PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_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 and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C13J3BPR
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 39 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 243
HIF-1-alpha transcription factor network 159
EGFR-dependent Endothelin signaling events 140
TCR signaling in naïve CD8+ T cells 134
FOXA2 and FOXA3 transcription factor networks 131
PDGFR-alpha signaling pathway 111
TCGA08_retinoblastoma 98
Syndecan-4-mediated signaling events 91
TCGA08_p53 89
Glypican 1 network 82
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 518 . 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 ( 518 ).

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 0.4691 243 8265 34 -0.49 0.029 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.3069 159 12102 76 -0.99 0.044 1000 -1000 -0.16 -1000
EGFR-dependent Endothelin signaling events 0.2703 140 2945 21 -0.54 0.041 1000 -1000 -0.053 -1000
TCR signaling in naïve CD8+ T cells 0.2587 134 12522 93 -0.41 0.19 1000 -1000 -0.065 -1000
FOXA2 and FOXA3 transcription factor networks 0.2529 131 6026 46 -1.1 0.034 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.2143 111 4909 44 -0.21 0.035 1000 -1000 -0.05 -1000
TCGA08_retinoblastoma 0.1892 98 787 8 -0.5 0.13 1000 -1000 -0.006 -1000
Syndecan-4-mediated signaling events 0.1757 91 6156 67 -0.37 0.083 1000 -1000 -0.05 -1000
TCGA08_p53 0.1718 89 629 7 -0.35 0.19 1000 -1000 -0.012 -1000
Glypican 1 network 0.1583 82 3948 48 -0.38 0.045 1000 -1000 -0.047 -1000
Aurora B signaling 0.1564 81 5428 67 -0.23 0.04 1000 -1000 -0.055 -1000
IL12-mediated signaling events 0.1525 79 6921 87 -0.38 0.097 1000 -1000 -0.11 -1000
amb2 Integrin signaling 0.1409 73 5993 82 -0.43 0.037 1000 -1000 -0.047 -1000
BMP receptor signaling 0.1371 71 5798 81 -0.5 0.052 1000 -1000 -0.081 -1000
Aurora C signaling 0.1313 68 476 7 -0.22 0.026 1000 -1000 -0.015 -1000
Glypican 2 network 0.1178 61 244 4 -0.03 -1000 1000 -1000 -0.004 -1000
FOXM1 transcription factor network 0.1158 60 3088 51 -0.48 0.029 1000 -1000 -0.11 -1000
JNK signaling in the CD4+ TCR pathway 0.1081 56 955 17 -0.19 0.028 1000 -1000 -0.046 -1000
Caspase cascade in apoptosis 0.1004 52 3890 74 -0.29 0.073 1000 -1000 -0.046 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0965 50 1670 33 -0.49 0.053 1000 -1000 -0.042 -1000
IL4-mediated signaling events 0.0946 49 4528 91 -0.77 0.47 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 0.0869 45 1539 34 -0.21 0.029 1000 -1000 -0.063 -1000
Fc-epsilon receptor I signaling in mast cells 0.0792 41 4000 97 -0.24 0.039 1000 -1000 -0.076 -1000
Arf6 signaling events 0.0753 39 2418 62 -0.54 0.062 1000 -1000 -0.044 -1000
Effects of Botulinum toxin 0.0734 38 1001 26 -0.2 0.04 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 0.0714 37 1608 43 -0.45 0.21 1000 -1000 -0.066 -1000
Calcium signaling in the CD4+ TCR pathway 0.0714 37 1152 31 -0.33 0.028 1000 -1000 -0.055 -1000
Reelin signaling pathway 0.0695 36 2030 56 -0.16 0.077 1000 -1000 -0.068 -1000
Signaling events mediated by the Hedgehog family 0.0676 35 1839 52 -0.24 0.064 1000 -1000 -0.056 -1000
LPA4-mediated signaling events 0.0637 33 396 12 -0.085 0.009 1000 -1000 -0.028 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0637 33 1815 54 -0.38 0.04 1000 -1000 -0.079 -1000
IL27-mediated signaling events 0.0618 32 1666 51 -0.59 0.048 1000 -1000 -0.058 -1000
Ephrin A reverse signaling 0.0598 31 217 7 -0.022 0.013 1000 -1000 -0.013 -1000
IL2 signaling events mediated by STAT5 0.0579 30 681 22 -0.25 0.034 1000 -1000 -0.061 -1000
Coregulation of Androgen receptor activity 0.0560 29 2277 76 -0.84 0.052 1000 -1000 -0.028 -1000
p75(NTR)-mediated signaling 0.0560 29 3695 125 -0.29 0.076 1000 -1000 -0.083 -1000
PLK1 signaling events 0.0560 29 2545 85 -0.16 0.041 1000 -1000 -0.054 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0560 29 2008 68 -0.28 0.052 1000 -1000 -0.11 -1000
S1P1 pathway 0.0541 28 1043 36 -0.21 0.028 1000 -1000 -0.057 -1000
Glucocorticoid receptor regulatory network 0.0463 24 2788 114 -0.33 0.14 1000 -1000 -0.068 -1000
Ceramide signaling pathway 0.0463 24 1830 76 -0.54 0.2 1000 -1000 -0.046 -1000
VEGFR1 specific signals 0.0463 24 1399 56 -0.27 0.029 1000 -1000 -0.06 -1000
Integrins in angiogenesis 0.0444 23 1956 84 -0.25 0.065 1000 -1000 -0.074 -1000
BCR signaling pathway 0.0444 23 2327 99 -0.19 0.056 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0444 23 1419 60 -0.22 0.028 1000 -1000 -0.085 -1000
Signaling events mediated by PTP1B 0.0425 22 1688 76 -0.55 0.067 1000 -1000 -0.058 -1000
IL2 signaling events mediated by PI3K 0.0425 22 1309 58 -0.25 0.045 1000 -1000 -0.058 -1000
Wnt signaling 0.0425 22 158 7 -0.042 0.027 1000 -1000 -0.036 -1000
Noncanonical Wnt signaling pathway 0.0405 21 546 26 -0.096 0.028 1000 -1000 -0.06 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0405 21 968 45 -0.31 0.075 1000 -1000 -0.067 -1000
Regulation of Telomerase 0.0405 21 2164 102 -0.54 0.059 1000 -1000 -0.075 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0405 21 1901 88 -0.17 0.037 1000 -1000 -0.084 -1000
FoxO family signaling 0.0386 20 1327 64 -0.55 0.086 1000 -1000 -0.062 -1000
Visual signal transduction: Rods 0.0386 20 1046 52 -0.13 0.041 1000 -1000 -0.064 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0386 20 1610 78 -0.23 0.043 1000 -1000 -0.063 -1000
Thromboxane A2 receptor signaling 0.0367 19 2011 105 -0.54 0.04 1000 -1000 -0.052 -1000
Syndecan-2-mediated signaling events 0.0347 18 1302 69 -0.43 0.061 1000 -1000 -0.046 -1000
EPO signaling pathway 0.0347 18 1041 55 -0.14 0.035 1000 -1000 -0.066 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0347 18 2183 120 -0.11 0.078 1000 -1000 -0.063 -1000
Signaling mediated by p38-alpha and p38-beta 0.0328 17 774 44 -0.041 0.05 1000 -1000 -0.036 -1000
Endothelins 0.0309 16 1617 96 -0.33 0.042 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.0309 16 1662 102 -0.21 0.046 1000 -1000 -0.065 -1000
Presenilin action in Notch and Wnt signaling 0.0290 15 964 61 -0.13 0.082 1000 -1000 -0.069 -1000
IFN-gamma pathway 0.0290 15 1040 68 -0.21 0.041 1000 -1000 -0.072 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0290 15 1154 74 -0.54 0.098 1000 -1000 -0.091 -1000
Signaling events regulated by Ret tyrosine kinase 0.0270 14 1174 82 -0.037 0.029 1000 -1000 -0.08 -1000
IL6-mediated signaling events 0.0270 14 1097 75 -0.2 0.053 1000 -1000 -0.058 -1000
Class I PI3K signaling events 0.0270 14 1059 73 -0.26 0.078 1000 -1000 -0.054 -1000
Canonical Wnt signaling pathway 0.0251 13 675 51 -0.13 0.094 1000 -1000 -0.06 -1000
Nongenotropic Androgen signaling 0.0251 13 724 52 -0.095 0.043 1000 -1000 -0.044 -1000
Regulation of Androgen receptor activity 0.0251 13 949 70 -0.91 0.052 1000 -1000 -0.051 -1000
Regulation of nuclear SMAD2/3 signaling 0.0232 12 1719 136 -0.28 0.096 1000 -1000 -0.059 -1000
PLK2 and PLK4 events 0.0232 12 36 3 0.006 0.025 1000 -1000 -0.015 -1000
Aurora A signaling 0.0232 12 738 60 -0.13 0.058 1000 -1000 -0.034 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0232 12 461 37 -0.14 0.057 1000 -1000 -0.037 -1000
S1P5 pathway 0.0232 12 211 17 -0.062 0.028 1000 -1000 -0.029 -1000
Plasma membrane estrogen receptor signaling 0.0232 12 1108 86 -0.13 0.052 1000 -1000 -0.08 -1000
S1P3 pathway 0.0232 12 524 42 -0.21 0.049 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0212 11 762 69 -0.16 0.096 1000 -1000 -0.059 -1000
FAS signaling pathway (CD95) 0.0212 11 555 47 -0.24 0.047 1000 -1000 -0.045 -1000
TCGA08_rtk_signaling 0.0212 11 307 26 -0.22 0.053 1000 -1000 -0.025 -1000
ceramide signaling pathway 0.0193 10 509 49 -0.054 0.044 1000 -1000 -0.05 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0193 10 1253 125 -0.21 0.041 1000 -1000 -0.067 -1000
S1P4 pathway 0.0193 10 266 25 -0.062 0.037 1000 -1000 -0.04 -1000
E-cadherin signaling events 0.0193 10 54 5 0.007 0.024 1000 -1000 -0.003 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0174 9 274 28 -0.062 0.047 1000 -1000 -0.033 -1000
a4b1 and a4b7 Integrin signaling 0.0174 9 45 5 0.012 0.028 1000 -1000 0 -1000
Visual signal transduction: Cones 0.0154 8 332 38 -0.012 0.044 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0154 8 733 85 -0.04 0.076 1000 -1000 -0.057 -1000
mTOR signaling pathway 0.0154 8 431 53 -0.059 0.05 1000 -1000 -0.054 -1000
Syndecan-3-mediated signaling events 0.0154 8 302 35 -0.009 0.076 1000 -1000 -0.05 -1000
E-cadherin signaling in keratinocytes 0.0154 8 382 43 -0.21 0.038 1000 -1000 -0.058 -1000
Ephrin B reverse signaling 0.0135 7 341 48 -0.047 0.052 1000 -1000 -0.043 -1000
Canonical NF-kappaB pathway 0.0116 6 267 39 -0.098 0.055 1000 -1000 -0.049 -1000
IL1-mediated signaling events 0.0116 6 373 62 -0.036 0.062 1000 -1000 -0.075 -1000
E-cadherin signaling in the nascent adherens junction 0.0116 6 495 76 -0.033 0.049 1000 -1000 -0.08 -1000
Signaling events mediated by PRL 0.0116 6 233 34 -0.037 0.06 1000 -1000 -0.051 -1000
ErbB2/ErbB3 signaling events 0.0097 5 355 65 -0.11 0.04 1000 -1000 -0.057 -1000
Cellular roles of Anthrax toxin 0.0097 5 214 39 -0.009 0.037 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 0.0097 5 171 32 -0.036 0.054 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 0.0097 5 218 40 -0.052 0.052 1000 -1000 -0.026 -1000
EPHB forward signaling 0.0097 5 443 85 -0.046 0.069 1000 -1000 -0.086 -1000
Regulation of p38-alpha and p38-beta 0.0097 5 278 54 -0.021 0.064 1000 -1000 -0.056 -1000
Arf6 trafficking events 0.0097 5 382 71 -0.11 0.059 1000 -1000 -0.05 -1000
PDGFR-beta signaling pathway 0.0097 5 520 97 -0.012 0.081 1000 -1000 -0.073 -1000
Class IB PI3K non-lipid kinase events 0.0097 5 15 3 -0.023 0.023 1000 -1000 -0.008 -1000
p38 MAPK signaling pathway 0.0097 5 251 44 -0.062 0.055 1000 -1000 -0.043 -1000
Ras signaling in the CD4+ TCR pathway 0.0097 5 100 17 -0.006 0.052 1000 -1000 -0.037 -1000
Signaling mediated by p38-gamma and p38-delta 0.0077 4 70 15 0 0.03 1000 -1000 -0.032 -1000
IGF1 pathway 0.0077 4 233 57 -0.054 0.075 1000 -1000 -0.064 -1000
Insulin Pathway 0.0077 4 298 74 -0.033 0.077 1000 -1000 -0.066 -1000
BARD1 signaling events 0.0058 3 208 57 -0.081 0.073 1000 -1000 -0.075 -1000
Hedgehog signaling events mediated by Gli proteins 0.0058 3 249 65 -0.005 0.097 1000 -1000 -0.056 -1000
Class I PI3K signaling events mediated by Akt 0.0058 3 228 68 -0.036 0.053 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0058 3 191 63 0 0.056 1000 -1000 -0.062 -1000
Osteopontin-mediated events 0.0039 2 105 38 0 0.08 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0039 2 149 52 -0.013 0.094 1000 -1000 -0.046 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0039 2 240 83 -0.036 0.068 1000 -1000 -0.057 -1000
Retinoic acid receptors-mediated signaling 0.0039 2 129 58 -0.021 0.051 1000 -1000 -0.056 -1000
Paxillin-dependent events mediated by a4b1 0.0039 2 76 36 -0.051 0.053 1000 -1000 -0.044 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 38 23 -0.029 0.054 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class II 0.0019 1 109 75 -0.038 0.059 1000 -1000 -0.034 -1000
Circadian rhythm pathway 0.0019 1 24 22 -0.012 0.065 1000 -1000 -0.036 -1000
Arf6 downstream pathway 0.0019 1 83 43 -0.045 0.046 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class I 0.0019 1 192 104 -0.055 0.073 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 0.0019 1 61 31 0 0.036 1000 -1000 -0.035 -1000
Arf1 pathway 0.0019 1 84 54 0 0.047 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0000 0 34 48 0 0.07 1000 -1000 -0.048 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 7 27 0 0.067 1000 -1000 -0.046 -1000
Rapid glucocorticoid signaling 0.0000 0 9 20 -0.007 0.035 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 0 0.059 1000 -1000 -0.003 -1000
Total NA 3530 191557 7203 -27 -990 131000 -131000 -7 -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 0.38 0.22 0.5 379 -10000 0 379
KIRREL -0.059 0.082 -10000 0 -0.6 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.38 0.22 -10000 0 -0.5 379 379
PLCG1 0.028 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.029 -10000 0 -0.62 1 1
WASL 0.026 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.4 0.27 -10000 0 -0.51 400 400
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.33 0.23 -10000 0 -0.44 375 375
FYN -0.38 0.24 0.26 1 -0.48 404 405
mol:Ca2+ -0.39 0.27 -10000 0 -0.51 397 397
mol:DAG -0.39 0.27 -10000 0 -0.51 397 397
NPHS2 -0.33 0.31 -10000 0 -0.66 235 235
mol:IP3 -0.39 0.27 -10000 0 -0.51 397 397
regulation of endocytosis -0.35 0.24 -10000 0 -0.46 397 397
Nephrin/NEPH1/podocin/Cholesterol -0.4 0.26 -10000 0 -0.51 404 404
establishment of cell polarity -0.38 0.22 -10000 0 -0.5 379 379
Nephrin/NEPH1/podocin/NCK1-2 -0.36 0.26 -10000 0 -0.62 210 210
Nephrin/NEPH1/beta Arrestin2 -0.36 0.24 -10000 0 -0.47 397 397
NPHS1 -0.49 0.27 -10000 0 -0.64 392 392
Nephrin/NEPH1/podocin -0.38 0.25 -10000 0 -0.48 404 404
TJP1 0.029 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.029 -10000 0 -0.61 1 1
NCK2 0.028 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.39 0.27 -10000 0 -0.51 397 397
CD2AP 0.028 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.39 0.27 -10000 0 -0.51 398 398
GRB2 0.028 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.37 0.24 0.28 1 -0.48 398 399
cytoskeleton organization -0.42 0.27 -10000 0 -0.56 358 358
Nephrin/NEPH1 -0.27 0.17 -10000 0 -0.37 379 379
Nephrin/NEPH1/ZO-1 -0.3 0.19 -10000 0 -0.41 377 377
HIF-1-alpha transcription factor network

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
PKM2 -0.79 0.46 -10000 0 -1.2 239 239
HDAC7 0.025 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.58 0.31 -10000 0 -0.88 193 193
SMAD4 0.029 0.005 -10000 0 -10000 0 0
ID2 -0.79 0.46 -10000 0 -1.2 239 239
AP1 0.028 0.074 -10000 0 -0.44 12 12
ABCG2 -0.79 0.46 -10000 0 -1.2 240 240
HIF1A -0.11 0.072 -10000 0 -0.74 2 2
TFF3 -0.8 0.46 -10000 0 -1.2 243 243
GATA2 0.014 0.09 -10000 0 -0.58 11 11
AKT1 -0.098 0.06 -10000 0 -0.31 1 1
response to hypoxia -0.12 0.059 -10000 0 -0.34 7 7
MCL1 -0.79 0.46 -10000 0 -1.2 236 236
NDRG1 -0.79 0.46 -10000 0 -1.2 240 240
SERPINE1 -0.8 0.49 -10000 0 -1.2 245 245
FECH -0.79 0.46 -10000 0 -1.2 242 242
FURIN -0.79 0.46 -10000 0 -1.2 240 240
NCOA2 0.013 0.079 -10000 0 -0.61 8 8
EP300 -0.1 0.075 -10000 0 -0.32 17 17
HMOX1 -0.8 0.47 -10000 0 -1.2 246 246
BHLHE40 -0.79 0.46 -10000 0 -1.2 239 239
BHLHE41 -0.84 0.49 -10000 0 -1.2 261 261
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.098 0.085 -10000 0 -0.52 2 2
ENG -0.086 0.086 0.43 1 -0.48 2 3
JUN 0.028 0.007 -10000 0 -10000 0 0
RORA -0.79 0.46 -10000 0 -1.2 243 243
ABCB1 -0.26 0.39 -10000 0 -1.3 64 64
TFRC -0.79 0.46 -10000 0 -1.2 241 241
CXCR4 -0.86 0.5 -10000 0 -1.2 274 274
TF -0.83 0.5 -10000 0 -1.2 251 251
CITED2 -0.79 0.46 -10000 0 -1.2 239 239
HIF1A/ARNT -0.94 0.64 -10000 0 -1.4 266 266
LDHA -0.079 0.12 -10000 0 -0.81 10 10
ETS1 -0.79 0.46 -10000 0 -1.2 240 240
PGK1 -0.79 0.46 -10000 0 -1.2 240 240
NOS2 -0.79 0.46 -10000 0 -1.2 241 241
ITGB2 -0.82 0.48 -10000 0 -1.2 256 256
ALDOA -0.79 0.46 -10000 0 -1.2 238 238
Cbp/p300/CITED2 -0.79 0.45 -10000 0 -1.2 226 226
FOS 0.012 0.096 -10000 0 -0.6 12 12
HK2 -0.93 0.49 -10000 0 -1.3 304 304
SP1 0.021 0.043 -10000 0 -10000 0 0
GCK -0.17 0.16 -10000 0 -0.88 10 10
HK1 -0.79 0.46 -10000 0 -1.2 240 240
NPM1 -0.76 0.46 -10000 0 -1.2 225 225
EGLN1 -0.79 0.46 -10000 0 -1.2 236 236
CREB1 0.034 0.009 -10000 0 -10000 0 0
PGM1 -0.79 0.46 -10000 0 -1.2 240 240
SMAD3 0.03 0.003 -10000 0 -10000 0 0
EDN1 -0.11 0.13 -10000 0 -0.69 7 7
IGFBP1 -0.82 0.5 -10000 0 -1.2 246 246
VEGFA -0.62 0.32 -10000 0 -0.93 199 199
HIF1A/JAB1 -0.062 0.056 -10000 0 -0.56 2 2
CP -0.93 0.5 -10000 0 -1.3 311 311
CXCL12 -0.8 0.46 -10000 0 -1.2 244 244
COPS5 0.024 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.044 0.008 -10000 0 -10000 0 0
BNIP3 -0.79 0.46 -10000 0 -1.2 240 240
EGLN3 -0.98 0.46 -10000 0 -1.3 327 327
CA9 -0.99 0.45 -10000 0 -1.3 338 338
TERT -0.81 0.47 -10000 0 -1.2 245 245
ENO1 -0.79 0.46 -10000 0 -1.2 243 243
PFKL -0.79 0.46 -10000 0 -1.2 238 238
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM -0.84 0.48 -10000 0 -1.2 261 261
ARNT -0.11 0.054 -10000 0 -10000 0 0
HNF4A -0.018 0.17 -10000 0 -0.61 38 38
ADFP -0.79 0.46 -10000 0 -1.2 261 261
SLC2A1 -0.55 0.28 -10000 0 -0.86 146 146
LEP -0.8 0.47 -10000 0 -1.2 246 246
HIF1A/ARNT/Cbp/p300 -0.6 0.31 -10000 0 -0.91 194 194
EPO -0.49 0.3 -10000 0 -0.83 167 167
CREBBP -0.1 0.074 -10000 0 -0.33 13 13
HIF1A/ARNT/Cbp/p300/HDAC7 -0.62 0.34 -10000 0 -0.95 192 192
PFKFB3 -0.79 0.46 -10000 0 -1.2 240 240
NT5E -0.79 0.46 -10000 0 -1.2 242 242
EGFR-dependent Endothelin signaling events

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
HRAS 0.028 0.024 -9999 0 -0.5 1 1
EGFR 0.019 0.06 -9999 0 -0.52 6 6
EGF/EGFR -0.28 0.12 -9999 0 -0.33 411 411
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.27 0.13 -9999 0 -0.33 389 389
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.027 0.024 -9999 0 -0.5 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.54 0.19 -9999 0 -0.61 460 460
EGF/EGFR dimer/SHC -0.32 0.14 -9999 0 -0.39 398 398
mol:GDP -0.27 0.13 -9999 0 -0.33 389 389
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.097 -9999 0 -0.51 17 17
GRB2/SOS1 0.041 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.25 0.12 -9999 0 -0.54 6 6
SHC1 0.027 0.006 -9999 0 -10000 0 0
HRAS/GDP -0.25 0.12 -9999 0 -0.54 6 6
FRAP1 -0.26 0.11 -9999 0 -0.32 389 389
EGF/EGFR dimer -0.39 0.16 -9999 0 -0.43 454 454
SOS1 0.028 0.005 -9999 0 -10000 0 0
GRB2 0.028 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.027 0.076 -9999 0 -0.37 18 18
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.21 0.27 0.3 6 -0.52 196 202
FYN -0.25 0.34 0.42 13 -0.62 203 216
LAT/GRAP2/SLP76 -0.25 0.31 0.34 4 -0.59 201 205
IKBKB 0.027 0.008 -10000 0 -10000 0 0
AKT1 -0.18 0.27 0.44 21 -0.45 212 233
B2M 0.025 0.007 -10000 0 -10000 0 0
IKBKG -0.051 0.082 0.15 13 -0.17 63 76
MAP3K8 0.026 0.033 -10000 0 -0.5 2 2
mol:Ca2+ -0.084 0.052 0.073 10 -0.12 283 293
integrin-mediated signaling pathway 0.026 0.058 -10000 0 -0.31 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.27 0.37 0.49 16 -0.66 213 229
TRPV6 -0.41 0.42 0.74 44 -0.61 394 438
CD28 -0.014 0.14 -10000 0 -0.51 38 38
SHC1 -0.27 0.34 0.39 8 -0.62 223 231
receptor internalization -0.29 0.34 0.48 1 -0.64 227 228
PRF1 -0.27 0.36 0.41 1 -0.74 158 159
KRAS 0.028 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.13 0.22 0.41 19 -0.36 191 210
LAT -0.32 0.38 0.46 7 -0.7 231 238
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.21 0.27 -10000 0 -0.51 228 228
CD3E -0.19 0.26 -10000 0 -0.51 204 204
CD3G -0.18 0.26 -10000 0 -0.51 200 200
RASGRP2 -0.012 0.028 0.089 5 -0.17 1 6
RASGRP1 -0.15 0.27 0.45 26 -0.44 189 215
HLA-A 0.022 0.035 -10000 0 -0.51 2 2
RASSF5 0.012 0.09 -10000 0 -0.5 15 15
RAP1A/GTP/RAPL 0.027 0.059 -10000 0 -0.31 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.14 0.23 61 -0.13 5 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.11 0.11 -10000 0 -0.25 162 162
PRKCA -0.1 0.16 0.18 32 -0.28 167 199
GRAP2 -0.008 0.14 -10000 0 -0.51 35 35
mol:IP3 -0.11 0.29 0.23 155 -0.43 192 347
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.3 0.28 1 -0.56 221 222
ORAI1 0.19 0.27 0.66 6 -0.59 44 50
CSK -0.28 0.34 0.38 5 -0.63 225 230
B7 family/CD28 -0.3 0.39 0.32 2 -0.73 205 207
CHUK 0.028 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.32 0.38 0.24 1 -0.71 227 228
PTPN6 -0.27 0.33 0.28 4 -0.63 211 215
VAV1 -0.32 0.38 0.42 7 -0.7 228 235
Monovalent TCR/CD3 -0.21 0.26 -10000 0 -0.5 221 221
CBL 0.027 0.028 -10000 0 -0.61 1 1
LCK -0.26 0.35 0.44 11 -0.63 211 222
PAG1 -0.28 0.33 0.32 3 -0.63 224 227
RAP1A 0.028 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.3 0.37 -10000 0 -0.7 216 216
CD80 -0.095 0.22 -10000 0 -0.51 114 114
CD86 -0.06 0.2 -10000 0 -0.51 81 81
PDK1/CARD11/BCL10/MALT1 -0.13 0.15 0.19 1 -0.3 172 173
HRAS 0.028 0.024 -10000 0 -0.5 1 1
GO:0035030 -0.25 0.31 0.42 3 -0.58 212 215
CD8A -0.22 0.27 -10000 0 -0.51 230 230
CD8B -0.17 0.26 -10000 0 -0.51 184 184
PTPRC -0.03 0.16 -10000 0 -0.51 53 53
PDK1/PKC theta -0.22 0.33 0.54 23 -0.56 209 232
CSK/PAG1 -0.27 0.33 0.42 5 -0.63 208 213
SOS1 0.028 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.032 0.029 -10000 0 -0.37 2 2
GRAP2/SLP76 -0.26 0.33 0.3 2 -0.63 202 204
STIM1 0.11 0.11 0.96 1 -0.63 3 4
RAS family/GTP -0.032 0.14 0.31 31 -0.18 41 72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.31 0.36 0.49 1 -0.68 227 228
mol:DAG -0.16 0.21 0.14 2 -0.39 205 207
RAP1A/GDP 0.003 0.083 0.19 33 -10000 0 33
PLCG1 0.028 0.006 -10000 0 -10000 0 0
CD247 -0.15 0.25 -10000 0 -0.51 166 166
cytotoxic T cell degranulation -0.26 0.35 0.41 1 -0.71 159 160
RAP1A/GTP -0.005 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.22 0.31 0.43 19 -0.54 213 232
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.18 0.36 0.26 116 -0.58 199 315
NRAS 0.028 0.005 -10000 0 -10000 0 0
ZAP70 -0.26 0.26 -10000 0 -0.5 276 276
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.26 0.31 0.28 3 -0.6 209 212
MALT1 0.028 0.005 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.25 0.33 -10000 0 -0.6 236 236
CARD11 -0.077 0.21 -10000 0 -0.5 98 98
PRKCB -0.11 0.16 0.17 30 -0.28 175 205
PRKCE -0.1 0.16 0.17 31 -0.28 172 203
PRKCQ -0.26 0.37 0.46 22 -0.64 210 232
LCP2 -0.009 0.12 -10000 0 -0.5 29 29
BCL10 0.028 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.15 0.23 0.42 22 -0.38 212 234
IKK complex -0.002 0.15 0.27 64 -0.13 6 70
RAS family/GDP -0.012 0.013 -10000 0 -10000 0 0
MAP3K14 -0.099 0.17 0.36 18 -0.28 163 181
PDPK1 -0.16 0.26 0.47 22 -0.43 206 228
TCR/CD3/MHC I/CD8/Fyn -0.3 0.36 0.44 1 -0.69 217 218
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.44 0.4 -10000 0 -0.98 130 130
PCK1 -0.9 0.66 -10000 0 -1.3 313 313
HNF4A -0.51 0.47 -10000 0 -1.2 131 131
KCNJ11 -0.45 0.43 -10000 0 -1 131 131
AKT1 -0.21 0.2 -10000 0 -0.53 56 56
response to starvation -0.013 0.024 -10000 0 -10000 0 0
DLK1 -0.54 0.5 -10000 0 -1.1 174 174
NKX2-1 -0.086 0.18 -10000 0 -0.7 4 4
ACADM -0.44 0.4 -10000 0 -0.98 133 133
TAT -0.48 0.3 -10000 0 -0.75 224 224
CEBPB -0.022 0.081 -10000 0 -0.56 8 8
CEBPA -0.023 0.084 -10000 0 -0.54 10 10
TTR -0.84 0.46 0.43 1 -1.1 354 355
PKLR -0.48 0.48 -10000 0 -1.1 138 138
APOA1 -0.53 0.47 -10000 0 -1.2 140 140
CPT1C -0.44 0.4 -10000 0 -0.97 134 134
ALAS1 -0.23 0.21 -10000 0 -0.72 14 14
TFRC -0.64 0.38 -10000 0 -0.9 289 289
FOXF1 0.019 0.066 -10000 0 -0.49 8 8
NF1 0.034 0.005 -10000 0 -10000 0 0
HNF1A (dimer) -0.014 0.081 -10000 0 -0.44 8 8
CPT1A -0.44 0.4 -10000 0 -0.98 132 132
HMGCS1 -0.43 0.4 -10000 0 -0.98 126 126
NR3C1 0.006 0.053 -10000 0 -0.57 1 1
CPT1B -0.45 0.42 -10000 0 -0.99 140 140
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.007 -10000 0 -10000 0 0
GCK -0.43 0.41 -10000 0 -0.99 127 127
CREB1 -0.04 0.08 -10000 0 -0.32 2 2
IGFBP1 -0.24 0.29 -10000 0 -0.73 92 92
PDX1 -0.2 0.2 -10000 0 -0.76 12 12
UCP2 -0.44 0.4 -10000 0 -0.98 132 132
ALDOB -0.87 0.55 -10000 0 -1.1 382 382
AFP -0.62 0.43 -10000 0 -0.76 378 378
BDH1 -0.56 0.49 -10000 0 -1.1 200 200
HADH -0.44 0.42 -10000 0 -1 130 130
F2 -0.57 0.48 -10000 0 -1.1 165 165
HNF1A -0.014 0.081 -10000 0 -0.45 8 8
G6PC -0.76 0.62 -10000 0 -1.4 241 241
SLC2A2 -0.32 0.43 -10000 0 -1.4 50 50
INS 0 0.058 -10000 0 -10000 0 0
FOXA1 -0.3 0.25 -10000 0 -0.55 191 191
FOXA3 -0.55 0.29 -10000 0 -0.67 392 392
FOXA2 -0.51 0.48 -10000 0 -1.1 152 152
ABCC8 -0.45 0.42 -10000 0 -1 135 135
ALB -1.1 0.42 -10000 0 -1.2 438 438
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 -0.21 0.31 -10000 0 -0.61 193 193
PDGF/PDGFRA/CRKL -0.14 0.23 -10000 0 -0.44 190 190
positive regulation of JUN kinase activity -0.079 0.19 -10000 0 -0.34 171 171
CRKL 0.028 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.23 -10000 0 -0.44 196 196
AP1 -0.12 0.21 0.47 1 -1.1 11 12
mol:IP3 -0.15 0.23 -10000 0 -0.45 187 187
PLCG1 -0.16 0.23 -10000 0 -0.45 187 187
PDGF/PDGFRA/alphaV Integrin -0.14 0.23 -10000 0 -0.44 184 184
RAPGEF1 0.028 0.005 -10000 0 -10000 0 0
CRK 0.028 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.23 -10000 0 -0.45 187 187
CAV3 0.012 0.044 -10000 0 -0.54 3 3
CAV1 -0.006 0.12 -10000 0 -0.5 30 30
SHC/Grb2/SOS1 -0.078 0.19 -10000 0 -0.34 171 171
PDGF/PDGFRA/Shf -0.14 0.23 -10000 0 -0.44 192 192
FOS -0.12 0.21 -10000 0 -1.1 11 11
JUN -0.025 0.022 -10000 0 -10000 0 0
oligodendrocyte development -0.14 0.23 -10000 0 -0.44 184 184
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:DAG -0.15 0.23 -10000 0 -0.45 187 187
PDGF/PDGFRA -0.21 0.31 -10000 0 -0.61 193 193
actin cytoskeleton reorganization -0.14 0.23 -10000 0 -0.44 192 192
SRF 0.023 0.01 -10000 0 -10000 0 0
SHC1 0.027 0.006 -10000 0 -10000 0 0
PI3K -0.1 0.2 -10000 0 -0.37 166 166
PDGF/PDGFRA/Crk/C3G -0.11 0.21 -10000 0 -0.37 190 190
JAK1 -0.15 0.22 -10000 0 -0.44 192 192
ELK1/SRF -0.11 0.17 -10000 0 -0.34 179 179
SHB 0.028 0.006 -10000 0 -10000 0 0
SHF 0.027 0.028 -10000 0 -0.61 1 1
CSNK2A1 0.035 0.016 -10000 0 -10000 0 0
GO:0007205 -0.17 0.23 -10000 0 -0.46 192 192
SOS1 0.028 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.079 0.19 -10000 0 -0.34 171 171
PDGF/PDGFRA/SHB -0.14 0.23 -10000 0 -0.44 192 192
PDGF/PDGFRA/Caveolin-1 -0.16 0.23 -10000 0 -0.44 194 194
ITGAV 0.027 0.006 -10000 0 -10000 0 0
ELK1 -0.14 0.2 -10000 0 -0.41 185 185
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
PDGF/PDGFRA/Crk -0.14 0.23 -10000 0 -0.44 191 191
JAK-STAT cascade -0.15 0.22 -10000 0 -0.44 192 192
cell proliferation -0.14 0.23 -10000 0 -0.44 192 192
TCGA08_retinoblastoma

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
CDKN2B 0.025 0.059 -10000 0 -0.51 6 6
CDKN2C 0.071 0.021 -10000 0 -10000 0 0
CDKN2A -0.5 0.11 -10000 0 -0.52 489 489
CCND2 0.11 0.05 0.23 46 -10000 0 46
RB1 -0.13 0.059 0.29 1 -0.25 54 55
CDK4 0.13 0.058 0.26 47 -10000 0 47
CDK6 0.13 0.062 0.23 84 -0.16 1 85
G1/S progression 0.13 0.061 0.26 58 -0.29 1 59
Syndecan-4-mediated signaling events

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
PTK2 -0.1 0.16 -10000 0 -0.68 16 16
Syndecan-4/Syndesmos -0.27 0.23 -10000 0 -0.52 169 169
positive regulation of JNK cascade -0.32 0.25 -10000 0 -0.59 189 189
Syndecan-4/ADAM12 -0.34 0.28 -10000 0 -0.61 212 212
CCL5 -0.2 0.26 -10000 0 -0.5 217 217
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 -0.007 0.13 -10000 0 -0.5 34 34
SDCBP 0.027 0.007 -10000 0 -10000 0 0
PLG -0.28 0.3 -10000 0 -0.57 265 265
ADAM12 -0.12 0.24 -10000 0 -0.5 136 136
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.08 0.06 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.28 0.23 -10000 0 -0.53 180 180
Syndecan-4/CXCL12/CXCR4 -0.34 0.27 -10000 0 -0.63 189 189
Syndecan-4/Laminin alpha3 -0.28 0.23 -10000 0 -0.52 178 178
MDK -0.011 0.14 -10000 0 -0.51 38 38
Syndecan-4/FZD7 -0.27 0.23 -10000 0 -0.52 181 181
Syndecan-4/Midkine -0.29 0.24 -10000 0 -0.59 141 141
FZD7 0.026 0.029 -10000 0 -0.61 1 1
Syndecan-4/FGFR1/FGF -0.26 0.22 -10000 0 -0.55 110 110
THBS1 0.025 0.049 -10000 0 -0.61 3 3
integrin-mediated signaling pathway -0.27 0.22 -10000 0 -0.51 180 180
positive regulation of MAPKKK cascade -0.32 0.25 -10000 0 -0.59 189 189
Syndecan-4/TACI -0.3 0.25 -10000 0 -0.53 222 222
CXCR4 -0.15 0.25 -10000 0 -0.5 174 174
cell adhesion 0.018 0.065 0.22 5 -0.25 9 14
Syndecan-4/Dynamin -0.28 0.23 -10000 0 -0.52 174 174
Syndecan-4/TSP1 -0.28 0.23 -10000 0 -0.52 175 175
Syndecan-4/GIPC -0.28 0.23 -10000 0 -0.52 179 179
Syndecan-4/RANTES -0.37 0.27 -10000 0 -0.61 241 241
ITGB1 0.028 0.004 -10000 0 -10000 0 0
LAMA1 0.013 0.095 -10000 0 -0.54 14 14
LAMA3 0.022 0.058 -10000 0 -0.5 6 6
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.083 0.13 0.99 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.28 0.23 -10000 0 -0.52 175 175
TFPI 0.019 0.067 -10000 0 -0.51 8 8
F2 -0.17 0.26 -10000 0 -0.5 191 191
alpha5/beta1 Integrin 0.014 0.1 -10000 0 -0.36 34 34
positive regulation of cell adhesion -0.28 0.23 -10000 0 -0.57 123 123
ACTN1 0.025 0.029 -10000 0 -0.61 1 1
TNC 0.014 0.093 -10000 0 -0.61 11 11
Syndecan-4/CXCL12 -0.28 0.23 -10000 0 -0.53 181 181
FGF6 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
CXCL12 0.018 0.078 -10000 0 -0.52 10 10
TNFRSF13B -0.025 0.16 -10000 0 -0.5 50 50
FGF2 0.022 0.061 -10000 0 -0.59 5 5
FGFR1 0.026 0.008 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.28 0.22 -10000 0 -0.5 212 212
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.003 0.14 -10000 0 -0.49 37 37
cell migration -0.027 0.02 -10000 0 -10000 0 0
PRKCD 0.028 0.032 -10000 0 -0.49 1 1
vasculogenesis -0.27 0.22 -10000 0 -0.5 176 176
SDC4 -0.29 0.24 -10000 0 -0.53 212 212
Syndecan-4/Tenascin C -0.28 0.23 -10000 0 -0.53 180 180
Syndecan-4/PI-4-5-P2/PKC alpha -0.063 0.047 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.27 0.23 -10000 0 -0.52 171 171
MMP9 -0.21 0.26 -10000 0 -0.5 230 230
Rac1/GTP 0.018 0.066 0.22 5 -0.26 9 14
cytoskeleton organization -0.26 0.22 -10000 0 -0.5 172 172
GIPC1 0.027 0.028 -10000 0 -0.61 1 1
Syndecan-4/TFPI -0.28 0.23 -10000 0 -0.57 125 125
TCGA08_p53

