PARADIGM pathway analysis of mRNASeq expression data
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1CJ8CPJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1CJ8CPJ
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 48 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
Nephrin/Neph1 signaling in the kidney podocyte 403
EGFR-dependent Endothelin signaling events 256
HIF-1-alpha transcription factor network 239
TCGA08_p53 223
PDGFR-alpha signaling pathway 212
FOXA2 and FOXA3 transcription factor networks 201
FOXM1 transcription factor network 190
TCR signaling in naïve CD8+ T cells 184
Aurora B signaling 182
Syndecan-4-mediated signaling events 172
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 889 . 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 ( 889 ).

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
Nephrin/Neph1 signaling in the kidney podocyte 0.4533 403 13711 34 -0.66 0.015 1000 -1000 -0.092 -1000
EGFR-dependent Endothelin signaling events 0.2880 256 5379 21 -0.71 0.015 1000 -1000 -0.093 -1000
HIF-1-alpha transcription factor network 0.2688 239 18205 76 -0.92 0.025 1000 -1000 -0.16 -1000
TCGA08_p53 0.2508 223 1565 7 -0.5 0.25 1000 -1000 -0.024 -1000
PDGFR-alpha signaling pathway 0.2385 212 9370 44 -0.33 0.034 1000 -1000 -0.095 -1000
FOXA2 and FOXA3 transcription factor networks 0.2261 201 9249 46 -1.2 0.024 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 0.2137 190 9690 51 -0.64 0.033 1000 -1000 -0.18 -1000
TCR signaling in naïve CD8+ T cells 0.2070 184 17115 93 -0.66 0.31 1000 -1000 -0.11 -1000
Aurora B signaling 0.2047 182 12244 67 -0.38 0.015 1000 -1000 -0.098 -1000
Syndecan-4-mediated signaling events 0.1935 172 11531 67 -0.48 0.099 1000 -1000 -0.12 -1000
Glypican 2 network 0.1879 167 670 4 -0.15 -1000 1000 -1000 -0.057 -1000
Glypican 1 network 0.1867 166 7997 48 -0.57 0.043 1000 -1000 -0.068 -1000
amb2 Integrin signaling 0.1564 139 11446 82 -0.59 0.015 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1552 138 12162 88 -0.52 0.03 1000 -1000 -0.17 -1000
IL12-mediated signaling events 0.1507 134 11694 87 -0.45 0.14 1000 -1000 -0.16 -1000
BMP receptor signaling 0.1305 116 9423 81 -0.67 0.015 1000 -1000 -0.13 -1000
Aurora C signaling 0.1237 110 773 7 -0.3 0.008 1000 -1000 -0.058 -1000
IL4-mediated signaling events 0.1226 109 9979 91 -0.76 0.55 1000 -1000 -0.18 -1000
TCGA08_retinoblastoma 0.1204 107 862 8 -0.66 0.17 1000 -1000 -0.039 -1000
Effects of Botulinum toxin 0.1024 91 2368 26 -0.36 0.015 1000 -1000 -0.089 -1000
Syndecan-1-mediated signaling events 0.1012 90 3078 34 -0.28 0.015 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0979 87 5428 62 -0.71 0.015 1000 -1000 -0.091 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0844 75 5166 68 -0.44 0.078 1000 -1000 -0.16 -1000
Endothelins 0.0821 73 7014 96 -0.5 0.016 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 0.0810 72 865 12 -0.16 0.026 1000 -1000 -0.041 -1000
Fc-epsilon receptor I signaling in mast cells 0.0810 72 7042 97 -0.31 0.041 1000 -1000 -0.13 -1000
Caspase cascade in apoptosis 0.0799 71 5272 74 -0.32 0.086 1000 -1000 -0.085 -1000
IL23-mediated signaling events 0.0787 70 4205 60 -0.3 0.021 1000 -1000 -0.19 -1000
S1P1 pathway 0.0754 67 2420 36 -0.22 0.015 1000 -1000 -0.087 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0754 67 2215 33 -0.65 0.015 1000 -1000 -0.086 -1000
Thromboxane A2 receptor signaling 0.0742 66 6981 105 -0.71 0.03 1000 -1000 -0.11 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0742 66 5175 78 -0.39 0.06 1000 -1000 -0.098 -1000
Signaling events mediated by the Hedgehog family 0.0731 65 3407 52 -0.23 0.099 1000 -1000 -0.11 -1000
JNK signaling in the CD4+ TCR pathway 0.0731 65 1119 17 -0.24 0.015 1000 -1000 -0.096 -1000
IL27-mediated signaling events 0.0697 62 3208 51 -0.72 0.064 1000 -1000 -0.11 -1000
Ephrin A reverse signaling 0.0664 59 413 7 -0.053 0 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 0.0664 59 2566 43 -0.4 0.13 1000 -1000 -0.11 -1000
Integrins in angiogenesis 0.0607 54 4568 84 -0.45 0.039 1000 -1000 -0.12 -1000
Calcium signaling in the CD4+ TCR pathway 0.0607 54 1698 31 -0.33 0.015 1000 -1000 -0.16 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0585 52 2820 54 -0.57 0.029 1000 -1000 -0.14 -1000
PLK1 signaling events 0.0585 52 4482 85 -0.32 0.015 1000 -1000 -0.079 -1000
Coregulation of Androgen receptor activity 0.0574 51 3936 76 -0.87 0.036 1000 -1000 -0.073 -1000
p75(NTR)-mediated signaling 0.0562 50 6355 125 -0.44 0.015 1000 -1000 -0.15 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0562 50 6292 125 -0.28 0.016 1000 -1000 -0.14 -1000
Reelin signaling pathway 0.0529 47 2659 56 -0.23 0.015 1000 -1000 -0.13 -1000
IL2 signaling events mediated by STAT5 0.0517 46 1024 22 -0.26 0.022 1000 -1000 -0.061 -1000
Signaling events mediated by PTP1B 0.0506 45 3423 76 -0.71 0.06 1000 -1000 -0.11 -1000
IL6-mediated signaling events 0.0506 45 3412 75 -0.23 0.075 1000 -1000 -0.12 -1000
Glucocorticoid receptor regulatory network 0.0495 44 5057 114 -0.44 0.17 1000 -1000 -0.11 -1000
IL2 signaling events mediated by PI3K 0.0484 43 2517 58 -0.26 0.032 1000 -1000 -0.11 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0484 43 5195 120 -0.25 0.17 1000 -1000 -0.12 -1000
Regulation of Telomerase 0.0461 41 4244 102 -0.71 0.035 1000 -1000 -0.14 -1000
BCR signaling pathway 0.0461 41 4060 99 -0.19 0.032 1000 -1000 -0.14 -1000
Visual signal transduction: Rods 0.0450 40 2114 52 -0.21 0.015 1000 -1000 -0.13 -1000
Syndecan-2-mediated signaling events 0.0394 35 2433 69 -0.59 0.047 1000 -1000 -0.095 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0382 34 962 28 -0.13 0.015 1000 -1000 -0.088 -1000
PLK2 and PLK4 events 0.0371 33 100 3 -0.023 0.011 1000 -1000 -0.038 -1000
Presenilin action in Notch and Wnt signaling 0.0371 33 2027 61 -0.22 0.098 1000 -1000 -0.096 -1000
Signaling events regulated by Ret tyrosine kinase 0.0371 33 2752 82 -0.12 0.015 1000 -1000 -0.12 -1000
Wnt signaling 0.0371 33 234 7 -0.084 0.015 1000 -1000 -0.077 -1000
Aurora A signaling 0.0360 32 1930 60 -0.22 0.05 1000 -1000 -0.092 -1000
VEGFR1 specific signals 0.0360 32 1820 56 -0.24 0.039 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 0.0337 30 4163 136 -0.44 0.099 1000 -1000 -0.11 -1000
E-cadherin signaling events 0.0326 29 149 5 -0.036 0.015 1000 -1000 -0.067 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0315 28 2123 74 -0.71 0.089 1000 -1000 -0.13 -1000
Nongenotropic Androgen signaling 0.0304 27 1440 52 -0.11 0.04 1000 -1000 -0.085 -1000
ErbB4 signaling events 0.0292 26 1796 69 -0.16 0.12 1000 -1000 -0.11 -1000
Regulation of Androgen receptor activity 0.0292 26 1860 70 -0.92 0.039 1000 -1000 -0.1 -1000
Ceramide signaling pathway 0.0281 25 1933 76 -0.71 0.23 1000 -1000 -0.092 -1000
FoxO family signaling 0.0281 25 1640 64 -0.66 0.12 1000 -1000 -0.1 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0281 25 1127 45 -0.34 0.068 1000 -1000 -0.13 -1000
Plasma membrane estrogen receptor signaling 0.0270 24 2118 86 -0.12 0.052 1000 -1000 -0.11 -1000
S1P3 pathway 0.0270 24 1032 42 -0.21 0.035 1000 -1000 -0.077 -1000
Noncanonical Wnt signaling pathway 0.0259 23 604 26 -0.15 0.015 1000 -1000 -0.12 -1000
Canonical Wnt signaling pathway 0.0259 23 1188 51 -0.22 0.1 1000 -1000 -0.086 -1000
LPA receptor mediated events 0.0247 22 2331 102 -0.28 0.043 1000 -1000 -0.13 -1000
Visual signal transduction: Cones 0.0236 21 805 38 -0.04 0.015 1000 -1000 -0.09 -1000
EPO signaling pathway 0.0236 21 1190 55 -0.15 0.038 1000 -1000 -0.14 -1000
S1P5 pathway 0.0236 21 365 17 -0.093 0.041 1000 -1000 -0.072 -1000
Ephrin B reverse signaling 0.0236 21 1044 48 -0.096 0.074 1000 -1000 -0.1 -1000
Class IB PI3K non-lipid kinase events 0.0236 21 63 3 -0.005 -1000 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0225 20 773 37 -0.15 0.015 1000 -1000 -0.12 -1000
FAS signaling pathway (CD95) 0.0214 19 933 47 -0.26 0.025 1000 -1000 -0.067 -1000
Osteopontin-mediated events 0.0202 18 697 38 -0.058 0.053 1000 -1000 -0.15 -1000
a4b1 and a4b7 Integrin signaling 0.0202 18 90 5 -0.019 0.015 1000 -1000 -0.056 -1000
Insulin-mediated glucose transport 0.0202 18 583 32 -0.15 0.071 1000 -1000 -0.092 -1000
IFN-gamma pathway 0.0202 18 1273 68 -0.28 0.04 1000 -1000 -0.13 -1000
IL1-mediated signaling events 0.0191 17 1098 62 -0.17 0.054 1000 -1000 -0.15 -1000
Signaling mediated by p38-alpha and p38-beta 0.0191 17 760 44 -0.093 0.021 1000 -1000 -0.07 -1000
TCGA08_rtk_signaling 0.0191 17 452 26 -0.33 0.037 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0191 17 1262 73 -0.24 0.033 1000 -1000 -0.11 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0169 15 1307 85 -0.062 0.059 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0169 15 1282 85 -0.096 0.054 1000 -1000 -0.14 -1000
S1P4 pathway 0.0169 15 385 25 -0.093 0.03 1000 -1000 -0.074 -1000
Syndecan-3-mediated signaling events 0.0157 14 513 35 -0.083 0.015 1000 -1000 -0.1 -1000
E-cadherin signaling in the nascent adherens junction 0.0157 14 1126 76 -0.038 0.056 1000 -1000 -0.12 -1000
BARD1 signaling events 0.0135 12 735 57 -0.16 0.031 1000 -1000 -0.092 -1000
Signaling events mediated by PRL 0.0135 12 409 34 -0.064 0.032 1000 -1000 -0.086 -1000
p38 MAPK signaling pathway 0.0135 12 570 44 -0.13 0.042 1000 -1000 -0.082 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0124 11 614 52 -0.12 0.081 1000 -1000 -0.095 -1000
PDGFR-beta signaling pathway 0.0124 11 1157 97 -0.13 0.078 1000 -1000 -0.13 -1000
Cellular roles of Anthrax toxin 0.0112 10 393 39 -0.09 0.026 1000 -1000 -0.05 -1000
Arf6 trafficking events 0.0112 10 775 71 -0.23 0.043 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 0.0112 10 173 17 -0.018 0.046 1000 -1000 -0.062 -1000
Canonical NF-kappaB pathway 0.0101 9 371 39 -0.12 0.085 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0101 9 506 54 -0.077 0.069 1000 -1000 -0.079 -1000
ErbB2/ErbB3 signaling events 0.0090 8 579 65 -0.15 0.048 1000 -1000 -0.093 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0090 8 682 83 -0.15 0.074 1000 -1000 -0.11 -1000
E-cadherin signaling in keratinocytes 0.0090 8 348 43 -0.34 0.049 1000 -1000 -0.11 -1000
Signaling mediated by p38-gamma and p38-delta 0.0079 7 114 15 0 0.033 1000 -1000 -0.053 -1000
Circadian rhythm pathway 0.0067 6 146 22 -0.035 0.049 1000 -1000 -0.09 -1000
Nectin adhesion pathway 0.0067 6 430 63 -0.04 0.07 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class III 0.0067 6 277 40 -0.037 0.029 1000 -1000 -0.058 -1000
IGF1 pathway 0.0067 6 368 57 -0.054 0.06 1000 -1000 -0.14 -1000
Signaling events mediated by HDAC Class II 0.0056 5 425 75 -0.065 0.05 1000 -1000 -0.093 -1000
Hedgehog signaling events mediated by Gli proteins 0.0056 5 363 65 -0.039 0.084 1000 -1000 -0.098 -1000
Signaling events mediated by HDAC Class I 0.0056 5 585 104 -0.065 0.061 1000 -1000 -0.1 -1000
Insulin Pathway 0.0056 5 372 74 -0.041 0.047 1000 -1000 -0.14 -1000
Class I PI3K signaling events mediated by Akt 0.0045 4 309 68 -0.15 0.057 1000 -1000 -0.099 -1000
ceramide signaling pathway 0.0045 4 200 49 -0.071 0.054 1000 -1000 -0.072 -1000
Retinoic acid receptors-mediated signaling 0.0045 4 282 58 -0.072 0.048 1000 -1000 -0.1 -1000
Paxillin-dependent events mediated by a4b1 0.0045 4 179 36 -0.052 0.029 1000 -1000 -0.11 -1000
Rapid glucocorticoid signaling 0.0045 4 82 20 -0.022 0.015 1000 -1000 -0.057 -1000
Arf6 downstream pathway 0.0034 3 151 43 -0.032 0.032 1000 -1000 -0.065 -1000
Atypical NF-kappaB pathway 0.0034 3 99 31 -0.023 0.033 1000 -1000 -0.11 -1000
mTOR signaling pathway 0.0022 2 114 53 -0.004 0.042 1000 -1000 -0.094 -1000
TRAIL signaling pathway 0.0022 2 125 48 -0.01 0.063 1000 -1000 -0.099 -1000
Arf1 pathway 0.0011 1 73 54 -0.016 0.033 1000 -1000 -0.072 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 12 23 -0.004 0.06 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.001 0.037 1000 -1000 -0.08 -1000
Alternative NF-kappaB pathway 0.0000 0 6 13 -0.001 0.015 1000 -1000 -0.099 -1000
Total NA 6714 368653 7203 -37 -2000 131000 -131000 -13 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.56 0.33 0.74 663 -10000 0 663
KIRREL -0.092 0.2 -10000 0 -0.92 47 47
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.56 0.33 -10000 0 -0.74 663 663
PLCG1 0.015 0 -10000 0 -10000 0 0
ARRB2 0.012 0.044 -10000 0 -0.74 3 3
WASL 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.61 0.38 -10000 0 -0.76 715 715
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.45 0.3 -10000 0 -0.77 353 353
FYN -0.58 0.37 -10000 0 -0.72 715 715
mol:Ca2+ -0.6 0.38 -10000 0 -0.75 715 715
mol:DAG -0.61 0.38 -10000 0 -0.76 715 715
NPHS2 -0.43 0.44 -10000 0 -0.92 385 385
mol:IP3 -0.61 0.38 -10000 0 -0.76 715 715
regulation of endocytosis -0.54 0.34 -10000 0 -0.9 365 365
Nephrin/NEPH1/podocin/Cholesterol -0.62 0.39 -10000 0 -0.77 715 715
establishment of cell polarity -0.56 0.33 -10000 0 -0.74 663 663
Nephrin/NEPH1/podocin/NCK1-2 -0.57 0.36 -10000 0 -0.96 353 353
Nephrin/NEPH1/beta Arrestin2 -0.56 0.35 -10000 0 -0.92 365 365
NPHS1 -0.66 0.39 -10000 0 -0.9 649 649
Nephrin/NEPH1/podocin -0.59 0.37 -10000 0 -0.73 715 715
TJP1 0.015 0 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
NCK2 0.015 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.61 0.38 -10000 0 -0.76 715 715
CD2AP 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.61 0.38 -10000 0 -0.76 715 715
GRB2 0.015 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.63 0.39 -10000 0 -0.76 739 739
cytoskeleton organization -0.6 0.39 -10000 0 -0.76 702 702
Nephrin/NEPH1 -0.43 0.26 -10000 0 -0.57 663 663
Nephrin/NEPH1/ZO-1 -0.46 0.28 -10000 0 -0.62 663 663
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0.025 -9999 0 -0.74 1 1
EGFR 0.002 0.099 -9999 0 -0.75 15 15
EGF/EGFR -0.44 0.22 -9999 0 -0.51 750 750
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.41 0.19 -9999 0 -0.49 741 741
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.014 0.16 -9999 0 -0.83 31 31
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.71 0.33 -9999 0 -0.86 739 739
EGF/EGFR dimer/SHC -0.48 0.22 -9999 0 -0.58 742 742
mol:GDP -0.4 0.19 -9999 0 -0.48 741 741
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.019 0.16 -9999 0 -0.78 38 38
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.37 0.17 -9999 0 -0.81 14 14
SHC1 0.014 0.025 -9999 0 -0.74 1 1
HRAS/GDP -0.38 0.17 -9999 0 -0.82 14 14
FRAP1 -0.39 0.18 -9999 0 -0.47 741 741
EGF/EGFR dimer -0.56 0.25 -9999 0 -0.67 742 742
SOS1 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.047 0.16 -9999 0 -0.61 69 69
HIF-1-alpha 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
PKM2 -0.66 0.64 -9999 0 -1.3 362 362
HDAC7 0.015 0.004 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.49 0.39 -9999 0 -0.92 322 322
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.66 0.64 -9999 0 -1.3 339 339
AP1 -0.044 0.16 -9999 0 -0.66 59 59
ABCG2 -0.67 0.64 -9999 0 -1.3 357 357
HIF1A -0.07 0.091 -9999 0 -1 2 2
TFF3 -0.72 0.64 -9999 0 -1.3 372 372
GATA2 -0.063 0.25 -9999 0 -0.86 81 81
AKT1 -0.058 0.086 -9999 0 -10000 0 0
response to hypoxia -0.086 0.095 -9999 0 -10000 0 0
MCL1 -0.66 0.64 -9999 0 -1.3 339 339
NDRG1 -0.66 0.64 -9999 0 -1.3 365 365
SERPINE1 -0.7 0.66 -9999 0 -1.4 369 369
FECH -0.66 0.64 -9999 0 -1.3 339 339
FURIN -0.66 0.64 -9999 0 -1.3 362 362
NCOA2 -0.027 0.18 -9999 0 -0.86 41 41
EP300 -0.05 0.12 -9999 0 -0.4 4 4
HMOX1 -0.69 0.66 -9999 0 -1.3 370 370
BHLHE40 -0.66 0.64 -9999 0 -1.3 362 362
BHLHE41 -0.74 0.7 -9999 0 -1.4 381 381
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.061 0.059 -9999 0 -0.69 2 2
ENG -0.019 0.1 -9999 0 -0.62 2 2
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.66 0.64 -9999 0 -1.3 355 355
ABCB1 -0.3 0.44 -9999 0 -1.3 135 135
TFRC -0.66 0.64 -9999 0 -1.3 341 341
CXCR4 -0.73 0.7 -9999 0 -1.4 381 381
TF -0.7 0.68 -9999 0 -1.4 367 367
CITED2 -0.66 0.64 -9999 0 -1.3 356 356
HIF1A/ARNT -0.89 0.82 -9999 0 -1.6 412 412
LDHA -0.065 0.071 -9999 0 -0.75 5 5
ETS1 -0.66 0.64 -9999 0 -1.3 356 356
PGK1 -0.66 0.64 -9999 0 -1.3 355 355
NOS2 -0.68 0.64 -9999 0 -1.3 372 372
ITGB2 -0.72 0.68 -9999 0 -1.4 381 381
ALDOA -0.66 0.64 -9999 0 -1.3 339 339
Cbp/p300/CITED2 -0.67 0.63 -9999 0 -1.3 334 334
FOS -0.042 0.22 -9999 0 -0.86 59 59
HK2 -0.85 0.71 -9999 0 -1.4 459 459
SP1 0.015 0.039 -9999 0 -10000 0 0
GCK -0.12 0.22 -9999 0 -1 13 13
HK1 -0.66 0.64 -9999 0 -1.3 356 356
NPM1 -0.66 0.64 -9999 0 -1.3 355 355
EGLN1 -0.66 0.64 -9999 0 -1.3 340 340
CREB1 0.025 0.002 -9999 0 -10000 0 0
PGM1 -0.66 0.64 -9999 0 -1.3 356 356
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.1 0.26 -9999 0 -0.89 58 58
IGFBP1 -0.72 0.67 -9999 0 -1.4 358 358
VEGFA -0.49 0.52 -9999 0 -1.1 266 266
HIF1A/JAB1 -0.04 0.047 -9999 0 -0.8 2 2
CP -0.85 0.71 -9999 0 -1.4 445 445
CXCL12 -0.7 0.65 -9999 0 -1.3 392 392
COPS5 0.013 0.007 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.66 0.64 -9999 0 -1.3 354 354
EGLN3 -0.83 0.73 -9999 0 -1.5 450 450
CA9 -0.92 0.69 -9999 0 -1.4 504 504
TERT -0.72 0.66 -9999 0 -1.3 385 385
ENO1 -0.66 0.64 -9999 0 -1.3 354 354
PFKL -0.66 0.64 -9999 0 -1.3 355 355
NCOA1 0.014 0.003 -9999 0 -10000 0 0
ADM -0.7 0.67 -9999 0 -1.4 368 368
ARNT -0.067 0.078 -9999 0 -10000 0 0
HNF4A -0.1 0.31 -9999 0 -0.86 127 127
ADFP -0.68 0.64 -9999 0 -1.3 381 381
SLC2A1 -0.41 0.45 -9999 0 -0.98 191 191
LEP -0.7 0.65 -9999 0 -1.3 374 374
HIF1A/ARNT/Cbp/p300 -0.51 0.4 -9999 0 -0.93 347 347
EPO -0.39 0.43 -9999 0 -1 203 203
CREBBP -0.05 0.12 -9999 0 -0.37 3 3
HIF1A/ARNT/Cbp/p300/HDAC7 -0.54 0.44 -9999 0 -1 327 327
PFKFB3 -0.67 0.64 -9999 0 -1.3 363 363
NT5E -0.67 0.64 -9999 0 -1.3 341 341
TCGA08_p53

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
CDKN2A -0.5 0.19 -10000 0 -0.56 782 782
TP53 -0.14 0.052 -10000 0 -10000 0 0
Senescence -0.14 0.052 -10000 0 -10000 0 0
Apoptosis -0.14 0.052 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.25 0.093 0.28 782 -10000 0 782
MDM4 0.014 0.025 -10000 0 -0.74 1 1
PDGFR-alpha signaling pathway

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
PDGFRA -0.33 0.43 -9999 0 -0.86 352 352
PDGF/PDGFRA/CRKL -0.26 0.32 -9999 0 -0.65 352 352
positive regulation of JUN kinase activity -0.2 0.24 -9999 0 -0.5 352 352
CRKL 0.015 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.26 0.32 -9999 0 -0.66 355 355
AP1 -0.25 0.39 -9999 0 -1.5 58 58
mol:IP3 -0.24 0.34 -9999 0 -0.66 352 352
PLCG1 -0.24 0.34 -9999 0 -0.67 352 352
PDGF/PDGFRA/alphaV Integrin -0.26 0.32 -9999 0 -0.65 353 353
RAPGEF1 0.015 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ -0.24 0.34 -9999 0 -0.66 352 352
CAV3 0.001 0.043 -9999 0 -0.74 3 3
CAV1 -0.027 0.17 -9999 0 -0.74 50 50
SHC/Grb2/SOS1 -0.2 0.24 -9999 0 -0.5 352 352
PDGF/PDGFRA/Shf -0.26 0.32 -9999 0 -0.65 352 352
FOS -0.21 0.4 -9999 0 -1.4 58 58
JUN -0.017 0.021 -9999 0 -10000 0 0
oligodendrocyte development -0.26 0.32 -9999 0 -0.65 353 353
GRB2 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:DAG -0.24 0.34 -9999 0 -0.66 352 352
PDGF/PDGFRA -0.33 0.43 -9999 0 -0.86 352 352
actin cytoskeleton reorganization -0.26 0.32 -9999 0 -0.65 352 352
SRF 0.034 0.01 -9999 0 -10000 0 0
SHC1 0.014 0.025 -9999 0 -0.74 1 1
PI3K -0.22 0.27 -9999 0 -0.55 352 352
PDGF/PDGFRA/Crk/C3G -0.22 0.27 -9999 0 -0.56 352 352
JAK1 -0.24 0.33 -9999 0 -0.65 352 352
ELK1/SRF -0.19 0.24 -9999 0 -0.49 352 352
SHB 0.015 0 -9999 0 -10000 0 0
SHF 0.015 0 -9999 0 -10000 0 0
CSNK2A1 0.02 0.024 -9999 0 -10000 0 0
GO:0007205 -0.24 0.35 -9999 0 -0.67 352 352
SOS1 0.015 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.2 0.24 -9999 0 -0.5 352 352
PDGF/PDGFRA/SHB -0.26 0.32 -9999 0 -0.65 352 352
PDGF/PDGFRA/Caveolin-1 -0.29 0.33 -9999 0 -0.65 393 393
ITGAV 0.013 0.039 -9999 0 -0.8 2 2
ELK1 -0.21 0.31 -9999 0 -0.59 352 352
PIK3CA 0.015 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.26 0.32 -9999 0 -0.65 352 352
JAK-STAT cascade -0.24 0.33 -9999 0 -0.64 352 352
cell proliferation -0.26 0.32 -9999 0 -0.65 352 352
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.47 0.5 -9999 0 -1.2 204 204
PCK1 -1 0.76 -9999 0 -1.6 526 526
HNF4A -0.6 0.63 -9999 0 -1.5 227 227
KCNJ11 -0.49 0.55 -9999 0 -1.3 196 196
AKT1 -0.19 0.18 -9999 0 -10000 0 0
response to starvation -0.014 0.032 -9999 0 -10000 0 0
DLK1 -0.55 0.58 -9999 0 -1.3 255 255
NKX2-1 -0.082 0.2 -9999 0 -0.75 10 10
ACADM -0.47 0.5 -9999 0 -1.2 204 204
TAT -0.5 0.35 -9999 0 -0.89 296 296
CEBPB -0.027 0.13 -9999 0 -0.79 23 23
CEBPA -0.042 0.17 -9999 0 -0.78 42 42
TTR -0.81 0.46 -9999 0 -1.1 515 515
PKLR -0.56 0.64 -9999 0 -1.5 239 239
APOA1 -0.56 0.58 -9999 0 -1.4 208 208
CPT1C -0.48 0.51 -9999 0 -1.2 222 222
ALAS1 -0.17 0.19 -9999 0 -10000 0 0
TFRC -0.61 0.43 -9999 0 -1 362 362
FOXF1 -0.005 0.12 -9999 0 -0.74 23 23
NF1 0.024 0.001 -9999 0 -10000 0 0
HNF1A (dimer) -0.021 0.13 -9999 0 -0.9 16 16
CPT1A -0.47 0.5 -9999 0 -1.2 201 201
HMGCS1 -0.47 0.5 -9999 0 -1.2 201 201
NR3C1 0.005 0.054 -9999 0 -0.83 1 1
CPT1B -0.49 0.53 -9999 0 -1.3 211 211
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.016 0.008 -9999 0 -10000 0 0
GCK -0.47 0.5 -9999 0 -1.2 218 218
CREB1 -0.038 0.068 -9999 0 -10000 0 0
IGFBP1 -0.3 0.41 -9999 0 -1 166 166
PDX1 -0.21 0.25 -9999 0 -1.1 26 26
UCP2 -0.47 0.5 -9999 0 -1.2 201 201
ALDOB -1.1 0.62 -9999 0 -1.3 731 731
AFP -0.62 0.47 -9999 0 -0.96 437 437
BDH1 -0.56 0.56 -9999 0 -1.3 288 288
HADH -0.47 0.52 -9999 0 -1.3 197 197
F2 -0.62 0.6 -9999 0 -1.4 275 275
HNF1A -0.021 0.13 -9999 0 -0.9 16 16
G6PC -0.89 0.69 -9999 0 -1.5 453 453
SLC2A2 -0.41 0.6 -9999 0 -1.7 134 134
INS 0.004 0.068 -9999 0 -0.76 3 3
FOXA1 -0.29 0.3 -9999 0 -0.85 161 161
FOXA3 -0.59 0.4 -9999 0 -0.8 576 576
FOXA2 -0.55 0.6 -9999 0 -1.4 238 238
ABCC8 -0.48 0.52 -9999 0 -1.3 199 199
ALB -1.2 0.51 -9999 0 -1.4 748 748
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.2 0.66 -10000 0 -1.2 226 226
PLK1 -0.08 0.34 -10000 0 -0.68 206 206
BIRC5 -0.13 0.37 -10000 0 -0.67 278 278
HSPA1B -0.2 0.66 -10000 0 -1.2 227 227
MAP2K1 0.033 0.046 -10000 0 -10000 0 0
BRCA2 -0.21 0.67 -10000 0 -1.2 218 218
FOXM1 -0.36 0.91 -10000 0 -1.7 232 232
XRCC1 -0.2 0.66 -10000 0 -1.2 226 226
FOXM1B/p19 -0.44 0.54 0.48 2 -1.2 255 257
Cyclin D1/CDK4 -0.2 0.59 -10000 0 -1.1 205 205
CDC2 -0.23 0.7 -10000 0 -1.3 231 231
TGFA -0.2 0.6 -10000 0 -1 218 218
SKP2 -0.2 0.66 -10000 0 -1.2 211 211
CCNE1 -0.005 0.12 -10000 0 -0.75 22 22
CKS1B -0.2 0.66 -10000 0 -1.2 226 226
RB1 -0.18 0.24 -10000 0 -0.64 152 152
FOXM1C/SP1 -0.29 0.75 -10000 0 -1.4 231 231
AURKB -0.19 0.39 -10000 0 -0.65 349 349
CENPF -0.23 0.71 -10000 0 -1.3 217 217
CDK4 0.018 0.02 -10000 0 -10000 0 0
MYC -0.16 0.58 -10000 0 -1 210 210
CHEK2 0.027 0.08 -10000 0 -0.76 6 6
ONECUT1 -0.21 0.64 -10000 0 -1.2 222 222
CDKN2A -0.64 0.24 -10000 0 -0.73 782 782
LAMA4 -0.27 0.67 -10000 0 -1.2 236 236
FOXM1B/HNF6 -0.29 0.77 -10000 0 -1.4 229 229
FOS -0.25 0.69 -10000 0 -1.2 252 252
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.2 0.66 -10000 0 -1.2 226 226
response to radiation 0.01 0.046 -10000 0 -10000 0 0
CENPB -0.2 0.66 -10000 0 -1.2 225 225
CENPA -0.28 0.74 -10000 0 -1.3 258 258
NEK2 -0.27 0.74 -10000 0 -1.3 253 253
HIST1H2BA -0.21 0.66 -10000 0 -1.2 217 217
CCNA2 -0.13 0.3 -10000 0 -0.75 168 168
EP300 0.014 0.029 -10000 0 -0.86 1 1
CCNB1/CDK1 -0.28 0.78 -10000 0 -1.5 228 228
CCNB2 -0.26 0.74 -10000 0 -1.3 255 255
CCNB1 -0.22 0.7 -10000 0 -1.3 228 228
ETV5 -0.2 0.66 -10000 0 -1.2 225 225
ESR1 -0.22 0.68 -10000 0 -1.2 243 243
CCND1 -0.2 0.61 -10000 0 -1.1 206 206
GSK3A 0.032 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.064 0.25 -10000 0 -0.55 166 166
CDK2 0.014 0.014 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.011 0.055 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.58 -10000 0 -1.3 239 239
GAS1 -0.24 0.69 -10000 0 -1.2 252 252
MMP2 -0.2 0.66 -10000 0 -1.2 218 218
RB1/FOXM1C -0.22 0.65 -10000 0 -1.2 213 213
CREBBP 0.015 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.22 0.3 -10000 0 -0.65 270 270
FYN -0.24 0.44 -10000 0 -0.86 275 275
LAT/GRAP2/SLP76 -0.24 0.36 -10000 0 -0.73 273 273
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.16 0.27 -10000 0 -0.52 284 284
B2M 0.011 0.009 -10000 0 -10000 0 0
IKBKG -0.061 0.068 -10000 0 -0.18 112 112
MAP3K8 0.013 0.036 -10000 0 -0.74 2 2
mol:Ca2+ -0.11 0.061 -10000 0 -0.14 671 671
integrin-mediated signaling pathway -0.018 0.09 -10000 0 -0.48 33 33
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.26 0.42 -10000 0 -0.81 297 297
TRPV6 -0.66 0.38 -10000 0 -0.87 671 671
CD28 -0.047 0.2 -10000 0 -0.74 67 67
SHC1 -0.26 0.44 -10000 0 -0.87 287 287
receptor internalization -0.3 0.49 -10000 0 -0.96 296 296
PRF1 -0.29 0.51 -10000 0 -1 263 263
KRAS 0.015 0 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
COT/AKT1 -0.11 0.22 -10000 0 -0.4 254 254
LAT -0.31 0.47 -10000 0 -0.92 294 294
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D -0.24 0.36 -10000 0 -0.75 292 292
CD3E -0.22 0.35 -10000 0 -0.75 270 270
CD3G -0.2 0.34 -10000 0 -0.74 250 250
RASGRP2 -0.015 0.029 -10000 0 -0.14 3 3
RASGRP1 -0.15 0.26 -10000 0 -0.49 273 273
HLA-A 0.007 0.051 -10000 0 -0.74 4 4
RASSF5 -0.013 0.14 -10000 0 -0.74 33 33
RAP1A/GTP/RAPL -0.018 0.091 -10000 0 -0.48 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.08 -10000 0 -0.13 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.11 0.12 -10000 0 -0.33 132 132
PRKCA -0.091 0.16 -10000 0 -0.31 209 209
GRAP2 -0.033 0.18 -10000 0 -0.74 56 56
mol:IP3 -0.068 0.32 0.28 315 -0.48 267 582
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.29 0.49 -10000 0 -0.96 286 286
ORAI1 0.31 0.17 0.4 670 -10000 0 670
CSK -0.27 0.46 -10000 0 -0.9 287 287
B7 family/CD28 -0.36 0.47 -10000 0 -0.98 295 295
CHUK 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.34 0.55 -10000 0 -1.1 291 291
PTPN6 -0.26 0.46 -10000 0 -0.91 278 278
VAV1 -0.31 0.49 -10000 0 -0.93 314 314
Monovalent TCR/CD3 -0.27 0.42 -10000 0 -0.82 295 295
CBL 0.014 0.029 -10000 0 -0.86 1 1
LCK -0.26 0.47 -10000 0 -0.92 275 275
PAG1 -0.28 0.46 -10000 0 -0.9 286 286
RAP1A 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.32 0.54 -10000 0 -1.1 287 287
CD80 -0.13 0.3 -10000 0 -0.74 170 170
CD86 -0.12 0.29 -10000 0 -0.74 157 157
PDK1/CARD11/BCL10/MALT1 -0.14 0.15 -10000 0 -0.36 209 209
HRAS 0.014 0.025 -10000 0 -0.74 1 1
GO:0035030 -0.23 0.39 -10000 0 -0.74 293 293
CD8A -0.22 0.35 -10000 0 -0.75 270 270
CD8B -0.18 0.33 -10000 0 -0.75 226 226
PTPRC -0.048 0.2 -10000 0 -0.74 69 69
PDK1/PKC theta -0.21 0.34 -10000 0 -0.66 284 284
CSK/PAG1 -0.26 0.44 -10000 0 -0.88 277 277
SOS1 0.015 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.038 -10000 0 -0.56 4 4
GRAP2/SLP76 -0.26 0.43 -10000 0 -0.86 274 274
STIM1 0.16 0.089 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.11 -10000 0 -0.18 89 89
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.34 0.55 -10000 0 -1.1 296 296
mol:DAG -0.13 0.24 -10000 0 -0.44 280 280
RAP1A/GDP -0.004 0.035 -10000 0 -10000 0 0
PLCG1 0.015 0 -10000 0 -10000 0 0
CD247 -0.16 0.32 -10000 0 -0.74 209 209
cytotoxic T cell degranulation -0.27 0.47 -10000 0 -0.95 263 263
RAP1A/GTP -0.007 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.2 0.33 -10000 0 -0.63 296 296
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.15 0.41 0.3 283 -0.67 277 560
NRAS 0.015 0 -10000 0 -10000 0 0
ZAP70 -0.24 0.36 -10000 0 -0.74 301 301
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.24 0.35 -10000 0 -0.7 296 296
MALT1 0.015 0 -10000 0 -10000 0 0
TRAF6 0.015 0 -10000 0 -10000 0 0
CD8 heterodimer -0.29 0.44 -10000 0 -0.91 284 284
CARD11 -0.15 0.31 -10000 0 -0.74 192 192
PRKCB -0.094 0.16 -10000 0 -0.31 231 231
PRKCE -0.091 0.16 -10000 0 -0.31 203 203
PRKCQ -0.26 0.39 -10000 0 -0.77 293 293
LCP2 -0.042 0.2 -10000 0 -0.74 67 67
BCL10 0.015 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.13 0.23 -10000 0 -0.43 283 283
IKK complex -0.005 0.083 -10000 0 -10000 0 0
RAS family/GDP -0.008 0.011 -10000 0 -0.092 1 1
MAP3K14 -0.073 0.17 -10000 0 -0.32 123 123
PDPK1 -0.14 0.26 -10000 0 -0.49 269 269
TCR/CD3/MHC I/CD8/Fyn -0.33 0.55 -10000 0 -1.1 291 291
Aurora B 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
Condensin I complex -0.18 0.26 -9999 0 -0.55 259 259
STMN1 -0.21 0.29 -9999 0 -0.55 379 379
Aurora B/RasGAP/Survivin -0.32 0.41 -9999 0 -0.76 383 383
Chromosomal passenger complex/Cul3 protein complex -0.14 0.21 -9999 0 -0.42 273 273
BIRC5 -0.23 0.36 -9999 0 -0.76 280 280
DES -0.38 0.35 -9999 0 -0.74 336 336
Aurora C/Aurora B/INCENP -0.17 0.23 -9999 0 -0.43 386 386
Aurora B/TACC1 -0.19 0.24 -9999 0 -0.47 379 379
Aurora B/PP2A -0.22 0.28 -9999 0 -0.55 379 379
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.052 0.078 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.32 0.42 -9999 0 -0.75 396 396
Cul3 protein complex -0.023 0.11 -9999 0 -0.57 36 36
KIF2C -0.14 0.16 -9999 0 -0.32 305 305
PEBP1 0.006 0.008 -9999 0 -10000 0 0
KIF20A -0.32 0.37 -9999 0 -0.74 392 392
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.22 0.28 -9999 0 -0.55 380 380
SEPT1 -0.036 0.19 -9999 0 -0.74 60 60
SMC2 0.015 0 -9999 0 -10000 0 0
SMC4 0.015 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.13 0.19 -9999 0 -0.38 204 204
PSMA3 0.015 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.004 -9999 0 -10000 0 0
H3F3B -0.12 0.17 -9999 0 -0.33 379 379
AURKB -0.3 0.38 -9999 0 -0.74 379 379
AURKC 0.008 0.071 -9999 0 -0.74 8 8
CDCA8 -0.039 0.18 -9999 0 -0.76 54 54
cytokinesis -0.29 0.31 -9999 0 -0.68 308 308
Aurora B/Septin1 -0.28 0.35 -9999 0 -0.73 288 288
AURKA 0 0.091 -9999 0 -0.74 13 13
INCENP 0.007 0.008 -9999 0 -10000 0 0
KLHL13 -0.019 0.17 -9999 0 -0.86 35 35
BUB1 -0.33 0.37 -9999 0 -0.74 405 405
hSgo1/Aurora B/Survivin -0.32 0.42 -9999 0 -0.75 392 392
EVI5 0.01 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.24 0.28 -9999 0 -0.63 277 277
SGOL1 -0.023 0.16 -9999 0 -0.74 45 45
CENPA -0.22 0.29 -9999 0 -0.52 389 389
NCAPG -0.24 0.36 -9999 0 -0.74 304 304
Aurora B/HC8 Proteasome -0.22 0.28 -9999 0 -0.55 379 379
NCAPD2 0.015 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.22 0.28 -9999 0 -0.55 379 379
RHOA 0.015 0 -9999 0 -10000 0 0
NCAPH -0.1 0.27 -9999 0 -0.74 139 139
NPM1 -0.16 0.19 -9999 0 -0.38 379 379
RASA1 0.014 0.029 -9999 0 -0.86 1 1
KLHL9 0.014 0.029 -9999 0 -0.86 1 1
mitotic prometaphase -0.009 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.22 0.28 -9999 0 -0.54 379 379
PPP1CC 0.015 0 -9999 0 -10000 0 0
Centraspindlin -0.27 0.32 -9999 0 -0.67 304 304
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.16 0.19 -9999 0 -0.38 359 359
MYLK -0.13 0.19 -9999 0 -0.34 389 389
KIF23 -0.001 0.076 -9999 0 -0.75 9 9
VIM -0.26 0.35 -9999 0 -0.62 403 403
RACGAP1 0.004 0.045 -9999 0 -0.75 3 3
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.16 0.19 -9999 0 -0.38 379 379
Chromosomal passenger complex -0.28 0.34 -9999 0 -0.65 368 368
Chromosomal passenger complex/EVI5 -0.28 0.42 -9999 0 -0.87 268 268
TACC1 0.014 0.029 -9999 0 -0.86 1 1
PPP2R5D 0.014 0.025 -9999 0 -0.74 1 1
CUL3 0.015 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.047 0.12 -9999 0 -0.43 74 74
Syndecan-4/Syndesmos -0.37 0.33 -9999 0 -0.74 322 322
positive regulation of JNK cascade -0.45 0.32 -9999 0 -0.74 421 421
Syndecan-4/ADAM12 -0.44 0.4 -9999 0 -0.85 372 372
CCL5 -0.2 0.34 -9999 0 -0.74 256 256
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.015 0 -9999 0 -10000 0 0
ITGA5 -0.025 0.17 -9999 0 -0.74 47 47
SDCBP 0.015 0 -9999 0 -10000 0 0
PLG -0.42 0.42 -9999 0 -0.84 446 446
ADAM12 -0.15 0.31 -9999 0 -0.74 192 192
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.093 0.065 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.38 0.34 -9999 0 -0.75 339 339
Syndecan-4/CXCL12/CXCR4 -0.48 0.36 -9999 0 -0.81 421 421
Syndecan-4/Laminin alpha3 -0.4 0.33 -9999 0 -0.75 356 356
MDK -0.066 0.23 -9999 0 -0.74 96 96
Syndecan-4/FZD7 -0.38 0.33 -9999 0 -0.74 327 327
Syndecan-4/Midkine -0.41 0.35 -9999 0 -0.77 359 359
FZD7 0 0.11 -9999 0 -0.84 16 16
Syndecan-4/FGFR1/FGF -0.36 0.28 -9999 0 -0.69 319 319
THBS1 -0.015 0.16 -9999 0 -0.86 31 31
integrin-mediated signaling pathway -0.37 0.31 -9999 0 -0.71 339 339
positive regulation of MAPKKK cascade -0.45 0.32 -9999 0 -0.74 421 421
Syndecan-4/TACI -0.39 0.35 -9999 0 -0.77 335 335
CXCR4 -0.18 0.33 -9999 0 -0.74 226 226
cell adhesion -0.006 0.1 -9999 0 -0.42 23 23
Syndecan-4/Dynamin -0.37 0.33 -9999 0 -0.74 322 322
Syndecan-4/TSP1 -0.38 0.33 -9999 0 -0.75 336 336
Syndecan-4/GIPC -0.37 0.33 -9999 0 -0.74 312 312
Syndecan-4/RANTES -0.47 0.39 -9999 0 -0.84 400 400
ITGB1 0.015 0 -9999 0 -10000 0 0
LAMA1 -0.017 0.16 -9999 0 -0.83 34 34
LAMA3 -0.05 0.21 -9999 0 -0.74 77 77
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.099 0.064 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.37 0.33 -9999 0 -0.74 323 323
TFPI -0.01 0.14 -9999 0 -0.82 27 27
F2 -0.2 0.34 -9999 0 -0.74 254 254
alpha5/beta1 Integrin -0.029 0.12 -9999 0 -0.55 47 47
positive regulation of cell adhesion -0.39 0.33 -9999 0 -0.73 360 360
ACTN1 0.013 0.039 -9999 0 -0.8 2 2
TNC -0.019 0.17 -9999 0 -0.83 36 36
Syndecan-4/CXCL12 -0.41 0.34 -9999 0 -0.76 364 364
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.25 -9999 0 -0.86 78 78
TNFRSF13B -0.029 0.17 -9999 0 -0.74 48 48
FGF2 -0.001 0.12 -9999 0 -0.85 16 16
FGFR1 0.014 0.025 -9999 0 -0.74 1 1
Syndecan-4/PI-4-5-P2 -0.38 0.33 -9999 0 -0.75 322 322
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.043 0.2 -9999 0 -0.71 74 74
cell migration -0.028 0.02 -9999 0 -10000 0 0
PRKCD 0.011 0.082 -9999 0 -0.73 10 10
vasculogenesis -0.37 0.31 -9999 0 -0.71 336 336
SDC4 -0.4 0.36 -9999 0 -0.8 322 322
Syndecan-4/Tenascin C -0.38 0.33 -9999 0 -0.75 339 339
Syndecan-4/PI-4-5-P2/PKC alpha -0.073 0.05 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.37 0.33 -9999 0 -0.74 322 322
MMP9 -0.28 0.37 -9999 0 -0.73 350 350
Rac1/GTP -0.015 0.099 -9999 0 -0.43 23 23
cytoskeleton organization -0.35 0.31 -9999 0 -0.7 322 322
GIPC1 0.014 0.029 -9999 0 -0.86 1 1
Syndecan-4/TFPI -0.38 0.33 -9999 0 -0.74 335 335
Glypican 2 network

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
MDK -0.066 0.23 -9999 0 -0.74 96 96
GPC2 -0.12 0.29 -9999 0 -0.74 156 156
GPC2/Midkine -0.15 0.29 -9999 0 -0.65 209 209
neuron projection morphogenesis -0.15 0.29 -9999 0 -0.64 209 209
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.012 0.08 -10000 0 -0.56 19 19
fibroblast growth factor receptor signaling pathway -0.012 0.08 -10000 0 -0.55 19 19
LAMA1 -0.017 0.16 -10000 0 -0.83 34 34
PRNP 0.015 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.1 0.24 -10000 0 -0.65 143 143
SMAD2 0.043 0.024 -10000 0 -0.52 1 1
GPC1/PrPc/Cu2+ -0.001 0.025 -10000 0 -0.53 2 2
GPC1/Laminin alpha1 -0.026 0.13 -10000 0 -0.65 35 35
TDGF1 -0.57 0.41 -10000 0 -0.86 594 594
CRIPTO/GPC1 -0.44 0.31 -10000 0 -0.66 594 594
APP/GPC1 -0.001 0.029 -10000 0 -0.61 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.37 0.28 -10000 0 -0.57 594 594
FLT1 0.002 0.1 -10000 0 -0.77 15 15
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.025 -10000 0 -0.52 2 2
SERPINC1 -0.037 0.2 -10000 0 -0.84 53 53
FYN -0.37 0.28 -10000 0 -0.57 594 594
FGR -0.38 0.29 -10000 0 -0.58 597 597
positive regulation of MAPKKK cascade -0.37 0.3 -10000 0 -0.58 592 592
SLIT2 -0.12 0.32 -10000 0 -0.85 141 141
GPC1/NRG -0.03 0.14 -10000 0 -0.66 40 40
NRG1 -0.023 0.18 -10000 0 -0.85 39 39
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.15 0.23 -10000 0 -0.49 278 278
LYN -0.37 0.28 -10000 0 -0.57 594 594
mol:Spermine 0.013 0.03 -10000 0 -0.62 2 2
cell growth -0.012 0.08 -10000 0 -0.55 19 19
BMP signaling pathway -0.013 0.039 0.8 2 -10000 0 2
SRC -0.37 0.28 -10000 0 -0.57 594 594
TGFBR1 0.015 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.06 0.22 -10000 0 -0.74 82 82
GPC1 0.013 0.039 -10000 0 -0.8 2 2
TGFBR1 (dimer) 0.015 0 -10000 0 -10000 0 0
VEGFA -0.22 0.35 -10000 0 -0.74 273 273
BLK -0.4 0.31 -10000 0 -0.6 603 603
HCK -0.4 0.3 -10000 0 -0.59 620 620
FGF2 -0.001 0.12 -10000 0 -0.85 16 16
FGFR1 0.014 0.025 -10000 0 -0.74 1 1
VEGFR1 homodimer 0.002 0.1 -10000 0 -0.77 15 15
TGFBR2 0.015 0 -10000 0 -10000 0 0
cell death -0.001 0.029 -10000 0 -0.6 2 2
ATIII/GPC1 -0.04 0.15 -10000 0 -0.64 55 55
PLA2G2A/GPC1 -0.052 0.16 -10000 0 -0.56 83 83
LCK -0.4 0.3 -10000 0 -0.59 606 606
neuron differentiation -0.03 0.14 -10000 0 -0.66 40 40
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.015 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.015 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.13 0.26 -9999 0 -0.61 184 184
alphaM/beta2 Integrin/GPIbA -0.13 0.26 -9999 0 -0.61 176 176
alphaM/beta2 Integrin/proMMP-9 -0.3 0.38 -9999 0 -0.65 411 411
PLAUR -0.022 0.16 -9999 0 -0.74 44 44
HMGB1 0.011 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.12 0.26 -9999 0 -0.61 175 175
AGER -0.068 0.23 -9999 0 -0.74 93 93
RAP1A 0.015 0 -9999 0 -10000 0 0
SELPLG -0.056 0.22 -9999 0 -0.74 84 84
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.18 0.26 -9999 0 -0.79 96 96
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.28 0.37 -9999 0 -0.74 350 350
CYR61 -0.029 0.19 -9999 0 -0.86 45 45
TLN1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.55 218 218
RHOA 0.015 0 -9999 0 -10000 0 0
P-selectin oligomer -0.06 0.24 -9999 0 -0.86 76 76
MYH2 -0.34 0.27 -9999 0 -0.63 324 324
MST1R -0.017 0.15 -9999 0 -0.76 36 36
leukocyte activation during inflammatory response -0.22 0.3 -9999 0 -0.73 160 160
APOB -0.19 0.34 -9999 0 -0.75 235 235
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.004 0.09 -9999 0 -0.77 12 12
JAM3 0.012 0.051 -9999 0 -0.86 3 3
GP1BA 0.012 0.048 -9999 0 -0.82 3 3
alphaM/beta2 Integrin/CTGF -0.14 0.27 -9999 0 -0.62 200 200
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.54 383 383
JAM3 homodimer 0.012 0.051 -9999 0 -0.86 3 3
ICAM2 0.015 0 -9999 0 -10000 0 0
ICAM1 0.002 0.097 -9999 0 -0.74 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.25 -9999 0 -0.53 377 377
cell adhesion -0.12 0.26 -9999 0 -0.61 176 176
NFKB1 -0.14 0.3 -9999 0 -0.79 102 102
THY1 -0.066 0.25 -9999 0 -0.86 82 82
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.14 0.23 -9999 0 -0.5 241 241
alphaM/beta2 Integrin/LRP/tPA -0.15 0.27 -9999 0 -0.69 133 133
IL6 -0.2 0.4 -9999 0 -0.9 177 177
ITGB2 -0.12 0.29 -9999 0 -0.74 160 160
elevation of cytosolic calcium ion concentration -0.16 0.28 -9999 0 -0.73 127 127
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.25 -9999 0 -0.75 83 83
JAM2 0.002 0.1 -9999 0 -0.85 13 13
alphaM/beta2 Integrin/ICAM1 -0.13 0.25 -9999 0 -0.84 64 64
alphaM/beta2 Integrin/uPA/Plg -0.4 0.37 -9999 0 -0.67 500 500
RhoA/GTP -0.36 0.27 -9999 0 -0.66 330 330
positive regulation of phagocytosis -0.26 0.26 -9999 0 -0.74 147 147
Ron/MSP -0.032 0.13 -9999 0 -0.58 50 50
alphaM/beta2 Integrin/uPAR/uPA -0.16 0.29 -9999 0 -0.74 127 127
alphaM/beta2 Integrin/uPAR -0.15 0.29 -9999 0 -0.63 200 200
PLAU -0.032 0.2 -9999 0 -0.86 48 48
PLAT -0.052 0.23 -9999 0 -0.86 68 68
actin filament polymerization -0.32 0.25 -9999 0 -0.59 324 324
MST1 0.003 0.097 -9999 0 -0.76 14 14
alphaM/beta2 Integrin/lipoprotein(a) -0.22 0.31 -9999 0 -0.74 160 160
TNF -0.13 0.3 -9999 0 -0.75 107 107
RAP1B 0.015 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.16 0.28 -9999 0 -0.61 221 221
fibrinolysis -0.4 0.36 -9999 0 -0.66 500 500
HCK -0.04 0.2 -9999 0 -0.74 65 65
dendritic cell antigen processing and presentation -0.3 0.25 -9999 0 -0.53 377 377
VTN -0.14 0.33 -9999 0 -0.84 162 162
alphaM/beta2 Integrin/CYR61 -0.15 0.28 -9999 0 -0.62 216 216
LPA -0.001 0.075 -9999 0 -0.74 9 9
LRP1 0.015 0 -9999 0 -10000 0 0
cell migration -0.28 0.36 -9999 0 -0.84 184 184
FN1 -0.048 0.21 -9999 0 -0.74 74 74
alphaM/beta2 Integrin/Thy1 -0.18 0.29 -9999 0 -0.61 253 253
MPO -0.015 0.14 -9999 0 -0.74 34 34
KNG1 -0.59 0.4 -9999 0 -0.86 612 612
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.32 0.26 -9999 0 -0.62 314 314
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.43 0.43 -9999 0 -0.86 446 446
CTGF -0.013 0.15 -9999 0 -0.86 28 28
alphaM/beta2 Integrin/Hck -0.16 0.33 -9999 0 -0.74 183 183
ITGAM -0.049 0.2 -9999 0 -0.74 71 71
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.2 0.34 -9999 0 -0.78 181 181
HP -0.15 0.31 -9999 0 -0.74 189 189
leukocyte adhesion -0.19 0.26 -9999 0 -0.75 115 115
SELP -0.06 0.24 -9999 0 -0.86 76 76
Angiopoietin receptor Tie2-mediated signaling

