PARADIGM pathway analysis of mRNASeq expression and copy number data
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1KH0MPX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0MPX
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
E-cadherin signaling events 141
Aurora B signaling 118
FOXM1 transcription factor network 95
Signaling events regulated by Ret tyrosine kinase 80
Aurora C signaling 70
Angiopoietin receptor Tie2-mediated signaling 59
TCGA08_p53 57
Signaling events mediated by VEGFR1 and VEGFR2 52
Plasma membrane estrogen receptor signaling 48
p75(NTR)-mediated signaling 47
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 304 . 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 ( 304 ).

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
E-cadherin signaling events 0.4638 141 707 5 0.019 0.17 1000 -1000 0.011 -1000
Aurora B signaling 0.3882 118 7968 67 -0.29 0.43 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.3125 95 4886 51 0.02 0.5 1000 -1000 -0.12 -1000
Signaling events regulated by Ret tyrosine kinase 0.2632 80 6574 82 -0.22 0.021 1000 -1000 -0.042 -1000
Aurora C signaling 0.2303 70 492 7 0 0.26 1000 -1000 -0.012 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1941 59 5246 88 -0.35 0.07 1000 -1000 -0.05 -1000
TCGA08_p53 0.1875 57 402 7 -0.086 0.026 1000 -1000 -0.011 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1711 52 6502 125 -0.17 0.043 1000 -1000 -0.037 -1000
Plasma membrane estrogen receptor signaling 0.1579 48 4197 86 -0.25 0.24 1000 -1000 -0.041 -1000
p75(NTR)-mediated signaling 0.1546 47 5963 125 -0.14 0.16 1000 -1000 -0.044 -1000
PLK1 signaling events 0.1546 47 4049 85 -0.076 0.29 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.1546 47 380 8 -0.083 0.27 1000 -1000 -0.004 -1000
HIF-1-alpha transcription factor network 0.1480 45 3461 76 -0.28 0.028 1000 -1000 -0.035 -1000
Endothelins 0.1480 45 4380 96 -0.18 0.19 1000 -1000 -0.046 -1000
IGF1 pathway 0.1447 44 2511 57 -0.1 0.036 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.1316 40 3401 84 -0.18 0.26 1000 -1000 -0.034 -1000
E-cadherin signaling in the nascent adherens junction 0.1250 38 2916 76 -0.008 0.26 1000 -1000 -0.04 -1000
Glucocorticoid receptor regulatory network 0.1217 37 4314 114 -0.28 0.39 1000 -1000 -0.047 -1000
PDGFR-alpha signaling pathway 0.1184 36 1593 44 -0.095 0.023 1000 -1000 -0.027 -1000
Reelin signaling pathway 0.1151 35 1970 56 -0.084 0.047 1000 -1000 -0.027 -1000
Nongenotropic Androgen signaling 0.1151 35 1835 52 -0.13 0.087 1000 -1000 -0.024 -1000
Signaling events mediated by the Hedgehog family 0.1053 32 1704 52 -0.12 0.072 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 0.1020 31 1054 34 -0.016 0.1 1000 -1000 -0.024 -1000
IL23-mediated signaling events 0.1020 31 1868 60 -0.013 0.37 1000 -1000 -0.082 -1000
Syndecan-2-mediated signaling events 0.0954 29 2059 69 -0.038 0.17 1000 -1000 -0.028 -1000
Aurora A signaling 0.0954 29 1778 60 -0.065 0.28 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0954 29 3487 120 -0.18 0.16 1000 -1000 -0.037 -1000
Cellular roles of Anthrax toxin 0.0921 28 1102 39 -0.095 0.023 1000 -1000 -0.016 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0855 26 1932 74 -0.14 0.26 1000 -1000 -0.045 -1000
E-cadherin signaling in keratinocytes 0.0855 26 1150 43 -0.073 0.26 1000 -1000 -0.023 -1000
LPA4-mediated signaling events 0.0822 25 310 12 -0.081 0 1000 -1000 -0.015 -1000
Coregulation of Androgen receptor activity 0.0822 25 1963 76 -0.069 0.27 1000 -1000 -0.018 -1000
Thromboxane A2 receptor signaling 0.0789 24 2579 105 -0.14 0.042 1000 -1000 -0.036 -1000
IL4-mediated signaling events 0.0789 24 2222 91 -0.6 0.36 1000 -1000 -0.13 -1000
Glypican 1 network 0.0789 24 1160 48 -0.089 0.065 1000 -1000 -0.021 -1000
HIF-2-alpha transcription factor network 0.0789 24 1061 43 -0.36 0.15 1000 -1000 -0.041 -1000
Effects of Botulinum toxin 0.0789 24 644 26 -0.11 0.039 1000 -1000 -0.012 -1000
amb2 Integrin signaling 0.0757 23 1926 82 -0.12 0.099 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0757 23 1435 62 -0.024 0.23 1000 -1000 -0.034 -1000
Nectin adhesion pathway 0.0691 21 1362 63 -0.076 0.26 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 0.0658 20 1984 97 -0.073 0.035 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0625 19 1555 81 -0.23 0.083 1000 -1000 -0.017 -1000
Canonical Wnt signaling pathway 0.0625 19 1012 51 -0.37 0.18 1000 -1000 -0.031 -1000
S1P3 pathway 0.0625 19 804 42 -0.077 0.035 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0625 19 1491 78 -0.11 0.039 1000 -1000 -0.052 -1000
S1P5 pathway 0.0592 18 311 17 -0.05 0.11 1000 -1000 -0.009 -1000
TCR signaling in naïve CD8+ T cells 0.0592 18 1680 93 -0.04 0.034 1000 -1000 -0.037 -1000
EPHB forward signaling 0.0592 18 1559 85 -0.063 0.06 1000 -1000 -0.039 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0592 18 605 33 -0.11 0.27 1000 -1000 -0.023 -1000
Arf6 signaling events 0.0559 17 1067 62 -0.094 0.036 1000 -1000 -0.046 -1000
S1P1 pathway 0.0559 17 622 36 -0.072 0.02 1000 -1000 -0.035 -1000
S1P4 pathway 0.0559 17 432 25 -0.05 0.11 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0526 16 465 28 -0.066 0.11 1000 -1000 -0.017 -1000
LPA receptor mediated events 0.0493 15 1554 102 -0.092 0.12 1000 -1000 -0.053 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0461 14 799 54 -0.084 0.033 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0461 14 1130 76 -0.14 0.064 1000 -1000 -0.024 -1000
FOXA2 and FOXA3 transcription factor networks 0.0461 14 682 46 -0.16 0.26 1000 -1000 -0.078 -1000
mTOR signaling pathway 0.0461 14 754 53 -0.032 0.045 1000 -1000 -0.028 -1000
BCR signaling pathway 0.0461 14 1406 99 -0.06 0.04 1000 -1000 -0.046 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0428 13 461 34 -0.016 0.03 1000 -1000 -0.022 -1000
Hedgehog signaling events mediated by Gli proteins 0.0428 13 892 65 -0.14 0.047 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 0.0428 13 844 61 -0.045 0.18 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 0.0395 12 257 21 -0.028 0.04 1000 -1000 -0.03 -1000
Insulin Pathway 0.0395 12 934 74 -0.096 0.07 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 0.0395 12 1227 97 -0.031 0.041 1000 -1000 -0.038 -1000
ErbB2/ErbB3 signaling events 0.0362 11 771 65 -0.031 0.066 1000 -1000 -0.049 -1000
Noncanonical Wnt signaling pathway 0.0362 11 300 26 -0.068 0.02 1000 -1000 -0.024 -1000
ErbB4 signaling events 0.0329 10 748 69 -0.11 0.14 1000 -1000 -0.028 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0329 10 850 85 -0.052 0.028 1000 -1000 -0.035 -1000
Insulin-mediated glucose transport 0.0329 10 333 32 -0.037 0.28 1000 -1000 -0.024 -1000
Class I PI3K signaling events mediated by Akt 0.0329 10 742 68 -0.057 0.28 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 0.0296 9 451 48 -0.026 0.026 1000 -1000 -0.026 -1000
Syndecan-3-mediated signaling events 0.0296 9 340 35 -0.099 0.17 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 0.0296 9 435 44 -0.06 0.045 1000 -1000 -0.021 -1000
Calcium signaling in the CD4+ TCR pathway 0.0296 9 282 31 -0.011 0.08 1000 -1000 -0.039 -1000
Syndecan-4-mediated signaling events 0.0296 9 621 67 -0.17 0.061 1000 -1000 -0.027 -1000
EPO signaling pathway 0.0263 8 476 55 -0.034 0.033 1000 -1000 -0.03 -1000
FAS signaling pathway (CD95) 0.0263 8 408 47 -0.021 0.05 1000 -1000 -0.028 -1000
Wnt signaling 0.0263 8 62 7 -0.025 0.019 1000 -1000 -0.01 -1000
Regulation of Telomerase 0.0263 8 883 102 -0.24 0.085 1000 -1000 -0.033 -1000
Regulation of Androgen receptor activity 0.0263 8 584 70 -0.066 0.14 1000 -1000 -0.041 -1000
IL12-mediated signaling events 0.0230 7 650 87 -0.06 0.074 1000 -1000 -0.068 -1000
IFN-gamma pathway 0.0230 7 509 68 -0.074 0.075 1000 -1000 -0.037 -1000
Ceramide signaling pathway 0.0230 7 571 76 -0.079 0.055 1000 -1000 -0.031 -1000
ceramide signaling pathway 0.0230 7 347 49 -0.017 0.038 1000 -1000 -0.026 -1000
TCGA08_rtk_signaling 0.0230 7 184 26 -0.049 0.047 1000 -1000 -0.008 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0230 7 491 68 -0.043 0.19 1000 -1000 -0.06 -1000
Regulation of nuclear SMAD2/3 signaling 0.0197 6 869 136 -0.12 0.056 1000 -1000 -0.032 -1000
Osteopontin-mediated events 0.0197 6 252 38 -0.058 0.034 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.0197 6 352 52 -0.017 0.086 1000 -1000 -0.03 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0164 5 421 83 -0.021 0.28 1000 -1000 -0.018 -1000
FoxO family signaling 0.0164 5 324 64 -0.027 0.28 1000 -1000 -0.052 -1000
Regulation of p38-alpha and p38-beta 0.0164 5 306 54 -0.055 0.064 1000 -1000 -0.04 -1000
Caspase cascade in apoptosis 0.0132 4 348 74 -0.019 0.12 1000 -1000 -0.033 -1000
Visual signal transduction: Cones 0.0132 4 179 38 -0.017 0.039 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0132 4 63 15 -0.015 0.02 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0132 4 181 45 -0.024 0.048 1000 -1000 -0.033 -1000
IL27-mediated signaling events 0.0132 4 216 51 -0.018 0.062 1000 -1000 -0.045 -1000
Signaling events mediated by PRL 0.0132 4 141 34 -0.049 0.035 1000 -1000 -0.037 -1000
Ras signaling in the CD4+ TCR pathway 0.0132 4 70 17 -0.013 0.031 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 0.0099 3 298 75 -0.082 0.038 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0099 3 177 52 -0.01 0.057 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 0.0099 3 178 58 -0.019 0.04 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0099 3 260 73 -0.029 0.064 1000 -1000 -0.027 -1000
VEGFR1 specific signals 0.0099 3 175 56 -0.03 0.031 1000 -1000 -0.031 -1000
p38 MAPK signaling pathway 0.0099 3 167 44 -0.033 0.046 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 0.0066 2 92 39 -0.02 0.041 1000 -1000 -0.02 -1000
BARD1 signaling events 0.0066 2 114 57 -0.031 0.048 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0066 2 42 17 -0.01 0.053 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0066 2 97 37 -0.029 0.049 1000 -1000 -0.02 -1000
TRAIL signaling pathway 0.0066 2 108 48 -0.019 0.035 1000 -1000 -0.021 -1000
IL2 signaling events mediated by PI3K 0.0066 2 166 58 -0.014 0.047 1000 -1000 -0.037 -1000
IL6-mediated signaling events 0.0066 2 213 75 -0.11 0.05 1000 -1000 -0.051 -1000
IL2 signaling events mediated by STAT5 0.0066 2 54 22 -0.032 0.031 1000 -1000 -0.026 -1000
Arf6 trafficking events 0.0066 2 154 71 -0.077 0.067 1000 -1000 -0.029 -1000
Rapid glucocorticoid signaling 0.0066 2 46 20 -0.017 0.026 1000 -1000 -0.01 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0033 1 27 23 -0.009 0.037 1000 -1000 -0.015 -1000
Ephrin A reverse signaling 0.0033 1 9 7 -0.019 0.025 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class III 0.0033 1 53 40 -0.038 0.038 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0033 1 144 104 -0.037 0.05 1000 -1000 -0.037 -1000
Glypican 2 network 0.0033 1 6 4 0.02 0.029 1000 -1000 0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0033 1 31 27 -0.021 0.045 1000 -1000 -0.026 -1000
Class IB PI3K non-lipid kinase events 0.0033 1 3 3 -0.021 0.021 1000 -1000 -0.011 -1000
Arf1 pathway 0.0033 1 63 54 -0.011 0.026 1000 -1000 -0.014 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.017 0.02 1000 -1000 -0.021 -1000
Circadian rhythm pathway 0.0000 0 5 22 -0.009 0.04 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.02 0.029 1000 -1000 0.013 -1000
Arf6 downstream pathway 0.0000 0 7 43 -0.04 0.042 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 30 36 -0.036 0.038 1000 -1000 -0.024 -1000
Atypical NF-kappaB pathway 0.0000 0 10 31 -0.02 0.024 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.053 1000 -1000 0 -1000
Total NA 2405 146559 7203 -10 13 131000 -131000 -4 -131000
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.16 0.08 0.21 226 -9999 0 226
E-cadherin/beta catenin 0.17 0.082 0.22 230 -9999 0 230
CTNNB1 0.019 0.006 -10000 0 -9999 0 0
JUP 0.02 0.003 -10000 0 -9999 0 0
CDH1 0.26 0.097 0.29 251 -9999 0 251
Aurora B signaling

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
Condensin I complex 0.17 0.11 0.23 206 -0.25 1 207
STMN1 0.12 0.052 0.14 254 -10000 0 254
Aurora B/RasGAP/Survivin 0.32 0.13 0.37 250 -10000 0 250
Chromosomal passenger complex/Cul3 protein complex 0.12 0.084 0.18 186 -0.15 1 187
BIRC5 0.28 0.073 0.3 273 -10000 0 273
DES -0.29 0.15 -10000 0 -0.53 39 39
Aurora C/Aurora B/INCENP 0.17 0.08 0.21 235 -0.098 1 236
Aurora B/TACC1 0.16 0.073 0.19 241 -0.15 1 242
Aurora B/PP2A 0.18 0.076 0.22 246 -10000 0 246
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.054 0.025 0.13 11 -10000 0 11
mitotic metaphase/anaphase transition -0.009 0.006 -10000 0 -10000 0 0
NDC80 0.12 0.061 0.15 251 -10000 0 251
Cul3 protein complex 0.003 0.078 -10000 0 -0.17 47 47
KIF2C 0.18 0.076 0.21 236 -10000 0 236
PEBP1 0.024 0.003 -10000 0 -10000 0 0
KIF20A 0.27 0.067 0.29 275 -10000 0 275
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.18 0.076 0.22 246 -10000 0 246
SEPT1 0.02 0.002 -10000 0 -10000 0 0
SMC2 0.02 0.003 -10000 0 -10000 0 0
SMC4 0.014 0.01 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.15 0.18 0.28 59 -0.42 22 81
PSMA3 0.02 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.12 0.049 0.13 254 -10000 0 254
AURKB 0.26 0.099 0.3 255 -10000 0 255
AURKC 0.019 0.019 -10000 0 -0.29 1 1
CDCA8 0.21 0.13 0.31 195 -10000 0 195
cytokinesis 0.18 0.099 0.23 219 -10000 0 219
Aurora B/Septin1 0.26 0.12 0.31 244 -10000 0 244
AURKA 0.003 0.064 0.29 13 -10000 0 13
INCENP 0.033 0.006 -10000 0 -10000 0 0
KLHL13 -0.029 0.11 -10000 0 -0.29 47 47
BUB1 0.17 0.15 0.29 176 -10000 0 176
hSgo1/Aurora B/Survivin 0.42 0.19 0.49 246 -10000 0 246
EVI5 0.031 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.094 0.24 191 -10000 0 191
SGOL1 0.26 0.098 0.29 251 -10000 0 251
CENPA 0.22 0.094 0.25 260 -10000 0 260
NCAPG 0.24 0.11 0.29 240 -10000 0 240
Aurora B/HC8 Proteasome 0.19 0.075 0.22 248 -10000 0 248
NCAPD2 0.019 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.19 0.069 0.22 255 -10000 0 255
RHOA 0.019 0.006 -10000 0 -10000 0 0
NCAPH 0.22 0.12 0.29 208 -10000 0 208
NPM1 0.12 0.12 0.2 6 -0.46 9 15
RASA1 0.02 0.004 -10000 0 -10000 0 0
KLHL9 0.02 0.004 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.18 0.075 0.22 248 -10000 0 248
PPP1CC 0.021 0.001 -10000 0 -10000 0 0
Centraspindlin 0.21 0.093 0.25 239 -10000 0 239
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
NSUN2 0.14 0.099 0.23 54 -0.32 6 60
MYLK 0.007 0.13 0.16 110 -0.13 120 230
KIF23 0.031 0.006 -10000 0 -10000 0 0
VIM 0.12 0.064 0.14 243 -0.14 5 248
RACGAP1 0.031 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.11 0.13 0.18 12 -0.46 11 23
Chromosomal passenger complex 0.25 0.085 0.27 268 -10000 0 268
Chromosomal passenger complex/EVI5 0.43 0.18 0.49 252 -10000 0 252
TACC1 0.018 0.019 -10000 0 -0.29 1 1
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
CUL3 0.019 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.4 0.38 0.76 110 -0.9 2 112
PLK1 0.21 0.17 0.55 27 -10000 0 27
BIRC5 0.34 0.14 0.45 108 -0.65 2 110
HSPA1B 0.41 0.39 0.77 110 -0.91 2 112
MAP2K1 0.1 0.095 0.22 86 -10000 0 86
BRCA2 0.4 0.38 0.76 111 -0.91 2 113
FOXM1 0.45 0.43 0.83 123 -1.1 2 125
XRCC1 0.4 0.39 0.77 110 -0.91 2 112
FOXM1B/p19 0.3 0.37 0.69 87 -0.97 3 90
Cyclin D1/CDK4 0.35 0.36 0.69 110 -0.84 2 112
CDC2 0.42 0.4 0.78 123 -0.96 2 125
TGFA 0.36 0.36 0.69 122 -0.81 2 124
SKP2 0.43 0.39 0.78 122 -0.91 2 124
CCNE1 0.036 0.042 0.31 4 -10000 0 4
CKS1B 0.4 0.38 0.73 123 -0.91 2 125
RB1 0.21 0.25 0.5 88 -0.58 1 89
FOXM1C/SP1 0.36 0.36 0.73 88 -1.1 2 90
AURKB 0.29 0.23 0.44 110 -0.71 9 119
CENPF 0.44 0.41 0.8 123 -0.91 2 125
CDK4 0.052 0.042 0.17 5 -10000 0 5
MYC 0.32 0.35 0.65 111 -0.94 3 114
CHEK2 0.11 0.096 0.22 89 -10000 0 89
ONECUT1 0.36 0.36 0.7 116 -0.88 2 118
CDKN2A 0.18 0.11 0.23 234 -0.15 9 243
LAMA4 0.33 0.5 0.75 111 -1 17 128
FOXM1B/HNF6 0.37 0.38 0.74 99 -0.99 2 101
FOS 0.35 0.46 0.76 109 -0.94 11 120
SP1 0.02 0.009 -10000 0 -0.11 1 1
CDC25B 0.41 0.38 0.76 112 -0.91 2 114
response to radiation 0.073 0.069 0.17 75 -10000 0 75
CENPB 0.41 0.38 0.76 111 -0.91 2 113
CENPA 0.47 0.4 0.86 107 -0.98 1 108
NEK2 0.5 0.4 0.84 131 -0.91 1 132
HIST1H2BA 0.4 0.38 0.76 109 -0.91 2 111
CCNA2 0.035 0.036 0.32 2 -10000 0 2
EP300 0.02 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.4 0.4 0.82 91 -1 2 93
CCNB2 0.48 0.39 0.82 131 -0.84 2 133
CCNB1 0.42 0.4 0.8 112 -0.96 2 114
ETV5 0.47 0.4 0.8 136 -0.86 1 137
ESR1 0.14 0.6 0.76 100 -0.94 21 121
CCND1 0.35 0.37 0.71 114 -0.85 2 116
GSK3A 0.084 0.077 0.18 75 -10000 0 75
Cyclin A-E1/CDK1-2 0.1 0.086 0.22 67 -10000 0 67
CDK2 0.033 0.027 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.092 0.086 0.18 111 -10000 0 111
FOXM1B/Cbp/p300 0.29 0.33 0.66 68 -0.97 2 70
GAS1 0.068 0.63 0.76 98 -0.96 26 124
MMP2 0.36 0.46 0.75 111 -1 11 122
RB1/FOXM1C 0.32 0.35 0.67 103 -0.9 2 105
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.048 0.099 -10000 0 -0.41 18 18
Crk/p130 Cas/Paxillin -0.15 0.089 -10000 0 -0.22 165 165
JUN -0.1 0.091 -10000 0 -0.28 19 19
HRAS 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.098 -10000 0 -0.17 187 187
RAP1A 0.021 0.002 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.098 0.098 -10000 0 -0.17 184 184
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.094 0.084 -10000 0 -0.16 189 189
RHOA 0.019 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.092 0.089 -10000 0 -0.16 189 189
GRB7 0.021 0.023 0.29 2 -10000 0 2
RET51/GFRalpha1/GDNF -0.099 0.097 -10000 0 -0.17 184 184
MAPKKK cascade -0.11 0.082 -10000 0 -0.19 139 139
BCAR1 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.098 0.088 -10000 0 -0.16 189 189
lamellipodium assembly -0.14 0.086 -10000 0 -0.22 123 123
RET51/GFRalpha1/GDNF/SHC -0.092 0.098 -10000 0 -0.17 172 172
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.086 0.085 -10000 0 -0.16 172 172
RET9/GFRalpha1/GDNF/Shank3 -0.094 0.084 -10000 0 -0.16 189 189
MAPK3 -0.097 0.085 0.2 2 -0.26 10 12
DOK1 0.02 0.003 -10000 0 -10000 0 0
DOK6 0.011 0.051 -10000 0 -0.29 8 8
PXN 0.021 0.001 -10000 0 -10000 0 0
neurite development -0.1 0.078 -10000 0 -0.25 16 16
DOK5 0.013 0.044 0.29 1 -0.29 5 6
GFRA1 -0.22 0.13 -10000 0 -0.29 228 228
MAPK8 -0.095 0.097 -10000 0 -0.19 146 146
HRAS/GTP -0.11 0.1 -10000 0 -0.2 146 146
tube development -0.089 0.082 0.19 1 -0.15 183 184
MAPK1 -0.097 0.087 0.17 8 -0.26 10 18
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.088 -10000 0 -0.18 181 181
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
SRC 0.019 0.006 -10000 0 -10000 0 0
PDLIM7 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.092 0.1 -10000 0 -0.17 176 176
SHC1 0.019 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.097 -10000 0 -0.17 189 189
RET51/GFRalpha1/GDNF/Dok5 -0.096 0.1 0.21 1 -0.17 177 178
PRKCA 0.014 0.044 -10000 0 -0.29 6 6
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.13 0.13 -10000 0 -0.24 163 163
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.092 -10000 0 -0.18 167 167
RET51/GFRalpha1/GDNF/Grb7 -0.097 0.096 -10000 0 -0.17 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.007 0.062 -10000 0 -0.29 12 12
DOK4 0.02 0.004 -10000 0 -10000 0 0
JNK cascade -0.1 0.089 -10000 0 -0.28 19 19
RET9/GFRalpha1/GDNF/FRS2 -0.093 0.085 -10000 0 -0.16 186 186
SHANK3 0.02 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.004 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.097 0.09 -10000 0 -0.18 162 162
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.12 0.098 -10000 0 -0.19 187 187
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.097 0.1 -10000 0 -0.19 150 150
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.1 -10000 0 -0.19 163 163
PI3K -0.18 0.13 -10000 0 -0.3 126 126
SOS1 0.02 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.087 0.084 -10000 0 -0.15 183 183
GRB10 0.019 0.018 -10000 0 -0.29 1 1
activation of MAPKK activity -0.11 0.089 -10000 0 -0.26 13 13
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.097 -10000 0 -0.17 186 186
GAB1 0.02 0.003 -10000 0 -10000 0 0
IRS1 0.008 0.056 -10000 0 -0.29 10 10
IRS2 0.011 0.051 -10000 0 -0.29 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.11 -10000 0 -0.2 167 167
RET51/GFRalpha1/GDNF/PKC alpha -0.1 0.098 -10000 0 -0.17 185 185
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GDNF -0.004 0.017 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.1 0.1 -10000 0 -0.17 189 189
Rac1/GTP -0.16 0.1 -10000 0 -0.25 123 123
RET9/GFRalpha1/GDNF -0.1 0.087 -10000 0 -0.17 189 189
GFRalpha1/GDNF -0.13 0.1 -10000 0 -0.2 189 189
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.02 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.16 0.076 0.2 235 -0.1 1 236
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.021 0.012 -10000 0 -10000 0 0
AURKB 0.26 0.096 0.29 255 -10000 0 255
AURKC 0.019 0.019 -10000 0 -0.29 1 1
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.27 0.41 -10000 0 -0.84 95 95
NCK1/PAK1/Dok-R -0.14 0.18 -10000 0 -0.39 96 96
NCK1/Dok-R -0.27 0.44 -10000 0 -0.86 95 95
PIK3CA 0.014 0.01 -10000 0 -10000 0 0
mol:beta2-estradiol 0.028 0.068 0.23 28 -10000 0 28
RELA 0.02 0.003 -10000 0 -10000 0 0
SHC1 0.007 0.018 -10000 0 -10000 0 0
Rac/GDP 0.015 0.002 -10000 0 -10000 0 0
F2 0.021 0.08 0.26 27 -10000 0 27
TNIP2 0.019 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.26 0.44 -10000 0 -0.85 95 95
FN1 0.01 0.051 -10000 0 -0.29 8 8
PLD2 -0.3 0.47 -10000 0 -0.94 94 94
PTPN11 0.021 0.001 -10000 0 -10000 0 0
GRB14 0.07 0.11 0.29 54 -10000 0 54
ELK1 -0.29 0.43 -10000 0 -0.88 95 95
GRB7 0.021 0.023 0.29 2 -10000 0 2
PAK1 0.019 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.27 0.46 -10000 0 -0.89 95 95
CDKN1A -0.19 0.29 -10000 0 -0.6 95 95
ITGA5 0.018 0.026 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.28 0.46 -10000 0 -0.9 95 95
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.2 0.3 -10000 0 -0.63 95 95
PLG -0.31 0.47 -10000 0 -0.94 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.26 0.38 -10000 0 -0.8 95 95
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.008 0.018 -10000 0 -10000 0 0
ANGPT2 -0.14 0.26 -10000 0 -0.72 36 36
BMX -0.35 0.48 -10000 0 -1 94 94
ANGPT1 -0.13 0.32 -10000 0 -1.1 27 27
tube development -0.22 0.32 -10000 0 -0.66 96 96
ANGPT4 0.006 0.018 -10000 0 -10000 0 0
response to hypoxia -0.021 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.28 0.5 -10000 0 -0.95 96 96
alpha5/beta1 Integrin 0.028 0.02 -10000 0 -0.2 2 2
FGF2 -0.073 0.14 -10000 0 -0.29 88 88
STAT5A (dimer) -0.24 0.37 -10000 0 -0.75 95 95
mol:L-citrulline -0.2 0.3 -10000 0 -0.63 95 95
AGTR1 -0.093 0.14 -10000 0 -0.29 99 99
MAPK14 -0.34 0.52 -10000 0 -1.1 95 95
Tie2/SHP2 -0.28 0.45 -10000 0 -0.92 91 91
TEK -0.31 0.48 -10000 0 -1 91 91
RPS6KB1 -0.26 0.4 -10000 0 -0.81 95 95
Angiotensin II/AT1 -0.06 0.097 -10000 0 -0.2 99 99
Tie2/Ang1/GRB2 -0.3 0.49 -10000 0 -0.95 96 96
MAPK3 -0.29 0.43 -10000 0 -0.88 94 94
MAPK1 -0.29 0.43 -10000 0 -0.88 94 94
Tie2/Ang1/GRB7 -0.3 0.49 -10000 0 -0.95 96 96
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.31 0.47 -10000 0 -0.94 96 96
PI3K -0.32 0.47 -10000 0 -0.97 95 95
FES -0.34 0.52 -10000 0 -1.1 95 95
Crk/Dok-R -0.28 0.46 -10000 0 -0.9 95 95
Tie2/Ang1/ABIN2 -0.3 0.49 -10000 0 -0.95 96 96
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.24 0.36 -10000 0 -0.75 95 95
STAT5A 0.02 0.002 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.26 0.39 -10000 0 -0.8 95 95
Tie2/Ang2 -0.29 0.44 -10000 0 -0.89 95 95
Tie2/Ang1 -0.32 0.51 -10000 0 -1 95 95
FOXO1 -0.24 0.37 -10000 0 -0.75 95 95
ELF1 -0.018 0.062 -10000 0 -0.12 74 74
ELF2 -0.3 0.47 -10000 0 -0.94 94 94
mol:Choline -0.29 0.44 -10000 0 -0.9 94 94
cell migration -0.08 0.1 -10000 0 -0.22 96 96
FYN -0.25 0.36 -10000 0 -0.75 96 96
DOK2 0.019 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.17 0.27 -10000 0 -0.54 95 95
ETS1 -0.012 0.071 -10000 0 -0.25 22 22
PXN -0.21 0.33 -10000 0 -0.67 95 95
ITGB1 0.02 0.003 -10000 0 -10000 0 0
NOS3 -0.23 0.35 -10000 0 -0.72 95 95
RAC1 0.02 0.003 -10000 0 -10000 0 0
TNF -0.015 0.082 0.28 3 -0.24 26 29
MAPKKK cascade -0.29 0.44 -10000 0 -0.9 94 94
RASA1 0.02 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.3 0.49 -10000 0 -0.95 96 96
NCK1 0.015 0.009 -10000 0 -10000 0 0
vasculogenesis -0.18 0.27 -10000 0 -0.56 95 95
mol:Phosphatidic acid -0.29 0.44 -10000 0 -0.9 94 94
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.2 0.3 -10000 0 -0.63 95 95
Rac1/GTP -0.24 0.37 -10000 0 -0.76 95 95
MMP2 -0.31 0.48 -10000 0 -0.95 95 95
TCGA08_p53

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
CDKN2A 0.13 0.043 0.14 270 -10000 0 270
TP53 0.026 0.062 -10000 0 -0.12 40 40
Senescence 0.026 0.061 -10000 0 -0.12 40 40
Apoptosis 0.026 0.061 -10000 0 -0.12 40 40
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.086 0.052 0.2 7 -0.18 5 12
MDM4 0.019 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.003 0.073 -10000 0 -0.2 33 33
AKT1 -0.11 0.21 0.24 3 -0.42 80 83
PTK2B -0.14 0.19 0.32 1 -0.43 84 85
VEGFR2 homodimer/Frs2 -0.15 0.21 -10000 0 -0.47 85 85
CAV1 -0.008 0.088 -10000 0 -0.29 26 26
CALM1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.21 -10000 0 -0.43 85 85
endothelial cell proliferation -0.1 0.21 0.32 10 -0.4 84 94
mol:Ca2+ -0.13 0.18 0.17 4 -0.4 84 88
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.093 0.21 -10000 0 -0.42 83 83
RP11-342D11.1 -0.13 0.18 0.16 4 -0.4 85 89
CDH5 0.013 0.048 -10000 0 -0.29 7 7
VEGFA homodimer 0.043 0.021 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
SHC2 0.007 0.062 -10000 0 -0.29 12 12
HRAS/GDP -0.13 0.16 -10000 0 -0.37 80 80
SH2D2A 0.028 0.048 0.29 9 -10000 0 9
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.098 0.21 0.25 2 -0.4 85 87
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.1 0.21 0.2 3 -0.43 85 88
VEGFR1 homodimer 0.019 0.019 -10000 0 -0.29 1 1
SHC/GRB2/SOS1 -0.083 0.2 -10000 0 -0.39 85 85
GRB10 -0.13 0.18 0.17 4 -0.42 80 84
PTPN11 0.021 0.001 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
PAK1 0.019 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.089 0.21 -10000 0 -0.41 84 84
HRAS 0.02 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.11 0.18 -10000 0 -0.35 86 86
HIF1A 0.02 0.003 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.093 0.2 -10000 0 -0.41 83 83
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.006 0.064 -10000 0 -0.29 13 13
Nck/Pak 0.021 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.21 -10000 0 -0.43 88 88
mol:GDP -0.087 0.19 -10000 0 -0.38 85 85
mol:NADP -0.094 0.19 0.29 5 -0.36 85 90
eNOS/Hsp90 -0.084 0.18 0.34 2 -0.34 85 87
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:IP3 -0.13 0.18 0.17 4 -0.41 84 88
HIF1A/ARNT 0.028 0.009 -10000 0 -10000 0 0
SHB 0.02 0.003 -10000 0 -10000 0 0
VEGFA 0.02 0.005 -10000 0 -10000 0 0
VEGFC 0.01 0.054 -10000 0 -0.29 9 9
FAK1/Vinculin -0.16 0.25 0.27 3 -0.52 87 90
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.22 -10000 0 -0.44 87 87
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.068 0.14 -10000 0 -0.28 86 86
mol:L-citrulline -0.094 0.19 0.29 5 -0.36 85 90
ITGAV 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.095 0.21 -10000 0 -0.41 84 84
VEGFR2 homodimer/VEGFA homodimer -0.11 0.21 -10000 0 -0.44 85 85
VEGFR2/3 heterodimer -0.16 0.22 -10000 0 -0.48 87 87
VEGFB 0.02 0.003 -10000 0 -10000 0 0
MAPK11 -0.12 0.19 0.22 4 -0.42 82 86
VEGFR2 homodimer -0.16 0.24 -10000 0 -0.55 80 80
FLT1 0.019 0.019 -10000 0 -0.29 1 1
NEDD4 0.02 0.005 -10000 0 -10000 0 0
MAPK3 -0.12 0.17 0.21 4 -0.38 82 86
MAPK1 -0.12 0.17 0.22 3 -0.38 82 85
VEGFA145/NRP2 0.023 0.032 -10000 0 -0.2 5 5
VEGFR1/2 heterodimer -0.15 0.21 -10000 0 -0.47 85 85
KDR -0.16 0.24 -10000 0 -0.55 80 80
VEGFA165/NRP1/VEGFR2 homodimer -0.1 0.2 -10000 0 -0.41 85 85
SRC 0.019 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.12 0.18 0.29 6 -0.38 84 90
PI3K -0.13 0.19 -10000 0 -0.43 78 78
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.1 0.2 -10000 0 -0.4 84 84
FES -0.13 0.18 0.17 4 -0.42 83 87
GAB1 -0.15 0.22 -10000 0 -0.47 86 86
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.21 -10000 0 -0.43 84 84
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
ARNT 0.019 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.089 0.18 0.27 4 -0.35 85 89
VEGFR2 homodimer/VEGFA homodimer/Yes -0.11 0.21 -10000 0 -0.43 85 85
PI3K/GAB1 -0.1 0.21 -10000 0 -0.44 74 74
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.084 0.19 -10000 0 -0.38 83 83
PRKACA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.12 0.22 -10000 0 -0.44 90 90
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.14 0.18 0.17 4 -0.42 83 87
actin cytoskeleton reorganization -0.1 0.21 0.2 3 -0.42 85 88
PTK2 -0.17 0.26 0.3 2 -0.55 87 89
EDG1 -0.13 0.18 0.16 4 -0.4 85 89
mol:DAG -0.13 0.18 0.17 4 -0.41 84 88
CaM/Ca2+ -0.12 0.17 0.16 3 -0.38 83 86
MAP2K3 -0.11 0.16 0.16 1 -0.35 81 82
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.2 -10000 0 -0.43 80 80
PLCG1 -0.13 0.18 0.17 4 -0.41 84 88
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.095 0.21 -10000 0 -0.41 84 84
IQGAP1 0.02 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.21 -10000 0 -0.44 85 85
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.21 -10000 0 -0.44 85 85
cell migration -0.15 0.22 0.28 3 -0.47 87 90
mol:PI-3-4-5-P3 -0.12 0.18 -10000 0 -0.4 78 78
FYN 0.015 0.04 -10000 0 -0.29 5 5
VEGFB/NRP1 -0.13 0.17 0.16 4 -0.39 85 89
mol:NO -0.094 0.19 0.29 5 -0.36 85 90
PXN 0.021 0.001 -10000 0 -10000 0 0
HRAS/GTP -0.13 0.15 -10000 0 -0.36 83 83
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.14 0.18 -10000 0 -0.43 80 80
VHL 0.019 0.005 -10000 0 -10000 0 0
ITGB3 -0.016 0.1 -10000 0 -0.29 34 34
NOS3 -0.11 0.21 0.32 4 -0.4 85 89
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.22 -10000 0 -0.43 90 90
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.13 0.17 0.16 3 -0.39 82 85
PRKCB -0.13 0.17 0.16 3 -0.39 83 86
VCL 0.02 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.13 0.18 0.16 4 -0.4 85 89
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.21 -10000 0 -0.43 86 86
VEGFA165/NRP2 0.023 0.032 -10000 0 -0.2 5 5
MAPKKK cascade -0.12 0.17 -10000 0 -0.38 78 78
NRP2 0.014 0.041 -10000 0 -0.29 5 5
VEGFC homodimer 0.01 0.054 -10000 0 -0.29 9 9
NCK1 0.015 0.009 -10000 0 -10000 0 0
ROCK1 0.02 0.002 -10000 0 -10000 0 0
FAK1/Paxillin -0.16 0.25 0.27 3 -0.52 87 90
MAP3K13 -0.11 0.16 0.17 1 -0.36 82 83
PDPK1 -0.11 0.16 -10000 0 -0.37 78 78
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.019 0.091 -10000 0 -0.15 92 92
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.19 -10000 0 -0.37 105 105
AKT1 -0.25 0.34 -10000 0 -0.67 112 112
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.25 0.34 -10000 0 -0.68 112 112
mol:Ca2+ -0.1 0.15 0.29 1 -0.33 79 80
IGF1R 0.018 0.026 -10000 0 -0.29 2 2
E2/ER alpha (dimer)/Striatin -0.037 0.09 -10000 0 -0.17 94 94
SHC1 0.019 0.006 -10000 0 -10000 0 0
apoptosis 0.24 0.32 0.64 112 -10000 0 112
RhoA/GTP -0.063 0.055 -10000 0 -0.15 78 78
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.19 -10000 0 -0.37 96 96
regulation of stress fiber formation 0.056 0.062 0.23 2 -0.2 3 5
E2/ERA-ERB (dimer) -0.037 0.09 -10000 0 -0.17 93 93
KRAS 0.019 0.005 -10000 0 -10000 0 0
G13/GTP -0.032 0.081 -10000 0 -0.15 93 93
pseudopodium formation -0.056 0.062 0.2 3 -0.23 2 5
E2/ER alpha (dimer)/PELP1 -0.038 0.089 -10000 0 -0.17 95 95
GRB2 0.02 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.003 -10000 0 -10000 0 0
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
HRAS 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.18 0.22 0.23 1 -0.43 116 117
E2/ER beta (dimer) 0.015 0.002 -10000 0 -10000 0 0
mol:GDP -0.11 0.13 -10000 0 -0.27 104 104
mol:NADP -0.18 0.22 0.23 1 -0.43 116 117
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:IP3 -0.11 0.15 -10000 0 -0.34 79 79
IGF-1R heterotetramer 0.018 0.026 -10000 0 -0.29 2 2
PLCB1 -0.11 0.15 -10000 0 -0.35 78 78
PLCB2 -0.11 0.16 -10000 0 -0.35 82 82
IGF1 -0.079 0.14 -10000 0 -0.29 93 93
mol:L-citrulline -0.18 0.22 0.23 1 -0.43 116 117
RHOA 0.019 0.006 -10000 0 -10000 0 0
Gai/GDP -0.11 0.23 -10000 0 -0.66 37 37
JNK cascade 0.015 0.002 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
ESR2 0.02 0.003 -10000 0 -10000 0 0
GNAQ 0.02 0.003 -10000 0 -10000 0 0
ESR1 -0.082 0.14 -10000 0 -0.29 95 95
Gq family/GDP/Gbeta gamma -0.077 0.19 -10000 0 -0.75 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.061 0.12 -10000 0 -0.68 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.14 0.19 -10000 0 -0.37 92 92
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
E2/ER alpha (dimer) -0.054 0.098 -10000 0 -0.2 95 95
STRN 0.02 0.003 -10000 0 -10000 0 0
GNAL 0.008 0.059 -10000 0 -0.29 11 11
PELP1 0.019 0.006 -10000 0 -10000 0 0
MAPK11 -0.014 0.004 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
HBEGF -0.13 0.2 0.33 11 -0.44 49 60
cAMP biosynthetic process -0.034 0.078 -10000 0 -0.14 97 97
SRC -0.14 0.19 0.25 2 -0.36 98 100
PI3K 0.019 0.015 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.067 0.14 -10000 0 -0.26 92 92
SOS1 0.02 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.16 -10000 0 -0.34 111 111
Gs family/GTP -0.031 0.082 -10000 0 -0.14 97 97
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.012 -10000 0 -10000 0 0
vasodilation -0.17 0.21 0.22 1 -0.41 116 117
mol:DAG -0.11 0.15 -10000 0 -0.34 79 79
Gs family/GDP/Gbeta gamma -0.11 0.11 -10000 0 -0.26 100 100
MSN -0.059 0.065 0.21 3 -0.24 2 5
Gq family/GTP -0.1 0.17 -10000 0 -0.36 82 82
mol:PI-3-4-5-P3 -0.24 0.33 -10000 0 -0.65 112 112
NRAS 0.021 0.002 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.17 0.21 0.41 116 -0.22 1 117
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.083 0.14 -10000 0 -0.27 100 100
NOS3 -0.19 0.24 0.23 1 -0.45 116 117
GNA11 0.019 0.019 -10000 0 -0.29 1 1
MAPKKK cascade -0.19 0.26 0.25 1 -0.51 109 110
E2/ER alpha (dimer)/PELP1/Src -0.14 0.2 0.24 2 -0.38 100 102
ruffle organization -0.056 0.062 0.2 3 -0.23 2 5
ROCK2 -0.057 0.07 0.21 4 -0.25 1 5
GNA14 -0.066 0.14 -10000 0 -0.29 81 81
GNA15 0.035 0.064 0.29 17 -10000 0 17
GNA13 0.02 0.003 -10000 0 -10000 0 0
MMP9 -0.12 0.19 0.36 11 -0.45 44 55
MMP2 -0.14 0.19 0.33 4 -0.45 49 53
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.029 0.007 -10000 0 -10000 0 0
Necdin/E2F1 -0.056 0.12 0.22 6 -0.2 107 113
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.048 0.12 -10000 0 -0.18 129 129
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.14 -10000 0 -0.23 190 190
NT-4/5 (dimer)/p75(NTR) 0.11 0.12 0.22 152 -0.2 17 169
IKBKB 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.025 0.12 0.17 51 -0.28 10 61
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF 0.035 0.063 0.29 16 -10000 0 16
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.057 -10000 0 -0.17 22 22
FURIN 0.02 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.034 0.063 0.21 13 -0.17 18 31
LINGO1 0.016 0.036 -10000 0 -0.29 4 4
Sortilin/TRAF6/NRIF -0.034 0.016 -10000 0 -10000 0 0
proBDNF (dimer) 0.035 0.063 0.29 16 -10000 0 16
NTRK1 0.017 0.009 -10000 0 -10000 0 0
RTN4R 0.02 0.003 -10000 0 -10000 0 0
neuron apoptosis -0.056 0.1 0.32 2 -0.3 18 20
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.087 0.088 -10000 0 -0.19 116 116
ARHGDIA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.014 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.051 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.051 0.12 -10000 0 -0.18 125 125
MAGEH1 0.008 0.059 -10000 0 -0.29 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.14 -10000 0 -0.22 174 174
Mammalian IAPs/DIABLO 0.042 0.024 0.21 1 -10000 0 1
proNGF (dimer) -0.11 0.15 -10000 0 -0.29 122 122
MAGED1 0.018 0.026 -10000 0 -0.29 2 2
APP 0.02 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.16 0.14 0.29 153 -10000 0 153
ZNF274 0.02 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.06 0.093 -10000 0 -0.16 126 126
NGF -0.11 0.15 -10000 0 -0.29 122 122
cell cycle arrest -0.046 0.092 0.24 5 -0.24 13 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.079 0.11 -10000 0 -0.2 119 119
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.11 0.11 0.21 146 -0.17 17 163
NCSTN 0.019 0.005 -10000 0 -10000 0 0
mol:GTP -0.059 0.12 -10000 0 -0.19 127 127
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.082 0.084 0.17 4 -0.18 118 122
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.047 0.088 -10000 0 -0.28 19 19
p75(NTR)/beta APP 0.015 0.056 -10000 0 -0.2 18 18
BEX1 -0.12 0.15 -10000 0 -0.29 126 126
mol:GDP -0.087 0.088 -10000 0 -0.18 127 127
NGF (dimer) -0.047 0.1 0.21 2 -0.17 121 123
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.032 0.057 -10000 0 -0.16 22 22
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
RAC1/GTP -0.048 0.099 -10000 0 -0.16 126 126
MYD88 0.019 0.005 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.059 0.12 -10000 0 -0.19 127 127
RHOB 0.019 0.019 -10000 0 -0.29 1 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.029 0.22 6 -10000 0 6
NT3 (dimer) -0.021 0.1 -10000 0 -0.29 36 36
TP53 -0.02 0.059 0.17 17 -10000 0 17
PRDM4 -0.087 0.084 0.17 4 -0.18 125 129
BDNF (dimer) 0.068 0.1 0.23 68 -0.14 17 85
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
SORT1 0.02 0.002 -10000 0 -10000 0 0
activation of caspase activity -0.05 0.12 -10000 0 -0.18 129 129
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.047 0.11 -10000 0 -0.18 124 124
RHOC 0.021 0.002 -10000 0 -10000 0 0
XIAP 0.021 0.002 -10000 0 -10000 0 0
MAPK10 -0.12 0.13 0.4 2 -0.32 57 59
DIABLO 0.021 0.001 -10000 0 -10000 0 0
SMPD2 -0.083 0.084 0.17 4 -0.18 118 122
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.059 0.12 -10000 0 -0.19 126 126
PSEN1 0.02 0.003 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.005 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.014 0.094 -10000 0 -0.22 50 50
MAPK8 -0.084 0.1 0.4 2 -0.27 28 30
MAPK9 -0.083 0.1 0.52 1 -0.27 30 31
APAF1 0.021 0.001 -10000 0 -10000 0 0
NTF3 -0.021 0.1 -10000 0 -0.29 36 36
NTF4 0.16 0.14 0.29 153 -10000 0 153
NDN -0.1 0.15 -10000 0 -0.29 114 114
RAC1/GDP 0.015 0.002 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.041 0.1 -10000 0 -0.16 120 120
p75 CTF/Sortilin/TRAF6/NRIF 0.047 0.018 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.059 0.12 -10000 0 -0.19 127 127
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.049 0.062 0.21 13 -0.16 15 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.044 0.063 0.21 13 -0.16 16 29
PRKACB 0.021 0.002 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.039 0.043 0.22 16 -10000 0 16
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.017 0.018 0.29 1 -10000 0 1
BIRC2 0.016 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.09 0.12 0.19 3 -0.24 92 95
BAD -0.11 0.12 0.38 2 -0.29 48 50
RIPK2 0.02 0.004 -10000 0 -10000 0 0
NGFR 0.001 0.075 -10000 0 -0.29 18 18
CYCS -0.083 0.088 0.24 5 -0.28 14 19
ADAM17 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.047 0.11 -10000 0 -0.18 122 122
BCL2L11 -0.11 0.12 0.38 2 -0.29 48 50
BDNF (dimer)/p75(NTR) 0.024 0.069 0.22 13 -0.2 18 31
PI3K -0.029 0.095 -10000 0 -0.18 77 77
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.047 0.12 -10000 0 -0.18 125 125
NDNL2 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.079 0.13 -10000 0 -0.22 127 127
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.046 0.12 -10000 0 -0.18 124 124
TRAF6 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.02 0.004 -10000 0 -10000 0 0
PLG -0.007 0.034 0.29 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.084 0.088 -10000 0 -0.18 119 119
SQSTM1 0.02 0.004 -10000 0 -10000 0 0
NGFRAP1 0.008 0.062 -10000 0 -0.29 12 12
CASP3 -0.1 0.11 0.36 2 -0.27 52 54
E2F1 0.024 0.04 0.29 6 -10000 0 6
CASP9 0.02 0.003 -10000 0 -10000 0 0
IKK complex -0.055 0.13 -10000 0 -0.25 72 72
NGF (dimer)/TRKA -0.062 0.11 -10000 0 -0.2 112 112
MMP7 -0.001 0.078 0.29 2 -0.29 18 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.037 0.11 -10000 0 -0.17 117 117
MMP3 0.08 0.12 0.29 68 -10000 0 68
APAF-1/Caspase 9 -0.086 0.067 -10000 0 -0.25 13 13
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.076 0.056 0.12 18 -0.096 247 265
BUB1B 0.088 0.046 0.12 116 -0.12 2 118
PLK1 0.025 0.03 0.09 28 -0.077 1 29
PLK1S1 0.016 0.031 0.11 8 -0.16 4 12
KIF2A 0.015 0.026 0.11 5 -10000 0 5
regulation of mitotic centrosome separation 0.025 0.03 0.09 27 -0.077 1 28
GOLGA2 0.021 0.002 -10000 0 -10000 0 0
Hec1/SPC24 0.054 0.056 0.22 24 -10000 0 24
WEE1 0.011 0.069 -10000 0 -0.31 11 11
cytokinesis 0.11 0.056 0.17 37 -0.16 1 38
PP2A-alpha B56 0.11 0.11 -10000 0 -0.5 5 5
AURKA 0.024 0.035 0.13 21 -0.17 1 22
PICH/PLK1 0.03 0.064 0.17 42 -10000 0 42
CENPE 0.015 0.027 0.098 11 -10000 0 11
RhoA/GTP 0.014 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.016 0.026 0.11 5 -10000 0 5
PPP2CA 0.02 0.005 -10000 0 -10000 0 0
FZR1 0.019 0.005 -10000 0 -10000 0 0
TPX2 0.11 0.023 0.11 280 -10000 0 280
PAK1 0.018 0.006 -10000 0 -10000 0 0
SPC24 0.043 0.077 0.29 25 -10000 0 25
FBXW11 0.02 0.004 -10000 0 -10000 0 0
CLSPN 0.11 0.039 0.14 117 -10000 0 117
GORASP1 0.019 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.011 1 -0.011 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.012 0.016 0.05 21 -0.041 1 22
G2 phase of mitotic cell cycle -0.001 0.002 0.012 1 -10000 0 1
STAG2 0.021 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.025 0.13 -10000 0 -0.49 22 22
spindle elongation 0.025 0.03 0.09 27 -0.077 1 28
ODF2 0.02 0.006 -10000 0 -10000 0 0
BUB1 0.11 0.12 -10000 0 -0.57 5 5
TPT1 0.006 0.047 -10000 0 -0.17 17 17
CDC25C 0.11 0.079 0.15 176 -0.22 11 187
CDC25B 0.019 0.009 -10000 0 -10000 0 0
SGOL1 0.076 0.056 0.096 247 -0.12 18 265
RHOA 0.019 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.025 -10000 0 -10000 0 0
CDC14B -0.01 0.003 -10000 0 -10000 0 0
CDC20 0.29 0.041 0.29 286 -10000 0 286
PLK1/PBIP1 0.039 0.05 0.1 106 -10000 0 106
mitosis -0.002 0.004 0.017 2 -0.015 9 11
FBXO5 0.01 0.026 0.095 4 -0.1 1 5
CDC2 0.001 0.002 -10000 0 -0.009 1 1
NDC80 0.02 0.004 -10000 0 -10000 0 0
metaphase plate congression 0.018 0.037 -10000 0 -0.22 5 5
ERCC6L 0.026 0.06 0.15 40 -10000 0 40
NLP/gamma Tubulin 0.014 0.018 0.073 10 -10000 0 10
microtubule cytoskeleton organization 0.006 0.047 -10000 0 -0.17 17 17
G2/M transition DNA damage checkpoint -0.001 0.003 0.013 10 -10000 0 10
PPP1R12A 0.021 0.003 -10000 0 -10000 0 0
interphase -0.001 0.003 0.013 10 -10000 0 10
PLK1/PRC1-2 0.19 0.064 0.21 264 -10000 0 264
GRASP65/GM130/RAB1/GTP/PLK1 0.044 0.028 -10000 0 -10000 0 0
RAB1A 0.02 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.018 0.026 0.083 28 -10000 0 28
mitotic prometaphase 0.001 0.003 0.017 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.057 0.18 4 -0.34 2 6
microtubule-based process 0.2 0.054 0.21 275 -10000 0 275
Golgi organization 0.025 0.03 0.09 27 -0.077 1 28
Cohesin/SA2 0.032 0.024 0.11 6 -10000 0 6
PPP1CB/MYPT1 0.03 0.007 -10000 0 -10000 0 0
KIF20A 0.28 0.068 0.29 275 -10000 0 275
APC/C/CDC20 0.21 0.038 0.21 286 -10000 0 286
PPP2R1A 0.02 0.004 -10000 0 -10000 0 0
chromosome segregation 0.038 0.049 0.1 106 -10000 0 106
PRC1 0.02 0.004 -10000 0 -10000 0 0
ECT2 0.093 0.11 0.23 108 -10000 0 108
C13orf34 0.019 0.025 0.077 27 -10000 0 27
NUDC 0.018 0.037 -10000 0 -0.22 5 5
regulation of attachment of spindle microtubules to kinetochore 0.088 0.046 0.12 119 -0.12 2 121
spindle assembly 0.018 0.025 0.086 17 -0.067 1 18
spindle stabilization 0.016 0.031 0.11 8 -0.16 4 12
APC/C/HCDH1 0.008 0.014 -10000 0 -10000 0 0
MKLP2/PLK1 0.2 0.054 0.21 275 -10000 0 275
CCNB1 0.02 0.007 -10000 0 -10000 0 0
PPP1CB 0.02 0.005 -10000 0 -10000 0 0
BTRC 0.02 0.004 -10000 0 -10000 0 0
ROCK2 0.015 0.051 0.17 1 -0.37 2 3
TUBG1 0.016 0.019 0.1 2 -0.15 1 3
G2/M transition of mitotic cell cycle 0.004 0.022 -10000 0 -10000 0 0
MLF1IP 0.049 0.075 0.14 109 -10000 0 109
INCENP 0.021 0.005 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.022 0.03 0.3 2 -10000 0 2
CDKN2C -0.031 0.019 -10000 0 -10000 0 0
CDKN2A 0.27 0.083 0.3 265 -10000 0 265
CCND2 -0.074 0.048 -10000 0 -0.18 25 25
RB1 0.079 0.048 0.21 19 -10000 0 19
CDK4 -0.082 0.048 -10000 0 -0.21 19 19
CDK6 -0.083 0.051 -10000 0 -0.19 28 28
G1/S progression -0.078 0.052 0.18 2 -0.2 20 22
HIF-1-alpha transcription factor network

