PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C118357G
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C118357G
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 53 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
Class IB PI3K non-lipid kinase events 294
Signaling events mediated by Stem cell factor receptor (c-Kit) 282
Reelin signaling pathway 247
Signaling mediated by p38-alpha and p38-beta 240
EGFR-dependent Endothelin signaling events 240
HIF-1-alpha transcription factor network 210
p75(NTR)-mediated signaling 161
FOXA2 and FOXA3 transcription factor networks 154
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 153
Glucocorticoid receptor regulatory network 149
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 1058 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 1058 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Class IB PI3K non-lipid kinase events 0.2779 294 882 3 -0.22 -1000 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2665 282 22061 78 -0.62 0.19 1000 -1000 -0.062 -1000
Reelin signaling pathway 0.2335 247 13844 56 -0.48 0 1000 -1000 -0.078 -1000
Signaling mediated by p38-alpha and p38-beta 0.2268 240 10576 44 -0.4 0 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.2268 240 5054 21 -0.34 0 1000 -1000 -0.055 -1000
HIF-1-alpha transcription factor network 0.1985 210 16029 76 -0.74 0.019 1000 -1000 -0.086 -1000
p75(NTR)-mediated signaling 0.1522 161 20165 125 -0.38 0 1000 -1000 -0.099 -1000
FOXA2 and FOXA3 transcription factor networks 0.1456 154 7097 46 -1.2 0.023 1000 -1000 -0.044 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1446 153 10470 68 -0.51 0.16 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.1408 149 16997 114 -0.93 0.35 1000 -1000 -0.07 -1000
Aurora B signaling 0.1361 144 9658 67 -0.32 0.009 1000 -1000 -0.071 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1352 143 7752 54 -0.48 0.022 1000 -1000 -0.084 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1342 142 12513 88 -0.37 0.039 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.1257 133 6789 51 -0.44 0.014 1000 -1000 -0.14 -1000
Arf6 signaling events 0.1248 132 8238 62 -0.34 0.017 1000 -1000 -0.063 -1000
IL4-mediated signaling events 0.1229 130 11909 91 -0.99 0.52 1000 -1000 -0.14 -1000
Endothelins 0.1219 129 12409 96 -0.37 0.039 1000 -1000 -0.07 -1000
ErbB2/ErbB3 signaling events 0.1172 124 8078 65 -0.39 0.018 1000 -1000 -0.059 -1000
EPHB forward signaling 0.1172 124 10583 85 -0.31 0.17 1000 -1000 -0.083 -1000
Ephrin B reverse signaling 0.1134 120 5767 48 -0.31 0.17 1000 -1000 -0.069 -1000
IGF1 pathway 0.1096 116 6625 57 -0.18 0.08 1000 -1000 -0.09 -1000
ErbB4 signaling events 0.1002 106 7342 69 -0.42 0.057 1000 -1000 -0.077 -1000
Signaling events regulated by Ret tyrosine kinase 0.1002 106 8702 82 -0.17 0 1000 -1000 -0.08 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0974 103 8760 85 -0.24 0.011 1000 -1000 -0.068 -1000
Nongenotropic Androgen signaling 0.0974 103 5381 52 -0.23 0.1 1000 -1000 -0.058 -1000
BMP receptor signaling 0.0964 102 8316 81 -0.54 0.026 1000 -1000 -0.087 -1000
Calcium signaling in the CD4+ TCR pathway 0.0955 101 3159 31 -0.32 0.012 1000 -1000 -0.088 -1000
Plasma membrane estrogen receptor signaling 0.0917 97 8420 86 -0.2 0.095 1000 -1000 -0.074 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0917 97 11756 120 -0.59 0.24 1000 -1000 -0.068 -1000
Glypican 1 network 0.0888 94 4548 48 -0.32 0.03 1000 -1000 -0.047 -1000
IL6-mediated signaling events 0.0888 94 7107 75 -0.28 0.051 1000 -1000 -0.083 -1000
Syndecan-1-mediated signaling events 0.0860 91 3112 34 -0.22 0 1000 -1000 -0.067 -1000
Visual signal transduction: Rods 0.0860 91 4772 52 -0.48 0 1000 -1000 -0.074 -1000
Aurora C signaling 0.0841 89 628 7 -0.17 0 1000 -1000 -0.039 -1000
Wnt signaling 0.0841 89 625 7 -0.17 -0.008 1000 -1000 -0.054 -1000
Signaling events mediated by PTP1B 0.0822 87 6662 76 -0.63 0.07 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 0.0784 83 2163 26 -0.17 0 1000 -1000 -0.076 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0728 77 4009 52 -0.19 0.029 1000 -1000 -0.054 -1000
Integrins in angiogenesis 0.0718 76 6424 84 -0.33 0 1000 -1000 -0.085 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0709 75 2563 34 -0.095 0 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.0709 75 7673 102 -0.3 0.028 1000 -1000 -0.075 -1000
Ephrin A reverse signaling 0.0690 73 511 7 -0.076 0 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.0690 73 6000 82 -0.49 0 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0671 71 4271 60 -0.46 0.017 1000 -1000 -0.15 -1000
Fc-epsilon receptor I signaling in mast cells 0.0662 70 6819 97 -0.24 0.028 1000 -1000 -0.08 -1000
Syndecan-3-mediated signaling events 0.0662 70 2457 35 -0.35 0 1000 -1000 -0.058 -1000
Signaling events mediated by the Hedgehog family 0.0605 64 3341 52 -0.22 0.03 1000 -1000 -0.08 -1000
PDGFR-alpha signaling pathway 0.0605 64 2818 44 -0.36 0.019 1000 -1000 -0.052 -1000
Visual signal transduction: Cones 0.0548 58 2208 38 -0.18 0.011 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0539 57 982 17 -0.12 -0.001 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 0.0529 56 1479 26 -0.3 0.027 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0510 54 3422 63 -0.087 0.001 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0501 53 1074 20 -0.19 0.027 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0491 52 1744 33 -0.54 0 1000 -1000 -0.063 -1000
PLK1 signaling events 0.0482 51 4368 85 -0.22 0.03 1000 -1000 -0.058 -1000
FAS signaling pathway (CD95) 0.0482 51 2408 47 -0.47 0.013 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 0.0473 50 2019 40 -0.56 0.02 1000 -1000 -0.036 -1000
Glypican 2 network 0.0473 50 200 4 -0.036 -0.03 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0473 50 3767 74 -0.3 0.072 1000 -1000 -0.085 -1000
LPA4-mediated signaling events 0.0444 47 567 12 -0.16 0.02 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.0444 47 1241 26 -0.1 0.001 1000 -1000 -0.055 -1000
Signaling events mediated by PRL 0.0444 47 1599 34 -0.17 0.02 1000 -1000 -0.061 -1000
S1P1 pathway 0.0435 46 1685 36 -0.33 0.008 1000 -1000 -0.065 -1000
IL27-mediated signaling events 0.0435 46 2355 51 -0.29 0.034 1000 -1000 -0.06 -1000
Presenilin action in Notch and Wnt signaling 0.0425 45 2801 61 -0.42 0.014 1000 -1000 -0.059 -1000
E-cadherin signaling in keratinocytes 0.0425 45 1954 43 -0.3 0.041 1000 -1000 -0.071 -1000
TCR signaling in naïve CD8+ T cells 0.0406 43 4026 93 -0.16 0.078 1000 -1000 -0.069 -1000
Regulation of Androgen receptor activity 0.0378 40 2869 70 -0.25 0.022 1000 -1000 -0.063 -1000
Coregulation of Androgen receptor activity 0.0359 38 2903 76 -0.18 0.034 1000 -1000 -0.044 -1000
Osteopontin-mediated events 0.0350 37 1436 38 -0.24 0.021 1000 -1000 -0.084 -1000
Insulin Pathway 0.0340 36 2685 74 -0.2 0.033 1000 -1000 -0.082 -1000
IL12-mediated signaling events 0.0331 35 3060 87 -0.35 0.047 1000 -1000 -0.12 -1000
Regulation of Telomerase 0.0331 35 3576 102 -0.34 0.021 1000 -1000 -0.092 -1000
Syndecan-4-mediated signaling events 0.0331 35 2369 67 -0.32 0.005 1000 -1000 -0.08 -1000
Regulation of nuclear SMAD2/3 signaling 0.0321 34 4679 136 -0.31 0.052 1000 -1000 -0.073 -1000
Canonical Wnt signaling pathway 0.0321 34 1778 51 -0.42 0.14 1000 -1000 -0.053 -1000
Regulation of p38-alpha and p38-beta 0.0312 33 1810 54 -0.35 0.029 1000 -1000 -0.064 -1000
Thromboxane A2 receptor signaling 0.0302 32 3421 105 -0.3 0.066 1000 -1000 -0.062 -1000
TCGA08_retinoblastoma 0.0302 32 257 8 -0.053 0.01 1000 -1000 -0.026 -1000
IL2 signaling events mediated by STAT5 0.0284 30 664 22 -0.12 0.063 1000 -1000 -0.037 -1000
BCR signaling pathway 0.0284 30 3007 99 -0.13 0.042 1000 -1000 -0.085 -1000
Aurora A signaling 0.0265 28 1695 60 -0.21 0.006 1000 -1000 -0.059 -1000
Arf6 trafficking events 0.0255 27 1958 71 -0.44 0.032 1000 -1000 -0.071 -1000
Syndecan-2-mediated signaling events 0.0246 26 1854 69 -0.2 0.034 1000 -1000 -0.051 -1000
Ceramide signaling pathway 0.0227 24 1836 76 -0.18 0.049 1000 -1000 -0.058 -1000
Hedgehog signaling events mediated by Gli proteins 0.0180 19 1256 65 -0.067 0.041 1000 -1000 -0.073 -1000
TRAIL signaling pathway 0.0180 19 932 48 -0.077 0.044 1000 -1000 -0.069 -1000
Caspase cascade in apoptosis 0.0170 18 1350 74 -0.05 0.045 1000 -1000 -0.06 -1000
Class I PI3K signaling events mediated by Akt 0.0170 18 1287 68 -0.25 0.053 1000 -1000 -0.054 -1000
E-cadherin signaling events 0.0170 18 90 5 -0.022 0 1000 -1000 -0.043 -1000
BARD1 signaling events 0.0161 17 1002 57 -0.11 0.024 1000 -1000 -0.063 -1000
Retinoic acid receptors-mediated signaling 0.0161 17 1029 58 -0.1 0.037 1000 -1000 -0.06 -1000
Cellular roles of Anthrax toxin 0.0151 16 661 39 -0.14 0.02 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 0.0151 16 976 58 -0.043 0.06 1000 -1000 -0.064 -1000
PLK2 and PLK4 events 0.0142 15 46 3 -0.012 0.013 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 0.0142 15 269 17 -0.02 0.042 1000 -1000 -0.057 -1000
Signaling mediated by p38-gamma and p38-delta 0.0142 15 231 15 -0.019 0.022 1000 -1000 -0.053 -1000
E-cadherin signaling in the nascent adherens junction 0.0123 13 1006 76 -0.022 0.049 1000 -1000 -0.073 -1000
IL1-mediated signaling events 0.0113 12 765 62 -0.037 0.032 1000 -1000 -0.092 -1000
S1P3 pathway 0.0113 12 513 42 -0.031 0.021 1000 -1000 -0.053 -1000
S1P4 pathway 0.0104 11 280 25 -0.043 0.009 1000 -1000 -0.053 -1000
mTOR signaling pathway 0.0095 10 546 53 -0.019 0.026 1000 -1000 -0.054 -1000
S1P5 pathway 0.0095 10 179 17 -0.043 0.023 1000 -1000 -0.059 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0095 10 844 83 -0.038 0.051 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class II 0.0085 9 742 75 -0.16 0 1000 -1000 -0.057 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0085 9 277 28 -0.043 0.017 1000 -1000 -0.052 -1000
a4b1 and a4b7 Integrin signaling 0.0085 9 46 5 -0.009 -0.002 1000 -1000 -0.038 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0085 9 1125 125 -0.17 0.082 1000 -1000 -0.098 -1000
HIF-2-alpha transcription factor network 0.0066 7 326 43 -0.17 0.18 1000 -1000 -0.069 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0066 7 353 45 -0.025 0.073 1000 -1000 -0.07 -1000
Class I PI3K signaling events 0.0066 7 581 73 -0.043 0.058 1000 -1000 -0.059 -1000
VEGFR1 specific signals 0.0066 7 430 56 -0.17 0.065 1000 -1000 -0.078 -1000
p38 MAPK signaling pathway 0.0066 7 326 44 -0.071 0.026 1000 -1000 -0.059 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0057 6 142 23 -0.03 0.041 1000 -1000 -0.065 -1000
PDGFR-beta signaling pathway 0.0057 6 670 97 -0.025 0.051 1000 -1000 -0.082 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0047 5 196 37 -0.048 0.034 1000 -1000 -0.069 -1000
Signaling events mediated by HDAC Class I 0.0047 5 542 104 -0.094 0.046 1000 -1000 -0.066 -1000
FoxO family signaling 0.0047 5 360 64 -0.039 0.09 1000 -1000 -0.07 -1000
Atypical NF-kappaB pathway 0.0047 5 178 31 -0.021 0.03 1000 -1000 -0.055 -1000
Circadian rhythm pathway 0.0038 4 91 22 -0.016 0.041 1000 -1000 -0.07 -1000
ceramide signaling pathway 0.0038 4 234 49 -0.028 0.054 1000 -1000 -0.045 -1000
Canonical NF-kappaB pathway 0.0028 3 124 39 -0.021 0.077 1000 -1000 -0.079 -1000
Arf6 downstream pathway 0.0028 3 137 43 -0.011 0.021 1000 -1000 -0.043 -1000
EPO signaling pathway 0.0028 3 215 55 -0.036 0.057 1000 -1000 -0.091 -1000
Paxillin-dependent events mediated by a4b1 0.0028 3 123 36 -0.011 0.022 1000 -1000 -0.069 -1000
Insulin-mediated glucose transport 0.0019 2 88 32 -0.13 0.032 1000 -1000 -0.063 -1000
IFN-gamma pathway 0.0019 2 191 68 -0.071 0.075 1000 -1000 -0.089 -1000
TCGA08_p53 0.0000 0 0 7 -0.025 0.017 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 -0.001 0.029 1000 -1000 -0.051 -1000
Arf1 pathway 0.0000 0 23 54 -0.001 0.025 1000 -1000 -0.04 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 -0.003 0 1000 -1000 -0.058 -1000
Total NA 7830 464392 7203 -31 -990 131000 -131000 -8.6 -131000
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.22 0.36 0.79 294 -10000 0 294
PI3K Class IB/PDE3B -0.22 0.36 -10000 0 -0.79 294 294
PDE3B -0.22 0.36 -10000 0 -0.8 294 294
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.22 -10000 0 -0.39 485 485
CRKL -0.17 0.23 -10000 0 -0.41 485 485
HRAS -0.16 0.18 -10000 0 -0.46 63 63
mol:PIP3 -0.17 0.21 -10000 0 -0.4 487 487
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 486 486
FOXO3 -0.15 0.21 -10000 0 -0.37 484 484
AKT1 -0.17 0.22 -10000 0 -0.41 485 485
BAD -0.15 0.21 -10000 0 -0.37 484 484
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 487 487
GSK3B -0.15 0.21 -10000 0 -0.37 484 484
RAF1 -0.093 0.17 -10000 0 -0.4 42 42
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 486 486
STAT1 -0.46 0.56 -10000 0 -1 496 496
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.39 44 44
cell proliferation -0.18 0.24 -10000 0 -0.44 487 487
PIK3CA 0 0.009 -10000 0 -10000 0 0
TEC -0.002 0.042 -10000 0 -0.8 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 486 486
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.39 44 44
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 486 486
MAPK3 -0.055 0.13 -10000 0 -0.32 22 22
STAP1 -0.2 0.24 -10000 0 -0.46 488 488
GRAP2 -0.015 0.11 -10000 0 -0.8 19 19
JAK2 -0.4 0.44 -10000 0 -0.87 496 496
STAT1 (dimer) -0.44 0.54 -10000 0 -1 496 496
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 486 486
actin filament polymerization -0.19 0.24 -10000 0 -0.44 486 486
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.34 -10000 0 -0.62 487 487
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.36 484 484
PI3K -0.19 0.21 -10000 0 -0.41 490 490
PTEN -0.002 0.034 -10000 0 -0.79 2 2
SCF/KIT/EPO/EPOR -0.57 0.7 -10000 0 -1.3 484 484
MAPK8 -0.19 0.24 -10000 0 -0.45 487 487
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 486 486
positive regulation of transcription -0.042 0.11 -10000 0 -0.26 22 22
mol:GDP -0.17 0.18 -10000 0 -0.49 60 60
PIK3C2B -0.18 0.24 -10000 0 -0.44 486 486
CBL/CRKL -0.15 0.22 -10000 0 -0.38 484 484
FER -0.19 0.24 -10000 0 -0.44 491 491
SH2B3 -0.18 0.24 -10000 0 -0.44 486 486
PDPK1 -0.15 0.2 -10000 0 -0.36 487 487
SNAI2 -0.19 0.25 -10000 0 -0.45 488 488
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.75 496 496
KITLG 0.001 0.069 -10000 0 -0.49 16 16
cell motility -0.32 0.41 -10000 0 -0.75 496 496
PTPN6 0.015 0.021 -10000 0 -0.29 2 2
EPOR -0.097 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 498 498
SOCS1 -0.005 0.042 -10000 0 -0.32 16 16
cell migration 0.19 0.24 0.44 494 -10000 0 494
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.31 104 104
VAV1 -0.003 0.044 -10000 0 -0.59 5 5
GRB10 -0.18 0.24 -10000 0 -0.44 486 486
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.23 -10000 0 -0.47 491 491
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.35 23 23
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.73 -10000 0 -1.4 482 482
MAP2K2 -0.064 0.14 -10000 0 -0.35 23 23
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 484 484
STAT5A -0.27 0.35 -10000 0 -0.64 498 498
GRB2 0 0.009 -10000 0 -0.29 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 488 488
SHC/GRAP2 -0.011 0.081 -10000 0 -0.61 19 19
PTPRO -0.18 0.24 -10000 0 -0.44 487 487
SH2B2 -0.19 0.24 -10000 0 -0.45 486 486
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
MATK -0.2 0.25 -10000 0 -0.45 494 494
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.5 37 37
Reelin signaling pathway

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
CDK5R1/CDK5 -0.007 0.035 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.8 32 32
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
ITGA3 -0.004 0.051 -9999 0 -0.58 7 7
RELN/VLDLR/Fyn -0.33 0.27 -9999 0 -0.54 639 639
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.045 -9999 0 -0.44 11 11
AKT1 -0.2 0.17 -9999 0 -0.32 644 644
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 63 63
RELN/LRP8/DAB1 -0.31 0.25 -9999 0 -0.51 632 632
LRPAP1/LRP8 -0.02 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.29 0.23 -9999 0 -0.48 632 632
DAB1/alpha3/beta1 Integrin -0.27 0.22 -9999 0 -0.44 642 642
long-term memory -0.35 0.3 -9999 0 -0.54 685 685
DAB1/LIS1 -0.28 0.23 -9999 0 -0.46 639 639
DAB1/CRLK/C3G -0.27 0.22 -9999 0 -0.44 639 639
PIK3CA 0 0.009 -9999 0 -10000 0 0
DAB1/NCK2 -0.28 0.23 -9999 0 -0.46 639 639
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.091 0.25 -9999 0 -0.75 129 129
CDK5R1 -0.009 0.049 -9999 0 -0.29 31 31
RELN -0.48 0.39 -9999 0 -0.79 634 634
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
RELN/LRP8/Fyn -0.33 0.26 -9999 0 -0.54 631 631
GRIN2A/RELN/LRP8/DAB1/Fyn -0.34 0.29 -9999 0 -0.54 651 651
MAPK8 -0.006 0.069 -9999 0 -0.8 8 8
RELN/VLDLR/DAB1 -0.31 0.26 -9999 0 -0.51 639 639
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.3 0.25 -9999 0 -0.49 643 643
RELN/LRP8 -0.33 0.26 -9999 0 -0.54 631 631
GRIN2B/RELN/LRP8/DAB1/Fyn -0.32 0.25 -9999 0 -0.5 669 669
PI3K -0.006 0.059 -9999 0 -0.61 10 10
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.038 -9999 0 -0.61 4 4
RAP1A -0.25 0.21 -9999 0 -0.54 140 140
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.047 -9999 0 -0.48 8 8
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.055 0.2 -9999 0 -0.78 75 75
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.13 -9999 0 -0.47 12 12
neuron adhesion -0.24 0.19 -9999 0 -0.51 142 142
LRP8 -0.031 0.09 -9999 0 -0.29 113 113
GSK3B -0.17 0.18 -9999 0 -0.45 67 67
RELN/VLDLR/DAB1/Fyn -0.29 0.24 -9999 0 -0.48 639 639
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.18 -9999 0 -0.35 644 644
CDK5 -0.002 0.024 -9999 0 -0.29 7 7
MAPT -0.047 0.24 -9999 0 -0.72 118 118
neuron migration -0.23 0.23 -9999 0 -0.41 632 632
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.11 -9999 0 -0.48 12 12
RELN/VLDLR -0.31 0.26 -9999 0 -0.51 639 639
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.62 -9999 0 -1.3 356 356
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.081 0.15 -9999 0 -0.3 356 356
ATF2/c-Jun -0.052 0.15 -9999 0 -0.79 14 14
MAPK11 -0.083 0.16 -9999 0 -0.3 359 359
MITF -0.093 0.2 -9999 0 -0.36 363 363
MAPKAPK5 -0.088 0.19 -9999 0 -0.35 359 359
KRT8 -0.095 0.2 -9999 0 -0.36 360 360
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -0.29 1 1
p38alpha-beta/CK2 -0.12 0.23 -9999 0 -0.45 359 359
CEBPB -0.088 0.19 -9999 0 -0.35 359 359
SLC9A1 -0.088 0.19 -9999 0 -0.35 359 359
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 360 360
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.35 359 359
JUN -0.051 0.15 -9999 0 -0.78 14 14
PPARGC1A -0.21 0.36 -9999 0 -0.57 439 439
USF1 -0.088 0.19 -9999 0 -0.35 359 359
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.38 16 16
NOS2 -0.092 0.21 -9999 0 -0.87 16 16
DDIT3 -0.088 0.19 -9999 0 -0.35 359 359
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.074 0.17 -9999 0 -0.44 51 51
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.35 359 359
CREB1 -0.093 0.2 -9999 0 -0.37 359 359
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.069 0.17 -9999 0 -0.5 16 16
RPS6KA4 -0.088 0.19 -9999 0 -0.35 359 359
PLA2G4A -0.13 0.27 -9999 0 -0.73 132 132
GDI1 -0.088 0.19 -9999 0 -0.35 359 359
TP53 -0.11 0.23 -9999 0 -0.44 359 359
RPS6KA5 -0.094 0.2 -9999 0 -0.36 367 367
ESR1 -0.18 0.26 -9999 0 -0.42 491 491
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.089 0.19 -9999 0 -0.35 359 359
MEF2A -0.089 0.19 -9999 0 -0.35 359 359
EIF4EBP1 -0.093 0.2 -9999 0 -0.37 359 359
KRT19 -0.1 0.21 -9999 0 -0.37 364 364
ELK4 -0.088 0.19 -9999 0 -0.35 359 359
ATF6 -0.088 0.19 -9999 0 -0.35 359 359
ATF1 -0.093 0.2 -9999 0 -0.37 359 359
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.52 20 20
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.53 19 19
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS -0.002 0.027 -9999 0 -0.29 9 9
EGFR -0.3 0.38 -9999 0 -0.79 396 396
EGF/EGFR -0.28 0.3 -9999 0 -0.54 543 543
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.25 0.27 -9999 0 -0.49 533 533
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.026 -9999 0 -0.54 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.79 206 206
EGF/EGFR dimer/SHC -0.29 0.31 -9999 0 -0.58 533 533
mol:GDP -0.25 0.26 -9999 0 -0.49 533 533
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.062 0.21 -9999 0 -0.79 83 83
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.23 0.24 -9999 0 -0.45 533 533
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.23 0.25 -9999 0 -0.46 533 533
FRAP1 -0.24 0.25 -9999 0 -0.47 533 533
EGF/EGFR dimer -0.34 0.35 -9999 0 -0.66 533 533
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
ETA receptor/Endothelin-1 -0.048 0.16 -9999 0 -0.61 83 83
HIF-1-alpha transcription factor network

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
PKM2 -0.4 0.46 -9999 0 -0.99 295 295
HDAC7 0 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.31 -9999 0 -0.76 243 243
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
ID2 -0.4 0.46 -9999 0 -0.99 294 294
AP1 -0.18 0.28 -9999 0 -0.62 314 314
ABCG2 -0.43 0.5 -9999 0 -1.1 307 307
HIF1A -0.05 0.065 -9999 0 -10000 0 0
TFF3 -0.48 0.53 -9999 0 -1.1 378 378
GATA2 -0.014 0.13 -9999 0 -0.63 42 42
AKT1 -0.051 0.081 -9999 0 -10000 0 0
response to hypoxia -0.073 0.088 -9999 0 -0.24 35 35
MCL1 -0.4 0.46 -9999 0 -0.99 294 294
NDRG1 -0.41 0.47 -9999 0 -1 294 294
SERPINE1 -0.41 0.47 -9999 0 -0.99 298 298
FECH -0.4 0.46 -9999 0 -0.99 294 294
FURIN -0.4 0.46 -9999 0 -0.99 295 295
NCOA2 -0.027 0.17 -9999 0 -0.8 48 48
EP300 -0.05 0.12 -9999 0 -0.35 55 55
HMOX1 -0.41 0.46 -9999 0 -0.99 294 294
BHLHE40 -0.4 0.46 -9999 0 -0.99 294 294
BHLHE41 -0.41 0.48 -9999 0 -1 295 295
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.049 0.055 -9999 0 -0.61 1 1
ENG -0.027 0.077 -9999 0 -0.55 1 1
JUN -0.001 0.065 -9999 0 -0.8 7 7
RORA -0.4 0.46 -9999 0 -0.99 294 294
ABCB1 -0.34 0.55 -9999 0 -1.4 209 209
TFRC -0.4 0.47 -9999 0 -0.99 296 296
CXCR4 -0.41 0.46 -9999 0 -0.99 297 297
TF -0.64 0.58 -9999 0 -1.1 569 569
CITED2 -0.4 0.46 -9999 0 -0.99 294 294
HIF1A/ARNT -0.48 0.53 -9999 0 -1.1 307 307
LDHA -0.048 0.047 -9999 0 -10000 0 0
ETS1 -0.4 0.47 -9999 0 -0.99 294 294
PGK1 -0.4 0.46 -9999 0 -0.99 296 296
NOS2 -0.41 0.47 -9999 0 -1 295 295
ITGB2 -0.4 0.46 -9999 0 -0.99 294 294
ALDOA -0.4 0.46 -9999 0 -0.99 295 295
Cbp/p300/CITED2 -0.42 0.45 -9999 0 -1 304 304
FOS -0.23 0.37 -9999 0 -0.8 313 313
HK2 -0.4 0.46 -9999 0 -0.99 294 294
SP1 0.012 0.024 -9999 0 -10000 0 0
GCK -0.13 0.37 -9999 0 -1.6 56 56
HK1 -0.4 0.46 -9999 0 -0.99 294 294
NPM1 -0.4 0.46 -9999 0 -0.99 295 295
EGLN1 -0.4 0.46 -9999 0 -0.99 294 294
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.4 0.46 -9999 0 -0.99 294 294
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.19 0.41 -9999 0 -1.2 124 124
IGFBP1 -0.5 0.53 -9999 0 -1.1 378 378
VEGFA -0.24 0.32 -9999 0 -0.75 126 126
HIF1A/JAB1 -0.028 0.026 -9999 0 -10000 0 0
CP -0.52 0.55 -9999 0 -1.1 407 407
CXCL12 -0.43 0.5 -9999 0 -1.1 308 308
COPS5 0.009 0.006 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.019 -9999 0 -0.6 1 1
BNIP3 -0.4 0.46 -9999 0 -0.99 294 294
EGLN3 -0.41 0.47 -9999 0 -1 303 303
CA9 -0.45 0.49 -9999 0 -1 324 324
TERT -0.42 0.48 -9999 0 -1 305 305
ENO1 -0.4 0.46 -9999 0 -0.99 294 294
PFKL -0.4 0.46 -9999 0 -0.99 294 294
NCOA1 -0.001 0.024 -9999 0 -0.8 1 1
ADM -0.43 0.5 -9999 0 -1 318 318
ARNT -0.05 0.065 -9999 0 -10000 0 0
HNF4A -0.002 0.043 -9999 0 -0.29 18 18
ADFP -0.41 0.46 -9999 0 -0.99 301 301
SLC2A1 -0.24 0.32 -9999 0 -0.75 135 135
LEP -0.74 0.54 -9999 0 -1.1 668 668
HIF1A/ARNT/Cbp/p300 -0.33 0.34 -9999 0 -0.79 246 246
EPO -0.23 0.28 -9999 0 -0.86 47 47
CREBBP -0.05 0.12 -9999 0 -0.36 53 53
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.31 -9999 0 -0.77 232 232
PFKFB3 -0.41 0.47 -9999 0 -1 295 295
NT5E -0.41 0.47 -9999 0 -1 294 294
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.019 -9999 0 -0.61 1 1
Necdin/E2F1 -0.082 0.15 -9999 0 -0.69 41 41
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.14 0.22 -9999 0 -0.45 337 337
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.32 -9999 0 -0.63 413 413
NT-4/5 (dimer)/p75(NTR) -0.38 0.41 -9999 0 -0.76 534 534
IKBKB -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.15 0.22 -9999 0 -0.45 340 340
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.066 0.21 -9999 0 -0.67 104 104
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.25 -9999 0 -0.56 327 327
FURIN -0.001 0.013 -9999 0 -0.29 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -9999 0 -0.57 370 370
LINGO1 -0.07 0.12 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.001 0.024 -9999 0 -0.78 1 1
proBDNF (dimer) -0.066 0.21 -9999 0 -0.67 104 104
NTRK1 -0.011 0.07 -9999 0 -0.37 31 31
RTN4R -0.012 0.058 -9999 0 -0.29 43 43
neuron apoptosis -0.14 0.26 -9999 0 -0.49 327 327
IRAK1 -0.001 0.018 -9999 0 -0.29 4 4
SHC1 -0.15 0.26 -9999 0 -0.53 335 335
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.014 -9999 0 -0.44 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.16 0.23 -9999 0 -0.49 335 335
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.17 0.26 -9999 0 -0.52 349 349
Mammalian IAPs/DIABLO -0.005 0.045 -9999 0 -0.47 9 9
proNGF (dimer) -0.014 0.1 -9999 0 -0.63 24 24
MAGED1 -0.001 0.018 -9999 0 -0.29 4 4
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.28 0.38 -9999 0 -0.79 371 371
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.14 0.22 -9999 0 -0.46 335 335
NGF -0.014 0.1 -9999 0 -0.63 24 24
cell cycle arrest -0.12 0.23 -9999 0 -0.44 335 335
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.16 -9999 0 -0.33 335 335
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.34 0.37 -9999 0 -0.67 534 534
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.18 0.26 -9999 0 -0.54 335 335
PSENEN 0 0.009 -9999 0 -0.29 1 1
mol:ceramide -0.13 0.24 -9999 0 -0.48 335 335
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.083 0.12 -9999 0 -0.48 13 13
p75(NTR)/beta APP -0.19 0.28 -9999 0 -0.61 327 327
BEX1 -0.15 0.27 -9999 0 -0.52 307 307
mol:GDP -0.16 0.26 -9999 0 -0.54 335 335
NGF (dimer) -0.082 0.18 -9999 0 -0.49 166 166
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.23 -9999 0 -0.51 327 327
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
RAC1/GTP -0.15 0.22 -9999 0 -0.47 335 335
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.18 0.26 -9999 0 -0.55 335 335
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.059 0.087 -9999 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -9999 0 -0.76 178 178
TP53 -0.16 0.23 -9999 0 -0.46 370 370
PRDM4 -0.13 0.24 -9999 0 -0.48 335 335
BDNF (dimer) -0.17 0.23 -9999 0 -0.57 217 217
PIK3CA 0 0.009 -9999 0 -10000 0 0
SORT1 -0.001 0.024 -9999 0 -0.8 1 1
activation of caspase activity -0.14 0.21 -9999 0 -0.45 337 337
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.16 0.23 -9999 0 -0.49 335 335
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.15 0.27 -9999 0 -0.49 341 341
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.13 0.24 -9999 0 -0.48 335 335
APH1B -0.001 0.024 -9999 0 -0.8 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.17 0.25 -9999 0 -0.54 335 335
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.28 0.36 -9999 0 -0.69 424 424
MAPK8 -0.11 0.24 -9999 0 -0.43 327 327
MAPK9 -0.11 0.24 -9999 0 -0.43 327 327
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.13 0.29 -9999 0 -0.76 178 178
NTF4 -0.28 0.38 -9999 0 -0.8 371 371
NDN -0.031 0.15 -9999 0 -0.8 41 41
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.2 -9999 0 -0.43 335 335
p75 CTF/Sortilin/TRAF6/NRIF 0 0.015 -9999 0 -0.47 1 1
RhoA-B-C/GTP -0.18 0.26 -9999 0 -0.54 335 335
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.49 370 370
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.26 -9999 0 -0.52 370 370
PRKACB -0.016 0.074 -9999 0 -0.32 51 51
proBDNF (dimer)/p75 ECD -0.05 0.16 -9999 0 -0.61 79 79
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.079 -9999 0 -0.51 21 21
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.12 0.25 -9999 0 -0.49 282 282
BAD -0.12 0.24 -9999 0 -0.45 330 330
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
NGFR -0.25 0.37 -9999 0 -0.8 327 327
CYCS -0.14 0.21 -9999 0 -0.45 335 335
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.16 0.23 -9999 0 -0.49 335 335
BCL2L11 -0.12 0.24 -9999 0 -0.45 330 330
BDNF (dimer)/p75(NTR) -0.23 0.32 -9999 0 -0.66 370 370
PI3K -0.16 0.23 -9999 0 -0.49 340 340
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.16 0.23 -9999 0 -0.49 335 335
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -0.29 1 1
NGF (dimer)/p75(NTR) -0.2 0.29 -9999 0 -0.62 335 335
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.16 0.23 -9999 0 -0.49 335 335
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.8 1 1
PLG -0.002 0.025 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.19 0.26 -9999 0 -0.52 378 378
SQSTM1 0 0.009 -9999 0 -0.29 1 1
NGFRAP1 -0.002 0.035 -9999 0 -0.8 2 2
CASP3 -0.11 0.22 -9999 0 -0.41 330 330
E2F1 -0.093 0.14 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.066 0.12 -9999 0 -0.57 22 22
NGF (dimer)/TRKA -0.018 0.09 -9999 0 -0.61 21 21
MMP7 -0.12 0.28 -9999 0 -0.71 183 183
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.14 0.22 -9999 0 -0.45 335 335
MMP3 -0.12 0.16 -9999 0 -0.31 406 406
APAF-1/Caspase 9 -0.11 0.16 -9999 0 -0.65 15 15
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.82 97 97
PCK1 -1 0.7 -9999 0 -1.6 645 645
HNF4A -0.25 0.28 -9999 0 -0.86 78 78
KCNJ11 -0.28 0.32 -9999 0 -0.91 111 111
AKT1 -0.15 0.14 -9999 0 -0.4 28 28
response to starvation -0.001 0.008 -9999 0 -10000 0 0
DLK1 -0.5 0.56 -9999 0 -1.2 353 353
NKX2-1 -0.055 0.15 -9999 0 -10000 0 0
ACADM -0.25 0.28 -9999 0 -0.82 104 104
TAT -1.2 0.68 -9999 0 -1.6 769 769
CEBPB 0.005 0.006 -9999 0 -10000 0 0
CEBPA -0.001 0.074 -9999 0 -0.79 9 9
TTR -0.46 0.29 -9999 0 -0.73 422 422
PKLR -0.25 0.28 -9999 0 -0.79 116 116
APOA1 -0.3 0.3 -9999 0 -0.87 114 114
CPT1C -0.25 0.28 -9999 0 -0.83 96 96
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.75 297 297
FOXF1 -0.003 0.055 -9999 0 -0.5 10 10
NF1 0.017 0.025 -9999 0 -0.79 1 1
HNF1A (dimer) 0.003 0.025 -9999 0 -10000 0 0
CPT1A -0.24 0.28 -9999 0 -0.84 85 85
HMGCS1 -0.25 0.28 -9999 0 -0.79 112 112
NR3C1 -0.11 0.13 -9999 0 -0.36 98 98
CPT1B -0.25 0.28 -9999 0 -0.81 106 106
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.007 -9999 0 -10000 0 0
GCK -0.28 0.35 -9999 0 -1 119 119
CREB1 -0.058 0.066 -9999 0 -10000 0 0
IGFBP1 -0.45 0.59 -9999 0 -1.5 238 238
PDX1 -0.13 0.15 -9999 0 -10000 0 0
UCP2 -0.25 0.28 -9999 0 -0.79 112 112
ALDOB -0.27 0.3 -9999 0 -0.92 82 82
AFP -0.69 0.61 -9999 0 -1.2 490 490
BDH1 -0.25 0.28 -9999 0 -0.82 100 100
HADH -0.27 0.3 -9999 0 -0.81 136 136
F2 -0.3 0.3 -9999 0 -0.92 85 85
HNF1A 0.003 0.026 -9999 0 -10000 0 0
G6PC -0.2 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.023 0.066 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.56 317 317
FOXA3 -0.43 0.23 -9999 0 -0.54 736 736
FOXA2 -0.32 0.34 -9999 0 -0.88 172 172
ABCC8 -0.35 0.43 -9999 0 -1.2 158 158
ALB -0.94 0.64 -9999 0 -1.4 693 693
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.077 0.16 -10000 0 -0.34 274 274
NFATC2 -0.054 0.27 -10000 0 -0.76 118 118
NFATC3 -0.052 0.12 -10000 0 -0.31 46 46
CD40LG -0.36 0.57 -10000 0 -1.1 338 338
ITCH 0.014 0.097 -10000 0 -10000 0 0
CBLB 0.014 0.097 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.36 -10000 0 -1.1 95 95
JUNB -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.035 0.1 -10000 0 -0.34 109 109
T cell anergy -0.026 0.16 -10000 0 -0.48 109 109
TLE4 -0.029 0.26 -10000 0 -0.73 94 94
Jun/NFAT1-c-4/p21SNFT -0.3 0.44 -10000 0 -0.91 308 308
AP-1/NFAT1-c-4 -0.51 0.65 -10000 0 -1.3 343 343
IKZF1 -0.018 0.21 -10000 0 -0.64 79 79
T-helper 2 cell differentiation -0.11 0.3 -10000 0 -0.85 107 107
AP-1/NFAT1 -0.22 0.32 -10000 0 -0.64 359 359
CALM1 -0.018 0.054 -10000 0 -10000 0 0
EGR2 -0.28 0.64 -10000 0 -1.6 168 168
EGR3 -0.37 0.72 -10000 0 -1.5 286 286
NFAT1/FOXP3 -0.12 0.22 -10000 0 -0.57 137 137
EGR1 -0.24 0.37 -10000 0 -0.79 333 333
JUN -0.001 0.067 -10000 0 -0.8 7 7
EGR4 -0.015 0.076 -10000 0 -0.29 75 75
mol:Ca2+ -0.021 0.062 -10000 0 -10000 0 0
GBP3 -0.023 0.22 -10000 0 -0.62 112 112
FOSL1 -0.009 0.06 -10000 0 -0.8 3 3
NFAT1-c-4/MAF/IRF4 -0.31 0.47 -10000 0 -0.93 332 332
DGKA -0.016 0.21 -10000 0 -0.61 86 86
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.39 0.52 -10000 0 -1.1 343 343
CTLA4 -0.087 0.24 -10000 0 -0.7 68 68
NFAT1-c-4 (dimer)/EGR1 -0.42 0.57 -10000 0 -1.2 342 342
NFAT1-c-4 (dimer)/EGR4 -0.29 0.45 -10000 0 -0.9 331 331
FOS -0.23 0.37 -10000 0 -0.81 313 313
IFNG -0.15 0.27 -10000 0 -0.87 95 95
T cell activation -0.17 0.35 -10000 0 -0.79 188 188
MAF -0.001 0.024 -10000 0 -0.8 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.36 0.66 327 -10000 0 327
TNF -0.31 0.52 -10000 0 -1 327 327
FASLG -0.35 0.67 -10000 0 -1.3 329 329
TBX21 -0.023 0.16 -10000 0 -0.67 55 55
BATF3 -0.002 0.03 -10000 0 -0.39 5 5
PRKCQ -0.026 0.17 -10000 0 -0.75 52 52
PTPN1 -0.018 0.21 -10000 0 -0.62 86 86
NFAT1-c-4/ICER1 -0.29 0.44 -10000 0 -0.9 329 329
GATA3 -0.035 0.16 -10000 0 -0.6 63 63
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.84 98 98
IL2RA -0.24 0.34 -10000 0 -0.96 122 122
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.016 0.21 -10000 0 -0.64 73 73
E2F1 -0.079 0.14 -10000 0 -10000 0 0
PPARG -0.19 0.34 -10000 0 -0.8 255 255
SLC3A2 -0.016 0.21 -10000 0 -0.61 86 86
IRF4 -0.072 0.22 -10000 0 -0.74 104 104
PTGS2 -0.46 0.65 -10000 0 -1.2 392 392
CSF2 -0.36 0.55 -10000 0 -1.1 323 323
JunB/Fra1/NFAT1-c-4 -0.28 0.42 -10000 0 -0.86 324 324
IL4 -0.12 0.32 -10000 0 -0.91 104 104
IL5 -0.35 0.55 -10000 0 -1.1 328 328
IL2 -0.17 0.36 -10000 0 -0.81 187 187
IL3 -0.063 0.065 -10000 0 -10000 0 0
RNF128 -0.049 0.27 -10000 0 -0.85 109 109
NFATC1 -0.16 0.36 -10000 0 -0.66 327 327
CDK4 0.083 0.23 0.6 42 -10000 0 42
PTPRK -0.022 0.23 -10000 0 -0.66 90 90
IL8 -0.36 0.56 -10000 0 -1.1 332 332
POU2F1 0.001 0.01 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 0.024 0.079 0.34 9 -10000 0 9
SMARCC2 0.012 0.01 -10000 0 -10000 0 0
SMARCC1 0.012 0.01 -10000 0 -10000 0 0
TBX21 -0.14 0.26 -10000 0 -0.73 101 101
SUMO2 0 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.014 0.041 -10000 0 -0.36 1 1
FKBP4 -0.002 0.027 -10000 0 -0.29 9 9
FKBP5 -0.013 0.096 -10000 0 -0.67 20 20
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.31 113 -0.4 19 132
PRL -0.088 0.12 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.27 0.3 0.54 450 -0.55 29 479
RELA -0.04 0.083 -10000 0 -0.3 1 1
FGG 0.24 0.22 0.49 294 -0.53 2 296
GR beta/TIF2 0.1 0.2 0.33 160 -0.57 50 210
IFNG -0.42 0.35 -10000 0 -0.79 428 428
apoptosis -0.28 0.3 0.59 3 -0.66 280 283
CREB1 -0.009 0.031 -10000 0 -10000 0 0
histone acetylation 0.021 0.14 0.4 41 -0.4 31 72
BGLAP -0.1 0.15 -10000 0 -0.54 16 16
GR/PKAc 0.12 0.12 0.33 61 -0.46 4 65
NF kappa B1 p50/RelA -0.066 0.15 -10000 0 -0.41 42 42
SMARCD1 0.012 0.01 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.26 224 -10000 0 224
GATA3 -0.026 0.16 -10000 0 -0.79 39 39
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.04 0.11 -10000 0 -0.62 6 6
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.27 0.56 3 -0.62 168 171
CSN2 0.2 0.18 0.43 169 -0.53 1 170
BRG1/BAF155/BAF170/BAF60A -0.002 0.032 -10000 0 -0.46 5 5
NFATC1 0 0.043 -10000 0 -0.8 3 3
POU2F1 0.007 0.013 -10000 0 -10000 0 0
CDKN1A 0.046 0.073 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN -0.017 0.1 -10000 0 -0.51 34 34
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 64 -0.38 25 89
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.37 0.43 0.54 3 -0.9 367 370
JUN -0.32 0.29 -10000 0 -0.61 426 426
IL4 -0.13 0.16 -10000 0 -0.53 36 36
CDK5R1 -0.008 0.051 -10000 0 -0.3 31 31
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.42 0.41 -10000 0 -0.74 574 574
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.33 66 -0.39 12 78
cortisol/GR alpha (monomer) 0.35 0.32 0.63 493 -0.51 3 496
NCOA2 -0.036 0.16 -10000 0 -0.8 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.28 0.38 -10000 0 -0.86 313 313
AP-1/NFAT1-c-4 -0.65 0.52 -10000 0 -1 637 637
AFP -0.62 0.7 -10000 0 -1.6 359 359
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.5 67 -10000 0 67
TP53 0.032 0.024 -10000 0 -0.5 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.83 0.8 -10000 0 -1.6 507 507
KRT14 -0.82 0.77 -10000 0 -1.6 555 555
TBP 0.019 0.006 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.28 416 -10000 0 416
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.66 0.52 -10000 0 -1 637 637
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.12 0.29 -10000 0 -0.8 165 165
MAPK11 -0.002 0.043 -10000 0 -0.8 3 3
KRT5 -0.93 0.81 -10000 0 -1.7 560 560
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.013 0.025 -10000 0 -0.79 1 1
STAT1 0.014 0.041 -10000 0 -0.36 1 1
CGA -0.16 0.18 -10000 0 -0.53 76 76
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.38 460 -10000 0 460
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.57 221 221
NFKB1 -0.04 0.083 -10000 0 -0.3 1 1
MAPK8 -0.24 0.22 -10000 0 -0.48 344 344
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.32 0.59 3 -0.7 285 288
BAX 0.048 0.032 -10000 0 -10000 0 0
POMC -0.19 0.31 -10000 0 -1.1 70 70
EP300 0.14 0.14 0.29 386 -10000 0 386
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.55 493 -0.57 1 494
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.079 0.24 55 -10000 0 55
SGK1 0.22 0.2 -10000 0 -1.2 6 6
IL13 -0.32 0.28 -10000 0 -0.85 93 93
IL6 -0.5 0.62 -10000 0 -1.3 398 398
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.23 -10000 0 -0.75 58 58
IL2 -0.41 0.35 -10000 0 -0.77 430 430
CDK5 -0.002 0.024 -10000 0 -0.3 7 7
PRKACB -0.016 0.074 -10000 0 -0.32 51 51
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
IL8 -0.2 0.3 -10000 0 -0.66 215 215
CDK5R1/CDK5 -0.007 0.037 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.056 0.098 -10000 0 -0.51 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.52 431 -0.5 2 433
SMARCA4 0.012 0.013 -10000 0 -0.29 1 1
chromatin remodeling 0.2 0.16 0.38 318 -0.34 1 319
NF kappa B1 p50/RelA/Cbp 0.061 0.17 0.34 79 -0.43 3 82
JUN (dimer) -0.32 0.29 -10000 0 -0.61 427 427
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.13 0.25 -10000 0 -0.57 167 167
NR3C1 0.2 0.2 0.43 338 -0.5 9 347
NR4A1 -0.057 0.23 -10000 0 -0.74 103 103
TIF2/SUV420H1 -0.028 0.13 -10000 0 -0.61 48 48
MAPKKK cascade -0.28 0.3 0.59 3 -0.66 280 283
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.55 468 -0.57 1 469
PBX1 0.005 0.038 -10000 0 -0.54 4 4
POU1F1 0.003 0.015 -10000 0 -0.29 2 2
SELE -0.23 0.36 -10000 0 -0.77 218 218
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.38 318 -0.34 1 319
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.52 431 -0.5 2 433
mol:cortisol 0.2 0.2 0.38 491 -10000 0 491
MMP1 -0.22 0.11 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex -0.053 0.067 -9999 0 -10000 0 0
STMN1 -0.11 0.12 -9999 0 -0.37 79 79
Aurora B/RasGAP/Survivin -0.18 0.13 -9999 0 -0.29 454 454
Chromosomal passenger complex/Cul3 protein complex -0.16 0.15 -9999 0 -0.33 426 426
BIRC5 -0.21 0.14 -9999 0 -0.3 757 757
DES -0.29 0.34 -9999 0 -0.65 484 484
Aurora C/Aurora B/INCENP -0.069 0.076 -9999 0 -0.62 1 1
Aurora B/TACC1 -0.1 0.13 -9999 0 -0.62 40 40
Aurora B/PP2A -0.099 0.096 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.008 0.017 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.17 -9999 0 -0.37 538 538
Cul3 protein complex -0.21 0.26 -9999 0 -0.52 426 426
KIF2C -0.045 0.033 -9999 0 -10000 0 0
PEBP1 0.002 0.005 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.3 797 797
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.099 0.096 -9999 0 -10000 0 0
SEPT1 -0.009 0.052 -9999 0 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.035 -9999 0 -0.29 15 15
NSUN2/NPM1/Nucleolin 0.005 0.019 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.036 0.044 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.3 515 515
AURKC -0.005 0.044 -9999 0 -0.32 18 18
CDCA8 -0.098 0.14 -9999 0 -0.3 358 358
cytokinesis -0.11 0.079 -9999 0 -10000 0 0
Aurora B/Septin1 -0.099 0.088 -9999 0 -10000 0 0
AURKA -0.14 0.15 -9999 0 -0.3 493 493
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.32 0.39 -9999 0 -0.8 425 425
BUB1 -0.2 0.14 -9999 0 -0.3 718 718
hSgo1/Aurora B/Survivin -0.26 0.18 -9999 0 -0.38 662 662
EVI5 0.009 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.1 -9999 0 -10000 0 0
SGOL1 -0.18 0.14 -9999 0 -0.29 669 669
CENPA -0.059 0.064 -9999 0 -10000 0 0
NCAPG -0.14 0.15 -9999 0 -0.29 517 517
Aurora B/HC8 Proteasome -0.099 0.096 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -0.29 8 8
Aurora B/PP1-gamma -0.099 0.096 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.11 0.14 -9999 0 -0.29 414 414
NPM1 -0.019 0.024 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.002 0.035 -9999 0 -0.8 2 2
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.099 0.096 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.11 -9999 0 -0.37 37 37
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.019 0.024 -9999 0 -10000 0 0
MYLK -0.089 0.15 -9999 0 -0.47 133 133
KIF23 -0.092 0.14 -9999 0 -0.3 334 334
VIM -0.095 0.1 -9999 0 -0.69 2 2
RACGAP1 -0.009 0.059 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.019 0.024 -9999 0 -10000 0 0
Chromosomal passenger complex -0.084 0.078 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.16 0.18 -9999 0 -0.36 296 296
TACC1 -0.03 0.15 -9999 0 -0.8 40 40
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.8 32 32
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.33 0.26 -9999 0 -0.54 631 631
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -0.29 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.28 0.25 -9999 0 -0.49 631 631
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 63 63
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.016 0.093 -9999 0 -0.43 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.009 -9999 0 -0.29 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.02 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.009 0.049 -9999 0 -0.29 31 31
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.044 0.1 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.34 0.28 -9999 0 -0.55 639 639
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.19 -9999 0 -0.45 180 180
MAP1B -0.007 0.05 -9999 0 -0.38 19 19
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.26 0.21 -9999 0 -0.43 631 631
RELN -0.48 0.39 -9999 0 -0.79 634 634
PAFAH/LIS1 -0.009 0.057 -9999 0 -0.52 11 11
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -9999 0 -0.41 25 25
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -9999 0 -0.33 642 642
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.25 0.2 -9999 0 -0.43 399 399
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.034 0.094 -9999 0 -0.29 123 123
PAFAH1B2 -0.004 0.055 -9999 0 -0.8 5 5
MAP1B/LIS1/Dynein heavy chain -0.004 0.032 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.18 -9999 0 -0.43 181 181
LRP8 -0.031 0.09 -9999 0 -0.29 113 113
NDEL1/Katanin 60 -0.23 0.19 -9999 0 -0.45 181 181
P39/CDK5 -0.28 0.22 -9999 0 -0.45 631 631
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.26 0.24 -9999 0 -0.45 631 631
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.29 0.24 -9999 0 -0.47 639 639
RELN/VLDLR -0.31 0.26 -9999 0 -0.51 639 639
CDC42 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.42 -10000 0 -0.9 230 230
NCK1/PAK1/Dok-R -0.092 0.17 -10000 0 -0.42 230 230
NCK1/Dok-R -0.25 0.47 -10000 0 -1.1 230 230
PIK3CA 0.003 0.011 -10000 0 -10000 0 0
mol:beta2-estradiol 0.037 0.1 0.24 193 -10000 0 193
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.007 0.006 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.039 0.11 0.26 91 -0.32 10 101
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.23 0.44 -10000 0 -1 230 230
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.2 0.53 -10000 0 -1.2 230 230
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.22 -10000 0 -0.8 81 81
ELK1 -0.16 0.47 -10000 0 -1 230 230
GRB7 -0.022 0.084 -10000 0 -0.31 75 75
PAK1 -0.006 0.043 -10000 0 -0.29 23 23
Tie2/Ang1/alpha5/beta1 Integrin -0.2 0.49 -10000 0 -1.1 230 230
CDKN1A -0.065 0.28 -10000 0 -0.62 159 159
ITGA5 0 0.009 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.25 0.47 -10000 0 -1.1 230 230
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.07 0.31 -10000 0 -0.66 230 230
PLG -0.21 0.52 -10000 0 -1.2 230 230
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.18 0.37 -10000 0 -0.88 230 230
GRB2 0 0.009 -10000 0 -0.29 1 1
PIK3R1 0 0.078 -10000 0 -0.8 10 10
ANGPT2 -0.11 0.27 -10000 0 -0.74 114 114
BMX -0.37 0.59 -10000 0 -1.4 230 230
ANGPT1 -0.24 0.57 -10000 0 -1.4 203 203
tube development -0.083 0.31 -10000 0 -0.67 193 193
ANGPT4 -0.24 0.37 -10000 0 -0.8 321 321
response to hypoxia -0.01 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.28 0.54 -10000 0 -1.3 230 230
alpha5/beta1 Integrin 0 0.006 -10000 0 -10000 0 0
FGF2 -0.32 0.39 -10000 0 -0.8 426 426
STAT5A (dimer) -0.099 0.35 -10000 0 -0.78 184 184
mol:L-citrulline -0.07 0.31 -10000 0 -0.66 230 230
AGTR1 -0.2 0.34 -10000 0 -0.79 254 254
MAPK14 -0.19 0.51 -10000 0 -1.1 230 230
Tie2/SHP2 -0.1 0.28 -10000 0 -1.3 51 51
TEK -0.1 0.33 -10000 0 -1.5 51 51
RPS6KB1 -0.12 0.4 -10000 0 -0.87 230 230
Angiotensin II/AT1 -0.15 0.26 -10000 0 -0.61 254 254
Tie2/Ang1/GRB2 -0.27 0.52 -10000 0 -1.2 230 230
MAPK3 -0.17 0.48 -10000 0 -1.1 230 230
MAPK1 -0.17 0.48 -10000 0 -1.1 230 230
Tie2/Ang1/GRB7 -0.26 0.52 -10000 0 -1.2 230 230
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.2 0.53 -10000 0 -1.2 230 230
PI3K -0.16 0.48 -10000 0 -1.1 230 230
FES -0.19 0.5 -10000 0 -1.1 230 230
Crk/Dok-R -0.25 0.47 -10000 0 -1.1 230 230
Tie2/Ang1/ABIN2 -0.27 0.52 -10000 0 -1.2 230 230
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.37 -10000 0 -0.8 230 230
STAT5A -0.006 0.069 -10000 0 -0.8 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.12 0.4 -10000 0 -0.87 230 230
Tie2/Ang2 -0.14 0.41 -10000 0 -0.94 185 185
Tie2/Ang1 -0.23 0.58 -10000 0 -1.3 230 230
FOXO1 -0.1 0.38 -10000 0 -0.81 230 230
ELF1 0.014 0.023 -10000 0 -10000 0 0
ELF2 -0.2 0.52 -10000 0 -1.2 230 230
mol:Choline -0.18 0.5 -10000 0 -1.1 230 230
cell migration -0.042 0.1 -10000 0 -0.25 41 41
FYN -0.1 0.35 -10000 0 -0.77 187 187
DOK2 -0.003 0.046 -10000 0 -0.51 7 7
negative regulation of cell cycle -0.055 0.26 -10000 0 -0.55 168 168
ETS1 -0.028 0.11 -10000 0 -0.97 5 5
PXN -0.082 0.33 -10000 0 -0.71 230 230
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.089 0.35 -10000 0 -0.75 230 230
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.04 0.14 -10000 0 -0.77 17 17
MAPKKK cascade -0.18 0.5 -10000 0 -1.1 230 230
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.23 0.54 -10000 0 -1.2 230 230
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.056 0.28 -10000 0 -0.58 230 230
mol:Phosphatidic acid -0.18 0.5 -10000 0 -1.1 230 230
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.07 0.31 -10000 0 -0.66 230 230
Rac1/GTP -0.18 0.33 -10000 0 -0.81 230 230
MMP2 -0.2 0.53 -10000 0 -1.2 230 230
FOXM1 transcription factor network

