PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1H994KH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1H994KH
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 211
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 92
Endothelins 76
LPA receptor mediated events 76
amb2 Integrin signaling 68
Ceramide signaling pathway 68
HIF-1-alpha transcription factor network 67
TCGA08_retinoblastoma 65
BARD1 signaling events 62
HIF-2-alpha transcription factor network 58
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 528 . 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 ( 528 ).

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 0.3996 211 846 4 -0.025 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1742 92 6298 68 -0.24 0.039 1000 -1000 -0.039 -1000
Endothelins 0.1439 76 7309 96 -0.47 0.032 1000 -1000 -0.035 -1000
LPA receptor mediated events 0.1439 76 7790 102 -0.042 0.044 1000 -1000 -0.046 -1000
amb2 Integrin signaling 0.1288 68 5634 82 -0.045 0.045 1000 -1000 -0.013 -1000
Ceramide signaling pathway 0.1288 68 5202 76 -0.092 0.066 1000 -1000 -0.021 -1000
HIF-1-alpha transcription factor network 0.1269 67 5157 76 -0.1 0.035 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.1231 65 525 8 -0.073 0.081 1000 -1000 0 -1000
BARD1 signaling events 0.1174 62 3558 57 -0.047 0.062 1000 -1000 -0.047 -1000
HIF-2-alpha transcription factor network 0.1098 58 2526 43 -0.081 0.051 1000 -1000 -0.023 -1000
EPO signaling pathway 0.1023 54 3019 55 -0.005 0.052 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1023 54 6870 125 -0.049 0.044 1000 -1000 -0.032 -1000
Arf6 signaling events 0.0871 46 2860 62 0 0.081 1000 -1000 -0.004 -1000
Osteopontin-mediated events 0.0852 45 1716 38 -0.088 0.043 1000 -1000 -0.018 -1000
Aurora B signaling 0.0758 40 2723 67 -0.044 0.049 1000 -1000 -0.028 -1000
Wnt signaling 0.0739 39 279 7 -0.002 0.032 1000 -1000 0.003 -1000
Syndecan-4-mediated signaling events 0.0739 39 2614 67 -0.063 0.032 1000 -1000 -0.029 -1000
Syndecan-1-mediated signaling events 0.0682 36 1257 34 -0.039 0.032 1000 -1000 -0.017 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0682 36 2809 78 -0.037 0.042 1000 -1000 -0.042 -1000
Ras signaling in the CD4+ TCR pathway 0.0663 35 611 17 -0.003 0.031 1000 -1000 -0.015 -1000
PLK1 signaling events 0.0625 33 2866 85 -0.038 0.056 1000 -1000 -0.012 -1000
VEGFR1 specific signals 0.0625 33 1856 56 -0.037 0.054 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0587 31 1436 45 -0.057 0.055 1000 -1000 -0.023 -1000
Caspase cascade in apoptosis 0.0568 30 2280 74 -0.053 0.054 1000 -1000 -0.026 -1000
JNK signaling in the CD4+ TCR pathway 0.0549 29 507 17 -0.11 0.057 1000 -1000 -0.012 -1000
Glypican 1 network 0.0549 29 1434 48 -0.031 0.06 1000 -1000 -0.026 -1000
S1P1 pathway 0.0549 29 1058 36 -0.056 0.035 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 0.0549 29 1378 47 -0.14 0.045 1000 -1000 -0.027 -1000
PDGFR-alpha signaling pathway 0.0530 28 1248 44 -0.042 0.049 1000 -1000 -0.023 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0530 28 939 33 -0.055 0.063 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 0.0511 27 1205 44 -0.038 0.062 1000 -1000 -0.015 -1000
Regulation of nuclear SMAD2/3 signaling 0.0492 26 3571 136 -0.2 0.059 1000 -1000 -0.035 -1000
Fc-epsilon receptor I signaling in mast cells 0.0492 26 2574 97 -0.1 0.056 1000 -1000 -0.049 -1000
IL1-mediated signaling events 0.0492 26 1636 62 -0.053 0.057 1000 -1000 -0.035 -1000
TCGA08_rtk_signaling 0.0492 26 686 26 -0.049 0.13 1000 -1000 -0.004 -1000
Plasma membrane estrogen receptor signaling 0.0473 25 2172 86 -0.43 0.052 1000 -1000 -0.03 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0455 24 923 37 -0.05 0.074 1000 -1000 -0.017 -1000
Integrins in angiogenesis 0.0455 24 2033 84 -0.05 0.078 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 0.0455 24 1235 51 -0.037 0.11 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 0.0455 24 510 21 -0.012 0.032 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0436 23 1025 43 -0.013 0.074 1000 -1000 -0.016 -1000
Signaling events regulated by Ret tyrosine kinase 0.0417 22 1864 82 -0.041 0.049 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0398 21 500 23 -0.019 0.036 1000 -1000 -0.008 -1000
Visual signal transduction: Cones 0.0398 21 809 38 -0.021 0.053 1000 -1000 -0.015 -1000
Nectin adhesion pathway 0.0398 21 1332 63 -0.016 0.073 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.0398 21 1114 51 -0.2 0.032 1000 -1000 -0.14 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0379 20 1125 54 -0.02 0.047 1000 -1000 -0.026 -1000
Signaling events mediated by the Hedgehog family 0.0379 20 1083 52 -0.015 0.067 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 0.0379 20 525 26 -0.024 0.032 1000 -1000 -0.027 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0379 20 1711 85 -0.02 0.11 1000 -1000 -0.039 -1000
BMP receptor signaling 0.0379 20 1680 81 -0.023 0.057 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0379 20 968 48 -0.031 0.07 1000 -1000 -0.021 -1000
TCGA08_p53 0.0379 20 143 7 -0.008 0.029 1000 -1000 -0.012 -1000
Arf6 trafficking events 0.0379 20 1447 71 -0.035 0.042 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0360 19 1516 76 -0.026 0.059 1000 -1000 -0.015 -1000
FOXA2 and FOXA3 transcription factor networks 0.0360 19 908 46 0 0.091 1000 -1000 -0.061 -1000
mTOR signaling pathway 0.0360 19 1059 53 -0.039 0.055 1000 -1000 -0.026 -1000
ceramide signaling pathway 0.0360 19 963 49 -0.016 0.045 1000 -1000 -0.017 -1000
Aurora A signaling 0.0341 18 1086 60 -0.036 0.065 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class I 0.0341 18 1959 104 -0.041 0.053 1000 -1000 -0.034 -1000
BCR signaling pathway 0.0341 18 1872 99 -0.049 0.05 1000 -1000 -0.033 -1000
LPA4-mediated signaling events 0.0322 17 215 12 -0.018 0.008 1000 -1000 -0.017 -1000
Coregulation of Androgen receptor activity 0.0322 17 1327 76 -0.053 0.058 1000 -1000 -0.018 -1000
Arf6 downstream pathway 0.0322 17 731 43 -0.025 0.047 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 0.0322 17 647 36 -0.043 0.046 1000 -1000 -0.038 -1000
E-cadherin signaling in the nascent adherens junction 0.0322 17 1333 76 -0.036 0.083 1000 -1000 -0.03 -1000
Regulation of Telomerase 0.0322 17 1760 102 -0.026 0.075 1000 -1000 -0.024 -1000
S1P3 pathway 0.0322 17 728 42 -0.031 0.033 1000 -1000 -0.013 -1000
Class I PI3K signaling events mediated by Akt 0.0303 16 1093 68 -0.025 0.06 1000 -1000 -0.021 -1000
TCR signaling in naïve CD8+ T cells 0.0303 16 1567 93 -0.33 0.38 1000 -1000 -0.024 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0303 16 1227 74 -0.21 0.069 1000 -1000 -0.041 -1000
Class I PI3K signaling events 0.0303 16 1203 73 -0.024 0.056 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 0.0284 15 1065 69 -0.021 0.054 1000 -1000 -0.021 -1000
Retinoic acid receptors-mediated signaling 0.0284 15 922 58 -0.014 0.058 1000 -1000 -0.018 -1000
Syndecan-3-mediated signaling events 0.0284 15 533 35 -0.009 0.073 1000 -1000 -0.019 -1000
EPHB forward signaling 0.0284 15 1306 85 -0.051 0.078 1000 -1000 -0.037 -1000
PDGFR-beta signaling pathway 0.0284 15 1529 97 -0.043 0.066 1000 -1000 -0.035 -1000
Signaling events mediated by PRL 0.0284 15 530 34 -0.027 0.047 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.0265 14 1832 125 -0.05 0.073 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0265 14 865 58 -0.18 0.044 1000 -1000 -0.032 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0265 14 386 27 -0.029 0.07 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 0.0246 13 526 39 -0.028 0.065 1000 -1000 -0.016 -1000
Hedgehog signaling events mediated by Gli proteins 0.0246 13 877 65 -0.004 0.053 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 0.0246 13 851 61 -0.009 0.072 1000 -1000 -0.034 -1000
IFN-gamma pathway 0.0246 13 914 68 -0.081 0.063 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class III 0.0246 13 533 40 -0.038 0.042 1000 -1000 -0.042 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0246 13 1147 83 -0.045 0.061 1000 -1000 -0.017 -1000
FoxO family signaling 0.0246 13 860 64 -0.098 0.043 1000 -1000 -0.046 -1000
IL6-mediated signaling events 0.0246 13 984 75 -0.017 0.069 1000 -1000 -0.064 -1000
IL2 signaling events mediated by STAT5 0.0246 13 294 22 -0.018 0.034 1000 -1000 -0.019 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0246 13 1640 120 -0.038 0.083 1000 -1000 -0.034 -1000
S1P4 pathway 0.0246 13 325 25 -0.033 0.041 1000 -1000 -0.007 -1000
Effects of Botulinum toxin 0.0227 12 316 26 0 0.053 1000 -1000 -0.011 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0227 12 1122 88 -0.07 0.037 1000 -1000 -0.042 -1000
Thromboxane A2 receptor signaling 0.0208 11 1212 105 -0.036 0.042 1000 -1000 -0.033 -1000
Glucocorticoid receptor regulatory network 0.0208 11 1365 114 -0.072 0.12 1000 -1000 -0.038 -1000
Arf1 pathway 0.0208 11 644 54 -0.06 0.042 1000 -1000 -0.011 -1000
ErbB2/ErbB3 signaling events 0.0189 10 709 65 -0.033 0.039 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 0.0189 10 417 39 -0.025 0.032 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 0.0189 10 587 54 -0.02 0.042 1000 -1000 -0.03 -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 9 311 34 -0.049 0.09 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class II 0.0170 9 684 75 -0.032 0.076 1000 -1000 -0.022 -1000
Nongenotropic Androgen signaling 0.0170 9 497 52 -0.064 0.055 1000 -1000 -0.017 -1000
Aurora C signaling 0.0152 8 60 7 0 0.05 1000 -1000 0 -1000
IL4-mediated signaling events 0.0152 8 771 91 -0.17 0.071 1000 -1000 -0.14 -1000
S1P5 pathway 0.0152 8 143 17 -0.033 0.032 1000 -1000 -0.007 -1000
Atypical NF-kappaB pathway 0.0152 8 266 31 -0.022 0.039 1000 -1000 -0.021 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0133 7 221 28 -0.022 0.033 1000 -1000 -0.021 -1000
Reelin signaling pathway 0.0133 7 427 56 -0.014 0.062 1000 -1000 -0.016 -1000
Signaling mediated by p38-gamma and p38-delta 0.0133 7 108 15 -0.026 0.032 1000 -1000 -0.023 -1000
Calcium signaling in the CD4+ TCR pathway 0.0133 7 230 31 -0.04 0.035 1000 -1000 -0.022 -1000
IGF1 pathway 0.0133 7 446 57 -0.038 0.061 1000 -1000 -0.025 -1000
Ephrin B reverse signaling 0.0114 6 290 48 -0.011 0.049 1000 -1000 -0.037 -1000
Insulin Pathway 0.0114 6 509 74 -0.043 0.078 1000 -1000 -0.026 -1000
p38 MAPK signaling pathway 0.0114 6 293 44 0 0.052 1000 -1000 -0.004 -1000
Regulation of Androgen receptor activity 0.0114 6 435 70 -0.036 0.058 1000 -1000 -0.03 -1000
IL12-mediated signaling events 0.0095 5 520 87 -0.067 0.058 1000 -1000 -0.063 -1000
ErbB4 signaling events 0.0095 5 381 69 -0.027 0.064 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 0.0095 5 185 32 -0.03 0.042 1000 -1000 -0.02 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0095 5 264 52 -0.066 0.091 1000 -1000 -0.006 -1000
IL27-mediated signaling events 0.0076 4 223 51 -0.02 0.056 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0057 3 86 22 -0.011 0.045 1000 -1000 -0.022 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 16 5 0.025 0.046 1000 -1000 0.028 -1000
Rapid glucocorticoid signaling 0.0057 3 73 20 -0.011 0.032 1000 -1000 -0.011 -1000
IL23-mediated signaling events 0.0038 2 154 60 -0.023 0.057 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0019 1 76 52 -0.035 0.074 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 0.0019 1 18 13 0 0.056 1000 -1000 0 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.016 0.032 1000 -1000 -0.02 -1000
Ephrin A reverse signaling 0.0000 0 3 7 -0.02 0.042 1000 -1000 -0.012 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.032 0.032 1000 -1000 -0.028 -1000
Total NA 2947 169703 7203 -6.8 7.5 131000 -131000 -3.4 -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 -0.025 0.05 -9999 0 -0.07 282 282
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.014 0.033 -9999 0 -0.043 282 282
neuron projection morphogenesis -0.014 0.033 -9999 0 -0.043 282 282
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 -0.029 6 6
NFATC2 -0.026 0.096 -10000 0 -0.14 198 198
NFATC3 -0.041 0.11 -10000 0 -0.16 214 214
CD40LG -0.14 0.17 0.26 1 -0.32 206 207
ITCH -0.012 0.012 -10000 0 -10000 0 0
CBLB -0.013 0.012 -10000 0 -0.061 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.16 -10000 0 -0.37 106 106
JUNB 0.03 0.014 -10000 0 -0.07 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.019 -10000 0 -0.056 14 14
T cell anergy -0.008 0.027 0.13 4 -0.1 5 9
TLE4 -0.019 0.06 0.1 1 -0.1 93 94
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.32 226 226
AP-1/NFAT1-c-4 -0.12 0.21 -10000 0 -0.34 211 211
IKZF1 -0.012 0.05 0.1 1 -0.1 59 60
T-helper 2 cell differentiation -0.12 0.17 -10000 0 -0.48 61 61
AP-1/NFAT1 -0.02 0.072 -10000 0 -0.11 23 23
CALM1 0.031 0.018 -10000 0 -0.048 14 14
EGR2 -0.091 0.18 -10000 0 -0.34 169 169
EGR3 0.007 0.12 -10000 0 -0.61 18 18
NFAT1/FOXP3 -0.005 0.081 -10000 0 -0.11 87 87
EGR1 0.029 0.018 -10000 0 -0.07 15 15
JUN 0.03 0.013 -10000 0 -0.033 10 10
EGR4 0.033 0.003 -10000 0 -0.027 1 1
mol:Ca2+ 0.003 0.007 -10000 0 -10000 0 0
GBP3 -0.019 0.054 0.08 4 -0.08 198 202
FOSL1 0.03 0.016 -10000 0 -0.07 12 12
NFAT1-c-4/MAF/IRF4 -0.096 0.22 -10000 0 -0.33 229 229
DGKA -0.02 0.06 0.1 1 -0.1 106 107
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.34 227 227
CTLA4 -0.022 0.054 0.085 1 -0.092 89 90
NFAT1-c-4 (dimer)/EGR1 -0.11 0.22 -10000 0 -0.34 230 230
NFAT1-c-4 (dimer)/EGR4 -0.11 0.22 -10000 0 -0.34 233 233
FOS 0.004 0.044 -10000 0 -0.07 127 127
IFNG -0.048 0.092 -10000 0 -0.25 33 33
T cell activation -0.077 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 0.039 0.16 0.33 104 -10000 0 104
TNF -0.13 0.19 -10000 0 -0.32 232 232
FASLG -0.24 0.29 -10000 0 -0.53 242 242
TBX21 0.034 0.005 -10000 0 -0.044 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.026 0.014 -10000 0 -10000 0 0
PTPN1 -0.019 0.059 0.1 1 -0.098 106 107
NFAT1-c-4/ICER1 -0.12 0.21 -10000 0 -0.34 233 233
GATA3 0.025 0.015 -10000 0 -0.069 2 2
T-helper 1 cell differentiation -0.047 0.091 -10000 0 -0.28 20 20
IL2RA -0.11 0.17 -10000 0 -0.37 106 106
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.031 0.065 0.1 1 -0.11 109 110
E2F1 -0.022 0.042 -10000 0 -0.055 304 304
PPARG 0.031 0.01 -10000 0 -0.07 4 4
SLC3A2 -0.02 0.062 0.1 1 -0.093 158 159
IRF4 0.032 0.006 -10000 0 -0.069 1 1
PTGS2 -0.14 0.17 0.26 1 -0.32 205 206
CSF2 -0.14 0.17 0.26 1 -0.32 206 207
JunB/Fra1/NFAT1-c-4 -0.098 0.22 -10000 0 -0.33 223 223
IL4 -0.12 0.18 -10000 0 -0.5 60 60
IL5 -0.14 0.17 0.26 1 -0.32 205 206
IL2 -0.077 0.11 -10000 0 -10000 0 0
IL3 -0.008 0.072 -10000 0 -0.54 6 6
RNF128 -0.017 0.013 -10000 0 -0.087 14 14
NFATC1 -0.034 0.15 -10000 0 -0.34 96 96
CDK4 0.009 0.11 0.27 67 -10000 0 67
PTPRK -0.019 0.059 0.1 1 -0.093 138 139
IL8 -0.14 0.17 0.26 1 -0.33 206 207
POU2F1 0.035 0.005 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.072 0.037 -10000 0 -0.12 91 91
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.17 0.36 1 -0.42 85 86
EDN1 -0.039 0.046 -10000 0 -0.067 344 344
EDN3 0.029 0.012 -10000 0 -0.07 3 3
EDN2 0.032 0.007 -10000 0 -0.07 1 1
HRAS/GDP -0.034 0.081 0.24 11 -0.29 15 26
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.042 -10000 0 -0.18 10 10
ADCY4 -0.058 0.026 0.014 1 -0.079 268 269
ADCY5 -0.058 0.026 0.014 1 -0.079 268 269
ADCY6 -0.061 0.035 0.18 1 -10000 0 1
ADCY7 -0.061 0.038 0.18 1 -10000 0 1
ADCY1 -0.045 0.04 -10000 0 -10000 0 0
ADCY2 -0.06 0.038 0.18 1 -10000 0 1
ADCY3 -0.058 0.026 0.014 1 -0.079 268 269
ADCY8 -0.06 0.038 0.18 1 -10000 0 1
ADCY9 -0.061 0.037 0.18 1 -10000 0 1
arachidonic acid secretion -0.052 0.095 0.31 7 -0.33 18 25
ETB receptor/Endothelin-1/Gq/GTP -0.01 0.035 -10000 0 -0.15 16 16
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 -0.035 0.057 -10000 0 -0.093 178 178
ETA receptor/Endothelin-1/Gs/GTP -0.042 0.06 -10000 0 -0.087 235 235
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.097 0.046 -10000 0 -0.14 240 240
EDNRB -0.01 0.038 -10000 0 -0.044 257 257
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.068 0.038 -10000 0 -0.12 87 87
CYSLTR1 -0.066 0.034 0.044 1 -0.084 349 350
SLC9A1 -0.035 0.035 -10000 0 -0.06 260 260
mol:GDP -0.036 0.079 0.22 13 -0.3 15 28
SLC9A3 -0.076 0.19 -10000 0 -0.62 42 42
RAF1 -0.035 0.083 0.26 10 -0.32 14 24
JUN -0.097 0.19 0.35 1 -0.45 93 94
JAK2 -0.068 0.04 -10000 0 -0.12 84 84
mol:IP3 -0.018 0.047 -10000 0 -0.22 14 14
ETA receptor/Endothelin-1 -0.064 0.071 0.13 1 -0.1 359 360
PLCB1 0.029 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.007 -10000 0 -0.028 2 2
ETA receptor/Endothelin-3 -0.032 0.047 -10000 0 -0.062 329 329
FOS -0.043 0.098 0.34 8 -0.35 12 20
Gai/GDP -0.47 0.17 -10000 0 -0.52 449 449
CRK 0.032 0.004 -10000 0 -10000 0 0
mol:Ca ++ -0.05 0.054 -10000 0 -0.2 21 21
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.019 0.047 -10000 0 -0.21 15 15
GNAQ 0.031 0.008 -10000 0 -0.027 4 4
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNAL 0.032 0.005 -10000 0 -10000 0 0
Gs family/GDP -0.034 0.075 0.2 11 -0.28 14 25
ETA receptor/Endothelin-1/Gq/GTP -0.025 0.038 -10000 0 -0.14 14 14
MAPK14 -0.013 0.036 -10000 0 -0.2 8 8
TRPC6 -0.092 0.18 0.36 1 -0.44 84 85
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
GNAI1 0.019 0.016 -10000 0 -0.07 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.006 0.039 -10000 0 -0.18 13 13
ETB receptor/Endothelin-2 0 0.041 -10000 0 -0.038 246 246
ETB receptor/Endothelin-3 -0.001 0.039 -10000 0 -0.038 236 236
ETB receptor/Endothelin-1 -0.037 0.05 -10000 0 -0.074 264 264
MAPK3 -0.038 0.099 0.35 8 -0.37 10 18
MAPK1 -0.046 0.1 0.34 8 -0.36 15 23
Rac1/GDP -0.03 0.06 0.21 3 -0.26 11 14
cAMP biosynthetic process -0.023 0.044 0.2 4 -0.15 1 5
MAPK8 -0.11 0.22 0.37 1 -0.5 106 107
SRC 0.03 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.006 0.026 -10000 0 -0.11 25 25
p130Cas/CRK/Src/PYK2 -0.028 0.085 0.31 9 -0.33 10 19
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.03 0.06 0.21 3 -0.26 12 15
COL1A2 -0.059 0.067 -10000 0 -0.14 184 184
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.033 0.048 -10000 0 -0.061 354 354
mol:DAG -0.018 0.047 -10000 0 -0.22 14 14
MAP2K2 -0.038 0.1 0.34 15 -0.32 14 29
MAP2K1 -0.045 0.085 0.27 7 -0.32 14 21
EDNRA -0.052 0.053 -10000 0 -0.081 361 361
positive regulation of muscle contraction -0.011 0.097 0.15 124 -0.13 5 129
Gq family/GDP 0.002 0.082 0.25 3 -0.26 14 17
HRAS/GTP -0.028 0.077 0.22 11 -0.3 16 27
PRKCH -0.024 0.05 0.21 1 -0.24 14 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.026 0.055 0.18 3 -0.23 19 22
PRKCB -0.019 0.047 -10000 0 -0.21 15 15
PRKCE -0.027 0.053 -10000 0 -0.23 19 19
PRKCD -0.026 0.053 0.17 2 -0.23 18 20
PRKCG -0.026 0.054 0.21 1 -0.24 17 18
regulation of vascular smooth muscle contraction -0.046 0.11 0.37 8 -0.45 7 15
PRKCQ -0.02 0.042 0.19 3 -0.25 8 11
PLA2G4A -0.054 0.099 0.31 7 -0.35 18 25
GNA14 0.031 0.01 -10000 0 -0.044 5 5
GNA15 0.03 0.014 -10000 0 -0.064 8 8
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.007 -10000 0 -0.026 1 1
Rac1/GTP -0.036 0.057 -10000 0 -0.093 180 180
MMP1 0.024 0.048 0.074 110 -0.094 25 135
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.007 0.031 -10000 0 -0.037 259 259
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.06 0.21 6 -0.18 23 29
AP1 -0.019 0.032 -10000 0 -0.043 300 300
mol:PIP3 -0.013 0.019 -10000 0 -0.059 13 13
AKT1 0.01 0.074 0.2 23 -0.24 7 30
PTK2B -0.01 0.028 0.11 2 -0.2 6 8
RHOA 0.01 0.061 0.16 9 -0.31 9 18
PIK3CB 0.032 0.006 -10000 0 -0.031 1 1
mol:Ca2+ -0.013 0.019 0.17 2 -0.12 6 8
MAGI3 0 0 -10000 0 -0.004 2 2
RELA 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.017 0.028 -10000 0 -0.041 272 272
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.012 0.039 0.17 11 -0.19 6 17
NF kappa B1 p50/RelA -0.039 0.021 0.067 1 -0.12 10 11
endothelial cell migration -0.028 0.045 -10000 0 -0.074 244 244
ADCY4 -0.001 0.007 -10000 0 -0.096 1 1
ADCY5 -0.001 0.007 -10000 0 -0.096 1 1
ADCY6 -0.001 0.011 0.085 3 -0.093 3 6
ADCY7 -0.001 0.011 0.085 4 -0.082 2 6
ADCY1 -0.001 0.008 -10000 0 -0.082 2 2
ADCY2 -0.001 0.011 0.085 4 -0.093 1 5
ADCY3 -0.001 0.007 -10000 0 -0.096 1 1
ADCY8 -0.001 0.01 0.085 3 -0.082 2 5
ADCY9 -0.001 0.011 0.085 4 -0.093 1 5
GSK3B -0.014 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.001 0.014 0.076 4 -0.11 5 9
GNG2 0 0.001 0.002 1 -0.004 28 29
TRIP6 -0.01 0.027 -10000 0 -0.047 163 163
GNAO1 -0.001 0.008 -10000 0 -0.043 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.022 0.049 0.18 8 -0.19 23 31
GAB1 0.031 0.009 -10000 0 -0.07 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.18 -10000 0 -0.69 31 31
JUN 0.032 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.001 0.023 -10000 0 -0.022 243 243
TIAM1 -0.01 0.22 -10000 0 -0.85 31 31
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.013 0.017 0.17 2 -0.12 3 5
PLCB3 -0.02 0.017 0.18 3 -10000 0 3
FOS 0.006 0.043 -10000 0 -0.07 121 121
positive regulation of mitosis -0.001 0.014 0.076 4 -0.11 5 9
LPA/LPA1-2-3 -0.013 0.017 -10000 0 -0.03 249 249
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 0.003 0.024 0.13 1 -0.14 3 4
GNAZ -0.012 0.026 -10000 0 -0.043 201 201
EGFR/PI3K-beta/Gab1 -0.014 0.02 0.023 2 -0.066 7 9
positive regulation of dendritic cell cytokine production -0.013 0.017 -10000 0 -0.03 249 249
LPA/LPA2/MAGI-3 -0.006 0.007 -10000 0 -0.013 249 249
ARHGEF1 0.026 0.094 0.17 144 -10000 0 144
GNAI2 -0.015 0.028 -10000 0 -0.043 242 242
GNAI3 -0.019 0.029 -10000 0 -0.045 269 269
GNAI1 -0.009 0.023 -10000 0 -0.043 153 153
LPA/LPA3 -0.008 0.009 -10000 0 -0.017 247 247
LPA/LPA2 -0.008 0.009 -10000 0 -0.017 247 247
LPA/LPA1 -0.019 0.024 -10000 0 -0.043 247 247
HB-EGF/EGFR -0.004 0.025 -10000 0 -0.052 82 82
HBEGF -0.031 0.018 -10000 0 -0.055 165 165
mol:DAG -0.013 0.017 0.17 2 -0.12 3 5
cAMP biosynthetic process 0.044 0.062 0.14 118 -0.1 1 119
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
SRC 0.03 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
LYN -0.018 0.039 0.18 8 -0.16 1 9
GNAQ -0.002 0.014 -10000 0 -0.017 235 235
LPAR2 0 0 -10000 0 -0.004 2 2
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.013 0.015 -10000 0 -0.028 246 246
IL8 -0.042 0.058 0.2 2 -0.23 8 10
PTK2 -0.007 0.027 -10000 0 -0.035 241 241
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
CASP3 -0.017 0.028 -10000 0 -0.041 272 272
EGFR 0.012 0.018 -10000 0 -0.07 5 5
PLCG1 0.002 0.009 -10000 0 -0.033 8 8
PLD2 -0.007 0.027 -10000 0 -0.035 242 242
G12/G13 0.001 0.038 -10000 0 -0.045 171 171
PI3K-beta -0.011 0.041 -10000 0 -0.2 13 13
cell migration -0.005 0.051 -10000 0 -0.22 21 21
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
PXN 0.003 0.024 0.13 1 -0.14 3 4
HRAS/GTP -0.001 0.013 0.077 4 -0.11 4 8
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.003 0.047 -10000 0 -0.07 166 166
PRKCE 0.032 0.006 -10000 0 -0.027 3 3
PRKCD -0.014 0.036 0.2 9 -0.12 4 13
Gi(beta/gamma) 0 0.015 0.086 4 -0.14 3 7
mol:LPA -0.013 0.015 -10000 0 -0.028 246 246
TRIP6/p130 Cas/FAK1/Paxillin -0.01 0.026 -10000 0 -0.11 6 6
MAPKKK cascade -0.001 0.014 0.076 4 -0.11 5 9
contractile ring contraction involved in cytokinesis 0.013 0.062 0.14 18 -0.31 9 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.002 0.014 -10000 0 -0.017 238 238
GNA15 -0.002 0.015 -10000 0 -0.018 232 232
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.07 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.002 0.014 -10000 0 -0.017 232 232
Rac1/GTP -0.005 0.19 -10000 0 -0.73 31 31
MMP2 -0.029 0.045 -10000 0 -0.075 244 244
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.02 0.059 -10000 0 -0.06 339 339
alphaM/beta2 Integrin/GPIbA 0.015 0.059 -10000 0 -0.053 213 213
alphaM/beta2 Integrin/proMMP-9 -0.008 0.061 -10000 0 -0.062 274 274
PLAUR 0.022 0.029 -10000 0 -0.07 44 44
HMGB1 0.025 0.019 -10000 0 -0.029 45 45
alphaM/beta2 Integrin/Talin 0.005 0.058 -10000 0 -0.055 231 231
AGER 0.026 0.02 -10000 0 -0.033 50 50
RAP1A 0.032 0.005 -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 0.016 0.074 -10000 0 -0.091 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.003 0.047 -10000 0 -0.07 166 166
CYR61 0.002 0.046 -10000 0 -0.07 150 150
TLN1 0.021 0.029 -10000 0 -0.07 43 43
Rap1/GTP 0.008 0.039 -10000 0 -0.15 4 4
RHOA 0.032 0.006 -10000 0 -10000 0 0
P-selectin oligomer 0.032 0.006 -10000 0 -0.07 1 1
MYH2 -0.001 0.039 0.14 4 -0.15 4 8
MST1R 0.031 0.008 -10000 0 -0.07 2 2
leukocyte activation during inflammatory response 0.011 0.059 -10000 0 -0.059 37 37
APOB 0.032 0.009 -10000 0 -0.07 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.017 0.051 -10000 0 -0.07 241 241
JAM3 0.03 0.009 -10000 0 -0.07 1 1
GP1BA 0.032 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.006 0.059 -10000 0 -0.055 227 227
alphaM/beta2 Integrin -0.001 0.038 -10000 0 -0.14 8 8
JAM3 homodimer 0.03 0.009 -10000 0 -0.07 1 1
ICAM2 0.032 0.008 -10000 0 -0.07 3 3
ICAM1 0.028 0.018 -10000 0 -0.07 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.001 0.038 -10000 0 -0.14 8 8
cell adhesion 0.014 0.058 -10000 0 -0.053 213 213
NFKB1 -0.044 0.034 0.18 6 -0.15 1 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 0.013 -10000 0 -0.046 3 3
alphaM/beta2 Integrin/LRP/tPA -0.015 0.067 -10000 0 -0.075 133 133
IL6 -0.034 0.04 0.16 4 -0.14 28 32
ITGB2 -0.012 0.05 -10000 0 -0.068 222 222
elevation of cytosolic calcium ion concentration -0.011 0.066 -10000 0 -0.08 115 115
alphaM/beta2 Integrin/JAM2/JAM3 0.007 0.068 -10000 0 -0.07 56 56
JAM2 0.017 0.036 -10000 0 -0.07 72 72
alphaM/beta2 Integrin/ICAM1 0.022 0.076 -10000 0 -0.081 12 12
alphaM/beta2 Integrin/uPA/Plg -0.01 0.066 -10000 0 -0.074 108 108
RhoA/GTP 0.003 0.039 0.1 17 -0.13 10 27
positive regulation of phagocytosis -0.004 0.055 0.16 4 -0.14 8 12
Ron/MSP 0.045 0.015 -10000 0 -0.054 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.01 0.068 -10000 0 -0.08 115 115
alphaM/beta2 Integrin/uPAR 0.01 0.06 -10000 0 -0.058 214 214
PLAU 0.006 0.038 -10000 0 -0.07 94 94
PLAT -0.015 0.051 -10000 0 -0.07 232 232
actin filament polymerization 0 0.04 0.15 6 -0.16 3 9
MST1 0.031 0.012 -10000 0 -0.07 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.015 0.063 -10000 0 -0.06 34 34
TNF -0.045 0.033 0.16 6 -0.14 2 8
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.005 0.058 -10000 0 -0.062 233 233
fibrinolysis -0.01 0.065 -10000 0 -0.074 108 108
HCK 0.013 0.038 -10000 0 -0.07 84 84
dendritic cell antigen processing and presentation -0.001 0.038 -10000 0 -0.14 8 8
VTN 0.032 0.007 -10000 0 -0.07 2 2
alphaM/beta2 Integrin/CYR61 -0.003 0.063 -10000 0 -0.061 268 268
LPA 0.03 0.008 -10000 0 -10000 0 0
LRP1 0.028 0.017 -10000 0 -0.07 13 13
cell migration -0.036 0.052 -10000 0 -0.07 337 337
FN1 0.013 0.04 -10000 0 -0.07 96 96
alphaM/beta2 Integrin/Thy1 0.006 0.051 -10000 0 -0.053 178 178
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 0.044 0.18 9 -0.16 3 12
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.009 -10000 0 -10000 0 0
CTGF 0.023 0.027 -10000 0 -0.07 36 36
alphaM/beta2 Integrin/Hck 0.008 0.062 -10000 0 -0.063 208 208
ITGAM 0.027 0.018 -10000 0 -0.029 47 47
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.023 0.068 -10000 0 -0.065 34 34
HP 0.016 0.037 -10000 0 -0.07 77 77
leukocyte adhesion -0.009 0.057 -10000 0 -0.11 10 10
SELP 0.032 0.006 -10000 0 -0.07 1 1
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 0 179 -0.054 2 181
MAP4K4 -0.009 0.039 -10000 0 -0.19 11 11
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.059 0.11 -10000 0 -0.2 161 161
NFKBIA 0.031 0.009 -10000 0 -0.07 1 1
BIRC3 0.026 0.024 -10000 0 -0.07 30 30
BAX -0.028 0.087 -10000 0 -0.36 24 24
RIPK1 0.03 0.014 -10000 0 -0.07 9 9
AKT1 0 0.069 0.75 4 -10000 0 4
BAD -0.065 0.11 0.19 2 -0.21 161 163
SMPD1 -0.006 0.037 0.11 10 -0.17 15 25
RB1 -0.065 0.11 0.2 1 -0.21 161 162
FADD/Caspase 8 -0.003 0.042 -10000 0 -0.24 7 7
MAP2K4 -0.064 0.11 0.19 4 -0.2 152 156
NSMAF 0.032 0.006 -10000 0 -0.07 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.066 0.11 0.17 6 -0.2 158 164
EGF 0.032 0.007 -10000 0 -0.07 2 2
mol:ceramide -0.062 0.12 -10000 0 -0.21 161 161
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 0 172 -0.054 2 174
ASAH1 0.032 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.065 0.11 0.2 1 -0.2 161 162
cell proliferation -0.037 0.1 0.16 1 -0.19 144 145
BID -0.024 0.15 -10000 0 -0.61 26 26
MAP3K1 -0.065 0.11 0.2 1 -0.21 160 161
EIF2A -0.066 0.1 0.17 1 -0.19 161 162
TRADD 0.032 0.004 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.059 0.096 0.18 4 -0.19 146 150
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 -0.047 0.12 -10000 0 -0.21 160 160
FADD -0.007 0.034 -10000 0 -0.17 8 8
KSR1 -0.065 0.11 0.19 2 -0.21 161 163
MAPK8 -0.092 0.15 0.15 3 -0.25 191 194
PRKRA -0.066 0.11 -10000 0 -0.21 161 161
PDGFA 0.022 0.016 -10000 0 -0.07 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0.031 0.01 -10000 0 -0.07 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.062 0.12 -10000 0 -0.21 161 161
CTSD 0.028 0.018 -10000 0 -0.07 15 15
regulation of nitric oxide biosynthetic process 0.046 0.012 -10000 0 -0.054 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.11 0.18 1 -0.2 144 145
PRKCD 0.032 0.005 -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 0 172 -0.054 2 174
RelA/NF kappa B1 0.046 0.012 -10000 0 -0.054 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 -0.003 0.04 -10000 0 -0.12 33 33
TNFR1A/BAG4/TNF-alpha 0.024 0.055 -10000 0 -0.052 163 163
mol:Sphingosine-1-phosphate -0.015 0.011 0 179 -0.054 2 181
MAP2K1 -0.067 0.1 0.17 6 -0.2 153 159
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
CYCS -0.017 0.064 0.12 1 -0.2 37 38
TNFRSF1A -0.002 0.047 -10000 0 -0.07 164 164
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
TNFR1A/BAG4 0.013 0.047 -10000 0 -0.054 162 162
EIF2AK2 -0.069 0.11 0.18 1 -0.2 161 162
TNF-alpha/TNFR1A/FAN 0.024 0.055 -10000 0 -0.052 163 163
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.048 -10000 0 -0.29 8 8
MAP2K2 -0.064 0.095 0.17 10 -0.19 151 161
SMPD3 -0.001 0.04 0.096 4 -0.23 10 14
TNF 0.032 0.007 -10000 0 -0.07 2 2
PKC zeta/PAR4 0.023 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.036 0.067 0.13 3 -0.13 153 156
NF kappa B1/RelA/I kappa B alpha 0.066 0.034 -10000 0 -0.057 1 1
AIFM1 -0.043 0.081 0.12 1 -0.22 40 41
BCL2 0.031 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.1 0.096 -10000 0 -0.21 198 198
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.082 0.11 -10000 0 -0.23 109 109
SMAD4 0.008 0.043 -10000 0 -0.07 114 114
ID2 -0.064 0.17 0.48 13 -0.28 55 68
AP1 0.021 0.043 -10000 0 -0.054 118 118
ABCG2 -0.067 0.17 0.5 9 -0.28 54 63
HIF1A -0.016 0.056 0.15 7 -0.085 44 51
TFF3 -0.064 0.17 0.52 8 -0.28 53 61
GATA2 0.031 0.01 -10000 0 -0.028 9 9
AKT1 -0.012 0.056 0.16 7 -0.092 6 13
response to hypoxia -0.02 0.026 0.091 6 -0.059 59 65
MCL1 -0.066 0.17 0.5 8 -0.28 54 62
NDRG1 -0.074 0.15 0.54 3 -0.28 52 55
SERPINE1 -0.058 0.15 0.48 8 -0.28 61 69
FECH -0.059 0.17 0.47 14 -0.28 53 67
FURIN -0.062 0.17 0.52 9 -0.28 52 61
NCOA2 0.033 0.004 -10000 0 -10000 0 0
EP300 -0.001 0.055 0.22 12 -0.2 2 14
HMOX1 -0.084 0.17 0.48 9 -0.28 84 93
BHLHE40 -0.1 0.096 -10000 0 -0.21 198 198
BHLHE41 -0.1 0.096 -10000 0 -0.21 198 198
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.005 0.095 0.23 6 -0.11 86 92
ENG -0.036 0.08 0.27 9 -0.16 4 13
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.063 0.17 0.52 9 -0.28 52 61
ABCB1 -0.012 0.045 -10000 0 -0.31 5 5
TFRC -0.065 0.17 0.5 11 -0.28 54 65
CXCR4 -0.082 0.16 0.53 5 -0.28 81 86
TF -0.087 0.12 0.41 1 -0.28 52 53
CITED2 -0.067 0.16 0.53 6 -0.28 53 59
HIF1A/ARNT -0.079 0.15 0.27 24 -0.25 142 166
LDHA 0.001 0.057 -10000 0 -0.46 6 6
ETS1 -0.062 0.17 0.5 10 -0.28 53 63
PGK1 -0.062 0.17 0.52 9 -0.28 53 62
NOS2 -0.1 0.096 -10000 0 -0.21 198 198
ITGB2 -0.071 0.18 0.5 11 -0.28 77 88
ALDOA -0.062 0.17 0.51 7 -0.28 53 60
Cbp/p300/CITED2 -0.1 0.11 -10000 0 -0.24 149 149
FOS 0.006 0.043 -10000 0 -0.07 121 121
HK2 -0.062 0.17 0.47 14 -0.28 54 68
SP1 0.035 0.007 -10000 0 -0.042 2 2
GCK 0.002 0.087 0.34 8 -0.3 6 14
HK1 -0.083 0.14 0.45 4 -0.28 55 59
NPM1 -0.066 0.17 0.54 6 -0.28 53 59
EGLN1 -0.066 0.17 0.51 7 -0.28 54 61
CREB1 0.035 0.008 -10000 0 -0.085 2 2
PGM1 -0.063 0.17 0.5 11 -0.28 51 62
SMAD3 0.032 0.005 -10000 0 -10000 0 0
EDN1 -0.019 0.08 -10000 0 -0.33 13 13
IGFBP1 -0.051 0.15 0.51 7 -0.28 41 48
VEGFA -0.084 0.14 0.36 12 -0.25 90 102
HIF1A/JAB1 0.006 0.053 0.14 4 -0.057 130 134
CP -0.072 0.17 0.49 8 -0.29 64 72
CXCL12 -0.074 0.15 0.47 7 -0.28 55 62
COPS5 0.033 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.023 0.042 -10000 0 -0.055 110 110
BNIP3 -0.08 0.14 0.42 3 -0.28 56 59
EGLN3 -0.065 0.17 0.47 12 -0.28 56 68
CA9 -0.066 0.17 0.49 11 -0.28 54 65
TERT -0.06 0.17 0.5 11 -0.28 54 65
ENO1 -0.065 0.17 0.48 11 -0.28 54 65
PFKL -0.061 0.17 0.5 11 -0.28 52 63
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.082 0.16 0.51 6 -0.28 79 85
ARNT -0.016 0.056 0.15 7 -0.083 46 53
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.1 0.096 -10000 0 -0.21 198 198
SLC2A1 -0.068 0.14 0.37 13 -0.25 56 69
LEP -0.051 0.15 0.48 7 -0.28 41 48
HIF1A/ARNT/Cbp/p300 -0.086 0.11 -10000 0 -0.23 118 118
EPO -0.034 0.11 0.33 11 -0.34 21 32
CREBBP 0 0.055 0.22 12 -0.19 2 14
HIF1A/ARNT/Cbp/p300/HDAC7 -0.089 0.11 -10000 0 -0.23 135 135
PFKFB3 -0.072 0.16 0.48 7 -0.28 52 59
NT5E -0.071 0.16 0.51 6 -0.28 54 60
TCGA08_retinoblastoma

