PARADIGM pathway analysis of mRNASeq expression and copy number data
Skin Cutaneous Melanoma (Metastatic)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C12B8WZG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12B8WZG
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
BCR signaling pathway 127
IL4-mediated signaling events 119
TCR signaling in naïve CD8+ T cells 106
IL23-mediated signaling events 101
Nephrin/Neph1 signaling in the kidney podocyte 81
IL12-mediated signaling events 76
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 64
Caspase cascade in apoptosis 60
Calcium signaling in the CD4+ TCR pathway 57
E-cadherin signaling events 55
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 366 . 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 ( 366 ).

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
BCR signaling pathway 0.3470 127 12645 99 -0.71 0.043 1000 -1000 -0.049 -1000
IL4-mediated signaling events 0.3251 119 10906 91 -1.3 1 1000 -1000 -0.048 -1000
TCR signaling in naïve CD8+ T cells 0.2896 106 9876 93 -0.56 0.12 1000 -1000 -0.031 -1000
IL23-mediated signaling events 0.2760 101 6102 60 -0.76 0.035 1000 -1000 -0.035 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.2213 81 2767 34 -0.15 0.035 1000 -1000 -0.029 -1000
IL12-mediated signaling events 0.2077 76 6687 87 -0.68 0.11 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1749 64 4367 68 -0.57 0.12 1000 -1000 -0.028 -1000
Caspase cascade in apoptosis 0.1639 60 4465 74 -0.16 0.12 1000 -1000 -0.016 -1000
Calcium signaling in the CD4+ TCR pathway 0.1557 57 1784 31 -0.35 0.035 1000 -1000 -0.012 -1000
E-cadherin signaling events 0.1503 55 276 5 -0.08 0.035 1000 -1000 0.019 -1000
JNK signaling in the CD4+ TCR pathway 0.1475 54 928 17 -0.22 0.033 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 0.1421 52 2456 47 -0.094 0.076 1000 -1000 -0.022 -1000
IL27-mediated signaling events 0.1421 52 2675 51 -0.26 0.17 1000 -1000 -0.037 -1000
Ras signaling in the CD4+ TCR pathway 0.1393 51 868 17 -0.14 0.063 1000 -1000 -0.013 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1284 47 3487 74 -0.08 0.08 1000 -1000 -0.044 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.1148 42 1930 45 -0.17 0.073 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 0.1120 41 207 5 -0.03 0.011 1000 -1000 0.022 -1000
E-cadherin signaling in the nascent adherens junction 0.1093 40 3064 76 -0.092 0.052 1000 -1000 -0.03 -1000
amb2 Integrin signaling 0.1066 39 3226 82 -0.18 0.044 1000 -1000 -0.012 -1000
IL2 signaling events mediated by PI3K 0.1066 39 2298 58 -0.15 0.06 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.1038 38 2631 68 -0.12 0.045 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 0.1038 38 3164 82 -0.069 0.035 1000 -1000 -0.033 -1000
Thromboxane A2 receptor signaling 0.1011 37 3951 105 -0.12 0.057 1000 -1000 -0.024 -1000
Class I PI3K signaling events 0.1011 37 2763 73 -0.38 0.069 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1011 37 3325 88 -0.21 0.046 1000 -1000 -0.049 -1000
Glucocorticoid receptor regulatory network 0.0984 36 4144 114 -0.42 0.23 1000 -1000 -0.033 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0984 36 1360 37 -0.22 0.049 1000 -1000 -0.011 -1000
IL2 signaling events mediated by STAT5 0.0984 36 800 22 -0.16 0.036 1000 -1000 -0.015 -1000
ceramide signaling pathway 0.0956 35 1751 49 -0.1 0.05 1000 -1000 -0.017 -1000
S1P4 pathway 0.0956 35 891 25 -0.11 0.045 1000 -1000 -0.013 -1000
Endothelins 0.0929 34 3337 96 -0.15 0.037 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 0.0847 31 1087 34 -0.096 0.035 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 0.0847 31 3088 97 -0.1 0.06 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0820 30 1326 43 -0.08 0.037 1000 -1000 -0.016 -1000
Syndecan-4-mediated signaling events 0.0765 28 1926 67 -0.17 0.046 1000 -1000 -0.027 -1000
LPA receptor mediated events 0.0738 27 2796 102 -0.073 0.045 1000 -1000 -0.039 -1000
Visual signal transduction: Cones 0.0683 25 982 38 -0.14 0.043 1000 -1000 -0.004 -1000
HIF-1-alpha transcription factor network 0.0683 25 1928 76 -0.08 0.11 1000 -1000 0 -1000
FOXA2 and FOXA3 transcription factor networks 0.0683 25 1180 46 -0.42 0.04 1000 -1000 -0.026 -1000
Glypican 1 network 0.0656 24 1167 48 -0.22 0.038 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 0.0656 24 747 31 -0.14 0.049 1000 -1000 -0.005 -1000
TRAIL signaling pathway 0.0628 23 1129 48 -0.03 0.053 1000 -1000 -0.021 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0628 23 1230 52 -0.18 0.079 1000 -1000 -0.009 -1000
Visual signal transduction: Rods 0.0628 23 1221 52 -0.14 0.047 1000 -1000 -0.005 -1000
Ceramide signaling pathway 0.0601 22 1739 76 -0.1 0.079 1000 -1000 -0.013 -1000
Osteopontin-mediated events 0.0574 21 814 38 -0.035 0.049 1000 -1000 -0.022 -1000
Aurora C signaling 0.0574 21 150 7 -0.056 0.032 1000 -1000 -0.007 -1000
Regulation of p38-alpha and p38-beta 0.0574 21 1181 54 -0.23 0.072 1000 -1000 -0.037 -1000
Ephrin A reverse signaling 0.0546 20 141 7 0 0.025 1000 -1000 0 -1000
Arf6 signaling events 0.0546 20 1283 62 -0.1 0.073 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0546 20 721 36 -0.04 0.059 1000 -1000 -0.03 -1000
EPO signaling pathway 0.0519 19 1056 55 -0.038 0.053 1000 -1000 -0.014 -1000
IL6-mediated signaling events 0.0519 19 1445 75 -0.19 0.056 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0492 18 1551 85 -0.054 0.067 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 0.0492 18 1610 86 -0.054 0.062 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0464 17 1304 76 -0.24 0.063 1000 -1000 -0.027 -1000
Nectin adhesion pathway 0.0437 16 1070 63 -0.18 0.072 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.0437 16 1360 84 -0.14 0.077 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 0.0410 15 1495 97 -0.3 0.087 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 0.0383 14 1766 125 -0.1 0.088 1000 -1000 -0.03 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0355 13 376 28 -0.11 0.066 1000 -1000 -0.006 -1000
Signaling events mediated by the Hedgehog family 0.0355 13 682 52 -0.2 0.058 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.0355 13 545 39 -0.12 0.041 1000 -1000 -0.016 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0355 13 1132 85 -0.038 0.074 1000 -1000 -0.031 -1000
BMP receptor signaling 0.0355 13 1105 81 -0.14 0.074 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0355 13 1094 83 -0.098 0.066 1000 -1000 -0.013 -1000
LPA4-mediated signaling events 0.0328 12 146 12 -0.048 0.01 1000 -1000 -0.009 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0328 12 1493 120 -0.075 0.084 1000 -1000 -0.031 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0328 12 988 78 -0.074 0.09 1000 -1000 -0.031 -1000
Syndecan-2-mediated signaling events 0.0301 11 823 69 -0.17 0.058 1000 -1000 -0.029 -1000
IL1-mediated signaling events 0.0301 11 696 62 -0.032 0.09 1000 -1000 -0.019 -1000
Ephrin B reverse signaling 0.0301 11 555 48 -0.1 0.048 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 0.0273 10 665 65 -0.023 0.06 1000 -1000 -0.044 -1000
Signaling events mediated by HDAC Class I 0.0273 10 1072 104 -0.064 0.081 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0273 10 526 51 -0.026 0.075 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 0.0273 10 225 21 -0.02 0.055 1000 -1000 -0.026 -1000
Presenilin action in Notch and Wnt signaling 0.0246 9 595 61 -0.067 0.089 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0219 8 315 39 -0.054 0.073 1000 -1000 -0.009 -1000
Noncanonical Wnt signaling pathway 0.0219 8 231 26 -0.001 0.052 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 0.0219 8 69 8 -0.002 0.027 1000 -1000 -0.004 -1000
Aurora B signaling 0.0219 8 547 67 -0.096 0.089 1000 -1000 -0.028 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0191 7 382 54 -0.078 0.064 1000 -1000 -0.01 -1000
Signaling mediated by p38-gamma and p38-delta 0.0191 7 115 15 -0.004 0.034 1000 -1000 -0.015 -1000
Effects of Botulinum toxin 0.0191 7 188 26 -0.026 0.046 1000 -1000 -0.001 -1000
mTOR signaling pathway 0.0164 6 327 53 -0.02 0.058 1000 -1000 -0.025 -1000
Glypican 2 network 0.0164 6 27 4 0.025 0.036 1000 -1000 0.016 -1000
TCGA08_rtk_signaling 0.0164 6 164 26 -0.04 0.082 1000 -1000 -0.007 -1000
Insulin Pathway 0.0164 6 463 74 -0.059 0.083 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0164 6 207 33 -0.009 0.077 1000 -1000 -0.023 -1000
Class IB PI3K non-lipid kinase events 0.0164 6 18 3 -0.027 0.027 1000 -1000 -0.019 -1000
PLK1 signaling events 0.0137 5 426 85 -0.008 0.069 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 0.0137 5 244 43 -0.16 0.17 1000 -1000 -0.041 -1000
FoxO family signaling 0.0137 5 362 64 -0.41 0.094 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 0.0137 5 238 44 -0.005 0.061 1000 -1000 -0.008 -1000
Wnt signaling 0.0137 5 41 7 0.007 0.033 1000 -1000 -0.004 -1000
Regulation of Telomerase 0.0137 5 586 102 -0.11 0.077 1000 -1000 -0.012 -1000
S1P3 pathway 0.0137 5 215 42 -0.037 0.054 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 0.0137 5 388 70 -0.057 0.055 1000 -1000 -0.036 -1000
Regulation of nuclear SMAD2/3 signaling 0.0109 4 585 136 -0.11 0.13 1000 -1000 -0.03 -1000
Arf6 downstream pathway 0.0109 4 207 43 -0.051 0.064 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0109 4 300 68 -0.054 0.066 1000 -1000 -0.015 -1000
S1P1 pathway 0.0109 4 173 36 0 0.052 1000 -1000 -0.013 -1000
VEGFR1 specific signals 0.0109 4 251 56 -0.047 0.084 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0109 4 146 34 -0.054 0.078 1000 -1000 -0.033 -1000
p38 MAPK signaling pathway 0.0109 4 185 44 -0.011 0.057 1000 -1000 -0.008 -1000
ErbB4 signaling events 0.0082 3 254 69 -0.031 0.055 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0082 3 204 58 -0.033 0.067 1000 -1000 -0.016 -1000
Syndecan-3-mediated signaling events 0.0082 3 132 35 -0.016 0.088 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.0082 3 157 52 -0.041 0.057 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 3 444 125 -0.075 0.087 1000 -1000 -0.02 -1000
Arf6 trafficking events 0.0082 3 250 71 -0.053 0.065 1000 -1000 -0.035 -1000
Arf1 pathway 0.0082 3 200 54 -0.008 0.05 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 0.0055 2 194 76 -0.015 0.06 1000 -1000 -0.018 -1000
Hedgehog signaling events mediated by Gli proteins 0.0055 2 188 65 0 0.081 1000 -1000 -0.033 -1000
Aurora A signaling 0.0055 2 121 60 0 0.075 1000 -1000 -0.009 -1000
PDGFR-alpha signaling pathway 0.0055 2 119 44 -0.019 0.071 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class III 0.0055 2 102 40 -0.056 0.057 1000 -1000 -0.033 -1000
Reelin signaling pathway 0.0055 2 138 56 -0.002 0.079 1000 -1000 -0.017 -1000
IGF1 pathway 0.0055 2 166 57 -0.025 0.085 1000 -1000 -0.024 -1000
FOXM1 transcription factor network 0.0055 2 123 51 0.008 0.26 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0.0027 1 149 75 -0.039 0.089 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 0.0027 1 48 32 0 0.064 1000 -1000 -0.014 -1000
Rapid glucocorticoid signaling 0.0027 1 36 20 -0.009 0.041 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 6 23 0.007 0.069 1000 -1000 -0.013 -1000
BARD1 signaling events 0.0000 0 38 57 -0.078 0.091 1000 -1000 -0.044 -1000
PLK2 and PLK4 events 0.0000 0 2 3 0.018 -1000 1000 -1000 -0.005 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.012 0.08 1000 -1000 -0.026 -1000
S1P5 pathway 0.0000 0 13 17 -0.039 0.04 1000 -1000 -0.008 -1000
TCGA08_p53 0.0000 0 1 7 0 0.031 1000 -1000 -0.004 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 5 27 0 0.082 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.089 1000 -1000 0 -1000
Total NA 2731 170838 7203 -16 -990 131000 -131000 -2.7 -131000
BCR signaling pathway

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
JUN -0.29 0.26 -10000 0 -0.48 218 218
IKBKB -0.12 0.14 0.22 1 -0.27 126 127
AKT1 -0.17 0.13 0.26 1 -0.27 226 227
IKBKG -0.12 0.14 -10000 0 -0.28 126 126
CALM1 -0.32 0.33 -10000 0 -0.58 193 193
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
MAP3K1 -0.44 0.38 -10000 0 -0.72 226 226
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.34 0.36 -10000 0 -0.59 211 211
DOK1 0.035 0.002 -10000 0 -10000 0 0
AP-1 -0.15 0.14 -10000 0 -0.27 196 196
LYN 0.016 0.084 -10000 0 -0.42 13 13
BLNK -0.11 0.21 -10000 0 -0.42 116 116
SHC1 0.032 0.011 -10000 0 -10000 0 0
BCR complex -0.27 0.26 -10000 0 -0.47 224 224
CD22 -0.47 0.42 -10000 0 -0.78 219 219
CAMK2G -0.29 0.3 -10000 0 -0.53 192 192
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
SHC/GRB2/SOS1 -0.24 0.26 -10000 0 -0.42 214 214
GO:0007205 -0.35 0.38 -10000 0 -0.6 211 211
SYK -0.012 0.13 -10000 0 -0.42 36 36
ELK1 -0.33 0.34 -10000 0 -0.59 194 194
NFATC1 -0.37 0.32 0.32 1 -0.6 224 225
B-cell antigen/BCR complex -0.27 0.26 -10000 0 -0.47 224 224
PAG1/CSK 0.043 0.031 -10000 0 -0.3 2 2
NFKBIB -0.025 0.053 0.13 1 -0.13 19 20
HRAS -0.3 0.31 -10000 0 -0.55 195 195
NFKBIA -0.024 0.053 0.13 1 -0.13 18 19
NF-kappa-B/RelA/I kappa B beta -0.013 0.045 0.14 1 -0.092 17 18
RasGAP/Csk -0.17 0.22 -10000 0 -0.34 217 217
mol:GDP -0.33 0.35 -10000 0 -0.6 194 194
PTEN 0.03 0.012 -10000 0 -10000 0 0
CD79B -0.2 0.22 -10000 0 -0.42 185 185
NF-kappa-B/RelA/I kappa B alpha -0.013 0.045 0.14 1 -0.091 15 16
GRB2 0.034 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.42 0.34 -10000 0 -0.66 234 234
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.35 0.38 -10000 0 -0.62 209 209
CSK 0.034 0.006 -10000 0 -10000 0 0
FOS -0.3 0.31 -10000 0 -0.54 193 193
CHUK -0.14 0.15 -10000 0 -0.3 133 133
IBTK 0.032 0.011 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.27 0.32 0.25 1 -0.53 190 191
PTPN6 -0.48 0.43 -10000 0 -0.79 218 218
RELA 0.034 0.007 -10000 0 -10000 0 0
BCL2A1 -0.01 0.037 -10000 0 -0.1 8 8
VAV2 -0.54 0.45 -10000 0 -0.86 228 228
ubiquitin-dependent protein catabolic process -0.02 0.052 0.14 1 -0.12 18 19
BTK -0.15 0.41 -10000 0 -1 65 65
CD19 -0.5 0.43 -10000 0 -0.8 225 225
MAP4K1 -0.044 0.17 -10000 0 -0.42 64 64
CD72 -0.065 0.18 -10000 0 -0.42 78 78
PAG1 0.029 0.035 -10000 0 -0.42 2 2
MAPK14 -0.34 0.31 0.24 1 -0.58 221 222
SH3BP5 0.035 0.005 -10000 0 -10000 0 0
PIK3AP1 -0.38 0.42 -10000 0 -0.67 208 208
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.51 0.58 -10000 0 -0.89 213 213
RAF1 -0.28 0.29 -10000 0 -0.51 194 194
RasGAP/p62DOK/SHIP -0.2 0.25 -10000 0 -0.38 221 221
CD79A -0.22 0.22 -10000 0 -0.42 209 209
re-entry into mitotic cell cycle -0.15 0.14 -10000 0 -0.27 198 198
RASA1 0.032 0.025 -10000 0 -0.42 1 1
MAPK3 -0.22 0.23 0.24 1 -0.42 185 186
MAPK1 -0.22 0.23 0.24 1 -0.42 182 183
CD72/SHP1 -0.47 0.42 0.26 1 -0.77 222 223
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.36 0.31 -10000 0 -0.59 223 223
actin cytoskeleton organization -0.42 0.35 -10000 0 -0.67 228 228
NF-kappa-B/RelA -0.019 0.087 0.25 1 -0.19 18 19
Calcineurin -0.25 0.28 -10000 0 -0.49 189 189
PI3K -0.39 0.31 -10000 0 -0.6 239 239
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.4 0.44 -10000 0 -0.7 211 211
SOS1 0.035 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.59 0.52 -10000 0 -0.97 227 227
DAPP1 -0.71 0.63 -10000 0 -1.2 227 227
cytokine secretion -0.34 0.29 0.32 1 -0.55 224 225
mol:DAG -0.35 0.38 -10000 0 -0.62 209 209
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
MAP2K1 -0.25 0.26 0.25 1 -0.47 189 190
B-cell antigen/BCR complex/FcgammaRIIB -0.22 0.24 -10000 0 -0.4 220 220
mol:PI-3-4-5-P3 -0.25 0.19 -10000 0 -0.39 234 234
ETS1 -0.26 0.26 -10000 0 -0.48 192 192
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.26 0.31 -10000 0 -0.48 223 223
B-cell antigen/BCR complex/LYN -0.42 0.4 -10000 0 -0.71 219 219
MALT1 0.033 0.024 -10000 0 -0.42 1 1
TRAF6 0.035 0.006 -10000 0 -10000 0 0
RAC1 -0.46 0.39 -10000 0 -0.74 227 227
B-cell antigen/BCR complex/LYN/SYK -0.44 0.43 -10000 0 -0.76 219 219
CARD11 -0.35 0.38 0.26 1 -0.65 190 191
FCGR2B 0.013 0.09 -10000 0 -0.42 15 15
PPP3CA 0.034 0.006 -10000 0 -10000 0 0
BCL10 0.035 0.006 -10000 0 -10000 0 0
IKK complex -0.043 0.055 0.16 1 -0.1 79 80
PTPRC -0.098 0.2 -10000 0 -0.42 104 104
PDPK1 -0.17 0.12 0.14 1 -0.26 229 230
PPP3CB 0.032 0.01 -10000 0 -10000 0 0
PPP3CC 0.033 0.008 -10000 0 -10000 0 0
POU2F2 -0.015 0.045 -10000 0 -0.097 33 33
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.85 0.61 -10000 0 -1.3 196 196
STAT6 (cleaved dimer) -0.92 0.66 -10000 0 -1.4 220 220
IGHG1 -0.23 0.17 -10000 0 -0.38 75 75
IGHG3 -0.82 0.58 -10000 0 -1.3 212 212
AKT1 -0.52 0.47 -10000 0 -1.1 135 135
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.56 0.62 -10000 0 -1.4 123 123
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.58 0.57 -10000 0 -1.3 130 130
THY1 -0.86 0.61 -10000 0 -1.3 197 197
MYB 0.015 0.084 -10000 0 -0.42 13 13
HMGA1 0.031 0.026 -10000 0 -0.42 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.62 0.54 -10000 0 -0.97 209 209
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.62 0.61 -10000 0 -1.3 135 135
SP1 0.036 0.013 -10000 0 -10000 0 0
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
SOCS5 0.048 0.023 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.91 0.66 -10000 0 -1.4 216 216
SOCS1 -0.53 0.36 -10000 0 -0.8 205 205
SOCS3 -0.48 0.4 -10000 0 -0.94 127 127
FCER2 -1.3 0.68 -10000 0 -1.6 292 292
PARP14 0.013 0.049 -10000 0 -0.42 3 3
CCL17 -0.89 0.64 -10000 0 -1.4 198 198
GRB2 0.034 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.45 0.45 -10000 0 -0.96 128 128
T cell proliferation -0.9 0.66 -10000 0 -1.4 210 210
IL4R/JAK1 -0.86 0.62 -10000 0 -1.3 202 202
EGR2 -0.97 0.63 -10000 0 -1.4 230 230
JAK2 -0.041 0.066 -10000 0 -0.44 5 5
JAK3 0.007 0.11 -10000 0 -0.39 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.001 0.028 -10000 0 -10000 0 0
COL1A2 -0.22 0.21 -10000 0 -1.2 8 8
CCL26 -0.86 0.61 -10000 0 -1.3 197 197
IL4R -0.92 0.68 -10000 0 -1.5 199 199
PTPN6 -0.061 0.19 -10000 0 -0.4 88 88
IL13RA2 -0.88 0.62 -10000 0 -1.4 202 202
IL13RA1 -0.04 0.045 -10000 0 -10000 0 0
IRF4 -0.66 0.6 -10000 0 -1.1 199 199
ARG1 -0.24 0.27 -10000 0 -0.76 50 50
CBL -0.58 0.49 -10000 0 -0.91 206 206
GTF3A 0.034 0.015 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.047 0.071 -10000 0 -0.31 5 5
IRF4/BCL6 -0.57 0.56 -10000 0 -1 198 198
CD40LG -0.21 0.22 -10000 0 -0.42 196 196
MAPK14 -0.56 0.49 -10000 0 -0.96 177 177
mitosis -0.48 0.42 -10000 0 -0.96 135 135
STAT6 -1.1 0.89 -10000 0 -1.7 207 207
SPI1 0.008 0.11 -10000 0 -0.42 23 23
RPS6KB1 -0.45 0.4 -10000 0 -0.91 134 134
STAT6 (dimer) -1.1 0.88 -10000 0 -1.7 207 207
STAT6 (dimer)/PARP14 -1 0.74 -10000 0 -1.5 236 236
mast cell activation 0.017 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.6 0.61 -10000 0 -1.3 133 133
FRAP1 -0.52 0.47 -10000 0 -1.1 135 135
LTA -1 0.73 -10000 0 -1.6 214 214
FES 0.024 0.066 -10000 0 -0.42 8 8
T-helper 1 cell differentiation 1 0.76 1.6 209 -10000 0 209
CCL11 -0.83 0.58 -10000 0 -1.3 197 197
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.58 0.59 -10000 0 -1.3 129 129
IL2RG -0.1 0.2 -10000 0 -0.4 112 112
IL10 -0.87 0.63 -10000 0 -1.4 202 202
IRS1 0.032 0.011 -10000 0 -10000 0 0
IRS2 0.034 0.008 -10000 0 -10000 0 0
IL4 -0.2 0.26 -10000 0 -1.3 17 17
IL5 -0.86 0.61 -10000 0 -1.3 197 197
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.68 0.52 -10000 0 -1 207 207
COL1A1 -0.25 0.25 -10000 0 -1.2 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.9 0.66 -10000 0 -1.4 197 197
IL2R gamma/JAK3 -0.071 0.18 -10000 0 -0.34 111 111
TFF3 -0.93 0.67 -10000 0 -1.4 206 206
ALOX15 -0.86 0.62 -10000 0 -1.3 201 201
MYBL1 0.029 0.035 -10000 0 -0.42 2 2
T-helper 2 cell differentiation -0.8 0.62 -10000 0 -1.2 212 212
SHC1 0.032 0.011 -10000 0 -10000 0 0
CEBPB 0.034 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.57 0.56 -10000 0 -1.2 131 131
mol:PI-3-4-5-P3 -0.52 0.47 -10000 0 -1.1 135 135
PI3K -0.57 0.55 -10000 0 -1.2 135 135
DOK2 -0.01 0.13 -10000 0 -0.42 35 35
ETS1 0.045 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.41 0.41 -10000 0 -0.89 127 127
ITGB3 -0.88 0.62 -10000 0 -1.4 204 204
PIGR -0.93 0.68 -10000 0 -1.5 204 204
IGHE 0.055 0.059 0.19 32 -10000 0 32
MAPKKK cascade -0.4 0.39 -10000 0 -0.86 127 127
BCL6 0.04 0.011 -10000 0 -10000 0 0
OPRM1 -0.86 0.61 -10000 0 -1.3 198 198
RETNLB -0.86 0.61 -10000 0 -1.4 197 197
SELP -0.97 0.71 -10000 0 -1.5 208 208
AICDA -1.1 0.67 -10000 0 -1.5 257 257
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.26 0.39 0.28 11 -0.68 161 172
FYN -0.43 0.56 0.24 3 -1 164 167
LAT/GRAP2/SLP76 -0.28 0.4 -10000 0 -0.71 163 163
IKBKB 0.034 0.007 -10000 0 -10000 0 0
AKT1 -0.22 0.3 0.18 1 -0.53 164 165
B2M 0.026 0.043 -10000 0 -0.43 3 3
IKBKG -0.05 0.089 0.11 10 -0.15 149 159
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
mol:Ca2+ -0.018 0.035 0.089 24 -0.054 109 133
integrin-mediated signaling pathway 0.013 0.085 -10000 0 -0.24 34 34
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.36 0.47 0.21 1 -0.85 166 167
TRPV6 0.12 0.37 1.2 39 -10000 0 39
CD28 -0.039 0.17 -10000 0 -0.42 58 58
SHC1 -0.4 0.52 0.29 11 -0.94 163 174
receptor internalization -0.48 0.61 -10000 0 -1.1 166 166
PRF1 -0.51 0.67 -10000 0 -1.2 156 156
KRAS 0.034 0.006 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.16 0.24 0.18 1 -0.42 157 158
LAT -0.41 0.53 0.2 1 -0.98 162 163
EntrezGene:6955 -0.003 0.004 -10000 0 -10000 0 0
CD3D -0.12 0.22 -10000 0 -0.43 122 122
CD3E -0.1 0.21 -10000 0 -0.43 105 105
CD3G -0.098 0.2 -10000 0 -0.42 102 102
RASGRP2 -0.088 0.097 0.072 1 -0.18 184 185
RASGRP1 -0.23 0.32 0.22 3 -0.57 162 165
HLA-A -0.004 0.007 -10000 0 -10000 0 0
RASSF5 -0.013 0.13 -10000 0 -0.42 36 36
RAP1A/GTP/RAPL 0.014 0.085 -10000 0 -0.25 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.091 0.15 8 -0.14 153 161
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.11 0.14 -10000 0 -0.26 158 158
PRKCA -0.12 0.17 -10000 0 -0.31 155 155
GRAP2 -0.014 0.14 -10000 0 -0.42 38 38
mol:IP3 -0.21 0.28 -10000 0 -0.51 162 162
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.48 0.64 -10000 0 -1.2 157 157
ORAI1 -0.11 0.31 -10000 0 -1 39 39
CSK -0.42 0.54 0.22 4 -0.99 162 166
B7 family/CD28 -0.41 0.59 -10000 0 -1 162 162
CHUK 0.032 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.53 0.68 0.2 2 -1.2 165 167
PTPN6 -0.45 0.58 0.19 3 -1.1 162 165
VAV1 -0.42 0.54 0.2 2 -0.98 163 165
Monovalent TCR/CD3 -0.31 0.43 -10000 0 -0.75 159 159
CBL 0.032 0.011 -10000 0 -10000 0 0
LCK -0.49 0.63 0.24 3 -1.2 162 165
PAG1 -0.41 0.54 0.22 14 -0.98 163 177
RAP1A 0.034 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.68 0.2 2 -1.2 166 168
CD80 -0.061 0.18 -10000 0 -0.42 75 75
CD86 -0.022 0.15 -10000 0 -0.42 44 44
PDK1/CARD11/BCL10/MALT1 -0.12 0.18 -10000 0 -0.32 157 157
HRAS 0.034 0.006 -10000 0 -10000 0 0
GO:0035030 -0.32 0.42 0.17 2 -0.76 163 165
CD8A -0.13 0.22 -10000 0 -0.43 132 132
CD8B -0.14 0.22 -10000 0 -0.43 134 134
PTPRC -0.1 0.2 -10000 0 -0.42 104 104
PDK1/PKC theta -0.28 0.37 0.21 2 -0.68 161 163
CSK/PAG1 -0.4 0.52 0.22 17 -0.95 162 179
SOS1 0.035 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.008 0.036 -10000 0 -0.31 3 3
GRAP2/SLP76 -0.36 0.49 -10000 0 -0.88 164 164
STIM1 -0.021 0.06 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.12 0.18 10 -0.19 148 158
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.56 0.72 -10000 0 -1.3 168 168
mol:DAG -0.2 0.24 -10000 0 -0.45 162 162
RAP1A/GDP -0.018 0.043 0.077 7 -0.066 135 142
PLCG1 0.033 0.01 -10000 0 -10000 0 0
CD247 -0.1 0.21 -10000 0 -0.42 107 107
cytotoxic T cell degranulation -0.47 0.61 -10000 0 -1.1 156 156
RAP1A/GTP -0.032 0.037 -10000 0 -0.068 180 180
mol:PI-3-4-5-P3 -0.27 0.36 0.2 1 -0.65 164 165
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.28 0.38 -10000 0 -0.69 162 162
NRAS 0.034 0.008 -10000 0 -10000 0 0
ZAP70 -0.12 0.22 -10000 0 -0.42 126 126
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.29 0.38 -10000 0 -0.69 163 163
MALT1 0.033 0.024 -10000 0 -0.42 1 1
TRAF6 0.034 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.17 0.28 -10000 0 -0.51 146 146
CARD11 -0.074 0.19 -10000 0 -0.42 85 85
PRKCB -0.15 0.2 0.2 1 -0.36 163 164
PRKCE -0.12 0.17 0.2 1 -0.31 158 159
PRKCQ -0.34 0.44 0.22 2 -0.81 164 166
LCP2 0.015 0.09 -10000 0 -0.42 15 15
BCL10 0.035 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.18 0.25 0.17 3 -0.44 163 166
IKK complex -0.034 0.08 0.14 14 -0.12 149 163
RAS family/GDP -0.014 0.021 -10000 0 -0.04 117 117
MAP3K14 -0.12 0.18 0.14 3 -0.31 156 159
PDPK1 -0.2 0.28 0.18 1 -0.5 163 164
TCR/CD3/MHC I/CD8/Fyn -0.55 0.71 -10000 0 -1.3 163 163
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.5 0.67 -9999 0 -1.2 151 151
IL23A -0.53 0.7 -9999 0 -1.3 154 154
NF kappa B1 p50/RelA/I kappa B alpha -0.53 0.73 -9999 0 -1.3 154 154
positive regulation of T cell mediated cytotoxicity -0.64 0.85 -9999 0 -1.5 154 154
ITGA3 -0.51 0.67 -9999 0 -1.2 150 150
IL17F -0.31 0.41 -9999 0 -0.75 154 154
IL12B -0.01 0.087 -9999 0 -0.45 8 8
STAT1 (dimer) -0.6 0.8 -9999 0 -1.5 154 154
CD4 -0.51 0.68 -9999 0 -1.3 151 151
IL23 -0.5 0.67 -9999 0 -1.2 154 154
IL23R -0.038 0.13 -9999 0 -1.3 2 2
IL1B -0.55 0.73 -9999 0 -1.4 151 151
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.59 0.72 -9999 0 -1.3 178 178
TYK2 0 0.046 -9999 0 -10000 0 0
STAT4 -0.079 0.2 -9999 0 -0.42 92 92
STAT3 0.035 0.006 -9999 0 -10000 0 0
IL18RAP -0.12 0.21 -9999 0 -0.42 117 117
IL12RB1 -0.11 0.21 -9999 0 -0.45 96 96
PIK3CA 0.034 0.006 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.072 0.17 -9999 0 -0.34 96 96
IL23R/JAK2 -0.03 0.16 -9999 0 -1.3 2 2
positive regulation of chronic inflammatory response -0.64 0.85 -9999 0 -1.5 154 154
natural killer cell activation 0.006 0.009 -9999 0 -10000 0 0
JAK2 -0.002 0.075 -9999 0 -0.45 5 5
PIK3R1 0.034 0.007 -9999 0 -10000 0 0
NFKB1 0.033 0.007 -9999 0 -10000 0 0
RELA 0.032 0.008 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.47 0.62 -9999 0 -1.1 154 154
ALOX12B -0.5 0.66 -9999 0 -1.2 151 151
CXCL1 -0.51 0.66 -9999 0 -1.2 156 156
T cell proliferation -0.64 0.85 -9999 0 -1.5 154 154
NFKBIA 0.033 0.006 -9999 0 -10000 0 0
IL17A -0.22 0.33 -9999 0 -0.57 151 151
PI3K -0.55 0.75 -9999 0 -1.4 154 154
IFNG -0.048 0.068 -9999 0 -0.12 151 151
STAT3 (dimer) -0.51 0.7 -9999 0 -1.3 154 154
IL18R1 -0.045 0.16 -9999 0 -0.42 57 57
IL23/IL23R/JAK2/TYK2/SOCS3 -0.31 0.47 -9999 0 -0.81 143 143
IL18/IL18R -0.14 0.25 -9999 0 -0.43 143 143
macrophage activation -0.02 0.024 -9999 0 -0.045 154 154
TNF -0.57 0.75 -9999 0 -1.4 153 153
STAT3/STAT4 -0.57 0.77 -9999 0 -1.4 158 158
STAT4 (dimer) -0.62 0.82 -9999 0 -1.5 158 158
IL18 -0.067 0.18 -9999 0 -0.42 72 72
IL19 -0.5 0.66 -9999 0 -1.2 151 151
STAT5A (dimer) -0.6 0.8 -9999 0 -1.5 154 154
STAT1 0.033 0.033 -9999 0 -0.42 2 2
SOCS3 0.03 0.041 -9999 0 -0.42 3 3
CXCL9 -0.65 0.78 -9999 0 -1.4 175 175
MPO -0.52 0.68 -9999 0 -1.3 156 156
positive regulation of humoral immune response -0.64 0.85 -9999 0 -1.5 154 154
IL23/IL23R/JAK2/TYK2 -0.76 1 -9999 0 -1.8 154 154
IL6 -0.51 0.68 -9999 0 -1.3 151 151
STAT5A 0.033 0.024 -9999 0 -0.42 1 1
IL2 0.004 0.031 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.009 -9999 0 -10000 0 0
CD3E -0.61 0.76 -9999 0 -1.5 156 156
keratinocyte proliferation -0.64 0.85 -9999 0 -1.5 154 154
NOS2 -0.5 0.66 -9999 0 -1.2 151 151
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.087 0.17 0.3 134 -10000 0 134
KIRREL 0.001 0.051 -10000 0 -0.42 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.087 0.17 -10000 0 -0.3 134 134
PLCG1 0.033 0.01 -10000 0 -10000 0 0
ARRB2 0.033 0.009 -10000 0 -10000 0 0
WASL 0.031 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.039 0.14 -10000 0 -0.23 122 122
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.06 0.12 -10000 0 -0.23 119 119
FYN -0.055 0.13 0.24 20 -0.22 133 153
mol:Ca2+ -0.041 0.14 -10000 0 -0.22 123 123
mol:DAG -0.04 0.14 -10000 0 -0.22 123 123
NPHS2 -0.01 0.038 -10000 0 -10000 0 0
mol:IP3 -0.04 0.14 -10000 0 -0.22 123 123
regulation of endocytosis -0.044 0.12 -10000 0 -0.2 132 132
Nephrin/NEPH1/podocin/Cholesterol -0.054 0.13 -10000 0 -0.22 133 133
establishment of cell polarity -0.087 0.17 -10000 0 -0.3 134 134
Nephrin/NEPH1/podocin/NCK1-2 -0.028 0.14 -10000 0 -0.21 131 131
Nephrin/NEPH1/beta Arrestin2 -0.044 0.12 -10000 0 -0.2 132 132
NPHS1 -0.15 0.22 -10000 0 -0.42 145 145
Nephrin/NEPH1/podocin -0.053 0.12 -10000 0 -0.22 133 133
TJP1 0.034 0.007 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.04 0.14 -10000 0 -0.23 123 123
CD2AP 0.031 0.026 -10000 0 -0.42 1 1
Nephrin/NEPH1/podocin/GRB2 -0.042 0.14 -10000 0 -0.23 130 130
GRB2 0.034 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.055 0.13 0.25 24 -0.2 127 151
cytoskeleton organization -0.082 0.14 0.2 5 -0.28 117 122
Nephrin/NEPH1 -0.056 0.12 -10000 0 -0.21 134 134
Nephrin/NEPH1/ZO-1 -0.054 0.14 -10000 0 -0.24 133 133
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.11 0.25 -10000 0 -0.44 114 114
TBX21 -0.48 0.77 -10000 0 -1.5 133 133
B2M 0.03 0.042 -10000 0 -0.42 3 3
TYK2 0.01 0.048 -10000 0 -10000 0 0
IL12RB1 -0.099 0.22 -10000 0 -0.45 96 96
GADD45B -0.38 0.66 -10000 0 -1.2 129 129
IL12RB2 -0.004 0.073 -10000 0 -0.43 7 7
GADD45G -0.42 0.69 -10000 0 -1.3 136 136
natural killer cell activation -0.005 0.026 0.046 1 -0.042 82 83
RELB 0.035 0.004 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
IL18 -0.057 0.18 -10000 0 -0.43 72 72
IL2RA -0.062 0.18 -10000 0 -0.42 76 76
IFNG -0.12 0.21 -10000 0 -0.42 119 119
STAT3 (dimer) -0.32 0.55 -10000 0 -1 136 136
HLA-DRB5 0.001 0.001 -10000 0 -10000 0 0
FASLG -0.5 0.79 -10000 0 -1.5 137 137
NF kappa B2 p52/RelB -0.43 0.74 -10000 0 -1.3 135 135
CD4 -0.007 0.13 -10000 0 -0.42 34 34
SOCS1 0.011 0.1 -10000 0 -0.42 19 19
EntrezGene:6955 0.001 0.003 -10000 0 -0.019 2 2
CD3D -0.12 0.21 -10000 0 -0.42 122 122
CD3E -0.097 0.2 -10000 0 -0.42 105 105
CD3G -0.094 0.2 -10000 0 -0.42 102 102
IL12Rbeta2/JAK2 0.004 0.084 -10000 0 -0.33 12 12
CCL3 -0.43 0.72 -10000 0 -1.3 130 130
CCL4 -0.46 0.76 -10000 0 -1.4 131 131
HLA-A 0 0.003 -10000 0 -0.02 2 2
IL18/IL18R -0.11 0.28 -10000 0 -0.42 143 143
NOS2 -0.44 0.73 -10000 0 -1.4 130 130
IL12/IL12R/TYK2/JAK2/SPHK2 -0.1 0.23 -10000 0 -0.41 114 114
IL1R1 -0.42 0.7 -10000 0 -1.3 129 129
IL4 0.004 0.041 -10000 0 -10000 0 0
JAK2 0.007 0.07 -10000 0 -0.46 5 5
EntrezGene:6957 0.001 0.003 -10000 0 -0.021 2 2
TCR/CD3/MHC I/CD8 -0.5 0.7 -10000 0 -1.2 156 156
RAB7A -0.27 0.5 -10000 0 -0.94 121 121
lysosomal transport -0.25 0.47 -10000 0 -0.87 123 123
FOS -0.31 0.51 -10000 0 -0.98 123 123
STAT4 (dimer) -0.39 0.68 -10000 0 -1.2 139 139
STAT5A (dimer) -0.47 0.74 -10000 0 -1.3 141 141
GZMA -0.49 0.78 -10000 0 -1.5 131 131
GZMB -0.51 0.79 -10000 0 -1.5 143 143
HLX 0.031 0.011 -10000 0 -10000 0 0
LCK -0.56 0.88 -10000 0 -1.6 140 140
TCR/CD3/MHC II/CD4 -0.28 0.4 -10000 0 -0.68 162 162
IL2/IL2R -0.097 0.25 -10000 0 -0.41 129 129
MAPK14 -0.4 0.69 -10000 0 -1.2 136 136
CCR5 -0.42 0.71 -10000 0 -1.3 127 127
IL1B -0.031 0.14 -10000 0 -0.45 34 34
STAT6 -0.055 0.19 -10000 0 -0.28 93 93
STAT4 -0.079 0.2 -10000 0 -0.42 92 92
STAT3 0.035 0.006 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
NFKB1 0.034 0.006 -10000 0 -10000 0 0
NFKB2 0.032 0.01 -10000 0 -10000 0 0
IL12B 0.003 0.08 -10000 0 -0.44 8 8
CD8A -0.13 0.22 -10000 0 -0.42 132 132
CD8B -0.13 0.22 -10000 0 -0.42 134 134
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.25 0.44 114 -10000 0 114
IL2RB -0.043 0.17 -10000 0 -0.42 61 61
proteasomal ubiquitin-dependent protein catabolic process -0.32 0.58 -10000 0 -1 139 139
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
IL12 -0.001 0.11 -10000 0 -0.33 27 27
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
CD247 -0.1 0.2 -10000 0 -0.42 107 107
IL2 0.022 0.009 -10000 0 -10000 0 0
SPHK2 0.035 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.013 0.11 -10000 0 -0.45 19 19
IL12/IL12R/TYK2/JAK2 -0.68 1.1 -10000 0 -2 135 135
MAP2K3 -0.43 0.72 -10000 0 -1.3 138 138
RIPK2 0.032 0.011 -10000 0 -10000 0 0
MAP2K6 -0.42 0.72 -10000 0 -1.3 136 136
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.001 -10000 0 -10000 0 0
IL18RAP -0.11 0.22 -10000 0 -0.42 117 117
IL12Rbeta1/TYK2 -0.06 0.18 -10000 0 -0.35 96 96
EOMES -0.14 0.4 -10000 0 -1.3 34 34
STAT1 (dimer) -0.38 0.57 -10000 0 -1 157 157
T cell proliferation -0.24 0.44 -10000 0 -0.77 139 139
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.036 0.17 -10000 0 -0.43 57 57
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.27 0.48 -10000 0 -0.85 138 138
ATF2 -0.34 0.6 -10000 0 -1.1 136 136
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.061 0.19 -10000 0 -0.4 79 79
NFATC2 -0.14 0.34 -10000 0 -0.62 102 102
NFATC3 -0.009 0.079 -10000 0 -0.2 13 13
CD40LG -0.42 0.49 -10000 0 -0.9 161 161
ITCH 0.031 0.019 -10000 0 -0.21 1 1
CBLB 0.033 0.018 -10000 0 -0.21 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.45 0.62 -10000 0 -1.1 149 149
JUNB 0.035 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.026 -10000 0 -0.25 1 1
T cell anergy 0.002 0.063 -10000 0 -0.32 1 1
TLE4 -0.11 0.28 -10000 0 -0.55 83 83
Jun/NFAT1-c-4/p21SNFT -0.21 0.41 -10000 0 -0.76 103 103
AP-1/NFAT1-c-4 -0.34 0.53 -10000 0 -0.96 134 134
IKZF1 -0.16 0.35 -10000 0 -0.75 87 87
T-helper 2 cell differentiation -0.24 0.4 -10000 0 -0.83 99 99
AP-1/NFAT1 -0.1 0.26 -10000 0 -0.46 98 98
CALM1 0.041 0.015 -10000 0 -0.16 1 1
EGR2 -0.16 0.34 -10000 0 -0.75 63 63
EGR3 -0.17 0.37 -10000 0 -0.83 58 58
NFAT1/FOXP3 -0.14 0.35 -10000 0 -0.61 109 109
EGR1 0.026 0.022 -10000 0 -10000 0 0
JUN -0.008 0.042 -10000 0 -10000 0 0
EGR4 0.024 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.01 -10000 0 -0.15 1 1
GBP3 -0.12 0.29 -10000 0 -0.56 89 89
FOSL1 0.015 0.09 -10000 0 -0.42 15 15
NFAT1-c-4/MAF/IRF4 -0.17 0.38 -10000 0 -0.73 85 85
DGKA -0.11 0.28 -10000 0 -0.54 83 83
CREM 0.032 0.01 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.39 -10000 0 -0.75 90 90
CTLA4 -0.16 0.34 -10000 0 -0.62 111 111
NFAT1-c-4 (dimer)/EGR1 -0.18 0.4 -10000 0 -0.77 91 91
NFAT1-c-4 (dimer)/EGR4 -0.18 0.41 -10000 0 -0.76 95 95
FOS -0.006 0.042 -10000 0 -10000 0 0
IFNG -0.57 0.7 -10000 0 -1.3 176 176
T cell activation -0.13 0.24 -10000 0 -0.63 37 37
MAF 0.034 0.007 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.12 0.29 0.91 23 -10000 0 23
TNF -0.23 0.41 -10000 0 -0.84 94 94
FASLG -0.55 0.8 -10000 0 -1.6 126 126
TBX21 -0.11 0.2 -10000 0 -0.35 137 137
BATF3 0.026 0.053 -10000 0 -0.42 5 5
PRKCQ -0.1 0.21 -10000 0 -0.42 106 106
PTPN1 -0.099 0.25 -10000 0 -0.5 83 83
NFAT1-c-4/ICER1 -0.17 0.39 -10000 0 -0.73 91 91
GATA3 -0.047 0.17 -10000 0 -0.42 64 64
T-helper 1 cell differentiation -0.55 0.66 -10000 0 -1.2 176 176
IL2RA -0.4 0.58 -10000 0 -1 147 147
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.099 0.25 -10000 0 -0.5 83 83
E2F1 0.038 0.011 -10000 0 -10000 0 0
PPARG 0.03 0.047 -10000 0 -0.42 4 4
SLC3A2 -0.097 0.25 -10000 0 -0.5 82 82
IRF4 -0.003 0.12 -10000 0 -0.42 28 28
PTGS2 -0.32 0.42 -10000 0 -0.82 131 131
CSF2 -0.32 0.43 -10000 0 -0.83 134 134
JunB/Fra1/NFAT1-c-4 -0.16 0.38 -10000 0 -0.74 83 83
IL4 -0.25 0.42 -10000 0 -0.88 98 98
IL5 -0.33 0.43 -10000 0 -0.83 135 135
IL2 -0.13 0.24 -10000 0 -0.65 35 35
IL3 -0.068 0.2 -10000 0 -0.92 16 16
RNF128 0.024 0.035 -10000 0 -0.52 1 1
NFATC1 -0.12 0.29 -10000 0 -0.92 23 23
CDK4 0.1 0.2 0.53 34 -10000 0 34
PTPRK -0.095 0.25 -10000 0 -0.51 76 76
IL8 -0.34 0.42 -10000 0 -0.83 136 136
POU2F1 0.032 0.011 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.11 0.23 0.29 1 -0.44 101 102
ACTA1 -0.14 0.25 0.23 5 -0.48 115 120
NUMA1 -0.11 0.24 0.26 1 -0.46 101 102
SPTAN1 -0.14 0.25 0.3 1 -0.49 115 116
LIMK1 -0.13 0.25 0.33 4 -0.47 114 118
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BIRC2 0.028 0.042 -10000 0 -0.42 3 3
BAX 0.035 0.004 -10000 0 -10000 0 0
CASP10 -0.12 0.2 -10000 0 -0.4 111 111
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
PTK2 -0.11 0.23 0.29 1 -0.45 101 102
DIABLO 0.035 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.14 0.25 0.3 1 -0.48 115 116
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.006 -10000 0 -10000 0 0
GSN -0.15 0.26 0.3 1 -0.49 115 116
MADD 0.035 0.006 -10000 0 -10000 0 0
TFAP2A -0.14 0.33 -10000 0 -0.74 79 79
BID -0.074 0.13 -10000 0 -0.25 118 118
MAP3K1 -0.042 0.13 -10000 0 -0.4 18 18
TRADD 0.034 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.16 0.28 0.51 1 -0.53 116 117
CASP9 0.035 0.005 -10000 0 -10000 0 0
DNA repair -0.008 0.08 0.2 14 -0.17 30 44
neuron apoptosis -0.007 0.13 -10000 0 -0.69 11 11
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.13 0.26 0.31 2 -0.47 119 121
APAF1 0.035 0.006 -10000 0 -10000 0 0
CASP6 -0.081 0.24 -10000 0 -0.62 33 33
TRAF2 0.033 0.009 -10000 0 -10000 0 0
ICAD/CAD -0.14 0.25 0.39 3 -0.47 115 118
CASP7 0.073 0.15 0.28 99 -0.67 1 100
KRT18 -0.088 0.25 -10000 0 -0.66 52 52
apoptosis -0.1 0.22 0.31 1 -0.43 96 97
DFFA -0.14 0.26 0.32 2 -0.49 115 117
DFFB -0.14 0.25 0.32 2 -0.49 115 117
PARP1 0.008 0.081 0.17 30 -0.2 14 44
actin filament polymerization 0.12 0.24 0.44 114 -0.31 4 118
TNF -0.054 0.18 -10000 0 -0.42 69 69
CYCS -0.05 0.089 -10000 0 -0.19 88 88
SATB1 -0.089 0.23 -10000 0 -0.59 42 42
SLK -0.14 0.25 0.3 1 -0.49 115 116
p15 BID/BAX -0.061 0.13 -10000 0 -0.26 96 96
CASP2 -0.049 0.15 0.22 13 -0.33 59 72
JNK cascade 0.042 0.13 0.4 18 -0.18 1 19
CASP3 -0.15 0.27 0.33 1 -0.51 115 116
LMNB2 -0.036 0.18 0.26 4 -0.38 53 57
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CASP4 0.031 0.026 -10000 0 -0.42 1 1
Mammalian IAPs/DIABLO -0.014 0.14 -10000 0 -0.23 108 108
negative regulation of DNA binding -0.13 0.33 -10000 0 -0.73 79 79
stress fiber formation -0.14 0.25 0.3 1 -0.48 115 116
GZMB -0.13 0.22 -10000 0 -0.45 112 112
CASP1 0.006 0.066 -10000 0 -0.31 14 14
LMNB1 -0.047 0.2 0.25 5 -0.39 67 72
APP -0.007 0.13 -10000 0 -0.7 11 11
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.001 -10000 0 -10000 0 0
VIM -0.099 0.21 0.32 1 -0.41 99 100
LMNA -0.037 0.17 0.25 4 -0.37 54 58
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.064 0.15 -10000 0 -0.32 77 77
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.14 0.25 0.32 2 -0.49 115 117
APAF-1/Caspase 9 0.038 0.093 0.37 3 -0.51 5 8
nuclear fragmentation during apoptosis -0.11 0.24 0.26 1 -0.45 101 102
CFL2 -0.13 0.24 0.31 4 -0.45 114 118
GAS2 -0.15 0.25 0.29 1 -0.49 114 115
positive regulation of apoptosis -0.035 0.18 0.22 16 -0.38 58 74
PRF1 -0.079 0.19 -10000 0 -0.42 90 90
Calcium signaling in the CD4+ TCR pathway