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
NFATC3 -0.24 0.43 -9999 0 -0.95 155 155
PLK1 -0.087 0.11 -9999 0 -10000 0 0
BIRC5 -0.1 0.1 -9999 0 -10000 0 0
HSPA1B -0.24 0.43 -9999 0 -0.97 139 139
MAP2K1 0.008 0.03 -9999 0 -10000 0 0
BRCA2 -0.24 0.44 -9999 0 -0.95 161 161
FOXM1 -0.29 0.51 -9999 0 -1.1 210 210
XRCC1 -0.24 0.43 -9999 0 -0.93 168 168
FOXM1B/p19 -0.29 0.42 -9999 0 -0.92 233 233
Cyclin D1/CDK4 -0.23 0.41 -9999 0 -0.92 132 132
CDC2 -0.26 0.45 -9999 0 -0.93 212 212
TGFA -0.22 0.42 -9999 0 -0.93 144 144
SKP2 -0.24 0.43 -9999 0 -0.98 136 136
CCNE1 -0.055 0.12 -9999 0 -0.3 213 213
CKS1B -0.24 0.44 -9999 0 -0.93 170 170
RB1 -0.12 0.13 -9999 0 -1.1 2 2
FOXM1C/SP1 -0.3 0.44 -9999 0 -0.98 214 214
AURKB -0.08 0.11 -9999 0 -10000 0 0
CENPF -0.27 0.45 -9999 0 -0.95 202 202
CDK4 0.007 0.02 -9999 0 -0.3 3 3
MYC -0.22 0.41 -9999 0 -0.89 152 152
CHEK2 0.007 0.033 -9999 0 -0.34 1 1
ONECUT1 -0.24 0.43 -9999 0 -0.92 172 172
CDKN2A -0.038 0.11 -9999 0 -0.29 122 122
LAMA4 -0.24 0.44 -9999 0 -0.99 139 139
FOXM1B/HNF6 -0.27 0.48 -9999 0 -1.1 167 167
FOS -0.44 0.67 -9999 0 -1.3 352 352
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.24 0.44 -9999 0 -1 126 126
response to radiation -0.007 0.03 -9999 0 -10000 0 0
CENPB -0.24 0.43 -9999 0 -0.97 139 139
CENPA -0.27 0.46 -9999 0 -0.97 187 187
NEK2 -0.29 0.44 -9999 0 -0.95 207 207
HIST1H2BA -0.25 0.43 -9999 0 -0.95 155 155
CCNA2 -0.11 0.15 -9999 0 -0.3 417 417
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.28 0.48 -9999 0 -1 187 187
CCNB2 -0.27 0.46 -9999 0 -0.96 198 198
CCNB1 -0.26 0.46 -9999 0 -0.98 188 188
ETV5 -0.24 0.44 -9999 0 -0.98 138 138
ESR1 -0.34 0.58 -9999 0 -1.3 233 233
CCND1 -0.23 0.42 -9999 0 -0.93 140 140
GSK3A 0.014 0.021 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.081 0.14 -9999 0 -0.33 183 183
CDK2 0.006 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.33 0.37 -9999 0 -0.93 216 216
GAS1 -0.27 0.49 -9999 0 -1.1 166 166
MMP2 -0.24 0.44 -9999 0 -1 139 139
RB1/FOXM1C -0.24 0.44 -9999 0 -0.94 171 171
CREBBP 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.044 -9999 0 -0.65 4 4
ARNO/beta Arrestin1-2 -0.13 0.19 -9999 0 -0.43 245 245
EGFR -0.3 0.38 -9999 0 -0.79 396 396
EPHA2 -0.005 0.06 -9999 0 -0.8 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.34 0.35 -9999 0 -0.66 533 533
ARRB2 -0.054 0.16 -9999 0 -0.44 148 148
mol:GTP 0.017 0.018 -9999 0 -0.15 6 6
ARRB1 -0.002 0.036 -9999 0 -0.63 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.037 0.16 -9999 0 -0.75 52 52
EGF -0.15 0.31 -9999 0 -0.79 206 206
somatostatin receptor activity 0 0 -9999 0 -0.001 365 365
ARAP2 -0.005 0.06 -9999 0 -0.8 6 6
mol:GDP -0.14 0.18 -9999 0 -0.35 337 337
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 268 268
ITGA2B -0.018 0.078 -9999 0 -0.32 61 61
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -9999 0 -0.47 6 6
ADAP1 -0.004 0.049 -9999 0 -0.43 11 11
KIF13B -0.002 0.035 -9999 0 -0.8 2 2
HGF/MET -0.14 0.28 -9999 0 -0.65 227 227
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.32 342 342
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.29 0.31 -9999 0 -0.58 533 533
ADRB2 -0.18 0.34 -9999 0 -0.8 244 244
receptor agonist activity 0 0 -9999 0 0 344 344
actin filament binding 0 0 -9999 0 -0.001 355 355
SRC 0 0.009 -9999 0 -0.29 1 1
ITGB3 -0.029 0.15 -9999 0 -0.8 37 37
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 319 319
ARF6/GDP -0.014 0.084 -9999 0 -0.42 18 18
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.52 172 172
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.096 -9999 0 -0.49 40 40
ACAP1 -0.019 0.095 -9999 0 -0.39 52 52
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.092 0.23 -9999 0 -0.66 148 148
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.052 0.2 -9999 0 -0.78 70 70
CYTH3 0.01 0.019 -9999 0 -0.62 1 1
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 282 282
endosomal lumen acidification 0 0 -9999 0 -0.001 288 288
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.052 0.2 -9999 0 -0.8 69 69
GNAQ/ARNO 0.004 0.021 -9999 0 -0.45 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 351 351
MET -0.14 0.3 -9999 0 -0.8 179 179
GNA14 -0.013 0.087 -9999 0 -0.46 31 31
GNA15 -0.003 0.034 -9999 0 -0.36 8 8
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
mol:PI-4-5-P2 0 0 -9999 0 -0.001 338 338
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
LHCGR -0.11 0.28 -9999 0 -0.8 148 148
AGTR1 -0.21 0.34 -9999 0 -0.8 254 254
desensitization of G-protein coupled receptor protein signaling pathway -0.091 0.23 -9999 0 -0.65 148 148
IPCEF1/ARNO -0.23 0.25 -9999 0 -0.46 533 533
alphaIIb/beta3 Integrin -0.034 0.12 -9999 0 -0.62 40 40
IL4-mediated signaling events

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
BCL2L1 -0.46 0.46 -10000 0 -1.1 238 238
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -1 385 385
IGHG1 -0.16 0.16 -10000 0 -0.35 141 141
IGHG3 -0.45 0.44 -10000 0 -0.98 338 338
AKT1 -0.21 0.24 -10000 0 -0.65 90 90
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.68 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.65 102 102
THY1 -0.46 0.46 -10000 0 -1.1 233 233
MYB -0.017 0.11 -10000 0 -0.74 25 25
HMGA1 -0.014 0.061 -10000 0 -0.29 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.68 226 226
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.63 67 67
SP1 0.018 0.004 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.029 -10000 0 -0.77 1 1
STAT6 (dimer)/ETS1 -0.49 0.44 -10000 0 -1 320 320
SOCS1 -0.3 0.31 -10000 0 -0.74 201 201
SOCS3 -0.23 0.26 -10000 0 -0.8 70 70
FCER2 -0.59 0.64 -10000 0 -1.4 365 365
PARP14 0.004 0.019 -10000 0 -0.3 3 3
CCL17 -0.47 0.46 -10000 0 -1.1 246 246
GRB2 0 0.009 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.72 15 15
T cell proliferation -0.46 0.48 -10000 0 -1.1 257 257
IL4R/JAK1 -0.46 0.46 -10000 0 -1.1 242 242
EGR2 -0.6 0.63 -10000 0 -1.4 316 316
JAK2 -0.008 0.036 -10000 0 -0.82 1 1
JAK3 0.01 0.036 -10000 0 -0.29 14 14
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
JAK1 0.004 0.027 -10000 0 -0.79 1 1
COL1A2 -0.14 0.16 -10000 0 -1.7 2 2
CCL26 -0.46 0.46 -10000 0 -1.2 219 219
IL4R -0.49 0.49 -10000 0 -1.2 243 243
PTPN6 0.022 0.018 -10000 0 -0.28 2 2
IL13RA2 -0.46 0.46 -10000 0 -1.1 240 240
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.5 112 112
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.66 193 193
GTF3A 0.013 0.016 -10000 0 -0.29 2 2
PIK3CA 0 0.009 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.014 0.041 -10000 0 -0.62 1 1
IRF4/BCL6 -0.2 0.43 -10000 0 -1.4 116 116
CD40LG -0.033 0.18 -10000 0 -0.72 66 66
MAPK14 -0.26 0.28 -10000 0 -0.67 180 180
mitosis -0.2 0.23 -10000 0 -0.62 90 90
STAT6 -0.53 0.54 -10000 0 -1.2 313 313
SPI1 0.007 0.022 -10000 0 -0.29 5 5
RPS6KB1 -0.19 0.22 -10000 0 -0.62 72 72
STAT6 (dimer) -0.53 0.55 -10000 0 -1.2 313 313
STAT6 (dimer)/PARP14 -0.52 0.51 -10000 0 -1.1 352 352
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.23 -10000 0 -0.67 65 65
FRAP1 -0.21 0.24 -10000 0 -0.65 90 90
LTA -0.47 0.46 -10000 0 -1.1 239 239
FES -0.002 0.042 -10000 0 -0.8 3 3
T-helper 1 cell differentiation 0.52 0.52 1.2 314 -10000 0 314
CCL11 -0.49 0.44 -10000 0 -1.1 282 282
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.23 -10000 0 -0.67 67 67
IL2RG -0.005 0.09 -10000 0 -0.41 30 30
IL10 -0.46 0.46 -10000 0 -1.2 217 217
IRS1 -0.032 0.16 -10000 0 -0.8 43 43
IRS2 -0.033 0.16 -10000 0 -0.8 44 44
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.46 -10000 0 -1.2 217 217
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.82 299 299
COL1A1 -0.18 0.17 -10000 0 -1.7 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.48 -10000 0 -1.2 204 204
IL2R gamma/JAK3 -0.012 0.072 -10000 0 -0.46 20 20
TFF3 -0.57 0.59 -10000 0 -1.3 300 300
ALOX15 -0.54 0.57 -10000 0 -1.3 290 290
MYBL1 -0.043 0.1 -10000 0 -0.29 154 154
T-helper 2 cell differentiation -0.4 0.38 -10000 0 -0.85 310 310
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.24 -10000 0 -0.63 89 89
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.65 90 90
PI3K -0.22 0.26 -10000 0 -0.7 89 89
DOK2 -0.003 0.046 -10000 0 -0.51 7 7
ETS1 0.019 0.055 -10000 0 -0.76 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.18 -10000 0 -0.9 8 8
ITGB3 -0.48 0.5 -10000 0 -1.2 226 226
PIGR -0.99 0.75 -10000 0 -1.5 662 662
IGHE 0.046 0.04 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.87 8 8
BCL6 0.001 0.061 -10000 0 -0.79 6 6
OPRM1 -0.47 0.46 -10000 0 -1.1 233 233
RETNLB -0.47 0.46 -10000 0 -1.1 239 239
SELP -0.63 0.68 -10000 0 -1.5 320 320
AICDA -0.45 0.44 -10000 0 -1.1 222 222
Endothelins

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
AKT1 -0.01 0.2 -9999 0 -0.6 87 87
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.022 0.2 -9999 0 -0.96 31 31
EDN1 -0.037 0.24 -9999 0 -0.82 85 85
EDN3 -0.37 0.4 -9999 0 -0.79 496 496
EDN2 -0.075 0.14 -9999 0 -0.31 259 259
HRAS/GDP -0.028 0.2 -9999 0 -0.52 101 101
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.14 -9999 0 -0.48 43 43
ADCY4 -0.15 0.29 -9999 0 -0.56 305 305
ADCY5 -0.28 0.36 -9999 0 -0.6 502 502
ADCY6 -0.13 0.27 -9999 0 -0.53 287 287
ADCY7 -0.13 0.27 -9999 0 -0.53 287 287
ADCY1 -0.15 0.29 -9999 0 -0.56 302 302
ADCY2 -0.17 0.32 -9999 0 -0.6 314 314
ADCY3 -0.13 0.27 -9999 0 -0.53 287 287
ADCY8 -0.14 0.27 -9999 0 -0.54 287 287
ADCY9 -0.13 0.27 -9999 0 -0.53 287 287
arachidonic acid secretion -0.1 0.29 -9999 0 -0.58 204 204
ETB receptor/Endothelin-1/Gq/GTP -0.033 0.17 -9999 0 -0.39 156 156
GNAO1 -0.03 0.13 -9999 0 -0.8 25 25
HRAS -0.002 0.027 -9999 0 -0.29 9 9
ETA receptor/Endothelin-1/G12/GTP 0.039 0.21 -9999 0 -0.56 87 87
ETA receptor/Endothelin-1/Gs/GTP -0.09 0.32 -9999 0 -0.57 287 287
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.019 0.21 -9999 0 -0.6 87 87
EDNRB -0.072 0.24 -9999 0 -0.79 107 107
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.023 0.24 -9999 0 -0.68 102 102
CYSLTR1 -0.02 0.23 -9999 0 -0.67 99 99
SLC9A1 0.002 0.1 -9999 0 -0.3 86 86
mol:GDP -0.036 0.22 -9999 0 -0.56 106 106
SLC9A3 -0.052 0.28 -9999 0 -0.63 178 178
RAF1 -0.082 0.25 -9999 0 -0.54 157 157
JUN 0.028 0.18 -9999 0 -0.85 28 28
JAK2 -0.01 0.2 -9999 0 -0.6 87 87
mol:IP3 -0.028 0.17 -9999 0 -0.52 71 71
ETA receptor/Endothelin-1 0.036 0.25 -9999 0 -0.68 89 89
PLCB1 -0.051 0.21 -9999 0 -0.8 77 77
PLCB2 0.007 0.027 -9999 0 -0.54 2 2
ETA receptor/Endothelin-3 -0.27 0.32 -9999 0 -0.61 495 495
FOS -0.25 0.49 -9999 0 -0.98 320 320
Gai/GDP -0.016 0.16 -9999 0 -0.83 25 25
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.049 0.25 -9999 0 -0.67 111 111
BCAR1 0.004 0.006 -9999 0 -10000 0 0
PRKCB1 -0.031 0.17 -9999 0 -0.46 87 87
GNAQ 0.008 0.036 -9999 0 -0.8 2 2
GNAZ -0.007 0.073 -9999 0 -0.8 9 9
GNAL -0.19 0.34 -9999 0 -0.8 253 253
Gs family/GDP -0.17 0.26 -9999 0 -0.54 299 299
ETA receptor/Endothelin-1/Gq/GTP 0.018 0.13 -9999 0 -0.42 45 45
MAPK14 -0.031 0.17 -9999 0 -0.47 92 92
TRPC6 0.02 0.22 -9999 0 -1.1 31 31
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.8 57 57
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.18 -9999 0 -0.45 122 122
ETB receptor/Endothelin-2 -0.11 0.2 -9999 0 -0.66 114 114
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.65 550 550
ETB receptor/Endothelin-1 -0.082 0.27 -9999 0 -0.66 178 178
MAPK3 -0.19 0.41 -9999 0 -0.79 324 324
MAPK1 -0.19 0.41 -9999 0 -0.79 324 324
Rac1/GDP -0.027 0.2 -9999 0 -0.52 98 98
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.6 301 301
MAPK8 0.019 0.19 -9999 0 -0.77 37 37
SRC 0 0.009 -9999 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.049 0.19 -9999 0 -0.54 84 84
p130Cas/CRK/Src/PYK2 -0.014 0.21 -9999 0 -0.62 73 73
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.027 0.2 -9999 0 -0.52 99 99
COL1A2 -0.055 0.25 -9999 0 -0.69 101 101
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.12 -9999 0 -0.44 21 21
mol:DAG -0.028 0.18 -9999 0 -0.52 71 71
MAP2K2 -0.13 0.31 -9999 0 -0.56 330 330
MAP2K1 -0.13 0.31 -9999 0 -0.56 330 330
EDNRA 0.027 0.07 -9999 0 -0.41 6 6
positive regulation of muscle contraction -0.011 0.17 -9999 0 -0.52 87 87
Gq family/GDP -0.073 0.16 -9999 0 -0.59 58 58
HRAS/GTP -0.051 0.21 -9999 0 -0.48 131 131
PRKCH -0.022 0.17 -9999 0 -0.52 64 64
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.034 0.2 -9999 0 -0.57 83 83
PRKCB -0.034 0.19 -9999 0 -0.6 66 66
PRKCE -0.022 0.17 -9999 0 -0.56 51 51
PRKCD -0.023 0.17 -9999 0 -0.52 64 64
PRKCG -0.032 0.17 -9999 0 -0.51 71 71
regulation of vascular smooth muscle contraction -0.29 0.56 -9999 0 -1.1 320 320
PRKCQ -0.045 0.21 -9999 0 -0.62 88 88
PLA2G4A -0.12 0.33 -9999 0 -0.65 204 204
GNA14 -0.004 0.089 -9999 0 -0.46 31 31
GNA15 0.007 0.035 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.035 -9999 0 -0.8 2 2
Rac1/GTP 0.039 0.21 -9999 0 -0.56 87 87
MMP1 -0.12 0.13 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.36 66 66
NFATC4 -0.088 0.16 -9999 0 -0.38 30 30
ERBB2IP 0.008 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -0.29 1 1
mammary gland morphogenesis -0.15 0.19 -9999 0 -0.39 388 388
JUN -0.018 0.08 -9999 0 -0.37 6 6
HRAS -0.002 0.027 -9999 0 -0.29 9 9
DOCK7 -0.12 0.19 -9999 0 -0.37 388 388
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.22 -9999 0 -0.47 388 388
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.007 -9999 0 -10000 0 0
MAPK10 -0.11 0.14 -9999 0 -0.35 176 176
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.42 388 388
RAF1 -0.08 0.16 -9999 0 -0.42 22 22
ErbB2/ErbB3/neuregulin 2 -0.25 0.25 -9999 0 -0.51 519 519
STAT3 0.001 0.004 -9999 0 -10000 0 0
cell migration -0.062 0.13 -9999 0 -0.3 98 98
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.22 -9999 0 -0.51 165 165
FOS -0.16 0.26 -9999 0 -0.53 317 317
NRAS -0.001 0.013 -9999 0 -0.3 1 1
mol:Ca2+ -0.15 0.19 -9999 0 -0.39 388 388
MAPK3 -0.11 0.19 -9999 0 -0.42 163 163
MAPK1 -0.11 0.19 -9999 0 -0.42 163 163
JAK2 -0.12 0.19 -9999 0 -0.37 389 389
NF2 -0.006 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.36 388 388
NRG1 -0.29 0.38 -9999 0 -0.79 391 391
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.33 392 392
MAPK9 -0.069 0.088 -9999 0 -0.23 25 25
ERBB2 -0.017 0.058 -9999 0 -0.63 1 1
ERBB3 0 0.055 -9999 0 -0.8 5 5
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.014 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.004 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.098 0.12 -9999 0 -0.33 25 25
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.046 -9999 0 -0.54 1 1
CHRNA1 -0.091 0.16 -9999 0 -0.41 58 58
myelination -0.081 0.16 -9999 0 -0.36 30 30
PPP3CB -0.13 0.16 -9999 0 -0.34 388 388
KRAS -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.4 26 26
NRG2 -0.39 0.4 -9999 0 -0.8 514 514
mol:GDP -0.12 0.18 -9999 0 -0.36 388 388
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.44 16 16
SRC 0 0.009 -9999 0 -0.29 1 1
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.37 388 388
MAP2K1 -0.13 0.21 -9999 0 -0.48 162 162
heart morphogenesis -0.15 0.19 -9999 0 -0.39 388 388
RAS family/GDP -0.11 0.14 -9999 0 -0.4 28 28
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA -0.01 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.023 -9999 0 -0.18 6 6
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.19 -9999 0 -0.39 388 388
CDC42 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.054 0.16 -10000 0 -0.53 101 101
cell-cell adhesion 0.17 0.22 0.67 76 -10000 0 76
Ephrin B/EPHB2/RasGAP -0.04 0.12 -10000 0 -0.44 92 92
ITSN1 -0.001 0.024 -10000 0 -0.8 1 1
PIK3CA 0 0.009 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.017 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.26 -10000 0 -0.53 412 412
HRAS/GDP -0.17 0.22 -10000 0 -0.64 100 100
Ephrin B/EPHB1/GRB7 -0.22 0.28 -10000 0 -0.52 436 436
Endophilin/SYNJ1 -0.038 0.12 -10000 0 -0.42 92 92
KRAS -0.001 0.013 -10000 0 -0.29 2 2
Ephrin B/EPHB1/Src -0.21 0.27 -10000 0 -0.51 434 434
endothelial cell migration -0.004 0.043 -10000 0 -0.44 10 10
GRB2 0 0.009 -10000 0 -0.29 1 1
GRB7 -0.022 0.084 -10000 0 -0.31 75 75
PAK1 -0.048 0.14 -10000 0 -0.46 103 103
HRAS -0.002 0.027 -10000 0 -0.29 9 9
RRAS -0.038 0.12 -10000 0 -0.42 92 92
DNM1 -0.006 0.065 -10000 0 -0.73 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.2 0.26 -10000 0 -0.49 434 434
lamellipodium assembly -0.17 0.22 -10000 0 -0.67 76 76
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.19 -10000 0 -0.36 412 412
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
EPHB2 -0.006 0.04 -10000 0 -0.29 20 20
EPHB3 -0.004 0.033 -10000 0 -0.29 14 14
EPHB1 -0.31 0.39 -10000 0 -0.79 413 413
EPHB4 0 0.009 -10000 0 -10000 0 0
mol:GDP -0.15 0.21 -10000 0 -0.64 93 93
Ephrin B/EPHB2 -0.041 0.13 -10000 0 -0.45 92 92
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.45 92 92
JNK cascade -0.17 0.21 -10000 0 -0.44 412 412
Ephrin B/EPHB1 -0.21 0.28 -10000 0 -0.52 434 434
RAP1/GDP -0.13 0.18 -10000 0 -0.55 91 91
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.069 0.22 -10000 0 -0.8 92 92
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.48 412 412
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.18 0.23 -10000 0 -0.67 97 97
Rap1/GTP -0.17 0.22 -10000 0 -0.7 75 75
axon guidance -0.053 0.16 -10000 0 -0.53 101 101
MAPK3 -0.096 0.19 -10000 0 -0.52 71 71
MAPK1 -0.096 0.19 -10000 0 -0.52 70 70
Rac1/GDP -0.14 0.19 -10000 0 -0.58 91 91
actin cytoskeleton reorganization -0.13 0.17 -10000 0 -0.51 80 80
CDC42/GDP -0.14 0.19 -10000 0 -0.58 91 91
PI3K -0.004 0.044 -10000 0 -0.45 10 10
EFNA5 -0.076 0.23 -10000 0 -0.79 102 102
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.029 0.095 -10000 0 -0.33 92 92
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.16 0.21 -10000 0 -0.66 79 79
PTK2 0.041 0.05 -10000 0 -10000 0 0
MAP4K4 -0.17 0.21 -10000 0 -0.44 412 412
SRC 0 0.009 -10000 0 -0.29 1 1
KALRN -0.016 0.11 -10000 0 -0.8 21 21
Intersectin/N-WASP -0.001 0.019 -10000 0 -0.61 1 1
neuron projection morphogenesis -0.13 0.17 -10000 0 -0.54 80 80
MAP2K1 -0.11 0.2 -10000 0 -0.55 71 71
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.23 -10000 0 -0.48 412 412
cell migration -0.12 0.22 -10000 0 -0.38 412 412
NRAS -0.001 0.013 -10000 0 -10000 0 0
SYNJ1 -0.038 0.12 -10000 0 -0.42 92 92
PXN 0 0 -10000 0 -10000 0 0
TF -0.24 0.27 -10000 0 -0.46 608 608
HRAS/GTP -0.18 0.23 -10000 0 -0.44 434 434
Ephrin B1/EPHB1-2 -0.19 0.24 -10000 0 -0.48 412 412
cell adhesion mediated by integrin 0.009 0.13 0.42 92 -10000 0 92
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.2 0.25 -10000 0 -0.47 434 434
RAC1-CDC42/GTP -0.17 0.22 -10000 0 -0.68 76 76
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.18 -10000 0 -0.6 70 70
ruffle organization -0.17 0.22 -10000 0 -0.7 76 76
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.002 0.14 -10000 0 -0.42 94 94
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.49 103 103
ROCK1 0.022 0.023 -10000 0 -0.48 1 1
RAS family/GDP -0.12 0.15 -10000 0 -0.52 71 71
Rac1/GTP -0.18 0.23 -10000 0 -0.74 76 76
Ephrin B/EPHB1/Src/Paxillin -0.15 0.2 -10000 0 -0.38 434 434
Ephrin B reverse signaling