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
CDKN2B 0.012 0.018 -10000 0 -0.038 5 5
CDKN2C -0.007 0.031 -10000 0 -0.059 106 106
CDKN2A 0.005 0.027 -10000 0 -0.054 52 52
CCND2 0.003 0.011 0.089 3 -10000 0 3
RB1 -0.073 0.1 0.1 1 -0.22 167 168
CDK4 0.002 0.012 0.1 3 -10000 0 3
CDK6 0.005 0.018 0.11 7 -10000 0 7
G1/S progression 0.081 0.11 0.22 180 -0.1 1 181
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 0.022 0.043 -10000 0 -0.054 113 113
ATM 0.027 0.022 -10000 0 -0.07 25 25
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.028 0.021 -10000 0 -0.07 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 0.012 -10000 0 -0.041 24 24
protein ubiquitination 0.042 0.067 -10000 0 -0.085 25 25
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
M/R/N Complex 0.062 0.018 -10000 0 -0.036 11 11
MRE11A 0.032 0.004 -10000 0 -10000 0 0
DNA-PK 0.054 0.034 -10000 0 -0.054 22 22
FA complex/FANCD2/Ubiquitin -0.005 0.08 -10000 0 -0.25 36 36
FANCF 0.031 0.008 -10000 0 -0.07 2 2
BRCA1 0.031 0.011 -10000 0 -0.07 5 5
CCNE1 0.03 0.012 -10000 0 -0.07 4 4
CDK2/Cyclin E1 0.04 0.025 -10000 0 -0.058 23 23
FANCG 0.018 0.033 -10000 0 -0.07 57 57
BRCA1/BACH1/BARD1 0.023 0.044 -10000 0 -0.055 120 120
FANCE 0.032 0.005 -10000 0 -0.07 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 -0.031 0.067 0.18 14 -0.22 25 39
BRCA1/BARD1/ubiquitin 0.023 0.044 -10000 0 -0.055 120 120
BARD1/DNA-PK 0.041 0.063 -10000 0 -0.069 23 23
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.042 0.054 113 -10000 0 113
BRCA1/BARD1/CTIP/M/R/N Complex -0.02 0.041 0.1 6 -0.14 25 31
BRCA1/BACH1/BARD1/TopBP1 0.035 0.051 -10000 0 -0.053 122 122
BRCA1/BARD1/P53 0.034 0.067 -10000 0 -0.058 158 158
BARD1/CSTF1/BRCA1 0.034 0.05 -10000 0 -0.053 114 114
BRCA1/BACH1 0.031 0.011 -10000 0 -0.07 5 5
BARD1 0.008 0.044 -10000 0 -0.07 122 122
PCNA -0.03 0.048 -10000 0 -0.07 297 297
BRCA1/BARD1/UbcH5C 0.036 0.052 -10000 0 -0.053 123 123
BRCA1/BARD1/UbcH7 0.034 0.052 -10000 0 -0.053 122 122
BRCA1/BARD1/RAD51/PCNA -0.012 0.066 -10000 0 -0.075 103 103
BARD1/DNA-PK/P53 0.037 0.076 -10000 0 -0.082 37 37
BRCA1/BARD1/Ubiquitin 0.023 0.044 -10000 0 -0.055 120 120
BRCA1/BARD1/CTIP -0.037 0.046 -10000 0 -0.061 392 392
FA complex 0.011 0.035 0.087 8 -0.15 16 24
BARD1/EWS 0.023 0.042 -10000 0 -0.054 110 110
RBBP8 -0.047 0.017 -10000 0 -0.056 379 379
TP53 0.018 0.034 -10000 0 -0.07 65 65
TOPBP1 0.032 0.007 -10000 0 -0.07 1 1
G1/S transition of mitotic cell cycle -0.032 0.065 0.058 158 -10000 0 158
BRCA1/BARD1 0.047 0.071 -10000 0 -0.086 25 25
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.008 0.029 -10000 0 -0.043 122 122
CDK2 0.027 0.022 -10000 0 -0.07 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 0.023 0.044 -10000 0 -0.055 120 120
EWSR1 0.031 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 -0.012 0.16 -10000 0 -0.65 31 31
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.023 0.075 -10000 0 -0.14 95 95
EPO -0.032 0.072 -10000 0 -0.2 46 46
FIH (dimer) 0.02 0.018 -10000 0 -0.028 31 31
APEX1 0.022 0.022 -10000 0 -0.03 67 67
SERPINE1 -0.046 0.073 -10000 0 -0.18 65 65
FLT1 -0.013 0.16 -10000 0 -0.61 33 33
ADORA2A -0.071 0.068 -10000 0 -0.17 123 123
germ cell development -0.064 0.07 -10000 0 -0.16 124 124
SLC11A2 -0.067 0.076 -10000 0 -0.17 124 124
BHLHE40 -0.066 0.072 -10000 0 -0.16 124 124
HIF1AN 0.02 0.018 -10000 0 -0.028 31 31
HIF2A/ARNT/SIRT1 -0.033 0.086 0.17 1 -0.17 97 98
ETS1 0.035 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 38 38
KDR 0.014 0.081 -10000 0 -0.55 9 9
PGK1 -0.067 0.076 -10000 0 -0.17 124 124
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.052 0.11 -10000 0 -0.2 89 89
EPAS1 -0.032 0.049 0.12 1 -0.12 98 99
SP1 0.034 0.006 -10000 0 -0.04 1 1
ABCG2 -0.068 0.076 -10000 0 -0.17 124 124
EFNA1 -0.068 0.077 -10000 0 -0.17 124 124
FXN -0.069 0.067 -10000 0 -0.17 113 113
POU5F1 -0.066 0.072 -10000 0 -0.16 124 124
neuron apoptosis 0.051 0.1 0.19 89 -10000 0 89
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.023 0.019 -10000 0 -0.033 43 43
EGLN2 0.025 0.016 -10000 0 -0.028 37 37
EGLN1 0.025 0.017 -10000 0 -0.029 39 39
VHL/Elongin B/Elongin C 0.043 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.024 0.021 -10000 0 -0.03 63 63
SLC2A1 -0.07 0.067 -10000 0 -0.17 114 114
TWIST1 -0.041 0.058 -10000 0 -0.17 52 52
ELK1 0.033 0.012 -10000 0 -0.04 13 13
HIF2A/ARNT/Cbp/p300 -0.025 0.095 0.19 1 -0.17 97 98
VEGFA -0.081 0.084 -10000 0 -0.18 141 141
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 0.037 0.048 0.18 20 -0.16 2 22
CRKL 0.028 0.094 0.16 134 -10000 0 134
mol:DAG 0.011 0.029 0.13 6 -0.14 2 8
HRAS 0.021 0.097 0.27 34 -10000 0 34
MAPK8 0.006 0.068 0.15 87 -10000 0 87
RAP1A 0.03 0.094 0.16 141 -10000 0 141
GAB1 0.03 0.095 0.16 140 -10000 0 140
MAPK14 0.021 0.084 0.15 148 -10000 0 148
EPO 0.023 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.03 0.14 6 -0.14 2 8
EPOR/TRPC2/IP3 Receptors 0.037 0.011 0.093 3 -10000 0 3
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.014 0.087 0.15 146 -10000 0 146
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.029 0.092 0.16 137 -10000 0 137
STAT1 0.012 0.033 0.14 6 -0.14 2 8
STAT5B 0.012 0.031 0.14 6 -0.14 2 8
cell proliferation 0.005 0.076 0.16 92 -10000 0 92
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.065 0.11 118 -10000 0 118
TEC 0.029 0.094 0.16 139 -10000 0 139
SOCS3 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.032 0.14 6 -0.14 2 8
JAK2 0.034 0.015 0.093 4 -10000 0 4
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 0.021 0.033 -10000 0 -0.069 60 60
TEC/VAV2 0.006 0.071 0.13 114 -10000 0 114
elevation of cytosolic calcium ion concentration 0.036 0.011 0.093 3 -10000 0 3
SHC1 0.024 0.028 -10000 0 -0.07 40 40
EPO/EPOR (dimer)/LYN 0.034 0.044 -10000 0 -0.056 47 47
mol:IP3 0.011 0.029 0.13 6 -0.14 2 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.022 0.091 0.16 126 -10000 0 126
SH2B3 0.037 0.016 0.093 1 -0.074 7 8
NFKB1 0.021 0.084 0.15 148 -10000 0 148
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 -10000 0 -10000 0 0
PTPN6 0.031 0.091 0.16 157 -10000 0 157
TEC/VAV2/GRB2 0.052 0.075 0.16 121 -10000 0 121
EPOR 0.037 0.011 0.093 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.088 0.15 146 -10000 0 146
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.015 -10000 0 -0.07 10 10
CRKL/CBL/C3G 0.052 0.075 0.16 118 -10000 0 118
VAV2 0.027 0.091 0.16 134 -10000 0 134
CBL 0.03 0.095 0.16 141 -10000 0 141
SHC/Grb2/SOS1 0.019 0.037 -10000 0 -0.087 1 1
STAT5A 0.012 0.031 0.14 6 -0.14 2 8
GRB2 0.031 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.042 0.18 4 -10000 0 4
LYN/PLCgamma2 0.034 0.036 -10000 0 -0.058 61 61
PTPN11 0.032 0.004 -10000 0 -10000 0 0
BTK 0.031 0.096 0.16 144 -10000 0 144
BCL2 0.037 0.052 0.17 22 -0.2 5 27
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.054 15 15
AKT1 -0.025 0.073 0.22 5 -0.28 15 20
PTK2B -0.036 0.057 0.15 37 -10000 0 37
VEGFR2 homodimer/Frs2 0.025 0.025 -10000 0 -0.097 13 13
CAV1 -0.021 0.044 -10000 0 -0.07 216 216
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.006 0.052 -10000 0 -0.056 248 248
endothelial cell proliferation -0.006 0.079 0.21 22 -0.26 10 32
mol:Ca2+ -0.032 0.052 0.15 32 -0.12 11 43
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.003 0.061 0.17 12 -0.082 63 75
RP11-342D11.1 -0.034 0.038 0.16 14 -0.11 11 25
CDH5 0.026 0.024 -10000 0 -0.07 29 29
VEGFA homodimer 0 0.053 -10000 0 -0.047 274 274
SHC1 0.024 0.028 -10000 0 -0.07 40 40
SHC2 0.031 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.019 0.055 -10000 0 -0.094 48 48
SH2D2A 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.003 0.061 0.2 1 -0.22 1 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.007 0.053 -10000 0 -0.056 255 255
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.005 0.069 0.16 13 -0.1 28 41
GRB10 -0.022 0.047 0.16 23 -0.11 13 36
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB2 0.031 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 -0.008 0.078 0.18 12 -0.11 28 40
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.006 0.051 0.13 11 -0.17 21 32
HIF1A 0.03 0.01 -10000 0 -0.07 2 2
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.004 0.059 0.17 12 -0.082 63 75
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.005 -10000 0 -10000 0 0
Nck/Pak 0.044 0.018 -10000 0 -0.054 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.052 -10000 0 -0.057 256 256
mol:GDP -0.013 0.057 -10000 0 -0.092 47 47
mol:NADP 0.003 0.058 0.26 3 -10000 0 3
eNOS/Hsp90 0.012 0.061 0.27 3 -0.2 1 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.032 0.052 0.15 32 -0.12 11 43
HIF1A/ARNT 0.044 0.014 -10000 0 -0.054 2 2
SHB 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.024 0.051 -10000 0 -0.071 275 275
VEGFC 0.029 0.016 -10000 0 -0.07 11 11
FAK1/Vinculin -0.005 0.061 0.2 11 -0.21 8 19
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 0.001 0.069 0.17 13 -0.09 35 48
PTPN6 0.029 0.016 -10000 0 -0.07 11 11
EPAS1 0.034 0.021 -10000 0 -0.076 17 17
mol:L-citrulline 0.003 0.058 0.26 3 -10000 0 3
ITGAV 0.029 0.018 -10000 0 -0.07 15 15
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.002 0.067 0.17 13 -0.091 26 39
VEGFR2 homodimer/VEGFA homodimer -0.007 0.057 -10000 0 -0.058 263 263
VEGFR2/3 heterodimer 0.025 0.026 -10000 0 -0.084 18 18
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.032 0.059 0.16 26 -0.16 14 40
VEGFR2 homodimer -0.021 0.016 -10000 0 -0.11 14 14
FLT1 0.031 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.02 -10000 0 -0.048 29 29
MAPK3 -0.02 0.065 0.19 12 -10000 0 12
MAPK1 -0.022 0.063 0.2 10 -10000 0 10
VEGFA145/NRP2 -0.008 0.051 -10000 0 -0.055 275 275
VEGFR1/2 heterodimer 0.024 0.026 -10000 0 -0.097 14 14
KDR -0.021 0.016 -10000 0 -0.11 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.004 0.062 0.16 14 -0.093 34 48
SRC 0.03 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.02 0.067 0.25 6 -10000 0 6
PI3K -0.021 0.065 0.17 7 -0.17 21 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.053 -10000 0 -0.056 264 264
FES -0.034 0.054 0.15 35 -0.12 11 46
GAB1 -0.02 0.067 0.16 10 -0.18 32 42
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.052 -10000 0 -0.056 236 236
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 -0.009 0.047 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.015 0.054 -10000 0 -0.059 289 289
PI3K/GAB1 -0.022 0.074 0.25 1 -0.24 17 18
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.003 0.074 0.18 12 -0.11 13 25
PRKACA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.032 -10000 0 -0.077 24 24
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
CDC42 -0.034 0.053 0.15 33 -0.12 11 44
actin cytoskeleton reorganization -0.007 0.053 -10000 0 -0.056 255 255
PTK2 -0.013 0.058 0.14 29 -0.19 11 40
EDG1 -0.034 0.038 0.16 14 -0.11 11 25
mol:DAG -0.032 0.052 0.15 32 -0.12 11 43
CaM/Ca2+ -0.033 0.051 0.15 29 -0.14 1 30
MAP2K3 -0.038 0.05 0.14 31 -0.14 1 32
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.044 0.096 0.18 139 -0.11 17 156
PLCG1 -0.032 0.052 0.15 32 -0.12 11 43
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.001 0.066 0.17 10 -0.092 28 38
IQGAP1 0.008 0.043 -10000 0 -0.07 120 120
YES1 0.017 0.036 -10000 0 -0.07 74 74
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.007 0.053 -10000 0 -0.056 260 260
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.053 -10000 0 -0.056 265 265
cell migration -0.009 0.076 0.2 12 -0.21 24 36
mol:PI-3-4-5-P3 -0.02 0.062 0.17 7 -0.16 21 28
FYN 0.029 0.011 -10000 0 -0.07 1 1
VEGFB/NRP1 -0.032 0.051 0.15 34 -0.11 11 45
mol:NO 0.003 0.058 0.26 3 -10000 0 3
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.049 0.025 -10000 0 -0.099 35 35
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.041 -10000 0 -0.059 169 169
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
NOS3 0.003 0.06 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.006 0.052 -10000 0 -0.056 246 246
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.035 0.05 0.14 31 -0.14 1 32
PRKCB -0.03 0.048 0.14 32 -0.13 2 34
VCL 0.025 0.014 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.033 0.042 0.17 16 -0.11 11 27
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.053 -10000 0 -0.056 259 259
VEGFA165/NRP2 -0.008 0.051 -10000 0 -0.055 275 275
MAPKKK cascade -0.033 0.04 0.18 6 -10000 0 6
NRP2 0.032 0.005 -10000 0 -0.07 1 1
VEGFC homodimer 0.029 0.016 -10000 0 -0.07 11 11
NCK1 0.029 0.016 -10000 0 -0.07 11 11
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.003 0.069 0.2 14 -0.21 8 22
MAP3K13 -0.035 0.051 0.15 31 -0.12 11 42
PDPK1 -0.035 0.054 0.15 8 -0.17 14 22
Arf6 signaling 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
CENTA1/KIF3B 0.021 0.005 -10000 0 -0.006 12 12
ARNO/beta Arrestin1-2 0.04 0.016 -10000 0 -0.063 9 9
EGFR 0.012 0.018 -10000 0 -0.07 5 5
EPHA2 0.029 0.016 -10000 0 -0.07 12 12
USP6 0.032 0.005 -10000 0 -10000 0 0
IQSEC1 0.032 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.017 0.025 -10000 0 -0.054 7 7
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0.013 0.1 4 -0.062 7 11
ARRB1 0.032 0.004 -10000 0 0 7 7
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -0.07 4 4
EGF 0.032 0.007 -10000 0 -0.07 2 2
somatostatin receptor activity 0 0 0 157 0 14 171
ARAP2 0 0 0 150 0 10 160
mol:GDP 0.061 0.064 0.15 138 -0.13 9 147
mol:PI-3-4-5-P3 0 0 0 147 0 12 159
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.043 -10000 0 -0.078 7 7
ADAP1 0 0 0 43 0 6 49
KIF13B 0.031 0.008 -10000 0 -0.07 2 2
HGF/MET 0.031 0.024 -10000 0 -0.054 3 3
PXN 0.032 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.074 0.086 0.18 148 -0.18 12 160
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.046 11 11
ADRB2 0.032 0.006 -10000 0 -0.07 1 1
receptor agonist activity 0 0 0 144 0 13 157
actin filament binding 0 0 0 148 0 14 162
SRC 0.03 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 0.001 0.001 0.001 162 -0.001 11 173
ARF6/GDP 0.026 0.064 0.13 28 -0.2 26 54
ARF6/GDP/GULP/ACAP1 0.081 0.062 0.16 127 -0.14 7 134
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.017 -10000 0 -0.054 2 2
ACAP1 0 0 0 41 -10000 0 41
ACAP2 0 0 0 148 0 10 158
LHCGR/beta Arrestin2 0.028 0.014 -10000 0 -0.079 9 9
EFNA1 0.028 0.021 -10000 0 -0.07 21 21
HGF 0.022 0.016 -10000 0 -0.07 1 1
CYTH3 0 0 0.001 148 0 12 160
CYTH2 0 0.001 0.002 3 -0.003 18 21
NCK1 0.029 0.016 -10000 0 -0.07 11 11
fibronectin binding 0 0 0 143 0 16 159
endosomal lumen acidification 0 0 0 157 0 16 173
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 0.032 0.009 -10000 0 -0.07 4 4
GNAQ/ARNO 0.024 0.006 0.039 5 0 18 23
mol:Phosphatidic acid 0 0 0 148 0 10 158
PIP3-E 0 0 0 85 0 14 99
MET 0.021 0.016 -10000 0 -0.07 2 2
GNA14 0.031 0.009 -10000 0 -0.07 2 2
GNA15 0.03 0.014 -10000 0 -0.07 7 7
GIT1 0.032 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 154 -0.001 11 165
GNA11 0.031 0.007 -10000 0 -10000 0 0
LHCGR 0.033 0 -10000 0 -10000 0 0
AGTR1 0.032 0.008 -10000 0 -0.07 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.028 0.014 -10000 0 -0.079 9 9
IPCEF1/ARNO 0.014 0.02 -10000 0 -0.031 7 7
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer -0.038 0.036 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.06 0.05 0.18 2 -0.2 10 12
alphaV/beta3 Integrin/Osteopontin/Src 0.008 0.052 -10000 0 -0.062 179 179
AP1 -0.065 0.069 -10000 0 -0.14 78 78
ILK -0.042 0.026 0.16 4 -10000 0 4
bone resorption -0.066 0.031 0.15 4 -10000 0 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.006 0.064 0.16 4 -0.093 18 22
ITGAV 0.022 0.026 -10000 0 -0.037 75 75
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.033 0.041 -10000 0 -0.054 395 395
alphaV/beta3 Integrin/Osteopontin 0.015 0.064 -10000 0 -0.075 76 76
MAP3K1 -0.044 0.027 0.16 5 -10000 0 5
JUN 0.031 0.004 -10000 0 -10000 0 0
MAPK3 -0.05 0.034 0.16 5 -10000 0 5
MAPK1 -0.047 0.036 0.16 5 -10000 0 5
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
MAPK8 -0.038 0.034 0.16 4 -10000 0 4
ITGB3 0.024 0.02 -10000 0 -0.028 63 63
NFKBIA -0.048 0.044 0.16 5 -0.17 14 19
FOS 0.005 0.043 -10000 0 -0.071 121 121
CD44 -0.048 0.041 -10000 0 -0.07 397 397
CHUK 0.025 0.015 -10000 0 -0.07 1 1
PLAU -0.073 0.069 -10000 0 -0.31 4 4
NF kappa B1 p50/RelA -0.069 0.05 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 0.043 0.02 -10000 0 -0.06 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.043 0.029 0.17 5 -10000 0 5
VAV3 -0.047 0.03 0.16 5 -10000 0 5
MAP3K14 -0.044 0.029 0.17 5 -10000 0 5
ROCK2 0.032 0.003 -10000 0 -10000 0 0
SPP1 -0.008 0.05 -10000 0 -0.069 197 197
RAC1 0.023 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.034 0.16 3 -10000 0 3
MMP2 -0.088 0.048 0.26 1 -0.17 4 5
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 -0.032 0.049 -10000 0 -0.13 77 77
STMN1 -0.024 0.009 -10000 0 -0.055 24 24
Aurora B/RasGAP/Survivin 0.016 0.059 -10000 0 -0.057 196 196
Chromosomal passenger complex/Cul3 protein complex -0.035 0.056 -10000 0 -0.1 163 163
BIRC5 -0.01 0.051 -10000 0 -0.073 201 201
DES 0.018 0.098 -10000 0 -0.68 9 9
Aurora C/Aurora B/INCENP 0.049 0.033 -10000 0 -0.047 37 37
Aurora B/TACC1 0.038 0.02 -10000 0 -0.044 23 23
Aurora B/PP2A 0.042 0.024 -10000 0 -0.055 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.005 0.005 -10000 0 -0.017 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.02 2 -10000 0 2
NDC80 -0.034 0.019 -10000 0 -0.06 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.007 0.045 -10000 0 -0.18 16 16
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.004 0.049 -10000 0 -0.071 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.023 -10000 0 -0.055 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.02 0.032 -10000 0 -0.07 56 56
SMC4 -0.044 0.044 -10000 0 -0.07 377 377
NSUN2/NPM1/Nucleolin -0.008 0.079 -10000 0 -0.54 9 9
PSMA3 0.031 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.009 0.012 -10000 0 -0.041 25 25
AURKB 0.026 0.024 -10000 0 -0.067 30 30
AURKC 0.03 0.01 -10000 0 -0.07 2 2
CDCA8 0.028 0.019 -10000 0 -0.07 17 17
cytokinesis -0.023 0.066 0.15 1 -0.21 33 34
Aurora B/Septin1 -0.015 0.07 0.14 1 -0.22 27 28
AURKA 0.027 0.019 -10000 0 -0.069 16 16
INCENP 0.031 0.005 -10000 0 -0.026 2 2
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.032 0.009 -10000 0 -0.069 4 4
hSgo1/Aurora B/Survivin 0.007 0.041 -10000 0 -0.043 201 201
EVI5 0.031 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.075 0.16 1 -0.16 31 32
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.001 0.045 -10000 0 -0.17 21 21
NCAPG 0.01 0.042 -10000 0 -0.07 111 111
Aurora B/HC8 Proteasome 0.041 0.023 -10000 0 -0.055 21 21
NCAPD2 0.012 0.04 -10000 0 -0.07 94 94
Aurora B/PP1-gamma 0.041 0.024 -10000 0 -0.055 25 25
RHOA 0.032 0.006 -10000 0 -10000 0 0
NCAPH 0.029 0.017 -10000 0 -0.07 15 15
NPM1 -0.002 0.075 -10000 0 -0.36 16 16
RASA1 0.032 0.006 -10000 0 -10000 0 0
KLHL9 0.021 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.023 -10000 0 -0.055 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0 0.071 0.16 1 -0.16 34 35
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.003 0.045 -10000 0 -0.31 9 9
MYLK 0.008 0.014 -10000 0 -0.042 34 34
KIF23 0.016 0.038 -10000 0 -0.073 77 77
VIM -0.02 0.014 0.021 1 -0.055 32 33
RACGAP1 0 0.048 -10000 0 -0.072 154 154
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.046 -10000 0 -0.28 11 11
Chromosomal passenger complex -0.011 0.044 0.086 1 -0.14 33 34
Chromosomal passenger complex/EVI5 0.027 0.076 -10000 0 -0.1 16 16
TACC1 0.032 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
CUL3 0.033 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Wnt signaling

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.002 0.04 -9999 0 -0.12 24 24
FZD6 0.013 0.039 -9999 0 -0.07 93 93
WNT6 0.032 0.001 -9999 0 -10000 0 0
WNT4 0.031 0.009 -9999 0 -0.07 2 2
FZD3 0.03 0.01 -9999 0 -0.07 3 3
WNT5A 0.001 0.047 -9999 0 -0.07 155 155
WNT11 0.032 0.008 -9999 0 -0.07 2 2
Syndecan-4-mediated signaling events

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
PTK2 -0.001 0.058 -10000 0 -0.32 10 10
Syndecan-4/Syndesmos -0.032 0.098 -10000 0 -0.38 21 21
positive regulation of JNK cascade -0.038 0.099 -10000 0 -0.32 28 28
Syndecan-4/ADAM12 -0.023 0.11 -10000 0 -0.37 23 23
CCL5 0.027 0.022 -10000 0 -0.07 25 25
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DNM2 0.031 0.007 -10000 0 -10000 0 0
ITGA5 0.018 0.035 -10000 0 -0.07 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.024 0.023 -10000 0 -0.056 10 10
ADAM12 0.024 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 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.032 0.098 -10000 0 -0.38 21 21
Syndecan-4/CXCL12/CXCR4 -0.039 0.1 -10000 0 -0.34 28 28
Syndecan-4/Laminin alpha3 -0.018 0.11 -10000 0 -0.38 21 21
MDK -0.025 0.05 -10000 0 -0.07 282 282
Syndecan-4/FZD7 -0.035 0.11 -10000 0 -0.39 21 21
Syndecan-4/Midkine -0.038 0.1 -10000 0 -0.35 27 27
FZD7 -0.015 0.051 -10000 0 -0.07 238 238
Syndecan-4/FGFR1/FGF -0.005 0.12 -10000 0 -0.34 26 26
THBS1 0.024 0.028 -10000 0 -0.07 39 39
integrin-mediated signaling pathway -0.049 0.092 -10000 0 -0.35 26 26
positive regulation of MAPKKK cascade -0.038 0.099 -10000 0 -0.32 28 28
Syndecan-4/TACI -0.016 0.11 -10000 0 -0.38 22 22
CXCR4 -0.02 0.051 -10000 0 -0.07 263 263
cell adhesion -0.007 0.032 0.2 4 -0.087 14 18
Syndecan-4/Dynamin -0.019 0.11 -10000 0 -0.39 20 20
Syndecan-4/TSP1 -0.019 0.11 -10000 0 -0.38 21 21
Syndecan-4/GIPC -0.019 0.11 -10000 0 -0.38 20 20
Syndecan-4/RANTES -0.018 0.11 -10000 0 -0.38 21 21
ITGB1 0.025 0.013 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.029 0.018 -10000 0 -0.07 15 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA 0.001 0.095 0.8 7 -10000 0 7
Syndecan-4/alpha-Actinin -0.02 0.11 -10000 0 -0.35 28 28
TFPI 0.01 0.042 -10000 0 -0.07 112 112
F2 0.028 0.02 -10000 0 -0.046 11 11
alpha5/beta1 Integrin 0.024 0.035 -10000 0 -0.054 61 61
positive regulation of cell adhesion -0.026 0.1 -10000 0 -0.33 28 28
ACTN1 0.022 0.028 -10000 0 -0.07 40 40
TNC -0.063 0.024 -10000 0 -0.07 469 469
Syndecan-4/CXCL12 -0.023 0.11 -10000 0 -0.35 28 28
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CXCL12 0.023 0.02 -10000 0 -0.07 12 12
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.07 2 2
FGFR1 0.032 0.006 -10000 0 -0.07 1 1
Syndecan-4/PI-4-5-P2 -0.032 0.098 -10000 0 -0.38 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.008 0.041 -10000 0 -0.063 107 107
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -0.058 8 8
vasculogenesis -0.018 0.11 -10000 0 -0.33 28 28
SDC4 -0.03 0.1 -10000 0 -0.37 25 25
Syndecan-4/Tenascin C -0.05 0.096 -10000 0 -0.36 26 26
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.017 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.016 0.11 -10000 0 -0.38 21 21
MMP9 -0.007 0.047 -10000 0 -0.067 177 177
Rac1/GTP -0.007 0.033 0.2 4 -0.088 14 18
cytoskeleton organization -0.031 0.094 -10000 0 -0.36 21 21
GIPC1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.025 0.11 -10000 0 -0.38 21 21
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.023 -10000 0 -0.07 26 26
CCL5 0.027 0.022 -10000 0 -0.07 25 25
SDCBP 0.032 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.013 0.049 0.1 17 -0.14 26 43
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 -0.01 0.054 0.17 2 -0.19 14 16
Syndecan-1/Syntenin 0.001 0.067 0.2 16 -0.2 10 26
MAPK3 -0.037 0.053 0.16 4 -0.16 28 32
HGF/MET 0.031 0.024 -10000 0 -0.054 3 3
TGFB1/TGF beta receptor Type II 0.026 0.023 -10000 0 -0.07 26 26
BSG 0.031 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.01 0.054 0.16 2 -0.19 14 16
Syndecan-1/RANTES 0 0.07 0.2 17 -0.18 16 33
Syndecan-1/CD147 -0.031 0.059 0.19 4 -0.17 25 29
Syndecan-1/Syntenin/PIP2 0.001 0.064 0.19 16 -0.19 10 26
LAMA5 0.027 0.018 -10000 0 -0.07 13 13
positive regulation of cell-cell adhesion 0 0.063 0.19 16 -0.19 10 26
MMP7 0.017 0.036 -10000 0 -0.07 75 75
HGF 0.022 0.016 -10000 0 -0.07 1 1
Syndecan-1/CASK -0.015 0.046 -10000 0 -0.18 14 14
Syndecan-1/HGF/MET 0 0.058 0.2 5 -0.2 8 13
regulation of cell adhesion -0.037 0.073 0.23 20 -0.21 13 33
HPSE 0.023 0.029 -10000 0 -0.07 44 44
positive regulation of cell migration -0.013 0.049 0.1 17 -0.14 26 43
SDC1 -0.012 0.044 0.1 17 -0.13 23 40
Syndecan-1/Collagen -0.013 0.049 0.1 17 -0.14 26 43
PPIB -0.039 0.046 -10000 0 -0.07 354 354
MET 0.021 0.016 -10000 0 -0.07 2 2
PRKACA 0.031 0.006 -10000 0 -10000 0 0
MMP9 -0.003 0.047 -10000 0 -0.07 166 166
MAPK1 -0.036 0.053 0.16 4 -0.17 26 30
homophilic cell adhesion -0.011 0.055 0.18 7 -0.19 14 21
MMP1 0.024 0.027 -10000 0 -0.07 38 38
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.021 0.096 0.19 15 -0.29 47 62
CRKL -0.021 0.095 0.18 1 -0.3 48 49
HRAS -0.005 0.097 0.16 3 -0.27 49 52
mol:PIP3 0.042 0.12 0.26 34 -0.28 36 70
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.003 -10000 0 -10000 0 0
GAB1 -0.014 0.099 -10000 0 -0.31 48 48
FOXO3 0.03 0.14 0.26 21 -0.35 17 38
AKT1 0.036 0.14 0.26 19 -0.38 16 35
BAD 0.03 0.13 0.24 17 -0.35 17 34
megakaryocyte differentiation -0.012 0.09 -10000 0 -0.3 44 44
GSK3B 0.031 0.14 0.26 21 -0.36 16 37
RAF1 -0.012 0.083 0.17 5 -0.23 48 53
SHC1 0.024 0.028 -10000 0 -0.07 40 40
STAT3 -0.016 0.099 -10000 0 -0.31 48 48
STAT1 -0.032 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.007 0.082 0.14 3 -0.22 49 52
cell proliferation -0.019 0.096 -10000 0 -0.31 48 48
PIK3CA 0.028 0.019 -10000 0 -0.069 17 17
TEC 0.031 0.006 -10000 0 -10000 0 0
RPS6KB1 0.019 0.11 0.2 2 -0.31 31 33
HRAS/SPRED2 0.006 0.093 0.19 3 -0.23 47 50
LYN/TEC/p62DOK 0.022 0.12 -10000 0 -0.31 48 48
MAPK3 -0.006 0.072 0.19 15 -0.18 36 51
STAP1 -0.015 0.099 -10000 0 -0.31 48 48
GRAP2 0.03 0.008 -10000 0 -10000 0 0
JAK2 -0.027 0.16 -10000 0 -0.5 47 47
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 0.031 0.12 -10000 0 -0.31 47 47
actin filament polymerization -0.009 0.098 -10000 0 -0.3 48 48
LYN 0.02 0.033 -10000 0 -0.07 60 60
STAP1/STAT5A (dimer) -0.024 0.13 0.21 1 -0.4 47 48
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.11 0.22 2 -0.29 48 50
PI3K 0.04 0.12 0.24 1 -0.3 31 32
PTEN 0.022 0.016 -10000 0 -0.07 2 2
SCF/KIT/EPO/EPOR -0.017 0.18 -10000 0 -0.57 46 46
MAPK8 -0.019 0.097 -10000 0 -0.31 48 48
STAT3 (dimer) -0.015 0.098 -10000 0 -0.31 48 48
positive regulation of transcription -0.003 0.063 0.18 17 -0.16 18 35
mol:GDP 0.001 0.1 -10000 0 -0.28 47 47
PIK3C2B -0.016 0.097 -10000 0 -0.31 46 46
CBL/CRKL -0.004 0.1 0.21 4 -0.3 48 52
FER -0.015 0.099 -10000 0 -0.31 47 47
SH2B3 -0.015 0.098 -10000 0 -0.31 48 48
PDPK1 0.035 0.12 0.24 34 -0.26 35 69
SNAI2 -0.021 0.099 -10000 0 -0.32 48 48
positive regulation of cell proliferation -0.028 0.15 -10000 0 -0.47 48 48
KITLG 0.027 0.024 -10000 0 -0.045 45 45
cell motility -0.028 0.15 -10000 0 -0.47 48 48
PTPN6 0.028 0.019 -10000 0 -0.048 22 22
EPOR 0.016 0.078 -10000 0 -0.48 4 4
STAT5A (dimer) -0.018 0.13 -10000 0 -0.4 47 47
SOCS1 0.032 0.004 -10000 0 -10000 0 0
cell migration 0.015 0.096 0.31 46 -10000 0 46
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.019 0.021 -10000 0 -10000 0 0
VAV1 0.031 0.007 -10000 0 -0.07 1 1
GRB10 -0.011 0.076 -10000 0 -0.32 28 28
PTPN11 0.031 0.01 -10000 0 -0.029 10 10
SCF/KIT -0.008 0.1 -10000 0 -0.32 48 48
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.07 0.16 6 -0.19 47 53
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.037 0.2 -10000 0 -0.63 52 52
MAP2K2 -0.013 0.078 0.21 17 -0.19 47 64
SHC/Grb2/SOS1 0.012 0.11 -10000 0 -0.3 48 48
STAT5A -0.017 0.13 -10000 0 -0.41 46 46
GRB2 0.031 0.006 -10000 0 -10000 0 0
response to radiation -0.02 0.098 -10000 0 -0.31 48 48
SHC/GRAP2 0.036 0.029 -10000 0 -0.054 38 38
PTPRO -0.012 0.092 -10000 0 -0.3 44 44
SH2B2 -0.01 0.099 -10000 0 -0.31 48 48
DOK1 0.032 0.001 -10000 0 -10000 0 0
MATK -0.015 0.097 -10000 0 -0.31 46 46
CREBBP 0.027 0.043 -10000 0 -0.1 47 47
BCL2 0.006 0.12 -10000 0 -0.67 10 10
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 0.019 0.069 -9999 0 -0.25 11 11
MAP3K8 0.017 0.028 -9999 0 -0.07 37 37
FOS 0.011 0.058 -9999 0 -0.25 9 9
PRKCA 0.031 0.004 -9999 0 0 8 8
PTPN7 0.03 0.009 -9999 0 -0.034 5 5
HRAS 0.031 0.007 -9999 0 -10000 0 0
PRKCB -0.001 0.002 -9999 0 -0.003 124 124
NRAS 0.007 0.044 -9999 0 -0.07 125 125
RAS family/GTP 0.029 0.047 -9999 0 -0.047 121 121
MAPK3 0.026 0.031 -9999 0 -0.36 2 2
MAP2K1 -0.003 0.025 -9999 0 -0.18 2 2
ELK1 0.031 0.007 -9999 0 -0.024 6 6
BRAF 0.003 0.016 -9999 0 -0.23 2 2
mol:GTP 0 0 -9999 0 -0.001 124 124
MAPK1 0.002 0.097 -9999 0 -0.35 33 33
RAF1 0.005 0.016 -9999 0 -0.22 2 2
KRAS 0.031 0.008 -9999 0 -10000 0 0
PLK1 signaling events

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.009 -10000 0 -0.028 29 29
BUB1B -0.015 0.036 0.089 8 -0.12 23 31
PLK1 0.006 0.023 0.069 35 -0.093 4 39
PLK1S1 0.002 0.013 0.042 35 -0.047 4 39
KIF2A -0.001 0.025 0.17 4 -0.1 2 6
regulation of mitotic centrosome separation 0.006 0.023 0.069 35 -0.093 4 39
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.029 0.1 3 -0.082 9 12
WEE1 -0.022 0.067 -10000 0 -0.35 15 15
cytokinesis -0.013 0.042 0.17 2 -0.16 11 13
PP2A-alpha B56 0.056 0.072 -10000 0 -0.56 6 6
AURKA 0.007 0.018 0.087 3 -0.14 2 5
PICH/PLK1 -0.034 0.022 -10000 0 -0.086 18 18
CENPE -0.004 0.027 0.17 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 0.15 6 -0.1 2 8
PPP2CA 0.032 0.005 -10000 0 -10000 0 0
FZR1 0.031 0.006 -10000 0 -10000 0 0
TPX2 -0.012 0.027 0.11 2 -0.09 2 4
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 -10000 0 -0.23 7 7
GORASP1 0.032 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 3 -0.011 4 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.042 35 -0.047 4 39
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.027 0.023 -10000 0 -0.07 26 26
GRASP65/GM130/RAB1/GTP 0.011 0.061 -10000 0 -0.5 7 7
spindle elongation 0.006 0.023 0.069 35 -0.093 4 39
ODF2 0.032 0.007 -10000 0 -10000 0 0
BUB1 0.024 0.068 -10000 0 -0.59 6 6
TPT1 -0.003 0.052 0.083 2 -0.19 34 36
CDC25C 0.011 0.031 -10000 0 -0.24 6 6
CDC25B 0.026 0.019 -10000 0 -0.066 16 16
SGOL1 0.001 0.009 0.028 29 -10000 0 29
RHOA 0.032 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 -0.015 0.049 -10000 0 -0.07 137 137
CDC14B -0.011 0.004 0.009 10 -10000 0 10
CDC20 -0.026 0.05 -10000 0 -0.07 287 287
PLK1/PBIP1 -0.02 0.015 0.062 1 -0.072 13 14
mitosis -0.003 0.003 0.016 5 -10000 0 5
FBXO5 -0.015 0.033 0.11 6 -0.098 33 39
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 -0.002 0.048 -10000 0 -0.07 168 168
metaphase plate congression 0.009 0.033 -10000 0 -0.23 8 8
ERCC6L -0.027 0.038 -10000 0 -0.097 40 40
NLP/gamma Tubulin 0.004 0.016 0.06 12 -0.068 6 18
microtubule cytoskeleton organization -0.003 0.052 0.082 2 -0.19 34 36
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 0.004 0.05 0.12 3 -0.083 26 29
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.03 0.14 1 -0.092 4 5
RAB1A 0.032 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.005 0.022 0.068 40 -0.061 4 44
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.093 0.13 2 -0.23 94 96
microtubule-based process 0.008 0.032 0.1 4 -0.082 11 15
Golgi organization 0.006 0.023 0.069 35 -0.093 4 39
Cohesin/SA2 0.021 0.023 0.096 3 -0.073 6 9
PPP1CB/MYPT1 0.047 0.011 -10000 0 -0.051 1 1
KIF20A -0.004 0.049 -10000 0 -0.07 178 178
APC/C/CDC20 -0.003 0.032 0.11 2 -0.078 14 16
PPP2R1A 0.03 0.009 -10000 0 -10000 0 0
chromosome segregation -0.02 0.015 0.061 1 -0.071 13 14
PRC1 -0.011 0.05 -10000 0 -0.07 213 213
ECT2 -0.006 0.037 0.18 13 -0.12 3 16
C13orf34 0.005 0.02 0.063 35 -0.07 4 39
NUDC 0.009 0.033 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.015 0.035 0.089 8 -0.12 23 31
spindle assembly 0.004 0.02 0.064 24 -0.08 4 28
spindle stabilization 0.002 0.013 0.041 35 -0.047 4 39
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.008 0.032 0.1 4 -0.083 11 15
CCNB1 -0.024 0.051 -10000 0 -0.07 280 280
PPP1CB 0.032 0.007 -10000 0 -0.065 2 2
BTRC 0.025 0.014 -10000 0 -10000 0 0
ROCK2 0.016 0.024 -10000 0 -0.29 1 1
TUBG1 0.008 0.022 0.087 1 -0.16 5 6
G2/M transition of mitotic cell cycle -0.028 0.032 -10000 0 -0.09 43 43
MLF1IP -0.038 0.013 -10000 0 -0.044 419 419
INCENP 0.032 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.028 0.019 -10000 0 -0.049 2 2
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.019 0.18 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.012 0.036 -10000 0 -0.044 274 274
CaM/Ca2+ -0.027 0.022 0.18 3 -10000 0 3
HIF1A 0.036 0.011 -10000 0 -0.068 2 2
GAB1 0.031 0.009 -10000 0 -0.07 3 3
AKT1 -0.023 0.035 0.13 17 -0.19 1 18
PLCG1 -0.024 0.02 0.18 3 -10000 0 3
NOS3 -0.006 0.041 0.18 5 -0.21 12 17
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.007 0.054 0.15 21 -0.21 12 33
FLT1 -0.017 0.006 -10000 0 -10000 0 0
PGF 0.026 0.021 -10000 0 -0.07 19 19
VEGFR1 homodimer/NRP2/VEGFR121 -0.008 0.051 -10000 0 -0.06 26 26
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
eNOS/Hsp90 0.024 0.073 0.19 14 -0.22 21 35
endothelial cell proliferation -0.009 0.049 0.12 39 -0.15 17 56
mol:Ca2+ -0.024 0.019 0.18 3 -10000 0 3
MAPK3 -0.035 0.02 0.15 3 -10000 0 3
MAPK1 -0.032 0.021 0.15 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PLGF homodimer 0.026 0.021 -10000 0 -0.07 19 19
PRKACA 0.031 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.021 0.044 -10000 0 -0.07 216 216
VEGFA homodimer -0.023 0.051 -10000 0 -0.07 275 275
VEGFR1 homodimer/VEGFA homodimer -0.014 0.04 -10000 0 -0.049 271 271
platelet activating factor biosynthetic process -0.037 0.022 0.14 3 -10000 0 3
PI3K 0.045 0.047 0.17 2 -0.08 1 3
PRKCA -0.028 0.02 0.17 3 -10000 0 3
PRKCB -0.022 0.018 0.17 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer 0.026 0.021 -10000 0 -0.049 21 21
VEGFA -0.023 0.051 -10000 0 -0.07 275 275
VEGFB 0.032 0.004 -10000 0 0 7 7
mol:IP3 -0.024 0.019 0.18 3 -10000 0 3
RASA1 -0.026 0.018 0.18 3 -10000 0 3
NRP2 0.032 0.005 -10000 0 -0.07 1 1
VEGFR1 homodimer -0.017 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.032 0.004 -10000 0 0 7 7
NCK1 0.029 0.016 -10000 0 -0.07 11 11
eNOS/Caveolin-1 -0.014 0.049 0.17 1 -0.22 14 15
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.046 0.16 2 -0.079 1 3
mol:L-citrulline 0.007 0.054 0.15 21 -0.21 12 33
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.01 0.061 0.17 1 -0.08 1 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.01 0.05 -10000 0 -0.061 29 29
CD2AP 0.022 0.03 -10000 0 -0.07 48 48
PI3K/GAB1 0.054 0.055 0.18 2 -10000 0 2
PDPK1 -0.031 0.036 0.15 17 -10000 0 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.008 0.051 -10000 0 -0.06 28 28
mol:NADP 0.007 0.054 0.15 21 -0.21 12 33
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.01 0.06 0.17 1 -0.08 1 2
VEGFR1 homodimer/NRP2 0.028 0.02 -10000 0 -0.049 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.004 0.078 0.15 3 -0.12 136 139
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.037 28 28
BIRC3 -0.033 0.024 0.17 4 -10000 0 4
CYCS 0.004 0.069 0.17 64 -0.1 41 105
RIPK1 0.03 0.014 -10000 0 -0.07 9 9
CD247 0.033 0.008 -10000 0 -0.07 2 2
MAP2K7 -0.007 0.087 -10000 0 -0.4 7 7
protein ubiquitination 0.001 0.052 0.2 7 -0.23 11 18
CRADD 0.032 0.004 -10000 0 -10000 0 0
DAXX 0.032 0.005 -10000 0 -0.07 1 1
FAS 0.013 0.032 -10000 0 -0.07 55 55
BID -0.019 0.044 0.16 3 -0.1 94 97
NF-kappa-B/RelA/I kappa B alpha 0.055 0.042 -10000 0 -0.067 34 34
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 -0.07 5 5
FADD 0.032 0.006 -10000 0 -0.07 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.055 0.042 -10000 0 -0.067 34 34
MAPK8 -0.006 0.081 -10000 0 -0.38 8 8
APAF1 0.032 0.004 -10000 0 -10000 0 0
TRAF1 0.031 0.008 -10000 0 -0.07 1 1
TRAF2 0.031 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.025 0.15 4 -0.12 7 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.054 -10000 0 -0.22 14 14
CHUK 0.002 0.052 0.2 7 -0.22 12 19
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.039 0.071 -10000 0 -0.075 6 6
TCRz/NEF 0.029 0.006 -10000 0 -0.043 2 2
TNF 0.032 0.007 -10000 0 -0.07 2 2
FASLG -0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.04 32 32
TNFR1A/BAG4/TNF-alpha 0.024 0.055 -10000 0 -0.052 163 163
CASP6 0.009 0.085 -10000 0 -0.44 5 5
CASP7 -0.057 0.11 0.18 5 -0.24 124 129
RELA 0.028 0.016 -10000 0 -0.035 30 30
CASP2 0.022 0.015 -10000 0 -10000 0 0
CASP3 -0.029 0.07 0.18 4 -0.23 26 30
TNFRSF1A -0.002 0.047 -10000 0 -0.07 164 164
TNFR1A/BAG4 0.013 0.047 -10000 0 -0.054 162 162
CASP8 0.031 0.014 -10000 0 -0.07 10 10
CASP9 0.031 0.009 -10000 0 -0.07 3 3
MAP3K14 0.009 0.056 0.14 4 -0.22 16 20
APAF-1/Caspase 9 -0.015 0.072 0.13 70 -0.16 6 76
BCL2 -0.017 0.082 0.24 2 -0.36 8 10
Caspase cascade in apoptosis