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.035 0.064 -10000 0 -0.2 21 21
NFATC2 -0.04 0.08 -10000 0 -0.29 24 24
NFATC3 -0.028 0.047 -10000 0 -0.12 12 12
CD40LG -0.35 0.35 0.39 1 -0.62 207 208
PTGS2 -0.24 0.28 0.39 1 -0.53 155 156
JUNB 0.035 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.015 0.036 -10000 0 -0.083 3 3
CaM/Ca2+ -0.015 0.036 -10000 0 -0.084 2 2
CALM1 0.005 0.034 -10000 0 -10000 0 0
JUN 0.001 0.035 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.017 -10000 0 -10000 0 0
FOSL1 0.015 0.09 -10000 0 -0.42 15 15
CREM 0.032 0.01 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.19 -10000 0 -0.33 129 129
FOS 0.004 0.034 -10000 0 -10000 0 0
IFNG -0.31 0.34 0.39 1 -0.61 181 182
AP-1/NFAT1-c-4 -0.28 0.37 -10000 0 -0.63 166 166
FASLG -0.29 0.34 0.39 1 -0.63 159 160
NFAT1-c-4/ICER1 -0.075 0.13 -10000 0 -0.24 90 90
IL2RA -0.29 0.33 0.39 1 -0.61 167 168
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSF2 -0.25 0.29 0.39 1 -0.54 160 161
JunB/Fra1/NFAT1-c-4 -0.07 0.14 -10000 0 -0.25 95 95
IL4 -0.26 0.29 0.39 1 -0.54 162 163
IL2 -0.008 0.14 -10000 0 -1 7 7
IL3 -0.038 0.18 -10000 0 -0.84 17 17
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
BATF3 0.025 0.053 -10000 0 -0.42 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.032 0.011 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.017 0.14 -9999 0 -0.25 92 92
E-cadherin/beta catenin -0.039 0.15 -9999 0 -0.3 92 92
CTNNB1 0.035 0.005 -9999 0 -10000 0 0
JUP 0.034 0.008 -9999 0 -10000 0 0
CDH1 -0.08 0.2 -9999 0 -0.42 92 92
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.032 0.21 -10000 0 -0.36 91 91
MAP4K1 -0.044 0.17 -10000 0 -0.42 64 64
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
PRKCB -0.098 0.21 -10000 0 -0.42 107 107
DBNL 0.031 0.011 -10000 0 -10000 0 0
CRKL 0.033 0.01 -10000 0 -10000 0 0
MAP3K1 -0.06 0.19 -10000 0 -0.49 50 50
JUN -0.21 0.37 -10000 0 -0.71 119 119
MAP3K7 -0.057 0.19 -10000 0 -0.49 49 49
GRAP2 -0.014 0.14 -10000 0 -0.42 38 38
CRK 0.033 0.009 -10000 0 -10000 0 0
MAP2K4 -0.064 0.22 0.25 5 -0.49 58 63
LAT -0.021 0.15 -10000 0 -0.42 45 45
LCP2 0.015 0.09 -10000 0 -0.42 15 15
MAPK8 -0.22 0.39 -10000 0 -0.74 122 122
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.06 0.21 -10000 0 -0.44 68 68
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.019 0.2 -10000 0 -0.34 88 88
FAS signaling pathway (CD95)

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
SPTAN1 0.033 0.073 0.17 80 -0.18 1 81
RFC1 0.036 0.077 0.17 87 -0.18 2 89
PRKDC 0.05 0.1 0.21 96 -0.18 2 98
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CASP7 0.004 0.19 -10000 0 -0.57 29 29
FASLG/FAS/FADD/FAF1 -0.001 0.12 0.2 42 -0.25 47 89
MAP2K4 -0.035 0.18 0.24 3 -0.42 43 46
mol:ceramide -0.045 0.16 -10000 0 -0.3 91 91
GSN 0.032 0.072 0.17 79 -0.18 2 81
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.13 0.23 1 -0.28 60 61
FAS 0.026 0.054 -10000 0 -0.42 5 5
BID 0.065 0.14 0.29 97 -10000 0 97
MAP3K1 -0.004 0.16 0.25 7 -0.48 24 31
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
RB1 0.038 0.076 0.17 91 -0.18 2 93
CFLAR 0.035 0.004 -10000 0 -10000 0 0
HGF/MET 0.033 0.09 -10000 0 -0.26 27 27
ARHGDIB 0.027 0.1 0.18 84 -0.23 18 102
FADD 0.033 0.012 -10000 0 -10000 0 0
actin filament polymerization -0.032 0.072 0.18 1 -0.17 79 80
NFKB1 -0.019 0.15 -10000 0 -0.7 13 13
MAPK8 -0.036 0.19 -10000 0 -0.45 40 40
DFFA 0.037 0.075 0.17 89 -0.18 1 90
DNA fragmentation during apoptosis 0.037 0.077 0.17 88 -0.18 2 90
FAS/FADD/MET 0.033 0.082 -10000 0 -0.25 24 24
CFLAR/RIP1 0.046 0.018 -10000 0 -10000 0 0
FAIM3 -0.094 0.2 -10000 0 -0.42 101 101
FAF1 0.034 0.011 -10000 0 -10000 0 0
PARP1 0.037 0.076 0.17 90 -0.18 2 92
DFFB 0.037 0.077 0.17 88 -0.18 2 90
CHUK -0.02 0.13 -10000 0 -0.64 12 12
FASLG -0.092 0.2 -10000 0 -0.42 99 99
FAS/FADD 0.041 0.041 -10000 0 -0.3 4 4
HGF 0.024 0.058 -10000 0 -0.42 6 6
LMNA 0.033 0.068 0.2 5 -10000 0 5
CASP6 0.036 0.073 0.17 86 -0.17 1 87
CASP10 0.027 0.058 -10000 0 -0.42 6 6
CASP3 0.047 0.089 0.2 87 -10000 0 87
PTPN13 0.029 0.047 -10000 0 -0.42 4 4
CASP8 0.076 0.16 0.34 98 -10000 0 98
IL6 -0.051 0.28 -10000 0 -1.2 20 20
MET 0.006 0.1 -10000 0 -0.42 20 20
ICAD/CAD 0.033 0.07 0.15 88 -0.17 1 89
FASLG/FAS/FADD/FAF1/Caspase 10 -0.045 0.16 -10000 0 -0.3 91 91
activation of caspase activity by cytochrome c 0.065 0.14 0.29 97 -10000 0 97
PAK2 0.038 0.078 0.17 89 -0.18 2 91
BCL2 0.035 0.005 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.033 0.034 -10000 0 -0.42 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.17 0.3 0.59 94 -10000 0 94
IL27/IL27R/JAK1 -0.12 0.32 -10000 0 -0.86 39 39
TBX21 -0.18 0.27 -10000 0 -0.55 106 106
IL12B 0.008 0.068 -10000 0 -0.42 8 8
IL12A -0.013 0.068 -10000 0 -0.3 19 19
IL6ST 0.005 0.071 -10000 0 -0.43 8 8
IL27RA/JAK1 -0.064 0.28 -10000 0 -1.2 20 20
IL27 -0.035 0.14 -10000 0 -0.43 39 39
TYK2 0.012 0.033 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.033 0.1 0.43 1 -0.57 1 2
T-helper 2 cell differentiation 0.17 0.3 0.59 94 -10000 0 94
T cell proliferation during immune response 0.17 0.3 0.59 94 -10000 0 94
MAPKKK cascade -0.17 0.3 -10000 0 -0.59 94 94
STAT3 0.035 0.006 -10000 0 -10000 0 0
STAT2 0.035 0.006 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
IL12RB1 -0.086 0.2 -10000 0 -0.42 96 96
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.15 0.23 0.36 1 -0.52 81 82
IL27/IL27R/JAK2/TYK2 -0.18 0.31 -10000 0 -0.6 94 94
positive regulation of T cell mediated cytotoxicity -0.17 0.3 -10000 0 -0.59 94 94
STAT1 (dimer) -0.16 0.34 0.51 1 -0.72 72 73
JAK2 0.012 0.058 -10000 0 -0.42 5 5
JAK1 0.035 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.16 0.3 -10000 0 -0.58 91 91
T cell proliferation -0.16 0.3 -10000 0 -0.6 85 85
IL12/IL12R/TYK2/JAK2 -0.18 0.34 -10000 0 -0.9 44 44
IL17A 0.033 0.1 0.43 1 -0.57 1 2
mast cell activation 0.17 0.3 0.59 94 -10000 0 94
IFNG -0.045 0.068 -10000 0 -0.12 149 149
T cell differentiation -0.009 0.011 -10000 0 -0.023 137 137
STAT3 (dimer) -0.16 0.3 -10000 0 -0.58 91 91
STAT5A (dimer) -0.16 0.3 -10000 0 -0.57 92 92
STAT4 (dimer) -0.2 0.34 -10000 0 -0.62 113 113
STAT4 -0.079 0.2 -10000 0 -0.42 92 92
T cell activation -0.003 0.029 0.12 18 -10000 0 18
IL27R/JAK2/TYK2 -0.068 0.29 -10000 0 -1.1 23 23
GATA3 -0.26 0.54 -10000 0 -1.3 80 80
IL18 -0.054 0.12 -10000 0 -0.3 72 72
positive regulation of mast cell cytokine production -0.15 0.29 -10000 0 -0.56 92 92
IL27/EBI3 -0.074 0.18 -10000 0 -0.36 97 97
IL27RA -0.081 0.3 -10000 0 -1.3 20 20
IL6 0.014 0.084 -10000 0 -0.42 13 13
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
monocyte differentiation -0.002 0.004 -10000 0 -0.013 1 1
IL2 0.023 0.11 0.48 20 -10000 0 20
IL1B -0.023 0.088 -10000 0 -0.3 34 34
EBI3 -0.076 0.18 -10000 0 -0.42 80 80
TNF -0.052 0.12 -10000 0 -0.3 69 69
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.3 -9999 0 -0.6 92 92
MAP3K8 0.021 0.07 -9999 0 -0.42 9 9
FOS -0.13 0.3 -9999 0 -0.61 95 95
PRKCA 0.033 0.025 -9999 0 -0.42 1 1
PTPN7 -0.061 0.18 -9999 0 -0.42 75 75
HRAS 0.035 0.006 -9999 0 -10000 0 0
PRKCB -0.097 0.21 -9999 0 -0.42 107 107
NRAS 0.034 0.008 -9999 0 -10000 0 0
RAS family/GTP 0.063 0.02 -9999 0 -10000 0 0
MAPK3 -0.14 0.31 -9999 0 -0.64 95 95
MAP2K1 -0.075 0.2 -9999 0 -0.37 105 105
ELK1 0.036 0.003 -9999 0 -10000 0 0
BRAF -0.064 0.17 -9999 0 -0.36 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
MAPK1 -0.14 0.31 -9999 0 -0.63 96 96
RAF1 -0.075 0.18 -9999 0 -0.35 104 104
KRAS 0.035 0.006 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.029 0.1 -10000 0 -0.21 92 92
epithelial cell differentiation -0.004 0.12 -10000 0 -0.21 91 91
CYFIP2 0.015 0.09 -10000 0 -0.42 15 15
ENAH -0.032 0.076 0.27 3 -0.26 1 4
EGFR 0.027 0.035 -10000 0 -0.42 2 2
EPHA2 0.03 0.047 -10000 0 -0.42 4 4
MYO6 -0.033 0.1 0.2 10 -0.2 91 101
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.066 -10000 0 -0.24 15 15
AQP5 -0.029 0.089 -10000 0 -0.32 3 3
CTNND1 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.1 0.19 10 -0.2 89 99
regulation of calcium-dependent cell-cell adhesion -0.037 0.11 0.19 10 -0.2 97 107
EGF 0.001 0.11 -10000 0 -0.42 25 25
NCKAP1 0.035 0.003 -10000 0 -10000 0 0
AQP3 -0.078 0.16 0.4 1 -0.4 51 52
cortical microtubule organization -0.004 0.12 -10000 0 -0.21 91 91
GO:0000145 -0.046 0.089 0.18 10 -0.19 89 99
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.001 0.13 -10000 0 -0.21 91 91
MLLT4 0.029 0.014 -10000 0 -10000 0 0
ARF6/GDP -0.051 0.074 -10000 0 -0.19 77 77
ARF6 0.035 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.044 -10000 0 -0.23 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.031 0.088 0.23 4 -0.24 3 7
PVRL2 0.035 0.004 -10000 0 -10000 0 0
ZYX -0.028 0.098 0.2 9 -0.2 81 90
ARF6/GTP 0.08 0.047 -10000 0 -0.21 3 3
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
EGFR/EGFR/EGF/EGF -0.026 0.12 -10000 0 -0.21 103 103
RhoA/GDP 0 0.12 -10000 0 -0.2 91 91
actin cytoskeleton organization -0.039 0.098 0.18 10 -0.2 91 101
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
IGF1R 0.034 0.006 -10000 0 -10000 0 0
IGF1 0.03 0.041 -10000 0 -0.42 3 3
DIAPH1 -0.017 0.22 -10000 0 -0.58 30 30
Wnt receptor signaling pathway 0.004 0.12 0.21 91 -10000 0 91
RHOA 0.035 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.051 0.074 -10000 0 -0.19 77 77
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
VCL -0.04 0.099 0.18 10 -0.2 91 101
EFNA1 0.032 0.011 -10000 0 -10000 0 0
LPP -0.049 0.09 0.19 9 -0.2 87 96
Ephrin A1/EPHA2 -0.006 0.11 -10000 0 -0.2 81 81
SEC6/SEC8 -0.032 0.083 -10000 0 -0.19 77 77
MGAT3 -0.038 0.11 0.2 10 -0.21 97 107
HGF/MET -0.019 0.13 -10000 0 -0.22 93 93
HGF 0.024 0.058 -10000 0 -0.42 6 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.03 0.1 -10000 0 -0.21 92 92
actin cable formation 0.004 0.11 0.26 22 -0.26 7 29
KIAA1543 -0.055 0.096 0.18 10 -0.2 102 112
KIFC3 -0.033 0.1 0.21 7 -0.2 91 98
NCK1 0.034 0.006 -10000 0 -10000 0 0
EXOC3 0.032 0.01 -10000 0 -10000 0 0
ACTN1 -0.032 0.1 0.2 11 -0.2 92 103
NCK1/GIT1 0.049 0.013 -10000 0 -10000 0 0
mol:GDP -0.004 0.12 -10000 0 -0.21 91 91
EXOC4 0.031 0.012 -10000 0 -10000 0 0
STX4 -0.032 0.1 0.2 11 -0.2 91 102
PIP5K1C -0.031 0.1 0.2 10 -0.2 89 99
LIMA1 0.035 0.005 -10000 0 -10000 0 0
ABI1 0.032 0.01 -10000 0 -10000 0 0
ROCK1 -0.025 0.1 0.33 7 -0.3 1 8
adherens junction assembly -0.041 0.1 0.3 3 -0.37 6 9
IGF-1R heterotetramer/IGF1 -0.007 0.11 -10000 0 -0.2 92 92
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.023 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PLEKHA7 -0.04 0.11 0.2 10 -0.21 102 112
mol:GTP 0.071 0.043 -10000 0 -0.23 3 3
establishment of epithelial cell apical/basal polarity -0.013 0.12 0.31 12 -10000 0 12
cortical actin cytoskeleton stabilization -0.029 0.1 -10000 0 -0.21 92 92
regulation of cell-cell adhesion -0.039 0.098 0.18 10 -0.2 91 101
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.03 0.1 -10000 0 -0.21 92 92
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.034 0.008 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.018 0.13 -10000 0 -0.3 28 28
NEF -0.036 0.067 -10000 0 -0.2 35 35
NFKBIA -0.007 0.062 -10000 0 -0.12 5 5
BIRC3 -0.12 0.22 -10000 0 -0.46 108 108
CYCS -0.032 0.12 0.2 17 -0.25 72 89
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CD247 -0.14 0.25 -10000 0 -0.48 123 123
MAP2K7 -0.034 0.17 -10000 0 -0.53 16 16
protein ubiquitination -0.02 0.14 0.25 6 -0.35 32 38
CRADD 0.034 0.006 -10000 0 -10000 0 0
DAXX 0.032 0.011 -10000 0 -10000 0 0
FAS 0.026 0.053 -10000 0 -0.42 5 5
BID -0.045 0.13 0.19 8 -0.26 83 91
NF-kappa-B/RelA/I kappa B alpha -0.028 0.15 -10000 0 -0.24 118 118
TRADD 0.034 0.007 -10000 0 -10000 0 0
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
CFLAR 0.035 0.003 -10000 0 -10000 0 0
FADD 0.033 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.028 0.15 -10000 0 -0.24 118 118
MAPK8 -0.03 0.16 -10000 0 -0.49 15 15
APAF1 0.034 0.006 -10000 0 -10000 0 0
TRAF1 0.025 0.058 -10000 0 -0.42 6 6
TRAF2 0.033 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.05 0.14 0.2 9 -0.27 89 98
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.046 0.17 -10000 0 -0.37 56 56
CHUK -0.024 0.15 0.25 6 -0.38 31 37
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.058 -10000 0 -0.21 5 5
TCRz/NEF -0.13 0.23 -10000 0 -0.44 123 123
TNF -0.054 0.18 -10000 0 -0.42 69 69
FASLG -0.17 0.29 -10000 0 -0.56 122 122
NFKB1 -0.006 0.061 -10000 0 -0.098 106 106
TNFR1A/BAG4/TNF-alpha 0.002 0.12 -10000 0 -0.25 66 66
CASP6 -0.003 0.15 -10000 0 -0.56 13 13
CASP7 -0.15 0.26 0.31 6 -0.48 132 138
RELA -0.006 0.061 -10000 0 -0.12 2 2
CASP2 0.031 0.011 -10000 0 -10000 0 0
CASP3 -0.14 0.26 0.31 6 -0.47 129 135
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.015 -10000 0 -10000 0 0
CASP8 0.035 0.004 -10000 0 -10000 0 0
CASP9 0.035 0.005 -10000 0 -10000 0 0
MAP3K14 -0.038 0.16 0.27 2 -0.36 50 52
APAF-1/Caspase 9 -0.093 0.19 -10000 0 -0.37 98 98
BCL2 -0.027 0.14 -10000 0 -0.46 14 14
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.032 0.011 -9999 0 -10000 0 0
ITGB7 -0.026 0.15 -9999 0 -0.42 49 49
ITGA4 -0.013 0.14 -9999 0 -0.42 39 39
alpha4/beta7 Integrin -0.03 0.16 -9999 0 -0.32 80 80
alpha4/beta1 Integrin 0.011 0.11 -9999 0 -0.29 39 39
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.089 0.2 -10000 0 -0.4 100 100
KLHL20 -0.012 0.097 0.21 7 -0.21 25 32
CYFIP2 0.015 0.09 -10000 0 -0.42 15 15
Rac1/GDP -0.032 0.13 0.26 1 -0.25 73 74
ENAH -0.085 0.19 -10000 0 -0.39 97 97
AP1M1 0.035 0.004 -10000 0 -10000 0 0
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.092 -10000 0 -0.21 1 1
ABI1/Sra1/Nap1 -0.036 0.051 -10000 0 -0.15 31 31
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.033 0.16 -10000 0 -0.25 123 123
RAPGEF1 -0.067 0.17 0.24 3 -0.35 88 91
CTNND1 0.035 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.086 0.21 -10000 0 -0.41 101 101
CRK -0.076 0.18 -10000 0 -0.38 90 90
E-cadherin/gamma catenin/alpha catenin -0.017 0.14 -10000 0 -0.25 91 91
alphaE/beta7 Integrin 0.004 0.12 -10000 0 -0.29 48 48
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
NCKAP1 0.035 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.031 -10000 0 -10000 0 0
DLG1 -0.088 0.2 -10000 0 -0.4 99 99
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.058 -10000 0 -0.14 4 4
MLLT4 0.029 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.069 -10000 0 -0.22 21 21
PI3K -0.026 0.076 -10000 0 -0.21 1 1
ARF6 0.035 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.04 0.15 -10000 0 -0.3 92 92
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
E-cadherin(dimer)/Ca2+ 0.001 0.13 -10000 0 -0.21 91 91
AKT1 -0.007 0.056 0.16 4 -10000 0 4
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
RhoA/GDP -0.027 0.14 0.28 4 -0.25 77 81
actin cytoskeleton organization -0.007 0.075 0.17 9 -0.16 25 34
CDC42/GDP -0.029 0.14 0.28 4 -0.25 77 81
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.036 0.1 -10000 0 -0.21 93 93
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.002 0.14 -10000 0 -0.23 91 91
E-cadherin/Ca2+/beta catenin/alpha catenin -0.012 0.12 -10000 0 -0.21 91 91
mol:GDP -0.048 0.14 0.28 4 -0.28 78 82
CDC42/GTP/IQGAP1 0.045 0.011 -10000 0 -10000 0 0
JUP 0.034 0.008 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.02 0.14 0.27 3 -0.25 76 79
RAC1/GTP/IQGAP1 0.041 0.017 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.052 0.007 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.001 0.056 0.14 13 -0.1 24 37
NME1 0.034 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.089 0.2 -10000 0 -0.4 99 99
regulation of cell-cell adhesion -0.018 0.075 -10000 0 -0.16 6 6
WASF2 -0.004 0.043 0.1 5 -0.09 15 20
Rap1/GTP -0.013 0.1 -10000 0 -0.24 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.022 0.16 -10000 0 -0.23 124 124
CCND1 0.001 0.066 0.16 12 -0.13 24 36
VAV2 -0.092 0.24 0.37 1 -0.45 97 98
RAP1/GDP -0.011 0.12 0.3 3 -0.24 6 9
adherens junction assembly -0.086 0.19 -10000 0 -0.39 99 99
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.032 0.01 -10000 0 -10000 0 0
PIP5K1C 0.035 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.029 0.15 -10000 0 -0.23 123 123
E-cadherin/beta catenin -0.069 0.14 -10000 0 -0.31 95 95
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.086 0.19 -10000 0 -0.39 98 98
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.058 0.12 -10000 0 -0.35 27 27
E-cadherin/beta catenin/alpha catenin -0.016 0.14 -10000 0 -0.25 91 91
ITGAE 0.033 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.088 0.21 -10000 0 -0.42 101 101
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.004 0.14 -10000 0 -0.35 44 44
alphaM/beta2 Integrin/GPIbA -0.13 0.2 -10000 0 -0.31 187 187
alphaM/beta2 Integrin/proMMP-9 -0.035 0.19 -10000 0 -0.37 74 74
PLAUR 0.033 0.024 -10000 0 -0.42 1 1
HMGB1 0.019 0.036 -10000 0 -0.15 1 1
alphaM/beta2 Integrin/Talin 0.004 0.14 -10000 0 -0.33 43 43
AGER 0.017 0.034 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
SELPLG -0.004 0.13 -10000 0 -0.42 31 31
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.006 0.18 -10000 0 -0.29 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
CYR61 0.032 0.034 -10000 0 -0.42 2 2
TLN1 0.032 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.072 0.19 -10000 0 -0.41 63 63
RHOA 0.035 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.096 0.2 -10000 0 -0.42 103 103
MYH2 -0.1 0.2 -10000 0 -0.44 67 67
MST1R 0.013 0.095 -10000 0 -0.42 17 17
leukocyte activation during inflammatory response -0.002 0.12 -10000 0 -0.3 42 42
APOB 0.023 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.027 0.036 -10000 0 -0.42 2 2
JAM3 0.029 0.014 -10000 0 -10000 0 0
GP1BA -0.18 0.22 -10000 0 -0.42 174 174
alphaM/beta2 Integrin/CTGF 0 0.14 -10000 0 -0.34 43 43
alphaM/beta2 Integrin -0.1 0.21 -10000 0 -0.45 70 70
JAM3 homodimer 0.029 0.014 -10000 0 -10000 0 0
ICAM2 0.006 0.11 -10000 0 -0.42 23 23
ICAM1 0.027 0.062 -10000 0 -0.42 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.21 -10000 0 -0.44 72 72
cell adhesion -0.13 0.2 -10000 0 -0.31 187 187
NFKB1 -0.052 0.23 0.4 3 -0.42 84 87
THY1 0.029 0.035 -10000 0 -0.42 2 2
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.019 0.14 -10000 0 -0.32 40 40
IL6 -0.064 0.22 0.38 3 -0.43 78 81
ITGB2 -0.032 0.15 -10000 0 -0.44 42 42
elevation of cytosolic calcium ion concentration 0.014 0.14 -10000 0 -0.32 42 42
alphaM/beta2 Integrin/JAM2/JAM3 0.016 0.14 -10000 0 -0.33 42 42
JAM2 0.032 0.034 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/ICAM1 0.026 0.16 -10000 0 -0.3 60 60
alphaM/beta2 Integrin/uPA/Plg 0.008 0.13 -10000 0 -0.32 42 42
RhoA/GTP -0.11 0.21 -10000 0 -0.35 119 119
positive regulation of phagocytosis -0.075 0.22 -10000 0 -0.45 69 69
Ron/MSP 0.033 0.076 -10000 0 -0.3 18 18
alphaM/beta2 Integrin/uPAR/uPA 0.016 0.14 -10000 0 -0.33 42 42
alphaM/beta2 Integrin/uPAR 0.002 0.14 -10000 0 -0.34 44 44
PLAU 0.03 0.026 -10000 0 -0.42 1 1
PLAT 0.032 0.025 -10000 0 -0.42 1 1
actin filament polymerization -0.099 0.19 -10000 0 -0.42 66 66
MST1 0.033 0.024 -10000 0 -0.42 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.001 0.12 -10000 0 -0.3 42 42
TNF -0.14 0.31 -10000 0 -0.69 80 80
RAP1B 0.034 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.001 0.14 -10000 0 -0.35 42 42
fibrinolysis 0.006 0.13 -10000 0 -0.32 42 42
HCK -0.002 0.12 -10000 0 -0.42 28 28
dendritic cell antigen processing and presentation -0.1 0.21 -10000 0 -0.44 72 72
VTN -0.02 0.14 -10000 0 -0.42 43 43
alphaM/beta2 Integrin/CYR61 0.001 0.14 -10000 0 -0.34 45 45
LPA 0.016 0.006 -10000 0 -10000 0 0
LRP1 0.034 0.007 -10000 0 -10000 0 0
cell migration -0.038 0.17 -10000 0 -0.34 75 75
FN1 0.021 0.077 -10000 0 -0.42 11 11
alphaM/beta2 Integrin/Thy1 0.001 0.14 -10000 0 -0.34 44 44
MPO -0.003 0.12 -10000 0 -0.42 29 29
KNG1 0.021 0.01 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.013 -10000 0 -10000 0 0
ROCK1 -0.1 0.2 0.28 1 -0.43 67 68
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.016 0.006 -10000 0 -10000 0 0
CTGF 0.03 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Hck -0.011 0.18 -10000 0 -0.46 44 44
ITGAM 0.005 0.086 -10000 0 -0.41 12 12
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.068 0.22 -10000 0 -0.34 120 120
HP -0.069 0.18 -10000 0 -0.42 80 80
leukocyte adhesion -0.015 0.16 -10000 0 -0.37 47 47
SELP -0.096 0.2 -10000 0 -0.42 103 103
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.13 0.28 -10000 0 -0.64 66 66
UGCG -0.054 0.23 -10000 0 -0.85 26 26
AKT1/mTOR/p70S6K/Hsp90/TERT -0.066 0.24 0.27 2 -0.42 86 88
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.053 0.23 -10000 0 -0.84 26 26
mol:DAG -0.084 0.28 -10000 0 -0.89 38 38
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.086 0.25 0.3 2 -0.44 109 111
FRAP1 -0.11 0.29 0.31 2 -0.51 109 111
FOXO3 -0.12 0.28 0.31 2 -0.5 113 115
AKT1 -0.13 0.31 0.32 2 -0.54 116 118
GAB2 0.034 0.009 -10000 0 -10000 0 0
SMPD1 -0.017 0.15 -10000 0 -0.99 8 8
SGMS1 -0.078 0.26 -10000 0 -0.82 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.004 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
cell proliferation -0.084 0.27 0.25 1 -0.7 47 48
EIF3A 0.032 0.01 -10000 0 -10000 0 0
PI3K 0.053 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.004 0.15 -10000 0 -1 6 6
mol:sphingomyelin -0.084 0.28 -10000 0 -0.89 38 38
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.006 0.12 -10000 0 -0.42 25 25
PIK3R1 0.036 0.008 -10000 0 -10000 0 0
JAK1 0.037 0.005 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MYC -0.079 0.26 0.38 2 -0.49 76 78
MYB -0.031 0.28 -10000 0 -1.2 19 19
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.15 0.32 -10000 0 -0.57 119 119
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.14 -10000 0 -0.92 6 6
mol:PI-3-4-5-P3 -0.14 0.31 -10000 0 -0.55 120 120
Rac1/GDP 0.029 0.014 -10000 0 -10000 0 0
T cell proliferation -0.13 0.29 -10000 0 -0.52 117 117
SHC1 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.016 -10000 0 -0.065 19 19
PRKCZ -0.14 0.3 -10000 0 -0.54 118 118
NF kappa B1 p50/RelA -0.076 0.26 0.32 2 -0.44 107 109
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.15 0.31 -10000 0 -0.56 111 111
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
RELA 0.034 0.007 -10000 0 -10000 0 0
IL2RA -0.062 0.18 -10000 0 -0.42 76 76
IL2RB -0.04 0.17 -10000 0 -0.42 61 61
TERT 0.029 0.013 -10000 0 -10000 0 0
E2F1 0.008 0.11 -10000 0 -0.45 19 19
SOS1 0.036 0.003 -10000 0 -10000 0 0
RPS6 0.031 0.012 -10000 0 -10000 0 0
mol:cAMP -0.001 0.007 0.032 17 -10000 0 17
PTPN11 0.035 0.006 -10000 0 -10000 0 0
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
actin cytoskeleton organization -0.13 0.29 -10000 0 -0.52 117 117
GRB2 0.035 0.007 -10000 0 -10000 0 0
IL2 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.037 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.06 0.029 -10000 0 -10000 0 0
LCK -0.13 0.22 -10000 0 -0.42 137 137
BCL2 -0.077 0.22 -10000 0 -0.43 80 80
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.024 0.13 0.23 1 -0.2 120 121
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.033 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.029 0.14 0.29 2 -0.3 36 38
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.022 0.066 -10000 0 -0.27 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.086 -10000 0 -0.22 27 27
CaM/Ca2+ -0.019 0.13 0.21 1 -0.19 119 120
RAP1A 0.034 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.043 0.12 0.28 1 -0.2 119 120
AKT1 -0.041 0.11 0.29 4 -0.24 18 22
MAP2K1 -0.049 0.1 0.21 3 -0.2 85 88
MAP3K11 -0.045 0.11 0.26 3 -0.2 112 115
IFNGR1 0.014 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.12 -10000 0 -0.36 28 28
Rap1/GTP -0.033 0.086 -10000 0 -0.17 76 76
CRKL/C3G 0.045 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.012 0.14 -10000 0 -0.21 118 118
CEBPB 0 0.11 0.41 2 -0.35 2 4
STAT3 0.035 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.29 -10000 0 -1.2 20 20
STAT1 -0.051 0.12 0.27 3 -0.2 112 115
CALM1 0.034 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.12 0.21 -10000 0 -0.42 119 119
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.035 0.12 0.26 2 -0.2 109 111
CEBPB/PTGES2/Cbp/p300 0.01 0.084 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.13 0.22 1 -0.2 120 121
MAPK3 -0.018 0.11 0.4 1 -0.69 2 3
STAT1 (dimer) -0.022 0.12 -10000 0 -0.3 26 26
MAPK1 -0.025 0.13 0.4 1 -0.72 5 6
JAK2 0.007 0.06 -10000 0 -0.43 5 5
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.014 0.033 -10000 0 -10000 0 0
CAMK2D 0.035 0.006 -10000 0 -10000 0 0
DAPK1 0.009 0.081 0.36 2 -10000 0 2
SMAD7 -0.004 0.054 0.17 5 -0.14 10 15
CBL/CRKL/C3G -0.019 0.11 0.31 2 -0.19 87 89
PI3K -0.018 0.13 -10000 0 -0.19 111 111
IFNG -0.12 0.21 -10000 0 -0.42 119 119
apoptosis 0.006 0.075 0.3 2 -0.32 1 3
CAMK2G 0.032 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.035 0.005 -10000 0 -10000 0 0
CAMK2A 0.024 0.048 -10000 0 -0.42 4 4
CAMK2B 0.021 0.063 -10000 0 -0.42 7 7
FRAP1 -0.051 0.093 0.23 6 -0.23 16 22
PRKCD -0.039 0.11 0.26 6 -0.23 22 28
RAP1B 0.034 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.086 -10000 0 -0.22 27 27
PTPN2 0.034 0.007 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
IRF1 -0.069 0.17 0.26 2 -0.44 46 48
STAT1 (dimer)/PIASy -0.035 0.12 0.35 2 -0.2 100 102
SOCS1 -0.038 0.31 -10000 0 -1.3 20 20
mol:GDP -0.02 0.11 0.29 2 -0.18 87 89
CASP1 -0.009 0.071 0.17 5 -0.23 19 24
PTGES2 0.033 0.009 -10000 0 -10000 0 0
IRF9 0.019 0.052 0.17 7 -10000 0 7
mol:PI-3-4-5-P3 -0.028 0.12 -10000 0 -0.19 111 111
RAP1/GDP -0.018 0.099 -10000 0 -0.2 17 17
CBL -0.042 0.11 0.26 3 -0.2 103 106
MAP3K1 -0.046 0.11 0.26 3 -0.2 114 117
PIAS1 0.035 0.005 -10000 0 -10000 0 0
PIAS4 0.035 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.086 -10000 0 -0.22 27 27
PTPN11 -0.05 0.11 0.18 9 -0.2 119 128
CREBBP 0.034 0.007 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0.058 -10000 0 -0.36 6 6
Crk/p130 Cas/Paxillin -0.05 0.1 -10000 0 -0.24 66 66
JUN -0.029 0.092 0.2 1 -0.28 9 10
HRAS 0.034 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.004 0.12 -10000 0 -0.23 78 78
RAP1A 0.034 0.007 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
RAP1A/GDP 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.002 0.13 -10000 0 -0.23 82 82
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.018 0.12 -10000 0 -0.23 81 81
RHOA 0.035 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.001 0.11 -10000 0 -0.2 79 79
GRB7 0.029 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.002 0.13 -10000 0 -0.23 82 82
MAPKKK cascade -0.023 0.11 -10000 0 -0.22 74 74
BCAR1 0.034 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.02 0.12 -10000 0 -0.23 80 80
lamellipodium assembly -0.034 0.11 -10000 0 -0.23 70 70
RET51/GFRalpha1/GDNF/SHC -0.002 0.12 -10000 0 -0.23 72 72
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.015 0.11 -10000 0 -0.23 71 71
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.12 -10000 0 -0.23 78 78
MAPK3 -0.026 0.1 0.2 15 -0.2 73 88
DOK1 0.035 0.002 -10000 0 -10000 0 0
DOK6 0.023 0.062 -10000 0 -0.42 7 7
PXN 0.034 0.006 -10000 0 -10000 0 0
neurite development -0.017 0.095 0.29 2 -0.28 5 7
DOK5 0.021 0.043 -10000 0 -0.42 3 3
GFRA1 -0.069 0.19 -10000 0 -0.42 81 81
MAPK8 -0.027 0.096 -10000 0 -0.2 80 80
HRAS/GTP -0.014 0.13 -10000 0 -0.24 80 80
tube development -0.013 0.11 0.22 5 -0.22 74 79
MAPK1 -0.024 0.099 0.19 17 -0.2 68 85
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.031 0.1 -10000 0 -0.21 77 77
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
PDLIM7 0.033 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.005 0.13 -10000 0 -0.23 73 73
SHC1 0.032 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.003 0.13 -10000 0 -0.23 82 82
RET51/GFRalpha1/GDNF/Dok5 -0.01 0.12 -10000 0 -0.23 74 74
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.026 0.004 -10000 0 -10000 0 0
CREB1 -0.032 0.11 -10000 0 -0.23 75 75
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.028 0.097 -10000 0 -0.21 71 71
RET51/GFRalpha1/GDNF/Grb7 -0.007 0.13 -10000 0 -0.23 81 81
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.03 0.026 -10000 0 -0.42 1 1
DOK4 0.034 0.007 -10000 0 -10000 0 0
JNK cascade -0.029 0.091 0.2 1 -0.27 9 10
RET9/GFRalpha1/GDNF/FRS2 -0.017 0.12 -10000 0 -0.23 80 80
SHANK3 0.032 0.01 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.029 0.098 -10000 0 -0.21 73 73
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.03 0.11 -10000 0 -0.21 88 88
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.11 -10000 0 -0.21 91 91
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.097 -10000 0 -0.21 70 70
PI3K -0.044 0.16 0.23 3 -0.32 73 76
SOS1 0.035 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.003 0.11 -10000 0 -0.22 74 74
GRB10 0.032 0.011 -10000 0 -10000 0 0
activation of MAPKK activity -0.022 0.1 -10000 0 -0.21 80 80
RET51/GFRalpha1/GDNF/FRS2 -0.003 0.13 -10000 0 -0.23 81 81
GAB1 0.035 0.005 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
IRS2 0.034 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.023 0.097 -10000 0 -0.21 69 69
RET51/GFRalpha1/GDNF/PKC alpha -0.003 0.13 -10000 0 -0.23 78 78
GRB2 0.034 0.007 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GDNF 0.019 0.058 -10000 0 -0.42 6 6
RAC1 0.031 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.005 0.13 -10000 0 -0.23 81 81
Rac1/GTP -0.035 0.13 -10000 0 -0.27 70 70
RET9/GFRalpha1/GDNF -0.032 0.12 -10000 0 -0.25 81 81
GFRalpha1/GDNF -0.04 0.14 -10000 0 -0.3 81 81
Thromboxane A2 receptor signaling

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
TGM2 0.031 0.026 -10000 0 -0.42 1 1
GNB1/GNG2 -0.055 0.083 -10000 0 -0.19 91 91
AKT1 -0.017 0.12 0.34 1 -0.23 48 49
EGF 0.001 0.11 -10000 0 -0.42 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.004 0.089 0.39 2 -0.22 28 30
mol:Ca2+ -0.042 0.17 -10000 0 -0.3 99 99
LYN 0.011 0.07 0.29 2 -0.23 12 14
RhoA/GTP -0.014 0.072 -10000 0 -0.13 82 82
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.19 -10000 0 -0.37 96 96
GNG2 0.027 0.058 -10000 0 -0.42 6 6
ARRB2 0.033 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.016 0.11 -10000 0 -0.41 18 18
G beta5/gamma2 -0.068 0.11 -10000 0 -0.25 90 90
PRKCH -0.053 0.18 -10000 0 -0.34 94 94
DNM1 0.029 0.013 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.013 0.019 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.022 0.074 -10000 0 -0.42 10 10
G12 family/GTP -0.051 0.15 -10000 0 -0.31 89 89
ADRBK1 0.034 0.007 -10000 0 -10000 0 0
ADRBK2 0.029 0.042 -10000 0 -0.42 3 3
RhoA/GTP/ROCK1 0.046 0.009 -10000 0 -10000 0 0
mol:GDP 0.017 0.13 0.35 23 -10000 0 23
mol:NADP 0.03 0.026 -10000 0 -0.42 1 1
RAB11A 0.035 0.006 -10000 0 -10000 0 0
PRKG1 0.018 0.018 -10000 0 -10000 0 0
mol:IP3 -0.06 0.2 -10000 0 -0.38 99 99
cell morphogenesis 0.045 0.009 -10000 0 -10000 0 0
PLCB2 -0.096 0.27 -10000 0 -0.52 96 96
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.091 0.1 -10000 0 -0.21 65 65
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.083 0.39 2 -0.22 25 27
RHOA 0.035 0.005 -10000 0 -10000 0 0
PTGIR 0.031 0.041 -10000 0 -0.42 3 3
PRKCB1 -0.059 0.2 -10000 0 -0.37 94 94
GNAQ 0.033 0.009 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.026 -10000 0 -0.42 1 1
TXA2/TXA2-R family -0.1 0.27 -10000 0 -0.54 95 95
LCK -0.046 0.11 -10000 0 -0.22 67 67
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.032 0.049 -10000 0 -0.2 11 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.02 0.087 -10000 0 -0.41 12 12
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.037 0.049 -10000 0 -0.19 13 13
MAPK14 -0.027 0.14 0.22 6 -0.25 85 91
TGM2/GTP -0.071 0.22 -10000 0 -0.43 92 92
MAPK11 -0.034 0.13 0.24 2 -0.24 90 92
ARHGEF1 -0.018 0.1 0.17 7 -0.18 83 90
GNAI2 0.035 0.005 -10000 0 -10000 0 0
JNK cascade -0.066 0.2 -10000 0 -0.4 95 95
RAB11/GDP 0.034 0.006 -10000 0 -10000 0 0
ICAM1 -0.042 0.15 -10000 0 -0.29 93 93
cAMP biosynthetic process -0.06 0.19 -10000 0 -0.36 95 95
Gq family/GTP/EBP50 -0.02 0.092 -10000 0 -0.18 82 82
actin cytoskeleton reorganization 0.045 0.009 -10000 0 -10000 0 0
SRC 0.018 0.063 0.36 3 -0.24 1 4
GNB5 0.033 0.024 -10000 0 -0.42 1 1
GNB1 0.034 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.093 0.14 0.25 5 -0.29 92 97
VCAM1 -0.062 0.18 -10000 0 -0.36 94 94
TP beta/Gq family/GDP/G beta5/gamma2 -0.016 0.11 -10000 0 -0.41 18 18
platelet activation -0.037 0.18 0.28 2 -0.31 93 95
PGI2/IP 0.023 0.029 -10000 0 -0.29 3 3
PRKACA 0.017 0.047 -10000 0 -0.22 13 13
Gq family/GDP/G beta5/gamma2 -0.014 0.11 -10000 0 -0.39 19 19
TXA2/TP beta/beta Arrestin2 0.004 0.062 -10000 0 -0.33 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.045 -10000 0 -0.21 14 14
mol:DAG -0.068 0.22 -10000 0 -0.42 94 94
EGFR 0.027 0.035 -10000 0 -0.42 2 2
TXA2/TP alpha -0.088 0.26 -10000 0 -0.5 94 94
Gq family/GTP -0.022 0.091 0.23 2 -0.21 62 64
YES1 0.019 0.058 0.22 3 -0.18 7 10
GNAI2/GTP 0.025 0.049 -10000 0 -0.18 15 15
PGD2/DP 0.017 0.052 -10000 0 -0.29 10 10
SLC9A3R1 0.034 0.007 -10000 0 -10000 0 0
FYN 0.02 0.061 0.39 2 -0.24 1 3
mol:NO 0.03 0.026 -10000 0 -0.42 1 1
GNA15 0.021 0.077 -10000 0 -0.42 11 11
PGK/cGMP 0.018 0.031 -10000 0 -0.26 1 1
RhoA/GDP 0.034 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.051 0.063 -10000 0 -0.19 14 14
NOS3 0.03 0.026 -10000 0 -0.42 1 1
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA -0.049 0.18 0.28 1 -0.35 90 91
PRKCB -0.083 0.21 -10000 0 -0.41 97 97
PRKCE -0.047 0.18 -10000 0 -0.34 94 94
PRKCD -0.061 0.2 -10000 0 -0.38 95 95
PRKCG -0.062 0.2 -10000 0 -0.39 94 94
muscle contraction -0.097 0.26 -10000 0 -0.51 95 95
PRKCZ -0.057 0.18 0.35 1 -0.35 94 95
ARR3 0.021 0.007 -10000 0 -10000 0 0
TXA2/TP beta 0.038 0.056 0.2 1 -0.19 16 17
PRKCQ -0.084 0.2 -10000 0 -0.4 97 97
MAPKKK cascade -0.09 0.25 -10000 0 -0.48 96 96
SELE -0.059 0.18 -10000 0 -0.35 94 94
TP beta/GNAI2/GDP/G beta/gamma 0.057 0.062 -10000 0 -0.19 15 15
ROCK1 0.035 0.005 -10000 0 -10000 0 0
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
chemotaxis -0.12 0.31 -10000 0 -0.63 94 94
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.009 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.027 0.046 0.3 5 -10000 0 5
DAPP1 -0.29 0.39 0.34 1 -0.65 155 156
Src family/SYK family/BLNK-LAT/BTK-ITK -0.38 0.44 0.4 1 -0.8 164 165
mol:DAG -0.12 0.16 0.23 6 -0.3 140 146
HRAS 0.038 0.009 -10000 0 -10000 0 0
RAP1A 0.036 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.007 0.12 0.2 2 -0.32 31 33
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
PLCG1 0.033 0.01 -10000 0 -10000 0 0
ARF5 0.031 0.011 -10000 0 -10000 0 0
mol:GTP -0.002 0.058 0.22 20 -10000 0 20
ARF1/GTP 0.012 0.054 0.3 8 -10000 0 8
RHOA 0.035 0.005 -10000 0 -10000 0 0
YES1 0.034 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.03 0.18 11 -10000 0 11
ADAP1 -0.011 0.053 0.26 6 -0.2 10 16
ARAP3 -0.002 0.057 0.22 20 -10000 0 20
INPPL1 0.033 0.009 -10000 0 -10000 0 0
PREX1 0.03 0.035 -10000 0 -0.42 2 2
ARHGEF6 0.016 0.093 -10000 0 -0.42 16 16
ARHGEF7 0.034 0.008 -10000 0 -10000 0 0
ARF1 0.032 0.011 -10000 0 -10000 0 0
NRAS 0.036 0.01 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
mol:Ca2+ -0.054 0.076 0.16 9 -0.14 124 133
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
ZAP70 -0.12 0.22 -10000 0 -0.42 126 126
mol:IP3 -0.08 0.1 0.18 7 -0.2 134 141
LYN 0.016 0.084 -10000 0 -0.42 13 13
ARF1/GDP 0.01 0.12 0.2 1 -0.31 30 31
RhoA/GDP 0.042 0.082 0.26 9 -0.26 5 14
PDK1/Src/Hsp90 0.064 0.023 -10000 0 -10000 0 0
BLNK -0.11 0.21 -10000 0 -0.42 116 116
actin cytoskeleton reorganization 0.02 0.12 0.26 21 -0.31 18 39
SRC 0.033 0.01 -10000 0 -10000 0 0
PLEKHA2 -0.029 0.091 -10000 0 -0.26 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
PTEN 0.027 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
ARF6/GTP 0.031 0.052 0.3 10 -10000 0 10
RhoA/GTP -0.002 0.059 0.24 19 -10000 0 19
Src family/SYK family/BLNK-LAT -0.38 0.46 -10000 0 -0.79 167 167
BLK -0.23 0.22 -10000 0 -0.42 215 215
PDPK1 0.035 0.003 -10000 0 -10000 0 0
CYTH1 -0.003 0.055 0.28 10 -10000 0 10
HCK -0.002 0.12 -10000 0 -0.42 28 28
CYTH3 -0.006 0.043 0.26 6 -10000 0 6
CYTH2 -0.002 0.057 0.28 11 -10000 0 11
KRAS 0.037 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.026 0.048 0.22 7 -0.29 3 10
SGK1 0.015 0.085 0.23 7 -0.31 19 26
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
mol:GDP -0.008 0.13 0.2 5 -0.32 35 40
SOS1 0.035 0.003 -10000 0 -10000 0 0
SYK -0.012 0.13 -10000 0 -0.42 36 36
ARF6/GDP 0.023 0.082 0.28 15 -0.23 8 23
mol:PI-3-4-5-P3 -0.003 0.055 0.27 11 -10000 0 11
ARAP3/RAP1A/GTP 0.021 0.03 0.18 11 -10000 0 11
VAV1 -0.052 0.18 -10000 0 -0.42 70 70
mol:PI-3-4-P2 -0.029 0.11 -10000 0 -0.3 54 54
RAS family/GTP/PI3K Class I 0.069 0.057 0.21 45 -10000 0 45
PLEKHA1 -0.024 0.082 -10000 0 -0.25 43 43
Rac1/GDP 0.004 0.12 0.2 2 -0.31 32 34
LAT -0.021 0.15 -10000 0 -0.42 45 45
Rac1/GTP -0.018 0.15 -10000 0 -0.39 36 36
ITK -0.043 0.088 0.28 5 -0.21 64 69
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.18 0.22 0.22 4 -0.43 144 148
LCK -0.14 0.22 -10000 0 -0.42 137 137
BTK -0.029 0.083 0.27 9 -0.21 45 54
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.092 0.34 -10000 0 -0.82 62 62
NCK1/PAK1/Dok-R -0.082 0.15 -10000 0 -0.41 61 61
NCK1/Dok-R -0.14 0.42 -10000 0 -1 62 62
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.03 0.088 0.22 61 -10000 0 61
RELA 0.034 0.007 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
Rac/GDP 0.023 0.009 -10000 0 -10000 0 0
F2 0.026 0.099 0.25 57 -10000 0 57
TNIP2 0.034 0.007 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.39 -10000 0 -0.94 62 62
FN1 0.021 0.077 -10000 0 -0.42 11 11
PLD2 -0.15 0.4 -10000 0 -1 62 62
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GRB14 0.027 0.013 -10000 0 -10000 0 0
ELK1 -0.13 0.37 -10000 0 -0.93 62 62
GRB7 0.029 0.012 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.41 -10000 0 -0.99 62 62
CDKN1A -0.036 0.22 -10000 0 -0.52 52 52
ITGA5 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.42 -10000 0 -1 62 62
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:NO -0.046 0.27 0.38 1 -0.62 62 63
PLG -0.15 0.4 -10000 0 -1 62 62
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.087 0.33 -10000 0 -0.8 62 62
GRB2 0.034 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
ANGPT2 -0.039 0.18 -10000 0 -0.57 7 7
BMX -0.18 0.42 -10000 0 -1.1 62 62
ANGPT1 -0.21 0.47 -10000 0 -1.2 60 60
tube development -0.056 0.24 -10000 0 -0.57 61 61
ANGPT4 0.01 0.015 -10000 0 -10000 0 0
response to hypoxia -0.011 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.42 -10000 0 -1.1 62 62
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
FGF2 0.029 0.035 -10000 0 -0.42 2 2
STAT5A (dimer) -0.051 0.28 -10000 0 -0.64 61 61
mol:L-citrulline -0.046 0.27 0.38 1 -0.62 62 63
AGTR1 0.017 0.009 -10000 0 -10000 0 0
MAPK14 -0.14 0.39 -10000 0 -0.98 62 62
Tie2/SHP2 -0.046 0.22 -10000 0 -0.74 20 20
TEK -0.05 0.23 -10000 0 -0.84 19 19
RPS6KB1 -0.086 0.33 -10000 0 -0.78 62 62
Angiotensin II/AT1 0.015 0.007 -10000 0 -10000 0 0
Tie2/Ang1/GRB2 -0.14 0.42 -10000 0 -1 62 62
MAPK3 -0.14 0.38 -10000 0 -0.95 62 62
MAPK1 -0.14 0.38 -10000 0 -0.95 62 62
Tie2/Ang1/GRB7 -0.15 0.42 -10000 0 -1.1 62 62
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.15 0.4 -10000 0 -1 62 62
PI3K -0.11 0.38 -10000 0 -0.93 62 62
FES -0.14 0.4 -10000 0 -0.98 62 62
Crk/Dok-R -0.14 0.42 -10000 0 -1 62 62
Tie2/Ang1/ABIN2 -0.15 0.42 -10000 0 -1.1 62 62
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.079 0.31 -10000 0 -0.74 62 62
STAT5A 0.034 0.024 -10000 0 -0.42 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.074 0.34 -10000 0 -0.78 61 61
Tie2/Ang2 -0.08 0.31 -10000 0 -0.73 61 61
Tie2/Ang1 -0.16 0.43 -10000 0 -1.1 62 62
FOXO1 -0.08 0.31 -10000 0 -0.74 62 62
ELF1 0.041 0.019 -10000 0 -0.12 2 2
ELF2 -0.14 0.4 -10000 0 -1 62 62
mol:Choline -0.14 0.39 -10000 0 -0.98 62 62
cell migration -0.046 0.086 -10000 0 -0.23 62 62
FYN -0.067 0.27 -10000 0 -0.64 61 61
DOK2 -0.01 0.13 -10000 0 -0.42 35 35
negative regulation of cell cycle -0.029 0.21 -10000 0 -0.47 52 52
ETS1 0.001 0.095 -10000 0 -0.24 49 49
PXN -0.053 0.29 0.38 1 -0.66 61 62
ITGB1 0.032 0.011 -10000 0 -10000 0 0
NOS3 -0.061 0.3 0.39 1 -0.7 62 63
RAC1 0.031 0.012 -10000 0 -10000 0 0
TNF -0.086 0.2 -10000 0 -0.39 105 105
MAPKKK cascade -0.14 0.39 -10000 0 -0.98 62 62
RASA1 0.032 0.025 -10000 0 -0.42 1 1
Tie2/Ang1/Shc -0.15 0.42 -10000 0 -1 62 62
NCK1 0.034 0.006 -10000 0 -10000 0 0
vasculogenesis -0.036 0.25 0.35 3 -0.55 62 65
mol:Phosphatidic acid -0.14 0.39 -10000 0 -0.98 62 62
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.046 0.27 0.38 1 -0.62 62 63
Rac1/GTP -0.079 0.31 -10000 0 -0.74 62 62
MMP2 -0.15 0.4 -10000 0 -1 62 62
Glucocorticoid receptor regulatory network