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 -0.27 0.48 -10000 0 -1 225 225
NCK1/PAK1/Dok-R -0.15 0.18 -10000 0 -0.45 225 225
NCK1/Dok-R -0.36 0.6 -10000 0 -1.4 227 227
PIK3CA 0.005 0.008 -10000 0 -10000 0 0
mol:beta2-estradiol 0.03 0.094 0.26 121 -10000 0 121
RELA 0.015 0 -10000 0 -10000 0 0
SHC1 0.006 0.026 -10000 0 -0.74 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.17 0.35 -10000 0 -0.7 254 254
TNIP2 0.015 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.31 0.54 -10000 0 -1.2 227 227
FN1 -0.048 0.21 -10000 0 -0.74 74 74
PLD2 -0.29 0.68 -10000 0 -1.4 227 227
PTPN11 0.015 0 -10000 0 -10000 0 0
GRB14 -0.032 0.2 -10000 0 -0.86 48 48
ELK1 -0.22 0.58 -10000 0 -1.2 227 227
GRB7 0.005 0.092 -10000 0 -0.86 10 10
PAK1 0.015 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.37 0.58 -10000 0 -1.3 227 227
CDKN1A -0.21 0.35 -10000 0 -0.7 185 185
ITGA5 -0.025 0.17 -10000 0 -0.74 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.36 0.6 -10000 0 -1.3 228 228
CRK 0.015 0 -10000 0 -10000 0 0
mol:NO -0.18 0.36 -10000 0 -0.73 225 225
PLG -0.52 0.67 -10000 0 -1.6 228 228
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.29 0.41 -10000 0 -0.97 227 227
GRB2 0.015 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.008 -10000 0 -10000 0 0
ANGPT2 -0.24 0.36 -10000 0 -0.64 286 286
BMX -0.33 0.68 -10000 0 -1.4 227 227
ANGPT1 -0.16 0.54 -10000 0 -1.5 125 125
tube development -0.25 0.39 -10000 0 -0.8 218 218
ANGPT4 -0.007 0.1 -10000 0 -0.74 17 17
response to hypoxia -0.016 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.38 0.7 -10000 0 -1.5 227 227
alpha5/beta1 Integrin -0.029 0.12 -10000 0 -0.55 47 47
FGF2 -0.001 0.12 -10000 0 -0.85 16 16
STAT5A (dimer) -0.28 0.45 -10000 0 -0.93 219 219
mol:L-citrulline -0.18 0.36 -10000 0 -0.73 225 225
AGTR1 -0.13 0.32 -10000 0 -0.86 143 143
MAPK14 -0.31 0.66 -10000 0 -1.4 227 227
Tie2/SHP2 -0.32 0.56 -10000 0 -1.3 215 215
TEK -0.35 0.64 -10000 0 -1.5 215 215
RPS6KB1 -0.24 0.46 -10000 0 -0.98 226 226
Angiotensin II/AT1 -0.11 0.25 -10000 0 -0.67 143 143
Tie2/Ang1/GRB2 -0.36 0.69 -10000 0 -1.5 227 227
MAPK3 -0.24 0.6 -10000 0 -1.2 227 227
MAPK1 -0.24 0.6 -10000 0 -1.2 227 227
Tie2/Ang1/GRB7 -0.37 0.69 -10000 0 -1.5 227 227
NFKB1 0.014 0.029 -10000 0 -0.86 1 1
MAPK8 -0.3 0.69 -10000 0 -1.4 227 227
PI3K -0.32 0.58 -10000 0 -1.3 226 226
FES -0.31 0.65 -10000 0 -1.4 227 227
Crk/Dok-R -0.36 0.6 -10000 0 -1.4 227 227
Tie2/Ang1/ABIN2 -0.36 0.69 -10000 0 -1.5 227 227
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.23 0.42 -10000 0 -0.9 226 226
STAT5A 0.015 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.24 0.46 -10000 0 -0.98 226 226
Tie2/Ang2 -0.37 0.55 -10000 0 -1.2 219 219
Tie2/Ang1 -0.36 0.8 -10000 0 -1.7 227 227
FOXO1 -0.25 0.43 -10000 0 -0.91 225 225
ELF1 -0.001 0.053 -10000 0 -0.84 1 1
ELF2 -0.3 0.7 -10000 0 -1.5 227 227
mol:Choline -0.26 0.63 -10000 0 -1.3 227 227
cell migration -0.09 0.1 -10000 0 -10000 0 0
FYN -0.29 0.45 -10000 0 -0.94 218 218
DOK2 -0.036 0.19 -10000 0 -0.74 60 60
negative regulation of cell cycle -0.18 0.32 -10000 0 -0.63 193 193
ETS1 -0.008 0.089 -10000 0 -10000 0 0
PXN -0.18 0.38 -10000 0 -0.78 225 225
ITGB1 0.015 0 -10000 0 -10000 0 0
NOS3 -0.22 0.41 -10000 0 -0.85 225 225
RAC1 0.015 0 -10000 0 -10000 0 0
TNF -0.035 0.16 -10000 0 -0.83 25 25
MAPKKK cascade -0.26 0.63 -10000 0 -1.3 227 227
RASA1 0.014 0.029 -10000 0 -0.86 1 1
Tie2/Ang1/Shc -0.34 0.71 -10000 0 -1.5 227 227
NCK1 0.015 0 -10000 0 -10000 0 0
vasculogenesis -0.16 0.32 -10000 0 -0.64 225 225
mol:Phosphatidic acid -0.26 0.63 -10000 0 -1.3 227 227
mol:Angiotensin II -0.011 0.018 -10000 0 -10000 0 0
mol:NADP -0.18 0.36 -10000 0 -0.73 225 225
Rac1/GTP -0.28 0.37 -10000 0 -0.9 227 227
MMP2 -0.3 0.68 -10000 0 -1.4 227 227
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.14 0.22 -10000 0 -0.57 94 94
TBX21 -0.37 0.6 -10000 0 -1.2 265 265
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.16 0.33 -10000 0 -0.78 202 202
GADD45B -0.2 0.39 -10000 0 -0.78 183 183
IL12RB2 -0.18 0.33 -10000 0 -0.74 233 233
GADD45G -0.22 0.4 -10000 0 -0.8 193 193
natural killer cell activation -0.003 0.03 -10000 0 -10000 0 0
RELB 0.015 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
IL18 -0.024 0.17 -10000 0 -0.74 46 46
IL2RA -0.11 0.28 -10000 0 -0.74 144 144
IFNG -0.21 0.34 -10000 0 -0.74 261 261
STAT3 (dimer) -0.26 0.43 -10000 0 -0.84 255 255
HLA-DRB5 -0.03 0.18 -10000 0 -0.75 52 52
FASLG -0.41 0.63 -10000 0 -1.2 298 298
NF kappa B2 p52/RelB -0.38 0.48 -10000 0 -1 264 264
CD4 -0.01 0.14 -10000 0 -0.74 30 30
SOCS1 0.002 0.1 -10000 0 -0.8 14 14
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D -0.23 0.36 -10000 0 -0.74 292 292
CD3E -0.22 0.35 -10000 0 -0.74 270 270
CD3G -0.2 0.34 -10000 0 -0.75 250 250
IL12Rbeta2/JAK2 -0.13 0.26 -10000 0 -0.56 233 233
CCL3 -0.35 0.57 -10000 0 -1.2 237 237
CCL4 -0.36 0.6 -10000 0 -1.2 233 233
HLA-A 0.009 0.051 -10000 0 -0.74 4 4
IL18/IL18R -0.076 0.25 -10000 0 -0.51 177 177
NOS2 -0.27 0.48 -10000 0 -0.93 246 246
IL12/IL12R/TYK2/JAK2/SPHK2 -0.13 0.22 -10000 0 -0.58 87 87
IL1R1 -0.31 0.54 -10000 0 -1.1 234 234
IL4 0.007 0.03 -10000 0 -10000 0 0
JAK2 0.015 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.4 0.64 -10000 0 -1.2 316 316
RAB7A -0.16 0.34 -10000 0 -0.75 66 66
lysosomal transport -0.15 0.33 -10000 0 -0.7 70 70
FOS -0.3 0.49 -10000 0 -0.97 265 265
STAT4 (dimer) -0.28 0.48 -10000 0 -0.96 234 234
STAT5A (dimer) -0.45 0.55 -10000 0 -1.2 289 289
GZMA -0.38 0.62 -10000 0 -1.2 271 271
GZMB -0.37 0.6 -10000 0 -1.2 273 273
HLX -0.047 0.21 -10000 0 -0.74 73 73
LCK -0.36 0.62 -10000 0 -1.2 255 255
TCR/CD3/MHC II/CD4 -0.23 0.38 -10000 0 -0.73 290 290
IL2/IL2R -0.26 0.34 -10000 0 -0.93 131 131
MAPK14 -0.21 0.4 -10000 0 -0.8 193 193
CCR5 -0.31 0.52 -10000 0 -1.1 247 247
IL1B -0.003 0.12 -10000 0 -0.82 19 19
STAT6 -0.056 0.14 -10000 0 -10000 0 0
STAT4 -0.026 0.17 -10000 0 -0.74 49 49
STAT3 0.015 0 -10000 0 -10000 0 0
STAT1 0.013 0.036 -10000 0 -0.74 2 2
NFKB1 0.014 0.029 -10000 0 -0.86 1 1
NFKB2 0.015 0 -10000 0 -10000 0 0
IL12B -0.068 0.24 -10000 0 -0.75 96 96
CD8A -0.22 0.35 -10000 0 -0.75 270 270
CD8B -0.18 0.33 -10000 0 -0.75 226 226
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.14 0.22 0.57 94 -10000 0 94
IL2RB -0.26 0.36 -10000 0 -0.74 331 331
proteasomal ubiquitin-dependent protein catabolic process -0.25 0.43 -10000 0 -0.85 234 234
IL2RG -0.025 0.17 -10000 0 -0.75 47 47
IL12 -0.044 0.19 -10000 0 -0.58 96 96
STAT5A 0.015 0 -10000 0 -10000 0 0
CD247 -0.16 0.32 -10000 0 -0.74 209 209
IL2 -0.006 0.099 -10000 0 -0.74 16 16
SPHK2 0.013 0.041 -10000 0 -0.86 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.02 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.39 0.66 -10000 0 -1.2 279 279
MAP2K3 -0.21 0.4 -10000 0 -0.78 214 214
RIPK2 0.014 0.025 -10000 0 -0.74 1 1
MAP2K6 -0.21 0.4 -10000 0 -0.79 212 212
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.11 -10000 0 -0.75 18 18
IL18RAP -0.12 0.3 -10000 0 -0.74 164 164
IL12Rbeta1/TYK2 -0.12 0.26 -10000 0 -0.6 202 202
EOMES -0.18 0.3 -10000 0 -0.62 273 273
STAT1 (dimer) -0.29 0.47 -10000 0 -0.91 273 273
T cell proliferation -0.17 0.35 -10000 0 -0.66 207 207
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.097 -10000 0 -0.82 12 12
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.29 0.31 -10000 0 -0.74 202 202
ATF2 -0.18 0.38 -10000 0 -0.74 175 175
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.64 0.38 -9999 0 -0.88 529 529
SMAD6-7/SMURF1 -0.001 0.027 -9999 0 -0.57 2 2
NOG -0.066 0.23 -9999 0 -0.75 92 92
SMAD9 -0.079 0.11 -9999 0 -0.55 39 39
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD5 -0.19 0.2 -9999 0 -0.51 47 47
BMP7/USAG1 -0.67 0.44 -9999 0 -0.88 677 677
SMAD5/SKI -0.18 0.19 -9999 0 -0.5 38 38
SMAD1 -0.001 0.048 -9999 0 -10000 0 0
BMP2 0.012 0.048 -9999 0 -0.82 3 3
SMAD1/SMAD1/SMAD4 -0.001 0.018 -9999 0 -10000 0 0
BMPR1A 0.014 0.029 -9999 0 -0.86 1 1
BMPR1B -0.52 0.42 -9999 0 -0.86 548 548
BMPR1A-1B/BAMBI -0.36 0.28 -9999 0 -0.57 560 560
AHSG -0.011 0.11 -9999 0 -0.74 21 21
CER1 0.004 0.026 -9999 0 -0.74 1 1
BMP2-4/CER1 -0.006 0.059 -9999 0 -0.56 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.15 0.13 -9999 0 -0.51 39 39
BMP2-4 (homodimer) -0.007 0.065 -9999 0 -0.65 9 9
RGMB 0.013 0.036 -9999 0 -0.74 2 2
BMP6/BMPR2/BMPR1A-1B -0.33 0.26 -9999 0 -0.53 548 548
RGMA -0.022 0.18 -9999 0 -0.86 38 38
SMURF1 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.17 0.15 -9999 0 -0.52 39 39
BMP2-4/USAG1 -0.31 0.29 -9999 0 -0.57 479 479
SMAD6/SMURF1/SMAD5 -0.18 0.19 -9999 0 -0.5 38 38
SOSTDC1 -0.45 0.43 -9999 0 -0.85 477 477
BMP7/BMPR2/BMPR1A-1B -0.6 0.37 -9999 0 -0.74 713 713
SKI 0.015 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.005 0.13 -9999 0 -0.86 20 20
HFE2 -0.009 0.12 -9999 0 -0.74 23 23
ZFYVE16 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.029 0.13 -9999 0 -0.6 44 44
SMAD5/SMAD5/SMAD4 -0.18 0.19 -9999 0 -0.5 38 38
MAPK1 0.015 0 -9999 0 -10000 0 0
TAK1/TAB family -0.14 0.11 -9999 0 -0.44 37 37
BMP7 (homodimer) -0.46 0.43 -9999 0 -0.86 483 483
NUP214 0.015 0 -9999 0 -10000 0 0
BMP6/FETUA -0.028 0.13 -9999 0 -0.62 40 40
SMAD1/SKI 0.008 0.045 -9999 0 -10000 0 0
SMAD6 0.013 0.041 -9999 0 -0.86 2 2
CTDSP2 0.015 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.017 0.09 -9999 0 -0.5 30 30
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.26 0.4 -9999 0 -0.85 280 280
BMPR2 (homodimer) 0.015 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.41 0.32 -9999 0 -0.66 549 549
CHRDL1 -0.41 0.44 -9999 0 -0.86 436 436
ENDOFIN/SMAD1 0.008 0.045 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.005 0.021 -9999 0 -10000 0 0
SMAD6/SMURF1 0.015 0 -9999 0 -10000 0 0
BAMBI 0 0.11 -9999 0 -0.86 15 15
SMURF2 0.014 0.029 -9999 0 -0.86 1 1
BMP2-4/CHRDL1 -0.28 0.29 -9999 0 -0.58 440 440
BMP2-4/GREM1 -0.18 0.27 -9999 0 -0.57 285 285
SMAD7 0.015 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.051 0.12 -9999 0 -0.52 36 36
SMAD1/SMAD6 0.008 0.045 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.46 0.43 -9999 0 -0.86 483 483
BMP6 -0.005 0.13 -9999 0 -0.86 20 20
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.14 -9999 0 -0.44 39 39
PPM1A 0.015 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.007 0.048 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.015 0 -9999 0 -10000 0 0
PPP1CA 0.015 0 -9999 0 -10000 0 0
XIAP 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.015 0 -9999 0 -10000 0 0
PPP1R15A 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.25 0.25 -9999 0 -0.74 133 133
CHRD -0.022 0.17 -9999 0 -0.84 38 38
BMPR2 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.18 0.14 -9999 0 -0.55 39 39
BMP4 0.009 0.071 -9999 0 -0.86 6 6
FST -0.12 0.31 -9999 0 -0.84 142 142
BMP2-4/NOG -0.056 0.16 -9999 0 -0.49 101 101
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.56 0.35 -9999 0 -0.7 713 713
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.015 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.19 0.22 -9999 0 -0.43 386 386
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.05 0.057 -9999 0 -10000 0 0
AURKB -0.3 0.37 -9999 0 -0.74 379 379
AURKC 0.008 0.071 -9999 0 -0.74 8 8
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.49 0.48 -10000 0 -1.2 165 165
STAT6 (cleaved dimer) -0.57 0.48 -10000 0 -1.1 291 291
IGHG1 -0.17 0.18 -10000 0 -0.59 23 23
IGHG3 -0.48 0.46 -10000 0 -1.1 229 229
AKT1 -0.26 0.29 -10000 0 -0.8 90 90
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.26 -10000 0 -0.75 93 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.27 -10000 0 -0.8 64 64
THY1 -0.56 0.57 -10000 0 -1.4 209 209
MYB -0.18 0.33 -10000 0 -0.74 233 233
HMGA1 0.008 0.071 -10000 0 -0.74 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.36 -10000 0 -0.9 160 160
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.27 -10000 0 -0.81 61 61
SP1 0.022 0.012 -10000 0 -10000 0 0
INPP5D 0.006 0.083 -10000 0 -0.74 11 11
SOCS5 0.026 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.47 -10000 0 -1.2 261 261
SOCS1 -0.33 0.33 -10000 0 -0.82 103 103
SOCS3 -0.28 0.31 -10000 0 -0.92 74 74
FCER2 -0.4 0.41 -10000 0 -1 134 134
PARP14 0.015 0.004 -10000 0 -10000 0 0
CCL17 -0.52 0.5 -10000 0 -1.3 175 175
GRB2 0.015 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.24 -10000 0 -0.82 43 43
T cell proliferation -0.51 0.51 -10000 0 -1.3 183 183
IL4R/JAK1 -0.49 0.48 -10000 0 -1.2 160 160
EGR2 -0.52 0.54 -10000 0 -1.3 181 181
JAK2 0.004 0.025 -10000 0 -10000 0 0
JAK3 -0.12 0.3 -10000 0 -0.74 167 167
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.006 0.015 -10000 0 -10000 0 0
COL1A2 -0.19 0.25 -10000 0 -0.82 82 82
CCL26 -0.5 0.49 -10000 0 -1.2 178 178
IL4R -0.52 0.52 -10000 0 -1.3 159 159
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.7 0.65 -10000 0 -1.4 321 321
IL13RA1 0.004 0.025 -10000 0 -10000 0 0
IRF4 -0.21 0.34 -10000 0 -0.88 151 151
ARG1 -0.17 0.23 -10000 0 -0.8 38 38
CBL -0.32 0.34 -10000 0 -0.88 142 142
GTF3A 0.014 0.035 -10000 0 -0.73 1 1
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.008 0.043 -10000 0 -10000 0 0
IRF4/BCL6 -0.21 0.3 -10000 0 -0.83 145 145
CD40LG -0.071 0.26 -10000 0 -0.78 103 103
MAPK14 -0.32 0.34 -10000 0 -0.88 138 138
mitosis -0.24 0.28 -10000 0 -0.75 89 89
STAT6 -0.56 0.57 -10000 0 -1.3 217 217
SPI1 -0.091 0.27 -10000 0 -0.73 130 130
RPS6KB1 -0.23 0.27 -10000 0 -0.76 65 65
STAT6 (dimer) -0.57 0.56 -10000 0 -1.3 217 217
STAT6 (dimer)/PARP14 -0.52 0.52 -10000 0 -1.2 212 212
mast cell activation 0.012 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.31 -10000 0 -0.84 114 114
FRAP1 -0.26 0.29 -10000 0 -0.8 91 91
LTA -0.56 0.52 -10000 0 -1.3 199 199
FES 0.012 0.051 -10000 0 -0.86 3 3
T-helper 1 cell differentiation 0.55 0.55 1.3 217 -10000 0 217
CCL11 -0.67 0.62 -10000 0 -1.4 330 330
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.29 -10000 0 -0.81 105 105
IL2RG -0.02 0.17 -10000 0 -0.75 47 47
IL10 -0.51 0.5 -10000 0 -1.2 186 186
IRS1 0.005 0.092 -10000 0 -0.86 10 10
IRS2 0 0.11 -10000 0 -0.74 18 18
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.5 0.48 -10000 0 -1.2 177 177
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.38 -10000 0 -0.92 144 144
COL1A1 -0.3 0.34 -10000 0 -0.84 186 186
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.49 0.49 -10000 0 -1.3 126 126
IL2R gamma/JAK3 -0.12 0.28 -10000 0 -0.66 178 178
TFF3 -0.58 0.6 -10000 0 -1.4 210 210
ALOX15 -0.5 0.49 -10000 0 -1.2 172 172
MYBL1 -0.036 0.19 -10000 0 -0.74 60 60
T-helper 2 cell differentiation -0.43 0.4 -10000 0 -0.97 189 189
SHC1 0.014 0.025 -10000 0 -0.74 1 1
CEBPB -0.001 0.12 -10000 0 -0.74 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.27 -10000 0 -0.77 69 69
mol:PI-3-4-5-P3 -0.26 0.29 -10000 0 -0.8 91 91
PI3K -0.27 0.31 -10000 0 -0.86 89 89
DOK2 -0.036 0.19 -10000 0 -0.74 60 60
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.24 -10000 0 -0.79 47 47
ITGB3 -0.51 0.52 -10000 0 -1.3 181 181
PIGR -0.76 0.68 -10000 0 -1.5 378 378
IGHE 0.029 0.081 -10000 0 -0.34 2 2
MAPKKK cascade -0.19 0.24 -10000 0 -0.77 47 47
BCL6 0.012 0.006 -10000 0 -10000 0 0
OPRM1 -0.5 0.48 -10000 0 -1.2 153 153
RETNLB -0.5 0.48 -10000 0 -1.3 149 149
SELP -0.55 0.57 -10000 0 -1.4 194 194
AICDA -0.58 0.51 -10000 0 -1.2 227 227
TCGA08_retinoblastoma

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
CDKN2B -0.009 0.085 -10000 0 -0.74 12 12
CDKN2C 0.064 0.042 -10000 0 -0.64 2 2
CDKN2A -0.66 0.24 -10000 0 -0.75 782 782
CCND2 0.14 0.065 0.4 13 -10000 0 13
RB1 -0.16 0.067 -10000 0 -0.41 13 13
CDK4 0.17 0.071 0.41 13 -10000 0 13
CDK6 0.16 0.07 0.43 13 -0.19 1 14
G1/S progression 0.16 0.073 0.41 13 -10000 0 13
Effects of Botulinum toxin

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
STX1A 0.009 0.059 -9999 0 -0.58 9 9
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.042 0.15 -9999 0 -0.55 68 68
STXBP1 0.014 0.029 -9999 0 -0.86 1 1
ACh/CHRNA1 -0.26 0.26 -9999 0 -0.52 442 442
RAB3GAP2/RIMS1/UNC13B -0.036 0.12 -9999 0 -0.47 68 68
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.047 0.2 -9999 0 -0.74 68 68
mol:ACh -0.017 0.055 -9999 0 -0.12 204 204
RAB3GAP2 0.015 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.055 0.11 -9999 0 -0.5 13 13
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.26 0.26 -9999 0 -0.52 442 442
UNC13B 0.015 0 -9999 0 -10000 0 0
CHRNA1 -0.36 0.38 -9999 0 -0.74 442 442
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.14 0.26 -9999 0 -0.63 195 195
SNAP25 -0.056 0.12 -9999 0 -0.28 198 198
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.18 0.36 -9999 0 -0.86 195 195
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.006 0.053 -9999 0 -0.5 10 10
STX1A/SNAP25 fragment 1/VAMP2 -0.055 0.11 -9999 0 -0.5 13 13
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.056 -9999 0 -0.74 5 5
CCL5 -0.2 0.34 -9999 0 -0.74 256 256
SDCBP 0.015 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.22 -9999 0 -0.56 134 134
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.16 0.21 -9999 0 -0.55 117 117
Syndecan-1/Syntenin -0.16 0.21 -9999 0 -0.55 115 115
MAPK3 -0.13 0.19 -9999 0 -0.61 49 49
HGF/MET -0.065 0.21 -9999 0 -0.69 84 84
TGFB1/TGF beta receptor Type II 0.011 0.056 -9999 0 -0.74 5 5
BSG 0.013 0.036 -9999 0 -0.74 2 2
keratinocyte migration -0.16 0.2 -9999 0 -0.54 117 117
Syndecan-1/RANTES -0.28 0.28 -9999 0 -0.64 255 255
Syndecan-1/CD147 -0.17 0.18 -9999 0 -0.64 55 55
Syndecan-1/Syntenin/PIP2 -0.17 0.18 -9999 0 -0.53 115 115
LAMA5 0.013 0.039 -9999 0 -0.8 2 2
positive regulation of cell-cell adhesion -0.17 0.17 -9999 0 -0.52 115 115
MMP7 -0.12 0.31 -9999 0 -0.82 144 144
HGF -0.049 0.22 -9999 0 -0.84 67 67
Syndecan-1/CASK -0.17 0.21 -9999 0 -0.53 134 134
Syndecan-1/HGF/MET -0.21 0.24 -9999 0 -0.68 119 119
regulation of cell adhesion -0.11 0.19 -9999 0 -0.68 21 21
HPSE -0.014 0.15 -9999 0 -0.83 30 30
positive regulation of cell migration -0.18 0.22 -9999 0 -0.56 134 134
SDC1 -0.18 0.22 -9999 0 -0.56 134 134
Syndecan-1/Collagen -0.18 0.22 -9999 0 -0.56 134 134
PPIB 0.015 0 -9999 0 -10000 0 0
MET -0.01 0.13 -9999 0 -0.74 29 29
PRKACA 0.015 0 -9999 0 -10000 0 0
MMP9 -0.28 0.37 -9999 0 -0.74 350 350
MAPK1 -0.13 0.19 -9999 0 -0.61 49 49
homophilic cell adhesion -0.17 0.22 -9999 0 -0.55 134 134
MMP1 -0.14 0.32 -9999 0 -0.79 173 173
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.003 0.044 -9999 0 -0.58 5 5
ARNO/beta Arrestin1-2 -0.024 0.074 -9999 0 -0.43 2 2
EGFR 0.002 0.099 -9999 0 -0.75 15 15
EPHA2 0.013 0.039 -9999 0 -0.8 2 2
USP6 0.004 0.09 -9999 0 -0.74 13 13
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.56 0.25 -9999 0 -0.67 742 742
ARRB2 -0.014 0.095 -9999 0 -0.33 73 73
mol:GTP 0.004 0.038 -9999 0 -0.26 2 2
ARRB1 0.014 0.029 -9999 0 -0.86 1 1
FBXO8 0.015 0 -9999 0 -10000 0 0
TSHR -0.053 0.21 -9999 0 -0.74 79 79
EGF -0.71 0.33 -9999 0 -0.86 739 739
somatostatin receptor activity 0 0 -9999 0 -0.001 126 126
ARAP2 0.013 0.041 -9999 0 -0.86 2 2
mol:GDP -0.088 0.12 -9999 0 -0.33 102 102
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 80 80
ITGA2B -0.006 0.12 -9999 0 -0.75 24 24
ARF6 0.015 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.026 -9999 0 -0.52 1 1
ADAP1 0.01 0.065 -9999 0 -0.86 5 5
KIF13B 0.015 0 -9999 0 -10000 0 0
HGF/MET -0.065 0.21 -9999 0 -0.69 84 84
PXN 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.13 -9999 0 -0.35 129 129
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.48 0.22 -9999 0 -0.58 742 742
ADRB2 -0.003 0.12 -9999 0 -0.74 21 21
receptor agonist activity 0 0 -9999 0 0 103 103
actin filament binding 0 0 -9999 0 -0.001 121 121
SRC 0.014 0.025 -9999 0 -0.74 1 1
ITGB3 -0.014 0.16 -9999 0 -0.85 30 30
GNAQ 0.013 0.005 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 86 86
ARF6/GDP -0.042 0.11 -9999 0 -0.41 1 1
ARF6/GDP/GULP/ACAP1 -0.17 0.2 -9999 0 -0.56 107 107
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.029 0.12 -9999 0 -0.53 30 30
ACAP1 -0.18 0.33 -9999 0 -0.74 226 226
ACAP2 0.015 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.039 0.13 -9999 0 -0.48 73 73
EFNA1 0.014 0.025 -9999 0 -0.74 1 1
HGF -0.049 0.22 -9999 0 -0.84 67 67
CYTH3 0.014 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 90 90
endosomal lumen acidification 0 0 -9999 0 -0.001 140 140
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.002 0.11 -9999 0 -0.84 14 14
GNAQ/ARNO 0.003 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 3 3
MET -0.01 0.13 -9999 0 -0.74 29 29
GNA14 -0.076 0.27 -9999 0 -0.86 93 93
GNA15 -0.014 0.14 -9999 0 -0.74 34 34
GIT1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 102 102
GNA11 0.007 0.082 -9999 0 -0.86 8 8
LHCGR -0.053 0.2 -9999 0 -0.74 70 70
AGTR1 -0.13 0.32 -9999 0 -0.86 143 143
desensitization of G-protein coupled receptor protein signaling pathway -0.039 0.13 -9999 0 -0.48 73 73
IPCEF1/ARNO -0.38 0.18 -9999 0 -0.46 741 741
alphaIIb/beta3 Integrin -0.037 0.15 -9999 0 -0.62 53 53
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.099 0.26 -10000 0 -0.9 78 78
NFATC2 -0.075 0.25 -10000 0 -0.65 77 77
NFATC3 -0.023 0.088 -10000 0 -10000 0 0
CD40LG -0.25 0.47 -10000 0 -1.1 142 142
ITCH 0.035 0.091 -10000 0 -10000 0 0
CBLB 0.035 0.091 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.39 0.48 -10000 0 -1.1 219 219
JUNB 0.013 0.041 -10000 0 -0.86 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.092 -10000 0 -10000 0 0
T cell anergy -0.002 0.14 -10000 0 -0.53 7 7
TLE4 -0.027 0.18 -10000 0 -0.67 17 17
Jun/NFAT1-c-4/p21SNFT -0.22 0.3 -10000 0 -1 62 62
AP-1/NFAT1-c-4 -0.33 0.43 -10000 0 -1.3 104 104
IKZF1 -0.11 0.33 -10000 0 -0.75 170 170
T-helper 2 cell differentiation -0.39 0.33 -10000 0 -0.79 242 242
AP-1/NFAT1 -0.12 0.2 -10000 0 -0.65 67 67
CALM1 0.017 0.057 -10000 0 -10000 0 0
EGR2 -0.14 0.43 -10000 0 -1.7 46 46
EGR3 -0.16 0.48 -10000 0 -1.6 68 68
NFAT1/FOXP3 -0.2 0.32 -10000 0 -0.8 160 160
EGR1 -0.031 0.2 -10000 0 -0.86 48 48
JUN 0.007 0.022 -10000 0 -10000 0 0
EGR4 0.003 0.075 -10000 0 -0.73 9 9
mol:Ca2+ -0.003 0.062 -10000 0 -10000 0 0
GBP3 -0.036 0.21 -10000 0 -0.71 37 37
FOSL1 -0.012 0.14 -10000 0 -0.74 32 32
NFAT1-c-4/MAF/IRF4 -0.24 0.35 -10000 0 -0.91 135 135
DGKA -0.033 0.2 -10000 0 -0.71 29 29
CREM 0.013 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.19 0.29 -10000 0 -1.1 53 53
CTLA4 -0.24 0.47 -10000 0 -0.9 270 270
NFAT1-c-4 (dimer)/EGR1 -0.21 0.35 -10000 0 -1.2 67 67
NFAT1-c-4 (dimer)/EGR4 -0.19 0.3 -10000 0 -1.1 53 53
FOS -0.052 0.22 -10000 0 -0.87 59 59
IFNG -0.31 0.42 -10000 0 -0.94 233 233
T cell activation -0.074 0.26 -10000 0 -0.82 46 46
MAF 0.015 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.078 0.25 0.9 34 -10000 0 34
TNF -0.13 0.36 -10000 0 -1.1 65 65
FASLG -0.29 0.52 -10000 0 -1.3 89 89
TBX21 -0.17 0.34 -10000 0 -0.79 201 201
BATF3 -0.014 0.14 -10000 0 -0.74 34 34
PRKCQ -0.052 0.2 -10000 0 -0.86 53 53
PTPN1 -0.027 0.18 -10000 0 -0.67 17 17
NFAT1-c-4/ICER1 -0.19 0.29 -10000 0 -1.1 53 53
GATA3 -0.44 0.44 -10000 0 -0.86 467 467
T-helper 1 cell differentiation -0.31 0.4 -10000 0 -0.92 234 234
IL2RA -0.3 0.39 -10000 0 -1 165 165
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.027 0.18 -10000 0 -0.67 17 17
E2F1 -0.13 0.3 -10000 0 -0.73 181 181
PPARG 0.014 0.025 -10000 0 -0.74 1 1
SLC3A2 -0.027 0.18 -10000 0 -0.67 17 17
IRF4 -0.11 0.28 -10000 0 -0.74 152 152
PTGS2 -0.25 0.48 -10000 0 -1.2 108 108
CSF2 -0.22 0.43 -10000 0 -1.1 98 98
JunB/Fra1/NFAT1-c-4 -0.19 0.29 -10000 0 -1.1 51 51
IL4 -0.4 0.35 -10000 0 -0.86 217 217
IL5 -0.21 0.42 -10000 0 -1.1 94 94
IL2 -0.075 0.26 -10000 0 -0.83 46 46
IL3 -0.05 0.052 -10000 0 -10000 0 0
RNF128 -0.018 0.26 -10000 0 -0.89 75 75
NFATC1 -0.078 0.26 -10000 0 -0.9 34 34
CDK4 0.023 0.2 0.62 4 -10000 0 4
PTPRK -0.028 0.18 -10000 0 -0.69 18 18
IL8 -0.24 0.46 -10000 0 -1.1 109 109
POU2F1 0.015 0.002 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.035 0.24 -10000 0 -0.74 45 45
PTK2B 0.014 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.39 -10000 0 -1 115 115
EDN1 -0.047 0.2 -10000 0 -0.74 41 41
EDN3 -0.009 0.11 -10000 0 -0.74 21 21
EDN2 -0.091 0.28 -10000 0 -0.81 113 113
HRAS/GDP -0.048 0.25 -10000 0 -0.64 81 81
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.066 0.24 -10000 0 -0.6 95 95
ADCY4 -0.04 0.22 -10000 0 -0.74 45 45
ADCY5 -0.059 0.24 -10000 0 -0.65 77 77
ADCY6 -0.029 0.2 -10000 0 -0.69 35 35
ADCY7 -0.044 0.21 -10000 0 -0.69 43 43
ADCY1 -0.12 0.29 -10000 0 -0.6 164 164
ADCY2 -0.18 0.28 -10000 0 -0.64 135 135
ADCY3 -0.029 0.2 -10000 0 -0.7 34 34
ADCY8 -0.12 0.25 -10000 0 -0.69 77 77
ADCY9 -0.029 0.2 -10000 0 -0.73 30 30
arachidonic acid secretion -0.041 0.27 -10000 0 -0.67 94 94
ETB receptor/Endothelin-1/Gq/GTP -0.02 0.16 -10000 0 -0.42 68 68
GNAO1 -0.02 0.17 -10000 0 -0.83 37 37
HRAS 0.013 0.025 -10000 0 -0.74 1 1
ETA receptor/Endothelin-1/G12/GTP -0.045 0.24 0.37 101 -0.7 45 146
ETA receptor/Endothelin-1/Gs/GTP -0.045 0.23 0.34 100 -0.67 46 146
mol:GTP 0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.076 0.33 -10000 0 -0.86 103 103
EDNRB 0.004 0.087 -10000 0 -0.81 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.12 0.37 -10000 0 -0.76 171 171
CYSLTR1 -0.036 0.25 -10000 0 -0.83 34 34
SLC9A1 -0.03 0.12 -10000 0 -0.38 23 23
mol:GDP -0.062 0.27 -10000 0 -0.68 89 89
SLC9A3 -0.5 0.38 -10000 0 -0.68 629 629
RAF1 -0.059 0.26 -10000 0 -0.68 89 89
JUN -0.024 0.25 -10000 0 -0.74 58 58
JAK2 -0.035 0.24 -10000 0 -0.74 45 45
mol:IP3 -0.071 0.24 -10000 0 -0.59 112 112
ETA receptor/Endothelin-1 -0.067 0.3 0.43 103 -0.62 116 219
PLCB1 -0.085 0.28 -10000 0 -0.86 101 101
PLCB2 -0.061 0.22 -10000 0 -0.74 89 89
ETA receptor/Endothelin-3 -0.039 0.18 -10000 0 -0.67 50 50
FOS -0.051 0.31 -10000 0 -0.96 68 68
Gai/GDP -0.005 0.17 -10000 0 -0.88 28 28
CRK 0.014 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.092 0.3 -10000 0 -0.76 92 92
BCAR1 0.013 0.029 -10000 0 -0.86 1 1
PRKCB1 -0.068 0.24 -10000 0 -0.57 112 112
GNAQ 0.016 0.007 -10000 0 -10000 0 0
GNAZ 0.012 0.051 -10000 0 -0.86 3 3
GNAL 0.013 0.039 -10000 0 -0.8 2 2
Gs family/GDP -0.11 0.19 -10000 0 -0.6 87 87
ETA receptor/Endothelin-1/Gq/GTP -0.036 0.23 -10000 0 -0.6 79 79
MAPK14 -0.041 0.18 -10000 0 -0.57 49 49
TRPC6 -0.1 0.42 -10000 0 -1.1 114 114
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.01 0.065 -10000 0 -0.86 5 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.054 0.19 -10000 0 -0.55 66 66
ETB receptor/Endothelin-2 -0.087 0.22 -10000 0 -0.62 121 121
ETB receptor/Endothelin-3 -0.022 0.1 -10000 0 -0.58 30 30
ETB receptor/Endothelin-1 -0.04 0.17 -10000 0 -0.61 45 45
MAPK3 -0.055 0.3 -10000 0 -0.83 87 87
MAPK1 -0.055 0.3 -10000 0 -0.84 85 85
Rac1/GDP -0.048 0.25 -10000 0 -0.65 78 78
cAMP biosynthetic process -0.12 0.23 -10000 0 -0.64 81 81
MAPK8 -0.052 0.31 -10000 0 -0.89 74 74
SRC 0.014 0.025 -10000 0 -0.74 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.013 0.092 -10000 0 -0.44 8 8
p130Cas/CRK/Src/PYK2 -0.065 0.3 -10000 0 -0.73 105 105
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.048 0.25 -10000 0 -0.66 72 72
COL1A2 -0.1 0.3 -10000 0 -0.8 103 103
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.1 0.26 -10000 0 -0.66 139 139
mol:DAG -0.071 0.24 -10000 0 -0.59 112 112
MAP2K2 -0.051 0.27 -10000 0 -0.72 87 87
MAP2K1 -0.051 0.27 -10000 0 -0.73 83 83
EDNRA -0.042 0.2 -10000 0 -0.9 31 31
positive regulation of muscle contraction -0.022 0.22 -10000 0 -0.72 34 34
Gq family/GDP -0.12 0.25 -10000 0 -0.72 107 107
HRAS/GTP -0.069 0.26 -10000 0 -0.64 104 104
PRKCH -0.059 0.24 -10000 0 -0.65 77 77
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.058 0.24 -10000 0 -0.64 77 77
PRKCB -0.064 0.25 -10000 0 -0.66 85 85
PRKCE -0.058 0.23 -10000 0 -0.64 76 76
PRKCD -0.063 0.24 -10000 0 -0.63 90 90
PRKCG -0.11 0.29 -10000 0 -0.72 120 120
regulation of vascular smooth muscle contraction -0.066 0.36 -10000 0 -1.1 72 72
PRKCQ -0.088 0.27 -10000 0 -0.66 111 111
PLA2G4A -0.052 0.3 -10000 0 -0.75 94 94
GNA14 -0.075 0.27 -10000 0 -0.86 93 93
GNA15 -0.014 0.14 -10000 0 -0.74 34 34
GNA12 0.015 0 -10000 0 -10000 0 0
GNA11 0.007 0.083 -10000 0 -0.86 8 8
Rac1/GTP -0.045 0.24 0.37 102 -0.69 45 147
MMP1 -0.13 0.4 -10000 0 -0.88 173 173
LPA4-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
ADCY4 0.012 0.093 -9999 0 -0.58 21 21
ADCY5 -0.011 0.15 -9999 0 -0.58 54 54
ADCY6 0.025 0.038 -9999 0 -1.1 1 1
ADCY7 0.007 0.098 -9999 0 -0.48 34 34
ADCY1 -0.092 0.24 -9999 0 -0.57 175 175
ADCY2 -0.16 0.25 -9999 0 -0.49 316 316
ADCY3 0.025 0.027 -9999 0 -0.53 2 2
ADCY8 -0.077 0.2 -9999 0 -0.48 176 176
PRKCE 0.014 0.023 -9999 0 -0.67 1 1
ADCY9 0.026 0.02 -9999 0 -0.58 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.097 0.15 -9999 0 -0.43 84 84
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.015 0 -9999 0 -10000 0 0
LAT2 -0.16 0.22 -9999 0 -0.61 124 124
AP1 -0.16 0.19 -9999 0 -0.51 138 138
mol:PIP3 -0.2 0.31 -9999 0 -0.69 196 196
IKBKB -0.078 0.16 -9999 0 -0.33 126 126
AKT1 -0.16 0.19 -9999 0 -0.64 48 48
IKBKG -0.078 0.16 -9999 0 -0.33 132 132
MS4A2 -0.18 0.32 -9999 0 -0.74 228 228
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.008 -9999 0 -10000 0 0
MAP3K1 -0.11 0.23 -9999 0 -0.53 149 149
mol:Ca2+ -0.14 0.22 -9999 0 -0.47 194 194
LYN 0.009 0.031 -9999 0 -0.89 1 1
CBLB -0.11 0.14 -9999 0 -0.48 49 49
SHC1 0.014 0.025 -9999 0 -0.74 1 1
RasGAP/p62DOK -0.003 0.039 -9999 0 -0.53 3 3
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.006 0.083 -9999 0 -0.74 11 11
PLD2 -0.17 0.25 -9999 0 -0.77 51 51
PTPN13 -0.074 0.16 -9999 0 -0.52 31 31
PTPN11 0.013 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.044 0.16 -9999 0 -0.43 5 5
SYK 0.005 0.066 -9999 0 -0.87 5 5
GRB2 0.014 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.25 0.29 -9999 0 -0.7 219 219
LAT -0.18 0.23 -9999 0 -0.63 148 148
PAK2 -0.13 0.26 -9999 0 -0.58 172 172
NFATC2 -0.093 0.16 -9999 0 -0.84 32 32
HRAS -0.16 0.28 -9999 0 -0.62 197 197
GAB2 0.013 0.036 -9999 0 -0.74 2 2
PLA2G1B 0.041 0.024 -9999 0 -10000 0 0
Fc epsilon R1 -0.25 0.29 -9999 0 -0.54 414 414
Antigen/IgE/Fc epsilon R1 -0.23 0.27 -9999 0 -0.5 414 414
mol:GDP -0.18 0.31 -9999 0 -0.7 197 197
JUN 0.015 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.008 -9999 0 -10000 0 0
FOS -0.043 0.22 -9999 0 -0.86 59 59
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.12 0.15 -9999 0 -0.51 51 51
CHUK -0.078 0.16 -9999 0 -0.34 115 115
KLRG1 -0.12 0.14 -9999 0 -0.49 51 51
VAV1 -0.2 0.26 -9999 0 -0.61 214 214
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.11 0.14 -9999 0 -0.48 52 52
negative regulation of mast cell degranulation -0.11 0.14 -9999 0 -0.5 49 49
BTK -0.17 0.21 -9999 0 -0.53 187 187
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.2 -9999 0 -0.51 171 171
GAB2/PI3K/SHP2 -0.18 0.21 -9999 0 -0.72 48 48
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.14 -9999 0 -0.5 51 51
RAF1 0.027 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.29 0.35 -9999 0 -0.89 171 171
FCER1G -0.16 0.31 -9999 0 -0.74 193 193
FCER1A -0.032 0.18 -9999 0 -0.84 43 43
Antigen/IgE/Fc epsilon R1/Fyn -0.21 0.25 -9999 0 -0.71 78 78
MAPK3 0.04 0.023 -9999 0 -10000 0 0
MAPK1 0.04 0.023 -9999 0 -10000 0 0
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
MAPK8 -0.017 0.088 -9999 0 -0.67 7 7
DUSP1 0.012 0.048 -9999 0 -0.82 3 3
NF-kappa-B/RelA -0.063 0.07 -9999 0 -0.31 1 1
actin cytoskeleton reorganization -0.072 0.14 -9999 0 -0.44 38 38
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.26 -9999 0 -0.64 193 193
FER -0.11 0.14 -9999 0 -0.48 53 53
RELA 0.015 0 -9999 0 -10000 0 0
ITK -0.089 0.14 -9999 0 -0.36 179 179
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG1 -0.18 0.31 -9999 0 -0.69 202 202
cytokine secretion -0.046 0.051 -9999 0 -10000 0 0
SPHK1 -0.19 0.22 -9999 0 -0.61 141 141
PTK2 -0.075 0.15 -9999 0 -0.46 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.23 0.29 -9999 0 -0.73 186 186
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.17 0.29 -9999 0 -0.64 187 187
MAP2K2 0.035 0.029 -9999 0 -0.52 1 1
MAP2K1 0.036 0.022 -9999 0 -10000 0 0
MAP2K7 0.015 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.14 -9999 0 -0.48 49 49
MAP2K4 0.016 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.31 0.36 -9999 0 -0.87 196 196
mol:Choline -0.17 0.25 -9999 0 -0.75 51 51
SHC/Grb2/SOS1 -0.1 0.13 -9999 0 -0.63 7 7
FYN 0.015 0 -9999 0 -10000 0 0
DOK1 0.013 0.036 -9999 0 -0.74 2 2
PXN -0.061 0.14 -9999 0 -0.61 5 5
HCLS1 -0.12 0.17 -9999 0 -0.56 71 71
PRKCB -0.13 0.21 -9999 0 -0.46 186 186
FCGR2B -0.14 0.31 -9999 0 -0.74 183 183
IGHE -0.006 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.15 -9999 0 -0.52 49 49
LCP2 -0.042 0.2 -9999 0 -0.74 67 67
PLA2G4A -0.12 0.16 -9999 0 -0.52 72 72
RASA1 0.014 0.029 -9999 0 -0.86 1 1
mol:Phosphatidic acid -0.17 0.25 -9999 0 -0.75 51 51
IKK complex -0.04 0.12 -9999 0 -0.28 2 2
WIPF1 0.014 0.025 -9999 0 -0.74 1 1
Caspase cascade in apoptosis