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
CDKN2A -0.35 0.085 0.19 3 -0.37 489 492
TP53 -0.1 0.071 -10000 0 -0.34 32 32
Senescence -0.1 0.071 -10000 0 -0.34 32 32
Apoptosis -0.1 0.071 -10000 0 -0.34 32 32
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.19 0.088 0.4 41 -10000 0 41
MDM4 0.028 0.006 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.045 0.05 -10000 0 -0.37 6 6
fibroblast growth factor receptor signaling pathway 0.045 0.05 -10000 0 -0.37 6 6
LAMA1 0.013 0.095 -10000 0 -0.54 14 14
PRNP 0.028 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.06 0.2 -10000 0 -0.45 100 100
SMAD2 0.019 0.026 -10000 0 -0.35 1 1
GPC1/PrPc/Cu2+ 0.035 0.022 -10000 0 -0.39 1 1
GPC1/Laminin alpha1 0.028 0.074 -10000 0 -0.44 11 11
TDGF1 -0.38 0.26 -10000 0 -0.52 383 383
CRIPTO/GPC1 -0.27 0.2 -10000 0 -0.45 262 262
APP/GPC1 0.038 0.025 -10000 0 -0.45 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.23 0.17 -10000 0 -0.39 259 259
FLT1 0.023 0.053 -10000 0 -0.5 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.033 -10000 0 -0.39 1 1
SERPINC1 -0.027 0.18 -10000 0 -0.6 44 44
FYN -0.23 0.18 -10000 0 -0.39 261 261
FGR -0.23 0.18 -10000 0 -0.39 262 262
positive regulation of MAPKKK cascade -0.27 0.19 0.38 3 -0.42 267 270
SLIT2 -0.1 0.26 -10000 0 -0.59 108 108
GPC1/NRG 0.023 0.08 -10000 0 -0.45 13 13
NRG1 0.009 0.1 -10000 0 -0.53 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.11 0.18 -10000 0 -0.31 222 222
LYN -0.22 0.17 -10000 0 -0.39 253 253
mol:Spermine 0.009 0.021 -10000 0 -0.45 1 1
cell growth 0.045 0.05 -10000 0 -0.37 6 6
BMP signaling pathway -0.026 0.029 0.61 1 -10000 0 1
SRC -0.23 0.17 -10000 0 -0.39 254 254
TGFBR1 0.028 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.02 0.15 -10000 0 -0.5 43 43
GPC1 0.026 0.029 -10000 0 -0.61 1 1
TGFBR1 (dimer) 0.028 0.006 -10000 0 -10000 0 0
VEGFA -0.21 0.26 -10000 0 -0.5 228 228
BLK -0.24 0.2 -10000 0 -0.41 266 266
HCK -0.24 0.18 -10000 0 -0.4 266 266
FGF2 0.022 0.061 -10000 0 -0.59 5 5
FGFR1 0.026 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer 0.023 0.053 -10000 0 -0.5 5 5
TGFBR2 0.021 0.013 -10000 0 -10000 0 0
cell death 0.038 0.025 -10000 0 -0.45 1 1
ATIII/GPC1 -0.004 0.14 -10000 0 -0.44 45 45
PLA2G2A/GPC1 0.002 0.11 -10000 0 -0.36 44 44
LCK -0.24 0.18 -10000 0 -0.4 270 270
neuron differentiation 0.023 0.08 -10000 0 -0.44 13 13
PrPc/Cu2+ 0.021 0.004 -10000 0 -10000 0 0
APP 0.028 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.021 0.013 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.1 0.16 -10000 0 -0.39 87 87
STMN1 -0.15 0.19 -10000 0 -0.36 239 239
Aurora B/RasGAP/Survivin -0.18 0.26 -10000 0 -0.45 227 227
Chromosomal passenger complex/Cul3 protein complex -0.075 0.13 -10000 0 -0.4 34 34
BIRC5 -0.13 0.25 -10000 0 -0.52 148 148
DES -0.23 0.29 -10000 0 -0.63 157 157
Aurora C/Aurora B/INCENP -0.096 0.17 -10000 0 -0.27 234 234
Aurora B/TACC1 -0.12 0.17 -10000 0 -0.3 236 236
Aurora B/PP2A -0.14 0.2 -10000 0 -0.36 238 238
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.028 0.049 -10000 0 -0.2 3 3
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.22 0.27 -10000 0 -0.48 241 241
Cul3 protein complex 0.04 0.077 -10000 0 -0.39 15 15
KIF2C -0.066 0.13 -10000 0 -0.38 42 42
PEBP1 0.023 0.01 -10000 0 -10000 0 0
KIF20A -0.16 0.25 -10000 0 -0.5 174 174
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.13 0.19 -10000 0 -0.36 213 213
SEPT1 -0.041 0.18 -10000 0 -0.5 66 66
SMC2 0.028 0.006 -10000 0 -10000 0 0
SMC4 0.027 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.034 0.15 0.28 1 -0.7 11 12
PSMA3 0.027 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -10000 0 -10000 0 0
H3F3B -0.079 0.11 -10000 0 -0.2 231 231
AURKB -0.22 0.27 -10000 0 -0.51 239 239
AURKC 0.026 0.033 -10000 0 -0.5 2 2
CDCA8 -0.002 0.1 -10000 0 -0.53 19 19
cytokinesis -0.13 0.18 -10000 0 -0.42 94 94
Aurora B/Septin1 -0.14 0.23 -10000 0 -0.53 82 82
AURKA 0.023 0.053 -10000 0 -0.51 5 5
INCENP 0.018 0.019 -10000 0 -10000 0 0
KLHL13 0.009 0.11 -10000 0 -0.59 16 16
BUB1 -0.2 0.26 -10000 0 -0.51 220 220
hSgo1/Aurora B/Survivin -0.19 0.26 -10000 0 -0.44 227 227
EVI5 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.11 0.18 -10000 0 -0.4 83 83
SGOL1 0.001 0.1 -10000 0 -0.52 18 18
CENPA -0.12 0.16 0.19 1 -0.32 158 159
NCAPG -0.15 0.25 -10000 0 -0.5 171 171
Aurora B/HC8 Proteasome -0.14 0.2 -10000 0 -0.35 238 238
NCAPD2 0.028 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.14 0.2 -10000 0 -0.36 229 229
RHOA 0.021 0.013 -10000 0 -10000 0 0
NCAPH -0.06 0.2 -10000 0 -0.5 84 84
NPM1 -0.072 0.11 -10000 0 -0.52 7 7
RASA1 0.024 0.03 -10000 0 -0.61 1 1
KLHL9 0.028 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.005 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.2 -10000 0 -0.35 238 238
PPP1CC 0.028 0.005 -10000 0 -10000 0 0
Centraspindlin -0.11 0.2 -10000 0 -0.43 92 92
RhoA/GDP 0.015 0.01 -10000 0 -10000 0 0
NSUN2 -0.076 0.12 -10000 0 -0.55 6 6
MYLK -0.085 0.12 -10000 0 -0.38 15 15
KIF23 0.018 0.067 -10000 0 -0.51 8 8
VIM -0.18 0.22 -10000 0 -0.4 250 250
RACGAP1 0.025 0.025 -10000 0 -0.52 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.09 0.15 -10000 0 -0.6 18 18
Chromosomal passenger complex -0.13 0.19 0.18 1 -0.37 164 165
Chromosomal passenger complex/EVI5 -0.14 0.27 -10000 0 -0.52 144 144
TACC1 0.026 0.008 -10000 0 -10000 0 0
PPP2R5D 0.028 0.006 -10000 0 -10000 0 0
CUL3 0.027 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.097 0.15 -10000 0 -0.4 58 58
TBX21 -0.35 0.46 0.74 1 -0.96 146 147
B2M 0.021 0.015 -10000 0 -10000 0 0
TYK2 0.002 0.037 -10000 0 -10000 0 0
IL12RB1 -0.16 0.26 -10000 0 -0.54 158 158
GADD45B -0.19 0.3 0.57 1 -0.69 52 53
IL12RB2 -0.074 0.19 -10000 0 -0.52 74 74
GADD45G -0.21 0.31 0.57 1 -0.68 70 71
natural killer cell activation -0.011 0.025 -10000 0 -10000 0 0
RELB 0.029 0.003 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
IL18 0.021 0.053 -10000 0 -0.5 5 5
IL2RA -0.076 0.21 -10000 0 -0.5 100 100
IFNG -0.21 0.26 -10000 0 -0.5 230 230
STAT3 (dimer) -0.26 0.35 -10000 0 -0.7 156 156
HLA-DRB5 -0.005 0.13 -10000 0 -0.5 31 31
FASLG -0.38 0.47 0.74 1 -0.96 163 164
NF kappa B2 p52/RelB -0.29 0.41 -10000 0 -0.83 151 151
CD4 0.018 0.071 -10000 0 -0.5 9 9
SOCS1 0.021 0.058 -10000 0 -0.5 6 6
EntrezGene:6955 -0.004 0.009 -10000 0 -10000 0 0
CD3D -0.22 0.27 -10000 0 -0.51 228 228
CD3E -0.19 0.26 -10000 0 -0.51 204 204
CD3G -0.19 0.27 -10000 0 -0.52 200 200
IL12Rbeta2/JAK2 -0.052 0.15 -10000 0 -0.38 74 74
CCL3 -0.32 0.44 0.74 1 -0.91 139 140
CCL4 -0.33 0.45 0.74 1 -0.97 134 135
HLA-A 0.019 0.036 -10000 0 -0.51 2 2
IL18/IL18R -0.053 0.18 -10000 0 -0.34 105 105
NOS2 -0.25 0.33 -10000 0 -0.74 100 100
IL12/IL12R/TYK2/JAK2/SPHK2 -0.095 0.15 -10000 0 -0.39 57 57
IL1R1 -0.3 0.41 0.74 1 -0.89 120 121
IL4 0.017 0.036 -10000 0 -10000 0 0
JAK2 0.001 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.32 0.38 -10000 0 -0.73 216 216
RAB7A -0.16 0.28 0.54 4 -0.65 18 22
lysosomal transport -0.15 0.27 0.52 5 -0.62 18 23
FOS -0.25 0.36 -10000 0 -0.71 140 140
STAT4 (dimer) -0.26 0.38 0.56 5 -0.77 132 137
STAT5A (dimer) -0.38 0.47 -10000 0 -0.9 200 200
GZMA -0.36 0.46 -10000 0 -0.97 148 148
GZMB -0.35 0.45 -10000 0 -0.93 156 156
HLX -0.033 0.17 -10000 0 -0.51 58 58
LCK -0.33 0.44 0.52 1 -0.91 155 156
TCR/CD3/MHC II/CD4 -0.18 0.23 -10000 0 -0.44 206 206
IL2/IL2R -0.19 0.25 -10000 0 -0.6 88 88
MAPK14 -0.19 0.32 0.58 1 -0.68 70 71
CCR5 -0.35 0.4 0.57 1 -0.84 158 159
IL1B -0.005 0.068 -10000 0 -0.54 6 6
STAT6 -0.07 0.11 -10000 0 -10000 0 0
STAT4 -0.003 0.12 -10000 0 -0.5 29 29
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.024 -10000 0 -0.5 1 1
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
NFKB2 0.028 0.006 -10000 0 -10000 0 0
IL12B -0.053 0.16 -10000 0 -0.53 52 52
CD8A -0.22 0.27 -10000 0 -0.52 230 230
CD8B -0.17 0.26 -10000 0 -0.52 184 184
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.097 0.15 0.39 58 -10000 0 58
IL2RB -0.25 0.27 -10000 0 -0.5 270 270
proteasomal ubiquitin-dependent protein catabolic process -0.23 0.36 0.53 6 -0.7 131 137
IL2RG -0.007 0.13 -10000 0 -0.51 34 34
IL12 -0.038 0.13 -10000 0 -0.4 52 52
STAT5A 0.028 0.004 -10000 0 -10000 0 0
CD247 -0.15 0.25 -10000 0 -0.51 166 166
IL2 0.014 0.073 -10000 0 -0.5 10 10
SPHK2 0.026 0.04 -10000 0 -0.61 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.001 0.036 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.35 0.45 -10000 0 -0.94 155 155
MAP2K3 -0.2 0.32 0.57 1 -0.66 90 91
RIPK2 0.026 0.024 -10000 0 -0.5 1 1
MAP2K6 -0.2 0.32 0.57 1 -0.68 80 81
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.023 0.048 -10000 0 -0.5 4 4
IL18RAP -0.11 0.24 -10000 0 -0.51 132 132
IL12Rbeta1/TYK2 -0.11 0.21 -10000 0 -0.41 158 158
EOMES -0.28 0.29 -10000 0 -0.82 69 69
STAT1 (dimer) -0.3 0.37 -10000 0 -0.75 159 159
T cell proliferation -0.19 0.28 0.45 5 -0.58 102 107
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.068 -10000 0 -0.55 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.24 0.28 -10000 0 -0.65 95 95
ATF2 -0.18 0.31 0.53 7 -0.65 64 71
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.034 0.17 -10000 0 -0.36 99 99
alphaM/beta2 Integrin/GPIbA -0.033 0.17 -10000 0 -0.36 97 97
alphaM/beta2 Integrin/proMMP-9 -0.18 0.25 -10000 0 -0.4 250 250
PLAUR 0.003 0.11 -10000 0 -0.5 24 24
HMGB1 0.023 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.033 0.17 -10000 0 -0.36 96 96
AGER -0.071 0.2 -10000 0 -0.51 90 90
RAP1A 0.028 0.005 -10000 0 -10000 0 0
SELPLG -0.005 0.13 -10000 0 -0.5 32 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.081 0.21 -10000 0 -0.5 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.21 0.26 -10000 0 -0.5 230 230
CYR61 0.022 0.055 -10000 0 -0.46 6 6
TLN1 0.028 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.18 0.15 -10000 0 -0.4 105 105
RHOA 0.021 0.013 -10000 0 -10000 0 0
P-selectin oligomer 0.002 0.12 -10000 0 -0.61 20 20
MYH2 -0.27 0.18 -10000 0 -0.47 173 173
MST1R 0.013 0.067 -10000 0 -0.54 7 7
leukocyte activation during inflammatory response -0.12 0.2 -10000 0 -0.46 82 82
APOB -0.15 0.25 -10000 0 -0.51 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.055 -10000 0 -0.52 5 5
JAM3 0.029 0.003 -10000 0 -10000 0 0
GP1BA 0.027 0.029 -10000 0 -0.61 1 1
alphaM/beta2 Integrin/CTGF -0.039 0.17 -10000 0 -0.36 101 101
alphaM/beta2 Integrin -0.21 0.17 -10000 0 -0.37 215 215
JAM3 homodimer 0.029 0.003 -10000 0 -10000 0 0
ICAM2 0.028 0.005 -10000 0 -10000 0 0
ICAM1 0.017 0.077 -10000 0 -0.5 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.21 0.17 -10000 0 -0.36 215 215
cell adhesion -0.033 0.17 -10000 0 -0.36 97 97
NFKB1 -0.097 0.22 0.39 5 -0.54 62 67
THY1 0.027 0.028 -10000 0 -0.61 1 1
RhoA/GDP 0.015 0.01 -10000 0 -10000 0 0
Lipoprotein(a) -0.083 0.17 -10000 0 -0.32 166 166
alphaM/beta2 Integrin/LRP/tPA -0.021 0.16 -10000 0 -0.44 37 37
IL6 -0.12 0.27 0.38 3 -0.64 76 79
ITGB2 -0.077 0.21 -10000 0 -0.5 96 96
elevation of cytosolic calcium ion concentration -0.033 0.18 -10000 0 -0.47 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.012 0.16 -10000 0 -0.45 28 28
JAM2 0.028 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.033 0.16 -10000 0 -0.48 30 30
alphaM/beta2 Integrin/uPA/Plg -0.21 0.25 -10000 0 -0.43 252 252
RhoA/GTP -0.28 0.2 -10000 0 -0.48 184 184
positive regulation of phagocytosis -0.17 0.17 -10000 0 -0.47 82 82
Ron/MSP 0.018 0.074 -10000 0 -0.4 14 14
alphaM/beta2 Integrin/uPAR/uPA -0.031 0.18 -10000 0 -0.47 42 42
alphaM/beta2 Integrin/uPAR -0.045 0.19 -10000 0 -0.37 109 109
PLAU 0.019 0.072 -10000 0 -0.53 8 8
PLAT 0.015 0.085 -10000 0 -0.58 10 10
actin filament polymerization -0.26 0.17 -10000 0 -0.45 172 172
MST1 0.012 0.07 -10000 0 -0.53 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.12 0.21 -10000 0 -0.46 82 82
TNF -0.093 0.22 0.39 4 -0.52 63 67
RAP1B 0.028 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.038 0.17 -10000 0 -0.36 102 102
fibrinolysis -0.21 0.24 -10000 0 -0.42 252 252
HCK 0.001 0.12 -10000 0 -0.5 26 26
dendritic cell antigen processing and presentation -0.21 0.17 -10000 0 -0.36 215 215
VTN -0.065 0.22 -10000 0 -0.59 76 76
alphaM/beta2 Integrin/CYR61 -0.035 0.17 -10000 0 -0.36 99 99
LPA 0.018 0.044 -10000 0 -0.54 3 3
LRP1 0.028 0.005 -10000 0 -10000 0 0
cell migration -0.16 0.23 -10000 0 -0.45 135 135
FN1 -0.012 0.14 -10000 0 -0.51 37 37
alphaM/beta2 Integrin/Thy1 -0.033 0.17 -10000 0 -0.36 97 97
MPO 0.01 0.096 -10000 0 -0.5 17 17
KNG1 -0.43 0.28 -10000 0 -0.6 370 370
RAP1/GDP 0.037 0.01 -10000 0 -10000 0 0
ROCK1 -0.26 0.18 -10000 0 -0.46 170 170
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.29 0.31 -10000 0 -0.58 265 265
CTGF 0.018 0.075 -10000 0 -0.61 7 7
alphaM/beta2 Integrin/Hck -0.046 0.2 -10000 0 -0.42 98 98
ITGAM 0.003 0.1 -10000 0 -0.5 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.041 0.2 -10000 0 -0.49 61 61
HP -0.1 0.23 -10000 0 -0.51 124 124
leukocyte adhesion -0.058 0.17 -10000 0 -0.44 41 41
SELP 0.002 0.12 -10000 0 -0.61 20 20
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 -0.44 0.26 -10000 0 -0.54 413 413
SMAD6-7/SMURF1 0.051 0.02 -10000 0 -10000 0 0
NOG -0.06 0.2 -10000 0 -0.52 81 81
SMAD9 -0.067 0.17 -10000 0 -0.62 38 38
SMAD4 0.028 0.005 -10000 0 -10000 0 0
SMAD5 -0.14 0.16 -10000 0 -0.47 32 32
BMP7/USAG1 -0.5 0.3 -10000 0 -0.62 416 416
SMAD5/SKI -0.14 0.16 0.31 3 -0.47 29 32
SMAD1 -0.026 0.056 -10000 0 -10000 0 0
BMP2 0.024 0.049 -10000 0 -0.61 3 3
SMAD1/SMAD1/SMAD4 0.005 0.058 -10000 0 -10000 0 0
BMPR1A 0.028 0.006 -10000 0 -10000 0 0
BMPR1B -0.41 0.3 -10000 0 -0.61 350 350
BMPR1A-1B/BAMBI -0.25 0.21 -10000 0 -0.39 344 344
AHSG 0.011 0.078 -10000 0 -0.51 11 11
CER1 0.02 0.006 -10000 0 -10000 0 0
BMP2-4/CER1 0.042 0.045 -10000 0 -0.4 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.12 -10000 0 -0.44 10 10
BMP2-4 (homodimer) 0.034 0.048 -10000 0 -0.45 4 4
RGMB 0.023 0.035 -10000 0 -0.5 2 2
BMP6/BMPR2/BMPR1A-1B -0.22 0.19 -10000 0 -0.36 334 334
RGMA 0.022 0.063 -10000 0 -0.61 5 5
SMURF1 0.026 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.13 -10000 0 -0.35 47 47
BMP2-4/USAG1 -0.21 0.22 -10000 0 -0.39 292 292
SMAD6/SMURF1/SMAD5 -0.14 0.15 0.3 1 -0.48 26 27
SOSTDC1 -0.34 0.31 -10000 0 -0.61 293 293
BMP7/BMPR2/BMPR1A-1B -0.44 0.26 -10000 0 -0.54 417 417
SKI 0.028 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.018 0.076 -10000 0 -0.57 8 8
HFE2 0.007 0.099 -10000 0 -0.51 18 18
ZFYVE16 0.026 0.009 -10000 0 -10000 0 0
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.042 0.069 -10000 0 -0.4 10 10
SMAD5/SMAD5/SMAD4 -0.15 0.16 0.29 2 -0.48 29 31
MAPK1 0.028 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.42 8 8
BMP7 (homodimer) -0.39 0.3 -10000 0 -0.61 332 332
NUP214 0.028 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.021 0.077 -10000 0 -0.39 15 15
SMAD1/SKI -0.023 0.068 0.34 1 -0.44 1 2
SMAD6 0.029 0.003 -10000 0 -10000 0 0
CTDSP2 0.028 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.037 0.066 -10000 0 -0.33 14 14
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.13 0.27 -10000 0 -0.6 126 126
BMPR2 (homodimer) 0.027 0.006 -10000 0 -10000 0 0
GADD34/PP1CA 0.052 0.019 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.3 0.23 -10000 0 -0.45 344 344
CHRDL1 -0.3 0.32 -10000 0 -0.61 265 265
ENDOFIN/SMAD1 -0.02 0.065 0.34 1 -0.45 1 2
SMAD6-7/SMURF1/SMAD1 0.008 0.068 -10000 0 -0.42 1 1
SMAD6/SMURF1 0.026 0.009 -10000 0 -10000 0 0
BAMBI 0.021 0.065 -10000 0 -0.56 6 6
SMURF2 0.027 0.029 -10000 0 -0.61 1 1
BMP2-4/CHRDL1 -0.18 0.22 -10000 0 -0.39 258 258
BMP2-4/GREM1 -0.056 0.19 -10000 0 -0.38 124 124
SMAD7 0.028 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.065 0.17 -10000 0 -0.57 46 46
SMAD1/SMAD6 -0.022 0.063 -10000 0 -0.45 1 1
TAK1/SMAD6 0.036 0.016 -10000 0 -10000 0 0
BMP7 -0.39 0.3 -10000 0 -0.61 332 332
BMP6 0.018 0.076 -10000 0 -0.57 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.098 0.11 -10000 0 -0.34 27 27
PPM1A 0.027 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.024 0.069 0.34 1 -0.45 1 2
SMAD7/SMURF1 0.037 0.014 -10000 0 -10000 0 0
CTDSPL 0.02 0.013 -10000 0 -10000 0 0
PPP1CA 0.029 0.003 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
CTDSP1 0.027 0.007 -10000 0 -10000 0 0
PPP1R15A 0.029 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.17 -10000 0 -0.46 75 75
CHRD 0.017 0.08 -10000 0 -0.57 9 9
BMPR2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.13 -10000 0 -0.36 48 48
BMP4 0.023 0.049 -10000 0 -0.61 3 3
FST -0.037 0.19 -10000 0 -0.59 52 52
BMP2-4/NOG -0.01 0.14 -10000 0 -0.33 79 79
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.4 0.25 -10000 0 -0.51 396 396
Aurora C signaling

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
INCENP 0.029 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.1 0.17 -9999 0 -0.28 234 234
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.024 0.051 -9999 0 -0.57 1 1
AURKB -0.22 0.27 -9999 0 -0.51 239 239
AURKC 0.026 0.033 -9999 0 -0.5 2 2
Glypican 2 network

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
MDK -0.011 0.14 -9999 0 -0.51 38 38
GPC2 -0.029 0.16 -9999 0 -0.5 52 52
GPC2/Midkine -0.03 0.16 -9999 0 -0.41 77 77
neuron projection morphogenesis -0.03 0.16 -9999 0 -0.4 77 77
FOXM1 transcription factor network

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
NFATC3 -0.11 0.48 0.75 1 -1 61 62
PLK1 -0.039 0.22 -10000 0 -1.5 1 1
BIRC5 -0.063 0.24 -10000 0 -0.74 9 9
HSPA1B -0.11 0.48 0.75 2 -1.1 59 61
MAP2K1 0.024 0.051 -10000 0 -10000 0 0
BRCA2 -0.12 0.48 -10000 0 -1.1 63 63
FOXM1 -0.16 0.59 -10000 0 -1.3 77 77
XRCC1 -0.11 0.48 -10000 0 -1 71 71
FOXM1B/p19 -0.23 0.45 -10000 0 -1.1 72 72
Cyclin D1/CDK4 -0.11 0.45 -10000 0 -0.96 61 61
CDC2 -0.12 0.5 -10000 0 -1.1 77 77
TGFA -0.11 0.44 -10000 0 -0.94 61 61
SKP2 -0.099 0.48 0.68 5 -1 68 73
CCNE1 0.023 0.06 -10000 0 -0.52 6 6
CKS1B -0.11 0.48 0.67 1 -1 65 66
RB1 -0.023 0.27 -10000 0 -0.89 12 12
FOXM1C/SP1 -0.14 0.53 -10000 0 -1.1 78 78
AURKB -0.13 0.28 -10000 0 -1.2 9 9
CENPF -0.13 0.52 0.67 1 -1.1 69 70
CDK4 0.024 0.025 -10000 0 -10000 0 0
MYC -0.097 0.43 -10000 0 -0.91 68 68
CHEK2 0.023 0.057 -10000 0 -0.56 1 1
ONECUT1 -0.12 0.47 -10000 0 -1 71 71
CDKN2A -0.48 0.11 -10000 0 -0.5 489 489
LAMA4 -0.16 0.49 0.75 1 -1.1 72 73
FOXM1B/HNF6 -0.15 0.54 -10000 0 -1.2 68 68
FOS -0.13 0.5 -10000 0 -1.1 74 74
SP1 0.028 0.009 -10000 0 -10000 0 0
CDC25B -0.11 0.48 -10000 0 -1 68 68
response to radiation 0.005 0.033 -10000 0 -10000 0 0
CENPB -0.11 0.48 -10000 0 -1 68 68
CENPA -0.17 0.54 0.66 1 -1.1 90 91
NEK2 -0.15 0.53 0.67 1 -1.1 86 87
HIST1H2BA -0.12 0.48 0.75 1 -1 69 70
CCNA2 -0.076 0.22 -10000 0 -0.52 100 100
EP300 0.027 0.029 -10000 0 -0.61 1 1
CCNB1/CDK1 -0.14 0.54 -10000 0 -1.2 71 71
CCNB2 -0.15 0.53 0.75 1 -1.1 95 96
CCNB1 -0.12 0.51 -10000 0 -1.1 70 70
ETV5 -0.11 0.48 -10000 0 -1 71 71
ESR1 -0.12 0.48 0.75 1 -1.1 62 63
CCND1 -0.11 0.45 -10000 0 -0.98 63 63
GSK3A 0.025 0.044 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.013 0.17 -10000 0 -0.35 93 93
CDK2 0.029 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.005 0.04 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.51 -10000 0 -1.1 75 75
GAS1 -0.16 0.52 -10000 0 -1.1 89 89
MMP2 -0.11 0.48 0.75 1 -1 69 70
RB1/FOXM1C -0.12 0.48 -10000 0 -1 69 69
CREBBP 0.028 0.006 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.17 0.3 -10000 0 -0.47 214 214
MAP4K1 -0.19 0.26 -10000 0 -0.5 207 207
MAP3K8 0.026 0.033 -10000 0 -0.5 2 2
PRKCB 0.022 0.057 -10000 0 -0.55 5 5
DBNL 0.026 0.009 -10000 0 -10000 0 0
CRKL 0.028 0.004 -10000 0 -10000 0 0
MAP3K1 -0.06 0.13 -10000 0 -0.41 37 37
JUN 0.015 0.11 0.34 1 -0.58 12 13
MAP3K7 -0.062 0.13 -10000 0 -0.41 37 37
GRAP2 -0.008 0.14 -10000 0 -0.51 35 35
CRK 0.028 0.005 -10000 0 -10000 0 0
MAP2K4 -0.025 0.16 0.29 29 -0.39 36 65
LAT -0.12 0.24 -10000 0 -0.5 141 141
LCP2 -0.009 0.12 -10000 0 -0.5 29 29
MAPK8 0.012 0.12 -10000 0 -0.6 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.066 0.14 -10000 0 -0.43 40 40
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.16 0.28 -10000 0 -0.6 117 117
Caspase cascade in apoptosis

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
TOP1 -0.062 0.15 -10000 0 -0.32 81 81
ACTA1 -0.1 0.18 -10000 0 -0.4 107 107
NUMA1 -0.063 0.15 0.23 1 -0.33 77 78
SPTAN1 -0.1 0.18 0.26 1 -0.4 107 108
LIMK1 -0.083 0.19 0.33 2 -0.4 100 102
BIRC3 -0.054 0.19 -10000 0 -0.5 79 79
BIRC2 0.028 0.004 -10000 0 -10000 0 0
BAX 0.029 0.003 -10000 0 -10000 0 0
CASP10 -0.16 0.24 -10000 0 -0.46 181 181
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.003 -10000 0 -10000 0 0
PTK2 -0.066 0.15 0.23 1 -0.33 82 83
DIABLO 0.028 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.098 0.18 0.26 1 -0.4 107 108
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.005 -10000 0 -10000 0 0
GSN -0.1 0.18 0.26 1 -0.4 107 108
MADD 0.029 0.003 -10000 0 -10000 0 0
TFAP2A -0.29 0.29 -10000 0 -0.52 287 287
BID -0.064 0.11 -10000 0 -0.25 108 108
MAP3K1 -0.025 0.068 -10000 0 -0.25 1 1
TRADD 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.094 0.18 0.3 3 -0.4 106 109
CASP9 0.028 0.006 -10000 0 -10000 0 0
DNA repair 0.015 0.077 0.3 13 -0.18 2 15
neuron apoptosis 0.005 0.12 -10000 0 -0.62 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.084 0.18 -10000 0 -0.4 84 84
APAF1 0.028 0.005 -10000 0 -10000 0 0
CASP6 -0.023 0.14 0.36 2 -0.9 7 9
TRAF2 0.028 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.095 0.17 0.4 1 -0.41 81 82
CASP7 0.027 0.1 -10000 0 -0.33 8 8
KRT18 0.012 0.038 -10000 0 -10000 0 0
apoptosis -0.094 0.18 0.42 2 -0.4 91 93
DFFA -0.099 0.18 -10000 0 -0.4 107 107
DFFB -0.099 0.18 -10000 0 -0.4 107 107
PARP1 -0.015 0.078 0.18 2 -0.3 13 15
actin filament polymerization 0.073 0.18 0.4 72 -0.4 2 74
TNF 0.018 0.073 -10000 0 -0.56 8 8
CYCS -0.04 0.095 0.18 6 -0.19 97 103
SATB1 -0.022 0.14 0.43 2 -0.83 7 9
SLK -0.099 0.18 0.34 1 -0.4 108 109
p15 BID/BAX -0.043 0.11 -10000 0 -0.25 2 2
CASP2 0.024 0.08 0.22 36 -0.44 2 38
JNK cascade 0.024 0.068 0.25 1 -10000 0 1
CASP3 -0.11 0.19 -10000 0 -0.42 107 107
LMNB2 0.025 0.11 0.36 11 -0.54 6 17
RIPK1 0.028 0.005 -10000 0 -10000 0 0
CASP4 0.028 0.003 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.018 0.12 -10000 0 -0.28 75 75
negative regulation of DNA binding -0.28 0.29 -10000 0 -0.52 287 287
stress fiber formation -0.099 0.18 0.34 1 -0.4 108 109
GZMB -0.18 0.28 -10000 0 -0.53 185 185
CASP1 0.019 0.002 -10000 0 -10000 0 0
LMNB1 0.02 0.099 0.37 9 -0.42 6 15
APP 0.004 0.12 -10000 0 -0.63 14 14
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.002 -10000 0 -10000 0 0
VIM -0.092 0.17 0.29 1 -0.39 90 91
LMNA 0.023 0.11 0.36 11 -0.38 11 22
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.014 0.059 -10000 0 -0.47 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.099 0.18 0.3 1 -0.4 107 108
APAF-1/Caspase 9 -0.014 0.13 -10000 0 -0.59 22 22
nuclear fragmentation during apoptosis -0.062 0.15 0.23 1 -0.33 77 78
CFL2 -0.077 0.18 0.4 2 -0.4 72 74
GAS2 -0.11 0.18 0.39 1 -0.4 116 117
positive regulation of apoptosis 0.027 0.11 0.36 11 -0.46 7 18
PRF1 -0.11 0.23 -10000 0 -0.5 131 131
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.013 0.097 -10000 0 -0.59 13 13
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.044 -10000 0 -0.54 3 3
TCEB1 0.027 0.007 -10000 0 -10000 0 0
HIF1A/p53 -0.061 0.077 0.26 1 -0.44 15 16
HIF1A -0.067 0.078 -10000 0 -0.46 15 15
COPS5 0.027 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.05 -10000 0 -0.33 1 1
FIH (dimer) 0.028 0.006 -10000 0 -10000 0 0
CDKN2A -0.49 0.11 -10000 0 -0.51 489 489
ARNT/IPAS 0.028 0.075 -10000 0 -0.43 13 13
HIF1AN 0.028 0.006 -10000 0 -10000 0 0
GNB2L1 0.022 0.012 -10000 0 -10000 0 0
HIF1A/ARNT -0.06 0.079 0.26 1 -0.44 15 16
CUL2 0.028 0.004 -10000 0 -10000 0 0
OS9 0.028 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.039 0.039 -10000 0 -0.33 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.053 0.077 -10000 0 -0.44 15 15
PHD1-3/OS9 -0.23 0.11 -10000 0 -0.36 21 21
HIF1A/RACK1/Elongin B/Elongin C -0.041 0.078 -10000 0 -0.42 14 14
VHL 0.02 0.019 -10000 0 -0.3 1 1
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.058 0.078 -10000 0 -0.44 15 15
EGLN3 -0.45 0.17 -10000 0 -0.51 451 451
EGLN2 0.029 0.003 -10000 0 -10000 0 0
EGLN1 0.028 0.006 -10000 0 -10000 0 0
TP53 0.028 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.13 0.26 -10000 0 -0.52 149 149
ARNT 0.027 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.028 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.3 0.095 -10000 0 -0.32 435 435
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.42 0.39 -10000 0 -1.1 69 69
STAT6 (cleaved dimer) -0.46 0.41 -10000 0 -1.1 110 110
IGHG1 -0.15 0.15 -10000 0 -0.44 10 10
IGHG3 -0.41 0.38 -10000 0 -0.99 93 93
AKT1 -0.22 0.24 -10000 0 -0.68 41 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.19 -10000 0 -0.62 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.24 -10000 0 -0.74 35 35
THY1 -0.42 0.4 -10000 0 -1.1 74 74
MYB -0.12 0.24 -10000 0 -0.51 139 139
HMGA1 0.027 0.024 -10000 0 -0.5 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.28 -10000 0 -0.75 81 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.24 -10000 0 -0.73 35 35
SP1 0.024 0.03 -10000 0 -10000 0 0
INPP5D 0.023 0.047 -10000 0 -0.5 4 4
SOCS5 0.039 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.44 0.41 -10000 0 -1.1 99 99
SOCS1 -0.3 0.28 -10000 0 -0.75 54 54
SOCS3 -0.25 0.24 -10000 0 -0.72 34 34
FCER2 -0.36 0.34 -10000 0 -0.96 63 63
PARP14 0.027 0.008 -10000 0 -10000 0 0
CCL17 -0.43 0.4 -10000 0 -1.1 72 72
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.21 -10000 0 -0.64 36 36
T cell proliferation -0.43 0.41 -10000 0 -1.1 83 83
IL4R/JAK1 -0.42 0.39 -10000 0 -1 83 83
EGR2 -0.44 0.41 -10000 0 -1.1 79 79
JAK2 -0.022 0.038 -10000 0 -10000 0 0
JAK3 -0.079 0.22 -10000 0 -0.51 103 103
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
JAK1 0.006 0.02 -10000 0 -10000 0 0
COL1A2 -0.16 0.18 -10000 0 -0.62 24 24
CCL26 -0.41 0.4 -10000 0 -1.1 70 70
IL4R -0.44 0.42 -10000 0 -1.1 81 81
PTPN6 0.039 0.014 -10000 0 -10000 0 0
IL13RA2 -0.49 0.48 -10000 0 -1.3 98 98
IL13RA1 -0.022 0.04 -10000 0 -10000 0 0
IRF4 -0.17 0.24 -10000 0 -0.66 53 53
ARG1 -0.14 0.17 -10000 0 -0.74 8 8
CBL -0.28 0.27 -10000 0 -0.72 76 76
GTF3A -0.001 0.045 -10000 0 -10000 0 0
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
IL13RA1/JAK2 -0.027 0.053 -10000 0 -10000 0 0
IRF4/BCL6 -0.15 0.23 -10000 0 -0.63 43 43
CD40LG -0.037 0.17 -10000 0 -0.55 51 51
MAPK14 -0.28 0.27 -10000 0 -0.72 71 71
mitosis -0.22 0.23 -10000 0 -0.65 41 41
STAT6 -0.48 0.44 -10000 0 -1.2 90 90
SPI1 -0.042 0.18 -10000 0 -0.5 70 70
RPS6KB1 -0.2 0.23 -10000 0 -0.65 30 30
STAT6 (dimer) -0.48 0.45 -10000 0 -1.2 90 90
STAT6 (dimer)/PARP14 -0.44 0.42 -10000 0 -1.1 91 91
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.23 0.24 -10000 0 -0.67 49 49
FRAP1 -0.22 0.24 -10000 0 -0.68 41 41
LTA -0.48 0.42 -10000 0 -1.1 90 90
FES 0.026 0.04 -10000 0 -0.61 2 2
T-helper 1 cell differentiation 0.47 0.44 1.1 90 -10000 0 90
CCL11 -0.63 0.56 -10000 0 -1.3 195 195
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.23 -10000 0 -0.66 34 34
IL2RG -0.005 0.14 -10000 0 -0.51 34 34
IL10 -0.43 0.4 -10000 0 -1.2 48 48
IRS1 0.022 0.057 -10000 0 -0.61 4 4
IRS2 0.02 0.068 -10000 0 -0.52 8 8
IL4 -0.11 0.13 -10000 0 -1.1 3 3
IL5 -0.39 0.41 -10000 0 -1.1 63 63
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.33 -10000 0 -0.91 53 53
COL1A1 -0.27 0.27 -10000 0 -0.66 94 94
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.42 0.4 -10000 0 -1.1 61 61
IL2R gamma/JAK3 -0.066 0.22 -10000 0 -0.46 107 107
TFF3 -0.44 0.42 -10000 0 -1.1 80 80
ALOX15 -0.43 0.4 -10000 0 -1.1 68 68
MYBL1 -0.004 0.12 -10000 0 -0.5 30 30
T-helper 2 cell differentiation -0.38 0.35 -10000 0 -0.92 85 85
SHC1 0.027 0.006 -10000 0 -10000 0 0
CEBPB 0.021 0.069 -10000 0 -0.52 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.23 -10000 0 -0.69 37 37
mol:PI-3-4-5-P3 -0.22 0.24 -10000 0 -0.68 41 41
PI3K -0.24 0.26 -10000 0 -0.72 42 42
DOK2 -0.007 0.13 -10000 0 -0.51 31 31
ETS1 0.039 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.21 -10000 0 -0.63 38 38
ITGB3 -0.43 0.4 -10000 0 -1.2 58 58
PIGR -0.77 0.66 -10000 0 -1.4 247 247
IGHE 0.032 0.068 0.29 5 -0.34 1 6
MAPKKK cascade -0.18 0.2 -10000 0 -0.61 38 38
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.43 0.4 -10000 0 -1.1 67 67
RETNLB -0.43 0.4 -10000 0 -1.1 85 85
SELP -0.45 0.44 -10000 0 -1.3 67 67
AICDA -0.48 0.41 -10000 0 -1 114 114
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.047 -10000 0 -0.5 4 4
CCL5 -0.2 0.26 -10000 0 -0.5 217 217
SDCBP 0.027 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.12 0.15 0.25 4 -0.42 51 55
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.11 0.14 -10000 0 -0.42 44 44
Syndecan-1/Syntenin -0.1 0.15 0.34 2 -0.43 42 44
MAPK3 -0.091 0.14 0.25 1 -0.46 22 23
HGF/MET 0.019 0.091 -10000 0 -0.42 20 20
TGFB1/TGF beta receptor Type II 0.024 0.047 -10000 0 -0.5 4 4
BSG 0.027 0.024 -10000 0 -0.5 1 1
keratinocyte migration -0.1 0.14 -10000 0 -0.42 44 44
Syndecan-1/RANTES -0.21 0.2 0.35 3 -0.42 181 184
Syndecan-1/CD147 -0.092 0.15 0.28 1 -0.49 22 23
Syndecan-1/Syntenin/PIP2 -0.1 0.14 0.26 1 -0.41 42 43
LAMA5 0.027 0.029 -10000 0 -0.61 1 1
positive regulation of cell-cell adhesion -0.099 0.14 -10000 0 -0.4 42 42
MMP7 -0.082 0.24 -10000 0 -0.6 89 89
HGF 0.003 0.11 -10000 0 -0.54 20 20
Syndecan-1/CASK -0.11 0.14 0.2 1 -0.4 51 52
Syndecan-1/HGF/MET -0.099 0.16 -10000 0 -0.48 35 35
regulation of cell adhesion -0.088 0.13 0.52 1 -0.47 18 19
HPSE 0.026 0.04 -10000 0 -0.61 2 2
positive regulation of cell migration -0.12 0.15 0.25 4 -0.42 51 55
SDC1 -0.12 0.15 0.24 3 -0.43 51 54
Syndecan-1/Collagen -0.12 0.15 0.25 4 -0.42 51 55
PPIB 0.029 0.003 -10000 0 -10000 0 0
MET 0.024 0.034 -10000 0 -0.5 2 2
PRKACA 0.029 0.002 -10000 0 -10000 0 0
MMP9 -0.21 0.26 -10000 0 -0.5 230 230
MAPK1 -0.09 0.14 0.26 2 -0.46 22 24
homophilic cell adhesion -0.11 0.15 0.26 3 -0.42 51 54
MMP1 -0.081 0.22 -10000 0 -0.54 99 99
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.008 -10000 0 -10000 0 0
LAT2 -0.061 0.13 -10000 0 -0.4 39 39
AP1 -0.028 0.14 -10000 0 -0.52 10 10
mol:PIP3 -0.072 0.27 0.44 40 -0.52 81 121
IKBKB -0.006 0.18 0.34 62 -0.29 31 93
AKT1 -0.058 0.17 0.42 13 -0.45 20 33
IKBKG -0.007 0.18 0.32 63 -0.3 29 92
MS4A2 -0.088 0.22 -10000 0 -0.51 111 111
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
MAP3K1 -0.033 0.18 0.33 41 -0.39 13 54
mol:Ca2+ -0.044 0.22 0.39 43 -0.38 81 124
LYN 0.024 0.011 -10000 0 -10000 0 0
CBLB -0.042 0.093 -10000 0 -0.34 9 9
SHC1 0.027 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.039 0.034 -10000 0 -0.32 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.023 0.047 -10000 0 -0.5 4 4
PLD2 -0.083 0.18 0.34 17 -0.51 20 37
PTPN13 -0.016 0.14 0.39 3 -0.69 8 11
PTPN11 0.025 0.014 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0 0.16 0.41 33 -0.36 2 35
SYK 0.023 0.034 -10000 0 -0.47 2 2
GRB2 0.028 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.21 -10000 0 -0.52 92 92
LAT -0.11 0.16 -10000 0 -0.39 87 87
PAK2 -0.053 0.17 0.35 21 -0.36 61 82
NFATC2 -0.03 0.068 -10000 0 -0.54 3 3
HRAS -0.067 0.17 0.32 8 -0.38 69 77
GAB2 0.029 0.003 -10000 0 -10000 0 0
PLA2G1B -0.21 0.38 -10000 0 -0.8 148 148
Fc epsilon R1 -0.11 0.2 -10000 0 -0.35 201 201
Antigen/IgE/Fc epsilon R1 -0.096 0.19 -10000 0 -0.32 200 200
mol:GDP -0.084 0.18 0.25 1 -0.42 73 74
JUN 0.028 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.029 -10000 0 -0.61 1 1
FOS 0.012 0.096 -10000 0 -0.6 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.042 0.099 -10000 0 -0.32 17 17
CHUK -0.008 0.18 0.33 61 -0.29 32 93
KLRG1 -0.045 0.098 -10000 0 -0.35 9 9
VAV1 -0.097 0.16 -10000 0 -0.38 93 93
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.041 0.096 -10000 0 -0.35 10 10
negative regulation of mast cell degranulation -0.034 0.1 0.23 1 -0.4 9 10
BTK -0.048 0.12 -10000 0 -0.37 13 13
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.055 0.14 -10000 0 -0.41 23 23
GAB2/PI3K/SHP2 -0.093 0.14 -10000 0 -0.49 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.042 0.1 -10000 0 -0.32 24 24
RAF1 -0.24 0.42 -10000 0 -0.9 148 148
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.24 -10000 0 -0.54 87 87
FCER1G -0.07 0.21 -10000 0 -0.51 93 93
FCER1A 0.001 0.12 -10000 0 -0.6 19 19
Antigen/IgE/Fc epsilon R1/Fyn -0.083 0.18 -10000 0 -0.47 30 30
MAPK3 -0.21 0.39 -10000 0 -0.81 148 148
MAPK1 -0.21 0.39 -10000 0 -0.81 148 148
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
MAPK8 0.01 0.14 -10000 0 -0.7 14 14
DUSP1 0.02 0.026 -10000 0 -0.5 1 1
NF-kappa-B/RelA -0.025 0.077 -10000 0 -0.26 1 1
actin cytoskeleton reorganization -0.013 0.13 0.4 3 -0.66 9 12
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.081 0.18 0.26 1 -0.42 71 72
FER -0.04 0.095 -10000 0 -0.37 10 10
RELA 0.029 0.003 -10000 0 -10000 0 0
ITK -0.041 0.092 -10000 0 -0.24 12 12
SOS1 0.028 0.005 -10000 0 -10000 0 0
PLCG1 -0.063 0.2 0.38 14 -0.43 71 85
cytokine secretion -0.025 0.049 -10000 0 -10000 0 0
SPHK1 -0.056 0.12 -10000 0 -0.41 26 26
PTK2 -0.014 0.14 0.4 3 -0.71 9 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.19 -10000 0 -0.53 55 55
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.036 0.26 0.4 57 -0.5 51 108
MAP2K2 -0.22 0.39 -10000 0 -0.83 148 148
MAP2K1 -0.22 0.39 -10000 0 -0.83 148 148
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.042 0.1 0.29 2 -0.36 7 9
MAP2K4 0.016 0.14 -10000 0 -0.82 12 12
Fc epsilon R1/FcgammaRIIB -0.13 0.25 -10000 0 -0.56 88 88
mol:Choline -0.082 0.17 0.34 17 -0.5 20 37
SHC/Grb2/SOS1 -0.012 0.11 -10000 0 -0.39 2 2
FYN 0.027 0.008 -10000 0 -10000 0 0
DOK1 0.028 0.005 -10000 0 -10000 0 0
PXN -0.006 0.14 0.42 10 -0.67 8 18
HCLS1 -0.047 0.11 -10000 0 -0.41 18 18
PRKCB -0.026 0.22 0.37 60 -0.36 66 126
FCGR2B -0.066 0.2 -10000 0 -0.5 89 89
IGHE -0.003 0.01 -10000 0 -10000 0 0
KLRG1/SHIP -0.035 0.11 0.23 1 -0.4 9 10
LCP2 -0.009 0.12 -10000 0 -0.51 29 29
PLA2G4A -0.042 0.098 -10000 0 -0.36 12 12
RASA1 0.024 0.03 -10000 0 -0.61 1 1
mol:Phosphatidic acid -0.082 0.17 0.34 17 -0.5 20 37
IKK complex 0.009 0.16 0.32 63 -0.24 3 66
WIPF1 0.028 0.006 -10000 0 -10000 0 0
Arf6 signaling events