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
PKM2 -0.19 0.25 0.35 6 -0.56 60 66
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.18 0.28 0.47 5 -0.63 51 56
SMAD4 0.019 0.005 -10000 0 -10000 0 0
ID2 -0.18 0.26 0.39 4 -0.57 55 59
AP1 0.011 0.062 -10000 0 -0.2 22 22
ABCG2 -0.24 0.29 0.39 4 -0.6 86 90
HIF1A -0.044 0.064 0.16 1 -0.19 6 7
TFF3 -0.19 0.3 0.44 9 -0.6 69 78
GATA2 0.009 0.048 -10000 0 -0.29 7 7
AKT1 -0.054 0.079 -10000 0 -0.21 29 29
response to hypoxia -0.051 0.067 0.13 1 -0.18 33 34
MCL1 -0.18 0.26 0.4 3 -0.57 58 61
NDRG1 -0.17 0.25 0.39 4 -0.57 52 56
SERPINE1 -0.18 0.26 0.39 4 -0.56 57 61
FECH -0.18 0.26 0.39 4 -0.57 58 62
FURIN -0.18 0.26 0.39 4 -0.57 57 61
NCOA2 0.012 0.039 -10000 0 -0.29 4 4
EP300 -0.062 0.11 0.19 1 -0.32 36 37
HMOX1 -0.18 0.26 0.39 4 -0.57 58 62
BHLHE40 -0.18 0.26 0.4 3 -0.57 58 61
BHLHE41 -0.18 0.26 0.39 4 -0.57 56 60
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.042 0.1 0.27 1 -0.32 2 3
ENG -0.05 0.094 0.25 2 -0.3 2 4
JUN 0.019 0.019 -10000 0 -0.29 1 1
RORA -0.18 0.26 0.39 4 -0.57 57 61
ABCB1 -0.28 0.4 -10000 0 -0.86 90 90
TFRC -0.15 0.23 0.4 3 -0.57 40 43
CXCR4 -0.18 0.26 0.39 4 -0.57 58 62
TF -0.16 0.25 0.42 6 -0.56 49 55
CITED2 -0.19 0.27 0.39 4 -0.57 65 69
HIF1A/ARNT -0.18 0.31 0.65 5 -0.65 45 50
LDHA -0.078 0.19 -10000 0 -0.66 24 24
ETS1 -0.18 0.26 0.4 3 -0.57 57 60
PGK1 -0.18 0.26 0.39 4 -0.56 60 64
NOS2 -0.18 0.27 0.44 6 -0.57 60 66
ITGB2 -0.18 0.26 0.39 4 -0.57 58 62
ALDOA -0.18 0.26 0.39 4 -0.57 58 62
Cbp/p300/CITED2 -0.23 0.32 0.48 1 -0.71 60 61
FOS -0.003 0.082 -10000 0 -0.29 22 22
HK2 -0.15 0.28 0.46 8 -0.56 56 64
SP1 -0.017 0.061 -10000 0 -0.12 41 41
GCK -0.16 0.36 -10000 0 -1.2 31 31
HK1 -0.18 0.26 0.39 4 -0.57 58 62
NPM1 -0.18 0.26 0.39 4 -0.56 59 63
EGLN1 -0.18 0.26 0.4 3 -0.57 56 59
CREB1 0.02 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.26 0.39 4 -0.57 57 61
SMAD3 0.02 0.003 -10000 0 -10000 0 0
EDN1 -0.068 0.17 0.37 1 -0.48 26 27
IGFBP1 -0.19 0.27 0.39 4 -0.58 61 65
VEGFA -0.16 0.25 0.38 1 -0.56 53 54
HIF1A/JAB1 -0.024 0.054 -10000 0 -0.15 1 1
CP -0.15 0.26 0.43 9 -0.59 46 55
CXCL12 -0.25 0.3 0.39 4 -0.59 97 101
COPS5 0.016 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.009 -10000 0 -10000 0 0
BNIP3 -0.18 0.26 0.39 4 -0.57 59 63
EGLN3 -0.18 0.26 0.4 3 -0.57 58 61
CA9 -0.13 0.29 0.46 10 -0.55 55 65
TERT -0.17 0.24 0.39 3 -0.57 47 50
ENO1 -0.18 0.26 0.39 4 -0.57 58 62
PFKL -0.18 0.26 0.39 4 -0.57 58 62
NCOA1 0.018 0.011 -10000 0 -10000 0 0
ADM -0.18 0.26 0.4 3 -0.57 58 61
ARNT -0.038 0.062 -10000 0 -0.21 2 2
HNF4A 0.008 0.06 0.3 5 -0.2 6 11
ADFP -0.19 0.25 0.35 6 -0.56 60 66
SLC2A1 -0.16 0.25 0.38 2 -0.56 53 55
LEP -0.17 0.27 0.44 4 -0.57 57 61
HIF1A/ARNT/Cbp/p300 -0.19 0.29 0.48 5 -0.64 55 60
EPO -0.17 0.27 0.39 1 -0.72 37 38
CREBBP -0.06 0.11 0.19 1 -0.32 35 36
HIF1A/ARNT/Cbp/p300/HDAC7 -0.17 0.29 0.47 5 -0.65 47 52
PFKFB3 -0.18 0.26 0.39 4 -0.57 58 62
NT5E -0.2 0.28 0.39 4 -0.58 74 78
Endothelins

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
AKT1 -0.079 0.097 -10000 0 -0.34 22 22
PTK2B 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.19 -10000 0 -0.61 19 19
EDN1 -0.023 0.061 -10000 0 -0.2 5 5
EDN3 -0.077 0.13 0.29 1 -0.29 75 76
EDN2 0.19 0.13 0.29 182 -10000 0 182
HRAS/GDP -0.13 0.17 0.26 1 -0.39 62 63
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.096 0.14 -10000 0 -0.31 70 70
ADCY4 -0.074 0.1 0.19 1 -0.28 37 38
ADCY5 -0.086 0.12 0.18 4 -0.27 65 69
ADCY6 -0.065 0.091 0.19 1 -0.27 27 28
ADCY7 -0.066 0.09 0.18 2 -0.27 27 29
ADCY1 -0.069 0.096 0.17 7 -0.28 30 37
ADCY2 -0.092 0.11 0.17 1 -0.26 68 69
ADCY3 -0.065 0.091 0.19 1 -0.28 26 27
ADCY8 -0.062 0.088 0.17 5 -0.28 23 28
ADCY9 -0.065 0.089 0.19 1 -0.28 26 27
arachidonic acid secretion -0.13 0.17 -10000 0 -0.4 63 63
ETB receptor/Endothelin-1/Gq/GTP -0.099 0.15 -10000 0 -0.28 100 100
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
HRAS 0.018 0.009 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.042 0.11 -10000 0 -0.31 20 20
ETA receptor/Endothelin-1/Gs/GTP -0.044 0.11 -10000 0 -0.28 28 28
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
COL3A1 -0.085 0.12 -10000 0 -0.43 21 21
EDNRB -0.052 0.13 -10000 0 -0.29 63 63
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.077 0.097 0.27 1 -0.34 21 22
CYSLTR1 -0.08 0.096 -10000 0 -0.34 20 20
SLC9A1 -0.043 0.073 -10000 0 -0.22 22 22
mol:GDP -0.14 0.17 0.23 3 -0.41 62 65
SLC9A3 -0.13 0.26 -10000 0 -0.58 59 59
RAF1 -0.14 0.17 0.23 1 -0.39 72 73
JUN -0.12 0.19 -10000 0 -0.59 23 23
JAK2 -0.079 0.097 -10000 0 -0.34 22 22
mol:IP3 -0.12 0.16 -10000 0 -0.37 68 68
ETA receptor/Endothelin-1 -0.064 0.13 -10000 0 -0.35 28 28
PLCB1 0.013 0.033 -10000 0 -0.29 3 3
PLCB2 0.016 0.013 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.087 0.13 0.22 1 -0.24 104 105
FOS -0.15 0.23 -10000 0 -0.71 32 32
Gai/GDP -0.11 0.25 -10000 0 -0.72 37 37
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.17 -10000 0 -0.39 74 74
BCAR1 0.02 0.004 -10000 0 -10000 0 0
PRKCB1 -0.12 0.15 -10000 0 -0.35 70 70
GNAQ 0.016 0.013 -10000 0 -10000 0 0
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
GNAL 0.008 0.059 -10000 0 -0.29 11 11
Gs family/GDP -0.13 0.16 0.25 1 -0.38 63 64
ETA receptor/Endothelin-1/Gq/GTP -0.1 0.14 -10000 0 -0.31 71 71
MAPK14 -0.097 0.14 -10000 0 -0.33 62 62
TRPC6 -0.11 0.2 -10000 0 -0.67 17 17
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.097 0.15 0.17 1 -0.34 66 67
ETB receptor/Endothelin-2 0.073 0.15 0.21 132 -0.16 61 193
ETB receptor/Endothelin-3 -0.076 0.12 0.22 1 -0.22 119 120
ETB receptor/Endothelin-1 -0.053 0.1 -10000 0 -0.23 66 66
MAPK3 -0.16 0.22 -10000 0 -0.58 46 46
MAPK1 -0.16 0.23 -10000 0 -0.59 45 45
Rac1/GDP -0.12 0.17 0.24 2 -0.39 62 64
cAMP biosynthetic process -0.13 0.14 0.29 4 -0.3 79 83
MAPK8 -0.13 0.22 -10000 0 -0.59 39 39
SRC 0.019 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.093 0.12 -10000 0 -0.3 49 49
p130Cas/CRK/Src/PYK2 -0.12 0.18 0.26 2 -0.42 54 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.17 0.24 2 -0.39 61 63
COL1A2 -0.11 0.18 -10000 0 -0.47 41 41
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.072 0.15 0.2 130 -0.2 42 172
mol:DAG -0.12 0.16 -10000 0 -0.37 68 68
MAP2K2 -0.15 0.19 -10000 0 -0.44 67 67
MAP2K1 -0.15 0.19 -10000 0 -0.44 67 67
EDNRA -0.063 0.13 -10000 0 -0.34 43 43
positive regulation of muscle contraction -0.07 0.083 0.18 1 -0.29 21 22
Gq family/GDP -0.11 0.17 0.28 1 -0.37 67 68
HRAS/GTP -0.13 0.17 0.24 2 -0.38 71 73
PRKCH -0.12 0.15 0.19 1 -0.36 69 70
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.12 0.16 0.19 1 -0.36 67 68
PRKCB -0.12 0.16 -10000 0 -0.36 68 68
PRKCE -0.11 0.15 -10000 0 -0.36 64 64
PRKCD -0.11 0.15 -10000 0 -0.36 66 66
PRKCG -0.11 0.15 -10000 0 -0.36 62 62
regulation of vascular smooth muscle contraction -0.18 0.28 -10000 0 -0.84 32 32
PRKCQ -0.12 0.15 -10000 0 -0.36 68 68
PLA2G4A -0.14 0.18 -10000 0 -0.43 63 63
GNA14 -0.069 0.14 -10000 0 -0.29 81 81
GNA15 0.032 0.066 0.29 17 -10000 0 17
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA11 0.015 0.022 -10000 0 -0.29 1 1
Rac1/GTP -0.043 0.11 -10000 0 -0.31 21 21
MMP1 0.1 0.17 0.34 85 -10000 0 85
IGF1 pathway

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
NCK2 0.02 0.002 -10000 0 -10000 0 0
PTK2 0.019 0.006 -10000 0 -10000 0 0
CRKL -0.059 0.073 -10000 0 -0.17 84 84
GRB2/SOS1/SHC 0.036 0.015 -10000 0 -10000 0 0
HRAS 0.02 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.062 0.071 -10000 0 -0.16 88 88
IGF-1R heterotetramer/IGF1/PTP1B -0.02 0.096 -10000 0 -0.17 82 82
AKT1 -0.005 0.1 0.15 65 -0.16 46 111
BAD -0.009 0.098 0.14 63 -0.16 45 108
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.056 0.073 -10000 0 -0.17 80 80
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.04 0.087 -10000 0 -0.17 88 88
RAF1 -0.014 0.14 0.26 4 -0.44 16 20
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.018 0.095 -10000 0 -0.16 81 81
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.039 0.094 -10000 0 -0.17 94 94
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.004 0.11 0.15 67 -0.16 47 114
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0 0.13 0.29 12 -0.33 16 28
PXN 0.021 0.001 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.059 0.063 -10000 0 -0.16 66 66
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.002 0.09 -10000 0 -0.15 76 76
IGF-1R heterotetramer -0.006 0.046 -10000 0 -0.16 4 4
IGF-1R heterotetramer/IGF1/IRS/Nck -0.029 0.095 -10000 0 -0.17 88 88
Crk/p130 Cas/Paxillin -0.023 0.093 -10000 0 -0.16 87 87
IGF1R -0.006 0.046 -10000 0 -0.16 4 4
IGF1 0.009 0.045 -10000 0 -0.34 4 4
IRS2/Crk -0.063 0.074 -10000 0 -0.17 88 88
PI3K -0.016 0.08 -10000 0 -0.16 61 61
apoptosis 0.002 0.098 0.26 2 -0.21 10 12
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.084 0.13 -10000 0 -0.27 87 87
RAF1/14-3-3 E -0.01 0.13 0.26 4 -0.37 18 22
BAD/14-3-3 -0.003 0.1 0.21 10 -0.27 2 12
PRKCZ -0.004 0.1 0.15 69 -0.16 47 116
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.084 -10000 0 -0.28 2 2
PTPN1 0.019 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.085 0.14 -10000 0 -0.28 89 89
BCAR1 0.02 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.009 0.093 -10000 0 -0.16 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.04 0.087 -10000 0 -0.17 88 88
GRB10 0.019 0.018 -10000 0 -0.29 1 1
PTPN11 -0.061 0.073 -10000 0 -0.17 88 88
IRS1 -0.055 0.077 0.12 2 -0.18 77 79
IRS2 -0.062 0.077 -10000 0 -0.17 88 88
IGF-1R heterotetramer/IGF1 -0.045 0.12 -10000 0 -0.23 88 88
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDPK1 -0.006 0.11 0.16 64 -0.16 48 112
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.1 0.15 -10000 0 -0.3 91 91
SHC1 0.019 0.006 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.041 0.11 -10000 0 -0.2 87 87
alphaV beta3 Integrin -0.043 0.12 -10000 0 -0.2 100 100
PTK2 -0.14 0.19 0.31 3 -0.42 73 76
IGF1R 0.018 0.026 -10000 0 -0.29 2 2
PI4KB 0.019 0.006 -10000 0 -10000 0 0
MFGE8 0.019 0.019 -10000 0 -0.29 1 1
SRC 0.019 0.006 -10000 0 -10000 0 0
CDKN1B -0.062 0.14 0.16 4 -0.43 33 37
VEGFA 0.02 0.004 -10000 0 -10000 0 0
ILK -0.062 0.14 -10000 0 -0.42 32 32
ROCK1 0.02 0.002 -10000 0 -10000 0 0
AKT1 -0.071 0.13 -10000 0 -0.38 37 37
PTK2B -0.065 0.093 0.2 9 -0.27 24 33
alphaV/beta3 Integrin/JAM-A -0.046 0.12 0.2 4 -0.19 104 108
CBL 0.017 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.015 0.068 -10000 0 -0.17 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.022 0.1 -10000 0 -0.17 94 94
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.086 0.14 -10000 0 -0.35 44 44
alphaV/beta3 Integrin/Syndecan-1 0.14 0.11 0.21 216 -0.12 28 244
PI4KA 0.02 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.083 0.14 -10000 0 -0.22 133 133
PI4 Kinase 0.027 0.01 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.02 0.075 0.21 9 -0.17 33 42
RPS6KB1 -0.12 0.11 -10000 0 -0.29 60 60
TLN1 0.02 0.003 -10000 0 -10000 0 0
MAPK3 -0.18 0.22 -10000 0 -0.45 105 105
GPR124 -0.044 0.12 -10000 0 -0.29 60 60
MAPK1 -0.18 0.22 -10000 0 -0.45 105 105
PXN 0.021 0.001 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.016 0.07 0.21 4 -0.17 33 37
cell adhesion 0.007 0.062 -10000 0 -0.19 25 25
ANGPTL3 0.008 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.024 0.094 -10000 0 -0.17 82 82
IGF-1R heterotetramer 0.018 0.026 -10000 0 -0.29 2 2
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
TGFBR2 0.017 0.026 -10000 0 -0.29 2 2
ITGB3 -0.016 0.1 -10000 0 -0.29 34 34
IGF1 -0.079 0.14 -10000 0 -0.29 93 93
RAC1 0.02 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.023 0.11 -10000 0 -0.2 74 74
apoptosis 0.02 0.004 -10000 0 -10000 0 0
CD47 0.017 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.016 0.06 -10000 0 -0.17 25 25
VCL 0.02 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.02 0.11 -10000 0 -0.21 68 68
CSF1 0.018 0.026 -10000 0 -0.29 2 2
PIK3C2A -0.062 0.14 0.16 4 -0.42 32 36
PI4 Kinase/Pyk2 -0.12 0.11 0.099 2 -0.3 63 65
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.03 0.12 -10000 0 -0.19 93 93
FAK1/Vinculin -0.11 0.16 0.33 4 -0.34 70 74
alphaV beta3/Integrin/ppsTEM5 -0.023 0.11 -10000 0 -0.2 74 74
RHOA 0.019 0.006 -10000 0 -10000 0 0
VTN -0.008 0.1 0.29 5 -0.29 29 34
BCAR1 0.02 0.004 -10000 0 -10000 0 0
FGF2 -0.074 0.14 -10000 0 -0.29 88 88
F11R -0.067 0.084 -10000 0 -0.2 80 80
alphaV/beta3 Integrin/Lactadherin 0.015 0.069 -10000 0 -0.18 32 32
alphaV/beta3 Integrin/TGFBR2 0.013 0.069 -10000 0 -0.17 34 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.041 0.027 -10000 0 -0.16 2 2
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.017 0.06 -10000 0 -0.15 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.051 -10000 0 -0.29 8 8
alphaV/beta3 Integrin/Pyk2 -0.039 0.1 0.16 4 -0.19 79 83
SDC1 0.26 0.09 0.29 258 -10000 0 258
VAV3 -0.023 0.028 0.16 5 -10000 0 5
PTPN11 0.021 0.001 -10000 0 -10000 0 0
IRS1 0.008 0.056 -10000 0 -0.29 10 10
FAK1/Paxillin -0.11 0.16 0.33 4 -0.34 70 74
cell migration -0.1 0.14 0.32 4 -0.31 70 74
ITGAV 0.02 0.004 -10000 0 -10000 0 0
PI3K -0.028 0.096 -10000 0 -0.18 68 68
SPP1 0.03 0.05 0.29 10 -10000 0 10
KDR -0.073 0.14 -10000 0 -0.29 87 87
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.02 0.004 -10000 0 -10000 0 0
COL4A3 0.02 0.034 0.29 4 -10000 0 4
angiogenesis -0.18 0.23 -10000 0 -0.46 106 106
Rac1/GTP -0.025 0.028 0.16 5 -10000 0 5
EDIL3 -0.039 0.12 -10000 0 -0.29 54 54
cell proliferation 0.012 0.069 -10000 0 -0.17 34 34
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.081 0.1 0.28 5 -0.27 6 11
KLHL20 0.041 0.052 0.16 11 -10000 0 11
CYFIP2 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.066 0.08 0.23 24 -10000 0 24
ENAH 0.083 0.12 0.29 13 -0.28 9 22
AP1M1 0.02 0.003 -10000 0 -10000 0 0
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.037 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.016 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.16 0.088 0.21 208 -10000 0 208
RAPGEF1 0.066 0.11 0.26 22 -0.26 10 32
CTNND1 0.02 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.097 0.12 0.26 1 -0.28 10 11
CRK 0.07 0.11 0.28 19 -0.27 10 29
E-cadherin/gamma catenin/alpha catenin 0.17 0.075 0.21 233 -10000 0 233
alphaE/beta7 Integrin 0.028 0.009 -10000 0 -10000 0 0
IQGAP1 0.02 0.004 -10000 0 -10000 0 0
NCKAP1 0.02 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.012 -10000 0 -10000 0 0
DLG1 0.12 0.14 0.29 77 -0.28 7 84
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.016 -10000 0 -10000 0 0
MLLT4 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.019 -10000 0 -0.16 2 2
PI3K 0.004 0.023 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.18 0.071 0.22 246 -10000 0 246
TIAM1 0.018 0.026 -10000 0 -0.29 2 2
E-cadherin(dimer)/Ca2+ 0.15 0.078 0.2 218 -10000 0 218
AKT1 0.007 0.026 0.099 15 -10000 0 15
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.26 0.097 0.29 251 -10000 0 251
RhoA/GDP 0.072 0.071 0.24 23 -10000 0 23
actin cytoskeleton organization 0.036 0.044 0.14 14 -10000 0 14
CDC42/GDP 0.065 0.08 0.24 23 -10000 0 23
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.076 0.036 0.14 2 -10000 0 2
ITGB7 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.16 0.083 0.21 218 -10000 0 218
E-cadherin/Ca2+/beta catenin/alpha catenin 0.14 0.073 0.18 219 -10000 0 219
mol:GDP 0.062 0.083 0.24 24 -10000 0 24
CDC42/GTP/IQGAP1 0.026 0.007 -10000 0 -10000 0 0
JUP 0.02 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.073 0.079 0.24 22 -10000 0 22
RAC1/GTP/IQGAP1 0.027 0.006 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.03 0.036 0.16 7 -10000 0 7
NME1 0.02 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.075 0.11 0.27 2 -0.28 10 12
regulation of cell-cell adhesion 0.014 0.029 -10000 0 -10000 0 0
WASF2 0.015 0.023 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.057 0.19 19 -10000 0 19
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.16 0.085 0.21 210 -10000 0 210
CCND1 0.033 0.037 0.16 5 -10000 0 5
VAV2 0.097 0.12 0.31 11 -10000 0 11
RAP1/GDP 0.057 0.066 0.22 21 -10000 0 21
adherens junction assembly 0.075 0.11 0.27 2 -0.27 10 12
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.02 0.004 -10000 0 -10000 0 0
PIP5K1C 0.019 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.14 0.082 0.19 201 -10000 0 201
E-cadherin/beta catenin 0.11 0.049 0.13 217 -10000 0 217
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.085 0.12 0.29 18 -0.28 10 28
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.008 0.03 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.16 0.083 0.21 219 -10000 0 219
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.096 0.12 -10000 0 -0.29 10 10
Glucocorticoid receptor regulatory network

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
PCK2 -0.092 0.07 -10000 0 -0.36 6 6
SMARCC2 0.021 0.002 -10000 0 -10000 0 0
SMARCC1 0.019 0.006 -10000 0 -10000 0 0
TBX21 0.11 0.086 0.58 2 -0.63 1 3
SUMO2 0.018 0.009 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.004 -10000 0 -10000 0 0
FKBP4 0.02 0.004 -10000 0 -10000 0 0
FKBP5 0.019 0.018 -10000 0 -0.29 1 1
GR alpha/HSP90/FKBP51/HSP90 -0.096 0.065 -10000 0 -0.18 16 16
PRL -0.17 0.47 0.38 10 -1 65 75
cortisol/GR alpha (dimer)/TIF2 -0.24 0.15 -10000 0 -0.4 101 101
RELA 0.018 0.088 -10000 0 -0.18 32 32
FGG -0.24 0.15 -10000 0 -0.39 109 109
GR beta/TIF2 -0.11 0.074 -10000 0 -0.2 47 47
IFNG 0.27 0.16 0.46 88 -10000 0 88
apoptosis -0.092 0.13 -10000 0 -0.5 10 10
CREB1 0.023 0.022 -10000 0 -10000 0 0
histone acetylation 0.005 0.069 0.24 4 -10000 0 4
BGLAP 0.11 0.077 0.32 8 -10000 0 8
GR/PKAc -0.088 0.065 -10000 0 -0.18 8 8
NF kappa B1 p50/RelA 0.044 0.16 0.28 7 -0.28 43 50
SMARCD1 0.021 0.003 -10000 0 -10000 0 0
MDM2 -0.07 0.044 -10000 0 -0.12 44 44
GATA3 0.047 0.08 0.3 27 -10000 0 27
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 0.02 0.048 -10000 0 -10000 0 0
GSK3B 0.015 0.011 -10000 0 -10000 0 0
NR1I3 -0.073 0.12 -10000 0 -0.49 6 6
CSN2 -0.22 0.14 -10000 0 -0.33 147 147
BRG1/BAF155/BAF170/BAF60A 0.048 0.018 -10000 0 -10000 0 0
NFATC1 0.019 0.019 -10000 0 -0.29 1 1
POU2F1 -0.051 0.13 -10000 0 -0.29 65 65
CDKN1A -0.001 0.057 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.002 -10000 0 -10000 0 0
SFN 0.28 0.067 0.29 274 -10000 0 274
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.076 0.1 0.26 3 -10000 0 3
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.091 0.15 -10000 0 -0.73 9 9
JUN 0.24 0.13 0.32 174 -0.28 1 175
IL4 0.1 0.068 0.33 1 -10000 0 1
CDK5R1 0.019 0.008 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.043 0.057 -10000 0 -0.22 9 9
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.087 0.065 -10000 0 -0.18 3 3
cortisol/GR alpha (monomer) -0.28 0.18 -10000 0 -0.45 114 114
NCOA2 0.015 0.036 -10000 0 -0.29 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.14 0.083 0.23 92 -0.29 2 94
AP-1/NFAT1-c-4 0.32 0.18 0.42 206 -10000 0 206
AFP 0.17 0.092 0.39 8 -10000 0 8
SUV420H1 0.02 0.004 -10000 0 -10000 0 0
IRF1 -0.14 0.11 -10000 0 -0.46 12 12
TP53 0.022 0.007 -10000 0 -10000 0 0
PPP5C 0.02 0.004 -10000 0 -10000 0 0
KRT17 0.39 0.16 0.47 191 -10000 0 191
KRT14 0.28 0.13 0.36 183 -10000 0 183
TBP 0.021 0.006 -10000 0 -10000 0 0
CREBBP -0.084 0.054 -10000 0 -10000 0 0
HDAC1 0.02 0.001 -10000 0 -10000 0 0
HDAC2 0.019 0.009 -10000 0 -10000 0 0
AP-1 0.33 0.18 0.42 207 -10000 0 207
MAPK14 0.018 0.009 -10000 0 -10000 0 0
MAPK10 -0.063 0.14 -10000 0 -0.29 76 76
MAPK11 0.018 0.009 -10000 0 -10000 0 0
KRT5 0.37 0.17 0.46 206 -10000 0 206
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
STAT1 0.021 0.004 -10000 0 -10000 0 0
CGA 0.1 0.078 0.38 4 -10000 0 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.18 0.097 -10000 0 -0.34 35 35
MAPK3 0.018 0.01 -10000 0 -10000 0 0
MAPK1 0.019 0.009 -10000 0 -10000 0 0
ICAM1 0.11 0.12 0.31 5 -0.35 1 6
NFKB1 0.019 0.088 -10000 0 -0.19 25 25
MAPK8 0.21 0.11 0.29 169 -10000 0 169
MAPK9 0.018 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.095 0.14 -10000 0 -0.53 10 10
BAX -0.001 0.058 -10000 0 -10000 0 0
POMC 0.13 0.12 0.49 7 -0.98 1 8
EP300 -0.085 0.055 -10000 0 -0.16 1 1
cortisol/GR alpha (dimer)/p53 -0.24 0.16 -10000 0 -0.41 96 96
proteasomal ubiquitin-dependent protein catabolic process -0.066 0.037 -10000 0 -10000 0 0
SGK1 -0.11 0.071 -10000 0 -10000 0 0
IL13 0.2 0.12 0.42 23 -10000 0 23
IL6 0.11 0.13 0.43 9 -10000 0 9
PRKACG -0.017 0.003 -10000 0 -10000 0 0
IL5 0.18 0.11 0.42 7 -10000 0 7
IL2 0.24 0.13 0.4 70 -10000 0 70
CDK5 0.018 0.009 -10000 0 -10000 0 0
PRKACB 0.021 0.002 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 0.21 0.18 0.38 124 -0.35 1 125
CDK5R1/CDK5 0.027 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.06 0.13 0.26 4 -0.25 22 26
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.22 0.15 -10000 0 -0.38 97 97
SMARCA4 0.02 0.004 -10000 0 -10000 0 0
chromatin remodeling -0.15 0.096 -10000 0 -0.31 20 20
NF kappa B1 p50/RelA/Cbp -0.078 0.13 -10000 0 -0.31 39 39
JUN (dimer) 0.24 0.13 0.32 173 -0.28 1 174
YWHAH 0.02 0.003 -10000 0 -10000 0 0
VIPR1 0.099 0.084 -10000 0 -0.75 1 1
NR3C1 -0.16 0.099 -10000 0 -0.27 89 89
NR4A1 0.014 0.057 -10000 0 -0.33 7 7
TIF2/SUV420H1 0.025 0.028 -10000 0 -0.2 4 4
MAPKKK cascade -0.092 0.13 -10000 0 -0.5 10 10
cortisol/GR alpha (dimer)/Src-1 -0.24 0.16 -10000 0 -0.4 102 102
PBX1 -0.062 0.14 -10000 0 -0.3 75 75
POU1F1 -0.063 0.12 -10000 0 -0.3 61 61
SELE -0.003 0.36 0.32 14 -0.76 52 66
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.15 0.097 -10000 0 -0.32 20 20
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.22 0.15 -10000 0 -0.38 97 97
mol:cortisol -0.16 0.087 -10000 0 -0.23 138 138
MMP1 0.18 0.19 0.44 73 -0.43 4 77
PDGFR-alpha signaling pathway

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
PDGFRA -0.044 0.12 -10000 0 -0.3 54 54
PDGF/PDGFRA/CRKL -0.023 0.092 -10000 0 -0.2 61 61
positive regulation of JUN kinase activity 0.003 0.077 -10000 0 -0.16 49 49
CRKL 0.02 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.026 0.091 -10000 0 -0.2 62 62
AP1 -0.095 0.19 0.29 1 -0.73 22 23
mol:IP3 -0.057 0.077 -10000 0 -0.21 57 57
PLCG1 -0.058 0.078 -10000 0 -0.21 57 57
PDGF/PDGFRA/alphaV Integrin -0.021 0.09 -10000 0 -0.2 59 59
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.077 -10000 0 -0.21 57 57
CAV3 -0.01 0.014 -10000 0 -10000 0 0
CAV1 -0.008 0.088 -10000 0 -0.29 26 26
SHC/Grb2/SOS1 0.004 0.078 -10000 0 -0.16 49 49
PDGF/PDGFRA/Shf -0.035 0.11 -10000 0 -0.23 65 65
FOS -0.092 0.19 0.3 3 -0.72 22 25
JUN -0.028 0.023 -10000 0 -0.18 1 1
oligodendrocyte development -0.021 0.09 -10000 0 -0.2 59 59
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:DAG -0.057 0.077 -10000 0 -0.21 57 57
PDGF/PDGFRA -0.044 0.12 -10000 0 -0.3 54 54
actin cytoskeleton reorganization -0.022 0.091 -10000 0 -0.2 60 60
SRF -0.013 0.013 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
PI3K -0.004 0.066 -10000 0 -0.17 36 36
PDGF/PDGFRA/Crk/C3G -0.01 0.083 -10000 0 -0.17 60 60
JAK1 -0.055 0.075 -10000 0 -0.2 60 60
ELK1/SRF -0.05 0.073 0.14 11 -0.19 52 63
SHB 0.02 0.003 -10000 0 -10000 0 0
SHF 0.002 0.073 -10000 0 -0.29 17 17
CSNK2A1 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 -0.06 0.091 -10000 0 -0.24 57 57
SOS1 0.02 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.003 0.077 -10000 0 -0.16 49 49
PDGF/PDGFRA/SHB -0.022 0.092 -10000 0 -0.2 60 60
PDGF/PDGFRA/Caveolin-1 -0.041 0.11 -10000 0 -0.22 78 78
ITGAV 0.02 0.004 -10000 0 -10000 0 0
ELK1 -0.055 0.077 -10000 0 -0.21 51 51
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.024 0.091 -10000 0 -0.2 62 62
JAK-STAT cascade -0.055 0.075 -10000 0 -0.2 60 60
cell proliferation -0.035 0.11 -10000 0 -0.23 65 65
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.029 0.008 -10000 0 -10000 0 0
VLDLR 0.019 0.005 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
LRPAP1 0.019 0.006 -10000 0 -10000 0 0
FYN 0.015 0.04 -10000 0 -0.29 5 5
ITGA3 0.02 0.002 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.032 0.099 -10000 0 -0.18 94 94
MAPK8IP1/MKK7/MAP3K11/JNK1 0.047 0.037 -10000 0 -0.16 5 5
AKT1 -0.04 0.07 0.16 1 -0.17 59 60
MAP2K7 0.02 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
DAB1 0.005 0.03 0.29 2 -10000 0 2
RELN/LRP8/DAB1 -0.024 0.09 0.2 2 -0.16 91 93
LRPAP1/LRP8 0.027 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.02 0.093 0.2 2 -0.15 94 96
DAB1/alpha3/beta1 Integrin -0.022 0.088 -10000 0 -0.15 84 84
long-term memory -0.048 0.11 0.23 2 -0.18 113 115
DAB1/LIS1 -0.015 0.093 0.19 2 -0.15 86 88
DAB1/CRLK/C3G -0.022 0.089 -10000 0 -0.15 87 87
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DAB1/NCK2 -0.014 0.095 0.19 2 -0.15 87 89
ARHGEF2 0.019 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.042 0.12 -10000 0 -0.29 53 53
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
RELN -0.084 0.14 -10000 0 -0.29 94 94
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.032 0.1 -10000 0 -0.18 95 95
GRIN2A/RELN/LRP8/DAB1/Fyn -0.044 0.12 0.21 2 -0.18 117 119
MAPK8 0.018 0.026 -10000 0 -0.29 2 2
RELN/VLDLR/DAB1 -0.024 0.089 0.2 2 -0.16 88 90
ITGB1 0.02 0.003 -10000 0 -10000 0 0
MAP1B -0.071 0.089 0.14 9 -0.18 85 94
RELN/LRP8 -0.03 0.097 -10000 0 -0.17 92 92
GRIN2B/RELN/LRP8/DAB1/Fyn -0.014 0.1 0.23 6 -0.16 93 99
PI3K 0.019 0.015 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.006 -10000 0 -10000 0 0
RAP1A -0.057 0.083 0.25 6 -10000 0 6
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.013 0.044 -10000 0 -0.29 6 6
CRLK/C3G 0.03 0.006 -10000 0 -10000 0 0
GRIN2B -0.005 0.042 0.29 5 -10000 0 5
NCK2 0.02 0.002 -10000 0 -10000 0 0
neuron differentiation -0.048 0.087 -10000 0 -0.28 15 15
neuron adhesion -0.061 0.085 0.26 6 -10000 0 6
LRP8 0.02 0.003 -10000 0 -10000 0 0
GSK3B -0.041 0.066 -10000 0 -0.17 56 56
RELN/VLDLR/DAB1/Fyn -0.02 0.092 0.2 2 -0.15 91 93
MAP3K11 0.02 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.034 0.075 -10000 0 -0.18 60 60
CDK5 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.004 0.028 -10000 0 -0.27 3 3
neuron migration -0.062 0.11 0.24 3 -0.24 57 60
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.048 0.088 -10000 0 -0.29 15 15
RELN/VLDLR -0.02 0.094 -10000 0 -0.16 89 89
Nongenotropic Androgen signaling

