Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 32 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Glypican 2 network 212
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 90
LPA receptor mediated events 78
Endothelins 74
amb2 Integrin signaling 69
TCGA08_retinoblastoma 65
BARD1 signaling events 60
TCGA08_p53 60
Ceramide signaling pathway 57
HIF-2-alpha transcription factor network 57
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • 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.

Pathway.Name 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 212 849 4 -0.022 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 90 6173 68 -0.24 0.065 1000 -1000 -0.039 -1000
LPA receptor mediated events 78 7985 102 -0.038 0.046 1000 -1000 -0.055 -1000
Endothelins 74 7109 96 -0.47 0.032 1000 -1000 -0.035 -1000
amb2 Integrin signaling 69 5702 82 -0.043 0.045 1000 -1000 -0.011 -1000
TCGA08_retinoblastoma 65 525 8 -0.073 0.081 1000 -1000 -0.003 -1000
BARD1 signaling events 60 3469 57 -0.043 0.062 1000 -1000 -0.047 -1000
TCGA08_p53 60 425 7 -0.007 0.029 1000 -1000 -0.012 -1000
Ceramide signaling pathway 57 4399 76 -0.092 0.065 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 57 2476 43 -0.075 0.043 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 52 158 3 -0.016 0.032 1000 -1000 -0.021 -1000
EPO signaling pathway 50 2788 55 -0.005 0.061 1000 -1000 -0.02 -1000
Effects of Botulinum toxin 50 1320 26 0 0.053 1000 -1000 -0.011 -1000
Arf6 signaling events 44 2757 62 0 0.081 1000 -1000 -0.009 -1000
Osteopontin-mediated events 41 1560 38 -0.083 0.044 1000 -1000 -0.017 -1000
HIF-1-alpha transcription factor network 41 3141 76 -0.095 0.035 1000 -1000 -0.03 -1000
Aurora B signaling 41 2764 67 -0.039 0.049 1000 -1000 -0.02 -1000
Wnt signaling 39 279 7 0 0.032 1000 -1000 0.002 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 37 2941 78 -0.037 0.038 1000 -1000 -0.04 -1000
VEGFR1 specific signals 36 2043 56 -0.037 0.052 1000 -1000 -0.023 -1000
Ras signaling in the CD4+ TCR pathway 36 614 17 -0.003 0.031 1000 -1000 -0.013 -1000
Syndecan-4-mediated signaling events 35 2395 67 -0.056 0.032 1000 -1000 -0.028 -1000
S1P1 pathway 34 1227 36 -0.055 0.035 1000 -1000 -0.016 -1000
Signaling events mediated by VEGFR1 and VEGFR2 34 4314 125 -0.047 0.044 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 33 1484 44 -0.04 0.049 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 32 2382 74 -0.055 0.054 1000 -1000 -0.032 -1000
Syndecan-1-mediated signaling events 32 1092 34 -0.035 0.032 1000 -1000 -0.018 -1000
PLK1 signaling events 32 2756 85 -0.039 0.056 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 29 1363 47 -0.15 0.045 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 29 988 33 -0.059 0.063 1000 -1000 -0.008 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 28 1261 45 -0.06 0.054 1000 -1000 -0.026 -1000
Signaling mediated by p38-alpha and p38-beta 27 1228 44 -0.037 0.059 1000 -1000 -0.016 -1000
Regulation of nuclear SMAD2/3 signaling 26 3579 136 -0.21 0.059 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 26 456 17 -0.12 0.057 1000 -1000 -0.015 -1000
Fc-epsilon receptor I signaling in mast cells 26 2543 97 -0.1 0.056 1000 -1000 -0.043 -1000
IL1-mediated signaling events 26 1658 62 -0.052 0.056 1000 -1000 -0.035 -1000
Signaling events regulated by Ret tyrosine kinase 26 2181 82 -0.043 0.048 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 26 690 26 -0.044 0.13 1000 -1000 -0.002 -1000
Paxillin-independent events mediated by a4b1 and a4b7 25 933 37 -0.048 0.074 1000 -1000 -0.019 -1000
Integrins in angiogenesis 25 2129 84 -0.048 0.079 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 24 1282 52 -0.015 0.066 1000 -1000 -0.021 -1000
Glypican 1 network 24 1169 48 -0.031 0.06 1000 -1000 -0.027 -1000
Canonical Wnt signaling pathway 24 1233 51 -0.034 0.11 1000 -1000 -0.018 -1000
Arf6 trafficking events 24 1740 71 -0.034 0.041 1000 -1000 -0.03 -1000
Plasma membrane estrogen receptor signaling 24 2143 86 -0.43 0.053 1000 -1000 -0.042 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 23 541 23 -0.021 0.037 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 23 1008 43 -0.012 0.075 1000 -1000 -0.014 -1000
Visual signal transduction: Cones 21 804 38 -0.02 0.053 1000 -1000 -0.012 -1000
Signaling events mediated by PTP1B 21 1665 76 -0.026 0.06 1000 -1000 -0.022 -1000
BMP receptor signaling 21 1747 81 -0.03 0.057 1000 -1000 -0.012 -1000
E-cadherin signaling in the nascent adherens junction 21 1609 76 -0.036 0.082 1000 -1000 -0.029 -1000
S1P3 pathway 21 885 42 -0.031 0.034 1000 -1000 -0.012 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 20 1725 85 -0.023 0.12 1000 -1000 -0.031 -1000
Aurora A signaling 20 1225 60 -0.034 0.065 1000 -1000 -0.02 -1000
EGFR-dependent Endothelin signaling events 20 426 21 -0.012 0.032 1000 -1000 -0.024 -1000
Noncanonical Wnt signaling pathway 19 503 26 -0.022 0.032 1000 -1000 -0.022 -1000
Arf6 downstream pathway 19 847 43 -0.024 0.047 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 19 2024 104 -0.041 0.053 1000 -1000 -0.034 -1000
Retinoic acid receptors-mediated signaling 19 1147 58 -0.013 0.057 1000 -1000 -0.014 -1000
Stabilization and expansion of the E-cadherin adherens junction 19 1434 74 -0.22 0.069 1000 -1000 -0.04 -1000
BCR signaling pathway 19 1901 99 -0.048 0.051 1000 -1000 -0.035 -1000
FOXM1 transcription factor network 19 980 51 -0.19 0.032 1000 -1000 -0.14 -1000
FOXA2 and FOXA3 transcription factor networks 18 840 46 0 0.09 1000 -1000 -0.059 -1000
mTOR signaling pathway 18 998 53 -0.033 0.05 1000 -1000 -0.02 -1000
Class I PI3K signaling events mediated by Akt 18 1234 68 -0.026 0.06 1000 -1000 -0.021 -1000
TRAIL signaling pathway 18 907 48 -0.034 0.072 1000 -1000 -0.021 -1000
ceramide signaling pathway 18 903 49 -0.016 0.045 1000 -1000 -0.018 -1000
Coregulation of Androgen receptor activity 17 1299 76 -0.047 0.059 1000 -1000 -0.018 -1000
Nectin adhesion pathway 17 1108 63 -0.015 0.075 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class III 17 698 40 -0.037 0.041 1000 -1000 -0.044 -1000
S1P5 pathway 17 292 17 -0.033 0.033 1000 -1000 -0.006 -1000
TCR signaling in naïve CD8+ T cells 17 1626 93 -0.33 0.38 1000 -1000 -0.027 -1000
EPHB forward signaling 17 1468 85 -0.05 0.078 1000 -1000 -0.039 -1000
Regulation of Telomerase 17 1756 102 -0.025 0.075 1000 -1000 -0.031 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 16 897 54 -0.02 0.047 1000 -1000 -0.023 -1000
IL2 signaling events mediated by PI3K 16 929 58 -0.18 0.042 1000 -1000 -0.023 -1000
Class I PI3K signaling events 16 1227 73 -0.025 0.057 1000 -1000 -0.017 -1000
PDGFR-beta signaling pathway 16 1600 97 -0.043 0.066 1000 -1000 -0.036 -1000
E-cadherin signaling events 16 84 5 0.029 0.057 1000 -1000 0.028 -1000
Syndecan-2-mediated signaling events 15 1064 69 -0.021 0.054 1000 -1000 -0.019 -1000
Syndecan-3-mediated signaling events 15 550 35 -0.008 0.072 1000 -1000 -0.017 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 408 27 -0.029 0.07 1000 -1000 -0.022 -1000
Arf1 pathway 15 824 54 -0.063 0.042 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 14 866 61 -0.005 0.071 1000 -1000 -0.028 -1000
p75(NTR)-mediated signaling 14 1861 125 -0.049 0.072 1000 -1000 -0.037 -1000
Paxillin-dependent events mediated by a4b1 14 533 36 -0.042 0.046 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 13 508 39 -0.028 0.065 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 13 1413 105 -0.035 0.042 1000 -1000 -0.03 -1000
Hedgehog signaling events mediated by Gli proteins 13 896 65 -0.005 0.053 1000 -1000 -0.014 -1000
IFN-gamma pathway 13 948 68 -0.056 0.063 1000 -1000 -0.029 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 13 1082 83 -0.046 0.061 1000 -1000 -0.015 -1000
FoxO family signaling 13 842 64 -0.093 0.043 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 13 293 22 -0.018 0.033 1000 -1000 -0.019 -1000
Neurotrophic factor-mediated Trk receptor signaling 13 1628 120 -0.038 0.084 1000 -1000 -0.031 -1000
Signaling events mediated by PRL 13 453 34 -0.026 0.047 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 12 828 65 -0.034 0.039 1000 -1000 -0.047 -1000
Cellular roles of Anthrax toxin 12 471 39 -0.028 0.032 1000 -1000 -0.015 -1000
IL6-mediated signaling events 12 963 75 -0.021 0.071 1000 -1000 -0.063 -1000
Angiopoietin receptor Tie2-mediated signaling 12 1123 88 -0.063 0.037 1000 -1000 -0.041 -1000
S1P4 pathway 12 315 25 -0.033 0.039 1000 -1000 -0.009 -1000
Glucocorticoid receptor regulatory network 11 1274 114 -0.073 0.12 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 11 617 54 -0.019 0.043 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 10 323 31 -0.022 0.039 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 10 560 52 -0.065 0.055 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 9 112 12 -0.018 0.009 1000 -1000 -0.016 -1000
Nephrin/Neph1 signaling in the kidney podocyte 9 331 34 -0.049 0.091 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class II 9 698 75 -0.032 0.077 1000 -1000 -0.022 -1000
IL12-mediated signaling events 9 851 87 -0.067 0.058 1000 -1000 -0.06 -1000
Aurora C signaling 8 61 7 0 0.05 1000 -1000 0 -1000
IL4-mediated signaling events 8 781 91 -0.17 0.069 1000 -1000 -0.14 -1000
Sphingosine 1-phosphate (S1P) pathway 7 222 28 -0.022 0.034 1000 -1000 -0.021 -1000
Reelin signaling pathway 7 422 56 -0.016 0.061 1000 -1000 -0.016 -1000
Calcium signaling in the CD4+ TCR pathway 7 222 31 -0.04 0.034 1000 -1000 -0.015 -1000
IGF1 pathway 7 399 57 -0.037 0.062 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 7 503 70 -0.036 0.058 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 6 200 32 -0.03 0.042 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 6 298 48 -0.011 0.05 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 6 90 15 -0.026 0.032 1000 -1000 -0.023 -1000
Insulin Pathway 6 488 74 -0.041 0.078 1000 -1000 -0.025 -1000
p38 MAPK signaling pathway 6 294 44 0 0.052 1000 -1000 -0.008 -1000
ErbB4 signaling events 5 377 69 -0.027 0.066 1000 -1000 -0.021 -1000
RXR and RAR heterodimerization with other nuclear receptor 4 246 52 -0.059 0.091 1000 -1000 -0.006 -1000
IL27-mediated signaling events 4 209 51 -0.022 0.056 1000 -1000 -0.03 -1000
Circadian rhythm pathway 3 74 22 -0.01 0.046 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 3 16 5 0.025 0.046 1000 -1000 0.027 -1000
IL23-mediated signaling events 3 183 60 -0.02 0.057 1000 -1000 -0.096 -1000
Rapid glucocorticoid signaling 3 60 20 -0.011 0.032 1000 -1000 -0.011 -1000
Visual signal transduction: Rods 2 116 52 -0.034 0.074 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 1 18 13 0 0.054 1000 -1000 0 -1000
Ephrin A reverse signaling 0 3 7 -0.02 0.043 1000 -1000 -0.013 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.032 0.032 1000 -1000 -0.028 -1000
Total 3059 167957 7203 -6.7 7.5 131000 -131000 -3.3 -131000
Glypican 2 network

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.022 0.046 -9999 0 -0.063 283 283
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.012 0.03 -9999 0 -0.039 283 283
neuron projection morphogenesis -0.012 0.03 -9999 0 -0.039 283 283
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.033 0.007 -10000 0 -0.028 6 6
NFATC2 -0.029 0.096 -10000 0 -0.14 199 199
NFATC3 -0.043 0.11 -10000 0 -0.16 215 215
CD40LG -0.14 0.17 0.26 1 -0.33 205 206
ITCH -0.015 0.009 -10000 0 -10000 0 0
CBLB -0.016 0.008 -10000 0 -0.058 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.13 0.17 -10000 0 -0.38 100 100
JUNB 0.03 0.013 -10000 0 -0.063 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.019 -10000 0 -0.051 14 14
T cell anergy -0.008 0.027 0.17 2 -0.1 5 7
TLE4 -0.021 0.059 0.097 1 -0.1 101 102
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.33 225 225
AP-1/NFAT1-c-4 -0.12 0.22 -10000 0 -0.35 208 208
IKZF1 -0.014 0.051 0.097 1 -0.1 61 62
T-helper 2 cell differentiation -0.13 0.17 -10000 0 -0.47 71 71
AP-1/NFAT1 -0.02 0.071 -10000 0 -0.11 20 20
CALM1 0.03 0.017 -10000 0 -0.045 14 14
EGR2 -0.092 0.18 -10000 0 -0.34 166 166
EGR3 0.005 0.12 -10000 0 -0.61 18 18
NFAT1/FOXP3 -0.006 0.08 -10000 0 -0.11 87 87
EGR1 0.029 0.017 -10000 0 -0.063 15 15
JUN 0.03 0.012 -10000 0 -0.032 4 4
EGR4 0.033 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.006 -10000 0 -10000 0 0
GBP3 -0.02 0.053 0.088 1 -0.082 199 200
FOSL1 0.03 0.015 -10000 0 -0.063 12 12
NFAT1-c-4/MAF/IRF4 -0.099 0.22 -10000 0 -0.33 227 227
DGKA -0.021 0.06 0.097 1 -0.098 116 117
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.35 225 225
CTLA4 -0.023 0.054 0.082 1 -0.092 87 88
NFAT1-c-4 (dimer)/EGR1 -0.11 0.22 -10000 0 -0.34 228 228
NFAT1-c-4 (dimer)/EGR4 -0.11 0.22 -10000 0 -0.35 230 230
FOS 0.006 0.041 -10000 0 -0.063 126 126
IFNG -0.05 0.094 -10000 0 -0.26 34 34
T cell activation -0.079 0.11 -10000 0 -10000 0 0
MAF 0.032 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.17 0.32 145 -10000 0 145
TNF -0.13 0.19 -10000 0 -0.33 231 231
FASLG -0.24 0.29 -10000 0 -0.53 240 240
TBX21 0.034 0.005 -10000 0 -0.041 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.015 -10000 0 -10000 0 0
PTPN1 -0.021 0.059 0.097 1 -0.098 117 118
NFAT1-c-4/ICER1 -0.12 0.21 -10000 0 -0.35 231 231
GATA3 0.025 0.016 -10000 0 -0.062 2 2
T-helper 1 cell differentiation -0.05 0.093 -10000 0 -0.29 22 22
IL2RA -0.12 0.18 -10000 0 -0.38 109 109
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.064 0.097 1 -0.12 95 96
E2F1 -0.019 0.04 -10000 0 -0.055 170 170
PPARG 0.031 0.009 -10000 0 -0.063 4 4
SLC3A2 -0.022 0.061 0.097 1 -0.1 104 105
IRF4 0.032 0.006 -10000 0 -0.062 1 1
PTGS2 -0.14 0.17 -10000 0 -0.33 204 204
CSF2 -0.14 0.17 -10000 0 -0.33 205 205
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.34 223 223
IL4 -0.13 0.18 -10000 0 -0.48 72 72
IL5 -0.14 0.17 -10000 0 -0.33 203 203
IL2 -0.08 0.11 -10000 0 -10000 0 0
IL3 -0.009 0.072 -10000 0 -0.54 6 6
RNF128 -0.017 0.012 -10000 0 -0.079 14 14
NFATC1 -0.052 0.16 -10000 0 -0.33 123 123
CDK4 0.011 0.11 0.27 66 -10000 0 66
PTPRK -0.02 0.059 0.097 1 -0.095 139 140
IL8 -0.15 0.17 0.26 1 -0.33 206 207
POU2F1 0.035 0.005 -10000 0 -10000 0 0
LPA receptor mediated events

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.006 0.029 -10000 0 -0.034 258 258
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.062 0.22 6 -0.18 28 34
AP1 -0.017 0.03 -10000 0 -0.04 295 295
mol:PIP3 -0.013 0.018 -10000 0 -0.056 13 13
AKT1 0.008 0.071 0.2 20 -0.24 7 27
PTK2B -0.009 0.027 0.11 2 -0.2 6 8
RHOA 0.011 0.061 0.14 13 -0.3 10 23
PIK3CB 0.031 0.006 -10000 0 -0.031 2 2
mol:Ca2+ -0.012 0.022 0.2 3 -0.12 7 10
MAGI3 0 0 -10000 0 -0.004 3 3
RELA 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.015 0.026 -10000 0 -0.037 273 273
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.039 0.17 12 -0.19 6 18
NF kappa B1 p50/RelA -0.038 0.02 -10000 0 -0.11 11 11
endothelial cell migration -0.025 0.041 -10000 0 -0.066 246 246
ADCY4 -0.001 0.007 -10000 0 -0.092 1 1
ADCY5 -0.001 0.007 -10000 0 -0.092 1 1
ADCY6 -0.001 0.01 0.086 2 -0.1 2 4
ADCY7 -0.001 0.01 0.086 3 -0.079 2 5
ADCY1 -0.001 0.007 -10000 0 -0.089 1 1
ADCY2 -0.001 0.01 0.086 3 -0.079 2 5
ADCY3 -0.001 0.007 -10000 0 -0.092 1 1
ADCY8 -0.001 0.009 0.086 2 -0.089 1 3
ADCY9 -0.001 0.01 0.086 3 -0.079 2 5
GSK3B -0.012 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.002 0.014 0.077 3 -0.11 5 8
GNG2 0 0.001 0.002 1 -0.004 28 29
TRIP6 -0.008 0.025 -10000 0 -0.041 167 167
GNAO1 0 0.008 -10000 0 -0.039 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.022 0.052 0.19 8 -0.18 28 36
GAB1 0.032 0.008 -10000 0 -0.063 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.17 -10000 0 -0.71 25 25
JUN 0.032 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.002 0.022 -10000 0 -0.021 243 243
TIAM1 -0.003 0.2 -10000 0 -0.84 27 27
PIK3R1 0.03 0.01 -10000 0 -0.032 1 1
mol:IP3 -0.012 0.016 0.17 2 -0.12 2 4
PLCB3 -0.019 0.018 0.18 4 -10000 0 4
FOS 0.007 0.04 -10000 0 -0.063 120 120
positive regulation of mitosis -0.002 0.014 0.077 3 -0.11 5 8
LPA/LPA1-2-3 -0.011 0.015 -10000 0 -0.027 250 250
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.004 0.023 0.13 1 -0.14 1 2
GNAZ -0.01 0.024 -10000 0 -0.039 203 203
EGFR/PI3K-beta/Gab1 -0.013 0.019 0.023 2 -0.063 7 9
positive regulation of dendritic cell cytokine production -0.011 0.015 -10000 0 -0.027 250 250
LPA/LPA2/MAGI-3 -0.005 0.007 -10000 0 -0.012 250 250
ARHGEF1 0.026 0.093 0.17 140 -10000 0 140
GNAI2 -0.013 0.026 -10000 0 -0.039 242 242
GNAI3 -0.016 0.027 -10000 0 -0.041 271 271
GNAI1 -0.008 0.021 -10000 0 -0.039 155 155
LPA/LPA3 -0.007 0.008 -10000 0 -0.015 248 248
LPA/LPA2 -0.007 0.008 -10000 0 -0.015 249 249
LPA/LPA1 -0.016 0.021 -10000 0 -0.038 248 248
HB-EGF/EGFR -0.001 0.024 -10000 0 -0.048 83 83
HBEGF -0.03 0.016 0 44 -0.05 165 209
mol:DAG -0.012 0.016 0.17 2 -0.12 2 4
cAMP biosynthetic process 0.046 0.063 0.14 117 -10000 0 117
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
SRC 0.031 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
LYN -0.017 0.039 0.19 8 -0.16 1 9
GNAQ -0.001 0.013 -10000 0 -0.015 235 235
LPAR2 0 0.001 -10000 0 -0.004 3 3
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.012 0.013 -10000 0 -0.025 247 247
IL8 -0.038 0.054 0.2 2 -0.29 4 6
PTK2 -0.006 0.025 -10000 0 -0.032 242 242
Rac1/GDP 0.017 0.011 -10000 0 0 151 151
CASP3 -0.015 0.026 -10000 0 -0.037 273 273
EGFR 0.012 0.018 -10000 0 -0.063 6 6
PLCG1 0.002 0.008 -10000 0 -0.03 8 8
PLD2 -0.006 0.025 -10000 0 -0.032 244 244
G12/G13 0.003 0.037 -10000 0 -0.042 174 174
PI3K-beta -0.011 0.041 -10000 0 -0.21 12 12
cell migration -0.002 0.048 -10000 0 -0.22 19 19
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
PXN 0.004 0.024 0.13 1 -0.14 1 2
HRAS/GTP -0.001 0.012 0.077 3 -0.1 4 7
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
PRKCE 0.032 0.005 -10000 0 -0.027 3 3
PRKCD -0.013 0.037 0.21 10 -0.13 1 11
Gi(beta/gamma) 0 0.014 0.078 4 -0.14 3 7
mol:LPA -0.012 0.013 -10000 0 -0.025 247 247
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.024 -10000 0 -0.12 4 4
MAPKKK cascade -0.002 0.014 0.077 3 -0.11 5 8
contractile ring contraction involved in cytokinesis 0.013 0.062 0.14 17 -0.29 10 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.001 0.013 -10000 0 -0.015 238 238
GNA15 -0.002 0.014 -10000 0 -0.016 234 234
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.001 0.013 -10000 0 -0.015 234 234
Rac1/GTP 0.002 0.18 -10000 0 -0.74 25 25
MMP2 -0.025 0.041 -10000 0 -0.066 246 246
Endothelins

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
AKT1 -0.066 0.034 -10000 0 -0.11 90 90
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.17 0.36 1 -0.41 94 95
EDN1 -0.036 0.043 -10000 0 -0.06 368 368
EDN3 0.029 0.012 -10000 0 -0.063 3 3
EDN2 0.032 0.006 -10000 0 -0.063 1 1
HRAS/GDP -0.028 0.081 0.23 15 -0.28 17 32
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.014 0.04 -10000 0 -0.18 10 10
ADCY4 -0.053 0.024 0.011 1 -0.073 258 259
ADCY5 -0.053 0.024 0.011 1 -0.073 258 259
ADCY6 -0.057 0.033 0.16 3 -10000 0 3
ADCY7 -0.057 0.036 0.16 4 -10000 0 4
ADCY1 -0.043 0.037 0.15 2 -10000 0 2
ADCY2 -0.056 0.036 0.16 4 -10000 0 4
ADCY3 -0.053 0.024 0.011 1 -0.073 258 259
ADCY8 -0.056 0.036 0.16 4 -10000 0 4
ADCY9 -0.057 0.035 0.16 4 -10000 0 4
arachidonic acid secretion -0.048 0.094 0.28 10 -0.32 20 30
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.033 -10000 0 -0.15 15 15
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.032 0.054 -10000 0 -0.085 182 182
ETA receptor/Endothelin-1/Gs/GTP -0.038 0.057 -10000 0 -0.079 235 235
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.088 0.041 -10000 0 -0.12 229 229
EDNRB -0.008 0.036 -10000 0 -0.041 256 256
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.063 0.035 -10000 0 -0.11 84 84
CYSLTR1 -0.06 0.03 0.04 1 -0.077 348 349
SLC9A1 -0.03 0.03 -10000 0 -0.054 258 258
mol:GDP -0.031 0.079 0.22 15 -0.28 17 32
SLC9A3 -0.074 0.19 -10000 0 -0.61 43 43
RAF1 -0.031 0.082 0.25 13 -0.3 15 28
JUN -0.096 0.19 0.32 2 -0.45 99 101
JAK2 -0.063 0.036 -10000 0 -0.11 84 84
mol:IP3 -0.014 0.046 -10000 0 -0.23 12 12
ETA receptor/Endothelin-1 -0.056 0.067 -10000 0 -0.095 356 356
PLCB1 0.03 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.006 -10000 0 -0.029 1 1
ETA receptor/Endothelin-3 -0.027 0.046 -10000 0 -0.057 339 339
FOS -0.039 0.097 0.32 10 -0.32 16 26
Gai/GDP -0.47 0.17 -10000 0 -0.52 441 441
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.044 0.05 -10000 0 -0.2 16 16
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.016 0.046 -10000 0 -0.23 12 12
GNAQ 0.031 0.007 -10000 0 -0.027 2 2
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
Gs family/GDP -0.03 0.074 0.21 14 -0.27 15 29
ETA receptor/Endothelin-1/Gq/GTP -0.021 0.036 -10000 0 -0.13 16 16
MAPK14 -0.011 0.035 -10000 0 -0.22 6 6
TRPC6 -0.091 0.18 0.36 1 -0.43 94 95
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.038 -10000 0 -0.16 16 16
ETB receptor/Endothelin-2 0.026 0.031 -10000 0 -0.044 63 63
ETB receptor/Endothelin-3 0.024 0.03 -10000 0 -0.045 59 59
ETB receptor/Endothelin-1 -0.031 0.048 -10000 0 -0.062 346 346
MAPK3 -0.034 0.096 0.31 12 -0.33 13 25
MAPK1 -0.042 0.1 0.31 11 -0.34 19 30
Rac1/GDP -0.026 0.06 0.2 4 -0.28 11 15
cAMP biosynthetic process -0.019 0.043 0.18 7 -0.14 1 8
MAPK8 -0.11 0.22 0.37 1 -0.5 111 112
SRC 0.031 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.024 -10000 0 -0.13 17 17
p130Cas/CRK/Src/PYK2 -0.026 0.084 0.26 15 -0.31 13 28
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.026 0.06 0.2 4 -0.28 11 15
COL1A2 -0.054 0.062 -10000 0 -0.13 191 191
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.028 0.047 -10000 0 -0.057 356 356
mol:DAG -0.015 0.046 -10000 0 -0.23 12 12
MAP2K2 -0.035 0.098 0.33 16 -0.31 15 31
MAP2K1 -0.04 0.083 0.26 10 -0.32 14 24
EDNRA -0.047 0.049 -10000 0 -0.074 362 362
positive regulation of muscle contraction -0.009 0.095 0.15 122 -0.12 4 126
Gq family/GDP 0.005 0.08 0.25 3 -0.25 14 17
HRAS/GTP -0.024 0.077 0.21 16 -0.3 16 32
PRKCH -0.02 0.047 0.21 1 -0.27 10 11
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.023 0.053 0.19 2 -0.25 16 18
PRKCB -0.016 0.046 -10000 0 -0.22 14 14
PRKCE -0.024 0.052 -10000 0 -0.26 15 15
PRKCD -0.022 0.05 0.17 2 -0.25 13 15
PRKCG -0.023 0.052 0.21 1 -0.25 16 17
regulation of vascular smooth muscle contraction -0.042 0.11 0.36 9 -0.38 12 21
PRKCQ -0.017 0.041 0.19 3 -0.28 6 9
PLA2G4A -0.05 0.098 0.28 10 -0.34 20 30
GNA14 0.031 0.009 -10000 0 -0.045 4 4
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.033 0.054 -10000 0 -0.085 185 185
MMP1 0.021 0.045 0.067 120 -0.086 25 145
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 -0.017 0.057 -10000 0 -0.056 339 339
alphaM/beta2 Integrin/GPIbA 0.016 0.057 -10000 0 -0.049 213 213
alphaM/beta2 Integrin/proMMP-9 -0.005 0.059 -10000 0 -0.057 273 273
PLAUR 0.023 0.027 -10000 0 -0.063 44 44
HMGB1 0.029 0.012 -10000 0 -0.029 11 11
alphaM/beta2 Integrin/Talin 0.007 0.057 -10000 0 -0.051 231 231
AGER 0.03 0.013 -10000 0 -0.039 17 17
RAP1A 0.032 0.004 -10000 0 -10000 0 0
SELPLG 0.032 0.004 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.072 -10000 0 -0.081 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
CYR61 0.004 0.043 -10000 0 -0.063 150 150
TLN1 0.021 0.027 -10000 0 -0.063 43 43
Rap1/GTP 0.01 0.037 -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 -0.063 1 1
MYH2 0 0.038 0.14 5 -0.16 3 8
MST1R 0.031 0.008 -10000 0 -0.063 2 2
leukocyte activation during inflammatory response 0.012 0.058 -10000 0 -0.047 212 212
APOB 0.032 0.008 -10000 0 -0.063 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.013 0.047 -10000 0 -0.063 241 241
JAM3 0.03 0.009 -10000 0 -0.063 1 1
GP1BA 0.032 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.008 0.056 -10000 0 -0.051 229 229
alphaM/beta2 Integrin 0.001 0.036 -10000 0 -0.14 8 8
JAM3 homodimer 0.03 0.009 -10000 0 -0.063 1 1
ICAM2 0.032 0.008 -10000 0 -0.063 3 3
ICAM1 0.028 0.018 -10000 0 -0.063 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor 0.001 0.036 -10000 0 -0.14 6 6
cell adhesion 0.016 0.056 -10000 0 -0.049 213 213
NFKB1 -0.041 0.037 0.21 7 -0.13 1 8
THY1 0.024 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.04 0.014 -10000 0 -0.042 3 3
alphaM/beta2 Integrin/LRP/tPA -0.011 0.065 -10000 0 -0.069 134 134
IL6 -0.033 0.037 0.16 4 -0.13 29 33
ITGB2 -0.008 0.047 -10000 0 -0.063 214 214
elevation of cytosolic calcium ion concentration -0.009 0.064 -10000 0 -0.073 116 116
alphaM/beta2 Integrin/JAM2/JAM3 0.009 0.066 -10000 0 -0.065 56 56
JAM2 0.018 0.033 -10000 0 -0.063 72 72
alphaM/beta2 Integrin/ICAM1 0.024 0.074 -10000 0 -0.079 6 6
alphaM/beta2 Integrin/uPA/Plg -0.008 0.064 -10000 0 -0.068 110 110
RhoA/GTP 0.005 0.037 0.14 1 -0.15 5 6
positive regulation of phagocytosis -0.002 0.052 0.14 7 -0.14 6 13
Ron/MSP 0.045 0.015 -10000 0 -0.05 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.008 0.065 -10000 0 -0.073 116 116
alphaM/beta2 Integrin/uPAR 0.012 0.058 -10000 0 -0.053 214 214
PLAU 0.007 0.036 -10000 0 -0.063 94 94
PLAT -0.011 0.047 -10000 0 -0.063 233 233
actin filament polymerization 0.001 0.039 0.15 7 -0.16 3 10
MST1 0.031 0.012 -10000 0 -0.063 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.061 -10000 0 -0.055 41 41
TNF -0.043 0.035 0.19 7 -0.13 2 9
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.055 -10000 0 -0.057 233 233
fibrinolysis -0.009 0.063 -10000 0 -0.068 110 110
HCK 0.014 0.036 -10000 0 -0.063 85 85
dendritic cell antigen processing and presentation 0.001 0.036 -10000 0 -0.14 6 6
VTN 0.032 0.007 -10000 0 -0.063 2 2
alphaM/beta2 Integrin/CYR61 0 0.061 -10000 0 -0.056 267 267
LPA 0.03 0.008 -10000 0 -10000 0 0
LRP1 0.029 0.016 -10000 0 -0.063 13 13
cell migration -0.032 0.05 -10000 0 -0.064 340 340
FN1 0.014 0.037 -10000 0 -0.063 96 96
alphaM/beta2 Integrin/Thy1 0.007 0.049 -10000 0 -0.049 178 178
MPO 0.032 0.004 -10000 0 -10000 0 0
KNG1 0.032 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.022 0.003 -10000 0 -10000 0 0
ROCK1 0.001 0.043 0.18 9 -0.16 3 12
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
CTGF 0.023 0.025 -10000 0 -0.063 36 36
alphaM/beta2 Integrin/Hck 0.01 0.06 -10000 0 -0.058 208 208
ITGAM 0.031 0.01 -10000 0 -0.03 13 13
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.024 0.066 -10000 0 -0.06 34 34
HP 0.017 0.034 -10000 0 -0.063 77 77
leukocyte adhesion -0.008 0.055 -10000 0 -0.1 12 12
SELP 0.032 0.006 -10000 0 -0.063 1 1
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.019 -10000 0 -0.037 6 6
CDKN2C -0.006 0.028 -10000 0 -0.053 106 106
CDKN2A 0.006 0.025 -10000 0 -0.049 52 52
CCND2 0.002 0.009 0.079 2 -10000 0 2
RB1 -0.073 0.1 0.1 1 -0.22 169 170
CDK4 0.002 0.01 0.09 2 -10000 0 2
CDK6 0.004 0.016 0.11 6 -10000 0 6
G1/S progression 0.081 0.11 0.22 180 -0.1 1 181
BARD1 signaling events

