PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1D21W4D
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 34 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 76
EGFR-dependent Endothelin signaling events 61
Angiopoietin receptor Tie2-mediated signaling 46
FOXA2 and FOXA3 transcription factor networks 43
Glypican 2 network 36
PDGFR-alpha signaling pathway 31
Thromboxane A2 receptor signaling 26
Glypican 1 network 24
Arf6 signaling events 22
amb2 Integrin signaling 20
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 161 . 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 ( 161 ).

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 0.4720 76 2604 34 -0.67 0.012 1000 -1000 -0.053 -1000
EGFR-dependent Endothelin signaling events 0.3789 61 1292 21 -0.76 0.012 1000 -1000 -0.07 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2857 46 4101 88 -0.9 0.075 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.2671 43 1978 46 -1.3 0.019 1000 -1000 -0.1 -1000
Glypican 2 network 0.2236 36 147 4 -0.13 -1000 1000 -1000 -0.036 -1000
PDGFR-alpha signaling pathway 0.1925 31 1405 44 -0.33 0.028 1000 -1000 -0.068 -1000
Thromboxane A2 receptor signaling 0.1615 26 2744 105 -0.76 0.073 1000 -1000 -0.075 -1000
Glypican 1 network 0.1491 24 1192 48 -0.47 0.033 1000 -1000 -0.042 -1000
Arf6 signaling events 0.1366 22 1400 62 -0.76 0.015 1000 -1000 -0.063 -1000
amb2 Integrin signaling 0.1242 20 1640 82 -0.54 0.012 1000 -1000 -0.079 -1000
TCGA08_retinoblastoma 0.1180 19 156 8 -0.26 0.069 1000 -1000 -0.019 -1000
FOXM1 transcription factor network 0.1180 19 982 51 -0.27 0.024 1000 -1000 -0.18 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1118 18 1476 78 -0.32 0.062 1000 -1000 -0.081 -1000
BMP receptor signaling 0.1056 17 1427 81 -0.53 0.012 1000 -1000 -0.1 -1000
Endothelins 0.1056 17 1644 96 -0.61 0.012 1000 -1000 -0.09 -1000
TCGA08_p53 0.1056 17 125 7 -0.18 0.11 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 0.1056 17 757 44 -0.15 0.012 1000 -1000 -0.053 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1056 17 2137 125 -0.17 0.014 1000 -1000 -0.097 -1000
IL4-mediated signaling events 0.0870 14 1361 91 -0.91 0.5 1000 -1000 -0.17 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0870 14 996 68 -0.6 0.08 1000 -1000 -0.12 -1000
Signaling events mediated by PTP1B 0.0807 13 1036 76 -0.76 0.1 1000 -1000 -0.082 -1000
Integrins in angiogenesis 0.0807 13 1143 84 -0.56 0.033 1000 -1000 -0.091 -1000
S1P1 pathway 0.0745 12 464 36 -0.16 0.012 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 0.0745 12 313 26 -0.24 0.015 1000 -1000 -0.071 -1000
Aurora B signaling 0.0745 12 864 67 -0.28 0.012 1000 -1000 -0.07 -1000
Aurora C signaling 0.0683 11 77 7 -0.15 0.012 1000 -1000 -0.043 -1000
TCR signaling in naïve CD8+ T cells 0.0683 11 1088 93 -0.57 0.26 1000 -1000 -0.082 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0683 11 886 74 -0.76 0.049 1000 -1000 -0.095 -1000
Syndecan-4-mediated signaling events 0.0683 11 743 67 -0.51 0.084 1000 -1000 -0.1 -1000
FoxO family signaling 0.0621 10 661 64 -0.99 0.084 1000 -1000 -0.078 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0621 10 1318 120 -0.34 0.16 1000 -1000 -0.091 -1000
Syndecan-1-mediated signaling events 0.0559 9 328 34 -0.12 0.012 1000 -1000 -0.064 -1000
Signaling events mediated by the Hedgehog family 0.0559 9 473 52 -0.1 0.038 1000 -1000 -0.08 -1000
E-cadherin signaling events 0.0559 9 45 5 -0.069 0.012 1000 -1000 -0.046 -1000
Coregulation of Androgen receptor activity 0.0497 8 609 76 -0.8 0.023 1000 -1000 -0.055 -1000
IL27-mediated signaling events 0.0497 8 429 51 -0.99 0.14 1000 -1000 -0.097 -1000
LPA4-mediated signaling events 0.0435 7 95 12 -0.23 0.019 1000 -1000 -0.028 -1000
ErbB4 signaling events 0.0435 7 483 69 -0.38 0.12 1000 -1000 -0.084 -1000
HIF-1-alpha transcription factor network 0.0435 7 539 76 -0.16 0.052 1000 -1000 -0.14 -1000
p75(NTR)-mediated signaling 0.0435 7 938 125 -0.52 0.035 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0435 7 858 114 -0.6 0.16 1000 -1000 -0.078 -1000
Signaling events regulated by Ret tyrosine kinase 0.0435 7 628 82 -0.13 0.012 1000 -1000 -0.088 -1000
Nongenotropic Androgen signaling 0.0435 7 406 52 -0.093 0.024 1000 -1000 -0.062 -1000
Wnt signaling 0.0435 7 53 7 -0.044 0.012 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0435 7 554 75 -0.27 0.055 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.0373 6 574 87 -0.19 0.023 1000 -1000 -0.14 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0373 6 193 28 -0.16 0.012 1000 -1000 -0.065 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0373 6 332 54 -0.25 0.026 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0373 6 43 7 -0.035 0 1000 -1000 -0.026 -1000
Noncanonical Wnt signaling pathway 0.0373 6 177 26 -0.22 0.012 1000 -1000 -0.084 -1000
Presenilin action in Notch and Wnt signaling 0.0373 6 368 61 -0.21 0.093 1000 -1000 -0.074 -1000
Reelin signaling pathway 0.0373 6 364 56 -0.19 0.012 1000 -1000 -0.092 -1000
Calcium signaling in the CD4+ TCR pathway 0.0373 6 211 31 -0.16 0.016 1000 -1000 -0.094 -1000
Plasma membrane estrogen receptor signaling 0.0373 6 553 86 -0.16 0.028 1000 -1000 -0.083 -1000
Visual signal transduction: Rods 0.0373 6 316 52 -0.23 0.012 1000 -1000 -0.091 -1000
Regulation of nuclear SMAD2/3 signaling 0.0311 5 743 136 -0.6 0.065 1000 -1000 -0.077 -1000
Syndecan-2-mediated signaling events 0.0311 5 359 69 -0.54 0.042 1000 -1000 -0.059 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0311 5 264 52 -0.36 0.059 1000 -1000 -0.064 -1000
Syndecan-3-mediated signaling events 0.0311 5 182 35 -0.19 0.012 1000 -1000 -0.07 -1000
Regulation of Telomerase 0.0311 5 563 102 -0.76 0.044 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.0311 5 351 60 -0.13 0.024 1000 -1000 -0.15 -1000
S1P3 pathway 0.0311 5 236 42 -0.16 0.017 1000 -1000 -0.061 -1000
E-cadherin signaling in keratinocytes 0.0311 5 215 43 -0.3 0.035 1000 -1000 -0.069 -1000
Class IB PI3K non-lipid kinase events 0.0311 5 15 3 -0.005 -1000 1000 -1000 -0.012 -1000
Regulation of Androgen receptor activity 0.0311 5 400 70 -0.9 0.029 1000 -1000 -0.065 -1000
Caspase cascade in apoptosis 0.0248 4 312 74 -0.41 0.039 1000 -1000 -0.06 -1000
PLK2 and PLK4 events 0.0248 4 14 3 -0.014 0.008 1000 -1000 -0.023 -1000
Osteopontin-mediated events 0.0248 4 173 38 -0.13 0.039 1000 -1000 -0.11 -1000
Fc-epsilon receptor I signaling in mast cells 0.0248 4 415 97 -0.14 0.031 1000 -1000 -0.087 -1000
Ceramide signaling pathway 0.0248 4 337 76 -0.76 0.25 1000 -1000 -0.072 -1000
S1P5 pathway 0.0248 4 82 17 -0.059 0.03 1000 -1000 -0.053 -1000
EPHB forward signaling 0.0248 4 368 85 -0.16 0.06 1000 -1000 -0.093 -1000
E-cadherin signaling in the nascent adherens junction 0.0248 4 364 76 -0.069 0.029 1000 -1000 -0.085 -1000
IL2 signaling events mediated by STAT5 0.0248 4 94 22 -0.055 0.041 1000 -1000 -0.038 -1000
BCR signaling pathway 0.0248 4 467 99 -0.097 0.027 1000 -1000 -0.093 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0248 4 164 33 -0.26 0.036 1000 -1000 -0.069 -1000
PDGFR-beta signaling pathway 0.0248 4 407 97 -0.13 0.047 1000 -1000 -0.089 -1000
BARD1 signaling events 0.0186 3 195 57 -0.12 0.027 1000 -1000 -0.07 -1000
JNK signaling in the CD4+ TCR pathway 0.0186 3 67 17 -0.045 0.027 1000 -1000 -0.056 -1000
PLK1 signaling events 0.0186 3 285 85 -0.12 0.021 1000 -1000 -0.059 -1000
Insulin-mediated glucose transport 0.0186 3 120 32 -0.14 0.067 1000 -1000 -0.068 -1000
IFN-gamma pathway 0.0186 3 216 68 -0.42 0.065 1000 -1000 -0.088 -1000
IL1-mediated signaling events 0.0186 3 210 62 -0.16 0.06 1000 -1000 -0.1 -1000
IL2 signaling events mediated by PI3K 0.0186 3 197 58 -0.061 0.057 1000 -1000 -0.088 -1000
Canonical Wnt signaling pathway 0.0186 3 153 51 -0.2 0.1 1000 -1000 -0.062 -1000
Regulation of p38-alpha and p38-beta 0.0186 3 163 54 -0.18 0.06 1000 -1000 -0.061 -1000
TCGA08_rtk_signaling 0.0186 3 86 26 -0.27 0.03 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 0.0186 3 106 34 -0.034 0.022 1000 -1000 -0.046 -1000
Ras signaling in the CD4+ TCR pathway 0.0186 3 60 17 -0.013 0.027 1000 -1000 -0.053 -1000
Cellular roles of Anthrax toxin 0.0124 2 79 39 -0.19 0.019 1000 -1000 -0.029 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0124 2 229 85 -0.13 0.042 1000 -1000 -0.068 -1000
Nectin adhesion pathway 0.0124 2 181 63 -0.12 0.05 1000 -1000 -0.075 -1000
Ephrin B reverse signaling 0.0124 2 104 48 -0.072 0.047 1000 -1000 -0.066 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0124 2 208 83 -0.29 0.049 1000 -1000 -0.082 -1000
FAS signaling pathway (CD95) 0.0124 2 94 47 -0.11 0.022 1000 -1000 -0.062 -1000
LPA receptor mediated events 0.0124 2 290 102 -0.13 0.034 1000 -1000 -0.098 -1000
Class I PI3K signaling events 0.0124 2 170 73 -0.06 0.027 1000 -1000 -0.08 -1000
Arf6 trafficking events 0.0124 2 160 71 -0.37 0.042 1000 -1000 -0.076 -1000
IGF1 pathway 0.0124 2 139 57 -0.037 0.042 1000 -1000 -0.098 -1000
S1P4 pathway 0.0124 2 68 25 -0.059 0.027 1000 -1000 -0.054 -1000
ErbB2/ErbB3 signaling events 0.0062 1 114 65 -0.13 0.032 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class II 0.0062 1 103 75 -0.16 0.038 1000 -1000 -0.073 -1000
Visual signal transduction: Cones 0.0062 1 52 38 -0.02 0.012 1000 -1000 -0.063 -1000
Hedgehog signaling events mediated by Gli proteins 0.0062 1 71 65 -0.059 0.066 1000 -1000 -0.067 -1000
Aurora A signaling 0.0062 1 111 60 -0.14 0.035 1000 -1000 -0.061 -1000
Class I PI3K signaling events mediated by Akt 0.0062 1 73 68 -0.14 0.049 1000 -1000 -0.067 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0062 1 39 37 -0.037 0.036 1000 -1000 -0.058 -1000
HIF-2-alpha transcription factor network 0.0062 1 74 43 -0.22 0.13 1000 -1000 -0.086 -1000
Signaling mediated by p38-gamma and p38-delta 0.0062 1 20 15 -0.004 0.025 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0062 1 93 58 -0.064 0.033 1000 -1000 -0.079 -1000
Insulin Pathway 0.0062 1 93 74 -0.042 0.035 1000 -1000 -0.098 -1000
VEGFR1 specific signals 0.0062 1 87 56 -0.014 0.045 1000 -1000 -0.072 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 4 23 -0.008 0.046 1000 -1000 -0.076 -1000
Canonical NF-kappaB pathway 0.0000 0 23 39 -0.016 0.079 1000 -1000 -0.076 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.012 0.039 1000 -1000 -0.067 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0 0.012 1000 -1000 -0.04 -1000
Arf6 downstream pathway 0.0000 0 3 43 -0.023 0.023 1000 -1000 -0.042 -1000
EPO signaling pathway 0.0000 0 41 55 -0.044 0.077 1000 -1000 -0.093 -1000
mTOR signaling pathway 0.0000 0 30 53 -0.007 0.029 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class III 0.0000 0 18 40 -0.02 0.022 1000 -1000 -0.047 -1000
TRAIL signaling pathway 0.0000 0 33 48 -0.018 0.045 1000 -1000 -0.073 -1000
ceramide signaling pathway 0.0000 0 26 49 -0.014 0.047 1000 -1000 -0.057 -1000
Signaling events mediated by HDAC Class I 0.0000 0 100 104 -0.16 0.055 1000 -1000 -0.071 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 15 36 -0.02 0.022 1000 -1000 -0.076 -1000
Atypical NF-kappaB pathway 0.0000 0 10 31 -0.001 0.046 1000 -1000 -0.052 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0000 0 37 45 -0.029 0.06 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.003 0.029 1000 -1000 -0.056 -1000
Rapid glucocorticoid signaling 0.0000 0 8 20 -0.004 0.012 1000 -1000 -0.042 -1000
p38 MAPK signaling pathway 0.0000 0 35 44 -0.042 0.041 1000 -1000 -0.072 -1000
Arf1 pathway 0.0000 0 7 54 -0.008 0.031 1000 -1000 -0.044 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.012 1000 -1000 -0.053 -1000
Total NA 1014 59160 7203 -33 -2000 131000 -131000 -9.6 -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 0.54 0.38 0.78 109 -10000 0 109
KIRREL -0.13 0.26 -10000 0 -0.93 15 15
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.54 0.38 -10000 0 -0.78 109 109
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.6 0.41 -10000 0 -0.78 124 124
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.45 0.33 -10000 0 -0.59 124 124
FYN -0.57 0.39 -10000 0 -0.74 124 124
mol:Ca2+ -0.59 0.4 -10000 0 -0.77 124 124
mol:DAG -0.6 0.4 -10000 0 -0.78 124 124
NPHS2 -0.43 0.44 -10000 0 -0.92 70 70
mol:IP3 -0.6 0.4 -10000 0 -0.78 124 124
regulation of endocytosis -0.54 0.36 -10000 0 -0.69 124 124
Nephrin/NEPH1/podocin/Cholesterol -0.61 0.41 -10000 0 -0.79 124 124
establishment of cell polarity -0.54 0.38 -10000 0 -0.78 109 109
Nephrin/NEPH1/podocin/NCK1-2 -0.56 0.39 -10000 0 -0.73 124 124
Nephrin/NEPH1/beta Arrestin2 -0.54 0.38 -10000 0 -0.71 124 124
NPHS1 -0.6 0.42 -10000 0 -0.91 106 106
Nephrin/NEPH1/podocin -0.58 0.39 -10000 0 -0.75 124 124
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.6 0.41 -10000 0 -0.78 124 124
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.6 0.41 -10000 0 -0.78 124 124
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.67 0.44 -10000 0 -0.83 132 132
cytoskeleton organization -0.59 0.42 -10000 0 -0.78 124 124
Nephrin/NEPH1 -0.42 0.3 -10000 0 -0.61 109 109
Nephrin/NEPH1/ZO-1 -0.45 0.33 -10000 0 -0.66 109 109
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 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
EGF/EGFR -0.45 0.18 -9999 0 -0.5 143 143
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.44 0.16 -9999 0 -0.5 142 142
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.02 0.16 -9999 0 -0.86 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.76 0.28 -9999 0 -0.86 142 142
EGF/EGFR dimer/SHC -0.51 0.19 -9999 0 -0.58 142 142
mol:GDP -0.43 0.16 -9999 0 -0.49 142 142
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.027 -9999 0 -0.34 1 1
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.4 0.14 -9999 0 -0.45 142 142
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.4 0.15 -9999 0 -0.46 142 142
FRAP1 -0.41 0.16 -9999 0 -0.47 142 142
EGF/EGFR dimer -0.59 0.21 -9999 0 -0.66 142 142
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.026 0.13 -9999 0 -0.66 6 6
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.47 0.56 -10000 0 -1 78 78
NCK1/PAK1/Dok-R -0.22 0.22 -10000 0 -0.45 78 78
NCK1/Dok-R -0.66 0.7 -10000 0 -1.3 78 78
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.075 0.12 0.25 49 -10000 0 49
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.011 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.06 0.14 -10000 0 -0.35 5 5
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.58 0.62 -10000 0 -1.2 78 78
FN1 -0.018 0.098 -10000 0 -0.34 14 14
PLD2 -0.66 0.78 -10000 0 -1.4 78 78
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.042 0.21 -10000 0 -0.86 10 10
ELK1 -0.54 0.65 -10000 0 -1.2 78 78
GRB7 0.012 0 -10000 0 -10000 0 0
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.64 0.67 -10000 0 -1.3 78 78
CDKN1A -0.31 0.38 -10000 0 -0.69 76 76
ITGA5 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.66 0.7 -10000 0 -1.3 78 78
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO -0.32 0.4 -10000 0 -0.73 78 78
PLG -0.9 0.72 -10000 0 -1.6 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.44 0.52 -10000 0 -0.97 78 78
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.002 -10000 0 -10000 0 0
ANGPT2 -0.27 0.35 -10000 0 -0.69 57 57
BMX -0.66 0.78 -10000 0 -1.4 78 78
ANGPT1 -0.44 0.67 -10000 0 -1.4 49 49
tube development -0.36 0.43 -10000 0 -0.79 76 76
ANGPT4 0.002 0.047 -10000 0 -0.34 3 3
response to hypoxia -0.031 0.037 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.71 0.82 -10000 0 -1.5 78 78
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.013 0.002 -10000 0 -10000 0 0
STAT5A (dimer) -0.42 0.5 -10000 0 -0.93 76 76
mol:L-citrulline -0.32 0.4 -10000 0 -0.73 78 78
AGTR1 -0.28 0.41 -10000 0 -0.86 54 54
MAPK14 -0.64 0.75 -10000 0 -1.4 78 78
Tie2/SHP2 -0.56 0.64 -10000 0 -1.3 67 67
TEK -0.61 0.74 -10000 0 -1.5 67 67
RPS6KB1 -0.44 0.53 -10000 0 -0.98 78 78
Angiotensin II/AT1 -0.22 0.32 -10000 0 -0.67 54 54
Tie2/Ang1/GRB2 -0.69 0.82 -10000 0 -1.5 78 78
MAPK3 -0.56 0.68 -10000 0 -1.2 78 78
MAPK1 -0.56 0.68 -10000 0 -1.2 78 78
Tie2/Ang1/GRB7 -0.69 0.82 -10000 0 -1.5 78 78
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.66 0.78 -10000 0 -1.4 78 78
PI3K -0.57 0.67 -10000 0 -1.2 78 78
FES -0.64 0.74 -10000 0 -1.4 78 78
Crk/Dok-R -0.66 0.7 -10000 0 -1.3 78 78
Tie2/Ang1/ABIN2 -0.69 0.82 -10000 0 -1.5 78 78
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.4 0.49 -10000 0 -0.9 78 78
STAT5A 0.012 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.44 0.53 -10000 0 -0.98 78 78
Tie2/Ang2 -0.56 0.63 -10000 0 -1.2 76 76
Tie2/Ang1 -0.77 0.92 -10000 0 -1.7 78 78
FOXO1 -0.4 0.5 -10000 0 -0.9 78 78
ELF1 -0.025 0.053 -10000 0 -10000 0 0
ELF2 -0.67 0.79 -10000 0 -1.4 78 78
mol:Choline -0.6 0.71 -10000 0 -1.3 78 78
cell migration -0.12 0.12 -10000 0 -0.25 76 76
FYN -0.43 0.5 -10000 0 -0.93 76 76
DOK2 -0.015 0.11 -10000 0 -0.38 11 11
negative regulation of cell cycle -0.27 0.34 -10000 0 -0.62 76 76
ETS1 -0.057 0.11 -10000 0 -10000 0 0
PXN -0.34 0.43 -10000 0 -0.78 78 78
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 -0.38 0.47 -10000 0 -0.85 78 78
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.082 0.16 -10000 0 -0.48 9 9
MAPKKK cascade -0.6 0.71 -10000 0 -1.3 78 78
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.69 0.82 -10000 0 -1.5 78 78
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis -0.28 0.36 -10000 0 -0.64 78 78
mol:Phosphatidic acid -0.6 0.71 -10000 0 -1.3 78 78
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.32 0.4 -10000 0 -0.73 78 78
Rac1/GTP -0.44 0.45 -10000 0 -0.9 78 78
MMP2 -0.66 0.78 -10000 0 -1.4 78 78
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.55 0.44 -9999 0 -1.1 53 53
PCK1 -1.2 0.7 -9999 0 -1.6 112 112
HNF4A -0.66 0.6 -9999 0 -1.4 54 54
KCNJ11 -0.57 0.45 -9999 0 -1.1 52 52
AKT1 -0.24 0.14 -9999 0 -0.46 2 2
response to starvation -0.005 0.016 -9999 0 -10000 0 0
DLK1 -0.59 0.46 -9999 0 -1.1 53 53
NKX2-1 -0.13 0.16 -9999 0 -0.58 1 1
ACADM -0.55 0.44 -9999 0 -1.1 49 49
TAT -0.46 0.23 -9999 0 -0.75 38 38
CEBPB -0.037 0.065 -9999 0 -0.4 4 4
CEBPA -0.06 0.12 -9999 0 -0.42 14 14
TTR -0.78 0.42 -9999 0 -0.99 103 103
PKLR -0.72 0.66 -9999 0 -1.5 57 57
APOA1 -0.71 0.62 -9999 0 -1.4 60 60
CPT1C -0.56 0.45 -9999 0 -1.1 52 52
ALAS1 -0.22 0.15 -9999 0 -10000 0 0
TFRC -0.6 0.29 -9999 0 -0.85 75 75
FOXF1 0 0.097 -9999 0 -0.86 2 2
NF1 0.019 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.052 0.13 -9999 0 -0.91 3 3
CPT1A -0.55 0.44 -9999 0 -1.1 50 50
HMGCS1 -0.55 0.44 -9999 0 -1.1 50 50
NR3C1 0.005 0.044 -9999 0 -10000 0 0
CPT1B -0.55 0.44 -9999 0 -1.1 50 50
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.008 -9999 0 -10000 0 0
GCK -0.55 0.44 -9999 0 -1.1 50 50
CREB1 -0.083 0.063 -9999 0 -10000 0 0
IGFBP1 -0.34 0.44 -9999 0 -1.5 19 19
PDX1 -0.28 0.22 -9999 0 -0.85 9 9
UCP2 -0.55 0.44 -9999 0 -1.1 51 51
ALDOB -1.3 0.42 -9999 0 -1.4 154 154
AFP -0.48 0.37 -9999 0 -0.86 48 48
BDH1 -0.55 0.44 -9999 0 -1.1 50 50
HADH -0.56 0.45 -9999 0 -1.1 51 51
F2 -0.65 0.53 -9999 0 -1.3 51 51
HNF1A -0.052 0.13 -9999 0 -0.91 3 3
G6PC -1.2 0.6 -9999 0 -1.5 117 117
SLC2A2 -0.52 0.6 -9999 0 -1.7 29 29
INS 0.006 0.047 -9999 0 -10000 0 0
FOXA1 -0.25 0.14 -9999 0 -0.52 21 21
FOXA3 -0.45 0.28 -9999 0 -0.52 131 131
FOXA2 -0.66 0.5 -9999 0 -1.2 63 63
ABCC8 -0.57 0.45 -9999 0 -1.1 55 55
ALB -1.2 0.41 -9999 0 -1.3 142 142
Glypican 2 network

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
MDK -0.066 0.14 -9999 0 -0.34 36 36
GPC2 -0.12 0.17 -9999 0 -0.34 63 63
GPC2/Midkine -0.13 0.16 -9999 0 -0.43 24 24
neuron projection morphogenesis -0.13 0.16 -9999 0 -0.42 24 24
PDGFR-alpha signaling pathway