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
PTK2 -0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.049 0.095 -10000 0 -0.16 129 129
regulation of S phase of mitotic cell cycle -0.047 0.088 -10000 0 -0.19 76 76
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
HRAS 0.017 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.004 -10000 0 -10000 0 0
PELP1 0.016 0.012 -10000 0 -10000 0 0
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.064 0.083 0.15 15 -0.25 11 26
T-DHT/AR -0.082 0.1 -10000 0 -0.2 132 132
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.005 22 22
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
mol:GDP -0.11 0.13 -10000 0 -0.25 124 124
cell proliferation -0.1 0.13 0.26 1 -0.39 33 34
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
FOS -0.1 0.2 0.26 1 -0.63 29 30
mol:Ca2+ -0.024 0.026 -10000 0 -0.06 85 85
MAPK3 -0.089 0.11 0.27 1 -0.3 30 31
MAPK1 -0.043 0.079 -10000 0 -0.26 20 20
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 20 20
cAMP biosynthetic process 0.012 0.021 0.083 1 -10000 0 1
GNG2 0.02 0.003 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 20 20
HRAS/GTP -0.047 0.087 -10000 0 -0.14 124 124
actin cytoskeleton reorganization 0.019 0.016 -10000 0 -10000 0 0
SRC 0.016 0.012 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 20 20
PI3K 0.017 0.014 -10000 0 -10000 0 0
apoptosis 0.087 0.14 0.41 39 -10000 0 39
T-DHT/AR/PELP1 -0.063 0.094 -10000 0 -0.17 132 132
HRAS/GDP -0.11 0.12 -10000 0 -0.28 86 86
CREB1 -0.093 0.15 -10000 0 -0.44 39 39
RAC1-CDC42/GTP 0.024 0.02 -10000 0 -10000 0 0
AR -0.13 0.15 -10000 0 -0.29 132 132
GNB1 0.02 0.004 -10000 0 -10000 0 0
RAF1 -0.061 0.082 0.16 15 -0.22 11 26
RAC1-CDC42/GDP -0.082 0.15 -10000 0 -0.28 79 79
T-DHT/AR/PELP1/Src -0.05 0.092 -10000 0 -0.16 124 124
MAP2K2 -0.061 0.082 0.15 15 -0.25 11 26
T-DHT/AR/PELP1/Src/PI3K -0.047 0.089 -10000 0 -0.19 76 76
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
SHBG 0.017 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.076 0.13 -10000 0 -0.37 29 29
mol:T-DHT 0 0.001 -10000 0 -0.004 5 5
RAC1 0.02 0.003 -10000 0 -10000 0 0
GNRH1 -0.008 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.085 0.1 -10000 0 -0.22 78 78
CDC42 0.02 0.003 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.047 0.088 -10000 0 -0.4 6 6
IHH 0.016 0.04 0.3 4 -0.13 5 9
SHH Np/Cholesterol/GAS1 -0.072 0.073 0.14 4 -0.16 119 123
LRPAP1 0.019 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.072 0.072 0.16 119 -0.14 4 123
SMO/beta Arrestin2 -0.089 0.16 -10000 0 -0.33 69 69
SMO -0.09 0.15 -10000 0 -0.34 62 62
AKT1 -0.04 0.11 -10000 0 -0.48 10 10
ARRB2 0.019 0.006 -10000 0 -10000 0 0
BOC -0.044 0.12 -10000 0 -0.29 57 57
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
heart looping -0.093 0.16 -10000 0 -0.34 65 65
STIL -0.04 0.083 0.17 11 -0.23 6 17
DHH N/PTCH2 0.013 0.06 -10000 0 -0.2 21 21
DHH N/PTCH1 -0.036 0.093 -10000 0 -0.19 71 71
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DHH 0.017 0.011 -10000 0 -10000 0 0
PTHLH -0.072 0.14 -10000 0 -0.55 6 6
determination of left/right symmetry -0.093 0.16 -10000 0 -0.34 65 65
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
skeletal system development -0.072 0.14 -10000 0 -0.54 6 6
IHH N/Hhip -0.027 0.1 0.2 5 -0.2 71 76
DHH N/Hhip 0.024 0.037 0.21 1 -0.2 7 8
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.093 0.16 -10000 0 -0.34 65 65
pancreas development 0.003 0.052 0.29 1 -0.29 7 8
HHAT 0.018 0.019 -10000 0 -0.29 1 1
PI3K 0.019 0.015 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.12 0.15 -10000 0 -0.29 130 130
somite specification -0.093 0.16 -10000 0 -0.34 65 65
SHH Np/Cholesterol/PTCH1 -0.047 0.073 0.21 3 -0.23 7 10
SHH Np/Cholesterol/PTCH2 -0.024 0.045 0.12 8 -0.16 22 30
SHH Np/Cholesterol/Megalin -0.01 0.04 0.16 13 -0.16 1 14
SHH -0.012 0.039 0.18 9 -0.2 1 10
catabolic process -0.05 0.097 -10000 0 -0.21 71 71
SMO/Vitamin D3 -0.064 0.11 0.34 1 -0.25 61 62
SHH Np/Cholesterol/Hhip -0.016 0.035 0.13 9 -0.15 7 16
LRP2 0.018 0.039 0.29 5 -10000 0 5
receptor-mediated endocytosis -0.064 0.11 0.29 1 -0.28 21 22
SHH Np/Cholesterol/BOC -0.037 0.062 0.13 6 -0.16 53 59
SHH Np/Cholesterol/CDO -0.019 0.042 0.12 8 -0.16 17 25
mesenchymal cell differentiation 0.016 0.035 0.15 7 -0.13 9 16
mol:Vitamin D3 -0.037 0.083 0.19 11 -0.23 7 18
IHH N/PTCH2 -0.038 0.11 0.19 4 -0.2 84 88
CDON -0.001 0.072 -10000 0 -0.29 17 17
IHH N/PTCH1 -0.036 0.1 -10000 0 -0.21 71 71
Megalin/LRPAP1 0.03 0.027 0.22 5 -10000 0 5
PTCH2 -0.004 0.082 -10000 0 -0.29 22 22
SHH Np/Cholesterol -0.01 0.015 -10000 0 -0.15 1 1
PTCH1 -0.05 0.097 -10000 0 -0.21 71 71
HHIP 0.003 0.052 0.29 1 -0.29 7 8
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.02 0.004 -10000 0 -10000 0 0
CCL5 0.02 0.003 -10000 0 -10000 0 0
SDCBP 0.02 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.1 0.1 0.26 57 -10000 0 57
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 0.081 0.1 0.25 42 -0.2 1 43
Syndecan-1/Syntenin 0.087 0.1 0.25 46 -0.2 1 47
MAPK3 0.066 0.096 0.22 42 -10000 0 42
HGF/MET 0.003 0.076 0.22 1 -0.2 34 35
TGFB1/TGF beta receptor Type II 0.02 0.004 -10000 0 -10000 0 0
BSG 0.019 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.081 0.1 0.25 42 -0.2 1 43
Syndecan-1/RANTES 0.089 0.1 0.25 48 -0.2 1 49
Syndecan-1/CD147 0.087 0.1 0.27 30 -10000 0 30
Syndecan-1/Syntenin/PIP2 0.081 0.098 0.23 46 -0.2 1 47
LAMA5 0.019 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.078 0.095 0.23 45 -0.19 1 46
MMP7 -0.001 0.078 0.29 2 -0.29 18 20
HGF -0.016 0.1 0.29 1 -0.29 34 35
Syndecan-1/CASK 0.066 0.091 0.16 100 -0.2 1 101
Syndecan-1/HGF/MET 0.071 0.11 0.27 26 -0.22 2 28
regulation of cell adhesion 0.056 0.092 0.21 42 -10000 0 42
HPSE 0.02 0.004 -10000 0 -10000 0 0
positive regulation of cell migration 0.1 0.1 0.26 57 -10000 0 57
SDC1 0.098 0.099 0.24 59 -10000 0 59
Syndecan-1/Collagen 0.1 0.1 0.26 57 -10000 0 57
PPIB 0.02 0.003 -10000 0 -10000 0 0
MET 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
MMP9 0.062 0.1 0.29 46 -10000 0 46
MAPK1 0.068 0.096 0.22 44 -10000 0 44
homophilic cell adhesion 0.094 0.11 0.26 58 -10000 0 58
MMP1 0.08 0.12 0.29 68 -10000 0 68
IL23-mediated 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
CCL2 0.32 0.24 0.75 37 -10000 0 37
IL23A 0.34 0.26 0.84 35 -10000 0 35
NF kappa B1 p50/RelA/I kappa B alpha 0.24 0.18 0.62 7 -10000 0 7
positive regulation of T cell mediated cytotoxicity 0.36 0.28 0.8 53 -10000 0 53
ITGA3 0.31 0.23 0.73 38 -10000 0 38
IL17F 0.28 0.21 0.54 81 -10000 0 81
IL12B 0.098 0.077 0.23 54 -10000 0 54
STAT1 (dimer) 0.3 0.22 0.69 35 -10000 0 35
CD4 0.32 0.24 0.74 40 -10000 0 40
IL23 0.3 0.24 0.76 33 -10000 0 33
IL23R 0.17 0.14 0.59 12 -10000 0 12
IL1B 0.34 0.26 0.8 46 -10000 0 46
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.35 0.27 0.77 58 -10000 0 58
TYK2 0.069 0.05 0.19 23 -10000 0 23
STAT4 0.02 0.004 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.011 0.022 -10000 0 -10000 0 0
IL12RB1 0.07 0.049 0.17 37 -10000 0 37
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.083 0.056 0.2 36 -10000 0 36
IL23R/JAK2 0.2 0.15 0.55 19 -10000 0 19
positive regulation of chronic inflammatory response 0.36 0.28 0.8 53 -10000 0 53
natural killer cell activation -0.013 0.013 -10000 0 -0.043 29 29
JAK2 0.092 0.071 0.22 49 -10000 0 49
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.028 0.01 -10000 0 -10000 0 0
RELA 0.028 0.01 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.3 0.24 0.75 34 -10000 0 34
ALOX12B 0.35 0.26 0.76 49 -10000 0 49
CXCL1 0.37 0.27 0.79 55 -10000 0 55
T cell proliferation 0.36 0.28 0.8 53 -10000 0 53
NFKBIA 0.027 0.01 -10000 0 -10000 0 0
IL17A 0.26 0.2 0.5 87 -10000 0 87
PI3K 0.18 0.21 0.64 17 -10000 0 17
IFNG 0.047 0.06 0.15 54 -10000 0 54
STAT3 (dimer) 0.17 0.2 0.61 13 -10000 0 13
IL18R1 0.01 0.028 -10000 0 -0.29 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.27 0.21 0.6 59 -10000 0 59
IL18/IL18R 0.037 0.056 0.26 3 -0.18 1 4
macrophage activation 0.023 0.027 0.057 83 -10000 0 83
TNF 0.34 0.26 0.8 40 -10000 0 40
STAT3/STAT4 0.27 0.2 0.62 24 -10000 0 24
STAT4 (dimer) 0.3 0.22 0.69 35 -10000 0 35
IL18 0.012 0.037 0.3 3 -10000 0 3
IL19 0.31 0.31 0.72 53 -0.83 8 61
STAT5A (dimer) 0.3 0.22 0.69 36 -10000 0 36
STAT1 0.02 0.004 -10000 0 -10000 0 0
SOCS3 0.02 0.004 -10000 0 -10000 0 0
CXCL9 0.34 0.26 0.79 43 -10000 0 43
MPO 0.32 0.24 0.75 38 -10000 0 38
positive regulation of humoral immune response 0.36 0.28 0.8 53 -10000 0 53
IL23/IL23R/JAK2/TYK2 0.35 0.28 0.8 53 -10000 0 53
IL6 0.32 0.24 0.74 40 -10000 0 40
STAT5A 0.02 0.002 -10000 0 -10000 0 0
IL2 -0.004 0.038 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.013 0.013 -10000 0 -0.043 29 29
CD3E 0.32 0.24 0.75 37 -10000 0 37
keratinocyte proliferation 0.36 0.28 0.8 53 -10000 0 53
NOS2 0.3 0.29 0.75 37 -0.84 2 39
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.016 0.069 -10000 0 -0.16 50 50
EPHB2 0.02 0.003 -10000 0 -10000 0 0
Syndecan-2/TACI -0.011 0.066 0.2 1 -0.16 44 45
LAMA1 0.032 0.066 0.29 15 -0.29 2 17
Syndecan-2/alpha2 ITGB1 0.009 0.069 0.2 2 -0.15 44 46
HRAS 0.02 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK -0.029 0.055 -10000 0 -0.16 44 44
ITGA5 0.018 0.026 -10000 0 -0.29 2 2
BAX -0.034 0.048 -10000 0 -10000 0 0
EPB41 0.02 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.009 0.058 -10000 0 -0.15 43 43
LAMA3 0.02 0.024 0.29 1 -0.29 1 2
EZR 0.019 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.019 -10000 0 -0.29 1 1
Syndecan-2/MMP2 -0.018 0.08 -10000 0 -0.19 48 48
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.029 0.014 0.22 1 -10000 0 1
dendrite morphogenesis -0.011 0.065 -10000 0 -0.16 44 44
Syndecan-2/GM-CSF -0.007 0.072 0.2 7 -0.16 44 51
determination of left/right symmetry -0.036 0.067 -10000 0 -0.19 44 44
Syndecan-2/PKC delta -0.012 0.065 -10000 0 -0.16 44 44
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.027 0.066 0.18 11 -0.15 44 55
MAPK1 -0.026 0.066 0.18 11 -0.15 42 53
Syndecan-2/RACK1 0 0.06 -10000 0 -0.14 44 44
NF1 0.02 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.036 0.067 -10000 0 -0.19 44 44
ITGA2 0.02 0.017 0.29 1 -10000 0 1
MAPK8 -0.035 0.055 -10000 0 -0.16 44 44
Syndecan-2/alpha2/beta1 Integrin 0.017 0.079 0.21 14 -0.15 41 55
Syndecan-2/Kininogen -0.006 0.049 -10000 0 -0.17 24 24
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.028 0.058 0.16 12 -10000 0 12
Syndecan-2/CASK/Protein 4.1 -0.01 0.059 -10000 0 -0.15 44 44
extracellular matrix organization -0.01 0.063 -10000 0 -0.16 41 41
actin cytoskeleton reorganization -0.016 0.069 -10000 0 -0.16 50 50
Syndecan-2/Caveolin-2/Ras -0.001 0.065 -10000 0 -0.15 43 43
Syndecan-2/Laminin alpha3 -0.011 0.067 0.2 1 -0.17 45 46
Syndecan-2/RasGAP 0.008 0.063 -10000 0 -0.14 40 40
alpha5/beta1 Integrin 0.028 0.02 -10000 0 -0.2 2 2
PRKCD 0.019 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer -0.011 0.065 -10000 0 -0.17 44 44
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.038 0.042 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
SDCBP 0.02 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.017 0.02 0.29 1 -10000 0 1
RASA1 0.02 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.029 0.014 0.22 1 -10000 0 1
Syndecan-2/Synbindin -0.012 0.063 -10000 0 -0.16 44 44
TGFB1 0.02 0.004 -10000 0 -10000 0 0
CASP3 -0.031 0.055 0.18 5 -0.15 37 42
FN1 0.01 0.051 -10000 0 -0.29 8 8
Syndecan-2/IL8 0.077 0.13 0.21 129 -0.13 44 173
SDC2 -0.036 0.067 -10000 0 -0.2 44 44
KNG1 -0.011 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin -0.011 0.065 -10000 0 -0.17 44 44
TRAPPC4 0.017 0.008 -10000 0 -10000 0 0
CSF2 0.024 0.043 0.29 7 -10000 0 7
Syndecan-2/TGFB1 -0.01 0.063 -10000 0 -0.17 41 41
Syndecan-2/Syntenin/PI-4-5-P2 -0.009 0.058 -10000 0 -0.15 43 43
Syndecan-2/Ezrin -0.002 0.065 -10000 0 -0.15 44 44
PRKACA -0.03 0.061 0.18 9 -0.15 42 51
angiogenesis 0.077 0.13 0.2 129 -0.13 44 173
MMP2 0.004 0.069 -10000 0 -0.29 15 15
IL8 0.17 0.14 0.29 159 -10000 0 159
calcineurin-NFAT signaling pathway -0.011 0.065 0.2 1 -0.16 44 45
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.018 0.044 -10000 0 -0.15 4 4
BIRC5 0.28 0.071 0.29 273 -10000 0 273
NFKBIA -0.023 0.037 0.19 2 -10000 0 2
CPEB1 -0.065 0.13 -10000 0 -0.29 74 74
AKT1 -0.023 0.036 0.19 2 -10000 0 2
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.016 0.039 -10000 0 -0.13 3 3
NDEL1/TACC3 -0.002 0.051 -10000 0 -10000 0 0
GADD45A 0.02 0.002 -10000 0 -10000 0 0
GSK3B -0.019 0.027 -10000 0 -10000 0 0
PAK1/Aurora A -0.016 0.043 -10000 0 -0.15 4 4
MDM2 0.02 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.15 0.049 0.16 286 -10000 0 286
TP53 -0.019 0.057 -10000 0 -0.22 19 19
DLG7 -0.02 0.03 0.14 2 -10000 0 2
AURKAIP1 0.02 0.004 -10000 0 -10000 0 0
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.002 0.054 -10000 0 -0.14 1 1
G2/M transition of mitotic cell cycle -0.016 0.038 -10000 0 -0.13 3 3
AURKA -0.022 0.04 0.17 2 -10000 0 2
AURKB 0.13 0.066 0.15 254 -10000 0 254
CDC25B -0.013 0.03 -10000 0 -0.22 1 1
G2/M transition checkpoint -0.018 0.028 -10000 0 -0.13 4 4
mRNA polyadenylation -0.048 0.07 -10000 0 -0.17 58 58
Aurora A/CPEB -0.048 0.07 -10000 0 -0.17 58 58
Aurora A/TACC1/TRAP/chTOG 0.001 0.061 -10000 0 -0.26 1 1
BRCA1 0.02 0.002 -10000 0 -10000 0 0
centrosome duplication -0.016 0.043 -10000 0 -0.15 4 4
regulation of centrosome cycle -0.003 0.05 -10000 0 -10000 0 0
spindle assembly 0.001 0.06 -10000 0 -0.26 1 1
TDRD7 0.02 0.002 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.16 0.071 0.21 135 -10000 0 135
CENPA 0.14 0.068 0.18 189 -10000 0 189
Aurora A/PP2A -0.018 0.043 -10000 0 -0.15 4 4
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.019 0.039 -10000 0 -0.17 4 4
negative regulation of DNA binding -0.018 0.057 -10000 0 -0.22 19 19
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.007 -10000 0 -10000 0 0
RASA1 0.02 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A -0.018 0.028 -10000 0 -0.13 4 4
mitotic prometaphase -0.024 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.022 0.04 0.17 2 -10000 0 2
TACC1 0.018 0.019 -10000 0 -0.29 1 1
TACC3 0.02 0.017 0.29 1 -10000 0 1
Aurora A/Antizyme1 -0.001 0.054 -10000 0 -0.14 1 1
Aurora A/RasGAP -0.017 0.042 -10000 0 -0.15 3 3
OAZ1 0.019 0.005 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.023 0.027 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.037 0.014 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.15 0.049 0.15 286 -10000 0 286
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.09 0.055 0.16 73 -10000 0 73
PAK1 0.019 0.005 -10000 0 -10000 0 0
CKAP5 0.02 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.074 0.077 -10000 0 -0.2 41 41
NT3 (dimer)/TRKC -0.12 0.13 -10000 0 -0.23 164 164
NT3 (dimer)/TRKB -0.028 0.11 0.21 1 -0.2 81 82
SHC/Grb2/SOS1/GAB1/PI3K 0.005 0.021 -10000 0 -0.18 1 1
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
BDNF 0.035 0.063 0.29 16 -10000 0 16
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
DYNLT1 0.019 0.005 -10000 0 -10000 0 0
NTRK1 0.017 0.009 -10000 0 -10000 0 0
NTRK2 -0.027 0.11 0.29 1 -0.29 45 46
NTRK3 -0.16 0.15 -10000 0 -0.29 163 163
NT-4/5 (dimer)/TRKB 0.073 0.14 0.21 127 -0.16 58 185
neuron apoptosis 0.072 0.14 0.31 46 -10000 0 46
SHC 2-3/Grb2 -0.078 0.15 -10000 0 -0.33 46 46
SHC1 0.019 0.006 -10000 0 -10000 0 0
SHC2 -0.087 0.16 -10000 0 -0.39 49 49
SHC3 -0.064 0.13 -10000 0 -0.34 34 34
STAT3 (dimer) 0.022 0.003 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.002 0.085 -10000 0 -0.19 49 49
RIN/GDP -0.051 0.077 0.19 4 -0.2 6 10
GIPC1 0.02 0.004 -10000 0 -10000 0 0
KRAS 0.019 0.005 -10000 0 -10000 0 0
DNAJA3 -0.052 0.1 0.15 1 -0.2 71 72
RIN/GTP 0.012 0.003 -10000 0 -10000 0 0
CCND1 -0.016 0.004 -10000 0 -10000 0 0
MAGED1 0.018 0.026 -10000 0 -0.29 2 2
PTPN11 0.021 0.001 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.16 0.14 0.29 153 -10000 0 153
SHC/GRB2/SOS1 0.036 0.015 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.045 0.1 -10000 0 -0.17 112 112
TRKA/NEDD4-2 0.027 0.01 -10000 0 -10000 0 0
ELMO1 0.019 0.018 -10000 0 -0.29 1 1
RhoG/GTP/ELMO1/DOCK1 0.026 0.013 -10000 0 -0.17 1 1
NGF -0.11 0.15 -10000 0 -0.29 122 122
HRAS 0.02 0.005 -10000 0 -10000 0 0
DOCK1 0.02 0.003 -10000 0 -10000 0 0
GAB2 0.018 0.019 -10000 0 -0.29 1 1
RIT2 -0.017 0.003 -10000 0 -10000 0 0
RIT1 0.019 0.006 -10000 0 -10000 0 0
FRS2 0.02 0.003 -10000 0 -10000 0 0
DNM1 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.042 0.11 -10000 0 -0.2 74 74
mol:GDP -0.073 0.1 0.24 4 -0.28 10 14
NGF (dimer) -0.11 0.15 -10000 0 -0.29 122 122
RhoG/GDP 0.014 0.012 -10000 0 -0.2 1 1
RIT1/GDP -0.054 0.071 0.23 1 -0.2 6 7
TIAM1 0.018 0.026 -10000 0 -0.29 2 2
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.014 0.086 0.22 12 -0.17 45 57
KIDINS220/CRKL/C3G 0.03 0.006 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2 0.04 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.044 0.02 -10000 0 -10000 0 0
RIT1/GTP 0.014 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.021 0.1 -10000 0 -0.29 36 36
RAP1/GDP -0.05 0.062 -10000 0 -0.18 6 6
KIDINS220/CRKL 0.02 0.003 -10000 0 -10000 0 0
BDNF (dimer) 0.035 0.063 0.29 16 -10000 0 16
ubiquitin-dependent protein catabolic process -0.045 0.1 -10000 0 -0.17 112 112
Schwann cell development -0.034 0.023 -10000 0 -10000 0 0
EHD4 0.02 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.046 -10000 0 -0.19 6 6
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.097 0.17 4 -0.28 43 47
ABL1 0.02 0.002 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.049 -10000 0 -0.31 1 1
STAT3 0.022 0.003 -10000 0 -10000 0 0
axon guidance -0.12 0.092 0.13 4 -0.28 43 47
MAPK3 -0.07 0.079 0.17 9 -0.16 105 114
MAPK1 -0.069 0.08 0.17 10 -0.16 105 115
CDC42/GDP -0.051 0.078 0.2 4 -0.2 5 9
NTF3 -0.021 0.1 -10000 0 -0.29 36 36
NTF4 0.16 0.14 0.29 153 -10000 0 153
NGF (dimer)/TRKA/FAIM -0.033 0.092 -10000 0 -0.17 84 84
PI3K 0.019 0.015 -10000 0 -10000 0 0
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.015 0.009 -10000 0 -10000 0 0
GAB1 0.02 0.003 -10000 0 -10000 0 0
RASGRF1 -0.052 0.1 0.15 2 -0.21 70 72
SOS1 0.02 0.003 -10000 0 -10000 0 0
MCF2L -0.12 0.1 -10000 0 -0.2 160 160
RGS19 0.019 0.005 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.008 0.083 0.28 1 -0.33 7 8
Rac1/GDP -0.051 0.077 0.2 4 -0.2 6 10
NGF (dimer)/TRKA/GRIT -0.049 0.094 -10000 0 -0.17 112 112
neuron projection morphogenesis -0.038 0.12 -10000 0 -0.58 1 1
NGF (dimer)/TRKA/NEDD4-2 -0.045 0.1 -10000 0 -0.17 112 112
MAP2K1 -0.002 0.069 0.17 38 -10000 0 38
NGFR 0.001 0.075 -10000 0 -0.29 18 18
NGF (dimer)/TRKA/GIPC/GAIP -0.063 0.096 -10000 0 -0.19 105 105
RAS family/GTP/PI3K 0.003 0.022 -10000 0 -0.17 2 2
FRS2 family/SHP2/GRB2/SOS1 0.054 0.021 -10000 0 -10000 0 0
NRAS 0.021 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.02 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.24 -10000 0 -0.46 119 119
RASA1 0.02 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.028 0.009 -10000 0 -10000 0 0
SQSTM1 0.02 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.024 0.083 0.22 11 -0.16 38 49
NGF (dimer)/TRKA/p62/Atypical PKCs -0.017 0.083 -10000 0 -0.16 70 70
MATK 0.02 0.005 -10000 0 -10000 0 0
NEDD4L 0.02 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.059 0.048 -10000 0 -0.15 20 20
NGF (dimer)/TRKA -0.049 0.1 0.17 1 -0.21 73 74
Rac1/GTP -0.084 0.077 -10000 0 -0.2 62 62
FRS2 family/SHP2/CRK family 0.051 0.025 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.019 0.018 -10000 0 -0.29 1 1
ANTXR2 -0.053 0.13 -10000 0 -0.29 69 69
negative regulation of myeloid dendritic cell antigen processing and presentation -0.011 0.016 -10000 0 -0.042 64 64
monocyte activation -0.004 0.077 -10000 0 -0.35 13 13
MAP2K2 -0.024 0.13 -10000 0 -0.58 15 15
MAP2K1 -0.016 0.015 -10000 0 -0.069 1 1
MAP2K7 -0.016 0.015 -10000 0 -0.069 1 1
MAP2K6 -0.016 0.016 0.048 1 -0.069 1 2
CYAA -0.04 0.054 -10000 0 -0.14 64 64
MAP2K4 -0.014 0.015 -10000 0 -10000 0 0
IL1B -0.012 0.036 0.18 1 -0.11 9 10
Channel -0.014 0.074 -10000 0 -0.15 64 64
NLRP1 -0.015 0.018 -10000 0 -0.12 2 2
CALM1 0.02 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.013 0.064 -10000 0 -0.4 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.011 0.016 0.042 64 -10000 0 64
MAPK3 -0.016 0.015 -10000 0 -0.069 1 1
MAPK1 -0.016 0.015 -10000 0 -0.069 1 1
PGR -0.095 0.069 -10000 0 -0.14 187 187
PA/Cellular Receptors -0.017 0.082 -10000 0 -0.17 64 64
apoptosis -0.011 0.016 -10000 0 -0.042 64 64
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.013 0.072 -10000 0 -0.15 64 64
macrophage activation -0.021 0.015 -10000 0 -10000 0 0
TNF 0.023 0.032 0.29 4 -10000 0 4
VCAM1 -0.004 0.077 -10000 0 -0.35 13 13
platelet activation -0.013 0.064 -10000 0 -0.4 7 7
MAPKKK cascade 0.015 0.023 0.084 4 -0.062 7 11
IL18 -0.012 0.016 -10000 0 -0.11 1 1
negative regulation of macrophage activation -0.011 0.016 -10000 0 -0.042 64 64
LEF -0.011 0.017 -10000 0 -0.042 64 64
CASP1 -0.009 0.015 -10000 0 -0.042 45 45
mol:cAMP -0.013 0.064 -10000 0 -0.4 7 7
necrosis -0.011 0.016 -10000 0 -0.042 64 64
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.012 0.069 -10000 0 -0.14 64 64
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.071 0.048 0.15 5 -0.16 1 6
epithelial cell differentiation 0.14 0.071 0.18 218 -10000 0 218
CYFIP2 0.02 0.004 -10000 0 -10000 0 0
ENAH 0.029 0.071 0.15 64 -10000 0 64
EGFR 0.018 0.026 -10000 0 -0.29 2 2
EPHA2 0.02 0.003 -10000 0 -10000 0 0
MYO6 0.037 0.03 0.18 4 -10000 0 4
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.013 -10000 0 -10000 0 0
AQP5 0.014 0.12 0.22 9 -0.36 24 33
CTNND1 0.02 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.036 0.029 0.18 4 -10000 0 4
regulation of calcium-dependent cell-cell adhesion 0.034 0.032 0.17 2 -10000 0 2
EGF 0.003 0.066 -10000 0 -0.29 14 14
NCKAP1 0.02 0.004 -10000 0 -10000 0 0
AQP3 0.079 0.078 0.22 21 -10000 0 21
cortical microtubule organization 0.14 0.071 0.18 218 -10000 0 218
GO:0000145 0.023 0.025 0.16 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.15 0.078 0.2 218 -10000 0 218
MLLT4 0.019 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.003 0.015 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.036 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.015 0.02 0.16 1 -10000 0 1
PVRL2 0.02 0.005 -10000 0 -10000 0 0
ZYX 0.036 0.03 0.18 4 -10000 0 4
ARF6/GTP 0.037 0.029 -10000 0 -10000 0 0
CDH1 0.26 0.097 0.29 251 -10000 0 251
EGFR/EGFR/EGF/EGF 0.085 0.069 0.21 2 -0.13 4 6
RhoA/GDP 0.12 0.062 -10000 0 -10000 0 0
actin cytoskeleton organization 0.027 0.028 0.17 4 -10000 0 4
IGF-1R heterotetramer 0.018 0.026 -10000 0 -0.29 2 2
GIT1 0.02 0.003 -10000 0 -10000 0 0
IGF1R 0.018 0.026 -10000 0 -0.29 2 2
IGF1 -0.079 0.14 -10000 0 -0.29 93 93
DIAPH1 -0.006 0.13 -10000 0 -0.53 9 9
Wnt receptor signaling pathway -0.14 0.071 -10000 0 -0.18 218 218
RHOA 0.019 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.003 0.016 -10000 0 -10000 0 0
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
VCL 0.028 0.028 0.17 4 -10000 0 4
EFNA1 0.019 0.006 -10000 0 -10000 0 0
LPP 0.014 0.021 0.16 1 -10000 0 1
Ephrin A1/EPHA2 0.089 0.055 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.023 -10000 0 -10000 0 0
MGAT3 0.034 0.032 0.17 2 -10000 0 2
HGF/MET 0.072 0.081 0.23 1 -0.14 3 4
HGF -0.016 0.1 0.29 1 -0.29 34 35
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.071 0.048 0.15 4 -0.17 1 5
actin cable formation 0.074 0.12 0.24 74 -0.23 3 77
KIAA1543 0.023 0.025 0.17 4 -10000 0 4
KIFC3 0.036 0.027 0.19 2 -10000 0 2
NCK1 0.015 0.009 -10000 0 -10000 0 0
EXOC3 0.017 0.008 -10000 0 -10000 0 0
ACTN1 0.037 0.029 0.18 4 -10000 0 4
NCK1/GIT1 0.023 0.014 -10000 0 -10000 0 0
mol:GDP 0.14 0.071 0.18 218 -10000 0 218
EXOC4 0.02 0.004 -10000 0 -10000 0 0
STX4 0.037 0.027 0.19 2 -10000 0 2
PIP5K1C 0.036 0.029 0.18 4 -10000 0 4
LIMA1 0.02 0.003 -10000 0 -10000 0 0
ABI1 0.02 0.004 -10000 0 -10000 0 0
ROCK1 0.059 0.09 0.19 78 -10000 0 78
adherens junction assembly 0.01 0.081 0.25 3 -0.45 5 8
IGF-1R heterotetramer/IGF1 0.035 0.1 -10000 0 -0.16 10 10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
MET 0.02 0.004 -10000 0 -10000 0 0
PLEKHA7 0.036 0.03 0.18 4 -10000 0 4
mol:GTP 0.035 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.055 0.08 0.2 57 -10000 0 57
cortical actin cytoskeleton stabilization 0.071 0.048 0.15 5 -0.16 1 6
regulation of cell-cell adhesion 0.027 0.028 0.17 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.071 0.048 0.15 4 -0.17 1 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.058 0.071 0.17 65 -10000 0 65
adherens junction organization 0.072 0.068 0.19 19 -0.21 1 20
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.07 0.079 0.19 72 -10000 0 72
FMN1 0.07 0.062 0.19 12 -0.19 1 13
mol:IP3 0.02 0.032 0.14 6 -10000 0 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.083 0.065 0.2 12 -0.19 1 13
CTNNB1 -0.001 0.019 -10000 0 -10000 0 0
AKT1 0.024 0.037 0.14 8 -10000 0 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.095 0.083 0.24 17 -0.25 1 18
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.078 0.074 0.23 25 -0.18 1 26
VASP 0.068 0.062 0.19 11 -0.19 1 12
ZYX 0.072 0.059 0.19 13 -10000 0 13
JUB 0.076 0.061 0.19 12 -0.18 1 13
EGFR(dimer) 0.083 0.067 0.2 10 -0.19 1 11
E-cadherin/beta catenin-gamma catenin 0.16 0.078 0.2 226 -10000 0 226
mol:PI-3-4-5-P3 0.039 0.047 0.22 1 -10000 0 1
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
PI3K 0.04 0.048 0.22 1 -10000 0 1
FYN 0.029 0.063 0.17 33 -0.22 4 37
mol:Ca2+ 0.019 0.032 0.14 6 -10000 0 6
JUP 0 0.02 -10000 0 -10000 0 0
PIK3R1 0.023 0.007 -10000 0 -10000 0 0
mol:DAG 0.02 0.032 0.14 6 -10000 0 6
CDH1 0.26 0.097 0.3 251 -10000 0 251
RhoA/GDP 0.068 0.078 0.19 73 -10000 0 73
establishment of polarity of embryonic epithelium 0.07 0.064 0.2 14 -0.18 1 15
SRC 0.019 0.006 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
EGFR 0.018 0.026 -10000 0 -0.29 2 2
CASR 0.034 0.058 0.16 41 -10000 0 41
RhoA/GTP 0.021 0.035 -10000 0 -10000 0 0
AKT2 0.022 0.038 0.14 6 -10000 0 6
actin cable formation 0.064 0.069 0.22 17 -10000 0 17
apoptosis -0.073 0.078 0.18 1 -0.19 71 72
CTNNA1 0.023 0.007 -10000 0 -10000 0 0
mol:GDP 0.059 0.075 0.17 79 -10000 0 79
PIP5K1A 0.066 0.062 0.18 11 -0.19 1 12
PLCG1 0.02 0.033 0.14 6 -10000 0 6
Rac1/GTP 0.081 0.064 0.19 8 -0.18 1 9
homophilic cell adhesion 0.003 0.005 -10000 0 -10000 0 0
LPA4-mediated signaling events

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.025 0.041 -10000 0 -0.17 22 22
ADCY5 -0.072 0.078 -10000 0 -0.17 116 116
ADCY6 -0.014 0.003 -10000 0 -10000 0 0
ADCY7 -0.014 0.004 -10000 0 -10000 0 0
ADCY1 -0.018 0.025 -10000 0 -0.17 8 8
ADCY2 -0.081 0.079 -10000 0 -0.17 132 132
ADCY3 -0.014 0.003 -10000 0 -10000 0 0
ADCY8 -0.014 0.007 0.081 1 -10000 0 1
PRKCE -0.009 0.002 -10000 0 -10000 0 0
ADCY9 -0.014 0.004 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.028 0.1 0.2 26 -0.19 5 31
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.005 -10000 0 -10000 0 0
SVIL 0.017 0.036 -10000 0 -0.29 4 4
ZNF318 0.017 0.014 -10000 0 -10000 0 0
JMJD2C 0.004 0.019 0.11 9 -10000 0 9
T-DHT/AR/Ubc9 -0.042 0.1 0.15 1 -0.15 129 130
CARM1 0.02 0.004 -10000 0 -10000 0 0
PRDX1 0.019 0.008 -10000 0 -10000 0 0
PELP1 0.017 0.009 -10000 0 -10000 0 0
CTNNB1 0.02 0.006 -10000 0 -10000 0 0
AKT1 0.018 0.01 -10000 0 -10000 0 0
PTK2B 0.019 0.006 -10000 0 -10000 0 0
MED1 0.018 0.009 -10000 0 -10000 0 0
MAK 0.03 0.061 0.29 14 -10000 0 14
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.017 0.032 -10000 0 -0.29 3 3
GSN 0.021 0.004 -10000 0 -10000 0 0
NCOA2 0.015 0.036 -10000 0 -0.29 4 4
NCOA6 0.019 0.007 -10000 0 -10000 0 0
DNA-PK 0.033 0.021 -10000 0 -10000 0 0
NCOA4 0.02 0.003 -10000 0 -10000 0 0
PIAS3 0.02 0.006 -10000 0 -10000 0 0
cell proliferation -0.004 0.1 0.24 15 -0.46 10 25
XRCC5 0.017 0.01 -10000 0 -10000 0 0
UBE3A 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.056 0.12 0.15 1 -0.17 140 141
FHL2 -0.022 0.083 -10000 0 -0.5 5 5
RANBP9 0.02 0.006 -10000 0 -10000 0 0
JMJD1A 0.044 0.056 0.12 106 -10000 0 106
CDK6 0.019 0.005 -10000 0 -10000 0 0
TGFB1I1 -0.013 0.097 -10000 0 -0.29 32 32
T-DHT/AR/CyclinD1 -0.038 0.1 0.16 1 -0.15 123 124
XRCC6 0.018 0.01 -10000 0 -10000 0 0
T-DHT/AR -0.018 0.12 0.3 1 -0.17 86 87
CTDSP1 0.019 0.007 -10000 0 -10000 0 0
CTDSP2 0.018 0.012 -10000 0 -10000 0 0
BRCA1 0.021 0.004 -10000 0 -10000 0 0
TCF4 0.015 0.028 -10000 0 -0.29 2 2
CDKN2A 0.27 0.082 0.29 265 -10000 0 265
SRF 0.019 0.016 -10000 0 -0.14 2 2
NKX3-1 0 0.068 0.11 60 -10000 0 60
KLK3 -0.007 0.061 -10000 0 -10000 0 0
TMF1 0.019 0.006 -10000 0 -10000 0 0
HNRNPA1 0.018 0.01 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 -0.017 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.041 0.1 -10000 0 -0.15 129 129
AR -0.069 0.14 -10000 0 -0.29 87 87
UBA3 0.019 0.006 -10000 0 -10000 0 0
PATZ1 0.018 0.01 -10000 0 -10000 0 0
PAWR 0.021 0.001 -10000 0 -10000 0 0
PRKDC 0.018 0.009 -10000 0 -10000 0 0
PA2G4 0.018 0.01 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.036 0.094 -10000 0 -0.14 129 129
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.042 0.1 0.15 1 -0.15 129 130
LATS2 0.018 0.01 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.036 0.094 -10000 0 -0.14 129 129
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.021 0.003 -10000 0 -10000 0 0
KLK2 -0.015 0.068 0.28 3 -0.32 2 5
CASP8 0.018 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.031 0.1 0.17 1 -0.15 122 123
TMPRSS2 0.063 0.14 0.27 61 -0.33 4 65
CCND1 0.02 0.005 -10000 0 -10000 0 0
PIAS1 0.021 0.006 -10000 0 -10000 0 0
mol:T-DHT 0.009 0.012 0.059 1 -10000 0 1
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.009 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.04 0.1 -10000 0 -0.15 126 126
CMTM2 0.018 0.009 -10000 0 -10000 0 0
SNURF -0.012 0.088 -10000 0 -0.29 26 26
ZMIZ1 0.028 0.014 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.018 0.009 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.023 0.1 -10000 0 -0.29 35 35
GNB1/GNG2 -0.052 0.068 -10000 0 -0.18 54 54
AKT1 -0.052 0.096 -10000 0 -0.24 24 24
EGF 0.003 0.066 -10000 0 -0.29 14 14
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.018 0.044 0.2 3 -10000 0 3
mol:Ca2+ -0.079 0.14 -10000 0 -0.3 62 62
LYN -0.017 0.044 0.2 3 -10000 0 3
RhoA/GTP -0.039 0.054 -10000 0 -0.13 49 49
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.086 0.15 -10000 0 -0.34 56 56
GNG2 0.02 0.003 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.046 0.15 0.27 2 -0.52 19 21
G beta5/gamma2 -0.066 0.09 -10000 0 -0.25 53 53
PRKCH -0.091 0.16 0.25 1 -0.36 56 57
DNM1 0.021 0.002 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.016 0.039 -10000 0 -0.51 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.016 0.032 -10000 0 -0.29 3 3
G12 family/GTP -0.077 0.13 -10000 0 -0.29 60 60
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
ADRBK2 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.025 0.008 -10000 0 -10000 0 0
mol:GDP 0.042 0.088 0.25 5 -0.19 1 6
mol:NADP 0.011 0.051 -10000 0 -0.29 8 8
RAB11A 0.02 0.003 -10000 0 -10000 0 0
PRKG1 -0.055 0.13 -10000 0 -0.29 68 68
mol:IP3 -0.1 0.17 -10000 0 -0.37 63 63
cell morphogenesis 0.025 0.008 -10000 0 -10000 0 0
PLCB2 -0.14 0.22 -10000 0 -0.5 64 64
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.01 0.071 0.2 7 -10000 0 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.018 0.041 0.2 3 -10000 0 3
RHOA 0.019 0.006 -10000 0 -10000 0 0
PTGIR 0.019 0.018 -10000 0 -0.29 1 1
PRKCB1 -0.097 0.16 -10000 0 -0.37 58 58
GNAQ 0.02 0.003 -10000 0 -10000 0 0
mol:L-citrulline 0.011 0.051 -10000 0 -0.29 8 8
TXA2/TXA2-R family -0.13 0.22 -10000 0 -0.51 57 57
LCK -0.018 0.044 0.2 3 -10000 0 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.038 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.074 -10000 0 -0.39 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.004 0.038 0.15 2 -10000 0 2
MAPK14 -0.058 0.1 0.28 1 -0.23 52 53
TGM2/GTP -0.12 0.19 -10000 0 -0.41 80 80
MAPK11 -0.06 0.099 -10000 0 -0.23 52 52
ARHGEF1 -0.051 0.074 -10000 0 -0.18 51 51
GNAI2 0.019 0.006 -10000 0 -10000 0 0
JNK cascade -0.095 0.16 -10000 0 -0.38 56 56
RAB11/GDP 0.02 0.007 -10000 0 -10000 0 0
ICAM1 -0.068 0.12 -10000 0 -0.28 55 55
cAMP biosynthetic process -0.097 0.16 -10000 0 -0.33 80 80
Gq family/GTP/EBP50 -0.023 0.079 0.23 5 -0.15 67 72
actin cytoskeleton reorganization 0.025 0.008 -10000 0 -10000 0 0
SRC -0.019 0.041 0.2 3 -10000 0 3
GNB5 0.02 0.005 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.001 0.059 0.18 8 -10000 0 8
VCAM1 -0.071 0.13 -10000 0 -0.3 55 55
TP beta/Gq family/GDP/G beta5/gamma2 -0.046 0.15 0.27 2 -0.52 19 21
platelet activation -0.078 0.13 0.29 1 -0.3 53 54
PGI2/IP 0.014 0.013 -10000 0 -0.2 1 1
PRKACA 0.005 0.019 -10000 0 -0.17 3 3
Gq family/GDP/G beta5/gamma2 -0.041 0.12 0.21 1 -0.45 18 19
TXA2/TP beta/beta Arrestin2 0.003 0.039 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.021 -10000 0 -0.16 5 5
mol:DAG -0.11 0.18 -10000 0 -0.42 59 59
EGFR 0.018 0.026 -10000 0 -0.29 2 2
TXA2/TP alpha -0.13 0.21 -10000 0 -0.45 80 80
Gq family/GTP -0.051 0.095 -10000 0 -0.19 80 80
YES1 -0.018 0.043 0.2 3 -10000 0 3
GNAI2/GTP -0.022 0.025 -10000 0 -0.16 3 3
PGD2/DP 0.012 0.022 -10000 0 -0.2 3 3
SLC9A3R1 0.033 0.059 0.29 14 -10000 0 14
FYN -0.02 0.047 0.2 3 -10000 0 3
mol:NO 0.011 0.051 -10000 0 -0.29 8 8
GNA15 0.035 0.064 0.29 17 -10000 0 17
PGK/cGMP -0.024 0.088 -10000 0 -0.17 73 73
RhoA/GDP 0.018 0.008 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.008 0.061 -10000 0 -0.23 3 3
NOS3 0.011 0.051 -10000 0 -0.29 8 8
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA -0.092 0.15 -10000 0 -0.35 56 56
PRKCB -0.093 0.16 0.24 1 -0.36 56 57
PRKCE -0.09 0.15 -10000 0 -0.36 54 54
PRKCD -0.098 0.16 -10000 0 -0.38 56 56
PRKCG -0.097 0.17 -10000 0 -0.39 53 53
muscle contraction -0.12 0.2 -10000 0 -0.48 57 57
PRKCZ -0.087 0.14 -10000 0 -0.34 57 57
ARR3 -0.008 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.007 0.041 -10000 0 -0.17 3 3
PRKCQ -0.093 0.15 -10000 0 -0.36 56 56
MAPKKK cascade -0.12 0.2 -10000 0 -0.45 59 59
SELE -0.082 0.15 -10000 0 -0.35 55 55
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.036 -10000 0 -0.16 3 3
ROCK1 0.02 0.002 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.29 81 81
chemotaxis -0.14 0.24 -10000 0 -0.58 55 55
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.003 -10000 0 -10000 0 0
GNA11 0.019 0.019 -10000 0 -0.29 1 1
Rac1/GTP 0.014 0.002 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.31 0.49 -10000 0 -1.1 46 46
STAT6 (cleaved dimer) -0.33 0.46 -10000 0 -1.1 54 54
IGHG1 -0.099 0.19 0.36 4 -10000 0 4
IGHG3 -0.32 0.46 -10000 0 -1.1 52 52
AKT1 -0.16 0.25 -10000 0 -0.8 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.2 -10000 0 -0.67 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.26 -10000 0 -0.75 15 15
THY1 -0.33 0.48 -10000 0 -1.1 51 51
MYB 0.052 0.088 0.29 34 -10000 0 34
HMGA1 0.024 0.032 0.29 4 -10000 0 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.18 0.28 0.45 2 -0.65 24 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.26 -10000 0 -0.75 15 15
SP1 0.013 0.033 -10000 0 -0.16 4 4
INPP5D 0.018 0.007 -10000 0 -10000 0 0
SOCS5 0.015 0.033 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.46 -10000 0 -1.1 53 53
SOCS1 -0.22 0.31 -10000 0 -0.71 44 44
SOCS3 -0.16 0.24 0.56 1 -0.66 6 7
FCER2 -0.28 0.4 -10000 0 -0.97 38 38
PARP14 0.017 0.008 -10000 0 -10000 0 0
CCL17 -0.32 0.49 0.63 3 -1.1 49 52
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.24 -10000 0 -0.71 15 15
T cell proliferation -0.33 0.47 -10000 0 -1.1 51 51
IL4R/JAK1 -0.33 0.47 -10000 0 -1.1 50 50
EGR2 -0.33 0.48 -10000 0 -1.1 46 46
JAK2 -0.017 0.056 -10000 0 -10000 0 0
JAK3 0.02 0.014 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
JAK1 -0.004 0.03 -10000 0 -10000 0 0
COL1A2 -0.16 0.34 -10000 0 -1.2 23 23
CCL26 -0.33 0.48 -10000 0 -1.1 50 50
IL4R -0.35 0.51 -10000 0 -1.2 51 51
PTPN6 0.019 0.027 -10000 0 -10000 0 0
IL13RA2 -0.33 0.48 -10000 0 -1.1 50 50
IL13RA1 -0.018 0.057 -10000 0 -10000 0 0
IRF4 -0.059 0.17 0.44 1 -0.75 9 10
ARG1 -0.081 0.18 -10000 0 -0.63 8 8
CBL -0.17 0.26 -10000 0 -0.62 23 23
GTF3A 0.021 0.008 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.015 0.08 0.2 4 -10000 0 4
IRF4/BCL6 -0.039 0.14 -10000 0 -0.68 9 9
CD40LG 0.022 0.011 -10000 0 -0.13 1 1
MAPK14 -0.17 0.27 -10000 0 -0.66 16 16
mitosis -0.15 0.24 -10000 0 -0.77 8 8
STAT6 -0.36 0.55 0.65 1 -1.3 52 53
SPI1 0.021 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.23 0.39 1 -0.75 8 9
STAT6 (dimer) -0.36 0.55 0.65 1 -1.3 52 53
STAT6 (dimer)/PARP14 -0.34 0.49 -10000 0 -1.2 48 48
mast cell activation 0.007 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.25 -10000 0 -0.67 18 18
FRAP1 -0.16 0.25 -10000 0 -0.8 9 9
LTA -0.32 0.48 0.64 1 -1.1 49 50
FES 0.02 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.36 0.54 1.2 52 -0.64 1 53
CCL11 -0.34 0.48 -10000 0 -1.1 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.24 -10000 0 -0.75 8 8
IL2RG 0.023 0.032 0.3 3 -10000 0 3
IL10 -0.32 0.48 0.62 1 -1.1 45 46
IRS1 0.008 0.056 -10000 0 -0.29 10 10
IRS2 0.011 0.051 -10000 0 -0.29 8 8
IL4 -0.091 0.23 -10000 0 -0.98 11 11
IL5 -0.33 0.48 -10000 0 -1.1 50 50
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.41 0.56 4 -0.91 46 50
COL1A1 -0.12 0.24 -10000 0 -0.92 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.48 -10000 0 -1.2 49 49
IL2R gamma/JAK3 0.031 0.024 0.22 3 -10000 0 3
TFF3 -0.44 0.63 0.62 2 -1.4 75 77
ALOX15 -0.31 0.49 0.63 3 -1.1 49 52
MYBL1 0.02 0.004 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.37 0.45 -10000 0 -1 65 65
SHC1 0.019 0.006 -10000 0 -10000 0 0
CEBPB 0.021 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.23 0.43 1 -0.65 7 8
mol:PI-3-4-5-P3 -0.16 0.25 -10000 0 -0.8 9 9
PI3K -0.16 0.26 -10000 0 -0.86 9 9
DOK2 0.019 0.006 -10000 0 -10000 0 0
ETS1 0.014 0.03 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.12 0.21 -10000 0 -0.66 9 9
ITGB3 -0.4 0.56 -10000 0 -1.3 63 63
PIGR -0.46 0.63 0.62 4 -1.3 88 92
IGHE 0.042 0.062 0.18 19 -10000 0 19
MAPKKK cascade -0.12 0.21 -10000 0 -0.64 9 9
BCL6 0.013 0.01 -10000 0 -10000 0 0
OPRM1 -0.33 0.48 -10000 0 -1.1 48 48
RETNLB -0.3 0.48 0.62 1 -1.1 48 49
SELP -0.6 0.68 0.62 1 -1.3 133 134
AICDA -0.32 0.46 -10000 0 -1.1 50 50
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.046 0.12 -10000 0 -0.2 103 103
fibroblast growth factor receptor signaling pathway -0.046 0.12 -10000 0 -0.2 103 103
LAMA1 0.032 0.066 0.29 15 -0.29 2 17
PRNP 0.014 0.04 -10000 0 -0.29 5 5
GPC1/SLIT2 -0.052 0.11 -10000 0 -0.2 99 99
SMAD2 -0.018 0.028 0.17 5 -0.16 1 6
GPC1/PrPc/Cu2+ 0.02 0.027 -10000 0 -0.17 5 5
GPC1/Laminin alpha1 0.033 0.046 0.22 14 -0.19 2 16
TDGF1 -0.01 0.076 0.29 1 -0.29 18 19
CRIPTO/GPC1 0.011 0.057 0.22 1 -0.2 18 19
APP/GPC1 0.026 0.011 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.026 0.039 0.092 1 -0.17 18 19
FLT1 0.019 0.019 -10000 0 -0.29 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.033 0.024 -10000 0 -0.17 2 2
SERPINC1 0.018 0.035 0.29 4 -10000 0 4
FYN -0.029 0.041 0.092 1 -0.17 21 22
FGR -0.027 0.038 0.092 1 -0.17 17 18
positive regulation of MAPKKK cascade -0.021 0.099 0.22 4 -0.25 21 25
SLIT2 -0.089 0.15 -10000 0 -0.29 100 100
GPC1/NRG 0.052 0.068 0.22 42 -10000 0 42
NRG1 0.065 0.1 0.29 50 -10000 0 50
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.034 0.02 -10000 0 -0.17 1 1
LYN -0.026 0.038 0.092 1 -0.17 17 18
mol:Spermine -0.008 0.003 -10000 0 -10000 0 0
cell growth -0.046 0.12 -10000 0 -0.2 103 103
BMP signaling pathway -0.018 0.007 -10000 0 -10000 0 0
SRC -0.026 0.039 0.092 1 -0.17 18 19
TGFBR1 0.02 0.003 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0 0.098 0.29 10 -0.29 22 32
GPC1 0.018 0.007 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.02 0.003 -10000 0 -10000 0 0
VEGFA 0.02 0.004 -10000 0 -10000 0 0
BLK 0.004 0.075 0.15 50 -0.17 14 64
HCK -0.024 0.036 0.092 1 -0.17 15 16
FGF2 -0.074 0.14 -10000 0 -0.29 88 88
FGFR1 -0.021 0.1 -10000 0 -0.29 38 38
VEGFR1 homodimer 0.019 0.019 -10000 0 -0.29 1 1
TGFBR2 0.017 0.026 -10000 0 -0.29 2 2
cell death 0.026 0.011 -10000 0 -10000 0 0
ATIII/GPC1 0.026 0.023 0.22 3 -10000 0 3
PLA2G2A/GPC1 0.016 0.071 0.22 10 -0.2 22 32
LCK -0.027 0.039 0.092 1 -0.17 18 19
neuron differentiation 0.052 0.068 0.22 42 -10000 0 42
PrPc/Cu2+ 0.011 0.028 -10000 0 -0.2 5 5
APP 0.02 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.017 0.026 -10000 0 -0.29 2 2
HIF-2-alpha transcription factor network

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
MMP14 -0.016 0.081 -10000 0 -0.64 4 4
oxygen homeostasis -0.011 0.012 -10000 0 -10000 0 0
TCEB2 0.02 0.004 -10000 0 -10000 0 0
TCEB1 0.02 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.041 0.082 -10000 0 -0.23 2 2
EPO -0.16 0.19 -10000 0 -0.47 44 44
FIH (dimer) -0.016 0.027 -10000 0 -10000 0 0
APEX1 -0.02 0.031 -10000 0 -10000 0 0
SERPINE1 -0.15 0.17 0.34 2 -0.43 40 42
FLT1 -0.16 0.27 -10000 0 -0.7 52 52
ADORA2A -0.15 0.17 0.33 2 -0.42 44 46
germ cell development -0.13 0.18 0.39 4 -0.42 38 42
SLC11A2 -0.15 0.18 0.34 2 -0.43 44 46
BHLHE40 -0.15 0.18 0.34 2 -0.42 44 46
HIF1AN -0.016 0.027 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.084 0.12 0.32 1 -0.3 8 9
ETS1 -0.011 0.052 -10000 0 -10000 0 0
CITED2 -0.12 0.3 -10000 0 -0.88 38 38
KDR -0.36 0.46 -10000 0 -0.91 117 117
PGK1 -0.15 0.18 0.34 2 -0.42 45 47
SIRT1 0.018 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.16 0.2 -10000 0 -0.47 44 44
EPAS1 -0.055 0.066 -10000 0 -0.22 8 8
SP1 0.021 0.003 -10000 0 -10000 0 0
ABCG2 -0.23 0.23 0.34 2 -0.46 123 125
EFNA1 -0.15 0.17 0.32 1 -0.43 44 45
FXN -0.15 0.17 0.33 2 -0.42 45 47
POU5F1 -0.14 0.19 0.39 4 -0.43 38 42
neuron apoptosis 0.15 0.2 0.46 44 -10000 0 44
EP300 0.02 0.003 -10000 0 -10000 0 0
EGLN3 -0.016 0.026 -10000 0 -10000 0 0
EGLN2 -0.016 0.026 -10000 0 -10000 0 0
EGLN1 -0.014 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.036 0.015 -10000 0 -10000 0 0
VHL 0.019 0.005 -10000 0 -10000 0 0
ARNT -0.018 0.029 -10000 0 -10000 0 0
SLC2A1 -0.15 0.17 0.32 3 -0.41 46 49
TWIST1 -0.18 0.2 0.33 2 -0.48 62 64
ELK1 0.01 0.035 -10000 0 -0.11 6 6
HIF2A/ARNT/Cbp/p300 -0.079 0.12 -10000 0 -0.29 7 7
VEGFA -0.15 0.17 0.36 1 -0.42 44 45
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.025 0.22 5 -10000 0 5
STXBP1 0.019 0.018 -10000 0 -0.29 1 1
ACh/CHRNA1 -0.012 0.058 0.2 6 -0.086 82 88
RAB3GAP2/RIMS1/UNC13B 0.039 0.026 0.21 5 -10000 0 5
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 0.006 0.042 0.29 5 -10000 0 5
mol:ACh -0.032 0.054 0.073 14 -0.1 91 105
RAB3GAP2 0.019 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.023 0.086 0.19 4 -0.2 15 19
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.012 0.058 0.2 6 -0.086 82 88
UNC13B 0.02 0.003 -10000 0 -10000 0 0
CHRNA1 0.021 0.042 0.29 6 -10000 0 6
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.099 -10000 0 -0.18 90 90
SNAP25 -0.063 0.097 -10000 0 -0.21 89 89
VAMP2 0.002 0 -10000 0 -10000 0 0
SYT1 -0.11 0.15 -10000 0 -0.29 123 123
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.011 -10000 0 -0.17 1 1
STX1A/SNAP25 fragment 1/VAMP2 -0.023 0.086 0.19 4 -0.2 15 19
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.03 0.047 -10000 0 -0.17 14 14
alphaM/beta2 Integrin/GPIbA 0.039 0.019 0.21 1 -10000 0 1
alphaM/beta2 Integrin/proMMP-9 0.065 0.064 0.21 44 -10000 0 44
PLAUR 0.02 0.004 -10000 0 -10000 0 0
HMGB1 0.021 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.041 0.013 -10000 0 -10000 0 0
AGER 0.021 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
SELPLG 0.021 0.001 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.053 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.062 0.1 0.29 46 -10000 0 46
CYR61 -0.015 0.098 -10000 0 -0.29 33 33
TLN1 0.02 0.003 -10000 0 -10000 0 0
Rap1/GTP -0.052 0.11 -10000 0 -0.24 40 40
RHOA 0.019 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.12 0.15 -10000 0 -0.29 128 128
MYH2 -0.075 0.14 -10000 0 -0.33 42 42
MST1R 0.099 0.12 0.29 85 -10000 0 85
leukocyte activation during inflammatory response 0.043 0.028 0.18 8 -10000 0 8
APOB 0.01 0.034 0.29 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.004 0.069 -10000 0 -0.29 15 15
JAM3 -0.013 0.091 -10000 0 -0.29 28 28
GP1BA 0.018 0.019 0.29 1 -10000 0 1
alphaM/beta2 Integrin/CTGF -0.014 0.094 -10000 0 -0.17 75 75
alphaM/beta2 Integrin -0.056 0.1 -10000 0 -0.28 32 32
JAM3 homodimer -0.013 0.091 -10000 0 -0.29 28 28
ICAM2 0.009 0.057 -10000 0 -0.29 10 10
ICAM1 0.02 0.004 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.049 0.11 -10000 0 -0.27 35 35
cell adhesion 0.039 0.019 0.21 1 -10000 0 1
NFKB1 -0.005 0.068 0.38 4 -10000 0 4
THY1 0.017 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.029 0.029 0.19 8 -10000 0 8
alphaM/beta2 Integrin/LRP/tPA 0.04 0.046 -10000 0 -0.16 12 12
IL6 -0.007 0.069 0.28 11 -10000 0 11
ITGB2 0.021 0.006 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.048 0.021 0.24 1 -10000 0 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.058 0.12 -10000 0 -0.18 132 132
JAM2 -0.12 0.15 -10000 0 -0.29 134 134
alphaM/beta2 Integrin/ICAM1 0.094 0.074 0.21 78 -10000 0 78
alphaM/beta2 Integrin/uPA/Plg 0.05 0.027 0.22 4 -10000 0 4
RhoA/GTP -0.088 0.14 -10000 0 -0.34 45 45
positive regulation of phagocytosis -0.038 0.087 -10000 0 -0.25 15 15
Ron/MSP 0.082 0.086 0.22 85 -10000 0 85
alphaM/beta2 Integrin/uPAR/uPA 0.05 0.021 0.24 1 -10000 0 1
alphaM/beta2 Integrin/uPAR 0.04 0.014 -10000 0 -10000 0 0
PLAU 0.021 0.016 0.29 1 -10000 0 1
PLAT 0.007 0.062 -10000 0 -0.29 12 12
actin filament polymerization -0.085 0.13 -10000 0 -0.32 44 44
MST1 0.019 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.048 0.03 0.2 8 -10000 0 8
TNF -0.013 0.064 0.35 6 -10000 0 6
RAP1B 0.02 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.042 0.018 0.24 1 -10000 0 1
fibrinolysis 0.048 0.026 0.21 4 -10000 0 4
HCK 0.019 0.006 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.049 0.11 -10000 0 -0.27 35 35
VTN -0.008 0.1 0.29 5 -0.29 29 34
alphaM/beta2 Integrin/CYR61 0.019 0.068 -10000 0 -0.17 32 32
LPA 0.01 0.042 0.29 5 -10000 0 5
LRP1 0.02 0.002 -10000 0 -10000 0 0
cell migration 0.034 0.055 0.19 3 -0.16 11 14
FN1 0.01 0.051 -10000 0 -0.29 8 8
alphaM/beta2 Integrin/Thy1 0.036 0.019 -10000 0 -10000 0 0
MPO 0.014 0.022 0.29 1 -10000 0 1
KNG1 -0.011 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.027 0.005 -10000 0 -10000 0 0
ROCK1 -0.08 0.14 -10000 0 -0.33 45 45
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.007 0.034 0.29 3 -10000 0 3
CTGF -0.063 0.14 -10000 0 -0.29 78 78
alphaM/beta2 Integrin/Hck 0.038 0.017 -10000 0 -10000 0 0
ITGAM 0.022 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.042 0.1 -10000 0 -0.16 124 124
HP -0.11 0.15 -10000 0 -0.29 119 119
leukocyte adhesion -0.06 0.11 -10000 0 -0.26 25 25
SELP -0.12 0.15 -10000 0 -0.29 128 128
IL1-mediated signaling events