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.081 0.097 0.28 30 -10000 0 30
SMARCC2 0.036 0.005 -10000 0 -10000 0 0
SMARCC1 0.036 0.005 -10000 0 -10000 0 0
TBX21 -0.21 0.32 -10000 0 -0.7 103 103
SUMO2 0.036 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.003 0.11 -10000 0 -0.28 45 45
FKBP4 0.034 0.007 -10000 0 -10000 0 0
FKBP5 0.003 0.11 -10000 0 -0.42 23 23
GR alpha/HSP90/FKBP51/HSP90 0.095 0.12 0.3 54 -0.21 7 61
PRL -0.045 0.11 -10000 0 -0.45 2 2
cortisol/GR alpha (dimer)/TIF2 0.19 0.26 0.56 99 -10000 0 99
RELA 0.015 0.072 -10000 0 -0.19 24 24
FGG 0.15 0.21 0.45 97 -10000 0 97
GR beta/TIF2 0.1 0.13 0.3 86 -10000 0 86
IFNG -0.42 0.53 -10000 0 -1.1 138 138
apoptosis 0.084 0.15 0.5 33 -10000 0 33
CREB1 0.036 0.01 -10000 0 -10000 0 0
histone acetylation -0.07 0.14 -10000 0 -0.34 60 60
BGLAP -0.061 0.14 -10000 0 -0.46 14 14
GR/PKAc 0.13 0.11 0.32 60 -10000 0 60
NF kappa B1 p50/RelA 0.022 0.13 -10000 0 -0.28 41 41
SMARCD1 0.036 0.006 -10000 0 -10000 0 0
MDM2 0.086 0.11 0.24 96 -10000 0 96
GATA3 -0.046 0.17 -10000 0 -0.42 64 64
AKT1 0.029 0.005 -10000 0 -10000 0 0
CSF2 -0.088 0.16 -10000 0 -0.56 14 14
GSK3B 0.037 0.011 -10000 0 -10000 0 0
NR1I3 0.11 0.16 0.53 28 -10000 0 28
CSN2 0.12 0.18 0.38 85 -10000 0 85
BRG1/BAF155/BAF170/BAF60A 0.093 0.023 -10000 0 -10000 0 0
NFATC1 0.025 0.07 -10000 0 -0.42 9 9
POU2F1 0.029 0.02 -10000 0 -10000 0 0
CDKN1A 0.023 0.056 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.009 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.12 0.32 41 -0.2 6 47
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.094 0.14 0.48 28 -10000 0 28
JUN -0.14 0.19 -10000 0 -0.41 90 90
IL4 -0.097 0.16 -10000 0 -0.5 26 26
CDK5R1 0.034 0.025 -10000 0 -0.42 1 1
PRKACA 0.035 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.052 0.11 0.22 17 -0.3 28 45
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.12 0.31 53 -0.19 6 59
cortisol/GR alpha (monomer) 0.23 0.32 0.66 109 -10000 0 109
NCOA2 0.032 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.02 0.074 -10000 0 -0.18 1 1
AP-1/NFAT1-c-4 -0.2 0.27 -10000 0 -0.51 137 137
AFP -0.11 0.14 -10000 0 -0.49 5 5
SUV420H1 0.034 0.008 -10000 0 -10000 0 0
IRF1 0.059 0.27 0.44 42 -0.66 33 75
TP53 0.05 0.015 -10000 0 -10000 0 0
PPP5C 0.035 0.004 -10000 0 -10000 0 0
KRT17 -0.19 0.27 -10000 0 -0.57 97 97
KRT14 -0.1 0.14 -10000 0 -0.49 12 12
TBP 0.039 0.015 -10000 0 -10000 0 0
CREBBP 0.042 0.012 -10000 0 -10000 0 0
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC2 0.03 0.012 -10000 0 -10000 0 0
AP-1 -0.2 0.28 -10000 0 -0.52 137 137
MAPK14 0.033 0.014 -10000 0 -10000 0 0
MAPK10 0.029 0.018 -10000 0 -10000 0 0
MAPK11 0.035 0.013 -10000 0 -10000 0 0
KRT5 -0.25 0.38 -10000 0 -0.84 84 84
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.037 0.006 -10000 0 -10000 0 0
STAT1 0.003 0.11 -10000 0 -0.28 45 45
CGA -0.084 0.15 -10000 0 -0.46 24 24
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.1 0.13 0.36 44 -10000 0 44
MAPK3 0.038 0.01 -10000 0 -10000 0 0
MAPK1 0.035 0.012 -10000 0 -10000 0 0
ICAM1 -0.12 0.23 -10000 0 -0.62 44 44
NFKB1 0.014 0.075 -10000 0 -0.18 34 34
MAPK8 -0.12 0.18 -10000 0 -0.39 86 86
MAPK9 0.035 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.081 0.15 0.51 32 -10000 0 32
BAX 0.014 0.043 -10000 0 -10000 0 0
POMC -0.25 0.5 -10000 0 -1.6 42 42
EP300 0.038 0.016 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.2 0.26 0.57 101 -10000 0 101
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.091 0.21 62 -10000 0 62
SGK1 0.057 0.073 -10000 0 -10000 0 0
IL13 -0.23 0.33 -10000 0 -0.77 78 78
IL6 -0.12 0.26 -10000 0 -0.62 55 55
PRKACG 0.019 0.009 -10000 0 -10000 0 0
IL5 -0.21 0.28 -10000 0 -0.74 61 61
IL2 -0.2 0.27 -10000 0 -0.63 75 75
CDK5 0.032 0.012 -10000 0 -10000 0 0
PRKACB 0.035 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
IL8 -0.12 0.22 -10000 0 -0.52 60 60
CDK5R1/CDK5 0.047 0.028 -10000 0 -0.3 1 1
NF kappa B1 p50/RelA/PKAc 0.056 0.11 -10000 0 -0.25 20 20
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.2 0.25 0.54 106 -10000 0 106
SMARCA4 0.037 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.16 0.37 95 -10000 0 95
NF kappa B1 p50/RelA/Cbp 0.062 0.11 0.34 1 -0.28 9 10
JUN (dimer) -0.14 0.19 -10000 0 -0.4 90 90
YWHAH 0.034 0.008 -10000 0 -10000 0 0
VIPR1 -0.2 0.32 -10000 0 -0.71 98 98
NR3C1 0.15 0.21 0.43 103 -10000 0 103
NR4A1 -0.015 0.16 -10000 0 -0.45 41 41
TIF2/SUV420H1 0.045 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.084 0.15 0.5 33 -10000 0 33
cortisol/GR alpha (dimer)/Src-1 0.21 0.27 0.56 110 -10000 0 110
PBX1 0.028 0.02 -10000 0 -10000 0 0
POU1F1 0.017 0.02 -10000 0 -10000 0 0
SELE -0.16 0.33 -10000 0 -0.74 75 75
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.16 0.37 95 -10000 0 95
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.2 0.25 0.54 106 -10000 0 106
mol:cortisol 0.14 0.19 0.38 111 -10000 0 111
MMP1 -0.14 0.33 -10000 0 -1 40 40
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.029 0.13 -10000 0 -0.29 64 64
CRKL 0.033 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
ITGA4 -0.013 0.14 -10000 0 -0.42 39 39
alpha4/beta7 Integrin/MAdCAM1 -0.14 0.19 -10000 0 -0.28 233 233
EPO 0.027 0.012 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.16 -10000 0 -0.32 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.011 0.11 -10000 0 -0.29 39 39
EPO/EPOR (dimer) 0.043 0.017 -10000 0 -10000 0 0
lamellipodium assembly 0.018 0.076 -10000 0 -0.54 5 5
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
JAK2 -0.003 0.1 -10000 0 -0.28 37 37
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
MADCAM1 -0.22 0.22 -10000 0 -0.42 202 202
cell adhesion -0.14 0.19 -10000 0 -0.27 233 233
CRKL/CBL 0.044 0.02 -10000 0 -10000 0 0
ITGB1 0.032 0.011 -10000 0 -10000 0 0
SRC -0.038 0.13 0.19 3 -0.3 67 70
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.16 -10000 0 -0.32 73 73
p130Cas/Crk/Dock1 -0.005 0.13 -10000 0 -0.27 61 61
VCAM1 -0.04 0.17 -10000 0 -0.42 60 60
RHOA 0.035 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.097 -10000 0 -0.22 39 39
BCAR1 -0.043 0.12 0.18 4 -0.28 67 71
EPOR 0.035 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.079 -10000 0 -0.57 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.033 0.009 -10000 0 -10000 0 0
ELF1 -0.039 0.15 -10000 0 -0.31 84 84
CCNA2 0.034 0.024 -10000 0 -0.42 1 1
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
JAK3 0.005 0.11 -10000 0 -0.42 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.035 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.16 0.33 -10000 0 -0.6 118 118
SHC1 0.032 0.011 -10000 0 -10000 0 0
SP1 0.019 0.094 -10000 0 -0.33 24 24
IL2RA -0.13 0.29 -10000 0 -0.63 88 88
IL2RB -0.042 0.17 -10000 0 -0.42 61 61
SOS1 0.036 0.003 -10000 0 -10000 0 0
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
G1/S transition of mitotic cell cycle -0.031 0.22 0.27 2 -0.68 33 35
PTPN11 0.035 0.006 -10000 0 -10000 0 0
CCND2 -0.019 0.18 -10000 0 -0.68 24 24
LCK -0.13 0.22 -10000 0 -0.42 137 137
GRB2 0.034 0.007 -10000 0 -10000 0 0
IL2 0.023 0.009 -10000 0 -10000 0 0
CDK6 0.029 0.042 -10000 0 -0.42 3 3
CCND3 -0.12 0.28 -10000 0 -0.56 88 88
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.083 0.19 0.23 1 -0.35 101 102
BAG4 0.034 0.008 -10000 0 -10000 0 0
BAD -0.018 0.069 0.15 7 -0.14 56 63
NFKBIA 0.035 0.004 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BAX -0.019 0.068 0.15 6 -0.14 50 56
EnzymeConsortium:3.1.4.12 -0.016 0.048 0.066 16 -0.096 68 84
IKBKB -0.077 0.18 0.24 5 -0.4 66 71
MAP2K2 -0.015 0.073 0.21 7 -0.19 15 22
MAP2K1 -0.014 0.073 0.21 7 -0.19 15 22
SMPD1 -0.014 0.052 0.093 2 -0.14 23 25
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.071 0.2 0.3 8 -0.41 63 71
MAP2K4 -0.014 0.064 0.18 2 -0.17 16 18
protein ubiquitination -0.08 0.19 0.24 2 -0.4 68 70
EnzymeConsortium:2.7.1.37 -0.014 0.078 0.22 6 -0.21 15 21
response to UV 0 0.001 0.003 8 -0.002 14 22
RAF1 -0.016 0.071 0.18 4 -0.18 19 23
CRADD 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide -0.02 0.07 0.13 5 -0.14 65 70
I-kappa-B-alpha/RELA/p50/ubiquitin 0.045 0.011 -10000 0 -10000 0 0
MADD 0.035 0.006 -10000 0 -10000 0 0
MAP3K1 -0.018 0.069 0.15 5 -0.14 50 55
TRADD 0.034 0.007 -10000 0 -10000 0 0
RELA/p50 0.034 0.007 -10000 0 -10000 0 0
MAPK3 -0.01 0.074 0.21 7 -0.19 12 19
MAPK1 -0.011 0.075 0.21 7 -0.2 14 21
p50/RELA/I-kappa-B-alpha 0.05 0.012 -10000 0 -10000 0 0
FADD -0.08 0.19 0.26 5 -0.36 94 99
KSR1 -0.017 0.07 0.17 5 -0.15 50 55
MAPK8 -0.013 0.059 0.17 2 -0.18 7 9
TRAF2 0.033 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.003 3 -0.002 3 6
CHUK -0.079 0.18 0.22 1 -0.39 68 69
TNF R/SODD 0.048 0.015 -10000 0 -10000 0 0
TNF -0.054 0.18 -10000 0 -0.42 69 69
CYCS -0.014 0.069 0.14 10 -0.15 45 55
IKBKG -0.079 0.18 0.22 3 -0.39 68 71
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.093 0.2 -10000 0 -0.36 108 108
RELA 0.034 0.007 -10000 0 -10000 0 0
RIPK1 0.031 0.012 -10000 0 -10000 0 0
AIFM1 -0.02 0.067 0.14 7 -0.14 50 57
TNF/TNF R/SODD 0.002 0.12 -10000 0 -0.25 66 66
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
response to heat 0 0.001 0.003 3 -0.002 3 6
CASP8 0.002 0.13 -10000 0 -0.69 10 10
NSMAF -0.072 0.19 0.23 9 -0.34 97 106
response to hydrogen peroxide 0 0.001 0.003 8 -0.002 14 22
BCL2 0.035 0.005 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
CDC42/GTP -0.033 0.12 -10000 0 -0.22 96 96
PLCG1 -0.04 0.11 -10000 0 -0.22 83 83
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
G12/G13 0.045 0.018 -10000 0 -10000 0 0
cell migration -0.033 0.12 -10000 0 -0.21 96 96
S1PR5 0.034 0.008 -10000 0 -10000 0 0
S1PR4 -0.11 0.21 -10000 0 -0.42 118 118
MAPK3 -0.045 0.11 -10000 0 -0.22 89 89
MAPK1 -0.042 0.11 -10000 0 -0.22 89 89
S1P/S1P5/Gi 0.022 0.037 -10000 0 -0.18 4 4
GNAI1 0.031 0.012 -10000 0 -10000 0 0
CDC42/GDP 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.04 0.019 -10000 0 -10000 0 0
RHOA -0.028 0.12 0.22 27 -0.21 97 124
S1P/S1P4/Gi -0.047 0.12 -10000 0 -0.23 91 91
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
S1P/S1P4/G12/G13 -0.022 0.13 -10000 0 -0.22 98 98
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
Endothelins

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
AKT1 0.006 0.13 0.29 22 -0.26 49 71
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
mol:Ca2+ -0.032 0.22 0.65 1 -0.52 42 43
EDN1 0.016 0.11 0.23 22 -0.21 37 59
EDN3 0 0.093 -10000 0 -0.42 17 17
EDN2 0.017 0.002 -10000 0 -10000 0 0
HRAS/GDP -0.048 0.2 0.34 2 -0.42 56 58
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.013 0.16 0.2 11 -0.39 37 48
ADCY4 0.024 0.13 0.22 29 -0.28 23 52
ADCY5 -0.018 0.15 0.23 13 -0.27 61 74
ADCY6 0.026 0.12 0.23 19 -0.3 17 36
ADCY7 0.024 0.12 0.26 11 -0.31 15 26
ADCY1 -0.007 0.13 0.26 11 -0.25 42 53
ADCY2 0.005 0.11 0.24 8 -0.3 16 24
ADCY3 0.025 0.12 0.26 10 -0.29 18 28
ADCY8 0.017 0.11 0.21 23 -0.23 28 51
ADCY9 0.028 0.12 0.22 33 -0.27 23 56
arachidonic acid secretion -0.03 0.18 0.36 3 -0.4 41 44
ETB receptor/Endothelin-1/Gq/GTP -0.003 0.11 -10000 0 -0.26 45 45
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
HRAS 0.035 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.037 0.14 0.37 18 -0.24 40 58
ETA receptor/Endothelin-1/Gs/GTP 0.031 0.13 0.34 21 -0.23 45 66
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 0.006 0.13 0.29 23 -0.31 23 46
EDNRB 0.03 0.028 -10000 0 -0.42 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.014 0.18 0.29 18 -0.42 43 61
CYSLTR1 -0.021 0.2 0.29 23 -0.5 43 66
SLC9A1 0.011 0.078 0.2 21 -0.22 12 33
mol:GDP -0.065 0.2 0.34 2 -0.45 58 60
SLC9A3 -0.15 0.3 0.43 1 -0.57 103 104
RAF1 -0.056 0.19 0.36 1 -0.43 51 52
JUN -0.042 0.23 0.48 1 -0.56 43 44
JAK2 0.004 0.13 0.29 20 -0.27 47 67
mol:IP3 -0.024 0.17 0.23 2 -0.4 44 46
ETA receptor/Endothelin-1 0.025 0.17 0.42 22 -0.3 50 72
PLCB1 0.019 0.081 -10000 0 -0.42 12 12
PLCB2 0.022 0.074 -10000 0 -0.42 10 10
ETA receptor/Endothelin-3 0.004 0.098 0.19 11 -0.23 32 43
FOS -0.028 0.16 0.46 1 -0.48 13 14
Gai/GDP -0.016 0.18 -10000 0 -0.75 19 19
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.016 0.18 0.27 11 -0.46 38 49
BCAR1 0.034 0.008 -10000 0 -10000 0 0
PRKCB1 -0.025 0.16 0.22 2 -0.37 47 49
GNAQ 0.035 0.01 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
GNAL 0.024 0.053 -10000 0 -0.42 5 5
Gs family/GDP -0.055 0.19 0.32 2 -0.42 53 55
ETA receptor/Endothelin-1/Gq/GTP -0.003 0.14 0.22 12 -0.36 34 46
MAPK14 -0.015 0.13 0.3 1 -0.37 28 29
TRPC6 -0.034 0.22 0.66 1 -0.54 41 42
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.01 0.14 -10000 0 -0.35 33 33
ETB receptor/Endothelin-2 0.03 0.027 -10000 0 -0.3 1 1
ETB receptor/Endothelin-3 0.01 0.075 -10000 0 -0.29 18 18
ETB receptor/Endothelin-1 0.027 0.083 -10000 0 -0.27 9 9
MAPK3 -0.038 0.17 0.46 1 -0.5 22 23
MAPK1 -0.04 0.18 0.46 1 -0.52 22 23
Rac1/GDP -0.046 0.19 0.39 1 -0.43 53 54
cAMP biosynthetic process -0.018 0.15 0.26 16 -0.35 33 49
MAPK8 -0.055 0.26 0.51 1 -0.62 52 53
SRC 0.033 0.01 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.013 0.05 -10000 0 -0.32 3 3
p130Cas/CRK/Src/PYK2 -0.053 0.21 0.44 2 -0.43 60 62
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.045 0.19 0.39 1 -0.43 52 53
COL1A2 0.013 0.12 0.29 22 -0.38 12 34
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.079 0.28 1 -0.18 18 19
mol:DAG -0.024 0.17 0.23 2 -0.4 44 46
MAP2K2 -0.048 0.18 0.41 2 -0.49 27 29
MAP2K1 -0.047 0.18 0.33 3 -0.46 33 36
EDNRA 0.016 0.11 0.24 23 -0.19 52 75
positive regulation of muscle contraction 0.02 0.12 0.25 39 -0.24 35 74
Gq family/GDP -0.045 0.21 -10000 0 -0.45 59 59
HRAS/GTP -0.062 0.2 0.37 1 -0.42 63 64
PRKCH -0.026 0.16 0.21 2 -0.4 40 42
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA -0.024 0.17 0.24 8 -0.39 43 51
PRKCB -0.081 0.22 -10000 0 -0.44 75 75
PRKCE -0.024 0.16 0.23 5 -0.39 42 47
PRKCD -0.025 0.16 0.23 3 -0.4 41 44
PRKCG -0.028 0.16 0.21 2 -0.38 45 47
regulation of vascular smooth muscle contraction -0.038 0.18 0.49 1 -0.57 13 14
PRKCQ -0.07 0.2 -10000 0 -0.43 64 64
PLA2G4A -0.034 0.18 0.37 3 -0.43 41 44
GNA14 -0.035 0.16 -10000 0 -0.42 56 56
GNA15 0.022 0.078 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA11 0.036 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.14 0.37 18 -0.24 40 58
MMP1 -0.041 0.2 0.56 4 -0.78 22 26
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 0.033 0.034 -10000 0 -0.42 2 2
CCL5 -0.096 0.2 -10000 0 -0.42 105 105
SDCBP 0.032 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.028 0.14 0.21 8 -0.28 68 76
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.022 0.15 0.22 8 -0.42 28 36
Syndecan-1/Syntenin -0.018 0.14 0.21 6 -0.38 28 34
MAPK3 -0.018 0.14 0.22 8 -0.41 24 32
HGF/MET 0.019 0.091 -10000 0 -0.3 25 25
TGFB1/TGF beta receptor Type II 0.033 0.034 -10000 0 -0.42 2 2
BSG 0.035 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.022 0.14 0.22 8 -0.41 28 36
Syndecan-1/RANTES -0.074 0.19 0.24 8 -0.41 62 70
Syndecan-1/CD147 0 0.15 0.32 2 -0.42 25 27
Syndecan-1/Syntenin/PIP2 -0.018 0.13 0.2 6 -0.37 28 34
LAMA5 0.032 0.025 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion -0.018 0.13 0.19 6 -0.36 28 34
MMP7 0.017 0.07 -10000 0 -0.42 9 9
HGF 0.024 0.058 -10000 0 -0.42 6 6
Syndecan-1/CASK -0.041 0.13 -10000 0 -0.27 72 72
Syndecan-1/HGF/MET -0.02 0.16 0.34 1 -0.45 31 32
regulation of cell adhesion -0.024 0.13 0.29 2 -0.39 23 25
HPSE 0.035 0.005 -10000 0 -10000 0 0
positive regulation of cell migration -0.028 0.14 0.21 8 -0.28 68 76
SDC1 -0.032 0.14 -10000 0 -0.28 71 71
Syndecan-1/Collagen -0.028 0.14 0.21 8 -0.28 68 76
PPIB 0.035 0.004 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PRKACA 0.035 0.003 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
MAPK1 -0.017 0.13 0.22 8 -0.39 24 32
homophilic cell adhesion -0.027 0.14 0.23 10 -0.28 68 78
MMP1 0.002 0.1 -10000 0 -0.42 21 21
Fc-epsilon receptor I signaling in mast cells

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.034 0.007 -10000 0 -10000 0 0
LAT2 -0.034 0.17 0.2 4 -0.43 44 48
AP1 -0.069 0.28 -10000 0 -0.57 75 75
mol:PIP3 -0.052 0.24 0.32 17 -0.51 63 80
IKBKB -0.027 0.14 0.23 25 -0.28 59 84
AKT1 0.024 0.12 0.32 40 -0.23 1 41
IKBKG -0.029 0.14 0.23 21 -0.28 59 80
MS4A2 0.027 0.021 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.034 0.007 -10000 0 -10000 0 0
MAP3K1 -0.05 0.2 0.26 10 -0.44 64 74
mol:Ca2+ -0.031 0.18 0.27 22 -0.37 61 83
LYN 0.017 0.087 -10000 0 -0.43 13 13
CBLB -0.019 0.13 0.2 3 -0.37 35 38
SHC1 0.032 0.011 -10000 0 -10000 0 0
RasGAP/p62DOK 0.06 0.026 -10000 0 -0.22 1 1
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
PLD2 0.024 0.11 0.33 33 -0.2 20 53
PTPN13 -0.007 0.16 -10000 0 -0.52 16 16
PTPN11 0.031 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.015 0.11 0.31 11 -0.3 10 21
SYK -0.011 0.14 -10000 0 -0.43 36 36
GRB2 0.034 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.064 0.22 -10000 0 -0.52 62 62
LAT -0.039 0.16 0.18 1 -0.4 49 50
PAK2 -0.058 0.23 0.26 9 -0.5 64 73
NFATC2 -0.019 0.12 -10000 0 -0.5 20 20
HRAS -0.065 0.25 0.28 8 -0.55 65 73
GAB2 0.033 0.009 -10000 0 -10000 0 0
PLA2G1B 0.011 0.13 -10000 0 -0.9 7 7
Fc epsilon R1 0.035 0.081 -10000 0 -0.25 24 24
Antigen/IgE/Fc epsilon R1 0.033 0.074 -10000 0 -0.22 24 24
mol:GDP -0.091 0.27 0.35 1 -0.6 70 71
JUN 0.032 0.011 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
FOS 0.034 0.008 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.016 0.14 0.22 1 -0.37 38 39
CHUK -0.029 0.14 0.23 19 -0.28 59 78
KLRG1 -0.021 0.12 -10000 0 -0.32 44 44
VAV1 -0.047 0.18 0.2 2 -0.44 52 54
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.015 0.12 0.21 1 -0.38 30 31
negative regulation of mast cell degranulation -0.023 0.18 0.22 9 -0.37 62 71
BTK -0.1 0.31 -10000 0 -0.68 72 72
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.15 -10000 0 -0.33 55 55
GAB2/PI3K/SHP2 -0.003 0.052 -10000 0 -0.21 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.018 0.14 -10000 0 -0.36 41 41
RAF1 0.005 0.14 -10000 0 -0.99 7 7
Fc epsilon R1/FcgammaRIIB/SHIP 0.021 0.15 -10000 0 -0.3 59 59
FCER1G 0.002 0.11 -10000 0 -0.42 23 23
FCER1A 0.026 0.029 -10000 0 -0.43 1 1
Antigen/IgE/Fc epsilon R1/Fyn 0.044 0.074 -10000 0 -0.2 24 24
MAPK3 0.011 0.13 -10000 0 -0.91 7 7
MAPK1 0.009 0.13 -10000 0 -0.91 7 7
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.056 0.28 -10000 0 -0.73 44 44
DUSP1 0.033 0.01 -10000 0 -10000 0 0
NF-kappa-B/RelA -0.008 0.088 0.16 10 -0.17 56 66
actin cytoskeleton reorganization -0.005 0.16 -10000 0 -0.52 18 18
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.03 0.22 0.36 1 -0.47 62 63
FER -0.016 0.13 0.2 3 -0.37 33 36
RELA 0.034 0.007 -10000 0 -10000 0 0
ITK -0.096 0.18 -10000 0 -0.37 105 105
SOS1 0.035 0.003 -10000 0 -10000 0 0
PLCG1 -0.07 0.27 0.3 11 -0.6 65 76
cytokine secretion -0.012 0.057 -10000 0 -0.14 36 36
SPHK1 -0.02 0.13 0.2 2 -0.38 34 36
PTK2 -0.006 0.16 -10000 0 -0.55 17 17
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.055 0.22 0.26 1 -0.51 62 63
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.039 0.22 0.31 21 -0.48 59 80
MAP2K2 0.004 0.14 -10000 0 -0.93 7 7
MAP2K1 0.005 0.14 -10000 0 -0.93 7 7
MAP2K7 0.035 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.006 0.12 0.23 6 -0.32 37 43
MAP2K4 -0.013 0.23 -10000 0 -0.87 24 24
Fc epsilon R1/FcgammaRIIB 0.042 0.11 -10000 0 -0.27 32 32
mol:Choline 0.024 0.11 0.32 33 -0.2 20 53
SHC/Grb2/SOS1 0.029 0.14 -10000 0 -0.36 32 32
FYN 0.031 0.012 -10000 0 -10000 0 0
DOK1 0.035 0.002 -10000 0 -10000 0 0
PXN -0.005 0.15 -10000 0 -0.52 15 15
HCLS1 -0.044 0.18 0.2 3 -0.44 53 56
PRKCB -0.05 0.19 0.27 18 -0.39 64 82
FCGR2B 0.013 0.09 -10000 0 -0.42 15 15
IGHE 0 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.023 0.18 0.22 9 -0.38 62 71
LCP2 0.015 0.09 -10000 0 -0.42 15 15
PLA2G4A -0.017 0.13 0.2 2 -0.38 33 35
RASA1 0.032 0.025 -10000 0 -0.42 1 1
mol:Phosphatidic acid 0.024 0.11 0.32 33 -0.2 20 53
IKK complex -0.014 0.11 0.24 18 -0.21 54 72
WIPF1 0.029 0.053 -10000 0 -0.42 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.069 0.23 2 -0.27 3 5
adherens junction organization -0.041 0.12 -10000 0 -0.23 91 91
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.072 0.25 1 -0.21 2 3
FMN1 -0.04 0.12 -10000 0 -0.23 88 88
mol:IP3 -0.011 0.066 0.22 1 -0.2 4 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.035 0.12 -10000 0 -0.23 88 88
CTNNB1 0.037 0.007 -10000 0 -10000 0 0
AKT1 -0.008 0.084 0.2 2 -0.24 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.059 0.18 -10000 0 -0.34 95 95
CTNND1 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.1 -10000 0 -0.22 75 75
VASP -0.036 0.11 -10000 0 -0.22 88 88
ZYX -0.033 0.1 -10000 0 -0.22 76 76
JUB -0.036 0.11 -10000 0 -0.22 88 88
EGFR(dimer) -0.025 0.12 -10000 0 -0.22 83 83
E-cadherin/beta catenin-gamma catenin -0.013 0.13 -10000 0 -0.23 92 92
mol:PI-3-4-5-P3 0.009 0.099 0.23 1 -0.25 5 6
PIK3CA 0.035 0.007 -10000 0 -10000 0 0
PI3K 0.009 0.1 0.23 1 -0.25 5 6
FYN -0.016 0.076 0.22 2 -0.25 17 19
mol:Ca2+ -0.011 0.065 0.22 1 -0.2 4 5
JUP 0.036 0.01 -10000 0 -10000 0 0
PIK3R1 0.035 0.008 -10000 0 -10000 0 0
mol:DAG -0.011 0.066 0.22 1 -0.2 4 5
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
RhoA/GDP 0.009 0.084 0.26 4 -0.21 1 5
establishment of polarity of embryonic epithelium -0.036 0.11 -10000 0 -0.22 88 88
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
CASR -0.016 0.062 0.2 3 -0.2 1 4
RhoA/GTP 0.003 0.072 0.22 2 -0.19 2 4
AKT2 -0.009 0.085 0.2 2 -0.23 5 7
actin cable formation -0.039 0.12 0.19 5 -0.31 15 20
apoptosis 0.007 0.084 0.25 6 -0.22 4 10
CTNNA1 0.034 0.009 -10000 0 -10000 0 0
mol:GDP -0.013 0.068 0.2 4 -0.22 3 7
PIP5K1A -0.031 0.1 -10000 0 -0.22 75 75
PLCG1 -0.011 0.067 0.22 1 -0.21 4 5
Rac1/GTP -0.015 0.12 -10000 0 -0.21 82 82
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.011 0.11 -10000 0 -0.48 15 15
Syndecan-4/Syndesmos -0.038 0.22 -10000 0 -0.5 56 56
positive regulation of JNK cascade -0.039 0.22 -10000 0 -0.49 58 58
Syndecan-4/ADAM12 -0.043 0.21 -10000 0 -0.49 56 56
CCL5 -0.096 0.2 -10000 0 -0.42 105 105
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DNM2 0.035 0.003 -10000 0 -10000 0 0
ITGA5 0.034 0.006 -10000 0 -10000 0 0
SDCBP 0.032 0.01 -10000 0 -10000 0 0
PLG 0.009 0.019 -10000 0 -10000 0 0
ADAM12 0.029 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.035 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.027 0.016 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.2 -10000 0 -0.5 55 55
Syndecan-4/CXCL12/CXCR4 -0.042 0.24 -10000 0 -0.52 58 58
Syndecan-4/Laminin alpha3 -0.044 0.22 -10000 0 -0.5 55 55
MDK 0.029 0.042 -10000 0 -0.42 3 3
Syndecan-4/FZD7 -0.038 0.22 -10000 0 -0.5 56 56
Syndecan-4/Midkine -0.041 0.22 -10000 0 -0.5 56 56
FZD7 0.034 0.024 -10000 0 -0.42 1 1
Syndecan-4/FGFR1/FGF -0.028 0.2 -10000 0 -0.47 54 54
THBS1 0.031 0.012 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.039 0.21 -10000 0 -0.48 58 58
positive regulation of MAPKKK cascade -0.039 0.22 -10000 0 -0.49 58 58
Syndecan-4/TACI -0.13 0.23 -10000 0 -0.58 58 58
CXCR4 0.001 0.12 -10000 0 -0.42 28 28
cell adhesion 0.014 0.054 0.2 7 -0.24 11 18
Syndecan-4/Dynamin -0.037 0.21 -10000 0 -0.49 56 56
Syndecan-4/TSP1 -0.043 0.21 -10000 0 -0.49 56 56
Syndecan-4/GIPC -0.037 0.21 -10000 0 -0.49 56 56
Syndecan-4/RANTES -0.092 0.25 -10000 0 -0.6 55 55
ITGB1 0.032 0.011 -10000 0 -10000 0 0
LAMA1 0.006 0.013 -10000 0 -10000 0 0
LAMA3 0.02 0.081 -10000 0 -0.42 12 12
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA 0.023 0.15 0.84 11 -0.39 1 12
Syndecan-4/alpha-Actinin -0.038 0.22 -10000 0 -0.49 56 56
TFPI 0.034 0.024 -10000 0 -0.42 1 1
F2 0.013 0.027 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.069 0.2 -10000 0 -0.49 55 55
ACTN1 0.033 0.024 -10000 0 -0.42 1 1
TNC 0.02 0.074 -10000 0 -0.42 10 10
Syndecan-4/CXCL12 -0.044 0.22 -10000 0 -0.5 56 56
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
CXCL12 0.018 0.077 -10000 0 -0.42 11 11
TNFRSF13B -0.17 0.22 -10000 0 -0.42 163 163
FGF2 0.03 0.035 -10000 0 -0.42 2 2
FGFR1 0.031 0.012 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.063 0.2 -10000 0 -0.49 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.016 0.076 -10000 0 -0.4 11 11
cell migration -0.013 0.012 -10000 0 -10000 0 0
PRKCD 0.029 0.023 -10000 0 -10000 0 0
vasculogenesis -0.04 0.2 -10000 0 -0.47 57 57
SDC4 -0.058 0.21 -10000 0 -0.52 56 56
Syndecan-4/Tenascin C -0.041 0.22 -10000 0 -0.5 58 58
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.037 0.21 -10000 0 -0.5 52 52
MMP9 -0.035 0.16 -10000 0 -0.42 55 55
Rac1/GTP 0.014 0.055 0.2 7 -0.25 11 18
cytoskeleton organization -0.035 0.21 -10000 0 -0.48 56 56
GIPC1 0.035 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.038 0.22 -10000 0 -0.5 56 56
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.017 0.11 -10000 0 -0.23 56 56
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.092 0.24 1 -0.27 13 14
AP1 0.006 0.089 -10000 0 -0.2 53 53
mol:PIP3 -0.016 0.074 -10000 0 -0.19 50 50
AKT1 0.013 0.089 0.25 6 -0.28 8 14
PTK2B -0.028 0.11 0.18 1 -0.28 34 35
RHOA 0.014 0.065 0.18 10 -0.27 8 18
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.064 0.22 6 -0.29 7 13
MAGI3 0.034 0.007 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
apoptosis -0.019 0.09 -10000 0 -0.23 54 54
HRAS/GDP 0.026 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.026 0.097 0.21 2 -0.32 17 19
NF kappa B1 p50/RelA -0.008 0.097 -10000 0 -0.27 25 25
endothelial cell migration -0.019 0.097 -10000 0 -0.25 51 51
ADCY4 -0.036 0.13 -10000 0 -0.32 57 57
ADCY5 -0.073 0.16 -10000 0 -0.38 68 68
ADCY6 -0.036 0.13 -10000 0 -0.31 59 59
ADCY7 -0.035 0.13 -10000 0 -0.32 57 57
ADCY1 -0.062 0.15 -10000 0 -0.35 61 61
ADCY2 -0.044 0.13 -10000 0 -0.31 61 61
ADCY3 -0.036 0.13 -10000 0 -0.3 61 61
ADCY8 -0.035 0.12 -10000 0 -0.31 53 53
ADCY9 -0.036 0.13 -10000 0 -0.31 60 60
GSK3B -0.026 0.1 0.22 2 -0.29 28 30
arachidonic acid secretion -0.038 0.13 -10000 0 -0.3 63 63
GNG2 0.027 0.057 -10000 0 -0.42 6 6
TRIP6 0.024 0.02 -10000 0 -10000 0 0
GNAO1 -0.025 0.091 -10000 0 -0.24 52 52
HRAS 0.034 0.006 -10000 0 -10000 0 0
NFKBIA -0.015 0.086 0.23 1 -0.3 13 14
GAB1 0.035 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.018 0.26 -10000 0 -0.88 29 29
JUN 0.032 0.011 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.045 0.029 -10000 0 -0.24 3 3
TIAM1 -0.043 0.3 -10000 0 -1.1 29 29
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.002 0.059 0.2 4 -0.3 7 11
PLCB3 0.023 0.032 0.19 6 -0.22 3 9
FOS 0.034 0.008 -10000 0 -10000 0 0
positive regulation of mitosis -0.038 0.13 -10000 0 -0.3 63 63
LPA/LPA1-2-3 0.009 0.1 -10000 0 -0.22 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
stress fiber formation -0.016 0.11 -10000 0 -0.35 18 18
GNAZ -0.02 0.091 -10000 0 -0.24 51 51
EGFR/PI3K-beta/Gab1 -0.006 0.082 -10000 0 -0.2 50 50
positive regulation of dendritic cell cytokine production 0.008 0.1 -10000 0 -0.22 54 54
LPA/LPA2/MAGI-3 0.044 0.03 -10000 0 -0.24 3 3
ARHGEF1 0.013 0.1 0.21 39 -0.2 47 86
GNAI2 -0.018 0.093 -10000 0 -0.24 53 53
GNAI3 -0.016 0.091 -10000 0 -0.24 50 50
GNAI1 -0.019 0.091 -10000 0 -0.24 51 51
LPA/LPA3 0.018 0.017 -10000 0 -0.11 2 2
LPA/LPA2 0.025 0.03 -10000 0 -0.22 5 5
LPA/LPA1 -0.02 0.11 -10000 0 -0.29 55 55
HB-EGF/EGFR -0.01 0.098 -10000 0 -0.25 50 50
HBEGF -0.024 0.1 -10000 0 -0.3 47 47
mol:DAG -0.002 0.059 0.2 4 -0.3 7 11
cAMP biosynthetic process -0.041 0.13 0.21 5 -0.3 65 70
NFKB1 0.034 0.006 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
LYN -0.018 0.12 0.24 2 -0.38 22 24
GNAQ 0.016 0.027 -10000 0 -0.25 3 3
LPAR2 0.031 0.041 -10000 0 -0.42 3 3
LPAR3 0.025 0.015 -10000 0 -10000 0 0
LPAR1 -0.032 0.16 -10000 0 -0.4 55 55
IL8 -0.032 0.13 0.33 1 -0.35 32 33
PTK2 -0.006 0.076 0.19 6 -0.21 40 46
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
CASP3 -0.019 0.09 -10000 0 -0.23 54 54
EGFR 0.027 0.035 -10000 0 -0.42 2 2
PLCG1 0 0.058 0.16 4 -0.29 7 11
PLD2 -0.012 0.086 0.19 6 -0.21 53 59
G12/G13 0.019 0.097 -10000 0 -0.22 48 48
PI3K-beta -0.005 0.079 -10000 0 -0.3 10 10
cell migration 0.004 0.09 0.2 1 -0.26 28 29
SLC9A3R2 0.035 0.004 -10000 0 -10000 0 0
PXN -0.016 0.11 -10000 0 -0.36 18 18
HRAS/GTP -0.039 0.13 -10000 0 -0.31 61 61
RAC1 0.031 0.012 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
PRKCE 0.035 0.004 -10000 0 -10000 0 0
PRKCD -0.004 0.065 0.21 5 -0.33 4 9
Gi(beta/gamma) -0.028 0.13 -10000 0 -0.3 59 59
mol:LPA 0.002 0.012 -10000 0 -0.16 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.016 0.11 -10000 0 -0.32 8 8
MAPKKK cascade -0.038 0.13 -10000 0 -0.3 63 63
contractile ring contraction involved in cytokinesis 0.014 0.065 0.19 7 -0.27 8 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.095 -10000 0 -0.24 56 56
GNA15 0.01 0.055 -10000 0 -0.26 13 13
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
MAPT -0.027 0.1 0.22 2 -0.34 17 19
GNA11 0.017 0.025 -10000 0 -0.23 3 3
Rac1/GTP -0.021 0.27 -10000 0 -0.94 29 29
MMP2 -0.019 0.098 -10000 0 -0.25 51 51
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.1 -10000 0 -0.21 64 64
RGS9BP 0.035 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
mol:Na + 0.023 0.012 -10000 0 -10000 0 0
mol:ADP -0.015 0.006 -10000 0 -10000 0 0
GNAT2 0.033 0.008 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.056 0.15 -10000 0 -0.25 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.036 0.013 -10000 0 -10000 0 0
GRK7 0.027 0.01 -10000 0 -10000 0 0
CNGB3 0.021 0.011 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.034 0.17 12 -10000 0 12
Cone PDE6 -0.038 0.14 -10000 0 -0.22 136 136
Cone Metarhodopsin II 0.027 0.01 -10000 0 -10000 0 0
Na + (4 Units) 0.027 0.018 -10000 0 -10000 0 0
GNAT2/GDP -0.035 0.14 -10000 0 -0.21 133 133
GNB5 0.033 0.024 -10000 0 -0.42 1 1
mol:GMP (4 units) 0 0.037 0.17 14 -10000 0 14
Cone Transducin 0.009 0.11 -10000 0 -0.22 64 64
SLC24A2 0.015 0.006 -10000 0 -10000 0 0
GNB3/GNGT2 -0.016 0.13 -10000 0 -0.3 68 68
GNB3 0.03 0.041 -10000 0 -0.42 3 3
GNAT2/GTP 0.024 0.006 -10000 0 -10000 0 0
CNGA3 0.018 0.001 -10000 0 -10000 0 0
ARR3 0.021 0.007 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.024 0.012 -10000 0 -10000 0 0
mol:Pi -0.056 0.15 -10000 0 -0.25 138 138
Cone CNG Channel 0.043 0.026 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.015 0.006 -10000 0 -10000 0 0
RGS9 -0.14 0.22 -10000 0 -0.42 144 144
PDE6C 0.016 0.005 -10000 0 -10000 0 0
GNGT2 -0.049 0.18 -10000 0 -0.42 67 67
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.023 0.01 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.005 0.28 0.42 2 -0.62 37 39
HDAC7 0.036 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.039 0.34 -10000 0 -0.67 38 38
SMAD4 0.036 0.005 -10000 0 -10000 0 0
ID2 0.029 0.3 -10000 0 -0.67 31 31
AP1 0.045 0.025 -10000 0 -10000 0 0
ABCG2 0.015 0.32 -10000 0 -0.71 35 35
HIF1A 0.029 0.077 -10000 0 -0.18 4 4
TFF3 -0.016 0.33 -10000 0 -0.64 50 50
GATA2 0.035 0.011 -10000 0 -10000 0 0
AKT1 0.017 0.099 -10000 0 -0.23 17 17
response to hypoxia -0.004 0.082 -10000 0 -0.16 51 51
MCL1 0.02 0.28 -10000 0 -0.66 30 30
NDRG1 0.03 0.29 -10000 0 -0.68 28 28
SERPINE1 0.018 0.28 -10000 0 -0.65 31 31
FECH 0.029 0.29 -10000 0 -0.66 32 32
FURIN 0.027 0.29 -10000 0 -0.66 31 31
NCOA2 0.033 0.011 -10000 0 -10000 0 0
EP300 0.014 0.14 -10000 0 -0.31 38 38
HMOX1 0.028 0.29 -10000 0 -0.66 32 32
BHLHE40 0.031 0.3 -10000 0 -0.67 31 31
BHLHE41 0.024 0.3 -10000 0 -0.64 37 37
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.11 0.11 -10000 0 -10000 0 0
ENG 0.055 0.088 0.33 3 -10000 0 3
JUN 0.032 0.013 -10000 0 -10000 0 0
RORA 0.028 0.29 -10000 0 -0.68 30 30
ABCB1 -0.039 0.32 -10000 0 -1 30 30
TFRC 0.031 0.3 -10000 0 -0.66 32 32
CXCR4 0.015 0.32 -10000 0 -0.74 35 35
TF -0.03 0.32 -10000 0 -0.69 42 42
CITED2 0.027 0.29 -10000 0 -0.67 31 31
HIF1A/ARNT 0.06 0.37 -10000 0 -0.76 29 29
LDHA 0.042 0.12 -10000 0 -0.83 4 4
ETS1 0.026 0.29 -10000 0 -0.67 31 31
PGK1 0.03 0.3 -10000 0 -0.63 36 36
NOS2 0.019 0.29 -10000 0 -0.67 31 31
ITGB2 0.003 0.33 -10000 0 -0.74 38 38
ALDOA 0.029 0.3 -10000 0 -0.68 30 30
Cbp/p300/CITED2 0.005 0.36 -10000 0 -0.75 42 42
FOS 0.034 0.01 -10000 0 -10000 0 0
HK2 0.03 0.3 -10000 0 -0.65 33 33
SP1 0.031 0.043 -10000 0 -0.13 13 13
GCK -0.08 0.45 -10000 0 -1.3 42 42
HK1 0.026 0.29 -10000 0 -0.64 34 34
NPM1 0.028 0.3 -10000 0 -0.64 34 34
EGLN1 0.022 0.28 -10000 0 -0.63 32 32
CREB1 0.042 0.009 -10000 0 -10000 0 0
PGM1 0.026 0.29 -10000 0 -0.65 34 34
SMAD3 0.036 0.005 -10000 0 -10000 0 0
EDN1 0.022 0.21 -10000 0 -0.65 15 15
IGFBP1 0.014 0.28 -10000 0 -0.65 32 32
VEGFA 0.023 0.27 -10000 0 -0.6 31 31
HIF1A/JAB1 0.048 0.058 -10000 0 -0.13 2 2
CP -0.047 0.35 -10000 0 -0.71 49 49
CXCL12 0.019 0.3 -10000 0 -0.68 35 35
COPS5 0.033 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.052 0.01 -10000 0 -10000 0 0
BNIP3 0.024 0.29 -10000 0 -0.67 31 31
EGLN3 0.027 0.3 -10000 0 -0.65 34 34
CA9 -0.005 0.28 -10000 0 -0.67 31 31
TERT 0.022 0.29 -10000 0 -0.66 31 31
ENO1 0.025 0.29 -10000 0 -0.66 32 32
PFKL 0.027 0.29 -10000 0 -0.67 31 31
NCOA1 0.035 0.006 -10000 0 -10000 0 0
ADM -0.005 0.28 -10000 0 -0.66 32 32
ARNT 0.032 0.068 -10000 0 -10000 0 0
HNF4A 0.009 0.045 -10000 0 -0.13 22 22
ADFP 0.005 0.28 0.42 2 -0.62 37 39
SLC2A1 0.03 0.28 -10000 0 -0.58 38 38
LEP -0.003 0.28 -10000 0 -0.63 34 34
HIF1A/ARNT/Cbp/p300 0.03 0.34 -10000 0 -0.69 38 38
EPO 0.051 0.2 -10000 0 -0.54 6 6
CREBBP 0.013 0.14 -10000 0 -0.3 43 43
HIF1A/ARNT/Cbp/p300/HDAC7 0.047 0.34 -10000 0 -0.69 34 34
PFKFB3 0.022 0.29 -10000 0 -0.66 32 32
NT5E 0.005 0.28 -10000 0 -0.64 35 35
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.15 0.27 -10000 0 -0.79 26 26
PCK1 -0.071 0.14 -10000 0 -0.57 3 3
HNF4A -0.15 0.27 0.56 1 -0.81 25 26
KCNJ11 -0.19 0.34 -10000 0 -0.89 42 42
AKT1 -0.096 0.17 -10000 0 -0.4 34 34
response to starvation 0.001 0.005 -10000 0 -10000 0 0
DLK1 -0.19 0.32 -10000 0 -0.73 65 65
NKX2-1 -0.077 0.15 0.31 4 -0.34 43 47
ACADM -0.16 0.27 -10000 0 -0.71 36 36
TAT -0.08 0.15 -10000 0 -0.59 6 6
CEBPB 0.031 0.016 -10000 0 -10000 0 0
CEBPA -0.005 0.13 -10000 0 -0.42 31 31
TTR -0.081 0.28 -10000 0 -0.93 25 25
PKLR -0.42 0.47 -10000 0 -0.84 189 189
APOA1 -0.18 0.32 -10000 0 -0.89 33 33
CPT1C -0.17 0.3 -10000 0 -0.88 30 30
ALAS1 -0.066 0.16 -10000 0 -0.6 3 3
TFRC -0.097 0.2 -10000 0 -0.67 8 8
FOXF1 0.007 0.1 -10000 0 -0.42 21 21
NF1 0.04 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.006 -10000 0 -10000 0 0
CPT1A -0.15 0.28 -10000 0 -0.61 64 64
HMGCS1 -0.15 0.27 -10000 0 -0.7 37 37
NR3C1 0.033 0.009 -10000 0 -10000 0 0
CPT1B -0.15 0.28 -10000 0 -0.69 43 43
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.005 -10000 0 -10000 0 0
GCK -0.19 0.36 -10000 0 -0.91 54 54
CREB1 0.031 0.018 -10000 0 -10000 0 0
IGFBP1 -0.061 0.14 -10000 0 -0.51 2 2
PDX1 -0.073 0.16 -10000 0 -0.75 2 2
UCP2 -0.2 0.35 -10000 0 -0.83 62 62
ALDOB -0.17 0.29 -10000 0 -0.76 36 36
AFP 0.002 0.053 -10000 0 -10000 0 0
BDH1 -0.16 0.28 -10000 0 -0.82 28 28
HADH -0.17 0.3 -10000 0 -0.68 56 56
F2 -0.18 0.32 -10000 0 -0.88 34 34
HNF1A 0.034 0.006 -10000 0 -10000 0 0
G6PC 0.001 0.085 -10000 0 -10000 0 0
SLC2A2 -0.095 0.19 -10000 0 -0.7 5 5
INS -0.022 0.005 -10000 0 -10000 0 0
FOXA1 0.032 0.021 -10000 0 -10000 0 0
FOXA3 0.016 0.094 -10000 0 -0.41 16 16
FOXA2 -0.19 0.34 -10000 0 -0.72 76 76
ABCC8 -0.18 0.29 -10000 0 -0.74 40 40
ALB 0.005 0.053 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.031 0.047 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.031 0.046 -10000 0 -0.26 2 2
LAMA1 0.006 0.013 -10000 0 -10000 0 0
PRNP 0.032 0.025 -10000 0 -0.42 1 1
GPC1/SLIT2 0.021 0.046 -10000 0 -0.29 4 4
SMAD2 0.01 0.019 0.19 1 -10000 0 1
GPC1/PrPc/Cu2+ 0.025 0.031 -10000 0 -0.25 1 1
GPC1/Laminin alpha1 -0.007 0.022 -10000 0 -10000 0 0
TDGF1 -0.053 0.17 -10000 0 -0.42 63 63
CRIPTO/GPC1 -0.033 0.12 -10000 0 -0.3 63 63
APP/GPC1 0.025 0.043 -10000 0 -0.3 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.036 0.096 -10000 0 -0.25 60 60
FLT1 0.034 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.038 0.04 -10000 0 -10000 0 0
SERPINC1 0.027 0.013 -10000 0 -10000 0 0
FYN -0.035 0.094 -10000 0 -0.25 58 58
FGR -0.059 0.12 -10000 0 -0.26 89 89
positive regulation of MAPKKK cascade -0.22 0.24 -10000 0 -0.44 154 154
SLIT2 0.026 0.048 -10000 0 -0.42 4 4
GPC1/NRG 0.023 0.042 -10000 0 -0.3 3 3
NRG1 0.026 0.042 -10000 0 -0.42 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.034 0.041 -10000 0 -10000 0 0
LYN -0.044 0.11 -10000 0 -0.26 70 70
mol:Spermine 0.007 0.005 -10000 0 -10000 0 0
cell growth 0.031 0.046 -10000 0 -0.26 2 2
BMP signaling pathway -0.022 0.017 -10000 0 -10000 0 0
SRC -0.035 0.096 -10000 0 -0.25 60 60
TGFBR1 0.033 0.009 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.005 0.097 -10000 0 -0.42 18 18
GPC1 0.022 0.017 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.033 0.009 -10000 0 -10000 0 0
VEGFA 0.03 0.013 -10000 0 -10000 0 0
BLK -0.18 0.16 -10000 0 -0.29 227 227
HCK -0.053 0.12 -10000 0 -0.26 81 81
FGF2 0.03 0.035 -10000 0 -0.42 2 2
FGFR1 0.031 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer 0.034 0.007 -10000 0 -10000 0 0
TGFBR2 0.035 0.005 -10000 0 -10000 0 0
cell death 0.025 0.043 -10000 0 -0.3 3 3
ATIII/GPC1 0.023 0.031 -10000 0 -10000 0 0
PLA2G2A/GPC1 0.004 0.075 -10000 0 -0.29 18 18
LCK -0.13 0.16 -10000 0 -0.28 168 168
neuron differentiation 0.023 0.042 -10000 0 -0.3 3 3
PrPc/Cu2+ 0.024 0.018 -10000 0 -0.29 1 1
APP 0.031 0.041 -10000 0 -0.42 3 3
TGFBR2 (dimer) 0.035 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0.049 0.022 -10000 0 -0.3 1 1
FBXW11 0.033 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.038 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.049 0.16 0.21 1 -0.35 57 58
NFKBIA -0.068 0.17 -10000 0 -0.29 111 111
MAPK14 0.032 0.011 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.036 0.014 -10000 0 -10000 0 0
ARRB2 0.017 0.008 -10000 0 -10000 0 0
REL 0.035 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.036 0.024 -10000 0 -0.25 2 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.036 0.013 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.027 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.018 0.005 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.066 0.14 -10000 0 -0.26 111 111
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.047 0.16 0.2 1 -0.35 58 59
SRC 0.033 0.01 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.14 -10000 0 -0.26 111 111
IKBKB 0.034 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -10000 0 -10000 0 0
SYK -0.012 0.13 -10000 0 -0.42 36 36
I kappa B alpha/PIK3R1 -0.056 0.16 0.21 1 -0.37 59 60
cell death -0.045 0.15 0.2 1 -0.33 58 59
NF kappa B1 p105/c-Rel 0.038 0.011 -10000 0 -10000 0 0
LCK -0.14 0.22 -10000 0 -0.42 137 137
BCL3 0.033 0.034 -10000 0 -0.42 2 2
TRAIL signaling pathway

