Head and Neck Squamous Cell Carcinoma: Paradigm Report
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/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 131 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
TCGA08_p53 29
TRAIL signaling pathway 27
E-cadherin signaling in keratinocytes 24
EPO signaling pathway 20
E-cadherin signaling events 20
Syndecan-2-mediated signaling events 18
FOXA2 and FOXA3 transcription factor networks 17
Glypican 1 network 17
TCR signaling in naïve CD8+ T cells 16
Syndecan-1-mediated signaling events 15
Results

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
TCGA08_p53 29 204 7 -0.018 0.006 1000 -1000 -0.017 -1000
TRAIL signaling pathway 27 1313 48 -0.018 0.038 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 24 1064 43 -0.028 0.027 1000 -1000 -0.018 -1000
EPO signaling pathway 20 1102 55 -0.029 0.034 1000 -1000 -0.028 -1000
E-cadherin signaling events 20 102 5 -0.018 0.028 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 18 1283 69 -0.024 0.025 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 17 809 46 -0.022 0.012 1000 -1000 -0.022 -1000
Glypican 1 network 17 852 48 -0.023 0.028 1000 -1000 -0.023 -1000
TCR signaling in naïve CD8+ T cells 16 1498 93 -0.046 0.025 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 15 512 34 -0.023 0.024 1000 -1000 -0.022 -1000
ErbB4 signaling events 14 991 69 -0.032 0.034 1000 -1000 -0.019 -1000
BARD1 signaling events 14 802 57 -0.033 0.041 1000 -1000 -0.034 -1000
Glypican 2 network 14 58 4 -0.018 0.022 1000 -1000 -0.018 -1000
Wnt signaling 14 100 7 -0.018 -0.016 1000 -1000 -0.018 -1000
VEGFR1 specific signals 14 792 56 -0.032 0.015 1000 -1000 -0.032 -1000
Noncanonical Wnt signaling pathway 13 363 26 -0.025 0.011 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 13 613 44 -0.025 0.038 1000 -1000 -0.021 -1000
Nectin adhesion pathway 13 861 63 -0.018 0.037 1000 -1000 -0.018 -1000
IL1-mediated signaling events 13 832 62 -0.038 0.037 1000 -1000 -0.038 -1000
ceramide signaling pathway 13 662 49 -0.02 0.033 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 13 423 31 -0.022 0.017 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 13 622 45 -0.023 0.031 1000 -1000 -0.028 -1000
EPHB forward signaling 13 1124 85 -0.044 0.055 1000 -1000 -0.038 -1000
Stabilization and expansion of the E-cadherin adherens junction 13 1013 74 -0.037 0.036 1000 -1000 -0.038 -1000
Signaling events mediated by PRL 13 470 34 -0.024 0.024 1000 -1000 -0.024 -1000
IL12-mediated signaling events 12 1065 87 -0.08 0.041 1000 -1000 -0.018 -1000
Signaling events mediated by the Hedgehog family 12 641 52 -0.021 0.026 1000 -1000 -0.02 -1000
Signaling events mediated by PTP1B 12 984 76 -0.027 0.029 1000 -1000 -0.018 -1000
BMP receptor signaling 12 1046 81 -0.034 0.041 1000 -1000 -0.027 -1000
Endothelins 12 1161 96 -0.083 0.028 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 12 624 51 -0.021 0.16 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 12 330 26 -0.03 0.041 1000 -1000 -0.018 -1000
IGF1 pathway 12 719 57 -0.032 0.049 1000 -1000 -0.032 -1000
LPA4-mediated signaling events 11 141 12 -0.017 0.025 1000 -1000 -0.016 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 11 609 54 -0.042 0.034 1000 -1000 -0.031 -1000
Arf6 signaling events 11 685 62 -0.018 0.043 1000 -1000 -0.018 -1000
mTOR signaling pathway 11 629 53 -0.034 0.025 1000 -1000 -0.027 -1000
IFN-gamma pathway 11 794 68 -0.037 0.036 1000 -1000 -0.037 -1000
Ceramide signaling pathway 11 874 76 -0.026 0.042 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 11 434 37 -0.035 0.041 1000 -1000 -0.022 -1000
S1P1 pathway 11 410 36 -0.044 0.012 1000 -1000 -0.019 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 11 788 68 -0.018 0.038 1000 -1000 -0.022 -1000
E-cadherin signaling in the nascent adherens junction 11 869 76 -0.037 0.045 1000 -1000 -0.036 -1000
Angiopoietin receptor Tie2-mediated signaling 11 988 88 -0.018 0.024 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 10 786 74 -0.025 0.027 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 10 426 39 -0.018 0.03 1000 -1000 -0.019 -1000
Visual signal transduction: Cones 10 393 38 -0.018 0.044 1000 -1000 -0.02 -1000
Fc-epsilon receptor I signaling in mast cells 10 981 97 -0.086 0.052 1000 -1000 -0.04 -1000
Insulin-mediated glucose transport 10 328 32 -0.02 0.023 1000 -1000 -0.02 -1000
Signaling events regulated by Ret tyrosine kinase 10 843 82 -0.029 0.038 1000 -1000 -0.033 -1000
FAS signaling pathway (CD95) 10 471 47 -0.023 0.035 1000 -1000 -0.022 -1000
IL2 signaling events mediated by PI3K 10 598 58 -0.018 0.028 1000 -1000 -0.02 -1000
Integrins in angiogenesis 10 892 84 -0.04 0.04 1000 -1000 -0.035 -1000
Nongenotropic Androgen signaling 10 569 52 -0.03 0.031 1000 -1000 -0.022 -1000
Plasma membrane estrogen receptor signaling 10 944 86 -0.072 0.036 1000 -1000 -0.029 -1000
Neurotrophic factor-mediated Trk receptor signaling 10 1222 120 -0.037 0.045 1000 -1000 -0.034 -1000
Visual signal transduction: Rods 10 533 52 -0.037 0.041 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 9 748 76 -0.018 0.029 1000 -1000 -0.018 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 9 226 23 -0.018 0.029 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 9 687 75 -0.022 0.043 1000 -1000 -0.02 -1000
PLK2 and PLK4 events 9 28 3 -0.02 -1000 1000 -1000 -0.02 -1000
Thromboxane A2 receptor signaling 9 967 105 -0.025 0.021 1000 -1000 -0.026 -1000
HIF-1-alpha transcription factor network 9 741 76 -0.025 0.041 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 9 821 85 -0.018 0.04 1000 -1000 -0.022 -1000
IL4-mediated signaling events 9 858 91 -0.07 0.024 1000 -1000 -0.018 -1000
amb2 Integrin signaling 9 779 82 -0.034 0.042 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 9 658 68 -0.022 0.037 1000 -1000 -0.025 -1000
Reelin signaling pathway 9 509 56 -0.036 0.043 1000 -1000 -0.034 -1000
Ephrin B reverse signaling 9 437 48 -0.026 0.027 1000 -1000 -0.026 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 9 773 83 -0.026 0.033 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 9 334 35 -0.018 0.045 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 9 1238 125 -0.038 0.027 1000 -1000 -0.032 -1000
IL27-mediated signaling events 9 490 51 -0.02 0.033 1000 -1000 -0.021 -1000
LPA receptor mediated events 9 968 102 -0.041 0.018 1000 -1000 -0.027 -1000
IL2 signaling events mediated by STAT5 9 199 22 -0.02 0.006 1000 -1000 -0.02 -1000
Class I PI3K signaling events 9 676 73 -0.024 0.021 1000 -1000 -0.022 -1000
Regulation of Telomerase 9 950 102 -0.022 0.05 1000 -1000 -0.022 -1000
EGFR-dependent Endothelin signaling events 9 200 21 -0.031 0.04 1000 -1000 -0.029 -1000
IL23-mediated signaling events 9 599 60 -0.018 0.029 1000 -1000 -0.018 -1000
Insulin Pathway 9 726 74 -0.04 0.047 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 9 954 97 -0.037 0.041 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 9 713 78 -0.041 0.026 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 9 402 44 -0.044 0.037 1000 -1000 -0.018 -1000
ErbB2/ErbB3 signaling events 8 530 65 -0.036 0.029 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 8 1208 136 -0.12 0.042 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 8 1105 125 -0.043 0.046 1000 -1000 -0.038 -1000
PLK1 signaling events 8 693 85 -0.058 0.049 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 8 1022 114 -0.032 0.042 1000 -1000 -0.028 -1000
S1P5 pathway 8 151 17 -0.018 0.011 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 8 880 104 -0.023 0.041 1000 -1000 -0.021 -1000
FoxO family signaling 8 530 64 -0.037 0.022 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 8 121 15 -0.024 0 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 8 290 36 -0.034 0.033 1000 -1000 -0.029 -1000
Effects of Botulinum toxin 8 219 26 -0.022 0.027 1000 -1000 -0.024 -1000
Calcium signaling in the CD4+ TCR pathway 8 267 31 -0.03 0.012 1000 -1000 -0.03 -1000
IL6-mediated signaling events 8 645 75 -0.025 0.037 1000 -1000 -0.024 -1000
FOXM1 transcription factor network 8 458 51 -0.018 0.05 1000 -1000 -0.018 -1000
Ephrin A reverse signaling 7 49 7 -0.019 0.021 1000 -1000 -0.018 -1000
Hedgehog signaling events mediated by Gli proteins 7 468 65 -0.018 0.041 1000 -1000 -0.018 -1000
Retinoic acid receptors-mediated signaling 7 406 58 -0.033 0.031 1000 -1000 -0.03 -1000
Regulation of p38-alpha and p38-beta 7 412 54 -0.018 0.04 1000 -1000 -0.018 -1000
BCR signaling pathway 7 715 99 -0.041 0.043 1000 -1000 -0.037 -1000
S1P3 pathway 7 319 42 -0.025 0.024 1000 -1000 -0.018 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 7 252 33 -0.04 0.04 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 7 142 20 -0.018 0.022 1000 -1000 -0.018 -1000
S1P4 pathway 7 184 25 -0.018 0.024 1000 -1000 -0.018 -1000
Regulation of Androgen receptor activity 7 533 70 -0.029 0.03 1000 -1000 -0.027 -1000
Ras signaling in the CD4+ TCR pathway 7 127 17 -0.018 0.028 1000 -1000 -0.018 -1000
Circadian rhythm pathway 6 149 22 -0.018 0.032 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 6 397 61 -0.021 0.045 1000 -1000 -0.018 -1000
RXR and RAR heterodimerization with other nuclear receptor 6 342 52 -0.029 0.045 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 6 298 43 -0.051 0.028 1000 -1000 -0.019 -1000
Arf6 trafficking events 6 433 71 -0.021 0.022 1000 -1000 -0.019 -1000
TCGA08_retinoblastoma 6 53 8 -0.012 0.032 1000 -1000 -0.018 -1000
Class IB PI3K non-lipid kinase events 6 18 3 -0.018 -1000 1000 -1000 -0.017 -1000
Arf1 pathway 6 365 54 -0.02 0.023 1000 -1000 -0.018 -1000
Aurora B signaling 6 405 67 -0.022 0.048 1000 -1000 -0.02 -1000
Osteopontin-mediated events 5 191 38 -0.042 0.032 1000 -1000 -0.031 -1000
JNK signaling in the CD4+ TCR pathway 5 100 17 -0.018 0.043 1000 -1000 -0.018 -1000
Cellular roles of Anthrax toxin 5 228 39 -0.023 0.022 1000 -1000 -0.018 -1000
Arf6 downstream pathway 5 225 43 -0.031 0.032 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class III 5 209 40 -0.033 0.033 1000 -1000 -0.029 -1000
Sumoylation by RanBP2 regulates transcriptional repression 5 137 27 -0.026 0.037 1000 -1000 -0.023 -1000
Syndecan-4-mediated signaling events 5 373 67 -0.039 0.024 1000 -1000 -0.028 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 168 34 -0.026 0.043 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 4 21 5 -0.018 0.025 1000 -1000 -0.017 -1000
Aurora A signaling 4 259 60 -0.019 0.035 1000 -1000 -0.02 -1000
Signaling mediated by p38-alpha and p38-beta 4 177 44 -0.027 0.029 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 4 61 13 -0.018 0.046 1000 -1000 -0.018 -1000
Sphingosine 1-phosphate (S1P) pathway 3 107 28 -0.022 0.024 1000 -1000 -0.02 -1000
Aurora C signaling 2 18 7 -0.018 0.031 1000 -1000 -0.018 -1000
Total 1287 74383 7203 -3.9 -2000 131000 -131000 -3.1 -131000
TCGA08_p53

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
CDKN2A -0.008 0.005 0 44 -9999 0 44
TP53 0.006 0.004 -10000 0 0 51 51
Senescence 0.006 0.004 -10000 0 0 51 51
Apoptosis 0.006 0.004 -10000 0 0 51 51
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 -0.004 0.034 0.3 2 -9999 0 2
MDM4 -0.018 0.003 0 5 -9999 0 5
TRAIL signaling pathway

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
TNFSF10 -0.013 0.008 0 47 -10000 0 47
positive regulation of NF-kappaB transcription factor activity 0.017 0.012 -10000 0 0 54 54
MAP2K4 0.007 0.04 -10000 0 -0.19 3 3
IKBKB -0.016 0.006 0 18 -10000 0 18
TNFRSF10B -0.017 0.004 0 9 -10000 0 9
TNFRSF10A -0.017 0.004 0 9 -10000 0 9
SMPD1 -0.005 0.003 0 54 -10000 0 54
IKBKG -0.018 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.017 0.004 0 9 -10000 0 9
TRAIL/TRAILR2 0.017 0.012 -10000 0 0 54 54
TRAIL/TRAILR3 0.017 0.012 -10000 0 0 54 54
TRAIL/TRAILR1 0.017 0.012 -10000 0 0 54 54
TRAIL/TRAILR4 0.017 0.012 -10000 0 0 54 54
TRAIL/TRAILR1/DAP3/GTP 0.021 0.016 -10000 0 0 59 59
IKK complex -0.008 0.017 -10000 0 -0.2 1 1
RIPK1 -0.017 0.004 0 10 -10000 0 10
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0.003 -10000 0 0 10 10
MAPK3 -0.016 0.01 0 49 -10000 0 49
MAP3K1 0.013 0.043 0.085 29 -0.2 3 32
TRAILR4 (trimer) -0.017 0.004 0 9 -10000 0 9
TRADD -0.017 0.004 0 10 -10000 0 10
TRAILR1 (trimer) -0.017 0.004 0 9 -10000 0 9
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.007 0.021 -10000 0 -0.13 4 4
CFLAR -0.018 0.003 0 4 -10000 0 4
MAPK1 -0.015 0.01 0 51 -10000 0 51
TRAIL/TRAILR1/FADD/TRADD/RIP 0.023 0.025 -10000 0 -0.008 2 2
mol:ceramide -0.005 0.003 0 54 -10000 0 54
FADD -0.012 0.009 0 54 -10000 0 54
MAPK8 0.02 0.059 0.14 13 -0.2 3 16
TRAF2 -0.018 0.002 0 3 -10000 0 3
TRAILR3 (trimer) -0.017 0.004 0 9 -10000 0 9
CHUK -0.018 0.002 0 3 -10000 0 3
TRAIL/TRAILR1/FADD 0.017 0.017 -10000 0 0 84 84
DAP3 -0.017 0.004 0 10 -10000 0 10
CASP10 0.038 0.074 0.14 55 -10000 0 55
JNK cascade 0.017 0.012 -10000 0 0 54 54
TRAIL (trimer) -0.013 0.008 0 47 -10000 0 47
TNFRSF10C -0.017 0.004 0 9 -10000 0 9
TRAIL/TRAILR1/DAP3/GTP/FADD 0.019 0.02 -10000 0 0 86 86
TRAIL/TRAILR2/FADD 0.017 0.017 -10000 0 0 84 84
cell death -0.005 0.003 0 54 -10000 0 54
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.021 -10000 0 -0.13 4 4
TRAILR2 (trimer) -0.017 0.004 0 9 -10000 0 9
CASP8 -0.006 0.083 -10000 0 -0.36 7 7
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.023 0.025 -10000 0 -0.008 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.067 0.12 33 -0.16 8 41
adherens junction organization -0.014 0.079 0.13 4 -0.21 17 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.077 0.13 45 -0.13 6 51
FMN1 -0.008 0.071 0.13 3 -0.2 13 16
mol:IP3 -0.016 0.024 0.061 3 -0.12 4 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.072 -10000 0 -0.2 14 14
CTNNB1 -0.006 0.017 0.02 43 -10000 0 43
AKT1 -0.019 0.039 0.1 4 -0.16 6 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.028 0.15 0.13 1 -0.32 21 22
CTNND1 -0.004 0.02 0.024 55 -10000 0 55
mol:PI-4-5-P2 -0.01 0.07 0.13 3 -0.2 14 17
VASP -0.009 0.071 0.13 3 -0.2 14 17
ZYX -0.008 0.07 0.13 3 -0.21 12 15
JUB -0.01 0.07 0.13 3 -0.2 13 16
EGFR(dimer) -0.011 0.076 0.14 1 -0.18 18 19
E-cadherin/beta catenin-gamma catenin 0.027 0.014 -10000 0 0 32 32
mol:PI-3-4-5-P3 0.005 0.049 0.14 5 -0.12 14 19
PIK3CA -0.01 0.013 0.022 14 -10000 0 14
PI3K 0.006 0.049 0.15 5 -0.12 14 19
FYN 0 0.067 0.12 28 -0.17 8 36
mol:Ca2+ -0.015 0.024 0.061 3 -0.12 4 7
JUP -0.003 0.02 0.021 67 -10000 0 67
PIK3R1 -0.004 0.02 0.023 58 -10000 0 58
mol:DAG -0.016 0.024 0.061 3 -0.12 4 7
CDH1 -0.004 0.019 0.02 59 -10000 0 59
RhoA/GDP 0.02 0.073 0.13 45 -0.12 3 48
establishment of polarity of embryonic epithelium -0.009 0.07 0.13 3 -0.2 14 17
SRC -0.017 0.005 0 14 -10000 0 14
RAC1 -0.017 0.004 0 10 -10000 0 10
RHOA -0.016 0.006 0 23 -10000 0 23
EGFR -0.016 0.006 0 20 -10000 0 20
CASR -0.001 0.056 0.12 26 -0.12 4 30
RhoA/GTP 0.006 0.061 0.12 35 -0.1 3 38
AKT2 -0.019 0.042 0.098 6 -0.17 6 12
actin cable formation -0.014 0.069 0.12 3 -0.2 13 16
apoptosis 0.011 0.049 0.16 8 -0.14 7 15
CTNNA1 -0.004 0.02 0.024 55 -10000 0 55
mol:GDP 0.006 0.063 0.13 31 -0.13 4 35
PIP5K1A -0.01 0.071 0.13 3 -0.2 14 17
PLCG1 -0.016 0.024 0.062 3 -0.12 4 7
Rac1/GTP 0.006 0.074 0.13 1 -0.18 18 19
homophilic cell adhesion 0.001 0.004 0.012 6 -10000 0 6
EPO signaling pathway

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
BCL2L1 0.015 0.055 0.15 14 -0.14 3 17
CRKL 0.006 0.075 0.16 29 -10000 0 29
mol:DAG -0.003 0.038 0.1 17 -0.1 3 20
HRAS -0.002 0.081 0.2 12 -10000 0 12
MAPK8 0.008 0.071 0.16 27 -10000 0 27
RAP1A 0.01 0.079 0.16 32 -10000 0 32
GAB1 0.009 0.079 0.16 31 -10000 0 31
MAPK14 0.004 0.068 0.16 24 -10000 0 24
EPO -0.012 0.019 0.032 23 -10000 0 23
PLCG1 -0.003 0.039 0.1 17 -0.1 3 20
EPOR/TRPC2/IP3 Receptors -0.009 0.024 0.035 36 -10000 0 36
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
EPO/EPOR (dimer)/SOCS3 0.034 0.015 0.066 7 0 18 25
GAB1/SHC/GRB2/SOS1 -0.005 0.073 0.14 31 -10000 0 31
EPO/EPOR (dimer) 0.025 0.015 0.061 7 -0.022 5 12
IRS2 0.01 0.079 0.16 32 -10000 0 32
STAT1 -0.003 0.038 0.1 16 -0.1 3 19
STAT5B -0.003 0.039 0.1 17 -0.1 3 20
cell proliferation 0.002 0.077 0.17 26 -10000 0 26
GAB1/SHIP/PIK3R1/SHP2/SHC -0.022 0.048 0.095 21 -10000 0 21
TEC 0.007 0.077 0.16 28 -10000 0 28
SOCS3 -0.018 0.001 0 1 -10000 0 1
STAT1 (dimer) -0.003 0.037 0.1 16 -0.1 3 19
JAK2 -0.013 0.017 0.035 15 -10000 0 15
PIK3R1 -0.018 0.004 0 8 -10000 0 8
EPO/EPOR (dimer)/JAK2 0.028 0.032 0.17 7 -10000 0 7
EPO/EPOR 0.025 0.015 0.061 7 -0.022 5 12
LYN -0.016 0.006 0 18 -10000 0 18
TEC/VAV2 -0.008 0.054 0.12 22 -10000 0 22
elevation of cytosolic calcium ion concentration -0.008 0.024 0.035 36 -10000 0 36
SHC1 -0.018 0.004 0 7 -10000 0 7
EPO/EPOR (dimer)/LYN 0.03 0.017 0.066 5 0 33 38
mol:IP3 -0.003 0.038 0.1 17 -0.1 3 20
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.003 0.08 0.16 31 -10000 0 31
SH2B3 -0.002 0.006 0.021 9 -10000 0 9
NFKB1 0.005 0.068 0.16 24 -10000 0 24
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.018 0.077 1 -0.14 2 3
PTPN6 0.008 0.072 0.17 25 -10000 0 25
TEC/VAV2/GRB2 -0.011 0.056 0.13 22 -10000 0 22
EPOR -0.009 0.024 0.035 36 -10000 0 36
INPP5D -0.018 0.004 0 8 -10000 0 8
mol:GDP -0.005 0.074 0.14 31 -10000 0 31
SOS1 -0.018 0.002 0 3 -10000 0 3
PLCG2 -0.017 0.005 0 11 -10000 0 11
CRKL/CBL/C3G -0.01 0.054 0.12 21 -10000 0 21
VAV2 0.01 0.08 0.16 32 -10000 0 32
CBL 0.011 0.077 0.16 30 -10000 0 30
SHC/Grb2/SOS1 -0.029 0.017 -10000 0 -10000 0 0
STAT5A -0.003 0.039 0.1 17 -0.1 3 20
GRB2 -0.018 0.001 0 1 -10000 0 1
STAT5 (dimer) -0.008 0.042 0.11 17 -10000 0 17
LYN/PLCgamma2 0.021 0.009 -10000 0 0 26 26
PTPN11 -0.018 0.001 0 1 -10000 0 1
BTK 0.009 0.08 0.16 32 -10000 0 32
BCL2 0.012 0.071 0.14 20 -0.17 9 29
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.028 0.014 -9999 0 0 32 32
E-cadherin/beta catenin 0.021 0.01 -9999 0 0 30 30
CTNNB1 -0.015 0.007 0 28 -9999 0 28
JUP -0.018 0.002 0 3 -9999 0 3
CDH1 -0.017 0.004 0 9 -9999 0 9
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.015 0.006 0 26 -9999 0 26
EPHB2 -0.018 0.003 0 5 -9999 0 5
Syndecan-2/TACI -0.015 0.006 0 24 -9999 0 24
LAMA1 -0.017 0.005 0 13 -9999 0 13
Syndecan-2/alpha2 ITGB1 0.025 0.014 -10000 0 0 38 38
HRAS -0.018 0.003 0 5 -9999 0 5
Syndecan-2/CASK -0.008 0.003 0 22 -9999 0 22
ITGA5 -0.018 0 -10000 0 -9999 0 0
BAX -0.019 0.008 0 27 -9999 0 27
EPB41 -0.018 0.002 0 3 -9999 0 3
positive regulation of cell-cell adhesion -0.013 0.005 0 23 -9999 0 23
LAMA3 -0.017 0.005 0 11 -9999 0 11
EZR 0 0 -10000 0 -9999 0 0
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
CAV2 -0.018 0.004 0 7 -9999 0 7
Syndecan-2/MMP2 -0.014 0.007 0 29 -9999 0 29
RP11-540L11.1 0 0 -10000 0 -9999 0 0
alpha2 ITGB1 0.024 0.006 -10000 0 0 11 11
dendrite morphogenesis -0.015 0.006 0 26 -9999 0 26
Syndecan-2/GM-CSF -0.015 0.007 0 28 -9999 0 28
determination of left/right symmetry -0.01 0.004 0 22 -9999 0 22
Syndecan-2/PKC delta -0.013 0.007 0 39 -9999 0 39
GNB2L1 -0.017 0.004 0 10 -9999 0 10
MAPK3 0 0.062 0.18 18 -9999 0 18
MAPK1 0.002 0.063 0.18 19 -9999 0 19
Syndecan-2/RACK1 0.018 0.008 -10000 0 0 31 31
NF1 -0.018 0.001 0 1 -9999 0 1
FGFR/FGF/Syndecan-2 -0.01 0.004 0 22 -9999 0 22
ITGA2 -0.018 0.004 0 8 -9999 0 8
MAPK8 -0.015 0.006 0 25 -9999 0 25
Syndecan-2/alpha2/beta1 Integrin 0.025 0.014 -10000 0 0 39 39
Syndecan-2/Kininogen -0.011 0.008 0 60 -9999 0 60
ITGB1 -0.018 0.003 0 5 -9999 0 5
SRC -0.004 0.056 0.16 16 -9999 0 16
Syndecan-2/CASK/Protein 4.1 -0.013 0.005 0 24 -9999 0 24
extracellular matrix organization -0.015 0.006 0 23 -9999 0 23
actin cytoskeleton reorganization -0.015 0.006 0 26 -9999 0 26
Syndecan-2/Caveolin-2/Ras -0.019 0.009 0 31 -9999 0 31
Syndecan-2/Laminin alpha3 -0.014 0.007 0 30 -9999 0 30
Syndecan-2/RasGAP 0.024 0.012 -10000 0 0 33 33
alpha5/beta1 Integrin 0.024 0.004 -10000 0 0 5 5
PRKCD -0.016 0.006 0 24 -9999 0 24
Syndecan-2 dimer -0.015 0.006 0 26 -9999 0 26
GO:0007205 0 0 -10000 0 -9999 0 0
DNA mediated transformation 0 0 -10000 0 -9999 0 0
Syndecan-2/RasGAP/Src -0.024 0.014 -10000 0 -9999 0 0
RHOA -0.016 0.006 0 23 -9999 0 23
SDCBP -0.017 0.006 0 17 -9999 0 17
TNFRSF13B -0.018 0.003 0 4 -9999 0 4
RASA1 -0.018 0.004 0 8 -9999 0 8
alpha2/beta1 Integrin 0.024 0.006 -10000 0 0 11 11
Syndecan-2/Synbindin -0.013 0.008 0 41 -9999 0 41
TGFB1 -0.018 0.001 0 1 -9999 0 1
CASP3 -0.001 0.056 0.18 15 -9999 0 15
FN1 -0.018 0.004 0 8 -9999 0 8
Syndecan-2/IL8 -0.015 0.006 0 27 -9999 0 27
SDC2 -0.01 0.004 0 22 -9999 0 22
KNG1 -0.013 0.008 0 45 -9999 0 45
Syndecan-2/Neurofibromin -0.015 0.006 0 23 -9999 0 23
TRAPPC4 -0.016 0.006 0 24 -9999 0 24
CSF2 -0.018 0.004 0 8 -9999 0 8
Syndecan-2/TGFB1 -0.015 0.006 0 23 -9999 0 23
Syndecan-2/Syntenin/PI-4-5-P2 -0.013 0.005 0 23 -9999 0 23
Syndecan-2/Ezrin -0.012 0.006 0 38 -9999 0 38
PRKACA 0.002 0.065 0.18 20 -9999 0 20
angiogenesis -0.015 0.006 0 27 -9999 0 27
MMP2 -0.017 0.004 0 10 -9999 0 10
IL8 -0.018 0.003 0 6 -9999 0 6
calcineurin-NFAT signaling pathway -0.015 0.006 0 24 -9999 0 24
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.019 0.008 0 25 -10000 0 25
PCK1 -0.005 0.002 -10000 0 -10000 0 0
HNF4A -0.019 0.008 0 27 -10000 0 27
KCNJ11 -0.022 0.009 0 25 -10000 0 25
AKT1 -0.017 0.005 0 13 -10000 0 13
response to starvation 0 0 -10000 0 -10000 0 0
DLK1 -0.022 0.01 0 27 -10000 0 27
NKX2-1 -0.004 0.002 0 31 -10000 0 31
ACADM -0.019 0.008 0 26 -10000 0 26
TAT -0.005 0.002 -10000 0 -10000 0 0
CEBPB -0.017 0.005 0 11 -10000 0 11
CEBPA -0.018 0.003 0 4 -10000 0 4
TTR 0.012 0.071 0.23 10 -0.27 2 12
PKLR -0.019 0.009 0 29 -10000 0 29
APOA1 0 0.038 0.18 7 -10000 0 7
CPT1C -0.02 0.008 0 24 -10000 0 24
ALAS1 -0.005 0.003 -10000 0 -10000 0 0
TFRC -0.003 0.002 0 59 -10000 0 59
FOXF1 -0.017 0.004 0 10 -10000 0 10
NF1 -0.018 0.001 0 1 -10000 0 1
HNF1A (dimer) 0 0 -10000 0 -10000 0 0
CPT1A -0.016 0.01 0 47 -10000 0 47
HMGCS1 -0.018 0.01 0 38 -10000 0 38
NR3C1 -0.018 0.003 0 5 -10000 0 5
CPT1B -0.019 0.009 0 28 -10000 0 28
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.018 0.001 0 1 -10000 0 1
GCK -0.019 0.008 0 27 -10000 0 27
CREB1 -0.018 0.003 0 6 -10000 0 6
IGFBP1 -0.004 0.002 -10000 0 -10000 0 0
PDX1 -0.006 0.002 0 24 -10000 0 24
UCP2 -0.018 0.009 0 35 -10000 0 35
ALDOB -0.022 0.009 0 25 -10000 0 25
AFP -0.004 0.001 0 15 -10000 0 15
BDH1 -0.015 0.011 0 57 -10000 0 57
HADH -0.015 0.006 0 23 -10000 0 23
F2 0 0.041 0.18 8 -10000 0 8
HNF1A 0 0 -10000 0 -10000 0 0
G6PC -0.006 0.002 -10000 0 -10000 0 0
SLC2A2 -0.004 0.003 0 60 -10000 0 60
INS -0.018 0.003 0 6 -10000 0 6
FOXA1 -0.018 0.004 0 8 -10000 0 8
FOXA3 -0.018 0.002 0 2 -10000 0 2
FOXA2 -0.019 0.008 0 23 -10000 0 23
ABCC8 -0.022 0.009 0 25 -10000 0 25
ALB -0.004 0.001 0 15 -10000 0 15
Glypican 1 network