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
TOP1 -0.015 0.095 -10000 0 -0.32 25 25
ACTA1 -0.044 0.084 -10000 0 -0.23 53 53
NUMA1 -0.013 0.083 -10000 0 -0.31 26 26
SPTAN1 -0.044 0.086 0.18 7 -0.31 30 37
LIMK1 0.001 0.1 0.18 79 -0.28 22 101
BIRC3 0.026 0.024 -10000 0 -0.07 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.07 6 6
CASP10 -0.021 0.014 -10000 0 -0.055 19 19
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0 1 -0.001 10 11
PTK2 -0.014 0.083 -10000 0 -0.3 27 27
DIABLO 0.032 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.04 0.089 0.17 7 -0.3 30 37
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.047 0.086 0.18 7 -0.27 40 47
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.029 0.093 -10000 0 -0.66 8 8
BID -0.005 0.014 -10000 0 -0.12 6 6
MAP3K1 -0.009 0.055 -10000 0 -0.38 7 7
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 -0.054 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.047 0.089 0.18 11 -0.27 41 52
CASP9 0.031 0.009 -10000 0 -0.07 3 3
DNA repair 0.025 0.058 0.17 28 -10000 0 28
neuron apoptosis 0.019 0.076 -10000 0 -0.64 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.089 0.2 2 -0.32 30 32
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.013 0.1 -10000 0 -0.93 4 4
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.052 0.087 0.27 5 -0.3 31 36
CASP7 -0.053 0.1 -10000 0 -0.22 128 128
KRT18 0.013 0.053 -10000 0 -0.47 4 4
apoptosis -0.048 0.095 -10000 0 -0.35 27 27
DFFA -0.048 0.085 0.18 3 -0.28 36 39
DFFB -0.048 0.085 0.18 3 -0.28 36 39
PARP1 -0.025 0.059 -10000 0 -0.18 28 28
actin filament polymerization -0.009 0.099 0.26 22 -0.17 79 101
TNF 0.032 0.007 -10000 0 -0.07 2 2
CYCS 0 0.026 -10000 0 -0.22 2 2
SATB1 0.017 0.1 0.31 1 -0.83 4 5
SLK -0.051 0.084 -10000 0 -0.26 47 47
p15 BID/BAX -0.01 0.062 -10000 0 -0.17 43 43
CASP2 0.041 0.089 0.19 119 -0.15 7 126
JNK cascade 0.008 0.055 0.38 7 -10000 0 7
CASP3 -0.045 0.087 -10000 0 -0.23 57 57
LMNB2 0.047 0.082 0.2 29 -0.27 5 34
RIPK1 0.03 0.014 -10000 0 -0.07 9 9
CASP4 0.012 0.041 -10000 0 -0.07 101 101
Mammalian IAPs/DIABLO 0.054 0.029 -10000 0 -0.045 36 36
negative regulation of DNA binding 0.029 0.092 -10000 0 -0.65 8 8
stress fiber formation -0.05 0.083 -10000 0 -0.26 44 44
GZMB -0.018 0.013 -10000 0 -0.057 19 19
CASP1 -0.014 0.037 -10000 0 -0.059 187 187
LMNB1 0.037 0.099 0.23 12 -0.36 11 23
APP 0.019 0.077 -10000 0 -0.65 6 6
TNFRSF1A -0.002 0.047 -10000 0 -0.07 164 164
response to stress 0 0 0.001 6 -0.001 21 27
CASP8 -0.012 0.004 -10000 0 -0.043 10 10
VIM -0.04 0.096 -10000 0 -0.34 27 27
LMNA 0.05 0.081 0.24 12 -0.31 3 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.001 0.04 -10000 0 -0.12 33 33
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.049 0.083 0.18 1 -0.29 35 36
APAF-1/Caspase 9 0.022 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.013 0.082 -10000 0 -0.3 26 26
CFL2 0.009 0.1 0.17 79 -0.26 22 101
GAS2 -0.05 0.084 0.18 2 -0.25 46 48
positive regulation of apoptosis 0.048 0.09 0.2 41 -0.32 7 48
PRF1 0.022 0.02 -10000 0 -0.07 12 12
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.061 0.048 -10000 0 -0.054 31 31
MAP4K1 0.031 0.008 -10000 0 -0.07 1 1
MAP3K8 0.018 0.028 -10000 0 -0.07 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 0.03 0.076 12 -0.1 29 41
JUN -0.11 0.22 0.23 2 -0.52 118 120
MAP3K7 0.001 0.029 0.076 12 -0.11 24 36
GRAP2 0.03 0.008 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
MAP2K4 -0.019 0.057 0.15 4 -0.21 30 34
LAT 0.032 0.005 -10000 0 -0.07 1 1
LCP2 0.026 0.024 -10000 0 -0.07 29 29
MAPK8 -0.11 0.24 -10000 0 -0.54 118 118
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.03 0.087 12 -0.12 16 28
LAT/GRAP2/SLP76/HPK1/HIP-55 0.057 0.044 -10000 0 -0.05 31 31
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.061 0.023 -10000 0 -0.052 10 10
fibroblast growth factor receptor signaling pathway 0.06 0.023 -10000 0 -0.052 10 10
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.028 0.011 -10000 0 -10000 0 0
GPC1/SLIT2 0.03 0.025 -10000 0 -0.054 5 5
SMAD2 -0.027 0.029 0.17 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.037 0.018 -10000 0 -0.043 7 7
GPC1/Laminin alpha1 0.023 0.008 -10000 0 -0.043 7 7
TDGF1 0.031 0.008 -10000 0 -0.07 2 2
CRIPTO/GPC1 0.045 0.016 -10000 0 -0.054 9 9
APP/GPC1 0.045 0.014 -10000 0 -0.054 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.029 0.012 -10000 0 -0.053 77 77
FLT1 0.031 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.058 0.027 -10000 0 -0.052 13 13
SERPINC1 0.032 0.006 -10000 0 -0.07 1 1
FYN -0.024 0.01 -10000 0 -0.052 7 7
FGR -0.026 0.009 -10000 0 -0.052 24 24
positive regulation of MAPKKK cascade -0.008 0.06 0.17 35 -0.19 5 40
SLIT2 0.02 0.017 -10000 0 -0.07 3 3
GPC1/NRG 0.046 0.014 -10000 0 -0.054 7 7
NRG1 0.032 0.005 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.058 -10000 0 -0.053 277 277
LYN -0.029 0.011 -10000 0 -0.052 67 67
mol:Spermine -0.012 0.004 -10000 0 -0.043 7 7
cell growth 0.06 0.023 -10000 0 -0.052 10 10
BMP signaling pathway -0.031 0.012 0.07 7 -10000 0 7
SRC -0.025 0.009 -10000 0 -0.052 8 8
TGFBR1 0.032 0.006 -10000 0 0 15 15
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.004 0.048 -10000 0 -0.07 179 179
GPC1 0.031 0.012 -10000 0 -0.07 7 7
TGFBR1 (dimer) 0.032 0.006 -10000 0 0 15 15
VEGFA -0.023 0.051 -10000 0 -0.07 275 275
BLK -0.026 0.007 -10000 0 -0.052 8 8
HCK -0.029 0.014 -10000 0 -0.052 90 90
FGF2 0.032 0.007 -10000 0 -0.07 2 2
FGFR1 0.032 0.006 -10000 0 -0.07 1 1
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.012 -10000 0 -0.07 6 6
cell death 0.045 0.014 -10000 0 -0.054 7 7
ATIII/GPC1 0.045 0.015 -10000 0 -0.054 8 8
PLA2G2A/GPC1 0.01 0.049 -10000 0 -0.054 182 182
LCK -0.026 0.007 -10000 0 -0.054 11 11
neuron differentiation 0.045 0.014 -10000 0 -0.054 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 0.012 -10000 0 -0.07 6 6
S1P1 pathway

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.007 0.049 -10000 0 -0.053 259 259
PDGFRB 0.032 0.008 -10000 0 -0.071 2 2
SPHK1 0.01 0.019 -10000 0 -10000 0 0
mol:S1P 0.004 0.024 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.068 -10000 0 -0.27 20 20
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.08 0.18 17 -0.23 18 35
PLCG1 -0.045 0.063 -10000 0 -0.24 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.008 -10000 0 -0.071 2 2
GNAI2 0.035 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.069 59 59
GNAI1 0.019 0.016 -10000 0 -0.067 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.027 0.015 0.011 1 -0.041 246 247
S1P1/S1P -0.005 0.034 0.18 1 -10000 0 1
negative regulation of cAMP metabolic process -0.04 0.067 -10000 0 -0.26 20 20
MAPK3 -0.05 0.07 -10000 0 -0.29 17 17
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 0.019 -10000 0 -0.069 14 14
PLCB2 -0.001 0.052 0.16 21 -10000 0 21
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.033 -10000 0 -10000 0 0
receptor internalization -0.005 0.032 0.17 1 -10000 0 1
PTGS2 -0.056 0.073 -10000 0 -0.34 10 10
Rac1/GTP -0.009 0.026 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.022 0.05 -10000 0 -0.068 275 275
negative regulation of T cell proliferation -0.04 0.067 -10000 0 -0.26 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 -0.3 15 15
S1P1/S1P/PDGFB-D/PDGFRB 0.007 0.054 0.18 11 -10000 0 11
ABCC1 0.031 0.013 -10000 0 -0.07 8 8
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 -0.019 0.044 0.21 8 -0.19 13 21
RFC1 -0.023 0.036 0.17 2 -0.19 15 17
PRKDC -0.024 0.038 0.19 3 -0.19 15 18
RIPK1 0.03 0.014 -10000 0 -0.069 9 9
CASP7 -0.14 0.26 -10000 0 -0.59 125 125
FASLG/FAS/FADD/FAF1 -0.021 0.057 0.11 1 -0.12 120 121
MAP2K4 -0.063 0.12 0.19 1 -0.24 127 128
mol:ceramide -0.018 0.066 -10000 0 -0.17 33 33
GSN -0.021 0.044 0.21 8 -0.19 14 22
FASLG/FAS/FADD/FAF1/Caspase 8 -0.028 0.065 0.14 1 -0.13 124 125
FAS 0.013 0.032 -10000 0 -0.071 55 55
BID -0.032 0.014 0.2 1 -10000 0 1
MAP3K1 -0.1 0.18 -10000 0 -0.39 130 130
MAP3K7 0.031 0.008 -10000 0 -0.07 1 1
RB1 -0.022 0.036 0.17 2 -0.19 15 17
CFLAR 0.032 0.01 -10000 0 -0.068 5 5
HGF/MET 0.036 0.037 -10000 0 -0.053 23 23
ARHGDIB -0.021 0.046 0.21 10 -0.2 12 22
FADD 0.032 0.007 -10000 0 -0.07 1 1
actin filament polymerization 0.02 0.044 0.19 14 -0.21 8 22
NFKB1 0.013 0.073 -10000 0 -0.62 6 6
MAPK8 -0.068 0.11 0.17 1 -0.24 122 123
DFFA -0.022 0.039 0.2 4 -0.2 14 18
DNA fragmentation during apoptosis -0.022 0.037 0.19 3 -0.19 14 17
FAS/FADD/MET 0.025 0.041 -10000 0 -0.052 53 53
CFLAR/RIP1 0.045 0.018 -10000 0 -0.053 14 14
FAIM3 0.031 0.007 -10000 0 -0.07 1 1
FAF1 0.03 0.008 -10000 0 -10000 0 0
PARP1 -0.024 0.038 0.22 2 -0.19 16 18
DFFB -0.022 0.037 0.19 3 -0.2 14 17
CHUK 0.004 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.035 -10000 0 -0.055 56 56
HGF 0.022 0.016 -10000 0 -0.07 1 1
LMNA -0.029 0.035 0.19 2 -0.18 14 16
CASP6 -0.024 0.035 0.17 2 -0.19 13 15
CASP10 0.032 0.001 -10000 0 -10000 0 0
CASP3 -0.017 0.034 0.16 1 -0.21 10 11
PTPN13 0.027 0.023 -10000 0 -0.07 26 26
CASP8 -0.031 0.008 0.059 1 -0.064 3 4
IL6 -0.028 0.09 -10000 0 -0.51 6 6
MET 0.021 0.016 -10000 0 -0.07 2 2
ICAD/CAD -0.027 0.041 0.25 4 -0.19 14 18
FASLG/FAS/FADD/FAF1/Caspase 10 -0.018 0.067 -10000 0 -0.17 33 33
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.021 0.042 0.21 7 -0.19 13 20
BCL2 0.031 0.006 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.015 0.028 -10000 0 -0.034 100 100
PDGF/PDGFRA/CRKL 0.037 0.022 -10000 0 -0.056 5 5
positive regulation of JUN kinase activity 0.039 0.035 -10000 0 -0.047 41 41
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.056 5 5
AP1 -0.029 0.076 0.14 58 -0.16 3 61
mol:IP3 -0.022 0.015 0.034 3 -0.072 2 5
PLCG1 -0.022 0.015 0.034 3 -0.072 2 5
PDGF/PDGFRA/alphaV Integrin 0.035 0.026 -10000 0 -0.057 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.015 0.034 3 -0.071 2 5
CAV3 0.032 0.005 -10000 0 -10000 0 0
CAV1 -0.021 0.044 -10000 0 -0.07 216 216
SHC/Grb2/SOS1 0.04 0.036 -10000 0 -0.047 41 41
PDGF/PDGFRA/Shf 0.019 0.012 -10000 0 -0.044 6 6
FOS -0.042 0.051 0.17 4 -0.14 96 100
JUN -0.026 0.022 0.053 3 -10000 0 3
oligodendrocyte development 0.035 0.026 -10000 0 -0.057 20 20
GRB2 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.015 0.034 3 -0.072 2 5
PDGF/PDGFRA 0.015 0.028 -10000 0 -0.034 100 100
actin cytoskeleton reorganization 0.036 0.022 -10000 0 -0.055 4 4
SRF -0.021 0.008 0.023 1 -10000 0 1
SHC1 0.024 0.028 -10000 0 -0.07 40 40
PI3K 0.045 0.035 -10000 0 -0.056 19 19
PDGF/PDGFRA/Crk/C3G 0.049 0.031 -10000 0 -0.041 18 18
JAK1 -0.018 0.014 0.021 27 -0.057 5 32
ELK1/SRF -0.009 0.06 0.13 74 -10000 0 74
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 -0.041 5 5
GO:0007205 -0.016 0.012 0.024 3 -0.062 5 8
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.039 0.035 -10000 0 -0.047 41 41
PDGF/PDGFRA/SHB 0.036 0.022 -10000 0 -0.055 4 4
PDGF/PDGFRA/Caveolin-1 -0.011 0.04 -10000 0 -0.058 184 184
ITGAV 0.029 0.018 -10000 0 -0.07 15 15
ELK1 -0.022 0.016 0.026 3 -0.077 2 5
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.055 5 5
JAK-STAT cascade -0.018 0.014 0.021 27 -0.057 5 32
cell proliferation 0.019 0.012 -10000 0 -0.044 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.031 0.007 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.045 0.13 0.16 1 -0.26 121 122
HIF1A -0.043 0.12 -10000 0 -0.32 83 83
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.049 0.049 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.014 -10000 0 -10000 0 0
CDKN2A 0.002 0.028 -10000 0 -0.07 53 53
ARNT/IPAS 0.045 0.013 -10000 0 -10000 0 0
HIF1AN 0.025 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.039 0.13 0.16 1 -0.26 119 120
CUL2 0.026 0.013 -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 -0.039 0.13 0.16 2 -0.26 121 123
PHD1-3/OS9 0.06 0.042 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.018 0.14 0.18 1 -0.26 120 121
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.04 0.13 0.16 1 -0.26 120 121
EGLN3 0.03 0.012 -10000 0 -0.07 4 4
EGLN2 0.031 0.007 -10000 0 -10000 0 0
EGLN1 0.032 0.007 -10000 0 -0.07 1 1
TP53 0.018 0.034 -10000 0 -0.07 65 65
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.003 0.069 -10000 0 -0.58 3 3
ARNT 0.032 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF -0.055 0.13 0.16 2 -0.27 120 122
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 0.028 0.081 2 -0.1 26 28
MKNK1 0.032 0.005 -10000 0 -10000 0 0
MAPK14 0.032 0.025 0.092 4 -0.072 26 30
ATF2/c-Jun 0.004 0.041 -10000 0 -0.11 49 49
MAPK11 0.029 0.026 0.089 3 -0.072 25 28
MITF 0.016 0.018 0.081 4 -0.048 28 32
MAPKAPK5 0.016 0.017 0.082 3 -0.049 26 29
KRT8 0.013 0.022 0.082 3 -0.05 45 48
MAPKAPK3 0.032 0.007 -10000 0 -0.07 1 1
MAPKAPK2 0.032 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.034 -10000 0 -0.09 25 25
CEBPB 0.014 0.02 0.072 2 -0.056 30 32
SLC9A1 0.015 0.017 0.1 1 -0.049 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.02 0.1 8 -0.051 25 33
p38alpha-beta/MNK1 0.053 0.037 -10000 0 -0.075 25 25
JUN 0 0.039 -10000 0 -0.11 49 49
PPARGC1A 0.016 0.018 0.081 4 -0.05 28 32
USF1 0.012 0.016 0.077 4 -0.05 26 30
RAB5/GDP/GDI1 0.014 0.048 -10000 0 -0.12 44 44
NOS2 0.012 0.016 0.076 4 -0.05 26 30
DDIT3 0.014 0.019 0.083 2 -0.051 28 30
RAB5A 0.032 0.004 -10000 0 -10000 0 0
HSPB1 0.062 0.12 0.27 127 -10000 0 127
p38alpha-beta/HBP1 0.037 0.04 -10000 0 -0.076 20 20
CREB1 0.004 0.056 -10000 0 -0.2 34 34
RAB5/GDP 0.024 0.003 -10000 0 -10000 0 0
EIF4E -0.032 0.027 0.22 5 -10000 0 5
RPS6KA4 0.016 0.018 0.081 4 -0.049 26 30
PLA2G4A -0.038 0.025 0.21 3 -10000 0 3
GDI1 0.016 0.016 0.081 4 -0.049 17 21
TP53 -0.016 0.018 0.067 4 -0.077 26 30
RPS6KA5 0.015 0.018 0.081 4 -0.049 26 30
ESR1 0.015 0.018 0.081 4 -0.049 25 29
HBP1 0.022 0.015 -10000 0 -10000 0 0
MEF2C 0.014 0.016 0.072 2 -0.049 17 19
MEF2A 0.016 0.018 0.081 4 -0.049 26 30
EIF4EBP1 -0.01 0.057 -10000 0 -0.21 33 33
KRT19 0.013 0.022 0.081 4 -0.049 45 49
ELK4 0.016 0.017 0.075 3 -0.049 25 28
ATF6 0.016 0.017 0.075 3 -0.049 25 28
ATF1 0.001 0.058 -10000 0 -0.19 38 38
p38alpha-beta/MAPKAPK2 0.054 0.037 -10000 0 -0.075 24 24
p38alpha-beta/MAPKAPK3 0.053 0.038 -10000 0 -0.075 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 0.015 0.025 -10000 0 -0.026 130 130
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.063 -10000 0 -0.085 12 12
AKT1 0.031 0.008 -10000 0 -10000 0 0
GSC 0.008 0.028 0.09 29 -10000 0 29
NKX2-5 0 0 -10000 0 -10000 0 0
muscle cell differentiation -0.013 0.069 0.24 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.011 0.08 -10000 0 -0.12 15 15
SMAD4 -0.01 0.053 -10000 0 -0.089 102 102
CBFB 0.031 0.01 -10000 0 -0.07 4 4
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.049 0.032 -10000 0 -0.056 24 24
SMAD3/SMAD4/VDR 0.037 0.078 -10000 0 -0.098 2 2
MYC 0.007 0.043 -10000 0 -0.071 119 119
CDKN2B -0.2 0.19 -10000 0 -0.36 288 288
AP1 -0.004 0.051 0.14 6 -0.088 20 26
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.069 -10000 0 -0.21 30 30
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.058 0.14 3 -0.24 21 24
SP3 0.017 0.037 -10000 0 -0.067 80 80
CREB1 0.033 0 -10000 0 -10000 0 0
FOXH1 0.035 0.011 0.089 6 -10000 0 6
SMAD3/SMAD4/GR 0.03 0.062 -10000 0 -0.09 13 13
GATA3 0.025 0.015 -10000 0 -0.07 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.002 0.066 -10000 0 -0.18 38 38
MEF2C/TIF2 -0.028 0.04 0.21 10 -10000 0 10
endothelial cell migration 0.04 0.072 0.46 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 0.014 0.039 -10000 0 -0.069 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.01 -10000 0 -0.07 3 3
RUNX1 0.032 0.005 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 0.036 0.007 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
CDKN1A -0.018 0.059 0.32 3 -0.42 1 4
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.027 0.05 -10000 0 -0.063 37 37
DCP1A 0.032 0.005 -10000 0 -10000 0 0
SKI 0.031 0.007 -10000 0 -10000 0 0
SERPINE1 -0.039 0.072 -10000 0 -0.46 2 2
SMAD3/SMAD4/ATF2 0.022 0.062 -10000 0 -0.083 36 36
SMAD3/SMAD4/ATF3 0.005 0.067 -10000 0 -0.087 70 70
SAP30 0.032 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.049 0.027 -10000 0 -0.045 5 5
JUN -0.027 0.04 0.14 10 -10000 0 10
SMAD3/SMAD4/IRF7 0.022 0.066 -10000 0 -0.091 26 26
TFE3 -0.007 0.038 -10000 0 -0.045 211 211
COL1A2 -0.028 0.056 -10000 0 -0.12 33 33
mesenchymal cell differentiation -0.021 0.062 0.084 31 -10000 0 31
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.006 -10000 0 -10000 0 0
FOS 0.002 0.047 -10000 0 -0.068 146 146
SMAD3/SMAD4/Max 0.029 0.063 -10000 0 -0.089 17 17
Cbp/p300/SNIP1 0.055 0.027 -10000 0 -10000 0 0
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.053 0.047 0.13 6 -0.13 21 27
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.06 -10000 0 -0.084 34 34
IRF7 0.029 0.017 -10000 0 -0.071 12 12
ESR1 0.038 0.015 0.13 3 -0.028 1 4
HNF4A 0.03 0.009 -10000 0 -10000 0 0
MEF2C -0.024 0.041 0.2 13 -10000 0 13
SMAD2-3/SMAD4 0.025 0.063 -10000 0 -0.09 16 16
Cbp/p300/Src-1 0.052 0.027 -10000 0 -0.045 3 3
IGHV3OR16-13 0.005 0.009 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.029 0.012 -10000 0 -0.07 4 4
CREBBP 0.03 0.006 -10000 0 -0.027 3 3
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.02 0.033 -10000 0 -0.069 61 61
HDAC2 0.03 0.012 -10000 0 -0.07 4 4
SNIP1 0.032 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.003 0.075 -10000 0 -0.098 87 87
MSG1/HSC70 0.043 0.023 -10000 0 -0.053 24 24
SMAD2 0.036 0.012 0.1 3 -10000 0 3
SMAD3 0 0.041 -10000 0 -0.069 9 9
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.002 0.043 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.01 0.039 0.13 8 -0.17 10 18
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 0.045 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.027 0.085 -10000 0 -0.12 4 4
IFNB1 -0.022 0.035 0.14 10 -10000 0 10
SMAD3/SMAD4/MEF2C -0.001 0.054 0.2 4 -10000 0 4
CITED1 0.028 0.022 -10000 0 -0.07 24 24
SMAD2-3/SMAD4/ARC105 0.038 0.069 -10000 0 -0.091 9 9
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.05 0.18 1 -0.23 13 14
RUNX1-3/PEBPB2 0.059 0.026 -10000 0 -0.041 27 27
SMAD7 -0.027 0.066 -10000 0 -0.18 37 37
MYC/MIZ-1 0.021 0.043 -10000 0 -0.056 116 116
SMAD3/SMAD4 -0.049 0.065 -10000 0 -0.24 28 28
IL10 -0.032 0.042 0.15 15 -10000 0 15
PIASy/HDAC complex 0.033 0.007 -10000 0 -10000 0 0
PIAS3 0.031 0.005 -10000 0 -10000 0 0
CDK2 0.025 0.022 -10000 0 -0.071 24 24
IL5 -0.033 0.041 0.15 14 -10000 0 14
CDK4 -0.025 0.047 -10000 0 -0.072 250 250
PIAS4 0.033 0.007 -10000 0 -10000 0 0
ATF3 0.011 0.041 -10000 0 -0.07 103 103
SMAD3/SMAD4/SP1 -0.01 0.072 -10000 0 -0.11 44 44
FOXG1 0.028 0.012 -10000 0 -10000 0 0
FOXO3 -0.019 0.007 -10000 0 -10000 0 0
FOXO1 -0.02 0.008 -10000 0 -0.056 2 2
FOXO4 -0.02 0.005 -10000 0 -10000 0 0
heart looping -0.024 0.041 0.2 13 -10000 0 13
CEBPB 0.028 0.017 -10000 0 -0.069 11 11
SMAD3/SMAD4/DLX1 0.006 0.049 -10000 0 -0.072 43 43
MYOD1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.022 0.059 -10000 0 -0.082 33 33
SMAD3/SMAD4/GATA3 0.015 0.067 -10000 0 -0.093 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.049 0.073 -10000 0 -0.093 5 5
SMAD3/SMAD4/SP1-3 0.003 0.084 -10000 0 -0.12 33 33
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.006 0.038 -10000 0 -0.053 63 63
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.029 0.048 -10000 0 -0.059 14 14
ITGB5 -0.045 0.053 0.23 9 -0.16 1 10
TGIF/SIN3/HDAC complex/CtBP -0.021 0.06 -10000 0 -0.19 35 35
SMAD3/SMAD4/AR 0.021 0.063 -10000 0 -0.083 43 43
AR 0.031 0.013 -10000 0 -0.07 8 8
negative regulation of cell growth -0.005 0.049 -10000 0 -0.23 12 12
SMAD3/SMAD4/MYOD 0.021 0.062 -10000 0 -0.083 36 36
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 0.046 0.065 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.002 0.04 0.15 1 -0.2 10 11
TFDP1 0.029 0.016 -10000 0 -0.07 11 11
SMAD3/SMAD4/AP1 0.011 0.066 -10000 0 -0.092 12 12
SMAD3/SMAD4/RUNX2 0.021 0.063 -10000 0 -0.084 31 31
TGIF2 0.029 0.012 -10000 0 -0.07 4 4
TGIF1 -0.038 0.047 -10000 0 -0.07 343 343
ATF2 0.032 0.002 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.007 -10000 0 -0.07 1 1
LAT2 -0.016 0.032 0.12 4 -0.14 7 11
AP1 -0.032 0.11 -10000 0 -0.28 34 34
mol:PIP3 0.025 0.099 0.26 32 -10000 0 32
IKBKB 0.015 0.072 0.19 36 -10000 0 36
AKT1 -0.034 0.076 0.28 13 -10000 0 13
IKBKG 0.015 0.071 0.19 36 -10000 0 36
MS4A2 0.035 0.005 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
MAP3K1 -0.012 0.06 0.21 13 -0.21 5 18
mol:Ca2+ 0.024 0.087 0.23 35 -10000 0 35
LYN 0.019 0.034 -10000 0 -0.07 64 64
CBLB -0.017 0.038 0.14 7 -0.14 9 16
SHC1 0.024 0.028 -10000 0 -0.07 40 40
RasGAP/p62DOK 0.056 0.024 -10000 0 -0.042 25 25
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.033 0.058 0.31 10 -10000 0 10
PTPN13 0.003 0.074 -10000 0 -0.58 5 5
PTPN11 0.031 0.01 -10000 0 -0.029 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.01 0.071 0.3 7 -0.28 5 12
SYK 0.024 0.027 -10000 0 -0.07 37 37
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.068 0.18 19 -0.15 5 24
LAT -0.017 0.039 0.14 7 -0.14 9 16
PAK2 -0.008 0.062 0.2 17 -0.22 5 22
NFATC2 -0.013 0.006 -10000 0 -10000 0 0
HRAS -0.004 0.057 0.17 22 -0.21 7 29
GAB2 0.032 0.006 -10000 0 -10000 0 0
PLA2G1B 0.022 0.065 -10000 0 -0.81 2 2
Fc epsilon R1 0.008 0.06 -10000 0 -0.053 240 240
Antigen/IgE/Fc epsilon R1 0.01 0.056 -10000 0 -0.048 238 238
mol:GDP 0.002 0.054 0.18 18 -0.22 1 19
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 0.006 0.043 -10000 0 -0.07 121 121
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.038 0.12 3 -0.14 6 9
CHUK 0.006 0.063 0.19 26 -10000 0 26
KLRG1 -0.015 0.03 0.082 3 -0.12 5 8
VAV1 -0.018 0.038 0.13 7 -0.14 9 16
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.038 0.14 7 -0.14 7 14
negative regulation of mast cell degranulation -0.015 0.03 0.076 2 -0.13 5 7
BTK 0.005 0.042 0.19 2 -0.22 1 3
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.01 0.031 -10000 0 -0.087 12 12
GAB2/PI3K/SHP2 -0.053 0.025 0.027 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.011 0.034 -10000 0 -0.095 34 34
RAF1 0.025 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.005 0.067 -10000 0 -0.065 144 144
FCER1G -0.018 0.053 -10000 0 -0.072 241 241
FCER1A 0.029 0.016 -10000 0 -0.061 14 14
Antigen/IgE/Fc epsilon R1/Fyn 0.007 0.063 -10000 0 -0.065 13 13
MAPK3 0.025 0.063 -10000 0 -0.82 2 2
MAPK1 0.015 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
MAPK8 -0.1 0.24 -10000 0 -0.52 118 118
DUSP1 0.029 0.018 -10000 0 -0.07 16 16
NF-kappa-B/RelA 0.007 0.052 0.13 27 -10000 0 27
actin cytoskeleton reorganization 0.009 0.076 -10000 0 -0.59 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.069 0.2 18 -0.2 6 24
FER -0.017 0.039 0.14 7 -0.14 9 16
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.024 -10000 0 -0.21 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.014 0.075 0.24 25 -0.18 3 28
cytokine secretion 0.001 0.033 0.075 24 -0.065 1 25
SPHK1 -0.019 0.038 0.14 5 -0.14 9 14
PTK2 0.009 0.078 -10000 0 -0.62 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.019 0.082 0.22 24 -0.16 4 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.019 0.09 0.24 32 -0.21 1 33
MAP2K2 0.022 0.072 -10000 0 -0.84 2 2
MAP2K1 0.016 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.003 0.047 0.19 11 -0.15 3 14
MAP2K4 0 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.005 0.073 -10000 0 -0.071 144 144
mol:Choline -0.033 0.057 0.31 10 -10000 0 10
SHC/Grb2/SOS1 0.006 0.06 0.17 4 -0.14 6 10
FYN 0.029 0.011 -10000 0 -0.07 1 1
DOK1 0.032 0.001 -10000 0 -10000 0 0
PXN 0.005 0.077 0.33 3 -0.58 5 8
HCLS1 -0.021 0.042 0.14 7 -0.12 27 34
PRKCB 0.02 0.082 0.22 34 -10000 0 34
FCGR2B 0.008 0.043 -10000 0 -0.07 120 120
IGHE -0.001 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.016 0.03 0.077 2 -0.13 5 7
LCP2 0.026 0.024 -10000 0 -0.07 29 29
PLA2G4A -0.023 0.04 0.14 7 -0.12 22 29
RASA1 0.032 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.033 0.057 0.31 10 -10000 0 10
IKK complex 0.007 0.063 0.19 25 -10000 0 25
WIPF1 0.03 0.015 -10000 0 -0.07 11 11
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.052 -10000 0 -0.18 25 25
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.031 4 4
IKBKB 0.032 0.004 -10000 0 -10000 0 0
IKBKG 0.032 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.028 -10000 0 -0.054 40 40
IL1A 0.032 0.008 -10000 0 -0.07 3 3
IL1B -0.033 0.016 -10000 0 -0.055 172 172
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.026 0.17 4 -10000 0 4
IL1R2 0.025 0.027 -10000 0 -0.07 37 37
IL1R1 0.032 0.008 -10000 0 -0.07 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.047 -10000 0 -0.18 20 20
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 -0.034 1 1
IKK complex/ELKS -0.022 0.091 -10000 0 -0.19 110 110
JUN -0.026 0.022 0.14 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 -0.07 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.018 0.07 0.18 2 -0.099 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.058 -10000 0 -0.075 11 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.057 0.066 -10000 0 -0.077 11 11
IL1 beta fragment/IL1R1/IL1RAP 0.007 0.052 -10000 0 -0.058 187 187
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
MAPK8 -0.022 0.023 0.16 5 -10000 0 5
IRAK1 -0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.048 0.008 -10000 0 -0.054 3 3
IRAK4 0.031 0.008 -10000 0 -0.07 1 1
PRKCI 0.032 0.007 -10000 0 -0.07 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.054 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.047 0.13 1 -0.19 19 20
CHUK 0.025 0.015 -10000 0 -0.07 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.007 0.052 -10000 0 -0.058 187 187
IL1 beta/IL1R2 0.003 0.046 -10000 0 -0.055 193 193
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.022 0.16 4 -10000 0 4
NF kappa B1 p50/RelA 0.006 0.066 -10000 0 -0.1 8 8
IRAK3 0.031 0.008 -10000 0 -0.07 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.014 0.059 0.16 2 -0.076 32 34
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.041 -10000 0 -0.12 33 33
IL1 alpha/IL1R1/IL1RAP 0.053 0.036 -10000 0 -0.05 53 53
RELA 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.007 -10000 0 -0.07 1 1
MYD88 0.019 0.034 -10000 0 -0.07 66 66
IRAK/TRAF6/MEKK3 0.05 0.017 0.18 4 -10000 0 4
IL1RAP 0.023 0.028 -10000 0 -0.07 41 41
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.053 0.017 0.035 1 -0.1 4 5
CASP1 -0.002 0.048 -10000 0 -0.07 167 167
IL1RN/IL1R2 0.041 0.027 -10000 0 -0.054 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.009 0.066 0.17 2 -0.081 67 69
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.047 -10000 0 -0.23 11 11
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
IL1RN 0.032 0.001 -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
TCGA08_rtk_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
PDGFRA 0.026 0.016 -10000 0 -0.07 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.07 5 5
AKT 0.12 0.093 0.22 203 -0.14 1 204
FOXO3 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.031 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.017 -10000 0 -0.07 11 11
AKT3 0.031 0.007 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.021 0.016 -10000 0 -0.07 2 2
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
PIK3CB 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.007 0.044 -10000 0 -0.07 125 125
PIK3CG 0.022 0.015 -10000 0 -10000 0 0
PIK3R3 0.032 0.006 -10000 0 -0.07 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.032 0.005 -10000 0 -10000 0 0
RAS 0.007 0.024 0.085 3 -0.084 8 11
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.049 0.065 0.29 6 -0.21 18 24
PI3K 0.051 0.077 0.18 99 -10000 0 99
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 0.22 179 -10000 0 179
AKT2 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -0.07 2 2
Plasma membrane estrogen receptor signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.046 0.03 -10000 0 -0.038 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.099 0.13 -10000 0 -0.38 59 59
AKT1 -0.032 0.18 -10000 0 -0.71 31 31
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.027 0.18 -10000 0 -0.72 31 31
mol:Ca2+ -0.004 0.046 0.17 19 -0.23 9 28
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 0.028 -10000 0 -0.07 40 40
apoptosis 0.03 0.17 0.68 31 -10000 0 31
RhoA/GTP -0.04 0.015 -10000 0 -0.081 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.069 0.11 0.17 10 -0.3 58 68
regulation of stress fiber formation 0.05 0.037 -10000 0 -0.28 1 1
E2/ERA-ERB (dimer) 0.04 0.013 -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 -0.05 0.037 0.28 1 -10000 0 1
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.031 0.006 -10000 0 -10000 0 0
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 -0.054 0.13 0.2 1 -0.46 36 37
E2/ER beta (dimer) 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.005 0.057 0.13 5 -0.18 42 47
mol:NADP -0.054 0.13 0.2 1 -0.46 36 37
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 0.015 -10000 0 -0.23 1 1
PLCB2 0.009 0.015 -10000 0 -0.23 1 1
IGF1 0.031 0.01 -10000 0 -0.07 4 4
mol:L-citrulline -0.054 0.13 0.2 1 -0.46 36 37
RHOA 0.032 0.006 -10000 0 -10000 0 0
Gai/GDP -0.43 0.16 -10000 0 -0.48 448 448
JNK cascade 0.023 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.031 0.008 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 0.03 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.014 0.071 -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 -0.069 0.12 0.2 12 -0.3 58 70
GNAZ 0.027 0.012 -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 0.005 -10000 0 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
MAPK11 -0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
GNAI1 0.019 0.016 -10000 0 -0.07 1 1
HBEGF -0.11 0.12 0.24 16 -0.35 58 74
cAMP biosynthetic process 0.031 0.02 -10000 0 -0.03 49 49
SRC -0.096 0.12 0.2 1 -0.37 53 54
PI3K 0.039 0.023 -10000 0 -0.054 16 16
GNB1 0.031 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.059 -10000 0 -0.15 44 44
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.077 0.089 -10000 0 -0.25 65 65
Gs family/GTP 0.039 0.024 -10000 0 -0.036 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.048 -10000 0 -0.046 119 119
vasodilation -0.052 0.13 0.2 1 -0.44 36 37
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 44 44
MSN -0.053 0.039 0.29 1 -10000 0 1
Gq family/GTP 0.023 0.019 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.026 0.17 -10000 0 -0.69 31 31
NRAS 0.007 0.044 -10000 0 -0.07 125 125
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.13 0.44 36 -0.2 1 37
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.062 0.14 5 -0.17 43 48
NOS3 -0.057 0.14 0.2 1 -0.48 36 37
GNA11 0.031 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.036 0.13 -10000 0 -0.48 35 35
E2/ER alpha (dimer)/PELP1/Src -0.068 0.12 0.2 12 -0.31 58 70
ruffle organization -0.05 0.037 0.28 1 -10000 0 1
ROCK2 -0.032 0.053 0.31 2 -10000 0 2
GNA14 0.031 0.009 -10000 0 -0.07 2 2
GNA15 0.03 0.013 -10000 0 -0.07 7 7
GNA13 0.032 0.007 -10000 0 -0.07 2 2
MMP9 -0.11 0.11 0.37 1 -0.35 57 58
MMP2 -0.11 0.11 0.19 1 -0.36 57 58
Paxillin-independent events mediated by a4b1 and a4b7