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
TOP1 -0.069 0.21 -10000 0 -0.5 134 134
ACTA1 -0.11 0.27 -10000 0 -0.66 139 139
NUMA1 -0.069 0.21 -10000 0 -0.5 134 134
SPTAN1 -0.1 0.26 -10000 0 -0.66 134 134
LIMK1 -0.1 0.27 -10000 0 -0.66 135 135
BIRC3 -0.072 0.24 -10000 0 -0.74 101 101
BIRC2 0.012 0.006 -10000 0 -10000 0 0
BAX 0.014 0.025 -10000 0 -0.74 1 1
CASP10 -0.16 0.35 -10000 0 -0.71 238 238
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0.006 -10000 0 -10000 0 0
PTK2 -0.069 0.21 -10000 0 -0.5 134 134
DIABLO 0.015 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.099 0.26 -10000 0 -0.64 134 134
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
GSN -0.1 0.27 -10000 0 -0.66 134 134
MADD 0.015 0 -10000 0 -10000 0 0
TFAP2A -0.32 0.29 -10000 0 -0.55 515 515
BID -0.051 0.14 -10000 0 -0.34 134 134
MAP3K1 -0.023 0.088 -10000 0 -10000 0 0
TRADD 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.1 0.27 -10000 0 -0.66 134 134
CASP9 0.015 0.001 -10000 0 -10000 0 0
DNA repair 0.006 0.073 -10000 0 -0.21 5 5
neuron apoptosis 0.018 0.029 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.089 0.26 -10000 0 -0.63 134 134
APAF1 0.015 0 -10000 0 -10000 0 0
CASP6 -0.018 0.12 -10000 0 -0.42 1 1
TRAF2 0.015 0 -10000 0 -10000 0 0
ICAD/CAD -0.089 0.26 -10000 0 -0.63 134 134
CASP7 0.028 0.1 0.33 62 -10000 0 62
KRT18 0.005 0.041 -10000 0 -0.24 7 7
apoptosis -0.1 0.26 -10000 0 -0.64 116 116
DFFA -0.1 0.26 -10000 0 -0.66 134 134
DFFB -0.1 0.26 -10000 0 -0.66 134 134
PARP1 -0.006 0.073 0.21 5 -10000 0 5
actin filament polymerization 0.086 0.25 0.6 135 -10000 0 135
TNF -0.007 0.13 -10000 0 -0.78 25 25
CYCS -0.037 0.11 -10000 0 -0.26 133 133
SATB1 -0.007 0.12 -10000 0 -0.42 2 2
SLK -0.1 0.27 -10000 0 -0.66 135 135
p15 BID/BAX -0.039 0.13 -10000 0 -0.42 1 1
CASP2 0.037 0.072 -10000 0 -0.43 2 2
JNK cascade 0.023 0.087 -10000 0 -10000 0 0
CASP3 -0.12 0.28 -10000 0 -0.7 134 134
LMNB2 0.025 0.067 -10000 0 -0.33 1 1
RIPK1 0.015 0 -10000 0 -10000 0 0
CASP4 0.015 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.048 0.13 -10000 0 -0.52 2 2
negative regulation of DNA binding -0.31 0.28 -10000 0 -0.55 515 515
stress fiber formation -0.1 0.26 -10000 0 -0.64 135 135
GZMB -0.2 0.39 -10000 0 -0.81 238 238
CASP1 0.02 0.024 -10000 0 -0.33 4 4
LMNB1 0.023 0.071 -10000 0 -0.33 1 1
APP 0.018 0.029 -10000 0 -10000 0 0
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.1 0.25 -10000 0 -0.58 149 149
LMNA 0.025 0.067 -10000 0 -0.33 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.021 0.057 -10000 0 -0.46 2 2
LRDD 0.004 0.091 -10000 0 -0.75 13 13
SREBF1 -0.1 0.26 -10000 0 -0.66 134 134
APAF-1/Caspase 9 -0.007 0.048 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.067 0.2 -10000 0 -0.49 134 134
CFL2 -0.089 0.25 -10000 0 -0.62 135 135
GAS2 -0.12 0.27 -10000 0 -0.66 145 145
positive regulation of apoptosis 0.028 0.068 -10000 0 -10000 0 0
PRF1 -0.12 0.29 -10000 0 -0.74 163 163
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.45 -10000 0 -1.1 77 77
IL23A -0.19 0.44 -10000 0 -1.1 58 58
NF kappa B1 p50/RelA/I kappa B alpha -0.27 0.34 -10000 0 -1 85 85
positive regulation of T cell mediated cytotoxicity -0.22 0.47 -10000 0 -1.1 107 107
ITGA3 -0.19 0.43 -10000 0 -1.1 69 69
IL17F -0.12 0.32 -10000 0 -0.74 34 34
IL12B -0.067 0.24 -10000 0 -0.75 96 96
STAT1 (dimer) -0.22 0.44 -10000 0 -1.1 97 97
CD4 -0.2 0.44 -10000 0 -1.1 77 77
IL23 -0.22 0.44 -10000 0 -1.1 74 74
IL23R -0.013 0.14 -10000 0 -0.69 21 21
IL1B -0.2 0.45 -10000 0 -1.2 69 69
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.19 0.43 -10000 0 -1.1 66 66
TYK2 0.015 0.023 -10000 0 -10000 0 0
STAT4 -0.026 0.17 -10000 0 -0.74 49 49
STAT3 0.015 0.001 -10000 0 -10000 0 0
IL18RAP -0.13 0.3 -10000 0 -0.75 164 164
IL12RB1 -0.16 0.33 -10000 0 -0.76 202 202
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.12 0.26 -10000 0 -0.59 202 202
IL23R/JAK2 -0.011 0.15 -10000 0 -0.68 15 15
positive regulation of chronic inflammatory response -0.22 0.47 -10000 0 -1.1 107 107
natural killer cell activation 0.002 0.012 0.058 22 -10000 0 22
JAK2 0.021 0.033 -10000 0 -10000 0 0
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0.03 -10000 0 -0.85 1 1
RELA 0.011 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.42 -10000 0 -1.1 74 74
ALOX12B -0.23 0.45 -10000 0 -1.1 83 83
CXCL1 -0.28 0.5 -10000 0 -1.2 125 125
T cell proliferation -0.22 0.47 -10000 0 -1.1 107 107
NFKBIA 0.011 0.009 -10000 0 -10000 0 0
IL17A -0.073 0.27 -10000 0 -0.6 9 9
PI3K -0.28 0.35 -10000 0 -1 109 109
IFNG -0.032 0.061 0.12 13 -0.12 107 120
STAT3 (dimer) -0.26 0.34 -10000 0 -0.98 92 92
IL18R1 0 0.096 -10000 0 -0.82 12 12
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.33 -10000 0 -0.77 78 78
IL18/IL18R -0.12 0.22 -10000 0 -0.5 216 216
macrophage activation -0.015 0.017 -10000 0 -0.045 15 15
TNF -0.21 0.45 -10000 0 -1.1 75 75
STAT3/STAT4 -0.3 0.38 -10000 0 -1 120 120
STAT4 (dimer) -0.24 0.47 -10000 0 -1.1 108 108
IL18 -0.028 0.17 -10000 0 -0.74 46 46
IL19 -0.2 0.42 -10000 0 -1.1 65 65
STAT5A (dimer) -0.22 0.44 -10000 0 -1.1 93 93
STAT1 0.013 0.036 -10000 0 -0.74 2 2
SOCS3 0.004 0.093 -10000 0 -0.79 12 12
CXCL9 -0.28 0.51 -10000 0 -1.1 130 130
MPO -0.2 0.43 -10000 0 -1.1 69 69
positive regulation of humoral immune response -0.22 0.47 -10000 0 -1.1 107 107
IL23/IL23R/JAK2/TYK2 -0.24 0.48 -10000 0 -1.2 105 105
IL6 -0.3 0.55 -10000 0 -1.2 164 164
STAT5A 0.015 0 -10000 0 -10000 0 0
IL2 -0.011 0.099 -10000 0 -0.74 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.058 22 -10000 0 22
CD3E -0.28 0.52 -10000 0 -1.1 137 137
keratinocyte proliferation -0.22 0.47 -10000 0 -1.1 107 107
NOS2 -0.22 0.46 -10000 0 -1.1 95 95
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.22 0.28 -9999 0 -0.58 338 338
PDGFRB 0.001 0.11 -9999 0 -0.85 14 14
SPHK1 -0.062 0.12 -9999 0 -0.34 84 84
mol:S1P -0.056 0.12 -9999 0 -0.38 45 45
S1P1/S1P/Gi -0.08 0.21 -9999 0 -0.65 70 70
GNAO1 -0.02 0.17 -9999 0 -0.84 37 37
PDGFB-D/PDGFRB/PLCgamma1 -0.092 0.18 -9999 0 -0.7 46 46
PLCG1 -0.063 0.2 -9999 0 -0.68 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.001 0.11 -9999 0 -0.84 14 14
GNAI2 0.015 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.007 -9999 0 -10000 0 0
GNAI1 0.007 0.066 -9999 0 -0.86 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.17 0.25 -9999 0 -0.5 338 338
S1P1/S1P -0.18 0.2 -9999 0 -0.58 95 95
negative regulation of cAMP metabolic process -0.077 0.21 -9999 0 -0.62 70 70
MAPK3 -0.082 0.25 -9999 0 -0.68 105 105
calcium-dependent phospholipase C activity 0 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.052 0.23 -9999 0 -0.86 67 67
PLCB2 -0.17 0.23 -9999 0 -0.56 139 139
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.15 0.16 -9999 0 -0.5 82 82
receptor internalization -0.17 0.18 -9999 0 -0.54 95 95
PTGS2 -0.12 0.37 -9999 0 -1.1 104 104
Rac1/GTP -0.15 0.16 -9999 0 -0.48 91 91
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFA -0.22 0.35 -9999 0 -0.74 273 273
negative regulation of T cell proliferation -0.077 0.21 -9999 0 -0.62 70 70
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.009 0.051 -9999 0 -0.86 3 3
MAPK1 -0.082 0.25 -9999 0 -0.7 98 98
S1P1/S1P/PDGFB-D/PDGFRB -0.16 0.24 -9999 0 -0.65 87 87
ABCC1 0.012 0.007 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.051 0.23 -9999 0 -0.84 68 68
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.058 -9999 0 -0.76 5 5
TCEB1 0.015 0 -9999 0 -10000 0 0
HIF1A/p53 -0.026 0.062 -9999 0 -0.41 1 1
HIF1A -0.052 0.049 -9999 0 -0.44 1 1
COPS5 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.002 0.031 -9999 0 -0.48 1 1
FIH (dimer) 0.015 0 -9999 0 -10000 0 0
CDKN2A -0.65 0.24 -9999 0 -0.74 782 782
ARNT/IPAS -0.05 0.17 -9999 0 -0.65 68 68
HIF1AN 0.015 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.025 -9999 0 -0.74 1 1
HIF1A/ARNT -0.026 0.062 -9999 0 -0.41 1 1
CUL2 0.015 0 -9999 0 -10000 0 0
OS9 0.015 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.003 0.04 -9999 0 -0.49 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.026 0.062 -9999 0 -0.41 1 1
PHD1-3/OS9 -0.23 0.21 -9999 0 -0.52 4 4
HIF1A/RACK1/Elongin B/Elongin C -0.034 0.046 -9999 0 -0.56 3 3
VHL 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.026 0.062 -9999 0 -0.41 1 1
EGLN3 -0.4 0.37 -9999 0 -0.74 490 490
EGLN2 0.015 0 -9999 0 -10000 0 0
EGLN1 0.015 0 -9999 0 -10000 0 0
TP53 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.018 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.015 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.38 0.16 -9999 0 -0.44 782 782
Thromboxane A2 receptor signaling

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
TGM2 -0.013 0.13 -10000 0 -0.74 27 27
GNB1/GNG2 -0.065 0.081 -10000 0 -0.21 65 65
AKT1 -0.009 0.13 -10000 0 -0.26 1 1
EGF -0.71 0.33 -10000 0 -0.86 739 739
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.027 0.079 -10000 0 -0.62 3 3
mol:Ca2+ -0.044 0.18 -10000 0 -0.31 218 218
LYN -0.023 0.069 -10000 0 -0.54 1 1
RhoA/GTP -0.04 0.053 -10000 0 -0.17 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.047 0.2 -10000 0 -0.36 148 148
GNG2 0.015 0 -10000 0 -10000 0 0
ARRB2 0.012 0.044 -10000 0 -0.74 3 3
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.1 -10000 0 -0.48 10 10
G beta5/gamma2 -0.085 0.11 -10000 0 -0.29 64 64
PRKCH -0.053 0.2 -10000 0 -0.38 109 109
DNM1 -0.096 0.27 -10000 0 -0.74 131 131
TXA2/TP beta/beta Arrestin3 -0.037 0.079 -10000 0 -0.24 62 62
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.053 0.22 -10000 0 -0.74 80 80
G12 family/GTP -0.099 0.13 -10000 0 -0.31 152 152
ADRBK1 0.015 0 -10000 0 -10000 0 0
ADRBK2 0.015 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.12 0.38 24 -10000 0 24
mol:NADP -0.003 0.12 -10000 0 -0.85 18 18
RAB11A 0.015 0 -10000 0 -10000 0 0
PRKG1 -0.078 0.27 -10000 0 -0.86 94 94
mol:IP3 -0.064 0.22 -10000 0 -0.39 224 224
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.1 0.28 -10000 0 -0.52 228 228
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.04 0.1 -10000 0 -0.5 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.046 0.11 -10000 0 -0.53 14 14
RHOA 0.015 0 -10000 0 -10000 0 0
PTGIR 0.009 0.07 -10000 0 -0.84 6 6
PRKCB1 -0.064 0.21 -10000 0 -0.38 228 228
GNAQ 0.015 0 -10000 0 -10000 0 0
mol:L-citrulline -0.003 0.12 -10000 0 -0.85 18 18
TXA2/TXA2-R family -0.1 0.29 -10000 0 -0.54 227 227
LCK -0.039 0.11 -10000 0 -0.52 21 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.031 0.09 -10000 0 -0.59 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.03 0.032 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.031 0.09 -10000 0 -0.74 1 1
MAPK14 -0.016 0.14 -10000 0 -0.32 3 3
TGM2/GTP -0.078 0.24 -10000 0 -0.47 152 152
MAPK11 -0.016 0.14 -10000 0 -0.34 4 4
ARHGEF1 -0.012 0.11 -10000 0 -0.28 1 1
GNAI2 0.015 0 -10000 0 -10000 0 0
JNK cascade -0.062 0.22 -10000 0 -0.39 227 227
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 -0.035 0.17 -10000 0 -0.29 156 156
cAMP biosynthetic process -0.062 0.21 -10000 0 -0.38 155 155
Gq family/GTP/EBP50 -0.003 0.098 -10000 0 -0.37 10 10
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.023 0.068 -10000 0 -0.54 1 1
GNB5 0.015 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
EGF/EGFR -0.086 0.11 -10000 0 -0.4 25 25
VCAM1 -0.048 0.19 -10000 0 -0.32 191 191
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.1 -10000 0 -0.48 10 10
platelet activation -0.025 0.19 -10000 0 -0.33 80 80
PGI2/IP -0.004 0.054 -10000 0 -0.66 6 6
PRKACA -0.028 0.086 -10000 0 -0.39 5 5
Gq family/GDP/G beta5/gamma2 0.007 0.096 -10000 0 -0.45 10 10
TXA2/TP beta/beta Arrestin2 -0.05 0.12 -10000 0 -0.34 94 94
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.12 -10000 0 -0.51 19 19
mol:DAG -0.074 0.24 -10000 0 -0.43 228 228
EGFR 0.002 0.099 -10000 0 -0.75 15 15
TXA2/TP alpha -0.093 0.27 -10000 0 -0.53 160 160
Gq family/GTP -0.036 0.099 -10000 0 -0.29 100 100
YES1 -0.023 0.067 -10000 0 -0.54 1 1
GNAI2/GTP -0.027 0.079 -10000 0 -0.65 1 1
PGD2/DP -0.051 0.16 -10000 0 -0.56 80 80
SLC9A3R1 0.015 0 -10000 0 -10000 0 0
FYN -0.023 0.067 -10000 0 -0.54 1 1
mol:NO -0.003 0.12 -10000 0 -0.85 18 18
GNA15 -0.014 0.14 -10000 0 -0.74 34 34
PGK/cGMP -0.073 0.21 -10000 0 -0.62 104 104
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.039 0.1 -10000 0 -0.8 3 3
NOS3 -0.003 0.12 -10000 0 -0.85 18 18
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.053 0.2 -10000 0 -0.38 108 108
PRKCB -0.057 0.21 -10000 0 -0.39 146 146
PRKCE -0.052 0.2 -10000 0 -0.39 101 101
PRKCD -0.063 0.22 -10000 0 -0.39 226 226
PRKCG -0.084 0.25 -10000 0 -0.44 231 231
muscle contraction -0.087 0.27 -10000 0 -0.5 228 228
PRKCZ -0.047 0.2 -10000 0 -0.36 159 159
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.03 0.09 -10000 0 -0.6 2 2
PRKCQ -0.071 0.22 -10000 0 -0.41 159 159
MAPKKK cascade -0.083 0.25 -10000 0 -0.46 227 227
SELE -0.072 0.22 -10000 0 -0.43 218 218
TP beta/GNAI2/GDP/G beta/gamma -0.029 0.086 -10000 0 -0.73 1 1
ROCK1 0.015 0 -10000 0 -10000 0 0
GNA14 -0.076 0.27 -10000 0 -0.86 93 93
chemotaxis -0.12 0.33 -10000 0 -0.62 228 228
GNA12 0.015 0 -10000 0 -10000 0 0
GNA13 0.015 0 -10000 0 -10000 0 0
GNA11 0.007 0.082 -10000 0 -0.86 8 8
Rac1/GTP 0 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.11 0.22 -10000 0 -0.71 25 25
CRKL -0.017 0.16 -10000 0 -0.71 9 9
HRAS -0.053 0.18 -10000 0 -0.54 29 29
mol:PIP3 -0.035 0.15 -10000 0 -0.42 97 97
SPRED1 0.015 0 -10000 0 -10000 0 0
SPRED2 0.014 0.029 -10000 0 -0.86 1 1
GAB1 -0.029 0.17 -10000 0 -0.47 97 97
FOXO3 -0.008 0.15 -10000 0 -0.62 9 9
AKT1 -0.02 0.16 -10000 0 -0.43 97 97
BAD -0.009 0.15 -10000 0 -0.6 10 10
megakaryocyte differentiation -0.12 0.28 -10000 0 -0.54 252 252
GSK3B -0.008 0.15 -10000 0 -0.62 9 9
RAF1 -0.024 0.16 -10000 0 -0.44 18 18
SHC1 0.014 0.025 -10000 0 -0.74 1 1
STAT3 -0.029 0.17 -10000 0 -0.47 97 97
STAT1 -0.088 0.36 -10000 0 -1 97 97
HRAS/SPRED1 -0.077 0.12 -10000 0 -0.42 28 28
cell proliferation -0.032 0.18 -10000 0 -0.46 102 102
PIK3CA 0.015 0 -10000 0 -10000 0 0
TEC 0.015 0 -10000 0 -10000 0 0
RPS6KB1 -0.029 0.17 -10000 0 -0.46 99 99
HRAS/SPRED2 -0.077 0.12 -10000 0 -0.43 29 29
LYN/TEC/p62DOK -0.055 0.15 -10000 0 -0.7 10 10
MAPK3 0.001 0.12 -10000 0 -0.34 4 4
STAP1 -0.39 0.28 -10000 0 -0.53 675 675
GRAP2 -0.033 0.18 -10000 0 -0.74 56 56
JAK2 -0.13 0.28 -10000 0 -0.89 97 97
STAT1 (dimer) -0.085 0.35 -10000 0 -1 97 97
mol:Gleevec -0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.2 -10000 0 -0.71 35 35
actin filament polymerization -0.032 0.18 -10000 0 -0.46 106 106
LYN 0.014 0.029 -10000 0 -0.86 1 1
STAP1/STAT5A (dimer) -0.38 0.3 -10000 0 -0.68 268 268
PIK3R1 0.015 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.047 0.13 -10000 0 -0.6 10 10
PI3K -0.055 0.15 -10000 0 -0.71 9 9
PTEN 0.015 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.44 -10000 0 -1.3 99 99
MAPK8 -0.033 0.18 -10000 0 -0.48 102 102
STAT3 (dimer) -0.028 0.17 -10000 0 -0.45 99 99
positive regulation of transcription 0.005 0.1 -10000 0 -10000 0 0
mol:GDP -0.12 0.18 -10000 0 -0.54 79 79
PIK3C2B -0.029 0.17 -10000 0 -0.46 99 99
CBL/CRKL -0.008 0.16 -10000 0 -0.63 10 10
FER -0.03 0.17 -10000 0 -0.46 101 101
SH2B3 -0.029 0.17 -10000 0 -0.47 97 97
PDPK1 -0.023 0.14 -10000 0 -0.59 9 9
SNAI2 -0.058 0.22 -10000 0 -0.54 126 126
positive regulation of cell proliferation -0.055 0.27 -10000 0 -0.77 97 97
KITLG -0.001 0.12 -10000 0 -0.88 16 16
cell motility -0.055 0.27 -10000 0 -0.77 97 97
PTPN6 0.009 0.013 -10000 0 -10000 0 0
EPOR 0.017 0.11 -10000 0 -10000 0 0
STAT5A (dimer) -0.042 0.23 -10000 0 -0.64 97 97
SOCS1 0.002 0.1 -10000 0 -0.8 14 14
cell migration 0.06 0.2 0.5 107 -10000 0 107
SOS1 0.015 0 -10000 0 -10000 0 0
EPO -0.15 0.31 -10000 0 -0.73 195 195
VAV1 -0.15 0.31 -10000 0 -0.74 193 193
GRB10 -0.029 0.17 -10000 0 -0.47 97 97
PTPN11 0.008 0.011 -10000 0 -10000 0 0
SCF/KIT -0.072 0.17 -10000 0 -0.49 104 104
GO:0007205 0 0.009 -10000 0 -10000 0 0
MAP2K1 -0.006 0.13 -10000 0 -0.38 4 4
CBL 0.014 0.029 -10000 0 -0.86 1 1
KIT -0.12 0.46 -10000 0 -1.4 97 97
MAP2K2 -0.006 0.13 -10000 0 -0.38 4 4
SHC/Grb2/SOS1 -0.054 0.14 -10000 0 -0.7 9 9
STAT5A -0.045 0.24 -10000 0 -0.66 97 97
GRB2 0.015 0 -10000 0 -10000 0 0
response to radiation -0.056 0.22 -10000 0 -0.53 126 126
SHC/GRAP2 -0.036 0.14 -10000 0 -0.56 57 57
PTPRO -0.13 0.28 -10000 0 -0.55 252 252
SH2B2 -0.034 0.18 -10000 0 -0.47 106 106
DOK1 0.013 0.036 -10000 0 -0.74 2 2
MATK -0.062 0.21 -10000 0 -0.51 107 107
CREBBP 0.04 0.017 -10000 0 -10000 0 0
BCL2 0.018 0.11 -10000 0 -1.4 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.14 0.25 -10000 0 -0.79 38 38
IHH -0.088 0.26 -10000 0 -0.88 85 85
SHH Np/Cholesterol/GAS1 -0.056 0.17 -10000 0 -0.54 92 92
LRPAP1 0.015 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.055 0.16 0.53 92 -10000 0 92
SMO/beta Arrestin2 -0.11 0.17 -10000 0 -0.66 42 42
SMO -0.079 0.21 -10000 0 -0.68 47 47
AKT1 -0.012 0.095 -10000 0 -10000 0 0
ARRB2 0.012 0.044 -10000 0 -0.74 3 3
BOC 0.013 0.041 -10000 0 -0.86 2 2
ADRBK1 0.015 0 -10000 0 -10000 0 0
heart looping -0.077 0.2 -10000 0 -0.58 82 82
STIL -0.065 0.19 -10000 0 -0.62 47 47
DHH N/PTCH2 -0.043 0.16 -10000 0 -0.63 61 61
DHH N/PTCH1 -0.13 0.19 -10000 0 -0.62 78 78
PIK3CA 0.015 0 -10000 0 -10000 0 0
DHH -0.029 0.19 -10000 0 -0.86 44 44
PTHLH -0.23 0.37 -10000 0 -1.1 39 39
determination of left/right symmetry -0.077 0.2 -10000 0 -0.58 82 82
PIK3R1 0.015 0 -10000 0 -10000 0 0
skeletal system development -0.23 0.36 -10000 0 -1.1 39 39
IHH N/Hhip -0.16 0.3 -10000 0 -0.7 201 201
DHH N/Hhip -0.13 0.27 -10000 0 -0.67 166 166
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.077 0.2 -10000 0 -0.58 82 82
pancreas development -0.11 0.3 -10000 0 -0.84 129 129
HHAT 0.015 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.035 0.2 -10000 0 -0.85 51 51
somite specification -0.077 0.2 -10000 0 -0.58 82 82
SHH Np/Cholesterol/PTCH1 -0.11 0.17 -10000 0 -0.65 45 45
SHH Np/Cholesterol/PTCH2 -0.034 0.12 -10000 0 -0.49 61 61
SHH Np/Cholesterol/Megalin -0.099 0.25 -10000 0 -0.64 137 137
SHH -0.005 0.15 -10000 0 -0.65 44 44
catabolic process -0.091 0.2 -10000 0 -0.58 81 81
SMO/Vitamin D3 -0.12 0.18 -10000 0 -0.68 47 47
SHH Np/Cholesterol/Hhip -0.1 0.23 -10000 0 -0.57 157 157
LRP2 -0.11 0.3 -10000 0 -0.86 125 125
receptor-mediated endocytosis -0.15 0.23 -10000 0 -0.76 83 83
SHH Np/Cholesterol/BOC -0.027 0.11 -10000 0 -0.52 46 46
SHH Np/Cholesterol/CDO -0.068 0.16 -10000 0 -0.46 130 130
mesenchymal cell differentiation 0.099 0.22 0.56 157 -10000 0 157
mol:Vitamin D3 -0.075 0.2 -10000 0 -0.66 45 45
IHH N/PTCH2 -0.068 0.19 -10000 0 -0.6 101 101
CDON -0.059 0.22 -10000 0 -0.74 87 87
IHH N/PTCH1 -0.094 0.2 -10000 0 -0.59 81 81
Megalin/LRPAP1 -0.093 0.23 -10000 0 -0.66 125 125
PTCH2 0 0.1 -10000 0 -0.74 17 17
SHH Np/Cholesterol -0.026 0.11 -10000 0 -0.53 44 44
PTCH1 -0.092 0.2 -10000 0 -0.58 81 81
HHIP -0.11 0.3 -10000 0 -0.84 129 129
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.24 0.41 -9999 0 -1.1 124 124
MAP4K1 -0.18 0.33 -9999 0 -0.74 235 235
MAP3K8 0.013 0.036 -9999 0 -0.74 2 2
PRKCB 0.004 0.097 -9999 0 -0.83 12 12
DBNL 0.015 0 -9999 0 -10000 0 0
CRKL 0.015 0 -9999 0 -10000 0 0
MAP3K1 -0.067 0.22 -9999 0 -0.73 61 61
JUN 0.01 0.1 -9999 0 -0.63 16 16
MAP3K7 -0.067 0.22 -9999 0 -0.73 61 61
GRAP2 -0.033 0.18 -9999 0 -0.74 56 56
CRK 0.015 0 -9999 0 -10000 0 0
MAP2K4 -0.053 0.22 -9999 0 -0.69 62 62
LAT -0.12 0.29 -9999 0 -0.74 161 161
LCP2 -0.042 0.2 -9999 0 -0.74 67 67
MAPK8 -0.001 0.11 -9999 0 -0.64 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.12 0.22 -9999 0 -0.6 122 122
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.23 0.39 -9999 0 -1.1 122 122
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.012 0.056 -10000 0 -0.74 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.064 0.18 0.57 45 -0.4 4 49
IL27/IL27R/JAK1 -0.067 0.31 0.55 1 -0.88 53 54
TBX21 -0.16 0.34 0.45 1 -0.72 162 163
IL12B -0.073 0.23 -10000 0 -0.74 96 96
IL12A 0.01 0.007 -10000 0 -10000 0 0
IL6ST -0.06 0.24 -10000 0 -0.86 73 73
IL27RA/JAK1 0.012 0.05 -10000 0 -0.59 1 1
IL27 -0.035 0.18 -10000 0 -0.75 52 52
TYK2 0.012 0.01 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.038 0.14 -10000 0 -0.62 2 2
T-helper 2 cell differentiation 0.064 0.18 0.57 45 -0.4 4 49
T cell proliferation during immune response 0.064 0.18 0.57 45 -0.4 4 49
MAPKKK cascade -0.064 0.18 0.4 4 -0.57 45 49
STAT3 0.015 0 -10000 0 -10000 0 0
STAT2 0.015 0 -10000 0 -10000 0 0
STAT1 0.014 0.036 -10000 0 -0.74 2 2
IL12RB1 -0.16 0.32 -10000 0 -0.74 202 202
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.18 0.34 0.45 1 -0.68 161 162
IL27/IL27R/JAK2/TYK2 -0.065 0.18 0.4 4 -0.58 45 49
positive regulation of T cell mediated cytotoxicity -0.064 0.18 0.4 4 -0.57 45 49
STAT1 (dimer) -0.031 0.45 0.54 186 -0.88 101 287
JAK2 0.012 0.01 -10000 0 -10000 0 0
JAK1 0.016 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.064 0.16 0.35 4 -0.56 38 42
T cell proliferation -0.13 0.25 0.39 1 -0.64 93 94
IL12/IL12R/TYK2/JAK2 -0.1 0.2 -10000 0 -0.66 41 41
IL17A -0.039 0.14 -10000 0 -0.62 2 2
mast cell activation 0.064 0.18 0.57 45 -0.4 4 49
IFNG -0.025 0.055 0.098 4 -0.1 216 220
T cell differentiation -0.009 0.01 0.026 4 -0.025 158 162
STAT3 (dimer) -0.064 0.16 0.35 4 -0.56 40 44
STAT5A (dimer) -0.064 0.16 0.35 4 -0.56 40 44
STAT4 (dimer) -0.086 0.2 0.35 3 -0.66 59 62
STAT4 -0.026 0.17 -10000 0 -0.74 49 49
T cell activation -0.012 0.007 0.091 1 -10000 0 1
IL27R/JAK2/TYK2 -0.055 0.15 -10000 0 -0.62 5 5
GATA3 -0.72 0.73 -10000 0 -1.4 467 467
IL18 -0.016 0.13 -10000 0 -0.57 46 46
positive regulation of mast cell cytokine production -0.063 0.16 0.35 4 -0.55 40 44
IL27/EBI3 -0.09 0.26 -10000 0 -0.67 133 133
IL27RA 0.003 0.051 -10000 0 -0.64 1 1
IL6 -0.12 0.31 -10000 0 -0.82 146 146
STAT5A 0.015 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.001 0.069 -10000 0 -0.51 9 9
IL1B 0 0.092 -10000 0 -0.62 19 19
EBI3 -0.083 0.25 -10000 0 -0.75 110 110
TNF -0.003 0.1 -10000 0 -0.6 25 25
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.053 0.17 -9999 0 -0.57 82 82
EFNA5 -0.048 0.22 -9999 0 -0.85 65 65
FYN -0.025 0.16 -9999 0 -0.52 82 82
neuron projection morphogenesis -0.053 0.17 -9999 0 -0.57 82 82
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.053 0.17 -9999 0 -0.58 82 82
EPHA5 -0.012 0.11 -9999 0 -0.74 20 20
HIF-2-alpha transcription factor network

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
MMP14 -0.024 0.097 -10000 0 -0.57 25 25
oxygen homeostasis 0.004 0.019 -10000 0 -10000 0 0
TCEB2 0.011 0.058 -10000 0 -0.76 5 5
TCEB1 0.015 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.13 0.14 -10000 0 -0.57 3 3
EPO -0.16 0.41 -10000 0 -0.81 171 171
FIH (dimer) 0.018 0.02 -10000 0 -10000 0 0
APEX1 0.017 0.017 -10000 0 -10000 0 0
SERPINE1 -0.15 0.42 -10000 0 -0.93 103 103
FLT1 -0.027 0.13 -10000 0 -0.87 15 15
ADORA2A -0.11 0.36 -10000 0 -0.76 98 98
germ cell development -0.19 0.43 -10000 0 -0.86 172 172
SLC11A2 -0.1 0.36 -10000 0 -0.83 51 51
BHLHE40 -0.1 0.36 -10000 0 -0.83 52 52
HIF1AN 0.018 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.17 0.2 -10000 0 -0.55 98 98
ETS1 0.03 0.021 -10000 0 -10000 0 0
CITED2 -0.01 0.024 -10000 0 -10000 0 0
KDR -0.097 0.33 -10000 0 -1.2 67 67
PGK1 -0.1 0.36 -10000 0 -0.83 51 51
SIRT1 0.013 0.005 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.14 0.41 -10000 0 -0.9 98 98
EPAS1 -0.1 0.23 -10000 0 -0.43 104 104
SP1 0.024 0.01 -10000 0 -10000 0 0
ABCG2 -0.11 0.36 -10000 0 -0.85 58 58
EFNA1 -0.11 0.36 -10000 0 -0.83 52 52
FXN -0.11 0.36 -10000 0 -0.75 96 96
POU5F1 -0.2 0.46 -10000 0 -0.91 172 172
neuron apoptosis 0.13 0.4 0.86 98 -10000 0 98
EP300 0.014 0.029 -10000 0 -0.86 1 1
EGLN3 -0.4 0.38 -10000 0 -0.74 490 490
EGLN2 0.017 0.019 -10000 0 -10000 0 0
EGLN1 0.018 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.037 -10000 0 -0.49 5 5
VHL 0.015 0 -10000 0 -10000 0 0
ARNT 0.017 0.017 -10000 0 -10000 0 0
SLC2A1 -0.13 0.38 -10000 0 -0.83 101 101
TWIST1 -0.12 0.37 -10000 0 -0.77 107 107
ELK1 0.025 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.15 0.18 -10000 0 -0.53 51 51
VEGFA -0.21 0.47 -10000 0 -0.88 222 222
CREBBP 0.015 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.22 0.28 -9999 0 -0.57 338 338
alphaV beta3 Integrin -0.03 0.13 -9999 0 -0.58 46 46
PTK2 -0.15 0.24 -9999 0 -0.69 55 55
IGF1R 0.015 0 -9999 0 -10000 0 0
PI4KB 0.015 0 -9999 0 -10000 0 0
MFGE8 0.013 0.039 -9999 0 -0.8 2 2
SRC 0.014 0.025 -9999 0 -0.74 1 1
CDKN1B -0.12 0.24 -9999 0 -0.61 162 162
VEGFA -0.22 0.35 -9999 0 -0.74 273 273
ILK -0.12 0.24 -9999 0 -0.61 162 162
ROCK1 0.015 0 -9999 0 -10000 0 0
AKT1 -0.11 0.22 -9999 0 -0.59 144 144
PTK2B -0.14 0.24 -9999 0 -0.51 90 90
alphaV/beta3 Integrin/JAM-A -0.11 0.22 -9999 0 -0.92 16 16
CBL 0.014 0.029 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.32 0.3 -9999 0 -0.59 493 493
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.025 0.1 -9999 0 -0.52 21 21
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.16 -9999 0 -0.55 70 70
alphaV/beta3 Integrin/Syndecan-1 -0.025 0.12 -9999 0 -0.6 37 37
PI4KA 0.015 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.072 0.17 -9999 0 -0.83 16 16
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.031 0.14 -9999 0 -0.62 45 45
RPS6KB1 -0.067 0.16 -9999 0 -0.76 16 16
TLN1 0.015 0 -9999 0 -10000 0 0
MAPK3 -0.077 0.16 -9999 0 -0.71 42 42
GPR124 0.011 0.052 -9999 0 -0.77 4 4
MAPK1 -0.077 0.16 -9999 0 -0.7 44 44
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.067 0.2 -9999 0 -0.61 97 97
cell adhesion -0.25 0.24 -9999 0 -0.77 31 31
ANGPTL3 -0.45 0.43 -9999 0 -0.86 476 476
VEGFR2 homodimer/VEGFA homodimer/Src -0.19 0.24 -9999 0 -0.49 339 339
IGF-1R heterotetramer 0.015 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.014 0.16 -9999 0 -0.85 30 30
IGF1 -0.018 0.16 -9999 0 -0.77 37 37
RAC1 0.015 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.022 0.11 -9999 0 -0.56 35 35
apoptosis 0.013 0.038 -9999 0 -0.79 2 2
CD47 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.02 0.11 -9999 0 -0.57 31 31
VCL 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.075 0.21 -9999 0 -0.6 110 110
CSF1 0.01 0.064 -9999 0 -0.83 5 5
PIK3C2A -0.12 0.24 -9999 0 -0.64 145 145
PI4 Kinase/Pyk2 -0.22 0.24 -9999 0 -0.77 76 76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.19 0.23 -9999 0 -0.55 90 90
FAK1/Vinculin -0.11 0.19 -9999 0 -0.53 44 44
alphaV beta3/Integrin/ppsTEM5 -0.022 0.11 -9999 0 -0.57 35 35
RHOA 0.015 0 -9999 0 -10000 0 0
VTN -0.14 0.33 -9999 0 -0.84 162 162
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
FGF2 -0.001 0.12 -9999 0 -0.85 16 16
F11R 0.017 0.091 -9999 0 -0.65 16 16
alphaV/beta3 Integrin/Lactadherin -0.021 0.11 -9999 0 -0.57 33 33
alphaV/beta3 Integrin/TGFBR2 -0.02 0.11 -9999 0 -0.57 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.005 0.055 -9999 0 -0.6 6 6
HSP90AA1 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.019 0.099 -9999 0 -0.53 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.048 0.21 -9999 0 -0.74 74 74
alphaV/beta3 Integrin/Pyk2 -0.17 0.21 -9999 0 -0.51 90 90
SDC1 0.007 0.081 -9999 0 -0.84 8 8
VAV3 0.039 0.083 -9999 0 -0.52 13 13
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 0.005 0.092 -9999 0 -0.86 10 10
FAK1/Paxillin -0.11 0.19 -9999 0 -0.53 42 42
cell migration -0.088 0.18 -9999 0 -0.5 30 30
ITGAV 0.013 0.039 -9999 0 -0.8 2 2
PI3K -0.099 0.2 -9999 0 -0.85 15 15
SPP1 -0.003 0.12 -9999 0 -0.83 19 19
KDR -0.05 0.23 -9999 0 -0.85 67 67
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.039 -9999 0 -0.8 2 2
COL4A3 -0.057 0.24 -9999 0 -0.86 73 73
angiogenesis -0.043 0.22 -9999 0 -0.71 44 44
Rac1/GTP -0.01 0.068 -9999 0 -0.87 1 1
EDIL3 -0.071 0.26 -9999 0 -0.83 90 90
cell proliferation -0.02 0.11 -9999 0 -0.57 31 31
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.001 0.044 -9999 0 -10000 0 0
NFATC2 -0.023 0.12 -9999 0 -0.59 32 32
NFATC3 -0.001 0.044 -9999 0 -10000 0 0
CD40LG -0.24 0.4 -9999 0 -0.92 144 144
PTGS2 -0.25 0.4 -9999 0 -0.82 210 210
JUNB 0.013 0.041 -9999 0 -0.86 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.017 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.017 -9999 0 -10000 0 0
CALM1 0.008 0.012 -9999 0 -10000 0 0
JUN 0.008 0.012 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.018 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.002 -9999 0 -10000 0 0
FOSL1 -0.012 0.14 -9999 0 -0.74 32 32
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.14 0.17 -9999 0 -0.67 33 33
FOS -0.05 0.22 -9999 0 -0.86 59 59
IFNG -0.3 0.46 -9999 0 -0.92 255 255
AP-1/NFAT1-c-4 -0.33 0.38 -9999 0 -0.97 168 168
FASLG -0.32 0.46 -9999 0 -0.91 273 273
NFAT1-c-4/ICER1 -0.072 0.11 -9999 0 -0.57 15 15
IL2RA -0.25 0.41 -9999 0 -0.95 146 146
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.21 0.36 -9999 0 -0.81 131 131
JunB/Fra1/NFAT1-c-4 -0.078 0.12 -9999 0 -0.57 23 23
IL4 -0.21 0.35 -9999 0 -0.8 125 125
IL2 -0.012 0.088 -9999 0 -0.65 16 16
IL3 -0.024 0.024 -9999 0 -10000 0 0
FKBP1A 0.015 0 -9999 0 -10000 0 0
BATF3 -0.014 0.14 -9999 0 -0.74 34 34
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.015 0.002 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.015 0 -10000 0 -10000 0 0
VLDLR 0.014 0.025 -10000 0 -0.74 1 1
LRPAP1 0.015 0 -10000 0 -10000 0 0
NUDC 0.015 0 -10000 0 -10000 0 0
RELN/LRP8 -0.15 0.24 -10000 0 -0.54 244 244
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
KATNA1 0.015 0.001 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.1 0.24 -10000 0 -0.52 172 172
IQGAP1/CaM 0 0 -10000 0 -10000 0 0
DAB1 -0.01 0.12 -10000 0 -0.74 22 22
IQGAP1 0.015 0 -10000 0 -10000 0 0
PLA2G7 -0.57 0.31 -10000 0 -0.74 696 696
CALM1 0.015 0 -10000 0 -10000 0 0
DYNLT1 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.004 0.045 -10000 0 -0.55 6 6
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.015 0 -10000 0 -10000 0 0
CDK5R1 0.008 0.071 -10000 0 -0.74 8 8
LIS1/Poliovirus Protein 3A 0 0 -10000 0 -10000 0 0
CDK5R2 -0.1 0.26 -10000 0 -0.74 131 131
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.25 -10000 0 -0.55 260 260
YWHAE 0.015 0 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.17 -10000 0 -0.58 29 29
MAP1B -0.006 0.041 0.26 1 -0.28 19 20
RAC1 0 0 -10000 0 -10000 0 0
p35/CDK5 -0.12 0.19 -10000 0 -0.81 1 1
RELN -0.21 0.37 -10000 0 -0.82 239 239
PAFAH/LIS1 -0.37 0.19 -10000 0 -0.47 696 696
LIS1/CLIP170 0 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.095 0.13 -10000 0 -0.52 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.086 0.14 -10000 0 -0.61 3 3
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.13 0.2 -10000 0 -0.63 29 29
LIS1/IQGAP1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PAFAH1B1 0.029 0 -10000 0 -10000 0 0
PAFAH1B3 0.013 0.039 -10000 0 -0.8 2 2
PAFAH1B2 0.012 0.051 -10000 0 -0.86 3 3
MAP1B/LIS1/Dynein heavy chain -0.004 0.025 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.16 -10000 0 -0.58 17 17
LRP8 0.01 0.062 -10000 0 -0.74 6 6
NDEL1/Katanin 60 -0.13 0.17 -10000 0 -0.58 29 29
P39/CDK5 -0.17 0.23 -10000 0 -0.8 29 29
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -10000 0 -10000 0 0
CDK5 -0.085 0.23 -10000 0 -0.86 1 1
PPP2R5D 0.014 0.025 -10000 0 -0.74 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.13 0.21 -10000 0 -0.89 2 2
RELN/VLDLR -0.14 0.22 -10000 0 -0.52 172 172
CDC42 0 0 -10000 0 -10000 0 0
PLK1 signaling events