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.028 0.014 -10000 0 0 33 33
fibroblast growth factor receptor signaling pathway 0.027 0.014 -10000 0 0 33 33
LAMA1 -0.017 0.005 0 13 -10000 0 13
PRNP -0.017 0.005 0 12 -10000 0 12
GPC1/SLIT2 0.022 0.009 -10000 0 0 22 22
SMAD2 -0.023 0.019 0.16 1 -10000 0 1
GPC1/PrPc/Cu2+ 0.02 0.008 -10000 0 0 20 20
GPC1/Laminin alpha1 0.022 0.009 -10000 0 0 22 22
TDGF1 -0.016 0.006 0 22 -10000 0 22
CRIPTO/GPC1 0.021 0.009 -10000 0 0 28 28
APP/GPC1 0.023 0.007 -10000 0 0 16 16
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.02 0.011 0 39 -10000 0 39
FLT1 -0.018 0.004 0 7 -10000 0 7
GPC1/TGFB/TGFBR1/TGFBR2 0.028 0.014 -10000 0 0 31 31
SERPINC1 -0.018 0.003 0 5 -10000 0 5
FYN -0.021 0.01 0 30 -10000 0 30
FGR -0.022 0.01 0 28 -10000 0 28
positive regulation of MAPKKK cascade -0.009 0.071 0.19 7 -0.29 4 11
SLIT2 -0.017 0.005 0 15 -10000 0 15
GPC1/NRG 0.022 0.008 -10000 0 0 20 20
NRG1 -0.017 0.005 0 12 -10000 0 12
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.021 0.007 -10000 0 0 17 17
LYN -0.02 0.011 0 37 -10000 0 37
mol:Spermine -0.01 0.003 0 11 -10000 0 11
cell growth 0.027 0.014 -10000 0 0 33 33
BMP signaling pathway 0.017 0.005 -10000 0 0 11 11
SRC -0.02 0.011 0 37 -10000 0 37
TGFBR1 -0.018 0.001 0 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.018 0.003 0 5 -10000 0 5
GPC1 -0.017 0.005 0 11 -10000 0 11
TGFBR1 (dimer) -0.018 0.001 0 1 -10000 0 1
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.021 0.01 0 30 -10000 0 30
HCK -0.02 0.011 0 42 -10000 0 42
FGF2 -0.018 0.004 0 7 -10000 0 7
FGFR1 -0.016 0.006 0 21 -10000 0 21
VEGFR1 homodimer -0.018 0.004 0 7 -10000 0 7
TGFBR2 -0.016 0.006 0 24 -10000 0 24
cell death 0.023 0.007 -10000 0 0 16 16
ATIII/GPC1 0.023 0.007 -10000 0 0 16 16
PLA2G2A/GPC1 0.023 0.007 -10000 0 0 16 16
LCK -0.022 0.01 0 28 -10000 0 28
neuron differentiation 0.022 0.008 -10000 0 0 20 20
PrPc/Cu2+ 0.012 0.003 -10000 0 0 12 12
APP -0.018 0.003 0 5 -10000 0 5
TGFBR2 (dimer) -0.016 0.006 0 24 -10000 0 24
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.028 0.1 0.18 10 -0.23 22 32
FYN -0.02 0.11 0.18 10 -0.25 19 29
LAT/GRAP2/SLP76 -0.031 0.097 0.16 6 -0.24 20 26
IKBKB -0.016 0.006 0 18 -10000 0 18
AKT1 -0.03 0.094 0.16 6 -0.22 25 31
B2M -0.01 0.016 0.024 4 -10000 0 4
IKBKG -0.018 0.031 0.057 9 -0.079 16 25
MAP3K8 -0.018 0.003 0 5 -10000 0 5
mol:Ca2+ -0.015 0.008 -10000 0 -0.033 15 15
integrin-mediated signaling pathway 0.022 0.005 -10000 0 0 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.033 0.11 0.19 6 -0.26 24 30
TRPV6 -0.006 0.091 1.2 1 -10000 0 1
CD28 -0.012 0.014 0.019 29 -10000 0 29
SHC1 -0.027 0.11 0.14 18 -0.26 23 41
receptor internalization -0.04 0.12 0.1 4 -0.32 23 27
PRF1 -0.024 0.1 -10000 0 -0.29 15 15
KRAS -0.017 0.005 0 11 -10000 0 11
GRB2 -0.018 0.001 0 1 -10000 0 1
COT/AKT1 -0.027 0.081 0.15 6 -0.18 25 31
LAT -0.03 0.11 0.12 15 -0.26 22 37
EntrezGene:6955 0 0.002 0.008 1 -10000 0 1
CD3D -0.008 0.016 0.025 2 -10000 0 2
CD3E -0.008 0.015 0.025 1 -10000 0 1
CD3G -0.011 0.014 0.02 22 -10000 0 22
RASGRP2 -0.003 0.01 -10000 0 -10000 0 0
RASGRP1 -0.029 0.089 0.17 5 -0.22 20 25
HLA-A -0.01 0.015 0.025 1 -10000 0 1
RASSF5 -0.018 0.003 0 5 -10000 0 5
RAP1A/GTP/RAPL 0.022 0.005 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.036 0.096 8 -0.089 5 13
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.031 0.037 -10000 0 -0.11 22 22
PRKCA -0.027 0.057 0.11 7 -0.14 18 25
GRAP2 -0.018 0.002 0 2 -10000 0 2
mol:IP3 -0.041 0.068 -10000 0 -0.2 19 19
EntrezGene:6957 0 0.002 0.008 2 -10000 0 2
TCR/CD3/MHC I/CD8 -0.006 0.042 -10000 0 -0.18 6 6
ORAI1 -0.005 0.077 -10000 0 -0.98 1 1
CSK -0.027 0.1 0.13 13 -0.26 20 33
B7 family/CD28 -0.023 0.075 0.14 4 -0.23 14 18
CHUK -0.018 0.002 0 3 -10000 0 3
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.031 0.1 0.11 4 -0.31 17 21
PTPN6 -0.026 0.092 0.13 9 -0.28 15 24
VAV1 -0.031 0.1 0.13 13 -0.25 23 36
Monovalent TCR/CD3 -0.001 0.007 0.016 15 -10000 0 15
CBL -0.016 0.006 0 24 -10000 0 24
LCK -0.018 0.1 0.19 8 -0.26 16 24
PAG1 -0.029 0.099 0.13 10 -0.26 20 30
RAP1A -0.018 0.003 0 6 -10000 0 6
TCR/CD3/MHC I/CD8/LCK -0.028 0.098 0.14 4 -0.3 16 20
CD80 -0.013 0.011 0.018 14 -10000 0 14
CD86 -0.013 0.011 0.018 14 -10000 0 14
PDK1/CARD11/BCL10/MALT1 -0.03 0.047 -10000 0 -0.13 21 21
HRAS -0.018 0.003 0 5 -10000 0 5
GO:0035030 -0.026 0.063 0.1 4 -0.21 14 18
CD8A -0.01 0.016 0.024 4 -10000 0 4
CD8B 0 0.002 0.008 1 -10000 0 1
PTPRC -0.013 0.013 0.02 5 -10000 0 5
PDK1/PKC theta -0.038 0.1 0.18 5 -0.24 24 29
CSK/PAG1 -0.018 0.1 0.19 11 -0.28 14 25
SOS1 -0.018 0.002 0 3 -10000 0 3
peptide-MHC class I 0.021 0.014 -10000 0 -0.026 9 9
GRAP2/SLP76 -0.03 0.11 0.16 8 -0.25 22 30
STIM1 -0.014 0.016 -10000 0 -10000 0 0
RAS family/GTP -0.009 0.051 0.12 5 -0.12 18 23
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.039 0.12 0.1 4 -0.36 20 24
mol:DAG -0.042 0.058 -10000 0 -0.18 20 20
RAP1A/GDP -0.002 0.017 0.042 6 -0.044 5 11
PLCG1 -0.017 0.005 0 11 -10000 0 11
CD247 0 0.002 0.008 1 -10000 0 1
cytotoxic T cell degranulation -0.024 0.1 -10000 0 -0.29 15 15
RAP1A/GTP -0.003 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.1 0.18 6 -0.23 24 30
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.046 0.085 0.1 2 -0.24 19 21
NRAS -0.017 0.004 0 9 -10000 0 9
ZAP70 -0.015 0.011 0.013 20 -10000 0 20
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
LAT/GRAP2/SLP76/VAV1 -0.039 0.09 0.14 4 -0.24 20 24
MALT1 -0.016 0.006 0 21 -10000 0 21
TRAF6 -0.018 0.003 0 6 -10000 0 6
CD8 heterodimer 0.01 0.009 0.028 1 -0.015 16 17
CARD11 -0.017 0.004 0 9 -10000 0 9
PRKCB -0.033 0.042 -10000 0 -0.13 21 21
PRKCE -0.026 0.056 0.11 7 -0.15 17 24
PRKCQ -0.037 0.11 0.19 5 -0.26 24 29
LCP2 -0.017 0.004 0 9 -10000 0 9
BCL10 -0.018 0.003 0 4 -10000 0 4
regulation of survival gene product expression -0.026 0.084 0.16 6 -0.19 25 31
IKK complex -0.007 0.037 0.11 7 -0.097 5 12
RAS family/GDP -0.006 0.007 -10000 0 -0.024 13 13
MAP3K14 -0.026 0.065 0.12 6 -0.15 25 31
PDPK1 -0.027 0.085 0.16 6 -0.2 22 28
TCR/CD3/MHC I/CD8/Fyn -0.046 0.12 0.13 1 -0.32 25 26
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.018 0.001 0 1 -10000 0 1
CCL5 -0.018 0.001 0 1 -10000 0 1
SDCBP -0.017 0.006 0 17 -10000 0 17
FGFR/FGF2/Syndecan-1 0 0.026 0.098 5 -10000 0 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.014 0.073 0.16 11 -0.18 16 27
Syndecan-1/Syntenin -0.008 0.074 0.16 13 -0.19 12 25
MAPK3 -0.019 0.076 0.14 16 -0.17 16 32
HGF/MET 0.024 0.006 -10000 0 0 10 10
TGFB1/TGF beta receptor Type II -0.018 0.001 0 1 -10000 0 1
BSG -0.018 0.003 0 5 -10000 0 5
keratinocyte migration -0.014 0.072 0.16 11 -0.18 16 27
Syndecan-1/RANTES -0.01 0.083 0.16 16 -0.18 16 32
Syndecan-1/CD147 -0.012 0.083 0.17 16 -0.18 16 32
Syndecan-1/Syntenin/PIP2 -0.008 0.071 0.16 13 -0.18 13 26
LAMA5 -0.017 0.004 0 10 -10000 0 10
positive regulation of cell-cell adhesion -0.012 0.063 0.13 11 -0.18 13 24
MMP7 -0.015 0.007 0 30 -10000 0 30
HGF -0.018 0.003 0 5 -10000 0 5
Syndecan-1/CASK -0.023 0.053 -10000 0 -0.17 18 18
Syndecan-1/HGF/MET -0.015 0.079 0.14 21 -0.18 16 37
regulation of cell adhesion -0.023 0.071 0.17 10 -0.18 14 24
HPSE -0.018 0.003 0 5 -10000 0 5
positive regulation of cell migration 0 0.026 0.098 5 -10000 0 5
SDC1 0 0.026 0.098 5 -10000 0 5
Syndecan-1/Collagen 0 0.026 0.098 5 -10000 0 5
PPIB -0.018 0.002 0 3 -10000 0 3
MET -0.018 0.004 0 7 -10000 0 7
PRKACA -0.018 0.003 0 4 -10000 0 4
MMP9 -0.017 0.005 0 11 -10000 0 11
MAPK1 -0.018 0.075 0.15 14 -0.18 14 28
homophilic cell adhesion -0.004 0.062 0.15 11 -0.17 11 22
MMP1 -0.015 0.007 0 28 -10000 0 28
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.034 0.1 12 -0.083 5 17
epithelial cell differentiation -0.012 0.04 0.11 2 -10000 0 2
ITCH -0.014 0.015 0.028 14 -10000 0 14
WWP1 0.003 0.042 0.19 8 -10000 0 8
FYN -0.018 0.003 0 6 -10000 0 6
EGFR -0.016 0.006 0 20 -10000 0 20
PRL -0.018 0.004 0 8 -10000 0 8
neuron projection morphogenesis -0.011 0.056 0.15 12 -10000 0 12
PTPRZ1 -0.018 0.003 0 5 -10000 0 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.003 0.048 0.099 15 -10000 0 15
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.002 0.025 0.043 33 -0.064 3 36
ADAM17 -0.016 0.015 0.028 17 -10000 0 17
ErbB4/ErbB4 -0.002 0.001 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.024 0.035 0.1 13 -0.083 5 18
NCOR1 -0.018 0.002 0 3 -10000 0 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.003 0.032 0.053 36 -10000 0 36
GRIN2B -0.006 0.041 0.14 8 -10000 0 8
ErbB4/ErbB2/betacellulin -0.003 0.033 0.053 38 -10000 0 38
STAT1 -0.018 0.004 0 7 -10000 0 7
HBEGF -0.018 0.003 0 5 -10000 0 5
PRLR -0.016 0.006 0 19 -10000 0 19
E4ICDs/ETO2 0.022 0.032 0.098 12 -0.082 4 16
axon guidance -0.003 0.039 0.11 7 -0.12 2 9
NEDD4 -0.016 0.014 0.027 14 -10000 0 14
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.009 -10000 0 0 26 26
CBFA2T3 -0.017 0.004 0 10 -10000 0 10
ErbB4/ErbB2/HBEGF -0.003 0.033 0.054 37 -10000 0 37
MAPK3 -0.006 0.057 0.15 13 -10000 0 13
STAT1 (dimer) 0.024 0.033 0.1 13 -0.087 3 16
MAPK1 -0.006 0.056 0.16 12 -10000 0 12
JAK2 -0.015 0.007 0 28 -10000 0 28
ErbB4/ErbB2/neuregulin 1 beta -0.008 0.023 0.035 32 -0.066 3 35
NRG1 -0.02 0.009 0.013 5 -10000 0 5
NRG3 -0.018 0.001 0 1 -10000 0 1
NRG2 -0.018 0.003 0 5 -10000 0 5
NRG4 -0.018 0.002 0 3 -10000 0 3
heart development -0.003 0.039 0.11 7 -0.12 2 9
neural crest cell migration -0.008 0.023 0.035 32 -0.066 3 35
ERBB2 -0.02 0.009 0.014 8 -10000 0 8
WWOX/E4ICDs 0.015 0.025 0.1 7 -0.087 1 8
SHC1 -0.018 0.004 0 7 -10000 0 7
ErbB4/EGFR/neuregulin 4 0.029 0.031 0.11 10 -0.086 3 13
apoptosis -0.022 0.031 0.067 3 -0.096 14 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.023 0.034 0.1 12 -0.083 5 17
ErbB4/ErbB2/epiregulin -0.003 0.033 0.053 38 -10000 0 38
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.033 0.1 12 -0.082 4 16
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.034 0.036 0.13 3 -0.085 4 7
MDM2 0 0.041 0.23 5 -10000 0 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.011 0.015 0.029 12 -0.047 3 15
STAT5A -0.007 0.045 0.17 3 -0.13 1 4
ErbB4/EGFR/neuregulin 1 beta -0.003 0.029 0.051 33 -10000 0 33
DLG4 -0.018 0.002 0 2 -10000 0 2
GRB2/SHC 0.024 0.005 -10000 0 0 8 8
E4ICDs/TAB2/NCoR1 0.03 0.032 0.1 11 -0.082 5 16
STAT5A (dimer) -0.009 0.048 0.12 10 -10000 0 10
MAP3K7IP2 -0.018 0.003 0 5 -10000 0 5
STAT5B (dimer) 0.011 0.05 0.15 4 -0.12 3 7
LRIG1 -0.016 0.007 0 25 -10000 0 25
EREG -0.018 0.003 0 6 -10000 0 6
BTC -0.018 0.004 0 7 -10000 0 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.003 0.039 0.11 7 -0.12 2 9
ERBB4 -0.002 0.001 -10000 0 -10000 0 0
STAT5B -0.018 0.002 0 3 -10000 0 3
YAP1 -0.032 0.1 -10000 0 -0.42 10 10
GRB2 -0.018 0.001 0 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 -0.003 0.032 0.053 38 -10000 0 38
glial cell differentiation -0.029 0.032 0.082 5 -0.1 11 16
WWOX -0.011 0.009 0 63 -10000 0 63
cell proliferation -0.003 0.048 0.18 7 -0.14 2 9
BARD1 signaling events

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.023 0.008 -10000 0 0 18 18
ATM -0.016 0.007 0 25 -10000 0 25
UBE2D3 -0.018 0.003 0 6 -10000 0 6
PRKDC -0.016 0.006 0 21 -10000 0 21
ATR -0.015 0.007 0 28 -10000 0 28
UBE2L3 -0.018 0.003 0 5 -10000 0 5
FANCD2 -0.004 0.003 -10000 0 -10000 0 0
protein ubiquitination 0.036 0.021 -10000 0 -0.008 23 23
XRCC5 -0.018 0.004 0 8 -10000 0 8
XRCC6 -0.018 0.002 0 2 -10000 0 2
M/R/N Complex 0.026 0.015 -10000 0 0 39 39
MRE11A -0.016 0.006 0 21 -10000 0 21
DNA-PK 0.029 0.013 -10000 0 0 27 27
FA complex/FANCD2/Ubiquitin -0.014 0.068 0.12 1 -0.28 8 9
FANCF -0.018 0.002 0 3 -10000 0 3
BRCA1 -0.018 0.002 0 3 -10000 0 3
CCNE1 -0.018 0.002 0 3 -10000 0 3
CDK2/Cyclin E1 0.025 0.004 -10000 0 0 4 4
FANCG -0.016 0.006 0 18 -10000 0 18
BRCA1/BACH1/BARD1 0.024 0.006 -10000 0 0 9 9
FANCE -0.018 0.004 0 8 -10000 0 8
FANCC -0.018 0.001 0 1 -10000 0 1
NBN -0.016 0.006 0 18 -10000 0 18
FANCA -0.017 0.004 0 9 -10000 0 9
DNA repair -0.022 0.051 0.17 4 -0.21 5 9
BRCA1/BARD1/ubiquitin 0.024 0.006 -10000 0 0 9 9
BARD1/DNA-PK 0.037 0.016 -10000 0 0 27 27
FANCL -0.018 0.003 0 4 -10000 0 4
mRNA polyadenylation -0.022 0.008 0 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex -0.015 0.054 0.097 4 -0.18 12 16
BRCA1/BACH1/BARD1/TopBP1 0.029 0.013 -10000 0 0 29 29
BRCA1/BARD1/P53 0.034 0.018 -10000 0 0 36 36
BARD1/CSTF1/BRCA1 0.031 0.011 -10000 0 0 19 19
BRCA1/BACH1 -0.018 0.002 0 3 -10000 0 3
BARD1 -0.018 0.004 0 8 -10000 0 8
PCNA -0.017 0.005 0 13 -10000 0 13
BRCA1/BARD1/UbcH5C 0.032 0.01 -10000 0 0 14 14
BRCA1/BARD1/UbcH7 0.032 0.009 -10000 0 0 13 13
BRCA1/BARD1/RAD51/PCNA 0.037 0.015 -10000 0 0 24 24
BARD1/DNA-PK/P53 0.041 0.02 -10000 0 -0.008 5 5
BRCA1/BARD1/Ubiquitin 0.024 0.006 -10000 0 0 9 9
BRCA1/BARD1/CTIP -0.024 0.012 0 34 -10000 0 34
FA complex 0.005 0.029 0.078 21 -0.089 1 22
BARD1/EWS 0.023 0.007 -10000 0 0 14 14
RBBP8 -0.018 0.009 0 31 -10000 0 31
TP53 -0.018 0.003 0 4 -10000 0 4
TOPBP1 -0.016 0.006 0 24 -10000 0 24
G1/S transition of mitotic cell cycle -0.033 0.017 0 36 -10000 0 36
BRCA1/BARD1 0.039 0.023 -10000 0 -0.008 23 23
CSTF1 -0.017 0.004 0 10 -10000 0 10
BARD1/EWS-Fli1 0.012 0.003 -10000 0 0 8 8
CDK2 -0.018 0.001 0 1 -10000 0 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.018 0.004 0 7 -10000 0 7
RAD50 -0.017 0.004 0 9 -10000 0 9
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.024 0.006 -10000 0 0 9 9
EWSR1 -0.018 0.003 0 6 -10000 0 6
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.018 0.003 0 6 -9999 0 6
GPC2 -0.017 0.005 0 14 -9999 0 14
GPC2/Midkine 0.022 0.008 -9999 0 0 19 19
neuron projection morphogenesis 0.022 0.008 -9999 0 0 19 19
Wnt signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.016 0.031 -9999 0 -0.11 15 15
FZD6 -0.016 0.006 0 22 -10000 0 22
WNT6 -0.018 0.004 0 8 -10000 0 8
WNT4 -0.018 0.003 0 5 -10000 0 5
FZD3 -0.017 0.004 0 10 -10000 0 10
WNT5A -0.016 0.007 0 25 -10000 0 25
WNT11 -0.017 0.005 0 15 -10000 0 15
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.023 0.009 0 21 -10000 0 21
VEGFR1 homodimer/NRP1 -0.016 0.005 0 14 -10000 0 14
mol:DAG -0.026 0.01 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 -0.014 0.004 0 14 -10000 0 14
CaM/Ca2+ -0.029 0.013 -10000 0 -10000 0 0
HIF1A -0.018 0.004 0 7 -10000 0 7
GAB1 -0.018 0.004 0 7 -10000 0 7
AKT1 0.009 0.077 0.13 40 -10000 0 40
PLCG1 -0.026 0.01 -10000 0 -10000 0 0
NOS3 -0.003 0.049 0.3 1 -0.2 3 4
CBL -0.016 0.006 0 24 -10000 0 24
mol:NO 0.003 0.078 0.28 6 -0.18 6 12
FLT1 -0.02 0.006 0 14 -10000 0 14
PGF -0.017 0.004 0 9 -10000 0 9
VEGFR1 homodimer/NRP2/VEGFR121 -0.021 0.007 0 16 -10000 0 16
CALM1 -0.017 0.005 0 14 -10000 0 14
PIK3CA -0.013 0.008 0 49 -10000 0 49
eNOS/Hsp90 -0.012 0.058 0.28 1 -0.18 8 9
endothelial cell proliferation -0.002 0.059 0.21 9 -0.14 1 10
mol:Ca2+ -0.026 0.01 -10000 0 -10000 0 0
MAPK3 -0.024 0.063 0.33 5 -10000 0 5
MAPK1 -0.028 0.05 0.33 3 -10000 0 3
PIK3R1 -0.018 0.004 0 8 -10000 0 8
PLGF homodimer -0.017 0.004 0 9 -10000 0 9
PRKACA -0.018 0.003 0 4 -10000 0 4
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.018 0.004 0 7 -10000 0 7
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.016 0.005 0 14 -10000 0 14
platelet activating factor biosynthetic process -0.032 0.049 0.31 3 -10000 0 3
PI3K -0.023 0.017 0 57 -10000 0 57
PRKCA -0.03 0.012 -10000 0 -10000 0 0
PRKCB -0.024 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.024 0.007 0 14 -10000 0 14
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB -0.018 0.004 0 7 -10000 0 7
mol:IP3 -0.026 0.01 -10000 0 -10000 0 0
RASA1 -0.021 0.035 0.17 5 -10000 0 5
NRP2 -0.018 0.003 0 4 -10000 0 4
VEGFR1 homodimer -0.02 0.006 0 14 -10000 0 14
VEGFB homodimer -0.018 0.004 0 7 -10000 0 7
NCK1 -0.015 0.007 0 27 -10000 0 27
eNOS/Caveolin-1 -0.002 0.091 0.33 6 -0.2 7 13
PTPN11 -0.018 0.001 0 1 -10000 0 1
mol:PI-3-4-5-P3 -0.022 0.017 0 57 -10000 0 57
mol:L-citrulline 0.003 0.078 0.28 6 -0.18 6 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.022 0.012 0 37 -10000 0 37
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.018 0.009 0 35 -10000 0 35
CD2AP -0.018 0.004 0 8 -10000 0 8
PI3K/GAB1 -0.026 0.019 0 54 -10000 0 54
PDPK1 0.015 0.086 0.15 44 -10000 0 44
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.021 0.006 0 14 -10000 0 14
mol:NADP 0.003 0.078 0.28 6 -0.18 6 12
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.022 0.012 0 37 -10000 0 37
VEGFR1 homodimer/NRP2 -0.024 0.008 0 16 -10000 0 16
Noncanonical Wnt signaling pathway

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
NFATC2 -0.017 0.005 0 11 -10000 0 11
GNB1/GNG2 0.011 0.058 -10000 0 -0.13 21 21
mol:DAG -0.024 0.045 0.075 14 -0.15 9 23
PLCG1 -0.025 0.046 0.076 14 -0.15 9 23
YES1 -0.018 0.028 -10000 0 -0.11 12 12
FZD3 -0.017 0.004 0 10 -10000 0 10
FZD6 -0.016 0.006 0 22 -10000 0 22
G protein -0.021 0.06 0.21 3 -0.16 10 13
MAP3K7 -0.024 0.046 0.14 4 -0.14 6 10
mol:Ca2+ -0.024 0.044 0.074 14 -0.15 9 23
mol:IP3 -0.024 0.045 0.075 14 -0.15 9 23
NLK 0.003 0.11 -10000 0 -0.78 3 3
GNB1 -0.018 0.003 0 5 -10000 0 5
CAMK2A -0.022 0.049 0.15 4 -0.14 8 12
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
Noncanonical Wnts/FZD -0.016 0.031 -10000 0 -0.11 15 15
CSNK1A1 -0.018 0.003 0 5 -10000 0 5
GNAS -0.019 0.029 -10000 0 -0.11 13 13
GO:0007205 -0.023 0.048 0.068 14 -0.13 18 32
WNT6 -0.018 0.004 0 8 -10000 0 8
WNT4 -0.018 0.003 0 5 -10000 0 5
NFAT1/CK1 alpha -0.019 0.063 0.18 8 -0.16 6 14
GNG2 -0.018 0.004 0 7 -10000 0 7
WNT5A -0.016 0.007 0 25 -10000 0 25
WNT11 -0.017 0.005 0 15 -10000 0 15
CDC42 -0.021 0.026 -10000 0 -0.11 11 11
PDGFR-alpha signaling pathway

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
PDGFRA -0.015 0.015 0.028 15 -10000 0 15
PDGF/PDGFRA/CRKL 0.022 0.008 -10000 0 0 18 18
positive regulation of JUN kinase activity 0.037 0.014 -10000 0 0 20 20
CRKL -0.018 0.004 0 7 -10000 0 7
PDGF/PDGFRA/Caveolin-3 0.021 0.01 -10000 0 0 28 28
AP1 -0.017 0.045 0.13 13 -10000 0 13
mol:IP3 -0.02 0.012 0.023 7 -10000 0 7
PLCG1 -0.02 0.012 0.023 7 -10000 0 7
PDGF/PDGFRA/alphaV Integrin 0.023 0.008 -10000 0 0 16 16
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
CRK -0.018 0.002 0 2 -10000 0 2
mol:Ca2+ -0.02 0.012 0.023 7 -10000 0 7
CAV3 -0.016 0.006 0 19 -10000 0 19
CAV1 -0.018 0.004 0 7 -10000 0 7
SHC/Grb2/SOS1 0.038 0.014 -10000 0 0 20 20
PDGF/PDGFRA/Shf 0.023 0.008 -10000 0 0 15 15
FOS -0.025 0.025 0.13 3 -10000 0 3
JUN -0.019 0.014 0.021 13 -10000 0 13
oligodendrocyte development 0.023 0.008 -10000 0 0 16 16
GRB2 -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:DAG -0.02 0.012 0.023 7 -10000 0 7
PDGF/PDGFRA -0.015 0.015 0.028 15 -10000 0 15
actin cytoskeleton reorganization 0.022 0.009 -10000 0 0 22 22
SRF -0.02 0.007 0 19 -10000 0 19
SHC1 -0.018 0.004 0 7 -10000 0 7
PI3K 0.022 0.017 -10000 0 0 59 59
PDGF/PDGFRA/Crk/C3G 0.031 0.01 -10000 0 0 15 15
JAK1 -0.021 0.007 0 14 -10000 0 14
ELK1/SRF -0.022 0.038 0.13 9 -10000 0 9
SHB -0.017 0.005 0 13 -10000 0 13
SHF -0.018 0.003 0 4 -10000 0 4
CSNK2A1 0.013 0.015 -10000 0 -0.028 14 14
GO:0007205 -0.015 0.009 0.017 7 -10000 0 7
SOS1 -0.018 0.002 0 3 -10000 0 3
Ras protein signal transduction 0.037 0.014 -10000 0 0 20 20
PDGF/PDGFRA/SHB 0.022 0.009 -10000 0 0 22 22
PDGF/PDGFRA/Caveolin-1 0.023 0.008 -10000 0 0 16 16
ITGAV -0.018 0.003 0 5 -10000 0 5
ELK1 -0.02 0.012 0.021 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
PDGF/PDGFRA/Crk 0.023 0.007 -10000 0 0 13 13
JAK-STAT cascade -0.021 0.007 0 14 -10000 0 14
cell proliferation 0.023 0.008 -10000 0 0 15 15
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.018 0.003 0 5 -10000 0 5
alphaV beta3 Integrin 0.024 0.004 -10000 0 0 5 5
PTK2 -0.003 0.052 -10000 0 -0.19 11 11
positive regulation of JNK cascade -0.008 0.08 -10000 0 -0.24 16 16
CDC42/GDP 0.003 0.093 -10000 0 -0.3 10 10
Rac1/GDP 0.004 0.089 -10000 0 -0.3 10 10
RAP1B -0.018 0.004 0 7 -10000 0 7
RAP1A -0.018 0.003 0 6 -10000 0 6
CTNNB1 -0.015 0.007 0 28 -10000 0 28
CDC42/GTP -0.005 0.098 -10000 0 -0.29 15 15
nectin-3/I-afadin 0.021 0.009 -10000 0 0 27 27
RAPGEF1 -0.004 0.077 0.22 1 -0.34 6 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.008 0.076 -10000 0 -0.38 6 6
PDGFB-D/PDGFRB -0.018 0.003 0 5 -10000 0 5
TLN1 -0.016 0.01 -10000 0 -0.049 4 4
Rap1/GTP -0.002 0.057 -10000 0 -0.27 6 6
IQGAP1 -0.018 0.003 0 4 -10000 0 4
Rap1/GTP/I-afadin 0.029 0.01 -10000 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.021 0.009 -10000 0 0 27 27
PVR -0.018 0.002 0 2 -10000 0 2
Necl-5(dimer) -0.018 0.002 0 2 -10000 0 2
mol:GDP -0.005 0.1 -10000 0 -0.35 10 10
MLLT4 -0.018 0.004 0 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
PI3K 0.032 0.025 -10000 0 -0.008 6 6
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.021 0.01 -10000 0 0 29 29
positive regulation of lamellipodium assembly 0.006 0.062 -10000 0 -0.26 7 7
PVRL1 -0.016 0.006 0 24 -10000 0 24
PVRL3 -0.016 0.006 0 20 -10000 0 20
PVRL2 -0.018 0.002 0 2 -10000 0 2
PIK3R1 -0.018 0.004 0 8 -10000 0 8
CDH1 -0.017 0.004 0 9 -10000 0 9
CLDN1 -0.014 0.008 0 43 -10000 0 43
JAM-A/CLDN1 0.029 0.021 -10000 0 0 54 54
SRC -0.004 0.082 -10000 0 -0.41 6 6
ITGB3 -0.018 0 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.021 0.01 -10000 0 0 29 29
FARP2 -0.017 0.14 -10000 0 -0.41 16 16
RAC1 -0.017 0.004 0 10 -10000 0 10
CTNNA1 -0.018 0.003 0 5 -10000 0 5
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.029 0.013 -10000 0 0 29 29
nectin-1/I-afadin 0.021 0.01 -10000 0 0 29 29
nectin-2/I-afadin 0.024 0.006 -10000 0 0 9 9
RAC1/GTP/IQGAP1/filamentous actin 0.021 0.006 -10000 0 0 13 13
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.015 -10000 0 0 41 41
CDC42/GTP/IQGAP1/filamentous actin 0.022 0.005 -10000 0 0 9 9
F11R -0.018 0.004 0 7 -10000 0 7
positive regulation of filopodium formation -0.008 0.08 -10000 0 -0.24 16 16
alphaV/beta3 Integrin/Talin 0.003 0.07 0.19 14 -10000 0 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.024 0.006 -10000 0 0 9 9
nectin-2(dimer)/I-afadin/I-afadin 0.024 0.006 -10000 0 0 9 9
PIP5K1C -0.011 0.006 0 35 -10000 0 35
VAV2 0.009 0.09 -10000 0 -0.4 6 6
RAP1/GDP 0.007 0.081 -10000 0 -0.31 7 7
ITGAV -0.018 0.003 0 5 -10000 0 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.029 0.013 -10000 0 0 29 29
nectin-3(dimer)/I-afadin/I-afadin 0.021 0.009 -10000 0 0 27 27
Rac1/GTP 0.009 0.074 -10000 0 -0.31 7 7
PTPRM -0.005 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.037 0.024 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 -0.018 0.003 0 5 -10000 0 5
IL1-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
UBC13/UEV1A 0.012 0.002 -10000 0 0 3 3
PRKCZ -0.018 0.003 0 5 -10000 0 5
MAP3K7IP2 -0.018 0.003 0 5 -10000 0 5
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.052 -10000 0 -0.2 11 11
IRAK/TOLLIP -0.022 0.005 0 7 -10000 0 7
IKBKB -0.016 0.006 0 18 -10000 0 18
IKBKG -0.018 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.025 0.003 -10000 0 0 3 3
IL1A -0.018 0.001 0 1 -10000 0 1
IL1B -0.019 0.008 0 25 -10000 0 25
IRAK/TRAF6/p62/Atypical PKCs -0.026 0.018 -10000 0 -10000 0 0
IL1R2 -0.018 0.002 0 3 -10000 0 3
IL1R1 -0.018 0.002 0 3 -10000 0 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.04 -10000 0 -0.24 1 1
TOLLIP -0.018 0.003 0 5 -10000 0 5
TICAM2 -0.018 0.003 0 6 -10000 0 6
MAP3K3 -0.018 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.033 0.008 -10000 0 0 10 10
IKK complex/ELKS -0.019 0.046 0.13 4 -0.2 6 10
JUN -0.038 0.031 0.12 5 -10000 0 5
MAP3K7 -0.018 0.003 0 6 -10000 0 6
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.025 0.019 0 55 -10000 0 55
IL1 alpha/IL1R1/IL1RAP/MYD88 0.029 0.021 -10000 0 0 57 57
PIK3R1 -0.018 0.004 0 8 -10000 0 8
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.033 0.025 -10000 0 -0.008 12 12
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.015 0 59 -10000 0 59
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAPK8 -0.034 0.032 0.14 5 -10000 0 5
IRAK1 -0.017 0.002 0 3 -10000 0 3
IL1RN/IL1R1 0.025 0.003 -10000 0 0 3 3
IRAK4 -0.018 0.002 0 2 -10000 0 2
PRKCI -0.013 0.008 0 47 -10000 0 47
TRAF6 -0.018 0.003 0 6 -10000 0 6
PI3K 0.017 0.012 -10000 0 0 53 53
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.043 0.11 2 -0.17 11 13
CHUK -0.018 0.002 0 3 -10000 0 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.015 0 59 -10000 0 59
IL1 beta/IL1R2 -0.022 0.01 -10000 0 -10000 0 0
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.034 0.018 0.15 1 -10000 0 1
NF kappa B1 p50/RelA -0.029 0.024 -10000 0 -10000 0 0
IRAK3 -0.018 0.004 0 7 -10000 0 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.026 0.018 0 49 -10000 0 49
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.013 0.027 -10000 0 -0.1 12 12
IL1 alpha/IL1R1/IL1RAP 0.025 0.015 -10000 0 0 44 44
RELA -0.017 0.005 0 11 -10000 0 11
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
SQSTM1 -0.018 0.004 0 8 -10000 0 8
MYD88 -0.016 0.006 0 22 -10000 0 22
IRAK/TRAF6/MEKK3 -0.027 0.006 0 8 -10000 0 8
IL1RAP -0.014 0.008 0 43 -10000 0 43
UBE2N -0.018 0.002 0 3 -10000 0 3
IRAK/TRAF6 -0.035 0.024 -10000 0 -10000 0 0
CASP1 -0.016 0.007 0 25 -10000 0 25
IL1RN/IL1R2 0.025 0.003 -10000 0 0 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.022 0.017 -10000 0 -10000 0 0
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.059 -10000 0 -0.22 12 12
PIK3CA -0.013 0.008 0 49 -10000 0 49
IL1RN -0.018 0.001 0 1 -10000 0 1
TRAF6/TAK1/TAB1/TAB2 0.037 0.014 -10000 0 -0.008 9 9
MAP2K6 -0.03 0.033 0.15 5 -10000 0 5
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.017 0.076 0.15 2 -0.23 15 17
BAG4 -0.016 0.006 0 21 -10000 0 21
BAD -0.003 0.046 0.16 8 -0.1 7 15
NFKBIA -0.017 0.004 0 9 -10000 0 9
BIRC3 -0.015 0.008 0.018 3 -10000 0 3
BAX -0.008 0.037 0.13 4 -0.1 8 12
EnzymeConsortium:3.1.4.12 -0.003 0.021 0.054 4 -0.059 13 17
IKBKB -0.005 0.084 0.23 9 -0.22 9 18
MAP2K2 -0.014 0.033 0.12 3 -0.12 3 6
MAP2K1 -0.014 0.03 0.11 2 -0.12 2 4
SMPD1 -0.006 0.026 0.071 1 -0.083 10 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.033 0.12 0.2 42 -0.24 12 54
MAP2K4 -0.014 0.03 -10000 0 -0.12 3 3
protein ubiquitination -0.015 0.08 0.2 3 -0.24 11 14
EnzymeConsortium:2.7.1.37 -0.017 0.035 0.12 2 -0.13 2 4
response to UV 0 0 0.001 3 -0.001 1 4
RAF1 -0.011 0.029 0.1 3 -0.11 3 6
CRADD -0.015 0.01 0.018 13 -10000 0 13
mol:ceramide -0.004 0.032 0.072 8 -0.098 8 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.021 0.007 -10000 0 0 17 17
MADD -0.015 0.01 0.018 12 -10000 0 12
MAP3K1 -0.01 0.029 0.088 2 -0.1 6 8
TRADD -0.015 0.01 0.018 12 -10000 0 12
RELA/p50 -0.017 0.005 0 11 -10000 0 11
MAPK3 -0.014 0.037 0.12 2 -0.14 4 6
MAPK1 -0.013 0.033 0.12 2 -0.12 2 4
p50/RELA/I-kappa-B-alpha 0.023 0.008 -10000 0 0 17 17
FADD 0.03 0.11 0.19 40 -0.24 11 51
KSR1 -0.008 0.033 0.11 3 -0.1 7 10
MAPK8 -0.018 0.031 0.14 1 -0.12 2 3
TRAF2 -0.015 0.01 0.018 14 -10000 0 14
response to radiation 0 0 0.001 1 -10000 0 1
CHUK -0.019 0.076 0.17 2 -0.23 13 15
TNF R/SODD 0.021 0.01 -10000 0 0 30 30
TNF -0.015 0.01 0.018 11 -10000 0 11
CYCS -0.001 0.049 0.11 16 -0.11 6 22
IKBKG -0.02 0.077 0.17 2 -0.23 13 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.01 0.075 0.14 1 -0.22 14 15
RELA -0.017 0.005 0 11 -10000 0 11
RIPK1 -0.015 0.01 0.018 10 -10000 0 10
AIFM1 0 0.047 0.11 16 -0.099 6 22
TNF/TNF R/SODD 0.027 0.014 -10000 0 0 36 36
TNFRSF1A -0.014 0.01 0.018 12 -10000 0 12
response to heat 0 0 0.001 1 -10000 0 1
CASP8 -0.004 0.099 -10000 0 -0.55 5 5
NSMAF 0 0.078 0.21 10 -0.22 8 18
response to hydrogen peroxide 0 0 0.001 3 -0.001 1 4
BCL2 -0.016 0.006 0 22 -10000 0 22
Atypical NF-kappaB pathway