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.043 -10000 0 -0.084 108 108
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 -0.07 5 5
alpha4/beta7 Integrin/MAdCAM1 0.074 0.03 -10000 0 -0.062 5 5
EPO 0.022 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.066 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.022 -10000 0 -0.054 4 4
EPO/EPOR (dimer) 0.032 0.023 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.075 0.16 1 -0.3 25 26
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
PI3K 0.039 0.023 -10000 0 -0.054 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
JAK2 0.009 0.027 -10000 0 -0.091 27 27
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 0.071 0.029 -10000 0 -0.062 5 5
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.013 -10000 0 -10000 0 0
SRC -0.043 0.021 0.17 2 -10000 0 2
ITGB7 0.032 0.008 -10000 0 -0.07 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.022 0.052 -10000 0 -0.054 335 335
p130Cas/Crk/Dock1 -0.05 0.024 0.18 3 -10000 0 3
VCAM1 -0.035 0.048 -10000 0 -0.07 333 333
RHOA 0.032 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.052 -10000 0 -0.061 1 1
BCAR1 -0.04 0.021 0.16 3 -10000 0 3
EPOR 0.031 0.007 -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 -0.004 0.078 0.16 1 -0.31 25 26
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.049 -10000 0 -0.055 259 259
alphaV beta3 Integrin 0.059 0.026 -10000 0 -0.052 17 17
PTK2 -0.013 0.064 0.27 8 -0.26 6 14
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 -0.07 2 2
SRC 0.03 0.008 -10000 0 -10000 0 0
CDKN1B 0.014 0.046 -10000 0 -0.26 14 14
VEGFA -0.023 0.051 -10000 0 -0.07 275 275
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0 0.041 -10000 0 -0.25 13 13
PTK2B -0.031 0.058 0.16 39 -10000 0 39
alphaV/beta3 Integrin/JAM-A 0.054 0.042 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 0.025 -10000 0 -0.052 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.078 0.025 -10000 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.01 0.045 -10000 0 -0.17 20 20
alphaV/beta3 Integrin/Syndecan-1 0.05 0.039 -10000 0 -0.054 55 55
PI4KA 0.012 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.041 0.062 -10000 0 -0.1 2 2
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
alphaV/beta3 Integrin/Osteopontin 0.021 0.057 -10000 0 -0.053 178 178
RPS6KB1 -0.05 0.03 -10000 0 -10000 0 0
TLN1 0.021 0.029 -10000 0 -0.07 43 43
MAPK3 -0.002 0.041 -10000 0 -0.28 9 9
GPR124 0.032 0.007 -10000 0 -0.07 2 2
MAPK1 -0.002 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 0.023 -10000 0 -0.052 15 15
cell adhesion 0.046 0.031 -10000 0 -0.082 5 5
ANGPTL3 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.001 0.055 -10000 0 -0.053 236 236
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 0.012 -10000 0 -0.07 6 6
ITGB3 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.031 0.01 -10000 0 -0.07 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.059 0.025 -10000 0 -0.051 18 18
apoptosis 0.029 0.017 -10000 0 -0.069 15 15
CD47 0.031 0.008 -10000 0 -0.07 2 2
alphaV/beta3 Integrin/CD47 0.059 0.027 -10000 0 -0.052 17 17
VCL 0.025 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.06 0.025 -10000 0 -0.052 15 15
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.008 0.014 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.021 0.035 0.096 8 -0.11 1 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.066 -10000 0 -0.075 20 20
FAK1/Vinculin -0.007 0.058 0.26 7 -0.23 6 13
alphaV beta3/Integrin/ppsTEM5 0.06 0.025 -10000 0 -0.051 18 18
RHOA 0.032 0.006 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -0.07 2 2
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.07 2 2
F11R -0.024 0.009 -10000 0 -0.054 33 33
alphaV/beta3 Integrin/Lactadherin 0.059 0.026 -10000 0 -0.052 17 17
alphaV/beta3 Integrin/TGFBR2 0.058 0.028 -10000 0 -0.052 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.023 -10000 0 -0.045 16 16
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.04 -10000 0 -0.048 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.013 0.04 -10000 0 -0.07 96 96
alphaV/beta3 Integrin/Pyk2 0 0.068 0.16 34 -0.078 18 52
SDC1 0.023 0.029 -10000 0 -0.07 45 45
VAV3 -0.029 0.022 0.18 5 -10000 0 5
PTPN11 0.032 0.004 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.07 4 4
FAK1/Paxillin -0.005 0.065 0.25 9 -0.22 6 15
cell migration -0.017 0.053 0.25 7 -0.22 6 13
ITGAV 0.029 0.018 -10000 0 -0.07 15 15
PI3K 0.06 0.05 0.16 5 -10000 0 5
SPP1 -0.004 0.048 -10000 0 -0.07 175 175
KDR 0.027 0.018 -10000 0 -0.07 14 14
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.017 -10000 0 -0.07 15 15
COL4A3 0.033 0 -10000 0 -10000 0 0
angiogenesis 0.001 0.045 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 0.028 -10000 0 -0.052 21 21
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.033 -10000 0 -0.064 61 61
AES 0.034 0.01 -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 0.031 0.024 -10000 0 -0.055 4 4
SMAD4 0.008 0.042 -10000 0 -0.07 114 114
DKK2 0.03 0.013 -10000 0 -0.07 8 8
TLE1 0.034 0.009 -10000 0 -10000 0 0
MACF1 0.032 0.006 -10000 0 -10000 0 0
CTNNB1 0.096 0.098 0.21 153 -0.27 7 160
WIF1 0.004 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.1 0.081 0.26 31 -0.28 4 35
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.005 0.039 -10000 0 -0.069 101 101
beta catenin/beta TrCP1 0.11 0.094 0.22 148 -0.26 7 155
FZD1 0.021 0.017 -10000 0 -0.07 4 4
AXIN2 -0.015 0.024 -10000 0 -0.14 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 0.086 -10000 0 -0.44 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.069 0.22 21 -0.23 8 29
Axin1/APC/GSK3 0.042 0.065 0.16 75 -0.22 6 81
Axin1/APC/GSK3/beta catenin/Macf1 0.066 0.095 0.2 129 -0.22 11 140
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.035 0.009 -10000 0 -10000 0 0
MYC -0.028 0.1 0.44 15 -10000 0 15
RANBP3 0.032 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.023 -10000 0 -0.051 8 8
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.034 0.01 -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 -0.063 1 1
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.036 0.054 0.22 2 -0.2 1 3
LEF1 0.035 0.011 -10000 0 -0.065 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.031 0.009 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.065 0.062 0.23 21 -0.23 2 23
DKK1/LRP6/Kremen 2 0.025 0.048 -10000 0 -0.05 109 109
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.009 -10000 0 -10000 0 0
NLK 0.031 0.005 -10000 0 -10000 0 0
CCND1 -0.037 0.06 0.35 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 0.025 0.014 -10000 0 -10000 0 0
PPP2R5D 0.032 0.037 -10000 0 -0.24 5 5
APC 0.034 0.1 0.18 156 -10000 0 156
WNT1/LRP6/FZD1 0 0.026 -10000 0 -0.24 4 4
CREBBP 0.035 0.007 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.018 -9999 0 -0.07 5 5
EGF/EGFR 0.007 0.036 -9999 0 -0.048 79 79
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.04 -9999 0 -0.063 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.002 0.046 -9999 0 -0.07 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.032 0.007 -9999 0 -0.07 2 2
EGF/EGFR dimer/SHC 0.018 0.036 -9999 0 -0.052 34 34
mol:GDP 0.019 0.037 -9999 0 -0.05 31 31
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.03 0.014 -9999 0 -0.07 9 9
GRB2/SOS1 0.023 0.004 -9999 0 -10000 0 0
HRAS/GTP 0.011 0.03 -9999 0 -0.062 3 3
SHC1 0.024 0.028 -9999 0 -0.07 40 40
HRAS/GDP 0.016 0.038 -9999 0 -0.072 1 1
FRAP1 -0.012 0.016 -9999 0 -0.06 2 2
EGF/EGFR dimer 0.017 0.025 -9999 0 -0.054 7 7
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.031 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.016 0.047 -9999 0 -0.055 149 149
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.037 0.14 14 -0.16 9 23
adherens junction organization 0.007 0.042 0.13 8 -0.15 20 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.044 0.07 0.16 125 -0.14 5 130
FMN1 0.012 0.038 0.13 8 -0.14 16 24
mol:IP3 0.004 0.025 0.085 1 -0.12 10 11
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.017 0.041 0.14 8 -0.15 16 24
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.012 0.035 0.1 31 -0.15 6 37
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.059 0.17 3 -0.25 14 17
CTNND1 0.031 0.015 -10000 0 -0.071 10 10
mol:PI-4-5-P2 0.007 0.038 0.12 8 -0.15 16 24
VASP 0.006 0.034 0.12 8 -0.14 14 22
ZYX 0 0.032 0.12 3 -0.17 10 13
JUB 0.012 0.038 0.13 8 -0.14 16 24
EGFR(dimer) 0.01 0.035 0.15 2 -0.16 8 10
E-cadherin/beta catenin-gamma catenin 0.058 0.027 -10000 0 -0.056 19 19
mol:PI-3-4-5-P3 0.041 0.05 0.16 33 -0.14 8 41
PIK3CA 0.028 0.02 -10000 0 -0.063 21 21
PI3K 0.042 0.051 0.16 33 -0.14 8 41
FYN -0.011 0.055 0.16 12 -0.2 26 38
mol:Ca2+ 0.004 0.025 0.084 1 -0.12 10 11
JUP 0.029 0.018 -10000 0 -0.069 16 16
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.025 0.085 1 -0.12 10 11
CDH1 0.031 0.013 -10000 0 -0.068 8 8
RhoA/GDP 0.074 0.077 0.16 221 -0.14 6 227
establishment of polarity of embryonic epithelium 0.006 0.036 0.12 8 -0.14 16 24
SRC 0.03 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 -0.07 5 5
CASR -0.013 0.032 0.14 13 -0.13 7 20
RhoA/GTP 0.02 0.036 0.14 12 -0.13 8 20
AKT2 0.01 0.034 0.1 24 -0.14 7 31
actin cable formation 0.003 0.035 0.12 8 -0.14 16 24
apoptosis -0.01 0.042 0.16 9 -0.17 11 20
CTNNA1 0.033 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.019 -10000 0 -0.14 6 6
PIP5K1A 0.007 0.038 0.12 8 -0.15 16 24
PLCG1 0.004 0.025 0.086 1 -0.13 10 11
Rac1/GTP 0.014 0.038 0.15 2 -0.16 8 10
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.014 0.05 -10000 0 -0.35 9 9
Crk/p130 Cas/Paxillin -0.035 0.079 -10000 0 -0.18 110 110
JUN -0.012 0.029 -10000 0 -0.18 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.043 0.049 -10000 0 -0.055 8 8
RAP1A 0.032 0.005 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.049 0.057 -10000 0 -0.056 3 3
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.037 0.042 -10000 0 -0.041 9 9
RHOA 0.032 0.006 -10000 0 -10000 0 0
RAP1A/GTP 0.044 0.056 -10000 0 -10000 0 0
GRB7 0.032 0.006 -10000 0 -0.07 1 1
RET51/GFRalpha1/GDNF 0.049 0.056 -10000 0 -0.057 2 2
MAPKKK cascade -0.006 0.075 -10000 0 -0.13 124 124
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.037 0.042 -10000 0 -0.044 9 9
lamellipodium assembly -0.012 0.059 -10000 0 -0.17 45 45
RET51/GFRalpha1/GDNF/SHC 0.039 0.062 -10000 0 -0.064 7 7
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
RET9/GFRalpha1/GDNF/SHC 0.03 0.046 -10000 0 -0.046 44 44
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.024 132 132
MAPK3 -0.038 0.032 0.22 3 -10000 0 3
DOK1 0.032 0.001 -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 0.03 0.21 4 -10000 0 4
DOK5 0.028 0.012 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.07 1 1
MAPK8 0 0.03 -10000 0 -0.12 26 26
HRAS/GTP 0.02 0.096 -10000 0 -0.14 128 128
tube development 0.021 0.036 0.17 12 -10000 0 12
MAPK1 -0.035 0.033 0.2 4 -10000 0 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.008 0.055 -10000 0 -0.11 115 115
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
PDLIM7 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.047 0.05 -10000 0 -10000 0 0
SHC1 0.024 0.028 -10000 0 -0.07 40 40
RET51/GFRalpha1/GDNF/Dok4 0.048 0.057 -10000 0 -0.055 7 7
RET51/GFRalpha1/GDNF/Dok5 0.047 0.053 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 0 8 8
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
CREB1 -0.035 0.095 -10000 0 -0.2 120 120
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.056 -10000 0 -0.11 119 119
RET51/GFRalpha1/GDNF/Grb7 0.049 0.058 -10000 0 -0.058 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.014 -10000 0 -0.07 1 1
DOK4 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.012 0.029 -10000 0 -0.18 6 6
RET9/GFRalpha1/GDNF/FRS2 0.037 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 0.029 0.016 -10000 0 -0.07 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.015 0.053 -10000 0 -0.11 120 120
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.026 0.094 -10000 0 -0.19 120 120
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.098 -10000 0 -0.19 135 135
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.035 -10000 0 -0.12 26 26
PI3K -0.041 0.11 -10000 0 -0.23 117 117
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.034 0.038 -10000 0 -0.037 5 5
GRB10 0.021 0.017 -10000 0 -0.07 4 4
activation of MAPKK activity -0.013 0.069 0.1 8 -0.15 98 106
RET51/GFRalpha1/GDNF/FRS2 0.047 0.057 -10000 0 -0.061 1 1
GAB1 0.031 0.009 -10000 0 -0.07 3 3
IRS1 0.032 0.009 -10000 0 -0.07 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.038 -10000 0 -0.12 28 28
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.057 -10000 0 -0.056 3 3
GRB2 0.031 0.006 -10000 0 -10000 0 0
PRKACA 0.031 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 0.048 0.058 -10000 0 -0.066 3 3
Rac1/GTP -0.012 0.069 -10000 0 -0.2 45 45
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.043 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.054 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.008 0.042 -10000 0 -0.07 114 114
SMAD2 -0.019 0.054 -10000 0 -0.22 22 22
SMAD3 0.015 0.042 0.1 35 -0.098 32 67
SMAD3/SMAD4 0.026 0.056 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.036 0.049 -10000 0 -0.052 106 106
SMAD2/SMAD2/SMAD4 0.018 0.082 -10000 0 -0.21 23 23
PPM1A 0.031 0.007 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.013 0.06 -10000 0 -0.19 33 33
MAP3K1 0.032 0.006 -10000 0 -0.07 1 1
TRAP-1/SMAD4 0.024 0.043 -10000 0 -0.054 114 114
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
CTDSP1 0.032 0.008 -10000 0 -0.07 3 3
CTDSP2 0.028 0.012 -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 0.002 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
NUP153 0.032 0.007 -10000 0 -0.07 2 2
KPNA2 0.03 0.015 -10000 0 -0.07 11 11
PIAS4 0.031 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.01 -10000 0 -0.022 7 7
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 + 0.012 0.041 -10000 0 -0.043 179 179
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 -10000 0 0
mol:Ca2+ -0.021 0.032 0.18 10 -10000 0 10
Cone PDE6 0.045 0.05 -10000 0 -10000 0 0
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.012 0.052 -10000 0 -0.044 232 232
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 0.032 0.18 12 -10000 0 12
Cone Transducin 0.039 0.011 -10000 0 -0.024 7 7
SLC24A2 0.026 0.013 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.005 -10000 0 -10000 0 0
GNB3 0.031 0.006 -10000 0 -10000 0 0
GNAT2/GTP 0.024 0.003 -10000 0 -10000 0 0
CNGA3 -0.004 0.049 -10000 0 -0.07 179 179
ARR3 0.032 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.012 0.041 -10000 0 -0.043 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.065 -10000 0 -0.067 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.026 0.013 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
PDE6C 0.025 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
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.07 2 2
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.054 15 15
PTK2 0.014 0.082 -10000 0 -0.23 46 46
positive regulation of JNK cascade 0.018 0.085 -10000 0 -0.25 36 36
CDC42/GDP 0.031 0.12 0.35 2 -0.32 42 44
Rac1/GDP 0.021 0.095 0.29 1 -0.32 22 23
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.1 -10000 0 -0.3 36 36
nectin-3/I-afadin 0.043 0.015 -10000 0 -0.054 1 1
RAPGEF1 0.003 0.11 0.24 5 -0.34 44 49
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.001 0.12 -10000 0 -0.37 44 44
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.07 2 2
TLN1 -0.016 0.016 -10000 0 -0.14 3 3
Rap1/GTP -0.001 0.081 -10000 0 -0.26 44 44
IQGAP1 0.008 0.043 -10000 0 -0.07 120 120
Rap1/GTP/I-afadin 0.036 0.019 -10000 0 -0.024 44 44
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -0.054 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 0.016 0.13 0.33 3 -0.38 43 46
MLLT4 0.03 0.009 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
PI3K 0.069 0.053 -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 0.012 0.078 -10000 0 -0.27 22 22
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.031 0.007 -10000 0 -0.07 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 -0.07 8 8
CLDN1 0.03 0.015 -10000 0 -0.07 9 9
JAM-A/CLDN1 0.06 0.049 -10000 0 -0.071 12 12
SRC 0.006 0.13 -10000 0 -0.39 44 44
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 0.022 0.13 0.37 1 -0.38 35 36
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) 0.053 0.033 -10000 0 -0.045 9 9
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 0.015 0.033 -10000 0 -0.043 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.055 0.032 -10000 0 -0.036 50 50
CDC42/GTP/IQGAP1/filamentous actin 0.022 0.037 -10000 0 -0.043 119 119
F11R 0.026 0.025 -10000 0 -0.07 32 32
positive regulation of filopodium formation 0.018 0.085 -10000 0 -0.25 36 36
alphaV/beta3 Integrin/Talin 0.024 0.066 0.2 28 -0.17 8 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 36 36
VAV2 0.015 0.15 0.31 2 -0.4 45 47
RAP1/GDP 0.021 0.11 0.32 2 -0.3 42 44
ITGAV 0.029 0.018 -10000 0 -0.07 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.053 0.033 -10000 0 -0.037 50 50
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -0.054 1 1
Rac1/GTP 0.016 0.094 0.25 1 -0.32 22 23
PTPRM 0.005 0.02 -10000 0 -0.061 40 40
E-cadherin/beta catenin/alpha catenin 0.073 0.053 -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
FOXM1 transcription factor network

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
NFATC3 -0.17 0.2 -9999 0 -0.72 14 14
PLK1 -0.003 0.12 -9999 0 -0.9 8 8
BIRC5 -0.033 0.078 -9999 0 -10000 0 0
HSPA1B -0.17 0.2 -9999 0 -0.68 19 19
MAP2K1 -0.014 0.038 -9999 0 -10000 0 0
BRCA2 -0.17 0.2 -9999 0 -0.72 13 13
FOXM1 -0.18 0.22 -9999 0 -0.73 25 25
XRCC1 -0.17 0.2 -9999 0 -0.71 13 13
FOXM1B/p19 -0.17 0.2 -9999 0 -0.7 19 19
Cyclin D1/CDK4 -0.17 0.19 -9999 0 -0.66 16 16
CDC2 -0.18 0.21 -9999 0 -0.73 15 15
TGFA -0.16 0.19 -9999 0 -0.65 15 15
SKP2 -0.17 0.2 -9999 0 -0.71 15 15
CCNE1 0.015 0.027 -9999 0 -0.079 4 4
CKS1B -0.17 0.2 -9999 0 -0.68 19 19
RB1 -0.11 0.19 -9999 0 -0.6 45 45
FOXM1C/SP1 -0.18 0.22 -9999 0 -0.73 21 21
AURKB -0.007 0.13 -9999 0 -0.94 9 9
CENPF -0.18 0.21 -9999 0 -0.71 18 18
CDK4 -0.032 0.049 -9999 0 -0.079 250 250
MYC -0.17 0.19 -9999 0 -0.62 23 23
CHEK2 -0.014 0.04 -9999 0 -0.11 15 15
ONECUT1 -0.17 0.2 -9999 0 -0.7 15 15
CDKN2A 0.002 0.028 -9999 0 -0.068 53 53
LAMA4 -0.17 0.2 -9999 0 -0.71 14 14
FOXM1B/HNF6 -0.18 0.22 -9999 0 -0.74 17 17
FOS -0.18 0.2 -9999 0 -0.75 14 14
SP1 0.031 0.006 -9999 0 -0.026 3 3
CDC25B -0.16 0.2 -9999 0 -0.7 14 14
response to radiation -0.011 0.013 -9999 0 -10000 0 0
CENPB -0.16 0.2 -9999 0 -0.72 12 12
CENPA -0.18 0.21 -9999 0 -0.73 18 18
NEK2 -0.17 0.2 -9999 0 -0.73 14 14
HIST1H2BA -0.17 0.2 -9999 0 -0.68 19 19
CCNA2 -0.002 0.048 -9999 0 -0.078 135 135
EP300 0.03 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.19 0.22 -9999 0 -0.78 15 15
CCNB2 -0.2 0.21 -9999 0 -0.73 18 18
CCNB1 -0.18 0.21 -9999 0 -0.74 16 16
ETV5 -0.17 0.2 -9999 0 -0.71 14 14
ESR1 -0.17 0.2 -9999 0 -0.71 14 14
CCND1 -0.17 0.2 -9999 0 -0.66 18 18
GSK3A -0.011 0.035 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.011 0.062 -9999 0 -0.11 14 14
CDK2 0.013 0.032 -9999 0 -0.08 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.17 0.22 -9999 0 -0.72 19 19
GAS1 -0.17 0.2 -9999 0 -0.72 15 15
MMP2 -0.19 0.21 -9999 0 -0.71 18 18
RB1/FOXM1C -0.18 0.21 -9999 0 -0.68 25 25
CREBBP 0.032 0.004 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.07 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.031 -10000 0 -0.052 2 2
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
KATNA1 0.029 0.013 -10000 0 -0.07 5 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.012 0.063 0.17 64 -10000 0 64
IQGAP1/CaM 0.02 0.042 -10000 0 -0.054 111 111
DAB1 0.031 0.006 -10000 0 -10000 0 0
IQGAP1 0.008 0.043 -10000 0 -0.07 120 120
PLA2G7 0.03 0.013 -10000 0 -0.07 8 8
CALM1 0.029 0.01 -10000 0 -10000 0 0
DYNLT1 0.016 0.036 -10000 0 -0.07 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 0.004 -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 0 313 313
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.018 0.032 -10000 0 -0.05 4 4
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.026 0.096 0.3 50 -10000 0 50
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.001 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.009 0.044 0.17 6 -10000 0 6
RELN 0.01 0.016 -10000 0 -0.07 2 2
PAFAH/LIS1 0.025 0.016 -10000 0 -0.043 18 18
LIS1/CLIP170 0.026 0.013 -10000 0 -0.036 12 12
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.039 0.14 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0 0.044 0.13 5 -0.22 17 22
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.02 0.076 0.3 30 -10000 0 30
LIS1/IQGAP1 0.007 0.034 -10000 0 -0.05 126 126
RHOA -0.001 0.029 -10000 0 -0.26 5 5
PAFAH1B1 -0.02 0.007 -10000 0 -10000 0 0
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 0.019 0.029 0.11 1 -0.14 7 8
NDEL1/Katanin 60/Dynein heavy chain 0.028 0.098 0.31 46 -10000 0 46
LRP8 0.032 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.092 0.3 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 0.013 -10000 0 -0.036 11 11
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 0.022 0.011 -10000 0 -0.029 13 13
CSNK2A1 0.03 0.009 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.036 0.17 6 -10000 0 6
RELN/VLDLR 0.023 0.039 -10000 0 -10000 0 0
CDC42 -0.002 0.035 -10000 0 -0.26 8 8
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.16 8 -0.092 14 22
IHH 0.038 0.022 0.13 8 -0.052 1 9
SHH Np/Cholesterol/GAS1 0.013 0.02 -10000 0 -0.044 36 36
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.013 0.02 0.044 36 -10000 0 36
SMO/beta Arrestin2 0.067 0.057 -10000 0 -10000 0 0
SMO 0.013 0.019 0.14 3 -10000 0 3
AKT1 0.004 0.081 -10000 0 -0.37 15 15
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 0.013 0.019 0.14 3 -10000 0 3
STIL 0.024 0.086 0.17 127 -10000 0 127
DHH N/PTCH2 0.024 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.015 -10000 0 -0.071 1 1
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.016 0.026 0.16 7 -10000 0 7
determination of left/right symmetry 0.013 0.019 0.14 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
skeletal system development 0.016 0.025 0.16 7 -10000 0 7
IHH N/Hhip 0.025 0.013 0.073 15 -10000 0 15
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.013 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 -0.054 16 16
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.032 -10000 0 -0.07 55 55
somite specification 0.013 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.018 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.018 0.014 -10000 0 -0.031 4 4
SHH Np/Cholesterol/Megalin 0.018 0.014 -10000 0 -0.034 5 5
SHH -0.015 0.011 -10000 0 -10000 0 0
catabolic process 0.021 0.018 -10000 0 -0.083 1 1
SMO/Vitamin D3 0.015 0.032 0.18 13 -10000 0 13
SHH Np/Cholesterol/Hhip -0.011 0.007 0 165 -10000 0 165
LRP2 0.032 0.005 -10000 0 -0.07 1 1
receptor-mediated endocytosis 0.012 0.027 0.15 12 -10000 0 12
SHH Np/Cholesterol/BOC -0.011 0.007 0 165 -10000 0 165
SHH Np/Cholesterol/CDO 0.018 0.014 -10000 0 -0.031 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 165 165
mol:Vitamin D3 0.064 0.083 0.19 146 -10000 0 146
IHH N/PTCH2 0.049 0.016 0.11 8 -0.037 1 9
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.036 0.022 -10000 0 -0.07 13 13
Megalin/LRPAP1 0.048 0.007 -10000 0 -0.054 1 1
PTCH2 0.032 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.011 0.007 -10000 0 -10000 0 0
PTCH1 0.021 0.018 -10000 0 -0.084 1 1
HHIP 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.05 -10000 0 -0.15 12 12
mol:DAG -0.007 0.042 0.15 4 -0.16 9 13
PLCG1 -0.007 0.042 0.16 4 -0.16 9 13
YES1 -0.017 0.037 -10000 0 -0.13 27 27
FZD3 0.03 0.01 -10000 0 -0.07 3 3
FZD6 0.013 0.039 -10000 0 -0.07 93 93
G protein 0.009 0.062 0.16 36 -0.16 10 46
MAP3K7 -0.024 0.035 0.14 7 -0.15 9 16
mol:Ca2+ -0.007 0.041 0.15 4 -0.15 9 13
mol:IP3 -0.007 0.042 0.15 4 -0.16 9 13
NLK 0.006 0.087 -10000 0 -0.73 7 7
GNB1 0.031 0.008 -10000 0 -10000 0 0
CAMK2A -0.021 0.038 0.16 8 -0.15 9 17
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.002 0.04 -10000 0 -0.12 24 24
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
GNAS -0.012 0.034 -10000 0 -0.12 23 23
GO:0007205 -0.011 0.036 0.14 5 -0.15 10 15
WNT6 0.032 0.001 -10000 0 -10000 0 0
WNT4 0.031 0.009 -10000 0 -0.07 2 2
NFAT1/CK1 alpha -0.008 0.055 0.19 7 -0.16 14 21
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.001 0.047 -10000 0 -0.07 155 155
WNT11 0.032 0.008 -10000 0 -0.07 2 2
CDC42 -0.024 0.034 0.18 4 -0.16 6 10
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.023 -10000 0 -0.054 2 2
CRKL 0.051 0.083 0.22 22 -0.41 5 27
mol:PIP3 0.012 0.037 -10000 0 -0.7 1 1
AKT1 0.005 0.042 -10000 0 -0.62 1 1
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.048 0.085 0.3 14 -0.34 6 20
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
HGF/MET/SHIP2 0.041 0.033 -10000 0 -0.05 4 4
MAP3K5 0.05 0.08 0.25 8 -0.41 4 12
HGF/MET/CIN85/CBL/ENDOPHILINS 0.039 0.032 -10000 0 -0.046 3 3
AP1 0.012 0.075 0.14 117 -10000 0 117
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.028 -10000 0 -0.07 40 40
apoptosis -0.019 0.21 -10000 0 -0.71 39 39
STAT3 (dimer) 0.011 0.027 -10000 0 -0.14 8 8
GAB1/CRKL/SHP2/PI3K 0.079 0.082 0.32 3 -0.38 5 8
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.068 0.08 0.23 8 -0.37 6 14
PTPN11 0.032 0.004 -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 0.022 0.016 -10000 0 -0.07 2 2
ELK1 0.11 0.18 0.35 172 -10000 0 172
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.027 0.16 1 -0.15 9 10
PAK1 0 0.044 -10000 0 -0.6 1 1
HGF/MET/RANBP10 0.041 0.033 -10000 0 -0.052 3 3
HRAS 0.015 0.039 -10000 0 -0.31 4 4
DOCK1 0.038 0.078 0.27 6 -0.37 6 12
GAB1 0.051 0.078 0.22 1 -0.47 4 5
CRK 0.053 0.08 0.2 23 -0.46 4 27
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.034 -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 9 -0.05 17 26
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.046 0.09 0.25 44 -0.31 3 47
GRB2/SHC 0.059 0.061 0.16 104 -0.11 8 112
FOS 0.006 0.043 -10000 0 -0.07 121 121
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.11 0.18 0.35 172 -10000 0 172
HGF/MET/MUC20 0.028 0.022 -10000 0 -0.043 3 3
cell migration 0.058 0.06 0.15 104 -0.11 8 112
GRB2 0.031 0.006 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.031 0.024 -10000 0 -0.054 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.043 2 2
RAP1B 0.048 0.081 0.28 14 -0.32 6 20
RAP1A 0.043 0.083 0.29 16 -0.35 5 21
HGF/MET/RANBP9 0.041 0.033 -10000 0 -0.043 7 7
RAF1 0.038 0.062 0.21 4 -0.28 6 10
STAT3 0.011 0.026 -10000 0 -0.14 7 7
cell proliferation 0.031 0.063 0.22 17 -0.26 2 19
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.078 0.16 0.36 14 -10000 0 14
MAPK1 0.11 0.21 0.62 39 -10000 0 39
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.02 0.14 0.26 3 -0.32 48 51
SRC 0.004 0.017 -10000 0 -0.12 7 7
PI3K 0.058 0.059 0.16 97 -0.11 7 104
MET/Glomulin 0.014 0.025 -10000 0 -0.085 20 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.063 0.25 5 -0.26 5 10
MET 0.021 0.016 -10000 0 -0.07 2 2
MAP4K1 0.058 0.085 0.26 7 -0.42 5 12
PTK2 0.031 0.006 -10000 0 0 18 18
MAP2K2 0.041 0.075 0.28 14 -0.27 6 20
BAD -0.002 0.041 -10000 0 -0.6 1 1
MAP2K4 0.044 0.077 0.23 15 -0.36 4 19
SHP2/GRB2/SOS1/GAB1 0.028 0.052 -10000 0 -0.35 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 9 -0.11 2 11
PLCgamma1/PKC 0.022 0.007 -10000 0 -10000 0 0
HGF 0.022 0.016 -10000 0 -0.07 1 1
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.016 -10000 0 -0.07 11 11
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.15 113 -0.11 9 122
PDPK1 0.012 0.041 0.31 1 -0.65 1 2
HGF/MET/SHIP 0.028 0.022 -10000 0 -0.043 3 3
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.055 0.062 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.042 0.033 -10000 0 -0.048 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.019 0.15 -10000 0 -0.48 43 43
SMAD4 0.008 0.042 -10000 0 -0.07 114 114
SMAD5 -0.023 0.085 0.12 1 -0.3 32 33
BMP7/USAG1 0.03 0.025 -10000 0 -0.054 6 6
SMAD5/SKI -0.011 0.091 -10000 0 -0.3 33 33
SMAD1 -0.007 0.066 -10000 0 -0.24 23 23
BMP2 0.021 0.029 -10000 0 -0.07 44 44
SMAD1/SMAD1/SMAD4 0.001 0.066 -10000 0 -0.24 16 16
BMPR1A 0.023 0.017 -10000 0 -0.07 6 6
BMPR1B 0.032 0.006 -10000 0 -0.07 1 1
BMPR1A-1B/BAMBI 0.031 0.051 -10000 0 -0.047 129 129
AHSG 0.031 0.009 -10000 0 -0.07 2 2
CER1 0.029 0.01 -10000 0 -10000 0 0
BMP2-4/CER1 0.039 0.045 -10000 0 -0.045 98 98
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.002 0.058 -10000 0 -0.19 36 36
BMP2-4 (homodimer) 0.033 0.032 -10000 0 -0.054 47 47
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.05 0.055 -10000 0 -0.061 4 4
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.022 0.015 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.014 0.055 -10000 0 -0.12 93 93
BMP2-4/USAG1 0.032 0.042 -10000 0 -0.051 55 55
SMAD6/SMURF1/SMAD5 -0.004 0.079 -10000 0 -0.29 28 28
SOSTDC1 0.021 0.018 -10000 0 -0.07 6 6
BMP7/BMPR2/BMPR1A-1B 0.052 0.052 -10000 0 -0.061 2 2
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.032 0.008 -10000 0 -0.07 2 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.031 0.011 -10000 0 -0.07 5 5
MAP3K7 0.031 0.008 -10000 0 -0.07 1 1
BMP2-4/CHRD 0.044 0.041 -10000 0 -0.048 66 66
SMAD5/SMAD5/SMAD4 -0.018 0.092 -10000 0 -0.31 33 33
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.009 0.051 -10000 0 -0.18 16 16
BMP7 (homodimer) 0.029 0.01 -10000 0 -0.07 1 1
NUP214 0.031 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.014 -10000 0 -0.054 4 4
SMAD1/SKI 0.006 0.076 -10000 0 -0.24 24 24
SMAD6 0.032 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.012 -10000 0 -10000 0 0
BMP2-4/FETUA 0.044 0.042 -10000 0 -0.052 53 53
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.021 -10000 0 -0.07 22 22
BMPR2 (homodimer) 0.032 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.057 0.028 -10000 0 -0.039 34 34
BMPR1A-1B (homodimer) 0.035 0.023 -10000 0 -0.054 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.004 0.077 -10000 0 -0.24 25 25
SMAD6-7/SMURF1/SMAD1 0.017 0.073 -10000 0 -0.24 15 15
SMAD6/SMURF1 0.022 0.015 -10000 0 -10000 0 0
BAMBI 0.02 0.025 -10000 0 -0.07 27 27
SMURF2 0.032 0.006 -10000 0 -0.07 1 1
BMP2-4/CHRDL1 0.03 0.028 -10000 0 -0.044 50 50
BMP2-4/GREM1 0.04 0.046 -10000 0 -0.049 95 95
SMAD7 0.031 0.007 -10000 0 -0.07 1 1
SMAD8A/SMAD8A/SMAD4 -0.017 0.15 -10000 0 -0.46 49 49
SMAD1/SMAD6 0.004 0.062 -10000 0 -0.24 16 16
TAK1/SMAD6 0.032 0.023 -10000 0 -0.054 1 1
BMP7 0.03 0.01 -10000 0 -0.07 1 1
BMP6 0.032 0.008 -10000 0 -0.07 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.002 0.045 -10000 0 -0.22 14 14
PPM1A 0.031 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.005 0.077 -10000 0 -0.24 25 25
SMAD7/SMURF1 0.032 0.023 -10000 0 -0.054 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 0.008 -10000 0 -0.07 3 3
PPP1R15A 0.031 0.009 -10000 0 -0.07 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.013 0.056 -10000 0 -0.12 94 94
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.032 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.015 0.055 -10000 0 -0.12 98 98
BMP4 0.029 0.014 -10000 0 -0.07 8 8
FST 0.029 0.018 -10000 0 -0.07 16 16
BMP2-4/NOG 0.03 0.028 -10000 0 -0.044 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.05 0.054 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.029 -10000 0 -0.07 45 45
positive regulation of NF-kappaB transcription factor activity 0.037 0.03 -10000 0 -0.054 44 44
MAP2K4 0.007 0.04 0.2 2 -0.18 11 13
IKBKB 0.032 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.031 0.012 -10000 0 -0.07 6 6
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.007 0.013 -10000 0 -0.057 8 8
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 0.031 -10000 0 -0.055 47 47
TRAIL/TRAILR3 0.037 0.03 -10000 0 -0.054 44 44
TRAIL/TRAILR1 0.018 0.019 -10000 0 -0.043 45 45
TRAIL/TRAILR4 0.037 0.03 -10000 0 -0.054 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.024 -10000 0 -0.037 46 46
IKK complex -0.031 0.11 -10000 0 -0.23 115 115
RIPK1 0.03 0.014 -10000 0 -0.07 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.025 0.01 -10000 0 -0.054 45 45
MAP3K1 0.013 0.038 -10000 0 -0.14 21 21
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 0.011 0.031 -10000 0 -0.12 21 21
CFLAR 0.032 0.01 -10000 0 -0.07 5 5
MAPK1 -0.023 0.011 -10000 0 -0.054 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.058 0.044 -10000 0 -0.051 52 52
mol:ceramide 0.007 0.013 -10000 0 -0.057 8 8
FADD 0.032 0.006 -10000 0 -0.07 1 1
MAPK8 -0.002 0.034 0.19 1 -0.18 9 10
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.032 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.015 -10000 0 -0.07 1 1
TRAIL/TRAILR1/FADD 0.035 0.026 -10000 0 -0.044 45 45
DAP3 0.032 0.005 -10000 0 -10000 0 0
CASP10 -0.014 0.027 0.14 11 -0.093 7 18
JNK cascade 0.037 0.03 -10000 0 -0.054 44 44
TRAIL (trimer) 0.023 0.029 -10000 0 -0.07 45 45
TNFRSF10C 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.031 -10000 0 -0.043 44 44
TRAIL/TRAILR2/FADD 0.05 0.039 -10000 0 -0.05 60 60
cell death 0.007 0.013 -10000 0 -0.057 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.035 -10000 0 -0.12 23 23
TRAILR2 (trimer) 0.031 0.012 -10000 0 -0.07 6 6
CASP8 0.016 0.022 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.07 0.056 -10000 0 -0.077 5 5
TCGA08_p53