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.001 0.058 0.24 45 -10000 0 45
BUB1B -0.019 0.11 -10000 0 -0.4 58 58
PLK1 -0.007 0.049 -10000 0 -0.19 14 14
PLK1S1 0.004 0.026 -10000 0 -10000 0 0
KIF2A 0.002 0.061 -10000 0 -0.5 6 6
regulation of mitotic centrosome separation -0.007 0.049 -10000 0 -0.19 14 14
GOLGA2 0.015 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.16 0.28 -10000 0 -0.6 236 236
WEE1 0.003 0.046 -10000 0 -0.28 2 2
cytokinesis -0.16 0.22 -10000 0 -0.4 392 392
PP2A-alpha B56 -0.11 0.12 -10000 0 -10000 0 0
AURKA 0.001 0.039 -10000 0 -0.23 13 13
PICH/PLK1 -0.045 0.15 -10000 0 -0.57 57 57
CENPE -0.046 0.17 -10000 0 -0.51 101 101
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.06 -10000 0 -0.5 6 6
PPP2CA 0.015 0 -10000 0 -10000 0 0
FZR1 0.014 0.029 -10000 0 -0.86 1 1
TPX2 -0.05 0.1 -10000 0 -0.2 271 271
PAK1 0.015 0.002 -10000 0 -10000 0 0
SPC24 -0.086 0.26 -10000 0 -0.74 119 119
FBXW11 0.015 0 -10000 0 -10000 0 0
CLSPN -0.025 0.088 -10000 0 -0.23 130 130
GORASP1 0.015 0 -10000 0 -10000 0 0
metaphase -0.003 0.008 -10000 0 -0.016 206 206
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.026 -10000 0 -0.087 14 14
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 7 7
STAG2 0.015 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.007 0.049 -10000 0 -0.19 14 14
ODF2 0.015 0.002 -10000 0 -10000 0 0
BUB1 -0.13 0.15 -10000 0 -10000 0 0
TPT1 0.004 0.026 -10000 0 -10000 0 0
CDC25C -0.096 0.14 -10000 0 -0.25 378 378
CDC25B 0.01 0.063 -10000 0 -0.75 6 6
SGOL1 -0.001 0.058 -10000 0 -0.25 45 45
RHOA 0.015 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.016 0.075 -10000 0 -0.54 15 15
CDC14B 0.015 0.002 -10000 0 -10000 0 0
CDC20 -0.055 0.22 -10000 0 -0.74 83 83
PLK1/PBIP1 -0.041 0.12 -10000 0 -0.49 53 53
mitosis 0 0.004 0.031 11 -10000 0 11
FBXO5 0.006 0.037 -10000 0 -10000 0 0
CDC2 0 0.003 -10000 0 -0.02 15 15
NDC80 -0.15 0.31 -10000 0 -0.74 195 195
metaphase plate congression -0.001 0.035 -10000 0 -10000 0 0
ERCC6L -0.038 0.14 -10000 0 -0.55 57 57
NLP/gamma Tubulin 0 0.029 -10000 0 -0.11 2 2
microtubule cytoskeleton organization 0.004 0.026 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.015 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.2 0.24 -10000 0 -0.46 392 392
GRASP65/GM130/RAB1/GTP/PLK1 -0.01 0.021 -10000 0 -10000 0 0
RAB1A 0.015 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.033 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.004 -10000 0 -0.012 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.038 -10000 0 -10000 0 0
microtubule-based process -0.19 0.25 -10000 0 -0.47 392 392
Golgi organization -0.007 0.049 -10000 0 -0.19 14 14
Cohesin/SA2 -0.019 0.036 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.32 0.37 -10000 0 -0.74 392 392
APC/C/CDC20 -0.038 0.16 -10000 0 -0.52 83 83
PPP2R1A 0.015 0 -10000 0 -10000 0 0
chromosome segregation -0.041 0.12 -10000 0 -0.48 53 53
PRC1 0.001 0.1 -10000 0 -0.74 16 16
ECT2 0.005 0.048 -10000 0 -0.55 1 1
C13orf34 0.007 0.036 -10000 0 -10000 0 0
NUDC -0.001 0.035 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.018 0.11 -10000 0 -0.39 58 58
spindle assembly -0.002 0.04 -10000 0 -0.14 12 12
spindle stabilization 0.004 0.026 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.02 -10000 0 -0.59 1 1
MKLP2/PLK1 -0.2 0.25 -10000 0 -0.48 392 392
CCNB1 0.004 0.091 -10000 0 -0.74 13 13
PPP1CB 0.015 0.002 -10000 0 -10000 0 0
BTRC 0.015 0 -10000 0 -10000 0 0
ROCK2 0.005 0.062 -10000 0 -0.52 9 9
TUBG1 0.004 0.026 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.019 0.071 -10000 0 -0.52 15 15
MLF1IP -0.022 0.14 -10000 0 -0.58 53 53
INCENP 0.008 0.008 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.032 -9999 0 -0.89 1 1
SVIL 0.013 0.007 -9999 0 -10000 0 0
ZNF318 0.022 0.032 -9999 0 -10000 0 0
JMJD2C -0.006 0.032 -9999 0 -0.1 83 83
T-DHT/AR/Ubc9 -0.088 0.14 -9999 0 -0.63 53 53
CARM1 0.014 0.004 -9999 0 -10000 0 0
PRDX1 0.016 0.002 -9999 0 -10000 0 0
PELP1 0.016 0.005 -9999 0 -10000 0 0
CTNNB1 0.014 0.005 -9999 0 -10000 0 0
AKT1 0.018 0.009 -9999 0 -10000 0 0
PTK2B 0.014 0.005 -9999 0 -10000 0 0
MED1 0.014 0.012 -9999 0 -10000 0 0
MAK 0.013 0.089 -9999 0 -0.73 11 11
response to oxidative stress 0.001 0.002 -9999 0 -10000 0 0
HIP1 0.007 0.073 -9999 0 -0.87 6 6
GSN 0.012 0.01 -9999 0 -10000 0 0
NCOA2 -0.027 0.18 -9999 0 -0.86 41 41
NCOA6 0.014 0.005 -9999 0 -10000 0 0
DNA-PK 0.014 0.039 -9999 0 -10000 0 0
NCOA4 0.014 0.004 -9999 0 -10000 0 0
PIAS3 0.014 0.005 -9999 0 -10000 0 0
cell proliferation -0.027 0.058 -9999 0 -0.44 11 11
XRCC5 0.017 0.007 -9999 0 -10000 0 0
UBE3A 0.01 0.017 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.19 -9999 0 -0.67 86 86
FHL2 -0.051 0.16 -9999 0 -1.2 17 17
RANBP9 0.014 0.005 -9999 0 -10000 0 0
JMJD1A -0.11 0.072 -9999 0 -0.15 661 661
CDK6 0.014 0.029 -9999 0 -0.86 1 1
TGFB1I1 0.008 0.07 -9999 0 -0.84 6 6
T-DHT/AR/CyclinD1 -0.11 0.17 -9999 0 -0.61 88 88
XRCC6 0.017 0.007 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.16 -9999 0 -0.67 53 53
CTDSP1 0.013 0.005 -9999 0 -10000 0 0
CTDSP2 0.019 0.024 -9999 0 -10000 0 0
BRCA1 0.01 0.051 -9999 0 -0.75 4 4
TCF4 0.012 0.066 -9999 0 -0.83 5 5
CDKN2A -0.64 0.24 -9999 0 -0.73 782 782
SRF 0.026 0.02 -9999 0 -10000 0 0
NKX3-1 -0.18 0.1 -9999 0 -1.5 1 1
KLK3 -0.026 0.2 -9999 0 -0.58 101 101
TMF1 0.012 0.03 -9999 0 -0.86 1 1
HNRNPA1 0.016 0.017 -9999 0 -10000 0 0
AOF2 -0.004 0.014 -9999 0 -10000 0 0
APPL1 0.036 0.019 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.086 0.14 -9999 0 -0.62 53 53
AR -0.083 0.2 -9999 0 -0.89 53 53
UBA3 0.013 0.005 -9999 0 -10000 0 0
PATZ1 0.016 0.017 -9999 0 -10000 0 0
PAWR 0.012 0.03 -9999 0 -0.86 1 1
PRKDC 0.017 0.007 -9999 0 -10000 0 0
PA2G4 0.016 0.017 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.079 0.13 -9999 0 -0.58 56 56
RPS6KA3 0.012 0.01 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.09 0.14 -9999 0 -0.63 53 53
LATS2 0.015 0.014 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.076 0.13 -9999 0 -0.58 53 53
Cyclin D3/CDK11 p58 -0.002 0.033 -9999 0 -0.56 3 3
VAV3 0.002 0.1 -9999 0 -0.86 12 12
KLK2 -0.12 0.19 -9999 0 -0.67 83 83
CASP8 0.016 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.098 0.19 -9999 0 -0.67 81 81
TMPRSS2 -0.87 0.5 -9999 0 -1.2 660 660
CCND1 -0.017 0.15 -9999 0 -0.74 36 36
PIAS1 0.01 0.017 -9999 0 -10000 0 0
mol:T-DHT -0.058 0.035 -9999 0 -0.076 656 656
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.007 0.026 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.088 0.14 -9999 0 -0.64 53 53
CMTM2 -0.009 0.13 -9999 0 -0.74 29 29
SNURF -0.024 0.18 -9999 0 -0.86 39 39
ZMIZ1 -0.03 0.028 -9999 0 -10000 0 0
CCND3 0.013 0.044 -9999 0 -0.74 3 3
TGIF1 0.016 0.017 -9999 0 -10000 0 0
FKBP4 0.014 0.005 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.022 -9999 0 -0.66 1 1
Necdin/E2F1 -0.13 0.25 -9999 0 -0.58 203 203
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.069 0.17 -9999 0 -0.82 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.22 0.3 -9999 0 -0.64 245 245
NT-4/5 (dimer)/p75(NTR) -0.067 0.18 -9999 0 -0.57 104 104
IKBKB 0.015 0 -9999 0 -10000 0 0
AKT1 -0.022 0.18 -9999 0 -0.8 16 16
IKBKG 0.015 0 -9999 0 -10000 0 0
BDNF -0.096 0.27 -9999 0 -0.74 131 131
MGDIs/NGR/p75(NTR)/LINGO1 -0.069 0.18 -9999 0 -0.51 121 121
FURIN 0.015 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.23 -9999 0 -0.53 186 186
LINGO1 -0.018 0.16 -9999 0 -0.75 38 38
Sortilin/TRAF6/NRIF -0.001 0.024 -9999 0 -10000 0 0
proBDNF (dimer) -0.096 0.27 -9999 0 -0.74 131 131
NTRK1 -0.062 0.24 -9999 0 -0.86 77 77
RTN4R 0.005 0.088 -9999 0 -0.75 12 12
neuron apoptosis -0.072 0.22 -9999 0 -0.73 30 30
IRAK1 0.015 0 -9999 0 -10000 0 0
SHC1 -0.049 0.21 -9999 0 -0.54 132 132
ARHGDIA 0.015 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.023 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.073 0.18 -9999 0 -0.67 37 37
MAGEH1 0.014 0.025 -9999 0 -0.74 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.089 0.21 -9999 0 -0.68 58 58
Mammalian IAPs/DIABLO -0.048 0.13 -9999 0 -0.52 2 2
proNGF (dimer) -0.045 0.21 -9999 0 -0.76 69 69
MAGED1 0.014 0.025 -9999 0 -0.74 1 1
APP 0.015 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.13 -9999 0 -0.74 27 27
ZNF274 0.015 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.068 0.17 -9999 0 -0.63 36 36
NGF -0.045 0.21 -9999 0 -0.76 69 69
cell cycle arrest -0.023 0.22 -9999 0 -0.83 17 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.041 0.1 -9999 0 -0.5 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.057 0.16 -9999 0 -0.49 104 104
NCSTN 0.015 0 -9999 0 -10000 0 0
mol:GTP -0.079 0.2 -9999 0 -0.72 36 36
PSENEN 0.015 0 -9999 0 -10000 0 0
mol:ceramide -0.035 0.2 -9999 0 -0.66 37 37
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.032 0.08 -9999 0 -0.54 2 2
p75(NTR)/beta APP -0.05 0.16 -9999 0 -0.57 78 78
BEX1 -0.2 0.37 -9999 0 -0.85 218 218
mol:GDP -0.061 0.21 -9999 0 -0.55 131 131
NGF (dimer) -0.37 0.33 -9999 0 -0.61 511 511
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.062 0.16 -9999 0 -0.64 21 21
PIK3R1 0.015 0 -9999 0 -10000 0 0
RAC1/GTP -0.07 0.18 -9999 0 -0.47 131 131
MYD88 0.015 0 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.08 0.2 -9999 0 -0.73 36 36
RHOB 0.015 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.11 0.22 -9999 0 -0.55 181 181
NT3 (dimer) -0.035 0.2 -9999 0 -0.85 51 51
TP53 -0.04 0.2 -9999 0 -0.77 24 24
PRDM4 -0.035 0.2 -9999 0 -0.66 37 37
BDNF (dimer) -0.44 0.36 -9999 0 -0.68 514 514
PIK3CA 0.015 0 -9999 0 -10000 0 0
SORT1 0.014 0.029 -9999 0 -0.86 1 1
activation of caspase activity -0.068 0.17 -9999 0 -0.8 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.073 0.18 -9999 0 -0.67 37 37
RHOC 0.015 0 -9999 0 -10000 0 0
XIAP 0.015 0 -9999 0 -10000 0 0
MAPK10 -0.018 0.19 -9999 0 -0.64 20 20
DIABLO 0.015 0 -9999 0 -10000 0 0
SMPD2 -0.035 0.2 -9999 0 -0.66 37 37
APH1B 0.013 0.041 -9999 0 -0.86 2 2
APH1A 0.015 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.08 0.2 -9999 0 -0.72 37 37
PSEN1 0.015 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.086 0.22 -9999 0 -0.63 122 122
MAPK8 -0.016 0.19 -9999 0 -0.64 20 20
MAPK9 -0.013 0.18 -9999 0 -0.64 20 20
APAF1 0.015 0 -9999 0 -10000 0 0
NTF3 -0.035 0.2 -9999 0 -0.85 51 51
NTF4 -0.016 0.13 -9999 0 -0.74 27 27
NDN -0.013 0.15 -9999 0 -0.86 28 28
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.061 0.16 -9999 0 -0.76 16 16
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.017 -9999 0 -0.52 1 1
RhoA-B-C/GTP -0.079 0.2 -9999 0 -0.72 36 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.094 0.19 -9999 0 -0.82 24 24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.21 -9999 0 -0.76 34 34
PRKACB 0.015 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.082 0.2 -9999 0 -0.56 131 131
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.071 0.24 -9999 0 -0.74 101 101
BIRC2 0.015 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.015 0.22 -9999 0 -0.68 36 36
BAD -0.005 0.18 -9999 0 -0.65 13 13
RIPK2 0.014 0.025 -9999 0 -0.74 1 1
NGFR -0.052 0.22 -9999 0 -0.75 78 78
CYCS -0.024 0.19 -9999 0 -0.81 17 17
ADAM17 0.015 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.073 0.18 -9999 0 -0.67 36 36
BCL2L11 -0.005 0.18 -9999 0 -0.65 13 13
BDNF (dimer)/p75(NTR) -0.13 0.26 -9999 0 -0.62 186 186
PI3K -0.072 0.18 -9999 0 -0.67 36 36
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.073 0.18 -9999 0 -0.67 37 37
NDNL2 0.015 0 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
PRKCI 0.015 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.092 0.23 -9999 0 -0.63 131 131
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.073 0.18 -9999 0 -0.67 37 37
TRAF6 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.051 -9999 0 -0.86 3 3
PLG -0.43 0.43 -9999 0 -0.86 446 446
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.11 0.21 -9999 0 -0.76 46 46
SQSTM1 0.009 0.066 -9999 0 -0.74 7 7
NGFRAP1 0.013 0.041 -9999 0 -0.86 2 2
CASP3 0 0.17 -9999 0 -0.58 13 13
E2F1 -0.14 0.3 -9999 0 -0.74 181 181
CASP9 0.015 0 -9999 0 -10000 0 0
IKK complex -0.072 0.15 -9999 0 -0.69 14 14
NGF (dimer)/TRKA -0.1 0.24 -9999 0 -0.64 141 141
MMP7 -0.12 0.31 -9999 0 -0.82 144 144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.068 0.17 -9999 0 -0.82 16 16
MMP3 -0.052 0.2 -9999 0 -0.74 69 69
APAF-1/Caspase 9 -0.078 0.14 -9999 0 -0.67 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.023 0.12 -9999 0 -0.66 31 31
AKT1 -0.034 0.22 -9999 0 -0.62 66 66
PTK2B -0.13 0.28 -9999 0 -0.8 67 67
VEGFR2 homodimer/Frs2 -0.07 0.25 -9999 0 -0.92 68 68
CAV1 -0.027 0.17 -9999 0 -0.74 50 50
CALM1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.19 0.27 -9999 0 -0.88 66 66
endothelial cell proliferation -0.022 0.22 -9999 0 -0.59 65 65
mol:Ca2+ -0.12 0.27 -9999 0 -0.78 66 66
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.18 0.25 -9999 0 -0.83 66 66
RP11-342D11.1 -0.13 0.27 -9999 0 -0.79 66 66
CDH5 0.012 0.046 -9999 0 -0.78 3 3
VEGFA homodimer -0.13 0.19 -9999 0 -0.52 2 2
SHC1 0.014 0.025 -9999 0 -0.74 1 1
SHC2 -0.002 0.12 -9999 0 -0.76 20 20
HRAS/GDP -0.14 0.2 -9999 0 -0.66 67 67
SH2D2A -0.15 0.31 -9999 0 -0.74 199 199
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.12 0.19 -9999 0 -0.66 66 66
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.28 0.31 -9999 0 -0.85 145 145
VEGFR1 homodimer 0.002 0.1 -9999 0 -0.77 15 15
SHC/GRB2/SOS1 -0.15 0.22 -9999 0 -0.75 66 66
GRB10 -0.12 0.27 -9999 0 -0.78 66 66
PTPN11 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
PAK1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.17 0.24 -9999 0 -0.81 67 67
HRAS 0.014 0.025 -9999 0 -0.74 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.081 0.12 -9999 0 -0.39 67 67
HIF1A 0.013 0.041 -9999 0 -0.86 2 2
FRS2 0.015 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.17 0.25 -9999 0 -0.82 66 66
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.006 0.087 -9999 0 -0.86 9 9
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.19 0.27 -9999 0 -0.88 66 66
mol:GDP -0.15 0.21 -9999 0 -0.72 66 66
mol:NADP -0.043 0.21 -9999 0 -0.56 66 66
eNOS/Hsp90 -0.033 0.2 -9999 0 -0.68 18 18
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 -0.12 0.28 -9999 0 -0.8 66 66
HIF1A/ARNT -0.001 0.031 -9999 0 -0.66 2 2
SHB 0.015 0 -9999 0 -10000 0 0
VEGFA -0.21 0.34 -9999 0 -0.73 273 273
VEGFC 0.012 0.05 -9999 0 -0.74 4 4
FAK1/Vinculin -0.089 0.26 -9999 0 -0.77 67 67
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.19 0.26 -9999 0 -0.86 67 67
PTPN6 0.015 0 -9999 0 -10000 0 0
EPAS1 -0.006 0.12 -9999 0 -0.41 65 65
mol:L-citrulline -0.043 0.21 -9999 0 -0.56 66 66
ITGAV 0.013 0.039 -9999 0 -0.8 2 2
PIK3CA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.18 0.25 -9999 0 -0.83 66 66
VEGFR2 homodimer/VEGFA homodimer -0.19 0.26 -9999 0 -0.87 66 66
VEGFR2/3 heterodimer -0.076 0.26 -9999 0 -0.96 70 70
VEGFB 0.015 0 -9999 0 -10000 0 0
MAPK11 -0.11 0.28 -9999 0 -0.8 67 67
VEGFR2 homodimer -0.037 0.29 -9999 0 -1 68 68
FLT1 0.002 0.1 -9999 0 -0.77 15 15
NEDD4 0.016 0.029 -9999 0 -0.85 1 1
MAPK3 -0.1 0.25 -9999 0 -0.71 66 66
MAPK1 -0.1 0.25 -9999 0 -0.71 66 66
VEGFA145/NRP2 -0.18 0.26 -9999 0 -0.55 288 288
VEGFR1/2 heterodimer -0.078 0.26 -9999 0 -0.96 68 68
KDR -0.037 0.29 -9999 0 -1 68 68
VEGFA165/NRP1/VEGFR2 homodimer -0.18 0.25 -9999 0 -0.8 72 72
SRC 0.014 0.025 -9999 0 -0.74 1 1
platelet activating factor biosynthetic process -0.1 0.26 -9999 0 -0.73 66 66
PI3K -0.14 0.22 -9999 0 -0.77 67 67
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.19 0.27 -9999 0 -0.87 67 67
FES -0.13 0.28 -9999 0 -0.82 67 67
GAB1 -0.15 0.23 -9999 0 -0.77 76 76
VEGFR2 homodimer/VEGFA homodimer/Src -0.19 0.27 -9999 0 -0.88 66 66
CTNNB1 0.015 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.052 0.21 -9999 0 -0.59 36 36
VEGFR2 homodimer/VEGFA homodimer/Yes -0.19 0.27 -9999 0 -0.87 67 67
PI3K/GAB1 -0.035 0.22 -9999 0 -0.63 66 66
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.16 0.24 -9999 0 -0.8 66 66
PRKACA 0.015 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.072 0.25 -9999 0 -0.9 70 70
HSP90AA1 0.015 0 -9999 0 -10000 0 0
CDC42 -0.12 0.28 -9999 0 -0.82 66 66
actin cytoskeleton reorganization -0.28 0.31 -9999 0 -0.84 145 145
PTK2 -0.1 0.28 -9999 0 -0.84 68 68
EDG1 -0.13 0.27 -9999 0 -0.79 66 66
mol:DAG -0.12 0.28 -9999 0 -0.8 66 66
CaM/Ca2+ -0.15 0.22 -9999 0 -0.73 66 66
MAP2K3 -0.11 0.27 -9999 0 -0.77 66 66
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.17 0.25 -9999 0 -0.83 66 66
PLCG1 -0.12 0.28 -9999 0 -0.82 66 66
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.18 0.25 -9999 0 -0.83 66 66
IQGAP1 0.015 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.19 0.27 -9999 0 -0.87 67 67
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.19 0.27 -9999 0 -0.88 66 66
cell migration -0.04 0.22 -9999 0 -0.63 66 66
mol:PI-3-4-5-P3 -0.13 0.2 -9999 0 -0.7 67 67
FYN 0.015 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.16 0.23 -9999 0 -0.74 66 66
mol:NO -0.043 0.21 -9999 0 -0.56 66 66
PXN 0.015 0 -9999 0 -10000 0 0
HRAS/GTP -0.14 0.2 -9999 0 -0.66 67 67
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.17 0.25 -9999 0 -0.83 66 66
VHL 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.014 0.16 -9999 0 -0.85 30 30
NOS3 -0.054 0.23 -9999 0 -0.66 66 66
VEGFR2 homodimer/VEGFA homodimer/Sck -0.2 0.28 -9999 0 -0.9 73 73
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA -0.1 0.26 -9999 0 -0.74 66 66
PRKCB -0.11 0.26 -9999 0 -0.74 67 67
VCL 0.015 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.18 0.24 -9999 0 -0.8 66 66
VEGFR1/2 heterodimer/VEGFA homodimer -0.2 0.28 -9999 0 -0.9 76 76
VEGFA165/NRP2 -0.18 0.26 -9999 0 -0.55 288 288
MAPKKK cascade -0.14 0.2 -9999 0 -0.66 67 67
NRP2 -0.002 0.11 -9999 0 -0.74 20 20
VEGFC homodimer 0.012 0.05 -9999 0 -0.74 4 4
NCK1 0.015 0 -9999 0 -10000 0 0
ROCK1 0.015 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.089 0.26 -9999 0 -0.77 67 67
MAP3K13 -0.12 0.28 -9999 0 -0.82 66 66
PDPK1 -0.047 0.22 -9999 0 -0.6 67 67
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.005 0.052 -9999 0 -0.55 8 8
VLDLR 0.014 0.025 -9999 0 -0.74 1 1
CRKL 0.015 0 -9999 0 -10000 0 0
LRPAP1 0.015 0 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
ITGA3 0.003 0.094 -9999 0 -0.74 14 14
RELN/VLDLR/Fyn -0.15 0.24 -9999 0 -0.54 240 240
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.006 0.058 -9999 0 -0.98 1 1
AKT1 -0.05 0.15 -9999 0 -0.55 2 2
MAP2K7 0.015 0 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
DAB1 -0.01 0.12 -9999 0 -0.74 22 22
RELN/LRP8/DAB1 -0.15 0.23 -9999 0 -0.5 264 264
LRPAP1/LRP8 -0.004 0.045 -9999 0 -0.55 6 6
RELN/LRP8/DAB1/Fyn -0.14 0.22 -9999 0 -0.5 172 172
DAB1/alpha3/beta1 Integrin -0.13 0.2 -9999 0 -0.77 8 8
long-term memory -0.23 0.27 -9999 0 -0.88 59 59
DAB1/LIS1 -0.13 0.2 -9999 0 -0.85 3 3
DAB1/CRLK/C3G -0.12 0.19 -9999 0 -0.82 3 3
PIK3CA 0.015 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.13 0.2 -9999 0 -0.85 3 3
ARHGEF2 0.015 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.16 0.34 -9999 0 -0.8 195 195
CDK5R1 0.008 0.071 -9999 0 -0.74 8 8
RELN -0.21 0.37 -9999 0 -0.82 239 239
PIK3R1 0.015 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.15 0.24 -9999 0 -0.54 244 244
GRIN2A/RELN/LRP8/DAB1/Fyn -0.23 0.28 -9999 0 -0.89 60 60
MAPK8 0.008 0.077 -9999 0 -0.86 7 7
RELN/VLDLR/DAB1 -0.15 0.23 -9999 0 -0.5 260 260
ITGB1 0.015 0 -9999 0 -10000 0 0
MAP1B -0.14 0.21 -9999 0 -0.5 173 173
RELN/LRP8 -0.15 0.24 -9999 0 -0.54 244 244
GRIN2B/RELN/LRP8/DAB1/Fyn -0.14 0.22 -9999 0 -0.88 5 5
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.009 0.069 -9999 0 -0.55 14 14
RAP1A -0.11 0.18 -9999 0 -0.75 3 3
PAFAH1B1 0.015 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.051 -9999 0 -0.86 3 3
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.001 0.079 -9999 0 -0.74 10 10
NCK2 0.015 0 -9999 0 -10000 0 0
neuron differentiation -0.018 0.12 -9999 0 -0.49 4 4
neuron adhesion -0.048 0.21 -9999 0 -0.66 8 8
LRP8 0.01 0.062 -9999 0 -0.74 6 6
GSK3B -0.037 0.15 -9999 0 -0.52 2 2
RELN/VLDLR/DAB1/Fyn -0.14 0.22 -9999 0 -0.5 172 172
MAP3K11 0.014 0.029 -9999 0 -0.86 1 1
RELN/VLDLR/DAB1/P13K -0.091 0.14 -9999 0 -0.59 2 2
CDK5 0.015 0 -9999 0 -10000 0 0
MAPT 0.006 0.11 -9999 0 -0.79 14 14
neuron migration -0.041 0.2 -9999 0 -0.61 3 3
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.044 0.1 -9999 0 -0.5 4 4
RELN/VLDLR -0.14 0.22 -9999 0 -0.52 172 172
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0.036 -9999 0 -0.74 2 2
ELF1 -0.028 0.12 -9999 0 -0.84 1 1
CCNA2 -0.13 0.29 -9999 0 -0.74 168 168
PIK3CA 0.016 0.001 -9999 0 -10000 0 0
JAK3 -0.12 0.29 -9999 0 -0.74 167 167
PIK3R1 0.016 0.001 -9999 0 -10000 0 0
JAK1 0.016 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.044 0.21 -9999 0 -0.72 41 41
SHC1 0.015 0.025 -9999 0 -0.74 1 1
SP1 0.017 0.05 -9999 0 -10000 0 0
IL2RA -0.074 0.26 -9999 0 -0.66 145 145
IL2RB -0.26 0.36 -9999 0 -0.74 331 331
SOS1 0.016 0.001 -9999 0 -10000 0 0
IL2RG -0.025 0.17 -9999 0 -0.75 47 47
G1/S transition of mitotic cell cycle -0.031 0.16 -9999 0 -0.74 4 4
PTPN11 0.016 0.001 -9999 0 -10000 0 0
CCND2 0.022 0.11 -9999 0 -0.66 22 22
LCK -0.022 0.17 -9999 0 -0.76 44 44
GRB2 0.016 0.001 -9999 0 -10000 0 0
IL2 -0.005 0.099 -9999 0 -0.74 16 16
CDK6 0.014 0.029 -9999 0 -0.86 1 1
CCND3 -0.026 0.18 -9999 0 -0.62 34 34
Signaling events mediated by PTP1B

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
PDGFRB 0.002 0.11 -10000 0 -0.84 14 14
Jak2/Leptin Receptor -0.07 0.12 -10000 0 -0.42 38 38
PTP1B/AKT1 -0.043 0.065 -10000 0 -0.43 6 6
FYN 0.015 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.06 0.074 -10000 0 -0.36 25 25
EGFR -0.01 0.1 -10000 0 -0.77 15 15
EGF/EGFR -0.42 0.19 -10000 0 -0.5 741 741
CSF1 0.01 0.064 -10000 0 -0.83 5 5
AKT1 0.015 0.001 -10000 0 -10000 0 0
INSR 0.015 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.096 0.16 -10000 0 -0.53 88 88
Insulin Receptor/Insulin -0.027 0.049 -10000 0 -0.41 3 3
HCK -0.04 0.2 -10000 0 -0.74 65 65
CRK 0.015 0 -10000 0 -10000 0 0
TYK2 -0.047 0.07 -10000 0 -0.46 6 6
EGF -0.71 0.33 -10000 0 -0.86 739 739
YES1 0.015 0 -10000 0 -10000 0 0
CAV1 -0.16 0.11 -10000 0 -0.4 71 71
TXN 0.002 0.026 -10000 0 -0.74 1 1
PTP1B/IRS1/GRB2 -0.05 0.081 -10000 0 -0.54 16 16
cell migration 0.06 0.074 0.36 25 -10000 0 25
STAT3 0.014 0.003 -10000 0 -10000 0 0
PRLR -0.14 0.32 -10000 0 -0.86 147 147
ITGA2B -0.018 0.12 -10000 0 -0.75 24 24
CSF1R -0.01 0.14 -10000 0 -0.74 29 29
Prolactin Receptor/Prolactin -0.11 0.25 -10000 0 -0.67 147 147
FGR 0.006 0.084 -10000 0 -0.75 11 11
PTP1B/p130 Cas -0.048 0.071 -10000 0 -0.45 8 8
Crk/p130 Cas -0.045 0.057 -10000 0 -0.44 7 7
DOK1 -0.034 0.076 -10000 0 -0.38 16 16
JAK2 -0.073 0.13 -10000 0 -0.35 144 144
Jak2/Leptin Receptor/Leptin -0.06 0.13 -10000 0 -0.63 14 14
PIK3R1 0.015 0 -10000 0 -10000 0 0
PTPN1 -0.061 0.074 -10000 0 -0.37 25 25
LYN 0.014 0.029 -10000 0 -0.86 1 1
CDH2 -0.068 0.26 -10000 0 -0.86 85 85
SRC -0.007 0.031 -10000 0 -0.38 1 1
ITGB3 -0.026 0.15 -10000 0 -0.85 30 30
CAT1/PTP1B -0.24 0.17 -10000 0 -0.53 114 114
CAPN1 0.003 0.006 -10000 0 -10000 0 0
CSK 0.015 0 -10000 0 -10000 0 0
PI3K -0.003 0.047 -10000 0 -10000 0 0
mol:H2O2 -0.007 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.051 0.12 -10000 0 -0.65 13 13
negative regulation of transcription -0.072 0.13 -10000 0 -0.35 144 144
FCGR2A -0.026 0.17 -10000 0 -0.74 49 49
FER 0 0.042 -10000 0 -0.87 2 2
alphaIIb/beta3 Integrin -0.037 0.15 -10000 0 -0.62 53 53
BLK -0.027 0.17 -10000 0 -0.74 48 48
Insulin Receptor/Insulin/Shc -0.002 0.031 -10000 0 -0.47 4 4
RHOA 0.003 0.006 -10000 0 -10000 0 0
LEPR 0.011 0.041 -10000 0 -0.86 2 2
BCAR1 0.014 0.029 -10000 0 -0.86 1 1
p210 bcr-abl/Grb2 0.015 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.004 -10000 0 -10000 0 0
TRPV6 -0.22 0.18 -10000 0 -0.58 101 101
PRL 0 0.003 -10000 0 -10000 0 0
SOCS3 0.017 0.12 -10000 0 -0.96 12 12
SPRY2 0.003 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.008 0.067 -10000 0 -0.56 13 13
CSF1/CSF1R -0.061 0.11 -10000 0 -0.53 35 35
Ras protein signal transduction 0.041 0.022 -10000 0 -10000 0 0
IRS1 0.005 0.092 -10000 0 -0.86 10 10
INS -0.002 0.043 -10000 0 -0.74 3 3
LEP -0.058 0.22 -10000 0 -0.74 81 81
STAT5B -0.06 0.085 -10000 0 -0.35 29 29
STAT5A -0.06 0.085 -10000 0 -0.35 29 29
GRB2 0.015 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.055 0.096 -10000 0 -0.53 21 21
CSN2 -0.017 0.083 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
LAT -0.066 0.13 -10000 0 -0.43 38 38
YBX1 0.004 0.009 -10000 0 -10000 0 0
LCK -0.023 0.17 -10000 0 -0.76 44 44
SHC1 0.014 0.025 -10000 0 -0.74 1 1
NOX4 -0.026 0.15 -10000 0 -0.87 29 29
IL6-mediated signaling events

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
BCL2L1 -0.097 0.27 -9999 0 -0.71 49 49
CRP -0.14 0.34 -9999 0 -0.82 116 116
cell cycle arrest -0.12 0.3 -9999 0 -0.75 90 90
TIMP1 -0.12 0.31 -9999 0 -0.74 106 106
IL6ST -0.058 0.24 -9999 0 -0.86 73 73
Rac1/GDP -0.13 0.24 -9999 0 -0.56 123 123
AP1 -0.004 0.14 -9999 0 -0.54 19 19
GAB2 0.01 0.036 -9999 0 -0.74 2 2
TNFSF11 -0.13 0.32 -9999 0 -0.8 79 79
HSP90B1 0.01 0.077 -9999 0 -10000 0 0
GAB1 0.013 0.006 -9999 0 -10000 0 0
MAPK14 -0.019 0.18 -9999 0 -0.74 22 22
AKT1 0.061 0.028 -9999 0 -10000 0 0
FOXO1 0.075 0.017 -9999 0 -10000 0 0
MAP2K6 -0.047 0.18 -9999 0 -0.73 24 24
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.11 0.25 -9999 0 -0.6 101 101
MITF -0.048 0.18 -9999 0 -0.69 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.015 0 -9999 0 -10000 0 0
A2M 0.023 0.087 -9999 0 -1.5 3 3
CEBPB 0.002 0.12 -9999 0 -0.73 23 23
GRB2/SOS1/GAB family/SHP2 -0.007 0.077 -9999 0 -10000 0 0
STAT3 -0.13 0.32 -9999 0 -0.8 90 90
STAT1 -0.007 0.023 -9999 0 -0.38 2 2
CEBPD -0.097 0.27 -9999 0 -0.72 48 48
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
JUN 0.01 0.007 -9999 0 -10000 0 0
PIAS3/MITF -0.043 0.17 -9999 0 -0.71 20 20
MAPK11 -0.019 0.18 -9999 0 -0.74 23 23
STAT3 (dimer)/FOXO1 -0.038 0.25 -9999 0 -0.64 15 15
GRB2/SOS1/GAB family -0.074 0.14 -9999 0 -0.68 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.071 0.19 -9999 0 -0.61 48 48
GRB2 0.013 0.006 -9999 0 -10000 0 0
JAK2 0.015 0 -9999 0 -10000 0 0
LBP -0.23 0.43 -9999 0 -0.9 219 219
PIK3R1 0.017 0 -9999 0 -10000 0 0
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.11 0.28 -9999 0 -0.74 53 53
FGG -0.18 0.36 -9999 0 -0.8 144 144
macrophage differentiation -0.12 0.3 -9999 0 -0.75 90 90
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.22 -9999 0 -0.58 78 78
JUNB -0.095 0.26 -9999 0 -0.74 36 36
FOS -0.048 0.22 -9999 0 -0.86 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.06 0.19 -9999 0 -0.54 53 53
STAT1/PIAS1 -0.06 0.18 -9999 0 -0.62 29 29
GRB2/SOS1/GAB family/SHP2/PI3K 0.025 0.034 -9999 0 -10000 0 0
STAT3 (dimer) -0.13 0.32 -9999 0 -0.79 90 90
PRKCD -0.11 0.27 -9999 0 -0.65 82 82
IL6R 0.013 0.042 -9999 0 -0.85 2 2
SOCS3 -0.011 0.19 -9999 0 -0.92 17 17
gp130 (dimer)/JAK1/JAK1/LMO4 -0.042 0.16 -9999 0 -0.57 73 73
Rac1/GTP -0.17 0.21 -9999 0 -0.54 163 163
HCK -0.042 0.2 -9999 0 -0.74 65 65
MAPKKK cascade 0.021 0.064 -9999 0 -10000 0 0
bone resorption -0.12 0.3 -9999 0 -0.75 80 80
IRF1 -0.097 0.27 -9999 0 -0.76 30 30
mol:GDP -0.14 0.25 -9999 0 -0.54 168 168
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.14 0.26 -9999 0 -0.55 167 167
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.039 0.18 -9999 0 -0.74 23 23
PTPN11 -0.006 0.014 -9999 0 -10000 0 0
IL6/IL6RA -0.1 0.23 -9999 0 -0.62 148 148
gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.16 -9999 0 -0.57 73 73
gp130 (dimer)/JAK2/JAK2/LMO4 -0.043 0.16 -9999 0 -0.57 73 73
IL6 -0.12 0.31 -9999 0 -0.82 146 146
PIAS3 0.015 0 -9999 0 -10000 0 0
PTPRE 0.012 0.028 -9999 0 -0.69 1 1
PIAS1 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.072 0.18 -9999 0 -0.55 44 44
LMO4 0.014 0.013 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.18 0.24 -9999 0 -0.75 86 86
MCL1 0.073 0.016 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.012 0.093 -10000 0 -1.3 2 2
SMARCC2 0.017 0.005 -10000 0 -10000 0 0
SMARCC1 0.017 0.005 -10000 0 -10000 0 0
TBX21 -0.16 0.31 -10000 0 -0.7 204 204
SUMO2 0.01 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.044 -10000 0 -0.87 2 2
FKBP4 0.015 0 -10000 0 -10000 0 0
FKBP5 -0.007 0.13 -10000 0 -0.8 24 24
GR alpha/HSP90/FKBP51/HSP90 0.046 0.13 0.38 4 -0.53 20 24
PRL -0.015 0.097 -10000 0 -0.58 1 1
cortisol/GR alpha (dimer)/TIF2 0.12 0.27 0.56 89 -0.58 9 98
RELA -0.035 0.1 -10000 0 -10000 0 0
FGG -0.021 0.35 0.58 12 -0.66 131 143
GR beta/TIF2 0.034 0.17 0.39 8 -0.6 42 50
IFNG -0.3 0.34 -10000 0 -0.81 174 174
apoptosis -0.082 0.21 0.57 3 -0.7 21 24
CREB1 -0.003 0.08 -10000 0 -0.43 1 1
histone acetylation 0.01 0.11 0.36 9 -0.47 9 18
BGLAP -0.008 0.1 -10000 0 -0.94 1 1
GR/PKAc 0.064 0.091 0.37 3 -0.5 1 4
NF kappa B1 p50/RelA -0.062 0.19 -10000 0 -0.54 30 30
SMARCD1 0.017 0.005 -10000 0 -10000 0 0
MDM2 0.055 0.081 0.32 8 -10000 0 8
GATA3 -0.44 0.44 -10000 0 -0.85 467 467
AKT1 0 0.007 -10000 0 -10000 0 0
CSF2 -0.028 0.12 -10000 0 -0.58 18 18
GSK3B 0.01 0.008 -10000 0 -10000 0 0
NR1I3 -0.038 0.22 0.54 3 -0.8 23 26
CSN2 0.075 0.16 0.49 3 -0.55 1 4
BRG1/BAF155/BAF170/BAF60A -0.001 0.014 -10000 0 -10000 0 0
NFATC1 0.017 0.005 -10000 0 -10000 0 0
POU2F1 0.018 0.004 -10000 0 -10000 0 0
CDKN1A 0.044 0.046 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.15 0.32 -10000 0 -0.76 188 188
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.049 0.22 0.38 1 -0.52 36 37
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.27 0.52 3 -0.92 49 52
JUN -0.18 0.22 -10000 0 -0.63 75 75
IL4 -0.025 0.1 -10000 0 -10000 0 0
CDK5R1 0.005 0.071 -10000 0 -0.74 8 8
PRKACA 0.015 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.2 0.25 0.32 1 -0.68 99 100
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.052 0.12 0.38 3 -0.51 9 12
cortisol/GR alpha (monomer) 0.17 0.29 0.63 116 -0.69 1 117
NCOA2 -0.025 0.18 -10000 0 -0.86 41 41
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.087 0.22 -10000 0 -0.88 59 59
AP-1/NFAT1-c-4 -0.29 0.32 -10000 0 -0.86 114 114
AFP -0.29 0.53 -10000 0 -1.4 148 148
SUV420H1 0.015 0 -10000 0 -10000 0 0
IRF1 0.098 0.14 0.54 4 -10000 0 4
TP53 0.042 0.019 -10000 0 -10000 0 0
PPP5C 0.015 0 -10000 0 -10000 0 0
KRT17 -0.28 0.43 -10000 0 -1.1 158 158
KRT14 -0.13 0.25 -10000 0 -0.73 114 114
TBP 0.027 0.007 -10000 0 -10000 0 0
CREBBP 0.04 0.073 -10000 0 -10000 0 0
HDAC1 0.01 0.007 -10000 0 -10000 0 0
HDAC2 0.01 0.011 -10000 0 -10000 0 0
AP-1 -0.29 0.33 -10000 0 -0.86 116 116
MAPK14 0.009 0.008 -10000 0 -10000 0 0
MAPK10 -0.005 0.11 -10000 0 -0.86 14 14
MAPK11 0.009 0.027 -10000 0 -0.76 1 1
KRT5 -0.24 0.33 -10000 0 -0.87 134 134
interleukin-1 receptor activity 0 0.008 -10000 0 -10000 0 0
NCOA1 0.019 0.003 -10000 0 -10000 0 0
STAT1 0.024 0.044 -10000 0 -0.87 2 2
CGA -0.092 0.31 -10000 0 -1.2 54 54
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.073 0.13 0.44 35 -10000 0 35
MAPK3 0.008 0.008 -10000 0 -10000 0 0
MAPK1 0.009 0.008 -10000 0 -10000 0 0
ICAM1 -0.1 0.23 -10000 0 -0.68 55 55
NFKB1 -0.036 0.11 -10000 0 -1 1 1
MAPK8 -0.12 0.18 -10000 0 -0.54 48 48
MAPK9 0.009 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.088 0.22 0.57 3 -0.74 22 25
BAX 0.045 0.036 -10000 0 -0.61 1 1
POMC -0.11 0.26 -10000 0 -0.86 40 40
EP300 0.039 0.077 -10000 0 -0.73 1 1
cortisol/GR alpha (dimer)/p53 0.17 0.24 0.57 101 -0.59 1 102
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.063 -10000 0 -10000 0 0
SGK1 0.091 0.13 -10000 0 -1.4 4 4
IL13 -0.4 0.32 -10000 0 -0.82 241 241
IL6 -0.23 0.47 -10000 0 -1.2 147 147
PRKACG 0.003 0.026 -10000 0 -0.74 1 1
IL5 -0.33 0.24 -10000 0 -0.68 192 192
IL2 -0.18 0.23 -10000 0 -0.78 37 37
CDK5 0.012 0.006 -10000 0 -10000 0 0
PRKACB 0.015 0 -10000 0 -10000 0 0
HSP90AA1 0.015 0 -10000 0 -10000 0 0
IL8 -0.15 0.33 -10000 0 -0.88 98 98
CDK5R1/CDK5 -0.004 0.053 -10000 0 -0.56 8 8
NF kappa B1 p50/RelA/PKAc -0.029 0.14 -10000 0 -0.66 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.22 0.55 78 -0.54 1 79
SMARCA4 0.017 0.005 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.14 0.41 31 -10000 0 31
NF kappa B1 p50/RelA/Cbp -0.001 0.17 -10000 0 -0.87 3 3
JUN (dimer) -0.18 0.22 -10000 0 -0.63 76 76
YWHAH 0.015 0 -10000 0 -10000 0 0
VIPR1 -0.054 0.22 -10000 0 -1 30 30
NR3C1 0.091 0.16 0.47 36 -0.82 1 37
NR4A1 -0.12 0.32 -10000 0 -0.85 145 145
TIF2/SUV420H1 -0.03 0.14 -10000 0 -0.66 41 41
MAPKKK cascade -0.082 0.21 0.57 3 -0.7 21 24
cortisol/GR alpha (dimer)/Src-1 0.16 0.24 0.57 94 -0.69 1 95
PBX1 0.004 0.11 -10000 0 -0.86 14 14
POU1F1 0.008 0.009 -10000 0 -10000 0 0
SELE -0.33 0.58 -10000 0 -1.3 212 212
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.14 0.41 30 -10000 0 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.22 0.55 78 -0.54 1 79
mol:cortisol 0.076 0.16 0.39 79 -10000 0 79
MMP1 -0.24 0.43 -10000 0 -1 173 173
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.058 0.2 -10000 0 -0.7 42 42
UGCG -0.017 0.055 -10000 0 -0.74 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT -0.036 0.17 -10000 0 -0.47 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.064 -10000 0 -0.73 4 4
mol:DAG -0.002 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.071 0.14 -10000 0 -0.53 39 39
FRAP1 -0.025 0.2 -10000 0 -0.6 46 46
FOXO3 -0.019 0.19 -10000 0 -0.61 39 39
AKT1 -0.032 0.2 -10000 0 -0.64 46 46
GAB2 0.014 0.036 -10000 0 -0.74 2 2
SMPD1 -0.014 0.026 -10000 0 -10000 0 0
SGMS1 -0.014 0.026 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.005 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
cell proliferation 0.002 0.091 -10000 0 -0.42 4 4
EIF3A 0.015 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 -0.017 0.078 -10000 0 -10000 0 0
mol:sphingomyelin -0.002 0.005 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.002 -10000 0 -0.012 1 1
JAK3 -0.12 0.29 -10000 0 -0.73 167 167
PIK3R1 0.018 0.003 -10000 0 -10000 0 0
JAK1 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.014 0.029 -10000 0 -0.86 1 1
MYC -0.02 0.2 -10000 0 -0.62 36 36
MYB -0.17 0.29 -10000 0 -0.63 233 233
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.054 0.22 -10000 0 -0.63 67 67
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.03 0.054 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.048 0.21 -10000 0 -0.61 67 67
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation -0.036 0.2 -10000 0 -0.63 47 47
SHC1 0.015 0.025 -10000 0 -0.74 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.007 0.024 -10000 0 -0.046 233 233
PRKCZ -0.039 0.21 -10000 0 -0.67 47 47
NF kappa B1 p50/RelA -0.069 0.13 -10000 0 -0.54 33 33
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.079 0.22 -10000 0 -0.73 50 50
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
IL2RA -0.11 0.28 -10000 0 -0.74 144 144
IL2RB -0.26 0.36 -10000 0 -0.73 331 331
TERT -0.1 0.26 -10000 0 -0.74 132 132
E2F1 -0.1 0.18 -10000 0 -0.36 233 233
SOS1 0.015 0.003 -10000 0 -10000 0 0
RPS6 0.013 0.036 -10000 0 -0.74 2 2
mol:cAMP 0.003 0.012 0.023 233 -10000 0 233
PTPN11 0.015 0.005 -10000 0 -10000 0 0
IL2RG -0.022 0.17 -10000 0 -0.75 47 47
actin cytoskeleton organization -0.036 0.2 -10000 0 -0.63 47 47
GRB2 0.015 0.003 -10000 0 -10000 0 0
IL2 -0.003 0.099 -10000 0 -0.74 16 16
PIK3CA 0.018 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.02 -10000 0 -10000 0 0
LCK -0.02 0.17 -10000 0 -0.76 44 44
BCL2 -0.006 0.16 -10000 0 -0.53 23 23
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.015 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.033 0.085 -10000 0 -0.58 1 1
NT3 (dimer)/TRKC -0.096 0.25 -10000 0 -0.71 121 121
NT3 (dimer)/TRKB -0.25 0.33 -10000 0 -0.63 346 346
SHC/Grb2/SOS1/GAB1/PI3K 0 0.007 -10000 0 -10000 0 0
RAPGEF1 0.015 0 -10000 0 -10000 0 0
BDNF -0.096 0.27 -10000 0 -0.74 131 131
PIK3CA 0.015 0 -10000 0 -10000 0 0
DYNLT1 0.015 0 -10000 0 -10000 0 0
NTRK1 -0.062 0.24 -10000 0 -0.86 77 77
NTRK2 -0.25 0.4 -10000 0 -0.86 271 271
NTRK3 -0.065 0.25 -10000 0 -0.86 81 81
NT-4/5 (dimer)/TRKB -0.23 0.31 -10000 0 -0.61 335 335
neuron apoptosis 0.17 0.2 0.57 123 -10000 0 123
SHC 2-3/Grb2 -0.18 0.23 -10000 0 -0.64 123 123
SHC1 0.014 0.025 -10000 0 -0.74 1 1
SHC2 -0.13 0.17 -10000 0 -0.54 91 91
SHC3 -0.18 0.26 -10000 0 -0.69 138 138
STAT3 (dimer) 0.012 0.064 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.12 0.26 -10000 0 -0.6 184 184
RIN/GDP 0.024 0.084 -10000 0 -0.32 2 2
GIPC1 0.014 0.029 -10000 0 -0.86 1 1
KRAS 0.015 0 -10000 0 -10000 0 0
DNAJA3 -0.072 0.15 -10000 0 -0.58 34 34
RIN/GTP -0.002 0.033 -10000 0 -0.56 3 3
CCND1 0.011 0.14 -10000 0 -0.67 36 36
MAGED1 0.014 0.025 -10000 0 -0.74 1 1
PTPN11 0.015 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.13 -10000 0 -0.74 27 27
SHC/GRB2/SOS1 -0.001 0.016 -10000 0 -0.47 1 1
GRB2 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.12 0.24 -10000 0 -0.54 204 204
TRKA/NEDD4-2 -0.058 0.19 -10000 0 -0.66 78 78
ELMO1 0.011 0.056 -10000 0 -0.74 5 5
RhoG/GTP/ELMO1/DOCK1 -0.003 0.041 -10000 0 -0.5 6 6
NGF -0.045 0.21 -10000 0 -0.76 69 69
HRAS 0.014 0.025 -10000 0 -0.74 1 1
DOCK1 0.014 0.029 -10000 0 -0.86 1 1
GAB2 0.013 0.036 -10000 0 -0.74 2 2
RIT2 0 0.043 -10000 0 -0.74 3 3
RIT1 0.015 0 -10000 0 -10000 0 0
FRS2 0.015 0 -10000 0 -10000 0 0
DNM1 -0.096 0.27 -10000 0 -0.74 131 131
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.072 0.15 -10000 0 -0.56 34 34
mol:GDP 0.029 0.12 -10000 0 -0.46 5 5
NGF (dimer) -0.045 0.21 -10000 0 -0.76 69 69
RhoG/GDP -0.003 0.042 -10000 0 -0.56 5 5
RIT1/GDP 0.031 0.083 -10000 0 -0.32 2 2
TIAM1 0.014 0.029 -10000 0 -0.86 1 1
PIK3R1 0.015 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.24 0.29 -10000 0 -0.56 382 382
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.029 -10000 0 -0.61 2 2
FRS2 family/SHP2 -0.002 0.027 -10000 0 -0.47 3 3
SHC/GRB2/SOS1/GAB1 0 0.014 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.035 0.2 -10000 0 -0.85 51 51
RAP1/GDP -0.018 0.048 -10000 0 -10000 0 0
KIDINS220/CRKL 0.015 0 -10000 0 -10000 0 0
BDNF (dimer) -0.096 0.27 -10000 0 -0.74 131 131
ubiquitin-dependent protein catabolic process -0.088 0.21 -10000 0 -0.55 142 142
Schwann cell development -0.037 0.036 -10000 0 -10000 0 0
EHD4 0.015 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.015 -10000 0 -10000 0 0
RAP1B 0.015 0 -10000 0 -10000 0 0
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.29 -10000 0 -0.89 93 93
ABL1 0.015 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.075 0.089 -10000 0 -10000 0 0
STAT3 0.012 0.063 -10000 0 -10000 0 0
axon guidance -0.23 0.27 -10000 0 -0.82 93 93
MAPK3 -0.079 0.23 -10000 0 -0.57 91 91
MAPK1 -0.079 0.23 -10000 0 -0.57 91 91
CDC42/GDP 0.031 0.083 -10000 0 -0.32 2 2
NTF3 -0.035 0.2 -10000 0 -0.85 51 51
NTF4 -0.016 0.13 -10000 0 -0.74 27 27
NGF (dimer)/TRKA/FAIM -0.088 0.21 -10000 0 -0.55 143 143
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.012 0.044 -10000 0 -0.74 3 3
FAIM 0.013 0.036 -10000 0 -0.74 2 2
GAB1 0.015 0 -10000 0 -10000 0 0
RASGRF1 -0.081 0.16 -10000 0 -0.59 42 42
SOS1 0.015 0 -10000 0 -10000 0 0
MCF2L -0.053 0.23 -10000 0 -0.61 121 121
RGS19 0.012 0.044 -10000 0 -0.74 3 3
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.031 0.083 -10000 0 -0.32 2 2
NGF (dimer)/TRKA/GRIT -0.089 0.21 -10000 0 -0.56 141 141
neuron projection morphogenesis -0.026 0.15 -10000 0 -0.65 13 13
NGF (dimer)/TRKA/NEDD4-2 -0.088 0.21 -10000 0 -0.55 142 142
MAP2K1 0.051 0.015 -10000 0 -10000 0 0
NGFR -0.052 0.22 -10000 0 -0.75 78 78
NGF (dimer)/TRKA/GIPC/GAIP -0.085 0.16 -10000 0 -0.67 27 27
RAS family/GTP/PI3K 0 0.008 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.023 -10000 0 -10000 0 0
NRAS 0.015 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.015 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.051 -10000 0 -0.86 3 3
MAPKKK cascade -0.096 0.21 -10000 0 -0.69 86 86
RASA1 0.014 0.029 -10000 0 -0.86 1 1
TRKA/c-Abl -0.057 0.18 -10000 0 -0.66 77 77
SQSTM1 0.009 0.066 -10000 0 -0.74 7 7
BDNF (dimer)/TRKB/GIPC -0.22 0.26 -10000 0 -0.55 274 274
NGF (dimer)/TRKA/p62/Atypical PKCs -0.078 0.18 -10000 0 -0.95 6 6
MATK -0.045 0.2 -10000 0 -0.74 71 71
NEDD4L 0.013 0.041 -10000 0 -0.86 2 2
RAS family/GDP -0.018 0.046 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.078 0.16 -10000 0 -0.62 34 34
Rac1/GTP -0.054 0.09 -10000 0 -0.41 14 14
FRS2 family/SHP2/CRK family -0.001 0.023 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.25 -9999 0 -0.75 137 137
RAD9A 0.013 0.036 -9999 0 -0.74 2 2
AP1 -0.044 0.16 -9999 0 -0.66 59 59
IFNAR2 0.014 0.006 -9999 0 -10000 0 0
AKT1 0.003 0.078 -9999 0 -0.35 20 20
ER alpha/Oestrogen -0.024 0.12 -9999 0 -0.67 32 32
NFX1/SIN3/HDAC complex 0.035 0.06 -9999 0 -10000 0 0
EGF -0.71 0.33 -9999 0 -0.86 739 739
SMG5 0.015 0 -9999 0 -10000 0 0
SMG6 0.015 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.23 -9999 0 -0.73 113 113
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex -0.001 0.019 -9999 0 -0.57 1 1
WT1 -0.41 0.43 -9999 0 -0.86 432 432
WRN 0.015 0 -9999 0 -10000 0 0
SP1 0.014 0.007 -9999 0 -10000 0 0
SP3 0.013 0.006 -9999 0 -10000 0 0
TERF2IP 0.015 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.19 0.21 -9999 0 -0.69 74 74
Mad/Max -0.001 0.018 -9999 0 -0.55 1 1
TERT -0.25 0.26 -9999 0 -0.78 134 134
CCND1 -0.22 0.25 -9999 0 -0.76 98 98
MAX 0.013 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.03 -9999 0 -0.86 1 1
TERF2 0 0.003 -9999 0 -10000 0 0
PTGES3 0.015 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 -0.002 0.025 -9999 0 -10000 0 0
CDKN1B -0.1 0.22 -9999 0 -0.87 2 2
RAD1 0.015 0 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
XRCC6 0.015 0 -9999 0 -10000 0 0
SAP30 -0.041 0.19 -9999 0 -0.74 63 63
TRF2/PARP2 0 0.003 -9999 0 -10000 0 0
UBE3A 0.013 0.006 -9999 0 -10000 0 0
JUN 0.013 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.045 0.22 -9999 0 -0.86 59 59
IFN-gamma/IRF1 -0.16 0.25 -9999 0 -0.54 261 261
PARP2 0.015 0 -9999 0 -10000 0 0
BLM -0.012 0.14 -9999 0 -0.74 32 32
Telomerase -0.019 0.12 -9999 0 -0.41 2 2
IRF1 0.016 0.036 -9999 0 -0.73 2 2
ESR1 -0.019 0.16 -9999 0 -0.86 32 32
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.02 -9999 0 -0.58 1 1
ubiquitin-dependent protein catabolic process 0.028 0.056 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.01 0.036 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.014 0.007 -9999 0 -10000 0 0
ATM -0.001 0.019 -9999 0 -0.58 1 1
SMAD3 0.027 0.043 -9999 0 -0.55 5 5
ABL1 0.015 0 -9999 0 -10000 0 0
MXD1 0.012 0.026 -9999 0 -0.74 1 1
MRE11A 0.015 0 -9999 0 -10000 0 0
HUS1 0.015 0 -9999 0 -10000 0 0
RPS6KB1 0.015 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.18 0.22 -9999 0 -0.72 78 78
NR2F2 0.006 0.031 -9999 0 -0.86 1 1
MAPK3 0.009 0.077 -9999 0 -0.55 16 16
MAPK1 0.009 0.077 -9999 0 -0.55 16 16
TGFB1/TGF beta receptor Type II 0.011 0.056 -9999 0 -0.73 5 5
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
HNRNPC 0.015 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.019 -9999 0 -0.58 1 1
NBN 0.015 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.75 15 15
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.56 0.25 -9999 0 -0.67 742 742
MYC -0.009 0.13 -9999 0 -0.74 26 26
IL2 -0.007 0.099 -9999 0 -0.74 16 16
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0.029 -9999 0 -0.86 1 1
HSP90AA1 0.015 0 -9999 0 -10000 0 0
TGFB1 0.011 0.056 -9999 0 -0.73 5 5
TRF2/BLM -0.018 0.096 -9999 0 -0.52 32 32
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.22 0.23 -9999 0 -0.73 106 106
SP1/HDAC2 0.004 0.01 -9999 0 -10000 0 0
PINX1 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.19 0.21 -9999 0 -0.69 74 74
Smad3/Myc -0.01 0.091 -9999 0 -0.48 30 30
911 complex -0.001 0.022 -9999 0 -0.47 2 2
IFNG -0.2 0.34 -9999 0 -0.72 261 261
Telomerase/PinX1 -0.19 0.21 -9999 0 -0.69 74 74
Telomerase/AKT1/mTOR/p70S6K -0.019 0.071 -9999 0 -0.44 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.19 0.21 -9999 0 -0.69 74 74
response to DNA damage stimulus 0.004 0.005 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.016 -9999 0 -10000 0 0
TRF2/WRN 0 0.003 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.19 0.21 -9999 0 -0.7 73 73
E2F1 -0.14 0.3 -9999 0 -0.74 181 181
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.076 0.25 -9999 0 -0.74 108 108
NCL 0.015 0 -9999 0 -10000 0 0
DKC1 0.015 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
BCR signaling 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
JUN -0.023 0.14 -10000 0 -0.39 31 31
IKBKB -0.019 0.091 -10000 0 -10000 0 0
AKT1 -0.02 0.11 -10000 0 -10000 0 0
IKBKG -0.018 0.096 -10000 0 -10000 0 0
CALM1 -0.034 0.1 -10000 0 -0.52 10 10
PIK3CA 0.015 0 -10000 0 -10000 0 0
MAP3K1 -0.06 0.2 -10000 0 -0.54 87 87
MAP3K7 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.046 0.11 -10000 0 -0.5 15 15
DOK1 0.013 0.036 -10000 0 -0.74 2 2
AP-1 -0.01 0.091 0.21 6 -0.29 7 13
LYN 0.014 0.029 -10000 0 -0.86 1 1
BLNK 0.002 0.1 -10000 0 -0.86 13 13
SHC1 0.014 0.025 -10000 0 -0.74 1 1
BCR complex -0.11 0.23 -10000 0 -0.56 176 176
CD22 -0.13 0.2 -10000 0 -0.6 77 77
CAMK2G -0.022 0.1 -10000 0 -0.53 6 6
CSNK2A1 0.015 0 -10000 0 -10000 0 0
INPP5D 0.006 0.083 -10000 0 -0.74 11 11
SHC/GRB2/SOS1 -0.075 0.15 -10000 0 -0.73 7 7
GO:0007205 -0.047 0.11 -10000 0 -0.5 15 15
SYK 0.01 0.065 -10000 0 -0.86 5 5
ELK1 -0.034 0.11 -10000 0 -0.53 10 10
NFATC1 -0.042 0.16 -10000 0 -0.47 53 53
B-cell antigen/BCR complex -0.11 0.23 -10000 0 -0.56 176 176
PAG1/CSK -0.004 0.049 -10000 0 -0.55 7 7
NFKBIB 0.005 0.035 0.098 10 -0.13 1 11
HRAS -0.025 0.11 -10000 0 -0.48 14 14
NFKBIA 0.005 0.035 0.098 10 -0.14 1 11
NF-kappa-B/RelA/I kappa B beta 0.013 0.03 -10000 0 -0.2 1 1
RasGAP/Csk -0.16 0.25 -10000 0 -0.81 63 63
mol:GDP -0.043 0.11 0.26 1 -0.5 14 15
PTEN 0.015 0 -10000 0 -10000 0 0
CD79B 0.009 0.071 -10000 0 -0.79 7 7
NF-kappa-B/RelA/I kappa B alpha 0.013 0.029 -10000 0 -0.2 1 1
GRB2 0.015 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.056 0.18 -10000 0 -0.5 93 93
PIK3R1 0.015 0 -10000 0 -10000 0 0
mol:IP3 -0.056 0.11 -10000 0 -0.51 15 15
CSK 0.015 0 -10000 0 -10000 0 0
FOS -0.054 0.15 -10000 0 -0.5 61 61
CHUK -0.018 0.096 -10000 0 -10000 0 0
IBTK 0.015 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.11 0.17 -10000 0 -0.5 60 60
PTPN6 -0.12 0.19 -10000 0 -0.66 41 41
RELA 0.015 0 -10000 0 -10000 0 0
BCL2A1 -0.01 0.061 -10000 0 -0.12 169 169
VAV2 -0.12 0.22 -10000 0 -0.67 97 97
ubiquitin-dependent protein catabolic process 0.011 0.034 0.1 10 -0.12 1 11
BTK -0.078 0.14 0.42 2 -10000 0 2
CD19 -0.13 0.25 -10000 0 -0.73 105 105
MAP4K1 -0.18 0.33 -10000 0 -0.74 235 235
CD72 -0.098 0.27 -10000 0 -0.74 134 134
PAG1 0.009 0.066 -10000 0 -0.74 7 7
MAPK14 -0.04 0.17 -10000 0 -0.49 51 51
SH3BP5 -0.007 0.14 -10000 0 -0.86 22 22
PIK3AP1 -0.029 0.11 -10000 0 -0.52 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.075 0.19 -10000 0 -0.53 81 81
RAF1 -0.014 0.11 -10000 0 -0.5 9 9
RasGAP/p62DOK/SHIP -0.16 0.24 -10000 0 -0.79 69 69
CD79A -0.13 0.3 -10000 0 -0.74 173 173
re-entry into mitotic cell cycle -0.01 0.09 0.21 6 -0.29 7 13
RASA1 0.014 0.029 -10000 0 -0.86 1 1
MAPK3 0.008 0.094 -10000 0 -0.61 1 1
MAPK1 0.008 0.094 -10000 0 -0.61 1 1
CD72/SHP1 -0.17 0.25 -10000 0 -0.73 108 108
NFKB1 0.014 0.029 -10000 0 -0.86 1 1
MAPK8 -0.043 0.18 -10000 0 -0.49 55 55
actin cytoskeleton organization -0.058 0.2 -10000 0 -0.56 97 97
NF-kappa-B/RelA 0.032 0.055 0.19 10 -10000 0 10
Calcineurin -0.037 0.069 -10000 0 -0.52 3 3
PI3K -0.12 0.18 -10000 0 -0.59 57 57
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.051 0.11 0.29 13 -0.54 15 28
SOS1 0.015 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.16 0.25 -10000 0 -0.64 147 147
DAPP1 -0.079 0.16 -10000 0 -0.64 31 31
cytokine secretion -0.038 0.15 -10000 0 -0.44 53 53
mol:DAG -0.056 0.11 -10000 0 -0.51 15 15
PLCG2 -0.025 0.18 -10000 0 -0.79 44 44
MAP2K1 -0.003 0.1 -10000 0 -0.46 7 7
B-cell antigen/BCR complex/FcgammaRIIB -0.19 0.29 -10000 0 -0.57 297 297
mol:PI-3-4-5-P3 -0.084 0.13 -10000 0 -0.42 30 30
ETS1 -0.011 0.093 -10000 0 -0.47 6 6
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.089 0.18 -10000 0 -0.86 6 6
B-cell antigen/BCR complex/LYN -0.097 0.16 -10000 0 -0.49 87 87
MALT1 0.015 0 -10000 0 -10000 0 0
TRAF6 0.015 0.002 -10000 0 -10000 0 0
RAC1 -0.064 0.22 -10000 0 -0.6 97 97
B-cell antigen/BCR complex/LYN/SYK -0.14 0.21 -10000 0 -0.74 40 40
CARD11 -0.12 0.22 -10000 0 -0.49 193 193
FCGR2B -0.14 0.31 -10000 0 -0.74 183 183
PPP3CA 0.015 0 -10000 0 -10000 0 0
BCL10 0.015 0 -10000 0 -10000 0 0
IKK complex 0.005 0.043 -10000 0 -10000 0 0
PTPRC -0.043 0.2 -10000 0 -0.74 69 69
PDPK1 -0.05 0.089 -10000 0 -10000 0 0
PPP3CB 0.015 0 -10000 0 -10000 0 0
PPP3CC 0.015 0 -10000 0 -10000 0 0
POU2F2 0.004 0.049 -10000 0 -0.13 91 91
Visual signal transduction: Rods