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
BCL3/RelA 0.023 0.007 -10000 0 0 13 13
FBXW11 -0.018 0.004 0 8 -10000 0 8
NF kappa B1 p50/c-Rel -0.022 0.009 0 24 -10000 0 24
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.029 0.087 9 -10000 0 9
NFKBIA -0.004 0.002 -10000 0 -10000 0 0
MAPK14 -0.018 0.004 0 8 -10000 0 8
NF kappa B1 p105/p50 -0.022 0.01 0 28 -10000 0 28
ARRB2 -0.004 0.001 -10000 0 -10000 0 0
REL -0.018 0.002 0 3 -10000 0 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.022 0.009 0 24 -10000 0 24
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.021 0.01 0 30 -10000 0 30
PIK3CA -0.013 0.008 0 49 -10000 0 49
NF kappa B1 p50 dimer -0.018 0.011 -10000 0 -10000 0 0
PIK3R1 -0.018 0.004 0 8 -10000 0 8
NFKB1 -0.019 0.008 0 22 -10000 0 22
RELA -0.017 0.005 0 11 -10000 0 11
positive regulation of anti-apoptosis -0.002 0.023 0.083 9 -0.1 2 11
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.018 0.029 0.081 9 -0.12 2 11
SRC -0.017 0.005 0 14 -10000 0 14
PI3K 0.017 0.012 -10000 0 0 53 53
NF kappa B1 p50/RelA -0.002 0.024 0.083 9 -0.1 2 11
IKBKB -0.016 0.006 0 18 -10000 0 18
beta TrCP1/SCF ubiquitin ligase complex -0.017 0.004 0 8 -10000 0 8
SYK -0.018 0.001 0 1 -10000 0 1
I kappa B alpha/PIK3R1 -0.003 0.041 0.098 18 -10000 0 18
cell death -0.017 0.028 0.078 9 -0.12 2 11
NF kappa B1 p105/c-Rel -0.022 0.009 0 24 -10000 0 24
LCK -0.018 0.003 0 4 -10000 0 4
BCL3 -0.018 0.002 0 2 -10000 0 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.016 0.006 0 21 -10000 0 21
Caspase 8 (4 units) 0.031 0.049 0.15 1 -0.1 11 12
NEF 0 0 -10000 0 -10000 0 0
NFKBIA -0.017 0.004 0 9 -10000 0 9
BIRC3 -0.017 0.037 0.16 6 -10000 0 6
CYCS 0 0.042 0.16 2 -0.17 2 4
RIPK1 -0.017 0.004 0 10 -10000 0 10
CD247 0 0 -10000 0 -10000 0 0
MAP2K7 0.01 0.12 -10000 0 -0.42 8 8
protein ubiquitination 0.003 0.089 0.16 13 -0.22 12 25
CRADD -0.018 0.002 0 2 -10000 0 2
DAXX -0.018 0.004 0 8 -10000 0 8
FAS -0.018 0.002 0 3 -10000 0 3
BID 0.005 0.04 0.064 42 -0.12 5 47
NF-kappa-B/RelA/I kappa B alpha 0.03 0.012 -10000 0 0 23 23
TRADD -0.017 0.004 0 10 -10000 0 10
MAP3K5 -0.018 0.003 0 6 -10000 0 6
CFLAR -0.018 0.003 0 4 -10000 0 4
FADD -0.012 0.009 0 54 -10000 0 54
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.03 0.012 -10000 0 0 23 23
MAPK8 0.006 0.11 -10000 0 -0.4 8 8
APAF1 -0.018 0.002 0 2 -10000 0 2
TRAF1 -0.018 0.002 0 3 -10000 0 3
TRAF2 -0.018 0.002 0 3 -10000 0 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.042 0.073 43 -0.12 5 48
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.008 0.085 0.13 4 -0.27 11 15
CHUK 0.004 0.091 0.16 13 -0.24 11 24
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.03 0.025 -10000 0 -0.008 7 7
TCRz/NEF 0 0 -10000 0 -10000 0 0
TNF -0.018 0.004 0 8 -10000 0 8
FASLG -0.009 0.002 0 5 -10000 0 5
NFKB1 -0.018 0.003 0 6 -10000 0 6
TNFR1A/BAG4/TNF-alpha 0.027 0.014 -10000 0 0 36 36
CASP6 0.014 0.1 -10000 0 -0.46 6 6
CASP7 0.002 0.097 0.19 20 -0.2 12 32
RELA -0.017 0.005 0 11 -10000 0 11
CASP2 -0.018 0.003 0 6 -10000 0 6
CASP3 -0.002 0.1 0.19 19 -0.2 16 35
TNFRSF1A -0.017 0.005 0 13 -10000 0 13
TNFR1A/BAG4 0.021 0.01 -10000 0 0 30 30
CASP8 -0.018 0.003 0 6 -10000 0 6
CASP9 -0.018 0.004 0 7 -10000 0 7
MAP3K14 -0.004 0.087 0.13 12 -0.26 11 23
APAF-1/Caspase 9 -0.023 0.039 0.09 1 -0.14 3 4
BCL2 0.001 0.1 0.22 2 -0.39 7 9
EPHB forward 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
Ephrin A5/EPHB2 0.022 0.005 -10000 0 0 9 9
cell-cell adhesion 0.035 0.02 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.046 0.016 -10000 0 -10000 0 0
ITSN1 -0.018 0.003 0 5 -10000 0 5
PIK3CA -0.013 0.008 0 49 -10000 0 49
SHC1 -0.018 0.004 0 7 -10000 0 7
Ephrin B1/EPHB3 0.017 0.01 -10000 0 0 44 44
Ephrin B1/EPHB1 0.019 0.008 -10000 0 0 26 26
HRAS/GDP -0.041 0.044 -10000 0 -0.16 17 17
Ephrin B/EPHB1/GRB7 0.04 0.021 -10000 0 -0.008 3 3
Endophilin/SYNJ1 -0.031 0.009 -10000 0 -10000 0 0
KRAS -0.017 0.005 0 11 -10000 0 11
Ephrin B/EPHB1/Src 0.038 0.023 -10000 0 -0.008 7 7
endothelial cell migration 0.024 0.017 -10000 0 0 58 58
GRB2 -0.018 0.001 0 1 -10000 0 1
GRB7 -0.018 0.003 0 6 -10000 0 6
PAK1 -0.023 0.048 0.15 11 -10000 0 11
HRAS -0.018 0.003 0 5 -10000 0 5
RRAS -0.032 0.008 -10000 0 -10000 0 0
DNM1 -0.018 0.002 0 2 -10000 0 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.003 0.069 0.16 26 -10000 0 26
lamellipodium assembly -0.035 0.02 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.004 0.022 0.078 7 -0.089 4 11
PIK3R1 -0.018 0.004 0 8 -10000 0 8
EPHB2 -0.018 0.003 0 5 -10000 0 5
EPHB3 -0.014 0.008 0 44 -10000 0 44
EPHB1 -0.016 0.007 0 26 -10000 0 26
EPHB4 -0.017 0.005 0 14 -10000 0 14
mol:GDP -0.028 0.05 0.13 4 -0.16 14 18
Ephrin B/EPHB2 0.038 0.009 -10000 0 0 9 9
Ephrin B/EPHB3 0.028 0.018 -10000 0 0 49 49
JNK cascade 0.015 0.12 0.31 23 -10000 0 23
Ephrin B/EPHB1 0.033 0.016 -10000 0 0 31 31
RAP1/GDP -0.036 0.055 0.14 4 -0.16 17 21
EFNB2 -0.018 0.002 0 3 -10000 0 3
EFNB3 -0.018 0.002 0 3 -10000 0 3
EFNB1 -0.018 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.027 0.013 -10000 0 0 30 30
RAP1B -0.018 0.004 0 7 -10000 0 7
RAP1A -0.018 0.003 0 6 -10000 0 6
CDC42/GTP -0.034 0.02 0.034 3 -10000 0 3
Rap1/GTP -0.042 0.021 -10000 0 -10000 0 0
axon guidance 0.022 0.005 -10000 0 0 9 9
MAPK3 -0.014 0.021 -10000 0 -10000 0 0
MAPK1 -0.014 0.022 -10000 0 -10000 0 0
Rac1/GDP -0.034 0.052 0.14 3 -0.16 17 20
actin cytoskeleton reorganization -0.041 0.038 0.028 14 -0.12 16 30
CDC42/GDP -0.032 0.055 0.14 5 -0.16 17 22
PI3K 0.026 0.019 -10000 0 0 58 58
EFNA5 -0.018 0.003 0 6 -10000 0 6
Ephrin B2/EPHB4 0.021 0.007 -10000 0 0 17 17
Ephrin B/EPHB2/Intersectin/N-WASP -0.017 0.03 -10000 0 -0.11 15 15
CDC42 -0.018 0.003 0 5 -10000 0 5
RAS family/GTP -0.04 0.022 -10000 0 -10000 0 0
PTK2 0.055 0.19 0.54 21 -10000 0 21
MAP4K4 0.015 0.12 0.32 23 -10000 0 23
SRC -0.017 0.005 0 14 -10000 0 14
KALRN -0.016 0.006 0 20 -10000 0 20
Intersectin/N-WASP 0.024 0.006 -10000 0 0 11 11
neuron projection morphogenesis -0.006 0.094 0.26 15 -10000 0 15
MAP2K1 -0.008 0.02 0.068 7 -0.09 3 10
WASL -0.018 0.004 0 7 -10000 0 7
Ephrin B1/EPHB1-2/NCK1 0.036 0.017 -10000 0 0 30 30
cell migration -0.001 0.049 0.15 6 -0.13 1 7
NRAS -0.017 0.004 0 9 -10000 0 9
SYNJ1 -0.031 0.009 -10000 0 -10000 0 0
PXN -0.018 0.001 0 1 -10000 0 1
TF -0.031 0.015 -10000 0 -10000 0 0
HRAS/GTP -0.035 0.017 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.027 0.012 -10000 0 0 28 28
cell adhesion mediated by integrin 0.008 0.033 -10000 0 -10000 0 0
RAC1 -0.017 0.004 0 10 -10000 0 10
mol:GTP -0.031 0.015 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.036 0.024 -10000 0 -10000 0 0
RASA1 -0.018 0.004 0 8 -10000 0 8
RAC1-CDC42/GDP -0.037 0.051 0.14 3 -0.16 17 20
ruffle organization -0.001 0.1 0.25 13 -10000 0 13
NCK1 -0.015 0.007 0 27 -10000 0 27
receptor internalization -0.035 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.042 0.019 -10000 0 -0.008 5 5
ROCK1 0.027 0.083 0.17 42 -10000 0 42
RAS family/GDP -0.044 0.039 -10000 0 -0.14 16 16
Rac1/GTP -0.036 0.021 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin -0.01 0.017 -10000 0 -0.091 7 7
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.005 0.002 0 32 -10000 0 32
epithelial cell differentiation 0.03 0.015 -10000 0 0 32 32
CYFIP2 -0.018 0.003 0 6 -10000 0 6
ENAH -0.013 0.072 0.18 11 -10000 0 11
EGFR -0.016 0.006 0 20 -10000 0 20
EPHA2 -0.018 0.004 0 7 -10000 0 7
MYO6 -0.019 0.044 0.16 8 -10000 0 8
CTNNB1 -0.015 0.007 0 28 -10000 0 28
ABI1/Sra1/Nap1 0.032 0.009 -10000 0 0 12 12
AQP5 -0.015 0.042 0.15 7 -0.27 1 8
CTNND1 -0.018 0.002 0 3 -10000 0 3
mol:PI-4-5-P2 -0.018 0.043 0.16 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.017 0.046 0.16 9 -10000 0 9
EGF -0.018 0.003 0 5 -10000 0 5
NCKAP1 -0.018 0.003 0 4 -10000 0 4
AQP3 -0.018 0.049 0.15 6 -0.27 3 9
cortical microtubule organization 0.03 0.015 -10000 0 0 32 32
GO:0000145 -0.017 0.041 0.16 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.016 -10000 0 0 32 32
MLLT4 -0.018 0.004 0 7 -10000 0 7
ARF6/GDP -0.037 0.024 -10000 0 -10000 0 0
ARF6 -0.017 0.004 0 9 -10000 0 9
Ephrin A1/EPHA2/NCK1/GIT1 0.034 0.018 -10000 0 0 37 37
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.033 0.16 5 -10000 0 5
PVRL2 -0.018 0.002 0 2 -10000 0 2
ZYX -0.018 0.044 0.16 8 -10000 0 8
ARF6/GTP 0.036 0.021 -10000 0 -10000 0 0
CDH1 -0.017 0.004 0 9 -10000 0 9
EGFR/EGFR/EGF/EGF -0.028 0.017 0 38 -10000 0 38
RhoA/GDP 0.03 0.015 -10000 0 -0.008 4 4
actin cytoskeleton organization -0.023 0.04 0.15 8 -10000 0 8
IGF-1R heterotetramer -0.018 0.003 0 4 -10000 0 4
GIT1 -0.018 0.002 0 2 -10000 0 2
IGF1R -0.018 0.003 0 4 -10000 0 4
IGF1 -0.018 0.002 0 2 -10000 0 2
DIAPH1 0.014 0.091 -10000 0 -0.5 5 5
Wnt receptor signaling pathway -0.03 0.015 0 32 -10000 0 32
RHOA -0.016 0.006 0 23 -10000 0 23
RhoA/GTP -0.036 0.024 -10000 0 -10000 0 0
CTNNA1 -0.018 0.003 0 5 -10000 0 5
VCL -0.023 0.04 0.15 8 -10000 0 8
EFNA1 -0.018 0.004 0 8 -10000 0 8
LPP -0.018 0.037 0.16 5 -10000 0 5
Ephrin A1/EPHA2 -0.031 0.015 0 27 -10000 0 27
SEC6/SEC8 -0.035 0.021 -10000 0 -10000 0 0
MGAT3 -0.017 0.046 0.17 9 -10000 0 9
HGF/MET -0.031 0.015 0 25 -10000 0 25
HGF -0.018 0.003 0 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.005 0.002 0 32 -10000 0 32
actin cable formation 0.02 0.093 0.19 30 -0.16 1 31
KIAA1543 -0.023 0.043 0.16 8 -10000 0 8
KIFC3 -0.02 0.04 0.16 7 -10000 0 7
NCK1 -0.015 0.007 0 27 -10000 0 27
EXOC3 -0.015 0.007 0 27 -10000 0 27
ACTN1 -0.019 0.042 0.17 7 -10000 0 7
NCK1/GIT1 0.021 0.009 -10000 0 0 28 28
mol:GDP 0.03 0.015 -10000 0 0 32 32
EXOC4 -0.018 0.003 0 4 -10000 0 4
STX4 -0.022 0.011 0 32 -10000 0 32
PIP5K1C -0.018 0.044 0.16 8 -10000 0 8
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 -0.018 0.002 0 3 -10000 0 3
ROCK1 -0.003 0.088 0.22 12 -10000 0 12
adherens junction assembly -0.023 0.066 0.15 8 -0.33 3 11
IGF-1R heterotetramer/IGF1 -0.032 0.014 0 22 -10000 0 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.024 0.006 -10000 0 0 9 9
MET -0.018 0.004 0 7 -10000 0 7
PLEKHA7 -0.017 0.046 0.17 9 -10000 0 9
mol:GTP 0.033 0.018 -10000 0 0 37 37
establishment of epithelial cell apical/basal polarity -0.015 0.064 0.13 23 -10000 0 23
cortical actin cytoskeleton stabilization -0.005 0.002 0 32 -10000 0 32
regulation of cell-cell adhesion -0.023 0.04 0.15 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.005 0.002 0 32 -10000 0 32
Signaling events mediated by PRL

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
CCNE1 -0.018 0.002 0 3 -10000 0 3
mol:Halofuginone 0 0 -10000 0 -10000 0 0
ITGA1 -0.018 0.004 0 8 -10000 0 8
CDKN1A -0.004 0.044 -10000 0 -0.32 3 3
PRL-3/alpha Tubulin 0.01 0.005 -10000 0 0 28 28
mol:Ca2+ -0.017 0.008 0 31 -10000 0 31
AGT -0.018 0.003 0 5 -10000 0 5
CCNA2 -0.024 0.01 0 27 -10000 0 27
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.011 0.002 0 5 -10000 0 5
CDK2/Cyclin E1 0.018 0.063 0.24 1 -0.22 8 9
MAPK3 -0.018 0.009 0 31 -10000 0 31
PRL-2 /Rab GGTase beta 0.024 0.005 -10000 0 0 8 8
MAPK1 -0.018 0.009 0 32 -10000 0 32
PTP4A1 -0.02 0.008 0 24 -10000 0 24
PTP4A3 -0.015 0.007 0 28 -10000 0 28
PTP4A2 -0.018 0.003 0 5 -10000 0 5
ITGB1 -0.018 0.009 0 32 -10000 0 32
SRC -0.017 0.005 0 14 -10000 0 14
RAC1 -0.001 0.025 -10000 0 -0.33 1 1
Rab GGTase beta/Rab GGTase alpha 0.023 0.007 -10000 0 0 12 12
PRL-1/ATF-5 -0.01 0.053 0.16 14 -10000 0 14
RABGGTA -0.018 0.003 0 6 -10000 0 6
BCAR1 -0.017 0.009 0 33 -10000 0 33
RHOC 0.001 0.001 -10000 0 -10000 0 0
RHOA -0.012 0.066 -10000 0 -0.33 7 7
cell motility 0.003 0.063 0.17 6 -0.29 2 8
PRL-1/alpha Tubulin -0.018 0.007 0 24 -10000 0 24
PRL-3/alpha1 Integrin 0.02 0.01 -10000 0 0 33 33
ROCK1 0.001 0.037 -10000 0 -0.14 7 7
RABGGTB -0.018 0.003 0 6 -10000 0 6
CDK2 -0.018 0.001 0 1 -10000 0 1
mitosis -0.02 0.008 0 24 -10000 0 24
ATF5 -0.018 0.001 0 1 -10000 0 1
IL12-mediated signaling 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.006 0.045 0.074 34 -0.16 5 39
TBX21 0.002 0.035 0.098 2 -0.18 2 4
B2M -0.018 0.003 0 4 -10000 0 4
TYK2 -0.006 0.018 0.025 7 -10000 0 7
IL12RB1 -0.006 0.018 0.026 6 -10000 0 6
GADD45B 0.002 0.066 0.16 1 -0.25 7 8
IL12RB2 -0.008 0.017 0.018 47 -10000 0 47
GADD45G 0.008 0.047 0.16 1 -0.16 5 6
natural killer cell activation 0 0.001 0.007 2 -10000 0 2
RELB -0.018 0.002 0 3 -10000 0 3
RELA -0.017 0.005 0 11 -10000 0 11
IL18 -0.008 0.015 0.018 37 -10000 0 37
IL2RA -0.018 0.003 0 4 -10000 0 4
IFNG -0.018 0.003 0 6 -10000 0 6
STAT3 (dimer) 0.006 0.07 0.14 1 -0.27 7 8
HLA-DRB5 -0.012 0.009 0 57 -10000 0 57
FASLG 0.007 0.046 0.16 6 -0.18 2 8
NF kappa B2 p52/RelB 0.028 0.042 0.11 7 -0.12 5 12
CD4 -0.017 0.005 0 12 -10000 0 12
SOCS1 -0.018 0.003 0 4 -10000 0 4
EntrezGene:6955 0 0 -10000 0 -10000 0 0
CD3D -0.016 0.006 0 24 -10000 0 24
CD3E -0.016 0.006 0 24 -10000 0 24
CD3G -0.016 0.006 0 24 -10000 0 24
IL12Rbeta2/JAK2 0.021 0.01 -10000 0 0 30 30
CCL3 0.002 0.035 0.1 1 -0.18 2 3
CCL4 0.003 0.037 0.13 3 -0.18 2 5
HLA-A -0.017 0.005 0 11 -10000 0 11
IL18/IL18R 0.03 0.013 -10000 0 0 27 27
NOS2 0.008 0.034 0.1 7 -0.14 2 9
IL12/IL12R/TYK2/JAK2/SPHK2 0.006 0.043 0.074 34 -0.14 5 39
IL1R1 0.003 0.041 0.19 2 -0.18 2 4
IL4 -0.017 0.007 0.019 3 -10000 0 3
JAK2 -0.009 0.015 0.023 2 -10000 0 2
EntrezGene:6957 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.042 -10000 0 -0.15 8 8
RAB7A 0.006 0.058 0.15 2 -0.17 8 10
lysosomal transport 0.006 0.057 0.11 7 -0.17 8 15
FOS -0.019 0.14 -10000 0 -0.67 5 5
STAT4 (dimer) 0.01 0.061 0.13 11 -0.2 6 17
STAT5A (dimer) 0.029 0.042 0.11 8 -0.12 5 13
GZMA 0.007 0.033 0.1 6 -0.14 1 7
GZMB 0.009 0.044 0.13 9 -0.16 2 11
HLX 0 0 -10000 0 -10000 0 0
LCK 0.003 0.025 0.1 1 -10000 0 1
TCR/CD3/MHC II/CD4 -0.006 0.049 0.065 27 -0.099 26 53
IL2/IL2R 0.041 0.011 -10000 0 0 12 12
MAPK14 0.006 0.063 0.16 2 -0.19 8 10
CCR5 0.005 0.045 0.1 8 -0.15 5 13
IL1B -0.006 0.018 0.024 8 -10000 0 8
STAT6 0.011 0.014 -10000 0 -10000 0 0
STAT4 -0.018 0.004 0 7 -10000 0 7
STAT3 -0.018 0.002 0 3 -10000 0 3
STAT1 -0.018 0.004 0 7 -10000 0 7
NFKB1 -0.018 0.003 0 6 -10000 0 6
NFKB2 -0.018 0.002 0 2 -10000 0 2
IL12B -0.008 0.016 0.018 44 -10000 0 44
CD8A -0.018 0.002 0 2 -10000 0 2
CD8B 0 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.006 0.044 0.15 5 -0.074 34 39
IL2RB -0.018 0.002 0 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.059 0.13 11 -0.19 6 17
IL2RG -0.018 0 -10000 0 -10000 0 0
IL12 0.019 0.011 -10000 0 0 42 42
STAT5A -0.018 0.002 0 3 -10000 0 3
CD247 0 0 -10000 0 -10000 0 0
IL2 -0.018 0.004 0 7 -10000 0 7
SPHK2 -0.018 0.002 0 2 -10000 0 2
FRAP1 -0.018 0.004 0 7 -10000 0 7
IL12A -0.01 0.013 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.001 0.015 -10000 0 -0.13 2 2
MAP2K3 0.003 0.066 0.17 1 -0.23 7 8
RIPK2 -0.016 0.006 0 18 -10000 0 18
MAP2K6 0.007 0.056 0.16 1 -0.21 5 6
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.017 0.004 0 9 -10000 0 9
IL18RAP -0.008 0.017 0.018 47 -10000 0 47
IL12Rbeta1/TYK2 0.025 0.005 0.041 2 0 4 6
EOMES -0.08 0.21 -10000 0 -0.6 23 23
STAT1 (dimer) 0.012 0.051 0.13 1 -0.2 5 6
T cell proliferation 0.012 0.049 0.14 8 -0.12 5 13
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.008 0.017 0.018 47 -10000 0 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.02 0.052 -10000 0 -0.2 4 4
ATF2 0.007 0.07 0.19 7 -0.21 6 13
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.01 0.003 0 13 -10000 0 13
IHH 0.02 0.005 -10000 0 0 8 8
SHH Np/Cholesterol/GAS1 -0.021 0.007 0 16 -10000 0 16
LRPAP1 -0.017 0.005 0 15 -10000 0 15
dorsoventral neural tube patterning 0.021 0.007 -10000 0 0 16 16
SMO/beta Arrestin2 0.009 0.064 -10000 0 -0.2 11 11
SMO -0.007 0.046 -10000 0 -0.22 7 7
AKT1 -0.009 0.078 -10000 0 -0.31 9 9
ARRB2 -0.018 0.002 0 2 -10000 0 2
BOC -0.016 0.006 0 20 -10000 0 20
ADRBK1 -0.017 0.006 0 17 -10000 0 17
heart looping -0.007 0.046 -10000 0 -0.22 7 7
STIL -0.012 0.044 0.16 10 -10000 0 10
DHH N/PTCH2 0.025 0.003 -10000 0 0 3 3
DHH N/PTCH1 0.009 0.017 -10000 0 -0.067 8 8
PIK3CA -0.013 0.008 0 49 -10000 0 49
DHH -0.018 0.002 0 2 -10000 0 2
PTHLH -0.012 0.034 -10000 0 -0.19 6 6
determination of left/right symmetry -0.007 0.046 -10000 0 -0.22 7 7
PIK3R1 -0.018 0.004 0 8 -10000 0 8
skeletal system development -0.012 0.034 -10000 0 -0.18 6 6
IHH N/Hhip 0.025 0.008 -10000 0 0 14 14
DHH N/Hhip 0.024 0.005 -10000 0 0 7 7
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.007 0.046 -10000 0 -0.22 7 7
pancreas development -0.018 0.004 0 7 -10000 0 7
HHAT -0.017 0.004 0 9 -10000 0 9
PI3K 0.017 0.012 -10000 0 0 53 53
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.018 0 -10000 0 -10000 0 0
somite specification -0.007 0.046 -10000 0 -0.22 7 7
SHH Np/Cholesterol/PTCH1 -0.016 0.011 -10000 0 -0.061 8 8
SHH Np/Cholesterol/PTCH2 -0.021 0.007 0 16 -10000 0 16
SHH Np/Cholesterol/Megalin -0.02 0.007 0 19 -10000 0 19
SHH -0.02 0.007 0 16 -10000 0 16
catabolic process -0.006 0.014 -10000 0 -0.069 8 8
SMO/Vitamin D3 -0.01 0.049 0.16 10 -0.14 7 17
SHH Np/Cholesterol/Hhip -0.02 0.008 0 20 -10000 0 20
LRP2 -0.018 0.003 0 4 -10000 0 4
receptor-mediated endocytosis -0.013 0.043 0.13 9 -0.14 6 15
SHH Np/Cholesterol/BOC -0.019 0.009 0 32 -10000 0 32
SHH Np/Cholesterol/CDO -0.018 0.009 0 34 -10000 0 34
mesenchymal cell differentiation 0.02 0.007 -10000 0 0 20 20
mol:Vitamin D3 -0.003 0.045 0.16 11 -10000 0 11
IHH N/PTCH2 0.026 0.006 -10000 0 0 9 9
CDON -0.016 0.006 0 22 -10000 0 22
IHH N/PTCH1 0.014 0.003 -10000 0 0 8 8
Megalin/LRPAP1 0.023 0.008 -10000 0 0 17 17
PTCH2 -0.018 0.001 0 1 -10000 0 1
SHH Np/Cholesterol -0.013 0.008 0.029 5 -10000 0 5
PTCH1 -0.006 0.014 -10000 0 -0.069 8 8
HHIP -0.018 0.004 0 7 -10000 0 7
Signaling events mediated by PTP1B

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
PDGFRB -0.018 0.003 0 5 -10000 0 5
Jak2/Leptin Receptor -0.009 0.11 -10000 0 -0.35 13 13
PTP1B/AKT1 -0.02 0.075 0.12 2 -0.18 21 23
FYN -0.018 0.003 0 6 -10000 0 6
p210 bcr-abl/PTP1B -0.022 0.08 0.12 2 -0.18 25 27
EGFR -0.015 0.011 0.024 1 -10000 0 1
EGF/EGFR -0.007 0.068 0.14 1 -0.15 24 25
CSF1 -0.018 0.003 0 4 -10000 0 4
AKT1 -0.016 0.01 0.019 8 -10000 0 8
INSR -0.016 0.01 0.019 12 -10000 0 12
PTP1B/N-cadherin -0.019 0.076 0.12 2 -0.18 22 24
Insulin Receptor/Insulin 0 0.08 0.14 1 -0.17 25 26
HCK -0.016 0.006 0 21 -10000 0 21
CRK -0.018 0.002 0 2 -10000 0 2
TYK2 -0.027 0.077 0.17 2 -0.2 18 20
EGF -0.012 0.015 0.025 2 -10000 0 2
YES1 -0.017 0.006 0 17 -10000 0 17
CAV1 -0.018 0.082 0.12 7 -0.19 21 28
TXN -0.011 0.015 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.006 0.082 0.12 2 -0.17 24 26
cell migration 0.022 0.08 0.18 25 -0.12 2 27
STAT3 -0.016 0.01 0.018 12 -10000 0 12
PRLR -0.016 0.007 0.018 3 -10000 0 3
ITGA2B -0.012 0.014 0.021 2 -10000 0 2
CSF1R -0.018 0.003 0 5 -10000 0 5
Prolactin Receptor/Prolactin 0.021 0.01 -10000 0 -0.001 27 27
FGR -0.018 0.003 0 4 -10000 0 4
PTP1B/p130 Cas -0.021 0.077 0.12 2 -0.18 23 25
Crk/p130 Cas -0.005 0.081 0.12 2 -0.17 24 26
DOK1 -0.027 0.081 0.12 1 -0.2 21 22
JAK2 -0.021 0.11 -10000 0 -0.36 13 13
Jak2/Leptin Receptor/Leptin -0.023 0.085 0.12 6 -0.22 16 22
PIK3R1 -0.018 0.004 0 8 -10000 0 8
PTPN1 -0.023 0.08 0.12 2 -0.18 25 27
LYN -0.016 0.006 0 18 -10000 0 18
CDH2 -0.017 0.005 0 15 -10000 0 15
SRC -0.008 0.095 -10000 0 -0.51 5 5
ITGB3 -0.012 0.014 0.021 2 -10000 0 2
CAT1/PTP1B -0.01 0.1 0.2 7 -0.24 15 22
CAPN1 -0.017 0.009 0.022 4 -10000 0 4
CSK -0.018 0.002 0 3 -10000 0 3
PI3K 0.008 0.064 0.12 1 -0.17 14 15
mol:H2O2 0 0.003 0.016 2 -10000 0 2
STAT3 (dimer) -0.022 0.078 0.11 6 -0.2 16 22
negative regulation of transcription -0.02 0.11 -10000 0 -0.36 13 13
FCGR2A -0.018 0.003 0 6 -10000 0 6
FER -0.011 0.015 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.024 0.007 -10000 0 -0.024 3 3
BLK -0.017 0.004 0 9 -10000 0 9
Insulin Receptor/Insulin/Shc 0.028 0.018 -10000 0 -0.012 24 24
RHOA -0.013 0.012 0.02 11 -10000 0 11
LEPR -0.018 0.003 0 3 -10000 0 3
BCAR1 -0.018 0.004 0 7 -10000 0 7
p210 bcr-abl/Grb2 -0.018 0.001 0 1 -10000 0 1
mol:NADPH 0 0.001 -10000 0 -10000 0 0
TRPV6 0.005 0.09 0.19 4 -0.26 10 14
PRL -0.016 0.008 0.018 7 -10000 0 7
SOCS3 0.016 0.009 -10000 0 -10000 0 0
SPRY2 -0.011 0.016 0.021 31 -10000 0 31
Insulin Receptor/Insulin/IRS1 0.029 0.016 -10000 0 -0.032 7 7
CSF1/CSF1R -0.005 0.082 0.12 2 -0.17 26 28
Ras protein signal transduction -0.005 0.049 0.55 1 -10000 0 1
IRS1 -0.018 0.004 0 8 -10000 0 8
INS -0.016 0.011 0.019 12 -10000 0 12
LEP -0.015 0.01 0.018 12 -10000 0 12
STAT5B -0.017 0.094 0.15 1 -0.24 18 19
STAT5A -0.017 0.094 0.15 1 -0.24 18 19
GRB2 -0.018 0.001 0 1 -10000 0 1
PDGFB-D/PDGFRB -0.02 0.078 0.12 2 -0.18 23 25
CSN2 0.009 0.052 0.14 6 -0.26 3 9
PIK3CA -0.013 0.008 0 49 -10000 0 49
LAT -0.003 0.077 -10000 0 -0.52 3 3
YBX1 -0.012 0.015 0.023 9 -10000 0 9
LCK -0.018 0.003 0 4 -10000 0 4
SHC1 -0.018 0.004 0 7 -10000 0 7
NOX4 -0.012 0.014 0.022 21 -10000 0 21
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.042 0.02 -10000 0 -0.008 14 14
SMAD6-7/SMURF1 0.029 0.013 -10000 0 0 29 29
NOG -0.018 0.001 0 1 -10000 0 1
SMAD9 -0.008 0.094 -10000 0 -0.41 8 8
SMAD4 -0.016 0.006 0 19 -10000 0 19
SMAD5 -0.009 0.047 0.11 2 -0.21 6 8
BMP7/USAG1 0.023 0.007 -10000 0 0 16 16
SMAD5/SKI -0.012 0.063 0.12 5 -0.22 9 14
SMAD1 -0.005 0.035 -10000 0 -0.25 1 1
BMP2 -0.017 0.005 0 13 -10000 0 13
SMAD1/SMAD1/SMAD4 -0.034 0.045 -10000 0 -0.22 5 5
BMPR1A -0.018 0.001 0 1 -10000 0 1
BMPR1B -0.018 0.003 0 6 -10000 0 6
BMPR1A-1B/BAMBI 0.033 0.007 -10000 0 0 8 8
AHSG -0.013 0.008 0 45 -10000 0 45
CER1 -0.016 0.006 0 20 -10000 0 20
BMP2-4/CER1 0.028 0.014 -10000 0 0 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.005 0.049 -10000 0 -0.22 4 4
BMP2-4 (homodimer) 0.022 0.008 -10000 0 0 20 20
RGMB -0.018 0.004 0 7 -10000 0 7
BMP6/BMPR2/BMPR1A-1B 0.039 0.014 -10000 0 0 20 20
RGMA -0.018 0.003 0 5 -10000 0 5
SMURF1 -0.017 0.005 0 13 -10000 0 13
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.004 0.036 0.066 8 -0.14 6 14
BMP2-4/USAG1 0.03 0.012 -10000 0 0 24 24
SMAD6/SMURF1/SMAD5 -0.012 0.061 0.12 5 -0.23 8 13
SOSTDC1 -0.018 0.004 0 8 -10000 0 8
BMP7/BMPR2/BMPR1A-1B 0.039 0.014 -10000 0 0 20 20
SKI -0.018 0.003 0 5 -10000 0 5
BMP6 (homodimer) -0.017 0.005 0 12 -10000 0 12
HFE2 -0.018 0.003 0 6 -10000 0 6
ZFYVE16 -0.018 0.004 0 8 -10000 0 8
MAP3K7 -0.018 0.003 0 6 -10000 0 6
BMP2-4/CHRD 0.023 0.016 -10000 0 0 55 55
SMAD5/SMAD5/SMAD4 -0.012 0.058 0.12 2 -0.22 8 10
MAPK1 -0.018 0.003 0 6 -10000 0 6
TAK1/TAB family 0.022 0.05 -10000 0 -0.19 4 4
BMP7 (homodimer) -0.017 0.004 0 10 -10000 0 10
NUP214 -0.018 0.002 0 2 -10000 0 2
BMP6/FETUA 0.017 0.012 -10000 0 0 52 52
SMAD1/SKI -0.016 0.061 0.14 4 -0.24 6 10
SMAD6 -0.018 0.002 0 3 -10000 0 3
CTDSP2 -0.018 0.002 0 2 -10000 0 2
BMP2-4/FETUA 0.023 0.016 -10000 0 0 56 56
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
GREM1 -0.018 0.003 0 4 -10000 0 4
BMPR2 (homodimer) -0.018 0.004 0 7 -10000 0 7
GADD34/PP1CA 0.03 0.012 -10000 0 0 24 24
BMPR1A-1B (homodimer) 0.024 0.005 -10000 0 0 6 6
CHRDL1 -0.018 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.015 0.061 0.14 4 -0.24 6 10
SMAD6-7/SMURF1/SMAD1 0.008 0.061 0.17 1 -0.24 5 6
SMAD6/SMURF1 -0.017 0.005 0 13 -10000 0 13
BAMBI -0.018 0.002 0 3 -10000 0 3
SMURF2 -0.018 0 -10000 0 -10000 0 0
BMP2-4/CHRDL1 0.03 0.011 -10000 0 0 20 20
BMP2-4/GREM1 0.03 0.012 -10000 0 0 22 22
SMAD7 -0.017 0.005 0 15 -10000 0 15
SMAD8A/SMAD8A/SMAD4 -0.008 0.11 -10000 0 -0.36 13 13
SMAD1/SMAD6 -0.015 0.059 0.14 4 -0.25 5 9
TAK1/SMAD6 0.023 0.008 -10000 0 0 18 18
BMP7 -0.017 0.004 0 10 -10000 0 10
BMP6 -0.017 0.005 0 12 -10000 0 12
MAP3K7IP2 -0.018 0.003 0 5 -10000 0 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.008 0.042 -10000 0 -0.24 4 4
PPM1A -0.018 0.004 0 8 -10000 0 8
SMAD1/SMURF2 -0.017 0.062 0.14 4 -0.25 6 10
SMAD7/SMURF1 0.021 0.009 -10000 0 0 27 27
CTDSPL -0.016 0.007 0 25 -10000 0 25
PPP1CA -0.017 0.006 0 17 -10000 0 17
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 -0.018 0.004 0 8 -10000 0 8
PPP1R15A -0.018 0.002 0 2 -10000 0 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.007 0.049 -10000 0 -0.18 8 8
CHRD -0.014 0.008 0 44 -10000 0 44
BMPR2 -0.018 0.004 0 7 -10000 0 7
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.012 0.035 -10000 0 -0.12 11 11
BMP4 -0.018 0.004 0 7 -10000 0 7
FST -0.018 0.004 0 8 -10000 0 8
BMP2-4/NOG 0.03 0.011 -10000 0 0 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.041 0.02 -10000 0 -0.008 7 7
Endothelins