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
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.04 -10000 0 -0.29 20 20
EFNB1 0.017 0.052 -10000 0 -0.61 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.16 0.2 -10000 0 -0.41 413 413
Ephrin B2/EPHB1-2 -0.19 0.23 -10000 0 -0.48 412 412
neuron projection morphogenesis -0.16 0.19 -10000 0 -0.4 413 413
Ephrin B1/EPHB1-2/Tiam1 -0.18 0.22 -10000 0 -0.45 413 413
DNM1 -0.006 0.065 -10000 0 -0.73 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.004 0.13 -10000 0 -0.74 33 33
YES1 -0.026 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/NCK2 -0.18 0.22 -10000 0 -0.45 413 413
PI3K -0.027 0.14 -10000 0 -0.7 41 41
mol:GDP -0.17 0.22 -10000 0 -0.44 413 413
ITGA2B -0.018 0.078 -10000 0 -0.32 61 61
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.026 0.17 -10000 0 -0.98 32 32
MAP3K7 -0.023 0.14 -10000 0 -0.8 32 32
FGR -0.028 0.17 -10000 0 -0.98 32 32
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.046 0.16 -10000 0 -0.62 70 70
LYN -0.026 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.027 0.16 -10000 0 -0.92 32 32
Ephrin B1/EPHB1-2 -0.03 0.15 -10000 0 -0.86 32 32
SRC -0.028 0.17 -10000 0 -0.98 32 32
ITGB3 -0.029 0.15 -10000 0 -0.8 37 37
EPHB1 -0.31 0.39 -10000 0 -0.79 413 413
EPHB4 0 0.009 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.034 0.12 -10000 0 -0.62 40 40
BLK -0.028 0.17 -10000 0 -0.98 32 32
HCK -0.028 0.17 -10000 0 -0.98 32 32
regulation of stress fiber formation 0.17 0.22 0.44 413 -10000 0 413
MAPK8 0.001 0.14 -10000 0 -0.71 37 37
Ephrin B1/EPHB1-2/RGS3 -0.18 0.22 -10000 0 -0.45 413 413
endothelial cell migration -0.017 0.12 -10000 0 -0.7 32 32
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.018 0.16 -10000 0 -0.91 32 32
regulation of focal adhesion formation 0.17 0.22 0.44 413 -10000 0 413
chemotaxis 0.17 0.22 0.44 413 -10000 0 413
PIK3CA 0 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.16 0.2 -10000 0 -0.4 413 413
angiogenesis -0.029 0.15 -10000 0 -0.85 32 32
LCK -0.03 0.17 -10000 0 -0.98 32 32
IGF1 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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.24 -10000 0 -0.49 259 259
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.002 0.027 -10000 0 -0.29 9 9
IRS1/Crk -0.12 0.23 -10000 0 -0.49 259 259
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.54 245 245
AKT1 -0.067 0.21 -10000 0 -0.73 48 48
BAD -0.054 0.2 -10000 0 -0.67 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.24 -10000 0 -0.49 259 259
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.49 259 259
RAF1 -0.047 0.19 -10000 0 -0.63 45 45
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.22 -10000 0 -0.46 259 259
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.24 -10000 0 -0.53 259 259
PIK3CA 0 0.009 -10000 0 -10000 0 0
RPS6KB1 -0.067 0.21 -10000 0 -0.73 48 48
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.04 0.16 -10000 0 -0.51 47 47
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.19 -10000 0 -0.42 246 246
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.19 -10000 0 -0.43 245 245
IGF-1R heterotetramer -0.033 0.14 -10000 0 -0.84 24 24
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.49 259 259
Crk/p130 Cas/Paxillin -0.11 0.2 -10000 0 -0.44 245 245
IGF1R -0.033 0.14 -10000 0 -0.84 24 24
IGF1 -0.18 0.34 -10000 0 -0.82 236 236
IRS2/Crk -0.13 0.25 -10000 0 -0.51 263 263
PI3K -0.12 0.22 -10000 0 -0.48 246 246
apoptosis 0.08 0.15 0.55 48 -10000 0 48
HRAS/GDP -0.002 0.018 -10000 0 -10000 0 0
PRKCD -0.094 0.25 -10000 0 -0.53 245 245
RAF1/14-3-3 E -0.032 0.16 -10000 0 -0.52 45 45
BAD/14-3-3 -0.085 0.16 -10000 0 -0.6 48 48
PRKCZ -0.067 0.21 -10000 0 -0.72 49 49
Crk/p130 Cas/Paxillin/FAK1 -0.084 0.16 -10000 0 -0.62 45 45
PTPN1 -0.003 0.03 -10000 0 -0.29 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.25 -10000 0 -0.57 245 245
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.47 245 245
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.22 -10000 0 -0.48 259 259
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.24 -10000 0 -0.49 259 259
IRS1 -0.12 0.25 -10000 0 -0.53 259 259
IRS2 -0.12 0.27 -10000 0 -0.53 273 273
IGF-1R heterotetramer/IGF1 -0.16 0.29 -10000 0 -0.66 245 245
GRB2 0 0.009 -10000 0 -0.29 1 1
PDPK1 -0.11 0.21 -10000 0 -0.45 246 246
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.57 258 258
SHC1 0 0 -10000 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.062 -10000 0 -0.49 2 2
epithelial cell differentiation -0.022 0.066 -10000 0 -0.5 9 9
ITCH 0.01 0.022 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.002 0.035 -10000 0 -0.8 2 2
EGFR -0.3 0.38 -10000 0 -0.79 396 396
PRL -0.004 0.033 -10000 0 -0.29 14 14
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.46 74 74
PTPRZ1 -0.42 0.4 -10000 0 -0.79 561 561
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.42 386 386
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.19 0.24 -10000 0 -0.5 386 386
ADAM17 0.01 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.056 0.13 -10000 0 -0.54 57 57
NCOR1 -0.001 0.024 -10000 0 -0.8 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.22 -10000 0 -0.47 386 386
GRIN2B -0.18 0.25 -10000 0 -0.46 436 436
ErbB4/ErbB2/betacellulin -0.05 0.12 -10000 0 -0.47 61 61
STAT1 -0.005 0.039 -10000 0 -10000 0 0
HBEGF -0.002 0.035 -10000 0 -0.8 2 2
PRLR -0.008 0.073 -10000 0 -0.8 8 8
E4ICDs/ETO2 -0.035 0.092 -10000 0 -0.55 19 19
axon guidance 0.044 0.12 -10000 0 -0.43 3 3
NEDD4 0.01 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.008 0.059 -10000 0 -0.61 8 8
CBFA2T3 -0.016 0.11 -10000 0 -0.69 24 24
ErbB4/ErbB2/HBEGF -0.025 0.054 -10000 0 -0.48 3 3
MAPK3 -0.15 0.19 -10000 0 -0.48 77 77
STAT1 (dimer) -0.028 0.063 -10000 0 -10000 0 0
MAPK1 -0.15 0.19 -10000 0 -0.48 77 77
JAK2 -0.001 0.024 -10000 0 -0.8 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.22 -10000 0 -0.47 386 386
NRG1 -0.21 0.31 -10000 0 -0.61 386 386
NRG3 -0.05 0.18 -10000 0 -0.8 57 57
NRG2 -0.39 0.4 -10000 0 -0.8 514 514
NRG4 -0.005 0.039 -10000 0 -0.29 19 19
heart development 0.044 0.12 -10000 0 -0.43 3 3
neural crest cell migration -0.19 0.22 -10000 0 -0.47 386 386
ERBB2 0.01 0.061 -10000 0 -0.6 1 1
WWOX/E4ICDs -0.026 0.059 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.21 -10000 0 -0.46 391 391
apoptosis 0.057 0.14 0.54 57 -10000 0 57
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.26 0.24 -10000 0 -0.5 514 514
ErbB4/ErbB2/epiregulin -0.084 0.15 -10000 0 -0.46 125 125
ErbB4/ErbB4/betacellulin/betacellulin -0.054 0.13 -10000 0 -0.51 61 61
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.023 0.068 -10000 0 -0.52 11 11
MDM2 0.008 0.075 -10000 0 -0.31 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.22 -10000 0 -0.47 386 386
STAT5A 0.044 0.12 -10000 0 -0.45 9 9
ErbB4/EGFR/neuregulin 1 beta -0.34 0.36 -10000 0 -0.66 537 537
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.056 -10000 0 -0.46 1 1
STAT5A (dimer) -0.022 0.071 -10000 0 -0.54 9 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.026 0.12 -10000 0 -0.42 6 6
LRIG1 -0.002 0.042 -10000 0 -0.8 3 3
EREG -0.11 0.26 -10000 0 -0.6 201 201
BTC -0.046 0.18 -10000 0 -0.78 62 62
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.12 -10000 0 -0.43 3 3
ERBB4 -0.032 0.072 -10000 0 -10000 0 0
STAT5B -0.002 0.042 -10000 0 -0.8 3 3
YAP1 -0.01 0.043 -10000 0 -0.64 4 4
GRB2 0 0.009 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 4 -0.027 0.055 -10000 0 -0.57 1 1
glial cell differentiation 0.024 0.055 0.46 1 -10000 0 1
WWOX -0.001 0.013 -10000 0 -0.29 2 2
cell proliferation -0.12 0.24 -10000 0 -0.46 208 208
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.036 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.082 0.16 -9999 0 -0.47 94 94
JUN -0.051 0.14 -9999 0 -0.53 26 26
HRAS -0.002 0.027 -9999 0 -0.29 9 9
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.52 204 204
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -0.29 10 10
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.52 204 204
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.49 195 195
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.47 204 204
GRB7 -0.022 0.084 -9999 0 -0.31 75 75
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.52 204 204
MAPKKK cascade -0.1 0.16 -9999 0 -0.42 201 201
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.23 -9999 0 -0.56 207 207
lamellipodium assembly -0.083 0.15 -9999 0 -0.37 203 203
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.52 204 204
PIK3CA 0 0.009 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.49 195 195
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.49 195 195
MAPK3 -0.12 0.17 -9999 0 -0.44 201 201
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
DOK6 -0.013 0.096 -9999 0 -0.65 21 21
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.53 56 56
DOK5 -0.019 0.12 -9999 0 -0.71 29 29
GFRA1 -0.16 0.31 -9999 0 -0.69 249 249
MAPK8 -0.077 0.13 -9999 0 -0.44 55 55
HRAS/GTP -0.12 0.19 -9999 0 -0.48 201 201
tube development -0.096 0.18 -9999 0 -0.46 195 195
MAPK1 -0.12 0.17 -9999 0 -0.44 201 201
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.066 0.13 -9999 0 -0.33 195 195
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.2 -9999 0 -0.51 210 210
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.52 204 204
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.55 219 219
PRKCA -0.021 0.13 -9999 0 -0.76 29 29
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
CREB1 -0.074 0.15 -9999 0 -0.38 195 195
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.13 -9999 0 -0.33 195 195
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.55 206 206
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.16 -9999 0 -0.31 388 388
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.05 0.14 -9999 0 -0.52 26 26
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.49 195 195
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.066 0.13 -9999 0 -0.34 195 195
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -9999 0 -0.35 201 201
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.14 -9999 0 -0.35 201 201
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.085 0.15 -9999 0 -0.36 201 201
PI3K -0.13 0.24 -9999 0 -0.59 205 205
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.096 0.18 -9999 0 -0.46 195 195
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.079 0.13 -9999 0 -0.34 195 195
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.52 204 204
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.8 43 43
IRS2 -0.033 0.16 -9999 0 -0.8 44 44
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.085 0.15 -9999 0 -0.36 201 201
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.54 229 229
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.015 0.065 -9999 0 -0.29 56 56
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.59 215 215
Rac1/GTP -0.1 0.18 -9999 0 -0.44 203 203
RET9/GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.54 199 199
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.61 199 199
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.61 179 179
CRKL -0.039 0.16 -10000 0 -0.35 179 179
mol:PIP3 -0.018 0.035 0.78 2 -10000 0 2
AKT1 0.003 0.022 0.49 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.029 0.15 -10000 0 -0.54 20 20
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.12 0.24 -10000 0 -0.56 227 227
MAP3K5 -0.02 0.15 -10000 0 -0.53 24 24
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.22 -10000 0 -0.51 227 227
AP1 -0.19 0.26 -10000 0 -0.58 314 314
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.23 0.36 -10000 0 -0.78 314 314
STAT3 (dimer) -0.038 0.16 -10000 0 -0.33 227 227
GAB1/CRKL/SHP2/PI3K -0.063 0.13 -10000 0 -0.51 30 30
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.03 0.15 -10000 0 -0.54 20 20
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.035 -10000 0 -0.8 2 2
ELK1 -0.044 0.1 -10000 0 -0.27 179 179
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.045 0.092 -10000 0 -0.22 179 179
PAK1 0.008 0.028 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.24 -10000 0 -0.56 227 227
HRAS -0.15 0.3 -10000 0 -0.77 179 179
DOCK1 -0.029 0.15 -10000 0 -0.32 179 179
GAB1 -0.049 0.16 -10000 0 -0.35 227 227
CRK -0.039 0.16 -10000 0 -0.35 179 179
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.7 227 227
JUN -0.005 0.064 -10000 0 -0.8 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.076 0.15 -10000 0 -0.36 227 227
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
cell morphogenesis -0.017 0.17 -10000 0 -0.59 26 26
GRB2/SHC -0.065 0.13 -10000 0 -0.33 179 179
FOS -0.24 0.36 -10000 0 -0.8 313 313
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.043 0.1 -10000 0 -0.27 179 179
HGF/MET/MUC20 -0.12 0.24 -10000 0 -0.57 227 227
cell migration -0.065 0.13 -10000 0 -0.32 179 179
GRB2 0 0.009 -10000 0 -0.29 1 1
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.1 0.23 -10000 0 -0.61 179 179
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.075 0.15 -10000 0 -0.35 227 227
MET/MUC20 -0.1 0.23 -10000 0 -0.62 179 179
RAP1B -0.019 0.14 -10000 0 -0.5 20 20
RAP1A -0.019 0.14 -10000 0 -0.5 20 20
HGF/MET/RANBP9 -0.12 0.24 -10000 0 -0.56 227 227
RAF1 -0.1 0.29 -10000 0 -0.71 179 179
STAT3 -0.072 0.14 -10000 0 -0.34 227 227
cell proliferation -0.059 0.23 -10000 0 -0.48 227 227
RPS6KB1 -0.026 0.052 -10000 0 -0.18 20 20
MAPK3 -0.044 0.092 -10000 0 -0.25 179 179
MAPK1 -0.044 0.092 -10000 0 -0.25 179 179
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.002 0.14 -10000 0 -0.48 31 31
SRC -0.07 0.14 -10000 0 -0.32 227 227
PI3K -0.07 0.14 -10000 0 -0.34 187 187
MET/Glomulin -0.094 0.21 -10000 0 -0.55 179 179
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.084 0.26 -10000 0 -0.64 179 179
MET -0.14 0.3 -10000 0 -0.8 179 179
MAP4K1 -0.028 0.15 -10000 0 -0.32 180 180
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.084 0.26 -10000 0 -0.64 179 179
BAD 0.011 0.02 0.45 2 -10000 0 2
MAP2K4 -0.01 0.14 -10000 0 -0.47 25 25
SHP2/GRB2/SOS1/GAB1 -0.095 0.19 -10000 0 -0.5 179 179
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.07 0.14 -10000 0 -0.35 179 179
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.052 0.2 -10000 0 -0.78 70 70
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.066 0.13 -10000 0 -0.33 179 179
PDPK1 -0.006 0.026 0.57 2 -10000 0 2
HGF/MET/SHIP -0.12 0.24 -10000 0 -0.56 227 227
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.068 0.17 -10000 0 -0.49 147 147
regulation of S phase of mitotic cell cycle -0.042 0.12 -10000 0 -0.35 139 139
GNAO1 -0.03 0.13 -10000 0 -0.8 25 25
HRAS -0.002 0.027 -10000 0 -0.29 9 9
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.001 -10000 0 -10000 0 0
MAP2K1 -0.043 0.16 -10000 0 -0.43 136 136
T-DHT/AR -0.08 0.21 -10000 0 -0.62 137 137
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 313 313
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.8 57 57
mol:GDP -0.081 0.21 -10000 0 -0.61 139 139
cell proliferation -0.1 0.24 -10000 0 -0.42 317 317
PIK3CA 0 0.009 -10000 0 -10000 0 0
FOS -0.23 0.42 -10000 0 -0.87 313 313
mol:Ca2+ -0.016 0.028 -10000 0 -0.076 142 142
MAPK3 -0.073 0.2 -10000 0 -0.46 138 138
MAPK1 -0.045 0.12 -10000 0 -0.3 62 62
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
mol:IP3 -0.001 0.002 -10000 0 -0.005 313 313
cAMP biosynthetic process 0.013 0.024 -10000 0 -10000 0 0
GNG2 -0.009 0.084 -10000 0 -0.8 12 12
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 313 313
HRAS/GTP -0.066 0.15 -10000 0 -0.46 136 136
actin cytoskeleton reorganization -0.004 0.041 -10000 0 -0.42 10 10
SRC 0 0.009 -10000 0 -0.29 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 313 313
PI3K -0.005 0.052 -10000 0 -0.53 10 10
apoptosis 0.1 0.23 0.43 315 -10000 0 315
T-DHT/AR/PELP1 -0.069 0.18 -10000 0 -0.54 136 136
HRAS/GDP -0.077 0.2 -10000 0 -0.59 137 137
CREB1 -0.11 0.24 -10000 0 -0.46 315 315
RAC1-CDC42/GTP -0.004 0.042 -10000 0 -0.43 10 10
AR -0.1 0.27 -10000 0 -0.79 137 137
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.043 0.16 -10000 0 -0.44 136 136
RAC1-CDC42/GDP -0.072 0.19 -10000 0 -0.56 136 136
T-DHT/AR/PELP1/Src -0.063 0.16 -10000 0 -0.49 136 136
MAP2K2 -0.043 0.16 -10000 0 -0.43 136 136
T-DHT/AR/PELP1/Src/PI3K -0.042 0.12 -10000 0 -0.35 139 139
GNAZ -0.007 0.073 -10000 0 -0.8 9 9
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.038 0.1 -10000 0 -0.49 36 36
mol:T-DHT -0.001 0.001 0.001 60 -0.003 251 311
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.006 0.058 -10000 0 -0.62 9 9
Gi family/GTP -0.05 0.1 -10000 0 -0.3 91 91
CDC42 0 0 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.21 -9999 0 -0.6 137 137
SMAD6-7/SMURF1 0 0.016 -9999 0 -0.52 1 1
NOG -0.026 0.13 -9999 0 -0.58 47 47
SMAD9 -0.11 0.26 -9999 0 -0.78 118 118
SMAD4 -0.001 0.024 -9999 0 -0.8 1 1
SMAD5 -0.075 0.18 -9999 0 -0.48 134 134
BMP7/USAG1 -0.35 0.35 -9999 0 -0.66 545 545
SMAD5/SKI -0.087 0.16 -9999 0 -0.48 106 106
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.3 -9999 0 -0.79 188 188
SMAD1/SMAD1/SMAD4 -0.002 0.014 -9999 0 -10000 0 0
BMPR1A -0.002 0.042 -9999 0 -0.8 3 3
BMPR1B -0.14 0.18 -9999 0 -0.32 456 456
BMPR1A-1B/BAMBI -0.093 0.14 -9999 0 -0.56 69 69
AHSG -0.005 0.039 -9999 0 -10000 0 0
CER1 -0.001 0.016 -9999 0 -0.29 3 3
BMP2-4/CER1 -0.13 0.24 -9999 0 -0.57 235 235
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.2 -9999 0 -0.52 145 145
BMP2-4 (homodimer) -0.14 0.28 -9999 0 -0.65 235 235
RGMB -0.001 0.024 -9999 0 -0.8 1 1
BMP6/BMPR2/BMPR1A-1B -0.097 0.16 -9999 0 -0.54 105 105
RGMA -0.1 0.27 -9999 0 -0.8 139 139
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.61 104 104
BMP2-4/USAG1 -0.37 0.36 -9999 0 -0.65 603 603
SMAD6/SMURF1/SMAD5 -0.087 0.16 -9999 0 -0.52 88 88
SOSTDC1 -0.39 0.4 -9999 0 -0.79 516 516
BMP7/BMPR2/BMPR1A-1B -0.11 0.17 -9999 0 -0.57 111 111
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.06 0.21 -9999 0 -0.78 81 81
HFE2 -0.003 0.03 -9999 0 -0.29 11 11
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.29 1 1
BMP2-4/CHRD -0.14 0.27 -9999 0 -0.6 239 239
SMAD5/SMAD5/SMAD4 -0.087 0.16 -9999 0 -0.49 101 101
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.086 0.17 -9999 0 -0.53 101 101
BMP7 (homodimer) -0.079 0.23 -9999 0 -0.65 129 129
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.049 0.16 -9999 0 -0.61 79 79
SMAD1/SKI 0.004 0.018 -9999 0 -10000 0 0
SMAD6 -0.001 0.024 -9999 0 -0.8 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.24 -9999 0 -0.57 235 235
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.038 0.12 -9999 0 -0.36 112 112
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.092 0.13 -9999 0 -0.62 28 28
CHRDL1 -0.54 0.37 -9999 0 -0.8 724 724
ENDOFIN/SMAD1 0.004 0.018 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.014 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.034 0.14 -9999 0 -0.51 71 71
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.47 0.37 -9999 0 -0.67 741 741
BMP2-4/GREM1 -0.14 0.25 -9999 0 -0.58 240 240
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.1 0.24 -9999 0 -0.73 118 118
SMAD1/SMAD6 0.004 0.018 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.079 0.23 -9999 0 -0.65 129 129
BMP6 -0.06 0.21 -9999 0 -0.78 81 81
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.19 -9999 0 -0.59 101 101
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.004 0.018 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.001 0.02 -9999 0 -0.29 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.53 200 200
CHRD -0.032 0.13 -9999 0 -0.8 21 21
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.23 -9999 0 -0.54 193 193
BMP4 -0.052 0.2 -9999 0 -0.79 70 70
FST -0.037 0.17 -9999 0 -0.76 52 52
BMP2-4/NOG -0.14 0.26 -9999 0 -0.59 251 251
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.097 0.16 -9999 0 -0.54 111 111
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.01 0.038 -9999 0 -0.54 3 3
NFATC2 -0.04 0.16 -9999 0 -0.55 96 96
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.21 0.36 -9999 0 -0.72 294 294
PTGS2 -0.32 0.46 -9999 0 -0.85 410 410
JUNB -0.001 0.013 -9999 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.003 -9999 0 -10000 0 0
JUN -0.005 0.065 -9999 0 -0.8 7 7
mol:Ca2+ -0.007 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
FOSL1 -0.009 0.06 -9999 0 -0.8 3 3
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.076 0.15 -9999 0 -0.53 76 76
FOS -0.24 0.37 -9999 0 -0.81 313 313
IFNG -0.21 0.35 -9999 0 -0.68 301 301
AP-1/NFAT1-c-4 -0.3 0.38 -9999 0 -0.82 307 307
FASLG -0.2 0.35 -9999 0 -0.69 289 289
NFAT1-c-4/ICER1 -0.058 0.14 -9999 0 -0.47 99 99
IL2RA -0.21 0.35 -9999 0 -0.69 291 291
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.68 287 287
JunB/Fra1/NFAT1-c-4 -0.056 0.14 -9999 0 -0.47 90 90
IL4 -0.2 0.34 -9999 0 -0.67 286 286
IL2 -0.01 0.024 -9999 0 -10000 0 0
IL3 -0.023 0.026 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -10000 0 0
BATF3 -0.002 0.03 -9999 0 -0.39 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.096 0.18 -10000 0 -0.47 190 190
ER alpha/Gai/GDP/Gbeta gamma -0.092 0.19 -10000 0 -0.48 173 173
AKT1 -0.1 0.32 -10000 0 -0.84 165 165
PIK3CA 0 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.32 -10000 0 -0.86 162 162
mol:Ca2+ -0.028 0.15 -10000 0 -0.45 88 88
IGF1R -0.02 0.12 -10000 0 -0.61 35 35
E2/ER alpha (dimer)/Striatin -0.11 0.2 -10000 0 -0.54 178 178
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.095 0.3 0.79 165 -10000 0 165
RhoA/GTP -0.071 0.14 -10000 0 -0.4 162 162
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.093 0.2 -10000 0 -0.54 171 171
regulation of stress fiber formation 0.024 0.14 0.36 32 -10000 0 32
E2/ERA-ERB (dimer) -0.11 0.2 -10000 0 -0.54 182 182
KRAS -0.001 0.013 -10000 0 -0.29 2 2
G13/GTP -0.091 0.17 -10000 0 -0.49 162 162
pseudopodium formation -0.024 0.14 -10000 0 -0.36 32 32
E2/ER alpha (dimer)/PELP1 -0.099 0.19 -10000 0 -0.53 162 162
GRB2 0 0.009 -10000 0 -0.29 1 1
GNG2 -0.009 0.084 -10000 0 -0.8 12 12
GNAO1 -0.03 0.13 -10000 0 -0.8 25 25
HRAS -0.002 0.027 -10000 0 -0.29 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.061 0.22 -10000 0 -0.54 172 172
E2/ER beta (dimer) -0.013 0.088 -10000 0 -0.62 22 22
mol:GDP -0.087 0.21 -10000 0 -0.54 182 182
mol:NADP -0.061 0.22 -10000 0 -0.54 172 172
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
mol:IP3 -0.03 0.15 -10000 0 -0.47 88 88
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.61 35 35
PLCB1 -0.064 0.14 -10000 0 -0.49 87 87
PLCB2 -0.034 0.092 -10000 0 -0.66 14 14
IGF1 -0.18 0.33 -10000 0 -0.8 236 236
mol:L-citrulline -0.061 0.22 -10000 0 -0.54 172 172
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.039 0.15 -10000 0 -0.85 25 25
JNK cascade -0.013 0.088 -10000 0 -0.61 22 22
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.017 0.11 -10000 0 -0.8 22 22
GNAQ -0.002 0.035 -10000 0 -0.8 2 2
ESR1 -0.16 0.29 -10000 0 -0.58 286 286
Gq family/GDP/Gbeta gamma -0.007 0.069 -10000 0 -0.71 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.025 0.13 -10000 0 -0.32 162 162
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.093 0.2 -10000 0 -0.54 171 171
GNAZ -0.007 0.073 -10000 0 -0.8 9 9
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.62 162 162
STRN -0.014 0.11 -10000 0 -0.8 19 19
GNAL -0.19 0.34 -10000 0 -0.8 253 253
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.005 0.083 -10000 0 -0.53 25 25
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.8 57 57
HBEGF -0.071 0.19 -10000 0 -0.45 182 182
cAMP biosynthetic process -0.19 0.26 -10000 0 -0.51 380 380
SRC -0.052 0.2 -10000 0 -0.44 173 173
PI3K -0.006 0.059 -10000 0 -0.61 10 10
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.19 -10000 0 -0.47 190 190
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.51 245 245
Gs family/GTP -0.2 0.26 -10000 0 -0.52 380 380
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.014 -10000 0 -10000 0 0
vasodilation -0.057 0.21 -10000 0 -0.52 172 172
mol:DAG -0.03 0.15 -10000 0 -0.47 88 88
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.45 381 381
MSN -0.028 0.15 -10000 0 -0.4 32 32
Gq family/GTP -0.038 0.097 -10000 0 -0.71 13 13
mol:PI-3-4-5-P3 -0.1 0.31 -10000 0 -0.82 162 162
NRAS -0.001 0.013 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.057 0.21 0.52 172 -10000 0 172
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.08 0.19 -10000 0 -0.5 182 182
NOS3 -0.066 0.24 -10000 0 -0.57 171 171
GNA11 -0.002 0.035 -10000 0 -0.8 2 2
MAPKKK cascade -0.069 0.26 -10000 0 -0.63 178 178
E2/ER alpha (dimer)/PELP1/Src -0.098 0.22 -10000 0 -0.57 171 171
ruffle organization -0.024 0.14 -10000 0 -0.36 32 32
ROCK2 -0.075 0.14 -10000 0 -0.37 188 188
GNA14 -0.013 0.087 -10000 0 -0.45 31 31
GNA15 -0.003 0.034 -10000 0 -0.36 8 8
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.097 0.2 -10000 0 -0.48 180 180
MMP2 -0.045 0.19 -10000 0 -0.43 178 178
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.1 0.12 -10000 0 -0.33 89 89
NT3 (dimer)/TRKC -0.3 0.36 -10000 0 -0.69 448 448
NT3 (dimer)/TRKB -0.5 0.44 -10000 0 -0.78 675 675
SHC/Grb2/SOS1/GAB1/PI3K -0.003 0.031 -10000 0 -0.32 10 10
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.066 0.21 -10000 0 -0.67 104 104
PIK3CA 0 0.009 -10000 0 -10000 0 0
DYNLT1 0 0.009 -10000 0 -0.29 1 1
NTRK1 -0.011 0.07 -10000 0 -0.37 31 31
NTRK2 -0.42 0.4 -10000 0 -0.8 556 556
NTRK3 -0.27 0.38 -10000 0 -0.79 366 366
NT-4/5 (dimer)/TRKB -0.59 0.48 -10000 0 -0.86 728 728
neuron apoptosis 0.24 0.24 0.59 293 -10000 0 293
SHC 2-3/Grb2 -0.26 0.28 -10000 0 -0.66 293 293
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.25 0.29 -10000 0 -0.68 278 278
SHC3 -0.25 0.28 -10000 0 -0.66 282 282
STAT3 (dimer) -0.006 0.032 -10000 0 -0.38 5 5
NT3 (dimer)/TRKA -0.25 0.32 -10000 0 -0.61 424 424
RIN/GDP -0.066 0.12 -10000 0 -0.26 111 111
GIPC1 -0.001 0.016 -10000 0 -0.29 3 3
KRAS -0.001 0.013 -10000 0 -0.29 2 2
DNAJA3 -0.14 0.2 -10000 0 -0.43 327 327
RIN/GTP 0 0.009 -10000 0 -10000 0 0
CCND1 0.017 0.082 -10000 0 -1 5 5
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.28 0.38 -10000 0 -0.79 371 371
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/TRKA/MATK -0.028 0.11 -10000 0 -0.55 38 38
TRKA/NEDD4-2 -0.008 0.054 -10000 0 -0.61 6 6
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.1 -10000 0 -0.63 24 24
HRAS -0.002 0.027 -10000 0 -0.29 9 9
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.004 0.044 -10000 0 -0.38 11 11
RIT2 -0.001 0.013 -10000 0 -0.29 2 2
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.028 -10000 0 -0.29 10 10
DNM1 -0.006 0.065 -10000 0 -0.73 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.13 0.2 -10000 0 -0.42 327 327
mol:GDP -0.1 0.18 -10000 0 -0.36 235 235
NGF (dimer) -0.014 0.1 -10000 0 -0.63 24 24
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.062 0.12 -10000 0 -0.27 75 75
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
BDNF (dimer)/TRKB -0.31 0.3 -10000 0 -0.57 581 581
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -10000 0 -0.76 178 178
RAP1/GDP -0.072 0.084 -10000 0 -0.24 38 38
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.066 0.21 -10000 0 -0.67 104 104
ubiquitin-dependent protein catabolic process -0.015 0.078 -10000 0 -0.52 22 22
Schwann cell development -0.059 0.044 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.43 0.38 -10000 0 -0.66 689 689
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.098 -10000 0 -10000 0 0
STAT3 -0.006 0.032 -10000 0 -0.38 5 5
axon guidance -0.4 0.35 -10000 0 -0.61 689 689
MAPK3 0.005 0.11 -10000 0 -0.5 38 38
MAPK1 0.005 0.11 -10000 0 -0.5 38 38
CDC42/GDP -0.062 0.12 -10000 0 -0.27 71 71
NTF3 -0.13 0.29 -10000 0 -0.76 178 178
NTF4 -0.28 0.38 -10000 0 -0.8 371 371
NGF (dimer)/TRKA/FAIM -0.015 0.077 -10000 0 -0.52 21 21
PI3K -0.006 0.059 -10000 0 -0.61 10 10
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.15 0.21 -10000 0 -0.45 331 331
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.24 0.33 -10000 0 -0.6 450 450
RGS19 -0.001 0.013 -10000 0 -0.29 2 2
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.082 -10000 0 -10000 0 0
Rac1/GDP -0.062 0.12 -10000 0 -0.28 64 64
NGF (dimer)/TRKA/GRIT -0.015 0.078 -10000 0 -0.53 21 21
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.67 21 21
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.078 -10000 0 -0.52 22 22
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.25 0.37 -10000 0 -0.8 327 327
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.054 -10000 0 -0.34 27 27
RAS family/GTP/PI3K -0.004 0.033 -10000 0 -0.34 10 10
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.01 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.8 1 1
MAPKKK cascade -0.065 0.12 -10000 0 -0.82 21 21
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.05 -10000 0 -0.61 5 5
SQSTM1 0 0.009 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB/GIPC -0.29 0.28 -10000 0 -0.52 581 581
NGF (dimer)/TRKA/p62/Atypical PKCs -0.013 0.065 -10000 0 -0.44 22 22
MATK -0.022 0.12 -10000 0 -0.49 48 48
NEDD4L -0.001 0.024 -10000 0 -0.8 1 1
RAS family/GDP -0.066 0.079 -10000 0 -0.24 2 2
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 335 335
Rac1/GTP -0.12 0.14 -10000 0 -0.34 244 244
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.26 -10000 0 -0.53 432 432
fibroblast growth factor receptor signaling pathway -0.22 0.26 -10000 0 -0.53 432 432
LAMA1 -0.091 0.25 -10000 0 -0.8 119 119
PRNP -0.013 0.1 -10000 0 -0.8 17 17
GPC1/SLIT2 -0.068 0.19 -10000 0 -0.61 116 116
SMAD2 0.01 0.1 -10000 0 -0.47 46 46
GPC1/PrPc/Cu2+ -0.01 0.07 -10000 0 -0.53 18 18
GPC1/Laminin alpha1 -0.071 0.19 -10000 0 -0.6 121 121
TDGF1 -0.008 0.077 -10000 0 -0.75 11 11
CRIPTO/GPC1 -0.008 0.064 -10000 0 -0.61 11 11
APP/GPC1 -0.002 0.024 -10000 0 -0.61 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.018 0.06 -10000 0 -0.52 12 12
FLT1 -0.001 0.024 -10000 0 -0.8 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.024 0.11 -10000 0 -0.52 46 46
SERPINC1 -0.017 0.068 -10000 0 -0.29 61 61
FYN 0.018 0.062 -10000 0 -0.52 13 13
FGR 0.018 0.06 -10000 0 -0.52 12 12
positive regulation of MAPKKK cascade 0.03 0.073 -10000 0 -0.52 13 13
SLIT2 -0.086 0.25 -10000 0 -0.8 115 115
GPC1/NRG -0.22 0.29 -10000 0 -0.61 387 387
NRG1 -0.29 0.38 -10000 0 -0.79 391 391
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.004 0.03 -10000 0 -0.52 2 2
LYN 0.019 0.057 -10000 0 -0.52 11 11
mol:Spermine 0.009 0.026 -10000 0 -0.62 1 1
cell growth -0.22 0.26 -10000 0 -0.53 432 432
BMP signaling pathway 0.003 0.034 0.36 8 -10000 0 8
SRC 0.019 0.058 -10000 0 -0.52 11 11
TGFBR1 0 0.009 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.26 0.37 -10000 0 -0.76 365 365
GPC1 -0.003 0.034 -10000 0 -0.36 8 8
TGFBR1 (dimer) 0 0.009 -10000 0 -10000 0 0
VEGFA -0.003 0.031 -10000 0 -0.29 12 12
BLK -0.007 0.087 -10000 0 -0.56 13 13
HCK 0.016 0.06 -10000 0 -0.52 11 11
FGF2 -0.32 0.39 -10000 0 -0.8 426 426
FGFR1 -0.009 0.082 -10000 0 -0.69 14 14
VEGFR1 homodimer -0.001 0.024 -10000 0 -0.79 1 1
TGFBR2 -0.034 0.16 -10000 0 -0.8 45 45
cell death -0.002 0.024 -10000 0 -0.6 1 1
ATIII/GPC1 -0.013 0.049 -10000 0 -0.62 1 1
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.61 338 338
LCK 0.006 0.089 -10000 0 -0.53 24 24
neuron differentiation -0.22 0.29 -10000 0 -0.61 387 387
PrPc/Cu2+ -0.01 0.077 -10000 0 -0.62 17 17
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.034 0.16 -10000 0 -0.79 45 45
IL6-mediated signaling events