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
mol:K + 0.015 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.062 -9999 0 -0.56 11 11
Metarhodopsin II/Arrestin -0.01 0.069 -9999 0 -0.49 18 18
PDE6G/GNAT1/GTP -0.018 0.098 -9999 0 -0.54 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.082 -9999 0 -0.74 11 11
GRK1 0.001 0.043 -9999 0 -0.74 3 3
CNG Channel -0.16 0.24 -9999 0 -0.94 28 28
mol:Na + -0.16 0.24 -9999 0 -0.81 43 43
mol:ADP 0.001 0.043 -9999 0 -0.74 3 3
RGS9-1/Gbeta5/R9AP -0.038 0.14 -9999 0 -0.55 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.25 -9999 0 -0.85 43 43
CNGB1 -0.034 0.18 -9999 0 -0.74 52 52
RDH5 -0.047 0.21 -9999 0 -0.75 72 72
SAG 0.001 0.025 -9999 0 -0.74 1 1
mol:Ca2+ -0.12 0.25 -9999 0 -0.78 43 43
Na + (4 Units) -0.14 0.22 -9999 0 -0.74 43 43
RGS9 -0.027 0.18 -9999 0 -0.81 45 45
GNB1/GNGT1 -0.16 0.25 -9999 0 -0.55 263 263
GNAT1/GDP -0.038 0.13 -9999 0 -0.52 45 45
GUCY2D -0.04 0.19 -9999 0 -0.74 61 61
GNGT1 -0.21 0.34 -9999 0 -0.74 263 263
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.037 0.14 -9999 0 -0.64 32 32
mol:11-cis-retinal -0.047 0.21 -9999 0 -0.75 72 72
mol:cGMP -0.04 0.13 -9999 0 -0.81 4 4
GNB1 0.015 0 -9999 0 -10000 0 0
Rhodopsin -0.056 0.17 -9999 0 -0.57 88 88
SLC24A1 0.015 0 -9999 0 -10000 0 0
CNGA1 -0.18 0.36 -9999 0 -0.86 200 200
Metarhodopsin II -0.01 0.069 -9999 0 -0.47 19 19
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.14 -9999 0 -0.84 4 4
RGS9BP -0.003 0.12 -9999 0 -0.84 18 18
Metarhodopsin II/Transducin -0.081 0.12 -9999 0 -0.51 12 12
GCAP Family/Ca ++ -0.013 0.077 -9999 0 -0.45 26 26
PDE6A/B -0.029 0.13 -9999 0 -0.58 45 45
mol:Pi -0.038 0.14 -9999 0 -0.54 62 62
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.14 0.21 -9999 0 -0.45 267 267
PDE6B 0.002 0.11 -9999 0 -0.84 14 14
PDE6A -0.014 0.14 -9999 0 -0.74 31 31
PDE6G -0.003 0.12 -9999 0 -0.84 19 19
RHO -0.006 0.1 -9999 0 -0.74 17 17
PDE6 -0.06 0.18 -9999 0 -0.94 16 16
GUCA1A -0.01 0.11 -9999 0 -0.74 19 19
GC2/GCAP Family -0.013 0.077 -9999 0 -0.86 1 1
GUCA1C 0.003 0.036 -9999 0 -0.74 2 2
GUCA1B 0.01 0.062 -9999 0 -0.74 6 6
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.04 0.13 -9999 0 -0.47 75 75
EPHB2 0.003 0.099 -9999 0 -0.81 13 13
Syndecan-2/TACI -0.026 0.11 -9999 0 -0.47 49 49
LAMA1 -0.017 0.16 -9999 0 -0.83 34 34
Syndecan-2/alpha2 ITGB1 -0.039 0.12 -9999 0 -0.48 9 9
HRAS 0.014 0.025 -9999 0 -0.74 1 1
Syndecan-2/CASK -0.001 0.017 -9999 0 -0.48 1 1
ITGA5 -0.025 0.17 -9999 0 -0.74 47 47
BAX 0.047 0.056 -9999 0 -0.6 1 1
EPB41 0.015 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.001 0.015 -9999 0 -0.43 1 1
LAMA3 -0.05 0.21 -9999 0 -0.74 77 77
EZR 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.001 0.1 -9999 0 -0.74 17 17
Syndecan-2/MMP2 -0.007 0.064 -9999 0 -0.53 12 12
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.007 0.066 -9999 0 -0.66 9 9
dendrite morphogenesis -0.008 0.07 -9999 0 -0.56 13 13
Syndecan-2/GM-CSF -0.01 0.067 -9999 0 -0.47 18 18
determination of left/right symmetry 0.025 0.02 -9999 0 -0.55 1 1
Syndecan-2/PKC delta -0.006 0.052 -9999 0 -0.47 11 11
GNB2L1 0.014 0.025 -9999 0 -0.74 1 1
MAPK3 0.027 0.065 -9999 0 -0.42 18 18
MAPK1 0.027 0.065 -9999 0 -0.42 18 18
Syndecan-2/RACK1 -0.001 0.023 -9999 0 -0.4 3 3
NF1 0.015 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.025 0.02 -9999 0 -0.55 1 1
ITGA2 0.006 0.087 -9999 0 -0.86 9 9
MAPK8 0.04 0.057 -9999 0 -0.55 8 8
Syndecan-2/alpha2/beta1 Integrin -0.023 0.1 -9999 0 -0.48 35 35
Syndecan-2/Kininogen -0.4 0.27 -9999 0 -0.57 612 612
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC 0.046 0.028 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.001 0.015 -9999 0 -0.43 1 1
extracellular matrix organization -0.003 0.039 -9999 0 -0.47 6 6
actin cytoskeleton reorganization -0.04 0.13 -9999 0 -0.47 75 75
Syndecan-2/Caveolin-2/Ras -0.009 0.064 -9999 0 -0.45 18 18
Syndecan-2/Laminin alpha3 -0.041 0.13 -9999 0 -0.47 78 78
Syndecan-2/RasGAP -0.002 0.034 -9999 0 -0.86 1 1
alpha5/beta1 Integrin -0.029 0.12 -9999 0 -0.55 47 47
PRKCD 0.007 0.079 -9999 0 -0.74 10 10
Syndecan-2 dimer -0.008 0.07 -9999 0 -0.57 13 13
GO:0007205 0.005 0.004 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.034 -9999 0 -0.82 1 1
RHOA 0.015 0 -9999 0 -10000 0 0
SDCBP 0.015 0 -9999 0 -10000 0 0
TNFRSF13B -0.029 0.17 -9999 0 -0.74 48 48
RASA1 0.014 0.029 -9999 0 -0.86 1 1
alpha2/beta1 Integrin -0.007 0.066 -9999 0 -0.66 9 9
Syndecan-2/Synbindin -0.001 0.016 -9999 0 -0.47 1 1
TGFB1 0.011 0.056 -9999 0 -0.74 5 5
CASP3 0.036 0.051 -9999 0 -0.42 11 11
FN1 -0.048 0.21 -9999 0 -0.74 74 74
Syndecan-2/IL8 -0.045 0.14 -9999 0 -0.5 80 80
SDC2 0.025 0.02 -9999 0 -0.55 1 1
KNG1 -0.59 0.4 -9999 0 -0.86 612 612
Syndecan-2/Neurofibromin -0.001 0.016 -9999 0 -0.47 1 1
TRAPPC4 0.015 0 -9999 0 -10000 0 0
CSF2 -0.008 0.1 -9999 0 -0.74 17 17
Syndecan-2/TGFB1 -0.003 0.039 -9999 0 -0.47 6 6
Syndecan-2/Syntenin/PI-4-5-P2 -0.001 0.015 -9999 0 -0.43 1 1
Syndecan-2/Ezrin -0.001 0.014 -9999 0 -0.42 1 1
PRKACA 0.042 0.016 -9999 0 -0.42 1 1
angiogenesis -0.045 0.14 -9999 0 -0.5 80 80
MMP2 0.004 0.09 -9999 0 -0.77 12 12
IL8 -0.055 0.22 -9999 0 -0.77 79 79
calcineurin-NFAT signaling pathway -0.026 0.11 -9999 0 -0.47 49 49
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0.041 -9999 0 -0.86 2 2
SPHK1 -0.13 0.3 -9999 0 -0.74 174 174
GNAI2 0.015 0 -9999 0 -10000 0 0
mol:S1P -0.028 0.12 -9999 0 -0.37 2 2
GNAO1 -0.02 0.17 -9999 0 -0.83 37 37
mol:Sphinganine-1-P -0.086 0.23 -9999 0 -0.55 176 176
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.032 0.066 -9999 0 -0.58 1 1
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.034 0.2 -9999 0 -0.86 50 50
S1PR2 0.014 0.025 -9999 0 -0.74 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.044 0.088 -9999 0 -0.32 2 2
S1PR5 -0.093 0.26 -9999 0 -0.74 127 127
S1PR4 -0.008 0.13 -9999 0 -0.74 27 27
GNAI1 0.01 0.065 -9999 0 -0.86 5 5
S1P/S1P5/G12 -0.095 0.16 -9999 0 -0.44 127 127
S1P/S1P3/Gq -0.083 0.18 -9999 0 -0.59 77 77
S1P/S1P4/Gi 0.009 0.1 -9999 0 -0.41 16 16
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.012 0.051 -9999 0 -0.86 3 3
GNA14 -0.076 0.27 -9999 0 -0.86 93 93
GNA15 -0.014 0.14 -9999 0 -0.74 34 34
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.007 0.082 -9999 0 -0.86 8 8
ABCC1 0.015 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.023 0.16 -9999 0 -0.74 45 45
PLK4 0.011 0.056 -9999 0 -0.74 5 5
regulation of centriole replication -0.003 0.13 -9999 0 -0.55 50 50
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.017 0.089 -10000 0 -0.49 26 26
HDAC1 0.003 0.01 -10000 0 -10000 0 0
AES 0.004 0.007 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
DTX1 -0.063 0.25 -10000 0 -0.86 79 79
LRP6/FZD1 -0.005 0.053 -10000 0 -0.56 8 8
TLE1 0.014 0.002 -10000 0 -10000 0 0
AP1 -0.13 0.22 -10000 0 -0.42 270 270
NCSTN 0.015 0 -10000 0 -10000 0 0
ADAM10 0.014 0.029 -10000 0 -0.86 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.066 -10000 0 -10000 0 0
NICD/RBPSUH -0.001 0.026 -10000 0 -0.72 1 1
WIF1 0.002 0.072 -10000 0 -0.75 8 8
NOTCH1 -0.001 0.028 -10000 0 -0.76 1 1
PSENEN 0.015 0 -10000 0 -10000 0 0
KREMEN2 -0.074 0.24 -10000 0 -0.74 104 104
DKK1 -0.017 0.15 -10000 0 -0.74 36 36
beta catenin/beta TrCP1 0.085 0.091 -10000 0 -10000 0 0
APH1B 0.013 0.041 -10000 0 -0.86 2 2
APH1A 0.015 0 -10000 0 -10000 0 0
AXIN1 -0.014 0.039 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.059 -10000 0 -10000 0 0
PSEN1 0.015 0 -10000 0 -10000 0 0
FOS -0.043 0.22 -10000 0 -0.86 59 59
JUN 0.015 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.007 -10000 0 -10000 0 0
CTNNB1 0.082 0.098 0.29 1 -10000 0 1
MAPK3 0.015 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.08 0.18 -10000 0 -0.49 145 145
HNF1A -0.011 0.12 -10000 0 -0.86 16 16
CTBP1 0.004 0.007 -10000 0 -10000 0 0
MYC -0.009 0.12 -10000 0 -0.65 26 26
NKD1 -0.22 0.38 -10000 0 -0.86 234 234
FZD1 0.008 0.072 -10000 0 -0.75 8 8
NOTCH1 precursor/Deltex homolog 1 -0.044 0.14 -10000 0 -0.48 80 80
apoptosis -0.13 0.22 -10000 0 -0.42 270 270
Delta 1/NOTCHprecursor -0.017 0.088 -10000 0 -0.49 26 26
DLL1 -0.015 0.16 -10000 0 -0.83 31 31
PPARD 0.009 0.023 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.023 -10000 0 -10000 0 0
APC -0.014 0.039 -10000 0 -10000 0 0
DVL1 -0.006 0.029 -10000 0 -0.53 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.074 0.18 -10000 0 -0.49 135 135
LRP6 0.015 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.004 0.013 -10000 0 -10000 0 0
CCND1 -0.015 0.13 -10000 0 -0.64 36 36
WNT1 -0.037 0.19 -10000 0 -0.74 59 59
Axin1/APC/beta catenin 0.079 0.053 -10000 0 -10000 0 0
DKK2 -0.026 0.17 -10000 0 -0.78 45 45
NOTCH1 precursor/DVL1 -0.003 0.031 -10000 0 -0.65 1 1
GSK3B 0.011 0.006 -10000 0 -10000 0 0
FRAT1 0.002 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.044 0.14 -10000 0 -0.48 80 80
PPP2R5D 0.098 0.17 0.38 234 -10000 0 234
MAPK1 0.015 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.036 0.12 -10000 0 -0.63 3 3
RBPJ 0.015 0 -10000 0 -10000 0 0
CREBBP 0.019 0.005 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.019 0.045 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.052 0.12 -9999 0 -0.52 10 10
JUN 0.005 0.14 -9999 0 -0.66 8 8
HRAS 0.014 0.025 -9999 0 -0.74 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.079 0.19 -9999 0 -0.55 114 114
RAP1A 0.015 0 -9999 0 -10000 0 0
FRS2 0.015 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.08 0.2 -9999 0 -0.56 114 114
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.061 0.17 -9999 0 -0.52 103 103
RHOA 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.07 0.17 -9999 0 -0.89 6 6
GRB7 0.005 0.092 -9999 0 -0.86 10 10
RET51/GFRalpha1/GDNF -0.079 0.19 -9999 0 -0.55 114 114
MAPKKK cascade -0.062 0.15 -9999 0 -0.72 9 9
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.065 0.18 -9999 0 -0.54 108 108
lamellipodium assembly -0.049 0.11 -9999 0 -0.46 11 11
RET51/GFRalpha1/GDNF/SHC -0.079 0.19 -9999 0 -0.55 114 114
PIK3CA 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.06 0.17 -9999 0 -0.52 102 102
RET9/GFRalpha1/GDNF/Shank3 -0.059 0.17 -9999 0 -0.52 101 101
MAPK3 -0.021 0.18 -9999 0 -0.83 6 6
DOK1 0.013 0.036 -9999 0 -0.74 2 2
DOK6 -0.066 0.25 -9999 0 -0.86 82 82
PXN 0.015 0 -9999 0 -10000 0 0
neurite development -0.074 0.17 -9999 0 -0.62 34 34
DOK5 -0.021 0.17 -9999 0 -0.85 37 37
GFRA1 -0.079 0.27 -9999 0 -0.84 97 97
MAPK8 -0.006 0.14 -9999 0 -0.62 13 13
HRAS/GTP -0.072 0.18 -9999 0 -0.85 9 9
tube development -0.055 0.16 -9999 0 -0.5 86 86
MAPK1 -0.021 0.18 -9999 0 -0.83 6 6
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.037 0.1 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0.025 -9999 0 -0.74 1 1
PDLIM7 0.012 0.044 -9999 0 -0.74 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.12 0.26 -9999 0 -0.98 39 39
SHC1 0.014 0.025 -9999 0 -0.74 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.079 0.19 -9999 0 -0.55 114 114
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.24 -9999 0 -0.62 130 130
PRKCA 0.015 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.019 -9999 0 -0.56 1 1
CREB1 -0.046 0.12 -9999 0 -0.62 5 5
PIK3R1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.038 0.1 -9999 0 -0.34 86 86
RET51/GFRalpha1/GDNF/Grb7 -0.085 0.21 -9999 0 -0.58 119 119
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.02 0.17 -9999 0 -0.84 36 36
DOK4 0.015 0 -9999 0 -10000 0 0
JNK cascade 0.005 0.14 -9999 0 -0.64 8 8
RET9/GFRalpha1/GDNF/FRS2 -0.059 0.17 -9999 0 -0.52 101 101
SHANK3 0.015 0 -9999 0 -10000 0 0
RASA1 0.014 0.029 -9999 0 -0.86 1 1
NCK1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.038 0.11 -9999 0 -0.35 86 86
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.05 0.12 -9999 0 -0.64 6 6
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.051 0.13 -9999 0 -0.64 8 8
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.13 -9999 0 -0.85 6 6
PI3K -0.074 0.17 -9999 0 -0.79 11 11
SOS1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.055 0.16 -9999 0 -0.5 86 86
GRB10 0.015 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.044 0.11 -9999 0 -0.55 6 6
RET51/GFRalpha1/GDNF/FRS2 -0.079 0.19 -9999 0 -0.55 114 114
GAB1 0.015 0 -9999 0 -10000 0 0
IRS1 0.005 0.092 -9999 0 -0.86 10 10
IRS2 0 0.11 -9999 0 -0.74 18 18
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.051 0.13 -9999 0 -0.85 6 6
RET51/GFRalpha1/GDNF/PKC alpha -0.079 0.19 -9999 0 -0.55 114 114
GRB2 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GDNF 0.001 0.05 -9999 0 -0.74 4 4
RAC1 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.085 0.2 -9999 0 -0.56 121 121
Rac1/GTP -0.058 0.13 -9999 0 -0.57 11 11
RET9/GFRalpha1/GDNF -0.065 0.18 -9999 0 -0.57 101 101
GFRalpha1/GDNF -0.074 0.21 -9999 0 -0.65 101 101
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.074 0.15 -9999 0 -0.66 16 16
FZD6 0.015 0 -9999 0 -10000 0 0
WNT6 -0.001 0.11 -9999 0 -0.74 18 18
WNT4 -0.048 0.22 -9999 0 -0.85 65 65
FZD3 0.015 0 -9999 0 -10000 0 0
WNT5A -0.013 0.14 -9999 0 -0.76 32 32
WNT11 -0.084 0.27 -9999 0 -0.84 103 103
Aurora A signaling

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
Aurora A/GADD45A 0.017 0.042 -9999 0 -10000 0 0
BIRC5 -0.22 0.35 -9999 0 -0.74 280 280
NFKBIA 0.044 0.037 -9999 0 -10000 0 0
CPEB1 -0.099 0.28 -9999 0 -0.82 120 120
AKT1 0.044 0.037 -9999 0 -10000 0 0
NDEL1 0.015 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.013 0.049 -9999 0 -0.47 4 4
NDEL1/TACC3 0.013 0.064 -9999 0 -0.6 6 6
GADD45A 0.015 0 -9999 0 -10000 0 0
GSK3B 0.012 0.017 -9999 0 -10000 0 0
PAK1/Aurora A 0.017 0.042 -9999 0 -10000 0 0
MDM2 0.015 0 -9999 0 -10000 0 0
JUB 0.007 0.082 -9999 0 -0.86 8 8
TPX2 -0.15 0.27 -9999 0 -0.55 271 271
TP53 0.022 0.034 -9999 0 -10000 0 0
DLG7 0.017 0.04 -9999 0 -10000 0 0
AURKAIP1 0.012 0.048 -9999 0 -0.82 3 3
ARHGEF7 0.015 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.014 0.068 -9999 0 -0.63 6 6
G2/M transition of mitotic cell cycle 0.013 0.049 -9999 0 -0.47 4 4
AURKA 0.023 0.051 -9999 0 -10000 0 0
AURKB -0.1 0.12 -9999 0 -0.24 379 379
CDC25B 0.015 0.052 -9999 0 -0.44 3 3
G2/M transition checkpoint 0.01 0.065 -9999 0 -0.55 8 8
mRNA polyadenylation -0.054 0.18 -9999 0 -0.49 120 120
Aurora A/CPEB -0.054 0.18 -9999 0 -0.49 120 120
Aurora A/TACC1/TRAP/chTOG -0.003 0.026 -9999 0 -0.47 1 1
BRCA1 0.012 0.05 -9999 0 -0.74 4 4
centrosome duplication 0.016 0.041 -9999 0 -10000 0 0
regulation of centrosome cycle -0.006 0.054 -9999 0 -0.6 6 6
spindle assembly -0.003 0.025 -9999 0 -0.46 1 1
TDRD7 0.015 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.12 0.18 -9999 0 -0.65 16 16
CENPA -0.09 0.11 -9999 0 -0.25 262 262
Aurora A/PP2A 0.016 0.044 -9999 0 -0.45 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.05 0.033 -9999 0 -10000 0 0
negative regulation of DNA binding 0.022 0.034 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.029 -9999 0 -0.86 1 1
Ajuba/Aurora A 0.01 0.065 -9999 0 -0.55 8 8
mitotic prometaphase 0.029 0.034 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.051 -9999 0 -10000 0 0
TACC1 0.014 0.029 -9999 0 -0.86 1 1
TACC3 0.008 0.071 -9999 0 -0.74 8 8
Aurora A/Antizyme1 0.016 0.051 -9999 0 -0.5 2 2
Aurora A/RasGAP 0.016 0.046 -9999 0 -0.57 1 1
OAZ1 0.014 0.025 -9999 0 -0.74 1 1
RAN 0.015 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.017 -9999 0 -10000 0 0
GIT1 0.015 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.15 0.27 -9999 0 -0.55 271 271
PPP2R5D 0.014 0.025 -9999 0 -0.74 1 1
Aurora A/TPX2 -0.096 0.21 -9999 0 -0.63 13 13
PAK1 0.015 0 -9999 0 -10000 0 0
CKAP5 0.015 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.012 0.092 -9999 0 -0.65 17 17
VEGFR1 homodimer/NRP1 -0.013 0.093 -9999 0 -0.66 17 17
mol:DAG -0.12 0.24 -9999 0 -0.89 15 15
VEGFR1 homodimer/NRP1/VEGFR 121 -0.14 0.22 -9999 0 -0.87 17 17
CaM/Ca2+ -0.14 0.2 -9999 0 -0.84 15 15
HIF1A 0.017 0.06 -9999 0 -0.53 6 6
GAB1 0.015 0 -9999 0 -10000 0 0
AKT1 -0.11 0.17 -9999 0 -0.74 15 15
PLCG1 -0.12 0.24 -9999 0 -0.9 15 15
NOS3 -0.064 0.21 -9999 0 -0.78 15 15
CBL 0.014 0.029 -9999 0 -0.86 1 1
mol:NO -0.061 0.2 -9999 0 -0.73 15 15
FLT1 0.024 0.11 -9999 0 -0.75 17 17
PGF -0.24 0.36 -9999 0 -0.74 302 302
VEGFR1 homodimer/NRP2/VEGFR121 -0.15 0.22 -9999 0 -0.89 20 20
CALM1 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.051 0.19 -9999 0 -0.7 15 15
endothelial cell proliferation -0.077 0.21 -9999 0 -0.76 17 17
mol:Ca2+ -0.12 0.24 -9999 0 -0.88 15 15
MAPK3 -0.081 0.21 -9999 0 -0.77 15 15
MAPK1 -0.081 0.21 -9999 0 -0.77 15 15
PIK3R1 0.015 0 -9999 0 -10000 0 0
PLGF homodimer -0.24 0.36 -9999 0 -0.74 302 302
PRKACA 0.015 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.027 0.17 -9999 0 -0.74 50 50
VEGFA homodimer -0.22 0.35 -9999 0 -0.74 273 273
VEGFR1 homodimer/VEGFA homodimer -0.15 0.24 -9999 0 -0.93 17 17
platelet activating factor biosynthetic process -0.069 0.21 -9999 0 -0.74 15 15
PI3K -0.14 0.2 -9999 0 -0.86 15 15
PRKCA -0.097 0.22 -9999 0 -0.82 15 15
PRKCB -0.1 0.23 -9999 0 -0.82 17 17
VEGFR1 homodimer/PLGF homodimer -0.17 0.24 -9999 0 -0.93 17 17
VEGFA -0.22 0.35 -9999 0 -0.74 273 273
VEGFB 0.015 0 -9999 0 -10000 0 0
mol:IP3 -0.12 0.24 -9999 0 -0.89 15 15
RASA1 0.039 0.096 -9999 0 -0.89 5 5
NRP2 -0.002 0.11 -9999 0 -0.74 20 20
VEGFR1 homodimer 0.024 0.11 -9999 0 -0.74 17 17
VEGFB homodimer 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.072 0.22 -9999 0 -0.67 50 50
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.2 -9999 0 -0.84 15 15
mol:L-citrulline -0.061 0.2 -9999 0 -0.73 15 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.13 0.2 -9999 0 -0.87 16 16
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.14 0.21 -9999 0 -0.91 15 15
CD2AP 0.015 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.13 0.19 -9999 0 -0.8 15 15
PDPK1 -0.085 0.22 -9999 0 -0.79 15 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.14 0.21 -9999 0 -0.91 15 15
mol:NADP -0.061 0.2 -9999 0 -0.73 15 15
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.13 0.2 -9999 0 -0.86 16 16
VEGFR1 homodimer/NRP2 -0.023 0.11 -9999 0 -0.65 18 18
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.013 0.03 -10000 0 -0.84 1 1
HSPA8 0.014 0.029 -10000 0 -0.85 1 1
SMAD3/SMAD4/ER alpha -0.003 0.13 -10000 0 -0.58 32 32
AKT1 0.019 0.006 -10000 0 -10000 0 0
GSC -0.002 0.16 -10000 0 -0.63 47 47
NKX2-5 -0.04 0.18 -10000 0 -0.73 57 57
muscle cell differentiation 0.023 0.075 0.55 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.041 0.073 -10000 0 -10000 0 0
SMAD4 0.028 0.031 -10000 0 -10000 0 0
CBFB 0.015 0 -10000 0 -10000 0 0
SAP18 0.015 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.001 0.054 -10000 0 -0.48 10 10
SMAD3/SMAD4/VDR 0.005 0.049 -10000 0 -10000 0 0
MYC -0.021 0.13 -10000 0 -0.74 26 26
CDKN2B 0.051 0.083 -10000 0 -0.61 10 10
AP1 0.035 0.13 -10000 0 -0.53 2 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.003 0.044 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.039 0.06 -10000 0 -0.45 1 1
SP3 0.019 0 -10000 0 -10000 0 0
CREB1 0.015 0 -10000 0 -10000 0 0
FOXH1 -0.046 0.21 -10000 0 -0.74 74 74
SMAD3/SMAD4/GR 0.005 0.037 -10000 0 -0.49 1 1
GATA3 -0.44 0.43 -10000 0 -0.85 467 467
SKI/SIN3/HDAC complex/NCoR1 0.048 0.048 -10000 0 -10000 0 0
MEF2C/TIF2 -0.074 0.2 -10000 0 -0.82 38 38
endothelial cell migration 0.099 0.31 0.84 113 -10000 0 113
MAX 0.008 0.019 -10000 0 -10000 0 0
RBBP7 0.015 0.004 -10000 0 -10000 0 0
RBBP4 0.014 0.029 -10000 0 -0.86 1 1
RUNX2 -0.015 0.15 -10000 0 -0.74 35 35
RUNX3 -0.21 0.35 -10000 0 -0.74 271 271
RUNX1 -0.042 0.2 -10000 0 -0.74 67 67
CTBP1 0.015 0 -10000 0 -10000 0 0
NR3C1 0.007 0.032 -10000 0 -0.74 1 1
VDR 0.01 0.065 -10000 0 -0.86 5 5
CDKN1A 0.078 0.066 -10000 0 -10000 0 0
KAT2B 0.012 0.03 -10000 0 -0.86 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.039 0.14 -10000 0 -0.48 63 63
DCP1A 0.015 0 -10000 0 -10000 0 0
SKI 0.015 0.004 -10000 0 -10000 0 0
SERPINE1 -0.1 0.32 -10000 0 -0.85 113 113
SMAD3/SMAD4/ATF2 0.003 0.035 -10000 0 -0.58 1 1
SMAD3/SMAD4/ATF3 -0.012 0.1 -10000 0 -0.59 24 24
SAP30 -0.039 0.19 -10000 0 -0.74 63 63
Cbp/p300/PIAS3 0.004 0.029 -10000 0 -0.55 1 1
JUN 0.048 0.12 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.002 0.06 -10000 0 -0.55 3 3
TFE3 0.021 0.011 -10000 0 -10000 0 0
COL1A2 -0.059 0.2 -10000 0 -0.63 95 95
mesenchymal cell differentiation 0.016 0.099 0.5 26 -10000 0 26
DLX1 -0.29 0.37 -10000 0 -0.74 359 359
TCF3 0.015 0 -10000 0 -10000 0 0
FOS -0.034 0.22 -10000 0 -0.84 59 59
SMAD3/SMAD4/Max 0.006 0.033 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.019 -10000 0 -0.56 1 1
ZBTB17 -0.001 0.04 -10000 0 -0.83 2 2
LAMC1 0.065 0.043 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.004 0.029 -10000 0 -10000 0 0
IRF7 0.008 0.08 -10000 0 -0.74 10 10
ESR1 -0.025 0.16 -10000 0 -0.86 32 32
HNF4A -0.11 0.3 -10000 0 -0.86 127 127
MEF2C 0.007 0.18 -10000 0 -0.75 18 18
SMAD2-3/SMAD4 0.002 0.03 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.003 0.024 -10000 0 -0.55 1 1
IGHV3OR16-13 -0.032 0.045 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.015 0 -10000 0 -10000 0 0
CREBBP 0.014 0.007 -10000 0 -10000 0 0
SKIL 0.015 0 -10000 0 -10000 0 0
HDAC1 0.015 0.004 -10000 0 -10000 0 0
HDAC2 0.015 0.004 -10000 0 -10000 0 0
SNIP1 0.015 0.004 -10000 0 -10000 0 0
GCN5L2 -0.002 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.005 0.032 -10000 0 -10000 0 0
MSG1/HSC70 -0.002 0.061 -10000 0 -0.56 10 10
SMAD2 0.022 0.015 -10000 0 -10000 0 0
SMAD3 0.027 0.03 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.057 0.034 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.03 -10000 0 -0.62 1 1
NCOR1 0.015 0.004 -10000 0 -10000 0 0
NCOA2 -0.025 0.18 -10000 0 -0.86 41 41
NCOA1 0.015 0 -10000 0 -10000 0 0
MYOD/E2A -0.016 0.091 -10000 0 -0.55 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.077 -10000 0 -10000 0 0
IFNB1 0.049 0.074 -10000 0 -0.66 3 3
SMAD3/SMAD4/MEF2C -0.007 0.17 -10000 0 -0.72 17 17
CITED1 0.006 0.075 -10000 0 -0.74 9 9
SMAD2-3/SMAD4/ARC105 0.004 0.028 -10000 0 -10000 0 0
RBL1 0.015 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.072 0.059 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.18 0.25 -10000 0 -0.51 310 310
SMAD7 0.036 0.1 -10000 0 -10000 0 0
MYC/MIZ-1 -0.016 0.1 -10000 0 -0.57 27 27
SMAD3/SMAD4 -0.025 0.12 0.32 1 -0.44 12 13
IL10 -0.27 0.32 -10000 0 -0.77 77 77
PIASy/HDAC complex 0.017 0.009 -10000 0 -10000 0 0
PIAS3 0.013 0.005 -10000 0 -10000 0 0
CDK2 0.014 0.007 -10000 0 -10000 0 0
IL5 -0.24 0.29 -10000 0 -0.63 65 65
CDK4 0.014 0.007 -10000 0 -10000 0 0
PIAS4 0.017 0.009 -10000 0 -10000 0 0
ATF3 -0.009 0.14 -10000 0 -0.86 24 24
SMAD3/SMAD4/SP1 -0.01 0.048 -10000 0 -10000 0 0
FOXG1 -0.024 0.14 -10000 0 -0.74 35 35
FOXO3 0.035 0.009 -10000 0 -10000 0 0
FOXO1 0.035 0.008 -10000 0 -10000 0 0
FOXO4 0.035 0.008 -10000 0 -10000 0 0
heart looping 0.007 0.18 -10000 0 -0.74 18 18
CEBPB -0.002 0.12 -10000 0 -0.74 23 23
SMAD3/SMAD4/DLX1 -0.19 0.24 -10000 0 -0.48 357 357
MYOD1 -0.017 0.12 -10000 0 -0.74 25 25
SMAD3/SMAD4/HNF4 -0.081 0.21 -10000 0 -0.59 127 127
SMAD3/SMAD4/GATA3 -0.31 0.29 -10000 0 -0.57 467 467
SnoN/SIN3/HDAC complex/NCoR1 0.015 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.14 0.22 -10000 0 -0.75 36 36
SMAD3/SMAD4/SP1-3 -0.005 0.038 -10000 0 -10000 0 0
MED15 0.015 0 -10000 0 -10000 0 0
SP1 0.016 0.041 -10000 0 -10000 0 0
SIN3B 0.015 0.004 -10000 0 -10000 0 0
SIN3A 0.015 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.06 0.17 -10000 0 -0.73 27 27
ITGB5 0.08 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.046 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.031 0.14 -10000 0 -0.59 52 52
AR -0.037 0.21 -10000 0 -0.85 53 53
negative regulation of cell growth 0.039 0.073 -10000 0 -0.49 1 1
SMAD3/SMAD4/MYOD -0.011 0.085 -10000 0 -0.49 19 19
E2F5 0.014 0.029 -10000 0 -0.86 1 1
E2F4 0.015 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.03 0.12 -10000 0 -0.57 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 0.069 0.043 -10000 0 -10000 0 0
TFDP1 0.015 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.015 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.016 0.1 -10000 0 -0.5 26 26
TGIF2 0.015 0 -10000 0 -10000 0 0
TGIF1 0.015 0 -10000 0 -10000 0 0
ATF2 0.014 0.029 -10000 0 -0.86 1 1
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.033 0.14 -9999 0 -0.58 50 50
E-cadherin/beta catenin -0.036 0.15 -9999 0 -0.66 48 48
CTNNB1 0.015 0 -9999 0 -10000 0 0
JUP 0.012 0.051 -9999 0 -0.86 3 3
CDH1 -0.032 0.2 -9999 0 -0.86 48 48
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.018 0.076 -10000 0 -10000 0 0
epithelial cell differentiation -0.026 0.11 -10000 0 -0.49 48 48
CYFIP2 0.004 0.096 -10000 0 -0.86 11 11
ENAH 0.069 0.083 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.75 15 15
EPHA2 0.013 0.039 -10000 0 -0.8 2 2
MYO6 0.021 0.12 -10000 0 -0.94 2 2
CTNNB1 0.015 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.063 -10000 0 -0.57 11 11
AQP5 -0.17 0.27 -10000 0 -0.61 223 223
CTNND1 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.11 -10000 0 -0.45 48 48
regulation of calcium-dependent cell-cell adhesion -0.004 0.16 -10000 0 -0.5 74 74
EGF -0.71 0.33 -10000 0 -0.86 739 739
NCKAP1 0.015 0 -10000 0 -10000 0 0
AQP3 -0.14 0.27 -10000 0 -0.64 187 187
cortical microtubule organization -0.026 0.11 -10000 0 -0.49 48 48
GO:0000145 0.023 0.11 -10000 0 -0.43 48 48
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.027 0.11 -10000 0 -0.49 48 48
MLLT4 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.021 0.085 -10000 0 -10000 0 0
ARF6 0.015 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.026 -10000 0 -0.52 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.039 0.11 -10000 0 -0.62 1 1
PVRL2 0.015 0 -10000 0 -10000 0 0
ZYX 0.022 0.12 -10000 0 -0.46 48 48
ARF6/GTP -0.001 0.024 -10000 0 -10000 0 0
CDH1 -0.032 0.2 -10000 0 -0.86 48 48
EGFR/EGFR/EGF/EGF -0.4 0.2 -10000 0 -0.89 54 54
RhoA/GDP -0.025 0.1 -10000 0 -0.45 48 48
actin cytoskeleton organization 0.031 0.12 -10000 0 -0.85 2 2
IGF-1R heterotetramer 0.015 0 -10000 0 -10000 0 0
GIT1 0.015 0 -10000 0 -10000 0 0
IGF1R 0.015 0 -10000 0 -10000 0 0
IGF1 -0.018 0.16 -10000 0 -0.77 37 37
DIAPH1 -0.01 0.081 -10000 0 -0.73 11 11
Wnt receptor signaling pathway 0.026 0.11 0.49 48 -10000 0 48
RHOA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.086 -10000 0 -10000 0 0
CTNNA1 0.015 0 -10000 0 -10000 0 0
VCL 0.031 0.12 -10000 0 -0.89 2 2
EFNA1 0.014 0.025 -10000 0 -0.74 1 1
LPP 0.032 0.11 -10000 0 -0.8 1 1
Ephrin A1/EPHA2 -0.025 0.1 -10000 0 -10000 0 0
SEC6/SEC8 -0.021 0.09 -10000 0 -10000 0 0
MGAT3 -0.005 0.17 -10000 0 -0.51 74 74
HGF/MET -0.068 0.18 -10000 0 -0.87 20 20
HGF -0.049 0.22 -10000 0 -0.84 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.018 0.077 -10000 0 -10000 0 0
actin cable formation 0.089 0.084 -10000 0 -0.42 1 1
KIAA1543 0.025 0.15 -10000 0 -1 8 8
KIFC3 0.019 0.12 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
EXOC3 0.015 0 -10000 0 -10000 0 0
ACTN1 0.021 0.12 -10000 0 -0.85 1 1
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.026 0.11 -10000 0 -0.49 48 48
EXOC4 0.015 0 -10000 0 -10000 0 0
STX4 0.022 0.12 -10000 0 -10000 0 0
PIP5K1C 0.022 0.12 -10000 0 -0.46 48 48
LIMA1 0.015 0 -10000 0 -10000 0 0
ABI1 0.015 0 -10000 0 -10000 0 0
ROCK1 -0.018 0.075 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.14 -10000 0 -0.91 9 9
IGF-1R heterotetramer/IGF1 -0.039 0.12 -10000 0 -0.9 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.01 0.13 -10000 0 -0.74 29 29
PLEKHA7 0.018 0.13 -10000 0 -0.76 8 8
mol:GTP -0.002 0.026 -10000 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.058 0.1 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.018 0.076 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.031 0.12 -10000 0 -0.85 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.018 0.077 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.031 0.12 -10000 0 -0.52 53 53
regulation of S phase of mitotic cell cycle -0.019 0.082 -10000 0 -0.66 1 1
GNAO1 -0.02 0.17 -10000 0 -0.83 37 37
HRAS 0.014 0.025 -10000 0 -0.74 1 1
SHBG/T-DHT -0.038 0.14 -10000 0 -0.59 57 57
PELP1 0.015 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.03 0.12 -10000 0 -0.55 9 9
T-DHT/AR -0.04 0.16 -10000 0 -0.67 53 53
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.008 51 51
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0.001 -10000 0 -10000 0 0
GNAI1 0.01 0.065 -10000 0 -0.86 5 5
mol:GDP -0.037 0.15 -10000 0 -0.62 53 53
cell proliferation 0.04 0.15 -10000 0 -0.68 10 10
PIK3CA 0.015 0 -10000 0 -10000 0 0
FOS 0.009 0.24 -10000 0 -0.85 59 59
mol:Ca2+ -0.007 0.02 -10000 0 -0.094 17 17
MAPK3 0.038 0.14 -10000 0 -0.63 10 10
MAPK1 0.029 0.075 -10000 0 -0.31 8 8
PIK3R1 0.015 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 59 59
cAMP biosynthetic process -0.03 0.14 -10000 0 -0.57 57 57
GNG2 0.015 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 59 59
HRAS/GTP -0.03 0.12 -10000 0 -0.48 52 52
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.014 0.025 -10000 0 -0.74 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 59 59
PI3K 0 0 -10000 0 -10000 0 0
apoptosis -0.033 0.14 0.41 58 -10000 0 58
T-DHT/AR/PELP1 -0.035 0.14 -10000 0 -0.58 53 53
HRAS/GDP -0.035 0.14 -10000 0 -0.59 52 52
CREB1 0.032 0.14 -10000 0 -0.44 58 58
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.037 0.21 -10000 0 -0.85 53 53
GNB1 0.015 0 -10000 0 -10000 0 0
RAF1 0.02 0.12 -10000 0 -0.55 10 10
RAC1-CDC42/GDP -0.033 0.13 -10000 0 -0.56 51 51
T-DHT/AR/PELP1/Src -0.032 0.13 -10000 0 -0.54 53 53
MAP2K2 0.029 0.12 -10000 0 -0.55 9 9
T-DHT/AR/PELP1/Src/PI3K -0.019 0.083 -10000 0 -0.67 1 1
GNAZ 0.012 0.051 -10000 0 -0.86 3 3
SHBG -0.041 0.21 -10000 0 -0.86 57 57
Gi family/GNB1/GNG2/GDP -0.021 0.079 -10000 0 -0.4 30 30
mol:T-DHT 0 0.001 -10000 0 -0.003 50 50
RAC1 0.015 0 -10000 0 -10000 0 0
GNRH1 -0.11 0.24 -10000 0 -0.56 187 187
Gi family/GTP -0.025 0.076 -10000 0 -0.54 4 4
CDC42 0.015 0 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.1 -10000 0 -0.58 6 6
epithelial cell differentiation -0.086 0.16 -10000 0 -0.55 7 7
ITCH 0.051 0.023 -10000 0 -10000 0 0
WWP1 -0.087 0.088 -10000 0 -10000 0 0
FYN 0.015 0 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.75 15 15
PRL 0.004 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.1 -10000 0 -0.67 1 1
PTPRZ1 -0.017 0.14 -10000 0 -0.82 28 28
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.065 0.095 -10000 0 -0.57 14 14
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.086 0.13 -10000 0 -0.57 39 39
ADAM17 0.051 0.023 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.11 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.13 0.13 -10000 0 -0.5 59 59
NCOR1 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.085 0.1 -10000 0 -0.54 37 37
GRIN2B -0.064 0.12 -10000 0 -0.56 21 21
ErbB4/ErbB2/betacellulin -0.12 0.17 -10000 0 -0.59 97 97
STAT1 0.013 0.036 -10000 0 -0.74 2 2
HBEGF 0.01 0.065 -10000 0 -0.86 5 5
PRLR -0.13 0.32 -10000 0 -0.86 147 147
E4ICDs/ETO2 -0.098 0.098 -10000 0 -0.57 4 4
axon guidance -0.031 0.064 -10000 0 -0.38 1 1
NEDD4 0.05 0.037 -10000 0 -0.83 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.25 -10000 0 -0.67 147 147
CBFA2T3 0.012 0.044 -10000 0 -0.74 3 3
ErbB4/ErbB2/HBEGF -0.067 0.058 -10000 0 -0.55 6 6
MAPK3 -0.033 0.11 -10000 0 -0.53 14 14
STAT1 (dimer) -0.097 0.095 -10000 0 -0.5 3 3
MAPK1 -0.033 0.11 -10000 0 -0.71 1 1
JAK2 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.086 0.11 -10000 0 -0.54 38 38
NRG1 0.02 0.15 -10000 0 -0.66 39 39
NRG3 -0.035 0.19 -10000 0 -0.75 58 58
NRG2 -0.028 0.18 -10000 0 -0.75 50 50
NRG4 -0.044 0.21 -10000 0 -0.79 64 64
heart development -0.031 0.064 -10000 0 -0.38 1 1
neural crest cell migration -0.085 0.1 -10000 0 -0.53 38 38
ERBB2 0.05 0.027 -10000 0 -0.66 1 1
WWOX/E4ICDs -0.097 0.095 -10000 0 -0.53 2 2
SHC1 0.014 0.025 -10000 0 -0.74 1 1
ErbB4/EGFR/neuregulin 4 -0.13 0.14 -10000 0 -0.61 47 47
apoptosis 0.12 0.086 0.45 10 -10000 0 10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.12 -10000 0 -0.46 51 51
ErbB4/ErbB2/epiregulin -0.14 0.17 -10000 0 -0.52 116 116
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.2 -10000 0 -0.68 97 97
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.16 0.19 -10000 0 -0.61 108 108
MDM2 -0.094 0.097 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.065 0.1 -10000 0 -0.54 37 37
STAT5A -0.019 0.06 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.093 0.12 -10000 0 -0.56 46 46
DLG4 0.015 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.018 -10000 0 -0.55 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.066 -10000 0 -0.42 1 1
STAT5A (dimer) -0.092 0.17 -10000 0 -0.61 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.02 0.058 -10000 0 -10000 0 0
LRIG1 0.015 0 -10000 0 -10000 0 0
EREG -0.12 0.28 -10000 0 -0.74 156 156
BTC -0.08 0.27 -10000 0 -0.86 96 96
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.031 0.064 -10000 0 -0.39 1 1
ERBB4 -0.12 0.11 -10000 0 -0.52 1 1
STAT5B 0.015 0 -10000 0 -10000 0 0
YAP1 -0.033 0.022 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.098 0.12 -10000 0 -0.59 37 37
glial cell differentiation 0.1 0.065 0.42 1 -10000 0 1
WWOX 0.014 0.025 -10000 0 -0.74 1 1
cell proliferation -0.075 0.17 -10000 0 -0.62 31 31
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.003 -9999 0 -10000 0 0
SMARCC1 0.021 0.012 -9999 0 -10000 0 0
REL 0.002 0.095 -9999 0 -0.84 11 11
HDAC7 -0.086 0.12 -9999 0 -0.7 9 9
JUN 0.013 0.005 -9999 0 -10000 0 0
EP300 0.012 0.03 -9999 0 -0.86 1 1
KAT2B 0.012 0.03 -9999 0 -0.86 1 1
KAT5 0.015 0.001 -9999 0 -10000 0 0
MAPK14 0.003 0.051 -9999 0 -0.65 5 5
FOXO1 0.014 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.1 0.12 -9999 0 -0.73 10 10
MAP2K6 -0.001 0.064 -9999 0 -0.84 5 5
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.003 0.007 -9999 0 -10000 0 0
SMARCA2 0.014 0.005 -9999 0 -10000 0 0
PDE9A -0.14 0.18 -9999 0 -0.71 57 57
NCOA2 -0.026 0.18 -9999 0 -0.86 41 41
CEBPA -0.02 0.16 -9999 0 -0.74 42 42
EHMT2 0.013 0.005 -9999 0 -10000 0 0
cell proliferation -0.11 0.15 -9999 0 -0.6 17 17
NR0B1 -0.076 0.23 -9999 0 -0.74 98 98
EGR1 -0.034 0.2 -9999 0 -0.86 48 48
RXRs/9cRA -0.005 0.049 -9999 0 -0.44 11 11
AR/RACK1/Src -0.027 0.082 -9999 0 -0.62 9 9
AR/GR -0.005 0.1 -9999 0 -0.65 9 9
GNB2L1 0.013 0.026 -9999 0 -0.74 1 1
PKN1 0.013 0.005 -9999 0 -10000 0 0
RCHY1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.001 0.064 -9999 0 -0.7 7 7
T-DHT/AR/TIF2/CARM1 -0.044 0.15 -9999 0 -0.77 22 22
SRC 0.004 0.069 -9999 0 -0.54 9 9
NR3C1 0.014 0.025 -9999 0 -0.74 1 1
KLK3 -0.12 0.25 -9999 0 -0.62 135 135
APPBP2 0.004 0.008 -9999 0 -10000 0 0
TRIM24 0.014 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.03 0.077 -9999 0 -0.64 10 10
TMPRSS2 -0.92 0.53 -9999 0 -1.2 660 660
RXRG 0 0.083 -9999 0 -0.74 11 11
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.015 0.001 -9999 0 -10000 0 0
RXRB 0.015 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.004 -9999 0 -10000 0 0
NR2C2 0.011 0.058 -9999 0 -0.86 4 4
KLK2 -0.058 0.19 -9999 0 -0.57 81 81
AR -0.018 0.11 -9999 0 -0.52 21 21
SENP1 0.015 0.001 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
MDM2 0.014 0.011 -9999 0 -10000 0 0
SRY 0.003 0.009 -9999 0 -10000 0 0
GATA2 -0.065 0.25 -9999 0 -0.86 81 81
MYST2 0.015 0.001 -9999 0 -10000 0 0
HOXB13 -0.15 0.31 -9999 0 -0.74 191 191
T-DHT/AR/RACK1/Src -0.021 0.081 -9999 0 -0.62 10 10
positive regulation of transcription -0.064 0.25 -9999 0 -0.86 81 81
DNAJA1 0.004 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.002 -9999 0 -10000 0 0
NCOA1 0.021 0.008 -9999 0 -10000 0 0
SPDEF -0.083 0.25 -9999 0 -0.74 113 113
T-DHT/AR/TIF2 0.007 0.099 -9999 0 -0.57 14 14
T-DHT/AR/Hsp90 -0.034 0.074 -9999 0 -0.65 10 10
GSK3B 0.003 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.015 0.072 -9999 0 -0.57 11 11
SIRT1 0.013 0.005 -9999 0 -10000 0 0
ZMIZ2 0.014 0.011 -9999 0 -10000 0 0
POU2F1 0.01 0.019 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.084 0.15 -9999 0 -0.73 13 13
CREBBP 0.013 0.005 -9999 0 -10000 0 0
SMARCE1 0.014 0.005 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.07 -10000 0 -0.58 12 12
MAP4K4 0.033 0.081 -10000 0 -0.71 1 1
BAG4 0.013 0.041 -10000 0 -0.86 2 2
PKC zeta/ceramide -0.099 0.056 -10000 0 -0.57 3 3
NFKBIA 0.015 0 -10000 0 -10000 0 0
BIRC3 -0.071 0.24 -10000 0 -0.74 101 101
BAX -0.043 0.026 -10000 0 -0.31 1 1
RIPK1 0.015 0 -10000 0 -10000 0 0
AKT1 0.045 0.011 -10000 0 -10000 0 0
BAD -0.098 0.052 -10000 0 -0.44 2 2
SMPD1 0.026 0.045 -10000 0 -0.26 8 8
RB1 -0.097 0.05 -10000 0 -10000 0 0
FADD/Caspase 8 0.047 0.074 -10000 0 -0.67 1 1
MAP2K4 -0.082 0.047 -10000 0 -10000 0 0
NSMAF 0.015 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.086 0.064 -10000 0 -0.51 9 9
EGF -0.71 0.33 -10000 0 -0.86 739 739
mol:ceramide -0.12 0.053 0.22 2 -10000 0 2
MADD 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.063 -10000 0 -0.56 10 10
ASAH1 0.015 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.096 0.05 -10000 0 -10000 0 0
cell proliferation -0.071 0.086 -10000 0 -0.47 27 27
BID -0.006 0.057 -10000 0 -0.4 1 1
MAP3K1 -0.097 0.05 -10000 0 -10000 0 0
EIF2A -0.069 0.045 -10000 0 -10000 0 0
TRADD 0.015 0 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
MAPK3 -0.067 0.059 -10000 0 -0.46 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.059 -10000 0 -0.46 9 9
Cathepsin D/ceramide -0.099 0.053 -10000 0 -0.48 3 3
FADD 0.033 0.079 -10000 0 -0.71 1 1
KSR1 -0.1 0.067 -10000 0 -0.54 9 9
MAPK8 -0.079 0.055 -10000 0 -0.38 9 9
PRKRA -0.097 0.05 -10000 0 -10000 0 0
PDGFA 0.006 0.081 -10000 0 -0.75 10 10
TRAF2 0.015 0 -10000 0 -10000 0 0
IGF1 -0.018 0.16 -10000 0 -0.77 37 37
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.053 0.22 2 -10000 0 2
CTSD 0.012 0.046 -10000 0 -0.78 3 3
regulation of nitric oxide biosynthetic process -0.001 0.022 -10000 0 -0.66 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.075 0.094 -10000 0 -0.51 27 27
PRKCD 0.007 0.079 -10000 0 -0.74 10 10
PRKCZ 0.012 0.051 -10000 0 -0.86 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.063 -10000 0 -0.56 10 10
RelA/NF kappa B1 -0.001 0.022 -10000 0 -0.66 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.029 -10000 0 -0.86 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.024 0.066 -10000 0 -0.53 3 3
TNFR1A/BAG4/TNF-alpha -0.015 0.087 -10000 0 -0.51 27 27
mol:Sphingosine-1-phosphate 0.021 0.07 -10000 0 -0.58 12 12
MAP2K1 -0.073 0.061 -10000 0 -0.48 9 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
CYCS -0.063 0.034 0.2 1 -0.22 2 3
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
NFKB1 0.014 0.029 -10000 0 -0.86 1 1
TNFR1A/BAG4 -0.001 0.031 -10000 0 -0.66 2 2
EIF2AK2 -0.082 0.047 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.014 0.083 -10000 0 -0.5 25 25
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.031 -10000 0 -10000 0 0
MAP2K2 -0.073 0.061 -10000 0 -0.48 9 9
SMPD3 0.027 0.051 -10000 0 -0.3 4 4
TNF -0.007 0.13 -10000 0 -0.78 25 25
PKC zeta/PAR4 -0.003 0.044 -10000 0 -0.66 4 4
mol:PHOSPHOCHOLINE 0.23 0.11 0.28 741 -10000 0 741
NF kappa B1/RelA/I kappa B alpha -0.003 0.036 -10000 0 -10000 0 0
AIFM1 -0.063 0.035 0.2 1 -0.22 2 3
BCL2 0.014 0.029 -10000 0 -0.86 1 1
FoxO family signaling

