Uterine Corpus Endometrioid Carcinoma: PARADIGM pathway analysis of mRNASeq expression data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 47 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
Signaling events mediated by the Hedgehog family 56
FOXA2 and FOXA3 transcription factor networks 38
IL23-mediated signaling events 38
Syndecan-1-mediated signaling events 37
Ephrin A reverse signaling 35
TCGA08_retinoblastoma 35
IL4-mediated signaling events 34
Wnt signaling 34
HIF-1-alpha transcription factor network 32
Signaling mediated by p38-alpha and p38-beta 28
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • 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.

Pathway.Name 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
Signaling events mediated by the Hedgehog family 56 2947 52 -0.28 0.14 1000 -1000 -0.041 -1000
FOXA2 and FOXA3 transcription factor networks 38 1759 46 -0.47 0.013 1000 -1000 -0.11 -1000
IL23-mediated signaling events 38 2311 60 -0.52 0.013 1000 -1000 -0.17 -1000
Syndecan-1-mediated signaling events 37 1280 34 -0.21 0.013 1000 -1000 -0.048 -1000
Ephrin A reverse signaling 35 248 7 -0.083 0 1000 -1000 -0.019 -1000
TCGA08_retinoblastoma 35 281 8 -0.1 0.052 1000 -1000 -0.018 -1000
IL4-mediated signaling events 34 3156 91 -0.7 0.54 1000 -1000 -0.17 -1000
Wnt signaling 34 243 7 -0.15 0.009 1000 -1000 -0.027 -1000
HIF-1-alpha transcription factor network 32 2466 76 -0.37 0.022 1000 -1000 -0.15 -1000
Signaling mediated by p38-alpha and p38-beta 28 1255 44 -0.19 0.013 1000 -1000 -0.037 -1000
TCR signaling in naïve CD8+ T cells 27 2548 93 -0.14 0.072 1000 -1000 -0.075 -1000
Noncanonical Wnt signaling pathway 26 686 26 -0.15 0.013 1000 -1000 -0.05 -1000
p75(NTR)-mediated signaling 25 3247 125 -0.31 0.034 1000 -1000 -0.092 -1000
Glypican 1 network 24 1155 48 -0.13 0.018 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 24 2030 82 -0.17 0.013 1000 -1000 -0.084 -1000
Ephrin B reverse signaling 24 1160 48 -0.12 0.078 1000 -1000 -0.065 -1000
BMP receptor signaling 23 1918 81 -0.21 0.043 1000 -1000 -0.087 -1000
EPHB forward signaling 23 2033 85 -0.16 0.13 1000 -1000 -0.086 -1000
IL12-mediated signaling events 22 1934 87 -0.25 0.031 1000 -1000 -0.14 -1000
Glucocorticoid receptor regulatory network 22 2619 114 -0.54 0.27 1000 -1000 -0.065 -1000
Syndecan-4-mediated signaling events 22 1477 67 -0.15 0.021 1000 -1000 -0.075 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 21 1710 78 -0.15 0.07 1000 -1000 -0.064 -1000
amb2 Integrin signaling 20 1680 82 -0.28 0.018 1000 -1000 -0.071 -1000
Nectin adhesion pathway 20 1271 63 -0.094 0.026 1000 -1000 -0.072 -1000
Endothelins 20 1964 96 -0.25 0.017 1000 -1000 -0.087 -1000
Osteopontin-mediated events 19 740 38 -0.069 0.013 1000 -1000 -0.089 -1000
Glypican 2 network 19 78 4 -0.018 -1000 1000 -1000 -0.014 -1000
LPA receptor mediated events 19 1946 102 -0.15 0.016 1000 -1000 -0.08 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 19 1340 68 -0.29 0.099 1000 -1000 -0.14 -1000
Caspase cascade in apoptosis 18 1395 74 -0.11 0.039 1000 -1000 -0.045 -1000
Nephrin/Neph1 signaling in the kidney podocyte 18 636 34 -0.058 0.013 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 18 1290 69 -0.08 0.02 1000 -1000 -0.028 -1000
BCR signaling pathway 18 1825 99 -0.17 0.017 1000 -1000 -0.083 -1000
Plasma membrane estrogen receptor signaling 18 1575 86 -0.098 0.088 1000 -1000 -0.082 -1000
FOXM1 transcription factor network 18 934 51 -0.21 0.028 1000 -1000 -0.16 -1000
Thromboxane A2 receptor signaling 16 1706 105 -0.1 0.022 1000 -1000 -0.064 -1000
Reelin signaling pathway 16 947 56 -0.16 0.023 1000 -1000 -0.075 -1000
Canonical Wnt signaling pathway 16 863 51 -0.28 0.11 1000 -1000 -0.059 -1000
Effects of Botulinum toxin 16 431 26 -0.12 0.014 1000 -1000 -0.059 -1000
IGF1 pathway 16 948 57 -0.067 0.027 1000 -1000 -0.084 -1000
Neurotrophic factor-mediated Trk receptor signaling 16 1944 120 -0.16 0.13 1000 -1000 -0.077 -1000
Presenilin action in Notch and Wnt signaling 15 929 61 -0.28 0.043 1000 -1000 -0.068 -1000
TCGA08_p53 15 105 7 -0.073 0.043 1000 -1000 -0.01 -1000
Integrins in angiogenesis 15 1282 84 -0.13 0.02 1000 -1000 -0.089 -1000
LPA4-mediated signaling events 14 174 12 -0.047 0.016 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 14 1115 76 -0.16 0.017 1000 -1000 -0.068 -1000
IL6-mediated signaling events 14 1117 75 -0.21 0.037 1000 -1000 -0.075 -1000
PDGFR-alpha signaling pathway 13 603 44 -0.068 0.021 1000 -1000 -0.069 -1000
Nongenotropic Androgen signaling 13 717 52 -0.085 0.013 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 12 934 76 -0.1 0.024 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 12 36 3 -0.007 -0.006 1000 -1000 -0.012 -1000
JNK signaling in the CD4+ TCR pathway 12 205 17 -0.048 0.013 1000 -1000 -0.035 -1000
Cellular roles of Anthrax toxin 12 489 39 -0.093 0.013 1000 -1000 -0.027 -1000
Arf6 signaling events 12 786 62 -0.085 0.019 1000 -1000 -0.045 -1000
IL1-mediated signaling events 12 780 62 -0.1 0.061 1000 -1000 -0.088 -1000
RXR and RAR heterodimerization with other nuclear receptor 12 627 52 -0.12 0.021 1000 -1000 -0.047 -1000
Calcium signaling in the CD4+ TCR pathway 12 391 31 -0.19 0.013 1000 -1000 -0.064 -1000
FAS signaling pathway (CD95) 11 523 47 -0.073 0.025 1000 -1000 -0.047 -1000
a4b1 and a4b7 Integrin signaling 10 53 5 -0.012 0 1000 -1000 -0.017 -1000
S1P1 pathway 10 382 36 -0.16 0.013 1000 -1000 -0.057 -1000
IL27-mediated signaling events 10 527 51 -0.11 0.039 1000 -1000 -0.095 -1000
IL2 signaling events mediated by STAT5 10 228 22 -0.037 0.014 1000 -1000 -0.057 -1000
EGFR-dependent Endothelin signaling events 10 229 21 -0.083 0.02 1000 -1000 -0.069 -1000
Visual signal transduction: Rods 10 552 52 -0.11 0.013 1000 -1000 -0.072 -1000
Regulation of nuclear SMAD2/3 signaling 9 1298 136 -0.26 0.06 1000 -1000 -0.059 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 9 797 85 -0.039 0.013 1000 -1000 -0.066 -1000
Fc-epsilon receptor I signaling in mast cells 9 945 97 -0.07 0.027 1000 -1000 -0.076 -1000
Paxillin-independent events mediated by a4b1 and a4b7 9 348 37 -0.059 0.019 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class III 9 380 40 -0.13 0.023 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 9 540 58 -0.11 0.025 1000 -1000 -0.076 -1000
Syndecan-3-mediated signaling events 9 320 35 -0.092 0.034 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 9 562 58 -0.088 0.021 1000 -1000 -0.084 -1000
Regulation of Telomerase 9 947 102 -0.19 0.036 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 9 846 88 -0.12 0.018 1000 -1000 -0.099 -1000
Signaling events mediated by PRL 9 326 34 -0.12 0.02 1000 -1000 -0.038 -1000
Regulation of Androgen receptor activity 9 680 70 -0.15 0.025 1000 -1000 -0.068 -1000
ErbB4 signaling events 8 616 69 -0.073 0.026 1000 -1000 -0.084 -1000
BARD1 signaling events 8 496 57 -0.03 0.032 1000 -1000 -0.06 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 8 461 54 -0.16 0.026 1000 -1000 -0.09 -1000
Hedgehog signaling events mediated by Gli proteins 8 563 65 -0.25 0.041 1000 -1000 -0.061 -1000
TRAIL signaling pathway 8 430 48 -0.04 0.026 1000 -1000 -0.072 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 274 33 -0.11 0.036 1000 -1000 -0.042 -1000
Ras signaling in the CD4+ TCR pathway 8 150 17 -0.03 0.02 1000 -1000 -0.036 -1000
Ceramide signaling pathway 7 586 76 -0.083 0.038 1000 -1000 -0.051 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 7 347 45 -0.079 0.032 1000 -1000 -0.086 -1000
Sphingosine 1-phosphate (S1P) pathway 6 172 28 -0.033 0.03 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 6 255 38 -0.04 0.009 1000 -1000 -0.042 -1000
EPO signaling pathway 6 360 55 -0.043 0.029 1000 -1000 -0.084 -1000
IFN-gamma pathway 6 434 68 -0.12 0.036 1000 -1000 -0.09 -1000
S1P5 pathway 6 114 17 -0.033 0.013 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 6 99 15 -0.013 0.018 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 6 172 26 -0.046 0.034 1000 -1000 -0.018 -1000
Insulin Pathway 6 483 74 -0.12 0.034 1000 -1000 -0.073 -1000
Aurora B signaling 6 443 67 -0.17 0.017 1000 -1000 -0.066 -1000
ErbB2/ErbB3 signaling events 5 372 65 -0.053 0.03 1000 -1000 -0.066 -1000
ceramide signaling pathway 5 261 49 -0.065 0.02 1000 -1000 -0.055 -1000
HIF-2-alpha transcription factor network 5 257 43 -0.049 0.05 1000 -1000 -0.075 -1000
Paxillin-dependent events mediated by a4b1 5 205 36 -0.059 0.026 1000 -1000 -0.071 -1000
S1P4 pathway 5 135 25 -0.033 0.018 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 5 253 44 -0.12 0.026 1000 -1000 -0.067 -1000
Signaling events mediated by HDAC Class II 4 331 75 -0.071 0.033 1000 -1000 -0.041 -1000
mTOR signaling pathway 4 242 53 -0.028 0.017 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 412 83 -0.1 0.053 1000 -1000 -0.077 -1000
Regulation of p38-alpha and p38-beta 4 259 54 -0.092 0.033 1000 -1000 -0.066 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 616 125 -0.065 0.047 1000 -1000 -0.093 -1000
Stabilization and expansion of the E-cadherin adherens junction 4 315 74 -0.083 0.056 1000 -1000 -0.086 -1000
Class I PI3K signaling events 4 346 73 -0.092 0.026 1000 -1000 -0.064 -1000
VEGFR1 specific signals 4 226 56 -0.024 0.038 1000 -1000 -0.061 -1000
PDGFR-beta signaling pathway 4 438 97 -0.076 0.036 1000 -1000 -0.081 -1000
Class IB PI3K non-lipid kinase events 4 12 3 -0.006 0.006 1000 -1000 -0.018 -1000
Canonical NF-kappaB pathway 3 141 39 -0.066 0.064 1000 -1000 -0.088 -1000
Arf6 downstream pathway 3 143 43 -0.019 0.02 1000 -1000 -0.04 -1000
Aurora C signaling 3 24 7 -0.005 0.009 1000 -1000 -0.037 -1000
PLK1 signaling events 3 265 85 -0.029 0.031 1000 -1000 -0.046 -1000
Class I PI3K signaling events mediated by Akt 3 224 68 -0.054 0.037 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 3 390 104 -0.066 0.049 1000 -1000 -0.062 -1000
FoxO family signaling 3 220 64 -0.11 0.098 1000 -1000 -0.074 -1000
Atypical NF-kappaB pathway 3 97 31 -0.024 0.032 1000 -1000 -0.045 -1000
S1P3 pathway 3 156 42 -0.018 0.022 1000 -1000 -0.046 -1000
E-cadherin signaling events 3 16 5 0.009 0.018 1000 -1000 -0.023 -1000
Aurora A signaling 2 174 60 -0.059 0.034 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 2 71 32 -0.054 0.028 1000 -1000 -0.054 -1000
E-cadherin signaling in the nascent adherens junction 2 193 76 -0.025 0.049 1000 -1000 -0.081 -1000
Sumoylation by RanBP2 regulates transcriptional repression 2 60 27 -0.009 0.029 1000 -1000 -0.049 -1000
Arf6 trafficking events 2 149 71 -0.019 0.033 1000 -1000 -0.077 -1000
Rapid glucocorticoid signaling 2 47 20 -0.007 0.013 1000 -1000 -0.018 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 35 23 -0.014 0.039 1000 -1000 -0.043 -1000
Circadian rhythm pathway 1 26 22 -0.013 0.044 1000 -1000 -0.05 -1000
E-cadherin signaling in keratinocytes 1 66 43 -0.023 0.027 1000 -1000 -0.051 -1000
Arf1 pathway 0 26 54 -0.002 0.028 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0 4 13 0 0.039 1000 -1000 -0.028 -1000
Total 1617 96411 7203 -15 -1000 131000 -131000 -8.2 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.29 -10000 0 -0.78 38 38
IHH -0.28 0.3 -10000 0 -0.57 133 133
SHH Np/Cholesterol/GAS1 -0.12 0.2 -10000 0 -0.41 70 70
LRPAP1 0.006 0.064 -10000 0 -0.6 3 3
dorsoventral neural tube patterning 0.12 0.2 0.41 70 -10000 0 70
SMO/beta Arrestin2 -0.18 0.26 -10000 0 -0.57 56 56
SMO -0.2 0.28 -10000 0 -0.51 93 93
AKT1 -0.092 0.18 -10000 0 -0.6 17 17
ARRB2 0.012 0.027 -10000 0 -0.43 1 1
BOC -0.024 0.13 -10000 0 -0.46 21 21
ADRBK1 0.012 0.027 -10000 0 -0.43 1 1
heart looping -0.19 0.27 -10000 0 -0.5 93 93
STIL -0.19 0.25 -10000 0 -0.57 57 57
DHH N/PTCH2 -0.032 0.15 -10000 0 -0.43 30 30
DHH N/PTCH1 -0.17 0.24 -10000 0 -0.58 41 41
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
DHH -0.027 0.15 -10000 0 -0.57 18 18
PTHLH -0.22 0.35 -10000 0 -0.95 35 35
determination of left/right symmetry -0.19 0.27 -10000 0 -0.5 93 93
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
skeletal system development -0.21 0.35 -10000 0 -0.93 35 35
IHH N/Hhip -0.25 0.27 -10000 0 -0.51 121 121
DHH N/Hhip -0.11 0.21 -10000 0 -0.42 76 76
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.19 0.27 -10000 0 -0.5 93 93
pancreas development -0.12 0.24 -10000 0 -0.56 62 62
HHAT -0.017 0.13 -10000 0 -0.6 13 13
PI3K -0.01 0.1 -10000 0 -0.37 20 20
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.092 0.21 -10000 0 -0.5 55 55
somite specification -0.19 0.27 -10000 0 -0.5 93 93
SHH Np/Cholesterol/PTCH1 -0.2 0.26 -10000 0 -0.6 59 59
SHH Np/Cholesterol/PTCH2 -0.085 0.17 -10000 0 -0.37 59 59
SHH Np/Cholesterol/Megalin -0.17 0.2 -10000 0 -0.41 86 86
SHH -0.097 0.2 -10000 0 -0.4 74 74
catabolic process -0.17 0.24 -10000 0 -0.42 102 102
SMO/Vitamin D3 -0.21 0.28 -10000 0 -0.64 59 59
SHH Np/Cholesterol/Hhip -0.14 0.21 -10000 0 -0.42 80 80
LRP2 -0.18 0.25 -10000 0 -0.49 101 101
receptor-mediated endocytosis -0.26 0.28 -10000 0 -0.61 81 81
SHH Np/Cholesterol/BOC -0.088 0.18 -10000 0 -0.4 53 53
SHH Np/Cholesterol/CDO -0.077 0.17 -10000 0 -0.38 51 51
mesenchymal cell differentiation 0.14 0.21 0.41 80 -10000 0 80
mol:Vitamin D3 -0.2 0.26 -10000 0 -0.6 59 59
IHH N/PTCH2 -0.18 0.21 -10000 0 -0.42 102 102
CDON -0.003 0.088 -10000 0 -0.47 9 9
IHH N/PTCH1 -0.17 0.24 -10000 0 -0.43 102 102
Megalin/LRPAP1 -0.12 0.19 -10000 0 -0.35 103 103
PTCH2 -0.017 0.13 -10000 0 -0.53 15 15
SHH Np/Cholesterol -0.076 0.15 -10000 0 -0.36 50 50
PTCH1 -0.17 0.24 -10000 0 -0.42 102 102
HHIP -0.12 0.24 -10000 0 -0.56 62 62
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.26 0.4 -9999 0 -0.95 48 48
PCK1 -0.39 0.49 -9999 0 -1 74 74
HNF4A -0.47 0.56 -9999 0 -1.1 91 91
KCNJ11 -0.27 0.41 -9999 0 -0.97 47 47
AKT1 -0.082 0.14 -9999 0 -0.42 10 10
response to starvation -0.008 0.024 -9999 0 -10000 0 0
DLK1 -0.29 0.43 -9999 0 -1 49 49
NKX2-1 -0.046 0.25 -9999 0 -0.63 10 10
ACADM -0.28 0.42 -9999 0 -0.98 53 53
TAT -0.22 0.28 -9999 0 -0.83 22 22
CEBPB 0.013 0.038 -9999 0 -0.59 1 1
CEBPA -0.014 0.13 -9999 0 -0.56 14 14
TTR -0.37 0.34 -9999 0 -0.91 56 56
PKLR -0.28 0.42 -9999 0 -0.99 50 50
APOA1 -0.45 0.58 -9999 0 -1.3 66 66
CPT1C -0.28 0.41 -9999 0 -0.99 47 47
ALAS1 -0.12 0.22 -9999 0 -1.4 3 3
TFRC -0.28 0.35 -9999 0 -0.93 36 36
FOXF1 -0.002 0.095 -9999 0 -0.44 11 11
NF1 0.012 0.066 -9999 0 -0.59 3 3
HNF1A (dimer) -0.083 0.2 -9999 0 -0.6 33 33
CPT1A -0.26 0.39 -9999 0 -0.95 45 45
HMGCS1 -0.26 0.39 -9999 0 -0.94 48 48
NR3C1 -0.005 0.11 -9999 0 -0.58 9 9
CPT1B -0.29 0.43 -9999 0 -1 49 49
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.011 0.06 -9999 0 -10000 0 0
GCK -0.3 0.44 -9999 0 -1 54 54
CREB1 -0.013 0.056 -9999 0 -10000 0 0
IGFBP1 -0.14 0.21 -9999 0 -0.78 9 9
PDX1 -0.33 0.49 -9999 0 -1.2 49 49
UCP2 -0.27 0.41 -9999 0 -0.98 48 48
ALDOB -0.28 0.41 -9999 0 -0.98 48 48
AFP -0.22 0.23 -9999 0 -0.61 46 46
BDH1 -0.27 0.4 -9999 0 -0.97 46 46
HADH -0.27 0.41 -9999 0 -0.98 46 46
F2 -0.4 0.5 -9999 0 -1.2 58 58
HNF1A -0.083 0.2 -9999 0 -0.6 33 33
G6PC -0.13 0.2 -9999 0 -0.7 16 16
SLC2A2 -0.23 0.33 -9999 0 -0.7 59 59
INS -0.002 0.029 -9999 0 -10000 0 0
FOXA1 -0.24 0.28 -9999 0 -0.54 116 116
FOXA3 -0.2 0.28 -9999 0 -0.57 88 88
FOXA2 -0.31 0.46 -9999 0 -1.1 53 53
ABCC8 -0.3 0.43 -9999 0 -1 51 51
ALB -0.28 0.34 -9999 0 -0.78 64 64
IL23-mediated 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
CCL2 -0.41 0.48 -10000 0 -1.2 54 54
IL23A -0.43 0.51 -10000 0 -1.2 58 58
NF kappa B1 p50/RelA/I kappa B alpha -0.43 0.47 -10000 0 -1.1 67 67
positive regulation of T cell mediated cytotoxicity -0.47 0.57 -10000 0 -1.3 66 66
ITGA3 -0.41 0.48 -10000 0 -1.1 59 59
IL17F -0.28 0.31 -10000 0 -0.7 64 64
IL12B -0.015 0.065 -10000 0 -0.48 4 4
STAT1 (dimer) -0.44 0.54 -10000 0 -1.2 67 67
CD4 -0.4 0.48 -10000 0 -1.2 54 54
IL23 -0.42 0.48 -10000 0 -1.2 58 58
IL23R -0.052 0.11 -10000 0 -1.4 1 1
IL1B -0.43 0.52 -10000 0 -1.2 57 57
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.41 0.48 -10000 0 -1.2 56 56
TYK2 -0.002 0.019 -10000 0 -10000 0 0
STAT4 0.001 0.083 -10000 0 -0.54 6 6
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.034 0.16 -10000 0 -0.55 22 22
IL12RB1 -0.008 0.059 -10000 0 -0.52 3 3
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
IL12Rbeta1/TYK2 -0.006 0.048 -10000 0 -0.39 3 3
IL23R/JAK2 -0.076 0.14 -10000 0 -0.91 2 2
positive regulation of chronic inflammatory response -0.47 0.57 -10000 0 -1.3 66 66
natural killer cell activation 0.005 0.008 0.08 1 -10000 0 1
JAK2 -0.02 0.12 -10000 0 -0.62 9 9
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
NFKB1 0.008 0.038 -10000 0 -0.6 1 1
RELA 0.011 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.46 -10000 0 -1.1 58 58
ALOX12B -0.46 0.53 -10000 0 -1.2 68 68
CXCL1 -0.51 0.56 -10000 0 -1.3 76 76
T cell proliferation -0.47 0.57 -10000 0 -1.3 66 66
NFKBIA 0.011 0.003 -10000 0 -10000 0 0
IL17A -0.21 0.25 -10000 0 -0.56 50 50
PI3K -0.46 0.48 -10000 0 -1.2 69 69
IFNG -0.026 0.041 0.16 1 -0.12 21 22
STAT3 (dimer) -0.43 0.45 -10000 0 -1.1 69 69
IL18R1 -0.028 0.15 -10000 0 -0.58 18 18
IL23/IL23R/JAK2/TYK2/SOCS3 -0.23 0.28 -10000 0 -0.72 29 29
IL18/IL18R -0.043 0.18 -10000 0 -0.44 39 39
macrophage activation -0.022 0.017 -10000 0 -0.044 50 50
TNF -0.45 0.54 -10000 0 -1.3 61 61
STAT3/STAT4 -0.44 0.48 -10000 0 -1.2 66 66
STAT4 (dimer) -0.44 0.54 -10000 0 -1.2 66 66
IL18 -0.016 0.13 -10000 0 -0.57 13 13
IL19 -0.52 0.56 -10000 0 -1.2 80 80
STAT5A (dimer) -0.44 0.54 -10000 0 -1.2 65 65
STAT1 0.006 0.06 -10000 0 -0.47 4 4
SOCS3 -0.014 0.12 -10000 0 -0.58 12 12
CXCL9 -0.5 0.56 -10000 0 -1.3 75 75
MPO -0.44 0.51 -10000 0 -1.2 67 67
positive regulation of humoral immune response -0.47 0.57 -10000 0 -1.3 66 66
IL23/IL23R/JAK2/TYK2 -0.51 0.69 -10000 0 -1.5 66 66
IL6 -0.44 0.51 -10000 0 -1.2 63 63
STAT5A 0.012 0.027 -10000 0 -0.43 1 1
IL2 -0.006 0.08 -10000 0 -0.43 9 9
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.008 0.08 1 -10000 0 1
CD3E -0.44 0.52 -10000 0 -1.2 60 60
keratinocyte proliferation -0.47 0.57 -10000 0 -1.3 66 66
NOS2 -0.42 0.49 -10000 0 -1.2 58 58
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.046 -9999 0 -0.51 2 2
CCL5 -0.001 0.084 -9999 0 -0.47 8 8
SDCBP 0.011 0.037 -9999 0 -0.6 1 1
FGFR/FGF2/Syndecan-1 -0.17 0.22 -9999 0 -0.48 59 59
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.16 0.21 -9999 0 -0.46 61 61
Syndecan-1/Syntenin -0.15 0.21 -9999 0 -0.46 59 59
MAPK3 -0.13 0.19 -9999 0 -0.46 39 39
HGF/MET -0.047 0.16 -9999 0 -0.4 42 42
TGFB1/TGF beta receptor Type II 0.009 0.046 -9999 0 -0.51 2 2
BSG 0.013 0 -9999 0 -10000 0 0
keratinocyte migration -0.15 0.21 -9999 0 -0.45 61 61
Syndecan-1/RANTES -0.16 0.21 -9999 0 -0.46 63 63
Syndecan-1/CD147 -0.14 0.2 -9999 0 -0.5 39 39
Syndecan-1/Syntenin/PIP2 -0.15 0.2 -9999 0 -0.44 59 59
LAMA5 0.007 0.059 -9999 0 -0.54 3 3
positive regulation of cell-cell adhesion -0.15 0.2 -9999 0 -0.43 59 59
MMP7 -0.21 0.28 -9999 0 -0.55 105 105
HGF -0.036 0.16 -9999 0 -0.53 24 24
Syndecan-1/CASK -0.16 0.21 -9999 0 -0.46 59 59
Syndecan-1/HGF/MET -0.18 0.24 -9999 0 -0.52 68 68
regulation of cell adhesion -0.12 0.18 -9999 0 -0.44 39 39
HPSE -0.03 0.14 -9999 0 -0.51 22 22
positive regulation of cell migration -0.17 0.22 -9999 0 -0.48 59 59
SDC1 -0.17 0.22 -9999 0 -0.49 59 59
Syndecan-1/Collagen -0.17 0.22 -9999 0 -0.48 59 59
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.029 0.15 -9999 0 -0.56 20 20
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.081 0.21 -9999 0 -0.52 47 47
MAPK1 -0.13 0.19 -9999 0 -0.46 39 39
homophilic cell adhesion -0.17 0.21 -9999 0 -0.48 59 59
MMP1 -0.11 0.23 -9999 0 -0.52 64 64
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.057 0.14 -9999 0 -0.34 53 53
EFNA5 -0.083 0.22 -9999 0 -0.57 44 44
FYN -0.045 0.13 -9999 0 -0.34 36 36
neuron projection morphogenesis -0.057 0.14 -9999 0 -0.34 53 53
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.057 0.14 -9999 0 -0.34 53 53
EPHA5 -0.01 0.079 -9999 0 -0.43 9 9
TCGA08_retinoblastoma

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
CDKN2B -0.025 0.14 -10000 0 -0.52 19 19
CDKN2C -0.006 0.11 -10000 0 -0.45 15 15
CDKN2A -0.1 0.2 -10000 0 -0.46 64 64
CCND2 0.038 0.092 0.24 33 -0.15 3 36
RB1 -0.038 0.11 0.16 1 -0.27 34 35
CDK4 0.052 0.1 0.27 37 -10000 0 37
CDK6 0.041 0.1 0.26 34 -0.18 6 40
G1/S progression 0.038 0.11 0.27 34 -0.16 1 35
IL4-mediated signaling events

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
BCL2L1 -0.48 0.53 -10000 0 -1.2 66 66
STAT6 (cleaved dimer) -0.54 0.51 -10000 0 -1.2 88 88
IGHG1 -0.16 0.18 -10000 0 -0.58 3 3
IGHG3 -0.47 0.5 -10000 0 -1.1 73 73
AKT1 -0.24 0.31 -10000 0 -0.84 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.29 -10000 0 -0.94 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.33 -10000 0 -0.98 25 25
THY1 -0.48 0.53 -10000 0 -1.2 66 66
MYB -0.005 0.1 -10000 0 -0.6 8 8
HMGA1 -0.006 0.099 -10000 0 -0.5 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.36 -10000 0 -0.9 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.33 -10000 0 -1 21 21
SP1 0.019 0.012 -10000 0 -10000 0 0
INPP5D 0 0.09 -10000 0 -0.6 6 6
SOCS5 0.027 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.49 0.54 -10000 0 -1.2 76 76
SOCS1 -0.3 0.34 -10000 0 -0.79 49 49
SOCS3 -0.28 0.36 -10000 0 -1.1 28 28
FCER2 -0.37 0.42 -10000 0 -1.1 30 30
PARP14 0.012 0.037 -10000 0 -0.6 1 1
CCL17 -0.55 0.6 -10000 0 -1.3 80 80
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.26 -10000 0 -0.82 19 19
T cell proliferation -0.49 0.55 -10000 0 -1.2 70 70
IL4R/JAK1 -0.48 0.53 -10000 0 -1.2 69 69
EGR2 -0.49 0.55 -10000 0 -1.3 61 61
JAK2 -0.031 0.12 -10000 0 -0.63 9 9
JAK3 0.01 0.049 -10000 0 -0.44 3 3
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
JAK1 -0.002 0.07 -10000 0 -0.56 4 4
COL1A2 -0.19 0.32 -10000 0 -1.3 15 15
CCL26 -0.48 0.53 -10000 0 -1.2 65 65
IL4R -0.51 0.57 -10000 0 -1.3 66 66
PTPN6 0.022 0.039 -10000 0 -0.58 1 1
IL13RA2 -0.55 0.59 -10000 0 -1.3 78 78
IL13RA1 -0.012 0.043 -10000 0 -0.48 1 1
IRF4 -0.26 0.47 -10000 0 -1.4 34 34
ARG1 -0.11 0.16 -10000 0 -0.68 6 6
CBL -0.29 0.34 -10000 0 -0.86 40 40
GTF3A 0.019 0.009 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
IL13RA1/JAK2 -0.027 0.097 -10000 0 -0.46 10 10
IRF4/BCL6 -0.24 0.43 -10000 0 -1.3 34 34
CD40LG -0.041 0.17 -10000 0 -0.56 26 26
MAPK14 -0.29 0.35 -10000 0 -0.91 39 39
mitosis -0.23 0.29 -10000 0 -0.78 30 30
STAT6 -0.56 0.66 -10000 0 -1.4 70 70
SPI1 0.005 0.075 -10000 0 -0.53 5 5
RPS6KB1 -0.22 0.28 -10000 0 -0.76 28 28
STAT6 (dimer) -0.56 0.66 -10000 0 -1.5 70 70
STAT6 (dimer)/PARP14 -0.51 0.58 -10000 0 -1.3 68 68
mast cell activation 0.011 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.32 -10000 0 -0.99 22 22
FRAP1 -0.24 0.31 -10000 0 -0.84 30 30
LTA -0.5 0.56 -10000 0 -1.3 67 67
FES 0.011 0.037 -10000 0 -0.6 1 1
T-helper 1 cell differentiation 0.54 0.61 1.4 70 -10000 0 70
CCL11 -0.56 0.59 -10000 0 -1.3 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.32 -10000 0 -0.95 23 23
IL2RG -0.019 0.14 -10000 0 -0.55 16 16
IL10 -0.48 0.53 -10000 0 -1.2 65 65
IRS1 -0.015 0.13 -10000 0 -0.57 13 13
IRS2 -0.042 0.16 -10000 0 -0.49 29 29
IL4 -0.1 0.12 -10000 0 -10000 0 0
IL5 -0.48 0.53 -10000 0 -1.2 72 72
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.44 -10000 0 -0.96 66 66
COL1A1 -0.17 0.26 -10000 0 -1.2 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.49 0.55 -10000 0 -1.3 65 65
IL2R gamma/JAK3 -0.009 0.11 -10000 0 -0.4 18 18
TFF3 -0.7 0.71 -10000 0 -1.6 95 95
ALOX15 -0.55 0.59 -10000 0 -1.3 74 74
MYBL1 0.004 0.066 -10000 0 -0.47 5 5
T-helper 2 cell differentiation -0.41 0.44 -10000 0 -0.99 69 69
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.013 0.038 -10000 0 -0.6 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.32 -10000 0 -0.92 26 26
mol:PI-3-4-5-P3 -0.24 0.31 -10000 0 -0.84 30 30
PI3K -0.26 0.34 -10000 0 -0.92 30 30
DOK2 0.001 0.083 -10000 0 -0.54 6 6
ETS1 0.023 0.038 -10000 0 -0.56 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.25 -10000 0 -0.77 20 20
ITGB3 -0.54 0.58 -10000 0 -1.3 77 77
PIGR -0.69 0.71 -10000 0 -1.5 96 96
IGHE 0.036 0.047 -10000 0 -0.31 1 1
MAPKKK cascade -0.18 0.24 -10000 0 -0.75 20 20
BCL6 0.01 0.037 -10000 0 -0.6 1 1
OPRM1 -0.48 0.53 -10000 0 -1.2 68 68
RETNLB -0.48 0.53 -10000 0 -1.2 72 72
SELP -0.54 0.61 -10000 0 -1.3 77 77
AICDA -0.47 0.51 -10000 0 -1.2 68 68
Wnt signaling

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
Noncanonical Wnts/FZD -0.14 0.24 -9999 0 -0.65 31 31
FZD6 0.009 0.053 -9999 0 -0.6 2 2
WNT6 -0.12 0.22 -9999 0 -0.48 73 73
WNT4 -0.068 0.2 -9999 0 -0.53 40 40
FZD3 0.006 0.064 -9999 0 -0.6 3 3
WNT5A -0.019 0.13 -9999 0 -0.56 15 15
WNT11 -0.15 0.25 -9999 0 -0.53 79 79
HIF-1-alpha transcription factor network