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.023 0.041 -10000 0 -0.05 114 114
ATM 0.027 0.021 -10000 0 -0.063 25 25
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.028 0.019 -10000 0 -0.063 21 21
ATR 0.032 0.005 -10000 0 0 13 13
UBE2L3 0.031 0.007 -10000 0 -10000 0 0
FANCD2 0.01 0.011 -10000 0 -0.036 25 25
protein ubiquitination 0.043 0.065 -10000 0 -0.089 10 10
XRCC5 0.032 0.002 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.062 0.019 -10000 0 -0.036 12 12
MRE11A 0.032 0.005 -10000 0 -10000 0 0
DNA-PK 0.054 0.034 -10000 0 -0.041 56 56
FA complex/FANCD2/Ubiquitin -0.005 0.08 -10000 0 -0.25 37 37
FANCF 0.031 0.008 -10000 0 -0.063 2 2
BRCA1 0.031 0.01 -10000 0 -0.063 5 5
CCNE1 0.03 0.011 -10000 0 -0.063 4 4
CDK2/Cyclin E1 0.04 0.024 -10000 0 -0.053 23 23
FANCG 0.019 0.03 -10000 0 -0.063 57 57
BRCA1/BACH1/BARD1 0.024 0.042 -10000 0 -0.05 120 120
FANCE 0.032 0.005 -10000 0 -0.063 1 1
FANCC 0.032 0.006 -10000 0 -10000 0 0
NBN 0.032 0.004 -10000 0 -10000 0 0
FANCA 0.031 0.006 -10000 0 -10000 0 0
DNA repair -0.029 0.066 0.18 16 -0.22 28 44
BRCA1/BARD1/ubiquitin 0.024 0.042 -10000 0 -0.05 120 120
BARD1/DNA-PK 0.042 0.062 -10000 0 -0.053 132 132
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.041 0.049 114 -10000 0 114
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.042 0.1 5 -0.14 26 31
BRCA1/BACH1/BARD1/TopBP1 0.036 0.05 -10000 0 -0.049 122 122
BRCA1/BARD1/P53 0.036 0.065 -10000 0 -0.07 32 32
BARD1/CSTF1/BRCA1 0.035 0.049 -10000 0 -0.049 115 115
BRCA1/BACH1 0.031 0.01 -10000 0 -0.063 5 5
BARD1 0.01 0.041 -10000 0 -0.063 122 122
PCNA -0.026 0.045 -10000 0 -0.063 299 299
BRCA1/BARD1/UbcH5C 0.036 0.05 -10000 0 -0.049 123 123
BRCA1/BARD1/UbcH7 0.035 0.051 -10000 0 -0.05 122 122
BRCA1/BARD1/RAD51/PCNA -0.01 0.064 -10000 0 -0.069 104 104
BARD1/DNA-PK/P53 0.038 0.075 -10000 0 -0.076 37 37
BRCA1/BARD1/Ubiquitin 0.024 0.042 -10000 0 -0.05 120 120
BRCA1/BARD1/CTIP -0.034 0.044 -10000 0 -0.057 392 392
FA complex 0.012 0.034 -10000 0 -0.15 16 16
BARD1/EWS 0.024 0.04 -10000 0 -0.05 107 107
RBBP8 -0.043 0.016 -10000 0 -0.051 379 379
TP53 0.019 0.032 -10000 0 -0.063 65 65
TOPBP1 0.032 0.006 -10000 0 -0.063 1 1
G1/S transition of mitotic cell cycle -0.034 0.063 0.07 32 -10000 0 32
BRCA1/BARD1 0.048 0.069 -10000 0 -0.09 10 10
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0.027 -10000 0 -0.039 122 122
CDK2 0.027 0.021 -10000 0 -0.063 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.032 0.006 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.024 0.042 -10000 0 -0.05 120 120
EWSR1 0.03 0.008 -10000 0 0 34 34
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.007 0.012 0 313 -0.039 52 365
TP53 -0.002 0.022 -10000 0 -0.2 5 5
Senescence -0.002 0.024 -10000 0 -0.2 6 6
Apoptosis -0.002 0.024 -10000 0 -0.2 6 6
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.009 0.022 43 -10000 0 43
MDM4 0.029 0.011 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.015 0.011 -10000 0 -0.05 2 2
MAP4K4 -0.008 0.038 -10000 0 -0.23 6 6
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.058 0.11 -10000 0 -0.2 158 158
NFKBIA 0.03 0.009 -10000 0 -0.063 1 1
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BAX -0.027 0.086 -10000 0 -0.36 24 24
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
AKT1 0 0.07 0.75 4 -10000 0 4
BAD -0.064 0.11 0.19 2 -0.21 158 160
SMPD1 -0.006 0.038 0.11 10 -0.17 15 25
RB1 -0.064 0.11 0.2 1 -0.21 158 159
FADD/Caspase 8 -0.002 0.04 -10000 0 -0.25 6 6
MAP2K4 -0.063 0.11 0.19 4 -0.2 150 154
NSMAF 0.032 0.005 -10000 0 -0.063 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.065 0.11 0.18 5 -0.2 155 160
EGF 0.032 0.007 -10000 0 -0.063 2 2
mol:ceramide -0.061 0.12 -10000 0 -0.21 158 158
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 -10000 0 -0.05 2 2
ASAH1 0.032 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.064 0.11 0.2 1 -0.2 158 159
cell proliferation -0.036 0.1 -10000 0 -0.19 142 142
BID -0.026 0.15 -10000 0 -0.65 26 26
MAP3K1 -0.064 0.11 0.2 1 -0.21 157 158
EIF2A -0.064 0.1 0.18 2 -0.19 157 159
TRADD 0.032 0.004 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.059 0.095 0.19 3 -0.19 138 141
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.1 0.19 3 -0.21 147 150
Cathepsin D/ceramide -0.046 0.12 -10000 0 -0.21 157 157
FADD -0.006 0.033 -10000 0 -0.24 3 3
KSR1 -0.064 0.11 0.2 1 -0.21 158 159
MAPK8 -0.092 0.15 0.15 3 -0.25 190 193
PRKRA -0.064 0.11 -10000 0 -0.21 157 157
PDGFA 0.022 0.016 -10000 0 -0.063 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.061 0.12 0.094 1 -0.21 158 159
CTSD 0.029 0.017 -10000 0 -0.063 15 15
regulation of nitric oxide biosynthetic process 0.046 0.012 -10000 0 -0.049 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.11 -10000 0 -0.2 142 142
PRKCD 0.032 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.015 0.011 -10000 0 -0.05 2 2
RelA/NF kappa B1 0.046 0.012 -10000 0 -0.05 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.031 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.039 -10000 0 -0.18 11 11
TNFR1A/BAG4/TNF-alpha 0.025 0.054 -10000 0 -0.048 165 165
mol:Sphingosine-1-phosphate -0.015 0.011 -10000 0 -0.049 2 2
MAP2K1 -0.066 0.1 0.19 4 -0.2 150 154
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 40 41
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
TNFR1A/BAG4 0.014 0.045 -10000 0 -0.05 164 164
EIF2AK2 -0.067 0.11 0.18 2 -0.2 157 159
TNF-alpha/TNFR1A/FAN 0.024 0.054 -10000 0 -0.048 165 165
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.048 -10000 0 -0.29 8 8
MAP2K2 -0.064 0.094 0.17 7 -0.2 149 156
SMPD3 0 0.04 0.1 1 -0.24 9 10
TNF 0.032 0.006 -10000 0 -0.063 2 2
PKC zeta/PAR4 0.023 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.035 0.066 0.13 3 -0.13 150 153
NF kappa B1/RelA/I kappa B alpha 0.065 0.035 -10000 0 -0.054 1 1
AIFM1 -0.042 0.081 0.12 1 -0.22 41 42
BCL2 0.032 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.014 0.17 -10000 0 -0.64 33 33
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.004 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.024 0.075 -10000 0 -0.14 100 100
EPO -0.031 0.072 -10000 0 -0.2 49 49
FIH (dimer) 0.02 0.017 -10000 0 -0.027 21 21
APEX1 0.025 0.019 -10000 0 -0.03 44 44
SERPINE1 -0.045 0.071 -10000 0 -0.18 69 69
FLT1 -0.015 0.16 -10000 0 -0.61 35 35
ADORA2A -0.067 0.07 0.3 2 -0.16 118 120
germ cell development -0.062 0.068 -10000 0 -0.15 129 129
SLC11A2 -0.065 0.074 -10000 0 -0.17 119 119
BHLHE40 -0.063 0.069 -10000 0 -0.16 129 129
HIF1AN 0.02 0.017 -10000 0 -0.027 21 21
HIF2A/ARNT/SIRT1 -0.03 0.086 0.17 1 -0.16 103 104
ETS1 0.034 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 39 39
KDR 0.016 0.076 -10000 0 -0.55 8 8
PGK1 -0.064 0.077 0.42 1 -0.17 120 121
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.032 0.11 -10000 0 -0.19 103 103
EPAS1 -0.03 0.048 0.11 1 -0.12 98 99
SP1 0.034 0.006 -10000 0 -0.038 1 1
ABCG2 -0.064 0.077 0.42 1 -0.17 120 121
EFNA1 -0.065 0.075 -10000 0 -0.17 119 119
FXN -0.067 0.065 -10000 0 -0.16 116 116
POU5F1 -0.063 0.069 -10000 0 -0.16 129 129
neuron apoptosis 0.032 0.11 0.18 104 -10000 0 104
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.024 0.017 -10000 0 -0.033 33 33
EGLN2 0.027 0.013 -10000 0 -0.027 23 23
EGLN1 0.026 0.015 -10000 0 -0.029 30 30
VHL/Elongin B/Elongin C 0.043 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.027 0.018 -10000 0 -0.029 41 41
SLC2A1 -0.067 0.066 0.18 1 -0.16 116 117
TWIST1 -0.041 0.057 -10000 0 -0.16 57 57
ELK1 0.033 0.012 -10000 0 -0.038 13 13
HIF2A/ARNT/Cbp/p300 -0.024 0.095 0.19 1 -0.16 99 100
VEGFA -0.075 0.083 0.42 1 -0.18 128 129
CREBBP 0.032 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.023 0.015 -9999 0 -9999 0 0
PLK4 0.032 0.004 -9999 0 -9999 0 0
regulation of centriole replication -0.016 0.01 0 158 -9999 0 158
EPO signaling pathway

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
BCL2L1 0.036 0.046 0.18 18 -0.16 2 20
CRKL 0.026 0.092 0.16 130 -10000 0 130
mol:DAG 0.011 0.028 0.14 4 -0.14 2 6
HRAS 0.019 0.095 0.28 29 -10000 0 29
MAPK8 0.005 0.067 0.15 84 -10000 0 84
RAP1A 0.026 0.09 0.16 136 -10000 0 136
GAB1 0.027 0.093 0.16 135 -10000 0 135
MAPK14 0.02 0.083 0.15 146 -10000 0 146
EPO 0.024 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.028 0.14 4 -0.14 2 6
EPOR/TRPC2/IP3 Receptors 0.037 0.011 0.084 5 -10000 0 5
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.013 0.085 0.15 124 -10000 0 124
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.027 0.091 0.16 134 -10000 0 134
STAT1 0.012 0.031 0.15 4 -0.14 2 6
STAT5B 0.012 0.03 0.15 4 -0.14 2 6
cell proliferation 0.004 0.073 0.16 88 -10000 0 88
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.065 0.11 117 -10000 0 117
TEC 0.027 0.093 0.16 133 -10000 0 133
SOCS3 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.031 0.15 4 -0.14 2 6
JAK2 0.034 0.015 0.086 6 -10000 0 6
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.051 0.05 0.23 5 -10000 0 5
EPO/EPOR 0.034 0.024 -10000 0 -10000 0 0
LYN 0.022 0.031 -10000 0 -0.062 60 60
TEC/VAV2 0.005 0.07 0.13 110 -10000 0 110
elevation of cytosolic calcium ion concentration 0.037 0.011 0.084 5 -10000 0 5
SHC1 0.024 0.026 -10000 0 -0.063 40 40
EPO/EPOR (dimer)/LYN 0.035 0.043 -10000 0 -0.052 47 47
mol:IP3 0.011 0.028 0.14 4 -0.14 2 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.089 0.16 123 -10000 0 123
SH2B3 0.036 0.016 0.078 3 -0.067 7 10
NFKB1 0.02 0.083 0.15 146 -10000 0 146
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 -10000 0 -10000 0 0
PTPN6 0.028 0.088 0.16 150 -10000 0 150
TEC/VAV2/GRB2 0.061 0.066 0.25 18 -10000 0 18
EPOR 0.037 0.011 0.084 5 -10000 0 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.086 0.15 124 -10000 0 124
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
CRKL/CBL/C3G 0.059 0.067 0.16 108 -10000 0 108
VAV2 0.024 0.088 0.16 129 -10000 0 129
CBL 0.028 0.093 0.16 136 -10000 0 136
SHC/Grb2/SOS1 0.02 0.036 -10000 0 -0.079 1 1
STAT5A 0.012 0.03 0.15 4 -0.14 2 6
GRB2 0.032 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.041 0.18 4 -10000 0 4
LYN/PLCgamma2 0.035 0.034 -10000 0 -0.053 61 61
PTPN11 0.032 0.003 -10000 0 -10000 0 0
BTK 0.028 0.094 0.16 139 -10000 0 139
BCL2 0.035 0.05 0.17 22 -0.19 6 28
Effects of Botulinum toxin

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
STX1A 0 0.002 0 499 -10000 0 499
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 0 467 467
ACh/CHRNA1 0.034 0.027 0.081 30 -0.036 40 70
RAB3GAP2/RIMS1/UNC13B 0.053 0.032 -10000 0 -0.037 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.031 0.006 -10000 0 -10000 0 0
mol:ACh 0.018 0.035 0.065 149 -0.059 7 156
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 -0.063 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.01 0.074 4 -10000 0 4
SNAP25 0 0.001 -10000 0 -10000 0 0
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.002 0.007 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.004 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.01 0.14 1 -10000 0 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.021 0.004 -10000 0 -0.006 11 11
ARNO/beta Arrestin1-2 0.04 0.017 -10000 0 -0.063 11 11
EGFR 0.012 0.018 -10000 0 -0.063 6 6
EPHA2 0.029 0.015 -10000 0 -0.063 12 12
USP6 0.032 0.005 -10000 0 -10000 0 0
IQSEC1 0.032 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.018 0.025 -10000 0 -0.05 8 8
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0.012 0.1 3 -0.074 4 7
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -0.063 4 4
EGF 0.032 0.007 -10000 0 -0.063 2 2
somatostatin receptor activity 0 0 0 153 0 14 167
ARAP2 0 0 0 145 0 6 151
mol:GDP 0.06 0.064 0.15 137 -0.15 7 144
mol:PI-3-4-5-P3 0 0 0 141 0 12 153
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.072 7 7
ADAP1 0 0 0 41 0 5 46
KIF13B 0.032 0.007 -10000 0 -0.063 2 2
HGF/MET 0.031 0.024 -10000 0 -0.05 3 3
PXN 0.032 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.072 0.088 0.18 142 -0.19 12 154
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.048 8 8
ADRB2 0.032 0.006 -10000 0 -0.063 1 1
receptor agonist activity 0 0 0 141 0 12 153
actin filament binding 0 0 0 144 0 13 157
SRC 0.031 0.008 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
GNAQ 0.032 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 158 -0.001 12 170
ARF6/GDP 0.024 0.068 0.14 21 -0.21 27 48
ARF6/GDP/GULP/ACAP1 0.08 0.063 0.16 126 -0.15 7 133
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.017 -10000 0 -10000 0 0
ACAP1 0 0 0 40 -10000 0 40
ACAP2 0 0 0 140 0 9 149
LHCGR/beta Arrestin2 0.028 0.016 -10000 0 -0.079 11 11
EFNA1 0.028 0.019 -10000 0 -0.063 20 20
HGF 0.022 0.016 -10000 0 -0.063 1 1
CYTH3 0 0 0.001 142 0 12 154
CYTH2 0 0.001 0.002 3 -0.003 16 19
NCK1 0.03 0.015 -10000 0 -0.063 11 11
fibronectin binding 0 0 0 138 0 16 154
endosomal lumen acidification 0 0 0 150 0 16 166
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 0.032 0.008 -10000 0 -0.063 3 3
GNAQ/ARNO 0.024 0.006 0.039 5 0 19 24
mol:Phosphatidic acid 0 0 0 140 0 9 149
PIP3-E 0 0 0 79 0 15 94
MET 0.022 0.016 -10000 0 -0.063 2 2
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GIT1 0.032 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 152 -0.001 12 164
GNA11 0.031 0.006 -10000 0 -10000 0 0
LHCGR 0.033 0.001 -10000 0 -10000 0 0
AGTR1 0.032 0.008 -10000 0 -0.063 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.027 0.016 -10000 0 -0.079 11 11
IPCEF1/ARNO 0.014 0.02 -10000 0 -0.029 8 8
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure 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
IKK alpha homodimer -0.035 0.035 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.058 0.053 0.23 3 -0.19 18 21
alphaV/beta3 Integrin/Osteopontin/Src 0.01 0.05 -10000 0 -0.057 179 179
AP1 -0.061 0.065 -10000 0 -0.14 59 59
ILK -0.04 0.026 0.16 5 -10000 0 5
bone resorption -0.063 0.029 0.15 4 -10000 0 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.01 0.062 0.16 4 -0.085 17 21
ITGAV 0.029 0.017 -10000 0 -0.066 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.029 0.039 -10000 0 -0.05 394 394
alphaV/beta3 Integrin/Osteopontin 0.02 0.061 -10000 0 -0.07 76 76
MAP3K1 -0.041 0.028 0.17 6 -10000 0 6
JUN 0.031 0.005 -10000 0 -10000 0 0
MAPK3 -0.047 0.032 0.16 5 -10000 0 5
MAPK1 -0.044 0.036 0.17 6 -10000 0 6
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.036 0.032 0.16 4 -10000 0 4
ITGB3 0.031 0.004 -10000 0 -10000 0 0
NFKBIA -0.047 0.043 0.16 5 -0.17 18 23
FOS 0.007 0.04 -10000 0 -0.064 120 120
CD44 -0.043 0.038 -10000 0 -0.063 397 397
CHUK 0.024 0.015 -10000 0 -0.063 1 1
PLAU -0.07 0.065 -10000 0 -0.3 4 4
NF kappa B1 p50/RelA -0.066 0.047 0.19 1 -10000 0 1
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.044 0.019 -10000 0 -0.055 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.027 0.17 5 -10000 0 5
VAV3 -0.044 0.029 0.16 5 -10000 0 5
MAP3K14 -0.042 0.03 0.17 6 -10000 0 6
ROCK2 0.032 0.003 -10000 0 -10000 0 0
SPP1 -0.003 0.047 -10000 0 -0.066 175 175
RAC1 0.023 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.032 0.16 3 -10000 0 3
MMP2 -0.083 0.044 0.26 1 -10000 0 1
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.054 0.17 0.52 8 -0.28 18 26
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.076 0.11 -10000 0 -0.23 85 85
SMAD4 0.009 0.04 -10000 0 -0.063 117 117
ID2 -0.055 0.17 0.53 9 -0.28 18 27
AP1 0.022 0.041 -10000 0 -0.05 117 117
ABCG2 -0.058 0.16 0.54 7 -0.29 15 22
HIF1A -0.013 0.054 0.15 7 -0.087 17 24
TFF3 -0.056 0.16 0.54 8 -0.29 16 24
GATA2 0.031 0.009 -10000 0 -0.027 9 9
AKT1 -0.009 0.055 0.17 6 -0.095 1 7
response to hypoxia -0.018 0.025 0.09 7 -0.06 22 29
MCL1 -0.058 0.16 0.52 7 -0.29 16 23
NDRG1 -0.066 0.15 0.58 3 -0.28 18 21
SERPINE1 -0.052 0.15 0.51 7 -0.29 19 26
FECH -0.05 0.17 0.53 9 -0.28 17 26
FURIN -0.053 0.17 0.53 9 -0.28 17 26
NCOA2 0.033 0.004 -10000 0 -10000 0 0
EP300 0.002 0.055 0.24 9 -0.2 2 11
HMOX1 -0.074 0.16 0.52 7 -0.29 27 34
BHLHE40 -0.094 0.09 -10000 0 -0.2 172 172
BHLHE41 -0.094 0.09 -10000 0 -0.2 172 172
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.01 0.093 0.23 6 -0.1 74 80
ENG -0.035 0.079 0.27 9 -10000 0 9
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.055 0.17 0.53 9 -0.28 18 27
ABCB1 -0.011 0.045 -10000 0 -0.34 5 5
TFRC -0.057 0.16 0.53 9 -0.28 18 27
CXCR4 -0.073 0.16 0.55 5 -0.29 27 32
TF -0.082 0.11 -10000 0 -0.28 17 17
CITED2 -0.059 0.16 0.55 6 -0.29 18 24
HIF1A/ARNT -0.07 0.14 0.26 23 -0.24 128 151
LDHA 0.003 0.057 -10000 0 -0.46 6 6
ETS1 -0.053 0.17 0.53 9 -0.29 14 23
PGK1 -0.054 0.17 0.53 9 -0.29 14 23
NOS2 -0.094 0.09 -10000 0 -0.2 172 172
ITGB2 -0.061 0.17 0.53 9 -0.3 22 31
ALDOA -0.055 0.17 0.52 7 -0.28 18 25
Cbp/p300/CITED2 -0.095 0.1 -10000 0 -0.24 115 115
FOS 0.008 0.04 -10000 0 -0.063 120 120
HK2 -0.054 0.17 0.53 9 -0.29 16 25
SP1 0.034 0.007 -10000 0 -0.041 2 2
GCK 0.004 0.088 0.39 5 -0.37 3 8
HK1 -0.076 0.13 0.5 3 -0.28 19 22
NPM1 -0.058 0.16 0.55 6 -0.29 16 22
EGLN1 -0.058 0.16 0.52 7 -0.29 14 21
CREB1 0.035 0.008 -10000 0 -0.085 2 2
PGM1 -0.054 0.17 0.5 11 -0.28 17 28
SMAD3 0.032 0.005 -10000 0 -10000 0 0
EDN1 -0.017 0.082 -10000 0 -0.33 13 13
IGFBP1 -0.045 0.15 0.51 8 -0.29 15 23
VEGFA -0.076 0.13 0.37 10 -0.28 34 44
HIF1A/JAB1 0.009 0.052 0.14 4 -0.054 146 150
CP -0.064 0.16 0.54 6 -0.3 23 29
CXCL12 -0.066 0.15 0.52 5 -0.29 21 26
COPS5 0.033 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.041 -10000 0 -0.05 113 113
BNIP3 -0.073 0.13 0.47 1 -0.28 19 20
EGLN3 -0.057 0.16 0.52 8 -0.28 19 27
CA9 -0.058 0.16 0.53 8 -0.29 16 24
TERT -0.051 0.17 0.53 9 -0.28 17 26
ENO1 -0.057 0.16 0.52 8 -0.29 16 24
PFKL -0.052 0.17 0.52 10 -0.28 20 30
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.072 0.16 0.5 8 -0.29 26 34
ARNT -0.014 0.055 0.15 6 -0.084 18 24
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.094 0.09 -10000 0 -0.2 172 172
SLC2A1 -0.063 0.13 0.38 11 -0.29 19 30
LEP -0.045 0.14 0.51 6 -0.28 13 19
HIF1A/ARNT/Cbp/p300 -0.077 0.1 -10000 0 -0.22 105 105
EPO -0.032 0.11 0.35 8 -0.37 19 27
CREBBP 0.002 0.055 0.24 9 -0.19 2 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.082 0.1 -10000 0 -0.22 109 109
PFKFB3 -0.065 0.15 0.52 5 -0.29 16 21
NT5E -0.062 0.16 0.53 6 -0.29 19 25
Aurora B signaling