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
UBC13/UEV1A 0.015 0.001 -10000 0 -10000 0 0
PRKCZ 0.02 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.041 -10000 0 -0.21 7 7
IRAK/TOLLIP 0.018 0.006 -10000 0 -10000 0 0
IKBKB 0.02 0.005 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.13 0.097 0.22 157 -10000 0 157
IL1A 0.16 0.14 0.29 148 -10000 0 148
IL1B 0.011 0.062 0.15 47 -10000 0 47
IRAK/TRAF6/p62/Atypical PKCs 0.026 0.026 -10000 0 -10000 0 0
IL1R2 0.033 0.057 0.29 13 -10000 0 13
IL1R1 0.017 0.031 -10000 0 -0.29 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.02 0.062 0.19 3 -0.33 4 7
TOLLIP 0.02 0.005 -10000 0 -10000 0 0
TICAM2 0.019 0.005 -10000 0 -10000 0 0
MAP3K3 0.02 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.014 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.013 0.061 -10000 0 -0.36 2 2
JUN -0.024 0.024 0.14 5 -10000 0 5
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.046 -10000 0 -0.16 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88 0.078 0.091 0.21 88 -0.16 2 90
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.08 0.09 0.21 88 -0.16 2 90
IL1 beta fragment/IL1R1/IL1RAP 0.027 0.041 0.26 1 -0.16 2 3
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.021 0.026 0.15 5 -0.14 1 6
IRAK1 -0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.17 0.087 0.22 219 -0.16 3 222
IRAK4 0.02 0.002 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
TRAF6 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.019 0.015 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.043 -10000 0 -0.24 1 1
CHUK 0.02 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.027 0.041 0.26 1 -0.16 2 3
IL1 beta/IL1R2 0.034 0.04 0.2 11 -10000 0 11
IRAK/TRAF6/TAK1/TAB1/TAB2 0.024 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.011 0.04 -10000 0 -10000 0 0
IRAK3 0.012 0.051 -10000 0 -0.29 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.037 0.046 -10000 0 -0.16 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.054 0.066 0.17 42 -0.22 2 44
IL1 alpha/IL1R1/IL1RAP 0.08 0.093 0.21 96 -0.17 2 98
RELA 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.004 -10000 0 -10000 0 0
MYD88 0.019 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.029 0.01 -10000 0 -10000 0 0
IL1RAP 0.013 0.01 -10000 0 -10000 0 0
UBE2N 0.021 0.001 -10000 0 -10000 0 0
IRAK/TRAF6 -0.014 0.034 -10000 0 -10000 0 0
CASP1 0.018 0.007 -10000 0 -10000 0 0
IL1RN/IL1R2 0.18 0.086 0.22 227 -10000 0 227
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.031 0.041 -10000 0 -0.16 2 2
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.035 0.078 -10000 0 -0.27 7 7
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
IL1RN 0.23 0.12 0.29 223 -10000 0 223
TRAF6/TAK1/TAB1/TAB2 0.028 0.008 -10000 0 -10000 0 0
MAP2K6 -0.015 0.029 0.16 7 -10000 0 7
Nectin adhesion pathway

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
PDGFRB 0.003 0.071 -10000 0 -0.29 16 16
alphaV beta3 Integrin 0.003 0.073 -10000 0 -0.2 33 33
PTK2 -0.037 0.12 -10000 0 -0.32 31 31
positive regulation of JNK cascade -0.043 0.13 -10000 0 -0.29 46 46
CDC42/GDP -0.04 0.16 -10000 0 -0.38 37 37
Rac1/GDP -0.037 0.15 -10000 0 -0.37 39 39
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.05 0.16 -10000 0 -0.37 43 43
nectin-3/I-afadin 0.008 0.057 -10000 0 -0.2 19 19
RAPGEF1 -0.04 0.14 0.25 1 -0.38 34 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.045 0.15 -10000 0 -0.42 34 34
PDGFB-D/PDGFRB 0.003 0.071 -10000 0 -0.29 16 16
TLN1 -0.025 0.051 -10000 0 -0.26 9 9
Rap1/GTP -0.028 0.1 -10000 0 -0.28 33 33
IQGAP1 0.02 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.012 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.008 0.057 -10000 0 -0.2 19 19
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.055 0.18 -10000 0 -0.45 39 39
MLLT4 0.019 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.021 0.056 -10000 0 -0.16 17 17
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.056 0.22 26 -10000 0 26
positive regulation of lamellipodium assembly -0.024 0.11 -10000 0 -0.28 35 35
PVRL1 0.045 0.085 0.29 30 -10000 0 30
PVRL3 -0.003 0.076 -10000 0 -0.29 19 19
PVRL2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.26 0.097 0.29 251 -10000 0 251
CLDN1 -0.001 0.063 -10000 0 -0.29 13 13
JAM-A/CLDN1 0.014 0.058 -10000 0 -0.17 22 22
SRC -0.046 0.16 -10000 0 -0.45 35 35
ITGB3 -0.016 0.1 -10000 0 -0.29 34 34
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.056 0.22 26 -10000 0 26
FARP2 -0.076 0.22 -10000 0 -0.49 53 53
RAC1 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.017 0.052 -10000 0 -0.17 18 18
nectin-1/I-afadin 0.041 0.056 0.22 26 -10000 0 26
nectin-2/I-afadin 0.027 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.027 0.006 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.027 0.074 0.21 23 -0.17 19 42
CDC42/GTP/IQGAP1/filamentous actin 0.026 0.007 -10000 0 -10000 0 0
F11R 0.019 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.043 0.13 -10000 0 -0.29 46 46
alphaV/beta3 Integrin/Talin -0.032 0.085 0.19 2 -0.26 16 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
PIP5K1C -0.02 0.053 -10000 0 -0.18 23 23
VAV2 -0.034 0.16 -10000 0 -0.44 27 27
RAP1/GDP -0.028 0.14 -10000 0 -0.34 37 37
ITGAV 0.02 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.018 0.051 -10000 0 -0.17 17 17
nectin-3(dimer)/I-afadin/I-afadin 0.008 0.057 -10000 0 -0.2 19 19
Rac1/GTP -0.026 0.13 -10000 0 -0.34 32 32
PTPRM -0.014 0.065 -10000 0 -0.21 25 25
E-cadherin/beta catenin/alpha catenin 0.13 0.1 0.32 22 -10000 0 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.02 0.005 -10000 0 -10000 0 0
LAT2 -0.04 0.086 -10000 0 -0.24 33 33
AP1 -0.012 0.13 0.26 1 -0.42 12 13
mol:PIP3 -0.035 0.12 0.25 10 -0.29 23 33
IKBKB -0.014 0.082 0.18 16 -0.2 10 26
AKT1 0.015 0.14 0.34 27 -0.23 7 34
IKBKG -0.012 0.086 0.19 15 -0.2 10 25
MS4A2 -0.021 0.097 -10000 0 -0.29 33 33
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
MAP3K1 0.031 0.14 0.22 73 -0.31 8 81
mol:Ca2+ -0.026 0.1 0.21 14 -0.23 23 37
LYN 0.015 0.016 -10000 0 -10000 0 0
CBLB -0.034 0.079 -10000 0 -0.24 28 28
SHC1 0.019 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.035 0.025 -10000 0 -0.16 4 4
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.007 -10000 0 -10000 0 0
PLD2 -0.03 0.11 0.29 22 -0.19 35 57
PTPN13 -0.033 0.13 -10000 0 -0.46 12 12
PTPN11 0.015 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.004 0.12 0.27 17 -0.28 9 26
SYK 0.015 0.016 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.11 -10000 0 -0.27 32 32
LAT -0.04 0.086 -10000 0 -0.24 33 33
PAK2 0.031 0.14 0.23 75 -0.32 9 84
NFATC2 -0.025 0.079 -10000 0 -0.44 9 9
HRAS -0.025 0.1 0.21 7 -0.27 25 32
GAB2 0.018 0.019 -10000 0 -0.29 1 1
PLA2G1B -0.037 0.2 -10000 0 -0.83 18 18
Fc epsilon R1 -0.012 0.098 -10000 0 -0.19 64 64
Antigen/IgE/Fc epsilon R1 -0.009 0.088 -10000 0 -0.17 63 63
mol:GDP -0.028 0.098 0.23 1 -0.34 12 13
JUN 0.019 0.018 -10000 0 -0.29 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.007 -10000 0 -10000 0 0
FOS -0.003 0.082 -10000 0 -0.29 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.033 0.091 -10000 0 -0.24 33 33
CHUK -0.017 0.08 0.19 13 -0.2 9 22
KLRG1 -0.036 0.074 -10000 0 -0.26 13 13
VAV1 -0.038 0.087 0.21 1 -0.24 32 33
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.034 0.081 -10000 0 -0.24 27 27
negative regulation of mast cell degranulation -0.031 0.076 0.19 3 -0.26 13 16
BTK -0.026 0.097 -10000 0 -0.34 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.1 -10000 0 -0.24 43 43
GAB2/PI3K/SHP2 -0.045 0.057 -10000 0 -0.18 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.033 0.082 -10000 0 -0.2 39 39
RAF1 -0.037 0.23 -10000 0 -0.91 18 18
Fc epsilon R1/FcgammaRIIB/SHIP 0.001 0.095 -10000 0 -0.17 60 60
FCER1G 0.016 0.019 -10000 0 -10000 0 0
FCER1A -0.028 0.11 -10000 0 -0.3 39 39
Antigen/IgE/Fc epsilon R1/Fyn -0.005 0.091 -10000 0 -0.17 66 66
MAPK3 -0.038 0.21 -10000 0 -0.84 18 18
MAPK1 -0.038 0.21 -10000 0 -0.84 18 18
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.038 0.19 -10000 0 -0.61 19 19
DUSP1 0.014 0.04 -10000 0 -0.29 5 5
NF-kappa-B/RelA -0.012 0.053 0.12 7 -0.14 8 15
actin cytoskeleton reorganization -0.03 0.13 -10000 0 -0.45 14 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.021 0.087 -10000 0 -0.26 21 21
FER -0.04 0.085 -10000 0 -0.24 32 32
RELA 0.02 0.003 -10000 0 -10000 0 0
ITK -0.012 0.044 -10000 0 -0.23 8 8
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG1 -0.018 0.11 0.25 3 -0.29 22 25
cytokine secretion -0.015 0.032 -10000 0 -10000 0 0
SPHK1 -0.04 0.086 -10000 0 -0.24 33 33
PTK2 -0.031 0.14 -10000 0 -0.49 12 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.027 0.11 -10000 0 -0.27 32 32
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.033 0.12 0.23 16 -0.28 25 41
MAP2K2 -0.043 0.21 -10000 0 -0.85 18 18
MAP2K1 -0.041 0.21 -10000 0 -0.85 18 18
MAP2K7 0.02 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.029 0.073 0.2 3 -0.23 13 16
MAP2K4 -0.073 0.29 -10000 0 -0.83 35 35
Fc epsilon R1/FcgammaRIIB -0.001 0.097 -10000 0 -0.18 62 62
mol:Choline -0.029 0.11 0.29 22 -0.18 35 57
SHC/Grb2/SOS1 -0.01 0.1 -10000 0 -0.25 24 24
FYN 0.015 0.04 -10000 0 -0.29 5 5
DOK1 0.02 0.003 -10000 0 -10000 0 0
PXN -0.034 0.13 -10000 0 -0.44 14 14
HCLS1 -0.033 0.077 -10000 0 -0.24 25 25
PRKCB -0.02 0.1 0.22 13 -0.25 13 26
FCGR2B 0.017 0.026 -10000 0 -0.29 2 2
IGHE -0.001 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.032 0.077 0.19 3 -0.26 13 16
LCP2 0.02 0.004 -10000 0 -10000 0 0
PLA2G4A -0.042 0.089 -10000 0 -0.25 35 35
RASA1 0.02 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.029 0.11 0.29 22 -0.18 35 57
IKK complex -0.01 0.073 0.19 10 -0.16 6 16
WIPF1 0.02 0.003 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.058 0.1 0.21 59 -0.16 24 83
SMAD6-7/SMURF1 0.037 0.013 -10000 0 -10000 0 0
NOG 0.019 0.025 0.29 2 -10000 0 2
SMAD9 -0.061 0.17 -10000 0 -0.44 45 45
SMAD4 0.019 0.005 -10000 0 -10000 0 0
SMAD5 -0.032 0.093 -10000 0 -0.32 15 15
BMP7/USAG1 0.083 0.096 0.23 84 -0.2 1 85
SMAD5/SKI -0.023 0.1 0.22 1 -0.3 16 17
SMAD1 -0.011 0.052 -10000 0 -0.25 4 4
BMP2 0.018 0.019 -10000 0 -0.29 1 1
SMAD1/SMAD1/SMAD4 0 0.059 -10000 0 -0.24 5 5
BMPR1A 0.02 0.004 -10000 0 -10000 0 0
BMPR1B -0.007 0.09 0.29 1 -0.29 26 27
BMPR1A-1B/BAMBI 0.013 0.076 0.21 1 -0.19 35 36
AHSG -0.011 0.008 -10000 0 -10000 0 0
CER1 -0.01 0.014 -10000 0 -10000 0 0
BMP2-4/CER1 0.026 0.045 -10000 0 -0.17 13 13
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.027 0.091 -10000 0 -0.29 18 18
BMP2-4 (homodimer) 0.018 0.048 -10000 0 -0.2 13 13
RGMB 0.02 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.025 0.065 0.21 1 -0.16 29 30
RGMA -0.001 0.078 -10000 0 -0.29 20 20
SMURF1 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.026 0.085 -10000 0 -0.3 13 13
BMP2-4/USAG1 0.041 0.063 0.21 21 -0.17 12 33
SMAD6/SMURF1/SMAD5 -0.022 0.098 0.22 1 -0.31 14 15
SOSTDC1 0.037 0.082 0.29 26 -10000 0 26
BMP7/BMPR2/BMPR1A-1B 0.055 0.093 0.21 54 -0.16 18 72
SKI 0.02 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.016 0.032 -10000 0 -0.29 3 3
HFE2 -0.006 0.017 -10000 0 -10000 0 0
ZFYVE16 0.02 0.004 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD -0.018 0.085 -10000 0 -0.19 55 55
SMAD5/SMAD5/SMAD4 -0.021 0.1 0.22 1 -0.31 14 15
MAPK1 0.02 0.002 -10000 0 -10000 0 0
TAK1/TAB family -0.012 0.086 -10000 0 -0.26 13 13
BMP7 (homodimer) 0.082 0.12 0.29 68 -0.29 1 69
NUP214 0.02 0.002 -10000 0 -10000 0 0
BMP6/FETUA 0.016 0.019 -10000 0 -0.2 1 1
SMAD1/SKI -0.005 0.061 -10000 0 -0.25 6 6
SMAD6 0.02 0.003 -10000 0 -10000 0 0
CTDSP2 0.02 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA 0.019 0.036 -10000 0 -0.17 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.015 0.04 -10000 0 -0.29 5 5
BMPR2 (homodimer) 0.019 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.038 0.013 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.009 0.068 0.22 1 -0.2 26 27
CHRDL1 -0.23 0.12 -10000 0 -0.29 229 229
ENDOFIN/SMAD1 -0.003 0.06 -10000 0 -0.25 6 6
SMAD6-7/SMURF1/SMAD1 0.009 0.065 -10000 0 -0.25 5 5
SMAD6/SMURF1 0.02 0.004 -10000 0 -10000 0 0
BAMBI 0.007 0.062 -10000 0 -0.29 12 12
SMURF2 0.02 0.003 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.094 -10000 0 -0.18 217 217
BMP2-4/GREM1 0.025 0.052 -10000 0 -0.18 16 16
SMAD7 0.02 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.057 0.17 -10000 0 -0.41 49 49
SMAD1/SMAD6 -0.004 0.06 -10000 0 -0.25 6 6
TAK1/SMAD6 0.028 0.008 -10000 0 -10000 0 0
BMP7 0.082 0.12 0.29 68 -0.29 1 69
BMP6 0.017 0.032 -10000 0 -0.29 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.023 0.091 0.2 1 -0.3 16 17
PPM1A 0.02 0.003 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.061 -10000 0 -0.26 6 6
SMAD7/SMURF1 0.028 0.009 -10000 0 -10000 0 0
CTDSPL 0.019 0.005 -10000 0 -10000 0 0
PPP1CA 0.02 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.002 -10000 0 -10000 0 0
CTDSP1 0.018 0.006 -10000 0 -10000 0 0
PPP1R15A 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.032 0.1 -10000 0 -0.34 18 18
CHRD -0.045 0.12 -10000 0 -0.29 55 55
BMPR2 0.019 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.033 0.085 -10000 0 -0.31 14 14
BMP4 0.007 0.062 -10000 0 -0.29 12 12
FST 0.02 0.068 0.29 9 -0.29 7 16
BMP2-4/NOG 0.028 0.046 0.21 1 -0.17 13 14
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.059 0.091 -10000 0 -0.16 17 17
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.045 0.037 0.22 3 -10000 0 3
AES 0.038 0.03 0.18 2 -10000 0 2
FBXW11 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.028 0.009 -10000 0 -10000 0 0
SMAD4 0.019 0.005 -10000 0 -10000 0 0
DKK2 0.015 0.044 0.29 1 -0.29 5 6
TLE1 0.04 0.03 0.19 2 -10000 0 2
MACF1 0.021 0.002 -10000 0 -10000 0 0
CTNNB1 0.052 0.11 0.29 17 -0.38 3 20
WIF1 -0.035 0.12 0.29 3 -0.29 51 54
beta catenin/RanBP3 0.12 0.16 0.36 82 -10000 0 82
KREMEN2 0.18 0.14 0.29 168 -10000 0 168
DKK1 0.006 0.076 0.29 3 -0.29 16 19
beta catenin/beta TrCP1 0.061 0.1 0.28 17 -0.38 2 19
FZD1 0.02 0.005 -10000 0 -10000 0 0
AXIN2 -0.37 0.55 0.54 5 -1.1 96 101
AXIN1 0.021 0.004 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.024 0.091 -10000 0 -0.56 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.12 -10000 0 -0.51 8 8
Axin1/APC/GSK3 0.011 0.056 0.19 2 -0.25 3 5
Axin1/APC/GSK3/beta catenin/Macf1 0.017 0.092 0.31 6 -0.4 6 12
HNF1A 0.044 0.04 0.25 5 -10000 0 5
CTBP1 0.037 0.032 0.19 2 -10000 0 2
MYC -0.042 0.21 0.56 13 -1 5 18
RANBP3 0.021 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.093 0.21 150 -0.12 5 155
NKD1 0.019 0.042 0.29 3 -0.29 3 6
TCF4 0.038 0.032 0.2 2 -10000 0 2
TCF3 0.038 0.032 0.19 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.047 0.018 -10000 0 -10000 0 0
Ran/GTP 0.017 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.1 0.2 0.4 79 -0.37 1 80
LEF1 0.041 0.033 0.2 3 -10000 0 3
DVL1 0.025 0.047 0.23 1 -0.23 2 3
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.044 0.15 0.27 1 -0.45 18 19
DKK1/LRP6/Kremen 2 0.12 0.11 0.21 151 -0.15 15 166
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.043 0.038 0.23 3 -10000 0 3
NLK 0.005 0.022 -10000 0 -10000 0 0
CCND1 -0.059 0.11 0.48 1 -0.62 2 3
WNT1 0.019 0.019 0.29 1 -10000 0 1
GSK3A 0.02 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.008 -10000 0 -10000 0 0
FRAT1 0.019 0.006 -10000 0 -10000 0 0
PPP2R5D 0.02 0.062 0.2 3 -0.26 7 10
APC -0.014 0.051 0.19 15 -10000 0 15
WNT1/LRP6/FZD1 0.025 0.055 0.17 8 -0.27 1 9
CREBBP 0.04 0.033 0.2 3 -10000 0 3
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.003 0.071 -10000 0 -0.29 16 16
mol:S1P -0.001 0.005 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.049 0.091 -10000 0 -0.19 72 72
GNAO1 0.014 0.034 -10000 0 -0.29 3 3
S1P/S1P3/G12/G13 0.015 0.062 -10000 0 -0.16 31 31
AKT1 -0.062 0.16 -10000 0 -0.48 33 33
AKT3 -0.077 0.23 -10000 0 -0.84 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.071 -10000 0 -0.29 16 16
GNAI2 0.017 0.014 -10000 0 -10000 0 0
GNAI3 0.018 0.012 -10000 0 -10000 0 0
GNAI1 0.016 0.022 -10000 0 -0.29 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.016 0.098 -10000 0 -0.29 32 32
S1PR2 0.02 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.063 0.12 -10000 0 -0.34 33 33
MAPK3 -0.071 0.11 -10000 0 -0.33 33 33
MAPK1 -0.07 0.11 -10000 0 -0.33 33 33
JAK2 -0.067 0.13 -10000 0 -0.33 36 36
CXCR4 -0.071 0.11 -10000 0 -0.33 33 33
FLT1 0.016 0.025 -10000 0 -0.3 1 1
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
SRC -0.067 0.11 -10000 0 -0.32 32 32
S1P/S1P3/Gi -0.064 0.12 -10000 0 -0.34 33 33
RAC1 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.06 0.12 -10000 0 -0.3 36 36
VEGFA 0.017 0.016 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.039 0.091 -10000 0 -0.28 17 17
VEGFR1 homodimer/VEGFA homodimer 0.024 0.027 -10000 0 -0.22 1 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.058 0.12 -10000 0 -0.22 90 90
GNAQ 0.02 0.003 -10000 0 -10000 0 0
GNAZ -0.052 0.13 -10000 0 -0.29 66 66
G12/G13 0.029 0.006 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.29 81 81
GNA15 0.035 0.064 0.29 17 -10000 0 17
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.003 -10000 0 -10000 0 0
GNA11 0.019 0.019 -10000 0 -0.29 1 1
Rac1/GTP -0.061 0.12 -10000 0 -0.3 36 36
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.035 0.12 0.23 1 -0.37 26 27
CRKL -0.043 0.12 -10000 0 -0.38 29 29
HRAS -0.02 0.11 -10000 0 -0.33 24 24
mol:PIP3 0.001 0.12 0.26 2 -0.33 26 28
SPRED1 0.02 0.004 -10000 0 -10000 0 0
SPRED2 0.02 0.003 -10000 0 -10000 0 0
GAB1 -0.038 0.12 -10000 0 -0.4 29 29
FOXO3 -0.025 0.13 -10000 0 -0.36 28 28
AKT1 -0.023 0.13 -10000 0 -0.38 28 28
BAD -0.026 0.13 -10000 0 -0.36 28 28
megakaryocyte differentiation -0.04 0.12 -10000 0 -0.38 29 29
GSK3B 0.006 0.14 0.33 4 -0.36 23 27
RAF1 -0.02 0.094 0.22 3 -0.28 23 26
SHC1 0.019 0.006 -10000 0 -10000 0 0
STAT3 -0.039 0.12 -10000 0 -0.4 28 28
STAT1 -0.093 0.28 -10000 0 -0.86 32 32
HRAS/SPRED1 -0.008 0.096 -10000 0 -0.28 22 22
cell proliferation -0.04 0.12 -10000 0 -0.39 29 29
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
TEC 0.019 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.025 0.13 -10000 0 -0.39 29 29
HRAS/SPRED2 -0.008 0.095 -10000 0 -0.28 22 22
LYN/TEC/p62DOK -0.006 0.13 -10000 0 -0.38 27 27
MAPK3 -0.016 0.074 0.19 3 -0.21 14 17
STAP1 -0.037 0.12 -10000 0 -0.4 29 29
GRAP2 0.02 0.003 -10000 0 -10000 0 0
JAK2 -0.078 0.24 -10000 0 -0.74 32 32
STAT1 (dimer) -0.092 0.27 -10000 0 -0.85 32 32
mol:Gleevec 0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.01 0.13 -10000 0 -0.39 27 27
actin filament polymerization -0.038 0.12 -10000 0 -0.39 29 29
LYN 0.02 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.055 0.18 -10000 0 -0.55 30 30
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.024 0.12 -10000 0 -0.36 28 28
PI3K -0.014 0.11 -10000 0 -0.37 20 20
PTEN 0.019 0.005 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.096 0.33 -10000 0 -1 29 29
MAPK8 -0.04 0.12 -10000 0 -0.4 29 29
STAT3 (dimer) -0.039 0.12 -10000 0 -0.39 28 28
positive regulation of transcription -0.012 0.063 0.18 3 -0.21 3 6
mol:GDP -0.02 0.11 -10000 0 -0.34 23 23
PIK3C2B -0.038 0.12 -10000 0 -0.4 28 28
CBL/CRKL -0.031 0.12 -10000 0 -0.37 28 28
FER -0.038 0.12 -10000 0 -0.4 29 29
SH2B3 -0.039 0.12 -10000 0 -0.4 29 29
PDPK1 0.001 0.12 0.29 4 -0.32 26 30
SNAI2 -0.044 0.13 -10000 0 -0.41 28 28
positive regulation of cell proliferation -0.067 0.21 -10000 0 -0.67 30 30
KITLG 0.01 0.024 -10000 0 -10000 0 0
cell motility -0.067 0.21 -10000 0 -0.67 30 30
PTPN6 0.019 0.014 -10000 0 -10000 0 0
EPOR -0.024 0.14 -10000 0 -0.69 7 7
STAT5A (dimer) -0.052 0.18 -10000 0 -0.56 30 30
SOCS1 0.02 0.005 -10000 0 -10000 0 0
cell migration 0.039 0.12 0.39 29 -10000 0 29
SOS1 0.02 0.003 -10000 0 -10000 0 0
EPO -0.006 0.079 -10000 0 -0.3 19 19
VAV1 0.02 0.004 -10000 0 -10000 0 0
GRB10 -0.04 0.12 -10000 0 -0.4 29 29
PTPN11 0.019 0.013 -10000 0 -10000 0 0
SCF/KIT -0.035 0.13 -10000 0 -0.41 29 29
GO:0007205 0.002 0.007 -10000 0 -10000 0 0
MAP2K1 -0.019 0.078 0.2 3 -0.22 22 25
CBL 0.017 0.008 -10000 0 -10000 0 0
KIT -0.11 0.34 -10000 0 -1 32 32
MAP2K2 -0.019 0.077 0.2 3 -0.23 21 24
SHC/Grb2/SOS1 -0.008 0.13 -10000 0 -0.39 25 25
STAT5A -0.055 0.18 -10000 0 -0.57 30 30
GRB2 0.02 0.005 -10000 0 -10000 0 0
response to radiation -0.044 0.13 -10000 0 -0.4 29 29
SHC/GRAP2 0.028 0.009 -10000 0 -10000 0 0
PTPRO -0.039 0.12 -10000 0 -0.4 28 28
SH2B2 -0.038 0.12 -10000 0 -0.4 28 28
DOK1 0.02 0.003 -10000 0 -10000 0 0
MATK -0.039 0.12 -10000 0 -0.4 29 29
CREBBP 0.007 0.043 -10000 0 -10000 0 0
BCL2 -0.055 0.23 -10000 0 -0.91 15 15
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.009 0.09 0.23 10 -10000 0 10
GNAI2 0.019 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.078 0.078 0.19 90 -10000 0 90
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
RhoA/GTP -0.009 0.092 -10000 0 -0.23 10 10
negative regulation of cAMP metabolic process -0.01 0.093 0.17 2 -0.22 17 19
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
GNAI3 0.02 0.002 -10000 0 -10000 0 0
GNA12 0.02 0.003 -10000 0 -10000 0 0
S1PR5 0.11 0.13 0.29 93 -10000 0 93
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.01 0.093 0.17 2 -0.22 17 19
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.005 0.12 0.26 12 -0.29 28 40
FYN -0.011 0.13 0.24 15 -0.31 30 45
LAT/GRAP2/SLP76 -0.004 0.12 0.24 7 -0.28 31 38
IKBKB 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.011 0.11 0.23 12 -0.26 32 44
B2M 0.018 0.011 -10000 0 -10000 0 0
IKBKG -0.009 0.042 0.11 9 -0.099 9 18
MAP3K8 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.014 0.019 4 -0.045 3 7
integrin-mediated signaling pathway 0.026 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.018 0.14 0.25 10 -0.33 32 42
TRPV6 0.029 0.11 1.2 2 -10000 0 2
CD28 0.018 0.02 -10000 0 -0.29 1 1
SHC1 -0.015 0.13 0.25 13 -0.32 33 46
receptor internalization -0.034 0.14 0.17 5 -0.35 45 50
PRF1 -0.025 0.15 -10000 0 -0.66 8 8
KRAS 0.019 0.005 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.007 0.099 0.21 12 -0.22 30 42
LAT -0.022 0.13 0.21 5 -0.31 36 41
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.019 0.018 0.3 1 -10000 0 1
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G 0.019 0.018 0.3 1 -10000 0 1
RASGRP2 -0.019 0.05 -10000 0 -0.15 33 33
RASGRP1 -0.015 0.12 0.28 6 -0.27 28 34
HLA-A 0 0.002 -10000 0 -10000 0 0
RASSF5 0.019 0.005 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.052 0.16 11 -0.11 6 17
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.03 0.044 -10000 0 -0.14 31 31
PRKCA -0.018 0.066 0.15 6 -0.17 21 27
GRAP2 0.02 0.003 -10000 0 -10000 0 0
mol:IP3 -0.036 0.077 -10000 0 -0.23 30 30
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.017 0.086 0.13 1 -0.28 27 28
ORAI1 -0.034 0.092 -10000 0 -1 2 2
CSK -0.019 0.12 0.2 11 -0.31 33 44
B7 family/CD28 -0.004 0.098 -10000 0 -0.26 29 29
CHUK 0.02 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.034 0.12 0.17 1 -0.33 36 37
PTPN6 -0.015 0.12 0.2 9 -0.3 33 42
VAV1 -0.02 0.13 0.2 9 -0.31 36 45
Monovalent TCR/CD3 0.01 0.01 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
LCK -0.006 0.12 0.24 17 -0.29 29 46
PAG1 -0.019 0.12 0.19 11 -0.32 33 44
RAP1A 0.021 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.029 0.12 0.18 4 -0.32 36 40
CD80 0.015 0.011 -10000 0 -10000 0 0
CD86 0.015 0.011 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.028 0.055 -10000 0 -0.17 31 31
HRAS 0.02 0.005 -10000 0 -10000 0 0
GO:0035030 -0.028 0.078 0.18 1 -0.23 30 31
CD8A 0.018 0.02 0.3 1 -10000 0 1
CD8B 0.021 0.042 0.29 5 -0.3 1 6
PTPRC 0.016 0.021 -10000 0 -0.29 1 1
PDK1/PKC theta -0.019 0.13 0.29 9 -0.3 31 40
CSK/PAG1 -0.012 0.12 0.24 10 -0.31 31 41
SOS1 0.02 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 -0.001 0.13 0.22 4 -0.31 33 37
STIM1 -0.015 0.022 -10000 0 -10000 0 0
RAS family/GTP 0.006 0.072 0.19 11 -0.17 14 25
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.034 0.15 0.17 3 -0.37 43 46
mol:DAG -0.04 0.064 -10000 0 -0.21 31 31
RAP1A/GDP 0.003 0.026 0.094 6 -10000 0 6
PLCG1 0.019 0.005 -10000 0 -10000 0 0
CD247 0.02 0.006 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.024 0.14 -10000 0 -0.64 8 8
RAP1A/GTP -0.009 0.019 -10000 0 -0.06 33 33
mol:PI-3-4-5-P3 -0.013 0.12 0.24 10 -0.29 32 42
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.016 0.1 -10000 0 -0.28 30 30
NRAS 0.021 0.002 -10000 0 -10000 0 0
ZAP70 0.021 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.028 0.11 0.21 1 -0.28 32 33
MALT1 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.02 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.034 0.031 0.22 6 -0.21 1 7
CARD11 0.02 0.003 -10000 0 -10000 0 0
PRKCB -0.018 0.065 0.15 5 -0.17 21 26
PRKCE -0.018 0.064 0.15 5 -0.17 21 26
PRKCQ -0.021 0.13 0.27 7 -0.32 32 39
LCP2 0.02 0.004 -10000 0 -10000 0 0
BCL10 0.021 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression -0.008 0.1 0.22 12 -0.22 32 44
IKK complex 0.004 0.056 0.16 17 -0.096 1 18
RAS family/GDP -0.006 0.009 -10000 0 -0.035 2 2
MAP3K14 -0.011 0.076 0.17 10 -0.18 29 39
PDPK1 -0.011 0.11 0.24 12 -0.25 31 43
TCR/CD3/MHC I/CD8/Fyn -0.04 0.15 -10000 0 -0.38 39 39
EPHB forward signaling