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
G6PC -0.66 0.72 -9999 0 -1.4 444 444
PLK1 -0.06 0.31 -9999 0 -0.68 122 122
CDKN1B 0.037 0.15 -9999 0 -0.38 1 1
FOXO3 0.005 0.2 -9999 0 -0.72 11 11
KAT2B 0.016 0.036 -9999 0 -0.9 1 1
FOXO1/SIRT1 -0.16 0.21 -9999 0 -0.4 10 10
CAT 0.013 0.2 -9999 0 -1.3 4 4
CTNNB1 0.015 0 -9999 0 -10000 0 0
AKT1 -0.003 0.033 -9999 0 -10000 0 0
FOXO1 -0.18 0.23 -9999 0 -0.41 444 444
MAPK10 0.028 0.07 -9999 0 -0.51 14 14
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.1 0.052 -9999 0 -10000 0 0
response to oxidative stress -0.026 0.04 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.036 0.18 -9999 0 -0.61 11 11
XPO1 0.016 0.001 -9999 0 -10000 0 0
EP300 -0.008 0.039 -9999 0 -0.86 1 1
BCL2L11 0.022 0.039 -9999 0 -10000 0 0
FOXO1/SKP2 -0.16 0.21 -9999 0 -10000 0 0
mol:GDP -0.026 0.04 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.091 -9999 0 -10000 0 0
YWHAQ 0.015 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.009 0.093 -9999 0 -0.45 1 1
MST1 0.005 0.099 -9999 0 -0.76 14 14
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.021 0.1 -9999 0 -10000 0 0
YWHAB 0.015 0 -9999 0 -10000 0 0
MAPK8 0.033 0.051 -9999 0 -0.51 7 7
MAPK9 0.036 0.017 -9999 0 -10000 0 0
YWHAG 0.015 0 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
YWHAZ 0.015 0 -9999 0 -10000 0 0
SIRT1 0.027 0.023 -9999 0 -10000 0 0
SOD2 0.018 0.18 -9999 0 -0.63 13 13
RBL2 0.051 0.15 -9999 0 -1.4 1 1
RAL/GDP 0.009 0.022 -9999 0 -10000 0 0
CHUK 0.017 0.019 -9999 0 -10000 0 0
Ran/GTP 0.015 0.005 -9999 0 -10000 0 0
CSNK1G2 0.014 0.029 -9999 0 -0.86 1 1
RAL/GTP 0.024 0.023 -9999 0 -10000 0 0
CSNK1G1 0.015 0 -9999 0 -10000 0 0
FASLG -0.19 0.31 -9999 0 -0.61 320 320
SKP2 0.015 0 -9999 0 -10000 0 0
USP7 0.017 0.001 -9999 0 -10000 0 0
IKBKB 0.017 0.019 -9999 0 -10000 0 0
CCNB1 0.011 0.2 -9999 0 -0.81 16 16
FOXO1-3a-4/beta catenin -0.056 0.089 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.21 -9999 0 -10000 0 0
CSNK1A1 0.015 0 -9999 0 -10000 0 0
SGK1 0.013 0.061 -9999 0 -0.85 4 4
CSNK1G3 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.047 -9999 0 -10000 0 0
SFN -0.15 0.32 -9999 0 -0.76 188 188
CDK2 -0.023 0.042 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.006 0.095 -9999 0 -10000 0 0
CREBBP -0.023 0.042 -9999 0 -10000 0 0
FBXO32 0.01 0.2 -9999 0 -0.78 11 11
BCL6 0.052 0.14 -9999 0 -10000 0 0
RALB 0.017 0 -9999 0 -10000 0 0
RALA 0.017 0 -9999 0 -10000 0 0
YWHAH 0.015 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.013 0.041 -9999 0 -0.86 2 2
Caspase 8 (4 units) -0.065 0.084 -9999 0 -10000 0 0
NEF -0.039 0.072 -9999 0 -10000 0 0
NFKBIA 0.006 0.037 -9999 0 -10000 0 0
BIRC3 -0.025 0.23 -9999 0 -0.68 101 101
CYCS -0.03 0.13 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
CD247 -0.22 0.39 -9999 0 -0.91 209 209
MAP2K7 -0.007 0.097 -9999 0 -10000 0 0
protein ubiquitination 0.067 0.058 -9999 0 -10000 0 0
CRADD 0.015 0 -9999 0 -10000 0 0
DAXX 0.015 0 -9999 0 -10000 0 0
FAS 0.014 0.029 -9999 0 -0.86 1 1
BID -0.042 0.14 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.034 0.095 -9999 0 -0.55 1 1
TRADD 0.015 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
CFLAR 0.015 0 -9999 0 -10000 0 0
FADD 0.015 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.034 0.096 -9999 0 -0.55 1 1
MAPK8 0 0.1 -9999 0 -0.41 7 7
APAF1 0.015 0 -9999 0 -10000 0 0
TRAF1 0.013 0.036 -9999 0 -0.74 2 2
TRAF2 0.015 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.089 0.12 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.054 0.062 -9999 0 -10000 0 0
CHUK 0.068 0.06 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.016 -9999 0 -10000 0 0
TCRz/NEF -0.25 0.36 -9999 0 -0.65 338 338
TNF -0.007 0.13 -9999 0 -0.78 25 25
FASLG -0.34 0.5 -9999 0 -0.94 338 338
NFKB1 0.005 0.047 -9999 0 -0.85 1 1
TNFR1A/BAG4/TNF-alpha -0.015 0.087 -9999 0 -0.51 27 27
CASP6 -0.032 0.047 -9999 0 -10000 0 0
CASP7 -0.004 0.18 -9999 0 -0.58 2 2
RELA 0.006 0.037 -9999 0 -10000 0 0
CASP2 0.015 0 -9999 0 -10000 0 0
CASP3 -0.004 0.18 -9999 0 -0.58 2 2
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.031 -9999 0 -0.66 2 2
CASP8 0.015 0 -9999 0 -10000 0 0
CASP9 0.015 0 -9999 0 -10000 0 0
MAP3K14 0.061 0.064 -9999 0 -0.46 1 1
APAF-1/Caspase 9 -0.081 0.15 -9999 0 -0.51 67 67
BCL2 0.01 0.096 -9999 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.021 0.098 -10000 0 -0.49 33 33
ER alpha/Gai/GDP/Gbeta gamma 0.024 0.14 -10000 0 -0.59 32 32
AKT1 0.017 0.17 -10000 0 -0.85 31 31
PIK3CA 0.015 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.013 0.17 -10000 0 -0.87 31 31
mol:Ca2+ -0.1 0.27 -10000 0 -0.63 126 126
IGF1R 0.015 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.029 0.13 -10000 0 -0.59 43 43
SHC1 0.014 0.025 -10000 0 -0.74 1 1
apoptosis -0.018 0.16 0.81 31 -10000 0 31
RhoA/GTP -0.016 0.08 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.03 0.12 -10000 0 -0.61 31 31
regulation of stress fiber formation -0.051 0.085 0.62 1 -10000 0 1
E2/ERA-ERB (dimer) -0.025 0.12 -10000 0 -0.57 39 39
KRAS 0.015 0 -10000 0 -10000 0 0
G13/GTP -0.019 0.1 -10000 0 -0.53 32 32
pseudopodium formation 0.051 0.085 -10000 0 -0.62 1 1
E2/ER alpha (dimer)/PELP1 -0.021 0.11 -10000 0 -0.58 32 32
GRB2 0.015 0 -10000 0 -10000 0 0
GNG2 0.015 0 -10000 0 -10000 0 0
GNAO1 -0.02 0.17 -10000 0 -0.83 37 37
HRAS 0.014 0.025 -10000 0 -0.74 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.032 0.14 -10000 0 -0.61 35 35
E2/ER beta (dimer) -0.005 0.053 -10000 0 -0.59 7 7
mol:GDP -0.023 0.11 -10000 0 -0.56 33 33
mol:NADP 0.032 0.14 -10000 0 -0.61 35 35
PIK3R1 0.015 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.29 -10000 0 -0.68 126 126
IGF-1R heterotetramer 0.015 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.25 -10000 0 -0.6 170 170
PLCB2 -0.11 0.22 -10000 0 -0.6 110 110
IGF1 -0.018 0.16 -10000 0 -0.77 37 37
mol:L-citrulline 0.032 0.14 -10000 0 -0.61 35 35
RHOA 0.015 0 -10000 0 -10000 0 0
Gai/GDP -0.03 0.14 -10000 0 -0.76 28 28
JNK cascade -0.005 0.053 -10000 0 -0.59 7 7
BCAR1 0.014 0.029 -10000 0 -0.86 1 1
ESR2 0.009 0.07 -10000 0 -0.77 7 7
GNAQ 0.015 0 -10000 0 -10000 0 0
ESR1 -0.016 0.16 -10000 0 -0.85 32 32
Gq family/GDP/Gbeta gamma -0.046 0.12 -10000 0 -0.59 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.037 0.072 -10000 0 -0.36 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.03 0.12 -10000 0 -0.61 31 31
GNAZ 0.012 0.051 -10000 0 -0.86 3 3
E2/ER alpha (dimer) -0.024 0.12 -10000 0 -0.67 32 32
STRN 0.003 0.1 -10000 0 -0.86 12 12
GNAL 0.013 0.039 -10000 0 -0.8 2 2
PELP1 0.015 0 -10000 0 -10000 0 0
MAPK11 0.019 0.05 -10000 0 -0.5 8 8
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.01 0.065 -10000 0 -0.86 5 5
HBEGF -0.037 0.16 -10000 0 -0.62 28 28
cAMP biosynthetic process -0.021 0.096 -10000 0 -0.46 41 41
SRC 0.034 0.14 -10000 0 -0.92 9 9
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.094 -10000 0 -0.49 31 31
SOS1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.034 0.11 -10000 0 -0.63 16 16
Gs family/GTP -0.022 0.098 -10000 0 -0.47 41 41
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0.014 -10000 0 -0.43 1 1
vasodilation 0.033 0.14 -10000 0 -0.57 35 35
mol:DAG -0.11 0.29 -10000 0 -0.68 126 126
Gs family/GDP/Gbeta gamma -0.019 0.087 -10000 0 -0.45 31 31
MSN 0.052 0.091 -10000 0 -0.7 1 1
Gq family/GTP -0.079 0.2 -10000 0 -0.62 93 93
mol:PI-3-4-5-P3 0.014 0.16 -10000 0 -0.83 31 31
NRAS 0.015 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.033 0.14 0.57 35 -10000 0 35
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.021 0.1 -10000 0 -0.52 33 33
NOS3 0.031 0.15 -10000 0 -0.65 35 35
GNA11 0.007 0.082 -10000 0 -0.86 8 8
MAPKKK cascade 0.04 0.15 -10000 0 -0.62 43 43
E2/ER alpha (dimer)/PELP1/Src -0.031 0.13 -10000 0 -0.65 31 31
ruffle organization 0.051 0.085 -10000 0 -0.62 1 1
ROCK2 -0.018 0.085 -10000 0 -0.82 1 1
GNA14 -0.076 0.27 -10000 0 -0.86 93 93
GNA15 -0.014 0.14 -10000 0 -0.74 34 34
GNA13 0.015 0 -10000 0 -10000 0 0
MMP9 -0.12 0.23 -10000 0 -0.7 31 31
MMP2 0.038 0.14 -10000 0 -0.8 13 13
S1P3 pathway

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
PDGFRB 0.002 0.11 -9999 0 -0.84 14 14
mol:S1P 0.002 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.029 0.069 -9999 0 -0.33 8 8
GNAO1 -0.018 0.17 -9999 0 -0.83 37 37
S1P/S1P3/G12/G13 -0.03 0.12 -9999 0 -0.53 50 50
AKT1 -0.02 0.092 -9999 0 -0.72 12 12
AKT3 -0.009 0.11 -9999 0 -1.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.002 0.11 -9999 0 -0.84 14 14
GNAI2 0.017 0.001 -9999 0 -10000 0 0
GNAI3 0.017 0.001 -9999 0 -10000 0 0
GNAI1 0.012 0.065 -9999 0 -0.86 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.032 0.2 -9999 0 -0.86 50 50
S1PR2 0.014 0.025 -9999 0 -0.74 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.017 0.14 -9999 0 -0.88 11 11
MAPK3 0.027 0.14 -9999 0 -0.84 11 11
MAPK1 0.027 0.14 -9999 0 -0.84 11 11
JAK2 -0.025 0.16 -9999 0 -0.78 13 13
CXCR4 -0.084 0.22 -9999 0 -0.82 13 13
FLT1 0.005 0.1 -9999 0 -0.77 15 15
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.026 0.14 -9999 0 -0.84 11 11
S1P/S1P3/Gi 0.017 0.14 -9999 0 -0.9 11 11
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.12 -9999 0 -0.82 11 11
VEGFA -0.21 0.35 -9999 0 -0.73 273 273
S1P/S1P2/Gi 0.035 0.077 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.15 0.28 -9999 0 -0.57 277 277
RHOA 0.015 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.047 0.18 -9999 0 -0.73 34 34
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ 0.014 0.051 -9999 0 -0.86 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.076 0.27 -9999 0 -0.86 93 93
GNA15 -0.014 0.14 -9999 0 -0.74 34 34
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.007 0.082 -9999 0 -0.86 8 8
Rac1/GTP -0.032 0.12 -9999 0 -0.82 11 11
Noncanonical Wnt signaling pathway

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
NFATC2 -0.016 0.16 -9999 0 -0.85 32 32
GNB1/GNG2 -0.063 0.13 -9999 0 -0.6 15 15
mol:DAG -0.003 0.14 -9999 0 -0.54 15 15
PLCG1 -0.003 0.14 -9999 0 -0.56 15 15
YES1 -0.024 0.16 -9999 0 -0.62 16 16
FZD3 0.015 0 -9999 0 -10000 0 0
FZD6 0.015 0 -9999 0 -10000 0 0
G protein -0.059 0.12 -9999 0 -0.57 15 15
MAP3K7 -0.13 0.25 -9999 0 -0.62 81 81
mol:Ca2+ -0.002 0.14 -9999 0 -0.52 15 15
mol:IP3 -0.003 0.14 -9999 0 -0.54 15 15
NLK -0.009 0.011 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.15 0.27 -9999 0 -0.68 87 87
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.074 0.15 -9999 0 -0.66 16 16
CSNK1A1 0.015 0 -9999 0 -10000 0 0
GNAS -0.024 0.16 -9999 0 -0.63 15 15
GO:0007205 -0.001 0.14 -9999 0 -0.53 15 15
WNT6 -0.001 0.11 -9999 0 -0.74 18 18
WNT4 -0.048 0.22 -9999 0 -0.85 65 65
NFAT1/CK1 alpha -0.07 0.13 -9999 0 -0.59 19 19
GNG2 0.015 0 -9999 0 -10000 0 0
WNT5A -0.013 0.14 -9999 0 -0.76 32 32
WNT11 -0.084 0.27 -9999 0 -0.84 103 103
CDC42 -0.012 0.15 -9999 0 -0.59 15 15
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.016 -10000 0 -10000 0 0
AES 0.004 0.014 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.005 0.053 -10000 0 -0.56 8 8
SMAD4 0.015 0 -10000 0 -10000 0 0
DKK2 -0.026 0.17 -10000 0 -0.78 45 45
TLE1 0.004 0.014 -10000 0 -10000 0 0
MACF1 0.015 0.004 -10000 0 -10000 0 0
CTNNB1 0.045 0.093 0.34 1 -10000 0 1
WIF1 -0.004 0.072 -10000 0 -0.75 8 8
beta catenin/RanBP3 0.001 0.094 0.4 7 -10000 0 7
KREMEN2 -0.074 0.24 -10000 0 -0.74 104 104
DKK1 -0.017 0.15 -10000 0 -0.74 36 36
beta catenin/beta TrCP1 0.051 0.087 0.33 1 -10000 0 1
FZD1 0.008 0.072 -10000 0 -0.75 8 8
AXIN2 0.016 0.086 -10000 0 -1.5 2 2
AXIN1 0.014 0.004 -10000 0 -10000 0 0
RAN 0.015 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.016 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.051 0.093 -10000 0 -0.58 1 1
Axin1/APC/GSK3 0.039 0.084 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.05 0.1 -10000 0 -0.61 1 1
HNF1A -0.012 0.12 -10000 0 -0.86 16 16
CTBP1 0.004 0.015 -10000 0 -10000 0 0
MYC 0.003 0.12 -10000 0 -0.67 26 26
RANBP3 0.015 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.08 0.18 -10000 0 -0.49 145 145
NKD1 -0.22 0.38 -10000 0 -0.86 234 234
TCF4 -0.001 0.065 -10000 0 -0.84 5 5
TCF3 0.004 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.032 0.11 -10000 0 -0.68 2 2
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.002 0.11 0.52 5 -0.62 1 6
LEF1 -0.052 0.21 -10000 0 -0.81 61 61
DVL1 0.002 0.031 -10000 0 -0.36 2 2
CSNK2A1 0.015 0.002 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.062 0.094 -10000 0 -0.56 1 1
DKK1/LRP6/Kremen 2 -0.074 0.18 -10000 0 -0.49 135 135
LRP6 0.015 0.002 -10000 0 -10000 0 0
CSNK1A1 0.004 0.016 -10000 0 -10000 0 0
NLK 0.015 0.004 -10000 0 -10000 0 0
CCND1 -0.002 0.14 -10000 0 -0.66 36 36
WNT1 -0.037 0.19 -10000 0 -0.74 59 59
GSK3A 0.014 0.004 -10000 0 -10000 0 0
GSK3B 0.014 0.005 -10000 0 -10000 0 0
FRAT1 0.013 0.004 -10000 0 -10000 0 0
PPP2R5D 0.1 0.16 0.38 234 -10000 0 234
APC -0.023 0.11 -10000 0 -0.78 1 1
WNT1/LRP6/FZD1 0.004 0.065 0.27 2 -0.45 1 3
CREBBP 0.004 0.015 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.017 0.085 -9999 0 -0.51 22 22
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.049 -9999 0 -0.52 1 1
AP1 -0.049 0.15 -9999 0 -0.81 8 8
mol:PIP3 -0.023 0.089 -9999 0 -0.68 3 3
AKT1 -0.011 0.054 -9999 0 -10000 0 0
PTK2B 0.029 0.055 -9999 0 -0.37 1 1
RHOA 0.036 0.033 -9999 0 -10000 0 0
PIK3CB 0.014 0.025 -9999 0 -0.74 1 1
mol:Ca2+ 0.031 0.07 -9999 0 -0.69 1 1
MAGI3 0.013 0.041 -9999 0 -0.86 2 2
RELA 0.015 0 -9999 0 -10000 0 0
apoptosis -0.018 0.08 -9999 0 -0.43 22 22
HRAS/GDP -0.001 0.019 -9999 0 -0.56 1 1
positive regulation of microtubule depolymerization 0.038 0.079 -9999 0 -0.46 13 13
NF kappa B1 p50/RelA -0.016 0.086 -9999 0 -0.67 4 4
endothelial cell migration 0.01 0.13 -9999 0 -0.61 36 36
ADCY4 0.02 0.13 -9999 0 -0.59 30 30
ADCY5 0.011 0.14 -9999 0 -0.57 34 34
ADCY6 0.026 0.12 -9999 0 -0.56 24 24
ADCY7 0.021 0.12 -9999 0 -0.56 24 24
ADCY1 -0.023 0.17 -9999 0 -0.62 44 44
ADCY2 -0.033 0.15 -9999 0 -0.54 45 45
ADCY3 0.026 0.12 -9999 0 -0.56 24 24
ADCY8 -0.006 0.13 -9999 0 -0.56 26 26
ADCY9 0.026 0.12 -9999 0 -0.56 24 24
GSK3B 0.038 0.052 -9999 0 -10000 0 0
arachidonic acid secretion 0.031 0.12 -9999 0 -0.52 23 23
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 -0.002 0.031 -9999 0 -0.54 3 3
GNAO1 -0.008 0.15 -9999 0 -0.55 61 61
HRAS 0.014 0.025 -9999 0 -0.74 1 1
NFKBIA 0.043 0.078 -9999 0 -0.52 4 4
GAB1 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.044 -9999 0 -0.93 2 2
JUN 0.015 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.027 -9999 0 -0.53 2 2
TIAM1 -0.002 0.053 -9999 0 -1.1 2 2
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.031 0.071 -9999 0 -0.71 1 1
PLCB3 0.035 0.027 -9999 0 -0.47 2 2
FOS -0.043 0.22 -9999 0 -0.86 59 59
positive regulation of mitosis 0.031 0.12 -9999 0 -0.52 23 23
LPA/LPA1-2-3 -0.023 0.1 -9999 0 -0.53 23 23
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
stress fiber formation 0.036 0.072 -9999 0 -0.49 1 1
GNAZ 0.014 0.11 -9999 0 -0.57 27 27
EGFR/PI3K-beta/Gab1 -0.024 0.093 -9999 0 -0.72 3 3
positive regulation of dendritic cell cytokine production -0.022 0.1 -9999 0 -0.53 23 23
LPA/LPA2/MAGI-3 -0.003 0.033 -9999 0 -0.54 3 3
ARHGEF1 0.033 0.089 -9999 0 -0.47 22 22
GNAI2 0.016 0.1 -9999 0 -0.56 24 24
GNAI3 0.016 0.1 -9999 0 -0.56 24 24
GNAI1 0.013 0.11 -9999 0 -0.56 29 29
LPA/LPA3 -0.009 0.063 -9999 0 -0.56 11 11
LPA/LPA2 -0.002 0.023 -9999 0 -0.56 1 1
LPA/LPA1 -0.022 0.11 -9999 0 -0.61 27 27
HB-EGF/EGFR -0.2 0.24 -9999 0 -0.48 362 362
HBEGF -0.2 0.29 -9999 0 -0.56 354 354
mol:DAG 0.031 0.071 -9999 0 -0.71 1 1
cAMP biosynthetic process 0.002 0.14 -9999 0 -0.52 48 48
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
SRC 0.014 0.025 -9999 0 -0.74 1 1
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.042 0.08 -9999 0 -0.52 4 4
GNAQ -0.005 0.041 -9999 0 -0.63 1 1
LPAR2 0.014 0.025 -9999 0 -0.74 1 1
LPAR3 -0.002 0.083 -9999 0 -0.74 11 11
LPAR1 -0.005 0.14 -9999 0 -0.84 24 24
IL8 -0.063 0.19 -9999 0 -0.49 74 74
PTK2 0.024 0.1 -9999 0 -0.79 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.018 0.081 -9999 0 -0.44 22 22
EGFR 0.001 0.099 -9999 0 -0.75 15 15
PLCG1 -0.003 0.074 -9999 0 -0.45 6 6
PLD2 0.024 0.1 -9999 0 -0.79 1 1
G12/G13 -0.017 0.085 -9999 0 -0.51 22 22
PI3K-beta -0.013 0.063 -9999 0 -10000 0 0
cell migration -0.002 0.037 -9999 0 -0.3 1 1
SLC9A3R2 0.014 0.029 -9999 0 -0.86 1 1
PXN 0.036 0.073 -9999 0 -0.5 1 1
HRAS/GTP -0.03 0.1 -9999 0 -0.54 23 23
RAC1 0.015 0 -9999 0 -10000 0 0
MMP9 -0.28 0.37 -9999 0 -0.74 350 350
PRKCE 0.013 0.029 -9999 0 -0.86 1 1
PRKCD 0.036 0.079 -9999 0 -0.66 1 1
Gi(beta/gamma) -0.028 0.099 -9999 0 -0.53 24 24
mol:LPA 0.003 0.024 -9999 0 -0.22 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.011 0.085 -9999 0 -0.8 1 1
MAPKKK cascade 0.031 0.12 -9999 0 -0.52 23 23
contractile ring contraction involved in cytokinesis 0.036 0.032 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.052 0.14 -9999 0 -0.45 94 94
GNA15 -0.018 0.084 -9999 0 -0.61 7 7
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
MAPT 0.039 0.081 -9999 0 -0.48 13 13
GNA11 -0.009 0.059 -9999 0 -0.47 9 9
Rac1/GTP -0.001 0.047 -9999 0 -0.99 2 2
MMP2 0.01 0.13 -9999 0 -0.62 36 36
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.018 0.087 -9999 0 -0.42 38 38
RGS9BP -0.003 0.12 -9999 0 -0.84 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.001 0.043 -9999 0 -0.74 3 3
mol:Na + -0.027 0.11 -9999 0 -0.48 49 49
mol:ADP 0.008 0.052 -9999 0 -0.56 7 7
GNAT2 0.013 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.038 0.14 -9999 0 -0.55 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.023 -9999 0 -0.48 2 2
GRK7 0.006 0.05 -9999 0 -0.74 4 4
CNGB3 -0.031 0.16 -9999 0 -0.74 44 44
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.032 0.15 -9999 0 -0.53 67 67
Cone PDE6 -0.035 0.12 -9999 0 -0.51 43 43
Cone Metarhodopsin II -0.004 0.04 -9999 0 -0.45 7 7
Na + (4 Units) -0.04 0.15 -9999 0 -0.53 67 67
GNAT2/GDP -0.033 0.12 -9999 0 -0.5 43 43
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.032 -9999 0 -0.44 4 4
Cone Transducin -0.019 0.092 -9999 0 -0.45 38 38
SLC24A2 -0.025 0.14 -9999 0 -0.74 33 33
GNB3/GNGT2 -0.024 0.12 -9999 0 -0.57 38 38
GNB3 -0.016 0.15 -9999 0 -0.74 36 36
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.056 -9999 0 -0.74 5 5
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.027 0.11 -9999 0 -0.49 49 49
mol:Pi -0.038 0.14 -9999 0 -0.54 62 62
Cone CNG Channel -0.023 0.095 -9999 0 -0.78 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.025 0.14 -9999 0 -0.74 33 33
RGS9 -0.027 0.18 -9999 0 -0.81 45 45
PDE6C 0.004 0.036 -9999 0 -0.74 2 2
GNGT2 0.012 0.046 -9999 0 -0.78 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.036 -9999 0 -0.74 2 2
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.039 0.12 -9999 0 -10000 0 0
CRKL -0.017 0.16 -9999 0 -10000 0 0
mol:DAG -0.059 0.11 -9999 0 -10000 0 0
HRAS -0.052 0.098 -9999 0 -0.57 1 1
MAPK8 -0.05 0.18 -9999 0 -0.53 8 8
RAP1A -0.017 0.16 -9999 0 -10000 0 0
GAB1 -0.017 0.16 -9999 0 -10000 0 0
MAPK14 -0.046 0.18 -9999 0 -0.52 1 1
EPO -0.15 0.31 -9999 0 -0.73 195 195
PLCG1 -0.061 0.11 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.013 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.1 0.19 -9999 0 -0.45 204 204
GAB1/SHC/GRB2/SOS1 -0.056 0.1 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.11 0.23 -9999 0 -0.54 195 195
IRS2 -0.025 0.16 -9999 0 -0.71 2 2
STAT1 0.007 0.15 -9999 0 -10000 0 0
STAT5B 0.002 0.14 -9999 0 -10000 0 0
cell proliferation -0.035 0.17 -9999 0 -0.49 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.056 0.1 -9999 0 -0.58 2 2
TEC -0.017 0.16 -9999 0 -10000 0 0
SOCS3 0.004 0.093 -9999 0 -0.79 12 12
STAT1 (dimer) 0.008 0.14 -9999 0 -10000 0 0
JAK2 0.011 0.013 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.019 0.17 -9999 0 -10000 0 0
EPO/EPOR -0.11 0.23 -9999 0 -0.54 195 195
LYN 0.016 0.029 -9999 0 -0.86 1 1
TEC/VAV2 -0.006 0.15 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.012 0.013 -9999 0 -10000 0 0
SHC1 0.014 0.025 -9999 0 -0.74 1 1
EPO/EPOR (dimer)/LYN -0.061 0.2 -9999 0 -0.44 196 196
mol:IP3 -0.059 0.11 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.069 0.12 -9999 0 -0.64 4 4
SH2B3 0.011 0.013 -9999 0 -10000 0 0
NFKB1 -0.046 0.18 -9999 0 -0.71 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.059 0.11 -9999 0 -0.44 3 3
PTPN6 -0.028 0.16 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.06 0.11 -9999 0 -10000 0 0
EPOR 0.012 0.013 -9999 0 -10000 0 0
INPP5D 0.006 0.083 -9999 0 -0.74 11 11
mol:GDP -0.057 0.11 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG2 -0.025 0.18 -9999 0 -0.79 44 44
CRKL/CBL/C3G -0.06 0.12 -9999 0 -0.73 1 1
VAV2 -0.017 0.16 -9999 0 -10000 0 0
CBL -0.017 0.16 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.06 0.11 -9999 0 -10000 0 0
STAT5A 0.002 0.14 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.025 0.14 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.03 0.13 -9999 0 -0.6 45 45
PTPN11 0.015 0 -9999 0 -10000 0 0
BTK -0.12 0.24 -9999 0 -0.71 57 57
BCL2 0.038 0.13 -9999 0 -0.96 1 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.041 0.085 0.41 1 -10000 0 1
GNAI2 0.015 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.069 0.17 -10000 0 -0.48 127 127
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.02 0.17 -10000 0 -0.83 37 37
RhoA/GTP -0.041 0.087 -10000 0 -0.42 1 1
negative regulation of cAMP metabolic process -0.047 0.099 -10000 0 -0.34 32 32
GNAZ 0.012 0.051 -10000 0 -0.86 3 3
GNAI3 0.015 0 -10000 0 -10000 0 0
GNA12 0.015 0 -10000 0 -10000 0 0
S1PR5 -0.093 0.26 -10000 0 -0.74 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.048 0.1 -10000 0 -0.34 32 32
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
GNAI1 0.01 0.065 -10000 0 -0.86 5 5
Ephrin B reverse signaling

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
EFNB2 0.015 0 -10000 0 -10000 0 0
EPHB2 0.002 0.1 -10000 0 -0.81 13 13
EFNB1 -0.056 0.21 -10000 0 -0.55 131 131
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.069 0.16 -10000 0 -0.81 14 14
Ephrin B2/EPHB1-2 -0.019 0.1 -10000 0 -0.53 32 32
neuron projection morphogenesis -0.066 0.15 -10000 0 -0.77 14 14
Ephrin B1/EPHB1-2/Tiam1 -0.075 0.18 -10000 0 -0.88 14 14
DNM1 -0.096 0.27 -10000 0 -0.74 131 131
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.01 0.12 -10000 0 -0.72 25 25
YES1 -0.025 0.16 -10000 0 -0.96 25 25
Ephrin B1/EPHB1-2/NCK2 -0.075 0.17 -10000 0 -0.87 13 13
PI3K -0.019 0.12 -10000 0 -0.73 25 25
mol:GDP -0.074 0.17 -10000 0 -0.86 14 14
ITGA2B -0.006 0.12 -10000 0 -0.75 24 24
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.025 0.16 -10000 0 -0.96 25 25
MAP3K7 -0.02 0.13 -10000 0 -0.77 25 25
FGR -0.026 0.16 -10000 0 -0.95 25 25
TIAM1 0.014 0.029 -10000 0 -0.86 1 1
PIK3R1 0.015 0 -10000 0 -10000 0 0
RGS3 0.015 0 -10000 0 -10000 0 0
cell adhesion -0.035 0.15 -10000 0 -0.61 41 41
LYN -0.025 0.16 -10000 0 -0.96 25 25
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.15 -10000 0 -0.9 25 25
Ephrin B1/EPHB1-2 -0.026 0.14 -10000 0 -0.83 25 25
SRC -0.025 0.16 -10000 0 -0.95 25 25
ITGB3 -0.014 0.16 -10000 0 -0.85 30 30
EPHB1 -0.006 0.13 -10000 0 -0.8 22 22
EPHB4 0.015 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.037 0.15 -10000 0 -0.62 53 53
BLK -0.03 0.16 -10000 0 -0.95 25 25
HCK -0.032 0.16 -10000 0 -0.96 25 25
regulation of stress fiber formation 0.074 0.17 0.86 13 -10000 0 13
MAPK8 0.016 0.13 -10000 0 -0.65 31 31
Ephrin B1/EPHB1-2/RGS3 -0.075 0.17 -10000 0 -0.87 13 13
endothelial cell migration -0.015 0.11 -10000 0 -0.66 25 25
NCK2 0.015 0 -10000 0 -10000 0 0
PTPN13 -0.02 0.16 -10000 0 -0.96 25 25
regulation of focal adhesion formation 0.074 0.17 0.86 13 -10000 0 13
chemotaxis 0.074 0.17 0.86 13 -10000 0 13
PIK3CA 0.015 0 -10000 0 -10000 0 0
Rac1/GTP -0.068 0.16 -10000 0 -0.8 14 14
angiogenesis -0.025 0.14 -10000 0 -0.83 25 25
LCK -0.03 0.16 -10000 0 -0.96 25 25
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.005 0.12 0.81 21 -10000 0 21
PI3K Class IB/PDE3B -0.005 0.13 -10000 0 -0.81 21 21
PDE3B -0.005 0.13 -10000 0 -0.81 21 21
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.014 0.075 -9999 0 -10000 0 0
CRKL 0.015 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.029 -9999 0 -0.86 1 1
ITGA4 -0.01 0.14 -9999 0 -0.74 30 30
alpha4/beta7 Integrin/MAdCAM1 -0.04 0.12 -9999 0 -0.84 1 1
EPO -0.15 0.31 -9999 0 -0.74 195 195
alpha4/beta7 Integrin -0.019 0.1 -9999 0 -0.55 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.1 -9999 0 -0.55 30 30
EPO/EPOR (dimer) -0.12 0.23 -9999 0 -0.55 195 195
lamellipodium assembly 0.003 0.015 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
JAK2 -0.068 0.12 -9999 0 -0.54 13 13
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
MADCAM1 -0.033 0.18 -9999 0 -0.74 54 54
cell adhesion -0.039 0.12 -9999 0 -0.83 1 1
CRKL/CBL -0.001 0.022 -9999 0 -0.66 1 1
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC -0.014 0.17 -9999 0 -0.57 35 35
ITGB7 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.058 0.17 -9999 0 -0.52 99 99
p130Cas/Crk/Dock1 -0.044 0.13 -9999 0 -0.77 6 6
VCAM1 -0.052 0.22 -9999 0 -0.78 75 75
RHOA 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.014 0.076 -9999 0 -10000 0 0
BCAR1 -0.002 0.16 -9999 0 -0.86 6 6
EPOR 0.015 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.029 -9999 0 -0.86 1 1
GIT1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP 0.003 0.015 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.039 0.3 1 -10000 0 1
RFC1 0.011 0.039 0.3 1 -10000 0 1
PRKDC 0.011 0.039 0.3 1 -10000 0 1
RIPK1 0.012 0.005 -10000 0 -10000 0 0
CASP7 -0.013 0.059 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.073 0.14 0.28 18 -10000 0 18
MAP2K4 -0.045 0.14 -10000 0 -0.44 8 8
mol:ceramide -0.082 0.16 -10000 0 -0.45 11 11
GSN 0.011 0.039 0.3 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 -0.096 0.14 0.32 1 -10000 0 1
FAS 0.013 0.03 -10000 0 -0.88 1 1
BID 0.016 0.058 -10000 0 -10000 0 0
MAP3K1 -0.012 0.09 -10000 0 -10000 0 0
MAP3K7 0.013 0.006 -10000 0 -10000 0 0
RB1 0.011 0.039 0.3 1 -10000 0 1
CFLAR 0.012 0.005 -10000 0 -10000 0 0
HGF/MET -0.072 0.2 -10000 0 -0.61 106 106
ARHGDIB 0.01 0.044 0.3 1 -0.41 2 3
FADD 0.014 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.039 -10000 0 -0.3 1 1
NFKB1 -0.056 0.076 -10000 0 -0.76 1 1
MAPK8 -0.059 0.18 -10000 0 -0.65 11 11
DFFA 0.011 0.039 0.3 1 -10000 0 1
DNA fragmentation during apoptosis 0.011 0.039 0.3 1 -10000 0 1
FAS/FADD/MET -0.016 0.086 -10000 0 -0.48 30 30
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.038 0.19 -10000 0 -0.74 63 63
FAF1 0.013 0.03 -10000 0 -0.86 1 1
PARP1 0.011 0.039 0.3 1 -10000 0 1
DFFB 0.011 0.039 0.3 1 -10000 0 1
CHUK -0.045 0.066 -10000 0 -0.7 1 1
FASLG -0.26 0.36 -10000 0 -0.74 320 320
FAS/FADD -0.001 0.023 -10000 0 -0.69 1 1
HGF -0.049 0.22 -10000 0 -0.84 67 67
LMNA 0.01 0.04 -10000 0 -0.42 1 1
CASP6 0.011 0.039 0.3 1 -10000 0 1
CASP10 0.014 0.006 -10000 0 -10000 0 0
CASP3 0.012 0.045 0.37 1 -10000 0 1
PTPN13 -0.01 0.14 -10000 0 -0.86 25 25
CASP8 0.025 0.09 0.35 63 -10000 0 63
IL6 -0.17 0.43 -10000 0 -1.1 146 146
MET -0.01 0.13 -10000 0 -0.74 29 29
ICAD/CAD 0.011 0.039 0.28 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.083 0.16 -10000 0 -0.45 11 11
activation of caspase activity by cytochrome c 0.016 0.058 -10000 0 -10000 0 0
PAK2 0.011 0.039 0.3 1 -10000 0 1
BCL2 0.014 0.029 -10000 0 -0.86 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.029 0.12 -9999 0 -0.76 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.031 0.11 -9999 0 -0.71 12 12
alphaV/beta3 Integrin/Osteopontin/Src -0.015 0.095 -9999 0 -0.62 21 21
AP1 -0.058 0.17 -9999 0 -0.84 21 21
ILK 0.033 0.14 -9999 0 -0.57 37 37
bone resorption -0.045 0.14 -9999 0 -0.82 13 13
PTK2B 0.015 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.028 0.12 -9999 0 -0.89 6 6
ITGAV 0.018 0.039 -9999 0 -0.79 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.035 0.14 -9999 0 -0.57 55 55
alphaV/beta3 Integrin/Osteopontin -0.032 0.14 -9999 0 -0.6 45 45
MAP3K1 0.033 0.14 -9999 0 -0.58 38 38
JUN 0.015 0.003 -9999 0 -10000 0 0
MAPK3 0.043 0.14 -9999 0 -0.77 12 12
MAPK1 0.043 0.14 -9999 0 -0.77 12 12
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
MAPK8 0.042 0.15 -9999 0 -0.74 15 15
ITGB3 -0.009 0.16 -9999 0 -0.84 30 30
NFKBIA 0.053 0.15 -9999 0 -0.77 12 12
FOS -0.043 0.22 -9999 0 -0.86 59 59
CD44 -0.024 0.17 -9999 0 -0.74 46 46
CHUK 0.015 0 -9999 0 -10000 0 0
PLAU 0.017 0.31 -9999 0 -1.1 53 53
NF kappa B1 p50/RelA -0.033 0.11 -9999 0 -0.71 12 12
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
RELA 0.015 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.023 0.12 -9999 0 -0.65 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.028 0.15 -9999 0 -0.57 43 43
VAV3 0.032 0.15 -9999 0 -0.72 14 14
MAP3K14 0.032 0.14 -9999 0 -0.58 38 38
ROCK2 0.006 0.087 -9999 0 -0.86 9 9
SPP1 0.002 0.12 -9999 0 -0.82 19 19
RAC1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.031 0.12 -9999 0 -0.76 9 9
MMP2 0.05 0.18 -9999 0 -0.71 20 20
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.015 0 -9999 0 -10000 0 0
ITGB7 0.015 0 -9999 0 -10000 0 0
ITGA4 -0.01 0.14 -9999 0 -0.74 30 30
alpha4/beta7 Integrin -0.019 0.1 -9999 0 -0.55 30 30
alpha4/beta1 Integrin -0.019 0.1 -9999 0 -0.55 30 30
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.011 0.044 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
AKT2 0.015 0 -10000 0 -10000 0 0
STXBP4 0.014 0.029 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.07 0.11 0.3 107 -0.39 3 110
YWHAZ 0.015 0 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.029 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.019 -10000 0 -0.57 1 1
YWHAG 0.015 0 -10000 0 -10000 0 0
ASIP -0.13 0.29 -10000 0 -0.74 164 164
PRKCI 0.015 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.015 0 -10000 0 -10000 0 0
GYS1 0.042 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.051 -10000 0 -0.86 3 3
TRIP10 0.015 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.035 0.07 -10000 0 -10000 0 0
VAMP2 0.015 0 -10000 0 -10000 0 0
SLC2A4 0.071 0.12 0.3 107 -0.44 3 110
STX4 0.015 0 -10000 0 -10000 0 0
GSK3B 0.033 0 -10000 0 -10000 0 0
SFN -0.15 0.32 -10000 0 -0.76 188 188
LNPEP 0.009 0.071 -10000 0 -0.86 6 6
YWHAE 0.015 0 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.1 0.16 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.077 0.12 -9999 0 -0.8 2 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.013 0.021 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.086 0.09 -9999 0 -0.39 5 5
CaM/Ca2+ -0.091 0.14 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.092 0.15 -9999 0 -0.84 1 1
AKT1 -0.079 0.12 -9999 0 -10000 0 0
MAP2K1 -0.035 0.16 -9999 0 -10000 0 0
MAP3K11 -0.051 0.17 -9999 0 -0.8 1 1
IFNGR1 0.008 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.26 0.28 -9999 0 -0.68 188 188
Rap1/GTP -0.066 0.1 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.11 0.17 -9999 0 -10000 0 0
CEBPB 0 0.16 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.11 0.18 -9999 0 -1.2 7 7
STAT1 -0.05 0.17 -9999 0 -0.85 1 1
CALM1 0.015 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.2 0.34 -9999 0 -0.73 261 261
PIK3CA 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.084 0.14 -9999 0 -0.79 1 1
CEBPB/PTGES2/Cbp/p300 -0.041 0.064 -9999 0 -0.48 1 1
mol:Ca2+ -0.099 0.15 -9999 0 -10000 0 0
MAPK3 -0.014 0.15 -9999 0 -10000 0 0
STAT1 (dimer) -0.11 0.12 -9999 0 -0.68 3 3
MAPK1 -0.014 0.15 -9999 0 -10000 0 0
JAK2 0.008 0.014 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
JAK1 0.008 0.014 -9999 0 -10000 0 0
CAMK2D 0.015 0 -9999 0 -10000 0 0
DAPK1 0.012 0.15 -9999 0 -0.65 22 22
SMAD7 -0.009 0.079 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.081 0.13 -9999 0 -10000 0 0
PI3K -0.087 0.14 -9999 0 -10000 0 0
IFNG -0.2 0.34 -9999 0 -0.73 261 261
apoptosis -0.004 0.12 -9999 0 -0.45 22 22
CAMK2G 0.015 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.28 0.41 -9999 0 -0.86 298 298
CAMK2B -0.13 0.31 -9999 0 -0.79 165 165
FRAP1 -0.023 0.15 -9999 0 -10000 0 0
PRKCD -0.057 0.15 -9999 0 -10000 0 0
RAP1B 0.015 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.086 0.09 -9999 0 -0.39 5 5
PTPN2 0.015 0 -9999 0 -10000 0 0
EP300 0.015 0.029 -9999 0 -0.86 1 1
IRF1 0.011 0.14 -9999 0 -0.79 2 2
STAT1 (dimer)/PIASy -0.084 0.14 -9999 0 -0.8 1 1
SOCS1 -0.005 0.14 -9999 0 -1 14 14
mol:GDP -0.078 0.12 -9999 0 -10000 0 0
CASP1 -0.01 0.082 -9999 0 -0.36 4 4
PTGES2 0.013 0.041 -9999 0 -0.86 2 2
IRF9 0.04 0.062 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.085 0.13 -9999 0 -10000 0 0
RAP1/GDP -0.066 0.1 -9999 0 -10000 0 0
CBL -0.053 0.17 -9999 0 -10000 0 0
MAP3K1 -0.05 0.17 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.086 0.09 -9999 0 -0.39 5 5
PTPN11 -0.065 0.18 -9999 0 -10000 0 0
CREBBP 0.016 0.001 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.051 -9999 0 -0.86 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.015 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.037 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.015 0 -9999 0 -10000 0 0
IKBKG 0.015 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.16 0.29 -9999 0 -0.65 225 225
IL1A -0.021 0.16 -9999 0 -0.74 41 41
IL1B 0.013 0.1 -9999 0 -0.6 23 23
IRAK/TRAF6/p62/Atypical PKCs -0.004 0.04 -9999 0 -10000 0 0
IL1R2 -0.17 0.35 -9999 0 -0.84 192 192
IL1R1 0.012 0.051 -9999 0 -0.86 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.036 -9999 0 -10000 0 0
TOLLIP 0.015 0 -9999 0 -10000 0 0
TICAM2 0.014 0.029 -9999 0 -0.86 1 1
MAP3K3 0.015 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.033 0.044 -9999 0 -10000 0 0
JUN 0.054 0.052 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.015 0.077 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.025 0.1 -9999 0 -0.53 4 4
PIK3R1 0.015 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.092 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.017 0.088 -9999 0 -0.52 14 14
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
MAPK8 0.045 0.056 -9999 0 -10000 0 0
IRAK1 0.029 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.025 0.12 -9999 0 -0.61 37 37
IRAK4 0.015 0 -9999 0 -10000 0 0
PRKCI 0.015 0 -9999 0 -10000 0 0
TRAF6 0.015 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.043 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.017 0.088 -9999 0 -0.52 14 14
IL1 beta/IL1R2 -0.13 0.24 -9999 0 -0.57 210 210
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.072 -9999 0 -0.85 1 1
IRAK3 0.013 0.036 -9999 0 -0.74 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.015 0.081 -9999 0 -0.94 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.013 0.054 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.027 0.11 -9999 0 -0.48 51 51
RELA 0.015 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.009 0.066 -9999 0 -0.74 7 7
MYD88 0.015 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.009 0.068 -9999 0 -0.75 7 7
UBE2N 0.015 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.012 0.065 -9999 0 -0.75 1 1
CASP1 0.012 0.05 -9999 0 -0.74 4 4
IL1RN/IL1R2 -0.16 0.29 -9999 0 -0.66 220 220
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.016 0.081 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.006 0.007 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.009 0.04 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
IL1RN -0.017 0.15 -9999 0 -0.76 36 36
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.04 0.037 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.091 0.42 -9999 0 -1.2 100 100
MKNK1 0.015 0 -9999 0 -10000 0 0
MAPK14 -0.006 0.12 -9999 0 -0.47 10 10
ATF2/c-Jun 0.021 0.096 -9999 0 -0.56 1 1
MAPK11 -0.006 0.12 -9999 0 -0.49 11 11
MITF 0.007 0.14 -9999 0 -0.57 12 12
MAPKAPK5 0.008 0.14 -9999 0 -0.6 10 10
KRT8 0.005 0.15 -9999 0 -0.61 13 13
MAPKAPK3 0.015 0 -9999 0 -10000 0 0
MAPKAPK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.011 0.18 -9999 0 -0.79 11 11
CEBPB -0.002 0.16 -9999 0 -0.64 14 14
SLC9A1 0.008 0.14 -9999 0 -0.6 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.016 0.14 -9999 0 -0.61 11 11
p38alpha-beta/MNK1 -0.048 0.12 -9999 0 -0.68 10 10
JUN 0.021 0.095 -9999 0 -0.56 1 1
PPARGC1A -0.021 0.18 -9999 0 -0.48 63 63
USF1 0.008 0.14 -9999 0 -0.6 10 10
RAB5/GDP/GDI1 -0.033 0.087 -9999 0 -0.46 10 10
NOS2 -0.021 0.27 -9999 0 -1.2 34 34
DDIT3 -0.001 0.16 -9999 0 -0.64 13 13
RAB5A 0.015 0 -9999 0 -10000 0 0
HSPB1 0.015 0.13 -9999 0 -0.56 18 18
p38alpha-beta/HBP1 -0.048 0.12 -9999 0 -0.68 10 10
CREB1 0.011 0.15 -9999 0 -0.64 11 11
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.016 0.13 -9999 0 -0.61 10 10
RPS6KA4 0.008 0.14 -9999 0 -0.6 10 10
PLA2G4A 0.002 0.17 -9999 0 -0.72 30 30
GDI1 0.008 0.14 -9999 0 -0.6 10 10
TP53 0.002 0.18 -9999 0 -0.78 10 10
RPS6KA5 0.005 0.15 -9999 0 -0.66 13 13
ESR1 -0.012 0.2 -9999 0 -0.67 39 39
HBP1 0.015 0 -9999 0 -10000 0 0
MEF2C 0.007 0.14 -9999 0 -0.6 10 10
MEF2A 0.008 0.14 -9999 0 -0.6 10 10
EIF4EBP1 0.007 0.15 -9999 0 -0.64 12 12
KRT19 -0.093 0.25 -9999 0 -0.5 172 172
ELK4 0.008 0.14 -9999 0 -0.6 10 10
ATF6 0.008 0.14 -9999 0 -0.6 10 10
ATF1 0.011 0.15 -9999 0 -0.64 11 11
p38alpha-beta/MAPKAPK2 -0.048 0.12 -9999 0 -0.68 10 10
p38alpha-beta/MAPKAPK3 -0.048 0.12 -9999 0 -0.68 10 10
TCGA08_rtk_signaling