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.029 0.047 -10000 0 -0.12 76 76
STMN1 -0.023 0.008 -10000 0 -0.05 24 24
Aurora B/RasGAP/Survivin 0.017 0.057 -10000 0 -0.053 196 196
Chromosomal passenger complex/Cul3 protein complex -0.034 0.056 -10000 0 -0.1 175 175
BIRC5 -0.007 0.048 -10000 0 -0.066 201 201
DES 0.016 0.11 -10000 0 -0.68 11 11
Aurora C/Aurora B/INCENP 0.049 0.033 -10000 0 -0.043 44 44
Aurora B/TACC1 0.038 0.019 -10000 0 -0.04 23 23
Aurora B/PP2A 0.042 0.023 -10000 0 -0.05 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.005 -10000 0 -0.014 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.018 2 -10000 0 2
NDC80 -0.032 0.017 -10000 0 -0.054 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.005 0.042 -10000 0 -0.16 16 16
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.002 0.046 -10000 0 -0.064 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.023 -10000 0 -0.051 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.021 0.03 -10000 0 -0.063 56 56
SMC4 -0.039 0.041 -10000 0 -0.063 378 378
NSUN2/NPM1/Nucleolin -0.009 0.086 -10000 0 -0.55 11 11
PSMA3 0.031 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 0.015 1 -10000 0 1
H3F3B 0.01 0.011 -10000 0 -0.037 25 25
AURKB 0.026 0.023 -10000 0 -0.062 29 29
AURKC 0.03 0.01 -10000 0 -0.063 2 2
CDCA8 0.028 0.018 -10000 0 -0.065 16 16
cytokinesis -0.02 0.064 0.15 1 -0.2 35 36
Aurora B/Septin1 -0.012 0.068 0.14 1 -0.21 28 29
AURKA 0.027 0.018 -10000 0 -0.062 16 16
INCENP 0.032 0.005 0.065 1 -0.026 1 2
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.032 0.009 -10000 0 -0.062 4 4
hSgo1/Aurora B/Survivin 0.008 0.039 -10000 0 -0.039 203 203
EVI5 0.031 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.072 0.16 1 -0.15 33 34
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0 0.044 -10000 0 -0.16 22 22
NCAPG 0.011 0.039 -10000 0 -0.063 111 111
Aurora B/HC8 Proteasome 0.04 0.023 -10000 0 -0.05 21 21
NCAPD2 0.014 0.037 -10000 0 -0.063 93 93
Aurora B/PP1-gamma 0.041 0.023 -10000 0 -0.05 25 25
RHOA 0.032 0.006 -10000 0 -10000 0 0
NCAPH 0.03 0.016 -10000 0 -0.063 15 15
NPM1 -0.003 0.084 -10000 0 -0.39 17 17
RASA1 0.032 0.006 -10000 0 -10000 0 0
KLHL9 0.021 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 0.015 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.023 -10000 0 -0.05 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0.002 0.068 0.16 1 -0.15 36 37
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.004 0.048 -10000 0 -0.31 11 11
MYLK 0.009 0.013 -10000 0 -0.038 34 34
KIF23 0.017 0.035 -10000 0 -0.066 77 77
VIM -0.019 0.013 0.021 1 -0.05 33 34
RACGAP1 0.002 0.045 -10000 0 -0.065 154 154
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.048 -10000 0 -0.29 12 12
Chromosomal passenger complex -0.009 0.043 0.086 1 -0.13 35 36
Chromosomal passenger complex/EVI5 0.028 0.075 -10000 0 -0.091 18 18
TACC1 0.032 0.004 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
CUL3 0.033 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD 0 0.039 -9999 0 -0.12 23 23
FZD6 0.014 0.037 -9999 0 -0.063 94 94
WNT6 0.032 0.002 -9999 0 -10000 0 0
WNT4 0.031 0.008 -9999 0 -0.063 2 2
FZD3 0.031 0.01 -9999 0 -0.063 3 3
WNT5A 0.003 0.044 -9999 0 -0.063 155 155
WNT11 0.032 0.007 -9999 0 -0.063 2 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure 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 -0.022 0.096 0.19 15 -0.3 47 62
CRKL -0.022 0.095 0.18 1 -0.31 48 49
HRAS -0.006 0.095 0.16 3 -0.27 48 51
mol:PIP3 0.038 0.12 0.25 33 -0.28 39 72
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.003 -10000 0 -10000 0 0
GAB1 -0.014 0.098 -10000 0 -0.31 47 47
FOXO3 0.025 0.13 0.25 24 -0.3 41 65
AKT1 0.03 0.14 0.24 27 -0.32 40 67
BAD 0.024 0.13 0.23 25 -0.3 40 65
megakaryocyte differentiation -0.012 0.089 -10000 0 -0.3 43 43
GSK3B 0.025 0.13 0.25 24 -0.3 39 63
RAF1 -0.012 0.081 0.16 6 -0.23 48 54
SHC1 0.024 0.026 -10000 0 -0.063 40 40
STAT3 -0.016 0.098 -10000 0 -0.31 47 47
STAT1 -0.033 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.008 0.081 0.14 2 -0.22 48 50
cell proliferation -0.019 0.095 -10000 0 -0.31 47 47
PIK3CA 0.028 0.018 -10000 0 -0.062 17 17
TEC 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 0.015 0.11 0.2 3 -0.31 34 37
HRAS/SPRED2 0.006 0.091 0.19 3 -0.23 47 50
LYN/TEC/p62DOK 0.024 0.12 -10000 0 -0.31 48 48
MAPK3 -0.007 0.07 0.19 13 -0.17 35 48
STAP1 -0.015 0.098 -10000 0 -0.31 47 47
GRAP2 0.03 0.008 -10000 0 -10000 0 0
JAK2 -0.029 0.16 -10000 0 -0.5 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 0.032 0.12 -10000 0 -0.31 47 47
actin filament polymerization -0.01 0.096 -10000 0 -0.3 47 47
LYN 0.021 0.031 -10000 0 -0.063 60 60
STAP1/STAT5A (dimer) -0.024 0.13 0.21 1 -0.4 48 49
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.007 0.1 0.21 1 -0.3 48 49
PI3K 0.038 0.12 0.22 3 -0.29 40 43
PTEN 0.023 0.016 -10000 0 -0.063 2 2
SCF/KIT/EPO/EPOR -0.016 0.18 -10000 0 -0.57 46 46
MAPK8 -0.019 0.096 -10000 0 -0.31 47 47
STAT3 (dimer) -0.016 0.097 -10000 0 -0.31 47 47
positive regulation of transcription -0.004 0.061 0.18 14 -0.16 17 31
mol:GDP 0.001 0.099 -10000 0 -0.28 46 46
PIK3C2B -0.017 0.097 -10000 0 -0.31 46 46
CBL/CRKL -0.005 0.1 0.2 3 -0.3 48 51
FER -0.015 0.098 -10000 0 -0.31 46 46
SH2B3 -0.015 0.097 -10000 0 -0.31 47 47
PDPK1 0.032 0.11 0.23 35 -0.26 38 73
SNAI2 -0.021 0.098 -10000 0 -0.32 47 47
positive regulation of cell proliferation -0.029 0.15 -10000 0 -0.47 49 49
KITLG 0.027 0.023 -10000 0 -0.044 45 45
cell motility -0.029 0.15 -10000 0 -0.47 49 49
PTPN6 0.029 0.017 -10000 0 -0.049 18 18
EPOR 0.016 0.077 -10000 0 -0.49 3 3
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 0.095 0.31 45 -10000 0 45
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.02 0.02 -10000 0 -0.033 27 27
VAV1 0.032 0.007 -10000 0 -0.063 1 1
GRB10 -0.011 0.076 -10000 0 -0.32 28 28
PTPN11 0.031 0.01 -10000 0 -0.028 11 11
SCF/KIT -0.008 0.1 -10000 0 -0.32 47 47
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.068 0.15 9 -0.19 46 55
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.037 0.2 -10000 0 -0.64 51 51
MAP2K2 -0.015 0.075 0.2 16 -0.19 46 62
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 0.032 0.006 -10000 0 -10000 0 0
response to radiation -0.02 0.096 -10000 0 -0.31 47 47
SHC/GRAP2 0.037 0.028 -10000 0 -0.05 38 38
PTPRO -0.012 0.091 -10000 0 -0.3 43 43
SH2B2 -0.01 0.098 -10000 0 -0.31 47 47
DOK1 0.032 0.002 -10000 0 -10000 0 0
MATK -0.015 0.096 -10000 0 -0.31 45 45
CREBBP 0.026 0.043 -10000 0 -0.1 47 47
BCL2 0.007 0.12 -10000 0 -0.64 9 9
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0.02 -10000 0 -0.045 2 2
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.017 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.01 0.035 -10000 0 -0.041 273 273
CaM/Ca2+ -0.027 0.019 0.18 2 -10000 0 2
HIF1A 0.035 0.011 -10000 0 -0.061 2 2
GAB1 0.032 0.008 -10000 0 -0.063 3 3
AKT1 -0.023 0.034 0.13 15 -0.19 1 16
PLCG1 -0.024 0.017 0.18 2 -10000 0 2
NOS3 -0.007 0.042 0.2 3 -0.21 14 17
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.006 0.055 0.19 4 -0.21 14 18
FLT1 -0.016 0.006 -10000 0 -10000 0 0
PGF 0.027 0.02 -10000 0 -0.063 19 19
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.049 -10000 0 -0.049 277 277
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
eNOS/Hsp90 0.022 0.075 0.19 12 -0.22 24 36
endothelial cell proliferation -0.011 0.047 0.12 33 -0.14 20 53
mol:Ca2+ -0.024 0.017 0.18 2 -10000 0 2
MAPK3 -0.035 0.017 0.15 2 -10000 0 2
MAPK1 -0.033 0.019 0.15 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PLGF homodimer 0.027 0.02 -10000 0 -0.063 19 19
PRKACA 0.032 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
VEGFA homodimer -0.019 0.047 -10000 0 -0.063 274 274
VEGFR1 homodimer/VEGFA homodimer -0.012 0.039 -10000 0 -0.046 269 269
platelet activating factor biosynthetic process -0.037 0.02 0.14 2 -10000 0 2
PI3K 0.044 0.047 0.17 1 -0.077 1 2
PRKCA -0.028 0.018 0.17 2 -10000 0 2
PRKCB -0.022 0.016 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.026 0.021 -10000 0 -0.045 21 21
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
VEGFB 0.032 0.004 -10000 0 -10000 0 0
mol:IP3 -0.024 0.017 0.18 2 -10000 0 2
RASA1 -0.027 0.015 0.18 2 -10000 0 2
NRP2 0.032 0.004 -10000 0 -0.063 1 1
VEGFR1 homodimer -0.016 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.032 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
eNOS/Caveolin-1 -0.015 0.051 0.17 1 -0.22 17 18
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.046 0.16 1 -0.077 1 2
mol:L-citrulline 0.006 0.055 0.19 4 -0.21 14 18
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.008 0.059 -10000 0 -0.076 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.049 -10000 0 -0.058 35 35
CD2AP 0.023 0.028 -10000 0 -0.063 48 48
PI3K/GAB1 0.052 0.055 0.18 1 -0.087 1 2
PDPK1 -0.031 0.035 0.15 16 -10000 0 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.049 -10000 0 -0.057 35 35
mol:NADP 0.006 0.055 0.19 4 -0.21 14 18
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.009 0.058 -10000 0 -0.075 2 2
VEGFR1 homodimer/NRP2 0.027 0.021 -10000 0 -0.045 3 3
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.02 0.071 0.3 1 -0.24 14 15
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
FOS 0.011 0.062 0.25 2 -0.24 14 16
PRKCA 0.031 0.004 -10000 0 -10000 0 0
PTPN7 0.03 0.008 0.066 1 -0.044 2 3
HRAS 0.031 0.007 -10000 0 -10000 0 0
PRKCB -0.001 0.002 0.018 1 -0.003 121 122
NRAS 0.008 0.041 -10000 0 -0.063 125 125
RAS family/GTP 0.03 0.046 -10000 0 -0.044 121 121
MAPK3 0.026 0.032 -10000 0 -0.36 2 2
MAP2K1 -0.003 0.026 0.12 1 -0.16 3 4
ELK1 0.031 0.005 -10000 0 -0.022 2 2
BRAF 0.004 0.017 0.098 1 -0.23 2 3
mol:GTP 0 0 0.003 1 -0.001 124 125
MAPK1 0 0.1 -10000 0 -0.35 36 36
RAF1 0.006 0.016 0.098 1 -0.22 2 3
KRAS 0.03 0.008 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0 0.059 -10000 0 -0.32 10 10
Syndecan-4/Syndesmos -0.031 0.11 -10000 0 -0.55 13 13
positive regulation of JNK cascade -0.036 0.11 -10000 0 -0.47 15 15
Syndecan-4/ADAM12 -0.022 0.12 -10000 0 -0.52 15 15
CCL5 0.028 0.021 -10000 0 -0.063 25 25
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
ITGA5 0.019 0.033 -10000 0 -0.063 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.024 0.022 -10000 0 -0.051 13 13
ADAM12 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.031 0.11 -10000 0 -0.55 13 13
Syndecan-4/CXCL12/CXCR4 -0.038 0.11 -10000 0 -0.52 14 14
Syndecan-4/Laminin alpha3 -0.016 0.12 -10000 0 -0.55 13 13
MDK -0.022 0.046 -10000 0 -0.063 283 283
Syndecan-4/FZD7 -0.034 0.12 -10000 0 -0.52 15 15
Syndecan-4/Midkine -0.037 0.11 -10000 0 -0.58 12 12
FZD7 -0.012 0.048 -10000 0 -0.063 238 238
Syndecan-4/FGFR1/FGF -0.005 0.12 -10000 0 -0.47 16 16
THBS1 0.024 0.026 -10000 0 -0.063 39 39
integrin-mediated signaling pathway -0.048 0.1 -10000 0 -0.44 19 19
positive regulation of MAPKKK cascade -0.036 0.11 -10000 0 -0.47 15 15
Syndecan-4/TACI -0.015 0.12 -10000 0 -0.56 13 13
CXCR4 -0.017 0.048 -10000 0 -0.063 263 263
cell adhesion -0.007 0.03 0.2 3 -0.085 14 17
Syndecan-4/Dynamin -0.018 0.12 -10000 0 -0.56 13 13
Syndecan-4/TSP1 -0.018 0.12 -10000 0 -0.52 15 15
Syndecan-4/GIPC -0.018 0.12 -10000 0 -0.55 13 13
Syndecan-4/RANTES -0.016 0.12 -10000 0 -0.56 13 13
ITGB1 0.025 0.014 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.029 0.017 -10000 0 -0.063 15 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.003 0.081 0.8 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.018 0.12 -10000 0 -0.54 14 14
TFPI 0.012 0.039 -10000 0 -0.063 111 111
F2 0.029 0.02 0.074 1 -0.039 28 29
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.05 61 61
positive regulation of cell adhesion -0.026 0.11 -10000 0 -0.49 15 15
ACTN1 0.023 0.026 -10000 0 -0.063 40 40
TNC -0.056 0.022 -10000 0 -0.063 469 469
Syndecan-4/CXCL12 -0.022 0.12 -10000 0 -0.56 13 13
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CXCL12 0.023 0.019 -10000 0 -0.063 12 12
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.063 2 2
FGFR1 0.032 0.005 -10000 0 -0.063 1 1
Syndecan-4/PI-4-5-P2 -0.031 0.11 -10000 0 -0.55 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.039 -10000 0 -0.057 105 105
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -0.051 12 12
vasculogenesis -0.017 0.12 -10000 0 -0.46 17 17
SDC4 -0.029 0.11 -10000 0 -0.48 19 19
Syndecan-4/Tenascin C -0.049 0.11 -10000 0 -0.46 19 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.015 0.12 -10000 0 -0.56 13 13
MMP9 -0.004 0.044 -10000 0 -0.06 177 177
Rac1/GTP -0.007 0.031 0.2 3 -0.087 14 17
cytoskeleton organization -0.03 0.1 -10000 0 -0.49 15 15
GIPC1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.023 0.12 -10000 0 -0.46 18 18
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.004 0.047 -10000 0 -0.049 258 258
PDGFRB 0.032 0.007 -10000 0 -0.064 2 2
SPHK1 0.011 0.018 -10000 0 -10000 0 0
mol:S1P 0.005 0.023 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.068 -10000 0 -0.24 27 27
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.08 0.2 16 -0.24 17 33
PLCG1 -0.04 0.061 -10000 0 -0.25 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.064 2 2
GNAI2 0.035 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.062 58 58
GNAI1 0.019 0.016 -10000 0 -0.06 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.014 0.01 3 -0.038 229 232
S1P1/S1P -0.003 0.033 0.2 2 -10000 0 2
negative regulation of cAMP metabolic process -0.04 0.067 -10000 0 -0.24 27 27
MAPK3 -0.05 0.069 -10000 0 -0.28 20 20
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 0 151 151
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
KDR 0.028 0.018 -10000 0 -0.062 14 14
PLCB2 0.001 0.052 0.16 30 -10000 0 30
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.032 -10000 0 -10000 0 0
receptor internalization -0.003 0.032 0.19 2 -10000 0 2
PTGS2 -0.055 0.072 -10000 0 -0.33 12 12
Rac1/GTP -0.007 0.025 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.018 0.047 -10000 0 -0.061 274 274
negative regulation of T cell proliferation -0.04 0.067 -10000 0 -0.24 27 27
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 16 16
S1P1/S1P/PDGFB-D/PDGFRB 0.01 0.054 0.2 11 -10000 0 11
ABCC1 0.031 0.012 -10000 0 -0.063 8 8
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.05 15 15
AKT1 -0.023 0.074 0.21 7 -0.26 18 25
PTK2B -0.034 0.059 0.16 38 -10000 0 38
VEGFR2 homodimer/Frs2 0.025 0.024 -10000 0 -0.089 13 13
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.004 0.05 -10000 0 -0.059 97 97
endothelial cell proliferation -0.005 0.079 0.21 25 -0.25 10 35
mol:Ca2+ -0.03 0.052 0.15 33 -0.12 2 35
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.002 0.059 0.17 12 -0.1 14 26
RP11-342D11.1 -0.032 0.037 0.16 15 -0.098 11 26
CDH5 0.027 0.022 -10000 0 -0.063 29 29
VEGFA homodimer 0.002 0.052 -10000 0 -0.043 273 273
SHC1 0.024 0.026 -10000 0 -0.063 40 40
SHC2 0.031 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.017 0.053 -10000 0 -0.096 30 30
SH2D2A 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.007 0.06 0.2 2 -0.2 4 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.005 0.051 -10000 0 -0.06 100 100
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.003 0.068 0.16 13 -0.1 22 35
GRB10 -0.021 0.047 0.16 24 -0.12 1 25
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.005 0.076 0.18 12 -0.1 27 39
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.046 0.13 11 -0.21 8 19
HIF1A 0.03 0.01 -10000 0 -0.063 2 2
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.002 0.058 0.17 12 -0.1 14 26
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.004 -10000 0 -10000 0 0
Nck/Pak 0.044 0.017 -10000 0 -0.05 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.007 0.05 -10000 0 -0.072 49 49
mol:GDP -0.011 0.056 -10000 0 -0.094 29 29
mol:NADP 0.005 0.058 0.25 4 -0.2 1 5
eNOS/Hsp90 0.014 0.06 0.26 4 -0.19 3 7
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.03 0.052 0.15 33 -0.12 2 35
HIF1A/ARNT 0.044 0.015 -10000 0 -0.05 2 2
SHB 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.019 0.048 -10000 0 -0.064 274 274
VEGFC 0.03 0.015 -10000 0 -0.063 11 11
FAK1/Vinculin -0.004 0.059 0.2 11 -0.2 9 20
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.067 0.17 13 -0.1 14 27
PTPN6 0.029 0.015 -10000 0 -0.063 11 11
EPAS1 0.034 0.019 -10000 0 -0.072 16 16
mol:L-citrulline 0.005 0.058 0.25 4 -0.2 1 5
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.004 0.065 0.17 13 -0.1 12 25
VEGFR2 homodimer/VEGFA homodimer -0.005 0.055 -10000 0 -0.064 111 111
VEGFR2/3 heterodimer 0.026 0.024 -10000 0 -0.089 14 14
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.03 0.06 0.18 14 -0.18 11 25
VEGFR2 homodimer -0.02 0.015 -10000 0 -0.099 14 14
FLT1 0.03 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.019 -10000 0 -0.044 29 29
MAPK3 -0.019 0.065 0.2 13 -10000 0 13
MAPK1 -0.021 0.062 0.2 10 -10000 0 10
VEGFA145/NRP2 -0.005 0.049 -10000 0 -0.05 275 275
VEGFR1/2 heterodimer 0.024 0.025 -10000 0 -0.089 14 14
KDR -0.02 0.015 -10000 0 -0.1 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.002 0.06 0.16 14 -0.087 31 45
SRC 0.031 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.018 0.066 0.2 13 -10000 0 13
PI3K -0.019 0.064 0.17 8 -0.16 25 33
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.006 0.051 -10000 0 -0.077 38 38
FES -0.032 0.054 0.16 36 -0.12 2 38
GAB1 -0.018 0.067 0.16 10 -0.19 31 41
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.05 -10000 0 -0.06 91 91
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.008 0.047 0.27 3 -0.19 2 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.013 0.051 -10000 0 -0.062 139 139
PI3K/GAB1 -0.02 0.076 0.21 3 -0.23 20 23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.006 0.073 0.18 12 -0.11 9 21
PRKACA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.031 -10000 0 -0.071 24 24
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
CDC42 -0.032 0.052 0.16 33 -0.12 2 35
actin cytoskeleton reorganization -0.005 0.051 -10000 0 -0.059 100 100
PTK2 -0.011 0.059 0.15 29 -0.19 11 40
EDG1 -0.032 0.037 0.16 15 -0.098 11 26
mol:DAG -0.03 0.052 0.15 33 -0.12 2 35
CaM/Ca2+ -0.031 0.051 0.15 30 -0.13 1 31
MAP2K3 -0.036 0.05 0.14 31 -10000 0 31
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.043 0.095 0.18 133 -0.098 20 153
PLCG1 -0.03 0.052 0.16 33 -0.12 2 35
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.003 0.065 0.17 11 -0.1 14 25
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
YES1 0.017 0.034 -10000 0 -0.063 75 75
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.005 0.051 -10000 0 -0.077 36 36
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.007 0.051 -10000 0 -0.06 107 107
cell migration -0.009 0.075 0.2 11 -0.2 28 39
mol:PI-3-4-5-P3 -0.018 0.062 0.16 8 -0.15 23 31
FYN 0.029 0.011 -10000 0 -0.063 1 1
VEGFB/NRP1 -0.03 0.051 0.15 35 -0.12 2 37
mol:NO 0.005 0.058 0.25 4 -0.2 1 5
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.047 0.023 -10000 0 -0.095 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.04 -10000 0 -0.09 25 25
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
NOS3 0.004 0.061 0.26 4 -0.22 1 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.004 0.05 -10000 0 -0.078 34 34
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.033 0.05 0.14 34 -10000 0 34
PRKCB -0.028 0.048 0.14 33 -0.12 1 34
VCL 0.025 0.014 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.031 0.041 0.17 17 -0.12 2 19
VEGFR1/2 heterodimer/VEGFA homodimer -0.006 0.051 -10000 0 -0.073 47 47
VEGFA165/NRP2 -0.005 0.049 -10000 0 -0.05 275 275
MAPKKK cascade -0.033 0.039 0.18 6 -10000 0 6
NRP2 0.032 0.004 -10000 0 -0.063 1 1
VEGFC homodimer 0.029 0.015 -10000 0 -0.063 11 11
NCK1 0.03 0.015 -10000 0 -0.063 11 11
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.068 0.2 14 -0.2 9 23
MAP3K13 -0.033 0.052 0.16 32 -0.12 2 34
PDPK1 -0.034 0.053 0.15 8 -0.16 14 22
PDGFR-alpha signaling 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
PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
PDGF/PDGFRA/CRKL 0.037 0.021 -10000 0 -0.051 5 5
positive regulation of JUN kinase activity 0.039 0.035 -10000 0 -0.044 42 42
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.051 5 5
AP1 -0.027 0.073 0.14 58 -0.13 97 155
mol:IP3 -0.022 0.014 0.033 4 -0.066 2 6
PLCG1 -0.022 0.015 0.033 4 -0.066 2 6
PDGF/PDGFRA/alphaV Integrin 0.036 0.026 -10000 0 -0.053 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.014 0.033 4 -0.066 2 6
CAV3 0.032 0.004 -10000 0 -10000 0 0
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
SHC/Grb2/SOS1 0.041 0.036 -10000 0 -0.044 42 42
PDGF/PDGFRA/Shf 0.019 0.011 0.046 1 -0.04 6 7
FOS -0.04 0.048 0.17 4 -0.12 98 102
JUN -0.026 0.021 0.025 36 -10000 0 36
oligodendrocyte development 0.036 0.025 -10000 0 -0.053 20 20
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.014 0.033 4 -0.066 2 6
PDGF/PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
actin cytoskeleton reorganization 0.036 0.022 -10000 0 -0.05 4 4
SRF -0.021 0.007 0.02 1 -10000 0 1
SHC1 0.024 0.026 -10000 0 -0.063 40 40
PI3K 0.045 0.034 -10000 0 -0.05 22 22
PDGF/PDGFRA/Crk/C3G 0.049 0.031 -10000 0 -0.044 8 8
JAK1 -0.018 0.014 0.022 25 -0.052 5 30
ELK1/SRF -0.01 0.059 0.13 72 -10000 0 72
SHB 0.03 0.009 -10000 0 0 40 40
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.024 -10000 0 -0.03 65 65
GO:0007205 -0.016 0.011 0.023 4 -0.057 5 9
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.039 0.035 -10000 0 -0.044 42 42
PDGF/PDGFRA/SHB 0.036 0.022 -10000 0 -0.05 4 4
PDGF/PDGFRA/Caveolin-1 -0.009 0.038 -10000 0 -0.054 186 186
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
ELK1 -0.022 0.015 0.026 4 -0.07 2 6
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.05 5 5
JAK-STAT cascade -0.018 0.014 0.022 25 -0.052 5 30
cell proliferation 0.019 0.011 -10000 0 -0.04 6 6
Caspase cascade in apoptosis

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
TOP1 -0.016 0.097 0.3 1 -0.32 27 28
ACTA1 -0.045 0.088 0.4 1 -0.25 49 50
NUMA1 -0.014 0.086 0.3 1 -0.33 23 24
SPTAN1 -0.045 0.091 0.21 8 -0.31 33 41
LIMK1 -0.002 0.1 0.18 75 -0.28 26 101
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.063 6 6
CASP10 -0.02 0.013 -10000 0 -0.051 19 19
CRMA 0 0 -10000 0 -0.001 2 2
XIAP 0 0 0.001 2 -0.001 10 12
PTK2 -0.015 0.086 0.3 1 -0.3 28 29
DIABLO 0.032 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.041 0.094 0.21 8 -0.31 33 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.048 0.091 0.21 8 -0.3 35 43
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.03 0.09 -10000 0 -0.66 7 7
BID -0.004 0.014 -10000 0 -0.13 5 5
MAP3K1 -0.009 0.056 -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 -0.05 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.092 0.2 10 -0.25 50 60
CASP9 0.031 0.009 -10000 0 -0.063 3 3
DNA repair 0.026 0.06 0.16 47 -0.14 1 48
neuron apoptosis 0.021 0.069 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.093 0.32 2 -0.35 26 28
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.013 0.1 0.36 1 -0.92 4 5
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.091 0.31 5 -0.33 29 34
CASP7 -0.055 0.1 -10000 0 -0.22 135 135
KRT18 0.013 0.059 -10000 0 -0.49 5 5
apoptosis -0.048 0.1 0.6 1 -0.34 29 30
DFFA -0.049 0.089 0.26 3 -0.3 35 38
DFFB -0.049 0.089 0.26 3 -0.3 34 37
PARP1 -0.026 0.061 0.14 1 -0.16 47 48
actin filament polymerization -0.006 0.1 0.26 26 -0.17 75 101
TNF 0.032 0.006 -10000 0 -0.063 2 2
CYCS 0 0.029 0.25 1 -0.22 2 3
SATB1 0.017 0.1 0.43 1 -0.83 4 5
SLK -0.052 0.09 0.42 1 -0.26 49 50
p15 BID/BAX -0.011 0.066 0.21 1 -0.2 39 40
CASP2 0.041 0.088 0.2 116 -0.18 3 119
JNK cascade 0.009 0.056 0.38 7 -10000 0 7
CASP3 -0.047 0.091 0.24 1 -0.26 51 52
LMNB2 0.047 0.082 0.24 11 -0.35 2 13
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
CASP4 0.013 0.038 -10000 0 -0.063 101 101
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
negative regulation of DNA binding 0.03 0.089 -10000 0 -0.65 7 7
stress fiber formation -0.052 0.089 0.42 1 -0.26 48 49
GZMB -0.018 0.012 0 138 -0.052 19 157
CASP1 -0.011 0.034 -10000 0 -0.053 186 186
LMNB1 0.038 0.1 0.24 12 -0.39 9 21
APP 0.021 0.069 -10000 0 -0.63 5 5
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
response to stress 0 0 0.001 6 -0.001 21 27
CASP8 -0.012 0.004 0 1 -0.039 9 10
VIM -0.042 0.099 0.43 1 -0.34 29 30
LMNA 0.05 0.081 0.26 10 -0.34 2 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.039 -10000 0 -0.17 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.086 0.2 2 -0.3 36 38
APAF-1/Caspase 9 0.021 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.014 0.085 0.29 1 -0.32 23 24
CFL2 0.006 0.1 0.17 75 -0.27 26 101
GAS2 -0.052 0.087 0.2 2 -0.29 39 41
positive regulation of apoptosis 0.049 0.09 0.25 12 -0.36 5 17
PRF1 0.022 0.019 -10000 0 -0.063 12 12
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.022 -10000 0 -0.063 26 26
CCL5 0.028 0.021 -10000 0 -0.063 25 25
SDCBP 0.032 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.011 0.046 -10000 0 -0.18 12 12
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.009 0.053 0.17 2 -0.23 9 11
Syndecan-1/Syntenin 0.003 0.066 0.2 16 -0.23 8 24
MAPK3 -0.034 0.052 0.16 4 -0.21 13 17
HGF/MET 0.031 0.024 -10000 0 -0.05 3 3
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.063 26 26
BSG 0.031 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.009 0.052 0.17 2 -0.23 9 11
Syndecan-1/RANTES 0.001 0.069 0.2 16 -0.22 11 27
Syndecan-1/CD147 -0.026 0.058 0.19 4 -0.21 13 17
Syndecan-1/Syntenin/PIP2 0.002 0.063 0.19 16 -0.22 8 24
LAMA5 0.027 0.017 -10000 0 -0.063 13 13
positive regulation of cell-cell adhesion 0.002 0.062 0.19 16 -0.22 8 24
MMP7 0.018 0.034 -10000 0 -0.063 75 75
HGF 0.022 0.016 -10000 0 -0.063 1 1
Syndecan-1/CASK -0.013 0.045 -10000 0 -0.2 12 12
Syndecan-1/HGF/MET 0.004 0.058 0.2 5 -0.24 7 12
regulation of cell adhesion -0.034 0.07 0.23 18 -0.22 12 30
HPSE 0.024 0.027 -10000 0 -0.063 44 44
positive regulation of cell migration -0.011 0.046 -10000 0 -0.18 12 12
SDC1 -0.009 0.042 0.1 17 -0.12 22 39
Syndecan-1/Collagen -0.011 0.046 -10000 0 -0.18 12 12
PPIB -0.035 0.043 -10000 0 -0.063 355 355
MET 0.022 0.016 -10000 0 -0.063 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
MAPK1 -0.033 0.051 0.16 4 -0.21 13 17
homophilic cell adhesion -0.009 0.052 0.18 6 -0.19 12 18
MMP1 0.025 0.025 -10000 0 -0.063 38 38
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.009 -10000 0 -0.029 31 31
BUB1B -0.012 0.035 0.084 12 -0.13 18 30
PLK1 0.007 0.023 0.071 35 -0.092 4 39
PLK1S1 0.003 0.014 0.042 35 -0.047 4 39
KIF2A -0.001 0.025 0.15 6 -0.1 2 8
regulation of mitotic centrosome separation 0.007 0.023 0.071 35 -0.092 4 39
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.028 0.11 2 -0.079 9 11
WEE1 -0.018 0.066 -10000 0 -0.34 15 15
cytokinesis -0.011 0.04 0.16 3 -0.15 11 14
PP2A-alpha B56 0.056 0.077 -10000 0 -0.56 7 7
AURKA 0.007 0.017 0.092 4 -0.14 2 6
PICH/PLK1 -0.031 0.021 0.098 2 -0.088 11 13
CENPE -0.003 0.026 0.14 7 -0.12 3 10
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.026 0.14 7 -0.1 2 9
PPP2CA 0.032 0.005 -10000 0 -10000 0 0
FZR1 0.031 0.006 -10000 0 -10000 0 0
TPX2 -0.01 0.025 0.13 1 -10000 0 1
PAK1 0.032 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
CLSPN 0.009 0.031 0.1 2 -0.23 7 9
GORASP1 0.032 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 4 -0.011 3 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.014 0.042 35 -0.047 4 39
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -0.011 1 9
STAG2 0.028 0.021 -10000 0 -0.063 26 26
GRASP65/GM130/RAB1/GTP 0.011 0.067 -10000 0 -0.51 8 8
spindle elongation 0.007 0.023 0.071 35 -0.092 4 39
ODF2 0.032 0.007 -10000 0 -10000 0 0
BUB1 0.023 0.074 -10000 0 -0.59 7 7
TPT1 -0.005 0.055 0.087 1 -0.19 39 40
CDC25C 0.011 0.031 -10000 0 -0.25 6 6
CDC25B 0.026 0.018 -10000 0 -0.059 17 17
SGOL1 0.001 0.009 0.029 31 -10000 0 31
RHOA 0.032 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 -0.011 0.047 -10000 0 -0.088 40 40
CDC14B -0.011 0.004 0.009 11 -10000 0 11
CDC20 -0.022 0.047 -10000 0 -0.063 287 287
PLK1/PBIP1 -0.017 0.015 0.054 3 -0.077 8 11
mitosis -0.003 0.003 0.015 5 -10000 0 5
FBXO5 -0.013 0.033 0.11 7 -0.099 31 38
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 0 0.045 -10000 0 -0.063 170 170
metaphase plate congression 0.009 0.033 0.099 1 -0.23 8 9
ERCC6L -0.024 0.036 -10000 0 -0.097 32 32
NLP/gamma Tubulin 0.004 0.016 0.065 11 -0.064 6 17
microtubule cytoskeleton organization -0.005 0.055 0.087 1 -0.19 39 40
G2/M transition DNA damage checkpoint 0 0.002 0.011 5 -10000 0 5
PPP1R12A 0.032 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.011 5 -10000 0 5
PLK1/PRC1-2 0.007 0.047 0.13 3 -0.091 14 17
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.029 0.14 1 -0.086 5 6
RAB1A 0.032 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.022 0.067 43 -0.06 4 47
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.097 0.13 3 -0.23 100 103
microtubule-based process 0.009 0.031 0.12 3 -0.083 9 12
Golgi organization 0.007 0.023 0.071 35 -0.092 4 39
Cohesin/SA2 0.021 0.022 0.09 4 -0.07 6 10
PPP1CB/MYPT1 0.047 0.01 -10000 0 -0.046 1 1
KIF20A -0.001 0.045 -10000 0 -0.063 178 178
APC/C/CDC20 -0.001 0.03 0.12 1 -0.078 12 13
PPP2R1A 0.03 0.009 -10000 0 -10000 0 0
chromosome segregation -0.017 0.015 0.054 3 -0.076 8 11
PRC1 -0.008 0.047 -10000 0 -0.063 213 213
ECT2 -0.005 0.036 0.18 11 -0.12 3 14
C13orf34 0.005 0.02 0.064 35 -0.068 4 39
NUDC 0.009 0.033 0.1 1 -0.23 8 9
regulation of attachment of spindle microtubules to kinetochore -0.012 0.034 0.084 12 -0.12 18 30
spindle assembly 0.004 0.02 0.065 25 -0.077 4 29
spindle stabilization 0.003 0.014 0.042 35 -0.047 4 39
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.031 0.12 3 -0.084 9 12
CCNB1 -0.02 0.048 -10000 0 -0.063 280 280
PPP1CB 0.032 0.007 -10000 0 -0.058 2 2
BTRC 0.024 0.014 -10000 0 -10000 0 0
ROCK2 0.016 0.025 0.14 1 -0.22 2 3
TUBG1 0.009 0.022 0.086 2 -0.18 4 6
G2/M transition of mitotic cell cycle -0.025 0.029 -10000 0 -0.092 32 32
MLF1IP -0.034 0.012 -10000 0 -0.04 420 420
INCENP 0.032 0.004 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.042 0.21 8 -0.19 12 20
RFC1 -0.022 0.035 0.17 2 -0.19 14 16
PRKDC -0.023 0.035 0.17 2 -0.19 14 16
RIPK1 0.03 0.013 -10000 0 -0.062 9 9
CASP7 -0.15 0.26 -10000 0 -0.59 132 132
FASLG/FAS/FADD/FAF1 -0.022 0.057 0.11 1 -0.12 124 125
MAP2K4 -0.059 0.12 0.34 2 -0.24 128 130
mol:ceramide -0.014 0.061 -10000 0 -0.16 20 20
GSN -0.019 0.043 0.21 8 -0.19 13 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.062 0.14 1 -0.12 128 129
FAS 0.013 0.03 -10000 0 -0.064 55 55
BID -0.031 0.014 0.2 1 -10000 0 1
MAP3K1 -0.1 0.18 0.42 1 -0.39 135 136
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
RB1 -0.02 0.034 0.17 2 -0.19 13 15
CFLAR 0.032 0.009 -10000 0 -0.061 5 5
HGF/MET 0.037 0.037 -10000 0 -0.049 23 23
ARHGDIB -0.02 0.044 0.21 9 -0.2 11 20
FADD 0.032 0.006 -10000 0 -0.062 1 1
actin filament polymerization 0.019 0.043 0.19 13 -0.21 8 21
NFKB1 0.014 0.072 -10000 0 -0.62 6 6
MAPK8 -0.064 0.12 0.42 2 -0.24 126 128
DFFA -0.02 0.038 0.2 4 -0.2 13 17
DNA fragmentation during apoptosis -0.021 0.036 0.19 3 -0.2 13 16
FAS/FADD/MET 0.026 0.04 -10000 0 -0.048 53 53
CFLAR/RIP1 0.045 0.017 -10000 0 -0.048 14 14
FAIM3 0.031 0.007 -10000 0 -0.063 1 1
FAF1 0.031 0.006 -10000 0 -10000 0 0
PARP1 -0.023 0.037 0.22 2 -0.19 15 17
DFFB -0.021 0.036 0.19 3 -0.2 13 16
CHUK 0.005 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.034 -10000 0 -0.051 56 56
HGF 0.022 0.016 -10000 0 -0.063 1 1
LMNA -0.027 0.034 0.19 2 -0.18 13 15
CASP6 -0.023 0.033 0.17 2 -0.19 12 14
CASP10 0.032 0.002 -10000 0 -10000 0 0
CASP3 -0.016 0.033 0.16 1 -0.22 9 10
PTPN13 0.027 0.021 -10000 0 -0.063 26 26
CASP8 -0.03 0.007 0.053 1 -0.059 3 4
IL6 -0.025 0.092 0.29 1 -0.52 7 8
MET 0.022 0.016 -10000 0 -0.063 2 2
ICAD/CAD -0.026 0.04 0.25 4 -0.19 13 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.015 0.061 -10000 0 -0.16 20 20
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.02 0.041 0.21 7 -0.19 12 19
BCL2 0.032 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure 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 0.004 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.05 0.14 0.22 2 -0.27 128 130
HIF1A -0.048 0.13 -10000 0 -0.32 90 90
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.014 -10000 0 -10000 0 0
CDKN2A 0.003 0.026 -10000 0 -0.063 52 52
ARNT/IPAS 0.045 0.013 -10000 0 -10000 0 0
HIF1AN 0.024 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.045 0.14 0.16 1 -0.27 124 125
CUL2 0.025 0.014 -10000 0 -10000 0 0
OS9 0.028 0.012 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.063 0.017 -10000 0 -0.053 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.044 0.14 0.2 3 -0.27 128 131
PHD1-3/OS9 0.059 0.043 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.023 0.15 0.18 1 -0.27 126 127
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.045 0.14 0.22 2 -0.27 127 129
EGLN3 0.03 0.011 -10000 0 -0.063 4 4
EGLN2 0.031 0.006 -10000 0 -10000 0 0
EGLN1 0.032 0.007 -10000 0 -0.063 1 1
TP53 0.019 0.032 -10000 0 -0.063 65 65
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.002 0.07 -10000 0 -0.57 3 3
ARNT 0.032 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF -0.059 0.13 0.2 3 -0.27 127 130
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.005 0.078 0.15 3 -0.17 34 37
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.035 27 27
BIRC3 -0.033 0.021 0.17 3 -10000 0 3
CYCS 0.004 0.068 0.17 61 -0.12 3 64
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
CD247 0.033 0.008 -10000 0 -0.063 2 2
MAP2K7 -0.007 0.088 -10000 0 -0.39 8 8
protein ubiquitination 0.002 0.05 0.2 7 -0.25 7 14
CRADD 0.032 0.004 -10000 0 -10000 0 0
DAXX 0.032 0.005 -10000 0 -0.063 1 1
FAS 0.013 0.03 -10000 0 -0.063 55 55
BID -0.018 0.044 0.16 3 -0.1 94 97
NF-kappa-B/RelA/I kappa B alpha 0.054 0.042 -10000 0 -0.062 35 35
TRADD 0.032 0.004 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
CFLAR 0.032 0.01 -10000 0 -0.063 5 5
FADD 0.032 0.006 -10000 0 -0.063 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.042 -10000 0 -0.062 35 35
MAPK8 -0.004 0.085 0.54 1 -0.38 8 9
APAF1 0.032 0.004 -10000 0 -10000 0 0
TRAF1 0.031 0.008 -10000 0 -0.063 1 1
TRAF2 0.031 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.024 0.18 3 -0.13 6 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.05 -10000 0 -0.26 7 7
CHUK 0.003 0.05 0.2 7 -0.25 7 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.071 -10000 0 -10000 0 0
TCRz/NEF 0.028 0.006 -10000 0 -0.039 2 2
TNF 0.032 0.006 -10000 0 -0.063 2 2
FASLG -0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.037 32 32
TNFR1A/BAG4/TNF-alpha 0.025 0.054 -10000 0 -0.048 165 165
CASP6 0.008 0.086 -10000 0 -0.47 4 4
CASP7 -0.06 0.11 0.21 2 -0.24 130 132
RELA 0.029 0.016 -10000 0 -0.033 30 30
CASP2 0.023 0.015 -10000 0 -10000 0 0
CASP3 -0.03 0.071 0.2 3 -0.25 22 25
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
TNFR1A/BAG4 0.014 0.045 -10000 0 -0.05 164 164
CASP8 0.031 0.013 -10000 0 -0.063 9 9
CASP9 0.031 0.009 -10000 0 -0.063 3 3
MAP3K14 0.01 0.054 0.16 2 -0.26 9 11
APAF-1/Caspase 9 -0.017 0.071 0.13 65 -0.16 7 72
BCL2 -0.016 0.086 0.3 4 -0.36 8 12
Signaling mediated by p38-alpha and p38-beta