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
PDGFRA -0.28 0.41 -9999 0 -0.87 52 52
PDGF/PDGFRA/CRKL -0.21 0.31 -9999 0 -0.66 52 52
positive regulation of JUN kinase activity -0.16 0.24 -9999 0 -0.51 52 52
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.31 -9999 0 -0.67 52 52
AP1 -0.33 0.51 -9999 0 -1.4 26 26
mol:IP3 -0.21 0.33 -9999 0 -0.68 52 52
PLCG1 -0.21 0.33 -9999 0 -0.68 52 52
PDGF/PDGFRA/alphaV Integrin -0.21 0.31 -9999 0 -0.66 52 52
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.21 0.33 -9999 0 -0.68 52 52
CAV3 0.003 0.005 -9999 0 -10000 0 0
CAV1 0.01 0.027 -9999 0 -0.34 1 1
SHC/Grb2/SOS1 -0.17 0.24 -9999 0 -0.52 52 52
PDGF/PDGFRA/Shf -0.21 0.31 -9999 0 -0.66 52 52
FOS -0.3 0.52 -9999 0 -1.4 26 26
JUN -0.02 0.026 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.31 -9999 0 -0.66 52 52
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG -0.21 0.33 -9999 0 -0.68 52 52
PDGF/PDGFRA -0.27 0.41 -9999 0 -0.87 52 52
actin cytoskeleton reorganization -0.21 0.31 -9999 0 -0.66 52 52
SRF 0.028 0.011 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.18 0.27 -9999 0 -0.57 52 52
PDGF/PDGFRA/Crk/C3G -0.18 0.27 -9999 0 -0.57 52 52
JAK1 -0.2 0.32 -9999 0 -0.66 52 52
ELK1/SRF -0.14 0.26 -9999 0 -0.51 52 52
SHB 0.012 0 -9999 0 -10000 0 0
SHF 0.012 0 -9999 0 -10000 0 0
CSNK2A1 0.02 0.025 -9999 0 -10000 0 0
GO:0007205 -0.21 0.33 -9999 0 -0.69 52 52
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.24 -9999 0 -0.51 52 52
PDGF/PDGFRA/SHB -0.21 0.31 -9999 0 -0.66 52 52
PDGF/PDGFRA/Caveolin-1 -0.22 0.31 -9999 0 -0.66 52 52
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 -0.18 0.3 -9999 0 -0.62 52 52
PIK3CA 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.21 0.31 -9999 0 -0.66 52 52
JAK-STAT cascade -0.2 0.32 -9999 0 -0.66 52 52
cell proliferation -0.21 0.31 -9999 0 -0.66 52 52
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.017 0.087 -10000 0 -0.34 11 11
GNB1/GNG2 -0.091 0.089 -10000 0 -0.19 53 53
AKT1 -0.073 0.12 -10000 0 -0.21 32 32
EGF -0.76 0.28 -10000 0 -0.86 142 142
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR 0.009 0.12 -10000 0 -0.4 10 10
mol:Ca2+ -0.13 0.17 -10000 0 -0.31 72 72
LYN 0.014 0.1 -10000 0 -0.36 10 10
RhoA/GTP -0.061 0.058 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.14 0.2 -10000 0 -0.34 72 72
GNG2 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.024 0.12 -10000 0 -0.47 4 4
G beta5/gamma2 -0.12 0.12 -10000 0 -0.27 42 42
PRKCH -0.15 0.2 -10000 0 -0.36 72 72
DNM1 -0.072 0.15 -10000 0 -0.34 39 39
TXA2/TP beta/beta Arrestin3 -0.024 0.041 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.012 0.001 -10000 0 -10000 0 0
G12 family/GTP -0.15 0.14 -10000 0 -0.3 72 72
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.073 0.13 0.4 9 -10000 0 9
mol:NADP -0.015 0.15 -10000 0 -0.86 5 5
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.18 0.36 -10000 0 -0.86 35 35
mol:IP3 -0.17 0.21 -10000 0 -0.39 72 72
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.23 0.28 -10000 0 -0.53 72 72
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK 0.001 0.1 -10000 0 -0.37 10 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.004 0.12 -10000 0 -0.4 10 10
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.001 0.096 -10000 0 -0.86 2 2
PRKCB1 -0.16 0.21 -10000 0 -0.38 72 72
GNAQ 0.012 0 -10000 0 -10000 0 0
mol:L-citrulline -0.015 0.15 -10000 0 -0.86 5 5
TXA2/TXA2-R family -0.23 0.29 -10000 0 -0.54 72 72
LCK 0.01 0.1 -10000 0 -0.36 10 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.031 0.12 -10000 0 -0.47 10 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.023 0.035 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.031 0.12 -10000 0 -0.47 10 10
MAPK14 -0.086 0.14 -10000 0 -0.24 33 33
TGM2/GTP -0.19 0.24 -10000 0 -0.43 72 72
MAPK11 -0.086 0.14 -10000 0 -0.23 53 53
ARHGEF1 -0.067 0.1 -10000 0 -0.18 19 19
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.16 0.22 -10000 0 -0.39 72 72
RAB11/GDP 0.013 0.002 -10000 0 -10000 0 0
ICAM1 -0.11 0.16 -10000 0 -0.28 72 72
cAMP biosynthetic process -0.16 0.2 -10000 0 -0.36 72 72
Gq family/GTP/EBP50 -0.037 0.12 -10000 0 -0.3 9 9
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.014 0.1 -10000 0 -0.36 10 10
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.09 -10000 0 -0.34 11 11
VCAM1 -0.12 0.17 -10000 0 -0.3 73 73
TP beta/Gq family/GDP/G beta5/gamma2 -0.024 0.12 -10000 0 -0.47 4 4
platelet activation -0.12 0.18 -10000 0 -0.3 72 72
PGI2/IP -0.008 0.075 -10000 0 -0.67 2 2
PRKACA 0.014 0.046 -10000 0 -0.4 2 2
Gq family/GDP/G beta5/gamma2 -0.019 0.11 -10000 0 -0.43 4 4
TXA2/TP beta/beta Arrestin2 -0.028 0.049 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.14 -10000 0 -0.52 11 11
mol:DAG -0.19 0.24 -10000 0 -0.44 72 72
EGFR 0.012 0 -10000 0 -10000 0 0
TXA2/TP alpha -0.21 0.26 -10000 0 -0.49 72 72
Gq family/GTP -0.067 0.12 -10000 0 -0.3 35 35
YES1 0.014 0.1 -10000 0 -0.36 10 10
GNAI2/GTP -0.028 0.11 -10000 0 -0.42 10 10
PGD2/DP 0 0 -10000 0 -10000 0 0
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.014 0.1 -10000 0 -0.36 10 10
mol:NO -0.015 0.15 -10000 0 -0.86 5 5
GNA15 -0.007 0.08 -10000 0 -0.34 9 9
PGK/cGMP -0.14 0.27 -10000 0 -0.61 38 38
RhoA/GDP 0.013 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.038 0.12 -10000 0 -0.47 10 10
NOS3 -0.015 0.15 -10000 0 -0.86 5 5
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.15 0.2 -10000 0 -0.36 72 72
PRKCB -0.15 0.2 -10000 0 -0.36 72 72
PRKCE -0.15 0.2 -10000 0 -0.36 72 72
PRKCD -0.16 0.21 -10000 0 -0.39 72 72
PRKCG -0.18 0.23 -10000 0 -0.42 73 73
muscle contraction -0.21 0.27 -10000 0 -0.49 72 72
PRKCZ -0.14 0.19 -10000 0 -0.34 72 72
ARR3 0.002 0.004 -10000 0 -10000 0 0
TXA2/TP beta -0.032 0.12 -10000 0 -0.48 10 10
PRKCQ -0.16 0.2 -10000 0 -0.36 75 75
MAPKKK cascade -0.2 0.25 -10000 0 -0.46 72 72
SELE -0.18 0.23 -10000 0 -0.43 72 72
TP beta/GNAI2/GDP/G beta/gamma -0.031 0.12 -10000 0 -0.46 10 10
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.16 0.34 -10000 0 -0.86 31 31
chemotaxis -0.27 0.33 -10000 0 -0.62 72 72
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.01 0.027 -10000 0 -0.34 1 1
GNA11 -0.009 0.14 -10000 0 -0.86 4 4
Rac1/GTP 0.003 0.004 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0 0 -9999 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0 0 -9999 0 -10000 0 0
LAMA1 -0.037 0.16 -9999 0 -0.46 17 17
PRNP 0.012 0 -9999 0 -10000 0 0
GPC1/SLIT2 -0.16 0.28 -9999 0 -0.66 37 37
SMAD2 0.033 0 -9999 0 -10000 0 0
GPC1/PrPc/Cu2+ 0 0 -9999 0 -10000 0 0
GPC1/Laminin alpha1 -0.034 0.12 -9999 0 -0.66 4 4
TDGF1 -0.47 0.43 -9999 0 -0.86 89 89
CRIPTO/GPC1 -0.37 0.33 -9999 0 -0.66 89 89
APP/GPC1 0 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.31 0.3 -9999 0 -0.58 89 89
FLT1 0.001 0.096 -9999 0 -0.86 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0 0 -9999 0 -10000 0 0
SERPINC1 -0.21 0.38 -9999 0 -0.86 41 41
FYN -0.31 0.3 -9999 0 -0.58 89 89
FGR -0.32 0.3 -9999 0 -0.58 89 89
positive regulation of MAPKKK cascade -0.3 0.31 -9999 0 -0.57 89 89
SLIT2 -0.19 0.37 -9999 0 -0.83 39 39
GPC1/NRG -0.016 0.094 -9999 0 -0.66 3 3
NRG1 -0.01 0.13 -9999 0 -0.6 6 6
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.008 0.065 -9999 0 -0.58 2 2
LYN -0.31 0.3 -9999 0 -0.58 89 89
mol:Spermine 0.011 0 -9999 0 -10000 0 0
cell growth 0 0 -9999 0 -10000 0 0
BMP signaling pathway -0.012 0 -9999 0 -10000 0 0
SRC -0.31 0.3 -9999 0 -0.58 89 89
TGFBR1 0.012 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.026 0.099 -9999 0 -0.34 15 15
GPC1 0.012 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.012 0 -9999 0 -10000 0 0
VEGFA 0.01 0.027 -9999 0 -0.34 1 1
BLK -0.32 0.3 -9999 0 -0.59 89 89
HCK -0.33 0.3 -9999 0 -0.6 89 89
FGF2 0.012 0 -9999 0 -10000 0 0
FGFR1 0.012 0 -9999 0 -10000 0 0
VEGFR1 homodimer 0.001 0.096 -9999 0 -0.86 2 2
TGFBR2 0.012 0 -9999 0 -10000 0 0
cell death 0 0 -9999 0 -10000 0 0
ATIII/GPC1 -0.17 0.29 -9999 0 -0.66 41 41
PLA2G2A/GPC1 -0.02 0.064 -9999 0 -10000 0 0
LCK -0.31 0.3 -9999 0 -0.58 89 89
neuron differentiation -0.016 0.094 -9999 0 -0.66 3 3
PrPc/Cu2+ 0 0 -9999 0 -10000 0 0
APP 0.012 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.012 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.014 0.035 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
EPHA2 0.01 0.027 -9999 0 -0.34 1 1
USP6 -0.001 0.066 -9999 0 -0.34 6 6
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.59 0.22 -9999 0 -0.66 142 142
ARRB2 -0.002 0.044 -9999 0 -10000 0 0
mol:GTP 0.015 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0 -9999 0 -10000 0 0
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR 0.008 0.028 -9999 0 -0.34 1 1
EGF -0.76 0.28 -9999 0 -0.86 142 142
somatostatin receptor activity 0 0 -9999 0 -0.001 61 61
ARAP2 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.13 0.12 -9999 0 -0.28 52 52
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 55 55
ITGA2B -0.016 0.095 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.012 -9999 0 -10000 0 0
ADAP1 0.012 0 -9999 0 -10000 0 0
KIF13B 0.012 0 -9999 0 -10000 0 0
HGF/MET -0.055 0.15 -9999 0 -0.69 7 7
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.18 0.13 -9999 0 -0.32 61 61
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.51 0.19 -9999 0 -0.58 142 142
ADRB2 -0.012 0.088 -9999 0 -0.34 11 11
receptor agonist activity 0 0 -9999 0 0 61 61
actin filament binding 0 0 -9999 0 -0.001 61 61
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.14 -9999 0 -0.6 8 8
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 -0.001 0 -9999 0 -0.001 60 60
ARF6/GDP -0.03 0.06 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.12 0.12 -9999 0 -0.38 10 10
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.029 0.091 -9999 0 -0.53 4 4
ACAP1 -0.031 0.12 -9999 0 -0.34 20 20
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.015 0.057 -9999 0 -10000 0 0
EFNA1 0.012 0 -9999 0 -10000 0 0
HGF -0.026 0.18 -9999 0 -0.86 7 7
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 35 35
endosomal lumen acidification 0 0 -9999 0 -0.001 61 61
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.01 0.027 -9999 0 -0.34 1 1
GNAQ/ARNO 0.007 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 53 53
MET -0.029 0.11 -9999 0 -0.34 19 19
GNA14 -0.16 0.34 -9999 0 -0.86 31 31
GNA15 -0.007 0.08 -9999 0 -0.34 9 9
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 60 60
GNA11 -0.01 0.14 -9999 0 -0.86 4 4
LHCGR -0.027 0.099 -9999 0 -0.34 15 15
AGTR1 -0.28 0.41 -9999 0 -0.86 54 54
desensitization of G-protein coupled receptor protein signaling pathway -0.014 0.057 -9999 0 -10000 0 0
IPCEF1/ARNO -0.4 0.15 -9999 0 -0.46 142 142
alphaIIb/beta3 Integrin -0.04 0.12 -9999 0 -0.66 4 4
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.057 0.12 -9999 0 -0.38 14 14
alphaM/beta2 Integrin/GPIbA -0.054 0.12 -9999 0 -0.39 13 13
alphaM/beta2 Integrin/proMMP-9 -0.12 0.17 -9999 0 -0.44 26 26
PLAUR -0.016 0.095 -9999 0 -0.34 13 13
HMGB1 0.008 0.016 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.051 0.1 -9999 0 -10000 0 0
AGER -0.027 0.11 -9999 0 -0.34 16 16
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG -0.022 0.1 -9999 0 -0.34 16 16
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.08 0.11 -9999 0 -0.46 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.19 -9999 0 -0.36 58 58
CYR61 -0.015 0.15 -9999 0 -0.86 5 5
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.22 0.15 -9999 0 -0.45 39 39
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.058 0.24 -9999 0 -0.86 13 13
MYH2 -0.32 0.23 -9999 0 -0.59 47 47
MST1R -0.032 0.13 -9999 0 -0.36 19 19
leukocyte activation during inflammatory response -0.12 0.19 -9999 0 -0.54 23 23
APOB -0.047 0.2 -9999 0 -0.62 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.003 0.078 -9999 0 -0.51 3 3
JAM3 0.012 0 -9999 0 -10000 0 0
GP1BA 0.007 0.068 -9999 0 -0.86 1 1
alphaM/beta2 Integrin/CTGF -0.055 0.11 -9999 0 -0.36 14 14
alphaM/beta2 Integrin -0.27 0.19 -9999 0 -0.48 52 52
JAM3 homodimer 0.012 0 -9999 0 -10000 0 0
ICAM2 0.012 0 -9999 0 -10000 0 0
ICAM1 0.01 0.027 -9999 0 -0.34 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.27 0.18 -9999 0 -0.47 53 53
cell adhesion -0.054 0.12 -9999 0 -0.39 13 13
NFKB1 -0.057 0.16 -9999 0 -0.5 4 4
THY1 -0.22 0.38 -9999 0 -0.86 43 43
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.089 0.2 -9999 0 -0.59 22 22
alphaM/beta2 Integrin/LRP/tPA -0.086 0.17 -9999 0 -0.58 13 13
IL6 -0.11 0.31 -9999 0 -0.99 15 15
ITGB2 -0.053 0.13 -9999 0 -0.34 28 28
elevation of cytosolic calcium ion concentration -0.059 0.13 -9999 0 -0.49 6 6
alphaM/beta2 Integrin/JAM2/JAM3 -0.053 0.11 -9999 0 -0.54 3 3
JAM2 -0.004 0.12 -9999 0 -0.86 3 3
alphaM/beta2 Integrin/ICAM1 -0.059 0.1 -9999 0 -0.47 3 3
alphaM/beta2 Integrin/uPA/Plg -0.37 0.27 -9999 0 -0.57 98 98
RhoA/GTP -0.33 0.24 -9999 0 -0.59 55 55
positive regulation of phagocytosis -0.21 0.16 -9999 0 -0.44 39 39
Ron/MSP -0.033 0.099 -9999 0 -0.66 2 2
alphaM/beta2 Integrin/uPAR/uPA -0.06 0.13 -9999 0 -0.49 6 6
alphaM/beta2 Integrin/uPAR -0.065 0.13 -9999 0 -0.4 19 19
PLAU 0.007 0.068 -9999 0 -0.86 1 1
PLAT -0.06 0.24 -9999 0 -0.82 14 14
actin filament polymerization -0.3 0.21 -9999 0 -0.55 47 47
MST1 0.007 0.068 -9999 0 -0.86 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.12 0.2 -9999 0 -0.54 23 23
TNF -0.057 0.19 -9999 0 -0.67 5 5
RAP1B 0.012 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.055 0.11 -9999 0 -0.37 14 14
fibrinolysis -0.36 0.27 -9999 0 -0.57 98 98
HCK -0.034 0.13 -9999 0 -0.36 20 20
dendritic cell antigen processing and presentation -0.27 0.18 -9999 0 -0.47 53 53
VTN -0.26 0.4 -9999 0 -0.82 52 52
alphaM/beta2 Integrin/CYR61 -0.069 0.14 -9999 0 -0.42 18 18
LPA -0.072 0.24 -9999 0 -0.86 14 14
LRP1 0.012 0 -9999 0 -10000 0 0
cell migration -0.11 0.16 -9999 0 -0.5 13 13
FN1 -0.018 0.098 -9999 0 -0.34 14 14
alphaM/beta2 Integrin/Thy1 -0.2 0.26 -9999 0 -0.56 54 54
MPO -0.012 0.088 -9999 0 -0.34 11 11
KNG1 -0.54 0.41 -9999 0 -0.86 102 102
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.31 0.23 -9999 0 -0.61 39 39
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.52 0.42 -9999 0 -0.86 97 97
CTGF 0.007 0.068 -9999 0 -0.86 1 1
alphaM/beta2 Integrin/Hck -0.076 0.16 -9999 0 -0.45 21 21
ITGAM -0.024 0.1 -9999 0 -0.33 15 15
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.1 0.18 -9999 0 -0.51 22 22
HP -0.032 0.11 -9999 0 -0.34 20 20
leukocyte adhesion -0.19 0.24 -9999 0 -0.54 44 44
SELP -0.058 0.24 -9999 0 -0.86 13 13
TCGA08_retinoblastoma

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
CDKN2B -0.005 0.059 -10000 0 -0.33 5 5
CDKN2C 0.034 0.03 -10000 0 -0.3 1 1
CDKN2A -0.26 0.15 -10000 0 -0.34 125 125
CCND2 0.054 0.044 0.19 5 -10000 0 5
RB1 -0.063 0.043 -10000 0 -0.19 5 5
CDK4 0.069 0.045 0.2 5 -10000 0 5
CDK6 0.065 0.044 0.2 5 -10000 0 5
G1/S progression 0.059 0.048 0.19 5 -10000 0 5
FOXM1 transcription factor 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
NFATC3 -0.11 0.49 -9999 0 -0.98 22 22
PLK1 -0.038 0.18 -9999 0 -10000 0 0
BIRC5 -0.098 0.21 -9999 0 -10000 0 0
HSPA1B -0.11 0.49 -9999 0 -0.98 22 22
MAP2K1 0.022 0.039 -9999 0 -10000 0 0
BRCA2 -0.12 0.5 -9999 0 -1 22 22
FOXM1 -0.15 0.57 -9999 0 -1.1 27 27
XRCC1 -0.11 0.49 -9999 0 -0.99 21 21
FOXM1B/p19 -0.19 0.43 -9999 0 -0.96 26 26
Cyclin D1/CDK4 -0.096 0.46 -9999 0 -0.95 17 17
CDC2 -0.12 0.51 -9999 0 -0.99 26 26
TGFA -0.091 0.46 -9999 0 -0.96 17 17
SKP2 -0.11 0.49 -9999 0 -0.99 21 21
CCNE1 -0.018 0.1 -9999 0 -0.35 14 14
CKS1B -0.11 0.49 -9999 0 -0.99 21 21
RB1 -0.12 0.18 -9999 0 -0.54 10 10
FOXM1C/SP1 -0.14 0.52 -9999 0 -1.1 24 24
AURKB -0.11 0.21 -9999 0 -10000 0 0
CENPF -0.14 0.53 -9999 0 -1 30 30
CDK4 0.016 0.015 -9999 0 -10000 0 0
MYC -0.087 0.44 -9999 0 -0.9 17 17
CHEK2 0.003 0.091 -9999 0 -0.33 9 9
ONECUT1 -0.11 0.48 -9999 0 -0.96 23 23
CDKN2A -0.25 0.14 -9999 0 -0.33 125 125
LAMA4 -0.12 0.49 -9999 0 -1 19 19
FOXM1B/HNF6 -0.14 0.53 -9999 0 -1.1 23 23
FOS -0.23 0.62 -9999 0 -1.2 38 38
SP1 0.013 0.002 -9999 0 -10000 0 0
CDC25B -0.11 0.49 -9999 0 -1 21 21
response to radiation 0.007 0.036 -9999 0 -10000 0 0
CENPB -0.11 0.49 -9999 0 -0.98 22 22
CENPA -0.15 0.53 -9999 0 -1 31 31
NEK2 -0.15 0.53 -9999 0 -1 28 28
HIST1H2BA -0.12 0.49 -9999 0 -0.99 22 22
CCNA2 -0.055 0.14 -9999 0 -0.35 31 31
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.14 0.53 -9999 0 -1.1 22 22
CCNB2 -0.15 0.53 -9999 0 -1 30 30
CCNB1 -0.12 0.51 -9999 0 -1 22 22
ETV5 -0.11 0.49 -9999 0 -0.98 22 22
ESR1 -0.15 0.53 -9999 0 -1 27 27
CCND1 -0.096 0.47 -9999 0 -0.95 19 19
GSK3A 0.024 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.021 0.14 -9999 0 -0.39 13 13
CDK2 0.013 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.007 0.043 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.39 -9999 0 -0.97 30 30
GAS1 -0.13 0.51 -9999 0 -1 26 26
MMP2 -0.12 0.49 -9999 0 -1 21 21
RB1/FOXM1C -0.11 0.49 -9999 0 -1 21 21
CREBBP 0.012 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.043 0.16 -10000 0 -0.38 28 28
CRKL -0.034 0.17 -10000 0 -0.41 28 28
HRAS -0.026 0.16 -10000 0 -0.44 6 6
mol:PIP3 -0.045 0.16 -10000 0 -0.39 28 28
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.044 0.18 -10000 0 -0.43 28 28
FOXO3 -0.025 0.16 -10000 0 -0.37 28 28
AKT1 -0.035 0.17 -10000 0 -0.4 28 28
BAD -0.025 0.16 -10000 0 -0.37 28 28
megakaryocyte differentiation -0.12 0.26 -10000 0 -0.51 46 46
GSK3B -0.025 0.16 -10000 0 -0.37 28 28
RAF1 -0.011 0.13 -10000 0 -0.42 2 2
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.044 0.18 -10000 0 -0.43 28 28
STAT1 -0.12 0.41 -10000 0 -1 28 28
HRAS/SPRED1 -0.055 0.11 -10000 0 -0.42 2 2
cell proliferation -0.054 0.2 -10000 0 -0.46 30 30
PIK3CA 0.012 0 -10000 0 -10000 0 0
TEC 0.012 0 -10000 0 -10000 0 0
RPS6KB1 -0.043 0.18 -10000 0 -0.43 28 28
HRAS/SPRED2 -0.055 0.11 -10000 0 -0.42 2 2
LYN/TEC/p62DOK -0.07 0.15 -10000 0 -0.4 28 28
MAPK3 0.006 0.1 -10000 0 -0.28 2 2
STAP1 -0.32 0.3 -10000 0 -0.53 100 100
GRAP2 0.006 0.047 -10000 0 -0.34 3 3
JAK2 -0.15 0.32 -10000 0 -0.85 28 28
STAT1 (dimer) -0.12 0.4 -10000 0 -0.99 28 28
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.18 -10000 0 -0.45 29 29
actin filament polymerization -0.042 0.18 -10000 0 -0.42 28 28
LYN 0.012 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.32 0.33 -10000 0 -0.54 100 100
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.063 0.14 -10000 0 -10000 0 0
PI3K -0.03 0.17 -10000 0 -0.4 28 28
PTEN 0.012 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.5 -10000 0 -1.3 28 28
MAPK8 -0.056 0.2 -10000 0 -0.47 30 30
STAT3 (dimer) -0.042 0.18 -10000 0 -0.42 28 28
positive regulation of transcription 0.009 0.086 -10000 0 -10000 0 0
mol:GDP -0.08 0.14 -10000 0 -0.5 6 6
PIK3C2B -0.044 0.18 -10000 0 -0.43 28 28
CBL/CRKL -0.025 0.16 -10000 0 -0.38 28 28
FER -0.044 0.18 -10000 0 -0.43 28 28
SH2B3 -0.044 0.18 -10000 0 -0.43 28 28
PDPK1 -0.035 0.15 -10000 0 -0.36 28 28
SNAI2 -0.081 0.23 -10000 0 -0.5 36 36
positive regulation of cell proliferation -0.081 0.3 -10000 0 -0.74 28 28
KITLG 0.01 0.039 -10000 0 -0.33 2 2
cell motility -0.081 0.3 -10000 0 -0.74 28 28
PTPN6 0.007 0.013 -10000 0 -10000 0 0
EPOR 0 0.12 -10000 0 -10000 0 0
STAT5A (dimer) -0.062 0.25 -10000 0 -0.61 28 28
SOCS1 -0.001 0.1 -10000 0 -0.68 3 3
cell migration 0.062 0.2 0.47 30 -10000 0 30
SOS1 0.012 0 -10000 0 -10000 0 0
EPO 0.004 0.039 -10000 0 -0.33 2 2
VAV1 -0.06 0.15 -10000 0 -0.35 32 32
GRB10 -0.044 0.18 -10000 0 -0.43 28 28
PTPN11 0.013 0.007 -10000 0 -10000 0 0
SCF/KIT -0.054 0.19 -10000 0 -0.46 28 28
GO:0007205 0.001 0.01 -10000 0 -10000 0 0
MAP2K1 0.002 0.11 -10000 0 -0.32 2 2
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.2 0.54 -10000 0 -1.4 28 28
MAP2K2 0.002 0.11 -10000 0 -0.32 2 2
SHC/Grb2/SOS1 -0.07 0.15 -10000 0 -0.4 28 28
STAT5A -0.065 0.26 -10000 0 -0.63 28 28
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.079 0.23 -10000 0 -0.48 36 36
SHC/GRAP2 -0.004 0.03 -10000 0 -10000 0 0
PTPRO -0.12 0.27 -10000 0 -0.52 46 46
SH2B2 -0.044 0.18 -10000 0 -0.43 28 28
DOK1 0.01 0.027 -10000 0 -0.34 1 1
MATK -0.064 0.2 -10000 0 -0.48 30 30
CREBBP 0.031 0.015 -10000 0 -10000 0 0
BCL2 0.001 0.12 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.53 0.37 -9999 0 -0.69 123 123
SMAD6-7/SMURF1 -0.004 0.045 -9999 0 -0.58 1 1
NOG 0.001 0.096 -9999 0 -0.86 2 2
SMAD9 -0.074 0.093 -9999 0 -0.42 7 7
SMAD4 0.012 0 -9999 0 -10000 0 0
SMAD5 -0.19 0.21 -9999 0 -0.41 35 35
BMP7/USAG1 -0.35 0.38 -9999 0 -0.75 69 69
SMAD5/SKI -0.17 0.2 -9999 0 -0.49 13 13
SMAD1 -0.009 0.048 -9999 0 -10000 0 0
BMP2 0.012 0 -9999 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.009 0.034 -9999 0 -10000 0 0
BMPR1A 0.012 0 -9999 0 -10000 0 0
BMPR1B -0.48 0.43 -9999 0 -0.86 91 91
BMPR1A-1B/BAMBI -0.33 0.29 -9999 0 -0.58 92 92
AHSG -0.01 0.07 -9999 0 -0.34 7 7
CER1 0.004 0.006 -9999 0 -10000 0 0
BMP2-4/CER1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.18 -9999 0 -0.56 11 11
BMP2-4 (homodimer) 0 0 -9999 0 -10000 0 0
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.3 0.26 -9999 0 -0.53 91 91
RGMA -0.058 0.24 -9999 0 -0.86 13 13
SMURF1 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.18 -9999 0 -0.49 13 13
BMP2-4/USAG1 -0.13 0.22 -9999 0 -0.58 30 30
SMAD6/SMURF1/SMAD5 -0.17 0.2 -9999 0 -0.49 13 13
SOSTDC1 -0.2 0.34 -9999 0 -0.62 55 55
BMP7/BMPR2/BMPR1A-1B -0.45 0.32 -9999 0 -0.62 117 117
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.012 0 -9999 0 -10000 0 0
HFE2 0.004 0.039 -9999 0 -0.34 2 2
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.025 0.12 -9999 0 -0.58 7 7
SMAD5/SMAD5/SMAD4 -0.17 0.2 -9999 0 -0.49 13 13
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.14 0.13 -9999 0 -0.43 11 11
BMP7 (homodimer) -0.25 0.4 -9999 0 -0.85 49 49
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.01 0.045 -9999 0 -10000 0 0
SMAD1/SKI -0.001 0.046 -9999 0 -10000 0 0
SMAD6 0.007 0.068 -9999 0 -0.86 1 1
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.008 0.035 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.34 -9999 0 -0.76 38 38
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.33 -9999 0 -0.66 91 91
CHRDL1 -0.32 0.42 -9999 0 -0.86 62 62
ENDOFIN/SMAD1 -0.001 0.046 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.018 0.04 -9999 0 -0.49 1 1
SMAD6/SMURF1 0.012 0 -9999 0 -10000 0 0
BAMBI 0.007 0.068 -9999 0 -0.86 1 1
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.22 0.28 -9999 0 -0.58 62 62
BMP2-4/GREM1 -0.12 0.23 -9999 0 -0.58 31 31
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.051 0.096 -9999 0 -0.44 5 5
SMAD1/SMAD6 -0.001 0.046 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.25 0.4 -9999 0 -0.85 49 49
BMP6 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.16 -9999 0 -0.44 13 13
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.001 0.046 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.27 0.33 -9999 0 -0.8 34 34
CHRD -0.026 0.18 -9999 0 -0.86 7 7
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.16 0.18 -9999 0 -0.53 13 13
BMP4 0.012 0 -9999 0 -10000 0 0
FST -0.17 0.34 -9999 0 -0.8 35 35
BMP2-4/NOG -0.007 0.064 -9999 0 -0.58 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.43 0.31 -9999 0 -0.59 117 117
Endothelins

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
AKT1 -0.013 0.17 -10000 0 -0.66 6 6
PTK2B 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.25 0.47 -10000 0 -1 43 43
EDN1 0 0.083 -10000 0 -0.43 1 1
EDN3 0.008 0.006 -10000 0 -10000 0 0
EDN2 -0.022 0.17 -10000 0 -0.78 7 7
HRAS/GDP -0.096 0.22 -10000 0 -0.53 23 23
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.092 0.22 -10000 0 -0.44 34 34
ADCY4 -0.038 0.2 -10000 0 -0.59 15 15
ADCY5 -0.033 0.18 -10000 0 -0.54 14 14
ADCY6 -0.003 0.14 -10000 0 -0.56 6 6
ADCY7 -0.011 0.14 -10000 0 -0.56 6 6
ADCY1 -0.22 0.29 -10000 0 -0.53 69 69
ADCY2 -0.089 0.16 -10000 0 -0.58 9 9
ADCY3 -0.003 0.14 -10000 0 -0.56 6 6
ADCY8 -0.015 0.14 -10000 0 -0.52 8 8
ADCY9 -0.003 0.14 -10000 0 -0.56 6 6
arachidonic acid secretion -0.14 0.28 -10000 0 -0.57 36 36
ETB receptor/Endothelin-1/Gq/GTP -0.068 0.18 -10000 0 -0.39 32 32
GNAO1 -0.059 0.23 -10000 0 -0.75 15 15
HRAS 0.011 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.026 0.17 0.34 8 -0.62 6 14
ETA receptor/Endothelin-1/Gs/GTP -0.026 0.16 0.32 8 -0.59 6 14
mol:GTP -0.003 0.008 -10000 0 -10000 0 0
COL3A1 -0.021 0.19 -10000 0 -0.74 6 6
EDNRB 0.008 0.069 -10000 0 -0.86 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.07 0.24 -10000 0 -0.76 11 11
CYSLTR1 -0.016 0.18 -10000 0 -0.69 7 7
SLC9A1 -0.019 0.084 0.2 2 -0.33 6 8
mol:GDP -0.11 0.24 -10000 0 -0.55 26 26
SLC9A3 -0.61 0.36 -10000 0 -0.73 131 131
RAF1 -0.13 0.26 -10000 0 -0.57 30 30
JUN -0.13 0.29 -10000 0 -0.71 20 20
JAK2 -0.013 0.17 -10000 0 -0.66 6 6
mol:IP3 -0.1 0.24 -10000 0 -0.52 30 30
ETA receptor/Endothelin-1 -0.041 0.2 0.41 8 -0.76 6 14
PLCB1 -0.044 0.21 -10000 0 -0.86 10 10
PLCB2 -0.034 0.11 -10000 0 -0.34 20 20
ETA receptor/Endothelin-3 -0.03 0.14 -10000 0 -0.72 6 6
FOS -0.18 0.39 -10000 0 -0.94 30 30
Gai/GDP -0.045 0.22 -10000 0 -0.81 12 12
CRK 0.012 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.26 -10000 0 -0.63 20 20
BCAR1 0.012 0.001 -10000 0 -10000 0 0
PRKCB1 -0.11 0.23 -10000 0 -0.5 30 30
GNAQ 0.01 0.007 -10000 0 -10000 0 0
GNAZ 0.012 0 -10000 0 -10000 0 0
GNAL 0.012 0 -10000 0 -10000 0 0
Gs family/GDP -0.13 0.19 -10000 0 -0.5 24 24
ETA receptor/Endothelin-1/Gq/GTP -0.093 0.25 -10000 0 -0.51 32 32
MAPK14 -0.063 0.16 -10000 0 -0.5 7 7
TRPC6 -0.28 0.52 -10000 0 -1.1 43 43
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.86 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.074 0.18 -10000 0 -0.38 26 26
ETB receptor/Endothelin-2 -0.03 0.14 -10000 0 -0.67 7 7
ETB receptor/Endothelin-3 -0.002 0.053 -10000 0 -0.67 1 1
ETB receptor/Endothelin-1 -0.007 0.083 -10000 0 -0.75 1 1
MAPK3 -0.17 0.35 -10000 0 -0.82 31 31
MAPK1 -0.17 0.35 -10000 0 -0.82 31 31
Rac1/GDP -0.096 0.22 -10000 0 -0.53 23 23
cAMP biosynthetic process -0.12 0.2 -10000 0 -0.55 16 16
MAPK8 -0.17 0.35 -10000 0 -0.73 34 34
SRC 0.012 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.001 0.093 -10000 0 -0.3 10 10
p130Cas/CRK/Src/PYK2 -0.15 0.29 -10000 0 -0.6 36 36
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.096 0.22 -10000 0 -0.53 22 22
COL1A2 -0.009 0.16 -10000 0 -0.58 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.053 0.2 -10000 0 -0.75 11 11
mol:DAG -0.1 0.24 -10000 0 -0.52 30 30
MAP2K2 -0.14 0.29 -10000 0 -0.63 33 33
MAP2K1 -0.14 0.29 -10000 0 -0.63 33 33
EDNRA -0.032 0.19 -10000 0 -0.91 6 6
positive regulation of muscle contraction -0.006 0.15 -10000 0 -0.58 6 6
Gq family/GDP -0.18 0.27 -10000 0 -0.65 35 35
HRAS/GTP -0.12 0.24 -10000 0 -0.53 31 31
PRKCH -0.097 0.23 -10000 0 -0.51 28 28
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.097 0.23 -10000 0 -0.51 28 28
PRKCB -0.099 0.23 -10000 0 -0.51 27 27
PRKCE -0.096 0.23 -10000 0 -0.53 24 24
PRKCD -0.097 0.23 -10000 0 -0.51 28 28
PRKCG -0.14 0.25 -10000 0 -0.57 30 30
regulation of vascular smooth muscle contraction -0.21 0.45 -10000 0 -1.1 30 30
PRKCQ -0.11 0.23 -10000 0 -0.5 31 31
PLA2G4A -0.16 0.32 -10000 0 -0.64 36 36
GNA14 -0.16 0.35 -10000 0 -0.87 31 31
GNA15 -0.01 0.08 -10000 0 -0.34 9 9
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 -0.012 0.14 -10000 0 -0.86 4 4
Rac1/GTP -0.026 0.16 0.34 8 -0.62 6 14
MMP1 -0.042 0.27 -10000 0 -1.2 8 8
TCGA08_p53