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
PDGFRA -0.33 0.43 -9999 0 -0.86 352 352
HRAS 0.014 0.025 -9999 0 -0.74 1 1
EGFR 0.002 0.099 -9999 0 -0.75 15 15
AKT 0.032 0.032 -9999 0 -0.43 1 1
FOXO3 0.015 0 -9999 0 -10000 0 0
AKT1 0.015 0 -9999 0 -10000 0 0
FOXO1 0.015 0 -9999 0 -10000 0 0
AKT3 0.014 0.029 -9999 0 -0.86 1 1
FOXO4 0.015 0 -9999 0 -10000 0 0
MET -0.01 0.13 -9999 0 -0.74 29 29
PIK3CA 0.015 0 -9999 0 -10000 0 0
PIK3CB 0.014 0.025 -9999 0 -0.74 1 1
NRAS 0.015 0 -9999 0 -10000 0 0
PIK3CG 0.002 0.1 -9999 0 -0.79 14 14
PIK3R3 0.014 0.029 -9999 0 -0.86 1 1
PIK3R2 0.015 0 -9999 0 -10000 0 0
NF1 0.015 0 -9999 0 -10000 0 0
RAS -0.053 0.11 -9999 0 -0.36 15 15
ERBB2 0.014 0.029 -9999 0 -0.86 1 1
proliferation/survival/translation -0.037 0.019 -9999 0 -10000 0 0
PI3K -0.033 0.099 -9999 0 -0.28 21 21
PIK3R1 0.015 0 -9999 0 -10000 0 0
KRAS 0.015 0 -9999 0 -10000 0 0
FOXO 0.037 0.033 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
PTEN 0.015 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.003 0.034 -9999 0 -10000 0 0
DAPP1 0.024 0.11 -9999 0 -0.54 18 18
Src family/SYK family/BLNK-LAT/BTK-ITK -0.069 0.22 -9999 0 -0.67 71 71
mol:DAG -0.031 0.13 -9999 0 -0.31 56 56
HRAS 0.015 0.025 -9999 0 -0.73 1 1
RAP1A 0.016 0.002 -9999 0 -10000 0 0
ARF5/GDP 0.025 0.062 -9999 0 -0.34 1 1
PLCG2 -0.025 0.18 -9999 0 -0.79 44 44
PLCG1 0.015 0 -9999 0 -10000 0 0
ARF5 0.015 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.037 -9999 0 -0.43 6 6
ARF1/GTP -0.003 0.035 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.003 0.037 -9999 0 -0.42 6 6
ADAP1 -0.006 0.048 -9999 0 -10000 0 0
ARAP3 -0.003 0.037 -9999 0 -0.43 6 6
INPPL1 0.015 0 -9999 0 -10000 0 0
PREX1 0.013 0.041 -9999 0 -0.86 2 2
ARHGEF6 0.015 0 -9999 0 -10000 0 0
ARHGEF7 0.015 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
NRAS 0.016 0.002 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
FGR 0.006 0.084 -9999 0 -0.75 11 11
mol:Ca2+ -0.003 0.069 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.029 -9999 0 -0.86 1 1
ZAP70 -0.24 0.36 -9999 0 -0.74 301 301
mol:IP3 -0.009 0.093 -9999 0 -10000 0 0
LYN 0.014 0.029 -9999 0 -0.86 1 1
ARF1/GDP 0.025 0.062 -9999 0 -0.34 1 1
RhoA/GDP -0.004 0.033 -9999 0 -0.46 1 1
PDK1/Src/Hsp90 -0.001 0.016 -9999 0 -0.47 1 1
BLNK 0.002 0.1 -9999 0 -0.86 13 13
actin cytoskeleton reorganization 0.048 0.077 -9999 0 -0.49 2 2
SRC 0.014 0.025 -9999 0 -0.74 1 1
PLEKHA2 0.033 0.056 -9999 0 -0.47 11 11
RAC1 0.015 0 -9999 0 -10000 0 0
PTEN 0 0.004 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.003 0.034 -9999 0 -10000 0 0
RhoA/GTP -0.003 0.034 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.12 0.19 -9999 0 -0.63 70 70
BLK -0.027 0.17 -9999 0 -0.74 48 48
PDPK1 0.015 0 -9999 0 -10000 0 0
CYTH1 -0.003 0.034 -9999 0 -10000 0 0
HCK -0.04 0.2 -9999 0 -0.74 65 65
CYTH3 -0.003 0.034 -9999 0 -10000 0 0
CYTH2 -0.003 0.034 -9999 0 -10000 0 0
KRAS 0.016 0.002 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.004 0.04 -9999 0 -0.54 4 4
SGK1 -0.004 0.044 -9999 0 -0.6 4 4
INPP5D 0.006 0.083 -9999 0 -0.74 11 11
mol:GDP 0.016 0.066 -9999 0 -0.34 2 2
SOS1 0.015 0 -9999 0 -10000 0 0
SYK 0.01 0.065 -9999 0 -0.86 5 5
ARF6/GDP -0.004 0.033 -9999 0 -0.46 1 1
mol:PI-3-4-5-P3 -0.003 0.037 -9999 0 -0.43 6 6
ARAP3/RAP1A/GTP -0.003 0.037 -9999 0 -0.43 6 6
VAV1 -0.15 0.31 -9999 0 -0.74 193 193
mol:PI-3-4-P2 0.022 0.064 -9999 0 -0.55 11 11
RAS family/GTP/PI3K Class I -0.003 0.037 -9999 0 -0.43 6 6
PLEKHA1 0.033 0.056 -9999 0 -0.47 11 11
Rac1/GDP 0.025 0.062 -9999 0 -0.34 1 1
LAT -0.12 0.29 -9999 0 -0.74 161 161
Rac1/GTP 0.009 0.088 -9999 0 -0.72 1 1
ITK -0.076 0.15 -9999 0 -0.45 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.053 0.18 -9999 0 -0.45 56 56
LCK -0.023 0.17 -9999 0 -0.76 44 44
BTK -0.093 0.16 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.018 0.098 -9999 0 -0.55 29 29
CRKL 0.023 0.094 -9999 0 -0.43 12 12
mol:PIP3 -0.028 0.005 -9999 0 -10000 0 0
AKT1 0.001 0.003 -9999 0 -10000 0 0
PTK2B 0.015 0 -9999 0 -10000 0 0
RAPGEF1 0.032 0.09 -9999 0 -0.44 7 7
RANBP10 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.056 0.18 -9999 0 -0.6 84 84
MAP3K5 -0.002 0.11 -9999 0 -0.42 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.052 0.17 -9999 0 -0.6 60 60
AP1 -0.044 0.15 -9999 0 -0.59 59 59
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.025 -9999 0 -0.74 1 1
apoptosis -0.031 0.19 -9999 0 -0.74 58 58
STAT3 (dimer) 0.022 0.11 -9999 0 -0.5 13 13
GAB1/CRKL/SHP2/PI3K -0.02 0.066 -9999 0 -10000 0 0
INPP5D 0.006 0.083 -9999 0 -0.74 11 11
CBL/CRK 0.03 0.093 -9999 0 -0.48 8 8
PTPN11 0.015 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.015 0 -9999 0 -10000 0 0
PTEN 0.015 0 -9999 0 -10000 0 0
ELK1 -0.006 0.048 -9999 0 -0.26 29 29
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.018 0.058 -9999 0 -0.32 12 12
PAK1 0.011 0.003 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.056 0.18 -9999 0 -0.6 84 84
HRAS 0.008 0.14 -9999 0 -0.66 13 13
DOCK1 0.032 0.093 -9999 0 -0.48 8 8
GAB1 0.013 0.099 -9999 0 -0.46 13 13
CRK 0.023 0.094 -9999 0 -0.43 12 12
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.048 0.16 -9999 0 -0.6 60 60
JUN 0.015 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.027 0.088 -9999 0 -0.49 12 12
PIK3R1 0.015 0 -9999 0 -10000 0 0
cell morphogenesis 0.059 0.11 -9999 0 -10000 0 0
GRB2/SHC -0.023 0.077 -9999 0 -0.46 12 12
FOS -0.043 0.22 -9999 0 -0.86 59 59
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.006 0.048 -9999 0 -0.26 29 29
HGF/MET/MUC20 -0.057 0.18 -9999 0 -0.61 84 84
cell migration -0.023 0.076 -9999 0 -0.45 12 12
GRB2 0.015 0 -9999 0 -10000 0 0
CBL 0.014 0.029 -9999 0 -0.86 1 1
MET/RANBP10 -0.018 0.098 -9999 0 -0.55 29 29
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.032 0.1 -9999 0 -0.55 13 13
MET/MUC20 -0.018 0.1 -9999 0 -0.56 29 29
RAP1B 0.041 0.086 -9999 0 -10000 0 0
RAP1A 0.041 0.086 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.056 0.18 -9999 0 -0.6 84 84
RAF1 0.018 0.13 -9999 0 -0.61 13 13
STAT3 -0.029 0.096 -9999 0 -0.51 13 13
cell proliferation 0.029 0.14 -9999 0 -0.63 13 13
RPS6KB1 -0.009 0.029 -9999 0 -10000 0 0
MAPK3 -0.012 0.043 -9999 0 -10000 0 0
MAPK1 -0.012 0.043 -9999 0 -10000 0 0
RANBP9 0.015 0 -9999 0 -10000 0 0
MAPK8 0.024 0.1 -9999 0 -0.57 7 7
SRC 0.022 0.11 -9999 0 -0.55 8 8
PI3K -0.022 0.074 -9999 0 -0.45 7 7
MET/Glomulin -0.002 0.092 -9999 0 -0.5 29 29
SOS1 0.015 0 -9999 0 -10000 0 0
MAP2K1 0.028 0.12 -9999 0 -0.56 13 13
MET -0.01 0.13 -9999 0 -0.74 29 29
MAP4K1 -0.013 0.11 -9999 0 -0.45 12 12
PTK2 0.015 0 -9999 0 -10000 0 0
MAP2K2 0.028 0.12 -9999 0 -0.56 13 13
BAD 0.01 0.022 -9999 0 -0.51 1 1
MAP2K4 0.009 0.1 -9999 0 -0.42 3 3
SHP2/GRB2/SOS1/GAB1 -0.025 0.083 -9999 0 -0.5 12 12
INPPL1 0.015 0 -9999 0 -10000 0 0
PXN 0.015 0 -9999 0 -10000 0 0
SH3KBP1 0.015 0 -9999 0 -10000 0 0
HGS -0.024 0.08 -9999 0 -0.45 12 12
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.049 0.22 -9999 0 -0.84 67 67
RASA1 0.014 0.029 -9999 0 -0.86 1 1
NCK1 0.015 0 -9999 0 -10000 0 0
PTPRJ 0.015 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.024 0.08 -9999 0 -0.45 12 12
PDPK1 -0.012 0.004 -9999 0 -10000 0 0
HGF/MET/SHIP -0.062 0.19 -9999 0 -0.58 95 95
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.05 0.16 -10000 0 -0.57 78 78
cell-cell adhesion 0.028 0.1 0.72 6 -10000 0 6
Ephrin B/EPHB2/RasGAP -0.025 0.11 -10000 0 -0.98 2 2
ITSN1 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
SHC1 0.014 0.025 -10000 0 -0.74 1 1
Ephrin B1/EPHB3 -0.07 0.19 -10000 0 -0.58 107 107
Ephrin B1/EPHB1 -0.013 0.084 -10000 0 -0.54 22 22
HRAS/GDP -0.022 0.085 -10000 0 -0.64 2 2
Ephrin B/EPHB1/GRB7 -0.035 0.12 -10000 0 -0.5 45 45
Endophilin/SYNJ1 0.023 0.11 -10000 0 -0.89 2 2
KRAS 0.015 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.03 0.11 -10000 0 -0.89 1 1
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
GRB7 0.005 0.092 -10000 0 -0.86 10 10
PAK1 0.033 0.12 -10000 0 -0.91 2 2
HRAS 0.014 0.025 -10000 0 -0.74 1 1
RRAS 0.023 0.11 -10000 0 -0.92 2 2
DNM1 -0.096 0.27 -10000 0 -0.74 131 131
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.019 0.12 -10000 0 -0.84 1 1
lamellipodium assembly -0.028 0.1 -10000 0 -0.72 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.016 0.064 -10000 0 -0.51 1 1
PIK3R1 0.015 0 -10000 0 -10000 0 0
EPHB2 0.003 0.099 -10000 0 -0.81 13 13
EPHB3 -0.09 0.28 -10000 0 -0.86 107 107
EPHB1 -0.005 0.13 -10000 0 -0.8 22 22
EPHB4 0.015 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.11 -10000 0 -0.61 2 2
Ephrin B/EPHB2 -0.025 0.11 -10000 0 -0.53 29 29
Ephrin B/EPHB3 -0.078 0.2 -10000 0 -0.55 119 119
JNK cascade 0.032 0.1 -10000 0 -0.86 4 4
Ephrin B/EPHB1 -0.03 0.12 -10000 0 -0.5 35 35
RAP1/GDP 0.003 0.097 -10000 0 -0.6 1 1
EFNB2 0.015 0 -10000 0 -10000 0 0
EFNB3 -0.019 0.16 -10000 0 -0.81 36 36
EFNB1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.019 0.1 -10000 0 -0.53 32 32
RAP1B 0.015 0 -10000 0 -10000 0 0
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.03 0.11 -10000 0 -0.79 6 6
Rap1/GTP -0.028 0.1 -10000 0 -0.74 6 6
axon guidance -0.05 0.16 -10000 0 -0.57 78 78
MAPK3 0.05 0.069 -10000 0 -10000 0 0
MAPK1 0.05 0.069 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.1 -10000 0 -0.64 1 1
actin cytoskeleton reorganization -0.02 0.075 -10000 0 -0.52 7 7
CDC42/GDP 0.002 0.1 -10000 0 -0.64 1 1
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.048 0.22 -10000 0 -0.85 65 65
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.016 0.072 -10000 0 -0.68 2 2
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.1 -10000 0 -0.7 7 7
PTK2 0.004 0.021 -10000 0 -10000 0 0
MAP4K4 0.032 0.11 -10000 0 -0.88 4 4
SRC 0.014 0.025 -10000 0 -0.74 1 1
KALRN 0.014 0.029 -10000 0 -0.86 1 1
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.081 -10000 0 -0.56 5 5
MAP2K1 0.042 0.073 -10000 0 -0.48 1 1
WASL 0.015 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.019 0.1 -10000 0 -0.59 19 19
cell migration 0.054 0.081 -10000 0 -0.54 1 1
NRAS 0.015 0 -10000 0 -10000 0 0
SYNJ1 0.023 0.12 -10000 0 -0.92 2 2
PXN 0.015 0 -10000 0 -10000 0 0
TF -0.03 0.18 -10000 0 -0.81 5 5
HRAS/GTP -0.031 0.12 -10000 0 -0.79 7 7
Ephrin B1/EPHB1-2 -0.019 0.1 -10000 0 -0.53 32 32
cell adhesion mediated by integrin 0.038 0.12 0.54 36 -10000 0 36
RAC1 0.015 0 -10000 0 -10000 0 0
mol:GTP -0.033 0.12 -10000 0 -0.86 6 6
RAC1-CDC42/GTP -0.074 0.18 -10000 0 -0.77 29 29
RASA1 0.014 0.029 -10000 0 -0.86 1 1
RAC1-CDC42/GDP 0.003 0.097 -10000 0 -0.6 1 1
ruffle organization 0.049 0.13 -10000 0 -0.74 6 6
NCK1 0.015 0 -10000 0 -10000 0 0
receptor internalization -0.027 0.19 -10000 0 -0.81 11 11
Ephrin B/EPHB2/KALRN -0.025 0.11 -10000 0 -0.98 2 2
ROCK1 -0.034 0.18 -10000 0 -0.52 107 107
RAS family/GDP -0.019 0.073 -10000 0 -0.53 5 5
Rac1/GTP -0.03 0.11 -10000 0 -0.79 6 6
Ephrin B/EPHB1/Src/Paxillin -0.019 0.074 -10000 0 -0.58 1 1
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.02 0.17 -9999 0 -0.83 37 37
CDC42/GTP -0.019 0.066 -9999 0 -10000 0 0
PLCG1 0.03 0.083 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.019 0.065 -9999 0 -10000 0 0
S1PR5 -0.093 0.26 -9999 0 -0.74 127 127
S1PR4 -0.008 0.13 -9999 0 -0.74 27 27
MAPK3 0.03 0.083 -9999 0 -10000 0 0
MAPK1 0.03 0.083 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.048 0.1 -9999 0 -0.34 32 32
GNAI1 0.01 0.065 -9999 0 -0.86 5 5
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.069 0.17 -9999 0 -0.48 127 127
RHOA 0.028 0.075 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.022 0.076 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.051 -9999 0 -0.86 3 3
S1P/S1P4/G12/G13 -0.013 0.074 -9999 0 -0.43 27 27
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.015 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.051 0.14 -9999 0 -0.64 2 2
Syndecan-3/Neurocan -0.018 0.081 -9999 0 -0.39 37 37
POMC 0.006 0.086 -9999 0 -0.84 9 9
EGFR 0.002 0.099 -9999 0 -0.75 15 15
Syndecan-3/EGFR -0.008 0.056 -9999 0 -0.41 15 15
AGRP 0.008 0.036 -9999 0 -0.74 2 2
NCSTN 0.015 0 -9999 0 -10000 0 0
PSENEN 0.015 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0.041 -9999 0 -0.86 2 2
APH1A 0.015 0 -9999 0 -10000 0 0
NCAN -0.021 0.15 -9999 0 -0.74 37 37
long-term memory -0.001 0.019 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.12 -9999 0 -0.42 79 79
PSEN1 0.015 0 -9999 0 -10000 0 0
Src/Cortactin -0.001 0.018 -9999 0 -0.55 1 1
FYN 0.015 0 -9999 0 -10000 0 0
limb bud formation -0.002 0.023 -9999 0 -0.33 4 4
MC4R -0.003 0.074 -9999 0 -0.74 9 9
SRC 0.014 0.025 -9999 0 -0.74 1 1
PTN -0.083 0.27 -9999 0 -0.85 101 101
FGFR/FGF/Syndecan-3 -0.002 0.023 -9999 0 -0.34 4 4
neuron projection morphogenesis -0.063 0.15 -9999 0 -0.73 9 9
Syndecan-3/AgRP -0.002 0.028 -9999 0 -0.39 2 2
Syndecan-3/AgRP/MC4R -0.006 0.046 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.002 0.023 -9999 0 -0.34 4 4
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.038 0.12 -9999 0 -0.41 79 79
IL8 -0.055 0.22 -9999 0 -0.77 79 79
Syndecan-3/Fyn/Cortactin -0.001 0.02 -9999 0 -10000 0 0
Syndecan-3/CASK -0.002 0.022 -9999 0 -0.32 4 4
alpha-MSH/MC4R -0.012 0.086 -9999 0 -0.6 18 18
Gamma Secretase -0.001 0.023 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.031 0.13 -9999 0 -0.58 48 48
KLHL20 -0.016 0.049 -9999 0 -0.34 2 2
CYFIP2 0.004 0.096 -9999 0 -0.86 11 11
Rac1/GDP 0.056 0.097 -9999 0 -10000 0 0
ENAH -0.031 0.13 -9999 0 -0.58 48 48
AP1M1 0.015 0 -9999 0 -10000 0 0
RAP1B 0.015 0 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.016 0.065 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.012 0.038 -9999 0 -0.24 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.028 0.12 -9999 0 -0.52 48 48
RAPGEF1 0.041 0.12 -9999 0 -0.48 48 48
CTNND1 0.015 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.14 -9999 0 -0.61 48 48
CRK 0.029 0.14 -9999 0 -0.53 48 48
E-cadherin/gamma catenin/alpha catenin -0.033 0.14 -9999 0 -0.58 50 50
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.015 0 -9999 0 -10000 0 0
NCKAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.031 0.13 -9999 0 -0.58 48 48
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.046 -9999 0 -10000 0 0
MLLT4 0.015 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.003 0.034 -9999 0 -0.45 5 5
PI3K -0.014 0.06 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.038 0.16 -9999 0 -0.67 50 50
TIAM1 0.014 0.029 -9999 0 -0.86 1 1
E-cadherin(dimer)/Ca2+ -0.027 0.11 -9999 0 -0.49 48 48
AKT1 -0.008 0.033 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
CDH1 -0.033 0.2 -9999 0 -0.86 48 48
RhoA/GDP 0.056 0.097 -9999 0 -10000 0 0
actin cytoskeleton organization -0.012 0.036 -9999 0 -0.24 2 2
CDC42/GDP 0.056 0.097 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.02 0.083 -9999 0 -0.36 50 50
ITGB7 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.12 -9999 0 -0.52 48 48
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.11 -9999 0 -0.5 48 48
mol:GDP 0.051 0.11 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.012 0.051 -9999 0 -0.86 3 3
p120 catenin/RhoA/GDP -0.019 0.08 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.031 0.063 -9999 0 -0.24 36 36
NME1 0.012 0.05 -9999 0 -0.74 4 4
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.031 0.13 -9999 0 -0.58 48 48
regulation of cell-cell adhesion -0.014 0.057 -9999 0 -10000 0 0
WASF2 -0.006 0.019 -9999 0 -10000 0 0
Rap1/GTP -0.018 0.075 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.028 0.12 -9999 0 -0.98 1 1
CCND1 -0.017 0.062 -9999 0 -0.3 36 36
VAV2 0.036 0.13 -9999 0 -0.51 48 48
RAP1/GDP -0.018 0.076 -9999 0 -10000 0 0
adherens junction assembly 0.019 0.14 -9999 0 -0.56 48 48
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.015 0 -9999 0 -10000 0 0
PIP5K1C 0.015 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.026 0.11 -9999 0 -0.93 1 1
E-cadherin/beta catenin -0.028 0.12 -9999 0 -0.51 48 48
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.032 0.13 -9999 0 -0.58 48 48
PIK3CA 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.025 0.079 -9999 0 -0.63 2 2
E-cadherin/beta catenin/alpha catenin -0.031 0.13 -9999 0 -0.57 48 48
ITGAE 0.015 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.034 0.14 -9999 0 -0.62 48 48
BARD1 signaling events

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
BARD1/CSTF1 -0.012 0.088 -10000 0 -0.66 16 16
ATM 0.014 0.029 -10000 0 -0.86 1 1
UBE2D3 0.015 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
ATR 0.015 0 -10000 0 -10000 0 0
UBE2L3 0.015 0 -10000 0 -10000 0 0
FANCD2 0.031 0.026 -10000 0 -0.35 4 4
protein ubiquitination -0.02 0.091 -10000 0 -0.48 17 17
XRCC5 0.015 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
M/R/N Complex -0.001 0.019 -10000 0 -0.57 1 1
MRE11A 0.015 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.031 0.059 -10000 0 -0.42 1 1
FANCF 0.015 0 -10000 0 -10000 0 0
BRCA1 0.012 0.05 -10000 0 -0.74 4 4
CCNE1 -0.004 0.12 -10000 0 -0.74 22 22
CDK2/Cyclin E1 -0.014 0.086 -10000 0 -0.55 22 22
FANCG 0.015 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.014 0.095 -10000 0 -0.64 20 20
FANCE 0.014 0.025 -10000 0 -0.74 1 1
FANCC 0.015 0 -10000 0 -10000 0 0
NBN 0.015 0 -10000 0 -10000 0 0
FANCA -0.16 0.32 -10000 0 -0.74 208 208
DNA repair 0.03 0.15 -10000 0 -0.57 23 23
BRCA1/BARD1/ubiquitin -0.014 0.095 -10000 0 -0.64 20 20
BARD1/DNA-PK -0.009 0.069 -10000 0 -0.52 16 16
FANCL 0.015 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.012 0.088 0.66 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex -0.008 0.054 -10000 0 -0.9 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.012 0.082 -10000 0 -0.55 20 20
BRCA1/BARD1/P53 -0.011 0.074 -10000 0 -0.52 16 16
BARD1/CSTF1/BRCA1 -0.012 0.082 -10000 0 -0.55 20 20
BRCA1/BACH1 0.012 0.05 -10000 0 -0.74 4 4
BARD1 -0.001 0.12 -10000 0 -0.86 16 16
PCNA 0.015 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.012 0.082 -10000 0 -0.55 20 20
BRCA1/BARD1/UbcH7 -0.012 0.082 -10000 0 -0.55 20 20
BRCA1/BARD1/RAD51/PCNA -0.03 0.12 -10000 0 -0.47 56 56
BARD1/DNA-PK/P53 -0.009 0.064 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.014 0.095 -10000 0 -0.64 20 20
BRCA1/BARD1/CTIP -0.013 0.083 -10000 0 -0.52 22 22
FA complex -0.051 0.093 -10000 0 -0.46 1 1
BARD1/EWS -0.012 0.088 -10000 0 -0.66 16 16
RBBP8 0.027 0.047 -10000 0 -0.93 2 2
TP53 0.015 0 -10000 0 -10000 0 0
TOPBP1 0.015 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.011 0.074 0.52 16 -10000 0 16
BRCA1/BARD1 -0.021 0.092 -10000 0 -0.48 17 17
CSTF1 0.015 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.012 0.089 -10000 0 -0.67 16 16
CDK2 0.015 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.018 0.15 -10000 0 -0.74 39 39
RAD50 0.014 0.029 -10000 0 -0.86 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.014 0.095 -10000 0 -0.64 20 20
EWSR1 0.015 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.004 0.12 -10000 0 -0.74 22 22
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.007 0.082 -10000 0 -0.86 8 8
CDKN1A 0.03 0.053 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.01 0.073 -10000 0 -0.55 16 16
mol:Ca2+ -0.055 0.19 0.35 14 -0.62 86 100
AGT -0.064 0.24 -10000 0 -0.8 86 86
CCNA2 -0.056 0.21 -10000 0 -0.86 11 11
TUBA1B 0.014 0.025 -10000 0 -0.74 1 1
EGR1 -0.006 0.16 -10000 0 -0.65 48 48
CDK2/Cyclin E1 -0.018 0.069 -10000 0 -0.55 3 3
MAPK3 0.02 0.075 -10000 0 -0.55 15 15
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.075 -10000 0 -0.55 15 15
PTP4A1 0.019 0.13 -10000 0 -10000 0 0
PTP4A3 0.002 0.097 -10000 0 -0.74 15 15
PTP4A2 0.015 0 -10000 0 -10000 0 0
ITGB1 0.02 0.075 -10000 0 -0.55 15 15
SRC 0.014 0.025 -10000 0 -0.74 1 1
RAC1 0.027 0.061 -10000 0 -0.46 1 1
Rab GGTase beta/Rab GGTase alpha -0.001 0.031 -10000 0 -0.66 2 2
PRL-1/ATF-5 0.022 0.12 -10000 0 -0.87 1 1
RABGGTA 0.013 0.041 -10000 0 -0.86 2 2
BCAR1 0.005 0.051 0.35 15 -0.68 1 16
RHOC 0.027 0.061 -10000 0 -0.46 1 1
RHOA 0.027 0.061 -10000 0 -0.46 1 1
cell motility 0.032 0.064 -10000 0 -0.46 1 1
PRL-1/alpha Tubulin 0.024 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.015 0.094 -10000 0 -0.59 23 23
ROCK1 0.032 0.065 -10000 0 -0.47 1 1
RABGGTB 0.015 0 -10000 0 -10000 0 0
CDK2 0.015 0 -10000 0 -10000 0 0
mitosis 0.019 0.12 -10000 0 -10000 0 0
ATF5 0.012 0.05 -10000 0 -0.74 4 4
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0.014 0.029 -9999 0 -0.86 1 1
MAP2K3 0.031 0.048 -9999 0 -0.35 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.042 0.047 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.023 0.16 -9999 0 -0.74 44 44
TXN 0.011 0.012 -9999 0 -0.34 1 1
CALM1 0.015 0 -9999 0 -10000 0 0
GADD45A 0.015 0 -9999 0 -10000 0 0
GADD45B 0.014 0.029 -9999 0 -0.86 1 1
MAP3K1 0.015 0 -9999 0 -10000 0 0
MAP3K6 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
MAP3K4 0.014 0.029 -9999 0 -0.86 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0.006 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.015 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.005 0.016 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.13 0.31 -9999 0 -0.79 165 165
CCM2 0.015 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.097 0.2 -9999 0 -0.52 165 165
MAPK11 0.014 0.025 -9999 0 -0.74 1 1
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.088 0.18 -9999 0 -0.47 165 165
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.013 0.064 -9999 0 -0.46 16 16
TAOK2 0.021 0.016 -9999 0 -0.46 1 1
TAOK3 0.021 0.016 -9999 0 -0.46 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.015 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
MAP3K10 0.014 0.029 -9999 0 -0.86 1 1
MAP3K3 0.015 0 -9999 0 -10000 0 0
TRX/ASK1 0 0.009 -9999 0 -0.28 1 1
GADD45/MTK1/MTK1 -0.021 0.091 -9999 0 -0.49 5 5
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.001 0.048 -9999 0 -0.61 5 5
VDR 0.01 0.065 -9999 0 -0.86 5 5
FAM120B 0.015 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.067 0.061 -9999 0 -0.46 2 2
RXRs/LXRs/DNA/Oxysterols 0.075 0.077 -9999 0 -0.5 2 2
MED1 0.015 0 -9999 0 -10000 0 0
mol:9cRA 0.007 0.01 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.015 0.069 -9999 0 -10000 0 0
RXRs/NUR77 -0.077 0.2 -9999 0 -0.52 142 142
RXRs/PPAR 0.052 0.034 -9999 0 -10000 0 0
NCOR2 0.015 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.004 0.05 -9999 0 -0.67 5 5
RARs/VDR/DNA/Vit D3 -0.004 0.046 -9999 0 -0.49 7 7
RARA 0.015 0 -9999 0 -10000 0 0
NCOA1 0.015 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.01 0.065 -9999 0 -0.86 5 5
RARs/RARs/DNA/9cRA -0.002 0.028 -9999 0 -0.47 3 3
RARG 0.014 0.025 -9999 0 -0.74 1 1
RPS6KB1 0.002 0.028 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.015 0.069 -9999 0 -10000 0 0
THRA 0.014 0.029 -9999 0 -0.86 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.004 0.05 -9999 0 -0.67 5 5
RXRs/PPAR/9cRA/PGJ2/DNA -0.007 0.052 -9999 0 -0.54 1 1
NR1H4 -0.047 0.22 -9999 0 -0.86 63 63
RXRs/LXRs/DNA 0.016 0.064 -9999 0 -0.6 1 1
NR1H2 0.022 0.031 -9999 0 -0.88 1 1
NR1H3 0.023 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.008 0.057 -9999 0 -0.48 6 6
NR4A1 -0.12 0.32 -9999 0 -0.86 141 141
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.019 0.11 -9999 0 -0.35 61 61
RXRG 0.008 0.083 -9999 0 -0.73 11 11
RXR alpha/CCPG 0 0.003 -9999 0 -10000 0 0
RXRA 0.023 0.006 -9999 0 -10000 0 0
RXRB 0.023 0.007 -9999 0 -10000 0 0
THRB -0.021 0.17 -9999 0 -0.86 37 37
PPARG 0.014 0.025 -9999 0 -0.74 1 1
PPARD 0.015 0 -9999 0 -10000 0 0
TNF 0.068 0.15 -9999 0 -0.75 25 25
mol:Oxysterols 0.008 0.009 -9999 0 -10000 0 0
cholesterol transport 0.075 0.077 -9999 0 -0.5 2 2
PPARA 0.015 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0.041 -9999 0 -0.86 2 2
RXRs/NUR77/BCL2 -0.057 0.13 -9999 0 -0.4 7 7
SREBF1 0.081 0.08 -9999 0 -0.74 1 1
RXRs/RXRs/DNA/9cRA 0.008 0.059 -9999 0 -0.54 1 1
ABCA1 0.079 0.088 -9999 0 -0.59 7 7
RARs/THRs -0.022 0.1 -9999 0 -10000 0 0
RXRs/FXR -0.026 0.15 -9999 0 -0.54 62 62
BCL2 0.014 0.029 -9999 0 -0.86 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.071 0.15 -9999 0 -0.51 30 30
PDGFB-D/PDGFRB/SLAP -0.039 0.15 -9999 0 -0.58 60 60
PDGFB-D/PDGFRB/APS/CBL -0.015 0.086 -9999 0 -0.52 25 25
AKT1 -0.006 0.045 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.035 0.17 -9999 0 -0.57 25 25
PIK3CA 0.015 0 -9999 0 -10000 0 0
FGR -0.015 0.079 -9999 0 -0.57 13 13
mol:Ca2+ 0.018 0.092 -9999 0 -0.64 13 13
MYC 0.026 0.13 -9999 0 -0.51 26 26
SHC1 0.014 0.025 -9999 0 -0.74 1 1
HRAS/GDP -0.008 0.063 -9999 0 -0.49 13 13
LRP1/PDGFRB/PDGFB -0.01 0.074 -9999 0 -0.56 16 16
GRB10 0.015 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
GO:0007205 0.018 0.094 -9999 0 -0.66 13 13
PTEN 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
GRB7 0.005 0.092 -9999 0 -0.86 10 10
PDGFB-D/PDGFRB/SHP2 -0.01 0.08 -9999 0 -0.64 14 14
PDGFB-D/PDGFRB/GRB10 -0.01 0.08 -9999 0 -0.64 14 14
cell cycle arrest -0.039 0.15 -9999 0 -0.58 60 60
HRAS 0.014 0.025 -9999 0 -0.74 1 1
HIF1A 0.078 0.055 -9999 0 -10000 0 0
GAB1 0.007 0.11 -9999 0 -0.64 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.008 0.11 -9999 0 -0.6 13 13
PDGFB-D/PDGFRB -0.005 0.072 -9999 0 -0.56 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.01 0.08 -9999 0 -0.64 14 14
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.071 0.14 -9999 0 -0.56 22 22
positive regulation of MAPKKK cascade -0.01 0.08 -9999 0 -0.64 14 14
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.095 -9999 0 -0.66 13 13
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.005 0.008 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.11 -9999 0 -0.68 23 23
SHB 0.015 0 -9999 0 -10000 0 0
BLK -0.025 0.09 -9999 0 -0.55 12 12
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.01 0.08 -9999 0 -0.64 14 14
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
VAV2 0.009 0.12 -9999 0 -0.58 17 17
CBL 0.014 0.029 -9999 0 -0.86 1 1
PDGFB-D/PDGFRB/DEP1 -0.01 0.08 -9999 0 -0.64 14 14
LCK -0.027 0.1 -9999 0 -0.57 20 20
PDGFRB 0 0.11 -9999 0 -0.84 14 14
ACP1 0.015 0 -9999 0 -10000 0 0
HCK -0.031 0.1 -9999 0 -0.6 15 15
ABL1 0.012 0.096 -9999 0 -0.59 13 13
PDGFB-D/PDGFRB/CBL 0.008 0.11 -9999 0 -0.68 13 13
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.015 0 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
STAT1 0.013 0.036 -9999 0 -0.74 2 2
cell proliferation 0.027 0.12 -9999 0 -0.45 31 31
SLA -0.025 0.17 -9999 0 -0.74 47 47
actin cytoskeleton reorganization -0.004 0.056 -9999 0 -10000 0 0
SRC -0.01 0.068 -9999 0 -0.55 12 12
PI3K -0.007 0.051 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.016 0.095 -9999 0 -0.58 24 24
SH2B2 0.007 0.079 -9999 0 -0.74 10 10
PLCgamma1/SPHK1 -0.036 0.18 -9999 0 -0.66 18 18
LYN -0.01 0.072 -9999 0 -0.55 14 14
LRP1 0.015 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
STAT5B 0.015 0 -9999 0 -10000 0 0
STAT5A 0.015 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.007 0.057 -9999 0 -10000 0 0
SPHK1 -0.13 0.3 -9999 0 -0.74 174 174
EDG1 0 0.004 -9999 0 -10000 0 0
mol:DAG 0.018 0.095 -9999 0 -0.66 13 13
PLCG1 0.017 0.097 -9999 0 -0.68 13 13
NHERF/PDGFRB -0.009 0.071 -9999 0 -0.55 15 15
YES1 -0.011 0.068 -9999 0 -0.54 13 13
cell migration -0.009 0.071 -9999 0 -0.55 15 15
SHC/Grb2/SOS1 -0.007 0.056 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.029 -9999 0 -0.86 1 1
SLC9A3R1 0.015 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.008 0.065 -9999 0 -0.51 13 13
FYN -0.01 0.068 -9999 0 -0.55 12 12
DOK1 0.032 0.072 -9999 0 -0.52 12 12
HRAS/GTP -0.001 0.019 -9999 0 -0.56 1 1
PDGFB 0.013 0.041 -9999 0 -0.86 2 2
RAC1 0.022 0.12 -9999 0 -0.54 16 16
PRKCD 0.023 0.085 -9999 0 -0.47 24 24
FER 0.027 0.075 -9999 0 -0.52 15 15
MAPKKK cascade -0.007 0.056 -9999 0 -10000 0 0
RASA1 0.027 0.072 -9999 0 -0.52 13 13
NCK1 0.015 0 -9999 0 -10000 0 0
NCK2 0.015 0 -9999 0 -10000 0 0
p62DOK/Csk 0.003 0.065 -9999 0 -0.47 12 12
PDGFB-D/PDGFRB/SHB -0.01 0.08 -9999 0 -0.64 14 14
chemotaxis 0.013 0.093 -9999 0 -0.57 13 13
STAT1-3-5/STAT1-3-5 -0.007 0.055 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.01 0.082 -9999 0 -0.66 14 14
PTPRJ 0.015 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.036 -10000 0 -0.74 2 2
ANTXR2 0.012 0.048 -10000 0 -0.82 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.007 -10000 0 -0.096 5 5
monocyte activation -0.017 0.12 -10000 0 -0.52 36 36
MAP2K2 -0.001 0.029 -10000 0 -0.86 1 1
MAP2K1 0 0.006 -10000 0 -10000 0 0
MAP2K7 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.003 0.038 -10000 0 -0.5 5 5
CYAA 0.018 0.036 -10000 0 -0.45 5 5
MAP2K4 0 0.006 -10000 0 -10000 0 0
IL1B 0.012 0.072 -10000 0 -0.46 19 19
Channel -0.003 0.036 -10000 0 -0.48 5 5
NLRP1 -0.003 0.035 -10000 0 -0.42 6 6
CALM1 0.015 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.007 0.096 5 -10000 0 5
MAPK3 0 0.006 -10000 0 -10000 0 0
MAPK1 0 0.006 -10000 0 -10000 0 0
PGR -0.09 0.2 -10000 0 -0.52 153 153
PA/Cellular Receptors -0.003 0.039 -10000 0 -0.52 5 5
apoptosis -0.001 0.007 -10000 0 -0.096 5 5
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.033 -10000 0 -0.44 5 5
macrophage activation 0.026 0.007 -10000 0 -10000 0 0
TNF -0.007 0.13 -10000 0 -0.78 25 25
VCAM1 -0.036 0.12 -10000 0 -0.52 36 36
platelet activation -0.001 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.021 0.012 -10000 0 -10000 0 0
IL18 0 0.098 -10000 0 -0.41 46 46
negative regulation of macrophage activation -0.001 0.007 -10000 0 -0.096 5 5
LEF -0.001 0.007 -10000 0 -0.096 5 5
CASP1 -0.002 0.017 -10000 0 -0.2 6 6
mol:cAMP -0.001 0.008 -10000 0 -10000 0 0
necrosis -0.001 0.007 -10000 0 -0.096 5 5
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.003 0.034 -10000 0 -0.46 5 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.033 0.19 -10000 0 -0.75 56 56
CLTC 0.04 0.019 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.035 0.001 -10000 0 -10000 0 0
Dynamin 2/GTP -0.002 0.029 -10000 0 -0.43 4 4
EXOC4 0.015 0 -10000 0 -10000 0 0
CD59 0.037 0.011 -10000 0 -10000 0 0
CPE 0.004 0.099 -10000 0 -0.49 34 34
CTNNB1 0.015 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.04 0.029 -10000 0 -10000 0 0
DNM2 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.042 0.008 -10000 0 -10000 0 0
TSHR -0.022 0.14 -10000 0 -0.48 79 79
INS 0.015 0.015 -10000 0 -0.23 3 3
BIN1 0.012 0.048 -10000 0 -0.82 3 3
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.034 -10000 0 -0.48 4 4
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.029 -10000 0 -0.43 4 4
JUP 0.036 0.021 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.004 0.046 -10000 0 -0.52 7 7
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.02 0.071 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 -0.015 0.15 -10000 0 -0.74 35 35
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.015 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.015 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.011 0.046 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.019 0.093 -10000 0 -0.48 35 35
ACAP1 -0.01 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.03 0.016 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.043 0.018 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.015 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.04 0.029 -10000 0 -10000 0 0
NME1 0.022 0.034 -10000 0 -0.48 4 4
clathrin coat assembly 0.04 0.018 -10000 0 -10000 0 0
IL2RA -0.001 0.086 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.023 0.086 -10000 0 -0.43 6 6
EXOC6 0.015 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.015 0 -10000 0 -10000 0 0
PIP5K1C 0.042 0.008 -10000 0 -10000 0 0
SDC1 0.034 0.031 -10000 0 -10000 0 0
ARF6/GDP -0.002 0.032 -10000 0 -0.48 4 4
EXOC7 0.015 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.011 0.047 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.004 0.045 0.51 7 -10000 0 7
SCAMP2 0.015 0 -10000 0 -10000 0 0
ADRB2 0.038 0.066 -10000 0 -0.46 1 1
EXOC3 0.015 0 -10000 0 -10000 0 0
ASAP2 0.011 0.058 -10000 0 -0.86 4 4
Dynamin 2/GDP -0.002 0.029 -10000 0 -0.43 4 4
KLC1 0.015 0 -10000 0 -10000 0 0
AVPR2 -0.23 0.25 -10000 0 -0.46 481 481
RALA 0.015 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.01 0.04 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.034 0.14 -9999 0 -0.74 10 10
MAP3K8 0.013 0.036 -9999 0 -0.74 2 2
FOS 0.035 0.11 -9999 0 -0.63 9 9
PRKCA 0.016 0.004 -9999 0 -10000 0 0
PTPN7 -0.018 0.16 -9999 0 -0.74 41 41
HRAS 0.013 0.025 -9999 0 -0.74 1 1
PRKCB 0.004 0.098 -9999 0 -0.84 12 12
NRAS 0.014 0.004 -9999 0 -10000 0 0
RAS family/GTP 0 0.014 -9999 0 -0.43 1 1
MAPK3 0.028 0.078 -9999 0 -0.58 5 5
MAP2K1 0.046 0.072 -9999 0 -0.54 11 11
ELK1 0.015 0.005 -9999 0 -10000 0 0
BRAF -0.007 0.059 -9999 0 -0.56 9 9
mol:GTP 0 0.002 -9999 0 -0.006 57 57
MAPK1 0.028 0.078 -9999 0 -0.58 5 5
RAF1 -0.007 0.059 -9999 0 -0.54 10 10
KRAS 0.014 0.004 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.085 0.058 -9999 0 -10000 0 0
ERC1 0.015 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.098 0.21 -9999 0 -0.56 156 156
NFKBIA 0.061 0.019 -9999 0 -10000 0 0
BIRC2 0.015 0 -9999 0 -10000 0 0
IKBKB 0.015 0 -9999 0 -10000 0 0
RIPK2 0.014 0.025 -9999 0 -0.74 1 1
IKBKG -0.028 0.061 -9999 0 -10000 0 0
IKK complex/A20 -0.03 0.073 -9999 0 -0.55 3 3
NEMO/A20/RIP2 0.014 0.025 -9999 0 -0.74 1 1
XPO1 0.015 0 -9999 0 -10000 0 0
NEMO/ATM -0.026 0.057 -9999 0 -0.45 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.02 0.043 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.12 0.29 -9999 0 -0.74 156 156
NFKB1 0.019 0.029 -9999 0 -0.85 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.015 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.029 -9999 0 -0.86 1 1
TNF/TNFR1A -0.016 0.097 -9999 0 -0.59 25 25
TRAF6 0.015 0 -9999 0 -10000 0 0
PRKCA 0.015 0 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
UBE2D3 0.015 0 -9999 0 -10000 0 0
TNF -0.007 0.13 -9999 0 -0.78 25 25
NF kappa B1 p50/RelA -0.001 0.018 -9999 0 -0.55 1 1
BCL10 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.061 0.018 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
IKK complex -0.023 0.049 -9999 0 -10000 0 0
CYLD 0.015 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.02 0.045 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.01 0.064 -9999 0 -0.83 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.015 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.004 0.026 -9999 0 -0.28 1 1
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.015 0 -9999 0 -10000 0 0
FYN 0.015 0 -9999 0 -10000 0 0
MAP3K12 0.013 0.039 -9999 0 -0.8 2 2
FGR 0.006 0.084 -9999 0 -0.75 11 11
p38 alpha/TAB1 -0.012 0.039 -9999 0 -0.29 2 2
PRKG1 -0.077 0.27 -9999 0 -0.86 94 94
DUSP8 0.012 0.046 -9999 0 -0.78 3 3
PGK/cGMP/p38 alpha -0.053 0.13 -9999 0 -0.41 94 94
apoptosis -0.012 0.038 -9999 0 -0.28 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.014 0.029 -9999 0 -0.86 1 1
DUSP1 0.012 0.048 -9999 0 -0.82 3 3
PAK1 0.015 0 -9999 0 -10000 0 0
SRC 0.014 0.025 -9999 0 -0.74 1 1
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.015 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.053 0.083 -9999 0 -0.44 1 1
BLK -0.027 0.17 -9999 0 -0.74 48 48
HCK -0.04 0.2 -9999 0 -0.74 65 65
MAP2K3 0.015 0 -9999 0 -10000 0 0
DUSP16 0.015 0 -9999 0 -10000 0 0
DUSP10 0.005 0.087 -9999 0 -0.74 12 12
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.053 0.066 -9999 0 -0.32 2 2
positive regulation of innate immune response 0.064 0.09 -9999 0 -0.49 1 1
LCK -0.023 0.17 -9999 0 -0.76 44 44
p38alpha-beta/MKP7 0.069 0.086 -9999 0 -0.46 1 1
p38alpha-beta/MKP5 0.064 0.096 -9999 0 -0.46 1 1
PGK/cGMP -0.071 0.21 -9999 0 -0.67 94 94
PAK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.068 0.089 -9999 0 -0.46 1 1
CDC42 0.015 0 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
PAK3 -0.001 0.1 -9999 0 -0.74 17 17
ErbB2/ErbB3 signaling events