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

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
EP300 0.022 0.019 -10000 0 -0.026 53 53
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.061 -10000 0 -0.079 13 13
AKT1 0.031 0.009 -10000 0 -10000 0 0
GSC 0.007 0.026 0.08 31 -10000 0 31
NKX2-5 0.036 0.012 0.089 9 -10000 0 9
muscle cell differentiation -0.013 0.07 0.25 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.018 0.076 0.2 1 -0.11 15 16
SMAD4 -0.008 0.05 0.11 2 -0.081 100 102
CBFB 0.031 0.009 -10000 0 -0.063 4 4
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.05 0.031 -10000 0 -0.049 34 34
SMAD3/SMAD4/VDR 0.042 0.075 -10000 0 -0.093 3 3
MYC 0.008 0.04 -10000 0 -0.064 119 119
CDKN2B -0.21 0.19 -10000 0 -0.36 299 299
AP1 -0.003 0.048 0.15 5 -0.084 15 20
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.07 -10000 0 -0.21 33 33
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.012 0.061 0.14 3 -0.25 23 26
SP3 0.018 0.034 -10000 0 -0.061 81 81
CREB1 0.033 0.001 -10000 0 -10000 0 0
FOXH1 0.035 0.011 0.1 5 -10000 0 5
SMAD3/SMAD4/GR 0.033 0.059 -10000 0 -0.08 19 19
GATA3 0.025 0.015 -10000 0 -0.063 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.068 -10000 0 -0.17 44 44
MEF2C/TIF2 -0.034 0.039 0.22 8 -10000 0 8
endothelial cell migration 0.034 0.067 0.45 2 -10000 0 2
MAX 0.034 0.01 -10000 0 -10000 0 0
RBBP7 0.033 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.009 -10000 0 -0.063 3 3
RUNX1 0.032 0.005 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 0.035 0.006 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
CDKN1A -0.015 0.053 0.33 3 -10000 0 3
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.029 0.05 0.26 1 -0.059 33 34
DCP1A 0.032 0.006 -10000 0 -10000 0 0
SKI 0.031 0.007 -10000 0 -10000 0 0
SERPINE1 -0.032 0.067 -10000 0 -0.46 2 2
SMAD3/SMAD4/ATF2 0.024 0.06 -10000 0 -0.075 42 42
SMAD3/SMAD4/ATF3 0.008 0.064 -10000 0 -0.079 73 73
SAP30 0.032 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.052 0.023 -10000 0 -0.042 12 12
JUN -0.026 0.037 0.13 10 -10000 0 10
SMAD3/SMAD4/IRF7 0.024 0.063 -10000 0 -0.086 23 23
TFE3 -0.006 0.037 -10000 0 -0.039 275 275
COL1A2 -0.025 0.052 -10000 0 -0.16 4 4
mesenchymal cell differentiation -0.023 0.06 0.077 34 -10000 0 34
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.006 -10000 0 -10000 0 0
FOS 0.004 0.044 -10000 0 -0.061 151 151
SMAD3/SMAD4/Max 0.031 0.061 -10000 0 -0.077 31 31
Cbp/p300/SNIP1 0.057 0.022 -10000 0 -0.039 10 10
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.05 0.042 0.14 4 -0.12 13 17
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.058 -10000 0 -0.076 37 37
IRF7 0.029 0.016 -10000 0 -0.064 12 12
ESR1 0.037 0.014 0.13 3 -10000 0 3
HNF4A 0.03 0.008 -10000 0 -10000 0 0
MEF2C -0.03 0.04 0.2 11 -10000 0 11
SMAD2-3/SMAD4 0.026 0.061 0.18 1 -0.082 17 18
Cbp/p300/Src-1 0.053 0.024 -10000 0 -0.041 12 12
IGHV3OR16-13 0.006 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.03 0.012 -10000 0 -0.063 4 4
CREBBP 0.03 0.006 -10000 0 -0.026 2 2
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.031 -10000 0 -0.063 61 61
HDAC2 0.03 0.012 -10000 0 -0.063 4 4
SNIP1 0.032 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0 0.072 -10000 0 -0.09 87 87
MSG1/HSC70 0.044 0.022 -10000 0 -0.049 24 24
SMAD2 0.036 0.012 0.13 3 -10000 0 3
SMAD3 0.001 0.039 -10000 0 -0.065 9 9
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.042 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.01 0.039 0.12 9 -0.17 12 21
NCOR1 0.032 0.004 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
MYOD/E2A 0.046 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.081 0.21 1 -0.12 3 4
IFNB1 -0.022 0.033 0.14 8 -10000 0 8
SMAD3/SMAD4/MEF2C -0.009 0.054 0.2 3 -10000 0 3
CITED1 0.028 0.02 -10000 0 -0.063 24 24
SMAD2-3/SMAD4/ARC105 0.041 0.066 0.19 1 -0.085 9 10
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.051 0.16 2 -0.23 15 17
RUNX1-3/PEBPB2 0.059 0.025 -10000 0 -0.049 8 8
SMAD7 -0.024 0.064 0.12 1 -0.18 38 39
MYC/MIZ-1 0.022 0.041 -10000 0 -0.051 116 116
SMAD3/SMAD4 -0.045 0.066 -10000 0 -0.23 33 33
IL10 -0.032 0.04 0.16 13 -10000 0 13
PIASy/HDAC complex 0.033 0.006 -10000 0 -10000 0 0
PIAS3 0.031 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.021 -10000 0 -0.064 24 24
IL5 -0.033 0.04 0.16 13 -10000 0 13
CDK4 -0.021 0.044 -10000 0 -0.064 251 251
PIAS4 0.033 0.006 -10000 0 -10000 0 0
ATF3 0.012 0.038 -10000 0 -0.063 103 103
SMAD3/SMAD4/SP1 -0.003 0.069 -10000 0 -0.11 32 32
FOXG1 0.027 0.012 -10000 0 -10000 0 0
FOXO3 -0.019 0.007 -10000 0 -10000 0 0
FOXO1 -0.019 0.008 -10000 0 -10000 0 0
FOXO4 -0.02 0.006 -10000 0 -10000 0 0
heart looping -0.03 0.04 0.2 11 -10000 0 11
CEBPB 0.029 0.016 -10000 0 -0.062 11 11
SMAD3/SMAD4/DLX1 0.007 0.047 -10000 0 -0.067 38 38
MYOD1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.024 0.058 -10000 0 -0.075 37 37
SMAD3/SMAD4/GATA3 0.017 0.065 -10000 0 -0.088 23 23
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.052 0.07 -10000 0 -0.088 2 2
SMAD3/SMAD4/SP1-3 0.01 0.081 -10000 0 -0.12 28 28
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.004 0.036 -10000 0 -0.052 50 50
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.04 0.06 -10000 0 -10000 0 0
ITGB5 -0.043 0.052 0.24 9 -10000 0 9
TGIF/SIN3/HDAC complex/CtBP -0.019 0.06 -10000 0 -0.16 53 53
SMAD3/SMAD4/AR 0.023 0.061 -10000 0 -0.076 48 48
AR 0.031 0.012 -10000 0 -0.063 8 8
negative regulation of cell growth -0.003 0.048 -10000 0 -0.23 13 13
SMAD3/SMAD4/MYOD 0.023 0.06 -10000 0 -0.076 38 38
E2F5 0.032 0.004 -10000 0 -10000 0 0
E2F4 0.032 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.043 0.066 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.042 0.13 2 -0.2 11 13
TFDP1 0.029 0.015 -10000 0 -0.063 11 11
SMAD3/SMAD4/AP1 0.012 0.064 -10000 0 -0.085 14 14
SMAD3/SMAD4/RUNX2 0.024 0.06 -10000 0 -0.077 34 34
TGIF2 0.03 0.012 -10000 0 -0.063 4 4
TGIF1 -0.033 0.043 -10000 0 -0.063 343 343
ATF2 0.032 0.002 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.061 0.047 -10000 0 -0.058 1 1
MAP4K1 0.031 0.008 -10000 0 -0.063 1 1
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
MAP3K1 0.001 0.034 0.076 14 -0.12 28 42
JUN -0.12 0.23 0.23 2 -0.52 121 123
MAP3K7 0.002 0.033 0.076 14 -0.13 19 33
GRAP2 0.03 0.008 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
MAP2K4 -0.02 0.063 0.15 5 -0.22 32 37
LAT 0.032 0.005 -10000 0 -0.063 1 1
LCP2 0.026 0.022 -10000 0 -0.063 29 29
MAPK8 -0.12 0.24 -10000 0 -0.55 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.035 0.088 14 -0.14 16 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.057 0.044 -10000 0 -0.054 1 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.006 -10000 0 -0.063 1 1
LAT2 -0.015 0.03 0.12 4 -0.12 8 12
AP1 -0.031 0.11 -10000 0 -0.3 23 23
mol:PIP3 0.026 0.1 0.26 37 -0.18 1 38
IKBKB 0.016 0.074 0.21 33 -0.14 1 34
AKT1 -0.033 0.077 0.3 12 -10000 0 12
IKBKG 0.016 0.073 0.2 34 -0.14 1 35
MS4A2 0.035 0.005 0.069 1 -10000 0 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
MAP3K1 -0.01 0.06 0.22 14 -0.21 5 19
mol:Ca2+ 0.025 0.09 0.23 40 -0.14 1 41
LYN 0.02 0.032 0.086 1 -0.065 62 63
CBLB -0.015 0.036 0.14 7 -0.12 10 17
SHC1 0.024 0.026 -10000 0 -0.063 40 40
RasGAP/p62DOK 0.056 0.024 -10000 0 -0.042 21 21
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.06 0.32 11 -10000 0 11
PTPN13 0.005 0.074 0.32 1 -0.57 5 6
PTPN11 0.032 0.01 -10000 0 -0.029 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.074 0.32 8 -0.28 5 13
SYK 0.024 0.025 -10000 0 -0.064 35 35
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.013 0.066 0.18 18 -0.16 5 23
LAT -0.015 0.037 0.14 7 -0.12 10 17
PAK2 -0.006 0.061 0.21 16 -0.21 6 22
NFATC2 -0.012 0.005 -10000 0 -10000 0 0
HRAS -0.002 0.057 0.18 21 -0.2 8 29
GAB2 0.032 0.006 -10000 0 -10000 0 0
PLA2G1B 0.021 0.064 -10000 0 -0.81 2 2
Fc epsilon R1 0.009 0.058 -10000 0 -0.05 240 240
Antigen/IgE/Fc epsilon R1 0.011 0.055 -10000 0 -0.045 238 238
mol:GDP 0.003 0.051 0.18 16 -0.19 1 17
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
FOS 0.007 0.04 -10000 0 -0.063 120 120
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.007 0.036 0.12 3 -0.12 7 10
CHUK 0.007 0.068 0.2 30 -0.14 1 31
KLRG1 -0.012 0.026 0.082 3 -0.089 6 9
VAV1 -0.015 0.037 0.11 11 -0.13 10 21
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.036 0.14 7 -0.12 8 15
negative regulation of mast cell degranulation -0.013 0.027 0.076 2 -0.1 5 7
BTK 0.007 0.04 0.2 1 -10000 0 1
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.008 0.029 -10000 0 -0.1 8 8
GAB2/PI3K/SHP2 -0.052 0.024 0.027 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.03 0.075 1 -0.083 35 36
RAF1 0.024 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.065 -10000 0 -0.065 101 101
FCER1G -0.014 0.049 -10000 0 -0.065 242 242
FCER1A 0.03 0.015 -10000 0 -0.06 12 12
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.062 -10000 0 -0.056 28 28
MAPK3 0.024 0.063 -10000 0 -0.82 2 2
MAPK1 0.014 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.1 0.25 -10000 0 -0.52 122 122
DUSP1 0.029 0.017 -10000 0 -0.063 16 16
NF-kappa-B/RelA 0.007 0.051 0.13 28 -0.099 1 29
actin cytoskeleton reorganization 0.012 0.076 0.33 1 -0.59 5 6
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.066 0.2 15 -0.19 7 22
FER -0.015 0.036 0.14 7 -0.12 9 16
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.025 -10000 0 -0.23 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.015 0.074 0.25 23 -0.19 1 24
cytokine secretion 0.001 0.032 0.071 26 -0.073 1 27
SPHK1 -0.016 0.035 0.13 6 -0.12 10 16
PTK2 0.012 0.079 0.34 1 -0.62 5 6
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.02 0.08 0.17 76 -0.16 5 81
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.02 0.091 0.25 33 -0.24 2 35
MAP2K2 0.02 0.07 -10000 0 -0.84 2 2
MAP2K1 0.015 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.045 0.2 11 -0.097 4 15
MAP2K4 0.001 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.007 0.071 -10000 0 -0.07 104 104
mol:Choline -0.03 0.06 0.32 11 -10000 0 11
SHC/Grb2/SOS1 0.008 0.058 0.17 4 -0.13 6 10
FYN 0.029 0.011 -10000 0 -0.063 1 1
DOK1 0.032 0.002 -10000 0 -10000 0 0
PXN 0.007 0.078 0.4 3 -0.57 5 8
HCLS1 -0.018 0.039 0.14 7 -0.13 10 17
PRKCB 0.021 0.084 0.23 34 -0.18 1 35
FCGR2B 0.01 0.04 -10000 0 -0.063 120 120
IGHE -0.001 0.004 0.053 1 -10000 0 1
KLRG1/SHIP -0.014 0.027 0.077 2 -0.1 5 7
LCP2 0.027 0.023 -10000 0 -0.063 29 29
PLA2G4A -0.02 0.038 0.14 7 -0.13 10 17
RASA1 0.032 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.03 0.06 0.32 11 -10000 0 11
IKK complex 0.007 0.068 0.22 23 -10000 0 23
WIPF1 0.03 0.014 -10000 0 -0.063 11 11
IL1-mediated signaling events

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
UBC13/UEV1A 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.053 -10000 0 -0.18 29 29
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.031 4 4
IKBKB 0.032 0.003 -10000 0 -10000 0 0
IKBKG 0.032 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.027 -10000 0 -0.05 40 40
IL1A 0.032 0.008 -10000 0 -0.063 3 3
IL1B -0.032 0.014 -10000 0 -0.051 171 171
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.026 0.17 4 -10000 0 4
IL1R2 0.025 0.025 -10000 0 -0.063 37 37
IL1R1 0.032 0.008 -10000 0 -0.063 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.047 -10000 0 -0.17 23 23
TOLLIP 0.031 0.006 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.005 -10000 0 -0.031 1 1
IKK complex/ELKS -0.026 0.096 -10000 0 -0.19 120 120
JUN -0.025 0.022 0.14 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.019 0.068 0.18 2 -0.091 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.057 -10000 0 -0.069 11 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.056 0.066 -10000 0 -0.071 11 11
IL1 beta fragment/IL1R1/IL1RAP 0.009 0.05 -10000 0 -0.054 186 186
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.022 0.023 0.16 5 -10000 0 5
IRAK1 -0.017 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.048 0.008 -10000 0 -0.05 3 3
IRAK4 0.031 0.008 -10000 0 -0.063 1 1
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.047 0.13 1 -0.18 22 23
CHUK 0.024 0.015 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.009 0.05 -10000 0 -0.054 186 186
IL1 beta/IL1R2 0.004 0.044 -10000 0 -0.051 192 192
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.023 0.16 4 -10000 0 4
NF kappa B1 p50/RelA 0.007 0.064 -10000 0 -0.098 7 7
IRAK3 0.031 0.008 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.015 0.057 0.16 2 -0.07 33 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.041 -10000 0 -0.12 37 37
IL1 alpha/IL1R1/IL1RAP 0.053 0.036 -10000 0 -0.047 54 54
RELA 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.006 -10000 0 -0.063 1 1
MYD88 0.019 0.032 -10000 0 -0.063 67 67
IRAK/TRAF6/MEKK3 0.05 0.018 0.18 4 -10000 0 4
IL1RAP 0.024 0.026 -10000 0 -0.063 41 41
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.052 0.016 0.035 1 -0.092 4 5
CASP1 0.001 0.044 -10000 0 -0.063 166 166
IL1RN/IL1R2 0.041 0.026 -10000 0 -0.05 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.011 0.064 0.17 2 -0.075 67 69
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.048 -10000 0 -0.23 12 12
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
IL1RN 0.032 0.002 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.02 -10000 0 -0.035 5 5
MAP2K6 -0.023 0.025 0.17 8 -10000 0 8
Signaling events regulated by Ret tyrosine kinase

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 0.013 0.052 -10000 0 -0.35 10 10
Crk/p130 Cas/Paxillin -0.037 0.081 -10000 0 -0.18 118 118
JUN -0.012 0.029 -10000 0 -0.18 7 7
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.043 0.05 -10000 0 -0.056 3 3
RAP1A 0.032 0.004 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.048 0.058 -10000 0 -0.056 2 2
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.036 0.042 -10000 0 -0.041 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 0.005 -10000 0 -0.063 1 1
RET51/GFRalpha1/GDNF 0.048 0.057 -10000 0 -0.058 1 1
MAPKKK cascade -0.005 0.076 -10000 0 -0.13 127 127
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.036 0.042 -10000 0 -0.043 8 8
lamellipodium assembly -0.013 0.061 -10000 0 -0.17 50 50
RET51/GFRalpha1/GDNF/SHC 0.038 0.061 -10000 0 -0.061 7 7
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
RET9/GFRalpha1/GDNF/SHC 0.029 0.046 -10000 0 -0.043 43 43
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.024 137 137
MAPK3 -0.038 0.03 0.17 9 -10000 0 9
DOK1 0.032 0.002 -10000 0 -10000 0 0
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
neurite development -0.027 0.029 0.18 7 -10000 0 7
DOK5 0.028 0.011 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.063 1 1
MAPK8 0.001 0.03 -10000 0 -0.12 25 25
HRAS/GTP 0.019 0.097 -10000 0 -0.14 131 131
tube development 0.02 0.035 0.16 10 -10000 0 10
MAPK1 -0.033 0.046 0.23 10 -10000 0 10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.055 -10000 0 -0.11 122 122
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
PDLIM7 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.046 0.05 -10000 0 -0.048 2 2
SHC1 0.024 0.026 -10000 0 -0.063 40 40
RET51/GFRalpha1/GDNF/Dok4 0.047 0.058 -10000 0 -0.055 7 7
RET51/GFRalpha1/GDNF/Dok5 0.047 0.053 -10000 0 -0.054 1 1
PRKCA 0.032 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
CREB1 -0.036 0.096 -10000 0 -0.2 125 125
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.055 -10000 0 -0.11 124 124
RET51/GFRalpha1/GDNF/Grb7 0.048 0.058 -10000 0 -0.057 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.014 -10000 0 -0.063 1 1
DOK4 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.012 0.029 -10000 0 -0.18 7 7
RET9/GFRalpha1/GDNF/FRS2 0.036 0.041 -10000 0 -0.032 127 127
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.053 -10000 0 -0.1 125 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.095 -10000 0 -0.19 125 125
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.098 -10000 0 -0.19 136 136
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.033 -10000 0 -0.12 26 26
PI3K -0.043 0.11 -10000 0 -0.23 121 121
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.039 -10000 0 -0.029 131 131
GRB10 0.021 0.018 -10000 0 -0.063 6 6
activation of MAPKK activity -0.014 0.069 0.1 7 -0.15 102 109
RET51/GFRalpha1/GDNF/FRS2 0.047 0.057 -10000 0 -0.055 4 4
GAB1 0.032 0.008 -10000 0 -0.063 3 3
IRS1 0.032 0.009 -10000 0 -0.063 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.036 -10000 0 -0.12 28 28
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.058 -10000 0 -0.056 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GDNF 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.047 0.058 -10000 0 -0.061 4 4
Rac1/GTP -0.013 0.071 -10000 0 -0.2 50 50
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.04 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.05 1 1
TCGA08_rtk_signaling