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
BCL2L1 -0.065 0.22 -9999 0 -0.63 60 60
CRP -0.069 0.22 -9999 0 -0.64 56 56
cell cycle arrest -0.083 0.24 -9999 0 -0.71 68 68
TIMP1 -0.062 0.2 -9999 0 -0.57 56 56
IL6ST -0.084 0.26 -9999 0 -0.79 129 129
Rac1/GDP -0.12 0.23 -9999 0 -0.64 98 98
AP1 -0.13 0.23 -9999 0 -0.48 271 271
GAB2 0.004 0.045 -9999 0 -0.38 11 11
TNFSF11 -0.075 0.22 -9999 0 -0.66 47 47
HSP90B1 0.015 0.047 -9999 0 -10000 0 0
GAB1 0.005 0.006 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.73 90 90
AKT1 0.038 0.039 -9999 0 -10000 0 0
FOXO1 0.047 0.057 -9999 0 -0.41 11 11
MAP2K6 -0.15 0.26 -9999 0 -0.5 221 221
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.086 0.23 -9999 0 -0.64 85 85
MITF -0.14 0.26 -9999 0 -0.46 255 255
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.014 0.12 -9999 0 -1.5 7 7
CEBPB 0.016 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.051 0.088 -9999 0 -0.48 8 8
STAT3 -0.091 0.26 -9999 0 -0.78 68 68
STAT1 -0.013 0.022 -9999 0 -10000 0 0
CEBPD -0.066 0.22 -9999 0 -0.68 47 47
PIK3CA 0.012 0.009 -9999 0 -10000 0 0
PI3K -0.006 0.059 -9999 0 -0.6 10 10
JUN -0.005 0.064 -9999 0 -0.8 7 7
PIAS3/MITF -0.16 0.22 -9999 0 -0.7 88 88
MAPK11 -0.13 0.25 -9999 0 -0.74 90 90
STAT3 (dimer)/FOXO1 -0.035 0.22 -9999 0 -0.58 65 65
GRB2/SOS1/GAB family -0.14 0.2 -9999 0 -0.72 68 68
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.25 -9999 0 -0.39 485 485
GRB2 0.004 0.011 -9999 0 -0.29 1 1
JAK2 -0.001 0.024 -9999 0 -0.8 1 1
LBP -0.24 0.44 -9999 0 -0.97 261 261
PIK3R1 0.004 0.078 -9999 0 -0.79 10 10
JAK1 0.007 0.026 -9999 0 -0.79 1 1
MYC -0.077 0.26 -9999 0 -0.85 56 56
FGG -0.074 0.22 -9999 0 -0.64 57 57
macrophage differentiation -0.083 0.24 -9999 0 -0.71 68 68
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.5 485 485
JUNB -0.063 0.21 -9999 0 -0.63 47 47
FOS -0.24 0.36 -9999 0 -0.8 313 313
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -9999 0 -0.4 443 443
STAT1/PIAS1 -0.13 0.23 -9999 0 -0.48 196 196
GRB2/SOS1/GAB family/SHP2/PI3K -0.002 0.03 -9999 0 -0.29 6 6
STAT3 (dimer) -0.086 0.26 -9999 0 -0.75 68 68
PRKCD -0.061 0.22 -9999 0 -0.61 77 77
IL6R -0.023 0.15 -9999 0 -0.79 40 40
SOCS3 -0.12 0.24 -9999 0 -0.75 81 81
gp130 (dimer)/JAK1/JAK1/LMO4 -0.056 0.18 -9999 0 -0.52 131 131
Rac1/GTP -0.15 0.21 -9999 0 -0.63 101 101
HCK -0.004 0.033 -9999 0 -0.29 14 14
MAPKKK cascade -0.005 0.084 -9999 0 -1 2 2
bone resorption -0.071 0.21 -9999 0 -0.61 55 55
IRF1 -0.065 0.22 -9999 0 -0.65 47 47
mol:GDP -0.13 0.25 -9999 0 -0.48 220 220
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.13 0.25 -9999 0 -0.48 220 220
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.25 -9999 0 -0.81 86 86
PTPN11 -0.013 0.019 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.31 -9999 0 -0.63 406 406
gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.18 -9999 0 -0.52 131 131
gp130 (dimer)/JAK2/JAK2/LMO4 -0.059 0.18 -9999 0 -0.52 131 131
IL6 -0.28 0.39 -9999 0 -0.79 389 389
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.026 -9999 0 -0.8 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.24 -9999 0 -0.4 484 484
LMO4 0.009 0.05 -9999 0 -0.44 10 10
STAT3 (dimer)/PIAS3 -0.15 0.21 -9999 0 -0.78 67 67
MCL1 0.051 0.032 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.001 0.016 -9999 0 -0.29 3 3
CCL5 -0.015 0.08 -9999 0 -0.8 6 6
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.08 0.11 -9999 0 -0.34 104 104
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.074 0.097 -9999 0 -0.35 45 45
Syndecan-1/Syntenin -0.074 0.097 -9999 0 -0.35 45 45
MAPK3 -0.047 0.096 -9999 0 -0.48 5 5
HGF/MET -0.14 0.27 -9999 0 -0.65 227 227
TGFB1/TGF beta receptor Type II -0.001 0.016 -9999 0 -0.29 3 3
BSG 0 0.009 -9999 0 -10000 0 0
keratinocyte migration -0.073 0.095 -9999 0 -0.35 45 45
Syndecan-1/RANTES -0.081 0.11 -9999 0 -0.4 49 49
Syndecan-1/CD147 -0.065 0.094 -9999 0 -0.49 6 6
Syndecan-1/Syntenin/PIP2 -0.071 0.093 -9999 0 -0.34 45 45
LAMA5 0 0.009 -9999 0 -0.29 1 1
positive regulation of cell-cell adhesion -0.07 0.092 -9999 0 -0.34 45 45
MMP7 -0.12 0.28 -9999 0 -0.71 183 183
HGF -0.052 0.2 -9999 0 -0.78 70 70
Syndecan-1/CASK -0.076 0.1 -9999 0 -0.33 104 104
Syndecan-1/HGF/MET -0.17 0.25 -9999 0 -0.59 230 230
regulation of cell adhesion -0.039 0.093 -9999 0 -0.48 4 4
HPSE -0.006 0.051 -9999 0 -0.34 20 20
positive regulation of cell migration -0.08 0.11 -9999 0 -0.34 104 104
SDC1 -0.08 0.11 -9999 0 -0.35 104 104
Syndecan-1/Collagen -0.08 0.11 -9999 0 -0.34 104 104
PPIB -0.001 0.016 -9999 0 -0.29 3 3
MET -0.14 0.3 -9999 0 -0.8 179 179
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 468 468
MAPK1 -0.047 0.096 -9999 0 -0.48 5 5
homophilic cell adhesion -0.079 0.11 -9999 0 -0.34 104 104
MMP1 -0.22 0.12 -9999 0 -0.29 801 801
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.023 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.039 -9999 0 -0.31 2 2
PDE6G/GNAT1/GTP -0.009 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.035 -9999 0 -0.29 15 15
GRK1 -0.003 0.03 -9999 0 -0.29 11 11
CNG Channel -0.14 0.2 -9999 0 -0.44 307 307
mol:Na + -0.13 0.19 -9999 0 -0.42 302 302
mol:ADP -0.003 0.03 -9999 0 -0.29 11 11
RGS9-1/Gbeta5/R9AP -0.063 0.16 -9999 0 -0.53 108 108
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.19 -9999 0 -0.43 302 302
CNGB1 -0.015 0.064 -9999 0 -0.29 54 54
RDH5 -0.48 0.39 -9999 0 -0.8 644 644
SAG -0.014 0.063 -9999 0 -0.29 51 51
mol:Ca2+ -0.12 0.18 -9999 0 -0.4 301 301
Na + (4 Units) -0.12 0.18 -9999 0 -0.39 301 301
RGS9 -0.083 0.24 -9999 0 -0.74 119 119
GNB1/GNGT1 -0.03 0.068 -9999 0 -10000 0 0
GNAT1/GDP -0.056 0.14 -9999 0 -0.46 105 105
GUCY2D -0.007 0.06 -9999 0 -0.39 20 20
GNGT1 -0.047 0.11 -9999 0 -10000 0 0
GUCY2F -0.001 0.013 -9999 0 -0.29 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.018 0.071 -9999 0 -0.45 22 22
mol:11-cis-retinal -0.48 0.39 -9999 0 -0.79 644 644
mol:cGMP -0.011 0.05 -9999 0 -0.46 9 9
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.37 0.3 -9999 0 -0.61 644 644
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.22 0.36 -9999 0 -0.79 302 302
Metarhodopsin II -0.003 0.022 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.011 0.053 -9999 0 -0.48 9 9
RGS9BP -0.019 0.073 -9999 0 -0.29 70 70
Metarhodopsin II/Transducin -0.009 0.02 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.043 -9999 0 -0.49 5 5
PDE6A/B -0.017 0.091 -9999 0 -0.61 22 22
mol:Pi -0.063 0.16 -9999 0 -0.52 108 108
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.023 0.051 -9999 0 -10000 0 0
PDE6B -0.017 0.11 -9999 0 -0.74 25 25
PDE6A -0.006 0.042 -9999 0 -0.29 22 22
PDE6G -0.012 0.058 -9999 0 -0.29 43 43
RHO -0.004 0.035 -9999 0 -0.29 15 15
PDE6 -0.064 0.15 -9999 0 -0.45 123 123
GUCA1A -0.012 0.058 -9999 0 -0.29 43 43
GC2/GCAP Family -0.008 0.043 -9999 0 -0.49 5 5
GUCA1C 0 0.009 -9999 0 -0.29 1 1
GUCA1B -0.004 0.055 -9999 0 -0.8 5 5
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.076 0.068 -9999 0 -0.62 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.02 0.018 -9999 0 -10000 0 0
AURKB -0.17 0.14 -9999 0 -0.29 609 609
AURKC -0.005 0.044 -9999 0 -0.32 18 18
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.7 114 114
FZD6 -0.008 0.077 -9999 0 -0.8 10 10
WNT6 -0.17 0.31 -9999 0 -0.8 204 204
WNT4 -0.022 0.12 -9999 0 -0.54 42 42
FZD3 -0.008 0.081 -9999 0 -0.8 11 11
WNT5A -0.014 0.098 -9999 0 -0.59 25 25
WNT11 -0.17 0.32 -9999 0 -0.8 219 219
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.049 -10000 0 -0.8 4 4
Jak2/Leptin Receptor -0.16 0.24 -10000 0 -0.53 285 285
PTP1B/AKT1 -0.07 0.11 -10000 0 -0.34 111 111
FYN -0.002 0.035 -10000 0 -0.8 2 2
p210 bcr-abl/PTP1B -0.07 0.13 -10000 0 -0.38 117 117
EGFR -0.3 0.39 -10000 0 -0.8 396 396
EGF/EGFR -0.29 0.3 -10000 0 -0.57 535 535
CSF1 -0.006 0.069 -10000 0 -0.8 8 8
AKT1 0 0.002 -10000 0 -10000 0 0
INSR 0 0.009 -10000 0 -0.29 1 1
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.37 121 121
Insulin Receptor/Insulin -0.049 0.08 -10000 0 -0.4 20 20
HCK -0.004 0.033 -10000 0 -0.29 14 14
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.059 0.12 -10000 0 -0.36 111 111
EGF -0.15 0.32 -10000 0 -0.8 206 206
YES1 -0.001 0.024 -10000 0 -0.8 1 1
CAV1 -0.17 0.24 -10000 0 -0.5 287 287
TXN 0 0.016 -10000 0 -0.29 3 3
PTP1B/IRS1/GRB2 -0.086 0.14 -10000 0 -0.4 144 144
cell migration 0.07 0.13 0.38 117 -10000 0 117
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.006 0.073 -10000 0 -0.8 8 8
ITGA2B -0.018 0.079 -10000 0 -0.32 61 61
CSF1R -0.001 0.026 -10000 0 -0.54 2 2
Prolactin Receptor/Prolactin -0.007 0.06 -10000 0 -0.61 8 8
FGR -0.001 0.026 -10000 0 -0.54 2 2
PTP1B/p130 Cas -0.074 0.11 -10000 0 -0.36 111 111
Crk/p130 Cas -0.068 0.11 -10000 0 -0.43 42 42
DOK1 -0.045 0.12 -10000 0 -0.32 113 113
JAK2 -0.041 0.08 -10000 0 -0.34 23 23
Jak2/Leptin Receptor/Leptin -0.36 0.19 -10000 0 -0.48 598 598
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
PTPN1 -0.071 0.13 -10000 0 -0.38 117 117
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.055 0.12 -10000 0 -0.3 196 196
SRC -0.013 0.047 -10000 0 -10000 0 0
ITGB3 -0.029 0.15 -10000 0 -0.76 40 40
CAT1/PTP1B -0.084 0.17 -10000 0 -0.38 180 180
CAPN1 0.001 0.01 -10000 0 -0.29 1 1
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.043 0.089 -10000 0 -0.54 16 16
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.16 -10000 0 -0.43 525 525
negative regulation of transcription -0.041 0.079 -10000 0 -0.33 23 23
FCGR2A -0.001 0.013 -10000 0 -0.29 2 2
FER -0.007 0.082 -10000 0 -0.81 11 11
alphaIIb/beta3 Integrin -0.034 0.12 -10000 0 -0.63 40 40
BLK -0.043 0.11 -10000 0 -0.3 150 150
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.002 0.004 -10000 0 -10000 0 0
LEPR -0.2 0.36 -10000 0 -0.8 279 279
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -0.29 1 1
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.031 0.13 -10000 0 -0.44 23 23
PRL -0.004 0.034 -10000 0 -0.29 14 14
SOCS3 0.017 0.12 -10000 0 -1.5 6 6
SPRY2 -0.092 0.26 -10000 0 -0.81 121 121
Insulin Receptor/Insulin/IRS1 -0.022 0.11 -10000 0 -0.54 43 43
CSF1/CSF1R -0.072 0.12 -10000 0 -0.36 117 117
Ras protein signal transduction 0.037 0.036 -10000 0 -0.21 1 1
IRS1 -0.032 0.16 -10000 0 -0.8 43 43
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.63 0.32 -10000 0 -0.8 839 839
STAT5B -0.058 0.11 -10000 0 -0.32 115 115
STAT5A -0.058 0.11 -10000 0 -0.32 118 118
GRB2 0 0.009 -10000 0 -0.29 1 1
PDGFB-D/PDGFRB -0.076 0.12 -10000 0 -0.38 113 113
CSN2 0.018 0.035 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
LAT -0.014 0.053 -10000 0 -0.57 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.021 0.1 -10000 0 -0.42 52 52
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.045 -10000 0 -0.38 12 12
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.072 0.23 -9999 0 -0.8 96 96
GNB1/GNG2 -0.14 0.22 -9999 0 -0.67 108 108
mol:DAG -0.094 0.22 -9999 0 -0.59 108 108
PLCG1 -0.13 0.21 -9999 0 -0.62 108 108
YES1 -0.14 0.23 -9999 0 -0.66 112 112
FZD3 -0.008 0.081 -9999 0 -0.8 11 11
FZD6 -0.008 0.077 -9999 0 -0.8 10 10
G protein -0.13 0.21 -9999 0 -0.63 109 109
MAP3K7 -0.067 0.18 -9999 0 -0.48 104 104
mol:Ca2+ -0.091 0.21 -9999 0 -0.57 108 108
mol:IP3 -0.094 0.22 -9999 0 -0.59 108 108
NLK -0.005 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.081 0.2 -9999 0 -0.53 106 106
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.7 114 114
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.14 0.23 -9999 0 -0.66 113 113
GO:0007205 -0.092 0.21 -9999 0 -0.58 108 108
WNT6 -0.17 0.31 -9999 0 -0.8 204 204
WNT4 -0.022 0.12 -9999 0 -0.54 42 42
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.62 139 139
GNG2 -0.009 0.084 -9999 0 -0.8 12 12
WNT5A -0.014 0.098 -9999 0 -0.59 25 25
WNT11 -0.17 0.32 -9999 0 -0.8 219 219
CDC42 -0.1 0.23 -9999 0 -0.66 99 99
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0.031 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.034 0.16 -9999 0 -0.3 263 263
RXRs/LXRs/DNA/Oxysterols -0.014 0.14 -9999 0 -0.42 31 31
MED1 -0.007 0.044 -9999 0 -0.29 24 24
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.023 0.091 -9999 0 -0.36 66 66
RXRs/NUR77 -0.15 0.24 -9999 0 -0.5 321 321
RXRs/PPAR -0.13 0.23 -9999 0 -0.38 436 436
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.007 0.051 -9999 0 -0.45 13 13
RARA -0.004 0.033 -9999 0 -0.29 14 14
NCOA1 -0.001 0.024 -9999 0 -0.8 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.007 0.052 -9999 0 -0.46 13 13
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.052 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.022 0.087 -9999 0 -0.35 66 66
THRA -0.001 0.024 -9999 0 -0.8 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.2 -9999 0 -0.47 260 260
NR1H4 -0.003 0.031 -9999 0 -0.29 12 12
RXRs/LXRs/DNA -0.11 0.18 -9999 0 -0.42 260 260
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.19 -9999 0 -0.44 260 260
NR4A1 -0.066 0.22 -9999 0 -0.8 88 88
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.043 0.13 -9999 0 -0.27 260 260
RXRG -0.18 0.35 -9999 0 -0.78 263 263
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.016 0.007 -9999 0 -10000 0 0
THRB -0.043 0.18 -9999 0 -0.8 57 57
PPARG -0.19 0.34 -9999 0 -0.8 255 255
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.014 0.18 -9999 0 -1.2 13 13
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.014 0.14 -9999 0 -0.42 31 31
PPARA -0.005 0.06 -9999 0 -0.8 6 6
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.088 -9999 0 -0.8 13 13
RXRs/NUR77/BCL2 -0.12 0.19 -9999 0 -0.38 343 343
SREBF1 -0.005 0.14 -9999 0 -0.63 7 7
RXRs/RXRs/DNA/9cRA -0.12 0.2 -9999 0 -0.47 260 260
ABCA1 -0.008 0.16 -9999 0 -1.1 9 9
RARs/THRs -0.031 0.12 -9999 0 -0.48 66 66
RXRs/FXR -0.12 0.2 -9999 0 -0.47 260 260
BCL2 -0.028 0.15 -9999 0 -0.8 37 37
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.046 -9999 0 -0.61 5 5
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.55 440 440
PTK2 -0.089 0.2 -9999 0 -0.65 47 47
IGF1R -0.02 0.12 -9999 0 -0.61 35 35
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.091 -9999 0 -0.8 13 13
SRC 0 0.009 -9999 0 -0.29 1 1
CDKN1B -0.088 0.13 -9999 0 -0.89 11 11
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
ILK -0.086 0.12 -9999 0 -0.83 8 8
ROCK1 -0.001 0.024 -9999 0 -0.8 1 1
AKT1 -0.076 0.1 -9999 0 -0.78 8 8
PTK2B -0.019 0.095 -9999 0 -0.49 38 38
alphaV/beta3 Integrin/JAM-A -0.2 0.25 -9999 0 -0.48 444 444
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.097 -9999 0 -0.53 37 37
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.25 -9999 0 -0.55 259 259
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.063 -9999 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.029 0.1 -9999 0 -0.54 38 38
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.35 -9999 0 -0.76 340 340
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.058 0.11 -9999 0 -0.55 37 37
RPS6KB1 -0.3 0.32 -9999 0 -0.7 341 341
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.77 440 440
GPR124 -0.009 0.084 -9999 0 -0.8 12 12
MAPK1 -0.33 0.39 -9999 0 -0.77 440 440
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
alphaV/beta3 Integrin/Tumstatin -0.11 0.22 -9999 0 -0.53 211 211
cell adhesion -0.024 0.11 -9999 0 -0.5 47 47
ANGPTL3 -0.001 0.018 -9999 0 -0.29 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.039 -9999 0 -0.52 5 5
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.61 35 35
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.034 0.16 -9999 0 -0.8 45 45
ITGB3 -0.029 0.15 -9999 0 -0.8 37 37
IGF1 -0.18 0.33 -9999 0 -0.8 236 236
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.024 0.12 -9999 0 -0.58 43 43
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.024 -9999 0 -0.8 1 1
alphaV/beta3 Integrin/CD47 -0.019 0.097 -9999 0 -0.52 38 38
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.05 0.18 -9999 0 -0.67 75 75
CSF1 -0.006 0.069 -9999 0 -0.8 8 8
PIK3C2A -0.087 0.12 -9999 0 -0.85 9 9
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.61 71 71
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.021 0.1 -9999 0 -0.53 38 38
FAK1/Vinculin -0.065 0.16 -9999 0 -0.49 45 45
alphaV beta3/Integrin/ppsTEM5 -0.024 0.12 -9999 0 -0.59 43 43
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.027 0.1 -9999 0 -0.8 8 8
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.39 -9999 0 -0.8 426 426
F11R -0.23 0.31 -9999 0 -0.61 426 426
alphaV/beta3 Integrin/Lactadherin -0.026 0.12 -9999 0 -0.56 46 46
alphaV/beta3 Integrin/TGFBR2 -0.04 0.17 -9999 0 -0.66 63 63
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.041 -9999 0 -0.47 8 8
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Talin -0.017 0.089 -9999 0 -0.48 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.019 0.096 -9999 0 -0.49 38 38
SDC1 -0.021 0.077 -9999 0 -0.3 73 73
VAV3 -0.008 0.054 -9999 0 -0.44 15 15
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.8 43 43
FAK1/Paxillin -0.065 0.16 -9999 0 -0.49 45 45
cell migration -0.051 0.15 -9999 0 -0.45 42 42
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.23 -9999 0 -0.67 69 69
SPP1 -0.079 0.13 -9999 0 -0.29 286 286
KDR -0.004 0.055 -9999 0 -0.8 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.14 0.3 -9999 0 -0.8 179 179
angiogenesis -0.3 0.39 -9999 0 -0.74 442 442
Rac1/GTP -0.007 0.048 -9999 0 -0.4 15 15
EDIL3 -0.05 0.19 -9999 0 -0.7 76 76
cell proliferation -0.04 0.16 -9999 0 -0.66 63 63
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.095 0.2 0.63 113 -10000 0 113
KIRREL -0.079 0.25 -10000 0 -0.8 113 113
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.095 0.2 -10000 0 -0.64 113 113
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.069 0.15 -10000 0 -0.48 113 113
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.042 0.11 -10000 0 -0.36 113 113
FYN -0.064 0.14 -10000 0 -0.46 113 113
mol:Ca2+ -0.068 0.15 -10000 0 -0.48 113 113
mol:DAG -0.068 0.15 -10000 0 -0.48 113 113
NPHS2 -0.008 0.03 -10000 0 -0.29 4 4
mol:IP3 -0.068 0.15 -10000 0 -0.48 113 113
regulation of endocytosis -0.054 0.14 -10000 0 -0.43 113 113
Nephrin/NEPH1/podocin/Cholesterol -0.071 0.15 -10000 0 -0.49 113 113
establishment of cell polarity -0.095 0.2 -10000 0 -0.63 113 113
Nephrin/NEPH1/podocin/NCK1-2 -0.061 0.14 -10000 0 -0.44 113 113
Nephrin/NEPH1/beta Arrestin2 -0.055 0.14 -10000 0 -0.44 113 113
NPHS1 -0.047 0.11 -10000 0 -0.29 175 175
Nephrin/NEPH1/podocin -0.064 0.14 -10000 0 -0.47 113 113
TJP1 -0.001 0.024 -10000 0 -0.8 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.069 0.15 -10000 0 -0.48 113 113
CD2AP 0 0.009 -10000 0 -0.29 1 1
Nephrin/NEPH1/podocin/GRB2 -0.069 0.15 -10000 0 -0.48 113 113
GRB2 0 0.009 -10000 0 -0.29 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.069 0.17 -10000 0 -0.5 121 121
cytoskeleton organization -0.053 0.14 -10000 0 -0.45 113 113
Nephrin/NEPH1 -0.069 0.15 -10000 0 -0.48 113 113
Nephrin/NEPH1/ZO-1 -0.075 0.16 -10000 0 -0.52 113 113
LPA receptor mediated events

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
GNB1/GNG2 -0.018 0.093 -9999 0 -0.51 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.11 -9999 0 -0.34 124 124
AP1 -0.18 0.25 -9999 0 -0.48 406 406
mol:PIP3 -0.2 0.24 -9999 0 -0.45 448 448
AKT1 -0.015 0.072 -9999 0 -0.58 7 7
PTK2B 0.014 0.061 -9999 0 -0.29 24 24
RHOA 0.028 0.027 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.13 -9999 0 -0.35 124 124
MAGI3 -0.001 0.024 -9999 0 -0.8 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.42 143 143
HRAS/GDP -0.002 0.018 -9999 0 -0.2 9 9
positive regulation of microtubule depolymerization -0.02 0.15 -9999 0 -0.41 121 121
NF kappa B1 p50/RelA -0.053 0.14 -9999 0 -0.39 128 128
endothelial cell migration 0.007 0.12 -9999 0 -0.64 32 32
ADCY4 -0.003 0.15 -9999 0 -0.63 39 39
ADCY5 -0.072 0.19 -9999 0 -0.59 78 78
ADCY6 0.007 0.13 -9999 0 -0.6 29 29
ADCY7 0.007 0.13 -9999 0 -0.6 29 29
ADCY1 -0.002 0.14 -9999 0 -0.63 35 35
ADCY2 -0.013 0.16 -9999 0 -0.62 45 45
ADCY3 0.007 0.13 -9999 0 -0.6 29 29
ADCY8 0.004 0.13 -9999 0 -0.61 29 29
ADCY9 0.007 0.13 -9999 0 -0.6 29 29
GSK3B 0.021 0.058 -9999 0 -0.35 9 9
arachidonic acid secretion 0.01 0.12 -9999 0 -0.55 32 32
GNG2 -0.009 0.084 -9999 0 -0.8 12 12
TRIP6 -0.001 0.017 -9999 0 -0.51 1 1
GNAO1 -0.006 0.13 -9999 0 -0.52 54 54
HRAS -0.002 0.027 -9999 0 -0.29 9 9
NFKBIA -0.003 0.15 -9999 0 -0.4 126 126
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.004 -9999 0 -10000 0 0
JUN -0.005 0.064 -9999 0 -0.8 7 7
LPA/LPA2/NHERF2 -0.002 0.016 -9999 0 -10000 0 0
TIAM1 0.001 0.004 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.79 10 10
mol:IP3 -0.007 0.13 -9999 0 -0.36 124 124
PLCB3 0.026 0.017 -9999 0 -10000 0 0
FOS -0.24 0.36 -9999 0 -0.8 313 313
positive regulation of mitosis 0.01 0.12 -9999 0 -0.55 32 32
LPA/LPA1-2-3 -0.073 0.17 -9999 0 -0.49 143 143
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.38 23 23
GNAZ 0.008 0.1 -9999 0 -0.48 40 40
EGFR/PI3K-beta/Gab1 -0.2 0.26 -9999 0 -0.48 447 447
positive regulation of dendritic cell cytokine production -0.072 0.17 -9999 0 -0.48 143 143
LPA/LPA2/MAGI-3 -0.002 0.02 -9999 0 -0.53 1 1
ARHGEF1 -0.011 0.069 -9999 0 -0.45 22 22
GNAI2 0.013 0.086 -9999 0 -0.46 32 32
GNAI3 0.013 0.086 -9999 0 -0.46 32 32
GNAI1 -0.016 0.16 -9999 0 -0.54 82 82
LPA/LPA3 -0.08 0.2 -9999 0 -0.51 164 164
LPA/LPA2 -0.002 0.016 -9999 0 -0.19 3 3
LPA/LPA1 -0.016 0.095 -9999 0 -0.54 32 32
HB-EGF/EGFR -0.26 0.26 -9999 0 -0.57 396 396
HBEGF -0.071 0.11 -9999 0 -0.61 3 3
mol:DAG -0.007 0.13 -9999 0 -0.36 124 124
cAMP biosynthetic process -0.011 0.15 -9999 0 -0.57 51 51
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.003 0.15 -9999 0 -0.4 124 124
GNAQ -0.053 0.13 -9999 0 -0.41 126 126
LPAR2 -0.001 0.016 -9999 0 -0.29 3 3
LPAR3 -0.1 0.26 -9999 0 -0.67 164 164
LPAR1 -0.018 0.12 -9999 0 -0.79 22 22
IL8 -0.19 0.23 -9999 0 -0.43 432 432
PTK2 -0.067 0.16 -9999 0 -0.46 142 142
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.062 0.15 -9999 0 -0.42 143 143
EGFR -0.3 0.38 -9999 0 -0.79 396 396
PLCG1 -0.03 0.15 -9999 0 -0.42 125 125
PLD2 -0.067 0.16 -9999 0 -0.46 142 142
G12/G13 -0.013 0.074 -9999 0 -0.48 22 22
PI3K-beta -0.017 0.085 -9999 0 -0.71 7 7
cell migration -0.021 0.053 -9999 0 -0.24 7 7
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
PXN 0.002 0.1 -9999 0 -0.39 23 23
HRAS/GTP -0.034 0.12 -9999 0 -0.57 32 32
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 468 468
PRKCE 0.01 0.002 -9999 0 -10000 0 0
PRKCD 0.001 0.12 -9999 0 -0.33 124 124
Gi(beta/gamma) -0.035 0.12 -9999 0 -0.58 36 36
mol:LPA -0.002 0.021 -9999 0 -0.22 10 10
TRIP6/p130 Cas/FAK1/Paxillin -0.055 0.14 -9999 0 -0.39 142 142
MAPKKK cascade 0.01 0.12 -9999 0 -0.55 32 32
contractile ring contraction involved in cytokinesis 0.028 0.027 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.058 0.14 -9999 0 -0.42 132 132
GNA15 -0.053 0.13 -9999 0 -0.41 125 125
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.022 0.15 -9999 0 -0.42 121 121
GNA11 -0.053 0.13 -9999 0 -0.41 126 126
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
MMP2 0.007 0.12 -9999 0 -0.65 32 32
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.051 0.16 -9999 0 -0.53 101 101
EFNA5 -0.076 0.23 -9999 0 -0.79 102 102
FYN -0.027 0.15 -9999 0 -0.49 102 102
neuron projection morphogenesis -0.051 0.16 -9999 0 -0.53 101 101
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.052 0.16 -9999 0 -0.54 101 101
EPHA5 -0.001 0.018 -9999 0 -0.29 4 4
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.063 -9999 0 -0.57 11 11
alphaM/beta2 Integrin/GPIbA -0.025 0.058 -9999 0 -0.55 8 8
alphaM/beta2 Integrin/proMMP-9 -0.083 0.082 -9999 0 -0.39 8 8
PLAUR -0.022 0.076 -9999 0 -0.29 78 78
HMGB1 -0.013 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.017 0.029 -9999 0 -10000 0 0
AGER -0.015 0.041 -9999 0 -0.66 3 3
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.074 0.096 -9999 0 -0.7 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 468 468
CYR61 -0.043 0.18 -9999 0 -0.8 57 57
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.058 0.11 -9999 0 -0.53 21 21
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.34 -9999 0 -0.79 248 248
MYH2 -0.07 0.16 -9999 0 -0.49 49 49
MST1R -0.011 0.085 -9999 0 -0.57 20 20
leukocyte activation during inflammatory response -0.3 0.22 -9999 0 -0.47 650 650
APOB -0.49 0.39 -9999 0 -0.8 650 650
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.009 0.081 -9999 0 -0.75 12 12
JAM3 -0.005 0.064 -9999 0 -0.8 7 7
GP1BA -0.012 0.078 -9999 0 -0.4 33 33
alphaM/beta2 Integrin/CTGF -0.024 0.069 -9999 0 -0.58 13 13
alphaM/beta2 Integrin -0.073 0.13 -9999 0 -0.37 87 87
JAM3 homodimer -0.005 0.064 -9999 0 -0.79 7 7
ICAM2 -0.004 0.055 -9999 0 -0.8 5 5
ICAM1 -0.005 0.037 -9999 0 -0.29 17 17
phagocytosis triggered by activation of immune response cell surface activating receptor -0.062 0.14 -9999 0 -0.36 87 87
cell adhesion -0.025 0.058 -9999 0 -0.55 8 8
NFKB1 -0.14 0.18 -9999 0 -0.66 14 14
THY1 -0.002 0.025 -9999 0 -0.29 8 8
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.33 0.26 -9999 0 -0.54 650 650
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.55 43 43
IL6 -0.3 0.48 -9999 0 -0.93 388 388
ITGB2 -0.017 0.038 -9999 0 -0.3 15 15
elevation of cytosolic calcium ion concentration -0.025 0.049 -9999 0 -0.4 1 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.043 0.13 -9999 0 -0.54 62 62
JAM2 -0.045 0.18 -9999 0 -0.8 60 60
alphaM/beta2 Integrin/ICAM1 -0.022 0.082 -9999 0 -0.54 21 21
alphaM/beta2 Integrin/uPA/Plg -0.019 0.033 -9999 0 -10000 0 0
RhoA/GTP -0.088 0.16 -9999 0 -0.42 120 120
positive regulation of phagocytosis -0.049 0.089 -9999 0 -0.46 18 18
Ron/MSP -0.016 0.1 -9999 0 -0.66 22 22
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.049 -9999 0 -0.4 1 1
alphaM/beta2 Integrin/uPAR -0.028 0.047 -9999 0 -0.39 2 2
PLAU -0.008 0.048 -9999 0 -0.29 29 29
PLAT -0.028 0.14 -9999 0 -0.74 40 40
actin filament polymerization -0.067 0.16 -9999 0 -0.42 72 72
MST1 -0.012 0.091 -9999 0 -0.62 20 20
alphaM/beta2 Integrin/lipoprotein(a) -0.3 0.23 -9999 0 -0.48 650 650
TNF -0.087 0.22 -9999 0 -0.96 16 16
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.037 -9999 0 -10000 0 0
fibrinolysis -0.019 0.033 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -0.29 14 14
dendritic cell antigen processing and presentation -0.062 0.14 -9999 0 -0.36 87 87
VTN -0.027 0.1 -9999 0 -0.8 8 8
alphaM/beta2 Integrin/CYR61 -0.046 0.13 -9999 0 -0.57 57 57
LPA -0.001 0.02 -9999 0 -0.29 5 5
LRP1 -0.008 0.081 -9999 0 -0.8 11 11
cell migration -0.073 0.085 -9999 0 -0.51 13 13
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.018 0.031 -9999 0 -10000 0 0
MPO -0.054 0.2 -9999 0 -0.8 71 71
KNG1 -0.006 0.042 -9999 0 -0.29 22 22
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.066 0.16 -9999 0 -0.4 114 114
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.025 -9999 0 -10000 0 0
CTGF -0.011 0.089 -9999 0 -0.7 16 16
alphaM/beta2 Integrin/Hck -0.019 0.036 -9999 0 -0.33 2 2
ITGAM -0.015 0.028 -9999 0 -0.31 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.21 -9999 0 -0.51 248 248
HP -0.16 0.31 -9999 0 -0.71 235 235
leukocyte adhesion -0.075 0.13 -9999 0 -0.59 42 42
SELP -0.19 0.34 -9999 0 -0.8 248 248
IL23-mediated signaling 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
CCL2 -0.17 0.39 -9999 0 -0.98 98 98
IL23A -0.17 0.4 -9999 0 -1.1 71 71
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.32 -9999 0 -0.89 133 133
positive regulation of T cell mediated cytotoxicity -0.19 0.42 -9999 0 -0.99 135 135
ITGA3 -0.17 0.38 -9999 0 -1 83 83
IL17F -0.11 0.28 -9999 0 -0.68 69 69
IL12B -0.05 0.12 -9999 0 -0.32 78 78
STAT1 (dimer) -0.22 0.37 -9999 0 -0.96 131 131
CD4 -0.16 0.38 -9999 0 -0.96 88 88
IL23 -0.18 0.38 -9999 0 -1.1 74 74
IL23R -0.013 0.087 -9999 0 -10000 0 0
IL1B -0.18 0.41 -9999 0 -1.2 72 72
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.38 -9999 0 -0.97 91 91
TYK2 0.011 0.017 -9999 0 -10000 0 0
STAT4 -0.034 0.16 -9999 0 -0.8 45 45
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.024 0.15 -9999 0 -0.74 43 43
IL12RB1 -0.002 0.071 -9999 0 -0.32 43 43
PIK3CA 0 0.009 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.053 -9999 0 -0.61 2 2
IL23R/JAK2 -0.011 0.11 -9999 0 -0.64 1 1
positive regulation of chronic inflammatory response -0.19 0.42 -9999 0 -0.99 135 135
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.017 0.034 -9999 0 -0.83 1 1
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
NFKB1 0.004 0.007 -9999 0 -10000 0 0
RELA 0.004 0.007 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.37 -9999 0 -1 74 74
ALOX12B -0.17 0.38 -9999 0 -1.1 62 62
CXCL1 -0.35 0.64 -9999 0 -1.4 271 271
T cell proliferation -0.19 0.42 -9999 0 -0.99 135 135
NFKBIA 0.004 0.007 -9999 0 -10000 0 0
IL17A -0.071 0.24 -9999 0 -0.54 54 54
PI3K -0.24 0.33 -9999 0 -0.91 134 134
IFNG -0.005 0.027 -9999 0 -0.11 3 3
STAT3 (dimer) -0.23 0.31 -9999 0 -0.91 110 110
IL18R1 -0.008 0.1 -9999 0 -0.79 18 18
IL23/IL23R/JAK2/TYK2/SOCS3 -0.085 0.24 -9999 0 -0.66 17 17
IL18/IL18R -0.031 0.12 -9999 0 -0.53 55 55
macrophage activation -0.013 0.016 -9999 0 -0.043 71 71
TNF -0.18 0.41 -9999 0 -1.1 85 85
STAT3/STAT4 -0.26 0.35 -9999 0 -0.95 147 147
STAT4 (dimer) -0.23 0.4 -9999 0 -0.99 148 148
IL18 -0.001 0.044 -9999 0 -0.29 23 23
IL19 -0.18 0.38 -9999 0 -0.99 85 85
STAT5A (dimer) -0.22 0.38 -9999 0 -0.95 135 135
STAT1 -0.005 0.039 -9999 0 -10000 0 0
SOCS3 -0.005 0.06 -9999 0 -0.8 6 6
CXCL9 -0.19 0.38 -9999 0 -0.92 128 128
MPO -0.21 0.47 -9999 0 -1.2 128 128
positive regulation of humoral immune response -0.19 0.42 -9999 0 -0.99 135 135
IL23/IL23R/JAK2/TYK2 -0.2 0.44 -9999 0 -1 135 135
IL6 -0.46 0.7 -9999 0 -1.3 396 396
STAT5A -0.006 0.069 -9999 0 -0.8 8 8
IL2 0.004 0.028 -9999 0 -0.3 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.18 0.41 -9999 0 -1.2 71 71
keratinocyte proliferation -0.19 0.42 -9999 0 -0.99 135 135
NOS2 -0.17 0.39 -9999 0 -0.99 91 91
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.002 0.035 -9999 0 -0.8 2 2
LAT2 -0.061 0.14 -9999 0 -0.42 89 89
AP1 -0.15 0.21 -9999 0 -0.56 149 149
mol:PIP3 -0.025 0.2 -9999 0 -0.42 205 205
IKBKB 0.003 0.12 -9999 0 -0.32 50 50
AKT1 -0.08 0.17 -9999 0 -0.66 42 42
IKBKG 0.003 0.12 -9999 0 -0.32 51 51
MS4A2 -0.066 0.22 -9999 0 -0.77 92 92
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
MAP3K1 0.007 0.13 -9999 0 -0.43 42 42
mol:Ca2+ -0.011 0.15 -9999 0 -0.31 205 205
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.06 0.13 -9999 0 -0.42 88 88
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.064 0.16 -9999 0 -0.48 139 139
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.094 0.2 -9999 0 -0.48 205 205
PTPN13 -0.029 0.17 -9999 0 -0.53 65 65
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.008 0.14 -9999 0 -0.4 43 43
SYK 0.011 0.01 -9999 0 -0.29 1 1
GRB2 0 0.009 -9999 0 -0.29 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.084 0.18 -9999 0 -0.43 205 205
LAT -0.062 0.14 -9999 0 -0.43 89 89
PAK2 -0.002 0.14 -9999 0 -0.48 42 42
NFATC2 -0.099 0.24 -9999 0 -0.8 96 96
HRAS -0.011 0.15 -9999 0 -0.41 91 91
GAB2 -0.004 0.044 -9999 0 -0.38 11 11
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.6 205 205
Antigen/IgE/Fc epsilon R1 -0.11 0.23 -9999 0 -0.55 205 205
mol:GDP -0.018 0.15 -9999 0 -0.42 91 91
JUN -0.005 0.064 -9999 0 -0.8 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
FOS -0.24 0.36 -9999 0 -0.8 313 313
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.065 0.14 -9999 0 -0.43 100 100
CHUK 0.003 0.12 -9999 0 -0.32 50 50
KLRG1 -0.06 0.13 -9999 0 -0.4 92 92
VAV1 -0.062 0.14 -9999 0 -0.43 91 91
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.06 0.13 -9999 0 -0.42 88 88
negative regulation of mast cell degranulation -0.054 0.12 -9999 0 -0.5 39 39
BTK -0.059 0.13 -9999 0 -0.42 89 89
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.084 0.2 -9999 0 -0.43 207 207
GAB2/PI3K/SHP2 -0.089 0.19 -9999 0 -0.74 43 43
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.067 0.16 -9999 0 -0.35 205 205
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.51 207 207
FCER1G 0.003 0.012 -9999 0 -0.29 1 1
FCER1A -0.11 0.29 -9999 0 -0.8 153 153
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.52 205 205
MAPK3 0.026 0.018 -9999 0 -10000 0 0
MAPK1 0.026 0.018 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.078 -9999 0 -0.67 9 9
DUSP1 -0.1 0.27 -9999 0 -0.8 139 139
NF-kappa-B/RelA -0.026 0.054 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.025 0.15 -9999 0 -0.42 88 88
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.056 0.13 -9999 0 -0.51 48 48
FER -0.064 0.15 -9999 0 -0.44 95 95
RELA 0 0 -9999 0 -10000 0 0
ITK -0.035 0.12 -9999 0 -0.6 39 39
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.015 0.16 -9999 0 -0.43 91 91
cytokine secretion -0.019 0.039 -9999 0 -10000 0 0
SPHK1 -0.063 0.14 -9999 0 -0.43 91 91
PTK2 -0.027 0.15 -9999 0 -0.44 88 88
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.087 0.19 -9999 0 -0.45 205 205
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.02 0.2 -9999 0 -0.4 205 205
MAP2K2 0.022 0.019 -9999 0 -10000 0 0
MAP2K1 0.022 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.056 0.12 -9999 0 -0.5 39 39
MAP2K4 0.017 0.033 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.23 -9999 0 -0.55 207 207
mol:Choline -0.093 0.2 -9999 0 -0.48 205 205
SHC/Grb2/SOS1 -0.054 0.12 -9999 0 -0.53 37 37
FYN -0.002 0.035 -9999 0 -0.8 2 2
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
PXN -0.017 0.14 -9999 0 -0.52 39 39
HCLS1 -0.06 0.13 -9999 0 -0.42 88 88
PRKCB -0.013 0.16 -9999 0 -0.32 205 205
FCGR2B -0.004 0.055 -9999 0 -0.71 6 6
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.055 0.12 -9999 0 -0.51 39 39
LCP2 0 0.009 -9999 0 -0.29 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.5 192 192
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.093 0.2 -9999 0 -0.48 205 205
IKK complex 0.02 0.092 -9999 0 -0.23 46 46
WIPF1 0 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN -0.002 0.027 -9999 0 -0.29 9 9
Syndecan-3/Src/Cortactin -0.18 0.2 -9999 0 -0.41 463 463
Syndecan-3/Neurocan -0.007 0.028 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.8 21 21
EGFR -0.3 0.38 -9999 0 -0.79 396 396
Syndecan-3/EGFR -0.16 0.21 -9999 0 -0.44 391 391
AGRP -0.003 0.028 -9999 0 -0.29 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.009 -9999 0 -0.29 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.024 -9999 0 -0.8 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.072 -9999 0 -0.29 69 69
long-term memory -0.002 0.02 -9999 0 -0.41 2 2
Syndecan-3/IL8 -0.015 0.065 -9999 0 -0.44 20 20
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.031 -9999 0 -0.29 12 12
SRC 0 0.009 -9999 0 -0.29 1 1
PTN -0.35 0.39 -9999 0 -0.8 463 463
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.18 0.2 -9999 0 -0.4 463 463
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.015 -9999 0 -10000 0 0
Fyn/Cortactin -0.003 0.031 -9999 0 -0.61 2 2
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.015 0.064 -9999 0 -0.44 20 20
IL8 -0.033 0.13 -9999 0 -0.41 85 85
Syndecan-3/Fyn/Cortactin -0.002 0.021 -9999 0 -0.42 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.02 0.094 -9999 0 -0.6 23 23
Gamma Secretase -0.001 0.014 -9999 0 -0.44 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.052 0.3 -10000 0 -0.81 125 125
IHH -0.014 0.082 -10000 0 -0.42 8 8
SHH Np/Cholesterol/GAS1 -0.03 0.11 -10000 0 -0.49 59 59
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.11 0.49 59 -10000 0 59
SMO/beta Arrestin2 -0.075 0.23 -10000 0 -0.84 79 79
SMO -0.036 0.26 -10000 0 -0.9 79 79
AKT1 0.008 0.11 -10000 0 -0.43 19 19
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.059 0.21 -10000 0 -0.8 79 79
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.034 0.26 -10000 0 -0.87 79 79
STIL -0.039 0.21 -10000 0 -0.7 81 81
DHH N/PTCH2 -0.064 0.2 -10000 0 -0.64 106 106
DHH N/PTCH1 -0.09 0.24 -10000 0 -0.74 111 111
PIK3CA 0 0.009 -10000 0 -10000 0 0
DHH -0.023 0.13 -10000 0 -0.8 30 30
PTHLH -0.079 0.38 -10000 0 -1.1 125 125
determination of left/right symmetry -0.034 0.26 -10000 0 -0.87 79 79
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
skeletal system development -0.077 0.37 -10000 0 -1 125 125
IHH N/Hhip -0.015 0.05 -10000 0 -0.41 6 6
DHH N/Hhip -0.02 0.11 -10000 0 -0.62 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.034 0.26 -10000 0 -0.87 79 79
pancreas development -0.004 0.043 -10000 0 -0.39 10 10
HHAT -0.001 0.024 -10000 0 -0.8 1 1
PI3K -0.006 0.059 -10000 0 -0.61 10 10
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.044 0.18 -10000 0 -0.8 58 58
somite specification -0.034 0.26 -10000 0 -0.87 79 79
SHH Np/Cholesterol/PTCH1 -0.071 0.2 -10000 0 -0.75 79 79
SHH Np/Cholesterol/PTCH2 -0.042 0.13 -10000 0 -0.49 84 84
SHH Np/Cholesterol/Megalin -0.14 0.22 -10000 0 -0.49 279 279
SHH 0.01 0.036 -10000 0 -0.62 1 1
catabolic process -0.046 0.26 -10000 0 -0.85 87 87
SMO/Vitamin D3 -0.074 0.22 -10000 0 -0.82 79 79
SHH Np/Cholesterol/Hhip -0.005 0.036 -10000 0 -0.37 7 7
LRP2 -0.22 0.35 -10000 0 -0.8 278 278
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.82 95 95
SHH Np/Cholesterol/BOC -0.04 0.13 -10000 0 -0.49 80 80
SHH Np/Cholesterol/CDO -0.01 0.06 -10000 0 -0.49 15 15
mesenchymal cell differentiation 0.005 0.036 0.36 7 -10000 0 7
mol:Vitamin D3 -0.029 0.22 -10000 0 -0.76 79 79
IHH N/PTCH2 -0.064 0.18 -10000 0 -0.68 83 83
CDON -0.011 0.091 -10000 0 -0.8 14 14
IHH N/PTCH1 -0.044 0.26 -10000 0 -0.86 87 87
Megalin/LRPAP1 -0.16 0.27 -10000 0 -0.61 278 278
PTCH2 -0.062 0.21 -10000 0 -0.8 83 83
SHH Np/Cholesterol -0.004 0.025 -10000 0 -0.5 1 1
PTCH1 -0.047 0.26 -10000 0 -0.86 87 87
HHIP -0.004 0.043 -10000 0 -0.39 10 10
PDGFR-alpha signaling pathway