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
AKT1 -0.022 0.01 0 28 -10000 0 28
PTK2B -0.016 0.007 0.006 15 -10000 0 15
mol:Ca2+ 0.002 0.072 0.19 10 -0.22 6 16
EDN1 -0.015 0.009 0.007 20 -10000 0 20
EDN3 -0.017 0.004 0 10 -10000 0 10
EDN2 -0.018 0.002 0 3 -10000 0 3
HRAS/GDP -0.023 0.057 0.18 2 -0.2 8 10
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.008 0.046 0.066 9 -0.17 10 19
ADCY4 -0.006 0.058 0.18 14 -10000 0 14
ADCY5 -0.006 0.056 0.18 13 -10000 0 13
ADCY6 -0.004 0.063 0.18 17 -10000 0 17
ADCY7 -0.003 0.062 0.18 17 -10000 0 17
ADCY1 -0.003 0.062 0.18 17 -10000 0 17
ADCY2 -0.006 0.053 0.16 14 -10000 0 14
ADCY3 -0.005 0.061 0.18 16 -10000 0 16
ADCY8 -0.007 0.053 0.18 11 -10000 0 11
ADCY9 -0.003 0.064 0.17 18 -10000 0 18
arachidonic acid secretion -0.012 0.049 0.16 3 -0.18 4 7
ETB receptor/Endothelin-1/Gq/GTP -0.011 0.04 0.079 5 -0.14 11 16
GNAO1 -0.017 0.004 0 10 -10000 0 10
HRAS -0.018 0.003 0 5 -10000 0 5
ETA receptor/Endothelin-1/G12/GTP 0.028 0.012 -10000 0 0 24 24
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.011 -10000 0 0 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
COL3A1 -0.023 0.009 0 21 -10000 0 21
EDNRB -0.016 0.008 0.01 12 -10000 0 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.022 0.009 0 25 -10000 0 25
CYSLTR1 -0.023 0.008 0 17 -10000 0 17
SLC9A1 -0.006 0.002 -10000 0 -10000 0 0
mol:GDP -0.02 0.058 0.18 2 -0.2 9 11
SLC9A3 -0.006 0.11 -10000 0 -0.43 10 10
RAF1 -0.018 0.046 0.16 1 -0.19 6 7
JUN -0.01 0.065 0.17 1 -0.25 8 9
JAK2 -0.02 0.011 0 39 -10000 0 39
mol:IP3 -0.007 0.028 0.071 1 -0.17 3 4
ETA receptor/Endothelin-1 0.023 0.008 -10000 0 0 17 17
PLCB1 -0.016 0.007 0.003 16 -10000 0 16
PLCB2 -0.015 0.011 0.018 14 -10000 0 14
ETA receptor/Endothelin-3 0.023 0.007 -10000 0 0 15 15
FOS -0.021 0.046 0.17 2 -0.18 5 7
Gai/GDP -0.083 0.24 -10000 0 -0.65 25 25
CRK -0.017 0.007 0.014 8 -10000 0 8
mol:Ca ++ -0.009 0.029 0.13 5 -0.096 3 8
BCAR1 -0.018 0.004 0 7 -10000 0 7
PRKCB1 -0.013 0.04 -10000 0 -0.19 5 5
GNAQ -0.015 0.011 0.018 16 -10000 0 16
GNAZ -0.018 0.003 0 6 -10000 0 6
GNAL -0.017 0.005 0 13 -10000 0 13
Gs family/GDP -0.025 0.047 -10000 0 -0.2 7 7
ETA receptor/Endothelin-1/Gq/GTP -0.011 0.041 0.079 5 -0.15 11 16
MAPK14 -0.014 0.042 0.056 8 -0.16 9 17
TRPC6 0.002 0.073 0.2 10 -0.23 6 16
GNAI2 -0.016 0.006 0 23 -10000 0 23
GNAI3 -0.018 0.003 0 4 -10000 0 4
GNAI1 -0.018 0.003 0 4 -10000 0 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.007 0.046 0.067 10 -0.16 10 20
ETB receptor/Endothelin-2 0.024 0.005 -10000 0 0 7 7
ETB receptor/Endothelin-3 0.023 0.007 -10000 0 0 15 15
ETB receptor/Endothelin-1 0.023 0.007 -10000 0 0 16 16
MAPK3 -0.023 0.049 0.17 2 -0.2 5 7
MAPK1 -0.021 0.046 0.17 2 -0.19 4 6
Rac1/GDP -0.023 0.054 0.18 2 -0.2 7 9
cAMP biosynthetic process 0.025 0.082 0.22 19 -0.22 1 20
MAPK8 -0.006 0.071 -10000 0 -0.27 8 8
SRC -0.016 0.006 0.002 16 -10000 0 16
ETB receptor/Endothelin-1/Gi/GTP -0.014 0.033 -10000 0 -0.11 15 15
p130Cas/CRK/Src/PYK2 -0.019 0.068 0.19 4 -0.21 8 12
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.023 0.054 0.18 2 -0.21 6 8
COL1A2 -0.015 0.008 -10000 0 -0.056 3 3
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.024 0.006 -10000 0 0 9 9
mol:DAG -0.007 0.028 0.071 1 -0.17 3 4
MAP2K2 -0.021 0.049 0.18 3 -0.19 5 8
MAP2K1 -0.024 0.044 0.15 1 -0.18 6 7
EDNRA -0.016 0.007 0.007 13 -10000 0 13
positive regulation of muscle contraction -0.016 0.039 0.18 6 -10000 0 6
Gq family/GDP -0.018 0.055 0.16 3 -0.16 6 9
HRAS/GTP -0.017 0.051 0.15 2 -0.21 6 8
PRKCH -0.008 0.051 0.18 5 -0.19 5 10
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCA -0.013 0.043 0.17 1 -0.19 5 6
PRKCB -0.007 0.036 -10000 0 -0.15 7 7
PRKCE -0.012 0.045 0.17 2 -0.19 5 7
PRKCD -0.008 0.028 -10000 0 -0.17 3 3
PRKCG -0.013 0.043 0.17 1 -0.19 5 6
regulation of vascular smooth muscle contraction -0.025 0.048 0.16 3 -0.18 5 8
PRKCQ -0.014 0.039 -10000 0 -0.21 4 4
PLA2G4A -0.013 0.051 0.16 3 -0.18 5 8
GNA14 -0.015 0.011 0.018 16 -10000 0 16
GNA15 -0.016 0.009 0.012 15 -10000 0 15
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA11 -0.016 0.009 0.012 15 -10000 0 15
Rac1/GTP 0.028 0.012 -10000 0 0 25 25
MMP1 -0.017 0.009 0 39 -10000 0 39
Canonical Wnt signaling pathway

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
HDAC1 -0.018 0.003 0 4 -10000 0 4
AES -0.018 0.003 0 5 -10000 0 5
FBXW11 -0.018 0.004 0 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.022 0.009 -10000 0 -0.001 18 18
SMAD4 -0.016 0.006 0 19 -10000 0 19
DKK2 -0.018 0.003 0 6 -10000 0 6
TLE1 -0.018 0 -10000 0 -10000 0 0
MACF1 -0.013 0.013 0.018 22 -10000 0 22
CTNNB1 -0.013 0.077 0.15 6 -0.2 13 19
WIF1 -0.018 0.004 0 8 -10000 0 8
beta catenin/RanBP3 -0.021 0.065 0.12 3 -0.19 12 15
KREMEN2 -0.017 0.005 0.009 6 -10000 0 6
DKK1 -0.018 0.003 0 4 -10000 0 4
beta catenin/beta TrCP1 -0.015 0.074 0.16 6 -0.22 8 14
FZD1 -0.014 0.011 0.018 16 -10000 0 16
AXIN2 -0.005 0.02 -10000 0 -10000 0 0
AXIN1 -0.013 0.013 0.019 22 -10000 0 22
RAN -0.018 0.001 0 1 -10000 0 1
Axin1/APC/GSK3/beta catenin -0.003 0.069 -10000 0 -0.49 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.018 0.087 0.16 1 -0.25 18 19
Axin1/APC/GSK3 -0.005 0.044 0.12 5 -0.19 4 9
Axin1/APC/GSK3/beta catenin/Macf1 -0.001 0.062 0.15 13 -0.22 5 18
HNF1A 0 0 -10000 0 -10000 0 0
CTBP1 -0.017 0.005 0 15 -10000 0 15
MYC 0.1 0.23 0.58 30 -10000 0 30
RANBP3 -0.018 0.003 0 4 -10000 0 4
DKK2/LRP6/Kremen 2 0.031 0.011 -10000 0 0 17 17
NKD1 -0.017 0.005 0 11 -10000 0 11
TCF4 -0.016 0.006 0 20 -10000 0 20
TCF3 -0.018 0.003 0 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.038 0.015 -10000 0 0 21 21
Ran/GTP 0.013 0.001 -10000 0 0 1 1
CtBP/CBP/TCF/TLE1/AES -0.02 0.057 -10000 0 -0.14 27 27
LEF1 -0.018 0.004 0 7 -10000 0 7
DVL1 -0.006 0.047 -10000 0 -0.26 4 4
CSNK2A1 -0.016 0.008 0.006 19 -10000 0 19
beta catenin/TCF/CtBP/CBP/TLE1/AES 0 0.059 0.14 2 -0.24 7 9
DKK1/LRP6/Kremen 2 0.031 0.011 -10000 0 0 17 17
LRP6 -0.014 0.011 0.018 13 -10000 0 13
CSNK1A1 -0.013 0.013 0.019 21 -10000 0 21
NLK -0.018 0.002 0 2 -10000 0 2
CCND1 0.16 0.27 0.58 47 -10000 0 47
WNT1 -0.014 0.012 0.018 20 -10000 0 20
GSK3A -0.013 0.014 0.018 26 -10000 0 26
GSK3B -0.013 0.012 0.018 15 -10000 0 15
FRAT1 -0.018 0.003 0 3 -10000 0 3
PPP2R5D 0.003 0.056 -10000 0 -0.29 5 5
APC -0.016 0.058 0.17 14 -10000 0 14
WNT1/LRP6/FZD1 -0.003 0.024 0.081 8 -0.086 5 13
CREBBP -0.018 0.002 0 3 -10000 0 3
TCGA08_rtk_signaling

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
PDGFRA -0.017 0.005 0 11 -10000 0 11
HRAS -0.018 0.003 0 5 -10000 0 5
EGFR -0.016 0.006 0 20 -10000 0 20
AKT 0.016 0.075 0.13 34 -0.17 1 35
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 -0.017 0.005 0 13 -10000 0 13
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.017 0.004 0 9 -10000 0 9
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.018 0.004 0 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
PIK3CB -0.015 0.007 0 27 -10000 0 27
NRAS -0.017 0.004 0 9 -10000 0 9
PIK3CG -0.017 0.005 0 11 -10000 0 11
PIK3R3 -0.018 0.001 0 1 -10000 0 1
PIK3R2 -0.018 0.001 0 1 -10000 0 1
NF1 -0.018 0.001 0 1 -10000 0 1
RAS -0.003 0.002 -10000 0 -10000 0 0
ERBB2 -0.018 0.003 0 6 -10000 0 6
proliferation/survival/translation -0.03 0.06 0.13 5 -0.17 19 24
PI3K 0.024 0.056 0.11 39 -10000 0 39
PIK3R1 -0.018 0.004 0 8 -10000 0 8
KRAS -0.017 0.005 0 11 -10000 0 11
FOXO 0.041 0.05 0.11 35 -10000 0 35
AKT2 -0.018 0.002 0 3 -10000 0 3
PTEN -0.018 0.003 0 5 -10000 0 5
IGF1 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
NCK2 -0.018 0.002 0 3 -10000 0 3
PTK2 -0.015 0.007 0 28 -10000 0 28
CRKL -0.018 0.015 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.033 0.008 -10000 0 0 10 10
HRAS -0.018 0.003 0 5 -10000 0 5
IRS1/Crk -0.021 0.007 0 12 -0.044 3 15
IGF-1R heterotetramer/IGF1/PTP1B 0.033 0.017 0.096 7 -10000 0 7
AKT1 0.017 0.082 0.15 43 -10000 0 43
BAD 0.01 0.077 0.14 41 -10000 0 41
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.021 0.006 -10000 0 -10000 0 0
RAF1 -0.013 0.13 0.2 7 -0.37 14 21
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.037 0.014 -10000 0 -0.048 3 3
YWHAZ -0.016 0.006 0 21 -10000 0 21
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.006 -10000 0 0 14 14
PIK3CA -0.013 0.008 0 49 -10000 0 49
RPS6KB1 0.021 0.087 0.15 49 -10000 0 49
GNB2L1 -0.017 0.004 0 10 -10000 0 10
positive regulation of MAPKKK cascade -0.013 0.12 0.22 7 -0.28 16 23
PXN -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
HRAS/GTP -0.032 0.015 0.023 6 -10000 0 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.049 0.02 0.11 7 -0.023 2 9
IGF-1R heterotetramer -0.018 0.016 0.052 8 -10000 0 8
IGF-1R heterotetramer/IGF1/IRS/Nck 0.028 0.013 -10000 0 -0.044 3 3
Crk/p130 Cas/Paxillin -0.028 0.017 -10000 0 -10000 0 0
IGF1R -0.018 0.016 0.052 8 -10000 0 8
IGF1 -0.017 0.018 0.048 11 -10000 0 11
IRS2/Crk -0.024 0.015 -10000 0 -10000 0 0
PI3K 0.027 0.019 -10000 0 -10000 0 0
apoptosis -0.014 0.08 -10000 0 -0.14 45 45
HRAS/GDP 0.012 0.002 -10000 0 0 5 5
PRKCD -0.01 0.014 -10000 0 -0.095 4 4
RAF1/14-3-3 E -0.017 0.13 0.2 7 -0.31 18 25
BAD/14-3-3 0.015 0.083 0.14 45 -10000 0 45
PRKCZ 0.019 0.086 0.15 46 -10000 0 46
Crk/p130 Cas/Paxillin/FAK1 -0.012 0.061 0.11 31 -10000 0 31
PTPN1 -0.017 0.005 0 11 -10000 0 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.008 0.022 -10000 0 -0.097 9 9
BCAR1 -0.018 0.004 0 7 -10000 0 7
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.04 0.018 0.1 6 -10000 0 6
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 -0.018 0.002 0 3 -10000 0 3
IRS1/NCK2 -0.019 0.019 0.11 3 -10000 0 3
GRB10 -0.018 0.004 0 8 -10000 0 8
PTPN11 -0.018 0.015 -10000 0 -10000 0 0
IRS1 -0.014 0.018 0.11 3 -10000 0 3
IRS2 -0.018 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.027 0.016 0.097 8 -10000 0 8
GRB2 -0.018 0.001 0 1 -10000 0 1
PDPK1 0.021 0.085 0.16 43 -10000 0 43
YWHAE -0.018 0.002 0 2 -10000 0 2
PRKD1 -0.012 0.02 -10000 0 -0.099 8 8
SHC1 -0.018 0.004 0 7 -10000 0 7
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.017 0.004 0 9 -9999 0 9
ADCY5 -0.015 0.006 0 21 -9999 0 21
ADCY6 -0.017 0.003 0 5 -9999 0 5
ADCY7 -0.016 0.005 0 13 -9999 0 13
ADCY1 -0.016 0.004 0 10 -9999 0 10
ADCY2 -0.015 0.006 0 24 -9999 0 24
ADCY3 -0.017 0.002 0 3 -9999 0 3
ADCY8 -0.014 0.007 0 32 -9999 0 32
PRKCE -0.011 0.001 0 3 -9999 0 3
ADCY9 -0.017 0.003 0 6 -9999 0 6
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.025 0.079 0.21 15 -9999 0 15
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 -0.017 0.006 0 17 -10000 0 17
VLDLR -0.016 0.006 0 19 -10000 0 19
LRPAP1 -0.017 0.005 0 15 -10000 0 15
NUDC -0.018 0.003 0 4 -10000 0 4
RELN/LRP8 0.029 0.013 -10000 0 0 26 26
CaM/Ca2+ 0.012 0.004 -10000 0 0 14 14
KATNA1 -0.018 0.003 0 5 -10000 0 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.017 0.044 0.16 9 -10000 0 9
IQGAP1/CaM 0.023 0.008 -10000 0 0 17 17
DAB1 -0.018 0.003 0 4 -10000 0 4
IQGAP1 -0.018 0.003 0 4 -10000 0 4
PLA2G7 -0.017 0.004 0 9 -10000 0 9
CALM1 -0.017 0.005 0 14 -10000 0 14
DYNLT1 -0.018 0.003 0 5 -10000 0 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.023 0.007 -10000 0 0 16 16
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 -0.018 0.001 0 1 -10000 0 1
LIS1/Poliovirus Protein 3A -0.016 0.005 0 15 -10000 0 15
CDK5R2 -0.018 0.004 0 8 -10000 0 8
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.028 0.014 -10000 0 0 31 31
YWHAE -0.018 0.002 0 2 -10000 0 2
NDEL1/14-3-3 E -0.025 0.052 0.16 11 -10000 0 11
MAP1B -0.002 0.001 -10000 0 -10000 0 0
RAC1 -0.005 0.002 0 26 -10000 0 26
p35/CDK5 -0.025 0.045 0.16 9 -10000 0 9
RELN -0.017 0.005 0 13 -10000 0 13
PAFAH/LIS1 -0.023 0.009 0 20 -10000 0 20
LIS1/CLIP170 -0.016 0.005 0 15 -10000 0 15
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.042 0.036 0.095 7 -10000 0 7
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.043 0.11 2 -0.2 7 9
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.022 0.041 0.15 8 -10000 0 8
LIS1/IQGAP1 -0.023 0.008 0 18 -10000 0 18
RHOA -0.005 0.002 0 31 -10000 0 31
PAFAH1B1 -0.02 0.006 0 15 -10000 0 15
PAFAH1B3 -0.018 0.001 0 1 -10000 0 1
PAFAH1B2 -0.015 0.007 0 28 -10000 0 28
MAP1B/LIS1/Dynein heavy chain -0.019 0.022 0.077 2 -0.09 8 10
NDEL1/Katanin 60/Dynein heavy chain -0.027 0.053 0.16 10 -10000 0 10
LRP8 -0.018 0.002 0 3 -10000 0 3
NDEL1/Katanin 60 -0.025 0.053 0.16 11 -10000 0 11
P39/CDK5 -0.025 0.043 0.16 8 -10000 0 8
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.024 0.008 0 17 -10000 0 17
CDK5 -0.022 0.042 0.16 8 -10000 0 8
PPP2R5D -0.017 0.004 0 10 -10000 0 10
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.013 0.004 0 15 -10000 0 15
CSNK2A1 -0.017 0.005 0 13 -10000 0 13
RELN/VLDLR/DAB1/LIS1 -0.027 0.015 -10000 0 -10000 0 0
RELN/VLDLR 0.034 0.018 -10000 0 0 38 38
CDC42 -0.005 0.002 0 20 -10000 0 20
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.011 0.003 -10000 0 0 9 9
ARNO/beta Arrestin1-2 0.014 0.013 -10000 0 -0.045 2 2
EGFR -0.016 0.006 0 20 -10000 0 20
EPHA2 -0.018 0.004 0 7 -10000 0 7
USP6 -0.018 0.002 0 2 -10000 0 2
IQSEC1 -0.016 0.006 0 20 -10000 0 20
EGFR/EGFR/EGF/EGF 0.021 0.009 -10000 0 0 25 25
ARRB2 -0.004 0.001 0 6 -10000 0 6
mol:GTP 0.001 0.01 0.04 2 -0.048 2 4
ARRB1 -0.017 0.005 0 15 -10000 0 15
FBXO8 -0.018 0.003 0 5 -10000 0 5
TSHR -0.017 0.004 0 9 -10000 0 9
EGF -0.018 0.003 0 5 -10000 0 5
somatostatin receptor activity 0 0 0 10 0 6 16
ARAP2 0 0 0 13 0 3 16
mol:GDP 0.005 0.051 0.11 9 -0.16 7 16
mol:PI-3-4-5-P3 0 0 0 12 0 4 16
ITGA2B -0.018 0.001 0 1 -10000 0 1
ARF6 -0.017 0.004 0 9 -10000 0 9
Ephrin A1/EPHA2/NCK1/GIT1 0.034 0.018 -10000 0 0 37 37
ADAP1 0 0 0 8 0 2 10
KIF13B -0.017 0.004 0 9 -10000 0 9
HGF/MET 0.024 0.006 -10000 0 0 10 10
PXN -0.018 0.001 0 1 -10000 0 1
ARF6/GTP 0.009 0.053 0.13 12 -0.13 5 17
EGFR/EGFR/EGF/EGF/ARFGEP100 0.026 0.015 -10000 0 0 40 40
ADRB2 -0.018 0.003 0 5 -10000 0 5
receptor agonist activity 0 0 0 13 -10000 0 13
actin filament binding 0 0 0 10 0 6 16
SRC -0.017 0.005 0 14 -10000 0 14
ITGB3 -0.018 0 -10000 0 -10000 0 0
GNAQ -0.018 0.003 0.018 1 -10000 0 1
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 3 18
ARF6/GDP 0.008 0.047 0.12 11 -0.14 4 15
ARF6/GDP/GULP/ACAP1 0.016 0.051 0.12 5 -0.15 7 12
alphaIIb/beta3 Integrin/paxillin/GIT1 0.043 0.007 -10000 0 -10000 0 0
ACAP1 0 0 0 8 -10000 0 8
ACAP2 0 0 0 12 0 3 15
LHCGR/beta Arrestin2 0.013 0.008 -10000 0 -0.052 2 2
EFNA1 -0.018 0.004 0 8 -10000 0 8
HGF -0.018 0.003 0 5 -10000 0 5
CYTH3 0 0 0 13 -10000 0 13
CYTH2 0 0.001 -10000 0 -0.002 8 8
NCK1 -0.015 0.007 0 27 -10000 0 27
fibronectin binding 0 0 0 9 0 3 12
endosomal lumen acidification 0 0 0 15 0 5 20
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.018 0.003 0 4 -10000 0 4
GNAQ/ARNO 0.011 0.006 -10000 0 -0.009 11 11
mol:Phosphatidic acid 0 0 0 12 0 3 15
PIP3-E -0.018 0.003 0 5 -10000 0 5
MET -0.018 0.004 0 7 -10000 0 7
GNA14 -0.018 0 -10000 0 -10000 0 0
GNA15 -0.018 0.003 0 5 -10000 0 5
GIT1 -0.018 0.002 0 2 -10000 0 2
mol:PI-4-5-P2 0 0 0.001 15 0 5 20
GNA11 -0.018 0.003 0 5 -10000 0 5
LHCGR -0.018 0.003 0 4 -10000 0 4
AGTR1 -0.015 0.008 0 35 -10000 0 35
desensitization of G-protein coupled receptor protein signaling pathway 0.013 0.008 -10000 0 -0.052 2 2
IPCEF1/ARNO 0.025 0.012 -10000 0 -0.001 30 30
alphaIIb/beta3 Integrin 0.025 0.002 -10000 0 0 1 1
mTOR 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
GBL -0.018 0.002 0 3 -10000 0 3
MKNK1 -0.018 0.001 0 1 -10000 0 1
mol:PIP3 -0.014 0.024 -10000 0 -0.17 3 3
FRAP1 0.01 0.091 -10000 0 -0.38 6 6
AKT1 0.019 0.072 0.14 38 -0.16 4 42
INSR -0.018 0.002 0 3 -10000 0 3
Insulin Receptor/Insulin 0.022 0.005 -10000 0 0 9 9
mol:GTP 0.009 0.075 0.14 37 -0.14 5 42
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.022 -10000 0 -0.17 2 2
TSC2 -0.017 0.008 0.012 10 -10000 0 10
RHEB/GDP -0.025 0.026 -10000 0 -0.13 5 5
TSC1 -0.016 0.009 0.018 10 -10000 0 10
Insulin Receptor/IRS1 0.004 0.045 -10000 0 -0.19 8 8
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.014 0.029 0.069 3 -0.2 2 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.025 0.07 0.18 6 -0.29 2 8
MAP3K5 -0.003 0.034 0.18 2 -0.17 4 6
PIK3R1 -0.008 0.016 0.018 43 -10000 0 43
apoptosis -0.003 0.034 0.18 2 -0.17 4 6
mol:LY294002 0 0 0.001 1 -0.001 12 13
EIF4B 0.019 0.064 0.17 5 -0.26 2 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.058 0.16 4 -0.25 2 6
eIF4E/eIF4G1/eIF4A1 -0.017 0.043 -10000 0 -0.3 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.011 0.029 -10000 0 -0.18 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.012 0.056 0.1 37 -0.17 2 39
FKBP1A -0.008 0.016 0.019 42 -10000 0 42
RHEB/GTP 0.001 0.066 0.12 34 -0.13 4 38
mol:Amino Acids 0 0 0.001 1 -0.001 12 13
FKBP12/Rapamycin 0.012 0.006 -10000 0 -0.013 3 3
PDPK1 -0.016 0.029 0.16 2 -0.18 2 4
EIF4E -0.018 0.003 0 6 -10000 0 6
ASK1/PP5C 0.013 0.12 -10000 0 -0.47 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.013 0.1 -10000 0 -0.29 12 12
TSC1/TSC2 0.012 0.082 0.15 37 -0.14 5 42
tumor necrosis factor receptor activity 0 0 0.001 12 -0.001 1 13
RPS6 -0.017 0.005 0 16 -10000 0 16
PPP5C -0.018 0.002 0 2 -10000 0 2
EIF4G1 -0.014 0.008 0 44 -10000 0 44
IRS1 -0.006 0.044 -10000 0 -0.2 8 8
INS -0.018 0.003 0 6 -10000 0 6
PTEN -0.017 0.007 0.019 4 -10000 0 4
PDK2 -0.016 0.03 0.16 2 -0.16 3 5
EIF4EBP1 -0.034 0.22 -10000 0 -1.1 7 7
PIK3CA -0.013 0.009 0.018 2 -10000 0 2
PPP2R5D 0.01 0.085 0.21 2 -0.37 5 7
peptide biosynthetic process -0.022 0.005 -10000 0 -10000 0 0
RHEB -0.016 0.009 0.018 8 -10000 0 8
EIF4A1 -0.018 0.002 0 2 -10000 0 2
mol:Rapamycin 0 0.001 0.002 45 -0.002 2 47
EEF2 -0.022 0.005 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.024 0.2 -10000 0 -0.98 7 7
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.03 0.02 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL -0.018 0.004 0 7 -10000 0 7
STAT1 (dimer)/Cbp/p300 -0.016 0.06 0.13 24 -10000 0 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.027 0.015 -10000 0 -0.026 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.022 0.021 0.02 1 -0.08 1 2
CaM/Ca2+ 0.028 0.022 -10000 0 -0.025 7 7
RAP1A -0.018 0.003 0 6 -10000 0 6
STAT1 (dimer)/SHP2 -0.011 0.053 0.12 22 -10000 0 22
AKT1 0.03 0.098 0.15 57 -10000 0 57
MAP2K1 -0.015 0.052 0.11 22 -10000 0 22
MAP3K11 -0.012 0.05 0.12 20 -10000 0 20
IFNGR1 -0.014 0.018 0.031 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.001 0.057 -10000 0 -0.17 14 14
Rap1/GTP -0.037 0.021 -10000 0 -10000 0 0
CRKL/C3G 0.024 0.006 -10000 0 0 9 9
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.036 0.024 -10000 0 -10000 0 0
CEBPB -0.003 0.084 0.17 2 -0.39 4 6
STAT3 -0.018 0.002 0 3 -10000 0 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.024 0.098 -10000 0 -0.67 3 3
STAT1 -0.011 0.052 0.12 22 -10000 0 22
CALM1 -0.017 0.005 0 14 -10000 0 14
IFN-gamma (dimer) -0.015 0.017 0.031 20 -10000 0 20
PIK3CA -0.013 0.008 0 49 -10000 0 49
STAT1 (dimer)/PIAS1 -0.013 0.057 0.13 23 -10000 0 23
CEBPB/PTGES2/Cbp/p300 -0.016 0.057 -10000 0 -0.24 5 5
mol:Ca2+ 0.028 0.019 -10000 0 -10000 0 0
MAPK3 -0.016 0.11 -10000 0 -0.64 4 4
STAT1 (dimer) -0.027 0.026 0.031 2 -0.1 1 3
MAPK1 -0.004 0.061 -10000 0 -0.44 1 1
JAK2 -0.017 0.012 0.031 6 -10000 0 6
PIK3R1 -0.018 0.004 0 8 -10000 0 8
JAK1 -0.014 0.018 0.031 23 -10000 0 23
CAMK2D -0.018 0.003 0 5 -10000 0 5
DAPK1 -0.003 0.059 0.16 1 -0.24 4 5
SMAD7 0.002 0.038 0.1 11 -10000 0 11
CBL/CRKL/C3G -0.013 0.057 0.13 22 -10000 0 22
PI3K 0.021 0.022 -10000 0 -0.03 5 5
IFNG -0.015 0.017 0.031 20 -10000 0 20
apoptosis 0.002 0.065 -10000 0 -0.28 5 5
CAMK2G -0.018 0.002 0 2 -10000 0 2
STAT3 (dimer) -0.018 0.002 0 3 -10000 0 3
CAMK2A -0.018 0.003 0 5 -10000 0 5
CAMK2B -0.018 0.003 0 6 -10000 0 6
FRAP1 0.018 0.088 0.14 53 -10000 0 53
PRKCD 0.023 0.09 0.14 53 -10000 0 53
RAP1B -0.018 0.004 0 7 -10000 0 7
negative regulation of cell growth -0.022 0.021 0.02 1 -0.08 1 2
PTPN2 -0.017 0.005 0 12 -10000 0 12
EP300 -0.018 0.002 0 2 -10000 0 2
IRF1 -0.019 0.047 0.11 4 -10000 0 4
STAT1 (dimer)/PIASy -0.012 0.058 0.12 24 -10000 0 24
SOCS1 -0.004 0.14 -10000 0 -1 3 3
mol:GDP -0.014 0.054 0.12 22 -10000 0 22
CASP1 0.004 0.039 0.1 13 -10000 0 13
PTGES2 -0.018 0.002 0 2 -10000 0 2
IRF9 -0.006 0.028 0.057 4 -0.11 4 8
mol:PI-3-4-5-P3 -0.023 0.019 -10000 0 -10000 0 0
RAP1/GDP -0.029 0.042 0.084 17 -10000 0 17
CBL -0.009 0.051 0.12 21 -10000 0 21
MAP3K1 -0.012 0.05 0.12 20 -10000 0 20
PIAS1 -0.018 0.002 0 3 -10000 0 3
PIAS4 -0.018 0.003 0 4 -10000 0 4
antigen processing and presentation of peptide antigen via MHC class II -0.022 0.021 0.02 1 -0.08 1 2
PTPN11 -0.004 0.058 0.14 24 -10000 0 24
CREBBP -0.018 0.002 0 3 -10000 0 3
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.02 0.006 0 13 -10000 0 13
MAP4K4 -0.019 0.042 -10000 0 -0.14 13 13
BAG4 -0.016 0.006 0 21 -10000 0 21
PKC zeta/ceramide 0.007 0.048 -10000 0 -0.18 10 10
NFKBIA -0.017 0.004 0 9 -10000 0 9
BIRC3 -0.015 0.007 0 30 -10000 0 30
BAX 0.005 0.02 -10000 0 -10000 0 0
RIPK1 -0.017 0.004 0 10 -10000 0 10
AKT1 0.001 0.11 0.68 4 -10000 0 4
BAD -0.003 0.058 0.2 6 -0.18 10 16
SMPD1 0.006 0.049 0.12 17 -0.12 4 21
RB1 -0.007 0.052 0.2 3 -0.18 10 13
FADD/Caspase 8 0.009 0.091 0.17 26 -0.23 10 36
MAP2K4 -0.015 0.041 -10000 0 -0.18 10 10
NSMAF -0.017 0.006 0 17 -10000 0 17
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.044 0.18 1 -0.17 10 11
EGF -0.018 0.003 0 5 -10000 0 5
mol:ceramide -0.003 0.047 -10000 0 -0.19 10 10
MADD -0.018 0.003 0 4 -10000 0 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.02 0.007 0 18 -10000 0 18
ASAH1 -0.017 0.004 0 9 -10000 0 9
negative regulation of cell cycle -0.006 0.051 0.2 3 -0.18 10 13
cell proliferation -0.024 0.042 0.13 2 -0.17 9 11
BID 0.005 0.065 -10000 0 -0.41 2 2
MAP3K1 -0.009 0.043 -10000 0 -0.18 10 10
EIF2A 0.026 0.096 0.18 38 -0.18 7 45
TRADD -0.017 0.004 0 10 -10000 0 10
CRADD -0.018 0.002 0 2 -10000 0 2
MAPK3 -0.017 0.046 0.12 3 -0.16 12 15
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.015 0.044 0.12 3 -0.17 10 13
Cathepsin D/ceramide 0.007 0.048 -10000 0 -0.18 10 10
FADD -0.015 0.04 -10000 0 -0.16 9 9
KSR1 -0.009 0.047 0.2 1 -0.18 10 11
MAPK8 -0.011 0.052 -10000 0 -0.17 15 15
PRKRA -0.005 0.046 0.2 2 -0.18 8 10
PDGFA -0.017 0.005 0 11 -10000 0 11
TRAF2 -0.018 0.002 0 3 -10000 0 3
IGF1 -0.018 0.002 0 2 -10000 0 2
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.003 0.047 -10000 0 -0.18 10 10
CTSD -0.018 0.003 0 5 -10000 0 5
regulation of nitric oxide biosynthetic process 0.023 0.008 -10000 0 0 17 17
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.026 0.045 0.14 2 -0.18 9 11
PRKCD -0.016 0.006 0 24 -10000 0 24
PRKCZ -0.018 0.003 0 5 -10000 0 5
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.02 0.007 0 18 -10000 0 18
RelA/NF kappa B1 0.023 0.008 -10000 0 0 17 17
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.018 0.002 0 2 -10000 0 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.027 -10000 0 -0.11 10 10
TNFR1A/BAG4/TNF-alpha 0.027 0.014 -10000 0 0 36 36
mol:Sphingosine-1-phosphate -0.02 0.006 0 13 -10000 0 13
MAP2K1 -0.019 0.042 0.17 1 -0.17 10 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA -0.017 0.005 0 11 -10000 0 11
CYCS 0.008 0.043 0.11 14 -0.11 5 19
TNFRSF1A -0.017 0.005 0 13 -10000 0 13
NFKB1 -0.018 0.003 0 6 -10000 0 6
TNFR1A/BAG4 0.021 0.01 -10000 0 0 30 30
EIF2AK2 -0.009 0.053 0.25 3 -0.18 8 11
TNF-alpha/TNFR1A/FAN 0.028 0.014 -10000 0 0 31 31
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.074 -10000 0 -0.33 7 7
MAP2K2 -0.017 0.046 0.17 3 -0.17 10 13
SMPD3 0.001 0.06 0.14 5 -0.31 4 9
TNF -0.018 0.004 0 8 -10000 0 8
PKC zeta/PAR4 0.024 0.004 -10000 0 0 5 5
mol:PHOSPHOCHOLINE 0.004 0.034 0.086 3 -0.11 9 12
NF kappa B1/RelA/I kappa B alpha 0.042 0.019 -10000 0 -0.008 6 6
AIFM1 0.009 0.043 0.11 14 -0.11 6 20
BCL2 -0.016 0.006 0 22 -10000 0 22
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.014 0.008 -10000 0 -0.057 2 2
CRKL -0.018 0.004 0 7 -10000 0 7
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
DOCK1 -0.018 0.002 0 2 -10000 0 2
ITGA4 -0.018 0.002 0 3 -10000 0 3
alpha4/beta7 Integrin/MAdCAM1 0.037 0.016 -10000 0 0 26 26
EPO -0.017 0.005 0 15 -10000 0 15
alpha4/beta7 Integrin 0.025 0.004 -10000 0 0 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.002 0 2 -10000 0 2
alpha4/beta1 Integrin 0.024 0.005 -10000 0 0 8 8
EPO/EPOR (dimer) 0.023 0.008 -10000 0 0 17 17
lamellipodium assembly 0.02 0.059 0.12 32 -0.28 1 33
PIK3CA -0.013 0.008 0 49 -10000 0 49
PI3K 0.017 0.012 -10000 0 0 53 53
ARF6 -0.017 0.004 0 9 -10000 0 9
JAK2 -0.009 0.005 -10000 0 -10000 0 0
PXN -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
MADCAM1 -0.018 0.003 0 5 -10000 0 5
cell adhesion 0.036 0.015 -10000 0 0 26 26
CRKL/CBL 0.021 0.009 -10000 0 0 28 28
ITGB1 -0.018 0.003 0 5 -10000 0 5
SRC -0.024 0.027 0.16 3 -10000 0 3
ITGB7 -0.018 0.001 0 1 -10000 0 1
RAC1 -0.017 0.004 0 10 -10000 0 10
alpha4/beta1 Integrin/VCAM1 0.032 0.009 -10000 0 0 11 11
p130Cas/Crk/Dock1 -0.035 0.034 0.16 4 -10000 0 4
VCAM1 -0.018 0.003 0 4 -10000 0 4
RHOA -0.016 0.006 0 23 -10000 0 23
alpha4/beta1 Integrin/Paxillin/GIT1 0.041 0.011 -10000 0 -10000 0 0
BCAR1 -0.027 0.028 0.16 3 -10000 0 3
EPOR -0.018 0.002 0 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
CBL -0.016 0.006 0 24 -10000 0 24
GIT1 -0.018 0.002 0 2 -10000 0 2
Rac1/GTP 0.021 0.06 0.13 32 -0.28 1 33
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.012 0.004 -10000 0 -0.012 1 1
PDGFRB -0.015 0.012 0.02 15 -10000 0 15
SPHK1 0.004 0.011 -10000 0 -10000 0 0
mol:S1P -0.004 0.012 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.097 0.086 2 -0.26 22 24
GNAO1 -0.012 0.014 0.02 23 -10000 0 23
PDGFB-D/PDGFRB/PLCgamma1 -0.033 0.083 0.15 5 -0.22 19 24
PLCG1 -0.041 0.084 0.071 2 -0.23 21 23
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.015 0.012 0.02 15 -10000 0 15
GNAI2 -0.013 0.012 0.019 14 -10000 0 14
GNAI3 -0.015 0.011 0.019 10 -10000 0 10
GNAI1 -0.016 0.011 0.02 9 -10000 0 9
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.015 0.007 0.005 17 -10000 0 17
S1P1/S1P -0.011 0.017 -10000 0 -10000 0 0
negative regulation of cAMP metabolic process -0.04 0.095 0.086 2 -0.25 22 24
MAPK3 -0.043 0.09 0.074 2 -0.24 21 23
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -0.003 5 5
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
RhoA/GDP 0.011 0.004 -10000 0 0 23 23
KDR -0.013 0.012 0.019 19 -10000 0 19
PLCB2 -0.014 0.024 0.15 2 -10000 0 2
RAC1 -0.017 0.004 0 10 -10000 0 10
RhoA/GTP -0.014 0.015 -10000 0 -10000 0 0
receptor internalization -0.011 0.016 -10000 0 -10000 0 0
PTGS2 -0.032 0.092 0.16 4 -0.27 15 19
Rac1/GTP -0.016 0.015 -10000 0 -10000 0 0
RHOA -0.016 0.006 0 23 -10000 0 23
VEGFA 0 0.001 0.003 6 -10000 0 6
negative regulation of T cell proliferation -0.04 0.095 0.086 2 -0.25 22 24
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.016 0.01 0.019 10 -10000 0 10
MAPK1 -0.044 0.092 0.08 1 -0.25 21 22
S1P1/S1P/PDGFB-D/PDGFRB -0.013 0.026 -10000 0 -10000 0 0
ABCC1 -0.015 0.011 0.019 15 -10000 0 15
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.018 0 -10000 0 -10000 0 0
NFATC2 -0.012 0.022 0.043 22 -10000 0 22
NFATC3 -0.012 0.023 0.046 21 -10000 0 21
CD40LG -0.013 0.046 0.14 12 -10000 0 12
ITCH -0.014 0.007 0 32 -10000 0 32
CBLB -0.014 0.007 0 31 -10000 0 31
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.01 0.026 0.083 3 -0.2 2 5
JUNB -0.018 0.002 0 3 -10000 0 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.004 -10000 0 0 14 14
T cell anergy -0.005 0.017 0.21 1 -10000 0 1
TLE4 -0.015 0.018 0.025 24 -10000 0 24
Jun/NFAT1-c-4/p21SNFT 0.03 0.012 -10000 0 0 21 21
AP-1/NFAT1-c-4 0.038 0.018 -10000 0 -0.017 4 4
IKZF1 -0.006 0.013 0.025 22 -10000 0 22
T-helper 2 cell differentiation -0.004 0.056 0.14 1 -0.26 6 7
AP-1/NFAT1 0.033 0.014 -10000 0 -0.028 1 1
CALM1 -0.017 0.005 0 14 -10000 0 14
EGR2 -0.002 0.001 -10000 0 -10000 0 0
EGR3 -0.002 0.001 -10000 0 -10000 0 0
NFAT1/FOXP3 0.027 0.011 -10000 0 -0.025 1 1
EGR1 -0.018 0.003 0 5 -10000 0 5
JUN -0.018 0.003 0 4 -10000 0 4
EGR4 -0.018 0.002 0 2 -10000 0 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
GBP3 -0.015 0.017 0.025 20 -10000 0 20
FOSL1 -0.017 0.005 0 12 -10000 0 12
NFAT1-c-4/MAF/IRF4 0.038 0.017 -10000 0 -0.017 2 2
DGKA -0.015 0.018 0.025 24 -10000 0 24
CREM -0.018 0.003 0 5 -10000 0 5
NFAT1-c-4/PPARG 0.029 0.015 -10000 0 0 32 32
CTLA4 -0.018 0.017 0.019 22 -10000 0 22
NFAT1-c-4 (dimer)/EGR1 0.031 0.013 -10000 0 0 21 21
NFAT1-c-4 (dimer)/EGR4 0.032 0.012 -10000 0 0 20 20
FOS -0.018 0.004 0 8 -10000 0 8
IFNG -0.001 0.026 -10000 0 -0.19 3 3
T cell activation -0.003 0.039 0.13 10 -10000 0 10
MAF -0.017 0.004 0 9 -10000 0 9
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.004 0.002 -10000 0 0 36 36
TNF -0.017 0.022 0.12 2 -10000 0 2
FASLG -0.008 0.048 0.088 3 -0.22 6 9
TBX21 -0.018 0 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.018 0.003 0 4 -10000 0 4
PTPN1 -0.015 0.018 0.025 24 -10000 0 24
NFAT1-c-4/ICER1 0.032 0.012 -10000 0 0 20 20
GATA3 -0.018 0.003 0 5 -10000 0 5
T-helper 1 cell differentiation -0.002 0.029 -10000 0 -0.18 4 4
IL2RA 0.008 0.029 -10000 0 -0.2 3 3
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.015 0.017 0.025 23 -10000 0 23
E2F1 -0.016 0.006 0 22 -10000 0 22
PPARG -0.016 0.006 0 20 -10000 0 20
SLC3A2 -0.015 0.018 0.025 24 -10000 0 24
IRF4 -0.017 0.004 0 10 -10000 0 10
PTGS2 -0.014 0.045 0.14 11 -10000 0 11
CSF2 -0.015 0.043 0.14 10 -10000 0 10
JunB/Fra1/NFAT1-c-4 0.036 0.019 -10000 0 -0.017 5 5
IL4 -0.003 0.057 0.14 1 -0.26 6 7
IL5 -0.015 0.043 0.14 10 -10000 0 10
IL2 -0.003 0.04 0.13 10 -10000 0 10
IL3 -0.003 0.077 -10000 0 -0.4 6 6
RNF128 -0.016 0.005 0 14 -10000 0 14
NFATC1 -0.004 0.002 0 36 -10000 0 36
CDK4 0.002 0.001 -10000 0 -10000 0 0
PTPRK -0.015 0.017 0.024 22 -10000 0 22
IL8 -0.013 0.046 0.14 12 -10000 0 12
POU2F1 -0.018 0.003 0 5 -10000 0 5
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.024 0.071 -10000 0 -0.29 11 11
KLHL20 -0.011 0.049 0.1 9 -0.16 5 14
CYFIP2 -0.018 0.003 0 6 -10000 0 6
Rac1/GDP -0.022 0.066 0.15 9 -0.16 12 21
ENAH -0.036 0.089 -10000 0 -0.29 18 18
AP1M1 -0.018 0.002 0 2 -10000 0 2
RAP1B -0.018 0.004 0 7 -10000 0 7
RAP1A -0.018 0.003 0 6 -10000 0 6
CTNNB1 -0.015 0.007 0 28 -10000 0 28
CDC42/GTP -0.034 0.032 0.082 8 -0.11 3 11
ABI1/Sra1/Nap1 -0.021 0.025 -10000 0 -0.091 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.036 0.017 -10000 0 0 31 31
RAPGEF1 -0.034 0.09 0.16 8 -0.25 19 27
CTNND1 -0.018 0.002 0 3 -10000 0 3
regulation of calcium-dependent cell-cell adhesion -0.021 0.09 -10000 0 -0.29 17 17
CRK -0.035 0.08 -10000 0 -0.28 16 16
E-cadherin/gamma catenin/alpha catenin 0.031 0.01 -10000 0 0 16 16
alphaE/beta7 Integrin 0.025 0.003 -10000 0 0 3 3
IQGAP1 -0.018 0.003 0 4 -10000 0 4
NCKAP1 -0.018 0.003 0 4 -10000 0 4
Rap1/GTP/I-afadin 0.029 0.01 -10000 0 0 18 18
DLG1 -0.025 0.075 -10000 0 -0.28 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.021 -10000 0 -0.077 1 1
MLLT4 -0.018 0.004 0 7 -10000 0 7
ARF6/GTP/NME1/Tiam1 0.03 0.009 -10000 0 0 13 13
PI3K -0.029 0.025 -10000 0 -0.095 1 1
ARF6 -0.017 0.004 0 9 -10000 0 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.023 0.007 -10000 0 0 12 12
TIAM1 -0.018 0.003 0 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.033 0.016 -10000 0 0 32 32
AKT1 -0.013 0.031 0.061 11 -10000 0 11
PIK3R1 -0.018 0.004 0 8 -10000 0 8
CDH1 -0.017 0.004 0 9 -10000 0 9
RhoA/GDP -0.017 0.06 0.16 8 -0.16 8 16
actin cytoskeleton organization -0.008 0.038 0.084 9 -0.12 5 14
CDC42/GDP -0.022 0.066 0.15 9 -0.16 14 23
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.005 0.002 -10000 0 -10000 0 0
ITGB7 -0.018 0.001 0 1 -10000 0 1
RAC1 -0.017 0.004 0 10 -10000 0 10
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.035 0.017 -10000 0 0 32 32
E-cadherin/Ca2+/beta catenin/alpha catenin 0.025 0.012 -10000 0 0 30 30
mol:GDP -0.021 0.073 0.17 6 -0.18 15 21
CDC42/GTP/IQGAP1 0.022 0.005 -10000 0 0 9 9
JUP -0.018 0.002 0 3 -10000 0 3
p120 catenin/RhoA/GDP -0.024 0.06 0.15 7 -0.15 8 15
RAC1/GTP/IQGAP1 0.021 0.006 -10000 0 0 13 13
PIP5K1C/AP1M1 0.024 0.004 -10000 0 0 5 5
RHOA -0.016 0.006 0 23 -10000 0 23
CDC42 -0.018 0.003 0 5 -10000 0 5
CTNNA1 -0.018 0.003 0 5 -10000 0 5
positive regulation of S phase of mitotic cell cycle -0.005 0.022 0.064 4 -0.076 5 9
NME1 -0.018 0 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.037 0.091 -10000 0 -0.29 19 19
regulation of cell-cell adhesion -0.034 0.019 0.038 1 -0.099 3 4
WASF2 -0.01 0.022 0.044 9 -0.068 4 13
Rap1/GTP -0.029 0.043 0.14 7 -0.13 2 9
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.017 -10000 0 -10000 0 0
CCND1 -0.006 0.026 0.073 4 -0.092 5 9
VAV2 -0.025 0.11 0.22 1 -0.31 15 16
RAP1/GDP -0.019 0.055 0.16 8 -0.14 1 9
adherens junction assembly -0.036 0.089 -10000 0 -0.28 19 19
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 -0.018 0.002 0 3 -10000 0 3
PIP5K1C -0.018 0.003 0 4 -10000 0 4
regulation of heterotypic cell-cell adhesion -0.032 0.025 0.16 2 -10000 0 2
E-cadherin/beta catenin -0.007 0.006 -10000 0 -0.048 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.035 0.088 -10000 0 -0.28 18 18
PIK3CA -0.013 0.008 0 49 -10000 0 49
Rac1/GTP -0.028 0.053 -10000 0 -0.18 13 13
E-cadherin/beta catenin/alpha catenin 0.028 0.013 -10000 0 0 30 30
ITGAE -0.018 0.002 0 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.092 -10000 0 -0.29 17 17
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.005 0.055 0.14 3 -0.21 7 10
NCK1/PAK1/Dok-R -0.018 0.03 -10000 0 -0.13 8 8
NCK1/Dok-R -0.01 0.044 0.1 1 -0.15 6 7
PIK3CA -0.012 0.01 0.002 54 -10000 0 54
mol:beta2-estradiol 0 0.004 -10000 0 -0.015 5 5
RELA -0.017 0.005 0 11 -10000 0 11
SHC1 -0.015 0.01 0.019 11 -10000 0 11
Rac/GDP 0.012 0.003 -10000 0 0 10 10
F2 0.004 0.018 -10000 0 -10000 0 0
TNIP2 -0.017 0.005 0 14 -10000 0 14
NF kappa B/RelA 0.012 0.047 -10000 0 -0.1 17 17
FN1 -0.018 0.004 0 8 -10000 0 8
PLD2 -0.012 0.032 0.044 13 -0.1 11 24
PTPN11 -0.018 0.001 0 1 -10000 0 1
GRB14 -0.018 0.003 0 4 -10000 0 4
ELK1 -0.016 0.042 0.15 1 -0.17 4 5
GRB7 -0.018 0.003 0 6 -10000 0 6
PAK1 -0.017 0.005 0 15 -10000 0 15
Tie2/Ang1/alpha5/beta1 Integrin 0.011 0.053 -10000 0 -0.11 19 19
CDKN1A 0.001 0.066 0.12 6 -0.2 10 16
ITGA5 -0.018 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.011 0.047 0.1 1 -0.14 6 7
CRK -0.018 0.002 0 2 -10000 0 2
mol:NO -0.006 0.055 0.18 4 -0.18 7 11
PLG -0.011 0.03 0.044 15 -0.1 10 25
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.01 0.051 -10000 0 -0.18 8 8
GRB2 -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.016 0.009 0.018 9 -10000 0 9
ANGPT2 0.009 0.094 0.15 5 -0.27 11 16
BMX -0.012 0.032 0.045 5 -0.1 11 16
ANGPT1 -0.002 0.004 0.026 2 -10000 0 2
tube development -0.003 0.062 0.13 1 -0.22 7 8
ANGPT4 -0.016 0.007 0.004 17 -10000 0 17
response to hypoxia -0.002 0.005 0.025 2 -0.012 8 10
Tie2/Ang1/GRB14 -0.016 0.043 -10000 0 -0.14 8 8
alpha5/beta1 Integrin 0.024 0.004 -10000 0 0 5 5
FGF2 -0.014 0.011 0.012 22 -10000 0 22
STAT5A (dimer) -0.002 0.073 0.13 3 -0.22 9 12
mol:L-citrulline -0.006 0.055 0.18 4 -0.18 7 11
AGTR1 -0.013 0.01 0.018 6 -10000 0 6
MAPK14 -0.01 0.068 -10000 0 -0.24 10 10
Tie2/SHP2 -0.015 0.094 -10000 0 -0.26 20 20
TEK -0.017 0.088 -10000 0 -0.29 15 15
RPS6KB1 -0.008 0.055 -10000 0 -0.22 7 7
Angiotensin II/AT1 0.01 0.005 -10000 0 0 36 36
Tie2/Ang1/GRB2 -0.017 0.044 -10000 0 -0.14 8 8
MAPK3 -0.018 0.032 -10000 0 -0.15 5 5
MAPK1 -0.017 0.03 -10000 0 -0.15 4 4
Tie2/Ang1/GRB7 -0.014 0.041 -10000 0 -0.18 3 3
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAPK8 -0.012 0.032 0.044 15 -0.1 11 26
PI3K -0.005 0.056 -10000 0 -0.21 8 8
FES 0.001 0.047 -10000 0 -0.2 6 6
Crk/Dok-R -0.012 0.048 0.1 1 -0.16 5 6
Tie2/Ang1/ABIN2 -0.014 0.042 -10000 0 -0.14 8 8
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.003 0.053 0.14 3 -0.2 7 10
STAT5A -0.018 0.002 0 3 -10000 0 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.014 0.082 0.21 17 -0.22 5 22
Tie2/Ang2 0.003 0.069 0.12 6 -0.24 8 14
Tie2/Ang1 -0.004 0.03 0.055 15 -0.092 9 24
FOXO1 -0.004 0.054 0.14 3 -0.19 7 10
ELF1 -0.011 0.018 0.04 10 -10000 0 10
ELF2 -0.007 0.028 0.05 15 -0.09 9 24
mol:Choline -0.012 0.033 0.043 15 -0.1 12 27
cell migration -0.015 0.021 -10000 0 -0.089 7 7
FYN -0.004 0.065 0.14 1 -0.24 7 8
DOK2 -0.017 0.004 0 9 -10000 0 9
negative regulation of cell cycle 0.002 0.063 0.11 6 -0.18 10 16
ETS1 -0.009 0.016 0.033 3 -10000 0 3
PXN 0.01 0.081 0.2 17 -0.21 6 23
ITGB1 -0.018 0.003 0 5 -10000 0 5
NOS3 -0.006 0.053 0.17 3 -0.2 5 8
RAC1 -0.017 0.004 0 10 -10000 0 10
TNF -0.008 0.018 0.033 5 -10000 0 5
MAPKKK cascade -0.012 0.033 0.043 15 -0.1 12 27
RASA1 -0.018 0.004 0 8 -10000 0 8
Tie2/Ang1/Shc -0.015 0.043 -10000 0 -0.15 7 7
NCK1 -0.015 0.007 0 27 -10000 0 27
vasculogenesis -0.006 0.056 0.18 4 -0.17 8 12
mol:Phosphatidic acid -0.012 0.033 0.043 15 -0.1 12 27
mol:Angiotensin II 0 0 -10000 0 -10000 0 0
mol:NADP -0.006 0.055 0.18 4 -0.18 7 11
Rac1/GTP 0.002 0.059 -10000 0 -0.2 8 8
MMP2 -0.01 0.03 0.045 5 -0.1 9 14
Caspase cascade in apoptosis