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
USP8 0.027 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.089 -10000 0 -0.8 6 6
NFATC4 0.034 0.095 -10000 0 -0.52 5 5
ERBB2IP 0.009 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.015 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.025 0.1 -10000 0 -0.73 4 4
JUN 0.021 0.078 -10000 0 -0.39 5 5
HRAS 0.013 0.025 -10000 0 -0.74 1 1
DOCK7 0.005 0.11 -10000 0 -0.68 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.032 0.13 -10000 0 -0.55 50 50
AKT1 0.015 0.002 -10000 0 -10000 0 0
BAD 0.026 0.027 -10000 0 -0.54 2 2
MAPK10 -0.016 0.06 -10000 0 -0.38 7 7
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.028 0.11 -10000 0 -0.84 4 4
RAF1 0.022 0.1 -10000 0 -0.73 6 6
ErbB2/ErbB3/neuregulin 2 -0.036 0.13 -10000 0 -0.55 33 33
STAT3 0 0.01 -10000 0 -10000 0 0
cell migration 0.048 0.068 -10000 0 -0.31 4 4
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.12 0.23 -10000 0 -0.56 33 33
FOS -0.073 0.2 -10000 0 -0.53 58 58
NRAS 0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.025 0.1 -10000 0 -0.73 4 4
MAPK3 -0.081 0.19 -10000 0 -0.55 15 15
MAPK1 -0.081 0.19 -10000 0 -0.55 15 15
JAK2 0.005 0.11 -10000 0 -0.68 4 4
NF2 -0.001 0.014 -10000 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.11 -10000 0 -0.42 49 49
NRG1 -0.03 0.18 -10000 0 -0.85 39 39
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.099 -10000 0 -0.44 7 7
MAPK9 -0.011 0.046 -10000 0 -0.29 4 4
ERBB2 -0.001 0.023 -10000 0 -0.68 1 1
ERBB3 -0.01 0.12 -10000 0 -0.86 17 17
SHC1 0.006 0.026 -10000 0 -0.74 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
apoptosis 0.002 0.018 0.38 1 -10000 0 1
STAT3 (dimer) 0 0.01 -10000 0 -10000 0 0
RNF41 0.036 0.007 -10000 0 -10000 0 0
FRAP1 0.014 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.016 0.066 -10000 0 -0.44 4 4
ErbB2/ErbB2/HSP90 (dimer) -0.001 0.02 -10000 0 -0.59 1 1
CHRNA1 -0.15 0.25 -10000 0 -0.53 34 34
myelination 0.039 0.093 -10000 0 -0.5 5 5
PPP3CB 0.006 0.1 -10000 0 -0.62 4 4
KRAS 0.014 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.02 0.091 -10000 0 -0.85 5 5
NRG2 -0.028 0.18 -10000 0 -0.75 50 50
mol:GDP -0.006 0.11 -10000 0 -0.42 49 49
SOS1 0.007 0.008 -10000 0 -10000 0 0
MAP2K2 0.027 0.1 -10000 0 -0.7 5 5
SRC 0.014 0.025 -10000 0 -0.74 1 1
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.004 0.11 -10000 0 -0.68 4 4
MAP2K1 -0.065 0.17 -10000 0 -0.55 18 18
heart morphogenesis -0.025 0.1 -10000 0 -0.73 4 4
RAS family/GDP -0.02 0.09 -10000 0 -0.8 6 6
GRB2 0.007 0.008 -10000 0 -10000 0 0
PRKACA -0.002 0.006 -10000 0 -10000 0 0
CHRNE 0.016 0.027 -10000 0 -0.22 5 5
HSP90AA1 0.015 0 -10000 0 -10000 0 0
activation of caspase activity -0.015 0.002 -10000 0 -10000 0 0
nervous system development -0.025 0.1 -10000 0 -0.73 4 4
CDC42 0.015 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.015 0 -10000 0 -10000 0 0
NFATC1 0.069 0.028 -10000 0 -10000 0 0
NFATC2 0.032 0.061 -10000 0 -0.42 3 3
NFATC3 0.024 0.035 -10000 0 -0.55 3 3
YWHAE 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.007 0.11 -10000 0 -0.65 10 10
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.031 0.092 -10000 0 -0.64 12 12
BCL2/BAX -0.001 0.029 -10000 0 -0.61 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX 0.014 0.025 -10000 0 -0.74 1 1
MAPK14 0.013 0.006 -10000 0 -10000 0 0
BAD 0.013 0.039 -10000 0 -0.8 2 2
CABIN1/MEF2D 0.012 0.1 -10000 0 -0.61 10 10
Calcineurin A alpha-beta B1/BCL2 0.014 0.029 -10000 0 -0.86 1 1
FKBP8 0.014 0.029 -10000 0 -0.86 1 1
activation-induced cell death of T cells -0.012 0.099 0.6 10 -10000 0 10
KPNB1 0.015 0 -10000 0 -10000 0 0
KPNA2 0.015 0 -10000 0 -10000 0 0
XPO1 0.013 0.005 -10000 0 -10000 0 0
SFN -0.15 0.32 -10000 0 -0.76 188 188
MAP3K8 0.012 0.036 -10000 0 -0.74 2 2
NFAT4/CK1 alpha -0.001 0.022 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.055 0.12 -10000 0 -0.49 17 17
CABIN1 0.007 0.11 -10000 0 -0.66 10 10
CALM1 0.013 0.006 -10000 0 -10000 0 0
RAN 0.013 0.005 -10000 0 -10000 0 0
MAP3K1 0.015 0 -10000 0 -10000 0 0
CAMK4 0.004 0.095 -10000 0 -0.85 11 11
mol:Ca2+ -0.002 0.008 -10000 0 -10000 0 0
MAPK3 0.015 0 -10000 0 -10000 0 0
YWHAH 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.011 0.085 -10000 0 -0.66 15 15
YWHAB 0.015 0 -10000 0 -10000 0 0
MAPK8 0.006 0.078 -10000 0 -0.86 7 7
MAPK9 0.015 0 -10000 0 -10000 0 0
YWHAG 0.015 0 -10000 0 -10000 0 0
FKBP1A 0.015 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.027 -10000 0 -10000 0 0
PRKCH 0.014 0.029 -10000 0 -0.86 1 1
CABIN1/Cbp/p300 -0.001 0.022 -10000 0 -0.66 1 1
CASP3 0.013 0.006 -10000 0 -10000 0 0
PIM1 0.012 0.044 -10000 0 -0.74 3 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.018 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.082 -10000 0 -0.46 2 2
PRKCB 0.004 0.097 -10000 0 -0.83 12 12
PRKCE 0.014 0.029 -10000 0 -0.86 1 1
JNK2/NFAT4 -0.002 0.029 -10000 0 -0.5 3 3
BAD/BCL-XL -0.001 0.029 -10000 0 -0.61 2 2
PRKCD 0.007 0.079 -10000 0 -0.74 10 10
NUP214 0.013 0.005 -10000 0 -10000 0 0
PRKCZ 0.01 0.051 -10000 0 -0.86 3 3
PRKCA 0.015 0 -10000 0 -10000 0 0
PRKCG -0.076 0.24 -10000 0 -0.74 100 100
PRKCQ -0.037 0.21 -10000 0 -0.86 53 53
FKBP38/BCL2 -0.001 0.031 -10000 0 -0.66 2 2
EP300 0.013 0.03 -10000 0 -0.86 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
NFATc/JNK1 0.063 0.058 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.02 -10000 0 -0.6 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.007 0.064 -10000 0 -0.58 11 11
NFATc/ERK1 0.074 0.026 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.03 0.091 -10000 0 -0.66 11 11
NR4A1 -0.045 0.31 -10000 0 -0.75 141 141
GSK3B 0.013 0.006 -10000 0 -10000 0 0
positive T cell selection 0.024 0.035 -10000 0 -0.55 3 3
NFAT1/CK1 alpha -0.011 0.034 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.015 0 -10000 0 -10000 0 0
PRKACA 0.013 0.006 -10000 0 -10000 0 0
AKAP5 0 0.11 -10000 0 -0.86 15 15
MEF2D 0.014 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.015 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.038 -10000 0 -10000 0 0
CREBBP 0.014 0.006 -10000 0 -10000 0 0
BCL2 0.014 0.029 -10000 0 -0.86 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.053 0.052 -10000 0 -0.54 1 1
adherens junction organization 0.031 0.096 -10000 0 -0.48 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.055 -10000 0 -0.51 2 2
FMN1 0.01 0.15 -10000 0 -0.51 50 50
mol:IP3 -0.009 0.041 -10000 0 -0.56 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.018 0.077 -10000 0 -0.8 1 1
CTNNB1 0.002 0.007 -10000 0 -10000 0 0
AKT1 0.049 0.06 -10000 0 -0.58 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.023 0.14 -10000 0 -0.6 48 48
CTNND1 0.016 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.084 -10000 0 -0.58 2 2
VASP 0.038 0.084 -10000 0 -0.75 1 1
ZYX 0.038 0.084 -10000 0 -0.75 1 1
JUB 0.033 0.096 -10000 0 -0.49 9 9
EGFR(dimer) -0.023 0.086 -10000 0 -0.59 4 4
E-cadherin/beta catenin-gamma catenin -0.032 0.13 -10000 0 -0.56 50 50
mol:PI-3-4-5-P3 -0.012 0.05 -10000 0 -0.63 1 1
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
PI3K -0.012 0.051 -10000 0 -0.65 1 1
FYN -0.27 0.17 -10000 0 -0.5 36 36
mol:Ca2+ -0.009 0.04 -10000 0 -0.54 1 1
JUP -0.001 0.05 -10000 0 -0.86 3 3
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
mol:DAG -0.009 0.041 -10000 0 -0.56 1 1
CDH1 -0.046 0.19 -10000 0 -0.86 48 48
RhoA/GDP -0.013 0.055 -10000 0 -0.51 2 2
establishment of polarity of embryonic epithelium 0.038 0.083 -10000 0 -0.73 1 1
SRC 0.014 0.025 -10000 0 -0.74 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.75 15 15
CASR -0.34 0.2 -10000 0 -0.62 37 37
RhoA/GTP -0.008 0.035 -10000 0 -0.49 1 1
AKT2 0.049 0.06 -10000 0 -0.58 1 1
actin cable formation 0.02 0.15 -10000 0 -0.74 9 9
apoptosis 0.01 0.045 0.56 1 -10000 0 1
CTNNA1 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.015 0.061 -10000 0 -0.56 2 2
PIP5K1A 0.037 0.086 -10000 0 -0.6 2 2
PLCG1 -0.01 0.041 -10000 0 -0.57 1 1
Rac1/GTP -0.021 0.078 -10000 0 -0.53 4 4
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0.065 -9999 0 -0.54 11 11
SNTA1 0.009 0.068 -9999 0 -0.82 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.033 0.06 -9999 0 -0.56 9 9
MAPK12 0.029 0.073 -9999 0 -0.44 20 20
CCND1 0.015 0.06 -9999 0 -0.43 4 4
p38 gamma/SNTA1 0.032 0.083 -9999 0 -0.54 8 8
MAP2K3 0.015 0 -9999 0 -10000 0 0
PKN1 0.015 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.029 0.072 -9999 0 -0.44 20 20
MAP2K6 0.028 0.045 -9999 0 -0.55 5 5
MAPT 0.029 0.068 -9999 0 -0.37 22 22
MAPK13 0.023 0.065 -9999 0 -0.66 8 8
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.012 -9999 0 -0.33 1 1
Circadian rhythm 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
chromatin modification -0.004 0.014 -10000 0 -10000 0 0
CLOCK 0.008 0.096 -10000 0 -0.85 11 11
TIMELESS/CRY2 0.047 0.032 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.018 -10000 0 -0.55 1 1
ATR 0.015 0 -10000 0 -10000 0 0
NR1D1 0.045 0.05 -10000 0 -0.59 3 3
ARNTL 0.019 0.002 -10000 0 -10000 0 0
TIMELESS 0.046 0.037 -10000 0 -10000 0 0
NPAS2 -0.035 0.21 -10000 0 -0.85 55 55
CRY2 0.015 0 -10000 0 -10000 0 0
mol:CO -0.018 0.007 0.1 3 -10000 0 3
CHEK1 0.015 0 -10000 0 -10000 0 0
mol:HEME 0.018 0.007 -10000 0 -0.1 3 3
PER1 0.015 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.007 0.16 -10000 0 -0.56 66 66
BMAL1/CLOCK 0.049 0.073 -10000 0 -10000 0 0
S phase of mitotic cell cycle -0.004 0.014 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.004 0.015 -10000 0 -10000 0 0
mol:NADPH 0.018 0.007 -10000 0 -0.1 3 3
PER1/TIMELESS 0.047 0.032 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.002 0.025 -10000 0 -0.74 1 1
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.002 0.11 -9999 0 -0.84 14 14
alphaV beta3 Integrin -0.023 0.12 -9999 0 -0.66 31 31
PTK2 -0.013 0.078 -9999 0 -0.65 10 10
positive regulation of JNK cascade -0.005 0.038 -9999 0 -0.4 4 4
CDC42/GDP 0.067 0.06 -9999 0 -0.49 9 9
Rac1/GDP 0.07 0.06 -9999 0 -0.48 9 9
RAP1B 0.015 0 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.006 0.047 -9999 0 -0.44 10 10
nectin-3/I-afadin -0.007 0.066 -9999 0 -0.66 9 9
RAPGEF1 0.064 0.068 -9999 0 -0.56 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.057 0.078 -9999 0 -0.66 9 9
PDGFB-D/PDGFRB 0.002 0.11 -9999 0 -0.84 14 14
TLN1 0.042 0.028 -9999 0 -10000 0 0
Rap1/GTP -0.005 0.039 -9999 0 -0.43 4 4
IQGAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.007 0.066 -9999 0 -0.66 9 9
PVR 0.014 0.025 -9999 0 -0.74 1 1
Necl-5(dimer) 0.014 0.025 -9999 0 -0.74 1 1
mol:GDP 0.068 0.074 -9999 0 -0.62 9 9
MLLT4 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K -0.012 0.075 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.001 0.018 -9999 0 -0.55 1 1
positive regulation of lamellipodium assembly -0.005 0.038 -9999 0 -0.37 9 9
PVRL1 0.014 0.025 -9999 0 -0.74 1 1
PVRL3 0.006 0.087 -9999 0 -0.86 9 9
PVRL2 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
CDH1 -0.032 0.2 -9999 0 -0.86 48 48
CLDN1 -0.04 0.2 -9999 0 -0.76 63 63
JAM-A/CLDN1 -0.036 0.12 -9999 0 -0.54 20 20
SRC -0.01 0.08 -9999 0 -0.76 9 9
ITGB3 -0.014 0.16 -9999 0 -0.85 30 30
nectin-1(dimer)/I-afadin/I-afadin -0.001 0.018 -9999 0 -0.55 1 1
FARP2 0.059 0.075 -9999 0 -0.6 10 10
RAC1 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.006 0.059 -9999 0 -0.56 10 10
nectin-1/I-afadin -0.001 0.018 -9999 0 -0.55 1 1
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.006 0.059 -9999 0 -0.56 10 10
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.015 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.005 0.038 -9999 0 -0.4 4 4
alphaV/beta3 Integrin/Talin -0.018 0.091 -9999 0 -0.72 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.003 0.026 -9999 0 -10000 0 0
VAV2 0.058 0.073 -9999 0 -0.62 9 9
RAP1/GDP -0.005 0.046 -9999 0 -0.44 9 9
ITGAV 0.013 0.039 -9999 0 -0.8 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.006 0.057 -9999 0 -0.57 9 9
nectin-3(dimer)/I-afadin/I-afadin -0.007 0.066 -9999 0 -0.66 9 9
Rac1/GTP -0.006 0.047 -9999 0 -0.46 9 9
PTPRM -0.003 0.03 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.025 0.1 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.029 -10000 0 -0.86 1 1
HDAC4 0.014 0.029 -10000 0 -0.86 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.028 0.55 2 -10000 0 2
CDKN1A -0.002 0.031 -10000 0 -0.54 3 3
KAT2B 0.014 0.029 -10000 0 -0.86 1 1
BAX 0.014 0.025 -10000 0 -0.74 1 1
FOXO3 0.001 0.02 0.58 1 -10000 0 1
FOXO1 0.015 0 -10000 0 -10000 0 0
FOXO4 0.029 0.013 -10000 0 -0.37 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
TAT -0.005 0.11 -10000 0 -0.74 20 20
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.002 0.097 -10000 0 -0.56 26 26
PPARGC1A -0.037 0.21 -10000 0 -0.86 53 53
FHL2 -0.002 0.12 -10000 0 -0.85 17 17
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A 0.025 0.028 -10000 0 -0.55 2 2
SIRT1/FOXO3a 0.001 0.013 0.34 1 -10000 0 1
SIRT1 0.001 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.02 -10000 0 -0.57 1 1
SIRT1/Histone H1b 0 0.015 -10000 0 -10000 0 0
apoptosis 0 0.017 0.47 1 -10000 0 1
SIRT1/PGC1A -0.035 0.14 -10000 0 -0.58 53 53
p53/SIRT1 0.001 0.02 -10000 0 -10000 0 0
SIRT1/FOXO4 0 0.013 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.01 0.072 -10000 0 -0.52 17 17
HIST1H1E 0.028 0.017 -10000 0 -0.38 1 1
SIRT1/p300 0 0.023 -10000 0 -0.66 1 1
muscle cell differentiation 0.013 0.08 0.47 26 -10000 0 26
TP53 0.001 0.009 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.017 -10000 0 -0.47 1 1
CREBBP 0.015 0 -10000 0 -10000 0 0
MEF2D 0.015 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.012 0.082 -10000 0 -0.55 20 20
ACSS2 0.026 0.004 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.013 0.08 -10000 0 -0.47 26 26
IGF1 pathway

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
NCK2 0.015 0 -9999 0 -10000 0 0
PTK2 0.015 0 -9999 0 -10000 0 0
CRKL 0.014 0.091 -9999 0 -0.46 11 11
GRB2/SOS1/SHC -0.001 0.016 -9999 0 -0.47 1 1
HRAS 0.014 0.025 -9999 0 -0.74 1 1
IRS1/Crk -0.02 0.084 -9999 0 -0.46 11 11
IGF-1R heterotetramer/IGF1/PTP1B -0.02 0.091 -9999 0 -0.54 11 11
AKT1 0.042 0.08 -9999 0 -10000 0 0
BAD 0.05 0.079 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.091 -9999 0 -0.46 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.02 0.084 -9999 0 -0.46 11 11
RAF1 0.056 0.072 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.018 0.078 -9999 0 -0.43 11 11
YWHAZ 0.015 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.022 0.092 -9999 0 -0.41 47 47
PIK3CA 0.015 0 -9999 0 -10000 0 0
RPS6KB1 0.042 0.08 -9999 0 -10000 0 0
GNB2L1 0.014 0.025 -9999 0 -0.74 1 1
positive regulation of MAPKKK cascade 0.048 0.064 -9999 0 -10000 0 0
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.016 0.069 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.015 0.072 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.02 0.084 -9999 0 -0.46 11 11
Crk/p130 Cas/Paxillin -0.017 0.074 -9999 0 -10000 0 0
IGF1R 0.011 0.019 -9999 0 -10000 0 0
IGF1 -0.018 0.16 -9999 0 -0.77 37 37
IRS2/Crk -0.026 0.095 -9999 0 -0.71 1 1
PI3K -0.018 0.077 -9999 0 -10000 0 0
apoptosis -0.054 0.07 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.019 -9999 0 -0.56 1 1
PRKCD 0.032 0.1 -9999 0 -0.56 16 16
RAF1/14-3-3 E 0.06 0.065 -9999 0 -10000 0 0
BAD/14-3-3 0.057 0.074 -9999 0 -10000 0 0
PRKCZ 0.041 0.084 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.013 0.054 -9999 0 -10000 0 0
PTPN1 0.015 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.027 0.086 -9999 0 -0.55 11 11
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.017 0.08 -9999 0 -0.47 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.019 0.083 -9999 0 -0.46 11 11
GRB10 0.015 0 -9999 0 -10000 0 0
PTPN11 0.014 0.091 -9999 0 -0.46 11 11
IRS1 0.002 0.098 -9999 0 -0.41 47 47
IRS2 0.004 0.11 -9999 0 -0.43 39 39
IGF-1R heterotetramer/IGF1 -0.025 0.12 -9999 0 -0.58 37 37
GRB2 0.015 0 -9999 0 -10000 0 0
PDPK1 0.032 0.083 -9999 0 -10000 0 0
YWHAE 0.015 0 -9999 0 -10000 0 0
PRKD1 0.033 0.094 -9999 0 -0.51 17 17
SHC1 0.014 0.025 -9999 0 -0.74 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.017 -10000 0 -0.52 1 1
HDAC3 0.015 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.015 -10000 0 -0.44 1 1
GATA1/HDAC4 -0.029 0.12 -10000 0 -0.55 46 46
GATA1/HDAC5 -0.029 0.12 -10000 0 -0.55 46 46
GATA2/HDAC5 -0.061 0.19 -10000 0 -0.66 82 82
HDAC5/BCL6/BCoR -0.001 0.019 -10000 0 -0.57 1 1
HDAC9 0.014 0.029 -10000 0 -0.86 1 1
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.016 -10000 0 -0.47 1 1
HDAC4/ANKRA2 -0.001 0.022 -10000 0 -0.66 1 1
HDAC5/YWHAB -0.001 0.022 -10000 0 -0.66 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.065 0.25 -10000 0 -0.86 81 81
HDAC4/RFXANK -0.001 0.029 -10000 0 -0.61 2 2
BCOR 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.029 -10000 0 -0.86 1 1
HDAC5 0.014 0.029 -10000 0 -0.86 1 1
GNB1/GNG2 0 0 -10000 0 -10000 0 0
Histones -0.002 0.022 -10000 0 -10000 0 0
ADRBK1 0.015 0 -10000 0 -10000 0 0
HDAC4 0.014 0.029 -10000 0 -0.86 1 1
XPO1 0.015 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.022 -10000 0 -0.66 1 1
HDAC4/Ubc9 -0.001 0.022 -10000 0 -0.66 1 1
HDAC7 0.015 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.022 -10000 0 -0.66 1 1
TUBA1B 0.014 0.025 -10000 0 -0.74 1 1
HDAC6 0.015 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.029 -10000 0 -0.61 2 2
CAMK4 0.004 0.095 -10000 0 -0.85 11 11
Tubulin/HDAC6 -0.001 0.025 -10000 0 -0.52 2 2
SUMO1 0.015 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
GATA1 -0.026 0.16 -10000 0 -0.74 45 45
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.015 0 -10000 0 -10000 0 0
NR3C1 0.014 0.025 -10000 0 -0.74 1 1
SUMO1/HDAC4 -0.001 0.016 -10000 0 -0.48 1 1
SRF 0.015 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.022 -10000 0 -0.66 1 1
Tubulin -0.001 0.029 -10000 0 -0.61 2 2
HDAC4/14-3-3 E -0.001 0.022 -10000 0 -0.66 1 1
GNB1 0.015 0 -10000 0 -10000 0 0
RANGAP1 0.015 0 -10000 0 -10000 0 0
BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.019 -10000 0 -0.57 1 1
HDAC4/SRF -0.008 0.065 -10000 0 -0.56 12 12
HDAC4/ER alpha -0.024 0.12 -10000 0 -0.66 33 33
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.05 0.025 -10000 0 -10000 0 0
cell motility -0.001 0.025 -10000 0 -0.52 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.015 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 0.015 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0.029 -10000 0 -0.86 1 1
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 -0.016 0.16 -10000 0 -0.85 32 32
HDAC6/HDAC11 -0.001 0.022 -10000 0 -0.66 1 1
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0.014 0.025 -10000 0 -0.74 1 1
RAN 0.015 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.021 -10000 0 -10000 0 0
GNG2 0.015 0 -10000 0 -10000 0 0
NCOR2 0.015 0 -10000 0 -10000 0 0
TUBB2A 0.014 0.029 -10000 0 -0.86 1 1
HDAC11 0.014 0.029 -10000 0 -0.86 1 1
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RANBP2 0.015 0 -10000 0 -10000 0 0
ANKRA2 0.015 0 -10000 0 -10000 0 0
RFXANK 0.014 0.025 -10000 0 -0.74 1 1
nuclear import 0.001 0.022 0.46 2 -10000 0 2
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.015 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.004 0.045 -9999 0 -0.55 6 6
forebrain development 0.051 0.095 -9999 0 -0.43 16 16
GNAO1 -0.02 0.17 -9999 0 -0.83 37 37
SMO/beta Arrestin2 -0.006 0.062 -9999 0 -0.61 9 9
SMO 0.011 0.07 -9999 0 -0.84 6 6
ARRB2 0.013 0.044 -9999 0 -0.74 3 3
GLI3/SPOP 0.058 0.031 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.015 0 -9999 0 -10000 0 0
GNAI2 0.015 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex -0.03 0.11 -9999 0 -10000 0 0
GNAI1 0.01 0.065 -9999 0 -0.86 5 5
XPO1 0.018 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.009 0.065 -9999 0 -10000 0 0
SAP30 -0.039 0.19 -9999 0 -0.74 63 63
mol:GDP 0.011 0.07 -9999 0 -0.84 6 6
MIM/GLI2A 0.019 0.042 -9999 0 -0.86 2 2
IFT88 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0.004 -9999 0 -10000 0 0
GLI2 0.052 0.042 -9999 0 -10000 0 0
GLI3 0.052 0.033 -9999 0 -10000 0 0
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
SAP18 0.015 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.015 0 -9999 0 -10000 0 0
GNG2 0.015 0 -9999 0 -10000 0 0
Gi family/GTP 0.03 0.089 -9999 0 -0.51 6 6
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.015 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.046 0.045 -9999 0 -10000 0 0
GLI2/Su(fu) 0.069 0.046 -9999 0 -10000 0 0
FOXA2 -0.035 0.15 -9999 0 -0.65 47 47
neural tube patterning 0.051 0.095 -9999 0 -0.43 16 16
SPOP 0.015 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.022 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.029 -9999 0 -0.86 1 1
CSNK1G3 0.015 0 -9999 0 -10000 0 0
MTSS1 0.019 0.042 -9999 0 -0.86 2 2
embryonic limb morphogenesis 0.051 0.095 -9999 0 -0.43 16 16
SUFU 0.034 0.031 -9999 0 -10000 0 0
LGALS3 -0.032 0.18 -9999 0 -0.74 55 55
catabolic process 0.084 0.04 -9999 0 -10000 0 0
GLI3A/CBP 0.014 0.063 -9999 0 -0.38 16 16
KIF3A 0.015 0 -9999 0 -10000 0 0
GLI1 0.051 0.097 -9999 0 -0.43 16 16
RAB23 0.015 0 -9999 0 -10000 0 0
CSNK1A1 0.015 0 -9999 0 -10000 0 0
IFT172 0.015 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.028 0.11 -9999 0 -0.55 6 6
GNAZ 0.012 0.051 -9999 0 -0.86 3 3
RBBP4 0.014 0.029 -9999 0 -0.86 1 1
CSNK1G1 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GLI2/SPOP 0.055 0.039 -9999 0 -10000 0 0
STK36 0.018 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.024 0.075 -9999 0 -0.65 2 2
PTCH1 0.059 0.089 -9999 0 -10000 0 0
MIM/GLI1 0.053 0.13 -9999 0 -0.55 7 7
CREBBP 0.014 0.063 -9999 0 -0.38 16 16
Su(fu)/SIN3/HDAC complex 0.047 0.055 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.012 0.071 -9999 0 -0.53 9 9
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.056 -9999 0 -0.64 1 1
SUMO1 0.015 0 -9999 0 -10000 0 0
ZFPM1 0.01 0.062 -9999 0 -0.81 5 5
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.015 0 -9999 0 -10000 0 0
Histones -0.005 0.028 -9999 0 -10000 0 0
YY1/LSF -0.001 0.028 -9999 0 -0.83 1 1
SMG5 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.051 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.006 0.034 -9999 0 -10000 0 0
SAP18 0.015 0 -9999 0 -10000 0 0
RELA 0.04 0.052 -9999 0 -0.32 8 8
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.015 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.006 0.034 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.061 0.019 -9999 0 -0.44 1 1
NF kappa B1 p50/RelA 0.043 0.053 -9999 0 -0.75 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.065 0.25 -9999 0 -0.86 81 81
GATA1 -0.026 0.16 -9999 0 -0.74 45 45
Mad/Max -0.001 0.018 -9999 0 -0.55 1 1
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.038 -9999 0 -0.53 2 2
RBBP7 0.015 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.014 0.029 -9999 0 -0.86 1 1
MAX 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.015 0 -9999 0 -10000 0 0
NFKBIA -0.006 0.04 -9999 0 -10000 0 0
KAT2B 0.014 0.029 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.012 0.042 -9999 0 -10000 0 0
SIN3 complex -0.03 0.11 -9999 0 -10000 0 0
SMURF1 0.015 0 -9999 0 -10000 0 0
CHD3 0.015 0 -9999 0 -10000 0 0
SAP30 -0.038 0.19 -9999 0 -0.74 63 63
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.006 0.038 -9999 0 -0.74 1 1
YY1/HDAC2 -0.001 0.028 -9999 0 -0.83 1 1
YY1/HDAC1 -0.001 0.028 -9999 0 -0.83 1 1
NuRD/MBD2 Complex (MeCP1) 0.061 0.009 -9999 0 -10000 0 0
PPARG -0.01 0.059 -9999 0 -0.46 8 8
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.006 0.034 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.015 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.018 -9999 0 -0.5 1 1
HDAC1 0.015 0 -9999 0 -10000 0 0
HDAC3 -0.006 0.04 -9999 0 -10000 0 0
HDAC2 0.015 0 -9999 0 -10000 0 0
YY1 0.038 0.032 -9999 0 -0.92 1 1
HDAC8 0.015 0 -9999 0 -10000 0 0
SMAD7 0.015 0 -9999 0 -10000 0 0
NCOR2 0.015 0 -9999 0 -10000 0 0
MXD1 0.014 0.025 -9999 0 -0.74 1 1
STAT3 0.032 0.016 -9999 0 -0.45 1 1
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.026 -9999 0 -0.77 1 1
YY1/SAP30/HDAC1 -0.03 0.11 -9999 0 -0.41 64 64
EP300 0.014 0.029 -9999 0 -0.86 1 1
STAT3 (dimer non-phopshorylated) 0.032 0.016 -9999 0 -0.44 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.04 -9999 0 -10000 0 0
histone deacetylation 0.061 0.009 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.032 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GATAD2B 0.015 0 -9999 0 -10000 0 0
GATAD2A 0.015 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.053 0.15 -9999 0 -0.52 81 81
GATA1/HDAC1 -0.028 0.12 -9999 0 -0.55 45 45
GATA1/HDAC3 -0.027 0.099 -9999 0 -0.43 45 45
CHD4 0.015 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.016 0.097 -9999 0 -0.59 25 25
SIN3/HDAC complex/Mad/Max 0.048 0.047 -9999 0 -10000 0 0
NuRD Complex -0.001 0.015 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.027 -9999 0 -10000 0 0
SIN3B 0.015 0 -9999 0 -10000 0 0
MTA2 0.015 0 -9999 0 -10000 0 0
SIN3A 0.015 0 -9999 0 -10000 0 0
XPO1 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.017 -9999 0 -0.52 1 1
GATA1/Fog1 -0.031 0.13 -9999 0 -0.56 50 50
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.007 0.13 -9999 0 -0.78 25 25
negative regulation of cell growth 0.048 0.047 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.061 0.009 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.009 0.056 -9999 0 -0.44 8 8
SIN3/HDAC complex/NCoR1 -0.009 0.032 -9999 0 -10000 0 0
TFCP2 0.015 0 -9999 0 -10000 0 0
NR2C1 0.015 0 -9999 0 -10000 0 0
MBD3 0.013 0.039 -9999 0 -0.8 2 2
MBD2 0.015 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.011 0.065 -9999 0 -10000 0 0
TC10/GTP -0.004 0.04 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.007 0.061 -9999 0 -0.54 10 10
HRAS 0.014 0.025 -9999 0 -0.74 1 1
APS homodimer 0.007 0.079 -9999 0 -0.74 10 10
GRB14 -0.032 0.2 -9999 0 -0.86 48 48
FOXO3 -0.007 0.043 -9999 0 -0.6 4 4
AKT1 -0.027 0.1 -9999 0 -0.78 3 3
INSR 0.017 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.001 0.02 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.015 0 -9999 0 -10000 0 0
SORBS1 0.015 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
PTPN1 0.046 0.022 -9999 0 -10000 0 0
CAV1 0.003 0.12 -9999 0 -0.43 60 60
CBL/APS/CAP/Crk-II/C3G -0.005 0.044 -9999 0 -0.48 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.007 0.061 -9999 0 -0.54 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.053 -9999 0 -0.47 10 10
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.004 0.033 -9999 0 -10000 0 0
RPS6KB1 0.047 0.11 -9999 0 -0.68 3 3
PARD6A 0.012 0.051 -9999 0 -0.86 3 3
CBL 0.014 0.029 -9999 0 -0.86 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.019 -9999 0 -0.4 2 2
PIK3R1 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.024 0.092 -9999 0 -0.72 3 3
HRAS/GTP -0.01 0.063 -9999 0 -0.73 2 2
Insulin Receptor 0.017 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.007 0.058 -9999 0 -0.5 10 10
PRKCI -0.006 0.024 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.029 0.11 -9999 0 -0.88 3 3
SHC1 0.014 0.025 -9999 0 -0.74 1 1
negative regulation of MAPKKK cascade -0.001 0.023 -9999 0 -0.5 1 1
PI3K -0.006 0.054 -9999 0 -0.48 10 10
NCK2 0.015 0 -9999 0 -10000 0 0
RHOQ 0.015 0 -9999 0 -10000 0 0
mol:H2O2 0 0.002 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.019 -9999 0 -0.56 1 1
AKT2 -0.027 0.1 -9999 0 -0.78 3 3
PRKCZ -0.009 0.051 -9999 0 -0.78 3 3
SH2B2 0.007 0.079 -9999 0 -0.74 10 10
SHC/SHIP -0.012 0.074 -9999 0 -0.55 10 10
F2RL2 -0.041 0.2 -9999 0 -0.77 63 63
TRIP10 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.002 0.028 -9999 0 -0.41 4 4
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.002 0.024 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
RASA1 0.014 0.029 -9999 0 -0.86 1 1
NCK1 0.015 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.005 0.048 -9999 0 -0.52 1 1
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.002 0.027 -9999 0 -10000 0 0
INPP5D 0.023 0.084 -9999 0 -0.58 10 10
SOS1 0.015 0 -9999 0 -10000 0 0
SGK1 -0.006 0.064 -9999 0 -0.95 4 4
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 0.005 0.092 -9999 0 -0.86 10 10
p62DOK/RasGAP -0.001 0.023 -9999 0 -0.51 1 1
INS 0.002 0.042 -9999 0 -0.73 3 3
mol:PI-3-4-P2 0.022 0.083 -9999 0 -0.58 10 10
GRB2 0.015 0 -9999 0 -10000 0 0
EIF4EBP1 0.035 0.14 -9999 0 -0.73 8 8
PTPRA 0.017 0.002 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.005 0.038 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.008 0.062 -9999 0 -0.51 13 13
Insulin Receptor/Insulin/IRS3 -0.002 0.031 -9999 0 -0.54 3 3
Par3/Par6 -0.031 0.11 -9999 0 -0.49 18 18
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.029 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.001 0.022 -9999 0 -0.52 1 1
CDKN1B 0.049 0.005 -9999 0 -10000 0 0
CDKN1A 0.047 0.025 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.015 0 -9999 0 -10000 0 0
FOXO3 0.049 0.005 -9999 0 -10000 0 0
AKT1 0 0.004 -9999 0 -10000 0 0
BAD 0.013 0.039 -9999 0 -0.8 2 2
AKT3 0.021 0.016 -9999 0 -0.46 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.049 0.005 -9999 0 -10000 0 0
AKT1/ASK1 0 0.003 -9999 0 -10000 0 0
BAD/YWHAZ -0.001 0.025 -9999 0 -0.52 2 2
RICTOR 0.015 0 -9999 0 -10000 0 0
RAF1 0.015 0 -9999 0 -10000 0 0
JNK cascade 0 0.003 -9999 0 -10000 0 0
TSC1 0.049 0.005 -9999 0 -10000 0 0
YWHAZ 0.015 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0.003 -9999 0 -10000 0 0
EP300 0.014 0.029 -9999 0 -0.86 1 1
mol:GDP 0 0.004 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.049 0.005 -9999 0 -10000 0 0
YWHAQ 0.015 0 -9999 0 -10000 0 0
TBC1D4 0.032 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
MAPKAP1 0.015 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.027 0.059 -9999 0 -10000 0 0
YWHAH 0.015 0 -9999 0 -10000 0 0
AKT1S1 0.049 0.005 -9999 0 -10000 0 0
CASP9 0.049 0.005 -9999 0 -10000 0 0
YWHAB 0.015 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.055 0.005 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.016 -9999 0 -0.47 1 1
YWHAE 0.015 0 -9999 0 -10000 0 0
SRC 0.014 0.025 -9999 0 -0.74 1 1
AKT2/p21CIP1 -0.001 0.021 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.002 -9999 0 -10000 0 0
CHUK 0.049 0.005 -9999 0 -10000 0 0
BAD/BCL-XL -0.001 0.018 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.022 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.044 0.066 -9999 0 -10000 0 0
PDPK1 0.015 0 -9999 0 -10000 0 0
MDM2 0.049 0.005 -9999 0 -10000 0 0
MAPKKK cascade 0 0.003 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.001 0.014 -9999 0 -10000 0 0
TSC1/TSC2 0.057 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.014 -9999 0 -10000 0 0
glucose import 0.011 0.11 -9999 0 -0.43 56 56
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.041 0.003 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.011 0.12 -9999 0 -0.43 56 56
GSK3A 0.049 0.005 -9999 0 -10000 0 0
FOXO1 0.049 0.005 -9999 0 -10000 0 0
GSK3B 0.049 0.005 -9999 0 -10000 0 0
SFN -0.15 0.32 -9999 0 -0.76 188 188
G1/S transition of mitotic cell cycle 0.057 0.005 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.017 0.088 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
KPNA1 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
YWHAG 0.015 0 -9999 0 -10000 0 0
RHEB 0.015 0 -9999 0 -10000 0 0
CREBBP 0.015 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.037 0.082 -10000 0 -0.56 1 1
BAG4 0.013 0.041 -10000 0 -0.86 2 2
BAD 0.033 0.037 -10000 0 -0.42 2 2
NFKBIA 0.015 0 -10000 0 -10000 0 0
BIRC3 -0.071 0.24 -10000 0 -0.74 101 101
BAX 0.033 0.033 -10000 0 -0.36 1 1
EnzymeConsortium:3.1.4.12 0.014 0.023 -10000 0 -0.12 1 1
IKBKB 0.046 0.078 -10000 0 -0.52 1 1
MAP2K2 0.047 0.049 -10000 0 -0.41 1 1
MAP2K1 0.047 0.046 -10000 0 -10000 0 0
SMPD1 0.021 0.023 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.047 0.079 -10000 0 -0.53 1 1
MAP2K4 0.043 0.03 -10000 0 -10000 0 0
protein ubiquitination 0.048 0.079 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.054 0.048 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAF1 0.04 0.048 -10000 0 -0.33 9 9
CRADD 0.015 0.002 -10000 0 -10000 0 0
mol:ceramide 0.025 0.032 -10000 0 -0.17 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.015 0.002 -10000 0 -10000 0 0
MAP3K1 0.034 0.031 -10000 0 -10000 0 0
TRADD 0.015 0.002 -10000 0 -10000 0 0
RELA/p50 0.015 0 -10000 0 -10000 0 0
MAPK3 0.05 0.046 -10000 0 -10000 0 0
MAPK1 0.05 0.046 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.038 0.081 -10000 0 -0.56 1 1
KSR1 0.031 0.05 -10000 0 -0.36 9 9
MAPK8 0.047 0.05 -10000 0 -0.41 7 7
TRAF2 0.015 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.046 0.078 -10000 0 -0.52 1 1
TNF R/SODD -0.001 0.031 -10000 0 -0.66 2 2
TNF -0.007 0.13 -10000 0 -0.78 25 25
CYCS 0.035 0.032 0.16 1 -10000 0 1
IKBKG 0.046 0.078 -10000 0 -0.52 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.084 -10000 0 -0.6 1 1
RELA 0.015 0 -10000 0 -10000 0 0
RIPK1 0.015 0.001 -10000 0 -10000 0 0
AIFM1 0.035 0.032 0.16 1 -10000 0 1
TNF/TNF R/SODD -0.015 0.087 -10000 0 -0.51 27 27
TNFRSF1A 0.015 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.024 -10000 0 -10000 0 0
NSMAF 0.038 0.08 -10000 0 -0.55 1 1
response to hydrogen peroxide 0.001 0 -10000 0 -10000 0 0
BCL2 0.014 0.029 -10000 0 -0.86 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.015 0 -9999 0 -10000 0 0
HDAC3 0.015 0 -9999 0 -10000 0 0
VDR 0.01 0.065 -9999 0 -0.86 5 5
Cbp/p300/PCAF -0.001 0.037 -9999 0 -1.1 1 1
EP300 0.014 0.029 -9999 0 -0.86 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.048 0.04 -9999 0 -0.48 1 1
KAT2B 0.014 0.029 -9999 0 -0.86 1 1
MAPK14 0.015 0 -9999 0 -10000 0 0
AKT1 0.021 0.045 -9999 0 -0.34 2 2
RAR alpha/9cRA/Cyclin H -0.018 0.057 -9999 0 -0.51 5 5
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.044 0.041 -9999 0 -0.53 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
response to UV 0.002 0.001 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.024 0.087 -9999 0 -0.82 7 7
NCOR2 0.015 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.004 0.05 -9999 0 -0.67 5 5
RXRs/RARs/NRIP1/9cRA 0.041 0.1 -9999 0 -0.53 1 1
NCOA2 -0.025 0.18 -9999 0 -0.86 41 41
NCOA3 0.015 0 -9999 0 -10000 0 0
NCOA1 0.015 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.01 0.065 -9999 0 -0.86 5 5
RARG 0.016 0.025 -9999 0 -0.74 1 1
RAR gamma1/9cRA -0.001 0.016 -9999 0 -0.48 1 1
MAPK3 0.016 0.001 -9999 0 -10000 0 0
MAPK1 0.015 0 -9999 0 -10000 0 0
MAPK8 0.01 0.077 -9999 0 -0.86 7 7
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.034 0.094 -9999 0 -0.52 9 9
RARA 0.007 0.087 -9999 0 -0.5 7 7
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.03 0.088 -9999 0 -0.4 19 19
PRKCA 0.019 0.001 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.033 0.1 -9999 0 -0.46 6 6
RXRG -0.013 0.12 -9999 0 -10000 0 0
RXRA 0.019 0.082 -9999 0 -0.57 5 5
RXRB -0.005 0.11 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.004 0.05 -9999 0 -0.67 5 5
RBP1 0.011 0.058 -9999 0 -0.76 5 5
CRBP1/9-cic-RA -0.003 0.044 -9999 0 -0.58 5 5
RARB 0.016 0.041 -9999 0 -0.86 2 2
PRKCG -0.072 0.24 -9999 0 -0.73 100 100
MNAT1 0.015 0 -9999 0 -10000 0 0
RAR alpha/RXRs 0.031 0.1 -9999 0 -0.48 5 5
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.039 0.095 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.065 -9999 0 -0.4 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 0.033 0.1 -9999 0 -0.46 6 6
positive regulation of DNA binding -0.017 0.054 -9999 0 -0.48 5 5
NRIP1 0.032 0.1 -9999 0 -1.3 1 1
RXRs/RARs 0.024 0.1 -9999 0 -0.43 6 6
RXRs/RXRs/DNA/9cRA -0.034 0.092 -9999 0 -0.5 5 5
PRKACA 0.015 0 -9999 0 -10000 0 0
CDK7 0.015 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.013 0.041 -9999 0 -10000 0 0
CCNH 0.015 0 -9999 0 -10000 0 0
CREBBP 0.015 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0.012 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.015 0 -9999 0 -10000 0 0
Rac1/GDP 0.002 0.012 -9999 0 -10000 0 0
DOCK1 0.014 0.029 -9999 0 -0.86 1 1
ITGA4 -0.01 0.14 -9999 0 -0.74 30 30
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.019 0.1 -9999 0 -0.55 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.016 0.085 -9999 0 -0.47 30 30
alpha4/beta7 Integrin/Paxillin -0.014 0.076 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.026 -9999 0 -0.54 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
TLN1 0.015 0 -9999 0 -10000 0 0
PXN 0.029 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.012 0.063 -9999 0 -10000 0 0
cell adhesion -0.013 0.069 -9999 0 -10000 0 0
CRKL/CBL -0.001 0.022 -9999 0 -0.66 1 1
alpha4/beta1 Integrin/Paxillin -0.014 0.076 -9999 0 -10000 0 0
ITGB1 0.015 0 -9999 0 -10000 0 0
ITGB7 0.015 0 -9999 0 -10000 0 0
ARF6/GDP 0.002 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.049 0.14 -9999 0 -0.8 6 6
p130Cas/Crk/Dock1 -0.001 0.027 -9999 0 -0.57 2 2
VCAM1 -0.052 0.22 -9999 0 -0.78 75 75
alpha4/beta1 Integrin/Paxillin/Talin -0.013 0.07 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.013 0.07 -9999 0 -10000 0 0
BCAR1 0.014 0.029 -9999 0 -0.86 1 1
mol:GDP 0.013 0.069 -9999 0 -10000 0 0
CBL 0.014 0.029 -9999 0 -0.86 1 1
PRKACA 0.015 0 -9999 0 -10000 0 0
GIT1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.013 0.07 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.029 -9999 0 -0.62 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.001 0.022 -10000 0 -0.46 2 2
MAPK9 0.011 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.016 0.11 -10000 0 -0.56 33 33
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
Gs family/GTP -0.001 0.024 -10000 0 -0.5 2 2
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 0.005 0.11 2 -10000 0 2
GNAL 0.013 0.039 -10000 0 -0.8 2 2
GNG2 0.015 0 -10000 0 -10000 0 0
CRH -0.022 0.14 -10000 0 -0.74 33 33
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.043 -10000 0 -0.47 7 7
MAPK11 0.011 0.012 -10000 0 -0.34 1 1
Arf6 downstream 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
PLAUR 0.024 0.14 -10000 0 -0.6 44 44
regulation of axonogenesis -0.032 0.031 -10000 0 -10000 0 0
myoblast fusion 0.014 0.062 0.28 44 -10000 0 44
mol:GTP -0.009 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.01 0.046 0.46 5 -10000 0 5
ARF1/GTP -0.006 0.026 -10000 0 -10000 0 0
mol:GM1 0.007 0.032 -10000 0 -10000 0 0
mol:Choline 0.032 0.027 -10000 0 -10000 0 0
lamellipodium assembly -0.014 0.064 -10000 0 -10000 0 0
MAPK3 0.024 0.061 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.01 0.047 -10000 0 -0.46 5 5
ARF1 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.014 0.062 -10000 0 -0.28 44 44
ARF1/GDP -0.012 0.055 -10000 0 -10000 0 0
ARF6 0.009 0.021 -10000 0 -10000 0 0
RAB11A 0.015 0 -10000 0 -10000 0 0
TIAM1 0.016 0.03 -10000 0 -0.86 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.061 -10000 0 -10000 0 0
actin filament bundle formation 0.012 0.054 -10000 0 -10000 0 0
KALRN -0.011 0.052 -10000 0 -0.52 1 1
RAB11FIP3/RAB11A -0.001 0.022 -10000 0 -0.66 1 1
RhoA/GDP -0.013 0.055 -10000 0 -10000 0 0
NME1 0.013 0.05 -10000 0 -0.73 4 4
Rac1/GDP -0.013 0.055 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.009 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.014 0.064 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
liver development -0.009 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.009 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.006 0.026 -10000 0 -10000 0 0
mol:GDP -0.014 0.063 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.005 0.026 -10000 0 -0.55 1 1
RHOA 0.015 0 -10000 0 -10000 0 0
PLD1 0.02 0.032 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.029 -10000 0 -0.86 1 1
tube morphogenesis -0.014 0.064 -10000 0 -10000 0 0
ruffle organization 0.032 0.031 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.009 0.039 -10000 0 -10000 0 0
PLD2 0.02 0.032 -10000 0 -10000 0 0
PIP5K1A 0.032 0.031 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.032 0.027 -10000 0 -10000 0 0
Rac1/GTP -0.014 0.065 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA -0.001 0.026 -9999 0 -0.55 2 2
FBXW11 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.008 0.065 -9999 0 -0.56 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.039 -9999 0 -10000 0 0
NFKBIA 0.025 0.057 -9999 0 -10000 0 0
MAPK14 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.019 -9999 0 -0.57 1 1
ARRB2 0.021 0.02 -9999 0 -0.33 3 3
REL 0.004 0.095 -9999 0 -0.85 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.002 0.029 -9999 0 -0.5 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.019 -9999 0 -0.57 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0.023 -9999 0 -0.66 1 1
PIK3R1 0.015 0 -9999 0 -10000 0 0
NFKB1 0.029 0.023 -9999 0 -0.66 1 1
RELA 0.015 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.033 0.056 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.009 0.037 -9999 0 -10000 0 0
SRC 0.014 0.025 -9999 0 -0.74 1 1
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.011 0.045 -9999 0 -10000 0 0
IKBKB 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
SYK 0.01 0.065 -9999 0 -0.86 5 5
I kappa B alpha/PIK3R1 0.031 0.053 -9999 0 -10000 0 0
cell death -0.009 0.036 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.008 0.065 -9999 0 -0.56 12 12
LCK -0.023 0.17 -9999 0 -0.76 44 44
BCL3 0.013 0.036 -9999 0 -0.74 2 2
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.015 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.037 -10000 0 -0.35 10 10
FRAP1 0.019 0.007 -10000 0 -10000 0 0
AKT1 -0.003 0.029 -10000 0 -10000 0 0
INSR 0.015 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.002 0.028 -10000 0 -0.48 3 3
mol:GTP -0.002 0.021 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.005 -10000 0 -10000 0 0
TSC2 0.015 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.018 -10000 0 -10000 0 0
TSC1 0.015 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.047 -10000 0 -0.42 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.015 0 -10000 0 -10000 0 0
RPS6KB1 0.035 0.018 -10000 0 -10000 0 0
MAP3K5 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.015 0 -10000 0 -10000 0 0
apoptosis 0.014 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 10 10
EIF4B 0.042 0.017 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.017 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.007 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.04 -10000 0 -0.38 10 10
mTOR/RHEB/GTP/Raptor/GBL 0.041 0.011 -10000 0 -10000 0 0
FKBP1A 0.015 0 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.017 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.002 10 10
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.003 0.033 -10000 0 -10000 0 0
EIF4E 0.015 0 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.005 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.022 0 -10000 0 -10000 0 0
TSC1/TSC2 -0.002 0.023 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.002 10 -10000 0 10
RPS6 0.013 0.036 -10000 0 -0.74 2 2
PPP5C 0.015 0 -10000 0 -10000 0 0
EIF4G1 0.015 0 -10000 0 -10000 0 0
IRS1 0.006 0.05 -10000 0 -0.46 10 10
INS -0.002 0.043 -10000 0 -0.74 3 3
PTEN 0 0.002 -10000 0 -10000 0 0
PDK2 -0.003 0.033 -10000 0 -10000 0 0
EIF4EBP1 0.002 0.066 -10000 0 -0.36 29 29
PIK3CA 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.028 0.014 -10000 0 -0.35 1 1
peptide biosynthetic process 0.02 0.026 -10000 0 -0.43 3 3
RHEB 0.015 0 -10000 0 -10000 0 0
EIF4A1 0.015 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.021 0.026 -10000 0 -0.43 3 3
eIF4E/4E-BP1 0.011 0.059 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.012 0.048 -10000 0 -0.82 3 3
positive regulation of NF-kappaB transcription factor activity -0.003 0.042 -10000 0 -0.63 4 4
MAP2K4 0.059 0.024 -10000 0 -10000 0 0
IKBKB 0.015 0 -10000 0 -10000 0 0
TNFRSF10B 0.013 0.036 -10000 0 -0.74 2 2
TNFRSF10A 0.01 0.065 -10000 0 -0.86 5 5
SMPD1 -0.001 0.019 -10000 0 -10000 0 0
IKBKG 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.014 0.029 -10000 0 -0.86 1 1
TRAIL/TRAILR2 -0.003 0.045 -10000 0 -0.6 5 5
TRAIL/TRAILR3 -0.01 0.076 -10000 0 -0.57 16 16
TRAIL/TRAILR1 -0.006 0.061 -10000 0 -0.65 8 8
TRAIL/TRAILR4 -0.003 0.043 -10000 0 -0.63 4 4
TRAIL/TRAILR1/DAP3/GTP -0.005 0.049 -10000 0 -0.53 7 7
IKK complex -0.001 0.014 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.027 0.038 -10000 0 -0.62 3 3
MAP3K1 -0.002 0.02 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.014 0.029 -10000 0 -0.86 1 1
TRADD 0.015 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.01 0.065 -10000 0 -0.86 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.03 -10000 0 -10000 0 0
CFLAR 0.015 0 -10000 0 -10000 0 0
MAPK1 0.027 0.038 -10000 0 -0.62 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.004 0.045 -10000 0 -10000 0 0
mol:ceramide -0.001 0.019 -10000 0 -10000 0 0
FADD 0.015 0 -10000 0 -10000 0 0
MAPK8 0.063 0.05 -10000 0 -10000 0 0
TRAF2 0.015 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.004 0.091 -10000 0 -0.74 13 13
CHUK 0.015 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.005 0.053 -10000 0 -0.56 8 8
DAP3 0.015 0 -10000 0 -10000 0 0
CASP10 -0.003 0.038 0.33 1 -0.54 2 3
JNK cascade -0.003 0.042 -10000 0 -0.63 4 4
TRAIL (trimer) 0.012 0.048 -10000 0 -0.82 3 3
TNFRSF10C 0.004 0.091 -10000 0 -0.75 13 13
TRAIL/TRAILR1/DAP3/GTP/FADD -0.004 0.046 -10000 0 -0.49 7 7
TRAIL/TRAILR2/FADD -0.003 0.038 -10000 0 -0.51 5 5
cell death -0.001 0.019 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.02 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.013 0.036 -10000 0 -0.74 2 2
CASP8 0 0.01 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.032 -10000 0 -10000 0 0
Arf1 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
coatomer protein complex -0.001 0.02 -9999 0 -0.6 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.008 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.002 -9999 0 -10000 0 0
CLTB 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 -0.01 0.14 -9999 0 -0.74 30 30
CLTA 0.015 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.014 0.023 -9999 0 -0.67 1 1
mol:PI-4-5-P2 0 0.015 -9999 0 -0.44 1 1
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.019 -9999 0 -0.55 1 1
mol:Choline 0 0.014 -9999 0 -0.43 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
DDEF1 0 0.015 -9999 0 -0.44 1 1
ARF1/GDP -0.001 0.019 -9999 0 -0.55 1 1
AP2M1 0.015 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.017 -9999 0 -0.51 1 1
ARFIP2 0 0.002 -9999 0 -10000 0 0
COPA 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.033 0.004 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.005 -9999 0 -10000 0 0
AP2A1 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.009 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.005 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.002 -9999 0 -10000 0 0
CYTH2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.001 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.006 0.032 -9999 0 -10000 0 0
PLD2 0 0.015 -9999 0 -0.43 1 1
ARF-GAP1/v-SNARE 0.014 0.023 -9999 0 -0.67 1 1
PIP5K1A 0 0.015 -9999 0 -0.44 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.008 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.014 -9999 0 -0.43 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.023 -9999 0 -0.67 1 1
GOSR2 0 0.006 -9999 0 -10000 0 0
USO1 0 0.006 -9999 0 -10000 0 0
GBF1 0 0.006 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.016 0.085 -9999 0 -0.47 30 30
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD2 0.018 0 -9999 0 -10000 0 0
SMAD3 0.054 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.06 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.015 0 -9999 0 -10000 0 0
CALM1 0.015 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.026 0 -9999 0 -10000 0 0
MAP3K1 0.015 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.004 0.054 -9999 0 -0.66 6 6
MAPK3 0.015 0 -9999 0 -10000 0 0
MAPK1 0.015 0 -9999 0 -10000 0 0
NUP214 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.015 0 -9999 0 -10000 0 0
CTDSP2 0.015 0 -9999 0 -10000 0 0
CTDSPL 0.015 0 -9999 0 -10000 0 0
KPNB1 0.015 0 -9999 0 -10000 0 0
TGFBRAP1 0.009 0.071 -9999 0 -0.86 6 6
UBE2I 0.015 0 -9999 0 -10000 0 0
NUP153 0.015 0 -9999 0 -10000 0 0
KPNA2 0.015 0 -9999 0 -10000 0 0
PIAS4 0.015 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.013 -9999 0 -0.4 1 1
MDM2/SUMO1 0 0 -9999 0 -10000 0 0
HDAC4 0.014 0.029 -9999 0 -0.86 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.037 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.016 -9999 0 -0.48 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0.015 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.015 0 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.001 0.026 -9999 0 -0.55 2 2
FBXW11 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
CHUK 0.015 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.018 -9999 0 -10000 0 0
NFKB1 0.014 0.029 -9999 0 -0.86 1 1
MAP3K14 0.013 0.036 -9999 0 -0.74 2 2
NF kappa B1 p50/RelB -0.001 0.022 -9999 0 -0.66 1 1
RELB 0.015 0 -9999 0 -10000 0 0
NFKB2 0.015 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 889 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Y8.A8S1 TCGA.Y8.A8S0 TCGA.Y8.A8RZ TCGA.Y8.A8RY
109_MAP3K5 -0.1 0.071 0.071 0.071
47_PPARGC1A 0.015 0.015 0.015 0.015
105_BMP4 0.015 0.015 0.015 0.015
105_BMP6 0.015 0.015 -0.86 0.015
105_BMP7 0.015 0.015 -0.86 0.015
105_BMP2 0.015 0.015 0.015 0.015
131_RELN/VLDLR 0 -0.42 0 0
30_TGFB1/TGF beta receptor Type II 0.015 0.015 0.015 0.015
84_STAT5B -0.038 -0.16 -0.14 -0.16
84_STAT5A -0.038 -0.16 -0.14 -0.16
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/KIPAN-TP/19438837/KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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