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
TNFSF10 -0.009 0.13 -10000 0 -0.42 35 35
positive regulation of NF-kappaB transcription factor activity 0.011 0.1 -10000 0 -0.3 35 35
MAP2K4 0.004 0.1 -10000 0 -0.34 21 21
IKBKB 0.034 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.058 -10000 0 -0.42 6 6
TNFRSF10A -0.016 0.14 -10000 0 -0.42 40 40
SMPD1 -0.002 0.066 -10000 0 -0.19 38 38
IKBKG 0.035 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.03 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR2 0.011 0.11 -10000 0 -0.31 38 38
TRAIL/TRAILR3 -0.001 0.13 -10000 0 -0.31 50 50
TRAIL/TRAILR1 -0.016 0.15 -10000 0 -0.35 59 59
TRAIL/TRAILR4 0.011 0.1 -10000 0 -0.3 35 35
TRAIL/TRAILR1/DAP3/GTP 0.01 0.12 -10000 0 -0.27 50 50
IKK complex 0.014 0.088 -10000 0 -0.33 10 10
RIPK1 0.031 0.012 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.008 -10000 0 -10000 0 0
MAPK3 -0.011 0.093 -10000 0 -0.3 35 35
MAP3K1 -0.007 0.12 -10000 0 -0.3 40 40
TRAILR4 (trimer) 0.03 0.026 -10000 0 -0.42 1 1
TRADD 0.034 0.007 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.016 0.14 -10000 0 -0.42 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.015 0.12 -10000 0 -0.29 52 52
CFLAR 0.035 0.003 -10000 0 -10000 0 0
MAPK1 -0.01 0.089 -10000 0 -0.3 32 32
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.13 -10000 0 -0.25 52 52
mol:ceramide -0.002 0.066 -10000 0 -0.19 38 38
FADD 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.002 0.1 -10000 0 -0.33 21 21
TRAF2 0.033 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.008 0.1 -10000 0 -0.42 20 20
CHUK 0.032 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.007 0.14 -10000 0 -0.3 56 56
DAP3 0.032 0.011 -10000 0 -10000 0 0
CASP10 -0.03 0.14 0.21 1 -0.36 40 41
JNK cascade 0.011 0.1 -10000 0 -0.3 35 35
TRAIL (trimer) -0.009 0.13 -10000 0 -0.42 35 35
TNFRSF10C 0.008 0.1 -10000 0 -0.42 20 20
TRAIL/TRAILR1/DAP3/GTP/FADD 0.024 0.12 -10000 0 -0.26 47 47
TRAIL/TRAILR2/FADD 0.032 0.099 -10000 0 -0.26 35 35
cell death -0.002 0.066 -10000 0 -0.19 38 38
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.007 0.083 -10000 0 -0.24 32 32
TRAILR2 (trimer) 0.026 0.058 -10000 0 -0.42 6 6
CASP8 0.013 0.085 -10000 0 -0.73 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.053 0.096 -10000 0 -0.22 32 32
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.012 0.1 0.33 7 -1.2 2 9
VDR 0.032 0.034 -10000 0 -0.42 2 2
FAM120B 0.031 0.012 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.3 62 62
RXRs/LXRs/DNA/Oxysterols -0.069 0.2 -10000 0 -0.42 76 76
MED1 0.034 0.006 -10000 0 -10000 0 0
mol:9cRA -0.005 0.024 -10000 0 -0.11 5 5
RARs/THRs/DNA/Src-1 0.028 0.051 -10000 0 -0.21 14 14
RXRs/NUR77 0.003 0.13 -10000 0 -0.24 62 62
RXRs/PPAR -0.02 0.1 -10000 0 -0.22 67 67
NCOR2 0.034 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.024 -10000 0 -0.29 2 2
RARs/VDR/DNA/Vit D3 0.067 0.061 -10000 0 -0.21 15 15
RARA 0.034 0.006 -10000 0 -10000 0 0
NCOA1 0.035 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.032 0.034 -10000 0 -0.42 2 2
RARs/RARs/DNA/9cRA 0.046 0.056 -10000 0 -0.22 13 13
RARG 0.035 0.005 -10000 0 -10000 0 0
RPS6KB1 0.03 0.086 0.54 8 -0.42 2 10
RARs/THRs/DNA/SMRT 0.029 0.051 -10000 0 -0.21 14 14
THRA 0.034 0.006 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.024 -10000 0 -0.29 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.011 0.13 0.31 1 -0.2 98 99
NR1H4 0.017 0.003 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.005 0.15 -10000 0 -0.22 97 97
NR1H2 0.022 0.037 -10000 0 -10000 0 0
NR1H3 0.02 0.051 -10000 0 -0.21 7 7
RXRs/VDR/DNA/Vit D3 0.001 0.12 -10000 0 -0.22 63 63
NR4A1 0.033 0.024 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.029 0.097 -10000 0 -0.2 72 72
RXRG -0.065 0.18 -10000 0 -0.42 72 72
RXR alpha/CCPG 0.036 0.034 -10000 0 -10000 0 0
RXRA 0.022 0.036 -10000 0 -10000 0 0
RXRB 0.019 0.037 -10000 0 -10000 0 0
THRB 0.027 0.036 -10000 0 -0.42 2 2
PPARG 0.03 0.047 -10000 0 -0.42 4 4
PPARD 0.031 0.011 -10000 0 -10000 0 0
TNF -0.18 0.41 -10000 0 -1 70 70
mol:Oxysterols -0.004 0.021 -10000 0 -0.094 3 3
cholesterol transport -0.068 0.2 -10000 0 -0.41 76 76
PPARA 0.032 0.01 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.084 -10000 0 -0.42 13 13
RXRs/NUR77/BCL2 -0.023 0.098 -10000 0 -0.22 64 64
SREBF1 -0.061 0.18 -10000 0 -0.49 28 28
RXRs/RXRs/DNA/9cRA -0.011 0.13 0.31 1 -0.2 98 99
ABCA1 -0.062 0.18 -10000 0 -0.48 29 29
RARs/THRs 0.079 0.069 -10000 0 -0.23 14 14
RXRs/FXR -0.003 0.12 -10000 0 -0.24 62 62
BCL2 0.035 0.005 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.035 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.006 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP -0.009 0.1 -10000 0 -0.25 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.017 0.003 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
CNG Channel -0.023 0.14 -10000 0 -0.26 84 84
mol:Na + 0.03 0.052 -10000 0 -0.21 10 10
mol:ADP 0.017 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.056 0.15 -10000 0 -0.25 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.042 0.056 -10000 0 -0.21 10 10
CNGB1 0.026 0.01 -10000 0 -10000 0 0
RDH5 0.029 0.047 -10000 0 -0.42 4 4
SAG 0.017 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.11 0.33 34 -0.21 1 35
Na + (4 Units) 0.029 0.047 -10000 0 -0.2 10 10
RGS9 -0.14 0.22 -10000 0 -0.42 144 144
GNB1/GNGT1 0.029 0.025 -10000 0 -10000 0 0
GNAT1/GDP -0.044 0.14 -10000 0 -0.22 138 138
GUCY2D 0.029 0.012 -10000 0 -10000 0 0
GNGT1 0.018 0.013 -10000 0 -10000 0 0
GUCY2F 0.018 0 -10000 0 -10000 0 0
GNB5 0.033 0.024 -10000 0 -0.42 1 1
mol:GMP (4 units) -0.041 0.13 -10000 0 -0.28 81 81
mol:11-cis-retinal 0.029 0.047 -10000 0 -0.42 4 4
mol:cGMP 0.032 0.045 -10000 0 -0.22 5 5
GNB1 0.034 0.007 -10000 0 -10000 0 0
Rhodopsin 0.033 0.037 -10000 0 -0.3 4 4
SLC24A1 0.035 0.005 -10000 0 -10000 0 0
CNGA1 0.026 0.053 -10000 0 -0.42 5 5
Metarhodopsin II 0.021 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.047 0.047 -10000 0 -0.23 5 5
RGS9BP 0.035 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.008 0.01 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.033 0.042 -10000 0 -0.23 5 5
PDE6A/B -0.008 0.12 -10000 0 -0.29 57 57
mol:Pi -0.056 0.15 -10000 0 -0.25 138 138
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.032 0.028 -10000 0 -10000 0 0
PDE6B -0.037 0.16 -10000 0 -0.42 57 57
PDE6A 0.031 0.011 -10000 0 -10000 0 0
PDE6G -0.033 0.16 -10000 0 -0.42 54 54
RHO 0.017 0.003 -10000 0 -10000 0 0
PDE6 -0.091 0.2 -10000 0 -0.29 168 168
GUCA1A 0.023 0.015 -10000 0 -10000 0 0
GC2/GCAP Family 0.04 0.048 -10000 0 -0.24 5 5
GUCA1C 0.017 0.003 -10000 0 -10000 0 0
GUCA1B 0.026 0.053 -10000 0 -0.42 5 5
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.04 -10000 0 -0.3 6 6
MAP4K4 -0.076 0.17 -10000 0 -0.41 63 63
BAG4 0.034 0.008 -10000 0 -10000 0 0
PKC zeta/ceramide -0.002 0.072 0.15 2 -0.19 41 43
NFKBIA 0.035 0.004 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BAX 0.004 0.043 -10000 0 -0.34 3 3
RIPK1 0.031 0.012 -10000 0 -10000 0 0
AKT1 -0.003 0.012 -10000 0 -10000 0 0
BAD -0.02 0.068 0.19 7 -0.18 42 49
SMPD1 -0.016 0.11 0.17 25 -0.21 67 92
RB1 -0.02 0.066 0.18 5 -0.18 41 46
FADD/Caspase 8 -0.065 0.18 0.25 4 -0.41 62 66
MAP2K4 -0.02 0.061 0.17 3 -0.18 37 40
NSMAF 0.032 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.02 0.062 0.17 5 -0.18 38 43
EGF 0.001 0.11 -10000 0 -0.42 25 25
mol:ceramide -0.022 0.067 0.13 6 -0.19 42 48
MADD 0.035 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.033 -10000 0 -0.3 4 4
ASAH1 0.033 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.02 0.066 0.18 5 -0.18 41 46
cell proliferation 0.015 0.068 -10000 0 -0.21 3 3
BID -0.049 0.18 -10000 0 -0.52 28 28
MAP3K1 -0.02 0.063 0.16 4 -0.18 39 43
EIF2A -0.021 0.059 0.17 4 -0.19 8 12
TRADD 0.034 0.007 -10000 0 -10000 0 0
CRADD 0.034 0.006 -10000 0 -10000 0 0
MAPK3 -0.012 0.06 0.17 4 -0.17 26 30
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.06 0.17 4 -0.18 9 13
Cathepsin D/ceramide -0.001 0.071 0.15 2 -0.18 42 44
FADD -0.072 0.17 0.22 2 -0.41 61 63
KSR1 -0.02 0.065 0.17 5 -0.18 40 45
MAPK8 -0.023 0.08 -10000 0 -0.25 16 16
PRKRA -0.022 0.062 0.14 2 -0.18 40 42
PDGFA 0.024 0.058 -10000 0 -0.42 6 6
TRAF2 0.033 0.009 -10000 0 -10000 0 0
IGF1 0.03 0.041 -10000 0 -0.42 3 3
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.066 0.13 6 -0.19 42 48
CTSD 0.034 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.013 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.017 0.073 -10000 0 -0.22 3 3
PRKCD 0.034 0.006 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.033 -10000 0 -0.3 4 4
RelA/NF kappa B1 0.049 0.013 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.016 0.09 -10000 0 -0.42 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.074 0.18 -10000 0 -0.31 115 115
TNFR1A/BAG4/TNF-alpha 0.002 0.12 -10000 0 -0.25 66 66
mol:Sphingosine-1-phosphate 0.012 0.04 -10000 0 -0.3 6 6
MAP2K1 -0.018 0.062 0.17 7 -0.18 31 38
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
CYCS 0.001 0.035 0.18 1 -0.16 5 6
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.022 0.058 -10000 0 -0.18 38 38
TNF-alpha/TNFR1A/FAN 0.003 0.12 -10000 0 -0.25 63 63
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.027 0.13 -10000 0 -0.43 21 21
MAP2K2 -0.019 0.061 0.17 6 -0.17 35 41
SMPD3 -0.034 0.14 0.16 13 -0.29 59 72
TNF -0.054 0.18 -10000 0 -0.42 69 69
PKC zeta/PAR4 0.033 0.074 -10000 0 -0.3 17 17
mol:PHOSPHOCHOLINE -0.005 0.071 0.18 26 -0.14 34 60
NF kappa B1/RelA/I kappa B alpha 0.079 0.072 -10000 0 -0.21 17 17
AIFM1 -0.007 0.048 0.18 2 -0.16 6 8
BCL2 0.035 0.005 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer 0.014 0.099 -10000 0 -0.23 47 47
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.1 0.34 3 -0.34 7 10
alphaV/beta3 Integrin/Osteopontin/Src 0.022 0.1 -10000 0 -0.29 36 36
AP1 0.035 0.1 -10000 0 -0.34 8 8
ILK -0.001 0.097 -10000 0 -0.24 47 47
bone resorption -0.008 0.12 -10000 0 -0.35 14 14
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
PYK2/p130Cas 0.018 0.14 -10000 0 -0.23 72 72
ITGAV 0.038 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.049 0.021 -10000 0 -0.3 1 1
alphaV/beta3 Integrin/Osteopontin 0.03 0.12 -10000 0 -0.27 48 48
MAP3K1 -0.003 0.098 0.2 4 -0.24 48 52
JUN 0.032 0.011 -10000 0 -10000 0 0
MAPK3 -0.009 0.091 0.2 2 -0.23 46 48
MAPK1 -0.01 0.087 0.2 2 -0.32 10 12
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.012 0.088 0.2 4 -0.23 42 46
ITGB3 0.012 0.098 -10000 0 -0.42 18 18
NFKBIA -0.01 0.087 0.2 2 -0.35 9 11
FOS 0.034 0.008 -10000 0 -10000 0 0
CD44 0.033 0.024 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
PLAU 0.002 0.11 -10000 0 -1.1 1 1
NF kappa B1 p50/RelA 0.045 0.1 -10000 0 -0.33 6 6
BCAR1 0.034 0.007 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.034 0.077 -10000 0 -0.29 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.027 0.12 0.2 3 -0.25 76 79
VAV3 -0.035 0.11 0.19 3 -0.24 72 75
MAP3K14 -0.001 0.098 0.2 2 -0.24 47 49
ROCK2 0.035 0.004 -10000 0 -10000 0 0
SPP1 -0.007 0.13 -10000 0 -0.41 36 36
RAC1 0.031 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.017 0.1 0.19 1 -0.22 63 64
MMP2 0.002 0.085 0.32 2 -0.32 9 11
Aurora C signaling

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
INCENP 0.034 0.006 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.003 0.12 -9999 0 -0.22 74 74
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.001 0.039 -9999 0 -0.29 2 2
AURKB 0.032 0.025 -9999 0 -0.42 1 1
AURKC -0.056 0.18 -9999 0 -0.42 73 73
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.04 0.018 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.031 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.058 -10000 0 -0.42 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.033 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.034 0.007 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
MAP3K12 0.035 0.005 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
p38 alpha/TAB1 -0.12 0.17 -10000 0 -0.35 92 92
PRKG1 0.018 0.018 -10000 0 -10000 0 0
DUSP8 0.028 0.014 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.095 0.18 0.2 2 -0.39 67 69
apoptosis -0.11 0.16 -10000 0 -0.33 92 92
RAL/GTP 0.042 0.016 -10000 0 -10000 0 0
LYN 0.016 0.084 -10000 0 -0.42 13 13
DUSP1 0.033 0.01 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.072 0.037 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.031 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.041 0.016 -10000 0 -10000 0 0
MAPK11 -0.13 0.21 0.29 3 -0.42 86 89
BLK -0.23 0.22 -10000 0 -0.42 215 215
HCK -0.002 0.12 -10000 0 -0.42 28 28
MAP2K3 0.033 0.009 -10000 0 -10000 0 0
DUSP16 0.034 0.006 -10000 0 -10000 0 0
DUSP10 0.027 0.048 -10000 0 -0.42 4 4
TRAF6/MEKK3 0.043 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.1 0.2 0.25 3 -0.43 72 75
positive regulation of innate immune response -0.14 0.24 0.32 3 -0.46 88 91
LCK -0.14 0.22 -10000 0 -0.42 137 137
p38alpha-beta/MKP7 -0.12 0.22 0.31 1 -0.48 72 73
p38alpha-beta/MKP5 -0.12 0.22 0.33 2 -0.48 71 73
PGK/cGMP 0.01 0.018 -10000 0 -10000 0 0
PAK2 0.035 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.23 0.32 3 -0.45 85 88
CDC42 0.035 0.005 -10000 0 -10000 0 0
RALB 0.035 0.003 -10000 0 -10000 0 0
RALA 0.031 0.011 -10000 0 -10000 0 0
PAK3 0.028 0.012 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.01 0.075 -10000 0 -0.25 26 26
EFNA5 0.025 0.062 -10000 0 -0.42 7 7
FYN 0 0.07 0.19 11 -0.22 26 37
neuron projection morphogenesis 0.01 0.075 -10000 0 -0.25 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.011 0.076 -10000 0 -0.25 26 26
EPHA5 0.002 0.099 -10000 0 -0.42 19 19
Arf6 signaling events

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
CENTA1/KIF3B 0.031 0.052 -10000 0 -0.25 11 11
ARNO/beta Arrestin1-2 0.043 0.084 -10000 0 -0.81 3 3
EGFR 0.027 0.035 -10000 0 -0.42 2 2
EPHA2 0.03 0.047 -10000 0 -0.42 4 4
USP6 0.033 0.009 -10000 0 -10000 0 0
IQSEC1 0.035 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.015 0.089 -10000 0 -0.3 26 26
ARRB2 0.012 0.003 -10000 0 -10000 0 0
mol:GTP -0.019 0.066 0.17 2 -0.16 36 38
ARRB1 0.033 0.009 -10000 0 -10000 0 0
FBXO8 0.035 0.006 -10000 0 -10000 0 0
TSHR -0.003 0.12 -10000 0 -0.42 29 29
EGF 0.001 0.11 -10000 0 -0.42 25 25
somatostatin receptor activity 0 0 0.001 19 -0.001 49 68
ARAP2 0.026 0.062 -10000 0 -0.42 7 7
mol:GDP 0.006 0.1 0.19 20 -0.25 31 51
mol:PI-3-4-5-P3 0 0 0.001 17 -0.001 22 39
ITGA2B 0.031 0.012 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.044 -10000 0 -0.23 3 3
ADAP1 0.018 0.077 -10000 0 -0.42 11 11
KIF13B 0.033 0.008 -10000 0 -10000 0 0
HGF/MET 0.019 0.091 -10000 0 -0.3 25 25
PXN 0.034 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.12 0.25 18 -0.25 44 62
EGFR/EGFR/EGF/EGF/ARFGEP100 0.031 0.084 -10000 0 -0.25 26 26
ADRB2 0.031 0.034 -10000 0 -0.42 2 2
receptor agonist activity 0 0 0 9 0 44 53
actin filament binding 0 0 0.001 18 0 47 65
SRC 0.033 0.01 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
GNAQ 0.033 0.009 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 24 -0.001 34 58
ARF6/GDP -0.065 0.19 0.23 4 -0.32 110 114
ARF6/GDP/GULP/ACAP1 -0.028 0.17 0.23 7 -0.3 75 82
alphaIIb/beta3 Integrin/paxillin/GIT1 0.061 0.072 -10000 0 -0.22 18 18
ACAP1 -0.1 0.21 -10000 0 -0.42 110 110
ACAP2 0.035 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.015 0.017 -10000 0 -10000 0 0
EFNA1 0.032 0.011 -10000 0 -10000 0 0
HGF 0.024 0.058 -10000 0 -0.42 6 6
CYTH3 0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.017 0.094 -10000 0 -1 3 3
NCK1 0.034 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 19 0 45 64
endosomal lumen acidification 0 0 0.001 19 0 35 54
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.014 0.095 -10000 0 -0.42 17 17
GNAQ/ARNO 0.036 0.089 -10000 0 -0.93 3 3
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 15 0 4 19
MET 0.006 0.1 -10000 0 -0.42 20 20
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GIT1 0.034 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 20 -0.001 37 57
GNA11 0.035 0.004 -10000 0 -10000 0 0
LHCGR 0.015 0.009 -10000 0 -10000 0 0
AGTR1 0.016 0.006 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.017 -10000 0 -10000 0 0
IPCEF1/ARNO 0.025 0.1 -10000 0 -0.86 3 3
alphaIIb/beta3 Integrin 0.023 0.077 -10000 0 -0.3 18 18
Paxillin-dependent events mediated by a4b1

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
CRKL 0.033 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.016 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
ITGA4 -0.013 0.14 -10000 0 -0.42 39 39
RAC1 0.031 0.012 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.16 -10000 0 -0.32 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.031 0.098 -10000 0 -0.25 39 39
alpha4/beta7 Integrin/Paxillin -0.007 0.13 -10000 0 -0.25 79 79
lamellipodium assembly 0.018 0.097 -10000 0 -0.4 15 15
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
TLN1 0.032 0.011 -10000 0 -10000 0 0
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
ARF6/GTP 0.041 0.085 -10000 0 -0.19 39 39
cell adhesion 0.039 0.088 -10000 0 -0.2 39 39
CRKL/CBL 0.044 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.025 0.087 -10000 0 -0.22 39 39
ITGB1 0.032 0.011 -10000 0 -10000 0 0
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
ARF6/GDP 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.002 0.15 -10000 0 -0.28 72 72
p130Cas/Crk/Dock1 0.059 0.027 -10000 0 -10000 0 0
VCAM1 -0.04 0.17 -10000 0 -0.42 60 60
alpha4/beta1 Integrin/Paxillin/Talin 0.041 0.09 -10000 0 -0.2 39 39
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.091 -10000 0 -0.21 39 39
BCAR1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP -0.04 0.089 0.21 39 -10000 0 39
CBL 0.032 0.011 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.041 0.09 -10000 0 -0.2 39 39
Rac1/GTP 0.016 0.11 -10000 0 -0.45 15 15
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.032 0.11 0.38 1 -0.41 6 7
CRKL -0.004 0.093 0.22 6 -0.2 19 25
mol:DAG 0.002 0.092 -10000 0 -0.35 15 15
HRAS 0.016 0.1 0.32 9 -0.32 1 10
MAPK8 0.029 0.085 0.2 42 -0.25 13 55
RAP1A -0.003 0.097 0.27 4 -0.23 8 12
GAB1 -0.004 0.098 0.25 5 -0.19 20 25
MAPK14 0.021 0.077 0.2 17 -0.25 13 30
EPO 0.016 0.029 -10000 0 -10000 0 0
PLCG1 0.002 0.094 -10000 0 -0.36 15 15
EPOR/TRPC2/IP3 Receptors 0.028 0.026 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.053 0.043 -10000 0 -0.28 3 3
GAB1/SHC/GRB2/SOS1 0.028 0.097 0.29 2 -0.22 4 6
EPO/EPOR (dimer) 0.035 0.035 -10000 0 -10000 0 0
IRS2 -0.001 0.096 0.24 6 -0.2 18 24
STAT1 0.014 0.11 -10000 0 -0.37 17 17
STAT5B 0.009 0.1 -10000 0 -0.35 17 17
cell proliferation 0.008 0.073 0.18 34 -0.23 13 47
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.13 -10000 0 -0.31 40 40
TEC -0.009 0.1 0.23 5 -0.22 24 29
SOCS3 0.03 0.041 -10000 0 -0.42 3 3
STAT1 (dimer) 0.014 0.11 -10000 0 -0.36 17 17
JAK2 0.018 0.058 -10000 0 -0.42 5 5
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.028 0.12 0.24 4 -0.18 80 84
EPO/EPOR 0.035 0.035 -10000 0 -10000 0 0
LYN 0.018 0.084 -10000 0 -0.42 13 13
TEC/VAV2 0.003 0.11 0.22 5 -0.23 23 28
elevation of cytosolic calcium ion concentration 0.028 0.026 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.048 0.071 -10000 0 -0.28 13 13
mol:IP3 0.002 0.092 -10000 0 -0.35 15 15
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.004 0.15 0.31 2 -0.32 55 57
SH2B3 0.024 0.029 -10000 0 -10000 0 0
NFKB1 0.032 0.089 0.21 41 -0.25 13 54
EPO/EPOR (dimer)/JAK2/SOCS3 0.016 0.038 -10000 0 -0.22 7 7
PTPN6 -0.01 0.097 -10000 0 -0.18 80 80
TEC/VAV2/GRB2 0.015 0.11 0.3 1 -0.24 14 15
EPOR 0.025 0.029 -10000 0 -10000 0 0
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
mol:GDP 0.027 0.098 0.29 2 -0.22 4 6
SOS1 0.035 0.003 -10000 0 -10000 0 0
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
CRKL/CBL/C3G 0.02 0.098 0.3 1 -0.26 4 5
VAV2 -0.001 0.098 0.24 6 -0.2 20 26
CBL 0.002 0.09 0.27 4 -0.22 10 14
SHC/Grb2/SOS1 0.009 0.087 -10000 0 -0.2 7 7
STAT5A 0.009 0.1 -10000 0 -0.34 18 18
GRB2 0.034 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.11 -10000 0 -0.35 14 14
LYN/PLCgamma2 0.013 0.11 -10000 0 -0.32 33 33
PTPN11 0.034 0.006 -10000 0 -10000 0 0
BTK -0.038 0.15 0.3 3 -0.33 63 66
BCL2 0.035 0.11 0.35 1 -0.38 11 12
IL6-mediated signaling events