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
TOP1 -0.011 0.095 0.17 5 -0.3 9 14
ACTA1 -0.009 0.057 0.16 6 -0.14 9 15
NUMA1 -0.02 0.11 0.18 2 -0.33 11 13
SPTAN1 -0.012 0.056 0.16 6 -0.14 9 15
LIMK1 -0.01 0.059 0.17 8 -0.14 9 17
BIRC3 -0.015 0.007 0 30 -10000 0 30
BIRC2 -0.015 0.007 0 30 -10000 0 30
BAX -0.018 0.002 0 2 -10000 0 2
CASP10 -0.025 0.007 0 11 -10000 0 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.006 0.068 0.2 2 -0.27 6 8
DIABLO -0.018 0.002 0 1 -10000 0 1
apoptotic nuclear changes -0.012 0.055 0.16 6 -0.14 9 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.018 0.002 0 2 -10000 0 2
GSN -0.013 0.056 0.16 6 -0.14 9 15
MADD -0.018 0.003 0 4 -10000 0 4
TFAP2A -0.022 0.18 -10000 0 -0.72 9 9
BID -0.008 0.003 0 16 -10000 0 16
MAP3K1 -0.017 0.097 0.12 2 -0.4 9 11
TRADD -0.017 0.004 0 10 -10000 0 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.021 0.014 -10000 0 -0.015 19 19
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.006 0.072 0.2 11 -0.14 9 20
CASP9 -0.018 0.004 0 7 -10000 0 7
DNA repair 0 0.044 0.11 14 -0.12 3 17
neuron apoptosis -0.013 0.11 -10000 0 -0.52 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.023 0.1 0.19 2 -0.38 7 9
APAF1 -0.018 0.002 0 2 -10000 0 2
CASP6 -0.019 0.15 -10000 0 -0.85 5 5
TRAF2 -0.018 0.002 0 3 -10000 0 3
ICAD/CAD -0.016 0.059 0.25 3 -0.15 4 7
CASP7 -0.009 0.091 0.12 1 -0.24 15 16
KRT18 0.004 0.042 -10000 0 -0.41 1 1
apoptosis -0.022 0.088 0.22 2 -0.32 8 10
DFFA -0.012 0.055 0.16 6 -0.14 8 14
DFFB -0.012 0.055 0.16 6 -0.14 7 13
PARP1 0 0.044 0.12 3 -0.11 14 17
actin filament polymerization 0.009 0.077 0.14 5 -0.27 8 13
TNF -0.018 0.004 0 8 -10000 0 8
CYCS -0.003 0.039 0.12 7 -0.22 3 10
SATB1 -0.022 0.14 -10000 0 -0.78 5 5
SLK -0.013 0.054 0.16 5 -0.14 9 14
p15 BID/BAX -0.01 0.032 0.1 10 -0.16 1 11
CASP2 -0.013 0.053 -10000 0 -0.16 13 13
JNK cascade 0.017 0.097 0.4 9 -0.12 2 11
CASP3 -0.007 0.058 0.18 5 -0.14 11 16
LMNB2 -0.011 0.09 0.15 2 -0.31 11 13
RIPK1 -0.017 0.004 0 10 -10000 0 10
CASP4 -0.016 0.007 0 25 -10000 0 25
Mammalian IAPs/DIABLO 0.027 0.013 -10000 0 0 30 30
negative regulation of DNA binding -0.022 0.17 -10000 0 -0.71 9 9
stress fiber formation -0.013 0.054 0.16 5 -0.14 9 14
GZMB -0.021 0.005 0 8 -10000 0 8
CASP1 -0.004 0.002 0 25 -10000 0 25
LMNB1 -0.017 0.11 0.15 2 -0.33 12 14
APP -0.013 0.11 -10000 0 -0.53 6 6
TNFRSF1A -0.017 0.005 0 13 -10000 0 13
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.011 0.002 0 6 -10000 0 6
VIM -0.016 0.092 0.2 3 -0.33 8 11
LMNA -0.006 0.079 0.15 2 -0.32 7 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.008 0.058 -10000 0 -0.17 14 14
LRDD -0.018 0.003 0 5 -10000 0 5
SREBF1 -0.014 0.054 0.16 5 -0.14 8 13
APAF-1/Caspase 9 0.002 0.094 -10000 0 -0.58 4 4
nuclear fragmentation during apoptosis -0.02 0.11 0.18 2 -0.33 11 13
CFL2 -0.009 0.077 0.27 8 -0.15 5 13
GAS2 -0.013 0.054 0.16 5 -0.14 8 13
positive regulation of apoptosis -0.011 0.093 0.16 2 -0.33 9 11
PRF1 -0.018 0.002 0 2 -10000 0 2
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 -0.018 0.004 0 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.066 0.14 6 -0.22 9 15
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.011 0.004 -10000 0 0 18 18
NFKBIA -0.017 0.044 0.19 7 -10000 0 7
BIRC2 -0.015 0.007 0 30 -10000 0 30
IKBKB -0.016 0.006 0 18 -10000 0 18
RIPK2 -0.016 0.006 0 18 -10000 0 18
IKBKG -0.004 0.026 -10000 0 -0.15 3 3
IKK complex/A20 0.011 0.074 0.16 1 -0.25 9 10
NEMO/A20/RIP2 -0.016 0.006 0 18 -10000 0 18
XPO1 -0.018 0.003 0 4 -10000 0 4
NEMO/ATM 0.005 0.067 0.16 1 -0.26 8 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN -0.018 0.001 0 1 -10000 0 1
Exportin 1/RanGTP 0.022 0.004 -10000 0 0 5 5
IKK complex/ELKS 0.001 0.066 -10000 0 -0.22 10 10
BCL10/MALT1/TRAF6 0.029 0.013 -10000 0 0 27 27
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 -0.018 0.003 0 6 -10000 0 6
RELA -0.017 0.005 0 11 -10000 0 11
MALT1 -0.016 0.006 0 21 -10000 0 21
cIAP1/UbcH5C 0.02 0.01 -10000 0 0 32 32
ATM -0.016 0.007 0 25 -10000 0 25
TNF/TNFR1A 0.022 0.008 -10000 0 0 20 20
TRAF6 -0.018 0.003 0 6 -10000 0 6
PRKCA -0.018 0.001 0 1 -10000 0 1
CHUK -0.018 0.002 0 3 -10000 0 3
UBE2D3 -0.018 0.003 0 6 -10000 0 6
TNF -0.018 0.004 0 8 -10000 0 8
NF kappa B1 p50/RelA 0.03 0.012 -10000 0 0 23 23
BCL10 -0.018 0.003 0 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.044 0.19 7 -10000 0 7
beta TrCP1/SCF ubiquitin ligase complex -0.017 0.004 0 8 -10000 0 8
TNFRSF1A -0.017 0.005 0 13 -10000 0 13
IKK complex 0.008 0.074 0.16 1 -0.27 8 9
CYLD -0.017 0.005 0 11 -10000 0 11
IKK complex/PKC alpha 0.013 0.075 0.16 1 -0.24 10 11
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.027 0.009 -10000 0 0 16 16
RGS9BP -0.018 0.003 0 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.018 0.004 0 7 -10000 0 7
mol:Na + 0.02 0.008 -10000 0 0 22 22
mol:ADP -0.018 0.009 0 34 -10000 0 34
GNAT2 -0.018 0.003 0 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.033 0.007 -10000 0 0 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.021 0.006 -10000 0 0 14 14
GRK7 -0.015 0.007 0 28 -10000 0 28
CNGB3 -0.016 0.006 0 18 -10000 0 18
Cone Metarhodopsin II/X-Arrestin 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.056 0.17 16 -10000 0 16
Cone PDE6 0.044 0.017 -10000 0 -10000 0 0
Cone Metarhodopsin II 0.017 0.009 -10000 0 0 34 34
Na + (4 Units) 0.026 0.013 -10000 0 0 33 33
GNAT2/GDP 0.037 0.01 -10000 0 0 11 11
GNB5 -0.018 0.003 0 4 -10000 0 4
mol:GMP (4 units) -0.013 0.039 0.17 7 -10000 0 7
Cone Transducin 0.03 0.01 -10000 0 0 16 16
SLC24A2 -0.017 0.005 0 16 -10000 0 16
GNB3/GNGT2 0.023 0.007 -10000 0 0 12 12
GNB3 -0.017 0.005 0 12 -10000 0 12
GNAT2/GTP 0.012 0.002 -10000 0 0 4 4
CNGA3 -0.018 0.003 0 6 -10000 0 6
ARR3 -0.018 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.02 0.008 -10000 0 0 22 22
mol:Pi 0.033 0.007 -10000 0 0 8 8
Cone CNG Channel 0.033 0.018 -10000 0 -0.008 8 8
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.017 0.005 0 16 -10000 0 16
RGS9 -0.018 0 -10000 0 -10000 0 0
PDE6C -0.018 0.002 0 3 -10000 0 3
GNGT2 -0.018 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.017 0.004 0 10 -10000 0 10
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.017 0.004 0 10 -10000 0 10
LAT2 -0.006 0.033 0.077 10 -0.089 5 15
AP1 0.04 0.055 0.18 4 -0.21 2 6
mol:PIP3 -0.004 0.067 0.18 11 -0.2 2 13
IKBKB 0.007 0.068 0.16 20 -0.14 1 21
AKT1 0.013 0.11 0.26 17 -10000 0 17
IKBKG -0.003 0.049 0.14 7 -0.14 1 8
MS4A2 -0.013 0.017 0.033 1 -10000 0 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.011 0.011 0.019 9 -10000 0 9
MAP3K1 0.045 0.1 0.2 41 -0.15 1 42
mol:Ca2+ -0.002 0.059 0.16 11 -0.16 2 13
LYN -0.011 0.017 0.032 12 -10000 0 12
CBLB -0.005 0.029 0.079 8 -0.087 4 12
SHC1 -0.017 0.005 0.002 8 -10000 0 8
RasGAP/p62DOK 0.03 0.009 -10000 0 0 14 14
positive regulation of cell migration -0.011 0.002 0 4 -10000 0 4
INPP5D -0.018 0.004 0 8 -10000 0 8
PLD2 -0.018 0.072 0.21 13 -10000 0 13
PTPN13 0.01 0.044 -10000 0 -10000 0 0
PTPN11 -0.01 0.022 0.041 14 -10000 0 14
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.025 0.091 0.24 16 -10000 0 16
SYK -0.009 0.019 0.033 15 -10000 0 15
GRB2 -0.015 0.011 0.018 18 -10000 0 18
LAT/PLCgamma1/GRB2/SLP76/GADs -0.013 0.042 0.088 7 -0.15 3 10
LAT -0.005 0.032 0.081 8 -0.087 4 12
PAK2 0.052 0.11 0.21 45 -0.16 1 46
NFATC2 -0.009 0.022 -10000 0 -0.28 1 1
HRAS 0.012 0.055 0.17 11 -0.16 1 12
GAB2 -0.017 0.005 0 15 -10000 0 15
PLA2G1B -0.081 0.26 -10000 0 -0.82 18 18
Fc epsilon R1 0.031 0.015 -10000 0 -0.035 5 5
Antigen/IgE/Fc epsilon R1 0.036 0.021 -10000 0 -0.023 9 9
mol:GDP 0.014 0.042 0.16 5 -0.17 1 6
JUN -0.018 0.003 0 4 -10000 0 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.007 0.017 0.018 49 -10000 0 49
FOS -0.018 0.004 0 8 -10000 0 8
Antigen/IgE/Fc epsilon R1/LYN/SYK 0 0.031 0.071 15 -0.085 5 20
CHUK -0.003 0.048 0.14 9 -10000 0 9
KLRG1 -0.008 0.029 0.063 14 -0.089 5 19
VAV1 -0.003 0.033 0.085 8 -0.088 3 11
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.004 0.026 0.082 6 -0.087 1 7
negative regulation of mast cell degranulation 0 0.049 0.18 7 -10000 0 7
BTK 0.015 0.035 0.16 2 -0.17 1 3
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.013 0.029 0.078 2 -0.097 14 16
GAB2/PI3K/SHP2 -0.034 0.028 0.012 2 -10000 0 2
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.011 0.021 0.082 1 -0.088 9 10
RAF1 -0.083 0.28 -10000 0 -0.89 18 18
Fc epsilon R1/FcgammaRIIB/SHIP 0.044 0.019 -10000 0 -0.013 5 5
FCER1G -0.013 0.016 0.037 1 -10000 0 1
FCER1A -0.01 0.018 0.032 9 -10000 0 9
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.024 -10000 0 -0.024 8 8
MAPK3 -0.084 0.26 -10000 0 -0.83 18 18
MAPK1 -0.082 0.26 -10000 0 -0.82 18 18
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAPK8 0.016 0.1 -10000 0 -0.43 7 7
DUSP1 -0.018 0.004 0 8 -10000 0 8
NF-kappa-B/RelA -0.008 0.032 0.077 10 -10000 0 10
actin cytoskeleton reorganization 0.016 0.044 -10000 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.038 0.14 3 -0.16 1 4
FER -0.006 0.031 0.088 6 -0.087 4 10
RELA -0.017 0.005 0 11 -10000 0 11
ITK -0.004 0.036 -10000 0 -0.2 5 5
SOS1 -0.018 0.002 0 3 -10000 0 3
PLCG1 0.017 0.062 0.18 13 -0.17 1 14
cytokine secretion -0.009 0.02 0.043 8 -0.06 1 9
SPHK1 -0.006 0.033 0.075 11 -0.087 5 16
PTK2 0.016 0.045 -10000 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.012 0.045 0.11 3 -0.18 4 7
EDG1 -0.011 0.002 0 4 -10000 0 4
mol:DAG -0.005 0.07 0.2 9 -0.22 2 11
MAP2K2 -0.084 0.26 -10000 0 -0.83 18 18
MAP2K1 -0.086 0.26 -10000 0 -0.83 18 18
MAP2K7 -0.018 0.002 0 3 -10000 0 3
KLRG1/SHP2 0.003 0.056 0.17 10 -10000 0 10
MAP2K4 -0.001 0.15 -10000 0 -0.77 6 6
Fc epsilon R1/FcgammaRIIB 0.04 0.015 -10000 0 -0.038 1 1
mol:Choline -0.018 0.071 0.21 13 -10000 0 13
SHC/Grb2/SOS1 0.035 0.043 0.17 4 -0.13 1 5
FYN -0.018 0.003 0 6 -10000 0 6
DOK1 -0.018 0.002 0 2 -10000 0 2
PXN 0.009 0.043 -10000 0 -10000 0 0
HCLS1 -0.004 0.028 0.092 5 -0.087 3 8
PRKCB 0 0.059 0.16 10 -0.17 1 11
FCGR2B -0.017 0.004 0 9 -10000 0 9
IGHE -0.009 0.019 0.033 14 -10000 0 14
KLRG1/SHIP 0 0.05 0.18 7 -10000 0 7
LCP2 -0.014 0.011 0.018 16 -10000 0 16
PLA2G4A -0.006 0.033 0.075 11 -0.087 4 15
RASA1 -0.018 0.004 0 8 -10000 0 8
mol:Phosphatidic acid -0.018 0.071 0.21 13 -10000 0 13
IKK complex 0.001 0.059 0.18 8 -10000 0 8
WIPF1 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.004 0.1 0.15 2 -0.22 25 27
CaM/Ca2+ 0.012 0.004 -10000 0 0 14 14
AKT1 -0.017 0.005 0 13 -10000 0 13
AKT2 -0.018 0.002 0 3 -10000 0 3
STXBP4 -0.018 0.001 0 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.008 0.11 0.16 3 -0.24 24 27
YWHAZ -0.016 0.006 0 21 -10000 0 21
CALM1 -0.017 0.005 0 14 -10000 0 14
YWHAQ -0.018 0.002 0 2 -10000 0 2
TBC1D4 -0.02 0.007 0 18 -10000 0 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.018 0.002 0 2 -10000 0 2
YWHAB -0.017 0.005 0 12 -10000 0 12
SNARE/Synip 0.023 0.003 -10000 0 0 3 3
YWHAG -0.018 0.003 0 5 -10000 0 5
ASIP -0.016 0.006 0 21 -10000 0 21
PRKCI -0.013 0.008 0 47 -10000 0 47
AS160/CaM/Ca2+ 0.012 0.004 -10000 0 0 14 14
RHOQ -0.018 0.003 0 4 -10000 0 4
GYS1 -0.009 0.019 0.23 1 -10000 0 1
PRKCZ -0.018 0.003 0 5 -10000 0 5
TRIP10 -0.018 0.002 0 3 -10000 0 3
TC10/GTP/CIP4/Exocyst 0.022 0.005 -10000 0 0 7 7
AS160/14-3-3 0.001 0.035 0.078 20 -0.14 3 23
VAMP2 -0.018 0.002 0 2 -10000 0 2
SLC2A4 -0.011 0.12 0.17 2 -0.27 24 26
STX4 0 0 -10000 0 -10000 0 0
GSK3B -0.005 0.002 -10000 0 -10000 0 0
SFN -0.018 0.003 0 4 -10000 0 4
LNPEP -0.018 0.004 0 7 -10000 0 7
YWHAE -0.018 0.002 0 2 -10000 0 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.073 -10000 0 -0.31 9 9
Crk/p130 Cas/Paxillin -0.021 0.026 -10000 0 -0.14 2 2
JUN -0.016 0.013 -10000 0 -0.094 2 2
HRAS -0.018 0.003 0 5 -10000 0 5
RET51/GFRalpha1/GDNF/GRB10 0.037 0.016 -10000 0 0 27 27
RAP1A -0.018 0.003 0 6 -10000 0 6
FRS2 -0.018 0.003 0 6 -10000 0 6
RAP1A/GDP 0.012 0.002 -10000 0 0 6 6
RET51/GFRalpha1/GDNF/DOK1 0.038 0.015 -10000 0 0 23 23
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 -0.018 0.001 0 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.002 0 2 -10000 0 2
RET9/GFRalpha1/GDNF/Enigma 0.028 0.011 -10000 0 0 23 23
RHOA -0.016 0.006 0 23 -10000 0 23
RAP1A/GTP 0.033 0.017 -10000 0 -0.008 10 10
GRB7 -0.018 0.003 0 6 -10000 0 6
RET51/GFRalpha1/GDNF 0.037 0.016 -10000 0 0 25 25
MAPKKK cascade -0.029 0.019 -10000 0 -10000 0 0
BCAR1 -0.018 0.004 0 7 -10000 0 7
RET9/GFRalpha1/GDNF/IRS1 0.027 0.012 -10000 0 0 27 27
lamellipodium assembly -0.006 0.029 0.068 2 -0.14 2 4
RET51/GFRalpha1/GDNF/SHC 0.036 0.016 -10000 0 0 28 28
PIK3CA -0.013 0.008 0 49 -10000 0 49
RET9/GFRalpha1/GDNF/SHC 0.028 0.012 -10000 0 0 26 26
RET9/GFRalpha1/GDNF/Shank3 0.028 0.012 -10000 0 0 25 25
MAPK3 -0.012 0.065 0.16 20 -10000 0 20
DOK1 -0.018 0.002 0 2 -10000 0 2
DOK6 -0.016 0.006 0 21 -10000 0 21
PXN -0.018 0.001 0 1 -10000 0 1
neurite development -0.012 0.057 0.14 18 -10000 0 18
DOK5 -0.017 0.004 0 10 -10000 0 10
GFRA1 -0.018 0.002 0 2 -10000 0 2
MAPK8 -0.012 0.013 -10000 0 -0.092 3 3
HRAS/GTP 0.029 0.02 -10000 0 -0.061 1 1
tube development -0.023 0.019 0.19 1 -10000 0 1
MAPK1 -0.009 0.068 0.16 22 -10000 0 22
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.006 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
SRC -0.017 0.005 0 14 -10000 0 14
PDLIM7 -0.018 0.004 0 7 -10000 0 7
RET51/GFRalpha1/GDNF/Dok6 0.035 0.024 -10000 0 -0.008 18 18
SHC1 -0.018 0.004 0 7 -10000 0 7
RET51/GFRalpha1/GDNF/Dok4 0.036 0.016 -10000 0 0 28 28
RET51/GFRalpha1/GDNF/Dok5 0.036 0.016 -10000 0 -10000 0 0
PRKCA -0.018 0.001 0 1 -10000 0 1
HRAS/GDP 0.012 0.002 -10000 0 0 5 5
CREB1 0.003 0.015 -10000 0 -0.13 2 2
PIK3R1 -0.018 0.004 0 8 -10000 0 8
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.006 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 0.037 0.016 -10000 0 0 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.018 0.002 0 3 -10000 0 3
DOK4 -0.017 0.004 0 9 -10000 0 9
JNK cascade -0.002 0.036 0.07 32 -10000 0 32
RET9/GFRalpha1/GDNF/FRS2 0.028 0.012 -10000 0 0 25 25
SHANK3 -0.018 0.004 0 7 -10000 0 7
RASA1 -0.018 0.004 0 8 -10000 0 8
NCK1 -0.015 0.007 0 27 -10000 0 27
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.007 -10000 0 -0.091 1 1
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.008 0.012 -10000 0 -0.091 3 3
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.008 0.01 -10000 0 -0.091 2 2
PI3K 0.002 0.041 -10000 0 -0.22 1 1
SOS1 -0.018 0.002 0 3 -10000 0 3
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.034 0.015 -10000 0 0 26 26
GRB10 -0.018 0.004 0 8 -10000 0 8
activation of MAPKK activity -0.006 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 0.037 0.016 -10000 0 -10000 0 0
GAB1 -0.018 0.004 0 7 -10000 0 7
IRS1 -0.018 0.004 0 8 -10000 0 8
IRS2 -0.018 0.003 0 5 -10000 0 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.01 -10000 0 -0.091 2 2
RET51/GFRalpha1/GDNF/PKC alpha 0.038 0.015 -10000 0 0 22 22
GRB2 -0.018 0.001 0 1 -10000 0 1
PRKACA -0.018 0.003 0 4 -10000 0 4
GDNF -0.016 0.006 0 18 -10000 0 18
RAC1 -0.017 0.004 0 10 -10000 0 10
RET51/GFRalpha1/GDNF/IRS1 0.036 0.017 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.038 0.084 2 -0.16 2 4
RET9/GFRalpha1/GDNF 0.02 0.007 -10000 0 0 19 19
GFRalpha1/GDNF 0.022 0.008 -10000 0 0 19 19
FAS signaling pathway (CD95)