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
CDKN2A -0.18 0.1 -9999 0 -0.23 125 125
TP53 -0.057 0.031 -9999 0 -10000 0 0
Senescence -0.057 0.031 -9999 0 -10000 0 0
Apoptosis -0.057 0.031 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.11 0.057 -9999 0 -10000 0 0
MDM4 0.012 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.47 -9999 0 -1.3 22 22
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.031 0.14 -9999 0 -0.48 3 3
ATF2/c-Jun -0.006 0.11 -9999 0 -0.43 3 3
MAPK11 -0.031 0.14 -9999 0 -0.48 3 3
MITF -0.027 0.17 -9999 0 -0.37 29 29
MAPKAPK5 -0.027 0.17 -9999 0 -0.37 29 29
KRT8 -0.03 0.17 -9999 0 -0.38 29 29
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.049 0.21 -9999 0 -0.48 29 29
CEBPB -0.032 0.17 -9999 0 -0.39 29 29
SLC9A1 -0.027 0.17 -9999 0 -0.37 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.02 0.16 -9999 0 -0.36 29 29
p38alpha-beta/MNK1 -0.029 0.17 -9999 0 -0.7 3 3
JUN -0.006 0.11 -9999 0 -0.42 3 3
PPARGC1A -0.045 0.2 -9999 0 -0.42 32 32
USF1 -0.027 0.17 -9999 0 -0.37 29 29
RAB5/GDP/GDI1 -0.048 0.11 -9999 0 -0.47 3 3
NOS2 -0.084 0.36 -9999 0 -1.4 10 10
DDIT3 -0.028 0.17 -9999 0 -0.37 29 29
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.018 0.14 -9999 0 -0.5 4 4
p38alpha-beta/HBP1 -0.029 0.17 -9999 0 -0.7 3 3
CREB1 -0.028 0.18 -9999 0 -0.4 29 29
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.019 0.15 -9999 0 -0.63 3 3
RPS6KA4 -0.027 0.17 -9999 0 -0.37 29 29
PLA2G4A -0.026 0.17 -9999 0 -0.65 5 5
GDI1 -0.027 0.17 -9999 0 -0.37 29 29
TP53 -0.041 0.21 -9999 0 -0.47 29 29
RPS6KA5 -0.032 0.18 -9999 0 -0.4 29 29
ESR1 -0.052 0.23 -9999 0 -0.44 33 33
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.027 0.17 -9999 0 -0.37 29 29
MEF2A -0.027 0.17 -9999 0 -0.37 29 29
EIF4EBP1 -0.029 0.18 -9999 0 -0.4 29 29
KRT19 -0.081 0.2 -9999 0 -0.41 41 41
ELK4 -0.027 0.17 -9999 0 -0.37 29 29
ATF6 -0.027 0.17 -9999 0 -0.37 29 29
ATF1 -0.028 0.18 -9999 0 -0.4 29 29
p38alpha-beta/MAPKAPK2 -0.029 0.17 -9999 0 -0.7 3 3
p38alpha-beta/MAPKAPK3 -0.029 0.17 -9999 0 -0.7 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.022 0.11 -9999 0 -0.66 4 4
AKT1 -0.038 0.27 -9999 0 -0.63 28 28
PTK2B -0.11 0.34 -9999 0 -0.82 28 28
VEGFR2 homodimer/Frs2 -0.14 0.38 -9999 0 -0.96 28 28
CAV1 0.01 0.027 -9999 0 -0.34 1 1
CALM1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.16 0.34 -9999 0 -0.89 28 28
endothelial cell proliferation -0.023 0.26 -9999 0 -0.6 28 28
mol:Ca2+ -0.094 0.32 -9999 0 -0.8 28 28
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.15 0.32 -9999 0 -0.85 28 28
RP11-342D11.1 -0.1 0.32 -9999 0 -0.81 28 28
CDH5 0.012 0 -9999 0 -10000 0 0
VEGFA homodimer -0.001 0.011 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
SHC2 -0.014 0.12 -9999 0 -0.45 9 9
HRAS/GDP -0.12 0.26 -9999 0 -0.68 28 28
SH2D2A -0.033 0.12 -9999 0 -0.34 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.12 0.26 -9999 0 -0.66 28 28
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.17 0.34 -9999 0 -0.9 28 28
VEGFR1 homodimer 0.001 0.096 -9999 0 -0.86 2 2
SHC/GRB2/SOS1 -0.13 0.29 -9999 0 -0.77 28 28
GRB10 -0.093 0.32 -9999 0 -0.8 28 28
PTPN11 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PAK1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.14 0.31 -9999 0 -0.81 28 28
HRAS 0.012 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.034 0.17 -9999 0 -0.4 28 28
HIF1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.14 0.32 -9999 0 -0.83 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.009 0.14 -9999 0 -0.86 4 4
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.16 0.34 -9999 0 -0.89 28 28
mol:GDP -0.13 0.28 -9999 0 -0.74 28 28
mol:NADP -0.034 0.25 -9999 0 -0.56 28 28
eNOS/Hsp90 -0.025 0.23 -9999 0 -0.52 28 28
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.096 0.33 -9999 0 -0.82 28 28
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
VEGFA 0.012 0.027 -9999 0 -0.33 1 1
VEGFC 0.01 0.027 -9999 0 -0.34 1 1
FAK1/Vinculin -0.087 0.33 -9999 0 -0.79 28 28
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.16 0.34 -9999 0 -0.83 31 31
PTPN6 0.012 0 -9999 0 -10000 0 0
EPAS1 -0.054 0.18 -9999 0 -0.42 28 28
mol:L-citrulline -0.034 0.25 -9999 0 -0.56 28 28
ITGAV 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.15 0.32 -9999 0 -0.85 28 28
VEGFR2 homodimer/VEGFA homodimer -0.16 0.34 -9999 0 -0.88 28 28
VEGFR2/3 heterodimer -0.15 0.4 -9999 0 -0.96 30 30
VEGFB 0.012 0 -9999 0 -10000 0 0
MAPK11 -0.096 0.34 -9999 0 -0.83 28 28
VEGFR2 homodimer -0.16 0.42 -9999 0 -1.1 28 28
FLT1 0.001 0.096 -9999 0 -0.86 2 2
NEDD4 0.014 0.001 -9999 0 -10000 0 0
MAPK3 -0.076 0.3 -9999 0 -0.72 28 28
MAPK1 -0.076 0.3 -9999 0 -0.72 28 28
VEGFA145/NRP2 -0.004 0.029 -9999 0 -10000 0 0
VEGFR1/2 heterodimer -0.14 0.39 -9999 0 -0.99 28 28
KDR -0.16 0.42 -9999 0 -1.1 28 28
VEGFA165/NRP1/VEGFR2 homodimer -0.14 0.31 -9999 0 -0.82 28 28
SRC 0.012 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.078 0.31 -9999 0 -0.74 28 28
PI3K -0.14 0.3 -9999 0 -0.79 28 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.16 0.34 -9999 0 -0.89 28 28
FES -0.099 0.34 -9999 0 -0.83 28 28
GAB1 -0.14 0.31 -9999 0 -0.82 28 28
VEGFR2 homodimer/VEGFA homodimer/Src -0.16 0.34 -9999 0 -0.89 28 28
CTNNB1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.026 0.23 -9999 0 -0.52 28 28
VEGFR2 homodimer/VEGFA homodimer/Yes -0.16 0.34 -9999 0 -0.89 28 28
PI3K/GAB1 -0.04 0.28 -9999 0 -0.65 28 28
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.14 0.31 -9999 0 -0.81 28 28
PRKACA 0.012 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.17 0.36 -9999 0 -0.9 30 30
HSP90AA1 0.012 0 -9999 0 -10000 0 0
CDC42 -0.099 0.34 -9999 0 -0.83 28 28
actin cytoskeleton reorganization -0.17 0.33 -9999 0 -0.89 28 28
PTK2 -0.1 0.36 -9999 0 -0.87 28 28
EDG1 -0.1 0.32 -9999 0 -0.81 28 28
mol:DAG -0.096 0.33 -9999 0 -0.82 28 28
CaM/Ca2+ -0.13 0.28 -9999 0 -0.74 28 28
MAP2K3 -0.09 0.34 -9999 0 -0.81 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.15 0.32 -9999 0 -0.84 28 28
PLCG1 -0.099 0.34 -9999 0 -0.83 28 28
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.15 0.32 -9999 0 -0.85 28 28
IQGAP1 0.012 0 -9999 0 -10000 0 0
YES1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.16 0.34 -9999 0 -0.89 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.16 0.34 -9999 0 -0.89 28 28
cell migration -0.044 0.28 -9999 0 -0.65 28 28
mol:PI-3-4-5-P3 -0.12 0.27 -9999 0 -0.71 28 28
FYN 0.012 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.09 0.31 -9999 0 -0.76 28 28
mol:NO -0.034 0.25 -9999 0 -0.56 28 28
PXN 0.012 0 -9999 0 -10000 0 0
HRAS/GTP -0.12 0.26 -9999 0 -0.68 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.34 -9999 0 -0.84 28 28
VHL 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.14 -9999 0 -0.6 8 8
NOS3 -0.049 0.28 -9999 0 -0.66 28 28
VEGFR2 homodimer/VEGFA homodimer/Sck -0.17 0.35 -9999 0 -0.9 30 30
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA -0.081 0.31 -9999 0 -0.75 28 28
PRKCB -0.083 0.31 -9999 0 -0.75 28 28
VCL 0.012 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.1 0.32 -9999 0 -0.81 28 28
VEGFR1/2 heterodimer/VEGFA homodimer -0.16 0.36 -9999 0 -0.92 28 28
VEGFA165/NRP2 -0.004 0.029 -9999 0 -10000 0 0
MAPKKK cascade -0.12 0.26 -9999 0 -0.68 28 28
NRP2 0.008 0.039 -9999 0 -0.34 2 2
VEGFC homodimer 0.01 0.027 -9999 0 -0.34 1 1
NCK1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.012 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.087 0.33 -9999 0 -0.79 28 28
MAP3K13 -0.1 0.35 -9999 0 -0.86 28 28
PDPK1 -0.041 0.26 -9999 0 -0.61 28 28
IL4-mediated signaling events

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
BCL2L1 -0.45 0.43 -10000 0 -1.2 27 27
STAT6 (cleaved dimer) -0.48 0.41 -10000 0 -1.1 40 40
IGHG1 -0.16 0.15 -10000 0 -0.47 2 2
IGHG3 -0.44 0.42 -10000 0 -1.1 34 34
AKT1 -0.2 0.21 -10000 0 -0.67 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.16 -10000 0 -0.61 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.21 -10000 0 -0.86 3 3
THY1 -0.66 0.65 -10000 0 -1.5 54 54
MYB -0.064 0.14 -10000 0 -0.34 35 35
HMGA1 -0.001 0.066 -10000 0 -0.34 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.25 -10000 0 -0.66 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.2 -10000 0 -0.71 2 2
SP1 0.02 0.004 -10000 0 -10000 0 0
INPP5D 0.001 0.06 -10000 0 -0.34 5 5
SOCS5 0.024 0.012 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.4 -10000 0 -1.1 34 34
SOCS1 -0.3 0.3 -10000 0 -0.78 20 20
SOCS3 -0.23 0.23 -10000 0 -0.92 4 4
FCER2 -0.35 0.33 -10000 0 -0.88 23 23
PARP14 0.012 0.003 -10000 0 -10000 0 0
CCL17 -0.47 0.44 -10000 0 -1.1 32 32
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.18 0.17 -10000 0 -0.62 2 2
T cell proliferation -0.44 0.44 -10000 0 -1.2 28 28
IL4R/JAK1 -0.44 0.43 -10000 0 -1.2 28 28
EGR2 -0.52 0.56 -10000 0 -1.5 32 32
JAK2 -0.009 0.026 -10000 0 -10000 0 0
JAK3 -0.05 0.14 -10000 0 -0.34 31 31
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.004 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.15 -10000 0 -10000 0 0
CCL26 -0.45 0.44 -10000 0 -1.2 28 28
IL4R -0.47 0.46 -10000 0 -1.2 28 28
PTPN6 0.025 0.011 -10000 0 -10000 0 0
IL13RA2 -0.91 0.68 -10000 0 -1.4 94 94
IL13RA1 -0.009 0.026 -10000 0 -10000 0 0
IRF4 -0.097 0.13 -10000 0 -0.57 4 4
ARG1 -0.14 0.14 -10000 0 -10000 0 0
CBL -0.25 0.23 -10000 0 -0.67 13 13
GTF3A 0.018 0.008 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.014 0.038 -10000 0 -10000 0 0
IRF4/BCL6 -0.087 0.12 -10000 0 -0.54 3 3
CD40LG 0.005 0.07 -10000 0 -0.35 6 6
MAPK14 -0.25 0.24 -10000 0 -0.73 9 9
mitosis -0.2 0.2 -10000 0 -0.64 5 5
STAT6 -0.51 0.5 -10000 0 -1.3 31 31
SPI1 -0.048 0.13 -10000 0 -0.33 29 29
RPS6KB1 -0.18 0.2 -10000 0 -0.69 2 2
STAT6 (dimer) -0.51 0.5 -10000 0 -1.3 31 31
STAT6 (dimer)/PARP14 -0.47 0.46 -10000 0 -1.2 31 31
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.2 -10000 0 -0.66 7 7
FRAP1 -0.2 0.21 -10000 0 -0.67 5 5
LTA -0.46 0.44 -10000 0 -1.2 28 28
FES 0.012 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.5 0.48 1.3 32 -10000 0 32
CCL11 -0.52 0.53 -10000 0 -1.3 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.2 -10000 0 -0.63 6 6
IL2RG 0.004 0.067 -10000 0 -0.34 6 6
IL10 -0.46 0.44 -10000 0 -1.2 28 28
IRS1 -0.006 0.12 -10000 0 -0.73 4 4
IRS2 0.01 0.027 -10000 0 -0.34 1 1
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.45 0.43 -10000 0 -1.2 28 28
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.87 30 30
COL1A1 -0.17 0.18 -10000 0 -0.65 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.44 -10000 0 -1.2 25 25
IL2R gamma/JAK3 -0.032 0.12 -10000 0 -0.44 5 5
TFF3 -0.56 0.59 -10000 0 -1.4 45 45
ALOX15 -0.45 0.44 -10000 0 -1.1 31 31
MYBL1 -0.009 0.084 -10000 0 -0.34 10 10
T-helper 2 cell differentiation -0.38 0.34 -10000 0 -0.89 31 31
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.006 0.054 -10000 0 -0.33 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.2 -10000 0 -0.64 3 3
mol:PI-3-4-5-P3 -0.2 0.21 -10000 0 -0.67 5 5
PI3K -0.21 0.22 -10000 0 -0.71 5 5
DOK2 -0.015 0.11 -10000 0 -0.38 11 11
ETS1 0.025 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.17 -10000 0 -0.59 2 2
ITGB3 -0.47 0.46 -10000 0 -1.2 32 32
PIGR -0.5 0.5 -10000 0 -1.3 33 33
IGHE 0.035 0.046 -10000 0 -10000 0 0
MAPKKK cascade -0.16 0.16 -10000 0 -0.58 2 2
BCL6 0.01 0.027 -10000 0 -0.34 1 1
OPRM1 -0.45 0.43 -10000 0 -1.2 28 28
RETNLB -0.45 0.43 -10000 0 -1.2 27 27
SELP -0.5 0.53 -10000 0 -1.4 32 32
AICDA -0.46 0.43 -10000 0 -1.1 32 32
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.015 0.093 -10000 0 -0.46 5 5
NFATC2 -0.025 0.22 -10000 0 -0.78 10 10
NFATC3 -0.026 0.11 -10000 0 -10000 0 0
CD40LG -0.2 0.45 -10000 0 -1.1 25 25
ITCH 0.041 0.045 -10000 0 -10000 0 0
CBLB 0.041 0.045 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.25 -10000 0 -0.82 10 10
JUNB 0.012 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.047 -10000 0 -0.35 3 3
T cell anergy 0.019 0.077 -10000 0 -0.45 3 3
TLE4 0.004 0.16 -10000 0 -0.59 9 9
Jun/NFAT1-c-4/p21SNFT -0.17 0.35 -10000 0 -0.98 21 21
AP-1/NFAT1-c-4 -0.26 0.54 -10000 0 -1.3 27 27
IKZF1 -0.01 0.18 -10000 0 -0.65 7 7
T-helper 2 cell differentiation -0.48 0.34 -10000 0 -0.82 55 55
AP-1/NFAT1 -0.14 0.26 -10000 0 -0.62 33 33
CALM1 0.023 0.028 -10000 0 -10000 0 0
EGR2 -0.17 0.56 -10000 0 -1.6 19 19
EGR3 -0.19 0.59 -10000 0 -1.7 20 20
NFAT1/FOXP3 -0.038 0.19 -10000 0 -0.59 12 12
EGR1 -0.052 0.23 -10000 0 -0.86 12 12
JUN 0.008 0.017 -10000 0 -10000 0 0
EGR4 0.005 0.029 -10000 0 -0.33 1 1
mol:Ca2+ 0.011 0.03 -10000 0 -10000 0 0
GBP3 0.004 0.16 -10000 0 -0.59 9 9
FOSL1 0.004 0.054 -10000 0 -0.34 4 4
NFAT1-c-4/MAF/IRF4 -0.16 0.36 -10000 0 -0.96 21 21
DGKA -0.005 0.17 -10000 0 -0.62 7 7
CREM 0.012 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.37 -10000 0 -0.95 25 25
CTLA4 -0.047 0.21 -10000 0 -0.62 10 10
NFAT1-c-4 (dimer)/EGR1 -0.2 0.44 -10000 0 -1.1 25 25
NFAT1-c-4 (dimer)/EGR4 -0.17 0.37 -10000 0 -0.96 25 25
FOS -0.14 0.32 -10000 0 -0.87 26 26
IFNG -0.093 0.18 -10000 0 -0.72 6 6
T cell activation -0.1 0.29 -10000 0 -0.79 18 18
MAF 0.012 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 0.08 0.3 0.78 20 -10000 0 20
TNF -0.13 0.41 -10000 0 -1.1 21 21
FASLG -0.2 0.57 -10000 0 -1.4 25 25
TBX21 -0.002 0.072 -10000 0 -0.36 6 6
BATF3 0.012 0 -10000 0 -10000 0 0
PRKCQ -0.004 0.12 -10000 0 -0.86 3 3
PTPN1 0.004 0.16 -10000 0 -0.59 9 9
NFAT1-c-4/ICER1 -0.17 0.36 -10000 0 -0.94 26 26
GATA3 -0.6 0.4 -10000 0 -0.86 114 114
T-helper 1 cell differentiation -0.07 0.2 -10000 0 -0.71 6 6
IL2RA -0.16 0.23 -10000 0 -0.78 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0 0.16 -10000 0 -0.59 9 9
E2F1 -0.089 0.16 -10000 0 -0.33 50 50
PPARG 0.012 0 -10000 0 -10000 0 0
SLC3A2 0.004 0.16 -10000 0 -0.59 9 9
IRF4 -0.014 0.091 -10000 0 -0.34 12 12
PTGS2 -0.24 0.52 -10000 0 -1.2 30 30
CSF2 -0.2 0.45 -10000 0 -1.1 25 25
JunB/Fra1/NFAT1-c-4 -0.16 0.35 -10000 0 -0.96 21 21
IL4 -0.5 0.36 -10000 0 -0.88 51 51
IL5 -0.2 0.45 -10000 0 -1.1 25 25
IL2 -0.1 0.3 -10000 0 -0.82 17 17
IL3 -0.042 0.057 -10000 0 -10000 0 0
RNF128 0.029 0.13 -10000 0 -0.91 3 3
NFATC1 -0.081 0.3 -10000 0 -0.78 20 20
CDK4 0.02 0.19 0.55 1 -10000 0 1
PTPRK 0.004 0.16 -10000 0 -0.59 9 9
IL8 -0.23 0.46 -10000 0 -1.1 28 28
POU2F1 0.012 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.02 0.16 -10000 0 -0.86 6 6
Jak2/Leptin Receptor -0.18 0.16 -10000 0 -0.35 72 72
PTP1B/AKT1 -0.081 0.076 -10000 0 -0.3 12 12
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.1 0.086 -10000 0 -0.34 14 14
EGFR 0.001 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.47 0.16 -10000 0 -0.52 142 142
CSF1 0.003 0.078 -10000 0 -0.51 3 3
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.11 0.15 -10000 0 -0.46 19 19
Insulin Receptor/Insulin -0.054 0.055 -10000 0 -10000 0 0
HCK -0.034 0.13 -10000 0 -0.36 20 20
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.087 0.082 -10000 0 -0.32 12 12
EGF -0.76 0.28 -10000 0 -0.86 142 142
YES1 0.012 0 -10000 0 -10000 0 0
CAV1 -0.19 0.092 -10000 0 -0.37 17 17
TXN -0.001 0.027 -10000 0 -0.34 1 1
PTP1B/IRS1/GRB2 -0.087 0.1 -10000 0 -0.5 4 4
cell migration 0.1 0.086 0.34 14 -10000 0 14
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.38 0.43 -10000 0 -0.86 73 73
ITGA2B -0.018 0.095 -10000 0 -10000 0 0
CSF1R -0.004 0.091 -10000 0 -0.42 6 6
Prolactin Receptor/Prolactin -0.31 0.34 -10000 0 -0.67 73 73
FGR -0.002 0.087 -10000 0 -0.44 5 5
PTP1B/p130 Cas -0.087 0.082 -10000 0 -0.32 13 13
Crk/p130 Cas -0.077 0.08 -10000 0 -0.31 11 11
DOK1 -0.08 0.089 -10000 0 -0.3 17 17
JAK2 -0.19 0.17 -10000 0 -0.37 72 72
Jak2/Leptin Receptor/Leptin -0.11 0.11 -10000 0 -0.6 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.1 0.087 -10000 0 -0.34 14 14
LYN 0.012 0 -10000 0 -10000 0 0
CDH2 -0.03 0.18 -10000 0 -0.74 9 9
SRC -0.026 0.032 -10000 0 -10000 0 0
ITGB3 -0.02 0.14 -10000 0 -0.6 8 8
CAT1/PTP1B -0.25 0.15 -10000 0 -0.44 33 33
CAPN1 0.01 0.003 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.038 0.051 -10000 0 -10000 0 0
mol:H2O2 -0.008 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.1 0.11 -10000 0 -0.59 3 3
negative regulation of transcription -0.19 0.17 -10000 0 -0.36 72 72
FCGR2A -0.003 0.071 -10000 0 -0.34 7 7
FER 0.001 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.04 0.12 -10000 0 -0.67 4 4
BLK -0.011 0.084 -10000 0 -0.34 10 10
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.01 0.003 -10000 0 -10000 0 0
LEPR 0.007 0.068 -10000 0 -0.86 1 1
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.19 0.16 -10000 0 -0.42 19 19
PRL -0.002 0.027 -10000 0 -0.34 1 1
SOCS3 0.02 0.12 -10000 0 -1.4 1 1
SPRY2 0.002 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.012 0.081 -10000 0 -0.59 3 3
CSF1/CSF1R -0.09 0.11 -10000 0 -0.51 5 5
Ras protein signal transduction 0.047 0.023 -10000 0 -10000 0 0
IRS1 -0.006 0.12 -10000 0 -0.73 4 4
INS 0.001 0.003 -10000 0 -10000 0 0
LEP -0.022 0.097 -10000 0 -0.34 14 14
STAT5B -0.13 0.1 -10000 0 -0.34 18 18
STAT5A -0.13 0.1 -10000 0 -0.34 18 18
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.11 0.12 -10000 0 -0.4 19 19
CSN2 -0.077 0.11 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
LAT -0.045 0.05 -10000 0 -10000 0 0
YBX1 0.015 0.002 -10000 0 -10000 0 0
LCK 0.004 0.054 -10000 0 -0.34 4 4
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.096 0.27 -10000 0 -0.87 18 18
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.12 0.25 -9999 0 -0.66 28 28
alphaV beta3 Integrin -0.019 0.093 -9999 0 -0.58 4 4
PTK2 -0.15 0.28 -9999 0 -0.73 20 20
IGF1R 0.012 0 -9999 0 -10000 0 0
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.2 0.29 -9999 0 -0.63 49 49
VEGFA 0.01 0.027 -9999 0 -0.34 1 1
ILK -0.2 0.29 -9999 0 -0.63 49 49
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.18 0.27 -9999 0 -0.59 48 48
PTK2B -0.071 0.22 -9999 0 -0.51 31 31
alphaV/beta3 Integrin/JAM-A -0.17 0.24 -9999 0 -0.51 51 51
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.4 0.28 -9999 0 -0.59 108 108
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.024 0.11 -9999 0 -0.53 7 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.24 -9999 0 -0.7 17 17
alphaV/beta3 Integrin/Syndecan-1 -0.023 0.11 -9999 0 -0.61 5 5
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.044 0.12 -9999 0 -0.46 11 11
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.035 0.13 -9999 0 -0.58 7 7
RPS6KB1 0.006 0.13 -9999 0 -0.55 1 1
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.081 0.13 -9999 0 -0.64 4 4
GPR124 0.007 0.068 -9999 0 -0.86 1 1
MAPK1 -0.081 0.13 -9999 0 -0.64 4 4
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.047 0.16 -9999 0 -0.62 11 11
cell adhesion -0.31 0.22 -9999 0 -0.46 108 108
ANGPTL3 -0.56 0.41 -9999 0 -0.86 106 106
VEGFR2 homodimer/VEGFA homodimer/Src -0.1 0.22 -9999 0 -0.58 28 28
IGF-1R heterotetramer 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.14 -9999 0 -0.6 8 8
IGF1 -0.009 0.14 -9999 0 -0.86 4 4
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.022 0.1 -9999 0 -0.57 5 5
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.019 0.093 -9999 0 -0.58 4 4
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.075 0.2 -9999 0 -0.62 17 17
CSF1 0.003 0.078 -9999 0 -0.51 3 3
PIK3C2A -0.2 0.29 -9999 0 -0.63 49 49
PI4 Kinase/Pyk2 -0.21 0.27 -9999 0 -0.8 17 17
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.22 -9999 0 -0.55 31 31
FAK1/Vinculin -0.11 0.22 -9999 0 -0.54 20 20
alphaV beta3/Integrin/ppsTEM5 -0.022 0.1 -9999 0 -0.58 5 5
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.26 0.4 -9999 0 -0.82 52 52
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 0.012 0 -9999 0 -10000 0 0
F11R 0.022 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.019 0.093 -9999 0 -0.58 4 4
alphaV/beta3 Integrin/TGFBR2 -0.019 0.093 -9999 0 -0.58 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.005 0.044 -9999 0 -0.53 1 1
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.086 -9999 0 -0.54 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.018 0.098 -9999 0 -0.34 14 14
alphaV/beta3 Integrin/Pyk2 -0.1 0.2 -9999 0 -0.51 31 31
SDC1 0.005 0.074 -9999 0 -0.6 2 2
VAV3 0.033 0.045 -9999 0 -0.49 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 -0.006 0.12 -9999 0 -0.73 4 4
FAK1/Paxillin -0.11 0.22 -9999 0 -0.54 20 20
cell migration -0.091 0.2 -9999 0 -0.47 20 20
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.15 0.22 -9999 0 -0.46 51 51
SPP1 -0.015 0.13 -9999 0 -0.53 8 8
KDR -0.14 0.33 -9999 0 -0.86 28 28
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.031 0.19 -9999 0 -0.86 8 8
angiogenesis -0.089 0.19 -9999 0 -0.67 4 4
Rac1/GTP -0.004 0.037 -9999 0 -0.45 1 1
EDIL3 -0.077 0.25 -9999 0 -0.7 20 20
cell proliferation -0.019 0.093 -9999 0 -0.57 4 4
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.12 0.25 -9999 0 -0.67 28 28
PDGFRB -0.022 0.16 -9999 0 -0.86 6 6
SPHK1 -0.058 0.059 -9999 0 -10000 0 0
mol:S1P -0.055 0.059 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.094 0.23 -9999 0 -0.58 22 22
GNAO1 -0.06 0.23 -9999 0 -0.76 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.081 0.22 -9999 0 -0.59 19 19
PLCG1 -0.082 0.22 -9999 0 -0.61 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.022 0.16 -9999 0 -0.86 6 6
GNAI2 0.011 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 0.005 0.068 -9999 0 -0.86 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.089 0.23 -9999 0 -0.58 28 28
S1P1/S1P -0.12 0.19 -9999 0 -0.52 28 28
negative regulation of cAMP metabolic process -0.091 0.23 -9999 0 -0.56 22 22
MAPK3 -0.11 0.28 -9999 0 -0.66 27 27
calcium-dependent phospholipase C activity -0.001 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 -0.14 0.33 -9999 0 -0.86 28 28
PLCB2 -0.1 0.18 -9999 0 -0.47 28 28
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.16 -9999 0 -0.43 28 28
receptor internalization -0.12 0.18 -9999 0 -0.48 28 28
PTGS2 -0.16 0.4 -9999 0 -1.1 25 25
Rac1/GTP -0.1 0.16 -9999 0 -0.43 28 28
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.009 0.027 -9999 0 -0.34 1 1
negative regulation of T cell proliferation -0.091 0.23 -9999 0 -0.56 22 22
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
MAPK1 -0.11 0.28 -9999 0 -0.67 26 26
S1P1/S1P/PDGFB-D/PDGFRB -0.12 0.23 -9999 0 -0.54 32 32
ABCC1 0.011 0.003 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.008 0.027 -9999 0 -0.23 2 2
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.014 0.053 -9999 0 -10000 0 0
STXBP1 0.012 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.15 0.1 -9999 0 -0.24 47 47
RAB3GAP2/RIMS1/UNC13B -0.011 0.042 -9999 0 -10000 0 0
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 -0.014 0.083 -9999 0 -0.34 10 10
mol:ACh -0.014 0.031 -9999 0 -0.13 2 2
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.023 0.041 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.15 0.1 -9999 0 -0.24 47 47
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.23 0.16 -9999 0 -0.34 110 110
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.18 0.28 -9999 0 -0.63 47 47
SNAP25 -0.042 0.068 -9999 0 -0.39 1 1
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.24 0.4 -9999 0 -0.86 47 47
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.015 0.022 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.023 0.041 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.065 0.12 -9999 0 -10000 0 0
STMN1 -0.09 0.12 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin -0.15 0.17 -9999 0 -0.35 64 64
Chromosomal passenger complex/Cul3 protein complex -0.075 0.13 -9999 0 -0.39 10 10
BIRC5 -0.15 0.18 -9999 0 -0.34 72 72
DES -0.28 0.29 -9999 0 -0.66 57 57
Aurora C/Aurora B/INCENP -0.063 0.088 -9999 0 -10000 0 0
Aurora B/TACC1 -0.077 0.096 -9999 0 -10000 0 0
Aurora B/PP2A -0.096 0.12 -9999 0 -0.42 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.018 0.037 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.12 0.16 -9999 0 -0.43 21 21
Cul3 protein complex -0.036 0.14 -9999 0 -0.58 10 10
KIF2C -0.065 0.1 -9999 0 -0.24 28 28
PEBP1 0.007 0.006 -9999 0 -10000 0 0
KIF20A -0.12 0.17 -9999 0 -0.34 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.095 0.12 -9999 0 -10000 0 0
SEPT1 0.004 0.054 -9999 0 -0.34 4 4
SMC2 0.012 0 -9999 0 -10000 0 0
SMC4 0.012 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.051 0.083 -9999 0 -10000 0 0
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B -0.054 0.077 -9999 0 -10000 0 0
AURKB -0.15 0.18 -9999 0 -0.34 77 77
AURKC 0.012 0 -9999 0 -10000 0 0
CDCA8 -0.041 0.12 -9999 0 -0.35 22 22
cytokinesis -0.15 0.14 -9999 0 -0.37 22 22
Aurora B/Septin1 -0.13 0.15 -9999 0 -0.42 7 7
AURKA 0.002 0.061 -9999 0 -0.34 5 5
INCENP 0.007 0.007 -9999 0 -10000 0 0
KLHL13 -0.036 0.2 -9999 0 -0.86 9 9
BUB1 -0.13 0.17 -9999 0 -0.34 67 67
hSgo1/Aurora B/Survivin -0.16 0.19 -9999 0 -0.36 64 64
EVI5 0.011 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.12 -9999 0 -0.48 1 1
SGOL1 -0.027 0.11 -9999 0 -0.34 18 18
CENPA -0.097 0.13 -9999 0 -0.27 52 52
NCAPG -0.1 0.16 -9999 0 -0.34 52 52
Aurora B/HC8 Proteasome -0.095 0.12 -9999 0 -10000 0 0
NCAPD2 0.012 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.095 0.12 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH -0.066 0.14 -9999 0 -0.34 36 36
NPM1 -0.064 0.077 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
KLHL9 0.007 0.068 -9999 0 -0.86 1 1
mitotic prometaphase -0.005 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.095 0.12 -9999 0 -10000 0 0
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.13 -9999 0 -0.35 22 22
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.064 0.077 -9999 0 -10000 0 0
MYLK -0.069 0.12 -9999 0 -0.55 5 5
KIF23 0.006 0.028 -9999 0 -0.35 1 1
VIM -0.093 0.12 -9999 0 -0.43 1 1
RACGAP1 0.008 0.006 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.064 0.077 -9999 0 -10000 0 0
Chromosomal passenger complex -0.12 0.16 -9999 0 -0.33 50 50
Chromosomal passenger complex/EVI5 -0.13 0.19 -9999 0 -0.44 22 22
TACC1 0.012 0 -9999 0 -10000 0 0
PPP2R5D 0.01 0.027 -9999 0 -0.34 1 1
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.074 0.077 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.021 0.022 -9999 0 -10000 0 0
AURKB -0.15 0.17 -9999 0 -0.34 77 77
AURKC 0.012 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.036 0.1 -10000 0 -0.44 7 7
FYN 0.008 0.15 -10000 0 -0.52 8 8
LAT/GRAP2/SLP76 -0.012 0.14 -10000 0 -0.47 11 11
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 -0.003 0.13 -10000 0 -0.38 11 11
B2M 0.013 0.003 -10000 0 -10000 0 0
IKBKG -0.018 0.037 -10000 0 -10000 0 0
MAP3K8 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.086 0.063 -10000 0 -0.13 105 105
integrin-mediated signaling pathway -0.002 0.02 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.018 0.17 -10000 0 -0.54 12 12
TRPV6 -0.57 0.41 -10000 0 -0.86 106 106
CD28 -0.006 0.095 -10000 0 -0.41 7 7
SHC1 0.003 0.15 -10000 0 -0.53 8 8
receptor internalization 0 0.14 -10000 0 -0.51 8 8
PRF1 0.004 0.14 -10000 0 -0.66 4 4
KRAS 0.012 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.006 0.1 -10000 0 -0.33 7 7
LAT -0.016 0.16 -10000 0 -0.56 9 9
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.045 0.13 -10000 0 -0.34 27 27
CD3E -0.018 0.12 -10000 0 -0.38 13 13
CD3G -0.011 0.09 -10000 0 -0.34 11 11
RASGRP2 -0.003 0.022 -10000 0 -0.17 1 1
RASGRP1 0.003 0.13 -10000 0 -0.39 10 10
HLA-A 0.011 0.027 -10000 0 -0.33 1 1
RASSF5 0.008 0.039 -10000 0 -0.34 2 2
RAP1A/GTP/RAPL -0.002 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.046 -10000 0 -0.11 2 2
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.036 0.063 -10000 0 -0.25 4 4
PRKCA 0 0.087 -10000 0 -0.27 6 6
GRAP2 0.006 0.047 -10000 0 -0.34 3 3
mol:IP3 0.12 0.2 0.27 91 -0.41 8 99
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.003 0.12 -10000 0 -0.4 11 11
ORAI1 0.26 0.18 0.4 105 -10000 0 105
CSK 0.001 0.15 -10000 0 -0.53 8 8
B7 family/CD28 -0.077 0.17 -10000 0 -0.59 12 12
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.007 0.16 -10000 0 -0.52 11 11
PTPN6 0 0.15 -10000 0 -0.52 8 8
VAV1 -0.026 0.19 -10000 0 -0.6 11 11
Monovalent TCR/CD3 -0.015 0.11 -10000 0 -0.36 11 11
CBL 0.012 0 -10000 0 -10000 0 0
LCK 0.003 0.15 -10000 0 -0.55 8 8
PAG1 0.001 0.15 -10000 0 -0.53 8 8
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.006 0.16 -10000 0 -0.53 10 10
CD80 -0.036 0.12 -10000 0 -0.34 22 22
CD86 -0.061 0.14 -10000 0 -0.34 34 34
PDK1/CARD11/BCL10/MALT1 -0.044 0.076 -10000 0 -0.29 7 7
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.021 0.17 -10000 0 -0.5 12 12
CD8A -0.021 0.11 -10000 0 -0.34 16 16
CD8B -0.015 0.097 -10000 0 -0.34 13 13
PTPRC 0.002 0.079 -10000 0 -0.52 3 3
PDK1/PKC theta -0.005 0.15 -10000 0 -0.48 10 10
CSK/PAG1 0.005 0.15 -10000 0 -0.51 8 8
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.016 0.02 -10000 0 -10000 0 0
GRAP2/SLP76 -0.005 0.16 -10000 0 -0.52 10 10
STIM1 0.14 0.096 -10000 0 -10000 0 0
RAS family/GTP 0.027 0.058 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.002 0.15 -10000 0 -0.54 8 8
mol:DAG 0.024 0.13 -10000 0 -0.37 9 9
RAP1A/GDP 0.011 0.02 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 -0.002 0.073 -10000 0 -0.34 7 7
cytotoxic T cell degranulation 0.005 0.14 -10000 0 -0.56 6 6
RAP1A/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.15 -10000 0 -0.45 12 12
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.1 0.23 0.3 69 -0.54 9 78
NRAS 0.012 0 -10000 0 -10000 0 0
ZAP70 -0.029 0.11 -10000 0 -0.34 19 19
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.031 0.16 -10000 0 -0.53 11 11
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.022 0.12 -10000 0 -0.44 10 10
CARD11 -0.087 0.16 -10000 0 -0.34 46 46
PRKCB -0.001 0.089 -10000 0 -0.29 6 6
PRKCE 0 0.087 -10000 0 -0.27 6 6
PRKCQ -0.016 0.17 -10000 0 -0.52 12 12
LCP2 0.004 0.054 -10000 0 -0.34 4 4
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.001 0.11 -10000 0 -0.33 11 11
IKK complex 0.027 0.047 -10000 0 -0.11 1 1
RAS family/GDP -0.002 0.005 -10000 0 -10000 0 0
MAP3K14 0.014 0.084 -10000 0 -0.27 4 4
PDPK1 0 0.12 -10000 0 -0.37 10 10
TCR/CD3/MHC I/CD8/Fyn -0.005 0.16 -10000 0 -0.57 8 8
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.005 0.11 -10000 0 -0.34 15 15
epithelial cell differentiation -0.046 0.14 -10000 0 -0.5 15 15
CYFIP2 0.012 0 -10000 0 -10000 0 0
ENAH 0.032 0.1 -10000 0 -10000 0 0
EGFR 0.012 0 -10000 0 -10000 0 0
EPHA2 0.01 0.027 -10000 0 -0.34 1 1
MYO6 -0.01 0.15 -10000 0 -0.47 15 15
CTNNB1 0.012 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -10000 0 -10000 0 0
AQP5 -0.094 0.21 -10000 0 -0.65 15 15
CTNND1 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.14 -10000 0 -0.46 15 15
regulation of calcium-dependent cell-cell adhesion -0.05 0.2 -10000 0 -0.5 26 26
EGF -0.76 0.28 -10000 0 -0.86 142 142
NCKAP1 0.012 0 -10000 0 -10000 0 0
AQP3 -0.24 0.32 -10000 0 -0.66 55 55
cortical microtubule organization -0.046 0.14 -10000 0 -0.5 15 15
GO:0000145 -0.009 0.14 -10000 0 -0.44 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.047 0.15 -10000 0 -0.5 15 15
MLLT4 0.012 0 -10000 0 -10000 0 0
ARF6/GDP -0.037 0.11 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.003 0.14 -10000 0 -0.43 15 15
PVRL2 0.012 0 -10000 0 -10000 0 0
ZYX -0.01 0.15 -10000 0 -0.47 15 15
ARF6/GTP -0.001 0.01 -10000 0 -10000 0 0
CDH1 -0.069 0.25 -10000 0 -0.86 15 15
EGFR/EGFR/EGF/EGF -0.44 0.2 -10000 0 -0.5 144 144
RhoA/GDP -0.043 0.14 -10000 0 -0.46 15 15
actin cytoskeleton organization -0.002 0.14 -10000 0 -0.44 15 15
IGF-1R heterotetramer 0.012 0 -10000 0 -10000 0 0
GIT1 0.012 0 -10000 0 -10000 0 0
IGF1R 0.012 0 -10000 0 -10000 0 0
IGF1 -0.009 0.14 -10000 0 -0.86 4 4
DIAPH1 -0.002 0.008 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.046 0.14 0.5 15 -10000 0 15
RHOA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP -0.037 0.11 -10000 0 -10000 0 0
CTNNA1 0.012 0 -10000 0 -10000 0 0
VCL -0.003 0.14 -10000 0 -0.46 15 15
EFNA1 0.012 0 -10000 0 -10000 0 0
LPP -0.002 0.14 -10000 0 -0.44 15 15
Ephrin A1/EPHA2 -0.043 0.13 -10000 0 -0.45 15 15
SEC6/SEC8 -0.039 0.12 -10000 0 -10000 0 0
MGAT3 -0.051 0.21 -10000 0 -0.51 26 26
HGF/MET -0.075 0.17 -10000 0 -0.49 21 21
HGF -0.026 0.18 -10000 0 -0.86 7 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.005 0.11 -10000 0 -0.35 15 15
actin cable formation 0.049 0.098 -10000 0 -10000 0 0
KIAA1543 -0.005 0.15 -10000 0 -0.44 16 16
KIFC3 -0.01 0.15 -10000 0 -0.47 15 15
NCK1 0.012 0 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ACTN1 -0.01 0.15 -10000 0 -0.47 15 15
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.046 0.14 -10000 0 -0.5 15 15
EXOC4 0.012 0 -10000 0 -10000 0 0
STX4 -0.01 0.15 -10000 0 -0.47 15 15
PIP5K1C -0.01 0.15 -10000 0 -0.47 15 15
LIMA1 0.012 0 -10000 0 -10000 0 0
ABI1 0.012 0 -10000 0 -10000 0 0
ROCK1 -0.032 0.099 -10000 0 -10000 0 0
adherens junction assembly 0.014 0.14 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.053 0.15 -10000 0 -0.45 19 19
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.029 0.11 -10000 0 -0.34 19 19
PLEKHA7 -0.013 0.15 -10000 0 -0.47 16 16
mol:GTP -0.001 0.011 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.019 0.13 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.005 0.11 -10000 0 -0.34 15 15
regulation of cell-cell adhesion -0.002 0.14 -10000 0 -0.44 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.005 0.11 -10000 0 -0.35 15 15
Syndecan-4-mediated signaling events