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.029 0.04 -10000 0 -0.38 4 4
ARNO/beta Arrestin1-2 0.022 0.061 -10000 0 -0.78 1 1
EGFR 0.019 0.06 -10000 0 -0.52 6 6
EPHA2 0.026 0.029 -10000 0 -0.61 1 1
USP6 0.027 0.024 -10000 0 -0.5 1 1
IQSEC1 0.02 0.013 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.39 0.16 -10000 0 -0.43 454 454
ARRB2 -0.002 0.061 -10000 0 -0.21 36 36
mol:GTP 0.003 0.043 0.18 7 -0.16 6 13
ARRB1 0.029 0.003 -10000 0 -10000 0 0
FBXO8 0.028 0.004 -10000 0 -10000 0 0
TSHR -0.034 0.17 -10000 0 -0.5 58 58
EGF -0.54 0.19 -10000 0 -0.61 460 460
somatostatin receptor activity 0 0 0.001 19 -0.001 26 45
ARAP2 0.026 0.04 -10000 0 -0.61 2 2
mol:GDP -0.044 0.097 0.23 7 -0.3 31 38
mol:PI-3-4-5-P3 0 0 0.001 9 -0.001 11 20
ITGA2B 0.009 0.099 -10000 0 -0.51 18 18
ARF6 0.027 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.039 -10000 0 -0.35 2 2
ADAP1 0.021 0.057 -10000 0 -0.61 4 4
KIF13B 0.026 0.009 -10000 0 -10000 0 0
HGF/MET 0.019 0.091 -10000 0 -0.42 20 20
PXN 0.028 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.062 0.11 0.28 12 -0.31 30 42
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.32 0.14 -10000 0 -0.38 411 411
ADRB2 0.019 0.041 -10000 0 -0.61 2 2
receptor agonist activity 0 0 0 20 0 15 35
actin filament binding 0 0 0.001 20 -0.001 29 49
SRC 0.028 0.006 -10000 0 -10000 0 0
ITGB3 0.024 0.049 -10000 0 -0.61 3 3
GNAQ 0.028 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 27 -0.001 14 41
ARF6/GDP -0.041 0.11 0.27 5 -0.38 19 24
ARF6/GDP/GULP/ACAP1 -0.12 0.17 0.26 1 -0.4 71 72
alphaIIb/beta3 Integrin/paxillin/GIT1 0.056 0.073 -10000 0 -0.35 4 4
ACAP1 -0.18 0.26 -10000 0 -0.5 195 195
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0 0.083 -10000 0 -0.3 36 36
EFNA1 0.026 0.024 -10000 0 -0.5 1 1
HGF 0.003 0.11 -10000 0 -0.54 20 20
CYTH3 0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.017 0.045 -10000 0 -0.99 1 1
NCK1 0.026 0.029 -10000 0 -0.61 1 1
fibronectin binding 0 0 0.001 31 -0.001 14 45
endosomal lumen acidification 0 0 0.001 3 -0.001 26 29
microtubule-based process 0 0 -10000 0 -0.001 1 1
GULP1 0.007 0.11 -10000 0 -0.59 17 17
GNAQ/ARNO 0.032 0.044 -10000 0 -0.93 1 1
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0.001 2 0 8 10
MET 0.024 0.034 -10000 0 -0.5 2 2
GNA14 0.02 0.069 -10000 0 -0.61 6 6
GNA15 0.013 0.09 -10000 0 -0.5 15 15
GIT1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 22 -0.001 20 42
GNA11 0.025 0.049 -10000 0 -0.61 3 3
LHCGR -0.031 0.13 -10000 0 -0.5 35 35
AGTR1 -0.003 0.14 -10000 0 -0.6 25 25
desensitization of G-protein coupled receptor protein signaling pathway 0 0.082 -10000 0 -0.3 36 36
IPCEF1/ARNO -0.24 0.11 -10000 0 -0.58 6 6
alphaIIb/beta3 Integrin 0.024 0.084 -10000 0 -0.38 21 21
Effects of Botulinum toxin

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
STX1A 0.007 0.037 0.19 2 -0.39 4 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.074 -10000 0 -0.39 15 15
STXBP1 0.027 0.029 -10000 0 -0.61 1 1
ACh/CHRNA1 -0.13 0.17 -10000 0 -0.32 217 217
RAB3GAP2/RIMS1/UNC13B 0.04 0.067 -10000 0 -0.33 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.009 0.097 -10000 0 -0.54 15 15
mol:ACh 0.004 0.043 0.1 43 -0.14 3 46
RAB3GAP2 0.028 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.077 -10000 0 -0.35 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.13 0.17 -10000 0 -0.32 217 217
UNC13B 0.028 0.006 -10000 0 -10000 0 0
CHRNA1 -0.2 0.26 -10000 0 -0.5 217 217
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.048 0.16 -10000 0 -0.4 80 80
SNAP25 -0.018 0.063 -10000 0 -0.17 71 71
VAMP2 0.007 0.001 -10000 0 -10000 0 0
SYT1 -0.071 0.23 -10000 0 -0.6 80 80
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.022 0.038 -10000 0 -0.34 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.077 -10000 0 -0.35 8 8
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.015 0.15 -10000 0 -0.71 19 19
oxygen homeostasis -0.003 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.044 -10000 0 -0.54 3 3
TCEB1 0.027 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.12 0.12 -10000 0 -0.41 9 9
EPO -0.25 0.27 -10000 0 -0.68 75 75
FIH (dimer) 0.02 0.022 -10000 0 -10000 0 0
APEX1 0.02 0.022 -10000 0 -10000 0 0
SERPINE1 -0.21 0.27 -10000 0 -0.71 63 63
FLT1 0.003 0.12 -10000 0 -0.73 9 9
ADORA2A -0.2 0.24 0.48 3 -0.67 42 45
germ cell development -0.26 0.3 -10000 0 -0.66 126 126
SLC11A2 -0.19 0.24 -10000 0 -0.67 38 38
BHLHE40 -0.2 0.23 -10000 0 -0.67 39 39
HIF1AN 0.02 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.18 0.18 -10000 0 -0.47 32 32
ETS1 0.042 0.011 -10000 0 -10000 0 0
CITED2 -0.034 0.17 -10000 0 -0.72 21 21
KDR 0.012 0.097 -10000 0 -0.78 6 6
PGK1 -0.19 0.24 -10000 0 -0.67 40 40
SIRT1 0.027 0.006 -10000 0 -10000 0 0
response to hypoxia -0.002 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.21 0.29 -10000 0 -0.78 43 43
EPAS1 -0.16 0.12 -10000 0 -0.37 42 42
SP1 0.034 0.012 -10000 0 -10000 0 0
ABCG2 -0.19 0.24 -10000 0 -0.68 40 40
EFNA1 -0.19 0.24 -10000 0 -0.67 41 41
FXN -0.2 0.24 0.48 2 -0.66 42 44
POU5F1 -0.27 0.31 -10000 0 -0.68 128 128
neuron apoptosis 0.21 0.28 0.76 43 -10000 0 43
EP300 0.027 0.029 -10000 0 -0.61 1 1
EGLN3 -0.45 0.18 -10000 0 -0.52 451 451
EGLN2 0.022 0.02 -10000 0 -10000 0 0
EGLN1 0.02 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.036 0.041 -10000 0 -0.33 3 3
VHL 0.02 0.019 -10000 0 -0.3 1 1
ARNT 0.019 0.023 -10000 0 -10000 0 0
SLC2A1 -0.21 0.26 0.45 2 -0.73 48 50
TWIST1 -0.2 0.24 0.48 2 -0.64 45 47
ELK1 0.035 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.14 0.16 -10000 0 -0.5 11 11
VEGFA -0.28 0.31 -10000 0 -0.68 138 138
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.024 0.044 -10000 0 -10000 0 0
NFATC2 -0.024 0.052 -10000 0 -0.42 3 3
NFATC3 -0.024 0.043 -10000 0 -10000 0 0
CD40LG -0.25 0.3 0.4 2 -0.71 101 103
PTGS2 -0.24 0.29 0.4 1 -0.66 100 101
JUNB 0.026 0.04 -10000 0 -0.61 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.031 -10000 0 -10000 0 0
CaM/Ca2+ -0.013 0.031 -10000 0 -10000 0 0
CALM1 0.003 0.027 -10000 0 -10000 0 0
JUN 0.002 0.028 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.015 -10000 0 -10000 0 0
FOSL1 0.004 0.11 -10000 0 -0.5 24 24
CREM 0.028 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.18 -10000 0 -0.53 27 27
FOS -0.013 0.096 -10000 0 -0.61 12 12
IFNG -0.32 0.36 0.4 1 -0.69 217 218
AP-1/NFAT1-c-4 -0.27 0.33 -10000 0 -0.77 98 98
FASLG -0.33 0.35 0.4 1 -0.69 220 221
NFAT1-c-4/ICER1 -0.062 0.1 -10000 0 -0.44 3 3
IL2RA -0.27 0.32 0.4 1 -0.74 107 108
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.22 0.27 0.4 1 -0.67 87 88
JunB/Fra1/NFAT1-c-4 -0.065 0.12 -10000 0 -0.42 9 9
IL4 -0.22 0.26 0.4 1 -0.65 82 83
IL2 -0.006 0.12 -10000 0 -0.86 7 7
IL3 -0.013 0.076 -10000 0 -0.69 1 1
FKBP1A 0.028 0.005 -10000 0 -10000 0 0
BATF3 -0.018 0.15 -10000 0 -0.5 44 44
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.014 -10000 0 -10000 0 0
VLDLR 0.028 0.006 -10000 0 -10000 0 0
CRKL 0.028 0.004 -10000 0 -10000 0 0
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
FYN 0.027 0.008 -10000 0 -10000 0 0
ITGA3 0.027 0.024 -10000 0 -0.5 1 1
RELN/VLDLR/Fyn -0.083 0.2 -10000 0 -0.38 153 153
MAPK8IP1/MKK7/MAP3K11/JNK1 0.077 0.045 -10000 0 -0.49 2 2
AKT1 -0.063 0.13 -10000 0 -0.37 13 13
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.028 0.005 -10000 0 -10000 0 0
DAB1 0.012 0.08 -10000 0 -0.5 12 12
RELN/LRP8/DAB1 -0.082 0.18 -10000 0 -0.35 162 162
LRPAP1/LRP8 0.04 0.02 -10000 0 -0.36 1 1
RELN/LRP8/DAB1/Fyn -0.069 0.18 -10000 0 -0.34 147 147
DAB1/alpha3/beta1 Integrin -0.06 0.17 -10000 0 -0.54 1 1
long-term memory -0.098 0.2 -10000 0 -0.56 18 18
DAB1/LIS1 -0.055 0.18 -10000 0 -0.56 1 1
DAB1/CRLK/C3G -0.061 0.17 -10000 0 -0.54 1 1
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
DAB1/NCK2 -0.055 0.18 -10000 0 -0.56 1 1
ARHGEF2 0.027 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.047 0.19 -10000 0 -0.53 68 68
CDK5R1 0.028 0.004 -10000 0 -10000 0 0
RELN -0.16 0.29 -10000 0 -0.61 153 153
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
RELN/LRP8/Fyn -0.083 0.2 -10000 0 -0.38 153 153
GRIN2A/RELN/LRP8/DAB1/Fyn -0.1 0.2 -10000 0 -0.57 20 20
MAPK8 0.027 0.029 -10000 0 -0.61 1 1
RELN/VLDLR/DAB1 -0.083 0.18 -10000 0 -0.35 161 161
ITGB1 0.028 0.004 -10000 0 -10000 0 0
MAP1B -0.083 0.17 -10000 0 -0.34 130 130
RELN/LRP8 -0.082 0.2 -10000 0 -0.38 153 153
GRIN2B/RELN/LRP8/DAB1/Fyn -0.061 0.19 -10000 0 -0.34 130 130
PI3K 0.036 0.034 -10000 0 -0.45 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.041 0.02 -10000 0 -0.36 1 1
RAP1A -0.055 0.17 0.4 7 -0.51 1 8
PAFAH1B1 0.028 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.04 -10000 0 -0.61 2 2
CRLK/C3G 0.041 0.009 -10000 0 -10000 0 0
GRIN2B 0.023 0.034 -10000 0 -0.5 2 2
NCK2 0.028 0.005 -10000 0 -10000 0 0
neuron differentiation -0.035 0.13 -10000 0 -0.38 29 29
neuron adhesion -0.048 0.17 0.38 10 -0.49 1 11
LRP8 0.027 0.024 -10000 0 -0.5 1 1
GSK3B -0.058 0.12 -10000 0 -0.35 9 9
RELN/VLDLR/DAB1/Fyn -0.07 0.18 -10000 0 -0.33 148 148
MAP3K11 0.027 0.028 -10000 0 -0.61 1 1
RELN/VLDLR/DAB1/P13K -0.067 0.14 -10000 0 -0.28 138 138
CDK5 0.026 0.009 -10000 0 -10000 0 0
MAPT 0.01 0.096 0.72 5 -0.57 6 11
neuron migration -0.067 0.18 0.45 4 -0.49 2 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.035 0.13 -10000 0 -0.38 29 29
RELN/VLDLR -0.064 0.19 -10000 0 -0.35 148 148
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.17 -10000 0 -0.55 27 27
IHH -0.075 0.18 -10000 0 -0.65 44 44
SHH Np/Cholesterol/GAS1 0.003 0.093 -10000 0 -0.35 29 29
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.003 0.092 0.35 29 -10000 0 29
SMO/beta Arrestin2 -0.076 0.14 -10000 0 -0.49 26 26
SMO -0.086 0.14 -10000 0 -0.51 25 25
AKT1 -0.034 0.11 -10000 0 -0.49 15 15
ARRB2 0.027 0.029 -10000 0 -0.62 1 1
BOC 0.027 0.008 -10000 0 -10000 0 0
ADRBK1 0.029 0.003 -10000 0 -10000 0 0
heart looping -0.085 0.14 -10000 0 -0.5 25 25
STIL -0.062 0.12 -10000 0 -0.4 27 27
DHH N/PTCH2 0.01 0.11 -10000 0 -0.39 35 35
DHH N/PTCH1 -0.094 0.14 -10000 0 -0.47 31 31
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
DHH 0.014 0.093 -10000 0 -0.61 11 11
PTHLH -0.24 0.24 -10000 0 -0.74 35 35
determination of left/right symmetry -0.085 0.14 -10000 0 -0.5 25 25
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
skeletal system development -0.24 0.23 -10000 0 -0.73 35 35
IHH N/Hhip -0.15 0.24 -10000 0 -0.5 153 153
DHH N/Hhip -0.087 0.22 -10000 0 -0.45 129 129
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.085 0.14 -10000 0 -0.5 25 25
pancreas development -0.12 0.27 -10000 0 -0.59 126 126
HHAT 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.036 0.034 -10000 0 -0.45 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.14 -10000 0 -0.56 31 31
somite specification -0.085 0.14 -10000 0 -0.5 25 25
SHH Np/Cholesterol/PTCH1 -0.074 0.12 -10000 0 -0.42 27 27
SHH Np/Cholesterol/PTCH2 0.008 0.08 -10000 0 -0.3 31 31
SHH Np/Cholesterol/Megalin -0.004 0.11 -10000 0 -0.39 35 35
SHH 0.009 0.066 -10000 0 -0.45 10 10
catabolic process -0.11 0.14 -10000 0 -0.48 32 32
SMO/Vitamin D3 -0.076 0.13 -10000 0 -0.46 27 27
SHH Np/Cholesterol/Hhip -0.064 0.17 -10000 0 -0.36 112 112
LRP2 -0.021 0.17 -10000 0 -0.56 42 42
receptor-mediated endocytosis -0.089 0.15 -10000 0 -0.62 17 17
SHH Np/Cholesterol/BOC 0.02 0.054 -10000 0 -0.35 10 10
SHH Np/Cholesterol/CDO -0.011 0.1 -10000 0 -0.29 60 60
mesenchymal cell differentiation 0.064 0.16 0.36 112 -10000 0 112
mol:Vitamin D3 -0.069 0.13 -10000 0 -0.42 27 27
IHH N/PTCH2 -0.053 0.15 -10000 0 -0.42 67 67
CDON -0.032 0.17 -10000 0 -0.5 58 58
IHH N/PTCH1 -0.11 0.14 -10000 0 -0.49 32 32
Megalin/LRPAP1 0.004 0.12 -10000 0 -0.45 34 34
PTCH2 0.002 0.12 -10000 0 -0.5 25 25
SHH Np/Cholesterol 0.01 0.052 -10000 0 -0.35 10 10
PTCH1 -0.11 0.14 -10000 0 -0.48 32 32
HHIP -0.13 0.27 -10000 0 -0.59 126 126
LPA4-mediated signaling events

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
ADCY4 0.008 0.018 -10000 0 -0.39 1 1
ADCY5 -0.007 0.076 -10000 0 -0.39 19 19
ADCY6 0.008 0.033 -10000 0 -0.73 1 1
ADCY7 -0.001 0.056 -10000 0 -0.31 16 16
ADCY1 0 0.057 0.18 1 -0.38 11 12
ADCY2 -0.054 0.14 0.18 20 -0.31 109 129
ADCY3 0.009 0.018 -10000 0 -0.39 1 1
ADCY8 -0.085 0.15 0.18 7 -0.31 151 158
PRKCE 0.009 0.021 -10000 0 -0.45 1 1
ADCY9 0.008 0.018 -10000 0 -0.39 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.032 0.12 0.28 21 -0.28 36 57
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.008 -10000 0 -10000 0 0
VLDLR 0.028 0.006 -10000 0 -10000 0 0
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
NUDC 0.028 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.082 0.2 -10000 0 -0.38 153 153
CaM/Ca2+ 0.02 0.006 -10000 0 -10000 0 0
KATNA1 0.026 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.077 0.18 -10000 0 -0.35 148 148
IQGAP1/CaM 0.039 0.012 -10000 0 -10000 0 0
DAB1 0.012 0.08 -10000 0 -0.5 12 12
IQGAP1 0.029 0.003 -10000 0 -10000 0 0
PLA2G7 -0.38 0.23 -10000 0 -0.51 389 389
CALM1 0.027 0.008 -10000 0 -10000 0 0
DYNLT1 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.02 -10000 0 -0.36 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.028 0.005 -10000 0 -10000 0 0
CDK5R1 0.028 0.004 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.015 0.004 -10000 0 -10000 0 0
CDK5R2 -0.041 0.18 -10000 0 -0.51 62 62
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.092 0.2 -10000 0 -0.38 161 161
YWHAE 0.028 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.05 0.18 0.32 30 -0.44 11 41
MAP1B 0.007 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.07 0.15 -10000 0 -10000 0 0
RELN -0.16 0.29 -10000 0 -0.61 153 153
PAFAH/LIS1 -0.22 0.15 -10000 0 -0.31 376 376
LIS1/CLIP170 0.034 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.052 0.12 -10000 0 -0.39 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.06 0.14 -10000 0 -0.42 12 12
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.081 0.15 -10000 0 -0.46 12 12
LIS1/IQGAP1 0.034 0.01 -10000 0 -10000 0 0
RHOA 0.014 0.01 -10000 0 -10000 0 0
PAFAH1B1 0.02 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.028 -10000 0 -0.61 1 1
PAFAH1B2 0.027 0.028 -10000 0 -0.61 1 1
MAP1B/LIS1/Dynein heavy chain 0.036 0.023 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.047 0.17 0.32 22 -0.43 10 32
LRP8 0.027 0.024 -10000 0 -0.5 1 1
NDEL1/Katanin 60 -0.052 0.17 0.32 27 -0.44 11 38
P39/CDK5 -0.096 0.17 -10000 0 -0.54 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.034 0.01 -10000 0 -10000 0 0
CDK5 -0.085 0.16 -10000 0 -10000 0 0
PPP2R5D 0.028 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.068 0.18 -10000 0 -0.34 56 56
RELN/VLDLR -0.064 0.19 -10000 0 -0.35 148 148
CDC42 0.02 0.006 -10000 0 -10000 0 0
IL27-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 0.025 0.047 -10000 0 -0.5 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.048 0.13 0.38 26 -0.31 1 27
IL27/IL27R/JAK1 -0.01 0.25 0.66 3 -0.6 28 31
TBX21 -0.11 0.31 0.57 9 -0.56 107 116
IL12B -0.038 0.16 -10000 0 -0.51 52 52
IL12A 0.006 0.011 0.19 1 -10000 0 1
IL6ST -0.003 0.11 -10000 0 -0.6 16 16
IL27RA/JAK1 0.014 0.06 -10000 0 -10000 0 0
IL27 -0.018 0.13 -10000 0 -0.52 32 32
TYK2 0.01 0.025 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.009 0.1 -10000 0 -0.46 1 1
T-helper 2 cell differentiation 0.048 0.13 0.38 26 -0.31 1 27
T cell proliferation during immune response 0.048 0.13 0.38 26 -0.31 1 27
MAPKKK cascade -0.048 0.13 0.31 1 -0.38 26 27
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT2 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.025 -10000 0 -0.51 1 1
IL12RB1 -0.14 0.25 -10000 0 -0.51 158 158
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.081 0.27 0.56 9 -0.54 64 73
IL27/IL27R/JAK2/TYK2 -0.049 0.13 0.31 1 -0.39 26 27
positive regulation of T cell mediated cytotoxicity -0.048 0.13 0.31 1 -0.38 26 27
STAT1 (dimer) 0.047 0.39 0.51 137 -0.64 56 193
JAK2 0.014 0.021 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.031 0.14 0.39 2 -0.44 7 9
T cell proliferation -0.075 0.15 -10000 0 -0.46 28 28
IL12/IL12R/TYK2/JAK2 -0.079 0.14 -10000 0 -0.75 3 3
IL17A -0.009 0.099 -10000 0 -0.46 1 1
mast cell activation 0.048 0.13 0.38 26 -0.31 1 27
IFNG -0.023 0.051 0.12 5 -0.089 52 57
T cell differentiation -0.007 0.01 0.017 4 -0.021 119 123
STAT3 (dimer) -0.032 0.14 0.39 2 -0.43 8 10
STAT5A (dimer) -0.032 0.14 0.39 2 -0.43 8 10
STAT4 (dimer) -0.047 0.16 0.39 2 -0.48 26 28
STAT4 -0.003 0.12 -10000 0 -0.5 29 29
T cell activation -0.008 0.005 0.06 1 -10000 0 1
IL27R/JAK2/TYK2 -0.01 0.1 -10000 0 -0.44 4 4
GATA3 -0.59 0.64 0.5 1 -1.3 245 246
IL18 0.006 0.038 0.19 1 -0.36 5 6
positive regulation of mast cell cytokine production -0.031 0.14 0.39 2 -0.43 8 10
IL27/EBI3 -0.054 0.19 -10000 0 -0.46 85 85
IL27RA -0.003 0.044 -10000 0 -10000 0 0
IL6 -0.041 0.18 -10000 0 -0.55 60 60
STAT5A 0.028 0.004 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.002 -10000 0 -10000 0 0
IL2 -0.01 0.048 -10000 0 -10000 0 0
IL1B 0.005 0.042 -10000 0 -0.38 6 6
EBI3 -0.058 0.19 -10000 0 -0.52 75 75
TNF 0.003 0.052 -10000 0 -0.41 8 8
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.008 0.12 -9999 0 -0.39 43 43
EFNA5 -0.022 0.16 -9999 0 -0.6 37 37
FYN 0.009 0.13 -9999 0 -0.36 43 43
neuron projection morphogenesis -0.008 0.12 -9999 0 -0.39 43 43
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.008 0.12 -9999 0 -0.39 43 43
EPHA5 0.013 0.068 -9999 0 -0.52 8 8
IL2 signaling events mediated by STAT5