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
Ephrin A5/EPHB2 0.026 0.007 -10000 0 -10000 0 0
cell-cell adhesion 0.042 0.047 0.16 32 -10000 0 32
Ephrin B/EPHB2/RasGAP 0.019 0.077 -10000 0 -0.16 43 43
ITSN1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.018 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.011 0.043 -10000 0 -0.17 15 15
HRAS/GDP -0.043 0.094 -10000 0 -0.2 43 43
Ephrin B/EPHB1/GRB7 0.01 0.081 0.21 1 -0.16 41 42
Endophilin/SYNJ1 -0.036 0.052 0.16 7 -10000 0 7
KRAS 0.019 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.007 0.076 -10000 0 -0.16 40 40
endothelial cell migration 0.025 0.022 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.023 0.29 2 -10000 0 2
PAK1 -0.01 0.092 0.21 8 -0.27 2 10
HRAS 0.02 0.005 -10000 0 -10000 0 0
RRAS -0.037 0.054 0.16 7 -10000 0 7
DNM1 0.021 0.002 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.003 0.097 0.16 57 -0.27 3 60
lamellipodium assembly -0.042 0.047 -10000 0 -0.16 32 32
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.018 0.074 -10000 0 -0.22 18 18
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
EPHB2 0.02 0.003 -10000 0 -10000 0 0
EPHB3 0.013 0.01 -10000 0 -10000 0 0
EPHB1 -0.001 0.068 -10000 0 -0.29 15 15
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.045 0.079 0.14 2 -0.22 34 36
Ephrin B/EPHB2 0.013 0.07 -10000 0 -0.15 43 43
Ephrin B/EPHB3 0.01 0.056 -10000 0 -0.15 27 27
JNK cascade 0.06 0.17 0.34 75 -10000 0 75
Ephrin B/EPHB1 0.002 0.072 -10000 0 -0.16 43 43
RAP1/GDP -0.062 0.085 -10000 0 -0.24 19 19
EFNB2 0.02 0.004 -10000 0 -10000 0 0
EFNB3 -0.028 0.11 -10000 0 -0.29 44 44
EFNB1 0.02 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.018 0.044 -10000 0 -0.16 15 15
RAP1B 0.02 0.003 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.08 -10000 0 -0.2 33 33
Rap1/GTP -0.046 0.05 -10000 0 -0.16 34 34
axon guidance 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.031 0.067 0.17 1 -0.25 8 9
MAPK1 -0.031 0.066 0.17 1 -0.25 8 9
Rac1/GDP -0.062 0.085 -10000 0 -0.24 20 20
actin cytoskeleton reorganization -0.056 0.062 -10000 0 -0.18 35 35
CDC42/GDP -0.063 0.086 -10000 0 -0.24 20 20
PI3K 0.028 0.024 -10000 0 -10000 0 0
EFNA5 0.02 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.026 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.031 0.08 -10000 0 -0.19 48 48
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.046 0.05 -10000 0 -0.16 34 34
PTK2 0.013 0.11 0.54 12 -10000 0 12
MAP4K4 0.06 0.17 0.34 75 -10000 0 75
SRC 0.019 0.006 -10000 0 -10000 0 0
KALRN 0.002 0.064 -10000 0 -0.29 13 13
Intersectin/N-WASP 0.028 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.013 0.12 0.26 38 -0.24 6 44
MAP2K1 -0.025 0.068 -10000 0 -0.21 18 18
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.027 0.05 -10000 0 -0.16 15 15
cell migration -0.027 0.11 0.24 4 -0.28 14 18
NRAS 0.021 0.002 -10000 0 -10000 0 0
SYNJ1 -0.036 0.053 0.16 7 -10000 0 7
PXN 0.021 0.001 -10000 0 -10000 0 0
TF -0.029 0.051 0.15 5 -10000 0 5
HRAS/GTP -0.003 0.066 -10000 0 -0.15 40 40
Ephrin B1/EPHB1-2 0.019 0.044 -10000 0 -0.16 15 15
cell adhesion mediated by integrin 0.012 0.059 0.15 23 -0.24 4 27
RAC1 0.02 0.003 -10000 0 -10000 0 0
mol:GTP -0.002 0.068 0.18 1 -0.15 43 44
RAC1-CDC42/GTP -0.04 0.049 -10000 0 -0.16 28 28
RASA1 0.02 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.086 -10000 0 -0.24 18 18
ruffle organization -0.014 0.092 0.29 4 -0.25 3 7
NCK1 0.015 0.009 -10000 0 -10000 0 0
receptor internalization -0.039 0.05 0.15 7 -10000 0 7
Ephrin B/EPHB2/KALRN 0.009 0.077 -10000 0 -0.16 42 42
ROCK1 0.047 0.091 0.17 100 -10000 0 100
RAS family/GDP -0.062 0.062 -10000 0 -0.18 36 36
Rac1/GTP -0.043 0.049 -10000 0 -0.16 36 36
Ephrin B/EPHB1/Src/Paxillin -0.026 0.076 -10000 0 -0.2 42 42
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.15 -10000 0 -0.29 120 120
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.02 0.004 -10000 0 -10000 0 0
TCEB1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.054 -10000 0 -0.25 8 8
HIF1A -0.003 0.047 -10000 0 -0.28 7 7
COPS5 0.02 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.05 0.026 -10000 0 -10000 0 0
FIH (dimer) 0.02 0.003 -10000 0 -10000 0 0
CDKN2A 0.27 0.082 0.29 265 -10000 0 265
ARNT/IPAS -0.06 0.11 -10000 0 -0.2 109 109
HIF1AN 0.02 0.003 -10000 0 -10000 0 0
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.054 0.25 1 -0.26 8 9
CUL2 0.02 0.004 -10000 0 -10000 0 0
OS9 0.02 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.015 0.054 0.25 1 -0.27 7 8
PHD1-3/OS9 0.046 0.018 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.056 -10000 0 -0.26 8 8
VHL 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.014 0.057 0.25 1 -0.26 8 9
EGLN3 0.02 0.004 -10000 0 -10000 0 0
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.019 0.005 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.01 0.14 -10000 0 -0.52 19 19
ARNT 0.019 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.16 0.088 0.26 36 -0.23 7 43
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 0.026 0.016 0.19 2 -10000 0 2
ARNO/beta Arrestin1-2 0.01 0.097 -10000 0 -0.77 4 4
EGFR 0.018 0.026 -10000 0 -0.29 2 2
EPHA2 0.02 0.003 -10000 0 -10000 0 0
USP6 0.019 0.006 -10000 0 -10000 0 0
IQSEC1 0.019 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.017 0.052 -10000 0 -0.2 15 15
ARRB2 0.005 0.002 -10000 0 -10000 0 0
mol:GTP 0.033 0.057 0.12 65 -0.12 4 69
ARRB1 0.02 0.005 -10000 0 -10000 0 0
FBXO8 0.02 0.005 -10000 0 -10000 0 0
TSHR 0.016 0.021 0.29 1 -10000 0 1
EGF 0.003 0.066 -10000 0 -0.29 14 14
somatostatin receptor activity 0 0 0.001 8 -0.001 44 52
ARAP2 0.019 0.005 -10000 0 -10000 0 0
mol:GDP -0.052 0.095 0.14 1 -0.23 37 38
mol:PI-3-4-5-P3 0 0 0.001 2 -0.001 11 13
ITGA2B 0.019 0.03 0.29 1 -0.29 2 3
ARF6 0.02 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.036 0.025 -10000 0 -10000 0 0
ADAP1 0.022 0.023 0.29 2 -10000 0 2
KIF13B 0.019 0.006 -10000 0 -10000 0 0
HGF/MET 0.002 0.076 0.22 1 -0.2 34 35
PXN 0.021 0.001 -10000 0 -10000 0 0
ARF6/GTP -0.057 0.1 0.22 4 -0.22 45 49
EGFR/EGFR/EGF/EGF/ARFGEP100 0.026 0.048 -10000 0 -0.17 15 15
ADRB2 0.015 0.04 -10000 0 -0.29 5 5
receptor agonist activity 0 0 0 6 0 36 42
actin filament binding 0 0 0 6 0 46 52
SRC 0.019 0.006 -10000 0 -10000 0 0
ITGB3 -0.016 0.1 -10000 0 -0.29 34 34
GNAQ 0.02 0.003 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0.001 10 -0.001 23 33
ARF6/GDP 0.001 0.13 0.22 16 -0.33 19 35
ARF6/GDP/GULP/ACAP1 -0.065 0.11 -10000 0 -0.26 39 39
alphaIIb/beta3 Integrin/paxillin/GIT1 0.026 0.072 0.21 1 -0.17 35 36
ACAP1 0.019 0.006 -10000 0 -10000 0 0
ACAP2 0.013 0.01 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.009 0.02 -10000 0 -10000 0 0
EFNA1 0.019 0.006 -10000 0 -10000 0 0
HGF -0.016 0.1 0.29 1 -0.29 34 35
CYTH3 -0.009 0.001 -10000 0 -10000 0 0
CYTH2 0 0.12 -10000 0 -0.97 4 4
NCK1 0.015 0.009 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 6 0 28 34
endosomal lumen acidification 0 0 0 9 0 48 57
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.043 0.12 -10000 0 -0.29 59 59
GNAQ/ARNO 0.011 0.11 -10000 0 -0.9 4 4
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 4 0 1 5
MET 0.02 0.004 -10000 0 -10000 0 0
GNA14 -0.066 0.14 -10000 0 -0.29 81 81
GNA15 0.035 0.064 0.29 17 -10000 0 17
GIT1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 12 -0.001 28 40
GNA11 0.018 0.019 -10000 0 -0.29 1 1
LHCGR -0.009 0.015 -10000 0 -10000 0 0
AGTR1 -0.094 0.14 -10000 0 -0.29 99 99
desensitization of G-protein coupled receptor protein signaling pathway 0.009 0.02 -10000 0 -10000 0 0
IPCEF1/ARNO 0.013 0.1 -10000 0 -0.78 4 4
alphaIIb/beta3 Integrin 0.002 0.079 0.22 1 -0.21 35 36
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.04 0.11 -10000 0 -0.2 87 87
PDGFRB -0.004 0.072 -10000 0 -0.29 16 16
SPHK1 -0.008 0.079 -10000 0 -0.59 5 5
mol:S1P -0.012 0.07 -10000 0 -0.48 5 5
S1P1/S1P/Gi -0.061 0.12 0.3 3 -0.3 31 34
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.06 0.12 0.26 3 -0.3 25 28
PLCG1 -0.065 0.1 0.26 2 -0.32 19 21
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.071 -10000 0 -0.29 16 16
GNAI2 0.019 0.01 -10000 0 -10000 0 0
GNAI3 0.018 0.012 -10000 0 -10000 0 0
GNAI1 0.017 0.021 -10000 0 -0.29 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.057 0.07 -10000 0 -0.16 87 87
S1P1/S1P -0.049 0.081 0.24 1 -0.31 7 8
negative regulation of cAMP metabolic process -0.06 0.12 0.3 3 -0.29 31 34
MAPK3 -0.062 0.12 0.37 3 -0.34 15 18
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.014 0.004 -10000 0 -10000 0 0
KDR -0.072 0.14 -10000 0 -0.29 87 87
PLCB2 -0.043 0.085 0.26 5 -0.28 7 12
RAC1 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.05 0.066 -10000 0 -0.27 7 7
receptor internalization -0.049 0.073 -10000 0 -0.29 7 7
PTGS2 -0.055 0.12 0.38 3 -0.43 1 4
Rac1/GTP -0.05 0.066 -10000 0 -0.27 7 7
RHOA 0.019 0.006 -10000 0 -10000 0 0
VEGFA 0.02 0.004 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.06 0.12 0.3 3 -0.29 31 34
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.052 0.13 -10000 0 -0.29 66 66
MAPK1 -0.063 0.11 0.32 3 -0.34 15 18
S1P1/S1P/PDGFB-D/PDGFRB -0.057 0.093 0.24 3 -0.29 14 17
ABCC1 0.01 0.018 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
CDC42/GTP -0.035 0.089 -10000 0 -0.26 15 15
PLCG1 -0.042 0.077 -10000 0 -0.24 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
G12/G13 0.029 0.006 -10000 0 -10000 0 0
cell migration -0.035 0.087 -10000 0 -0.26 15 15
S1PR5 0.11 0.13 0.29 93 -10000 0 93
S1PR4 0.02 0.005 -10000 0 -10000 0 0
MAPK3 -0.043 0.078 -10000 0 -0.24 18 18
MAPK1 -0.042 0.077 -10000 0 -0.25 15 15
S1P/S1P5/Gi -0.01 0.093 0.17 2 -0.22 17 19
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.078 0.078 0.19 90 -10000 0 90
RHOA -0.015 0.035 0.17 10 -10000 0 10
S1P/S1P4/Gi -0.034 0.086 -10000 0 -0.18 69 69
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
S1P/S1P4/G12/G13 0.036 0.012 -10000 0 -10000 0 0
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.003 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.02 0.004 -10000 0 -10000 0 0
SPHK1 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.019 0.006 -10000 0 -10000 0 0
mol:S1P 0.005 0.002 -10000 0 -10000 0 0
GNAO1 0.016 0.032 -10000 0 -0.29 3 3
mol:Sphinganine-1-P -0.017 0.005 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.039 0.031 -10000 0 -10000 0 0
GNAI3 0.02 0.002 -10000 0 -10000 0 0
G12/G13 0.029 0.006 -10000 0 -10000 0 0
S1PR3 -0.014 0.097 -10000 0 -0.29 32 32
S1PR2 0.02 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.019 -10000 0 -10000 0 0
S1PR5 0.11 0.13 0.29 93 -10000 0 93
S1PR4 0.02 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.29 1 1
S1P/S1P5/G12 0.081 0.083 0.2 85 -10000 0 85
S1P/S1P3/Gq -0.06 0.13 0.19 1 -0.26 68 69
S1P/S1P4/Gi -0.034 0.089 -10000 0 -0.26 17 17
GNAQ 0.02 0.003 -10000 0 -10000 0 0
GNAZ -0.05 0.13 -10000 0 -0.29 66 66
GNA14 -0.066 0.14 -10000 0 -0.29 81 81
GNA15 0.035 0.064 0.29 17 -10000 0 17
GNA12 0.02 0.003 -10000 0 -10000 0 0
GNA13 0.02 0.003 -10000 0 -10000 0 0
GNA11 0.019 0.019 -10000 0 -0.29 1 1
ABCC1 0.02 0.004 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.023 0.055 -10000 0 -0.18 18 18
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.067 0.23 3 -0.3 1 4
AP1 0.035 0.081 0.18 6 -0.15 38 44
mol:PIP3 -0.024 0.031 -10000 0 -0.15 10 10
AKT1 0.004 0.096 0.27 7 -0.27 3 10
PTK2B -0.025 0.079 -10000 0 -0.28 16 16
RHOA -0.03 0.081 -10000 0 -0.29 22 22
PIK3CB 0.015 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.051 0.2 4 -0.17 1 5
MAGI3 0.02 0.002 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.002 0.048 -10000 0 -0.18 15 15
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.1 0.23 9 -0.29 8 17
NF kappa B1 p50/RelA 0.02 0.09 0.18 10 -0.24 6 16
endothelial cell migration -0.032 0.087 -10000 0 -0.38 16 16
ADCY4 -0.046 0.097 -10000 0 -0.31 26 26
ADCY5 -0.083 0.11 -10000 0 -0.28 49 49
ADCY6 -0.037 0.078 -10000 0 -0.26 21 21
ADCY7 -0.036 0.075 -10000 0 -0.26 19 19
ADCY1 -0.042 0.087 -10000 0 -0.27 26 26
ADCY2 -0.092 0.11 -10000 0 -0.28 52 52
ADCY3 -0.036 0.077 -10000 0 -0.26 21 21
ADCY8 -0.033 0.074 -10000 0 -0.26 19 19
ADCY9 -0.038 0.079 -10000 0 -0.26 22 22
GSK3B 0.005 0.1 0.19 34 -0.26 13 47
arachidonic acid secretion -0.046 0.081 -10000 0 -0.27 22 22
GNG2 0.018 0.009 -10000 0 -10000 0 0
TRIP6 0.008 0.011 -10000 0 -10000 0 0
GNAO1 -0.023 0.045 -10000 0 -0.19 19 19
HRAS 0.02 0.005 -10000 0 -10000 0 0
NFKBIA -0.016 0.06 0.22 3 -0.28 2 5
GAB1 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.004 0.16 -10000 0 -0.81 11 11
JUN 0.019 0.019 -10000 0 -0.29 1 1
LPA/LPA2/NHERF2 0.023 0.024 -10000 0 -10000 0 0
TIAM1 -0.014 0.18 -10000 0 -0.93 11 11
PIK3R1 0.018 0.008 -10000 0 -10000 0 0
mol:IP3 -0.02 0.044 0.18 3 -10000 0 3
PLCB3 -0.015 0.032 0.17 7 -10000 0 7
FOS -0.003 0.082 -10000 0 -0.29 22 22
positive regulation of mitosis -0.046 0.081 -10000 0 -0.27 22 22
LPA/LPA1-2-3 0.036 0.063 0.2 10 -0.17 18 28
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
stress fiber formation -0.011 0.066 -10000 0 -0.28 8 8
GNAZ -0.055 0.077 -10000 0 -0.18 74 74
EGFR/PI3K-beta/Gab1 -0.007 0.041 -10000 0 -0.16 9 9
positive regulation of dendritic cell cytokine production 0.035 0.062 0.2 10 -0.17 18 28
LPA/LPA2/MAGI-3 0.023 0.024 -10000 0 -10000 0 0
ARHGEF1 -0.022 0.055 0.18 12 -0.17 13 25
GNAI2 -0.021 0.041 -10000 0 -0.19 15 15
GNAI3 -0.023 0.044 -10000 0 -0.19 18 18
GNAI1 -0.022 0.041 -10000 0 -0.18 17 17
LPA/LPA3 0.019 0.043 0.19 12 -0.088 13 25
LPA/LPA2 0.011 0.023 -10000 0 -0.089 1 1
LPA/LPA1 0.002 0.059 -10000 0 -0.22 18 18
HB-EGF/EGFR 0.022 0.049 0.12 44 -0.17 1 45
HBEGF 0.009 0.059 0.15 44 -10000 0 44
mol:DAG -0.02 0.044 0.18 3 -10000 0 3
cAMP biosynthetic process -0.061 0.086 0.2 3 -0.26 23 26
NFKB1 0.02 0.003 -10000 0 -10000 0 0
SRC 0.019 0.006 -10000 0 -10000 0 0
GNB1 0.018 0.009 -10000 0 -10000 0 0
LYN -0.016 0.059 0.31 1 -0.3 2 3
GNAQ 0.001 0.027 0.2 1 -10000 0 1
LPAR2 0.021 0.004 -10000 0 -10000 0 0
LPAR3 0.032 0.055 0.3 12 -10000 0 12
LPAR1 0.008 0.053 -10000 0 -0.18 18 18
IL8 0.12 0.16 0.27 112 -0.34 5 117
PTK2 -0.018 0.046 0.18 7 -0.17 10 17
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
CASP3 -0.002 0.048 -10000 0 -0.18 15 15
EGFR 0.019 0.026 -10000 0 -0.29 2 2
PLCG1 -0.016 0.043 0.12 1 -0.16 3 4
PLD2 -0.019 0.05 0.18 8 -0.17 14 22
G12/G13 0.026 0.052 -10000 0 -0.17 17 17
PI3K-beta -0.032 0.056 -10000 0 -0.22 13 13
cell migration 0.004 0.06 -10000 0 -0.25 11 11
SLC9A3R2 0.02 0.004 -10000 0 -10000 0 0
PXN -0.012 0.067 -10000 0 -0.28 8 8
HRAS/GTP -0.048 0.081 -10000 0 -0.27 22 22
RAC1 0.02 0.003 -10000 0 -10000 0 0
MMP9 0.063 0.1 0.3 46 -10000 0 46
PRKCE 0.019 0.006 -10000 0 -10000 0 0
PRKCD -0.023 0.048 0.18 4 -10000 0 4
Gi(beta/gamma) -0.041 0.076 -10000 0 -0.24 21 21
mol:LPA -0.005 0.028 -10000 0 -0.13 14 14
TRIP6/p130 Cas/FAK1/Paxillin 0.006 0.067 0.2 1 -0.29 4 5
MAPKKK cascade -0.046 0.081 -10000 0 -0.27 22 22
contractile ring contraction involved in cytokinesis -0.028 0.082 -10000 0 -0.29 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.045 0.08 -10000 0 -0.18 73 73
GNA15 0.008 0.041 0.14 18 -10000 0 18
GNA12 0.02 0.004 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.002 0.1 0.24 8 -0.3 8 16
GNA11 0 0.029 0.2 1 -0.18 1 2
Rac1/GTP 0.003 0.17 -10000 0 -0.85 11 11
MMP2 -0.032 0.087 -10000 0 -0.39 16 16
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.019 0.005 -10000 0 -10000 0 0
LRPAP1 0.019 0.006 -10000 0 -10000 0 0
NUDC 0.02 0.003 -10000 0 -10000 0 0
RELN/LRP8 -0.03 0.097 -10000 0 -0.17 92 92
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.02 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.062 0.07 0.17 4 -0.16 80 84
IQGAP1/CaM 0.028 0.009 -10000 0 -10000 0 0
DAB1 0.005 0.03 0.29 2 -10000 0 2
IQGAP1 0.02 0.004 -10000 0 -10000 0 0
PLA2G7 0.033 0.059 0.29 14 -10000 0 14
CALM1 0.02 0.005 -10000 0 -10000 0 0
DYNLT1 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.027 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.002 -10000 0 -10000 0 0
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.013 0.005 -10000 0 -10000 0 0
CDK5R2 0.011 0.048 0.29 7 -10000 0 7
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.028 0.098 0.21 2 -0.17 88 90
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.062 0.068 0.16 4 -0.2 5 9
MAP1B -0.019 0.064 -10000 0 -0.21 30 30
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.063 0.064 0.16 5 -10000 0 5
RELN -0.084 0.14 -10000 0 -0.29 94 94
PAFAH/LIS1 -0.008 0.048 0.2 14 -10000 0 14
LIS1/CLIP170 -0.019 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.068 0.057 -10000 0 -0.2 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.083 0.2 1 -0.19 31 32
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.057 0.069 0.15 5 -0.2 10 15
LIS1/IQGAP1 -0.018 0.008 -10000 0 -10000 0 0
RHOA 0.004 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.02 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.017 0.008 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.008 0.055 -10000 0 -0.15 27 27
NDEL1/Katanin 60/Dynein heavy chain -0.067 0.068 -10000 0 -0.22 2 2
LRP8 0.02 0.003 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.064 0.068 0.16 4 -0.21 7 11
P39/CDK5 -0.058 0.073 0.16 11 -10000 0 11
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.019 0.008 -10000 0 -10000 0 0
CDK5 -0.063 0.066 0.16 4 -0.16 80 84
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.015 0.006 -10000 0 -10000 0 0
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.023 0.088 0.25 2 -0.16 84 86
RELN/VLDLR -0.02 0.094 -10000 0 -0.16 89 89
CDC42 0.004 0.002 -10000 0 -10000 0 0
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 0.003 0.071 -10000 0 -0.29 16 16
Jak2/Leptin Receptor -0.14 0.14 -10000 0 -0.34 51 51
PTP1B/AKT1 -0.017 0.079 0.21 2 -0.26 12 14
FYN 0.015 0.04 -10000 0 -0.29 5 5
p210 bcr-abl/PTP1B -0.027 0.08 0.23 2 -0.26 14 16
EGFR 0.013 0.03 -10000 0 -0.3 2 2
EGF/EGFR -0.012 0.083 0.2 1 -0.28 10 11
CSF1 0.018 0.026 -10000 0 -0.29 2 2
AKT1 0.015 0.014 -10000 0 -10000 0 0
INSR 0.016 0.013 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.026 0.092 0.23 2 -0.28 18 20
Insulin Receptor/Insulin -0.006 0.083 0.22 1 -0.29 7 8
HCK 0.019 0.006 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 -0.027 0.077 0.2 4 -0.29 8 12
EGF 0.002 0.068 -10000 0 -0.3 14 14
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.035 0.087 0.2 1 -0.26 19 20
TXN 0.018 0.019 0.3 1 -10000 0 1
PTP1B/IRS1/GRB2 -0.017 0.082 -10000 0 -0.27 11 11
cell migration 0.027 0.08 0.26 14 -0.23 2 16
STAT3 0.02 0.006 -10000 0 -10000 0 0
PRLR -0.11 0.15 -10000 0 -0.29 123 123
ITGA2B 0.015 0.033 0.29 1 -0.29 2 3
CSF1R 0.018 0.026 -10000 0 -0.29 2 2
Prolactin Receptor/Prolactin -0.11 0.13 -10000 0 -0.23 148 148
FGR 0.02 0.002 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.02 0.081 0.24 1 -0.26 13 14
Crk/p130 Cas -0.013 0.083 0.24 1 -0.27 10 11
DOK1 -0.036 0.094 0.2 2 -0.28 21 23
JAK2 -0.14 0.14 0.26 2 -0.33 61 63
Jak2/Leptin Receptor/Leptin -0.045 0.1 -10000 0 -0.31 13 13
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
PTPN1 -0.027 0.08 0.23 2 -0.26 14 16
LYN 0.02 0.004 -10000 0 -10000 0 0
CDH2 -0.008 0.092 0.29 1 -0.29 27 28
SRC 0.001 0.06 -10000 0 -0.4 4 4
ITGB3 -0.017 0.1 -10000 0 -0.29 34 34
CAT1/PTP1B -0.001 0.1 0.24 12 -0.29 9 21
CAPN1 0.017 0.01 -10000 0 -10000 0 0
CSK 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.002 0.065 -10000 0 -0.47 1 1
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.041 0.096 -10000 0 -0.28 12 12
negative regulation of transcription -0.14 0.14 0.25 2 -0.33 61 63
FCGR2A 0.019 0.006 -10000 0 -10000 0 0
FER 0.016 0.021 -10000 0 -0.3 1 1
alphaIIb/beta3 Integrin 0.001 0.08 0.21 1 -0.21 35 36
BLK 0.064 0.11 0.29 52 -10000 0 52
Insulin Receptor/Insulin/Shc 0.033 0.015 -10000 0 -10000 0 0
RHOA 0.018 0.007 -10000 0 -10000 0 0
LEPR 0.011 0.054 -10000 0 -0.29 9 9
BCAR1 0.02 0.004 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.02 0.005 -10000 0 -10000 0 0
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.022 0.09 0.26 5 -0.26 4 9
PRL -0.066 0.12 -10000 0 -0.29 61 61
SOCS3 -0.004 0.19 -10000 0 -1.1 9 9
SPRY2 0.015 0.033 -10000 0 -0.3 3 3
Insulin Receptor/Insulin/IRS1 0.026 0.041 -10000 0 -0.18 10 10
CSF1/CSF1R -0.013 0.086 -10000 0 -0.26 13 13
Ras protein signal transduction 0.017 0.11 0.55 11 -10000 0 11
IRS1 0.008 0.056 -10000 0 -0.29 10 10
INS 0.004 0.017 -10000 0 -10000 0 0
LEP 0.032 0.08 0.29 24 -10000 0 24
STAT5B -0.064 0.093 0.26 2 -0.28 21 23
STAT5A -0.064 0.093 0.26 2 -0.29 19 21
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.022 0.091 0.21 2 -0.27 21 23
CSN2 -0.06 0.098 -10000 0 -0.47 7 7
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
LAT 0.004 0.053 -10000 0 -0.4 3 3
YBX1 0.022 0.003 -10000 0 -10000 0 0
LCK 0.021 0.001 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
NOX4 0.009 0.049 -10000 0 -0.3 7 7
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.096 0.17 -10000 0 -0.53 10 10
PCK1 -0.026 0.13 0.43 6 -10000 0 6
HNF4A -0.096 0.18 0.57 1 -0.75 3 4
KCNJ11 -0.1 0.18 -10000 0 -0.58 10 10
AKT1 -0.048 0.13 -10000 0 -0.51 3 3
response to starvation 0.001 0.005 -10000 0 -10000 0 0
DLK1 -0.15 0.28 -10000 0 -0.77 36 36
NKX2-1 -0.15 0.13 -10000 0 -0.38 30 30
ACADM -0.099 0.16 -10000 0 -0.53 10 10
TAT -0.039 0.12 0.36 1 -0.5 1 2
CEBPB 0.021 0.01 -10000 0 -10000 0 0
CEBPA 0.023 0.015 -10000 0 -10000 0 0
TTR 0.12 0.14 0.54 17 -10000 0 17
PKLR -0.093 0.16 -10000 0 -0.54 9 9
APOA1 -0.12 0.22 0.56 1 -0.77 3 4
CPT1C -0.098 0.17 -10000 0 -0.57 10 10
ALAS1 -0.061 0.12 -10000 0 -0.54 1 1
TFRC -0.02 0.13 0.44 4 -10000 0 4
FOXF1 0.014 0.04 -10000 0 -0.29 5 5
NF1 0.021 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.022 0.023 0.29 2 -10000 0 2
CPT1A -0.093 0.16 -10000 0 -0.7 1 1
HMGCS1 -0.082 0.16 -10000 0 -0.54 9 9
NR3C1 0.009 0.051 -10000 0 -0.19 18 18
CPT1B -0.099 0.16 0.41 1 -0.53 10 11
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.02 0.003 -10000 0 -10000 0 0
GCK -0.13 0.24 -10000 0 -0.7 30 30
CREB1 0.024 0.022 -10000 0 -10000 0 0
IGFBP1 -0.1 0.26 -10000 0 -1 19 19
PDX1 -0.058 0.12 -10000 0 -0.54 1 1
UCP2 -0.094 0.16 -10000 0 -0.53 10 10
ALDOB -0.1 0.19 0.5 2 -0.57 12 14
AFP 0.11 0.062 0.29 6 -10000 0 6
BDH1 -0.064 0.16 0.41 2 -0.54 8 10
HADH -0.1 0.18 -10000 0 -0.58 10 10
F2 -0.12 0.21 -10000 0 -0.8 2 2
HNF1A 0.023 0.023 0.29 2 -10000 0 2
G6PC 0.022 0.057 0.35 1 -10000 0 1
SLC2A2 -0.045 0.12 -10000 0 -10000 0 0
INS -0.006 0.048 0.2 11 -10000 0 11
FOXA1 0.26 0.11 0.31 247 -10000 0 247
FOXA3 0.076 0.1 0.31 43 -10000 0 43
FOXA2 -0.11 0.22 0.5 2 -0.65 12 14
ABCC8 -0.16 0.28 -10000 0 -0.77 41 41
ALB 0.11 0.073 0.3 19 -10000 0 19
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.02 0.002 -10000 0 -10000 0 0
mol:PIP3 -0.02 0.044 -10000 0 -0.19 17 17
FRAP1 0.023 0.074 0.23 1 -0.4 5 6
AKT1 0.022 0.084 0.14 79 -0.2 5 84
INSR 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.088 0.22 8 -0.18 3 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.013 0.02 -10000 0 -0.16 1 1
TSC2 0.02 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.02 0.032 -10000 0 -0.16 3 3
TSC1 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.012 0.079 -10000 0 -0.21 39 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.005 0.029 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 0.039 0.077 0.25 10 -0.26 1 11
MAP3K5 -0.006 0.034 -10000 0 -0.18 10 10
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
apoptosis -0.006 0.034 -10000 0 -0.18 10 10
mol:LY294002 0 0 -10000 0 -0.001 38 38
EIF4B 0.034 0.076 0.24 13 -0.24 1 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.045 0.067 0.24 7 -0.23 1 8
eIF4E/eIF4G1/eIF4A1 -0.012 0.034 -10000 0 -0.28 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.059 -10000 0 -0.2 21 21
mTOR/RHEB/GTP/Raptor/GBL 0.03 0.071 0.21 18 -0.14 3 21
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.016 0.076 0.2 2 -10000 0 2
mol:Amino Acids 0 0 -10000 0 -0.001 38 38
FKBP12/Rapamycin 0.016 0.005 -10000 0 -10000 0 0
PDPK1 0.014 0.086 0.15 73 -0.18 16 89
EIF4E 0.02 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.017 0.12 -10000 0 -0.5 14 14
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.009 0.071 -10000 0 -0.53 2 2
TSC1/TSC2 0.029 0.098 0.25 10 -0.19 3 13
tumor necrosis factor receptor activity 0 0 0.001 38 -10000 0 38
RPS6 0.02 0.004 -10000 0 -10000 0 0
PPP5C 0.02 0.004 -10000 0 -10000 0 0
EIF4G1 0.013 0.01 -10000 0 -10000 0 0
IRS1 -0.024 0.079 -10000 0 -0.22 39 39
INS -0.016 0.004 -10000 0 -10000 0 0
PTEN 0.017 0.009 -10000 0 -10000 0 0
PDK2 0.014 0.085 0.15 72 -0.18 17 89
EIF4EBP1 -0.032 0.23 -10000 0 -1 14 14
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PPP2R5D 0.022 0.073 0.26 3 -0.37 5 8
peptide biosynthetic process -0.018 0.006 -10000 0 -10000 0 0
RHEB 0.02 0.004 -10000 0 -10000 0 0
EIF4A1 0.019 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 96 -10000 0 96
EEF2 -0.018 0.006 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.02 0.21 -10000 0 -0.97 14 14
BCR 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
JUN -0.025 0.12 0.54 1 -0.3 33 34
IKBKB 0.01 0.086 0.28 4 -0.29 5 9
AKT1 0.025 0.12 0.24 33 -0.19 15 48
IKBKG 0.018 0.079 0.26 7 -0.28 3 10
CALM1 0.015 0.1 0.32 6 -0.31 3 9
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
MAP3K1 -0.037 0.16 0.4 2 -0.42 39 41
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.016 0.099 0.28 8 -0.32 3 11
DOK1 0.02 0.003 -10000 0 -10000 0 0
AP-1 -0.003 0.088 0.26 8 -0.24 4 12
LYN 0.02 0.004 -10000 0 -10000 0 0
BLNK 0.021 0.016 0.29 1 -10000 0 1
SHC1 0.019 0.006 -10000 0 -10000 0 0
BCR complex 0.002 0.078 0.22 2 -0.2 35 37
CD22 -0.052 0.13 -10000 0 -0.4 34 34
CAMK2G 0.011 0.095 0.3 6 -0.31 2 8
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.044 0.043 -10000 0 -10000 0 0
GO:0007205 0.015 0.1 0.29 7 -0.32 3 10
SYK 0.02 0.003 -10000 0 -10000 0 0
ELK1 0.014 0.1 0.32 7 -0.31 3 10
NFATC1 -0.027 0.12 0.32 3 -0.32 31 34
B-cell antigen/BCR complex 0.002 0.078 0.22 2 -0.2 35 37
PAG1/CSK 0.028 0.009 -10000 0 -10000 0 0
NFKBIB 0.017 0.041 0.13 7 -0.12 7 14
HRAS 0.008 0.089 0.25 8 -0.26 4 12
NFKBIA 0.017 0.04 0.13 7 -0.12 8 15
NF-kappa-B/RelA/I kappa B beta 0.02 0.036 0.13 7 -10000 0 7
RasGAP/Csk 0.025 0.072 0.21 2 -0.16 33 35
mol:GDP 0.016 0.094 0.28 6 -0.3 3 9
PTEN 0.019 0.005 -10000 0 -10000 0 0
CD79B -0.017 0.1 -10000 0 -0.29 35 35
NF-kappa-B/RelA/I kappa B alpha 0.02 0.036 0.14 5 -10000 0 5
GRB2 0.02 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.029 0.17 0.39 2 -0.43 36 38
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:IP3 0.007 0.094 0.28 7 -0.33 3 10
CSK 0.02 0.004 -10000 0 -10000 0 0
FOS 0.002 0.1 0.31 7 -0.3 3 10
CHUK 0.012 0.089 0.29 4 -0.32 6 10
IBTK 0.02 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.024 0.088 0.28 2 -0.28 3 5
PTPN6 -0.054 0.13 -10000 0 -0.39 35 35
RELA 0.02 0.003 -10000 0 -10000 0 0
BCL2A1 0.014 0.027 0.16 2 -10000 0 2
VAV2 -0.041 0.15 -10000 0 -0.42 34 34
ubiquitin-dependent protein catabolic process 0.018 0.04 0.13 7 -0.12 8 15
BTK 0.019 0.012 -10000 0 -10000 0 0
CD19 -0.053 0.13 -10000 0 -0.4 35 35
MAP4K1 0.019 0.005 -10000 0 -10000 0 0
CD72 0.02 0.003 -10000 0 -10000 0 0
PAG1 0.02 0.005 -10000 0 -10000 0 0
MAPK14 -0.032 0.15 0.46 2 -0.36 38 40
SH3BP5 -0.005 0.084 -10000 0 -0.29 23 23
PIK3AP1 -0.003 0.1 0.23 5 -0.33 5 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.064 -10000 0 -0.37 3 3
RAF1 0.003 0.085 0.24 7 -0.26 3 10
RasGAP/p62DOK/SHIP 0.022 0.071 -10000 0 -0.16 31 31
CD79A 0.022 0.023 0.29 2 -10000 0 2
re-entry into mitotic cell cycle -0.003 0.087 0.26 8 -0.23 5 13
RASA1 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.003 0.08 0.27 5 -0.24 2 7
MAPK1 -0.003 0.079 0.24 5 -0.24 2 7
CD72/SHP1 -0.035 0.14 0.26 11 -0.38 33 44
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.036 0.14 0.37 2 -0.36 38 40
actin cytoskeleton organization -0.036 0.14 0.3 4 -0.38 33 37
NF-kappa-B/RelA 0.04 0.071 0.24 7 -0.2 3 10
Calcineurin 0.026 0.087 0.33 2 -0.29 2 4
PI3K -0.05 0.092 -10000 0 -0.3 31 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.002 0.1 0.25 5 -0.3 9 14
SOS1 0.02 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.04 0.21 -10000 0 -0.54 40 40
DAPP1 -0.06 0.22 -10000 0 -0.6 38 38
cytokine secretion -0.024 0.11 0.32 3 -0.31 30 33
mol:DAG 0.007 0.094 0.28 7 -0.33 3 10
PLCG2 0.02 0.004 -10000 0 -10000 0 0
MAP2K1 0 0.083 0.23 7 -0.25 3 10
B-cell antigen/BCR complex/FcgammaRIIB 0.011 0.073 0.21 2 -0.18 35 37
mol:PI-3-4-5-P3 -0.01 0.097 0.19 12 -0.25 19 31
ETS1 0.005 0.089 0.28 7 -0.29 2 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.03 0.071 -10000 0 -0.16 28 28
B-cell antigen/BCR complex/LYN -0.037 0.14 -10000 0 -0.41 35 35
MALT1 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.02 0.004 -10000 0 -10000 0 0
RAC1 -0.041 0.14 0.24 3 -0.4 33 36
B-cell antigen/BCR complex/LYN/SYK -0.015 0.14 -10000 0 -0.38 33 33
CARD11 0.013 0.1 0.31 6 -0.31 3 9
FCGR2B 0.017 0.026 -10000 0 -0.29 2 2
PPP3CA 0.02 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.002 -10000 0 -10000 0 0
IKK complex 0.015 0.051 0.17 10 -0.13 1 11
PTPRC 0.018 0.019 -10000 0 -0.29 1 1
PDPK1 0.005 0.095 0.21 26 -0.18 17 43
PPP3CB 0.02 0.003 -10000 0 -10000 0 0
PPP3CC 0.019 0.006 -10000 0 -10000 0 0
POU2F2 0.013 0.029 0.17 3 -10000 0 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.011 0.064 0.21 20 -0.21 3 23
KIRREL 0.018 0.013 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.011 0.064 0.21 3 -0.21 20 23
PLCG1 0.019 0.005 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.029 0.056 0.2 3 -0.16 18 21
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.004 0.047 -10000 0 -0.19 15 15
FYN -0.002 0.084 0.21 30 -0.16 16 46
mol:Ca2+ 0.029 0.052 0.2 2 -0.16 16 18
mol:DAG 0.029 0.053 0.2 2 -0.16 16 18
NPHS2 -0.015 0.019 -10000 0 -10000 0 0
mol:IP3 0.029 0.053 0.2 2 -0.16 16 18
regulation of endocytosis 0.019 0.053 0.18 3 -0.15 17 20
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.052 0.19 3 -0.15 20 23
establishment of cell polarity 0.011 0.064 0.21 3 -0.21 20 23
Nephrin/NEPH1/podocin/NCK1-2 0.029 0.054 -10000 0 -0.15 14 14
Nephrin/NEPH1/beta Arrestin2 0.021 0.055 0.19 3 -0.15 17 20
NPHS1 0.007 0.05 0.3 6 -10000 0 6
Nephrin/NEPH1/podocin 0.018 0.053 0.19 3 -0.14 25 28
TJP1 0.02 0.004 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
NCK2 0.02 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.03 0.053 0.2 2 -0.16 16 18
CD2AP 0.02 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.029 0.057 0.2 3 -0.16 18 21
GRB2 0.02 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.006 0.077 0.21 24 -0.15 16 40
cytoskeleton organization -0.016 0.054 0.18 8 -0.2 14 22
Nephrin/NEPH1 0.012 0.045 0.18 3 -0.14 20 23
Nephrin/NEPH1/ZO-1 0.021 0.057 0.2 3 -0.17 18 21
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.021 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.054 -10000 0 -0.17 19 19
forebrain development -0.13 0.22 -10000 0 -0.48 64 64
GNAO1 0.012 0.034 -10000 0 -0.29 3 3
SMO/beta Arrestin2 0.006 0.058 -10000 0 -0.2 19 19
SMO -0.005 0.077 -10000 0 -0.29 19 19
ARRB2 0.015 0.013 -10000 0 -10000 0 0
GLI3/SPOP 0.01 0.1 -10000 0 -0.32 8 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.008 -10000 0 -10000 0 0
GNAI2 0.015 0.013 -10000 0 -10000 0 0
SIN3/HDAC complex 0.047 0.019 -10000 0 -10000 0 0
GNAI1 0.014 0.022 -10000 0 -0.29 1 1
XPO1 0.015 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.12 0.22 -10000 0 -0.56 44 44
SAP30 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.076 -10000 0 -0.29 19 19
MIM/GLI2A 0.005 0.043 -10000 0 -0.12 23 23
IFT88 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.016 0.013 -10000 0 -10000 0 0
GLI2 -0.015 0.087 0.2 3 -0.29 10 13
GLI3 0.002 0.1 0.21 3 -0.33 8 11
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.003 -10000 0 -10000 0 0
SAP18 0.02 0.004 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.004 -10000 0 -10000 0 0
GNG2 0.02 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.053 0.1 -10000 0 -0.24 45 45
SIN3B 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.002 0.098 -10000 0 -0.34 13 13
GLI2/Su(fu) -0.026 0.098 0.21 1 -0.31 15 16
FOXA2 -0.12 0.31 -10000 0 -0.88 41 41
neural tube patterning -0.13 0.22 -10000 0 -0.48 64 64
SPOP 0.02 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.013 0.063 -10000 0 -0.18 1 1
GNB1 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.019 0.005 -10000 0 -10000 0 0
CSNK1G3 0.02 0.004 -10000 0 -10000 0 0
MTSS1 0.005 0.043 -10000 0 -0.12 23 23
embryonic limb morphogenesis -0.13 0.22 -10000 0 -0.48 64 64
SUFU -0.002 0.035 -10000 0 -10000 0 0
LGALS3 0.02 0.003 -10000 0 -10000 0 0
catabolic process -0.016 0.12 0.28 1 -0.37 11 12
GLI3A/CBP -0.03 0.11 -10000 0 -0.29 44 44
KIF3A 0.02 0.005 -10000 0 -10000 0 0
GLI1 -0.13 0.22 -10000 0 -0.5 64 64
RAB23 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.02 0.004 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.014 0.064 -10000 0 -0.18 1 1
GNAZ -0.053 0.13 -10000 0 -0.29 66 66
RBBP4 0.021 0.001 -10000 0 -10000 0 0
CSNK1G1 0.02 0.003 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GLI2/SPOP -0.009 0.087 0.22 1 -0.28 10 11
STK36 0.014 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.055 0.096 -10000 0 -0.29 23 23
PTCH1 -0.12 0.21 -10000 0 -0.59 33 33
MIM/GLI1 -0.14 0.24 -10000 0 -0.48 81 81
CREBBP -0.03 0.11 -10000 0 -0.29 44 44
Su(fu)/SIN3/HDAC complex -0.004 0.048 -10000 0 -0.27 3 3
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.019 0.075 -10000 0 -0.39 9 9
HDAC1 0.02 0.004 -10000 0 -10000 0 0
AES 0.02 0.005 -10000 0 -10000 0 0
FBXW11 0.02 0.004 -10000 0 -10000 0 0
DTX1 0.021 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.028 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.003 -10000 0 -10000 0 0
AP1 -0.008 0.056 -10000 0 -0.19 22 22
NCSTN 0.019 0.005 -10000 0 -10000 0 0
ADAM10 0.02 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.003 0.09 -10000 0 -0.62 5 5
NICD/RBPSUH 0.02 0.08 -10000 0 -0.39 10 10
WIF1 -0.045 0.12 0.29 3 -0.29 51 54
NOTCH1 0 0.077 -10000 0 -0.41 10 10
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.18 0.14 0.29 168 -10000 0 168
DKK1 0.005 0.077 0.29 3 -0.29 16 19
beta catenin/beta TrCP1 0.001 0.072 -10000 0 -0.29 5 5
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
AXIN1 0.009 0.058 -10000 0 -0.36 4 4
CtBP/CBP/TCF1/TLE1/AES 0 0.04 -10000 0 -10000 0 0
PSEN1 0.02 0.003 -10000 0 -10000 0 0
FOS -0.003 0.082 -10000 0 -0.29 22 22
JUN 0.019 0.018 -10000 0 -0.29 1 1
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 -0.009 0.073 -10000 0 -0.3 5 5
MAPK3 0.02 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.093 0.21 150 -0.12 5 155
HNF1A 0.022 0.023 0.29 2 -10000 0 2
CTBP1 0.019 0.006 -10000 0 -10000 0 0
MYC -0.003 0.14 -10000 0 -1 5 5
NKD1 0.019 0.042 0.29 3 -0.29 3 6
FZD1 0.02 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.022 0.082 -10000 0 -0.39 10 10
apoptosis -0.008 0.055 -10000 0 -0.19 22 22
Delta 1/NOTCHprecursor 0.021 0.078 -10000 0 -0.39 9 9
DLL1 0.019 0.005 -10000 0 -10000 0 0
PPARD 0.005 0.095 -10000 0 -0.79 4 4
Gamma Secretase 0.051 0.024 -10000 0 -10000 0 0
APC -0.003 0.089 -10000 0 -0.39 11 11
DVL1 -0.005 0.037 -10000 0 -0.24 6 6
CSNK2A1 0.019 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.11 0.11 0.21 151 -0.15 15 166
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.019 0.006 -10000 0 -10000 0 0
NLK 0.006 0.005 -10000 0 -10000 0 0
CCND1 -0.009 0.14 -10000 0 -0.79 9 9
WNT1 0.017 0.02 0.29 1 -10000 0 1
Axin1/APC/beta catenin -0.002 0.094 0.25 3 -0.32 11 14
DKK2 0.014 0.044 0.29 1 -0.29 5 6
NOTCH1 precursor/DVL1 -0.009 0.096 -10000 0 -0.41 12 12
GSK3B 0.017 0.008 -10000 0 -10000 0 0
FRAT1 0.02 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.02 0.079 -10000 0 -0.39 10 10
PPP2R5D 0.003 0.054 -10000 0 -0.3 7 7
MAPK1 0.02 0.002 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.013 0.083 0.21 4 -0.16 51 55
RBPJ 0.019 0.006 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.02 0.005 -10000 0 -10000 0 0
EGFR 0.018 0.026 -10000 0 -0.29 2 2
EGF/EGFR 0.004 0.071 -10000 0 -0.15 50 50
EGF/EGFR dimer/SHC/GRB2/SOS1 0.04 0.053 -10000 0 -0.16 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.024 0.11 -10000 0 -0.29 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.003 0.066 -10000 0 -0.29 14 14
EGF/EGFR dimer/SHC 0.026 0.049 -10000 0 -0.17 15 15
mol:GDP 0.034 0.05 -10000 0 -0.16 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.019 -10000 0 -0.29 1 1
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.02 0.044 -10000 0 -0.15 15 15
SHC1 0.019 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.031 0.049 -10000 0 -0.15 15 15
FRAP1 -0.028 0.033 0.15 2 -0.15 15 17
EGF/EGFR dimer 0.017 0.052 -10000 0 -0.2 15 15
SOS1 0.02 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.005 0.081 -10000 0 -0.2 42 42
Insulin Pathway