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
BCL2L1 -0.053 0.26 0.6 2 -0.68 25 27
CRP -0.051 0.26 0.69 2 -0.65 32 34
cell cycle arrest -0.078 0.29 0.54 2 -0.7 43 45
TIMP1 -0.027 0.23 0.52 2 -0.56 24 26
IL6ST 0.018 0.07 -10000 0 -0.42 8 8
Rac1/GDP -0.012 0.15 -10000 0 -0.36 38 38
AP1 0.042 0.14 -10000 0 -0.53 12 12
GAB2 0.033 0.009 -10000 0 -10000 0 0
TNFSF11 -0.19 0.46 0.57 1 -1 82 83
HSP90B1 0.013 0.16 -10000 0 -0.86 10 10
GAB1 0.035 0.005 -10000 0 -10000 0 0
MAPK14 0.025 0.11 0.26 2 -0.54 6 8
AKT1 0.035 0.091 -10000 0 -0.45 9 9
FOXO1 0.037 0.089 -10000 0 -0.47 7 7
MAP2K6 0.015 0.099 0.23 3 -0.33 17 20
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.031 0.17 0.38 1 -0.42 40 41
MITF 0.006 0.1 0.2 1 -0.28 23 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.035 0.003 -10000 0 -10000 0 0
A2M 0.006 0.16 -10000 0 -1.1 7 7
CEBPB 0.034 0.016 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.11 -10000 0 -0.45 11 11
STAT3 -0.084 0.3 0.54 2 -0.74 42 44
STAT1 0.015 0.098 -10000 0 -0.89 4 4
CEBPD -0.056 0.26 0.57 1 -0.68 28 29
PIK3CA 0.036 0.007 -10000 0 -10000 0 0
PI3K 0.051 0.014 -10000 0 -10000 0 0
JUN 0.031 0.011 -10000 0 -10000 0 0
PIAS3/MITF 0.028 0.11 0.24 12 -0.3 16 28
MAPK11 0.024 0.1 0.26 2 -0.53 6 8
STAT3 (dimer)/FOXO1 -0.033 0.23 -10000 0 -0.55 29 29
GRB2/SOS1/GAB family 0.055 0.13 -10000 0 -0.37 15 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.003 0.12 -10000 0 -0.33 33 33
GRB2 0.034 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.053 -10000 0 -0.42 5 5
LBP -0.18 0.43 0.58 2 -0.86 90 92
PIK3R1 0.035 0.007 -10000 0 -10000 0 0
JAK1 0.032 0.018 -10000 0 -10000 0 0
MYC -0.045 0.26 0.57 1 -0.66 24 25
FGG -0.068 0.26 0.56 1 -0.66 32 33
macrophage differentiation -0.078 0.29 0.54 2 -0.7 43 45
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.05 0.1 -10000 0 -0.29 20 20
JUNB -0.061 0.25 0.55 1 -0.64 28 29
FOS 0.033 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.008 0.097 -10000 0 -0.32 20 20
STAT1/PIAS1 0.02 0.12 -10000 0 -0.31 20 20
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.093 -10000 0 -0.5 8 8
STAT3 (dimer) -0.084 0.3 0.54 2 -0.74 42 44
PRKCD -0.032 0.22 0.38 11 -0.49 43 54
IL6R 0.026 0.052 -10000 0 -0.44 4 4
SOCS3 0.05 0.15 0.39 3 -1.1 3 6
gp130 (dimer)/JAK1/JAK1/LMO4 0.049 0.069 -10000 0 -0.25 9 9
Rac1/GTP -0.02 0.16 -10000 0 -0.38 39 39
HCK -0.002 0.12 -10000 0 -0.42 28 28
MAPKKK cascade 0.035 0.13 0.34 2 -0.57 11 13
bone resorption -0.17 0.43 0.57 1 -0.91 83 84
IRF1 -0.13 0.39 0.57 1 -1 48 49
mol:GDP -0.017 0.14 -10000 0 -0.34 44 44
SOS1 0.035 0.004 -10000 0 -10000 0 0
VAV1 -0.018 0.14 -10000 0 -0.34 45 45
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.037 0.11 0.27 2 -0.52 7 9
PTPN11 0.009 0.12 -10000 0 -0.81 7 7
IL6/IL6RA 0.025 0.077 -10000 0 -0.34 13 13
gp130 (dimer)/TYK2/TYK2/LMO4 0.056 0.058 -10000 0 -0.25 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.073 -10000 0 -0.31 11 11
IL6 0.009 0.088 -10000 0 -0.43 13 13
PIAS3 0.032 0.011 -10000 0 -10000 0 0
PTPRE 0.025 0.054 -10000 0 -0.4 5 5
PIAS1 0.035 0.005 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.008 0.074 -10000 0 -0.26 19 19
LMO4 0.026 0.034 -10000 0 -0.42 1 1
STAT3 (dimer)/PIAS3 -0.07 0.28 -10000 0 -0.7 39 39
MCL1 0.056 0.1 -10000 0 -0.6 3 3
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.027 0.069 -10000 0 -0.24 22 22
cell-cell adhesion 0.01 0.061 0.19 33 -10000 0 33
Ephrin B/EPHB2/RasGAP 0.056 0.096 -10000 0 -0.21 35 35
ITSN1 0.035 0.006 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.04 0.019 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.036 0.043 -10000 0 -0.25 7 7
HRAS/GDP 0.018 0.083 -10000 0 -0.23 23 23
Ephrin B/EPHB1/GRB7 0.058 0.087 -10000 0 -0.21 27 27
Endophilin/SYNJ1 0.001 0.07 0.18 10 -0.2 34 44
KRAS 0.034 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.059 0.086 -10000 0 -0.21 25 25
endothelial cell migration 0.061 0.03 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
GRB7 0.029 0.012 -10000 0 -10000 0 0
PAK1 0.001 0.073 0.19 1 -0.21 26 27
HRAS 0.034 0.006 -10000 0 -10000 0 0
RRAS 0.002 0.072 0.19 12 -0.2 34 46
DNM1 0.029 0.013 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.003 0.065 0.18 9 -0.2 28 37
lamellipodium assembly -0.01 0.061 -10000 0 -0.19 33 33
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.062 -10000 0 -0.22 9 9
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
EPHB2 0.016 0.09 -10000 0 -0.42 15 15
EPHB3 0.032 0.011 -10000 0 -10000 0 0
EPHB1 0.024 0.062 -10000 0 -0.42 7 7
EPHB4 0.032 0.01 -10000 0 -10000 0 0
mol:GDP -0.005 0.072 0.22 3 -0.24 22 25
Ephrin B/EPHB2 0.043 0.087 -10000 0 -0.21 34 34
Ephrin B/EPHB3 0.049 0.073 -10000 0 -0.21 21 21
JNK cascade 0.01 0.071 0.24 10 -0.23 20 30
Ephrin B/EPHB1 0.046 0.081 -10000 0 -0.21 28 28
RAP1/GDP 0.032 0.098 0.24 22 -0.22 24 46
EFNB2 0.033 0.009 -10000 0 -10000 0 0
EFNB3 0.007 0.1 -10000 0 -0.42 21 21
EFNB1 0.034 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.04 0.075 -10000 0 -0.24 20 20
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.033 0.1 -10000 0 -0.24 34 34
Rap1/GTP 0.009 0.072 -10000 0 -0.2 32 32
axon guidance 0.027 0.069 -10000 0 -0.24 22 22
MAPK3 0.016 0.063 0.2 4 -0.24 3 7
MAPK1 0.021 0.067 0.2 13 -0.24 3 16
Rac1/GDP 0.01 0.085 0.23 10 -0.23 22 32
actin cytoskeleton reorganization -0.011 0.064 -10000 0 -0.2 23 23
CDC42/GDP 0.021 0.098 0.23 25 -0.23 25 50
PI3K 0.067 0.033 -10000 0 -10000 0 0
EFNA5 0.025 0.062 -10000 0 -0.42 7 7
Ephrin B2/EPHB4 0.04 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.076 -10000 0 -0.22 34 34
CDC42 0.035 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.069 -10000 0 -0.2 31 31
PTK2 0.061 0.18 0.54 43 -10000 0 43
MAP4K4 0.01 0.072 0.24 10 -0.23 20 30
SRC 0.033 0.01 -10000 0 -10000 0 0
KALRN 0.032 0.034 -10000 0 -0.42 2 2
Intersectin/N-WASP 0.045 0.018 -10000 0 -10000 0 0
neuron projection morphogenesis 0.028 0.12 0.31 33 -0.27 6 39
MAP2K1 0.011 0.059 -10000 0 -0.21 8 8
WASL 0.031 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.063 0.08 -10000 0 -0.24 20 20
cell migration 0.023 0.092 0.26 6 -0.27 6 12
NRAS 0.034 0.008 -10000 0 -10000 0 0
SYNJ1 0.001 0.071 0.18 10 -0.2 34 44
PXN 0.034 0.006 -10000 0 -10000 0 0
TF -0.054 0.098 0.18 8 -0.22 76 84
HRAS/GTP 0.032 0.086 -10000 0 -0.2 38 38
Ephrin B1/EPHB1-2 0.042 0.075 -10000 0 -0.24 20 20
cell adhesion mediated by integrin 0.013 0.056 0.21 21 -0.19 7 28
RAC1 0.031 0.012 -10000 0 -10000 0 0
mol:GTP 0.034 0.091 -10000 0 -0.2 40 40
RAC1-CDC42/GTP -0.006 0.065 -10000 0 -0.2 30 30
RASA1 0.032 0.025 -10000 0 -0.42 1 1
RAC1-CDC42/GDP 0.022 0.088 0.23 9 -0.22 22 31
ruffle organization 0.011 0.12 0.34 22 -0.33 2 24
NCK1 0.034 0.006 -10000 0 -10000 0 0
receptor internalization -0.021 0.062 0.18 7 -0.2 27 34
Ephrin B/EPHB2/KALRN 0.056 0.098 -10000 0 -0.22 35 35
ROCK1 0.02 0.021 0.19 4 -10000 0 4
RAS family/GDP -0.016 0.062 -10000 0 -0.21 23 23
Rac1/GTP -0.001 0.068 -10000 0 -0.2 33 33
Ephrin B/EPHB1/Src/Paxillin 0.015 0.066 -10000 0 -0.21 25 25
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.053 0.075 -10000 0 -0.22 21 21
ER alpha/Gai/GDP/Gbeta gamma -0.018 0.15 -10000 0 -0.42 31 31
AKT1 -0.054 0.27 -10000 0 -0.69 52 52
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.27 -10000 0 -0.7 52 52
mol:Ca2+ -0.049 0.16 -10000 0 -0.37 60 60
IGF1R 0.034 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.037 0.04 -10000 0 -0.25 6 6
SHC1 0.032 0.011 -10000 0 -10000 0 0
apoptosis 0.05 0.26 0.66 52 -10000 0 52
RhoA/GTP 0.025 0.032 -10000 0 -0.19 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.026 0.14 0.25 4 -0.36 26 30
regulation of stress fiber formation -0.007 0.057 -10000 0 -0.22 7 7
E2/ERA-ERB (dimer) 0.027 0.063 -10000 0 -0.25 17 17
KRAS 0.034 0.006 -10000 0 -10000 0 0
G13/GTP 0.034 0.037 -10000 0 -0.22 6 6
pseudopodium formation 0.007 0.057 0.22 7 -10000 0 7
E2/ER alpha (dimer)/PELP1 0.036 0.038 -10000 0 -0.25 5 5
GRB2 0.034 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.058 -10000 0 -0.42 6 6
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
HRAS 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.18 0.27 1 -0.42 48 49
E2/ER beta (dimer) 0.016 0.055 -10000 0 -0.29 11 11
mol:GDP 0 0.081 -10000 0 -0.29 17 17
mol:NADP -0.012 0.18 0.27 1 -0.42 48 49
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.054 0.16 -10000 0 -0.38 60 60
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
PLCB1 -0.044 0.15 -10000 0 -0.38 58 58
PLCB2 -0.046 0.16 -10000 0 -0.38 61 61
IGF1 0.03 0.041 -10000 0 -0.42 3 3
mol:L-citrulline -0.012 0.18 0.27 1 -0.42 48 49
RHOA 0.035 0.005 -10000 0 -10000 0 0
Gai/GDP -0.006 0.15 -10000 0 -0.61 19 19
JNK cascade 0.016 0.055 -10000 0 -0.29 11 11
BCAR1 0.034 0.007 -10000 0 -10000 0 0
ESR2 0.021 0.077 -10000 0 -0.42 11 11
GNAQ 0.033 0.009 -10000 0 -10000 0 0
ESR1 0.023 0.058 -10000 0 -0.42 6 6
Gq family/GDP/Gbeta gamma -0.009 0.14 -10000 0 -0.51 18 18
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.04 0.082 -10000 0 -0.51 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.025 0.13 0.25 3 -0.36 22 25
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
E2/ER alpha (dimer) 0.018 0.041 -10000 0 -0.29 6 6
STRN 0.035 0.004 -10000 0 -10000 0 0
GNAL 0.024 0.053 -10000 0 -0.42 5 5
PELP1 0.033 0.009 -10000 0 -10000 0 0
MAPK11 0.012 0.042 -10000 0 -0.25 9 9
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
HBEGF -0.007 0.18 0.34 22 -0.42 38 60
cAMP biosynthetic process 0.017 0.058 -10000 0 -0.21 20 20
SRC -0.012 0.14 0.24 4 -0.42 27 31
PI3K 0.049 0.014 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.094 -10000 0 -0.26 20 20
SOS1 0.035 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.006 0.091 -10000 0 -0.31 19 19
Gs family/GTP 0.024 0.062 -10000 0 -0.21 20 20
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.062 0.02 -10000 0 -10000 0 0
vasodilation -0.01 0.17 0.26 1 -0.4 48 49
mol:DAG -0.054 0.16 -10000 0 -0.38 60 60
Gs family/GDP/Gbeta gamma 0.001 0.085 -10000 0 -0.27 17 17
MSN 0.006 0.059 0.22 7 -10000 0 7
Gq family/GTP -0.036 0.16 -10000 0 -0.38 60 60
mol:PI-3-4-5-P3 -0.048 0.26 -10000 0 -0.68 52 52
NRAS 0.034 0.008 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.01 0.17 0.4 48 -0.26 1 49
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.09 -10000 0 -0.27 17 17
NOS3 -0.015 0.19 0.27 1 -0.44 48 49
GNA11 0.035 0.004 -10000 0 -10000 0 0
MAPKKK cascade 0.001 0.19 0.29 6 -0.45 46 52
E2/ER alpha (dimer)/PELP1/Src 0.023 0.14 0.28 8 -0.38 26 34
ruffle organization 0.007 0.057 0.22 7 -10000 0 7
ROCK2 0.028 0.057 0.23 7 -10000 0 7
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA13 0.034 0.007 -10000 0 -10000 0 0
MMP9 -0.027 0.17 0.37 10 -0.44 35 45
MMP2 0.001 0.14 0.31 8 -0.39 27 35
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.003 0.15 -10000 0 -0.38 43 43
PTP1B/AKT1 0.03 0.078 0.29 1 -0.26 12 13
FYN 0.031 0.012 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.014 0.077 0.25 2 -0.28 12 14
EGFR 0.026 0.037 -10000 0 -0.42 2 2
EGF/EGFR 0.013 0.094 -10000 0 -0.24 29 29
CSF1 0.029 0.047 -10000 0 -0.42 4 4
AKT1 0.035 0.006 -10000 0 -10000 0 0
INSR 0.036 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.003 0.1 0.29 1 -0.26 31 32
Insulin Receptor/Insulin 0.047 0.078 0.28 1 -0.3 7 8
HCK -0.002 0.12 -10000 0 -0.42 28 28
CRK 0.033 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.075 0.25 3 -0.28 10 13
EGF 0.002 0.12 -10000 0 -0.42 25 25
YES1 0.034 0.007 -10000 0 -10000 0 0
CAV1 0.028 0.092 0.26 11 -0.29 10 21
TXN 0.033 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.038 0.082 -10000 0 -0.27 10 10
cell migration -0.014 0.077 0.28 12 -0.25 2 14
STAT3 0.035 0.006 -10000 0 -10000 0 0
PRLR 0.024 0.016 -10000 0 -10000 0 0
ITGA2B 0.03 0.013 -10000 0 -10000 0 0
CSF1R 0.015 0.09 -10000 0 -0.42 15 15
Prolactin Receptor/Prolactin 0.02 0.028 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
PTP1B/p130 Cas 0.03 0.077 0.24 2 -0.27 11 13
Crk/p130 Cas 0.043 0.081 0.3 1 -0.26 10 11
DOK1 0.017 0.083 0.28 1 -0.3 12 13
JAK2 -0.018 0.15 0.3 1 -0.39 44 45
Jak2/Leptin Receptor/Leptin 0.022 0.12 -10000 0 -0.32 19 19
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
PTPN1 0.014 0.077 0.26 2 -0.28 12 14
LYN 0.016 0.084 -10000 0 -0.42 13 13
CDH2 -0.017 0.14 -10000 0 -0.42 40 40
SRC 0.039 0.049 -10000 0 -0.67 1 1
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
CAT1/PTP1B -0.12 0.24 0.34 2 -0.46 89 91
CAPN1 0.034 0.007 -10000 0 -10000 0 0
CSK 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.063 0.075 0.26 1 -0.31 5 6
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.11 -10000 0 -0.31 18 18
negative regulation of transcription -0.018 0.15 0.3 1 -0.39 44 45
FCGR2A 0.027 0.048 -10000 0 -0.42 4 4
FER 0.034 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.022 0.077 -10000 0 -0.3 18 18
BLK -0.23 0.22 -10000 0 -0.42 215 215
Insulin Receptor/Insulin/Shc 0.052 0.022 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
LEPR 0.034 0.005 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.24 0.3 0.36 1 -0.56 137 138
PRL 0.013 0.02 -10000 0 -10000 0 0
SOCS3 0.005 0.18 -10000 0 -1.2 8 8
SPRY2 0.034 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.051 0.025 -10000 0 -10000 0 0
CSF1/CSF1R 0.033 0.099 -10000 0 -0.28 19 19
Ras protein signal transduction 0.006 0.09 0.49 11 -10000 0 11
IRS1 0.032 0.011 -10000 0 -10000 0 0
INS 0.015 0.011 -10000 0 -10000 0 0
LEP 0.021 0.018 -10000 0 -10000 0 0
STAT5B 0.007 0.11 0.25 2 -0.35 18 20
STAT5A 0.007 0.11 0.25 2 -0.35 18 20
GRB2 0.034 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.031 0.075 0.29 1 -0.26 11 12
CSN2 0.009 0.047 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
LAT -0.026 0.18 -10000 0 -0.49 46 46
YBX1 0.045 0.007 -10000 0 -10000 0 0
LCK -0.14 0.22 -10000 0 -0.42 137 137
SHC1 0.032 0.011 -10000 0 -10000 0 0
NOX4 0.024 0.037 -10000 0 -0.42 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.076 -10000 0 -0.3 18 18
PTK2 0 0.1 -10000 0 -0.35 13 13
positive regulation of JNK cascade 0.002 0.11 -10000 0 -0.3 20 20
CDC42/GDP 0.01 0.16 -10000 0 -0.39 29 29
Rac1/GDP 0.009 0.15 -10000 0 -0.39 29 29
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.14 -10000 0 -0.36 20 20
nectin-3/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
RAPGEF1 0 0.13 -10000 0 -0.38 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.14 -10000 0 -0.39 33 33
PDGFB-D/PDGFRB 0.033 0.01 -10000 0 -10000 0 0
TLN1 0.003 0.021 -10000 0 -0.14 7 7
Rap1/GTP 0.004 0.1 -10000 0 -0.3 14 14
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.031 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
PVR 0.034 0.024 -10000 0 -0.42 1 1
Necl-5(dimer) 0.034 0.024 -10000 0 -0.42 1 1
mol:GDP -0.01 0.18 -10000 0 -0.48 30 30
MLLT4 0.029 0.014 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.072 0.059 -10000 0 -0.2 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.025 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.002 0.12 -10000 0 -0.33 33 33
PVRL1 0.031 0.012 -10000 0 -10000 0 0
PVRL3 0.022 0.067 -10000 0 -0.42 8 8
PVRL2 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
CLDN1 -0.18 0.22 -10000 0 -0.42 169 169
JAM-A/CLDN1 -0.065 0.15 -10000 0 -0.24 151 151
SRC -0.011 0.15 -10000 0 -0.4 42 42
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.025 -10000 0 -10000 0 0
FARP2 -0.008 0.18 -10000 0 -0.51 21 21
RAC1 0.031 0.012 -10000 0 -10000 0 0
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.044 0.058 -10000 0 -0.25 9 9
nectin-1/I-afadin 0.039 0.025 -10000 0 -10000 0 0
nectin-2/I-afadin 0.041 0.023 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.041 0.017 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.042 0.056 -10000 0 -0.24 8 8
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.011 -10000 0 -10000 0 0
F11R 0.024 0.058 -10000 0 -0.42 6 6
positive regulation of filopodium formation 0.002 0.11 -10000 0 -0.3 20 20
alphaV/beta3 Integrin/Talin 0.027 0.068 0.24 3 -0.2 15 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.041 0.023 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.041 0.023 -10000 0 -10000 0 0
PIP5K1C 0.007 0.024 -10000 0 -0.15 8 8
VAV2 -0.019 0.21 -10000 0 -0.56 34 34
RAP1/GDP 0.017 0.14 -10000 0 -0.35 28 28
ITGAV 0.035 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.056 -10000 0 -0.25 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
Rac1/GTP -0.001 0.15 -10000 0 -0.4 33 33
PTPRM 0.012 0.028 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin 0.005 0.13 -10000 0 -0.2 91 91
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.042 0.023 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.077 -10000 0 -0.25 20 20
PTK2 -0.01 0.14 0.34 12 -0.35 20 32
IGF1R 0.034 0.006 -10000 0 -10000 0 0
PI4KB 0.032 0.011 -10000 0 -10000 0 0
MFGE8 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
CDKN1B -0.03 0.15 -10000 0 -0.41 47 47
VEGFA 0.03 0.013 -10000 0 -10000 0 0
ILK -0.032 0.15 -10000 0 -0.41 48 48
ROCK1 0.035 0.005 -10000 0 -10000 0 0
AKT1 -0.034 0.14 -10000 0 -0.39 47 47
PTK2B 0.021 0.079 0.2 36 -0.21 17 53
alphaV/beta3 Integrin/JAM-A 0.025 0.12 -10000 0 -0.23 57 57
CBL 0.032 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.034 0.07 -10000 0 -0.25 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.077 0.04 -10000 0 -0.23 3 3
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.084 -10000 0 -0.23 15 15
alphaV/beta3 Integrin/Syndecan-1 0.038 0.086 -10000 0 -0.27 23 23
PI4KA 0.033 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.045 0.086 -10000 0 -0.24 26 26
PI4 Kinase 0.044 0.02 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.015 0.12 -10000 0 -0.28 48 48
RPS6KB1 -0.021 0.072 0.34 1 -0.37 5 6
TLN1 0.032 0.011 -10000 0 -10000 0 0
MAPK3 -0.017 0.12 -10000 0 -0.42 22 22
GPR124 0.033 0.008 -10000 0 -10000 0 0
MAPK1 -0.018 0.12 -10000 0 -0.42 22 22
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.069 0.16 -10000 0 -0.26 143 143
cell adhesion 0.033 0.072 -10000 0 -0.26 18 18
ANGPTL3 0.017 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.053 0.033 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
TGFBR2 0.035 0.005 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
IGF1 0.03 0.041 -10000 0 -0.42 3 3
RAC1 0.031 0.012 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.042 0.071 -10000 0 -0.25 17 17
apoptosis 0.035 0.004 -10000 0 -10000 0 0
CD47 0.034 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.044 0.073 -10000 0 -0.25 18 18
VCL 0.032 0.01 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.024 0.074 -10000 0 -0.25 18 18
CSF1 0.029 0.047 -10000 0 -0.42 4 4
PIK3C2A -0.031 0.15 -10000 0 -0.41 48 48
PI4 Kinase/Pyk2 0.004 0.085 -10000 0 -0.2 40 40
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.056 0.068 -10000 0 -0.23 14 14
FAK1/Vinculin 0.007 0.12 0.32 13 -0.3 16 29
alphaV beta3/Integrin/ppsTEM5 0.043 0.071 -10000 0 -0.25 17 17
RHOA 0.035 0.005 -10000 0 -10000 0 0
VTN -0.02 0.14 -10000 0 -0.42 43 43
BCAR1 0.034 0.007 -10000 0 -10000 0 0
FGF2 0.03 0.035 -10000 0 -0.42 2 2
F11R 0.008 0.047 -10000 0 -0.3 8 8
alphaV/beta3 Integrin/Lactadherin 0.041 0.073 -10000 0 -0.25 18 18
alphaV/beta3 Integrin/TGFBR2 0.045 0.073 -10000 0 -0.25 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.073 0.046 -10000 0 -0.22 4 4
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Talin 0.039 0.066 -10000 0 -0.22 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.077 -10000 0 -0.42 11 11
alphaV/beta3 Integrin/Pyk2 0.046 0.075 -10000 0 -0.21 17 17
SDC1 0.026 0.062 -10000 0 -0.42 7 7
VAV3 0.017 0.041 0.19 6 -0.25 5 11
PTPN11 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
FAK1/Paxillin 0.007 0.13 0.32 13 -0.29 18 31
cell migration 0.004 0.12 0.29 15 -0.29 12 27
ITGAV 0.035 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.12 -10000 0 -0.21 52 52
SPP1 -0.01 0.14 -10000 0 -0.42 36 36
KDR 0.034 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.035 0.004 -10000 0 -10000 0 0
COL4A3 -0.14 0.22 -10000 0 -0.42 137 137
angiogenesis -0.018 0.15 0.27 1 -0.44 24 25
Rac1/GTP 0.03 0.04 -10000 0 -0.29 2 2
EDIL3 0.024 0.017 -10000 0 -10000 0 0
cell proliferation 0.044 0.072 -10000 0 -0.25 18 18
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.006 0.13 0.24 2 -0.43 21 23
PDGFB-D/PDGFRB/SLAP -0.007 0.12 -10000 0 -0.3 54 54
PDGFB-D/PDGFRB/APS/CBL 0.049 0.051 -10000 0 -0.24 7 7
AKT1 0.023 0.079 0.36 8 -10000 0 8
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.008 0.14 0.29 3 -0.46 23 26
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
FGR -0.034 0.2 0.33 1 -0.54 39 40
mol:Ca2+ -0.02 0.15 0.25 5 -0.52 21 26
MYC 0.016 0.14 0.39 11 -0.4 14 25
SHC1 0.032 0.011 -10000 0 -10000 0 0
HRAS/GDP 0.052 0.048 0.18 39 -0.21 1 40
LRP1/PDGFRB/PDGFB 0.06 0.028 -10000 0 -10000 0 0
GRB10 0.032 0.011 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GO:0007205 -0.021 0.15 0.25 5 -0.53 21 26
PTEN 0.031 0.012 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
GRB7 0.029 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.048 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.043 0.021 -10000 0 -10000 0 0
cell cycle arrest -0.007 0.12 -10000 0 -0.3 54 54
HRAS 0.034 0.006 -10000 0 -10000 0 0
HIF1A 0.018 0.074 0.32 9 -10000 0 9
GAB1 -0.036 0.15 0.29 4 -0.51 22 26
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.028 0.14 0.3 6 -0.44 22 28
PDGFB-D/PDGFRB 0.061 0.031 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.017 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.12 0.26 1 -0.39 19 20
positive regulation of MAPKKK cascade 0.048 0.017 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.021 0.15 0.25 5 -0.54 21 26
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.034 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.022 -10000 0 -10000 0 0
SHB 0.028 0.035 -10000 0 -0.42 2 2
BLK -0.3 0.27 -10000 0 -0.5 225 225
PTPN2 0.035 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.018 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
VAV2 -0.037 0.16 0.31 5 -0.52 24 29
CBL 0.032 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.048 0.017 -10000 0 -10000 0 0
LCK -0.18 0.28 -10000 0 -0.52 138 138
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
ACP1 0.035 0.005 -10000 0 -10000 0 0
HCK -0.02 0.19 0.34 1 -0.6 29 30
ABL1 -0.059 0.16 0.26 4 -0.4 43 47
PDGFB-D/PDGFRB/CBL -0.053 0.17 -10000 0 -0.57 25 25
PTPN1 0.032 0.011 -10000 0 -10000 0 0
SNX15 0.034 0.007 -10000 0 -10000 0 0
STAT3 0.035 0.006 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
cell proliferation 0.017 0.14 0.38 12 -0.36 15 27
SLA -0.036 0.16 -10000 0 -0.42 54 54
actin cytoskeleton reorganization 0.047 0.059 0.32 5 -0.21 2 7
SRC 0.02 0.059 0.3 2 -10000 0 2
PI3K 0.013 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.052 0.032 -10000 0 -10000 0 0
SH2B2 0.023 0.062 -10000 0 -0.42 7 7
PLCgamma1/SPHK1 -0.008 0.15 0.29 3 -0.48 23 26
LYN 0.001 0.14 0.3 2 -0.57 14 16
LRP1 0.034 0.007 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
STAT5B 0.035 0.006 -10000 0 -10000 0 0
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
NCK1-2/p130 Cas 0.087 0.048 -10000 0 -10000 0 0
SPHK1 0.03 0.042 -10000 0 -0.42 3 3
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.021 0.15 0.25 5 -0.54 21 26
PLCG1 -0.022 0.15 0.26 5 -0.55 21 26
NHERF/PDGFRB 0.063 0.025 -10000 0 -10000 0 0
YES1 0.016 0.095 0.32 2 -0.53 6 8
cell migration 0.063 0.024 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.079 0.052 -10000 0 -10000 0 0
SLC9A3R2 0.035 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.071 0.038 -10000 0 -10000 0 0
FYN -0.029 0.18 0.31 2 -0.48 43 45
DOK1 0.037 0.054 0.18 42 -10000 0 42
HRAS/GTP 0.026 0.004 -10000 0 -10000 0 0
PDGFB 0.033 0.009 -10000 0 -10000 0 0
RAC1 -0.013 0.16 0.33 8 -0.5 21 29
PRKCD 0.037 0.054 0.18 41 -10000 0 41
FER 0.036 0.054 0.18 40 -10000 0 40
MAPKKK cascade 0.029 0.089 0.28 21 -10000 0 21
RASA1 0.036 0.056 0.18 41 -0.24 1 42
NCK1 0.034 0.006 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.059 0.049 0.19 42 -10000 0 42
PDGFB-D/PDGFRB/SHB 0.041 0.033 -10000 0 -0.3 2 2
chemotaxis -0.057 0.15 0.24 6 -0.39 43 49
STAT1-3-5/STAT1-3-5 0.071 0.046 -10000 0 -0.21 3 3
Bovine Papilomavirus E5/PDGFRB 0.023 0.009 -10000 0 -10000 0 0
PTPRJ 0.034 0.006 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.046 0.038 -10000 0 -0.3 4 4
Necdin/E2F1 0.04 0.053 -10000 0 -0.3 8 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.068 0.06 -10000 0 -0.22 8 8
NGF (dimer)/p75(NTR)/BEX1 0.038 0.049 -10000 0 -0.25 4 4
NT-4/5 (dimer)/p75(NTR) 0.025 0.041 -10000 0 -0.3 4 4
IKBKB 0.034 0.007 -10000 0 -10000 0 0
AKT1 0.023 0.055 0.2 23 -0.21 4 27
IKBKG 0.035 0.004 -10000 0 -10000 0 0
BDNF -0.075 0.19 -10000 0 -0.42 88 88
MGDIs/NGR/p75(NTR)/LINGO1 0.033 0.062 -10000 0 -0.28 8 8
FURIN 0.034 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.026 0.14 -10000 0 -0.26 92 92
LINGO1 0.028 0.027 -10000 0 -0.42 1 1
Sortilin/TRAF6/NRIF 0.037 0.036 -10000 0 -0.2 6 6
proBDNF (dimer) -0.075 0.19 -10000 0 -0.42 88 88
NTRK1 0.018 0.077 -10000 0 -0.42 11 11
RTN4R 0.026 0.048 -10000 0 -0.42 4 4
neuron apoptosis -0.025 0.14 0.33 6 -0.41 14 20
IRAK1 0.035 0.004 -10000 0 -10000 0 0
SHC1 0.011 0.031 -10000 0 -0.25 4 4
ARHGDIA 0.034 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.026 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.088 0.044 -10000 0 -0.2 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.065 0.055 -10000 0 -0.23 8 8
MAGEH1 0.035 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.056 0.07 -10000 0 -0.23 16 16
Mammalian IAPs/DIABLO -0.013 0.14 -10000 0 -0.23 108 108
proNGF (dimer) 0.031 0.011 -10000 0 -10000 0 0
MAGED1 0.035 0.003 -10000 0 -10000 0 0
APP 0.031 0.041 -10000 0 -0.42 3 3
NT-4/5 (dimer) 0.017 0.002 -10000 0 -10000 0 0
ZNF274 0.035 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.046 0.038 0.18 10 -0.21 4 14
NGF 0.031 0.011 -10000 0 -10000 0 0
cell cycle arrest -0.001 0.082 0.31 18 -0.2 8 26
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.029 0.032 -10000 0 -0.24 3 3
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.043 -10000 0 -0.25 4 4
NCSTN 0.032 0.011 -10000 0 -10000 0 0
mol:GTP 0.047 0.047 -10000 0 -0.25 4 4
PSENEN 0.035 0.004 -10000 0 -10000 0 0
mol:ceramide 0.012 0.048 0.19 9 -0.22 9 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.037 0.043 -10000 0 -0.29 2 2
p75(NTR)/beta APP 0.034 0.053 -10000 0 -0.3 7 7
BEX1 0.027 0.014 -10000 0 -10000 0 0
mol:GDP 0.001 0.027 -10000 0 -0.25 4 4
NGF (dimer) 0.048 0.055 -10000 0 -0.22 9 9
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.053 0.061 -10000 0 -0.25 8 8
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RAC1/GTP 0.038 0.041 -10000 0 -0.21 4 4
MYD88 0.034 0.024 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.048 0.047 -10000 0 -0.25 4 4
RHOB 0.035 0.006 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.047 0.016 -10000 0 -10000 0 0
NT3 (dimer) 0.028 0.012 -10000 0 -10000 0 0
TP53 -0.036 0.11 0.19 14 -0.21 84 98
PRDM4 0.014 0.048 0.19 10 -0.23 8 18
BDNF (dimer) -0.032 0.12 -10000 0 -0.23 92 92
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
SORT1 0.029 0.047 -10000 0 -0.42 4 4
activation of caspase activity 0.061 0.056 -10000 0 -0.21 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.064 0.055 -10000 0 -0.23 8 8
RHOC 0.034 0.007 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
MAPK10 -0.014 0.11 0.32 10 -0.3 8 18
DIABLO 0.034 0.006 -10000 0 -10000 0 0
SMPD2 0.012 0.049 0.19 9 -0.22 9 18
APH1B 0.031 0.041 -10000 0 -0.42 3 3
APH1A 0.032 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.056 -10000 0 -0.25 8 8
PSEN1 0.035 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.05 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.031 0.044 -10000 0 -0.3 4 4
MAPK8 -0.012 0.11 0.33 10 -0.29 10 20
MAPK9 -0.01 0.11 0.33 10 -0.29 10 20
APAF1 0.034 0.006 -10000 0 -10000 0 0
NTF3 0.028 0.012 -10000 0 -10000 0 0
NTF4 0.017 0.002 -10000 0 -10000 0 0
NDN 0.022 0.074 -10000 0 -0.42 10 10
RAC1/GDP 0.023 0.009 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.073 0.044 -10000 0 -0.2 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.042 -10000 0 -0.23 4 4
RhoA-B-C/GTP 0.046 0.046 -10000 0 -0.25 4 4
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.14 -10000 0 -0.22 90 90
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.14 -10000 0 -0.23 91 91
PRKACB 0.035 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.033 0.15 -10000 0 -0.3 88 88
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BIRC2 0.029 0.042 -10000 0 -0.42 3 3
neuron projection morphogenesis -0.005 0.041 0.18 2 -0.22 8 10
BAD -0.015 0.11 0.32 11 -0.3 11 22
RIPK2 0.032 0.011 -10000 0 -10000 0 0
NGFR 0.024 0.048 -10000 0 -0.42 4 4
CYCS 0.015 0.057 0.24 12 -0.21 8 20
ADAM17 0.035 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.061 0.049 -10000 0 -0.23 4 4
BCL2L11 -0.016 0.11 0.32 11 -0.3 11 22
BDNF (dimer)/p75(NTR) -0.045 0.15 -10000 0 -0.3 90 90
PI3K 0.065 0.047 -10000 0 -0.22 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.063 0.056 -10000 0 -0.23 8 8
NDNL2 0.034 0.007 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.033 0.044 -10000 0 -0.3 4 4
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.065 0.055 -10000 0 -0.23 8 8
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
PLG 0.016 0.006 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.035 0.11 -10000 0 -0.22 89 89
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
NGFRAP1 0.031 0.012 -10000 0 -10000 0 0
CASP3 -0.013 0.11 0.3 12 -0.28 11 23
E2F1 0.033 0.009 -10000 0 -10000 0 0
CASP9 0.035 0.005 -10000 0 -10000 0 0
IKK complex 0.055 0.075 -10000 0 -0.25 6 6
NGF (dimer)/TRKA 0.031 0.062 -10000 0 -0.3 11 11
MMP7 0.017 0.07 -10000 0 -0.42 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.076 0.058 -10000 0 -0.21 8 8
MMP3 0.014 0.016 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.034 0.093 -10000 0 -0.19 79 79
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.035 0.004 -10000 0 -10000 0 0
SPHK1 0.03 0.041 -10000 0 -0.42 3 3
GNAI2 0.035 0.005 -10000 0 -10000 0 0
mol:S1P 0.018 0.028 -10000 0 -0.24 4 4
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
mol:Sphinganine-1-P 0.016 0.029 -10000 0 -0.3 3 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.066 0.046 -10000 0 -0.18 4 4
GNAI3 0.034 0.007 -10000 0 -10000 0 0
G12/G13 0.045 0.018 -10000 0 -10000 0 0
S1PR3 0.029 0.042 -10000 0 -0.42 3 3
S1PR2 0.035 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.01 0.028 -10000 0 -0.2 4 4
S1PR5 0.034 0.008 -10000 0 -10000 0 0
S1PR4 -0.11 0.21 -10000 0 -0.42 118 118
GNAI1 0.031 0.012 -10000 0 -10000 0 0
S1P/S1P5/G12 0.048 0.042 -10000 0 -0.19 4 4
S1P/S1P3/Gq -0.029 0.15 -10000 0 -0.29 80 80
S1P/S1P4/Gi -0.029 0.12 0.2 1 -0.22 81 82
GNAQ 0.033 0.009 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
ABCC1 0.034 0.024 -10000 0 -0.42 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 0.035 0.062 -10000 0 -0.43 4 4
IHH 0.043 0.033 -10000 0 -0.16 4 4
SHH Np/Cholesterol/GAS1 0.023 0.014 -10000 0 -10000 0 0
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.022 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.057 0.083 -10000 0 -0.37 4 4
SMO 0.027 0.07 -10000 0 -0.39 4 4
AKT1 0.032 0.08 -10000 0 -0.37 6 6
ARRB2 0.033 0.009 -10000 0 -10000 0 0
BOC 0.034 0.007 -10000 0 -10000 0 0
ADRBK1 0.034 0.007 -10000 0 -10000 0 0
heart looping 0.027 0.069 -10000 0 -0.38 4 4
STIL 0.046 0.077 0.36 5 -0.3 2 7
DHH N/PTCH2 0.035 0.064 -10000 0 -0.3 12 12
DHH N/PTCH1 0.039 0.074 -10000 0 -0.33 7 7
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DHH 0.019 0.077 -10000 0 -0.42 11 11
PTHLH 0.026 0.099 -10000 0 -0.67 6 6
determination of left/right symmetry 0.027 0.069 -10000 0 -0.38 4 4
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
skeletal system development 0.026 0.098 -10000 0 -0.66 6 6
IHH N/Hhip 0.04 0.023 -10000 0 -10000 0 0
DHH N/Hhip 0.025 0.059 -10000 0 -0.3 11 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.069 -10000 0 -0.38 4 4
pancreas development 0.017 0.002 -10000 0 -10000 0 0
HHAT 0.03 0.026 -10000 0 -0.42 1 1
PI3K 0.049 0.014 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.032 0.025 -10000 0 -0.42 1 1
somite specification 0.027 0.069 -10000 0 -0.38 4 4
SHH Np/Cholesterol/PTCH1 0.027 0.04 -10000 0 -0.32 2 2
SHH Np/Cholesterol/PTCH2 0.023 0.019 -10000 0 -0.23 1 1
SHH Np/Cholesterol/Megalin -0.086 0.12 -10000 0 -0.23 156 156
SHH -0.01 0.005 -10000 0 -10000 0 0
catabolic process 0.034 0.062 -10000 0 -0.42 6 6
SMO/Vitamin D3 0.036 0.064 -10000 0 -0.28 4 4
SHH Np/Cholesterol/Hhip 0.015 0.008 -10000 0 -10000 0 0
LRP2 -0.2 0.22 -10000 0 -0.42 192 192
receptor-mediated endocytosis -0.058 0.12 -10000 0 -0.39 10 10
SHH Np/Cholesterol/BOC 0.024 0.014 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.023 0.014 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.015 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.058 0.083 0.38 6 -0.32 2 8
IHH N/PTCH2 0.051 0.033 -10000 0 -0.32 1 1
CDON 0.032 0.011 -10000 0 -10000 0 0
IHH N/PTCH1 0.043 0.067 -10000 0 -0.42 6 6
Megalin/LRPAP1 -0.13 0.17 -10000 0 -0.3 189 189
PTCH2 0.033 0.024 -10000 0 -0.42 1 1
SHH Np/Cholesterol 0.015 0.007 -10000 0 -10000 0 0
PTCH1 0.034 0.063 -10000 0 -0.42 6 6
HHIP 0.017 0.002 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.008 -10000 0 -10000 0 0
ANTXR2 0.032 0.034 -10000 0 -0.42 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.004 -10000 0 -0.057 2 2
monocyte activation -0.12 0.26 -10000 0 -0.5 104 104
MAP2K2 0.019 0.046 -10000 0 -0.6 2 2
MAP2K1 -0.002 0.004 -10000 0 -10000 0 0
MAP2K7 -0.002 0.003 -10000 0 -10000 0 0
MAP2K6 -0.006 0.027 -10000 0 -0.21 6 6
CYAA -0.005 0.015 -10000 0 -0.21 2 2
MAP2K4 -0.002 0.008 0.14 1 -10000 0 1
IL1B -0.036 0.095 0.11 2 -0.26 47 49
Channel 0.039 0.025 -10000 0 -0.22 2 2
NLRP1 -0.022 0.061 -10000 0 -0.21 35 35
CALM1 0.034 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.005 0.069 -10000 0 -0.38 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.004 0.057 2 -10000 0 2
MAPK3 -0.002 0.004 -10000 0 -10000 0 0
MAPK1 -0.002 0.008 0.14 1 -10000 0 1
PGR -0.002 0.008 0.14 1 -10000 0 1
PA/Cellular Receptors 0.041 0.027 -10000 0 -0.25 2 2
apoptosis -0.001 0.004 -10000 0 -0.057 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.038 0.024 -10000 0 -0.21 2 2
macrophage activation -0.003 0.007 0.13 1 -10000 0 1
TNF -0.054 0.18 -10000 0 -0.42 69 69
VCAM1 -0.12 0.26 -10000 0 -0.5 102 102
platelet activation 0.005 0.069 -10000 0 -0.38 11 11
MAPKKK cascade -0.002 0.017 -10000 0 -0.07 15 15
IL18 -0.049 0.11 0.11 2 -0.25 72 74
negative regulation of macrophage activation -0.001 0.004 -10000 0 -0.057 2 2
LEF -0.001 0.004 -10000 0 -0.057 2 2
CASP1 -0.011 0.054 -10000 0 -0.18 28 28
mol:cAMP 0.005 0.069 -10000 0 -0.39 11 11
necrosis -0.001 0.004 -10000 0 -0.057 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.039 0.023 -10000 0 -0.21 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.028 0.068 -10000 0 -0.3 14 14
CRKL 0.036 0.12 0.33 12 -0.4 9 21
mol:PIP3 -0.003 0.012 -10000 0 -10000 0 0
AKT1 -0.006 0.019 -10000 0 -10000 0 0
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
RAPGEF1 0.034 0.11 0.31 12 -0.38 9 21
RANBP10 0.034 0.007 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.034 0.084 -10000 0 -0.26 24 24
MAP3K5 -0.01 0.16 0.3 5 -0.44 25 30
HGF/MET/CIN85/CBL/ENDOPHILINS 0.048 0.085 -10000 0 -0.23 25 25
AP1 0.038 0.05 0.17 7 -10000 0 7
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
apoptosis 0.018 0.14 -10000 0 -0.78 9 9
STAT3 (dimer) 0.01 0.085 -10000 0 -0.38 7 7
GAB1/CRKL/SHP2/PI3K 0.074 0.12 0.33 8 -0.37 8 16
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
CBL/CRK 0.041 0.11 0.32 3 -0.37 10 13
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.01 -10000 0 -10000 0 0
PTEN 0.031 0.012 -10000 0 -10000 0 0
ELK1 0.021 0.13 0.36 38 -10000 0 38
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.01 0.057 -10000 0 -0.24 8 8
PAK1 0.003 0.045 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.036 0.085 -10000 0 -0.26 25 25
HRAS -0.003 0.14 -10000 0 -0.53 23 23
DOCK1 0.033 0.11 0.31 13 -0.38 8 21
GAB1 0.022 0.11 0.25 2 -0.4 11 13
CRK 0.025 0.11 0.32 3 -0.4 10 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.14 -10000 0 -0.48 24 24
JUN 0.032 0.011 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.004 0.065 -10000 0 -0.23 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
cell morphogenesis 0.042 0.13 0.36 19 -0.41 6 25
GRB2/SHC 0.036 0.075 -10000 0 -0.21 20 20
FOS 0.034 0.008 -10000 0 -10000 0 0
GLMN 0.002 0.026 -10000 0 -0.24 4 4
cell motility 0.021 0.13 0.35 38 -10000 0 38
HGF/MET/MUC20 0.019 0.078 -10000 0 -0.26 25 25
cell migration 0.035 0.073 -10000 0 -0.2 20 20
GRB2 0.034 0.007 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
MET/RANBP10 0.025 0.079 -10000 0 -0.29 20 20
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.011 0.074 -10000 0 -0.36 6 6
MET/MUC20 0.005 0.072 -10000 0 -0.29 20 20
RAP1B 0.037 0.11 0.31 14 -0.36 8 22
RAP1A 0.036 0.11 0.32 12 -0.36 8 20
HGF/MET/RANBP9 0.036 0.076 -10000 0 -0.25 20 20
RAF1 0.015 0.14 -10000 0 -0.5 23 23
STAT3 0.01 0.086 -10000 0 -0.38 7 7
cell proliferation 0.032 0.12 0.29 15 -0.36 18 33
RPS6KB1 0.006 0.051 -10000 0 -0.32 6 6
MAPK3 0.007 0.13 0.48 13 -10000 0 13
MAPK1 0.016 0.14 0.57 14 -10000 0 14
RANBP9 0.031 0.012 -10000 0 -10000 0 0
MAPK8 -0.01 0.17 0.32 4 -0.43 27 31
SRC 0.008 0.077 -10000 0 -0.33 7 7
PI3K 0.037 0.081 -10000 0 -0.22 22 22
MET/Glomulin 0.003 0.073 -10000 0 -0.25 23 23
SOS1 0.035 0.003 -10000 0 -10000 0 0
MAP2K1 0.019 0.14 0.33 1 -0.47 22 23
MET 0.006 0.1 -10000 0 -0.42 20 20
MAP4K1 -0.011 0.17 0.31 5 -0.46 26 31
PTK2 0.031 0.012 -10000 0 -10000 0 0
MAP2K2 0.017 0.14 0.36 2 -0.48 21 23
BAD -0.005 0.027 -10000 0 -10000 0 0
MAP2K4 -0.007 0.15 0.29 5 -0.41 23 28
SHP2/GRB2/SOS1/GAB1 0.034 0.11 -10000 0 -0.32 25 25
INPPL1 0.033 0.009 -10000 0 -10000 0 0
PXN 0.034 0.006 -10000 0 -10000 0 0
SH3KBP1 0.035 0.004 -10000 0 -10000 0 0
HGS -0.007 0.06 -10000 0 -0.22 25 25
PLCgamma1/PKC 0.024 0.007 -10000 0 -10000 0 0
HGF 0.024 0.058 -10000 0 -0.42 6 6
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
PTPRJ 0.034 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.043 0.079 -10000 0 -0.21 23 23
PDPK1 -0.005 0.021 -10000 0 -10000 0 0
HGF/MET/SHIP -0.009 0.14 -10000 0 -0.28 69 69
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.09 -10000 0 -0.22 39 39
SMAD6-7/SMURF1 0.062 0.026 -10000 0 -10000 0 0
NOG -0.1 0.2 -10000 0 -0.42 105 105
SMAD9 0.007 0.12 -10000 0 -0.45 22 22
SMAD4 0.035 0.005 -10000 0 -10000 0 0
SMAD5 0.023 0.07 -10000 0 -0.34 7 7
BMP7/USAG1 -0.11 0.16 -10000 0 -0.32 134 134
SMAD5/SKI 0.035 0.096 0.22 1 -0.37 10 11
SMAD1 0.043 0.043 -10000 0 -10000 0 0
BMP2 0.025 0.058 -10000 0 -0.42 6 6
SMAD1/SMAD1/SMAD4 0.048 0.052 -10000 0 -0.35 1 1
BMPR1A 0.032 0.01 -10000 0 -10000 0 0
BMPR1B 0.014 0.017 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.013 0.054 -10000 0 -0.25 7 7
AHSG 0.022 0.011 -10000 0 -10000 0 0
CER1 0.019 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 0.038 0.059 -10000 0 -0.24 12 12
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.017 0.073 -10000 0 -0.33 7 7
BMP2-4 (homodimer) 0.033 0.066 -10000 0 -0.29 13 13
RGMB 0.031 0.011 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.042 0.034 -10000 0 -10000 0 0
RGMA 0.029 0.035 -10000 0 -0.42 2 2
SMURF1 0.032 0.01 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.01 0.055 -10000 0 -0.29 6 6
BMP2-4/USAG1 -0.075 0.15 -10000 0 -0.26 139 139
SMAD6/SMURF1/SMAD5 0.031 0.095 0.26 1 -0.37 10 11
SOSTDC1 -0.14 0.21 -10000 0 -0.42 133 133
BMP7/BMPR2/BMPR1A-1B 0.019 0.067 -10000 0 -0.23 19 19
SKI 0.034 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.03 0.012 -10000 0 -10000 0 0
HFE2 0.016 0.006 -10000 0 -10000 0 0
ZFYVE16 0.034 0.008 -10000 0 -10000 0 0
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
BMP2-4/CHRD 0.045 0.065 -10000 0 -0.25 13 13
SMAD5/SMAD5/SMAD4 0.037 0.098 0.24 2 -0.37 10 12
MAPK1 0.033 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.031 0.067 -10000 0 -0.26 6 6
BMP7 (homodimer) -0.001 0.099 -10000 0 -0.42 19 19
NUP214 0.033 0.009 -10000 0 -10000 0 0
BMP6/FETUA 0.034 0.021 -10000 0 -10000 0 0
SMAD1/SKI 0.056 0.06 -10000 0 -0.35 2 2
SMAD6 0.034 0.007 -10000 0 -10000 0 0
CTDSP2 0.034 0.007 -10000 0 -10000 0 0
BMP2-4/FETUA 0.039 0.063 -10000 0 -0.25 13 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.012 0.092 -10000 0 -0.42 16 16
BMPR2 (homodimer) 0.035 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.065 0.022 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.011 0.031 -10000 0 -10000 0 0
CHRDL1 -0.013 0.13 -10000 0 -0.42 36 36
ENDOFIN/SMAD1 0.056 0.059 -10000 0 -0.35 2 2
SMAD6-7/SMURF1/SMAD1 0.074 0.066 -10000 0 -0.41 1 1
SMAD6/SMURF1 0.032 0.01 -10000 0 -10000 0 0
BAMBI 0.023 0.062 -10000 0 -0.42 7 7
SMURF2 0.034 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 0.015 0.12 -10000 0 -0.28 43 43
BMP2-4/GREM1 0.033 0.09 -10000 0 -0.26 27 27
SMAD7 0.035 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.024 0.12 -10000 0 -0.41 24 24
SMAD1/SMAD6 0.051 0.06 -10000 0 -0.35 2 2
TAK1/SMAD6 0.043 0.02 -10000 0 -10000 0 0
BMP7 -0.001 0.099 -10000 0 -0.42 19 19
BMP6 0.03 0.012 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.014 0.061 -10000 0 -0.3 6 6
PPM1A 0.035 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.057 0.061 -10000 0 -0.35 2 2
SMAD7/SMURF1 0.047 0.017 -10000 0 -10000 0 0
CTDSPL 0.035 0.005 -10000 0 -10000 0 0
PPP1CA 0.034 0.007 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
CTDSP1 0.035 0.004 -10000 0 -10000 0 0
PPP1R15A 0.035 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.003 0.087 -10000 0 -0.32 15 15
CHRD 0.032 0.01 -10000 0 -10000 0 0
BMPR2 0.035 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.006 0.055 -10000 0 -0.32 5 5
BMP4 0.026 0.062 -10000 0 -0.42 7 7
FST 0.001 0.11 -10000 0 -0.42 24 24
BMP2-4/NOG -0.043 0.15 -10000 0 -0.26 113 113
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.029 0.068 -10000 0 -0.22 17 17
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.033 0.009 -10000 0 -10000 0 0
NFATC1 0.041 0.085 0.28 3 -0.37 4 7
NFATC2 0.009 0.083 0.17 3 -0.26 19 22
NFATC3 0.026 0.028 -10000 0 -0.33 2 2
YWHAE 0.033 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.09 0.17 0.19 1 -0.35 97 98
Exportin 1/Ran/NUP214 0.066 0.02 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.068 0.19 -10000 0 -0.36 92 92
BCL2/BAX 0.051 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
BAX 0.035 0.004 -10000 0 -10000 0 0
MAPK14 0.032 0.011 -10000 0 -10000 0 0
BAD 0.034 0.006 -10000 0 -10000 0 0
CABIN1/MEF2D -0.066 0.17 -10000 0 -0.34 79 79
Calcineurin A alpha-beta B1/BCL2 0.035 0.005 -10000 0 -10000 0 0
FKBP8 0.035 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.16 0.34 79 -10000 0 79
KPNB1 0.034 0.006 -10000 0 -10000 0 0
KPNA2 0.034 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
NFAT4/CK1 alpha 0.041 0.03 0.18 3 -0.18 2 5
MEF2D/NFAT1/Cbp/p300 0.054 0.09 -10000 0 -0.28 11 11
CABIN1 -0.091 0.17 0.19 1 -0.35 97 98
CALM1 0.035 0.006 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 -10000 0 0
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
CAMK4 -0.026 0.15 -10000 0 -0.42 48 48
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.035 0.004 -10000 0 -10000 0 0
YWHAH 0.034 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.005 0.13 -10000 0 -0.3 59 59
YWHAB 0.033 0.01 -10000 0 -10000 0 0
MAPK8 0.032 0.011 -10000 0 -10000 0 0
MAPK9 0.033 0.009 -10000 0 -10000 0 0
YWHAG 0.033 0.01 -10000 0 -10000 0 0
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.059 0.099 0.25 4 -0.34 6 10
PRKCH 0.033 0.024 -10000 0 -0.42 1 1
CABIN1/Cbp/p300 0.048 0.017 -10000 0 -10000 0 0
CASP3 0.035 0.006 -10000 0 -10000 0 0
PIM1 0.031 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.006 -10000 0 -10000 0 0
apoptosis 0.024 0.021 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.037 -10000 0 -10000 0 0
PRKCB -0.098 0.21 -10000 0 -0.42 107 107
PRKCE 0.035 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.036 0.046 -10000 0 -0.3 2 2
BAD/BCL-XL 0.047 0.016 -10000 0 -10000 0 0
PRKCD 0.034 0.006 -10000 0 -10000 0 0
NUP214 0.033 0.009 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
PRKCG 0.028 0.01 -10000 0 -10000 0 0
PRKCQ -0.088 0.2 -10000 0 -0.42 97 97
FKBP38/BCL2 0.051 0.008 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.084 0.28 3 -0.36 4 7
CaM/Ca2+/FKBP38 0.047 0.009 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSNK1A1 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.007 0.099 -10000 0 -0.24 48 48
NFATc/ERK1 0.059 0.086 0.28 3 -0.39 3 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.075 0.2 -10000 0 -0.36 104 104
NR4A1 0.047 0.09 0.23 15 -0.28 9 24
GSK3B 0.035 0.006 -10000 0 -10000 0 0
positive T cell selection 0.026 0.028 -10000 0 -0.33 2 2
NFAT1/CK1 alpha 0.014 0.059 -10000 0 -0.24 10 10
RCH1/ KPNB1 0.05 0.012 -10000 0 -10000 0 0
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
PRKACA 0.036 0.003 -10000 0 -10000 0 0
AKAP5 -0.04 0.17 -10000 0 -0.42 60 60
MEF2D 0.032 0.011 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.082 0.28 2 -0.45 2 4
CREBBP 0.035 0.004 -10000 0 -10000 0 0
BCL2 0.035 0.005 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.002 0.026 -10000 0 -0.25 4 4
ADCY5 -0.048 0.1 -10000 0 -0.25 74 74
ADCY6 0.005 0.002 -10000 0 -10000 0 0
ADCY7 0.004 0.013 -10000 0 -0.25 1 1
ADCY1 -0.031 0.088 -10000 0 -0.25 51 51
ADCY2 -0.003 0.008 -10000 0 -10000 0 0
ADCY3 0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.003 0.007 -10000 0 -10000 0 0
PRKCE 0.01 0.001 -10000 0 -10000 0 0
ADCY9 0.005 0.001 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.006 0.065 0.2 15 -0.17 1 16
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.033 0.01 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.006 0.068 -10000 0 -0.21 22 22
NT3 (dimer)/TRKC 0.018 0.088 -10000 0 -0.3 25 25
NT3 (dimer)/TRKB 0.034 0.057 -10000 0 -0.24 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0.018 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
BDNF -0.075 0.19 -10000 0 -0.42 88 88
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DYNLT1 0.031 0.011 -10000 0 -10000 0 0
NTRK1 0.018 0.077 -10000 0 -0.42 11 11
NTRK2 0.024 0.048 -10000 0 -0.42 4 4
NTRK3 0.002 0.11 -10000 0 -0.42 25 25
NT-4/5 (dimer)/TRKB 0.031 0.054 -10000 0 -0.25 8 8
neuron apoptosis 0.029 0.12 0.35 18 -10000 0 18
SHC 2-3/Grb2 -0.032 0.13 -10000 0 -0.38 18 18
SHC1 0.032 0.011 -10000 0 -10000 0 0
SHC2 -0.037 0.11 -10000 0 -0.4 17 17
SHC3 -0.044 0.13 -10000 0 -0.41 27 27
STAT3 (dimer) 0.041 0.014 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.033 0.07 -10000 0 -0.26 14 14
RIN/GDP 0.043 0.091 0.26 16 -0.22 10 26
GIPC1 0.035 0.003 -10000 0 -10000 0 0
KRAS 0.034 0.006 -10000 0 -10000 0 0
DNAJA3 -0.002 0.056 -10000 0 -0.24 15 15
RIN/GTP 0.013 0.002 -10000 0 -10000 0 0
CCND1 0.025 0.011 -10000 0 -10000 0 0
MAGED1 0.035 0.003 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.061 0.026 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.018 0.11 -10000 0 -0.27 42 42
TRKA/NEDD4-2 0.033 0.068 -10000 0 -0.29 14 14
ELMO1 0.014 0.087 -10000 0 -0.42 14 14
RhoG/GTP/ELMO1/DOCK1 0.028 0.057 -10000 0 -0.24 14 14
NGF 0.031 0.011 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
GAB2 0.033 0.009 -10000 0 -10000 0 0
RIT2 0.017 0.003 -10000 0 -10000 0 0
RIT1 0.032 0.011 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
DNM1 0.029 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.017 0.074 -10000 0 -0.24 17 17
mol:GDP 0.048 0.12 0.33 16 -0.33 11 27
NGF (dimer) 0.031 0.011 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.061 -10000 0 -0.29 14 14
RIT1/GDP 0.035 0.08 0.24 7 -0.23 9 16
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.024 0.13 -10000 0 -0.25 91 91
KIDINS220/CRKL/C3G 0.045 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.044 0.026 -10000 0 -0.3 1 1
FRS2 family/SHP2 0.06 0.027 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.077 0.034 -10000 0 -10000 0 0
RIT1/GTP 0.024 0.008 -10000 0 -10000 0 0
NT3 (dimer) 0.028 0.012 -10000 0 -10000 0 0
RAP1/GDP 0.032 0.066 0.16 6 -0.2 7 13
KIDINS220/CRKL 0.033 0.01 -10000 0 -10000 0 0
BDNF (dimer) -0.075 0.19 -10000 0 -0.42 88 88
ubiquitin-dependent protein catabolic process 0.044 0.065 -10000 0 -0.25 14 14
Schwann cell development -0.014 0.022 -10000 0 -10000 0 0
EHD4 0.034 0.008 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.074 0.036 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.044 -10000 0 -0.25 1 1
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.12 -10000 0 -0.22 96 96
ABL1 0.033 0.009 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
Rap1/GTP 0.011 0.085 -10000 0 -0.36 7 7
STAT3 0.041 0.014 -10000 0 -10000 0 0
axon guidance -0.034 0.11 -10000 0 -0.21 96 96
MAPK3 0.002 0.1 0.19 29 -0.25 42 71
MAPK1 0.001 0.098 0.19 27 -0.24 42 69
CDC42/GDP 0.051 0.093 0.26 18 -0.23 9 27
NTF3 0.028 0.012 -10000 0 -10000 0 0
NTF4 0.017 0.002 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.044 0.066 -10000 0 -0.25 14 14
PI3K 0.049 0.014 -10000 0 -10000 0 0
FRS3 0.032 0.011 -10000 0 -10000 0 0
FAIM 0.031 0.041 -10000 0 -0.42 3 3
GAB1 0.035 0.005 -10000 0 -10000 0 0
RASGRF1 -0.013 0.075 -10000 0 -0.24 23 23
SOS1 0.035 0.003 -10000 0 -10000 0 0
MCF2L -0.01 0.065 -10000 0 -0.25 23 23
RGS19 0.032 0.01 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.068 0.088 0.31 8 -0.4 5 13
Rac1/GDP 0.041 0.086 0.25 14 -0.23 9 23
NGF (dimer)/TRKA/GRIT 0.029 0.053 -10000 0 -0.25 11 11
neuron projection morphogenesis 0.02 0.14 -10000 0 -0.8 9 9
NGF (dimer)/TRKA/NEDD4-2 0.045 0.066 -10000 0 -0.25 14 14
MAP2K1 0.043 0.061 0.2 46 -10000 0 46
NGFR 0.024 0.048 -10000 0 -0.42 4 4
NGF (dimer)/TRKA/GIPC/GAIP 0.02 0.054 -10000 0 -0.27 9 9
RAS family/GTP/PI3K 0.032 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.084 0.043 -10000 0 -10000 0 0
NRAS 0.034 0.008 -10000 0 -10000 0 0
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
MAPKKK cascade -0.012 0.14 -10000 0 -0.54 23 23
RASA1 0.032 0.025 -10000 0 -0.42 1 1
TRKA/c-Abl 0.034 0.06 -10000 0 -0.29 11 11
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.003 0.13 -10000 0 -0.23 89 89
NGF (dimer)/TRKA/p62/Atypical PKCs 0.07 0.067 -10000 0 -0.21 12 12
MATK -0.018 0.15 -10000 0 -0.42 43 43
NEDD4L 0.031 0.041 -10000 0 -0.42 3 3
RAS family/GDP -0.011 0.036 -10000 0 -0.18 6 6
NGF (dimer)/TRKA 0.004 0.058 -10000 0 -0.24 15 15
Rac1/GTP -0.009 0.067 -10000 0 -0.23 17 17
FRS2 family/SHP2/CRK family 0.079 0.046 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.018 0.09 0.31 3 -0.38 7 10
CRKL 0.046 0.09 0.3 9 -0.36 6 15
HRAS 0.014 0.11 0.24 2 -0.34 14 16
mol:PIP3 0.071 0.1 0.29 24 -0.36 5 29
SPRED1 0.033 0.008 -10000 0 -10000 0 0
SPRED2 0.035 0.003 -10000 0 -10000 0 0
GAB1 0.046 0.085 0.22 8 -0.37 6 14
FOXO3 0.065 0.11 0.34 9 -0.34 7 16
AKT1 0.069 0.11 0.35 9 -0.35 9 18
BAD 0.068 0.11 0.34 11 -0.33 9 20
megakaryocyte differentiation 0.031 0.084 0.22 7 -0.35 8 15
GSK3B 0.067 0.11 0.34 12 -0.33 9 21
RAF1 0.023 0.099 0.26 8 -0.3 12 20
SHC1 0.032 0.011 -10000 0 -10000 0 0
STAT3 0.043 0.084 0.22 4 -0.37 6 10
STAT1 0.032 0.16 -10000 0 -0.84 9 9
HRAS/SPRED1 0.032 0.1 0.26 3 -0.3 12 15
cell proliferation 0.038 0.083 0.22 7 -0.36 7 14
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
TEC 0.023 0.07 -10000 0 -0.42 9 9
RPS6KB1 0.063 0.097 0.29 7 -0.38 6 13
HRAS/SPRED2 0.034 0.1 0.26 3 -0.28 14 17
LYN/TEC/p62DOK 0.075 0.099 0.28 1 -0.33 9 10
MAPK3 0.025 0.084 0.24 10 -0.25 5 15
STAP1 -0.066 0.12 -10000 0 -0.43 8 8
GRAP2 -0.014 0.14 -10000 0 -0.42 38 38
JAK2 0.039 0.14 -10000 0 -0.74 9 9
STAT1 (dimer) 0.033 0.16 -10000 0 -0.82 9 9
mol:Gleevec -0.003 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.04 0.11 -10000 0 -0.32 16 16
actin filament polymerization 0.042 0.095 0.35 9 -0.38 6 15
LYN 0.016 0.084 -10000 0 -0.42 13 13
STAP1/STAT5A (dimer) -0.071 0.14 0.33 1 -0.61 9 10
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.069 0.092 0.31 6 -0.32 7 13
PI3K 0.09 0.099 0.31 6 -0.39 5 11
PTEN 0.03 0.012 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.045 0.18 -10000 0 -1.1 7 7
MAPK8 0.038 0.084 0.22 6 -0.37 7 13
STAT3 (dimer) 0.043 0.083 0.22 7 -0.37 6 13
positive regulation of transcription 0.025 0.074 0.22 11 -0.21 4 15
mol:GDP 0.013 0.11 -10000 0 -0.34 18 18
PIK3C2B 0.047 0.1 0.32 16 -0.37 7 23
CBL/CRKL 0.058 0.09 0.3 7 -0.33 7 14
FER 0.042 0.089 0.29 5 -0.37 7 12
SH2B3 0.045 0.085 0.22 4 -0.37 6 10
PDPK1 0.069 0.1 0.28 25 -0.34 5 30
SNAI2 0.041 0.09 0.24 8 -0.37 7 15
positive regulation of cell proliferation 0.038 0.14 -10000 0 -0.74 7 7
KITLG 0.035 0.027 -10000 0 -0.42 1 1
cell motility 0.038 0.14 -10000 0 -0.74 7 7
PTPN6 -0.074 0.19 -10000 0 -0.41 88 88
EPOR 0.054 0.064 -10000 0 -10000 0 0
STAT5A (dimer) 0.041 0.12 0.34 2 -0.61 7 9
SOCS1 0.011 0.1 -10000 0 -0.42 19 19
cell migration -0.027 0.091 0.39 7 -0.3 2 9
SOS1 0.035 0.003 -10000 0 -10000 0 0
EPO 0.028 0.015 -10000 0 -10000 0 0
VAV1 -0.052 0.18 -10000 0 -0.42 70 70
GRB10 0.038 0.087 0.31 3 -0.37 7 10
PTPN11 0.032 0.008 -10000 0 -10000 0 0
SCF/KIT 0.05 0.093 0.23 7 -0.38 7 14
GO:0007205 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 0.022 0.088 0.25 9 -0.26 8 17
CBL 0.032 0.011 -10000 0 -10000 0 0
KIT 0.021 0.19 -10000 0 -1.3 7 7
MAP2K2 0.02 0.087 0.25 10 -0.26 8 18
SHC/Grb2/SOS1 0.081 0.092 0.28 1 -0.35 7 8
STAT5A 0.04 0.13 0.34 2 -0.63 7 9
GRB2 0.034 0.007 -10000 0 -10000 0 0
response to radiation 0.042 0.09 0.25 9 -0.36 7 16
SHC/GRAP2 0.016 0.094 -10000 0 -0.3 29 29
PTPRO 0.031 0.085 0.22 7 -0.36 8 15
SH2B2 0.035 0.083 0.21 1 -0.38 6 7
DOK1 0.035 0.002 -10000 0 -10000 0 0
MATK 0.025 0.09 -10000 0 -0.4 7 7
CREBBP 0.05 0.024 -10000 0 -10000 0 0
BCL2 0.049 0.097 -10000 0 -0.71 3 3
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.025 0.051 -10000 0 -0.24 12 12
EPHB2 0.016 0.09 -10000 0 -0.42 15 15
Syndecan-2/TACI -0.079 0.13 -10000 0 -0.24 142 142
LAMA1 0.006 0.013 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.053 0.061 -10000 0 -0.24 10 10
HRAS 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.01 0.019 -10000 0 -0.24 2 2
ITGA5 0.034 0.006 -10000 0 -10000 0 0
BAX 0.01 0.017 -10000 0 -10000 0 0
EPB41 0.034 0.024 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.03 0.022 -10000 0 -0.22 2 2
LAMA3 0.02 0.081 -10000 0 -0.42 12 12
EZR 0.028 0.042 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.032 0.011 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.026 0.033 -10000 0 -0.24 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.044 0.026 -10000 0 -0.3 1 1
dendrite morphogenesis 0.021 0.058 -10000 0 -0.24 16 16
Syndecan-2/GM-CSF 0.027 0.028 -10000 0 -0.24 3 3
determination of left/right symmetry 0.014 0.023 -10000 0 -0.28 2 2
Syndecan-2/PKC delta 0.032 0.024 -10000 0 -0.24 2 2
GNB2L1 0.034 0.008 -10000 0 -10000 0 0
MAPK3 0.032 0.056 0.19 33 -0.22 3 36
MAPK1 0.03 0.054 0.19 30 -0.22 3 33
Syndecan-2/RACK1 0.046 0.028 -10000 0 -0.2 2 2
NF1 0.034 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.023 -10000 0 -0.28 2 2
ITGA2 0.032 0.025 -10000 0 -0.42 1 1
MAPK8 0.013 0.02 -10000 0 -0.24 2 2
Syndecan-2/alpha2/beta1 Integrin 0.021 0.029 -10000 0 -0.21 2 2
Syndecan-2/Kininogen 0.023 0.023 -10000 0 -0.24 2 2
ITGB1 0.032 0.011 -10000 0 -10000 0 0
SRC 0.034 0.051 0.19 32 -0.2 2 34
Syndecan-2/CASK/Protein 4.1 0.029 0.026 -10000 0 -0.22 3 3
extracellular matrix organization 0.032 0.028 -10000 0 -0.24 3 3
actin cytoskeleton reorganization 0.025 0.051 -10000 0 -0.24 12 12
Syndecan-2/Caveolin-2/Ras 0.045 0.031 -10000 0 -0.22 2 2
Syndecan-2/Laminin alpha3 0.025 0.056 -10000 0 -0.28 10 10
Syndecan-2/RasGAP 0.058 0.037 -10000 0 -0.2 3 3
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
PRKCD 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.058 -10000 0 -0.24 16 16
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.041 0.034 0.2 4 -0.19 3 7
RHOA 0.035 0.005 -10000 0 -10000 0 0
SDCBP 0.032 0.01 -10000 0 -10000 0 0
TNFRSF13B -0.17 0.22 -10000 0 -0.42 163 163
RASA1 0.032 0.025 -10000 0 -0.42 1 1
alpha2/beta1 Integrin 0.044 0.026 -10000 0 -0.3 1 1
Syndecan-2/Synbindin 0.03 0.025 -10000 0 -0.24 2 2
TGFB1 0.033 0.034 -10000 0 -0.42 2 2
CASP3 0.037 0.056 0.2 36 -0.22 2 38
FN1 0.021 0.077 -10000 0 -0.42 11 11
Syndecan-2/IL8 0.022 0.036 -10000 0 -0.24 5 5
SDC2 0.014 0.023 -10000 0 -0.29 2 2
KNG1 0.021 0.01 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.032 0.025 -10000 0 -0.24 2 2
TRAPPC4 0.032 0.011 -10000 0 -10000 0 0
CSF2 0.026 0.026 -10000 0 -0.42 1 1
Syndecan-2/TGFB1 0.032 0.028 -10000 0 -0.24 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.03 0.022 -10000 0 -0.22 2 2
Syndecan-2/Ezrin 0.043 0.039 -10000 0 -0.22 5 5
PRKACA 0.037 0.055 0.2 34 -0.22 2 36
angiogenesis 0.021 0.036 -10000 0 -0.24 5 5
MMP2 0.027 0.036 -10000 0 -0.42 2 2
IL8 0.022 0.043 -10000 0 -0.42 3 3
calcineurin-NFAT signaling pathway -0.079 0.13 -10000 0 -0.24 142 142
IL1-mediated signaling events