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
GAB2 0.029 0.003 -10000 0 -10000 0 0
ELF1 -0.02 0.11 -10000 0 -0.47 4 4
CCNA2 -0.076 0.21 -10000 0 -0.51 100 100
PIK3CA 0.027 0.029 -10000 0 -0.61 1 1
JAK3 -0.078 0.21 -10000 0 -0.5 103 103
PIK3R1 0.026 0.029 -10000 0 -0.61 1 1
JAK1 0.028 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.039 0.14 -10000 0 -0.46 19 19
SHC1 0.028 0.007 -10000 0 -10000 0 0
SP1 0.034 0.017 -10000 0 -10000 0 0
IL2RA -0.063 0.18 -10000 0 -0.43 101 101
IL2RB -0.25 0.27 -10000 0 -0.5 270 270
SOS1 0.029 0.005 -10000 0 -10000 0 0
IL2RG -0.006 0.13 -10000 0 -0.51 34 34
G1/S transition of mitotic cell cycle 0.006 0.11 0.43 7 -0.46 4 11
PTPN11 0.029 0.005 -10000 0 -10000 0 0
CCND2 0.025 0.029 -10000 0 -0.43 2 2
LCK 0.005 0.11 -10000 0 -0.51 22 22
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL2 0.014 0.073 -10000 0 -0.5 10 10
CDK6 0.024 0.03 -10000 0 -0.61 1 1
CCND3 -0.026 0.13 0.49 1 -0.49 1 2
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 0.027 0.01 -9999 0 -10000 0 0
SVIL 0.027 0.009 -9999 0 -10000 0 0
ZNF318 0.028 0.011 -9999 0 -10000 0 0
JMJD2C 0 0.015 -9999 0 -0.076 17 17
T-DHT/AR/Ubc9 -0.081 0.087 -9999 0 -0.45 21 21
CARM1 0.029 0.003 -9999 0 -10000 0 0
PRDX1 0.028 0.006 -9999 0 -10000 0 0
PELP1 0.028 0.005 -9999 0 -10000 0 0
CTNNB1 0.019 0.015 -9999 0 -10000 0 0
AKT1 0.027 0.009 -9999 0 -10000 0 0
PTK2B 0.025 0.01 -9999 0 -10000 0 0
MED1 0.028 0.005 -9999 0 -10000 0 0
MAK 0.027 0.026 -9999 0 -0.5 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.02 0.058 -9999 0 -0.62 4 4
GSN 0.026 0.012 -9999 0 -10000 0 0
NCOA2 0.017 0.08 -9999 0 -0.61 8 8
NCOA6 0.026 0.011 -9999 0 -10000 0 0
DNA-PK 0.052 0.021 -9999 0 -10000 0 0
NCOA4 0.028 0.005 -9999 0 -10000 0 0
PIAS3 0.027 0.009 -9999 0 -10000 0 0
cell proliferation -0.044 0.099 -9999 0 -0.53 18 18
XRCC5 0.028 0.007 -9999 0 -10000 0 0
UBE3A 0.027 0.014 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.096 0.11 -9999 0 -0.47 36 36
FHL2 -0.052 0.11 -9999 0 -0.71 9 9
RANBP9 0.027 0.01 -9999 0 -10000 0 0
JMJD1A -0.12 0.052 -9999 0 -0.14 442 442
CDK6 0.024 0.03 -9999 0 -0.61 1 1
TGFB1I1 0.025 0.026 -9999 0 -0.5 1 1
T-DHT/AR/CyclinD1 -0.094 0.1 -9999 0 -0.41 40 40
XRCC6 0.029 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.1 -9999 0 -0.42 31 31
CTDSP1 0.027 0.007 -9999 0 -10000 0 0
CTDSP2 0.029 0.01 -9999 0 -10000 0 0
BRCA1 0.027 0.009 -9999 0 -10000 0 0
TCF4 0.029 0.008 -9999 0 -10000 0 0
CDKN2A -0.49 0.11 -9999 0 -0.51 489 489
SRF 0.034 0.015 -9999 0 -10000 0 0
NKX3-1 -0.21 0.12 -9999 0 -0.51 45 45
KLK3 0.017 0.075 -9999 0 -10000 0 0
TMF1 0.023 0.012 -9999 0 -10000 0 0
HNRNPA1 0.029 0.007 -9999 0 -10000 0 0
AOF2 -0.001 0.005 -9999 0 -10000 0 0
APPL1 0.015 0.012 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.082 0.087 -9999 0 -0.44 22 22
AR -0.08 0.13 -9999 0 -0.65 23 23
UBA3 0.022 0.012 -9999 0 -10000 0 0
PATZ1 0.029 0.006 -9999 0 -10000 0 0
PAWR 0.027 0.029 -9999 0 -0.61 1 1
PRKDC 0.027 0.008 -9999 0 -10000 0 0
PA2G4 0.029 0.007 -9999 0 -10000 0 0
UBE2I 0.028 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.074 0.08 -9999 0 -0.4 23 23
RPS6KA3 0.026 0.031 -9999 0 -0.63 1 1
T-DHT/AR/ARA70 -0.083 0.086 -9999 0 -0.44 22 22
LATS2 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.074 0.08 -9999 0 -0.4 23 23
Cyclin D3/CDK11 p58 0.021 0.004 -9999 0 -10000 0 0
VAV3 0.01 0.1 -9999 0 -0.61 14 14
KLK2 -0.074 0.081 -9999 0 -0.45 18 18
CASP8 0.028 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.075 0.097 -9999 0 -0.44 24 24
TMPRSS2 -0.84 0.32 -9999 0 -0.95 446 446
CCND1 0.01 0.098 -9999 0 -0.5 18 18
PIAS1 0.027 0.014 -9999 0 -10000 0 0
mol:T-DHT -0.057 0.024 -9999 0 -0.067 432 432
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.026 0.017 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.076 0.09 -9999 0 -0.45 20 20
CMTM2 0.016 0.077 -9999 0 -0.5 11 11
SNURF 0.008 0.11 -9999 0 -0.61 16 16
ZMIZ1 -0.049 0.033 -9999 0 -10000 0 0
CCND3 0.028 0.006 -9999 0 -10000 0 0
TGIF1 0.029 0.006 -9999 0 -10000 0 0
FKBP4 0.026 0.011 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.04 0.023 -10000 0 -0.45 1 1
Necdin/E2F1 -0.002 0.12 -10000 0 -0.36 54 54
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.027 0.13 -10000 0 -0.49 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.24 -10000 0 -0.4 241 241
NT-4/5 (dimer)/p75(NTR) 0.006 0.11 -10000 0 -0.38 38 38
IKBKB 0.027 0.008 -10000 0 -10000 0 0
AKT1 -0.005 0.13 0.41 4 -0.46 11 15
IKBKG 0.028 0.004 -10000 0 -10000 0 0
BDNF -0.042 0.18 -10000 0 -0.51 67 67
MGDIs/NGR/p75(NTR)/LINGO1 0.014 0.12 -10000 0 -0.33 56 56
FURIN 0.029 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.015 0.15 -10000 0 -0.33 94 94
LINGO1 0.008 0.1 -10000 0 -0.5 20 20
Sortilin/TRAF6/NRIF 0.035 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.042 0.18 -10000 0 -0.51 67 67
NTRK1 -0.016 0.16 -10000 0 -0.58 36 36
RTN4R 0.022 0.06 -10000 0 -0.52 6 6
neuron apoptosis -0.019 0.13 0.45 6 -0.55 7 13
IRAK1 0.029 0.003 -10000 0 -10000 0 0
SHC1 -0.027 0.13 -10000 0 -0.33 73 73
ARHGDIA 0.027 0.029 -10000 0 -0.61 1 1
RhoA/GTP 0.015 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.076 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.016 0.14 -10000 0 -0.46 11 11
MAGEH1 0.029 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.014 0.14 -10000 0 -0.44 13 13
Mammalian IAPs/DIABLO 0.018 0.12 -10000 0 -0.28 75 75
proNGF (dimer) -0.021 0.15 -10000 0 -0.5 47 47
MAGED1 0.029 0.003 -10000 0 -10000 0 0
APP 0.028 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.049 -10000 0 -0.53 4 4
ZNF274 0.029 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.014 0.12 -10000 0 -0.43 11 11
NGF -0.021 0.15 -10000 0 -0.5 47 47
cell cycle arrest 0.016 0.15 0.36 10 -0.54 7 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.003 0.084 -10000 0 -0.34 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.024 0.098 -10000 0 -0.32 38 38
NCSTN 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.14 -10000 0 -0.33 73 73
PSENEN 0.029 0.003 -10000 0 -10000 0 0
mol:ceramide -0.022 0.12 -10000 0 -0.45 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.059 -10000 0 -0.43 3 3
p75(NTR)/beta APP 0.014 0.1 -10000 0 -0.37 33 33
BEX1 -0.21 0.31 -10000 0 -0.61 189 189
mol:GDP -0.039 0.12 -10000 0 -0.34 73 73
NGF (dimer) -0.23 0.24 -10000 0 -0.42 294 294
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.03 0.12 -10000 0 -0.31 55 55
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
RAC1/GTP -0.001 0.12 -10000 0 -0.29 67 67
MYD88 0.02 0.013 -10000 0 -10000 0 0
CHUK 0.028 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0 0.14 -10000 0 -0.33 73 73
RHOB 0.028 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
MAGE-G1/E2F1 0 0.12 -10000 0 -0.36 52 52
NT3 (dimer) 0.022 0.059 -10000 0 -0.57 5 5
TP53 -0.024 0.12 0.34 3 -0.49 6 9
PRDM4 -0.021 0.12 -10000 0 -0.47 10 10
BDNF (dimer) -0.27 0.27 -10000 0 -0.46 297 297
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
SORT1 0.027 0.029 -10000 0 -0.61 1 1
activation of caspase activity 0.022 0.13 -10000 0 -0.48 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.016 0.14 -10000 0 -0.46 11 11
RHOC 0.028 0.005 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
MAPK10 -0.009 0.13 0.45 7 -0.44 6 13
DIABLO 0.028 0.005 -10000 0 -10000 0 0
SMPD2 -0.022 0.12 -10000 0 -0.46 11 11
APH1B 0.029 0.003 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.001 0.14 -10000 0 -0.34 74 74
PSEN1 0.027 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.009 0.11 -10000 0 -0.38 38 38
MAPK8 -0.009 0.12 0.43 7 -0.41 5 12
MAPK9 -0.013 0.11 0.45 6 -0.41 5 11
APAF1 0.028 0.005 -10000 0 -10000 0 0
NTF3 0.022 0.059 -10000 0 -0.57 5 5
NTF4 0.017 0.049 -10000 0 -0.53 4 4
NDN 0.026 0.04 -10000 0 -0.61 2 2
RAC1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.007 0.12 -10000 0 -0.47 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.068 0.027 -10000 0 -0.35 1 1
RhoA-B-C/GTP -0.001 0.14 -10000 0 -0.33 73 73
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.014 0.14 -10000 0 -0.44 10 10
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.003 0.15 -10000 0 -0.47 10 10
PRKACB 0.028 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.012 0.14 -10000 0 -0.36 66 66
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.054 0.19 -10000 0 -0.5 79 79
BIRC2 0.028 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.035 0.14 0.32 5 -0.42 7 12
BAD 0.007 0.13 0.47 10 -0.43 5 15
RIPK2 0.026 0.024 -10000 0 -0.5 1 1
NGFR -0.008 0.14 -10000 0 -0.51 34 34
CYCS -0.017 0.12 0.44 2 -0.49 9 11
ADAM17 0.028 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.013 0.14 -10000 0 -0.48 10 10
BCL2L11 0.008 0.13 0.46 10 -0.44 5 15
BDNF (dimer)/p75(NTR) -0.037 0.17 -10000 0 -0.38 94 94
PI3K 0.01 0.13 -10000 0 -0.31 68 68
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.016 0.14 -10000 0 -0.46 11 11
NDNL2 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.028 0.005 -10000 0 -10000 0 0
PRKCI 0.027 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.022 0.16 -10000 0 -0.39 73 73
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.016 0.14 -10000 0 -0.46 11 11
TRAF6 0.029 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCZ 0.024 0.049 -10000 0 -0.61 3 3
PLG -0.29 0.31 -10000 0 -0.58 265 265
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.038 0.13 -10000 0 -0.43 22 22
SQSTM1 0.021 0.013 -10000 0 -10000 0 0
NGFRAP1 0.029 0.003 -10000 0 -10000 0 0
CASP3 0.011 0.13 0.46 10 -0.4 5 15
E2F1 -0.027 0.16 -10000 0 -0.5 52 52
CASP9 0.028 0.006 -10000 0 -10000 0 0
IKK complex 0.023 0.12 -10000 0 -0.46 1 1
NGF (dimer)/TRKA -0.03 0.16 -10000 0 -0.4 79 79
MMP7 -0.082 0.24 -10000 0 -0.6 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.13 -10000 0 -0.49 8 8
MMP3 -0.024 0.15 -10000 0 -0.5 46 46
APAF-1/Caspase 9 -0.044 0.11 -10000 0 -0.4 9 9
PLK1 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
regulation of centriole-centriole cohesion 0.038 0.067 0.14 148 -0.14 2 150
BUB1B -0.003 0.073 0.2 8 -0.25 27 35
PLK1 -0.002 0.042 0.15 11 -0.14 7 18
PLK1S1 0.008 0.03 0.15 9 -0.19 1 10
KIF2A 0.016 0.083 0.24 46 -0.31 3 49
regulation of mitotic centrosome separation -0.002 0.042 0.15 11 -0.14 7 18
GOLGA2 0.028 0.006 -10000 0 -10000 0 0
Hec1/SPC24 -0.056 0.19 0.18 1 -0.37 119 120
WEE1 0.013 0.053 0.23 4 -0.76 1 5
cytokinesis -0.034 0.15 0.24 17 -0.25 91 108
PP2A-alpha B56 -0.011 0.1 -10000 0 -0.74 3 3
AURKA 0.006 0.03 0.14 6 -0.14 3 9
PICH/PLK1 -0.011 0.092 -10000 0 -0.44 17 17
CENPE -0.032 0.11 0.27 3 -0.32 60 63
RhoA/GTP 0.015 0.01 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.016 0.083 0.24 46 -0.31 3 49
PPP2CA 0.022 0.012 -10000 0 -10000 0 0
FZR1 0.027 0.028 -10000 0 -0.61 1 1
TPX2 -0.011 0.062 0.15 15 -0.12 82 97
PAK1 0.029 0.003 -10000 0 -10000 0 0
SPC24 -0.026 0.16 -10000 0 -0.51 52 52
FBXW11 0.022 0.013 -10000 0 -10000 0 0
CLSPN -0.013 0.068 0.14 3 -0.18 58 61
GORASP1 0.02 0.013 -10000 0 -10000 0 0
metaphase -0.001 0.005 0.017 20 -0.013 9 29
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.002 0.024 0.08 13 -0.069 9 22
G2 phase of mitotic cell cycle 0 0.003 0.019 3 -10000 0 3
STAG2 0.029 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.46 143 143
spindle elongation -0.002 0.042 0.15 11 -0.14 7 18
ODF2 0.028 0.006 -10000 0 -10000 0 0
BUB1 -0.035 0.1 -10000 0 -0.64 7 7
TPT1 0.003 0.038 0.15 4 -0.2 11 15
CDC25C -0.016 0.091 0.17 12 -0.19 10 22
CDC25B 0.024 0.048 -10000 0 -0.51 4 4
SGOL1 -0.039 0.067 0.14 2 -0.14 148 150
RHOA 0.021 0.013 -10000 0 -10000 0 0
CCNB1/CDK1 0.019 0.061 -10000 0 -0.39 6 6
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.017 0.15 -10000 0 -0.51 42 42
PLK1/PBIP1 -0.009 0.066 0.14 3 -0.3 17 20
mitosis -0.002 0.003 0.022 1 -10000 0 1
FBXO5 0 0.044 0.19 7 -0.18 4 11
CDC2 0 0.003 -10000 0 -0.015 6 6
NDC80 -0.083 0.22 -10000 0 -0.5 106 106
metaphase plate congression -0.003 0.061 0.14 3 -0.26 22 25
ERCC6L 0.001 0.087 -10000 0 -0.42 17 17
NLP/gamma Tubulin 0.001 0.029 0.12 8 -0.12 8 16
microtubule cytoskeleton organization 0.003 0.038 0.15 4 -0.2 11 15
G2/M transition DNA damage checkpoint 0 0.002 0.012 2 -10000 0 2
PPP1R12A 0.028 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 -0.08 0.16 -10000 0 -0.29 172 172
GRASP65/GM130/RAB1/GTP/PLK1 0.021 0.042 -10000 0 -10000 0 0
RAB1A 0.028 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.002 0.032 0.12 13 -0.11 7 20
mitotic prometaphase -0.001 0.004 0.017 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.054 -10000 0 -0.47 3 3
microtubule-based process -0.09 0.15 0.21 1 -0.3 174 175
Golgi organization -0.002 0.042 0.15 11 -0.14 7 18
Cohesin/SA2 0.01 0.041 0.17 3 -10000 0 3
PPP1CB/MYPT1 0.041 0.01 -10000 0 -10000 0 0
KIF20A -0.16 0.25 -10000 0 -0.5 174 174
APC/C/CDC20 -0.01 0.1 0.18 4 -0.33 41 45
PPP2R1A 0.029 0.003 -10000 0 -10000 0 0
chromosome segregation -0.009 0.065 0.14 3 -0.3 17 20
PRC1 0.023 0.053 -10000 0 -0.5 5 5
ECT2 0.006 0.054 0.24 15 -10000 0 15
C13orf34 0.001 0.033 0.13 11 -0.12 7 18
NUDC -0.003 0.061 0.14 3 -0.26 22 25
regulation of attachment of spindle microtubules to kinetochore -0.003 0.072 0.2 8 -0.24 27 35
spindle assembly 0 0.037 0.14 11 -0.12 6 17
spindle stabilization 0.008 0.03 0.15 9 -0.19 1 10
APC/C/HCDH1 0.027 0.02 -10000 0 -0.39 1 1
MKLP2/PLK1 -0.09 0.15 0.21 1 -0.3 174 175
CCNB1 0.019 0.067 -10000 0 -0.51 8 8
PPP1CB 0.029 0.005 -10000 0 -10000 0 0
BTRC 0.028 0.006 -10000 0 -10000 0 0
ROCK2 -0.022 0.074 0.19 2 -0.37 9 11
TUBG1 0.005 0.036 0.15 4 -0.24 6 10
G2/M transition of mitotic cell cycle -0.007 0.05 -10000 0 -0.38 6 6
MLF1IP -0.004 0.07 -10000 0 -0.38 17 17
INCENP 0.028 0.003 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.12 0.22 -10000 0 -0.62 72 72
NFATC2 -0.067 0.19 -10000 0 -0.67 10 10
NFATC3 -0.018 0.061 -10000 0 -0.33 1 1
CD40LG -0.17 0.31 -10000 0 -0.88 39 39
ITCH 0.036 0.045 -10000 0 -10000 0 0
CBLB 0.034 0.046 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.37 -10000 0 -0.89 92 92
JUNB 0.026 0.04 -10000 0 -0.61 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.054 -10000 0 -0.29 11 11
T cell anergy 0.022 0.071 -10000 0 -0.41 10 10
TLE4 -0.034 0.13 -10000 0 -0.53 6 6
Jun/NFAT1-c-4/p21SNFT -0.11 0.25 -10000 0 -0.98 8 8
AP-1/NFAT1-c-4 -0.16 0.32 -10000 0 -1.1 16 16
IKZF1 -0.08 0.22 -10000 0 -0.53 86 86
T-helper 2 cell differentiation -0.26 0.24 0.49 2 -0.65 60 62
AP-1/NFAT1 -0.046 0.16 -10000 0 -0.54 11 11
CALM1 0.034 0.034 -10000 0 -10000 0 0
EGR2 -0.08 0.22 -10000 0 -1.3 8 8
EGR3 -0.08 0.21 -10000 0 -1.3 7 7
NFAT1/FOXP3 -0.15 0.28 -10000 0 -0.67 85 85
EGR1 0.013 0.08 -10000 0 -0.61 8 8
JUN 0.01 0.031 -10000 0 -10000 0 0
EGR4 0.021 0.048 -10000 0 -0.5 4 4
mol:Ca2+ -0.002 0.038 -10000 0 -0.32 3 3
GBP3 -0.037 0.14 -10000 0 -0.59 8 8
FOSL1 0.004 0.11 -10000 0 -0.5 24 24
NFAT1-c-4/MAF/IRF4 -0.12 0.27 -10000 0 -0.87 12 12
DGKA -0.035 0.14 -10000 0 -0.66 8 8
CREM 0.028 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.088 0.2 -10000 0 -1 6 6
CTLA4 -0.24 0.34 -10000 0 -0.62 200 200
NFAT1-c-4 (dimer)/EGR1 -0.071 0.21 -10000 0 -1.1 6 6
NFAT1-c-4 (dimer)/EGR4 -0.076 0.22 -10000 0 -0.94 8 8
FOS -0.006 0.098 -10000 0 -0.6 12 12
IFNG -0.23 0.29 -10000 0 -0.64 121 121
T cell activation -0.04 0.16 0.46 1 -0.69 6 7
MAF 0.028 0.005 -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 0.052 0.14 0.78 5 -10000 0 5
TNF -0.055 0.21 -10000 0 -1.1 6 6
FASLG -0.18 0.3 -10000 0 -1.3 9 9
TBX21 -0.18 0.26 -10000 0 -0.55 167 167
BATF3 -0.018 0.15 -10000 0 -0.5 44 44
PRKCQ -0.023 0.098 -10000 0 -0.55 14 14
PTPN1 -0.033 0.13 -10000 0 -0.53 6 6
NFAT1-c-4/ICER1 -0.075 0.21 -10000 0 -0.92 8 8
GATA3 -0.28 0.32 -10000 0 -0.61 245 245
T-helper 1 cell differentiation -0.22 0.29 -10000 0 -0.62 122 122
IL2RA -0.19 0.31 -10000 0 -0.8 69 69
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.033 0.13 -10000 0 -0.53 6 6
E2F1 -0.021 0.16 -10000 0 -0.5 52 52
PPARG 0.02 0.013 -10000 0 -10000 0 0
SLC3A2 -0.033 0.13 -10000 0 -0.53 6 6
IRF4 -0.096 0.22 -10000 0 -0.51 118 118
PTGS2 -0.16 0.29 -10000 0 -0.94 23 23
CSF2 -0.15 0.27 -10000 0 -0.98 19 19
JunB/Fra1/NFAT1-c-4 -0.072 0.22 -10000 0 -0.96 6 6
IL4 -0.27 0.25 0.49 2 -0.69 53 55
IL5 -0.14 0.26 -10000 0 -0.96 13 13
IL2 -0.04 0.16 0.46 1 -0.7 6 7
IL3 -0.026 0.058 -10000 0 -0.9 1 1
RNF128 0.023 0.12 -10000 0 -0.6 16 16
NFATC1 -0.052 0.15 -10000 0 -0.79 5 5
CDK4 0.038 0.12 0.54 1 -10000 0 1
PTPRK -0.036 0.13 -10000 0 -0.53 6 6
IL8 -0.16 0.3 -10000 0 -0.96 26 26
POU2F1 0.028 0.006 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.14 0.2 -10000 0 -0.36 228 228
PDGFRB 0.022 0.013 -10000 0 -10000 0 0
SPHK1 -0.007 0.076 -10000 0 -0.6 6 6
mol:S1P -0.003 0.07 -10000 0 -0.5 6 6
S1P1/S1P/Gi -0.047 0.12 0.32 1 -0.45 20 21
GNAO1 0.025 0.05 -10000 0 -0.53 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.026 0.1 0.33 1 -0.43 11 12
PLCG1 -0.038 0.11 0.32 2 -0.44 16 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.013 -10000 0 -10000 0 0
GNAI2 0.021 0.015 -10000 0 -10000 0 0
GNAI3 0.028 0.008 -10000 0 -10000 0 0
GNAI1 0.025 0.03 -10000 0 -0.62 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.13 0.16 0.18 1 -0.3 227 228
S1P1/S1P -0.075 0.13 0.25 1 -0.33 23 24
negative regulation of cAMP metabolic process -0.046 0.12 0.32 1 -0.44 20 21
MAPK3 -0.048 0.14 0.42 2 -0.58 23 25
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.01 -10000 0 -10000 0 0
KDR 0.027 0.029 -10000 0 -0.61 1 1
PLCB2 -0.085 0.15 0.31 10 -0.37 50 60
RAC1 0.026 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.074 0.099 -10000 0 -0.29 20 20
receptor internalization -0.074 0.12 -10000 0 -0.31 24 24
PTGS2 -0.049 0.23 0.45 8 -0.94 24 32
Rac1/GTP -0.067 0.1 -10000 0 -0.29 21 21
RHOA 0.021 0.013 -10000 0 -10000 0 0
VEGFA -0.21 0.26 -10000 0 -0.5 228 228
negative regulation of T cell proliferation -0.046 0.12 0.32 1 -0.44 20 21
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.05 -10000 0 -0.61 3 3
MAPK1 -0.05 0.15 0.32 1 -0.58 25 26
S1P1/S1P/PDGFB-D/PDGFRB -0.067 0.12 0.29 1 -0.34 12 13
ABCC1 0.028 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.033 0.083 -10000 0 -1.1 1 1
SMARCC2 0.03 0.005 -10000 0 -10000 0 0
SMARCC1 0.022 0.014 -10000 0 -10000 0 0
TBX21 -0.16 0.23 0.54 1 -0.47 169 170
SUMO2 0.022 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.032 -10000 0 -0.68 1 1
FKBP4 0.028 0.006 -10000 0 -10000 0 0
FKBP5 0.02 0.064 -10000 0 -0.52 7 7
GR alpha/HSP90/FKBP51/HSP90 0.061 0.091 0.33 7 -0.35 2 9
PRL -0.027 0.1 -10000 0 -0.65 4 4
cortisol/GR alpha (dimer)/TIF2 0.12 0.21 0.51 51 -0.41 2 53
RELA 0.008 0.079 -10000 0 -0.3 1 1
FGG -0.027 0.25 0.46 16 -0.44 63 79
GR beta/TIF2 0.046 0.1 0.33 7 -0.42 5 12
IFNG -0.26 0.26 -10000 0 -0.6 123 123
apoptosis -0.083 0.21 -10000 0 -0.53 55 55
CREB1 -0.004 0.1 -10000 0 -0.35 40 40
histone acetylation -0.005 0.094 0.27 3 -0.38 7 10
BGLAP -0.018 0.089 -10000 0 -0.52 3 3
GR/PKAc 0.07 0.086 0.36 3 -10000 0 3
NF kappa B1 p50/RelA 0.013 0.14 -10000 0 -0.45 23 23
SMARCD1 0.03 0.005 -10000 0 -10000 0 0
MDM2 0.035 0.073 0.26 10 -10000 0 10
GATA3 -0.27 0.32 -10000 0 -0.6 245 245
AKT1 0.02 0.008 -10000 0 -10000 0 0
CSF2 -0.024 0.095 -10000 0 -0.57 4 4
GSK3B 0.022 0.013 -10000 0 -10000 0 0
NR1I3 -0.048 0.22 -10000 0 -0.66 20 20
CSN2 0.061 0.15 0.37 21 -10000 0 21
BRG1/BAF155/BAF170/BAF60A 0.057 0.038 -10000 0 -10000 0 0
NFATC1 0.029 0.006 -10000 0 -10000 0 0
POU2F1 0.03 0.008 -10000 0 -10000 0 0
CDKN1A 0.03 0.058 0.86 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.036 0.18 -10000 0 -0.52 59 59
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.033 0.13 0.34 3 -0.37 10 13
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.021 0.24 -10000 0 -0.66 19 19
JUN -0.18 0.2 -10000 0 -0.53 78 78
IL4 -0.026 0.084 -10000 0 -0.5 1 1
CDK5R1 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.029 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.16 0.2 0.25 12 -0.47 92 104
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.07 0.092 0.36 4 -0.35 1 5
cortisol/GR alpha (monomer) 0.12 0.24 0.57 56 -10000 0 56
NCOA2 0.017 0.08 -10000 0 -0.61 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.042 0.11 -10000 0 -0.65 12 12
AP-1/NFAT1-c-4 -0.24 0.25 -10000 0 -0.64 82 82
AFP -0.33 0.52 -10000 0 -1.3 106 106
SUV420H1 0.029 0.003 -10000 0 -10000 0 0
IRF1 0.059 0.1 0.45 5 -10000 0 5
TP53 0.047 0.016 -10000 0 -10000 0 0
PPP5C 0.029 0.003 -10000 0 -10000 0 0
KRT17 -0.2 0.32 -10000 0 -0.94 61 61
KRT14 -0.098 0.16 -10000 0 -0.57 18 18
TBP 0.034 0.013 -10000 0 -10000 0 0
CREBBP 0.047 0.048 -10000 0 -10000 0 0
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.027 0.01 -10000 0 -10000 0 0
AP-1 -0.24 0.25 -10000 0 -0.64 83 83
MAPK14 0.024 0.011 -10000 0 -10000 0 0
MAPK10 0.018 0.064 -10000 0 -0.62 5 5
MAPK11 0.022 0.027 -10000 0 -0.52 1 1
KRT5 -0.18 0.23 -10000 0 -0.62 69 69
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.03 0.007 -10000 0 -10000 0 0
STAT1 0.034 0.032 -10000 0 -0.68 1 1
CGA -0.12 0.32 -10000 0 -1.1 48 48
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.069 0.1 0.4 13 -10000 0 13
MAPK3 0.024 0.01 -10000 0 -10000 0 0
MAPK1 0.024 0.01 -10000 0 -10000 0 0
ICAM1 -0.05 0.17 -10000 0 -0.57 30 30
NFKB1 0.007 0.086 -10000 0 -0.34 7 7
MAPK8 -0.11 0.15 -10000 0 -0.42 42 42
MAPK9 0.019 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.088 0.22 -10000 0 -0.56 57 57
BAX 0.032 0.032 -10000 0 -10000 0 0
POMC -0.049 0.14 0.48 1 -0.73 6 7
EP300 0.048 0.055 -10000 0 -0.53 1 1
cortisol/GR alpha (dimer)/p53 0.14 0.21 0.52 55 -10000 0 55
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.056 0.22 4 -10000 0 4
SGK1 0.064 0.083 -10000 0 -10000 0 0
IL13 -0.27 0.24 -10000 0 -0.66 86 86
IL6 -0.098 0.29 -10000 0 -0.8 57 57
PRKACG 0.02 0.006 -10000 0 -10000 0 0
IL5 -0.22 0.19 -10000 0 -0.62 35 35
IL2 -0.15 0.19 -10000 0 -0.62 30 30
CDK5 0.024 0.009 -10000 0 -10000 0 0
PRKACB 0.028 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
IL8 -0.07 0.23 -10000 0 -0.67 43 43
CDK5R1/CDK5 0.034 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.046 0.12 -10000 0 -0.42 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.19 0.5 50 -10000 0 50
SMARCA4 0.03 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.063 0.11 0.37 17 -10000 0 17
NF kappa B1 p50/RelA/Cbp 0.064 0.14 -10000 0 -0.47 7 7
JUN (dimer) -0.18 0.2 -10000 0 -0.53 78 78
YWHAH 0.028 0.004 -10000 0 -10000 0 0
VIPR1 -0.05 0.15 -10000 0 -0.69 17 17
NR3C1 0.059 0.14 0.44 17 -0.52 1 18
NR4A1 0.016 0.11 -10000 0 -0.59 15 15
TIF2/SUV420H1 0.032 0.062 -10000 0 -0.45 8 8
MAPKKK cascade -0.083 0.21 -10000 0 -0.53 55 55
cortisol/GR alpha (dimer)/Src-1 0.13 0.21 0.51 55 -0.42 1 56
PBX1 0.011 0.11 -10000 0 -0.61 15 15
POU1F1 0.021 0.01 -10000 0 -10000 0 0
SELE -0.094 0.31 -10000 0 -1 42 42
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.063 0.11 0.38 17 -10000 0 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.19 0.5 50 -10000 0 50
mol:cortisol 0.043 0.15 0.3 58 -0.26 28 86
MMP1 -0.15 0.3 -10000 0 -0.88 54 54
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.037 -10000 0 -0.45 3 3
MAP4K4 0.012 0.058 -10000 0 -0.47 2 2
BAG4 0.025 0.029 -10000 0 -0.61 1 1
PKC zeta/ceramide -0.099 0.085 -10000 0 -0.3 54 54
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 -0.054 0.19 -10000 0 -0.5 79 79
BAX -0.035 0.036 -10000 0 -0.3 4 4
RIPK1 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.069 0.89 3 -10000 0 3
BAD -0.1 0.079 -10000 0 -0.3 48 48
SMPD1 0.02 0.053 0.27 9 -0.19 5 14
RB1 -0.098 0.079 -10000 0 -0.3 47 47
FADD/Caspase 8 0.018 0.073 -10000 0 -0.43 4 4
MAP2K4 -0.078 0.077 -10000 0 -0.28 36 36
NSMAF 0.027 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.075 0.086 -10000 0 -0.28 50 50
EGF -0.54 0.19 -10000 0 -0.61 460 460
mol:ceramide -0.11 0.084 0.17 2 -0.3 56 58
MADD 0.029 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.016 0.022 -10000 0 -0.45 1 1
ASAH1 0.026 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.098 0.078 -10000 0 -0.29 47 47
cell proliferation -0.058 0.071 -10000 0 -0.39 7 7
BID -0.005 0.075 -10000 0 -0.57 5 5
MAP3K1 -0.089 0.073 0.18 2 -0.29 37 39
EIF2A -0.074 0.084 0.29 7 -0.6 3 10
TRADD 0.028 0.006 -10000 0 -10000 0 0
CRADD 0.028 0.005 -10000 0 -10000 0 0
MAPK3 -0.077 0.072 -10000 0 -0.38 10 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.077 0.073 -10000 0 -0.43 7 7
Cathepsin D/ceramide -0.098 0.08 -10000 0 -0.28 54 54
FADD 0.013 0.058 -10000 0 -0.47 2 2
KSR1 -0.1 0.082 0.18 1 -0.29 56 57
MAPK8 -0.08 0.086 -10000 0 -0.3 42 42
PRKRA -0.096 0.081 0.18 2 -0.29 51 53
PDGFA 0.024 0.03 -10000 0 -0.61 1 1
TRAF2 0.028 0.005 -10000 0 -10000 0 0
IGF1 0.023 0.053 -10000 0 -0.5 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.083 0.17 2 -0.3 56 58
CTSD 0.027 0.028 -10000 0 -0.61 1 1
regulation of nitric oxide biosynthetic process 0.041 0.023 -10000 0 -0.45 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.061 0.077 -10000 0 -0.42 7 7
PRKCD 0.02 0.027 -10000 0 -0.5 1 1
PRKCZ 0.024 0.049 -10000 0 -0.61 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.016 0.022 -10000 0 -0.45 1 1
RelA/NF kappa B1 0.041 0.023 -10000 0 -0.45 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.029 -10000 0 -0.61 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.062 -10000 0 -0.5 2 2
TNFR1A/BAG4/TNF-alpha 0.044 0.057 -10000 0 -0.35 9 9
mol:Sphingosine-1-phosphate 0.016 0.037 -10000 0 -0.45 3 3
MAP2K1 -0.082 0.075 -10000 0 -0.4 10 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
CYCS -0.053 0.035 -10000 0 -0.24 8 8
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
TNFR1A/BAG4 0.037 0.026 -10000 0 -0.45 1 1
EIF2AK2 -0.085 0.089 0.27 7 -0.28 46 53
TNF-alpha/TNFR1A/FAN 0.045 0.053 -10000 0 -0.35 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.026 0.07 -10000 0 -0.4 7 7
MAP2K2 -0.083 0.073 -10000 0 -0.4 9 9
SMPD3 0.015 0.051 0.2 3 -0.32 4 7
TNF 0.018 0.073 -10000 0 -0.56 8 8
PKC zeta/PAR4 0.036 0.045 -10000 0 -0.45 4 4
mol:PHOSPHOCHOLINE 0.2 0.086 0.24 413 -10000 0 413
NF kappa B1/RelA/I kappa B alpha 0.072 0.045 -10000 0 -0.33 3 3
AIFM1 -0.06 0.049 -10000 0 -0.28 7 7
BCL2 0.028 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.049 -10000 0 -0.37 7 7
VEGFR1 homodimer/NRP1 0.013 0.046 -10000 0 -0.37 7 7
mol:DAG -0.14 0.15 -10000 0 -0.44 15 15
VEGFR1 homodimer/NRP1/VEGFR 121 -0.11 0.16 -10000 0 -0.45 9 9
CaM/Ca2+ -0.12 0.15 -10000 0 -0.57 6 6
HIF1A 0.029 0.046 -10000 0 -0.6 2 2
GAB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 -0.092 0.14 -10000 0 -0.58 6 6
PLCG1 -0.14 0.16 -10000 0 -0.44 15 15
NOS3 -0.08 0.12 -10000 0 -0.46 11 11
CBL 0.027 0.028 -10000 0 -0.61 1 1
mol:NO -0.074 0.13 0.72 1 -0.44 11 12
FLT1 0.019 0.054 -10000 0 -0.44 7 7
PGF -0.27 0.27 -10000 0 -0.51 282 282
VEGFR1 homodimer/NRP2/VEGFR121 -0.098 0.17 -10000 0 -0.46 11 11
CALM1 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
eNOS/Hsp90 -0.063 0.14 0.43 2 -0.49 5 7
endothelial cell proliferation -0.098 0.13 0.58 1 -0.44 13 14
mol:Ca2+ -0.14 0.15 -10000 0 -0.44 15 15
MAPK3 -0.12 0.14 0.46 2 -0.5 6 8
MAPK1 -0.12 0.14 0.46 2 -0.53 6 8
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
PLGF homodimer -0.27 0.27 -10000 0 -0.51 282 282
PRKACA 0.029 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.006 0.12 -10000 0 -0.5 30 30
VEGFA homodimer -0.21 0.26 -10000 0 -0.5 228 228
VEGFR1 homodimer/VEGFA homodimer -0.12 0.17 -10000 0 -0.49 9 9
platelet activating factor biosynthetic process -0.12 0.13 0.44 2 -0.49 6 8
PI3K -0.11 0.16 -10000 0 -0.62 6 6
PRKCA -0.13 0.14 0.58 1 -0.56 6 7
PRKCB -0.13 0.14 0.58 1 -0.52 8 9
VEGFR1 homodimer/PLGF homodimer -0.16 0.18 -10000 0 -0.46 18 18
VEGFA -0.21 0.26 -10000 0 -0.5 228 228
VEGFB 0.029 0.003 -10000 0 -10000 0 0
mol:IP3 -0.14 0.15 -10000 0 -0.44 15 15
RASA1 0.019 0.05 -10000 0 -0.67 1 1
NRP2 0.02 0.062 -10000 0 -0.5 7 7
VEGFR1 homodimer 0.019 0.054 -10000 0 -0.43 7 7
VEGFB homodimer 0.029 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.029 -10000 0 -0.61 1 1
eNOS/Caveolin-1 -0.084 0.14 -10000 0 -0.44 27 27
PTPN11 0.028 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.11 0.16 -10000 0 -0.61 6 6
mol:L-citrulline -0.074 0.13 0.72 1 -0.44 11 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.083 0.16 -10000 0 -0.58 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.098 0.17 -10000 0 -0.57 6 6
CD2AP 0.028 0.006 -10000 0 -10000 0 0
PI3K/GAB1 -0.1 0.16 -10000 0 -0.59 6 6
PDPK1 -0.11 0.15 0.34 1 -0.6 6 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.097 0.16 -10000 0 -0.55 5 5
mol:NADP -0.074 0.13 0.72 1 -0.44 11 12
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.083 0.16 -10000 0 -0.57 5 5
VEGFR1 homodimer/NRP2 0.028 0.06 -10000 0 -0.37 7 7
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.14 0.2 -10000 0 -0.36 228 228
alphaV beta3 Integrin 0.047 0.06 -10000 0 -0.42 7 7
PTK2 -0.079 0.15 0.51 3 -0.55 6 9
IGF1R 0.029 0.003 -10000 0 -10000 0 0
PI4KB 0.027 0.006 -10000 0 -10000 0 0
MFGE8 0.028 0.024 -10000 0 -0.5 1 1
SRC 0.028 0.006 -10000 0 -10000 0 0
CDKN1B -0.041 0.17 -10000 0 -0.47 69 69
VEGFA -0.21 0.26 -10000 0 -0.5 228 228
ILK -0.042 0.18 -10000 0 -0.47 71 71
ROCK1 0.028 0.004 -10000 0 -10000 0 0
AKT1 -0.041 0.16 -10000 0 -0.44 68 68
PTK2B -0.095 0.14 0.36 2 -0.56 1 3
alphaV/beta3 Integrin/JAM-A 0.004 0.14 -10000 0 -0.65 1 1
CBL 0.027 0.028 -10000 0 -0.61 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.14 0.21 -10000 0 -0.39 213 213
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.061 0.054 -10000 0 -0.35 4 4
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.084 0.14 -10000 0 -0.4 55 55
alphaV/beta3 Integrin/Syndecan-1 0.047 0.06 -10000 0 -0.39 9 9
PI4KA 0.028 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.029 0.1 -10000 0 -0.56 4 4
PI4 Kinase 0.04 0.011 -10000 0 -10000 0 0
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
alphaV/beta3 Integrin/Osteopontin 0.049 0.047 -10000 0 -0.39 5 5
RPS6KB1 0.018 0.12 0.47 13 -0.53 4 17
TLN1 0.028 0.006 -10000 0 -10000 0 0
MAPK3 0 0.1 -10000 0 -0.61 7 7
GPR124 0.025 0.025 -10000 0 -0.5 1 1
MAPK1 0.001 0.1 -10000 0 -0.61 7 7
PXN 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
alphaV/beta3 Integrin/Tumstatin 0.005 0.14 -10000 0 -0.39 54 54
cell adhesion -0.11 0.18 -10000 0 -0.36 23 23
ANGPTL3 -0.25 0.31 -10000 0 -0.59 232 232
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.18 -10000 0 -0.31 224 224
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
TGFBR2 0.021 0.013 -10000 0 -10000 0 0
ITGB3 0.024 0.049 -10000 0 -0.61 3 3
IGF1 0.023 0.053 -10000 0 -0.5 5 5
RAC1 0.026 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.047 0.039 -10000 0 -0.38 3 3
apoptosis 0.027 0.006 -10000 0 -10000 0 0
CD47 0.026 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.048 0.039 -10000 0 -0.39 3 3
VCL 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.037 0.076 -10000 0 -0.38 14 14
CSF1 0.027 0.029 -10000 0 -0.61 1 1
PIK3C2A -0.044 0.18 -10000 0 -0.48 72 72
PI4 Kinase/Pyk2 -0.12 0.17 -10000 0 -0.5 39 39
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.085 0.17 -10000 0 -0.4 5 5
FAK1/Vinculin -0.056 0.14 0.59 3 -0.49 3 6
alphaV beta3/Integrin/ppsTEM5 0.048 0.04 -10000 0 -0.39 3 3
RHOA 0.021 0.013 -10000 0 -10000 0 0
VTN -0.065 0.22 -10000 0 -0.59 76 76
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
FGF2 0.022 0.061 -10000 0 -0.59 5 5
F11R 0.016 0.042 -10000 0 -0.45 4 4
alphaV/beta3 Integrin/Lactadherin 0.051 0.04 -10000 0 -0.37 4 4
alphaV/beta3 Integrin/TGFBR2 0.038 0.042 -10000 0 -0.38 3 3
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.044 -10000 0 -0.52 2 2
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.048 0.035 -10000 0 -0.35 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.14 -10000 0 -0.51 37 37
alphaV/beta3 Integrin/Pyk2 -0.085 0.15 -10000 0 -0.39 4 4
SDC1 0.02 0.069 -10000 0 -0.61 6 6
VAV3 0.026 0.083 0.36 7 -0.64 1 8
PTPN11 0.028 0.005 -10000 0 -10000 0 0
IRS1 0.022 0.057 -10000 0 -0.61 4 4
FAK1/Paxillin -0.057 0.13 0.53 2 -0.44 5 7
cell migration -0.053 0.12 0.52 2 -0.44 3 5
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.013 0.13 -10000 0 -0.88 1 1
SPP1 0.025 0.049 -10000 0 -0.61 3 3
KDR 0.027 0.029 -10000 0 -0.61 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.006 -10000 0 -10000 0 0
COL4A3 -0.041 0.2 -10000 0 -0.58 57 57
angiogenesis -0.008 0.13 0.31 4 -0.63 7 11
Rac1/GTP 0.031 0.063 -10000 0 -0.59 1 1
EDIL3 0.011 0.092 -10000 0 -0.55 13 13
cell proliferation 0.037 0.042 -10000 0 -0.38 3 3
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.012 0.14 0.37 13 -0.46 10 23
IKBKB 0.01 0.12 0.33 19 -0.3 5 24
AKT1 0.005 0.13 0.39 27 -0.26 6 33
IKBKG 0.024 0.1 0.32 15 -0.28 1 16
CALM1 0.003 0.082 0.36 1 -0.31 4 5
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
MAP3K1 -0.029 0.17 0.38 21 -0.42 23 44
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.087 0.26 1 -0.33 4 5
DOK1 0.028 0.005 -10000 0 -10000 0 0
AP-1 0.017 0.1 0.29 22 -0.27 8 30
LYN 0.027 0.007 -10000 0 -10000 0 0
BLNK 0.026 0.029 -10000 0 -0.61 1 1
SHC1 0.027 0.006 -10000 0 -10000 0 0
BCR complex -0.058 0.18 -10000 0 -0.37 122 122
CD22 -0.05 0.13 -10000 0 -0.42 27 27
CAMK2G 0.009 0.081 0.35 1 -10000 0 1
CSNK2A1 0.028 0.005 -10000 0 -10000 0 0
INPP5D 0.023 0.047 -10000 0 -0.5 4 4
SHC/GRB2/SOS1 -0.031 0.12 -10000 0 -0.45 3 3
GO:0007205 0.003 0.088 0.26 1 -0.33 4 5
SYK 0.026 0.032 -10000 0 -0.46 2 2
ELK1 0.007 0.087 0.3 1 -0.32 3 4
NFATC1 -0.03 0.13 0.37 7 -0.34 18 25
B-cell antigen/BCR complex -0.058 0.18 -10000 0 -0.37 122 122
PAG1/CSK 0.04 0.011 -10000 0 -10000 0 0
NFKBIB 0.021 0.051 0.16 19 -0.13 8 27
HRAS 0.004 0.084 0.29 3 -0.33 1 4
NFKBIA 0.022 0.05 0.16 19 -0.12 5 24
NF-kappa-B/RelA/I kappa B beta 0.027 0.047 0.16 19 -0.17 1 20
RasGAP/Csk -0.059 0.2 -10000 0 -0.51 46 46
mol:GDP 0.004 0.085 0.27 2 -0.35 4 6
PTEN 0.028 0.006 -10000 0 -10000 0 0
CD79B 0.025 0.041 -10000 0 -0.5 3 3
NF-kappa-B/RelA/I kappa B alpha 0.027 0.047 0.16 19 -0.17 1 20
GRB2 0.028 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.003 0.16 0.39 15 -0.45 8 23
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:IP3 0.002 0.086 0.26 2 -0.33 5 7
CSK 0.029 0.003 -10000 0 -10000 0 0
FOS 0.001 0.098 0.32 3 -0.51 3 6
CHUK 0.016 0.11 0.32 15 -0.31 9 24
IBTK 0.027 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.14 0.39 1 -0.41 4 5
PTPN6 -0.046 0.12 -10000 0 -0.5 12 12
RELA 0.029 0.003 -10000 0 -10000 0 0
BCL2A1 0.006 0.054 0.15 12 -0.14 1 13
VAV2 -0.059 0.16 -10000 0 -0.45 42 42
ubiquitin-dependent protein catabolic process 0.025 0.05 0.15 22 -0.12 5 27
BTK -0.03 0.14 -10000 0 -0.89 11 11
CD19 -0.072 0.17 -10000 0 -0.46 64 64
MAP4K1 -0.19 0.26 -10000 0 -0.5 207 207
CD72 -0.1 0.23 -10000 0 -0.51 122 122
PAG1 0.027 0.007 -10000 0 -10000 0 0
MAPK14 -0.02 0.16 0.37 21 -0.38 9 30
SH3BP5 0.019 0.031 -10000 0 -0.61 1 1
PIK3AP1 0.008 0.087 0.3 1 -0.43 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.046 0.12 -10000 0 -0.4 13 13
RAF1 0 0.079 0.31 3 -10000 0 3
RasGAP/p62DOK/SHIP -0.058 0.19 -10000 0 -0.5 47 47
CD79A -0.1 0.23 -10000 0 -0.5 124 124
re-entry into mitotic cell cycle 0.017 0.1 0.29 22 -0.28 6 28
RASA1 0.024 0.03 -10000 0 -0.61 1 1
MAPK3 0.021 0.095 0.34 14 -10000 0 14
MAPK1 0.017 0.086 0.34 7 -10000 0 7
CD72/SHP1 -0.085 0.2 0.35 1 -0.48 61 62
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
MAPK8 -0.022 0.16 0.37 22 -0.38 9 31
actin cytoskeleton organization -0.036 0.16 0.33 8 -0.4 35 43
NF-kappa-B/RelA 0.056 0.085 0.29 19 -10000 0 19
Calcineurin 0.027 0.081 -10000 0 -10000 0 0
PI3K -0.062 0.14 -10000 0 -0.42 39 39
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0 0.083 0.31 1 -0.4 4 5
SOS1 0.028 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.2 -10000 0 -0.53 30 30
DAPP1 -0.03 0.14 -10000 0 -0.66 13 13
cytokine secretion -0.027 0.13 0.36 7 -0.32 17 24
mol:DAG 0.002 0.086 0.26 2 -0.33 5 7
PLCG2 0.02 0.068 -10000 0 -0.55 7 7
MAP2K1 0.014 0.086 0.33 6 -10000 0 6
B-cell antigen/BCR complex/FcgammaRIIB -0.088 0.22 -10000 0 -0.39 161 161
mol:PI-3-4-5-P3 -0.049 0.1 -10000 0 -0.32 28 28
ETS1 0.012 0.082 0.43 2 -10000 0 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.01 0.15 -10000 0 -0.42 6 6
B-cell antigen/BCR complex/LYN -0.049 0.11 -10000 0 -0.36 19 19
MALT1 0.028 0.005 -10000 0 -10000 0 0
TRAF6 0.029 0.003 -10000 0 -10000 0 0
RAC1 -0.042 0.16 0.31 4 -0.42 35 39
B-cell antigen/BCR complex/LYN/SYK -0.042 0.16 -10000 0 -0.45 27 27
CARD11 -0.026 0.16 0.32 14 -0.34 54 68
FCGR2B -0.066 0.2 -10000 0 -0.5 89 89
PPP3CA 0.028 0.004 -10000 0 -10000 0 0
BCL10 0.028 0.005 -10000 0 -10000 0 0
IKK complex 0.021 0.069 0.21 31 -10000 0 31
PTPRC -0.028 0.16 -10000 0 -0.5 53 53
PDPK1 -0.017 0.1 0.3 13 -0.26 9 22
PPP3CB 0.028 0.005 -10000 0 -10000 0 0
PPP3CC 0.026 0.009 -10000 0 -10000 0 0
POU2F2 0.013 0.049 0.15 12 -10000 0 12
IL23-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
CCL2 -0.15 0.33 -10000 0 -1.1 12 12
IL23A -0.13 0.33 -10000 0 -1.1 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.13 0.32 -10000 0 -0.99 15 15
positive regulation of T cell mediated cytotoxicity -0.16 0.34 -10000 0 -1 22 22
ITGA3 -0.14 0.32 -10000 0 -1 10 10
IL17F -0.092 0.25 0.66 2 -0.71 9 11
IL12B -0.049 0.16 -10000 0 -0.52 52 52
STAT1 (dimer) -0.15 0.33 -10000 0 -1 19 19
CD4 -0.14 0.32 -10000 0 -1 14 14
IL23 -0.16 0.3 -10000 0 -1 16 16
IL23R -0.019 0.15 -10000 0 -0.81 8 8
IL1B -0.14 0.33 -10000 0 -1 13 13
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.14 0.32 -10000 0 -0.95 17 17
TYK2 0.012 0.034 -10000 0 -10000 0 0
STAT4 -0.003 0.12 -10000 0 -0.5 29 29
STAT3 0.028 0.004 -10000 0 -10000 0 0
IL18RAP -0.12 0.23 -10000 0 -0.52 132 132
IL12RB1 -0.15 0.26 -10000 0 -0.53 158 158
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
IL12Rbeta1/TYK2 -0.097 0.2 -10000 0 -0.39 158 158
IL23R/JAK2 -0.022 0.15 -10000 0 -0.8 6 6
positive regulation of chronic inflammatory response -0.16 0.34 -10000 0 -1 22 22
natural killer cell activation 0.002 0.009 0.044 9 -10000 0 9
JAK2 0.008 0.039 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
RELA 0.028 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.3 -10000 0 -0.95 17 17
ALOX12B -0.17 0.33 -10000 0 -1 17 17
CXCL1 -0.18 0.37 -10000 0 -1.1 35 35
T cell proliferation -0.16 0.34 -10000 0 -1 22 22
NFKBIA 0.027 0.008 -10000 0 -10000 0 0
IL17A -0.068 0.21 -10000 0 -0.58 5 5
PI3K -0.14 0.32 -10000 0 -1 15 15
IFNG -0.035 0.053 0.11 8 -0.1 61 69
STAT3 (dimer) -0.13 0.31 -10000 0 -0.98 14 14
IL18R1 0.012 0.068 -10000 0 -0.55 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.24 -10000 0 -0.7 12 12
IL18/IL18R -0.078 0.17 -10000 0 -0.34 137 137
macrophage activation -0.011 0.016 -10000 0 -0.044 6 6
TNF -0.15 0.33 -10000 0 -1.1 15 15
STAT3/STAT4 -0.15 0.34 -10000 0 -1 21 21
STAT4 (dimer) -0.16 0.35 -10000 0 -1 23 23
IL18 0.016 0.053 -10000 0 -0.5 5 5
IL19 -0.14 0.32 -10000 0 -0.97 14 14
STAT5A (dimer) -0.15 0.33 -10000 0 -1 19 19
STAT1 0.026 0.024 -10000 0 -0.5 1 1
SOCS3 0.026 0.034 -10000 0 -0.5 2 2
CXCL9 -0.22 0.37 -10000 0 -0.92 42 42
MPO -0.15 0.32 -10000 0 -1 14 14
positive regulation of humoral immune response -0.16 0.34 -10000 0 -1 22 22
IL23/IL23R/JAK2/TYK2 -0.17 0.34 -10000 0 -1.1 18 18
IL6 -0.17 0.4 -10000 0 -1.1 41 41
STAT5A 0.028 0.004 -10000 0 -10000 0 0
IL2 -0.01 0.075 -10000 0 -0.51 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.009 0.044 9 -10000 0 9
CD3E -0.21 0.37 -10000 0 -0.93 37 37
keratinocyte proliferation -0.16 0.34 -10000 0 -1 22 22
NOS2 -0.14 0.32 -10000 0 -0.99 13 13
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.012 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.065 0.13 -10000 0 -0.43 30 30
PTP1B/AKT1 -0.053 0.072 0.21 1 -0.33 5 6
FYN 0.027 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.067 0.076 0.37 1 -0.31 10 11
EGFR -0.015 0.059 -10000 0 -0.54 6 6
EGF/EGFR -0.29 0.13 -10000 0 -0.35 395 395
CSF1 0.027 0.029 -10000 0 -0.61 1 1
AKT1 0.027 0.008 -10000 0 -10000 0 0
INSR 0.029 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.068 0.085 -10000 0 -0.38 14 14
Insulin Receptor/Insulin -0.043 0.077 0.3 1 -10000 0 1
HCK 0.001 0.12 -10000 0 -0.5 26 26
CRK 0.028 0.005 -10000 0 -10000 0 0
TYK2 -0.062 0.073 0.28 2 -0.36 4 6
EGF -0.55 0.2 -10000 0 -0.61 457 457
YES1 0.028 0.004 -10000 0 -10000 0 0
CAV1 -0.14 0.11 0.33 5 -0.34 26 31
TXN 0.022 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.056 0.08 0.33 1 -0.38 8 9
cell migration 0.067 0.076 0.31 10 -0.37 1 11
STAT3 0.028 0.004 -10000 0 -10000 0 0
PRLR -0.049 0.2 -10000 0 -0.61 59 59
ITGA2B 0.009 0.099 -10000 0 -0.51 18 18
CSF1R 0.017 0.053 -10000 0 -0.5 5 5
Prolactin Receptor/Prolactin -0.026 0.16 -10000 0 -0.46 59 59
FGR 0.025 0.041 -10000 0 -0.5 3 3
PTP1B/p130 Cas -0.06 0.072 -10000 0 -0.34 5 5
Crk/p130 Cas -0.055 0.072 -10000 0 -0.34 4 4
DOK1 -0.029 0.082 0.28 5 -0.32 4 9
JAK2 -0.07 0.14 0.32 1 -0.42 42 43
Jak2/Leptin Receptor/Leptin -0.045 0.1 -10000 0 -0.41 2 2
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
PTPN1 -0.067 0.076 0.37 1 -0.32 10 11
LYN 0.027 0.007 -10000 0 -10000 0 0
CDH2 0.011 0.1 -10000 0 -0.59 14 14
SRC 0.001 0.044 0.34 1 -0.66 1 2
ITGB3 0.024 0.049 -10000 0 -0.61 3 3
CAT1/PTP1B -0.21 0.15 0.37 6 -0.43 71 77
CAPN1 0.027 0.003 -10000 0 -10000 0 0
CSK 0.029 0.003 -10000 0 -10000 0 0
PI3K -0.003 0.085 -10000 0 -0.54 1 1
mol:H2O2 -0.006 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.037 0.098 -10000 0 -0.41 2 2
negative regulation of transcription -0.069 0.14 0.32 1 -0.41 43 44
FCGR2A 0.004 0.11 -10000 0 -0.5 22 22
FER 0.016 0.041 -10000 0 -0.62 2 2
alphaIIb/beta3 Integrin 0.022 0.084 -10000 0 -0.38 21 21
BLK -0.009 0.13 -10000 0 -0.5 33 33
Insulin Receptor/Insulin/Shc 0.048 0.013 -10000 0 -10000 0 0
RHOA 0.019 0.013 -10000 0 -10000 0 0
LEPR 0.028 0.006 -10000 0 -10000 0 0
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
p210 bcr-abl/Grb2 0.028 0.005 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.19 0.16 0.36 4 -0.44 75 79
PRL 0.001 0.022 -10000 0 -10000 0 0
SOCS3 0.025 0.11 -10000 0 -0.98 6 6
SPRY2 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.044 0.042 -10000 0 -0.4 4 4
CSF1/CSF1R -0.049 0.073 0.33 1 -0.45 3 4
Ras protein signal transduction 0.033 0.071 0.5 10 -10000 0 10
IRS1 0.022 0.057 -10000 0 -0.61 4 4
INS 0.006 0.019 -10000 0 -10000 0 0
LEP -0.032 0.15 -10000 0 -0.5 46 46
STAT5B -0.061 0.093 0.36 1 -0.34 24 25
STAT5A -0.061 0.093 0.36 1 -0.34 24 25
GRB2 0.028 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.068 0.33 1 -0.36 3 4
CSN2 0.004 0.071 -10000 0 -0.61 1 1
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
LAT -0.045 0.092 -10000 0 -0.45 8 8
YBX1 0.031 0.007 -10000 0 -10000 0 0
LCK 0.004 0.11 -10000 0 -0.51 22 22
SHC1 0.027 0.006 -10000 0 -10000 0 0
NOX4 0.02 0.051 -10000 0 -0.54 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.05 0.13 -10000 0 -0.49 3 3
UGCG -0.011 0.11 -10000 0 -0.57 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.025 0.14 0.32 4 -0.44 15 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.01 0.11 -10000 0 -0.56 19 19
mol:DAG -0.013 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.13 0.28 1 -0.42 7 8
FRAP1 -0.025 0.14 0.36 3 -0.46 9 12
FOXO3 -0.023 0.14 0.36 4 -0.47 7 11
AKT1 -0.029 0.14 0.3 1 -0.44 21 22
GAB2 0.029 0.003 -10000 0 -10000 0 0
SMPD1 0.009 0.043 -10000 0 -0.74 1 1
SGMS1 -0.006 0.11 -10000 0 -0.7 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.026 -10000 0 -0.38 2 2
CALM1 0.027 0.008 -10000 0 -10000 0 0
cell proliferation -0.01 0.12 0.29 4 -0.49 16 20
EIF3A 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.035 -10000 0 -0.45 2 2
RPS6KB1 -0.014 0.11 -10000 0 -0.91 6 6
mol:sphingomyelin -0.013 0.13 -10000 0 -0.84 12 12
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.077 0.21 -10000 0 -0.5 103 103
PIK3R1 0.027 0.03 -10000 0 -0.61 1 1
JAK1 0.03 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
MYC -0.019 0.14 0.42 4 -0.53 4 8
MYB -0.078 0.18 -10000 0 -0.46 24 24
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.04 0.14 0.26 1 -0.43 30 31
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.009 0.12 -10000 0 -0.86 6 6
mol:PI-3-4-5-P3 -0.038 0.14 0.26 1 -0.42 30 31
Rac1/GDP 0.025 0.027 -10000 0 -0.35 2 2
T cell proliferation -0.033 0.13 0.27 2 -0.43 20 22
SHC1 0.028 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.006 0.018 -10000 0 -0.036 139 139
PRKCZ -0.035 0.14 0.25 1 -0.45 20 21
NF kappa B1 p50/RelA -0.005 0.14 0.3 1 -0.44 5 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.064 0.13 -10000 0 -0.39 46 46
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
IL2RA -0.076 0.21 -10000 0 -0.5 100 100
IL2RB -0.25 0.27 -10000 0 -0.5 270 270
TERT -0.04 0.17 -10000 0 -0.51 59 59
E2F1 -0.038 0.12 -10000 0 -0.33 26 26
SOS1 0.028 0.005 -10000 0 -10000 0 0
RPS6 0.026 0.034 -10000 0 -0.5 2 2
mol:cAMP 0.003 0.009 0.017 137 -10000 0 137
PTPN11 0.028 0.006 -10000 0 -10000 0 0
IL2RG -0.005 0.13 -10000 0 -0.51 34 34
actin cytoskeleton organization -0.033 0.13 0.27 2 -0.43 20 22
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.016 0.074 -10000 0 -0.5 10 10
PIK3CA 0.028 0.029 -10000 0 -0.61 1 1
Rac1/GTP 0.045 0.035 -10000 0 -0.33 2 2
LCK 0.007 0.11 -10000 0 -0.51 22 22
BCL2 -0.013 0.12 0.44 2 -0.45 1 3
Wnt signaling