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
PTK2 -0.028 0.055 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.25 0.21 -9999 0 -0.66 10 10
positive regulation of JNK cascade -0.28 0.2 -9999 0 -0.64 20 20
Syndecan-4/ADAM12 -0.28 0.21 -9999 0 -0.67 15 15
CCL5 -0.024 0.11 -9999 0 -0.34 17 17
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.51 0.41 -9999 0 -0.84 97 97
ADAM12 -0.042 0.13 -9999 0 -0.34 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.07 0.046 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.28 0.23 -9999 0 -0.68 16 16
Syndecan-4/CXCL12/CXCR4 -0.29 0.23 -9999 0 -0.69 20 20
Syndecan-4/Laminin alpha3 -0.3 0.22 -9999 0 -0.64 20 20
MDK -0.066 0.14 -9999 0 -0.34 36 36
Syndecan-4/FZD7 -0.27 0.22 -9999 0 -0.72 13 13
Syndecan-4/Midkine -0.29 0.21 -9999 0 -0.65 17 17
FZD7 -0.015 0.15 -9999 0 -0.86 5 5
Syndecan-4/FGFR1/FGF -0.24 0.18 -9999 0 -0.61 10 10
THBS1 0.001 0.096 -9999 0 -0.86 2 2
integrin-mediated signaling pathway -0.26 0.2 -9999 0 -0.62 12 12
positive regulation of MAPKKK cascade -0.28 0.2 -9999 0 -0.64 20 20
Syndecan-4/TACI -0.27 0.22 -9999 0 -0.67 13 13
CXCR4 -0.009 0.084 -9999 0 -0.34 10 10
cell adhesion 0.032 0.037 -9999 0 -10000 0 0
Syndecan-4/Dynamin -0.25 0.21 -9999 0 -0.66 10 10
Syndecan-4/TSP1 -0.26 0.22 -9999 0 -0.69 12 12
Syndecan-4/GIPC -0.25 0.21 -9999 0 -0.66 10 10
Syndecan-4/RANTES -0.27 0.21 -9999 0 -0.66 13 13
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.037 0.16 -9999 0 -0.46 17 17
LAMA3 -0.087 0.16 -9999 0 -0.34 46 46
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.084 0.053 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.25 0.21 -9999 0 -0.66 10 10
TFPI 0.006 0.047 -9999 0 -0.34 3 3
F2 -0.027 0.1 -9999 0 -0.34 10 10
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.3 0.23 -9999 0 -0.63 28 28
ACTN1 0.012 0 -9999 0 -10000 0 0
TNC -0.015 0.11 -9999 0 -0.38 11 11
Syndecan-4/CXCL12 -0.3 0.23 -9999 0 -0.73 18 18
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.069 0.25 -9999 0 -0.86 15 15
TNFRSF13B -0.016 0.087 -9999 0 -0.34 11 11
FGF2 0.012 0 -9999 0 -10000 0 0
FGFR1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.26 0.21 -9999 0 -0.59 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.017 0.094 -9999 0 -0.32 12 12
cell migration -0.02 0.014 -9999 0 -10000 0 0
PRKCD 0.014 0.013 -9999 0 -10000 0 0
vasculogenesis -0.25 0.21 -9999 0 -0.66 12 12
SDC4 -0.27 0.22 -9999 0 -0.71 10 10
Syndecan-4/Tenascin C -0.26 0.21 -9999 0 -0.65 12 12
Syndecan-4/PI-4-5-P2/PKC alpha -0.056 0.036 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.25 0.21 -9999 0 -0.66 10 10
MMP9 -0.12 0.19 -9999 0 -0.35 58 58
Rac1/GTP 0.008 0.036 -9999 0 -10000 0 0
cytoskeleton organization -0.24 0.2 -9999 0 -0.63 10 10
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.26 0.21 -9999 0 -0.66 11 11
FoxO family signaling

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
G6PC -0.99 0.63 -9999 0 -1.4 117 117
PLK1 0.017 0.16 -9999 0 -10000 0 0
CDKN1B -0.048 0.099 -9999 0 -10000 0 0
FOXO3 0.046 0.11 -9999 0 -10000 0 0
KAT2B 0.018 0.013 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.27 0.18 -9999 0 -0.38 117 117
CAT 0.051 0.1 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.018 0.026 -9999 0 -10000 0 0
FOXO1 -0.29 0.2 -9999 0 -0.42 117 117
MAPK10 0.02 0.012 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.064 0.053 -9999 0 -10000 0 0
response to oxidative stress -0.036 0.029 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.049 0.11 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 -0.026 0.025 -9999 0 -10000 0 0
BCL2L11 0.027 0.021 -9999 0 -10000 0 0
FOXO1/SKP2 -0.26 0.19 -9999 0 -0.38 117 117
mol:GDP -0.036 0.029 -9999 0 -10000 0 0
RAN 0.014 0.001 -9999 0 -10000 0 0
GADD45A 0.084 0.059 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family -0.032 0.059 -9999 0 -10000 0 0
MST1 0.013 0.071 -9999 0 -0.87 1 1
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.013 0.048 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 0.008 0.086 -9999 0 -0.52 4 4
MAPK9 0.02 0.012 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
SIRT1 0.015 0.009 -9999 0 -10000 0 0
SOD2 -0.057 0.13 -9999 0 -10000 0 0
RBL2 0.064 0.083 -9999 0 -10000 0 0
RAL/GDP 0.003 0.015 -9999 0 -10000 0 0
CHUK 0.018 0.013 -9999 0 -10000 0 0
Ran/GTP 0.013 0.003 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
RAL/GTP 0.006 0.017 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
FASLG -0.004 0.1 -9999 0 -10000 0 0
SKP2 0.012 0 -9999 0 -10000 0 0
USP7 0.014 0.001 -9999 0 -10000 0 0
IKBKB 0.018 0.013 -9999 0 -10000 0 0
CCNB1 0.048 0.12 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.07 0.074 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.19 -9999 0 -0.38 117 117
CSNK1A1 0.012 0 -9999 0 -10000 0 0
SGK1 0.018 0.013 -9999 0 -10000 0 0
CSNK1G3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.005 -9999 0 -10000 0 0
ZFAND5 0.067 0.046 -9999 0 -10000 0 0
SFN -0.14 0.17 -9999 0 -0.34 71 71
CDK2 -0.049 0.038 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.05 -9999 0 -10000 0 0
CREBBP -0.049 0.038 -9999 0 -10000 0 0
FBXO32 0.047 0.12 -9999 0 -10000 0 0
BCL6 0.063 0.087 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk 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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.066 0.11 -10000 0 -0.35 4 4
NT3 (dimer)/TRKC -0.19 0.33 -10000 0 -0.72 43 43
NT3 (dimer)/TRKB -0.32 0.34 -10000 0 -0.64 82 82
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.031 0.12 -10000 0 -0.34 20 20
PIK3CA 0.012 0 -10000 0 -10000 0 0
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.15 0.33 -10000 0 -0.86 29 29
NTRK2 -0.34 0.43 -10000 0 -0.86 66 66
NTRK3 -0.12 0.32 -10000 0 -0.86 25 25
NT-4/5 (dimer)/TRKB -0.27 0.29 -10000 0 -0.6 68 68
neuron apoptosis 0.16 0.17 0.53 18 -10000 0 18
SHC 2-3/Grb2 -0.17 0.19 -10000 0 -0.59 18 18
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.15 0.18 -10000 0 -0.56 17 17
SHC3 -0.15 0.18 -10000 0 -0.57 18 18
STAT3 (dimer) 0.02 0 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.19 0.33 -10000 0 -0.68 45 45
RIN/GDP -0.023 0.094 -10000 0 -0.3 2 2
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS 0.012 0 -10000 0 -10000 0 0
DNAJA3 -0.074 0.15 -10000 0 -0.65 3 3
RIN/GTP -0.001 0.018 -10000 0 -0.23 1 1
CCND1 0.03 0 -10000 0 -10000 0 0
MAGED1 0.012 0 -10000 0 -10000 0 0
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.03 0.1 -10000 0 -0.34 17 17
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.14 0.24 -10000 0 -0.58 36 36
TRKA/NEDD4-2 -0.12 0.26 -10000 0 -0.66 30 30
ELMO1 0.012 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.012 0.14 -10000 0 -0.75 5 5
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.012 0 -10000 0 -10000 0 0
RIT2 -0.001 0.027 -10000 0 -0.34 1 1
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.012 0 -10000 0 -10000 0 0
DNM1 -0.072 0.15 -10000 0 -0.34 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.072 0.14 -10000 0 -0.63 3 3
mol:GDP -0.036 0.14 -10000 0 -0.43 3 3
NGF (dimer) -0.012 0.14 -10000 0 -0.75 5 5
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.017 0.095 -10000 0 -0.29 2 2
TIAM1 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.26 0.28 -10000 0 -0.59 66 66
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.003 0.023 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.3 -10000 0 -0.86 22 22
RAP1/GDP -0.038 0.063 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.031 0.12 -10000 0 -0.34 20 20
ubiquitin-dependent protein catabolic process -0.12 0.24 -10000 0 -0.57 34 34
Schwann cell development -0.048 0.037 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.003 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.037 0.015 -10000 0 -10000 0 0
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.32 0.3 -10000 0 -0.82 25 25
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.084 0.096 -10000 0 -10000 0 0
STAT3 0.02 0 -10000 0 -10000 0 0
axon guidance -0.3 0.28 -10000 0 -0.76 25 25
MAPK3 -0.11 0.23 -10000 0 -0.53 36 36
MAPK1 -0.11 0.23 -10000 0 -0.53 36 36
CDC42/GDP -0.017 0.095 -10000 0 -0.29 2 2
NTF3 -0.11 0.3 -10000 0 -0.86 22 22
NTF4 -0.03 0.1 -10000 0 -0.34 17 17
NGF (dimer)/TRKA/FAIM -0.12 0.23 -10000 0 -0.58 33 33
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.006 0.047 -10000 0 -0.34 3 3
FAIM 0.008 0.039 -10000 0 -0.34 2 2
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.078 0.16 -10000 0 -0.69 4 4
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.15 0.3 -10000 0 -0.62 43 43
RGS19 0.01 0.027 -10000 0 -0.34 1 1
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP 0.027 0.062 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.095 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.12 0.24 -10000 0 -0.58 33 33
neuron projection morphogenesis -0.036 0.15 -10000 0 -0.67 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.12 0.24 -10000 0 -0.58 34 34
MAP2K1 0.039 0 -10000 0 -10000 0 0
NGFR -0.004 0.12 -10000 0 -0.86 3 3
NGF (dimer)/TRKA/GIPC/GAIP -0.071 0.16 -10000 0 -0.37 33 33
RAS family/GTP/PI3K 0.03 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.002 0.017 -10000 0 -10000 0 0
NRAS 0.012 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.012 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.26 -10000 0 -0.64 33 33
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.12 0.26 -10000 0 -0.66 29 29
SQSTM1 -0.001 0.066 -10000 0 -0.34 6 6
BDNF (dimer)/TRKB/GIPC -0.24 0.26 -10000 0 -0.54 66 66
NGF (dimer)/TRKA/p62/Atypical PKCs -0.11 0.2 -10000 0 -0.5 33 33
MATK -0.028 0.14 -10000 0 -0.45 14 14
NEDD4L 0.007 0.068 -10000 0 -0.86 1 1
RAS family/GDP -0.036 0.062 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.079 0.16 -10000 0 -0.37 34 34
Rac1/GTP -0.07 0.1 -10000 0 -0.38 4 4
FRS2 family/SHP2/CRK family -0.002 0.017 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.039 -9999 0 -0.34 2 2
CCL5 -0.024 0.11 -9999 0 -0.34 17 17
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.078 0.17 -9999 0 -0.5 13 13
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 -0.067 0.16 -9999 0 -0.57 8 8
Syndecan-1/Syntenin -0.067 0.16 -9999 0 -0.57 8 8
MAPK3 -0.047 0.14 -9999 0 -0.92 2 2
HGF/MET -0.055 0.15 -9999 0 -0.69 7 7
TGFB1/TGF beta receptor Type II 0.008 0.038 -9999 0 -0.34 2 2
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.066 0.16 -9999 0 -0.56 8 8
Syndecan-1/RANTES -0.084 0.17 -9999 0 -0.6 8 8
Syndecan-1/CD147 -0.057 0.15 -9999 0 -0.61 6 6
Syndecan-1/Syntenin/PIP2 -0.081 0.14 -9999 0 -0.55 8 8
LAMA5 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.079 0.14 -9999 0 -0.53 8 8
MMP7 -0.092 0.19 -9999 0 -0.39 42 42
HGF -0.026 0.18 -9999 0 -0.86 7 7
Syndecan-1/CASK -0.075 0.16 -9999 0 -0.48 13 13
Syndecan-1/HGF/MET -0.097 0.2 -9999 0 -0.58 15 15
regulation of cell adhesion -0.038 0.14 -9999 0 -0.87 2 2
HPSE -0.02 0.16 -9999 0 -0.86 6 6
positive regulation of cell migration -0.078 0.17 -9999 0 -0.5 13 13
SDC1 -0.079 0.17 -9999 0 -0.5 13 13
Syndecan-1/Collagen -0.078 0.17 -9999 0 -0.5 13 13
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.029 0.11 -9999 0 -0.34 19 19
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.12 0.19 -9999 0 -0.36 58 58
MAPK1 -0.047 0.14 -9999 0 -0.92 2 2
homophilic cell adhesion -0.077 0.16 -9999 0 -0.49 13 13
MMP1 -0.047 0.2 -9999 0 -0.62 15 15
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 -0.01 0.17 -10000 0 -0.65 2 2
IHH -0.086 0.29 -10000 0 -0.88 19 19
SHH Np/Cholesterol/GAS1 -0.023 0.1 -10000 0 -0.54 6 6
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.023 0.1 0.53 6 -10000 0 6
SMO/beta Arrestin2 -0.014 0.19 -10000 0 -0.51 20 20
SMO -0.021 0.2 -10000 0 -0.54 20 20
AKT1 0.015 0.09 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC 0.012 0 -10000 0 -10000 0 0
ADRBK1 0.012 0 -10000 0 -10000 0 0
heart looping -0.02 0.2 -10000 0 -0.53 20 20
STIL -0.01 0.16 -10000 0 -0.48 7 7
DHH N/PTCH2 -0.034 0.14 -10000 0 -0.66 8 8
DHH N/PTCH1 -0.046 0.2 -10000 0 -0.5 26 26
PIK3CA 0.012 0 -10000 0 -10000 0 0
DHH -0.032 0.19 -10000 0 -0.86 8 8
PTHLH -0.02 0.2 -10000 0 -0.83 2 2
determination of left/right symmetry -0.02 0.2 -10000 0 -0.53 20 20
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.019 0.2 -10000 0 -0.82 2 2
IHH N/Hhip -0.089 0.25 -10000 0 -0.63 27 27
DHH N/Hhip -0.067 0.22 -10000 0 -0.74 14 14
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.02 0.2 -10000 0 -0.53 20 20
pancreas development -0.036 0.19 -10000 0 -0.75 10 10
HHAT 0.012 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.86 4 4
somite specification -0.02 0.2 -10000 0 -0.53 20 20
SHH Np/Cholesterol/PTCH1 -0.016 0.16 -10000 0 -0.5 5 5
SHH Np/Cholesterol/PTCH2 -0.01 0.063 -10000 0 -0.53 2 2
SHH Np/Cholesterol/Megalin -0.079 0.2 -10000 0 -0.56 22 22
SHH 0.009 0.083 -10000 0 -0.67 2 2
catabolic process -0.024 0.18 -10000 0 -0.52 19 19
SMO/Vitamin D3 -0.017 0.18 -10000 0 -0.61 4 4
SHH Np/Cholesterol/Hhip -0.038 0.13 -10000 0 -0.54 10 10
LRP2 -0.1 0.29 -10000 0 -0.86 21 21
receptor-mediated endocytosis -0.1 0.22 -10000 0 -0.72 13 13
SHH Np/Cholesterol/BOC -0.01 0.062 -10000 0 -0.53 2 2
SHH Np/Cholesterol/CDO -0.013 0.066 -10000 0 -0.53 2 2
mesenchymal cell differentiation 0.038 0.13 0.53 10 -10000 0 10
mol:Vitamin D3 -0.013 0.16 -10000 0 -0.5 5 5
IHH N/PTCH2 -0.05 0.2 -10000 0 -0.58 19 19
CDON 0.004 0.054 -10000 0 -0.34 4 4
IHH N/PTCH1 -0.025 0.19 -10000 0 -0.53 19 19
Megalin/LRPAP1 -0.087 0.22 -10000 0 -0.66 21 21
PTCH2 0.01 0.027 -10000 0 -0.34 1 1
SHH Np/Cholesterol -0.01 0.064 -10000 0 -0.54 2 2
PTCH1 -0.024 0.18 -10000 0 -0.52 19 19
HHIP -0.036 0.19 -10000 0 -0.75 10 10
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.054 0.17 -9999 0 -0.58 15 15
E-cadherin/beta catenin -0.062 0.19 -9999 0 -0.66 15 15
CTNNB1 0.012 0 -9999 0 -10000 0 0
JUP 0.012 0 -9999 0 -10000 0 0
CDH1 -0.069 0.25 -9999 0 -0.86 15 15
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.007 -9999 0 -10000 0 0
SVIL 0.012 0.006 -9999 0 -10000 0 0
ZNF318 0.01 0.017 -9999 0 -10000 0 0
JMJD2C -0.002 0.019 -9999 0 -0.065 12 12
T-DHT/AR/Ubc9 -0.067 0.13 -9999 0 -0.65 6 6
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.012 0.001 -9999 0 -10000 0 0
PELP1 0.012 0.003 -9999 0 -10000 0 0
CTNNB1 0.012 0.005 -9999 0 -10000 0 0
AKT1 0.013 0.005 -9999 0 -10000 0 0
PTK2B 0.012 0.005 -9999 0 -10000 0 0
MED1 0.013 0.005 -9999 0 -10000 0 0
MAK -0.007 0.077 -9999 0 -0.34 8 8
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.007 0.069 -9999 0 -0.86 1 1
GSN 0.012 0.007 -9999 0 -10000 0 0
NCOA2 -0.064 0.25 -9999 0 -0.86 14 14
NCOA6 0.012 0.006 -9999 0 -10000 0 0
DNA-PK 0.004 0.02 -9999 0 -10000 0 0
NCOA4 0.012 0.001 -9999 0 -10000 0 0
PIAS3 0.012 0.005 -9999 0 -10000 0 0
cell proliferation -0.038 0.044 -9999 0 -10000 0 0
XRCC5 0.013 0.003 -9999 0 -10000 0 0
UBE3A 0.012 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.19 -9999 0 -0.64 17 17
FHL2 -0.036 0.063 -9999 0 -0.54 1 1
RANBP9 0.012 0.006 -9999 0 -10000 0 0
JMJD1A -0.095 0.077 -9999 0 -0.15 109 109
CDK6 0.012 0.001 -9999 0 -10000 0 0
TGFB1I1 0.001 0.096 -9999 0 -0.86 2 2
T-DHT/AR/CyclinD1 -0.067 0.13 -9999 0 -0.65 6 6
XRCC6 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.16 -9999 0 -0.7 6 6
CTDSP1 0.012 0.003 -9999 0 -10000 0 0
CTDSP2 0.013 0.011 -9999 0 -10000 0 0
BRCA1 0.008 0.04 -9999 0 -0.35 2 2
TCF4 0.013 0.008 -9999 0 -10000 0 0
CDKN2A -0.26 0.14 -9999 0 -0.34 125 125
SRF 0.02 0.006 -9999 0 -10000 0 0
NKX3-1 -0.16 0.11 -9999 0 -10000 0 0
KLK3 0.005 0.14 -9999 0 -1.5 1 1
TMF1 0.012 0.003 -9999 0 -10000 0 0
HNRNPA1 0.013 0.006 -9999 0 -10000 0 0
AOF2 0 0.007 -9999 0 -0.071 1 1
APPL1 0.023 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.071 0.12 -9999 0 -0.65 6 6
AR -0.066 0.17 -9999 0 -0.82 7 7
UBA3 0.012 0.003 -9999 0 -10000 0 0
PATZ1 0.013 0.006 -9999 0 -10000 0 0
PAWR 0.012 0.003 -9999 0 -10000 0 0
PRKDC 0.013 0.003 -9999 0 -10000 0 0
PA2G4 0.013 0.007 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.063 0.12 -9999 0 -0.56 7 7
RPS6KA3 0.012 0.007 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.067 0.13 -9999 0 -0.65 6 6
LATS2 0.013 0.006 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.06 0.12 -9999 0 -0.61 6 6
Cyclin D3/CDK11 p58 -0.004 0.031 -9999 0 -0.23 3 3
VAV3 0.012 0.005 -9999 0 -10000 0 0
KLK2 -0.075 0.092 -9999 0 -0.38 4 4
CASP8 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.098 0.23 -9999 0 -0.73 16 16
TMPRSS2 -0.8 0.55 -9999 0 -1.2 109 109
CCND1 0.012 0.003 -9999 0 -10000 0 0
PIAS1 0.012 0.01 -9999 0 -10000 0 0
mol:T-DHT -0.049 0.04 -9999 0 -0.078 105 105
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.011 0.014 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.068 0.13 -9999 0 -0.65 6 6
CMTM2 -0.008 0.08 -9999 0 -0.34 9 9
SNURF -0.049 0.22 -9999 0 -0.86 11 11
ZMIZ1 -0.03 0.035 -9999 0 -10000 0 0
CCND3 0.006 0.047 -9999 0 -0.34 3 3
TGIF1 0.013 0.006 -9999 0 -10000 0 0
FKBP4 0.012 0.006 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.039 -10000 0 -0.34 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.036 0.15 0.48 7 -10000 0 7
IL27/IL27R/JAK1 0.013 0.28 -10000 0 -0.7 8 8
TBX21 -0.024 0.21 -10000 0 -0.61 5 5
IL12B 0.004 0.028 -10000 0 -0.34 1 1
IL12A 0.009 0.005 -10000 0 -10000 0 0
IL6ST -0.11 0.31 -10000 0 -0.86 23 23
IL27RA/JAK1 0.023 0.028 -10000 0 -10000 0 0
IL27 -0.011 0.081 -10000 0 -0.34 9 9
TYK2 0.012 0.005 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.03 0.12 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.036 0.15 0.48 7 -10000 0 7
T cell proliferation during immune response 0.036 0.15 0.48 7 -10000 0 7
MAPKKK cascade -0.036 0.15 -10000 0 -0.48 7 7
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.04 -10000 0 -0.34 2 2
IL12RB1 -0.01 0.085 -10000 0 -0.34 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.08 0.23 -10000 0 -0.56 15 15
IL27/IL27R/JAK2/TYK2 -0.037 0.15 -10000 0 -0.48 7 7
positive regulation of T cell mediated cytotoxicity -0.036 0.15 -10000 0 -0.48 7 7
STAT1 (dimer) 0.14 0.38 0.5 52 -0.73 7 59
JAK2 0.012 0.005 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.15 -10000 0 -0.48 5 5
T cell proliferation -0.083 0.22 -10000 0 -0.58 19 19
IL12/IL12R/TYK2/JAK2 0.008 0.055 -10000 0 -10000 0 0
IL17A -0.03 0.12 -10000 0 -10000 0 0
mast cell activation 0.036 0.15 0.48 7 -10000 0 7
IFNG -0.004 0.03 -10000 0 -0.095 2 2
T cell differentiation -0.004 0.006 -10000 0 -0.021 1 1
STAT3 (dimer) -0.028 0.15 -10000 0 -0.48 5 5
STAT5A (dimer) -0.028 0.15 -10000 0 -0.49 4 4
STAT4 (dimer) -0.041 0.16 -10000 0 -0.59 5 5
STAT4 -0.016 0.095 -10000 0 -0.34 13 13
T cell activation -0.01 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.062 0.18 -10000 0 -0.57 1 1
GATA3 -0.99 0.66 -10000 0 -1.4 114 114
IL18 0.008 0.027 -10000 0 -0.23 2 2
positive regulation of mast cell cytokine production -0.028 0.14 -10000 0 -0.47 5 5
IL27/EBI3 -0.036 0.13 -10000 0 -0.47 7 7
IL27RA 0.009 0.024 -10000 0 -10000 0 0
IL6 -0.087 0.26 -10000 0 -0.66 24 24
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0 0.019 -10000 0 -10000 0 0
IL1B -0.007 0.11 -10000 0 -0.68 4 4
EBI3 -0.048 0.14 -10000 0 -0.36 27 27
TNF -0.007 0.088 -10000 0 -0.34 8 8
LPA4-mediated signaling events

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
ADCY4 -0.022 0.15 -9999 0 -0.59 11 11
ADCY5 -0.016 0.14 -9999 0 -0.59 9 9
ADCY6 0.019 0 -9999 0 -10000 0 0
ADCY7 0.009 0.044 -9999 0 -10000 0 0
ADCY1 -0.23 0.3 -9999 0 -0.59 67 67
ADCY2 -0.089 0.1 -9999 0 -10000 0 0
ADCY3 0.019 0 -9999 0 -10000 0 0
ADCY8 0.009 0.038 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.019 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.081 0.1 -9999 0 -0.38 8 8
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.12 -10000 0 -0.72 2 2
epithelial cell differentiation -0.22 0.21 -10000 0 -0.46 56 56
ITCH 0.045 0.023 -10000 0 -10000 0 0
WWP1 -0.091 0.09 -10000 0 -10000 0 0
FYN 0.012 0 -10000 0 -10000 0 0
EGFR 0.012 0 -10000 0 -10000 0 0
PRL -0.001 0.027 -10000 0 -0.34 1 1
neuron projection morphogenesis -0.031 0.088 -10000 0 -0.51 2 2
PTPRZ1 -0.01 0.12 -10000 0 -0.86 3 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.067 0.077 -10000 0 -0.53 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.082 0.11 -10000 0 -0.62 3 3
ADAM17 0.045 0.023 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.12 -10000 0 -0.72 2 2
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.078 0.092 -10000 0 -0.58 3 3
GRIN2B -0.064 0.099 -10000 0 -0.55 3 3
ErbB4/ErbB2/betacellulin -0.075 0.096 -10000 0 -0.63 3 3
STAT1 0.008 0.039 -10000 0 -0.34 2 2
HBEGF 0.001 0.096 -10000 0 -0.86 2 2
PRLR -0.38 0.43 -10000 0 -0.86 73 73
E4ICDs/ETO2 -0.1 0.098 -10000 0 -0.34 1 1
axon guidance -0.036 0.059 -10000 0 -10000 0 0
NEDD4 0.045 0.023 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.31 0.33 -10000 0 -0.67 73 73
CBFA2T3 0.01 0.027 -10000 0 -0.34 1 1
ErbB4/ErbB2/HBEGF -0.072 0.085 -10000 0 -0.63 2 2
MAPK3 -0.04 0.09 -10000 0 -0.54 2 2
STAT1 (dimer) -0.1 0.1 -10000 0 -0.34 2 2
MAPK1 -0.04 0.09 -10000 0 -0.54 2 2
JAK2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.078 0.092 -10000 0 -0.58 3 3
NRG1 0.024 0.1 -10000 0 -0.66 3 3
NRG3 -0.005 0.11 -10000 0 -0.55 5 5
NRG2 0.001 0.096 -10000 0 -0.86 2 2
NRG4 0.003 0.073 -10000 0 -0.6 2 2
heart development -0.036 0.059 -10000 0 -10000 0 0
neural crest cell migration -0.069 0.099 -10000 0 -0.57 3 3
ERBB2 0.042 0.014 -10000 0 -10000 0 0
WWOX/E4ICDs -0.1 0.097 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.1 0.083 -10000 0 -0.67 1 1
apoptosis 0.12 0.095 0.58 2 -10000 0 2
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.11 -10000 0 -0.63 2 2
ErbB4/ErbB2/epiregulin -0.14 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.11 0.13 -10000 0 -0.72 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.31 0.26 -10000 0 -0.58 75 75
MDM2 -0.099 0.099 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.063 0.081 -10000 0 -0.57 3 3
STAT5A -0.026 0.055 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.078 0.092 -10000 0 -0.58 3 3
DLG4 0.012 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.1 0.073 -10000 0 -10000 0 0
STAT5A (dimer) -0.24 0.23 -10000 0 -0.5 56 56
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.027 0.054 -10000 0 -10000 0 0
LRIG1 0.012 0 -10000 0 -10000 0 0
EREG -0.14 0.17 -10000 0 -0.34 72 72
BTC -0.004 0.12 -10000 0 -0.86 3 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.036 0.059 -10000 0 -10000 0 0
ERBB4 -0.12 0.12 -10000 0 -10000 0 0
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.034 0.025 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.071 0.072 -10000 0 -0.63 1 1
glial cell differentiation 0.1 0.073 -10000 0 -10000 0 0
WWOX 0.012 0 -10000 0 -10000 0 0
cell proliferation -0.039 0.1 -10000 0 -0.49 3 3
HIF-1-alpha transcription factor network