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
PDGFRA -0.049 0.2 -9999 0 -0.81 68 68
PDGF/PDGFRA/CRKL -0.039 0.15 -9999 0 -0.61 67 67
positive regulation of JUN kinase activity -0.03 0.11 -9999 0 -0.47 67 67
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.042 0.15 -9999 0 -0.62 67 67
AP1 -0.36 0.53 -9999 0 -1.2 313 313
mol:IP3 -0.033 0.16 -9999 0 -0.64 67 67
PLCG1 -0.033 0.16 -9999 0 -0.64 67 67
PDGF/PDGFRA/alphaV Integrin -0.039 0.15 -9999 0 -0.61 67 67
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.16 -9999 0 -0.63 67 67
CAV3 -0.001 0.016 -9999 0 -0.29 3 3
CAV1 -0.17 0.33 -9999 0 -0.8 228 228
SHC/Grb2/SOS1 -0.03 0.12 -9999 0 -0.47 67 67
PDGF/PDGFRA/Shf -0.039 0.15 -9999 0 -0.62 67 67
FOS -0.32 0.54 -9999 0 -1.1 313 313
JUN -0.024 0.06 -9999 0 -0.68 7 7
oligodendrocyte development -0.039 0.15 -9999 0 -0.61 67 67
GRB2 0 0.009 -9999 0 -0.29 1 1
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
mol:DAG -0.033 0.16 -9999 0 -0.64 67 67
PDGF/PDGFRA -0.049 0.2 -9999 0 -0.81 68 68
actin cytoskeleton reorganization -0.04 0.15 -9999 0 -0.61 68 68
SRF 0.015 0.021 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.038 0.14 -9999 0 -0.53 76 76
PDGF/PDGFRA/Crk/C3G -0.033 0.13 -9999 0 -0.52 67 67
JAK1 -0.023 0.15 -9999 0 -0.61 68 68
ELK1/SRF -0.026 0.12 -9999 0 -0.48 67 67
SHB -0.001 0.026 -9999 0 -0.8 1 1
SHF -0.001 0.026 -9999 0 -0.8 1 1
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.035 0.16 -9999 0 -0.65 67 67
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.03 0.11 -9999 0 -0.47 67 67
PDGF/PDGFRA/SHB -0.04 0.15 -9999 0 -0.61 68 68
PDGF/PDGFRA/Caveolin-1 -0.17 0.31 -9999 0 -0.71 251 251
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.033 0.15 -9999 0 -0.59 67 67
PIK3CA 0 0.009 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.039 0.15 -9999 0 -0.61 67 67
JAK-STAT cascade -0.023 0.15 -9999 0 -0.61 68 68
cell proliferation -0.039 0.15 -9999 0 -0.62 67 67
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.055 -9999 0 -0.46 15 15
RGS9BP -0.019 0.073 -9999 0 -0.29 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.03 -9999 0 -0.29 11 11
mol:Na + -0.02 0.053 -9999 0 -10000 0 0
mol:ADP 0.008 0.027 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -0.29 4 4
RGS9-1/Gbeta5/R9AP -0.063 0.16 -9999 0 -0.53 108 108
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
GRK7 -0.002 0.024 -9999 0 -0.29 7 7
CNGB3 -0.011 0.055 -9999 0 -0.29 39 39
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.093 0.088 -9999 0 -0.28 39 39
Cone PDE6 -0.055 0.14 -9999 0 -0.46 105 105
Cone Metarhodopsin II -0.002 0.018 -9999 0 -10000 0 0
Na + (4 Units) -0.098 0.081 -9999 0 -0.28 39 39
GNAT2/GDP -0.054 0.14 -9999 0 -0.46 105 105
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.016 -9999 0 -10000 0 0
Cone Transducin -0.008 0.058 -9999 0 -0.48 15 15
SLC24A2 -0.18 0.14 -9999 0 -0.29 638 638
GNB3/GNGT2 -0.009 0.073 -9999 0 -0.61 15 15
GNB3 -0.011 0.09 -9999 0 -0.66 18 18
GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
CNGA3 -0.027 0.085 -9999 0 -0.29 99 99
ARR3 -0.002 0.025 -9999 0 -0.29 8 8
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.02 0.053 -9999 0 -10000 0 0
mol:Pi -0.063 0.16 -9999 0 -0.52 108 108
Cone CNG Channel -0.016 0.04 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.14 -9999 0 -0.29 638 638
RGS9 -0.083 0.24 -9999 0 -0.74 119 119
PDE6C 0 0.009 -9999 0 -10000 0 0
GNGT2 -0.002 0.035 -9999 0 -0.8 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.022 -9999 0 -0.29 6 6
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 314 314
MAP3K8 -0.007 0.074 -9999 0 -0.75 10 10
FOS -0.034 0.14 -9999 0 -0.46 37 37
PRKCA -0.013 0.13 -9999 0 -0.77 29 29
PTPN7 -0.008 0.072 -9999 0 -0.3 60 60
HRAS -0.003 0.027 -9999 0 -0.29 9 9
PRKCB -0.011 0.12 -9999 0 -0.55 38 38
NRAS -0.001 0.013 -9999 0 -0.3 2 2
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.007 0.073 -9999 0 -0.25 32 32
MAP2K1 -0.012 0.14 -9999 0 -0.6 45 45
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.57 45 45
mol:GTP -0.002 0.003 -9999 0 -0.006 313 313
MAPK1 -0.007 0.073 -9999 0 -0.29 1 1
RAF1 -0.032 0.12 -9999 0 -0.57 45 45
KRAS -0.001 0.013 -9999 0 -0.29 2 2
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.051 0.19 -10000 0 -0.79 68 68
HRAS -0.002 0.027 -10000 0 -0.29 9 9
EGFR -0.3 0.38 -10000 0 -0.79 396 396
AKT 0.014 0.078 -10000 0 -0.56 17 17
FOXO3 -0.002 0.042 -10000 0 -0.8 3 3
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.008 0.081 -10000 0 -0.8 11 11
AKT3 -0.013 0.1 -10000 0 -0.8 17 17
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.3 -10000 0 -0.8 179 179
PIK3CA 0 0.009 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
PIK3CG -0.013 0.099 -10000 0 -0.69 20 20
PIK3R3 0 0.009 -10000 0 -0.29 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.024 -10000 0 -0.8 1 1
RAS -0.094 0.16 0.26 1 -0.26 437 438
ERBB2 -0.024 0.082 -10000 0 -0.3 84 84
proliferation/survival/translation -0.005 0.057 0.27 12 -10000 0 12
PI3K -0.085 0.16 -10000 0 -0.35 208 208
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
KRAS -0.001 0.013 -10000 0 -0.29 2 2
FOXO 0.027 0.029 -10000 0 -0.49 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.035 -10000 0 -0.8 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.049 -9999 0 -0.8 4 4
alphaV beta3 Integrin -0.022 0.11 -9999 0 -0.61 37 37
PTK2 -0.066 0.19 -9999 0 -0.57 117 117
positive regulation of JNK cascade -0.038 0.11 -9999 0 -0.34 117 117
CDC42/GDP -0.001 0.16 -9999 0 -0.46 117 117
Rac1/GDP 0.001 0.16 -9999 0 -0.46 117 117
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.047 0.13 -9999 0 -0.42 117 117
nectin-3/I-afadin -0.07 0.2 -9999 0 -0.63 117 117
RAPGEF1 -0.01 0.18 -9999 0 -0.52 117 117
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.024 0.21 -9999 0 -0.61 117 117
PDGFB-D/PDGFRB -0.003 0.049 -9999 0 -0.79 4 4
TLN1 0.001 0.1 -9999 0 -0.54 13 13
Rap1/GTP -0.04 0.11 -9999 0 -0.36 117 117
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.036 -9999 0 -0.48 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.07 0.2 -9999 0 -0.63 117 117
PVR 0 0.009 -9999 0 -0.29 1 1
Necl-5(dimer) 0 0.009 -9999 0 -0.29 1 1
mol:GDP -0.013 0.2 -9999 0 -0.58 117 117
MLLT4 -0.005 0.06 -9999 0 -0.72 7 7
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.057 0.17 -9999 0 -0.49 122 122
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.61 6 6
positive regulation of lamellipodium assembly -0.04 0.11 -9999 0 -0.36 117 117
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.087 0.25 -9999 0 -0.8 116 116
PVRL2 -0.001 0.016 -9999 0 -0.29 3 3
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
CDH1 -0.022 0.13 -9999 0 -0.8 29 29
CLDN1 -0.036 0.15 -9999 0 -0.58 66 66
JAM-A/CLDN1 -0.075 0.19 -9999 0 -0.52 145 145
SRC -0.078 0.22 -9999 0 -0.7 117 117
ITGB3 -0.029 0.15 -9999 0 -0.8 37 37
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.61 6 6
FARP2 -0.018 0.2 -9999 0 -0.57 117 117
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.06 0.17 -9999 0 -0.54 117 117
nectin-1/I-afadin -0.004 0.046 -9999 0 -0.61 6 6
nectin-2/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.06 0.17 -9999 0 -0.54 117 117
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.038 0.11 -9999 0 -0.34 117 117
alphaV/beta3 Integrin/Talin -0.041 0.13 -9999 0 -0.59 42 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
PIP5K1C -0.033 0.1 -9999 0 -0.56 14 14
VAV2 -0.02 0.2 -9999 0 -0.58 117 117
RAP1/GDP -0.047 0.13 -9999 0 -0.42 117 117
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.061 0.17 -9999 0 -0.54 117 117
nectin-3(dimer)/I-afadin/I-afadin -0.07 0.2 -9999 0 -0.63 117 117
Rac1/GTP -0.049 0.14 -9999 0 -0.44 117 117
PTPRM -0.037 0.11 -9999 0 -0.32 121 121
E-cadherin/beta catenin/alpha catenin -0.014 0.077 -9999 0 -0.43 34 34
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.47 256 256
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.021 -10000 0 -0.2 12 12
GNB1/GNG2 -0.006 0.056 -10000 0 -0.53 12 12
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.21 -10000 0 -0.5 253 253
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.027 0.048 0.11 253 -10000 0 253
GNAL -0.19 0.34 -10000 0 -0.8 253 253
GNG2 -0.009 0.084 -10000 0 -0.8 12 12
CRH -0.003 0.031 -10000 0 -0.29 12 12
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.04 -10000 0 -0.45 8 8
MAPK11 0.007 0.024 -10000 0 -0.45 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.54 0.37 -9999 0 -0.8 724 724
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.007 0.046 -9999 0 -0.29 27 27
TCEB1 -0.001 0.013 -9999 0 -0.29 2 2
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.007 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.017 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.051 0.11 -9999 0 -0.29 184 184
ARNT/IPAS -0.42 0.28 -9999 0 -0.61 724 724
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0.009 -9999 0 -0.29 1 1
RACK1/Elongin B/Elongin C -0.004 0.023 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.006 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.038 -9999 0 -0.47 2 2
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.015 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
HIF1A/JAB1 -0.001 0.005 -9999 0 -10000 0 0
EGLN3 -0.022 0.08 -9999 0 -0.3 78 78
EGLN2 -0.001 0.02 -9999 0 -10000 0 0
EGLN1 -0.001 0.024 -9999 0 -0.8 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.005 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.019 0.04 -9999 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion 0.03 0.03 -9999 0 -10000 0 0
BUB1B -0.041 0.052 -9999 0 -10000 0 0
PLK1 -0.008 0.024 -9999 0 -10000 0 0
PLK1S1 0 0.014 -9999 0 -10000 0 0
KIF2A 0.002 0.021 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.008 0.024 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.17 0.12 -9999 0 -0.28 518 518
WEE1 -0.003 0.024 -9999 0 -10000 0 0
cytokinesis -0.055 0.057 -9999 0 -0.28 8 8
PP2A-alpha B56 0.028 0.019 -9999 0 -10000 0 0
AURKA 0 0.015 -9999 0 -10000 0 0
PICH/PLK1 -0.073 0.098 -9999 0 -0.34 11 11
CENPE -0.051 0.086 -9999 0 -0.19 17 17
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.021 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.006 0.017 -9999 0 -10000 0 0
PAK1 -0.006 0.042 -9999 0 -0.29 23 23
SPC24 -0.18 0.14 -9999 0 -0.29 654 654
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.006 0.019 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.005 0.013 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.024 -9999 0 -0.8 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.008 0.024 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.021 0.015 -9999 0 -10000 0 0
TPT1 0 0.014 -9999 0 -10000 0 0
CDC25C -0.009 0.016 -9999 0 -10000 0 0
CDC25B 0.001 0.041 -9999 0 -10000 0 0
SGOL1 -0.03 0.03 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.021 0.044 -9999 0 -10000 0 0
CDC14B -0.01 0.11 -9999 0 -0.63 34 34
CDC20 -0.16 0.15 -9999 0 -0.29 570 570
PLK1/PBIP1 -0.029 0.054 -9999 0 -0.18 4 4
mitosis -0.006 0.007 -9999 0 -0.022 2 2
FBXO5 0 0.022 -9999 0 -0.15 1 1
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.14 -9999 0 -0.29 648 648
metaphase plate congression -0.002 0.016 -9999 0 -10000 0 0
ERCC6L -0.064 0.089 -9999 0 -10000 0 0
NLP/gamma Tubulin -0.001 0.013 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0 0.014 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.1 -9999 0 -0.29 267 267
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.004 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.003 0.024 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.051 -9999 0 -0.3 28 28
microtubule-based process -0.12 0.068 -9999 0 -0.21 2 2
Golgi organization -0.008 0.024 -9999 0 -10000 0 0
Cohesin/SA2 -0.01 0.018 -9999 0 -0.46 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.29 797 797
APC/C/CDC20 -0.088 0.081 -9999 0 -0.18 204 204
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.029 0.053 -9999 0 -0.18 4 4
PRC1 -0.074 0.13 -9999 0 -0.29 269 269
ECT2 -0.004 0.039 -9999 0 -0.18 25 25
C13orf34 -0.001 0.022 -9999 0 -10000 0 0
NUDC -0.002 0.016 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.041 0.052 -9999 0 -10000 0 0
spindle assembly -0.004 0.02 -9999 0 -10000 0 0
spindle stabilization 0 0.014 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.094 -9999 0 -0.54 34 34
MKLP2/PLK1 -0.12 0.069 -9999 0 -0.21 2 2
CCNB1 -0.054 0.12 -9999 0 -0.29 215 215
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 -0.009 0.086 -9999 0 -0.51 29 29
TUBG1 0 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.041 -9999 0 -10000 0 0
MLF1IP -0.027 0.075 -9999 0 -10000 0 0
INCENP 0 0.002 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.053 0.28 38 -10000 0 38
RFC1 0.011 0.053 0.28 37 -10000 0 37
PRKDC 0.01 0.054 0.28 38 -10000 0 38
RIPK1 0 0.001 -10000 0 -10000 0 0
CASP7 -0.023 0.037 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.016 0.067 0.25 16 -0.38 16 32
MAP2K4 -0.058 0.16 -10000 0 -0.51 19 19
mol:ceramide -0.032 0.11 -10000 0 -0.55 19 19
GSN 0.004 0.076 0.28 37 -0.5 13 50
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.072 0.23 14 -0.46 16 30
FAS 0.004 0.05 -10000 0 -0.8 4 4
BID 0.001 0.011 0.32 1 -10000 0 1
MAP3K1 -0.021 0.094 -10000 0 -0.29 15 15
MAP3K7 0 0.009 -10000 0 -0.29 1 1
RB1 0.01 0.055 0.28 36 -0.41 2 38
CFLAR 0 0.001 -10000 0 -10000 0 0
HGF/MET -0.14 0.26 -10000 0 -0.59 243 243
ARHGDIB 0.01 0.054 0.28 37 -10000 0 37
FADD 0.003 0.039 -10000 0 -0.31 16 16
actin filament polymerization -0.004 0.076 0.49 13 -0.28 37 50
NFKB1 -0.076 0.1 -10000 0 -0.29 16 16
MAPK8 -0.12 0.24 -10000 0 -0.43 391 391
DFFA 0.011 0.053 0.28 38 -10000 0 38
DNA fragmentation during apoptosis 0.011 0.053 0.28 37 -10000 0 37
FAS/FADD/MET -0.095 0.21 -10000 0 -0.55 180 180
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.052 -10000 0 -0.31 26 26
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.011 0.053 0.28 38 -10000 0 38
DFFB 0.011 0.053 0.28 37 -10000 0 37
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.015 0.11 -10000 0 -0.42 55 55
FAS/FADD -0.005 0.047 -10000 0 -0.66 4 4
HGF -0.052 0.2 -10000 0 -0.78 70 70
LMNA 0.01 0.048 0.26 37 -10000 0 37
CASP6 0.011 0.053 0.28 38 -10000 0 38
CASP10 0.004 0.05 -10000 0 -0.81 4 4
CASP3 0.013 0.064 0.34 38 -10000 0 38
PTPN13 -0.024 0.14 -10000 0 -0.8 32 32
CASP8 0.003 0.02 0.45 1 -10000 0 1
IL6 -0.47 0.67 -10000 0 -1.4 388 388
MET -0.14 0.3 -10000 0 -0.8 179 179
ICAD/CAD 0.01 0.049 0.26 37 -10000 0 37
FASLG/FAS/FADD/FAF1/Caspase 10 -0.032 0.12 -10000 0 -0.56 19 19
activation of caspase activity by cytochrome c 0.001 0.011 0.32 1 -10000 0 1
PAK2 0.011 0.052 0.28 37 -10000 0 37
BCL2 -0.023 0.15 -10000 0 -0.79 37 37
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.8 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.077 0.61 1 -10000 0 1
CDKN1A -0.002 0.041 -10000 0 -0.94 2 2
KAT2B -0.001 0.024 -10000 0 -0.8 1 1
BAX -0.001 0.02 -10000 0 -0.29 5 5
FOXO3 -0.001 0.018 -10000 0 -0.33 3 3
FOXO1 -0.008 0.081 -10000 0 -0.8 11 11
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.56 0.36 -10000 0 -0.78 764 764
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.03 -10000 0 -0.61 1 1
PPARGC1A -0.17 0.32 -10000 0 -0.77 233 233
FHL2 -0.005 0.06 -10000 0 -0.8 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A -0.012 0.077 -10000 0 -0.61 1 1
SIRT1/FOXO3a 0 0.015 -10000 0 -0.25 3 3
SIRT1 0 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.017 -10000 0 -0.52 1 1
SIRT1/Histone H1b -0.003 0.012 -10000 0 -10000 0 0
apoptosis 0 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.22 -10000 0 -0.53 222 222
p53/SIRT1 0.001 0.019 0.43 2 -10000 0 2
SIRT1/FOXO4 0 0.007 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.061 -10000 0 -0.48 17 17
HIST1H1E -0.005 0.015 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.024 0.52 1 -10000 0 1
TP53 0 0.009 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0 0.012 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.43 0.27 -10000 0 -0.61 738 738
ACSS2 0.02 0.02 -10000 0 -0.61 1 1
SIRT1/PCAF/MYOD -0.002 0.024 -10000 0 -0.52 1 1
Glypican 2 network

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
MDK -0.011 0.056 -9999 0 -0.29 41 41
GPC2 -0.036 0.1 -9999 0 -0.3 125 125
GPC2/Midkine -0.03 0.08 -9999 0 -0.41 17 17
neuron projection morphogenesis -0.03 0.079 -9999 0 -0.41 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.009 0.054 -10000 0 -0.32 30 30
epithelial cell differentiation -0.012 0.073 -10000 0 -0.44 29 29
CYFIP2 -0.011 0.067 -10000 0 -0.36 32 32
ENAH 0.057 0.059 -10000 0 -10000 0 0
EGFR -0.3 0.38 -10000 0 -0.79 396 396
EPHA2 -0.005 0.06 -10000 0 -0.8 6 6
MYO6 -0.012 0.07 -10000 0 -0.42 30 30
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.039 -10000 0 -0.52 4 4
AQP5 -0.23 0.29 -10000 0 -0.59 416 416
CTNND1 0 0.009 -10000 0 -0.29 1 1
mol:PI-4-5-P2 -0.011 0.068 -10000 0 -0.41 29 29
regulation of calcium-dependent cell-cell adhesion -0.034 0.11 -10000 0 -0.42 84 84
EGF -0.15 0.31 -10000 0 -0.79 206 206
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.038 0.14 -10000 0 -0.58 57 57
cortical microtubule organization -0.012 0.073 -10000 0 -0.44 29 29
GO:0000145 0.026 0.071 -10000 0 -0.4 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.073 -10000 0 -0.45 29 29
MLLT4 -0.005 0.06 -10000 0 -0.72 7 7
ARF6/GDP -0.012 0.062 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -10000 0 -0.47 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.074 -10000 0 -0.39 29 29
PVRL2 -0.001 0.016 -10000 0 -0.29 3 3
ZYX -0.012 0.069 -10000 0 -0.42 29 29
ARF6/GTP -0.003 0.033 -10000 0 -0.44 6 6
CDH1 -0.022 0.13 -10000 0 -0.8 29 29
EGFR/EGFR/EGF/EGF -0.24 0.26 -10000 0 -0.47 544 544
RhoA/GDP -0.011 0.068 -10000 0 -0.42 29 29
actin cytoskeleton organization 0.032 0.073 -10000 0 -0.4 30 30
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.61 35 35
GIT1 -0.001 0.02 -10000 0 -0.29 5 5
IGF1R -0.02 0.12 -10000 0 -0.61 35 35
IGF1 -0.18 0.33 -10000 0 -0.8 236 236
DIAPH1 -0.002 0.044 -10000 0 -0.7 4 4
Wnt receptor signaling pathway 0.012 0.073 0.44 29 -10000 0 29
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.062 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.032 0.075 -10000 0 -0.41 30 30
EFNA1 0 0 -10000 0 -10000 0 0
LPP 0.03 0.081 -10000 0 -0.4 37 37
Ephrin A1/EPHA2 -0.013 0.072 -10000 0 -0.4 35 35
SEC6/SEC8 -0.012 0.068 -10000 0 -0.75 1 1
MGAT3 -0.034 0.12 -10000 0 -0.43 84 84
HGF/MET -0.11 0.2 -10000 0 -0.45 250 250
HGF -0.052 0.2 -10000 0 -0.78 70 70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.009 0.054 -10000 0 -0.33 30 30
actin cable formation 0.072 0.057 -10000 0 -0.32 1 1
KIAA1543 0.031 0.09 -10000 0 -0.46 30 30
KIFC3 -0.012 0.071 -10000 0 -0.42 31 31
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.012 0.07 -10000 0 -0.42 30 30
NCK1/GIT1 -0.001 0.013 -10000 0 -10000 0 0
mol:GDP -0.012 0.073 -10000 0 -0.44 29 29
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.012 0.069 -10000 0 -0.42 29 29
PIP5K1C -0.012 0.069 -10000 0 -0.42 29 29
LIMA1 -0.001 0.024 -10000 0 -0.8 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.011 0.055 -10000 0 -10000 0 0
adherens junction assembly 0.047 0.086 -10000 0 -0.63 7 7
IGF-1R heterotetramer/IGF1 -0.11 0.2 -10000 0 -0.44 269 269
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.047 -10000 0 -0.61 6 6
MET -0.14 0.3 -10000 0 -0.8 179 179
PLEKHA7 -0.013 0.079 -10000 0 -0.47 29 29
mol:GTP -0.003 0.036 -10000 0 -0.47 6 6
establishment of epithelial cell apical/basal polarity -0.012 0.064 -10000 0 -0.71 1 1
cortical actin cytoskeleton stabilization -0.009 0.054 -10000 0 -0.32 30 30
regulation of cell-cell adhesion 0.032 0.073 -10000 0 -0.4 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.009 0.054 -10000 0 -0.33 30 30
LPA4-mediated signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.001 0.1 -9999 0 -0.53 40 40
ADCY5 -0.16 0.26 -9999 0 -0.53 347 347
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.007 0.097 -9999 0 -0.53 27 27
ADCY2 -0.029 0.15 -9999 0 -0.53 82 82
ADCY3 0.02 0.005 -9999 0 -10000 0 0
ADCY8 0.009 0.028 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.031 0.1 -9999 0 -0.31 71 71
Effects of Botulinum toxin

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
STX1A 0.003 0.04 -9999 0 -0.2 40 40
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.047 0.13 -9999 0 -0.61 45 45
STXBP1 -0.005 0.06 -9999 0 -0.8 6 6
ACh/CHRNA1 -0.062 0.082 -9999 0 -0.22 34 34
RAB3GAP2/RIMS1/UNC13B -0.038 0.11 -9999 0 -0.52 45 45
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.067 0.18 -9999 0 -0.43 164 164
mol:ACh 0.001 0.031 -9999 0 -0.12 61 61
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.037 0.093 -9999 0 -0.39 51 51
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.082 -9999 0 -0.22 34 34
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.14 -9999 0 -0.29 361 361
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.06 0.12 -9999 0 -0.47 58 58
SNAP25 -0.016 0.068 -9999 0 -0.38 35 35
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.089 0.18 -9999 0 -0.38 250 250
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.009 0.049 -9999 0 -0.53 6 6
STX1A/SNAP25 fragment 1/VAMP2 -0.037 0.093 -9999 0 -0.39 51 51
Signaling events mediated by PRL

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
CCNE1 -0.059 0.12 -9999 0 -0.29 213 213
mol:Halofuginone 0 0.003 -9999 0 -10000 0 0
ITGA1 -0.008 0.077 -9999 0 -0.8 10 10
CDKN1A -0.057 0.088 -9999 0 -0.84 2 2
PRL-3/alpha Tubulin -0.002 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.096 -9999 0 -0.62 14 14
AGT -0.048 0.13 -9999 0 -0.34 149 149
CCNA2 -0.16 0.24 -9999 0 -0.56 178 178
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.17 0.29 -9999 0 -0.6 333 333
CDK2/Cyclin E1 -0.067 0.091 -9999 0 -0.65 3 3
MAPK3 0.02 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.008 -9999 0 -10000 0 0
MAPK1 0.02 0.02 -9999 0 -10000 0 0
PTP4A1 -0.12 0.23 -9999 0 -0.46 333 333
PTP4A3 -0.003 0.028 -9999 0 -0.29 10 10
PTP4A2 -0.001 0.013 -9999 0 -0.29 2 2
ITGB1 0.02 0.02 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1 -0.055 0.082 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.14 0.2 -9999 0 -0.59 2 2
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.055 0.082 -9999 0 -10000 0 0
RHOA -0.055 0.082 -9999 0 -10000 0 0
cell motility -0.034 0.1 -9999 0 -0.24 1 1
PRL-1/alpha Tubulin -0.14 0.2 -9999 0 -0.63 1 1
PRL-3/alpha1 Integrin -0.007 0.061 -9999 0 -0.61 10 10
ROCK1 -0.034 0.1 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.23 -9999 0 -0.46 333 333
ATF5 -0.001 0.018 -9999 0 -0.29 4 4
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.047 -9999 0 -0.62 5 5
PDGFRB 0.005 0.05 -9999 0 -0.8 4 4
SPHK1 -0.025 0.055 -9999 0 -1.1 2 2
mol:S1P -0.031 0.058 -9999 0 -0.97 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.59 93 93
GNAO1 -0.023 0.14 -9999 0 -0.59 45 45
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.59 71 71
PLCG1 -0.089 0.22 -9999 0 -0.62 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.05 -9999 0 -0.8 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.008 0.006 -9999 0 -10000 0 0
GNAI1 -0.036 0.18 -9999 0 -0.81 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.044 -9999 0 -0.55 5 5
S1P1/S1P -0.044 0.075 -9999 0 -0.62 7 7
negative regulation of cAMP metabolic process -0.097 0.22 -9999 0 -0.57 93 93
MAPK3 -0.16 0.31 -9999 0 -0.57 357 357
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.004 0.055 -9999 0 -0.8 5 5
PLCB2 -0.008 0.086 -9999 0 -0.53 8 8
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.061 -9999 0 -0.5 7 7
receptor internalization -0.042 0.07 -9999 0 -0.56 7 7
PTGS2 -0.33 0.55 -9999 0 -1.1 356 356
Rac1/GTP -0.037 0.061 -9999 0 -0.5 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
negative regulation of T cell proliferation -0.097 0.22 -9999 0 -0.57 93 93
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.075 -9999 0 -0.8 9 9
MAPK1 -0.16 0.31 -9999 0 -0.57 357 357
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.11 -9999 0 -0.67 9 9
ABCC1 0 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.001 0.017 -10000 0 -0.29 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.034 0.13 0.41 50 -10000 0 50
IL27/IL27R/JAK1 -0.072 0.18 -10000 0 -0.59 71 71
TBX21 -0.043 0.21 -10000 0 -0.59 87 87
IL12B -0.055 0.12 -10000 0 -0.3 92 92
IL12A -0.029 0.14 -10000 0 -0.62 59 59
IL6ST -0.089 0.26 -10000 0 -0.8 129 129
IL27RA/JAK1 -0.007 0.062 -10000 0 -1.1 3 3
IL27 -0.024 0.094 -10000 0 -0.29 115 115
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.034 0.13 0.41 50 -10000 0 50
T cell proliferation during immune response 0.034 0.13 0.41 50 -10000 0 50
MAPKKK cascade -0.034 0.13 -10000 0 -0.41 50 50
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.04 -10000 0 -0.3 3 3
IL12RB1 -0.006 0.068 -10000 0 -0.32 43 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.23 -10000 0 -0.61 102 102
IL27/IL27R/JAK2/TYK2 -0.034 0.13 -10000 0 -0.41 49 49
positive regulation of T cell mediated cytotoxicity -0.034 0.13 -10000 0 -0.41 50 50
STAT1 (dimer) -0.092 0.22 0.46 20 -0.72 61 81
JAK2 0.004 0.026 -10000 0 -0.8 1 1
JAK1 0 0.025 -10000 0 -0.79 1 1
STAT2 (dimer) -0.043 0.11 -10000 0 -0.45 22 22
T cell proliferation -0.18 0.25 -10000 0 -0.47 408 408
IL12/IL12R/TYK2/JAK2 0.011 0.071 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -10000 0 0
mast cell activation 0.034 0.13 0.41 50 -10000 0 50
IFNG -0.001 0.025 -10000 0 -0.084 3 3
T cell differentiation -0.004 0.006 -10000 0 -0.02 15 15
STAT3 (dimer) -0.043 0.11 -10000 0 -0.44 24 24
STAT5A (dimer) -0.046 0.12 -10000 0 -0.44 37 37
STAT4 (dimer) -0.062 0.15 -10000 0 -0.49 67 67
STAT4 -0.034 0.16 -10000 0 -0.8 45 45
T cell activation -0.009 0.008 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 -0.06 0.16 -10000 0 -0.55 47 47
GATA3 -0.04 0.28 -10000 0 -1.4 39 39
IL18 0.007 0.03 -10000 0 -0.2 23 23
positive regulation of mast cell cytokine production -0.043 0.11 -10000 0 -0.43 25 25
IL27/EBI3 -0.026 0.083 -10000 0 -0.54 13 13
IL27RA 0 0.066 -10000 0 -1.4 2 2
IL6 -0.29 0.38 -10000 0 -0.79 388 388
STAT5A -0.006 0.069 -10000 0 -0.8 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.004 0.026 0.48 2 -10000 0 2
IL1B 0.001 0.075 -10000 0 -0.62 15 15
EBI3 -0.004 0.076 -10000 0 -0.51 19 19
TNF -0.001 0.073 -10000 0 -0.62 12 12
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.051 -10000 0 -0.53 9 9
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.004 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.07 0.22 -10000 0 -0.8 93 93
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
TLE1 -0.005 0.069 -10000 0 -0.8 8 8
AP1 -0.11 0.17 -10000 0 -0.37 316 316
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.002 0.042 -10000 0 -0.8 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.045 -10000 0 -10000 0 0
NICD/RBPSUH -0.002 0.038 -10000 0 -0.7 3 3
WIF1 -0.42 0.39 -10000 0 -0.78 569 569
NOTCH1 -0.002 0.04 -10000 0 -0.75 3 3
PSENEN 0 0.009 -10000 0 -0.29 1 1
KREMEN2 -0.14 0.15 -10000 0 -10000 0 0
DKK1 -0.079 0.19 -10000 0 -0.42 198 198
beta catenin/beta TrCP1 -0.009 0.025 0.22 2 -10000 0 2
APH1B -0.001 0.024 -10000 0 -0.8 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.014 -10000 0 -0.22 1 1
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.33 8 8
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.36 -10000 0 -0.8 313 313
JUN -0.005 0.064 -10000 0 -0.8 7 7
MAP3K7 0.001 0.01 -10000 0 -0.3 1 1
CTNNB1 -0.003 0.035 0.23 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.083 0.11 -10000 0 -0.61 29 29
HNF1A -0.001 0.024 -10000 0 -0.29 7 7
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.032 0.22 -10000 0 -1.5 23 23
NKD1 -0.009 0.07 -10000 0 -0.42 23 23
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.04 0.13 -10000 0 -0.44 96 96
apoptosis -0.11 0.17 -10000 0 -0.37 316 316
Delta 1/NOTCHprecursor -0.005 0.05 -10000 0 -0.53 9 9
DLL1 -0.005 0.06 -10000 0 -0.8 6 6
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.44 1 1
APC 0.003 0.014 -10000 0 -10000 0 0
DVL1 -0.038 0.036 -10000 0 -10000 0 0
CSNK2A1 0.011 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 53 53
LRP6 -0.001 0.013 -10000 0 -0.29 2 2
CSNK1A1 0.011 0.003 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.013 0.11 -10000 0 -1.5 5 5
WNT1 -0.001 0.013 -10000 0 -0.29 2 2
Axin1/APC/beta catenin 0.011 0.037 -10000 0 -10000 0 0
DKK2 -0.022 0.13 -10000 0 -0.76 31 31
NOTCH1 precursor/DVL1 -0.019 0.038 -10000 0 -0.65 3 3
GSK3B 0.001 0.003 -10000 0 -10000 0 0
FRAT1 0.001 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.04 0.13 -10000 0 -0.45 96 96
PPP2R5D -0.015 0.038 0.35 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.25 0.24 -10000 0 -0.48 555 555
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.048 -10000 0 -0.42 10 10
adherens junction organization 0.032 0.064 -10000 0 -0.3 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.56 20 20
FMN1 0.023 0.092 -10000 0 -0.45 24 24
mol:IP3 -0.008 0.046 -10000 0 -0.39 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.053 -10000 0 -0.32 30 30
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.009 0.048 -10000 0 -0.38 10 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.082 -10000 0 -0.5 29 29
CTNND1 0.011 0.01 -10000 0 -0.29 1 1
mol:PI-4-5-P2 0.033 0.057 -10000 0 -10000 0 0
VASP 0.033 0.057 -10000 0 -10000 0 0
ZYX 0.033 0.057 -10000 0 -10000 0 0
JUB 0.031 0.064 -10000 0 -0.42 4 4
EGFR(dimer) -0.16 0.21 -10000 0 -0.43 392 392
E-cadherin/beta catenin-gamma catenin -0.014 0.084 -10000 0 -0.51 30 30
mol:PI-3-4-5-P3 -0.01 0.052 -10000 0 -0.41 10 10
PIK3CA 0 0.009 -10000 0 -10000 0 0
PI3K -0.01 0.053 -10000 0 -0.42 10 10
FYN 0.041 0.052 -10000 0 -0.38 2 2
mol:Ca2+ -0.008 0.045 -10000 0 -0.38 10 10
JUP 0 0.026 -10000 0 -0.54 2 2
PIK3R1 -0.007 0.077 -10000 0 -0.79 10 10
mol:DAG -0.008 0.046 -10000 0 -0.39 10 10
CDH1 -0.022 0.13 -10000 0 -0.79 29 29
RhoA/GDP -0.14 0.18 -10000 0 -0.56 20 20
establishment of polarity of embryonic epithelium 0.033 0.057 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.3 0.38 -10000 0 -0.79 396 396
CASR 0.009 0.052 -10000 0 -0.36 10 10
RhoA/GTP -0.007 0.041 -10000 0 -0.35 10 10
AKT2 -0.009 0.048 -10000 0 -0.38 10 10
actin cable formation 0.03 0.09 -10000 0 -0.43 24 24
apoptosis 0.009 0.049 0.4 10 -10000 0 10
CTNNA1 0.012 0.002 -10000 0 -10000 0 0
mol:GDP -0.15 0.2 -10000 0 -0.4 398 398
PIP5K1A 0.033 0.057 -10000 0 -10000 0 0
PLCG1 -0.009 0.047 -10000 0 -0.4 10 10
Rac1/GTP -0.15 0.19 -10000 0 -0.39 392 392
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.036 0.12 -10000 0 -0.59 41 41
FYN 0.015 0.18 -10000 0 -0.71 47 47
LAT/GRAP2/SLP76 -0.03 0.15 -10000 0 -0.64 44 44
IKBKB -0.001 0.013 -10000 0 -10000 0 0
AKT1 0.029 0.12 -10000 0 -0.46 45 45
B2M 0.011 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.14 14 14
MAP3K8 -0.007 0.074 -10000 0 -0.74 10 10
mol:Ca2+ -0.024 0.047 -10000 0 -0.12 206 206
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.53 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.02 0.18 -10000 0 -0.68 48 48
TRPV6 -0.16 0.32 -10000 0 -0.77 219 219
CD28 -0.006 0.075 -10000 0 -0.52 18 18
SHC1 0.009 0.18 -10000 0 -0.76 44 44
receptor internalization -0.003 0.2 -10000 0 -0.64 72 72
PRF1 -0.002 0.23 -10000 0 -1 39 39
KRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2 0 0.009 -10000 0 -0.29 1 1
COT/AKT1 0.03 0.1 -10000 0 -0.37 48 48
LAT 0.007 0.19 -10000 0 -0.74 48 48
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.024 0.14 -10000 0 -0.49 75 75
CD3E -0.018 0.14 -10000 0 -0.8 25 25
CD3G -0.035 0.17 -10000 0 -0.56 81 81
RASGRP2 0.003 0.042 -10000 0 -0.18 45 45
RASGRP1 0.035 0.13 -10000 0 -0.47 45 45
HLA-A 0.009 0.027 -10000 0 -0.29 8 8
RASSF5 -0.003 0.043 -10000 0 -0.67 4 4
RAP1A/GTP/RAPL -0.002 0.029 -10000 0 -0.53 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.043 -10000 0 -0.12 39 39
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.048 -10000 0 -0.23 33 33
PRKCA -0.013 0.085 -10000 0 -0.31 58 58
GRAP2 -0.015 0.11 -10000 0 -0.8 19 19
mol:IP3 0.018 0.15 0.27 176 -0.44 44 220
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.21 -10000 0 -0.83 46 46
ORAI1 0.078 0.15 0.38 205 -10000 0 205
CSK 0.007 0.19 -10000 0 -0.76 45 45
B7 family/CD28 -0.027 0.18 -10000 0 -0.66 59 59
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.004 0.22 -10000 0 -0.75 63 63
PTPN6 0.006 0.19 -10000 0 -0.76 45 45
VAV1 0.008 0.19 -10000 0 -0.75 46 46
Monovalent TCR/CD3 -0.025 0.21 -10000 0 -0.68 68 68
CBL 0 0 -10000 0 -10000 0 0
LCK 0.008 0.19 -10000 0 -0.76 48 48
PAG1 0.007 0.19 -10000 0 -0.77 45 45
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.003 0.22 -10000 0 -0.76 59 59
CD80 -0.078 0.13 -10000 0 -0.29 284 284
CD86 0.001 0.023 -10000 0 -0.29 6 6
PDK1/CARD11/BCL10/MALT1 -0.018 0.058 -10000 0 -0.28 35 35
HRAS -0.002 0.027 -10000 0 -0.29 9 9
GO:0035030 -0.003 0.15 -10000 0 -0.54 59 59
CD8A -0.001 0.079 -10000 0 -0.38 35 35
CD8B -0.023 0.15 -10000 0 -0.55 66 66
PTPRC -0.002 0.076 -10000 0 -0.51 19 19
PDK1/PKC theta 0.032 0.16 -10000 0 -0.58 49 49
CSK/PAG1 0.012 0.18 -10000 0 -0.75 43 43
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.036 0.17 -10000 0 -0.74 47 47
STIM1 0.041 0.078 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.055 -10000 0 -0.17 33 33
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.007 0.22 -10000 0 -0.7 72 72
mol:DAG -0.008 0.1 -10000 0 -0.4 44 44
RAP1A/GDP 0.015 0.019 -10000 0 -0.063 6 6
PLCG1 0 0.002 -10000 0 -10000 0 0
CD247 -0.012 0.12 -10000 0 -0.8 21 21
cytotoxic T cell degranulation 0.001 0.21 -10000 0 -0.94 40 40
RAP1A/GTP -0.003 0.013 -10000 0 -0.068 28 28
mol:PI-3-4-5-P3 0.025 0.14 -10000 0 -0.54 48 48
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.011 0.18 0.29 166 -0.6 44 210
NRAS -0.001 0.013 -10000 0 -10000 0 0
ZAP70 -0.031 0.12 -10000 0 -0.42 76 76
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.027 0.14 -10000 0 -0.62 44 44
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.033 0.14 -10000 0 -0.57 54 54
CARD11 -0.007 0.053 -10000 0 -0.34 22 22
PRKCB -0.012 0.086 -10000 0 -0.33 49 49
PRKCE -0.007 0.069 -10000 0 -0.29 37 37
PRKCQ 0.022 0.18 -10000 0 -0.68 50 50
LCP2 0 0.009 -10000 0 -0.29 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.031 0.11 -10000 0 -0.39 45 45
IKK complex 0.041 0.045 -10000 0 -0.12 26 26
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.035 0.082 -10000 0 -0.29 39 39
PDPK1 0.032 0.12 -10000 0 -0.43 45 45
TCR/CD3/MHC I/CD8/Fyn -0.007 0.23 -10000 0 -0.92 51 51
Regulation 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
HDAC1 0.021 0.003 -9999 0 -10000 0 0
SMARCC1 0.005 0.02 -9999 0 -0.56 1 1
REL -0.006 0.089 -9999 0 -0.8 13 13
HDAC7 0.01 0.13 -9999 0 -0.58 16 16
JUN -0.001 0.065 -9999 0 -0.8 7 7
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.8 1 1
KAT5 0.002 0.005 -9999 0 -10000 0 0
MAPK14 0.007 0.092 -9999 0 -0.62 22 22
FOXO1 -0.008 0.081 -9999 0 -0.8 11 11
T-DHT/AR -0.003 0.14 -9999 0 -0.52 31 31
MAP2K6 -0.009 0.12 -9999 0 -0.78 23 23
BRM/BAF57 -0.001 0.011 -9999 0 -10000 0 0
MAP2K4 0.008 0.026 -9999 0 -0.8 1 1
SMARCA2 0 0.001 -9999 0 -10000 0 0
PDE9A -0.087 0.28 -9999 0 -1.2 60 60
NCOA2 -0.035 0.17 -9999 0 -0.8 48 48
CEBPA -0.005 0.073 -9999 0 -0.79 9 9
EHMT2 0.004 0.006 -9999 0 -10000 0 0
cell proliferation 0.015 0.14 -9999 0 -0.5 24 24
NR0B1 -0.01 0.058 -9999 0 -0.31 36 36
EGR1 -0.25 0.37 -9999 0 -0.8 333 333
RXRs/9cRA -0.12 0.21 -9999 0 -0.48 260 260
AR/RACK1/Src -0.003 0.11 -9999 0 -0.48 30 30
AR/GR -0.053 0.13 -9999 0 -0.33 149 149
GNB2L1 0.001 0.004 -9999 0 -10000 0 0
PKN1 0 0.009 -9999 0 -0.29 1 1
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.015 0.06 -9999 0 -0.61 9 9
T-DHT/AR/TIF2/CARM1 -0.015 0.15 -9999 0 -0.51 70 70
SRC 0.022 0.091 -9999 0 -0.47 30 30
NR3C1 -0.011 0.094 -9999 0 -0.8 15 15
KLK3 -0.21 0.42 -9999 0 -1.2 144 144
APPBP2 0.005 0.017 -9999 0 -0.29 3 3
TRIM24 0.004 0.011 -9999 0 -0.29 1 1
T-DHT/AR/TIP60 -0.026 0.096 -9999 0 -0.52 30 30
TMPRSS2 -0.17 0.42 -9999 0 -1.2 136 136
RXRG -0.2 0.34 -9999 0 -0.79 263 263
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.001 0.004 -9999 0 -10000 0 0
NR2C2 -0.008 0.077 -9999 0 -0.8 10 10
KLK2 -0.041 0.24 -9999 0 -0.76 92 92
AR -0.026 0.14 -9999 0 -0.34 159 159
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
MDM2 0.004 0.024 -9999 0 -0.29 5 5
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.025 0.13 -9999 0 -0.63 42 42
MYST2 0.001 0.01 -9999 0 -0.29 1 1
HOXB13 -0.14 0.15 -9999 0 -0.3 487 487
T-DHT/AR/RACK1/Src -0.013 0.1 -9999 0 -0.5 30 30
positive regulation of transcription -0.025 0.13 -9999 0 -0.63 42 42
DNAJA1 0.006 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.012 0.026 -9999 0 -0.82 1 1
SPDEF -0.059 0.21 -9999 0 -0.64 106 106
T-DHT/AR/TIF2 0.013 0.099 -9999 0 -0.47 21 21
T-DHT/AR/Hsp90 -0.033 0.092 -9999 0 -0.52 30 30
GSK3B 0.008 0.006 -9999 0 -10000 0 0
NR2C1 0.003 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.015 0.096 -9999 0 -0.5 30 30
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.006 0.013 -9999 0 -10000 0 0
POU2F1 0.021 0.026 -9999 0 -0.42 1 1
T-DHT/AR/DAX-1 -0.035 0.097 -9999 0 -0.52 31 31
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.016 -9999 0 -0.3 3 3
Coregulation of Androgen receptor activity