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
PKM2 -0.24 0.54 -9999 0 -1.2 43 43
HDAC7 0.013 0.028 -9999 0 -0.44 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.36 -9999 0 -0.88 40 40
SMAD4 0.015 0 -9999 0 -10000 0 0
ID2 -0.25 0.54 -9999 0 -1.2 46 46
AP1 -0.013 0.11 -9999 0 -0.36 23 23
ABCG2 -0.26 0.56 -9999 0 -1.2 48 48
HIF1A -0.027 0.11 -9999 0 -0.67 4 4
TFF3 -0.36 0.61 -9999 0 -1.2 63 63
GATA2 -0.06 0.2 -9999 0 -0.58 33 33
AKT1 -0.022 0.092 -9999 0 -10000 0 0
response to hypoxia -0.039 0.097 -9999 0 -0.24 2 2
MCL1 -0.24 0.54 -9999 0 -1.2 44 44
NDRG1 -0.26 0.56 -9999 0 -1.2 45 45
SERPINE1 -0.25 0.55 -9999 0 -1.2 45 45
FECH -0.25 0.54 -9999 0 -1.2 45 45
FURIN -0.24 0.54 -9999 0 -1.2 44 44
NCOA2 -0.023 0.14 -9999 0 -0.56 17 17
EP300 -0.014 0.13 -9999 0 -0.3 5 5
HMOX1 -0.25 0.54 -9999 0 -1.2 45 45
BHLHE40 -0.24 0.54 -9999 0 -1.2 43 43
BHLHE41 -0.28 0.57 -9999 0 -1.2 50 50
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.021 0.089 -9999 0 -0.47 3 3
ENG 0.02 0.11 -9999 0 -0.44 2 2
JUN 0.008 0.054 -9999 0 -0.49 3 3
RORA -0.26 0.55 -9999 0 -1.2 45 45
ABCB1 -0.14 0.33 -9999 0 -1.2 19 19
TFRC -0.25 0.54 -9999 0 -1.2 44 44
CXCR4 -0.25 0.55 -9999 0 -1.2 46 46
TF -0.28 0.56 -9999 0 -1.2 47 47
CITED2 -0.25 0.55 -9999 0 -1.2 43 43
HIF1A/ARNT -0.37 0.61 -9999 0 -1.4 47 47
LDHA -0.036 0.048 -9999 0 -10000 0 0
ETS1 -0.24 0.54 -9999 0 -1.2 44 44
PGK1 -0.25 0.55 -9999 0 -1.2 44 44
NOS2 -0.26 0.55 -9999 0 -1.2 46 46
ITGB2 -0.25 0.55 -9999 0 -1.2 45 45
ALDOA -0.25 0.54 -9999 0 -1.2 44 44
Cbp/p300/CITED2 -0.27 0.55 -9999 0 -1.3 42 42
FOS -0.028 0.14 -9999 0 -0.48 22 22
HK2 -0.25 0.54 -9999 0 -1.2 44 44
SP1 0.018 0.017 -9999 0 -10000 0 0
GCK -0.14 0.34 -9999 0 -0.88 27 27
HK1 -0.24 0.54 -9999 0 -1.2 43 43
NPM1 -0.24 0.54 -9999 0 -1.2 44 44
EGLN1 -0.24 0.54 -9999 0 -1.2 44 44
CREB1 0.021 0 -9999 0 -10000 0 0
PGM1 -0.25 0.54 -9999 0 -1.2 44 44
SMAD3 0.015 0 -9999 0 -10000 0 0
EDN1 -0.082 0.3 -9999 0 -1.1 14 14
IGFBP1 -0.27 0.54 -9999 0 -1.2 45 45
VEGFA -0.13 0.38 -9999 0 -0.8 34 34
HIF1A/JAB1 -0.022 0.07 -9999 0 -0.5 4 4
CP -0.3 0.57 -9999 0 -1.2 51 51
CXCL12 -0.26 0.56 -9999 0 -1.2 48 48
COPS5 0.013 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 0.022 0.001 -9999 0 -10000 0 0
BNIP3 -0.26 0.55 -9999 0 -1.2 43 43
EGLN3 -0.26 0.56 -9999 0 -1.2 46 46
CA9 -0.31 0.59 -9999 0 -1.3 53 53
TERT -0.29 0.57 -9999 0 -1.2 56 56
ENO1 -0.25 0.54 -9999 0 -1.2 44 44
PFKL -0.24 0.54 -9999 0 -1.2 44 44
NCOA1 0.013 0.002 -9999 0 -10000 0 0
ADM -0.26 0.56 -9999 0 -1.2 49 49
ARNT -0.016 0.081 -9999 0 -10000 0 0
HNF4A -0.19 0.27 -9999 0 -0.53 97 97
ADFP -0.27 0.53 -9999 0 -1.2 47 47
SLC2A1 -0.13 0.4 -9999 0 -0.84 35 35
LEP -0.25 0.54 -9999 0 -1.2 44 44
HIF1A/ARNT/Cbp/p300 -0.2 0.42 -9999 0 -0.92 39 39
EPO -0.12 0.35 -9999 0 -1 14 14
CREBBP -0.014 0.13 -9999 0 -0.29 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.37 -9999 0 -0.92 39 39
PFKFB3 -0.26 0.56 -9999 0 -1.3 44 44
NT5E -0.3 0.59 -9999 0 -1.3 52 52
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.19 0.41 -9999 0 -1.1 42 42
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.052 0.13 -9999 0 -0.4 6 6
ATF2/c-Jun -0.03 0.12 -9999 0 -0.56 4 4
MAPK11 -0.057 0.14 -9999 0 -0.44 9 9
MITF -0.06 0.16 -9999 0 -0.36 47 47
MAPKAPK5 -0.053 0.16 -9999 0 -0.36 43 43
KRT8 -0.058 0.16 -9999 0 -0.37 44 44
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.079 0.2 -9999 0 -0.45 47 47
CEBPB -0.054 0.16 -9999 0 -0.36 43 43
SLC9A1 -0.053 0.16 -9999 0 -0.35 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.051 0.16 -9999 0 -0.5 7 7
p38alpha-beta/MNK1 -0.051 0.16 -9999 0 -0.53 7 7
JUN -0.029 0.12 -9999 0 -0.56 4 4
PPARGC1A -0.13 0.23 -9999 0 -0.48 62 62
USF1 -0.053 0.16 -9999 0 -0.36 43 43
RAB5/GDP/GDI1 -0.04 0.12 -9999 0 -0.4 11 11
NOS2 -0.087 0.25 -9999 0 -0.9 15 15
DDIT3 -0.053 0.16 -9999 0 -0.36 43 43
RAB5A 0.004 0.074 -9999 0 -0.6 4 4
HSPB1 -0.04 0.13 -9999 0 -0.4 9 9
p38alpha-beta/HBP1 -0.051 0.16 -9999 0 -0.36 43 43
CREB1 -0.059 0.18 -9999 0 -0.4 43 43
RAB5/GDP 0.003 0.055 -9999 0 -0.44 4 4
EIF4E -0.042 0.14 -9999 0 -0.45 8 8
RPS6KA4 -0.053 0.16 -9999 0 -0.49 7 7
PLA2G4A -0.1 0.21 -9999 0 -0.5 38 38
GDI1 -0.053 0.16 -9999 0 -0.35 47 47
TP53 -0.079 0.19 -9999 0 -0.44 48 48
RPS6KA5 -0.068 0.19 -9999 0 -0.42 46 46
ESR1 -0.11 0.26 -9999 0 -0.48 68 68
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.058 0.16 -9999 0 -0.36 46 46
MEF2A -0.053 0.16 -9999 0 -0.36 43 43
EIF4EBP1 -0.059 0.18 -9999 0 -0.4 44 44
KRT19 -0.073 0.18 -9999 0 -0.38 50 50
ELK4 -0.053 0.16 -9999 0 -0.35 47 47
ATF6 -0.054 0.16 -9999 0 -0.36 43 43
ATF1 -0.059 0.18 -9999 0 -0.4 43 43
p38alpha-beta/MAPKAPK2 -0.051 0.16 -9999 0 -0.53 7 7
p38alpha-beta/MAPKAPK3 -0.051 0.16 -9999 0 -0.36 43 43
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.1 0.2 -10000 0 -0.56 35 35
FYN -0.094 0.29 -10000 0 -0.7 41 41
LAT/GRAP2/SLP76 -0.11 0.24 -10000 0 -0.59 46 46
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.052 0.2 -10000 0 -0.46 42 42
B2M 0.002 0.08 -10000 0 -0.57 5 5
IKBKG -0.028 0.052 -10000 0 -0.16 19 19
MAP3K8 0 0.09 -10000 0 -0.6 6 6
mol:Ca2+ -0.027 0.039 -10000 0 -0.1 37 37
integrin-mediated signaling pathway 0.012 0.044 -10000 0 -0.34 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.093 0.29 -10000 0 -0.67 45 45
TRPV6 -0.14 0.25 0.22 1 -0.57 67 68
CD28 -0.027 0.15 -10000 0 -0.57 18 18
SHC1 -0.092 0.28 -10000 0 -0.67 43 43
receptor internalization -0.093 0.28 -10000 0 -0.69 40 40
PRF1 -0.11 0.35 -10000 0 -0.97 31 31
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.036 0.16 -10000 0 -0.37 41 41
LAT -0.095 0.29 -10000 0 -0.68 43 43
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D -0.065 0.2 -10000 0 -0.57 36 36
CD3E -0.058 0.19 -10000 0 -0.56 33 33
CD3G -0.007 0.1 -10000 0 -0.5 10 10
RASGRP2 -0.002 0.031 -10000 0 -0.14 6 6
RASGRP1 -0.051 0.2 -10000 0 -0.45 42 42
HLA-A 0.002 0.075 -10000 0 -0.53 5 5
RASSF5 0.005 0.07 -10000 0 -0.56 4 4
RAP1A/GTP/RAPL 0.013 0.044 -10000 0 -0.34 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.06 -10000 0 -0.12 29 29
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.053 0.093 -10000 0 -0.26 36 36
PRKCA -0.05 0.12 -10000 0 -0.29 38 38
GRAP2 -0.048 0.18 -10000 0 -0.55 29 29
mol:IP3 -0.046 0.21 0.22 51 -0.44 41 92
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.082 0.25 -10000 0 -0.61 40 40
ORAI1 0.072 0.15 0.31 67 -0.53 4 71
CSK -0.096 0.29 -10000 0 -0.67 44 44
B7 family/CD28 -0.1 0.3 -10000 0 -0.73 42 42
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.12 0.33 -10000 0 -0.78 44 44
PTPN6 -0.095 0.29 -10000 0 -0.7 41 41
VAV1 -0.1 0.3 -10000 0 -0.68 46 46
Monovalent TCR/CD3 -0.075 0.25 -10000 0 -0.57 44 44
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.1 0.31 -10000 0 -0.73 44 44
PAG1 -0.098 0.29 -10000 0 -0.68 44 44
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.11 0.33 -10000 0 -0.76 44 44
CD80 -0.022 0.14 -10000 0 -0.56 16 16
CD86 -0.011 0.12 -10000 0 -0.57 11 11
PDK1/CARD11/BCL10/MALT1 -0.064 0.11 -10000 0 -0.31 39 39
HRAS 0.013 0 -10000 0 -10000 0 0
GO:0035030 -0.083 0.25 -10000 0 -0.59 42 42
CD8A -0.01 0.11 -10000 0 -0.5 12 12
CD8B -0.071 0.19 -10000 0 -0.5 44 44
PTPRC -0.04 0.16 -10000 0 -0.55 25 25
PDK1/PKC theta -0.074 0.24 -10000 0 -0.57 43 43
CSK/PAG1 -0.091 0.28 -10000 0 -0.68 40 40
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.003 0.081 -10000 0 -0.4 10 10
GRAP2/SLP76 -0.13 0.28 -10000 0 -0.66 51 51
STIM1 0.041 0.073 -10000 0 -0.45 1 1
RAS family/GTP 0.002 0.083 -10000 0 -0.18 28 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.1 0.3 -10000 0 -0.75 40 40
mol:DAG -0.065 0.16 -10000 0 -0.4 42 42
RAP1A/GDP 0.004 0.026 -10000 0 -0.063 2 2
PLCG1 0.011 0.037 -10000 0 -0.6 1 1
CD247 -0.028 0.15 -10000 0 -0.56 19 19
cytotoxic T cell degranulation -0.1 0.32 -10000 0 -0.9 31 31
RAP1A/GTP -0.004 0.009 -10000 0 -0.067 2 2
mol:PI-3-4-5-P3 -0.069 0.23 -10000 0 -0.54 45 45
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.071 0.26 0.24 44 -0.58 42 86
NRAS 0.004 0.074 -10000 0 -0.6 4 4
ZAP70 -0.043 0.17 -10000 0 -0.52 28 28
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.11 0.23 -10000 0 -0.58 44 44
MALT1 0.001 0.076 -10000 0 -0.46 7 7
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.057 0.16 -10000 0 -0.37 52 52
CARD11 -0.046 0.17 -10000 0 -0.5 31 31
PRKCB -0.057 0.13 -10000 0 -0.31 42 42
PRKCE -0.045 0.11 -10000 0 -0.28 36 36
PRKCQ -0.096 0.28 -10000 0 -0.64 46 46
LCP2 -0.004 0.098 -10000 0 -0.56 8 8
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.04 0.17 -10000 0 -0.38 42 42
IKK complex 0.009 0.061 -10000 0 -0.12 20 20
RAS family/GDP -0.006 0.013 -10000 0 -0.08 4 4
MAP3K14 -0.02 0.12 -10000 0 -0.29 35 35
PDPK1 -0.046 0.18 -10000 0 -0.43 42 42
TCR/CD3/MHC I/CD8/Fyn -0.12 0.34 -10000 0 -0.8 45 45
Noncanonical Wnt signaling pathway

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
NFATC2 -0.034 0.16 -9999 0 -0.56 22 22
GNB1/GNG2 -0.13 0.23 -9999 0 -0.59 34 34
mol:DAG -0.11 0.2 -9999 0 -0.54 31 31
PLCG1 -0.12 0.21 -9999 0 -0.56 31 31
YES1 -0.13 0.23 -9999 0 -0.6 32 32
FZD3 0.006 0.064 -9999 0 -0.6 3 3
FZD6 0.009 0.053 -9999 0 -0.6 2 2
G protein -0.12 0.21 -9999 0 -0.57 31 31
MAP3K7 -0.087 0.16 -9999 0 -0.46 26 26
mol:Ca2+ -0.11 0.19 -9999 0 -0.52 31 31
mol:IP3 -0.11 0.2 -9999 0 -0.54 31 31
NLK -0.008 0.061 -9999 0 -1 1 1
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.1 0.18 -9999 0 -0.49 29 29
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.24 -9999 0 -0.65 31 31
CSNK1A1 0.011 0.037 -9999 0 -0.6 1 1
GNAS -0.13 0.23 -9999 0 -0.61 31 31
GO:0007205 -0.11 0.2 -9999 0 -0.53 31 31
WNT6 -0.12 0.22 -9999 0 -0.48 73 73
WNT4 -0.068 0.2 -9999 0 -0.53 40 40
NFAT1/CK1 alpha -0.12 0.22 -9999 0 -0.55 38 38
GNG2 -0.007 0.1 -9999 0 -0.51 10 10
WNT5A -0.019 0.13 -9999 0 -0.56 15 15
WNT11 -0.15 0.25 -9999 0 -0.53 79 79
CDC42 -0.12 0.22 -9999 0 -0.56 33 33
p75(NTR)-mediated 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
Sortilin/TRAF6 0.018 0.028 -9999 0 -0.43 1 1
Necdin/E2F1 -0.015 0.11 -9999 0 -0.36 24 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.055 0.16 -9999 0 -0.51 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.17 0.24 -9999 0 -0.46 83 83
NT-4/5 (dimer)/p75(NTR) -0.13 0.22 -9999 0 -0.4 95 95
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.072 0.16 -9999 0 -0.36 51 51
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.09 0.21 -9999 0 -0.49 54 54
MGDIs/NGR/p75(NTR)/LINGO1 -0.086 0.19 -9999 0 -0.46 41 41
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.1 0.19 -9999 0 -0.43 47 47
LINGO1 -0.044 0.16 -9999 0 -0.49 30 30
Sortilin/TRAF6/NRIF -0.005 0.035 -9999 0 -10000 0 0
proBDNF (dimer) -0.089 0.21 -9999 0 -0.49 54 54
NTRK1 -0.038 0.16 -9999 0 -0.5 26 26
RTN4R -0.01 0.11 -9999 0 -0.5 12 12
neuron apoptosis -0.081 0.17 -9999 0 -0.55 14 14
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.075 0.17 -9999 0 -0.4 41 41
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0.01 0 -9999 0 -10000 0 0
Gamma Secretase 0.034 0.043 -9999 0 -0.3 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.073 0.17 -9999 0 -0.38 48 48
MAGEH1 -0.009 0.11 -9999 0 -0.52 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.19 -9999 0 -0.41 50 50
Mammalian IAPs/DIABLO -0.007 0.12 -9999 0 -0.35 22 22
proNGF (dimer) -0.045 0.17 -9999 0 -0.56 27 27
MAGED1 0.002 0.083 -9999 0 -0.6 5 5
APP 0.009 0.053 -9999 0 -0.6 2 2
NT-4/5 (dimer) -0.095 0.22 -9999 0 -0.53 52 52
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.056 0.15 -9999 0 -0.34 41 41
NGF -0.045 0.17 -9999 0 -0.56 27 27
cell cycle arrest -0.048 0.16 -9999 0 -0.5 7 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.035 0.12 -9999 0 -0.52 4 4
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.1 0.19 -9999 0 -0.42 52 52
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.079 0.17 -9999 0 -0.4 44 44
PSENEN 0.011 0.037 -9999 0 -0.6 1 1
mol:ceramide -0.064 0.16 -9999 0 -0.36 43 43
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.022 0.11 -9999 0 -0.4 6 6
p75(NTR)/beta APP -0.06 0.16 -9999 0 -0.36 56 56
BEX1 -0.15 0.25 -9999 0 -0.52 82 82
mol:GDP -0.084 0.17 -9999 0 -0.34 76 76
NGF (dimer) -0.19 0.22 -9999 0 -0.42 103 103
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.07 0.18 -9999 0 -0.41 41 41
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
RAC1/GTP -0.064 0.15 -9999 0 -0.35 41 41
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.079 0.18 -9999 0 -0.4 44 44
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.009 0.061 -9999 0 -0.33 8 8
NT3 (dimer) -0.064 0.18 -9999 0 -0.5 40 40
TP53 -0.074 0.16 -9999 0 -0.45 16 16
PRDM4 -0.063 0.16 -9999 0 -0.36 42 42
BDNF (dimer) -0.31 0.26 -9999 0 -0.51 143 143
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
SORT1 0.011 0.037 -9999 0 -0.6 1 1
activation of caspase activity -0.057 0.16 -9999 0 -0.5 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.061 0.16 -9999 0 -0.36 42 42
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 -0.087 0.19 -9999 0 -0.51 26 26
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.064 0.16 -9999 0 -0.36 43 43
APH1B 0.006 0.064 -9999 0 -0.6 3 3
APH1A 0.012 0.027 -9999 0 -0.43 1 1
proNGF (dimer)/p75(NTR)/Sortilin -0.076 0.17 -9999 0 -0.4 42 42
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.11 0.21 -9999 0 -0.41 80 80
MAPK8 -0.065 0.17 -9999 0 -0.52 14 14
MAPK9 -0.061 0.16 -9999 0 -0.51 13 13
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.064 0.18 -9999 0 -0.5 40 40
NTF4 -0.096 0.22 -9999 0 -0.53 52 52
NDN -0.02 0.13 -9999 0 -0.54 16 16
RAC1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.073 0.12 -9999 0 -0.5 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.03 0.038 -9999 0 -0.32 3 3
RhoA-B-C/GTP -0.079 0.17 -9999 0 -0.4 44 44
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.072 0.16 -9999 0 -0.48 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.084 0.17 -9999 0 -0.39 47 47
PRKACB 0.006 0.064 -9999 0 -0.6 3 3
proBDNF (dimer)/p75 ECD -0.058 0.16 -9999 0 -0.36 55 55
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.052 0.18 -9999 0 -0.54 31 31
BIRC2 0.006 0.064 -9999 0 -0.6 3 3
neuron projection morphogenesis -0.055 0.18 -9999 0 -0.4 38 38
BAD -0.067 0.17 -9999 0 -0.48 19 19
RIPK2 0.009 0.046 -9999 0 -0.51 2 2
NGFR -0.093 0.21 -9999 0 -0.5 55 55
CYCS -0.061 0.16 -9999 0 -0.54 9 9
ADAM17 0.009 0.053 -9999 0 -0.6 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.062 0.16 -9999 0 -0.36 42 42
BCL2L11 -0.067 0.17 -9999 0 -0.48 19 19
BDNF (dimer)/p75(NTR) -0.13 0.22 -9999 0 -0.4 93 93
PI3K -0.081 0.18 -9999 0 -0.38 51 51
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.061 0.16 -9999 0 -0.36 42 42
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.002 0.075 -9999 0 -0.49 6 6
NGF (dimer)/p75(NTR) -0.099 0.2 -9999 0 -0.39 76 76
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.067 0.16 -9999 0 -0.36 46 46
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.11 0.22 -9999 0 -0.48 65 65
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.1 0.19 -9999 0 -0.47 34 34
SQSTM1 0.012 0.027 -9999 0 -0.43 1 1
NGFRAP1 0.004 0.074 -9999 0 -0.6 4 4
CASP3 -0.06 0.16 -9999 0 -0.44 19 19
E2F1 -0.001 0.084 -9999 0 -0.47 8 8
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.069 0.12 -9999 0 -0.49 11 11
NGF (dimer)/TRKA -0.06 0.17 -9999 0 -0.4 50 50
MMP7 -0.21 0.28 -9999 0 -0.55 105 105
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.05 0.15 -9999 0 -0.54 6 6
MMP3 -0.17 0.26 -9999 0 -0.52 89 89
APAF-1/Caspase 9 -0.086 0.14 -9999 0 -0.45 20 20
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.1 -10000 0 -0.42 11 11
fibroblast growth factor receptor signaling pathway -0.003 0.1 -10000 0 -0.41 11 11
LAMA1 -0.08 0.21 -10000 0 -0.54 45 45
PRNP -0.015 0.13 -10000 0 -0.57 13 13
GPC1/SLIT2 -0.069 0.17 -10000 0 -0.38 59 59
SMAD2 0.018 0.064 -10000 0 -0.32 8 8
GPC1/PrPc/Cu2+ -0.006 0.094 -10000 0 -0.36 17 17
GPC1/Laminin alpha1 -0.056 0.16 -10000 0 -0.39 49 49
TDGF1 -0.12 0.24 -10000 0 -0.54 65 65
CRIPTO/GPC1 -0.087 0.19 -10000 0 -0.4 68 68
APP/GPC1 0.009 0.067 -10000 0 -0.39 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.067 0.16 -10000 0 -0.38 46 46
FLT1 0.009 0.046 -10000 0 -0.51 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.013 0.07 -10000 0 -0.36 8 8
SERPINC1 0.006 0.047 -10000 0 -0.43 3 3
FYN -0.066 0.16 -10000 0 -0.38 45 45
FGR -0.075 0.17 -10000 0 -0.39 49 49
positive regulation of MAPKKK cascade -0.096 0.2 -10000 0 -0.46 52 52
SLIT2 -0.098 0.22 -10000 0 -0.52 56 56
GPC1/NRG -0.028 0.13 -10000 0 -0.38 31 31
NRG1 -0.042 0.16 -10000 0 -0.52 27 27
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.014 0.063 -10000 0 -0.36 4 4
LYN -0.067 0.16 -10000 0 -0.38 46 46
mol:Spermine 0.003 0.055 -10000 0 -0.39 5 5
cell growth -0.003 0.1 -10000 0 -0.41 11 11
BMP signaling pathway -0.003 0.075 0.53 5 -10000 0 5
SRC -0.067 0.16 -10000 0 -0.38 46 46
TGFBR1 0.013 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.076 0.19 -10000 0 -0.49 46 46
GPC1 0.003 0.075 -10000 0 -0.53 5 5
TGFBR1 (dimer) 0.013 0 -10000 0 -10000 0 0
VEGFA 0.007 0.054 -10000 0 -0.43 4 4
BLK -0.13 0.2 -10000 0 -0.42 67 67
HCK -0.076 0.17 -10000 0 -0.38 50 50
FGF2 -0.012 0.11 -10000 0 -0.47 14 14
FGFR1 0.001 0.083 -10000 0 -0.54 6 6
VEGFR1 homodimer 0.009 0.046 -10000 0 -0.51 2 2
TGFBR2 0.002 0.083 -10000 0 -0.6 5 5
cell death 0.009 0.067 -10000 0 -0.39 7 7
ATIII/GPC1 0.007 0.064 -10000 0 -0.35 8 8
PLA2G2A/GPC1 -0.052 0.15 -10000 0 -0.35 50 50
LCK -0.085 0.19 -10000 0 -0.42 51 51
neuron differentiation -0.028 0.13 -10000 0 -0.38 31 31
PrPc/Cu2+ -0.011 0.093 -10000 0 -0.42 13 13
APP 0.009 0.053 -10000 0 -0.6 2 2
TGFBR2 (dimer) 0.002 0.083 -10000 0 -0.6 5 5
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.028 0.053 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.11 0.14 -9999 0 -0.42 26 26
JUN -0.066 0.15 -9999 0 -0.44 22 22
HRAS 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.13 0.21 -9999 0 -0.43 67 67
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.2 -9999 0 -0.42 64 64
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0.037 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.053 0.14 -9999 0 -0.36 32 32
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.12 0.17 -9999 0 -0.38 64 64
GRB7 -0.015 0.11 -9999 0 -0.45 16 16
RET51/GFRalpha1/GDNF -0.12 0.2 -9999 0 -0.42 63 63
MAPKKK cascade -0.11 0.15 -9999 0 -0.49 18 18
BCAR1 0.011 0.037 -9999 0 -0.6 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.068 0.16 -9999 0 -0.39 41 41
lamellipodium assembly -0.1 0.13 -9999 0 -0.36 35 35
RET51/GFRalpha1/GDNF/SHC -0.12 0.2 -9999 0 -0.42 63 63
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
RET9/GFRalpha1/GDNF/SHC -0.052 0.14 -9999 0 -0.36 32 32
RET9/GFRalpha1/GDNF/Shank3 -0.052 0.14 -9999 0 -0.36 32 32
MAPK3 -0.095 0.17 -9999 0 -0.45 30 30
DOK1 0.011 0.037 -9999 0 -0.6 1 1
DOK6 -0.064 0.18 -9999 0 -0.5 40 40
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.095 0.18 -9999 0 -0.44 32 32
DOK5 -0.083 0.2 -9999 0 -0.5 50 50
GFRA1 -0.099 0.22 -9999 0 -0.52 56 56
MAPK8 -0.073 0.15 -9999 0 -0.45 20 20
HRAS/GTP -0.12 0.17 -9999 0 -0.48 31 31
tube development -0.043 0.13 -9999 0 -0.34 32 32
MAPK1 -0.095 0.17 -9999 0 -0.45 30 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.028 0.1 -9999 0 -0.27 33 33
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC 0.011 0.037 -9999 0 -0.6 1 1
PDLIM7 0.012 0.027 -9999 0 -0.43 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.22 -9999 0 -0.53 49 49
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.12 0.2 -9999 0 -0.42 64 64
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.24 -9999 0 -0.48 79 79
PRKCA -0.004 0.1 -9999 0 -0.58 8 8
HRAS/GDP 0.01 0 -9999 0 -10000 0 0
CREB1 -0.053 0.14 -9999 0 -0.37 31 31
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.027 0.1 -9999 0 -0.27 32 32
RET51/GFRalpha1/GDNF/Grb7 -0.14 0.21 -9999 0 -0.42 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.13 0.23 -9999 0 -0.49 76 76
DOK4 0.011 0.037 -9999 0 -0.6 1 1
JNK cascade -0.064 0.15 -9999 0 -0.43 22 22
RET9/GFRalpha1/GDNF/FRS2 -0.052 0.14 -9999 0 -0.36 32 32
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.6 1 1
NCK1 0.011 0.037 -9999 0 -0.6 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.027 0.1 -9999 0 -0.28 32 32
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.077 0.15 -9999 0 -0.46 16 16
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.079 0.16 -9999 0 -0.48 18 18
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.08 0.16 -9999 0 -0.54 16 16
PI3K -0.12 0.22 -9999 0 -0.53 43 43
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.042 0.13 -9999 0 -0.34 32 32
GRB10 -0.003 0.098 -9999 0 -0.6 7 7
activation of MAPKK activity -0.062 0.13 -9999 0 -0.4 16 16
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.2 -9999 0 -0.42 63 63
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.015 0.13 -9999 0 -0.57 13 13
IRS2 -0.042 0.16 -9999 0 -0.49 29 29
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.08 0.16 -9999 0 -0.54 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.13 0.21 -9999 0 -0.43 68 68
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.012 0.088 -9999 0 -0.43 11 11
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.14 0.22 -9999 0 -0.44 70 70
Rac1/GTP -0.12 0.15 -9999 0 -0.44 34 34
RET9/GFRalpha1/GDNF -0.067 0.15 -9999 0 -0.33 62 62
GFRalpha1/GDNF -0.079 0.18 -9999 0 -0.39 62 62
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.006 0.1 -10000 0 -0.54 9 9
EPHB2 -0.077 0.21 -10000 0 -0.54 44 44
EFNB1 0.002 0.082 -10000 0 -0.34 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.076 0.18 -10000 0 -0.47 24 24
Ephrin B2/EPHB1-2 -0.094 0.19 -10000 0 -0.41 56 56
neuron projection morphogenesis -0.099 0.15 -10000 0 -0.45 24 24
Ephrin B1/EPHB1-2/Tiam1 -0.087 0.19 -10000 0 -0.41 47 47
DNM1 -0.006 0.092 -10000 0 -0.45 11 11
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.049 0.2 -10000 0 -0.66 25 25
YES1 -0.083 0.26 -10000 0 -0.9 24 24
Ephrin B1/EPHB1-2/NCK2 -0.079 0.18 -10000 0 -0.49 19 19
PI3K -0.067 0.21 -10000 0 -0.57 35 35
mol:GDP -0.087 0.18 -10000 0 -0.4 47 47
ITGA2B -0.052 0.18 -10000 0 -0.53 32 32
endothelial cell proliferation 0.003 0.072 -10000 0 -0.34 11 11
FYN -0.082 0.26 -10000 0 -0.9 24 24
MAP3K7 -0.058 0.21 -10000 0 -0.71 24 24
FGR -0.086 0.26 -10000 0 -0.91 24 24
TIAM1 -0.003 0.095 -10000 0 -0.54 8 8
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.25 -10000 0 -0.67 34 34
LYN -0.083 0.26 -10000 0 -0.9 24 24
Ephrin B1/EPHB1-2/Src Family Kinases -0.08 0.24 -10000 0 -0.85 24 24
Ephrin B1/EPHB1-2 -0.076 0.22 -10000 0 -0.77 24 24
SRC -0.083 0.26 -10000 0 -0.9 24 24
ITGB3 -0.065 0.19 -10000 0 -0.5 41 41
EPHB1 -0.094 0.21 -10000 0 -0.5 55 55
EPHB4 0.009 0.053 -10000 0 -0.6 2 2
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.003 0.072 -10000 0 -0.34 11 11
alphaIIb/beta3 Integrin -0.085 0.18 -10000 0 -0.37 71 71
BLK -0.1 0.27 -10000 0 -0.93 24 24
HCK -0.085 0.26 -10000 0 -0.9 24 24
regulation of stress fiber formation 0.078 0.17 0.49 19 -10000 0 19
MAPK8 -0.045 0.19 -10000 0 -0.62 25 25
Ephrin B1/EPHB1-2/RGS3 -0.079 0.18 -10000 0 -0.39 42 42
endothelial cell migration -0.055 0.19 -10000 0 -0.56 31 31
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 -0.059 0.22 -10000 0 -0.66 29 29
regulation of focal adhesion formation 0.078 0.17 0.49 19 -10000 0 19
chemotaxis 0.078 0.17 0.38 42 -10000 0 42
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
Rac1/GTP -0.099 0.16 -10000 0 -0.46 24 24
angiogenesis -0.076 0.22 -10000 0 -0.76 24 24
LCK -0.091 0.26 -10000 0 -0.87 25 25
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.19 -9999 0 -0.49 32 32
SMAD6-7/SMURF1 0.024 0.041 -9999 0 -0.59 1 1
NOG -0.099 0.22 -9999 0 -0.53 55 55
SMAD9 -0.079 0.2 -9999 0 -0.61 26 26
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.051 0.15 -9999 0 -0.47 19 19
BMP7/USAG1 -0.18 0.23 -9999 0 -0.42 121 121
SMAD5/SKI -0.042 0.14 -9999 0 -0.47 16 16
SMAD1 0.03 0.058 -9999 0 -0.53 2 2
BMP2 -0.095 0.21 -9999 0 -0.5 56 56
SMAD1/SMAD1/SMAD4 -0.005 0.047 -9999 0 -0.42 3 3
BMPR1A 0.009 0.053 -9999 0 -0.6 2 2
BMPR1B -0.057 0.19 -9999 0 -0.58 31 31
BMPR1A-1B/BAMBI -0.089 0.2 -9999 0 -0.43 53 53
AHSG -0.004 0.076 -9999 0 -0.43 8 8
CER1 -0.002 0.054 -9999 0 -0.43 4 4
BMP2-4/CER1 -0.11 0.19 -9999 0 -0.46 37 37
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.075 0.17 -9999 0 -0.53 18 18
BMP2-4 (homodimer) -0.13 0.21 -9999 0 -0.38 98 98
RGMB 0.012 0.027 -9999 0 -0.43 1 1
BMP6/BMPR2/BMPR1A-1B -0.014 0.13 -9999 0 -0.36 30 30
RGMA -0.062 0.2 -9999 0 -0.57 34 34
SMURF1 0.012 0.027 -9999 0 -0.43 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.082 0.18 -9999 0 -0.44 35 35
BMP2-4/USAG1 -0.21 0.23 -9999 0 -0.47 88 88
SMAD6/SMURF1/SMAD5 -0.043 0.14 -9999 0 -0.48 16 16
SOSTDC1 -0.16 0.26 -9999 0 -0.54 85 85
BMP7/BMPR2/BMPR1A-1B -0.067 0.16 -9999 0 -0.39 37 37
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.005 0.061 -9999 0 -0.43 5 5
HFE2 0.002 0.038 -9999 0 -0.43 2 2
ZFYVE16 0.011 0.037 -9999 0 -0.6 1 1
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.14 0.21 -9999 0 -0.46 54 54
SMAD5/SMAD5/SMAD4 -0.042 0.14 -9999 0 -0.47 16 16
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.083 0.14 -9999 0 -0.47 20 20
BMP7 (homodimer) -0.092 0.2 -9999 0 -0.45 60 60
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA 0.002 0.068 -9999 0 -0.3 13 13
SMAD1/SKI 0.036 0.055 -9999 0 -0.5 2 2
SMAD6 0.009 0.046 -9999 0 -0.51 2 2
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.11 0.19 -9999 0 -0.47 40 40
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.095 0.22 -9999 0 -0.53 53 53
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.024 0.033 -9999 0 -0.36 1 1
BMPR1A-1B (homodimer) -0.035 0.15 -9999 0 -0.44 32 32
CHRDL1 -0.13 0.24 -9999 0 -0.52 69 69
ENDOFIN/SMAD1 0.035 0.058 -9999 0 -0.5 2 2
SMAD6-7/SMURF1/SMAD1 0.043 0.062 -9999 0 -0.47 3 3
SMAD6/SMURF1 0.012 0.027 -9999 0 -0.43 1 1
BAMBI -0.099 0.22 -9999 0 -0.52 56 56
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.18 0.23 -9999 0 -0.49 70 70
BMP2-4/GREM1 -0.16 0.23 -9999 0 -0.49 64 64
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.067 0.19 -9999 0 -0.6 24 24
SMAD1/SMAD6 0.035 0.058 -9999 0 -0.5 2 2
TAK1/SMAD6 0.019 0.019 -9999 0 -0.3 1 1
BMP7 -0.092 0.2 -9999 0 -0.46 60 60
BMP6 0.005 0.061 -9999 0 -0.43 5 5
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.071 0.16 -9999 0 -0.46 24 24
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.036 0.055 -9999 0 -0.5 2 2
SMAD7/SMURF1 0.019 0.019 -9999 0 -0.3 1 1
CTDSPL 0.011 0.037 -9999 0 -0.6 1 1
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.01 0.039 -9999 0 -0.43 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.14 0.21 -9999 0 -0.48 52 52
CHRD -0.044 0.17 -9999 0 -0.55 27 27
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.095 0.19 -9999 0 -0.48 35 35
BMP4 -0.088 0.2 -9999 0 -0.46 57 57
FST -0.12 0.23 -9999 0 -0.5 68 68
BMP2-4/NOG -0.17 0.22 -9999 0 -0.47 71 71
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.057 0.16 -9999 0 -0.53 11 11
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.098 0.18 -10000 0 -0.37 80 80
cell-cell adhesion 0.13 0.17 0.52 28 -10000 0 28
Ephrin B/EPHB2/RasGAP -0.083 0.19 -10000 0 -0.58 19 19
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.043 0.13 -10000 0 -0.31 49 49
Ephrin B1/EPHB1 -0.052 0.13 -10000 0 -0.3 59 59
HRAS/GDP -0.1 0.15 -10000 0 -0.46 25 25
Ephrin B/EPHB1/GRB7 -0.1 0.2 -10000 0 -0.5 30 30
Endophilin/SYNJ1 -0.081 0.18 -10000 0 -0.51 20 20
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.091 0.19 -10000 0 -0.51 25 25
endothelial cell migration -0.005 0.096 -10000 0 -0.31 20 20
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.015 0.11 -10000 0 -0.45 16 16
PAK1 -0.078 0.19 -10000 0 -0.56 20 20
HRAS 0.013 0 -10000 0 -10000 0 0
RRAS -0.08 0.18 -10000 0 -0.36 64 64
DNM1 -0.006 0.092 -10000 0 -0.45 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.087 0.18 -10000 0 -0.5 22 22
lamellipodium assembly -0.13 0.17 -10000 0 -0.52 28 28
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.057 0.15 -10000 0 -0.47 15 15
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
EPHB2 -0.077 0.2 -10000 0 -0.53 44 44
EPHB3 -0.078 0.2 -10000 0 -0.51 46 46
EPHB1 -0.093 0.21 -10000 0 -0.5 55 55
EPHB4 0.009 0.053 -10000 0 -0.6 2 2
mol:GDP -0.07 0.18 -10000 0 -0.45 27 27
Ephrin B/EPHB2 -0.089 0.19 -10000 0 -0.38 64 64
Ephrin B/EPHB3 -0.089 0.2 -10000 0 -0.4 60 60
JNK cascade -0.072 0.16 -10000 0 -0.49 16 16
Ephrin B/EPHB1 -0.097 0.19 -10000 0 -0.38 66 66
RAP1/GDP -0.051 0.16 -10000 0 -0.43 18 18
EFNB2 -0.006 0.1 -10000 0 -0.54 9 9
EFNB3 -0.096 0.23 -10000 0 -0.55 51 51
EFNB1 0.006 0.06 -10000 0 -0.47 4 4
Ephrin B2/EPHB1-2 -0.095 0.19 -10000 0 -0.41 56 56
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.19 -10000 0 -0.58 28 28
Rap1/GTP -0.13 0.17 -10000 0 -0.53 27 27
axon guidance -0.098 0.18 -10000 0 -0.37 80 80
MAPK3 -0.04 0.14 -10000 0 -0.47 10 10
MAPK1 -0.039 0.14 -10000 0 -0.47 10 10
Rac1/GDP -0.058 0.17 -10000 0 -0.44 21 21
actin cytoskeleton reorganization -0.1 0.14 -10000 0 -0.42 26 26
CDC42/GDP -0.059 0.17 -10000 0 -0.44 21 21
PI3K -0.003 0.098 -10000 0 -0.31 20 20
EFNA5 -0.083 0.22 -10000 0 -0.57 44 44
Ephrin B2/EPHB4 0.003 0.072 -10000 0 -0.34 11 11
Ephrin B/EPHB2/Intersectin/N-WASP -0.063 0.16 -10000 0 -0.55 14 14
CDC42 0.011 0.037 -10000 0 -0.6 1 1
RAS family/GTP -0.13 0.17 -10000 0 -0.52 28 28
PTK2 0.025 0.037 -10000 0 -10000 0 0
MAP4K4 -0.072 0.17 -10000 0 -0.49 16 16
SRC 0.011 0.037 -10000 0 -0.6 1 1
KALRN 0.006 0.064 -10000 0 -0.6 3 3
Intersectin/N-WASP 0.02 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.07 0.18 -10000 0 -0.45 26 26
MAP2K1 -0.047 0.14 -10000 0 -0.44 15 15
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.082 0.18 -10000 0 -0.38 54 54
cell migration -0.048 0.16 -10000 0 -0.48 15 15
NRAS 0.004 0.074 -10000 0 -0.6 4 4
SYNJ1 -0.082 0.18 -10000 0 -0.52 20 20
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.11 0.19 -10000 0 -0.52 28 28
HRAS/GTP -0.14 0.19 -10000 0 -0.5 38 38
Ephrin B1/EPHB1-2 -0.089 0.18 -10000 0 -0.39 53 53
cell adhesion mediated by integrin 0.076 0.16 0.38 43 -10000 0 43
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.22 -10000 0 -0.54 38 38
RAC1-CDC42/GTP -0.16 0.2 -10000 0 -0.53 42 42
RASA1 0.011 0.037 -10000 0 -0.6 1 1
RAC1-CDC42/GDP -0.052 0.16 -10000 0 -0.45 15 15
ruffle organization -0.097 0.2 -10000 0 -0.53 28 28
NCK1 0.011 0.037 -10000 0 -0.6 1 1
receptor internalization -0.081 0.18 -10000 0 -0.51 24 24
Ephrin B/EPHB2/KALRN -0.085 0.2 -10000 0 -0.39 64 64
ROCK1 -0.034 0.12 -10000 0 -0.34 25 25
RAS family/GDP -0.099 0.14 -10000 0 -0.42 26 26
Rac1/GTP -0.14 0.19 -10000 0 -0.56 28 28
Ephrin B/EPHB1/Src/Paxillin -0.067 0.16 -10000 0 -0.51 15 15
IL12-mediated signaling events