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
PKM2 -0.064 0.38 -9999 0 -1.1 7 7
HDAC7 0.014 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.075 0.25 -9999 0 -0.8 6 6
SMAD4 0.014 0 -9999 0 -10000 0 0
ID2 -0.064 0.38 -9999 0 -1.1 7 7
AP1 -0.1 0.24 -9999 0 -0.66 26 26
ABCG2 -0.068 0.38 -9999 0 -1.1 8 8
HIF1A 0.002 0.071 -9999 0 -10000 0 0
TFF3 -0.14 0.45 -9999 0 -1.1 16 16
GATA2 -0.16 0.35 -9999 0 -0.86 32 32
AKT1 0.007 0.073 -9999 0 -10000 0 0
response to hypoxia -0.009 0.079 -9999 0 -10000 0 0
MCL1 -0.064 0.38 -9999 0 -1.1 7 7
NDRG1 -0.064 0.38 -9999 0 -1.1 7 7
SERPINE1 -0.09 0.42 -9999 0 -1.1 10 10
FECH -0.064 0.38 -9999 0 -1.1 7 7
FURIN -0.064 0.38 -9999 0 -1.1 7 7
NCOA2 -0.062 0.24 -9999 0 -0.86 14 14
EP300 0.03 0.1 -9999 0 -10000 0 0
HMOX1 -0.077 0.4 -9999 0 -1.2 7 7
BHLHE40 -0.064 0.38 -9999 0 -1.1 7 7
BHLHE41 -0.089 0.4 -9999 0 -1.1 9 9
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.013 0.045 -9999 0 -10000 0 0
ENG 0.052 0.091 -9999 0 -10000 0 0
JUN 0.013 0.001 -9999 0 -10000 0 0
RORA -0.068 0.38 -9999 0 -1.1 8 8
ABCB1 -0.11 0.32 -9999 0 -1.3 10 10
TFRC -0.065 0.38 -9999 0 -1.1 7 7
CXCR4 -0.074 0.39 -9999 0 -1.1 8 8
TF -0.082 0.4 -9999 0 -1.1 10 10
CITED2 -0.064 0.38 -9999 0 -1.1 7 7
HIF1A/ARNT -0.14 0.37 -9999 0 -1.2 9 9
LDHA -0.015 0.036 -9999 0 -10000 0 0
ETS1 -0.064 0.38 -9999 0 -1.1 7 7
PGK1 -0.064 0.38 -9999 0 -1.1 7 7
NOS2 -0.093 0.44 -9999 0 -1.2 12 12
ITGB2 -0.091 0.4 -9999 0 -1 10 10
ALDOA -0.064 0.38 -9999 0 -1.1 7 7
Cbp/p300/CITED2 -0.047 0.37 -9999 0 -1.1 6 6
FOS -0.13 0.32 -9999 0 -0.86 26 26
HK2 -0.16 0.41 -9999 0 -1.1 12 12
SP1 0.017 0.021 -9999 0 -10000 0 0
GCK 0.006 0.19 -9999 0 -10000 0 0
HK1 -0.064 0.38 -9999 0 -1.1 7 7
NPM1 -0.064 0.38 -9999 0 -1.1 7 7
EGLN1 -0.064 0.38 -9999 0 -1.1 7 7
CREB1 0.02 0 -9999 0 -10000 0 0
PGM1 -0.064 0.38 -9999 0 -1.1 7 7
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.08 0.29 -9999 0 -0.86 12 12
IGFBP1 -0.12 0.45 -9999 0 -1.1 15 15
VEGFA 0.012 0.29 -9999 0 -0.93 2 2
HIF1A/JAB1 -0.01 0.023 -9999 0 -10000 0 0
CP -0.11 0.42 -9999 0 -1 15 15
CXCL12 -0.11 0.46 -9999 0 -1.1 17 17
COPS5 0.013 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.064 0.38 -9999 0 -1.1 7 7
EGLN3 -0.069 0.39 -9999 0 -1.1 8 8
CA9 -0.16 0.41 -9999 0 -1.1 11 11
TERT -0.092 0.39 -9999 0 -1.1 8 8
ENO1 -0.064 0.38 -9999 0 -1.1 7 7
PFKL -0.064 0.38 -9999 0 -1.1 7 7
NCOA1 0.013 0.001 -9999 0 -10000 0 0
ADM -0.071 0.39 -9999 0 -1.2 7 7
ARNT 0.002 0.07 -9999 0 -10000 0 0
HNF4A -0.1 0.3 -9999 0 -0.86 22 22
ADFP -0.074 0.38 -9999 0 -1.1 8 8
SLC2A1 0.006 0.3 -9999 0 -0.9 4 4
LEP -0.081 0.39 -9999 0 -1.2 7 7
HIF1A/ARNT/Cbp/p300 -0.073 0.27 -9999 0 -0.83 6 6
EPO -0.024 0.27 -9999 0 -0.74 4 4
CREBBP 0.03 0.1 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.076 0.26 -9999 0 -0.83 7 7
PFKFB3 -0.064 0.38 -9999 0 -1.1 7 7
NT5E -0.064 0.38 -9999 0 -1.1 7 7
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.12 0.19 -9999 0 -0.69 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.022 0.12 -9999 0 -0.58 6 6
NGF (dimer)/p75(NTR)/BEX1 -0.074 0.2 -9999 0 -0.62 19 19
NT-4/5 (dimer)/p75(NTR) -0.036 0.11 -9999 0 -0.67 3 3
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 0.015 0.12 -9999 0 -0.57 6 6
IKBKG 0.012 0 -9999 0 -10000 0 0
BDNF -0.031 0.12 -9999 0 -0.34 20 20
MGDIs/NGR/p75(NTR)/LINGO1 -0.021 0.1 -9999 0 -0.58 5 5
FURIN 0.012 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.032 0.1 -9999 0 -0.63 3 3
LINGO1 0.001 0.096 -9999 0 -0.86 2 2
Sortilin/TRAF6/NRIF -0.003 0.033 -9999 0 -10000 0 0
proBDNF (dimer) -0.031 0.12 -9999 0 -0.34 20 20
NTRK1 -0.15 0.33 -9999 0 -0.86 29 29
RTN4R 0.006 0.047 -9999 0 -0.34 3 3
neuron apoptosis -0.005 0.11 -9999 0 -0.6 3 3
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 0 0.14 -9999 0 -0.66 6 6
ARHGDIA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.003 0.039 -9999 0 -0.5 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.025 0.12 -9999 0 -0.61 6 6
MAGEH1 0.01 0.027 -9999 0 -0.34 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.062 0.22 -9999 0 -0.7 14 14
Mammalian IAPs/DIABLO -0.011 0.038 -9999 0 -10000 0 0
proNGF (dimer) -0.012 0.14 -9999 0 -0.75 5 5
MAGED1 0.012 0 -9999 0 -10000 0 0
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.03 0.1 -9999 0 -0.34 17 17
ZNF274 0.012 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.022 0.12 -9999 0 -0.58 6 6
NGF -0.012 0.14 -9999 0 -0.75 5 5
cell cycle arrest -0.006 0.13 -9999 0 -0.56 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.019 0.087 -9999 0 -0.4 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.029 0.093 -9999 0 -0.58 3 3
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.026 0.13 -9999 0 -0.66 6 6
PSENEN 0.012 0 -9999 0 -10000 0 0
mol:ceramide 0.008 0.12 -9999 0 -0.6 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.025 0.073 -9999 0 -0.56 1 1
p75(NTR)/beta APP -0.012 0.09 -9999 0 -0.66 3 3
BEX1 -0.062 0.24 -9999 0 -0.86 13 13
mol:GDP -0.009 0.14 -9999 0 -0.67 6 6
NGF (dimer) -0.38 0.28 -9999 0 -0.58 100 100
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.019 0.093 -9999 0 -0.53 5 5
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.023 0.12 -9999 0 -0.59 6 6
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.026 0.13 -9999 0 -0.66 6 6
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.068 0.1 -9999 0 -10000 0 0
NT3 (dimer) -0.11 0.3 -9999 0 -0.86 22 22
TP53 0.015 0.089 -9999 0 -0.51 3 3
PRDM4 0.008 0.13 -9999 0 -0.61 6 6
BDNF (dimer) -0.4 0.27 -9999 0 -0.6 99 99
PIK3CA 0.012 0 -9999 0 -10000 0 0
SORT1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.022 0.11 -9999 0 -0.57 6 6
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.024 0.12 -9999 0 -0.61 6 6
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 0.03 0.11 -9999 0 -0.62 2 2
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 0.008 0.13 -9999 0 -0.61 6 6
APH1B 0.007 0.068 -9999 0 -0.86 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.026 0.13 -9999 0 -0.66 6 6
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.1 0.25 -9999 0 -0.69 24 24
MAPK8 0.022 0.12 -9999 0 -0.62 2 2
MAPK9 0.03 0.11 -9999 0 -0.62 2 2
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.11 0.3 -9999 0 -0.86 22 22
NTF4 -0.03 0.1 -9999 0 -0.34 17 17
NDN -0.053 0.23 -9999 0 -0.86 12 12
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.021 0.11 -9999 0 -0.53 6 6
p75 CTF/Sortilin/TRAF6/NRIF 0 0 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.025 0.13 -9999 0 -0.66 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.025 0.083 -9999 0 -0.55 3 3
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.028 0.09 -9999 0 -0.58 3 3
PRKACB 0.012 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.027 0.072 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.014 0.091 -9999 0 -0.34 12 12
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.023 0.18 -9999 0 -0.77 6 6
BAD 0.034 0.11 -9999 0 -0.6 2 2
RIPK2 0.012 0 -9999 0 -10000 0 0
NGFR -0.004 0.12 -9999 0 -0.86 3 3
CYCS 0.015 0.12 -9999 0 -0.57 6 6
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.024 0.12 -9999 0 -0.61 6 6
BCL2L11 0.034 0.11 -9999 0 -0.6 2 2
BDNF (dimer)/p75(NTR) -0.039 0.12 -9999 0 -0.72 3 3
PI3K -0.024 0.12 -9999 0 -0.61 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.024 0.12 -9999 0 -0.61 6 6
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.029 0.15 -9999 0 -0.75 6 6
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.024 0.12 -9999 0 -0.61 6 6
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
PLG -0.52 0.42 -9999 0 -0.86 97 97
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.005 0.13 -9999 0 -0.59 6 6
SQSTM1 -0.001 0.066 -9999 0 -0.34 6 6
NGFRAP1 0.012 0 -9999 0 -10000 0 0
CASP3 0.035 0.1 -9999 0 -0.54 2 2
E2F1 -0.096 0.16 -9999 0 -0.34 50 50
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.091 0.18 -9999 0 -0.55 6 6
NGF (dimer)/TRKA -0.14 0.27 -9999 0 -0.66 33 33
MMP7 -0.092 0.19 -9999 0 -0.39 42 42
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.022 0.12 -9999 0 -0.58 6 6
MMP3 -0.022 0.089 -9999 0 -0.34 12 12
APAF-1/Caspase 9 -0.021 0.084 -9999 0 -0.7 1 1
Glucocorticoid receptor regulatory network

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
PCK2 -0.007 0.13 -10000 0 -1.1 2 2
SMARCC2 0.014 0 -10000 0 -10000 0 0
SMARCC1 0.014 0 -10000 0 -10000 0 0
TBX21 -0.025 0.09 -10000 0 -0.39 1 1
SUMO2 0.01 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.038 -10000 0 -0.33 2 2
FKBP4 0.012 0 -10000 0 -10000 0 0
FKBP5 0.007 0.068 -10000 0 -0.86 1 1
GR alpha/HSP90/FKBP51/HSP90 0.054 0.076 -10000 0 -0.46 1 1
PRL -0.02 0.075 -10000 0 -0.46 2 2
cortisol/GR alpha (dimer)/TIF2 0.091 0.24 0.49 8 -0.52 13 21
RELA -0.085 0.099 -10000 0 -10000 0 0
FGG 0.088 0.16 0.45 2 -10000 0 2
GR beta/TIF2 0.007 0.21 0.28 1 -0.63 14 15
IFNG -0.14 0.19 -10000 0 -0.7 4 4
apoptosis -0.066 0.21 -10000 0 -0.64 8 8
CREB1 0.003 0.057 -10000 0 -0.34 4 4
histone acetylation -0.003 0.068 -10000 0 -10000 0 0
BGLAP -0.009 0.063 -10000 0 -10000 0 0
GR/PKAc 0.063 0.062 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.18 -10000 0 -0.48 15 15
SMARCD1 0.014 0 -10000 0 -10000 0 0
MDM2 0.052 0.055 -10000 0 -10000 0 0
GATA3 -0.6 0.4 -10000 0 -0.86 114 114
AKT1 0.002 0.02 -10000 0 -10000 0 0
CSF2 -0.024 0.063 -10000 0 -10000 0 0
GSK3B 0.01 0.005 -10000 0 -10000 0 0
NR1I3 -0.037 0.26 -10000 0 -0.99 7 7
CSN2 0.092 0.11 -10000 0 -10000 0 0
BRG1/BAF155/BAF170/BAF60A 0.038 0.01 -10000 0 -10000 0 0
NFATC1 0.014 0.004 -10000 0 -10000 0 0
POU2F1 0.012 0.008 -10000 0 -10000 0 0
CDKN1A 0.024 0.055 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.006 -10000 0 -10000 0 0
SFN -0.14 0.17 -10000 0 -0.34 71 71
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.014 0.11 -10000 0 -0.42 1 1
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.056 0.29 -10000 0 -0.88 14 14
JUN -0.083 0.17 -10000 0 -0.59 8 8
IL4 -0.021 0.068 -10000 0 -10000 0 0
CDK5R1 0.008 0.028 -10000 0 -0.34 1 1
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.12 0.24 -10000 0 -0.62 23 23
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.061 0.073 -10000 0 -0.42 1 1
cortisol/GR alpha (monomer) 0.16 0.18 0.54 11 -10000 0 11
NCOA2 -0.063 0.24 -10000 0 -0.86 14 14
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.33 -10000 0 -0.88 26 26
AP-1/NFAT1-c-4 -0.19 0.32 -10000 0 -0.8 27 27
AFP -0.17 0.42 -10000 0 -1.3 18 18
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.096 0.09 -10000 0 -10000 0 0
TP53 0.029 0.026 -10000 0 -10000 0 0
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.19 0.33 -10000 0 -1.1 12 12
KRT14 -0.066 0.11 -10000 0 -0.44 2 2
TBP 0.022 0 -10000 0 -10000 0 0
CREBBP 0.024 0.032 -10000 0 -10000 0 0
HDAC1 0.01 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.003 -10000 0 -10000 0 0
AP-1 -0.19 0.32 -10000 0 -0.82 26 26
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 0.01 0.005 -10000 0 -10000 0 0
MAPK11 0.01 0.005 -10000 0 -10000 0 0
KRT5 -0.15 0.27 -10000 0 -0.96 8 8
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.014 0.01 -10000 0 -10000 0 0
STAT1 0.016 0.038 -10000 0 -0.33 2 2
CGA -0.053 0.22 -10000 0 -1.3 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.032 0.075 0.33 1 -10000 0 1
MAPK3 0.01 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
ICAM1 -0.15 0.18 -10000 0 -0.52 8 8
NFKB1 -0.085 0.099 -10000 0 -10000 0 0
MAPK8 -0.075 0.16 -10000 0 -0.83 4 4
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.073 0.22 -10000 0 -0.68 8 8
BAX 0.028 0.038 -10000 0 -10000 0 0
POMC -0.23 0.31 -10000 0 -0.92 11 11
EP300 0.024 0.032 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.16 0.16 0.51 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.043 -10000 0 -10000 0 0
SGK1 0.067 0.041 -10000 0 -10000 0 0
IL13 -0.45 0.3 -10000 0 -0.77 57 57
IL6 -0.26 0.42 -10000 0 -1.3 18 18
PRKACG 0 0.027 -10000 0 -0.34 1 1
IL5 -0.37 0.24 -10000 0 -0.69 32 32
IL2 -0.12 0.18 -10000 0 -0.66 3 3
CDK5 0.01 0.005 -10000 0 -10000 0 0
PRKACB 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.2 0.21 -10000 0 -0.62 11 11
CDK5R1/CDK5 0 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.09 0.14 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.15 0.48 7 -10000 0 7
SMARCA4 0.014 0 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.091 0.35 2 -10000 0 2
NF kappa B1 p50/RelA/Cbp -0.085 0.15 -10000 0 -10000 0 0
JUN (dimer) -0.082 0.17 -10000 0 -0.59 8 8
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.066 0.26 -10000 0 -1.1 9 9
NR3C1 0.086 0.096 0.35 4 -10000 0 4
NR4A1 -0.36 0.44 -10000 0 -0.86 69 69
TIF2/SUV420H1 -0.058 0.19 -10000 0 -0.66 14 14
MAPKKK cascade -0.066 0.21 -10000 0 -0.64 8 8
cortisol/GR alpha (dimer)/Src-1 0.15 0.16 0.5 8 -10000 0 8
PBX1 0.002 0.097 -10000 0 -0.86 2 2
POU1F1 0.006 0.011 -10000 0 -10000 0 0
SELE -0.59 0.65 -10000 0 -1.3 72 72
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.091 0.35 2 -10000 0 2
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.15 0.48 7 -10000 0 7
mol:cortisol 0.074 0.1 0.31 8 -10000 0 8
MMP1 -0.12 0.31 -10000 0 -1.4 8 8
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.015 0.042 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.042 0.12 -9999 0 -0.53 3 3
JUN -0.009 0.15 -9999 0 -0.58 6 6
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.062 0.18 -9999 0 -0.56 17 17
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.063 0.18 -9999 0 -0.57 17 17
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.14 -9999 0 -0.54 11 11
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.056 0.16 -9999 0 -0.5 17 17
GRB7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.062 0.18 -9999 0 -0.56 17 17
MAPKKK cascade -0.05 0.14 -9999 0 -0.46 17 17
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.05 0.17 -9999 0 -0.62 12 12
lamellipodium assembly -0.038 0.11 -9999 0 -0.37 11 11
RET51/GFRalpha1/GDNF/SHC -0.062 0.18 -9999 0 -0.56 17 17
PIK3CA 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.04 0.14 -9999 0 -0.54 11 11
RET9/GFRalpha1/GDNF/Shank3 -0.04 0.14 -9999 0 -0.54 11 11
MAPK3 -0.019 0.16 -9999 0 -0.47 17 17
DOK1 0.01 0.027 -9999 0 -0.34 1 1
DOK6 -0.11 0.3 -9999 0 -0.86 22 22
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.031 0.17 -9999 0 -0.65 4 4
DOK5 -0.004 0.12 -9999 0 -0.86 3 3
GFRA1 -0.054 0.22 -9999 0 -0.75 14 14
MAPK8 -0.017 0.16 -9999 0 -0.62 6 6
HRAS/GTP -0.058 0.17 -9999 0 -0.53 17 17
tube development -0.037 0.13 -9999 0 -0.51 11 11
MAPK1 -0.019 0.16 -9999 0 -0.47 17 17
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.002 0.096 -9999 0 -0.35 11 11
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.25 -9999 0 -0.56 36 36
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.062 0.18 -9999 0 -0.56 17 17
RET51/GFRalpha1/GDNF/Dok5 -0.072 0.19 -9999 0 -0.56 20 20
PRKCA 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.005 0.12 -9999 0 -0.4 11 11
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.002 0.096 -9999 0 -0.35 11 11
RET51/GFRalpha1/GDNF/Grb7 -0.062 0.18 -9999 0 -0.56 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.026 0.18 -9999 0 -0.86 7 7
DOK4 0.012 0 -9999 0 -10000 0 0
JNK cascade -0.008 0.15 -9999 0 -0.57 6 6
RET9/GFRalpha1/GDNF/FRS2 -0.04 0.14 -9999 0 -0.54 11 11
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.002 0.096 -9999 0 -0.35 11 11
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.012 0.13 -9999 0 -0.37 17 17
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.013 0.13 -9999 0 -0.38 17 17
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.014 0.14 -9999 0 -0.38 17 17
PI3K -0.01 0.19 -9999 0 -0.6 11 11
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.037 0.13 -9999 0 -0.51 11 11
GRB10 0.012 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.008 0.11 -9999 0 -0.35 11 11
RET51/GFRalpha1/GDNF/FRS2 -0.062 0.18 -9999 0 -0.56 17 17
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 -0.006 0.12 -9999 0 -0.73 4 4
IRS2 0.01 0.027 -9999 0 -0.34 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.14 -9999 0 -0.38 17 17
RET51/GFRalpha1/GDNF/PKC alpha -0.062 0.18 -9999 0 -0.56 17 17
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF 0.003 0.005 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.073 0.2 -9999 0 -0.62 18 18
Rac1/GTP -0.046 0.13 -9999 0 -0.45 11 11
RET9/GFRalpha1/GDNF -0.044 0.15 -9999 0 -0.59 11 11
GFRalpha1/GDNF -0.05 0.17 -9999 0 -0.67 11 11
Nongenotropic Androgen 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
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.021 0.1 -10000 0 -0.54 6 6
regulation of S phase of mitotic cell cycle 0.014 0.072 -10000 0 -0.35 6 6
GNAO1 -0.059 0.23 -10000 0 -0.75 15 15
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.025 0.12 -10000 0 -0.59 7 7
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 0.01 0.1 -10000 0 -0.46 6 6
T-DHT/AR -0.026 0.13 -10000 0 -0.61 7 7
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 24 24
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.86 1 1
mol:GDP -0.025 0.12 -10000 0 -0.64 6 6
cell proliferation -0.016 0.18 -10000 0 -0.62 3 3
PIK3CA 0.012 0 -10000 0 -10000 0 0
FOS -0.093 0.34 -10000 0 -0.86 26 26
mol:Ca2+ -0.01 0.024 -10000 0 -0.078 15 15
MAPK3 -0.002 0.14 -10000 0 -0.65 2 2
MAPK1 -0.003 0.091 -10000 0 -0.31 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 26 26
cAMP biosynthetic process -0.017 0.12 -10000 0 -0.57 7 7
GNG2 0.012 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 26 26
HRAS/GTP -0.024 0.095 -10000 0 -0.5 6 6
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 26 26
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.024 0.18 0.41 26 -10000 0 26
T-DHT/AR/PELP1 -0.022 0.11 -10000 0 -0.59 6 6
HRAS/GDP -0.022 0.12 -10000 0 -0.6 6 6
CREB1 -0.028 0.19 -10000 0 -0.44 26 26
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.023 0.17 -10000 0 -0.79 7 7
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 0.007 0.1 -10000 0 -0.48 6 6
RAC1-CDC42/GDP -0.022 0.11 -10000 0 -0.58 6 6
T-DHT/AR/PELP1/Src -0.021 0.1 -10000 0 -0.54 6 6
MAP2K2 0.01 0.1 -10000 0 -0.46 6 6
T-DHT/AR/PELP1/Src/PI3K 0.014 0.072 -10000 0 -0.35 6 6
GNAZ 0.012 0 -10000 0 -10000 0 0
SHBG -0.026 0.18 -10000 0 -0.86 7 7
Gi family/GNB1/GNG2/GDP 0.003 0.12 -10000 0 -0.41 12 12
mol:T-DHT 0 0.001 -10000 0 -0.003 23 23
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 -0.039 0.097 -10000 0 -0.23 33 33
Gi family/GTP -0.032 0.083 -10000 0 -0.28 13 13
CDC42 0.012 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.011 0.1 -9999 0 -0.37 10 10
FZD6 0.012 0 -9999 0 -10000 0 0
WNT6 0.003 0.073 -9999 0 -0.6 2 2
WNT4 -0.003 0.1 -9999 0 -0.6 4 4
FZD3 0.012 0 -9999 0 -10000 0 0
WNT5A -0.044 0.13 -9999 0 -0.34 26 26
WNT11 -0.035 0.18 -9999 0 -0.67 11 11
IL6-mediated signaling events

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
BCL2L1 -0.046 0.19 -9999 0 -0.71 2 2
CRP -0.06 0.2 -9999 0 -0.68 4 4
cell cycle arrest -0.063 0.21 -9999 0 -0.74 5 5
TIMP1 -0.079 0.21 -9999 0 -0.6 8 8
IL6ST -0.11 0.3 -9999 0 -0.86 23 23
Rac1/GDP -0.077 0.21 -9999 0 -0.66 10 10
AP1 -0.07 0.19 -9999 0 -0.47 24 24
GAB2 0.011 0.006 -9999 0 -10000 0 0
TNFSF11 -0.061 0.2 -9999 0 -0.68 4 4
HSP90B1 0.014 0.047 -9999 0 -10000 0 0
GAB1 0.013 0.002 -9999 0 -10000 0 0
MAPK14 -0.042 0.19 -9999 0 -0.69 7 7
AKT1 0.049 0.015 -9999 0 -10000 0 0
FOXO1 0.055 0.013 -9999 0 -10000 0 0
MAP2K6 -0.054 0.2 -9999 0 -0.67 8 8
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.064 0.2 -9999 0 -0.63 9 9
MITF -0.061 0.2 -9999 0 -0.57 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0 -9999 0 -10000 0 0
A2M 0.004 0.16 -9999 0 -1.5 2 2
CEBPB 0.007 0.055 -9999 0 -0.33 4 4
GRB2/SOS1/GAB family/SHP2 -0.01 0.076 -9999 0 -10000 0 0
STAT3 -0.067 0.22 -9999 0 -0.8 5 5
STAT1 -0.01 0.023 -9999 0 -10000 0 0
CEBPD -0.046 0.19 -9999 0 -0.68 3 3
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K 0.021 0.002 -9999 0 -10000 0 0
JUN 0.012 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.047 0.19 -9999 0 -0.72 6 6
MAPK11 -0.042 0.19 -9999 0 -0.69 7 7
STAT3 (dimer)/FOXO1 -0.017 0.19 -9999 0 -0.58 4 4
GRB2/SOS1/GAB family -0.079 0.16 -9999 0 -0.75 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.077 0.21 -9999 0 -0.53 19 19
GRB2 0.013 0.002 -9999 0 -10000 0 0
JAK2 0.012 0 -9999 0 -10000 0 0
LBP -0.27 0.45 -9999 0 -0.96 44 44
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.014 0.003 -9999 0 -10000 0 0
MYC -0.048 0.19 -9999 0 -0.68 3 3
FGG -0.066 0.21 -9999 0 -0.68 3 3
macrophage differentiation -0.063 0.21 -9999 0 -0.74 5 5
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.24 -9999 0 -0.55 34 34
JUNB -0.046 0.18 -9999 0 -0.63 4 4
FOS -0.13 0.32 -9999 0 -0.86 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.071 0.21 -9999 0 -0.53 17 17
STAT1/PIAS1 -0.062 0.19 -9999 0 -0.69 7 7
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.022 -9999 0 -10000 0 0
STAT3 (dimer) -0.066 0.22 -9999 0 -0.77 5 5
PRKCD -0.051 0.19 -9999 0 -0.68 5 5
IL6R 0.014 0.003 -9999 0 -10000 0 0
SOCS3 -0.038 0.2 -9999 0 -0.81 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 -0.063 0.21 -9999 0 -0.58 23 23
Rac1/GTP -0.083 0.2 -9999 0 -0.66 10 10
HCK -0.035 0.13 -9999 0 -0.36 20 20
MAPKKK cascade 0.01 0.059 -9999 0 -10000 0 0
bone resorption -0.057 0.19 -9999 0 -0.65 4 4
IRF1 -0.046 0.19 -9999 0 -0.65 4 4
mol:GDP -0.092 0.22 -9999 0 -0.59 16 16
SOS1 0.01 0.006 -9999 0 -10000 0 0
VAV1 -0.093 0.22 -9999 0 -0.6 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.052 0.2 -9999 0 -0.73 7 7
PTPN11 -0.007 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.062 0.2 -9999 0 -0.66 15 15
gp130 (dimer)/TYK2/TYK2/LMO4 -0.067 0.21 -9999 0 -0.58 23 23
gp130 (dimer)/JAK2/JAK2/LMO4 -0.067 0.21 -9999 0 -0.58 23 23
IL6 -0.088 0.26 -9999 0 -0.66 24 24
PIAS3 0.012 0 -9999 0 -10000 0 0
PTPRE 0.009 0.01 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.08 0.21 -9999 0 -0.43 34 34
LMO4 0.013 0.008 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.19 -9999 0 -0.82 5 5
MCL1 0.055 0.013 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.019 0.1 -10000 0 -0.4 2 2
TBX21 -0.03 0.28 -10000 0 -0.86 8 8
B2M 0.013 0.004 -10000 0 -10000 0 0
TYK2 0.016 0.017 -10000 0 -10000 0 0
IL12RB1 -0.006 0.094 -10000 0 -0.37 10 10
GADD45B -0.007 0.24 -10000 0 -0.83 3 3
IL12RB2 -0.13 0.18 -10000 0 -0.34 67 67
GADD45G -0.012 0.26 -10000 0 -0.91 5 5
natural killer cell activation 0.006 0.02 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.012 0.039 -10000 0 -0.33 2 2
IL2RA -0.022 0.1 -10000 0 -0.34 16 16
IFNG -0.024 0.1 -10000 0 -0.34 15 15
STAT3 (dimer) -0.013 0.25 -10000 0 -0.66 10 10
HLA-DRB5 -0.019 0.12 -10000 0 -0.43 11 11
FASLG -0.039 0.3 -10000 0 -0.81 12 12
NF kappa B2 p52/RelB -0.11 0.21 -10000 0 -0.66 15 15
CD4 -0.004 0.071 -10000 0 -0.34 7 7
SOCS1 -0.001 0.1 -10000 0 -0.68 3 3
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D -0.047 0.13 -10000 0 -0.34 27 27
CD3E -0.02 0.12 -10000 0 -0.38 13 13
CD3G -0.013 0.091 -10000 0 -0.35 11 11
IL12Rbeta2/JAK2 -0.077 0.13 -10000 0 -0.7 1 1
CCL3 -0.048 0.32 -10000 0 -1 8 8
CCL4 -0.04 0.3 -10000 0 -0.83 11 11
HLA-A 0.01 0.028 -10000 0 -0.33 1 1
IL18/IL18R 0.023 0.097 -10000 0 -0.56 1 1
NOS2 -0.064 0.39 -10000 0 -1.1 15 15
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.096 -10000 0 -0.42 1 1
IL1R1 -0.025 0.27 -10000 0 -0.83 7 7
IL4 -0.003 0.021 -10000 0 -10000 0 0
JAK2 0.016 0.017 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.022 0.16 -10000 0 -0.59 8 8
RAB7A 0.016 0.22 -10000 0 -0.81 1 1
lysosomal transport 0.018 0.21 -10000 0 -0.76 1 1
FOS -0.19 0.52 -10000 0 -1.3 28 28
STAT4 (dimer) -0.01 0.25 -10000 0 -0.75 7 7
STAT5A (dimer) -0.12 0.23 -10000 0 -0.72 14 14
GZMA -0.031 0.28 -10000 0 -0.91 8 8
GZMB -0.041 0.3 -10000 0 -0.93 9 9
HLX 0.01 0.027 -10000 0 -0.34 1 1
LCK -0.034 0.29 -10000 0 -0.75 15 15
TCR/CD3/MHC II/CD4 -0.041 0.15 -10000 0 -0.45 9 9
IL2/IL2R -0.041 0.1 -10000 0 -0.53 3 3
MAPK14 0.002 0.25 -10000 0 -0.67 7 7
CCR5 -0.02 0.26 -10000 0 -0.7 10 10
IL1B -0.008 0.14 -10000 0 -0.78 5 5
STAT6 0.01 0.097 -10000 0 -10000 0 0
STAT4 -0.016 0.095 -10000 0 -0.34 13 13
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.008 0.039 -10000 0 -0.34 2 2
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.011 0.031 -10000 0 -0.3 1 1
CD8A -0.022 0.11 -10000 0 -0.35 16 16
CD8B -0.016 0.097 -10000 0 -0.34 13 13
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.019 0.1 0.4 2 -10000 0 2
IL2RB -0.031 0.12 -10000 0 -0.34 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.24 -10000 0 -0.69 7 7
IL2RG -0.001 0.066 -10000 0 -0.34 6 6
IL12 0.022 0.034 -10000 0 -10000 0 0
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 -0.004 0.073 -10000 0 -0.34 7 7
IL2 0.002 0.027 -10000 0 -0.34 1 1
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.017 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.037 0.3 -10000 0 -0.76 15 15
MAP2K3 -0.003 0.24 -10000 0 -0.67 7 7
RIPK2 0.012 0 -10000 0 -10000 0 0
MAP2K6 -0.003 0.24 -10000 0 -0.67 7 7
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.079 -10000 0 -0.51 3 3
IL18RAP -0.027 0.12 -10000 0 -0.34 20 20
IL12Rbeta1/TYK2 0.007 0.072 -10000 0 -10000 0 0
EOMES -0.017 0.089 -10000 0 -10000 0 0
STAT1 (dimer) -0.018 0.25 -10000 0 -0.72 8 8
T cell proliferation 0.01 0.21 -10000 0 -0.56 6 6
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.01 0.068 -10000 0 -0.85 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.087 0.18 -10000 0 -0.62 6 6
ATF2 0.011 0.23 -10000 0 -0.65 5 5
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.012 0 -9999 0 -10000 0 0
SPHK1 -0.13 0.17 -9999 0 -0.34 67 67
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P -0.031 0.063 -9999 0 -10000 0 0
GNAO1 -0.059 0.23 -9999 0 -0.75 15 15
mol:Sphinganine-1-P -0.078 0.12 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.022 0.027 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.017 -9999 0 -10000 0 0
S1PR3 -0.047 0.22 -9999 0 -0.86 11 11
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.037 0.044 -9999 0 -10000 0 0
S1PR5 -0.007 0.11 -9999 0 -0.51 6 6
S1PR4 0.006 0.047 -9999 0 -0.34 3 3
GNAI1 0.007 0.068 -9999 0 -0.86 1 1
S1P/S1P5/G12 -0.037 0.069 -9999 0 -0.56 2 2
S1P/S1P3/Gq -0.09 0.19 -9999 0 -0.43 31 31
S1P/S1P4/Gi -0.011 0.1 -9999 0 -0.35 12 12
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ 0.012 0 -9999 0 -10000 0 0
GNA14 -0.16 0.34 -9999 0 -0.86 31 31
GNA15 -0.007 0.08 -9999 0 -0.34 9 9
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.01 0.027 -9999 0 -0.34 1 1
GNA11 -0.009 0.14 -9999 0 -0.86 4 4
ABCC1 0.012 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.098 0.14 -9999 0 -0.6 8 8
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.067 0.14 -9999 0 -0.54 8 8
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.01 0.07 -9999 0 -0.34 7 7
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 -0.25 0.15 -9999 0 -0.34 122 122
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.008 0.042 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 0.01 0.027 -9999 0 -0.34 1 1
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.087 0.16 -9999 0 -0.34 45 45
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.14 -9999 0 -0.6 8 8
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.053 0.12 -9999 0 -0.51 2 2
MAP1B 0 0.014 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.045 0.13 -9999 0 -0.48 8 8
RELN -0.16 0.23 -9999 0 -0.4 67 67
PAFAH/LIS1 -0.12 0.085 -9999 0 -10000 0 0
LIS1/CLIP170 0.026 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.048 0.077 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.03 0.098 -9999 0 -0.36 9 9
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.063 0.12 -9999 0 -0.55 2 2
LIS1/IQGAP1 0.026 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 0.01 0.027 -9999 0 -0.34 1 1
PAFAH1B2 0.007 0.068 -9999 0 -0.86 1 1
MAP1B/LIS1/Dynein heavy chain 0.024 0.008 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.067 0.094 -9999 0 -0.49 2 2
LRP8 -0.001 0.066 -9999 0 -0.34 6 6
NDEL1/Katanin 60 -0.053 0.12 -9999 0 -0.51 2 2
P39/CDK5 -0.09 0.13 -9999 0 -0.49 8 8
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0 -9999 0 -10000 0 0
CDK5 -0.054 0.13 -9999 0 -0.51 8 8
PPP2R5D 0.01 0.027 -9999 0 -0.34 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.08 0.12 -9999 0 -0.52 8 8
RELN/VLDLR -0.085 0.13 -9999 0 -0.55 8 8
CDC42 0 0 -9999 0 -10000 0 0
Ephrin A reverse signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.035 0.12 -9999 0 -0.59 7 7
EFNA5 -0.028 0.18 -9999 0 -0.79 8 8
FYN -0.014 0.12 -9999 0 -0.54 7 7
neuron projection morphogenesis -0.035 0.12 -9999 0 -0.59 7 7
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.035 0.12 -9999 0 -0.59 7 7
EPHA5 -0.011 0.069 -9999 0 -0.34 7 7
Noncanonical Wnt signaling pathway