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
CDKN2A -0.008 0.013 -10000 0 -0.043 53 53
TP53 -0.003 0.025 -10000 0 -0.12 15 15
Senescence -0.003 0.027 -10000 0 -0.13 16 16
Apoptosis -0.003 0.027 -10000 0 -0.13 16 16
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.01 0.025 43 -10000 0 43
MDM4 0.029 0.011 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.032 0.005 -10000 0 -10000 0 0
CLTC 0.013 0.083 0.15 7 -0.34 24 31
calcium ion-dependent exocytosis 0.023 0.045 0.091 117 -0.13 13 130
Dynamin 2/GTP 0.022 0.011 -10000 0 -0.023 23 23
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.009 0.07 -10000 0 -0.29 23 23
CPE -0.015 0.006 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
membrane fusion 0.027 0.044 0.093 136 -0.11 12 148
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.053 0.14 12 -0.17 24 36
TSHR -0.017 0.005 -10000 0 -0.043 4 4
INS 0.006 0.093 -10000 0 -0.46 18 18
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.027 0.044 0.093 136 -0.11 12 148
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.002 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.011 -10000 0 -0.023 23 23
JUP 0.009 0.067 -10000 0 -0.28 22 22
ASAP2/amphiphysin II 0.035 0.017 -10000 0 -0.023 23 23
ARF6/GTP 0.023 0.005 -10000 0 -10000 0 0
CDH1 0.009 0.066 -10000 0 -0.28 22 22
clathrin-independent pinocytosis 0.023 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.005 -10000 0 -10000 0 0
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.004 0.038 -10000 0 -0.13 30 30
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.006 -10000 0 -0.07 1 1
regulation of calcium-dependent cell-cell adhesion -0.035 0.07 0.27 23 -10000 0 23
positive regulation of phagocytosis -0.016 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.042 0.01 -10000 0 -10000 0 0
ACAP1 0.028 0.042 0.091 136 -0.094 12 148
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.002 0.061 -10000 0 -0.29 18 18
clathrin heavy chain/ACAP1 0.021 0.073 0.15 21 -0.25 23 44
JIP4/KLC1 0.041 0.032 -10000 0 -0.035 23 23
EXOC1 0.03 0.009 -10000 0 -0.07 1 1
exocyst 0.004 0.038 -10000 0 -0.13 30 30
RALA/GTP 0.015 0.014 -10000 0 -0.043 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.043 1 1
receptor recycling 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.009 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.014 0.082 0.18 1 -0.33 24 25
IL2RA 0.001 0.074 -10000 0 -0.33 21 21
VAMP3 -0.016 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.038 0.07 -10000 0 -0.24 24 24
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.011 -10000 0 -0.052 12 12
PLD2 0.006 0.011 -10000 0 -0.054 10 10
EXOC5 0.028 0.018 -10000 0 -0.07 15 15
PIP5K1C 0.014 0.049 0.12 5 -0.17 22 27
SDC1 0.007 0.069 -10000 0 -0.29 23 23
ARF6/GDP 0.023 0.005 -10000 0 -10000 0 0
EXOC7 0.032 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.038 0.072 -10000 0 -0.28 23 23
mol:Phosphatidic acid 0.027 0.044 0.093 136 -0.11 12 148
endocytosis -0.034 0.017 0.023 23 -10000 0 23
SCAMP2 0.032 0.005 -10000 0 -10000 0 0
ADRB2 0.008 0.079 0.22 2 -0.32 24 26
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.01 -10000 0 -0.023 23 23
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.009 0.08 0.2 5 -0.32 24 29
RALA 0.02 0.02 -10000 0 -0.07 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.071 0.21 3 -0.27 23 26
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.07 2 2
Jak2/Leptin Receptor 0.019 0.11 -10000 0 -0.3 46 46
PTP1B/AKT1 0.039 0.057 0.17 7 -0.27 7 14
FYN 0.029 0.011 -10000 0 -0.07 1 1
p210 bcr-abl/PTP1B 0.026 0.057 0.16 10 -0.26 8 18
EGFR 0.012 0.018 -10000 0 -0.054 8 8
EGF/EGFR 0.011 0.039 -10000 0 -0.23 6 6
CSF1 0.032 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.009 -10000 0 -0.027 2 2
INSR 0.031 0.009 -10000 0 -0.027 5 5
PTP1B/N-cadherin 0.038 0.058 0.16 5 -0.25 8 13
Insulin Receptor/Insulin 0.054 0.062 0.18 1 -0.22 10 11
HCK 0.013 0.038 -10000 0 -0.07 84 84
CRK 0.032 0.004 -10000 0 -10000 0 0
TYK2 0.027 0.076 0.27 26 -0.27 7 33
EGF 0.033 0.008 -10000 0 -0.057 3 3
YES1 0.017 0.036 -10000 0 -0.07 74 74
CAV1 0.05 0.083 0.16 113 -0.27 8 121
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.063 0.18 7 -0.25 8 15
cell migration -0.026 0.057 0.26 8 -0.16 10 18
STAT3 0.031 0.015 -10000 0 -0.069 10 10
PRLR 0.033 0.005 -10000 0 -10000 0 0
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
CSF1R 0.024 0.028 -10000 0 -0.07 40 40
Prolactin Receptor/Prolactin 0.049 0.014 -10000 0 -10000 0 0
FGR 0.029 0.018 -10000 0 -0.07 15 15
PTP1B/p130 Cas 0.022 0.053 0.12 24 -0.23 9 33
Crk/p130 Cas 0.038 0.057 0.16 7 -0.23 9 16
DOK1 0.023 0.059 0.17 13 -0.26 10 23
JAK2 0.005 0.11 0.2 1 -0.3 51 52
Jak2/Leptin Receptor/Leptin 0.026 0.074 -10000 0 -0.26 12 12
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.057 0.14 25 -0.24 9 34
LYN 0.02 0.033 -10000 0 -0.07 60 60
CDH2 0.03 0.01 -10000 0 -0.07 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 0.093 0.24 42 -0.3 10 52
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.054 0.067 -10000 0 -0.22 10 10
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.025 0.068 -10000 0 -0.23 12 12
negative regulation of transcription 0.005 0.11 0.2 1 -0.3 51 52
FCGR2A -0.019 0.051 -10000 0 -0.07 253 253
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 -0.049 56 56
RHOA 0.032 0.006 -10000 0 -10000 0 0
LEPR 0.031 0.009 -10000 0 -0.07 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.031 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.03 0.081 0.2 25 -0.28 11 36
PRL 0.033 0.011 -10000 0 -0.067 6 6
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.032 0.016 -10000 0 -0.068 8 8
Insulin Receptor/Insulin/IRS1 0.059 0.024 -10000 0 -0.044 13 13
CSF1/CSF1R 0.052 0.065 0.2 3 -0.25 8 11
Ras protein signal transduction -0.01 0.089 0.54 12 -10000 0 12
IRS1 0.032 0.009 -10000 0 -0.07 4 4
INS 0.032 0.007 -10000 0 -0.027 1 1
LEP 0.022 0.015 -10000 0 -10000 0 0
STAT5B 0.023 0.072 0.17 6 -0.25 17 23
STAT5A 0.022 0.072 0.19 3 -0.25 17 20
GRB2 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.041 0.059 0.17 7 -0.25 8 15
CSN2 0 0.034 -10000 0 -0.28 4 4
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
LAT 0.005 0.047 -10000 0 -0.3 3 3
YBX1 0.037 0.017 -10000 0 -0.067 12 12
LCK 0.031 0.01 -10000 0 -0.07 4 4
SHC1 0.024 0.028 -10000 0 -0.07 40 40
NOX4 0.021 0.036 -10000 0 -0.067 70 70
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.043 0.063 0.23 38 -10000 0 38
PCK1 0.037 0.032 -10000 0 -10000 0 0
HNF4A 0.036 0.045 0.26 5 -0.31 1 6
KCNJ11 0.056 0.063 0.26 29 -10000 0 29
AKT1 0.069 0.043 -10000 0 -0.28 1 1
response to starvation 0.002 0.004 -10000 0 -0.081 1 1
DLK1 0.048 0.076 0.26 34 -0.26 1 35
NKX2-1 0.036 0.042 0.17 33 -10000 0 33
ACADM 0.043 0.062 0.23 36 -10000 0 36
TAT 0.044 0.044 -10000 0 -10000 0 0
CEBPB 0.029 0.018 -10000 0 -0.068 11 11
CEBPA 0.03 0.019 -10000 0 -0.068 15 15
TTR 0.056 0.094 0.36 33 -0.43 1 34
PKLR 0.047 0.068 0.23 46 -10000 0 46
APOA1 0.061 0.073 0.41 10 -10000 0 10
CPT1C 0.043 0.058 0.24 29 -0.23 1 30
ALAS1 0.047 0.052 -10000 0 -10000 0 0
TFRC 0.056 0.052 0.21 26 -10000 0 26
FOXF1 0.024 0.026 -10000 0 -0.07 35 35
NF1 0.034 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.039 0.005 -10000 0 -10000 0 0
CPT1A 0.043 0.063 0.23 39 -10000 0 39
HMGCS1 0.044 0.063 0.23 39 -10000 0 39
NR3C1 0.035 0.015 -10000 0 -10000 0 0
CPT1B 0.036 0.056 0.23 26 -10000 0 26
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.005 -10000 0 -10000 0 0
GCK 0.079 0.1 0.24 125 -10000 0 125
CREB1 0.036 0.009 -10000 0 -10000 0 0
IGFBP1 0.051 0.048 -10000 0 -10000 0 0
PDX1 0.046 0.05 -10000 0 -10000 0 0
UCP2 0.037 0.069 0.23 36 -10000 0 36
ALDOB 0.059 0.075 0.26 46 -10000 0 46
AFP 0.012 0.01 -10000 0 -0.086 4 4
BDH1 0.047 0.069 0.24 47 -10000 0 47
HADH 0.056 0.073 0.26 41 -10000 0 41
F2 0.059 0.076 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 0.062 0.053 0.21 30 -10000 0 30
INS 0.028 0.01 0.15 1 -10000 0 1
FOXA1 0.008 0.006 -10000 0 -0.057 3 3
FOXA3 0.016 0.012 -10000 0 -0.11 3 3
FOXA2 0.091 0.073 0.29 29 -10000 0 29
ABCC8 0.055 0.071 0.25 39 -10000 0 39
ALB 0.012 0.01 -10000 0 -0.086 4 4
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.007 0.015 -10000 0 -10000 0 0
FRAP1 0.044 0.061 0.21 8 -0.36 3 11
AKT1 0.038 0.083 0.16 139 -0.14 4 143
INSR 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.011 -10000 0 -10000 0 0
mol:GTP 0.042 0.09 0.17 141 -0.15 2 143
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.021 -10000 0 -0.17 1 1
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.004 0.044 0.11 52 -0.14 3 55
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 0.044 0.043 0.13 9 -0.19 1 10
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.014 -10000 0 -10000 0 0
RPS6KB1 0.055 0.071 0.2 40 -0.26 1 41
MAP3K5 -0.012 0.055 0.16 2 -0.2 39 41
PIK3R1 0.03 0.01 -10000 0 -10000 0 0
apoptosis -0.012 0.055 0.16 2 -0.2 39 41
mol:LY294002 0 0 0.001 1 -0.001 1 2
EIF4B 0.048 0.069 0.19 43 -0.24 1 44
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.047 0.22 5 -10000 0 5
eIF4E/eIF4G1/eIF4A1 0.025 0.033 -10000 0 -0.25 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.026 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.012 0.051 0.12 70 -10000 0 70
FKBP1A 0.03 0.01 -10000 0 -0.07 1 1
RHEB/GTP 0.036 0.054 0.15 64 -0.14 3 67
mol:Amino Acids 0 0 0.001 1 -0.001 1 2
FKBP12/Rapamycin 0.023 0.008 -10000 0 -0.044 1 1
PDPK1 -0.012 0.02 0.16 4 -10000 0 4
EIF4E 0.031 0.011 -10000 0 -0.07 5 5
ASK1/PP5C 0.016 0.16 -10000 0 -0.52 41 41
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.032 -10000 0 -0.24 4 4
TSC1/TSC2 0.046 0.098 0.19 142 -0.16 2 144
tumor necrosis factor receptor activity 0 0 0.001 1 -0.001 1 2
RPS6 0.029 0.011 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
EIF4G1 0.031 0.006 -10000 0 -10000 0 0
IRS1 0.011 0.007 -10000 0 -10000 0 0
INS 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -0.069 2 2
PDK2 -0.013 0.02 0.16 4 -10000 0 4
EIF4EBP1 -0.039 0.097 -10000 0 -0.97 3 3
PIK3CA 0.029 0.019 -10000 0 -0.07 17 17
PPP2R5D 0.036 0.059 0.22 7 -0.33 3 10
peptide biosynthetic process -0.022 0.013 0.18 2 -10000 0 2
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.03 0.015 -10000 0 -0.07 10 10
mol:Rapamycin 0 0.001 0.002 124 -0.003 1 125
EEF2 -0.022 0.014 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.028 0.098 -10000 0 -0.91 3 3
ceramide signaling pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.052 -10000 0 -0.21 20 20
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.008 0.025 0.15 2 -0.12 8 10
NFKBIA 0.031 0.009 -10000 0 -0.07 1 1
BIRC3 0.026 0.024 -10000 0 -0.07 30 30
BAX -0.005 0.037 0.19 11 -0.12 9 20
EnzymeConsortium:3.1.4.12 0 0.016 0.052 4 -0.066 10 14
IKBKB -0.009 0.054 0.19 4 -0.27 9 13
MAP2K2 -0.012 0.046 0.17 23 -0.14 5 28
MAP2K1 -0.016 0.033 0.17 7 -0.14 5 12
SMPD1 -0.002 0.024 0.093 2 -0.1 17 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.057 0.22 2 -0.28 11 13
MAP2K4 -0.013 0.027 0.16 4 -0.14 5 9
protein ubiquitination -0.012 0.054 -10000 0 -0.28 9 9
EnzymeConsortium:2.7.1.37 -0.015 0.041 0.18 7 -0.15 5 12
response to UV 0 0 0.002 10 -0.002 2 12
RAF1 -0.012 0.032 0.17 7 -0.14 5 12
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.003 0.024 0.088 3 -0.11 12 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.011 -10000 0 -0.043 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.027 0.16 3 -0.12 8 11
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 0.17 9 -0.14 2 11
MAPK1 -0.015 0.047 0.18 7 -0.18 9 16
p50/RELA/I-kappa-B-alpha 0.045 0.013 -10000 0 -0.054 1 1
FADD -0.003 0.05 0.19 2 -0.2 18 20
KSR1 -0.008 0.025 0.11 2 -0.12 8 10
MAPK8 -0.013 0.029 0.15 4 -0.14 5 9
TRAF2 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.011 0.05 -10000 0 -0.26 10 10
TNF R/SODD 0.013 0.047 -10000 0 -0.054 162 162
TNF 0.032 0.007 -10000 0 -0.07 2 2
CYCS 0.011 0.044 0.13 21 -0.12 4 25
IKBKG -0.009 0.054 0.18 4 -0.26 10 14
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.003 0.055 0.15 1 -0.21 21 22
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.03 0.014 -10000 0 -0.07 9 9
AIFM1 -0.01 0.031 0.13 12 -0.12 6 18
TNF/TNF R/SODD 0.024 0.055 -10000 0 -0.052 163 163
TNFRSF1A -0.002 0.047 -10000 0 -0.07 164 164
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.004 0.055 0.18 6 -0.2 20 26
response to hydrogen peroxide 0 0 0.002 10 -0.002 2 12
BCL2 0.031 0.006 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.028 0.033 -10000 0 -0.12 8 8
BIRC5 -0.008 0.05 -10000 0 -0.07 201 201
NFKBIA -0.007 0.015 0.17 2 -10000 0 2
CPEB1 0.024 0.014 -10000 0 -10000 0 0
AKT1 -0.006 0.015 0.24 1 -10000 0 1
NDEL1 0.031 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.024 0.099 2 -0.12 8 10
NDEL1/TACC3 0.033 0.04 -10000 0 -0.12 8 8
GADD45A 0.024 0.027 -10000 0 -0.07 39 39
GSK3B 0.032 0.008 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 -0.07 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.036 0.019 -10000 0 -0.054 252 252
TP53 0.007 0.038 -10000 0 -0.2 14 14
DLG7 0.006 0.009 0.095 2 -0.037 1 3
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 0.043 -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 0.014 0.13 2 -0.046 1 3
AURKB 0.007 0.025 -10000 0 -0.086 25 25
CDC25B 0.011 0.019 0.097 2 -0.14 4 6
G2/M transition checkpoint 0.007 0.017 0.075 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 0.011 -10000 0 -0.07 5 5
centrosome duplication 0.034 0.029 -10000 0 -0.12 8 8
regulation of centrosome cycle 0.032 0.04 -10000 0 -0.12 8 8
spindle assembly 0.063 0.037 -10000 0 -0.12 7 7
TDRD7 0.031 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.024 0.055 -10000 0 -0.13 8 8
CENPA 0.009 0.026 -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 -10000 0 -0.19 8 8
negative regulation of DNA binding 0.007 0.038 -10000 0 -0.2 14 14
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 0.011 0.071 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.014 0.13 2 -0.046 1 3
TACC1 0.032 0.005 -10000 0 -10000 0 0
TACC3 0.014 0.039 -10000 0 -0.07 90 90
Aurora A/Antizyme1 0.049 0.032 -10000 0 -0.12 8 8
Aurora A/RasGAP 0.034 0.029 -10000 0 -0.13 7 7
OAZ1 0.031 0.007 -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 0.059 0.024 -10000 0 -0.044 2 2
Importin alpha/Importin beta/TPX2 -0.036 0.019 -10000 0 -0.054 252 252
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.026 0.021 -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
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.022 0.071 -10000 0 -0.14 19 19
Ran/GTP/Exportin 1/HDAC1 -0.027 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.06 -10000 0 -0.18 22 22
SUMO1 0.033 0 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.029 -10000 0 -0.098 37 37
FKBP3 0.031 0.007 -10000 0 -10000 0 0
Histones 0.032 0.044 -10000 0 -0.2 7 7
YY1/LSF 0.013 0.059 -10000 0 -0.15 56 56
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 28 28
I kappa B alpha/HDAC1 0 0.058 -10000 0 -0.18 31 31
SAP18 0.031 0.008 -10000 0 -10000 0 0
RELA 0 0.048 0.11 12 -0.15 34 46
HDAC1/Smad7 0.034 0.04 -10000 0 -0.05 45 45
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
HDAC3/TR2 0.015 0.045 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.047 -10000 0 -0.17 24 24
NF kappa B1 p50/RelA 0.006 0.059 -10000 0 -0.21 13 13
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 0.046 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.003 0.047 -10000 0 -0.17 22 22
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.039 -10000 0 -0.07 89 89
MAX 0.031 0.007 -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 0.02 -10000 0 -0.056 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.006 0.051 -10000 0 -0.13 55 55
SIN3 complex 0.053 0.027 -10000 0 -0.032 35 35
SMURF1 0.022 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 -0.002 0.049 -10000 0 -0.18 20 20
YY1/HDAC2 0.013 0.059 -10000 0 -0.15 51 51
YY1/HDAC1 0.008 0.06 -10000 0 -0.15 51 51
NuRD/MBD2 Complex (MeCP1) 0.002 0.051 -10000 0 -0.18 25 25
PPARG 0.002 0.038 0.12 10 -0.16 12 22
HDAC8/hEST1B 0.041 0.011 -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 -0.002 0.047 -10000 0 -0.07 164 164
HDAC3/SMRT (N-CoR2) 0.015 0.045 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.04 -10000 0 -0.05 45 45
CREBBP 0.032 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.046 -10000 0 -0.16 22 22
HDAC1 0.019 0.033 -10000 0 -0.07 61 61
HDAC3 0.006 0.021 -10000 0 -0.059 6 6
HDAC2 0.03 0.012 -10000 0 -0.07 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 -0.07 1 1
NCOR2 0.032 0.004 -10000 0 -10000 0 0
MXD1 0.033 0 -10000 0 -10000 0 0
STAT3 0.017 0.009 -10000 0 -0.039 9 9
NFKB1 0.031 0.01 -10000 0 -0.07 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 0.065 -10000 0 -0.14 54 54
YY1/SAP30/HDAC1 0.021 0.066 -10000 0 -0.14 55 55
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.009 -10000 0 -0.039 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.02 -10000 0 -0.056 5 5
histone deacetylation 0.002 0.051 -10000 0 -0.17 25 25
STAT3 (dimer non-phopshorylated)/HDAC3 0.004 0.042 -10000 0 -0.11 40 40
nuclear export -0.041 0.01 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.023 0.028 -10000 0 -0.07 41 41
GATA2/HDAC3 0.015 0.045 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.034 -10000 0 -0.054 61 61
GATA1/HDAC3 0.016 0.045 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.013 0.047 -10000 0 -0.054 165 165
SIN3/HDAC complex/Mad/Max -0.004 0.065 -10000 0 -0.18 42 42
NuRD Complex 0.004 0.05 -10000 0 -0.18 18 18
positive regulation of chromatin silencing 0.03 0.043 -10000 0 -0.2 7 7
SIN3B 0.031 0.007 -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 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.044 -10000 0 -0.1 36 36
HDAC complex 0.039 0.065 -10000 0 -0.057 136 136
GATA1/Fog1 0.024 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.041 0.047 -10000 0 -0.053 68 68
TNF 0.032 0.007 -10000 0 -0.07 2 2
negative regulation of cell growth -0.004 0.064 -10000 0 -0.18 42 42
NuRD/MBD2/PRMT5 Complex 0.002 0.051 -10000 0 -0.18 25 25
Ran/GTP/Exportin 1 0.038 0.039 -10000 0 -0.098 36 36
NF kappa B/RelA/I kappa B alpha -0.006 0.048 -10000 0 -0.17 24 24
SIN3/HDAC complex/NCoR1 0.006 0.042 -10000 0 -0.17 17 17
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 0.031 0.006 -10000 0 -10000 0 0
BCR 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
JUN 0.009 0.076 0.21 10 -0.23 19 29
IKBKB 0.016 0.057 0.26 4 -0.25 7 11
AKT1 0.014 0.075 0.21 37 -0.16 1 38
IKBKG 0.013 0.048 0.23 4 -0.22 6 10
CALM1 -0.009 0.049 0.2 2 -0.18 15 17
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
MAP3K1 0.032 0.092 0.26 17 -0.39 7 24
MAP3K7 0.031 0.008 -10000 0 -0.07 1 1
mol:Ca2+ -0.006 0.054 0.22 1 -0.18 20 21
DOK1 0.032 0.001 -10000 0 -10000 0 0
AP-1 -0.008 0.058 0.17 5 -0.17 23 28
LYN 0.02 0.033 -10000 0 -0.07 60 60
BLNK 0.013 0.033 -10000 0 -0.07 60 60
SHC1 0.024 0.028 -10000 0 -0.07 40 40
BCR complex 0.045 0.014 -10000 0 -0.069 2 2
CD22 -0.009 0.032 -10000 0 -0.24 2 2
CAMK2G -0.001 0.03 0.18 2 -0.2 5 7
CSNK2A1 0.03 0.009 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.049 0.022 -10000 0 -0.095 43 43
GO:0007205 -0.007 0.055 0.22 1 -0.18 20 21
SYK 0.025 0.026 -10000 0 -0.07 35 35
ELK1 -0.013 0.053 0.2 1 -0.18 19 20
NFATC1 -0.018 0.061 0.21 9 -0.21 18 27
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -0.069 2 2
PAG1/CSK 0.024 0.003 -10000 0 -10000 0 0
NFKBIB 0.021 0.032 0.14 3 -0.12 14 17
HRAS -0.014 0.053 0.18 5 -0.16 22 27
NFKBIA 0.021 0.031 0.14 3 -0.12 14 17
NF-kappa-B/RelA/I kappa B beta 0.024 0.029 0.13 4 -0.096 14 18
RasGAP/Csk 0.05 0.067 -10000 0 -0.097 2 2
mol:GDP -0.005 0.055 0.22 1 -0.18 17 18
PTEN 0.022 0.016 -10000 0 -0.07 2 2
CD79B 0.032 0.006 -10000 0 -0.069 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.028 0.13 4 -0.093 14 18
GRB2 0.031 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.007 0.077 0.3 3 -0.31 4 7
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.006 0.054 0.22 1 -0.18 20 21
CSK 0.032 0.005 -10000 0 -10000 0 0
FOS -0.021 0.052 0.17 2 -0.19 16 18
CHUK -0.044 0.12 0.23 4 -0.25 113 117
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.072 -10000 0 -0.18 16 16
PTPN6 -0.02 0.032 0.14 4 -0.2 3 7
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.012 0.02 0.09 4 -0.069 14 18
VAV2 -0.015 0.059 0.16 3 -0.26 18 21
ubiquitin-dependent protein catabolic process 0.022 0.032 0.14 3 -0.12 14 17
BTK 0.015 0.012 -10000 0 -10000 0 0
CD19 -0.009 0.033 -10000 0 -0.2 3 3
MAP4K1 0.031 0.008 -10000 0 -0.07 1 1
CD72 0.03 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.025 0.084 0.24 17 -0.35 7 24
SH3BP5 0.029 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.007 0.053 -10000 0 -0.18 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.001 0.06 -10000 0 -0.27 15 15
RAF1 -0.017 0.051 0.18 6 -0.18 12 18
RasGAP/p62DOK/SHIP 0.041 0.059 -10000 0 -0.078 3 3
CD79A 0.03 0.01 -10000 0 -0.07 2 2
re-entry into mitotic cell cycle -0.008 0.057 0.17 5 -0.17 23 28
RASA1 0.032 0.006 -10000 0 -10000 0 0
MAPK3 -0.024 0.05 0.18 5 -0.2 6 11
MAPK1 -0.022 0.05 0.2 7 -0.21 4 11
CD72/SHP1 0.006 0.065 0.22 27 -0.23 2 29
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
MAPK8 0.023 0.082 0.24 16 -0.35 7 23
actin cytoskeleton organization 0.029 0.092 0.19 53 -0.25 9 62
NF-kappa-B/RelA 0.047 0.055 0.24 4 -0.19 13 17
Calcineurin 0.007 0.066 0.2 1 -0.18 12 13
PI3K -0.029 0.049 -10000 0 -0.16 10 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.001 0.045 -10000 0 -0.21 6 6
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.034 0.079 -10000 0 -0.57 6 6
DAPP1 0.018 0.075 -10000 0 -0.64 5 5
cytokine secretion -0.017 0.059 0.21 9 -0.2 17 26
mol:DAG -0.006 0.054 0.22 1 -0.18 20 21
PLCG2 0.03 0.015 -10000 0 -0.07 10 10
MAP2K1 -0.022 0.05 0.18 6 -0.2 7 13
B-cell antigen/BCR complex/FcgammaRIIB 0.033 0.051 -10000 0 -0.052 123 123
mol:PI-3-4-5-P3 -0.021 0.051 0.2 11 -0.22 1 12
ETS1 0.02 0.065 0.17 24 -0.19 6 30
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.027 0.075 -10000 0 -0.089 35 35
B-cell antigen/BCR complex/LYN 0.004 0.038 -10000 0 -0.24 2 2
MALT1 0.027 0.021 -10000 0 -0.07 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.089 0.19 51 -0.26 9 60
B-cell antigen/BCR complex/LYN/SYK 0.042 0.065 0.22 18 -0.22 2 20
CARD11 -0.007 0.053 0.21 1 -0.17 20 21
FCGR2B 0.008 0.043 -10000 0 -0.07 120 120
PPP3CA 0.026 0.013 -10000 0 -10000 0 0
BCL10 0.031 0.01 -10000 0 -0.07 4 4
IKK complex 0.004 0.035 0.14 7 -0.12 8 15
PTPRC 0.007 0.044 -10000 0 -0.07 122 122
PDPK1 -0.015 0.052 0.19 16 -0.16 1 17
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.032 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.02 0.13 4 -0.068 10 14
LPA4-mediated signaling events

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
ADCY4 -0.009 0.001 -10000 0 -10000 0 0
ADCY5 -0.009 0.001 -10000 0 -10000 0 0
ADCY6 -0.017 0.003 0 19 -10000 0 19
ADCY7 -0.018 0.004 -10000 0 -0.043 5 5
ADCY1 -0.012 0.008 0 158 -10000 0 158
ADCY2 -0.017 0.004 -10000 0 -10000 0 0
ADCY3 -0.009 0.001 -10000 0 -10000 0 0
ADCY8 -0.018 0.004 -10000 0 -0.043 5 5
PRKCE -0.011 0.001 -10000 0 -10000 0 0
ADCY9 -0.018 0.003 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.008 0.041 0.13 24 -0.12 4 28
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.008 -9999 0 -0.069 2 2
SVIL 0.022 0.021 -9999 0 -0.069 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 0.043 0.016 -9999 0 -0.042 9 9
CARM1 0.031 0.007 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 -10000 0 0
PELP1 0.032 0.004 -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 0.004 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -0.071 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.016 0.027 -9999 0 -0.069 31 31
GSN 0.029 0.018 -9999 0 -0.069 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.031 0.009 -9999 0 -10000 0 0
DNA-PK 0.053 0.034 -9999 0 -0.054 22 22
NCOA4 0.025 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.005 -9999 0 -10000 0 0
cell proliferation 0.007 0.046 -9999 0 -0.42 5 5
XRCC5 0.032 0.001 -9999 0 -10000 0 0
UBE3A 0.033 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.023 0.01 -9999 0 -0.029 14 14
FHL2 0.012 0.028 -9999 0 -0.22 4 4
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.003 0.002 -9999 0 -0.027 3 3
CDK6 0.022 0.015 -9999 0 -10000 0 0
TGFB1I1 -0.053 0.038 -9999 0 -0.069 425 425
T-DHT/AR/CyclinD1 0.029 0.036 -9999 0 -0.043 92 92
XRCC6 0.03 0.008 -9999 0 -10000 0 0
T-DHT/AR 0.037 0.029 -9999 0 -0.048 13 13
CTDSP1 0.032 0.008 -9999 0 -0.07 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.032 0.011 -9999 0 -0.069 5 5
TCF4 0.03 0.007 -9999 0 -10000 0 0
CDKN2A 0.002 0.028 -9999 0 -0.07 53 53
SRF 0.033 0.01 -9999 0 -0.049 3 3
NKX3-1 -0.003 0.007 -9999 0 -0.039 15 15
KLK3 0.02 0.033 -9999 0 -10000 0 0
TMF1 0.031 0.01 -9999 0 -0.07 4 4
HNRNPA1 0.031 0.005 -9999 0 -10000 0 0
AOF2 0.001 0 -9999 0 -10000 0 0
APPL1 -0.021 0.007 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.042 0.019 -9999 0 -0.045 18 18
AR 0.03 0.016 -9999 0 -0.052 14 14
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 0.021 -9999 0 -0.07 21 21
PA2G4 0.031 0.006 -9999 0 -10000 0 0
UBE2I 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.041 0.015 -9999 0 -0.038 8 8
RPS6KA3 0.033 0.005 -9999 0 -0.069 1 1
T-DHT/AR/ARA70 0.033 0.024 -9999 0 -0.045 10 10
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.04 0.016 -9999 0 -0.038 8 8
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.025 0.026 -9999 0 -0.069 36 36
KLK2 0.003 0.025 -9999 0 -0.27 3 3
CASP8 0.03 0.014 -9999 0 -0.07 10 10
T-DHT/AR/TIF2/CARM1 0.058 0.024 -9999 0 -0.045 8 8
TMPRSS2 0.004 0.022 -9999 0 -0.15 4 4
CCND1 0.014 0.039 -9999 0 -0.069 90 90
PIAS1 0.033 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.011 6 6
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.032 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.029 0.024 -9999 0 -0.043 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.023 0.017 -9999 0 -0.03 3 3
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 -0.038 0.047 -9999 0 -0.07 343 343
FKBP4 0.032 0.006 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0 0.039 0.073 1 -0.11 57 58
regulation of axonogenesis 0.009 0.055 0.26 22 -10000 0 22
myoblast fusion -0.014 0.04 0.35 3 -10000 0 3
mol:GTP 0.011 0.047 -10000 0 -0.18 24 24
regulation of calcium-dependent cell-cell adhesion -0.025 0.039 0.12 20 -10000 0 20
ARF1/GTP 0.028 0.045 -10000 0 -0.14 23 23
mol:GM1 0 0.032 -10000 0 -0.13 24 24
mol:Choline -0.02 0.024 -10000 0 -0.13 21 21
lamellipodium assembly -0.004 0.06 -10000 0 -0.38 11 11
MAPK3 0.007 0.038 -10000 0 -0.12 24 24
ARF6/GTP/NME1/Tiam1 0.025 0.04 -10000 0 -0.12 20 20
ARF1 0.032 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.04 -10000 0 -0.35 3 3
ARF1/GDP 0.01 0.064 -10000 0 -0.24 23 23
ARF6 0.033 0.025 -10000 0 -0.042 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.028 0.013 -10000 0 -0.029 17 17
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.12 16 16
actin filament bundle formation -0.018 0.066 0.25 23 -10000 0 23
KALRN 0.001 0.043 -10000 0 -0.26 11 11
RAB11FIP3/RAB11A 0.047 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.067 -10000 0 -0.25 23 23
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.053 -10000 0 -0.24 13 13
substrate adhesion-dependent cell spreading 0.011 0.047 -10000 0 -0.18 24 24
cortical actin cytoskeleton organization -0.004 0.06 -10000 0 -0.38 11 11
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.011 0.047 -10000 0 -0.18 24 24
ARF6/GTP 0.011 0.047 -10000 0 -0.18 24 24
RhoA/GTP 0.028 0.045 -10000 0 -0.14 23 23
mol:GDP -0.007 0.057 -10000 0 -0.26 22 22
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.05 -10000 0 -0.13 24 24
RHOA 0.032 0.006 -10000 0 -10000 0 0
PLD1 0.006 0.037 -10000 0 -0.14 23 23
RAB11FIP3 0.032 0.003 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.06 -10000 0 -0.38 11 11
ruffle organization -0.009 0.055 -10000 0 -0.26 22 22
regulation of epithelial cell migration 0.011 0.047 -10000 0 -0.18 24 24
PLD2 0.007 0.036 -10000 0 -0.14 22 22
PIP5K1A -0.009 0.055 -10000 0 -0.26 22 22
mol:Phosphatidic acid -0.02 0.024 -10000 0 -0.13 21 21
Rac1/GTP -0.005 0.06 -10000 0 -0.38 11 11
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.018 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.07 5 5
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.066 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.043 0.042 -10000 0 -0.037 102 102
alpha4/beta7 Integrin/Paxillin 0.045 0.016 -10000 0 -0.062 5 5
lamellipodium assembly -0.01 0.08 -10000 0 -0.34 18 18
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
PI3K 0.039 0.023 -10000 0 -0.054 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
TLN1 0.021 0.029 -10000 0 -0.07 43 43
PXN -0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.042 0.05 0.14 10 -10000 0 10
cell adhesion 0.033 0.054 0.16 9 -0.073 2 11
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.023 -10000 0 -0.055 5 5
ITGB1 0.025 0.013 -10000 0 -10000 0 0
ITGB7 0.032 0.008 -10000 0 -0.07 2 2
ARF6/GDP 0.033 0.014 -10000 0 -0.026 10 10
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.022 0.056 0.17 3 -0.077 2 5
p130Cas/Crk/Dock1 0.032 0.02 -10000 0 -10000 0 0
VCAM1 -0.035 0.048 -10000 0 -0.07 333 333
alpha4/beta1 Integrin/Paxillin/Talin 0.034 0.055 0.17 9 -0.074 2 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.045 0.048 0.17 10 -10000 0 10
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.043 0.047 -10000 0 -0.16 10 10
CBL 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.034 0.055 0.17 9 -0.074 2 11
Rac1/GTP -0.011 0.088 -10000 0 -0.37 18 18
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 0.008 0.05 -10000 0 -0.3 12 12
KLHL20 0.027 0.071 0.17 33 -0.19 17 50
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.005 0.042 0.17 10 -0.16 8 18
ENAH 0.005 0.054 -10000 0 -0.3 14 14
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.033 0.11 21 -0.12 6 27
ABI1/Sra1/Nap1 -0.011 0.024 -10000 0 -0.12 16 16
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.073 0.034 -10000 0 -0.056 10 10
RAPGEF1 -0.001 0.059 0.16 33 -0.28 10 43
CTNND1 0.03 0.015 -10000 0 -0.07 10 10
regulation of calcium-dependent cell-cell adhesion 0.02 0.055 -10000 0 -0.3 13 13
CRK 0.006 0.06 0.17 25 -0.29 12 37
E-cadherin/gamma catenin/alpha catenin 0.057 0.03 -10000 0 -0.058 20 20
alphaE/beta7 Integrin 0.046 0.011 -10000 0 -0.054 2 2
IQGAP1 0.008 0.043 -10000 0 -0.07 120 120
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.019 -10000 0 -0.024 44 44
DLG1 0.006 0.054 -10000 0 -0.29 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.018 -10000 0 -0.093 10 10
MLLT4 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.017 -10000 0 -0.024 26 26
PI3K -0.036 0.022 -10000 0 -0.12 10 10
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.043 0.022 -10000 0 -0.062 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 0.037 0.14 8 -0.098 1 9
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.07 8 8
RhoA/GDP 0.01 0.061 0.17 28 -0.16 15 43
actin cytoskeleton organization 0.023 0.056 0.14 34 -0.14 17 51
CDC42/GDP 0.01 0.059 0.17 24 -0.16 15 39
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.026 -10000 0 -0.1 20 20
ITGB7 0.032 0.008 -10000 0 -0.07 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.072 0.037 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.022 -10000 0 -0.043 9 9
mol:GDP -0.002 0.063 0.17 29 -0.18 15 44
CDC42/GTP/IQGAP1 0.022 0.037 -10000 0 -0.043 119 119
JUP 0.029 0.018 -10000 0 -0.07 16 16
p120 catenin/RhoA/GDP 0.024 0.064 0.18 27 -0.17 15 42
RAC1/GTP/IQGAP1 0.015 0.033 -10000 0 -0.043 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 0.014 0.041 0.11 30 -0.093 17 47
NME1 0 0 -10000 0 0 2 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.006 0.053 -10000 0 -0.29 14 14
regulation of cell-cell adhesion -0.03 0.017 0.043 2 -0.099 11 13
WASF2 -0.006 0.013 -10000 0 -0.066 17 17
Rap1/GTP -0.022 0.045 0.14 30 -0.13 3 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.083 0.043 -10000 0 -0.081 5 5
CCND1 0.016 0.048 0.12 29 -0.11 17 46
VAV2 0.01 0.12 -10000 0 -0.55 17 17
RAP1/GDP -0.011 0.052 0.16 32 -0.18 1 33
adherens junction assembly 0.006 0.052 -10000 0 -0.29 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.014 -10000 0 -10000 0 0
PIP5K1C 0.03 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 3 -0.084 5 8
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.15 6 6
mol:GTP 0 0 -10000 0 0 2 2
SRC 0.006 0.052 -10000 0 -0.29 13 13
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
Rac1/GTP -0.009 0.06 -10000 0 -0.28 18 18
E-cadherin/beta catenin/alpha catenin 0.059 0.025 -10000 0 -0.052 9 9
ITGAE 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.056 -10000 0 -0.3 13 13
Regulation of Telomerase

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
Telomerase catalytic core complex 0.02 0.086 0.24 1 -0.34 12 13
RAD9A 0.032 0.006 -10000 0 -0.07 1 1
AP1 0.02 0.043 -10000 0 -0.054 118 118
IFNAR2 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.016 -10000 0 -0.054 20 20
ER alpha/Oestrogen 0.022 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.052 -10000 0 -0.15 44 44
EGF 0.032 0.007 -10000 0 -0.069 2 2
SMG5 0.032 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.004 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.036 -10000 0 -0.057 65 65
TERT/c-Abl 0.033 0.088 0.24 1 -0.33 11 12
SAP18 0.031 0.008 -10000 0 -10000 0 0
MRN complex 0.062 0.018 -10000 0 -0.036 11 11
WT1 0.031 0.012 -10000 0 -0.071 5 5
WRN 0.031 0.01 -10000 0 -0.07 4 4
SP1 0.031 0.007 -10000 0 -0.026 4 4
SP3 0.018 0.036 -10000 0 -0.07 73 73
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.33 11 11
Mad/Max 0.046 0.011 -10000 0 -10000 0 0
TERT 0.02 0.087 0.25 1 -0.35 12 13
CCND1 0.009 0.089 -10000 0 -0.39 8 8
MAX 0.031 0.007 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.039 -10000 0 -0.07 89 89
TERF2 -0.02 0.02 0.048 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.044 0.062 -10000 0 -0.31 7 7
CDKN1B -0.026 0.012 -10000 0 -0.061 1 1
RAD1 0.032 0.008 -10000 0 -0.07 2 2
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.039 0.018 -10000 0 -10000 0 0
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 0.023 0.004 -10000 0 -10000 0 0
FOS 0.006 0.043 -10000 0 -0.07 121 121
IFN-gamma/IRF1 0.037 0.037 -10000 0 -0.054 62 62
PARP2 0.031 0.008 -10000 0 -10000 0 0
BLM 0.008 0.043 -10000 0 -0.07 119 119
Telomerase 0.007 0.063 -10000 0 -0.24 28 28
IRF1 0.02 0.035 -10000 0 -0.07 66 66
ESR1 0.03 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 -0.064 30 30
ubiquitin-dependent protein catabolic process -0.002 0.052 -10000 0 -0.16 31 31
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.002 0.052 -10000 0 -0.16 30 30
HDAC1 0.019 0.033 -10000 0 -0.07 61 61
HDAC2 0.029 0.013 -10000 0 -0.053 7 7
ATM 0.012 0.019 0.091 6 -0.059 25 31
SMAD3 -0.023 0.009 -10000 0 -0.054 26 26
ABL1 0.031 0.008 -10000 0 -0.07 1 1
MXD1 0.033 0.001 -10000 0 -10000 0 0
MRE11A 0.032 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.015 -10000 0 -10000 0 0
RPS6KB1 0.032 0.006 -10000 0 -0.07 1 1
TERT/NF kappa B1/14-3-3 0.041 0.11 -10000 0 -0.37 17 17
NR2F2 0.031 0.01 -10000 0 -0.067 4 4
MAPK3 -0.022 0.003 -10000 0 -10000 0 0
MAPK1 -0.021 0.007 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.023 -10000 0 -0.069 26 26
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
HNRNPC 0.031 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.019 0.091 6 -0.058 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.07 5 5
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.025 -10000 0 -0.054 7 7
MYC 0.008 0.043 -10000 0 -0.07 119 119
IL2 0.032 0.005 -10000 0 -0.027 1 1
KU 0.045 0.013 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.023 -10000 0 -0.07 26 26
TRF2/BLM 0.017 0.043 -10000 0 -0.057 116 116
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.097 0.26 1 -0.34 12 13
SP1/HDAC2 0.043 0.017 -10000 0 -0.053 5 5
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.098 -10000 0 -0.33 11 11
Smad3/Myc 0.006 0.037 -10000 0 -0.053 137 137
911 complex 0.043 0.033 -10000 0 -0.041 9 9
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.035 0.09 -10000 0 -0.32 11 11
Telomerase/AKT1/mTOR/p70S6K 0.011 0.091 0.17 1 -0.3 33 34
SIN3B 0.031 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.096 -10000 0 -0.34 10 10
response to DNA damage stimulus 0.003 0.013 -10000 0 -0.1 5 5
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.04 0.018 -10000 0 -0.056 4 4
Telomerase/hnRNP C1/C2 0.045 0.098 -10000 0 -0.33 11 11
E2F1 0.03 0.009 -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 0.012 -10000 0 -0.07 7 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P3 pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -9999 0 -0.07 2 2
mol:S1P 0 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.019 0.028 -9999 0 -0.081 32 32
GNAO1 0.003 0.009 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.029 0.02 -9999 0 -0.023 2 2
AKT1 -0.007 0.068 -9999 0 -0.44 12 12
AKT3 -0.007 0.045 -9999 0 -0.28 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -9999 0 -0.07 2 2
GNAI2 0.032 0.006 -9999 0 -0.029 1 1
GNAI3 0.021 0.033 -9999 0 -0.069 59 59
GNAI1 0.019 0.017 -9999 0 -0.069 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0 -9999 0 -0.01 1 1
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 0.012 -9999 0 -0.12 1 1
MAPK1 0.001 0.01 -9999 0 -10000 0 0
JAK2 -0.009 0.036 -9999 0 -0.16 15 15
CXCR4 0 0.009 -9999 0 -0.12 1 1
FLT1 0.031 0.009 -9999 0 -0.03 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 0.011 -9999 0 -0.12 1 1
S1P/S1P3/Gi 0.002 0.013 -9999 0 -0.13 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 -0.023 0.051 -9999 0 -0.069 276 276
S1P/S1P2/Gi 0.002 0.013 -9999 0 -0.11 2 2
VEGFR1 homodimer/VEGFA homodimer -0.005 0.05 -9999 0 -0.053 257 257
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 0.033 0.022 -9999 0 -10000 0 0
GNA14 0.031 0.009 -9999 0 -0.07 2 2
GNA15 0.03 0.013 -9999 0 -0.07 7 7
GNA12 0.023 0.015 -9999 0 -10000 0 0
GNA13 0.032 0.007 -9999 0 -0.07 2 2
GNA11 0.031 0.007 -9999 0 -10000 0 0
Rac1/GTP -0.027 0.036 -9999 0 -0.13 16 16
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.021 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.005 0.083 0.2 8 -0.33 28 36
CDKN1A -0.01 0.081 -10000 0 -0.33 29 29
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.021 -10000 0 -0.07 21 21
FOXO3 -0.003 0.076 0.2 4 -0.32 24 28
AKT1 0 0.085 -10000 0 -0.34 28 28
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 -0.008 0.081 -10000 0 -0.32 29 29
AKT1/ASK1 0.015 0.086 -10000 0 -0.31 31 31
BAD/YWHAZ 0.06 0.021 -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 -0.014 0.084 0.3 31 -10000 0 31
TSC1 -0.009 0.083 0.19 2 -0.33 30 32
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.017 0.09 -10000 0 -0.32 31 31
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP 0 0.084 -10000 0 -0.34 28 28
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.009 0.083 -10000 0 -0.32 31 31
YWHAQ 0.032 0.003 -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 0.012 0.052 0.19 20 -0.14 1 21
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.002 0.082 -10000 0 -0.32 29 29
CASP9 -0.007 0.084 0.2 4 -0.33 30 34
YWHAB 0.03 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.014 0.09 0.22 10 -0.32 30 40
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.056 0.028 -10000 0 -0.044 2 2
YWHAE 0.032 0.005 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.009 0.076 0.23 1 -0.29 31 32
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.028 -10000 0 -0.14 2 2
CHUK -0.005 0.063 -10000 0 -0.34 17 17
BAD/BCL-XL 0.014 0.086 -10000 0 -0.32 29 29
mTORC2 0.02 0.006 -10000 0 -0.016 9 9
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.025 0.078 -10000 0 -0.28 29 29
PDPK1 0.032 0.004 -10000 0 -10000 0 0
MDM2 0.008 0.097 0.2 42 -0.32 28 70
MAPKKK cascade -0.017 0.089 0.32 31 -10000 0 31
MDM2/Cbp/p300 0.04 0.1 0.22 44 -0.31 28 72
TSC1/TSC2 -0.009 0.089 0.23 13 -0.32 30 43
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.099 0.21 44 -0.3 28 72
glucose import -0.011 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.051 -10000 0 -0.19 30 30
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.017 0.2 3 -10000 0 3
GSK3A -0.006 0.079 0.2 4 -0.33 26 30
FOXO1 -0.006 0.073 -10000 0 -0.32 24 24
GSK3B -0.007 0.083 0.2 4 -0.32 30 34
SFN 0.025 0.025 -10000 0 -0.07 31 31
G1/S transition of mitotic cell cycle -0.009 0.09 0.22 16 -0.32 30 46
p27Kip1/14-3-3 family 0.007 0.03 -10000 0 -0.25 4 4
PRKACA 0.031 0.006 -10000 0 -10000 0 0
KPNA1 0.032 0.005 -10000 0 -10000 0 0
HSP90AA1 0.031 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
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.016 0.048 0.2 11 -0.26 4 15
FYN -0.001 0.051 0.17 6 -0.27 5 11
LAT/GRAP2/SLP76 0.021 0.048 0.19 3 -0.29 4 7
IKBKB 0.032 0.004 -10000 0 -10000 0 0
AKT1 -0.001 0.051 0.15 9 -0.23 8 17
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.01 0.024 0.096 10 -0.088 4 14
MAP3K8 0.018 0.028 -10000 0 -0.07 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.04 1 1
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.001 0.059 0.18 9 -0.28 8 17
TRPV6 0.38 0.59 1.3 158 -10000 0 158
CD28 0.033 0.001 -10000 0 -10000 0 0
SHC1 0.005 0.049 0.22 10 -0.33 3 13
receptor internalization 0.013 0.046 -10000 0 -0.32 6 6
PRF1 -0.12 0.27 -10000 0 -0.6 121 121
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.031 0.006 -10000 0 -10000 0 0
COT/AKT1 0.006 0.046 0.16 5 -0.2 8 13
LAT 0.004 0.045 0.18 5 -0.33 4 9
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.028 0.021 -10000 0 -0.071 20 20
CD3E 0.032 0.007 -10000 0 -0.049 2 2
CD3G 0.032 0.006 -10000 0 -0.075 1 1
RASGRP2 0.003 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.047 0.083 0.2 11 -0.22 23 34
HLA-A 0 0.002 -10000 0 -10000 0 0
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 -0.005 0.039 0.13 16 -0.094 10 26
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.023 -10000 0 -0.11 9 9
PRKCA -0.012 0.039 0.18 4 -0.16 4 8
GRAP2 0.03 0.008 -10000 0 -10000 0 0
mol:IP3 0.004 0.041 -10000 0 -0.2 6 6
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.009 0.031 -10000 0 -0.2 6 6
ORAI1 -0.33 0.5 -10000 0 -1.1 158 158
CSK 0.005 0.044 0.17 8 -0.32 4 12
B7 family/CD28 0.05 0.056 0.21 4 -0.23 6 10
CHUK 0.025 0.015 -10000 0 -0.07 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.009 0.043 0.12 2 -0.31 5 7
PTPN6 0 0.041 0.14 9 -0.27 5 14
VAV1 0.009 0.053 0.19 18 -0.33 4 22
Monovalent TCR/CD3 0.014 0.026 -10000 0 -0.19 6 6
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.003 0.049 0.16 11 -0.26 5 16
PAG1 0.007 0.041 0.12 3 -0.32 4 7
RAP1A 0.032 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.008 0.043 0.12 4 -0.27 6 10
CD80 0.032 0.007 -10000 0 -0.072 1 1
CD86 0.027 0.022 -10000 0 -0.07 24 24
PDK1/CARD11/BCL10/MALT1 -0.002 0.031 -10000 0 -0.13 8 8
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 0 0.04 0.14 7 -0.19 7 14
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.008 -10000 0 -0.044 5 5
PTPRC 0.007 0.044 -10000 0 -0.07 122 122
PDK1/PKC theta -0.006 0.058 0.19 13 -0.28 6 19
CSK/PAG1 0.003 0.041 0.16 3 -0.3 4 7
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.023 0.008 -10000 0 -0.019 12 12
GRAP2/SLP76 0.032 0.053 0.19 4 -0.32 4 8
STIM1 -0.067 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.009 0.045 0.13 9 -0.16 17 26
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.013 0.047 -10000 0 -0.34 6 6
mol:DAG -0.022 0.024 -10000 0 -0.18 6 6
RAP1A/GDP 0 0.021 0.062 15 -0.046 9 24
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.032 0.008 -10000 0 -0.075 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 121 121
RAP1A/GTP 0.003 0.006 -10000 0 -0.057 4 4
mol:PI-3-4-5-P3 0.001 0.054 0.17 9 -0.25 8 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.01 0.05 -10000 0 -0.28 4 4
NRAS 0.007 0.044 -10000 0 -0.07 125 125
ZAP70 0.032 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.004 0.05 0.18 10 -0.28 4 14
MALT1 0.027 0.021 -10000 0 -0.07 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.023 14 14
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.017 0.018 -10000 0 -0.14 6 6
PRKCE -0.012 0.04 0.17 5 -0.16 4 9
PRKCQ -0.003 0.06 0.2 11 -0.27 8 19
LCP2 0.026 0.024 -10000 0 -0.07 29 29
BCL10 0.031 0.01 -10000 0 -0.07 4 4
regulation of survival gene product expression -0.001 0.047 0.14 9 -0.21 7 16
IKK complex -0.007 0.029 0.15 5 -0.082 4 9
RAS family/GDP -0.007 0.01 -10000 0 -0.029 12 12
MAP3K14 -0.004 0.036 0.12 7 -0.15 9 16
PDPK1 -0.003 0.048 0.15 10 -0.21 8 18
TCR/CD3/MHC I/CD8/Fyn 0.011 0.05 -10000 0 -0.36 5 5
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.025 0.03 -10000 0 -0.13 23 23
epithelial cell differentiation 0.06 0.032 -10000 0 -0.049 18 18
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
ENAH -0.045 0.052 0.41 4 -10000 0 4
EGFR 0.012 0.018 -10000 0 -0.07 5 5
EPHA2 0.029 0.016 -10000 0 -0.07 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 -0.013 0.044 0.16 8 -0.32 7 15
CTNND1 0.03 0.015 -10000 0 -0.07 10 10
mol:PI-4-5-P2 -0.03 0.025 0.16 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.028 0.03 0.16 11 -10000 0 11
EGF 0.032 0.007 -10000 0 -0.07 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.077 0.16 5 -0.32 31 36
cortical microtubule organization 0.06 0.032 -10000 0 -0.049 18 18
GO:0000145 -0.028 0.023 0.15 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.066 0.034 -10000 0 -10000 0 0
MLLT4 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP -0.054 0.016 -10000 0 -0.11 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.043 -10000 0 -0.078 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.025 0.15 3 -0.19 1 4
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.025 0.027 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.051 -10000 0 -0.079 7 7
CDH1 0.03 0.013 -10000 0 -0.07 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 0.027 0.14 8 -10000 0 8
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 0.031 0.01 -10000 0 -0.07 4 4
DIAPH1 -0.21 0.26 -10000 0 -0.45 262 262
Wnt receptor signaling pathway -0.06 0.032 0.049 18 -10000 0 18
RHOA 0.032 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.017 -10000 0 -0.11 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.027 0.14 8 -10000 0 8
EFNA1 0.028 0.021 -10000 0 -0.07 21 21
LPP -0.035 0.025 0.15 6 -10000 0 6
Ephrin A1/EPHA2 0.046 0.042 -10000 0 -0.076 8 8
SEC6/SEC8 -0.043 0.011 -10000 0 -10000 0 0
MGAT3 -0.029 0.03 0.16 11 -10000 0 11
HGF/MET 0.034 0.038 -10000 0 -0.077 1 1
HGF 0.022 0.016 -10000 0 -0.07 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.025 0.031 -10000 0 -0.13 23 23
actin cable formation -0.039 0.075 0.32 11 -0.21 11 22
KIAA1543 -0.024 0.024 0.15 9 -10000 0 9
KIFC3 -0.031 0.026 0.16 8 -10000 0 8
NCK1 0.029 0.016 -10000 0 -0.07 11 11
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ACTN1 -0.031 0.029 0.16 9 -10000 0 9
NCK1/GIT1 0.044 0.017 -10000 0 -0.054 11 11
mol:GDP 0.06 0.032 -10000 0 -0.049 18 18
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.031 0.028 0.16 10 -10000 0 10
PIP5K1C -0.03 0.025 0.16 7 -10000 0 7
LIMA1 -0.054 0.036 -10000 0 -0.07 425 425
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.042 0.066 0.41 7 -10000 0 7
adherens junction assembly -0.022 0.043 0.21 5 -0.2 9 14
IGF-1R heterotetramer/IGF1 0.052 0.035 -10000 0 -0.077 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 0.021 0.016 -10000 0 -0.07 2 2
PLEKHA7 -0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0.064 0.042 -10000 0 -0.059 33 33
establishment of epithelial cell apical/basal polarity -0.04 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.025 0.03 -10000 0 -0.13 23 23
regulation of cell-cell adhesion -0.024 0.027 0.14 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.025 0.031 -10000 0 -0.13 23 23
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.019 0.032 0.15 8 -10000 0 8
DAPP1 0.004 0.062 0.15 25 -0.24 10 35
Src family/SYK family/BLNK-LAT/BTK-ITK -0.003 0.072 0.32 1 -0.28 13 14
mol:DAG -0.002 0.057 0.22 13 -0.14 3 16
HRAS 0.035 0.01 0.078 2 -10000 0 2
RAP1A 0.036 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.018 0.053 0.15 2 -0.21 16 18
PLCG2 0.03 0.015 -10000 0 -0.07 10 10
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARF5 0.022 0.015 -10000 0 -10000 0 0
mol:GTP -0.02 0.041 0.18 13 -10000 0 13
ARF1/GTP -0.013 0.032 0.15 11 -0.11 1 12
RHOA 0.032 0.006 -10000 0 -10000 0 0
YES1 0.017 0.036 -10000 0 -0.07 74 74
RAP1A/GTP -0.021 0.032 0.15 10 -10000 0 10
ADAP1 -0.02 0.036 0.16 12 -10000 0 12
ARAP3 -0.02 0.041 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 0.013 -10000 0 -0.07 7 7
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
NRAS 0.011 0.044 -10000 0 -0.065 124 124
FYN 0.029 0.011 -10000 0 -0.07 1 1
ARF6 0.031 0.007 -10000 0 -10000 0 0
FGR 0.029 0.018 -10000 0 -0.07 15 15
mol:Ca2+ 0 0.043 0.13 34 -10000 0 34
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 -0.004 0.049 0.15 30 -10000 0 30
LYN 0.02 0.033 -10000 0 -0.07 60 60
ARF1/GDP 0.03 0.065 0.2 2 -0.21 23 25
RhoA/GDP 0.04 0.066 0.17 28 -0.12 4 32
PDK1/Src/Hsp90 0.056 0.028 -10000 0 -0.044 2 2
BLNK 0.013 0.033 -10000 0 -0.07 60 60
actin cytoskeleton reorganization 0.031 0.08 0.17 75 -0.18 4 79
SRC 0.03 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 0.022 0.02 -10000 0 -0.057 5 5
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.043 0.18 13 -10000 0 13
RhoA/GTP -0.022 0.044 0.18 13 -10000 0 13
Src family/SYK family/BLNK-LAT -0.02 0.069 -10000 0 -0.2 38 38
BLK 0.032 0.005 -10000 0 -10000 0 0
PDPK1 0.032 0.004 -10000 0 -10000 0 0
CYTH1 -0.02 0.036 0.16 12 -10000 0 12
HCK 0.013 0.038 -10000 0 -0.07 84 84
CYTH3 -0.02 0.036 0.16 12 -10000 0 12
CYTH2 -0.02 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 0.03 -10000 0 -0.17 11 11
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.064 0.15 10 -0.21 23 33
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.026 -10000 0 -0.07 35 35
ARF6/GDP -0.017 0.043 0.19 12 -0.13 1 13
mol:PI-3-4-5-P3 -0.022 0.032 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.021 0.032 0.15 10 -10000 0 10
VAV1 0.031 0.007 -10000 0 -0.07 1 1
mol:PI-3-4-P2 -0.011 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.054 0.084 0.2 105 -0.079 1 106
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.056 0.2 2 -0.21 18 20
LAT 0.032 0.005 -10000 0 -0.07 1 1
Rac1/GTP 0.023 0.06 0.16 1 -0.24 16 17
ITK -0.024 0.039 0.16 11 -10000 0 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.007 0.063 0.24 9 -0.18 4 13
LCK 0.031 0.01 -10000 0 -0.07 4 4
BTK -0.024 0.041 0.17 13 -10000 0 13
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.015 0.029 -10000 0 -0.064 6 6
EPHB2 0.031 0.008 -10000 0 -0.07 1 1
Syndecan-2/TACI 0.027 0.012 -10000 0 -0.056 5 5
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.054 -10000 0 -0.077 4 4
HRAS 0.031 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.005 -10000 0 -0.069 1 1
ITGA5 0.018 0.035 -10000 0 -0.07 68 68
BAX -0.013 0.012 -10000 0 -0.14 3 3
EPB41 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.025 0.01 -10000 0 -0.05 5 5
LAMA3 0.029 0.018 -10000 0 -0.07 15 15
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.03 -10000 0 -0.07 48 48
Syndecan-2/MMP2 -0.005 0.035 -10000 0 -0.073 7 7
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.036 -10000 0 -0.054 65 65
dendrite morphogenesis 0.026 0.013 -10000 0 -0.056 5 5
Syndecan-2/GM-CSF 0.027 0.012 -10000 0 -0.056 5 5
determination of left/right symmetry -0.009 0.007 -10000 0 -0.086 1 1
Syndecan-2/PKC delta 0.027 0.012 -10000 0 -0.056 5 5
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.018 0.028 0.18 9 -10000 0 9
MAPK1 -0.017 0.028 0.18 9 -10000 0 9
Syndecan-2/RACK1 0.041 0.02 -10000 0 -0.071 1 1
NF1 0.032 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.007 -10000 0 -0.086 1 1
ITGA2 0.014 0.039 -10000 0 -0.07 90 90
MAPK8 -0.011 0.009 -10000 0 -0.11 1 1
Syndecan-2/alpha2/beta1 Integrin 0.016 0.04 -10000 0 -0.06 4 4
Syndecan-2/Kininogen 0.027 0.012 -10000 0 -0.058 4 4
ITGB1 0.025 0.013 -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 5 5
extracellular matrix organization 0.023 0.019 -10000 0 -0.058 6 6
actin cytoskeleton reorganization 0.015 0.029 -10000 0 -0.064 6 6
Syndecan-2/Caveolin-2/Ras 0.023 0.032 -10000 0 -0.065 3 3
Syndecan-2/Laminin alpha3 0.025 0.016 -10000 0 -0.061 5 5
Syndecan-2/RasGAP 0.054 0.027 -10000 0 -0.074 1 1
alpha5/beta1 Integrin 0.024 0.035 -10000 0 -0.054 61 61
PRKCD 0.032 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.026 0.013 -10000 0 -0.056 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 0.036 -10000 0 -0.054 65 65
Syndecan-2/Synbindin 0.027 0.012 -10000 0 -0.056 5 5
TGFB1 0.026 0.023 -10000 0 -0.07 26 26
CASP3 -0.021 0.029 0.19 8 -10000 0 8
FN1 0.013 0.04 -10000 0 -0.07 96 96
Syndecan-2/IL8 0.012 0.03 -10000 0 -0.058 6 6
SDC2 -0.009 0.007 -10000 0 -0.086 1 1
KNG1 0.032 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.027 0.011 -10000 0 -0.056 5 5
TRAPPC4 0.032 0.004 -10000 0 -10000 0 0
CSF2 0.032 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.019 -10000 0 -0.058 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.025 0.01 -10000 0 -0.05 5 5
Syndecan-2/Ezrin 0.024 0.011 -10000 0 -0.054 3 3
PRKACA -0.016 0.029 0.18 10 -10000 0 10
angiogenesis 0.012 0.03 -10000 0 -0.058 6 6
MMP2 -0.017 0.051 -10000 0 -0.07 241 241
IL8 0.01 0.042 -10000 0 -0.07 110 110
calcineurin-NFAT signaling pathway 0.027 0.012 -10000 0 -0.056 5 5
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.033 -10000 0 -0.07 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 -0.001 0.054 -10000 0 -0.18 29 29
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.07 1 1
AKT1 0.007 0.052 0.14 5 -0.19 14 19
RAR alpha/9cRA/Cyclin H 0.008 0.086 0.18 2 -0.22 15 17
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.002 0.048 0.097 3 -0.14 40 43
CDC2 0 0 -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 -10000 0 0
VDR/VDR/Vit D3 0.023 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.002 0.07 0.25 2 -0.31 12 14
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA3 0.029 0.011 -10000 0 -0.07 2 2
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 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.033 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -0.028 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.071 -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 0.049 0.091 7 -0.15 38 45
PRKCA 0.033 0.007 -10000 0 -0.034 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.067 -10000 0 -0.31 11 11
RXRG 0.019 0.008 -10000 0 -0.038 2 2
RXRA -0.013 0.045 0.1 9 -0.099 6 15
RXRB 0.019 0.006 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.004 -10000 0 -10000 0 0
RBP1 -0.014 0.05 -10000 0 -0.07 222 222
CRBP1/9-cic-RA -0.006 0.033 -10000 0 -0.043 222 222
RARB 0.032 0.006 -10000 0 -0.026 3 3
PRKCG 0.031 0.009 -10000 0 -0.034 3 3
MNAT1 0.031 0.009 -10000 0 -0.07 1 1
RAR alpha/RXRs 0.006 0.079 0.2 1 -0.33 16 17
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.003 0.065 0.2 1 -0.27 15 16
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.062 0.16 2 -0.18 32 34
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.066 -10000 0 -0.31 9 9
positive regulation of DNA binding 0.002 0.079 0.15 2 -0.2 17 19
NRIP1 0.008 0.066 0.27 1 -0.35 4 5
RXRs/RARs 0.008 0.066 -10000 0 -0.29 14 14
RXRs/RXRs/DNA/9cRA -0.004 0.064 -10000 0 -0.28 18 18
PRKACA 0.031 0.006 -10000 0 -10000 0 0
CDK7 0.032 0.008 -10000 0 -0.07 2 2
TFIIH 0.058 0.027 -10000 0 -0.048 8 8
RAR alpha/9cRA 0.025 0.08 -10000 0 -0.14 26 26
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.055 0.032 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.032 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.029 0.07 -10000 0 -0.27 16 16
Syndecan-3/Neurocan 0.01 0.071 -10000 0 -0.3 22 22
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.07 5 5
Syndecan-3/EGFR 0 0.064 -10000 0 -0.33 14 14
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.026 0.024 -10000 0 -0.07 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 0.013 -10000 0 -0.07 7 7
NCAN 0.026 0.014 -10000 0 -0.07 2 2
long-term memory 0.028 0.079 -10000 0 -0.3 23 23
Syndecan-3/IL8 0.002 0.085 -10000 0 -0.36 23 23
PSEN1 0.031 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.044 0.014 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.07 1 1
limb bud formation -0.007 0.076 -10000 0 -0.37 21 21
MC4R 0.031 0.008 -10000 0 -0.07 1 1
SRC 0.03 0.008 -10000 0 -10000 0 0
PTN 0.021 0.016 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.007 0.077 -10000 0 -0.37 21 21
neuron projection morphogenesis 0.015 0.087 0.16 94 -0.29 6 100
Syndecan-3/AgRP 0.014 0.084 -10000 0 -0.35 23 23
Syndecan-3/AgRP/MC4R 0.029 0.087 -10000 0 -0.35 23 23
Fyn/Cortactin 0.043 0.016 -10000 0 -0.054 1 1
SDC3 -0.008 0.078 -10000 0 -0.37 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.002 0.083 -10000 0 -0.35 23 23
IL8 0.01 0.042 -10000 0 -0.07 110 110
Syndecan-3/Fyn/Cortactin 0.029 0.08 -10000 0 -0.31 23 23
Syndecan-3/CASK -0.009 0.075 -10000 0 -0.35 22 22
alpha-MSH/MC4R 0.046 0.011 -10000 0 -0.054 1 1
Gamma Secretase 0.073 0.052 -10000 0 -0.081 2 2
EPHB forward signaling