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.031 0.14 -10000 0 -0.42 15 15
TBX21 -0.19 0.5 -10000 0 -1.2 43 43
B2M 0.001 0.08 -10000 0 -0.57 5 5
TYK2 0.012 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.062 -10000 0 -0.53 3 3
GADD45B -0.12 0.39 -10000 0 -0.98 33 33
IL12RB2 -0.033 0.15 -10000 0 -0.49 25 25
GADD45G -0.13 0.41 -10000 0 -0.98 36 36
natural killer cell activation -0.001 0.025 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.014 0.13 -10000 0 -0.58 13 13
IL2RA -0.028 0.15 -10000 0 -0.56 19 19
IFNG -0.041 0.15 -10000 0 -0.47 28 28
STAT3 (dimer) -0.12 0.37 -10000 0 -0.82 44 44
HLA-DRB5 -0.11 0.23 -10000 0 -0.52 61 61
FASLG -0.22 0.54 -10000 0 -1.2 50 50
NF kappa B2 p52/RelB -0.23 0.39 -10000 0 -1 43 43
CD4 -0.001 0.09 -10000 0 -0.6 6 6
SOCS1 0.009 0.046 -10000 0 -0.51 2 2
EntrezGene:6955 -0.002 0.012 -10000 0 -10000 0 0
CD3D -0.066 0.2 -10000 0 -0.57 36 36
CD3E -0.059 0.19 -10000 0 -0.56 33 33
CD3G -0.008 0.1 -10000 0 -0.51 10 10
IL12Rbeta2/JAK2 -0.027 0.14 -10000 0 -0.39 33 33
CCL3 -0.17 0.47 -10000 0 -1.1 44 44
CCL4 -0.18 0.5 -10000 0 -1.2 41 41
HLA-A 0.002 0.076 -10000 0 -0.54 5 5
IL18/IL18R -0.024 0.2 -10000 0 -0.47 36 36
NOS2 -0.17 0.47 -10000 0 -1.1 40 40
IL12/IL12R/TYK2/JAK2/SPHK2 -0.03 0.14 -10000 0 -0.42 13 13
IL1R1 -0.18 0.48 -10000 0 -1.1 45 45
IL4 0.005 0.038 -10000 0 -0.45 1 1
JAK2 -0.009 0.12 -10000 0 -0.62 9 9
EntrezGene:6957 -0.002 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.35 -10000 0 -0.81 44 44
RAB7A -0.087 0.33 -10000 0 -0.8 29 29
lysosomal transport -0.08 0.32 -10000 0 -0.75 29 29
FOS -0.14 0.38 -10000 0 -0.97 35 35
STAT4 (dimer) -0.13 0.41 -10000 0 -0.92 41 41
STAT5A (dimer) -0.25 0.4 -10000 0 -1 46 46
GZMA -0.21 0.55 -10000 0 -1.3 46 46
GZMB -0.24 0.55 -10000 0 -1.2 56 56
HLX 0.013 0 -10000 0 -10000 0 0
LCK -0.19 0.51 -10000 0 -1.2 45 45
TCR/CD3/MHC II/CD4 -0.12 0.32 -10000 0 -0.71 44 44
IL2/IL2R -0.049 0.19 -10000 0 -0.46 38 38
MAPK14 -0.13 0.41 -10000 0 -0.96 38 38
CCR5 -0.15 0.44 -10000 0 -1.2 33 33
IL1B -0.024 0.15 -10000 0 -0.58 17 17
STAT6 -0.025 0.14 -10000 0 -0.84 2 2
STAT4 0.001 0.083 -10000 0 -0.54 6 6
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.06 -10000 0 -0.47 4 4
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0.001 0.059 -10000 0 -0.43 4 4
CD8A -0.011 0.11 -10000 0 -0.49 12 12
CD8B -0.072 0.19 -10000 0 -0.5 44 44
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.031 0.14 0.42 15 -10000 0 15
IL2RB -0.036 0.16 -10000 0 -0.56 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.37 -10000 0 -0.82 41 41
IL2RG -0.021 0.14 -10000 0 -0.56 16 16
IL12 -0.039 0.14 -10000 0 -0.39 28 28
STAT5A 0.012 0.027 -10000 0 -0.43 1 1
CD247 -0.029 0.15 -10000 0 -0.56 19 19
IL2 -0.01 0.08 -10000 0 -0.43 9 9
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.06 0.18 -10000 0 -0.5 37 37
IL12/IL12R/TYK2/JAK2 -0.21 0.58 -10000 0 -1.3 43 43
MAP2K3 -0.13 0.41 -10000 0 -0.94 39 39
RIPK2 0.009 0.046 -10000 0 -0.51 2 2
MAP2K6 -0.14 0.43 -10000 0 -0.98 42 42
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.031 0.16 -10000 0 -0.57 20 20
IL18RAP -0.032 0.16 -10000 0 -0.56 22 22
IL12Rbeta1/TYK2 0.014 0.055 -10000 0 -0.4 3 3
EOMES -0.082 0.31 -10000 0 -1.3 14 14
STAT1 (dimer) -0.13 0.37 -10000 0 -0.84 42 42
T cell proliferation -0.08 0.3 -10000 0 -0.68 36 36
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.026 0.15 -10000 0 -0.59 18 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.18 0.28 -10000 0 -0.74 40 40
ATF2 -0.11 0.38 -10000 0 -0.87 38 38
Glucocorticoid receptor regulatory network

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
PCK2 0.033 0.081 0.34 1 -10000 0 1
SMARCC2 0.014 0.01 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.7 34 34
SUMO2 0.016 0.015 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.067 -10000 0 -0.51 4 4
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 -0.017 0.12 -10000 0 -0.49 16 16
GR alpha/HSP90/FKBP51/HSP90 0.084 0.13 0.32 14 -0.39 6 20
PRL -0.083 0.15 -10000 0 -0.56 5 5
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.55 64 -0.42 6 70
RELA -0.025 0.08 -10000 0 -0.27 3 3
FGG 0.17 0.19 0.47 38 -0.45 3 41
GR beta/TIF2 0.08 0.16 0.32 23 -0.4 15 38
IFNG -0.3 0.32 -10000 0 -0.81 51 51
apoptosis 0.037 0.25 0.54 24 -0.66 11 35
CREB1 0.006 0.041 -10000 0 -10000 0 0
histone acetylation -0.021 0.14 0.33 6 -0.34 18 24
BGLAP -0.066 0.12 -10000 0 -0.54 2 2
GR/PKAc 0.096 0.11 0.29 18 -0.36 3 21
NF kappa B1 p50/RelA -0.041 0.15 -10000 0 -0.43 13 13
SMARCD1 0.013 0.01 -10000 0 -10000 0 0
MDM2 0.093 0.091 0.26 27 -0.28 2 29
GATA3 -0.037 0.15 -10000 0 -0.48 27 27
AKT1 0.005 0.003 -10000 0 -10000 0 0
CSF2 -0.057 0.13 -10000 0 -0.54 4 4
GSK3B 0.016 0.015 -10000 0 -10000 0 0
NR1I3 0.023 0.32 0.56 17 -0.9 19 36
CSN2 0.16 0.15 0.36 58 -0.39 2 60
BRG1/BAF155/BAF170/BAF60A 0.034 0.045 -10000 0 -0.32 2 2
NFATC1 0.003 0.087 -10000 0 -0.56 6 6
POU2F1 0.011 0.029 -10000 0 -10000 0 0
CDKN1A -0.073 0.36 -10000 0 -1.5 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.016 -10000 0 -10000 0 0
SFN -0.054 0.18 -10000 0 -0.53 33 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.17 0.31 10 -0.42 10 20
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.041 0.26 0.53 18 -0.82 10 28
JUN -0.2 0.21 -10000 0 -0.52 46 46
IL4 -0.086 0.14 -10000 0 -0.54 5 5
CDK5R1 0.005 0.071 -10000 0 -0.5 5 5
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.16 0.23 0.22 13 -0.51 59 72
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.09 0.12 0.31 13 -0.38 4 17
cortisol/GR alpha (monomer) 0.27 0.28 0.64 70 -0.5 2 72
NCOA2 -0.023 0.14 -10000 0 -0.56 17 17
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.092 0.15 -10000 0 -0.54 22 22
AP-1/NFAT1-c-4 -0.35 0.34 -10000 0 -0.77 78 78
AFP -0.14 0.18 -10000 0 -0.78 6 6
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.15 0.14 0.42 19 -10000 0 19
TP53 -0.014 0.16 -10000 0 -0.52 22 22
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.41 0.47 -10000 0 -1.1 74 74
KRT14 -0.34 0.49 -10000 0 -1.1 61 61
TBP 0.022 0 -10000 0 -10000 0 0
CREBBP 0.074 0.11 0.28 37 -10000 0 37
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC2 0.013 0.007 -10000 0 -10000 0 0
AP-1 -0.35 0.34 -10000 0 -0.77 78 78
MAPK14 0.016 0.013 -10000 0 -10000 0 0
MAPK10 -0.054 0.19 -10000 0 -0.55 33 33
MAPK11 0.011 0.049 -10000 0 -0.43 3 3
KRT5 -0.54 0.55 -10000 0 -1.1 108 108
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0.012 0.067 -10000 0 -0.51 4 4
CGA -0.098 0.16 -10000 0 -0.59 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.14 0.15 0.39 46 -10000 0 46
MAPK3 0.015 0.032 -10000 0 -0.43 1 1
MAPK1 0.016 0.013 -10000 0 -10000 0 0
ICAM1 -0.14 0.23 -10000 0 -0.7 22 22
NFKB1 -0.027 0.087 -10000 0 -0.58 1 1
MAPK8 -0.16 0.18 -10000 0 -0.48 40 40
MAPK9 0.016 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.027 0.26 0.54 25 -0.7 11 36
BAX -0.006 0.12 -10000 0 -0.53 2 2
POMC -0.23 0.38 -10000 0 -1.3 24 24
EP300 0.074 0.11 0.29 35 -10000 0 35
cortisol/GR alpha (dimer)/p53 0.22 0.26 0.56 60 -0.49 4 64
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.071 0.24 6 -0.24 2 8
SGK1 0.1 0.24 -10000 0 -1.4 5 5
IL13 -0.23 0.23 -10000 0 -0.74 24 24
IL6 -0.19 0.31 -10000 0 -0.87 33 33
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.2 0.19 -10000 0 -0.44 71 71
IL2 -0.27 0.26 -10000 0 -0.73 38 38
CDK5 0.015 0.008 -10000 0 -10000 0 0
PRKACB 0.006 0.064 -10000 0 -0.6 3 3
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.22 0.36 -10000 0 -1 37 37
CDK5R1/CDK5 0.015 0.055 0.21 1 -0.35 5 6
NF kappa B1 p50/RelA/PKAc -0.014 0.11 -10000 0 -0.38 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.22 0.53 64 -0.38 2 66
SMARCA4 0.009 0.053 -10000 0 -0.6 2 2
chromatin remodeling 0.16 0.15 0.39 38 -0.38 1 39
NF kappa B1 p50/RelA/Cbp 0.041 0.17 0.34 15 -0.48 5 20
JUN (dimer) -0.2 0.2 -10000 0 -0.52 46 46
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.28 -10000 0 -0.78 34 34
NR3C1 0.15 0.18 0.44 44 -0.51 4 48
NR4A1 -0.048 0.16 -10000 0 -0.48 28 28
TIF2/SUV420H1 -0.007 0.1 -10000 0 -0.4 17 17
MAPKKK cascade 0.037 0.25 0.54 24 -0.66 11 35
cortisol/GR alpha (dimer)/Src-1 0.24 0.23 0.56 65 -0.42 2 67
PBX1 -0.003 0.094 -10000 0 -0.59 6 6
POU1F1 -0.003 0.031 -10000 0 -10000 0 0
SELE -0.2 0.34 -10000 0 -0.84 46 46
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.15 0.39 38 -0.38 1 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.22 0.53 64 -0.38 2 66
mol:cortisol 0.16 0.16 0.36 77 -10000 0 77
MMP1 -0.27 0.43 -10000 0 -1 55 55
Syndecan-4-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
PTK2 -0.015 0.098 -9999 0 -0.55 6 6
Syndecan-4/Syndesmos -0.1 0.19 -9999 0 -0.52 33 33
positive regulation of JNK cascade -0.11 0.19 -9999 0 -0.49 40 40
Syndecan-4/ADAM12 -0.12 0.2 -9999 0 -0.52 37 37
CCL5 -0.001 0.084 -9999 0 -0.47 8 8
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.011 0.037 -9999 0 -0.6 1 1
SDCBP 0.011 0.037 -9999 0 -0.6 1 1
PLG -0.11 0.22 -9999 0 -0.48 65 65
ADAM12 -0.021 0.13 -9999 0 -0.5 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.036 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.15 0.23 -9999 0 -0.57 45 45
Syndecan-4/CXCL12/CXCR4 -0.12 0.21 -9999 0 -0.53 37 37
Syndecan-4/Laminin alpha3 -0.12 0.21 -9999 0 -0.55 38 38
MDK -0.009 0.11 -9999 0 -0.58 10 10
Syndecan-4/FZD7 -0.15 0.22 -9999 0 -0.52 51 51
Syndecan-4/Midkine -0.11 0.21 -9999 0 -0.54 36 36
FZD7 -0.079 0.21 -9999 0 -0.53 45 45
Syndecan-4/FGFR1/FGF -0.13 0.17 -9999 0 -0.49 35 35
THBS1 -0.02 0.13 -9999 0 -0.5 17 17
integrin-mediated signaling pathway -0.12 0.22 -9999 0 -0.55 40 40
positive regulation of MAPKKK cascade -0.11 0.19 -9999 0 -0.49 40 40
Syndecan-4/TACI -0.12 0.2 -9999 0 -0.53 37 37
CXCR4 0.004 0.074 -9999 0 -0.6 4 4
cell adhesion 0.005 0.081 -9999 0 -0.3 13 13
Syndecan-4/Dynamin -0.1 0.19 -9999 0 -0.52 33 33
Syndecan-4/TSP1 -0.12 0.21 -9999 0 -0.54 39 39
Syndecan-4/GIPC -0.1 0.19 -9999 0 -0.52 33 33
Syndecan-4/RANTES -0.11 0.2 -9999 0 -0.52 38 38
ITGB1 0.011 0.037 -9999 0 -0.6 1 1
LAMA1 -0.08 0.21 -9999 0 -0.54 45 45
LAMA3 -0.028 0.15 -9999 0 -0.56 19 19
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.021 0.1 -9999 0 -0.52 8 8
Syndecan-4/alpha-Actinin -0.1 0.2 -9999 0 -0.53 33 33
TFPI -0.045 0.16 -9999 0 -0.49 31 31
F2 -0.034 0.13 -9999 0 -0.44 26 26
alpha5/beta1 Integrin 0.016 0.039 -9999 0 -0.43 2 2
positive regulation of cell adhesion -0.15 0.24 -9999 0 -0.6 43 43
ACTN1 0.011 0.037 -9999 0 -0.6 1 1
TNC -0.039 0.17 -9999 0 -0.57 24 24
Syndecan-4/CXCL12 -0.12 0.2 -9999 0 -0.52 38 38
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.036 0.16 -9999 0 -0.54 24 24
TNFRSF13B -0.036 0.14 -9999 0 -0.43 28 28
FGF2 -0.012 0.11 -9999 0 -0.47 14 14
FGFR1 0.001 0.083 -9999 0 -0.54 6 6
Syndecan-4/PI-4-5-P2 -0.11 0.19 -9999 0 -0.53 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.023 0.13 -9999 0 -0.47 20 20
cell migration -0.008 0.015 -9999 0 -10000 0 0
PRKCD 0.015 0.011 -9999 0 -10000 0 0
vasculogenesis -0.11 0.2 -9999 0 -0.52 39 39
SDC4 -0.11 0.2 -9999 0 -0.56 33 33
Syndecan-4/Tenascin C -0.13 0.23 -9999 0 -0.58 40 40
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.029 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.1 0.2 -9999 0 -0.52 34 34
MMP9 -0.08 0.21 -9999 0 -0.52 47 47
Rac1/GTP 0.005 0.082 -9999 0 -0.3 13 13
cytoskeleton organization -0.098 0.19 -9999 0 -0.5 33 33
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.13 0.22 -9999 0 -0.54 42 42
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.048 0.16 -10000 0 -0.42 26 26
CRKL -0.048 0.16 -10000 0 -0.44 28 28
HRAS -0.049 0.18 -10000 0 -0.5 20 20
mol:PIP3 -0.061 0.16 -10000 0 -0.43 29 29
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.057 0.17 -10000 0 -0.44 32 32
FOXO3 -0.044 0.16 -10000 0 -0.44 24 24
AKT1 -0.054 0.17 -10000 0 -0.47 26 26
BAD -0.044 0.16 -10000 0 -0.44 24 24
megakaryocyte differentiation -0.066 0.18 -10000 0 -0.44 39 39
GSK3B -0.044 0.16 -10000 0 -0.44 24 24
RAF1 -0.031 0.15 -10000 0 -0.41 18 18
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.057 0.17 -10000 0 -0.44 32 32
STAT1 -0.13 0.36 -10000 0 -0.88 40 40
HRAS/SPRED1 -0.033 0.14 -10000 0 -0.41 18 18
cell proliferation -0.06 0.18 -10000 0 -0.45 31 31
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
TEC -0.003 0.095 -10000 0 -0.54 8 8
RPS6KB1 -0.059 0.18 -10000 0 -0.44 35 35
HRAS/SPRED2 -0.033 0.14 -10000 0 -0.41 18 18
LYN/TEC/p62DOK -0.05 0.18 -10000 0 -0.49 25 25
MAPK3 -0.011 0.11 -10000 0 -0.29 13 13
STAP1 -0.072 0.18 -10000 0 -0.46 32 32
GRAP2 -0.048 0.18 -10000 0 -0.55 29 29
JAK2 -0.12 0.31 -10000 0 -0.76 40 40
STAT1 (dimer) -0.13 0.35 -10000 0 -0.86 40 40
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.055 0.18 -10000 0 -0.47 29 29
actin filament polymerization -0.059 0.17 -10000 0 -0.41 36 36
LYN 0.011 0.037 -10000 0 -0.6 1 1
STAP1/STAT5A (dimer) -0.087 0.23 -10000 0 -0.62 30 30
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
CBL/CRKL/GRB2 -0.031 0.15 -10000 0 -0.42 21 21
PI3K -0.062 0.19 -10000 0 -0.52 27 27
PTEN 0.006 0.064 -10000 0 -0.6 3 3
SCF/KIT/EPO/EPOR -0.15 0.42 -10000 0 -1.3 26 26
MAPK8 -0.061 0.18 -10000 0 -0.46 31 31
STAT3 (dimer) -0.055 0.17 -10000 0 -0.43 32 32
positive regulation of transcription -0.005 0.092 -10000 0 -0.25 8 8
mol:GDP -0.058 0.18 -10000 0 -0.52 23 23
PIK3C2B -0.057 0.17 -10000 0 -0.46 29 29
CBL/CRKL -0.038 0.16 -10000 0 -0.42 25 25
FER -0.059 0.17 -10000 0 -0.45 30 30
SH2B3 -0.057 0.17 -10000 0 -0.46 29 29
PDPK1 -0.051 0.14 -10000 0 -0.42 24 24
SNAI2 -0.065 0.18 -10000 0 -0.46 33 33
positive regulation of cell proliferation -0.095 0.27 -10000 0 -0.66 40 40
KITLG -0.044 0.17 -10000 0 -0.54 28 28
cell motility -0.095 0.27 -10000 0 -0.66 40 40
PTPN6 0.013 0.038 -10000 0 -0.58 1 1
EPOR -0.044 0.23 -10000 0 -1.2 7 7
STAT5A (dimer) -0.078 0.23 -10000 0 -0.58 34 34
SOCS1 0.009 0.046 -10000 0 -0.51 2 2
cell migration 0.07 0.17 0.4 43 -10000 0 43
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.016 0.1 -10000 0 -0.44 15 15
VAV1 -0.014 0.12 -10000 0 -0.58 12 12
GRB10 -0.065 0.19 -10000 0 -0.45 36 36
PTPN11 0.012 0.037 -10000 0 -0.59 1 1
SCF/KIT -0.066 0.18 -10000 0 -0.42 42 42
GO:0007205 0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.016 0.12 -10000 0 -0.32 15 15
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.11 0.36 -10000 0 -1.2 23 23
MAP2K2 -0.016 0.12 -10000 0 -0.32 14 14
SHC/Grb2/SOS1 -0.04 0.16 -10000 0 -0.45 24 24
STAT5A -0.081 0.24 -10000 0 -0.6 34 34
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.064 0.18 -10000 0 -0.45 33 33
SHC/GRAP2 -0.026 0.13 -10000 0 -0.4 29 29
PTPRO -0.067 0.19 -10000 0 -0.45 39 39
SH2B2 -0.06 0.17 -10000 0 -0.42 36 36
DOK1 0.011 0.037 -10000 0 -0.6 1 1
MATK -0.072 0.18 -10000 0 -0.41 43 43
CREBBP 0.024 0.028 -10000 0 -10000 0 0
BCL2 -0.059 0.28 -10000 0 -1.4 10 10
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.049 0.17 -9999 0 -0.46 31 31
alphaM/beta2 Integrin/GPIbA -0.03 0.14 -9999 0 -0.45 22 22
alphaM/beta2 Integrin/proMMP-9 -0.072 0.19 -9999 0 -0.45 43 43
PLAUR 0 0.084 -9999 0 -0.5 7 7
HMGB1 -0.004 0.076 -9999 0 -0.6 4 4
alphaM/beta2 Integrin/Talin -0.015 0.12 -9999 0 -0.51 13 13
AGER -0.005 0.077 -9999 0 -0.54 5 5
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.001 0.083 -9999 0 -0.54 6 6
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.16 -9999 0 -0.46 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.081 0.21 -9999 0 -0.52 47 47
CYR61 -0.001 0.087 -9999 0 -0.53 7 7
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.11 0.14 -9999 0 -0.45 23 23
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.068 0.2 -9999 0 -0.55 38 38
MYH2 -0.14 0.18 -9999 0 -0.48 32 32
MST1R -0.034 0.16 -9999 0 -0.58 21 21
leukocyte activation during inflammatory response -0.062 0.13 -9999 0 -0.43 21 21
APOB -0.01 0.088 -9999 0 -0.43 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.044 0.17 -9999 0 -0.53 28 28
JAM3 0.006 0.06 -9999 0 -0.47 4 4
GP1BA -0.011 0.11 -9999 0 -0.55 11 11
alphaM/beta2 Integrin/CTGF -0.024 0.14 -9999 0 -0.5 18 18
alphaM/beta2 Integrin -0.12 0.17 -9999 0 -0.46 33 33
JAM3 homodimer 0.006 0.06 -9999 0 -0.47 4 4
ICAM2 0.004 0.074 -9999 0 -0.6 4 4
ICAM1 0.002 0.079 -9999 0 -0.56 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.17 -9999 0 -0.46 33 33
cell adhesion -0.03 0.14 -9999 0 -0.45 22 22
NFKB1 -0.06 0.2 -9999 0 -0.56 19 19
THY1 0.003 0.071 -9999 0 -0.46 6 6
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.029 0.11 -9999 0 -0.28 39 39
alphaM/beta2 Integrin/LRP/tPA -0.028 0.14 -9999 0 -0.45 19 19
IL6 -0.086 0.25 -9999 0 -0.68 28 28
ITGB2 -0.016 0.11 -9999 0 -0.56 10 10
elevation of cytosolic calcium ion concentration -0.025 0.15 -9999 0 -0.51 18 18
alphaM/beta2 Integrin/JAM2/JAM3 -0.027 0.15 -9999 0 -0.45 21 21
JAM2 -0.02 0.13 -9999 0 -0.5 17 17
alphaM/beta2 Integrin/ICAM1 -0.037 0.16 -9999 0 -0.4 36 36
alphaM/beta2 Integrin/uPA/Plg -0.086 0.17 -9999 0 -0.42 39 39
RhoA/GTP -0.14 0.18 -9999 0 -0.49 34 34
positive regulation of phagocytosis -0.1 0.17 -9999 0 -0.59 20 20
Ron/MSP -0.028 0.14 -9999 0 -0.42 29 29
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.15 -9999 0 -0.52 18 18
alphaM/beta2 Integrin/uPAR -0.023 0.14 -9999 0 -0.5 17 17
PLAU -0.01 0.11 -9999 0 -0.5 12 12
PLAT -0.019 0.12 -9999 0 -0.47 18 18
actin filament polymerization -0.13 0.17 -9999 0 -0.45 32 32
MST1 -0.005 0.098 -9999 0 -0.52 9 9
alphaM/beta2 Integrin/lipoprotein(a) -0.045 0.14 -9999 0 -0.43 21 21
TNF -0.095 0.27 -9999 0 -0.73 31 31
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.029 0.14 -9999 0 -0.49 19 19
fibrinolysis -0.086 0.17 -9999 0 -0.41 39 39
HCK -0.005 0.098 -9999 0 -0.52 9 9
dendritic cell antigen processing and presentation -0.12 0.17 -9999 0 -0.46 33 33
VTN -0.009 0.096 -9999 0 -0.43 13 13
alphaM/beta2 Integrin/CYR61 -0.023 0.14 -9999 0 -0.5 17 17
LPA -0.043 0.14 -9999 0 -0.43 32 32
LRP1 0.004 0.07 -9999 0 -0.5 5 5
cell migration -0.089 0.21 -9999 0 -0.45 51 51
FN1 -0.024 0.13 -9999 0 -0.48 20 20
alphaM/beta2 Integrin/Thy1 -0.021 0.13 -9999 0 -0.46 17 17
MPO -0.048 0.17 -9999 0 -0.52 30 30
KNG1 -0.02 0.11 -9999 0 -0.43 17 17
RAP1/GDP 0.018 0 -9999 0 -10000 0 0
ROCK1 -0.13 0.18 -9999 0 -0.48 30 30
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.11 0.22 -9999 0 -0.48 65 65
CTGF -0.002 0.091 -9999 0 -0.55 7 7
alphaM/beta2 Integrin/Hck -0.025 0.16 -9999 0 -0.57 16 16
ITGAM -0.025 0.12 -9999 0 -0.52 15 15
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.057 0.19 -9999 0 -0.46 37 37
HP -0.28 0.27 -9999 0 -0.52 147 147
leukocyte adhesion -0.076 0.14 -9999 0 -0.53 16 16
SELP -0.068 0.2 -9999 0 -0.55 38 38
Nectin adhesion pathway

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
PDGFRB 0 0.084 -9999 0 -0.5 7 7
alphaV beta3 Integrin -0.053 0.17 -9999 0 -0.4 46 46
PTK2 -0.094 0.19 -9999 0 -0.52 35 35
positive regulation of JNK cascade -0.047 0.11 -9999 0 -0.32 35 35
CDC42/GDP -0.026 0.17 -9999 0 -0.44 36 36
Rac1/GDP -0.023 0.17 -9999 0 -0.43 36 36
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.009 0.053 -9999 0 -0.6 2 2
CDC42/GTP -0.058 0.14 -9999 0 -0.4 35 35
nectin-3/I-afadin -0.047 0.16 -9999 0 -0.41 41 41
RAPGEF1 -0.038 0.18 -9999 0 -0.49 36 36
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.052 0.21 -9999 0 -0.56 36 36
PDGFB-D/PDGFRB 0 0.084 -9999 0 -0.5 7 7
TLN1 -0.035 0.13 -9999 0 -0.38 23 23
Rap1/GTP -0.049 0.12 -9999 0 -0.34 35 35
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.047 0.16 -9999 0 -0.41 41 41
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP -0.041 0.2 -9999 0 -0.54 36 36
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
PI3K -0.039 0.15 -9999 0 -0.32 48 48
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.015 0.044 -9999 0 -0.39 3 3
positive regulation of lamellipodium assembly -0.05 0.12 -9999 0 -0.34 36 36
PVRL1 0.007 0.059 -9999 0 -0.54 3 3
PVRL3 -0.077 0.21 -9999 0 -0.57 41 41
PVRL2 0.011 0.037 -9999 0 -0.6 1 1
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
CDH1 0.009 0.053 -9999 0 -0.6 2 2
CLDN1 -0.075 0.2 -9999 0 -0.54 43 43
JAM-A/CLDN1 -0.069 0.17 -9999 0 -0.36 57 57
SRC -0.067 0.23 -9999 0 -0.64 36 36
ITGB3 -0.065 0.19 -9999 0 -0.5 41 41
nectin-1(dimer)/I-afadin/I-afadin 0.015 0.044 -9999 0 -0.39 3 3
FARP2 -0.043 0.2 -9999 0 -0.53 36 36
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.03 0.14 -9999 0 -0.36 35 35
nectin-1/I-afadin 0.015 0.044 -9999 0 -0.39 3 3
nectin-2/I-afadin 0.018 0.028 -9999 0 -0.43 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.034 0.14 -9999 0 -0.37 37 37
CDC42/GTP/IQGAP1/filamentous actin 0.017 0.024 -9999 0 -0.37 1 1
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.047 0.11 -9999 0 -0.32 35 35
alphaV/beta3 Integrin/Talin -0.067 0.18 -9999 0 -0.53 22 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.028 -9999 0 -0.43 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.018 0.028 -9999 0 -0.43 1 1
PIP5K1C -0.044 0.14 -9999 0 -0.41 24 24
VAV2 -0.048 0.21 -9999 0 -0.55 37 37
RAP1/GDP -0.056 0.14 -9999 0 -0.4 36 36
ITGAV -0.011 0.12 -9999 0 -0.57 11 11
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.032 0.14 -9999 0 -0.36 36 36
nectin-3(dimer)/I-afadin/I-afadin -0.047 0.16 -9999 0 -0.41 41 41
Rac1/GTP -0.061 0.14 -9999 0 -0.42 36 36
PTPRM -0.057 0.15 -9999 0 -0.32 56 56
E-cadherin/beta catenin/alpha catenin -0.008 0.046 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0.037 -9999 0 -0.6 1 1
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.001 0.19 -10000 0 -0.61 12 12
PTK2B 0.005 0.07 -10000 0 -0.56 4 4
mol:Ca2+ -0.025 0.23 -10000 0 -0.77 13 13
EDN1 -0.007 0.16 -10000 0 -0.49 17 17
EDN3 -0.25 0.27 -10000 0 -0.52 130 130
EDN2 -0.079 0.2 -10000 0 -0.52 46 46
HRAS/GDP -0.033 0.2 -10000 0 -0.63 15 15
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.011 0.16 -10000 0 -0.46 19 19
ADCY4 -0.009 0.16 -10000 0 -0.54 12 12
ADCY5 -0.055 0.2 -10000 0 -0.51 25 25
ADCY6 -0.003 0.16 -10000 0 -0.55 12 12
ADCY7 -0.004 0.16 -10000 0 -0.55 11 11
ADCY1 -0.041 0.18 -10000 0 -0.48 22 22
ADCY2 -0.046 0.2 -10000 0 -0.55 25 25
ADCY3 -0.004 0.16 -10000 0 -0.57 12 12
ADCY8 -0.013 0.16 -10000 0 -0.51 13 13
ADCY9 -0.017 0.18 -10000 0 -0.51 20 20
arachidonic acid secretion -0.05 0.21 -10000 0 -0.56 23 23
ETB receptor/Endothelin-1/Gq/GTP -0.023 0.15 -10000 0 -0.45 16 16
GNAO1 -0.013 0.11 -10000 0 -0.48 14 14
HRAS 0.013 0.001 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.016 0.2 0.33 32 -0.62 11 43
ETA receptor/Endothelin-1/Gs/GTP -0.008 0.19 0.3 36 -0.58 11 47
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.026 0.26 -10000 0 -0.78 21 21
EDNRB -0.026 0.14 -10000 0 -0.52 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.01 0.2 -10000 0 -0.65 12 12
CYSLTR1 -0.023 0.24 -10000 0 -0.75 16 16
SLC9A1 -0.009 0.1 0.2 22 -0.34 7 29
mol:GDP -0.043 0.21 -10000 0 -0.6 21 21
SLC9A3 -0.059 0.27 -10000 0 -0.71 28 28
RAF1 -0.038 0.2 -10000 0 -0.6 18 18
JUN -0.005 0.19 -10000 0 -0.74 8 8
JAK2 -0.011 0.21 -10000 0 -0.57 19 19
mol:IP3 -0.021 0.17 -10000 0 -0.54 17 17
ETA receptor/Endothelin-1 -0.012 0.24 0.38 36 -0.6 18 54
PLCB1 -0.024 0.14 -10000 0 -0.57 17 17
PLCB2 0.005 0.065 -10000 0 -0.52 4 4
ETA receptor/Endothelin-3 -0.18 0.23 -10000 0 -0.4 120 120
FOS -0.032 0.22 -10000 0 -0.78 13 13
Gai/GDP -0.006 0.12 -10000 0 -0.67 5 5
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.032 0.24 -10000 0 -0.66 21 21
BCAR1 0.011 0.037 -10000 0 -0.6 1 1
PRKCB1 -0.021 0.17 -10000 0 -0.52 17 17
GNAQ 0.007 0.065 -10000 0 -0.6 3 3
GNAZ -0.015 0.12 -10000 0 -0.53 14 14
GNAL 0.005 0.061 -10000 0 -0.43 5 5
Gs family/GDP -0.077 0.16 -10000 0 -0.53 22 22
ETA receptor/Endothelin-1/Gq/GTP -0.006 0.16 -10000 0 -0.5 15 15
MAPK14 -0.018 0.14 -10000 0 -0.48 13 13
TRPC6 -0.029 0.24 -10000 0 -0.86 12 12
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.11 -10000 0 -0.54 11 11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.025 0.15 -10000 0 -0.46 17 17
ETB receptor/Endothelin-2 -0.075 0.18 -10000 0 -0.39 62 62
ETB receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.39 140 140
ETB receptor/Endothelin-1 -0.022 0.16 -10000 0 -0.44 22 22
MAPK3 -0.035 0.22 -10000 0 -0.77 14 14
MAPK1 -0.035 0.22 -10000 0 -0.77 14 14
Rac1/GDP -0.032 0.2 -10000 0 -0.63 15 15
cAMP biosynthetic process -0.049 0.19 -10000 0 -0.5 27 27
MAPK8 -0.019 0.22 -10000 0 -0.75 12 12
SRC 0.011 0.037 -10000 0 -0.6 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.11 -10000 0 -0.41 7 7
p130Cas/CRK/Src/PYK2 -0.046 0.22 -10000 0 -0.64 19 19
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.033 0.2 -10000 0 -0.65 15 15
COL1A2 -0.035 0.27 -10000 0 -0.82 21 21
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.052 0.19 -10000 0 -0.4 49 49
mol:DAG -0.021 0.17 -10000 0 -0.54 17 17
MAP2K2 -0.034 0.2 -10000 0 -0.65 16 16
MAP2K1 -0.034 0.2 -10000 0 -0.65 16 16
EDNRA 0.005 0.14 -10000 0 -0.52 10 10
positive regulation of muscle contraction 0.008 0.17 -10000 0 -0.56 11 11
Gq family/GDP -0.088 0.19 -10000 0 -0.66 18 18
HRAS/GTP -0.044 0.19 -10000 0 -0.58 20 20
PRKCH -0.017 0.18 -10000 0 -0.61 13 13
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.023 0.18 -10000 0 -0.56 19 19
PRKCB -0.035 0.2 -10000 0 -0.53 27 27
PRKCE -0.014 0.16 -10000 0 -0.52 16 16
PRKCD -0.015 0.17 -10000 0 -0.52 16 16
PRKCG -0.069 0.2 -10000 0 -0.57 22 22
regulation of vascular smooth muscle contraction -0.04 0.25 -10000 0 -0.96 12 12
PRKCQ -0.057 0.21 -10000 0 -0.53 28 28
PLA2G4A -0.057 0.23 -10000 0 -0.63 23 23
GNA14 -0.013 0.12 -10000 0 -0.57 12 12
GNA15 -0.001 0.087 -10000 0 -0.52 7 7
GNA12 0.011 0.037 -10000 0 -0.6 1 1
GNA11 -0.017 0.13 -10000 0 -0.57 14 14
Rac1/GTP 0.017 0.2 0.33 32 -0.59 11 43
MMP1 -0.14 0.34 -10000 0 -0.69 62 62
Osteopontin-mediated events

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
IKK alpha homodimer -0.045 0.18 -9999 0 -0.52 21 21
NF kappa B1 p50/RelA/I kappa B alpha -0.021 0.18 -9999 0 -0.62 11 11
alphaV/beta3 Integrin/Osteopontin/Src -0.045 0.17 -9999 0 -0.4 44 44
AP1 -0.065 0.24 -9999 0 -0.66 25 25
ILK -0.055 0.19 -9999 0 -0.55 20 20
bone resorption -0.048 0.2 -9999 0 -0.61 18 18
PTK2B 0.005 0.07 -9999 0 -0.56 4 4
PYK2/p130Cas -0.045 0.19 -9999 0 -0.53 22 22
ITGAV -0.008 0.12 -9999 0 -0.56 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.11 -9999 0 -0.42 17 17
alphaV/beta3 Integrin/Osteopontin -0.068 0.21 -9999 0 -0.46 47 47
MAP3K1 -0.059 0.2 -9999 0 -0.43 47 47
JUN 0.007 0.054 -9999 0 -0.49 3 3
MAPK3 -0.045 0.19 -9999 0 -0.53 21 21
MAPK1 -0.045 0.19 -9999 0 -0.53 21 21
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
NFKB1 0.011 0.037 -9999 0 -0.6 1 1
MAPK8 -0.055 0.2 -9999 0 -0.55 24 24
ITGB3 -0.062 0.19 -9999 0 -0.49 41 41
NFKBIA -0.036 0.18 -9999 0 -0.52 20 20
FOS -0.028 0.14 -9999 0 -0.48 22 22
CD44 -0.022 0.14 -9999 0 -0.58 16 16
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.044 0.23 -9999 0 -0.89 12 12
NF kappa B1 p50/RelA -0.068 0.15 -9999 0 -0.62 11 11
BCAR1 0.011 0.037 -9999 0 -0.6 1 1
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.047 0.17 -9999 0 -0.4 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.06 0.2 -9999 0 -0.43 48 48
VAV3 -0.069 0.2 -9999 0 -0.54 27 27
MAP3K14 -0.056 0.19 -9999 0 -0.42 47 47
ROCK2 0.011 0.037 -9999 0 -0.6 1 1
SPP1 -0.058 0.19 -9999 0 -0.52 37 37
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.057 0.19 -9999 0 -0.51 25 25
MMP2 -0.069 0.24 -9999 0 -0.62 29 29
Glypican 2 network