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
SPTAN1 -0.009 0.004 -10000 0 -10000 0 0
RFC1 -0.007 0.018 0.22 1 -10000 0 1
PRKDC 0.007 0.056 0.22 11 -10000 0 11
RIPK1 -0.017 0.004 0 10 -10000 0 10
CASP7 0.008 0.055 -10000 0 -0.47 2 2
FASLG/FAS/FADD/FAF1 0.002 0.017 -10000 0 -0.09 5 5
MAP2K4 0.021 0.054 0.15 7 -0.15 2 9
mol:ceramide -0.009 0.016 -10000 0 -0.092 5 5
GSN -0.009 0.004 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 0.01 0.042 0.13 1 -0.11 5 6
FAS -0.018 0.002 0 3 -10000 0 3
BID -0.023 0.007 0 15 -10000 0 15
MAP3K1 0.03 0.068 0.15 19 -0.26 2 21
MAP3K7 -0.018 0.003 0 6 -10000 0 6
RB1 -0.004 0.03 0.22 3 -10000 0 3
CFLAR -0.018 0.003 0 4 -10000 0 4
HGF/MET 0.031 0.01 -10000 0 0 15 15
ARHGDIB 0 0.042 0.22 6 -10000 0 6
FADD -0.012 0.009 0 54 -10000 0 54
actin filament polymerization 0.017 0.036 0.18 8 -10000 0 8
NFKB1 0.012 0.074 -10000 0 -0.52 3 3
MAPK8 0.016 0.052 0.16 5 -0.15 2 7
DFFA -0.009 0.004 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.017 0.036 -10000 0 -0.18 8 8
FAS/FADD/MET 0.023 0.016 -10000 0 0 57 57
CFLAR/RIP1 0.023 0.007 -10000 0 0 12 12
FAIM3 -0.018 0.003 0 5 -10000 0 5
FAF1 -0.018 0.001 0 1 -10000 0 1
PARP1 -0.009 0.004 -10000 0 -10000 0 0
DFFB -0.009 0.004 -10000 0 -10000 0 0
CHUK 0.004 0.06 -10000 0 -0.5 2 2
FASLG -0.018 0.003 0 5 -10000 0 5
FAS/FADD 0.017 0.012 -10000 0 0 55 55
HGF -0.018 0.003 0 5 -10000 0 5
LMNA -0.019 0.041 0.19 2 -0.17 8 10
CASP6 -0.009 0.004 -10000 0 -10000 0 0
CASP10 -0.018 0.003 0 4 -10000 0 4
CASP3 -0.003 0.001 -10000 0 -10000 0 0
PTPN13 -0.018 0.003 0 6 -10000 0 6
CASP8 -0.02 0.005 0 11 -10000 0 11
IL6 0.006 0.1 -10000 0 -0.46 7 7
MET -0.018 0.004 0 7 -10000 0 7
ICAD/CAD -0.022 0.034 -10000 0 -0.17 8 8
FASLG/FAS/FADD/FAF1/Caspase 10 -0.01 0.016 -10000 0 -0.093 5 5
activation of caspase activity by cytochrome c -0.023 0.007 0 15 -10000 0 15
PAK2 0.035 0.089 0.22 32 -10000 0 32
BCL2 -0.016 0.006 0 22 -10000 0 22
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.062 0.18 15 -0.16 1 16
UGCG 0.01 0.01 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.05 0.14 3 -0.16 5 8
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.012 -10000 0 -10000 0 0
mol:DAG -0.001 0.022 0.16 3 -10000 0 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.058 0.12 8 -0.18 7 15
FRAP1 0.001 0.059 0.15 3 -0.2 6 9
FOXO3 0.003 0.064 0.12 7 -0.22 7 14
AKT1 0.006 0.059 0.13 7 -0.23 5 12
GAB2 -0.017 0.005 0 15 -10000 0 15
SMPD1 -0.006 0.1 -10000 0 -0.65 4 4
SGMS1 0.002 0.01 -10000 0 -0.046 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 -0.012 0.008 0 53 -10000 0 53
CALM1 -0.017 0.005 0 14 -10000 0 14
cell proliferation 0.02 0.039 0.12 7 -10000 0 7
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.012 -10000 0 0 53 53
RPS6KB1 0.011 0.008 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.022 0.16 3 -10000 0 3
natural killer cell activation 0 0 -10000 0 -10000 0 0
JAK3 -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
JAK1 -0.018 0.002 0 3 -10000 0 3
NFKB1 -0.018 0.003 0 6 -10000 0 6
MYC 0.028 0.077 0.18 22 -0.19 4 26
MYB 0.006 0.02 0.19 2 -10000 0 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.006 0.045 -10000 0 -0.21 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.004 0.048 -10000 0 -0.2 5 5
Rac1/GDP -0.015 0.011 0 57 -10000 0 57
T cell proliferation 0.002 0.052 0.12 8 -0.2 4 12
SHC1 -0.018 0.004 0 7 -10000 0 7
RAC1 -0.017 0.004 0 10 -10000 0 10
positive regulation of cyclin-dependent protein kinase activity 0 0 -10000 0 -10000 0 0
PRKCZ 0 0.051 0.12 6 -0.21 4 10
NF kappa B1 p50/RelA 0.012 0.06 0.16 2 -0.19 7 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.008 0.021 -10000 0 -0.097 8 8
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA -0.017 0.005 0 11 -10000 0 11
IL2RA -0.018 0.003 0 4 -10000 0 4
IL2RB -0.018 0.002 0 2 -10000 0 2
TERT -0.016 0.006 0 24 -10000 0 24
E2F1 0.01 0.005 -10000 0 -10000 0 0
SOS1 -0.018 0.002 0 3 -10000 0 3
RPS6 -0.017 0.005 0 16 -10000 0 16
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 -0.018 0.001 0 1 -10000 0 1
IL2RG -0.018 0 -10000 0 -10000 0 0
actin cytoskeleton organization 0.002 0.052 0.12 8 -0.2 4 12
GRB2 -0.018 0.001 0 1 -10000 0 1
IL2 -0.018 0.004 0 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
Rac1/GTP 0.02 0.014 -10000 0 0 57 57
LCK -0.018 0.003 0 4 -10000 0 4
BCL2 0.001 0.057 0.15 5 -0.2 5 10
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.003 -10000 0 0 8 8
alphaV beta3 Integrin 0.032 0.009 -10000 0 0 12 12
PTK2 -0.008 0.057 0.18 6 -0.16 4 10
IGF1R -0.018 0.003 0 4 -10000 0 4
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 -0.018 0.003 0 4 -10000 0 4
SRC -0.017 0.005 0 14 -10000 0 14
CDKN1B 0.005 0.005 -10000 0 -0.015 7 7
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.005 0.004 -10000 0 -0.015 6 6
ROCK1 -0.018 0.004 0 7 -10000 0 7
AKT1 -0.014 0.023 -10000 0 -0.22 2 2
PTK2B -0.022 0.027 0.16 3 -10000 0 3
alphaV/beta3 Integrin/JAM-A -0.032 0.011 -10000 0 -10000 0 0
CBL -0.016 0.006 0 24 -10000 0 24
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.007 -10000 0 0 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.04 0.012 -10000 0 0 14 14
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.037 -10000 0 -0.14 12 12
alphaV/beta3 Integrin/Syndecan-1 0.033 0.006 -10000 0 0 6 6
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.04 0.013 0 13 -10000 0 13
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA -0.013 0.008 0 49 -10000 0 49
alphaV/beta3 Integrin/Osteopontin 0.032 0.009 -10000 0 0 12 12
RPS6KB1 -0.038 0.038 0.14 6 -10000 0 6
TLN1 -0.016 0.006 0 18 -10000 0 18
MAPK3 -0.021 0.044 -10000 0 -0.24 6 6
GPR124 -0.016 0.006 0 19 -10000 0 19
MAPK1 -0.023 0.051 -10000 0 -0.25 7 7
PXN -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
alphaV/beta3 Integrin/Tumstatin 0.032 0.009 -10000 0 0 11 11
cell adhesion -0.023 0.01 0 25 -10000 0 25
ANGPTL3 -0.018 0.002 0 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.008 -10000 0 0 21 21
IGF-1R heterotetramer -0.018 0.003 0 4 -10000 0 4
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
TGFBR2 -0.016 0.006 0 24 -10000 0 24
ITGB3 -0.018 0 -10000 0 -10000 0 0
IGF1 -0.018 0.002 0 2 -10000 0 2
RAC1 -0.017 0.004 0 10 -10000 0 10
regulation of cell-matrix adhesion 0.03 0.012 -10000 0 0 22 22
apoptosis -0.018 0.003 0 5 -10000 0 5
CD47 -0.016 0.006 0 20 -10000 0 20
alphaV/beta3 Integrin/CD47 0.03 0.012 -10000 0 0 24 24
VCL -0.018 0.002 0 2 -10000 0 2
alphaV/beta3 Integrin/Del1 0.032 0.009 -10000 0 0 13 13
CSF1 -0.018 0.003 0 4 -10000 0 4
PIK3C2A 0.005 0.004 -10000 0 -0.015 6 6
PI4 Kinase/Pyk2 -0.033 0.011 0 11 -10000 0 11
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.03 0.009 -10000 0 0 13 13
FAK1/Vinculin -0.004 0.063 0.16 11 -0.14 3 14
alphaV beta3/Integrin/ppsTEM5 0.03 0.012 -10000 0 0 22 22
RHOA -0.016 0.006 0 23 -10000 0 23
VTN -0.018 0.002 0 2 -10000 0 2
BCAR1 -0.018 0.004 0 7 -10000 0 7
FGF2 -0.018 0.004 0 7 -10000 0 7
F11R -0.02 0.006 0 13 -10000 0 13
alphaV/beta3 Integrin/Lactadherin 0.033 0.008 -10000 0 0 9 9
alphaV/beta3 Integrin/TGFBR2 0.029 0.013 -10000 0 0 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.035 0.017 -10000 0 0 32 32
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.029 0.011 -10000 0 0 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.018 0.004 0 8 -10000 0 8
alphaV/beta3 Integrin/Pyk2 -0.025 0.009 0 20 -10000 0 20
SDC1 -0.018 0.002 0 2 -10000 0 2
VAV3 -0.027 0.024 0.16 2 -10000 0 2
PTPN11 -0.018 0.001 0 1 -10000 0 1
IRS1 -0.018 0.004 0 8 -10000 0 8
FAK1/Paxillin -0.004 0.062 0.16 11 -0.14 3 14
cell migration -0.009 0.059 0.15 11 -0.14 3 14
ITGAV -0.018 0.003 0 5 -10000 0 5
PI3K -0.029 0.021 0 56 -10000 0 56
SPP1 -0.018 0.004 0 7 -10000 0 7
KDR -0.018 0.004 0 8 -10000 0 8
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.018 0.003 0 5 -10000 0 5
COL4A3 -0.018 0.004 0 8 -10000 0 8
angiogenesis -0.014 0.057 0.17 5 -0.27 5 10
Rac1/GTP -0.029 0.024 0.15 2 -10000 0 2
EDIL3 -0.018 0.004 0 8 -10000 0 8
cell proliferation 0.029 0.013 -10000 0 0 27 27
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.009 0.004 0 28 -10000 0 28
GNB1/GNG2 0.031 0.008 -10000 0 0 11 11
regulation of S phase of mitotic cell cycle -0.004 0.003 -10000 0 -10000 0 0
GNAO1 -0.017 0.004 0 10 -10000 0 10
HRAS -0.018 0.003 0 5 -10000 0 5
SHBG/T-DHT 0.011 0.002 -10000 0 0 3 3
PELP1 -0.018 0.002 0 2 -10000 0 2
AKT1 -0.01 0.003 0 13 -10000 0 13
MAP2K1 -0.023 0.041 0.14 9 -10000 0 9
T-DHT/AR 0.013 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 -0.016 0.006 0 23 -10000 0 23
GNAI3 -0.018 0.003 0 4 -10000 0 4
GNAI1 -0.018 0.003 0 4 -10000 0 4
mol:GDP -0.011 0.008 -10000 0 -10000 0 0
cell proliferation -0.03 0.057 0.14 9 -0.19 5 14
PIK3CA -0.013 0.008 0 49 -10000 0 49
FOS -0.018 0.056 0.15 5 -0.21 6 11
mol:Ca2+ -0.001 0.001 -10000 0 -10000 0 0
MAPK3 -0.03 0.049 0.14 9 -0.18 3 12
MAPK1 -0.008 0.028 0.14 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.006 0.004 -10000 0 -10000 0 0
GNG2 -0.018 0.004 0 7 -10000 0 7
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.029 0.01 -10000 0 0 18 18
actin cytoskeleton reorganization -0.017 0.013 0 58 -10000 0 58
SRC -0.017 0.005 0 14 -10000 0 14
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.011 -10000 0 0 53 53
apoptosis 0.02 0.058 0.25 6 -0.19 1 7
T-DHT/AR/PELP1 0.023 0.003 -10000 0 0 2 2
HRAS/GDP -0.014 0.011 -10000 0 -10000 0 0
CREB1 -0.021 0.061 0.19 1 -0.26 6 7
RAC1-CDC42/GTP 0.022 0.016 -10000 0 0 58 58
AR -0.018 0 -10000 0 -10000 0 0
GNB1 -0.018 0.003 0 5 -10000 0 5
RAF1 -0.018 0.042 0.15 9 -10000 0 9
RAC1-CDC42/GDP 0.007 0.053 0.094 43 -10000 0 43
T-DHT/AR/PELP1/Src 0.03 0.01 -10000 0 0 16 16
MAP2K2 -0.023 0.039 0.14 8 -10000 0 8
T-DHT/AR/PELP1/Src/PI3K -0.004 0.003 -10000 0 -10000 0 0
GNAZ -0.018 0.003 0 6 -10000 0 6
SHBG -0.018 0.002 0 3 -10000 0 3
Gi family/GNB1/GNG2/GDP -0.029 0.11 -10000 0 -0.27 22 22
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 -0.017 0.004 0 10 -10000 0 10
GNRH1 -0.01 0.003 0 11 -10000 0 11
Gi family/GTP -0.007 0.003 -10000 0 -10000 0 0
CDC42 -0.018 0.003 0 5 -10000 0 5
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.036 0.013 -10000 0 0 19 19
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.13 -10000 0 -0.32 23 23
AKT1 -0.013 0.11 -10000 0 -0.72 4 4
PIK3CA -0.013 0.008 0 49 -10000 0 49
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.12 -10000 0 -0.74 4 4
mol:Ca2+ -0.012 0.015 -10000 0 -10000 0 0
IGF1R -0.018 0.003 0 4 -10000 0 4
E2/ER alpha (dimer)/Striatin 0.022 0.005 -10000 0 0 8 8
SHC1 -0.018 0.004 0 7 -10000 0 7
apoptosis 0.013 0.11 0.68 4 -10000 0 4
RhoA/GTP -0.031 0.014 0 23 -10000 0 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.004 0.11 0.15 7 -0.25 20 27
regulation of stress fiber formation 0.029 0.037 -10000 0 -0.12 8 8
E2/ERA-ERB (dimer) 0.021 0.006 -10000 0 0 14 14
KRAS -0.017 0.005 0 11 -10000 0 11
G13/GTP 0.021 0.004 -10000 0 0 5 5
pseudopodium formation -0.029 0.037 0.12 8 -10000 0 8
E2/ER alpha (dimer)/PELP1 0.022 0.005 -10000 0 0 7 7
GRB2 -0.018 0.001 0 1 -10000 0 1
GNG2 -0.018 0.004 0 7 -10000 0 7
GNAO1 -0.017 0.004 0 10 -10000 0 10
HRAS -0.018 0.003 0 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.024 0.11 0.21 3 -0.32 15 18
E2/ER beta (dimer) 0.012 0.003 -10000 0 0 9 9
mol:GDP -0.02 0.023 -10000 0 -0.13 6 6
mol:NADP -0.024 0.11 0.21 3 -0.32 15 18
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:IP3 -0.013 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.018 0.003 0 4 -10000 0 4
PLCB1 -0.007 0.016 0.068 7 -10000 0 7
PLCB2 -0.008 0.015 0.068 6 -10000 0 6
IGF1 -0.018 0.002 0 2 -10000 0 2
mol:L-citrulline -0.024 0.11 0.21 3 -0.32 15 18
RHOA -0.016 0.006 0 23 -10000 0 23
Gai/GDP -0.072 0.22 -10000 0 -0.59 25 25
JNK cascade 0.012 0.003 -10000 0 0 9 9
BCAR1 -0.018 0.004 0 7 -10000 0 7
ESR2 -0.017 0.004 0 9 -10000 0 9
GNAQ -0.018 0 -10000 0 -10000 0 0
ESR1 -0.018 0.003 0 5 -10000 0 5
Gq family/GDP/Gbeta gamma -0.013 0.11 0.14 1 -0.44 8 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.027 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.004 0.11 0.15 7 -0.25 20 27
GNAZ -0.018 0.003 0 6 -10000 0 6
E2/ER alpha (dimer) 0.012 0.002 -10000 0 0 5 5
STRN -0.018 0.002 0 3 -10000 0 3
GNAL -0.017 0.005 0 13 -10000 0 13
PELP1 -0.018 0.002 0 2 -10000 0 2
MAPK11 -0.016 0.005 0 15 -10000 0 15
GNAI2 -0.016 0.006 0 23 -10000 0 23
GNAI3 -0.018 0.003 0 4 -10000 0 4
GNAI1 -0.018 0.003 0 4 -10000 0 4
HBEGF -0.028 0.13 0.21 9 -0.31 20 29
cAMP biosynthetic process -0.017 0.007 0 21 -10000 0 21
SRC -0.033 0.13 0.17 7 -0.31 21 28
PI3K 0.017 0.012 -10000 0 0 53 53
GNB1 -0.018 0.003 0 5 -10000 0 5
G13/GDP/Gbeta gamma 0.022 0.031 0.11 2 -0.12 5 7
SOS1 -0.018 0.002 0 3 -10000 0 3
IGF-1R heterotetramer/IGF1 -0.042 0.075 -10000 0 -0.22 20 20
Gs family/GTP 0.022 0.008 -10000 0 0 21 21
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.028 0.011 -10000 0 0 22 22
vasodilation -0.023 0.11 0.21 3 -0.3 15 18
mol:DAG -0.013 0.016 -10000 0 -10000 0 0
Gs family/GDP/Gbeta gamma -0.031 0.022 -10000 0 -0.13 5 5
MSN -0.03 0.038 0.12 8 -10000 0 8
Gq family/GTP 0.007 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.11 -10000 0 -0.71 4 4
NRAS -0.017 0.004 0 9 -10000 0 9
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.023 0.11 0.3 15 -0.21 3 18
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
RhoA/GDP -0.023 0.022 -10000 0 -0.14 4 4
NOS3 -0.025 0.12 0.21 3 -0.33 15 18
GNA11 -0.018 0.003 0 5 -10000 0 5
MAPKKK cascade -0.01 0.098 -10000 0 -0.4 7 7
E2/ER alpha (dimer)/PELP1/Src -0.008 0.11 0.17 8 -0.26 20 28
ruffle organization -0.029 0.037 0.12 8 -10000 0 8
ROCK2 -0.026 0.041 0.14 8 -10000 0 8
GNA14 -0.018 0 -10000 0 -10000 0 0
GNA15 -0.018 0.003 0 5 -10000 0 5
GNA13 -0.018 0 -10000 0 -10000 0 0
MMP9 -0.026 0.13 0.26 7 -0.3 19 26
MMP2 -0.031 0.12 0.17 8 -0.3 20 28
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL -0.018 0.004 0 7 -10000 0 7
RAS family/GTP/Tiam1 -0.014 0.021 -10000 0 -0.088 12 12
NT3 (dimer)/TRKC 0.023 0.008 -10000 0 0 18 18
NT3 (dimer)/TRKB 0.032 0.009 -10000 0 0 13 13
SHC/Grb2/SOS1/GAB1/PI3K -0.01 0.021 -10000 0 -0.1 7 7
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
BDNF -0.018 0.003 0 4 -10000 0 4
PIK3CA -0.013 0.008 0 49 -10000 0 49
DYNLT1 -0.018 0.003 0 5 -10000 0 5
NTRK1 -0.018 0.004 0 7 -10000 0 7
NTRK2 -0.018 0 -10000 0 -10000 0 0
NTRK3 -0.018 0.003 0 5 -10000 0 5
NT-4/5 (dimer)/TRKB 0.023 0 -10000 0 -10000 0 0
neuron apoptosis -0.026 0.044 0.14 4 -0.12 5 9
SHC 2-3/Grb2 0.027 0.046 0.13 5 -0.15 4 9
SHC1 -0.018 0.004 0 7 -10000 0 7
SHC2 0.018 0.043 -10000 0 -0.36 1 1
SHC3 0.021 0.033 -10000 0 -0.13 2 2
STAT3 (dimer) -0.018 0.002 0 3 -10000 0 3
NT3 (dimer)/TRKA 0.031 0.011 -10000 0 0 18 18
RIN/GDP 0.011 0.051 0.13 11 -0.2 2 13
GIPC1 -0.018 0.002 0 3 -10000 0 3
KRAS -0.017 0.005 0 11 -10000 0 11
DNAJA3 -0.009 0.008 -10000 0 -10000 0 0
RIN/GTP 0.012 0.003 -10000 0 0 13 13
CCND1 -0.015 0.01 0 52 -10000 0 52
MAGED1 -0.018 0 -10000 0 -10000 0 0
PTPN11 -0.018 0.001 0 1 -10000 0 1
RICS -0.016 0.006 0 20 -10000 0 20
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.033 0.008 -10000 0 0 10 10
GRB2 -0.018 0.001 0 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.022 0.006 -10000 0 0 11 11
TRKA/NEDD4-2 0.021 0.009 -10000 0 0 26 26
ELMO1 -0.018 0.003 0 6 -10000 0 6
RhoG/GTP/ELMO1/DOCK1 0.022 0.005 -10000 0 0 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS -0.018 0.003 0 5 -10000 0 5
DOCK1 -0.018 0.002 0 2 -10000 0 2
GAB2 -0.017 0.005 0 15 -10000 0 15
RIT2 -0.017 0.005 0 13 -10000 0 13
RIT1 -0.018 0.004 0 7 -10000 0 7
FRS2 -0.018 0.003 0 6 -10000 0 6
DNM1 -0.018 0.002 0 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.002 0 2 -10000 0 2
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.028 0.029 0.078 38 -10000 0 38
mol:GDP 0.015 0.069 0.18 10 -0.28 2 12
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.012 0.002 -10000 0 0 6 6
RIT1/GDP 0.007 0.05 0.13 9 -0.2 2 11
TIAM1 -0.018 0.003 0 4 -10000 0 4
PIK3R1 -0.018 0.004 0 8 -10000 0 8
BDNF (dimer)/TRKB 0.033 0.008 -10000 0 0 9 9
KIDINS220/CRKL/C3G 0.024 0.006 -10000 0 0 9 9
SHC/RasGAP 0.023 0.007 -10000 0 0 15 15
FRS2 family/SHP2 0.031 0.01 -10000 0 0 16 16
SHC/GRB2/SOS1/GAB1 0.04 0.013 -10000 0 0 16 16
RIT1/GTP 0.012 0.003 -10000 0 0 7 7
NT3 (dimer) -0.017 0.005 0 13 -10000 0 13
RAP1/GDP 0.001 0.039 0.098 5 -0.17 2 7
KIDINS220/CRKL -0.018 0.004 0 7 -10000 0 7
BDNF (dimer) -0.018 0.003 0 4 -10000 0 4
ubiquitin-dependent protein catabolic process 0.019 0.008 -10000 0 0 26 26
Schwann cell development -0.01 0.009 -10000 0 -0.032 1 1
EHD4 -0.018 0.003 0 6 -10000 0 6
FRS2 family/GRB2/SOS1 0.039 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.008 0.034 0.078 9 -0.11 11 20
RAP1B -0.018 0.004 0 7 -10000 0 7
RAP1A -0.018 0.003 0 6 -10000 0 6
CDC42/GTP -0.037 0.016 0 24 -10000 0 24
ABL1 -0.018 0.002 0 2 -10000 0 2
SH2B family/GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
Rap1/GTP -0.001 0.043 -10000 0 -0.18 7 7
STAT3 -0.018 0.002 0 3 -10000 0 3
axon guidance -0.036 0.015 0 24 -10000 0 24
MAPK3 -0.013 0.041 0.17 8 -10000 0 8
MAPK1 -0.012 0.041 0.17 8 -10000 0 8
CDC42/GDP 0.011 0.054 0.14 12 -0.2 2 14
NTF3 -0.017 0.005 0 13 -10000 0 13
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.019 0.009 -10000 0 0 32 32
PI3K 0.017 0.012 -10000 0 0 53 53
FRS3 -0.017 0.004 0 10 -10000 0 10
FAIM -0.015 0.007 0 28 -10000 0 28
GAB1 -0.018 0.004 0 7 -10000 0 7
RASGRF1 -0.01 0.008 -10000 0 -10000 0 0
SOS1 -0.018 0.002 0 3 -10000 0 3
MCF2L -0.022 0.009 0 25 -10000 0 25
RGS19 -0.017 0.004 0 10 -10000 0 10
CDC42 -0.018 0.003 0 5 -10000 0 5
RAS family/GTP 0.017 0.054 0.18 4 -0.25 2 6
Rac1/GDP 0.011 0.052 0.14 10 -0.2 2 12
NGF (dimer)/TRKA/GRIT 0.019 0.008 -10000 0 0 26 26
neuron projection morphogenesis 0.023 0.075 -10000 0 -0.77 1 1
NGF (dimer)/TRKA/NEDD4-2 0.019 0.008 -10000 0 0 26 26
MAP2K1 -0.023 0.048 0.18 8 -10000 0 8
NGFR -0.018 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP -0.007 0.013 -10000 0 -0.17 1 1
RAS family/GTP/PI3K -0.005 0.013 -10000 0 -0.17 1 1
FRS2 family/SHP2/GRB2/SOS1 0.045 0.017 -10000 0 -10000 0 0
NRAS -0.017 0.004 0 9 -10000 0 9
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
PRKCI -0.013 0.008 0 47 -10000 0 47
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCZ -0.018 0.003 0 5 -10000 0 5
MAPKKK cascade 0.013 0.014 -10000 0 -10000 0 0
RASA1 -0.018 0.004 0 8 -10000 0 8
TRKA/c-Abl 0.024 0.006 -10000 0 0 9 9
SQSTM1 -0.018 0.004 0 8 -10000 0 8
BDNF (dimer)/TRKB/GIPC 0.041 0.011 -10000 0 0 12 12
NGF (dimer)/TRKA/p62/Atypical PKCs 0.026 0.019 -10000 0 0 57 57
MATK -0.018 0.003 0 4 -10000 0 4
NEDD4L -0.016 0.006 0 21 -10000 0 21
RAS family/GDP -0.014 0.021 -10000 0 -0.1 5 5
NGF (dimer)/TRKA -0.005 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.021 0.02 -10000 0 -0.094 4 4
FRS2 family/SHP2/CRK family 0.043 0.019 -10000 0 -0.008 7 7
Visual signal transduction: Rods

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
mol:K + -0.018 0.002 0 3 -9999 0 3
GNAT1/GTP 0.011 0.004 -10000 0 0 23 23
Metarhodopsin II/Arrestin 0.02 0.008 -10000 0 0 24 24
PDE6G/GNAT1/GTP 0.02 0.008 -10000 0 0 25 25
mol:GTP 0 0 -10000 0 -9999 0 0
absorption of light 0 0 -10000 0 -9999 0 0
GNAT1 -0.016 0.006 0 23 -9999 0 23
GRK1 -0.018 0.004 0 7 -9999 0 7
CNG Channel -0.032 0.014 0 21 -9999 0 21
mol:Na + -0.034 0.018 -10000 0 -9999 0 0
mol:ADP -0.018 0.004 0 7 -9999 0 7
RGS9-1/Gbeta5/R9AP 0.033 0.007 -10000 0 0 8 8
mol:GDP 0 0 -10000 0 -9999 0 0
cGMP/CNG Channel -0.034 0.018 -10000 0 -9999 0 0
CNGB1 -0.017 0.004 0 9 -9999 0 9
RDH5 -0.018 0.001 0 1 -9999 0 1
SAG -0.018 0.004 0 8 -9999 0 8
mol:Ca2+ -0.01 0.085 0.25 9 -9999 0 9
Na + (4 Units) -0.037 0.02 -10000 0 -9999 0 0
RGS9 -0.018 0 -10000 0 -9999 0 0
GNB1/GNGT1 0.023 0.007 -10000 0 0 15 15
GNAT1/GDP 0.034 0.015 -10000 0 0 27 27
GUCY2D -0.018 0.002 0 2 -9999 0 2
GNGT1 -0.017 0.004 0 10 -9999 0 10
GUCY2F -0.018 0 -10000 0 -9999 0 0
GNB5 -0.018 0.003 0 4 -9999 0 4
mol:GMP (4 units) -0.023 0.011 0 32 -9999 0 32
mol:11-cis-retinal -0.018 0.001 0 1 -9999 0 1
mol:cGMP -0.029 0.014 -10000 0 -9999 0 0
GNB1 -0.018 0.003 0 5 -9999 0 5
Rhodopsin 0.022 0.009 -10000 0 0 22 22
SLC24A1 -0.018 0.002 0 3 -9999 0 3
CNGA1 -0.017 0.005 0 11 -9999 0 11
Metarhodopsin II 0.018 0.008 -10000 0 0 27 27
mol:Ca ++ 0 0 -10000 0 -9999 0 0
GC1/GCAP Family 0.035 0.017 -10000 0 -9999 0 0
RGS9BP -0.018 0.003 0 4 -9999 0 4
Metarhodopsin II/Transducin -0.004 0.003 -10000 0 -9999 0 0
GCAP Family/Ca ++ 0.027 0.013 -10000 0 0 30 30
PDE6A/B 0.023 0.008 -10000 0 0 18 18
mol:Pi 0.033 0.007 -10000 0 0 8 8
mol:all-trans-retinal 0 0 -10000 0 -9999 0 0
Transducin 0.026 0.013 -10000 0 0 33 33
PDE6B -0.017 0.005 0 14 -9999 0 14
PDE6A -0.018 0.003 0 5 -9999 0 5
PDE6G -0.018 0.002 0 3 -9999 0 3
RHO -0.016 0.006 0 21 -9999 0 21
PDE6 0.041 0.022 -10000 0 -9999 0 0
GUCA1A -0.017 0.004 0 10 -9999 0 10
GC2/GCAP Family 0.036 0.017 -10000 0 0 30 30
GUCA1C -0.016 0.006 0 20 -9999 0 20
GUCA1B -0.017 0.004 0 10 -9999 0 10
Coregulation of Androgen receptor activity