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.037 0.2 -9999 0 -0.86 9 9
GNB1/GNG2 -0.03 0.079 -9999 0 -0.42 2 2
mol:DAG 0.012 0.088 -9999 0 -10000 0 0
PLCG1 0.012 0.09 -9999 0 -10000 0 0
YES1 -0.002 0.098 -9999 0 -0.44 2 2
FZD3 0.012 0 -9999 0 -10000 0 0
FZD6 0.012 0 -9999 0 -10000 0 0
G protein 0.011 0.09 -9999 0 -10000 0 0
MAP3K7 -0.2 0.23 -9999 0 -0.49 19 19
mol:Ca2+ 0.012 0.086 -9999 0 -10000 0 0
mol:IP3 0.012 0.088 -9999 0 -10000 0 0
NLK -0.012 0.013 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.22 0.25 -9999 0 -0.46 79 79
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.011 0.1 -9999 0 -0.37 10 10
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.002 0.098 -9999 0 -0.44 2 2
GO:0007205 0.012 0.086 -9999 0 -10000 0 0
WNT6 0.003 0.073 -9999 0 -0.6 2 2
WNT4 -0.003 0.1 -9999 0 -0.6 4 4
NFAT1/CK1 alpha -0.05 0.12 -9999 0 -0.43 9 9
GNG2 0.012 0 -9999 0 -10000 0 0
WNT5A -0.044 0.13 -9999 0 -0.34 26 26
WNT11 -0.035 0.18 -9999 0 -0.67 11 11
CDC42 0.005 0.093 -9999 0 -0.42 2 2
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.036 0.12 -10000 0 -0.49 10 10
HDAC1 0.001 0.003 -10000 0 -10000 0 0
AES 0.011 0.001 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.007 0.068 -10000 0 -0.86 1 1
LRP6/FZD1 -0.005 0.034 -10000 0 -10000 0 0
TLE1 0.011 0 -10000 0 -10000 0 0
AP1 -0.15 0.25 -10000 0 -0.43 61 61
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.01 0.027 -10000 0 -0.34 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.046 -10000 0 -10000 0 0
NICD/RBPSUH -0.002 0.013 -10000 0 -10000 0 0
WIF1 0.002 0.047 -10000 0 -0.34 3 3
NOTCH1 -0.002 0.014 -10000 0 -10000 0 0
PSENEN 0.012 0 -10000 0 -10000 0 0
KREMEN2 -0.034 0.12 -10000 0 -0.34 21 21
DKK1 -0.014 0.087 -10000 0 -0.34 11 11
beta catenin/beta TrCP1 0.078 0.088 0.25 1 -10000 0 1
APH1B 0.007 0.068 -10000 0 -0.86 1 1
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 -0.015 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.014 0.052 -10000 0 -0.36 3 3
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.13 0.32 -10000 0 -0.86 26 26
JUN 0.012 0 -10000 0 -10000 0 0
MAP3K7 0.01 0.001 -10000 0 -10000 0 0
CTNNB1 0.076 0.095 0.24 34 -10000 0 34
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.028 0.08 -10000 0 -0.58 1 1
HNF1A -0.005 0.12 -10000 0 -0.86 3 3
CTBP1 0.011 0.001 -10000 0 -10000 0 0
MYC 0.024 0.036 -10000 0 -10000 0 0
NKD1 -0.21 0.38 -10000 0 -0.86 40 40
FZD1 0.004 0.054 -10000 0 -0.34 4 4
NOTCH1 precursor/Deltex homolog 1 -0.005 0.04 -10000 0 -0.49 1 1
apoptosis -0.15 0.25 -10000 0 -0.43 61 61
Delta 1/NOTCHprecursor -0.036 0.12 -10000 0 -0.49 10 10
DLL1 -0.053 0.22 -10000 0 -0.68 15 15
PPARD 0.027 0.007 -10000 0 -10000 0 0
Gamma Secretase -0.003 0.039 -10000 0 -0.49 1 1
APC -0.015 0.037 -10000 0 -10000 0 0
DVL1 0 0.007 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.035 0.081 -10000 0 -10000 0 0
LRP6 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0 -10000 0 -10000 0 0
NLK 0.012 0.002 -10000 0 -10000 0 0
CCND1 0.027 0.007 -10000 0 -10000 0 0
WNT1 -0.021 0.1 -10000 0 -0.34 15 15
Axin1/APC/beta catenin 0.067 0.046 -10000 0 -10000 0 0
DKK2 0.002 0.078 -10000 0 -0.51 3 3
NOTCH1 precursor/DVL1 0.001 0.011 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
FRAT1 0.011 0 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.04 -10000 0 -0.49 1 1
PPP2R5D 0.093 0.16 0.38 40 -10000 0 40
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.02 0.051 -10000 0 -10000 0 0
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.016 0.002 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.017 -9999 0 -10000 0 0
VLDLR 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 -0.005 0.076 -9999 0 -0.34 8 8
RELN/VLDLR/Fyn -0.092 0.14 -9999 0 -0.58 8 8
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.077 -9999 0 -0.5 4 4
AKT1 -0.028 0.088 -9999 0 -0.34 7 7
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.01 0.07 -9999 0 -0.34 7 7
RELN/LRP8/DAB1 -0.098 0.14 -9999 0 -0.58 8 8
LRPAP1/LRP8 -0.008 0.042 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.088 0.13 -9999 0 -0.55 8 8
DAB1/alpha3/beta1 Integrin -0.078 0.11 -9999 0 -0.59 2 2
long-term memory -0.18 0.23 -9999 0 -0.56 40 40
DAB1/LIS1 -0.077 0.12 -9999 0 -0.51 8 8
DAB1/CRLK/C3G -0.072 0.11 -9999 0 -0.49 8 8
PIK3CA 0.012 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.078 0.12 -9999 0 -0.51 8 8
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.18 0.36 -9999 0 -0.84 35 35
CDK5R1 0.01 0.027 -9999 0 -0.34 1 1
RELN -0.16 0.23 -9999 0 -0.4 67 67
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.098 0.14 -9999 0 -0.6 8 8
GRIN2A/RELN/LRP8/DAB1/Fyn -0.19 0.24 -9999 0 -0.58 40 40
MAPK8 -0.009 0.14 -9999 0 -0.86 4 4
RELN/VLDLR/DAB1 -0.092 0.13 -9999 0 -0.56 8 8
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.065 0.13 -9999 0 -0.53 8 8
RELN/LRP8 -0.098 0.14 -9999 0 -0.6 8 8
GRIN2B/RELN/LRP8/DAB1/Fyn -0.089 0.12 -9999 0 -0.54 8 8
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.011 0.048 -9999 0 -10000 0 0
RAP1A -0.038 0.12 -9999 0 -0.55 2 2
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.001 0.047 -9999 0 -0.34 3 3
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.014 0.078 -9999 0 -0.31 4 4
neuron adhesion -0.03 0.12 -9999 0 -0.52 2 2
LRP8 -0.001 0.066 -9999 0 -0.34 6 6
GSK3B -0.019 0.084 -9999 0 -0.4 1 1
RELN/VLDLR/DAB1/Fyn -0.083 0.12 -9999 0 -0.53 8 8
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.039 0.093 -9999 0 -0.37 8 8
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.02 0.17 -9999 0 -0.81 7 7
neuron migration -0.014 0.12 -9999 0 -0.44 8 8
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.078 -9999 0 -0.31 4 4
RELN/VLDLR -0.085 0.13 -9999 0 -0.55 8 8
Calcium signaling in the CD4+ TCR 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
NFATC1 0.016 0.024 -9999 0 -10000 0 0
NFATC2 -0.018 0.14 -9999 0 -0.59 9 9
NFATC3 0.016 0.024 -9999 0 -10000 0 0
CD40LG -0.092 0.27 -9999 0 -0.67 16 16
PTGS2 -0.14 0.37 -9999 0 -0.91 23 23
JUNB 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.008 -9999 0 -10000 0 0
CaM/Ca2+ -0.003 0.008 -9999 0 -10000 0 0
CALM1 0.012 0.006 -9999 0 -10000 0 0
JUN 0.012 0.007 -9999 0 -10000 0 0
mol:Ca2+ -0.003 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 0.004 0.054 -9999 0 -0.34 4 4
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.05 0.12 -9999 0 -0.56 3 3
FOS -0.13 0.32 -9999 0 -0.87 26 26
IFNG -0.1 0.28 -9999 0 -0.66 21 21
AP-1/NFAT1-c-4 -0.16 0.28 -9999 0 -0.79 18 18
FASLG -0.1 0.28 -9999 0 -0.66 21 21
NFAT1-c-4/ICER1 -0.039 0.11 -9999 0 -0.48 9 9
IL2RA -0.1 0.27 -9999 0 -0.64 20 20
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.092 0.27 -9999 0 -0.67 16 16
JunB/Fra1/NFAT1-c-4 -0.037 0.11 -9999 0 -0.46 9 9
IL4 -0.092 0.26 -9999 0 -0.67 16 16
IL2 -0.007 0.032 -9999 0 -10000 0 0
IL3 -0.015 0.022 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.012 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.023 0.1 -10000 0 -0.5 7 7
ER alpha/Gai/GDP/Gbeta gamma -0.01 0.17 -10000 0 -0.61 7 7
AKT1 -0.005 0.18 -10000 0 -0.86 7 7
PIK3CA 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.008 0.19 -10000 0 -0.88 7 7
mol:Ca2+ -0.13 0.27 -10000 0 -0.57 39 39
IGF1R 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.033 0.13 -10000 0 -0.58 9 9
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.003 0.17 0.81 7 -10000 0 7
RhoA/GTP -0.02 0.09 -10000 0 -0.44 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.043 0.14 -10000 0 -0.63 7 7
regulation of stress fiber formation -0.028 0.09 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.027 0.12 -10000 0 -0.58 7 7
KRAS 0.012 0 -10000 0 -10000 0 0
G13/GTP -0.025 0.11 -10000 0 -0.54 7 7
pseudopodium formation 0.028 0.09 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.025 0.12 -10000 0 -0.58 7 7
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.012 0 -10000 0 -10000 0 0
GNAO1 -0.059 0.23 -10000 0 -0.75 15 15
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.001 0.17 -10000 0 -0.66 8 8
E2/ER beta (dimer) -0.001 0.018 -10000 0 -10000 0 0
mol:GDP -0.026 0.12 -10000 0 -0.58 7 7
mol:NADP 0.001 0.17 -10000 0 -0.66 8 8
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.14 0.29 -10000 0 -0.6 39 39
IGF-1R heterotetramer 0.012 0 -10000 0 -10000 0 0
PLCB1 -0.13 0.29 -10000 0 -0.61 39 39
PLCB2 -0.12 0.27 -10000 0 -0.62 32 32
IGF1 -0.009 0.14 -10000 0 -0.86 4 4
mol:L-citrulline 0.001 0.17 -10000 0 -0.66 8 8
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.059 0.2 -10000 0 -0.74 12 12
JNK cascade -0.001 0.018 -10000 0 -10000 0 0
BCAR1 0.012 0 -10000 0 -10000 0 0
ESR2 0.01 0.027 -10000 0 -0.34 1 1
GNAQ 0.012 0 -10000 0 -10000 0 0
ESR1 -0.026 0.18 -10000 0 -0.86 7 7
Gq family/GDP/Gbeta gamma -0.047 0.16 -10000 0 -0.53 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.079 -10000 0 -0.37 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.043 0.14 -10000 0 -0.63 7 7
GNAZ 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.029 0.14 -10000 0 -0.67 7 7
STRN 0.001 0.096 -10000 0 -0.86 2 2
GNAL 0.012 0 -10000 0 -10000 0 0
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.017 0.016 -10000 0 -10000 0 0
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.86 1 1
HBEGF -0.028 0.16 -10000 0 -0.68 5 5
cAMP biosynthetic process -0.022 0.098 -10000 0 -0.48 7 7
SRC -0.001 0.16 -10000 0 -0.57 7 7
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.023 0.1 -10000 0 -0.5 7 7
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.13 -10000 0 -0.52 8 8
Gs family/GTP -0.022 0.1 -10000 0 -0.49 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.003 0.16 -10000 0 -0.62 8 8
mol:DAG -0.14 0.29 -10000 0 -0.6 39 39
Gs family/GDP/Gbeta gamma -0.021 0.095 -10000 0 -0.46 7 7
MSN 0.028 0.097 -10000 0 -10000 0 0
Gq family/GTP -0.14 0.26 -10000 0 -0.64 32 32
mol:PI-3-4-5-P3 -0.006 0.18 -10000 0 -0.83 7 7
NRAS 0.012 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.003 0.16 0.62 8 -10000 0 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.024 0.11 -10000 0 -0.54 7 7
NOS3 -0.002 0.18 -10000 0 -0.71 8 8
GNA11 -0.009 0.14 -10000 0 -0.86 4 4
MAPKKK cascade 0.01 0.16 -10000 0 -0.63 9 9
E2/ER alpha (dimer)/PELP1/Src -0.046 0.15 -10000 0 -0.67 7 7
ruffle organization 0.028 0.09 -10000 0 -10000 0 0
ROCK2 0.021 0.1 -10000 0 -10000 0 0
GNA14 -0.16 0.34 -10000 0 -0.86 31 31
GNA15 -0.007 0.08 -10000 0 -0.34 9 9
GNA13 0.01 0.027 -10000 0 -0.34 1 1
MMP9 -0.054 0.17 -10000 0 -0.54 10 10
MMP2 0.002 0.16 -10000 0 -0.83 3 3
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.004 0.031 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.005 0.029 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.019 0.095 -9999 0 -0.59 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.003 0.046 -9999 0 -0.34 3 3
GRK1 0 0.027 -9999 0 -0.34 1 1
CNG Channel -0.16 0.23 -9999 0 -0.49 48 48
mol:Na + -0.15 0.22 -9999 0 -0.5 44 44
mol:ADP 0 0.027 -9999 0 -0.34 1 1
RGS9-1/Gbeta5/R9AP -0.02 0.1 -9999 0 -0.62 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.23 -9999 0 -0.52 44 44
CNGB1 -0.008 0.075 -9999 0 -0.34 8 8
RDH5 -0.015 0.11 -9999 0 -0.86 1 1
SAG 0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.23 -9999 0 -0.62 10 10
Na + (4 Units) -0.14 0.21 -9999 0 -0.6 10 10
RGS9 -0.013 0.13 -9999 0 -0.56 7 7
GNB1/GNGT1 -0.023 0.068 -9999 0 -10000 0 0
GNAT1/GDP -0.02 0.09 -9999 0 -0.54 4 4
GUCY2D -0.023 0.1 -9999 0 -0.34 15 15
GNGT1 -0.029 0.11 -9999 0 -0.34 17 17
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.004 0.1 -9999 0 -0.51 5 5
mol:11-cis-retinal -0.015 0.11 -9999 0 -0.86 1 1
mol:cGMP -0.02 0.061 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.024 0.081 -9999 0 -0.67 1 1
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.23 0.39 -9999 0 -0.86 44 44
Metarhodopsin II -0.005 0.034 -9999 0 -0.33 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.025 0.064 -9999 0 -10000 0 0
RGS9BP 0.004 0.074 -9999 0 -0.6 2 2
Metarhodopsin II/Transducin -0.002 0.045 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.011 0.044 -9999 0 -10000 0 0
PDE6A/B -0.014 0.069 -9999 0 -0.67 1 1
mol:Pi -0.02 0.099 -9999 0 -0.62 4 4
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.02 0.059 -9999 0 -10000 0 0
PDE6B 0.003 0.078 -9999 0 -0.51 3 3
PDE6A -0.001 0.06 -9999 0 -0.34 5 5
PDE6G -0.012 0.14 -9999 0 -0.75 5 5
RHO -0.003 0.054 -9999 0 -0.34 4 4
PDE6 -0.037 0.12 -9999 0 -0.5 9 9
GUCA1A -0.012 0.074 -9999 0 -0.34 8 8
GC2/GCAP Family -0.011 0.043 -9999 0 -10000 0 0
GUCA1C 0.005 0.028 -9999 0 -10000 0 0
GUCA1B 0.008 0.039 -9999 0 -0.34 2 2
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.011 0.007 -10000 0 -10000 0 0
HSPA8 0.013 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.028 0.12 -10000 0 -0.6 7 7
AKT1 0.015 0.005 -10000 0 -10000 0 0
GSC 0.013 0.061 -10000 0 -10000 0 0
NKX2-5 -0.018 0.085 -10000 0 -0.33 11 11
muscle cell differentiation 0.008 0.029 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.059 0.049 -10000 0 -10000 0 0
SMAD4 0.016 0.029 -10000 0 -10000 0 0
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.007 0.069 -10000 0 -0.5 3 3
MYC 0.006 0.039 -10000 0 -0.34 2 2
CDKN2B 0.03 0.059 -10000 0 -10000 0 0
AP1 -0.024 0.19 -10000 0 -0.45 19 19
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.061 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.044 0.033 -10000 0 -10000 0 0
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.006 0.085 -10000 0 -0.33 10 10
SMAD3/SMAD4/GR -0.005 0.019 -10000 0 -10000 0 0
GATA3 -0.6 0.39 -10000 0 -0.85 114 114
SKI/SIN3/HDAC complex/NCoR1 0.046 0.012 -10000 0 -10000 0 0
MEF2C/TIF2 -0.022 0.17 -10000 0 -0.53 13 13
endothelial cell migration 0.065 0.31 1.4 8 -10000 0 8
MAX 0.013 0.012 -10000 0 -10000 0 0
RBBP7 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.001 -10000 0 -10000 0 0
RUNX2 0.001 0.06 -10000 0 -0.34 5 5
RUNX3 -0.035 0.12 -10000 0 -0.34 22 22
RUNX1 -0.018 0.098 -10000 0 -0.34 14 14
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.013 0.012 -10000 0 -10000 0 0
VDR -0.004 0.12 -10000 0 -0.86 3 3
CDKN1A 0.05 0.06 -10000 0 -10000 0 0
KAT2B 0.012 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.008 0.054 -10000 0 -10000 0 0
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.001 -10000 0 -10000 0 0
SERPINE1 -0.068 0.32 -10000 0 -1.5 8 8
SMAD3/SMAD4/ATF2 -0.004 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.036 0.13 -10000 0 -0.61 8 8
SAP30 0.01 0.027 -10000 0 -0.34 1 1
Cbp/p300/PIAS3 0.002 0.016 -10000 0 -10000 0 0
JUN -0.021 0.18 -10000 0 -0.47 3 3
SMAD3/SMAD4/IRF7 -0.005 0.025 -10000 0 -10000 0 0
TFE3 0.016 0.015 -10000 0 -10000 0 0
COL1A2 0.001 0.074 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.009 0.033 -10000 0 -10000 0 0
DLX1 -0.012 0.084 -10000 0 -0.34 10 10
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.12 0.32 -10000 0 -0.85 26 26
SMAD3/SMAD4/Max -0.005 0.019 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.001 0.006 -10000 0 -10000 0 0
ZBTB17 0.011 0.005 -10000 0 -10000 0 0
LAMC1 0.043 0.049 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.004 0.019 -10000 0 -10000 0 0
IRF7 0.012 0.01 -10000 0 -10000 0 0
ESR1 -0.027 0.18 -10000 0 -0.86 7 7
HNF4A -0.11 0.3 -10000 0 -0.86 22 22
MEF2C 0.029 0.065 -10000 0 -10000 0 0
SMAD2-3/SMAD4 -0.003 0.02 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.002 0.011 -10000 0 -10000 0 0
IGHV3OR16-13 -0.006 0.017 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0.005 -10000 0 -10000 0 0
SKIL 0.012 0 -10000 0 -10000 0 0
HDAC1 0.012 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.001 -10000 0 -10000 0 0
SNIP1 0.013 0.002 -10000 0 -10000 0 0
GCN5L2 -0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.017 0.04 -10000 0 -10000 0 0
MSG1/HSC70 -0.001 0.025 -10000 0 -10000 0 0
SMAD2 0.018 0.007 -10000 0 -10000 0 0
SMAD3 0.014 0.028 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.039 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.014 -10000 0 -10000 0 0
NCOR1 0.012 0.001 -10000 0 -10000 0 0
NCOA2 -0.063 0.24 -10000 0 -0.86 14 14
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A -0.005 0.034 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.065 0.047 -10000 0 -10000 0 0
IFNB1 0.029 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.035 0.07 -10000 0 -10000 0 0
CITED1 0.007 0.039 -10000 0 -0.34 2 2
SMAD2-3/SMAD4/ARC105 0.001 0.019 -10000 0 -10000 0 0
RBL1 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.052 0.04 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.039 0.087 -10000 0 -10000 0 0
SMAD7 0.026 0.14 -10000 0 -10000 0 0
MYC/MIZ-1 0 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.016 0.098 -10000 0 -0.42 8 8
IL10 -0.37 0.26 -10000 0 -0.53 113 113
PIASy/HDAC complex 0.013 0.007 -10000 0 -10000 0 0
PIAS3 0.012 0.003 -10000 0 -10000 0 0
CDK2 0.012 0.004 -10000 0 -10000 0 0
IL5 -0.37 0.25 -10000 0 -0.53 114 114
CDK4 0.012 0.004 -10000 0 -10000 0 0
PIAS4 0.013 0.007 -10000 0 -10000 0 0
ATF3 -0.033 0.19 -10000 0 -0.8 9 9
SMAD3/SMAD4/SP1 0.024 0.046 -10000 0 -10000 0 0
FOXG1 -0.012 0.069 -10000 0 -0.34 7 7
FOXO3 0.026 0.008 -10000 0 -10000 0 0
FOXO1 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.025 0.008 -10000 0 -10000 0 0
heart looping 0.029 0.064 -10000 0 -10000 0 0
CEBPB 0.005 0.054 -10000 0 -0.33 4 4
SMAD3/SMAD4/DLX1 -0.016 0.054 -10000 0 -10000 0 0
MYOD1 -0.007 0.053 -10000 0 -0.34 4 4
SMAD3/SMAD4/HNF4 -0.087 0.21 -10000 0 -0.62 22 22
SMAD3/SMAD4/GATA3 -0.43 0.26 -10000 0 -0.59 114 114
SnoN/SIN3/HDAC complex/NCoR1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.028 0.071 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.048 0.046 -10000 0 -10000 0 0
MED15 0.012 0 -10000 0 -10000 0 0
SP1 0.02 0.014 -10000 0 -10000 0 0
SIN3B 0.012 0.001 -10000 0 -10000 0 0
SIN3A 0.012 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.011 0.07 -10000 0 -10000 0 0
ITGB5 0.058 0.038 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.047 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.028 0.12 -10000 0 -0.64 6 6
AR -0.022 0.17 -10000 0 -0.78 7 7
negative regulation of cell growth 0.031 0.063 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.01 0.034 -10000 0 -10000 0 0
E2F5 0.012 0 -10000 0 -10000 0 0
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.003 0.035 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.051 0.033 -10000 0 -10000 0 0
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.023 0.19 -10000 0 -0.48 3 3
SMAD3/SMAD4/RUNX2 -0.009 0.033 -10000 0 -10000 0 0
TGIF2 0.012 0 -10000 0 -10000 0 0
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling 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
Syndecan-2/Fibronectin 0.006 0.056 -9999 0 -10000 0 0
EPHB2 0.004 0.054 -9999 0 -0.34 4 4
Syndecan-2/TACI 0.001 0.049 -9999 0 -10000 0 0
LAMA1 -0.037 0.16 -9999 0 -0.46 17 17
Syndecan-2/alpha2 ITGB1 -0.038 0.059 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0.006 -9999 0 -10000 0 0
ITGA5 0.012 0 -9999 0 -10000 0 0
BAX 0.024 0.089 -9999 0 -0.51 4 4
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0.005 -9999 0 -10000 0 0
LAMA3 -0.087 0.16 -9999 0 -0.34 46 46
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.039 -9999 0 -0.34 2 2
Syndecan-2/MMP2 0.017 0.053 -9999 0 -0.58 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis 0.018 0.032 -9999 0 -10000 0 0
Syndecan-2/GM-CSF 0.007 0.025 -9999 0 -10000 0 0
determination of left/right symmetry 0.019 0.009 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.023 0.007 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 0.024 0.021 -9999 0 -10000 0 0
MAPK1 0.024 0.021 -9999 0 -10000 0 0
Syndecan-2/RACK1 0 0.004 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.019 0.009 -9999 0 -10000 0 0
ITGA2 0.012 0 -9999 0 -10000 0 0
MAPK8 0.018 0.095 -9999 0 -0.57 4 4
Syndecan-2/alpha2/beta1 Integrin -0.023 0.083 -9999 0 -0.5 4 4
Syndecan-2/Kininogen -0.37 0.28 -9999 0 -0.58 102 102
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.035 0.006 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0 0.005 -9999 0 -10000 0 0
extracellular matrix organization 0.021 0.023 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.006 0.056 -9999 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras -0.002 0.017 -9999 0 -10000 0 0
Syndecan-2/Laminin alpha3 -0.034 0.089 -9999 0 -10000 0 0
Syndecan-2/RasGAP 0 0.003 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.018 0.032 -9999 0 -10000 0 0
GO:0007205 0.003 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.042 0.006 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.016 0.087 -9999 0 -0.34 11 11
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.023 0.007 -9999 0 -10000 0 0
TGFB1 0.008 0.039 -9999 0 -0.34 2 2
CASP3 0.029 0.021 -9999 0 -10000 0 0
FN1 -0.018 0.098 -9999 0 -0.34 14 14
Syndecan-2/IL8 -0.027 0.096 -9999 0 -0.58 1 1
SDC2 0.019 0.009 -9999 0 -10000 0 0
KNG1 -0.54 0.41 -9999 0 -0.86 102 102
Syndecan-2/Neurofibromin 0.023 0.007 -9999 0 -10000 0 0
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 0.001 0.038 -9999 0 -0.34 2 2
Syndecan-2/TGFB1 0.021 0.023 -9999 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0 0.005 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0.004 -9999 0 -10000 0 0
PRKACA 0.031 0.007 -9999 0 -10000 0 0
angiogenesis -0.027 0.096 -9999 0 -0.58 1 1
MMP2 0.003 0.078 -9999 0 -0.51 3 3
IL8 -0.075 0.16 -9999 0 -0.35 39 39
calcineurin-NFAT signaling pathway 0.001 0.049 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.001 0.034 -9999 0 -10000 0 0
VDR -0.004 0.12 -9999 0 -0.86 3 3
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.049 0.044 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.054 0.063 -9999 0 -0.38 2 2
MED1 0.012 0 -9999 0 -10000 0 0
mol:9cRA 0.005 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.022 0.072 -9999 0 -0.34 6 6
RXRs/NUR77 -0.2 0.28 -9999 0 -0.53 68 68
RXRs/PPAR 0.039 0.015 -9999 0 -10000 0 0
NCOR2 0.012 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.013 0.091 -9999 0 -0.67 3 3
RARs/VDR/DNA/Vit D3 -0.01 0.069 -9999 0 -0.5 3 3
RARA 0.012 0 -9999 0 -10000 0 0
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.004 0.12 -9999 0 -0.86 3 3
RARs/RARs/DNA/9cRA -0.001 0.012 -9999 0 -10000 0 0
RARG 0.01 0.027 -9999 0 -0.34 1 1
RPS6KB1 0.001 0.021 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.022 0.072 -9999 0 -0.34 6 6
THRA 0.012 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.013 0.091 -9999 0 -0.67 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.035 0.029 -9999 0 -10000 0 0
NR1H4 -0.006 0.12 -9999 0 -0.73 4 4
RXRs/LXRs/DNA 0.055 0.034 -9999 0 -10000 0 0
NR1H2 0.018 0.006 -9999 0 -10000 0 0
NR1H3 0.018 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.026 0.075 -9999 0 -0.5 3 3
NR4A1 -0.36 0.43 -9999 0 -0.86 68 68
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.057 -9999 0 -0.36 3 3
RXRG 0.007 0.028 -9999 0 -0.33 1 1
RXR alpha/CCPG 0.021 0.006 -9999 0 -10000 0 0
RXRA 0.017 0.006 -9999 0 -10000 0 0
RXRB 0.018 0.007 -9999 0 -10000 0 0
THRB -0.02 0.16 -9999 0 -0.86 6 6
PPARG 0.012 0 -9999 0 -10000 0 0
PPARD 0.012 0 -9999 0 -10000 0 0
TNF 0.043 0.15 -9999 0 -1.2 2 2
mol:Oxysterols 0.005 0.008 -9999 0 -10000 0 0
cholesterol transport 0.053 0.063 -9999 0 -0.38 2 2
PPARA 0.012 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.012 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.13 0.19 -9999 0 -0.35 68 68
SREBF1 0.058 0.062 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.035 0.03 -9999 0 -10000 0 0
ABCA1 0.059 0.059 -9999 0 -10000 0 0
RARs/THRs -0.019 0.094 -9999 0 -0.5 6 6
RXRs/FXR 0.027 0.081 -9999 0 -0.53 3 3
BCL2 0.012 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.11 0.19 -9999 0 -0.46 37 37
Syndecan-3/Neurocan -0.016 0.043 -9999 0 -10000 0 0
POMC -0.004 0.12 -9999 0 -0.86 3 3
EGFR 0.012 0 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.001 0.011 -9999 0 -10000 0 0
AGRP 0.008 0.006 -9999 0 -10000 0 0
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.007 0.068 -9999 0 -0.86 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.028 0.11 -9999 0 -0.34 17 17
long-term memory -0.001 0.009 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.036 0.068 -9999 0 -0.49 1 1
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.012 -9999 0 -10000 0 0
MC4R -0.003 0.046 -9999 0 -0.34 3 3
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.19 0.37 -9999 0 -0.83 39 39
FGFR/FGF/Syndecan-3 -0.001 0.012 -9999 0 -10000 0 0
neuron projection morphogenesis -0.11 0.19 -9999 0 -0.46 37 37
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.004 0.02 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.012 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.036 0.068 -9999 0 -0.49 1 1
IL8 -0.075 0.16 -9999 0 -0.35 39 39
Syndecan-3/Fyn/Cortactin -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.012 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.017 0.095 -9999 0 -0.67 3 3
Gamma Secretase -0.003 0.039 -9999 0 -0.5 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.21 0.14 -9999 0 -0.56 5 5
RAD9A 0.012 0 -9999 0 -10000 0 0
AP1 -0.1 0.25 -9999 0 -0.67 26 26
IFNAR2 0.011 0.005 -9999 0 -10000 0 0
AKT1 0.002 0.066 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.029 0.14 -9999 0 -0.67 7 7
NFX1/SIN3/HDAC complex 0.039 0.018 -9999 0 -10000 0 0
EGF -0.76 0.28 -9999 0 -0.86 142 142
SMG5 0.012 0 -9999 0 -10000 0 0
SMG6 0.012 0 -9999 0 -10000 0 0
SP3/HDAC2 0.005 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.19 0.13 -9999 0 -0.52 4 4
SAP18 0.012 0.001 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.48 0.43 -9999 0 -0.85 92 92
WRN 0.012 0 -9999 0 -10000 0 0
SP1 0.012 0.005 -9999 0 -10000 0 0
SP3 0.011 0.004 -9999 0 -10000 0 0
TERF2IP 0.012 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.16 0.12 -9999 0 -10000 0 0
Mad/Max 0.003 0.008 -9999 0 -10000 0 0
TERT -0.21 0.15 -9999 0 -0.57 5 5
CCND1 -0.18 0.13 -9999 0 -10000 0 0
MAX 0.011 0.004 -9999 0 -10000 0 0
RBBP7 0.012 0.001 -9999 0 -10000 0 0
RBBP4 0.012 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
Telomerase/911 0.003 0.021 -9999 0 -10000 0 0
CDKN1B 0.015 0.057 -9999 0 -10000 0 0
RAD1 0.012 0 -9999 0 -10000 0 0
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
SAP30 0.01 0.027 -9999 0 -0.34 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.011 0.004 -9999 0 -10000 0 0
JUN 0.011 0.004 -9999 0 -10000 0 0
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.005 -9999 0 -10000 0 0
FOS -0.13 0.32 -9999 0 -0.86 26 26
IFN-gamma/IRF1 -0.019 0.06 -9999 0 -10000 0 0
PARP2 0.012 0 -9999 0 -10000 0 0
BLM -0.022 0.1 -9999 0 -0.34 16 16
Telomerase -0.028 0.045 -9999 0 -10000 0 0
IRF1 0.016 0.005 -9999 0 -10000 0 0
ESR1 -0.026 0.18 -9999 0 -0.86 7 7
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.043 0.019 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.019 -9999 0 -10000 0 0
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.012 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.02 0.027 -9999 0 -10000 0 0
ABL1 0.012 0 -9999 0 -10000 0 0
MXD1 0.011 0.004 -9999 0 -10000 0 0
MRE11A 0.012 0 -9999 0 -10000 0 0
HUS1 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.012 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.12 -9999 0 -10000 0 0
NR2F2 0.013 0.004 -9999 0 -10000 0 0
MAPK3 0.012 0.02 -9999 0 -10000 0 0
MAPK1 0.012 0.02 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.039 -9999 0 -0.34 2 2
NFKB1 0.012 0 -9999 0 -10000 0 0
HNRNPC 0.012 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0.001 -9999 0 -10000 0 0
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.59 0.22 -9999 0 -0.66 142 142
MYC 0.007 0.039 -9999 0 -0.34 2 2
IL2 0.001 0.028 -9999 0 -0.33 1 1
KU 0 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
TGFB1 0.008 0.039 -9999 0 -0.34 2 2
TRF2/BLM -0.02 0.06 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.18 0.14 -9999 0 -10000 0 0
SP1/HDAC2 0.014 0.011 -9999 0 -10000 0 0
PINX1 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.16 0.12 -9999 0 -10000 0 0
Smad3/Myc 0.021 0.031 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.02 0.099 -9999 0 -0.33 15 15
Telomerase/PinX1 -0.16 0.12 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.022 0.042 -9999 0 -10000 0 0
SIN3B 0.012 0.001 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.16 0.12 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.16 0.12 -9999 0 -10000 0 0
E2F1 -0.096 0.16 -9999 0 -0.34 50 50
ZNFX1 0.012 0.001 -9999 0 -10000 0 0
PIF1 -0.027 0.11 -9999 0 -0.34 18 18
NCL 0.012 0 -9999 0 -10000 0 0
DKC1 0.012 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.035 0.32 -10000 0 -0.91 8 8
IL23A -0.039 0.33 -10000 0 -1.1 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.13 0.23 -10000 0 -0.84 9 9
positive regulation of T cell mediated cytotoxicity -0.041 0.33 -10000 0 -0.91 10 10
ITGA3 -0.036 0.31 -10000 0 -0.9 7 7
IL17F -0.006 0.24 -10000 0 -0.65 4 4
IL12B 0.014 0.04 -10000 0 -0.33 1 1
STAT1 (dimer) -0.041 0.31 -10000 0 -0.92 8 8
CD4 -0.034 0.31 -10000 0 -0.86 8 8
IL23 -0.055 0.32 -10000 0 -1.1 5 5
IL23R 0.011 0.1 -10000 0 -0.42 1 1
IL1B -0.048 0.36 -10000 0 -1.2 7 7
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.033 0.3 -10000 0 -0.86 9 9
TYK2 0.017 0.018 -10000 0 -10000 0 0
STAT4 -0.016 0.095 -10000 0 -0.34 13 13
STAT3 0.012 0.001 -10000 0 -10000 0 0
IL18RAP -0.032 0.12 -10000 0 -0.34 20 20
IL12RB1 -0.005 0.092 -10000 0 -0.36 10 10
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.003 0.068 -10000 0 -10000 0 0
IL23R/JAK2 0.02 0.12 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.041 0.33 -10000 0 -0.91 10 10
natural killer cell activation 0 0.01 0.037 5 -10000 0 5
JAK2 0.024 0.024 -10000 0 -10000 0 0
PIK3R1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.049 0.31 -10000 0 -1 5 5
ALOX12B -0.032 0.3 -10000 0 -0.87 8 8
CXCL1 -0.091 0.37 -10000 0 -1.1 11 11
T cell proliferation -0.041 0.33 -10000 0 -0.91 10 10
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A 0.018 0.2 -10000 0 -0.51 2 2
PI3K -0.12 0.24 -10000 0 -0.86 9 9
IFNG 0 0.032 0.092 1 -0.092 1 2
STAT3 (dimer) -0.12 0.22 -10000 0 -0.85 8 8
IL18R1 0.006 0.069 -10000 0 -0.86 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.001 0.22 -10000 0 -0.68 2 2
IL18/IL18R -0.018 0.08 -10000 0 -0.58 1 1
macrophage activation -0.009 0.013 -10000 0 -0.043 6 6
TNF -0.045 0.34 -10000 0 -1 9 9
STAT3/STAT4 -0.13 0.25 -10000 0 -0.89 9 9
STAT4 (dimer) -0.051 0.32 -10000 0 -0.96 8 8
IL18 0.007 0.039 -10000 0 -0.34 2 2
IL19 -0.035 0.3 -10000 0 -0.86 8 8
STAT5A (dimer) -0.039 0.31 -10000 0 -0.9 9 9
STAT1 0.008 0.039 -10000 0 -0.34 2 2
SOCS3 0.003 0.078 -10000 0 -0.51 3 3
CXCL9 -0.046 0.33 -10000 0 -0.98 8 8
MPO -0.037 0.31 -10000 0 -0.87 8 8
positive regulation of humoral immune response -0.041 0.33 -10000 0 -0.91 10 10
IL23/IL23R/JAK2/TYK2 -0.043 0.33 -10000 0 -0.96 9 9
IL6 -0.12 0.46 -10000 0 -1.2 20 20
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.001 0.029 -10000 0 -0.34 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0.01 0.037 5 -10000 0 5
CD3E -0.041 0.33 -10000 0 -0.94 9 9
keratinocyte proliferation -0.041 0.33 -10000 0 -0.91 10 10
NOS2 -0.079 0.42 -10000 0 -1.2 15 15
S1P3 pathway