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
UBC13/UEV1A 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.034 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.01 0.076 -10000 0 -0.3 10 10
IRAK/TOLLIP 0.04 0.01 -10000 0 -10000 0 0
IKBKB 0.034 0.007 -10000 0 -10000 0 0
IKBKG 0.035 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.003 0.12 -10000 0 -0.3 53 53
IL1A 0.03 0.01 -10000 0 -10000 0 0
IL1B -0.018 0.1 -10000 0 -0.32 37 37
IRAK/TRAF6/p62/Atypical PKCs 0.077 0.039 -10000 0 -0.2 2 2
IL1R2 -0.031 0.16 -10000 0 -0.42 53 53
IL1R1 0.033 0.033 -10000 0 -0.42 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.084 -10000 0 -0.39 9 9
TOLLIP 0.034 0.006 -10000 0 -10000 0 0
TICAM2 0.028 0.048 -10000 0 -0.42 4 4
MAP3K3 0.034 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.037 0.064 -10000 0 -0.3 1 1
JUN -0.008 0.023 0.16 1 -0.18 5 6
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.046 0.11 -10000 0 -0.23 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88 0.077 0.037 -10000 0 -0.23 3 3
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.09 0.04 -10000 0 -0.2 3 3
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.1 -10000 0 -0.25 43 43
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 0.006 0.025 0.17 1 -0.19 5 6
IRAK1 0.02 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.041 0.06 -10000 0 -0.3 11 11
IRAK4 0.034 0.006 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.082 -10000 0 -0.31 12 12
CHUK 0.032 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.1 -10000 0 -0.25 43 43
IL1 beta/IL1R2 -0.032 0.15 -10000 0 -0.3 82 82
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.095 -10000 0 -0.22 39 39
IRAK3 0.028 0.053 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.11 -10000 0 -0.24 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.035 0.032 -10000 0 -0.28 3 3
IL1 alpha/IL1R1/IL1RAP 0.057 0.036 -10000 0 -0.25 2 2
RELA 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
MYD88 0.034 0.024 -10000 0 -0.42 1 1
IRAK/TRAF6/MEKK3 0.057 0.018 -10000 0 -10000 0 0
IL1RAP 0.032 0.01 -10000 0 -10000 0 0
UBE2N 0.035 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 0.014 0.088 -10000 0 -0.22 39 39
CASP1 0.015 0.087 -10000 0 -0.42 14 14
IL1RN/IL1R2 -0.007 0.13 -10000 0 -0.3 60 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.033 0.11 -10000 0 -0.24 43 43
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.033 0.061 -10000 0 -0.36 7 7
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
IL1RN 0.024 0.07 -10000 0 -0.42 9 9
TRAF6/TAK1/TAB1/TAB2 0.046 0.018 -10000 0 -10000 0 0
MAP2K6 0.017 0.031 0.18 2 -0.2 6 8
Ephrin B reverse signaling

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
EFNB2 0.033 0.009 -10000 0 -10000 0 0
EPHB2 0.015 0.091 -10000 0 -0.42 15 15
EFNB1 0.013 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.097 -10000 0 -0.24 30 30
Ephrin B2/EPHB1-2 0.038 0.075 -10000 0 -0.25 20 20
neuron projection morphogenesis 0.021 0.085 -10000 0 -0.23 30 30
Ephrin B1/EPHB1-2/Tiam1 0.033 0.1 -10000 0 -0.25 36 36
DNM1 0.029 0.013 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.014 0.087 -10000 0 -0.5 11 11
YES1 -0.003 0.13 -10000 0 -0.75 11 11
Ephrin B1/EPHB1-2/NCK2 0.048 0.075 -10000 0 -0.23 20 20
PI3K 0.03 0.1 -10000 0 -0.52 11 11
mol:GDP 0.031 0.1 -10000 0 -0.24 36 36
ITGA2B 0.031 0.012 -10000 0 -10000 0 0
endothelial cell proliferation 0.039 0.018 -10000 0 -10000 0 0
FYN -0.015 0.14 -10000 0 -0.75 11 11
MAP3K7 -0.014 0.096 -10000 0 -0.54 11 11
FGR -0.018 0.14 -10000 0 -0.76 11 11
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RGS3 0.033 0.009 -10000 0 -10000 0 0
cell adhesion 0.004 0.11 -10000 0 -0.49 12 12
LYN -0.008 0.13 -10000 0 -0.73 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.012 0.12 -10000 0 -0.69 11 11
Ephrin B1/EPHB1-2 -0.016 0.1 -10000 0 -0.59 11 11
SRC -0.002 0.13 -10000 0 -0.73 11 11
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
EPHB1 0.023 0.063 -10000 0 -0.42 7 7
EPHB4 0.032 0.01 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.04 0.018 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.077 -10000 0 -0.3 18 18
BLK -0.1 0.15 -10000 0 -0.79 11 11
HCK -0.015 0.14 -10000 0 -0.74 11 11
regulation of stress fiber formation -0.046 0.074 0.23 20 -10000 0 20
MAPK8 -0.013 0.083 -10000 0 -0.47 11 11
Ephrin B1/EPHB1-2/RGS3 0.048 0.075 -10000 0 -0.24 19 19
endothelial cell migration 0 0.09 0.19 7 -0.46 9 16
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTPN13 0.036 0.054 -10000 0 -0.54 3 3
regulation of focal adhesion formation -0.046 0.074 0.23 20 -10000 0 20
chemotaxis -0.046 0.074 0.24 19 -10000 0 19
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.031 0.091 -10000 0 -0.24 30 30
angiogenesis -0.015 0.1 -10000 0 -0.58 11 11
LCK -0.063 0.15 -10000 0 -0.78 11 11
ErbB2/ErbB3 signaling events

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.004 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.084 -10000 0 -0.22 14 14
NFATC4 -0.014 0.051 0.24 2 -0.2 4 6
ERBB2IP 0.034 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.024 -10000 0 -0.42 1 1
mammary gland morphogenesis 0.023 0.066 -10000 0 -0.23 17 17
JUN 0.037 0.066 0.24 4 -10000 0 4
HRAS 0.034 0.006 -10000 0 -10000 0 0
DOCK7 -0.003 0.059 -10000 0 -0.22 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.039 0.068 -10000 0 -0.23 16 16
AKT1 0.009 0.005 -10000 0 -10000 0 0
BAD -0.004 0.004 -10000 0 -10000 0 0
MAPK10 -0.001 0.051 0.2 7 -10000 0 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.026 0.071 -10000 0 -0.24 17 17
RAF1 0.031 0.094 0.29 8 -0.25 10 18
ErbB2/ErbB3/neuregulin 2 0.029 0.063 -10000 0 -0.25 16 16
STAT3 0.02 0.13 -10000 0 -0.83 8 8
cell migration 0.013 0.062 0.23 13 -0.16 1 14
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.001 0.24 0.38 2 -0.58 48 50
FOS 0.023 0.15 0.32 2 -0.33 47 49
NRAS 0.034 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.066 -10000 0 -0.23 17 17
MAPK3 0.009 0.19 0.38 2 -0.45 47 49
MAPK1 0.004 0.2 0.38 2 -0.46 48 50
JAK2 -0.008 0.059 -10000 0 -0.22 17 17
NF2 0.016 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.011 0.057 -10000 0 -0.23 16 16
NRG1 0.025 0.043 -10000 0 -0.42 3 3
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
MAPK8 0.018 0.069 0.22 3 -0.25 13 16
MAPK9 0.003 0.055 0.2 10 -10000 0 10
ERBB2 -0.023 0.007 -10000 0 -10000 0 0
ERBB3 0.017 0.087 -10000 0 -0.42 14 14
SHC1 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
apoptosis -0.002 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.13 -10000 0 -0.81 8 8
RNF41 -0.006 0.005 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.005 0.04 -10000 0 -0.17 13 13
ErbB2/ErbB2/HSP90 (dimer) 0.017 0.019 -10000 0 -10000 0 0
CHRNA1 -0.015 0.25 0.31 4 -0.63 48 52
myelination -0.012 0.054 0.24 3 -10000 0 3
PPP3CB -0.003 0.055 -10000 0 -0.21 17 17
KRAS 0.034 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.049 0.067 -10000 0 -0.21 13 13
NRG2 0.029 0.042 -10000 0 -0.42 3 3
mol:GDP 0.011 0.057 -10000 0 -0.23 16 16
SOS1 0.035 0.003 -10000 0 -10000 0 0
MAP2K2 0.016 0.1 0.29 7 -0.28 10 17
SRC 0.033 0.01 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.003 0.059 -10000 0 -0.22 17 17
MAP2K1 0.017 0.17 0.35 1 -0.54 10 11
heart morphogenesis 0.023 0.066 -10000 0 -0.23 17 17
RAS family/GDP 0.06 0.081 -10000 0 -0.21 14 14
GRB2 0.034 0.007 -10000 0 -10000 0 0
PRKACA 0.021 0.007 -10000 0 -10000 0 0
CHRNE 0.016 0.019 0.12 1 -10000 0 1
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
activation of caspase activity -0.009 0.005 -10000 0 -10000 0 0
nervous system development 0.023 0.066 -10000 0 -0.23 17 17
CDC42 0.035 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.009 0.14 -10000 0 -0.27 68 68
Ran/GTP/Exportin 1/HDAC1 0.009 0.011 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0 0.15 0.24 1 -0.28 69 70
SUMO1 0.035 0.003 -10000 0 -10000 0 0
ZFPM1 0.032 0.025 -10000 0 -0.42 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.02 0.007 -10000 0 -10000 0 0
FKBP3 0.035 0.004 -10000 0 -10000 0 0
Histones 0.038 0.11 0.23 2 -0.31 13 15
YY1/LSF 0.04 0.056 -10000 0 -0.22 9 9
SMG5 0.032 0.01 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.089 -10000 0 -0.21 57 57
I kappa B alpha/HDAC1 0.01 0.1 -10000 0 -0.34 12 12
SAP18 0.034 0.008 -10000 0 -10000 0 0
RELA 0.006 0.087 0.29 1 -0.19 44 45
HDAC1/Smad7 0.063 0.024 -10000 0 -10000 0 0
RANGAP1 0.032 0.01 -10000 0 -10000 0 0
HDAC3/TR2 0.01 0.1 -10000 0 -0.18 67 67
NuRD/MBD3 Complex 0.036 0.048 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.015 0.12 0.22 11 -0.21 57 68
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.034 0.008 -10000 0 -10000 0 0
GATA1 0.018 0.002 -10000 0 -10000 0 0
Mad/Max 0.051 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.068 -10000 0 -0.31 6 6
RBBP7 0.035 0.003 -10000 0 -10000 0 0
NPC 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.035 0.005 -10000 0 -10000 0 0
MAX 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
NFKBIA -0.011 0.089 -10000 0 -0.19 66 66
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.037 0.031 -10000 0 -0.34 1 1
SIN3 complex 0.081 0.029 -10000 0 -10000 0 0
SMURF1 0.032 0.01 -10000 0 -10000 0 0
CHD3 0.033 0.009 -10000 0 -10000 0 0
SAP30 0.035 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.033 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.007 0.078 -10000 0 -0.34 8 8
YY1/HDAC2 0.042 0.04 -10000 0 -0.2 2 2
YY1/HDAC1 0.043 0.046 -10000 0 -0.21 3 3
NuRD/MBD2 Complex (MeCP1) 0.037 0.051 -10000 0 -0.33 2 2
PPARG -0.023 0.15 -10000 0 -0.3 71 71
HDAC8/hEST1B 0.065 0.022 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.01 0.1 -10000 0 -0.35 12 12
MBD3L2 0.017 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.062 0.024 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.042 0.057 -10000 0 -0.32 1 1
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC3 -0.003 0.07 -10000 0 -0.16 57 57
HDAC2 0.031 0.012 -10000 0 -10000 0 0
YY1 0.024 0.022 -10000 0 -0.23 2 2
HDAC8 0.035 0 -10000 0 -10000 0 0
SMAD7 0.035 0.006 -10000 0 -10000 0 0
NCOR2 0.034 0.006 -10000 0 -10000 0 0
MXD1 0.035 0.002 -10000 0 -10000 0 0
STAT3 0.027 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.055 0.06 -10000 0 -0.21 8 8
YY1/SAP30/HDAC1 0.06 0.047 -10000 0 -0.19 3 3
EP300 0.032 0.011 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.089 -10000 0 -0.18 66 66
histone deacetylation 0.034 0.057 -10000 0 -0.26 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.072 -10000 0 -0.27 6 6
nuclear export -0.064 0.021 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GATAD2B 0.032 0.011 -10000 0 -10000 0 0
GATAD2A 0.035 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.008 0.1 -10000 0 -0.29 18 18
GATA1/HDAC1 0.037 0.019 -10000 0 -0.3 1 1
GATA1/HDAC3 -0.002 0.1 -10000 0 -0.18 72 72
CHD4 0.034 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.019 0.13 -10000 0 -0.3 68 68
SIN3/HDAC complex/Mad/Max 0.033 0.044 -10000 0 -0.33 1 1
NuRD Complex 0.044 0.059 -10000 0 -0.3 2 2
positive regulation of chromatin silencing 0.035 0.11 0.22 2 -0.31 13 15
SIN3B 0.035 0.003 -10000 0 -10000 0 0
MTA2 0.035 0.006 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.059 0.032 -10000 0 -0.18 1 1
HDAC complex 0.078 0.035 -10000 0 -0.23 1 1
GATA1/Fog1 0.036 0.02 -10000 0 -0.3 1 1
FKBP25/HDAC1/HDAC2 0.061 0.03 -10000 0 -0.25 1 1
TNF -0.054 0.18 -10000 0 -0.42 69 69
negative regulation of cell growth 0.031 0.051 -10000 0 -0.25 5 5
NuRD/MBD2/PRMT5 Complex 0.037 0.051 -10000 0 -0.33 2 2
Ran/GTP/Exportin 1 0.061 0.029 -10000 0 -0.16 1 1
NF kappa B/RelA/I kappa B alpha -0.023 0.13 -10000 0 -0.28 67 67
SIN3/HDAC complex/NCoR1 0.03 0.04 -10000 0 -0.23 1 1
TFCP2 0.026 0.062 -10000 0 -0.42 7 7
NR2C1 0.034 0.006 -10000 0 -10000 0 0
MBD3 0.032 0.034 -10000 0 -0.42 2 2
MBD2 0.035 0.005 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.029 0.024 -10000 0 -0.42 1 1
AES 0.031 0.005 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.046 0.018 -10000 0 -10000 0 0
SMAD4 0.035 0.005 -10000 0 -10000 0 0
DKK2 0.029 0.042 -10000 0 -0.42 3 3
TLE1 0.028 0.025 -10000 0 -0.42 1 1
MACF1 0.035 0.005 -10000 0 -10000 0 0
CTNNB1 0.013 0.092 0.33 2 -0.36 7 9
WIF1 0.02 0.016 -10000 0 -10000 0 0
beta catenin/RanBP3 -0.003 0.076 0.36 1 -0.34 5 6
KREMEN2 -0.026 0.15 -10000 0 -0.42 49 49
DKK1 -0.023 0.14 -10000 0 -0.42 42 42
beta catenin/beta TrCP1 0.03 0.09 0.33 2 -0.32 7 9
FZD1 0.032 0.011 -10000 0 -10000 0 0
AXIN2 0.018 0.12 0.56 10 -1.4 1 11
AXIN1 0.035 0.003 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.091 -10000 0 -0.52 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.03 0.11 0.25 1 -0.47 8 9
Axin1/APC/GSK3 0.029 0.063 0.3 3 -0.28 4 7
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.1 0.37 3 -0.34 9 12
HNF1A 0.031 0.006 -10000 0 -10000 0 0
CTBP1 0.03 0.008 -10000 0 -10000 0 0
MYC 0.075 0.19 0.58 41 -10000 0 41
RANBP3 0.035 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.019 0.11 -10000 0 -0.25 51 51
NKD1 0.025 0.058 -10000 0 -0.42 6 6
TCF4 0.027 0.041 -10000 0 -0.42 3 3
TCF3 0.031 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.057 0.08 -10000 0 -0.23 23 23
Ran/GTP 0.025 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.01 0.084 0.43 1 -0.6 2 3
LEF1 0.016 0.081 -10000 0 -0.42 12 12
DVL1 0.02 0.055 -10000 0 -0.41 3 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.039 0.12 0.27 1 -0.52 8 9
DKK1/LRP6/Kremen 2 -0.016 0.14 -10000 0 -0.27 78 78
LRP6 0.035 0.006 -10000 0 -10000 0 0
CSNK1A1 0.029 0.009 -10000 0 -10000 0 0
NLK 0.035 0.007 -10000 0 -10000 0 0
CCND1 0.039 0.14 0.57 20 -10000 0 20
WNT1 -0.002 0.12 -10000 0 -0.42 28 28
GSK3A 0.035 0.004 -10000 0 -10000 0 0
GSK3B 0.034 0.006 -10000 0 -10000 0 0
FRAT1 0.031 0.026 -10000 0 -0.42 1 1
PPP2R5D 0.026 0.042 0.25 5 -0.25 1 6
APC 0.019 0.082 0.21 31 -0.21 22 53
WNT1/LRP6/FZD1 0.013 0.063 -10000 0 -0.2 21 21
CREBBP 0.031 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.006 -9999 0 -10000 0 0
EGFR 0.027 0.035 -9999 0 -0.42 2 2
EGF/EGFR 0.029 0.073 -9999 0 -0.2 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 0.055 0.083 -9999 0 -0.21 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.033 0.009 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.001 0.11 -9999 0 -0.42 25 25
EGF/EGFR dimer/SHC 0.028 0.081 -9999 0 -0.25 24 24
mol:GDP 0.049 0.079 -9999 0 -0.21 23 23
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.027 0.042 -9999 0 -0.42 3 3
GRB2/SOS1 0.05 0.011 -9999 0 -10000 0 0
HRAS/GTP 0.033 0.067 -9999 0 -0.2 23 23
SHC1 0.032 0.011 -9999 0 -10000 0 0
HRAS/GDP 0.049 0.077 -9999 0 -0.2 23 23
FRAP1 -0.02 0.048 -9999 0 -0.2 23 23
EGF/EGFR dimer 0.015 0.089 -9999 0 -0.3 26 26
SOS1 0.035 0.003 -9999 0 -10000 0 0
GRB2 0.034 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.039 0.038 -9999 0 -0.3 3 3
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.11 -10000 0 -0.37 24 24
HDAC1 0.03 0.024 -10000 0 -0.42 1 1
AES 0.034 0.004 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
DTX1 -0.067 0.19 -10000 0 -0.42 82 82
LRP6/FZD1 0.046 0.018 -10000 0 -10000 0 0
TLE1 0.031 0.025 -10000 0 -0.42 1 1
AP1 0.019 0.037 -10000 0 -0.22 6 6
NCSTN 0.032 0.011 -10000 0 -10000 0 0
ADAM10 0.034 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.054 -10000 0 -0.57 2 2
NICD/RBPSUH 0.033 0.11 -10000 0 -0.38 23 23
WIF1 0.022 0.012 -10000 0 -10000 0 0
NOTCH1 0.008 0.11 -10000 0 -0.4 23 23
PSENEN 0.035 0.004 -10000 0 -10000 0 0
KREMEN2 -0.026 0.15 -10000 0 -0.42 49 49
DKK1 -0.023 0.14 -10000 0 -0.42 42 42
beta catenin/beta TrCP1 0.058 0.058 0.31 4 -10000 0 4
APH1B 0.031 0.041 -10000 0 -0.42 3 3
APH1A 0.032 0.011 -10000 0 -10000 0 0
AXIN1 0.012 0.054 0.3 2 -0.32 1 3
CtBP/CBP/TCF1/TLE1/AES 0.017 0.04 -10000 0 -0.21 2 2
PSEN1 0.035 0.006 -10000 0 -10000 0 0
FOS 0.034 0.008 -10000 0 -10000 0 0
JUN 0.032 0.011 -10000 0 -10000 0 0
MAP3K7 0.03 0.01 -10000 0 -10000 0 0
CTNNB1 0.04 0.062 0.29 5 -10000 0 5
MAPK3 0.035 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.019 0.11 -10000 0 -0.25 51 51
HNF1A 0.034 0.006 -10000 0 -10000 0 0
CTBP1 0.033 0.007 -10000 0 -10000 0 0
MYC 0.031 0.019 -10000 0 -10000 0 0
NKD1 0.024 0.058 -10000 0 -0.42 6 6
FZD1 0.032 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.013 0.15 -10000 0 -0.44 26 26
apoptosis 0.019 0.037 -10000 0 -0.23 5 5
Delta 1/NOTCHprecursor 0.029 0.11 -10000 0 -0.37 24 24
DLL1 0.029 0.035 -10000 0 -0.42 2 2
PPARD 0.029 0.041 -10000 0 -0.67 1 1
Gamma Secretase 0.089 0.044 -10000 0 -0.2 2 2
APC -0.001 0.099 0.3 2 -0.45 11 13
DVL1 0.026 0.046 -10000 0 -0.38 3 3
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.016 0.14 -10000 0 -0.27 78 78
LRP6 0.034 0.006 -10000 0 -10000 0 0
CSNK1A1 0.034 0.009 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.026 0.075 -10000 0 -0.77 3 3
WNT1 -0.003 0.12 -10000 0 -0.42 28 28
Axin1/APC/beta catenin 0.045 0.11 0.35 7 -0.42 6 13
DKK2 0.029 0.042 -10000 0 -0.42 3 3
NOTCH1 precursor/DVL1 0.018 0.13 -10000 0 -0.49 12 12
GSK3B 0.034 0.006 -10000 0 -10000 0 0
FRAT1 0.03 0.025 -10000 0 -0.42 1 1
NOTCH/Deltex homolog 1 -0.017 0.15 -10000 0 -0.44 26 26
PPP2R5D 0.027 0.033 0.25 5 -10000 0 5
MAPK1 0.033 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.047 0.079 -10000 0 -0.23 23 23
RBPJ 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.038 0.005 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.036 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.051 0.094 0.28 5 -0.26 13 18
ERC1 0.034 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.07 -10000 0 -0.3 15 15
NFKBIA 0.023 0.028 0.22 7 -10000 0 7
BIRC2 0.029 0.042 -10000 0 -0.42 3 3
IKBKB 0.034 0.007 -10000 0 -10000 0 0
RIPK2 0.032 0.011 -10000 0 -10000 0 0
IKBKG 0.033 0.067 -10000 0 -0.39 4 4
IKK complex/A20 0.015 0.15 -10000 0 -0.38 27 27
NEMO/A20/RIP2 0.032 0.011 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.039 0.1 -10000 0 -0.34 18 18
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.047 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.1 -10000 0 -0.32 18 18
BCL10/MALT1/TRAF6 0.066 0.024 -10000 0 -0.25 1 1
NOD2 0.01 0.1 -10000 0 -0.42 19 19
NFKB1 0.037 0.006 -10000 0 -10000 0 0
RELA 0.036 0.008 -10000 0 -10000 0 0
MALT1 0.033 0.024 -10000 0 -0.42 1 1
cIAP1/UbcH5C 0.044 0.035 -10000 0 -0.3 3 3
ATM 0.032 0.011 -10000 0 -10000 0 0
TNF/TNFR1A -0.019 0.13 -10000 0 -0.3 68 68
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
UBE2D3 0.034 0.006 -10000 0 -10000 0 0
TNF -0.054 0.18 -10000 0 -0.42 69 69
NF kappa B1 p50/RelA 0.073 0.027 -10000 0 -10000 0 0
BCL10 0.035 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.028 0.22 7 -10000 0 7
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
IKK complex 0.048 0.11 0.26 1 -0.34 18 19
CYLD 0.034 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.055 0.11 -10000 0 -0.33 17 17
Noncanonical Wnt signaling pathway

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
NFATC2 0.003 0.11 -10000 0 -0.42 23 23
GNB1/GNG2 0.044 0.085 -10000 0 -0.27 13 13
mol:DAG 0.02 0.072 0.19 4 -0.28 8 12
PLCG1 0.02 0.073 0.19 3 -0.29 8 11
YES1 0.003 0.063 -10000 0 -0.23 19 19
FZD3 0.033 0.009 -10000 0 -10000 0 0
FZD6 0.014 0.087 -10000 0 -0.42 14 14
G protein 0.052 0.089 0.28 4 -0.31 7 11
MAP3K7 0.003 0.059 0.25 1 -0.29 5 6
mol:Ca2+ 0.02 0.07 0.19 4 -0.28 8 12
mol:IP3 0.02 0.072 0.19 4 -0.28 8 12
NLK -0.001 0.13 -10000 0 -0.75 10 10
GNB1 0.034 0.007 -10000 0 -10000 0 0
CAMK2A 0.008 0.066 0.26 1 -0.28 7 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.007 0.064 -10000 0 -0.25 19 19
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
GNAS 0.004 0.06 -10000 0 -0.25 13 13
GO:0007205 0.012 0.071 0.26 2 -0.31 6 8
WNT6 0.033 0.008 -10000 0 -10000 0 0
WNT4 0.021 0.017 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.093 0.29 5 -0.31 8 13
GNG2 0.027 0.058 -10000 0 -0.42 6 6
WNT5A 0.024 0.066 -10000 0 -0.42 8 8
WNT11 0.023 0.017 -10000 0 -10000 0 0
CDC42 0.004 0.064 0.2 3 -0.26 10 13
TCGA08_retinoblastoma

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
CDKN2B 0.021 0.022 -10000 0 -10000 0 0
CDKN2C 0.025 0.018 -10000 0 -10000 0 0
CDKN2A 0.01 0.017 -10000 0 -10000 0 0
CCND2 -0.002 0.017 0.1 1 -0.11 2 3
RB1 -0.001 0.019 -10000 0 -0.24 1 1
CDK4 0 0.012 0.12 1 -10000 0 1
CDK6 -0.001 0.018 0.12 1 -0.13 3 4
G1/S progression 0.027 0.067 0.18 59 -0.14 1 60
Aurora B signaling

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
Condensin I complex 0.023 0.049 -10000 0 -0.38 1 1
STMN1 0.017 0.024 -10000 0 -0.29 2 2
Aurora B/RasGAP/Survivin 0.061 0.035 -10000 0 -0.25 2 2
Chromosomal passenger complex/Cul3 protein complex 0.002 0.069 -10000 0 -0.26 13 13
BIRC5 0.035 0.008 -10000 0 -10000 0 0
DES -0.058 0.24 -10000 0 -0.61 55 55
Aurora C/Aurora B/INCENP 0.003 0.12 -10000 0 -0.22 74 74
Aurora B/TACC1 0.042 0.021 -10000 0 -0.24 1 1
Aurora B/PP2A 0.043 0.027 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.013 0.009 -10000 0 -0.13 1 1
mitotic metaphase/anaphase transition 0 0.003 -10000 0 -10000 0 0
NDC80 0.015 0.034 -10000 0 -0.3 4 4
Cul3 protein complex 0.038 0.059 -10000 0 -0.24 10 10
KIF2C 0.022 0.023 -10000 0 -10000 0 0
PEBP1 0.035 0.006 -10000 0 -10000 0 0
KIF20A 0.033 0.025 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.046 0.03 -10000 0 -0.29 2 2
SEPT1 -0.096 0.2 -10000 0 -0.42 106 106
SMC2 0.032 0.025 -10000 0 -0.42 1 1
SMC4 0.034 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.002 0.15 0.26 1 -0.52 27 28
PSMA3 0.035 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -10000 0 -10000 0 0
H3F3B 0.018 0.017 -10000 0 -0.28 1 1
AURKB 0.033 0.026 -10000 0 -0.42 1 1
AURKC -0.056 0.18 -10000 0 -0.42 73 73
CDCA8 0.036 0.005 -10000 0 -10000 0 0
cytokinesis 0.03 0.056 0.2 2 -0.28 7 9
Aurora B/Septin1 -0.007 0.14 0.31 1 -0.34 23 24
AURKA 0.033 0.01 -10000 0 -10000 0 0
INCENP 0.036 0.006 -10000 0 -10000 0 0
KLHL13 0.017 0.074 -10000 0 -0.42 10 10
BUB1 0.036 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.06 0.027 -10000 0 -0.23 1 1
EVI5 0.035 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.064 0.062 -10000 0 -0.22 7 7
SGOL1 0.035 0.005 -10000 0 -10000 0 0
CENPA 0.021 0.062 -10000 0 -0.24 11 11
NCAPG 0.032 0.034 -10000 0 -0.42 2 2
Aurora B/HC8 Proteasome 0.048 0.023 -10000 0 -0.29 1 1
NCAPD2 0.034 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.048 0.023 -10000 0 -0.29 1 1
RHOA 0.035 0.005 -10000 0 -10000 0 0
NCAPH 0.034 0.024 -10000 0 -0.42 1 1
NPM1 -0.011 0.13 -10000 0 -0.38 28 28
RASA1 0.032 0.025 -10000 0 -0.42 1 1
KLHL9 0.029 0.014 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -10000 0 -0.29 1 1
PPP1CC 0.034 0.006 -10000 0 -10000 0 0
Centraspindlin 0.054 0.062 -10000 0 -0.23 7 7
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
NSUN2 -0.008 0.14 -10000 0 -0.42 24 24
MYLK 0.016 0.032 -10000 0 -0.28 4 4
KIF23 0.035 0.024 -10000 0 -0.42 1 1
VIM 0.017 0.018 -10000 0 -0.29 1 1
RACGAP1 0.036 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.001 0.093 -10000 0 -0.3 26 26
Chromosomal passenger complex 0.021 0.049 -10000 0 -0.21 9 9
Chromosomal passenger complex/EVI5 0.089 0.045 -10000 0 -0.23 1 1
TACC1 0.034 0.008 -10000 0 -10000 0 0
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
CUL3 0.035 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.006 -10000 0 -10000 0 0
VLDLR 0.021 0.067 -10000 0 -0.42 8 8
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
NUDC 0.035 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.043 0.038 -10000 0 -10000 0 0
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
KATNA1 0.031 0.012 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.032 0.057 0.19 40 -10000 0 40
IQGAP1/CaM 0.049 0.013 -10000 0 -10000 0 0
DAB1 0.021 0.012 -10000 0 -10000 0 0
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
PLA2G7 -0.078 0.19 -10000 0 -0.42 89 89
CALM1 0.034 0.006 -10000 0 -10000 0 0
DYNLT1 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.013 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.034 0.006 -10000 0 -10000 0 0
CDK5R1 0.033 0.024 -10000 0 -0.42 1 1
LIS1/Poliovirus Protein 3A 0.013 0.005 -10000 0 -10000 0 0
CDK5R2 0.025 0.015 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.024 0.054 -10000 0 -0.25 7 7
YWHAE 0.033 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.057 0.085 0.32 27 -10000 0 27
MAP1B 0.007 0.005 -10000 0 -10000 0 0
RAC1 0.016 0.009 -10000 0 -10000 0 0
p35/CDK5 0.028 0.033 0.19 10 -0.21 1 11
RELN 0.024 0.016 -10000 0 -10000 0 0
PAFAH/LIS1 -0.032 0.12 -10000 0 -0.24 84 84
LIS1/CLIP170 0.036 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.038 0.037 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.003 0.072 -10000 0 -0.22 23 23
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.027 0.067 0.33 12 -10000 0 12
LIS1/IQGAP1 0.035 0.014 -10000 0 -10000 0 0
RHOA 0.018 0.008 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.032 0.011 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.025 0.035 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.064 0.081 0.32 23 -10000 0 23
LRP8 0.035 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.051 0.081 0.32 23 -10000 0 23
P39/CDK5 0.02 0.035 0.19 9 -10000 0 9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.036 0.014 -10000 0 -10000 0 0
CDK5 0.008 0.033 0.19 11 -10000 0 11
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.031 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.035 0.054 -10000 0 -0.22 7 7
RELN/VLDLR 0.051 0.055 -10000 0 -0.23 7 7
CDC42 0.018 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0 0.037 -10000 0 -0.25 8 8
SNTA1 0.032 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0 0.04 -10000 0 -0.25 9 9
MAPK12 -0.004 0.041 -10000 0 -0.24 10 10
CCND1 0.015 0.041 -10000 0 -0.33 2 2
p38 gamma/SNTA1 0.029 0.063 0.2 23 -0.22 11 34
MAP2K3 0.033 0.009 -10000 0 -10000 0 0
PKN1 0.034 0.024 -10000 0 -0.42 1 1
G2/M transition checkpoint 0 0.05 0.21 7 -0.24 10 17
MAP2K6 0.001 0.033 -10000 0 -0.24 7 7
MAPT 0.007 0.076 0.19 7 -0.29 11 18
MAPK13 0.01 0.046 -10000 0 -0.3 8 8
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.016 -10000 0 -0.29 1 1
Effects of Botulinum toxin

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
STX1A 0.009 0.003 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.027 -10000 0 -0.3 1 1
STXBP1 0.033 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 -0.011 0.096 0.11 2 -0.25 48 50
RAB3GAP2/RIMS1/UNC13B 0.046 0.034 -10000 0 -0.25 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.022 0.012 -10000 0 -10000 0 0
mol:ACh 0.006 0.031 0.088 31 -0.11 1 32
RAB3GAP2 0.032 0.011 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.039 0.041 -10000 0 -0.19 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.011 0.096 0.11 2 -0.25 48 50
UNC13B 0.03 0.026 -10000 0 -0.42 1 1
CHRNA1 -0.026 0.15 -10000 0 -0.42 48 48
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.022 0.029 -10000 0 -0.17 2 2
SNAP25 0.005 0.004 -10000 0 -10000 0 0
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.027 0.027 -10000 0 -0.42 1 1
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.027 0.014 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.039 0.041 -10000 0 -0.19 1 1
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.035 0.005 -10000 0 -10000 0 0
mol:PIP3 0.007 0.021 -10000 0 -0.18 2 2
FRAP1 0.02 0.065 -10000 0 -0.38 7 7
AKT1 0.021 0.053 0.17 14 -0.19 1 15
INSR 0.035 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.035 0.007 -10000 0 -10000 0 0
mol:GTP 0.053 0.05 0.24 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.027 -10000 0 -0.17 3 3
TSC2 0.035 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.025 0.024 -10000 0 -10000 0 0
TSC1 0.033 0.009 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.027 0.032 -10000 0 -0.19 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.043 0.042 -10000 0 -0.2 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.032 0.01 -10000 0 -10000 0 0
RPS6KB1 0.04 0.068 0.22 5 -0.29 5 10
MAP3K5 -0.015 0.064 -10000 0 -0.18 45 45
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
apoptosis -0.015 0.064 -10000 0 -0.18 45 45
mol:LY294002 0 0 -10000 0 -0.001 5 5
EIF4B 0.037 0.063 0.21 5 -0.26 5 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.053 0.059 0.22 3 -0.25 4 7
eIF4E/eIF4G1/eIF4A1 0.022 0.038 -10000 0 -0.22 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.049 0.032 -10000 0 -0.17 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.041 0.17 8 -10000 0 8
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.048 0.044 0.22 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 5 5
FKBP12/Rapamycin 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.004 0.027 0.16 5 -0.19 1 6
EIF4E 0.034 0.006 -10000 0 -10000 0 0
ASK1/PP5C -0.02 0.21 -10000 0 -0.55 46 46
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.048 -10000 0 -10000 0 0
TSC1/TSC2 0.058 0.054 0.26 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 5 -10000 0 5
RPS6 0.031 0.012 -10000 0 -10000 0 0
PPP5C 0.035 0.004 -10000 0 -10000 0 0
EIF4G1 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.007 0.029 -10000 0 -0.2 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.03 0.012 -10000 0 -10000 0 0
PDK2 -0.004 0.027 0.16 5 -0.19 1 6
EIF4EBP1 0.001 0.18 -10000 0 -1 11 11
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
PPP2R5D 0.034 0.079 0.24 8 -0.34 7 15
peptide biosynthetic process 0.017 0.013 0.18 2 -10000 0 2
RHEB 0.031 0.011 -10000 0 -10000 0 0
EIF4A1 0.033 0.009 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 33 -10000 0 33
EEF2 0.017 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 0.018 0.17 -10000 0 -0.96 11 11
Glypican 2 network

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
MDK 0.029 0.042 -9999 0 -0.42 3 3
GPC2 0.025 0.058 -9999 0 -0.42 6 6
GPC2/Midkine 0.036 0.056 -9999 0 -0.3 9 9
neuron projection morphogenesis 0.036 0.056 -9999 0 -0.3 9 9
TCGA08_rtk_signaling