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
NRIP1 -0.018 0.003 0 5 -10000 0 5
SVIL -0.018 0.003 0 4 -10000 0 4
ZNF318 -0.017 0.004 0 10 -10000 0 10
JMJD2C -0.016 0.006 0 18 -10000 0 18
T-DHT/AR/Ubc9 0.023 0.003 -10000 0 0 3 3
CARM1 -0.018 0.002 0 3 -10000 0 3
PRDX1 -0.018 0.001 0 1 -10000 0 1
PELP1 -0.018 0.002 0 2 -10000 0 2
CTNNB1 -0.015 0.007 0 28 -10000 0 28
AKT1 -0.017 0.005 0 13 -10000 0 13
PTK2B -0.017 0.004 0 10 -10000 0 10
MED1 0 0 -10000 0 -10000 0 0
MAK -0.017 0.005 0 12 -10000 0 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 -0.018 0.004 0 8 -10000 0 8
GSN -0.018 0.002 0 2 -10000 0 2
NCOA2 -0.016 0.006 0 19 -10000 0 19
NCOA6 -0.016 0.006 0 19 -10000 0 19
DNA-PK 0.029 0.013 -10000 0 0 27 27
NCOA4 -0.018 0.002 0 2 -10000 0 2
PIAS3 -0.018 0.003 0 6 -10000 0 6
cell proliferation -0.003 0.073 -10000 0 -0.38 6 6
XRCC5 -0.018 0.004 0 8 -10000 0 8
UBE3A -0.018 0.003 0 5 -10000 0 5
T-DHT/AR/SNURF 0.022 0.004 -10000 0 0 5 5
FHL2 0.009 0.002 -10000 0 0 12 12
RANBP9 -0.017 0.005 0 11 -10000 0 11
JMJD1A -0.018 0.002 0 2 -10000 0 2
CDK6 -0.017 0.004 0 10 -10000 0 10
TGFB1I1 -0.018 0.002 0 3 -10000 0 3
T-DHT/AR/CyclinD1 0.016 0.011 -10000 0 0 50 50
XRCC6 -0.018 0.002 0 2 -10000 0 2
T-DHT/AR 0.012 0 -10000 0 -10000 0 0
CTDSP1 -0.018 0.004 0 8 -10000 0 8
CTDSP2 -0.018 0.002 0 2 -10000 0 2
BRCA1 -0.018 0.002 0 3 -10000 0 3
TCF4 -0.016 0.006 0 20 -10000 0 20
CDKN2A -0.014 0.008 0 44 -10000 0 44
SRF -0.017 0.004 0 10 -10000 0 10
NKX3-1 0.009 0.002 -10000 0 0 11 11
KLK3 0.009 0.032 0.095 5 -0.1 4 9
TMF1 -0.016 0.006 0 24 -10000 0 24
HNRNPA1 0 0 -10000 0 -10000 0 0
AOF2 -0.018 0.003 0 5 -10000 0 5
APPL1 -0.01 0.003 0 13 -10000 0 13
T-DHT/AR/Caspase 8 0.022 0.004 -10000 0 0 6 6
AR -0.018 0 -10000 0 -10000 0 0
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0 0 -10000 0 -10000 0 0
PAWR -0.018 0.002 0 2 -10000 0 2
PRKDC -0.016 0.006 0 21 -10000 0 21
PA2G4 -0.018 0.001 0 1 -10000 0 1
UBE2I -0.018 0.002 0 3 -10000 0 3
T-DHT/AR/Cyclin D3/CDK11 p58 0.027 0.013 -10000 0 0 31 31
RPS6KA3 -0.018 0 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.023 0.003 -10000 0 0 2 2
LATS2 -0.018 0.004 0 7 -10000 0 7
T-DHT/AR/PRX1 0.022 0.002 -10000 0 0 1 1
Cyclin D3/CDK11 p58 0.021 0.01 -10000 0 0 31 31
VAV3 -0.018 0.003 0 6 -10000 0 6
KLK2 0.008 0.003 -10000 0 0 19 19
CASP8 -0.018 0.003 0 6 -10000 0 6
T-DHT/AR/TIF2/CARM1 0.028 0.011 -10000 0 0 22 22
TMPRSS2 0.009 0.002 -10000 0 0 7 7
CCND1 -0.013 0.008 0 50 -10000 0 50
PIAS1 -0.018 0.002 0 3 -10000 0 3
mol:T-DHT 0 0 -10000 0 -10000 0 0
CDC2L1 -0.016 0.006 0 23 -10000 0 23
PIAS4 -0.018 0.003 0 4 -10000 0 4
T-DHT/AR/CDK6 0.022 0.006 -10000 0 0 10 10
CMTM2 -0.017 0.004 0 9 -10000 0 9
SNURF -0.018 0.003 0 5 -10000 0 5
ZMIZ1 0 0 -10000 0 -10000 0 0
CCND3 -0.017 0.004 0 10 -10000 0 10
TGIF1 0 0 -10000 0 -10000 0 0
FKBP4 -0.017 0.005 0 14 -10000 0 14
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 -0.016 0.006 0 19 -10000 0 19
SMAD2 -0.007 0.054 0.19 4 -0.17 5 9
SMAD3 -0.008 0.036 0.098 8 -0.089 16 24
SMAD3/SMAD4 -0.003 0.078 -10000 0 -0.42 5 5
SMAD4/Ubc9/PIASy 0.029 0.012 -10000 0 0 25 25
SMAD2/SMAD2/SMAD4 0.014 0.057 0.17 2 -0.13 12 14
PPM1A -0.018 0.004 0 8 -10000 0 8
CALM1 -0.017 0.005 0 14 -10000 0 14
SMAD2/SMAD4 -0.014 0.045 0.11 8 -0.18 4 12
MAP3K1 -0.017 0.004 0 9 -10000 0 9
TRAP-1/SMAD4 0.022 0.008 -10000 0 0 20 20
MAPK3 -0.018 0.003 0 4 -10000 0 4
MAPK1 -0.018 0.003 0 6 -10000 0 6
NUP214 -0.018 0.002 0 2 -10000 0 2
CTDSP1 -0.018 0.004 0 8 -10000 0 8
CTDSP2 -0.018 0.002 0 2 -10000 0 2
CTDSPL -0.016 0.007 0 25 -10000 0 25
KPNB1 -0.018 0 -10000 0 -10000 0 0
TGFBRAP1 -0.018 0.002 0 2 -10000 0 2
UBE2I -0.018 0.002 0 3 -10000 0 3
NUP153 -0.017 0.004 0 10 -10000 0 10
KPNA2 -0.018 0.001 0 1 -10000 0 1
PIAS4 -0.018 0.003 0 4 -10000 0 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.037 0.016 -10000 0 0 27 27
HDAC3 -0.018 0.003 0 6 -10000 0 6
Ran/GTP/Exportin 1/HDAC4 -0.022 0.007 -0.001 15 -10000 0 15
GATA1/HDAC4 0.024 0.006 -10000 0 0 10 10
GATA1/HDAC5 0.025 0.002 -10000 0 0 1 1
GATA2/HDAC5 0.022 0.008 -10000 0 0 21 21
HDAC5/BCL6/BCoR 0.025 0.016 -10000 0 0 46 46
HDAC9 -0.018 0.003 0 6 -10000 0 6
Glucocorticoid receptor/Hsp90/HDAC6 0.022 0.004 -10000 0 0 5 5
HDAC4/ANKRA2 0.023 0.008 -10000 0 0 17 17
HDAC5/YWHAB 0.023 0.007 -10000 0 0 13 13
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.001 -10000 0 -10000 0 0
GATA2 -0.016 0.006 0 20 -10000 0 20
HDAC4/RFXANK 0.024 0.006 -10000 0 0 11 11
BCOR -0.018 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.018 0.004 0 7 -10000 0 7
HDAC5 -0.018 0.001 0 1 -10000 0 1
GNB1/GNG2 0.024 0.006 -10000 0 0 11 11
Histones -0.01 0.026 -10000 0 -0.11 8 8
ADRBK1 -0.017 0.006 0 17 -10000 0 17
HDAC4 -0.017 0.004 0 10 -10000 0 10
XPO1 -0.018 0.003 0 4 -10000 0 4
HDAC5/ANKRA2 0.024 0.006 -10000 0 0 9 9
HDAC4/Ubc9 0.023 0.007 -10000 0 0 12 12
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.025 0.003 -10000 0 0 2 2
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 -0.018 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.025 0.003 -10000 0 0 2 2
CAMK4 -0.018 0.003 0 6 -10000 0 6
Tubulin/HDAC6 0.022 0.006 -10000 0 0 10 10
SUMO1 -0.018 0.004 0 7 -10000 0 7
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB -0.017 0.005 0 12 -10000 0 12
GATA1 -0.018 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE -0.018 0.002 0 2 -10000 0 2
NR3C1 -0.018 0.003 0 5 -10000 0 5
SUMO1/HDAC4 0.017 0.022 0.084 1 -0.098 5 6
SRF -0.017 0.004 0 10 -10000 0 10
HDAC4/YWHAB 0.022 0.008 -10000 0 0 21 21
Tubulin 0.012 0.003 -10000 0 0 10 10
HDAC4/14-3-3 E 0.023 0.007 -10000 0 0 12 12
GNB1 -0.018 0.003 0 5 -10000 0 5
RANGAP1 -0.018 0.002 0 2 -10000 0 2
BCL6/BCoR 0.018 0.011 -10000 0 0 45 45
HDAC4/HDAC3/SMRT (N-CoR2) 0.031 0.011 -10000 0 0 19 19
HDAC4/SRF 0.03 0.012 -10000 0 0 23 23
HDAC4/ER alpha 0.023 0.007 -10000 0 0 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.029 0.077 4 -0.11 8 12
cell motility 0.021 0.005 -10000 0 0 10 10
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I -0.018 0.002 0 3 -10000 0 3
HDAC7/HDAC3 0.012 0.002 -10000 0 0 6 6
BCL6 -0.013 0.008 0 45 -10000 0 45
HDAC4/CaMK II delta B -0.017 0.004 0 10 -10000 0 10
Hsp90/HDAC6 0.013 0 -10000 0 -10000 0 0
ESR1 -0.018 0.003 0 5 -10000 0 5
HDAC6/HDAC11 0.022 0.008 -10000 0 0 21 21
Ran/GTP/Exportin 1 0.017 0.026 -10000 0 -0.097 7 7
NPC 0.01 0.001 -10000 0 0 2 2
MEF2C -0.018 0.004 0 7 -10000 0 7
RAN -0.018 0.001 0 1 -10000 0 1
HDAC4/MEF2C 0.043 0.019 -10000 0 -0.008 14 14
GNG2 -0.018 0.004 0 7 -10000 0 7
NCOR2 -0.018 0.003 0 4 -10000 0 4
TUBB2A -0.017 0.004 0 10 -10000 0 10
HDAC11 -0.016 0.006 0 21 -10000 0 21
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 -0.018 0.002 0 2 -10000 0 2
ANKRA2 -0.018 0.004 0 8 -10000 0 8
RFXANK -0.018 0.001 0 1 -10000 0 1
nuclear import -0.014 0.005 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 -0.017 0.004 0 9 -9999 0 9
PLK4 -0.018 0.003 0 6 -9999 0 6
regulation of centriole replication -0.02 0.006 0 13 -9999 0 13
Thromboxane A2 receptor signaling

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.015 0.01 0.019 11 -10000 0 11
GNB1/GNG2 -0.021 0.018 -10000 0 -0.11 4 4
AKT1 -0.019 0.074 0.15 3 -0.22 15 18
EGF -0.018 0.003 0 5 -10000 0 5
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.005 0.064 0.15 18 -10000 0 18
mol:Ca2+ -0.011 0.065 0.18 3 -0.25 8 11
LYN -0.006 0.06 0.16 15 -10000 0 15
RhoA/GTP -0.015 0.023 0.062 1 -0.095 8 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.015 0.062 0.18 3 -0.24 8 11
GNG2 -0.018 0.004 0 7 -10000 0 7
ARRB2 -0.018 0.002 0 2 -10000 0 2
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.074 -10000 0 -0.34 6 6
G beta5/gamma2 -0.025 0.021 -10000 0 -0.12 4 4
PRKCH -0.013 0.069 0.19 5 -0.26 8 13
DNM1 -0.018 0.002 0 2 -10000 0 2
TXA2/TP beta/beta Arrestin3 0.01 0.009 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.018 0.004 0 7 -10000 0 7
G12 family/GTP -0.023 0.049 -10000 0 -0.22 8 8
ADRBK1 -0.016 0.006 0.001 18 -10000 0 18
ADRBK2 -0.018 0.003 0 4 -10000 0 4
RhoA/GTP/ROCK1 0.019 0.009 -10000 0 0 28 28
mol:GDP 0.004 0.049 0.18 7 -0.16 2 9
mol:NADP -0.017 0.005 0.002 10 -10000 0 10
RAB11A -0.018 0.002 0 3 -10000 0 3
PRKG1 -0.018 0.004 0.003 7 -10000 0 7
mol:IP3 -0.014 0.077 0.22 2 -0.31 8 10
cell morphogenesis 0.019 0.009 -10000 0 0 28 28
PLCB2 -0.021 0.097 0.24 2 -0.4 8 10
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.005 0.064 0.15 18 -10000 0 18
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.004 0.061 0.16 16 -10000 0 16
RHOA -0.016 0.006 0 23 -10000 0 23
PTGIR -0.018 0.003 0.006 3 -10000 0 3
PRKCB1 -0.014 0.07 0.19 3 -0.28 8 11
GNAQ -0.018 0 -10000 0 -10000 0 0
mol:L-citrulline -0.017 0.005 0.002 10 -10000 0 10
TXA2/TXA2-R family -0.018 0.083 0.21 3 -0.33 8 11
LCK -0.005 0.064 0.15 18 -10000 0 18
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.033 0.097 11 -10000 0 11
TXA2-R family/G12 family/GDP/G beta/gamma 0 0.072 -10000 0 -0.4 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.033 0.097 11 -10000 0 11
MAPK14 -0.013 0.047 0.13 5 -0.17 8 13
TGM2/GTP -0.022 0.079 0.21 2 -0.34 8 10
MAPK11 -0.013 0.05 0.16 5 -0.16 8 13
ARHGEF1 -0.016 0.034 0.1 2 -0.14 8 10
GNAI2 -0.016 0.006 0 23 -10000 0 23
JNK cascade -0.013 0.068 0.2 3 -0.26 8 11
RAB11/GDP -0.016 0.008 0.019 8 -10000 0 8
ICAM1 -0.009 0.051 0.15 4 -0.19 8 12
cAMP biosynthetic process -0.014 0.074 0.22 2 -0.29 8 10
Gq family/GTP/EBP50 -0.002 0.001 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.019 0.009 -10000 0 0 28 28
SRC -0.005 0.062 0.16 16 -10000 0 16
GNB5 -0.018 0.004 0.004 5 -10000 0 5
GNB1 -0.018 0.003 0 5 -10000 0 5
EGF/EGFR 0.011 0.069 0.17 17 -0.15 4 21
VCAM1 -0.009 0.051 0.16 3 -0.19 8 11
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.074 -10000 0 -0.34 6 6
platelet activation -0.013 0.066 0.2 4 -0.23 8 12
PGI2/IP 0.012 0.004 -10000 0 -0.008 6 6
PRKACA -0.006 0.004 0.007 8 -10000 0 8
Gq family/GDP/G beta5/gamma2 -0.008 0.064 0.11 5 -0.29 6 11
TXA2/TP beta/beta Arrestin2 0.004 0.015 -10000 0 -0.11 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.004 -10000 0 -10000 0 0
mol:DAG -0.014 0.077 0.22 2 -0.31 8 10
EGFR -0.016 0.006 0 20 -10000 0 20
TXA2/TP alpha -0.019 0.095 0.25 2 -0.39 8 10
Gq family/GTP -0.006 0.032 0.21 1 -0.18 4 5
YES1 -0.007 0.057 0.16 13 -10000 0 13
GNAI2/GTP -0.023 0.014 0.021 1 -0.078 1 2
PGD2/DP 0.011 0.004 -10000 0 -0.004 11 11
SLC9A3R1 -0.018 0.001 0 1 -10000 0 1
FYN -0.006 0.061 0.15 17 -10000 0 17
mol:NO -0.017 0.005 0.002 10 -10000 0 10
GNA15 -0.018 0.003 0 5 -10000 0 5
PGK/cGMP 0.021 0.006 -10000 0 0 14 14
RhoA/GDP -0.015 0.008 0.019 3 -10000 0 3
TP alpha/TGM2/GDP/G beta/gamma -0.022 0.03 0.11 6 -10000 0 6
NOS3 -0.017 0.005 0.002 10 -10000 0 10
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCA -0.014 0.066 0.17 4 -0.26 8 12
PRKCB -0.011 0.063 0.2 2 -0.25 8 10
PRKCE -0.014 0.065 0.19 3 -0.25 8 11
PRKCD -0.015 0.062 0.17 3 -0.25 8 11
PRKCG -0.014 0.071 0.19 3 -0.28 8 11
muscle contraction -0.019 0.083 0.21 3 -0.33 8 11
PRKCZ -0.015 0.062 0.17 4 -0.24 8 12
ARR3 -0.018 0 -10000 0 -10000 0 0
TXA2/TP beta -0.016 0.032 0.1 9 -0.099 1 10
PRKCQ -0.014 0.065 0.2 3 -0.25 8 11
MAPKKK cascade -0.017 0.083 0.22 2 -0.33 8 10
SELE -0.009 0.05 0.16 3 -0.19 8 11
TP beta/GNAI2/GDP/G beta/gamma -0.021 0.029 0.11 6 -10000 0 6
ROCK1 -0.018 0.004 0 7 -10000 0 7
GNA14 -0.018 0 -10000 0 -10000 0 0
chemotaxis -0.018 0.082 0.21 3 -0.33 8 11
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA13 -0.018 0 -10000 0 -10000 0 0
GNA11 -0.018 0.003 0 5 -10000 0 5
Rac1/GTP 0.011 0.005 -10000 0 -0.012 6 6
HIF-1-alpha transcription factor network

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
PKM2 -0.011 0.062 0.22 10 -10000 0 10
HDAC7 0 0 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.021 0.039 -10000 0 -0.11 12 12
SMAD4 -0.016 0.006 0 19 -10000 0 19
ID2 -0.011 0.062 0.22 10 -10000 0 10
AP1 0.024 0.006 -10000 0 0 11 11
ABCG2 -0.01 0.062 0.22 10 -10000 0 10
HIF1A -0.018 0.004 0 7 -10000 0 7
TFF3 -0.011 0.062 0.22 10 -10000 0 10
GATA2 -0.016 0.006 0 20 -10000 0 20
AKT1 -0.017 0.005 0 13 -10000 0 13
response to hypoxia 0 0 -10000 0 -10000 0 0
MCL1 -0.015 0.055 0.25 6 -10000 0 6
NDRG1 -0.01 0.058 0.23 8 -10000 0 8
SERPINE1 -0.01 0.06 0.22 9 -10000 0 9
FECH -0.014 0.046 0.19 7 -10000 0 7
FURIN -0.012 0.06 0.22 9 -10000 0 9
NCOA2 -0.016 0.006 0 19 -10000 0 19
EP300 -0.004 0.001 -10000 0 -10000 0 0
HMOX1 -0.011 0.062 0.22 10 -10000 0 10
BHLHE40 -0.018 0.007 0 20 -10000 0 20
BHLHE41 -0.018 0.007 0 20 -10000 0 20
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.041 0.021 -10000 0 -0.008 14 14
ENG -0.021 0.052 0.15 13 -10000 0 13
JUN -0.018 0.003 0 4 -10000 0 4
RORA -0.011 0.062 0.22 10 -10000 0 10
ABCB1 0.007 0.024 -10000 0 -0.3 1 1
TFRC -0.01 0.05 0.22 6 -10000 0 6
CXCR4 -0.012 0.06 0.22 9 -10000 0 9
TF -0.012 0.053 0.21 8 -10000 0 8
CITED2 -0.012 0.06 0.22 9 -10000 0 9
HIF1A/ARNT 0.029 0.011 -10000 0 0 20 20
LDHA -0.001 0.079 -10000 0 -0.44 5 5
ETS1 -0.013 0.052 0.21 7 -10000 0 7
PGK1 -0.011 0.062 0.22 10 -10000 0 10
NOS2 -0.018 0.007 0 20 -10000 0 20
ITGB2 -0.011 0.062 0.22 10 -10000 0 10
ALDOA -0.011 0.062 0.22 10 -10000 0 10
Cbp/p300/CITED2 -0.025 0.037 0.15 5 -0.12 7 12
FOS -0.018 0.004 0 8 -10000 0 8
HK2 -0.012 0.06 0.22 9 -10000 0 9
SP1 -0.018 0.001 0 1 -10000 0 1
GCK -0.008 0.045 0.14 3 -0.17 9 12
HK1 -0.011 0.062 0.22 10 -10000 0 10
NPM1 -0.013 0.055 0.2 9 -10000 0 9
EGLN1 -0.014 0.057 0.24 7 -10000 0 7
CREB1 -0.018 0.003 0 6 -10000 0 6
PGM1 -0.013 0.055 0.2 9 -10000 0 9
SMAD3 -0.018 0.003 0 4 -10000 0 4
EDN1 -0.001 0.061 0.15 5 -0.17 10 15
IGFBP1 -0.015 0.052 0.21 7 -10000 0 7
VEGFA -0.021 0.024 0.076 1 -0.12 8 9
HIF1A/JAB1 0.022 0.009 -10000 0 0 23 23
CP -0.014 0.041 0.2 5 -10000 0 5
CXCL12 -0.011 0.062 0.22 10 -10000 0 10
COPS5 -0.017 0.006 0 17 -10000 0 17
SMAD3/SMAD4 0.022 0.008 -10000 0 0 21 21
BNIP3 -0.011 0.062 0.22 10 -10000 0 10
EGLN3 -0.016 0.045 0.19 7 -10000 0 7
CA9 -0.012 0.053 0.21 8 -10000 0 8
TERT -0.012 0.052 0.21 7 -10000 0 7
ENO1 -0.011 0.062 0.22 10 -10000 0 10
PFKL -0.011 0.062 0.22 10 -10000 0 10
NCOA1 -0.018 0.002 0 2 -10000 0 2
ADM -0.011 0.062 0.22 10 -10000 0 10
ARNT -0.018 0.003 0 6 -10000 0 6
HNF4A -0.017 0.005 0 12 -10000 0 12
ADFP -0.012 0.053 0.21 8 -10000 0 8
SLC2A1 -0.022 0.04 0.14 7 -0.13 8 15
LEP -0.012 0.06 0.22 9 -10000 0 9
HIF1A/ARNT/Cbp/p300 0.013 0.036 -10000 0 -0.11 12 12
EPO -0.002 0.04 0.12 4 -0.41 1 5
CREBBP -0.004 0.001 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 0.012 0.034 -10000 0 -0.1 12 12
PFKFB3 -0.012 0.06 0.22 9 -10000 0 9
NT5E -0.012 0.06 0.22 9 -10000 0 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.023 0.008 -10000 0 0 17 17
CRKL -0.001 0.089 0.19 6 -0.36 7 13
mol:PIP3 0.006 0.088 -10000 0 -0.78 2 2
AKT1 -0.004 0.083 -10000 0 -0.69 2 2
PTK2B -0.017 0.004 0 10 -10000 0 10
RAPGEF1 -0.006 0.089 0.19 8 -0.38 6 14
RANBP10 -0.017 0.004 0 9 -10000 0 9
PIK3CA -0.013 0.008 0 49 -10000 0 49
HGF/MET/SHIP2 0.028 0.014 -10000 0 0 32 32
MAP3K5 -0.011 0.093 0.2 4 -0.41 6 10
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.018 -10000 0 0 33 33
AP1 -0.015 0.031 0.078 11 -10000 0 11
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.018 0.004 0 7 -10000 0 7
apoptosis -0.013 0.16 -10000 0 -0.82 6 6
STAT3 (dimer) 0.003 0.034 -10000 0 -0.11 5 5
GAB1/CRKL/SHP2/PI3K 0.012 0.078 0.22 3 -0.35 5 8
INPP5D -0.018 0.004 0 8 -10000 0 8
CBL/CRK 0.002 0.079 0.19 1 -0.36 6 7
PTPN11 -0.018 0.001 0 1 -10000 0 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.017 0.005 0 11 -10000 0 11
PTEN -0.018 0.003 0 5 -10000 0 5
ELK1 0 0.061 0.26 7 -10000 0 7
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.03 -10000 0 -0.12 8 8
PAK1 -0.006 0.083 -10000 0 -0.65 2 2
HGF/MET/RANBP10 0.031 0.011 -10000 0 0 18 18
HRAS -0.01 0.086 -10000 0 -0.38 8 8
DOCK1 -0.006 0.087 0.19 7 -0.37 6 13
GAB1 0.002 0.071 0.16 1 -0.42 4 5
CRK -0.007 0.082 0.2 1 -0.39 6 7
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.071 -10000 0 -0.31 8 8
JUN -0.018 0.003 0 4 -10000 0 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.004 0.008 0.021 4 -0.051 4 8
PIK3R1 -0.018 0.004 0 8 -10000 0 8
cell morphogenesis 0.04 0.11 0.18 50 -0.21 5 55
GRB2/SHC 0.021 0.028 0.086 5 -0.091 7 12
FOS -0.018 0.004 0 8 -10000 0 8
GLMN 0.001 0 -10000 0 -10000 0 0
cell motility 0 0.061 0.26 7 -10000 0 7
HGF/MET/MUC20 0.022 0.006 -10000 0 0 10 10
cell migration 0.02 0.027 0.084 5 -0.09 7 12
GRB2 -0.018 0.001 0 1 -10000 0 1
CBL -0.016 0.006 0 24 -10000 0 24
MET/RANBP10 0.023 0.007 -10000 0 0 15 15
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.017 -10000 0 -0.091 7 7
MET/MUC20 0.012 0.003 -10000 0 0 7 7
RAP1B -0.006 0.085 0.2 3 -0.37 5 8
RAP1A -0.011 0.084 0.18 7 -0.36 6 13
HGF/MET/RANBP9 0.03 0.011 -10000 0 0 20 20
RAF1 -0.012 0.081 -10000 0 -0.36 8 8
STAT3 0.003 0.034 -10000 0 -0.11 5 5
cell proliferation 0.001 0.05 0.17 7 -0.28 1 8
RPS6KB1 0.004 0.016 -10000 0 -0.1 1 1
MAPK3 0.003 0.11 0.56 5 -10000 0 5
MAPK1 -0.009 0.047 0.28 2 -10000 0 2
RANBP9 -0.017 0.005 0 11 -10000 0 11
MAPK8 -0.004 0.09 0.2 3 -0.36 7 10
SRC -0.013 0.015 -10000 0 -0.092 5 5
PI3K 0.014 0.021 -10000 0 -0.071 6 6
MET/Glomulin 0.009 0.023 -10000 0 -0.085 8 8
SOS1 -0.018 0.002 0 3 -10000 0 3
MAP2K1 -0.017 0.077 -10000 0 -0.34 8 8
MET -0.018 0.004 0 7 -10000 0 7
MAP4K1 -0.009 0.1 0.23 3 -0.41 7 10
PTK2 -0.015 0.007 0 28 -10000 0 28
MAP2K2 -0.015 0.079 0.18 2 -0.34 8 10
BAD -0.003 0.078 -10000 0 -0.58 2 2
MAP2K4 -0.017 0.086 0.19 4 -0.38 6 10
SHP2/GRB2/SOS1/GAB1 0.016 0.076 -10000 0 -0.32 7 7
INPPL1 -0.016 0.007 0 26 -10000 0 26
PXN -0.018 0.001 0 1 -10000 0 1
SH3KBP1 -0.018 0 -10000 0 -10000 0 0
HGS -0.009 0.013 0.07 3 -0.054 4 7
PLCgamma1/PKC 0.012 0.003 -10000 0 0 11 11
HGF -0.018 0.003 0 5 -10000 0 5
RASA1 -0.018 0.004 0 8 -10000 0 8
NCK1 -0.015 0.007 0 27 -10000 0 27
PTPRJ -0.018 0.002 0 2 -10000 0 2
NCK/PLCgamma1 0.02 0.017 0.085 5 -0.091 1 6
PDPK1 -0.003 0.081 -10000 0 -0.72 2 2
HGF/MET/SHIP 0.031 0.011 -10000 0 0 17 17
IL4-mediated signaling events

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
BCL2L1 0.016 0.073 0.18 24 -0.12 4 28
STAT6 (cleaved dimer) -0.002 0.035 0.11 1 -0.12 7 8
IGHG1 -0.009 0.078 -10000 0 -0.31 10 10
IGHG3 -0.002 0.047 0.18 8 -0.12 4 12
AKT1 -0.013 0.07 -10000 0 -0.27 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.003 0.05 0.14 1 -0.19 7 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.009 0.052 -10000 0 -0.18 8 8
THY1 -0.006 0.025 0.14 2 -0.12 2 4
MYB -0.018 0.003 0 6 -10000 0 6
HMGA1 -0.017 0.004 0 9 -10000 0 9
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.002 0.032 0.1 1 -0.11 9 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.009 0.052 -10000 0 -0.18 8 8
SP1 -0.018 0.001 0 1 -10000 0 1
INPP5D -0.018 0.004 0 8 -10000 0 8
SOCS5 -0.018 0.009 0.022 7 -10000 0 7
STAT6 (dimer)/ETS1 0.008 0.034 0.12 2 -0.13 5 7
SOCS1 -0.02 0.036 0.14 1 -0.2 2 3
SOCS3 -0.01 0.039 0.18 3 -10000 0 3
FCER2 -0.015 0.038 0.12 2 -0.12 5 7
PARP14 -0.016 0.006 0 20 -10000 0 20
CCL17 -0.01 0.032 0.17 2 -0.12 4 6
GRB2 -0.018 0.001 0 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.01 0.05 -10000 0 -0.14 17 17
T cell proliferation -0.01 0.034 0.12 3 -0.12 6 9
IL4R/JAK1 -0.009 0.03 0.13 3 -0.085 3 6
EGR2 -0.01 0.031 0.17 2 -0.12 4 6
JAK2 -0.015 0.012 0.028 5 -10000 0 5
JAK3 0.011 0.015 -10000 0 -0.035 1 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
JAK1 -0.012 0.016 0.028 6 -10000 0 6
COL1A2 0.006 0.033 -10000 0 -0.37 1 1
CCL26 -0.008 0.04 0.19 4 -0.12 5 9
IL4R -0.006 0.028 0.17 2 -0.088 4 6
PTPN6 -0.016 0.008 0.02 5 -10000 0 5
IL13RA2 -0.012 0.029 0.15 1 -0.12 5 6
IL13RA1 -0.011 0.02 0.041 15 -10000 0 15
IRF4 0.001 0.063 -10000 0 -0.34 5 5
ARG1 -0.008 0.062 0.099 6 -0.2 11 17
CBL -0.005 0.024 -10000 0 -0.11 6 6
GTF3A -0.018 0.003 0 5 -10000 0 5
PIK3CA -0.013 0.008 0 49 -10000 0 49
IL13RA1/JAK2 -0.013 0.022 0.067 5 -10000 0 5
IRF4/BCL6 0.007 0.056 -10000 0 -0.29 5 5
CD40LG -0.018 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.04 0.2 3 -0.11 3 6
mitosis -0.012 0.068 -10000 0 -0.26 9 9
STAT6 -0.004 0.027 0.11 1 -0.12 7 8
SPI1 -0.018 0.003 0 5 -10000 0 5
RPS6KB1 -0.018 0.066 -10000 0 -0.26 9 9
STAT6 (dimer) -0.004 0.031 0.14 2 -0.12 7 9
STAT6 (dimer)/PARP14 0.004 0.032 0.12 2 -0.11 7 9
mast cell activation 0.001 0.002 0.009 1 -0.008 4 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.008 0.057 -10000 0 -0.21 8 8
FRAP1 -0.012 0.07 -10000 0 -0.27 9 9
LTA -0.007 0.043 0.19 5 -0.12 5 10
FES -0.018 0.002 0 3 -10000 0 3
T-helper 1 cell differentiation 0.004 0.031 0.12 7 -0.14 2 9
CCL11 -0.012 0.027 0.14 1 -0.11 5 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.002 0.045 -10000 0 -0.2 4 4
IL2RG 0.011 0.015 -10000 0 -0.035 1 1
IL10 -0.006 0.045 0.17 7 -0.11 7 14
IRS1 -0.018 0.004 0 8 -10000 0 8
IRS2 -0.018 0.003 0 5 -10000 0 5
IL4 -0.018 0.12 -10000 0 -0.51 9 9
IL5 -0.009 0.024 0.12 2 -0.12 2 4
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.004 0.044 0.13 2 -0.18 8 10
COL1A1 -0.001 0.057 -10000 0 -0.31 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.012 0.033 0.14 3 -0.11 4 7
IL2R gamma/JAK3 0.024 0.013 -10000 0 -0.034 6 6
TFF3 -0.011 0.027 0.15 1 -0.12 3 4
ALOX15 -0.01 0.032 0.17 2 -0.12 4 6
MYBL1 -0.017 0.006 0 17 -10000 0 17
T-helper 2 cell differentiation -0.07 0.12 0.13 2 -0.25 49 51
SHC1 -0.018 0.004 0 7 -10000 0 7
CEBPB -0.017 0.005 0 11 -10000 0 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.007 0.049 -10000 0 -0.18 8 8
mol:PI-3-4-5-P3 -0.013 0.07 -10000 0 -0.27 9 9
PI3K -0.013 0.072 -10000 0 -0.28 9 9
DOK2 -0.017 0.004 0 9 -10000 0 9
ETS1 -0.013 0.012 0.02 13 -10000 0 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.009 0.041 -10000 0 -0.14 9 9
ITGB3 -0.012 0.029 0.12 2 -0.12 5 7
PIGR -0.006 0.045 0.18 6 -0.12 5 11
IGHE 0.003 0.05 0.12 13 -0.1 12 25
MAPKKK cascade -0.009 0.041 -10000 0 -0.13 9 9
BCL6 -0.013 0.008 0 45 -10000 0 45
OPRM1 -0.011 0.033 0.17 2 -0.12 5 7
RETNLB 0.01 0.07 0.19 19 -0.12 5 24
SELP -0.006 0.045 0.18 6 -0.12 5 11
AICDA -0.002 0.047 0.16 9 -0.12 4 13
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.031 0.01 -10000 0 0 15 15
alphaM/beta2 Integrin/GPIbA 0.033 0.008 -10000 0 0 10 10
alphaM/beta2 Integrin/proMMP-9 0.031 0.01 -10000 0 0 16 16
PLAUR -0.018 0.001 0 1 -10000 0 1
HMGB1 -0.018 0.004 0 7 -10000 0 7
alphaM/beta2 Integrin/Talin 0.03 0.012 -10000 0 0 22 22
AGER -0.018 0.004 0 7 -10000 0 7
RAP1A -0.018 0.003 0 6 -10000 0 6
SELPLG -0.018 0.001 0 1 -10000 0 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.039 0.014 -10000 0 0 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.017 0.005 0 11 -10000 0 11
CYR61 -0.018 0.003 0 4 -10000 0 4
TLN1 -0.016 0.006 0 18 -10000 0 18
Rap1/GTP 0.016 0.044 0.11 2 -0.15 4 6
RHOA -0.016 0.006 0 23 -10000 0 23
P-selectin oligomer -0.018 0.003 0 5 -10000 0 5
MYH2 -0.006 0.055 0.15 1 -0.16 11 12
MST1R -0.016 0.006 0 23 -10000 0 23
leukocyte activation during inflammatory response 0.03 0.014 -10000 0 -10000 0 0
APOB -0.018 0.002 0 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.017 0.004 0 10 -10000 0 10
JAM3 -0.016 0.006 0 19 -10000 0 19
GP1BA -0.018 0.002 0 2 -10000 0 2
alphaM/beta2 Integrin/CTGF 0.032 0.009 -10000 0 0 13 13
alphaM/beta2 Integrin -0.005 0.027 -10000 0 -0.1 11 11
JAM3 homodimer -0.016 0.006 0 19 -10000 0 19
ICAM2 -0.018 0 -10000 0 -10000 0 0
ICAM1 -0.018 0.002 0 3 -10000 0 3
phagocytosis triggered by activation of immune response cell surface activating receptor 0.009 0.039 -10000 0 -0.17 2 2
cell adhesion 0.032 0.008 -10000 0 0 10 10
NFKB1 -0.027 0.031 0.16 4 -10000 0 4
THY1 -0.016 0.006 0 24 -10000 0 24
RhoA/GDP 0.011 0.004 -10000 0 0 23 23
Lipoprotein(a) 0.02 0.008 -10000 0 0 22 22
alphaM/beta2 Integrin/LRP/tPA 0.038 0.015 -10000 0 -10000 0 0
IL6 -0.03 0.03 0.15 4 -10000 0 4
ITGB2 -0.018 0.003 0 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.04 0.01 -10000 0 0 10 10
alphaM/beta2 Integrin/JAM2/JAM3 0.037 0.015 -10000 0 -10000 0 0
JAM2 -0.018 0.003 0 5 -10000 0 5
alphaM/beta2 Integrin/ICAM1 0.042 0.019 -10000 0 -0.008 2 2
alphaM/beta2 Integrin/uPA/Plg 0.04 0.012 -10000 0 0 13 13
RhoA/GTP -0.011 0.04 -10000 0 -0.16 10 10
positive regulation of phagocytosis -0.009 0.037 0.098 2 -0.13 2 4
Ron/MSP 0.022 0.009 -10000 0 0 23 23
alphaM/beta2 Integrin/uPAR/uPA 0.041 0.01 -10000 0 0 10 10
alphaM/beta2 Integrin/uPAR 0.033 0.008 -10000 0 0 9 9
PLAU -0.018 0.002 0 2 -10000 0 2
PLAT -0.017 0.005 0 14 -10000 0 14
actin filament polymerization -0.007 0.055 0.15 1 -0.19 8 9
MST1 -0.016 0.006 0 23 -10000 0 23
alphaM/beta2 Integrin/lipoprotein(a) 0.034 0.015 -10000 0 -10000 0 0
TNF -0.034 0.018 0.15 1 -10000 0 1
RAP1B -0.018 0.004 0 7 -10000 0 7
alphaM/beta2 Integrin/uPA 0.033 0.008 -10000 0 0 9 9
fibrinolysis 0.039 0.011 -10000 0 0 13 13
HCK -0.016 0.006 0 21 -10000 0 21
dendritic cell antigen processing and presentation 0.009 0.039 -10000 0 -0.17 2 2
VTN -0.018 0.002 0 2 -10000 0 2
alphaM/beta2 Integrin/CYR61 0.032 0.009 -10000 0 0 11 11
LPA -0.016 0.006 0 21 -10000 0 21
LRP1 -0.018 0.002 0 2 -10000 0 2
cell migration -0.027 0.01 -10000 0 -10000 0 0
FN1 -0.018 0.004 0 8 -10000 0 8
alphaM/beta2 Integrin/Thy1 0.029 0.013 -10000 0 0 29 29
MPO -0.018 0 -10000 0 -10000 0 0
KNG1 -0.013 0.008 0 45 -10000 0 45
RAP1/GDP 0.022 0.006 -10000 0 0 11 11
ROCK1 -0.007 0.055 0.15 1 -0.16 12 13
ELA2 -0.018 0.003 0 5 -10000 0 5
PLG -0.018 0.003 0 5 -10000 0 5
CTGF -0.018 0.003 0 6 -10000 0 6
alphaM/beta2 Integrin/Hck 0.029 0.013 -10000 0 0 26 26
ITGAM -0.018 0.002 0 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.04 0.012 -10000 0 0 13 13
HP -0.018 0.004 0 8 -10000 0 8
leukocyte adhesion -0.03 0.014 -10000 0 -10000 0 0
SELP -0.018 0.003 0 5 -10000 0 5
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.018 0.008 0 28 -10000 0 28
BAD/BCL-XL/YWHAZ -0.022 0.014 0 44 -10000 0 44
CDKN1B -0.008 0.065 0.17 5 -0.27 7 12
CDKN1A -0.012 0.058 0.17 1 -0.27 7 8
FRAP1 -0.018 0.004 0 7 -10000 0 7
PRKDC -0.016 0.006 0 21 -10000 0 21
FOXO3 -0.008 0.056 -10000 0 -0.26 7 7
AKT1 -0.013 0.055 -10000 0 -0.28 7 7
BAD -0.018 0.004 0 7 -10000 0 7
AKT3 -0.004 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.008 0.056 -10000 0 -0.26 7 7
AKT1/ASK1 0.009 0.064 -10000 0 -0.26 7 7
BAD/YWHAZ 0.028 0.013 -10000 0 0 30 30
RICTOR -0.016 0.006 0 19 -10000 0 19
RAF1 -0.016 0.006 0 18 -10000 0 18
JNK cascade -0.009 0.062 0.25 7 -10000 0 7
TSC1 -0.014 0.056 -10000 0 -0.27 7 7
YWHAZ -0.016 0.006 0 21 -10000 0 21
AKT1/RAF1 0.007 0.068 0.18 1 -0.26 8 9
EP300 -0.018 0.002 0 2 -10000 0 2
mol:GDP -0.011 0.056 -10000 0 -0.27 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.013 0.056 -10000 0 -0.27 7 7
YWHAQ -0.018 0.002 0 2 -10000 0 2
TBC1D4 -0.011 0.003 0 12 -10000 0 12
MAP3K5 -0.018 0.003 0 6 -10000 0 6
MAPKAP1 -0.018 0.002 0 2 -10000 0 2
negative regulation of cell cycle -0.008 0.057 0.2 5 -0.15 5 10
YWHAH -0.018 0.002 0 2 -10000 0 2
AKT1S1 -0.012 0.058 0.17 1 -0.27 7 8
CASP9 -0.013 0.056 -10000 0 -0.27 7 7
YWHAB -0.017 0.005 0 12 -10000 0 12
p27Kip1/KPNA1 0.006 0.07 0.18 11 -0.25 4 15
GBL -0.018 0.002 0 3 -10000 0 3
PDK1/Src/Hsp90 0.021 0.007 -10000 0 0 16 16
YWHAE -0.018 0.002 0 2 -10000 0 2
SRC -0.017 0.005 0 14 -10000 0 14
AKT2/p21CIP1 -0.009 0.055 0.17 2 -0.22 8 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL -0.001 0.081 -10000 0 -0.36 7 7
CHUK -0.012 0.053 -10000 0 -0.27 6 6
BAD/BCL-XL -0.015 0.057 0.13 2 -0.26 6 8
mTORC2 0.037 0.016 -10000 0 0 27 27
AKT2 -0.004 0.001 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.009 0.073 0.15 6 -0.22 10 16
PDPK1 -0.018 0.002 0 3 -10000 0 3
MDM2 -0.009 0.063 0.17 4 -0.27 7 11
MAPKKK cascade -0.007 0.067 0.26 8 -0.18 1 9
MDM2/Cbp/p300 -0.003 0.081 0.18 9 -0.25 8 17
TSC1/TSC2 -0.017 0.058 0.21 1 -0.27 7 8
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.077 0.17 9 -0.24 8 17
glucose import -0.014 0.023 0.19 2 -10000 0 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 -0.008 0.062 -10000 0 -0.19 14 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.017 0.005 0 13 -10000 0 13
GSK3A -0.012 0.058 0.17 1 -0.27 7 8
FOXO1 -0.008 0.056 -10000 0 -0.26 7 7
GSK3B 0.004 0.058 0.17 10 -0.26 3 13
SFN -0.018 0.003 0 4 -10000 0 4
G1/S transition of mitotic cell cycle 0.007 0.067 0.17 15 -0.26 3 18
p27Kip1/14-3-3 family 0.003 0.048 0.12 1 -0.23 5 6
PRKACA -0.018 0.003 0 4 -10000 0 4
KPNA1 -0.016 0.006 0 21 -10000 0 21
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG -0.018 0.003 0 5 -10000 0 5
RHEB -0.018 0.004 0 8 -10000 0 8
CREBBP -0.018 0.002 0 3 -10000 0 3
Reelin signaling pathway