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.036 0.091 -10000 0 -0.16 91 91
TC10/GTP -0.031 0.083 -10000 0 -0.14 99 99
Insulin Receptor/Insulin/IRS1/Shp2 0.039 0.045 -10000 0 -0.16 10 10
HRAS 0.02 0.005 -10000 0 -10000 0 0
APS homodimer 0.02 0.004 -10000 0 -10000 0 0
GRB14 0.07 0.11 0.29 54 -10000 0 54
FOXO3 0.016 0.097 -10000 0 -0.63 6 6
AKT1 0.039 0.094 0.2 36 -10000 0 36
INSR 0.022 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.038 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.018 -10000 0 -0.29 1 1
SORBS1 -0.096 0.15 -10000 0 -0.29 109 109
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.015 0.017 0.15 3 -10000 0 3
CAV1 -0.03 0.048 -10000 0 -0.17 26 26
CBL/APS/CAP/Crk-II/C3G -0.025 0.097 -10000 0 -0.15 104 104
Insulin Receptor/Insulin/IRS1/NCK2 0.039 0.045 -10000 0 -0.16 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.02 0.032 -10000 0 -0.15 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.001 0.079 -10000 0 -0.32 12 12
RPS6KB1 0.029 0.087 0.18 37 -10000 0 37
PARD6A 0.02 0.004 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.007 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.017 0.072 0.15 15 -10000 0 15
HRAS/GTP -0.03 0.027 -10000 0 -0.15 6 6
Insulin Receptor 0.022 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.041 0.046 -10000 0 -0.16 7 7
PRKCI 0.005 0.053 -10000 0 -0.3 8 8
Insulin Receptor/Insulin/GRB14/PDK1 -0.007 0.041 0.1 4 -0.15 3 7
SHC1 0.019 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.028 0.02 -10000 0 -10000 0 0
PI3K 0.025 0.036 -10000 0 -0.15 5 5
NCK2 0.02 0.002 -10000 0 -10000 0 0
RHOQ 0.02 0.004 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 0.036 0.092 0.2 32 -10000 0 32
PRKCZ -0.002 0.072 -10000 0 -0.3 15 15
SH2B2 0.02 0.004 -10000 0 -10000 0 0
SHC/SHIP -0.021 0.031 -10000 0 -10000 0 0
F2RL2 0.002 0.073 -10000 0 -0.29 17 17
TRIP10 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.035 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.049 0.03 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
RASA1 0.02 0.004 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.031 0.097 -10000 0 -0.16 106 106
TC10/GDP 0.015 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.045 0.026 -10000 0 -0.17 1 1
INPP5D -0.021 0.03 -10000 0 -0.15 9 9
SOS1 0.02 0.003 -10000 0 -10000 0 0
SGK1 -0.01 0.1 -10000 0 -0.61 8 8
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.001 -10000 0 -10000 0 0
IRS1 0.008 0.056 -10000 0 -0.29 10 10
p62DOK/RasGAP 0.028 0.021 -10000 0 -10000 0 0
INS -0.014 0.017 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.021 0.03 -10000 0 -0.15 9 9
GRB2 0.02 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.028 0.087 0.18 40 -10000 0 40
PTPRA 0.02 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.026 0.007 -10000 0 -10000 0 0
PDPK1 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0 0.042 -10000 0 -0.18 10 10
Insulin Receptor/Insulin/IRS1 0.029 0.04 -10000 0 -0.16 10 10
Insulin Receptor/Insulin/IRS3 0.029 0.017 -10000 0 -10000 0 0
Par3/Par6 0.032 0.047 -10000 0 -0.15 16 16
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.014 0.099 0.2 1 -0.33 22 23
PDGFB-D/PDGFRB/SLAP 0.017 0.048 -10000 0 -0.2 13 13
PDGFB-D/PDGFRB/APS/CBL 0.024 0.047 -10000 0 -0.16 15 15
AKT1 0.041 0.11 0.32 19 -10000 0 19
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.001 0.12 0.22 4 -0.36 22 26
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
FGR -0.013 0.072 -10000 0 -0.36 4 4
mol:Ca2+ -0.009 0.13 0.21 15 -0.38 22 37
MYC 0 0.13 0.32 4 -0.66 5 9
SHC1 0.019 0.006 -10000 0 -10000 0 0
HRAS/GDP -0.014 0.059 0.16 24 -0.16 1 25
LRP1/PDGFRB/PDGFB 0.029 0.048 -10000 0 -0.17 15 15
GRB10 0.019 0.018 -10000 0 -0.29 1 1
PTPN11 0.021 0.001 -10000 0 -10000 0 0
GO:0007205 -0.009 0.13 0.22 14 -0.39 22 36
PTEN 0.019 0.005 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.023 0.29 2 -10000 0 2
PDGFB-D/PDGFRB/SHP2 0.017 0.054 -10000 0 -0.2 16 16
PDGFB-D/PDGFRB/GRB10 0.017 0.055 -10000 0 -0.21 15 15
cell cycle arrest 0.017 0.048 -10000 0 -0.2 13 13
HRAS 0.02 0.005 -10000 0 -10000 0 0
HIF1A 0.033 0.1 0.27 23 -10000 0 23
GAB1 -0.008 0.12 0.27 1 -0.39 18 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.007 0.12 0.21 13 -0.36 17 30
PDGFB-D/PDGFRB 0.026 0.049 -10000 0 -0.18 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.052 -10000 0 -0.2 15 15
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.01 0.091 -10000 0 -0.32 18 18
positive regulation of MAPKKK cascade 0.017 0.053 -10000 0 -0.2 16 16
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
mol:IP3 -0.009 0.13 0.22 14 -0.39 22 36
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.016 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.055 0.22 2 -0.2 15 17
SHB 0.02 0.003 -10000 0 -10000 0 0
BLK -0.021 0.16 0.32 4 -0.44 27 31
PTPN2 0.017 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.054 -10000 0 -0.2 16 16
BCAR1 0.02 0.004 -10000 0 -10000 0 0
VAV2 -0.007 0.13 0.24 6 -0.39 19 25
CBL 0.017 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.016 0.053 -10000 0 -0.2 16 16
LCK -0.009 0.06 -10000 0 -10000 0 0
PDGFRB 0.003 0.07 -10000 0 -0.3 15 15
ACP1 0.02 0.004 -10000 0 -10000 0 0
HCK -0.011 0.057 -10000 0 -10000 0 0
ABL1 -0.001 0.11 0.21 16 -0.32 18 34
PDGFB-D/PDGFRB/CBL -0.018 0.14 0.25 1 -0.44 23 24
PTPN1 0.015 0.014 -10000 0 -10000 0 0
SNX15 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation 0.002 0.12 0.31 4 -0.58 5 9
SLA 0.019 0.005 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.1 0.19 55 -10000 0 55
SRC -0.012 0.062 -10000 0 -0.38 1 1
PI3K -0.022 0.028 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.026 0.05 0.21 2 -0.17 14 16
SH2B2 0.02 0.004 -10000 0 -10000 0 0
PLCgamma1/SPHK1 -0.002 0.12 0.23 4 -0.37 22 26
LYN -0.013 0.073 -10000 0 -0.78 1 1
LRP1 0.02 0.002 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.002 -10000 0 -10000 0 0
STAT5A 0.02 0.002 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.034 0.043 -10000 0 -0.16 6 6
SPHK1 0.017 0.012 -10000 0 -10000 0 0
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.009 0.13 0.22 14 -0.39 22 36
PLCG1 -0.01 0.13 0.23 5 -0.4 22 27
NHERF/PDGFRB 0.035 0.061 0.21 13 -0.17 15 28
YES1 -0.02 0.09 -10000 0 -0.42 8 8
cell migration 0.034 0.061 0.21 13 -0.17 15 28
SHC/Grb2/SOS1 0.037 0.051 -10000 0 -0.16 12 12
SLC9A3R2 0.02 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.033 0.059 0.29 14 -10000 0 14
NHERF1-2/PDGFRB/PTEN 0.041 0.061 0.21 13 -0.16 15 28
FYN -0.031 0.14 -10000 0 -0.59 13 13
DOK1 -0.018 0.055 0.16 17 -0.17 14 31
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.02 0.002 -10000 0 -10000 0 0
RAC1 -0.01 0.13 0.27 1 -0.42 16 17
PRKCD -0.012 0.061 0.17 23 -0.17 11 34
FER -0.014 0.063 0.17 24 -0.17 14 38
MAPKKK cascade 0.001 0.088 0.2 22 -10000 0 22
RASA1 -0.014 0.063 0.17 24 -0.17 14 38
NCK1 0.015 0.009 -10000 0 -10000 0 0
NCK2 0.02 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.018 0.058 0.16 23 -0.16 13 36
PDGFB-D/PDGFRB/SHB 0.016 0.054 -10000 0 -0.2 16 16
chemotaxis -0.001 0.11 0.21 16 -0.31 18 34
STAT1-3-5/STAT1-3-5 0.03 0.049 -10000 0 -0.16 14 14
Bovine Papilomavirus E5/PDGFRB 0.002 0.049 -10000 0 -0.2 16 16
PTPRJ 0.02 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.013 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.06 0.22 2 -10000 0 2
NFATC4 -0.016 0.068 0.19 13 -0.17 3 16
ERBB2IP 0.016 0.012 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.014 0.088 0.18 56 -10000 0 56
JUN 0.015 0.06 0.24 5 -10000 0 5
HRAS 0.019 0.006 -10000 0 -10000 0 0
DOCK7 0 0.072 0.21 17 -10000 0 17
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.066 0.083 0.22 61 -10000 0 61
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.014 0.004 -10000 0 -10000 0 0
MAPK10 -0.025 0.058 0.15 9 -0.14 6 15
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.015 0.094 0.19 56 -10000 0 56
RAF1 0.008 0.066 0.23 7 -10000 0 7
ErbB2/ErbB3/neuregulin 2 -0.018 0.073 0.22 14 -0.17 27 41
STAT3 0.018 0.073 -10000 0 -0.85 2 2
cell migration -0.031 0.061 0.19 6 -0.17 5 11
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.007 0.14 0.4 1 -0.48 4 5
FOS -0.013 0.14 0.35 3 -0.42 23 26
NRAS 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.088 0.18 56 -10000 0 56
MAPK3 -0.001 0.12 0.35 1 -0.46 6 7
MAPK1 -0.002 0.12 0.35 1 -0.46 7 8
JAK2 0.001 0.071 0.21 16 -10000 0 16
NF2 0 0.053 -10000 0 -0.64 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.031 0.061 0.18 24 -10000 0 24
NRG1 0.064 0.1 0.3 50 -10000 0 50
GRB2/SOS1 0.028 0.008 -10000 0 -10000 0 0
MAPK8 0.008 0.081 0.23 12 -0.24 2 14
MAPK9 -0.012 0.043 0.17 6 -10000 0 6
ERBB2 -0.014 0.04 0.26 6 -10000 0 6
ERBB3 0.029 0.053 0.29 11 -10000 0 11
SHC1 0.019 0.006 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
apoptosis 0.01 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.018 0.072 -10000 0 -0.84 2 2
RNF41 -0.016 0.008 -10000 0 -10000 0 0
FRAP1 -0.007 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.022 0.029 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.017 0.03 0.19 5 -10000 0 5
CHRNA1 0.006 0.1 0.33 5 -0.33 3 8
myelination -0.012 0.074 0.24 11 -10000 0 11
PPP3CB -0.001 0.068 0.2 16 -10000 0 16
KRAS 0.019 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.048 0.06 0.22 2 -10000 0 2
NRG2 -0.014 0.094 -10000 0 -0.29 30 30
mol:GDP 0.031 0.061 0.18 24 -10000 0 24
SOS1 0.02 0.003 -10000 0 -10000 0 0
MAP2K2 0.003 0.065 0.22 6 -10000 0 6
SRC 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.001 0.072 0.21 17 -10000 0 17
MAP2K1 -0.002 0.15 0.38 1 -0.52 11 12
heart morphogenesis 0.014 0.088 0.18 56 -10000 0 56
RAS family/GDP 0.05 0.063 0.22 3 -10000 0 3
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.006 0.056 -10000 0 -0.67 2 2
CHRNE 0.006 0.015 0.12 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development 0.014 0.088 0.18 56 -10000 0 56
CDC42 0.02 0.003 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.008 0.054 -10000 0 -0.29 9 9
GNB1/GNG2 -0.011 0.09 -10000 0 -0.26 12 12
mol:DAG -0.042 0.068 0.17 1 -0.24 11 12
PLCG1 -0.043 0.07 0.17 1 -0.24 11 12
YES1 -0.036 0.067 -10000 0 -0.2 30 30
FZD3 0.009 0.054 -10000 0 -0.29 9 9
FZD6 0.019 0.005 -10000 0 -10000 0 0
G protein -0.009 0.093 0.24 1 -0.24 11 12
MAP3K7 -0.067 0.085 0.18 2 -0.25 27 29
mol:Ca2+ -0.041 0.067 0.16 1 -0.23 11 12
mol:IP3 -0.042 0.068 0.17 1 -0.24 11 12
NLK -0.003 0.081 -10000 0 -0.8 3 3
GNB1 0.02 0.004 -10000 0 -10000 0 0
CAMK2A -0.068 0.091 0.19 2 -0.25 32 34
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.025 0.077 -10000 0 -0.21 33 33
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.035 0.065 -10000 0 -0.19 32 32
GO:0007205 -0.039 0.068 0.16 1 -0.23 12 13
WNT6 0.011 0.048 -10000 0 -0.29 7 7
WNT4 0.016 0.036 -10000 0 -0.29 4 4
NFAT1/CK1 alpha -0.02 0.086 0.24 1 -0.27 8 9
GNG2 0.02 0.003 -10000 0 -10000 0 0
WNT5A 0.019 0.006 -10000 0 -10000 0 0
WNT11 0.012 0.053 0.29 1 -0.29 8 9
CDC42 -0.036 0.066 -10000 0 -0.29 7 7
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.044 -10000 0 -10000 0 0
epithelial cell differentiation -0.087 0.096 -10000 0 -0.34 6 6
ITCH 0.019 0.017 -10000 0 -10000 0 0
WWP1 0.006 0.032 -10000 0 -10000 0 0
FYN 0.015 0.04 -10000 0 -0.29 5 5
EGFR 0.018 0.026 -10000 0 -0.29 2 2
PRL -0.068 0.12 -10000 0 -0.29 61 61
neuron projection morphogenesis 0.005 0.07 0.28 3 -10000 0 3
PTPRZ1 0.14 0.14 0.29 135 -10000 0 135
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.037 0.058 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.017 0.054 0.26 2 -10000 0 2
ADAM17 0.017 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 0.009 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.019 0.047 -10000 0 -10000 0 0
NCOR1 0.019 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.029 0.051 0.24 1 -10000 0 1
GRIN2B 0.005 0.052 0.25 3 -10000 0 3
ErbB4/ErbB2/betacellulin 0.019 0.04 -10000 0 -10000 0 0
STAT1 0.02 0.004 -10000 0 -10000 0 0
HBEGF 0.02 0.004 -10000 0 -10000 0 0
PRLR -0.11 0.15 -10000 0 -0.29 123 123
E4ICDs/ETO2 0.016 0.044 -10000 0 -10000 0 0
axon guidance -0.025 0.064 -10000 0 -10000 0 0
NEDD4 0.015 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.13 -10000 0 -0.23 148 148
CBFA2T3 0.014 0.04 -10000 0 -0.29 5 5
ErbB4/ErbB2/HBEGF 0.02 0.04 -10000 0 -10000 0 0
MAPK3 0.008 0.068 0.29 2 -10000 0 2
STAT1 (dimer) 0.02 0.043 -10000 0 -10000 0 0
MAPK1 0.009 0.068 0.29 2 -10000 0 2
JAK2 0.019 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.011 0.054 0.23 3 -10000 0 3
NRG1 0.015 0.068 0.16 51 -10000 0 51
NRG3 0 0.035 0.29 3 -10000 0 3
NRG2 -0.014 0.094 -10000 0 -0.29 30 30
NRG4 0.042 0.076 0.29 24 -10000 0 24
heart development -0.025 0.064 -10000 0 -10000 0 0
neural crest cell migration 0.011 0.053 0.23 3 -10000 0 3
ERBB2 -0.008 0.046 0.27 7 -10000 0 7
WWOX/E4ICDs 0.018 0.042 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.041 0.064 0.33 1 -10000 0 1
apoptosis -0.027 0.048 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.014 0.045 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.061 0.085 0.3 6 -10000 0 6
ErbB4/ErbB4/betacellulin/betacellulin 0.018 0.043 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.063 0.1 -10000 0 -0.31 5 5
MDM2 0.006 0.033 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.026 0.04 -10000 0 -10000 0 0
STAT5A -0.029 0.063 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.03 0.051 0.24 1 -10000 0 1
DLG4 0.009 0.054 -10000 0 -0.29 9 9
GRB2/SHC 0.027 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.04 -10000 0 -10000 0 0
STAT5A (dimer) -0.09 0.1 -10000 0 -0.39 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.019 0.072 -10000 0 -10000 0 0
LRIG1 0.019 0.006 -10000 0 -10000 0 0
EREG 0.082 0.12 0.29 67 -10000 0 67
BTC 0.018 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.025 0.063 -10000 0 -10000 0 0
ERBB4 0.009 0.021 -10000 0 -10000 0 0
STAT5B 0.02 0.002 -10000 0 -10000 0 0
YAP1 -0.033 0.14 -10000 0 -0.46 28 28
GRB2 0.02 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.037 0.066 0.32 4 -10000 0 4
glial cell differentiation -0.014 0.039 -10000 0 -10000 0 0
WWOX 0.019 0.005 -10000 0 -10000 0 0
cell proliferation 0.005 0.069 0.28 3 -0.31 1 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.028 0.009 -10000 0 -10000 0 0
CRKL -0.026 0.1 -10000 0 -0.47 8 8
mol:PIP3 0.009 0.072 -10000 0 -0.84 2 2
AKT1 0.003 0.073 -10000 0 -0.74 2 2
PTK2B 0.019 0.006 -10000 0 -10000 0 0
RAPGEF1 -0.029 0.1 0.25 1 -0.45 8 9
RANBP10 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.014 0.07 0.21 1 -0.17 34 35
MAP3K5 -0.036 0.1 -10000 0 -0.44 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS 0.02 0.067 0.21 1 -0.16 33 34
AP1 -0.025 0.05 -10000 0 -0.18 19 19
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
apoptosis -0.045 0.2 -10000 0 -0.67 26 26
STAT3 (dimer) -0.028 0.086 -10000 0 -0.28 18 18
GAB1/CRKL/SHP2/PI3K -0.003 0.094 -10000 0 -0.48 5 5
INPP5D 0.018 0.007 -10000 0 -10000 0 0
CBL/CRK -0.014 0.099 -10000 0 -0.44 8 8
PTPN11 0.021 0.001 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.005 -10000 0 -10000 0 0
PTEN 0.019 0.005 -10000 0 -10000 0 0
ELK1 -0.008 0.052 0.24 8 -0.18 1 9
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.018 0.058 -10000 0 -0.23 5 5
PAK1 0 0.073 -10000 0 -0.71 2 2
HGF/MET/RANBP10 0.014 0.07 0.21 1 -0.17 34 35
HRAS -0.04 0.13 -10000 0 -0.47 17 17
DOCK1 -0.031 0.098 -10000 0 -0.45 8 8
GAB1 -0.021 0.11 -10000 0 -0.48 8 8
CRK -0.027 0.1 -10000 0 -0.46 8 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.052 0.16 -10000 0 -0.4 44 44
JUN 0.019 0.018 -10000 0 -0.29 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.014 0.049 -10000 0 -0.15 33 33
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.014 0.13 0.25 12 -0.34 12 24
GRB2/SHC -0.002 0.062 -10000 0 -0.17 10 10
FOS -0.003 0.082 -10000 0 -0.29 22 22
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility -0.008 0.052 0.24 8 -0.18 1 9
HGF/MET/MUC20 0.004 0.063 0.19 1 -0.17 34 35
cell migration -0.002 0.062 -10000 0 -0.16 10 10
GRB2 0.02 0.005 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.028 0.008 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.074 -10000 0 -0.2 36 36
MET/MUC20 0.015 0.003 -10000 0 -10000 0 0
RAP1B -0.029 0.1 0.25 3 -0.42 8 11
RAP1A -0.033 0.096 0.23 1 -0.42 8 9
HGF/MET/RANBP9 0.015 0.068 0.21 1 -0.17 32 33
RAF1 -0.042 0.12 -10000 0 -0.45 17 17
STAT3 -0.027 0.086 -10000 0 -0.28 18 18
cell proliferation -0.031 0.12 0.25 1 -0.32 35 36
RPS6KB1 -0.005 0.031 -10000 0 -0.26 1 1
MAPK3 -0.01 0.068 0.66 2 -10000 0 2
MAPK1 -0.008 0.08 0.53 5 -10000 0 5
RANBP9 0.019 0.005 -10000 0 -10000 0 0
MAPK8 -0.025 0.11 -10000 0 -0.45 10 10
SRC -0.032 0.064 -10000 0 -0.24 11 11
PI3K 0.001 0.051 -10000 0 -0.16 7 7
MET/Glomulin 0.012 0.02 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
MAP2K1 -0.042 0.12 -10000 0 -0.42 16 16
MET 0.02 0.004 -10000 0 -10000 0 0
MAP4K1 -0.033 0.11 -10000 0 -0.47 10 10
PTK2 0.019 0.006 -10000 0 -10000 0 0
MAP2K2 -0.042 0.12 -10000 0 -0.43 16 16
BAD -0.001 0.071 -10000 0 -0.71 2 2
MAP2K4 -0.035 0.095 -10000 0 -0.42 9 9
SHP2/GRB2/SOS1/GAB1 -0.006 0.1 -10000 0 -0.41 8 8
INPPL1 0.02 0.004 -10000 0 -10000 0 0
PXN 0.021 0.001 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.024 0.047 -10000 0 -0.14 36 36
PLCgamma1/PKC 0.014 0.004 -10000 0 -10000 0 0
HGF -0.016 0.1 0.29 1 -0.29 34 35
RASA1 0.02 0.004 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
PTPRJ 0.02 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0 0.059 -10000 0 -0.16 29 29
PDPK1 0.006 0.074 -10000 0 -0.78 2 2
HGF/MET/SHIP 0.013 0.069 0.21 1 -0.17 34 35
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.026 0.12 -10000 0 -0.32 11 11
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.033 0.12 0.2 3 -0.32 16 19
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.017 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
YWHAB 0.019 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.037 0.014 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
ASIP 0.004 0.018 -10000 0 -10000 0 0
PRKCI 0.013 0.01 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.02 0.004 -10000 0 -10000 0 0
GYS1 -0.006 0.003 -10000 0 -10000 0 0
PRKCZ 0.02 0.004 -10000 0 -10000 0 0
TRIP10 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.007 -10000 0 -10000 0 0
AS160/14-3-3 0.068 0.056 0.21 13 -10000 0 13
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.037 0.13 -10000 0 -0.35 16 16
STX4 0.02 0.002 -10000 0 -10000 0 0
GSK3B 0.007 0.004 -10000 0 -10000 0 0
SFN 0.28 0.067 0.29 274 -10000 0 274
LNPEP 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.012 -10000 0 -10000 0 0
CDKN1B 0.002 0.052 -10000 0 -0.29 7 7
CDKN1A 0.001 0.055 0.18 1 -0.29 8 9
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.02 0.004 -10000 0 -10000 0 0
FOXO3 0.001 0.055 -10000 0 -0.29 8 8
AKT1 -0.004 0.05 -10000 0 -0.3 8 8
BAD 0.02 0.003 -10000 0 -10000 0 0
AKT3 -0.005 0.051 -10000 0 -0.23 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.001 0.055 -10000 0 -0.29 8 8
AKT1/ASK1 0.025 0.062 0.22 1 -0.28 8 9
BAD/YWHAZ 0.038 0.013 -10000 0 -10000 0 0
RICTOR 0.018 0.007 -10000 0 -10000 0 0
RAF1 0.019 0.005 -10000 0 -10000 0 0
JNK cascade -0.023 0.059 0.28 8 -10000 0 8
TSC1 0.001 0.054 -10000 0 -0.29 8 8
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.025 0.065 0.23 1 -0.29 8 9
EP300 0.02 0.003 -10000 0 -10000 0 0
mol:GDP 0 0.053 -10000 0 -0.3 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0 0.053 -10000 0 -0.29 8 8
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.007 0.002 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
MAPKAP1 0.021 0.002 -10000 0 -10000 0 0
negative regulation of cell cycle -0.057 0.057 -10000 0 -0.19 14 14
YWHAH 0.02 0.003 -10000 0 -10000 0 0
AKT1S1 0.003 0.05 -10000 0 -0.29 6 6
CASP9 0.001 0.055 0.18 1 -0.29 8 9
YWHAB 0.019 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.016 0.056 0.22 2 -0.28 6 8
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.036 0.015 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.019 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0 0.047 0.18 1 -0.26 7 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL -0.001 0.067 -10000 0 -0.32 11 11
CHUK 0.001 0.054 -10000 0 -0.29 8 8
BAD/BCL-XL 0.018 0.058 -10000 0 -0.28 8 8
mTORC2 0.023 0.01 -10000 0 -10000 0 0
AKT2 0.006 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.063 0.072 0.23 9 -0.24 1 10
PDPK1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.003 0.057 0.18 3 -0.29 8 11
MAPKKK cascade -0.025 0.064 0.28 8 -0.22 2 10
MDM2/Cbp/p300 0.034 0.064 0.26 4 -0.28 6 10
TSC1/TSC2 0 0.066 0.3 5 -0.29 8 13
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.061 0.25 4 -0.27 6 10
glucose import -0.048 0.064 0.2 1 -0.15 83 84
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.005 0.057 0.21 4 -0.22 5 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.049 0.062 -10000 0 -0.15 83 83
GSK3A 0.003 0.049 -10000 0 -0.29 6 6
FOXO1 0.001 0.052 -10000 0 -0.29 7 7
GSK3B 0.021 0.074 -10000 0 -0.3 6 6
SFN 0.28 0.067 0.29 274 -10000 0 274
G1/S transition of mitotic cell cycle 0.034 0.092 0.25 19 -0.29 5 24
p27Kip1/14-3-3 family 0.073 0.063 0.23 8 -0.25 1 9
PRKACA 0.02 0.004 -10000 0 -10000 0 0
KPNA1 0.017 0.008 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
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 0.02 0.004 -10000 0 -10000 0 0
EPHB2 0.021 0.005 -10000 0 -10000 0 0
EFNB1 -0.016 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.05 -10000 0 -0.15 16 16
Ephrin B2/EPHB1-2 0.018 0.044 -10000 0 -0.15 15 15
neuron projection morphogenesis -0.021 0.04 -10000 0 -0.15 14 14
Ephrin B1/EPHB1-2/Tiam1 0.019 0.048 -10000 0 -0.16 16 16
DNM1 0.021 0.003 -10000 0 -10000 0 0
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.018 0.076 -10000 0 -0.4 10 10
YES1 -0.015 0.12 -10000 0 -0.62 11 11
Ephrin B1/EPHB1-2/NCK2 0.021 0.046 -10000 0 -0.16 14 14
PI3K 0.006 0.077 -10000 0 -0.36 11 11
mol:GDP 0.018 0.046 -10000 0 -0.15 16 16
ITGA2B 0.019 0.03 0.29 1 -0.29 2 3
endothelial cell proliferation 0.026 0.008 -10000 0 -10000 0 0
FYN -0.016 0.12 -10000 0 -0.62 11 11
MAP3K7 -0.016 0.078 -10000 0 -0.42 10 10
FGR -0.012 0.12 -10000 0 -0.61 12 12
TIAM1 0.018 0.026 -10000 0 -0.29 2 2
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
RGS3 0.02 0.003 -10000 0 -10000 0 0
cell adhesion -0.026 0.078 -10000 0 -0.36 11 11
LYN -0.014 0.12 -10000 0 -0.62 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.022 0.12 -10000 0 -0.53 15 15
Ephrin B1/EPHB1-2 -0.013 0.086 -10000 0 -0.47 10 10
SRC -0.01 0.12 -10000 0 -0.62 11 11
ITGB3 -0.016 0.1 -10000 0 -0.29 34 34
EPHB1 0.001 0.066 -10000 0 -0.29 14 14
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.026 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.002 0.079 0.22 1 -0.21 35 36
BLK -0.007 0.14 -10000 0 -0.62 12 12
HCK -0.011 0.12 -10000 0 -0.62 11 11
regulation of stress fiber formation -0.02 0.045 0.16 14 -10000 0 14
MAPK8 -0.024 0.077 -10000 0 -0.38 12 12
Ephrin B1/EPHB1-2/RGS3 0.021 0.046 -10000 0 -0.16 14 14
endothelial cell migration -0.011 0.071 0.18 8 -0.35 10 18
NCK2 0.02 0.002 -10000 0 -10000 0 0
PTPN13 0.017 0.026 -10000 0 -0.4 1 1
regulation of focal adhesion formation -0.02 0.045 0.16 14 -10000 0 14
chemotaxis -0.02 0.045 0.16 14 -10000 0 14
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.046 -10000 0 -0.15 16 16
angiogenesis -0.013 0.086 -10000 0 -0.47 10 10
LCK -0.012 0.12 -10000 0 -0.61 12 12
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.019 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.02 0.085 -10000 0 -0.49 1 1
Syndecan-3/Neurocan 0.019 0.029 -10000 0 -0.4 1 1
POMC 0.024 0.044 0.29 6 -0.29 1 7
EGFR 0.018 0.026 -10000 0 -0.29 2 2
Syndecan-3/EGFR 0.017 0.029 -10000 0 -0.4 1 1
AGRP -0.017 0.003 -10000 0 -10000 0 0
NCSTN 0.019 0.005 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.003 -10000 0 -10000 0 0
APH1A 0.019 0.005 -10000 0 -10000 0 0
NCAN 0.015 0.022 0.29 1 -10000 0 1
long-term memory 0.031 0.039 -10000 0 -0.38 1 1
Syndecan-3/IL8 0.12 0.097 0.28 13 -0.4 1 14
PSEN1 0.02 0.003 -10000 0 -10000 0 0
Src/Cortactin 0.027 0.01 -10000 0 -10000 0 0
FYN 0.015 0.04 -10000 0 -0.29 5 5
limb bud formation 0.004 0.024 -10000 0 -0.4 1 1
MC4R -0.004 0.025 0.29 1 -10000 0 1
SRC 0.019 0.006 -10000 0 -10000 0 0
PTN -0.099 0.15 -10000 0 -0.29 111 111
FGFR/FGF/Syndecan-3 0.004 0.024 -10000 0 -0.41 1 1
neuron projection morphogenesis -0.045 0.072 -10000 0 -0.48 1 1
Syndecan-3/AgRP 0.017 0.026 -10000 0 -0.38 1 1
Syndecan-3/AgRP/MC4R 0.033 0.036 0.28 1 -0.36 1 2
Fyn/Cortactin 0.024 0.031 -10000 0 -0.2 5 5
SDC3 0.004 0.024 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.11 0.096 0.28 13 -0.39 1 14
IL8 0.17 0.14 0.29 159 -10000 0 159
Syndecan-3/Fyn/Cortactin 0.032 0.04 -10000 0 -0.39 1 1
Syndecan-3/CASK 0.003 0.023 -10000 0 -0.39 1 1
alpha-MSH/MC4R 0.031 0.032 0.22 7 -0.18 1 8
Gamma Secretase 0.051 0.024 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.025 0.094 0.41 3 -10000 0 3
MKNK1 0.02 0.002 -10000 0 -10000 0 0
MAPK14 0.028 0.063 -10000 0 -0.28 8 8
ATF2/c-Jun 0.003 0.057 -10000 0 -0.33 2 2
MAPK11 0.028 0.061 -10000 0 -0.28 7 7
MITF -0.027 0.11 -10000 0 -0.25 47 47
MAPKAPK5 0.015 0.069 -10000 0 -0.33 8 8
KRT8 0.042 0.085 0.25 11 -0.31 6 17
MAPKAPK3 0.019 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.037 0.086 -10000 0 -0.38 8 8
CEBPB 0.017 0.072 0.27 3 -0.33 8 11
SLC9A1 0.015 0.072 -10000 0 -0.35 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.072 0.27 1 -0.32 8 9
p38alpha-beta/MNK1 0.045 0.074 -10000 0 -0.33 7 7
JUN 0.001 0.056 -10000 0 -0.33 2 2
PPARGC1A -0.002 0.1 -10000 0 -0.31 20 20
USF1 0.015 0.07 0.31 1 -0.33 8 9
RAB5/GDP/GDI1 0.014 0.053 -10000 0 -0.24 8 8
NOS2 0.007 0.15 -10000 0 -0.84 8 8
DDIT3 0.015 0.069 -10000 0 -0.33 8 8
RAB5A 0.019 0.005 -10000 0 -10000 0 0
HSPB1 0.001 0.059 0.26 4 -0.27 7 11
p38alpha-beta/HBP1 0.043 0.073 -10000 0 -0.33 7 7
CREB1 0.012 0.073 -10000 0 -0.36 8 8
RAB5/GDP 0.014 0.004 -10000 0 -10000 0 0
EIF4E -0.015 0.062 0.22 2 -0.29 7 9
RPS6KA4 0.015 0.069 -10000 0 -0.33 8 8
PLA2G4A -0.018 0.065 0.2 3 -0.29 7 10
GDI1 0.015 0.07 0.27 1 -0.33 8 9
TP53 -0.005 0.078 -10000 0 -0.39 8 8
RPS6KA5 0.016 0.067 0.27 1 -0.33 7 8
ESR1 -0.06 0.13 -10000 0 -0.25 76 76
HBP1 0.02 0.004 -10000 0 -10000 0 0
MEF2C -0.003 0.087 -10000 0 -0.28 20 20
MEF2A 0.016 0.066 -10000 0 -0.33 7 7
EIF4EBP1 0.012 0.069 -10000 0 -0.34 8 8
KRT19 0.026 0.08 0.25 4 -0.32 9 13
ELK4 0.017 0.074 0.32 3 -0.33 8 11
ATF6 0.015 0.07 0.31 1 -0.33 8 9
ATF1 0.014 0.07 0.22 1 -0.34 8 9
p38alpha-beta/MAPKAPK2 0.042 0.074 -10000 0 -0.33 7 7
p38alpha-beta/MAPKAPK3 0.042 0.073 -10000 0 -0.33 7 7
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.001 0.024 0.093 2 -0.17 1 3
NFATC2 -0.004 0.033 0.093 2 -0.17 7 9
NFATC3 -0.001 0.022 0.093 2 -10000 0 2
CD40LG 0.023 0.1 0.31 11 -10000 0 11
PTGS2 0.031 0.11 0.29 26 -10000 0 26
JUNB 0.02 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.022 0.007 -10000 0 -10000 0 0
JUN 0.022 0.019 -10000 0 -0.29 1 1
mol:Ca2+ 0.002 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.005 -10000 0 -10000 0 0
FOSL1 0.039 0.069 0.29 20 -10000 0 20
CREM 0.02 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.048 0.068 0.25 13 -10000 0 13
FOS -0.001 0.082 -10000 0 -0.29 22 22
IFNG 0.047 0.14 0.29 53 -10000 0 53
AP-1/NFAT1-c-4 0.08 0.13 0.44 14 -10000 0 14
FASLG 0.023 0.1 0.34 11 -10000 0 11
NFAT1-c-4/ICER1 0.002 0.055 0.19 3 -10000 0 3
IL2RA 0.026 0.11 0.33 17 -10000 0 17
FKBP12/FK506 0.014 0.004 -10000 0 -10000 0 0
CSF2 0.025 0.11 0.32 16 -10000 0 16
JunB/Fra1/NFAT1-c-4 0.045 0.065 0.21 20 -10000 0 20
IL4 0.02 0.098 0.26 21 -10000 0 21
IL2 -0.011 0.14 -10000 0 -0.82 8 8
IL3 -0.006 0.12 -10000 0 -0.56 12 12
FKBP1A 0.019 0.005 -10000 0 -10000 0 0
BATF3 0.019 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.005 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.03 0.14 -10000 0 -0.44 18 18
Syndecan-4/Syndesmos 0.015 0.1 -10000 0 -0.73 1 1
positive regulation of JNK cascade -0.057 0.12 -10000 0 -0.41 8 8
Syndecan-4/ADAM12 0.017 0.1 -10000 0 -0.73 1 1
CCL5 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
DNM2 0.02 0.004 -10000 0 -10000 0 0
ITGA5 0.018 0.026 -10000 0 -0.29 2 2
SDCBP 0.02 0.004 -10000 0 -10000 0 0
PLG 0.011 0.036 0.29 3 -0.12 1 4
ADAM12 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.02 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.023 0.11 0.29 3 -0.56 2 5
Syndecan-4/CXCL12/CXCR4 -0.059 0.13 -10000 0 -0.44 8 8
Syndecan-4/Laminin alpha3 0.017 0.1 0.29 1 -0.71 1 2
MDK 0.02 0.004 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.018 0.098 -10000 0 -0.73 1 1
Syndecan-4/Midkine 0.017 0.1 -10000 0 -0.73 1 1
FZD7 0.01 0.054 -10000 0 -0.29 9 9
Syndecan-4/FGFR1/FGF -0.029 0.13 -10000 0 -0.4 10 10
THBS1 -0.03 0.11 -10000 0 -0.29 47 47
integrin-mediated signaling pathway 0.013 0.11 -10000 0 -0.78 1 1
positive regulation of MAPKKK cascade -0.057 0.12 -10000 0 -0.41 8 8
Syndecan-4/TACI 0.018 0.1 0.29 1 -0.73 1 2
CXCR4 0.02 0.002 -10000 0 -10000 0 0
cell adhesion -0.006 0.049 0.18 8 -0.21 8 16
Syndecan-4/Dynamin 0.018 0.1 -10000 0 -0.73 1 1
Syndecan-4/TSP1 0.004 0.11 -10000 0 -0.46 4 4
Syndecan-4/GIPC 0.016 0.1 -10000 0 -0.73 1 1
Syndecan-4/RANTES 0.016 0.1 -10000 0 -0.73 1 1
ITGB1 0.02 0.003 -10000 0 -10000 0 0
LAMA1 0.032 0.066 0.29 15 -0.29 2 17
LAMA3 0.02 0.024 0.29 1 -0.29 1 2
RAC1 0.02 0.003 -10000 0 -10000 0 0
PRKCA 0.004 0.13 0.77 8 -10000 0 8
Syndecan-4/alpha-Actinin 0.015 0.1 -10000 0 -0.73 1 1
TFPI -0.009 0.09 -10000 0 -0.29 27 27
F2 0.02 0.015 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.028 0.02 -10000 0 -0.2 2 2
positive regulation of cell adhesion 0.012 0.1 -10000 0 -0.54 2 2
ACTN1 0.02 0.003 -10000 0 -10000 0 0
TNC 0.011 0.054 -10000 0 -0.29 9 9
Syndecan-4/CXCL12 -0.024 0.12 -10000 0 -0.44 8 8
FGF6 -0.016 0.004 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
CXCL12 -0.17 0.15 -10000 0 -0.29 177 177
TNFRSF13B 0.017 0.02 0.29 1 -10000 0 1
FGF2 -0.074 0.14 -10000 0 -0.29 88 88
FGFR1 -0.021 0.1 -10000 0 -0.29 38 38
Syndecan-4/PI-4-5-P2 -0.002 0.09 0.24 1 -0.72 1 2
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.005 0.051 -10000 0 -0.26 9 9
cell migration -0.016 0.012 -10000 0 -10000 0 0
PRKCD 0.013 0.022 -10000 0 -0.12 1 1
vasculogenesis 0.004 0.11 -10000 0 -0.44 4 4
SDC4 0.009 0.077 0.27 2 -10000 0 2
Syndecan-4/Tenascin C 0.013 0.11 -10000 0 -0.83 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.017 0.1 -10000 0 -0.73 1 1
MMP9 0.061 0.1 0.29 46 -10000 0 46
Rac1/GTP -0.007 0.05 0.18 8 -0.21 8 16
cytoskeleton organization 0.015 0.099 -10000 0 -0.37 5 5
GIPC1 0.02 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.012 0.11 -10000 0 -0.5 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.007 0.085 0.33 1 -0.38 1 2
CRKL -0.02 0.059 0.22 5 -10000 0 5
mol:DAG -0.007 0.062 -10000 0 -0.22 17 17
HRAS -0.015 0.079 0.35 4 -10000 0 4
MAPK8 -0.022 0.056 0.16 15 -0.16 20 35
RAP1A -0.02 0.06 0.21 6 -10000 0 6
GAB1 -0.02 0.059 0.28 3 -10000 0 3
MAPK14 -0.021 0.053 0.16 14 -0.16 17 31
EPO -0.003 0.076 -10000 0 -0.3 18 18
PLCG1 -0.008 0.063 -10000 0 -0.22 17 17
EPOR/TRPC2/IP3 Receptors 0.016 0.017 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.053 -10000 0 -0.17 18 18
GAB1/SHC/GRB2/SOS1 -0.027 0.054 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.014 0.059 -10000 0 -0.21 18 18
IRS2 -0.023 0.062 0.22 5 -10000 0 5
STAT1 -0.006 0.07 -10000 0 -0.23 21 21
STAT5B -0.006 0.069 -10000 0 -0.23 19 19
cell proliferation -0.022 0.064 0.19 17 -0.15 19 36
GAB1/SHIP/PIK3R1/SHP2/SHC -0.034 0.046 -10000 0 -10000 0 0
TEC -0.02 0.056 0.21 4 -10000 0 4
SOCS3 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer) -0.005 0.069 -10000 0 -0.22 21 21
JAK2 0.016 0.017 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.033 0.056 -10000 0 -0.15 18 18
EPO/EPOR 0.014 0.059 -10000 0 -0.21 18 18
LYN 0.019 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.026 0.053 0.19 3 -10000 0 3
elevation of cytosolic calcium ion concentration 0.016 0.017 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.025 0.053 -10000 0 -0.17 18 18
mol:IP3 -0.007 0.062 -10000 0 -0.22 17 17
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.026 0.064 0.25 4 -10000 0 4
SH2B3 0.017 0.017 -10000 0 -10000 0 0
NFKB1 -0.021 0.054 0.16 15 -0.16 17 32
EPO/EPOR (dimer)/JAK2/SOCS3 -0.007 0.055 -10000 0 -0.19 21 21
PTPN6 -0.019 0.053 0.15 18 -10000 0 18
TEC/VAV2/GRB2 -0.029 0.053 0.26 1 -10000 0 1
EPOR 0.017 0.017 -10000 0 -10000 0 0
INPP5D 0.018 0.007 -10000 0 -10000 0 0
mol:GDP -0.028 0.054 0.18 1 -10000 0 1
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.004 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.027 0.052 0.19 3 -10000 0 3
VAV2 -0.021 0.057 0.28 2 -10000 0 2
CBL -0.018 0.052 0.21 4 -10000 0 4
SHC/Grb2/SOS1 0.008 0.047 -10000 0 -10000 0 0
STAT5A -0.006 0.069 -10000 0 -0.23 19 19
GRB2 0.02 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.006 0.07 -10000 0 -0.3 3 3
LYN/PLCgamma2 0.028 0.011 -10000 0 -10000 0 0
PTPN11 0.021 0.001 -10000 0 -10000 0 0
BTK -0.021 0.06 0.21 6 -10000 0 6
BCL2 -0.019 0.12 0.33 1 -0.59 7 8
FAS signaling pathway (CD95)

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
SPTAN1 -0.011 0.042 0.17 6 -0.18 11 17
RFC1 -0.008 0.032 0.16 4 -0.18 6 10
PRKDC -0.005 0.052 0.19 12 -0.18 10 22
RIPK1 0.018 0.009 -10000 0 -10000 0 0
CASP7 -0.004 0.098 -10000 0 -0.58 8 8
FASLG/FAS/FADD/FAF1 0.005 0.029 0.15 1 -0.18 1 2
MAP2K4 0.007 0.094 0.28 1 -0.32 11 12
mol:ceramide 0.009 0.036 -10000 0 -10000 0 0
GSN -0.011 0.042 0.17 6 -0.18 11 17
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.041 -10000 0 -0.3 1 1
FAS 0.02 0.005 -10000 0 -10000 0 0
BID -0.021 0.009 -10000 0 -10000 0 0
MAP3K1 0.023 0.11 0.26 3 -0.4 10 13
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
RB1 -0.012 0.036 -10000 0 -0.18 10 10
CFLAR 0.018 0.009 -10000 0 -10000 0 0
HGF/MET 0.013 0.072 0.21 1 -0.18 35 36
ARHGDIB -0.01 0.044 0.22 3 -0.18 11 14
FADD 0.02 0.006 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.042 0.18 11 -0.17 6 17
NFKB1 0.011 0.079 -10000 0 -0.56 5 5
MAPK8 0.002 0.091 0.25 2 -0.56 2 4
DFFA -0.011 0.037 -10000 0 -0.18 10 10
DNA fragmentation during apoptosis -0.011 0.037 0.14 4 -0.18 10 14
FAS/FADD/MET 0.037 0.015 -10000 0 -10000 0 0
CFLAR/RIP1 0.026 0.014 -10000 0 -10000 0 0
FAIM3 0.018 0.008 -10000 0 -10000 0 0
FAF1 0.021 0.004 -10000 0 -10000 0 0
PARP1 -0.011 0.04 0.16 5 -0.18 11 16
DFFB -0.011 0.037 0.14 4 -0.18 10 14
CHUK 0.004 0.066 -10000 0 -0.52 4 4
FASLG 0.023 0.028 0.29 3 -10000 0 3
FAS/FADD 0.028 0.01 -10000 0 -10000 0 0
HGF -0.016 0.1 0.29 1 -0.29 34 35
LMNA -0.01 0.04 0.22 4 -0.17 6 10
CASP6 -0.01 0.032 0.14 4 -0.18 7 11
CASP10 0.02 0.006 -10000 0 -10000 0 0
CASP3 0 0.021 0.18 4 -10000 0 4
PTPN13 0.017 0.026 -10000 0 -0.29 2 2
CASP8 -0.019 0.007 -10000 0 -10000 0 0
IL6 0.02 0.083 -10000 0 -0.53 2 2
MET 0.02 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.015 0.034 -10000 0 -0.17 10 10
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.036 -10000 0 -10000 0 0
activation of caspase activity by cytochrome c -0.021 0.009 -10000 0 -10000 0 0
PAK2 0.05 0.1 0.22 76 -0.18 4 80
BCL2 0.014 0.04 -10000 0 -0.29 5 5
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.025 0.077 -10000 0 -0.21 33 33
FZD6 0.019 0.005 -10000 0 -10000 0 0
WNT6 0.011 0.048 -10000 0 -0.29 7 7
WNT4 0.016 0.036 -10000 0 -0.29 4 4
FZD3 0.009 0.054 -10000 0 -0.29 9 9
WNT5A 0.019 0.006 -10000 0 -10000 0 0
WNT11 0.012 0.053 0.29 1 -0.29 8 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.085 0.089 -10000 0 -0.45 3 3
RAD9A 0.02 0.003 -10000 0 -10000 0 0
AP1 0.012 0.062 -10000 0 -0.2 22 22
IFNAR2 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.039 0.075 -10000 0 -0.32 6 6
ER alpha/Oestrogen -0.054 0.098 -10000 0 -0.2 95 95
NFX1/SIN3/HDAC complex 0.01 0.03 -10000 0 -0.18 1 1
EGF 0.003 0.066 -10000 0 -0.29 14 14
SMG5 0.019 0.005 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.029 0.007 -10000 0 -10000 0 0
TERT/c-Abl -0.089 0.086 -10000 0 -0.44 3 3
SAP18 0.02 0.004 -10000 0 -10000 0 0
MRN complex 0.034 0.017 -10000 0 -10000 0 0
WT1 -0.24 0.12 -10000 0 -0.29 240 240
WRN 0.019 0.006 -10000 0 -10000 0 0
SP1 0.02 0.003 -10000 0 -10000 0 0
SP3 0.02 0.003 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.083 0.087 -10000 0 -0.41 3 3
Mad/Max 0.03 0.006 -10000 0 -10000 0 0
TERT -0.086 0.09 -10000 0 -0.46 3 3
CCND1 -0.079 0.083 -10000 0 -10000 0 0
MAX 0.02 0.003 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.001 -10000 0 -10000 0 0
TERF2 -0.009 0.03 -10000 0 -10000 0 0
PTGES3 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
Telomerase/911 0.008 0.041 -10000 0 -10000 0 0
CDKN1B 0.001 0.042 -10000 0 -10000 0 0
RAD1 0.018 0.007 -10000 0 -10000 0 0
XRCC5 0.019 0.006 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
TRF2/PARP2 0.032 0.016 -10000 0 -10000 0 0
UBE3A 0.02 0.004 -10000 0 -10000 0 0
JUN 0.019 0.018 -10000 0 -0.29 1 1
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.003 -10000 0 -10000 0 0
FOS -0.003 0.082 -10000 0 -0.29 22 22
IFN-gamma/IRF1 0.062 0.071 0.22 50 -10000 0 50
PARP2 0.02 0.003 -10000 0 -10000 0 0
BLM 0.085 0.12 0.29 69 -10000 0 69
Telomerase -0.014 0.062 -10000 0 -0.42 2 2
IRF1 0.02 0.005 -10000 0 -10000 0 0
ESR1 -0.082 0.14 -10000 0 -0.29 95 95
KU/TER 0.027 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.019 0.028 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.012 0.039 -10000 0 -0.23 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.012 0.04 -10000 0 -0.23 2 2
HDAC1 0.021 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
ATM 0.008 0.009 -10000 0 -10000 0 0
SMAD3 -0.018 0.004 -10000 0 -10000 0 0
ABL1 0.02 0.002 -10000 0 -10000 0 0
MXD1 0.02 0.003 -10000 0 -10000 0 0
MRE11A 0.018 0.007 -10000 0 -10000 0 0
HUS1 0.02 0.002 -10000 0 -10000 0 0
RPS6KB1 0.02 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.084 0.1 -10000 0 -0.44 6 6
NR2F2 -0.006 0.085 -10000 0 -0.29 24 24
MAPK3 -0.018 0.004 -10000 0 -10000 0 0
MAPK1 -0.018 0.004 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.003 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.008 0.009 -10000 0 -10000 0 0
NBN 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.018 0.026 -10000 0 -0.29 2 2
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.052 -10000 0 -0.2 15 15
MYC 0.015 0.036 -10000 0 -0.29 4 4
IL2 0.018 0.004 -10000 0 -10000 0 0
KU 0.027 0.01 -10000 0 -10000 0 0
RAD50 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.02 0.004 -10000 0 -10000 0 0
TRF2/BLM 0.073 0.079 0.21 67 -10000 0 67
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.082 0.09 -10000 0 -0.42 3 3
SP1/HDAC2 0.03 0.007 -10000 0 -10000 0 0
PINX1 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1A -0.084 0.088 -10000 0 -0.41 3 3
Smad3/Myc -0.021 0.02 -10000 0 -0.17 4 4
911 complex 0.034 0.016 -10000 0 -10000 0 0
IFNG 0.069 0.1 0.3 51 -10000 0 51
Telomerase/PinX1 -0.085 0.085 -10000 0 -0.41 3 3
Telomerase/AKT1/mTOR/p70S6K -0.035 0.072 -10000 0 -0.31 11 11
SIN3B 0.02 0.003 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.08 0.086 -10000 0 -0.42 3 3
response to DNA damage stimulus -0.011 0.036 -10000 0 -0.1 40 40
MRN complex/TRF2/Rap1 0.046 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.03 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.083 0.088 -10000 0 -0.41 3 3
E2F1 0.024 0.04 0.29 6 -10000 0 6
ZNFX1 0.019 0.005 -10000 0 -10000 0 0
PIF1 0.025 0.036 0.29 5 -10000 0 5
NCL 0.018 0.007 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.017 0.006 -10000 0 -10000 0 0
SMARCC1 0.003 0.011 -10000 0 -10000 0 0
REL 0.018 0.011 -10000 0 -10000 0 0
HDAC7 -0.009 0.086 0.19 2 -0.25 8 10
JUN 0.019 0.019 -10000 0 -0.29 1 1
EP300 0.02 0.003 -10000 0 -10000 0 0
KAT2B 0.02 0.005 -10000 0 -10000 0 0
KAT5 0.02 0.004 -10000 0 -10000 0 0
MAPK14 -0.005 0.022 0.14 1 -10000 0 1
FOXO1 0.017 0.026 -10000 0 -0.29 2 2
T-DHT/AR 0.021 0.12 0.23 12 -0.26 8 20
MAP2K6 0.021 0.021 0.29 1 -10000 0 1
BRM/BAF57 0.03 0.01 -10000 0 -10000 0 0
MAP2K4 0.018 0.015 -10000 0 -10000 0 0
SMARCA2 0.02 0.006 -10000 0 -10000 0 0
PDE9A -0.019 0.25 -10000 0 -0.75 26 26
NCOA2 0.016 0.036 -10000 0 -0.29 4 4
CEBPA 0.018 0.009 -10000 0 -10000 0 0
EHMT2 0.02 0.005 -10000 0 -10000 0 0
cell proliferation 0.025 0.13 0.32 19 -0.32 6 25
NR0B1 0.013 0.056 0.29 10 -10000 0 10
EGR1 0.012 0.051 -10000 0 -0.29 8 8
RXRs/9cRA 0.035 0.02 0.2 1 -0.16 1 2
AR/RACK1/Src -0.008 0.079 0.21 11 -10000 0 11
AR/GR -0.066 0.11 0.29 1 -0.21 72 73
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
PKN1 0.02 0.004 -10000 0 -10000 0 0
RCHY1 0.02 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.006 0.023 -10000 0 -0.2 1 1
T-DHT/AR/TIF2/CARM1 -0.014 0.077 0.28 1 -0.32 2 3
SRC -0.009 0.045 0.2 9 -0.15 1 10
NR3C1 0.02 0.004 -10000 0 -10000 0 0
KLK3 0.057 0.12 0.4 4 -10000 0 4
APPBP2 0.021 0.015 -10000 0 -10000 0 0
TRIM24 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.018 0.065 0.19 1 -0.29 1 2
TMPRSS2 0.084 0.17 0.46 15 -0.53 5 20
RXRG 0.008 0.03 0.29 1 -0.29 1 2
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.021 0.002 -10000 0 -10000 0 0
RXRB 0.02 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.004 -10000 0 -10000 0 0
NR2C2 0.017 0.026 -10000 0 -0.29 2 2
KLK2 -0.004 0.084 0.32 7 -10000 0 7
AR -0.062 0.095 0.13 1 -0.2 91 92
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.018 0.012 -10000 0 -10000 0 0
SRY -0.001 0.005 -10000 0 -0.025 11 11
GATA2 0.009 0.048 -10000 0 -0.29 7 7
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.14 0.14 0.3 134 -10000 0 134
T-DHT/AR/RACK1/Src -0.008 0.078 0.21 12 -10000 0 12
positive regulation of transcription 0.009 0.048 -10000 0 -0.29 7 7
DNAJA1 0.021 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.003 -10000 0 -10000 0 0
NCOA1 0.025 0.02 -10000 0 -10000 0 0
SPDEF 0.054 0.12 0.3 45 -0.29 8 53
T-DHT/AR/TIF2 -0.023 0.07 0.18 1 -0.27 7 8
T-DHT/AR/Hsp90 -0.018 0.065 0.18 2 -0.29 1 3
GSK3B 0.016 0.013 -10000 0 -10000 0 0
NR2C1 0.019 0.009 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.031 0.24 1 -0.16 1 2
SIRT1 0.02 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.012 -10000 0 -10000 0 0
POU2F1 0.05 0.066 -10000 0 -0.12 1 1
T-DHT/AR/DAX-1 -0.013 0.074 0.21 8 -0.29 1 9
CREBBP 0.02 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.045 0.068 0.22 2 -10000 0 2
TBX21 0.029 0.16 -10000 0 -1 1 1
B2M 0.02 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.028 -10000 0 -10000 0 0
IL12RB1 0.014 0.028 -10000 0 -10000 0 0
GADD45B 0.009 0.16 -10000 0 -0.59 6 6
IL12RB2 0.074 0.12 0.29 61 -10000 0 61
GADD45G -0.05 0.33 -10000 0 -0.99 28 28
natural killer cell activation 0 0.014 0.057 3 -0.046 2 5
RELB 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL18 0.014 0.036 0.3 3 -10000 0 3
IL2RA 0.027 0.042 0.29 7 -10000 0 7
IFNG 0.067 0.1 0.29 51 -10000 0 51
STAT3 (dimer) 0.017 0.15 -10000 0 -0.55 4 4
HLA-DRB5 -0.001 0.006 -10000 0 -0.022 19 19
FASLG 0.044 0.16 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.035 0.14 -10000 0 -0.53 3 3
CD4 0.016 0.015 -10000 0 -10000 0 0
SOCS1 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.007 0.025 2 -0.024 21 23
CD3D 0.015 0.024 0.32 1 -10000 0 1
CD3E 0.014 0.016 -10000 0 -10000 0 0
CD3G 0.015 0.024 0.32 1 -10000 0 1
IL12Rbeta2/JAK2 0.062 0.084 0.22 56 -10000 0 56
CCL3 0.032 0.15 -10000 0 -10000 0 0
CCL4 0.032 0.15 -10000 0 -10000 0 0
HLA-A 0 0.002 0.025 2 -10000 0 2
IL18/IL18R 0.034 0.053 0.22 3 -0.18 1 4
NOS2 0.009 0.22 -10000 0 -0.99 9 9
IL12/IL12R/TYK2/JAK2/SPHK2 0.042 0.068 0.2 1 -10000 0 1
IL1R1 0.024 0.17 -10000 0 -1 3 3
IL4 -0.007 0.027 -10000 0 -10000 0 0
JAK2 0.014 0.027 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.006 0.023 2 -0.021 19 21
TCR/CD3/MHC I/CD8 -0.028 0.096 0.28 2 -0.28 35 37
RAB7A 0.019 0.22 -10000 0 -0.67 8 8
lysosomal transport 0.02 0.21 -10000 0 -0.64 8 8
FOS -0.06 0.3 -10000 0 -1 24 24
STAT4 (dimer) 0.015 0.18 -10000 0 -0.6 5 5
STAT5A (dimer) 0.065 0.17 0.48 4 -0.53 3 7
GZMA 0.027 0.15 -10000 0 -1.1 1 1
GZMB 0.037 0.15 -10000 0 -10000 0 0
HLX 0.019 0.005 -10000 0 -10000 0 0
LCK 0.027 0.15 -10000 0 -0.56 3 3
TCR/CD3/MHC II/CD4 -0.015 0.077 -10000 0 -0.26 22 22
IL2/IL2R 0.054 0.032 0.21 10 -10000 0 10
MAPK14 -0.018 0.23 -10000 0 -0.77 11 11
CCR5 0.002 0.16 -10000 0 -0.58 2 2
IL1B 0.064 0.11 0.29 51 -10000 0 51
STAT6 0.028 0.068 -10000 0 -0.36 1 1
STAT4 0.02 0.004 -10000 0 -10000 0 0
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
NFKB2 0.02 0.003 -10000 0 -10000 0 0
IL12B 0.017 0.043 0.3 4 -10000 0 4
CD8A 0.022 0.018 0.32 1 -10000 0 1
CD8B 0.024 0.041 0.3 5 -0.29 1 6
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.045 0.068 -10000 0 -0.22 2 2
IL2RB 0.02 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.17 -10000 0 -0.56 5 5
IL2RG 0.023 0.028 0.29 3 -10000 0 3
IL12 0.024 0.053 0.22 11 -10000 0 11
STAT5A 0.02 0.002 -10000 0 -10000 0 0
CD247 0.016 0.015 -10000 0 -10000 0 0
IL2 -0.001 0.019 -10000 0 -10000 0 0
SPHK2 0.02 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.017 0.051 0.3 7 -10000 0 7
IL12/IL12R/TYK2/JAK2 0.023 0.15 -10000 0 -0.58 3 3
MAP2K3 -0.021 0.24 -10000 0 -0.81 11 11
RIPK2 0.02 0.004 -10000 0 -10000 0 0
MAP2K6 -0.013 0.22 -10000 0 -0.71 11 11
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.006 -10000 0 -0.025 21 21
IL18RAP 0.014 0.022 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.021 0.036 -10000 0 -10000 0 0
EOMES -0.038 0.14 -10000 0 -0.53 19 19
STAT1 (dimer) 0.044 0.17 0.46 4 -0.55 4 8
T cell proliferation -0.002 0.16 -10000 0 -0.5 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.013 0.028 -10000 0 -0.29 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.17 -10000 0 -0.5 17 17
ATF2 -0.018 0.22 -10000 0 -0.72 11 11
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.068 0.061 0.2 48 -10000 0 48
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.05 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.017 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.019 0.036 -10000 0 -10000 0 0
CaM/Ca2+ 0.063 0.055 -10000 0 -10000 0 0
RAP1A 0.021 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.002 0.049 0.18 2 -10000 0 2
AKT1 0.046 0.088 0.23 16 -10000 0 16
MAP2K1 -0.012 0.04 0.16 2 -10000 0 2
MAP3K11 -0.006 0.044 0.18 2 -10000 0 2
IFNGR1 0.021 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.073 0.15 -10000 0 -0.3 80 80
Rap1/GTP -0.025 0.026 -10000 0 -10000 0 0
CRKL/C3G 0.03 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.075 0.063 -10000 0 -10000 0 0
CEBPB 0.01 0.065 -10000 0 -0.32 3 3
STAT3 0.02 0.002 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.069 0.1 -10000 0 -0.72 3 3
STAT1 -0.007 0.042 0.18 2 -10000 0 2
CALM1 0.02 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.066 0.11 0.3 51 -10000 0 51
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.007 0.047 0.18 2 -10000 0 2
CEBPB/PTGES2/Cbp/p300 0.016 0.043 -10000 0 -0.23 2 2
mol:Ca2+ 0.064 0.058 0.19 48 -10000 0 48
MAPK3 0.002 0.074 -10000 0 -0.71 2 2
STAT1 (dimer) -0.023 0.049 -10000 0 -10000 0 0
MAPK1 -0.002 0.083 -10000 0 -0.69 3 3
JAK2 0.02 0.009 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
JAK1 0.02 0.01 -10000 0 -10000 0 0
CAMK2D 0.02 0.003 -10000 0 -10000 0 0
DAPK1 0.008 0.059 0.24 1 -0.52 1 2
SMAD7 0.006 0.043 0.15 4 -10000 0 4
CBL/CRKL/C3G -0.006 0.049 0.18 2 -10000 0 2
PI3K 0.042 0.052 -10000 0 -10000 0 0
IFNG 0.066 0.11 0.3 51 -10000 0 51
apoptosis 0.01 0.062 -10000 0 -0.36 4 4
CAMK2G 0.02 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.002 -10000 0 -10000 0 0
CAMK2A -0.074 0.14 -10000 0 -0.29 87 87
CAMK2B 0.041 0.072 0.29 22 -10000 0 22
FRAP1 0.04 0.082 0.21 19 -10000 0 19
PRKCD 0.045 0.089 0.23 17 -10000 0 17
RAP1B 0.02 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.019 0.036 -10000 0 -10000 0 0
PTPN2 0.02 0.004 -10000 0 -10000 0 0
EP300 0.02 0.003 -10000 0 -10000 0 0
IRF1 -0.01 0.046 0.26 3 -10000 0 3
STAT1 (dimer)/PIASy -0.008 0.046 0.18 2 -10000 0 2
SOCS1 0.007 0.11 -10000 0 -1 3 3
mol:GDP -0.006 0.046 0.17 2 -10000 0 2
CASP1 0.005 0.043 0.17 4 -10000 0 4
PTGES2 0.021 0.002 -10000 0 -10000 0 0
IRF9 0.002 0.029 0.15 1 -10000 0 1
mol:PI-3-4-5-P3 0.031 0.04 -10000 0 -10000 0 0
RAP1/GDP -0.019 0.039 -10000 0 -10000 0 0
CBL -0.004 0.041 0.18 2 -10000 0 2
MAP3K1 -0.006 0.043 0.18 2 -10000 0 2
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.019 0.036 -10000 0 -10000 0 0
PTPN11 -0.002 0.045 0.15 16 -10000 0 16
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.002 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.018 0.004 -10000 0 -10000 0 0
MAP4K4 -0.003 0.049 0.22 1 -0.26 1 2
BAG4 0.019 0.005 -10000 0 -10000 0 0
PKC zeta/ceramide 0.008 0.041 -10000 0 -0.19 11 11
NFKBIA 0.02 0.003 -10000 0 -10000 0 0
BIRC3 0.017 0.018 0.29 1 -10000 0 1
BAX 0.002 0.044 -10000 0 -0.35 4 4
RIPK1 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.003 0.087 0.65 5 -10000 0 5
BAD -0.007 0.036 0.2 1 -0.18 10 11
SMPD1 -0.001 0.063 0.16 10 -0.23 11 21
RB1 -0.009 0.036 -10000 0 -0.18 11 11
FADD/Caspase 8 -0.007 0.076 0.21 3 -0.33 7 10
MAP2K4 -0.012 0.038 0.18 2 -0.18 11 13
NSMAF 0.02 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.037 0.18 2 -0.18 10 12
EGF 0.003 0.066 -10000 0 -0.29 14 14
mol:ceramide -0.003 0.039 -10000 0 -0.19 11 11
MADD 0.02 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.006 -10000 0 -10000 0 0
ASAH1 0.019 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.009 0.036 -10000 0 -0.18 11 11
cell proliferation -0.049 0.066 0.16 2 -0.26 8 10
BID -0.003 0.12 -10000 0 -0.6 7 7
MAP3K1 -0.007 0.04 0.19 2 -0.18 11 13
EIF2A 0.039 0.091 0.17 83 -0.18 6 89
TRADD 0.02 0.004 -10000 0 -10000 0 0
CRADD 0.021 0.001 -10000 0 -10000 0 0
MAPK3 -0.013 0.037 0.17 2 -0.17 10 12
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.037 0.17 2 -0.17 11 13
Cathepsin D/ceramide 0.009 0.041 -10000 0 -0.19 11 11
FADD 0 0.046 0.22 1 -0.26 1 2
KSR1 -0.008 0.037 0.2 1 -0.19 10 11
MAPK8 -0.012 0.052 -10000 0 -0.18 12 12
PRKRA -0.005 0.046 0.19 6 -0.19 11 17
PDGFA 0.02 0.003 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
IGF1 -0.079 0.14 -10000 0 -0.29 93 93
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.003 0.039 -10000 0 -0.19 11 11
CTSD 0.02 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.052 0.07 0.18 2 -0.28 8 10
PRKCD 0.019 0.006 -10000 0 -10000 0 0
PRKCZ 0.02 0.004 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.03 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.001 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0 0.043 0.25 1 -10000 0 1
TNFR1A/BAG4/TNF-alpha 0.038 0.025 0.21 4 -10000 0 4
mol:Sphingosine-1-phosphate -0.018 0.004 -10000 0 -10000 0 0
MAP2K1 -0.015 0.038 0.16 4 -0.18 10 14
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
CYCS 0.002 0.039 0.13 3 -0.18 4 7
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.01 -10000 0 -10000 0 0
EIF2AK2 -0.005 0.049 0.18 11 -0.18 9 20
TNF-alpha/TNFR1A/FAN 0.038 0.025 0.21 4 -10000 0 4
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.1 -10000 0 -0.39 15 15
MAP2K2 -0.016 0.035 0.17 2 -0.18 10 12
SMPD3 0.003 0.052 0.19 3 -0.26 6 9
TNF 0.023 0.032 0.29 4 -10000 0 4
PKC zeta/PAR4 0.03 0.006 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.012 0.043 0.16 12 -0.12 8 20
NF kappa B1/RelA/I kappa B alpha 0.055 0.02 -10000 0 -10000 0 0
AIFM1 0.002 0.039 0.13 4 -0.18 4 8
BCL2 0.014 0.04 -10000 0 -0.29 5 5
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.013 0.098 0.22 2 -0.32 15 17
BAG4 0.019 0.005 -10000 0 -10000 0 0
BAD -0.007 0.041 0.13 6 -0.14 7 13
NFKBIA 0.02 0.003 -10000 0 -10000 0 0
BIRC3 0.017 0.018 0.29 1 -10000 0 1
BAX -0.004 0.048 0.16 9 -0.14 8 17
EnzymeConsortium:3.1.4.12 -0.001 0.026 0.075 6 -0.079 10 16
IKBKB -0.015 0.096 0.2 2 -0.4 7 9
MAP2K2 -0.012 0.04 0.21 3 -0.19 2 5
MAP2K1 -0.011 0.044 0.17 6 -0.19 2 8
SMPD1 -0.005 0.035 0.096 2 -0.14 11 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.011 0.1 0.24 4 -0.36 11 15
MAP2K4 -0.008 0.038 0.15 4 -0.18 2 6
protein ubiquitination -0.014 0.1 0.21 6 -0.42 7 13
EnzymeConsortium:2.7.1.37 -0.013 0.044 0.19 4 -0.2 2 6
response to UV 0 0 0.002 5 -0.002 1 6
RAF1 -0.009 0.042 0.19 4 -0.19 2 6
CRADD 0.021 0.001 -10000 0 -10000 0 0
mol:ceramide -0.003 0.041 0.11 6 -0.13 12 18
I-kappa-B-alpha/RELA/p50/ubiquitin 0.027 0.006 -10000 0 -10000 0 0
MADD 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 -0.006 0.041 0.13 6 -0.14 7 13
TRADD 0.02 0.004 -10000 0 -10000 0 0
RELA/p50 0.02 0.003 -10000 0 -10000 0 0
MAPK3 -0.01 0.043 0.2 3 -0.22 1 4
MAPK1 -0.01 0.043 0.21 3 -0.19 2 5
p50/RELA/I-kappa-B-alpha 0.029 0.006 -10000 0 -10000 0 0
FADD -0.008 0.094 0.2 3 -0.33 12 15
KSR1 -0.006 0.044 0.17 5 -0.16 4 9
MAPK8 -0.014 0.037 0.14 3 -0.2 1 4
TRAF2 0.02 0.003 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.017 0.093 0.2 2 -0.4 7 9
TNF R/SODD 0.027 0.01 -10000 0 -10000 0 0
TNF 0.023 0.032 0.29 4 -10000 0 4
CYCS -0.003 0.047 0.16 6 -0.17 3 9
IKBKG -0.012 0.1 0.24 5 -0.4 7 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.009 0.1 0.25 1 -0.32 17 18
RELA 0.02 0.003 -10000 0 -10000 0 0
RIPK1 0.02 0.005 -10000 0 -10000 0 0
AIFM1 -0.004 0.046 0.16 6 -0.17 3 9
TNF/TNF R/SODD 0.038 0.025 0.21 4 -10000 0 4
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 -0.016 0.16 -10000 0 -0.57 18 18
NSMAF -0.008 0.1 0.21 12 -0.31 16 28
response to hydrogen peroxide 0 0 0.002 5 -0.002 1 6
BCL2 0.014 0.04 -10000 0 -0.29 5 5
TCGA08_rtk_signaling