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
PDGFRA 0.026 0.015 -10000 0 -0.063 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
AKT 0.12 0.092 0.22 197 -0.14 1 198
FOXO3 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.016 -10000 0 -0.063 11 11
AKT3 0.031 0.007 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.063 2 2
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PIK3CB 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.009 0.041 -10000 0 -0.063 125 125
PIK3CG 0.023 0.015 -10000 0 -10000 0 0
PIK3R3 0.032 0.006 -10000 0 -0.063 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.032 0.003 -10000 0 -10000 0 0
RAS 0.006 0.024 -10000 0 -0.084 9 9
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.044 0.07 0.3 9 -0.21 15 24
PI3K 0.049 0.072 0.17 95 -10000 0 95
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 0.21 194 -10000 0 194
AKT2 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.063 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.043 -10000 0 -0.085 111 111
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.063 5 5
alpha4/beta7 Integrin/MAdCAM1 0.074 0.031 -10000 0 -0.069 2 2
EPO 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.06 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.022 -10000 0 -0.05 4 4
EPO/EPOR (dimer) 0.033 0.023 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.082 -10000 0 -0.3 30 30
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.039 0.023 -10000 0 -0.05 16 16
ARF6 0.031 0.008 -10000 0 -10000 0 0
JAK2 0.009 0.028 -10000 0 -0.091 31 31
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
MADCAM1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0.072 0.03 -10000 0 -0.069 2 2
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.041 0.02 0.17 2 -10000 0 2
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.02 0.05 -10000 0 -0.05 335 335
p130Cas/Crk/Dock1 -0.048 0.023 0.18 3 -10000 0 3
VCAM1 -0.03 0.045 -10000 0 -0.063 333 333
RHOA 0.032 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.053 -10000 0 -0.058 1 1
BCAR1 -0.037 0.035 0.27 4 -10000 0 4
EPOR 0.031 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.084 -10000 0 -0.31 30 30
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.006 0.047 -10000 0 -0.051 258 258
alphaV beta3 Integrin 0.06 0.025 -10000 0 -0.044 26 26
PTK2 -0.01 0.063 0.29 7 -0.26 6 13
IGF1R 0.032 0.004 -10000 0 -10000 0 0
PI4KB 0.032 0.005 -10000 0 -10000 0 0
MFGE8 0.032 0.007 -10000 0 -0.063 2 2
SRC 0.031 0.008 -10000 0 -10000 0 0
CDKN1B 0.013 0.051 -10000 0 -0.26 17 17
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.041 -10000 0 -0.25 13 13
PTK2B -0.029 0.058 0.16 40 -10000 0 40
alphaV/beta3 Integrin/JAM-A 0.055 0.041 0.17 6 -10000 0 6
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.06 0.024 -10000 0 -0.044 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.079 0.023 -10000 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.044 -10000 0 -0.16 24 24
alphaV/beta3 Integrin/Syndecan-1 0.051 0.038 -10000 0 -0.048 62 62
PI4KA 0.012 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.043 0.06 -10000 0 -0.094 2 2
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
alphaV/beta3 Integrin/Osteopontin 0.022 0.055 -10000 0 -0.049 186 186
RPS6KB1 -0.048 0.043 0.68 1 -10000 0 1
TLN1 0.021 0.027 -10000 0 -0.063 43 43
MAPK3 0 0.039 -10000 0 -0.28 8 8
GPR124 0.032 0.007 -10000 0 -0.063 2 2
MAPK1 -0.001 0.039 -10000 0 -0.28 8 8
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.022 -10000 0 -0.046 19 19
cell adhesion 0.047 0.03 -10000 0 -0.082 4 4
ANGPTL3 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.003 0.054 -10000 0 -0.049 237 237
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
TGFBR2 0.031 0.01 -10000 0 -0.063 5 5
ITGB3 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.059 0.024 -10000 0 -0.045 23 23
apoptosis 0.029 0.016 -10000 0 -0.063 15 15
CD47 0.031 0.008 -10000 0 -0.063 2 2
alphaV/beta3 Integrin/CD47 0.059 0.026 -10000 0 -0.044 26 26
VCL 0.025 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.06 0.024 -10000 0 -0.043 24 24
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.009 0.013 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.02 0.034 0.098 8 -0.1 1 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.005 0.064 -10000 0 -0.069 20 20
FAK1/Vinculin -0.005 0.056 0.28 6 -0.23 6 12
alphaV beta3/Integrin/ppsTEM5 0.06 0.024 -10000 0 -0.045 23 23
RHOA 0.032 0.006 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -0.063 2 2
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.063 2 2
F11R -0.024 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.025 -10000 0 -0.044 26 26
alphaV/beta3 Integrin/TGFBR2 0.059 0.027 -10000 0 -0.044 29 29
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.023 -10000 0 -0.039 23 23
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.039 -10000 0 -0.039 87 87
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.037 -10000 0 -0.063 96 96
alphaV/beta3 Integrin/Pyk2 0.002 0.067 0.17 34 -0.072 18 52
SDC1 0.024 0.027 -10000 0 -0.063 45 45
VAV3 -0.028 0.021 0.18 5 -10000 0 5
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.063 4 4
FAK1/Paxillin -0.003 0.062 0.26 7 -0.22 6 13
cell migration -0.016 0.051 0.25 7 -0.21 6 13
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
PI3K 0.061 0.049 0.16 5 -10000 0 5
SPP1 -0.001 0.045 -10000 0 -0.063 175 175
KDR 0.028 0.017 -10000 0 -0.063 14 14
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.016 -10000 0 -0.063 15 15
COL4A3 0.033 0.001 -10000 0 -10000 0 0
angiogenesis 0.002 0.044 0.18 3 -0.31 8 11
Rac1/GTP -0.023 0.024 0.18 4 -10000 0 4
EDIL3 0.032 0.004 -10000 0 -10000 0 0
cell proliferation 0.058 0.027 -10000 0 -0.044 29 29
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.16 9 -0.082 15 24
IHH 0.038 0.021 0.11 17 -0.044 13 30
SHH Np/Cholesterol/GAS1 0.014 0.02 -10000 0 -0.041 37 37
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.013 0.02 0.041 37 -10000 0 37
SMO/beta Arrestin2 0.066 0.056 0.16 116 -0.14 1 117
SMO 0.014 0.019 0.14 3 -10000 0 3
AKT1 0.003 0.083 -10000 0 -0.34 20 20
ARRB2 0.032 0.005 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
heart looping 0.014 0.019 0.14 3 -10000 0 3
STIL 0.024 0.085 0.17 125 -10000 0 125
DHH N/PTCH2 0.024 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.014 -10000 0 -0.056 7 7
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.015 0.024 0.16 7 -0.094 6 13
determination of left/right symmetry 0.014 0.019 0.14 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
skeletal system development 0.015 0.024 0.16 7 -0.093 6 13
IHH N/Hhip 0.025 0.012 0.071 17 -0.021 7 24
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.014 0.019 0.14 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.03 -10000 0 -0.063 55 55
somite specification 0.014 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.017 -10000 0 -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 -0.033 5 5
SHH -0.015 0.011 -10000 0 -10000 0 0
catabolic process 0.02 0.017 -10000 0 -0.063 13 13
SMO/Vitamin D3 0.016 0.032 0.18 14 -10000 0 14
SHH Np/Cholesterol/Hhip -0.011 0.007 0 163 -10000 0 163
LRP2 0.032 0.005 -10000 0 -0.063 1 1
receptor-mediated endocytosis 0.012 0.027 0.15 13 -10000 0 13
SHH Np/Cholesterol/BOC -0.011 0.007 0 163 -10000 0 163
SHH Np/Cholesterol/CDO 0.018 0.014 -10000 0 -0.031 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 163 163
mol:Vitamin D3 0.041 0.096 0.19 146 -10000 0 146
IHH N/PTCH2 0.05 0.012 0.11 8 -0.036 1 9
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.036 0.021 -10000 0 -0.06 20 20
Megalin/LRPAP1 0.047 0.007 -10000 0 -0.05 1 1
PTCH2 0.032 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.011 0.007 -10000 0 -10000 0 0
PTCH1 0.02 0.017 -10000 0 -0.063 13 13
HHIP 0 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.061 0.022 -10000 0 -0.042 21 21
fibroblast growth factor receptor signaling pathway 0.06 0.022 -10000 0 -0.041 21 21
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.028 0.011 -10000 0 -10000 0 0
GPC1/SLIT2 0.03 0.024 -10000 0 -0.05 5 5
SMAD2 -0.027 0.029 0.17 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.037 0.018 -10000 0 -0.04 7 7
GPC1/Laminin alpha1 0.023 0.008 -10000 0 -0.039 7 7
TDGF1 0.031 0.008 -10000 0 -0.063 2 2
CRIPTO/GPC1 0.045 0.016 -10000 0 -0.05 9 9
APP/GPC1 0.046 0.014 -10000 0 -0.05 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.011 -10000 0 -0.069 4 4
FLT1 0.03 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.026 -10000 0 -0.048 13 13
SERPINC1 0.032 0.006 -10000 0 -0.063 1 1
FYN -0.024 0.009 -10000 0 -10000 0 0
FGR -0.026 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.06 0.18 32 -0.2 6 38
SLIT2 0.021 0.017 -10000 0 -0.063 3 3
GPC1/NRG 0.046 0.014 -10000 0 -0.05 7 7
NRG1 0.032 0.004 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0 0.056 -10000 0 -0.049 276 276
LYN -0.028 0.01 -10000 0 -0.069 1 1
mol:Spermine -0.012 0.003 -10000 0 -0.039 7 7
cell growth 0.06 0.022 -10000 0 -0.041 21 21
BMP signaling pathway -0.031 0.012 0.063 7 -10000 0 7
SRC -0.024 0.008 -10000 0 -0.048 8 8
TGFBR1 0.032 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.002 0.045 -10000 0 -0.058 194 194
GPC1 0.031 0.012 -10000 0 -0.063 7 7
TGFBR1 (dimer) 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
BLK -0.025 0.007 -10000 0 -10000 0 0
HCK -0.028 0.013 -10000 0 -0.069 1 1
FGF2 0.032 0.007 -10000 0 -0.063 2 2
FGFR1 0.032 0.005 -10000 0 -0.063 1 1
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.01 -10000 0 -0.063 5 5
cell death 0.045 0.014 -10000 0 -0.049 7 7
ATIII/GPC1 0.046 0.014 -10000 0 -0.05 8 8
PLA2G2A/GPC1 0.011 0.047 -10000 0 -0.05 182 182
LCK -0.026 0.007 -10000 0 -0.069 1 1
neuron differentiation 0.046 0.014 -10000 0 -0.049 7 7
PrPc/Cu2+ 0.021 0.008 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.031 0.01 -10000 0 -0.063 5 5
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.031 -10000 0 -0.057 61 61
AES 0.034 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.024 -10000 0 -0.05 4 4
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
DKK2 0.031 0.012 -10000 0 -0.063 8 8
TLE1 0.034 0.008 -10000 0 -10000 0 0
MACF1 0.032 0.006 -10000 0 -10000 0 0
CTNNB1 0.096 0.099 0.21 154 -0.27 6 160
WIF1 0.004 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.098 0.078 0.23 51 -0.3 3 54
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.006 0.037 -10000 0 -0.062 101 101
beta catenin/beta TrCP1 0.11 0.095 0.22 149 -0.26 6 155
FZD1 0.022 0.017 -10000 0 -0.063 4 4
AXIN2 -0.014 0.022 -10000 0 -0.11 4 4
AXIN1 0.034 0.004 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.045 0.085 -10000 0 -0.45 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.07 0.23 20 -0.22 9 29
Axin1/APC/GSK3 0.041 0.063 0.16 74 -0.3 3 77
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.092 0.2 121 -0.25 7 128
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.034 0.008 -10000 0 -10000 0 0
MYC -0.025 0.098 0.45 15 -10000 0 15
RANBP3 0.032 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.023 -10000 0 -0.043 14 14
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.034 0.009 -10000 0 -10000 0 0
TCF3 0.034 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.053 0.042 -10000 0 -0.06 1 1
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.035 0.05 0.21 2 -0.2 2 4
LEF1 0.034 0.01 -10000 0 -0.059 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.062 0.26 16 -0.22 2 18
DKK1/LRP6/Kremen 2 0.025 0.047 -10000 0 -0.047 103 103
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.008 -10000 0 -10000 0 0
NLK 0.032 0.004 -10000 0 -10000 0 0
CCND1 -0.034 0.058 0.41 3 -10000 0 3
WNT1 0.032 0.006 -10000 0 -10000 0 0
GSK3A 0.032 0.007 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.024 0.014 -10000 0 -10000 0 0
PPP2R5D 0.032 0.037 -10000 0 -0.24 5 5
APC 0.032 0.11 0.18 150 -10000 0 150
WNT1/LRP6/FZD1 0 0.025 0.087 1 -0.24 4 5
CREBBP 0.035 0.007 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.032 0.005 -10000 0 -10000 0 0
CLTC 0.008 0.089 -10000 0 -0.34 29 29
calcium ion-dependent exocytosis 0.022 0.045 0.093 89 -0.19 6 95
Dynamin 2/GTP 0.022 0.012 -10000 0 -0.023 28 28
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.006 0.075 -10000 0 -0.28 28 28
CPE -0.015 0.007 0 82 -10000 0 82
CTNNB1 0.032 0.005 -10000 0 0 14 14
membrane fusion 0.026 0.044 0.093 126 -0.1 13 139
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.055 0.13 9 -0.17 28 37
TSHR -0.017 0.005 0 40 -0.04 4 44
INS 0.004 0.095 -10000 0 -0.46 19 19
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.026 0.044 0.093 126 -0.1 13 139
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.002 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.012 -10000 0 -0.023 28 28
JUP 0.005 0.072 -10000 0 -0.28 27 27
ASAP2/amphiphysin II 0.035 0.018 -10000 0 -0.023 27 27
ARF6/GTP 0.023 0.006 -10000 0 -10000 0 0
CDH1 0.006 0.072 -10000 0 -0.28 27 27
clathrin-independent pinocytosis 0.023 0.006 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.004 -10000 0 0 6 6
positive regulation of endocytosis 0.023 0.006 -10000 0 -10000 0 0
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.003 0.04 -10000 0 -0.13 34 34
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.005 -10000 0 -0.063 1 1
regulation of calcium-dependent cell-cell adhesion -0.033 0.076 0.27 28 -10000 0 28
positive regulation of phagocytosis -0.016 0.006 0 63 -10000 0 63
ARF6/GTP/JIP3 0.041 0.011 -10000 0 -10000 0 0
ACAP1 0.027 0.042 0.091 126 -0.2 3 129
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.066 -10000 0 -0.29 21 21
clathrin heavy chain/ACAP1 0.017 0.077 0.18 9 -0.25 28 37
JIP4/KLC1 0.041 0.033 -10000 0 -0.039 11 11
EXOC1 0.03 0.009 -10000 0 -0.063 1 1
exocyst 0.003 0.041 -10000 0 -0.13 34 34
RALA/GTP 0.015 0.014 -10000 0 -0.039 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.04 1 1
receptor recycling 0.023 0.006 -10000 0 -10000 0 0
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.008 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.009 0.088 0.18 1 -0.33 29 30
IL2RA -0.003 0.08 -10000 0 -0.33 26 26
VAMP3 -0.016 0.006 0 63 -10000 0 63
GLUT4/clathrin heavy chain/ACAP1 0.034 0.075 -10000 0 -0.25 28 28
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.012 -10000 0 -0.054 13 13
PLD2 0.006 0.011 -10000 0 -0.054 11 11
EXOC5 0.028 0.018 -10000 0 -0.063 15 15
PIP5K1C 0.011 0.051 0.12 4 -0.17 26 30
SDC1 0.003 0.074 -10000 0 -0.28 28 28
ARF6/GDP 0.023 0.006 -10000 0 0 29 29
EXOC7 0.032 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.035 0.079 -10000 0 -0.28 28 28
mol:Phosphatidic acid 0.026 0.044 0.093 126 -0.1 13 139
endocytosis -0.034 0.018 0.023 27 -10000 0 27
SCAMP2 0.032 0.005 -10000 0 -10000 0 0
ADRB2 0.003 0.085 0.22 2 -0.32 29 31
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.011 -10000 0 -0.023 28 28
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.004 0.086 0.2 4 -0.32 29 33
RALA 0.021 0.019 -10000 0 -0.063 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.076 0.22 2 -0.27 28 30
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.045 0.031 -10000 0 -0.038 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.13 -10000 0 -0.38 60 60
AKT1 -0.032 0.18 -10000 0 -0.71 31 31
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.028 0.18 -10000 0 -0.73 31 31
mol:Ca2+ -0.004 0.045 0.17 18 -0.23 9 27
IGF1R 0.032 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.041 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
apoptosis 0.03 0.17 0.68 31 -10000 0 31
RhoA/GTP -0.039 0.014 -10000 0 -0.076 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.071 0.12 0.18 9 -0.31 55 64
regulation of stress fiber formation 0.045 0.044 -10000 0 -0.16 8 8
E2/ERA-ERB (dimer) 0.039 0.014 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
G13/GTP 0.037 0.017 -10000 0 -0.025 32 32
pseudopodium formation -0.045 0.044 0.16 8 -10000 0 8
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -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 -0.055 0.14 0.21 2 -0.48 35 37
E2/ER beta (dimer) 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.005 0.058 0.13 5 -0.17 45 50
mol:NADP -0.055 0.14 0.21 2 -0.48 35 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 0.016 -10000 0 -0.23 1 1
PLCB2 0.009 0.016 -10000 0 -0.23 1 1
IGF1 0.032 0.009 -10000 0 -0.063 4 4
mol:L-citrulline -0.055 0.14 0.21 2 -0.48 35 37
RHOA 0.032 0.006 -10000 0 -10000 0 0
Gai/GDP -0.43 0.16 -10000 0 -0.48 436 436
JNK cascade 0.022 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.03 0.008 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 0.031 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.014 0.07 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.071 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.07 0.12 0.2 9 -0.32 54 63
GNAZ 0.027 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.023 0.006 -10000 0 -10000 0 0
STRN 0.032 0.002 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
HBEGF -0.11 0.13 0.24 16 -0.36 56 72
cAMP biosynthetic process 0.03 0.021 -10000 0 -0.035 15 15
SRC -0.098 0.12 0.2 1 -0.38 54 55
PI3K 0.039 0.023 -10000 0 -0.05 16 16
GNB1 0.031 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.059 -10000 0 -0.15 46 46
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.078 0.091 -10000 0 -0.26 62 62
Gs family/GTP 0.039 0.025 -10000 0 -0.036 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.046 -10000 0 -0.043 119 119
vasodilation -0.053 0.13 0.21 2 -0.45 35 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 46 46
MSN -0.051 0.039 0.16 8 -10000 0 8
Gq family/GTP 0.022 0.019 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.026 0.18 -10000 0 -0.7 31 31
NRAS 0.009 0.041 -10000 0 -0.063 125 125
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.13 0.45 35 -0.21 2 37
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.063 0.14 5 -0.17 46 51
NOS3 -0.058 0.14 0.22 2 -0.5 35 37
GNA11 0.031 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.035 0.14 0.24 1 -0.5 34 35
E2/ER alpha (dimer)/PELP1/Src -0.07 0.12 0.21 11 -0.33 54 65
ruffle organization -0.045 0.044 0.16 8 -10000 0 8
ROCK2 -0.032 0.052 0.31 2 -10000 0 2
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA13 0.032 0.007 -10000 0 -0.063 2 2
MMP9 -0.11 0.12 0.37 1 -0.36 56 57
MMP2 -0.11 0.12 0.19 1 -0.36 58 59
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
SMAD2 -0.021 0.058 0.14 1 -0.22 28 29
SMAD3 0.013 0.042 0.1 30 -0.097 35 65
SMAD3/SMAD4 0.026 0.056 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.037 0.048 -10000 0 -0.047 117 117
SMAD2/SMAD2/SMAD4 0.017 0.084 -10000 0 -0.19 38 38
PPM1A 0.031 0.008 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.014 0.063 -10000 0 -0.19 39 39
MAP3K1 0.032 0.006 -10000 0 -0.063 1 1
TRAP-1/SMAD4 0.024 0.041 -10000 0 -0.05 116 116
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
NUP214 0.031 0.007 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.063 3 3
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
KPNB1 0.032 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.032 0.003 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
NUP153 0.032 0.005 -10000 0 -0.063 1 1
KPNA2 0.03 0.014 -10000 0 -0.063 11 11
PIAS4 0.032 0.006 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.038 0.15 15 -0.17 9 24
adherens junction organization 0.007 0.041 0.13 7 -0.16 17 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.071 0.16 130 -0.15 5 135
FMN1 0.013 0.038 0.13 7 -0.14 16 23
mol:IP3 0.004 0.024 0.085 1 -0.12 9 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.018 0.04 0.14 7 -0.15 16 23
CTNNB1 0.032 0.006 -10000 0 -10000 0 0
AKT1 0.012 0.035 0.1 29 -0.16 6 35
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.06 0.17 3 -0.25 15 18
CTNND1 0.031 0.014 -10000 0 -0.064 10 10
mol:PI-4-5-P2 0.007 0.037 0.13 7 -0.15 16 23
VASP 0.007 0.034 0.13 7 -0.14 14 21
ZYX 0.001 0.03 0.13 2 -0.17 9 11
JUB 0.013 0.038 0.13 7 -0.14 16 23
EGFR(dimer) 0.011 0.035 0.15 2 -0.16 9 11
E-cadherin/beta catenin-gamma catenin 0.058 0.026 -10000 0 -0.052 19 19
mol:PI-3-4-5-P3 0.041 0.049 0.16 31 -0.15 8 39
PIK3CA 0.029 0.019 -10000 0 -0.057 21 21
PI3K 0.042 0.05 0.16 31 -0.15 8 39
FYN -0.011 0.054 0.15 11 -0.2 28 39
mol:Ca2+ 0.004 0.025 0.085 1 -0.13 10 11
JUP 0.03 0.017 -10000 0 -0.062 16 16
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.024 0.085 1 -0.12 9 10
CDH1 0.031 0.013 -10000 0 -0.061 8 8
RhoA/GDP 0.075 0.077 0.16 223 -0.14 6 229
establishment of polarity of embryonic epithelium 0.006 0.035 0.13 7 -0.14 16 23
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
CASR -0.012 0.033 0.15 12 -0.14 7 19
RhoA/GTP 0.02 0.037 0.14 12 -0.13 8 20
AKT2 0.01 0.034 0.1 22 -0.15 7 29
actin cable formation 0.004 0.034 0.12 7 -0.14 16 23
apoptosis -0.01 0.043 0.17 9 -0.17 12 21
CTNNA1 0.033 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.021 0.14 1 -0.14 6 7
PIP5K1A 0.007 0.038 0.13 7 -0.15 16 23
PLCG1 0.004 0.025 0.086 1 -0.13 9 10
Rac1/GTP 0.015 0.039 -10000 0 -0.18 5 5
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.011 -10000 0 -0.022 9 9
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.039 -10000 0 -0.039 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.032 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.032 0.004 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.024 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.033 0.18 11 -10000 0 11
Cone PDE6 0.044 0.051 -10000 0 -10000 0 0
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.014 0.051 -10000 0 -0.044 178 178
GNAT2/GDP 0.053 0.018 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.03 0.18 11 -10000 0 11
Cone Transducin 0.039 0.012 -10000 0 -0.023 9 9
SLC24A2 0.027 0.013 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.005 -10000 0 -10000 0 0
GNB3 0.031 0.007 -10000 0 0 22 22
GNAT2/GTP 0.024 0.003 -10000 0 -10000 0 0
CNGA3 -0.001 0.045 -10000 0 -0.063 179 179
ARR3 0.032 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.014 0.04 -10000 0 -0.04 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.064 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.013 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
PDE6C 0.024 0.014 -10000 0 -10000 0 0
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.007 -10000 0 0 27 27
Signaling events mediated by PTP1B

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
PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
Jak2/Leptin Receptor 0.019 0.12 -10000 0 -0.28 56 56
PTP1B/AKT1 0.039 0.059 0.17 10 -0.22 12 22
FYN 0.029 0.011 -10000 0 -0.063 1 1
p210 bcr-abl/PTP1B 0.026 0.06 0.15 17 -0.23 11 28
EGFR 0.012 0.019 -10000 0 -0.052 9 9
EGF/EGFR 0.01 0.041 -10000 0 -0.19 10 10
CSF1 0.032 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.009 -10000 0 -0.026 2 2
INSR 0.031 0.008 -10000 0 -0.026 5 5
PTP1B/N-cadherin 0.038 0.061 0.16 9 -0.23 11 20
Insulin Receptor/Insulin 0.054 0.064 0.18 3 -0.19 17 20
HCK 0.014 0.036 -10000 0 -0.063 85 85
CRK 0.032 0.005 -10000 0 -10000 0 0
TYK2 0.026 0.077 0.27 25 -0.25 9 34
EGF 0.034 0.008 -10000 0 -0.053 3 3
YES1 0.017 0.034 -10000 0 -0.063 75 75
CAV1 0.05 0.085 0.17 110 -0.25 10 120
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.065 0.18 7 -0.23 11 18
cell migration -0.026 0.06 0.23 11 -0.15 17 28
STAT3 0.031 0.014 -10000 0 -0.062 10 10
PRLR 0.033 0.005 -10000 0 -10000 0 0
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
CSF1R 0.025 0.026 -10000 0 -0.063 40 40
Prolactin Receptor/Prolactin 0.049 0.014 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.063 15 15
PTP1B/p130 Cas 0.022 0.055 0.12 27 -0.19 15 42
Crk/p130 Cas 0.038 0.06 0.16 10 -0.22 11 21
DOK1 0.022 0.062 0.18 14 -0.25 12 26
JAK2 0.005 0.12 0.2 2 -0.3 56 58
Jak2/Leptin Receptor/Leptin 0.026 0.076 -10000 0 -0.24 17 17
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.06 0.14 27 -0.22 13 40
LYN 0.021 0.031 -10000 0 -0.063 60 60
CDH2 0.031 0.009 -10000 0 -0.063 2 2
SRC 0.033 0.059 -10000 0 -0.41 7 7
ITGB3 0.032 0.003 -10000 0 -10000 0 0
CAT1/PTP1B 0.045 0.094 0.24 43 -0.27 13 56
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.053 0.07 -10000 0 -0.2 15 15
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.025 0.07 -10000 0 -0.22 17 17
negative regulation of transcription 0.005 0.12 0.2 2 -0.3 56 58
FCGR2A -0.015 0.047 -10000 0 -0.063 253 253
FER 0.034 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.032 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.05 0.038 -10000 0 -0.046 57 57
RHOA 0.032 0.006 -10000 0 -10000 0 0
LEPR 0.031 0.009 -10000 0 -0.063 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.031 0.08 0.2 25 -0.28 11 36
PRL 0.033 0.011 -10000 0 -0.06 6 6
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.032 0.015 -10000 0 -0.061 8 8
Insulin Receptor/Insulin/IRS1 0.06 0.024 -10000 0 -0.041 21 21
CSF1/CSF1R 0.051 0.067 0.18 6 -0.23 11 17
Ras protein signal transduction -0.012 0.082 0.51 11 -10000 0 11
IRS1 0.032 0.009 -10000 0 -0.063 4 4
INS 0.032 0.007 -10000 0 -0.026 1 1
LEP 0.023 0.015 -10000 0 -10000 0 0
STAT5B 0.023 0.075 0.17 8 -0.24 21 29
STAT5A 0.023 0.075 0.2 4 -0.24 21 25
GRB2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.041 0.062 0.17 10 -0.23 11 21
CSN2 0 0.034 -10000 0 -0.28 5 5
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
LAT 0.009 0.044 -10000 0 -0.29 2 2
YBX1 0.037 0.017 -10000 0 -0.061 12 12
LCK 0.031 0.01 -10000 0 -0.063 4 4
SHC1 0.024 0.026 -10000 0 -0.063 40 40
NOX4 0.022 0.033 -10000 0 -0.06 70 70
BMP receptor signaling