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
MDK -0.009 0.11 -9999 0 -0.58 10 10
GPC2 -0.016 0.12 -9999 0 -0.47 16 16
GPC2/Midkine -0.018 0.12 -9999 0 -0.36 26 26
neuron projection morphogenesis -0.018 0.12 -9999 0 -0.36 26 26
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.018 0.12 -9999 0 -0.38 18 18
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.14 -9999 0 -0.42 11 11
AP1 -0.12 0.16 -9999 0 -0.47 26 26
mol:PIP3 -0.11 0.16 -9999 0 -0.48 23 23
AKT1 0.004 0.12 -9999 0 -0.45 8 8
PTK2B -0.024 0.099 -9999 0 -0.37 11 11
RHOA 0.013 0.046 -9999 0 -10000 0 0
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.057 0.14 -9999 0 -0.39 19 19
MAGI3 0.011 0.037 -9999 0 -0.6 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.092 0.17 -9999 0 -0.37 55 55
HRAS/GDP 0.01 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.021 0.11 -9999 0 -0.4 9 9
NF kappa B1 p50/RelA -0.096 0.15 -9999 0 -0.46 22 22
endothelial cell migration -0.052 0.21 -9999 0 -0.54 37 37
ADCY4 -0.028 0.15 -9999 0 -0.5 16 16
ADCY5 -0.055 0.18 -9999 0 -0.5 23 23
ADCY6 -0.026 0.15 -9999 0 -0.5 16 16
ADCY7 -0.026 0.15 -9999 0 -0.48 17 17
ADCY1 -0.043 0.16 -9999 0 -0.53 17 17
ADCY2 -0.049 0.18 -9999 0 -0.5 24 24
ADCY3 -0.026 0.15 -9999 0 -0.48 18 18
ADCY8 -0.029 0.15 -9999 0 -0.5 16 16
ADCY9 -0.033 0.16 -9999 0 -0.48 20 20
GSK3B -0.016 0.094 -9999 0 -0.37 9 9
arachidonic acid secretion -0.021 0.14 -9999 0 -0.44 18 18
GNG2 -0.007 0.1 -9999 0 -0.51 10 10
TRIP6 0.006 0.077 -9999 0 -0.42 8 8
GNAO1 -0.033 0.14 -9999 0 -0.36 34 34
HRAS 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.061 0.16 -9999 0 -0.44 21 21
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.006 0.13 -9999 0 -0.9 5 5
JUN 0.008 0.053 -9999 0 -0.49 3 3
LPA/LPA2/NHERF2 0.009 0.039 -9999 0 -0.3 2 2
TIAM1 -0.018 0.15 -9999 0 -1.1 5 5
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
mol:IP3 -0.058 0.14 -9999 0 -0.4 19 19
PLCB3 0.016 0.035 -9999 0 -0.33 1 1
FOS -0.028 0.14 -9999 0 -0.48 22 22
positive regulation of mitosis -0.021 0.14 -9999 0 -0.44 18 18
LPA/LPA1-2-3 -0.1 0.18 -9999 0 -0.39 54 54
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.011 0.037 -9999 0 -0.6 1 1
stress fiber formation -0.043 0.12 -9999 0 -0.37 16 16
GNAZ -0.035 0.14 -9999 0 -0.35 37 37
EGFR/PI3K-beta/Gab1 -0.11 0.16 -9999 0 -0.51 23 23
positive regulation of dendritic cell cytokine production -0.1 0.18 -9999 0 -0.39 54 54
LPA/LPA2/MAGI-3 0.011 0.036 -9999 0 -0.37 1 1
ARHGEF1 -0.002 0.1 -9999 0 -0.35 13 13
GNAI2 -0.018 0.12 -9999 0 -0.34 25 25
GNAI3 -0.018 0.12 -9999 0 -0.34 25 25
GNAI1 -0.032 0.14 -9999 0 -0.35 35 35
LPA/LPA3 -0.12 0.18 -9999 0 -0.39 81 81
LPA/LPA2 0.002 0.033 -9999 0 -10000 0 0
LPA/LPA1 -0.032 0.14 -9999 0 -0.35 37 37
HB-EGF/EGFR -0.045 0.14 -9999 0 -0.37 31 31
HBEGF -0.049 0.15 -9999 0 -0.37 48 48
mol:DAG -0.058 0.14 -9999 0 -0.4 19 19
cAMP biosynthetic process -0.038 0.16 -9999 0 -0.51 17 17
NFKB1 0.011 0.037 -9999 0 -0.6 1 1
SRC 0.011 0.037 -9999 0 -0.6 1 1
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN -0.062 0.16 -9999 0 -0.44 22 22
GNAQ -0.071 0.14 -9999 0 -0.32 49 49
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.15 0.25 -9999 0 -0.52 81 81
LPAR1 -0.027 0.14 -9999 0 -0.63 12 12
IL8 -0.12 0.21 -9999 0 -0.48 47 47
PTK2 -0.087 0.17 -9999 0 -0.36 54 54
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
CASP3 -0.093 0.17 -9999 0 -0.37 55 55
EGFR -0.002 0.094 -9999 0 -0.57 7 7
PLCG1 -0.079 0.16 -9999 0 -0.36 48 48
PLD2 -0.089 0.17 -9999 0 -0.36 55 55
G12/G13 -0.008 0.11 -9999 0 -0.38 13 13
PI3K-beta -0.046 0.11 -9999 0 -0.52 8 8
cell migration -0.018 0.082 -9999 0 -0.27 6 6
SLC9A3R2 0.009 0.046 -9999 0 -0.51 2 2
PXN -0.044 0.12 -9999 0 -0.38 16 16
HRAS/GTP -0.022 0.14 -9999 0 -0.46 18 18
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.081 0.21 -9999 0 -0.52 47 47
PRKCE 0.013 0 -9999 0 -10000 0 0
PRKCD -0.049 0.14 -9999 0 -0.43 12 12
Gi(beta/gamma) -0.025 0.14 -9999 0 -0.44 20 20
mol:LPA -0.013 0.051 -9999 0 -0.19 13 13
TRIP6/p130 Cas/FAK1/Paxillin -0.096 0.15 -9999 0 -0.48 18 18
MAPKKK cascade -0.021 0.14 -9999 0 -0.44 18 18
contractile ring contraction involved in cytokinesis 0.013 0.046 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.082 0.15 -9999 0 -0.34 53 53
GNA15 -0.075 0.15 -9999 0 -0.35 47 47
GNA12 0.011 0.037 -9999 0 -0.6 1 1
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.022 0.11 -9999 0 -0.41 9 9
GNA11 -0.085 0.16 -9999 0 -0.35 54 54
Rac1/GTP 0.006 0.13 -9999 0 -0.96 5 5
MMP2 -0.052 0.21 -9999 0 -0.54 37 37
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.012 0.087 -10000 0 -0.48 4 4
NFATC2 -0.086 0.26 -10000 0 -0.71 26 26
NFATC3 -0.017 0.073 -10000 0 -10000 0 0
CD40LG -0.24 0.4 -10000 0 -1.1 31 31
ITCH -0.029 0.12 -10000 0 -0.67 2 2
CBLB -0.025 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.45 -10000 0 -1.2 40 40
JUNB 0.009 0.053 -10000 0 -0.6 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.046 0.13 -10000 0 -0.3 11 11
T cell anergy -0.074 0.16 -10000 0 -0.4 31 31
TLE4 -0.065 0.23 -10000 0 -0.71 18 18
Jun/NFAT1-c-4/p21SNFT -0.17 0.37 -10000 0 -1.1 23 23
AP-1/NFAT1-c-4 -0.26 0.46 -10000 0 -1.3 29 29
IKZF1 -0.07 0.26 -10000 0 -0.85 19 19
T-helper 2 cell differentiation -0.091 0.26 -10000 0 -0.77 22 22
AP-1/NFAT1 -0.086 0.21 -10000 0 -0.58 22 22
CALM1 -0.02 0.072 -10000 0 -10000 0 0
EGR2 -0.12 0.36 -10000 0 -1.5 11 11
EGR3 -0.15 0.41 -10000 0 -1.5 16 16
NFAT1/FOXP3 -0.077 0.23 -10000 0 -0.63 24 24
EGR1 -0.023 0.13 -10000 0 -0.51 17 17
JUN -0.006 0.057 -10000 0 -0.49 3 3
EGR4 -0.021 0.11 -10000 0 -0.44 17 17
mol:Ca2+ -0.035 0.076 -10000 0 -10000 0 0
GBP3 -0.083 0.28 -10000 0 -0.86 23 23
FOSL1 -0.025 0.14 -10000 0 -0.5 20 20
NFAT1-c-4/MAF/IRF4 -0.18 0.38 -10000 0 -1.1 28 28
DGKA -0.047 0.2 -10000 0 -0.66 14 14
CREM 0.013 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.2 0.38 -10000 0 -1.1 26 26
CTLA4 -0.11 0.3 -10000 0 -0.74 39 39
NFAT1-c-4 (dimer)/EGR1 -0.16 0.38 -10000 0 -1.1 25 25
NFAT1-c-4 (dimer)/EGR4 -0.16 0.38 -10000 0 -1.1 22 22
FOS -0.042 0.14 -10000 0 -0.5 22 22
IFNG -0.16 0.33 -10000 0 -0.9 29 29
T cell activation -0.1 0.23 -10000 0 -0.78 8 8
MAF 0 0.084 -10000 0 -0.5 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.099 0.3 1.5 7 -10000 0 7
TNF -0.19 0.4 -10000 0 -1 35 35
FASLG -0.26 0.56 -10000 0 -1.5 38 38
TBX21 -0.046 0.17 -10000 0 -0.55 27 27
BATF3 -0.01 0.11 -10000 0 -0.5 12 12
PRKCQ -0.073 0.21 -10000 0 -0.57 38 38
PTPN1 -0.044 0.19 -10000 0 -0.63 12 12
NFAT1-c-4/ICER1 -0.14 0.35 -10000 0 -1.1 21 21
GATA3 -0.036 0.15 -10000 0 -0.49 27 27
T-helper 1 cell differentiation -0.16 0.32 -10000 0 -0.88 29 29
IL2RA -0.22 0.36 -10000 0 -1.1 33 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.044 0.19 -10000 0 -0.62 13 13
E2F1 0.005 0.084 -10000 0 -0.47 8 8
PPARG -0.1 0.22 -10000 0 -0.53 55 55
SLC3A2 -0.044 0.19 -10000 0 -0.6 14 14
IRF4 -0.084 0.21 -10000 0 -0.51 49 49
PTGS2 -0.29 0.42 -10000 0 -1 41 41
CSF2 -0.23 0.38 -10000 0 -1 28 28
JunB/Fra1/NFAT1-c-4 -0.15 0.36 -10000 0 -1.1 23 23
IL4 -0.096 0.28 -10000 0 -0.82 21 21
IL5 -0.23 0.37 -10000 0 -1 30 30
IL2 -0.1 0.23 -10000 0 -0.8 8 8
IL3 -0.048 0.051 -10000 0 -10000 0 0
RNF128 -0.12 0.25 -10000 0 -0.49 78 78
NFATC1 -0.1 0.3 -10000 0 -1.5 7 7
CDK4 0.07 0.18 0.74 4 -10000 0 4
PTPRK -0.048 0.2 -10000 0 -0.66 14 14
IL8 -0.26 0.41 -10000 0 -1.1 37 37
POU2F1 0.013 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.037 0.15 -10000 0 -0.37 35 35
ACTA1 -0.055 0.19 0.24 3 -0.46 36 39
NUMA1 -0.035 0.15 -10000 0 -0.37 36 36
SPTAN1 -0.049 0.18 0.24 2 -0.45 35 37
LIMK1 -0.049 0.18 0.24 3 -0.45 35 38
BIRC3 -0.052 0.18 -10000 0 -0.54 31 31
BIRC2 0.006 0.064 -10000 0 -0.6 3 3
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.071 0.19 -10000 0 -0.46 44 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 -0.035 0.15 -10000 0 -0.37 35 35
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.047 0.18 0.24 2 -0.44 35 37
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.006 0.064 -10000 0 -0.6 3 3
GSN -0.05 0.19 0.24 3 -0.46 35 38
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.11 0.25 -10000 0 -0.61 48 48
BID -0.028 0.1 -10000 0 -0.24 43 43
MAP3K1 -0.013 0.073 -10000 0 -0.24 11 11
TRADD 0.011 0.037 -10000 0 -0.6 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.18 -10000 0 -0.45 35 35
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair 0.001 0.087 0.74 2 -0.19 10 12
neuron apoptosis 0.006 0.094 -10000 0 -1 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.041 0.18 -10000 0 -0.43 36 36
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 -0.018 0.12 -10000 0 -0.5 7 7
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD -0.041 0.18 -10000 0 -0.43 35 35
CASP7 0.023 0.1 0.31 21 -0.46 3 24
KRT18 0.005 0.03 -10000 0 -10000 0 0
apoptosis -0.05 0.18 0.25 3 -0.56 16 19
DFFA -0.049 0.18 0.24 3 -0.45 35 38
DFFB -0.049 0.18 0.24 2 -0.45 35 37
PARP1 -0.001 0.088 0.2 10 -0.76 2 12
actin filament polymerization 0.039 0.17 0.42 35 -10000 0 35
TNF -0.066 0.19 -10000 0 -0.51 40 40
CYCS -0.022 0.084 -10000 0 -0.23 20 20
SATB1 -0.043 0.14 -10000 0 -0.51 8 8
SLK -0.051 0.18 -10000 0 -0.45 36 36
p15 BID/BAX -0.018 0.09 -10000 0 -0.31 9 9
CASP2 -0.003 0.1 -10000 0 -0.4 9 9
JNK cascade 0.012 0.073 0.24 11 -10000 0 11
CASP3 -0.058 0.19 0.25 3 -0.48 35 38
LMNB2 0 0.084 -10000 0 -0.33 7 7
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.009 0.053 -10000 0 -0.6 2 2
Mammalian IAPs/DIABLO -0.007 0.12 -10000 0 -0.35 22 22
negative regulation of DNA binding -0.11 0.25 -10000 0 -0.6 48 48
stress fiber formation -0.05 0.18 0.24 2 -0.44 36 38
GZMB -0.087 0.22 -10000 0 -0.47 59 59
CASP1 -0.002 0.075 -10000 0 -0.3 15 15
LMNB1 -0.006 0.095 -10000 0 -0.39 7 7
APP 0.006 0.097 -10000 0 -1.1 2 2
TNFRSF1A 0.011 0.037 -10000 0 -0.6 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM -0.052 0.18 0.25 3 -0.42 35 38
LMNA 0 0.084 -10000 0 -0.33 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.01 0.11 -10000 0 -0.43 9 9
LRDD 0.011 0.037 -10000 0 -0.6 1 1
SREBF1 -0.05 0.18 0.24 3 -0.45 36 39
APAF-1/Caspase 9 0.005 0.057 0.38 3 -10000 0 3
nuclear fragmentation during apoptosis -0.035 0.15 0.2 1 -0.36 36 37
CFL2 -0.041 0.18 -10000 0 -0.43 35 35
GAS2 -0.092 0.21 0.24 2 -0.45 52 54
positive regulation of apoptosis 0 0.088 -10000 0 -0.36 6 6
PRF1 -0.034 0.16 -10000 0 -0.53 23 23
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.038 0.14 0.39 37 -10000 0 37
KIRREL -0.058 0.19 -10000 0 -0.54 34 34
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.038 0.14 -10000 0 -0.39 37 37
PLCG1 0.011 0.037 -10000 0 -0.6 1 1
ARRB2 0.012 0.027 -10000 0 -0.43 1 1
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.036 0.14 -10000 0 -0.35 37 37
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.005 0.094 -10000 0 -0.28 24 24
FYN -0.02 0.1 -10000 0 -0.32 24 24
mol:Ca2+ -0.019 0.11 -10000 0 -0.34 24 24
mol:DAG -0.019 0.11 -10000 0 -0.34 24 24
NPHS2 -0.005 0.019 -10000 0 -10000 0 0
mol:IP3 -0.019 0.11 -10000 0 -0.34 24 24
regulation of endocytosis -0.011 0.099 -10000 0 -0.29 24 24
Nephrin/NEPH1/podocin/Cholesterol -0.026 0.11 -10000 0 -0.29 37 37
establishment of cell polarity -0.038 0.14 -10000 0 -0.39 37 37
Nephrin/NEPH1/podocin/NCK1-2 -0.008 0.1 -10000 0 -0.3 24 24
Nephrin/NEPH1/beta Arrestin2 -0.01 0.1 -10000 0 -0.29 24 24
NPHS1 0.001 0.062 -10000 0 -0.48 4 4
Nephrin/NEPH1/podocin -0.02 0.1 -10000 0 -0.32 24 24
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.011 0.037 -10000 0 -0.6 1 1
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.018 0.11 -10000 0 -0.34 24 24
CD2AP -0.018 0.13 -10000 0 -0.58 14 14
Nephrin/NEPH1/podocin/GRB2 -0.017 0.11 -10000 0 -0.32 24 24
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.042 0.13 -10000 0 -0.3 47 47
cytoskeleton organization -0.005 0.11 -10000 0 -0.32 24 24
Nephrin/NEPH1 -0.025 0.1 -10000 0 -0.28 37 37
Nephrin/NEPH1/ZO-1 -0.02 0.12 -10000 0 -0.35 24 24
Syndecan-2-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
Syndecan-2/Fibronectin -0.022 0.12 -9999 0 -0.32 36 36
EPHB2 -0.077 0.2 -9999 0 -0.53 44 44
Syndecan-2/TACI -0.029 0.12 -9999 0 -0.29 43 43
LAMA1 -0.08 0.21 -9999 0 -0.54 45 45
Syndecan-2/alpha2 ITGB1 -0.039 0.16 -9999 0 -0.35 44 44
HRAS 0.013 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.009 0.089 -9999 0 -0.35 17 17
ITGA5 0.011 0.037 -9999 0 -0.6 1 1
BAX 0.01 0.094 -9999 0 -0.62 1 1
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.001 0.084 -9999 0 -0.31 18 18
LAMA3 -0.028 0.15 -9999 0 -0.56 19 19
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.053 -9999 0 -0.6 2 2
Syndecan-2/MMP2 -0.035 0.14 -9999 0 -0.33 44 44
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.027 0.13 -9999 0 -0.39 30 30
dendrite morphogenesis -0.055 0.16 -9999 0 -0.36 55 55
Syndecan-2/GM-CSF -0.01 0.1 -9999 0 -0.33 23 23
determination of left/right symmetry -0.009 0.1 -9999 0 -0.41 17 17
Syndecan-2/PKC delta 0.001 0.09 -9999 0 -0.34 17 17
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.002 0.092 -9999 0 -0.34 14 14
MAPK1 -0.001 0.091 -9999 0 -0.34 14 14
Syndecan-2/RACK1 0.009 0.078 -9999 0 -0.3 14 14
NF1 0.006 0.064 -9999 0 -0.6 3 3
FGFR/FGF/Syndecan-2 -0.009 0.1 -9999 0 -0.41 17 17
ITGA2 -0.048 0.18 -9999 0 -0.55 29 29
MAPK8 0.002 0.1 -9999 0 -0.38 17 17
Syndecan-2/alpha2/beta1 Integrin -0.066 0.18 -9999 0 -0.37 56 56
Syndecan-2/Kininogen -0.02 0.11 -9999 0 -0.32 29 29
ITGB1 0.011 0.037 -9999 0 -0.6 1 1
SRC 0.013 0.076 -9999 0 -0.28 15 15
Syndecan-2/CASK/Protein 4.1 0.001 0.082 -9999 0 -0.31 17 17
extracellular matrix organization -0.002 0.093 -9999 0 -0.34 19 19
actin cytoskeleton reorganization -0.022 0.12 -9999 0 -0.31 36 36
Syndecan-2/Caveolin-2/Ras 0.007 0.087 -9999 0 -0.32 16 16
Syndecan-2/Laminin alpha3 -0.025 0.13 -9999 0 -0.35 35 35
Syndecan-2/RasGAP 0.014 0.077 -9999 0 -0.29 15 15
alpha5/beta1 Integrin 0.016 0.039 -9999 0 -0.43 2 2
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.055 0.16 -9999 0 -0.36 55 55
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.02 0.077 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.011 0.037 -9999 0 -0.6 1 1
TNFRSF13B -0.036 0.14 -9999 0 -0.43 28 28
RASA1 0.011 0.037 -9999 0 -0.6 1 1
alpha2/beta1 Integrin -0.027 0.13 -9999 0 -0.39 30 30
Syndecan-2/Synbindin 0.001 0.09 -9999 0 -0.34 17 17
TGFB1 0.009 0.046 -9999 0 -0.51 2 2
CASP3 0.009 0.082 -9999 0 -0.32 14 14
FN1 -0.024 0.13 -9999 0 -0.48 20 20
Syndecan-2/IL8 -0.055 0.16 -9999 0 -0.39 37 37
SDC2 -0.009 0.1 -9999 0 -0.41 17 17
KNG1 -0.02 0.11 -9999 0 -0.43 17 17
Syndecan-2/Neurofibromin -0.004 0.1 -9999 0 -0.36 19 19
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.004 0.071 -9999 0 -0.43 7 7
Syndecan-2/TGFB1 -0.002 0.094 -9999 0 -0.34 19 19
Syndecan-2/Syntenin/PI-4-5-P2 -0.001 0.084 -9999 0 -0.31 18 18
Syndecan-2/Ezrin 0.009 0.082 -9999 0 -0.32 14 14
PRKACA 0.005 0.092 -9999 0 -0.34 17 17
angiogenesis -0.054 0.15 -9999 0 -0.39 37 37
MMP2 -0.044 0.17 -9999 0 -0.53 28 28
IL8 -0.076 0.2 -9999 0 -0.53 44 44
calcineurin-NFAT signaling pathway -0.029 0.12 -9999 0 -0.29 43 43
BCR signaling pathway

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
JUN -0.047 0.14 -10000 0 -0.38 22 22
IKBKB -0.024 0.071 -10000 0 -0.25 2 2
AKT1 -0.061 0.11 0.22 1 -0.24 34 35
IKBKG -0.023 0.074 -10000 0 -0.27 2 2
CALM1 -0.042 0.11 0.26 2 -0.34 15 17
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
MAP3K1 -0.08 0.2 -10000 0 -0.54 27 27
MAP3K7 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.051 0.11 0.26 2 -0.36 15 17
DOK1 0.011 0.037 -10000 0 -0.6 1 1
AP-1 -0.022 0.082 -10000 0 -0.24 11 11
LYN 0.011 0.037 -10000 0 -0.6 1 1
BLNK 0 0.09 -10000 0 -0.6 6 6
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.12 0.22 -10000 0 -0.42 84 84
CD22 -0.17 0.24 -10000 0 -0.59 45 45
CAMK2G -0.034 0.1 0.26 2 -0.36 8 10
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D 0 0.091 -10000 0 -0.6 6 6
SHC/GRB2/SOS1 -0.086 0.14 -10000 0 -0.4 23 23
GO:0007205 -0.052 0.11 0.26 2 -0.37 15 17
SYK 0.006 0.064 -10000 0 -0.6 3 3
ELK1 -0.043 0.11 0.26 2 -0.35 15 17
NFATC1 -0.084 0.19 -10000 0 -0.47 35 35
B-cell antigen/BCR complex -0.12 0.22 -10000 0 -0.42 84 84
PAG1/CSK 0.013 0.047 -10000 0 -0.32 5 5
NFKBIB 0 0.028 -10000 0 -0.13 1 1
HRAS -0.043 0.11 0.24 2 -0.34 15 17
NFKBIA 0 0.027 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.006 0.024 -10000 0 -0.17 1 1
RasGAP/Csk -0.084 0.19 -10000 0 -0.49 30 30
mol:GDP -0.048 0.1 0.27 2 -0.35 15 17
PTEN 0.006 0.064 -10000 0 -0.6 3 3
CD79B -0.037 0.15 -10000 0 -0.48 27 27
NF-kappa-B/RelA/I kappa B alpha 0.006 0.024 -10000 0 -0.17 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.12 0.21 -10000 0 -0.49 49 49
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
mol:IP3 -0.052 0.11 0.27 2 -0.37 15 17
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.053 0.12 0.26 2 -0.39 16 18
CHUK -0.023 0.074 -10000 0 -0.26 3 3
IBTK 0.006 0.064 -10000 0 -0.6 3 3
CARD11/BCL10/MALT1/TAK1 -0.071 0.11 -10000 0 -0.39 17 17
PTPN6 -0.14 0.24 -10000 0 -0.58 42 42
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 0.003 0.031 -10000 0 -0.1 12 12
VAV2 -0.12 0.24 -10000 0 -0.6 41 41
ubiquitin-dependent protein catabolic process 0.004 0.027 -10000 0 -0.13 1 1
BTK -0.035 0.18 0.36 2 -1 9 11
CD19 -0.16 0.24 -10000 0 -0.58 48 48
MAP4K1 -0.005 0.095 -10000 0 -0.48 10 10
CD72 0.004 0.07 -10000 0 -0.5 5 5
PAG1 0.004 0.066 -10000 0 -0.47 5 5
MAPK14 -0.062 0.17 -10000 0 -0.45 26 26
SH3BP5 0.006 0.064 -10000 0 -0.6 3 3
PIK3AP1 -0.054 0.13 -10000 0 -0.41 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.07 0.18 -10000 0 -0.43 38 38
RAF1 -0.034 0.11 0.24 1 -0.36 9 10
RasGAP/p62DOK/SHIP -0.11 0.18 -10000 0 -0.5 32 32
CD79A -0.13 0.24 -10000 0 -0.5 76 76
re-entry into mitotic cell cycle -0.023 0.082 -10000 0 -0.24 11 11
RASA1 0.011 0.037 -10000 0 -0.6 1 1
MAPK3 -0.018 0.093 0.23 1 -0.33 5 6
MAPK1 -0.017 0.093 0.23 1 -0.33 5 6
CD72/SHP1 -0.13 0.23 -10000 0 -0.58 39 39
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
MAPK8 -0.065 0.17 -10000 0 -0.45 28 28
actin cytoskeleton organization -0.1 0.21 -10000 0 -0.51 39 39
NF-kappa-B/RelA 0.017 0.044 -10000 0 -0.2 1 1
Calcineurin -0.035 0.1 -10000 0 -0.38 10 10
PI3K -0.16 0.19 -10000 0 -0.48 54 54
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.054 0.12 0.24 1 -0.42 15 16
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.089 0.22 -10000 0 -0.69 21 21
DAPP1 -0.11 0.23 -10000 0 -0.83 17 17
cytokine secretion -0.078 0.17 -10000 0 -0.43 35 35
mol:DAG -0.052 0.11 0.27 2 -0.37 15 17
PLCG2 0.004 0.07 -10000 0 -0.5 5 5
MAP2K1 -0.025 0.1 0.24 1 -0.36 6 7
B-cell antigen/BCR complex/FcgammaRIIB -0.11 0.22 -10000 0 -0.47 60 60
mol:PI-3-4-5-P3 -0.12 0.13 0.29 1 -0.33 54 55
ETS1 -0.027 0.095 0.25 2 -0.35 6 8
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.077 0.18 -10000 0 -0.37 58 58
B-cell antigen/BCR complex/LYN -0.12 0.21 -10000 0 -0.45 55 55
MALT1 0.001 0.076 -10000 0 -0.46 7 7
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 -0.11 0.22 -10000 0 -0.55 39 39
B-cell antigen/BCR complex/LYN/SYK -0.16 0.22 -10000 0 -0.59 39 39
CARD11 -0.071 0.14 -10000 0 -0.39 27 27
FCGR2B -0.024 0.14 -10000 0 -0.57 17 17
PPP3CA 0.004 0.074 -10000 0 -0.6 4 4
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex -0.004 0.034 -10000 0 -10000 0 0
PTPRC -0.039 0.16 -10000 0 -0.54 25 25
PDPK1 -0.061 0.1 0.2 1 -0.24 33 34
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC -0.003 0.098 -10000 0 -0.6 7 7
POU2F2 0.007 0.024 -10000 0 -0.1 3 3
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.027 0.14 -10000 0 -0.35 39 39
ER alpha/Gai/GDP/Gbeta gamma -0.044 0.18 -10000 0 -0.42 39 39
AKT1 -0.093 0.3 -10000 0 -0.82 37 37
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.098 0.3 -10000 0 -0.84 37 37
mol:Ca2+ -0.037 0.18 -10000 0 -0.53 22 22
IGF1R -0.019 0.14 -10000 0 -0.6 14 14
E2/ER alpha (dimer)/Striatin -0.043 0.14 -10000 0 -0.38 41 41
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.088 0.28 0.78 37 -10000 0 37
RhoA/GTP -0.041 0.1 -10000 0 -0.55 2 2
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.08 0.16 -10000 0 -0.46 40 40
regulation of stress fiber formation -0.005 0.1 0.41 4 -10000 0 4
E2/ERA-ERB (dimer) -0.037 0.14 -10000 0 -0.38 37 37
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.032 0.12 -10000 0 -0.34 37 37
pseudopodium formation 0.005 0.1 -10000 0 -0.41 4 4
E2/ER alpha (dimer)/PELP1 -0.036 0.13 -10000 0 -0.37 37 37
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 -0.007 0.1 -10000 0 -0.51 10 10
GNAO1 -0.013 0.11 -10000 0 -0.48 14 14
HRAS 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.048 0.2 -10000 0 -0.52 38 38
E2/ER beta (dimer) 0.008 0.028 -10000 0 -0.44 1 1
mol:GDP -0.061 0.15 -10000 0 -0.43 37 37
mol:NADP -0.048 0.2 -10000 0 -0.52 38 38
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
mol:IP3 -0.04 0.18 -10000 0 -0.56 22 22
IGF-1R heterotetramer -0.019 0.14 -10000 0 -0.6 14 14
PLCB1 -0.044 0.18 -10000 0 -0.57 22 22
PLCB2 -0.029 0.16 -10000 0 -0.58 16 16
IGF1 -0.058 0.18 -10000 0 -0.51 36 36
mol:L-citrulline -0.048 0.2 -10000 0 -0.52 38 38
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.008 0.12 -10000 0 -0.64 5 5
JNK cascade 0.008 0.028 -10000 0 -0.44 1 1
BCAR1 0.011 0.037 -10000 0 -0.6 1 1
ESR2 0.011 0.037 -10000 0 -0.6 1 1
GNAQ 0.006 0.064 -10000 0 -0.6 3 3
ESR1 -0.071 0.21 -10000 0 -0.6 37 37
Gq family/GDP/Gbeta gamma -0.018 0.15 -10000 0 -0.49 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.008 0.11 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.079 0.16 -10000 0 -0.46 39 39
GNAZ -0.015 0.12 -10000 0 -0.53 14 14
E2/ER alpha (dimer) -0.053 0.16 -10000 0 -0.44 37 37
STRN 0.002 0.083 -10000 0 -0.6 5 5
GNAL 0.005 0.061 -10000 0 -0.43 5 5
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.013 0.037 -10000 0 -0.28 4 4
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.11 -10000 0 -0.54 11 11
HBEGF -0.063 0.18 -10000 0 -0.49 27 27
cAMP biosynthetic process -0.046 0.11 -10000 0 -0.31 37 37
SRC -0.036 0.17 -10000 0 -0.48 18 18
PI3K -0.01 0.1 -10000 0 -0.37 20 20
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.061 0.15 -10000 0 -0.4 37 37
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.095 0.17 -10000 0 -0.44 41 41
Gs family/GTP -0.046 0.11 -10000 0 -0.31 37 37
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.043 -10000 0 -0.33 4 4
vasodilation -0.044 0.19 -10000 0 -0.49 38 38
mol:DAG -0.04 0.18 -10000 0 -0.56 22 22
Gs family/GDP/Gbeta gamma -0.059 0.14 -10000 0 -0.38 37 37
MSN 0.004 0.11 -10000 0 -0.44 4 4
Gq family/GTP -0.034 0.16 -10000 0 -0.61 15 15
mol:PI-3-4-5-P3 -0.092 0.29 -10000 0 -0.8 37 37
NRAS 0.004 0.074 -10000 0 -0.6 4 4
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.044 0.19 0.49 38 -10000 0 38
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
RhoA/GDP -0.057 0.14 -10000 0 -0.4 37 37
NOS3 -0.052 0.21 -10000 0 -0.55 38 38
GNA11 -0.018 0.13 -10000 0 -0.57 14 14
MAPKKK cascade -0.052 0.23 -10000 0 -0.59 38 38
E2/ER alpha (dimer)/PELP1/Src -0.083 0.17 -10000 0 -0.48 39 39
ruffle organization 0.005 0.1 -10000 0 -0.41 4 4
ROCK2 -0.002 0.11 -10000 0 -0.51 3 3
GNA14 -0.013 0.12 -10000 0 -0.57 12 12
GNA15 -0.001 0.087 -10000 0 -0.53 7 7
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.072 0.19 -10000 0 -0.49 27 27
MMP2 -0.054 0.19 -10000 0 -0.52 25 25
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.007 0.43 -9999 0 -1.1 19 19
PLK1 0.021 0.19 -9999 0 -1.5 4 4
BIRC5 0.026 0.17 -9999 0 -1.5 3 3
HSPA1B -0.014 0.44 -9999 0 -1.1 22 22
MAP2K1 0.028 0.036 -9999 0 -10000 0 0
BRCA2 -0.043 0.49 -9999 0 -1.2 29 29
FOXM1 -0.059 0.58 -9999 0 -1.5 23 23
XRCC1 -0.007 0.43 -9999 0 -1.1 19 19
FOXM1B/p19 -0.21 0.4 -9999 0 -1.2 29 29
Cyclin D1/CDK4 -0.044 0.44 -9999 0 -1.1 23 23
CDC2 -0.017 0.45 -9999 0 -1.1 22 22
TGFA -0.066 0.46 -9999 0 -1.1 26 26
SKP2 -0.013 0.44 -9999 0 -1.1 21 21
CCNE1 -0.022 0.14 -9999 0 -0.54 18 18
CKS1B -0.019 0.45 -9999 0 -1.1 22 22
RB1 -0.13 0.26 -9999 0 -0.92 19 19
FOXM1C/SP1 -0.037 0.49 -9999 0 -1.3 23 23
AURKB 0.017 0.2 -9999 0 -1.4 5 5
CENPF -0.023 0.47 -9999 0 -1.2 21 21
CDK4 0.018 0.015 -9999 0 -10000 0 0
MYC -0.012 0.41 -9999 0 -0.96 25 25
CHEK2 0.027 0.047 -9999 0 -0.45 1 1
ONECUT1 -0.042 0.44 -9999 0 -1.1 27 27
CDKN2A -0.11 0.21 -9999 0 -0.47 64 64
LAMA4 -0.009 0.43 -9999 0 -1.1 19 19
FOXM1B/HNF6 -0.071 0.52 -9999 0 -1.3 26 26
FOS -0.028 0.46 -9999 0 -1.2 20 20
SP1 0.014 0.004 -9999 0 -10000 0 0
CDC25B -0.009 0.43 -9999 0 -1.1 19 19
response to radiation 0.012 0.033 -9999 0 -10000 0 0
CENPB -0.007 0.43 -9999 0 -1.1 19 19
CENPA -0.02 0.46 -9999 0 -1.2 21 21
NEK2 -0.015 0.45 -9999 0 -1.2 20 20
HIST1H2BA -0.015 0.43 -9999 0 -1.1 23 23
CCNA2 0 0.1 -9999 0 -0.61 7 7
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.034 0.5 -9999 0 -1.4 20 20
CCNB2 -0.013 0.44 -9999 0 -1.2 20 20
CCNB1 -0.016 0.45 -9999 0 -1.2 20 20
ETV5 -0.045 0.49 -9999 0 -1.2 29 29
ESR1 -0.1 0.57 -9999 0 -1.2 47 47
CCND1 -0.045 0.46 -9999 0 -1.1 23 23
GSK3A 0.027 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.005 0.12 -9999 0 -0.4 18 18
CDK2 0.014 0.03 -9999 0 -0.45 1 1
G2/M transition of mitotic cell cycle 0.014 0.039 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.37 -9999 0 -1.2 23 23
GAS1 -0.083 0.52 -9999 0 -1.2 34 34
MMP2 -0.056 0.5 -9999 0 -1.2 31 31
RB1/FOXM1C -0.058 0.46 -9999 0 -1.1 29 29
CREBBP 0.013 0 -9999 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.012 0.11 -10000 0 -0.5 13 13
GNB1/GNG2 -0.05 0.07 -10000 0 -0.2 32 32
AKT1 -0.019 0.098 -10000 0 -0.22 11 11
EGF -0.083 0.2 -10000 0 -0.5 50 50
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.015 0.075 -10000 0 -0.44 2 2
mol:Ca2+ -0.046 0.14 -10000 0 -0.3 42 42
LYN 0.021 0.063 -10000 0 -0.44 1 1
RhoA/GTP -0.031 0.046 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.052 0.16 -10000 0 -0.35 41 41
GNG2 -0.007 0.1 -10000 0 -0.52 10 10
ARRB2 0.012 0.027 -10000 0 -0.43 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.12 -10000 0 -0.39 20 20
G beta5/gamma2 -0.063 0.092 -10000 0 -0.26 30 30
PRKCH -0.052 0.16 -10000 0 -0.35 40 40
DNM1 -0.006 0.092 -10000 0 -0.45 11 11
TXA2/TP beta/beta Arrestin3 -0.009 0.031 -10000 0 -0.24 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.033 0.16 -10000 0 -0.56 21 21
G12 family/GTP -0.076 0.11 -10000 0 -0.31 41 41
ADRBK1 0.012 0.027 -10000 0 -0.43 1 1
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.015 0.034 -10000 0 -0.37 2 2
mol:GDP 0.022 0.091 0.3 5 -10000 0 5
mol:NADP 0.006 0.06 -10000 0 -0.47 4 4
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.044 0.17 -10000 0 -0.53 28 28
mol:IP3 -0.061 0.17 -10000 0 -0.38 42 42
cell morphogenesis 0.015 0.033 -10000 0 -0.37 2 2
PLCB2 -0.087 0.22 -10000 0 -0.51 42 42
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.027 0.11 -10000 0 -0.41 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.014 0.072 -10000 0 -0.36 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.006 0.06 -10000 0 -0.47 4 4
PRKCB1 -0.059 0.16 -10000 0 -0.37 42 42
GNAQ 0.006 0.064 -10000 0 -0.6 3 3
mol:L-citrulline 0.006 0.06 -10000 0 -0.47 4 4
TXA2/TXA2-R family -0.091 0.22 -10000 0 -0.54 41 41
LCK 0.007 0.088 -10000 0 -0.44 3 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.004 0.064 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.048 -10000 0 -0.47 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.069 -10000 0 -0.42 1 1
MAPK14 -0.027 0.11 -10000 0 -0.24 20 20
TGM2/GTP -0.074 0.19 -10000 0 -0.44 43 43
MAPK11 -0.028 0.11 -10000 0 -0.23 30 30
ARHGEF1 -0.02 0.085 -10000 0 -0.19 16 16
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.062 0.17 -10000 0 -0.39 41 41
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.041 0.13 -10000 0 -0.29 40 40
cAMP biosynthetic process -0.062 0.16 -10000 0 -0.36 43 43
Gq family/GTP/EBP50 -0.007 0.092 -10000 0 -0.28 21 21
actin cytoskeleton reorganization 0.015 0.033 -10000 0 -0.37 2 2
SRC 0.021 0.059 -10000 0 -10000 0 0
GNB5 0.009 0.053 -10000 0 -0.6 2 2
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.008 0.092 -10000 0 -0.32 5 5
VCAM1 -0.057 0.16 -10000 0 -0.36 41 41
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.12 -10000 0 -0.39 20 20
platelet activation -0.036 0.14 -10000 0 -0.3 41 41
PGI2/IP 0.004 0.043 -10000 0 -0.34 4 4
PRKACA -0.005 0.078 -10000 0 -0.28 17 17
Gq family/GDP/G beta5/gamma2 -0.011 0.11 -10000 0 -0.37 20 20
TXA2/TP beta/beta Arrestin2 -0.011 0.047 -10000 0 -0.4 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.074 -10000 0 -0.26 4 4
mol:DAG -0.067 0.18 -10000 0 -0.42 43 43
EGFR -0.002 0.094 -10000 0 -0.57 7 7
TXA2/TP alpha -0.085 0.21 -10000 0 -0.49 43 43
Gq family/GTP -0.025 0.079 -10000 0 -0.25 26 26
YES1 0.021 0.059 -10000 0 -10000 0 0
GNAI2/GTP -0.016 0.052 -10000 0 -10000 0 0
PGD2/DP -0.024 0.11 -10000 0 -0.41 21 21
SLC9A3R1 0.005 0.07 -10000 0 -0.56 4 4
FYN 0.022 0.058 -10000 0 -10000 0 0
mol:NO 0.006 0.06 -10000 0 -0.47 4 4
GNA15 -0.001 0.087 -10000 0 -0.53 7 7
PGK/cGMP -0.022 0.11 -10000 0 -0.32 31 31
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.002 0.098 -10000 0 -0.5 2 2
NOS3 0.006 0.06 -10000 0 -0.47 4 4
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.056 0.16 -10000 0 -0.35 42 42
PRKCB -0.062 0.17 -10000 0 -0.37 41 41
PRKCE -0.048 0.15 -10000 0 -0.35 40 40
PRKCD -0.056 0.16 -10000 0 -0.38 41 41
PRKCG -0.08 0.18 -10000 0 -0.42 41 41
muscle contraction -0.083 0.21 -10000 0 -0.5 41 41
PRKCZ -0.05 0.15 -10000 0 -0.34 41 41
ARR3 0.004 0.028 -10000 0 -0.43 1 1
TXA2/TP beta 0.01 0.068 -10000 0 -10000 0 0
PRKCQ -0.074 0.18 -10000 0 -0.39 47 47
MAPKKK cascade -0.078 0.2 -10000 0 -0.46 42 42
SELE -0.058 0.16 -10000 0 -0.35 44 44
TP beta/GNAI2/GDP/G beta/gamma 0.013 0.087 -10000 0 -0.5 2 2
ROCK1 0.009 0.053 -10000 0 -0.6 2 2
GNA14 -0.013 0.12 -10000 0 -0.57 12 12
chemotaxis -0.1 0.25 -10000 0 -0.62 41 41
GNA12 0.011 0.037 -10000 0 -0.6 1 1
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.018 0.13 -10000 0 -0.57 14 14
Rac1/GTP 0.008 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.013 0.051 -9999 0 -0.35 5 5
VLDLR -0.005 0.1 -9999 0 -0.6 8 8
CRKL 0.012 0.027 -9999 0 -0.43 1 1
LRPAP1 0.006 0.064 -9999 0 -0.6 3 3
FYN 0.012 0.027 -9999 0 -0.43 1 1
ITGA3 -0.004 0.095 -9999 0 -0.5 9 9
RELN/VLDLR/Fyn -0.091 0.16 -9999 0 -0.37 48 48
MAPK8IP1/MKK7/MAP3K11/JNK1 0.023 0.072 -9999 0 -10000 0 0
AKT1 -0.057 0.12 -9999 0 -0.39 6 6
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.008 0.053 -9999 0 -0.49 3 3
RELN/LRP8/DAB1 -0.081 0.15 -9999 0 -0.34 47 47
LRPAP1/LRP8 0.005 0.077 -9999 0 -0.38 10 10
RELN/LRP8/DAB1/Fyn -0.07 0.14 -9999 0 -0.32 48 48
DAB1/alpha3/beta1 Integrin -0.096 0.13 -9999 0 -0.43 11 11
long-term memory -0.12 0.18 -9999 0 -0.48 28 28
DAB1/LIS1 -0.092 0.12 -9999 0 -0.42 6 6
DAB1/CRLK/C3G -0.088 0.12 -9999 0 -0.4 7 7
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
DAB1/NCK2 -0.093 0.13 -9999 0 -0.42 6 6
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.089 0.21 -9999 0 -0.5 52 52
CDK5R1 0.004 0.07 -9999 0 -0.5 5 5
RELN -0.16 0.25 -9999 0 -0.51 86 86
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
RELN/LRP8/Fyn -0.087 0.16 -9999 0 -0.38 46 46
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.47 21 21
MAPK8 0.004 0.074 -9999 0 -0.6 4 4
RELN/VLDLR/DAB1 -0.084 0.15 -9999 0 -0.34 49 49
ITGB1 0.011 0.037 -9999 0 -0.6 1 1
MAP1B -0.1 0.18 -9999 0 -0.38 53 53
RELN/LRP8 -0.091 0.17 -9999 0 -0.38 48 48
GRIN2B/RELN/LRP8/DAB1/Fyn -0.081 0.16 -9999 0 -0.35 40 40
PI3K -0.01 0.1 -9999 0 -0.37 20 20
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.005 0.074 -9999 0 -0.36 10 10
RAP1A -0.051 0.14 -9999 0 -0.44 2 2
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 -0.007 0.11 -9999 0 -0.58 9 9
CRLK/C3G 0.019 0.019 -9999 0 -0.3 1 1
GRIN2B -0.023 0.11 -9999 0 -0.43 18 18
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.024 0.097 -9999 0 -0.37 4 4
neuron adhesion -0.046 0.14 -9999 0 -0.42 6 6
LRP8 0 0.084 -9999 0 -0.5 7 7
GSK3B -0.047 0.12 -9999 0 -0.37 6 6
RELN/VLDLR/DAB1/Fyn -0.073 0.14 -9999 0 -0.32 50 50
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.067 0.13 -9999 0 -0.28 62 62
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT -0.006 0.11 -9999 0 -0.45 14 14
neuron migration -0.051 0.15 -9999 0 -0.41 6 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.024 0.098 -9999 0 -0.38 4 4
RELN/VLDLR -0.085 0.16 -9999 0 -0.34 56 56
Canonical Wnt signaling pathway