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.039 0.15 -9999 0 -0.42 44 44
FZD6 0.027 0.007 -9999 0 -10000 0 0
WNT6 0.009 0.097 -9999 0 -0.51 17 17
WNT4 -0.042 0.2 -9999 0 -0.59 57 57
FZD3 0.026 0.009 -9999 0 -10000 0 0
WNT5A 0.018 0.037 -9999 0 -0.41 3 3
WNT11 -0.017 0.16 -9999 0 -0.6 37 37
Noncanonical Wnt signaling pathway

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
NFATC2 0.024 0.047 -9999 0 -0.57 3 3
GNB1/GNG2 -0.028 0.15 -9999 0 -0.45 24 24
mol:DAG -0.036 0.13 -9999 0 -0.42 22 22
PLCG1 -0.037 0.13 -9999 0 -0.44 22 22
YES1 -0.038 0.14 -9999 0 -0.4 42 42
FZD3 0.026 0.009 -9999 0 -10000 0 0
FZD6 0.027 0.007 -9999 0 -10000 0 0
G protein -0.025 0.14 -9999 0 -0.44 22 22
MAP3K7 -0.089 0.16 -9999 0 -0.46 41 41
mol:Ca2+ -0.035 0.12 -9999 0 -0.41 22 22
mol:IP3 -0.036 0.13 -9999 0 -0.42 22 22
NLK -0.002 0.09 -9999 0 -0.82 6 6
GNB1 0.028 0.006 -9999 0 -10000 0 0
CAMK2A -0.096 0.18 -9999 0 -0.46 60 60
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.039 0.15 -9999 0 -0.42 44 44
CSNK1A1 0.022 0.012 -9999 0 -10000 0 0
GNAS -0.038 0.14 -9999 0 -0.4 44 44
GO:0007205 -0.04 0.12 -9999 0 -0.42 22 22
WNT6 0.009 0.097 -9999 0 -0.51 17 17
WNT4 -0.042 0.2 -9999 0 -0.59 57 57
NFAT1/CK1 alpha -0.017 0.12 -9999 0 -0.46 12 12
GNG2 0.027 0.008 -9999 0 -10000 0 0
WNT5A 0.018 0.037 -9999 0 -0.41 3 3
WNT11 -0.017 0.16 -9999 0 -0.6 37 37
CDC42 -0.035 0.13 -9999 0 -0.44 24 24
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.029 -10000 0 -0.61 1 1
Caspase 8 (4 units) -0.058 0.1 -10000 0 -0.36 1 1
NEF -0.054 0.069 -10000 0 -0.41 5 5
NFKBIA 0.012 0.043 -10000 0 -10000 0 0
BIRC3 -0.044 0.18 -10000 0 -0.46 79 79
CYCS -0.067 0.1 -10000 0 -0.39 1 1
RIPK1 0.028 0.005 -10000 0 -10000 0 0
CD247 -0.22 0.3 -10000 0 -0.63 166 166
MAP2K7 -0.041 0.13 0.38 2 -0.59 15 17
protein ubiquitination 0.027 0.097 0.36 10 -0.49 4 14
CRADD 0.028 0.005 -10000 0 -10000 0 0
DAXX 0.028 0.006 -10000 0 -10000 0 0
FAS 0.028 0.005 -10000 0 -10000 0 0
BID -0.075 0.11 -10000 0 -0.34 2 2
NF-kappa-B/RelA/I kappa B alpha 0.014 0.11 -10000 0 -0.43 2 2
TRADD 0.028 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.008 -10000 0 -10000 0 0
CFLAR 0.028 0.006 -10000 0 -10000 0 0
FADD 0.029 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.014 0.12 -10000 0 -0.43 2 2
MAPK8 -0.036 0.13 0.43 3 -0.57 13 16
APAF1 0.028 0.005 -10000 0 -10000 0 0
TRAF1 0.027 0.024 -10000 0 -0.5 1 1
TRAF2 0.028 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.081 0.11 -10000 0 -0.31 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.009 0.094 -10000 0 -0.52 7 7
CHUK 0.025 0.091 0.3 6 -0.54 4 10
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.029 -10000 0 -10000 0 0
TCRz/NEF -0.23 0.27 -10000 0 -0.44 271 271
TNF 0.018 0.073 -10000 0 -0.56 8 8
FASLG -0.31 0.34 -10000 0 -0.63 255 255
NFKB1 0.011 0.053 -10000 0 -0.6 1 1
TNFR1A/BAG4/TNF-alpha 0.044 0.057 -10000 0 -0.35 9 9
CASP6 -0.022 0.11 -10000 0 -0.55 13 13
CASP7 -0.061 0.14 0.37 1 -0.43 8 9
RELA 0.012 0.045 -10000 0 -10000 0 0
CASP2 0.026 0.009 -10000 0 -10000 0 0
CASP3 -0.058 0.14 0.37 1 -0.44 4 5
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.026 -10000 0 -0.45 1 1
CASP8 0.028 0.006 -10000 0 -10000 0 0
CASP9 0.028 0.006 -10000 0 -10000 0 0
MAP3K14 0.017 0.092 -10000 0 -0.57 5 5
APAF-1/Caspase 9 -0.082 0.14 -10000 0 -0.41 47 47
BCL2 -0.03 0.12 0.47 3 -0.54 11 14
Regulation of Telomerase