Figure 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
BMP7/BMPR2/BMPR1A-1B/FS 0.054 0.063 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.043 0.033 -10000 0 -0.046 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.03 0.16 -10000 0 -0.49 53 53
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
SMAD5 -0.028 0.093 0.12 2 -0.31 39 41
BMP7/USAG1 0.031 0.024 -10000 0 -0.05 6 6
SMAD5/SKI -0.016 0.097 -10000 0 -0.3 40 40
SMAD1 -0.01 0.072 -10000 0 -0.25 26 26
BMP2 0.022 0.027 -10000 0 -0.063 44 44
SMAD1/SMAD1/SMAD4 0 0.071 -10000 0 -0.25 19 19
BMPR1A 0.023 0.017 -10000 0 -0.063 6 6
BMPR1B 0.032 0.006 -10000 0 -0.063 1 1
BMPR1A-1B/BAMBI 0.029 0.052 -10000 0 -0.046 134 134
AHSG 0.031 0.008 -10000 0 -0.063 2 2
CER1 0.029 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 0.039 0.045 -10000 0 -0.05 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.003 0.061 -10000 0 -0.19 40 40
BMP2-4 (homodimer) 0.033 0.031 -10000 0 -0.05 47 47
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.048 0.056 -10000 0 -0.057 5 5
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.023 0.015 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.058 0.069 1 -0.12 102 103
BMP2-4/USAG1 0.032 0.041 -10000 0 -0.05 49 49
SMAD6/SMURF1/SMAD5 -0.008 0.087 -10000 0 -0.3 34 34
SOSTDC1 0.022 0.017 -10000 0 -0.063 6 6
BMP7/BMPR2/BMPR1A-1B 0.05 0.053 -10000 0 -0.058 2 2
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.032 0.007 -10000 0 -0.063 2 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.031 0.01 -10000 0 -0.063 5 5
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
BMP2-4/CHRD 0.044 0.041 -10000 0 -0.049 52 52
SMAD5/SMAD5/SMAD4 -0.022 0.099 -10000 0 -0.31 40 40
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.01 0.053 -10000 0 -0.18 20 20
BMP7 (homodimer) 0.03 0.01 -10000 0 -0.063 1 1
NUP214 0.031 0.007 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.014 -10000 0 -0.05 4 4
SMAD1/SKI 0.003 0.081 -10000 0 -0.25 30 30
SMAD6 0.032 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
BMP2-4/FETUA 0.044 0.041 -10000 0 -0.045 74 74
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.02 -10000 0 -0.063 22 22
BMPR2 (homodimer) 0.032 0.001 -10000 0 -10000 0 0
GADD34/PP1CA 0.057 0.028 -10000 0 -0.038 34 34
BMPR1A-1B (homodimer) 0.034 0.023 -10000 0 -0.05 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.002 0.084 0.29 1 -0.25 30 31
SMAD6-7/SMURF1/SMAD1 0.016 0.079 -10000 0 -0.25 19 19
SMAD6/SMURF1 0.023 0.015 -10000 0 -10000 0 0
BAMBI 0.02 0.024 -10000 0 -0.063 27 27
SMURF2 0.032 0.005 -10000 0 -0.063 1 1
BMP2-4/CHRDL1 0.03 0.027 -10000 0 -0.04 50 50
BMP2-4/GREM1 0.039 0.045 -10000 0 -0.049 75 75
SMAD7 0.031 0.007 -10000 0 -0.063 1 1
SMAD8A/SMAD8A/SMAD4 -0.027 0.16 -10000 0 -0.46 59 59
SMAD1/SMAD6 0.002 0.068 -10000 0 -0.25 20 20
TAK1/SMAD6 0.033 0.023 -10000 0 -0.05 1 1
BMP7 0.03 0.01 -10000 0 -0.063 1 1
BMP6 0.032 0.007 -10000 0 -0.063 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.005 0.051 -10000 0 -0.22 19 19
PPM1A 0.031 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.083 0.29 1 -0.25 28 29
SMAD7/SMURF1 0.033 0.023 -10000 0 -0.05 1 1
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
PPP1CA 0.032 0.004 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.063 3 3
PPP1R15A 0.031 0.009 -10000 0 -0.063 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.015 0.059 -10000 0 -0.12 103 103
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.033 0.001 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.018 0.059 -10000 0 -0.12 108 108
BMP4 0.029 0.014 -10000 0 -0.063 8 8
FST 0.029 0.017 -10000 0 -0.063 16 16
BMP2-4/NOG 0.03 0.027 -10000 0 -0.04 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.05 0.055 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.053 -10000 0 -0.3 14 14
KLHL20 0.028 0.068 0.17 32 -0.19 13 45
CYFIP2 0.018 0.016 -10000 0 0 221 221
Rac1/GDP 0.005 0.039 0.17 9 -0.16 10 19
ENAH 0.005 0.055 -10000 0 -0.3 15 15
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 0 14 14
CDC42/GTP -0.028 0.033 0.11 20 -0.12 9 29
ABI1/Sra1/Nap1 -0.01 0.022 -10000 0 -0.12 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.072 0.035 -10000 0 -0.053 10 10
RAPGEF1 -0.003 0.059 0.16 30 -0.28 11 41
CTNND1 0.03 0.014 -10000 0 -0.063 10 10
regulation of calcium-dependent cell-cell adhesion 0.02 0.056 -10000 0 -0.3 14 14
CRK 0.005 0.061 0.17 25 -0.29 13 38
E-cadherin/gamma catenin/alpha catenin 0.058 0.029 -10000 0 -0.046 35 35
alphaE/beta7 Integrin 0.046 0.012 -10000 0 -0.05 2 2
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.024 40 40
DLG1 0.006 0.055 -10000 0 -0.29 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.03 0.018 -10000 0 -0.092 13 13
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.018 -10000 0 -0.024 30 30
PI3K -0.036 0.022 -10000 0 -0.12 12 12
ARF6 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.043 0.021 -10000 0 -0.057 19 19
TIAM1 0.031 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.066 0.034 -10000 0 -10000 0 0
AKT1 -0.016 0.036 0.14 9 -0.1 2 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.063 8 8
RhoA/GDP 0.012 0.061 0.18 28 -0.17 16 44
actin cytoskeleton organization 0.023 0.054 0.14 32 -0.14 13 45
CDC42/GDP 0.011 0.057 0.18 21 -0.17 16 37
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.026 -10000 0 -0.11 19 19
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.072 0.036 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.022 -10000 0 -0.032 28 28
mol:GDP -0.002 0.063 0.18 29 -0.18 16 45
CDC42/GTP/IQGAP1 0.023 0.035 -10000 0 -0.04 118 118
JUP 0.029 0.017 -10000 0 -0.063 16 16
p120 catenin/RhoA/GDP 0.025 0.064 0.19 27 -0.18 16 43
RAC1/GTP/IQGAP1 0.016 0.032 -10000 0 -0.04 89 89
PIP5K1C/AP1M1 0.022 0.006 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.041 0.11 29 -0.095 14 43
NME1 0 0 -10000 0 0 2 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.006 0.055 -10000 0 -0.3 15 15
regulation of cell-cell adhesion -0.03 0.017 0.043 1 -0.1 13 14
WASF2 -0.006 0.012 -10000 0 -0.067 14 14
Rap1/GTP -0.022 0.045 0.14 29 -0.14 4 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.082 0.043 -10000 0 -0.075 5 5
CCND1 0.017 0.047 0.13 29 -0.12 14 43
VAV2 0.013 0.11 -10000 0 -0.58 13 13
RAP1/GDP -0.011 0.052 0.16 31 -0.17 3 34
adherens junction assembly 0.006 0.053 -10000 0 -0.29 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.014 -10000 0 -10000 0 0
PIP5K1C 0.03 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 2 -0.078 5 7
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.14 7 7
mol:GTP 0 0 -10000 0 0 2 2
SRC 0.005 0.053 -10000 0 -0.3 14 14
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
Rac1/GTP -0.007 0.055 -10000 0 -0.28 14 14
E-cadherin/beta catenin/alpha catenin 0.059 0.025 -10000 0 -0.04 28 28
ITGAE 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.057 -10000 0 -0.3 14 14
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.018 0.026 -10000 0 -0.15 3 3
GNAO1 0.003 0.009 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.03 0.02 -10000 0 -0.023 2 2
AKT1 -0.008 0.069 -10000 0 -0.43 13 13
AKT3 -0.008 0.046 -10000 0 -0.27 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
GNAI2 0.032 0.006 -10000 0 -0.028 1 1
GNAI3 0.022 0.03 -10000 0 -0.062 58 58
GNAI1 0.02 0.017 -10000 0 -0.062 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0 -10000 0 -0.009 1 1
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.013 -10000 0 -0.11 2 2
MAPK3 0.001 0.013 0.076 6 -0.12 3 9
MAPK1 0.001 0.01 0.076 6 -0.093 1 7
JAK2 -0.009 0.036 -10000 0 -0.16 19 19
CXCR4 0 0.009 0.076 2 -0.11 2 4
FLT1 0.031 0.009 -10000 0 -0.028 1 1
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 0 151 151
SRC 0.001 0.013 0.076 5 -0.12 3 8
S1P/S1P3/Gi 0.002 0.013 -10000 0 -0.11 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.041 -10000 0 -0.14 24 24
VEGFA -0.019 0.047 -10000 0 -0.062 275 275
S1P/S1P2/Gi 0.002 0.013 0.085 6 -0.11 2 8
VEGFR1 homodimer/VEGFA homodimer -0.003 0.048 -10000 0 -0.049 254 254
RHOA 0.032 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.017 0.009 -10000 0 -0.1 1 1
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
G12/G13 0.034 0.022 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.037 -10000 0 -0.13 17 17
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.023 -10000 0 -0.05 2 2
CRKL 0.049 0.083 0.27 5 -0.43 5 10
mol:PIP3 0.012 0.039 -10000 0 -0.76 1 1
AKT1 0.004 0.037 0.24 3 -0.5 1 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.047 0.085 0.3 13 -0.38 5 18
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
HGF/MET/SHIP2 0.042 0.033 -10000 0 -0.047 4 4
MAP3K5 0.048 0.08 0.24 6 -0.38 5 11
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.031 -10000 0 -0.043 3 3
AP1 0.012 0.074 0.14 114 -10000 0 114
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
apoptosis -0.023 0.22 -10000 0 -0.72 42 42
STAT3 (dimer) 0.012 0.028 -10000 0 -0.17 3 3
GAB1/CRKL/SHP2/PI3K 0.079 0.081 0.3 2 -0.4 5 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.067 0.081 0.25 4 -0.38 6 10
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.03 0.009 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.063 2 2
ELK1 0.11 0.18 0.35 169 -10000 0 169
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.029 0.16 1 -0.15 11 12
PAK1 -0.001 0.041 0.24 1 -0.48 1 2
HGF/MET/RANBP10 0.042 0.033 -10000 0 -0.048 3 3
HRAS 0.015 0.039 -10000 0 -0.3 4 4
DOCK1 0.036 0.078 0.28 5 -0.41 5 10
GAB1 0.051 0.078 0.22 2 -0.47 4 6
CRK 0.052 0.081 0.23 8 -0.43 5 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.036 -10000 0 -0.35 3 3
JUN 0.032 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.016 0.081 8 -0.051 16 24
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.044 0.089 0.25 43 -0.3 3 46
GRB2/SHC 0.059 0.062 0.16 104 -0.11 10 114
FOS 0.007 0.04 -10000 0 -0.063 120 120
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.11 0.18 0.35 169 -10000 0 169
HGF/MET/MUC20 0.028 0.022 -10000 0 -0.04 3 3
cell migration 0.058 0.061 0.15 104 -0.11 10 114
GRB2 0.032 0.006 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.032 0.023 -10000 0 -0.05 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.039 2 2
RAP1B 0.046 0.081 0.29 13 -0.36 5 18
RAP1A 0.042 0.084 0.31 15 -0.38 4 19
HGF/MET/RANBP9 0.042 0.033 -10000 0 -0.048 3 3
RAF1 0.038 0.061 0.22 2 -0.28 5 7
STAT3 0.012 0.027 -10000 0 -0.2 2 2
cell proliferation 0.03 0.061 0.21 15 -0.25 2 17
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.076 0.16 0.46 4 -10000 0 4
MAPK1 0.12 0.21 0.41 140 -10000 0 140
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.14 0.25 4 -0.32 55 59
SRC 0.004 0.017 -10000 0 -0.12 7 7
PI3K 0.058 0.059 0.16 96 -0.11 9 105
MET/Glomulin 0.015 0.025 0.085 1 -0.086 19 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.062 0.25 5 -0.28 4 9
MET 0.022 0.016 -10000 0 -0.063 2 2
MAP4K1 0.056 0.085 0.26 5 -0.44 5 10
PTK2 0.031 0.006 -10000 0 -10000 0 0
MAP2K2 0.04 0.073 0.28 12 -0.27 5 17
BAD -0.002 0.037 -10000 0 -0.48 1 1
MAP2K4 0.043 0.077 0.23 14 -0.34 5 19
SHP2/GRB2/SOS1/GAB1 0.028 0.052 -10000 0 -0.36 5 5
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.004 0.014 0.071 8 -0.11 2 10
PLCgamma1/PKC 0.022 0.006 -10000 0 -10000 0 0
HGF 0.022 0.016 -10000 0 -0.063 1 1
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.16 112 -0.11 10 122
PDPK1 0.011 0.036 0.25 3 -0.53 1 4
HGF/MET/SHIP 0.028 0.022 -10000 0 -0.04 3 3
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.033 -10000 0 -0.12 8 8
BIRC5 -0.006 0.046 -10000 0 -0.063 202 202
NFKBIA -0.006 0.015 0.17 2 -10000 0 2
CPEB1 0.024 0.014 -10000 0 0 136 136
AKT1 -0.006 0.015 0.14 3 -10000 0 3
NDEL1 0.031 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.025 0.024 0.099 2 -0.12 8 10
NDEL1/TACC3 0.033 0.039 -10000 0 -0.12 8 8
GADD45A 0.024 0.026 -10000 0 -0.063 39 39
GSK3B 0.032 0.007 0.082 2 -10000 0 2
PAK1/Aurora A 0.034 0.029 -10000 0 -0.12 8 8
MDM2 0.029 0.011 -10000 0 -0.063 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.034 0.017 -10000 0 -0.05 254 254
TP53 0.009 0.034 -10000 0 -0.2 10 10
DLG7 0.006 0.009 0.096 2 -0.033 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 0.042 -10000 0 -0.13 8 8
G2/M transition of mitotic cell cycle 0.024 0.024 0.098 2 -0.11 8 10
AURKA 0.014 0.013 0.13 2 -0.042 1 3
AURKB 0.007 0.025 -10000 0 -0.1 18 18
CDC25B 0.012 0.019 0.097 2 -0.21 2 4
G2/M transition checkpoint 0.007 0.017 0.076 2 -0.1 8 10
mRNA polyadenylation 0.019 0.021 0.098 1 -0.11 5 6
Aurora A/CPEB 0.019 0.021 0.099 1 -0.11 5 6
Aurora A/TACC1/TRAP/chTOG 0.065 0.037 -10000 0 -0.12 7 7
BRCA1 0.031 0.01 -10000 0 -0.063 5 5
centrosome duplication 0.034 0.029 -10000 0 -0.12 8 8
regulation of centrosome cycle 0.032 0.039 -10000 0 -0.12 8 8
spindle assembly 0.063 0.036 -10000 0 -0.12 7 7
TDRD7 0.031 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.025 0.054 -10000 0 -0.13 8 8
CENPA 0.01 0.024 -10000 0 -0.24 2 2
Aurora A/PP2A 0.035 0.027 -10000 0 -0.12 5 5
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.03 0.1 1 -0.19 8 9
negative regulation of DNA binding 0.009 0.034 -10000 0 -0.2 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.012 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.007 0.017 0.076 2 -0.1 8 10
mitotic prometaphase -0.002 0.012 0.071 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.013 0.13 2 -0.041 1 3
TACC1 0.032 0.004 -10000 0 -10000 0 0
TACC3 0.015 0.037 -10000 0 -0.058 100 100
Aurora A/Antizyme1 0.049 0.031 -10000 0 -0.12 8 8
Aurora A/RasGAP 0.034 0.029 -10000 0 -0.13 7 7
OAZ1 0.031 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.008 0.082 2 -10000 0 2
GIT1 0.032 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.06 0.024 -10000 0 -0.044 2 2
Importin alpha/Importin beta/TPX2 -0.034 0.017 -10000 0 -0.05 254 254
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.025 0.02 -10000 0 -0.14 8 8
PAK1 0.032 0.004 -10000 0 -10000 0 0
CKAP5 0.032 0.006 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.018 -9999 0 -0.063 6 6
EGF/EGFR 0.007 0.035 -9999 0 -0.056 8 8
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.04 -9999 0 -0.059 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.005 0.043 -9999 0 -0.063 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.032 0.007 -9999 0 -0.063 2 2
EGF/EGFR dimer/SHC 0.018 0.035 -9999 0 -0.049 33 33
mol:GDP 0.019 0.037 -9999 0 -0.058 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.03 0.013 -9999 0 -0.063 9 9
GRB2/SOS1 0.023 0.004 -9999 0 0 15 15
HRAS/GTP 0.011 0.03 -9999 0 -0.059 3 3
SHC1 0.024 0.026 -9999 0 -0.063 40 40
HRAS/GDP 0.017 0.038 -9999 0 -0.067 1 1
FRAP1 -0.012 0.015 -9999 0 -0.056 2 2
EGF/EGFR dimer 0.018 0.025 -9999 0 -0.05 8 8
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.032 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.018 0.045 -9999 0 -0.05 149 149
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.008 0.048 -10000 0 -0.14 11 11
mol:DAG -0.005 0.039 0.14 4 -0.14 9 13
PLCG1 -0.006 0.04 0.14 4 -0.14 9 13
YES1 -0.014 0.034 -10000 0 -0.12 24 24
FZD3 0.031 0.01 -10000 0 -0.063 3 3
FZD6 0.014 0.037 -10000 0 -0.063 94 94
G protein 0.01 0.06 0.17 34 -0.15 9 43
MAP3K7 -0.022 0.037 0.17 7 -0.14 9 16
mol:Ca2+ -0.005 0.039 0.14 4 -0.14 9 13
mol:IP3 -0.005 0.039 0.14 4 -0.14 9 13
NLK 0.007 0.08 -10000 0 -0.72 6 6
GNB1 0.031 0.008 -10000 0 -10000 0 0
CAMK2A -0.019 0.039 0.19 8 -0.16 5 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.039 -10000 0 -0.12 23 23
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
GNAS -0.009 0.03 -10000 0 -0.13 16 16
GO:0007205 -0.009 0.034 0.14 4 -0.13 11 15
WNT6 0.032 0.002 -10000 0 -10000 0 0
WNT4 0.031 0.008 -10000 0 -0.063 2 2
NFAT1/CK1 alpha -0.006 0.053 0.2 7 -0.16 8 15
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.003 0.044 -10000 0 -0.063 155 155
WNT11 0.032 0.007 -10000 0 -0.063 2 2
CDC42 -0.022 0.031 0.13 6 -0.14 7 13
Arf6 downstream 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
PLAUR 0 0.037 -10000 0 -0.1 59 59
regulation of axonogenesis 0.01 0.059 0.26 26 -10000 0 26
myoblast fusion -0.014 0.038 0.35 3 -10000 0 3
mol:GTP 0.009 0.05 -10000 0 -0.18 29 29
regulation of calcium-dependent cell-cell adhesion -0.024 0.041 0.12 25 -10000 0 25
ARF1/GTP 0.027 0.047 -10000 0 -0.14 27 27
mol:GM1 -0.001 0.034 -10000 0 -0.13 29 29
mol:Choline -0.021 0.026 0.033 1 -0.13 25 26
lamellipodium assembly -0.006 0.064 -10000 0 -0.38 13 13
MAPK3 0.006 0.039 -10000 0 -0.12 29 29
ARF6/GTP/NME1/Tiam1 0.024 0.041 -10000 0 -0.12 25 25
ARF1 0.032 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.038 -10000 0 -0.35 3 3
ARF1/GDP 0.008 0.067 -10000 0 -0.24 27 27
ARF6 0.033 0.024 -10000 0 -0.039 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.029 0.011 -10000 0 -0.031 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.12 18 18
actin filament bundle formation -0.016 0.071 0.25 28 -10000 0 28
KALRN -0.001 0.047 -10000 0 -0.26 14 14
RAB11FIP3/RAB11A 0.047 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.071 -10000 0 -0.25 28 28
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.055 -10000 0 -0.24 15 15
substrate adhesion-dependent cell spreading 0.009 0.05 -10000 0 -0.18 29 29
cortical actin cytoskeleton organization -0.006 0.064 -10000 0 -0.38 13 13
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.009 0.05 -10000 0 -0.18 29 29
ARF6/GTP 0.009 0.05 -10000 0 -0.18 29 29
RhoA/GTP 0.027 0.047 -10000 0 -0.14 28 28
mol:GDP -0.009 0.062 -10000 0 -0.26 27 27
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.052 -10000 0 -0.13 29 29
RHOA 0.032 0.006 -10000 0 -10000 0 0
PLD1 0.005 0.039 -10000 0 -0.14 28 28
RAB11FIP3 0.032 0.004 -10000 0 -10000 0 0
tube morphogenesis -0.006 0.064 -10000 0 -0.38 13 13
ruffle organization -0.01 0.059 -10000 0 -0.26 26 26
regulation of epithelial cell migration 0.009 0.05 -10000 0 -0.18 29 29
PLD2 0.006 0.038 -10000 0 -0.14 26 26
PIP5K1A -0.011 0.06 -10000 0 -0.26 26 26
mol:Phosphatidic acid -0.021 0.026 0.033 1 -0.13 25 26
Rac1/GTP -0.006 0.065 -10000 0 -0.38 13 13
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.022 0.071 -10000 0 -0.14 22 22
Ran/GTP/Exportin 1/HDAC1 -0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.062 0.16 1 -0.2 18 19
SUMO1 0.033 0.001 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.028 -10000 0 -0.095 39 39
FKBP3 0.03 0.008 -10000 0 -10000 0 0
Histones 0.032 0.044 -10000 0 -0.2 7 7
YY1/LSF 0.012 0.061 -10000 0 -0.15 59 59
SMG5 0.032 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.001 0.036 -10000 0 -0.1 32 32
I kappa B alpha/HDAC1 0 0.059 -10000 0 -0.18 34 34
SAP18 0.031 0.008 -10000 0 -10000 0 0
RELA 0 0.05 0.11 12 -0.15 37 49
HDAC1/Smad7 0.035 0.04 -10000 0 -0.047 47 47
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.044 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.048 -10000 0 -0.18 19 19
NF kappa B1 p50/RelA 0.016 0.059 0.17 1 -0.2 16 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.048 -10000 0 -0.19 17 17
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
MAX 0.03 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.019 -10000 0 -0.055 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.006 0.052 -10000 0 -0.13 59 59
SIN3 complex 0.053 0.028 -10000 0 -0.032 39 39
SMURF1 0.023 0.015 -10000 0 -10000 0 0
CHD3 0.032 0.005 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
YY1/HDAC3 -0.003 0.051 -10000 0 -0.18 24 24
YY1/HDAC2 0.012 0.06 -10000 0 -0.15 54 54
YY1/HDAC1 0.007 0.061 -10000 0 -0.15 55 55
NuRD/MBD2 Complex (MeCP1) 0.002 0.052 -10000 0 -0.19 21 21
PPARG 0.004 0.038 0.12 10 -0.15 14 24
HDAC8/hEST1B 0.042 0.01 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
HDAC3/SMRT (N-CoR2) 0.016 0.044 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.039 -10000 0 -0.047 47 47
CREBBP 0.032 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.047 -10000 0 -0.18 15 15
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC3 0.007 0.02 -10000 0 -0.059 7 7
HDAC2 0.03 0.012 -10000 0 -0.063 4 4
YY1 0.01 0.004 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.031 0.007 -10000 0 -0.063 1 1
NCOR2 0.032 0.004 -10000 0 -10000 0 0
MXD1 0.033 0.001 -10000 0 0 1 1
STAT3 0.017 0.009 -10000 0 -0.035 8 8
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.066 -10000 0 -0.14 58 58
YY1/SAP30/HDAC1 0.02 0.067 -10000 0 -0.14 59 59
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.009 -10000 0 -0.035 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.019 -10000 0 -0.055 5 5
histone deacetylation 0.002 0.051 -10000 0 -0.19 21 21
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.041 -10000 0 -0.15 14 14
nuclear export -0.041 0.01 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.023 0.027 -10000 0 -0.063 43 43
GATA2/HDAC3 0.016 0.044 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.032 -10000 0 -0.05 61 61
GATA1/HDAC3 0.016 0.045 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.014 0.045 -10000 0 -0.05 166 166
SIN3/HDAC complex/Mad/Max -0.006 0.067 -10000 0 -0.18 47 47
NuRD Complex 0.004 0.051 -10000 0 -0.19 17 17
positive regulation of chromatin silencing 0.031 0.042 -10000 0 -0.2 7 7
SIN3B 0.031 0.006 -10000 0 -10000 0 0
MTA2 0.032 0.004 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.033 0.001 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.043 -10000 0 -0.1 38 38
HDAC complex 0.04 0.063 -10000 0 -0.053 136 136
GATA1/Fog1 0.024 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.04 0.046 -10000 0 -0.044 112 112
TNF 0.032 0.006 -10000 0 -0.063 2 2
negative regulation of cell growth -0.006 0.067 -10000 0 -0.18 47 47
NuRD/MBD2/PRMT5 Complex 0.002 0.052 -10000 0 -0.19 21 21
Ran/GTP/Exportin 1 0.037 0.039 -10000 0 -0.096 39 39
NF kappa B/RelA/I kappa B alpha -0.005 0.049 -10000 0 -0.17 26 26
SIN3/HDAC complex/NCoR1 0.006 0.044 -10000 0 -0.17 21 21
TFCP2 0.032 0.005 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
MBD3 0.031 0.006 -10000 0 -10000 0 0
MBD2 0.032 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC3 0.032 0.004 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.057 -10000 0 -0.18 32 32
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.013 5 5
AKT1 0.004 0.053 0.14 5 -0.19 16 21
RAR alpha/9cRA/Cyclin H 0.007 0.088 0.2 3 -0.17 39 42
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.052 0.091 7 -0.15 43 50
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.045 0.15 1 -0.16 22 23
NCOR2 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.002 0.073 0.3 3 -0.29 16 19
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA3 0.03 0.011 -10000 0 -0.063 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 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.033 0.003 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -0.027 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.072 -10000 0 -0.28 18 18
RARA 0.011 0.007 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.051 0.098 8 -0.15 40 48
PRKCA 0.033 0.007 -10000 0 -0.036 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.069 0.27 2 -0.28 18 20
RXRG 0.019 0.007 -10000 0 -0.033 2 2
RXRA -0.013 0.044 0.1 8 -0.093 111 119
RXRB 0.019 0.007 -10000 0 -0.04 1 1
VDR/Vit D3/DNA 0.023 0.005 -10000 0 -10000 0 0
RBP1 -0.01 0.046 -10000 0 -0.063 222 222
CRBP1/9-cic-RA -0.004 0.031 -10000 0 -0.039 222 222
RARB 0.032 0.007 -10000 0 -0.025 4 4
PRKCG 0.031 0.01 -10000 0 -0.036 4 4
MNAT1 0.03 0.009 -10000 0 -0.063 1 1
RAR alpha/RXRs 0.003 0.08 0.2 1 -0.33 17 18
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.067 0.24 2 -0.25 19 21
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.064 0.16 3 -0.18 36 39
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.068 0.3 1 -0.27 18 19
positive regulation of DNA binding 0.001 0.08 0.15 2 -0.16 39 41
NRIP1 0.008 0.068 0.3 2 -0.33 6 8
RXRs/RARs 0.008 0.067 -10000 0 -0.27 20 20
RXRs/RXRs/DNA/9cRA -0.004 0.065 -10000 0 -0.28 18 18
PRKACA 0.032 0.006 -10000 0 -10000 0 0
CDK7 0.032 0.007 -10000 0 -0.063 2 2
TFIIH 0.057 0.029 -10000 0 -0.048 8 8
RAR alpha/9cRA 0.024 0.082 -10000 0 -0.14 32 32
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.053 0.034 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.022 0.03 -10000 0 -0.13 24 24
epithelial cell differentiation 0.06 0.032 -10000 0 -10000 0 0
CYFIP2 0.018 0.016 -10000 0 0 221 221
ENAH -0.045 0.051 0.41 4 -10000 0 4
EGFR 0.012 0.018 -10000 0 -0.063 6 6
EPHA2 0.029 0.015 -10000 0 -0.063 12 12
MYO6 -0.029 0.03 0.16 11 -10000 0 11
CTNNB1 0.032 0.005 -10000 0 0 14 14
ABI1/Sra1/Nap1 0.024 0.039 -10000 0 -0.036 70 70
AQP5 -0.014 0.045 0.16 7 -0.31 8 15
CTNND1 0.03 0.014 -10000 0 -0.063 10 10
mol:PI-4-5-P2 -0.029 0.026 0.16 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.028 0.03 0.16 11 -10000 0 11
EGF 0.032 0.007 -10000 0 -0.063 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.076 -10000 0 -0.32 31 31
cortical microtubule organization 0.06 0.032 -10000 0 -10000 0 0
GO:0000145 -0.028 0.024 0.15 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.066 0.034 -10000 0 -10000 0 0
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.053 0.015 -10000 0 -0.098 2 2
ARF6 0.031 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.072 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.022 0.16 2 -0.19 1 3
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.025 0.026 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.051 -10000 0 -0.088 1 1
CDH1 0.03 0.013 -10000 0 -0.063 8 8
EGFR/EGFR/EGF/EGF 0.019 0.035 -10000 0 -10000 0 0
RhoA/GDP 0.061 0.034 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.025 0.14 7 -10000 0 7
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
IGF1R 0.032 0.004 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
DIAPH1 -0.22 0.26 -10000 0 -0.45 264 264
Wnt receptor signaling pathway -0.06 0.032 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.015 -10000 0 -0.098 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.026 0.14 7 -10000 0 7
EFNA1 0.028 0.019 -10000 0 -0.063 20 20
LPP -0.035 0.023 0.15 5 -10000 0 5
Ephrin A1/EPHA2 0.047 0.041 -10000 0 -0.072 7 7
SEC6/SEC8 -0.043 0.011 -10000 0 -10000 0 0
MGAT3 -0.028 0.03 0.16 11 -10000 0 11
HGF/MET 0.035 0.038 -10000 0 -0.072 1 1
HGF 0.022 0.016 -10000 0 -0.063 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.022 0.03 -10000 0 -0.13 24 24
actin cable formation -0.039 0.079 0.4 9 -0.23 10 19
KIAA1543 -0.024 0.023 0.15 9 -10000 0 9
KIFC3 -0.031 0.024 0.16 7 -10000 0 7
NCK1 0.03 0.015 -10000 0 -0.063 11 11
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ACTN1 -0.03 0.027 0.16 8 -10000 0 8
NCK1/GIT1 0.044 0.017 -10000 0 -0.05 11 11
mol:GDP 0.06 0.032 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.031 0.027 0.16 9 -10000 0 9
PIP5K1C -0.029 0.026 0.16 8 -10000 0 8
LIMA1 -0.048 0.034 -10000 0 -0.061 438 438
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.041 0.069 0.41 8 -10000 0 8
adherens junction assembly -0.023 0.045 0.24 5 -0.2 9 14
IGF-1R heterotetramer/IGF1 0.053 0.035 -10000 0 -0.072 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.063 2 2
PLEKHA7 -0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0.065 0.041 -10000 0 -0.071 7 7
establishment of epithelial cell apical/basal polarity -0.04 0.041 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.022 0.03 -10000 0 -0.13 24 24
regulation of cell-cell adhesion -0.024 0.025 0.14 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.022 0.03 -10000 0 -0.13 24 24
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 0.011 0.08 0.24 13 -0.24 18 31
IKBKB 0.017 0.059 0.27 6 -0.24 8 14
AKT1 0.013 0.077 0.22 37 -0.13 1 38
IKBKG 0.012 0.05 0.27 4 -0.22 7 11
CALM1 -0.009 0.047 0.2 2 -0.18 14 16
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
MAP3K1 0.034 0.094 0.28 18 -0.37 8 26
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
mol:Ca2+ -0.006 0.053 0.21 1 -0.18 19 20
DOK1 0.032 0.002 -10000 0 -10000 0 0
AP-1 -0.006 0.062 0.23 6 -0.17 22 28
LYN 0.021 0.031 -10000 0 -0.063 60 60
BLNK 0.013 0.031 -10000 0 -0.063 59 59
SHC1 0.024 0.026 -10000 0 -0.063 40 40
BCR complex 0.045 0.014 -10000 0 -0.063 2 2
CD22 -0.007 0.03 -10000 0 -0.24 2 2
CAMK2G 0 0.032 0.23 3 -0.2 5 8
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.048 0.02 -10000 0 -0.096 25 25
GO:0007205 -0.007 0.053 0.21 1 -0.18 19 20
SYK 0.025 0.024 -10000 0 -0.063 34 34
ELK1 -0.013 0.053 0.18 2 -0.18 18 20
NFATC1 -0.015 0.064 0.27 8 -0.24 13 21
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -0.063 2 2
PAG1/CSK 0.024 0.003 -10000 0 -10000 0 0
NFKBIB 0.021 0.033 0.15 5 -0.13 14 19
HRAS -0.013 0.053 0.19 5 -0.16 23 28
NFKBIA 0.021 0.033 0.15 5 -0.12 14 19
NF-kappa-B/RelA/I kappa B beta 0.024 0.03 0.14 6 -0.096 14 20
RasGAP/Csk 0.051 0.066 -10000 0 -0.09 2 2
mol:GDP -0.005 0.054 0.19 2 -0.18 17 19
PTEN 0.023 0.016 -10000 0 -0.063 2 2
CD79B 0.032 0.005 -10000 0 -0.062 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.029 0.14 6 -0.093 14 20
GRB2 0.032 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.005 0.081 0.37 4 -0.29 5 9
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.006 0.053 0.22 1 -0.18 19 20
CSK 0.032 0.005 -10000 0 -10000 0 0
FOS -0.02 0.051 0.17 3 -0.18 16 19
CHUK -0.048 0.12 0.25 5 -0.25 122 127
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.071 -10000 0 -0.18 17 17
PTPN6 -0.018 0.031 0.14 4 -0.23 2 6
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.012 0.021 0.1 5 -0.069 14 19
VAV2 -0.011 0.055 0.16 3 -0.28 13 16
ubiquitin-dependent protein catabolic process 0.022 0.033 0.15 5 -0.12 14 19
BTK 0.016 0.011 -10000 0 -10000 0 0
CD19 -0.008 0.032 -10000 0 -0.24 2 2
MAP4K1 0.031 0.008 -10000 0 -0.063 1 1
CD72 0.03 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.086 0.26 18 -0.33 8 26
SH3BP5 0.029 0.01 -10000 0 0 53 53
PIK3AP1 -0.007 0.051 -10000 0 -0.18 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.06 -10000 0 -0.24 22 22
RAF1 -0.017 0.052 0.2 5 -0.19 11 16
RasGAP/p62DOK/SHIP 0.042 0.057 -10000 0 -0.079 2 2
CD79A 0.031 0.009 -10000 0 -0.063 2 2
re-entry into mitotic cell cycle -0.006 0.061 0.23 6 -0.17 22 28
RASA1 0.032 0.006 -10000 0 -10000 0 0
MAPK3 -0.023 0.052 0.22 5 -0.19 7 12
MAPK1 -0.022 0.05 0.2 7 -0.2 5 12
CD72/SHP1 0.007 0.064 0.22 26 -0.23 2 28
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 0.026 0.087 0.27 17 -0.33 8 25
actin cytoskeleton organization 0.031 0.088 0.2 49 -0.26 5 54
NF-kappa-B/RelA 0.047 0.057 0.27 5 -0.19 13 18
Calcineurin 0.009 0.065 0.2 1 -0.18 12 13
PI3K -0.025 0.049 -10000 0 -0.17 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.001 0.043 -10000 0 -0.21 6 6
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.036 0.079 -10000 0 -0.57 6 6
DAPP1 0.019 0.074 -10000 0 -0.64 5 5
cytokine secretion -0.014 0.062 0.24 10 -0.22 13 23
mol:DAG -0.006 0.053 0.22 1 -0.18 19 20
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
MAP2K1 -0.021 0.05 0.18 6 -0.2 8 14
B-cell antigen/BCR complex/FcgammaRIIB 0.034 0.049 -10000 0 -0.049 121 121
mol:PI-3-4-5-P3 -0.02 0.05 0.19 12 -10000 0 12
ETS1 0.021 0.066 0.19 14 -0.19 6 20
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.027 0.073 -10000 0 -0.081 34 34
B-cell antigen/BCR complex/LYN 0.006 0.036 -10000 0 -0.24 2 2
MALT1 0.028 0.02 -10000 0 -0.063 21 21
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.028 0.085 0.19 46 -0.27 5 51
B-cell antigen/BCR complex/LYN/SYK 0.043 0.062 0.22 16 -0.22 2 18
CARD11 -0.007 0.052 0.19 2 -0.17 19 21
FCGR2B 0.01 0.04 -10000 0 -0.063 120 120
PPP3CA 0.026 0.013 -10000 0 -10000 0 0
BCL10 0.031 0.009 -10000 0 -0.063 3 3
IKK complex 0.003 0.039 0.16 9 -0.12 10 19
PTPRC 0.009 0.04 -10000 0 -0.063 121 121
PDPK1 -0.015 0.051 0.19 17 -10000 0 17
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.032 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.021 0.12 6 -0.067 11 17
FOXM1 transcription factor network