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
HDAC1 0.02 0.029 -10000 0 -10000 0 0
AES 0.017 0.044 -10000 0 -0.58 1 1
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.011 0.061 -10000 0 -0.35 7 7
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.085 0.21 -10000 0 -0.52 49 49
TLE1 0.016 0.044 -10000 0 -0.6 1 1
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.07 0.099 0.38 3 -0.43 2 5
WIF1 -0.28 0.26 -10000 0 -0.5 148 148
beta catenin/RanBP3 0.054 0.16 0.46 21 -0.44 1 22
KREMEN2 -0.049 0.17 -10000 0 -0.49 33 33
DKK1 -0.2 0.26 -10000 0 -0.49 114 114
beta catenin/beta TrCP1 0.073 0.094 0.36 3 -0.39 2 5
FZD1 0 0.084 -10000 0 -0.5 7 7
AXIN2 -0.067 0.28 -10000 0 -1.2 11 11
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.009 0.052 -10000 0 -0.59 2 2
Axin1/APC/GSK3/beta catenin 0.028 0.052 -10000 0 -0.5 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.14 0.32 1 -0.42 9 10
Axin1/APC/GSK3 0.051 0.066 0.28 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.056 0.068 0.32 1 -0.45 1 2
HNF1A -0.056 0.2 -10000 0 -0.58 33 33
CTBP1 0.019 0.023 -10000 0 -10000 0 0
MYC -0.044 0.27 -10000 0 -1.5 9 9
RANBP3 0.014 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.072 0.16 -10000 0 -0.4 39 39
NKD1 -0.11 0.2 -10000 0 -0.45 68 68
TCF4 0.013 0.067 -10000 0 -0.57 3 3
TCF3 0.016 0.04 -10000 0 -0.53 1 1
WNT1/LRP6/FZD1/Axin1 0.021 0.061 -10000 0 -0.32 3 3
Ran/GTP 0.007 0.039 -10000 0 -0.44 2 2
CtBP/CBP/TCF/TLE1/AES 0.008 0.17 0.48 14 -0.42 5 19
LEF1 -0.083 0.22 -10000 0 -0.57 45 45
DVL1 0.065 0.054 0.23 1 -0.37 1 2
CSNK2A1 0.014 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.007 0.17 -10000 0 -0.53 12 12
DKK1/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.42 56 56
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.019 0.048 -10000 0 -0.6 1 1
NLK 0.01 0.037 -10000 0 -0.6 1 1
CCND1 -0.055 0.31 -10000 0 -1.4 12 12
WNT1 0 0.071 -10000 0 -0.43 7 7
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
PPP2R5D 0.087 0.098 0.25 67 -10000 0 67
APC 0.023 0.06 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.11 0.094 0.24 61 -10000 0 61
CREBBP 0.019 0.023 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.008 0.034 -9999 0 -0.37 2 2
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.005 0.063 -9999 0 -0.3 11 11
STXBP1 -0.004 0.098 -9999 0 -0.56 8 8
ACh/CHRNA1 -0.075 0.15 -9999 0 -0.35 57 57
RAB3GAP2/RIMS1/UNC13B 0.014 0.053 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.008 0.088 -9999 0 -0.43 11 11
mol:ACh -0.012 0.043 -9999 0 -0.13 21 21
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.034 0.074 -9999 0 -0.38 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.075 0.15 -9999 0 -0.35 57 57
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.22 -9999 0 -0.52 57 57
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.085 0.15 -9999 0 -0.34 67 67
SNAP25 -0.037 0.093 -9999 0 -0.21 54 54
VAMP2 0.005 0.017 -9999 0 -0.27 1 1
SYT1 -0.12 0.23 -9999 0 -0.51 67 67
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.005 0.068 -9999 0 -0.33 10 10
STX1A/SNAP25 fragment 1/VAMP2 -0.034 0.074 -9999 0 -0.38 4 4
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.039 0.14 -10000 0 -0.38 31 31
GRB2/SOS1/SHC 0.027 0 -10000 0 -10000 0 0
HRAS 0.013 0 -10000 0 -10000 0 0
IRS1/Crk -0.037 0.14 -10000 0 -0.36 34 34
IGF-1R heterotetramer/IGF1/PTP1B -0.038 0.14 -10000 0 -0.37 31 31
AKT1 -0.033 0.14 -10000 0 -0.46 15 15
BAD -0.025 0.13 -10000 0 -0.45 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.038 0.14 -10000 0 -0.36 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.039 0.14 -10000 0 -0.36 35 35
RAF1 -0.017 0.13 -10000 0 -0.42 13 13
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.027 0.14 -10000 0 -0.35 31 31
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.048 0.15 -10000 0 -0.39 36 36
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
RPS6KB1 -0.035 0.14 -10000 0 -0.47 16 16
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.017 0.11 -10000 0 -0.37 13 13
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
HRAS/GTP -0.047 0.11 -10000 0 -0.49 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.11 -10000 0 -0.36 9 9
IGF-1R heterotetramer -0.03 0.14 -10000 0 -0.63 14 14
IGF-1R heterotetramer/IGF1/IRS/Nck -0.036 0.14 -10000 0 -0.38 31 31
Crk/p130 Cas/Paxillin -0.021 0.13 -10000 0 -0.5 10 10
IGF1R -0.03 0.14 -10000 0 -0.63 14 14
IGF1 -0.065 0.19 -10000 0 -0.53 36 36
IRS2/Crk -0.056 0.16 -10000 0 -0.36 45 45
PI3K -0.048 0.16 -10000 0 -0.37 41 41
apoptosis 0.014 0.12 0.39 13 -10000 0 13
HRAS/GDP 0.01 0 -10000 0 -10000 0 0
PRKCD -0.022 0.14 -10000 0 -0.38 31 31
RAF1/14-3-3 E -0.007 0.11 -10000 0 -0.36 13 13
BAD/14-3-3 -0.015 0.13 -10000 0 -0.41 13 13
PRKCZ -0.033 0.14 -10000 0 -0.46 15 15
Crk/p130 Cas/Paxillin/FAK1 -0.054 0.11 -10000 0 -0.42 14 14
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.03 0.15 -10000 0 -0.41 31 31
BCAR1 0.011 0.037 -10000 0 -0.6 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.033 0.14 -10000 0 -0.35 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.037 0.14 -10000 0 -0.38 31 31
GRB10 -0.003 0.098 -10000 0 -0.6 7 7
PTPN11 -0.039 0.14 -10000 0 -0.36 35 35
IRS1 -0.049 0.15 -10000 0 -0.38 36 36
IRS2 -0.067 0.16 -10000 0 -0.38 45 45
IGF-1R heterotetramer/IGF1 -0.063 0.17 -10000 0 -0.41 49 49
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.041 0.15 -10000 0 -0.43 22 22
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.03 0.16 -10000 0 -0.45 26 26
SHC1 0.013 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0.027 -10000 0 -0.43 1 1
RAS family/GTP/Tiam1 -0.025 0.097 -10000 0 -0.33 8 8
NT3 (dimer)/TRKC -0.094 0.2 -10000 0 -0.4 71 71
NT3 (dimer)/TRKB -0.14 0.22 -10000 0 -0.48 59 59
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.063 -10000 0 -10000 0 0
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.09 0.21 -10000 0 -0.49 54 54
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.038 0.16 -10000 0 -0.5 26 26
NTRK2 -0.079 0.2 -10000 0 -0.51 47 47
NTRK3 -0.069 0.19 -10000 0 -0.52 41 41
NT-4/5 (dimer)/TRKB -0.16 0.22 -10000 0 -0.46 71 71
neuron apoptosis 0.13 0.2 0.52 34 -10000 0 34
SHC 2-3/Grb2 -0.14 0.22 -10000 0 -0.58 34 34
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.14 0.2 -10000 0 -0.56 29 29
SHC3 -0.14 0.23 0.21 2 -0.57 41 43
STAT3 (dimer) 0.003 0.079 -10000 0 -0.35 12 12
NT3 (dimer)/TRKA -0.12 0.21 -10000 0 -0.46 54 54
RIN/GDP -0.02 0.076 -10000 0 -0.25 5 5
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.075 0.16 0.24 3 -0.4 32 35
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.013 0.18 -10000 0 -0.76 14 14
MAGED1 0.002 0.083 -10000 0 -0.6 5 5
PTPN11 0.011 0.037 -10000 0 -0.6 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.095 0.22 -10000 0 -0.53 52 52
SHC/GRB2/SOS1 0.027 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.06 0.17 -10000 0 -0.41 41 41
TRKA/NEDD4-2 -0.019 0.12 -10000 0 -0.36 27 27
ELMO1 0.003 0.075 -10000 0 -0.53 5 5
RhoG/GTP/ELMO1/DOCK1 0.012 0.047 -10000 0 -0.32 5 5
NGF -0.045 0.17 -10000 0 -0.56 27 27
HRAS 0.013 0 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
GAB2 0.008 0.047 -10000 0 -0.43 3 3
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.006 0.092 -10000 0 -0.45 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.078 0.15 0.23 3 -0.38 36 39
mol:GDP -0.029 0.11 -10000 0 -0.37 5 5
NGF (dimer) -0.045 0.17 -10000 0 -0.56 27 27
RhoG/GDP 0.002 0.055 -10000 0 -0.39 5 5
RIT1/GDP -0.014 0.077 -10000 0 -0.26 2 2
TIAM1 -0.003 0.095 -10000 0 -0.54 8 8
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
BDNF (dimer)/TRKB -0.093 0.18 -10000 0 -0.41 42 42
KIDINS220/CRKL/C3G 0.019 0.019 -10000 0 -0.3 1 1
SHC/RasGAP 0.018 0.028 -10000 0 -0.43 1 1
FRS2 family/SHP2 0.024 0.034 -10000 0 -0.36 2 2
SHC/GRB2/SOS1/GAB1 0.034 0 -10000 0 -10000 0 0
RIT1/GTP 0.01 0 -10000 0 -10000 0 0
NT3 (dimer) -0.064 0.18 -10000 0 -0.5 40 40
RAP1/GDP -0.03 0.051 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0.027 -10000 0 -0.43 1 1
BDNF (dimer) -0.089 0.21 -10000 0 -0.49 54 54
ubiquitin-dependent protein catabolic process -0.043 0.15 -10000 0 -0.39 32 32
Schwann cell development -0.04 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.033 0.022 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.029 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.18 -10000 0 -0.48 43 43
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.076 -10000 0 -10000 0 0
STAT3 0.003 0.079 -10000 0 -0.35 12 12
axon guidance -0.15 0.17 -10000 0 -0.46 43 43
MAPK3 -0.049 0.16 -10000 0 -0.37 41 41
MAPK1 -0.048 0.16 -10000 0 -0.37 41 41
CDC42/GDP -0.015 0.079 -10000 0 -0.29 3 3
NTF3 -0.064 0.18 -10000 0 -0.5 40 40
NTF4 -0.096 0.22 -10000 0 -0.53 52 52
NGF (dimer)/TRKA/FAIM -0.043 0.15 -10000 0 -0.39 32 32
PI3K -0.01 0.1 -10000 0 -0.37 20 20
FRS3 0.011 0.037 -10000 0 -0.6 1 1
FAIM 0.011 0.037 -10000 0 -0.6 1 1
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.15 0.19 0.24 3 -0.42 68 71
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.087 0.19 -10000 0 -0.45 45 45
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.011 0.037 -10000 0 -0.6 1 1
RAS family/GTP -0.015 0.074 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.077 -10000 0 -0.26 2 2
NGF (dimer)/TRKA/GRIT -0.05 0.15 -10000 0 -0.34 50 50
neuron projection morphogenesis -0.068 0.16 -10000 0 -0.52 11 11
NGF (dimer)/TRKA/NEDD4-2 -0.043 0.15 -10000 0 -0.39 32 32
MAP2K1 0.036 0 -10000 0 -10000 0 0
NGFR -0.093 0.21 -10000 0 -0.5 55 55
NGF (dimer)/TRKA/GIPC/GAIP -0.018 0.12 -10000 0 -0.47 6 6
RAS family/GTP/PI3K 0.008 0.08 -10000 0 -0.29 14 14
FRS2 family/SHP2/GRB2/SOS1 0.037 0.029 -10000 0 -0.3 2 2
NRAS 0.004 0.074 -10000 0 -0.6 4 4
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
PRKCI 0.002 0.075 -10000 0 -0.49 6 6
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.1 0.2 -10000 0 -0.62 32 32
RASA1 0.011 0.037 -10000 0 -0.6 1 1
TRKA/c-Abl -0.017 0.11 -10000 0 -0.36 26 26
SQSTM1 0.012 0.027 -10000 0 -0.43 1 1
BDNF (dimer)/TRKB/GIPC -0.076 0.16 -10000 0 -0.37 42 42
NGF (dimer)/TRKA/p62/Atypical PKCs -0.026 0.14 -10000 0 -0.53 5 5
MATK -0.017 0.13 -10000 0 -0.53 15 15
NEDD4L 0.011 0.037 -10000 0 -0.6 1 1
RAS family/GDP -0.029 0.051 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.097 0.16 0.26 3 -0.35 59 62
Rac1/GTP -0.11 0.11 -10000 0 -0.32 34 34
FRS2 family/SHP2/CRK family 0.036 0.032 -10000 0 -0.3 2 2
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.038 0.14 -10000 0 -0.63 12 12
HDAC1 0.013 0.011 -10000 0 -10000 0 0
AES 0.011 0.037 -10000 0 -0.59 1 1
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.01 0.11 -10000 0 -0.55 11 11
LRP6/FZD1 0.01 0.061 -10000 0 -0.36 7 7
TLE1 0.011 0.037 -10000 0 -0.6 1 1
AP1 -0.038 0.11 -10000 0 -0.34 15 15
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.014 0.12 -10000 0 -0.58 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.11 -10000 0 -0.47 4 4
NICD/RBPSUH 0.003 0.13 -10000 0 -0.63 11 11
WIF1 -0.28 0.26 -10000 0 -0.5 148 148
NOTCH1 -0.03 0.14 -10000 0 -0.67 11 11
PSENEN 0.011 0.037 -10000 0 -0.6 1 1
KREMEN2 -0.049 0.17 -10000 0 -0.49 33 33
DKK1 -0.2 0.26 -10000 0 -0.49 114 114
beta catenin/beta TrCP1 0.033 0.072 -10000 0 -0.38 2 2
APH1B 0.006 0.064 -10000 0 -0.6 3 3
APH1A 0.012 0.027 -10000 0 -0.43 1 1
AXIN1 -0.016 0.048 -10000 0 -0.24 6 6
CtBP/CBP/TCF1/TLE1/AES -0.004 0.11 0.28 2 -0.54 1 3
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.028 0.14 -10000 0 -0.48 22 22
JUN 0.008 0.053 -10000 0 -0.49 3 3
MAP3K7 0.013 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.076 -10000 0 -0.41 2 2
MAPK3 0.012 0.027 -10000 0 -0.43 1 1
DKK2/LRP6/Kremen 2 -0.073 0.16 -10000 0 -0.4 39 39
HNF1A -0.061 0.2 -10000 0 -0.59 33 33
CTBP1 0.013 0.004 -10000 0 -10000 0 0
MYC -0.033 0.26 -10000 0 -1.4 9 9
NKD1 -0.11 0.2 -10000 0 -0.45 68 68
FZD1 0 0.084 -10000 0 -0.5 7 7
NOTCH1 precursor/Deltex homolog 1 -0.009 0.15 -10000 0 -0.65 11 11
apoptosis -0.038 0.11 -10000 0 -0.34 15 15
Delta 1/NOTCHprecursor -0.007 0.14 -10000 0 -0.61 12 12
DLL1 -0.006 0.1 -10000 0 -0.56 9 9
PPARD 0.018 0.027 -10000 0 -10000 0 0
Gamma Secretase 0.034 0.044 -10000 0 -0.3 4 4
APC -0.018 0.055 -10000 0 -0.27 7 7
DVL1 -0.013 0.059 -10000 0 -0.53 2 2
CSNK2A1 0.013 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.42 56 56
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.011 0.037 -10000 0 -0.6 1 1
NLK 0.014 0.026 -10000 0 -0.36 1 1
CCND1 -0.044 0.3 -10000 0 -1.4 12 12
WNT1 -0.001 0.071 -10000 0 -0.43 7 7
Axin1/APC/beta catenin 0.012 0.076 -10000 0 -0.48 3 3
DKK2 -0.085 0.21 -10000 0 -0.52 49 49
NOTCH1 precursor/DVL1 -0.032 0.12 -10000 0 -0.57 13 13
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.039 0.14 -10000 0 -0.67 11 11
PPP2R5D 0.043 0.097 0.21 64 -0.22 1 65
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.16 -10000 0 -0.35 71 71
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.015 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.073 0.15 -10000 0 -0.34 64 64
TP53 -0.034 0.082 -10000 0 -0.41 8 8
Senescence -0.034 0.082 -10000 0 -0.41 8 8
Apoptosis -0.034 0.082 -10000 0 -0.41 8 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.043 0.091 0.27 15 -0.35 2 17
MDM4 0.013 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.061 -9999 0 -0.33 8 8
alphaV beta3 Integrin -0.051 0.16 -9999 0 -0.43 29 29
PTK2 -0.038 0.18 -9999 0 -0.55 19 19
IGF1R -0.019 0.14 -9999 0 -0.6 14 14
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.003 0.095 -9999 0 -0.54 8 8
SRC 0.011 0.037 -9999 0 -0.6 1 1
CDKN1B -0.049 0.17 -9999 0 -0.59 18 18
VEGFA 0.007 0.054 -9999 0 -0.43 4 4
ILK -0.014 0.077 -9999 0 -0.33 2 2
ROCK1 0.009 0.053 -9999 0 -0.6 2 2
AKT1 -0.005 0.071 -9999 0 -0.3 2 2
PTK2B -0.03 0.15 -9999 0 -0.53 12 12
alphaV/beta3 Integrin/JAM-A -0.04 0.15 -9999 0 -0.48 13 13
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.051 0.16 -9999 0 -0.44 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.042 0.16 -9999 0 -0.41 35 35
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.008 0.11 -9999 0 -0.39 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.054 0.17 -9999 0 -0.45 31 31
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.21 -9999 0 -0.6 31 31
PI4 Kinase 0.02 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
alphaV/beta3 Integrin/Osteopontin -0.08 0.21 -9999 0 -0.4 66 66
RPS6KB1 -0.088 0.21 -9999 0 -0.56 32 32
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.065 0.2 -9999 0 -0.56 28 28
GPR124 0.001 0.079 -9999 0 -0.51 6 6
MAPK1 -0.065 0.2 -9999 0 -0.56 28 28
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
alphaV/beta3 Integrin/Tumstatin -0.086 0.2 -9999 0 -0.47 43 43
cell adhesion -0.044 0.16 -9999 0 -0.45 24 24
ANGPTL3 -0.011 0.096 -9999 0 -0.43 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0.017 0.057 -9999 0 -0.36 3 3
IGF-1R heterotetramer -0.019 0.14 -9999 0 -0.6 14 14
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
TGFBR2 0.002 0.083 -9999 0 -0.6 5 5
ITGB3 -0.065 0.19 -9999 0 -0.5 41 41
IGF1 -0.058 0.18 -9999 0 -0.51 36 36
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.043 0.15 -9999 0 -0.42 27 27
apoptosis -0.011 0.12 -9999 0 -0.56 11 11
CD47 0.009 0.046 -9999 0 -0.51 2 2
alphaV/beta3 Integrin/CD47 -0.038 0.15 -9999 0 -0.43 24 24
VCL 0.012 0.027 -9999 0 -0.43 1 1
alphaV/beta3 Integrin/Del1 -0.077 0.2 -9999 0 -0.49 40 40
CSF1 0 0.087 -9999 0 -0.57 6 6
PIK3C2A -0.017 0.09 -9999 0 -0.48 3 3
PI4 Kinase/Pyk2 -0.064 0.13 -9999 0 -0.56 10 10
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.031 0.15 -9999 0 -0.4 28 28
FAK1/Vinculin -0.022 0.15 -9999 0 -0.42 19 19
alphaV beta3/Integrin/ppsTEM5 -0.043 0.16 -9999 0 -0.43 27 27
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.009 0.096 -9999 0 -0.43 13 13
BCAR1 0.011 0.037 -9999 0 -0.6 1 1
FGF2 -0.012 0.11 -9999 0 -0.47 14 14
F11R 0.003 0.079 -9999 0 -0.33 14 14
alphaV/beta3 Integrin/Lactadherin -0.045 0.17 -9999 0 -0.48 25 25
alphaV/beta3 Integrin/TGFBR2 -0.042 0.17 -9999 0 -0.48 24 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.012 0.095 -9999 0 -0.37 13 13
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.032 0.14 -9999 0 -0.4 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.024 0.13 -9999 0 -0.48 20 20
alphaV/beta3 Integrin/Pyk2 -0.028 0.15 -9999 0 -0.4 29 29
SDC1 -0.017 0.13 -9999 0 -0.56 14 14
VAV3 -0.005 0.12 -9999 0 -0.39 18 18
PTPN11 0.011 0.037 -9999 0 -0.6 1 1
IRS1 -0.015 0.13 -9999 0 -0.57 13 13
FAK1/Paxillin -0.022 0.14 -9999 0 -0.42 19 19
cell migration -0.012 0.14 -9999 0 -0.43 10 10
ITGAV -0.011 0.12 -9999 0 -0.57 11 11
PI3K -0.078 0.14 -9999 0 -0.49 19 19
SPP1 -0.061 0.19 -9999 0 -0.52 37 37
KDR 0.005 0.065 -9999 0 -0.51 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.011 0.12 -9999 0 -0.56 11 11
COL4A3 -0.071 0.19 -9999 0 -0.5 43 43
angiogenesis -0.06 0.2 -9999 0 -0.59 25 25
Rac1/GTP 0.002 0.12 -9999 0 -0.56 5 5
EDIL3 -0.056 0.19 -9999 0 -0.55 33 33
cell proliferation -0.042 0.17 -9999 0 -0.48 24 24
LPA4-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
ADCY4 0.01 0.049 -9999 0 -0.28 7 7
ADCY5 -0.047 0.14 -9999 0 -0.32 50 50
ADCY6 0.016 0.024 -9999 0 -0.37 1 1
ADCY7 0.015 0.029 -9999 0 -0.31 2 2
ADCY1 -0.031 0.11 -9999 0 -0.28 44 44
ADCY2 -0.036 0.12 -9999 0 -0.3 45 45
ADCY3 0.015 0.034 -9999 0 -0.37 2 2
ADCY8 0.009 0 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 -0.001 0.074 -9999 0 -0.28 17 17
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.025 0.073 -9999 0 -0.28 6 6
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 0.084 -10000 0 -0.5 7 7
Jak2/Leptin Receptor -0.054 0.16 0.2 3 -0.52 19 22
PTP1B/AKT1 -0.007 0.082 -10000 0 -0.31 10 10
FYN 0.012 0.027 -10000 0 -0.43 1 1
p210 bcr-abl/PTP1B -0.015 0.09 -10000 0 -0.31 15 15
EGFR -0.004 0.096 -10000 0 -0.58 7 7
EGF/EGFR -0.048 0.15 -10000 0 -0.39 30 30
CSF1 0 0.087 -10000 0 -0.57 6 6
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.011 0.038 -10000 0 -0.6 1 1
PTP1B/N-cadherin -0.095 0.17 -10000 0 -0.38 55 55
Insulin Receptor/Insulin -0.023 0.059 -10000 0 -0.34 3 3
HCK -0.005 0.098 -10000 0 -0.52 9 9
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.007 0.086 -10000 0 -0.32 11 11
EGF -0.084 0.2 -10000 0 -0.5 50 50
YES1 0.011 0.037 -10000 0 -0.6 1 1
CAV1 -0.014 0.1 -10000 0 -0.38 10 10
TXN 0.011 0.027 -10000 0 -0.43 1 1
PTP1B/IRS1/GRB2 -0.013 0.11 -10000 0 -0.39 14 14
cell migration 0.015 0.09 0.31 15 -10000 0 15
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.07 0.2 -10000 0 -0.56 39 39
ITGA2B -0.053 0.18 -10000 0 -0.53 32 32
CSF1R -0.015 0.13 -10000 0 -0.57 13 13
Prolactin Receptor/Prolactin -0.066 0.17 -10000 0 -0.38 56 56
FGR -0.003 0.095 -10000 0 -0.54 8 8
PTP1B/p130 Cas -0.008 0.088 -10000 0 -0.32 11 11
Crk/p130 Cas 0 0.085 -10000 0 -0.37 5 5
DOK1 -0.004 0.089 -10000 0 -0.37 7 7
JAK2 -0.05 0.17 -10000 0 -0.49 24 24
Jak2/Leptin Receptor/Leptin -0.058 0.14 -10000 0 -0.5 20 20
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
PTPN1 -0.015 0.091 -10000 0 -0.31 15 15
LYN 0.011 0.037 -10000 0 -0.6 1 1
CDH2 -0.16 0.25 -10000 0 -0.52 86 86
SRC 0.008 0.054 -10000 0 -0.68 1 1
ITGB3 -0.066 0.19 -10000 0 -0.5 41 41
CAT1/PTP1B -0.069 0.16 -10000 0 -0.43 26 26
CAPN1 0.007 0.065 -10000 0 -0.6 3 3
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.033 0.083 -10000 0 -0.34 9 9
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.054 0.14 -10000 0 -0.5 20 20
negative regulation of transcription -0.049 0.16 -10000 0 -0.48 24 24
FCGR2A 0.004 0.074 -10000 0 -0.6 4 4
FER 0.009 0.046 -10000 0 -0.52 2 2
alphaIIb/beta3 Integrin -0.085 0.18 -10000 0 -0.37 71 71
BLK -0.092 0.21 -10000 0 -0.51 52 52
Insulin Receptor/Insulin/Shc 0.017 0.024 -10000 0 -0.37 1 1
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.007 0.055 -10000 0 -0.44 4 4
BCAR1 0.011 0.037 -10000 0 -0.6 1 1
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.076 0.16 -10000 0 -0.48 22 22
PRL -0.021 0.11 -10000 0 -0.43 19 19
SOCS3 -0.043 0.27 -10000 0 -1.4 11 11
SPRY2 -0.024 0.14 -10000 0 -0.56 17 17
Insulin Receptor/Insulin/IRS1 -0.001 0.085 -10000 0 -0.36 14 14
CSF1/CSF1R -0.02 0.12 -10000 0 -0.4 15 15
Ras protein signal transduction 0.017 0.026 -10000 0 -10000 0 0
IRS1 -0.015 0.13 -10000 0 -0.57 13 13
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.001 0.066 -10000 0 -0.43 6 6
STAT5B -0.024 0.1 -10000 0 -0.3 21 21
STAT5A -0.024 0.1 -10000 0 -0.3 21 21
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.099 -10000 0 -0.34 13 13
CSN2 -0.021 0.062 0.1 1 -0.14 45 46
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
LAT -0.001 0.083 -10000 0 -0.53 5 5
YBX1 0.016 0.052 -10000 0 -0.58 2 2
LCK -0.021 0.14 -10000 0 -0.56 16 16
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.007 0.099 -10000 0 -0.5 10 10
IL6-mediated signaling events