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
NRIP1 -0.003 0.033 -10000 0 -0.79 1 1
SVIL -0.004 0.052 -10000 0 -0.79 4 4
ZNF318 0.023 0.057 -10000 0 -10000 0 0
JMJD2C -0.003 0.041 -10000 0 -0.14 77 77
T-DHT/AR/Ubc9 -0.079 0.18 -10000 0 -0.54 137 137
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.002 0.012 -10000 0 -10000 0 0
PELP1 0.005 0.013 -10000 0 -10000 0 0
CTNNB1 0 0.015 -10000 0 -10000 0 0
AKT1 0.007 0.019 -10000 0 -10000 0 0
PTK2B 0.001 0.013 -10000 0 -10000 0 0
MED1 0.002 0.048 -10000 0 -0.29 20 20
MAK 0.012 0.1 0.26 1 -0.56 20 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.063 -10000 0 -0.79 6 6
GSN -0.012 0.09 -10000 0 -0.79 13 13
NCOA2 -0.036 0.16 -10000 0 -0.8 48 48
NCOA6 -0.001 0.021 -10000 0 -0.29 1 1
DNA-PK 0.022 0.058 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0 0.015 -10000 0 -10000 0 0
cell proliferation -0.007 0.11 -10000 0 -0.88 11 11
XRCC5 0.006 0.016 -10000 0 -10000 0 0
UBE3A -0.005 0.031 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.092 0.21 -10000 0 -0.58 151 151
FHL2 -0.018 0.12 -10000 0 -1.3 6 6
RANBP9 -0.001 0.019 -10000 0 -10000 0 0
JMJD1A -0.01 0.055 -10000 0 -0.14 146 146
CDK6 -0.007 0.086 -10000 0 -0.8 12 12
TGFB1I1 -0.004 0.053 -10000 0 -0.8 4 4
T-DHT/AR/CyclinD1 -0.092 0.19 -10000 0 -0.55 142 142
XRCC6 0.006 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.065 0.21 -10000 0 -0.53 154 154
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0.015 0.039 -10000 0 -10000 0 0
BRCA1 -0.002 0.035 -10000 0 -0.49 3 3
TCF4 0.004 0.083 -10000 0 -0.79 10 10
CDKN2A -0.042 0.11 -10000 0 -0.29 156 156
SRF 0.024 0.019 -10000 0 -10000 0 0
NKX3-1 -0.079 0.19 -10000 0 -1.3 18 18
KLK3 -0.18 0.51 -10000 0 -1.5 127 127
TMF1 0 0 -10000 0 -10000 0 0
HNRNPA1 0.009 0.022 -10000 0 -10000 0 0
AOF2 -0.008 0.024 -10000 0 -0.072 127 127
APPL1 0.034 0.033 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.072 0.19 -10000 0 -0.54 137 137
AR -0.099 0.27 -10000 0 -0.8 137 137
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.009 0.022 -10000 0 -10000 0 0
PAWR -0.001 0.024 -10000 0 -0.8 1 1
PRKDC 0.005 0.024 -10000 0 -0.29 4 4
PA2G4 0.011 0.028 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.067 0.17 -10000 0 -0.5 136 136
RPS6KA3 -0.008 0.072 -10000 0 -0.79 8 8
T-DHT/AR/ARA70 -0.083 0.18 -10000 0 -0.55 136 136
LATS2 0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.062 0.18 -10000 0 -0.5 136 136
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.01 0.077 -10000 0 -0.43 26 26
KLK2 -0.12 0.32 -10000 0 -1.2 77 77
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.096 0.2 -10000 0 -0.54 168 168
TMPRSS2 -0.18 0.39 -10000 0 -1.2 137 137
CCND1 -0.016 0.078 -10000 0 -0.35 44 44
PIAS1 -0.005 0.031 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.033 -10000 0 -0.078 176 176
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.011 0.049 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.082 0.19 -10000 0 -0.55 147 147
CMTM2 0.003 0.013 -10000 0 -0.29 1 1
SNURF -0.02 0.12 -10000 0 -0.8 26 26
ZMIZ1 0.004 0.03 -10000 0 -0.36 1 1
CCND3 0.002 0.011 -10000 0 -0.29 1 1
TGIF1 0.009 0.022 -10000 0 -10000 0 0
FKBP4 -0.003 0.033 -10000 0 -0.3 9 9
Osteopontin-mediated events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.038 0.086 -9999 0 -0.44 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.024 0.07 -9999 0 -0.44 9 9
alphaV/beta3 Integrin/Osteopontin/Src -0.047 0.077 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.57 121 121
ILK -0.008 0.11 -9999 0 -0.47 37 37
bone resorption -0.038 0.11 -9999 0 -0.68 19 19
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.004 0.091 -9999 0 -0.42 37 37
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.017 0.099 -9999 0 -0.61 29 29
alphaV/beta3 Integrin/Osteopontin -0.052 0.11 -9999 0 -0.53 37 37
MAP3K1 -0.009 0.12 -9999 0 -0.49 37 37
JUN -0.005 0.064 -9999 0 -0.79 7 7
MAPK3 0.007 0.11 -9999 0 -0.44 37 37
MAPK1 0.007 0.11 -9999 0 -0.44 37 37
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.001 0.13 -9999 0 -0.53 39 39
ITGB3 -0.029 0.14 -9999 0 -0.79 37 37
NFKBIA 0.021 0.1 -9999 0 -0.42 37 37
FOS -0.24 0.36 -9999 0 -0.79 313 313
CD44 -0.001 0.016 -9999 0 -0.29 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.019 0.1 -9999 0 -0.48 6 6
NF kappa B1 p50/RelA -0.023 0.067 -9999 0 -0.45 6 6
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.01 0.11 -9999 0 -0.48 37 37
VAV3 -0.004 0.11 -9999 0 -0.45 44 44
MAP3K14 -0.006 0.11 -9999 0 -0.48 37 37
ROCK2 -0.022 0.13 -9999 0 -0.8 29 29
SPP1 -0.077 0.13 -9999 0 -0.28 286 286
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.037 0.085 -9999 0 -0.41 44 44
MMP2 -0.075 0.21 -9999 0 -0.68 37 37
Insulin 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
CBL/APS/CAP -0.13 0.22 -9999 0 -0.47 284 284
TC10/GTP -0.11 0.18 -9999 0 -0.41 269 269
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.097 -9999 0 -0.49 43 43
HRAS -0.002 0.027 -9999 0 -0.29 9 9
APS homodimer -0.014 0.061 -9999 0 -0.29 49 49
GRB14 -0.1 0.22 -9999 0 -0.8 81 81
FOXO3 -0.014 0.066 -9999 0 -0.68 9 9
AKT1 -0.056 0.12 -9999 0 -0.52 11 11
INSR 0 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insulin -0.003 0.026 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.2 0.35 -9999 0 -0.8 269 269
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.12 0.22 -9999 0 -0.51 246 246
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.45 269 269
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.097 -9999 0 -0.49 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.094 -9999 0 -0.43 53 53
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.008 0.13 -9999 0 -0.46 11 11
PARD6A -0.002 0.024 -9999 0 -0.29 7 7
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.049 0.11 -9999 0 -0.48 11 11
HRAS/GTP -0.016 0.073 -9999 0 -0.47 2 2
Insulin Receptor 0 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.09 -9999 0 -0.46 43 43
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.062 0.14 -9999 0 -0.42 90 90
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.003 -9999 0 -10000 0 0
PI3K -0.022 0.095 -9999 0 -0.44 53 53
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
AKT2 -0.056 0.12 -9999 0 -0.52 11 11
PRKCZ -0.014 0.036 -9999 0 -0.6 1 1
SH2B2 -0.014 0.061 -9999 0 -0.29 49 49
SHC/SHIP -0.018 0.085 -9999 0 -0.43 43 43
F2RL2 -0.06 0.15 -9999 0 -0.35 181 181
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.13 0.21 -9999 0 -0.48 269 269
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D -0.019 0.091 -9999 0 -0.46 43 43
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.009 0.074 -9999 0 -0.98 6 6
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.8 43 43
p62DOK/RasGAP 0 0.003 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.09 -9999 0 -0.46 43 43
GRB2 0 0.009 -9999 0 -0.29 1 1
EIF4EBP1 -0.013 0.14 -9999 0 -0.46 23 23
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.064 -9999 0 -0.32 43 43
Insulin Receptor/Insulin/IRS1 -0.021 0.099 -9999 0 -0.5 43 43
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.027 0.074 -9999 0 -0.46 22 22
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.005 0.13 -10000 0 -0.4 52 52
TBX21 -0.014 0.34 -10000 0 -1.3 55 55
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.004 0.073 -10000 0 -0.33 43 43
GADD45B 0.032 0.22 -10000 0 -0.88 27 27
IL12RB2 -0.058 0.19 -10000 0 -0.43 180 180
GADD45G 0.022 0.22 -10000 0 -0.93 24 24
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.003 0.028 -10000 0 -0.29 10 10
RELA 0 0 -10000 0 -10000 0 0
IL18 0.008 0.045 -10000 0 -0.29 23 23
IL2RA -0.03 0.12 -10000 0 -0.38 81 81
IFNG -0.041 0.1 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.22 -10000 0 -0.71 45 45
HLA-DRB5 -0.018 0.097 -10000 0 -0.33 84 84
FASLG 0.002 0.29 -10000 0 -1.1 44 44
NF kappa B2 p52/RelB -0.079 0.2 -10000 0 -0.85 47 47
CD4 0.008 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.042 -10000 0 -0.32 16 16
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.027 0.14 -10000 0 -0.5 75 75
CD3E -0.021 0.13 -10000 0 -0.78 26 26
CD3G -0.035 0.17 -10000 0 -0.57 81 81
IL12Rbeta2/JAK2 -0.027 0.15 -10000 0 -0.62 50 50
CCL3 0.012 0.26 -10000 0 -1 38 38
CCL4 0.014 0.26 -10000 0 -0.95 38 38
HLA-A 0.009 0.028 -10000 0 -0.3 8 8
IL18/IL18R 0.02 0.14 -10000 0 -0.54 55 55
NOS2 0.018 0.25 -10000 0 -0.94 40 40
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.13 -10000 0 -0.42 41 41
IL1R1 0.002 0.3 -10000 0 -1.2 44 44
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.03 -10000 0 -0.82 1 1
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.032 0.25 -10000 0 -1 48 48
RAB7A 0.046 0.19 -10000 0 -0.75 24 24
lysosomal transport 0.047 0.19 -10000 0 -0.7 25 25
FOS -0.35 0.66 -10000 0 -1.3 328 328
STAT4 (dimer) 0.02 0.26 -10000 0 -0.88 54 54
STAT5A (dimer) -0.086 0.22 -10000 0 -0.82 54 54
GZMA 0.002 0.28 -10000 0 -1.1 39 39
GZMB -0.011 0.31 -10000 0 -1.2 49 49
HLX -0.001 0.016 -10000 0 -10000 0 0
LCK 0.003 0.29 -10000 0 -0.92 58 58
TCR/CD3/MHC II/CD4 -0.065 0.2 -10000 0 -0.54 89 89
IL2/IL2R -0.03 0.1 -10000 0 -0.48 40 40
MAPK14 0.035 0.22 -10000 0 -0.86 32 32
CCR5 0.025 0.22 -10000 0 -0.86 34 34
IL1B 0.004 0.1 -10000 0 -0.81 15 15
STAT6 0.025 0.087 -10000 0 -0.25 12 12
STAT4 -0.034 0.16 -10000 0 -0.8 45 45
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.039 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -0.29 1 1
IL12B -0.047 0.12 -10000 0 -0.31 82 82
CD8A -0.002 0.079 -10000 0 -0.39 35 35
CD8B -0.023 0.15 -10000 0 -0.55 66 66
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.005 0.13 0.4 52 -10000 0 52
IL2RB -0.012 0.065 -10000 0 -0.32 41 41
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.24 -10000 0 -0.78 54 54
IL2RG -0.018 0.087 -10000 0 -0.8 7 7
IL12 -0.054 0.16 -10000 0 -0.6 65 65
STAT5A -0.006 0.069 -10000 0 -0.8 8 8
CD247 -0.012 0.12 -10000 0 -0.69 27 27
IL2 -0.002 0.025 -10000 0 -0.29 8 8
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.034 0.19 -10000 0 -0.75 66 66
IL12/IL12R/TYK2/JAK2 0.007 0.29 -10000 0 -0.86 65 65
MAP2K3 0.031 0.22 -10000 0 -0.85 34 34
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
MAP2K6 0.027 0.23 -10000 0 -0.86 35 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.027 -10000 0 -0.54 2 2
IL18RAP -0.016 0.15 -10000 0 -0.74 43 43
IL12Rbeta1/TYK2 0.013 0.056 -10000 0 -0.64 2 2
EOMES -0.022 0.18 -10000 0 -1.5 15 15
STAT1 (dimer) 0.028 0.22 -10000 0 -0.76 33 33
T cell proliferation 0.031 0.2 -10000 0 -0.66 46 46
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.11 -10000 0 -0.8 18 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.17 -10000 0 -0.75 45 45
ATF2 0.042 0.21 -10000 0 -0.79 31 31
Regulation of Telomerase

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
Telomerase catalytic core complex -0.054 0.12 -9999 0 -0.59 5 5
RAD9A 0 0.009 -9999 0 -0.29 1 1
AP1 -0.18 0.28 -9999 0 -0.62 314 314
IFNAR2 0.011 0.005 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.28 162 162
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.44 274 274
NFX1/SIN3/HDAC complex 0.013 0.023 -9999 0 -10000 0 0
EGF -0.15 0.32 -9999 0 -0.79 206 206
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.066 0.089 -9999 0 -0.58 4 4
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.15 -9999 0 -0.29 538 538
WRN 0 0 -9999 0 -10000 0 0
SP1 0.011 0.005 -9999 0 -10000 0 0
SP3 0.009 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.078 -9999 0 -0.59 2 2
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.055 0.12 -9999 0 -0.64 4 4
CCND1 -0.048 0.14 -9999 0 -1.3 5 5
MAX 0.009 0.005 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.29 8 8
RBBP4 -0.001 0.024 -9999 0 -0.8 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 0.011 0.024 -9999 0 -10000 0 0
CDKN1B 0.009 0.075 -9999 0 -0.87 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.009 0.005 -9999 0 -10000 0 0
JUN 0.001 0.065 -9999 0 -0.8 7 7
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.23 0.37 -9999 0 -0.8 313 313
IFN-gamma/IRF1 -0.025 0.063 -9999 0 -0.36 3 3
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.031 0.09 -9999 0 -0.29 112 112
Telomerase -0.005 0.028 -9999 0 -10000 0 0
IRF1 0.011 0.021 -9999 0 -0.28 2 2
ESR1 -0.16 0.29 -9999 0 -0.58 286 286
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.007 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.011 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.008 0.011 -9999 0 -0.29 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.016 -9999 0 -0.29 3 3
TERT/NF kappa B1/14-3-3 -0.066 0.1 -9999 0 -0.67 3 3
NR2F2 0.001 0.043 -9999 0 -0.8 3 3
MAPK3 0.014 0.019 -9999 0 -10000 0 0
MAPK1 0.014 0.019 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.016 -9999 0 -0.29 3 3
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.38 -9999 0 -0.79 396 396
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.34 0.35 -9999 0 -0.66 533 533
MYC -0.008 0.12 -9999 0 -0.79 23 23
IL2 0.004 0.027 -9999 0 -0.29 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
TGFB1 0 0.016 -9999 0 -0.29 3 3
TRF2/BLM -0.018 0.051 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.063 0.087 -9999 0 -0.58 4 4
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.052 0.078 -9999 0 -0.59 2 2
Smad3/Myc -0.012 0.077 -9999 0 -0.52 23 23
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.03 0.1 -9999 0 -10000 0 0
Telomerase/PinX1 -0.052 0.078 -9999 0 -0.59 2 2
Telomerase/AKT1/mTOR/p70S6K 0.002 0.055 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.052 0.078 -9999 0 -0.59 2 2
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.052 0.078 -9999 0 -0.59 2 2
E2F1 -0.085 0.14 -9999 0 -0.3 97 97
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.059 0.12 -9999 0 -0.29 213 213
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.002 0.036 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.025 0.036 -9999 0 -0.64 1 1
positive regulation of JNK cascade -0.051 0.1 -9999 0 -0.46 7 7
Syndecan-4/ADAM12 -0.033 0.054 -9999 0 -0.54 2 2
CCL5 -0.015 0.08 -9999 0 -0.8 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0.009 -9999 0 -0.29 1 1
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.026 -9999 0 -0.3 2 2
ADAM12 -0.019 0.078 -9999 0 -0.31 67 67
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.002 0.022 -9999 0 -0.29 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.055 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.073 0.13 -9999 0 -0.57 6 6
Syndecan-4/CXCL12/CXCR4 -0.053 0.11 -9999 0 -0.51 4 4
Syndecan-4/Laminin alpha3 -0.13 0.19 -9999 0 -0.49 164 164
MDK -0.011 0.056 -9999 0 -0.29 41 41
Syndecan-4/FZD7 -0.033 0.066 -9999 0 -0.47 13 13
Syndecan-4/Midkine -0.029 0.041 -9999 0 -0.64 1 1
FZD7 -0.015 0.11 -9999 0 -0.8 20 20
Syndecan-4/FGFR1/FGF -0.19 0.21 -9999 0 -0.5 114 114
THBS1 -0.003 0.049 -9999 0 -0.8 4 4
integrin-mediated signaling pathway -0.035 0.072 -9999 0 -0.46 16 16
positive regulation of MAPKKK cascade -0.051 0.1 -9999 0 -0.46 7 7
Syndecan-4/TACI -0.036 0.066 -9999 0 -0.5 7 7
CXCR4 -0.007 0.045 -9999 0 -0.29 26 26
cell adhesion -0.02 0.061 -9999 0 -0.34 27 27
Syndecan-4/Dynamin -0.024 0.036 -9999 0 -0.64 1 1
Syndecan-4/TSP1 -0.026 0.044 -9999 0 -0.49 4 4
Syndecan-4/GIPC -0.025 0.036 -9999 0 -0.64 1 1
Syndecan-4/RANTES -0.031 0.053 -9999 0 -0.54 3 3
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.091 0.25 -9999 0 -0.8 119 119
LAMA3 -0.2 0.34 -9999 0 -0.8 264 264
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.12 -9999 0 -0.72 29 29
Syndecan-4/alpha-Actinin -0.025 0.038 -9999 0 -0.54 2 2
TFPI -0.038 0.17 -9999 0 -0.8 50 50
F2 0 0.033 -9999 0 -0.29 13 13
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.23 -9999 0 -0.59 108 108
ACTN1 -0.001 0.024 -9999 0 -0.8 1 1
TNC -0.021 0.12 -9999 0 -0.64 35 35
Syndecan-4/CXCL12 -0.057 0.11 -9999 0 -0.46 29 29
FGF6 -0.002 0.035 -9999 0 -0.8 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.21 -9999 0 -0.8 82 82
TNFRSF13B -0.027 0.11 -9999 0 -0.4 73 73
FGF2 -0.32 0.39 -9999 0 -0.8 426 426
FGFR1 -0.009 0.082 -9999 0 -0.69 14 14
Syndecan-4/PI-4-5-P2 -0.018 0.048 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.15 -9999 0 -0.3 18 18
cell migration -0.024 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.014 -9999 0 -0.28 1 1
vasculogenesis -0.025 0.042 -9999 0 -0.48 4 4
SDC4 -0.018 0.051 -9999 0 -0.68 1 1
Syndecan-4/Tenascin C -0.036 0.075 -9999 0 -0.49 14 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.036 -9999 0 -0.64 1 1
MMP9 -0.12 0.15 -9999 0 -0.29 468 468
Rac1/GTP -0.028 0.057 -9999 0 -0.35 27 27
cytoskeleton organization -0.024 0.035 -9999 0 -0.61 1 1
GIPC1 -0.001 0.016 -9999 0 -0.29 3 3
Syndecan-4/TFPI -0.045 0.095 -9999 0 -0.47 32 32
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.2 0.25 1 -0.56 162 163
AKT1 0.014 0.006 -10000 0 -10000 0 0
GSC -0.036 0.3 -10000 0 -1.5 41 41
NKX2-5 -0.044 0.1 -10000 0 -0.29 163 163
muscle cell differentiation 0.006 0.049 0.77 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.04 -10000 0 -0.46 2 2
SMAD4 0.014 0.041 -10000 0 -0.83 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.2 0.25 -10000 0 -0.52 404 404
SMAD3/SMAD4/VDR 0.005 0.03 -10000 0 -0.44 2 2
MYC -0.017 0.12 -10000 0 -0.8 23 23
CDKN2B 0.029 0.13 -10000 0 -1.5 7 7
AP1 -0.12 0.2 -10000 0 -0.41 314 314
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.002 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.041 -10000 0 -0.32 3 3
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.043 0.12 -10000 0 -0.37 6 6
SMAD3/SMAD4/GR -0.01 0.072 -10000 0 -0.56 16 16
GATA3 -0.037 0.15 -10000 0 -0.79 39 39
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.052 0.12 -10000 0 -0.58 36 36
endothelial cell migration -0.009 0.04 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -0.29 8 8
RBBP4 0 0.025 -10000 0 -0.8 1 1
RUNX2 -0.004 0.036 -10000 0 -0.29 16 16
RUNX3 -0.006 0.066 -10000 0 -0.64 10 10
RUNX1 -0.001 0.024 -10000 0 -0.8 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.01 0.095 -10000 0 -0.8 15 15
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.051 0.079 -10000 0 -1.5 2 2
KAT2B 0 0.025 -10000 0 -0.8 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.029 0.071 -10000 0 -0.47 5 5
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0.002 -10000 0 -10000 0 0
SERPINE1 0.008 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.002 0.037 -10000 0 -0.55 3 3
SMAD3/SMAD4/ATF3 -0.081 0.2 -10000 0 -0.56 152 152
SAP30 -0.001 0.018 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.005 0.023 -10000 0 -10000 0 0
JUN -0.073 0.22 -10000 0 -0.4 313 313
SMAD3/SMAD4/IRF7 -0.019 0.066 -10000 0 -0.36 15 15
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.029 0.1 -10000 0 -1.3 2 2
mesenchymal cell differentiation 0.004 0.034 0.54 1 -10000 0 1
DLX1 -0.054 0.13 -10000 0 -0.32 180 180
TCF3 0 0.009 -10000 0 -0.29 1 1
FOS -0.22 0.37 -10000 0 -0.79 313 313
SMAD3/SMAD4/Max -0.002 0.028 -10000 0 -0.55 1 1
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0.001 0.006 -10000 0 -10000 0 0
LAMC1 0.042 0.048 -10000 0 -0.62 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.028 -10000 0 -0.55 1 1
IRF7 -0.03 0.09 -10000 0 -0.31 97 97
ESR1 -0.16 0.29 -10000 0 -0.58 285 285
HNF4A -0.005 0.038 -10000 0 -0.29 18 18
MEF2C 0.002 0.093 -10000 0 -0.66 3 3
SMAD2-3/SMAD4 -0.003 0.033 -10000 0 -0.54 1 1
Cbp/p300/Src-1 0.003 0.022 -10000 0 -0.52 1 1
IGHV3OR16-13 -0.001 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.003 0.03 -10000 0 -0.29 11 11
HDAC1 0 0.002 -10000 0 -10000 0 0
HDAC2 0 0.002 -10000 0 -10000 0 0
SNIP1 0.001 0.003 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.03 -10000 0 -0.42 2 2
MSG1/HSC70 -0.23 0.29 -10000 0 -0.61 404 404
SMAD2 0.015 0.02 -10000 0 -10000 0 0
SMAD3 0.015 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.037 -10000 0 -0.33 3 3
SMAD2/SMAD2/SMAD4 0.027 0.04 -10000 0 -1.1 1 1
NCOR1 0 0.025 -10000 0 -0.8 1 1
NCOA2 -0.036 0.16 -10000 0 -0.8 48 48
NCOA1 -0.001 0.024 -10000 0 -0.8 1 1
MYOD/E2A -0.003 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.016 0.045 -10000 0 -0.42 2 2
IFNB1 0.012 0.091 -10000 0 -0.42 17 17
SMAD3/SMAD4/MEF2C -0.026 0.072 -10000 0 -0.77 2 2
CITED1 -0.31 0.38 -10000 0 -0.78 419 419
SMAD2-3/SMAD4/ARC105 0 0.029 -10000 0 -0.48 1 1
RBL1 -0.002 0.037 -10000 0 -0.54 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.047 0.063 -10000 0 -0.49 7 7
RUNX1-3/PEBPB2 -0.004 0.05 -10000 0 -0.59 7 7
SMAD7 -0.067 0.14 -10000 0 -0.59 8 8
MYC/MIZ-1 -0.012 0.09 -10000 0 -0.61 23 23
SMAD3/SMAD4 0.018 0.059 0.28 30 -0.45 1 31
IL10 0.019 0.12 -10000 0 -0.51 41 41
PIASy/HDAC complex 0.001 0.004 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.014 0.11 -10000 0 -0.51 37 37
CDK4 0.001 0.018 -10000 0 -0.29 3 3
PIAS4 0.001 0.004 -10000 0 -10000 0 0
ATF3 -0.11 0.28 -10000 0 -0.79 152 152
SMAD3/SMAD4/SP1 0 0.033 -10000 0 -0.52 2 2
FOXG1 -0.022 0.076 -10000 0 -0.29 75 75
FOXO3 0.025 0.035 -10000 0 -0.6 3 3
FOXO1 0.02 0.064 -10000 0 -0.6 11 11
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping 0.002 0.092 -10000 0 -0.65 3 3
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.03 0.081 -10000 0 -0.56 11 11
MYOD1 -0.004 0.033 -10000 0 -0.29 14 14
SMAD3/SMAD4/HNF4 -0.006 0.036 -10000 0 -0.69 1 1
SMAD3/SMAD4/GATA3 -0.024 0.11 -10000 0 -0.57 39 39
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.03 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.052 -10000 0 -0.53 8 8
SMAD3/SMAD4/SP1-3 0.003 0.029 -10000 0 -0.45 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.014 -10000 0 -10000 0 0
SIN3B 0 0.002 -10000 0 -10000 0 0
SIN3A 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.013 0.089 -10000 0 -0.47 6 6
ITGB5 0.052 0.046 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.002 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.072 0.19 -10000 0 -0.56 137 137
AR -0.1 0.27 -10000 0 -0.79 137 137
negative regulation of cell growth -0.025 0.073 -10000 0 -0.48 2 2
SMAD3/SMAD4/MYOD -0.006 0.034 -10000 0 -0.55 1 1
E2F5 -0.006 0.041 -10000 0 -0.29 21 21
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.003 0.056 -10000 0 -0.54 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.046 -10000 0 -0.34 6 6
TFDP1 -0.001 0.018 -10000 0 -0.29 4 4
SMAD3/SMAD4/AP1 -0.12 0.2 -10000 0 -0.42 283 283
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.55 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.002 0.035 -10000 0 -0.8 2 2
Canonical Wnt signaling pathway

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
HDAC1 0.005 0.018 -10000 0 -10000 0 0
AES 0.004 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
SMAD4 -0.001 0.024 -10000 0 -0.8 1 1
DKK2 -0.022 0.13 -10000 0 -0.76 31 31
TLE1 -0.002 0.071 -10000 0 -0.8 8 8
MACF1 0.005 0.006 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.42 0.39 -10000 0 -0.78 569 569
beta catenin/RanBP3 0.014 0.079 0.38 40 -10000 0 40
KREMEN2 -0.14 0.15 -10000 0 -10000 0 0
DKK1 -0.079 0.19 -10000 0 -0.42 198 198
beta catenin/beta TrCP1 0.1 0.084 -10000 0 -10000 0 0
FZD1 0 0.001 -10000 0 -10000 0 0
AXIN2 -0.015 0.22 -10000 0 -1.6 20 20
AXIN1 0.007 0.006 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.078 0.3 1 -0.52 5 6
Axin1/APC/GSK3 0.001 0.014 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.078 0.033 -10000 0 -10000 0 0
HNF1A 0.002 0.028 -10000 0 -0.3 3 3
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC -0.019 0.23 -10000 0 -1.5 24 24
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.083 0.11 -10000 0 -0.61 29 29
NKD1 -0.009 0.07 -10000 0 -0.42 23 23
TCF4 -0.004 0.078 -10000 0 -0.79 10 10
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.007 -10000 0 -10000 0 0
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.1 0.45 45 -0.43 1 46
LEF1 -0.034 0.1 -10000 0 -0.3 131 131
DVL1 0.072 0.065 0.22 1 -10000 0 1
CSNK2A1 0 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.099 0.089 -10000 0 -0.63 4 4
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 53 53
LRP6 0 0.013 -10000 0 -0.29 2 2
CSNK1A1 0.005 0.018 -10000 0 -10000 0 0
NLK 0.01 0.014 -10000 0 -0.3 2 2
CCND1 0 0.12 -10000 0 -1.6 5 5
WNT1 0.002 0.013 -10000 0 -0.29 2 2
GSK3A 0.007 0.006 -10000 0 -10000 0 0
GSK3B 0 0.001 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.044 0.045 0.26 14 -10000 0 14
APC 0.001 0.01 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 555 -10000 0 555
CREBBP 0.004 0.016 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.017 0.11 -9999 0 -0.77 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.024 -9999 0 -0.8 1 1
RAC1-CDC42/GTP/PAK family -0.12 0.14 -9999 0 -0.27 471 471
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.8 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.026 -9999 0 -0.54 2 2
p38 alpha/TAB1 -0.007 0.033 -9999 0 -0.32 4 4
PRKG1 -0.053 0.2 -9999 0 -0.8 70 70
DUSP8 -0.003 0.043 -9999 0 -0.8 3 3
PGK/cGMP/p38 alpha -0.032 0.1 -9999 0 -0.39 73 73
apoptosis -0.006 0.032 -9999 0 -0.31 4 4
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.1 0.27 -9999 0 -0.8 139 139
PAK1 -0.006 0.043 -9999 0 -0.29 23 23
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 -0.001 0.013 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.018 0.068 -9999 0 -0.35 19 19
BLK -0.043 0.11 -9999 0 -0.3 150 150
HCK -0.004 0.033 -9999 0 -0.29 14 14
MAP2K3 0 0.009 -9999 0 -0.29 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.016 -9999 0 -0.29 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.029 0.047 -9999 0 -0.34 4 4
positive regulation of innate immune response 0.025 0.073 -9999 0 -0.37 19 19
LCK -0.021 0.1 -9999 0 -0.42 52 52
p38alpha-beta/MKP7 -0.011 0.053 -9999 0 -0.35 18 18
p38alpha-beta/MKP5 -0.011 0.054 -9999 0 -0.35 18 18
PGK/cGMP -0.041 0.15 -9999 0 -0.62 70 70
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.14 -9999 0 -0.37 154 154
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.35 0.4 -9999 0 -0.8 471 471
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.037 -10000 0 -0.29 16 16
GNB1/GNG2 -0.015 0.048 -10000 0 -0.19 66 66
AKT1 0.05 0.072 -10000 0 -0.2 61 61
EGF -0.15 0.31 -10000 0 -0.79 206 206
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.051 -10000 0 -0.41 5 5
mol:Ca2+ 0.047 0.099 -10000 0 -0.31 61 61
LYN -0.01 0.048 -10000 0 -0.36 4 4
RhoA/GTP -0.008 0.03 -10000 0 -0.14 6 6
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.053 0.11 -10000 0 -0.35 61 61
GNG2 -0.009 0.084 -10000 0 -0.8 12 12
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.03 0.054 -10000 0 -0.53 6 6
G beta5/gamma2 -0.019 0.064 -10000 0 -0.25 66 66
PRKCH 0.048 0.11 -10000 0 -0.35 61 61
DNM1 -0.006 0.065 -10000 0 -0.73 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.027 -10000 0 -0.31 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.03 0.15 -10000 0 -0.72 45 45
G12 family/GTP -0.021 0.073 -10000 0 -0.31 61 61
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.003 0.049 -10000 0 -0.8 4 4
RhoA/GTP/ROCK1 -0.001 0.016 -10000 0 -0.53 1 1
mol:GDP -0.036 0.079 0.33 25 -10000 0 25
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
PRKG1 -0.053 0.2 -10000 0 -0.8 70 70
mol:IP3 0.047 0.12 -10000 0 -0.38 61 61
cell morphogenesis 0 0.016 -10000 0 -0.53 1 1
PLCB2 0.045 0.15 -10000 0 -0.52 61 61
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.006 0.061 -10000 0 -0.39 8 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.01 0.049 -10000 0 -0.36 4 4
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.002 0.027 -10000 0 -0.29 9 9
PRKCB1 0.045 0.12 -10000 0 -0.38 61 61
GNAQ -0.002 0.035 -10000 0 -0.8 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.047 0.16 -10000 0 -0.55 61 61
LCK -0.014 0.071 -10000 0 -0.45 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.057 -10000 0 -0.35 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.025 0.035 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.055 -10000 0 -0.34 1 1
MAPK14 0.051 0.079 -10000 0 -0.23 61 61
TGM2/GTP 0.047 0.13 -10000 0 -0.43 61 61
MAPK11 0.051 0.081 -10000 0 -0.24 61 61
ARHGEF1 0.039 0.061 -10000 0 -0.18 61 61
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.049 0.12 -10000 0 -0.4 61 61
RAB11/GDP -0.001 0.013 -10000 0 -0.29 2 2
ICAM1 0.046 0.092 -10000 0 -0.28 61 61
cAMP biosynthetic process 0.043 0.11 -10000 0 -0.36 61 61
Gq family/GTP/EBP50 0.018 0.037 -10000 0 -0.24 15 15
actin cytoskeleton reorganization 0 0.016 -10000 0 -0.53 1 1
SRC -0.01 0.048 -10000 0 -0.34 5 5
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.028 0.1 -10000 0 -0.3 46 46
VCAM1 0.044 0.1 -10000 0 -0.32 61 61
TP beta/Gq family/GDP/G beta5/gamma2 0.03 0.054 -10000 0 -0.53 6 6
platelet activation 0.066 0.1 -10000 0 -0.31 61 61
PGI2/IP -0.002 0.018 -10000 0 -10000 0 0
PRKACA -0.014 0.07 -10000 0 -0.37 38 38
Gq family/GDP/G beta5/gamma2 0.027 0.056 -10000 0 -0.53 6 6
TXA2/TP beta/beta Arrestin2 -0.006 0.054 -10000 0 -0.66 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.064 -10000 0 -0.34 38 38
mol:DAG 0.046 0.13 -10000 0 -0.42 61 61
EGFR -0.3 0.38 -10000 0 -0.79 396 396
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 61 61
Gq family/GTP -0.003 0.034 -10000 0 -0.28 15 15
YES1 -0.01 0.049 -10000 0 -0.36 5 5
GNAI2/GTP -0.011 0.056 -10000 0 -0.4 5 5
PGD2/DP -0.023 0.12 -10000 0 -0.62 38 38
SLC9A3R1 -0.025 0.082 -10000 0 -0.29 92 92
FYN -0.01 0.052 -10000 0 -0.4 6 6
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.034 -10000 0 -0.36 8 8
PGK/cGMP -0.035 0.13 -10000 0 -0.53 70 70
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.017 0.078 -10000 0 -0.57 12 12
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.042 0.12 -10000 0 -0.36 78 78
PRKCB 0.043 0.12 -10000 0 -0.36 74 74
PRKCE 0.05 0.11 -10000 0 -0.35 61 61
PRKCD 0.048 0.12 -10000 0 -0.38 61 61
PRKCG 0.044 0.12 -10000 0 -0.39 61 61
muscle contraction 0.05 0.15 -10000 0 -0.5 61 61
PRKCZ 0.052 0.11 -10000 0 -0.35 61 61
ARR3 -0.002 0.025 -10000 0 -0.29 8 8
TXA2/TP beta -0.013 0.063 -10000 0 -0.37 12 12
PRKCQ 0.036 0.14 -10000 0 -0.37 92 92
MAPKKK cascade 0.045 0.14 -10000 0 -0.48 61 61
SELE 0.038 0.12 -10000 0 -0.42 61 61
TP beta/GNAI2/GDP/G beta/gamma -0.015 0.078 -10000 0 -0.57 12 12
ROCK1 -0.001 0.024 -10000 0 -0.8 1 1
GNA14 -0.013 0.087 -10000 0 -0.45 31 31
chemotaxis 0.046 0.18 -10000 0 -0.62 61 61
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.002 0.035 -10000 0 -0.8 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.003 0.065 -10000 0 -0.67 9 9
CDKN2C 0.006 0.038 -10000 0 -0.78 2 2
CDKN2A -0.053 0.12 -10000 0 -0.31 179 179
CCND2 0.007 0.033 0.24 8 -0.19 7 15
RB1 -0.008 0.032 0.19 4 -0.25 8 12
CDK4 0.01 0.031 0.25 9 -10000 0 9
CDK6 0.007 0.038 0.27 8 -0.22 11 19
G1/S progression -0.006 0.036 0.25 8 -0.19 4 12
IL2 signaling events mediated by STAT5