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
Ephrin A5/EPHB2 0.042 0.011 -10000 0 -0.043 1 1
cell-cell adhesion 0.028 0.025 -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 0.019 -10000 0 -0.07 17 17
SHC1 0.024 0.028 -10000 0 -0.07 40 40
Ephrin B1/EPHB3 0.041 0.014 -10000 0 -0.043 7 7
Ephrin B1/EPHB1 0.041 0.014 -10000 0 -0.043 9 9
HRAS/GDP 0.021 0.05 -10000 0 -0.15 22 22
Ephrin B/EPHB1/GRB7 0.078 0.045 -10000 0 -0.078 1 1
Endophilin/SYNJ1 -0.022 0.04 0.18 15 -10000 0 15
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.073 0.048 -10000 0 -0.078 1 1
endothelial cell migration 0.037 0.038 -10000 0 -0.05 11 11
GRB2 0.031 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.006 -10000 0 -0.07 1 1
PAK1 -0.028 0.05 0.2 16 -10000 0 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.046 0.19 17 -10000 0 17
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.04 0.17 15 -10000 0 15
lamellipodium assembly -0.028 0.025 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.035 -10000 0 -0.2 5 5
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.008 -10000 0 -0.07 1 1
EPHB3 0.03 0.013 -10000 0 -0.07 7 7
EPHB1 0.03 0.014 -10000 0 -0.07 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.043 0.14 17 -0.16 17 34
Ephrin B/EPHB2 0.063 0.035 -10000 0 -10000 0 0
Ephrin B/EPHB3 0.062 0.036 -10000 0 -0.057 2 2
JNK cascade -0.027 0.056 0.25 18 -10000 0 18
Ephrin B/EPHB1 0.062 0.036 -10000 0 -0.052 9 9
RAP1/GDP 0.032 0.1 0.19 133 -0.17 13 146
EFNB2 0.029 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 0.031 -10000 0 -0.045 13 13
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.058 0.047 0.14 1 -0.12 9 10
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.043 1 1
MAPK3 -0.006 0.036 0.17 3 -0.2 4 7
MAPK1 -0.007 0.033 0.16 2 -0.2 4 6
Rac1/GDP -0.006 0.064 0.2 29 -0.18 13 42
actin cytoskeleton reorganization -0.035 0.033 0.034 1 -0.13 18 19
CDC42/GDP 0.038 0.11 0.2 135 -0.18 13 148
PI3K 0.04 0.042 -10000 0 -0.05 11 11
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 0.03 -10000 0 -0.12 18 18
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.051 0.023 -10000 0 -0.1 1 1
PTK2 -0.006 0.086 0.55 12 -10000 0 12
MAP4K4 -0.027 0.056 0.25 18 -10000 0 18
SRC 0.03 0.008 -10000 0 -10000 0 0
KALRN 0.032 0.006 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.023 -10000 0 -10000 0 0
neuron projection morphogenesis 0.062 0.17 0.32 134 -0.17 2 136
MAP2K1 0.004 0.036 -10000 0 -0.2 4 4
WASL 0.022 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.071 0.037 -10000 0 -10000 0 0
cell migration 0 0.055 0.17 8 -0.22 7 15
NRAS 0.007 0.044 -10000 0 -0.07 125 125
SYNJ1 -0.023 0.04 0.18 15 -10000 0 15
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.034 0.17 8 -10000 0 8
HRAS/GTP 0.045 0.041 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.056 0.024 -10000 0 -0.046 10 10
cell adhesion mediated by integrin 0.013 0.04 -10000 0 -0.2 10 10
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0.051 0.039 0.14 5 -0.072 1 6
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 0.063 0.21 26 -0.17 15 41
ruffle organization 0.07 0.16 0.32 136 -10000 0 136
NCK1 0.029 0.016 -10000 0 -0.07 11 11
receptor internalization -0.005 0.024 0.21 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.077 0.045 -10000 0 -10000 0 0
ROCK1 -0.015 0.039 0.18 20 -10000 0 20
RAS family/GDP -0.035 0.034 -10000 0 -0.14 22 22
Rac1/GTP -0.029 0.027 0.046 5 -10000 0 5
Ephrin B/EPHB1/Src/Paxillin 0.015 0.036 -10000 0 -0.12 29 29
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.072 0.23 28 -0.31 5 33
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -0.056 34 34
PDGFB-D/PDGFRB/APS/CBL 0.043 0.009 -10000 0 -0.043 2 2
AKT1 -0.019 0.079 0.3 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.034 0.076 0.24 33 -0.34 5 38
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
FGR 0.009 0.063 0.2 13 -0.37 7 20
mol:Ca2+ 0.024 0.072 0.22 28 -0.38 5 33
MYC 0.044 0.12 0.31 40 -0.34 3 43
SHC1 0.024 0.028 -10000 0 -0.07 40 40
HRAS/GDP -0.017 0.054 0.17 37 -10000 0 37
LRP1/PDGFRB/PDGFB 0.054 0.031 -10000 0 -0.045 32 32
GRB10 0.021 0.017 -10000 0 -0.07 4 4
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.22 28 -0.38 5 33
PTEN 0.022 0.016 -10000 0 -0.07 2 2
GRB2 0.031 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.006 -10000 0 -0.07 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.01 -10000 0 -0.054 2 2
PDGFB-D/PDGFRB/GRB10 0.031 0.025 -10000 0 -0.054 6 6
cell cycle arrest 0.04 0.027 -10000 0 -0.056 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.024 0.072 0.28 13 -10000 0 13
GAB1 0.019 0.078 0.24 23 -0.31 9 32
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.085 0.24 39 -0.26 9 48
PDGFB-D/PDGFRB 0.055 0.027 -10000 0 -0.055 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.011 -10000 0 -0.054 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.055 0.2 11 -0.25 5 16
positive regulation of MAPKKK cascade 0.047 0.01 -10000 0 -0.054 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.073 0.22 28 -0.38 5 33
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.03 0.01 -10000 0 -0.032 11 11
PDGFB-D/PDGFRB/GRB7 0.047 0.011 -10000 0 -0.054 3 3
SHB 0.03 0.009 -10000 0 -10000 0 0
BLK 0.009 0.059 0.34 1 -0.37 7 8
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -0.054 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.015 0.085 0.25 26 -0.32 9 35
CBL 0.032 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.046 0.011 -10000 0 -0.054 2 2
LCK 0.012 0.057 0.29 2 -0.35 5 7
PDGFRB 0.032 0.009 -10000 0 -0.049 4 4
ACP1 0.032 0.005 -10000 0 -10000 0 0
HCK -0.002 0.036 -10000 0 -10000 0 0
ABL1 0.02 0.074 0.21 33 -0.25 9 42
PDGFB-D/PDGFRB/CBL 0.023 0.08 0.26 14 -0.35 9 23
PTPN1 0.03 0.009 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.015 -10000 0 -0.07 10 10
STAT1 0.029 0.019 -10000 0 -0.07 18 18
cell proliferation 0.044 0.12 0.3 41 -0.32 3 44
SLA 0.025 0.026 -10000 0 -0.07 33 33
actin cytoskeleton reorganization -0.017 0.067 0.2 40 -10000 0 40
SRC 0.009 0.043 -10000 0 -0.73 1 1
PI3K -0.043 0.022 -10000 0 -0.096 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.053 0.035 -10000 0 -0.052 46 46
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.077 0.25 30 -0.35 5 35
LYN 0.003 0.043 -10000 0 -0.35 1 1
LRP1 0.028 0.017 -10000 0 -0.07 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.004 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.07 1 1
NCK1-2/p130 Cas 0.066 0.038 -10000 0 -10000 0 0
SPHK1 0.029 0.02 -10000 0 -0.07 18 18
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.024 0.073 0.22 28 -0.38 5 33
PLCG1 0.024 0.073 0.22 28 -0.39 5 33
NHERF/PDGFRB 0.063 0.018 -10000 0 -0.045 9 9
YES1 -0.005 0.089 0.19 9 -0.54 10 19
cell migration 0.062 0.018 -10000 0 -0.045 9 9
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.078 2 2
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.07 2 2
NHERF1-2/PDGFRB/PTEN 0.042 0.058 -10000 0 -0.064 1 1
FYN -0.02 0.11 -10000 0 -0.36 44 44
DOK1 -0.016 0.053 0.17 39 -10000 0 39
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.056 0.13 0.25 93 -0.4 4 97
PRKCD -0.015 0.054 0.17 38 -10000 0 38
FER -0.016 0.054 0.17 37 -10000 0 37
MAPKKK cascade -0.011 0.073 0.18 57 -10000 0 57
RASA1 -0.015 0.054 0.17 37 -10000 0 37
NCK1 0.029 0.016 -10000 0 -0.07 11 11
NCK2 0.032 0.003 -10000 0 -10000 0 0
p62DOK/Csk -0.02 0.053 0.16 38 -10000 0 38
PDGFB-D/PDGFRB/SHB 0.044 0.015 -10000 0 -0.054 2 2
chemotaxis 0.02 0.073 0.21 33 -0.25 9 42
STAT1-3-5/STAT1-3-5 0.063 0.044 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.023 0.006 0.052 2 -0.035 3 5
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.03 0.012 -10000 0 -0.07 4 4
mol:Halofuginone 0.002 0.004 -10000 0 -0.041 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.004 0.052 -10000 0 -0.34 10 10
PRL-3/alpha Tubulin 0.04 0.025 -10000 0 -0.054 28 28
mol:Ca2+ -0.022 0.022 0.058 27 -10000 0 27
AGT 0.029 0.01 -10000 0 -10000 0 0
CCNA2 -0.027 0.014 -10000 0 -0.078 5 5
TUBA1B 0.032 0.005 -10000 0 -10000 0 0
EGR1 0.008 0.009 -10000 0 -0.042 16 16
CDK2/Cyclin E1 0.035 0.064 -10000 0 -0.32 9 9
MAPK3 -0.024 0.009 0 18 -0.054 30 48
PRL-2 /Rab GGTase beta 0.047 0.009 -10000 0 -10000 0 0
MAPK1 -0.022 0.011 -10000 0 -0.054 30 30
PTP4A1 -0.017 0.008 -10000 0 -0.11 1 1
PTP4A3 0.025 0.025 -10000 0 -0.07 30 30
PTP4A2 0.032 0.005 -10000 0 -10000 0 0
ITGB1 -0.019 0.012 0 123 -0.054 23 146
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.006 0.034 -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 -0.013 0.045 0.18 24 -10000 0 24
RABGGTA 0.031 0.007 -10000 0 -10000 0 0
BCAR1 -0.015 0.018 0.054 30 -10000 0 30
RHOC -0.009 0.048 -10000 0 -0.34 6 6
RHOA 0.006 0.05 -10000 0 -0.32 10 10
cell motility 0.011 0.053 -10000 0 -0.29 5 5
PRL-1/alpha Tubulin -0.011 0.051 0.18 32 -10000 0 32
PRL-3/alpha1 Integrin 0.019 0.016 -10000 0 -0.043 30 30
ROCK1 0.012 0.051 -10000 0 -0.28 5 5
RABGGTB 0.032 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.022 -10000 0 -0.07 24 24
mitosis -0.017 0.008 -10000 0 -0.11 1 1
ATF5 0.03 0.009 -10000 0 -0.07 1 1
p75(NTR)-mediated signaling

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.009 -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 0.067 0.032 -10000 0 -0.057 1 1
NGF (dimer)/p75(NTR)/BEX1 0.028 0.024 -10000 0 -0.043 16 16
NT-4/5 (dimer)/p75(NTR) 0.021 0.014 -10000 0 -0.043 21 21
IKBKB 0.032 0.004 -10000 0 -10000 0 0
AKT1 -0.014 0.047 0.18 23 -10000 0 23
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 0.019 0.011 -10000 0 -0.034 21 21
FURIN 0.032 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.052 8 8
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.05 0.016 -10000 0 -0.094 1 1
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.032 0.005 -10000 0 -10000 0 0
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.08 0.22 7 -0.31 18 25
IRAK1 0.032 0.003 -10000 0 -10000 0 0
SHC1 -0.02 0.009 -10000 0 -0.044 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 0.073 0.052 -10000 0 -0.081 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.028 -10000 0 -0.046 18 18
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.034 0.034 -10000 0 -0.046 14 14
Mammalian IAPs/DIABLO 0.054 0.029 -10000 0 -0.045 36 36
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 0.029 0.012 -10000 0 -0.07 4 4
RhoA/GDP/RHOGDI 0.037 0.019 -10000 0 -0.042 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.018 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.026 -10000 0 -0.1 12 12
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.019 -10000 0 -0.043 21 21
NCSTN 0.026 0.024 -10000 0 -0.07 28 28
mol:GTP 0.035 0.021 -10000 0 -0.043 20 20
PSENEN 0.031 0.007 -10000 0 -10000 0 0
mol:ceramide -0.021 0.023 0.18 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.022 -10000 0 -0.097 18 18
p75(NTR)/beta APP 0.043 0.021 -10000 0 -0.054 20 20
BEX1 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.005 -10000 0 -0.034 21 21
NGF (dimer) 0.038 0.044 -10000 0 -0.046 75 75
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.017 -10000 0 -0.037 22 22
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.021 -10000 0 -0.033 21 21
MYD88 0.019 0.034 -10000 0 -0.07 66 66
CHUK 0.025 0.015 -10000 0 -0.07 1 1
NGF (dimer)/p75(NTR)/PKA 0.035 0.021 -10000 0 -0.044 20 20
RHOB 0.03 0.011 -10000 0 -0.07 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 0.006 -10000 0 -10000 0 0
TP53 0.032 0.064 0.23 25 -10000 0 25
PRDM4 -0.022 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.013 0.039 -10000 0 -0.072 4 4
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
SORT1 0.032 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.061 0.03 -10000 0 -0.056 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.055 0.027 -10000 0 -0.046 20 20
RHOC 0.001 0.047 -10000 0 -0.07 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.038 0.074 0.19 80 -10000 0 80
DIABLO 0.032 0.004 -10000 0 -10000 0 0
SMPD2 -0.021 0.023 0.18 6 -10000 0 6
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.013 -10000 0 -0.07 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.018 -10000 0 -0.043 20 20
PSEN1 0.031 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.054 3 3
NT3 (dimer)/p75(NTR) 0.042 0.022 -10000 0 -0.054 20 20
MAPK8 0.035 0.066 0.18 73 -0.14 1 74
MAPK9 0.064 0.086 0.19 138 -10000 0 138
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.031 0.006 -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 0.022 0.057 -10000 0 -0.071 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.036 -10000 0 -0.054 8 8
RhoA-B-C/GTP 0.034 0.021 -10000 0 -0.043 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.022 0.043 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.038 -10000 0 -0.054 8 8
PRKACB 0.029 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.022 -10000 0 -0.054 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.024 -10000 0 -0.07 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.024 -10000 0 -0.12 2 2
BAD 0.047 0.08 0.19 85 -0.16 2 87
RIPK2 0.032 0.006 -10000 0 -0.07 1 1
NGFR 0.028 0.021 -10000 0 -0.07 21 21
CYCS -0.018 0.023 0.17 4 -10000 0 4
ADAM17 0.031 0.011 -10000 0 -0.07 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.055 0.026 -10000 0 -0.041 30 30
BCL2L11 0.047 0.08 0.19 85 -0.16 2 87
BDNF (dimer)/p75(NTR) 0.012 0.023 -10000 0 -0.054 9 9
PI3K 0.047 0.033 -10000 0 -0.047 32 32
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.017 -10000 0 -0.035 25 25
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKCI 0.032 0.007 -10000 0 -0.07 1 1
NGF (dimer)/p75(NTR) 0.021 0.014 -10000 0 -0.043 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 -0.046 20 20
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 0.009 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.006 0.013 0.14 1 -0.075 1 2
SQSTM1 0.032 0.007 -10000 0 -0.07 1 1
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.045 0.078 0.19 82 -0.18 3 85
E2F1 0.03 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -0.07 3 3
IKK complex 0.037 0.047 -10000 0 -0.13 3 3
NGF (dimer)/TRKA 0.024 0.004 -10000 0 -10000 0 0
MMP7 0.017 0.036 -10000 0 -0.07 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.062 0.039 -10000 0 -0.05 23 23
MMP3 0.031 0.013 -10000 0 -0.07 7 7
APAF-1/Caspase 9 -0.036 0.027 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.011 0.048 0.2 12 -0.2 6 18
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.002 0.091 0.22 1 -0.32 22 23
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 -0.8 120 120
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.077 0.24 1 -0.27 8 9
FRAP1 -0.007 0.079 0.25 1 -0.29 10 11
FOXO3 -0.013 0.08 0.23 3 -0.28 14 17
AKT1 -0.01 0.082 0.26 1 -0.29 15 16
GAB2 0.031 0.006 -10000 0 -10000 0 0
SMPD1 -0.001 0.11 -10000 0 -0.6 15 15
SGMS1 -0.12 0.26 -10000 0 -0.6 120 120
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 0.008 -10000 0 -0.043 16 16
CALM1 0.029 0.01 -10000 0 -10000 0 0
cell proliferation -0.062 0.16 -10000 0 -0.35 107 107
EIF3A 0.024 0.014 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.054 16 16
RPS6KB1 0.022 0.015 -10000 0 -10000 0 0
mol:sphingomyelin -0.18 0.35 -10000 0 -0.8 120 120
natural killer cell activation 0 0.001 -10000 0 -0.005 1 1
JAK3 0.032 0.007 -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 0.01 -10000 0 -0.07 4 4
MYC -0.016 0.087 0.24 1 -0.31 9 10
MYB 0.016 0.026 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.008 0.071 0.14 3 -0.22 21 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.044 0.034 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.07 0.14 3 -0.22 21 24
Rac1/GDP 0.005 0.02 -10000 0 -0.049 2 2
T cell proliferation -0.009 0.066 -10000 0 -0.2 21 21
SHC1 0.023 0.028 -10000 0 -0.071 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 -0.009 0.067 0.13 3 -0.21 21 24
NF kappa B1 p50/RelA 0.008 0.092 0.26 1 -0.27 10 11
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.044 -10000 0 -0.21 9 9
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL2RA 0.024 0.017 -10000 0 -0.07 6 6
IL2RB 0.03 0.012 -10000 0 -0.071 4 4
TERT 0.031 0.006 -10000 0 -10000 0 0
E2F1 0.024 0.023 -10000 0 -0.38 1 1
SOS1 0 0.001 -10000 0 -10000 0 0
RPS6 0.029 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -10000 0 -10000 0 0
IL2RG 0.031 0.014 -10000 0 -0.071 9 9
actin cytoskeleton organization -0.009 0.066 -10000 0 -0.2 21 21
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
Rac1/GTP 0.031 0.032 -10000 0 -10000 0 0
LCK 0.031 0.01 -10000 0 -0.07 4 4
BCL2 -0.005 0.074 0.25 7 -0.27 3 10
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.019 0.033 -9999 0 -0.07 61 61
Ran/GTP/Exportin 1/HDAC4 -0.028 0.011 -9999 0 -0.064 36 36
MDM2/SUMO1 0.034 0.039 -9999 0 -0.1 33 33
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.029 0.013 -9999 0 -0.068 35 35
SUMO1 0.033 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.009 -9999 0 -0.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.026 -9999 0 -0.099 37 37
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 -0.099 37 37
SUMO1/HDAC1 0.03 0.044 -9999 0 -0.1 36 36
RANGAP1 0.03 0.008 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.07 0.034 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.029 -9999 0 -0.098 37 37
Ran/GTP 0.022 0.033 -9999 0 -0.095 36 36
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.011 -9999 0 -0.07 1 1
UBE2I 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 -9999 0 -0.098 36 36
NPC 0.019 0.002 -9999 0 -10000 0 0
PIAS2 0.031 0.006 -9999 0 -10000 0 0
PIAS1 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.032 0.005 -10000 0 -0.036 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.07 0.18 5 -0.25 16 21
ERC1 0.031 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.045 0.016 -10000 0 -0.054 9 9
NFKBIA -0.028 0.02 0.2 3 -10000 0 3
BIRC2 0.032 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.004 -10000 0 -10000 0 0
RIPK2 0.032 0.006 -10000 0 -0.07 1 1
IKBKG 0.017 0.051 -10000 0 -0.29 10 10
IKK complex/A20 0.034 0.069 -10000 0 -0.37 6 6
NEMO/A20/RIP2 0.032 0.006 -10000 0 -0.07 1 1
XPO1 0.033 0 -10000 0 -10000 0 0
NEMO/ATM 0.035 0.055 -10000 0 -0.38 6 6
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 -0.045 46 46
NOD2 0.03 0.013 -10000 0 -0.07 8 8
NFKB1 0.031 0.011 -10000 0 -0.064 5 5
RELA 0.032 0.005 -10000 0 -0.036 1 1
MALT1 0.027 0.021 -10000 0 -0.07 20 20
cIAP1/UbcH5C 0.047 0.009 -10000 0 -10000 0 0
ATM 0.027 0.022 -10000 0 -0.07 25 25
TNF/TNFR1A 0.013 0.047 -10000 0 -0.054 165 165
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
CHUK 0.025 0.015 -10000 0 -0.07 1 1
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.07 2 2
NF kappa B1 p50/RelA 0.065 0.025 -10000 0 -0.058 5 5
BCL10 0.031 0.01 -10000 0 -0.07 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.019 0.2 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -0.036 1 1
TNFRSF1A -0.002 0.047 -10000 0 -0.07 164 164
IKK complex 0.041 0.061 -10000 0 -0.38 6 6
CYLD 0.032 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.05 0.066 -10000 0 -0.38 6 6
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 0.019 0.033 -10000 0 -0.07 61 61
HDAC2 0.03 0.012 -10000 0 -0.07 4 4
GNB1/GNG2 0.028 0.021 -10000 0 -10000 0 0
forebrain development 0.026 0.052 0.21 10 -10000 0 10
GNAO1 0.003 0.009 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.033 0.023 -10000 0 -10000 0 0
SMO 0.022 0.015 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
GLI3/SPOP 0.011 0.069 -10000 0 -0.2 22 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.007 -10000 0 -0.027 2 2
SIN3/HDAC complex 0.053 0.027 -10000 0 -0.032 35 35
GNAI1 0.019 0.017 -10000 0 -0.069 1 1
XPO1 0.033 0.007 -10000 0 -0.028 6 6
GLI1/Su(fu) 0.006 0.023 -10000 0 -0.24 1 1
SAP30 0.032 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.015 -10000 0 -10000 0 0
MIM/GLI2A 0.034 0.009 -10000 0 -0.042 3 3
IFT88 0.031 0.007 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
GLI2 0.013 0.049 0.16 13 -0.22 9 22
GLI3 -0.004 0.062 -10000 0 -0.2 21 21
CSNK1D 0.032 0.007 -10000 0 -0.07 2 2
CSNK1E 0.031 0.008 -10000 0 -10000 0 0
SAP18 0.031 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.007 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.01 0.088 1 -0.12 2 3
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.003 0.044 0.1 1 -0.18 17 18
GLI2/Su(fu) 0.006 0.034 0.12 3 -0.19 7 10
FOXA2 0.036 0.045 -10000 0 -0.49 3 3
neural tube patterning 0.026 0.052 0.21 10 -10000 0 10
SPOP 0.032 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.034 0.093 155 -0.063 6 161
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 0.009 -10000 0 -0.042 3 3
embryonic limb morphogenesis 0.026 0.052 0.21 10 -10000 0 10
SUFU -0.002 0.002 -10000 0 -10000 0 0
LGALS3 0.018 0.033 -10000 0 -0.07 61 61
catabolic process 0.028 0.078 0.2 9 -0.27 15 24
GLI3A/CBP 0.036 0.017 -10000 0 -0.092 8 8
KIF3A 0.029 0.01 -10000 0 -10000 0 0
GLI1 0.026 0.053 0.21 10 -10000 0 10
RAB23 0.031 0.01 -10000 0 -0.07 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 0.093 128 -0.062 5 133
GNAZ 0.027 0.013 -10000 0 -10000 0 0
RBBP4 0.014 0.039 -10000 0 -0.07 89 89
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.03 0.051 0.16 13 -0.21 9 22
STK36 0.001 0.001 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0 0.012 -10000 0 -0.14 3 3
PTCH1 0.025 0.058 0.31 5 -10000 0 5
MIM/GLI1 0.043 0.056 0.22 5 -10000 0 5
CREBBP 0.036 0.017 -10000 0 -0.092 8 8
Su(fu)/SIN3/HDAC complex 0.006 0.058 0.12 4 -0.18 33 37
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) 0.012 0.082 -10000 0 -0.39 18 18
HDAC1 0.021 0.033 -10000 0 -0.065 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 0.031 0.024 -10000 0 -0.054 4 4
TLE1 0.032 0.006 -10000 0 -10000 0 0
AP1 0.001 0.023 -10000 0 -0.14 4 4
NCSTN 0.026 0.024 -10000 0 -0.07 28 28
ADAM10 0.028 0.019 -10000 0 -0.07 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.059 -10000 0 -0.52 4 4
NICD/RBPSUH 0.029 0.087 -10000 0 -0.39 18 18
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.08 -10000 0 -0.44 14 14
PSENEN 0.031 0.007 -10000 0 -10000 0 0
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.004 0.039 -10000 0 -0.07 101 101
beta catenin/beta TrCP1 0.062 0.079 0.2 70 -0.23 6 76
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.013 -10000 0 -0.07 7 7
AXIN1 0.025 0.049 0.26 5 -0.29 2 7
CtBP/CBP/TCF1/TLE1/AES 0.021 0.034 -10000 0 -0.12 14 14
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.006 0.043 -10000 0 -0.07 121 121
JUN 0.032 0.005 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -0.07 1 1
CTNNB1 0.046 0.081 0.19 86 -0.24 6 92
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.025 -10000 0 -0.052 8 8
HNF1A 0.033 0.004 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.009 0.07 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.021 0.017 -10000 0 -0.07 4 4
NOTCH1 precursor/Deltex homolog 1 0.005 0.08 -10000 0 -0.39 18 18
apoptosis 0.001 0.023 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.005 0.08 -10000 0 -0.39 18 18
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.017 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.072 0.052 -10000 0 -0.081 2 2
APC 0.007 0.091 0.26 4 -0.35 22 26
DVL1 0.017 0.021 -10000 0 -0.21 2 2
CSNK2A1 0.03 0.009 -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 -0.052 100 100
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -0.042 1 1
CCND1 -0.009 0.11 -10000 0 -0.81 7 7
WNT1 0.032 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.041 0.088 0.26 18 -0.4 5 23
DKK2 0.03 0.013 -10000 0 -0.07 8 8
NOTCH1 precursor/DVL1 0.034 0.091 0.25 1 -0.38 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 0.012 0.082 -10000 0 -0.39 18 18
PPP2R5D 0.014 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 0.003 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -0.021 2 2
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 0.05 -10000 0 -10000 0 0
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 0.055 0.2 20 -10000 0 20
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.046 0.043 0.16 2 -0.055 26 28
antigen processing and presentation of peptide antigen via MHC class I -0.039 0.035 -10000 0 -0.11 35 35
CaM/Ca2+ 0.047 0.055 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.034 0.037 0.14 18 -10000 0 18
AKT1 -0.022 0.064 0.21 18 -10000 0 18
MAP2K1 -0.032 0.044 0.15 20 -10000 0 20
MAP3K11 -0.028 0.05 0.18 21 -10000 0 21
IFNGR1 0.029 0.018 0.092 1 -0.071 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.081 0.095 -10000 0 -0.21 152 152
Rap1/GTP -0.045 0.018 -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 0.059 -10000 0 -10000 0 0
CEBPB -0.008 0.091 0.34 5 -0.32 17 22
STAT3 0.03 0.015 -10000 0 -0.07 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.058 0.087 -10000 0 -0.74 4 4
STAT1 -0.03 0.051 0.18 22 -10000 0 22
CALM1 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.03 0.011 -10000 0 -0.028 8 8
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
STAT1 (dimer)/PIAS1 -0.034 0.054 0.18 23 -10000 0 23
CEBPB/PTGES2/Cbp/p300 0.007 0.071 -10000 0 -0.23 24 24
mol:Ca2+ 0.047 0.049 -10000 0 -10000 0 0
MAPK3 -0.001 0.06 0.51 1 -0.57 2 3
STAT1 (dimer) -0.048 0.046 0.08 3 -0.15 26 29
MAPK1 -0.047 0.18 0.51 1 -0.67 37 38
JAK2 0.029 0.012 0.092 1 -0.028 3 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.01 0.07 2 -0.029 8 10
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.003 0.068 0.27 7 -0.21 17 24
SMAD7 -0.016 0.038 0.13 16 -0.086 3 19
CBL/CRKL/C3G -0.035 0.056 0.19 23 -10000 0 23
PI3K 0.041 0.056 -10000 0 -10000 0 0
IFNG 0.03 0.011 -10000 0 -0.029 8 8
apoptosis 0.002 0.063 0.28 5 -0.38 3 8
CAMK2G 0.012 0.016 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.015 -10000 0 -0.07 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 0.059 0.18 23 -10000 0 23
PRKCD -0.024 0.067 0.27 11 -10000 0 11
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.039 0.035 -10000 0 -0.11 35 35
PTPN2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
IRF1 -0.044 0.043 0.23 5 -10000 0 5
STAT1 (dimer)/PIASy -0.034 0.051 0.18 16 -10000 0 16
SOCS1 0.017 0.093 -10000 0 -1 4 4
mol:GDP -0.035 0.053 0.18 23 -10000 0 23
CASP1 -0.021 0.043 0.13 18 -0.093 11 29
PTGES2 0.031 0.006 -10000 0 -10000 0 0
IRF9 -0.007 0.037 0.15 7 -0.12 9 16
mol:PI-3-4-5-P3 0.027 0.047 -10000 0 -10000 0 0
RAP1/GDP -0.042 0.032 0.097 18 -10000 0 18
CBL -0.027 0.05 0.17 23 -10000 0 23
MAP3K1 -0.029 0.044 0.16 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 -0.039 0.035 -10000 0 -0.11 35 35
PTPN11 -0.024 0.045 0.16 25 -10000 0 25
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
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 -0.001 0.042 0.065 118 -0.08 46 164
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.07 6 6
FOXO3 0 0.012 0.027 74 -10000 0 74
FOXO1 0.028 0.017 -10000 0 -0.07 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 0.008 -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 -0.07 3 3
FHL2 0.03 0.01 -10000 0 -0.07 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 0.02 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 0.042 0.044 -10000 0 -0.039 2 2
SIRT1/Histone H1b 0.023 0.027 -10000 0 -0.14 9 9
apoptosis -0.038 0.047 0.048 37 -10000 0 37
SIRT1/PGC1A 0.034 0.021 -10000 0 -0.045 3 3
p53/SIRT1 0.031 0.036 0.11 37 -0.06 30 67
SIRT1/FOXO4 0.024 0.023 -10000 0 -0.12 7 7
FOXO1/FHL2/SIRT1 0.035 0.044 -10000 0 -0.045 28 28
HIST1H1E 0.011 0.004 -10000 0 -0.032 1 1
SIRT1/p300 0.038 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.01 0.016 -10000 0 -10000 0 0
TP53 0.019 0.035 -10000 0 -0.068 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 0 12 12
HIV-1 Tat/SIRT1 0.038 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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.03 0.008 -10000 0 -10000 0 0
NFATC1 0.018 0.051 0.2 3 -0.23 11 14
NFATC2 -0.035 0.077 0.1 2 -0.17 117 119
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 -0.022 0.074 0.15 2 -0.23 38 40
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 0.011 0.088 0.16 1 -0.22 36 37
BCL2/BAX 0.043 0.017 -10000 0 -0.054 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 -0.07 6 6
MAPK14 0.032 0.005 -10000 0 -0.07 1 1
BAD 0.032 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.08 0.15 2 -0.23 36 38
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 0.006 0.079 0.22 36 -0.15 2 38
KPNB1 0.032 0.003 -10000 0 -10000 0 0
KPNA2 0.03 0.015 -10000 0 -0.07 11 11
XPO1 0.033 0 -10000 0 -10000 0 0
SFN 0.025 0.025 -10000 0 -0.07 31 31
MAP3K8 0.018 0.028 -10000 0 -0.07 37 37
NFAT4/CK1 alpha 0.022 0.029 -10000 0 -0.078 35 35
MEF2D/NFAT1/Cbp/p300 0.012 0.1 -10000 0 -0.17 106 106
CABIN1 -0.021 0.074 0.15 2 -0.24 36 38
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 -0.07 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 0.014 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
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 0.01 -10000 0 -0.07 1 1
NFAT1-c-4/YWHAQ 0.008 0.071 0.2 2 -0.22 23 25
PRKCH 0.03 0.01 -10000 0 -0.07 2 2
CABIN1/Cbp/p300 0.045 0.013 -10000 0 -10000 0 0
CASP3 0.013 0.04 -10000 0 -0.07 94 94
PIM1 0.032 0.005 -10000 0 -0.07 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.001 38 38
apoptosis 0.017 0.024 -10000 0 -0.099 16 16
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.034 -10000 0 -0.19 10 10
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.032 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.031 0.099 1 -0.079 34 35
BAD/BCL-XL 0.044 0.014 -10000 0 -10000 0 0
PRKCD 0.032 0.005 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 0 8 8
PRKCG 0.031 0.008 -10000 0 0 31 31
PRKCQ 0.025 0.014 -10000 0 -10000 0 0
FKBP38/BCL2 0.045 0.013 -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 0.009 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.049 0.27 1 -0.23 11 12
CaM/Ca2+/FKBP38 0.038 0.016 -10000 0 -10000 0 0
FKBP12/FK506 0.022 0.007 -10000 0 -0.043 1 1
CSNK1A1 -0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.039 0.014 -10000 0 -10000 0 0
NFATc/ERK1 0.035 0.054 0.23 2 -0.23 11 13
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.011 0.088 0.16 1 -0.22 36 37
NR4A1 -0.045 0.066 0.14 7 -0.16 98 105
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 -0.023 0.058 0.068 3 -0.12 109 112
RCH1/ KPNB1 0.045 0.016 -10000 0 -0.054 11 11
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
AKAP5 0.031 0.007 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 0 12 12
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.054 0.23 2 -0.23 11 13
CREBBP 0.032 0.004 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.014 0.046 -10000 0 -0.26 4 4
PLK1 -0.054 0.081 -10000 0 -0.35 10 10
CDKN1B -0.091 0.15 0.23 2 -0.33 124 126
FOXO3 -0.052 0.084 -10000 0 -0.3 19 19
KAT2B -0.003 0.006 -10000 0 -10000 0 0
FOXO1/SIRT1 0.006 0.051 -10000 0 -0.19 20 20
CAT -0.051 0.078 -10000 0 -0.34 8 8
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.014 0.027 -10000 0 -10000 0 0
FOXO1 -0.012 0.053 -10000 0 -0.2 20 20
MAPK10 0.022 0.073 0.18 89 -10000 0 89
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 0 0.076 0.2 10 -0.24 1 11
response to oxidative stress -0.003 0.006 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.043 0.087 -10000 0 -0.31 15 15
XPO1 0.033 0 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
BCL2L11 0.019 0.012 -10000 0 -10000 0 0
FOXO1/SKP2 0.007 0.056 -10000 0 -0.2 19 19
mol:GDP -0.003 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
GADD45A -0.065 0.14 -10000 0 -0.45 23 23
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.019 0.076 -10000 0 -0.27 22 22
MST1 0.007 0.031 -10000 0 -0.073 6 6
CSNK1D 0.032 0.007 -10000 0 -0.07 2 2
CSNK1E 0.031 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.045 0.088 -10000 0 -0.32 18 18
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.014 0.074 0.18 80 -10000 0 80
MAPK9 0.041 0.095 0.18 159 -10000 0 159
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 0.016 -10000 0 -0.026 14 14
SOD2 -0.098 0.12 -10000 0 -0.43 34 34
RBL2 -0.028 0.098 -10000 0 -0.71 6 6
RAL/GDP 0.026 0.024 -10000 0 -10000 0 0
CHUK 0.003 0.027 -10000 0 -0.066 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 0.023 0.024 -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 0.008 -10000 0 -0.07 2 2
USP7 0.032 0.003 -10000 0 -10000 0 0
IKBKB 0.009 0.03 -10000 0 -10000 0 0
CCNB1 -0.078 0.093 -10000 0 -0.38 10 10
FOXO1-3a-4/beta catenin -0.028 0.081 0.21 1 -0.3 3 4
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.056 -10000 0 -0.19 19 19
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
SGK1 -0.003 0.006 -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 0.076 0.26 9 -10000 0 9
SFN 0.025 0.025 -10000 0 -0.07 31 31
CDK2 0.028 0.022 -10000 0 -0.067 24 24
FOXO3A/14-3-3 -0.047 0.074 -10000 0 -0.26 22 22
CREBBP 0.033 0.004 -10000 0 -10000 0 0
FBXO32 -0.048 0.077 -10000 0 -0.31 12 12
BCL6 -0.035 0.11 -10000 0 -0.66 8 8
RALB 0.032 0.005 -10000 0 -0.069 1 1
RALA 0.02 0.02 -10000 0 -0.07 11 11
YWHAH 0.015 0.016 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.055 0.13 0.4 31 -10000 0 31
CRP 0.045 0.12 0.45 10 -10000 0 10
cell cycle arrest 0.048 0.12 0.38 12 -10000 0 12
TIMP1 0.007 0.12 0.37 6 -0.53 1 7
IL6ST 0.03 0.013 -10000 0 -0.048 1 1
Rac1/GDP 0.016 0.058 0.23 11 -0.22 3 14
AP1 0.03 0.068 -10000 0 -0.35 6 6
GAB2 0.032 0.007 -10000 0 -0.027 1 1
TNFSF11 0.042 0.11 0.42 7 -10000 0 7
HSP90B1 0.041 0.052 -10000 0 -0.5 2 2
GAB1 0.032 0.009 -10000 0 -0.059 4 4
MAPK14 0.009 0.045 0.18 2 -0.21 3 5
AKT1 0.02 0.043 -10000 0 -0.35 4 4
FOXO1 0.014 0.045 0.2 3 -0.38 3 6
MAP2K6 0.006 0.038 0.11 20 -0.22 3 23
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.001 0.064 0.26 12 -0.27 1 13
MITF 0.004 0.038 0.11 20 -0.22 2 22
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 -0.017 0.17 -10000 0 -0.92 16 16
CEBPB 0.03 0.018 -10000 0 -0.066 12 12
GRB2/SOS1/GAB family/SHP2 0.02 0.046 0.23 1 -0.26 5 6
STAT3 0.046 0.12 0.45 7 -10000 0 7
STAT1 0.016 0.024 -10000 0 -10000 0 0
CEBPD 0.044 0.11 0.4 10 -10000 0 10
PIK3CA 0.028 0.019 -10000 0 -0.067 18 18
PI3K 0.04 0.024 -10000 0 -0.053 17 17
JUN 0.032 0.004 -10000 0 -10000 0 0
PIAS3/MITF 0.053 0.076 0.19 77 -0.21 2 79
MAPK11 0.007 0.042 0.18 2 -0.21 3 5
STAT3 (dimer)/FOXO1 -0.008 0.069 0.34 1 -0.41 1 2
GRB2/SOS1/GAB family 0.056 0.059 0.17 6 -0.21 3 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.003 0.034 -10000 0 -0.18 5 5
GRB2 0.032 0.007 -10000 0 -0.028 1 1
JAK2 0.029 0.01 -10000 0 -10000 0 0
LBP 0.057 0.12 0.36 24 -0.62 1 25
PIK3R1 0.03 0.01 -10000 0 -0.027 1 1
JAK1 0.031 0.008 -10000 0 -10000 0 0
MYC 0.037 0.12 0.42 11 -10000 0 11
FGG 0.042 0.11 0.42 7 -10000 0 7
macrophage differentiation 0.048 0.12 0.38 12 -10000 0 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.059 -10000 0 -10000 0 0
JUNB 0.047 0.12 0.39 23 -10000 0 23
FOS 0.005 0.043 -10000 0 -0.07 121 121
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.011 0.041 0.13 9 -0.23 3 12
STAT1/PIAS1 0.039 0.065 0.21 18 -0.2 1 19
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.044 -10000 0 -0.36 4 4
STAT3 (dimer) 0.047 0.12 0.41 9 -10000 0 9
PRKCD 0.069 0.15 0.3 125 -10000 0 125
IL6R 0.032 0.007 -10000 0 -10000 0 0
SOCS3 0.047 0.083 0.38 8 -10000 0 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.06 0.024 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.051 0.19 3 -0.22 3 6
HCK 0.013 0.038 -10000 0 -0.07 84 84
MAPKKK cascade 0.04 0.062 0.28 1 -0.37 6 7
bone resorption 0.042 0.11 0.41 7 -10000 0 7
IRF1 0.037 0.12 0.4 8 -10000 0 8
mol:GDP 0.003 0.039 0.11 18 -0.22 3 21
SOS1 0 0.002 -10000 0 -10000 0 0
VAV1 0.003 0.039 0.11 18 -0.23 3 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.017 0.046 0.19 2 -0.28 6 8
PTPN11 0.015 0.056 -10000 0 -0.68 3 3
IL6/IL6RA 0.026 0.032 -10000 0 -0.063 9 9
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 0.014 0.029 -10000 0 -0.072 36 36
PIAS3 0.032 0.005 -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 0.014 0.034 0.11 34 -0.11 4 38
LMO4 0.03 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.019 0.081 -10000 0 -10000 0 0
MCL1 0.02 0.051 0.26 2 -0.41 2 4
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.006 -10000 0 -10000 0 0
ELF1 0.034 0.018 -10000 0 -0.071 11 11
CCNA2 0.005 0.045 -10000 0 -0.07 135 135
PIK3CA 0.028 0.019 -10000 0 -0.069 17 17
JAK3 0.031 0.007 -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 0.011 0.055 0.16 1 -0.23 8 9
SHC1 0.024 0.028 -10000 0 -0.069 40 40
SP1 0.033 0.021 -10000 0 -0.079 14 14
IL2RA -0.015 0.013 -10000 0 -0.11 5 5
IL2RB 0.03 0.012 -10000 0 -0.07 4 4
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.031 0.014 -10000 0 -0.069 9 9
G1/S transition of mitotic cell cycle 0.023 0.093 0.26 13 -0.33 16 29
PTPN11 0.032 0.004 -10000 0 -10000 0 0
CCND2 -0.018 0.012 -10000 0 -0.11 8 8
LCK 0.031 0.01 -10000 0 -0.07 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 0.008 0.054 0.17 5 -0.26 4 9
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.004 0.033 -10000 0 -0.12 20 20
NT3 (dimer)/TRKC 0.044 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.05 0.033 -10000 0 -0.052 18 18
SHC/Grb2/SOS1/GAB1/PI3K 0.012 0.025 -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 0.019 -10000 0 -0.07 17 17
DYNLT1 0.016 0.036 -10000 0 -0.07 72 72
NTRK1 0.032 0.005 -10000 0 -10000 0 0
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 -0.043 18 18
neuron apoptosis 0.03 0.056 0.18 11 -0.15 2 13
SHC 2-3/Grb2 -0.032 0.059 -10000 0 -0.19 11 11
SHC1 0.024 0.028 -10000 0 -0.07 40 40
SHC2 -0.033 0.045 -10000 0 -0.25 4 4
SHC3 -0.038 0.062 -10000 0 -0.3 16 16
STAT3 (dimer) 0.016 0.045 -10000 0 -0.074 99 99
NT3 (dimer)/TRKA 0.057 0.028 -10000 0 -0.052 19 19
RIN/GDP 0.004 0.039 0.13 6 -0.16 10 16
GIPC1 0.031 0.006 -10000 0 -10000 0 0
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 -0.043 2 2
CCND1 -0.033 0.034 -10000 0 -0.1 93 93
MAGED1 0.032 0.003 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -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 0.025 -10000 0 -0.043 39 39
GRB2 0.031 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.041 0.011 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.046 0.011 -10000 0 -10000 0 0
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 -0.07 2 2
RIT1 0.002 0.047 -10000 0 -0.07 151 151
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 0.004 -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 -0.003 0.069 0.21 13 -0.2 20 33
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.012 -10000 0 -10000 0 0
RIT1/GDP -0.001 0.053 0.16 11 -0.15 19 30
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 0.029 -10000 0 -0.047 16 16
KIDINS220/CRKL/C3G 0.044 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.029 -10000 0 -0.054 40 40
FRS2 family/SHP2 0.062 0.018 -10000 0 -0.044 2 2
SHC/GRB2/SOS1/GAB1 0.049 0.033 -10000 0 -0.046 42 42
RIT1/GTP 0.004 0.031 -10000 0 -0.043 151 151
NT3 (dimer) 0.031 0.006 -10000 0 -10000 0 0
RAP1/GDP -0.001 0.039 0.082 4 -0.12 22 26
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 -10000 0 0
Schwann cell development -0.002 0.006 -10000 0 -10000 0 0
EHD4 0.025 0.025 -10000 0 -0.07 31 31
FRS2 family/GRB2/SOS1 0.057 0.019 -10000 0 -0.039 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.036 -10000 0 -0.13 21 21
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.027 0.15 4 -10000 0 4
ABL1 0.031 0.008 -10000 0 -0.07 1 1
SH2B family/GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP 0 0.038 -10000 0 -0.2 14 14
STAT3 0.016 0.045 -10000 0 -0.074 99 99
axon guidance -0.008 0.018 0.04 2 -10000 0 2
MAPK3 -0.012 0.047 0.18 29 -10000 0 29
MAPK1 -0.013 0.042 0.18 23 -10000 0 23
CDC42/GDP 0.007 0.053 0.15 13 -0.15 15 28
NTF3 0.031 0.006 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.019 -10000 0 -0.043 19 19
PI3K 0.039 0.023 -10000 0 -0.054 16 16
FRS3 0.032 0.002 -10000 0 -10000 0 0
FAIM 0.028 0.02 -10000 0 -0.07 19 19
GAB1 0.031 0.009 -10000 0 -0.07 3 3
RASGRF1 -0.009 0.018 0.074 13 -0.15 1 14
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.021 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 0.22 3 -0.26 10 13
Rac1/GDP 0.005 0.043 0.17 8 -0.14 8 16
NGF (dimer)/TRKA/GRIT 0.021 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis 0.012 0.081 -10000 0 -0.72 5 5
NGF (dimer)/TRKA/NEDD4-2 0.042 0.01 -10000 0 -10000 0 0
MAP2K1 -0.02 0.044 0.17 24 -10000 0 24
NGFR 0.028 0.021 -10000 0 -0.07 21 21
NGF (dimer)/TRKA/GIPC/GAIP 0.002 0.014 -10000 0 -0.14 3 3
RAS family/GTP/PI3K 0.002 0.036 -10000 0 -0.12 25 25
FRS2 family/SHP2/GRB2/SOS1 0.07 0.024 -10000 0 -10000 0 0
NRAS 0.007 0.044 -10000 0 -0.07 125 125
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
PRKCI 0.032 0.007 -10000 0 -0.07 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 0.022 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 -0.054 1 1
SQSTM1 0.032 0.007 -10000 0 -0.07 1 1
BDNF (dimer)/TRKB/GIPC 0.013 0.035 -10000 0 -0.054 13 13
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.018 -10000 0 -0.042 2 2
MATK 0.031 0.006 -10000 0 -10000 0 0
NEDD4L 0.031 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.013 0.034 -10000 0 -0.1 35 35
NGF (dimer)/TRKA 0.01 0.016 -10000 0 -0.16 1 1
Rac1/GTP -0.003 0.028 -10000 0 -0.13 9 9
FRS2 family/SHP2/CRK family 0.083 0.04 -10000 0 -10000 0 0
S1P4 pathway