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 -0.092 0.23 -9999 0 -0.72 11 11
CRP -0.1 0.24 -9999 0 -0.75 12 12
cell cycle arrest -0.12 0.26 -9999 0 -0.74 18 18
TIMP1 -0.08 0.22 -9999 0 -0.76 9 9
IL6ST -0.067 0.2 -9999 0 -0.57 36 36
Rac1/GDP -0.072 0.18 -9999 0 -0.5 21 21
AP1 -0.014 0.11 -9999 0 -0.46 4 4
GAB2 0.009 0.047 -9999 0 -0.43 3 3
TNFSF11 -0.21 0.41 -9999 0 -1.1 42 42
HSP90B1 0.006 0.064 -9999 0 -0.72 1 1
GAB1 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.074 0.21 -9999 0 -0.59 28 28
AKT1 0.031 0.057 -9999 0 -10000 0 0
FOXO1 0.035 0.059 -9999 0 -10000 0 0
MAP2K6 -0.083 0.2 -9999 0 -0.54 30 30
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.074 0.19 -9999 0 -0.55 17 17
MITF -0.071 0.18 -9999 0 -0.48 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.012 0.093 -9999 0 -1.4 1 1
CEBPB 0.016 0.038 -9999 0 -0.6 1 1
GRB2/SOS1/GAB family/SHP2 -0.008 0.07 -9999 0 -10000 0 0
STAT3 -0.12 0.27 -9999 0 -0.79 18 18
STAT1 -0.011 0.068 -9999 0 -1 1 1
CEBPD -0.098 0.24 -9999 0 -0.78 13 13
PIK3CA 0.011 0.039 -9999 0 -0.43 2 2
PI3K -0.007 0.1 -9999 0 -0.37 20 20
JUN 0.007 0.053 -9999 0 -0.49 3 3
PIAS3/MITF -0.061 0.17 -9999 0 -0.48 21 21
MAPK11 -0.077 0.21 -9999 0 -0.61 28 28
STAT3 (dimer)/FOXO1 -0.059 0.22 -9999 0 -0.65 10 10
GRB2/SOS1/GAB family -0.067 0.13 -9999 0 -0.48 14 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.067 0.17 -9999 0 -0.49 21 21
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 -0.007 0.11 -9999 0 -0.6 9 9
LBP -0.18 0.34 -9999 0 -0.88 38 38
PIK3R1 -0.023 0.14 -9999 0 -0.53 18 18
JAK1 0.004 0.072 -9999 0 -0.57 4 4
MYC -0.11 0.28 -9999 0 -0.98 15 15
FGG -0.11 0.24 -9999 0 -0.77 11 11
macrophage differentiation -0.12 0.26 -9999 0 -0.74 18 18
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.08 0.2 -9999 0 -0.53 24 24
JUNB -0.094 0.23 -9999 0 -0.73 13 13
FOS -0.028 0.14 -9999 0 -0.48 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.076 0.18 -9999 0 -0.47 27 27
STAT1/PIAS1 -0.065 0.16 -9999 0 -0.45 20 20
GRB2/SOS1/GAB family/SHP2/PI3K 0.02 0.059 -9999 0 -0.3 2 2
STAT3 (dimer) -0.12 0.27 -9999 0 -0.78 18 18
PRKCD -0.078 0.21 -9999 0 -0.65 12 12
IL6R -0.025 0.14 -9999 0 -0.54 18 18
SOCS3 -0.086 0.29 -9999 0 -0.99 18 18
gp130 (dimer)/JAK1/JAK1/LMO4 -0.037 0.15 -9999 0 -0.38 38 38
Rac1/GTP -0.076 0.18 -9999 0 -0.52 21 21
HCK -0.005 0.098 -9999 0 -0.52 9 9
MAPKKK cascade 0.001 0.066 -9999 0 -0.42 1 1
bone resorption -0.19 0.37 -9999 0 -0.96 42 42
IRF1 -0.093 0.23 -9999 0 -0.72 12 12
mol:GDP -0.08 0.18 -9999 0 -0.48 28 28
SOS1 0.013 0.002 -9999 0 -10000 0 0
VAV1 -0.081 0.18 -9999 0 -0.49 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.077 0.23 -9999 0 -0.66 27 27
PTPN11 -0.008 0.059 -9999 0 -0.92 1 1
IL6/IL6RA -0.057 0.16 -9999 0 -0.38 50 50
gp130 (dimer)/TYK2/TYK2/LMO4 -0.033 0.14 -9999 0 -0.37 35 35
gp130 (dimer)/JAK2/JAK2/LMO4 -0.046 0.16 -9999 0 -0.39 41 41
IL6 -0.055 0.17 -9999 0 -0.5 35 35
PIAS3 0.011 0.037 -9999 0 -0.6 1 1
PTPRE 0.004 0.073 -9999 0 -0.46 6 6
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.16 -9999 0 -0.42 25 25
LMO4 0.003 0.076 -9999 0 -0.6 4 4
STAT3 (dimer)/PIAS3 -0.11 0.25 -9999 0 -0.76 16 16
MCL1 0.037 0.057 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.033 0.16 -9999 0 -0.54 22 22
PDGF/PDGFRA/CRKL -0.014 0.11 -9999 0 -0.37 23 23
positive regulation of JUN kinase activity 0.008 0.085 -9999 0 -0.31 14 14
CRKL 0.012 0.027 -9999 0 -0.43 1 1
PDGF/PDGFRA/Caveolin-3 -0.023 0.11 -9999 0 -0.38 22 22
AP1 -0.068 0.2 -9999 0 -1 8 8
mol:IP3 -0.015 0.12 -9999 0 -0.39 23 23
PLCG1 -0.015 0.12 -9999 0 -0.39 23 23
PDGF/PDGFRA/alphaV Integrin -0.03 0.15 -9999 0 -0.42 30 30
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.015 0.12 -9999 0 -0.39 23 23
CAV3 0 0 -9999 0 -10000 0 0
CAV1 0.008 0.053 -9999 0 -0.49 3 3
SHC/Grb2/SOS1 0.009 0.086 -9999 0 -0.31 14 14
PDGF/PDGFRA/Shf -0.017 0.12 -9999 0 -0.39 24 24
FOS -0.033 0.21 -9999 0 -1 8 8
JUN -0.01 0.044 -9999 0 -0.39 3 3
oligodendrocyte development -0.03 0.15 -9999 0 -0.42 30 30
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
mol:DAG -0.015 0.12 -9999 0 -0.39 23 23
PDGF/PDGFRA -0.033 0.15 -9999 0 -0.54 22 22
actin cytoskeleton reorganization -0.013 0.11 -9999 0 -0.37 22 22
SRF 0.021 0.006 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.026 0.13 -9999 0 -0.37 24 24
PDGF/PDGFRA/Crk/C3G -0.001 0.094 -9999 0 -0.36 14 14
JAK1 -0.018 0.12 -9999 0 -0.38 26 26
ELK1/SRF 0.009 0.088 -9999 0 -0.36 4 4
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.007 0.059 -9999 0 -0.54 3 3
CSNK2A1 0.006 0.015 -9999 0 -10000 0 0
GO:0007205 -0.015 0.12 -9999 0 -0.46 15 15
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.008 0.085 -9999 0 -0.31 14 14
PDGF/PDGFRA/SHB -0.013 0.11 -9999 0 -0.38 22 22
PDGF/PDGFRA/Caveolin-1 -0.017 0.12 -9999 0 -0.37 25 25
ITGAV -0.011 0.12 -9999 0 -0.57 11 11
ELK1 -0.007 0.11 -9999 0 -0.41 15 15
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
PDGF/PDGFRA/Crk -0.013 0.11 -9999 0 -0.38 22 22
JAK-STAT cascade -0.018 0.12 -9999 0 -0.38 26 26
cell proliferation -0.017 0.12 -9999 0 -0.39 24 24
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.042 0.14 -10000 0 -0.36 32 32
regulation of S phase of mitotic cell cycle -0.03 0.12 -10000 0 -0.3 37 37
GNAO1 -0.013 0.11 -10000 0 -0.48 14 14
HRAS 0.013 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.004 0.068 -10000 0 -0.36 9 9
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.01 0.11 -10000 0 -0.38 2 2
T-DHT/AR -0.062 0.16 -10000 0 -0.39 48 48
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.005 22 22
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.11 -10000 0 -0.54 11 11
mol:GDP -0.078 0.17 -10000 0 -0.51 31 31
cell proliferation -0.006 0.13 -10000 0 -0.43 7 7
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
FOS -0.012 0.16 -10000 0 -0.7 10 10
mol:Ca2+ -0.012 0.022 -10000 0 -0.083 11 11
MAPK3 -0.007 0.12 -10000 0 -0.5 2 2
MAPK1 0.003 0.063 -10000 0 -0.28 2 2
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
mol:IP3 0 0.001 -10000 0 -0.003 22 22
cAMP biosynthetic process 0 0.067 -10000 0 -0.34 9 9
GNG2 -0.007 0.1 -10000 0 -0.51 10 10
potassium channel inhibitor activity 0 0.001 -10000 0 -0.003 22 22
HRAS/GTP -0.048 0.1 -10000 0 -0.29 30 30
actin cytoskeleton reorganization -0.019 0.072 -10000 0 -0.32 11 11
SRC 0.011 0.037 -10000 0 -0.6 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.003 22 22
PI3K -0.007 0.09 -10000 0 -0.32 20 20
apoptosis 0.001 0.11 0.39 10 -10000 0 10
T-DHT/AR/PELP1 -0.044 0.13 -10000 0 -0.32 48 48
HRAS/GDP -0.072 0.16 -10000 0 -0.48 31 31
CREB1 -0.003 0.11 -10000 0 -0.42 10 10
RAC1-CDC42/GTP -0.018 0.074 -10000 0 -0.32 11 11
AR -0.085 0.21 -10000 0 -0.53 48 48
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.017 0.11 -10000 0 -0.36 2 2
RAC1-CDC42/GDP -0.068 0.16 -10000 0 -0.47 30 30
T-DHT/AR/PELP1/Src -0.032 0.12 -10000 0 -0.33 30 30
MAP2K2 -0.01 0.11 -10000 0 -0.38 2 2
T-DHT/AR/PELP1/Src/PI3K -0.03 0.12 -10000 0 -0.3 37 37
GNAZ -0.015 0.12 -10000 0 -0.53 14 14
SHBG -0.007 0.11 -10000 0 -0.58 9 9
Gi family/GNB1/GNG2/GDP -0.008 0.1 -10000 0 -0.49 3 3
mol:T-DHT 0 0.001 -10000 0 -0.003 5 5
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 -0.009 0.092 -10000 0 -0.43 12 12
Gi family/GTP -0.025 0.098 -10000 0 -0.36 9 9
CDC42 0.011 0.037 -10000 0 -0.6 1 1
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.1 -9999 0 -0.58 8 8
SVIL -0.01 0.11 -9999 0 -0.58 10 10
ZNF318 0.018 0.019 -9999 0 -10000 0 0
JMJD2C -0.005 0.031 -9999 0 -0.09 30 30
T-DHT/AR/Ubc9 -0.055 0.15 -9999 0 -0.35 48 48
CARM1 0.013 0.001 -9999 0 -10000 0 0
PRDX1 0.014 0.001 -9999 0 -10000 0 0
PELP1 0.014 0.003 -9999 0 -10000 0 0
CTNNB1 0.008 0.053 -9999 0 -0.6 2 2
AKT1 0.015 0.005 -9999 0 -10000 0 0
PTK2B 0.004 0.07 -9999 0 -0.56 4 4
MED1 0.015 0.006 -9999 0 -10000 0 0
MAK 0.001 0.091 -9999 0 -0.44 10 10
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.005 0.065 -9999 0 -0.6 3 3
GSN 0.009 0.038 -9999 0 -0.6 1 1
NCOA2 -0.023 0.14 -9999 0 -0.56 17 17
NCOA6 0.013 0.004 -9999 0 -10000 0 0
DNA-PK 0.023 0.059 -9999 0 -0.36 5 5
NCOA4 0.007 0.059 -9999 0 -0.54 3 3
PIAS3 0.01 0.037 -9999 0 -0.6 1 1
cell proliferation -0.022 0.083 -9999 0 -0.68 2 2
XRCC5 0.014 0.004 -9999 0 -10000 0 0
UBE3A 0.011 0.011 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.08 0.18 -9999 0 -0.38 62 62
FHL2 -0.035 0.21 -9999 0 -1.1 10 10
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.009 0.057 -9999 0 -0.14 39 39
CDK6 -0.025 0.14 -9999 0 -0.53 19 19
TGFB1I1 0.001 0.076 -9999 0 -0.49 6 6
T-DHT/AR/CyclinD1 -0.075 0.17 -9999 0 -0.4 49 49
XRCC6 0.014 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.061 0.18 -9999 0 -0.42 39 39
CTDSP1 0.013 0.003 -9999 0 -10000 0 0
CTDSP2 0.016 0.013 -9999 0 -10000 0 0
BRCA1 0.007 0.053 -9999 0 -0.6 2 2
TCF4 0.009 0.064 -9999 0 -0.59 3 3
CDKN2A -0.1 0.21 -9999 0 -0.47 64 64
SRF 0.017 0.027 -9999 0 -10000 0 0
NKX3-1 -0.099 0.3 -9999 0 -1 22 22
KLK3 -0.023 0.12 -9999 0 -10000 0 0
TMF1 0.013 0.003 -9999 0 -10000 0 0
HNRNPA1 0.015 0.007 -9999 0 -10000 0 0
AOF2 -0.002 0.008 -9999 0 -10000 0 0
APPL1 0.024 0.011 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.054 0.15 -9999 0 -0.35 48 48
AR -0.095 0.22 -9999 0 -0.55 48 48
UBA3 0.01 0.037 -9999 0 -0.6 1 1
PATZ1 0.015 0.007 -9999 0 -10000 0 0
PAWR 0.013 0.003 -9999 0 -10000 0 0
PRKDC 0.001 0.087 -9999 0 -0.57 6 6
PA2G4 0.015 0.008 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.048 0.14 -9999 0 -0.32 48 48
RPS6KA3 0.01 0.028 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.059 0.16 -9999 0 -0.36 49 49
LATS2 0.015 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.047 0.14 -9999 0 -0.32 48 48
Cyclin D3/CDK11 p58 0.01 0.001 -9999 0 -10000 0 0
VAV3 -0.024 0.14 -9999 0 -0.6 16 16
KLK2 -0.062 0.17 -9999 0 -0.68 8 8
CASP8 0.014 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.063 0.17 -9999 0 -0.39 47 47
TMPRSS2 -0.096 0.32 -9999 0 -1.2 20 20
CCND1 -0.018 0.13 -9999 0 -0.57 14 14
PIAS1 0.011 0.011 -9999 0 -10000 0 0
mol:T-DHT -0.01 0.03 -9999 0 -0.075 30 30
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.009 0.018 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.18 -9999 0 -0.37 62 62
CMTM2 -0.008 0.11 -9999 0 -0.55 10 10
SNURF -0.028 0.15 -9999 0 -0.6 18 18
ZMIZ1 0.005 0.027 -9999 0 -10000 0 0
CCND3 0.013 0.001 -9999 0 -10000 0 0
TGIF1 0.013 0.038 -9999 0 -0.6 1 1
FKBP4 0.013 0.004 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.004 0.092 -9999 0 -0.49 9 9
PLK4 -0.007 0.11 -9999 0 -0.6 9 9
regulation of centriole replication -0.006 0.1 -9999 0 -0.39 18 18
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.025 0.16 -9999 0 -0.44 27 27
MAP4K1 -0.005 0.095 -9999 0 -0.48 10 10
MAP3K8 0 0.09 -9999 0 -0.6 6 6
PRKCB -0.03 0.15 -9999 0 -0.53 21 21
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.012 0.027 -9999 0 -0.43 1 1
MAP3K1 -0.003 0.13 -9999 0 -0.54 10 10
JUN -0.021 0.18 -9999 0 -0.64 17 17
MAP3K7 -0.001 0.13 -9999 0 -0.54 9 9
GRAP2 -0.048 0.18 -9999 0 -0.55 29 29
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.001 0.13 -9999 0 -0.56 9 9
LAT 0.004 0.066 -9999 0 -0.47 5 5
LCP2 -0.004 0.098 -9999 0 -0.56 8 8
MAPK8 -0.026 0.18 -9999 0 -0.67 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.13 -9999 0 -0.57 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.017 0.15 -9999 0 -0.41 27 27
Cellular roles of Anthrax toxin

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
ANTXR1 -0.007 0.11 -10000 0 -0.6 9 9
ANTXR2 -0.007 0.11 -10000 0 -0.58 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.019 -10000 0 -0.078 17 17
monocyte activation -0.072 0.2 -10000 0 -0.5 38 38
MAP2K2 -0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.004 0.016 -10000 0 -10000 0 0
MAP2K7 -0.004 0.016 -10000 0 -10000 0 0
MAP2K6 -0.024 0.083 -10000 0 -0.33 17 17
CYAA -0.008 0.086 -10000 0 -0.33 17 17
MAP2K4 -0.005 0.025 -10000 0 -0.32 1 1
IL1B -0.018 0.094 -10000 0 -0.33 18 18
Channel -0.006 0.092 -10000 0 -0.35 17 17
NLRP1 -0.018 0.063 -10000 0 -0.27 14 14
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.006 0.022 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.019 0.078 17 -10000 0 17
MAPK3 -0.005 0.021 -10000 0 -0.22 1 1
MAPK1 -0.004 0.016 -10000 0 -10000 0 0
PGR -0.093 0.14 -10000 0 -0.32 77 77
PA/Cellular Receptors -0.008 0.1 -10000 0 -0.38 17 17
apoptosis -0.005 0.019 -10000 0 -0.078 17 17
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.005 0.087 -10000 0 -0.33 17 17
macrophage activation 0.012 0.022 -10000 0 -0.2 1 1
TNF -0.066 0.19 -10000 0 -0.51 40 40
VCAM1 -0.073 0.2 -10000 0 -0.51 38 38
platelet activation -0.006 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.004 0.032 0.14 6 -10000 0 6
IL18 -0.014 0.085 -10000 0 -0.32 16 16
negative regulation of macrophage activation -0.005 0.019 -10000 0 -0.078 17 17
LEF -0.005 0.019 -10000 0 -0.079 17 17
CASP1 -0.014 0.042 -10000 0 -0.15 17 17
mol:cAMP -0.006 0.022 -10000 0 -10000 0 0
necrosis -0.005 0.019 -10000 0 -0.078 17 17
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0.087 -10000 0 -0.33 17 17
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.005 0.068 -9999 0 -0.36 9 9
ARNO/beta Arrestin1-2 -0.009 0.083 -9999 0 -0.54 1 1
EGFR -0.002 0.094 -9999 0 -0.57 7 7
EPHA2 -0.004 0.098 -9999 0 -0.56 8 8
USP6 0.01 0.039 -9999 0 -0.43 2 2
IQSEC1 0.011 0.037 -9999 0 -0.6 1 1
EGFR/EGFR/EGF/EGF -0.061 0.17 -9999 0 -0.38 54 54
ARRB2 0.007 0.012 -9999 0 -0.19 1 1
mol:GTP 0.009 0.036 -9999 0 -0.16 7 7
ARRB1 0.005 0.065 -9999 0 -0.51 4 4
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.04 0.14 -9999 0 -0.43 30 30
EGF -0.083 0.2 -9999 0 -0.5 50 50
somatostatin receptor activity 0 0 -9999 0 -0.001 15 15
ARAP2 -0.011 0.12 -9999 0 -0.58 11 11
mol:GDP -0.022 0.079 -9999 0 -0.28 12 12
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 10 10
ITGA2B -0.052 0.18 -9999 0 -0.53 32 32
ARF6 0.009 0.053 -9999 0 -0.6 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.019 0.076 -9999 0 -0.36 9 9
ADAP1 0 0.09 -9999 0 -0.6 6 6
KIF13B 0.007 0.059 -9999 0 -0.54 3 3
HGF/MET -0.047 0.16 -9999 0 -0.4 42 42
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.029 0.096 -9999 0 -0.31 15 15
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.044 0.14 -9999 0 -0.39 27 27
ADRB2 -0.051 0.16 -9999 0 -0.47 35 35
receptor agonist activity 0 0 -9999 0 0 15 15
actin filament binding 0 0 -9999 0 -0.001 15 15
SRC 0.011 0.037 -9999 0 -0.6 1 1
ITGB3 -0.065 0.19 -9999 0 -0.5 41 41
GNAQ 0.006 0.064 -9999 0 -0.6 3 3
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 13 13
ARF6/GDP 0.015 0.078 -9999 0 -0.42 3 3
ARF6/GDP/GULP/ACAP1 -0.025 0.12 -9999 0 -0.4 16 16
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.048 0.14 -9999 0 -0.34 35 35
ACAP1 0.008 0.047 -9999 0 -0.43 3 3
ACAP2 0.011 0.037 -9999 0 -0.6 1 1
LHCGR/beta Arrestin2 -0.001 0.011 -9999 0 -0.18 1 1
EFNA1 0.006 0.064 -9999 0 -0.6 3 3
HGF -0.036 0.16 -9999 0 -0.53 24 24
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.011 0.037 -9999 0 -0.6 1 1
fibronectin binding 0 0 -9999 0 0 16 16
endosomal lumen acidification 0 0 -9999 0 0 15 15
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.031 0.16 -9999 0 -0.58 20 20
GNAQ/ARNO 0.013 0.034 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 3 3
MET -0.03 0.15 -9999 0 -0.56 20 20
GNA14 -0.013 0.12 -9999 0 -0.57 12 12
GNA15 -0.001 0.087 -9999 0 -0.53 7 7
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 13 13
GNA11 -0.018 0.13 -9999 0 -0.57 14 14
LHCGR 0 0 -9999 0 -0.001 15 15
AGTR1 -0.005 0.076 -9999 0 -0.43 8 8
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.011 -9999 0 -0.18 1 1
IPCEF1/ARNO -0.031 0.11 -9999 0 -0.47 3 3
alphaIIb/beta3 Integrin -0.085 0.18 -9999 0 -0.37 71 71
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.087 -9999 0 -0.35 9 9
IRAK/TOLLIP 0.032 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.19 -9999 0 -0.39 78 78
IL1A -0.081 0.2 -9999 0 -0.49 49 49
IL1B -0.024 0.15 -9999 0 -0.46 25 25
IRAK/TRAF6/p62/Atypical PKCs 0.04 0.039 -9999 0 -10000 0 0
IL1R2 -0.06 0.19 -9999 0 -0.56 34 34
IL1R1 -0.009 0.11 -9999 0 -0.58 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.096 -9999 0 -0.48 3 3
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0 0.09 -9999 0 -0.6 6 6
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.009 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.061 0.014 -9999 0 -10000 0 0
JUN 0.019 0.092 -9999 0 -0.57 3 3
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.032 0.17 -9999 0 -0.59 14 14
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.14 -9999 0 -0.34 33 33
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.035 0.13 -9999 0 -0.32 33 33
IL1 beta fragment/IL1R1/IL1RAP -0.028 0.16 -9999 0 -0.44 27 27
NFKB1 0.011 0.037 -9999 0 -0.6 1 1
MAPK8 0.016 0.086 -9999 0 -0.55 2 2
IRAK1 0.026 0 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.045 0.16 -9999 0 -0.39 42 42
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.002 0.075 -9999 0 -0.49 6 6
TRAF6 0.013 0 -9999 0 -10000 0 0
PI3K -0.01 0.1 -9999 0 -0.37 20 20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.11 -9999 0 -0.42 9 9
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.028 0.16 -9999 0 -0.44 27 27
IL1 beta/IL1R2 -0.057 0.2 -9999 0 -0.5 34 34
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.061 0.14 -9999 0 -0.53 15 15
IRAK3 -0.017 0.12 -9999 0 -0.49 16 16
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.16 -9999 0 -0.6 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.1 -9999 0 -0.31 5 5
IL1 alpha/IL1R1/IL1RAP -0.059 0.15 -9999 0 -0.31 67 67
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0.027 -9999 0 -0.43 1 1
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.039 0 -9999 0 -10000 0 0
IL1RAP -0.009 0.11 -9999 0 -0.52 11 11
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.044 0.12 -9999 0 -0.5 11 11
CASP1 -0.013 0.12 -9999 0 -0.53 13 13
IL1RN/IL1R2 -0.08 0.2 -9999 0 -0.42 60 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.018 0.15 -9999 0 -0.41 27 27
TMEM189-UBE2V1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.096 -9999 0 -0.34 9 9
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
IL1RN -0.054 0.18 -9999 0 -0.51 34 34
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.014 0.074 -9999 0 -0.28 15 15
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.091 -9999 0 -1.2 1 1
VDR 0.009 0.053 -9999 0 -0.6 2 2
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.034 0.15 -9999 0 -0.46 14 14
RXRs/LXRs/DNA/Oxysterols -0.038 0.18 -9999 0 -0.47 28 28
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA -0.001 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.03 0.12 -9999 0 -0.46 2 2
RXRs/NUR77 -0.052 0.15 -9999 0 -0.36 36 36
RXRs/PPAR -0.069 0.15 -9999 0 -0.39 23 23
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.006 0.039 -9999 0 -0.44 2 2
RARs/VDR/DNA/Vit D3 0.021 0.06 -9999 0 -0.32 7 7
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.009 0.053 -9999 0 -0.6 2 2
RARs/RARs/DNA/9cRA 0.015 0.053 -9999 0 -0.34 5 5
RARG 0.01 0.039 -9999 0 -0.43 2 2
RPS6KB1 0.019 0.07 -9999 0 -0.52 3 3
RARs/THRs/DNA/SMRT -0.03 0.12 -9999 0 -0.46 2 2
THRA 0.009 0.046 -9999 0 -0.51 2 2
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.006 0.039 -9999 0 -0.44 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.05 0.15 -9999 0 -0.36 34 34
NR1H4 -0.017 0.098 -9999 0 -0.43 14 14
RXRs/LXRs/DNA -0.032 0.15 -9999 0 -0.44 13 13
NR1H2 0.014 0.014 -9999 0 -10000 0 0
NR1H3 0.013 0.015 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.041 0.14 -9999 0 -0.33 35 35
NR4A1 -0.009 0.099 -9999 0 -0.45 13 13
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.11 -9999 0 -0.32 17 17
RXRG -0.12 0.23 -9999 0 -0.51 65 65
RXR alpha/CCPG 0.018 0.03 -9999 0 -0.44 1 1
RXRA 0.011 0.04 -9999 0 -0.61 1 1
RXRB 0.013 0.015 -9999 0 -10000 0 0
THRB -0.12 0.24 -9999 0 -0.56 60 60
PPARG -0.1 0.22 -9999 0 -0.53 55 55
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.091 0.32 -9999 0 -1 24 24
mol:Oxysterols 0 0.016 -9999 0 -10000 0 0
cholesterol transport -0.037 0.18 -9999 0 -0.46 28 28
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.001 0.083 -9999 0 -0.54 6 6
RXRs/NUR77/BCL2 -0.051 0.15 -9999 0 -0.44 19 19
SREBF1 -0.029 0.17 -9999 0 -0.65 9 9
RXRs/RXRs/DNA/9cRA -0.05 0.15 -9999 0 -0.36 34 34
ABCA1 -0.04 0.22 -9999 0 -0.81 12 12
RARs/THRs -0.041 0.14 -9999 0 -0.54 3 3
RXRs/FXR -0.057 0.16 -9999 0 -0.38 35 35
BCL2 -0.02 0.13 -9999 0 -0.54 16 16
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.007 0.066 -9999 0 -0.38 6 6
NFATC2 -0.029 0.1 -9999 0 -0.36 22 22
NFATC3 0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.15 0.28 -9999 0 -0.72 32 32
PTGS2 -0.19 0.3 -9999 0 -0.65 57 57
JUNB 0.009 0.053 -9999 0 -0.6 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.017 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.017 -9999 0 -10000 0 0
CALM1 0.009 0.01 -9999 0 -10000 0 0
JUN 0.003 0.055 -9999 0 -0.5 3 3
mol:Ca2+ -0.009 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.006 -9999 0 -10000 0 0
FOSL1 -0.025 0.14 -9999 0 -0.5 20 20
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.07 0.17 -9999 0 -0.48 12 12
FOS -0.033 0.14 -9999 0 -0.49 22 22
IFNG -0.14 0.27 -9999 0 -0.65 35 35
AP-1/NFAT1-c-4 -0.15 0.29 -9999 0 -0.73 31 31
FASLG -0.15 0.29 -9999 0 -0.7 40 40
NFAT1-c-4/ICER1 -0.045 0.12 -9999 0 -0.42 11 11
IL2RA -0.14 0.27 -9999 0 -0.73 28 28
FKBP12/FK506 0.01 0 -9999 0 -10000 0 0
CSF2 -0.13 0.24 -9999 0 -0.68 21 21
JunB/Fra1/NFAT1-c-4 -0.052 0.14 -9999 0 -0.43 17 17
IL4 -0.13 0.24 -9999 0 -0.67 20 20
IL2 -0.016 0.069 -9999 0 -10000 0 0
IL3 -0.016 0.019 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.01 0.11 -9999 0 -0.5 12 12
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.016 0.058 0.26 11 -10000 0 11
RFC1 0.016 0.058 0.26 11 -10000 0 11
PRKDC 0.008 0.075 0.26 11 -0.33 5 16
RIPK1 0.014 0.003 -10000 0 -10000 0 0
CASP7 -0.017 0.073 0.25 1 -0.61 3 4
FASLG/FAS/FADD/FAF1 -0.01 0.1 0.22 19 -0.28 20 39
MAP2K4 -0.007 0.12 -10000 0 -0.39 4 4
mol:ceramide -0.015 0.12 -10000 0 -0.43 3 3
GSN 0.014 0.062 0.26 11 -0.35 1 12
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.12 -10000 0 -0.34 20 20
FAS 0.009 0.039 -10000 0 -0.44 2 2
BID 0.005 0.032 0.3 2 -10000 0 2
MAP3K1 0.004 0.086 0.29 1 -0.37 3 4
MAP3K7 0.013 0.003 -10000 0 -10000 0 0
RB1 -0.003 0.1 0.26 11 -0.35 14 25
CFLAR 0.014 0.003 -10000 0 -10000 0 0
HGF/MET -0.07 0.18 -10000 0 -0.4 51 51
ARHGDIB 0.016 0.058 0.26 11 -10000 0 11
FADD 0.012 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.014 0.062 0.35 1 -0.26 11 12
NFKB1 -0.03 0.073 -10000 0 -0.84 1 1
MAPK8 -0.016 0.15 -10000 0 -0.43 16 16
DFFA 0.016 0.058 0.26 11 -10000 0 11
DNA fragmentation during apoptosis 0.016 0.058 0.26 11 -10000 0 11
FAS/FADD/MET -0.004 0.1 -10000 0 -0.36 17 17
CFLAR/RIP1 0.017 0.006 -10000 0 -10000 0 0
FAIM3 0.001 0.08 -10000 0 -0.48 7 7
FAF1 0.012 0.006 -10000 0 -10000 0 0
PARP1 0.013 0.063 0.26 11 -0.35 1 12
DFFB 0.016 0.058 0.26 11 -10000 0 11
CHUK -0.026 0.066 -10000 0 -0.78 1 1
FASLG -0.062 0.19 -10000 0 -0.55 35 35
FAS/FADD 0.016 0.029 -10000 0 -0.31 2 2
HGF -0.036 0.16 -10000 0 -0.53 24 24
LMNA 0.025 0.054 0.24 10 -0.32 1 11
CASP6 0.014 0.062 0.26 11 -0.35 1 12
CASP10 0.005 0.06 -10000 0 -0.47 4 4
CASP3 0.019 0.07 0.31 12 -10000 0 12
PTPN13 -0.05 0.18 -10000 0 -0.57 29 29
CASP8 0.007 0.045 0.4 2 -10000 0 2
IL6 -0.073 0.3 -10000 0 -1.2 14 14
MET -0.029 0.15 -10000 0 -0.56 20 20
ICAD/CAD 0.015 0.054 0.24 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 -0.015 0.12 -10000 0 -0.44 3 3
activation of caspase activity by cytochrome c 0.005 0.032 0.3 2 -10000 0 2
PAK2 0.015 0.06 0.26 11 -0.24 1 12
BCL2 -0.02 0.13 -10000 0 -0.54 16 16
a4b1 and a4b7 Integrin 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
ITGB1 0.011 0.037 -9999 0 -0.6 1 1
ITGB7 -0.002 0.091 -9999 0 -0.55 7 7
ITGA4 -0.012 0.11 -9999 0 -0.51 13 13
alpha4/beta7 Integrin -0.009 0.11 -9999 0 -0.39 19 19
alpha4/beta1 Integrin 0 0.093 -9999 0 -0.39 13 13
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.006 0.062 -9999 0 -0.34 8 8
PDGFRB -0.001 0.084 -9999 0 -0.5 7 7
SPHK1 -0.029 0.087 -9999 0 -0.77 3 3
mol:S1P -0.032 0.079 -9999 0 -0.68 3 3
S1P1/S1P/Gi -0.06 0.17 -9999 0 -0.38 38 38
GNAO1 -0.016 0.11 -9999 0 -0.48 14 14
PDGFB-D/PDGFRB/PLCgamma1 -0.053 0.16 -9999 0 -0.44 15 15
PLCG1 -0.054 0.16 -9999 0 -0.47 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.084 -9999 0 -0.5 7 7
GNAI2 0.01 0.006 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GNAI1 -0.013 0.11 -9999 0 -0.54 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.002 0.054 -9999 0 -0.29 8 8
S1P1/S1P -0.018 0.093 -9999 0 -0.44 5 5
negative regulation of cAMP metabolic process -0.059 0.16 -9999 0 -0.37 38 38
MAPK3 -0.088 0.23 -9999 0 -0.55 40 40
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
KDR 0.004 0.065 -9999 0 -0.52 4 4
PLCB2 -0.012 0.093 -9999 0 -0.37 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.034 0.066 -9999 0 -0.37 5 5
receptor internalization -0.039 0.074 -9999 0 -0.39 6 6
PTGS2 -0.16 0.38 -9999 0 -0.95 43 43
Rac1/GTP -0.034 0.066 -9999 0 -0.4 4 4
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.005 0.055 -9999 0 -0.44 4 4
negative regulation of T cell proliferation -0.059 0.16 -9999 0 -0.37 38 38
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.018 0.12 -9999 0 -0.53 14 14
MAPK1 -0.087 0.22 -9999 0 -0.55 39 39
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.11 -9999 0 -0.42 6 6
ABCC1 0.012 0.003 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.046 -10000 0 -0.51 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.039 0.15 0.53 8 -10000 0 8
IL27/IL27R/JAK1 -0.048 0.19 -10000 0 -0.78 6 6
TBX21 -0.067 0.23 -10000 0 -0.61 26 26
IL12B 0.001 0.055 -10000 0 -0.44 4 4
IL12A -0.042 0.13 -10000 0 -0.36 37 37
IL6ST -0.067 0.2 -10000 0 -0.58 36 36
IL27RA/JAK1 0.002 0.12 -10000 0 -1.2 2 2
IL27 -0.007 0.087 -10000 0 -0.44 10 10
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.022 0.084 -10000 0 -0.3 15 15
T-helper 2 cell differentiation 0.039 0.15 0.53 8 -10000 0 8
T cell proliferation during immune response 0.039 0.15 0.53 8 -10000 0 8
MAPKKK cascade -0.039 0.15 -10000 0 -0.53 8 8
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.06 -10000 0 -0.48 4 4
IL12RB1 0.007 0.054 -10000 0 -0.49 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.065 0.22 -10000 0 -0.58 20 20
IL27/IL27R/JAK2/TYK2 -0.039 0.15 -10000 0 -0.54 8 8
positive regulation of T cell mediated cytotoxicity -0.039 0.15 -10000 0 -0.53 8 8
STAT1 (dimer) -0.11 0.23 0.47 5 -0.78 13 18
JAK2 -0.006 0.11 -10000 0 -0.6 9 9
JAK1 0.005 0.07 -10000 0 -0.55 4 4
STAT2 (dimer) -0.031 0.14 -10000 0 -0.5 8 8
T cell proliferation -0.064 0.17 -10000 0 -0.58 10 10
IL12/IL12R/TYK2/JAK2 -0.02 0.11 -10000 0 -0.64 2 2
IL17A -0.022 0.084 -10000 0 -0.3 15 15
mast cell activation 0.039 0.15 0.53 8 -10000 0 8
IFNG -0.008 0.038 -10000 0 -0.11 13 13
T cell differentiation -0.004 0.008 0.015 4 -0.022 15 19
STAT3 (dimer) -0.031 0.14 -10000 0 -0.5 8 8
STAT5A (dimer) -0.032 0.14 -10000 0 -0.5 8 8
STAT4 (dimer) -0.037 0.16 -10000 0 -0.57 10 10
STAT4 0.001 0.083 -10000 0 -0.54 6 6
T cell activation -0.008 0.012 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 -0.036 0.18 -10000 0 -0.86 5 5
GATA3 -0.047 0.25 -10000 0 -1.3 9 9
IL18 -0.011 0.094 -10000 0 -0.42 13 13
positive regulation of mast cell cytokine production -0.03 0.14 -10000 0 -0.5 8 8
IL27/EBI3 -0.019 0.12 -10000 0 -0.38 25 25
IL27RA -0.001 0.12 -10000 0 -1.3 2 2
IL6 -0.054 0.17 -10000 0 -0.49 35 35
STAT5A 0.012 0.027 -10000 0 -0.43 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.002 0.07 0.47 2 -10000 0 2
IL1B -0.016 0.1 -10000 0 -0.41 17 17
EBI3 -0.022 0.14 -10000 0 -0.54 17 17
TNF -0.047 0.14 -10000 0 -0.37 40 40
IL2 signaling events mediated by STAT5

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
GAB2 0.009 0.047 -9999 0 -0.43 3 3
ELF1 -0.005 0.1 -9999 0 -0.39 15 15
CCNA2 -0.003 0.098 -9999 0 -0.6 7 7
PIK3CA 0.011 0.039 -9999 0 -0.43 2 2
JAK3 0.009 0.047 -9999 0 -0.43 3 3
PIK3R1 -0.023 0.14 -9999 0 -0.53 18 18
JAK1 0.005 0.07 -9999 0 -0.56 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.001 0.15 -9999 0 -0.5 12 12
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 -0.002 0.08 -9999 0 -0.35 9 9
IL2RA -0.025 0.21 -9999 0 -0.75 19 19
IL2RB -0.036 0.16 -9999 0 -0.56 23 23
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.02 0.14 -9999 0 -0.56 16 16
G1/S transition of mitotic cell cycle -0.037 0.21 -9999 0 -0.57 28 28
PTPN11 0.012 0.037 -9999 0 -0.6 1 1
CCND2 -0.019 0.17 -9999 0 -0.58 21 21
LCK -0.02 0.14 -9999 0 -0.56 16 16
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 -0.009 0.08 -9999 0 -0.43 9 9
CDK6 -0.025 0.14 -9999 0 -0.53 19 19
CCND3 0.011 0.13 -9999 0 -0.57 3 3
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR -0.002 0.094 -9999 0 -0.57 7 7
EGF/EGFR -0.07 0.12 -9999 0 -0.32 36 36
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.02 0.12 -9999 0 -0.51 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.084 -9999 0 -0.47 8 8
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.083 0.2 -9999 0 -0.5 50 50
EGF/EGFR dimer/SHC -0.042 0.14 -9999 0 -0.39 26 26
mol:GDP -0.023 0.12 -9999 0 -0.5 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.014 0.12 -9999 0 -0.55 13 13
GRB2/SOS1 0.02 0 -9999 0 -10000 0 0
HRAS/GTP -0.046 0.098 -9999 0 -0.46 3 3
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.047 0.1 -9999 0 -0.47 3 3
FRAP1 -0.024 0.12 -9999 0 -0.48 3 3
EGF/EGFR dimer -0.061 0.17 -9999 0 -0.38 54 54
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.011 0.11 -9999 0 -0.38 20 20
Visual signal transduction: Rods