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
PDGFRB -0.02 0.16 -9999 0 -0.86 6 6
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.006 0.088 -9999 0 -0.29 13 13
GNAO1 -0.057 0.23 -9999 0 -0.75 15 15
S1P/S1P3/G12/G13 -0.037 0.14 -9999 0 -0.53 11 11
AKT1 -0.038 0.13 -9999 0 -0.62 6 6
AKT3 0.017 0.092 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.02 0.16 -9999 0 -0.86 6 6
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
GNAI1 0.008 0.068 -9999 0 -0.86 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.045 0.22 -9999 0 -0.86 11 11
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.019 0.19 -9999 0 -0.46 19 19
MAPK3 -0.011 0.18 -9999 0 -0.92 4 4
MAPK1 -0.011 0.18 -9999 0 -0.92 4 4
JAK2 -0.013 0.18 -9999 0 -0.92 4 4
CXCR4 -0.021 0.18 -9999 0 -0.92 4 4
FLT1 0.004 0.097 -9999 0 -0.86 2 2
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.011 0.18 -9999 0 -0.92 4 4
S1P/S1P3/Gi -0.019 0.19 -9999 0 -0.47 19 19
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.052 0.16 -9999 0 -0.89 4 4
VEGFA 0.013 0.027 -9999 0 -0.33 1 1
S1P/S1P2/Gi 0.009 0.1 -9999 0 -0.34 12 12
VEGFR1 homodimer/VEGFA homodimer 0.017 0.079 -9999 0 -0.66 2 2
RHOA 0.012 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.082 0.2 -9999 0 -0.42 39 39
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.017 -9999 0 -10000 0 0
GNA14 -0.16 0.34 -9999 0 -0.86 31 31
GNA15 -0.007 0.08 -9999 0 -0.34 9 9
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.01 0.027 -9999 0 -0.34 1 1
GNA11 -0.009 0.14 -9999 0 -0.86 4 4
Rac1/GTP -0.052 0.16 -9999 0 -0.89 4 4
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.029 0.061 -9999 0 -10000 0 0
adherens junction organization 0.008 0.1 -9999 0 -0.31 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.035 0.06 -9999 0 -10000 0 0
FMN1 -0.005 0.13 -9999 0 -0.46 5 5
mol:IP3 -0.016 0.05 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.003 0.11 -9999 0 -0.33 15 15
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.025 0.072 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.042 0.18 -9999 0 -0.59 15 15
CTNND1 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.011 0.1 -9999 0 -10000 0 0
VASP 0.011 0.1 -9999 0 -10000 0 0
ZYX 0.011 0.1 -9999 0 -10000 0 0
JUB 0.011 0.1 -9999 0 -0.31 15 15
EGFR(dimer) 0.01 0.1 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin -0.052 0.16 -9999 0 -0.56 15 15
mol:PI-3-4-5-P3 -0.02 0.063 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
PI3K -0.02 0.064 -9999 0 -10000 0 0
FYN -0.24 0.2 -9999 0 -0.52 9 9
mol:Ca2+ 0.021 0.061 -9999 0 -10000 0 0
JUP 0.013 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:DAG -0.016 0.05 -9999 0 -10000 0 0
CDH1 -0.069 0.25 -9999 0 -0.86 15 15
RhoA/GDP 0.035 0.06 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.011 0.1 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
CASR -0.3 0.24 -9999 0 -0.46 106 106
RhoA/GTP -0.014 0.044 -9999 0 -10000 0 0
AKT2 0.025 0.072 -9999 0 -10000 0 0
actin cable formation 0.002 0.13 -9999 0 -0.44 5 5
apoptosis 0.018 0.056 -9999 0 -10000 0 0
CTNNA1 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0.029 0.063 -9999 0 -10000 0 0
PIP5K1A 0.011 0.1 -9999 0 -10000 0 0
PLCG1 -0.016 0.051 -9999 0 -10000 0 0
Rac1/GTP -0.026 0.081 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.005 0.11 0.54 5 -10000 0 5
PI3K Class IB/PDE3B -0.005 0.11 -10000 0 -0.54 5 5
PDE3B -0.005 0.11 -10000 0 -0.55 5 5
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.001 -9999 0 -10000 0 0
SMARCC1 0.011 0.009 -9999 0 -10000 0 0
REL 0.01 0.028 -9999 0 -0.34 1 1
HDAC7 -0.095 0.14 -9999 0 -0.74 3 3
JUN 0.012 0.003 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.012 0 -9999 0 -10000 0 0
KAT5 0.012 0 -9999 0 -10000 0 0
MAPK14 0.003 0.016 -9999 0 -10000 0 0
FOXO1 0.012 0 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.15 -9999 0 -0.71 4 4
MAP2K6 0.004 0.007 -9999 0 -10000 0 0
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.004 0.007 -9999 0 -10000 0 0
SMARCA2 0.012 0.003 -9999 0 -10000 0 0
PDE9A -0.19 0.2 -9999 0 -0.64 20 20
NCOA2 -0.064 0.25 -9999 0 -0.86 14 14
CEBPA -0.021 0.12 -9999 0 -0.37 14 14
EHMT2 0.012 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.19 -9999 0 -0.52 22 22
NR0B1 -0.069 0.14 -9999 0 -0.34 36 36
EGR1 -0.053 0.23 -9999 0 -0.86 12 12
RXRs/9cRA -0.001 0.012 -9999 0 -10000 0 0
AR/RACK1/Src -0.033 0.1 -9999 0 -0.61 4 4
AR/GR -0.01 0.1 -9999 0 -0.56 4 4
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 -0.014 0.11 -9999 0 -0.69 4 4
T-DHT/AR/TIF2/CARM1 -0.075 0.21 -9999 0 -0.71 14 14
SRC -0.016 0.091 -9999 0 -0.54 4 4
NR3C1 0.012 0 -9999 0 -10000 0 0
KLK3 -0.11 0.24 -9999 0 -0.71 9 9
APPBP2 0.005 0.007 -9999 0 -10000 0 0
TRIM24 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.11 -9999 0 -0.64 4 4
TMPRSS2 -0.9 0.57 -9999 0 -1.3 109 109
RXRG 0.003 0.027 -9999 0 -0.34 1 1
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.003 -9999 0 -10000 0 0
NR2C2 0.007 0.068 -9999 0 -0.86 1 1
KLK2 -0.046 0.17 -9999 0 -0.65 8 8
AR -0.019 0.12 -9999 0 -0.46 8 8
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 0.012 0.004 -9999 0 -10000 0 0
SRY 0 0.004 -9999 0 -10000 0 0
GATA2 -0.16 0.35 -9999 0 -0.86 32 32
MYST2 0.012 0.001 -9999 0 -10000 0 0
HOXB13 -0.1 0.16 -9999 0 -0.36 5 5
T-DHT/AR/RACK1/Src -0.024 0.11 -9999 0 -0.62 4 4
positive regulation of transcription -0.16 0.35 -9999 0 -0.86 32 32
DNAJA1 0.005 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.001 -9999 0 -10000 0 0
NCOA1 0.019 0.004 -9999 0 -10000 0 0
SPDEF -0.019 0.099 -9999 0 -0.34 14 14
T-DHT/AR/TIF2 -0.019 0.14 -9999 0 -0.64 5 5
T-DHT/AR/Hsp90 -0.032 0.11 -9999 0 -0.64 4 4
GSK3B 0.007 0.005 -9999 0 -10000 0 0
NR2C1 0.012 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.026 0.096 -9999 0 -0.57 4 4
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0.004 -9999 0 -10000 0 0
POU2F1 -0.036 0.048 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.13 -9999 0 -0.72 4 4
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 0.012 0.003 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.016 0.061 -10000 0 -0.41 1 1
ACTA1 0.008 0.074 -10000 0 -0.54 1 1
NUMA1 0.016 0.061 -10000 0 -0.41 1 1
SPTAN1 0.009 0.074 -10000 0 -0.54 1 1
LIMK1 0.006 0.078 -10000 0 -0.54 1 1
BIRC3 -0.014 0.091 -10000 0 -0.34 12 12
BIRC2 0.012 0 -10000 0 -10000 0 0
BAX 0.01 0.027 -10000 0 -0.34 1 1
CASP10 -0.001 0.091 -10000 0 -0.4 5 5
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 0.016 0.061 -10000 0 -0.41 1 1
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.009 0.073 -10000 0 -0.53 1 1
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN 0.009 0.074 -10000 0 -0.54 1 1
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.41 0.25 -10000 0 -0.54 122 122
BID 0.009 0.047 -10000 0 -0.28 1 1
MAP3K1 0.009 0.03 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.074 -10000 0 -0.54 1 1
CASP9 0.012 0 -10000 0 -10000 0 0
DNA repair -0.008 0.029 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.01 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.071 -10000 0 -0.51 1 1
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.027 0.039 -10000 0 -10000 0 0
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD 0.016 0.071 -10000 0 -0.51 1 1
CASP7 0.001 0.042 -10000 0 -10000 0 0
KRT18 0.015 0.019 -10000 0 -10000 0 0
apoptosis 0.021 0.071 -10000 0 -0.46 1 1
DFFA 0.009 0.074 -10000 0 -0.54 1 1
DFFB 0.009 0.074 -10000 0 -0.54 1 1
PARP1 0.008 0.03 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.073 0.49 1 -10000 0 1
TNF -0.012 0.12 -10000 0 -0.47 8 8
CYCS 0.01 0.038 -10000 0 -0.2 1 1
SATB1 0.03 0.053 -10000 0 -0.46 1 1
SLK 0.009 0.074 -10000 0 -0.54 1 1
p15 BID/BAX 0.013 0.043 -10000 0 -10000 0 0
CASP2 0.037 0.042 -10000 0 -10000 0 0
JNK cascade -0.009 0.03 -10000 0 -10000 0 0
CASP3 0.002 0.078 -10000 0 -0.57 1 1
LMNB2 0.039 0.032 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.011 0.038 -10000 0 -10000 0 0
negative regulation of DNA binding -0.4 0.25 -10000 0 -0.54 122 122
stress fiber formation 0.009 0.073 -10000 0 -0.53 1 1
GZMB -0.013 0.11 -10000 0 -0.47 5 5
CASP1 0.016 0.012 -10000 0 -10000 0 0
LMNB1 0.034 0.036 -10000 0 -10000 0 0
APP 0.023 0.01 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.015 0.07 -10000 0 -0.4 2 2
LMNA 0.039 0.032 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.031 0.045 -10000 0 -10000 0 0
LRDD 0.012 0 -10000 0 -10000 0 0
SREBF1 0.008 0.075 -10000 0 -0.54 1 1
APAF-1/Caspase 9 0.001 0.019 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.016 0.06 -10000 0 -0.4 1 1
CFL2 0.013 0.075 -10000 0 -0.5 1 1
GAS2 -0.004 0.12 -10000 0 -0.57 5 5
positive regulation of apoptosis 0.039 0.033 -10000 0 -10000 0 0
PRF1 -0.001 0.066 -10000 0 -0.34 6 6
PLK2 and PLK4 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
PLK2 -0.014 0.091 -9999 0 -0.34 12 12
PLK4 0.008 0.039 -9999 0 -0.34 2 2
regulation of centriole replication 0.001 0.068 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.023 0.11 -9999 0 -0.47 7 7
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.086 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.019 0.094 -9999 0 -0.65 3 3
AP1 -0.1 0.21 -9999 0 -0.83 6 6
ILK 0.016 0.12 -9999 0 -0.5 7 7
bone resorption -0.038 0.12 -9999 0 -0.7 2 2
PTK2B 0.012 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.029 0.1 -9999 0 -0.45 6 6
ITGAV 0.017 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.027 0.095 -9999 0 -0.66 2 2
alphaV/beta3 Integrin/Osteopontin -0.033 0.12 -9999 0 -0.56 7 7
MAP3K1 0.015 0.12 -9999 0 -0.5 7 7
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 0.029 0.12 -9999 0 -0.46 7 7
MAPK1 0.029 0.12 -9999 0 -0.46 7 7
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.012 0.15 -9999 0 -0.52 10 10
ITGB3 -0.013 0.14 -9999 0 -0.59 8 8
NFKBIA 0.039 0.11 -9999 0 -0.45 7 7
FOS -0.13 0.32 -9999 0 -0.86 26 26
CD44 -0.018 0.098 -9999 0 -0.34 14 14
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU 0.037 0.14 -9999 0 -1.2 1 1
NF kappa B1 p50/RelA -0.023 0.083 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.65 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.011 0.13 -9999 0 -0.51 8 8
VAV3 0.019 0.12 -9999 0 -0.47 8 8
MAP3K14 0.018 0.12 -9999 0 -0.5 7 7
ROCK2 0.001 0.096 -9999 0 -0.86 2 2
SPP1 -0.01 0.13 -9999 0 -0.52 8 8
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.027 0.097 -9999 0 -0.43 3 3
MMP2 -0.02 0.21 -9999 0 -0.68 6 6
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0 -9999 0 -10000 0 0
LAT2 -0.043 0.11 -9999 0 -0.34 7 7
AP1 -0.12 0.17 -9999 0 -0.46 27 27
mol:PIP3 -0.067 0.16 -9999 0 -0.47 6 6
IKBKB -0.024 0.092 -9999 0 -0.28 2 2
AKT1 -0.028 0.11 -9999 0 -10000 0 0
IKBKG -0.024 0.092 -9999 0 -0.28 2 2
MS4A2 -0.09 0.17 -9999 0 -0.35 46 46
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.028 0.12 -9999 0 -0.47 1 1
mol:Ca2+ -0.049 0.12 -9999 0 -0.35 7 7
LYN 0.008 0.007 -9999 0 -10000 0 0
CBLB -0.026 0.084 -9999 0 -0.33 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.004 0.044 -9999 0 -0.54 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.001 0.06 -9999 0 -0.34 5 5
PLD2 -0.06 0.12 -9999 0 -0.46 6 6
PTPN13 -0.014 0.077 -9999 0 -10000 0 0
PTPN11 0.012 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.088 -9999 0 -10000 0 0
SYK 0.002 0.069 -9999 0 -0.86 1 1
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.098 0.13 -9999 0 -0.47 7 7
LAT -0.046 0.1 -9999 0 -0.36 4 4
PAK2 -0.038 0.13 -9999 0 -0.54 1 1
NFATC2 -0.073 0.18 -9999 0 -0.77 9 9
HRAS -0.049 0.14 -9999 0 -0.59 1 1
GAB2 0.012 0 -9999 0 -10000 0 0
PLA2G1B 0.031 0.014 -9999 0 -10000 0 0
Fc epsilon R1 -0.11 0.14 -9999 0 -0.43 18 18
Antigen/IgE/Fc epsilon R1 -0.1 0.13 -9999 0 -0.4 17 17
mol:GDP -0.062 0.15 -9999 0 -0.39 10 10
JUN 0.012 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.13 0.32 -9999 0 -0.86 26 26
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.054 0.073 -9999 0 -0.36 1 1
CHUK -0.024 0.092 -9999 0 -0.28 2 2
KLRG1 -0.031 0.085 -9999 0 -10000 0 0
VAV1 -0.058 0.13 -9999 0 -0.73 1 1
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.026 0.084 -9999 0 -0.33 1 1
negative regulation of mast cell degranulation -0.027 0.086 -9999 0 -10000 0 0
BTK -0.05 0.11 -9999 0 -0.32 2 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.065 0.13 -9999 0 -0.43 8 8
GAB2/PI3K/SHP2 -0.067 0.096 -9999 0 -0.43 4 4
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.034 0.088 -9999 0 -0.32 2 2
RAF1 0.019 0.016 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.17 -9999 0 -0.51 16 16
FCER1G -0.072 0.15 -9999 0 -0.34 39 39
FCER1A -0.018 0.14 -9999 0 -0.69 6 6
Antigen/IgE/Fc epsilon R1/Fyn -0.089 0.12 -9999 0 -0.49 6 6
MAPK3 0.029 0.014 -9999 0 -10000 0 0
MAPK1 0.029 0.014 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.011 0.11 -9999 0 -0.67 4 4
DUSP1 0.007 0.068 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.027 0.043 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.021 0.079 -9999 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.074 0.12 -9999 0 -0.64 1 1
FER -0.026 0.084 -9999 0 -0.33 1 1
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.017 0.034 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.057 0.15 -9999 0 -0.42 6 6
cytokine secretion -0.02 0.032 -9999 0 -10000 0 0
SPHK1 -0.092 0.12 -9999 0 -0.35 7 7
PTK2 -0.022 0.08 -9999 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.096 0.14 -9999 0 -0.46 10 10
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.053 0.15 -9999 0 -0.44 5 5
MAP2K2 0.026 0.014 -9999 0 -10000 0 0
MAP2K1 0.026 0.014 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.049 0.065 -9999 0 -10000 0 0
MAP2K4 0.016 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.18 -9999 0 -0.54 15 15
mol:Choline -0.059 0.12 -9999 0 -0.45 6 6
SHC/Grb2/SOS1 -0.04 0.059 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.01 0.027 -9999 0 -0.34 1 1
PXN -0.014 0.077 -9999 0 -10000 0 0
HCLS1 -0.028 0.088 -9999 0 -0.33 2 2
PRKCB -0.043 0.12 -9999 0 -0.37 4 4
FCGR2B -0.09 0.17 -9999 0 -0.35 46 46
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.027 0.087 -9999 0 -10000 0 0
LCP2 0.003 0.054 -9999 0 -0.34 4 4
PLA2G4A -0.032 0.1 -9999 0 -0.46 3 3
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.059 0.12 -9999 0 -0.45 6 6
IKK complex -0.005 0.075 -9999 0 -10000 0 0
WIPF1 0.012 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.013 0.046 -10000 0 -10000 0 0
MAP4K4 0.034 0.044 -10000 0 -10000 0 0
BAG4 0.012 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.1 0.041 -10000 0 -10000 0 0
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 -0.014 0.091 -10000 0 -0.34 12 12
BAX -0.046 0.021 -10000 0 -0.16 1 1
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.038 0.008 -10000 0 -10000 0 0
BAD -0.1 0.041 -10000 0 -10000 0 0
SMPD1 0.021 0.037 -10000 0 -0.26 2 2
RB1 -0.1 0.041 -10000 0 -10000 0 0
FADD/Caspase 8 0.044 0.042 -10000 0 -10000 0 0
MAP2K4 -0.089 0.039 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.09 0.041 -10000 0 -0.26 1 1
EGF -0.76 0.28 -10000 0 -0.86 142 142
mol:ceramide -0.12 0.044 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.046 -10000 0 -10000 0 0
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.1 0.041 -10000 0 -10000 0 0
cell proliferation -0.07 0.069 -10000 0 -0.46 4 4
BID -0.007 0.033 -10000 0 -10000 0 0
MAP3K1 -0.1 0.041 -10000 0 -10000 0 0
EIF2A -0.078 0.037 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 -0.074 0.039 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.074 0.039 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.1 0.041 -10000 0 -10000 0 0
FADD 0.034 0.044 -10000 0 -10000 0 0
KSR1 -0.1 0.043 -10000 0 -0.28 1 1
MAPK8 -0.09 0.061 -10000 0 -0.38 4 4
PRKRA -0.1 0.041 -10000 0 -10000 0 0
PDGFA -0.001 0.066 -10000 0 -0.34 6 6
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.009 0.14 -10000 0 -0.86 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.043 -10000 0 -10000 0 0
CTSD 0.012 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.07 0.079 -10000 0 -0.5 4 4
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.046 -10000 0 -10000 0 0
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.028 0.047 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.014 0.071 -10000 0 -0.58 2 2
mol:Sphingosine-1-phosphate 0.013 0.046 -10000 0 -10000 0 0
MAP2K1 -0.079 0.039 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS -0.067 0.028 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.089 0.039 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.014 0.071 -10000 0 -0.58 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.035 0.028 -10000 0 -10000 0 0
MAP2K2 -0.079 0.039 -10000 0 -10000 0 0
SMPD3 0.023 0.039 -10000 0 -0.26 2 2
TNF -0.012 0.12 -10000 0 -0.47 8 8
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.25 0.099 0.29 142 -10000 0 142
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 -0.067 0.028 -10000 0 -10000 0 0
BCL2 0.012 0 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.03 0.086 0.3 14 -10000 0 14
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.012 0.07 -10000 0 -0.58 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.059 0.23 -10000 0 -0.75 15 15
RhoA/GTP -0.031 0.088 -10000 0 -0.3 14 14
negative regulation of cAMP metabolic process -0.005 0.11 -10000 0 -0.34 15 15
GNAZ 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 -0.007 0.11 -10000 0 -0.51 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.11 -10000 0 -0.34 15 15
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.86 1 1
EPHB forward 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
Ephrin A5/EPHB2 -0.031 0.12 -10000 0 -0.58 7 7
cell-cell adhesion 0.03 0.083 0.4 6 -10000 0 6
Ephrin B/EPHB2/RasGAP -0.028 0.08 -10000 0 -0.5 3 3
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.12 0.23 -10000 0 -0.58 32 32
Ephrin B1/EPHB1 -0.015 0.083 -10000 0 -0.58 3 3
HRAS/GDP -0.025 0.075 -10000 0 -0.42 3 3
Ephrin B/EPHB1/GRB7 -0.037 0.1 -10000 0 -0.5 6 6
Endophilin/SYNJ1 0.005 0.086 -10000 0 -0.46 3 3
KRAS 0.012 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.037 0.1 -10000 0 -0.5 6 6
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 0.012 0 -10000 0 -10000 0 0
PAK1 0.012 0.088 -10000 0 -0.46 3 3
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS 0.005 0.088 -10000 0 -0.47 3 3
DNM1 -0.072 0.15 -10000 0 -0.34 39 39
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.11 -10000 0 -0.47 6 6
lamellipodium assembly -0.03 0.083 -10000 0 -0.4 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.013 0.072 -10000 0 -0.34 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 0.004 0.054 -10000 0 -0.34 4 4
EPHB3 -0.16 0.35 -10000 0 -0.86 32 32
EPHB1 -0.013 0.13 -10000 0 -0.56 7 7
EPHB4 0.012 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.11 -10000 0 -0.46 2 2
Ephrin B/EPHB2 -0.029 0.083 -10000 0 -0.5 3 3
Ephrin B/EPHB3 -0.12 0.22 -10000 0 -0.53 34 34
JNK cascade 0.02 0.08 -10000 0 -0.48 3 3
Ephrin B/EPHB1 -0.038 0.1 -10000 0 -0.5 6 6
RAP1/GDP 0.014 0.1 -10000 0 -0.4 2 2
EFNB2 0.012 0 -10000 0 -10000 0 0
EFNB3 -0.045 0.16 -10000 0 -0.41 22 22
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.018 0.081 -10000 0 -0.48 4 4
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.031 0.087 -10000 0 -0.44 3 3
Rap1/GTP -0.029 0.083 -10000 0 -10000 0 0
axon guidance -0.031 0.12 -10000 0 -0.58 7 7
MAPK3 0.027 0.065 -10000 0 -10000 0 0
MAPK1 0.027 0.065 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.11 -10000 0 -0.42 2 2
actin cytoskeleton reorganization -0.019 0.058 -10000 0 -10000 0 0
CDC42/GDP 0.046 0.11 -10000 0 -0.42 2 2
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.028 0.18 -10000 0 -0.79 8 8
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.013 0.064 -10000 0 -0.34 3 3
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.029 0.08 -10000 0 -10000 0 0
PTK2 0.004 0.018 -10000 0 -10000 0 0
MAP4K4 0.021 0.081 -10000 0 -0.49 3 3
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.012 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.037 0.086 -10000 0 -10000 0 0
MAP2K1 0.02 0.068 -10000 0 -0.31 3 3
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.017 0.079 -10000 0 -0.53 3 3
cell migration 0.034 0.079 -10000 0 -0.34 1 1
NRAS 0.012 0 -10000 0 -10000 0 0
SYNJ1 0.005 0.088 -10000 0 -0.47 3 3
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.005 0.11 -10000 0 -0.45 6 6
HRAS/GTP -0.033 0.09 -10000 0 -0.42 6 6
Ephrin B1/EPHB1-2 -0.018 0.081 -10000 0 -0.48 4 4
cell adhesion mediated by integrin 0.06 0.11 0.45 6 -10000 0 6
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.036 0.097 -10000 0 -0.45 7 7
RAC1-CDC42/GTP -0.11 0.19 -10000 0 -0.63 7 7
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.1 -10000 0 -0.4 2 2
ruffle organization 0.02 0.1 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.025 0.11 -10000 0 -0.44 3 3
Ephrin B/EPHB2/KALRN -0.028 0.08 -10000 0 -0.5 3 3
ROCK1 -0.086 0.22 -10000 0 -0.53 32 32
RAS family/GDP -0.018 0.055 -10000 0 -10000 0 0
Rac1/GTP -0.032 0.088 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.006 0.08 -10000 0 -0.34 6 6
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.017 0.18 -9999 0 -0.59 15 15
KLHL20 -0.016 0.05 -9999 0 -10000 0 0
CYFIP2 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.022 0.12 -9999 0 -10000 0 0
ENAH -0.017 0.18 -9999 0 -0.59 15 15
AP1M1 0.012 0 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.028 0.088 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.033 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.049 0.15 -9999 0 -0.53 15 15
RAPGEF1 0.002 0.16 -9999 0 -0.5 15 15
CTNND1 0.012 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.057 0.18 -9999 0 -0.62 15 15
CRK -0.007 0.17 -9999 0 -0.55 15 15
E-cadherin/gamma catenin/alpha catenin -0.054 0.17 -9999 0 -0.58 15 15
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.012 0 -9999 0 -10000 0 0
NCKAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.017 0.18 -9999 0 -0.59 15 15
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.063 -9999 0 -10000 0 0
MLLT4 0.012 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.003 0.021 -9999 0 -10000 0 0
PI3K -0.026 0.081 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.062 0.19 -9999 0 -0.66 15 15
TIAM1 0.012 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.047 0.15 -9999 0 -0.5 15 15
AKT1 -0.015 0.045 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 -0.069 0.25 -9999 0 -0.86 15 15
RhoA/GDP 0.021 0.12 -9999 0 -10000 0 0
actin cytoskeleton organization -0.012 0.037 -9999 0 -10000 0 0
CDC42/GDP 0.021 0.12 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.11 -9999 0 -0.36 15 15
ITGB7 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.049 0.15 -9999 0 -0.53 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin -0.047 0.15 -9999 0 -0.51 15 15
mol:GDP 0.013 0.14 -9999 0 -0.43 15 15
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.012 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.034 0.11 -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 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.025 0.034 -9999 0 -10000 0 0
NME1 0.006 0.047 -9999 0 -0.34 3 3
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.017 0.18 -9999 0 -0.59 15 15
regulation of cell-cell adhesion -0.025 0.077 -9999 0 -10000 0 0
WASF2 -0.005 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.032 0.1 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.046 0.14 -9999 0 -0.5 15 15
CCND1 0.029 0.04 -9999 0 -10000 0 0
VAV2 -0.001 0.17 -9999 0 -0.52 15 15
RAP1/GDP -0.032 0.1 -9999 0 -10000 0 0
adherens junction assembly -0.016 0.18 -9999 0 -0.57 15 15
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.012 0 -9999 0 -10000 0 0
PIP5K1C 0.012 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.044 0.14 -9999 0 -0.47 15 15
E-cadherin/beta catenin -0.048 0.15 -9999 0 -0.52 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.017 0.18 -9999 0 -0.59 15 15
PIK3CA 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.026 0.079 -9999 0 -0.33 1 1
E-cadherin/beta catenin/alpha catenin -0.054 0.17 -9999 0 -0.58 15 15
ITGAE 0.012 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.059 0.18 -9999 0 -0.63 15 15
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0.002 -9999 0 -10000 0 0
ELF1 0.002 0.055 -9999 0 -10000 0 0
CCNA2 -0.055 0.14 -9999 0 -0.34 31 31
PIK3CA 0.013 0.002 -9999 0 -10000 0 0
JAK3 -0.054 0.14 -9999 0 -0.34 31 31
PIK3R1 0.013 0.002 -9999 0 -10000 0 0
JAK1 0.013 0.002 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.075 -9999 0 -0.4 1 1
SHC1 0.013 0.002 -9999 0 -10000 0 0
SP1 -0.007 0.065 -9999 0 -10000 0 0
IL2RA -0.002 0.1 -9999 0 -10000 0 0
IL2RB -0.03 0.12 -9999 0 -0.34 20 20
SOS1 0.013 0.002 -9999 0 -10000 0 0
IL2RG 0 0.066 -9999 0 -0.34 6 6
G1/S transition of mitotic cell cycle -0.014 0.086 -9999 0 -10000 0 0
PTPN11 0.013 0.002 -9999 0 -10000 0 0
CCND2 -0.02 0.12 -9999 0 -10000 0 0
LCK 0.004 0.054 -9999 0 -0.34 4 4
GRB2 0.013 0.002 -9999 0 -10000 0 0
IL2 0.002 0.027 -9999 0 -0.34 1 1
CDK6 0.012 0 -9999 0 -10000 0 0
CCND3 0.041 0.076 -9999 0 -10000 0 0
BCR 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
JUN 0 0.09 -10000 0 -0.38 3 3
IKBKB -0.008 0.062 -10000 0 -0.26 1 1
AKT1 -0.001 0.068 -10000 0 -0.24 1 1
IKBKG -0.007 0.065 -10000 0 -0.28 1 1
CALM1 -0.03 0.12 -10000 0 -0.56 6 6
PIK3CA 0.012 0 -10000 0 -10000 0 0
MAP3K1 -0.007 0.11 -10000 0 -0.48 4 4
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.04 0.13 0.24 2 -0.6 6 8
DOK1 0.01 0.027 -10000 0 -0.34 1 1
AP-1 -0.024 0.099 0.19 1 -0.27 7 8
LYN 0.012 0 -10000 0 -10000 0 0
BLNK -0.026 0.18 -10000 0 -0.86 7 7
SHC1 0.012 0 -10000 0 -10000 0 0
BCR complex -0.053 0.13 -10000 0 -0.62 5 5
CD22 -0.051 0.11 -10000 0 -0.51 6 6
CAMK2G -0.021 0.12 -10000 0 -0.54 5 5
CSNK2A1 0.012 0 -10000 0 -10000 0 0
INPP5D 0.001 0.06 -10000 0 -0.34 5 5
SHC/GRB2/SOS1 -0.048 0.12 -10000 0 -0.85 1 1
GO:0007205 -0.04 0.14 0.24 2 -0.61 6 8
SYK 0.007 0.068 -10000 0 -0.86 1 1
ELK1 -0.031 0.13 -10000 0 -0.57 6 6
NFATC1 -0.013 0.1 -10000 0 -0.46 4 4
B-cell antigen/BCR complex -0.053 0.13 -10000 0 -0.62 5 5
PAG1/CSK 0 0 -10000 0 -10000 0 0
NFKBIB 0.006 0.025 0.087 2 -10000 0 2
HRAS -0.022 0.13 -10000 0 -0.55 6 6
NFKBIA 0.006 0.024 0.087 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.012 0.021 -10000 0 -10000 0 0
RasGAP/Csk -0.075 0.11 -10000 0 -0.49 5 5
mol:GDP -0.038 0.13 0.23 2 -0.59 6 8
PTEN 0.012 0 -10000 0 -10000 0 0
CD79B -0.001 0.1 -10000 0 -0.68 3 3
NF-kappa-B/RelA/I kappa B alpha 0.012 0.02 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.023 0.13 -10000 0 -0.52 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.045 0.14 0.24 2 -0.62 6 8
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.097 0.22 -10000 0 -0.53 28 28
CHUK -0.007 0.065 -10000 0 -0.28 1 1
IBTK 0.012 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.067 0.11 -10000 0 -0.5 5 5
PTPN6 -0.046 0.1 -10000 0 -0.53 4 4
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 -0.006 0.032 -10000 0 -10000 0 0
VAV2 -0.052 0.12 -10000 0 -0.56 5 5
ubiquitin-dependent protein catabolic process 0.01 0.024 0.09 2 -10000 0 2
BTK -0.03 0.066 -10000 0 -10000 0 0
CD19 -0.056 0.12 -10000 0 -0.53 6 6
MAP4K1 -0.031 0.12 -10000 0 -0.34 20 20
CD72 -0.022 0.1 -10000 0 -0.34 16 16
PAG1 0.012 0 -10000 0 -10000 0 0
MAPK14 0.002 0.096 -10000 0 -0.43 3 3
SH3BP5 -0.004 0.12 -10000 0 -0.86 3 3
PIK3AP1 -0.029 0.14 0.28 2 -0.62 6 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.046 0.17 -10000 0 -0.71 7 7
RAF1 -0.013 0.12 -10000 0 -0.54 5 5
RasGAP/p62DOK/SHIP -0.073 0.11 -10000 0 -0.46 7 7
CD79A -0.055 0.16 -10000 0 -0.37 28 28
re-entry into mitotic cell cycle -0.024 0.098 0.2 1 -0.27 7 8
RASA1 0.012 0 -10000 0 -10000 0 0
MAPK3 0.004 0.099 -10000 0 -0.43 5 5
MAPK1 0.004 0.099 -10000 0 -0.43 5 5
CD72/SHP1 -0.03 0.12 -10000 0 -0.57 3 3
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.12 -10000 0 -0.44 7 7
actin cytoskeleton organization -0.017 0.12 -10000 0 -0.51 4 4
NF-kappa-B/RelA 0.027 0.04 0.17 2 -10000 0 2
Calcineurin -0.03 0.094 -10000 0 -0.48 5 5
PI3K -0.047 0.098 -10000 0 -0.44 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.047 0.14 0.28 2 -0.67 6 8
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.033 0.13 -10000 0 -0.65 4 4
DAPP1 -0.04 0.12 -10000 0 -0.8 3 3
cytokine secretion -0.012 0.097 -10000 0 -0.43 4 4
mol:DAG -0.045 0.14 0.24 2 -0.62 6 8
PLCG2 -0.044 0.21 -10000 0 -0.81 11 11
MAP2K1 -0.005 0.11 -10000 0 -0.49 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.096 0.14 -10000 0 -0.44 14 14
mol:PI-3-4-5-P3 -0.036 0.072 -10000 0 -0.32 4 4
ETS1 -0.012 0.11 -10000 0 -0.48 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.059 0.14 -10000 0 -0.54 11 11
B-cell antigen/BCR complex/LYN -0.046 0.1 -10000 0 -0.55 5 5
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.019 0.12 -10000 0 -0.55 4 4
B-cell antigen/BCR complex/LYN/SYK -0.046 0.11 -10000 0 -0.54 4 4
CARD11 -0.075 0.14 -10000 0 -0.49 9 9
FCGR2B -0.09 0.17 -10000 0 -0.35 46 46
PPP3CA 0.012 0 -10000 0 -10000 0 0
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex 0.006 0.029 0.091 2 -10000 0 2
PTPRC 0.003 0.078 -10000 0 -0.51 3 3
PDPK1 -0.003 0.063 -10000 0 -10000 0 0
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0.012 0 -10000 0 -10000 0 0
POU2F2 0.011 0.02 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.075 0.26 -9999 0 -0.77 18 18
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.027 -9999 0 -0.34 1 1
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.03 0.009 -9999 0 -10000 0 0
HIF1A 0.023 0.01 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.01 -9999 0 -10000 0 0
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.26 0.14 -9999 0 -0.34 125 125
ARNT/IPAS -0.066 0.19 -9999 0 -0.66 15 15
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.03 0.009 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.014 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.03 0.009 -9999 0 -10000 0 0
PHD1-3/OS9 -0.005 0.025 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.001 0.008 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.03 0.009 -9999 0 -10000 0 0
EGLN3 0.001 0.06 -9999 0 -0.34 5 5
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.008 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.089 0.065 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.06 0.12 -9999 0 -0.61 6 6
PDGFB-D/PDGFRB/SLAP -0.033 0.14 -9999 0 -0.69 6 6
PDGFB-D/PDGFRB/APS/CBL -0.021 0.11 -9999 0 -0.57 6 6
AKT1 0.041 0.083 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.044 0.14 -9999 0 -0.65 6 6
PIK3CA 0.012 0 -9999 0 -10000 0 0
FGR -0.023 0.12 -9999 0 -0.57 7 7
mol:Ca2+ -0.005 0.13 -9999 0 -0.66 6 6
MYC 0.013 0.095 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.016 0.09 -9999 0 -0.47 6 6
LRP1/PDGFRB/PDGFB -0.025 0.12 -9999 0 -0.57 7 7
GRB10 0.012 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 -0.006 0.13 -9999 0 -0.67 6 6
PTEN 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 -0.025 0.12 -9999 0 -0.66 6 6
PDGFB-D/PDGFRB/GRB10 -0.025 0.12 -9999 0 -0.66 6 6
cell cycle arrest -0.033 0.14 -9999 0 -0.69 6 6
HRAS 0.012 0 -9999 0 -10000 0 0
HIF1A 0.047 0.075 -9999 0 -10000 0 0
GAB1 -0.012 0.13 -9999 0 -0.64 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.012 0.12 -9999 0 -0.59 6 6
PDGFB-D/PDGFRB -0.018 0.11 -9999 0 -0.58 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.025 0.12 -9999 0 -0.66 6 6
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.055 0.12 -9999 0 -0.6 6 6
positive regulation of MAPKKK cascade -0.025 0.12 -9999 0 -0.66 6 6
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.006 0.13 -9999 0 -0.68 6 6
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.025 0.12 -9999 0 -0.66 6 6
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.023 0.11 -9999 0 -0.55 6 6
PTPN2 0.012 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.025 0.12 -9999 0 -0.66 6 6
BCAR1 0.012 0 -9999 0 -10000 0 0
VAV2 -0.008 0.13 -9999 0 -0.59 7 7
CBL 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.025 0.12 -9999 0 -0.66 6 6
LCK -0.019 0.11 -9999 0 -0.55 6 6
PDGFRB -0.021 0.17 -9999 0 -0.86 6 6
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.033 0.12 -9999 0 -0.58 7 7
ABL1 -0.007 0.12 -9999 0 -0.59 6 6
PDGFB-D/PDGFRB/CBL -0.012 0.14 -9999 0 -0.69 6 6
PTPN1 0.012 0.003 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 0.008 0.039 -9999 0 -0.34 2 2
cell proliferation 0.013 0.089 -9999 0 -0.38 3 3
SLA -0.001 0.066 -9999 0 -0.34 6 6
actin cytoskeleton reorganization 0.012 0.094 -9999 0 -0.45 6 6
SRC -0.016 0.1 -9999 0 -0.55 6 6
PI3K -0.016 0.079 -9999 0 -0.42 6 6
PDGFB-D/PDGFRB/GRB7/SHC -0.021 0.11 -9999 0 -0.57 6 6
SH2B2 0.012 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.046 0.14 -9999 0 -0.68 6 6
LYN -0.016 0.1 -9999 0 -0.55 6 6
LRP1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.017 0.088 -9999 0 -0.47 6 6
SPHK1 -0.13 0.17 -9999 0 -0.34 67 67
EDG1 -0.001 0.003 -9999 0 -10000 0 0
mol:DAG -0.006 0.13 -9999 0 -0.68 6 6
PLCG1 -0.007 0.14 -9999 0 -0.7 6 6
NHERF/PDGFRB -0.021 0.11 -9999 0 -0.57 6 6
YES1 -0.017 0.1 -9999 0 -0.55 6 6
cell migration -0.021 0.11 -9999 0 -0.57 6 6
SHC/Grb2/SOS1 -0.017 0.088 -9999 0 -0.47 6 6
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.019 0.099 -9999 0 -0.52 6 6
FYN -0.016 0.1 -9999 0 -0.55 6 6
DOK1 0.009 0.11 -9999 0 -0.52 6 6
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.007 0.068 -9999 0 -0.86 1 1
RAC1 0.002 0.12 -9999 0 -0.55 6 6
PRKCD 0.011 0.11 -9999 0 -0.53 6 6
FER 0.011 0.11 -9999 0 -0.53 6 6
MAPKKK cascade -0.017 0.086 -9999 0 -0.46 6 6
RASA1 0.011 0.11 -9999 0 -0.53 6 6
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.002 0.098 -9999 0 -0.48 6 6
PDGFB-D/PDGFRB/SHB -0.025 0.12 -9999 0 -0.66 6 6
chemotaxis -0.006 0.12 -9999 0 -0.57 6 6
STAT1-3-5/STAT1-3-5 -0.018 0.085 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.025 0.13 -9999 0 -0.67 6 6
PTPRJ 0.012 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.017 0.1 -10000 0 -0.66 4 4
ATM 0.012 0 -10000 0 -10000 0 0
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.012 0 -10000 0 -10000 0 0
ATR 0.012 0 -10000 0 -10000 0 0
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.024 0.012 -10000 0 -10000 0 0
protein ubiquitination -0.025 0.085 -10000 0 -0.49 4 4
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.012 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.013 0.028 -10000 0 -10000 0 0
FANCF 0.012 0 -10000 0 -10000 0 0
BRCA1 0.008 0.039 -10000 0 -0.34 2 2
CCNE1 -0.018 0.098 -10000 0 -0.34 14 14
CDK2/Cyclin E1 -0.019 0.062 -10000 0 -10000 0 0
FANCG 0.012 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.019 0.11 -10000 0 -0.66 4 4
FANCE 0.012 0 -10000 0 -10000 0 0
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.012 0 -10000 0 -10000 0 0
FANCA -0.12 0.17 -10000 0 -0.34 62 62
DNA repair 0.006 0.11 -10000 0 -0.45 4 4
BRCA1/BARD1/ubiquitin -0.019 0.11 -10000 0 -0.66 4 4
BARD1/DNA-PK -0.013 0.082 -10000 0 -0.53 4 4
FANCL 0.012 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.016 0.1 0.66 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.062 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.017 0.092 -10000 0 -0.58 4 4
BRCA1/BARD1/P53 -0.015 0.083 -10000 0 -0.53 4 4
BARD1/CSTF1/BRCA1 -0.017 0.092 -10000 0 -0.58 4 4
BRCA1/BACH1 0.008 0.038 -10000 0 -0.34 2 2
BARD1 -0.01 0.14 -10000 0 -0.86 4 4
PCNA 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.017 0.092 -10000 0 -0.58 4 4
BRCA1/BARD1/UbcH7 -0.017 0.092 -10000 0 -0.58 4 4
BRCA1/BARD1/RAD51/PCNA -0.038 0.099 -10000 0 -0.53 4 4
BARD1/DNA-PK/P53 -0.012 0.077 -10000 0 -0.5 4 4
BRCA1/BARD1/Ubiquitin -0.019 0.11 -10000 0 -0.66 4 4
BRCA1/BARD1/CTIP -0.018 0.093 -10000 0 -0.53 5 5
FA complex -0.004 0.055 -10000 0 -10000 0 0
BARD1/EWS -0.017 0.1 -10000 0 -0.66 4 4
RBBP8 0.018 0.054 -10000 0 -0.67 1 1
TP53 0.012 0 -10000 0 -10000 0 0
TOPBP1 0.012 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.015 0.083 0.52 4 -10000 0 4
BRCA1/BARD1 -0.025 0.086 -10000 0 -0.5 4 4
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.017 0.1 -10000 0 -0.67 4 4
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.042 0.13 -10000 0 -0.34 25 25
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.019 0.11 -10000 0 -0.66 4 4
EWSR1 0.012 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.045 0.096 -9999 0 -0.48 3 3
MAP4K1 -0.031 0.12 -9999 0 -0.34 20 20
MAP3K8 0.012 0 -9999 0 -10000 0 0
PRKCB 0.008 0.039 -9999 0 -0.34 2 2
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 0.018 0.058 -9999 0 -10000 0 0
JUN 0.015 0.1 -9999 0 -0.6 4 4
MAP3K7 0.018 0.058 -9999 0 -10000 0 0
GRAP2 0.006 0.047 -9999 0 -0.34 3 3
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.027 0.056 -9999 0 -10000 0 0
LAT -0.033 0.12 -9999 0 -0.34 21 21
LCP2 0.004 0.054 -9999 0 -0.34 4 4
MAPK8 0.008 0.11 -9999 0 -0.64 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.011 0.061 -9999 0 -0.26 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.041 0.088 -9999 0 -0.45 3 3
PLK1 signaling events