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
GAB2 0.007 0.045 -9999 0 -0.38 11 11
ELF1 -0.012 0.051 -9999 0 -0.38 15 15
CCNA2 -0.12 0.14 -9999 0 -0.29 417 417
PIK3CA 0.011 0.01 -9999 0 -10000 0 0
JAK3 0.007 0.035 -9999 0 -0.29 14 14
PIK3R1 0.004 0.078 -9999 0 -0.79 10 10
JAK1 0.011 0.025 -9999 0 -0.79 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.058 0.079 -9999 0 -0.61 8 8
SHC1 0.011 0.002 -9999 0 -10000 0 0
SP1 -0.005 0.042 -9999 0 -0.38 13 13
IL2RA 0.002 0.13 -9999 0 -1 15 15
IL2RB -0.001 0.067 -9999 0 -0.32 41 41
SOS1 0.011 0.003 -9999 0 -10000 0 0
IL2RG -0.007 0.089 -9999 0 -0.79 7 7
G1/S transition of mitotic cell cycle 0.004 0.13 -9999 0 -0.84 21 21
PTPN11 0.011 0.002 -9999 0 -10000 0 0
CCND2 0.017 0.12 -9999 0 -1 13 13
LCK -0.01 0.1 -9999 0 -0.42 52 52
GRB2 0.011 0.01 -9999 0 -0.29 1 1
IL2 0.004 0.026 -9999 0 -0.29 8 8
CDK6 -0.01 0.085 -9999 0 -0.8 12 12
CCND3 0.063 0.07 -9999 0 -0.58 5 5
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.11 -10000 0 -0.45 34 34
IKBKB 0.016 0.053 -10000 0 -0.26 3 3
AKT1 0.003 0.082 0.25 2 -0.27 23 25
IKBKG 0.018 0.055 -10000 0 -0.28 3 3
CALM1 -0.011 0.092 -10000 0 -0.45 29 29
PIK3CA 0 0.009 -10000 0 -10000 0 0
MAP3K1 -0.009 0.15 -10000 0 -0.67 30 30
MAP3K7 0 0.009 -10000 0 -0.29 1 1
mol:Ca2+ -0.02 0.097 -10000 0 -0.48 29 29
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
AP-1 -0.04 0.11 -10000 0 -0.27 65 65
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.079 0.21 -10000 0 -0.63 114 114
CD22 -0.062 0.18 -10000 0 -0.54 97 97
CAMK2G -0.002 0.086 -10000 0 -0.48 17 17
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.13 -10000 0 -0.77 15 15
GO:0007205 -0.02 0.098 -10000 0 -0.49 29 29
SYK 0 0.009 -10000 0 -0.29 1 1
ELK1 -0.011 0.093 -10000 0 -0.46 29 29
NFATC1 -0.017 0.13 -10000 0 -0.56 33 33
B-cell antigen/BCR complex -0.079 0.21 -10000 0 -0.63 114 114
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.009 0.1 -10000 0 -0.47 30 30
NFKBIA 0.016 0.02 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.16 -10000 0 -0.52 97 97
mol:GDP -0.02 0.09 -10000 0 -0.46 29 29
PTEN -0.002 0.035 -10000 0 -0.8 2 2
CD79B -0.027 0.14 -10000 0 -0.8 29 29
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
PI3K/BCAP/CD19 -0.027 0.16 -10000 0 -0.47 96 96
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
mol:IP3 -0.029 0.096 -10000 0 -0.5 29 29
CSK 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.44 332 332
CHUK 0.018 0.055 -10000 0 -0.28 3 3
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.077 -10000 0 -0.48 17 17
PTPN6 -0.057 0.16 -10000 0 -0.74 39 39
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.07 0.16 -10000 0 -0.8 32 32
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.005 -10000 0 -10000 0 0
CD19 -0.081 0.17 -10000 0 -0.54 93 93
MAP4K1 -0.014 0.068 -10000 0 -0.31 47 47
CD72 -0.009 0.054 -10000 0 -0.31 30 30
PAG1 -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.002 0.13 -10000 0 -0.54 30 30
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.01 0.1 -10000 0 -0.53 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.042 0.13 -10000 0 -0.47 82 82
RAF1 0 0.096 -10000 0 -0.44 29 29
RasGAP/p62DOK/SHIP -0.055 0.15 -10000 0 -0.49 97 97
CD79A -0.082 0.22 -10000 0 -0.54 161 161
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.27 65 65
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.082 -10000 0 -0.42 16 16
MAPK1 0.016 0.082 -10000 0 -0.42 16 16
CD72/SHP1 -0.055 0.16 -10000 0 -0.68 40 40
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.54 34 34
actin cytoskeleton organization -0.026 0.15 -10000 0 -0.64 32 32
NF-kappa-B/RelA 0.042 0.032 -10000 0 -10000 0 0
Calcineurin -0.02 0.071 -10000 0 -0.44 16 16
PI3K -0.059 0.13 -10000 0 -0.53 41 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.032 0.11 -10000 0 -0.57 29 29
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.048 0.17 -10000 0 -0.83 34 34
DAPP1 -0.05 0.19 -10000 0 -0.98 33 33
cytokine secretion -0.015 0.12 -10000 0 -0.52 33 33
mol:DAG -0.029 0.096 -10000 0 -0.5 29 29
PLCG2 -0.002 0.036 -10000 0 -0.63 3 3
MAP2K1 0.008 0.089 -10000 0 -0.48 16 16
B-cell antigen/BCR complex/FcgammaRIIB -0.07 0.19 -10000 0 -0.6 97 97
mol:PI-3-4-5-P3 -0.043 0.092 0.34 2 -0.37 36 38
ETS1 0.004 0.088 -10000 0 -0.49 19 19
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.056 0.16 -10000 0 -0.51 94 94
B-cell antigen/BCR complex/LYN -0.057 0.18 -10000 0 -0.57 94 94
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0.002 -10000 0 -10000 0 0
RAC1 -0.029 0.16 -10000 0 -0.71 32 32
B-cell antigen/BCR complex/LYN/SYK -0.057 0.18 -10000 0 -0.56 94 94
CARD11 -0.015 0.1 -10000 0 -0.48 29 29
FCGR2B -0.004 0.055 -10000 0 -0.71 6 6
PPP3CA -0.001 0.013 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.009 0.075 -10000 0 -0.5 19 19
PDPK1 -0.028 0.062 0.22 2 -0.27 23 25
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.014 -10000 0 -0.14 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.026 0.031 -9999 0 -10000 0 0
BIRC5 -0.21 0.13 -9999 0 -0.29 757 757
NFKBIA -0.024 0.034 -9999 0 -10000 0 0
CPEB1 -0.15 0.31 -9999 0 -0.79 196 196
AKT1 -0.024 0.034 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.033 -9999 0 -0.55 1 1
NDEL1/TACC3 -0.04 0.061 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.039 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
JUB -0.003 0.049 -9999 0 -0.8 4 4
TPX2 -0.11 0.1 -9999 0 -10000 0 0
TP53 -0.011 0.017 -9999 0 -10000 0 0
DLG7 -0.03 0.037 -9999 0 -10000 0 0
AURKAIP1 -0.004 0.032 -9999 0 -0.29 13 13
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.043 0.065 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -0.55 1 1
AURKA -0.038 0.046 -9999 0 -10000 0 0
AURKB -0.009 0.011 -9999 0 -10000 0 0
CDC25B -0.018 0.026 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.04 -9999 0 -0.5 4 4
mRNA polyadenylation -0.11 0.2 -9999 0 -0.52 195 195
Aurora A/CPEB -0.11 0.2 -9999 0 -0.53 195 195
Aurora A/TACC1/TRAP/chTOG -0.032 0.089 -9999 0 -0.48 40 40
BRCA1 -0.001 0.028 -9999 0 -0.46 3 3
centrosome duplication -0.029 0.039 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.06 -9999 0 -10000 0 0
spindle assembly -0.032 0.088 -9999 0 -0.47 40 40
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.072 -9999 0 -0.4 3 3
CENPA -0.006 0.012 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.031 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.029 -9999 0 -10000 0 0
negative regulation of DNA binding -0.009 0.02 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.013 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.025 0.04 -9999 0 -0.5 4 4
mitotic prometaphase -0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.046 -9999 0 -10000 0 0
TACC1 -0.03 0.15 -9999 0 -0.8 40 40
TACC3 -0.046 0.11 -9999 0 -0.29 166 166
Aurora A/Antizyme1 -0.022 0.026 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.031 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.003 0.003 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
GIT1/beta-PIX/PAK1 -0.004 0.023 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.1 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.09 -9999 0 -10000 0 0
PAK1 -0.006 0.043 -9999 0 -0.29 23 23
CKAP5 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.44 0.4 -10000 0 -0.8 590 590
CLTC 0.027 0.018 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.007 0.028 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.017 -10000 0 -10000 0 0
CPE 0.006 0.082 -10000 0 -0.53 24 24
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.002 0.019 -10000 0 -10000 0 0
CTNND1 0.025 0.031 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.014 -10000 0 -10000 0 0
TSHR -0.007 0.11 -10000 0 -0.53 47 47
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.007 0.074 -10000 0 -0.74 10 10
mol:Choline -0.002 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.038 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.028 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.005 0.047 -10000 0 -0.48 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.017 0.05 -10000 0 -0.37 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -0.29 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.005 0.038 -10000 0 -0.29 18 18
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.033 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.005 -10000 0 -10000 0 0
ACAP1 -0.001 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.022 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.025 0.031 -10000 0 -10000 0 0
NME1 0.009 0.038 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.018 -10000 0 -10000 0 0
IL2RA 0.017 0.045 -10000 0 -0.37 7 7
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.22 0.2 -10000 0 -0.4 590 590
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.003 0.033 -10000 0 -0.34 10 10
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.014 -10000 0 -10000 0 0
SDC1 0.021 0.024 -10000 0 -0.35 1 1
ARF6/GDP -0.008 0.034 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.019 -10000 0 -10000 0 0
endocytosis 0.005 0.046 0.48 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.072 0.19 -10000 0 -0.43 244 244
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.024 -10000 0 -0.8 1 1
Dynamin 2/GDP -0.006 0.028 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.14 0.22 -10000 0 -0.42 394 394
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.029 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.06 0.076 -9999 0 -0.41 6 6
EPHB2 -0.006 0.04 -9999 0 -0.29 20 20
Syndecan-2/TACI -0.018 0.075 -9999 0 -0.52 18 18
LAMA1 -0.091 0.25 -9999 0 -0.8 119 119
Syndecan-2/alpha2 ITGB1 -0.12 0.21 -9999 0 -0.47 280 280
HRAS -0.002 0.027 -9999 0 -0.29 9 9
Syndecan-2/CASK -0.002 0.03 -9999 0 -0.53 3 3
ITGA5 0 0.009 -9999 0 -0.29 1 1
BAX 0.034 0.057 -9999 0 -0.51 11 11
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.027 -9999 0 -0.48 3 3
LAMA3 -0.2 0.34 -9999 0 -0.8 264 264
EZR -0.001 0.016 -9999 0 -0.29 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.1 0.27 -9999 0 -0.8 139 139
Syndecan-2/MMP2 -0.007 0.07 -9999 0 -0.65 11 11
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.015 0.096 -9999 0 -0.61 27 27
dendrite morphogenesis -0.005 0.035 -9999 0 -0.52 3 3
Syndecan-2/GM-CSF -0.005 0.036 -9999 0 -0.53 3 3
determination of left/right symmetry 0.017 0.036 -9999 0 -0.6 3 3
Syndecan-2/PKC delta -0.002 0.029 -9999 0 -0.52 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.036 -9999 0 -0.48 3 3
MAPK1 0.022 0.036 -9999 0 -0.48 3 3
Syndecan-2/RACK1 -0.003 0.027 -9999 0 -0.45 3 3
NF1 -0.001 0.024 -9999 0 -0.8 1 1
FGFR/FGF/Syndecan-2 0.017 0.036 -9999 0 -0.6 3 3
ITGA2 -0.02 0.12 -9999 0 -0.8 27 27
MAPK8 0.028 0.06 -9999 0 -0.55 11 11
Syndecan-2/alpha2/beta1 Integrin -0.063 0.18 -9999 0 -0.51 131 131
Syndecan-2/Kininogen -0.005 0.036 -9999 0 -0.53 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.003 0.025 -9999 0 -0.42 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.027 -9999 0 -0.48 3 3
extracellular matrix organization -0.002 0.03 -9999 0 -0.52 3 3
actin cytoskeleton reorganization -0.06 0.076 -9999 0 -0.41 6 6
Syndecan-2/Caveolin-2/Ras -0.065 0.17 -9999 0 -0.49 139 139
Syndecan-2/Laminin alpha3 -0.13 0.23 -9999 0 -0.52 267 267
Syndecan-2/RasGAP -0.002 0.025 -9999 0 -0.42 3 3
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.29 1 1
Syndecan-2 dimer -0.005 0.035 -9999 0 -0.52 3 3
GO:0007205 0 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.024 -9999 0 -0.4 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.027 0.11 -9999 0 -0.4 73 73
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.015 0.096 -9999 0 -0.61 27 27
Syndecan-2/Synbindin -0.002 0.029 -9999 0 -0.52 3 3
TGFB1 -0.001 0.016 -9999 0 -0.29 3 3
CASP3 0.03 0.029 -9999 0 -0.47 3 3
FN1 -0.12 0.14 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.021 0.083 -9999 0 -0.52 23 23
SDC2 0.017 0.036 -9999 0 -0.61 3 3
KNG1 -0.006 0.042 -9999 0 -0.29 22 22
Syndecan-2/Neurofibromin -0.003 0.033 -9999 0 -0.52 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.007 0.044 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.002 0.03 -9999 0 -0.52 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.027 -9999 0 -0.48 3 3
Syndecan-2/Ezrin -0.002 0.027 -9999 0 -0.47 3 3
PRKACA 0.03 0.032 -9999 0 -0.47 4 4
angiogenesis -0.021 0.083 -9999 0 -0.52 23 23
MMP2 -0.009 0.081 -9999 0 -0.75 12 12
IL8 -0.033 0.13 -9999 0 -0.41 85 85
calcineurin-NFAT signaling pathway -0.017 0.075 -9999 0 -0.52 18 18
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.022 0.02 -10000 0 -0.61 1 1
MAP4K4 0.041 0.044 -10000 0 -0.68 1 1
BAG4 -0.006 0.056 -10000 0 -0.8 4 4
PKC zeta/ceramide -0.023 0.047 0.18 1 -0.58 1 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.079 -10000 0 -0.51 21 21
BAX -0.008 0.021 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.009 -10000 0 -10000 0 0
BAD -0.021 0.045 0.2 1 -0.25 1 2
SMPD1 0.026 0.032 -10000 0 -0.25 12 12
RB1 -0.022 0.049 0.2 1 -0.48 2 3
FADD/Caspase 8 0.049 0.046 -10000 0 -0.44 3 3
MAP2K4 -0.014 0.046 -10000 0 -0.45 2 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.045 0.2 1 -0.3 3 4
EGF -0.15 0.31 -10000 0 -0.79 206 206
mol:ceramide -0.033 0.047 0.21 1 -0.13 199 200
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.023 -10000 0 -0.61 1 1
ASAH1 -0.001 0.016 -10000 0 -0.29 3 3
negative regulation of cell cycle -0.022 0.048 0.2 1 -0.47 2 3
cell proliferation -0.094 0.16 -10000 0 -0.38 236 236
BID 0.024 0.033 -10000 0 -0.39 1 1
MAP3K1 -0.022 0.047 0.2 1 -0.48 1 2
EIF2A -0.004 0.04 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.001 0.043 -10000 0 -0.41 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.043 -10000 0 -0.41 1 1
Cathepsin D/ceramide -0.027 0.05 0.18 1 -0.25 2 3
FADD 0.039 0.049 -10000 0 -0.47 3 3
KSR1 -0.022 0.048 0.2 1 -0.33 3 4
MAPK8 -0.012 0.054 -10000 0 -0.35 10 10
PRKRA -0.021 0.045 0.2 1 -10000 0 1
PDGFA -0.001 0.026 -10000 0 -0.54 2 2
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
IGF1 -0.18 0.33 -10000 0 -0.8 236 236
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.032 0.047 0.21 1 -0.13 199 200
CTSD -0.01 0.054 -10000 0 -0.29 37 37
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.1 0.17 -10000 0 -0.41 236 236
PRKCD 0 0.009 -10000 0 -0.29 1 1
PRKCZ -0.001 0.024 -10000 0 -0.8 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.61 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.001 0.024 -10000 0 -0.8 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.04 -10000 0 -0.73 1 1
TNFR1A/BAG4/TNF-alpha -0.012 0.069 -10000 0 -0.53 16 16
mol:Sphingosine-1-phosphate 0.022 0.02 -10000 0 -0.6 1 1
MAP2K1 -0.005 0.043 -10000 0 -0.42 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.007 0.044 0.18 25 -0.13 1 26
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.041 -10000 0 -0.61 4 4
EIF2AK2 -0.013 0.042 0.2 1 -10000 0 1
TNF-alpha/TNFR1A/FAN -0.009 0.059 -10000 0 -0.52 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -0.33 1 1
MAP2K2 -0.005 0.043 -10000 0 -0.42 1 1
SMPD3 0.026 0.041 -10000 0 -0.28 16 16
TNF -0.016 0.094 -10000 0 -0.46 36 36
PKC zeta/PAR4 -0.001 0.026 -10000 0 -0.61 2 2
mol:PHOSPHOCHOLINE 0.044 0.11 0.27 205 -10000 0 205
NF kappa B1/RelA/I kappa B alpha -0.001 0.019 -10000 0 -0.44 2 2
AIFM1 -0.007 0.044 0.18 25 -10000 0 25
BCL2 -0.028 0.15 -10000 0 -0.8 37 37
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.004 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.01 0.074 -9999 0 -0.55 19 19
forebrain development -0.024 0.2 -9999 0 -0.51 131 131
GNAO1 -0.028 0.13 -9999 0 -0.8 25 25
SMO/beta Arrestin2 -0.005 0.053 -9999 0 -0.61 8 8
SMO 0.005 0.071 -9999 0 -0.8 8 8
ARRB2 0.011 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.002 0.037 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.003 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.041 0.18 -9999 0 -0.8 57 57
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.054 0.16 -9999 0 -0.49 89 89
SAP30 0 0.019 -9999 0 -0.29 4 4
mol:GDP 0.005 0.071 -9999 0 -0.8 8 8
MIM/GLI2A 0.002 0.029 -9999 0 -0.3 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.002 0.005 -9999 0 -10000 0 0
GLI2 0.041 0.035 -9999 0 -10000 0 0
GLI3 0.04 0.04 -9999 0 -0.3 12 12
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.004 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.009 0.084 -9999 0 -0.8 12 12
Gi family/GTP -0.023 0.096 -9999 0 -0.36 48 48
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.004 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.026 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.007 0.046 -9999 0 -0.39 6 6
FOXA2 -0.012 0.032 -9999 0 -10000 0 0
neural tube patterning -0.024 0.2 -9999 0 -0.51 131 131
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.025 -9999 0 -0.46 1 1
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.002 0.029 -9999 0 -0.3 9 9
embryonic limb morphogenesis -0.024 0.2 -9999 0 -0.51 131 131
SUFU 0.003 0.032 -9999 0 -0.3 9 9
LGALS3 -0.011 0.091 -9999 0 -0.8 14 14
catabolic process -0.004 0.027 -9999 0 -10000 0 0
GLI3A/CBP -0.021 0.095 -9999 0 -0.38 68 68
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.026 0.21 -9999 0 -0.53 131 131
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.024 -9999 0 -0.8 1 1
RBBP7 -0.001 0.026 -9999 0 -0.29 8 8
Su(fu)/Galectin3 -0.009 0.065 -9999 0 -0.53 15 15
GNAZ -0.004 0.073 -9999 0 -0.79 9 9
RBBP4 0.001 0.025 -9999 0 -0.8 1 1
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.004 0.026 -9999 0 -10000 0 0
STK36 0.011 0.025 -9999 0 -0.79 1 1
Gi family/GNB1/GNG2/GDP -0.029 0.099 -9999 0 -0.63 13 13
PTCH1 -0.067 0.34 -9999 0 -1.2 79 79
MIM/GLI1 -0.051 0.18 -9999 0 -0.49 130 130
CREBBP -0.02 0.095 -9999 0 -0.38 68 68
Su(fu)/SIN3/HDAC complex 0.006 0.021 -9999 0 -10000 0 0
TRAIL signaling 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.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.074 -10000 0 -0.8 9 9
positive regulation of NF-kappaB transcription factor activity -0.064 0.18 -10000 0 -0.6 111 111
MAP2K4 0.041 0.039 -10000 0 -0.37 2 2
IKBKB -0.001 0.013 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.064 -10000 0 -0.8 7 7
SMPD1 -0.002 0.026 -10000 0 -0.28 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.077 0.24 -10000 0 -0.79 103 103
TRAIL/TRAILR2 -0.005 0.056 -10000 0 -0.61 9 9
TRAIL/TRAILR3 -0.008 0.07 -10000 0 -0.65 11 11
TRAIL/TRAILR1 -0.009 0.074 -10000 0 -0.61 16 16
TRAIL/TRAILR4 -0.064 0.19 -10000 0 -0.61 111 111
TRAIL/TRAILR1/DAP3/GTP -0.008 0.059 -10000 0 -0.48 16 16
IKK complex -0.003 0.02 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.058 -10000 0 -0.6 9 9
MAP3K1 -0.004 0.033 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.077 0.23 -10000 0 -0.79 103 103
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.064 -10000 0 -0.79 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.006 0.04 -10000 0 -0.32 16 16
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.058 -10000 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.056 -10000 0 -0.45 16 16
mol:ceramide -0.002 0.026 -10000 0 -0.28 9 9
FADD -0.004 0.036 -10000 0 -0.29 16 16
MAPK8 0.044 0.057 -10000 0 -0.44 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
TRAILR3 (trimer) -0.004 0.049 -10000 0 -0.43 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.067 -10000 0 -0.53 16 16
DAP3 0 0.009 -10000 0 -0.29 1 1
CASP10 0.021 0.11 0.31 96 -0.49 13 109
JNK cascade -0.064 0.18 -10000 0 -0.6 111 111
TRAIL (trimer) -0.007 0.073 -10000 0 -0.79 9 9
TNFRSF10C -0.004 0.049 -10000 0 -0.43 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.009 0.057 -10000 0 -0.46 16 16
TRAIL/TRAILR2/FADD -0.007 0.051 -10000 0 -0.52 9 9
cell death -0.002 0.026 -10000 0 -0.28 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.03 -10000 0 -0.32 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.015 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.042 -10000 0 -0.44 9 9
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.005 0.095 0.23 1 -0.45 37 38
ACTA1 -0.018 0.13 0.27 1 -0.62 38 39
NUMA1 0.005 0.095 0.23 1 -0.45 37 38
SPTAN1 -0.005 0.13 0.27 1 -0.62 34 35
LIMK1 -0.005 0.13 0.27 1 -0.62 34 35
BIRC3 -0.01 0.079 -10000 0 -0.51 21 21
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
CASP10 -0.016 0.15 -10000 0 -0.66 38 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.095 0.23 1 -0.45 37 38
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.12 0.27 1 -0.6 34 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.011 0.14 0.27 1 -0.62 43 44
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.015 0.08 -10000 0 -0.68 13 13
BID 0.005 0.063 -10000 0 -0.29 37 37
MAP3K1 0.004 0.042 -10000 0 -0.27 9 9
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.006 0.13 0.27 1 -0.62 34 35
CASP9 0.002 0.004 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 7 -0.22 4 11
neuron apoptosis 0.022 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.12 0.26 1 -0.59 34 35
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.057 -10000 0 -0.35 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
ICAD/CAD 0.003 0.12 -10000 0 -0.59 34 34
CASP7 -0.007 0.037 0.36 9 -10000 0 9
KRT18 0.015 0.025 -10000 0 -0.59 1 1
apoptosis 0.008 0.11 0.3 1 -0.52 34 35
DFFA -0.005 0.13 0.27 1 -0.59 37 38
DFFB -0.005 0.13 0.27 1 -0.62 34 35
PARP1 0.002 0.031 0.22 4 -0.18 7 11
actin filament polymerization -0.002 0.12 0.56 37 -0.26 1 38
TNF -0.016 0.094 -10000 0 -0.46 36 36
CYCS 0.007 0.05 -10000 0 -0.21 37 37
SATB1 0.017 0.099 -10000 0 -0.47 31 31
SLK -0.005 0.13 0.27 1 -0.62 34 35
p15 BID/BAX -0.014 0.05 -10000 0 -0.34 9 9
CASP2 0.044 0.039 -10000 0 -0.45 1 1
JNK cascade -0.004 0.042 0.27 9 -10000 0 9
CASP3 -0.014 0.13 0.28 1 -0.62 38 39
LMNB2 0.04 0.036 -10000 0 -0.33 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.024 -10000 0 -0.8 1 1
Mammalian IAPs/DIABLO -0.005 0.045 -10000 0 -0.47 9 9
negative regulation of DNA binding 0.015 0.079 -10000 0 -0.67 13 13
stress fiber formation -0.005 0.12 0.27 1 -0.6 34 35
GZMB -0.029 0.15 -10000 0 -0.65 46 46
CASP1 0.014 0.034 -10000 0 -0.44 6 6
LMNB1 0.044 0.037 -10000 0 -0.38 2 2
APP 0.022 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.003 0.1 0.26 4 -0.5 35 39
LMNA 0.04 0.036 -10000 0 -0.38 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.034 -10000 0 -0.48 1 1
LRDD -0.001 0.02 -10000 0 -0.29 5 5
SREBF1 -0.008 0.13 0.27 1 -0.62 34 35
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.094 0.23 1 -0.44 37 38
CFL2 0.001 0.12 -10000 0 -0.58 37 37
GAS2 -0.05 0.19 0.27 1 -0.52 128 129
positive regulation of apoptosis 0.045 0.036 -10000 0 -0.37 2 2
PRF1 -0.018 0.11 -10000 0 -0.64 29 29
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.036 0.025 -10000 0 -0.42 3 3
CDKN1A 0.036 0.021 -10000 0 -0.42 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 0.036 0.025 -10000 0 -0.42 3 3
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
AKT3 0.009 0.057 -10000 0 -0.44 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.025 -10000 0 -0.41 4 4
BAD/YWHAZ -0.001 0.009 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.025 0.4 4 -10000 0 4
TSC1 0.037 0.003 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.003 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.021 0.041 -10000 0 -0.52 6 6
MAP3K5 -0.003 0.049 -10000 0 -0.8 4 4
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.022 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.003 -10000 0 -10000 0 0
CASP9 0.037 0.003 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.021 -10000 0 -0.4 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
AKT2/p21CIP1 -0.001 0.018 -10000 0 -0.41 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.003 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.03 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.044 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.25 0.25 -10000 0 -0.47 592 592
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.25 0.25 -10000 0 -0.48 592 592
GSK3A 0.037 0.003 -10000 0 -10000 0 0
FOXO1 0.032 0.047 -10000 0 -0.42 11 11
GSK3B 0.037 0.003 -10000 0 -10000 0 0
SFN -0.017 0.1 -10000 0 -0.51 34 34
G1/S transition of mitotic cell cycle 0.044 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.042 0.033 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.015 0.087 -9999 0 -0.52 30 30
E-cadherin/beta catenin -0.017 0.099 -9999 0 -0.61 29 29
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.026 -9999 0 -0.54 2 2
CDH1 -0.022 0.13 -9999 0 -0.8 29 29
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.01 0.077 -10000 0 -0.61 17 17
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.024 0.01 -10000 0 -10000 0 0
protein ubiquitination -0.028 0.073 -10000 0 -0.48 18 18
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.009 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.001 0.011 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -0.29 1 1
BRCA1 -0.001 0.028 -10000 0 -0.46 3 3
CCNE1 -0.059 0.12 -10000 0 -0.29 213 213
CDK2/Cyclin E1 -0.037 0.075 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.011 0.079 -10000 0 -0.61 18 18
FANCE 0 0 -10000 0 -10000 0 0
FANCC 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
FANCA -0.052 0.11 -10000 0 -10000 0 0
DNA repair 0.007 0.094 -10000 0 -0.44 11 11
BRCA1/BARD1/ubiquitin -0.011 0.079 -10000 0 -0.61 18 18
BARD1/DNA-PK -0.008 0.06 -10000 0 -0.47 17 17
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.01 0.076 0.6 17 -10000 0 17
BRCA1/BARD1/CTIP/M/R/N Complex -0.005 0.04 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.009 0.068 -10000 0 -0.52 18 18
BRCA1/BARD1/P53 -0.008 0.062 -10000 0 -0.47 18 18
BARD1/CSTF1/BRCA1 -0.009 0.068 -10000 0 -0.52 18 18
BRCA1/BACH1 -0.001 0.027 -10000 0 -0.46 3 3
BARD1 -0.013 0.1 -10000 0 -0.8 17 17
PCNA -0.001 0.016 -10000 0 -0.29 3 3
BRCA1/BARD1/UbcH5C -0.009 0.068 -10000 0 -0.52 18 18
BRCA1/BARD1/UbcH7 -0.009 0.068 -10000 0 -0.52 18 18
BRCA1/BARD1/RAD51/PCNA -0.053 0.086 -10000 0 -0.53 18 18
BARD1/DNA-PK/P53 -0.008 0.056 -10000 0 -0.44 17 17
BRCA1/BARD1/Ubiquitin -0.011 0.079 -10000 0 -0.61 18 18
BRCA1/BARD1/CTIP -0.009 0.062 -10000 0 -0.47 18 18
FA complex -0.005 0.011 -10000 0 -10000 0 0
BARD1/EWS -0.01 0.076 -10000 0 -0.61 17 17
RBBP8 0.022 0.006 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.008 0.061 0.47 18 -10000 0 18
BRCA1/BARD1 -0.029 0.073 -10000 0 -0.49 18 18
CSTF1 0 0.009 -10000 0 -0.29 1 1
BARD1/EWS-Fli1 -0.01 0.078 -10000 0 -0.62 17 17
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -0.29 392 392
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.011 0.079 -10000 0 -0.61 18 18
EWSR1 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0.016 -10000 0 -0.52 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.039 -10000 0 -0.32 4 4
KAT2B -0.001 0.024 -10000 0 -0.8 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.02 0.05 0.24 4 -0.34 12 16
RAR alpha/9cRA/Cyclin H -0.012 0.064 -10000 0 -0.38 27 27
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.034 0.049 -10000 0 -0.32 14 14
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.069 -10000 0 -0.63 9 9
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.12 -10000 0 -0.56 32 32
NCOA2 -0.036 0.16 -10000 0 -0.8 48 48
NCOA3 0 0.009 -10000 0 -0.29 1 1
NCOA1 -0.001 0.024 -10000 0 -0.8 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.008 0.005 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.07 -10000 0 -0.79 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.62 27 27
RARA 0.014 0.063 -10000 0 -0.31 34 34
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.021 0.084 -10000 0 -0.3 59 59
PRKCA -0.007 0.13 -10000 0 -0.76 29 29
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.005 0.13 -10000 0 -0.57 34 34
RXRG -0.1 0.21 -10000 0 -0.44 281 281
RXRA 0.022 0.065 -10000 0 -0.32 34 34
RXRB 0.011 0.075 -10000 0 -0.43 27 27
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.025 0.096 -10000 0 -0.34 78 78
CRBP1/9-cic-RA -0.017 0.069 -10000 0 -0.62 7 7
RARB 0.003 0.089 -10000 0 -0.8 13 13
PRKCG -0.002 0.061 -10000 0 -0.29 45 45
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.008 0.12 -10000 0 -0.6 31 31
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.013 0.1 -10000 0 -0.48 32 32
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.057 -10000 0 -0.44 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.005 0.13 -10000 0 -0.57 34 34
positive regulation of DNA binding -0.011 0.06 -10000 0 -0.36 27 27
NRIP1 -0.003 0.12 -10000 0 -0.86 8 8
RXRs/RARs -0.012 0.13 -10000 0 -0.57 34 34
RXRs/RXRs/DNA/9cRA -0.045 0.11 -10000 0 -0.65 27 27
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.006 0.035 -10000 0 -0.52 1 1
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.002 0.036 -10000 0 -0.8 2 2
ANTXR2 -0.008 0.081 -10000 0 -0.8 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 12 12
monocyte activation 0.004 0.071 -10000 0 -0.46 24 24
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.011 0.068 -10000 0 -0.48 22 22
CYAA 0.01 0.056 -10000 0 -0.5 12 12
MAP2K4 -0.001 0.017 -10000 0 -0.47 1 1
IL1B 0.007 0.065 -10000 0 -0.34 30 30
Channel -0.006 0.058 -10000 0 -0.53 12 12
NLRP1 -0.008 0.059 -10000 0 -0.49 15 15
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 12 -10000 0 12
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.47 302 302
PA/Cellular Receptors -0.007 0.062 -10000 0 -0.57 12 12
apoptosis -0.001 0.011 -10000 0 -0.1 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.006 0.054 -10000 0 -0.49 12 12
macrophage activation 0.02 0.01 -10000 0 -10000 0 0
TNF -0.016 0.094 -10000 0 -0.46 36 36
VCAM1 -0.011 0.069 -10000 0 -0.46 24 24
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.021 0.11 23 -10000 0 23
IL18 0.011 0.036 -10000 0 -0.22 15 15
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 12 12
LEF -0.001 0.011 -10000 0 -0.1 12 12
CASP1 -0.004 0.03 -10000 0 -0.18 24 24
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.006 0.055 -10000 0 -0.5 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.064 -10000 0 -0.51 5 5
UGCG -0.011 0.095 -10000 0 -0.81 14 14
AKT1/mTOR/p70S6K/Hsp90/TERT 0.054 0.091 -10000 0 -0.38 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.014 0.097 -10000 0 -0.79 14 14
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.09 -10000 0 -0.36 63 63
FRAP1 0.052 0.13 -10000 0 -0.41 65 65
FOXO3 0.06 0.11 -10000 0 -0.42 33 33
AKT1 0.055 0.11 -10000 0 -0.45 32 32
GAB2 0.007 0.045 -10000 0 -0.38 11 11
SMPD1 -0.002 0.014 -10000 0 -10000 0 0
SGMS1 -0.002 0.014 -10000 0 -10000 0 0
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 0.017 0.054 -10000 0 -0.53 10 10
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.032 0.09 -10000 0 -0.36 36 36
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.059 -10000 0 -0.61 10 10
RPS6KB1 0.021 0.034 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 21 21
JAK3 0.009 0.035 -10000 0 -0.29 14 14
PIK3R1 0.006 0.078 -10000 0 -0.8 10 10
JAK1 0.012 0.025 -10000 0 -0.79 1 1
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.047 0.18 -10000 0 -0.94 28 28
MYB 0.006 0.19 -10000 0 -1.3 22 22
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.053 0.094 -10000 0 -0.56 11 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.022 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.092 -10000 0 -0.54 11 11
Rac1/GDP -0.005 0.047 -10000 0 -0.48 10 10
T cell proliferation 0.058 0.087 -10000 0 -0.52 10 10
SHC1 0.011 0.003 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.01 -10000 0 -0.066 22 22
PRKCZ 0.058 0.09 -10000 0 -0.55 10 10
NF kappa B1 p50/RelA -0.025 0.089 -10000 0 -0.38 43 43
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.039 0.069 -10000 0 -0.57 5 5
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.019 0.12 -10000 0 -0.38 81 81
IL2RB 0.001 0.067 -10000 0 -0.31 41 41
TERT -0.043 0.1 -10000 0 -0.29 154 154
E2F1 0.02 0.068 -10000 0 -0.44 22 22
SOS1 0.011 0.003 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.03 22 -10000 0 22
PTPN11 0.011 0.003 -10000 0 -10000 0 0
IL2RG -0.005 0.089 -10000 0 -0.79 7 7
actin cytoskeleton organization 0.058 0.087 -10000 0 -0.52 10 10
GRB2 0.011 0.01 -10000 0 -0.29 1 1
IL2 0.006 0.027 -10000 0 -0.29 8 8
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.026 0.048 -10000 0 -0.46 10 10
LCK -0.008 0.1 -10000 0 -0.42 52 52
BCL2 0.038 0.2 -10000 0 -0.86 43 43
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0.009 -9999 0 -0.29 1 1
PLK4 -0.012 0.059 -9999 0 -0.29 45 45
regulation of centriole replication 0.013 0.042 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.018 0.085 -9999 0 -0.52 24 24
MAP4K1 -0.014 0.068 -9999 0 -0.31 47 47
MAP3K8 -0.007 0.074 -9999 0 -0.74 10 10
PRKCB -0.02 0.11 -9999 0 -0.54 38 38
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.036 0.055 -9999 0 -0.47 4 4
JUN 0.017 0.12 -9999 0 -0.6 33 33
MAP3K7 0.036 0.054 -9999 0 -0.48 3 3
GRAP2 -0.015 0.11 -9999 0 -0.8 19 19
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.042 0.058 -9999 0 -0.46 5 5
LAT -0.005 0.048 -9999 0 -0.36 16 16
LCP2 0 0.009 -9999 0 -0.29 1 1
MAPK8 0.012 0.12 -9999 0 -0.69 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.05 -9999 0 -0.35 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.079 -9999 0 -0.48 24 24
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.03 0.008 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.046 -9999 0 -10000 0 0
MAPK12 0.018 0.08 -9999 0 -0.46 27 27
CCND1 0.014 0.045 -9999 0 -0.42 6 6
p38 gamma/SNTA1 -0.012 0.07 -9999 0 -0.46 22 22
MAP2K3 0 0.009 -9999 0 -0.29 1 1
PKN1 0 0.009 -9999 0 -0.29 1 1
G2/M transition checkpoint 0.018 0.08 -9999 0 -0.46 27 27
MAP2K6 0.011 0.082 -9999 0 -0.49 27 27
MAPT -0.019 0.14 -9999 0 -0.4 115 115
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.031 -9999 0 -0.44 5 5
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.017 0.096 -9999 0 -0.58 29 29
KLHL20 -0.008 0.033 -9999 0 -0.24 4 4
CYFIP2 -0.011 0.067 -9999 0 -0.36 32 32
Rac1/GDP 0.049 0.067 -9999 0 -0.34 29 29
ENAH -0.016 0.095 -9999 0 -0.58 29 29
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.008 0.047 -9999 0 -0.5 1 1
ABI1/Sra1/Nap1 -0.006 0.024 -9999 0 -0.21 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.082 -9999 0 -0.47 31 31
RAPGEF1 0.039 0.088 -9999 0 -0.48 29 29
CTNND1 0 0.009 -9999 0 -0.29 1 1
regulation of calcium-dependent cell-cell adhesion -0.017 0.099 -9999 0 -0.6 29 29
CRK 0.03 0.096 -9999 0 -0.53 29 29
E-cadherin/gamma catenin/alpha catenin -0.015 0.087 -9999 0 -0.52 30 30
alphaE/beta7 Integrin -0.006 0.04 -9999 0 -0.61 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.036 -9999 0 -0.48 6 6
DLG1 -0.016 0.095 -9999 0 -0.58 29 29
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.039 -9999 0 -0.31 2 2
MLLT4 -0.005 0.06 -9999 0 -0.72 7 7
ARF6/GTP/NME1/Tiam1 -0.007 0.029 -9999 0 -10000 0 0
PI3K -0.01 0.05 -9999 0 -0.42 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.017 0.1 -9999 0 -0.61 30 30
TIAM1 -0.001 0.018 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.012 0.073 -9999 0 -0.45 29 29
AKT1 -0.006 0.028 -9999 0 -0.22 2 2
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
CDH1 -0.022 0.13 -9999 0 -0.8 29 29
RhoA/GDP 0.049 0.067 -9999 0 -0.34 29 29
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 3 3
CDC42/GDP 0.049 0.067 -9999 0 -0.34 29 29
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.056 -9999 0 -0.34 30 30
ITGB7 -0.009 0.058 -9999 0 -0.33 30 30
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.013 0.077 -9999 0 -0.47 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin -0.013 0.075 -9999 0 -0.46 29 29
mol:GDP 0.046 0.078 -9999 0 -0.41 29 29
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.026 -9999 0 -0.54 2 2
p120 catenin/RhoA/GDP -0.01 0.058 -9999 0 -0.35 29 29
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.03 -9999 0 -0.22 8 8
NME1 -0.015 0.064 -9999 0 -0.29 54 54
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.017 0.095 -9999 0 -0.57 30 30
regulation of cell-cell adhesion -0.007 0.042 -9999 0 -0.42 1 1
WASF2 -0.003 0.013 -9999 0 -10000 0 0
Rap1/GTP -0.01 0.055 -9999 0 -0.59 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.077 -9999 0 -0.44 32 32
CCND1 -0.009 0.037 -9999 0 -0.32 6 6
VAV2 0.035 0.092 -9999 0 -0.51 29 29
RAP1/GDP -0.009 0.055 -9999 0 -0.57 1 1
adherens junction assembly -0.016 0.092 -9999 0 -0.55 30 30
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.015 0.073 -9999 0 -0.42 32 32
E-cadherin/beta catenin -0.013 0.08 -9999 0 -0.49 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.016 0.095 -9999 0 -0.58 29 29
PIK3CA 0 0.009 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.054 -9999 0 -0.4 4 4
E-cadherin/beta catenin/alpha catenin -0.014 0.085 -9999 0 -0.52 29 29
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.1 -9999 0 -0.62 29 29
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.8 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.042 -10000 0 -0.48 4 4
IRAK/TOLLIP -0.001 0.01 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.031 0.12 -10000 0 -0.59 41 41
IL1A -0.006 0.041 -10000 0 -0.29 21 21
IL1B 0.01 0.094 -10000 0 -0.7 17 17
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -0.4 1 1
IL1R2 -0.037 0.15 -10000 0 -0.57 69 69
IL1R1 -0.015 0.11 -10000 0 -0.8 20 20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.062 0.24 32 -0.33 16 48
TOLLIP 0 0.009 -10000 0 -0.29 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.032 0.078 -10000 0 -0.39 23 23
MAP3K7 0 0.009 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.021 0.1 -10000 0 -1 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.012 0.071 -10000 0 -0.5 20 20
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.066 -10000 0 -0.46 20 20
IL1 beta fragment/IL1R1/IL1RAP -0.019 0.11 -10000 0 -0.55 35 35
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.028 0.072 -10000 0 -0.39 30 30
IRAK1 0.021 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.019 0.092 -10000 0 -0.61 22 22
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.059 -10000 0 -0.61 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.011 0.061 -10000 0 -0.37 21 21
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.019 0.11 -10000 0 -0.55 35 35
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.57 53 53
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.018 0.092 -10000 0 -0.92 4 4
IRAK3 -0.03 0.15 -10000 0 -0.78 41 41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.017 0.096 -10000 0 -0.49 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.047 -10000 0 -0.34 20 20
IL1 alpha/IL1R1/IL1RAP -0.013 0.078 -10000 0 -0.55 20 20
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0.009 -10000 0 -0.29 1 1
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.008 -10000 0 -10000 0 0
IL1RAP -0.001 0.024 -10000 0 -0.8 1 1
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.014 0.076 -10000 0 -0.81 4 4
CASP1 -0.004 0.055 -10000 0 -0.8 5 5
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.58 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.017 0.1 -10000 0 -0.52 35 35
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.29 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.053 -10000 0 -0.39 20 20
PIK3CA 0 0.009 -10000 0 -10000 0 0
IL1RN -0.012 0.065 -10000 0 -0.8 2 2
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.009 0.06 -10000 0 -0.42 22 22
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.049 -9999 0 -0.8 4 4
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.094 -9999 0 -0.36 67 67
GNAO1 -0.018 0.13 -9999 0 -0.78 26 26
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.011 0.052 -9999 0 -0.68 4 4
AKT3 0.015 0.18 -9999 0 -1.4 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.049 -9999 0 -0.79 4 4
GNAI2 0.012 0.002 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.031 0.18 -9999 0 -0.8 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.03 -9999 0 -0.3 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.1 -9999 0 -0.39 38 38
MAPK3 0.018 0.1 -9999 0 -0.47 16 16
MAPK1 0.018 0.1 -9999 0 -0.51 13 13
JAK2 0.021 0.1 -9999 0 -0.45 19 19
CXCR4 0.015 0.1 -9999 0 -0.48 18 18
FLT1 0.013 0.025 -9999 0 -0.81 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.1 -9999 0 -0.36 38 38
S1P/S1P3/Gi 0.01 0.1 -9999 0 -0.39 38 38
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.025 0.083 -9999 0 -0.5 13 13
VEGFA 0.01 0.033 -9999 0 -0.3 12 12
S1P/S1P2/Gi 0.009 0.099 -9999 0 -0.37 37 37
VEGFR1 homodimer/VEGFA homodimer 0.021 0.031 -9999 0 -0.63 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.006 0.04 -9999 0 -0.34 15 15
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
GNAZ 0.005 0.074 -9999 0 -0.8 9 9
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.087 -9999 0 -0.45 31 31
GNA15 -0.003 0.034 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
Rac1/GTP -0.025 0.083 -9999 0 -0.5 13 13
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.03 0.13 -9999 0 -0.8 25 25
CDC42/GTP -0.025 0.077 -9999 0 -0.49 4 4
PLCG1 0.009 0.091 -9999 0 -0.51 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.075 -9999 0 -0.48 4 4
S1PR5 -0.008 0.059 -9999 0 -0.8 3 3
S1PR4 -0.015 0.08 -9999 0 -0.36 44 44
MAPK3 0.009 0.091 -9999 0 -0.32 38 38
MAPK1 0.009 0.091 -9999 0 -0.51 4 4
S1P/S1P5/Gi -0.027 0.087 -9999 0 -0.37 35 35
GNAI1 -0.043 0.18 -9999 0 -0.8 57 57
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -9999 0 -0.53 3 3
RHOA -0.006 0.039 -9999 0 -0.45 6 6
S1P/S1P4/Gi -0.029 0.086 -9999 0 -0.35 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.073 -9999 0 -0.8 9 9
S1P/S1P4/G12/G13 -0.007 0.043 -9999 0 -0.48 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.079 0.33 1 -0.36 52 53
FRAP1 0.011 0.021 -10000 0 -10000 0 0
AKT1 -0.015 0.068 0.24 1 -0.41 11 12
INSR 0 0.009 -10000 0 -0.29 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.012 0.052 -10000 0 -0.33 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.017 -10000 0 -10000 0 0
TSC2 0 0.001 -10000 0 -10000 0 0
RHEB/GDP -0.01 0.045 -10000 0 -0.3 11 11
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.082 -10000 0 -0.42 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.019 0.043 0.19 1 -0.25 11 12
MAP3K5 0.009 0.028 -10000 0 -0.44 4 4
PIK3R1 -0.008 0.077 -10000 0 -0.8 10 10
apoptosis 0.009 0.028 -10000 0 -0.44 4 4
mol:LY294002 0 0 -10000 0 -0.002 43 43
EIF4B 0.025 0.039 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.006 0.029 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.007 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.019 0.084 -10000 0 -0.38 53 53
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.03 0.18 1 -0.18 10 11
FKBP1A 0 0.009 -10000 0 -10000 0 0
RHEB/GTP -0.01 0.045 -10000 0 -0.3 11 11
mol:Amino Acids 0 0 -10000 0 -0.002 43 43
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.016 0.071 0.26 1 -0.32 52 53
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.004 0.04 -10000 0 -0.62 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.013 0.056 -10000 0 -0.36 11 11
tumor necrosis factor receptor activity 0 0 0.002 43 -10000 0 43
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.01 0.09 -10000 0 -0.45 43 43
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
PDK2 -0.017 0.077 0.26 1 -0.34 55 56
EIF4EBP1 0.013 0.01 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
PPP2R5D 0.018 0.02 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.006 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -0.003 10 12
EEF2 0.016 0.006 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.023 0.076 0.5 6 -10000 0 6
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -10000 0 -0.53 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.03 0.13 -10000 0 -0.8 25 25
RhoA/GTP -0.024 0.078 -10000 0 -0.52 6 6
negative regulation of cAMP metabolic process -0.027 0.087 -10000 0 -0.36 35 35
GNAZ -0.007 0.073 -10000 0 -0.8 9 9
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.059 -10000 0 -0.8 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.027 0.087 -10000 0 -0.37 35 35
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.8 57 57
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.029 -10000 0 -0.36 4 4
NFATC2 0.016 0.064 -10000 0 -0.31 11 11
NFATC3 0 0.016 -10000 0 -0.51 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.096 -10000 0 -0.4 36 36
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.019 0.078 -10000 0 -0.49 18 18
BCL2/BAX -0.022 0.11 -10000 0 -0.61 37 37
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
CABIN1/MEF2D -0.02 0.082 -10000 0 -0.52 18 18
Calcineurin A alpha-beta B1/BCL2 -0.028 0.15 -10000 0 -0.79 37 37
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.02 0.081 0.51 18 -10000 0 18
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.03 0.088 -10000 0 -0.29 107 107
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.017 0.1 -10000 0 -0.51 34 34
MAP3K8 -0.007 0.073 -10000 0 -0.74 10 10
NFAT4/CK1 alpha -0.001 0.017 -10000 0 -0.38 2 2
MEF2D/NFAT1/Cbp/p300 -0.036 0.091 -10000 0 -0.46 3 3
CABIN1 0.011 0.097 -10000 0 -0.41 36 36
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.8 1 1
CAMK4 -0.011 0.06 -10000 0 -0.3 39 39
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.045 -10000 0 -0.61 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.07 -10000 0 -0.79 8 8
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.021 -10000 0 -0.4 1 1
PRKCH -0.001 0.024 -10000 0 -0.8 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.007 0.036 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.025 -10000 0 -10000 0 0
PRKCB -0.02 0.11 -10000 0 -0.54 38 38
PRKCE 0 0 -10000 0 -10000 0 0
JNK2/NFAT4 0 0.014 -10000 0 -0.46 1 1