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
mol:K + 0.011 0.037 -9999 0 -0.6 1 1
GNAT1/GTP -0.002 0.046 -9999 0 -0.31 6 6
Metarhodopsin II/Arrestin -0.004 0.057 -9999 0 -0.25 13 13
PDE6G/GNAT1/GTP -0.038 0.12 -9999 0 -0.32 42 42
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.003 0.066 -9999 0 -0.43 6 6
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.11 0.16 -9999 0 -0.47 25 25
mol:Na + -0.068 0.13 -9999 0 -0.5 10 10
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.029 0.13 -9999 0 -0.42 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.068 0.13 -9999 0 -0.51 10 10
CNGB1 -0.057 0.18 -9999 0 -0.5 36 36
RDH5 0 0.076 -9999 0 -0.43 8 8
SAG -0.003 0.071 -9999 0 -0.43 7 7
mol:Ca2+ -0.038 0.14 -9999 0 -0.48 11 11
Na + (4 Units) -0.064 0.12 -9999 0 -0.46 11 11
RGS9 -0.04 0.15 -9999 0 -0.47 29 29
GNB1/GNGT1 0.011 0.058 -9999 0 -0.36 6 6
GNAT1/GDP -0.025 0.12 -9999 0 -0.38 19 19
GUCY2D -0.005 0.08 -9999 0 -0.43 9 9
GNGT1 0.001 0.079 -9999 0 -0.51 6 6
GUCY2F 0.001 0.047 -9999 0 -0.43 3 3
GNB5 0.009 0.053 -9999 0 -0.6 2 2
mol:GMP (4 units) -0.042 0.14 -9999 0 -0.37 28 28
mol:11-cis-retinal 0 0.076 -9999 0 -0.43 8 8
mol:cGMP 0.003 0.068 -9999 0 -0.36 2 2
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.003 0.07 -9999 0 -0.3 14 14
SLC24A1 0.011 0.037 -9999 0 -0.6 1 1
CNGA1 -0.04 0.17 -9999 0 -0.55 25 25
Metarhodopsin II -0.002 0.035 -9999 0 -0.23 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.002 0.068 -9999 0 -0.39 2 2
RGS9BP -0.022 0.12 -9999 0 -0.43 20 20
Metarhodopsin II/Transducin 0.006 0.048 -9999 0 -0.27 5 5
GCAP Family/Ca ++ 0.004 0.05 -9999 0 -0.24 11 11
PDE6A/B -0.015 0.1 -9999 0 -0.31 28 28
mol:Pi -0.029 0.13 -9999 0 -0.42 15 15
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.01 0.057 -9999 0 -0.34 3 3
PDE6B -0.035 0.14 -9999 0 -0.44 28 28
PDE6A 0.013 0 -9999 0 -10000 0 0
PDE6G -0.062 0.18 -9999 0 -0.5 39 39
RHO -0.005 0.065 -9999 0 -0.43 6 6
PDE6 -0.093 0.16 -9999 0 -0.5 24 24
GUCA1A -0.005 0.076 -9999 0 -0.43 8 8
GC2/GCAP Family 0.005 0.056 -9999 0 -0.34 1 1
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.053 -9999 0 -0.49 3 3
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.016 -10000 0 -10000 0 0
HSPA8 -0.018 0.13 -10000 0 -0.6 13 13
SMAD3/SMAD4/ER alpha -0.049 0.15 0.21 2 -0.4 37 39
AKT1 0.011 0.018 -10000 0 -10000 0 0
GSC -0.26 0.56 -10000 0 -1.4 51 51
NKX2-5 -0.048 0.15 -10000 0 -0.43 34 34
muscle cell differentiation 0.045 0.079 0.39 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.021 0.1 -10000 0 -0.39 4 4
SMAD4 -0.001 0.051 -10000 0 -0.24 1 1
CBFB 0.009 0.053 -10000 0 -0.6 2 2
SAP18 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.001 0.11 -10000 0 -0.29 26 26
SMAD3/SMAD4/VDR 0.026 0.064 -10000 0 -0.37 2 2
MYC -0.013 0.12 -10000 0 -0.51 14 14
CDKN2B -0.049 0.3 -10000 0 -1.4 12 12
AP1 0.018 0.11 -10000 0 -0.58 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.034 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.041 0.12 -10000 0 -0.44 7 7
SP3 0.015 0.004 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.012 0.073 -10000 0 -0.56 3 3
SMAD3/SMAD4/GR 0.012 0.087 -10000 0 -0.39 7 7
GATA3 -0.038 0.15 -10000 0 -0.48 27 27
SKI/SIN3/HDAC complex/NCoR1 0.032 0.032 -10000 0 -10000 0 0
MEF2C/TIF2 -0.044 0.15 -10000 0 -0.52 9 9
endothelial cell migration -0.011 0.13 1.3 2 -10000 0 2
MAX 0.012 0.006 -10000 0 -10000 0 0
RBBP7 0.009 0.039 -10000 0 -0.43 2 2
RBBP4 0.012 0.002 -10000 0 -10000 0 0
RUNX2 -0.071 0.19 -10000 0 -0.49 45 45
RUNX3 -0.033 0.16 -10000 0 -0.54 22 22
RUNX1 0.006 0.064 -10000 0 -0.6 3 3
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 -0.007 0.1 -10000 0 -0.56 9 9
VDR 0.009 0.053 -10000 0 -0.6 2 2
CDKN1A -0.018 0.33 -10000 0 -1.3 16 16
KAT2B -0.002 0.1 -10000 0 -0.6 8 8
SMAD2/SMAD2/SMAD4/FOXH1 -0.019 0.12 -10000 0 -0.36 6 6
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.002 -10000 0 -10000 0 0
SERPINE1 0.011 0.13 -10000 0 -1.3 2 2
SMAD3/SMAD4/ATF2 0.024 0.065 -10000 0 -0.43 2 2
SMAD3/SMAD4/ATF3 0.008 0.096 -10000 0 -0.36 7 7
SAP30 0.003 0.074 -10000 0 -0.6 4 4
Cbp/p300/PIAS3 0.046 0.047 -10000 0 -0.36 1 1
JUN 0.016 0.11 -10000 0 -0.58 4 4
SMAD3/SMAD4/IRF7 0.017 0.079 -10000 0 -0.38 5 5
TFE3 0.016 0.017 -10000 0 -10000 0 0
COL1A2 -0.036 0.22 -10000 0 -1 12 12
mesenchymal cell differentiation 0.029 0.14 0.39 23 -10000 0 23
DLX1 -0.031 0.13 -10000 0 -0.43 24 24
TCF3 0.011 0.037 -10000 0 -0.6 1 1
FOS -0.024 0.14 -10000 0 -0.49 22 22
SMAD3/SMAD4/Max 0.025 0.051 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.033 0.014 -10000 0 -10000 0 0
ZBTB17 0.014 0.012 -10000 0 -10000 0 0
LAMC1 0.027 0.087 -10000 0 -0.48 6 6
TGIF2/HDAC complex/SMAD3/SMAD4 0.018 0.079 -10000 0 -0.38 6 6
IRF7 -0.001 0.087 -10000 0 -0.53 7 7
ESR1 -0.07 0.21 -10000 0 -0.58 37 37
HNF4A -0.18 0.26 -10000 0 -0.52 97 97
MEF2C -0.035 0.14 -10000 0 -0.48 9 9
SMAD2-3/SMAD4 0.01 0.072 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.039 0.024 -10000 0 -10000 0 0
IGHV3OR16-13 -0.008 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0.09 -10000 0 -0.6 6 6
CREBBP 0.019 0.011 -10000 0 -10000 0 0
SKIL 0.002 0.079 -10000 0 -0.56 5 5
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.012 0.002 -10000 0 -10000 0 0
SNIP1 0.012 0.003 -10000 0 -10000 0 0
GCN5L2 0.006 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.068 -10000 0 -0.33 2 2
MSG1/HSC70 -0.051 0.16 -10000 0 -0.4 43 43
SMAD2 -0.007 0.046 -10000 0 -10000 0 0
SMAD3 0.015 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.032 0.042 -10000 0 -0.25 1 1
SMAD2/SMAD2/SMAD4 0.002 0.074 -10000 0 -0.38 8 8
NCOR1 0.012 0.002 -10000 0 -10000 0 0
NCOA2 -0.023 0.14 -10000 0 -0.56 17 17
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.017 0.093 -10000 0 -0.3 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.029 0.1 -10000 0 -0.39 2 2
IFNB1 0.011 0.067 -10000 0 -0.33 5 5
SMAD3/SMAD4/MEF2C -0.021 0.14 -10000 0 -0.67 3 3
CITED1 -0.05 0.17 -10000 0 -0.49 33 33
SMAD2-3/SMAD4/ARC105 0.02 0.065 -10000 0 -10000 0 0
RBL1 0.01 0.039 -10000 0 -0.43 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.015 0.13 -10000 0 -0.51 12 12
RUNX1-3/PEBPB2 -0.009 0.11 -10000 0 -0.38 19 19
SMAD7 0.036 0.11 -10000 0 -0.68 2 2
MYC/MIZ-1 0.002 0.09 -10000 0 -0.36 14 14
SMAD3/SMAD4 0.06 0.13 0.29 42 -0.77 1 43
IL10 -0.008 0.13 -10000 0 -0.4 12 12
PIASy/HDAC complex 0.008 0.011 -10000 0 -10000 0 0
PIAS3 0.014 0.038 -10000 0 -0.6 1 1
CDK2 0.017 0.03 -10000 0 -0.43 1 1
IL5 -0.008 0.1 -10000 0 -0.34 12 12
CDK4 0.02 0.013 -10000 0 -10000 0 0
PIAS4 0.008 0.011 -10000 0 -10000 0 0
ATF3 -0.017 0.12 -10000 0 -0.46 17 17
SMAD3/SMAD4/SP1 0.024 0.1 -10000 0 -0.43 4 4
FOXG1 -0.19 0.27 -10000 0 -0.55 95 95
FOXO3 0.018 0.023 -10000 0 -10000 0 0
FOXO1 0.016 0.036 -10000 0 -0.3 2 2
FOXO4 0.019 0.023 -10000 0 -10000 0 0
heart looping -0.035 0.13 -10000 0 -0.47 9 9
CEBPB 0.01 0.04 -10000 0 -0.63 1 1
SMAD3/SMAD4/DLX1 -0.001 0.1 -10000 0 -0.35 6 6
MYOD1 -0.035 0.12 -10000 0 -0.43 24 24
SMAD3/SMAD4/HNF4 -0.11 0.18 -10000 0 -0.38 62 62
SMAD3/SMAD4/GATA3 -0.005 0.12 -10000 0 -0.38 12 12
SnoN/SIN3/HDAC complex/NCoR1 0.002 0.079 -10000 0 -0.56 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.008 0.11 -10000 0 -0.42 6 6
SMAD3/SMAD4/SP1-3 0.038 0.094 -10000 0 -0.42 4 4
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.007 0.044 -10000 0 -10000 0 0
SIN3B 0.012 0.002 -10000 0 -10000 0 0
SIN3A 0.012 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.037 0.13 -10000 0 -0.42 9 9
ITGB5 0.031 0.095 -10000 0 -0.68 2 2
TGIF/SIN3/HDAC complex/CtBP 0.038 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.038 0.16 -10000 0 -0.41 29 29
AR -0.085 0.21 -10000 0 -0.53 48 48
negative regulation of cell growth 0.03 0.061 -10000 0 -0.42 1 1
SMAD3/SMAD4/MYOD -0.004 0.1 -10000 0 -0.35 7 7
E2F5 0.008 0.053 -10000 0 -0.49 3 3
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.009 0.086 -10000 0 -0.38 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.018 0.093 -10000 0 -0.37 4 4
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.11 -10000 0 -0.59 4 4
SMAD3/SMAD4/RUNX2 -0.028 0.14 -10000 0 -0.39 23 23
TGIF2 0 0.09 -10000 0 -0.6 6 6
TGIF1 0.011 0.037 -10000 0 -0.6 1 1
ATF2 0.009 0.053 -10000 0 -0.6 2 2
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.012 0.11 -10000 0 -0.4 20 20
CRKL -0.002 0.096 -10000 0 -0.38 5 5
mol:PIP3 -0.013 0.059 0.54 3 -10000 0 3
AKT1 0.004 0.04 0.37 3 -10000 0 3
PTK2B 0.005 0.07 -10000 0 -0.56 4 4
RAPGEF1 0.005 0.092 -10000 0 -0.38 4 4
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
HGF/MET/SHIP2 -0.03 0.14 -10000 0 -0.38 28 28
MAP3K5 0.004 0.1 -10000 0 -0.43 6 6
HGF/MET/CIN85/CBL/ENDOPHILINS -0.021 0.13 -10000 0 -0.35 30 30
AP1 -0.02 0.11 -10000 0 -0.33 23 23
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.02 0.15 -10000 0 -0.88 7 7
STAT3 (dimer) -0.005 0.12 -10000 0 -0.54 5 5
GAB1/CRKL/SHP2/PI3K -0.004 0.12 -10000 0 -0.42 9 9
INPP5D 0 0.09 -10000 0 -0.6 6 6
CBL/CRK 0.007 0.092 -10000 0 -0.36 5 5
PTPN11 0.011 0.037 -10000 0 -0.6 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.011 0.037 -10000 0 -0.6 1 1
PTEN 0.006 0.064 -10000 0 -0.6 3 3
ELK1 -0.016 0.054 -10000 0 -0.2 20 20
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.021 0.056 -10000 0 -0.29 2 2
PAK1 0.009 0.042 0.35 3 -0.32 1 4
HGF/MET/RANBP10 -0.03 0.14 -10000 0 -0.38 28 28
HRAS -0.027 0.17 -10000 0 -0.63 16 16
DOCK1 0.005 0.092 -10000 0 -0.38 4 4
GAB1 -0.008 0.1 -10000 0 -0.32 17 17
CRK -0.001 0.095 -10000 0 -0.38 5 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.038 0.18 -10000 0 -0.55 28 28
JUN 0.008 0.053 -10000 0 -0.49 3 3
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.022 0.09 -10000 0 -0.26 28 28
PIK3R1 -0.024 0.14 -10000 0 -0.53 18 18
cell morphogenesis 0 0.14 -10000 0 -0.51 9 9
GRB2/SHC -0.004 0.082 -10000 0 -0.36 2 2
FOS -0.028 0.14 -10000 0 -0.48 22 22
GLMN -0.015 0.063 -10000 0 -0.27 15 15
cell motility -0.016 0.054 -10000 0 -0.2 20 20
HGF/MET/MUC20 -0.039 0.14 -10000 0 -0.34 42 42
cell migration -0.004 0.08 -10000 0 -0.36 2 2
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.012 0.11 -10000 0 -0.4 20 20
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.011 0.12 -10000 0 -0.58 4 4
MET/MUC20 -0.021 0.11 -10000 0 -0.41 20 20
RAP1B 0.011 0.087 -10000 0 -0.37 3 3
RAP1A 0.011 0.087 -10000 0 -0.37 3 3
HGF/MET/RANBP9 -0.03 0.14 -10000 0 -0.38 28 28
RAF1 -0.019 0.16 -10000 0 -0.59 16 16
STAT3 -0.006 0.12 -10000 0 -0.55 5 5
cell proliferation -0.007 0.14 -10000 0 -0.44 17 17
RPS6KB1 -0.011 0.062 -10000 0 -0.3 6 6
MAPK3 -0.019 0.049 -10000 0 -10000 0 0
MAPK1 -0.019 0.049 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 0.01 0.12 -10000 0 -0.5 7 7
SRC -0.004 0.11 -10000 0 -0.54 5 5
PI3K -0.024 0.12 -10000 0 -0.39 13 13
MET/Glomulin -0.027 0.11 -10000 0 -0.31 33 33
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.01 0.15 -10000 0 -0.54 16 16
MET -0.029 0.15 -10000 0 -0.56 20 20
MAP4K1 0.002 0.095 -10000 0 -0.35 5 5
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.01 0.15 -10000 0 -0.54 16 16
BAD 0.01 0.037 0.35 3 -10000 0 3
MAP2K4 0.01 0.098 -10000 0 -0.39 6 6
SHP2/GRB2/SOS1/GAB1 -0.037 0.1 -10000 0 -0.38 16 16
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.009 0.053 -10000 0 -0.6 2 2
HGS -0.013 0.084 -10000 0 -0.28 16 16
PLCgamma1/PKC 0.008 0.028 -10000 0 -0.44 1 1
HGF -0.036 0.16 -10000 0 -0.53 24 24
RASA1 0.011 0.037 -10000 0 -0.6 1 1
NCK1 0.011 0.037 -10000 0 -0.6 1 1
PTPRJ 0.01 0.039 -10000 0 -0.43 2 2
NCK/PLCgamma1 -0.006 0.09 -10000 0 -0.42 3 3
PDPK1 -0.004 0.046 0.42 3 -10000 0 3
HGF/MET/SHIP -0.039 0.15 -10000 0 -0.4 32 32
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0 -9999 0 -10000 0 0
LAT2 -0.012 0.12 -9999 0 -0.55 7 7
AP1 -0.064 0.14 -9999 0 -0.52 16 16
mol:PIP3 -0.019 0.16 -9999 0 -0.54 14 14
IKBKB -0.001 0.098 -9999 0 -0.28 15 15
AKT1 -0.018 0.13 -9999 0 -0.44 8 8
IKBKG -0.001 0.098 -9999 0 -0.28 15 15
MS4A2 -0.006 0.098 -9999 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.038 -9999 0 -0.43 2 2
MAP3K1 -0.003 0.13 -9999 0 -0.46 12 12
mol:Ca2+ -0.009 0.12 -9999 0 -0.39 14 14
LYN 0.011 0.038 -9999 0 -0.61 1 1
CBLB -0.01 0.11 -9999 0 -0.46 7 7
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.015 0.056 -9999 0 -0.33 4 4
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0.09 -9999 0 -0.6 6 6
PLD2 -0.024 0.13 -9999 0 -0.33 27 27
PTPN13 -0.032 0.15 -9999 0 -0.53 11 11
PTPN11 0.01 0.038 -9999 0 -0.61 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.11 -9999 0 -0.34 7 7
SYK 0.006 0.066 -9999 0 -0.61 3 3
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.066 0.15 -9999 0 -0.56 14 14
LAT -0.014 0.12 -9999 0 -0.54 7 7
PAK2 -0.01 0.14 -9999 0 -0.5 12 12
NFATC2 -0.058 0.14 -9999 0 -0.52 20 20
HRAS -0.017 0.15 -9999 0 -0.55 12 12
GAB2 0.008 0.047 -9999 0 -0.43 3 3
PLA2G1B 0.027 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.065 0.14 -9999 0 -0.4 33 33
Antigen/IgE/Fc epsilon R1 -0.043 0.14 -9999 0 -0.36 33 33
mol:GDP -0.027 0.16 -9999 0 -0.56 15 15
JUN 0.008 0.053 -9999 0 -0.49 3 3
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
FOS -0.028 0.14 -9999 0 -0.48 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.018 0.12 -9999 0 -0.41 11 11
CHUK -0.001 0.098 -9999 0 -0.28 15 15
KLRG1 -0.015 0.11 -9999 0 -0.5 6 6
VAV1 -0.024 0.14 -9999 0 -0.44 16 16
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.01 0.11 -9999 0 -0.39 11 11
negative regulation of mast cell degranulation -0.013 0.13 -9999 0 -0.51 9 9
BTK -0.029 0.17 -9999 0 -0.63 14 14
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.037 0.16 -9999 0 -0.58 13 13
GAB2/PI3K/SHP2 -0.064 0.12 -9999 0 -0.46 10 10
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.017 0.12 -9999 0 -0.42 10 10
RAF1 0.016 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.052 0.18 -9999 0 -0.42 39 39
FCER1G -0.001 0.088 -9999 0 -0.57 6 6
FCER1A -0.07 0.2 -9999 0 -0.54 40 40
Antigen/IgE/Fc epsilon R1/Fyn -0.033 0.13 -9999 0 -0.33 33 33
MAPK3 0.025 0.017 -9999 0 -10000 0 0
MAPK1 0.025 0.017 -9999 0 -10000 0 0
NFKB1 0.011 0.037 -9999 0 -0.6 1 1
MAPK8 0.007 0.083 -9999 0 -0.5 5 5
DUSP1 -0.001 0.084 -9999 0 -0.47 8 8
NF-kappa-B/RelA -0.023 0.048 -9999 0 -0.24 2 2
actin cytoskeleton reorganization -0.008 0.11 -9999 0 -0.6 4 4
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.063 0.13 -9999 0 -0.53 13 13
FER -0.012 0.11 -9999 0 -0.47 8 8
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.036 0.12 -9999 0 -0.48 15 15
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.024 0.16 -9999 0 -0.59 13 13
cytokine secretion -0.017 0.035 -9999 0 -10000 0 0
SPHK1 -0.021 0.12 -9999 0 -0.41 13 13
PTK2 -0.009 0.12 -9999 0 -0.63 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.066 0.15 -9999 0 -0.59 13 13
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.015 0.16 -9999 0 -0.55 12 12
MAP2K2 0.022 0.017 -9999 0 -10000 0 0
MAP2K1 0.022 0.017 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.014 0.11 -9999 0 -0.45 7 7
MAP2K4 0.016 0.055 -9999 0 -0.88 1 1
Fc epsilon R1/FcgammaRIIB -0.055 0.17 -9999 0 -0.41 41 41
mol:Choline -0.024 0.12 -9999 0 -0.32 27 27
SHC/Grb2/SOS1 0.003 0.11 -9999 0 -0.56 4 4
FYN 0.012 0.027 -9999 0 -0.43 1 1
DOK1 0.011 0.037 -9999 0 -0.6 1 1
PXN -0.002 0.11 -9999 0 -0.58 4 4
HCLS1 -0.018 0.12 -9999 0 -0.44 13 13
PRKCB -0.015 0.13 -9999 0 -0.38 19 19
FCGR2B -0.024 0.14 -9999 0 -0.57 17 17
IGHE 0 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.013 0.13 -9999 0 -0.52 9 9
LCP2 -0.004 0.098 -9999 0 -0.56 8 8
PLA2G4A -0.065 0.16 -9999 0 -0.35 41 41
RASA1 0.011 0.037 -9999 0 -0.6 1 1
mol:Phosphatidic acid -0.024 0.12 -9999 0 -0.32 27 27
IKK complex 0.013 0.078 -9999 0 -0.23 7 7
WIPF1 0.009 0.053 -9999 0 -0.6 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.097 -9999 0 -0.41 11 11
CRKL 0.012 0.027 -9999 0 -0.43 1 1
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DOCK1 0.013 0 -9999 0 -10000 0 0
ITGA4 -0.012 0.11 -9999 0 -0.51 13 13
alpha4/beta7 Integrin/MAdCAM1 -0.019 0.12 -9999 0 -0.35 18 18
EPO -0.015 0.1 -9999 0 -0.43 15 15
alpha4/beta7 Integrin -0.009 0.11 -9999 0 -0.39 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0.093 -9999 0 -0.39 13 13
EPO/EPOR (dimer) -0.018 0.11 -9999 0 -0.34 27 27
lamellipodium assembly 0.008 0.085 -9999 0 -0.51 2 2
PIK3CA 0.01 0.039 -9999 0 -0.43 2 2
PI3K -0.01 0.1 -9999 0 -0.37 20 20
ARF6 0.009 0.053 -9999 0 -0.6 2 2
JAK2 -0.017 0.13 -9999 0 -0.51 12 12
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 -0.024 0.14 -9999 0 -0.53 18 18
MADCAM1 -0.041 0.15 -9999 0 -0.47 29 29
cell adhesion -0.02 0.12 -9999 0 -0.35 18 18
CRKL/CBL 0.019 0.019 -9999 0 -0.3 1 1
ITGB1 0.011 0.037 -9999 0 -0.6 1 1
SRC -0.027 0.14 -9999 0 -0.39 26 26
ITGB7 -0.002 0.091 -9999 0 -0.55 7 7
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.035 0.15 -9999 0 -0.44 25 25
p130Cas/Crk/Dock1 -0.003 0.12 -9999 0 -0.51 6 6
VCAM1 -0.059 0.19 -9999 0 -0.54 35 35
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.019 0.074 -9999 0 -0.38 6 6
BCAR1 -0.019 0.13 -9999 0 -0.57 6 6
EPOR -0.012 0.11 -9999 0 -0.51 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.018 0.08 -9999 0 -0.53 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.009 0.046 -10000 0 -0.51 2 2
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.006 0.087 0.37 12 -10000 0 12
CDKN1A -0.045 0.19 -10000 0 -0.78 16 16
KAT2B -0.005 0.1 -10000 0 -0.6 8 8
BAX 0.013 0 -10000 0 -10000 0 0
FOXO3 0.002 0.016 -10000 0 -10000 0 0
FOXO1 0.01 0.039 -10000 0 -0.43 2 2
FOXO4 0.021 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.007 0.059 -10000 0 -0.54 3 3
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.028 0.12 -10000 0 -0.34 31 31
PPARGC1A -0.13 0.23 -10000 0 -0.5 71 71
FHL2 -0.01 0.12 -10000 0 -0.6 10 10
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.015 0.067 -10000 0 -0.41 5 5
HIST2H4A 0.006 0.087 -10000 0 -0.37 12 12
SIRT1/FOXO3a 0.001 0.058 -10000 0 -0.35 5 5
SIRT1 0.008 0.091 -10000 0 -0.57 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.021 0.063 -10000 0 -0.34 6 6
SIRT1/Histone H1b 0.011 0.075 -10000 0 -0.29 12 12
apoptosis -0.023 0.058 0.34 5 -10000 0 5
SIRT1/PGC1A -0.073 0.15 -10000 0 -0.31 71 71
p53/SIRT1 0.002 0.13 0.38 15 -0.44 10 25
SIRT1/FOXO4 0.022 0.058 -10000 0 -0.34 5 5
FOXO1/FHL2/SIRT1 0.007 0.087 -10000 0 -0.33 15 15
HIST1H1E 0.009 0.057 -10000 0 -0.3 7 7
SIRT1/p300 0.015 0.067 -10000 0 -0.41 5 5
muscle cell differentiation 0.019 0.12 0.44 11 -10000 0 11
TP53 0.001 0.11 -10000 0 -0.57 8 8
KU70/SIRT1/BAX 0.023 0.058 -10000 0 -0.35 5 5
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.011 0.083 -10000 0 -0.46 7 7
ACSS2 0.017 0.065 -10000 0 -0.41 5 5
SIRT1/PCAF/MYOD -0.019 0.12 -10000 0 -0.44 11 11
Retinoic acid receptors-mediated 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
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.009 0.053 -10000 0 -0.6 2 2
Cbp/p300/PCAF 0.015 0.067 -10000 0 -0.36 8 8
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.012 0.07 -10000 0 -0.39 4 4
KAT2B -0.005 0.1 -10000 0 -0.6 8 8
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.025 0.089 0.22 26 -0.25 7 33
RAR alpha/9cRA/Cyclin H -0.04 0.086 -10000 0 -0.42 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.081 -10000 0 -0.41 6 6
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.023 0.095 -10000 0 -0.48 6 6
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.006 0.039 -10000 0 -0.44 2 2
RXRs/RARs/NRIP1/9cRA -0.039 0.18 -10000 0 -0.66 12 12
NCOA2 -0.023 0.14 -10000 0 -0.56 17 17
NCOA3 0.012 0.027 -10000 0 -0.43 1 1
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.009 0.053 -10000 0 -0.6 2 2
RARG 0.01 0.039 -10000 0 -0.44 2 2
RAR gamma1/9cRA 0.016 0.023 -10000 0 -0.25 2 2
MAPK3 0.012 0.027 -10000 0 -0.43 1 1
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.005 0.075 -10000 0 -0.6 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.055 0.17 -10000 0 -0.56 19 19
RARA -0.024 0.096 -10000 0 -0.29 20 20
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.006 0.096 -10000 0 -0.34 12 12
PRKCA -0.003 0.1 -10000 0 -0.58 8 8
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.058 0.19 -10000 0 -0.7 15 15
RXRG -0.11 0.19 -10000 0 -0.42 52 52
RXRA -0.017 0.095 -10000 0 -0.38 6 6
RXRB -0.039 0.12 -10000 0 -0.39 17 17
VDR/Vit D3/DNA 0.006 0.039 -10000 0 -0.44 2 2
RBP1 -0.087 0.22 -10000 0 -0.57 46 46
CRBP1/9-cic-RA -0.064 0.16 -10000 0 -0.42 46 46
RARB 0.002 0.083 -10000 0 -0.54 6 6
PRKCG -0.099 0.2 -10000 0 -0.46 64 64
MNAT1 0.011 0.037 -10000 0 -0.6 1 1
RAR alpha/RXRs -0.027 0.17 -10000 0 -0.56 16 16
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.022 0.14 -10000 0 -0.5 11 11
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.094 -10000 0 -0.45 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.058 0.19 -10000 0 -0.7 15 15
positive regulation of DNA binding -0.038 0.082 -10000 0 -0.4 7 7
NRIP1 -0.066 0.25 -10000 0 -1.1 11 11
RXRs/RARs -0.059 0.18 -10000 0 -0.55 21 21
RXRs/RXRs/DNA/9cRA -0.062 0.17 -10000 0 -0.57 18 18
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.011 0.037 -10000 0 -0.6 1 1
TFIIH 0.024 0.034 -10000 0 -0.36 2 2
RAR alpha/9cRA -0.025 0.056 -10000 0 -0.38 2 2
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.003 0.028 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.019 0.11 -9999 0 -0.56 1 1
Syndecan-3/Neurocan 0.001 0.058 -9999 0 -0.6 1 1
POMC -0.069 0.19 -9999 0 -0.5 43 43
EGFR -0.002 0.094 -9999 0 -0.57 7 7
Syndecan-3/EGFR 0.012 0.064 -9999 0 -0.34 7 7
AGRP 0.007 0.028 -9999 0 -0.43 1 1
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.011 0.037 -9999 0 -0.6 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.064 -9999 0 -0.6 3 3
APH1A 0.012 0.027 -9999 0 -0.43 1 1
NCAN -0.011 0.088 -9999 0 -0.43 11 11
long-term memory 0.026 0.041 -9999 0 -0.56 1 1
Syndecan-3/IL8 -0.026 0.12 -9999 0 -0.33 25 25
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.018 0.028 -9999 0 -0.43 1 1
FYN 0.012 0.027 -9999 0 -0.43 1 1
limb bud formation -0.004 0.04 -9999 0 -0.63 1 1
MC4R -0.023 0.11 -9999 0 -0.43 18 18
SRC 0.011 0.037 -9999 0 -0.6 1 1
PTN -0.092 0.22 -9999 0 -0.52 52 52
FGFR/FGF/Syndecan-3 -0.004 0.041 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.037 0.11 -9999 0 -0.41 5 5
Syndecan-3/AgRP 0.011 0.044 -9999 0 -0.6 1 1
Syndecan-3/AgRP/MC4R -0.007 0.066 -9999 0 -0.58 1 1
Fyn/Cortactin 0.019 0.019 -9999 0 -0.3 1 1
SDC3 -0.004 0.041 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.025 0.12 -9999 0 -0.32 25 25
IL8 -0.076 0.2 -9999 0 -0.53 44 44
Syndecan-3/Fyn/Cortactin 0.027 0.042 -9999 0 -0.58 1 1
Syndecan-3/CASK -0.004 0.039 -9999 0 -0.61 1 1
alpha-MSH/MC4R -0.066 0.16 -9999 0 -0.35 59 59
Gamma Secretase 0.034 0.043 -9999 0 -0.3 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.011 0.15 -10000 0 -0.56 11 11
UGCG -0.03 0.19 -10000 0 -0.8 14 14
AKT1/mTOR/p70S6K/Hsp90/TERT -0.029 0.17 -10000 0 -0.45 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.029 0.18 -10000 0 -0.78 14 14
mol:DAG -0.014 0.1 -10000 0 -0.99 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.065 0.14 -10000 0 -0.52 15 15
FRAP1 -0.016 0.19 -10000 0 -0.6 16 16
FOXO3 -0.004 0.17 -10000 0 -0.55 13 13
AKT1 -0.013 0.18 -10000 0 -0.51 22 22
GAB2 0.008 0.047 -10000 0 -0.43 3 3
SMPD1 0.01 0.034 -10000 0 -10000 0 0
SGMS1 0 0.094 -10000 0 -0.8 3 3
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 -0.006 0.089 -10000 0 -0.31 20 20
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.023 0.18 -10000 0 -0.49 23 23
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K -0.006 0.1 -10000 0 -0.37 20 20
RPS6KB1 0.006 0.085 -10000 0 -0.82 2 2
mol:sphingomyelin -0.014 0.1 -10000 0 -0.99 3 3
natural killer cell activation 0 0.003 -10000 0 -0.012 7 7
JAK3 0.01 0.047 -10000 0 -0.43 3 3
PIK3R1 -0.022 0.14 -10000 0 -0.53 18 18
JAK1 0.007 0.07 -10000 0 -0.55 4 4
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
MYC -0.021 0.23 -10000 0 -0.91 12 12
MYB -0.014 0.22 -10000 0 -1.3 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.012 0.17 -10000 0 -0.54 15 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.079 -10000 0 -0.75 2 2
mol:PI-3-4-5-P3 -0.011 0.16 -10000 0 -0.52 15 15
Rac1/GDP 0.003 0.081 -10000 0 -0.33 11 11
T cell proliferation -0.003 0.15 -10000 0 -0.48 15 15
SHC1 0.013 0.003 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.011 -10000 0 -0.06 8 8
PRKCZ -0.004 0.16 -10000 0 -0.5 15 15
NF kappa B1 p50/RelA -0.063 0.14 -10000 0 -0.54 13 13
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.02 0.16 -10000 0 -0.55 15 15
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.028 0.15 -10000 0 -0.56 19 19
IL2RB -0.034 0.16 -10000 0 -0.56 23 23
TERT -0.088 0.22 -10000 0 -0.54 49 49
E2F1 0.004 0.1 -10000 0 -0.49 10 10
SOS1 0.013 0.003 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.006 0.03 8 -10000 0 8
PTPN11 0.011 0.038 -10000 0 -0.6 1 1
IL2RG -0.019 0.14 -10000 0 -0.56 16 16
actin cytoskeleton organization -0.003 0.15 -10000 0 -0.48 15 15
GRB2 0.013 0.003 -10000 0 -10000 0 0
IL2 -0.008 0.08 -10000 0 -0.43 9 9
PIK3CA 0.012 0.039 -10000 0 -0.43 2 2
Rac1/GTP 0.01 0.079 -10000 0 -0.31 11 11
LCK -0.019 0.14 -10000 0 -0.55 16 16
BCL2 -0.021 0.22 -10000 0 -0.75 17 17
Regulation of Telomerase

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
Telomerase catalytic core complex -0.18 0.4 -10000 0 -1.1 36 36
RAD9A 0.013 0 -10000 0 -10000 0 0
AP1 -0.016 0.11 -10000 0 -0.37 23 23
IFNAR2 0.01 0.038 -10000 0 -0.6 1 1
AKT1 -0.029 0.094 -10000 0 -0.26 18 18
ER alpha/Oestrogen -0.054 0.16 -10000 0 -0.44 37 37
NFX1/SIN3/HDAC complex 0.031 0.038 -10000 0 -10000 0 0
EGF -0.085 0.2 -10000 0 -0.5 50 50
SMG5 0.013 0 -10000 0 -10000 0 0
SMG6 0.013 0 -10000 0 -10000 0 0
SP3/HDAC2 0.017 0.013 -10000 0 -10000 0 0
TERT/c-Abl -0.16 0.37 -10000 0 -1 35 35
SAP18 0.013 0.002 -10000 0 -10000 0 0
MRN complex 0.026 0.024 -10000 0 -0.36 1 1
WT1 -0.14 0.24 -10000 0 -0.52 74 74
WRN 0.011 0.037 -10000 0 -0.6 1 1
SP1 0.011 0.011 -10000 0 -10000 0 0
SP3 0.012 0.005 -10000 0 -10000 0 0
TERF2IP 0.013 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.16 0.31 -10000 0 -0.89 36 36
Mad/Max 0.013 0.044 -10000 0 -0.39 3 3
TERT -0.19 0.42 -10000 0 -1.2 35 35
CCND1 -0.18 0.4 -10000 0 -1 43 43
MAX 0.012 0.005 -10000 0 -10000 0 0
RBBP7 0.009 0.039 -10000 0 -0.43 2 2
RBBP4 0.013 0.002 -10000 0 -10000 0 0
TERF2 0.011 0.034 -10000 0 -0.54 1 1
PTGES3 0.011 0.037 -10000 0 -0.6 1 1
SIN3A 0.013 0.002 -10000 0 -10000 0 0
Telomerase/911 0.019 0.045 -10000 0 -10000 0 0
CDKN1B -0.046 0.19 -10000 0 -0.59 25 25
RAD1 0.013 0 -10000 0 -10000 0 0
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
SAP30 0.003 0.074 -10000 0 -0.6 4 4
TRF2/PARP2 0.018 0.028 -10000 0 -0.42 1 1
UBE3A 0.012 0.005 -10000 0 -10000 0 0
JUN 0.006 0.053 -10000 0 -0.49 3 3
E6 -0.002 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -10000 0 -10000 0 0
FOS -0.03 0.14 -10000 0 -0.49 22 22
IFN-gamma/IRF1 -0.037 0.14 -10000 0 -0.34 43 43
PARP2 0.013 0 -10000 0 -10000 0 0
BLM 0.004 0.074 -10000 0 -0.6 4 4
Telomerase 0 0.078 -10000 0 -0.46 4 4
IRF1 0 0.064 -10000 0 -0.43 3 3
ESR1 -0.072 0.21 -10000 0 -0.6 37 37
KU/TER 0.02 0 -10000 0 -10000 0 0
ATM/TRF2 0.016 0.041 -10000 0 -0.36 3 3
ubiquitin-dependent protein catabolic process 0.036 0.035 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.036 -10000 0 -10000 0 0
HDAC1 0.013 0.002 -10000 0 -10000 0 0
HDAC2 0.011 0.011 -10000 0 -10000 0 0
ATM -0.003 0.041 0.22 1 -0.45 2 3
SMAD3 0.02 0.035 -10000 0 -0.36 2 2
ABL1 0.013 0 -10000 0 -10000 0 0
MXD1 0.005 0.059 -10000 0 -0.54 3 3
MRE11A 0.013 0 -10000 0 -10000 0 0
HUS1 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.053 -10000 0 -0.6 2 2
TERT/NF kappa B1/14-3-3 -0.15 0.36 -10000 0 -1 34 34
NR2F2 0.003 0.088 -10000 0 -0.57 6 6
MAPK3 0.001 0.061 -10000 0 -0.3 10 10
MAPK1 0.002 0.058 -10000 0 -0.3 9 9
TGFB1/TGF beta receptor Type II 0.01 0.046 -10000 0 -0.51 2 2
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
HNRNPC 0.013 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.003 0.041 0.22 1 -0.45 2 3
NBN 0.011 0.037 -10000 0 -0.6 1 1
EGFR -0.003 0.094 -10000 0 -0.57 7 7
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.064 0.16 -10000 0 -0.38 54 54
MYC -0.018 0.12 -10000 0 -0.54 14 14
IL2 -0.013 0.081 -10000 0 -0.44 9 9
KU 0.02 0 -10000 0 -10000 0 0
RAD50 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
TGFB1 0.01 0.046 -10000 0 -0.52 2 2
TRF2/BLM 0.012 0.058 -10000 0 -0.41 5 5
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.15 0.37 -10000 0 -1 35 35
SP1/HDAC2 0.017 0.018 -10000 0 -10000 0 0
PINX1 0.013 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.16 0.31 -10000 0 -0.89 36 36
Smad3/Myc 0.007 0.088 -10000 0 -0.4 9 9
911 complex 0.027 0 -10000 0 -10000 0 0
IFNG -0.049 0.16 -10000 0 -0.47 28 28
Telomerase/PinX1 -0.16 0.31 -10000 0 -0.89 36 36
Telomerase/AKT1/mTOR/p70S6K -0.019 0.096 -10000 0 -0.37 3 3
SIN3B 0.013 0.002 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.16 0.31 -10000 0 -0.89 36 36
response to DNA damage stimulus 0.002 0.013 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.036 0.03 -10000 0 -0.31 1 1
TRF2/WRN 0.017 0.038 -10000 0 -0.41 2 2
Telomerase/hnRNP C1/C2 -0.16 0.31 -10000 0 -0.89 36 36
E2F1 -0.003 0.085 -10000 0 -0.48 8 8
ZNFX1 0.013 0.002 -10000 0 -10000 0 0
PIF1 0.004 0.074 -10000 0 -0.6 4 4
NCL 0.013 0 -10000 0 -10000 0 0
DKC1 0.013 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 0 0.24 -10000 0 -0.97 11 11
NCK1/PAK1/Dok-R -0.039 0.097 -10000 0 -0.43 11 11
NCK1/Dok-R -0.003 0.24 -10000 0 -1 11 11
PIK3CA 0.01 0.039 -10000 0 -0.43 2 2
mol:beta2-estradiol -0.006 0.024 0.24 1 -10000 0 1
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.002 -10000 0 -10000 0 0
Rac/GDP 0.01 0 -10000 0 -10000 0 0
F2 -0.04 0.14 0.25 1 -0.44 26 27
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.002 0.22 -10000 0 -0.97 11 11
FN1 -0.024 0.13 -10000 0 -0.48 20 20
PLD2 -0.004 0.24 -10000 0 -1.1 11 11
PTPN11 0.011 0.037 -10000 0 -0.6 1 1
GRB14 -0.12 0.24 -10000 0 -0.53 64 64
ELK1 0.007 0.22 -10000 0 -0.98 11 11
GRB7 -0.015 0.11 -10000 0 -0.45 16 16
PAK1 0.011 0.037 -10000 0 -0.6 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.02 0.24 -10000 0 -1 11 11
CDKN1A -0.013 0.27 -10000 0 -0.76 27 27
ITGA5 0.011 0.037 -10000 0 -0.6 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.003 0.23 -10000 0 -1 11 11
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.015 0.19 -10000 0 -0.7 11 11
PLG -0.064 0.26 -10000 0 -1.1 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.009 0.22 -10000 0 -0.9 11 11
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 -0.023 0.14 -10000 0 -0.53 18 18
ANGPT2 0.006 0.19 -10000 0 -1.2 5 5
BMX -0.055 0.28 -10000 0 -1.2 11 11
ANGPT1 0.004 0.13 -10000 0 -1.3 1 1
tube development 0.007 0.22 -10000 0 -0.74 15 15
ANGPT4 -0.014 0.095 -10000 0 -0.43 13 13
response to hypoxia -0.001 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.071 0.28 -10000 0 -1.1 13 13
alpha5/beta1 Integrin 0.016 0.039 -10000 0 -0.43 2 2
FGF2 -0.013 0.11 -10000 0 -0.47 14 14
STAT5A (dimer) -0.006 0.27 -10000 0 -0.89 15 15
mol:L-citrulline 0.015 0.19 -10000 0 -0.7 11 11
AGTR1 -0.004 0.076 -10000 0 -0.43 8 8
MAPK14 -0.007 0.26 -10000 0 -1.2 11 11
Tie2/SHP2 -0.017 0.23 -10000 0 -1.1 10 10
TEK -0.022 0.25 -10000 0 -1.2 10 10
RPS6KB1 0.004 0.23 -10000 0 -0.89 12 12
Angiotensin II/AT1 -0.001 0.054 -10000 0 -0.3 8 8
Tie2/Ang1/GRB2 -0.004 0.24 -10000 0 -1.1 11 11
MAPK3 0.003 0.22 -10000 0 -1 11 11
MAPK1 0.004 0.22 -10000 0 -1 11 11
Tie2/Ang1/GRB7 -0.018 0.25 -10000 0 -1.1 11 11
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
MAPK8 -0.007 0.25 -10000 0 -1.1 11 11
PI3K -0.008 0.26 -10000 0 -1.1 11 11
FES -0.008 0.26 -10000 0 -1.2 11 11
Crk/Dok-R -0.002 0.23 -10000 0 -1 11 11
Tie2/Ang1/ABIN2 -0.004 0.24 -10000 0 -1.1 11 11
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.006 0.21 -10000 0 -0.85 11 11
STAT5A 0.012 0.027 -10000 0 -0.43 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.006 0.22 -10000 0 -0.92 11 11
Tie2/Ang2 -0.016 0.29 -10000 0 -1.1 15 15
Tie2/Ang1 -0.011 0.25 -10000 0 -1.2 11 11
FOXO1 0.004 0.23 -10000 0 -0.82 13 13
ELF1 0.014 0.044 -10000 0 -0.6 1 1
ELF2 -0.008 0.24 -10000 0 -1.1 11 11
mol:Choline -0.002 0.23 -10000 0 -1 11 11
cell migration -0.025 0.056 -10000 0 -0.24 11 11
FYN 0 0.24 -10000 0 -0.86 15 15
DOK2 0.001 0.083 -10000 0 -0.54 6 6
negative regulation of cell cycle -0.005 0.24 -10000 0 -0.68 27 27
ETS1 0.016 0.044 -10000 0 -0.6 1 1
PXN 0.018 0.19 -10000 0 -0.74 11 11
ITGB1 0.011 0.037 -10000 0 -0.6 1 1
NOS3 0.01 0.21 -10000 0 -0.81 11 11
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.06 0.19 -10000 0 -0.51 40 40
MAPKKK cascade -0.002 0.23 -10000 0 -1 11 11
RASA1 0.011 0.037 -10000 0 -0.6 1 1
Tie2/Ang1/Shc -0.005 0.24 -10000 0 -1.1 11 11
NCK1 0.011 0.037 -10000 0 -0.6 1 1
vasculogenesis 0.018 0.17 -10000 0 -0.62 11 11
mol:Phosphatidic acid -0.002 0.23 -10000 0 -1 11 11
mol:Angiotensin II 0 0.006 -10000 0 -10000 0 0
mol:NADP 0.015 0.19 -10000 0 -0.7 11 11
Rac1/GTP -0.06 0.18 -10000 0 -0.85 11 11
MMP2 -0.031 0.26 -10000 0 -1.1 12 12
Signaling events mediated by PRL