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
PDGFRA 0.028 0.048 -10000 0 -0.42 4 4
HRAS 0.034 0.006 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
AKT 0.061 0.079 0.26 20 -0.19 1 21
FOXO3 0.031 0.012 -10000 0 -10000 0 0
AKT1 0.035 0.006 -10000 0 -10000 0 0
FOXO1 0.034 0.007 -10000 0 -10000 0 0
AKT3 0.031 0.011 -10000 0 -10000 0 0
FOXO4 0.035 0 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
NRAS 0.034 0.008 -10000 0 -10000 0 0
PIK3CG -0.023 0.15 -10000 0 -0.42 44 44
PIK3R3 0.035 0.005 -10000 0 -10000 0 0
PIK3R2 0.035 0.003 -10000 0 -10000 0 0
NF1 0.034 0.007 -10000 0 -10000 0 0
RAS 0.021 0.044 -10000 0 -10000 0 0
ERBB2 0.034 0.006 -10000 0 -10000 0 0
proliferation/survival/translation -0.04 0.078 0.28 7 -0.21 1 8
PI3K 0.039 0.082 0.23 31 -0.22 5 36
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
KRAS 0.034 0.006 -10000 0 -10000 0 0
FOXO 0.082 0.068 0.23 29 -10000 0 29
AKT2 0.035 0.004 -10000 0 -10000 0 0
PTEN 0.031 0.012 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP 0.045 0.053 -10000 0 -0.2 11 11
TC10/GTP 0.043 0.051 -10000 0 -0.19 11 11
Insulin Receptor/Insulin/IRS1/Shp2 0.075 0.029 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
APS homodimer 0.023 0.062 -10000 0 -0.42 7 7
GRB14 0.027 0.013 -10000 0 -10000 0 0
FOXO3 -0.042 0.21 -10000 0 -0.61 45 45
AKT1 0 0.042 0.21 2 -10000 0 2
INSR 0.039 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.074 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.032 0.011 -10000 0 -10000 0 0
SORBS1 0.027 0.048 -10000 0 -0.42 4 4
CRK 0.033 0.009 -10000 0 -10000 0 0
PTPN1 0.01 0.016 -10000 0 -10000 0 0
CAV1 0.02 0.025 0.17 7 -10000 0 7
CBL/APS/CAP/Crk-II/C3G 0.068 0.067 -10000 0 -0.2 11 11
Insulin Receptor/Insulin/IRS1/NCK2 0.076 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.06 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.039 0.044 -10000 0 -0.32 3 3
RPS6KB1 -0.003 0.037 0.19 3 -10000 0 3
PARD6A 0.034 0.007 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.033 -10000 0 -0.56 1 1
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.046 0.032 0.19 2 -10000 0 2
HRAS/GTP -0.002 0.066 -10000 0 -0.19 38 38
Insulin Receptor 0.039 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.079 0.041 -10000 0 -10000 0 0
PRKCI 0.045 0.037 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.037 0.019 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.055 0.04 -10000 0 -0.48 1 1
PI3K 0.073 0.03 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
RHOQ 0.035 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.004 -10000 0 -10000 0 0
AKT2 0 0.041 0.2 3 -10000 0 3
PRKCZ 0.035 0.07 -10000 0 -0.35 4 4
SH2B2 0.023 0.062 -10000 0 -0.42 7 7
SHC/SHIP 0.01 0.082 0.19 3 -0.2 43 46
F2RL2 -0.014 0.14 -10000 0 -0.42 37 37
TRIP10 0.035 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.053 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.047 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.083 0.04 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.058 0.063 -10000 0 -0.22 11 11
TC10/GDP 0.026 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.066 0.036 -10000 0 -10000 0 0
INPP5D -0.016 0.088 0.17 6 -0.21 57 63
SOS1 0.035 0.003 -10000 0 -10000 0 0
SGK1 -0.059 0.22 -10000 0 -0.65 44 44
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
p62DOK/RasGAP 0.055 0.041 -10000 0 -0.48 1 1
INS 0.022 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.015 0.087 0.17 6 -0.21 57 63
GRB2 0.034 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.003 0.037 0.2 1 -10000 0 1
PTPRA 0.037 0.01 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.047 0.007 -10000 0 -10000 0 0
PDPK1 0.035 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.054 0.026 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.045 0.016 -10000 0 -10000 0 0
Par3/Par6 0.044 0.089 -10000 0 -0.21 36 36
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.02 0.067 -9999 0 -0.42 8 8
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.034 0.024 -9999 0 -0.42 1 1
TCEB1 0.032 0.011 -9999 0 -10000 0 0
HIF1A/p53 0.018 0.085 -9999 0 -0.26 28 28
HIF1A 0.003 0.078 -9999 0 -0.27 26 26
COPS5 0.032 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.077 0.049 -9999 0 -0.21 1 1
FIH (dimer) 0.031 0.026 -9999 0 -0.42 1 1
CDKN2A 0.009 0.016 -9999 0 -10000 0 0
ARNT/IPAS 0.032 0.052 -9999 0 -0.3 7 7
HIF1AN 0.031 0.026 -9999 0 -0.42 1 1
GNB2L1 0.034 0.008 -9999 0 -10000 0 0
HIF1A/ARNT 0.013 0.082 -9999 0 -0.26 27 27
CUL2 0.032 0.01 -9999 0 -10000 0 0
OS9 0.034 0.008 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.06 0.031 -9999 0 -0.25 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.02 0.087 -9999 0 -0.26 28 28
PHD1-3/OS9 0.074 0.041 -9999 0 -0.23 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.045 0.085 -9999 0 -0.25 20 20
VHL 0.035 0.005 -9999 0 -10000 0 0
HSP90AA1 0.033 0.024 -9999 0 -0.42 1 1
HIF1A/JAB1 0.019 0.079 -9999 0 -0.26 21 21
EGLN3 0.032 0.034 -9999 0 -0.42 2 2
EGLN2 0.035 0.004 -9999 0 -10000 0 0
EGLN1 0.032 0.011 -9999 0 -10000 0 0
TP53 0.033 0.009 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.04 0.076 -9999 0 -0.6 4 4
ARNT 0.032 0.011 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.032 0.01 -9999 0 -10000 0 0
HIF1A/p19ARF -0.009 0.073 -9999 0 -0.25 28 28
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.027 0.057 0.42 6 -10000 0 6
PI3K Class IB/PDE3B 0.027 0.058 -10000 0 -0.42 6 6
PDE3B 0.027 0.058 -10000 0 -0.42 6 6
PLK1 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
regulation of centriole-centriole cohesion -0.008 0.019 0.13 5 -0.1 1 6
BUB1B 0.013 0.032 0.12 2 -0.18 2 4
PLK1 0.014 0.024 0.079 16 -0.11 2 18
PLK1S1 0.016 0.028 0.094 10 -0.19 4 14
KIF2A 0.013 0.031 0.21 5 -10000 0 5
regulation of mitotic centrosome separation 0.014 0.024 0.079 16 -0.11 2 18
GOLGA2 0.033 0.009 -10000 0 -10000 0 0
Hec1/SPC24 0.05 0.039 0.15 1 -0.2 4 5
WEE1 0.021 0.058 -10000 0 -0.31 9 9
cytokinesis 0.021 0.052 0.17 3 -0.2 10 13
PP2A-alpha B56 0.069 0.086 -10000 0 -0.52 7 7
AURKA 0.016 0.019 0.11 1 -0.17 1 2
PICH/PLK1 0.025 0.026 0.14 1 -0.18 2 3
CENPE 0.007 0.034 -10000 0 -0.19 7 7
RhoA/GTP 0.026 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.013 0.031 0.21 5 -10000 0 5
PPP2CA 0.033 0.008 -10000 0 -10000 0 0
FZR1 0.035 0.005 -10000 0 -10000 0 0
TPX2 0.019 0.023 0.14 1 -0.14 1 2
PAK1 0.033 0.009 -10000 0 -10000 0 0
SPC24 0.034 0.024 -10000 0 -0.42 1 1
FBXW11 0.033 0.008 -10000 0 -10000 0 0
CLSPN 0.016 0.031 -10000 0 -0.24 4 4
GORASP1 0.035 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.013 0.044 16 -0.05 3 19
G2 phase of mitotic cell cycle 0 0.003 0.011 24 -10000 0 24
STAG2 0.035 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.067 -10000 0 -0.53 5 5
spindle elongation 0.014 0.024 0.079 16 -0.11 2 18
ODF2 0.034 0.009 -10000 0 -10000 0 0
BUB1 0.032 0.084 -10000 0 -0.56 7 7
TPT1 0.011 0.035 -10000 0 -0.16 12 12
CDC25C 0.006 0.07 -10000 0 -0.28 20 20
CDC25B 0.035 0.008 -10000 0 -10000 0 0
SGOL1 0.008 0.019 0.1 1 -0.13 5 6
RHOA 0.035 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.049 0.032 -10000 0 -0.16 1 1
CDC14B 0.009 0.003 -10000 0 -10000 0 0
CDC20 0.035 0.004 -10000 0 -10000 0 0
PLK1/PBIP1 0.012 0.028 0.12 1 -0.17 5 6
mitosis -0.002 0.003 0.021 2 -10000 0 2
FBXO5 0.005 0.034 0.093 2 -0.1 12 14
CDC2 0.002 0.002 -10000 0 -0.009 6 6
NDC80 0.03 0.041 -10000 0 -0.42 3 3
metaphase plate congression 0.019 0.023 0.12 1 -0.23 2 3
ERCC6L 0.028 0.034 -10000 0 -0.17 3 3
NLP/gamma Tubulin 0.009 0.016 0.082 1 -0.074 4 5
microtubule cytoskeleton organization 0.011 0.035 -10000 0 -0.16 12 12
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 8 -10000 0 8
PPP1R12A 0.035 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 8 -10000 0 8
PLK1/PRC1-2 0.05 0.032 0.15 1 -0.22 1 2
GRASP65/GM130/RAB1/GTP/PLK1 0.066 0.027 -10000 0 -10000 0 0
RAB1A 0.035 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.012 0.023 0.081 16 -0.09 1 17
mitotic prometaphase -0.001 0.002 0.018 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.052 -10000 0 -0.51 3 3
microtubule-based process 0.033 0.027 0.14 1 -0.23 1 2
Golgi organization 0.014 0.024 0.079 16 -0.11 2 18
Cohesin/SA2 0.03 0.023 -10000 0 -0.12 1 1
PPP1CB/MYPT1 0.05 0.011 -10000 0 -10000 0 0
KIF20A 0.032 0.025 -10000 0 -0.42 1 1
APC/C/CDC20 0.034 0.026 0.14 1 -0.12 1 2
PPP2R1A 0.035 0.005 -10000 0 -10000 0 0
chromosome segregation 0.012 0.027 0.11 1 -0.17 5 6
PRC1 0.034 0.006 -10000 0 -10000 0 0
ECT2 0.012 0.029 0.2 4 -0.12 1 5
C13orf34 0.012 0.022 0.073 16 -0.11 1 17
NUDC 0.019 0.023 0.12 1 -0.23 2 3
regulation of attachment of spindle microtubules to kinetochore 0.012 0.032 0.12 2 -0.18 2 4
spindle assembly 0.011 0.02 0.076 7 -0.09 2 9
spindle stabilization 0.016 0.028 0.1 1 -0.19 4 5
APC/C/HCDH1 0.031 0.009 -10000 0 -10000 0 0
MKLP2/PLK1 0.033 0.027 0.14 1 -0.23 1 2
CCNB1 0.035 0.007 -10000 0 -10000 0 0
PPP1CB 0.035 0.005 -10000 0 -10000 0 0
BTRC 0.032 0.01 -10000 0 -10000 0 0
ROCK2 0.023 0.038 -10000 0 -0.25 4 4
TUBG1 0.012 0.029 -10000 0 -0.16 8 8
G2/M transition of mitotic cell cycle 0.015 0.023 -10000 0 -0.15 1 1
MLF1IP 0.006 0.032 -10000 0 -0.3 4 4
INCENP 0.035 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.058 0.08 -10000 0 -0.48 6 6
oxygen homeostasis 0.009 0.008 -10000 0 -10000 0 0
TCEB2 0.034 0.024 -10000 0 -0.42 1 1
TCEB1 0.032 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.07 -10000 0 -10000 0 0
EPO 0.11 0.1 -10000 0 -10000 0 0
FIH (dimer) 0.038 0.029 -10000 0 -0.41 1 1
APEX1 0.043 0.017 -10000 0 -10000 0 0
SERPINE1 0.12 0.11 0.38 5 -0.37 1 6
FLT1 0.026 0.16 -10000 0 -0.53 20 20
ADORA2A 0.11 0.13 0.36 17 -0.41 9 26
germ cell development 0.11 0.11 0.37 7 -0.36 1 8
SLC11A2 0.13 0.11 0.37 12 -0.37 1 13
BHLHE40 0.14 0.11 0.38 11 -0.37 1 12
HIF1AN 0.038 0.028 -10000 0 -0.41 1 1
HIF2A/ARNT/SIRT1 0.11 0.087 0.33 1 -10000 0 1
ETS1 0.044 0.016 -10000 0 -10000 0 0
CITED2 0.011 0.16 -10000 0 -0.52 18 18
KDR 0.023 0.16 -10000 0 -0.56 13 13
PGK1 0.13 0.11 0.37 12 -0.37 1 13
SIRT1 0.033 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.17 0.13 -10000 0 -0.41 1 1
EPAS1 0.068 0.059 0.21 15 -10000 0 15
SP1 0.041 0.006 -10000 0 -10000 0 0
ABCG2 0.12 0.15 0.38 9 -0.41 18 27
EFNA1 0.12 0.1 -10000 0 -0.37 1 1
FXN 0.12 0.11 0.37 17 -0.36 1 18
POU5F1 0.12 0.11 0.37 7 -0.37 1 8
neuron apoptosis -0.16 0.13 0.4 1 -10000 0 1
EP300 0.032 0.011 -10000 0 -10000 0 0
EGLN3 0.04 0.036 -10000 0 -0.41 2 2
EGLN2 0.043 0.013 -10000 0 -10000 0 0
EGLN1 0.04 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.062 0.029 -10000 0 -0.25 1 1
VHL 0.035 0.005 -10000 0 -10000 0 0
ARNT 0.041 0.017 -10000 0 -10000 0 0
SLC2A1 0.12 0.11 0.37 16 -0.36 1 17
TWIST1 0.086 0.1 0.37 6 -0.36 1 7
ELK1 0.042 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.093 -10000 0 -10000 0 0
VEGFA 0.12 0.11 0.38 6 -0.37 1 7
CREBBP 0.035 0.004 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.015 0.039 -10000 0 -10000 0 0
PLK1 -0.026 0.19 -10000 0 -0.75 4 4
CDKN1B 0.094 0.14 0.34 3 -0.34 18 21
FOXO3 -0.024 0.21 -10000 0 -0.51 30 30
KAT2B 0.018 0.049 -10000 0 -0.41 2 2
FOXO1/SIRT1 0.055 0.045 0.25 1 -10000 0 1
CAT -0.025 0.19 -10000 0 -0.75 4 4
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.023 0.038 -10000 0 -10000 0 0
FOXO1 0.024 0.042 0.24 2 -10000 0 2
MAPK10 0.036 0.045 0.19 25 -10000 0 25
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.067 0.064 0.3 1 -10000 0 1
response to oxidative stress 0.002 0.019 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.072 0.15 -10000 0 -0.52 7 7
XPO1 0.036 0.002 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 -10000 0 0
BCL2L11 0.015 0.1 -10000 0 -1.2 2 2
FOXO1/SKP2 0.039 0.036 -10000 0 -10000 0 0
mol:GDP 0.002 0.019 -10000 0 -10000 0 0
RAN 0.036 0.006 -10000 0 -10000 0 0
GADD45A 0.079 0.13 -10000 0 -0.58 3 3
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.06 0.082 0.26 1 -0.31 6 7
MST1 0.02 0.044 -10000 0 -0.43 1 1
CSNK1D 0.034 0.008 -10000 0 -10000 0 0
CSNK1E 0.033 0.01 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.065 -10000 0 -0.34 4 4
YWHAB 0.033 0.01 -10000 0 -10000 0 0
MAPK8 0.044 0.049 0.2 33 -10000 0 33
MAPK9 0.045 0.049 0.2 34 -10000 0 34
YWHAG 0.033 0.01 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
SIRT1 0.047 0.033 -10000 0 -10000 0 0
SOD2 0.05 0.16 -10000 0 -0.56 12 12
RBL2 -0.006 0.21 -10000 0 -0.75 16 16
RAL/GDP 0.048 0.021 -10000 0 -10000 0 0
CHUK 0.022 0.035 -10000 0 -10000 0 0
Ran/GTP 0.029 0.005 -10000 0 -10000 0 0
CSNK1G2 0.035 0.005 -10000 0 -10000 0 0
RAL/GTP 0.052 0.022 -10000 0 -10000 0 0
CSNK1G1 0.035 0.004 -10000 0 -10000 0 0
FASLG -0.41 0.66 -10000 0 -1.4 119 119
SKP2 0.033 0.009 -10000 0 -10000 0 0
USP7 0.036 0.004 -10000 0 -10000 0 0
IKBKB 0.021 0.037 -10000 0 -10000 0 0
CCNB1 -0.024 0.19 -10000 0 -0.59 10 10
FOXO1-3a-4/beta catenin 0.06 0.14 -10000 0 -0.35 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.036 -10000 0 -10000 0 0
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
SGK1 0.021 0.036 -10000 0 -10000 0 0
CSNK1G3 0.033 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.052 0.009 -10000 0 -10000 0 0
ZFAND5 0.065 0.058 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
CDK2 0.035 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.035 0.076 -10000 0 -0.35 5 5
CREBBP 0.035 0.004 -10000 0 -10000 0 0
FBXO32 -0.008 0.2 -10000 0 -0.7 8 8
BCL6 0.008 0.18 -10000 0 -0.68 9 9
RALB 0.036 0.003 -10000 0 -10000 0 0
RALA 0.032 0.012 -10000 0 -10000 0 0
YWHAH 0.034 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.02 0.093 -10000 0 -0.76 4 4
MKNK1 0.035 0.005 -10000 0 -10000 0 0
MAPK14 0.037 0.047 -10000 0 -0.33 4 4
ATF2/c-Jun 0.032 0.042 -10000 0 -0.25 4 4
MAPK11 0.038 0.046 -10000 0 -0.33 4 4
MITF 0.018 0.074 -10000 0 -0.3 17 17
MAPKAPK5 0.03 0.048 -10000 0 -0.37 4 4
KRT8 -0.005 0.11 -10000 0 -0.29 43 43
MAPKAPK3 0.035 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.031 0.011 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.047 0.07 -10000 0 -0.51 4 4
CEBPB 0.028 0.048 -10000 0 -0.37 4 4
SLC9A1 0.03 0.048 -10000 0 -0.37 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.034 0.05 0.22 1 -0.36 4 5
p38alpha-beta/MNK1 0.061 0.064 -10000 0 -0.42 4 4
JUN 0.033 0.045 -10000 0 -0.25 4 4
PPARGC1A 0.013 0.068 -10000 0 -0.3 14 14
USF1 0.028 0.046 -10000 0 -0.35 4 4
RAB5/GDP/GDI1 0.042 0.042 -10000 0 -0.28 3 3
NOS2 0.027 0.072 -10000 0 -0.74 2 2
DDIT3 0.03 0.048 -10000 0 -0.37 4 4
RAB5A 0.035 0.005 -10000 0 -10000 0 0
HSPB1 0.029 0.067 0.29 16 -0.3 4 20
p38alpha-beta/HBP1 0.057 0.065 -10000 0 -0.41 4 4
CREB1 0.032 0.051 -10000 0 -0.36 4 4
RAB5/GDP 0.026 0.003 -10000 0 -10000 0 0
EIF4E 0.038 0.069 0.25 3 -0.37 4 7
RPS6KA4 0.031 0.044 -10000 0 -0.38 3 3
PLA2G4A 0.03 0.063 0.25 1 -0.29 6 7
GDI1 0.032 0.044 -10000 0 -0.38 3 3
TP53 0.016 0.06 -10000 0 -0.5 4 4
RPS6KA5 0.028 0.053 -10000 0 -0.33 6 6
ESR1 0.021 0.072 -10000 0 -0.37 10 10
HBP1 0.032 0.011 -10000 0 -10000 0 0
MEF2C 0.028 0.05 -10000 0 -0.34 5 5
MEF2A 0.03 0.048 -10000 0 -0.37 4 4
EIF4EBP1 0.03 0.056 -10000 0 -0.41 4 4
KRT19 0.024 0.05 -10000 0 -0.35 5 5
ELK4 0.028 0.046 -10000 0 -0.35 4 4
ATF6 0.029 0.046 -10000 0 -0.35 4 4
ATF1 0.032 0.051 -10000 0 -0.36 4 4
p38alpha-beta/MAPKAPK2 0.057 0.061 -10000 0 -0.37 4 4
p38alpha-beta/MAPKAPK3 0.061 0.064 -10000 0 -0.41 4 4
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.007 0.064 -9999 0 -0.25 19 19
FZD6 0.014 0.087 -9999 0 -0.42 14 14
WNT6 0.033 0.008 -9999 0 -10000 0 0
WNT4 0.021 0.017 -9999 0 -10000 0 0
FZD3 0.033 0.009 -9999 0 -10000 0 0
WNT5A 0.024 0.066 -9999 0 -0.42 8 8
WNT11 0.023 0.017 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.015 0.13 -10000 0 -0.9 3 3
RAD9A 0.034 0.007 -10000 0 -10000 0 0
AP1 0.045 0.024 -10000 0 -10000 0 0
IFNAR2 0.036 0.008 -10000 0 -10000 0 0
AKT1 0.02 0.027 -10000 0 -0.16 6 6
ER alpha/Oestrogen 0.018 0.041 -10000 0 -0.29 6 6
NFX1/SIN3/HDAC complex 0.042 0.036 -10000 0 -0.23 1 1
EGF 0.002 0.11 -10000 0 -0.42 25 25
SMG5 0.032 0.01 -10000 0 -10000 0 0
SMG6 0.033 0.009 -10000 0 -10000 0 0
SP3/HDAC2 0.049 0.019 -10000 0 -10000 0 0
TERT/c-Abl 0.027 0.13 -10000 0 -0.83 3 3
SAP18 0.034 0.008 -10000 0 -10000 0 0
MRN complex 0.056 0.037 -10000 0 -0.25 2 2
WT1 0.016 0.012 -10000 0 -10000 0 0
WRN 0.034 0.008 -10000 0 -10000 0 0
SP1 0.037 0.008 -10000 0 -10000 0 0
SP3 0.036 0.004 -10000 0 -10000 0 0
TERF2IP 0.034 0.007 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.052 0.12 -10000 0 -0.67 3 3
Mad/Max 0.053 0.011 -10000 0 -10000 0 0
TERT 0.014 0.13 -10000 0 -0.94 3 3
CCND1 0.026 0.12 -10000 0 -0.7 3 3
MAX 0.035 0.006 -10000 0 -10000 0 0
RBBP7 0.036 0.003 -10000 0 -10000 0 0
RBBP4 0.035 0.005 -10000 0 -10000 0 0
TERF2 0.033 0.016 -10000 0 -10000 0 0
PTGES3 0.034 0.006 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
Telomerase/911 0.052 0.058 -10000 0 -0.28 1 1
CDKN1B -0.075 0.14 -10000 0 -0.26 129 129
RAD1 0.033 0.009 -10000 0 -10000 0 0
XRCC5 0.035 0.004 -10000 0 -10000 0 0
XRCC6 0.032 0.01 -10000 0 -10000 0 0
SAP30 0.035 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.051 0.016 -10000 0 -10000 0 0
UBE3A 0.035 0.007 -10000 0 -10000 0 0
JUN 0.032 0.012 -10000 0 -10000 0 0
E6 0.001 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.027 0.006 -10000 0 -10000 0 0
FOS 0.034 0.009 -10000 0 -10000 0 0
IFN-gamma/IRF1 -0.08 0.18 -10000 0 -0.31 135 135
PARP2 0.035 0.006 -10000 0 -10000 0 0
BLM 0.034 0.007 -10000 0 -10000 0 0
Telomerase 0.056 0.07 -10000 0 -0.33 4 4
IRF1 -0.002 0.13 -10000 0 -0.41 32 32
ESR1 0.024 0.058 -10000 0 -0.42 6 6
KU/TER 0.047 0.016 -10000 0 -10000 0 0
ATM/TRF2 0.047 0.017 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.047 0.042 0.18 2 -0.28 1 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.048 0.041 0.19 2 -0.29 1 3
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC2 0.033 0.013 -10000 0 -10000 0 0
ATM 0.013 0.009 -10000 0 -10000 0 0
SMAD3 0.017 0.023 -10000 0 -0.3 2 2
ABL1 0.033 0.009 -10000 0 -10000 0 0
MXD1 0.036 0.004 -10000 0 -10000 0 0
MRE11A 0.032 0.01 -10000 0 -10000 0 0
HUS1 0.031 0.011 -10000 0 -10000 0 0
RPS6KB1 0.034 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.053 0.13 -10000 0 -1 2 2
NR2F2 0.033 0.007 -10000 0 -10000 0 0
MAPK3 0.01 0.012 -10000 0 -10000 0 0
MAPK1 0.01 0.012 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.034 -10000 0 -0.42 2 2
NFKB1 0.034 0.006 -10000 0 -10000 0 0
HNRNPC 0.035 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.009 -10000 0 -10000 0 0
NBN 0.032 0.011 -10000 0 -10000 0 0
EGFR 0.027 0.036 -10000 0 -0.42 2 2
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.016 0.09 -10000 0 -0.3 26 26
MYC 0.032 0.012 -10000 0 -10000 0 0
IL2 0.022 0.016 -10000 0 -10000 0 0
KU 0.047 0.016 -10000 0 -10000 0 0
RAD50 0.031 0.034 -10000 0 -0.42 2 2
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
TGFB1 0.032 0.034 -10000 0 -0.42 2 2
TRF2/BLM 0.05 0.018 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.043 0.13 -10000 0 -0.84 3 3
SP1/HDAC2 0.05 0.02 -10000 0 -10000 0 0
PINX1 0.033 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.052 0.12 -10000 0 -0.67 3 3
Smad3/Myc 0.034 0.014 -10000 0 -10000 0 0
911 complex 0.058 0.029 -10000 0 -10000 0 0
IFNG -0.11 0.21 -10000 0 -0.41 119 119
Telomerase/PinX1 0.05 0.12 -10000 0 -0.67 3 3
Telomerase/AKT1/mTOR/p70S6K 0.027 0.089 -10000 0 -0.4 9 9
SIN3B 0.035 0.003 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
Telomerase/EST1B 0.048 0.12 -10000 0 -0.67 3 3
response to DNA damage stimulus -0.003 0.031 -10000 0 -0.1 30 30
MRN complex/TRF2/Rap1 0.077 0.048 -10000 0 -0.22 2 2
TRF2/WRN 0.049 0.018 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.12 -10000 0 -0.67 3 3
E2F1 0.034 0.011 -10000 0 -10000 0 0
ZNFX1 0.033 0.01 -10000 0 -10000 0 0
PIF1 0.031 0.041 -10000 0 -0.42 3 3
NCL 0.035 0.005 -10000 0 -10000 0 0
DKC1 0.035 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.017 0.033 -10000 0 -0.18 6 6
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
S1P/S1P3/G12/G13 0.054 0.038 -10000 0 -0.22 3 3
AKT1 0.026 0.089 -10000 0 -0.4 14 14
AKT3 0.041 0.044 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.01 -10000 0 -10000 0 0
GNAI2 0.036 0.005 -10000 0 -10000 0 0
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 0.032 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.031 0.042 -10000 0 -0.42 3 3
S1PR2 0.035 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.047 -10000 0 -0.23 6 6
MAPK3 0.027 0.045 -10000 0 -0.24 4 4
MAPK1 0.023 0.043 -10000 0 -0.24 4 4
JAK2 0.021 0.084 0.23 1 -0.34 11 12
CXCR4 0.017 0.069 -10000 0 -0.3 9 9
FLT1 0.036 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
SRC 0.025 0.042 -10000 0 -0.26 3 3
S1P/S1P3/Gi 0.029 0.047 -10000 0 -0.23 6 6
RAC1 0.031 0.012 -10000 0 -10000 0 0
RhoA/GTP 0.042 0.059 -10000 0 -0.23 4 4
VEGFA 0.032 0.014 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.029 0.037 -10000 0 -0.18 3 3
VEGFR1 homodimer/VEGFA homodimer 0.049 0.024 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.013 0.11 -10000 0 -0.24 63 63
GNAQ 0.033 0.009 -10000 0 -10000 0 0
GNAZ 0.028 0.036 -10000 0 -0.42 2 2
G12/G13 0.045 0.018 -10000 0 -10000 0 0
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.056 -10000 0 -0.22 5 5
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.017 -10000 0 -0.3 1 1
SMARCC1 0.02 0.012 -10000 0 -10000 0 0
REL 0.035 0.003 -10000 0 -10000 0 0
HDAC7 0.026 0.07 0.22 1 -10000 0 1
JUN 0.032 0.011 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
KAT5 0.034 0.007 -10000 0 -10000 0 0
MAPK14 0.012 0.042 -10000 0 -0.3 6 6
FOXO1 0.034 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.055 0.08 -10000 0 -10000 0 0
MAP2K6 0.027 0.058 -10000 0 -0.42 6 6
BRM/BAF57 0.045 0.019 -10000 0 -10000 0 0
MAP2K4 0.033 0.011 -10000 0 -10000 0 0
SMARCA2 0.031 0.012 -10000 0 -10000 0 0
PDE9A 0.013 0.12 -10000 0 -0.68 8 8
NCOA2 0.032 0.011 -10000 0 -10000 0 0
CEBPA -0.004 0.13 -10000 0 -0.42 31 31
EHMT2 0.032 0.011 -10000 0 -10000 0 0
cell proliferation 0.054 0.13 0.34 27 -0.3 6 33
NR0B1 0.018 0.001 -10000 0 -10000 0 0
EGR1 0.031 0.012 -10000 0 -10000 0 0
RXRs/9cRA 0.003 0.11 -10000 0 -0.22 62 62
AR/RACK1/Src 0.043 0.076 0.26 6 -0.22 4 10
AR/GR 0.033 0.051 -10000 0 -0.23 1 1
GNB2L1 0.034 0.008 -10000 0 -10000 0 0
PKN1 0.034 0.024 -10000 0 -0.42 1 1
RCHY1 0.035 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.017 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.047 0.061 0.24 1 -0.22 4 5
SRC 0.019 0.073 0.19 52 -0.21 4 56
NR3C1 0.033 0.009 -10000 0 -10000 0 0
KLK3 -0.003 0.044 -10000 0 -10000 0 0
APPBP2 0.033 0.014 -10000 0 -10000 0 0
TRIM24 0.031 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.035 0.066 0.21 3 -0.23 6 9
TMPRSS2 -0.014 0.22 -10000 0 -0.95 17 17
RXRG -0.057 0.18 -10000 0 -0.42 72 72
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.033 0.009 -10000 0 -10000 0 0
RXRB 0.032 0.011 -10000 0 -10000 0 0
CARM1 0.035 0.003 -10000 0 -10000 0 0
NR2C2 0.035 0.006 -10000 0 -10000 0 0
KLK2 0.033 0.059 0.28 1 -10000 0 1
AR 0.015 0.04 0.17 3 -0.17 2 5
SENP1 0.034 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
MDM2 0.034 0.008 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.034 0.008 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.012 0.016 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.046 0.078 0.27 6 -0.22 5 11
positive regulation of transcription 0.033 0.008 -10000 0 -10000 0 0
DNAJA1 0.03 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.013 -10000 0 -0.17 1 1
NCOA1 0.039 0.012 -10000 0 -10000 0 0
SPDEF 0.024 0.015 -10000 0 -10000 0 0
T-DHT/AR/TIF2 0.04 0.075 0.24 16 -0.26 4 20
T-DHT/AR/Hsp90 0.037 0.068 0.21 4 -0.22 7 11
GSK3B 0.035 0.007 -10000 0 -10000 0 0
NR2C1 0.034 0.006 -10000 0 -10000 0 0
mol:T-DHT 0 0.04 0.22 6 -0.22 4 10
SIRT1 0.032 0.01 -10000 0 -10000 0 0
ZMIZ2 0.031 0.011 -10000 0 -10000 0 0
POU2F1 0.034 0.034 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.022 0.064 0.22 1 -0.23 6 7
CREBBP 0.035 0.004 -10000 0 -10000 0 0
SMARCE1 0.034 0.006 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.032 0.012 -10000 0 -10000 0 0
HSPA8 0.032 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.065 0.065 -10000 0 -0.27 5 5
AKT1 0.035 0.016 -10000 0 -10000 0 0
GSC 0.008 0.065 -10000 0 -10000 0 0
NKX2-5 0.001 0.005 -10000 0 -10000 0 0
muscle cell differentiation -0.063 0.06 0.51 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.12 0.054 -10000 0 -10000 0 0
SMAD4 0.043 0.034 -10000 0 -10000 0 0
CBFB 0.034 0.007 -10000 0 -10000 0 0
SAP18 0.034 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.068 -10000 0 -0.25 15 15
SMAD3/SMAD4/VDR 0.1 0.059 -10000 0 -0.22 2 2
MYC 0.03 0.013 -10000 0 -10000 0 0
CDKN2B -0.11 0.25 -10000 0 -0.72 22 22
AP1 0.061 0.039 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.041 0.066 -10000 0 -0.36 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.031 0.047 -10000 0 -0.32 5 5
SP3 0.037 0.002 -10000 0 -10000 0 0
CREB1 0.035 0.003 -10000 0 -10000 0 0
FOXH1 0.031 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.075 0.047 -10000 0 -10000 0 0
GATA3 -0.052 0.18 -10000 0 -0.44 64 64
SKI/SIN3/HDAC complex/NCoR1 0.028 0.056 -10000 0 -0.37 3 3
MEF2C/TIF2 0.05 0.052 0.36 2 -0.38 2 4
endothelial cell migration -0.02 0.085 1.3 1 -10000 0 1
MAX 0.033 0.006 -10000 0 -10000 0 0
RBBP7 0.035 0.003 -10000 0 -10000 0 0
RBBP4 0.035 0.005 -10000 0 -10000 0 0
RUNX2 0.029 0.035 -10000 0 -0.42 2 2
RUNX3 0.005 0.11 -10000 0 -0.42 24 24
RUNX1 0.031 0.041 -10000 0 -0.42 3 3
CTBP1 0.034 0.008 -10000 0 -10000 0 0
NR3C1 0.032 0.009 -10000 0 -10000 0 0
VDR 0.032 0.034 -10000 0 -0.42 2 2
CDKN1A 0.037 0.046 -10000 0 -0.54 1 1
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.073 0.043 -10000 0 -10000 0 0
DCP1A 0.034 0.006 -10000 0 -10000 0 0
SKI 0.034 0.007 -10000 0 -10000 0 0
SERPINE1 0.02 0.086 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.079 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.071 0.049 -10000 0 -10000 0 0
SAP30 0.035 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.058 0.03 -10000 0 -10000 0 0
JUN 0.04 0.034 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.077 0.06 -10000 0 -0.27 4 4
TFE3 0.041 0.007 -10000 0 -10000 0 0
COL1A2 0.025 0.025 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.07 0.055 0.29 2 -10000 0 2
DLX1 0.008 0.1 -10000 0 -0.42 19 19
TCF3 0.035 0.005 -10000 0 -10000 0 0
FOS 0.04 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.076 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.064 0.024 -10000 0 -10000 0 0
ZBTB17 0.034 0.006 -10000 0 -10000 0 0
LAMC1 0.039 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.074 0.049 -10000 0 -10000 0 0
IRF7 0.03 0.047 -10000 0 -0.42 4 4
ESR1 0.023 0.058 -10000 0 -0.42 6 6
HNF4A 0.022 0.013 -10000 0 -10000 0 0
MEF2C 0.052 0.076 0.28 14 -0.4 2 16
SMAD2-3/SMAD4 0.086 0.048 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.063 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.013 0.045 -10000 0 -0.43 3 3
TGIF2/HDAC complex 0.033 0.009 -10000 0 -10000 0 0
CREBBP 0.035 0.006 -10000 0 -10000 0 0
SKIL 0.034 0.006 -10000 0 -10000 0 0
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC2 0.031 0.012 -10000 0 -10000 0 0
SNIP1 0.035 0.004 -10000 0 -10000 0 0
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.094 0.045 -10000 0 -10000 0 0
MSG1/HSC70 0.029 0.072 -10000 0 -0.29 16 16
SMAD2 0.037 0.016 -10000 0 -10000 0 0
SMAD3 0.041 0.032 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.036 0.044 -10000 0 -0.26 3 3
SMAD2/SMAD2/SMAD4 0.023 0.046 0.2 3 -0.26 2 5
NCOR1 0.033 0.009 -10000 0 -10000 0 0
NCOA2 0.032 0.011 -10000 0 -10000 0 0
NCOA1 0.035 0.006 -10000 0 -10000 0 0
MYOD/E2A 0.044 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.13 0.061 -10000 0 -10000 0 0
IFNB1 0.024 0.041 0.22 1 -0.24 3 4
SMAD3/SMAD4/MEF2C 0.093 0.07 -10000 0 -0.38 2 2
CITED1 0.014 0.093 -10000 0 -0.42 16 16
SMAD2-3/SMAD4/ARC105 0.097 0.053 -10000 0 -10000 0 0
RBL1 0.033 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.04 0.069 -10000 0 -0.48 5 5
RUNX1-3/PEBPB2 0.043 0.087 -10000 0 -0.26 25 25
SMAD7 0.077 0.033 -10000 0 -10000 0 0
MYC/MIZ-1 0.043 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.044 -10000 0 -0.36 2 2
IL10 -0.024 0.15 -10000 0 -0.31 65 65
PIASy/HDAC complex 0.035 0.005 -10000 0 -10000 0 0
PIAS3 0.032 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.006 -10000 0 -10000 0 0
IL5 -0.023 0.12 -10000 0 -0.25 68 68
CDK4 0.034 0.009 -10000 0 -10000 0 0
PIAS4 0.035 0.005 -10000 0 -10000 0 0
ATF3 0.031 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.093 0.047 -10000 0 -10000 0 0
FOXG1 0.013 0.024 -10000 0 -10000 0 0
FOXO3 0.017 0.018 -10000 0 -10000 0 0
FOXO1 0.018 0.018 -10000 0 -10000 0 0
FOXO4 0.019 0.018 -10000 0 -10000 0 0
heart looping 0.052 0.075 0.26 19 -0.4 2 21
CEBPB 0.032 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.057 0.088 -10000 0 -0.26 19 19
MYOD1 0.026 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.064 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.012 0.16 -10000 0 -0.28 74 74
SnoN/SIN3/HDAC complex/NCoR1 0.034 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.082 0.099 -10000 0 -0.23 25 25
SMAD3/SMAD4/SP1-3 0.12 0.049 -10000 0 -10000 0 0
MED15 0.033 0.009 -10000 0 -10000 0 0
SP1 0.041 0.007 -10000 0 -10000 0 0
SIN3B 0.035 0.003 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.074 0.045 -10000 0 -0.21 2 2
ITGB5 0.043 0.034 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.034 0.052 -10000 0 -0.39 2 2
SMAD3/SMAD4/AR 0.056 0.05 -10000 0 -10000 0 0
AR 0.02 0.017 -10000 0 -10000 0 0
negative regulation of cell growth 0.052 0.052 -10000 0 -0.33 1 1
SMAD3/SMAD4/MYOD 0.073 0.046 -10000 0 -10000 0 0
E2F5 0.023 0.062 -10000 0 -0.42 7 7
E2F4 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.092 0.055 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.037 0.053 -10000 0 -0.36 5 5
TFDP1 0.033 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.089 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.071 0.056 -10000 0 -0.29 2 2
TGIF2 0.033 0.009 -10000 0 -10000 0 0
TGIF1 0.034 0.007 -10000 0 -10000 0 0
ATF2 0.035 0.002 -10000 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.026 0.06 -10000 0 -1 1 1
regulation of axonogenesis -0.014 0.032 0.22 6 -10000 0 6
myoblast fusion -0.035 0.033 0.39 1 -10000 0 1
mol:GTP 0.024 0.026 -10000 0 -0.16 6 6
regulation of calcium-dependent cell-cell adhesion -0.051 0.075 0.23 22 -10000 0 22
ARF1/GTP 0.041 0.027 -10000 0 -0.12 7 7
mol:GM1 0.011 0.018 -10000 0 -0.12 6 6
mol:Choline 0.014 0.017 -10000 0 -0.15 1 1
lamellipodium assembly 0.022 0.049 -10000 0 -0.34 5 5
MAPK3 0.03 0.026 -10000 0 -0.34 1 1
ARF6/GTP/NME1/Tiam1 0.052 0.076 -10000 0 -0.23 22 22
ARF1 0.032 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.035 0.033 -10000 0 -0.4 1 1
ARF1/GDP 0.037 0.043 -10000 0 -0.21 6 6
ARF6 0.042 0.012 -10000 0 -0.14 1 1
RAB11A 0.035 0.006 -10000 0 -10000 0 0
TIAM1 0.01 0.11 -10000 0 -0.42 21 21
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.029 0.027 -10000 0 -0.34 1 1
actin filament bundle formation -0.045 0.041 0.21 6 -10000 0 6
KALRN 0.021 0.029 -10000 0 -0.24 3 3
RAB11FIP3/RAB11A 0.051 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.041 -10000 0 -0.21 6 6
NME1 0.036 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.042 0.041 -10000 0 -0.21 6 6
substrate adhesion-dependent cell spreading 0.024 0.026 -10000 0 -0.16 6 6
cortical actin cytoskeleton organization 0.022 0.049 -10000 0 -0.34 5 5
RAC1 0.031 0.012 -10000 0 -10000 0 0
liver development 0.024 0.026 -10000 0 -0.16 6 6
ARF6/GTP 0.024 0.026 -10000 0 -0.16 6 6
RhoA/GTP 0.044 0.025 -10000 0 -0.12 7 7
mol:GDP 0.02 0.039 -10000 0 -0.23 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.064 0.027 -10000 0 -0.15 1 1
RHOA 0.035 0.005 -10000 0 -10000 0 0
PLD1 0.025 0.021 -10000 0 -0.12 6 6
RAB11FIP3 0.035 0.003 -10000 0 -10000 0 0
tube morphogenesis 0.022 0.049 -10000 0 -0.34 5 5
ruffle organization 0.014 0.032 -10000 0 -0.22 6 6
regulation of epithelial cell migration 0.024 0.026 -10000 0 -0.16 6 6
PLD2 0.024 0.021 -10000 0 -0.12 6 6
PIP5K1A 0.014 0.032 -10000 0 -0.22 6 6
mol:Phosphatidic acid 0.014 0.017 -10000 0 -0.15 1 1
Rac1/GTP 0.022 0.049 -10000 0 -0.34 5 5
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.05 0.024 -10000 0 -10000 0 0
CDKN1B 0.026 0.051 0.23 3 -0.28 7 10
CDKN1A 0.036 0.07 0.27 2 -0.28 7 9
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.033 0.009 -10000 0 -10000 0 0
FOXO3 0.024 0.039 -10000 0 -0.27 4 4
AKT1 0.028 0.042 -10000 0 -0.28 5 5
BAD 0.034 0.006 -10000 0 -10000 0 0
AKT3 0.018 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.05 -10000 0 -0.28 8 8
AKT1/ASK1 0.043 0.058 -10000 0 -0.26 9 9
BAD/YWHAZ 0.062 0.025 -10000 0 -10000 0 0
RICTOR 0.031 0.025 -10000 0 -0.42 1 1
RAF1 0.035 0.005 -10000 0 -10000 0 0
JNK cascade -0.041 0.057 0.25 9 -10000 0 9
TSC1 0.024 0.045 -10000 0 -0.27 6 6
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.052 0.06 -10000 0 -0.27 9 9
EP300 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.026 0.051 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.05 -10000 0 -0.28 7 7
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
TBC1D4 0.015 0.032 0.24 6 -0.23 1 7
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
MAPKAP1 0.033 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.054 0.058 0.28 1 -0.23 8 9
YWHAH 0.034 0.008 -10000 0 -10000 0 0
AKT1S1 0.024 0.051 -10000 0 -0.28 8 8
CASP9 0.025 0.051 0.23 3 -0.28 7 10
YWHAB 0.033 0.01 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.052 0.064 0.29 5 -0.26 9 14
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.064 0.023 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
AKT2/p21CIP1 0.046 0.072 0.22 33 -0.24 7 40
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.032 -10000 0 -0.25 3 3
CHUK 0.025 0.039 -10000 0 -0.27 4 4
BAD/BCL-XL 0.052 0.057 -10000 0 -0.27 7 7
mTORC2 0.038 0.021 -10000 0 -0.22 1 1
AKT2 0.02 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.06 0.065 0.25 7 -0.28 2 9
PDPK1 0.035 0.003 -10000 0 -10000 0 0
MDM2 0.029 0.054 0.21 10 -0.28 6 16
MAPKKK cascade -0.051 0.059 0.27 9 -10000 0 9
MDM2/Cbp/p300 0.066 0.067 0.29 4 -0.26 6 10
TSC1/TSC2 0.021 0.042 -10000 0 -0.28 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.064 0.28 4 -0.25 6 10
glucose import 0.009 0.024 0.21 5 -10000 0 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.028 0.038 0.18 1 -0.17 3 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.009 0.024 0.21 5 -10000 0 5
GSK3A 0.024 0.051 -10000 0 -0.28 8 8
FOXO1 0.025 0.05 0.21 2 -0.28 7 9
GSK3B 0.024 0.052 0.21 2 -0.28 8 10
SFN 0.027 0.015 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.028 0.057 0.25 2 -0.28 7 9
p27Kip1/14-3-3 family 0.044 0.044 -10000 0 -0.29 1 1
PRKACA 0.035 0.003 -10000 0 -10000 0 0
KPNA1 0.034 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
YWHAG 0.033 0.01 -10000 0 -10000 0 0
RHEB 0.031 0.011 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.042 0.023 -10000 0 -10000 0 0
PDGFRB 0.034 0.01 -10000 0 -10000 0 0
SPHK1 0.006 0.099 -10000 0 -0.68 7 7
mol:S1P 0.01 0.089 -10000 0 -0.58 7 7
S1P1/S1P/Gi 0.023 0.074 0.24 2 -0.3 10 12
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/PLCgamma1 0.052 0.086 0.27 11 -0.32 5 16
PLCG1 0.015 0.068 0.25 4 -0.3 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.01 -10000 0 -10000 0 0
GNAI2 0.035 0.008 -10000 0 -10000 0 0
GNAI3 0.035 0.008 -10000 0 -10000 0 0
GNAI1 0.032 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.009 -10000 0 -10000 0 0
S1P1/S1P 0.017 0.071 0.18 1 -0.41 7 8
negative regulation of cAMP metabolic process 0.023 0.073 0.24 2 -0.3 10 12
MAPK3 0.018 0.085 0.31 3 -0.41 7 10
calcium-dependent phospholipase C activity 0 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
KDR 0.034 0.008 -10000 0 -10000 0 0
PLCB2 0.034 0.094 0.24 17 -0.36 9 26
RAC1 0.031 0.012 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.058 -10000 0 -0.35 7 7
receptor internalization 0.015 0.065 -10000 0 -0.38 7 7
PTGS2 0.035 0.13 0.36 4 -1 3 7
Rac1/GTP 0.015 0.058 -10000 0 -0.34 7 7
RHOA 0.035 0.005 -10000 0 -10000 0 0
VEGFA 0.03 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation 0.023 0.073 0.24 2 -0.3 10 12
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
MAPK1 0.018 0.082 0.24 1 -0.41 7 8
S1P1/S1P/PDGFB-D/PDGFRB 0.039 0.075 0.24 5 -0.35 7 12
ABCC1 0.035 0.024 -10000 0 -0.42 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.043 0.014 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.02 0.006 -10000 0 -10000 0 0
mol:DAG 0.017 0.044 0.2 5 -0.22 8 13
VEGFR1 homodimer/NRP1/VEGFR 121 0.034 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.036 0.045 -10000 0 -0.21 8 8
HIF1A 0.044 0.007 -10000 0 -10000 0 0
GAB1 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.019 0.047 -10000 0 -10000 0 0
PLCG1 0.017 0.044 0.2 5 -0.22 8 13
NOS3 0.04 0.065 0.28 1 -0.52 1 2
CBL 0.032 0.011 -10000 0 -10000 0 0
mol:NO 0.041 0.064 0.28 1 -0.5 1 2
FLT1 0.027 0.008 -10000 0 -10000 0 0
PGF 0.022 0.074 -10000 0 -0.42 10 10
VEGFR1 homodimer/NRP2/VEGFR121 0.053 0.028 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 0.06 0.065 0.29 1 -0.49 1 2
endothelial cell proliferation -0.027 0.11 -10000 0 -0.42 10 10
mol:Ca2+ 0.017 0.044 0.2 5 -0.22 8 13
MAPK3 -0.007 0.038 0.18 5 -10000 0 5
MAPK1 -0.006 0.036 0.18 5 -10000 0 5
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
PLGF homodimer 0.022 0.074 -10000 0 -0.42 10 10
PRKACA 0.035 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
VEGFA homodimer 0.03 0.013 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.038 0.02 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.016 0.069 -10000 0 -10000 0 0
PI3K 0.072 0.053 -10000 0 -0.21 8 8
PRKCA 0.006 0.041 0.19 5 -10000 0 5
PRKCB -0.047 0.11 0.19 3 -0.23 86 89
VEGFR1 homodimer/PLGF homodimer 0.037 0.046 -10000 0 -0.24 9 9
VEGFA 0.03 0.013 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 0.017 0.044 0.2 5 -0.22 8 13
RASA1 0.024 0.029 0.2 7 -0.22 1 8
NRP2 0.035 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.047 0.067 0.29 1 -0.49 1 2
PTPN11 0.034 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.069 0.052 -10000 0 -0.21 8 8
mol:L-citrulline 0.041 0.064 0.28 1 -0.5 1 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.067 0.041 -10000 0 -0.21 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.052 0.029 -10000 0 -10000 0 0
CD2AP 0.031 0.026 -10000 0 -0.42 1 1
PI3K/GAB1 0.084 0.057 -10000 0 -0.2 8 8
PDPK1 0.022 0.045 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.053 0.028 -10000 0 -10000 0 0
mol:NADP 0.041 0.064 0.28 1 -0.5 1 2
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.064 0.04 -10000 0 -0.21 1 1
VEGFR1 homodimer/NRP2 0.044 0.013 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.035 0.005 -10000 0 -10000 0 0
mol:Halofuginone 0.005 0.003 -10000 0 -10000 0 0
ITGA1 0.033 0.009 -10000 0 -10000 0 0
CDKN1A 0.022 0.039 -10000 0 -0.3 4 4
PRL-3/alpha Tubulin 0.044 0.026 -10000 0 -0.3 1 1
mol:Ca2+ -0.054 0.095 -10000 0 -0.31 44 44
AGT -0.032 0.15 -10000 0 -0.42 49 49
CCNA2 0.018 0.052 -10000 0 -10000 0 0
TUBA1B 0.035 0.006 -10000 0 -10000 0 0
EGR1 0.018 0.01 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.078 0.053 0.28 1 -0.27 5 6
MAPK3 0.016 0.018 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.051 0.009 -10000 0 -10000 0 0
MAPK1 0.015 0.018 -10000 0 -0.3 1 1
PTP4A1 0.007 0.006 -10000 0 -10000 0 0
PTP4A3 0.03 0.026 -10000 0 -0.42 1 1
PTP4A2 0.035 0.005 -10000 0 -10000 0 0
ITGB1 0.015 0.018 -10000 0 -0.3 1 1
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1 0.019 0.046 -10000 0 -0.32 5 5
Rab GGTase beta/Rab GGTase alpha 0.051 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 0.05 0.059 0.36 4 -10000 0 4
RABGGTA 0.035 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.021 0.34 1 -10000 0 1
RHOC 0.022 0.044 -10000 0 -0.33 4 4
RHOA 0.022 0.047 -10000 0 -0.32 5 5
cell motility 0.05 0.065 0.32 5 -0.33 3 8
PRL-1/alpha Tubulin 0.049 0.058 0.36 4 -10000 0 4
PRL-3/alpha1 Integrin 0.041 0.028 -10000 0 -0.3 1 1
ROCK1 0.049 0.059 0.32 4 -0.35 2 6
RABGGTB 0.035 0.005 -10000 0 -10000 0 0
CDK2 0.035 0.005 -10000 0 -10000 0 0
mitosis 0.007 0.006 -10000 0 -10000 0 0
ATF5 0.035 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.023 0.021 -10000 0 -0.2 1 1
TRAF2/ASK1 0.04 0.023 -10000 0 -0.25 1 1
ATM 0.032 0.011 -10000 0 -10000 0 0
MAP2K3 -0.011 0.12 -10000 0 -0.35 24 24
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.002 0.1 0.25 1 -0.32 24 25
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.011 0.13 -10000 0 -0.42 35 35
TXN 0.01 0.003 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
GADD45A 0.035 0.006 -10000 0 -10000 0 0
GADD45B 0.035 0.004 -10000 0 -10000 0 0
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
MAP3K6 0.035 0.005 -10000 0 -10000 0 0
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
MAP3K4 0.031 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.044 0.025 -10000 0 -0.3 1 1
TAK1/TAB family -0.009 0.031 -10000 0 -0.14 16 16
RAC1/OSM/MEKK3 0.057 0.025 -10000 0 -10000 0 0
TRAF2 0.033 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.099 -10000 0 -0.28 23 23
TRAF6 0.01 0.002 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.42 7 7
CCM2 0.031 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.033 0.044 -10000 0 -0.25 7 7
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.044 0.05 -10000 0 -0.22 8 8
OSM/MEKK3 0.045 0.019 -10000 0 -10000 0 0
TAOK1 0.018 0.007 -10000 0 -10000 0 0
TAOK2 0.018 0.007 -10000 0 -10000 0 0
TAOK3 0.018 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.011 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
MAP3K10 0.035 0.004 -10000 0 -10000 0 0
MAP3K3 0.034 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.027 0.024 -10000 0 -0.24 1 1
GADD45/MTK1/MTK1 0.043 0.088 -10000 0 -0.21 35 35
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.031 0.065 -10000 0 -10000 0 0
epithelial cell differentiation 0.027 0.056 -10000 0 -10000 0 0
ITCH 0.039 0.018 -10000 0 -10000 0 0
WWP1 0.024 0.068 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
PRL 0.02 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis 0.036 0.08 0.3 10 -10000 0 10
PTPRZ1 -0.011 0.13 -10000 0 -0.42 33 33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.055 0.07 -10000 0 -0.27 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.02 0.053 -10000 0 -0.3 1 1
ADAM17 0.041 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 0.018 0.062 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.1 -10000 0 -0.34 8 8
NCOR1 0.033 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.033 0.055 -10000 0 -0.27 1 1
GRIN2B 0.014 0.049 0.26 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.031 0.052 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
HBEGF 0.033 0.009 -10000 0 -10000 0 0
PRLR 0.025 0.016 -10000 0 -10000 0 0
E4ICDs/ETO2 0.017 0.087 -10000 0 -0.32 2 2
axon guidance 0.033 0.067 -10000 0 -10000 0 0
NEDD4 0.04 0.016 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.029 -10000 0 -10000 0 0
CBFA2T3 0.001 0.12 -10000 0 -0.42 26 26
ErbB4/ErbB2/HBEGF 0.038 0.052 -10000 0 -10000 0 0
MAPK3 0.044 0.08 0.28 11 -10000 0 11
STAT1 (dimer) 0.034 0.069 -10000 0 -10000 0 0
MAPK1 0.039 0.076 0.29 8 -10000 0 8
JAK2 0.024 0.053 -10000 0 -0.42 5 5
ErbB4/ErbB2/neuregulin 1 beta 0.021 0.05 -10000 0 -0.29 1 1
NRG1 0.015 0.032 -10000 0 -0.3 3 3
NRG3 -0.031 0.14 -10000 0 -0.42 44 44
NRG2 0.029 0.042 -10000 0 -0.42 3 3
NRG4 0.018 0.074 -10000 0 -0.42 10 10
heart development 0.033 0.067 -10000 0 -10000 0 0
neural crest cell migration 0.021 0.05 -10000 0 -0.28 1 1
ERBB2 0.023 0.01 -10000 0 -10000 0 0
WWOX/E4ICDs 0.034 0.066 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.032 0.081 -10000 0 -0.32 4 4
apoptosis 0.027 0.13 0.34 45 -10000 0 45
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.029 0.07 -10000 0 -0.34 1 1
ErbB4/ErbB2/epiregulin 0.033 0.052 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.024 0.065 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.036 0.074 -10000 0 -10000 0 0
MDM2 0.019 0.07 0.26 7 -10000 0 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.03 0.044 -10000 0 -0.27 1 1
STAT5A 0.031 0.065 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.028 0.057 -10000 0 -0.29 1 1
DLG4 0.033 0.009 -10000 0 -10000 0 0
GRB2/SHC 0.045 0.018 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.028 0.06 -10000 0 -10000 0 0
STAT5A (dimer) 0.038 0.068 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.051 0.068 -10000 0 -10000 0 0
LRIG1 0.033 0.024 -10000 0 -0.42 1 1
EREG 0.026 0.012 -10000 0 -10000 0 0
BTC 0.023 0.012 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.029 0.062 -10000 0 -10000 0 0
ERBB4 0.018 0.062 -10000 0 -10000 0 0
STAT5B 0.035 0.006 -10000 0 -10000 0 0
YAP1 0.005 0.086 -10000 0 -0.37 16 16
GRB2 0.034 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.032 0.066 -10000 0 -0.29 4 4
glial cell differentiation -0.028 0.059 -10000 0 -10000 0 0
WWOX 0.034 0.008 -10000 0 -10000 0 0
cell proliferation 0.026 0.061 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC3 0.033 0.008 -10000 0 -10000 0 0
VDR 0.032 0.034 -10000 0 -0.42 2 2
Cbp/p300/PCAF 0.061 0.033 -10000 0 -0.25 2 2
EP300 0.032 0.011 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.035 0.059 0.18 6 -0.28 2 8
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
MAPK14 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.009 0.069 0.23 4 -0.24 18 22
RAR alpha/9cRA/Cyclin H 0.054 0.063 -10000 0 -0.25 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.056 -10000 0 -0.21 7 7
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.035 0.03 -10000 0 -0.17 1 1
NCOR2 0.034 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.024 -10000 0 -0.29 2 2
RXRs/RARs/NRIP1/9cRA 0.028 0.081 -10000 0 -0.41 2 2
NCOA2 0.032 0.011 -10000 0 -10000 0 0
NCOA3 0.033 0.01 -10000 0 -10000 0 0
NCOA1 0.035 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.032 0.034 -10000 0 -0.42 2 2
RARG 0.036 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.047 0.008 -10000 0 -10000 0 0
MAPK3 0.036 0.004 -10000 0 -10000 0 0
MAPK1 0.033 0.009 -10000 0 -10000 0 0
MAPK8 0.033 0.011 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.03 0.07 -10000 0 -0.35 3 3
RARA 0.024 0.016 -10000 0 -0.2 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.019 0.053 -10000 0 -0.21 7 7
PRKCA 0.035 0.025 -10000 0 -0.42 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.023 0.087 -10000 0 -0.38 4 4
RXRG -0.033 0.12 -10000 0 -0.28 70 70
RXRA 0.026 0.024 -10000 0 -0.2 1 1
RXRB 0.025 0.02 -10000 0 -0.27 1 1
VDR/Vit D3/DNA 0.024 0.024 -10000 0 -0.29 2 2
RBP1 0.026 0.058 -10000 0 -0.42 6 6
CRBP1/9-cic-RA 0.019 0.041 -10000 0 -0.29 6 6
RARB 0.021 0.084 -10000 0 -0.42 13 13
PRKCG 0.031 0.01 -10000 0 -10000 0 0
MNAT1 0.035 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.072 -10000 0 -0.38 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.089 0.26 1 -0.4 7 8
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.077 0.26 2 -0.29 5 7
RXRs/RARs/NRIP1/9cRA/HDAC3 0.022 0.087 -10000 0 -0.38 4 4
positive regulation of DNA binding 0.042 0.056 -10000 0 -0.22 2 2
NRIP1 0.024 0.086 -10000 0 -0.49 1 1
RXRs/RARs 0.024 0.09 -10000 0 -0.35 8 8
RXRs/RXRs/DNA/9cRA 0.007 0.056 -10000 0 -0.36 3 3
PRKACA 0.035 0.003 -10000 0 -10000 0 0
CDK7 0.034 0.007 -10000 0 -10000 0 0
TFIIH 0.067 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.066 0.057 -10000 0 -10000 0 0
CCNH 0.034 0.008 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.06 0.027 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.033 0.008 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.051 0.056 -9999 0 -0.36 3 3
Syndecan-3/Neurocan 0.035 0.045 -9999 0 -0.37 3 3
POMC -0.016 0.14 -9999 0 -0.42 41 41
EGFR 0.027 0.035 -9999 0 -0.42 2 2
Syndecan-3/EGFR 0.037 0.045 -9999 0 -0.36 2 2
AGRP 0.026 0.011 -9999 0 -10000 0 0
NCSTN 0.032 0.011 -9999 0 -10000 0 0
PSENEN 0.035 0.004 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.031 0.041 -9999 0 -0.42 3 3
APH1A 0.032 0.011 -9999 0 -10000 0 0
NCAN 0.028 0.011 -9999 0 -10000 0 0
long-term memory 0.053 0.049 -9999 0 -0.34 3 3
Syndecan-3/IL8 0.032 0.052 -9999 0 -0.37 3 3
PSEN1 0.035 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.046 0.017 -9999 0 -10000 0 0
FYN 0.031 0.012 -9999 0 -10000 0 0
limb bud formation 0.014 0.037 -9999 0 -0.39 3 3
MC4R 0.023 0.014 -9999 0 -10000 0 0
SRC 0.033 0.01 -9999 0 -10000 0 0
PTN 0.023 0.017 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-3 0.014 0.038 -9999 0 -0.39 3 3
neuron projection morphogenesis 0.052 0.067 -9999 0 -0.35 3 3
Syndecan-3/AgRP 0.033 0.043 -9999 0 -0.37 3 3
Syndecan-3/AgRP/MC4R 0.043 0.051 -9999 0 -0.36 3 3
Fyn/Cortactin 0.044 0.02 -9999 0 -10000 0 0
SDC3 0.014 0.038 -9999 0 -0.39 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.032 0.051 -9999 0 -0.36 3 3
IL8 0.022 0.043 -9999 0 -0.42 3 3
Syndecan-3/Fyn/Cortactin 0.054 0.05 -9999 0 -0.35 3 3
Syndecan-3/CASK 0.012 0.036 -9999 0 -0.37 3 3
alpha-MSH/MC4R -0.002 0.11 -9999 0 -0.3 40 40
Gamma Secretase 0.088 0.044 -9999 0 -0.2 2 2
Nongenotropic Androgen signaling