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.046 0.13 -10000 0 -0.29 62 62
HRAS 0.02 0.005 -10000 0 -10000 0 0
EGFR 0.018 0.026 -10000 0 -0.29 2 2
AKT 0.024 0.089 0.25 8 -0.23 10 18
FOXO3 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.004 -10000 0 -10000 0 0
FOXO1 0.017 0.026 -10000 0 -0.29 2 2
AKT3 0.004 0.066 -10000 0 -0.29 14 14
FOXO4 0.02 0.002 -10000 0 -10000 0 0
MET 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PIK3CB 0.015 0.009 -10000 0 -10000 0 0
NRAS 0.021 0.002 -10000 0 -10000 0 0
PIK3CG 0.019 0.019 -10000 0 -0.29 1 1
PIK3R3 0.02 0.002 -10000 0 -10000 0 0
PIK3R2 0.02 0.003 -10000 0 -10000 0 0
NF1 0.02 0.004 -10000 0 -10000 0 0
RAS -0.009 0.054 0.22 1 -0.12 49 50
ERBB2 0.019 0.005 -10000 0 -10000 0 0
proliferation/survival/translation -0.049 0.089 0.26 7 -0.22 8 15
PI3K 0.022 0.069 0.23 10 -0.15 2 12
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
KRAS 0.019 0.005 -10000 0 -10000 0 0
FOXO 0.047 0.06 0.24 8 -10000 0 8
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.019 0.005 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.032 0.053 0.31 9 -10000 0 9
NFATC2 0.068 0.058 0.37 1 -10000 0 1
NFATC3 0.034 0.031 -10000 0 -0.29 1 1
CD40LG 0.1 0.12 0.4 5 -0.53 1 6
ITCH 0.022 0.052 -10000 0 -10000 0 0
CBLB 0.02 0.05 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.062 0.11 0.43 10 -10000 0 10
JUNB 0.02 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.062 0.068 0.17 82 -10000 0 82
T cell anergy 0.047 0.077 0.22 15 -10000 0 15
TLE4 0.029 0.055 -10000 0 -0.52 1 1
Jun/NFAT1-c-4/p21SNFT 0.13 0.12 0.49 2 -0.55 2 4
AP-1/NFAT1-c-4 0.19 0.19 0.6 10 -0.58 1 11
IKZF1 0.031 0.045 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.03 0.11 -10000 0 -10000 0 0
AP-1/NFAT1 0.088 0.1 0.31 10 -0.29 2 12
CALM1 0.041 0.032 -10000 0 -10000 0 0
EGR2 0.041 0.089 -10000 0 -0.73 2 2
EGR3 0.04 0.074 -10000 0 -0.56 1 1
NFAT1/FOXP3 0.068 0.085 0.37 11 -10000 0 11
EGR1 0.012 0.051 -10000 0 -0.29 8 8
JUN 0.032 0.023 -10000 0 -0.29 1 1
EGR4 0.028 0.045 0.29 8 -10000 0 8
mol:Ca2+ 0.022 0.031 -10000 0 -10000 0 0
GBP3 0.031 0.045 -10000 0 -10000 0 0
FOSL1 0.039 0.069 0.29 20 -10000 0 20
NFAT1-c-4/MAF/IRF4 0.095 0.099 -10000 0 -0.64 1 1
DGKA 0.031 0.045 -10000 0 -10000 0 0
CREM 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.08 0.11 -10000 0 -0.67 1 1
CTLA4 0.03 0.072 0.38 8 -10000 0 8
NFAT1-c-4 (dimer)/EGR1 0.091 0.1 -10000 0 -0.67 1 1
NFAT1-c-4 (dimer)/EGR4 0.1 0.099 -10000 0 -0.67 1 1
FOS 0.016 0.074 -10000 0 -0.28 16 16
IFNG 0.068 0.12 0.37 3 -0.6 1 4
T cell activation 0.038 0.088 -10000 0 -10000 0 0
MAF 0.015 0.036 -10000 0 -0.29 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.043 0.074 0.65 2 -10000 0 2
TNF 0.053 0.089 0.38 1 -0.61 1 2
FASLG 0.06 0.097 -10000 0 -0.72 1 1
TBX21 0.037 0.041 -10000 0 -0.29 1 1
BATF3 0.019 0.005 -10000 0 -10000 0 0
PRKCQ 0.021 0.007 -10000 0 -10000 0 0
PTPN1 0.031 0.045 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 0.095 0.094 -10000 0 -0.67 1 1
GATA3 0.045 0.08 0.29 27 -10000 0 27
T-helper 1 cell differentiation 0.069 0.12 0.37 3 -0.59 1 4
IL2RA 0.074 0.12 0.47 8 -10000 0 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.03 0.044 -10000 0 -10000 0 0
E2F1 0.025 0.04 0.3 6 -10000 0 6
PPARG 0 0.075 -10000 0 -0.29 18 18
SLC3A2 0.031 0.045 -10000 0 -10000 0 0
IRF4 0.019 0.025 0.29 1 -0.29 1 2
PTGS2 0.1 0.13 0.42 16 -0.53 1 17
CSF2 0.1 0.13 0.44 10 -0.53 1 11
JunB/Fra1/NFAT1-c-4 0.11 0.11 0.42 2 -0.64 1 3
IL4 0.03 0.11 -10000 0 -10000 0 0
IL5 0.095 0.12 0.41 4 -0.53 1 5
IL2 0.038 0.089 -10000 0 -10000 0 0
IL3 0.014 0.057 -10000 0 -0.41 4 4
RNF128 0.07 0.13 0.27 83 -10000 0 83
NFATC1 0.043 0.074 -10000 0 -0.66 2 2
CDK4 -0.029 0.06 -10000 0 -10000 0 0
PTPRK 0.031 0.045 -10000 0 -10000 0 0
IL8 0.19 0.18 0.41 54 -0.48 1 55
POU2F1 0.019 0.005 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.008 -10000 0 -10000 0 0
HSPA8 0.017 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.03 0.11 -10000 0 -0.19 84 84
AKT1 0.021 0.005 -10000 0 -10000 0 0
GSC 0 0.083 0.4 1 -0.43 3 4
NKX2-5 -0.003 0.013 -10000 0 -10000 0 0
muscle cell differentiation 0.005 0.1 0.42 7 -10000 0 7
SMAD2-3/SMAD4/SP1 0.035 0.06 -10000 0 -10000 0 0
SMAD4 0.013 0.028 -10000 0 -10000 0 0
CBFB 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.038 0.021 0.21 2 -10000 0 2
SMAD3/SMAD4/VDR 0.044 0.043 -10000 0 -10000 0 0
MYC 0.014 0.037 -10000 0 -0.29 4 4
CDKN2B -0.008 0.082 -10000 0 -0.51 4 4
AP1 0.005 0.052 -10000 0 -0.31 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.012 0.064 -10000 0 -0.28 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.004 0.047 -10000 0 -0.22 4 4
SP3 0.02 0.003 -10000 0 -10000 0 0
CREB1 0.019 0.006 -10000 0 -10000 0 0
FOXH1 0.028 0.065 0.29 15 -10000 0 15
SMAD3/SMAD4/GR 0.03 0.035 -10000 0 -10000 0 0
GATA3 0.046 0.08 0.3 27 -10000 0 27
SKI/SIN3/HDAC complex/NCoR1 -0.005 0.049 -10000 0 -0.31 2 2
MEF2C/TIF2 -0.03 0.08 0.19 7 -0.3 18 25
endothelial cell migration 0.004 0.12 0.54 11 -10000 0 11
MAX 0.02 0.004 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.001 -10000 0 -10000 0 0
RUNX2 0.02 0.004 -10000 0 -10000 0 0
RUNX3 0.021 0.016 0.29 1 -10000 0 1
RUNX1 0.02 0.004 -10000 0 -10000 0 0
CTBP1 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.02 0.005 -10000 0 -10000 0 0
VDR 0.02 0.003 -10000 0 -10000 0 0
CDKN1A -0.006 0.052 -10000 0 -10000 0 0
KAT2B 0.019 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.036 0.058 0.22 10 -10000 0 10
DCP1A 0.019 0.006 -10000 0 -10000 0 0
SKI 0.02 0.004 -10000 0 -10000 0 0
SERPINE1 -0.004 0.12 -10000 0 -0.55 11 11
SMAD3/SMAD4/ATF2 0.031 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.029 0.035 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.035 0.018 -10000 0 -10000 0 0
JUN -0.023 0.045 -10000 0 -0.31 1 1
SMAD3/SMAD4/IRF7 0.031 0.035 -10000 0 -10000 0 0
TFE3 0.021 0.006 -10000 0 -10000 0 0
COL1A2 -0.006 0.17 -10000 0 -0.57 21 21
mesenchymal cell differentiation -0.029 0.035 -10000 0 -10000 0 0
DLX1 0.054 0.099 0.29 42 -10000 0 42
TCF3 0.019 0.005 -10000 0 -10000 0 0
FOS 0.015 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.03 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.038 0.014 -10000 0 -10000 0 0
ZBTB17 0.019 0.007 -10000 0 -10000 0 0
LAMC1 -0.016 0.03 0.19 3 -10000 0 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.029 0.035 -10000 0 -10000 0 0
IRF7 0.02 0.005 -10000 0 -10000 0 0
ESR1 -0.075 0.15 -10000 0 -0.29 92 92
HNF4A 0.013 0.05 0.29 5 -0.29 3 8
MEF2C -0.022 0.09 0.18 16 -0.3 19 35
SMAD2-3/SMAD4 0.03 0.041 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.037 0.016 -10000 0 -10000 0 0
IGHV3OR16-13 -0.022 0.094 -10000 0 -0.36 21 21
TGIF2/HDAC complex 0.019 0.005 -10000 0 -10000 0 0
CREBBP 0.019 0.008 -10000 0 -10000 0 0
SKIL 0.013 0.01 -10000 0 -10000 0 0
HDAC1 0.021 0.001 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
SNIP1 0.021 0.002 -10000 0 -10000 0 0
GCN5L2 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.034 0.035 -10000 0 -10000 0 0
MSG1/HSC70 0.027 0.02 0.22 2 -10000 0 2
SMAD2 0.016 0.02 -10000 0 -10000 0 0
SMAD3 0.015 0.024 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.033 -10000 0 -0.2 1 1
SMAD2/SMAD2/SMAD4 -0.01 0.06 -10000 0 -0.26 7 7
NCOR1 0.019 0.006 -10000 0 -10000 0 0
NCOA2 0.015 0.036 -10000 0 -0.29 4 4
NCOA1 0.02 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.025 0.009 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.041 0.063 -10000 0 -10000 0 0
IFNB1 -0.019 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.014 0.095 0.23 1 -0.3 19 20
CITED1 0.022 0.023 0.29 2 -10000 0 2
SMAD2-3/SMAD4/ARC105 0.038 0.045 -10000 0 -10000 0 0
RBL1 0.019 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.046 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.039 0.015 0.21 1 -10000 0 1
SMAD7 -0.008 0.064 -10000 0 -10000 0 0
MYC/MIZ-1 0.023 0.03 -10000 0 -0.2 4 4
SMAD3/SMAD4 -0.001 0.058 -10000 0 -0.49 2 2
IL10 -0.009 0.043 0.31 2 -10000 0 2
PIASy/HDAC complex 0.02 0.005 -10000 0 -10000 0 0
PIAS3 0.019 0.008 -10000 0 -10000 0 0
CDK2 0.02 0.007 -10000 0 -10000 0 0
IL5 -0.011 0.04 0.34 1 -10000 0 1
CDK4 0.02 0.007 -10000 0 -10000 0 0
PIAS4 0.02 0.005 -10000 0 -10000 0 0
ATF3 0.019 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.027 0.054 -10000 0 -0.2 2 2
FOXG1 0.008 0.071 0.29 16 -10000 0 16
FOXO3 -0.016 0.007 -10000 0 -10000 0 0
FOXO1 -0.017 0.017 -10000 0 -0.2 2 2
FOXO4 -0.017 0.007 -10000 0 -10000 0 0
heart looping -0.021 0.089 0.18 16 -0.3 19 35
CEBPB 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.056 0.069 0.22 30 -10000 0 30
MYOD1 -0.017 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.029 0.044 0.22 3 -0.19 2 5
SMAD3/SMAD4/GATA3 0.045 0.06 0.24 1 -10000 0 1
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.047 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.037 0.055 -10000 0 -10000 0 0
MED15 0.02 0.003 -10000 0 -10000 0 0
SP1 0.013 0.034 -10000 0 -0.14 4 4
SIN3B 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.031 0.068 0.21 10 -0.19 15 25
ITGB5 -0.019 0.038 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.001 0.042 -10000 0 -0.26 1 1
SMAD3/SMAD4/AR -0.064 0.11 -10000 0 -0.19 126 126
AR -0.12 0.15 -10000 0 -0.29 132 132
negative regulation of cell growth 0.002 0.049 -10000 0 -0.26 1 1
SMAD3/SMAD4/MYOD 0.028 0.035 -10000 0 -10000 0 0
E2F5 0.019 0.019 -10000 0 -0.29 1 1
E2F4 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.048 0.06 0.24 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.033 -10000 0 -10000 0 0
TFDP1 0.02 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.025 0.061 -10000 0 -0.31 1 1
SMAD3/SMAD4/RUNX2 0.03 0.035 -10000 0 -10000 0 0
TGIF2 0.019 0.005 -10000 0 -10000 0 0
TGIF1 0.02 0.004 -10000 0 -10000 0 0
ATF2 0.02 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.033 0.054 0.17 6 -10000 0 6
NF kappa B1 p50/RelA/I kappa B alpha -0.031 0.061 0.33 1 -10000 0 1
alphaV/beta3 Integrin/Osteopontin/Src 0.034 0.037 0.22 10 -10000 0 10
AP1 -0.058 0.08 -10000 0 -0.31 9 9
ILK -0.028 0.058 0.23 1 -10000 0 1
bone resorption -0.037 0.064 0.29 3 -0.26 1 4
PTK2B 0.019 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.025 0.073 0.3 1 -10000 0 1
ITGAV 0.018 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.027 0.021 -10000 0 -0.2 2 2
alphaV/beta3 Integrin/Osteopontin 0.02 0.077 0.21 9 -0.17 33 42
MAP3K1 -0.029 0.058 0.18 7 -0.19 5 12
JUN 0.017 0.021 -10000 0 -0.29 1 1
MAPK3 -0.034 0.053 0.17 6 -10000 0 6
MAPK1 -0.034 0.053 0.17 6 -10000 0 6
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MAPK8 -0.033 0.056 0.18 7 -0.2 5 12
ITGB3 -0.017 0.1 -10000 0 -0.29 34 34
NFKBIA -0.028 0.053 -10000 0 -10000 0 0
FOS -0.005 0.082 -10000 0 -0.29 22 22
CD44 0.02 0.004 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
PLAU -0.028 0.065 0.4 1 -10000 0 1
NF kappa B1 p50/RelA -0.044 0.055 -10000 0 -10000 0 0
BCAR1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.002 0.074 -10000 0 -0.2 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.031 0.056 0.17 7 -10000 0 7
VAV3 -0.036 0.049 0.17 4 -10000 0 4
MAP3K14 -0.031 0.056 0.17 6 -10000 0 6
ROCK2 0.018 0.026 -10000 0 -0.29 2 2
SPP1 0.028 0.051 0.3 10 -10000 0 10
RAC1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.046 0.16 4 -10000 0 4
MMP2 -0.057 0.093 0.27 1 -0.36 15 16
Visual signal transduction: Rods

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
mol:K + 0.02 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.012 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.017 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.023 0.013 0.19 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.016 0.005 -10000 0 -10000 0 0
GRK1 -0.017 0.003 -10000 0 -10000 0 0
CNG Channel 0.05 0.049 0.24 2 -10000 0 2
mol:Na + 0.035 0.064 0.26 2 -10000 0 2
mol:ADP -0.017 0.003 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.016 0.065 0.2 1 -0.17 30 31
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.059 0.067 0.3 3 -10000 0 3
CNGB1 0.086 0.12 0.29 72 -10000 0 72
RDH5 0.019 0.018 -10000 0 -0.29 1 1
SAG -0.013 0.026 -10000 0 -0.29 2 2
mol:Ca2+ 0.014 0.087 0.25 16 -10000 0 16
Na + (4 Units) -0.001 0.057 0.11 47 -10000 0 47
RGS9 -0.016 0.098 -10000 0 -0.29 33 33
GNB1/GNGT1 0.026 0.007 -10000 0 -10000 0 0
GNAT1/GDP 0.019 0.059 -10000 0 -0.15 30 30
GUCY2D 0.016 0.02 0.29 1 -10000 0 1
GNGT1 -0.017 0.004 -10000 0 -10000 0 0
GUCY2F -0.013 0.013 -10000 0 -10000 0 0
GNB5 0.02 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.017 0.022 0.13 5 -10000 0 5
mol:11-cis-retinal 0.019 0.018 -10000 0 -0.29 1 1
mol:cGMP 0.03 0.031 0.2 6 -10000 0 6
GNB1 0.02 0.004 -10000 0 -10000 0 0
Rhodopsin 0.022 0.018 -10000 0 -0.2 1 1
SLC24A1 0.02 0.003 -10000 0 -10000 0 0
CNGA1 0.02 0.005 -10000 0 -10000 0 0
Metarhodopsin II 0.017 0.01 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.041 0.035 0.21 7 -10000 0 7
RGS9BP 0.02 0.017 0.29 1 -10000 0 1
Metarhodopsin II/Transducin 0.004 0.011 -10000 0 -0.17 1 1
GCAP Family/Ca ++ 0.033 0.028 0.2 6 -10000 0 6
PDE6A/B 0.03 0.026 0.22 5 -10000 0 5
mol:Pi 0.016 0.065 0.2 1 -0.17 30 31
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.03 0.012 -10000 0 -10000 0 0
PDE6B 0.019 0.006 -10000 0 -10000 0 0
PDE6A 0.022 0.041 0.29 6 -10000 0 6
PDE6G 0.02 0.017 0.29 1 -10000 0 1
RHO -0.003 0.016 -10000 0 -10000 0 0
PDE6 0.029 0.068 -10000 0 -0.15 26 26
GUCA1A 0.015 0.04 0.29 5 -10000 0 5
GC2/GCAP Family 0.042 0.031 0.21 6 -10000 0 6
GUCA1C -0.007 0.028 0.29 2 -10000 0 2
GUCA1B 0.019 0.019 -10000 0 -0.29 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.018 0.007 -10000 0 -10000 0 0
NFATC1 0.02 0.083 0.27 8 -0.37 2 10
NFATC2 0.007 0.061 0.19 7 -0.3 3 10
NFATC3 0.009 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.003 0.061 0.18 6 -0.23 2 8
Exportin 1/Ran/NUP214 0.04 0.008 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.02 0.057 -10000 0 -0.21 2 2
BCL2/BAX 0.024 0.031 -10000 0 -0.2 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.006 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.019 0.007 -10000 0 -10000 0 0
BAD 0.02 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D 0.012 0.058 0.18 2 -0.23 2 4
Calcineurin A alpha-beta B1/BCL2 0.014 0.04 -10000 0 -0.29 5 5
FKBP8 0.02 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.012 0.057 0.23 2 -0.18 2 4
KPNB1 0.021 0.002 -10000 0 -10000 0 0
KPNA2 0.02 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
SFN 0.28 0.067 0.29 274 -10000 0 274
MAP3K8 0.019 0.007 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.021 0.009 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.025 0.067 -10000 0 -0.25 5 5
CABIN1 0.003 0.061 0.18 6 -0.24 2 8
CALM1 0.019 0.008 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.02 0.002 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.029 0.007 -10000 0 -10000 0 0
YWHAB 0.019 0.006 -10000 0 -10000 0 0
MAPK8 0.017 0.026 -10000 0 -0.29 2 2
MAPK9 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
FKBP1A 0.019 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.018 0.081 0.3 3 -0.37 4 7
PRKCH 0.02 0.003 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.027 0.013 -10000 0 -10000 0 0
CASP3 0.019 0.008 -10000 0 -10000 0 0
PIM1 0.02 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.005 -10000 0 -10000 0 0
apoptosis 0.009 0.021 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.059 0.048 -10000 0 -10000 0 0
PRKCB 0.018 0.026 -10000 0 -0.29 2 2
PRKCE 0.02 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.016 0.037 -10000 0 -0.17 2 2
BAD/BCL-XL 0.026 0.011 -10000 0 -10000 0 0
PRKCD 0.019 0.006 -10000 0 -10000 0 0
NUP214 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.014 0.044 -10000 0 -0.29 6 6
PRKCG 0.03 0.077 0.29 22 -10000 0 22
PRKCQ 0.02 0.003 -10000 0 -10000 0 0
FKBP38/BCL2 0.025 0.028 -10000 0 -0.2 4 4
EP300 0.019 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.019 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.028 0.08 0.31 4 -0.36 2 6
CaM/Ca2+/FKBP38 0.025 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.014 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.014 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.024 0.011 -10000 0 -10000 0 0
NFATc/ERK1 0.029 0.08 0.28 4 -0.36 2 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.058 -10000 0 -0.21 2 2
NR4A1 0.001 0.081 0.26 4 -0.33 6 10
GSK3B 0.016 0.01 -10000 0 -10000 0 0
positive T cell selection 0.009 0.005 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.005 0.042 0.11 2 -0.24 3 5
RCH1/ KPNB1 0.03 0.005 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.019 0.007 -10000 0 -10000 0 0
AKAP5 0.02 0.003 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.028 0.078 0.27 5 -0.36 2 7
CREBBP 0.019 0.008 -10000 0 -10000 0 0
BCL2 0.014 0.04 -10000 0 -0.29 5 5
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.007 0.044 -10000 0 -10000 0 0
PLK1 0.083 0.15 0.46 2 -10000 0 2
CDKN1B 0.042 0.096 -10000 0 -0.33 3 3
FOXO3 0.069 0.11 -10000 0 -10000 0 0
KAT2B 0.03 0.019 -10000 0 -10000 0 0
FOXO1/SIRT1 0.005 0.041 -10000 0 -10000 0 0
CAT 0.054 0.11 0.41 1 -10000 0 1
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.031 0.019 -10000 0 -10000 0 0
FOXO1 -0.002 0.043 -10000 0 -10000 0 0
MAPK10 -0.003 0.019 0.18 1 -0.16 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.027 0.064 -10000 0 -10000 0 0
response to oxidative stress 0.012 0.016 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.06 0.11 -10000 0 -0.38 2 2
XPO1 0.02 0.003 -10000 0 -10000 0 0
EP300 0.02 0.003 -10000 0 -10000 0 0
BCL2L11 0.024 0.078 -10000 0 -0.7 3 3
FOXO1/SKP2 0.007 0.038 -10000 0 -10000 0 0
mol:GDP 0.012 0.016 -10000 0 -10000 0 0
RAN 0.021 0.002 -10000 0 -10000 0 0
GADD45A 0.033 0.088 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.09 0.22 2 -0.33 5 7
MST1 0.03 0.02 -10000 0 -10000 0 0
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.003 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.066 0.071 0.24 1 -0.32 2 3
YWHAB 0.019 0.006 -10000 0 -10000 0 0
MAPK8 -0.003 0.022 0.18 2 -10000 0 2
MAPK9 -0.003 0.022 0.18 2 -10000 0 2
YWHAG 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.02 0.005 -10000 0 -10000 0 0
SIRT1 0.008 0.019 -10000 0 -10000 0 0
SOD2 0.024 0.096 -10000 0 -10000 0 0
RBL2 0.025 0.17 -10000 0 -0.65 11 11
RAL/GDP 0.036 0.014 -10000 0 -10000 0 0
CHUK 0.031 0.019 -10000 0 -10000 0 0
Ran/GTP 0.016 0.002 -10000 0 -10000 0 0
CSNK1G2 0.019 0.005 -10000 0 -10000 0 0
RAL/GTP 0.035 0.013 -10000 0 -10000 0 0
CSNK1G1 0.02 0.003 -10000 0 -10000 0 0
FASLG 0.032 0.036 -10000 0 -10000 0 0
SKP2 0.018 0.007 -10000 0 -10000 0 0
USP7 0.02 0.005 -10000 0 -10000 0 0
IKBKB 0.03 0.019 -10000 0 -10000 0 0
CCNB1 0.052 0.11 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.031 0.08 0.3 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.038 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.031 0.019 -10000 0 -10000 0 0
CSNK1G3 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.005 -10000 0 -10000 0 0
ZFAND5 -0.025 0.06 -10000 0 -10000 0 0
SFN 0.28 0.067 0.29 274 -10000 0 274
CDK2 0.019 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.073 0.066 0.22 2 -10000 0 2
CREBBP 0.019 0.006 -10000 0 -10000 0 0
FBXO32 0.053 0.18 0.46 3 -0.98 5 8
BCL6 0.037 0.093 -10000 0 -10000 0 0
RALB 0.021 0.002 -10000 0 -10000 0 0
RALA 0.021 0.002 -10000 0 -10000 0 0
YWHAH 0.02 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.007 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.016 0.29 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.003 0.011 -10000 0 -0.17 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -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 0.02 0.004 -10000 0 -10000 0 0
FYN 0.015 0.04 -10000 0 -0.29 5 5
MAP3K12 0.019 0.018 -10000 0 -0.29 1 1
FGR 0.02 0.002 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.025 0.062 -10000 0 -0.26 12 12
PRKG1 -0.055 0.13 -10000 0 -0.29 68 68
DUSP8 0.019 0.019 -10000 0 -0.29 1 1
PGK/cGMP/p38 alpha -0.018 0.098 -10000 0 -0.28 18 18
apoptosis -0.024 0.06 -10000 0 -0.26 12 12
RAL/GTP 0.028 0.004 -10000 0 -10000 0 0
LYN 0.02 0.004 -10000 0 -10000 0 0
DUSP1 0.014 0.04 -10000 0 -0.29 5 5
PAK1 0.019 0.005 -10000 0 -10000 0 0
SRC 0.019 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.048 0.016 -10000 0 -10000 0 0
TRAF6 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.02 0.003 -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 0.02 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.006 -10000 0 -10000 0 0
MAPK11 0.016 0.079 0.21 5 -0.27 4 9
BLK 0.064 0.11 0.29 52 -10000 0 52
HCK 0.019 0.006 -10000 0 -10000 0 0
MAP2K3 0.02 0.005 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.019 0.005 -10000 0 -10000 0 0
TRAF6/MEKK3 0.025 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.088 0.2 3 -0.29 11 14
positive regulation of innate immune response 0.014 0.094 0.23 6 -0.31 7 13
LCK 0.021 0.001 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.022 0.093 0.27 2 -0.32 5 7
p38alpha-beta/MKP5 0.019 0.093 0.24 2 -0.32 6 8
PGK/cGMP -0.034 0.089 -10000 0 -0.2 68 68
PAK2 0.013 0.01 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.02 0.096 0.26 3 -0.32 7 10
CDC42 0.02 0.003 -10000 0 -10000 0 0
RALB 0.021 0.002 -10000 0 -10000 0 0
RALA 0.02 0.002 -10000 0 -10000 0 0
PAK3 0.004 0.025 0.29 1 -10000 0 1
Caspase cascade in apoptosis

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
TOP1 0.002 0.079 0.24 1 -0.38 7 8
ACTA1 -0.003 0.069 0.22 4 -0.34 2 6
NUMA1 -0.005 0.092 0.24 1 -0.44 7 8
SPTAN1 -0.009 0.067 0.23 4 -0.34 2 6
LIMK1 -0.006 0.07 0.24 5 -0.32 2 7
BIRC3 0.017 0.018 0.29 1 -10000 0 1
BIRC2 0.016 0.008 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.012 0.027 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
PTK2 0.001 0.08 0.24 1 -0.38 7 8
DIABLO 0.021 0.001 -10000 0 -10000 0 0
apoptotic nuclear changes -0.008 0.067 0.23 4 -0.33 2 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.021 0.001 -10000 0 -10000 0 0
GSN -0.009 0.067 0.23 4 -0.34 2 6
MADD 0.02 0.004 -10000 0 -10000 0 0
TFAP2A 0.12 0.14 0.34 3 -0.51 9 12
BID 0 0.015 -10000 0 -10000 0 0
MAP3K1 -0.01 0.092 -10000 0 -0.4 13 13
TRADD 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.005 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.006 0.07 0.24 5 -0.34 2 7
CASP9 0.02 0.003 -10000 0 -10000 0 0
DNA repair -0.001 0.052 0.36 1 -0.16 1 2
neuron apoptosis -0.011 0.13 -10000 0 -0.68 9 9
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.01 0.086 0.24 1 -0.42 6 7
APAF1 0.02 0.001 -10000 0 -10000 0 0
CASP6 -0.004 0.13 -10000 0 -0.89 6 6
TRAF2 0.02 0.003 -10000 0 -10000 0 0
ICAD/CAD -0.013 0.064 0.29 2 -0.31 2 4
CASP7 -0.019 0.1 -10000 0 -0.32 11 11
KRT18 0.037 0.077 -10000 0 -0.51 2 2
apoptosis -0.017 0.091 0.22 1 -0.43 7 8
DFFA -0.009 0.064 0.21 2 -0.33 2 4
DFFB -0.009 0.064 0.2 3 -0.33 2 5
PARP1 0.001 0.053 0.16 1 -0.36 1 2
actin filament polymerization 0.01 0.073 0.3 2 -0.27 5 7
TNF 0.023 0.032 0.29 4 -10000 0 4
CYCS 0.003 0.032 0.16 5 -0.2 1 6
SATB1 -0.008 0.12 -10000 0 -0.83 6 6
SLK -0.009 0.063 0.2 2 -0.33 2 4
p15 BID/BAX 0.009 0.032 0.2 1 -0.17 2 3
CASP2 -0.005 0.054 0.22 1 -0.24 5 6
JNK cascade 0.01 0.091 0.4 13 -10000 0 13
CASP3 -0.004 0.068 0.21 3 -0.35 2 5
LMNB2 -0.007 0.11 0.21 1 -0.39 13 14
RIPK1 0.02 0.005 -10000 0 -10000 0 0
CASP4 0.018 0.007 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.042 0.024 0.21 1 -10000 0 1
negative regulation of DNA binding 0.12 0.13 0.34 4 -0.51 9 13
stress fiber formation -0.009 0.063 0.2 2 -0.32 2 4
GZMB -0.006 0.042 0.14 23 -10000 0 23
CASP1 0.006 0.002 -10000 0 -10000 0 0
LMNB1 -0.007 0.11 0.21 1 -0.42 13 14
APP -0.011 0.13 -10000 0 -0.69 9 9
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.002 -10000 0 -10000 0 0
VIM -0.012 0.094 0.23 1 -0.48 6 7
LMNA 0.007 0.064 0.21 1 -0.29 6 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0 0.062 0.24 1 -0.19 16 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.008 0.063 0.2 2 -0.34 2 4
APAF-1/Caspase 9 0.005 0.085 -10000 0 -0.56 6 6
nuclear fragmentation during apoptosis -0.005 0.09 0.24 1 -0.43 7 8
CFL2 -0.011 0.073 0.27 5 -0.31 2 7
GAS2 -0.01 0.063 0.21 2 -0.33 2 4
positive regulation of apoptosis -0.002 0.1 0.22 1 -0.48 7 8
PRF1 0.02 0.003 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.014 -10000 0 -0.15 1 1
RGS9BP 0.02 0.017 0.29 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.017 0.003 -10000 0 -10000 0 0
mol:Na + 0.024 0.006 -10000 0 -10000 0 0
mol:ADP -0.013 0.019 0.26 1 -10000 0 1
GNAT2 0.011 0.016 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.016 0.065 0.2 1 -0.17 30 31
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.006 -10000 0 -10000 0 0
GRK7 0.011 0.013 -10000 0 -10000 0 0
CNGB3 0.006 0.018 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.013 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.037 0.17 11 -10000 0 11
Cone PDE6 0.029 0.067 -10000 0 -0.15 30 30
Cone Metarhodopsin II 0.017 0.011 -10000 0 -10000 0 0
Na + (4 Units) 0.033 0.011 -10000 0 -10000 0 0
GNAT2/GDP 0.023 0.061 0.19 1 -0.15 30 31
GNB5 0.02 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.016 0.027 0.17 6 -10000 0 6
Cone Transducin 0.036 0.015 -10000 0 -0.16 1 1
SLC24A2 0 0.019 -10000 0 -10000 0 0
GNB3/GNGT2 0.028 0.015 -10000 0 -0.2 1 1
GNB3 0.018 0.019 -10000 0 -0.29 1 1
GNAT2/GTP 0.015 0.002 -10000 0 -10000 0 0
CNGA3 0.003 0.019 -10000 0 -10000 0 0
ARR3 -0.008 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.025 0.006 -10000 0 -10000 0 0
mol:Pi 0.016 0.065 0.2 1 -0.17 30 31
Cone CNG Channel 0.039 0.017 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0.019 -10000 0 -10000 0 0
RGS9 -0.016 0.098 -10000 0 -0.29 33 33
PDE6C -0.017 0.003 -10000 0 -10000 0 0
GNGT2 0.02 0.002 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.016 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.015 0.028 0.099 13 -10000 0 13
SNTA1 0.019 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.028 0.099 13 -10000 0 13
MAPK12 -0.012 0.005 -10000 0 -10000 0 0
CCND1 -0.007 0.055 -10000 0 -0.34 8 8
p38 gamma/SNTA1 -0.011 0.029 0.18 4 -10000 0 4
MAP2K3 0.02 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.011 0.005 -10000 0 -10000 0 0
MAP2K6 -0.007 0.005 -10000 0 -10000 0 0
MAPT -0.007 0.049 0.19 5 -0.23 7 12
MAPK13 -0.01 0.038 0.16 13 -10000 0 13
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.001 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.005 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.016 0.046 -10000 0 -0.27 1 1
NEF 0.002 0.007 -10000 0 -10000 0 0
NFKBIA 0.021 0.007 -10000 0 -10000 0 0
BIRC3 -0.01 0.048 0.22 11 -10000 0 11
CYCS -0.01 0.048 0.15 13 -0.18 3 16
RIPK1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.021 0.009 -10000 0 -10000 0 0
MAP2K7 -0.008 0.14 -10000 0 -0.63 11 11
protein ubiquitination -0.008 0.075 0.31 3 -0.36 4 7
CRADD 0.021 0.001 -10000 0 -10000 0 0
DAXX 0.02 0.004 -10000 0 -10000 0 0
FAS 0.02 0.004 -10000 0 -10000 0 0
BID -0.002 0.047 0.16 13 -0.18 4 17
NF-kappa-B/RelA/I kappa B alpha 0.045 0.031 0.26 5 -10000 0 5
TRADD 0.02 0.004 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
CFLAR 0.019 0.005 -10000 0 -10000 0 0
FADD 0.019 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.045 0.031 0.26 5 -10000 0 5
MAPK8 -0.012 0.13 -10000 0 -0.58 11 11
APAF1 0.021 0.001 -10000 0 -10000 0 0
TRAF1 0.021 0.002 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.034 -10000 0 -0.18 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.006 0.081 0.21 1 -0.43 5 6
CHUK -0.011 0.076 0.3 2 -0.4 4 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.048 0.027 -10000 0 -10000 0 0
TCRz/NEF 0.017 0.016 0.17 3 -10000 0 3
TNF 0.023 0.032 0.29 4 -10000 0 4
FASLG -0.009 0.029 0.27 3 -10000 0 3
NFKB1 0.021 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.038 0.025 0.21 4 -10000 0 4
CASP6 -0.005 0.14 -10000 0 -0.47 21 21
CASP7 -0.015 0.096 0.26 5 -0.36 7 12
RELA 0.022 0.007 -10000 0 -10000 0 0
CASP2 0.02 0.005 -10000 0 -10000 0 0
CASP3 -0.019 0.099 0.26 6 -0.35 9 15
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.01 -10000 0 -10000 0 0
CASP8 0.019 0.005 -10000 0 -10000 0 0
CASP9 0.02 0.003 -10000 0 -10000 0 0
MAP3K14 -0.008 0.078 0.19 2 -0.4 5 7
APAF-1/Caspase 9 -0.024 0.043 -10000 0 -0.21 1 1
BCL2 -0.016 0.12 -10000 0 -0.55 11 11
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.01 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.018 0.083 0.47 1 -10000 0 1
IL27/IL27R/JAK1 0.059 0.083 -10000 0 -10000 0 0
TBX21 0.01 0.088 0.29 3 -10000 0 3
IL12B 0.026 0.035 0.31 4 -10000 0 4
IL12A 0.008 0.049 0.21 15 -10000 0 15
IL6ST 0.01 0.059 -10000 0 -0.3 10 10
IL27RA/JAK1 0.023 0.038 -10000 0 -10000 0 0
IL27 0.017 0.02 -10000 0 -10000 0 0
TYK2 0.026 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.013 0.059 0.39 1 -10000 0 1
T-helper 2 cell differentiation -0.018 0.083 0.47 1 -10000 0 1
T cell proliferation during immune response -0.018 0.083 0.47 1 -10000 0 1
MAPKKK cascade 0.018 0.083 -10000 0 -0.47 1 1
STAT3 0.02 0.002 -10000 0 -10000 0 0
STAT2 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.018 0.011 -10000 0 -10000 0 0
IL12RB1 0.022 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.031 0.12 0.3 20 -10000 0 20
IL27/IL27R/JAK2/TYK2 0.018 0.084 -10000 0 -0.48 1 1
positive regulation of T cell mediated cytotoxicity 0.018 0.083 -10000 0 -0.47 1 1
STAT1 (dimer) 0.062 0.12 -10000 0 -10000 0 0
JAK2 0.023 0.014 -10000 0 -10000 0 0
JAK1 0.018 0.011 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.087 -10000 0 -0.46 1 1
T cell proliferation 0.012 0.081 0.3 1 -0.46 1 2
IL12/IL12R/TYK2/JAK2 0.019 0.18 -10000 0 -0.65 15 15
IL17A 0.013 0.052 -10000 0 -10000 0 0
mast cell activation -0.018 0.083 0.47 1 -10000 0 1
IFNG 0.021 0.04 0.1 47 -0.1 2 49
T cell differentiation 0.001 0.004 0.012 16 -10000 0 16
STAT3 (dimer) 0.025 0.087 -10000 0 -0.46 1 1
STAT5A (dimer) 0.025 0.087 -10000 0 -0.46 1 1
STAT4 (dimer) 0.025 0.086 -10000 0 -0.46 1 1
STAT4 0.02 0.004 -10000 0 -10000 0 0
T cell activation -0.003 0.002 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.046 0.07 -10000 0 -10000 0 0
GATA3 0.002 0.072 0.65 1 -10000 0 1
IL18 -0.005 0.016 0.14 3 -10000 0 3
positive regulation of mast cell cytokine production 0.025 0.086 -10000 0 -0.45 1 1
IL27/EBI3 0.034 0.022 -10000 0 -10000 0 0
IL27RA 0.013 0.04 -10000 0 -10000 0 0
IL6 0.029 0.043 0.3 7 -10000 0 7
STAT5A 0.02 0.002 -10000 0 -10000 0 0
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.016 -10000 0 -10000 0 0
IL1B 0.019 0.059 0.14 52 -10000 0 52
EBI3 0.02 0.016 -10000 0 -10000 0 0
TNF -0.003 0.028 0.18 6 -10000 0 6
Signaling events mediated by PRL

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
CCNE1 0.024 0.032 0.29 4 -10000 0 4
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.02 0.005 -10000 0 -10000 0 0
CDKN1A 0.006 0.011 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.028 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.07 -10000 0 -0.21 48 48
AGT -0.039 0.12 -10000 0 -0.29 54 54
CCNA2 -0.021 0.022 -10000 0 -10000 0 0
TUBA1B 0.02 0.002 -10000 0 -10000 0 0
EGR1 -0.012 0.031 -10000 0 -0.19 8 8
CDK2/Cyclin E1 0.035 0.046 -10000 0 -0.29 3 3
MAPK3 -0.017 0.005 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.03 0.003 -10000 0 -10000 0 0
MAPK1 -0.017 0.005 -10000 0 -10000 0 0
PTP4A1 -0.018 0.022 -10000 0 -10000 0 0
PTP4A3 0.019 0.005 -10000 0 -10000 0 0
PTP4A2 0.021 0.002 -10000 0 -10000 0 0
ITGB1 -0.017 0.006 -10000 0 -10000 0 0
SRC 0.019 0.006 -10000 0 -10000 0 0
RAC1 0.002 0.035 -10000 0 -0.32 3 3
Rab GGTase beta/Rab GGTase alpha 0.03 0.005 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.01 0.052 -10000 0 -10000 0 0
RABGGTA 0.02 0.003 -10000 0 -10000 0 0
BCAR1 -0.02 0.007 -10000 0 -10000 0 0
RHOC 0.002 0.035 -10000 0 -0.32 3 3
RHOA -0.011 0.071 -10000 0 -0.32 14 14
cell motility 0.007 0.06 -10000 0 -0.34 2 2
PRL-1/alpha Tubulin -0.008 0.057 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.01 -10000 0 -10000 0 0
ROCK1 0.007 0.057 -10000 0 -0.34 2 2
RABGGTB 0.021 0.002 -10000 0 -10000 0 0
CDK2 0.02 0.002 -10000 0 -10000 0 0
mitosis -0.018 0.022 -10000 0 -10000 0 0
ATF5 0.02 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.004 0.1 -10000 0 -0.42 5 5
MAP3K8 0.017 0.012 -10000 0 -10000 0 0
FOS -0.004 0.077 0.25 1 -0.4 4 5
PRKCA 0.01 0.046 -10000 0 -0.29 6 6
PTPN7 0.015 0.015 -10000 0 -10000 0 0
HRAS 0.017 0.011 -10000 0 -10000 0 0
PRKCB 0.015 0.029 -10000 0 -0.29 2 2
NRAS 0.018 0.011 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.021 -10000 0 -10000 0 0
MAPK3 0.004 0.064 -10000 0 -0.63 2 2
MAP2K1 -0.013 0.076 -10000 0 -0.36 9 9
ELK1 0.016 0.016 -10000 0 -10000 0 0
BRAF -0.003 0.049 -10000 0 -0.3 7 7
mol:GTP 0 0.001 -10000 0 -0.004 22 22
MAPK1 0.003 0.057 -10000 0 -0.42 3 3
RAF1 -0.006 0.062 -10000 0 -0.33 9 9
KRAS 0.017 0.011 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.049 0.015 -10000 0 -10000 0 0
HDAC3 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.026 0.015 0.22 1 -10000 0 1
GATA1/HDAC5 0.03 0.012 0.22 1 -10000 0 1
GATA2/HDAC5 0.019 0.037 -10000 0 -0.2 7 7
HDAC5/BCL6/BCoR 0.026 0.02 -10000 0 -10000 0 0
HDAC9 0.009 0.059 -10000 0 -0.29 11 11
Glucocorticoid receptor/Hsp90/HDAC6 0.038 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.026 0.011 -10000 0 -10000 0 0
HDAC5/YWHAB 0.028 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.005 0.002 -10000 0 -10000 0 0
GATA2 0.009 0.048 -10000 0 -0.29 7 7
HDAC4/RFXANK 0.026 0.011 -10000 0 -10000 0 0
BCOR 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.02 0.004 -10000 0 -10000 0 0
HDAC5 0.02 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.007 -10000 0 -10000 0 0
Histones -0.013 0.062 -10000 0 -0.21 16 16
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
HDAC4 0.018 0.007 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.029 0.007 -10000 0 -10000 0 0
HDAC4/Ubc9 0.026 0.011 -10000 0 -10000 0 0
HDAC7 0.02 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.009 -10000 0 -10000 0 0
TUBA1B 0.02 0.002 -10000 0 -10000 0 0
HDAC6 0.02 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.03 0.006 -10000 0 -10000 0 0
CAMK4 0.019 0.006 -10000 0 -10000 0 0
Tubulin/HDAC6 0.038 0.012 -10000 0 -10000 0 0
SUMO1 0.019 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.019 0.006 -10000 0 -10000 0 0
GATA1 0.012 0.023 0.29 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.02 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.021 0.031 -10000 0 -0.16 4 4
SRF 0.02 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.025 0.012 -10000 0 -10000 0 0
Tubulin 0.029 0.008 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.025 0.012 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
BCL6/BCoR 0.019 0.015 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.036 0.015 -10000 0 -10000 0 0
HDAC4/SRF 0.035 0.016 -10000 0 -10000 0 0
HDAC4/ER alpha -0.047 0.11 -10000 0 -0.2 94 94
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.012 0.061 -10000 0 -0.2 16 16
cell motility 0.038 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.029 0.007 -10000 0 -10000 0 0
BCL6 0.013 0.01 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.018 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.028 0.008 -10000 0 -10000 0 0
ESR1 -0.082 0.14 -10000 0 -0.29 95 95
HDAC6/HDAC11 0.028 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.039 -10000 0 -0.16 4 4
NPC 0.012 0.002 -10000 0 -10000 0 0
MEF2C -0.003 0.08 -10000 0 -0.29 21 21
RAN 0.02 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.035 0.058 -10000 0 -0.16 20 20
GNG2 0.02 0.003 -10000 0 -10000 0 0
NCOR2 0.021 0.002 -10000 0 -10000 0 0
TUBB2A 0.019 0.005 -10000 0 -10000 0 0
HDAC11 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.003 -10000 0 -10000 0 0
nuclear import -0.017 0.01 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.005 0.069 0.39 7 -10000 0 7
VDR 0.02 0.003 -10000 0 -10000 0 0
FAM120B 0.019 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.016 0.028 0.22 2 -10000 0 2
RXRs/LXRs/DNA/Oxysterols 0.015 0.033 0.27 2 -10000 0 2
MED1 0.02 0.003 -10000 0 -10000 0 0
mol:9cRA 0.002 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.01 0.062 -10000 0 -0.18 33 33
RXRs/NUR77 0.046 0.039 -10000 0 -0.16 6 6
RXRs/PPAR -0.006 0.056 -10000 0 -0.27 2 2
NCOR2 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.042 0.022 -10000 0 -0.15 2 2
RARA 0.02 0.002 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.033 0.019 -10000 0 -0.14 2 2
RARG 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.046 0.54 2 -10000 0 2
RARs/THRs/DNA/SMRT -0.01 0.062 -10000 0 -0.18 34 34
THRA 0.02 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.041 0.03 0.22 2 -0.15 1 3
NR1H4 -0.005 0.03 0.29 2 -10000 0 2
RXRs/LXRs/DNA 0.057 0.037 -10000 0 -10000 0 0
NR1H2 0.022 0.006 -10000 0 -10000 0 0
NR1H3 0.022 0.007 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.046 0.026 -10000 0 -0.15 1 1
NR4A1 0.014 0.044 -10000 0 -0.29 6 6
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.009 0.018 0.16 1 -10000 0 1
RXRG 0.019 0.025 0.3 1 -0.29 1 2
RXR alpha/CCPG 0.03 0.009 -10000 0 -10000 0 0
RXRA 0.022 0.005 -10000 0 -10000 0 0
RXRB 0.022 0.007 -10000 0 -10000 0 0
THRB 0.007 0.062 -10000 0 -0.29 12 12
PPARG 0 0.075 -10000 0 -0.29 18 18
PPARD 0.02 0.003 -10000 0 -10000 0 0
TNF 0.016 0.053 0.45 2 -10000 0 2
mol:Oxysterols 0.002 0.005 -10000 0 -10000 0 0
cholesterol transport 0.021 0.038 0.27 2 -10000 0 2
PPARA 0.02 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.026 -10000 0 -0.29 2 2
RXRs/NUR77/BCL2 0.004 0.038 -10000 0 -0.18 10 10
SREBF1 0.012 0.033 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.041 0.03 0.22 2 -0.15 1 3
ABCA1 0.012 0.036 -10000 0 -10000 0 0
RARs/THRs 0.043 0.05 -10000 0 -0.16 14 14
RXRs/FXR 0.049 0.031 0.3 1 -0.16 1 2
BCL2 0.014 0.04 -10000 0 -0.29 5 5
Retinoic acid receptors-mediated signaling