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
NFATC3 -0.16 0.2 -9999 0 -0.71 13 13
PLK1 0 0.11 -9999 0 -0.86 7 7
BIRC5 -0.028 0.073 -9999 0 -10000 0 0
HSPA1B -0.16 0.2 -9999 0 -0.7 14 14
MAP2K1 -0.013 0.038 -9999 0 -10000 0 0
BRCA2 -0.16 0.2 -9999 0 -0.71 12 12
FOXM1 -0.18 0.22 -9999 0 -0.78 16 16
XRCC1 -0.16 0.2 -9999 0 -0.71 11 11
FOXM1B/p19 -0.17 0.2 -9999 0 -0.72 14 14
Cyclin D1/CDK4 -0.16 0.19 -9999 0 -0.66 12 12
CDC2 -0.17 0.2 -9999 0 -0.73 14 14
TGFA -0.16 0.19 -9999 0 -0.65 13 13
SKP2 -0.16 0.2 -9999 0 -0.71 13 13
CCNE1 0.015 0.026 -9999 0 -0.072 4 4
CKS1B -0.17 0.2 -9999 0 -0.72 14 14
RB1 -0.11 0.19 -9999 0 -0.59 46 46
FOXM1C/SP1 -0.17 0.22 -9999 0 -0.75 15 15
AURKB -0.009 0.14 -9999 0 -0.92 11 11
CENPF -0.17 0.21 -9999 0 -0.73 13 13
CDK4 -0.028 0.046 -9999 0 -0.073 232 232
MYC -0.16 0.19 -9999 0 -0.64 16 16
CHEK2 -0.012 0.04 -9999 0 -0.1 15 15
ONECUT1 -0.16 0.2 -9999 0 -0.7 13 13
CDKN2A 0.003 0.026 -9999 0 -0.061 52 52
LAMA4 -0.16 0.2 -9999 0 -0.7 14 14
FOXM1B/HNF6 -0.17 0.21 -9999 0 -0.76 13 13
FOS -0.18 0.2 -9999 0 -0.74 14 14
SP1 0.031 0.006 -9999 0 -0.025 2 2
CDC25B -0.16 0.2 -9999 0 -0.7 12 12
response to radiation -0.011 0.013 -9999 0 -10000 0 0
CENPB -0.16 0.2 -9999 0 -0.7 12 12
CENPA -0.17 0.21 -9999 0 -0.72 16 16
NEK2 -0.16 0.2 -9999 0 -0.72 13 13
HIST1H2BA -0.16 0.2 -9999 0 -0.7 14 14
CCNA2 0.001 0.046 -9999 0 -0.072 135 135
EP300 0.03 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.18 0.21 -9999 0 -0.79 12 12
CCNB2 -0.19 0.21 -9999 0 -0.73 15 15
CCNB1 -0.18 0.21 -9999 0 -0.75 13 13
ETV5 -0.16 0.2 -9999 0 -0.7 13 13
ESR1 -0.16 0.2 -9999 0 -0.7 12 12
CCND1 -0.16 0.2 -9999 0 -0.68 14 14
GSK3A -0.009 0.036 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.013 0.06 -9999 0 -0.11 4 4
CDK2 0.014 0.03 -9999 0 -0.073 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.22 -9999 0 -0.75 13 13
GAS1 -0.17 0.2 -9999 0 -0.71 14 14
MMP2 -0.18 0.2 -9999 0 -0.73 13 13
RB1/FOXM1C -0.18 0.21 -9999 0 -0.7 18 18
CREBBP 0.032 0.004 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.042 0.06 0.23 35 -10000 0 35
PCK1 0.037 0.031 -10000 0 -10000 0 0
HNF4A 0.035 0.043 0.25 5 -10000 0 5
KCNJ11 0.055 0.061 0.26 28 -10000 0 28
AKT1 0.068 0.042 -10000 0 -0.25 1 1
response to starvation 0.002 0.004 -10000 0 -0.075 1 1
DLK1 0.049 0.072 0.26 32 -10000 0 32
NKX2-1 0.04 0.048 0.21 4 -10000 0 4
ACADM 0.042 0.06 0.23 35 -10000 0 35
TAT 0.043 0.043 -10000 0 -10000 0 0
CEBPB 0.029 0.017 -10000 0 -0.061 11 11
CEBPA 0.03 0.018 -10000 0 -0.061 15 15
TTR 0.053 0.092 0.36 31 -0.44 1 32
PKLR 0.045 0.065 0.23 43 -10000 0 43
APOA1 0.06 0.071 0.41 10 -10000 0 10
CPT1C 0.044 0.056 0.24 29 -10000 0 29
ALAS1 0.047 0.058 -10000 0 -0.62 1 1
TFRC 0.055 0.051 0.21 25 -10000 0 25
FOXF1 0.023 0.024 -10000 0 -0.063 35 35
NF1 0.034 0.01 -10000 0 -0.17 1 1
HNF1A (dimer) 0.039 0.005 -10000 0 -10000 0 0
CPT1A 0.042 0.06 0.23 36 -10000 0 36
HMGCS1 0.043 0.061 0.23 37 -10000 0 37
NR3C1 0.035 0.014 -10000 0 -10000 0 0
CPT1B 0.035 0.053 0.23 24 -10000 0 24
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.005 -10000 0 -10000 0 0
GCK 0.077 0.098 0.25 119 -10000 0 119
CREB1 0.035 0.009 -10000 0 -10000 0 0
IGFBP1 0.05 0.047 -10000 0 -10000 0 0
PDX1 0.045 0.052 -10000 0 -0.31 1 1
UCP2 0.037 0.066 0.23 35 -10000 0 35
ALDOB 0.061 0.071 0.26 44 -10000 0 44
AFP 0.01 0.009 -10000 0 -0.082 4 4
BDH1 0.046 0.067 0.24 45 -10000 0 45
HADH 0.059 0.068 0.26 39 -10000 0 39
F2 0.058 0.074 0.41 10 -10000 0 10
HNF1A 0.039 0.005 -10000 0 -10000 0 0
G6PC 0.021 0.03 -10000 0 -10000 0 0
SLC2A2 0.061 0.051 0.21 30 -10000 0 30
INS 0.028 0.01 0.18 1 -10000 0 1
FOXA1 0.006 0.006 -10000 0 -0.087 1 1
FOXA3 0.015 0.011 -10000 0 -0.12 2 2
FOXA2 0.09 0.071 0.29 28 -10000 0 28
ABCC8 0.058 0.066 0.25 37 -10000 0 37
ALB 0.01 0.009 -10000 0 -0.082 4 4
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.008 0.014 0.054 2 -10000 0 2
FRAP1 0.04 0.06 0.22 5 -0.44 2 7
AKT1 0.033 0.08 0.16 123 -0.13 9 132
INSR 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.011 -10000 0 -10000 0 0
mol:GTP 0.036 0.088 0.18 125 -0.14 1 126
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.023 -10000 0 -0.17 2 2
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.042 0.1 44 -0.13 5 49
TSC1 0.031 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.03 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.043 0.042 0.13 9 -0.18 2 11
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.015 -10000 0 -10000 0 0
RPS6KB1 0.05 0.07 0.2 37 -0.25 2 39
MAP3K5 -0.012 0.056 0.16 2 -0.2 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
apoptosis -0.012 0.056 0.16 2 -0.2 40 42
mol:LY294002 0 0 0.001 1 -0.001 1 2
EIF4B 0.044 0.069 0.19 39 -0.23 2 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.045 0.21 6 -0.23 1 7
eIF4E/eIF4G1/eIF4A1 0.025 0.032 -10000 0 -0.24 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.026 0.15 1 -10000 0 1
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.046 0.12 58 -10000 0 58
FKBP1A 0.03 0.009 -10000 0 -0.063 1 1
RHEB/GTP 0.034 0.051 0.15 52 -0.13 5 57
mol:Amino Acids 0 0 0.001 1 -0.001 1 2
FKBP12/Rapamycin 0.023 0.007 -10000 0 -0.04 1 1
PDPK1 -0.013 0.021 0.16 5 -10000 0 5
EIF4E 0.031 0.009 -10000 0 -0.063 4 4
ASK1/PP5C 0.013 0.16 -10000 0 -0.52 42 42
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.031 -10000 0 -0.24 4 4
TSC1/TSC2 0.041 0.096 0.19 126 -0.15 1 127
tumor necrosis factor receptor activity 0 0 0.001 1 -0.001 1 2
RPS6 0.028 0.011 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 0 26 26
EIF4G1 0.031 0.006 -10000 0 -10000 0 0
IRS1 0.01 0.007 -10000 0 -10000 0 0
INS 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.062 2 2
PDK2 -0.013 0.021 0.16 5 -10000 0 5
EIF4EBP1 -0.033 0.094 -10000 0 -0.97 3 3
PIK3CA 0.029 0.018 -10000 0 -0.063 17 17
PPP2R5D 0.033 0.058 0.22 6 -0.4 2 8
peptide biosynthetic process -0.022 0.016 0.18 3 -10000 0 3
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.03 0.014 -10000 0 -0.063 10 10
mol:Rapamycin 0 0.001 0.002 108 -0.003 1 109
EEF2 -0.022 0.016 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.023 0.094 -10000 0 -0.91 3 3
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.021 0.006 0 41 -10000 0 41
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.006 0.084 0.2 7 -0.33 29 36
CDKN1A -0.012 0.085 -10000 0 -0.33 32 32
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.019 -10000 0 -0.063 21 21
FOXO3 -0.005 0.08 0.2 4 -0.33 26 30
AKT1 -0.002 0.088 -10000 0 -0.34 31 31
BAD 0.032 0.004 -10000 0 -10000 0 0
AKT3 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.009 0.084 -10000 0 -0.33 31 31
AKT1/ASK1 0.014 0.09 -10000 0 -0.32 33 33
BAD/YWHAZ 0.06 0.02 -10000 0 -0.036 8 8
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.032 0.004 -10000 0 -10000 0 0
JNK cascade -0.013 0.087 0.31 33 -10000 0 33
TSC1 -0.01 0.085 0.19 1 -0.33 32 33
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.093 -10000 0 -0.33 33 33
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.002 0.087 -10000 0 -0.34 31 31
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.011 0.085 -10000 0 -0.33 33 33
YWHAQ 0.032 0.004 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAPKAP1 0.031 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle 0.013 0.054 0.18 24 -0.16 2 26
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.003 0.084 -10000 0 -0.32 31 31
CASP9 -0.008 0.085 0.2 3 -0.33 31 34
YWHAB 0.03 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.013 0.093 0.23 10 -0.32 32 42
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.055 0.029 -10000 0 -0.036 32 32
YWHAE 0.032 0.005 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.01 0.079 0.23 1 -0.3 33 34
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.029 -10000 0 -0.14 2 2
CHUK -0.004 0.062 -10000 0 -0.34 16 16
BAD/BCL-XL 0.013 0.09 -10000 0 -0.32 31 31
mTORC2 0.02 0.006 -10000 0 -0.016 8 8
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.026 0.08 0.17 1 -0.27 35 36
PDPK1 0.032 0.004 -10000 0 -10000 0 0
MDM2 0.006 0.099 0.2 41 -0.33 30 71
MAPKKK cascade -0.016 0.092 0.32 33 -10000 0 33
MDM2/Cbp/p300 0.038 0.11 0.22 44 -0.32 30 74
TSC1/TSC2 -0.01 0.094 0.25 12 -0.32 33 45
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.1 0.21 44 -0.31 30 74
glucose import -0.01 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.007 0.053 -10000 0 -0.19 33 33
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.017 0.2 3 -10000 0 3
GSK3A -0.007 0.081 0.2 4 -0.33 28 32
FOXO1 -0.007 0.077 -10000 0 -0.33 26 26
GSK3B -0.008 0.086 0.2 4 -0.33 32 36
SFN 0.026 0.023 -10000 0 -0.063 31 31
G1/S transition of mitotic cell cycle -0.011 0.093 0.22 16 -0.33 33 49
p27Kip1/14-3-3 family 0.006 0.033 -10000 0 -0.26 5 5
PRKACA 0.032 0.006 -10000 0 -10000 0 0
KPNA1 0.032 0.005 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.022 0.015 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

Figure 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
TNFSF10 0.024 0.027 -10000 0 -0.063 45 45
positive regulation of NF-kappaB transcription factor activity 0.038 0.028 -10000 0 -0.049 44 44
MAP2K4 0.008 0.037 0.2 2 -0.16 11 13
IKBKB 0.032 0.003 -10000 0 -10000 0 0
TNFRSF10B 0.031 0.01 -10000 0 -0.063 5 5
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.007 0.013 -10000 0 -0.058 7 7
IKBKG 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.005 -10000 0 0 10 10
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.05 48 48
TRAIL/TRAILR3 0.038 0.029 -10000 0 -0.05 44 44
TRAIL/TRAILR1 0.018 0.018 -10000 0 -0.039 45 45
TRAIL/TRAILR4 0.038 0.029 -10000 0 -0.05 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.023 -10000 0 -0.034 46 46
IKK complex -0.034 0.11 -10000 0 -0.23 123 123
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.024 0.009 -10000 0 -0.049 45 45
MAP3K1 0.014 0.035 -10000 0 -0.16 11 11
TRAILR4 (trimer) 0.032 0.005 -10000 0 0 10 10
TRADD 0.032 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.029 -10000 0 -0.11 20 20
CFLAR 0.032 0.01 -10000 0 -0.063 5 5
MAPK1 -0.022 0.01 -10000 0 -0.049 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.043 -10000 0 -0.064 3 3
mol:ceramide 0.007 0.013 -10000 0 -0.058 7 7
FADD 0.032 0.006 -10000 0 -0.063 1 1
MAPK8 -0.001 0.031 0.19 1 -0.24 2 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.032 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.063 1 1
TRAIL/TRAILR1/FADD 0.035 0.025 -10000 0 -0.04 45 45
DAP3 0.032 0.005 -10000 0 -10000 0 0
CASP10 -0.013 0.026 0.14 10 -0.092 7 17
JNK cascade 0.038 0.028 -10000 0 -0.049 44 44
TRAIL (trimer) 0.023 0.027 -10000 0 -0.063 45 45
TNFRSF10C 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.031 -10000 0 -0.04 44 44
TRAIL/TRAILR2/FADD 0.051 0.038 -10000 0 -0.049 49 49
cell death 0.007 0.012 -10000 0 -0.058 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.033 -10000 0 -0.11 22 22
TRAILR2 (trimer) 0.031 0.01 -10000 0 -0.063 5 5
CASP8 0.016 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.055 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.003 0.051 -10000 0 -0.26 9 9
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.008 0.025 0.14 3 -0.12 7 10
NFKBIA 0.03 0.009 -10000 0 -0.063 1 1
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BAX -0.005 0.037 0.18 12 -0.12 7 19
EnzymeConsortium:3.1.4.12 0 0.016 0.068 3 -0.072 7 10
IKBKB -0.008 0.053 0.2 3 -0.27 8 11
MAP2K2 -0.012 0.045 0.17 22 -0.14 5 27
MAP2K1 -0.016 0.034 0.17 8 -0.14 5 13
SMPD1 -0.002 0.025 0.096 3 -0.11 16 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.056 0.29 1 -0.27 11 12
MAP2K4 -0.012 0.027 0.16 5 -0.14 5 10
protein ubiquitination -0.01 0.059 0.5 1 -0.27 9 10
EnzymeConsortium:2.7.1.37 -0.016 0.042 0.18 8 -0.15 5 13
response to UV 0 0 0.002 6 -0.002 1 7
RAF1 -0.012 0.033 0.17 8 -0.14 5 13
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.002 0.025 0.1 3 -0.1 13 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.012 -10000 0 -0.04 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.027 0.15 4 -0.12 8 12
TRADD 0.032 0.004 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.009 0.04 0.19 7 -0.15 1 8
MAPK1 -0.016 0.047 0.19 6 -0.17 11 17
p50/RELA/I-kappa-B-alpha 0.045 0.013 -10000 0 -0.05 1 1
FADD -0.002 0.049 0.24 1 -0.27 6 7
KSR1 -0.008 0.026 0.13 3 -0.13 7 10
MAPK8 -0.012 0.031 0.18 5 -0.14 5 10
TRAF2 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.049 -10000 0 -0.27 8 8
TNF R/SODD 0.014 0.045 -10000 0 -0.05 164 164
TNF 0.032 0.006 -10000 0 -0.063 2 2
CYCS 0.011 0.045 0.15 17 -0.13 3 20
IKBKG -0.008 0.053 0.19 3 -0.27 8 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.054 0.15 1 -0.27 9 10
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
AIFM1 -0.009 0.031 0.13 12 -0.13 5 17
TNF/TNF R/SODD 0.025 0.054 -10000 0 -0.048 172 172
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.002 0.054 0.18 5 -0.26 9 14
response to hydrogen peroxide 0 0 0.002 6 -0.002 1 7
BCL2 0.032 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.008 -9999 0 -0.062 2 2
SVIL 0.023 0.02 -9999 0 -0.062 14 14
ZNF318 0.031 0.003 -9999 0 -10000 0 0
JMJD2C 0.003 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.044 0.016 -9999 0 -0.039 9 9
CARM1 0.031 0.006 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 -10000 0 0
PELP1 0.032 0.005 -9999 0 -10000 0 0
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
AKT1 0.03 0.008 -9999 0 -10000 0 0
PTK2B 0.032 0.005 -9999 0 -10000 0 0
MED1 0.032 0.003 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -0.064 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.017 0.025 -9999 0 -0.062 30 30
GSN 0.029 0.017 -9999 0 -0.062 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.031 0.008 -9999 0 -10000 0 0
DNA-PK 0.053 0.034 -9999 0 -0.051 22 22
NCOA4 0.025 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.004 -9999 0 -10000 0 0
cell proliferation 0.006 0.053 -9999 0 -0.42 7 7
XRCC5 0.032 0.002 -9999 0 -10000 0 0
UBE3A 0.033 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.024 0.01 -9999 0 -0.026 14 14
FHL2 0.012 0.028 -9999 0 -0.25 3 3
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.006 0.002 -9999 0 -0.023 3 3
CDK6 0.022 0.015 -9999 0 -10000 0 0
TGFB1I1 -0.047 0.035 -9999 0 -0.062 424 424
T-DHT/AR/CyclinD1 0.031 0.034 -9999 0 -0.039 92 92
XRCC6 0.03 0.009 -9999 0 -10000 0 0
T-DHT/AR 0.039 0.03 -9999 0 -0.046 12 12
CTDSP1 0.032 0.007 -9999 0 -0.063 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.032 0.01 -9999 0 -0.062 5 5
TCF4 0.031 0.007 -9999 0 -10000 0 0
CDKN2A 0.003 0.026 -9999 0 -0.063 52 52
SRF 0.033 0.01 -9999 0 -0.045 3 3
NKX3-1 0.006 0.016 -9999 0 -10000 0 0
KLK3 0.02 0.033 -9999 0 -10000 0 0
TMF1 0.031 0.01 -9999 0 -0.063 4 4
HNRNPA1 0.031 0.005 -9999 0 -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 0.043 0.019 -9999 0 -0.041 17 17
AR 0.031 0.014 -9999 0 -0.051 12 12
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.03 0.008 -9999 0 -10000 0 0
PAWR 0.032 0.006 -9999 0 -10000 0 0
PRKDC 0.028 0.019 -9999 0 -0.063 21 21
PA2G4 0.031 0.007 -9999 0 -10000 0 0
UBE2I 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.042 0.014 -9999 0 -0.032 10 10
RPS6KA3 0.033 0.005 -9999 0 -0.062 1 1
T-DHT/AR/ARA70 0.034 0.025 -9999 0 -0.042 10 10
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.041 0.015 -9999 0 -0.035 8 8
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.026 0.025 -9999 0 -0.062 36 36
KLK2 0.004 0.019 -9999 0 -0.28 1 1
CASP8 0.031 0.013 -9999 0 -0.063 9 9
T-DHT/AR/TIF2/CARM1 0.059 0.024 -9999 0 -10000 0 0
TMPRSS2 0.004 0.026 -9999 0 -0.17 6 6
CCND1 0.015 0.036 -9999 0 -0.063 90 90
PIAS1 0.033 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.009 6 6
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.033 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.03 0.025 -9999 0 -0.039 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.024 0.016 -9999 0 -0.029 3 3
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 -0.033 0.043 -9999 0 -0.063 343 343
FKBP4 0.032 0.007 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.05 15 15
PTK2 0.016 0.078 -10000 0 -0.23 40 40
positive regulation of JNK cascade 0.021 0.081 -10000 0 -0.25 28 28
CDC42/GDP 0.035 0.11 0.35 2 -0.34 32 34
Rac1/GDP 0.024 0.093 0.29 1 -0.34 17 18
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.099 -10000 0 -0.31 28 28
nectin-3/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
RAPGEF1 0.006 0.11 0.24 5 -0.34 39 44
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.004 0.11 -10000 0 -0.37 39 39
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
TLN1 -0.015 0.015 -10000 0 -0.14 3 3
Rap1/GTP 0.001 0.077 -10000 0 -0.26 39 39
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.023 40 40
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
PVR 0.031 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.021 0.13 0.33 3 -0.4 33 36
MLLT4 0.03 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.07 0.052 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.015 0.076 -10000 0 -0.28 19 19
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.032 0.006 -10000 0 -0.063 1 1
PVRL2 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.063 8 8
CLDN1 0.03 0.014 -10000 0 -0.063 9 9
JAM-A/CLDN1 0.062 0.047 -10000 0 -0.067 11 11
SRC 0.01 0.12 -10000 0 -0.4 39 39
ITGB3 0.032 0.003 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
FARP2 0.026 0.12 0.37 1 -0.43 15 16
RAC1 0.023 0.015 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.055 0.031 -10000 0 -0.045 10 10
nectin-1/I-afadin 0.044 0.014 -10000 0 -10000 0 0
nectin-2/I-afadin 0.043 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.016 0.032 -10000 0 -0.04 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.056 0.03 -10000 0 -0.046 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.023 0.035 -10000 0 -0.04 118 118
F11R 0.026 0.023 -10000 0 -0.063 31 31
positive regulation of filopodium formation 0.021 0.081 -10000 0 -0.25 28 28
alphaV/beta3 Integrin/Talin 0.024 0.065 0.21 26 -0.17 9 35
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
PIP5K1C -0.011 0.014 -10000 0 -0.062 32 32
VAV2 0.021 0.14 0.31 2 -0.44 31 33
RAP1/GDP 0.025 0.1 0.32 2 -0.31 38 40
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.055 0.031 -10000 0 -0.045 10 10
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
Rac1/GTP 0.021 0.092 0.25 1 -0.34 18 19
PTPRM 0.006 0.019 -10000 0 -0.061 35 35
E-cadherin/beta catenin/alpha catenin 0.075 0.052 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.03 0.008 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.007 0.011 -10000 0 -10000 0 0
CDKN1A 0 0.04 0.065 118 -0.073 45 163
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.063 6 6
FOXO3 0 0.012 0.027 76 -10000 0 76
FOXO1 0.028 0.016 -10000 0 -0.063 11 11
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
TAT 0.032 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.002 -10000 0 -10000 0 0
PPARGC1A 0.032 0.008 -10000 0 -0.063 3 3
FHL2 0.03 0.01 -10000 0 -0.063 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.022 -10000 0 -10000 0 0
HIST2H4A -0.007 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.019 0.019 0.15 4 -10000 0 4
SIRT1 0.026 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.044 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.023 0.026 -10000 0 -0.14 8 8
apoptosis -0.037 0.047 0.04 125 -10000 0 125
SIRT1/PGC1A 0.033 0.021 -10000 0 -0.041 3 3
p53/SIRT1 0.032 0.034 0.1 37 -0.055 30 67
SIRT1/FOXO4 0.024 0.022 -10000 0 -0.12 6 6
FOXO1/FHL2/SIRT1 0.035 0.044 -10000 0 -0.043 32 32
HIST1H1E 0.011 0.004 -10000 0 -0.028 1 1
SIRT1/p300 0.037 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.01 0.016 -10000 0 -10000 0 0
TP53 0.02 0.033 -10000 0 -0.061 65 65
KU70/SIRT1/BAX 0.038 0.047 -10000 0 -0.04 125 125
CREBBP 0.032 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.037 0.022 -10000 0 -10000 0 0
ACSS2 -0.007 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.01 0.016 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.033 0.04 0.12 33 -10000 0 33
GNAI2 0.032 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 0 151 151
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.041 -10000 0 -0.13 33 33
negative regulation of cAMP metabolic process 0.002 0.012 0.082 6 -0.11 2 8
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNA12 0.023 0.015 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.012 0.083 6 -0.11 2 8
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.051 0.21 10 -0.23 7 17
FYN 0.002 0.057 0.22 6 -0.25 9 15
LAT/GRAP2/SLP76 0.023 0.051 0.2 3 -0.26 6 9
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.06 0.19 10 -0.24 10 20
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.01 0.023 0.084 12 -0.087 5 17
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.039 2 2
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.003 0.066 0.24 6 -0.28 9 15
TRPV6 0.38 0.59 1.3 155 -10000 0 155
CD28 0.033 0.002 -10000 0 -10000 0 0
SHC1 0.007 0.052 0.24 9 -0.27 6 15
receptor internalization 0.014 0.05 -10000 0 -0.36 6 6
PRF1 -0.13 0.27 -10000 0 -0.6 126 126
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
COT/AKT1 0.007 0.05 0.17 5 -0.2 10 15
LAT 0.007 0.049 0.19 5 -0.28 7 12
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.029 0.019 -10000 0 -0.064 20 20
CD3E 0.032 0.006 -10000 0 -0.064 1 1
CD3G 0.032 0.006 -10000 0 -0.068 1 1
RASGRP2 0.004 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.045 0.086 0.22 12 -0.25 20 32
HLA-A 0.032 0.006 -10000 0 -0.063 1 1
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.022 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.042 0.15 17 -0.095 10 27
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.027 -10000 0 -0.11 12 12
PRKCA -0.012 0.039 0.18 4 -0.16 5 9
GRAP2 0.03 0.008 -10000 0 -10000 0 0
mol:IP3 0.005 0.043 -10000 0 -0.21 7 7
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.01 0.036 -10000 0 -0.26 5 5
ORAI1 -0.33 0.5 -10000 0 -1.1 155 155
CSK 0.008 0.048 0.19 5 -0.27 7 12
B7 family/CD28 0.05 0.058 0.22 4 -0.27 5 9
CHUK 0.024 0.015 -10000 0 -0.063 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.012 0.048 -10000 0 -0.3 7 7
PTPN6 0.004 0.047 0.17 9 -0.26 7 16
VAV1 0.011 0.056 0.19 16 -0.28 7 23
Monovalent TCR/CD3 0.014 0.029 -10000 0 -0.22 6 6
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.005 0.052 0.19 7 -0.25 7 14
PAG1 0.01 0.046 0.21 2 -0.27 7 9
RAP1A 0.032 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.011 0.048 0.14 1 -0.29 7 8
CD80 0.032 0.007 -10000 0 -0.005 13 13
CD86 0.027 0.021 -10000 0 -0.063 24 24
PDK1/CARD11/BCL10/MALT1 0.002 0.033 -10000 0 -0.14 9 9
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 -0.001 0.041 0.16 5 -0.24 5 10
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.064 2 2
PTPRC 0.009 0.041 -10000 0 -0.063 121 121
PDK1/PKC theta -0.003 0.069 0.24 12 -0.29 6 18
CSK/PAG1 0.006 0.044 0.18 1 -0.26 7 8
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.046 0.011 -10000 0 -0.05 1 1
GRAP2/SLP76 0.034 0.057 0.2 4 -0.27 7 11
STIM1 -0.065 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.007 0.049 0.16 9 -0.15 20 29
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.014 0.052 -10000 0 -0.38 6 6
mol:DAG -0.021 0.026 -10000 0 -0.19 7 7
RAP1A/GDP 0 0.021 0.063 15 -0.046 9 24
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.032 0.008 -10000 0 -0.068 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 126 126
RAP1A/GTP 0.003 0.007 -10000 0 -0.056 4 4
mol:PI-3-4-5-P3 0.004 0.06 0.2 10 -0.24 9 19
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.053 -10000 0 -0.25 7 7
NRAS 0.009 0.041 -10000 0 -0.063 125 125
ZAP70 0.032 0.003 -10000 0 0 3 3
GRB2/SOS1 0.023 0.004 -10000 0 0 15 15
LAT/GRAP2/SLP76/VAV1 0.011 0.052 0.19 8 -0.26 6 14
MALT1 0.028 0.02 -10000 0 -0.063 21 21
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.022 13 13
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.02 -10000 0 -0.14 7 7
PRKCE -0.011 0.039 0.18 4 -0.16 5 9
PRKCQ 0 0.068 0.23 13 -0.28 8 21
LCP2 0.026 0.022 -10000 0 -0.063 29 29
BCL10 0.031 0.009 -10000 0 -0.063 3 3
regulation of survival gene product expression 0.001 0.056 0.18 10 -0.21 10 20
IKK complex -0.006 0.036 0.19 7 -0.085 5 12
RAS family/GDP -0.006 0.01 -10000 0 -0.031 11 11
MAP3K14 -0.003 0.038 0.13 5 -0.17 9 14
PDPK1 -0.001 0.056 0.19 11 -0.22 8 19
TCR/CD3/MHC I/CD8/Fyn 0.014 0.055 0.25 1 -0.39 5 6
EPHB forward signaling

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
Ephrin A5/EPHB2 0.042 0.01 -10000 0 -0.04 1 1
cell-cell adhesion 0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.077 0.045 -10000 0 -10000 0 0
ITSN1 0.032 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
SHC1 0.024 0.026 -10000 0 -0.063 40 40
Ephrin B1/EPHB3 0.041 0.013 -10000 0 -0.04 7 7
Ephrin B1/EPHB1 0.042 0.013 -10000 0 -0.04 9 9
HRAS/GDP 0.021 0.051 -10000 0 -0.15 26 26
Ephrin B/EPHB1/GRB7 0.078 0.046 -10000 0 -0.075 1 1
Endophilin/SYNJ1 -0.023 0.038 0.18 13 -10000 0 13
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.073 0.048 -10000 0 -0.075 1 1
endothelial cell migration 0.037 0.038 -10000 0 -0.047 11 11
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.063 1 1
PAK1 -0.028 0.047 0.19 14 -10000 0 14
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.045 0.19 16 -10000 0 16
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.038 0.17 13 -10000 0 13
lamellipodium assembly -0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.035 0.091 30 -0.15 9 39
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.063 1 1
EPHB3 0.03 0.013 -10000 0 -0.063 7 7
EPHB1 0.03 0.013 -10000 0 -0.063 9 9
EPHB4 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.011 0.043 0.15 15 -0.16 19 34
Ephrin B/EPHB2 0.063 0.035 -10000 0 -0.044 6 6
Ephrin B/EPHB3 0.062 0.036 -10000 0 -0.049 7 7
JNK cascade -0.027 0.053 0.24 17 -10000 0 17
Ephrin B/EPHB1 0.062 0.037 -10000 0 -0.048 11 11
RAP1/GDP 0.029 0.1 0.19 128 -0.18 13 141
EFNB2 0.03 0.01 -10000 0 -10000 0 0
EFNB3 0.031 0.006 -10000 0 -10000 0 0
EFNB1 0.032 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.035 41 41
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.057 0.049 0.14 1 -0.11 21 22
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.039 1 1
MAPK3 -0.007 0.035 0.17 3 -0.19 4 7
MAPK1 -0.007 0.032 0.16 2 -0.19 4 6
Rac1/GDP -0.006 0.066 0.21 31 -0.18 13 44
actin cytoskeleton reorganization -0.035 0.033 0.034 1 -0.13 20 21
CDC42/GDP 0.036 0.11 0.2 134 -0.18 13 147
PI3K 0.041 0.042 -10000 0 -0.054 1 1
EFNA5 0.032 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.021 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.032 -10000 0 -0.12 23 23
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.022 -10000 0 -0.095 1 1
PTK2 -0.006 0.086 0.55 12 -10000 0 12
MAP4K4 -0.027 0.053 0.24 17 -10000 0 17
SRC 0.031 0.008 -10000 0 -10000 0 0
KALRN 0.032 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.022 -10000 0 -10000 0 0
neuron projection morphogenesis 0.059 0.16 0.33 128 -0.17 2 130
MAP2K1 0.004 0.035 0.078 29 -0.12 20 49
WASL 0.023 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.072 0.035 -10000 0 -0.05 21 21
cell migration -0.001 0.055 0.17 10 -0.21 9 19
NRAS 0.009 0.041 -10000 0 -0.063 125 125
SYNJ1 -0.023 0.039 0.18 13 -10000 0 13
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.034 0.18 8 -10000 0 8
HRAS/GTP 0.046 0.04 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.057 0.023 -10000 0 -0.036 22 22
cell adhesion mediated by integrin 0.014 0.039 -10000 0 -0.2 9 9
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0.051 0.039 0.14 5 -0.069 1 6
RAC1-CDC42/GTP -0.034 0.028 0.022 5 -10000 0 5
RASA1 0.032 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.019 0.065 0.21 29 -0.16 22 51
ruffle organization 0.066 0.16 0.32 130 -10000 0 130
NCK1 0.03 0.015 -10000 0 -0.063 11 11
receptor internalization -0.005 0.024 0.22 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.077 0.045 -10000 0 -10000 0 0
ROCK1 -0.015 0.04 0.18 21 -10000 0 21
RAS family/GDP -0.035 0.034 -10000 0 -0.13 24 24
Rac1/GTP -0.029 0.026 0.047 4 -10000 0 4
Ephrin B/EPHB1/Src/Paxillin 0.015 0.037 -10000 0 -0.12 32 32
Regulation of Telomerase