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
PTK2 0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.048 -10000 0 -0.22 5 5
regulation of S phase of mitotic cell cycle 0.023 0.015 -10000 0 -10000 0 0
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
HRAS 0.035 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.02 0.01 -10000 0 -10000 0 0
PELP1 0.033 0.009 -10000 0 -10000 0 0
AKT1 0.01 0.002 -10000 0 -10000 0 0
MAP2K1 0.02 0.054 0.18 32 -10000 0 32
T-DHT/AR 0.011 0.018 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
mol:GDP -0.001 0.014 -10000 0 -10000 0 0
cell proliferation 0.038 0.061 0.27 9 -10000 0 9
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
FOS 0.039 0.049 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.007 -10000 0 -0.047 3 3
MAPK3 0.028 0.055 0.3 4 -10000 0 4
MAPK1 0.028 0.051 -10000 0 -0.34 3 3
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.008 -10000 0 -10000 0 0
GNG2 0.027 0.058 -10000 0 -0.42 6 6
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.045 0.028 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.045 0.022 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.045 0.012 -10000 0 -10000 0 0
apoptosis -0.041 0.054 0.28 2 -0.26 4 6
T-DHT/AR/PELP1 0.022 0.028 -10000 0 -10000 0 0
HRAS/GDP 0.012 0.025 -10000 0 -10000 0 0
CREB1 0.042 0.055 0.26 4 -0.3 2 6
RAC1-CDC42/GTP 0.057 0.028 -10000 0 -10000 0 0
AR 0.02 0.017 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
RAF1 0.034 0.052 0.2 31 -10000 0 31
RAC1-CDC42/GDP 0.041 0.028 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.038 0.031 -10000 0 -10000 0 0
MAP2K2 0.019 0.053 0.18 30 -10000 0 30
T-DHT/AR/PELP1/Src/PI3K 0.023 0.015 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
SHBG 0.03 0.013 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.009 0.081 -10000 0 -0.4 8 8
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
GNRH1 0.003 0.042 -10000 0 -0.29 7 7
Gi family/GTP 0.01 0.03 -10000 0 -0.17 4 4
CDC42 0.035 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.027 0.076 -10000 0 -0.3 18 18
AKT1 0.061 0.079 0.41 3 -0.34 1 4
PTK2B 0.03 0.075 0.36 3 -10000 0 3
VEGFR2 homodimer/Frs2 0.045 0.017 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.056 0.031 -10000 0 -10000 0 0
endothelial cell proliferation 0.021 0.13 0.31 15 -0.32 2 17
mol:Ca2+ 0.041 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.072 0.042 -10000 0 -10000 0 0
RP11-342D11.1 0.018 0.026 -10000 0 -10000 0 0
CDH5 0.034 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.071 0.038 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
SHC2 0.022 0.036 -10000 0 -0.42 2 2
HRAS/GDP 0.053 0.032 -10000 0 -10000 0 0
SH2D2A -0.001 0.12 -10000 0 -0.42 27 27
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.035 0.1 -10000 0 -0.43 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.037 0.073 -10000 0 -0.22 23 23
VEGFR1 homodimer 0.034 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.085 0.05 -10000 0 -10000 0 0
GRB10 0.039 0.042 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.087 0.045 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.037 0.057 -10000 0 -0.29 3 3
HIF1A 0.035 0.005 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.069 0.041 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.01 -10000 0 -10000 0 0
Nck/Pak 0.047 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.052 0.034 -10000 0 -10000 0 0
mol:GDP 0.066 0.039 -10000 0 -10000 0 0
mol:NADP 0.071 0.075 0.33 8 -0.31 2 10
eNOS/Hsp90 0.087 0.072 0.34 8 -0.32 1 9
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 0.041 0.046 -10000 0 -10000 0 0
HIF1A/ARNT 0.046 0.017 -10000 0 -10000 0 0
SHB 0.028 0.035 -10000 0 -0.42 2 2
VEGFA 0.032 0.013 -10000 0 -10000 0 0
VEGFC 0.034 0.006 -10000 0 -10000 0 0
FAK1/Vinculin 0.065 0.073 0.34 4 -10000 0 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.06 0.066 -10000 0 -10000 0 0
PTPN6 -0.075 0.19 -10000 0 -0.42 88 88
EPAS1 0.045 0.01 -10000 0 -10000 0 0
mol:L-citrulline 0.071 0.075 0.33 8 -0.31 2 10
ITGAV 0.035 0.004 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.072 0.04 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.063 0.031 -10000 0 -10000 0 0
VEGFR2/3 heterodimer 0.044 0.019 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
MAPK11 0.038 0.067 0.32 7 -10000 0 7
VEGFR2 homodimer 0.03 0.011 -10000 0 -10000 0 0
FLT1 0.034 0.007 -10000 0 -10000 0 0
NEDD4 0.036 0.007 -10000 0 -10000 0 0
MAPK3 0.013 0.087 0.33 8 -10000 0 8
MAPK1 0.017 0.091 0.32 12 -10000 0 12
VEGFA145/NRP2 0.045 0.021 -10000 0 -10000 0 0
VEGFR1/2 heterodimer 0.045 0.017 -10000 0 -10000 0 0
KDR 0.03 0.011 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.067 0.034 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.023 0.091 0.33 10 -10000 0 10
PI3K 0.054 0.054 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.057 0.031 -10000 0 -10000 0 0
FES 0.038 0.056 -10000 0 -10000 0 0
GAB1 0.051 0.043 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.054 0.032 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
ARNT 0.032 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.074 0.072 0.34 6 -0.32 1 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.056 0.031 -10000 0 -10000 0 0
PI3K/GAB1 0.061 0.073 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.08 0.047 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.06 0.026 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
CDC42 0.045 0.047 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.036 0.072 -10000 0 -0.22 23 23
PTK2 0.04 0.062 0.32 2 -10000 0 2
EDG1 0.018 0.026 -10000 0 -10000 0 0
mol:DAG 0.041 0.046 -10000 0 -10000 0 0
CaM/Ca2+ 0.055 0.044 -10000 0 -10000 0 0
MAP2K3 0.036 0.063 0.36 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.072 0.052 -10000 0 -10000 0 0
PLCG1 0.041 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.063 0.049 -10000 0 -10000 0 0
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
YES1 0.034 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.057 0.031 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.003 0.12 -10000 0 -0.22 77 77
cell migration 0.077 0.089 0.32 15 -10000 0 15
mol:PI-3-4-5-P3 0.052 0.053 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
VEGFB/NRP1 0.036 0.027 -10000 0 -10000 0 0
mol:NO 0.071 0.075 0.33 8 -0.31 2 10
PXN 0.034 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.032 0.02 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.031 -10000 0 -10000 0 0
VHL 0.035 0.005 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
NOS3 0.073 0.078 0.34 8 -0.38 1 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.039 -10000 0 -0.22 2 2
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA 0.033 0.061 0.36 4 -10000 0 4
PRKCB -0.018 0.11 0.36 4 -10000 0 4
VCL 0.032 0.01 -10000 0 -10000 0 0
VEGFA165/NRP1 0.04 0.03 -10000 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.057 0.031 -10000 0 -10000 0 0
VEGFA165/NRP2 0.045 0.021 -10000 0 -10000 0 0
MAPKKK cascade 0.05 0.051 0.36 1 -10000 0 1
NRP2 0.035 0.004 -10000 0 -10000 0 0
VEGFC homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
ROCK1 0.035 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.067 0.076 0.34 4 -10000 0 4
MAP3K13 0.043 0.048 -10000 0 -10000 0 0
PDPK1 0.046 0.053 0.25 3 -10000 0 3
Arf6 trafficking 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
SLC2A4 0.03 0.013 -10000 0 -10000 0 0
CLTC 0.031 0.058 0.22 1 -0.37 6 7
calcium ion-dependent exocytosis 0.026 0.029 -10000 0 -0.14 1 1
Dynamin 2/GTP 0.035 0.008 -10000 0 -10000 0 0
EXOC4 0.031 0.012 -10000 0 -10000 0 0
CD59 0.022 0.042 -10000 0 -0.29 5 5
CPE 0.017 0.025 -10000 0 -0.25 3 3
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
membrane fusion 0.025 0.03 -10000 0 -10000 0 0
CTNND1 0.02 0.02 0.19 5 -10000 0 5
DNM2 0.035 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.038 0.17 3 -0.18 6 9
TSHR -0.003 0.072 -10000 0 -0.25 29 29
INS 0.006 0.082 -10000 0 -0.46 10 10
BIN1 0.017 0.09 -10000 0 -0.42 15 15
mol:Choline 0.025 0.03 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.035 0.008 -10000 0 -10000 0 0
JUP 0.021 0.041 -10000 0 -0.29 5 5
ASAP2/amphiphysin II 0.055 0.058 -10000 0 -0.22 15 15
ARF6/GTP 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.024 0.093 -10000 0 -0.28 13 13
clathrin-independent pinocytosis 0.026 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.035 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.026 0.003 -10000 0 -10000 0 0
EXOC2 0.031 0.012 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.028 0.046 -10000 0 -0.2 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.015 0.089 0.32 6 -10000 0 6
positive regulation of phagocytosis 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.047 0.008 -10000 0 -10000 0 0
ACAP1 -0.005 0.063 -10000 0 -0.19 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.019 0.049 -10000 0 -0.3 6 6
clathrin heavy chain/ACAP1 0.023 0.053 0.24 2 -0.29 6 8
JIP4/KLC1 0.065 0.016 -10000 0 -10000 0 0
EXOC1 0.035 0.005 -10000 0 -10000 0 0
exocyst 0.028 0.046 -10000 0 -0.21 2 2
RALA/GTP 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.046 0.01 -10000 0 -10000 0 0
receptor recycling 0.026 0.003 -10000 0 -10000 0 0
CTNNA1 0.019 0.021 0.19 5 -10000 0 5
NME1 0.019 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.031 0.06 0.22 1 -0.36 6 7
IL2RA -0.015 0.088 -10000 0 -0.31 11 11
VAMP3 0.019 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.034 0.052 -10000 0 -0.27 7 7
EXOC6 0.031 0.026 -10000 0 -0.42 1 1
PLD1 0.018 0.011 -10000 0 -10000 0 0
PLD2 0.017 0.011 -10000 0 -10000 0 0
EXOC5 0.035 0.005 -10000 0 -10000 0 0
PIP5K1C 0.023 0.034 0.14 1 -0.18 6 7
SDC1 0.017 0.052 0.15 1 -0.23 12 13
ARF6/GDP 0.032 0.007 -10000 0 -10000 0 0
EXOC7 0.034 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.016 0.092 -10000 0 -0.33 6 6
mol:Phosphatidic acid 0.025 0.03 -10000 0 -10000 0 0
endocytosis -0.053 0.057 0.22 15 -10000 0 15
SCAMP2 0.034 0.006 -10000 0 -10000 0 0
ADRB2 0.028 0.06 0.21 5 -0.34 6 11
EXOC3 0.032 0.01 -10000 0 -10000 0 0
ASAP2 0.035 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.04 0.009 -10000 0 -10000 0 0
KLC1 0.034 0.006 -10000 0 -10000 0 0
AVPR2 0.03 0.061 0.21 6 -0.35 6 12
RALA 0.031 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.089 0.36 1 -0.31 6 7
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.018 0.033 0.15 19 -10000 0 19
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.044 0.14 20 -0.2 2 22
AP2 0.05 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.018 -10000 0 -10000 0 0
CLTB 0.033 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.022 0.013 -10000 0 -10000 0 0
CD4 -0.008 0.13 -10000 0 -0.42 34 34
CLTA 0.032 0.011 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.011 -10000 0 -10000 0 0
ARF1/GTP 0.039 0.018 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
mol:Choline 0.009 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.033 0.011 -10000 0 -10000 0 0
DDEF1 0.008 0.011 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.014 -10000 0 -0.11 1 1
AP2M1 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.009 -10000 0 -10000 0 0
Rac/GTP 0.025 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.021 -10000 0 -10000 0 0
ARFIP2 0.026 0.019 -10000 0 -10000 0 0
COPA 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.048 -10000 0 -0.2 9 9
ARF1/GTP/ARHGAP10 0.022 0.009 -10000 0 -10000 0 0
GGA3 0.034 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.044 -10000 0 -0.23 8 8
AP2A1 0.035 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.044 -10000 0 -0.21 11 11
ARF1/GDP/Membrin 0.025 0.05 -10000 0 -0.24 11 11
Arfaptin 2/Rac/GDP 0.04 0.017 -10000 0 -10000 0 0
CYTH2 0.038 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.042 0.018 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.023 0.009 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.074 -10000 0 -0.22 27 27
PLD2 0.009 0.011 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0.003 -10000 0 -10000 0 0
PIP5K1A 0.01 0.011 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.022 0.027 -10000 0 -0.12 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.011 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.003 -10000 0 -10000 0 0
GOSR2 0.013 0.036 -10000 0 -0.31 4 4
USO1 0.015 0.026 -10000 0 -0.32 2 2
GBF1 0.002 0.067 -10000 0 -0.31 16 16
ARF1/GTP/Arfaptin 2 0.045 0.018 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.094 -10000 0 -0.25 34 34
Coregulation of Androgen receptor activity

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
NRIP1 0.034 0.007 -9999 0 -10000 0 0
SVIL 0.032 0.01 -9999 0 -10000 0 0
ZNF318 0.032 0.011 -9999 0 -10000 0 0
JMJD2C 0.003 0.007 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.025 0.041 -9999 0 -0.19 2 2
CARM1 0.035 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.053 -9999 0 -0.42 5 5
PELP1 0.033 0.009 -9999 0 -10000 0 0
CTNNB1 0.035 0.005 -9999 0 -10000 0 0
AKT1 0.035 0.006 -9999 0 -10000 0 0
PTK2B 0.028 0.048 -9999 0 -0.42 4 4
MED1 0.034 0.006 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.032 0.01 -9999 0 -10000 0 0
GSN 0.033 0.009 -9999 0 -10000 0 0
NCOA2 0.032 0.011 -9999 0 -10000 0 0
NCOA6 0.033 0.009 -9999 0 -10000 0 0
DNA-PK 0.06 0.027 -9999 0 -10000 0 0
NCOA4 0.032 0.011 -9999 0 -10000 0 0
PIAS3 0.032 0.011 -9999 0 -10000 0 0
cell proliferation 0.019 0.016 -9999 0 -10000 0 0
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.034 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.015 0.061 -9999 0 -0.24 13 13
FHL2 0.021 0.11 -9999 0 -0.79 6 6
RANBP9 0.031 0.012 -9999 0 -10000 0 0
JMJD1A 0.001 0.028 -9999 0 -0.13 15 15
CDK6 0.029 0.042 -9999 0 -0.42 3 3
TGFB1I1 0.034 0.024 -9999 0 -0.42 1 1
T-DHT/AR/CyclinD1 0.022 0.04 -9999 0 -0.12 6 6
XRCC6 0.032 0.01 -9999 0 -10000 0 0
T-DHT/AR 0.027 0.061 -9999 0 -0.19 18 18
CTDSP1 0.035 0.004 -9999 0 -10000 0 0
CTDSP2 0.034 0.007 -9999 0 -10000 0 0
BRCA1 0.035 0.006 -9999 0 -10000 0 0
TCF4 0.03 0.041 -9999 0 -0.42 3 3
CDKN2A 0.009 0.016 -9999 0 -10000 0 0
SRF 0.037 0.022 -9999 0 -0.15 3 3
NKX3-1 -0.002 0.05 -9999 0 -0.24 15 15
KLK3 0.001 0.037 -9999 0 -10000 0 0
TMF1 0.034 0.007 -9999 0 -10000 0 0
HNRNPA1 0.035 0.004 -9999 0 -10000 0 0
AOF2 0 0 -9999 0 -10000 0 0
APPL1 0.019 0.004 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.025 0.041 -9999 0 -0.17 3 3
AR 0.017 0.03 -9999 0 -0.14 2 2
UBA3 0.034 0.007 -9999 0 -10000 0 0
PATZ1 0.034 0.007 -9999 0 -10000 0 0
PAWR 0.016 0.09 -9999 0 -0.42 15 15
PRKDC 0.033 0.009 -9999 0 -10000 0 0
PA2G4 0.035 0.005 -9999 0 -10000 0 0
UBE2I 0.035 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.023 0.034 -9999 0 -10000 0 0
RPS6KA3 0.035 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.022 0.04 -9999 0 -0.1 15 15
LATS2 0.034 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.02 0.047 -9999 0 -0.19 8 8
Cyclin D3/CDK11 p58 0.024 0.008 -9999 0 -10000 0 0
VAV3 0.029 0.042 -9999 0 -0.42 3 3
KLK2 0.008 0.03 -9999 0 -10000 0 0
CASP8 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.038 0.044 -9999 0 -0.17 2 2
TMPRSS2 -0.015 0.18 -9999 0 -0.88 15 15
CCND1 0.033 0.01 -9999 0 -10000 0 0
PIAS1 0.035 0.005 -9999 0 -10000 0 0
mol:T-DHT 0 0.017 -9999 0 -0.067 19 19
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.021 0.047 -9999 0 -0.22 5 5
CMTM2 0.031 0.01 -9999 0 -10000 0 0
SNURF 0.02 0.077 -9999 0 -0.42 11 11
ZMIZ1 0.03 0.027 -9999 0 -0.14 2 2
CCND3 0.032 0.011 -9999 0 -10000 0 0
TGIF1 0.034 0.007 -9999 0 -10000 0 0
FKBP4 0.034 0.007 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.033 0.024 -10000 0 -0.42 1 1
HDAC2 0.031 0.012 -10000 0 -10000 0 0
GNB1/GNG2 0.049 0.063 -10000 0 -0.25 13 13
forebrain development 0.05 0.07 -10000 0 -0.36 1 1
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
SMO/beta Arrestin2 0.038 0.053 -10000 0 -0.29 8 8
SMO 0.022 0.067 -10000 0 -0.42 8 8
ARRB2 0.034 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.049 0.074 0.24 1 -0.29 2 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.081 0.028 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
XPO1 0.037 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) 0.04 0.073 -10000 0 -0.37 1 1
SAP30 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0.022 0.067 -10000 0 -0.42 8 8
MIM/GLI2A 0.027 0.042 -10000 0 -0.42 3 3
IFT88 0.032 0.025 -10000 0 -0.42 1 1
GNAI3 0.034 0.008 -10000 0 -10000 0 0
GLI2 0.036 0.058 0.22 6 -0.24 3 9
GLI3 0.032 0.073 0.23 1 -0.26 5 6
CSNK1D 0.034 0.008 -10000 0 -10000 0 0
CSNK1E 0.033 0.01 -10000 0 -10000 0 0
SAP18 0.034 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.032 0.025 -10000 0 -0.42 1 1
GNG2 0.027 0.058 -10000 0 -0.42 6 6
Gi family/GTP 0.018 0.052 -10000 0 -0.24 10 10
SIN3B 0.035 0.003 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.087 -10000 0 -0.31 14 14
GLI2/Su(fu) 0.042 0.065 0.24 3 -0.25 8 11
FOXA2 0.028 0.074 -10000 0 -0.56 5 5
neural tube patterning 0.05 0.07 -10000 0 -0.36 1 1
SPOP 0.034 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.038 0.062 -10000 0 -0.19 1 1
GNB1 0.034 0.007 -10000 0 -10000 0 0
CSNK1G2 0.035 0.005 -10000 0 -10000 0 0
CSNK1G3 0.033 0.008 -10000 0 -10000 0 0
MTSS1 0.027 0.042 -10000 0 -0.42 3 3
embryonic limb morphogenesis 0.05 0.07 -10000 0 -0.36 1 1
SUFU 0.024 0.03 -10000 0 -0.15 5 5
LGALS3 0.016 0.09 -10000 0 -0.42 15 15
catabolic process 0.072 0.091 0.33 3 -0.33 3 6
GLI3A/CBP 0.042 0.029 -10000 0 -0.32 2 2
KIF3A 0.034 0.008 -10000 0 -10000 0 0
GLI1 0.05 0.071 -10000 0 -0.36 1 1
RAB23 0.032 0.01 -10000 0 -10000 0 0
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
IFT172 0.03 0.047 -10000 0 -0.42 4 4
RBBP7 0.035 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.03 0.076 -10000 0 -0.24 11 11
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
RBBP4 0.035 0.005 -10000 0 -10000 0 0
CSNK1G1 0.035 0.004 -10000 0 -10000 0 0
PIAS1 0.035 0.005 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.052 0.057 0.25 3 -0.21 3 6
STK36 0.036 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.021 0.058 -10000 0 -0.27 8 8
PTCH1 0.046 0.1 -10000 0 -1 2 2
MIM/GLI1 0.06 0.069 -10000 0 -10000 0 0
CREBBP 0.042 0.029 -10000 0 -0.32 2 2
Su(fu)/SIN3/HDAC complex 0.037 0.063 0.22 2 -0.32 6 8
Aurora A signaling

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
Aurora A/GADD45A 0.047 0.028 -10000 0 -10000 0 0
BIRC5 0.034 0.007 -10000 0 -10000 0 0
NFKBIA 0.013 0.013 -10000 0 -10000 0 0
CPEB1 0.001 0.12 -10000 0 -0.42 27 27
AKT1 0.013 0.013 -10000 0 -10000 0 0
NDEL1 0.033 0.009 -10000 0 -10000 0 0
Aurora A/BRCA1 0.034 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.056 0.03 -10000 0 -10000 0 0
GADD45A 0.035 0.006 -10000 0 -10000 0 0
GSK3B 0.033 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.045 0.027 -10000 0 -10000 0 0
MDM2 0.034 0.008 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.018 0.006 -10000 0 -10000 0 0
TP53 0.026 0.025 0.17 1 -0.18 3 4
DLG7 0.014 0.013 -10000 0 -10000 0 0
AURKAIP1 0.034 0.007 -10000 0 -10000 0 0
ARHGEF7 0.034 0.008 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.06 0.032 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.034 0.021 -10000 0 -10000 0 0
AURKA 0.024 0.017 -10000 0 -10000 0 0
AURKB 0.017 0.025 -10000 0 -0.27 2 2
CDC25B 0.024 0.013 -10000 0 -10000 0 0
G2/M transition checkpoint 0.013 0.016 -10000 0 -10000 0 0
mRNA polyadenylation 0.016 0.066 -10000 0 -0.21 24 24
Aurora A/CPEB 0.016 0.066 -10000 0 -0.21 24 24
Aurora A/TACC1/TRAP/chTOG 0.075 0.041 -10000 0 -0.2 1 1
BRCA1 0.035 0.006 -10000 0 -10000 0 0
centrosome duplication 0.045 0.027 -10000 0 -10000 0 0
regulation of centrosome cycle 0.055 0.03 -10000 0 -10000 0 0
spindle assembly 0.073 0.04 -10000 0 -0.2 1 1
TDRD7 0.032 0.025 -10000 0 -0.42 1 1
Aurora A/RasGAP/Survivin 0.071 0.038 -10000 0 -0.2 1 1
CENPA 0.019 0.037 -10000 0 -0.27 5 5
Aurora A/PP2A 0.042 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.034 0.04 0.19 7 -10000 0 7
negative regulation of DNA binding 0.018 0.05 0.17 2 -0.18 20 22
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.049 0.014 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
Ajuba/Aurora A 0.013 0.016 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.017 -10000 0 -10000 0 0
TACC1 0.034 0.008 -10000 0 -10000 0 0
TACC3 0.034 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.063 0.03 -10000 0 -10000 0 0
Aurora A/RasGAP 0.045 0.032 -10000 0 -0.24 1 1
OAZ1 0.035 0.004 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.034 0.008 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.062 0.025 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.018 0.006 -10000 0 -10000 0 0
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
Aurora A/TPX2 0.031 0.021 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
CKAP5 0.034 0.006 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.03 0.048 -10000 0 -0.42 4 4
PDGF/PDGFRA/CRKL 0.042 0.04 -10000 0 -0.28 4 4
positive regulation of JUN kinase activity 0.069 0.043 -10000 0 -0.21 3 3
CRKL 0.033 0.01 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.033 0.036 -10000 0 -0.28 4 4
AP1 0.016 0.044 -10000 0 -10000 0 0
mol:IP3 0.014 0.031 -10000 0 -0.3 3 3
PLCG1 0.014 0.031 -10000 0 -0.3 3 3
PDGF/PDGFRA/alphaV Integrin 0.046 0.038 -10000 0 -0.28 4 4
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.03 -10000 0 -0.3 3 3
CAV3 0.017 0.002 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.071 0.044 -10000 0 -0.21 3 3
PDGF/PDGFRA/Shf 0.043 0.039 -10000 0 -0.28 4 4
FOS -0.001 0.036 0.32 1 -10000 0 1
JUN -0.019 0.014 -10000 0 -10000 0 0
oligodendrocyte development 0.045 0.038 -10000 0 -0.28 4 4
GRB2 0.034 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:DAG 0.014 0.031 -10000 0 -0.3 3 3
PDGF/PDGFRA 0.03 0.048 -10000 0 -0.42 4 4
actin cytoskeleton reorganization 0.037 0.045 -10000 0 -0.29 5 5
SRF 0.014 0.01 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
PI3K 0.06 0.039 -10000 0 -0.22 4 4
PDGF/PDGFRA/Crk/C3G 0.056 0.042 -10000 0 -0.23 4 4
JAK1 0.015 0.033 -10000 0 -0.28 4 4
ELK1/SRF 0.019 0.04 0.16 21 -0.23 2 23
SHB 0.028 0.035 -10000 0 -0.42 2 2
SHF 0.034 0.007 -10000 0 -10000 0 0
CSNK2A1 0.029 0.015 -10000 0 -10000 0 0
GO:0007205 0.006 0.031 -10000 0 -0.32 3 3
SOS1 0.035 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.069 0.043 -10000 0 -0.21 3 3
PDGF/PDGFRA/SHB 0.037 0.045 -10000 0 -0.29 5 5
PDGF/PDGFRA/Caveolin-1 0.04 0.04 -10000 0 -0.28 4 4
ITGAV 0.035 0.004 -10000 0 -10000 0 0
ELK1 0.003 0.026 0.25 1 -0.28 2 3
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.042 0.04 -10000 0 -0.28 4 4
JAK-STAT cascade 0.015 0.033 -10000 0 -0.28 4 4
cell proliferation 0.043 0.039 -10000 0 -0.28 4 4
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.011 -10000 0 -10000 0 0
HDAC4 0.034 0.008 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.005 0.051 0.3 10 -10000 0 10
CDKN1A -0.006 0.005 -10000 0 -10000 0 0
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
BAX 0.035 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.005 -10000 0 -10000 0 0
FOXO1 0.034 0.007 -10000 0 -10000 0 0
FOXO4 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.01 -10000 0 -10000 0 0
TAT 0.017 0.003 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.003 0.028 -10000 0 -0.3 2 2
PPARGC1A 0.009 0.074 -10000 0 -0.42 10 10
FHL2 0.029 0.053 -10000 0 -0.42 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.041 0.019 -10000 0 -10000 0 0
HIST2H4A 0.005 0.051 -10000 0 -0.3 10 10
SIRT1/FOXO3a -0.002 0.059 -10000 0 -0.19 30 30
SIRT1 0.028 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.054 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.047 0.038 0.18 10 -10000 0 10
apoptosis -0.056 0.026 -10000 0 -10000 0 0
SIRT1/PGC1A 0.014 0.051 -10000 0 -0.25 10 10
p53/SIRT1 0.036 0.015 -10000 0 -10000 0 0
SIRT1/FOXO4 0.04 0.03 0.18 2 -10000 0 2
FOXO1/FHL2/SIRT1 0.054 0.039 -10000 0 -0.22 5 5
HIST1H1E 0.018 0.009 -10000 0 -10000 0 0
SIRT1/p300 0.04 0.019 -10000 0 -10000 0 0
muscle cell differentiation -0.038 0.027 0.25 2 -0.23 1 3
TP53 0.029 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.057 0.026 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.011 -10000 0 -10000 0 0
ACSS2 0.014 0.007 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.038 0.027 0.23 1 -0.25 2 3
Reelin signaling pathway

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
CDK5R1/CDK5 0.044 0.025 -10000 0 -0.3 1 1
VLDLR 0.021 0.067 -10000 0 -0.42 8 8
CRKL 0.033 0.01 -10000 0 -10000 0 0
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
ITGA3 0.032 0.01 -10000 0 -10000 0 0
RELN/VLDLR/Fyn 0.03 0.055 -10000 0 -0.25 7 7
MAPK8IP1/MKK7/MAP3K11/JNK1 0.079 0.047 -10000 0 -0.2 1 1
AKT1 0.002 0.043 -10000 0 -0.2 7 7
MAP2K7 0.035 0.004 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
DAB1 0.021 0.012 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.034 0.035 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.013 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.046 0.036 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin 0.041 0.05 -10000 0 -0.2 7 7
long-term memory 0.048 0.042 -10000 0 -10000 0 0
DAB1/LIS1 0.052 0.058 -10000 0 -0.21 7 7
DAB1/CRLK/C3G 0.043 0.05 -10000 0 -0.2 7 7
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DAB1/NCK2 0.055 0.059 -10000 0 -0.21 7 7
ARHGEF2 0.031 0.026 -10000 0 -0.42 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.031 0.011 -10000 0 -10000 0 0
CDK5R1 0.033 0.024 -10000 0 -0.42 1 1
RELN 0.024 0.016 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.039 0.039 -10000 0 -10000 0 0
GRIN2A/RELN/LRP8/DAB1/Fyn 0.058 0.044 -10000 0 -10000 0 0
MAPK8 0.032 0.01 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.024 0.049 -10000 0 -0.23 7 7
ITGB1 0.032 0.011 -10000 0 -10000 0 0
MAP1B 0.016 0.049 -10000 0 -0.21 7 7
RELN/LRP8 0.043 0.038 -10000 0 -10000 0 0
GRIN2B/RELN/LRP8/DAB1/Fyn 0.052 0.044 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.022 -10000 0 -10000 0 0
RAP1A 0.015 0.08 0.33 7 -10000 0 7
PAFAH1B1 0.033 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.008 -10000 0 -10000 0 0
CRLK/C3G 0.045 0.018 -10000 0 -10000 0 0
GRIN2B 0.022 0.013 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
neuron differentiation 0.02 0.062 -10000 0 -0.28 6 6
neuron adhesion 0.015 0.08 0.32 7 -10000 0 7
LRP8 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.004 0.045 -10000 0 -0.21 2 2
RELN/VLDLR/DAB1/Fyn 0.037 0.051 -10000 0 -0.22 7 7
MAP3K11 0.034 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.014 0.036 -10000 0 -0.21 7 7
CDK5 0.031 0.011 -10000 0 -10000 0 0
MAPT -0.002 0.063 0.68 3 -10000 0 3
neuron migration 0.02 0.078 0.25 18 -0.24 1 19
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.06 -10000 0 -0.28 5 5
RELN/VLDLR 0.051 0.055 -10000 0 -0.23 7 7
IGF1 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
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTK2 0.031 0.012 -10000 0 -10000 0 0
CRKL 0.019 0.027 0.17 3 -0.22 3 6
GRB2/SOS1/SHC 0.061 0.026 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.029 0.027 -10000 0 -0.22 3 3
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.039 -10000 0 -0.24 3 3
AKT1 0.014 0.038 0.19 7 -0.19 3 10
BAD -0.002 0.038 0.18 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.026 0.17 2 -0.22 3 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.041 0.032 0.22 2 -0.22 3 5
RAF1 0.024 0.067 0.28 1 -0.38 7 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.075 0.038 -10000 0 -0.21 2 2
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.041 0.03 0.17 1 -0.24 3 4
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 0.014 0.035 0.19 6 -0.19 2 8
GNB2L1 0.034 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.023 0.071 0.28 4 -0.33 6 10
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.036 0.025 -10000 0 -0.19 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.085 0.045 -10000 0 -0.19 1 1
IGF-1R heterotetramer 0.035 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.06 0.036 -10000 0 -0.22 3 3
Crk/p130 Cas/Paxillin 0.072 0.038 0.24 1 -0.2 3 4
IGF1R 0.035 0.015 -10000 0 -10000 0 0
IGF1 0.034 0.044 -10000 0 -0.43 3 3
IRS2/Crk 0.031 0.028 0.17 2 -0.21 3 5
PI3K 0.074 0.039 -10000 0 -0.21 3 3
apoptosis -0.025 0.038 -10000 0 -0.22 2 2
HRAS/GDP 0.026 0.004 -10000 0 -10000 0 0
PRKCD 0.026 0.057 0.21 2 -0.29 7 9
RAF1/14-3-3 E 0.038 0.065 0.28 1 -0.33 7 8
BAD/14-3-3 0.026 0.039 0.23 2 -10000 0 2
PRKCZ 0.013 0.04 0.19 6 -0.2 2 8
Crk/p130 Cas/Paxillin/FAK1 0.043 0.033 -10000 0 -10000 0 0
PTPN1 0.032 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.022 0.053 -10000 0 -0.29 8 8
BCAR1 0.034 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.068 0.041 -10000 0 -0.19 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.038 0.032 -10000 0 -0.22 3 3
GRB10 0.032 0.011 -10000 0 -10000 0 0
PTPN11 0.021 0.027 0.17 3 -0.22 3 6
IRS1 0.019 0.03 -10000 0 -0.23 3 3
IRS2 0.02 0.027 0.17 3 -0.22 3 6
IGF-1R heterotetramer/IGF1 0.046 0.038 -10000 0 -0.32 3 3
GRB2 0.034 0.007 -10000 0 -10000 0 0
PDPK1 0.025 0.038 0.2 7 -0.2 3 10
YWHAE 0.033 0.009 -10000 0 -10000 0 0
PRKD1 0.027 0.052 -10000 0 -0.29 6 6
SHC1 0.032 0.011 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.24 0.15 -10000 0 -1 2 2
PLK1 0.084 0.062 -10000 0 -0.56 2 2
BIRC5 0.08 0.076 -10000 0 -0.67 2 2
HSPA1B 0.26 0.17 0.7 2 -1 2 4
MAP2K1 0.07 0.027 -10000 0 -10000 0 0
BRCA2 0.24 0.2 0.7 1 -1.1 6 7
FOXM1 0.26 0.17 -10000 0 -1.2 2 2
XRCC1 0.24 0.15 -10000 0 -1 2 2
FOXM1B/p19 0.048 0.15 -10000 0 -1.1 2 2
Cyclin D1/CDK4 0.22 0.16 -10000 0 -0.86 2 2
CDC2 0.25 0.16 -10000 0 -1.1 2 2
TGFA 0.19 0.18 -10000 0 -0.85 3 3
SKP2 0.25 0.16 -10000 0 -0.96 2 2
CCNE1 0.043 0.007 -10000 0 -10000 0 0
CKS1B 0.24 0.15 -10000 0 -1 2 2
RB1 0.16 0.13 -10000 0 -0.87 2 2
FOXM1C/SP1 0.25 0.16 -10000 0 -1.1 2 2
AURKB 0.041 0.18 -10000 0 -0.67 15 15
CENPF 0.26 0.17 0.69 1 -1.2 2 3
CDK4 0.048 0.014 -10000 0 -10000 0 0
MYC 0.21 0.16 -10000 0 -0.88 2 2
CHEK2 0.067 0.03 -10000 0 -10000 0 0
ONECUT1 0.14 0.18 -10000 0 -0.96 2 2
CDKN2A 0.008 0.013 -10000 0 -10000 0 0
LAMA4 0.24 0.15 -10000 0 -1 2 2
FOXM1B/HNF6 0.14 0.19 -10000 0 -1.1 2 2
FOS 0.24 0.15 -10000 0 -1 2 2
SP1 0.036 0.005 -10000 0 -10000 0 0
CDC25B 0.25 0.16 -10000 0 -1 2 2
response to radiation 0.033 0.016 -10000 0 -10000 0 0
CENPB 0.25 0.16 -10000 0 -1 2 2
CENPA 0.24 0.17 -10000 0 -1.4 2 2
NEK2 0.26 0.19 0.69 1 -1.3 3 4
HIST1H2BA 0.26 0.17 0.69 2 -1 2 4
CCNA2 0.042 0.026 -10000 0 -0.43 1 1
EP300 0.032 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 0.25 0.16 -10000 0 -1.2 2 2
CCNB2 0.24 0.2 0.73 2 -0.99 6 8
CCNB1 0.25 0.16 -10000 0 -1.1 2 2
ETV5 0.24 0.16 0.7 1 -1 3 4
ESR1 0.23 0.22 -10000 0 -0.99 9 9
CCND1 0.2 0.16 -10000 0 -0.93 2 2
GSK3A 0.067 0.023 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.1 0.031 -10000 0 -10000 0 0
CDK2 0.043 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.038 0.018 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.23 0.17 -10000 0 -1.1 2 2
GAS1 0.24 0.18 -10000 0 -1 5 5
MMP2 0.24 0.18 -10000 0 -1 4 4
RB1/FOXM1C 0.22 0.17 0.6 1 -0.88 3 4
CREBBP 0.035 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.077 0.041 -9999 0 -0.22 3 3
HDAC3 0.033 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.009 0.003 -9999 0 -10000 0 0
GATA1/HDAC4 0.037 0.009 -9999 0 -10000 0 0
GATA1/HDAC5 0.038 0.008 -9999 0 -10000 0 0
GATA2/HDAC5 0.048 0.016 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.067 0.018 -9999 0 -10000 0 0
HDAC9 0.012 0.09 -9999 0 -0.42 15 15
Glucocorticoid receptor/Hsp90/HDAC6 0.065 0.025 -9999 0 -0.23 1 1
HDAC4/ANKRA2 0.047 0.024 -9999 0 -0.3 1 1
HDAC5/YWHAB 0.047 0.016 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.02 0.007 -9999 0 -10000 0 0
GATA2 0.034 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.049 0.014 -9999 0 -10000 0 0
BCOR 0.035 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.033 0.01 -9999 0 -10000 0 0
HDAC5 0.034 0.006 -9999 0 -10000 0 0
GNB1/GNG2 0.045 0.042 -9999 0 -0.29 5 5
Histones 0.032 0.062 -9999 0 -0.29 4 4
ADRBK1 0.034 0.007 -9999 0 -10000 0 0
HDAC4 0.034 0.008 -9999 0 -10000 0 0
XPO1 0.035 0.002 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.048 0.023 -9999 0 -0.3 1 1
HDAC4/Ubc9 0.049 0.013 -9999 0 -10000 0 0
HDAC7 0.034 0.006 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.048 0.015 -9999 0 -10000 0 0
TUBA1B 0.035 0.006 -9999 0 -10000 0 0
HDAC6 0.035 0.003 -9999 0 -10000 0 0
HDAC5/RFXANK 0.05 0.011 -9999 0 -10000 0 0
CAMK4 -0.026 0.15 -9999 0 -0.42 48 48
Tubulin/HDAC6 0.061 0.026 -9999 0 -10000 0 0
SUMO1 0.035 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.033 0.01 -9999 0 -10000 0 0
GATA1 0.018 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.033 0.009 -9999 0 -10000 0 0
NR3C1 0.033 0.009 -9999 0 -10000 0 0
SUMO1/HDAC4 0.059 0.029 -9999 0 -10000 0 0
SRF 0.032 0.011 -9999 0 -10000 0 0
HDAC4/YWHAB 0.046 0.017 -9999 0 -10000 0 0
Tubulin 0.045 0.019 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.046 0.017 -9999 0 -10000 0 0
GNB1 0.034 0.007 -9999 0 -10000 0 0
RANGAP1 0.032 0.01 -9999 0 -10000 0 0
BCL6/BCoR 0.051 0.01 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.063 0.024 -9999 0 -10000 0 0
HDAC4/SRF 0.022 0.1 -9999 0 -0.25 41 41
HDAC4/ER alpha 0.039 0.047 -9999 0 -0.29 6 6
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.061 -9999 0 -0.29 4 4
cell motility 0.061 0.025 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.035 0.003 -9999 0 -10000 0 0
HDAC7/HDAC3 0.048 0.015 -9999 0 -10000 0 0
BCL6 0.034 0.006 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.033 0.008 -9999 0 -10000 0 0
Hsp90/HDAC6 0.05 0.02 -9999 0 -0.3 1 1
ESR1 0.023 0.058 -9999 0 -0.42 6 6
HDAC6/HDAC11 0.051 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.061 0.029 -9999 0 -0.16 1 1
NPC 0.021 0.002 -9999 0 -10000 0 0
MEF2C 0.031 0.034 -9999 0 -0.42 2 2
RAN 0.034 0.006 -9999 0 -10000 0 0
HDAC4/MEF2C 0.089 0.042 -9999 0 -0.18 2 2
GNG2 0.027 0.058 -9999 0 -0.42 6 6
NCOR2 0.034 0.006 -9999 0 -10000 0 0
TUBB2A 0.031 0.012 -9999 0 -10000 0 0
HDAC11 0.035 0.005 -9999 0 -10000 0 0
HSP90AA1 0.033 0.024 -9999 0 -0.42 1 1
RANBP2 0.035 0.003 -9999 0 -10000 0 0
ANKRA2 0.033 0.025 -9999 0 -0.42 1 1
RFXANK 0.035 0.005 -9999 0 -10000 0 0
nuclear import -0.039 0.02 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.036 0.11 -9999 0 -0.33 13 13
CaM/Ca2+ 0.025 0.004 -9999 0 -10000 0 0
AKT1 0.035 0.006 -9999 0 -10000 0 0
AKT2 0.035 0.004 -9999 0 -10000 0 0
STXBP4 0.034 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.012 0.11 -9999 0 -0.36 14 14
YWHAZ 0.032 0.011 -9999 0 -10000 0 0
CALM1 0.034 0.006 -9999 0 -10000 0 0
YWHAQ 0.035 0.004 -9999 0 -10000 0 0
TBC1D4 0.017 0.017 -9999 0 -0.3 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.034 0.008 -9999 0 -10000 0 0
YWHAB 0.033 0.01 -9999 0 -10000 0 0
SNARE/Synip 0.064 0.023 -9999 0 -10000 0 0
YWHAG 0.033 0.01 -9999 0 -10000 0 0
ASIP 0.027 0.013 -9999 0 -10000 0 0
PRKCI 0.034 0.006 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.004 -9999 0 -10000 0 0
RHOQ 0.035 0.003 -9999 0 -10000 0 0
GYS1 0.018 0.005 -9999 0 -10000 0 0
PRKCZ 0.032 0.034 -9999 0 -0.42 2 2
TRIP10 0.035 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.047 0.007 -9999 0 -10000 0 0
AS160/14-3-3 0.029 0.044 -9999 0 -0.22 4 4
VAMP2 0.033 0.009 -9999 0 -10000 0 0
SLC2A4 0.01 0.12 -9999 0 -0.4 14 14
STX4 0.035 0.004 -9999 0 -10000 0 0
GSK3B 0.029 0.008 -9999 0 -10000 0 0
SFN 0.027 0.015 -9999 0 -10000 0 0
LNPEP 0.034 0.008 -9999 0 -10000 0 0
YWHAE 0.033 0.009 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.042 0.05 -10000 0 -0.21 10 10
MAPK9 0.01 0.003 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.041 0.035 -10000 0 -0.24 5 5
GNB1 0.034 0.007 -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 0.009 0.003 -10000 0 -10000 0 0
Gs family/GTP 0.015 0.03 -10000 0 -0.22 5 5
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 0.002 0.007 0.062 5 -10000 0 5
GNAL 0.024 0.053 -10000 0 -0.42 5 5
GNG2 0.027 0.058 -10000 0 -0.42 6 6
CRH 0.016 0.005 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.003 -10000 0 -10000 0 0
MAPK11 0.01 0.003 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.035 0.005 -10000 0 -10000 0 0
SMAD2 0.007 0.035 0.17 1 -0.2 1 2
SMAD3 0.039 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4 0.053 0.05 -10000 0 -0.39 3 3
SMAD4/Ubc9/PIASy 0.069 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.064 0.047 -10000 0 -10000 0 0
PPM1A 0.035 0.005 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.027 0.037 -10000 0 -0.19 1 1
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.051 0.008 -10000 0 -10000 0 0
MAPK3 0.035 0.004 -10000 0 -10000 0 0
MAPK1 0.033 0.009 -10000 0 -10000 0 0
NUP214 0.033 0.009 -10000 0 -10000 0 0
CTDSP1 0.035 0.004 -10000 0 -10000 0 0
CTDSP2 0.034 0.007 -10000 0 -10000 0 0
CTDSPL 0.035 0.005 -10000 0 -10000 0 0
KPNB1 0.034 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.035 0.003 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
NUP153 0.031 0.012 -10000 0 -10000 0 0
KPNA2 0.034 0.007 -10000 0 -10000 0 0
PIAS4 0.035 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.048 0.015 -9999 0 -10000 0 0
ATM 0.032 0.011 -9999 0 -10000 0 0
UBE2D3 0.034 0.006 -9999 0 -10000 0 0
PRKDC 0.033 0.009 -9999 0 -10000 0 0
ATR 0.034 0.006 -9999 0 -10000 0 0
UBE2L3 0.033 0.009 -9999 0 -10000 0 0
FANCD2 0.027 0.01 -9999 0 -10000 0 0
protein ubiquitination 0.083 0.034 -9999 0 -10000 0 0
XRCC5 0.035 0.004 -9999 0 -10000 0 0
XRCC6 0.032 0.01 -9999 0 -10000 0 0
M/R/N Complex 0.056 0.037 -9999 0 -0.25 2 2
MRE11A 0.032 0.01 -9999 0 -10000 0 0
DNA-PK 0.06 0.027 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.006 0.13 -9999 0 -0.47 21 21
FANCF 0.035 0.006 -9999 0 -10000 0 0
BRCA1 0.035 0.006 -9999 0 -10000 0 0
CCNE1 0.035 0.005 -9999 0 -10000 0 0
CDK2/Cyclin E1 0.051 0.009 -9999 0 -10000 0 0
FANCG 0.032 0.011 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 0.051 0.01 -9999 0 -10000 0 0
FANCE 0.032 0.011 -9999 0 -10000 0 0
FANCC 0.033 0.009 -9999 0 -10000 0 0
NBN 0.032 0.011 -9999 0 -10000 0 0
FANCA 0.033 0.008 -9999 0 -10000 0 0
DNA repair 0.018 0.072 -9999 0 -0.4 5 5
BRCA1/BARD1/ubiquitin 0.051 0.01 -9999 0 -10000 0 0
BARD1/DNA-PK 0.076 0.034 -9999 0 -10000 0 0
FANCL 0.035 0.003 -9999 0 -10000 0 0
mRNA polyadenylation -0.048 0.015 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.023 0.056 -9999 0 -0.23 4 4
BRCA1/BACH1/BARD1/TopBP1 0.068 0.016 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.081 0.029 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.064 0.023 -9999 0 -10000 0 0
BRCA1/BACH1 0.035 0.005 -9999 0 -10000 0 0
BARD1 0.035 0.004 -9999 0 -10000 0 0
PCNA 0.034 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.068 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.064 0.022 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.08 0.03 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.083 0.043 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.051 0.01 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.053 0.021 -9999 0 -10000 0 0
FA complex 0.029 0.038 -9999 0 -0.25 4 4
BARD1/EWS 0.049 0.013 -9999 0 -10000 0 0
RBBP8 0.017 0.006 -9999 0 -10000 0 0
TP53 0.033 0.009 -9999 0 -10000 0 0
TOPBP1 0.034 0.006 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.078 0.028 -9999 0 -10000 0 0
BRCA1/BARD1 0.091 0.037 -9999 0 -10000 0 0
CSTF1 0.032 0.01 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0.026 0.003 -9999 0 -10000 0 0
CDK2 0.035 0.005 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 0.034 0.008 -9999 0 -10000 0 0
RAD50 0.031 0.034 -9999 0 -0.42 2 2
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.051 0.01 -9999 0 -10000 0 0
EWSR1 0.034 0.008 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.034 0.007 -9999 0 -10000 0 0
PLK4 0.034 0.024 -9999 0 -0.42 1 1
regulation of centriole replication 0.018 0.017 -9999 0 -0.3 1 1
Circadian rhythm 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
chromatin modification 0.062 0.031 -9999 0 -10000 0 0
CLOCK 0.038 0.006 -9999 0 -10000 0 0
TIMELESS/CRY2 0.051 0.021 -9999 0 -10000 0 0
DEC1/BMAL1 0.038 0.011 -9999 0 -10000 0 0
ATR 0.034 0.006 -9999 0 -10000 0 0
NR1D1 0.032 0.01 -9999 0 -10000 0 0
ARNTL 0.038 0.006 -9999 0 -10000 0 0
TIMELESS 0.031 0.01 -9999 0 -10000 0 0
NPAS2 0.034 0.041 -9999 0 -0.41 3 3
CRY2 0.034 0.006 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 0.032 0.011 -9999 0 -10000 0 0
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 0.033 0.009 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.08 0.034 -9999 0 -0.24 3 3
BMAL1/CLOCK 0.042 0.039 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.062 0.031 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.063 0.032 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.049 0.02 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.016 0.005 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.039 0.044 0.18 1 -10000 0 1
GNAI2 0.035 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.04 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.029 -10000 0 -0.42 1 1
RhoA/GTP 0.04 0.045 -10000 0 -0.18 1 1
negative regulation of cAMP metabolic process 0.022 0.037 -10000 0 -0.18 4 4
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNA12 0.031 0.011 -10000 0 -10000 0 0
S1PR5 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.037 -10000 0 -0.18 4 4
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.003 0.005 -10000 0 -9999 0 0
TP53 0.002 0.004 -10000 0 -9999 0 0
Senescence 0.002 0.004 -10000 0 -9999 0 0
Apoptosis 0.002 0.004 -10000 0 -9999 0 0
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 0.003 0.017 0.29 1 -9999 0 1
MDM4 0.031 0.012 -10000 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.034 0.024 -9999 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.009 0.006 -9999 0 -10000 0 0
MDM2/SUMO1 0.058 0.031 -9999 0 -10000 0 0
HDAC4 0.034 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.008 0.012 -9999 0 -0.17 1 1
SUMO1 0.035 0.003 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0.013 -9999 0 -0.18 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.016 0.006 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.034 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.035 0.003 -9999 0 -10000 0 0
SUMO1/HDAC4 0.059 0.029 -9999 0 -10000 0 0
SUMO1/HDAC1 0.059 0.032 -9999 0 -0.18 1 1
RANGAP1 0.032 0.01 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.082 0.027 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.02 0.007 -9999 0 -10000 0 0
Ran/GTP 0.043 0.026 -9999 0 -0.16 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.034 0.008 -9999 0 -10000 0 0
UBE2I 0.035 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.025 -9999 0 -10000 0 0
NPC 0.021 0.002 -9999 0 -10000 0 0
PIAS2 0.035 0.006 -9999 0 -10000 0 0
PIAS1 0.035 0.005 -9999 0 -10000 0 0
EntrezGene:9972 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 0.046 0.017 -9999 0 -9999 0 0
FBXW11 0.033 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -9999 0 -9999 0 0
CHUK 0.032 0.01 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.089 0.038 -9999 0 -9999 0 0
NFKB1 0.034 0.006 -9999 0 -9999 0 0
MAP3K14 0.034 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.051 0.01 -9999 0 -9999 0 0
RELB 0.035 0.004 -9999 0 -9999 0 0
NFKB2 0.032 0.01 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.043 0.014 -9999 0 -9999 0 0
regulation of B cell activation 0.043 0.014 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 365 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z2.AA3V TCGA.Z2.AA3S TCGA.Z2.A8RT TCGA.YG.AA3P
109_MAP3K5 0.045 -0.34 0.045 -0.46
47_PPARGC1A 0.035 0.035 0.035 0.035
105_BMP4 0.035 0.035 0.035 0
105_BMP6 0.035 0.035 0.035 0.035
105_BMP7 0 0.035 0.035 0
105_BMP2 0.035 0.035 0.035 0.035
131_RELN/VLDLR 0.091 0 0 0.091
30_TGFB1/TGF beta receptor Type II 0.035 0.035 0.035 0.035
84_STAT5B 0.045 -0.22 0.027 -0.24
84_STAT5A 0.045 -0.22 0.027 -0.24
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/SKCM-TM/11493712/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/SKCM-TM/11541685/GDAC_Gistic2Report_11573311/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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