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
HDAC1 0.021 0.001 -10000 0 -10000 0 0
HDAC3 0.02 0.004 -10000 0 -10000 0 0
VDR 0.02 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.037 0.014 -10000 0 -10000 0 0
EP300 0.02 0.003 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.006 0.037 -10000 0 -0.43 1 1
KAT2B 0.019 0.005 -10000 0 -10000 0 0
MAPK14 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.019 0.061 0.19 3 -0.23 3 6
RAR alpha/9cRA/Cyclin H 0.025 0.056 -10000 0 -0.23 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.056 0.16 1 -0.24 3 4
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.018 0.037 -10000 0 -0.29 1 1
NCOR2 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.006 0.081 0.29 1 -0.36 6 7
NCOA2 0.015 0.036 -10000 0 -0.29 4 4
NCOA3 0.019 0.005 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.003 -10000 0 -10000 0 0
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.006 -10000 0 -10000 0 0
MAPK3 0.021 0.002 -10000 0 -10000 0 0
MAPK1 0.02 0.002 -10000 0 -10000 0 0
MAPK8 0.018 0.026 -10000 0 -0.29 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.02 0.071 -10000 0 -0.34 7 7
RARA 0.008 0.039 -10000 0 -0.19 7 7
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.003 0.056 0.16 1 -0.24 4 5
PRKCA 0.014 0.044 -10000 0 -0.29 6 6
RXRs/RARs/NRIP1/9cRA/HDAC1 0.005 0.094 0.39 2 -0.36 6 8
RXRG 0.012 0.051 -10000 0 -0.23 7 7
RXRA 0.002 0.033 -10000 0 -0.17 6 6
RXRB 0.014 0.049 0.24 1 -0.23 6 7
VDR/Vit D3/DNA 0.015 0.002 -10000 0 -10000 0 0
RBP1 0.009 0.044 -10000 0 -0.29 6 6
CRBP1/9-cic-RA 0.007 0.03 -10000 0 -0.2 6 6
RARB 0.017 0.026 -10000 0 -0.29 2 2
PRKCG 0.04 0.073 0.3 22 -10000 0 22
MNAT1 0.02 0.003 -10000 0 -10000 0 0
RAR alpha/RXRs -0.013 0.088 0.25 2 -0.4 7 9
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.003 0.075 -10000 0 -0.32 7 7
proteasomal ubiquitin-dependent protein catabolic process 0 0.079 0.35 2 -0.27 7 9
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.095 0.39 2 -0.36 6 8
positive regulation of DNA binding 0.018 0.051 -10000 0 -0.22 7 7
NRIP1 0.002 0.099 0.43 1 -0.54 1 2
RXRs/RARs 0.004 0.1 0.49 1 -0.36 6 7
RXRs/RXRs/DNA/9cRA 0.005 0.068 -10000 0 -0.34 7 7
PRKACA 0.02 0.004 -10000 0 -10000 0 0
CDK7 0.02 0.004 -10000 0 -10000 0 0
TFIIH 0.039 0.011 -10000 0 -10000 0 0
RAR alpha/9cRA 0.036 0.046 -10000 0 -0.19 1 1
CCNH 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.035 0.015 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.029 0.035 0.28 1 -10000 0 1
DAPP1 0.011 0.072 0.2 5 -0.23 3 8
Src family/SYK family/BLNK-LAT/BTK-ITK 0.019 0.085 0.25 1 -0.3 5 6
mol:DAG 0.008 0.063 0.21 12 -10000 0 12
HRAS 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
ARF5/GDP 0.012 0.057 0.22 1 -0.22 6 7
PLCG2 0.02 0.004 -10000 0 -10000 0 0
PLCG1 0.019 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.023 0.033 0.15 8 -10000 0 8
ARF1/GTP -0.018 0.027 0.22 1 -10000 0 1
RHOA 0.019 0.006 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.023 0.029 0.15 7 -10000 0 7
ADAP1 -0.025 0.033 0.2 2 -10000 0 2
ARAP3 -0.023 0.032 0.15 8 -10000 0 8
INPPL1 0.02 0.004 -10000 0 -10000 0 0
PREX1 0.019 0.005 -10000 0 -10000 0 0
ARHGEF6 0.017 0.031 -10000 0 -0.29 3 3
ARHGEF7 0.02 0.004 -10000 0 -10000 0 0
ARF1 0.019 0.005 -10000 0 -10000 0 0
NRAS 0.021 0.004 -10000 0 -10000 0 0
FYN 0.015 0.04 -10000 0 -0.29 5 5
ARF6 0.02 0.003 -10000 0 -10000 0 0
FGR 0.02 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.046 0.14 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.018 0.026 -10000 0 -0.29 2 2
ZAP70 0.02 0.002 -10000 0 -10000 0 0
mol:IP3 0.003 0.057 0.17 19 -10000 0 19
LYN 0.02 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.011 0.054 -10000 0 -0.22 4 4
RhoA/GDP -0.016 0.043 0.2 1 -10000 0 1
PDK1/Src/Hsp90 0.036 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.016 0.29 1 -10000 0 1
actin cytoskeleton reorganization -0.005 0.061 0.39 1 -0.25 1 2
SRC 0.019 0.006 -10000 0 -10000 0 0
PLEKHA2 -0.018 0.008 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
PTEN 0.02 0.011 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.043 0.28 1 -10000 0 1
RhoA/GTP -0.025 0.033 0.29 1 -10000 0 1
Src family/SYK family/BLNK-LAT 0.008 0.06 -10000 0 -0.32 1 1
BLK 0.064 0.11 0.29 52 -10000 0 52
PDPK1 0.02 0.004 -10000 0 -10000 0 0
CYTH1 -0.027 0.025 0.14 1 -10000 0 1
HCK 0.019 0.006 -10000 0 -10000 0 0
CYTH3 -0.026 0.033 0.2 2 -10000 0 2
CYTH2 -0.025 0.033 0.2 2 -10000 0 2
KRAS 0.02 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.007 0.031 -10000 0 -10000 0 0
SGK1 -0.004 0.058 -10000 0 -0.33 6 6
INPP5D 0.018 0.007 -10000 0 -10000 0 0
mol:GDP 0.001 0.057 0.22 1 -0.21 9 10
SOS1 0.02 0.003 -10000 0 -10000 0 0
SYK 0.02 0.003 -10000 0 -10000 0 0
ARF6/GDP -0.018 0.045 0.24 3 -10000 0 3
mol:PI-3-4-5-P3 -0.023 0.032 0.14 9 -10000 0 9
ARAP3/RAP1A/GTP -0.023 0.029 0.15 7 -10000 0 7
VAV1 0.02 0.004 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.016 0.006 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.015 0.052 0.18 19 -10000 0 19
PLEKHA1 -0.019 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.058 0.22 1 -0.21 9 10
LAT 0.02 0.002 -10000 0 -10000 0 0
Rac1/GTP 0 0.047 -10000 0 -0.24 6 6
ITK -0.026 0.032 0.27 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.005 0.07 0.22 10 -0.21 1 11
LCK 0.021 0.001 -10000 0 -10000 0 0
BTK -0.027 0.032 0.2 2 -10000 0 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.021 0.028 -10000 0 -0.48 1 1
VEGFR1 homodimer/NRP1 -0.014 0.027 -10000 0 -0.48 1 1
mol:DAG -0.021 0.031 0.18 2 -0.45 1 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.018 0.026 -10000 0 -0.45 1 1
CaM/Ca2+ -0.024 0.03 0.17 2 -0.43 1 3
HIF1A 0.021 0.018 -10000 0 -0.29 1 1
GAB1 0.02 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.081 0.35 3 -0.27 1 4
PLCG1 -0.021 0.031 0.18 2 -0.45 1 3
NOS3 0.007 0.078 0.31 4 -0.29 5 9
CBL 0.017 0.008 -10000 0 -10000 0 0
mol:NO 0.017 0.099 0.36 9 -0.34 3 12
FLT1 -0.018 0.032 -10000 0 -0.55 1 1
PGF 0.02 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.039 -10000 0 -0.45 1 1
CALM1 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
eNOS/Hsp90 0.009 0.09 0.28 5 -0.31 5 10
endothelial cell proliferation 0.006 0.076 0.37 6 -0.42 1 7
mol:Ca2+ -0.021 0.031 0.18 2 -0.44 1 3
MAPK3 -0.026 0.051 0.26 5 -0.41 1 6
MAPK1 -0.026 0.051 0.26 5 -0.41 1 6
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
PLGF homodimer 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.008 0.088 -10000 0 -0.29 26 26
VEGFA homodimer 0.02 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.02 0.028 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.03 0.049 0.32 3 -0.4 1 4
PI3K 0.024 0.027 -10000 0 -0.26 1 1
PRKCA -0.027 0.035 0.16 2 -0.42 1 3
PRKCB -0.025 0.031 0.16 2 -0.42 1 3
VEGFR1 homodimer/PLGF homodimer -0.021 0.028 -10000 0 -0.48 1 1
VEGFA 0.02 0.004 -10000 0 -10000 0 0
VEGFB 0.02 0.003 -10000 0 -10000 0 0
mol:IP3 -0.021 0.031 0.18 2 -0.45 1 3
RASA1 -0.02 0.038 0.18 6 -0.45 1 7
NRP2 0.014 0.041 -10000 0 -0.29 5 5
VEGFR1 homodimer -0.018 0.032 -10000 0 -0.55 1 1
VEGFB homodimer 0.02 0.003 -10000 0 -10000 0 0
NCK1 0.015 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.011 0.1 0.39 7 -0.34 5 12
PTPN11 0.021 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.026 -10000 0 -0.25 1 1
mol:L-citrulline 0.017 0.099 0.36 9 -0.34 3 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.031 0.032 -10000 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.02 0.022 -10000 0 -0.27 1 1
CD2AP 0.02 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.029 0.032 -10000 0 -0.25 1 1
PDPK1 0.031 0.09 0.32 4 -0.25 1 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.027 0.03 -10000 0 -0.45 1 1
mol:NADP 0.017 0.099 0.36 9 -0.34 3 12
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.032 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 -0.022 0.035 -10000 0 -0.48 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.012 0.015 -10000 0 -0.085 5 5
TRAF2/ASK1 0.027 0.006 -10000 0 -10000 0 0
ATM 0.018 0.007 -10000 0 -10000 0 0
MAP2K3 -0.033 0.11 -10000 0 -0.33 19 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.028 0.086 0.19 1 -0.33 10 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.008 0.09 -10000 0 -0.29 27 27
TXN 0.004 0.007 0.12 1 -10000 0 1
CALM1 0.02 0.005 -10000 0 -10000 0 0
GADD45A 0.02 0.002 -10000 0 -10000 0 0
GADD45B 0.019 0.005 -10000 0 -10000 0 0
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.02 0.003 -10000 0 -10000 0 0
MAP3K7 0.02 0.004 -10000 0 -10000 0 0
MAP3K4 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.029 0.007 -10000 0 -10000 0 0
TAK1/TAB family 0.003 0.014 -10000 0 -0.13 1 1
RAC1/OSM/MEKK3 0.038 0.009 -10000 0 -10000 0 0
TRAF2 0.02 0.003 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.012 0.094 -10000 0 -0.27 17 17
TRAF6 0.003 0.001 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.041 0.072 0.29 22 -10000 0 22
CCM2 0.02 0.002 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.037 0.042 0.19 19 -10000 0 19
MAPK11 0.02 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.046 0.041 0.2 18 -10000 0 18
OSM/MEKK3 0.03 0.006 -10000 0 -10000 0 0
TAOK1 0.006 0.002 -10000 0 -10000 0 0
TAOK2 0.006 0.002 -10000 0 -10000 0 0
TAOK3 0.006 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.004 -10000 0 -10000 0 0
MAP3K10 0.02 0.005 -10000 0 -10000 0 0
MAP3K3 0.02 0.004 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.006 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.026 0.058 -10000 0 -0.15 27 27
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.077 0.3 1 -0.26 8 9
ERC1 0.02 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.021 0.22 3 -10000 0 3
NFKBIA -0.02 0.019 0.19 2 -10000 0 2
BIRC2 0.016 0.008 -10000 0 -10000 0 0
IKBKB 0.02 0.005 -10000 0 -10000 0 0
RIPK2 0.02 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.073 -10000 0 -0.45 6 6
IKK complex/A20 0.023 0.095 0.32 1 -0.38 10 11
NEMO/A20/RIP2 0.02 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.087 -10000 0 -0.38 11 11
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.027 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.015 0.089 -10000 0 -0.38 10 10
BCL10/MALT1/TRAF6 0.038 0.012 -10000 0 -10000 0 0
NOD2 0.023 0.028 0.29 3 -10000 0 3
NFKB1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
MALT1 0.02 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.024 0.013 -10000 0 -10000 0 0
ATM 0.018 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.03 0.024 0.22 4 -10000 0 4
TRAF6 0.02 0.004 -10000 0 -10000 0 0
PRKCA 0.014 0.044 -10000 0 -0.29 6 6
CHUK 0.02 0.003 -10000 0 -10000 0 0
UBE2D3 0.02 0.003 -10000 0 -10000 0 0
TNF 0.023 0.032 0.29 4 -10000 0 4
NF kappa B1 p50/RelA 0.041 0.012 -10000 0 -10000 0 0
BCL10 0.021 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.019 0.19 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
IKK complex 0.017 0.095 -10000 0 -0.4 10 10
CYLD 0.02 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.019 0.098 -10000 0 -0.39 11 11
BARD1 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
BARD1/CSTF1 0.026 0.012 -10000 0 -10000 0 0
ATM 0.018 0.007 -10000 0 -10000 0 0
UBE2D3 0.02 0.003 -10000 0 -10000 0 0
PRKDC 0.02 0.004 -10000 0 -10000 0 0
ATR 0.015 0.009 -10000 0 -10000 0 0
UBE2L3 0.02 0.003 -10000 0 -10000 0 0
FANCD2 0.006 0.005 -10000 0 -10000 0 0
protein ubiquitination 0.042 0.034 0.19 4 -0.16 1 5
XRCC5 0.019 0.006 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
M/R/N Complex 0.034 0.017 -10000 0 -10000 0 0
MRE11A 0.018 0.007 -10000 0 -10000 0 0
DNA-PK 0.036 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.006 0.068 -10000 0 -0.36 3 3
FANCF 0.019 0.019 -10000 0 -0.29 1 1
BRCA1 0.02 0.002 -10000 0 -10000 0 0
CCNE1 0.024 0.032 0.29 4 -10000 0 4
CDK2/Cyclin E1 0.032 0.023 0.22 4 -10000 0 4
FANCG 0.02 0.003 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.016 -10000 0 -0.2 1 1
FANCE 0.02 0.003 -10000 0 -10000 0 0
FANCC 0.02 0.002 -10000 0 -10000 0 0
NBN 0.02 0.004 -10000 0 -10000 0 0
FANCA 0.039 0.071 0.29 21 -10000 0 21
DNA repair -0.004 0.073 0.23 10 -0.3 3 13
BRCA1/BARD1/ubiquitin 0.027 0.016 -10000 0 -0.2 1 1
BARD1/DNA-PK 0.044 0.023 -10000 0 -0.16 1 1
FANCL 0.02 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.025 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex -0.015 0.068 -10000 0 -0.21 29 29
BRCA1/BACH1/BARD1/TopBP1 0.029 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.033 0.026 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.035 0.016 -10000 0 -10000 0 0
BRCA1/BACH1 0.02 0.002 -10000 0 -10000 0 0
BARD1 0.018 0.019 -10000 0 -0.29 1 1
PCNA 0.019 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.036 0.018 -10000 0 -0.17 1 1
BRCA1/BARD1/UbcH7 0.036 0.019 -10000 0 -0.17 1 1
BRCA1/BARD1/RAD51/PCNA 0.043 0.028 0.21 2 -0.16 1 3
BARD1/DNA-PK/P53 0.047 0.029 -10000 0 -0.16 1 1
BRCA1/BARD1/Ubiquitin 0.027 0.016 -10000 0 -0.2 1 1
BRCA1/BARD1/CTIP 0.023 0.017 -10000 0 -0.16 1 1
FA complex 0.029 0.05 0.17 5 -0.2 4 9
BARD1/EWS 0.027 0.016 -10000 0 -0.2 1 1
RBBP8 -0.015 0.007 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
TOPBP1 0.016 0.009 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.031 0.025 -10000 0 -10000 0 0
BRCA1/BARD1 0.048 0.037 0.21 4 -0.16 1 5
CSTF1 0.019 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.013 0.013 -10000 0 -0.2 1 1
CDK2 0.02 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.024 0.036 0.29 5 -10000 0 5
RAD50 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.016 -10000 0 -0.2 1 1
EWSR1 0.02 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.047 0.018 -10000 0 -10000 0 0
MAP4K1 0.019 0.005 -10000 0 -10000 0 0
MAP3K8 0.02 0.004 -10000 0 -10000 0 0
PRKCB 0.018 0.026 -10000 0 -0.29 2 2
DBNL 0.02 0.002 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
MAP3K1 -0.007 0.03 -10000 0 -0.19 1 1
JUN -0.01 0.12 -10000 0 -0.53 14 14
MAP3K7 -0.008 0.035 -10000 0 -0.21 3 3
GRAP2 0.02 0.003 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.009 0.045 0.16 1 -0.24 2 3
LAT 0.02 0.002 -10000 0 -10000 0 0
LCP2 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.12 -10000 0 -0.55 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.041 -10000 0 -0.2 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 0.053 0.023 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.008 -10000 0 -10000 0 0
CRKL 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.002 -10000 0 -10000 0 0
DOCK1 0.02 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.045 0.021 0.21 1 -10000 0 1
EPO -0.004 0.076 -10000 0 -0.29 19 19
alpha4/beta7 Integrin 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.029 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.014 0.056 -10000 0 -0.2 18 18
lamellipodium assembly 0.037 0.057 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.019 0.015 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
JAK2 -0.001 0.046 -10000 0 -0.18 18 18
PXN 0.021 0.001 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
MADCAM1 0.014 0.022 0.29 1 -10000 0 1
cell adhesion 0.044 0.021 0.2 1 -10000 0 1
CRKL/CBL 0.025 0.012 -10000 0 -10000 0 0
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.023 0.034 0.17 5 -0.16 7 12
ITGB7 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.034 0.036 -10000 0 -0.17 8 8
p130Cas/Crk/Dock1 -0.029 0.037 0.17 6 -10000 0 6
VCAM1 0.012 0.051 -10000 0 -0.29 8 8
RHOA 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.015 -10000 0 -10000 0 0
BCAR1 -0.026 0.033 0.16 5 -10000 0 5
EPOR 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.017 0.008 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.058 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.013 0.01 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.018 0.015 -10000 0 -10000 0 0
MAP2K4 0.001 0.023 -10000 0 -0.24 1 1
IKBKB 0.02 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.019 0.006 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.006 -10000 0 -10000 0 0
SMPD1 0.003 0.003 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR3 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR1 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR4 0.018 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP 0.023 0.02 -10000 0 -10000 0 0
IKK complex 0.001 0.035 -10000 0 -10000 0 0
RIPK1 0.02 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.004 -10000 0 -10000 0 0
MAPK3 -0.011 0.018 0.26 1 -10000 0 1
MAP3K1 0.005 0.025 -10000 0 -0.25 1 1
TRAILR4 (trimer) 0.019 0.006 -10000 0 -10000 0 0
TRADD 0.02 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.003 0.026 -10000 0 -0.18 1 1
CFLAR 0.019 0.005 -10000 0 -10000 0 0
MAPK1 -0.011 0.019 0.26 1 -10000 0 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.033 0.033 -10000 0 -10000 0 0
mol:ceramide 0.003 0.003 -10000 0 -10000 0 0
FADD 0.019 0.005 -10000 0 -10000 0 0
MAPK8 0.01 0.049 -10000 0 -0.25 2 2
TRAF2 0.02 0.003 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.024 0.021 -10000 0 -10000 0 0
DAP3 0.019 0.005 -10000 0 -10000 0 0
CASP10 0.035 0.072 0.15 86 -10000 0 86
JNK cascade 0.018 0.015 -10000 0 -10000 0 0
TRAIL (trimer) 0.013 0.01 -10000 0 -10000 0 0
TNFRSF10C 0.019 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.027 0.025 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.024 0.021 -10000 0 -10000 0 0
cell death 0.003 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.003 0.026 0.14 1 -0.18 1 2
TRAILR2 (trimer) 0.019 0.006 -10000 0 -10000 0 0
CASP8 -0.019 0.12 -10000 0 -0.57 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.033 0.033 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.032 0.059 -10000 0 -10000 0 0
UGCG 0.016 0.029 -10000 0 -0.4 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.04 0.078 0.26 1 -0.39 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.018 0.029 -10000 0 -0.4 1 1
mol:DAG -0.002 0.12 -10000 0 -0.78 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.08 -10000 0 -0.34 5 5
FRAP1 0.031 0.086 -10000 0 -0.38 5 5
FOXO3 0.027 0.074 -10000 0 -0.36 3 3
AKT1 0.031 0.078 -10000 0 -0.38 3 3
GAB2 0.017 0.02 -10000 0 -0.29 1 1
SMPD1 -0.008 0.12 -10000 0 -0.55 14 14
SGMS1 0.006 0.086 -10000 0 -0.57 6 6
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 -0.009 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
cell proliferation 0.03 0.07 -10000 0 -0.39 3 3
EIF3A 0.02 0.003 -10000 0 -10000 0 0
PI3K 0.019 0.017 -10000 0 -10000 0 0
RPS6KB1 0.029 0.056 -10000 0 -0.7 1 1
mol:sphingomyelin -0.002 0.12 -10000 0 -0.78 6 6
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.02 0.008 -10000 0 -10000 0 0
PIK3R1 0.019 0.009 -10000 0 -10000 0 0
JAK1 0.02 0.008 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
MYC 0.034 0.12 -10000 0 -0.82 4 4
MYB 0.045 0.086 0.37 5 -10000 0 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.029 0.055 -10000 0 -0.28 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.047 0.053 -10000 0 -0.66 1 1
mol:PI-3-4-5-P3 0.028 0.055 -10000 0 -0.27 1 1
Rac1/GDP -0.01 0.011 -10000 0 -10000 0 0
T cell proliferation 0.026 0.055 -10000 0 -0.26 1 1
SHC1 0.018 0.009 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.01 0.025 0.079 34 -10000 0 34
PRKCZ 0.027 0.055 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA 0.046 0.084 -10000 0 -0.35 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.003 0.025 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL2RA 0.026 0.043 0.3 7 -10000 0 7
IL2RB 0.02 0.007 -10000 0 -10000 0 0
TERT -0.014 0.007 -10000 0 -10000 0 0
E2F1 0.045 0.073 0.34 5 -10000 0 5
SOS1 0.019 0.008 -10000 0 -10000 0 0
RPS6 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.005 0.014 -10000 0 -0.043 34 34
PTPN11 0.02 0.008 -10000 0 -10000 0 0
IL2RG 0.023 0.029 0.3 3 -10000 0 3
actin cytoskeleton organization 0.026 0.055 -10000 0 -0.26 1 1
GRB2 0.019 0.009 -10000 0 -10000 0 0
IL2 0.018 0.009 -10000 0 -10000 0 0
PIK3CA 0.013 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.024 0.021 -10000 0 -10000 0 0
LCK 0.02 0.008 -10000 0 -10000 0 0
BCL2 0.02 0.12 0.34 1 -0.74 5 6
IL6-mediated signaling events

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
BCL2L1 0.044 0.1 0.54 1 -10000 0 1
CRP 0.037 0.11 0.49 2 -10000 0 2
cell cycle arrest 0.03 0.093 -10000 0 -10000 0 0
TIMP1 0.033 0.1 -10000 0 -0.52 3 3
IL6ST 0.01 0.06 -10000 0 -0.29 11 11
Rac1/GDP 0.024 0.063 -10000 0 -0.3 2 2
AP1 0.042 0.11 -10000 0 -0.39 3 3
GAB2 0.02 0.02 -10000 0 -0.29 1 1
TNFSF11 0.031 0.1 0.43 1 -10000 0 1
HSP90B1 0.03 0.039 -10000 0 -10000 0 0
GAB1 0.021 0.005 -10000 0 -10000 0 0
MAPK14 -0.005 0.052 -10000 0 -0.32 1 1
AKT1 0.023 0.047 0.27 1 -10000 0 1
FOXO1 0.018 0.048 0.24 1 -10000 0 1
MAP2K6 0.001 0.05 -10000 0 -0.33 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.022 0.065 0.26 2 -0.35 1 3
MITF -0.013 0.066 0.19 2 -0.29 3 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.004 -10000 0 -10000 0 0
A2M -0.11 0.36 -10000 0 -1.1 32 32
CEBPB 0.021 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.032 0.083 -10000 0 -0.36 3 3
STAT3 0.031 0.093 -10000 0 -10000 0 0
STAT1 0.007 0.1 -10000 0 -0.68 6 6
CEBPD 0.031 0.092 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
PI3K 0.019 0.015 -10000 0 -10000 0 0
JUN 0.019 0.018 -10000 0 -0.29 1 1
PIAS3/MITF -0.009 0.076 -10000 0 -0.28 3 3
MAPK11 -0.004 0.051 -10000 0 -0.32 1 1
STAT3 (dimer)/FOXO1 0.024 0.11 0.4 2 -0.57 1 3
GRB2/SOS1/GAB family 0.049 0.074 0.23 1 -0.3 2 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.011 0.051 -10000 0 -0.27 2 2
GRB2 0.021 0.006 -10000 0 -10000 0 0
JAK2 0.019 0.005 -10000 0 -10000 0 0
LBP 0.05 0.097 0.46 3 -10000 0 3
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
JAK1 0.022 0.006 -10000 0 -10000 0 0
MYC 0.031 0.14 -10000 0 -0.85 4 4
FGG 0.023 0.087 -10000 0 -10000 0 0
macrophage differentiation 0.03 0.093 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.062 0.23 5 -0.23 2 7
JUNB 0.027 0.09 -10000 0 -10000 0 0
FOS -0.003 0.082 -10000 0 -0.29 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.016 0.056 0.23 1 -0.31 2 3
STAT1/PIAS1 0.035 0.068 0.26 2 -10000 0 2
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.045 -10000 0 -0.26 1 1
STAT3 (dimer) 0.029 0.094 -10000 0 -10000 0 0
PRKCD 0.011 0.074 -10000 0 -0.42 1 1
IL6R 0.016 0.037 -10000 0 -0.29 4 4
SOCS3 -0.002 0.057 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.038 0.045 -10000 0 -0.17 11 11
Rac1/GTP 0.025 0.064 -10000 0 -0.31 2 2
HCK 0.019 0.007 -10000 0 -10000 0 0
MAPKKK cascade 0.037 0.098 -10000 0 -0.4 5 5
bone resorption 0.031 0.099 0.43 1 -10000 0 1
IRF1 0.026 0.086 -10000 0 -10000 0 0
mol:GDP 0.005 0.054 0.2 2 -0.3 2 4
SOS1 0.022 0.007 -10000 0 -10000 0 0
VAV1 0.005 0.055 0.21 2 -0.3 2 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.01 0.06 -10000 0 -0.34 4 4
PTPN11 0.022 0.041 -10000 0 -0.63 1 1
IL6/IL6RA 0.033 0.043 0.23 7 -0.2 4 11
gp130 (dimer)/TYK2/TYK2/LMO4 0.034 0.044 -10000 0 -0.17 11 11
gp130 (dimer)/JAK2/JAK2/LMO4 0.033 0.044 -10000 0 -0.17 11 11
IL6 0.029 0.044 0.3 7 -10000 0 7
PIAS3 0.019 0.005 -10000 0 -10000 0 0
PTPRE 0.013 0.017 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.02 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.005 0.054 -10000 0 -0.27 3 3
LMO4 0.023 0.007 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.034 0.088 -10000 0 -10000 0 0
MCL1 0.034 0.073 0.33 1 -10000 0 1
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0.019 -10000 0 -0.29 1 1
ELF1 0.024 0.022 0.16 7 -10000 0 7
CCNA2 0.022 0.023 0.29 2 -10000 0 2
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
JAK3 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.004 -10000 0 -10000 0 0
JAK1 0.021 0.002 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.031 0.051 -10000 0 -10000 0 0
SHC1 0.019 0.006 -10000 0 -10000 0 0
SP1 0.012 0.055 -10000 0 -0.28 10 10
IL2RA -0.008 0.044 0.27 7 -10000 0 7
IL2RB 0.021 0.002 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
IL2RG 0.023 0.028 0.29 3 -10000 0 3
G1/S transition of mitotic cell cycle -0.022 0.13 0.27 2 -0.56 12 14
PTPN11 0.021 0.001 -10000 0 -10000 0 0
CCND2 -0.032 0.093 -10000 0 -0.55 9 9
LCK 0.021 0.001 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.018 0.005 -10000 0 -10000 0 0
CDK6 0.02 0.005 -10000 0 -10000 0 0
CCND3 0.027 0.054 0.28 1 -10000 0 1
Arf6 trafficking events

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
SLC2A4 -0.077 0.14 -10000 0 -0.29 90 90
CLTC 0.017 0.023 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.004 0.017 -10000 0 -0.16 1 1
Dynamin 2/GTP -0.018 0.005 -10000 0 -10000 0 0
EXOC4 0.02 0.004 -10000 0 -10000 0 0
CD59 0.004 0.012 -10000 0 -10000 0 0
CPE -0.022 0.034 -10000 0 -0.17 15 15
CTNNB1 0.019 0.006 -10000 0 -10000 0 0
membrane fusion 0.004 0.015 -10000 0 -10000 0 0
CTNND1 -0.016 0.035 0.17 10 -10000 0 10
DNM2 0.02 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.028 0.16 2 -10000 0 2
TSHR -0.014 0.01 0.15 1 -10000 0 1
INS -0.008 0.099 -10000 0 -0.43 15 15
BIN1 0.02 0.002 -10000 0 -10000 0 0
mol:Choline 0.004 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.005 -10000 0 -10000 0 0
JUP 0.004 0.013 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.037 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.064 0.038 0.2 1 -10000 0 1
clathrin-independent pinocytosis 0.015 0.002 -10000 0 -10000 0 0
MAPK8IP3 0.02 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.002 -10000 0 -10000 0 0
EXOC2 0.02 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.004 0.039 -10000 0 -0.33 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.02 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.041 0.022 -10000 0 -10000 0 0
positive regulation of phagocytosis -0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.026 0.007 -10000 0 -10000 0 0
ACAP1 0.006 0.018 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.012 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.007 0.025 0.23 1 -10000 0 1
JIP4/KLC1 0.037 0.01 -10000 0 -10000 0 0
EXOC1 0.02 0.004 -10000 0 -10000 0 0
exocyst -0.004 0.039 -10000 0 -0.34 1 1
RALA/GTP 0.015 0.002 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.006 -10000 0 -10000 0 0
receptor recycling 0.015 0.002 -10000 0 -10000 0 0
CTNNA1 -0.016 0.034 0.17 9 -10000 0 9
NME1 -0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.019 0.03 0.25 1 -10000 0 1
IL2RA 0.005 0.015 -10000 0 -10000 0 0
VAMP3 -0.014 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.013 0.063 -10000 0 -10000 0 0
EXOC6 0.02 0.004 -10000 0 -10000 0 0
PLD1 0.003 0.003 -10000 0 -10000 0 0
PLD2 0.004 0.002 -10000 0 -10000 0 0
EXOC5 0.02 0.003 -10000 0 -10000 0 0
PIP5K1C 0.002 0.025 0.16 1 -10000 0 1
SDC1 0.067 0.036 0.2 1 -10000 0 1
ARF6/GDP 0.016 0.003 -10000 0 -10000 0 0
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.044 0.023 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.015 -10000 0 -10000 0 0
endocytosis -0.036 0.01 -10000 0 -10000 0 0
SCAMP2 0.02 0.004 -10000 0 -10000 0 0
ADRB2 0.011 0.038 0.23 1 -10000 0 1
EXOC3 0.017 0.008 -10000 0 -10000 0 0
ASAP2 0.02 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.018 0.005 -10000 0 -10000 0 0
KLC1 0.02 0.004 -10000 0 -10000 0 0
AVPR2 -0.011 0.069 0.37 1 -0.27 1 2
RALA 0.02 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.023 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.027 0.036 -10000 0 -0.15 11 11
MAPK9 0.003 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.007 -10000 0 -10000 0 0
GNB1 0.02 0.004 -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 0.003 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.007 0.03 -10000 0 -0.14 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0.008 0.042 11 -10000 0 11
GNAL 0.008 0.059 -10000 0 -0.29 11 11
GNG2 0.02 0.003 -10000 0 -10000 0 0
CRH -0.017 0.004 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.019 -10000 0 -0.23 2 2
MAPK11 0.003 0.001 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.005 -9999 0 -10000 0 0
SMAD2 -0.009 0.054 -9999 0 -0.25 5 5
SMAD3 -0.006 0.038 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.069 -9999 0 -0.37 8 8
SMAD4/Ubc9/PIASy 0.037 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.021 0.06 -9999 0 -0.23 5 5
PPM1A 0.02 0.003 -9999 0 -10000 0 0
CALM1 0.02 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0.052 -9999 0 -0.24 5 5
MAP3K1 0.02 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.021 -9999 0 -0.2 2 2
MAPK3 0.02 0.002 -9999 0 -10000 0 0
MAPK1 0.02 0.002 -9999 0 -10000 0 0
NUP214 0.02 0.002 -9999 0 -10000 0 0
CTDSP1 0.018 0.006 -9999 0 -10000 0 0
CTDSP2 0.02 0.002 -9999 0 -10000 0 0
CTDSPL 0.019 0.005 -9999 0 -10000 0 0
KPNB1 0.021 0.002 -9999 0 -10000 0 0
TGFBRAP1 0.018 0.026 -9999 0 -0.29 2 2
UBE2I 0.02 0.004 -9999 0 -10000 0 0
NUP153 0.02 0.005 -9999 0 -10000 0 0
KPNA2 0.02 0.004 -9999 0 -10000 0 0
PIAS4 0.02 0.005 -9999 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.025 0.012 0.19 1 -10000 0 1
EFNA5 0.02 0.005 -10000 0 -10000 0 0
FYN -0.019 0.021 0.17 1 -0.16 4 5
neuron projection morphogenesis 0.025 0.012 0.19 1 -10000 0 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.025 0.012 0.19 1 -10000 0 1
EPHA5 0.003 0.025 0.29 1 -10000 0 1
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.003 -10000 0 -10000 0 0
HDAC4 0.018 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.018 0.005 -10000 0 -10000 0 0
CDKN1A -0.012 0.004 -10000 0 -10000 0 0
KAT2B 0.019 0.005 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.002 0.003 -10000 0 -10000 0 0
FOXO1 0.017 0.026 -10000 0 -0.29 2 2
FOXO4 0.005 0.001 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
TAT 0.004 0.025 0.29 1 -10000 0 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.006 -10000 0 -10000 0 0
PPARGC1A -0.001 0.078 0.29 1 -0.29 19 20
FHL2 0.018 0.026 -10000 0 -0.29 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.007 -10000 0 -10000 0 0
HIST2H4A -0.018 0.005 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.016 0.021 -10000 0 -0.2 1 1
SIRT1 0.019 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.033 0.017 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.038 -10000 0 -0.22 2 2
apoptosis -0.038 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A 0.013 0.049 0.19 1 -0.17 19 20
p53/SIRT1 0.026 0.009 -10000 0 -10000 0 0
SIRT1/FOXO4 0.016 0.028 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.033 0.025 -10000 0 -0.15 4 4
HIST1H1E 0.007 0.016 -10000 0 -10000 0 0
SIRT1/p300 0.029 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.02 0.012 -10000 0 -10000 0 0
TP53 0.018 0.006 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.038 0.011 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
MEF2D 0.019 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.013 0.22 1 -10000 0 1
ACSS2 -0.017 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.02 0.012 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.036 0.052 0.24 1 -10000 0 1
Ran/GTP/Exportin 1/HDAC1 -0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.014 0.061 0.21 1 -0.24 7 8
SUMO1 0.019 0.005 -10000 0 -10000 0 0
ZFPM1 0.019 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.005 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.003 -10000 0 -10000 0 0
Histones 0.039 0.047 -10000 0 -10000 0 0
YY1/LSF 0.008 0.044 -10000 0 -0.22 2 2
SMG5 0.019 0.005 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.01 0.022 0.15 2 -10000 0 2
I kappa B alpha/HDAC1 0.019 0.041 -10000 0 -10000 0 0
SAP18 0.02 0.004 -10000 0 -10000 0 0
RELA 0.012 0.031 0.16 1 -10000 0 1
HDAC1/Smad7 0.038 0.012 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
HDAC3/TR2 0.019 0.044 -10000 0 -0.17 8 8
NuRD/MBD3 Complex 0.002 0.048 -10000 0 -0.26 2 2
NF kappa B1 p50/RelA 0.015 0.06 0.2 1 -0.24 7 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.009 0.048 -10000 0 -0.29 7 7
GATA1 0.012 0.023 0.29 1 -10000 0 1
Mad/Max 0.029 0.006 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.003 0.058 -10000 0 -0.23 6 6
RBBP7 0.02 0.004 -10000 0 -10000 0 0
NPC 0.012 0.002 -10000 0 -10000 0 0
RBBP4 0.021 0.001 -10000 0 -10000 0 0
MAX 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.004 -10000 0 -10000 0 0
NFKBIA 0.011 0.013 -10000 0 -10000 0 0
KAT2B 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.001 0.03 -10000 0 -10000 0 0
SIN3 complex 0.046 0.018 -10000 0 -10000 0 0
SMURF1 0.02 0.004 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.019 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.006 0.036 -10000 0 -0.22 1 1
YY1/HDAC2 0.009 0.044 -10000 0 -0.22 2 2
YY1/HDAC1 0.008 0.045 -10000 0 -0.22 2 2
NuRD/MBD2 Complex (MeCP1) 0.001 0.051 -10000 0 -0.3 3 3
PPARG 0 0.067 0.18 1 -0.24 15 16
HDAC8/hEST1B 0.037 0.013 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.043 -10000 0 -0.17 8 8
MBD3L2 -0.017 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.012 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.06 -10000 0 -0.26 7 7
HDAC1 0.021 0.001 -10000 0 -10000 0 0
HDAC3 0.011 0.013 -10000 0 -10000 0 0
HDAC2 0.02 0.003 -10000 0 -10000 0 0
YY1 0.006 0.003 -10000 0 -10000 0 0
HDAC8 0.02 0.002 -10000 0 -10000 0 0
SMAD7 0.02 0.004 -10000 0 -10000 0 0
NCOR2 0.021 0.002 -10000 0 -10000 0 0
MXD1 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.009 0.003 -10000 0 -10000 0 0
NFKB1 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.046 -10000 0 -0.21 2 2
YY1/SAP30/HDAC1 0.018 0.047 -10000 0 -0.21 2 2
EP300 0.02 0.003 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.009 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.013 -10000 0 -10000 0 0
histone deacetylation 0.001 0.05 -10000 0 -0.3 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.01 0.024 -10000 0 -10000 0 0
nuclear export -0.037 0.013 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
GATAD2B 0.019 0.005 -10000 0 -10000 0 0
GATAD2A 0.02 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.01 0.048 -10000 0 -0.18 1 1
GATA1/HDAC1 0.03 0.012 0.22 1 -10000 0 1
GATA1/HDAC3 0.018 0.045 0.2 1 -0.17 8 9
CHD4 0.019 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.03 0.024 0.22 4 -10000 0 4
SIN3/HDAC complex/Mad/Max 0.006 0.04 -10000 0 -0.26 2 2
NuRD Complex 0 0.056 -10000 0 -0.26 4 4
positive regulation of chromatin silencing 0.037 0.046 -10000 0 -10000 0 0
SIN3B 0.02 0.003 -10000 0 -10000 0 0
MTA2 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.004 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.019 0.04 -10000 0 -0.17 4 4
HDAC complex 0.05 0.013 -10000 0 -10000 0 0
GATA1/Fog1 0.028 0.014 0.22 1 -10000 0 1
FKBP25/HDAC1/HDAC2 0.04 0.009 -10000 0 -10000 0 0
TNF 0.023 0.032 0.29 4 -10000 0 4
negative regulation of cell growth 0.006 0.04 -10000 0 -0.26 2 2
NuRD/MBD2/PRMT5 Complex 0.001 0.051 -10000 0 -0.3 3 3
Ran/GTP/Exportin 1 0.018 0.039 -10000 0 -0.16 4 4
NF kappa B/RelA/I kappa B alpha 0.004 0.046 0.19 2 -0.22 5 7
SIN3/HDAC complex/NCoR1 -0.004 0.049 -10000 0 -0.25 6 6
TFCP2 0.02 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.001 -10000 0 -10000 0 0
MBD3 0.019 0.005 -10000 0 -10000 0 0
MBD2 0.02 0.005 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.02 0.004 -10000 0 -9999 0 0
GPC2 0.022 0.023 0.29 2 -9999 0 2
GPC2/Midkine 0.029 0.018 0.22 2 -9999 0 2
neuron projection morphogenesis 0.029 0.018 0.22 2 -9999 0 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.021 0.001 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.018 0.04 -10000 0 -0.17 4 4
HDAC4 0.018 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.021 0.008 -10000 0 -10000 0 0
SUMO1 0.019 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 -0.001 0.025 -10000 0 -0.19 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.012 0.027 -10000 0 -0.17 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.02 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.021 0.031 -10000 0 -0.16 4 4
SUMO1/HDAC1 0.019 0.04 -10000 0 -0.17 4 4
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.019 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.005 0.002 -10000 0 -10000 0 0
Ran/GTP 0.009 0.036 -10000 0 -0.16 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.004 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.008 0.044 0.18 7 -0.16 4 11
NPC 0.012 0.002 -10000 0 -10000 0 0
PIAS2 0.02 0.004 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.021 0.017 -10000 0 -0.29 1 1
PI3K Class IB/PDE3B 0.021 0.017 0.29 1 -10000 0 1
PDE3B 0.021 0.017 0.29 1 -10000 0 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.004 0.035 0.14 17 -10000 0 17
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.009 0.037 0.13 12 -0.13 1 13
AP2 0.02 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.023 0.015 -10000 0 -10000 0 0
CLTB 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.005 -10000 0 -10000 0 0
CD4 0.02 0.005 -10000 0 -10000 0 0
CLTA 0.02 0.003 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ARFGAP1 -0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.014 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.011 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.004 0.007 -10000 0 -10000 0 0
mol:Choline -0.001 0.014 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.02 0.008 -10000 0 -10000 0 0
DDEF1 0 0.014 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.018 -10000 0 -0.087 8 8
AP2M1 0.013 0.01 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.016 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.012 -10000 0 -10000 0 0
ARFIP2 0.012 0.019 -10000 0 -10000 0 0
COPA 0.019 0.005 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.018 -10000 0 -0.15 2 2
ARF1/GTP/ARHGAP10 0.013 0.006 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.013 0.019 -10000 0 -0.23 1 1
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.002 0.031 -10000 0 -0.16 10 10
ARF1/GDP/Membrin 0.015 0.022 -10000 0 -0.26 1 1
Arfaptin 2/Rac/GDP 0.021 0.017 -10000 0 -10000 0 0
CYTH2 0.023 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.015 0.002 -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 0.007 0.017 -10000 0 -0.16 1 1
PLD2 -0.001 0.014 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0.002 -10000 0 -10000 0 0
PIP5K1A -0.001 0.014 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.014 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.006 0.02 -10000 0 -0.32 1 1
USO1 0.001 0.043 -10000 0 -0.32 5 5
GBF1 0.003 0.038 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.023 0.016 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.026 0.021 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.02 0.004 -9999 0 -9999 0 0
PLK4 0.02 0.003 -9999 0 -9999 0 0
regulation of centriole replication -0.017 0.005 -9999 0 -9999 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.017 0.019 -9999 0 -10000 0 0
CLOCK 0.02 0.004 -9999 0 -10000 0 0
TIMELESS/CRY2 0.017 0.016 -9999 0 -10000 0 0
DEC1/BMAL1 0.027 0.007 -9999 0 -10000 0 0
ATR 0.015 0.009 -9999 0 -10000 0 0
NR1D1 0.004 0.004 -9999 0 -10000 0 0
ARNTL 0.02 0.004 -9999 0 -10000 0 0
TIMELESS 0.004 0.004 -9999 0 -10000 0 0
NPAS2 0.019 0.026 -9999 0 -0.29 2 2
CRY2 0.02 0.004 -9999 0 -10000 0 0
mol:CO -0.002 0 -9999 0 -10000 0 0
CHEK1 0.017 0.008 -9999 0 -10000 0 0
mol:HEME 0.002 0 -9999 0 -10000 0 0
PER1 0.019 0.006 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.04 0.021 -9999 0 -0.16 2 2
BMAL1/CLOCK 0.002 0.048 -9999 0 -0.33 1 1
S phase of mitotic cell cycle 0.017 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.018 0.019 -9999 0 -10000 0 0
mol:NADPH 0.002 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.017 0.013 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.009 0.015 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.02 0.003 -9999 0 -9999 0 0
ITGB7 0.02 0.003 -9999 0 -9999 0 0
ITGA4 0.02 0.004 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.029 0.007 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.029 0.007 -9999 0 -9999 0 0
Arf6 downstream 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
PLAUR 0.01 0.013 -10000 0 -10000 0 0
regulation of axonogenesis 0.002 0.005 -10000 0 -10000 0 0
myoblast fusion -0.027 0.039 -10000 0 -10000 0 0
mol:GTP 0.02 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.04 0.024 0.16 2 -10000 0 2
ARF1/GTP 0.028 0.018 -10000 0 -10000 0 0
mol:GM1 0.009 0.012 -10000 0 -10000 0 0
mol:Choline -0.007 0.008 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.01 -10000 0 -10000 0 0
MAPK3 0.013 0.012 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.025 -10000 0 -0.16 2 2
ARF1 0.019 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.039 -10000 0 -10000 0 0
ARF1/GDP 0.027 0.031 -10000 0 -10000 0 0
ARF6 0.03 0.019 -10000 0 -10000 0 0
RAB11A 0.02 0.003 -10000 0 -10000 0 0
TIAM1 0.018 0.027 -10000 0 -0.29 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.012 -10000 0 -10000 0 0
actin filament bundle formation -0.026 0.029 -10000 0 -10000 0 0
KALRN -0.001 0.032 -10000 0 -0.16 1 1
RAB11FIP3/RAB11A 0.029 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.03 -10000 0 -10000 0 0
NME1 0.02 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.029 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.02 0.016 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.007 0.01 -10000 0 -10000 0 0
RAC1 0.02 0.003 -10000 0 -10000 0 0
liver development 0.02 0.016 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.016 -10000 0 -10000 0 0
RhoA/GTP 0.028 0.019 -10000 0 -10000 0 0
mol:GDP 0.006 0.006 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.016 -10000 0 -10000 0 0
RHOA 0.019 0.006 -10000 0 -10000 0 0
PLD1 0.006 0.009 -10000 0 -10000 0 0
RAB11FIP3 0.02 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.01 -10000 0 -10000 0 0
ruffle organization -0.002 0.005 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.02 0.016 -10000 0 -10000 0 0
PLD2 0.013 0.014 -10000 0 -10000 0 0
PIP5K1A -0.002 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.007 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.01 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.022 0.01 -9999 0 -10000 0 0
DOCK1 0.02 0.003 -9999 0 -10000 0 0
ITGA4 0.02 0.004 -9999 0 -10000 0 0
RAC1 0.02 0.003 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.012 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.028 0.008 -9999 0 -10000 0 0
lamellipodium assembly -0.011 0.069 -9999 0 -0.4 7 7
PIK3CA 0.013 0.01 -9999 0 -10000 0 0
PI3K 0.019 0.015 -9999 0 -10000 0 0
ARF6 0.02 0.003 -9999 0 -10000 0 0
TLN1 0.02 0.003 -9999 0 -10000 0 0
PXN -0.018 0.003 -9999 0 -10000 0 0
PIK3R1 0.02 0.004 -9999 0 -10000 0 0
ARF6/GTP 0.035 0.016 -9999 0 -10000 0 0
cell adhesion 0.036 0.012 -9999 0 -10000 0 0
CRKL/CBL 0.025 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.009 -9999 0 -10000 0 0
ITGB1 0.02 0.003 -9999 0 -10000 0 0
ITGB7 0.02 0.003 -9999 0 -10000 0 0
ARF6/GDP 0.022 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.033 0.034 -9999 0 -0.16 8 8
p130Cas/Crk/Dock1 0.037 0.014 -9999 0 -10000 0 0
VCAM1 0.012 0.051 -9999 0 -0.29 8 8
alpha4/beta1 Integrin/Paxillin/Talin 0.038 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.037 0.013 -9999 0 -10000 0 0
BCAR1 0.02 0.004 -9999 0 -10000 0 0
mol:GDP -0.036 0.013 -9999 0 -10000 0 0
CBL 0.017 0.008 -9999 0 -10000 0 0
PRKACA 0.02 0.004 -9999 0 -10000 0 0
GIT1 0.02 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.038 0.013 -9999 0 -10000 0 0
Rac1/GTP -0.012 0.076 -9999 0 -0.44 7 7
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.029 0.008 -10000 0 -9999 0 0
FBXW11 0.02 0.004 -10000 0 -9999 0 0
NF kappa B1 p50/c-Rel -0.02 0.006 -10000 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.034 0.22 3 -9999 0 3
NFKBIA 0.001 0 -10000 0 -9999 0 0
MAPK14 0.02 0.003 -10000 0 -9999 0 0
NF kappa B1 p105/p50 -0.02 0.007 -10000 0 -9999 0 0
ARRB2 0.006 0.002 -10000 0 -9999 0 0
REL 0.02 0.003 -10000 0 -9999 0 0
response to oxidative stress 0 0 -10000 0 -9999 0 0
BCL3/NF kappa B1 p50 -0.019 0.007 -10000 0 -9999 0 0
response to UV 0 0 -10000 0 -9999 0 0
NF kappa B1 p105/RelA -0.02 0.006 -10000 0 -9999 0 0
PIK3CA 0.013 0.01 -10000 0 -9999 0 0
NF kappa B1 p50 dimer -0.017 0.008 -10000 0 -9999 0 0
PIK3R1 0.02 0.004 -10000 0 -9999 0 0
NFKB1 -0.017 0.005 -10000 0 -9999 0 0
RELA 0.02 0.003 -10000 0 -9999 0 0
positive regulation of anti-apoptosis 0.009 0.022 -10000 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.019 0.035 0.17 2 -9999 0 2
SRC 0.019 0.006 -10000 0 -9999 0 0
PI3K 0.019 0.015 -10000 0 -9999 0 0
NF kappa B1 p50/RelA 0.009 0.022 -10000 0 -9999 0 0
IKBKB 0.02 0.005 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.004 -10000 0 -9999 0 0
SYK 0.02 0.003 -10000 0 -9999 0 0
I kappa B alpha/PIK3R1 0.024 0.037 0.23 3 -9999 0 3
cell death 0.018 0.034 0.16 2 -9999 0 2
NF kappa B1 p105/c-Rel -0.02 0.006 -10000 0 -9999 0 0
LCK 0.021 0.001 -10000 0 -9999 0 0
BCL3 0.02 0.005 -10000 0 -9999 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 0.03 0.006 -9999 0 -9999 0 0
FBXW11 0.02 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.004 -9999 0 -9999 0 0
CHUK 0.02 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.053 0.022 -9999 0 -9999 0 0
NFKB1 0.02 0.003 -9999 0 -9999 0 0
MAP3K14 0.02 0.002 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.029 0.008 -9999 0 -9999 0 0
RELB 0.02 0.004 -9999 0 -9999 0 0
NFKB2 0.02 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.026 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.026 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 292 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZX.AA5X TCGA.ZJ.AB0I TCGA.ZJ.AB0H TCGA.ZJ.AAXU
109_MAP3K5 0.0056 -0.14 0.0056 0.0056
47_PPARGC1A 0.021 0 0.021 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 0.021 0.021 0.021
105_BMP7 0.021 0.021 0.021 0.021
105_BMP2 0.021 0.021 0.021 0.021
131_RELN/VLDLR 0.053 -0.12 -0.16 0.053
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.021 0.021
84_STAT5B -0.067 -0.35 -0.063 -0.099
84_STAT5A -0.067 -0.35 -0.063 -0.099
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/CESC-TP/22312681/CESC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/CESC-TP/22489353/Gistic2_Analysis_22506437/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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