BAD/BCL-XL 0 0.006 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.29 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.025 -10000 0 -0.79 1 1
PRKCA -0.021 0.13 -10000 0 -0.76 29 29
PRKCG -0.012 0.059 -10000 0 -0.29 45 45
PRKCQ -0.038 0.17 -10000 0 -0.8 47 47
FKBP38/BCL2 -0.021 0.11 -10000 0 -0.61 37 37
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.048 -10000 0 -0.38 9 9
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.033 -10000 0 -0.53 1 1
NFATc/ERK1 0.051 0.03 -10000 0 -0.36 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.019 0.077 -10000 0 -0.49 18 18
NR4A1 -0.008 0.22 -10000 0 -0.7 88 88
GSK3B 0.01 0.004 -10000 0 -10000 0 0
positive T cell selection 0 0.016 -10000 0 -0.51 1 1
NFAT1/CK1 alpha -0.015 0.039 -10000 0 -0.29 3 3
RCH1/ KPNB1 -0.019 0.056 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.015 0.068 -10000 0 -0.3 54 54
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
NFATc/p38 alpha 0.051 0.031 -10000 0 -0.36 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.028 0.15 -10000 0 -0.8 37 37
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.005 0.05 -10000 0 -0.47 12 12
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.012 -10000 0 -0.4 1 1
GATA1/HDAC4 -0.004 0.03 -10000 0 -0.61 1 1
GATA1/HDAC5 -0.003 0.024 -10000 0 -10000 0 0
GATA2/HDAC5 -0.019 0.099 -10000 0 -0.61 28 28
HDAC5/BCL6/BCoR -0.004 0.045 -10000 0 -0.52 8 8
HDAC9 -0.01 0.079 -10000 0 -0.51 21 21
Glucocorticoid receptor/Hsp90/HDAC6 -0.008 0.062 -10000 0 -0.52 15 15
HDAC4/ANKRA2 -0.001 0.019 -10000 0 -0.61 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.025 0.13 -10000 0 -0.63 42 42
HDAC4/RFXANK -0.001 0.023 -10000 0 -0.61 1 1
BCOR -0.002 0.035 -10000 0 -0.8 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.001 0.013 -10000 0 -0.29 2 2
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.064 -10000 0 -0.61 12 12
Histones -0.003 0.025 -10000 0 -0.26 10 10
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.8 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.019 -10000 0 -0.61 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -10000 0 -10000 0 0
CAMK4 -0.011 0.06 -10000 0 -0.3 39 39
Tubulin/HDAC6 -0.001 0.017 -10000 0 -0.52 1 1
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.005 0.038 -10000 0 -0.29 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.094 -10000 0 -0.8 15 15
SUMO1/HDAC4 0 0.013 -10000 0 -0.44 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.019 -10000 0 -0.61 1 1
Tubulin -0.001 0.02 -10000 0 -0.61 1 1
HDAC4/14-3-3 E -0.001 0.019 -10000 0 -0.61 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.005 0.053 -10000 0 -0.61 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0 0.016 -10000 0 -0.52 1 1
HDAC4/SRF -0.006 0.035 -10000 0 -0.52 2 2
HDAC4/ER alpha -0.12 0.22 -10000 0 -0.61 163 163
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.025 -10000 0 -0.26 10 10
cell motility -0.001 0.017 -10000 0 -0.52 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.005 0.06 -10000 0 -0.8 6 6
HDAC4/CaMK II delta B -0.001 0.024 -10000 0 -0.79 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.16 0.29 -10000 0 -0.58 286 286
HDAC6/HDAC11 -0.001 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.024 -10000 0 -0.8 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.019 -10000 0 -0.44 2 2
GNG2 -0.009 0.084 -10000 0 -0.8 12 12
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.028 -10000 0 -0.46 3 3
HDAC11 -0.001 0.018 -10000 0 -0.29 4 4
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.001 0.02 -10000 0 -0.29 5 5
nuclear import 0 0.013 0.43 1 -10000 0 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.007 0.053 -9999 0 -0.34 23 23
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.002 0.017 -9999 0 -0.36 2 2
GNAO1 -0.03 0.13 -9999 0 -0.8 25 25
mol:Sphinganine-1-P 0.017 0.04 -9999 0 -0.61 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.028 -9999 0 -0.29 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.015 -9999 0 -0.31 2 2
S1PR5 -0.008 0.059 -9999 0 -0.8 3 3
S1PR4 -0.015 0.08 -9999 0 -0.36 44 44
GNAI1 -0.043 0.18 -9999 0 -0.8 57 57
S1P/S1P5/G12 -0.005 0.033 -9999 0 -0.47 3 3
S1P/S1P3/Gq -0.004 0.035 -9999 0 -0.29 15 15
S1P/S1P4/Gi -0.027 0.083 -9999 0 -0.34 39 39
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
GNAZ -0.007 0.073 -9999 0 -0.8 9 9
GNA14 -0.013 0.087 -9999 0 -0.45 31 31
GNA15 -0.003 0.034 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
ABCC1 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.33 30 30
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.022 0.11 -9999 0 -0.61 37 37
AKT1 0.08 0.068 -9999 0 -0.68 6 6
PTK2B -0.021 0.11 -9999 0 -1 7 7
VEGFR2 homodimer/Frs2 -0.008 0.08 -9999 0 -0.8 9 9
CAV1 -0.17 0.33 -9999 0 -0.8 228 228
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.008 0.075 -9999 0 -0.74 9 9
endothelial cell proliferation 0.082 0.084 -9999 0 -0.69 6 6
mol:Ca2+ 0.05 0.072 -9999 0 -0.87 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.007 0.071 -9999 0 -0.94 5 5
RP11-342D11.1 0.042 0.072 -9999 0 -0.67 9 9
CDH5 -0.007 0.073 -9999 0 -0.8 9 9
VEGFA homodimer -0.001 0.012 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.021 0.13 -9999 0 -0.78 28 28
HRAS/GDP -0.006 0.057 -9999 0 -0.76 5 5
SH2D2A -0.035 0.1 -9999 0 -0.3 122 122
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.053 -9999 0 -0.68 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.021 0.086 -9999 0 -0.7 12 12
VEGFR1 homodimer -0.001 0.024 -9999 0 -0.79 1 1
SHC/GRB2/SOS1 -0.004 0.064 -9999 0 -0.84 5 5
GRB10 0.05 0.072 -9999 0 -0.87 5 5
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
PAK1 -0.006 0.043 -9999 0 -0.29 23 23
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.091 -9999 0 -1 7 7
HRAS -0.002 0.027 -9999 0 -0.29 9 9
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.064 -9999 0 -0.59 7 7
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -0.29 10 10
oxygen and reactive oxygen species metabolic process -0.007 0.069 -9999 0 -0.69 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.042 -9999 0 -0.8 3 3
Nck/Pak -0.004 0.027 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.008 0.082 -9999 0 -0.77 10 10
mol:GDP -0.004 0.06 -9999 0 -0.8 5 5
mol:NADP 0.073 0.05 -9999 0 -0.56 5 5
eNOS/Hsp90 0.075 0.047 -9999 0 -0.51 5 5
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
mol:IP3 0.05 0.073 -9999 0 -0.89 5 5
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.026 -9999 0 -0.8 1 1
VEGFA -0.003 0.03 -9999 0 -0.29 12 12
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.055 0.1 -9999 0 -0.96 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.55 38 38
PTPN6 -0.001 0.013 -9999 0 -0.29 2 2
EPAS1 -0.006 0.072 -9999 0 -0.73 9 9
mol:L-citrulline 0.073 0.05 -9999 0 -0.56 5 5
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.071 -9999 0 -0.7 9 9
VEGFR2 homodimer/VEGFA homodimer -0.007 0.074 -9999 0 -0.74 9 9
VEGFR2/3 heterodimer -0.008 0.09 -9999 0 -0.87 10 10
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.054 0.078 -9999 0 -0.94 5 5
VEGFR2 homodimer 0.028 0.091 -9999 0 -0.9 9 9
FLT1 -0.001 0.024 -9999 0 -0.8 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.051 0.081 -9999 0 -0.84 6 6
MAPK1 0.051 0.081 -9999 0 -0.84 6 6
VEGFA145/NRP2 -0.004 0.04 -9999 0 -0.66 3 3
VEGFR1/2 heterodimer -0.007 0.085 -9999 0 -0.85 9 9
KDR 0.028 0.091 -9999 0 -0.9 9 9
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.081 -9999 0 -0.97 6 6
SRC 0 0.009 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process 0.053 0.083 -9999 0 -0.87 6 6
PI3K -0.008 0.074 -9999 0 -0.89 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.074 -9999 0 -0.74 9 9
FES 0.049 0.079 -9999 0 -0.73 8 8
GAB1 -0.006 0.069 -9999 0 -0.94 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.075 -9999 0 -0.74 9 9
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.17 -9999 0 -0.6 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.076 -9999 0 -0.72 10 10
PI3K/GAB1 0.079 0.075 -9999 0 -0.71 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.002 0.069 -9999 0 -0.9 5 5
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.008 0.084 -9999 0 -0.81 10 10
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
CDC42 0.05 0.075 -9999 0 -0.92 5 5
actin cytoskeleton reorganization -0.02 0.084 -9999 0 -0.69 12 12
PTK2 0.051 0.11 -9999 0 -1 7 7
EDG1 0.042 0.072 -9999 0 -0.67 9 9
mol:DAG 0.05 0.073 -9999 0 -0.89 5 5
CaM/Ca2+ -0.006 0.061 -9999 0 -0.81 5 5
MAP2K3 0.056 0.078 -9999 0 -0.86 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.07 -9999 0 -0.93 5 5
PLCG1 0.05 0.075 -9999 0 -0.92 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.008 0.072 -9999 0 -0.85 6 6
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.008 0.074 -9999 0 -0.74 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.075 -9999 0 -0.74 9 9
cell migration 0.078 0.089 -9999 0 -0.79 6 6
mol:PI-3-4-5-P3 -0.007 0.066 -9999 0 -0.78 6 6
FYN -0.002 0.035 -9999 0 -0.8 2 2
VEGFB/NRP1 -0.006 0.062 -9999 0 -0.83 5 5
mol:NO 0.073 0.05 -9999 0 -0.56 5 5
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.057 -9999 0 -0.76 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.07 -9999 0 -0.93 5 5
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.029 0.15 -9999 0 -0.8 37 37
NOS3 0.075 0.057 -9999 0 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.1 -9999 0 -0.54 36 36
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.045 0.11 -9999 0 -0.98 5 5
PRKCB 0.047 0.1 -9999 0 -0.9 7 7
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.007 0.067 -9999 0 -0.67 9 9
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.08 -9999 0 -0.79 9 9
VEGFA165/NRP2 -0.004 0.04 -9999 0 -0.66 3 3
MAPKKK cascade -0.004 0.058 -9999 0 -0.76 5 5
NRP2 -0.003 0.043 -9999 0 -0.67 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.024 -9999 0 -0.8 1 1
FAK1/Paxillin 0.055 0.1 -9999 0 -0.96 6 6
MAP3K13 0.048 0.082 -9999 0 -0.67 10 10
PDPK1 0.074 0.066 -9999 0 -0.66 6 6
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0 0.017 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.007 0.046 -10000 0 -0.29 27 27
TCEB1 -0.001 0.013 -10000 0 -0.29 2 2
VHL/Elongin B/Elongin C/HIF2A -0.006 0.039 -10000 0 -0.43 2 2
EPO 0.14 0.15 -10000 0 -0.72 2 2
FIH (dimer) 0.023 0.012 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.31 1 1
SERPINE1 0.16 0.15 -10000 0 -0.68 4 4
FLT1 -0.003 0.08 -10000 0 -1.1 5 5
ADORA2A 0.14 0.16 -10000 0 -0.64 5 5
germ cell development 0.16 0.15 -10000 0 -0.65 6 6
SLC11A2 0.16 0.15 -10000 0 -0.68 4 4
BHLHE40 0.16 0.16 -10000 0 -0.81 5 5
HIF1AN 0.023 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.013 0.07 -10000 0 -0.42 5 5
ETS1 0.022 0.057 -10000 0 -0.81 5 5
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.007 0.11 -10000 0 -1.2 8 8
PGK1 0.16 0.15 -10000 0 -0.68 4 4
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.18 0.16 -10000 0 -0.77 5 5
EPAS1 0.092 0.083 -10000 0 -0.41 5 5
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.13 0.25 -10000 0 -0.7 73 73
EFNA1 0.16 0.15 -10000 0 -0.68 4 4
FXN 0.15 0.15 -10000 0 -0.67 4 4
POU5F1 0.16 0.16 -10000 0 -0.68 6 6
neuron apoptosis -0.17 0.16 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.083 -10000 0 -0.29 78 78
EGLN2 0.021 0.024 -10000 0 -0.31 2 2
EGLN1 0.022 0.028 -10000 0 -0.8 1 1
VHL/Elongin B/Elongin C -0.004 0.023 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.01 -10000 0 -10000 0 0
SLC2A1 0.15 0.15 -10000 0 -0.65 6 6
TWIST1 0.13 0.21 -10000 0 -0.7 44 44
ELK1 0.019 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.008 0.063 -10000 0 -0.43 4 4
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 -0.006 0.056 -9999 0 -0.8 4 4
Caspase 8 (4 units) -0.009 0.047 -9999 0 -0.99 1 1
NEF -0.006 0.027 -9999 0 -0.22 10 10
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.035 0.083 -9999 0 -0.8 9 9
CYCS 0.04 0.059 -9999 0 -0.94 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.12 -9999 0 -0.69 30 30
MAP2K7 0.042 0.049 -9999 0 -0.81 1 1
protein ubiquitination 0.066 0.034 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.003 0.049 -9999 0 -0.8 4 4
BID 0.033 0.062 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.033 -9999 0 -0.33 9 9
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.003 0.049 -9999 0 -0.8 4 4
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.004 0.036 -9999 0 -0.29 16 16
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -0.34 9 9
MAPK8 0.045 0.062 -9999 0 -0.47 9 9
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.016 -9999 0 -0.29 3 3
TRAF2 -0.001 0.018 -9999 0 -0.29 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.012 0.057 -9999 0 -0.34 21 21
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.031 -9999 0 -0.37 2 2
CHUK 0.068 0.035 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.047 -9999 0 -0.52 7 7
TCRz/NEF -0.025 0.11 -9999 0 -0.52 40 40
TNF -0.016 0.094 -9999 0 -0.46 36 36
FASLG -0.007 0.15 -9999 0 -0.66 40 40
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.012 0.069 -9999 0 -0.53 16 16
CASP6 -0.004 0.031 -9999 0 -0.7 1 1
CASP7 0.073 0.076 -9999 0 -0.62 9 9
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.073 0.076 -9999 0 -0.62 9 9
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.041 -9999 0 -0.61 4 4
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.038 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.009 0.054 -9999 0 -0.51 9 9
BCL2 0.036 0.1 -9999 0 -0.43 43 43
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.025 0.3 2 -0.37 3 5
DAPP1 0.035 0.053 -10000 0 -0.58 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.079 -10000 0 -0.54 11 11
mol:DAG 0.051 0.051 0.21 1 -0.27 7 8
HRAS -0.002 0.026 -10000 0 -0.29 9 9
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.003 0.026 -10000 0 -0.3 2 2
PLCG2 -0.002 0.036 -10000 0 -0.63 3 3
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.29 1 1
mol:GTP -0.001 0.023 0.26 2 -0.39 2 4
ARF1/GTP -0.001 0.022 0.28 2 -0.37 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.024 -10000 0 -0.8 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.39 2 4
ADAP1 -0.003 0.032 0.26 2 -0.39 5 7
ARAP3 -0.001 0.023 0.26 2 -0.39 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.058 -10000 0 -0.31 36 36
ARHGEF6 -0.011 0.094 -10000 0 -0.8 15 15
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
FYN -0.002 0.035 -10000 0 -0.8 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.026 -10000 0 -0.54 2 2
mol:Ca2+ 0.039 0.029 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
ZAP70 -0.031 0.12 -10000 0 -0.42 76 76
mol:IP3 0.047 0.038 -10000 0 -0.21 2 2
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.026 -10000 0 -0.3 2 2
RhoA/GDP -0.002 0.022 0.28 2 -0.34 2 4
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.061 0.035 0.26 2 -10000 0 2
SRC 0 0.009 -10000 0 -0.29 1 1
PLEKHA2 0.03 0.008 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.77 2 2
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
ARF6/GTP -0.001 0.021 0.3 2 -10000 0 2
RhoA/GTP -0.001 0.021 0.25 2 -0.36 2 4
Src family/SYK family/BLNK-LAT -0.011 0.057 -10000 0 -0.54 6 6
BLK -0.043 0.11 -10000 0 -0.3 150 150
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 0.26 2 -0.36 2 4
HCK -0.004 0.033 -10000 0 -0.29 14 14
CYTH3 -0.001 0.025 0.26 2 -0.38 3 5
CYTH2 -0.001 0.021 0.26 2 -0.36 2 4
KRAS -0.001 0.013 -10000 0 -0.29 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.053 -10000 0 -0.55 9 9
SGK1 -0.004 0.055 0.23 2 -0.71 6 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.033 -10000 0 -0.28 4 4
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.29 1 1
ARF6/GDP -0.002 0.023 0.29 2 -0.34 2 4
mol:PI-3-4-5-P3 -0.001 0.025 0.36 2 -0.39 2 4
ARAP3/RAP1A/GTP -0.001 0.022 0.25 2 -0.39 2 4
VAV1 -0.003 0.044 -10000 0 -0.59 5 5
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.002 0.019 -10000 0 -0.39 2 2
PLEKHA1 0.03 0.018 -10000 0 -0.52 1 1
Rac1/GDP -0.003 0.026 -10000 0 -0.3 2 2
LAT -0.005 0.048 -10000 0 -0.36 16 16
Rac1/GTP -0.006 0.046 -10000 0 -0.37 15 15
ITK -0.02 0.085 0.26 1 -0.44 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.058 0.066 0.24 1 -0.39 7 8
LCK -0.021 0.1 -10000 0 -0.42 52 52
BTK -0.001 0.022 0.26 2 -0.36 2 4
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.001 0.028 -9999 0 -0.9 1 1
VEGFR1 homodimer/NRP1 -0.001 0.028 -9999 0 -0.91 1 1
mol:DAG 0.038 0.032 -9999 0 -0.64 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.029 -9999 0 -0.85 1 1
CaM/Ca2+ -0.002 0.028 -9999 0 -0.61 2 2
HIF1A 0 0.012 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.047 -9999 0 -0.71 1 1
PLCG1 0.038 0.033 -9999 0 -0.65 2 2
NOS3 0.061 0.032 -9999 0 -0.7 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.061 0.031 -9999 0 -0.67 1 1
FLT1 0.029 0.032 -9999 0 -1 1 1
PGF -0.002 0.032 -9999 0 -0.38 6 6
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.047 -9999 0 -0.78 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
eNOS/Hsp90 0.065 0.03 -9999 0 -0.64 1 1
endothelial cell proliferation 0.036 0.088 -9999 0 -0.64 5 5
mol:Ca2+ 0.038 0.032 -9999 0 -0.64 2 2
MAPK3 0.039 0.082 -9999 0 -0.44 27 27
MAPK1 0.039 0.082 -9999 0 -1.1 1 1
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
PLGF homodimer -0.002 0.032 -9999 0 -0.38 6 6
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.33 -9999 0 -0.8 228 228
VEGFA homodimer -0.003 0.031 -9999 0 -0.29 12 12
VEGFR1 homodimer/VEGFA homodimer -0.002 0.031 -9999 0 -0.9 1 1
platelet activating factor biosynthetic process 0.046 0.079 -9999 0 -1.1 1 1
PI3K -0.006 0.051 -9999 0 -0.47 12 12
PRKCA 0.032 0.086 -9999 0 -0.47 28 28
PRKCB 0.034 0.077 -9999 0 -0.48 20 20
VEGFR1 homodimer/PLGF homodimer -0.002 0.033 -9999 0 -0.71 2 2
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.032 -9999 0 -0.64 2 2
RASA1 0.039 0.027 -9999 0 -0.83 1 1
NRP2 -0.003 0.043 -9999 0 -0.67 4 4
VEGFR1 homodimer 0.029 0.032 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.18 -9999 0 -0.63 6 6
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.05 -9999 0 -0.46 12 12
mol:L-citrulline 0.061 0.031 -9999 0 -0.67 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.027 -9999 0 -0.8 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.028 -9999 0 -0.84 1 1
CD2AP 0 0.009 -9999 0 -0.29 1 1
PI3K/GAB1 -0.005 0.048 -9999 0 -0.74 1 1
PDPK1 -0.005 0.047 -9999 0 -0.73 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.028 -9999 0 -0.84 1 1
mol:NADP 0.061 0.031 -9999 0 -0.67 1 1
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
ubiquitin-dependent protein catabolic process -0.002 0.027 -9999 0 -0.78 1 1
VEGFR1 homodimer/NRP2 -0.002 0.047 -9999 0 -0.79 3 3
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.028 -10000 0 -0.46 4 4
TRAF2/ASK1 -0.003 0.034 -10000 0 -0.53 4 4
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.046 -10000 0 -0.39 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.063 -10000 0 -0.38 8 8
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.036 0.096 -10000 0 -10000 0 0
TXN 0.008 0.005 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.8 1 1
MAP3K6 -0.001 0.024 -10000 0 -0.8 1 1
MAP3K7 0 0.009 -10000 0 -0.29 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.003 0.042 -10000 0 -0.61 5 5
TAK1/TAB family 0.001 0.012 0.22 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.006 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
RAC1/OSM/MEKK3/MKK3 -0.006 0.024 -10000 0 -0.4 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.071 0.21 -10000 0 -0.8 76 76
CCM2 -0.001 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.045 0.14 -10000 0 -0.53 76 76
MAPK11 -0.002 0.042 -10000 0 -0.8 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.042 0.13 -10000 0 -0.49 79 79
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 -0.004 0.095 -10000 0 -0.44 48 48
TAOK2 0.017 0 -10000 0 -10000 0 0
TAOK3 0.017 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.003 0.049 -10000 0 -0.8 4 4
MAP3K10 0 0.009 -10000 0 -0.29 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.032 -10000 0 -0.52 4 4
GADD45/MTK1/MTK1 -0.013 0.036 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.001 0.024 -9999 0 -0.8 1 1
SMAD2 0.014 0.004 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.016 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0.016 -9999 0 -0.52 1 1
SMAD2/SMAD2/SMAD4 -0.01 0.031 -9999 0 -0.53 1 1
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0.015 -9999 0 -0.47 1 1
MAP3K1 -0.001 0.024 -9999 0 -0.8 1 1
TRAP-1/SMAD4 -0.009 0.072 -9999 0 -0.61 15 15
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.011 0.091 -9999 0 -0.8 14 14
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.29 1 1
KPNA2 -0.03 0.088 -9999 0 -0.29 107 107
PIAS4 0 0 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.046 -9999 0 -0.56 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.041 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/APS/CBL -0.009 0.044 -9999 0 -0.52 4 4
AKT1 -0.011 0.049 -9999 0 -0.52 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.036 0.053 -9999 0 -0.59 6 6
PIK3CA 0 0.009 -9999 0 -10000 0 0
FGR -0.003 0.039 -9999 0 -0.53 5 5
mol:Ca2+ 0.033 0.049 -9999 0 -0.68 4 4
MYC 0.039 0.14 -9999 0 -0.83 25 25
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.029 -9999 0 -0.42 4 4
LRP1/PDGFRB/PDGFB -0.007 0.068 -9999 0 -0.6 13 13
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.049 -9999 0 -0.7 4 4
PTEN -0.002 0.035 -9999 0 -0.8 2 2
GRB2 0 0.009 -9999 0 -0.29 1 1
GRB7 -0.022 0.084 -9999 0 -0.31 75 75
PDGFB-D/PDGFRB/SHP2 -0.002 0.037 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.037 -9999 0 -0.6 4 4
cell cycle arrest -0.004 0.041 -9999 0 -0.6 4 4
HRAS -0.002 0.027 -9999 0 -0.29 9 9
HIF1A 0.051 0.058 -9999 0 -0.45 3 3
GAB1 0.035 0.056 -9999 0 -0.68 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.039 0.054 -9999 0 -0.62 4 4
PDGFB-D/PDGFRB -0.003 0.036 -9999 0 -0.53 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.037 -9999 0 -0.6 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.05 -9999 0 -0.57 6 6
positive regulation of MAPKKK cascade -0.002 0.037 -9999 0 -0.6 4 4
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
mol:IP3 0.033 0.05 -9999 0 -0.7 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.067 -9999 0 -0.61 7 7
SHB -0.001 0.026 -9999 0 -0.8 1 1
BLK -0.002 0.05 -9999 0 -0.58 7 7
PTPN2 0.002 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.037 -9999 0 -0.6 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.063 -9999 0 -0.61 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.037 -9999 0 -0.6 4 4
LCK -0.01 0.082 -9999 0 -0.64 16 16
PDGFRB 0.009 0.05 -9999 0 -0.8 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.034 -9999 0 -0.51 4 4
ABL1 0.034 0.05 -9999 0 -0.63 4 4
PDGFB-D/PDGFRB/CBL 0.034 0.061 -9999 0 -0.79 4 4
PTPN1 -0.001 0.03 -9999 0 -0.29 11 11
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.039 -9999 0 -10000 0 0
cell proliferation 0.041 0.12 -9999 0 -0.72 25 25
SLA -0.002 0.027 -9999 0 -0.29 9 9
actin cytoskeleton reorganization -0.003 0.029 -9999 0 -10000 0 0
SRC -0.002 0.034 -9999 0 -0.51 4 4
PI3K -0.013 0.055 -9999 0 -0.58 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.013 0.055 -9999 0 -0.52 7 7
SH2B2 -0.014 0.061 -9999 0 -0.29 49 49
PLCgamma1/SPHK1 0.036 0.055 -9999 0 -0.61 6 6
LYN -0.002 0.034 -9999 0 -0.51 4 4
LRP1 -0.008 0.081 -9999 0 -0.8 11 11
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.042 -9999 0 -0.8 3 3
STAT5A -0.006 0.069 -9999 0 -0.8 8 8
NCK1-2/p130 Cas -0.002 0.027 -9999 0 -0.42 4 4
SPHK1 0.003 0.055 -9999 0 -0.33 23 23
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.05 -9999 0 -0.7 4 4
PLCG1 0.033 0.051 -9999 0 -0.73 4 4
NHERF/PDGFRB -0.015 0.053 -9999 0 -0.45 6 6
YES1 -0.003 0.039 -9999 0 -0.53 5 5
cell migration -0.015 0.052 -9999 0 -0.44 6 6
SHC/Grb2/SOS1 -0.003 0.027 -9999 0 -0.42 4 4
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
SLC9A3R1 -0.025 0.082 -9999 0 -0.29 92 92
NHERF1-2/PDGFRB/PTEN -0.014 0.05 -9999 0 -0.47 6 6
FYN -0.004 0.062 -9999 0 -0.9 4 4
DOK1 0.029 0.036 -9999 0 -0.47 4 4
HRAS/GTP -0.002 0.018 -9999 0 -0.2 9 9
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.083 -9999 0 -0.44 27 27
PRKCD 0.03 0.036 -9999 0 -0.48 4 4
FER 0.025 0.063 -9999 0 -0.48 15 15
MAPKKK cascade -0.002 0.028 -9999 0 -0.41 4 4
RASA1 0.03 0.035 -9999 0 -0.48 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.03 -9999 0 -0.44 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.042 -9999 0 -0.61 5 5
chemotaxis 0.034 0.049 -9999 0 -0.61 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.055 -9999 0 -0.69 3 3
Bovine Papilomavirus E5/PDGFRB -0.002 0.038 -9999 0 -0.62 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.004 0.025 -9999 0 -0.4 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.01 0.043 -9999 0 -0.45 3 3
EPO -0.048 0.11 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.031 0.069 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.039 -9999 0 -0.4 10 10
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.006 0.059 -9999 0 -0.61 10 10
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.01 0.025 -9999 0 -0.5 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
MADCAM1 -0.011 0.056 -9999 0 -0.29 41 41
cell adhesion -0.01 0.043 -9999 0 -0.45 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.025 0.057 -9999 0 -0.47 12 12
ITGB7 -0.009 0.058 -9999 0 -0.33 30 30
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.058 -9999 0 -0.52 12 12
p130Cas/Crk/Dock1 -0.006 0.042 -9999 0 -10000 0 0
VCAM1 -0.011 0.087 -9999 0 -0.63 18 18
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.034 0.053 -9999 0 -0.44 12 12
EPOR 0 0.009 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
Rac1/GTP -0.003 0.041 -9999 0 -0.41 10 10
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.004 0.052 -9999 0 -0.48 12 12
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.043 -9999 0 -0.4 12 12
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.025 -9999 0 -0.29 8 8
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.021 -9999 0 -10000 0 0
YY1/LSF -0.001 0.018 -9999 0 -0.4 2 2
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.039 -9999 0 -0.36 12 12
I kappa B alpha/HDAC1 -0.004 0.026 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.033 -9999 0 -0.31 12 12
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.026 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -0.28 12 12
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.025 0.13 -9999 0 -0.63 42 42
GATA1 -0.005 0.038 -9999 0 -0.29 18 18
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.007 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.29 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.024 -9999 0 -0.8 1 1
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.03 -9999 0 -0.28 12 12
KAT2B -0.001 0.024 -9999 0 -0.8 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.008 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.024 -9999 0 -0.8 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -0.3 1 1
YY1/HDAC1 0 0.009 -9999 0 -0.3 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.006 -9999 0 -10000 0 0
PPARG -0.094 0.17 -9999 0 -0.38 263 263
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.026 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -0.29 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.03 -9999 0 -0.28 12 12
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 0.011 -9999 0 -0.35 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.29 1 1
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.016 -9999 0 -0.46 1 1
YY1/SAP30/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.03 -9999 0 -0.27 12 12
histone deacetylation 0.046 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.023 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.018 0.081 -9999 0 -0.48 28 28
GATA1/HDAC1 -0.003 0.024 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.03 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.07 -9999 0 -0.61 12 12
SIN3/HDAC complex/Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD Complex 0 0.007 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.021 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.018 -9999 0 -0.47 1 1
GATA1/Fog1 -0.005 0.029 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.094 -9999 0 -0.46 36 36
negative regulation of cell growth 0.046 0.009 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.045 -9999 0 -0.43 12 12
SIN3/HDAC complex/NCoR1 0 0.01 -9999 0 -10000 0 0
TFCP2 -0.001 0.024 -9999 0 -0.8 1 1
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.29 1 1
MBD2 0 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.029 0.039 -9999 0 -10000 0 0
PLK1 0.005 0.12 -9999 0 -0.67 5 5
CDKN1B 0.079 0.071 -9999 0 -0.54 3 3
FOXO3 0.039 0.11 -9999 0 -0.56 12 12
KAT2B 0.008 0.029 -9999 0 -0.83 1 1
FOXO1/SIRT1 0.007 0.038 -9999 0 -0.32 11 11
CAT 0.042 0.12 -9999 0 -1 6 6
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.032 0.041 -9999 0 -0.36 11 11
MAPK10 -0.039 0.18 -9999 0 -0.45 165 165
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.089 -9999 0 -0.39 2 2
response to oxidative stress 0.005 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.016 0.069 -9999 0 -0.52 8 8
XPO1 0.001 0.004 -9999 0 -10000 0 0
EP300 0.01 0.005 -9999 0 -10000 0 0
BCL2L11 0.028 0.02 -9999 0 -10000 0 0
FOXO1/SKP2 -0.004 0.033 -9999 0 -0.32 11 11
mol:GDP 0.005 0.012 -9999 0 -10000 0 0
RAN 0.012 0.001 -9999 0 -10000 0 0
GADD45A 0.067 0.064 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.028 -9999 0 -10000 0 0
MST1 -0.003 0.093 -9999 0 -0.62 20 20
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.048 0.046 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.033 0.043 -9999 0 -0.45 8 8
MAPK9 0.036 0.007 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.016 -9999 0 -0.29 3 3
SIRT1 0.002 0.008 -9999 0 -10000 0 0
SOD2 0.09 0.078 -9999 0 -0.45 1 1
RBL2 0.06 0.083 -9999 0 -0.56 2 2
RAL/GDP 0.011 0.016 -9999 0 -10000 0 0
CHUK 0.009 0.013 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.03 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.003 0.18 -9999 0 -1.5 14 14
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.012 0.001 -9999 0 -10000 0 0
IKBKB 0.008 0.018 -9999 0 -10000 0 0
CCNB1 0.032 0.12 -9999 0 -0.64 6 6
FOXO1-3a-4/beta catenin -0.009 0.043 -9999 0 -0.41 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.033 -9999 0 -0.32 11 11
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.062 -9999 0 -0.8 6 6
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.068 0.079 -9999 0 -10000 0 0
SFN -0.017 0.1 -9999 0 -0.51 34 34
CDK2 0.004 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.027 0.051 -9999 0 -10000 0 0
CREBBP 0.004 0.006 -9999 0 -10000 0 0
FBXO32 0.041 0.13 -9999 0 -1.2 6 6
BCL6 0.054 0.13 -9999 0 -1.2 7 7
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.01 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.007 0.058 -9999 0 -0.52 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.024 -9999 0 -10000 0 0
NFKBIA 0.024 0.034 -9999 0 -0.27 13 13
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0.017 0 -9999 0 -10000 0 0
REL -0.01 0.088 -9999 0 -0.8 13 13
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.01 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
NFKB1 0.022 0.009 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.034 -9999 0 -0.26 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.023 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PI3K -0.006 0.059 -9999 0 -0.61 10 10
NF kappa B1 p50/RelA -0.004 0.029 -9999 0 -0.27 13 13
IKBKB -0.001 0.013 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.29 1 1
I kappa B alpha/PIK3R1 -0.008 0.05 -9999 0 -0.33 23 23
cell death -0.003 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.007 0.058 -9999 0 -0.52 13 13
LCK -0.021 0.1 -9999 0 -0.42 52 52
BCL3 -0.001 0.016 -9999 0 -0.29 3 3
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.004 0.019 -9999 0 -10000 0 0
CLOCK 0.005 0.085 -9999 0 -0.79 12 12
TIMELESS/CRY2 -0.002 0.011 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.014 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.017 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.04 0.02 -9999 0 -10000 0 0
NPAS2 0.009 0.062 -9999 0 -0.62 9 9
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.014 0.003 -9999 0 -10000 0 0
CHEK1 -0.007 0.044 -9999 0 -0.29 25 25
mol:HEME 0.014 0.003 -9999 0 -10000 0 0
PER1 -0.016 0.11 -9999 0 -0.8 21 21
BMAL/CLOCK/NPAS2 0.029 0.072 -9999 0 -0.51 18 18
BMAL1/CLOCK 0.041 0.054 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.004 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.004 0.019 -9999 0 -10000 0 0
mol:NADPH 0.014 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.011 0.064 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.002 0.022 -9999 0 -0.29 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.045 -10000 0 -0.55 1 1
BAG4 -0.006 0.056 -10000 0 -0.8 4 4
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.079 -10000 0 -0.51 21 21
BAX 0.032 0.019 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.1 2 2
IKBKB 0.052 0.044 -10000 0 -0.51 1 1
MAP2K2 0.044 0.024 -10000 0 -0.46 1 1
MAP2K1 0.044 0.024 -10000 0 -0.46 1 1
SMPD1 0.021 0.012 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.05 0.048 -10000 0 -0.45 3 3
MAP2K4 0.038 0.025 -10000 0 -0.38 2 2
protein ubiquitination 0.054 0.044 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.05 0.026 -10000 0 -0.49 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.024 -10000 0 -0.5 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.017 -10000 0 -0.14 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.022 -10000 0 -0.41 1 1
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.047 0.023 -10000 0 -0.45 1 1
MAPK1 0.047 0.023 -10000 0 -0.45 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.044 0.05 -10000 0 -0.47 3 3
KSR1 0.032 0.024 -10000 0 -0.52 1 1
MAPK8 0.041 0.047 -10000 0 -0.42 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.052 0.043 -10000 0 -0.51 1 1
TNF R/SODD -0.004 0.041 -10000 0 -0.61 4 4
TNF -0.016 0.094 -10000 0 -0.46 36 36
CYCS 0.037 0.026 0.15 32 -10000 0 32
IKBKG 0.052 0.043 -10000 0 -0.51 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.039 0.048 -10000 0 -0.36 9 9
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.026 0.15 32 -10000 0 32
TNF/TNF R/SODD -0.012 0.069 -10000 0 -0.53 16 16
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.028 0.012 -10000 0 -10000 0 0
NSMAF 0.046 0.045 -10000 0 -0.54 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.028 0.15 -10000 0 -0.8 37 37
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.077 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.007 0.04 -9999 0 -0.49 2 2
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -10000 0 0
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.002 0.042 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.02 -9999 0 -0.29 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.007 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.007 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.01 0.057 -9999 0 -0.31 35 35
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.011 0.07 -9999 0 -0.61 12 12
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.021 0.13 -9999 0 -0.76 29 29
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.094 -9999 0 -0.46 36 36
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0 0.008 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.06 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.028 0.046 -10000 0 -10000 0 0
regulation of axonogenesis 0.004 0.03 0.31 10 -10000 0 10
myoblast fusion 0.008 0.027 -10000 0 -10000 0 0
mol:GTP -0.005 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.03 -10000 0 -10000 0 0
ARF1/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GM1 0.006 0.014 -10000 0 -10000 0 0
mol:Choline 0.02 0.053 -10000 0 -0.51 10 10
lamellipodium assembly -0.004 0.032 -10000 0 -10000 0 0
MAPK3 0.021 0.025 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.031 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.027 -10000 0 -10000 0 0
ARF1/GDP -0.004 0.025 -10000 0 -10000 0 0
ARF6 0.007 0.008 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
TIAM1 0.011 0.019 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.025 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.022 -10000 0 -10000 0 0
KALRN -0.011 0.069 -10000 0 -0.48 21 21
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.022 -10000 0 -10000 0 0
NME1 -0.004 0.066 -10000 0 -0.29 54 54
Rac1/GDP -0.006 0.022 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.016 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.032 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.016 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.016 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GDP -0.005 0.03 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.011 0.059 -10000 0 -0.58 10 10
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.032 -10000 0 -10000 0 0
ruffle organization -0.004 0.03 -10000 0 -0.31 10 10
regulation of epithelial cell migration -0.005 0.016 -10000 0 -10000 0 0
PLD2 0.016 0.014 -10000 0 -10000 0 0
PIP5K1A -0.004 0.03 -10000 0 -0.31 10 10
mol:Phosphatidic acid 0.02 0.053 -10000 0 -0.51 10 10
Rac1/GTP -0.004 0.032 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.077 -9999 0 -0.52 1 1
CRKL 0.028 0.05 -9999 0 -0.49 1 1
mol:DAG -0.007 0.026 -9999 0 -0.39 1 1
HRAS -0.006 0.022 -9999 0 -10000 0 0
MAPK8 0.011 0.069 -9999 0 -0.51 8 8
RAP1A 0.028 0.05 -9999 0 -0.49 1 1
GAB1 0.028 0.05 -9999 0 -0.49 1 1
MAPK14 0.014 0.052 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.31 10 10
PLCG1 -0.008 0.027 -9999 0 -0.4 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -0.28 1 1
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.066 -9999 0 -0.63 6 6
GAB1/SHC/GRB2/SOS1 -0.008 0.022 -9999 0 -0.42 1 1
EPO/EPOR (dimer) -0.029 0.066 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.47 45 45
STAT1 0.048 0.057 -9999 0 -0.5 1 1
STAT5B -0.004 0.044 -9999 0 -0.44 4 4
cell proliferation 0.02 0.065 -9999 0 -0.47 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.01 0.041 -9999 0 -10000 0 0
TEC 0.027 0.057 -9999 0 -0.48 4 4
SOCS3 -0.005 0.06 -9999 0 -0.8 6 6
STAT1 (dimer) 0.048 0.057 -9999 0 -0.49 1 1
JAK2 0.011 0.025 -9999 0 -0.81 1 1
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
EPO/EPOR (dimer)/JAK2 0.054 0.04 -9999 0 -0.52 1 1
EPO/EPOR -0.029 0.066 -9999 0 -10000 0 0
LYN 0.013 0.002 -9999 0 -10000 0 0
TEC/VAV2 -0.006 0.043 -9999 0 -0.48 3 3
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -0.28 1 1
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.018 0.05 -9999 0 -10000 0 0
mol:IP3 -0.007 0.026 -9999 0 -0.39 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.029 0.094 -9999 0 -0.49 22 22
SH2B3 0.012 0.004 -9999 0 -10000 0 0
NFKB1 0.014 0.052 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.031 -9999 0 -0.32 7 7
PTPN6 0.02 0.052 -9999 0 -0.51 1 1
TEC/VAV2/GRB2 -0.011 0.034 -9999 0 -0.46 3 3
EPOR 0.012 0.01 -9999 0 -0.28 1 1
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.008 0.023 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.036 -9999 0 -0.63 3 3
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.45 1 1
VAV2 0.028 0.05 -9999 0 -0.49 1 1
CBL 0.028 0.05 -9999 0 -0.49 1 1
SHC/Grb2/SOS1 0.004 0.028 -9999 0 -0.45 1 1
STAT5A -0.007 0.056 -9999 0 -0.48 9 9
GRB2 0 0.009 -9999 0 -0.29 1 1
STAT5 (dimer) 0.057 0.087 -9999 0 -0.57 5 5
LYN/PLCgamma2 -0.001 0.027 -9999 0 -0.61 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.027 0.051 -9999 0 -0.49 1 1
BCL2 0.035 0.2 -9999 0 -0.98 37 37
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.033 -9999 0 -0.47 2 2
lamellipodium assembly -0.004 0.045 -9999 0 -0.46 10 10
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.006 0.059 -9999 0 -0.61 10 10
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.011 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.33 30 30
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.007 0.048 -9999 0 -0.44 12 12
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.087 -9999 0 -0.63 18 18
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.004 0.05 -9999 0 -0.51 10 10
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.5 9 9
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -0.29 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.35 12 12
YWHAZ -0.001 0.016 -9999 0 -0.29 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.047 -9999 0 -0.61 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.003 0.03 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -0.29 1 1
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.032 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.8 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.005 0.032 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.13 0.16 -9999 0 -0.39 12 12
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.017 0.1 -9999 0 -0.51 34 34
LNPEP -0.006 0.069 -9999 0 -0.8 8 8
YWHAE 0 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.035 -9999 0 -0.42 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.028 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.023 -9999 0 -0.52 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.039 -9999 0 -0.4 1 1
CaM/Ca2+ 0.009 0.031 -9999 0 -0.38 2 2
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.012 0.036 -9999 0 -0.4 1 1
AKT1 -0.01 0.042 -9999 0 -0.46 2 2
MAP2K1 0.04 0.044 -9999 0 -0.4 1 1
MAP3K11 0.03 0.043 -9999 0 -0.4 1 1
IFNGR1 0.009 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.096 -9999 0 -0.41 23 23
Rap1/GTP -0.004 0.016 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.012 0.036 -9999 0 -0.43 2 2
CEBPB 0.075 0.039 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.007 0.056 -9999 0 -1.2 1 1
STAT1 -0.012 0.036 -9999 0 -0.4 1 1
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.031 0.1 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.01 0.032 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.001 0.013 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.034 -9999 0 -0.41 2 2
MAPK3 0.054 0.04 -9999 0 -0.43 1 1
STAT1 (dimer) -0.007 0.054 -9999 0 -0.59 1 1
MAPK1 0.054 0.04 -9999 0 -10000 0 0
JAK2 0.008 0.025 -9999 0 -0.79 1 1
PIK3R1 -0.008 0.077 -9999 0 -0.8 10 10
JAK1 0.008 0.025 -9999 0 -0.79 1 1
CAMK2D -0.002 0.042 -9999 0 -0.8 3 3
DAPK1 0.07 0.033 -9999 0 -10000 0 0
SMAD7 0.05 0.038 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.007 0.022 -9999 0 -10000 0 0
PI3K 0.004 0.05 -9999 0 -0.5 2 2
IFNG -0.031 0.1 -9999 0 -10000 0 0
apoptosis 0.053 0.029 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.009 0.051 -9999 0 -0.29 33 33
CAMK2B -0.071 0.21 -9999 0 -0.8 76 76
FRAP1 0.038 0.054 -9999 0 -0.42 2 2
PRKCD -0.01 0.043 -9999 0 -0.46 2 2
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.039 -9999 0 -0.4 1 1
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.047 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.033 -9999 0 -10000 0 0
SOCS1 0 0.05 -9999 0 -1.5 1 1
mol:GDP -0.007 0.021 -9999 0 -10000 0 0
CASP1 0.049 0.045 -9999 0 -0.36 5 5
PTGES2 0 0.009 -9999 0 -0.29 1 1
IRF9 0.057 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.046 -9999 0 -0.48 2 2
RAP1/GDP -0.004 0.016 -9999 0 -10000 0 0
CBL -0.01 0.029 -9999 0 -0.39 2 2
MAP3K1 0.03 0.045 -9999 0 -0.4 3 3
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.039 -9999 0 -0.4 1 1
PTPN11 -0.011 0.032 -9999 0 -0.41 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.025 0.079 -9999 0 -9999 0 0
TP53 -0.008 0.02 -9999 0 -9999 0 0
Senescence -0.008 0.02 -9999 0 -9999 0 0
Apoptosis -0.008 0.02 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.017 0.041 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.011 -9999 0 -0.37 1 1
MDM2/SUMO1 -0.001 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.024 -9999 0 -0.8 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0.013 -9999 0 -0.44 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.009 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB -0.001 0.02 -9999 0 -0.29 5 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.003 -9999 0 -10000 0 0
CD4 0 0 -9999 0 -10000 0 0
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.016 -9999 0 -0.2 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.007 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.009 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.009 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.003 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0.001 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.016 -9999 0 -0.2 6 6
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.016 -9999 0 -0.2 6 6
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.01 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.018 -9999 0 -10000 0 0
RELB -0.003 0.028 -9999 0 -0.29 10 10
NFKB2 0 0.009 -9999 0 -0.29 1 1
NF kappa B2 p52/RelB -0.002 0.015 -9999 0 -10000 0 0
regulation of B cell activation -0.002 0.015 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1058 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.XX.A89A TCGA.XX.A899 TCGA.W8.A86G TCGA.V7.A7HQ
109_MAP3K5 0.054 0.054 0.054 -0.27
47_PPARGC1A 0 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 -0.79
131_RELN/VLDLR 0 0 -0.47 -0.47
30_TGFB1/TGF beta receptor Type II 0.013 0 0 0
84_STAT5B 0.032 0.046 0.02 -0.43
84_STAT5A 0.032 0.046 0.02 -0.43
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/9828739/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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