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
Telomerase catalytic core complex -0.16 0.19 0.49 1 -0.6 40 41
RAD9A 0.029 0.003 -10000 0 -10000 0 0
AP1 0.026 0.074 -10000 0 -0.44 12 12
IFNAR2 0.027 0.009 -10000 0 -10000 0 0
AKT1 0.013 0.044 -10000 0 -0.3 4 4
ER alpha/Oestrogen 0.016 0.036 -10000 0 -0.37 4 4
NFX1/SIN3/HDAC complex 0.026 0.064 -10000 0 -0.38 5 5
EGF -0.54 0.19 -10000 0 -0.61 460 460
SMG5 0.027 0.006 -10000 0 -10000 0 0
SMG6 0.028 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.036 0.017 -10000 0 -10000 0 0
TERT/c-Abl -0.15 0.18 -10000 0 -0.58 36 36
SAP18 0.028 0.005 -10000 0 -10000 0 0
MRN complex 0.042 0.026 -10000 0 -10000 0 0
WT1 -0.27 0.32 -10000 0 -0.61 235 235
WRN 0.026 0.009 -10000 0 -10000 0 0
SP1 0.025 0.014 -10000 0 -10000 0 0
SP3 0.027 0.006 -10000 0 -10000 0 0
TERF2IP 0.028 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.16 -10000 0 -0.59 17 17
Mad/Max 0.038 0.014 -10000 0 -10000 0 0
TERT -0.16 0.19 0.49 1 -0.62 39 40
CCND1 -0.15 0.19 0.65 1 -0.65 21 22
MAX 0.026 0.008 -10000 0 -10000 0 0
RBBP7 0.028 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.029 -10000 0 -0.61 1 1
TERF2 0.025 0.007 -10000 0 -10000 0 0
PTGES3 0.028 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.003 -10000 0 -10000 0 0
Telomerase/911 0.025 0.042 -10000 0 -10000 0 0
CDKN1B -0.1 0.15 -10000 0 -0.56 1 1
RAD1 0.026 0.009 -10000 0 -10000 0 0
XRCC5 0.027 0.007 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
SAP30 0.01 0.096 -10000 0 -0.5 17 17
TRF2/PARP2 0.038 0.012 -10000 0 -10000 0 0
UBE3A 0.028 0.004 -10000 0 -10000 0 0
JUN 0.027 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.009 -10000 0 -10000 0 0
FOS 0.011 0.096 -10000 0 -0.6 12 12
IFN-gamma/IRF1 -0.12 0.18 -10000 0 -0.35 189 189
PARP2 0.027 0.007 -10000 0 -10000 0 0
BLM 0.018 0.074 -10000 0 -0.5 10 10
Telomerase -0.019 0.11 -10000 0 -0.6 3 3
IRF1 0.024 0.027 -10000 0 -0.5 1 1
ESR1 0.022 0.049 -10000 0 -0.51 4 4
KU/TER 0.04 0.011 -10000 0 -10000 0 0
ATM/TRF2 0.041 0.022 -10000 0 -0.41 1 1
ubiquitin-dependent protein catabolic process 0.036 0.052 -10000 0 -0.44 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.053 -10000 0 -0.45 1 1
HDAC1 0.028 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.014 -10000 0 -10000 0 0
ATM 0.01 0.021 -10000 0 -0.45 1 1
SMAD3 0.018 0.035 0.22 1 -0.36 4 5
ABL1 0.028 0.005 -10000 0 -10000 0 0
MXD1 0.028 0.006 -10000 0 -10000 0 0
MRE11A 0.028 0.004 -10000 0 -10000 0 0
HUS1 0.026 0.009 -10000 0 -10000 0 0
RPS6KB1 0.028 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.18 -10000 0 -0.62 20 20
NR2F2 0.029 0.006 -10000 0 -10000 0 0
MAPK3 0.006 0.054 -10000 0 -0.36 10 10
MAPK1 0.006 0.054 -10000 0 -0.36 10 10
TGFB1/TGF beta receptor Type II 0.025 0.047 -10000 0 -0.5 4 4
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
HNRNPC 0.027 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.021 -10000 0 -0.45 1 1
NBN 0.027 0.007 -10000 0 -10000 0 0
EGFR 0.019 0.06 -10000 0 -0.52 6 6
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.39 0.16 -10000 0 -0.44 446 446
MYC 0.009 0.096 -10000 0 -0.5 17 17
IL2 0.009 0.075 -10000 0 -0.5 10 10
KU 0.04 0.011 -10000 0 -10000 0 0
RAD50 0.022 0.012 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
TGFB1 0.025 0.047 -10000 0 -0.5 4 4
TRF2/BLM 0.032 0.053 -10000 0 -0.34 10 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.14 0.18 -10000 0 -0.6 29 29
SP1/HDAC2 0.034 0.024 -10000 0 -10000 0 0
PINX1 0.026 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.13 0.17 -10000 0 -0.58 19 19
Smad3/Myc 0.021 0.071 -10000 0 -0.32 20 20
911 complex 0.049 0.022 -10000 0 -10000 0 0
IFNG -0.21 0.26 -10000 0 -0.49 230 230
Telomerase/PinX1 -0.13 0.16 -10000 0 -0.58 18 18
Telomerase/AKT1/mTOR/p70S6K -0.02 0.094 -10000 0 -0.42 8 8
SIN3B 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.028 0.005 -10000 0 -10000 0 0
Telomerase/EST1B -0.13 0.17 -10000 0 -0.57 21 21
response to DNA damage stimulus 0.005 0.012 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.059 0.038 -10000 0 -10000 0 0
TRF2/WRN 0.036 0.014 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.13 0.17 -10000 0 -0.59 16 16
E2F1 -0.028 0.16 -10000 0 -0.51 52 52
ZNFX1 0.028 0.006 -10000 0 -10000 0 0
PIF1 -0.064 0.2 -10000 0 -0.5 89 89
NCL 0.027 0.007 -10000 0 -10000 0 0
DKC1 0.028 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.064 0.25 -10000 0 -0.88 29 29
NCK1/PAK1/Dok-R -0.057 0.098 -10000 0 -0.42 26 26
NCK1/Dok-R 0.001 0.27 -10000 0 -1 29 29
PIK3CA 0.025 0.029 -10000 0 -0.61 1 1
mol:beta2-estradiol -0.002 0.035 0.26 8 -10000 0 8
RELA 0.029 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.006 -10000 0 -10000 0 0
Rac/GDP 0.019 0.007 -10000 0 -10000 0 0
F2 -0.17 0.25 0.27 3 -0.5 186 189
TNIP2 0.028 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.037 0.26 -10000 0 -0.96 29 29
FN1 -0.012 0.14 -10000 0 -0.51 37 37
PLD2 -0.005 0.27 -10000 0 -1.1 29 29
PTPN11 0.028 0.005 -10000 0 -10000 0 0
GRB14 -0.006 0.14 -10000 0 -0.61 27 27
ELK1 0.009 0.24 -10000 0 -0.94 29 29
GRB7 0.021 0.069 -10000 0 -0.61 6 6
PAK1 0.029 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.003 0.28 -10000 0 -1 28 28
CDKN1A -0.066 0.21 -10000 0 -0.64 21 21
ITGA5 -0.007 0.13 -10000 0 -0.5 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.003 0.27 -10000 0 -1 29 29
CRK 0.028 0.005 -10000 0 -10000 0 0
mol:NO -0.025 0.2 0.42 6 -0.64 28 34
PLG -0.16 0.3 -10000 0 -1.2 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.043 0.22 -10000 0 -0.83 28 28
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.029 -10000 0 -0.61 1 1
ANGPT2 -0.11 0.23 -10000 0 -0.59 27 27
BMX -0.043 0.28 -10000 0 -1.1 29 29
ANGPT1 0.034 0.17 -10000 0 -1.2 8 8
tube development -0.083 0.23 -10000 0 -0.71 26 26
ANGPT4 0.005 0.093 -10000 0 -0.51 16 16
response to hypoxia -0.005 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.012 0.3 -10000 0 -1.1 29 29
alpha5/beta1 Integrin 0.014 0.1 -10000 0 -0.36 34 34
FGF2 0.027 0.062 -10000 0 -0.59 5 5
STAT5A (dimer) -0.082 0.26 -10000 0 -0.8 26 26
mol:L-citrulline -0.025 0.2 0.42 6 -0.64 28 34
AGTR1 -0.023 0.13 -10000 0 -0.6 25 25
MAPK14 -0.032 0.3 -10000 0 -1.1 30 30
Tie2/SHP2 -0.008 0.26 -10000 0 -1.1 27 27
TEK -0.012 0.29 -10000 0 -1.2 27 27
RPS6KB1 -0.04 0.24 -10000 0 -0.84 29 29
Angiotensin II/AT1 -0.025 0.1 -10000 0 -0.45 25 25
Tie2/Ang1/GRB2 0.007 0.28 -10000 0 -1.1 29 29
MAPK3 0.001 0.25 -10000 0 -0.95 29 29
MAPK1 -0.001 0.25 -10000 0 -0.96 29 29
Tie2/Ang1/GRB7 0.004 0.29 -10000 0 -1.1 29 29
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
MAPK8 -0.006 0.27 -10000 0 -1.1 29 29
PI3K -0.058 0.28 -10000 0 -1 29 29
FES -0.027 0.29 -10000 0 -1.1 29 29
Crk/Dok-R 0.004 0.27 -10000 0 -1 28 28
Tie2/Ang1/ABIN2 0.006 0.29 -10000 0 -1.1 29 29
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.054 0.23 0.43 1 -0.78 29 30
STAT5A 0.028 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.038 0.24 -10000 0 -0.85 28 28
Tie2/Ang2 -0.11 0.29 -10000 0 -0.99 26 26
Tie2/Ang1 -0.008 0.3 -10000 0 -1.2 29 29
FOXO1 -0.07 0.24 0.45 1 -0.8 28 29
ELF1 0.029 0.041 -10000 0 -0.6 1 1
ELF2 -0.006 0.28 -10000 0 -1.1 29 29
mol:Choline -0.002 0.26 -10000 0 -1 29 29
cell migration -0.038 0.061 -10000 0 -0.24 23 23
FYN -0.096 0.25 -10000 0 -0.82 26 26
DOK2 -0.007 0.13 -10000 0 -0.51 31 31
negative regulation of cell cycle -0.059 0.2 -10000 0 -0.58 21 21
ETS1 0.032 0.04 -10000 0 -0.28 4 4
PXN -0.021 0.21 0.49 6 -0.69 28 34
ITGB1 0.028 0.004 -10000 0 -10000 0 0
NOS3 -0.033 0.22 0.58 1 -0.73 28 29
RAC1 0.026 0.009 -10000 0 -10000 0 0
TNF 0.019 0.083 -10000 0 -0.45 13 13
MAPKKK cascade -0.002 0.26 -10000 0 -1 29 29
RASA1 0.024 0.03 -10000 0 -0.61 1 1
Tie2/Ang1/Shc -0.001 0.28 -10000 0 -1.1 29 29
NCK1 0.026 0.029 -10000 0 -0.61 1 1
vasculogenesis -0.02 0.19 0.39 10 -0.57 28 38
mol:Phosphatidic acid -0.002 0.26 -10000 0 -1 29 29
mol:Angiotensin II -0.009 0.012 -10000 0 -10000 0 0
mol:NADP -0.025 0.2 0.42 6 -0.64 28 34
Rac1/GTP -0.039 0.22 -10000 0 -0.78 28 28
MMP2 -0.009 0.27 -10000 0 -1.1 29 29
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.55 0.64 -10000 0 -1.2 237 237
PLK1 -0.12 0.21 -10000 0 -0.71 10 10
CDKN1B -0.021 0.14 0.52 1 -0.38 1 2
FOXO3 -0.06 0.16 -10000 0 -0.6 10 10
KAT2B 0.012 0.038 -10000 0 -0.65 1 1
FOXO1/SIRT1 -0.14 0.22 -10000 0 -0.38 216 216
CAT -0.082 0.18 0.47 1 -1.2 3 4
CTNNB1 0.02 0.013 -10000 0 -10000 0 0
AKT1 -0.011 0.05 -10000 0 -0.3 1 1
FOXO1 -0.17 0.23 0.3 1 -0.41 232 233
MAPK10 0.032 0.069 0.34 3 -0.35 4 7
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.084 0.085 0.38 13 -10000 0 13
response to oxidative stress -0.028 0.04 -10000 0 -0.29 1 1
FOXO3A/SIRT1 -0.028 0.18 -10000 0 -0.59 9 9
XPO1 0.029 0.005 -10000 0 -10000 0 0
EP300 -0.012 0.055 -10000 0 -0.47 2 2
BCL2L11 0.003 0.085 -10000 0 -0.74 6 6
FOXO1/SKP2 -0.14 0.21 -10000 0 -0.39 198 198
mol:GDP -0.028 0.04 -10000 0 -0.29 1 1
RAN 0.029 0.006 -10000 0 -10000 0 0
GADD45A 0.049 0.15 -10000 0 -0.64 13 13
YWHAQ 0.028 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.026 0.11 0.27 1 -0.54 9 10
MST1 0.005 0.073 -10000 0 -0.54 8 8
CSNK1D 0.028 0.005 -10000 0 -10000 0 0
CSNK1E 0.028 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.024 0.11 -10000 0 -0.62 7 7
YWHAB 0.028 0.006 -10000 0 -10000 0 0
MAPK8 0.034 0.061 0.34 2 -0.35 1 3
MAPK9 0.021 0.048 0.35 2 -10000 0 2
YWHAG 0.026 0.009 -10000 0 -10000 0 0
YWHAE 0.028 0.005 -10000 0 -10000 0 0
YWHAZ 0.027 0.007 -10000 0 -10000 0 0
SIRT1 0.041 0.016 -10000 0 -10000 0 0
SOD2 -0.059 0.18 0.45 1 -0.54 11 12
RBL2 -0.023 0.16 -10000 0 -0.95 6 6
RAL/GDP 0.016 0.034 -10000 0 -10000 0 0
CHUK 0.02 0.025 -10000 0 -10000 0 0
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CSNK1G2 0.027 0.029 -10000 0 -0.61 1 1
RAL/GTP 0.023 0.033 -10000 0 -10000 0 0
CSNK1G1 0.029 0.003 -10000 0 -10000 0 0
FASLG -0.18 0.2 -10000 0 -0.7 8 8
SKP2 0.026 0.009 -10000 0 -10000 0 0
USP7 0.029 0.006 -10000 0 -10000 0 0
IKBKB 0.02 0.024 -10000 0 -10000 0 0
CCNB1 -0.068 0.17 -10000 0 -0.68 7 7
FOXO1-3a-4/beta catenin -0.043 0.14 0.38 4 -0.41 2 6
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -10000 0 -0.38 198 198
CSNK1A1 0.022 0.012 -10000 0 -10000 0 0
SGK1 0.019 0.025 -10000 0 -10000 0 0
CSNK1G3 0.022 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.011 -10000 0 -10000 0 0
ZFAND5 0.086 0.085 0.45 8 -10000 0 8
SFN -0.036 0.18 -10000 0 -0.52 59 59
CDK2 -0.021 0.059 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.004 0.11 -10000 0 -0.52 12 12
CREBBP -0.02 0.058 -10000 0 -10000 0 0
FBXO32 -0.074 0.16 0.47 1 -0.68 4 5
BCL6 -0.029 0.16 -10000 0 -0.74 11 11
RALB 0.029 0.005 -10000 0 -10000 0 0
RALA 0.027 0.009 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.029 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.006 0.05 -10000 0 -0.41 7 7
Metarhodopsin II/Arrestin 0.017 0.059 -10000 0 -0.31 15 15
PDE6G/GNAT1/GTP 0.015 0.06 -10000 0 -0.36 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.068 -10000 0 -0.55 7 7
GRK1 0.02 0.005 -10000 0 -10000 0 0
CNG Channel -0.039 0.14 -10000 0 -0.62 7 7
mol:Na + -0.04 0.16 -10000 0 -0.51 18 18
mol:ADP 0.02 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.027 0.11 -10000 0 -0.36 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.034 0.17 -10000 0 -0.52 18 18
CNGB1 0.014 0.07 -10000 0 -0.5 9 9
RDH5 0.02 0.066 -10000 0 -0.53 7 7
SAG 0.017 0.024 -10000 0 -0.5 1 1
mol:Ca2+ -0.068 0.15 0.38 3 -0.5 17 20
Na + (4 Units) -0.041 0.15 -10000 0 -0.48 17 17
RGS9 0.013 0.091 -10000 0 -0.52 14 14
GNB1/GNGT1 -0.082 0.18 -10000 0 -0.36 150 150
GNAT1/GDP 0.015 0.1 -10000 0 -0.34 29 29
GUCY2D 0 0.11 -10000 0 -0.5 25 25
GNGT1 -0.13 0.24 -10000 0 -0.5 150 150
GUCY2F 0.019 0.004 -10000 0 -10000 0 0
GNB5 0.029 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.003 0.082 -10000 0 -0.43 10 10
mol:11-cis-retinal 0.02 0.066 -10000 0 -0.53 7 7
mol:cGMP 0.019 0.091 -10000 0 -0.43 4 4
GNB1 0.028 0.006 -10000 0 -10000 0 0
Rhodopsin 0.019 0.084 -10000 0 -0.37 22 22
SLC24A1 0.029 0.003 -10000 0 -10000 0 0
CNGA1 -0.086 0.24 -10000 0 -0.6 93 93
Metarhodopsin II 0.017 0.053 -10000 0 -0.28 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.028 0.098 -10000 0 -0.45 4 4
RGS9BP -0.001 0.13 -10000 0 -0.61 23 23
Metarhodopsin II/Transducin -0.051 0.11 -10000 0 -0.32 48 48
GCAP Family/Ca ++ 0.031 0.062 -10000 0 -0.31 15 15
PDE6A/B 0.016 0.082 -10000 0 -0.41 17 17
mol:Pi 0.026 0.11 -10000 0 -0.36 34 34
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.064 0.15 -10000 0 -0.28 152 152
PDE6B 0.022 0.063 -10000 0 -0.61 5 5
PDE6A 0.007 0.084 -10000 0 -0.5 13 13
PDE6G 0.022 0.061 -10000 0 -0.59 5 5
RHO 0.008 0.089 -10000 0 -0.5 15 15
PDE6 0.026 0.12 -10000 0 -0.6 5 5
GUCA1A 0.012 0.07 -10000 0 -0.5 9 9
GC2/GCAP Family 0.041 0.066 -10000 0 -0.43 3 3
GUCA1C 0.016 0.04 -10000 0 -0.61 2 2
GUCA1B 0.022 0.053 -10000 0 -0.5 5 5
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.09 0.16 -10000 0 -0.58 20 20
CRKL 0.005 0.11 -10000 0 -0.47 20 20
HRAS -0.009 0.13 -10000 0 -0.51 10 10
mol:PIP3 0.011 0.11 0.27 1 -0.45 19 20
SPRED1 0.029 0.003 -10000 0 -10000 0 0
SPRED2 0.027 0.029 -10000 0 -0.61 1 1
GAB1 0.004 0.12 -10000 0 -0.5 21 21
FOXO3 0.01 0.14 0.34 3 -0.53 18 21
AKT1 0.008 0.16 0.3 4 -0.52 25 29
BAD 0.011 0.15 0.33 4 -0.53 18 22
megakaryocyte differentiation -0.051 0.17 -10000 0 -0.43 54 54
GSK3B 0.012 0.15 0.31 7 -0.52 19 26
RAF1 -0.016 0.1 0.3 2 -0.41 9 11
SHC1 0.027 0.006 -10000 0 -10000 0 0
STAT3 0.003 0.12 -10000 0 -0.5 21 21
STAT1 -0.012 0.24 -10000 0 -1.1 21 21
HRAS/SPRED1 0.006 0.11 -10000 0 -0.41 9 9
cell proliferation 0.002 0.12 -10000 0 -0.51 21 21
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
TEC 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 0.009 0.13 -10000 0 -0.51 23 23
HRAS/SPRED2 0.004 0.11 -10000 0 -0.42 9 9
LYN/TEC/p62DOK 0.041 0.12 -10000 0 -0.46 20 20
MAPK3 0.011 0.092 0.29 10 -0.31 5 15
STAP1 -0.23 0.18 -10000 0 -0.38 154 154
GRAP2 -0.008 0.14 -10000 0 -0.51 35 35
JAK2 -0.012 0.22 -10000 0 -1 21 21
STAT1 (dimer) -0.009 0.23 -10000 0 -1.1 21 21
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.027 0.16 -10000 0 -0.53 20 20
actin filament polymerization -0.001 0.11 -10000 0 -0.49 20 20
LYN 0.027 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.2 0.2 -10000 0 -0.72 30 30
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
CBL/CRKL/GRB2 0.034 0.11 -10000 0 -0.45 15 15
PI3K 0.03 0.13 -10000 0 -0.5 18 18
PTEN 0.027 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.045 0.27 -10000 0 -1.2 21 21
MAPK8 0.002 0.12 -10000 0 -0.52 21 21
STAT3 (dimer) 0.003 0.12 -10000 0 -0.49 21 21
positive regulation of transcription 0.014 0.082 0.27 12 -0.27 3 15
mol:GDP -0.023 0.15 -10000 0 -0.58 9 9
PIK3C2B 0.003 0.12 -10000 0 -0.49 21 21
CBL/CRKL 0.021 0.11 -10000 0 -0.45 18 18
FER -0.002 0.12 -10000 0 -0.5 20 20
SH2B3 0.004 0.12 -10000 0 -0.5 21 21
PDPK1 0.02 0.11 0.34 6 -0.42 17 23
SNAI2 0.002 0.12 -10000 0 -0.51 21 21
positive regulation of cell proliferation 0.009 0.18 -10000 0 -0.8 21 21
KITLG 0.017 0.092 -10000 0 -0.63 10 10
cell motility 0.009 0.18 -10000 0 -0.8 21 21
PTPN6 0.026 0.008 -10000 0 -10000 0 0
EPOR 0.039 0.094 -10000 0 -1.1 2 2
STAT5A (dimer) 0.021 0.16 -10000 0 -0.65 22 22
SOCS1 0.021 0.058 -10000 0 -0.5 6 6
cell migration 0.022 0.14 0.51 26 -10000 0 26
SOS1 0.028 0.005 -10000 0 -10000 0 0
EPO -0.14 0.24 -10000 0 -0.5 163 163
VAV1 -0.099 0.23 -10000 0 -0.5 122 122
GRB10 0 0.11 0.24 1 -0.5 20 21
PTPN11 0.027 0.007 -10000 0 -10000 0 0
SCF/KIT 0.004 0.12 -10000 0 -0.52 22 22
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.01 0.086 0.3 3 -0.35 5 8
CBL 0.027 0.028 -10000 0 -0.61 1 1
KIT -0.007 0.27 -10000 0 -1.3 21 21
MAP2K2 -0.01 0.086 0.35 3 -0.35 5 8
SHC/Grb2/SOS1 0.042 0.12 -10000 0 -0.48 15 15
STAT5A 0.02 0.17 -10000 0 -0.68 22 22
GRB2 0.028 0.005 -10000 0 -10000 0 0
response to radiation 0.003 0.12 0.28 1 -0.49 21 22
SHC/GRAP2 0.013 0.1 -10000 0 -0.36 34 34
PTPRO -0.052 0.18 -10000 0 -0.44 54 54
SH2B2 -0.001 0.12 -10000 0 -0.5 20 20
DOK1 0.028 0.005 -10000 0 -10000 0 0
MATK -0.023 0.15 -10000 0 -0.53 26 26
CREBBP 0.043 0.03 -10000 0 -10000 0 0
BCL2 0.038 0.094 -10000 0 -0.86 2 2
Thromboxane A2 receptor 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
TGM2 0.022 0.058 -10000 0 -0.5 6 6
GNB1/GNG2 -0.025 0.051 -10000 0 -0.18 33 33
AKT1 0.021 0.11 0.3 6 -0.3 23 29
EGF -0.54 0.19 -10000 0 -0.61 460 460
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.011 0.067 0.33 3 -0.33 2 5
mol:Ca2+ 0.034 0.12 0.32 6 -0.3 32 38
LYN 0.01 0.061 0.37 2 -10000 0 2
RhoA/GTP 0.007 0.044 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.03 0.12 0.35 5 -0.34 33 38
GNG2 0.027 0.008 -10000 0 -10000 0 0
ARRB2 0.027 0.029 -10000 0 -0.62 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.013 0.075 0.31 2 -0.48 5 7
G beta5/gamma2 -0.032 0.068 -10000 0 -0.24 33 33
PRKCH 0.027 0.12 0.37 3 -0.34 32 35
DNM1 0.018 0.072 -10000 0 -0.52 9 9
TXA2/TP beta/beta Arrestin3 0.005 0.031 -10000 0 -0.42 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.052 0.19 -10000 0 -0.5 75 75
G12 family/GTP 0.007 0.095 -10000 0 -0.3 27 27
ADRBK1 0.029 0.003 -10000 0 -10000 0 0
ADRBK2 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.028 0.018 -10000 0 -10000 0 0
mol:GDP -0.028 0.086 0.42 4 -0.32 3 7
mol:NADP 0.026 0.009 -10000 0 -10000 0 0
RAB11A 0.029 0.003 -10000 0 -10000 0 0
PRKG1 0.013 0.097 -10000 0 -0.61 12 12
mol:IP3 0.032 0.14 0.38 4 -0.37 32 36
cell morphogenesis 0.027 0.018 -10000 0 -10000 0 0
PLCB2 0.026 0.17 0.45 3 -0.5 33 36
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.005 0.088 0.37 2 -0.33 15 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.081 0.38 1 -0.32 9 10
RHOA 0.021 0.013 -10000 0 -10000 0 0
PTGIR 0.026 0.037 -10000 0 -0.56 2 2
PRKCB1 0.029 0.13 0.36 4 -0.37 35 39
GNAQ 0.028 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.025 0.18 0.45 3 -0.51 35 38
LCK 0.003 0.084 0.33 3 -0.33 12 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.008 0.069 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.012 0.083 -10000 0 -0.42 15 15
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.07 -10000 0 -0.3 1 1
MAPK14 0.03 0.092 0.27 10 -0.24 16 26
TGM2/GTP 0.031 0.15 0.38 2 -0.41 30 32
MAPK11 0.032 0.092 0.27 10 -0.25 15 25
ARHGEF1 0.017 0.064 -10000 0 -0.19 10 10
GNAI2 0.02 0.013 -10000 0 -10000 0 0
JNK cascade 0.031 0.14 0.37 5 -0.38 35 40
RAB11/GDP 0.028 0.003 -10000 0 -10000 0 0
ICAM1 0.031 0.11 0.32 5 -0.29 37 42
cAMP biosynthetic process 0.028 0.13 0.36 5 -0.35 31 36
Gq family/GTP/EBP50 0.015 0.05 0.23 3 -0.24 4 7
actin cytoskeleton reorganization 0.027 0.018 -10000 0 -10000 0 0
SRC 0.01 0.058 0.38 1 -10000 0 1
GNB5 0.029 0.003 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.08 0.27 2 -0.3 15 17
VCAM1 0.029 0.12 0.29 7 -0.3 36 43
TP beta/Gq family/GDP/G beta5/gamma2 0.013 0.075 0.31 2 -0.48 5 7
platelet activation 0.04 0.12 0.34 11 -0.3 30 41
PGI2/IP 0.02 0.027 -10000 0 -0.41 2 2
PRKACA -0.005 0.07 -10000 0 -0.29 2 2
Gq family/GDP/G beta5/gamma2 0.01 0.072 0.26 1 -0.44 5 6
TXA2/TP beta/beta Arrestin2 0.002 0.044 -10000 0 -0.35 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.065 -10000 0 -0.28 2 2
mol:DAG 0.031 0.15 0.39 4 -0.41 35 39
EGFR 0.019 0.06 -10000 0 -0.52 6 6
TXA2/TP alpha 0.029 0.17 0.47 3 -0.47 32 35
Gq family/GTP 0.011 0.046 -10000 0 -0.27 9 9
YES1 0.012 0.063 0.37 2 -10000 0 2
GNAI2/GTP 0.001 0.058 -10000 0 -10000 0 0
PGD2/DP -0.037 0.14 -10000 0 -0.36 75 75
SLC9A3R1 0.028 0.005 -10000 0 -10000 0 0
FYN 0.011 0.062 0.33 3 -10000 0 3
mol:NO 0.026 0.009 -10000 0 -10000 0 0
GNA15 0.013 0.09 -10000 0 -0.5 15 15
PGK/cGMP 0.025 0.062 -10000 0 -0.39 10 10
RhoA/GDP 0.02 0.013 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.025 0.08 -10000 0 -0.37 1 1
NOS3 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.032 0.13 0.36 6 -0.35 30 36
PRKCB 0.033 0.13 0.34 12 -0.36 34 46
PRKCE 0.032 0.13 0.34 5 -0.35 32 37
PRKCD 0.009 0.13 0.41 3 -0.37 36 39
PRKCG 0.025 0.14 0.42 3 -0.39 38 41
muscle contraction 0.028 0.16 0.42 4 -0.48 35 39
PRKCZ 0.029 0.12 0.33 6 -0.34 34 40
ARR3 0.021 0.005 -10000 0 -10000 0 0
TXA2/TP beta 0.018 0.071 -10000 0 -10000 0 0
PRKCQ 0.025 0.13 0.36 5 -0.37 33 38
MAPKKK cascade 0.026 0.16 0.43 3 -0.44 34 37
SELE 0.023 0.14 0.29 7 -0.4 37 44
TP beta/GNAI2/GDP/G beta/gamma 0.016 0.072 -10000 0 -10000 0 0
ROCK1 0.028 0.004 -10000 0 -10000 0 0
GNA14 0.02 0.069 -10000 0 -0.61 6 6
chemotaxis 0.022 0.2 0.46 3 -0.59 37 40
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.049 -10000 0 -0.61 3 3
Rac1/GTP 0.019 0.007 -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 0.009 0.084 -10000 0 -0.3 33 33
EPHB2 0.019 0.07 -10000 0 -0.48 9 9
Syndecan-2/TACI -0.001 0.098 -10000 0 -0.3 49 49
LAMA1 0.013 0.095 -10000 0 -0.54 14 14
Syndecan-2/alpha2 ITGB1 0.051 0.05 -10000 0 -0.33 3 3
HRAS 0.028 0.024 -10000 0 -0.5 1 1
Syndecan-2/CASK 0.013 0.003 -10000 0 -10000 0 0
ITGA5 -0.007 0.13 -10000 0 -0.5 34 34
BAX 0.018 0.017 -10000 0 -10000 0 0
EPB41 0.028 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.03 0.008 -10000 0 -10000 0 0
LAMA3 0.022 0.058 -10000 0 -0.5 6 6
EZR 0.026 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.053 -10000 0 -0.5 5 5
Syndecan-2/MMP2 0.029 0.033 -10000 0 -0.32 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.046 -10000 0 -0.45 4 4
dendrite morphogenesis 0.027 0.041 -10000 0 -0.38 4 4
Syndecan-2/GM-CSF 0.014 0.053 -10000 0 -0.3 13 13
determination of left/right symmetry 0.018 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.024 0.022 -10000 0 -0.3 1 1
GNB2L1 0.022 0.012 -10000 0 -10000 0 0
MAPK3 0.011 0.052 -10000 0 -0.27 13 13
MAPK1 0.012 0.053 -10000 0 -0.27 13 13
Syndecan-2/RACK1 0.035 0.026 -10000 0 -0.26 1 1
NF1 0.028 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.018 0.004 -10000 0 -10000 0 0
ITGA2 0.021 0.059 -10000 0 -0.55 5 5
MAPK8 0.02 0.019 -10000 0 -0.38 1 1
Syndecan-2/alpha2/beta1 Integrin 0.047 0.066 -10000 0 -0.32 12 12
Syndecan-2/Kininogen -0.26 0.18 -10000 0 -0.38 351 351
ITGB1 0.028 0.004 -10000 0 -10000 0 0
SRC 0.061 0.067 0.35 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.029 0.009 -10000 0 -10000 0 0
extracellular matrix organization 0.03 0.031 -10000 0 -0.3 4 4
actin cytoskeleton reorganization 0.009 0.084 -10000 0 -0.3 33 33
Syndecan-2/Caveolin-2/Ras 0.041 0.037 -10000 0 -0.27 5 5
Syndecan-2/Laminin alpha3 0.029 0.035 -10000 0 -0.3 5 5
Syndecan-2/RasGAP 0.044 0.039 -10000 0 -0.56 1 1
alpha5/beta1 Integrin 0.014 0.1 -10000 0 -0.36 34 34
PRKCD 0.02 0.027 -10000 0 -0.5 1 1
Syndecan-2 dimer 0.028 0.041 -10000 0 -0.38 4 4
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.057 0.057 -10000 0 -0.54 1 1
RHOA 0.021 0.013 -10000 0 -10000 0 0
SDCBP 0.027 0.007 -10000 0 -10000 0 0
TNFRSF13B -0.025 0.16 -10000 0 -0.5 50 50
RASA1 0.024 0.03 -10000 0 -0.61 1 1
alpha2/beta1 Integrin 0.034 0.046 -10000 0 -0.45 4 4
Syndecan-2/Synbindin 0.033 0.009 -10000 0 -10000 0 0
TGFB1 0.024 0.047 -10000 0 -0.5 4 4
CASP3 0.022 0.033 -10000 0 -0.27 1 1
FN1 -0.012 0.14 -10000 0 -0.51 37 37
Syndecan-2/IL8 0.01 0.087 -10000 0 -0.32 32 32
SDC2 0.018 0.004 -10000 0 -10000 0 0
KNG1 -0.43 0.28 -10000 0 -0.6 370 370
Syndecan-2/Neurofibromin 0.033 0.009 -10000 0 -10000 0 0
TRAPPC4 0.029 0.003 -10000 0 -10000 0 0
CSF2 0.003 0.086 -10000 0 -0.5 14 14
Syndecan-2/TGFB1 0.03 0.031 -10000 0 -0.3 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.03 0.008 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.034 0.025 -10000 0 -10000 0 0
PRKACA 0.03 0.031 -10000 0 -10000 0 0
angiogenesis 0.01 0.087 -10000 0 -0.32 32 32
MMP2 0.022 0.055 -10000 0 -0.52 5 5
IL8 -0.009 0.14 -10000 0 -0.53 34 34
calcineurin-NFAT signaling pathway -0.001 0.098 -10000 0 -0.3 49 49
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.026 0.096 0.45 3 -10000 0 3
CRKL -0.019 0.14 0.37 15 -10000 0 15
mol:DAG -0.014 0.099 -10000 0 -10000 0 0
HRAS -0.001 0.14 0.39 20 -10000 0 20
MAPK8 -0.045 0.15 0.31 2 -0.36 1 3
RAP1A -0.02 0.14 0.37 16 -10000 0 16
GAB1 -0.021 0.14 0.36 14 -10000 0 14
MAPK14 -0.044 0.15 0.31 2 -10000 0 2
EPO -0.14 0.24 -10000 0 -0.5 163 163
PLCG1 -0.015 0.1 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.03 -10000 0 -10000 0 0
RAPGEF1 0.028 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.057 0.16 -10000 0 -0.29 161 161
GAB1/SHC/GRB2/SOS1 -0.004 0.13 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.086 0.19 -10000 0 -0.36 163 163
IRS2 -0.024 0.14 0.36 14 -0.45 1 15
STAT1 -0.008 0.1 -10000 0 -10000 0 0
STAT5B -0.011 0.1 -10000 0 -10000 0 0
cell proliferation -0.04 0.14 0.36 7 -0.33 1 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.024 0.1 -10000 0 -0.39 1 1
TEC -0.021 0.14 0.36 14 -10000 0 14
SOCS3 0.026 0.034 -10000 0 -0.5 2 2
STAT1 (dimer) -0.006 0.1 -10000 0 -10000 0 0
JAK2 0.014 0.03 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
EPO/EPOR (dimer)/JAK2 -0.013 0.14 -10000 0 -10000 0 0
EPO/EPOR -0.086 0.19 -10000 0 -0.36 163 163
LYN 0.029 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.015 0.13 0.29 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.016 0.03 -10000 0 -10000 0 0
SHC1 0.027 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.051 0.16 -10000 0 -0.28 153 153
mol:IP3 -0.014 0.099 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.012 0.13 0.34 6 -0.42 2 8
SH2B3 0.013 0.028 -10000 0 -10000 0 0
NFKB1 -0.044 0.15 0.31 2 -0.59 1 3
EPO/EPOR (dimer)/JAK2/SOCS3 -0.036 0.083 -10000 0 -0.31 4 4
PTPN6 -0.031 0.13 0.3 3 -10000 0 3
TEC/VAV2/GRB2 -0.007 0.13 0.29 4 -10000 0 4
EPOR 0.016 0.03 -10000 0 -10000 0 0
INPP5D 0.023 0.047 -10000 0 -0.5 4 4
mol:GDP -0.005 0.13 -10000 0 -10000 0 0
SOS1 0.028 0.005 -10000 0 -10000 0 0
PLCG2 0.02 0.068 -10000 0 -0.55 7 7
CRKL/CBL/C3G -0.006 0.13 0.29 5 -0.48 1 6
VAV2 -0.02 0.14 0.37 14 -10000 0 14
CBL -0.022 0.14 0.35 13 -0.52 1 14
SHC/Grb2/SOS1 -0.03 0.11 -10000 0 -10000 0 0
STAT5A -0.011 0.1 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.004 0.11 -10000 0 -10000 0 0
LYN/PLCgamma2 0.035 0.05 -10000 0 -0.39 6 6
PTPN11 0.028 0.005 -10000 0 -10000 0 0
BTK -0.074 0.18 0.37 14 -0.45 28 42
BCL2 0.028 0.099 0.42 4 -10000 0 4
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.022 0.051 -10000 0 -0.32 3 3
NT3 (dimer)/TRKC 0.012 0.12 -10000 0 -0.47 26 26
NT3 (dimer)/TRKB -0.044 0.19 -10000 0 -0.38 105 105
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.03 -10000 0 -0.44 1 1
RAPGEF1 0.028 0.005 -10000 0 -10000 0 0
BDNF -0.042 0.18 -10000 0 -0.51 67 67
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
DYNLT1 0.026 0.008 -10000 0 -10000 0 0
NTRK1 -0.016 0.16 -10000 0 -0.58 36 36
NTRK2 -0.087 0.24 -10000 0 -0.59 95 95
NTRK3 -0.007 0.15 -10000 0 -0.61 28 28
NT-4/5 (dimer)/TRKB -0.052 0.19 -10000 0 -0.39 111 111
neuron apoptosis 0.074 0.18 0.5 41 -10000 0 41
SHC 2-3/Grb2 -0.081 0.19 -10000 0 -0.55 41 41
SHC1 0.027 0.006 -10000 0 -10000 0 0
SHC2 -0.04 0.13 -10000 0 -0.5 21 21
SHC3 -0.11 0.22 -10000 0 -0.56 85 85
STAT3 (dimer) 0.026 0.048 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.004 0.14 -10000 0 -0.36 68 68
RIN/GDP 0.044 0.084 0.29 15 -0.3 6 21
GIPC1 0.027 0.028 -10000 0 -0.61 1 1
KRAS 0.028 0.005 -10000 0 -10000 0 0
DNAJA3 -0.027 0.097 -10000 0 -0.38 16 16
RIN/GTP 0.014 0.017 -10000 0 -0.36 1 1
CCND1 0.011 0.084 -10000 0 -0.43 18 18
MAGED1 0.029 0.003 -10000 0 -10000 0 0
PTPN11 0.028 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.049 -10000 0 -0.53 4 4
SHC/GRB2/SOS1 0.054 0.016 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.043 0.18 -10000 0 -0.35 120 120
TRKA/NEDD4-2 0.006 0.12 -10000 0 -0.44 33 33
ELMO1 0.025 0.025 -10000 0 -0.5 1 1
RhoG/GTP/ELMO1/DOCK1 0.032 0.027 -10000 0 -0.35 2 2
NGF -0.021 0.15 -10000 0 -0.5 47 47
HRAS 0.028 0.024 -10000 0 -0.5 1 1
DOCK1 0.026 0.029 -10000 0 -0.61 1 1
GAB2 0.029 0.003 -10000 0 -10000 0 0
RIT2 0.019 0.024 -10000 0 -0.5 1 1
RIT1 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.028 0.005 -10000 0 -10000 0 0
DNM1 0.018 0.072 -10000 0 -0.52 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.011 0.1 -10000 0 -0.37 15 15
mol:GDP 0.05 0.12 0.4 15 -0.44 9 24
NGF (dimer) -0.021 0.15 -10000 0 -0.5 47 47
RhoG/GDP 0.018 0.018 -10000 0 -0.36 1 1
RIT1/GDP 0.045 0.078 0.3 12 -0.3 5 17
TIAM1 0.028 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
BDNF (dimer)/TRKB -0.068 0.2 -10000 0 -0.38 142 142
KIDINS220/CRKL/C3G 0.041 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.027 -10000 0 -0.45 1 1
FRS2 family/SHP2 0.054 0.016 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.068 0.022 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.022 0.059 -10000 0 -0.57 5 5
RAP1/GDP 0.03 0.055 -10000 0 -0.26 4 4
KIDINS220/CRKL 0.028 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.042 0.18 -10000 0 -0.51 67 67
ubiquitin-dependent protein catabolic process -0.009 0.14 -10000 0 -0.34 78 78
Schwann cell development -0.018 0.025 -10000 0 -10000 0 0
EHD4 0.029 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.067 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.037 0.024 -10000 0 -10000 0 0
RAP1B 0.028 0.005 -10000 0 -10000 0 0
RAP1A 0.028 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.057 0.18 -10000 0 -0.57 25 25
ABL1 0.028 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.1 -10000 0 -0.46 8 8
STAT3 0.026 0.048 -10000 0 -10000 0 0
axon guidance -0.064 0.17 -10000 0 -0.55 25 25
MAPK3 -0.054 0.15 -10000 0 -0.41 37 37
MAPK1 -0.053 0.15 -10000 0 -0.41 37 37
CDC42/GDP 0.052 0.086 0.33 16 -0.31 4 20
NTF3 0.022 0.059 -10000 0 -0.57 5 5
NTF4 0.017 0.049 -10000 0 -0.53 4 4
NGF (dimer)/TRKA/FAIM -0.01 0.14 -10000 0 -0.39 32 32
PI3K 0.036 0.034 -10000 0 -0.45 2 2
FRS3 0.028 0.006 -10000 0 -10000 0 0
FAIM 0.027 0.007 -10000 0 -10000 0 0
GAB1 0.028 0.004 -10000 0 -10000 0 0
RASGRF1 -0.031 0.1 -10000 0 -0.38 20 20
SOS1 0.028 0.005 -10000 0 -10000 0 0
MCF2L 0.001 0.098 -10000 0 -0.4 26 26
RGS19 0.028 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.093 0.31 6 -0.57 6 12
Rac1/GDP 0.041 0.073 0.28 7 -0.31 5 12
NGF (dimer)/TRKA/GRIT -0.024 0.14 -10000 0 -0.34 79 79
neuron projection morphogenesis 0.003 0.15 0.38 2 -0.97 7 9
NGF (dimer)/TRKA/NEDD4-2 -0.009 0.14 -10000 0 -0.34 78 78
MAP2K1 0.037 0.048 0.43 3 -10000 0 3
NGFR -0.008 0.14 -10000 0 -0.51 34 34
NGF (dimer)/TRKA/GIPC/GAIP -0.005 0.097 -10000 0 -0.39 11 11
RAS family/GTP/PI3K 0.027 0.031 -10000 0 -0.42 2 2
FRS2 family/SHP2/GRB2/SOS1 0.077 0.027 -10000 0 -10000 0 0
NRAS 0.028 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
PRKCI 0.027 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCZ 0.024 0.049 -10000 0 -0.61 3 3
MAPKKK cascade -0.061 0.2 -10000 0 -0.61 51 51
RASA1 0.024 0.03 -10000 0 -0.61 1 1
TRKA/c-Abl 0.006 0.12 -10000 0 -0.44 33 33
SQSTM1 0.021 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.051 0.19 -10000 0 -0.38 90 90
NGF (dimer)/TRKA/p62/Atypical PKCs 0.012 0.12 -10000 0 -0.34 18 18
MATK -0.026 0.16 -10000 0 -0.51 52 52
NEDD4L 0.027 0.029 -10000 0 -0.61 1 1
RAS family/GDP -0.009 0.035 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.027 0.1 -10000 0 -0.32 39 39
Rac1/GTP -0.013 0.07 -10000 0 -0.32 6 6
FRS2 family/SHP2/CRK family 0.078 0.026 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.002 0.22 -10000 0 -1.1 20 20
MKNK1 0.028 0.006 -10000 0 -10000 0 0
MAPK14 0.028 0.073 -10000 0 -0.3 20 20
ATF2/c-Jun 0.024 0.059 -10000 0 -0.38 1 1
MAPK11 0.028 0.079 -10000 0 -0.31 22 22
MITF 0.017 0.09 -10000 0 -0.38 21 21
MAPKAPK5 0.027 0.083 -10000 0 -0.35 20 20
KRT8 0.027 0.085 -10000 0 -0.35 21 21
MAPKAPK3 0.021 0.013 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.036 0.11 -10000 0 -0.46 21 21
CEBPB 0.025 0.088 -10000 0 -0.35 20 20
SLC9A1 0.026 0.088 -10000 0 -0.36 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.03 0.087 -10000 0 -0.34 22 22
p38alpha-beta/MNK1 0.05 0.096 -10000 0 -0.37 20 20
JUN 0.026 0.06 -10000 0 -0.38 1 1
PPARGC1A -0.008 0.14 -10000 0 -0.35 66 66
USF1 0.027 0.08 -10000 0 -0.34 20 20
RAB5/GDP/GDI1 0.019 0.063 -10000 0 -0.39 2 2
NOS2 0.028 0.09 -10000 0 -0.5 2 2
DDIT3 0.026 0.088 -10000 0 -0.36 22 22
RAB5A 0.021 0.013 -10000 0 -10000 0 0
HSPB1 0.04 0.1 0.3 41 -0.42 4 45
p38alpha-beta/HBP1 0.045 0.093 -10000 0 -0.37 18 18
CREB1 0.027 0.092 -10000 0 -0.39 20 20
RAB5/GDP 0.015 0.01 -10000 0 -10000 0 0
EIF4E 0.024 0.077 -10000 0 -0.5 2 2
RPS6KA4 0.028 0.085 -10000 0 -0.36 20 20
PLA2G4A 0.018 0.087 -10000 0 -0.45 6 6
GDI1 0.028 0.085 -10000 0 -0.35 21 21
TP53 0.017 0.1 -10000 0 -0.45 21 21
RPS6KA5 0.025 0.09 -10000 0 -0.38 20 20
ESR1 0.023 0.093 -10000 0 -0.37 23 23
HBP1 0.026 0.009 -10000 0 -10000 0 0
MEF2C 0.025 0.08 -10000 0 -0.36 17 17
MEF2A 0.029 0.083 -10000 0 -0.36 19 19
EIF4EBP1 0.022 0.099 -10000 0 -0.41 20 20
KRT19 -0.041 0.18 -10000 0 -0.37 97 97
ELK4 0.027 0.082 -10000 0 -0.35 20 20
ATF6 0.027 0.08 -10000 0 -0.34 20 20
ATF1 0.027 0.092 -10000 0 -0.39 20 20
p38alpha-beta/MAPKAPK2 0.05 0.094 -10000 0 -0.36 21 21
p38alpha-beta/MAPKAPK3 0.034 0.095 -10000 0 -0.58 2 2
Endothelins

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
AKT1 0.002 0.15 0.37 2 -0.45 5 7
PTK2B 0.026 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.041 0.14 0.47 2 -0.67 6 8
EDN1 0.003 0.14 0.45 1 -0.44 21 22
EDN3 0.012 0.077 -10000 0 -0.5 11 11
EDN2 -0.04 0.18 -10000 0 -0.51 64 64
HRAS/GDP 0.029 0.14 0.31 5 -0.54 12 17
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.018 0.11 0.27 1 -0.5 10 11
ADCY4 0.004 0.12 0.34 1 -0.39 4 5
ADCY5 -0.01 0.14 0.35 2 -0.49 14 16
ADCY6 0.003 0.12 0.34 1 -0.43 4 5
ADCY7 -0.005 0.13 0.34 1 -0.42 8 9
ADCY1 -0.004 0.12 0.34 1 -0.44 6 7
ADCY2 -0.056 0.15 0.35 1 -0.4 27 28
ADCY3 0.006 0.12 0.35 2 -0.43 4 6
ADCY8 -0.076 0.16 0.34 1 -0.45 25 26
ADCY9 0.004 0.12 0.35 2 -0.43 4 6
arachidonic acid secretion 0.036 0.14 0.36 7 -0.55 12 19
ETB receptor/Endothelin-1/Gq/GTP 0.024 0.08 -10000 0 -0.51 5 5
GNAO1 0.023 0.05 -10000 0 -0.53 4 4
HRAS 0.028 0.024 -10000 0 -0.5 1 1
ETA receptor/Endothelin-1/G12/GTP 0.037 0.16 0.4 19 -0.47 4 23
ETA receptor/Endothelin-1/Gs/GTP 0.038 0.16 0.38 22 -0.41 6 28
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.019 0.2 0.44 1 -0.56 48 49
EDNRB 0.017 0.053 -10000 0 -0.47 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.022 0.2 0.63 1 -0.49 39 40
CYSLTR1 0.003 0.15 0.44 1 -0.52 5 6
SLC9A1 0.013 0.089 0.28 2 -0.31 4 6
mol:GDP 0.02 0.14 0.32 7 -0.57 13 20
SLC9A3 -0.33 0.28 0.38 1 -0.65 130 131
RAF1 0.011 0.14 0.33 4 -0.62 11 15
JUN 0.042 0.14 -10000 0 -0.67 5 5
JAK2 0.003 0.15 0.37 2 -0.49 5 7
mol:IP3 0.013 0.12 0.25 1 -0.56 10 11
ETA receptor/Endothelin-1 0.027 0.21 0.45 27 -0.53 7 34
PLCB1 0.02 0.075 -10000 0 -0.61 7 7
PLCB2 -0.031 0.17 -10000 0 -0.5 58 58
ETA receptor/Endothelin-3 0.022 0.096 -10000 0 -0.37 11 11
FOS 0.022 0.18 0.39 4 -0.81 16 20
Gai/GDP -0.11 0.26 -10000 0 -0.56 90 90
CRK 0.028 0.005 -10000 0 -10000 0 0
mol:Ca ++ 0.001 0.16 0.32 1 -0.57 12 13
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
PRKCB1 0.013 0.12 0.24 1 -0.53 10 11
GNAQ 0.03 0.007 -10000 0 -10000 0 0
GNAZ 0.025 0.049 -10000 0 -0.61 3 3
GNAL 0.028 0.005 -10000 0 -10000 0 0
Gs family/GDP 0.025 0.13 0.29 5 -0.54 11 16
ETA receptor/Endothelin-1/Gq/GTP 0.032 0.1 0.23 1 -0.51 4 5
MAPK14 0.012 0.095 0.33 1 -0.47 10 11
TRPC6 0.041 0.14 0.47 2 -0.71 6 8
GNAI2 0.02 0.013 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.03 -10000 0 -0.61 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.1 -10000 0 -0.49 11 11
ETB receptor/Endothelin-2 -0.02 0.14 -10000 0 -0.39 60 60
ETB receptor/Endothelin-3 0.02 0.07 -10000 0 -0.37 13 13
ETB receptor/Endothelin-1 0.015 0.12 -10000 0 -0.36 16 16
MAPK3 0.025 0.17 0.38 5 -0.72 16 21
MAPK1 0.025 0.17 0.39 5 -0.7 17 22
Rac1/GDP 0.021 0.13 0.3 2 -0.55 11 13
cAMP biosynthetic process -0.017 0.14 0.36 9 -0.48 8 17
MAPK8 0.039 0.16 0.4 1 -0.67 12 13
SRC 0.028 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.01 0.072 -10000 0 -0.45 5 5
p130Cas/CRK/Src/PYK2 0.034 0.14 0.42 9 -0.6 9 18
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.021 0.13 0.3 2 -0.55 11 13
COL1A2 -0.017 0.21 0.7 1 -0.54 50 51
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.017 0.15 0.3 1 -0.38 59 60
mol:DAG 0.013 0.12 0.25 1 -0.56 10 11
MAP2K2 0.022 0.15 0.46 3 -0.58 18 21
MAP2K1 0.024 0.15 0.37 5 -0.58 17 22
EDNRA 0.021 0.11 0.43 1 -0.4 2 3
positive regulation of muscle contraction 0.021 0.14 0.42 7 -0.41 4 11
Gq family/GDP 0.033 0.14 -10000 0 -0.55 12 12
HRAS/GTP 0.016 0.14 0.29 7 -0.58 12 19
PRKCH 0.013 0.11 -10000 0 -0.55 8 8
RAC1 0.026 0.009 -10000 0 -10000 0 0
PRKCA 0.016 0.12 0.24 4 -0.56 9 13
PRKCB 0.016 0.13 0.28 14 -0.55 13 27
PRKCE 0.015 0.12 0.24 5 -0.53 10 15
PRKCD 0 0.11 -10000 0 -0.55 9 9
PRKCG 0 0.13 -10000 0 -0.59 12 12
regulation of vascular smooth muscle contraction 0.02 0.2 0.42 5 -0.93 16 21
PRKCQ 0.007 0.13 0.28 1 -0.61 11 12
PLA2G4A 0.035 0.15 0.37 7 -0.6 12 19
GNA14 0.023 0.069 -10000 0 -0.61 6 6
GNA15 0.015 0.09 -10000 0 -0.5 15 15
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA11 0.027 0.049 -10000 0 -0.61 3 3
Rac1/GTP 0.038 0.16 0.4 19 -0.47 4 23
MMP1 -0.097 0.26 0.65 1 -0.58 91 92
LPA receptor mediated events