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.003 0.038 0.11 18 -10000 0 18
BUB1B -0.015 0.07 -10000 0 -0.22 3 3
PLK1 0.004 0.025 -10000 0 -10000 0 0
PLK1S1 0.008 0.013 -10000 0 -10000 0 0
KIF2A 0.012 0.023 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.004 0.025 -10000 0 -10000 0 0
GOLGA2 0.012 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.035 0.12 -10000 0 -0.34 16 16
WEE1 0.011 0.024 -10000 0 -10000 0 0
cytokinesis -0.042 0.094 -10000 0 -10000 0 0
PP2A-alpha B56 -0.014 0.058 -10000 0 -10000 0 0
AURKA 0.006 0.022 -10000 0 -10000 0 0
PICH/PLK1 -0.004 0.085 -10000 0 -0.43 1 1
CENPE -0.006 0.068 -10000 0 -0.22 6 6
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.012 0.023 -10000 0 -10000 0 0
PPP2CA 0.012 0 -10000 0 -10000 0 0
FZR1 0.012 0 -10000 0 -10000 0 0
TPX2 -0.015 0.047 -10000 0 -0.11 3 3
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 -0.053 0.14 -10000 0 -0.34 30 30
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN -0.012 0.047 -10000 0 -10000 0 0
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase -0.001 0.003 -10000 0 -0.009 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 -10000 0 -10000 0 0
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.008 -10000 0 -10000 0 0
spindle elongation 0.004 0.025 -10000 0 -10000 0 0
ODF2 0.012 0.002 -10000 0 -10000 0 0
BUB1 -0.045 0.054 -10000 0 -10000 0 0
TPT1 0.008 0.013 -10000 0 -10000 0 0
CDC25C -0.023 0.059 -10000 0 -10000 0 0
CDC25B 0.008 0.039 -10000 0 -0.34 2 2
SGOL1 -0.003 0.038 -10000 0 -0.11 18 18
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.005 0.036 -10000 0 -10000 0 0
CDC14B 0.011 0.001 -10000 0 -10000 0 0
CDC20 -0.04 0.12 -10000 0 -0.34 24 24
PLK1/PBIP1 -0.024 0.063 -10000 0 -0.21 5 5
mitosis 0 0.003 0.017 3 -10000 0 3
FBXO5 0.011 0.02 -10000 0 -10000 0 0
CDC2 0 0.002 -10000 0 -0.014 1 1
NDC80 -0.033 0.12 -10000 0 -0.34 21 21
metaphase plate congression 0.006 0.017 -10000 0 -10000 0 0
ERCC6L -0.023 0.074 -10000 0 -0.42 1 1
NLP/gamma Tubulin 0.006 0.015 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.008 0.013 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.012 0 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.053 0.11 -10000 0 -0.35 8 8
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.007 -10000 0 -10000 0 0
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.012 0.018 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.029 -10000 0 -10000 0 0
microtubule-based process -0.056 0.1 -10000 0 -0.23 6 6
Golgi organization 0.004 0.025 -10000 0 -10000 0 0
Cohesin/SA2 -0.007 0.014 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.12 0.17 -10000 0 -0.34 62 62
APC/C/CDC20 -0.015 0.079 -10000 0 -0.23 6 6
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation -0.024 0.062 -10000 0 -0.21 5 5
PRC1 -0.005 0.076 -10000 0 -0.34 8 8
ECT2 0.011 0.028 -10000 0 -0.19 1 1
C13orf34 0.011 0.019 -10000 0 -10000 0 0
NUDC 0.006 0.017 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.015 0.069 -10000 0 -0.21 3 3
spindle assembly 0.006 0.02 -10000 0 -10000 0 0
spindle stabilization 0.008 0.013 -10000 0 -10000 0 0
APC/C/HCDH1 0.018 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.056 0.1 -10000 0 -0.23 6 6
CCNB1 0.004 0.055 -10000 0 -0.34 4 4
PPP1CB 0.012 0 -10000 0 -10000 0 0
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.008 0.061 -10000 0 -0.51 2 2
TUBG1 0.008 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.008 0.034 -10000 0 -10000 0 0
MLF1IP -0.021 0.082 -10000 0 -0.24 20 20
INCENP 0.011 0.001 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.006 0.016 -9999 0 -10000 0 0
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0.012 0 -9999 0 -10000 0 0
AKT2 0.012 0 -9999 0 -10000 0 0
STXBP4 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.065 0.065 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
TBC1D4 0.022 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
ASIP -0.095 0.16 -9999 0 -0.34 49 49
PRKCI 0.012 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0.012 0 -9999 0 -10000 0 0
GYS1 0.031 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
TRIP10 0.012 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 0.005 0.046 -9999 0 -10000 0 0
VAMP2 0.012 0 -9999 0 -10000 0 0
SLC2A4 0.067 0.067 -9999 0 -10000 0 0
STX4 0.012 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.14 0.17 -9999 0 -0.34 71 71
LNPEP 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.025 0.043 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.024 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.001 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.08 0.085 -9999 0 -0.33 1 1
CaM/Ca2+ -0.009 0.027 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.03 0.047 -9999 0 -10000 0 0
AKT1 0.042 0.037 -9999 0 -10000 0 0
MAP2K1 0.04 0.039 -9999 0 -10000 0 0
MAP3K11 0.031 0.04 -9999 0 -10000 0 0
IFNGR1 0.013 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.27 0.26 -9999 0 -0.54 79 79
Rap1/GTP -0.005 0.015 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.011 0.034 -9999 0 -10000 0 0
CEBPB 0.065 0.04 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.025 0.14 -9999 0 -1.2 2 2
STAT1 0.03 0.047 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.022 0.099 -9999 0 -0.33 15 15
PIK3CA 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.036 0.045 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0 0.007 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.031 -9999 0 -10000 0 0
MAPK3 0.049 0.035 -9999 0 -10000 0 0
STAT1 (dimer) -0.1 0.11 -9999 0 -0.47 1 1
MAPK1 0.049 0.035 -9999 0 -10000 0 0
JAK2 0.013 0.003 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
JAK1 0.013 0.003 -9999 0 -10000 0 0
CAMK2D 0.012 0 -9999 0 -10000 0 0
DAPK1 0.063 0.031 -9999 0 -10000 0 0
SMAD7 -0.015 0.069 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.007 0.021 -9999 0 -10000 0 0
PI3K -0.008 0.024 -9999 0 -10000 0 0
IFNG -0.022 0.099 -9999 0 -0.33 15 15
apoptosis 0.036 0.03 -9999 0 -10000 0 0
CAMK2G 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.42 0.43 -9999 0 -0.86 79 79
CAMK2B -0.042 0.16 -9999 0 -0.45 19 19
FRAP1 0.041 0.035 -9999 0 -10000 0 0
PRKCD 0.044 0.037 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.08 0.085 -9999 0 -0.33 1 1
PTPN2 0.012 0 -9999 0 -10000 0 0
EP300 0.013 0.001 -9999 0 -10000 0 0
IRF1 0.059 0.053 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.006 0.039 -9999 0 -10000 0 0
SOCS1 -0.017 0.16 -9999 0 -1.5 2 2
mol:GDP -0.007 0.021 -9999 0 -10000 0 0
CASP1 -0.016 0.07 -9999 0 -0.26 1 1
PTGES2 0.012 0 -9999 0 -10000 0 0
IRF9 0.053 0.016 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.024 -9999 0 -10000 0 0
RAP1/GDP -0.005 0.015 -9999 0 -10000 0 0
CBL 0.03 0.04 -9999 0 -10000 0 0
MAP3K1 0.032 0.041 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.08 0.085 -9999 0 -0.33 1 1
PTPN11 0.024 0.042 -9999 0 -10000 0 0
CREBBP 0.013 0.001 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.039 -9999 0 -10000 0 0
IRAK/TOLLIP 0.026 0.003 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.16 0.26 -9999 0 -0.68 30 30
IL1A -0.045 0.13 -9999 0 -0.34 26 26
IL1B 0.002 0.11 -9999 0 -0.67 4 4
IRAK/TRAF6/p62/Atypical PKCs -0.004 0.021 -9999 0 -10000 0 0
IL1R2 -0.15 0.34 -9999 0 -0.84 31 31
IL1R1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.031 0.04 -9999 0 -10000 0 0
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.007 0.068 -9999 0 -0.86 1 1
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.06 0.009 -9999 0 -10000 0 0
JUN 0.031 0.072 -9999 0 -0.42 4 4
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.015 0.075 -9999 0 -0.47 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.026 0.059 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.052 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.017 0.085 -9999 0 -0.53 4 4
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.025 0.076 -9999 0 -0.45 4 4
IRAK1 0.02 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.019 0.075 -9999 0 -0.66 1 1
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.012 0 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.03 0.05 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.017 0.085 -9999 0 -0.53 4 4
IL1 beta/IL1R2 -0.12 0.24 -9999 0 -0.58 34 34
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.067 -9999 0 -10000 0 0
IRAK3 0.01 0.027 -9999 0 -0.34 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.017 0.098 -9999 0 -0.59 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.016 0.045 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.03 0.069 -9999 0 -0.36 1 1
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 -0.001 0.066 -9999 0 -0.34 6 6
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.024 0.013 -9999 0 -10000 0 0
IL1RAP 0.008 0.039 -9999 0 -0.34 2 2
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.014 0.08 -9999 0 -0.76 1 1
CASP1 0.01 0.027 -9999 0 -0.34 1 1
IL1RN/IL1R2 -0.14 0.27 -9999 0 -0.68 31 31
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.015 0.079 -9999 0 -0.49 4 4
TMEM189-UBE2V1 0.003 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.026 0.035 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
IL1RN -0.017 0.11 -9999 0 -0.38 12 12
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.031 0.003 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.028 0.067 -10000 0 -10000 0 0
UGCG 0.01 0.018 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.037 0.07 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.021 0.017 -10000 0 -10000 0 0
mol:DAG 0.001 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.04 -10000 0 -10000 0 0
FRAP1 0.053 0.072 -10000 0 -10000 0 0
FOXO3 0.057 0.068 -10000 0 -10000 0 0
AKT1 0.051 0.071 -10000 0 -10000 0 0
GAB2 0.013 0.002 -10000 0 -10000 0 0
SMPD1 0.01 0.018 -10000 0 -10000 0 0
SGMS1 0.01 0.018 -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 0.022 0.003 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.036 0.036 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.006 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0.001 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.052 0.14 -10000 0 -0.33 31 31
PIK3R1 0.015 0.002 -10000 0 -10000 0 0
JAK1 0.015 0.001 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
MYC 0.055 0.07 -10000 0 -10000 0 0
MYB -0.061 0.14 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.073 -10000 0 -0.41 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.02 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.072 -10000 0 -0.4 1 1
Rac1/GDP 0.028 0.003 -10000 0 -10000 0 0
T cell proliferation 0.048 0.069 -10000 0 -0.37 1 1
SHC1 0.013 0.002 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.014 -10000 0 -0.029 35 35
PRKCZ 0.048 0.07 -10000 0 -0.38 1 1
NF kappa B1 p50/RelA -0.009 0.039 -10000 0 -10000 0 0
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.021 0.073 -10000 0 -0.41 1 1
HSP90AA1 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.022 0.1 -10000 0 -0.34 16 16
IL2RB -0.028 0.12 -10000 0 -0.33 20 20
TERT -0.045 0.12 -10000 0 -0.34 23 23
E2F1 -0.045 0.1 -10000 0 -0.27 20 20
SOS1 0.013 0.002 -10000 0 -10000 0 0
RPS6 0.012 0 -10000 0 -10000 0 0
mol:cAMP 0.001 0.007 0.014 35 -10000 0 35
PTPN11 0.013 0.002 -10000 0 -10000 0 0
IL2RG 0.002 0.066 -10000 0 -0.33 6 6
actin cytoskeleton organization 0.048 0.069 -10000 0 -0.37 1 1
GRB2 0.013 0.002 -10000 0 -10000 0 0
IL2 0.005 0.027 -10000 0 -0.34 1 1
PIK3CA 0.015 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.015 -10000 0 -10000 0 0
LCK 0.006 0.054 -10000 0 -0.33 4 4
BCL2 0.057 0.063 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0.004 -10000 0 -10000 0 0
AES 0.001 0.004 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 -0.005 0.034 -10000 0 -10000 0 0
SMAD4 0.012 0 -10000 0 -10000 0 0
DKK2 0.002 0.078 -10000 0 -0.51 3 3
TLE1 0.001 0.004 -10000 0 -10000 0 0
MACF1 0.013 0 -10000 0 -10000 0 0
CTNNB1 0.045 0.058 -10000 0 -10000 0 0
WIF1 0.001 0.047 -10000 0 -0.34 3 3
beta catenin/RanBP3 -0.006 0.026 -10000 0 -10000 0 0
KREMEN2 -0.034 0.12 -10000 0 -0.34 21 21
DKK1 -0.014 0.087 -10000 0 -0.34 11 11
beta catenin/beta TrCP1 0.05 0.054 -10000 0 -10000 0 0
FZD1 0.004 0.054 -10000 0 -0.34 4 4
AXIN2 0.023 0.022 -10000 0 -10000 0 0
AXIN1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.012 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.003 0.009 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.031 0.094 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.037 0.07 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.045 0.049 -10000 0 -10000 0 0
HNF1A -0.015 0.12 -10000 0 -0.86 3 3
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC 0.02 0.041 -10000 0 -10000 0 0
RANBP3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.028 0.08 -10000 0 -0.58 1 1
NKD1 -0.2 0.38 -10000 0 -0.86 40 40
TCF4 0.001 0.004 -10000 0 -10000 0 0
TCF3 0.001 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.017 0.046 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.021 0.077 -10000 0 -10000