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
CCNE1 -0.024 0.14 -10000 0 -0.54 18 18
mol:Halofuginone 0.002 0.027 -10000 0 -0.23 3 3
ITGA1 0.001 0.076 -10000 0 -0.46 7 7
CDKN1A -0.013 0.15 -10000 0 -0.48 18 18
PRL-3/alpha Tubulin 0.015 0.044 -10000 0 -0.39 3 3
mol:Ca2+ -0.092 0.17 0.34 3 -0.37 69 72
AGT -0.12 0.23 -10000 0 -0.5 69 69
CCNA2 -0.006 0.17 -10000 0 -0.96 6 6
TUBA1B 0.013 0 -10000 0 -10000 0 0
EGR1 -0.009 0.12 -10000 0 -0.4 20 20
CDK2/Cyclin E1 -0.018 0.15 -10000 0 -0.43 19 19
MAPK3 0.015 0.048 -10000 0 -0.36 4 4
PRL-2 /Rab GGTase beta 0.02 0 -10000 0 -10000 0 0
MAPK1 0.017 0.044 -10000 0 -0.39 3 3
PTP4A1 -0.004 0.16 -10000 0 -0.98 6 6
PTP4A3 0.007 0.059 -10000 0 -0.54 3 3
PTP4A2 0.013 0 -10000 0 -10000 0 0
ITGB1 0.015 0.052 -10000 0 -0.4 4 4
SRC 0.011 0.037 -10000 0 -0.6 1 1
RAC1 0.013 0.082 -10000 0 -0.4 7 7
Rab GGTase beta/Rab GGTase alpha 0.02 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.001 0.16 -10000 0 -0.92 6 6
RABGGTA 0.013 0 -10000 0 -10000 0 0
BCAR1 0.002 0.046 0.34 3 -0.45 1 4
RHOC 0.013 0.082 -10000 0 -0.4 7 7
RHOA 0.013 0.082 -10000 0 -0.4 7 7
cell motility 0.015 0.092 -10000 0 -0.46 7 7
PRL-1/alpha Tubulin 0.003 0.16 -10000 0 -0.92 6 6
PRL-3/alpha1 Integrin 0.006 0.069 -10000 0 -0.34 10 10
ROCK1 0.015 0.093 -10000 0 -0.46 7 7
RABGGTB 0.013 0 -10000 0 -10000 0 0
CDK2 0.012 0.027 -10000 0 -0.43 1 1
mitosis -0.004 0.16 -10000 0 -0.96 6 6
ATF5 0.01 0.039 -10000 0 -0.43 2 2
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.002 -9999 0 -10000 0 0
SMARCC1 0.006 0.011 -9999 0 -10000 0 0
REL 0.011 0.037 -9999 0 -0.6 1 1
HDAC7 0.004 0.14 -9999 0 -0.63 7 7
JUN 0.007 0.053 -9999 0 -0.49 3 3
EP300 0.013 0 -9999 0 -10000 0 0
KAT2B -0.005 0.1 -9999 0 -0.6 8 8
KAT5 0.011 0.037 -9999 0 -0.6 1 1
MAPK14 -0.007 0.11 -9999 0 -0.42 17 17
FOXO1 0.01 0.039 -9999 0 -0.43 2 2
T-DHT/AR 0.004 0.15 -9999 0 -0.57 11 11
MAP2K6 -0.025 0.15 -9999 0 -0.58 17 17
BRM/BAF57 0.015 0.039 -9999 0 -0.43 2 2
MAP2K4 0.011 0.037 -9999 0 -0.59 1 1
SMARCA2 0.008 0.053 -9999 0 -0.6 2 2
PDE9A -0.073 0.24 -9999 0 -1.2 9 9
NCOA2 -0.024 0.14 -9999 0 -0.56 17 17
CEBPA -0.017 0.13 -9999 0 -0.56 14 14
EHMT2 0.013 0.003 -9999 0 -10000 0 0
cell proliferation -0.017 0.17 -9999 0 -0.5 13 13
NR0B1 -0.025 0.11 -9999 0 -0.43 18 18
EGR1 -0.021 0.13 -9999 0 -0.51 17 17
RXRs/9cRA -0.05 0.14 -9999 0 -0.34 31 31
AR/RACK1/Src -0.006 0.13 -9999 0 -0.49 11 11
AR/GR -0.034 0.15 -9999 0 -0.46 21 21
GNB2L1 0.013 0.002 -9999 0 -10000 0 0
PKN1 0.012 0.027 -9999 0 -0.43 1 1
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.012 0.064 -9999 0 -0.44 5 5
T-DHT/AR/TIF2/CARM1 -0.018 0.15 -9999 0 -0.56 11 11
SRC 0.005 0.1 -9999 0 -0.43 7 7
NR3C1 -0.006 0.1 -9999 0 -0.56 9 9
KLK3 -0.14 0.22 -9999 0 -0.6 33 33
APPBP2 0.013 0.005 -9999 0 -10000 0 0
TRIM24 0.012 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.008 0.13 -9999 0 -0.53 12 12
TMPRSS2 -0.11 0.33 -9999 0 -1.2 20 20
RXRG -0.12 0.23 -9999 0 -0.51 65 65
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.011 0.037 -9999 0 -0.6 1 1
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.013 0.002 -9999 0 -10000 0 0
NR2C2 0.013 0 -9999 0 -10000 0 0
KLK2 -0.035 0.17 -9999 0 -0.57 9 9
AR -0.031 0.15 -9999 0 -0.55 14 14
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.01 0.053 -9999 0 -0.6 2 2
SRY 0.001 0.005 -9999 0 -10000 0 0
GATA2 -0.06 0.2 -9999 0 -0.58 33 33
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 -0.15 0.27 -9999 0 -0.59 70 70
T-DHT/AR/RACK1/Src -0.003 0.13 -9999 0 -0.5 11 11
positive regulation of transcription -0.06 0.2 -9999 0 -0.58 33 33
DNAJA1 0.013 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.031 -9999 0 -0.33 2 2
NCOA1 0.016 0.005 -9999 0 -10000 0 0
SPDEF -0.12 0.25 -9999 0 -0.59 60 60
T-DHT/AR/TIF2 -0.006 0.12 -9999 0 -0.41 12 12
T-DHT/AR/Hsp90 -0.007 0.13 -9999 0 -0.53 11 11
GSK3B 0.013 0.002 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.11 -9999 0 -0.38 18 18
SIRT1 0.002 0.083 -9999 0 -0.6 5 5
ZMIZ2 0.014 0.005 -9999 0 -10000 0 0
POU2F1 0.02 0.028 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.027 0.14 -9999 0 -0.54 13 13
CREBBP 0.013 0 -9999 0 -10000 0 0
SMARCE1 0.013 0.003 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.001 0.074 -10000 0 -0.36 3 3
epithelial cell differentiation -0.069 0.13 -10000 0 -0.48 15 15
ITCH 0.017 0.054 -10000 0 -0.58 2 2
WWP1 0.004 0.067 -10000 0 -10000 0 0
FYN 0.012 0.027 -10000 0 -0.43 1 1
EGFR -0.002 0.094 -10000 0 -0.57 7 7
PRL -0.021 0.11 -10000 0 -0.43 19 19
neuron projection morphogenesis 0.008 0.097 -10000 0 -0.4 1 1
PTPRZ1 -0.047 0.14 -10000 0 -0.43 33 33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.003 0.1 -10000 0 -0.45 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.023 0.11 -10000 0 -0.39 6 6
ADAM17 0.017 0.054 -10000 0 -0.58 2 2
ErbB4/ErbB4 -0.004 0.085 -10000 0 -0.42 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.034 0.1 -10000 0 -0.4 7 7
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.015 0.11 -10000 0 -0.41 5 5
GRIN2B -0.025 0.12 -10000 0 -0.47 5 5
ErbB4/ErbB2/betacellulin -0.013 0.11 -10000 0 -0.41 7 7
STAT1 0.006 0.06 -10000 0 -0.47 4 4
HBEGF 0.012 0.027 -10000 0 -0.43 1 1
PRLR -0.071 0.2 -10000 0 -0.56 39 39
E4ICDs/ETO2 -0.018 0.1 -10000 0 -0.38 10 10
axon guidance -0.001 0.084 -10000 0 -0.34 1 1
NEDD4 0.008 0.088 -10000 0 -0.56 6 6
Prolactin receptor/Prolactin receptor/Prolactin -0.066 0.17 -10000 0 -0.38 56 56
CBFA2T3 -0.021 0.13 -10000 0 -0.49 18 18
ErbB4/ErbB2/HBEGF 0.009 0.075 -10000 0 -0.42 3 3
MAPK3 0.002 0.099 -10000 0 -0.42 1 1
STAT1 (dimer) -0.002 0.084 -10000 0 -0.39 5 5
MAPK1 0.003 0.099 -10000 0 -0.42 1 1
JAK2 -0.007 0.11 -10000 0 -0.6 9 9
ErbB4/ErbB2/neuregulin 1 beta -0.02 0.11 -10000 0 -0.39 5 5
NRG1 -0.018 0.13 -10000 0 -0.38 29 29
NRG3 -0.036 0.13 -10000 0 -0.43 27 27
NRG2 -0.05 0.18 -10000 0 -0.53 31 31
NRG4 -0.031 0.15 -10000 0 -0.51 22 22
heart development -0.001 0.084 -10000 0 -0.34 1 1
neural crest cell migration -0.02 0.11 -10000 0 -0.39 5 5
ERBB2 0.015 0.065 -10000 0 -0.34 8 8
WWOX/E4ICDs 0.001 0.078 -10000 0 -0.4 4 4
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.022 0.12 -10000 0 -0.47 7 7
apoptosis 0.026 0.082 0.38 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.035 0.13 -10000 0 -0.39 21 21
ErbB4/ErbB2/epiregulin -0.02 0.11 -10000 0 -0.4 5 5
ErbB4/ErbB4/betacellulin/betacellulin -0.023 0.12 -10000 0 -0.37 21 21
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.047 0.17 -10000 0 -0.49 22 22
MDM2 0.001 0.087 -10000 0 -0.48 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.015 0.11 -10000 0 -0.38 6 6
STAT5A 0.005 0.081 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.023 0.12 -10000 0 -0.43 6 6
DLG4 0.004 0.074 -10000 0 -0.6 4 4
GRB2/SHC 0.02 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.001 0.066 -10000 0 -0.34 3 3
STAT5A (dimer) -0.073 0.14 -10000 0 -0.52 14 14
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.005 0.079 -10000 0 -10000 0 0
LRIG1 -0.031 0.16 -10000 0 -0.58 20 20
EREG -0.046 0.16 -10000 0 -0.45 34 34
BTC -0.028 0.15 -10000 0 -0.6 18 18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.085 -10000 0 -0.34 1 1
ERBB4 -0.004 0.085 -10000 0 -0.42 3 3
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 0.005 0.042 -10000 0 -0.56 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.015 0.11 -10000 0 -0.47 6 6
glial cell differentiation -0.001 0.066 0.34 3 -10000 0 3
WWOX 0.011 0.037 -10000 0 -0.6 1 1
cell proliferation -0.031 0.14 -10000 0 -0.51 9 9
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.012 0.11 -10000 0 -0.41 20 20
ATM 0.009 0.053 -10000 0 -0.6 2 2
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0 0.087 -10000 0 -0.57 6 6
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.022 0.032 -10000 0 -0.35 2 2
protein ubiquitination -0.013 0.12 -10000 0 -0.5 3 3
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0.026 0.024 -10000 0 -0.36 1 1
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0.019 0.055 -10000 0 -0.36 5 5
FA complex/FANCD2/Ubiquitin 0.032 0.057 -10000 0 -0.42 2 2
FANCF 0 0.09 -10000 0 -0.6 6 6
BRCA1 0.009 0.053 -10000 0 -0.6 2 2
CCNE1 -0.024 0.14 -10000 0 -0.54 18 18
CDK2/Cyclin E1 -0.009 0.1 -10000 0 -0.38 19 19
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.016 0.12 -10000 0 -0.41 22 22
FANCE 0.011 0.037 -10000 0 -0.6 1 1
FANCC 0.011 0.037 -10000 0 -0.6 1 1
NBN 0.011 0.037 -10000 0 -0.6 1 1
FANCA 0.012 0.027 -10000 0 -0.43 1 1
DNA repair 0.027 0.099 -10000 0 -0.54 2 2
BRCA1/BARD1/ubiquitin -0.016 0.12 -10000 0 -0.41 22 22
BARD1/DNA-PK 0.002 0.11 -10000 0 -0.38 18 18
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.012 0.11 0.4 20 -10000 0 20
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.082 -10000 0 -0.42 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.003 0.1 -10000 0 -0.36 18 18
BRCA1/BARD1/P53 -0.004 0.11 -10000 0 -0.32 26 26
BARD1/CSTF1/BRCA1 -0.003 0.1 -10000 0 -0.36 18 18
BRCA1/BACH1 0.009 0.053 -10000 0 -0.6 2 2
BARD1 -0.03 0.15 -10000 0 -0.56 20 20
PCNA 0.012 0.027 -10000 0 -0.43 1 1
BRCA1/BARD1/UbcH5C -0.003 0.1 -10000 0 -0.36 18 18
BRCA1/BARD1/UbcH7 -0.003 0.1 -10000 0 -0.36 18 18
BRCA1/BARD1/RAD51/PCNA 0.002 0.1 -10000 0 -0.34 20 20
BARD1/DNA-PK/P53 -0.001 0.12 -10000 0 -0.34 26 26
BRCA1/BARD1/Ubiquitin -0.016 0.12 -10000 0 -0.41 22 22
BRCA1/BARD1/CTIP -0.002 0.1 -10000 0 -0.32 23 23
FA complex 0.03 0.044 -10000 0 -10000 0 0
BARD1/EWS -0.012 0.11 -10000 0 -0.41 20 20
RBBP8 0.013 0.062 -10000 0 -0.43 5 5
TP53 -0.005 0.1 -10000 0 -0.6 8 8
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.005 0.11 0.32 26 -10000 0 26
BRCA1/BARD1 -0.01 0.12 -10000 0 -0.51 3 3
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.022 0.11 -10000 0 -0.41 20 20
CDK2 0.012 0.027 -10000 0 -0.43 1 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.006 0.064 -10000 0 -0.6 3 3
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.016 0.12 -10000 0 -0.41 22 22
EWSR1 0.013 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.005 0.1 -9999 0 -0.6 8 8
LRPAP1 0.006 0.064 -9999 0 -0.6 3 3
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.091 0.17 -9999 0 -0.38 48 48
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.076 0.15 -9999 0 -0.33 48 48
IQGAP1/CaM 0.02 0 -9999 0 -10000 0 0
DAB1 0.008 0.053 -9999 0 -0.49 3 3
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.02 0.13 -9999 0 -0.51 17 17
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.005 0.077 -9999 0 -0.38 10 10
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0.037 -9999 0 -0.6 1 1
CDK5R1 0.004 0.07 -9999 0 -0.5 5 5
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.038 0.14 -9999 0 -0.43 28 28
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.093 0.16 -9999 0 -0.37 49 49
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.052 0.13 -9999 0 -0.41 5 5
MAP1B -0.028 0.084 -9999 0 -0.31 19 19
RAC1 0.021 0 -9999 0 -10000 0 0
p35/CDK5 -0.058 0.14 -9999 0 -0.43 6 6
RELN -0.16 0.25 -9999 0 -0.51 86 86
PAFAH/LIS1 0.005 0.081 -9999 0 -0.36 8 8
LIS1/CLIP170 0.024 0.024 -9999 0 -0.36 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.061 0.084 -9999 0 -0.36 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.048 0.12 -9999 0 -0.45 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.062 0.14 -9999 0 -0.42 7 7
LIS1/IQGAP1 0.026 0 -9999 0 -10000 0 0
RHOA 0.021 0 -9999 0 -10000 0 0
PAFAH1B1 0.021 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.027 -9999 0 -0.43 1 1
PAFAH1B2 -0.003 0.098 -9999 0 -0.6 7 7
MAP1B/LIS1/Dynein heavy chain 0.005 0.059 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.045 0.13 -9999 0 -0.42 3 3
LRP8 0 0.084 -9999 0 -0.5 7 7
NDEL1/Katanin 60 -0.052 0.13 -9999 0 -0.41 5 5
P39/CDK5 -0.078 0.15 -9999 0 -0.42 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0 -9999 0 -10000 0 0
CDK5 -0.064 0.14 -9999 0 -0.43 4 4
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.02 -9999 0 -0.31 1 1
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.065 0.14 -9999 0 -0.37 5 5
RELN/VLDLR -0.085 0.16 -9999 0 -0.34 56 56
CDC42 0.019 0.028 -9999 0 -0.43 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.013 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.09 -9999 0 -0.36 12 12
forebrain development -0.079 0.25 -9999 0 -0.58 40 40
GNAO1 -0.013 0.11 -9999 0 -0.48 14 14
SMO/beta Arrestin2 0.003 0.08 -9999 0 -0.39 10 10
SMO -0.007 0.1 -9999 0 -0.56 9 9
ARRB2 0.01 0.028 -9999 0 -0.43 1 1
GLI3/SPOP 0.022 0.083 -9999 0 -0.49 1 1
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.013 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.03 0.044 -9999 0 -0.32 4 4
GNAI1 -0.01 0.11 -9999 0 -0.54 11 11
XPO1 0.006 0.065 -9999 0 -0.6 3 3
GLI1/Su(fu) -0.058 0.21 -9999 0 -0.58 24 24
SAP30 0.004 0.074 -9999 0 -0.6 4 4
mol:GDP -0.007 0.1 -9999 0 -0.56 9 9
MIM/GLI2A -0.022 0.13 -9999 0 -0.53 15 15
IFT88 0.011 0.037 -9999 0 -0.6 1 1
GNAI3 0.013 0.003 -9999 0 -10000 0 0
GLI2 0.024 0.055 -9999 0 -10000 0 0
GLI3 0.015 0.086 -9999 0 -0.52 1 1
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.013 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.011 0.037 -9999 0 -0.6 1 1
GNG2 -0.007 0.1 -9999 0 -0.51 10 10
Gi family/GTP -0.009 0.1 -9999 0 -0.47 5 5
SIN3B 0.013 0.001 -9999 0 -10000 0 0
SIN3A 0.013 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.028 0.077 -9999 0 -0.5 2 2
GLI2/Su(fu) 0.027 0.068 -9999 0 -0.34 1 1
FOXA2 -0.25 0.49 -9999 0 -1.2 55 55
neural tube patterning -0.079 0.25 -9999 0 -0.58 40 40
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.044 -9999 0 -0.36 1 1
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.022 0.13 -9999 0 -0.53 15 15
embryonic limb morphogenesis -0.079 0.25 -9999 0 -0.58 40 40
SUFU 0.014 0.049 -9999 0 -0.4 1 1
LGALS3 -0.002 0.091 -9999 0 -0.55 7 7
catabolic process 0.034 0.092 -9999 0 -0.57 1 1
GLI3A/CBP -0.031 0.12 -9999 0 -0.35 32 32
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.082 0.26 -9999 0 -0.61 39 39
RAB23 0.006 0.064 -9999 0 -0.6 3 3
CSNK1A1 0.011 0.037 -9999 0 -0.6 1 1
IFT172 0.012 0.027 -9999 0 -0.43 1 1
RBBP7 0.01 0.039 -9999 0 -0.43 2 2
Su(fu)/Galectin3 0.013 0.067 -9999 0 -0.33 6 6
GNAZ -0.016 0.12 -9999 0 -0.53 14 14
RBBP4 0.013 0.001 -9999 0 -10000 0 0
CSNK1G1 0.011 0.037 -9999 0 -0.6 1 1
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.029 0.051 -9999 0 -10000 0 0
STK36 0.011 0.038 -9999 0 -0.6 1 1
Gi family/GNB1/GNG2/GDP -0.004 0.1 -9999 0 -0.45 6 6
PTCH1 -0.073 0.26 -9999 0 -0.73 24 24
MIM/GLI1 -0.13 0.34 -9999 0 -0.67 63 63
CREBBP -0.031 0.12 -9999 0 -0.35 32 32
Su(fu)/SIN3/HDAC complex 0.041 0.034 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.019 0.13 -10000 0 -0.52 16 16
positive regulation of NF-kappaB transcription factor activity -0.032 0.14 -10000 0 -0.38 34 34
MAP2K4 0.026 0.063 -10000 0 -10000 0 0
IKBKB 0.013 0 -10000 0 -10000 0 0
TNFRSF10B 0.011 0.037 -10000 0 -0.6 1 1
TNFRSF10A 0.006 0.064 -10000 0 -0.6 3 3
SMPD1 0.006 0.05 -10000 0 -0.22 10 10
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.025 0.14 -10000 0 -0.53 19 19
TRAIL/TRAILR2 -0.006 0.099 -10000 0 -0.38 17 17
TRAIL/TRAILR3 -0.04 0.16 -10000 0 -0.42 36 36
TRAIL/TRAILR1 -0.009 0.1 -10000 0 -0.38 19 19
TRAIL/TRAILR4 -0.032 0.14 -10000 0 -0.38 34 34
TRAIL/TRAILR1/DAP3/GTP 0.003 0.082 -10000 0 -0.33 12 12
IKK complex -0.008 0.028 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.004 0.097 -10000 0 -0.37 17 17
MAP3K1 0.021 0.063 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.025 0.14 -10000 0 -0.53 19 19
TRADD 0.011 0.037 -10000 0 -0.6 1 1
TRAILR1 (trimer) 0.006 0.064 -10000 0 -0.6 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.066 -10000 0 -10000 0 0
CFLAR 0.013 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.095 -10000 0 -0.37 16 16
TRAIL/TRAILR1/FADD/TRADD/RIP 0.017 0.081 -10000 0 -10000 0 0
mol:ceramide 0.006 0.05 -10000 0 -0.22 10 10
FADD 0.013 0 -10000 0 -10000 0 0
MAPK8 0.026 0.078 -10000 0 -0.52 2 2
TRAF2 0.013 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.037 0.16 -10000 0 -0.55 24 24
CHUK 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.002 0.09 -10000 0 -0.36 12 12
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 -0.007 0.096 0.27 8 -0.36 10 18
JNK cascade -0.032 0.14 -10000 0 -0.38 34 34
TRAIL (trimer) -0.019 0.13 -10000 0 -0.52 16 16
TNFRSF10C -0.037 0.16 -10000 0 -0.55 24 24
TRAIL/TRAILR1/DAP3/GTP/FADD 0.01 0.078 -10000 0 -0.31 12 12
TRAIL/TRAILR2/FADD 0.005 0.085 -10000 0 -0.36 10 10
cell death 0.006 0.05 -10000 0 -0.22 10 10
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.019 0.061 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.011 0.037 -10000 0 -0.6 1 1
CASP8 0.006 0.027 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.02 0.076 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.21 -9999 0 -0.46 69 69
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.013 0 -9999 0 -10000 0 0
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.012 0.064 -9999 0 -0.28 8 8
HIF1A 0.014 0.039 -9999 0 -0.24 4 4
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.036 0.036 -9999 0 -10000 0 0
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.1 0.21 -9999 0 -0.47 64 64
ARNT/IPAS -0.069 0.15 -9999 0 -0.32 69 69
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.021 0.038 -9999 0 -10000 0 0
CUL2 0.011 0.037 -9999 0 -0.6 1 1
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.027 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.021 0.038 -9999 0 -10000 0 0
PHD1-3/OS9 0.016 0.079 -9999 0 -0.32 13 13
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.036 -9999 0 -10000 0 0
VHL 0.009 0.053 -9999 0 -0.6 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.021 0.038 -9999 0 -10000 0 0
EGLN3 -0.018 0.13 -9999 0 -0.58 14 14
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 -0.005 0.1 -9999 0 -0.6 8 8
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.053 -9999 0 -0.53 2 2
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.034 0.11 -9999 0 -0.3 20 20
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0 0.16 -9999 0 -0.69 7 7
MAP3K8 -0.001 0.091 -9999 0 -0.6 6 6
FOS -0.002 0.14 -9999 0 -0.67 7 7
PRKCA -0.004 0.1 -9999 0 -0.58 8 8
PTPN7 -0.003 0.095 -9999 0 -0.54 8 8
HRAS 0.013 0.001 -9999 0 -10000 0 0
PRKCB -0.03 0.15 -9999 0 -0.53 21 21
NRAS 0.004 0.074 -9999 0 -0.6 4 4
RAS family/GTP 0.02 0.044 -9999 0 -0.33 4 4
MAPK3 0 0.12 -9999 0 -0.67 6 6
MAP2K1 -0.011 0.15 -9999 0 -0.5 18 18
ELK1 0.013 0.005 -9999 0 -10000 0 0
BRAF -0.013 0.15 -9999 0 -0.5 18 18
mol:GTP 0 0.001 -9999 0 -0.005 20 20
MAPK1 0 0.12 -9999 0 -0.76 5 5
RAF1 -0.013 0.15 -9999 0 -0.5 18 18
KRAS 0.013 0.001 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.001 0.086 -10000 0 -0.36 14 14
MAP4K4 -0.011 0.12 -10000 0 -0.56 8 8
BAG4 0.009 0.053 -10000 0 -0.6 2 2
PKC zeta/ceramide -0.003 0.042 0.16 5 -10000 0 5
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.052 0.18 -10000 0 -0.54 31 31
BAX 0.002 0.023 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.017 0.008 -10000 0 -10000 0 0
BAD -0.004 0.044 0.17 5 -10000 0 5
SMPD1 -0.005 0.071 -10000 0 -0.27 7 7
RB1 -0.021 0.083 0.17 4 -0.32 14 18
FADD/Caspase 8 0 0.12 -10000 0 -0.53 8 8
MAP2K4 -0.001 0.049 0.18 1 -0.31 2 3
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.001 0.05 0.18 1 -0.34 2 3
EGF -0.083 0.2 -10000 0 -0.5 50 50
mol:ceramide -0.012 0.047 0.17 5 -10000 0 5
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0 0.09 -10000 0 -0.36 15 15
ASAH1 0.011 0.037 -10000 0 -0.6 1 1
negative regulation of cell cycle -0.021 0.082 0.17 4 -0.32 14 18
cell proliferation -0.015 0.088 -10000 0 -0.27 20 20
BID -0.002 0.08 -10000 0 -0.34 7 7
MAP3K1 -0.006 0.048 0.17 4 -0.25 2 6
EIF2A 0.001 0.063 -10000 0 -0.34 5 5
TRADD 0.011 0.037 -10000 0 -0.6 1 1
CRADD 0.006 0.064 -10000 0 -0.6 3 3
MAPK3 0.01 0.048 0.18 1 -0.31 2 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.01 0.048 0.18 1 -0.31 2 3
Cathepsin D/ceramide -0.004 0.044 0.16 5 -0.19 1 6
FADD -0.011 0.12 -10000 0 -0.56 8 8
KSR1 -0.007 0.053 0.17 5 -0.36 2 7
MAPK8 0.002 0.051 0.17 2 -0.23 4 6
PRKRA -0.004 0.044 0.17 5 -10000 0 5
PDGFA -0.014 0.12 -10000 0 -0.5 14 14
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.058 0.18 -10000 0 -0.51 36 36
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.047 0.17 5 -10000 0 5
CTSD 0.012 0.027 -10000 0 -0.43 1 1
regulation of nitric oxide biosynthetic process 0.018 0.028 -10000 0 -0.43 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.015 0.095 -10000 0 -0.29 20 20
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0 0.09 -10000 0 -0.36 15 15
RelA/NF kappa B1 0.018 0.028 -10000 0 -0.43 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.018 0.13 -10000 0 -0.56 9 9
TNFR1A/BAG4/TNF-alpha -0.026 0.13 -10000 0 -0.4 20 20
mol:Sphingosine-1-phosphate 0.001 0.085 -10000 0 -0.36 14 14
MAP2K1 0.006 0.048 -10000 0 -0.32 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.006 0.046 0.16 10 -0.22 1 11
TNFRSF1A 0.011 0.037 -10000 0 -0.6 1 1
NFKB1 0.011 0.037 -10000 0 -0.6 1 1
TNFR1A/BAG4 0.015 0.048 -10000 0 -0.43 3 3
EIF2AK2 -0.002 0.053 0.18 1 -0.3 3 4
TNF-alpha/TNFR1A/FAN -0.023 0.12 -10000 0 -0.38 19 19
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.075 -10000 0 -0.38 2 2
MAP2K2 0.006 0.048 -10000 0 -0.32 2 2
SMPD3 -0.04 0.14 -10000 0 -0.41 25 25
TNF -0.066 0.19 -10000 0 -0.51 40 40
PKC zeta/PAR4 0.02 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.02 0.084 0.19 41 -10000 0 41
NF kappa B1/RelA/I kappa B alpha 0.038 0.021 -10000 0 -10000 0 0
AIFM1 0.007 0.046 0.16 9 -0.22 1 10
BCL2 -0.02 0.13 -10000 0 -0.54 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.009 0.053 -9999 0 -0.6 2 2
Caspase 8 (4 units) 0.006 0.086 -9999 0 -0.39 2 2
NEF -0.016 0.055 -9999 0 -10000 0 0
NFKBIA 0.004 0.034 -9999 0 -10000 0 0
BIRC3 -0.029 0.19 -9999 0 -0.55 31 31
CYCS 0.004 0.1 -9999 0 -0.44 3 3
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.046 0.18 -9999 0 -0.65 19 19
MAP2K7 0.008 0.089 -9999 0 -0.43 3 3
protein ubiquitination 0.02 0.095 -9999 0 -0.43 5 5
CRADD 0.006 0.064 -9999 0 -0.6 3 3
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.01 0.039 -9999 0 -0.43 2 2
BID 0 0.1 -9999 0 -0.42 2 2
NF-kappa-B/RelA/I kappa B alpha 0.001 0.099 -9999 0 -0.35 1 1
TRADD 0.011 0.037 -9999 0 -0.6 1 1
MAP3K5 0.003 0.075 -9999 0 -0.53 5 5
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.001 0.1 -9999 0 -0.35 1 1
MAPK8 0.01 0.097 -9999 0 -0.59 2 2
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 0.006 0.064 -9999 0 -0.6 3 3
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.007 0.11 -9999 0 -0.28 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.006 0.12 -9999 0 -0.6 5 5
CHUK 0.019 0.1 -9999 0 -0.48 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.032 0.045 -9999 0 -10000 0 0
TCRz/NEF -0.051 0.17 -9999 0 -0.44 37 37
TNF -0.066 0.19 -9999 0 -0.51 40 40
FASLG -0.079 0.26 -9999 0 -0.64 42 42
NFKB1 0.002 0.05 -9999 0 -0.59 1 1
TNFR1A/BAG4/TNF-alpha -0.026 0.13 -9999 0 -0.4 20 20
CASP6 0.021 0.075 -9999 0 -0.53 1 1
CASP7 -0.007 0.18 -9999 0 -0.53 23 23
RELA 0.004 0.034 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 -0.004 0.18 -9999 0 -0.54 22 22
TNFRSF1A 0.011 0.037 -9999 0 -0.6 1 1
TNFR1A/BAG4 0.015 0.048 -9999 0 -0.43 3 3
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.013 0.11 -9999 0 -0.54 5 5
APAF-1/Caspase 9 -0.058 0.13 -9999 0 -0.41 25 25
BCL2 0.001 0.11 -9999 0 -0.44 5 5
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 -0.01 0.1 -9999 0 -0.47 13 13
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.012 0.045 -9999 0 -0.3 3 3
GNAO1 -0.013 0.11 -9999 0 -0.48 14 14
mol:Sphinganine-1-P 0.004 0.076 -9999 0 -0.33 13 13
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.039 -9999 0 -0.3 1 1
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.018 0.028 -9999 0 -0.43 1 1
S1PR3 0.007 0.059 -9999 0 -0.54 3 3
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.007 0.038 -9999 0 -0.26 3 3
S1PR5 -0.033 0.15 -9999 0 -0.52 23 23
S1PR4 -0.013 0.12 -9999 0 -0.53 13 13
GNAI1 -0.009 0.11 -9999 0 -0.54 11 11
S1P/S1P5/G12 -0.003 0.098 -9999 0 -0.34 14 14
S1P/S1P3/Gq -0.003 0.1 -9999 0 -0.47 5 5
S1P/S1P4/Gi -0.003 0.098 -9999 0 -0.42 4 4
GNAQ 0.006 0.064 -9999 0 -0.6 3 3
GNAZ -0.015 0.12 -9999 0 -0.53 14 14
GNA14 -0.013 0.12 -9999 0 -0.57 12 12
GNA15 -0.001 0.087 -9999 0 -0.53 7 7
GNA12 0.011 0.037 -9999 0 -0.6 1 1
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.018 0.13 -9999 0 -0.57 14 14
ABCC1 0.013 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.01 0.098 -9999 0 -0.35 14 14
RGS9BP -0.022 0.12 -9999 0 -0.43 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0 0.05 -9999 0 -0.25 10 10
mol:ADP 0.005 0.02 -9999 0 -0.31 1 1
GNAT2 0.006 0.047 -9999 0 -0.43 3 3
RGS9-1/Gbeta5/R9AP -0.029 0.13 -9999 0 -0.42 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.005 0.028 -9999 0 -0.26 3 3
GRK7 0.007 0.028 -9999 0 -0.43 1 1
CNGB3 -0.005 0.071 -9999 0 -0.43 7 7
Cone Metarhodopsin II/X-Arrestin 0.003 0.02 -9999 0 -0.31 1 1
mol:Ca2+ -0.003 0.059 -9999 0 -0.45 1 1
Cone PDE6 -0.021 0.11 -9999 0 -0.36 15 15
Cone Metarhodopsin II 0.004 0.015 -9999 0 -0.23 1 1
Na + (4 Units) -0.002 0.06 -9999 0 -0.45 1 1
GNAT2/GDP -0.02 0.11 -9999 0