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
GNB1/GNG2 0.036 0.084 -10000 0 -0.34 21 21
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.077 0.28 2 -10000 0 2
AP1 0.019 0.091 -10000 0 -0.34 8 8
mol:PIP3 0 0.063 -10000 0 -0.47 1 1
AKT1 0.004 0.11 0.31 4 -0.38 10 14
PTK2B 0.002 0.085 0.22 2 -0.35 11 13
RHOA -0.044 0.12 -10000 0 -0.35 24 24
PIK3CB 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.057 0.42 2 -0.38 2 4
MAGI3 0.025 0.04 -10000 0 -0.61 2 2
RELA 0.029 0.003 -10000 0 -10000 0 0
apoptosis 0.008 0.074 -10000 0 -0.32 22 22
HRAS/GDP 0.02 0.017 -10000 0 -0.36 1 1
positive regulation of microtubule depolymerization 0.006 0.086 0.26 8 -0.32 12 20
NF kappa B1 p50/RelA 0.024 0.075 -10000 0 -0.39 1 1
endothelial cell migration 0.005 0.094 -10000 0 -0.4 25 25
ADCY4 0.003 0.098 -10000 0 -0.44 20 20
ADCY5 -0.003 0.11 -10000 0 -0.42 26 26
ADCY6 0.003 0.097 -10000 0 -0.44 20 20
ADCY7 0 0.098 -10000 0 -0.44 20 20
ADCY1 -0.001 0.096 0.21 1 -0.43 21 22
ADCY2 -0.02 0.11 -10000 0 -0.43 24 24
ADCY3 0.003 0.097 -10000 0 -0.43 21 21
ADCY8 -0.027 0.11 0.21 1 -0.42 27 28
ADCY9 0.002 0.096 -10000 0 -0.44 20 20
GSK3B 0.005 0.082 0.26 5 -0.37 8 13
arachidonic acid secretion 0.003 0.099 -10000 0 -0.42 22 22
GNG2 0.027 0.008 -10000 0 -10000 0 0
TRIP6 0.026 0.011 -10000 0 -10000 0 0
GNAO1 0.006 0.088 -10000 0 -0.36 25 25
HRAS 0.028 0.024 -10000 0 -0.5 1 1
NFKBIA 0.025 0.077 0.33 5 -0.38 2 7
GAB1 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.17 -10000 0 -0.83 19 19
JUN 0.028 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.038 0.024 -10000 0 -0.38 1 1
TIAM1 -0.004 0.2 -10000 0 -0.98 20 20
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:IP3 0.024 0.057 0.42 2 -0.39 2 4
PLCB3 0.032 0.039 -10000 0 -0.35 1 1
FOS 0.012 0.096 -10000 0 -0.6 12 12
positive regulation of mitosis 0.003 0.099 -10000 0 -0.42 22 22
LPA/LPA1-2-3 0.034 0.088 -10000 0 -0.34 24 24
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
stress fiber formation 0.015 0.085 0.31 2 -0.36 7 9
GNAZ 0.007 0.089 -10000 0 -0.38 24 24
EGFR/PI3K-beta/Gab1 0.01 0.069 -10000 0 -0.5 1 1
positive regulation of dendritic cell cytokine production 0.032 0.087 -10000 0 -0.33 24 24
LPA/LPA2/MAGI-3 0.037 0.031 -10000 0 -0.38 2 2
ARHGEF1 0.031 0.088 0.36 6 -0.32 14 20
GNAI2 0.003 0.079 -10000 0 -0.36 21 21
GNAI3 0.008 0.084 -10000 0 -0.37 22 22
GNAI1 0.008 0.078 -10000 0 -0.36 19 19
LPA/LPA3 0.017 0.033 -10000 0 -0.36 3 3
LPA/LPA2 0.023 0.014 -10000 0 -0.17 1 1
LPA/LPA1 0.006 0.098 -10000 0 -0.4 26 26
HB-EGF/EGFR -0.1 0.16 -10000 0 -0.31 178 178
HBEGF -0.13 0.18 -10000 0 -0.36 184 184
mol:DAG 0.024 0.057 0.42 2 -0.39 2 4
cAMP biosynthetic process 0.008 0.11 0.36 10 -0.39 21 31
NFKB1 0.027 0.029 -10000 0 -0.61 1 1
SRC 0.028 0.006 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
LYN 0.028 0.08 0.33 7 -0.38 3 10
GNAQ 0.02 0.023 -10000 0 -10000 0 0
LPAR2 0.029 0.003 -10000 0 -10000 0 0
LPAR3 0.02 0.041 -10000 0 -0.5 3 3
LPAR1 0.004 0.12 -10000 0 -0.57 22 22
IL8 -0.024 0.14 0.29 1 -0.48 9 10
PTK2 0.011 0.077 -10000 0 -0.32 20 20
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
CASP3 0.008 0.075 -10000 0 -0.32 22 22
EGFR 0.019 0.06 -10000 0 -0.52 6 6
PLCG1 0.018 0.037 -10000 0 -0.43 1 1
PLD2 0.012 0.077 -10000 0 -0.32 20 20
G12/G13 0.037 0.075 -10000 0 -0.34 14 14
PI3K-beta -0.026 0.1 -10000 0 -0.43 10 10
cell migration 0.024 0.064 -10000 0 -0.26 13 13
SLC9A3R2 0.026 0.029 -10000 0 -0.61 1 1
PXN 0.015 0.086 0.31 2 -0.36 7 9
HRAS/GTP 0.003 0.099 -10000 0 -0.44 21 21
RAC1 0.026 0.009 -10000 0 -10000 0 0
MMP9 -0.21 0.26 -10000 0 -0.5 230 230
PRKCE 0.027 0.029 -10000 0 -0.61 1 1
PRKCD 0.021 0.06 0.36 4 -0.37 2 6
Gi(beta/gamma) 0.007 0.095 -10000 0 -0.41 22 22
mol:LPA -0.002 0.019 -10000 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.031 0.085 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.099 -10000 0 -0.42 22 22
contractile ring contraction involved in cytokinesis -0.046 0.12 -10000 0 -0.36 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.016 0.046 -10000 0 -0.38 5 5
GNA15 0.014 0.045 -10000 0 -0.38 1 1
GNA12 0.026 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
MAPT 0.005 0.088 0.26 7 -0.32 13 20
GNA11 0.019 0.034 -10000 0 -0.32 3 3
Rac1/GTP 0.012 0.18 -10000 0 -0.88 19 19
MMP2 0.005 0.095 -10000 0 -0.4 25 25
Presenilin action in Notch and Wnt signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.034 0.079 -10000 0 -0.62 1 1
HDAC1 0.025 0.007 -10000 0 -10000 0 0
AES 0.028 0.003 -10000 0 -10000 0 0
FBXW11 0.022 0.013 -10000 0 -10000 0 0
DTX1 -0.028 0.18 -10000 0 -0.6 45 45
LRP6/FZD1 0.037 0.014 -10000 0 -10000 0 0
TLE1 0.027 0.006 -10000 0 -10000 0 0
AP1 -0.066 0.15 -10000 0 -0.31 133 133
NCSTN 0.027 0.006 -10000 0 -10000 0 0
ADAM10 0.027 0.028 -10000 0 -0.61 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.057 -10000 0 -0.74 1 1
NICD/RBPSUH 0.036 0.079 -10000 0 -0.61 1 1
WIF1 0.016 0.061 -10000 0 -0.59 5 5
NOTCH1 0.02 0.08 -10000 0 -0.64 1 1
PSENEN 0.029 0.003 -10000 0 -10000 0 0
KREMEN2 -0.034 0.17 -10000 0 -0.5 58 58
DKK1 0.005 0.11 -10000 0 -0.54 21 21
beta catenin/beta TrCP1 0.033 0.089 0.29 4 -10000 0 4
APH1B 0.029 0.003 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
AXIN1 0.011 0.067 0.27 6 -0.3 2 8
CtBP/CBP/TCF1/TLE1/AES 0.025 0.036 -10000 0 -0.35 2 2
PSEN1 0.027 0.008 -10000 0 -10000 0 0
FOS 0.012 0.096 -10000 0 -0.6 12 12
JUN 0.028 0.006 -10000 0 -10000 0 0
MAP3K7 0.026 0.007 -10000 0 -10000 0 0
CTNNB1 0.033 0.11 0.28 15 -0.33 4 19
MAPK3 0.028 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.001 0.13 -10000 0 -0.32 72 72
HNF1A 0.022 0.057 -10000 0 -0.61 4 4
CTBP1 0.028 0.004 -10000 0 -10000 0 0
MYC 0.009 0.12 -10000 0 -0.76 8 8
NKD1 -0.13 0.28 -10000 0 -0.6 130 130
FZD1 0.026 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.12 -10000 0 -0.6 4 4
apoptosis -0.065 0.15 -10000 0 -0.31 133 133
Delta 1/NOTCHprecursor 0.033 0.079 -10000 0 -0.61 1 1
DLL1 0.026 0.008 -10000 0 -10000 0 0
PPARD 0.008 0.15 -10000 0 -0.75 18 18
Gamma Secretase 0.076 0.029 -10000 0 -10000 0 0
APC 0.011 0.073 0.28 6 -0.4 3 9
DVL1 0.018 0.034 -10000 0 -0.42 2 2
CSNK2A1 0.028 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0 0.14 -10000 0 -0.33 66 66
LRP6 0.028 0.005 -10000 0 -10000 0 0
CSNK1A1 0.022 0.013 -10000 0 -10000 0 0
NLK 0.016 0.007 -10000 0 -10000 0 0
CCND1 0.021 0.087 -10000 0 -0.72 2 2
WNT1 0.001 0.12 -10000 0 -0.5 25 25
Axin1/APC/beta catenin 0.077 0.099 0.36 22 -10000 0 22
DKK2 0.003 0.12 -10000 0 -0.54 23 23
NOTCH1 precursor/DVL1 0.042 0.081 -10000 0 -0.55 1 1
GSK3B 0.027 0.008 -10000 0 -10000 0 0
FRAT1 0.027 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.008 0.12 -10000 0 -0.6 4 4
PPP2R5D 0.082 0.15 0.33 116 -0.39 8 124
MAPK1 0.028 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.041 0.085 -10000 0 -0.35 4 4
RBPJ 0.028 0.004 -10000 0 -10000 0 0
CREBBP 0.03 0.008 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.063 0.14 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.038 0.13 0.32 2 -0.66 1 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.058 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.055 0.081 -10000 0 -0.29 3 3
CaM/Ca2+ -0.057 0.14 -10000 0 -10000 0 0
RAP1A 0.028 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.068 0.12 -10000 0 -0.55 1 1
AKT1 -0.044 0.14 0.36 12 -10000 0 12
MAP2K1 -0.062 0.12 0.3 6 -10000 0 6
MAP3K11 -0.07 0.13 0.3 10 -0.52 1 11
IFNGR1 0.005 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.16 0.24 -10000 0 -0.51 136 136
Rap1/GTP -0.06 0.095 -10000 0 -10000 0 0
CRKL/C3G 0.041 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.068 0.16 -10000 0 -10000 0 0
CEBPB 0.001 0.14 0.51 10 -10000 0 10
STAT3 0.028 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.046 0.15 -10000 0 -0.66 1 1
STAT1 -0.067 0.13 0.31 11 -0.55 1 12
CALM1 0.027 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.21 0.26 -10000 0 -0.5 230 230
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
STAT1 (dimer)/PIAS1 -0.054 0.13 0.31 6 -0.52 1 7
CEBPB/PTGES2/Cbp/p300 -0.003 0.074 -10000 0 -0.38 1 1
mol:Ca2+ -0.064 0.14 -10000 0 -10000 0 0
MAPK3 -0.029 0.11 0.42 3 -0.63 1 4
STAT1 (dimer) -0.069 0.11 -10000 0 -0.42 2 2
MAPK1 -0.028 0.12 0.45 4 -0.6 2 6
JAK2 0.005 0.029 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
JAK1 0.005 0.03 -10000 0 -10000 0 0
CAMK2D 0.028 0.004 -10000 0 -10000 0 0
DAPK1 0.011 0.12 0.42 14 -0.61 3 17
SMAD7 -0.011 0.073 0.23 19 -10000 0 19
CBL/CRKL/C3G -0.048 0.13 0.3 9 -10000 0 9
PI3K -0.055 0.13 -10000 0 -10000 0 0
IFNG -0.21 0.26 -10000 0 -0.5 230 230
apoptosis 0.004 0.12 0.4 14 -0.44 7 21
CAMK2G 0.028 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.004 -10000 0 -10000 0 0
CAMK2A -0.13 0.27 -10000 0 -0.61 122 122
CAMK2B -0.062 0.22 -10000 0 -0.6 71 71
FRAP1 -0.046 0.13 0.35 12 -10000 0 12
PRKCD -0.055 0.12 0.33 10 -10000 0 10
RAP1B 0.028 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.055 0.081 -10000 0 -0.29 3 3
PTPN2 0.028 0.005 -10000 0 -10000 0 0
EP300 0.028 0.029 -10000 0 -0.61 1 1
IRF1 -0.03 0.1 0.41 5 -0.66 1 6
STAT1 (dimer)/PIASy -0.057 0.13 0.33 5 -0.52 1 6
SOCS1 0.027 0.063 -10000 0 -0.99 1 1
mol:GDP -0.048 0.13 0.28 6 -10000 0 6
CASP1 -0.011 0.073 0.23 19 -10000 0 19
PTGES2 0.025 0.04 -10000 0 -0.61 2 2
IRF9 0.022 0.065 0.24 18 -10000 0 18
mol:PI-3-4-5-P3 -0.061 0.12 -10000 0 -10000 0 0
RAP1/GDP -0.049 0.11 -10000 0 -10000 0 0
CBL -0.071 0.13 0.3 10 -0.32 1 11
MAP3K1 -0.067 0.12 0.32 6 -10000 0 6
PIAS1 0.029 0.003 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.055 0.081 -10000 0 -0.29 3 3
PTPN11 -0.079 0.13 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
RAPGEF1 0.028 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.011 0.055 -10000 0 -0.29 13 13
epithelial cell differentiation 0.027 0.067 -10000 0 -0.32 13 13
CYFIP2 0.013 0.075 -10000 0 -0.61 7 7
ENAH 0.056 0.1 0.38 17 -10000 0 17
EGFR 0.019 0.06 -10000 0 -0.52 6 6
EPHA2 0.026 0.029 -10000 0 -0.61 1 1
MYO6 0.055 0.11 0.38 13 -0.45 2 15
CTNNB1 0.02 0.013 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.036 0.056 -10000 0 -0.38 7 7
AQP5 -0.11 0.24 -10000 0 -0.5 108 108
CTNND1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.059 0.11 0.39 13 -10000 0 13
regulation of calcium-dependent cell-cell adhesion 0.05 0.11 0.4 11 -0.39 1 12
EGF -0.54 0.19 -10000 0 -0.61 460 460
NCKAP1 0.028 0.006 -10000 0 -10000 0 0
AQP3 0.004 0.15 -10000 0 -0.53 29 29
cortical microtubule organization 0.027 0.067 -10000 0 -0.32 13 13
GO:0000145 0.049 0.1 0.39 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.069 -10000 0 -0.33 13 13
MLLT4 0.026 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.044 -10000 0 -10000 0 0
ARF6 0.027 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.039 -10000 0 -0.35 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.081 0.37 2 -10000 0 2
PVRL2 0.029 0.003 -10000 0 -10000 0 0
ZYX 0.045 0.092 0.36 5 -10000 0 5
ARF6/GTP 0.066 0.042 -10000 0 -10000 0 0
CDH1 0.007 0.11 -10000 0 -0.59 17 17
EGFR/EGFR/EGF/EGF -0.23 0.14 -10000 0 -0.55 18 18
RhoA/GDP 0.028 0.064 -10000 0 -10000 0 0
actin cytoskeleton organization 0.047 0.1 0.34 12 -0.42 2 14
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
GIT1 0.028 0.004 -10000 0 -10000 0 0
IGF1R 0.029 0.003 -10000 0 -10000 0 0
IGF1 0.023 0.053 -10000 0 -0.5 5 5
DIAPH1 0.029 0.11 -10000 0 -0.66 7 7
Wnt receptor signaling pathway -0.027 0.067 0.32 13 -10000 0 13
RHOA 0.021 0.013 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.045 -10000 0 -10000 0 0
CTNNA1 0.022 0.012 -10000 0 -10000 0 0
VCL 0.048 0.1 0.35 12 -0.43 2 14
EFNA1 0.026 0.024 -10000 0 -0.5 1 1
LPP 0.043 0.092 0.39 6 -10000 0 6
Ephrin A1/EPHA2 0.022 0.061 -10000 0 -10000 0 0
SEC6/SEC8 0.001 0.047 -10000 0 -10000 0 0
MGAT3 0.05 0.11 0.41 11 -0.4 1 12
HGF/MET 0.013 0.083 -10000 0 -0.52 3 3
HGF 0.003 0.11 -10000 0 -0.54 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.056 -10000 0 -0.29 13 13
actin cable formation 0.098 0.13 0.32 72 -10000 0 72
KIAA1543 0.045 0.1 0.35 10 -0.5 2 12
KIFC3 0.048 0.092 -10000 0 -10000 0 0
NCK1 0.026 0.029 -10000 0 -0.61 1 1
EXOC3 0.026 0.009 -10000 0 -10000 0 0
ACTN1 0.05 0.099 0.43 7 -10000 0 7
NCK1/GIT1 0.039 0.025 -10000 0 -0.45 1 1
mol:GDP 0.027 0.067 -10000 0 -0.32 13 13
EXOC4 0.026 0.009 -10000 0 -10000 0 0
STX4 0.048 0.09 -10000 0 -10000 0 0
PIP5K1C 0.059 0.11 0.4 13 -10000 0 13
LIMA1 0.028 0.005 -10000 0 -10000 0 0
ABI1 0.028 0.004 -10000 0 -10000 0 0
ROCK1 0.068 0.11 0.4 20 -10000 0 20
adherens junction assembly 0.067 0.14 0.5 16 -0.7 2 18
IGF-1R heterotetramer/IGF1 0.022 0.064 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.013 -10000 0 -10000 0 0
MET 0.024 0.034 -10000 0 -0.5 2 2
PLEKHA7 0.055 0.1 0.36 10 -0.53 2 12
mol:GTP 0.06 0.038 -10000 0 -0.35 2 2
establishment of epithelial cell apical/basal polarity 0.077 0.13 0.37 49 -10000 0 49
cortical actin cytoskeleton stabilization 0.011 0.055 -10000 0 -0.29 13 13
regulation of cell-cell adhesion 0.047 0.1 0.34 12 -0.42 2 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.056 -10000 0 -0.29 13 13
Signaling events regulated by Ret tyrosine kinase

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.037 0.14 -10000 0 -0.53 14 14
Crk/p130 Cas/Paxillin -0.029 0.081 -10000 0 -0.41 5 5
JUN 0.005 0.086 -10000 0 -0.45 7 7
HRAS 0.028 0.024 -10000 0 -0.5 1 1
RET51/GFRalpha1/GDNF/GRB10 0.021 0.12 -10000 0 -0.37 33 33
RAP1A 0.028 0.005 -10000 0 -10000 0 0
FRS2 0.028 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.021 0.12 -10000 0 -0.37 41 41
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.012 0.09 -10000 0 -0.33 26 26
RHOA 0.021 0.013 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.11 -10000 0 -0.34 35 35
GRB7 0.021 0.069 -10000 0 -0.61 6 6
RET51/GFRalpha1/GDNF 0.022 0.12 -10000 0 -0.37 38 38
MAPKKK cascade 0.01 0.1 -10000 0 -0.47 4 4
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
RET9/GFRalpha1/GDNF/IRS1 0.014 0.1 -10000 0 -0.35 35 35
lamellipodium assembly 0.001 0.086 -10000 0 -0.29 25 25
RET51/GFRalpha1/GDNF/SHC 0.021 0.12 -10000 0 -0.37 39 39
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
RET9/GFRalpha1/GDNF/SHC 0.018 0.096 -10000 0 -0.34 30 30
RET9/GFRalpha1/GDNF/Shank3 0.018 0.098 -10000 0 -0.34 32 32
MAPK3 0.004 0.11 0.52 1 -0.53 3 4
DOK1 0.028 0.005 -10000 0 -10000 0 0
DOK6 0.015 0.09 -10000 0 -0.58 11 11
PXN 0.028 0.005 -10000 0 -10000 0 0
neurite development 0.002 0.1 -10000 0 -0.45 6 6
DOK5 0.015 0.087 -10000 0 -0.6 10 10
GFRA1 -0.013 0.15 -10000 0 -0.55 36 36
MAPK8 0 0.091 -10000 0 -0.43 11 11
HRAS/GTP 0.019 0.12 -10000 0 -0.37 33 33
tube development 0.021 0.096 -10000 0 -0.34 26 26
MAPK1 0.009 0.12 0.43 6 -0.53 3 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.008 0.069 -10000 0 -0.27 22 22
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC 0.028 0.006 -10000 0 -10000 0 0
PDLIM7 0.018 0.042 -10000 0 -0.5 3 3
RET51/GFRalpha1/GDNF/Dok6 0.026 0.14 -10000 0 -0.39 39 39
SHC1 0.027 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.021 0.12 -10000 0 -0.37 37 37
RET51/GFRalpha1/GDNF/Dok5 0.016 0.14 -10000 0 -0.42 39 39
PRKCA 0.028 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.017 -10000 0 -0.36 1 1
CREB1 0.005 0.092 -10000 0 -0.43 9 9
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.006 0.077 -10000 0 -0.29 27 27
RET51/GFRalpha1/GDNF/Grb7 0.017 0.14 -10000 0 -0.41 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.007 0.11 -10000 0 -0.58 18 18
DOK4 0.028 0.006 -10000 0 -10000 0 0
JNK cascade 0.004 0.087 -10000 0 -0.43 8 8
RET9/GFRalpha1/GDNF/FRS2 0.019 0.094 -10000 0 -0.34 28 28
SHANK3 0.028 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.03 -10000 0 -0.61 1 1
NCK1 0.026 0.029 -10000 0 -0.61 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.005 0.08 -10000 0 -0.3 28 28
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.004 0.09 -10000 0 -0.37 8 8
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.001 0.1 -10000 0 -0.32 40 40
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.003 0.097 -10000 0 -0.44 10 10
PI3K 0.002 0.13 -10000 0 -0.44 28 28
SOS1 0.028 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.029 0.097 -10000 0 -0.34 26 26
GRB10 0.026 0.009 -10000 0 -10000 0 0
activation of MAPKK activity 0.004 0.08 -10000 0 -0.39 3 3
RET51/GFRalpha1/GDNF/FRS2 0.023 0.12 -10000 0 -0.38 35 35
GAB1 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.022 0.057 -10000 0 -0.61 4 4
IRS2 0.02 0.068 -10000 0 -0.52 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.001 0.1 -10000 0 -0.4 15 15
RET51/GFRalpha1/GDNF/PKC alpha 0.021 0.12 -10000 0 -0.37 38 38
GRB2 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.002 -10000 0 -10000 0 0
GDNF 0.017 0.041 -10000 0 -0.5 3 3
RAC1 0.026 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.017 0.13 -10000 0 -0.37 45 45
Rac1/GTP 0.009 0.1 -10000 0 -0.35 24 24
RET9/GFRalpha1/GDNF 0.002 0.1 -10000 0 -0.37 33 33
GFRalpha1/GDNF 0 0.12 -10000 0 -0.44 33 33
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.079 0.22 0.54 4 -0.66 6 10
CRP -0.11 0.26 0.5 2 -0.62 45 47
cell cycle arrest -0.1 0.23 -10000 0 -0.62 29 29
TIMP1 -0.08 0.22 0.45 1 -0.59 32 33
IL6ST 0.005 0.11 -10000 0 -0.61 15 15
Rac1/GDP -0.07 0.15 -10000 0 -0.42 28 28
AP1 0.026 0.12 0.45 1 -0.74 4 5
GAB2 0.028 0.003 -10000 0 -10000 0 0
TNFSF11 -0.11 0.24 0.59 1 -0.66 30 31
HSP90B1 0.026 0.058 -10000 0 -10000 0 0
GAB1 0.029 0.004 -10000 0 -10000 0 0
MAPK14 0.005 0.093 -10000 0 -0.53 4 4
AKT1 0.04 0.04 -10000 0 -0.5 1 1
FOXO1 0.047 0.045 -10000 0 -0.48 1 1
MAP2K6 -0.015 0.093 -10000 0 -0.58 4 4
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.084 0.16 -10000 0 -0.44 33 33
MITF -0.023 0.093 -10000 0 -0.46 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.003 -10000 0 -10000 0 0
A2M 0.029 0.051 -10000 0 -1.1 1 1
CEBPB 0.023 0.067 -10000 0 -0.5 8 8
GRB2/SOS1/GAB family/SHP2 0.013 0.079 -10000 0 -0.76 3 3
STAT3 -0.12 0.22 -10000 0 -0.65 28 28
STAT1 -0.002 0.11 -10000 0 -0.76 9 9
CEBPD -0.081 0.21 0.53 2 -0.66 6 8
PIK3CA 0.027 0.029 -10000 0 -0.61 1 1
PI3K 0.038 0.034 -10000 0 -0.45 2 2
JUN 0.027 0.006 -10000 0 -10000 0 0
PIAS3/MITF -0.01 0.099 -10000 0 -0.56 3 3
MAPK11 0.005 0.095 -10000 0 -0.52 5 5
STAT3 (dimer)/FOXO1 -0.054 0.18 0.41 1 -0.62 4 5
GRB2/SOS1/GAB family 0.03 0.11 -10000 0 -0.56 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.015 0.1 -10000 0 -0.39 13 13
GRB2 0.028 0.005 -10000 0 -10000 0 0
JAK2 0.027 0.007 -10000 0 -10000 0 0
LBP -0.2 0.38 0.53 4 -0.79 119 123
PIK3R1 0.026 0.03 -10000 0 -0.61 1 1
JAK1 0.027 0.01 -10000 0 -10000 0 0
MYC -0.086 0.22 0.52 3 -0.68 9 12
FGG -0.15 0.27 0.51 1 -0.65 46 47
macrophage differentiation -0.1 0.23 -10000 0 -0.62 29 29
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.13 -10000 0 -0.37 17 17
JUNB -0.085 0.21 -10000 0 -0.75 8 8
FOS 0.011 0.096 -10000 0 -0.6 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.023 0.1 -10000 0 -0.46 7 7
STAT1/PIAS1 -0.024 0.12 -10000 0 -0.51 5 5
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.043 -10000 0 -0.53 1 1
STAT3 (dimer) -0.1 0.24 -10000 0 -0.65 29 29
PRKCD -0.095 0.18 0.41 7 -0.49 32 39
IL6R 0.027 0.009 -10000 0 -10000 0 0
SOCS3 0.032 0.11 0.45 1 -0.66 2 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.033 0.079 -10000 0 -0.38 15 15
Rac1/GTP -0.077 0.16 -10000 0 -0.42 36 36
HCK 0 0.12 -10000 0 -0.5 26 26
MAPKKK cascade 0.031 0.095 -10000 0 -0.61 6 6
bone resorption -0.1 0.24 0.59 1 -0.62 31 32
IRF1 -0.05 0.23 0.53 7 -0.62 10 17
mol:GDP -0.085 0.15 -10000 0 -0.38 52 52
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.086 0.15 -10000 0 -0.39 52 52
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.007 0.11 -10000 0 -0.57 6 6
PTPN11 0.011 0.038 -10000 0 -0.71 1 1
IL6/IL6RA -0.017 0.14 -10000 0 -0.4 59 59
gp130 (dimer)/TYK2/TYK2/LMO4 0.035 0.077 -10000 0 -0.38 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 0.033 0.077 -10000 0 -0.38 15 15
IL6 -0.045 0.19 -10000 0 -0.55 60 60
PIAS3 0.028 0.006 -10000 0 -10000 0 0
PTPRE 0.029 0.017 -10000 0 -10000 0 0
PIAS1 0.029 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.016 0.093 -10000 0 -0.35 13 13
LMO4 0.024 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.22 -10000 0 -0.63 24 24
MCL1 0.053 0.057 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.021 0.027 0.3 1 -10000 0 1
DAPP1 0.008 0.11 0.34 8 -0.42 10 18
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.17 0.36 2 -0.51 25 27
mol:DAG -0.009 0.15 0.28 57 -0.25 13 70
HRAS 0.032 0.025 -10000 0 -0.5 1 1
RAP1A 0.032 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.031 0.072 0.25 2 -0.39 4 6
PLCG2 0.02 0.068 -10000 0 -0.55 7 7
PLCG1 0.028 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.007 0.029 0.3 2 -10000 0 2
ARF1/GTP 0.034 0.057 0.31 3 -10000 0 3
RHOA 0.021 0.013 -10000 0 -10000 0 0
YES1 0.028 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.027 0.3 1 -10000 0 1
ADAP1 0.032 0.07 0.29 3 -10000 0 3
ARAP3 0.007 0.029 0.3 2 -10000 0 2
INPPL1 0.029 0.003 -10000 0 -10000 0 0
PREX1 0.028 0.006 -10000 0 -10000 0 0
ARHGEF6 0.029 0.003 -10000 0 -10000 0 0
ARHGEF7 0.028 0.004 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
NRAS 0.032 0.009 -10000 0 -10000 0 0
FYN 0.027 0.008 -10000 0 -10000 0 0
ARF6 0.027 0.008 -10000 0 -10000 0 0
FGR 0.025 0.041 -10000 0 -0.5 3 3
mol:Ca2+ 0.005 0.094 0.31 20 -10000 0 20
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.006 -10000 0 -10000 0 0
ZAP70 -0.26 0.26 -10000 0 -0.5 276 276
mol:IP3 -0.001 0.11 0.32 24 -10000 0 24
LYN 0.027 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.042 0.077 0.25 7 -0.38 4 11
RhoA/GDP 0.016 0.044 0.38 1 -10000 0 1
PDK1/Src/Hsp90 0.05 0.028 -10000 0 -0.39 1 1
BLNK 0.026 0.029 -10000 0 -0.61 1 1
actin cytoskeleton reorganization 0.038 0.095 0.36 14 -10000 0 14
SRC 0.028 0.006 -10000 0 -10000 0 0
PLEKHA2 0.01 0.028 -10000 0 -0.3 4 4
RAC1 0.026 0.009 -10000 0 -10000 0 0
PTEN 0.017 0.017 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.021 0.026 0.3 1 -10000 0 1
RhoA/GTP 0.016 0.029 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.084 0.14 -10000 0 -0.43 27 27
BLK -0.009 0.13 -10000 0 -0.5 33 33
PDPK1 0.026 0.029 -10000 0 -0.61 1 1
CYTH1 0.045 0.073 0.29 11 -10000 0 11
HCK 0.001 0.12 -10000 0 -0.5 26 26
CYTH3 0.034 0.063 0.29 3 -10000 0 3
CYTH2 0.044 0.073 0.29 11 -10000 0 11
KRAS 0.032 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.039 0.055 -10000 0 -0.38 1 1
SGK1 0.035 0.071 -10000 0 -0.41 1 1
INPP5D 0.023 0.047 -10000 0 -0.5 4 4
mol:GDP 0.031 0.079 0.23 12 -0.41 4 16
SOS1 0.028 0.005 -10000 0 -10000 0 0
SYK 0.026 0.032 -10000 0 -0.46 2 2
ARF6/GDP 0.016 0.043 0.32 2 -10000 0 2
mol:PI-3-4-5-P3 0.037 0.062 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.027 0.3 1 -10000 0 1
VAV1 -0.099 0.23 -10000 0 -0.5 122 122
mol:PI-3-4-P2 0.017 0.034 -10000 0 -0.36 4 4
RAS family/GTP/PI3K Class I 0.078 0.066 0.33 1 -10000 0 1
PLEKHA1 0.01 0.028 -10000 0 -0.3 4 4
Rac1/GDP 0.031 0.071 0.24 1 -0.39 4 5
LAT -0.12 0.24 -10000 0 -0.5 141 141
Rac1/GTP 0.018 0.064 -10000 0 -0.41 1 1
ITK -0.044 0.13 0.28 25 -10000 0 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.03 0.17 0.3 48 -0.33 36 84
LCK 0.004 0.11 -10000 0 -0.51 22 22
BTK -0.007 0.14 0.29 12 -10000 0 12
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.011 -10000 0 -10000 0 0
AES 0.026 0.009 -10000 0 -10000 0 0
FBXW11 0.022 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.015 -10000 0 -10000 0 0
SMAD4 0.028 0.005 -10000 0 -10000 0 0
DKK2 0.003 0.12 -10000 0 -0.54 23 23
TLE1 0.026 0.01 -10000 0 -10000 0 0
MACF1 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.036 0.11 0.38 13 -0.39 1 14
WIF1 0.002 0.063 -10000 0 -0.59 5 5
beta catenin/RanBP3 -0.004 0.082 0.34 5 -10000 0 5
KREMEN2 -0.034 0.17 -10000 0 -0.5 58 58
DKK1 0.005 0.11 -10000 0 -0.54 21 21
beta catenin/beta TrCP1 0.018 0.082 0.38 1 -0.36 1 2
FZD1 0.026 0.009 -10000 0 -10000 0 0
AXIN2 -0.003 0.12 0.55 9 -1.4 2 11
AXIN1 0.028 0.007 -10000 0 -10000 0 0
RAN 0.028 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.12 -10000 0 -0.52 17 17
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.057 0.085 0.31 2 -0.76 1 3
Axin1/APC/GSK3 0.071 0.085 0.3 25 -10000 0 25
Axin1/APC/GSK3/beta catenin/Macf1 0.048 0.096 0.36 10 -10000 0 10
HNF1A 0.021 0.057 -10000 0 -0.61 4 4
CTBP1 0.026 0.01 -10000 0 -10000 0 0
MYC -0.001 0.12 0.59 12 -10000 0 12
RANBP3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0 0.13 -10000 0 -0.32 72 72
NKD1 -0.13 0.28 -10000 0 -0.6 130 130
TCF4 0.026 0.01 -10000 0 -10000 0 0
TCF3 0.026 0.01 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.077 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.012 0.083 0.39 6 -0.53 2 8
LEF1 0.01 0.091 -10000 0 -0.51 15 15
DVL1 0.019 0.029 -10000 0 -0.3 2 2
CSNK2A1 0.028 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.065 0.086 0.33 2 -0.61 2 4
DKK1/LRP6/Kremen 2 0 0.14 -10000 0 -0.33 66 66
LRP6 0.028 0.006 -10000 0 -10000 0 0
CSNK1A1 0.02 0.014 -10000 0 -10000 0 0
NLK 0.029 0.005 -10000 0 -10000 0 0
CCND1 -0.016 0.089 0.57 2 -0.47 1 3
WNT1 0.002 0.12 -10000 0 -0.5 25 25
GSK3A 0.03 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.008 -10000 0 -10000 0 0
FRAT1 0.027 0.006 -10000 0 -10000 0 0
PPP2R5D 0.094 0.14 0.32 121 -0.37 7 128
APC 0.026 0.088 0.38 9 -10000 0 9
WNT1/LRP6/FZD1 0.035 0.048 0.25 3 -10000 0 3
CREBBP 0.025 0.011 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.084 -10000 0 -0.34 23 23
regulation of S phase of mitotic cell cycle 0.017 0.066 -10000 0 -0.3 17 17
GNAO1 0.023 0.05 -10000 0 -0.53 4 4
HRAS 0.028 0.024 -10000 0 -0.5 1 1
SHBG/T-DHT -0.023 0.12 -10000 0 -0.38 53 53
PELP1 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.01 0.003 -10000 0 -10000 0 0
MAP2K1 0.006 0.068 0.35 1 -0.39 3 4
T-DHT/AR -0.001 0.099 -10000 0 -0.44 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.009 13 13
GNAI2 0.02 0.013 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.03 -10000 0 -0.61 1 1
mol:GDP -0.007 0.096 -10000 0 -0.45 22 22
cell proliferation -0.002 0.1 0.3 6 -0.48 10 16
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
FOS 0.003 0.14 -10000 0 -0.76 13 13
mol:Ca2+ 0.002 0.015 -10000 0 -0.078 10 10
MAPK3 0.004 0.088 0.3 6 -0.47 5 11
MAPK1 0.008 0.064 -10000 0 -0.51 3 3
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:IP3 0 0.001 -10000 0 -0.005 12 12
cAMP biosynthetic process -0.038 0.11 0.24 2 -0.37 52 54
GNG2 0.027 0.008 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 12 12
HRAS/GTP 0.04 0.074 -10000 0 -0.32 18 18
actin cytoskeleton reorganization 0.034 0.029 -10000 0 -0.31 2 2
SRC 0.028 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 12 12
PI3K 0.033 0.029 -10000 0 -0.39 2 2
apoptosis -0.008 0.1 0.5 12 -0.25 3 15
T-DHT/AR/PELP1 0.019 0.087 -10000 0 -0.38 22 22
HRAS/GDP 0.009 0.096 -10000 0 -0.43 22 22
CREB1 0.007 0.11 0.26 3 -0.54 12 15
RAC1-CDC42/GTP 0.043 0.032 -10000 0 -0.31 2 2
AR -0.001 0.13 -10000 0 -0.6 24 24
GNB1 0.028 0.006 -10000 0 -10000 0 0
RAF1 0.009 0.071 0.35 1 -0.38 3 4
RAC1-CDC42/GDP 0.029 0.095 -10000 0 -0.42 19 19
T-DHT/AR/PELP1/Src 0.037 0.079 -10000 0 -0.35 18 18
MAP2K2 0.005 0.068 0.35 1 -0.39 3 4
T-DHT/AR/PELP1/Src/PI3K 0.017 0.067 -10000 0 -0.3 17 17
GNAZ 0.025 0.049 -10000 0 -0.61 3 3
SHBG -0.038 0.19 -10000 0 -0.6 53 53
Gi family/GNB1/GNG2/GDP -0.013 0.12 -10000 0 -0.48 16 16
mol:T-DHT 0 0.001 -10000 0 -0.007 9 9
RAC1 0.026 0.009 -10000 0 -10000 0 0
GNRH1 -0.095 0.17 0.19 1 -0.37 141 142
Gi family/GTP 0.006 0.055 -10000 0 -0.3 10 10
CDC42 0.028 0.006 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.005 -10000 0 -10000 0 0
SMARCC1 0.006 0.046 -10000 0 -0.66 2 2
REL 0.025 0.043 -10000 0 -0.51 3 3
HDAC7 -0.13 0.093 -10000 0 -0.5 7 7
JUN 0.028 0.006 -10000 0 -10000 0 0
EP300 0.027 0.029 -10000 0 -0.61 1 1
KAT2B 0.019 0.031 -10000 0 -0.61 1 1
KAT5 0.029 0.003 -10000 0 -10000 0 0
MAPK14 -0.02 0.04 -10000 0 -0.48 3 3
FOXO1 0.028 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.14 0.1 -10000 0 -0.53 7 7
MAP2K6 0 0.052 -10000 0 -0.63 3 3
BRM/BAF57 0.04 0.012 -10000 0 -10000 0 0
MAP2K4 0.004 0.02 -10000 0 -10000 0 0
SMARCA2 0.027 0.007 -10000 0 -10000 0 0
PDE9A -0.12 0.14 -10000 0 -0.79 16 16
NCOA2 0.017 0.08 -10000 0 -0.61 8 8
CEBPA 0.018 0.074 -10000 0 -0.5 10 10
EHMT2 0.028 0.006 -10000 0 -10000 0 0
cell proliferation -0.12 0.13 0.47 5 -0.46 19 24
NR0B1 -0.012 0.13 -10000 0 -0.51 32 32
EGR1 0.012 0.08 -10000 0 -0.61 8 8
RXRs/9cRA 0.047 0.033 -10000 0 -0.3 3 3
AR/RACK1/Src -0.04 0.064 -10000 0 -0.45 4 4
AR/GR -0.024 0.086 -10000 0 -0.42 16 16
GNB2L1 0.022 0.012 -10000 0 -10000 0 0
PKN1 0.029 0.002 -10000 0 -10000 0 0
RCHY1 0.029 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.015 1 1
MAPK8 -0.018 0.027 -10000 0 -0.47 1 1
T-DHT/AR/TIF2/CARM1 -0.051 0.084 -10000 0 -0.47 11 11
SRC -0.04 0.039 -10000 0 -0.38 3 3
NR3C1 0.021 0.026 -10000 0 -0.5 1 1
KLK3 -0.019 0.13 -10000 0 -0.67 9 9
APPBP2 -0.003 0.019 -10000 0 -10000 0 0
TRIM24 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.055 0.067 -10000 0 -0.46 6 6
TMPRSS2 -0.91 0.35 -10000 0 -1 449 449
RXRG 0.021 0.05 -10000 0 -0.54 4 4
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.028 0.005 -10000 0 -10000 0 0
RXRB 0.028 0.006 -10000 0 -10000 0 0
CARM1 0.029 0.003 -10000 0 -10000 0 0
NR2C2 0.019 0.031 -10000 0 -0.61 1 1
KLK2 -0.038 0.096 -10000 0 -0.5 13 13
AR -0.025 0.071 -10000 0 -0.36 18 18
SENP1 0.028 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 -10000 0 0
SRY 0 0.003 0.017 18 -10000 0 18
GATA2 0.014 0.09 -10000 0 -0.58 11 11
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.082 0.21 -10000 0 -0.5 101 101
T-DHT/AR/RACK1/Src -0.04 0.065 -10000 0 -0.44 4 4
positive regulation of transcription 0.014 0.09 -10000 0 -0.58 11 11
DNAJA1 -0.003 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.008 -10000 0 -10000 0 0
NCOA1 0.052 0.031 -10000 0 -10000 0 0
SPDEF -0.088 0.22 -10000 0 -0.51 109 109
T-DHT/AR/TIF2 -0.035 0.091 -10000 0 -0.48 10 10
T-DHT/AR/Hsp90 -0.053 0.065 -10000 0 -0.45 5 5
GSK3B 0.023 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.047 0.044 -10000 0 -0.41 4 4
SIRT1 0.028 0.005 -10000 0 -10000 0 0
ZMIZ2 0.026 0.01 -10000 0 -10000 0 0
POU2F1 -0.074 0.047 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.076 0.095 -10000 0 -0.5 11 11
CREBBP 0.028 0.006 -10000 0 -10000 0 0
SMARCE1 0.028 0.005 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.022 0.033 -10000 0 -0.6 1 1
HSPA8 0.029 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.072 0.066 0.32 1 -0.41 2 3
AKT1 0.029 0.011 -10000 0 -10000 0 0
GSC -0.024 0.14 -10000 0 -0.63 3 3
NKX2-5 -0.005 0.11 -10000 0 -0.5 22 22
muscle cell differentiation -0.03 0.079 0.45 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.089 0.082 -10000 0 -10000 0 0
SMAD4 0.038 0.033 -10000 0 -10000 0 0
CBFB 0.028 0.006 -10000 0 -10000 0 0
SAP18 0.028 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.047 0.039 -10000 0 -0.32 3 3
SMAD3/SMAD4/VDR 0.087 0.058 -10000 0 -10000 0 0
MYC 0.007 0.096 -10000 0 -0.51 17 17
CDKN2B 0.017 0.11 -10000 0 -0.61 1 1
AP1 0.057 0.064 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.048 0.063 -10000 0 -0.41 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.04 0.038 -10000 0 -10000 0 0
SP3 0.03 0.007 -10000 0 -10000 0 0
CREB1 0.028 0.006 -10000 0 -10000 0 0
FOXH1 -0.014 0.14 -10000 0 -0.51 38 38
SMAD3/SMAD4/GR 0.059 0.053 -10000 0 -10000 0 0
GATA3 -0.28 0.32 -10000 0 -0.61 242 242
SKI/SIN3/HDAC complex/NCoR1 0.039 0.032 -10000 0 -0.32 1 1
MEF2C/TIF2 0.029 0.12 -10000 0 -0.49 8 8
endothelial cell migration 0.044 0.14 0.45 14 -10000 0 14
MAX 0.029 0.013 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.027 0.029 -10000 0 -0.61 1 1
RUNX2 0.013 0.087 -10000 0 -0.5 14 14
RUNX3 -0.21 0.26 -10000 0 -0.51 225 225
RUNX1 -0.008 0.13 -10000 0 -0.5 34 34
CTBP1 0.028 0.004 -10000 0 -10000 0 0
NR3C1 0.023 0.029 -10000 0 -0.51 1 1
VDR 0.024 0.049 -10000 0 -0.61 3 3
CDKN1A 0.044 0.077 -10000 0 -10000 0 0
KAT2B 0.019 0.031 -10000 0 -0.61 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.04 0.11 -10000 0 -0.4 13 13
DCP1A 0.021 0.013 -10000 0 -10000 0 0
SKI 0.028 0.006 -10000 0 -10000 0 0
SERPINE1 -0.044 0.14 -10000 0 -0.45 14 14
SMAD3/SMAD4/ATF2 0.069 0.048 -10000 0 -0.4 1 1
SMAD3/SMAD4/ATF3 0.067 0.056 -10000 0 -0.41 3 3
SAP30 0.011 0.096 -10000 0 -0.5 17 17
Cbp/p300/PIAS3 0.045 0.039 -10000 0 -0.37 1 1
JUN 0.045 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.06 0.081 -10000 0 -0.36 2 2
TFE3 0.028 0.02 -10000 0 -10000 0 0
COL1A2 -0.021 0.13 -10000 0 -0.39 55 55
mesenchymal cell differentiation -0.06 0.075 0.42 2 -10000 0 2
DLX1 -0.25 0.26 -10000 0 -0.5 263 263
TCF3 0.029 0.003 -10000 0 -10000 0 0
FOS 0.019 0.096 -10000 0 -0.6 12 12
SMAD3/SMAD4/Max 0.074 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.051 0.026 -10000 0 -0.38 1 1
ZBTB17 0.024 0.039 -10000 0 -0.59 2 2
LAMC1 0.047 0.036 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.071 0.042 -10000 0 -10000 0 0
IRF7 0.01 0.1 -10000 0 -0.5 19 19
ESR1 0.024 0.05 -10000 0 -0.5 4 4
HNF4A -0.02 0.17 -10000 0 -0.61 38 38
MEF2C 0.032 0.13 0.46 8 -0.48 6 14
SMAD2-3/SMAD4 0.078 0.045 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.05 0.029 -10000 0 -0.37 1 1
IGHV3OR16-13 -0.022 0.063 -10000 0 -0.4 8 8
TGIF2/HDAC complex 0.028 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.01 -10000 0 -10000 0 0
SKIL 0.027 0.007 -10000 0 -10000 0 0
HDAC1 0.028 0.006 -10000 0 -10000 0 0
HDAC2 0.027 0.008 -10000 0 -10000 0 0
SNIP1 0.028 0.006 -10000 0 -10000 0 0
GCN5L2 -0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.076 0.048 -10000 0 -10000 0 0
MSG1/HSC70 0.041 0.026 -10000 0 -0.36 2 2
SMAD2 0.03 0.022 -10000 0 -10000 0 0
SMAD3 0.039 0.032 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.047 0.03 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.018 0.068 0.21 1 -0.45 4 5
NCOR1 0.028 0.005 -10000 0 -10000 0 0
NCOA2 0.017 0.08 -10000 0 -0.61 8 8
NCOA1 0.028 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.015 0.093 -10000 0 -0.36 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.096 0.086 -10000 0 -10000 0 0
IFNB1 0.027 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.051 0.12 -10000 0 -0.45 6 6
CITED1 0.026 0.034 -10000 0 -0.5 2 2
SMAD2-3/SMAD4/ARC105 0.092 0.044 -10000 0 -10000 0 0
RBL1 0.028 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.05 0.039 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.12 0.19 -10000 0 -0.32 237 237
SMAD7 0.072 0.063 -10000 0 -10000 0 0
MYC/MIZ-1 0.02 0.078 -10000 0 -0.37 19 19
SMAD3/SMAD4 0.015 0.08 -10000 0 -0.42 1 1
IL10 -0.15 0.22 -10000 0 -0.76 17 17
PIASy/HDAC complex 0.03 0.008 -10000 0 -10000 0 0
PIAS3 0.027 0.007 -10000 0 -10000 0 0
CDK2 0.027 0.009 -10000 0 -10000 0 0
IL5 -0.12 0.18 -10000 0 -0.56 12 12
CDK4 0.026 0.011 -10000 0 -10000 0 0
PIAS4 0.03 0.008 -10000 0 -10000 0 0
ATF3 0.023 0.051 -10000 0 -0.53 4 4
SMAD3/SMAD4/SP1 0.065 0.08 -10000 0 -10000 0 0
FOXG1 -0.008 0.098 -10000 0 -0.5 18 18
FOXO3 0.021 0.011 -10000 0 -10000 0 0
FOXO1 0.022 0.01 -10000 0 -10000 0 0
FOXO4 0.023 0.01 -10000 0 -10000 0 0
heart looping 0.032 0.13 0.46 8 -0.48 6 14
CEBPB 0.02 0.067 -10000 0 -0.5 8 8
SMAD3/SMAD4/DLX1 -0.13 0.19 -10000 0 -0.37 26 26
MYOD1 -0.008 0.12 -10000 0 -0.5 29 29
SMAD3/SMAD4/HNF4 0.036 0.13 -10000 0 -0.4 38 38
SMAD3/SMAD4/GATA3 -0.15 0.24 -10000 0 -0.49 41 41
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.078 0.18 -10000 0 -0.52 14 14
SMAD3/SMAD4/SP1-3 0.081 0.078 -10000 0 -10000 0 0
MED15 0.028 0.004 -10000 0 -10000 0 0
SP1 0.022 0.045 -10000 0 -10000 0 0
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.027 0.12 -10000 0 -0.44 14 14
ITGB5 0.052 0.073 0.42 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.036 0.047 -10000 0 -0.45 3 3
SMAD3/SMAD4/AR 0.053 0.11 -10000 0 -0.4 23 23
AR -0.001 0.13 -10000 0 -0.6 24 24
negative regulation of cell growth 0.05 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.047 0.097 -10000 0 -0.4 6 6
E2F5 0.026 0.029 -10000 0 -0.61 1 1
E2F4 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.041 0.11 -10000 0 -0.39 6 6
SMAD2-3/SMAD4/FOXO1-3a-4 0.048 0.031 -10000 0 -10000 0 0
TFDP1 0.028 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.076 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.06 0.075 -10000 0 -0.42 2 2
TGIF2 0.028 0.006 -10000 0 -10000 0 0
TGIF1 0.028 0.005 -10000 0 -10000 0 0
ATF2 0.026 0.029 -10000 0 -0.61 1 1
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.011 0.09 -9999 0 -0.5 15 15
PLK4 0.025 0.041 -9999 0 -0.5 3 3
regulation of centriole replication 0.006 0.072 -9999 0 -0.36 18 18
Aurora A signaling