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
Telomerase catalytic core complex 0.021 0.087 0.3 2 -0.38 8 10
RAD9A 0.032 0.006 -10000 0 -0.063 1 1
AP1 0.021 0.041 -10000 0 -0.05 117 117
IFNAR2 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.016 -10000 0 -0.054 20 20
ER alpha/Oestrogen 0.023 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.051 -10000 0 -0.14 46 46
EGF 0.032 0.007 -10000 0 -0.062 2 2
SMG5 0.032 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.035 -10000 0 -0.052 65 65
TERT/c-Abl 0.033 0.088 -10000 0 -0.36 8 8
SAP18 0.031 0.008 -10000 0 -10000 0 0
MRN complex 0.062 0.019 -10000 0 -0.036 12 12
WT1 0.031 0.011 -10000 0 -0.064 5 5
WRN 0.031 0.009 -10000 0 -0.063 4 4
SP1 0.032 0.005 -10000 0 -10000 0 0
SP3 0.019 0.034 -10000 0 -0.063 74 74
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.37 7 7
Mad/Max 0.045 0.013 -10000 0 -10000 0 0
TERT 0.021 0.088 0.3 2 -0.39 8 10
CCND1 0.011 0.089 0.32 1 -0.4 7 8
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
TERF2 -0.02 0.02 0.047 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.043 0.062 -10000 0 -0.34 6 6
CDKN1B -0.025 0.011 -10000 0 -0.057 1 1
RAD1 0.032 0.007 -10000 0 -0.063 2 2
XRCC5 0.032 0.002 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.018 -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 0.024 0.004 -10000 0 -10000 0 0
FOS 0.008 0.04 -10000 0 -0.063 120 120
IFN-gamma/IRF1 0.037 0.035 -10000 0 -0.05 62 62
PARP2 0.031 0.008 -10000 0 -10000 0 0
BLM 0.01 0.04 -10000 0 -0.063 119 119
Telomerase 0.006 0.065 -10000 0 -0.24 31 31
IRF1 0.021 0.033 -10000 0 -0.063 66 66
ESR1 0.031 0.008 -10000 0 -10000 0 0
KU/TER 0.045 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.029 -10000 0 -0.06 30 30
ubiquitin-dependent protein catabolic process -0.003 0.053 -10000 0 -0.16 34 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.002 0.053 -10000 0 -0.16 34 34
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
ATM 0.012 0.017 0.091 6 -0.053 25 31
SMAD3 -0.023 0.008 -10000 0 -0.049 26 26
ABL1 0.031 0.008 -10000 0 -0.063 1 1
MXD1 0.033 0.002 -10000 0 -10000 0 0
MRE11A 0.032 0.005 -10000 0 -10000 0 0
HUS1 0.023 0.015 -10000 0 -10000 0 0
RPS6KB1 0.032 0.006 -10000 0 -0.063 1 1
TERT/NF kappa B1/14-3-3 0.042 0.11 0.29 1 -0.39 14 15
NR2F2 0.031 0.009 -10000 0 -0.06 4 4
MAPK3 -0.022 0.004 -10000 0 -10000 0 0
MAPK1 -0.02 0.007 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.062 26 26
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
HNRNPC 0.031 0.008 -10000 0 0 29 29
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.017 0.091 6 -0.053 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.018 0.025 -10000 0 -0.05 8 8
MYC 0.009 0.04 -10000 0 -0.063 119 119
IL2 0.032 0.005 -10000 0 -10000 0 0
KU 0.045 0.013 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.063 26 26
TRF2/BLM 0.018 0.041 -10000 0 -0.053 114 114
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.097 -10000 0 -0.38 8 8
SP1/HDAC2 0.043 0.017 -10000 0 -0.053 4 4
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.098 -10000 0 -0.38 7 7
Smad3/Myc 0.007 0.035 -10000 0 -0.05 137 137
911 complex 0.045 0.032 -10000 0 -0.041 8 8
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.035 0.09 -10000 0 -0.37 7 7
Telomerase/AKT1/mTOR/p70S6K 0.009 0.094 0.2 1 -0.3 34 35
SIN3B 0.031 0.006 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.096 -10000 0 -0.37 7 7
response to DNA damage stimulus 0.003 0.014 -10000 0 -0.1 6 6
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.04 0.018 -10000 0 -0.052 4 4
Telomerase/hnRNP C1/C2 0.045 0.098 -10000 0 -0.38 7 7
E2F1 0.03 0.008 -10000 0 -10000 0 0
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.032 0.002 -10000 0 -10000 0 0
DKC1 0.031 0.011 -10000 0 -0.063 7 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.063 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.032 0.006 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.031 -10000 0 -0.048 2 2
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
KATNA1 0.029 0.012 -10000 0 -0.063 5 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.012 0.063 0.18 63 -10000 0 63
IQGAP1/CaM 0.021 0.04 -10000 0 -0.05 111 111
DAB1 0.032 0.005 -10000 0 -10000 0 0
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
PLA2G7 0.031 0.012 -10000 0 -0.063 8 8
CALM1 0.029 0.01 -10000 0 -10000 0 0
DYNLT1 0.017 0.033 -10000 0 -0.063 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.009 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.003 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 0 101 101
LIS1/Poliovirus Protein 3A -0.016 0.005 -10000 0 -10000 0 0
CDK5R2 0.012 0.016 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.019 0.032 -10000 0 -0.048 3 3
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.095 0.3 49 -10000 0 49
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.002 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.009 0.044 0.17 5 -10000 0 5
RELN 0.01 0.016 -10000 0 -0.063 2 2
PAFAH/LIS1 0.025 0.015 -10000 0 -0.042 16 16
LIS1/CLIP170 0.026 0.012 -10000 0 -0.035 10 10
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.039 0.15 3 -10000 0 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.046 0.13 4 -0.21 21 25
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.019 0.074 0.3 29 -10000 0 29
LIS1/IQGAP1 0.009 0.033 -10000 0 -0.047 124 124
RHOA 0 0.031 -10000 0 -0.26 6 6
PAFAH1B1 -0.02 0.007 -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 0.02 0.027 0.11 1 -0.15 5 6
NDEL1/Katanin 60/Dynein heavy chain 0.027 0.095 0.3 45 -10000 0 45
LRP8 0.032 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.091 0.29 44 -10000 0 44
P39/CDK5 0.003 0.03 0.17 3 -10000 0 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -0.035 9 9
CDK5 0.011 0.043 0.18 10 -10000 0 10
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.01 -10000 0 -0.029 10 10
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.035 0.17 5 -10000 0 5
RELN/VLDLR 0.024 0.04 -10000 0 -10000 0 0
CDC42 -0.001 0.033 -10000 0 -0.26 7 7
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.047 0.2 10 -0.2 4 14
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.003 0.092 0.24 2 -0.32 23 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.071 -10000 0 -0.57 7 7
mol:DAG -0.18 0.35 -10000 0 -0.8 122 122
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.077 0.26 2 -0.26 9 11
FRAP1 -0.007 0.079 0.28 2 -0.27 13 15
FOXO3 -0.013 0.079 0.25 3 -0.26 19 22
AKT1 -0.01 0.08 0.26 1 -0.27 19 20
GAB2 0.031 0.006 -10000 0 -10000 0 0
SMPD1 -0.001 0.1 -10000 0 -0.59 15 15
SGMS1 -0.13 0.26 -10000 0 -0.6 122 122
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.016 0.007 -10000 0 -0.042 6 6
CALM1 0.029 0.01 -10000 0 -10000 0 0
cell proliferation -0.063 0.16 0.19 1 -0.34 116 117
EIF3A 0.024 0.015 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.049 16 16
RPS6KB1 0.02 0.037 -10000 0 -0.74 1 1
mol:sphingomyelin -0.18 0.35 -10000 0 -0.8 122 122
natural killer cell activation 0 0.001 -10000 0 -0.004 2 2
JAK3 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MYC -0.015 0.085 0.25 3 -0.28 14 17
MYB 0.015 0.026 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.009 0.071 0.14 3 -0.21 27 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.047 -10000 0 -0.71 1 1
mol:PI-3-4-5-P3 -0.009 0.07 0.14 3 -0.2 27 30
Rac1/GDP 0.005 0.019 -10000 0 -0.046 3 3
T cell proliferation -0.009 0.066 0.13 1 -0.2 25 26
SHC1 0.024 0.026 -10000 0 -0.064 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.002 -10000 0 -10000 0 0
PRKCZ -0.01 0.067 0.13 3 -0.2 26 29
NF kappa B1 p50/RelA 0.008 0.091 0.28 2 -0.26 13 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.044 -10000 0 -0.2 10 10
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL2RA 0.023 0.017 -10000 0 -0.063 6 6
IL2RB 0.03 0.012 -10000 0 -0.064 4 4
TERT 0.032 0.006 -10000 0 -10000 0 0
E2F1 0.024 0.024 -10000 0 -0.38 1 1
SOS1 0 0.001 -10000 0 -10000 0 0
RPS6 0.028 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.064 9 9
actin cytoskeleton organization -0.009 0.066 0.13 1 -0.2 25 26
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.029 0.018 -10000 0 -0.063 17 17
Rac1/GTP 0.032 0.032 -10000 0 -10000 0 0
LCK 0.031 0.01 -10000 0 -0.063 4 4
BCL2 -0.005 0.074 0.26 7 -0.25 5 12
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.02 0.031 0.16 7 -10000 0 7
DAPP1 0.005 0.061 0.15 22 -0.24 10 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.004 0.07 0.32 1 -0.26 16 17
mol:DAG -0.005 0.054 0.23 11 -0.14 3 14
HRAS 0.035 0.01 0.08 3 -10000 0 3
RAP1A 0.035 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.056 -10000 0 -0.23 17 17
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARF5 0.023 0.015 -10000 0 -10000 0 0
mol:GTP -0.021 0.041 0.18 13 -10000 0 13
ARF1/GTP -0.014 0.031 0.15 11 -0.11 1 12
RHOA 0.032 0.006 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.063 75 75
RAP1A/GTP -0.022 0.032 0.15 10 -10000 0 10
ADAP1 -0.021 0.036 0.16 12 -10000 0 12
ARAP3 -0.021 0.04 0.18 13 -10000 0 13
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.03 0.012 -10000 0 -0.063 7 7
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
NRAS 0.012 0.042 -10000 0 -0.059 124 124
FYN 0.029 0.011 -10000 0 -0.063 1 1
ARF6 0.031 0.008 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.063 15 15
mol:Ca2+ -0.004 0.037 0.13 23 -10000 0 23
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 0 3 3
mol:IP3 -0.008 0.042 0.14 22 -10000 0 22
LYN 0.021 0.031 -10000 0 -0.063 60 60
ARF1/GDP 0.028 0.066 0.26 1 -0.22 23 24
RhoA/GDP 0.037 0.065 0.18 23 -0.12 6 29
PDK1/Src/Hsp90 0.055 0.029 -10000 0 -0.036 32 32
BLNK 0.013 0.031 -10000 0 -0.063 59 59
actin cytoskeleton reorganization 0.027 0.08 0.17 84 -0.18 6 90
SRC 0.031 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.003 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PTEN 0.023 0.019 -10000 0 -0.039 15 15
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.042 0.19 12 -10000 0 12
RhoA/GTP -0.023 0.043 0.19 13 -10000 0 13
Src family/SYK family/BLNK-LAT -0.019 0.068 -10000 0 -0.19 40 40
BLK 0.032 0.005 -10000 0 -10000 0 0
PDPK1 0.032 0.004 -10000 0 -10000 0 0
CYTH1 -0.021 0.036 0.16 12 -10000 0 12
HCK 0.014 0.036 -10000 0 -0.063 85 85
CYTH3 -0.021 0.036 0.16 12 -10000 0 12
CYTH2 -0.021 0.036 0.16 12 -10000 0 12
KRAS 0.034 0.011 0.079 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.028 0.3 1 -0.17 7 8
SGK1 0.001 0.03 -10000 0 -0.17 11 11
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.066 0.16 10 -0.22 24 34
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.024 -10000 0 -0.063 34 34
ARF6/GDP -0.018 0.043 0.2 11 -0.13 3 14
mol:PI-3-4-5-P3 -0.023 0.031 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.022 0.033 0.15 10 -10000 0 10
VAV1 0.032 0.007 -10000 0 -0.063 1 1
mol:PI-3-4-P2 -0.011 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.057 0.081 0.2 95 -0.069 3 98
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.058 0.26 1 -0.23 18 19
LAT 0.032 0.005 -10000 0 -0.063 1 1
Rac1/GTP 0.022 0.061 0.16 1 -0.24 18 19
ITK -0.025 0.038 0.16 11 -10000 0 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.059 0.26 8 -0.17 5 13
LCK 0.031 0.01 -10000 0 -0.063 4 4
BTK -0.025 0.041 0.17 13 -10000 0 13
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.07 0.22 31 -0.32 5 36
PDGFB-D/PDGFRB/SLAP 0.04 0.026 -10000 0 -0.051 34 34
PDGFB-D/PDGFRB/APS/CBL 0.043 0.009 -10000 0 -0.04 2 2
AKT1 -0.019 0.078 0.29 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.075 0.23 33 -0.36 5 38
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
FGR 0.009 0.063 0.2 10 -0.37 7 17
mol:Ca2+ 0.024 0.071 0.22 29 -0.39 5 34
MYC 0.045 0.12 0.3 41 -0.31 4 45
SHC1 0.024 0.026 -10000 0 -0.063 40 40
HRAS/GDP -0.017 0.053 0.17 36 -10000 0 36
LRP1/PDGFRB/PDGFB 0.054 0.031 -10000 0 -0.043 33 33
GRB10 0.021 0.018 -10000 0 -0.063 6 6
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.22 29 -0.4 5 34
PTEN 0.023 0.016 -10000 0 -0.063 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.063 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.01 -10000 0 -0.05 2 2
PDGFB-D/PDGFRB/GRB10 0.031 0.025 -10000 0 -0.05 8 8
cell cycle arrest 0.04 0.026 -10000 0 -0.051 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.023 0.071 0.27 13 -10000 0 13
GAB1 0.019 0.077 0.24 23 -0.34 8 31
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.083 0.24 36 -0.28 8 44
PDGFB-D/PDGFRB 0.055 0.026 -10000 0 -0.046 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.011 -10000 0 -0.05 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.053 0.2 10 -0.26 5 15
positive regulation of MAPKKK cascade 0.047 0.01 -10000 0 -0.05 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.072 0.22 29 -0.4 5 34
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.031 0.01 -10000 0 -0.032 10 10
PDGFB-D/PDGFRB/GRB7 0.047 0.011 -10000 0 -0.05 3 3
SHB 0.03 0.009 -10000 0 0 40 40
BLK 0.009 0.058 0.22 5 -0.36 7 12
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -0.05 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.016 0.084 0.25 25 -0.34 8 33
CBL 0.032 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.046 0.011 -10000 0 -0.05 2 2
LCK 0.013 0.057 0.21 10 -0.34 5 15
PDGFRB 0.032 0.008 -10000 0 -0.052 3 3
ACP1 0.032 0.005 -10000 0 -10000 0 0
HCK 0 0.035 -10000 0 -10000 0 0
ABL1 0.02 0.073 0.22 31 -0.27 8 39
PDGFB-D/PDGFRB/CBL 0.023 0.08 0.26 13 -0.38 8 21
PTPN1 0.03 0.009 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.063 10 10
STAT1 0.029 0.018 -10000 0 -0.063 18 18
cell proliferation 0.045 0.11 0.29 42 -0.29 4 46
SLA 0.026 0.024 -10000 0 -0.063 33 33
actin cytoskeleton reorganization -0.016 0.067 0.2 41 -10000 0 41
SRC 0.01 0.044 0.18 3 -0.73 1 4
PI3K -0.043 0.021 -10000 0 -0.093 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.035 -10000 0 -0.048 46 46
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.076 0.24 32 -0.37 5 37
LYN 0.004 0.041 0.18 4 -0.35 1 5
LRP1 0.029 0.016 -10000 0 -0.063 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.004 -10000 0 -10000 0 0
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
NCK1-2/p130 Cas 0.066 0.038 -10000 0 -0.068 1 1
SPHK1 0.029 0.019 -10000 0 -0.063 19 19
EDG1 0 0.003 0.025 1 -10000 0 1
mol:DAG 0.024 0.072 0.22 29 -0.4 5 34
PLCG1 0.024 0.073 0.22 29 -0.41 5 34
NHERF/PDGFRB 0.063 0.018 -10000 0 -0.043 9 9
YES1 -0.006 0.095 0.19 9 -0.57 11 20
cell migration 0.062 0.018 -10000 0 -0.043 9 9
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.073 2 2
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.063 2 2
NHERF1-2/PDGFRB/PTEN 0.046 0.056 -10000 0 -0.052 8 8
FYN -0.019 0.11 -10000 0 -0.36 44 44
DOK1 -0.016 0.053 0.17 38 -10000 0 38
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.055 0.12 0.25 93 -0.42 4 97
PRKCD -0.015 0.053 0.17 37 -10000 0 37
FER -0.016 0.053 0.17 36 -10000 0 36
MAPKKK cascade -0.011 0.072 0.18 57 -10000 0 57
RASA1 -0.015 0.053 0.17 36 -10000 0 36
NCK1 0.03 0.015 -10000 0 -0.063 11 11
NCK2 0.032 0.004 -10000 0 -10000 0 0
p62DOK/Csk -0.02 0.052 0.17 37 -10000 0 37
PDGFB-D/PDGFRB/SHB 0.044 0.015 -10000 0 -0.05 2 2
chemotaxis 0.02 0.072 0.21 32 -0.27 8 40
STAT1-3-5/STAT1-3-5 0.063 0.043 -10000 0 -0.092 1 1
Bovine Papilomavirus E5/PDGFRB 0.023 0.006 0.052 2 -0.04 2 4
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.057 0.03 -9999 0 -0.045 38 38
E-cadherin/beta catenin 0.045 0.016 -9999 0 -0.05 8 8
CTNNB1 0.032 0.005 -9999 0 0 14 14
JUP 0.029 0.017 -9999 0 -0.063 16 16
CDH1 0.03 0.013 -9999 0 -0.063 8 8
Syndecan-2-mediated signaling events

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

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
CTTN 0.032 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.07 -10000 0 -0.24 21 21
Syndecan-3/Neurocan 0.011 0.068 -10000 0 -0.29 21 21
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
Syndecan-3/EGFR 0 0.063 -10000 0 -0.26 22 22
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
PSENEN 0.031 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
NCAN 0.026 0.014 -10000 0 -0.063 2 2
long-term memory 0.029 0.076 -10000 0 -0.3 22 22
Syndecan-3/IL8 0.003 0.082 -10000 0 -0.35 22 22
PSEN1 0.03 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.045 0.013 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.063 1 1
limb bud formation -0.006 0.074 -10000 0 -0.36 20 20
MC4R 0.031 0.007 -10000 0 -0.063 1 1
SRC 0.031 0.008 -10000 0 -10000 0 0
PTN 0.021 0.015 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.006 0.074 -10000 0 -0.36 20 20
neuron projection morphogenesis 0.014 0.086 0.16 105 -0.25 9 114
Syndecan-3/AgRP 0.015 0.081 -10000 0 -0.35 22 22
Syndecan-3/AgRP/MC4R 0.031 0.084 -10000 0 -0.34 22 22
Fyn/Cortactin 0.043 0.016 -10000 0 -0.05 1 1
SDC3 -0.006 0.075 -10000 0 -0.37 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.081 -10000 0 -0.35 22 22
IL8 0.012 0.039 -10000 0 -0.063 110 110
Syndecan-3/Fyn/Cortactin 0.03 0.077 -10000 0 -0.3 22 22
Syndecan-3/CASK -0.008 0.073 -10000 0 -0.34 22 22
alpha-MSH/MC4R 0.046 0.011 -10000 0 -0.05 1 1
Gamma Secretase 0.072 0.053 -10000 0 -0.078 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.031 -9999 0 -0.063 61 61
Ran/GTP/Exportin 1/HDAC4 -0.027 0.011 -9999 0 -0.062 39 39
MDM2/SUMO1 0.034 0.039 -9999 0 -0.098 36 36
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.029 0.012 -9999 0 -0.066 38 38
SUMO1 0.033 0.001 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.026 -9999 0 -0.096 39 39
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.039 -9999 0 -0.097 39 39
SUMO1/HDAC1 0.03 0.043 -9999 0 -0.1 38 38
RANGAP1 0.03 0.008 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.07 0.034 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.028 -9999 0 -0.095 39 39
Ran/GTP 0.021 0.033 -9999 0 -0.092 39 39
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.011 -9999 0 -0.063 1 1
UBE2I 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 -9999 0 -0.096 39 39
NPC 0.019 0.001 -9999 0 -10000 0 0
PIAS2 0.031 0.006 -9999 0 -10000 0 0
PIAS1 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.006 0.034 0.13 31 -0.14 3 34
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.041 0.12 4 -0.13 11 15
AP2 0.023 0.005 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.022 -10000 0 -0.04 1 1
CLTB 0.032 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.031 -10000 0 -0.1 35 35
CD4 0.028 0.019 -10000 0 -0.063 18 18
CLTA 0.03 0.009 -10000 0 -10000 0 0
mol:GTP -0.003 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.01 0.003 0 43 -10000 0 43
mol:PI-4-5-P2 0.004 0.007 0.074 4 -0.034 1 5
ARF1/GTP 0.018 0.009 -10000 0 -0.036 10 10
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.02 -10000 0 -0.09 24 24
mol:Choline 0.004 0.007 0.075 4 -0.034 1 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
DDEF1 0.002 0.007 0.074 4 -0.034 1 5
ARF1/GDP 0.004 0.012 -10000 0 -0.082 7 7
AP2M1 0.031 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.017 0.011 0.047 1 -10000 0 1
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.015 -10000 0 -0.031 1 1
ARFIP2 0.029 0.014 -10000 0 -0.04 11 11
COPA 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.039 0.1 1 -0.14 30 31
ARF1/GTP/ARHGAP10 0.02 0.004 -10000 0 -10000 0 0
GGA3 0.032 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.024 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.028 -10000 0 -0.1 27 27
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.03 0.021 -10000 0 -0.038 1 1
CYTH2 -0.003 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.041 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.011 -10000 0 0 151 151
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 0.071 9 -0.092 29 38
PLD2 0.004 0.007 0.075 4 -0.034 1 5
ARF-GAP1/v-SNARE -0.01 0.003 0 43 -10000 0 43
PIP5K1A 0.004 0.007 0.074 4 -0.034 1 5
ARF1/GTP/Membrin/GBF1/p115 0.003 0.033 -10000 0 -0.056 116 116
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.007 0.075 4 -0.034 1 5
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 0 43 -10000 0 43
GOSR2 0.011 0.029 -10000 0 -0.36 3 3
USO1 0.012 0.02 -10000 0 -0.29 2 2
GBF1 -0.063 0.14 -10000 0 -0.32 115 115
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.02 -10000 0 -0.04 18 18
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.083 -10000 0 -0.39 19 19
HDAC1 0.022 0.031 -10000 0 -0.059 61 61
AES 0.032 0.007 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.024 -10000 0 -0.05 4 4
TLE1 0.032 0.006 -10000 0 -10000 0 0
AP1 0.002 0.022 -10000 0 -0.14 4 4
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
ADAM10 0.028 0.018 -10000 0 -0.063 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.058 -10000 0 -0.51 4 4
NICD/RBPSUH 0.028 0.088 -10000 0 -0.39 19 19
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.082 -10000 0 -0.44 15 15
PSENEN 0.031 0.007 -10000 0 -10000 0 0
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.006 0.037 -10000 0 -0.063 101 101
beta catenin/beta TrCP1 0.063 0.078 0.19 87 -0.23 6 93
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
AXIN1 0.026 0.047 0.26 4 -0.25 1 5
CtBP/CBP/TCF1/TLE1/AES 0.022 0.031 -10000 0 -0.12 11 11
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.007 0.04 -10000 0 -0.063 120 120
JUN 0.032 0.005 -10000 0 -10000 0 0
MAP3K7 0.031 0.009 -10000 0 -0.063 1 1
CTNNB1 0.048 0.08 0.19 88 -0.23 6 94
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.025 -10000 0 -0.048 9 9
HNF1A 0.033 0.003 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.005 0.065 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.022 0.017 -10000 0 -0.063 4 4
NOTCH1 precursor/Deltex homolog 1 0.005 0.081 -10000 0 -0.39 19 19
apoptosis 0.002 0.022 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.005 0.081 -10000 0 -0.39 19 19
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.018 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.071 0.053 -10000 0 -0.076 2 2
APC 0.01 0.084 0.26 3 -0.33 19 22
DVL1 0.018 0.021 -10000 0 -0.21 2 2
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.017 0.053 -10000 0 -0.048 102 102
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -0.038 1 1
CCND1 -0.005 0.1 -10000 0 -0.8 7 7
WNT1 0.031 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.085 0.26 17 -0.46 3 20
DKK2 0.031 0.012 -10000 0 -0.063 8 8
NOTCH1 precursor/DVL1 0.034 0.091 0.25 1 -0.38 16 17
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.014 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.083 -10000 0 -0.39 19 19
PPP2R5D 0.015 0.03 -10000 0 -0.39 2 2
MAPK1 0.03 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.007 0.024 -10000 0 -10000 0 0
RBPJ 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.005 -10000 0 -0.022 1 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.01 -10000 0 -10000 0 0
Necdin/E2F1 0.028 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.068 0.032 -10000 0 -0.047 20 20
NGF (dimer)/p75(NTR)/BEX1 0.028 0.024 -10000 0 -0.04 16 16
NT-4/5 (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.039 21 21
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 -0.014 0.046 0.17 22 -10000 0 22
IKBKG 0.032 0.003 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.02 0.011 -10000 0 -0.031 21 21
FURIN 0.032 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.047 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.049 0.015 -10000 0 -10000 0 0
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.032 0.006 -10000 0 -0.063 1 1
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.079 0.22 7 -0.3 19 26
IRAK1 0.032 0.003 -10000 0 -10000 0 0
SHC1 -0.02 0.008 -10000 0 -0.04 59 59
ARHGDIA 0.032 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.053 -10000 0 -0.078 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.027 -10000 0 -0.04 23 23
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.034 0.034 -10000 0 -0.038 23 23
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.003 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.03 0.011 -10000 0 -0.063 3 3
RhoA/GDP/RHOGDI 0.037 0.018 -10000 0 -0.039 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.028 -10000 0 -0.11 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.018 -10000 0 -0.04 21 21
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
mol:GTP 0.035 0.021 -10000 0 -0.04 20 20
PSENEN 0.031 0.007 -10000 0 -10000 0 0
mol:ceramide -0.02 0.025 0.18 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.023 -10000 0 -0.1 16 16
p75(NTR)/beta APP 0.043 0.021 -10000 0 -0.05 20 20
BEX1 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.004 -10000 0 -10000 0 0
NGF (dimer) 0.039 0.043 -10000 0 -0.043 75 75
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.016 -10000 0 -0.034 22 22
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.021 -10000 0 -0.031 21 21
MYD88 0.019 0.032 -10000 0 -0.063 67 67
CHUK 0.024 0.015 -10000 0 -0.063 1 1
NGF (dimer)/p75(NTR)/PKA 0.036 0.021 -10000 0 -0.04 20 20
RHOB 0.03 0.011 -10000 0 -0.063 4 4
RHOA 0.032 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
TP53 0.033 0.064 0.23 25 -10000 0 25
PRDM4 -0.021 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.014 0.038 -10000 0 -0.069 3 3
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
SORT1 0.032 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.061 0.03 -10000 0 -0.047 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.055 0.027 -10000 0 -0.043 20 20
RHOC 0.003 0.044 -10000 0 -0.063 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.038 0.074 0.19 80 -0.13 1 81
DIABLO 0.032 0.004 -10000 0 -10000 0 0
SMPD2 -0.02 0.025 0.18 7 -10000 0 7
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.018 -10000 0 -0.04 20 20
PSEN1 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.05 3 3
NT3 (dimer)/p75(NTR) 0.042 0.021 -10000 0 -0.05 20 20
MAPK8 0.035 0.066 0.18 69 -0.13 2 71
MAPK9 0.065 0.087 0.19 137 -10000 0 137
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.016 -10000 0 -10000 0 0
RAC1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.023 0.056 -10000 0 -0.065 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.071 0.036 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.035 0.021 -10000 0 -0.04 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.023 0.043 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.038 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.022 -10000 0 -0.05 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.023 -10000 0 -0.12 2 2
BAD 0.048 0.082 0.2 81 -0.16 3 84
RIPK2 0.032 0.006 -10000 0 -0.063 1 1
NGFR 0.028 0.019 -10000 0 -0.063 21 21
CYCS -0.018 0.022 0.17 4 -10000 0 4
ADAM17 0.031 0.01 -10000 0 -0.063 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.055 0.026 -10000 0 -0.042 22 22
BCL2L11 0.048 0.083 0.2 81 -0.16 3 84
BDNF (dimer)/p75(NTR) 0.012 0.023 -10000 0 -0.05 9 9
PI3K 0.048 0.033 -10000 0 -0.041 40 40
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.017 -10000 0 -0.033 25 25
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
NGF (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.039 21 21
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.024 -10000 0 -0.04 25 25
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.012 0.14 1 -0.075 1 2
SQSTM1 0.032 0.006 -10000 0 -0.063 1 1
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.046 0.081 0.19 84 -0.17 3 87
E2F1 0.03 0.008 -10000 0 0 35 35
CASP9 0.031 0.009 -10000 0 -0.063 3 3
IKK complex 0.037 0.049 -10000 0 -0.17 3 3
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -0.039 1 1
MMP7 0.018 0.034 -10000 0 -0.063 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.062 0.038 -10000 0 -10000 0 0
MMP3 0.031 0.012 -10000 0 -0.063 7 7
APAF-1/Caspase 9 -0.036 0.026 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.018 -10000 0 -0.026 4 4
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.063 5 5
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.06 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.043 -10000 0 -0.05 5 5
alpha4/beta7 Integrin/Paxillin 0.046 0.015 -10000 0 -0.058 5 5
lamellipodium assembly -0.011 0.081 -10000 0 -0.34 18 18
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.039 0.023 -10000 0 -0.05 16 16
ARF6 0.031 0.008 -10000 0 -10000 0 0
TLN1 0.021 0.027 -10000 0 -0.063 43 43
PXN -0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.05 0.15 7 -10000 0 7
cell adhesion 0.031 0.053 0.16 6 -0.069 2 8
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.023 -10000 0 -0.052 5 5
ITGB1 0.025 0.014 -10000 0 -10000 0 0
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
ARF6/GDP 0.033 0.013 -10000 0 -0.026 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.021 0.054 0.17 3 -0.071 2 5
p130Cas/Crk/Dock1 0.031 0.02 -10000 0 -10000 0 0
VCAM1 -0.03 0.045 -10000 0 -0.063 333 333
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.054 0.17 6 -0.07 2 8
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.048 0.17 7 -10000 0 7
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.047 -10000 0 -0.16 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.054 0.17 6 -0.07 2 8
Rac1/GTP -0.013 0.089 -10000 0 -0.38 18 18
Canonical NF-kappaB pathway

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.

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