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
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 33 33
PLCG1 0.001 0.011 0.073 6 -0.11 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
G12/G13 0.033 0.022 -10000 0 -10000 0 0
cell migration -0.032 0.041 -10000 0 -0.13 33 33
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 0.001 0.012 0.073 7 -0.11 2 9
MAPK1 0.001 0.01 0.073 7 -0.096 1 8
S1P/S1P5/Gi 0.002 0.013 0.082 7 -0.11 2 9
GNAI1 0.019 0.016 -10000 0 -0.07 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 0.041 0.095 0.18 152 -10000 0 152
S1P/S1P4/Gi 0.002 0.013 0.082 7 -0.11 2 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.029 0.02 -10000 0 -0.024 2 2
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.07 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
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 -0.036 40 70
RAB3GAP2/RIMS1/UNC13B 0.053 0.032 -10000 0 -0.044 7 7
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 0.007 -10000 0 -10000 0 0
mol:ACh 0.019 0.035 0.065 154 -0.059 6 160
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 -0.036 40 70
UNC13B 0.03 0.009 -10000 0 -10000 0 0
CHRNA1 0.032 0.008 -10000 0 -0.07 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
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.056 0.076 -10000 0 -0.36 1 1
NCK1/PAK1/Dok-R -0.032 0.041 -10000 0 -0.24 1 1
NCK1/Dok-R -0.007 0.061 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
mol:beta2-estradiol 0.005 0.014 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
SHC1 0.023 0.028 -10000 0 -0.071 40 40
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
F2 0.037 0.021 -10000 0 -0.071 2 2
TNIP2 0.03 0.015 -10000 0 -0.07 11 11
NF kappa B/RelA 0.014 0.082 -10000 0 -0.25 1 1
FN1 0.013 0.04 -10000 0 -0.07 96 96
PLD2 -0.014 0.042 -10000 0 -0.25 1 1
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB14 0.029 0.019 -10000 0 -0.07 18 18
ELK1 -0.025 0.051 -10000 0 -10000 0 0
GRB7 0.032 0.006 -10000 0 -0.07 1 1
PAK1 0.032 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.012 0.08 -10000 0 -10000 0 0
CDKN1A -0.062 0.082 -10000 0 -0.34 4 4
ITGA5 0.018 0.035 -10000 0 -0.07 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.006 0.062 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
mol:NO -0.009 0.095 0.3 3 -0.3 1 4
PLG -0.012 0.039 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.015 0.084 -10000 0 -10000 0 0
GRB2 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ANGPT2 -0.056 0.074 -10000 0 -0.35 3 3
BMX -0.014 0.042 -10000 0 -0.25 1 1
ANGPT1 -0.009 0.042 -10000 0 -0.21 1 1
tube development -0.066 0.077 -10000 0 -0.32 2 2
ANGPT4 0.028 0.008 -10000 0 -10000 0 0
response to hypoxia -0.003 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.007 0.064 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.024 0.035 -10000 0 -0.054 61 61
FGF2 0.034 0.008 -10000 0 -0.068 2 2
STAT5A (dimer) -0.067 0.095 -10000 0 -0.35 1 1
mol:L-citrulline -0.009 0.095 0.3 3 -0.3 1 4
AGTR1 0.001 0.03 -10000 0 -0.027 263 263
MAPK14 -0.023 0.074 -10000 0 -0.57 3 3
Tie2/SHP2 -0.026 0.12 -10000 0 -0.27 93 93
TEK -0.035 0.12 -10000 0 -0.29 90 90
RPS6KB1 -0.05 0.073 -10000 0 -0.37 1 1
Angiotensin II/AT1 -0.001 0.024 -10000 0 -0.023 265 265
Tie2/Ang1/GRB2 -0.005 0.064 -10000 0 -10000 0 0
MAPK3 -0.03 0.046 -10000 0 -0.25 1 1
MAPK1 -0.027 0.045 -10000 0 -0.25 1 1
Tie2/Ang1/GRB7 -0.006 0.065 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
MAPK8 -0.009 0.033 -10000 0 -0.25 1 1
PI3K -0.046 0.075 -10000 0 -0.4 1 1
FES -0.024 0.073 -10000 0 -0.42 4 4
Crk/Dok-R -0.006 0.062 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 -0.007 0.064 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.054 0.074 -10000 0 -0.34 1 1
STAT5A 0.032 0.006 -10000 0 -0.07 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.048 0.079 0.3 2 -10000 0 2
Tie2/Ang2 -0.066 0.088 -10000 0 -0.35 4 4
Tie2/Ang1 -0.005 0.044 -10000 0 -0.26 1 1
FOXO1 -0.064 0.077 -10000 0 -10000 0 0
ELF1 0.035 0.018 -10000 0 -0.07 6 6
ELF2 -0.009 0.039 -10000 0 -0.22 1 1
mol:Choline -0.014 0.042 -10000 0 -0.25 1 1
cell migration -0.023 0.03 -10000 0 -0.12 2 2
FYN -0.07 0.081 -10000 0 -0.34 2 2
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.059 0.078 -10000 0 -0.32 4 4
ETS1 0.022 0.033 -10000 0 -10000 0 0
PXN -0.048 0.076 0.29 2 -10000 0 2
ITGB1 0.025 0.013 -10000 0 -10000 0 0
NOS3 -0.022 0.09 0.33 2 -0.33 1 3
RAC1 0.023 0.015 -10000 0 -10000 0 0
TNF 0.021 0.033 -10000 0 -0.07 1 1
MAPKKK cascade -0.014 0.042 -10000 0 -0.25 1 1
RASA1 0.032 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.012 0.064 -10000 0 -10000 0 0
NCK1 0.029 0.016 -10000 0 -0.07 11 11
vasculogenesis -0.005 0.093 0.28 4 -0.28 1 5
mol:Phosphatidic acid -0.014 0.042 -10000 0 -0.25 1 1
mol:Angiotensin II -0.004 0.004 -10000 0 -10000 0 0
mol:NADP -0.009 0.095 0.3 3 -0.3 1 4
Rac1/GTP -0.028 0.066 -10000 0 -0.36 1 1
MMP2 -0.022 0.042 -10000 0 -0.27 1 1
Thromboxane A2 receptor signaling

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
TGM2 0.029 0.011 -10000 0 -0.07 3 3
GNB1/GNG2 -0.032 0.027 -10000 0 -0.13 9 9
AKT1 -0.007 0.082 0.23 13 -0.26 23 36
EGF 0.032 0.007 -10000 0 -0.07 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.02 0.064 0.26 20 -0.15 4 24
mol:Ca2+ -0.01 0.076 0.27 9 -0.26 15 24
LYN -0.021 0.067 0.26 21 -0.16 4 25
RhoA/GTP -0.007 0.037 -10000 0 -0.11 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.022 0.078 0.28 11 -0.26 11 22
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 0.008 0.05 0.14 6 -0.22 14 20
G beta5/gamma2 -0.036 0.037 -10000 0 -0.17 4 4
PRKCH -0.017 0.077 0.27 9 -0.28 14 23
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 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.025 0.052 -10000 0 -0.24 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 0.081 0.3 16 -0.26 10 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 -0.015 0.087 0.29 9 -0.33 15 24
cell morphogenesis 0.041 0.01 -10000 0 -10000 0 0
PLCB2 -0.021 0.11 0.34 6 -0.43 15 21
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.018 0.067 0.28 19 -0.15 4 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.027 0.048 0.22 12 -0.16 3 15
RHOA 0.032 0.006 -10000 0 -10000 0 0
PTGIR 0.031 0.007 -10000 0 -10000 0 0
PRKCB1 -0.018 0.08 0.29 6 -0.3 14 20
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 -0.028 0.095 0.33 6 -0.38 11 17
LCK -0.019 0.066 0.26 20 -0.15 4 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.029 0.036 0.19 3 -0.14 5 8
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 0.028 0.037 0.19 3 -0.13 7 10
MAPK14 -0.019 0.06 0.23 11 -0.19 9 20
TGM2/GTP -0.014 0.093 0.34 4 -0.36 14 18
MAPK11 -0.018 0.059 0.24 9 -0.19 9 18
ARHGEF1 -0.02 0.032 -10000 0 -0.15 7 7
GNAI2 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.021 0.08 0.28 9 -0.29 11 20
RAB11/GDP 0.031 0.009 -10000 0 -0.03 8 8
ICAM1 -0.017 0.063 0.22 9 -0.2 15 24
cAMP biosynthetic process -0.015 0.083 0.28 9 -0.3 15 24
Gq family/GTP/EBP50 0.013 0.039 0.22 8 -0.2 8 16
actin cytoskeleton reorganization 0.041 0.01 -10000 0 -10000 0 0
SRC -0.025 0.047 0.22 12 -0.16 3 15
GNB5 0.031 0.006 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.078 0.29 23 -0.18 6 29
VCAM1 -0.024 0.066 0.23 9 -0.21 15 24
TP beta/Gq family/GDP/G beta5/gamma2 0.008 0.05 0.14 6 -0.22 14 20
platelet activation -0.021 0.078 0.3 11 -0.25 11 22
PGI2/IP 0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.01 0.026 -10000 0 -0.091 30 30
Gq family/GDP/G beta5/gamma2 0.01 0.044 0.14 7 -0.2 15 22
TXA2/TP beta/beta Arrestin2 -0.005 0.049 -10000 0 -0.32 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.022 -10000 0 -0.097 31 31
mol:DAG -0.017 0.089 0.31 6 -0.34 14 20
EGFR 0.012 0.018 -10000 0 -0.07 5 5
TXA2/TP alpha -0.019 0.1 0.33 9 -0.4 15 24
Gq family/GTP 0.008 0.028 0.21 7 -0.21 2 9
YES1 -0.023 0.061 0.26 17 -0.16 4 21
GNAI2/GTP 0.017 0.035 -10000 0 -0.11 24 24
PGD2/DP 0.023 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.07 2 2
FYN -0.017 0.065 0.27 20 -0.15 4 24
mol:NO 0.022 0.015 -10000 0 -10000 0 0
GNA15 0.03 0.013 -10000 0 -0.07 7 7
PGK/cGMP 0.025 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 0.027 0.037 0.18 2 -0.12 9 11
NOS3 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.017 0.077 0.25 11 -0.28 13 24
PRKCB -0.015 0.076 0.26 9 -0.27 13 22
PRKCE -0.018 0.076 0.26 9 -0.28 13 22
PRKCD -0.02 0.079 0.28 8 -0.28 13 21
PRKCG -0.019 0.083 0.3 9 -0.3 14 23
muscle contraction -0.029 0.094 0.33 6 -0.36 14 20
PRKCZ -0.019 0.073 0.26 9 -0.26 11 20
ARR3 0.032 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.029 0.039 0.18 2 -0.13 10 12
PRKCQ -0.022 0.069 0.3 5 -0.28 14 19
MAPKKK cascade -0.023 0.092 0.32 6 -0.36 14 20
SELE -0.017 0.063 0.23 9 -0.2 15 24
TP beta/GNAI2/GDP/G beta/gamma 0.029 0.038 0.18 3 -0.13 9 12
ROCK1 0.032 0.005 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.07 2 2
chemotaxis -0.034 0.096 0.33 6 -0.39 9 15
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.07 2 2
GNA11 0.031 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.011 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.006 0.028 -10000 0 -0.25 5 5
SMARCC2 0.031 0.006 -10000 0 -10000 0 0
SMARCC1 0.028 0.019 -10000 0 -0.07 17 17
TBX21 0.006 0.017 -10000 0 -10000 0 0
SUMO2 0.032 0.006 -10000 0 -0.026 2 2
STAT1 (dimer) 0.021 0.038 -10000 0 -0.068 74 74
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 0.027 0.023 -10000 0 -0.07 26 26
GR alpha/HSP90/FKBP51/HSP90 0.08 0.054 -10000 0 -0.079 4 4
PRL -0.041 0.059 -10000 0 -0.21 2 2
cortisol/GR alpha (dimer)/TIF2 -0.014 0.04 -10000 0 -10000 0 0
RELA 0.014 0.041 -10000 0 -0.074 41 41
FGG 0.11 0.14 0.27 28 -10000 0 28
GR beta/TIF2 0.006 0.05 -10000 0 -10000 0 0
IFNG -0.06 0.093 -10000 0 -0.2 46 46
apoptosis 0.022 0.09 -10000 0 -0.36 8 8
CREB1 0.036 0.012 -10000 0 -0.073 6 6
histone acetylation 0.009 0.015 -10000 0 -10000 0 0
BGLAP 0.01 0.018 -10000 0 -10000 0 0
GR/PKAc 0.09 0.057 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.063 -10000 0 -0.11 41 41
SMARCD1 0.032 0.005 -10000 0 -10000 0 0
MDM2 0.004 0.029 0.11 25 -10000 0 25
GATA3 0.029 0.017 -10000 0 -0.065 2 2
AKT1 0.03 0.009 0.067 4 -10000 0 4
CSF2 -0.072 0.072 -10000 0 -0.24 2 2
GSK3B 0.032 0.006 -10000 0 -0.027 1 1
NR1I3 0.025 0.089 -10000 0 -0.33 7 7
CSN2 0.12 0.14 0.25 79 -10000 0 79
BRG1/BAF155/BAF170/BAF60A 0.069 0.037 -10000 0 -0.055 14 14
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.034 0.01 -10000 0 -0.059 3 3
CDKN1A -0.017 0.055 -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 0.025 0.025 -10000 0 -0.07 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.086 0.064 -10000 0 -0.092 4 4
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.026 0.091 -10000 0 -0.36 7 7
JUN 0.002 0.023 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 0.031 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.027 0.039 -10000 0 -0.12 4 4
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.092 0.059 -10000 0 -0.081 2 2
cortisol/GR alpha (monomer) -0.018 0.042 0.2 1 -10000 0 1
NCOA2 0.032 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.009 0.046 -10000 0 -0.08 11 11
AP-1/NFAT1-c-4 -0.015 0.044 0.24 1 -0.2 2 3
AFP -0.052 0.058 0.23 1 -0.37 1 2
SUV420H1 0.032 0.005 -10000 0 -10000 0 0
IRF1 0.002 0.049 0.17 22 -0.14 10 32
TP53 0.014 0.047 -10000 0 -0.18 2 2
PPP5C 0.031 0.007 -10000 0 -10000 0 0
KRT17 -0.062 0.094 0.17 1 -0.2 51 52
KRT14 -0.042 0.069 0.17 12 -0.14 30 42
TBP 0.035 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.007 -10000 0 -10000 0 0
HDAC1 0.017 0.033 -10000 0 -0.072 61 61
HDAC2 0.029 0.012 -10000 0 -0.07 4 4
AP-1 -0.015 0.044 0.24 1 -0.2 3 4
MAPK14 0.032 0.007 -10000 0 -0.04 3 3
MAPK10 0.018 0.016 -10000 0 -10000 0 0
MAPK11 0.03 0.01 -10000 0 -0.026 2 2
KRT5 -0.061 0.093 -10000 0 -0.2 39 39
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.03 0.011 -10000 0 -0.034 8 8
STAT1 0.021 0.038 -10000 0 -0.068 74 74
CGA 0.01 0.02 -10000 0 -0.12 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.052 0.079 0.16 2 -0.22 7 9
MAPK3 0.032 0.005 -10000 0 -0.026 3 3
MAPK1 0.03 0.01 -10000 0 -0.026 2 2
ICAM1 -0.018 0.073 0.14 2 -0.18 76 78
NFKB1 0.014 0.041 -10000 0 -0.075 42 42
MAPK8 0.005 0.019 -10000 0 -0.12 1 1
MAPK9 0.032 0.006 -10000 0 -0.026 2 2
cortisol/GR alpha (dimer) 0.018 0.089 0.25 1 -0.37 8 9
BAX -0.014 0.059 -10000 0 -0.37 3 3
POMC -0.072 0.079 0.26 2 -10000 0 2
EP300 0.028 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.016 0.043 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.22 2 -10000 0 2
SGK1 0.018 0.048 -10000 0 -0.16 13 13
IL13 -0.043 0.068 -10000 0 -0.25 3 3
IL6 -0.017 0.07 0.14 2 -0.19 64 66
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 -0.049 0.07 -10000 0 -0.29 3 3
IL2 -0.06 0.093 0.17 1 -0.2 45 46
CDK5 0.021 0.016 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
IL8 -0.03 0.09 0.14 2 -0.21 88 90
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.048 0.078 -10000 0 -0.12 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.012 0.044 -10000 0 -10000 0 0
SMARCA4 0.031 0.008 -10000 0 -10000 0 0
chromatin remodeling 0.072 0.079 0.17 23 -0.2 2 25
NF kappa B1 p50/RelA/Cbp 0.039 0.077 -10000 0 -0.14 5 5
JUN (dimer) 0.002 0.023 0.28 2 -10000 0 2
YWHAH 0.015 0.016 -10000 0 -10000 0 0
VIPR1 0.009 0.034 0.34 4 -10000 0 4
NR3C1 -0.014 0.032 -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 0.022 0.09 -10000 0 -0.36 8 8
cortisol/GR alpha (dimer)/Src-1 -0.013 0.04 -10000 0 -10000 0 0
PBX1 0.034 0.01 -10000 0 -10000 0 0
POU1F1 0.034 0.011 -10000 0 -0.06 6 6
SELE -0.017 0.071 0.14 2 -0.17 79 81
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.079 0.17 23 -0.2 2 25
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.012 0.044 -10000 0 -10000 0 0
mol:cortisol -0.012 0.021 -10000 0 -10000 0 0
MMP1 0.001 0.047 -10000 0 -0.48 3 3
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.005 0.04 0.12 4 -0.13 10 14
AP2 0.022 0.006 -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 0.03 -10000 0 -0.1 33 33
CD4 0.027 0.02 -10000 0 -0.07 19 19
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 44 -10000 0 44
mol:PI-4-5-P2 0.004 0.007 0.074 4 -0.038 1 5
ARF1/GTP 0.018 0.008 -10000 0 -0.036 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.019 -10000 0 -0.09 22 22
mol:Choline 0.004 0.007 0.075 4 -0.038 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 -0.037 1 5
ARF1/GDP 0.004 0.013 -10000 0 -0.083 8 8
AP2M1 0.03 0.008 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.008 -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 -10000 0 0
ARFIP2 0.029 0.013 -10000 0 -0.04 9 9
COPA 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.038 0.1 1 -0.14 28 29
ARF1/GTP/ARHGAP10 0.02 0.004 -10000 0 -10000 0 0
GGA3 0.032 0.005 -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 25 25
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.029 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 0.072 3 -0.094 25 28
PLD2 0.004 0.007 0.075 4 -0.038 1 5
ARF-GAP1/v-SNARE -0.01 0.003 0 44 -10000 0 44
PIP5K1A 0.004 0.007 0.074 4 -0.038 1 5
ARF1/GTP/Membrin/GBF1/p115 0.004 0.033 -10000 0 -0.056 111 111
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.007 0.075 4 -0.038 1 5
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 0 44 -10000 0 44
GOSR2 0.011 0.029 -10000 0 -0.36 3 3
USO1 0.012 0.02 -10000 0 -0.29 2 2
GBF1 -0.06 0.14 -10000 0 -0.32 110 110
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0.021 -10000 0 -0.043 19 19
ErbB2/ErbB3 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
USP8 -0.017 0.008 0.016 11 -10000 0 11
RAS family/GTP 0.014 0.057 -10000 0 -0.12 4 4
NFATC4 -0.025 0.042 0.26 6 -10000 0 6
ERBB2IP 0.026 0.025 -10000 0 -0.066 32 32
HSP90 (dimer) 0.031 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.032 0.14 5 -10000 0 5
JUN 0.001 0.042 0.15 4 -10000 0 4
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 0.046 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 0.004 0.051 0.19 15 -10000 0 15
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 -0.02 0.06 0.22 16 -10000 0 16
ErbB2/ErbB3/neuregulin 2 0.032 0.03 -10000 0 -0.061 27 27
STAT3 0.025 0.099 -10000 0 -0.93 5 5
cell migration -0.013 0.048 0.21 10 -0.14 2 12
mol:PI-3-4-5-P3 -0.001 0.001 0.005 7 -10000 0 7
cell proliferation -0.005 0.097 0.43 2 -0.45 9 11
FOS -0.008 0.075 0.3 4 -0.27 11 15
NRAS 0.007 0.044 -10000 0 -0.07 125 125
mol:Ca2+ -0.031 0.032 0.14 5 -10000 0 5
MAPK3 0.007 0.064 0.37 3 -10000 0 3
MAPK1 -0.016 0.12 0.42 2 -0.53 12 14
JAK2 -0.03 0.036 0.13 4 -10000 0 4
NF2 0.009 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.022 0.1 12 -0.06 1 13
NRG1 0.032 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.016 0.055 0.2 1 -0.18 27 28
MAPK9 0.007 0.067 0.19 26 -10000 0 26
ERBB2 -0.025 0.022 0.056 32 -10000 0 32
ERBB3 0.022 0.025 -10000 0 -0.071 28 28
SHC1 0.024 0.028 -10000 0 -0.07 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
apoptosis 0.009 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.096 -10000 0 -0.9 5 5
RNF41 -0.022 0.009 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 0.007 15 -10000 0 15
RAC1-CDC42/GTP -0.026 0.022 -10000 0 -0.088 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.027 0.052 48 -10000 0 48
CHRNA1 0.005 0.067 0.4 2 -0.26 4 6
myelination -0.028 0.057 0.29 11 -10000 0 11
PPP3CB -0.026 0.03 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 3 3
NRG2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.022 0.1 12 -0.06 1 13
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.025 0.054 0.19 15 -10000 0 15
SRC 0.03 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 0.003 4 -10000 0 4
PTPN11 -0.033 0.038 0.13 4 -10000 0 4
MAP2K1 -0.012 0.12 0.42 2 -0.53 21 23
heart morphogenesis -0.031 0.032 0.14 5 -10000 0 5
RAS family/GDP 0.018 0.061 -10000 0 -0.12 5 5
GRB2 0.031 0.006 -10000 0 -10000 0 0
PRKACA 0.017 0.006 -10000 0 -10000 0 0
CHRNE 0.001 0.012 0.048 5 -10000 0 5
HSP90AA1 0.031 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 0.032 0.14 5 -10000 0 5
CDC42 0.031 0.006 -10000 0 -10000 0 0
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 -0.07 3 3
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.001 -10000 0 -0.009 3 3
monocyte activation -0.022 0.048 -10000 0 -0.33 8 8
MAP2K2 0.017 0.027 -10000 0 -0.58 1 1
MAP2K1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K7 -0.009 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.001 -10000 0 -10000 0 0
CYAA -0.007 0.002 -10000 0 -0.028 3 3
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B -0.014 0.015 0.13 3 -0.079 5 8
Channel 0.021 0.004 -10000 0 -0.027 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 -0.025 0.12 -10000 0 -0.37 52 52
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.001 0.009 3 -10000 0 3
MAPK3 -0.009 0.001 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 -10000 0 -10000 0 0
PGR -0.009 0.001 -10000 0 -10000 0 0
PA/Cellular Receptors 0.022 0.004 -10000 0 -0.034 3 3
apoptosis -0.002 0.001 -10000 0 -0.009 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.004 -10000 0 -0.028 4 4
macrophage activation -0.014 0.004 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.07 2 2
VCAM1 -0.022 0.048 -10000 0 -0.33 8 8
platelet activation -0.025 0.12 -10000 0 -0.37 52 52
MAPKKK cascade 0.004 0.018 0.065 1 -0.068 26 27
IL18 -0.015 0.013 0.11 2 -0.079 2 4
negative regulation of macrophage activation -0.002 0.001 -10000 0 -0.009 3 3
LEF -0.002 0.001 -10000 0 -0.009 3 3
CASP1 -0.007 0.007 -10000 0 -0.017 164 164
mol:cAMP -0.025 0.12 -10000 0 -0.37 52 52
necrosis -0.002 0.001 -10000 0 -0.009 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 -0.025 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.014 -10000 0 -0.043 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.03 0.014 -10000 0 -0.07 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 6 6
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.017 0.036 -10000 0 -0.07 74 74
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 -0.07 1 1
MAP3K12 0.032 0.004 -10000 0 -10000 0 0
FGR 0.029 0.018 -10000 0 -0.07 15 15
p38 alpha/TAB1 -0.02 0.048 -10000 0 -0.22 17 17
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 -0.23 15 18
apoptosis -0.019 0.046 -10000 0 -0.21 17 17
RAL/GTP 0.028 0.023 -10000 0 -0.043 12 12
LYN 0.02 0.033 -10000 0 -0.07 60 60
DUSP1 0.029 0.018 -10000 0 -0.07 16 16
PAK1 0.032 0.004 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0.03 -10000 0 -0.039 1 1
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 0.021 -10000 0 -10000 0 0
MAPK11 0.004 0.08 0.17 24 -0.3 10 34
BLK 0.032 0.005 -10000 0 -10000 0 0
HCK 0.013 0.038 -10000 0 -0.07 84 84
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.03 0.012 -10000 0 -0.07 6 6
TRAF6/MEKK3 0.04 0.01 -10000 0 -0.024 8 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.075 0.16 17 -0.25 15 32
positive regulation of innate immune response 0.004 0.09 0.18 23 -0.32 12 35
LCK 0.031 0.01 -10000 0 -0.07 4 4
p38alpha-beta/MKP7 0.001 0.086 0.17 23 -0.3 13 36
p38alpha-beta/MKP5 0.012 0.094 0.2 19 -0.32 10 29
PGK/cGMP 0.018 0.01 -10000 0 -10000 0 0
PAK2 0.027 0.021 -10000 0 -0.07 22 22
p38alpha-beta/MKP1 0.011 0.096 0.2 19 -0.33 11 30
CDC42 0.031 0.006 -10000 0 -10000 0 0
RALB 0.032 0.005 -10000 0 -0.07 1 1
RALA 0.02 0.02 -10000 0 -0.07 11 11
PAK3 0.005 0.012 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.057 0.031 -9999 0 -0.058 20 20
E-cadherin/beta catenin 0.045 0.016 -9999 0 -0.054 8 8
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
JUP 0.029 0.018 -9999 0 -0.07 16 16
CDH1 0.03 0.013 -9999 0 -0.07 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.018 0.058 1 -0.12 3 4
KIRREL 0.035 0.011 0.084 1 -0.039 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.018 0.12 3 -0.058 1 4
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
WASL 0.022 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.068 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 -0.01 0.044 0.16 28 -10000 0 28
mol:Ca2+ 0.074 0.036 0.17 19 -10000 0 19
mol:DAG 0.075 0.037 0.17 19 -10000 0 19
NPHS2 0.035 0.01 0.084 1 -0.03 4 5
mol:IP3 0.075 0.037 0.17 19 -10000 0 19
regulation of endocytosis 0.056 0.029 0.13 1 -0.061 2 3
Nephrin/NEPH1/podocin/Cholesterol 0.062 0.029 0.16 19 -0.045 1 20
establishment of cell polarity 0.049 0.018 0.12 3 -0.058 1 4
Nephrin/NEPH1/podocin/NCK1-2 0.09 0.039 0.2 2 -10000 0 2
Nephrin/NEPH1/beta Arrestin2 0.058 0.03 0.14 1 -0.061 2 3
NPHS1 0.034 0.011 0.076 6 -10000 0 6
Nephrin/NEPH1/podocin 0.059 0.024 0.17 3 -0.056 4 7
TJP1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.016 -10000 0 -0.07 11 11
NCK2 0.032 0.003 -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 0.022 0.03 -10000 0 -0.07 48 48
Nephrin/NEPH1/podocin/GRB2 0.078 0.035 0.18 16 -10000 0 16
GRB2 0.031 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.051 0.17 30 -10000 0 30
cytoskeleton organization -0.007 0.034 0.18 11 -0.15 3 14
Nephrin/NEPH1 0.041 0.016 0.097 3 -0.03 5 8
Nephrin/NEPH1/ZO-1 0.062 0.024 -10000 0 -0.045 5 5
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.056 0.023 -10000 0 -0.039 3 3
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 0.057 0.029 -10000 0 -0.046 31 31
HDAC9 0.022 0.016 -10000 0 -0.07 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.059 0.026 -10000 0 -0.044 3 3
HDAC4/ANKRA2 0.047 0.009 -10000 0 -0.054 1 1
HDAC5/YWHAB 0.044 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.029 -10000 0 -0.098 37 37
GATA2 0.032 0.005 -10000 0 -10000 0 0
HDAC4/RFXANK 0.037 0.03 -10000 0 -0.054 45 45
BCOR 0.031 0.01 -10000 0 -0.07 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.032 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.006 -10000 0 -10000 0 0
Histones 0.036 0.032 0.082 154 -0.095 4 158
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
XPO1 0.033 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.047 0.009 -10000 0 -0.054 1 1
HDAC4/Ubc9 0.047 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 0.005 -10000 0 -10000 0 0
HDAC6 0.032 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.037 0.03 -10000 0 -0.054 43 43
CAMK4 0.032 0.004 -10000 0 -10000 0 0
Tubulin/HDAC6 0.059 0.023 -10000 0 -0.037 10 10
SUMO1 0.033 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
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 -0.099 37 37
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 0.008 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.021 -10000 0 -0.054 19 19
HDAC4/HDAC3/SMRT (N-CoR2) 0.063 0.018 -10000 0 -0.036 13 13
HDAC4/SRF 0.063 0.018 -10000 0 -10000 0 0
HDAC4/ER alpha 0.045 0.013 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.032 0.082 154 -0.094 4 158
cell motility 0.058 0.023 -10000 0 -0.037 10 10
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 0.028 0.018 -10000 0 -0.07 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 0.03 0.008 -10000 0 -10000 0 0
HDAC6/HDAC11 0.047 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.039 -10000 0 -0.098 36 36
NPC 0.019 0.002 -10000 0 -0.014 1 1
MEF2C 0.027 0.012 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.076 0.042 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.032 0.004 -10000 0 -10000 0 0
TUBB2A 0.03 0.009 -10000 0 -10000 0 0
HDAC11 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
ANKRA2 0.032 0.006 -10000 0 -0.07 1 1
RFXANK 0.022 0.029 -10000 0 -0.07 45 45
nuclear import -0.032 0.023 0.11 10 -10000 0 10
Nongenotropic Androgen signaling

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
PTK2 -0.011 0.002 0 18 -10000 0 18
GNB1/GNG2 0.037 0.017 -10000 0 -0.028 27 27
regulation of S phase of mitotic cell cycle 0.014 0.021 -10000 0 -0.11 10 10
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 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
AKT1 -0.011 0.003 -10000 0 -10000 0 0
MAP2K1 -0.029 0.051 0.15 32 -0.14 2 34
T-DHT/AR 0.023 0.009 -10000 0 -0.044 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 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
GNAI1 0.019 0.016 -10000 0 -0.07 1 1
mol:GDP -0.012 0.009 -10000 0 -0.081 1 1
cell proliferation -0.024 0.07 0.22 11 -0.26 4 15
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
FOS -0.025 0.07 0.21 4 -0.33 4 8
mol:Ca2+ 0 0.002 -10000 0 -0.033 2 2
MAPK3 -0.021 0.064 0.21 13 -0.24 2 15
MAPK1 -0.023 0.094 -10000 0 -0.35 32 32
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 0.031 -10000 0 -0.068 4 4
actin cytoskeleton reorganization 0.028 0.029 -10000 0 -0.047 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 -0.043 16 16
apoptosis 0.015 0.066 0.25 6 -0.21 4 10
T-DHT/AR/PELP1 0.041 0.013 -10000 0 -0.045 9 9
HRAS/GDP 0.016 0.034 0.1 37 -0.086 1 38
CREB1 -0.016 0.068 0.22 4 -0.26 6 10
RAC1-CDC42/GTP 0.036 0.035 -10000 0 -0.054 1 1
AR 0.031 0.013 -10000 0 -0.07 8 8
GNB1 0.031 0.008 -10000 0 -10000 0 0
RAF1 -0.022 0.053 0.16 37 -10000 0 37
RAC1-CDC42/GDP 0.027 0.031 0.14 2 -0.087 1 3
T-DHT/AR/PELP1/Src 0.055 0.022 -10000 0 -0.046 9 9
MAP2K2 -0.032 0.045 0.15 26 -0.14 2 28
T-DHT/AR/PELP1/Src/PI3K 0.014 0.021 -10000 0 -0.11 10 10
GNAZ 0.027 0.012 -10000 0 -10000 0 0
SHBG 0.031 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.064 0.1 -10000 0 -0.36 35 35
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 -10000 0 -10000 0 0
Gi family/GTP 0 0.008 -10000 0 -0.11 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Aurora C 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
INCENP 0.032 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.05 0.032 -9999 0 -0.046 31 31
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 0.023 -9999 0 -0.07 26 26
AURKC 0.03 0.01 -9999 0 -0.07 2 2
IL4-mediated signaling events