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
Aurora A/GADD45A 0.033 0.038 -10000 0 -10000 0 0
BIRC5 -0.13 0.24 -10000 0 -0.5 148 148
NFKBIA 0.02 0.023 0.25 1 -10000 0 1
CPEB1 -0.097 0.25 -10000 0 -0.6 101 101
AKT1 0.019 0.021 -10000 0 -10000 0 0
NDEL1 0.028 0.005 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.033 -10000 0 -10000 0 0
NDEL1/TACC3 0.044 0.048 -10000 0 -0.38 3 3
GADD45A 0.028 0.006 -10000 0 -10000 0 0
GSK3B 0.029 0.011 -10000 0 -10000 0 0
PAK1/Aurora A 0.035 0.04 -10000 0 -10000 0 0
MDM2 0.028 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.059 0.16 -10000 0 -0.36 108 108
TP53 0.029 0.024 -10000 0 -0.31 1 1
DLG7 0.017 0.021 -10000 0 -10000 0 0
AURKAIP1 0.024 0.047 -10000 0 -0.57 3 3
ARHGEF7 0.028 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.05 -10000 0 -0.4 3 3
G2/M transition of mitotic cell cycle 0.027 0.033 -10000 0 -10000 0 0
AURKA 0.027 0.028 -10000 0 -10000 0 0
AURKB -0.049 0.074 -10000 0 -0.21 14 14
CDC25B 0.025 0.027 -10000 0 -0.27 1 1
G2/M transition checkpoint 0.01 0.028 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.15 -10000 0 -0.34 99 99
Aurora A/CPEB -0.045 0.15 -10000 0 -0.34 99 99
Aurora A/TACC1/TRAP/chTOG 0.058 0.043 -10000 0 -10000 0 0
BRCA1 0.028 0.004 -10000 0 -10000 0 0
centrosome duplication 0.035 0.039 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.047 -10000 0 -0.37 3 3
spindle assembly 0.057 0.042 -10000 0 -10000 0 0
TDRD7 0.028 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.025 0.13 -10000 0 -0.35 13 13
CENPA -0.035 0.066 -10000 0 -0.21 13 13
Aurora A/PP2A 0.034 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.025 0.029 0.19 1 -10000 0 1
negative regulation of DNA binding 0.029 0.024 -10000 0 -0.31 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.008 -10000 0 -10000 0 0
RASA1 0.024 0.03 -10000 0 -0.61 1 1
Ajuba/Aurora A 0.011 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.018 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.028 -10000 0 -10000 0 0
TACC1 0.026 0.008 -10000 0 -10000 0 0
TACC3 0.024 0.047 -10000 0 -0.5 4 4
Aurora A/Antizyme1 0.045 0.049 -10000 0 -0.34 2 2
Aurora A/RasGAP 0.031 0.041 -10000 0 -0.38 1 1
OAZ1 0.027 0.024 -10000 0 -0.5 1 1
RAN 0.028 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.009 -10000 0 -10000 0 0
GIT1 0.028 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.056 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.059 0.16 -10000 0 -0.36 108 108
PPP2R5D 0.028 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 -0.037 0.12 -10000 0 -0.37 9 9
PAK1 0.029 0.003 -10000 0 -10000 0 0
CKAP5 0.029 0.003 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.022 0.048 -10000 0 -10000 0 0
CRKL 0.028 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DOCK1 0.026 0.029 -10000 0 -0.61 1 1
ITGA4 0.012 0.09 -10000 0 -0.5 15 15
alpha4/beta7 Integrin/MAdCAM1 0.032 0.08 -10000 0 -0.31 3 3
EPO -0.14 0.25 -10000 0 -0.5 163 163
alpha4/beta7 Integrin 0.028 0.069 -10000 0 -0.36 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.069 -10000 0 -0.36 15 15
EPO/EPOR (dimer) -0.092 0.19 -10000 0 -0.36 163 163
lamellipodium assembly 0.019 0.091 0.31 1 -0.52 7 8
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
PI3K 0.036 0.034 -10000 0 -0.45 2 2
ARF6 0.027 0.008 -10000 0 -10000 0 0
JAK2 -0.033 0.099 -10000 0 -0.33 9 9
PXN 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
MADCAM1 0.015 0.079 -10000 0 -0.51 11 11
cell adhesion 0.03 0.078 -10000 0 -0.31 3 3
CRKL/CBL 0.041 0.023 -10000 0 -0.45 1 1
ITGB1 0.028 0.004 -10000 0 -10000 0 0
SRC 0.014 0.072 -10000 0 -0.33 1 1
ITGB7 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.035 0.081 -10000 0 -0.31 25 25
p130Cas/Crk/Dock1 0.035 0.073 -10000 0 -0.53 1 1
VCAM1 0.016 0.079 -10000 0 -0.47 13 13
RHOA 0.021 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.062 -10000 0 -10000 0 0
BCAR1 0.006 0.07 -10000 0 -0.58 1 1
EPOR 0.029 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.028 -10000 0 -0.61 1 1
GIT1 0.028 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.093 0.31 1 -0.54 7 8
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.002 0.082 0.53 1 -10000 0 1
GNAI2 0.02 0.013 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.02 0.12 -10000 0 -0.31 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.05 -10000 0 -0.53 4 4
RhoA/GTP -0.001 0.084 -10000 0 -0.54 1 1
negative regulation of cAMP metabolic process -0.011 0.088 -10000 0 -0.31 18 18
GNAZ 0.025 0.049 -10000 0 -0.61 3 3
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.009 -10000 0 -10000 0 0
S1PR5 -0.062 0.2 -10000 0 -0.5 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.011 0.088 -10000 0 -0.31 18 18
RhoA/GDP 0.015 0.01 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
GNAI1 0.024 0.03 -10000 0 -0.61 1 1
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.052 0.053 -10000 0 -0.33 3 3
ER alpha/Gai/GDP/Gbeta gamma -0.035 0.17 -10000 0 -0.53 36 36
AKT1 -0.034 0.22 -10000 0 -0.73 44 44
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.034 0.23 -10000 0 -0.75 45 45
mol:Ca2+ -0.015 0.11 -10000 0 -0.41 17 17
IGF1R 0.029 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.03 0.053 -10000 0 -0.43 6 6
SHC1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.031 0.21 0.68 46 -10000 0 46
RhoA/GTP 0.017 0.028 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.001 0.14 -10000 0 -0.57 12 12
regulation of stress fiber formation -0.029 0.053 -10000 0 -0.36 4 4
E2/ERA-ERB (dimer) 0.026 0.052 -10000 0 -0.34 9 9
KRAS 0.028 0.005 -10000 0 -10000 0 0
G13/GTP 0.031 0.031 -10000 0 -0.33 3 3
pseudopodium formation 0.029 0.053 0.36 4 -10000 0 4
E2/ER alpha (dimer)/PELP1 0.033 0.034 -10000 0 -0.36 3 3
GRB2 0.028 0.005 -10000 0 -10000 0 0
GNG2 0.027 0.008 -10000 0 -10000 0 0
GNAO1 0.023 0.05 -10000 0 -0.53 4 4
HRAS 0.028 0.024 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.009 0.17 0.31 5 -0.53 41 46
E2/ER beta (dimer) 0.015 0.045 -10000 0 -0.35 7 7
mol:GDP 0.019 0.047 -10000 0 -0.4 3 3
mol:NADP -0.009 0.17 0.31 5 -0.53 41 46
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:IP3 -0.015 0.11 -10000 0 -0.43 16 16
IGF-1R heterotetramer 0.029 0.003 -10000 0 -10000 0 0
PLCB1 0.014 0.081 -10000 0 -0.47 9 9
PLCB2 -0.011 0.11 -10000 0 -0.42 15 15
IGF1 0.023 0.053 -10000 0 -0.5 5 5
mol:L-citrulline -0.009 0.17 0.31 5 -0.53 41 46
RHOA 0.021 0.013 -10000 0 -10000 0 0
Gai/GDP -0.11 0.26 -10000 0 -0.54 122 122
JNK cascade 0.015 0.044 -10000 0 -0.35 7 7
BCAR1 0.027 0.029 -10000 0 -0.61 1 1
ESR2 0.02 0.061 -10000 0 -0.49 7 7
GNAQ 0.028 0.006 -10000 0 -10000 0 0
ESR1 0.022 0.049 -10000 0 -0.51 4 4
Gq family/GDP/Gbeta gamma 0.018 0.11 -10000 0 -0.71 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.026 0.14 -10000 0 -0.92 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.001 0.14 -10000 0 -0.59 11 11
GNAZ 0.025 0.049 -10000 0 -0.61 3 3
E2/ER alpha (dimer) 0.017 0.036 -10000 0 -0.37 4 4
STRN 0.023 0.057 -10000 0 -0.61 4 4
GNAL 0.028 0.005 -10000 0 -10000 0 0
PELP1 0.028 0.005 -10000 0 -10000 0 0
MAPK11 0.013 0.04 -10000 0 -0.32 7 7
GNAI2 0.02 0.013 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.024 0.03 -10000 0 -0.61 1 1
HBEGF -0.076 0.17 0.38 9 -0.54 28 37
cAMP biosynthetic process 0.023 0.042 -10000 0 -0.27 9 9
SRC -0.029 0.16 -10000 0 -0.51 34 34
PI3K 0.036 0.034 -10000 0 -0.45 2 2
GNB1 0.028 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.039 0.061 -10000 0 -0.38 2 2
SOS1 0.028 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.039 0.097 -10000 0 -0.47 13 13
Gs family/GTP 0.03 0.045 -10000 0 -0.27 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.051 0.021 -10000 0 -0.28 1 1
vasodilation -0.007 0.17 0.31 5 -0.5 41 46
mol:DAG -0.015 0.11 -10000 0 -0.43 16 16
Gs family/GDP/Gbeta gamma 0.019 0.053 -10000 0 -0.36 2 2
MSN 0.029 0.055 0.37 4 -10000 0 4
Gq family/GTP 0.021 0.072 -10000 0 -0.46 8 8
mol:PI-3-4-5-P3 -0.031 0.22 -10000 0 -0.71 46 46
NRAS 0.028 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.007 0.17 0.5 41 -0.31 5 46
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.06 -10000 0 -0.37 3 3
NOS3 -0.011 0.18 0.33 4 -0.56 41 45
GNA11 0.025 0.049 -10000 0 -0.61 3 3
MAPKKK cascade 0 0.18 0.38 4 -0.55 43 47
E2/ER alpha (dimer)/PELP1/Src -0.003 0.15 -10000 0 -0.52 20 20
ruffle organization 0.029 0.053 0.36 4 -10000 0 4
ROCK2 0.035 0.057 0.38 4 -10000 0 4
GNA14 0.02 0.069 -10000 0 -0.61 6 6
GNA15 0.013 0.09 -10000 0 -0.5 15 15
GNA13 0.028 0.005 -10000 0 -10000 0 0
MMP9 -0.13 0.18 0.38 7 -0.54 37 44
MMP2 -0.025 0.16 0.33 2 -0.58 20 22
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.012 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.007 0.049 -9999 0 -0.27 4 4
GNAO1 0.025 0.05 -9999 0 -0.53 4 4
S1P/S1P3/G12/G13 0.049 0.021 -9999 0 -10000 0 0
AKT1 0.024 0.04 -9999 0 -0.38 1 1
AKT3 -0.009 0.082 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.012 -9999 0 -10000 0 0
GNAI2 0.022 0.014 -9999 0 -10000 0 0
GNAI3 0.029 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.03 -9999 0 -0.61 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.029 0.006 -9999 0 -10000 0 0
S1PR2 0.029 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.029 0.039 -9999 0 -0.28 2 2
MAPK3 0.026 0.036 -9999 0 -10000 0 0
MAPK1 0.027 0.037 -9999 0 -10000 0 0
JAK2 -0.022 0.086 -9999 0 -0.46 3 3
CXCR4 -0.066 0.13 -9999 0 -0.35 5 5
FLT1 0.025 0.053 -9999 0 -0.5 5 5
RhoA/GDP 0.015 0.01 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.007 -9999 0 -10000 0 0
SRC 0.026 0.036 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.029 0.04 -9999 0 -0.29 2 2
RAC1 0.026 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.034 0.048 -9999 0 -10000 0 0
VEGFA -0.21 0.26 -9999 0 -0.5 228 228
S1P/S1P2/Gi 0.027 0.041 -9999 0 -0.29 2 2
VEGFR1 homodimer/VEGFA homodimer -0.14 0.21 -9999 0 -0.36 228 228
RHOA 0.021 0.013 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.025 0.051 -9999 0 -0.29 9 9
GNAQ 0.028 0.006 -9999 0 -10000 0 0
GNAZ 0.026 0.049 -9999 0 -0.61 3 3
G12/G13 0.037 0.015 -9999 0 -10000 0 0
GNA14 0.02 0.069 -9999 0 -0.61 6 6
GNA15 0.013 0.09 -9999 0 -0.5 15 15
GNA12 0.026 0.009 -9999 0 -10000 0 0
GNA13 0.028 0.005 -9999 0 -10000 0 0
GNA11 0.025 0.049 -9999 0 -0.61 3 3
Rac1/GTP 0.023 0.054 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.078 0.082 -10000 0 -0.37 1 1
epithelial cell differentiation -0.05 0.1 -10000 0 -0.45 3 3
ITCH 0.061 0.02 -10000 0 -10000 0 0
WWP1 -0.092 0.064 -10000 0 -10000 0 0
FYN 0.027 0.008 -10000 0 -10000 0 0
EGFR 0.019 0.06 -10000 0 -0.52 6 6
PRL 0.021 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.051 0.078 0.37 2 -0.51 1 3
PTPRZ1 -0.046 0.2 -10000 0 -0.6 56 56
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.061 0.077 -10000 0 -0.44 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.08 0.08 -10000 0 -0.45 10 10
ADAM17 0.062 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.083 -10000 0 -0.42 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.086 -10000 0 -0.41 9 9
NCOR1 0.028 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.071 0.078 -10000 0 -0.44 8 8
GRIN2B -0.069 0.074 -10000 0 -0.42 8 8
ErbB4/ErbB2/betacellulin -0.11 0.13 -10000 0 -0.43 59 59
STAT1 0.026 0.024 -10000 0 -0.5 1 1
HBEGF 0.022 0.012 -10000 0 -10000 0 0
PRLR -0.048 0.2 -10000 0 -0.61 59 59
E4ICDs/ETO2 -0.1 0.078 -10000 0 -0.41 3 3
axon guidance -0.046 0.08 -10000 0 -10000 0 0
NEDD4 0.06 0.045 -10000 0 -0.6 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.024 0.16 -10000 0 -0.46 59 59
CBFA2T3 0.026 0.034 -10000 0 -0.5 2 2
ErbB4/ErbB2/HBEGF -0.048 0.064 -10000 0 -0.43 1 1
MAPK3 -0.055 0.077 0.44 1 -0.52 1 2
STAT1 (dimer) -0.1 0.075 -10000 0 -0.37 1 1
MAPK1 -0.055 0.079 0.35 3 -0.52 1 4
JAK2 0.027 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.077 0.076 -10000 0 -0.44 9 9
NRG1 0.025 0.076 -10000 0 -0.44 12 12
NRG3 0.017 0.076 -10000 0 -0.52 10 10
NRG2 0.012 0.072 -10000 0 -0.52 9 9
NRG4 -0.027 0.18 -10000 0 -0.59 45 45
heart development -0.046 0.08 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.075 -10000 0 -0.44 9 9
ERBB2 0.039 0.033 -10000 0 -0.45 2 2
WWOX/E4ICDs -0.1 0.077 -10000 0 -0.37 2 2
SHC1 0.027 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.12 -10000 0 -0.45 35 35
apoptosis 0.089 0.076 0.34 11 -10000 0 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.083 0.087 -10000 0 -0.4 5 5
ErbB4/ErbB2/epiregulin -0.082 0.087 -10000 0 -0.36 21 21
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.15 -10000 0 -0.48 69 69
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.093 0.12 -10000 0 -0.44 32 32
MDM2 -0.1 0.071 -10000 0 -0.37 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.068 -10000 0 -0.4 10 10
STAT5A -0.041 0.075 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.073 0.082 -10000 0 -0.42 12 12
DLG4 0.028 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.04 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.096 0.068 -10000 0 -0.35 1 1
STAT5A (dimer) -0.049 0.11 -10000 0 -0.48 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.039 0.084 0.35 1 -10000 0 1
LRIG1 0.022 0.012 -10000 0 -10000 0 0
EREG -0.005 0.13 -10000 0 -0.51 31 31
BTC -0.063 0.22 -10000 0 -0.6 74 74
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.047 0.079 -10000 0 -10000 0 0
ERBB4 -0.12 0.083 -10000 0 -0.42 1 1
STAT5B 0.028 0.004 -10000 0 -10000 0 0
YAP1 -0.021 0.039 -10000 0 -0.53 2 2
GRB2 0.028 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.096 0.11 -10000 0 -0.42 34 34
glial cell differentiation 0.096 0.067 0.34 1 -10000 0 1
WWOX 0.026 0.024 -10000 0 -0.5 1 1
cell proliferation -0.079 0.14 0.34 1 -0.55 16 17
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.022 -10000 0 -10000 0 0
RFC1 0.005 0.02 -10000 0 -10000 0 0
PRKDC 0.008 0.033 0.31 1 -10000 0 1
RIPK1 0.028 0.006 -10000 0 -10000 0 0
CASP7 -0.009 0.11 -10000 0 -0.63 12 12
FASLG/FAS/FADD/FAF1 -0.059 0.092 0.23 6 -0.27 3 9
MAP2K4 -0.043 0.14 0.31 5 -0.55 18 23
mol:ceramide -0.066 0.11 -10000 0 -0.34 10 10
GSN 0.006 0.022 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.068 0.099 -10000 0 -0.39 4 4
FAS 0.026 0.011 -10000 0 -10000 0 0
BID -0.001 0.033 -10000 0 -10000 0 0
MAP3K1 -0.013 0.12 0.31 5 -0.5 16 21
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
RB1 0.006 0.026 -10000 0 -10000 0 0
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET 0.029 0.097 -10000 0 -0.38 25 25
ARHGDIB 0.01 0.035 -10000 0 -10000 0 0
FADD 0.026 0.011 -10000 0 -10000 0 0
actin filament polymerization -0.006 0.022 -10000 0 -10000 0 0
NFKB1 -0.023 0.089 -10000 0 -0.59 7 7
MAPK8 -0.05 0.16 0.34 6 -0.52 31 37
DFFA 0.005 0.02 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.005 0.02 -10000 0 -10000 0 0
FAS/FADD/MET 0.047 0.031 -10000 0 -0.3 2 2
CFLAR/RIP1 0.041 0.012 -10000 0 -10000 0 0
FAIM3 -0.009 0.13 -10000 0 -0.5 35 35
FAF1 0.025 0.014 -10000 0 -10000 0 0
PARP1 0.005 0.02 -10000 0 -10000 0 0
DFFB 0.005 0.02 -10000 0 -10000 0 0
CHUK -0.017 0.076 -10000 0 -0.55 5 5
FASLG -0.24 0.26 -10000 0 -0.5 255 255
FAS/FADD 0.038 0.017 -10000 0 -10000 0 0
HGF 0.003 0.11 -10000 0 -0.54 20 20
LMNA 0.004 0.029 0.27 1 -10000 0 1
CASP6 0.005 0.02 -10000 0 -10000 0 0
CASP10 0.026 0.011 -10000 0 -10000 0 0
CASP3 0.004 0.026 -10000 0 -10000 0 0
PTPN13 0.017 0.084 -10000 0 -0.61 9 9
CASP8 0.001 0.059 0.22 35 -10000 0 35
IL6 -0.076 0.29 -10000 0 -1.1 32 32
MET 0.024 0.034 -10000 0 -0.5 2 2
ICAD/CAD 0.007 0.019 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.067 0.11 -10000 0 -0.35 10 10
activation of caspase activity by cytochrome c -0.001 0.033 -10000 0 -10000 0 0
PAK2 0.009 0.036 -10000 0 -10000 0 0
BCL2 0.028 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.31 -10000 0 -0.61 196 196
HRAS 0.028 0.024 -10000 0 -0.5 1 1
EGFR 0.019 0.06 -10000 0 -0.52 6 6
AKT 0.028 0.089 0.28 24 -10000 0 24
FOXO3 0.027 0.008 -10000 0 -10000 0 0
AKT1 0.027 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.005 -10000 0 -10000 0 0
AKT3 0.028 0.006 -10000 0 -10000 0 0
FOXO4 0.029 0.001 -10000 0 -10000 0 0
MET 0.024 0.034 -10000 0 -0.5 2 2
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
PIK3CB 0.027 0.007 -10000 0 -10000 0 0
NRAS 0.028 0.005 -10000 0 -10000 0 0
PIK3CG 0.023 0.041 -10000 0 -0.5 3 3
PIK3R3 0.028 0.006 -10000 0 -10000 0 0
PIK3R2 0.029 0.003 -10000 0 -10000 0 0
NF1 0.028 0.004 -10000 0 -10000 0 0
RAS -0.029 0.081 0.19 2 -0.25 3 5
ERBB2 0.026 0.04 -10000 0 -0.61 2 2
proliferation/survival/translation -0.041 0.061 0.26 8 -0.21 5 13
PI3K -0.002 0.1 0.3 24 -0.25 6 30
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
KRAS 0.028 0.005 -10000 0 -10000 0 0
FOXO 0.053 0.072 0.27 23 -10000 0 23
AKT2 0.029 0.003 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 0.017 0.08 -10000 0 -0.48 5 5
BAG4 0.025 0.029 -10000 0 -0.61 1 1
BAD 0.018 0.054 0.34 6 -0.24 3 9
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 -0.054 0.19 -10000 0 -0.5 79 79
BAX 0.02 0.048 0.25 11 -0.19 1 12
EnzymeConsortium:3.1.4.12 0.01 0.031 0.12 12 -0.1 5 17
IKBKB 0.023 0.081 0.33 3 -0.47 4 7
MAP2K2 0.025 0.059 0.29 11 -0.27 1 12
MAP2K1 0.026 0.061 0.3 12 -10000 0 12
SMPD1 0.015 0.034 0.21 6 -0.15 2 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.024 0.087 0.37 1 -0.49 5 6
MAP2K4 0.034 0.072 0.22 45 -10000 0 45
protein ubiquitination 0.028 0.097 0.38 9 -0.46 5 14
EnzymeConsortium:2.7.1.37 0.032 0.069 0.34 11 -10000 0 11
response to UV 0 0.001 0.004 20 -0.003 1 21
RAF1 0.016 0.056 0.28 11 -10000 0 11
CRADD 0.028 0.005 -10000 0 -10000 0 0
mol:ceramide 0.017 0.045 0.2 10 -0.17 3 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.01 -10000 0 -10000 0 0
MADD 0.029 0.003 -10000 0 -10000 0 0
MAP3K1 0.032 0.07 0.22 43 -0.2 1 44
TRADD 0.028 0.006 -10000 0 -10000 0 0
RELA/p50 0.029 0.003 -10000 0 -10000 0 0
MAPK3 0.029 0.059 0.28 13 -10000 0 13
MAPK1 0.029 0.059 0.29 12 -10000 0 12
p50/RELA/I-kappa-B-alpha 0.04 0.011 -10000 0 -10000 0 0
FADD 0.013 0.081 0.37 1 -0.48 5 6
KSR1 0.02 0.053 0.26 10 -0.21 5 15
MAPK8 0.034 0.074 0.31 15 -0.27 1 16
TRAF2 0.028 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 8 -10000 0 8
CHUK 0.024 0.081 0.29 3 -0.51 3 6
TNF R/SODD 0.037 0.026 -10000 0 -0.45 1 1
TNF 0.019 0.073 -10000 0 -0.56 8 8
CYCS 0.024 0.059 0.25 15 -0.19 1 16
IKBKG 0.024 0.085 0.3 4 -0.51 3 7
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.013 0.085 -10000 0 -0.5 5 5
RELA 0.029 0.003 -10000 0 -10000 0 0
RIPK1 0.028 0.006 -10000 0 -10000 0 0
AIFM1 0.018 0.051 0.24 12 -0.19 1 13
TNF/TNF R/SODD 0.044 0.057 -10000 0 -0.35 9 9
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 8 -10000 0 8
CASP8 0.022 0.098 -10000 0 -0.61 11 11
NSMAF 0.016 0.084 0.32 2 -0.47 5 7
response to hydrogen peroxide 0 0.001 0.004 20 -0.003 1 21
BCL2 0.028 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.039 -10000 0 -0.45 3 3
AKT1 -0.007 0.12 0.44 7 -0.52 4 11
PTK2B -0.08 0.14 0.35 2 -0.83 1 3
VEGFR2 homodimer/Frs2 0.04 0.041 -10000 0 -0.56 2 2
CAV1 -0.006 0.12 -10000 0 -0.5 30 30
CALM1 0.027 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.084 0.16 -10000 0 -0.64 2 2
endothelial cell proliferation 0.012 0.14 0.47 20 -0.45 2 22
mol:Ca2+ -0.082 0.14 -10000 0 -0.69 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.065 0.15 -10000 0 -0.73 1 1
RP11-342D11.1 -0.088 0.14 -10000 0 -0.84 1 1
CDH5 0.027 0.024 -10000 0 -0.5 1 1
VEGFA homodimer -0.089 0.16 -10000 0 -0.34 4 4
SHC1 0.027 0.006 -10000 0 -10000 0 0
SHC2 0.023 0.057 -10000 0 -0.55 5 5
HRAS/GDP -0.061 0.13 -10000 0 -0.55 2 2
SH2D2A -0.14 0.25 -10000 0 -0.5 160 160
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.012 0.12 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.18 0.2 -10000 0 -0.52 64 64
VEGFR1 homodimer 0.023 0.053 -10000 0 -0.5 5 5
SHC/GRB2/SOS1 -0.052 0.15 -10000 0 -0.67 1 1
GRB10 -0.076 0.14 -10000 0 -0.69 1 1
PTPN11 0.028 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
PAK1 0.029 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.063 0.15 -10000 0 -0.67 2 2
HRAS 0.028 0.024 -10000 0 -0.5 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.04 0.1 -10000 0 -0.37 14 14
HIF1A 0.024 0.041 -10000 0 -0.61 2 2
FRS2 0.028 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.065 0.15 -10000 0 -0.72 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.013 -10000 0 -10000 0 0
Nck/Pak 0.039 0.024 -10000 0 -0.45 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.086 0.16 -10000 0 -0.93 1 1
mol:GDP -0.059 0.14 -10000 0 -0.64 1 1
mol:NADP -0.01 0.11 0.46 5 -0.46 1 6
eNOS/Hsp90 -0.005 0.1 0.36 2 -0.42 1 3
PIK3R1 0.025 0.029 -10000 0 -0.61 1 1
mol:IP3 -0.082 0.14 -10000 0 -0.7 1 1
HIF1A/ARNT 0.036 0.034 -10000 0 -0.45 2 2
SHB 0.028 0.006 -10000 0 -10000 0 0
VEGFA -0.21 0.26 -10000 0 -0.5 228 228
VEGFC 0.027 0.024 -10000 0 -0.5 1 1
FAK1/Vinculin -0.051 0.13 0.45 2 -0.54 4 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.069 0.16 -10000 0 -0.89 1 1
PTPN6 0.028 0.006 -10000 0 -10000 0 0
EPAS1 0.035 0.033 -10000 0 -0.47 2 2
mol:L-citrulline -0.01 0.11 0.46 5 -0.46 1 6
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.029 -10000 0 -0.61 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.069 0.16 -10000 0 -0.89 1 1
VEGFR2 homodimer/VEGFA homodimer -0.081 0.16 -10000 0 -0.92 1 1
VEGFR2/3 heterodimer 0.03 0.038 -10000 0 -0.47 2 2
VEGFB 0.029 0.003 -10000 0 -10000 0 0
MAPK11 -0.078 0.13 0.34 1 -0.62 2 3
VEGFR2 homodimer 0.028 0.044 -10000 0 -0.63 2 2
FLT1 0.023 0.053 -10000 0 -0.5 5 5
NEDD4 0.028 0.04 -10000 0 -0.61 2 2
MAPK3 -0.078 0.13 0.32 3 -0.66 1 4
MAPK1 -0.076 0.13 0.32 3 -0.6 1 4
VEGFA145/NRP2 -0.14 0.2 -10000 0 -0.36 225 225
VEGFR1/2 heterodimer 0.037 0.052 -10000 0 -0.55 2 2
KDR 0.028 0.044 -10000 0 -0.63 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.068 0.16 -10000 0 -0.77 2 2
SRC 0.028 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.067 0.14 0.38 8 -0.64 1 9
PI3K -0.037 0.12 -10000 0 -0.52 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.086 0.16 -10000 0 -0.48 3 3
FES -0.084 0.15 -10000 0 -0.72 2 2
GAB1 -0.043 0.11 -10000 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.085 0.16 -10000 0 -0.56 2 2
CTNNB1 0.02 0.013 -10000 0 -10000 0 0
SOS1 0.028 0.005 -10000 0 -10000 0 0
ARNT 0.027 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.023 0.1 0.32 1 -0.38 1 2
VEGFR2 homodimer/VEGFA homodimer/Yes -0.083 0.16 -10000 0 -0.64 2 2
PI3K/GAB1 -0.005 0.1 -10000 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.06 0.16 -10000 0 -0.71 1 1
PRKACA 0.029 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.043 -10000 0 -0.53 1 1
HSP90AA1 0.027 0.008 -10000 0 -10000 0 0
CDC42 -0.083 0.15 -10000 0 -0.85 1 1
actin cytoskeleton reorganization -0.18 0.2 -10000 0 -0.52 64 64
PTK2 -0.06 0.12 -10000 0 -0.6 3 3
EDG1 -0.088 0.14 -10000 0 -0.84 1 1
mol:DAG -0.082 0.14 -10000 0 -0.7 1 1
CaM/Ca2+ -0.069 0.13 -10000 0 -0.63 1 1
MAP2K3 -0.08 0.13 0.38 1 -0.68 1 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.05 0.16 -10000 0 -0.72 1 1
PLCG1 -0.083 0.14 -10000 0 -0.71 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.07 0.16 -10000 0 -0.73 1 1
IQGAP1 0.029 0.003 -10000 0 -10000 0 0
YES1 0.028 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.085 0.16 -10000 0 -0.64 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.085 0.16 -10000 0 -0.64 2 2
cell migration -0.023 0.12 0.42 3 -0.49 4 7
mol:PI-3-4-5-P3 -0.035 0.11 -10000 0 -0.49 3 3
FYN 0.027 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.074 0.14 -10000 0 -0.79 1 1
mol:NO -0.01 0.11 0.46 5 -0.46 1 6
PXN 0.028 0.005 -10000 0 -10000 0 0
HRAS/GTP -0.072 0.12 -10000 0