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
BCL2L1 -0.056 0.16 0.46 1 -0.69 2 3
STAT6 (cleaved dimer) -0.053 0.15 -10000 0 -0.71 2 2
IGHG1 -0.023 0.085 -10000 0 -0.49 1 1
IGHG3 -0.065 0.15 -10000 0 -0.66 2 2
AKT1 -0.023 0.11 0.26 1 -0.62 3 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.001 0.079 -10000 0 -0.61 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.016 0.1 -10000 0 -0.64 1 1
THY1 -0.17 0.31 -10000 0 -0.74 51 51
MYB 0.029 0.014 -10000 0 -0.07 7 7
HMGA1 0.032 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.11 -10000 0 -0.65 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.02 0.1 -10000 0 -0.65 1 1
SP1 -0.006 0.041 -10000 0 -0.047 252 252
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.026 0.025 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.046 0.16 -10000 0 -0.75 1 1
SOCS1 -0.044 0.13 0.29 1 -0.55 1 2
SOCS3 -0.03 0.096 -10000 0 -0.57 1 1
FCER2 -0.048 0.13 -10000 0 -0.63 2 2
PARP14 0.001 0 -10000 0 -10000 0 0
CCL17 -0.071 0.15 -10000 0 -0.69 2 2
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.019 0.087 -10000 0 -0.6 1 1
T cell proliferation -0.058 0.15 -10000 0 -0.87 1 1
IL4R/JAK1 -0.062 0.16 -10000 0 -0.66 2 2
EGR2 -0.073 0.15 -10000 0 -0.7 2 2
JAK2 0.004 0.039 -10000 0 -10000 0 0
JAK3 0.031 0.014 -10000 0 -0.042 1 1
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.019 0.027 -10000 0 -10000 0 0
COL1A2 -0.059 0.11 -10000 0 -0.72 5 5
CCL26 -0.068 0.15 -10000 0 -0.69 2 2
IL4R -0.072 0.16 -10000 0 -0.7 2 2
PTPN6 0.03 0.018 -10000 0 -0.048 20 20
IL13RA2 -0.092 0.16 -10000 0 -0.69 2 2
IL13RA1 -0.004 0.052 -10000 0 -0.1 10 10
IRF4 0.012 0.065 -10000 0 -0.44 3 3
ARG1 -0.021 0.091 -10000 0 -0.4 4 4
CBL -0.031 0.1 0.29 1 -0.63 1 2
GTF3A 0.023 0.027 -10000 0 -0.045 63 63
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
IL13RA1/JAK2 0.002 0.056 -10000 0 -10000 0 0
IRF4/BCL6 0.019 0.068 -10000 0 -0.42 3 3
CD40LG 0.035 0.004 -10000 0 -0.042 1 1
MAPK14 -0.031 0.1 0.28 1 -0.63 1 2
mitosis -0.02 0.11 0.26 1 -0.59 3 4
STAT6 -0.07 0.17 -10000 0 -0.75 2 2
SPI1 0.032 0.014 -10000 0 -0.068 8 8
RPS6KB1 -0.024 0.11 0.26 1 -0.57 3 4
STAT6 (dimer) -0.069 0.17 -10000 0 -0.75 2 2
STAT6 (dimer)/PARP14 -0.071 0.15 -10000 0 -0.72 2 2
mast cell activation 0.003 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.091 -10000 0 -0.65 1 1
FRAP1 -0.021 0.12 -10000 0 -0.62 3 3
LTA -0.072 0.15 -10000 0 -0.71 2 2
FES 0.032 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.071 0.17 0.74 2 -10000 0 2
CCL11 -0.069 0.15 -10000 0 -0.66 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.011 0.097 -10000 0 -0.9 1 1
IL2RG 0.03 0.02 -10000 0 -0.064 11 11
IL10 -0.066 0.16 -10000 0 -0.69 2 2
IRS1 0.032 0.009 -10000 0 -0.07 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
IL4 -0.011 0.086 -10000 0 -0.59 5 5
IL5 -0.071 0.15 -10000 0 -0.69 2 2
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.068 0.15 -10000 0 -0.72 2 2
COL1A1 -0.04 0.12 -10000 0 -0.58 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.064 0.16 -10000 0 -0.73 1 1
IL2R gamma/JAK3 0.048 0.02 -10000 0 -0.05 12 12
TFF3 -0.071 0.16 -10000 0 -0.69 2 2
ALOX15 -0.071 0.15 -10000 0 -0.69 2 2
MYBL1 0.016 0.037 -10000 0 -0.07 78 78
T-helper 2 cell differentiation -0.054 0.15 -10000 0 -0.79 2 2
SHC1 0.024 0.028 -10000 0 -0.07 40 40
CEBPB 0.03 0.017 -10000 0 -0.068 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.021 0.11 -10000 0 -0.69 2 2
mol:PI-3-4-5-P3 -0.021 0.12 0.27 1 -0.62 3 4
PI3K -0.022 0.12 -10000 0 -0.65 3 3
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.032 0.014 -10000 0 -0.035 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.016 0.084 -10000 0 -0.54 1 1
ITGB3 -0.071 0.15 -10000 0 -0.69 2 2
PIGR -0.066 0.16 -10000 0 -0.69 2 2
IGHE 0.015 0.041 0.14 25 -0.094 3 28
MAPKKK cascade -0.016 0.084 -10000 0 -0.53 1 1
BCL6 0.028 0.018 -10000 0 -0.07 15 15
OPRM1 -0.071 0.15 -10000 0 -0.69 2 2
RETNLB -0.068 0.15 -10000 0 -0.69 2 2
SELP -0.068 0.16 -10000 0 -0.69 2 2
AICDA -0.064 0.15 0.42 1 -0.69 2 3
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.041 0.13 33 -10000 0 33
GNAI2 0.032 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
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 32 32
negative regulation of cAMP metabolic process 0.002 0.013 0.082 7 -0.11 2 9
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNAI3 0.02 0.033 -10000 0 -0.07 59 59
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 0.013 0.082 7 -0.11 2 9
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 -0.07 1 1
Atypical NF-kappaB 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
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 -0.041 12 12
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.049 0.12 25 -0.21 7 32
NFKBIA 0.004 0.032 0.1 24 -0.098 24 48
MAPK14 0.032 0.005 -10000 0 -0.07 1 1
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -0.04 11 11
ARRB2 0.012 0.003 -10000 0 -0.041 1 1
REL 0.032 0.001 -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 -0.042 10 10
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.012 -10000 0 -0.041 12 12
PIK3CA 0.028 0.019 -10000 0 -0.07 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 0.005 -10000 0 -0.054 4 4
RELA 0.032 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.009 0.029 0.11 3 -0.14 6 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.051 0.17 2 -0.2 9 11
SRC 0.03 0.008 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.054 16 16
NF kappa B1 p50/RelA 0.011 0.027 0.11 3 -0.14 6 9
IKBKB 0.032 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
SYK 0.025 0.026 -10000 0 -0.07 35 35
I kappa B alpha/PIK3R1 0.02 0.047 0.18 2 -0.21 7 9
cell death 0.023 0.05 0.17 2 -0.2 9 11
NF kappa B1 p105/c-Rel 0.028 0.011 -10000 0 -0.041 12 12
LCK 0.031 0.01 -10000 0 -0.07 4 4
BCL3 0.031 0.007 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.031 0.008 -10000 0 -10000 0 0
SPHK1 0.029 0.019 -10000 0 -0.07 18 18
GNAI2 0.032 0.005 -10000 0 -10000 0 0
mol:S1P 0.009 0.01 -10000 0 -0.036 23 23
GNAO1 0.003 0.009 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.022 0.008 -10000 0 -0.054 18 18
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 0.02 0.033 -10000 0 -0.07 59 59
G12/G13 0.033 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 0.001 0.025 -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 -0.07 1 1
S1P/S1P5/G12 0.016 0.028 -10000 0 -0.11 14 14
S1P/S1P3/Gq 0.019 0.044 0.15 8 -0.28 8 16
S1P/S1P4/Gi -0.005 0.043 -10000 0 -0.22 18 18
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.012 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.07 2 2
GNA15 0.03 0.013 -10000 0 -0.07 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.07 2 2
GNA11 0.031 0.007 -10000 0 -10000 0 0
ABCC1 0.031 0.013 -10000 0 -0.07 8 8
Reelin signaling pathway

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
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.07 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 -0.07 1 1
ITGA3 0.029 0.019 -10000 0 -0.07 17 17
RELN/VLDLR/Fyn 0.017 0.031 -10000 0 -0.049 5 5
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.059 -10000 0 -10000 0 0
AKT1 -0.004 0.028 -10000 0 -0.13 22 22
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.031 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.019 0.03 -10000 0 -0.042 4 4
LRPAP1/LRP8 0.047 0.009 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.021 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 0.036 0.17 5 -10000 0 5
DAB1/LIS1 0.025 0.045 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.019 0.038 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
DAB1/NCK2 0.026 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 -0.07 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.018 0.031 -10000 0 -0.052 2 2
GRIN2A/RELN/LRP8/DAB1/Fyn 0.019 0.04 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.017 0.03 -10000 0 -0.044 4 4
ITGB1 0.025 0.013 -10000 0 -10000 0 0
MAP1B 0.008 0.052 0.15 58 -10000 0 58
RELN/LRP8 0.02 0.031 -10000 0 -0.052 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn 0.024 0.044 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.054 16 16
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.025 -10000 0 -0.054 15 15
RAP1A 0.054 0.094 0.32 19 -10000 0 19
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 0.003 -10000 0 -10000 0 0
neuron differentiation -0.014 0.058 -10000 0 -0.17 36 36
neuron adhesion 0.041 0.093 0.31 20 -10000 0 20
LRP8 0.032 0.005 -10000 0 -10000 0 0
GSK3B -0.003 0.04 0.077 48 -0.14 24 72
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 0.02 0.016 -10000 0 -10000 0 0
MAPT 0.004 0.056 0.72 1 -10000 0 1
neuron migration -0.014 0.081 0.19 47 -0.16 14 61
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.058 -10000 0 -0.17 36 36
RELN/VLDLR 0.023 0.039 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.005 -10000 0 -0.043 15 15
SNTA1 0.03 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.026 0.008 -10000 0 -0.052 15 15
MAPK12 -0.013 0.006 -10000 0 -0.046 6 6
CCND1 -0.009 0.047 -10000 0 -0.36 7 7
p38 gamma/SNTA1 -0.016 0.024 0.18 4 -10000 0 4
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.013 -10000 0 -0.07 7 7
G2/M transition checkpoint -0.013 0.006 -10000 0 -0.045 6 6
MAP2K6 -0.008 0.004 -10000 0 -0.043 7 7
MAPT -0.025 0.046 0.14 3 -0.14 16 19
MAPK13 -0.023 0.006 -10000 0 -0.054 15 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.006 -10000 0 -0.042 7 7
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.017 0.007 -10000 0 -10000 0 0
NFATC2 -0.01 0.004 -10000 0 -10000 0 0
NFATC3 -0.018 0.007 -10000 0 -10000 0 0
CD40LG -0.039 0.043 0.32 2 -10000 0 2
PTGS2 -0.04 0.04 0.3 1 -10000 0 1
JUNB 0.03 0.014 -10000 0 -0.07 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.009 -10000 0 -0.021 4 4
CaM/Ca2+ 0.021 0.009 -10000 0 -0.021 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 38 38
FOSL1 0.03 0.016 -10000 0 -0.07 12 12
CREM 0.025 0.013 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.025 0.033 0.15 1 -0.075 3 4
FOS 0.006 0.043 -10000 0 -0.07 121 121
IFNG -0.037 0.039 0.34 1 -10000 0 1
AP-1/NFAT1-c-4 0.032 0.075 0.2 4 -0.12 3 7
FASLG -0.039 0.039 0.3 1 -10000 0 1
NFAT1-c-4/ICER1 0.004 0.036 -10000 0 -10000 0 0
IL2RA -0.029 0.042 0.32 2 -10000 0 2
FKBP12/FK506 0.022 0.007 -10000 0 -0.043 1 1
CSF2 -0.039 0.04 0.3 1 -10000 0 1
JunB/Fra1/NFAT1-c-4 0.032 0.041 0.16 6 -10000 0 6
IL4 -0.039 0.04 0.19 4 -10000 0 4
IL2 0.016 0.088 -10000 0 -0.86 5 5
IL3 0.028 0.073 -10000 0 -0.59 7 7
FKBP1A 0.03 0.01 -10000 0 -0.07 1 1
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.035 0.005 -10000 0 -10000 0 0
IGF1 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
NCK2 0.032 0.003 -10000 0 -10000 0 0
PTK2 0.031 0.006 -10000 0 0 18 18
CRKL -0.021 0.008 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.035 0.025 -10000 0 -0.043 39 39
HRAS 0.031 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.024 0.014 -10000 0 -0.061 10 10
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.023 -10000 0 -0.049 10 10
AKT1 -0.023 0.046 0.17 19 -10000 0 19
BAD -0.027 0.044 0.15 19 -10000 0 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.032 0.018 0.21 1 -0.073 7 8
RAF1 -0.007 0.055 0.24 4 -0.43 3 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.053 0.02 -10000 0 -0.058 11 11
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.016 -10000 0 -0.06 11 11
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
RPS6KB1 -0.024 0.047 0.17 20 -10000 0 20
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.012 0.053 0.21 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 0.022 0.029 -10000 0 -0.07 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.06 0.04 -10000 0 -0.067 1 1
IGF-1R heterotetramer 0.033 0.008 -10000 0 -0.033 6 6
IGF-1R heterotetramer/IGF1/IRS/Nck 0.058 0.02 -10000 0 -0.062 11 11
Crk/p130 Cas/Paxillin 0.047 0.019 0.21 1 -0.072 7 8
IGF1R 0.033 0.008 -10000 0 -0.033 6 6
IGF1 0.033 0.013 -10000 0 -0.055 9 9
IRS2/Crk -0.026 0.009 -10000 0 -10000 0 0
PI3K 0.061 0.038 -10000 0 -0.074 5 5
apoptosis 0.028 0.05 -10000 0 -0.16 20 20
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
PRKCD 0.001 0.02 -10000 0 -0.14 5 5
RAF1/14-3-3 E -0.006 0.057 0.24 4 -0.38 3 7
BAD/14-3-3 -0.029 0.052 0.16 21 -10000 0 21
PRKCZ -0.019 0.045 0.17 20 -10000 0 20
Crk/p130 Cas/Paxillin/FAK1 -0.038 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 0.009 0.024 -10000 0 -0.15 6 6
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.043 0.048 -10000 0 -0.07 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.033 0.018 0.13 5 -0.071 7 12
GRB10 0.021 0.017 -10000 0 -0.07 4 4
PTPN11 -0.022 0.006 -10000 0 -10000 0 0
IRS1 -0.016 0.015 0.12 5 -10000 0 5
IRS2 -0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.045 0.012 -10000 0 -0.059 4 4
GRB2 0.031 0.006 -10000 0 -10000 0 0
PDPK1 -0.019 0.048 0.18 20 -10000 0 20
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKD1 -0.005 0.023 -10000 0 -0.14 9 9
SHC1 0.024 0.028 -10000 0 -0.07 40 40
Ephrin B reverse signaling

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
EFNB2 0.029 0.01 -10000 0 -10000 0 0
EPHB2 0.031 0.008 -10000 0 -0.071 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 0.049 0.031 -10000 0 -0.041 17 17
neuron projection morphogenesis 0.006 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.027 0.16 2 -10000 0 2
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 0.038 0.2 1 -0.39 4 5
YES1 0.008 0.061 -10000 0 -0.61 4 4
Ephrin B1/EPHB1-2/NCK2 0.011 0.027 0.16 2 -10000 0 2
PI3K 0.038 0.049 -10000 0 -0.36 4 4
mol:GDP 0.011 0.026 0.16 2 -10000 0 2
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
endothelial cell proliferation 0.027 0.021 -10000 0 -10000 0 0
FYN 0.009 0.063 -10000 0 -0.61 4 4
MAP3K7 -0.002 0.033 -10000 0 -0.39 3 3
FGR 0.012 0.058 -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 -0.07 1 1
cell adhesion 0.019 0.043 -10000 0 -0.34 4 4
LYN 0.01 0.059 -10000 0 -0.6 4 4
Ephrin B1/EPHB1-2/Src Family Kinases 0.006 0.054 -10000 0 -0.57 4 4
Ephrin B1/EPHB1-2 0.004 0.041 -10000 0 -0.43 4 4
SRC 0.013 0.058 -10000 0 -0.6 4 4
ITGB3 0.032 0.003 -10000 0 -10000 0 0
EPHB1 0.03 0.014 -10000 0 -0.068 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.021 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.013 0.058 -10000 0 -0.58 4 4
HCK 0.009 0.058 -10000 0 -0.59 4 4
regulation of stress fiber formation -0.011 0.026 -10000 0 -0.16 2 2
MAPK8 -0.009 0.039 -10000 0 -0.38 4 4
Ephrin B1/EPHB1-2/RGS3 0.011 0.026 0.16 1 -10000 0 1
endothelial cell migration 0.048 0.095 0.19 141 -0.33 3 144
NCK2 0.032 0.003 -10000 0 -10000 0 0
PTPN13 0.026 0.026 -10000 0 -0.081 25 25
regulation of focal adhesion formation -0.011 0.026 -10000 0 -0.16 2 2
chemotaxis -0.011 0.025 -10000 0 -0.16 1 1
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
Rac1/GTP 0.008 0.022 -10000 0 -10000 0 0
angiogenesis 0.005 0.041 -10000 0 -0.43 4 4
LCK 0.012 0.058 -10000 0 -0.6 4 4
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.034 0.041 -10000 0 -10000 0 0
TC10/GTP 0.027 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.078 0.034 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.029 0.019 -10000 0 -0.07 18 18
FOXO3 -0.019 0.13 -10000 0 -0.57 28 28
AKT1 -0.023 0.06 0.24 6 -10000 0 6
INSR 0.034 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.058 0.032 0.22 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.017 -10000 0 -0.07 4 4
SORBS1 0.024 0.014 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
PTPN1 -0.018 0.025 0.14 10 -10000 0 10
CAV1 -0.026 0.03 0.18 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.046 0.05 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.078 0.033 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.053 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.038 0.18 17 -0.19 3 20
RPS6KB1 -0.028 0.055 0.22 6 -10000 0 6
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 0.019 0.015 -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 22 -10000 0 22
HRAS/GTP -0.032 0.018 0.03 22 -0.072 1 23
Insulin Receptor 0.034 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.055 -10000 0 -0.079 1 1
PRKCI 0.034 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 0.028 -10000 0 -0.07 40 40
negative regulation of MAPKKK cascade 0.031 0.044 -10000 0 -10000 0 0
PI3K 0.065 0.044 -10000 0 -10000 0 0
NCK2 0.032 0.003 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -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 -0.027 0.055 0.23 5 -10000 0 5
PRKCZ 0.016 0.017 -10000 0 -0.29 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.018 0.04 0.16 19 -10000 0 19
F2RL2 0.032 0.004 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.07 6 6
Insulin Receptor/Insulin/Shc 0.05 0.038 -10000 0 -0.046 40 40
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.043 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.045 -10000 0 -0.05 35 35
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.016 -10000 0 -0.07 11 11
CBL/APS/CAP/Crk-II 0.038 0.041 -10000 0 -0.039 8 8
TC10/GDP 0.024 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.051 -10000 0 -0.056 34 34
INPP5D -0.019 0.013 0.034 25 -10000 0 25
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 0.004 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.07 4 4
p62DOK/RasGAP 0.032 0.045 -10000 0 -10000 0 0
INS 0.036 0.013 0.078 33 -10000 0 33
mol:PI-3-4-P2 -0.018 0.013 0.034 25 -10000 0 25
GRB2 0.031 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.043 0.038 0.13 4 -10000 0 4
PTPRA 0.031 0.01 0.07 1 -10000 0 1
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
TC10/GTP/CIP4 0.042 0.012 -10000 0 -0.043 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 16 16
Insulin Receptor/Insulin/IRS1 0.06 0.026 -10000 0 -0.047 2 2
Insulin Receptor/Insulin/IRS3 0.049 0.019 0.11 21 -10000 0 21
Par3/Par6 0.07 0.026 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.016 -10000 0 -0.1 7 7
TRAF2/ASK1 0.039 0.014 -10000 0 -10000 0 0
ATM 0.027 0.022 -10000 0 -0.07 25 25
MAP2K3 0.029 0.058 0.17 4 -0.24 11 15
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.054 0.18 6 -0.2 12 18
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.029 0.016 -10000 0 -0.03 28 28
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
GADD45A 0.024 0.027 -10000 0 -0.07 39 39
GADD45B 0.03 0.014 -10000 0 -0.07 8 8
MAP3K1 0.032 0.006 -10000 0 -0.07 1 1
MAP3K6 0.031 0.008 -10000 0 -0.07 2 2
MAP3K7 0.031 0.008 -10000 0 -0.07 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 -0.054 2 2
TAK1/TAB family 0.002 0.022 0.074 40 -0.069 6 46
RAC1/OSM/MEKK3 0.029 0.02 -10000 0 -0.024 3 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.022 0.047 -10000 0 -0.21 11 11
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 0.03 0.009 -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 -10000 0 0
OSM/MEKK3 0.024 0.002 -10000 0 -10000 0 0
TAOK1 0.004 0.01 -10000 0 -0.042 25 25
TAOK2 0.01 0.012 -10000 0 -0.041 25 25
TAOK3 0.01 0.012 -10000 0 -0.041 25 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.07 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 0.048 -10000 0 -0.06 6 6
Regulation of Androgen receptor activity

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
HDAC1 -0.015 0.011 -10000 0 -0.043 61 61
SMARCC1 0.003 0.034 -10000 0 -0.6 1 1
REL 0.032 0.001 -10000 0 -10000 0 0
HDAC7 -0.036 0.031 0.16 2 -0.14 2 4
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 0.02 28 -0.055 1 29
FOXO1 0.028 0.017 -10000 0 -0.07 11 11
T-DHT/AR 0.01 0.053 0.19 3 -0.14 3 6
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 -10000 0 0
CEBPA 0.028 0.018 -10000 0 -0.07 15 15
EHMT2 0.032 0.003 -10000 0 -10000 0 0
cell proliferation -0.021 0.073 0.26 6 -0.24 20 26
NR0B1 0.023 0.029 -10000 0 -0.07 46 46
EGR1 0.029 0.018 -10000 0 -0.069 15 15
RXRs/9cRA 0.058 0.021 -10000 0 -0.044 4 4
AR/RACK1/Src -0.021 0.053 0.17 13 -0.15 1 14
AR/GR 0.003 0.044 0.14 5 -0.18 8 13
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.013 -10000 0 -0.07 7 7
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 -0.029 0.043 0.2 6 -0.15 1 7
SRC -0.024 0.025 0.18 4 -10000 0 4
NR3C1 0.032 0.004 -10000 0 -10000 0 0
KLK3 -0.02 0.061 0.22 1 -0.34 5 6
APPBP2 0.033 0.004 -10000 0 -10000 0 0
TRIM24 0.022 0.016 -10000 0 -0.069 2 2
T-DHT/AR/TIP60 -0.029 0.021 0.042 3 -0.084 18 21
TMPRSS2 0.013 0.068 -10000 0 -0.5 8 8
RXRG 0.032 0.009 -10000 0 -0.021 10 10
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.031 0.007 -10000 0 -10000 0 0
RXRB 0.032 0.002 -10000 0 -10000 0 0
CARM1 0.031 0.007 -10000 0 -10000 0 0
NR2C2 0.032 0.004 -10000 0 -10000 0 0
KLK2 -0.015 0.044 0.17 6 -0.18 11 17
AR -0.003 0.018 0.14 4 -0.16 2 6
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.031 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.011 -10000 0 -0.07 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 -0.022 0.055 0.18 13 -0.16 1 14
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 0.009 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 -0.034 0.079 0.13 4 -0.24 42 46
T-DHT/AR/Hsp90 -0.028 0.037 0.18 5 -0.16 1 6
GSK3B 0.032 0.006 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.023 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 0.036 0.18 5 -0.15 1 6
CREBBP 0.032 0.004 -10000 0 -10000 0 0
SMARCE1 0.032 0.004 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 0.003 0.056 -10000 0 -0.17 22 22
TBX21 -0.019 0.12 -10000 0 -0.41 3 3
B2M 0.032 0.006 -10000 0 -10000 0 0
TYK2 0.02 0.029 -10000 0 -10000 0 0
IL12RB1 0.02 0.03 -10000 0 -10000 0 0
GADD45B 0.003 0.095 -10000 0 -0.41 2 2
IL12RB2 0.02 0.031 -10000 0 -10000 0 0
GADD45G 0.001 0.1 -10000 0 -0.46 4 4
natural killer cell activation -0.002 0.01 -10000 0 -0.028 16 16
RELB 0.031 0.008 -10000 0 -0.07 1 1
RELA 0.032 0.004 -10000 0 -10000 0 0
IL18 0.024 0.029 -10000 0 -0.07 43 43
IL2RA 0.024 0.017 -10000 0 -0.07 6 6
IFNG 0.031 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.006 0.11 -10000 0 -0.39 5 5
HLA-DRB5 -0.001 0.002 -10000 0 -10000 0 0
FASLG -0.017 0.12 0.28 1 -0.42 2 3
NF kappa B2 p52/RelB -0.007 0.13 -10000 0 -0.4 4 4
CD4 0.026 0.021 -10000 0 -0.068 21 21
SOCS1 0.032 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.003 -10000 0 -10000 0 0
CD3D 0.027 0.021 -10000 0 -0.068 22 22
CD3E 0.031 0.008 -10000 0 -0.048 3 3
CD3G 0.03 0.008 -10000 0 -0.05 3 3
IL12Rbeta2/JAK2 0.03 0.041 -10000 0 -10000 0 0
CCL3 -0.018 0.12 -10000 0 -0.39 4 4
CCL4 -0.067 0.23 -10000 0 -0.61 71 71
HLA-A 0 0 -10000 0 -10000 0 0
IL18/IL18R 0.058 0.043 -10000 0 -10000 0 0
NOS2 -0.013 0.11 -10000 0 -0.39 4 4
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.057 -10000 0 -0.18 22 22
IL1R1 -0.02 0.12 -10000 0 -0.42 2 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 0.007 0.031 -10000 0 -0.13 17 17
RAB7A 0.013 0.098 0.31 4 -0.42 2 6
lysosomal transport 0.014 0.096 0.31 4 -0.4 2 6
FOS -0.048 0.16 -10000 0 -0.55 37 37
STAT4 (dimer) -0.015 0.12 0.38 1 -0.45 4 5
STAT5A (dimer) 0 0.13 -10000 0 -0.38 3 3
GZMA -0.024 0.12 0.28 1 -0.4 3 4
GZMB -0.024 0.12 -10000 0 -0.42 2 2
HLX 0.031 0.01 -10000 0 -0.07 3 3
LCK -0.024 0.12 0.28 2 -0.38 10 12
TCR/CD3/MHC II/CD4 0.003 0.028 -10000 0 -0.14 1 1
IL2/IL2R 0.05 0.056 -10000 0 -0.072 6 6
MAPK14 0.014 0.1 -10000 0 -0.47 2 2
CCR5 -0.002 0.11 -10000 0 -0.53 4 4
IL1B 0.018 0.034 -10000 0 -0.072 13 13
STAT6 0.003 0.065 -10000 0 -0.39 7 7
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.015 -10000 0 -0.07 10 10
STAT1 0.029 0.019 -10000 0 -0.07 18 18
NFKB1 0.031 0.01 -10000 0 -0.07 4 4
NFKB2 0.025 0.014 -10000 0 -10000 0 0
IL12B 0.02 0.031 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.07 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 0.012 -10000 0 -0.07 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.11 0.37 1 -0.43 4 5
IL2RG 0.031 0.014 -10000 0 -0.07 9 9
IL12 0.031 0.043 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.07 1 1
CD247 0.03 0.009 -10000 0 -0.049 5 5
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 0.031 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.017 0.12 -10000 0 -0.38 15 15
MAP2K3 0.009 0.1 -10000 0 -0.53 2 2
RIPK2 0.032 0.006 -10000 0 -0.07 1 1
MAP2K6 0.011 0.1 -10000 0 -0.47 1 1
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.003 -10000 0 -10000 0 0
IL18RAP 0.033 0.007 -10000 0 -0.028 2 2
IL12Rbeta1/TYK2 0.032 0.039 -10000 0 -10000 0 0
EOMES 0.004 0.019 0.068 5 -0.07 4 9
STAT1 (dimer) 0 0.11 -10000 0 -0.46 1 1
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 0.007 -10000 0 -0.028 1 1
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 0.42 1 -0.45 2 3
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 0.009 0.065 -10000 0 -10000 0 0
ITCH 0.031 0.012 -10000 0 -0.048 3 3
WWP1 0.009 0.023 0.21 6 -10000 0 6
FYN 0.029 0.011 -10000 0 -0.07 1 1
EGFR 0.012 0.018 -10000 0 -0.07 5 5
PRL 0.031 0.011 -10000 0 -0.07 6 6
neuron projection morphogenesis -0.022 0.05 0.18 22 -10000 0 22
PTPRZ1 0.018 0.022 -10000 0 -0.07 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.052 0.049 0.23 2 -10000 0 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.014 0.019 -10000 0 -10000 0 0
ADAM17 0.029 0.017 -10000 0 -0.061 5 5
ErbB4/ErbB4 0.014 0.015 0.12 6 -0.065 2 8
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.018 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.029 0.026 -10000 0 -10000 0 0
GRIN2B -0.012 0.025 0.2 3 -10000 0 3
ErbB4/ErbB2/betacellulin 0.031 0.027 -10000 0 -10000 0 0
STAT1 0.029 0.019 -10000 0 -0.07 18 18
HBEGF 0.032 0.008 -10000 0 -0.07 2 2
PRLR 0.032 0.005 -10000 0 -10000 0 0
E4ICDs/ETO2 0.03 0.029 -10000 0 -10000 0 0
axon guidance -0.007 0.044 0.21 2 -0.24 1 3
NEDD4 0.027 0.022 -10000 0 -0.067 15 15
Prolactin receptor/Prolactin receptor/Prolactin 0.046 0.014 -10000 0 -0.054 6 6
CBFA2T3 0.031 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.031 0.027 -10000 0 -10000 0 0
MAPK3 -0.017 0.051 0.18 24 -10000 0 24
STAT1 (dimer) 0.029 0.031 -10000 0 -0.16 1 1
MAPK1 -0.016 0.05 0.18 22 -10000 0 22
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 13 -10000 0 13
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 -0.007 0.044 0.21 2 -0.24 1 3
neural crest cell migration 0.012 0.019 -10000 0 -10000 0 0
ERBB2 -0.021 0.012 0.024 13 -10000 0 13
WWOX/E4ICDs 0.03 0.03 -10000 0 -10000 0 0
SHC1 0.024 0.028 -10000 0 -0.07 40 40
ErbB4/EGFR/neuregulin 4 0.012 0.021 -10000 0 -10000 0 0
apoptosis -0.015 0.023 -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 0.03 0.028 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.03 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.064 0.051 -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 -0.016 0.047 0.2 4 -0.23 1 5
ErbB4/EGFR/neuregulin 1 beta 0.012 0.022 -10000 0 -10000 0 0
DLG4 0.032 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.029 -10000 0 -0.054 39 39
E4ICDs/TAB2/NCoR1 0.027 0.027 -10000 0 -10000 0 0
STAT5A (dimer) 0.016 0.073 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.002 0.059 0.21 3 -0.23 1 4
LRIG1 0.027 0.021 -10000 0 -0.07 21 21
EREG 0.03 0.014 -10000 0 -0.07 9 9
BTC 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.007 0.045 0.21 2 -0.24 1 3
ERBB4 0.014 0.015 0.12 6 -0.065 2 8
STAT5B 0.032 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.056 -10000 0 -0.44 6 6
GRB2 0.031 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 0.027 -10000 0 -10000 0 0
WWOX 0.031 0.006 -10000 0 -10000 0 0
cell proliferation -0.002 0.031 0.2 3 -0.22 2 5
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.009 0.08 -10000 0 -0.23 38 38
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
AKT1 0.031 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 0.075 -10000 0 -0.24 43 43
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
YWHAQ 0.032 0.003 -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 -10000 0 0
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 0.007 -10000 0 -0.07 1 1
AS160/CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -10000 0 -10000 0 0
GYS1 -0.006 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.07 6 6
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.043 6 6
AS160/14-3-3 -0.021 0.043 0.1 1 -0.16 15 16
VAMP2 0.029 0.01 -10000 0 -10000 0 0
SLC2A4 -0.03 0.081 -10000 0 -0.26 43 43
STX4 0.032 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN 0.025 0.025 -10000 0 -0.07 31 31
LNPEP 0.032 0.006 -10000 0 -0.07 1 1
YWHAE 0.032 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.011 0.061 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 -0.027 0.041 -10000 0 -0.16 15 15
RXRs/LXRs/DNA/Oxysterols -0.035 0.048 -10000 0 -0.18 17 17
MED1 0.032 0.004 -10000 0 -10000 0 0
mol:9cRA -0.007 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.02 0.035 -10000 0 -0.15 18 18
RXRs/NUR77 0.057 0.031 -10000 0 -10000 0 0
RXRs/PPAR 0.002 0.046 -10000 0 -0.12 54 54
NCOR2 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.004 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.071 0.025 -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 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.06 0.56 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.022 0.033 -10000 0 -0.16 14 14
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 0.004 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.013 0.054 -10000 0 -10000 0 0
NR1H4 0.032 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.019 0.075 -10000 0 -10000 0 0
NR1H2 -0.009 0.027 -10000 0 -10000 0 0
NR1H3 -0.011 0.029 -10000 0 -0.073 4 4
RXRs/VDR/DNA/Vit D3 0.052 0.031 -10000 0 -10000 0 0
NR4A1 0.032 0.005 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.005 0.028 -10000 0 -0.12 17 17
RXRG -0.008 0.029 -10000 0 -0.061 5 5
RXR alpha/CCPG 0.018 0.008 -10000 0 -10000 0 0
RXRA -0.008 0.028 -10000 0 -10000 0 0
RXRB -0.009 0.03 -10000 0 -0.042 1 1
THRB 0.032 0.004 -10000 0 -10000 0 0
PPARG 0.031 0.01 -10000 0 -0.07 4 4
PPARD 0.032 0.002 -10000 0 -10000 0 0
TNF -0.036 0.043 -10000 0 -0.16 16 16
mol:Oxysterols -0.006 0.005 -10000 0 -10000 0 0
cholesterol transport -0.035 0.048 -10000 0 -0.17 17 17
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 0.01 0.033 -10000 0 -0.12 29 29
SREBF1 -0.036 0.043 -10000 0 -0.17 16 16
RXRs/RXRs/DNA/9cRA -0.013 0.054 -10000 0 -10000 0 0
ABCA1 -0.066 0.06 -10000 0 -0.19 18 18
RARs/THRs 0.091 0.027 -10000 0 -10000 0 0
RXRs/FXR 0.058 0.03 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.029 0.023 -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 0.001 0.054 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.05 0.03 -10000 0 -10000 0 0
TBX21 -0.018 0.071 0.32 15 -10000 0 15
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 0.026 0.044 -10000 0 -10000 0 0
IL27 -0.001 0.003 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -0.027 1 1
T-helper cell lineage commitment 0.047 0.083 -10000 0 -0.29 1 1
T-helper 2 cell differentiation 0.001 0.054 -10000 0 -10000 0 0
T cell proliferation during immune response 0.001 0.054 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.054 -10000 0 -10000 0 0
STAT3 0.03 0.015 -10000 0 -0.07 10 10
STAT2 0.031 0.006 -10000 0 -10000 0 0
STAT1 0.029 0.019 -10000 0 -0.07 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 -0.02 0.066 0.32 14 -10000 0 14
IL27/IL27R/JAK2/TYK2 -0.001 0.055 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.001 0.054 -10000 0 -10000 0 0
STAT1 (dimer) 0.056 0.036 -10000 0 -10000 0 0
JAK2 0.029 0.011 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.023 0.07 0.23 10 -10000 0 10
T cell proliferation -0.003 0.033 -10000 0 -0.18 2 2
IL12/IL12R/TYK2/JAK2 0.032 0.086 -10000 0 -0.67 7 7
IL17A 0.046 0.083 -10000 0 -0.29 1 1
mast cell activation 0.001 0.054 -10000 0 -10000 0 0
IFNG 0.005 0.022 0.072 1 -0.084 12 13
T cell differentiation -0.001 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.072 0.23 11 -10000 0 11
STAT5A (dimer) 0.023 0.073 0.23 12 -10000 0 12
STAT4 (dimer) 0.014 0.049 0.23 3 -10000 0 3
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 0.039 -10000 0 -10000 0 0
GATA3 0 0.072 0.64 6 -10000 0 6
IL18 -0.014 0.009 -10000 0 -0.043 43 43
positive regulation of mast cell cytokine production 0.021 0.072 0.23 11 -10000 0 11
IL27/EBI3 0.023 0.009 -10000 0 -0.043 3 3
IL27RA 0.004 0.032 0.26 7 -10000 0 7
IL6 0.017 0.028 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.07 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 0.005 -10000 0 -0.043 13 13
EBI3 0.031 0.011 -10000 0 -0.07 3 3
TNF -0.011 0.002 -10000 0 -0.043 2 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.018 0.068 -9999 0 -0.28 1 1
CLOCK 0.021 0.024 -9999 0 -0.031 5 5
TIMELESS/CRY2 0.009 0.056 -9999 0 -0.27 1 1
DEC1/BMAL1 0.045 0.011 -9999 0 -10000 0 0
ATR 0.032 0.005 -9999 0 -10000 0 0
NR1D1 -0.003 0.031 -9999 0 -0.24 1 1
ARNTL 0.022 0.024 -9999 0 -0.035 1 1
TIMELESS -0.011 0.048 -9999 0 -0.28 1 1
NPAS2 0.022 0.025 -9999 0 -0.037 10 10
CRY2 0.032 0.006 -9999 0 -10000 0 0
mol:CO 0.001 0.012 -9999 0 -10000 0 0
CHEK1 0.02 0.033 -9999 0 -0.07 59 59
mol:HEME -0.001 0.012 -9999 0 -10000 0 0
PER1 0.031 0.009 -9999 0 -0.07 3 3
BMAL/CLOCK/NPAS2 0.045 0.048 -9999 0 -10000 0 0
BMAL1/CLOCK 0.009 0.045 -9999 0 -0.35 1 1
S phase of mitotic cell cycle 0.018 0.068 -9999 0 -0.28 1 1
TIMELESS/CHEK1/ATR 0.019 0.068 -9999 0 -0.28 1 1
mol:NADPH -0.001 0.012 -9999 0 -10000 0 0
PER1/TIMELESS 0.007 0.057 -9999 0 -0.29 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.031 0.006 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.025 0.013 -9999 0 -10000 0 0
ITGB7 0.032 0.008 -9999 0 -0.07 2 2
ITGA4 0.031 0.01 -9999 0 -0.07 5 5
alpha4/beta7 Integrin 0.046 0.013 -9999 0 -0.066 5 5
alpha4/beta1 Integrin 0.037 0.022 -9999 0 -0.054 4 4
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.034 0.015 -9999 0 -0.022 25 25
MAPK9 0.006 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.002 -9999 0 -0.043 1 1
GNB1/GNG2 0.021 0.005 -9999 0 0 31 31
GNB1 0.031 0.008 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.006 0.002 -9999 0 -0.042 1 1
Gs family/GTP 0.02 0.005 -9999 0 -0.016 7 7
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 0 7 7
GNAL 0.032 0.005 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.032 0.006 -9999 0 -0.07 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.005 0.003 -9999 0 -10000 0 0
MAPK11 0.006 0.002 -9999 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.023 0.15 -10000 0 -0.63 13 13
IL23A 0.006 0.096 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.13 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.004 0.12 -10000 0 -10000 0 0
ITGA3 0.002 0.11 -10000 0 -10000 0 0
IL17F -0.012 0.088 -10000 0 -10000 0 0
IL12B 0.026 0.031 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.13 -10000 0 -10000 0 0
CD4 0.004 0.12 0.39 1 -10000 0 1
IL23 0.022 0.1 -10000 0 -10000 0 0
IL23R 0.003 0.032 0.092 2 -10000 0 2
IL1B 0.005 0.1 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.005 0.12 -10000 0 -10000 0 0
TYK2 0.022 0.028 -10000 0 -10000 0 0
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.015 -10000 0 -0.07 10 10
IL18RAP 0.033 0.003 -10000 0 -0.027 1 1
IL12RB1 0.022 0.028 -10000 0 -10000 0 0
PIK3CA 0.028 0.019 -10000 0 -0.07 17 17
IL12Rbeta1/TYK2 0.04 0.03 -10000 0 -10000 0 0
IL23R/JAK2 0.026 0.048 0.15 1 -10000 0 1
positive regulation of chronic inflammatory response 0.004 0.12 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK2 0.024 0.031 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.01 -10000 0 -0.073 4 4
RELA 0.033 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.022 0.1 -10000 0 -10000 0 0
ALOX12B 0 0.12 -10000 0 -10000 0 0
CXCL1 -0.002 0.12 -10000 0 -10000 0 0
T cell proliferation 0.004 0.12 -10000 0 -10000 0 0
NFKBIA 0.031 0.009 -10000 0 -0.074 1 1
IL17A 0.008 0.084 0.26 1 -10000 0 1
PI3K 0.021 0.12 -10000 0 -10000 0 0
IFNG 0.005 0.016 0.072 2 -0.068 15 17
STAT3 (dimer) 0.03 0.13 -10000 0 -10000 0 0
IL18R1 0.033 0.003 -10000 0 -0.027 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.009 0.094 0.27 2 -10000 0 2
IL18/IL18R 0.057 0.034 -10000 0 -0.052 8 8
macrophage activation -0.001 0.007 -10000 0 -10000 0 0
TNF 0.005 0.1 -10000 0 -10000 0 0
STAT3/STAT4 -0.001 0.11 -10000 0 -10000 0 0
STAT4 (dimer) -0.002 0.1 -10000 0 -10000 0 0
IL18 0.024 0.028 -10000 0 -0.068 44 44
IL19 0.005 0.12 -10000 0 -10000 0 0
STAT5A (dimer) 0.013 0.13 -10000 0 -10000 0 0
STAT1 0.029 0.019 -10000 0 -0.07 18 18
SOCS3 0.032 0.004 -10000 0 -10000 0 0
CXCL9 -0.005 0.12 -10000 0 -10000 0 0
MPO 0.002 0.12 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.004 0.12 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.004 0.12 -10000 0 -10000 0 0
IL6 0.055 0.14 0.4 10 -10000 0 10
STAT5A 0.032 0.006 -10000 0 -0.07 1 1
IL2 0.033 0.006 -10000 0 -0.031 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0 0.003 -10000 0 -10000 0 0
CD3E 0.001 0.12 -10000 0 -10000 0 0
keratinocyte proliferation 0.004 0.12 -10000 0 -10000 0 0
NOS2 0.003 0.11 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.032 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.023 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.042 0.009 -10000 0 -10000 0 0
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 0.06 0.025 -10000 0 -10000 0 0
mol:Na + 0.037 0.017 -10000 0 -10000 0 0
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 -0.07 1 1
SAG 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.035 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 0.019 -10000 0 -10000 0 0
GUCY2D 0.032 0.005 -10000 0 -10000 0 0
GNGT1 0.022 0.015 -10000 0 -10000 0 0
GUCY2F 0.032 0.002 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.028 0.005 -10000 0 -10000 0 0
mol:11-cis-retinal 0.031 0.007 -10000 0 -0.07 1 1
mol:cGMP 0.024 0.009 -10000 0 -0.03 13 13
GNB1 0.031 0.008 -10000 0 -10000 0 0
Rhodopsin 0.045 0.012 -10000 0 -0.054 1 1
SLC24A1 0.032 0.004 -10000 0 -10000 0 0
CNGA1 0.032 0.003 -10000 0 -10000 0 0
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 0.01 -10000 0 -0.024 12 12
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.007 0.027 -10000 0 -0.11 22 22
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 0.038 0.032 -10000 0 -0.039 2 2
PDE6B 0.032 0.003 -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 0.008 -10000 0 -0.024 6 6
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.032 0.004 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.036 0.022 -9999 0 -0.054 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 0.025 0.015 -9999 0 -0.07 1 1
NF kappa B2 p100/RelB 0.056 0.065 -9999 0 -10000 0 0
NFKB1 0.031 0.01 -9999 0 -0.07 4 4
MAP3K14 0.032 0.007 -9999 0 -0.07 2 2
NF kappa B1 p50/RelB 0.044 0.015 -9999 0 -0.054 5 5
RELB 0.031 0.008 -9999 0 -0.07 1 1
NFKB2 0.025 0.014 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.032 0.02 -9999 0 -0.043 1 1
regulation of B cell activation 0.032 0.019 -9999 0 -0.043 1 1
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 0.011 -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 0.008 -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 0.008 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.042 0.008 -10000 0 -9999 0 0
EPHA5 0.032 0.005 -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 508 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.14 0.018 -0.37 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 -0.07 0.033
131_RELN/VLDLR 0 0 0.084 0
30_TGFB1/TGF beta receptor Type II 0 0.032 0 -0.07
84_STAT5B 0.04 0.031 -0.32 0.031
84_STAT5A 0.04 0.031 -0.32 0.031
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/22215716/GDAC_MergeDataFiles_12184161/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/GDAC_Gistic2/GBM-TP/22506698/GDAC_Gistic2Report_22535714/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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