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
CDK5R1/CDK5 0.024 0.005 -10000 0 0 8 8
VLDLR -0.016 0.006 0 19 -10000 0 19
CRKL -0.018 0.004 0 7 -10000 0 7
LRPAP1 -0.017 0.005 0 15 -10000 0 15
FYN -0.018 0.003 0 6 -10000 0 6
ITGA3 -0.018 0 -10000 0 -10000 0 0
RELN/VLDLR/Fyn 0.028 0.014 -10000 0 0 32 32
MAPK8IP1/MKK7/MAP3K11/JNK1 0.042 0.02 -10000 0 -0.008 4 4
AKT1 -0.01 0.014 -10000 0 -0.091 4 4
MAP2K7 -0.018 0.002 0 3 -10000 0 3
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
DAB1 -0.018 0.003 0 4 -10000 0 4
RELN/LRP8/DAB1 0.029 0.01 -10000 0 0 17 17
LRPAP1/LRP8 0.023 0.007 -10000 0 0 16 16
RELN/LRP8/DAB1/Fyn 0.035 0.013 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin -0.036 0.017 -10000 0 -10000 0 0
long-term memory -0.033 0.015 -10000 0 -10000 0 0
DAB1/LIS1 0.036 0.024 -10000 0 -10000 0 0
DAB1/CRLK/C3G -0.035 0.018 -10000 0 -10000 0 0
PIK3CA -0.013 0.008 0 49 -10000 0 49
DAB1/NCK2 0.037 0.024 -10000 0 -10000 0 0
ARHGEF2 -0.018 0.004 0 7 -10000 0 7
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.018 0.003 0 4 -10000 0 4
CDK5R1 -0.018 0.001 0 1 -10000 0 1
RELN -0.017 0.005 0 13 -10000 0 13
PIK3R1 -0.018 0.004 0 8 -10000 0 8
RELN/LRP8/Fyn 0.03 0.011 -10000 0 0 20 20
GRIN2A/RELN/LRP8/DAB1/Fyn 0.043 0.019 -10000 0 -10000 0 0
MAPK8 -0.018 0.002 0 3 -10000 0 3
RELN/VLDLR/DAB1 0.027 0.013 -10000 0 0 31 31
ITGB1 -0.018 0.003 0 5 -10000 0 5
MAP1B -0.021 0.027 0.14 4 -10000 0 4
RELN/LRP8 0.029 0.013 -10000 0 0 26 26
GRIN2B/RELN/LRP8/DAB1/Fyn 0.041 0.02 -10000 0 -10000 0 0
PI3K 0.017 0.012 -10000 0 0 53 53
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.024 0.004 -10000 0 0 5 5
RAP1A -0.017 0.068 0.19 5 -10000 0 5
PAFAH1B1 -0.018 0.002 0 2 -10000 0 2
MAPK8IP1 -0.018 0.004 0 7 -10000 0 7
CRLK/C3G 0.024 0.006 -10000 0 0 9 9
GRIN2B -0.017 0.004 0 10 -10000 0 10
NCK2 -0.018 0.002 0 3 -10000 0 3
neuron differentiation 0 0.028 0.065 14 -0.1 6 20
neuron adhesion -0.025 0.069 0.21 3 -10000 0 3
LRP8 -0.018 0.002 0 3 -10000 0 3
GSK3B -0.013 0.016 -10000 0 -0.093 4 4
RELN/VLDLR/DAB1/Fyn 0.032 0.016 -10000 0 -10000 0 0
MAP3K11 -0.017 0.005 0 11 -10000 0 11
RELN/VLDLR/DAB1/P13K -0.004 0.003 -10000 0 -10000 0 0
CDK5 -0.018 0.004 0 8 -10000 0 8
MAPT -0.008 0.007 -10000 0 -10000 0 0
neuron migration -0.01 0.039 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0 0.028 0.065 14 -0.1 6 20
RELN/VLDLR 0.034 0.018 -10000 0 0 38 38
Ephrin B reverse signaling

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
EFNB2 -0.018 0.002 0 3 -10000 0 3
EPHB2 -0.007 0.018 0.032 4 -10000 0 4
EFNB1 -0.021 0.008 0.02 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.016 0.034 0.057 7 -10000 0 7
Ephrin B2/EPHB1-2 0.027 0.013 0.058 3 0 30 33
neuron projection morphogenesis -0.026 0.022 0.038 9 -10000 0 9
Ephrin B1/EPHB1-2/Tiam1 -0.022 0.026 0.044 16 -10000 0 16
DNM1 -0.008 0.018 0.024 7 -10000 0 7
cell-cell signaling 0 0.003 0.016 5 -10000 0 5
MAP2K4 -0.016 0.057 -10000 0 -0.37 4 4
YES1 -0.004 0.083 -10000 0 -0.62 3 3
Ephrin B1/EPHB1-2/NCK2 -0.022 0.026 0.044 16 -10000 0 16
PI3K 0.01 0.063 -10000 0 -0.38 4 4
mol:GDP -0.022 0.026 0.042 16 -10000 0 16
ITGA2B -0.018 0.001 0 1 -10000 0 1
endothelial cell proliferation 0.02 0.007 -10000 0 0 17 17
FYN -0.006 0.085 -10000 0 -0.62 3 3
MAP3K7 -0.011 0.055 -10000 0 -0.41 3 3
FGR -0.004 0.092 -10000 0 -0.59 4 4
TIAM1 -0.018 0.003 0 4 -10000 0 4
PIK3R1 -0.018 0.004 0 8 -10000 0 8
RGS3 -0.018 0.001 0 1 -10000 0 1
cell adhesion -0.019 0.057 -10000 0 -0.36 4 4
LYN -0.007 0.092 -10000 0 -0.58 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.082 -10000 0 -0.52 4 4
Ephrin B1/EPHB1-2 -0.004 0.051 -10000 0 -0.47 2 2
SRC -0.004 0.092 -10000 0 -0.59 4 4
ITGB3 -0.018 0 -10000 0 -10000 0 0
EPHB1 -0.011 0.014 0.021 16 -10000 0 16
EPHB4 -0.017 0.005 0 14 -10000 0 14
RAC1 -0.017 0.004 0 10 -10000 0 10
Ephrin B2/EPHB4 0.021 0.007 -10000 0 0 17 17
alphaIIb/beta3 Integrin 0.025 0.002 -10000 0 0 1 1
BLK -0.005 0.093 -10000 0 -0.6 4 4
HCK -0.005 0.092 -10000 0 -0.59 4 4
regulation of stress fiber formation 0.022 0.026 -10000 0 -0.043 16 16
MAPK8 -0.019 0.057 0.17 1 -0.36 4 5
Ephrin B1/EPHB1-2/RGS3 -0.022 0.027 0.044 17 -10000 0 17
endothelial cell migration 0 0.051 0.18 9 -0.35 1 10
NCK2 -0.018 0.002 0 3 -10000 0 3
PTPN13 0.016 0.008 -10000 0 -0.001 25 25
regulation of focal adhesion formation 0.022 0.026 -10000 0 -0.043 16 16
chemotaxis 0.022 0.026 -10000 0 -0.042 17 17
PIK3CA -0.013 0.008 0 49 -10000 0 49
Rac1/GTP -0.024 0.027 0.042 15 -10000 0 15
angiogenesis -0.007 0.059 -10000 0 -0.44 3 3
LCK -0.004 0.092 -10000 0 -0.59 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 -0.016 0.006 0 24 -10000 0 24
NFATC1 -0.012 0.069 0.17 2 -0.2 12 14
NFATC2 -0.004 0.051 0.098 4 -0.18 7 11
NFATC3 0.005 0.002 -10000 0 -10000 0 0
YWHAE -0.018 0.002 0 2 -10000 0 2
Calcineurin A alpha-beta B1/CABIN1 -0.012 0.054 0.16 4 -0.17 8 12
Exportin 1/Ran/NUP214 0.033 0.007 -10000 0 0 7 7
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.009 0.049 0.14 3 -0.12 16 19
BCL2/BAX 0.022 0.009 -10000 0 0 24 24
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.004 -10000 0 0 14 14
CaM/Ca2+ 0.012 0.004 -10000 0 0 14 14
BAX -0.018 0.002 0 2 -10000 0 2
MAPK14 -0.018 0.004 0 8 -10000 0 8
BAD -0.018 0.004 0 7 -10000 0 7
CABIN1/MEF2D -0.001 0.053 0.15 4 -0.17 7 11
Calcineurin A alpha-beta B1/BCL2 -0.016 0.006 0 22 -10000 0 22
FKBP8 -0.018 0.001 0 1 -10000 0 1
activation-induced cell death of T cells 0.001 0.052 0.17 7 -0.15 4 11
KPNB1 -0.018 0 -10000 0 -10000 0 0
KPNA2 -0.018 0.001 0 1 -10000 0 1
XPO1 -0.018 0.003 0 4 -10000 0 4
SFN -0.018 0.003 0 4 -10000 0 4
MAP3K8 -0.018 0.003 0 5 -10000 0 5
NFAT4/CK1 alpha -0.026 0.01 0 16 -0.058 5 21
MEF2D/NFAT1/Cbp/p300 0.021 0.054 -10000 0 -0.15 8 8
CABIN1 -0.011 0.053 0.16 4 -0.18 7 11
CALM1 -0.017 0.005 0 14 -10000 0 14
RAN -0.018 0.001 0 1 -10000 0 1
MAP3K1 -0.017 0.004 0 9 -10000 0 9
CAMK4 -0.018 0.003 0 6 -10000 0 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 -0.018 0.003 0 4 -10000 0 4
YWHAH -0.018 0.002 0 2 -10000 0 2
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.007 -10000 0 0 12 12
YWHAB -0.017 0.005 0 12 -10000 0 12
MAPK8 -0.018 0.002 0 3 -10000 0 3
MAPK9 -0.018 0.004 0 8 -10000 0 8
YWHAG -0.018 0.003 0 5 -10000 0 5
FKBP1A -0.017 0.005 0 12 -10000 0 12
NFAT1-c-4/YWHAQ -0.024 0.071 0.18 1 -0.19 15 16
PRKCH -0.018 0.004 0 7 -10000 0 7
CABIN1/Cbp/p300 0.024 0.004 -10000 0 0 5 5
CASP3 -0.017 0.004 0 9 -10000 0 9
PIM1 -0.018 0.004 0 8 -10000 0 8
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.003 -10000 0 0 12 12
apoptosis -0.009 0.01 -10000 0 -0.12 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.029 -10000 0 -0.17 2 2
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE -0.018 0.002 0 3 -10000 0 3
JNK2/NFAT4 0.007 0.038 0.089 2 -0.14 9 11
BAD/BCL-XL 0.021 0.009 -10000 0 0 28 28
PRKCD -0.016 0.006 0 24 -10000 0 24
NUP214 -0.018 0.002 0 2 -10000 0 2
PRKCZ -0.018 0.003 0 5 -10000 0 5
PRKCA -0.018 0.001 0 1 -10000 0 1
PRKCG -0.018 0.001 0 1 -10000 0 1
PRKCQ -0.018 0.003 0 4 -10000 0 4
FKBP38/BCL2 0.022 0.009 -10000 0 0 23 23
EP300 -0.018 0.002 0 2 -10000 0 2
PRKCB1 -0.018 0.003 0 4 -10000 0 4
CSNK2A1 -0.017 0.005 0 13 -10000 0 13
NFATc/JNK1 -0.007 0.073 0.17 2 -0.2 13 15
CaM/Ca2+/FKBP38 0.021 0.006 -10000 0 0 14 14
FKBP12/FK506 0.012 0.003 -10000 0 0 12 12
CSNK1A1 -0.016 0.005 0 17 -10000 0 17
CaM/Ca2+/CAMK IV 0.021 0.007 -10000 0 0 18 18
NFATc/ERK1 -0.007 0.073 0.17 2 -0.2 13 15
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.007 0.049 0.13 1 -0.12 18 19
NR4A1 -0.017 0.05 0.14 5 -0.19 4 9
GSK3B -0.016 0.006 0 20 -10000 0 20
positive T cell selection 0.005 0.002 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.007 0.036 0.048 20 -0.14 5 25
RCH1/ KPNB1 0.025 0.002 -10000 0 0 1 1
YWHAQ -0.018 0.002 0 2 -10000 0 2
PRKACA -0.018 0.003 0 4 -10000 0 4
AKAP5 -0.017 0.004 0 9 -10000 0 9
MEF2D -0.018 0.004 0 7 -10000 0 7
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.016 0.006 0 21 -10000 0 21
NFATc/p38 alpha -0.007 0.071 0.2 1 -0.2 13 14
CREBBP -0.018 0.002 0 3 -10000 0 3
BCL2 -0.016 0.006 0 22 -10000 0 22
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 -0.012 0.009 0 53 -10000 0 53
Syndecan-3/Src/Cortactin 0.018 0.04 -9999 0 -0.29 2 2
Syndecan-3/Neurocan -0.007 0.041 -9999 0 -0.38 2 2
POMC -0.018 0.002 0 2 -10000 0 2
EGFR -0.016 0.006 0 20 -10000 0 20
Syndecan-3/EGFR 0.008 0.045 -9999 0 -0.38 2 2
AGRP -0.017 0.004 0 9 -10000 0 9
NCSTN -0.018 0.004 0 7 -10000 0 7
PSENEN -0.018 0.002 0 3 -10000 0 3
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.018 0.002 0 3 -10000 0 3
APH1A -0.018 0.004 0 7 -10000 0 7
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.012 0.045 -9999 0 -0.37 2 2
Syndecan-3/IL8 0.01 0.045 -9999 0 -0.38 2 2
PSEN1 -0.018 0.004 0 7 -10000 0 7
Src/Cortactin 0.016 0.012 -9999 0 0 61 61
FYN -0.018 0.003 0 6 -10000 0 6
limb bud formation -0.008 0.043 -9999 0 -0.39 2 2
MC4R -0.016 0.006 0 21 -10000 0 21
SRC -0.017 0.005 0 14 -10000 0 14
PTN -0.018 0.004 0 7 -10000 0 7
FGFR/FGF/Syndecan-3 -0.008 0.043 -9999 0 -0.4 2 2
neuron projection morphogenesis -0.016 0.033 -9999 0 -0.28 2 2
Syndecan-3/AgRP 0.009 0.045 -9999 0 -0.38 2 2
Syndecan-3/AgRP/MC4R 0.019 0.046 -9999 0 -0.37 2 2
Fyn/Cortactin 0.017 0.012 -9999 0 0 57 57
SDC3 -0.008 0.043 -9999 0 -0.4 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.01 0.044 -9999 0 -0.38 2 2
IL8 -0.018 0.003 0 6 -10000 0 6
Syndecan-3/Fyn/Cortactin 0.013 0.046 -9999 0 -0.38 2 2
Syndecan-3/CASK -0.007 0.041 -9999 0 -0.38 2 2
alpha-MSH/MC4R 0.022 0.009 -9999 0 0 23 23
Gamma Secretase 0.045 0.017 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.024 0.004 -10000 0 0 5 5
AKT1 0.004 0.063 0.17 11 -0.19 2 13
PTK2B -0.026 0.03 0.15 4 -10000 0 4
VEGFR2 homodimer/Frs2 -0.024 0.008 0 16 -10000 0 16
CAV1 -0.018 0.004 0 7 -10000 0 7
CALM1 -0.017 0.005 0 14 -10000 0 14
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.021 0.007 0 16 -10000 0 16
endothelial cell proliferation -0.001 0.078 0.2 9 -0.19 7 16
mol:Ca2+ -0.02 0.03 0.16 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.024 0.01 0 23 -10000 0 23
RP11-342D11.1 -0.019 0.006 0 15 -10000 0 15
CDH5 -0.017 0.004 0 9 -10000 0 9
VEGFA homodimer 0.027 0.012 -10000 0 0 29 29
SHC1 -0.018 0.004 0 7 -10000 0 7
SHC2 -0.018 0.003 0 5 -10000 0 5
HRAS/GDP -0.038 0.013 -10000 0 -10000 0 0
SH2D2A -0.018 0.004 0 7 -10000 0 7
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.073 0.12 4 -0.29 8 12
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.021 0.007 0 16 -10000 0 16
VEGFR1 homodimer -0.018 0.004 0 7 -10000 0 7
SHC/GRB2/SOS1 -0.035 0.011 -10000 0 -10000 0 0
GRB10 -0.02 0.03 0.16 4 -10000 0 4
PTPN11 -0.018 0.001 0 1 -10000 0 1
GRB2 -0.018 0.001 0 1 -10000 0 1
PAK1 -0.017 0.005 0 15 -10000 0 15
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.026 0.014 -10000 0 -10000 0 0
HRAS -0.018 0.003 0 5 -10000 0 5
VEGF/Rho/ROCK1/Integrin Complex -0.017 0.04 -10000 0 -0.12 19 19
HIF1A -0.018 0.004 0 7 -10000 0 7
FRS2 -0.018 0.003 0 6 -10000 0 6
oxygen and reactive oxygen species metabolic process -0.024 0.01 0 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.018 0.004 0 8 -10000 0 8
Nck/Pak 0.02 0.01 -10000 0 0 32 32
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.021 0.007 0 17 -10000 0 17
mol:GDP -0.034 0.011 -10000 0 -10000 0 0
mol:NADP -0.011 0.078 0.19 4 -0.28 8 12
eNOS/Hsp90 -0.01 0.074 0.18 4 -0.26 8 12
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:IP3 -0.02 0.03 0.16 4 -10000 0 4
HIF1A/ARNT 0.023 0.007 -10000 0 0 12 12
SHB -0.017 0.005 0 13 -10000 0 13
VEGFA 0 0 -10000 0 -10000 0 0
VEGFC -0.018 0.003 0 5 -10000 0 5
FAK1/Vinculin -0.009 0.05 0.13 9 -0.15 3 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA -0.016 0.006 0 23 -10000 0 23
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.026 0.008 0 15 -10000 0 15
PTPN6 -0.017 0.005 0 12 -10000 0 12
EPAS1 -0.018 0.002 0 3 -10000 0 3
mol:L-citrulline -0.011 0.078 0.19 4 -0.28 8 12
ITGAV -0.018 0.003 0 5 -10000 0 5
PIK3CA -0.013 0.008 0 49 -10000 0 49
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.026 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer -0.021 0.007 0 15 -10000 0 15
VEGFR2/3 heterodimer -0.024 0.008 0 16 -10000 0 16
VEGFB -0.018 0.004 0 7 -10000 0 7
MAPK11 -0.009 0.043 0.22 5 -10000 0 5
VEGFR2 homodimer -0.021 0.006 0 11 -10000 0 11
FLT1 -0.018 0.004 0 7 -10000 0 7
NEDD4 -0.018 0.003 0 4 -10000 0 4
MAPK3 -0.014 0.049 0.16 10 -10000 0 10
MAPK1 -0.012 0.051 0.17 10 -10000 0 10
VEGFA145/NRP2 0.012 0.002 -10000 0 0 4 4
VEGFR1/2 heterodimer -0.024 0.008 0 16 -10000 0 16
KDR -0.021 0.006 0 11 -10000 0 11
VEGFA165/NRP1/VEGFR2 homodimer -0.024 0.008 0 18 -10000 0 18
SRC -0.017 0.005 0 14 -10000 0 14
platelet activating factor biosynthetic process -0.013 0.052 0.17 10 -10000 0 10
PI3K -0.019 0.031 0.09 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.018 0.009 0 33 -10000 0 33
FES -0.021 0.03 0.16 4 -10000 0 4
GAB1 -0.025 0.026 0.13 2 -0.14 4 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.02 0.008 0 24 -10000 0 24
CTNNB1 -0.015 0.007 0 28 -10000 0 28
SOS1 -0.018 0.002 0 3 -10000 0 3
ARNT -0.018 0.003 0 6 -10000 0 6
eNOS/Caveolin-1 -0.013 0.075 0.19 3 -0.26 8 11
VEGFR2 homodimer/VEGFA homodimer/Yes -0.02 0.008 0 25 -10000 0 25
PI3K/GAB1 -0.02 0.041 0.18 1 -0.19 5 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.025 0.014 -10000 0 -10000 0 0
PRKACA -0.018 0.003 0 4 -10000 0 4
VEGFR2/3 heterodimer/VEGFC homodimer -0.027 0.01 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 -0.021 0.03 0.16 4 -10000 0 4
actin cytoskeleton reorganization -0.021 0.007 0 16 -10000 0 16
PTK2 -0.011 0.027 0.14 3 -10000 0 3
EDG1 -0.021 0.03 0.16 4 -10000 0 4
mol:DAG -0.02 0.03 0.16 4 -10000 0 4
CaM/Ca2+ -0.022 0.03 0.15 4 -10000 0 4
MAP2K3 -0.022 0.02 0.15 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.017 0.041 0.18 7 -10000 0 7
PLCG1 -0.02 0.03 0.16 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.022 0.011 0 34 -10000 0 34
IQGAP1 -0.018 0.003 0 4 -10000 0 4
YES1 -0.017 0.006 0 17 -10000 0 17
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.021 0.006 0 11 -10000 0 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.02 0.008 0 22 -10000 0 22
cell migration -0.007 0.052 0.14 9 -0.15 2 11
mol:PI-3-4-5-P3 -0.018 0.03 0.088 8 -10000 0 8
FYN -0.018 0.003 0 6 -10000 0 6
VEGFB/NRP1 -0.019 0.029 0.16 4 -10000 0 4
mol:NO -0.011 0.078 0.19 4 -0.28 8 12
PXN -0.018 0.001 0 1 -10000 0 1
HRAS/GTP -0.037 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.024 0.01 0 23 -10000 0 23
VHL -0.016 0.006 0 19 -10000 0 19
ITGB3 -0.018 0 -10000 0 -10000 0 0
NOS3 -0.012 0.085 0.2 4 -0.31 8 12
VEGFR2 homodimer/VEGFA homodimer/Sck -0.021 0.007 0 16 -10000 0 16
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCA -0.026 0.026 0.15 3 -10000 0 3
PRKCB -0.019 0.029 0.16 4 -10000 0 4
VCL -0.018 0.002 0 2 -10000 0 2
VEGFA165/NRP1 -0.019 0.006 0 15 -10000 0 15
VEGFR1/2 heterodimer/VEGFA homodimer -0.021 0.007 0 16 -10000 0 16
VEGFA165/NRP2 0.012 0.002 -10000 0 0 4 4
MAPKKK cascade -0.037 0.03 0.13 4 -10000 0 4
NRP2 -0.018 0.003 0 4 -10000 0 4
VEGFC homodimer -0.018 0.003 0 5 -10000 0 5
NCK1 -0.015 0.007 0 27 -10000 0 27
ROCK1 -0.018 0.004 0 7 -10000 0 7
FAK1/Paxillin -0.009 0.05 0.13 9 -0.15 3 12
MAP3K13 -0.02 0.013 -10000 0 -10000 0 0
PDPK1 -0.019 0.035 0.16 2 -10000 0 2
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.018 0.001 0 1 -10000 0 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.006 0.061 0.21 11 -0.13 2 13
IL27/IL27R/JAK1 0.033 0.028 0.19 3 -0.084 1 4
TBX21 -0.02 0.04 0.13 6 -10000 0 6
IL12B -0.018 0.003 0 6 -10000 0 6
IL12A -0.009 0.005 0 39 -10000 0 39
IL6ST -0.012 0.014 0.021 23 -10000 0 23
IL27RA/JAK1 -0.007 0.032 0.19 3 -0.15 1 4
IL27 -0.013 0.014 0.021 24 -10000 0 24
TYK2 -0.013 0.014 0.02 25 -10000 0 25
T-helper cell lineage commitment 0.001 0.033 0.18 5 -0.1 2 7
T-helper 2 cell differentiation 0.006 0.061 0.21 11 -0.13 2 13
T cell proliferation during immune response 0.006 0.061 0.21 11 -0.13 2 13
MAPKKK cascade -0.006 0.061 0.13 2 -0.21 11 13
STAT3 -0.018 0.002 0 3 -10000 0 3
STAT2 -0.018 0.001 0 1 -10000 0 1
STAT1 -0.018 0.004 0 7 -10000 0 7
IL12RB1 -0.018 0.002 0 2 -10000 0 2
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.02 0.04 0.13 6 -10000 0 6
IL27/IL27R/JAK2/TYK2 -0.006 0.061 0.13 2 -0.22 11 13
positive regulation of T cell mediated cytotoxicity -0.006 0.061 0.13 2 -0.21 11 13
STAT1 (dimer) 0.031 0.033 0.17 2 -0.08 8 10
JAK2 -0.014 0.01 0.021 7 -10000 0 7
JAK1 -0.018 0.002 0 3 -10000 0 3
STAT2 (dimer) 0.001 0.069 0.15 3 -0.22 12 15
T cell proliferation -0.014 0.054 0.12 2 -0.22 9 11
IL12/IL12R/TYK2/JAK2 -0.016 0.15 -10000 0 -0.7 7 7
IL17A 0.002 0.031 0.18 5 -10000 0 5
mast cell activation 0.006 0.061 0.21 11 -0.13 2 13
IFNG 0.002 0.019 0.053 1 -0.07 7 8
T cell differentiation -0.001 0.001 -10000 0 -0.008 6 6
STAT3 (dimer) 0.001 0.069 0.15 3 -0.22 12 15
STAT5A (dimer) 0.001 0.069 0.15 3 -0.22 12 15
STAT4 (dimer) 0.003 0.066 0.15 3 -0.21 11 14
STAT4 -0.018 0.004 0 7 -10000 0 7
T cell activation -0.001 0.001 -10000 0 -0.008 6 6
IL27R/JAK2/TYK2 0.024 0.023 0.19 2 -0.081 1 3
GATA3 -0.011 0.048 0.58 1 -10000 0 1
IL18 -0.009 0.004 0 26 -10000 0 26
positive regulation of mast cell cytokine production 0.001 0.068 0.15 3 -0.21 12 15
IL27/EBI3 0.024 0.007 0.041 5 0 8 13
IL27RA 0.001 0.036 0.24 3 -0.16 1 4
IL6 -0.018 0.004 0 8 -10000 0 8
STAT5A -0.018 0.002 0 3 -10000 0 3
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.006 0.025 0.3 1 -10000 0 1
IL1B -0.011 0.001 0 1 -10000 0 1
EBI3 -0.012 0.015 0.019 29 -10000 0 29
TNF -0.011 0.002 0 8 -10000 0 8
LPA receptor mediated events

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
GNB1/GNG2 0.016 0.016 -10000 0 -0.022 21 21
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.029 0.09 4 -0.12 1 5
AP1 -0.01 0.007 0.006 22 -10000 0 22
mol:PIP3 -0.016 0.011 -10000 0 -10000 0 0
AKT1 -0.018 0.074 0.14 18 -0.18 13 31
PTK2B -0.009 0.042 0.068 4 -0.18 9 13
RHOA -0.037 0.09 -10000 0 -0.28 19 19
PIK3CB -0.012 0.011 0.006 40 -10000 0 40
mol:Ca2+ -0.007 0.036 0.17 6 -10000 0 6
MAGI3 -0.017 0.004 0 8 -10000 0 8
RELA -0.017 0.005 0 11 -10000 0 11
apoptosis 0.003 0.004 -10000 0 -0.008 4 4
HRAS/GDP 0.012 0.002 -10000 0 0 5 5
positive regulation of microtubule depolymerization 0 0.066 0.16 18 -0.16 7 25
NF kappa B1 p50/RelA -0.026 0.017 0.025 1 -0.081 4 5
endothelial cell migration -0.007 0.004 0.003 19 -0.015 1 20
ADCY4 -0.007 0.009 0.1 1 -10000 0 1
ADCY5 -0.007 0.009 0.1 1 -10000 0 1
ADCY6 -0.008 0.009 0.1 1 -10000 0 1
ADCY7 -0.008 0.004 -10000 0 -10000 0 0
ADCY1 -0.007 0.009 0.1 1 -10000 0 1
ADCY2 -0.007 0.013 0.1 1 -0.11 1 2
ADCY3 -0.008 0.009 0.1 1 -10000 0 1
ADCY8 -0.006 0.01 0.1 1 -10000 0 1
ADCY9 -0.008 0.009 0.1 1 -10000 0 1
GSK3B 0.007 0.07 0.18 18 -0.17 7 25
arachidonic acid secretion -0.01 0.015 0.058 6 -10000 0 6
GNG2 -0.015 0.01 0.012 20 -10000 0 20
TRIP6 0.006 0.003 -10000 0 0 26 26
GNAO1 -0.007 0.004 0.003 19 -0.015 1 20
HRAS -0.018 0.003 0 5 -10000 0 5
NFKBIA -0.006 0.042 0.15 7 -0.12 1 8
GAB1 -0.018 0.004 0 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.004 0.14 -10000 0 -0.77 5 5
JUN -0.018 0.003 0 4 -10000 0 4
LPA/LPA2/NHERF2 0.011 0.004 -10000 0 -0.011 5 5
TIAM1 -0.008 0.16 -10000 0 -0.92 5 5
PIK3R1 -0.015 0.01 0.01 19 -10000 0 19
mol:IP3 -0.007 0.036 0.17 6 -10000 0 6
PLCB3 -0.014 0.004 0 9 -10000 0 9
FOS -0.018 0.004 0 8 -10000 0 8
positive regulation of mitosis -0.01 0.015 0.058 6 -10000 0 6
LPA/LPA1-2-3 0 0.001 0.004 1 -0.006 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 -0.018 0.004 0 7 -10000 0 7
stress fiber formation 0.006 0.028 -10000 0 -0.12 2 2
GNAZ -0.007 0.004 0.005 18 -0.015 1 19
EGFR/PI3K-beta/Gab1 -0.016 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production 0 0.001 -10000 0 -0.006 4 4
LPA/LPA2/MAGI-3 0.008 0.009 -10000 0 -0.012 22 22
ARHGEF1 -0.013 0.038 0.16 7 -10000 0 7
GNAI2 -0.007 0.003 0 23 -0.015 1 24
GNAI3 -0.007 0.004 0.005 15 -0.015 1 16
GNAI1 -0.007 0.005 0.005 17 -0.015 1 18
LPA/LPA3 0 0 -10000 0 -0.003 3 3
LPA/LPA2 0 0.001 0.002 3 -0.004 4 7
LPA/LPA1 0 0.001 -10000 0 -0.006 5 5
HB-EGF/EGFR -0.021 0.01 0 33 -10000 0 33
HBEGF -0.02 0.006 0 15 -10000 0 15
mol:DAG -0.007 0.036 0.17 6 -10000 0 6
cAMP biosynthetic process -0.005 0.031 0.12 6 -10000 0 6
NFKB1 -0.018 0.003 0 6 -10000 0 6
SRC -0.017 0.005 0 14 -10000 0 14
GNB1 -0.015 0.009 0.012 16 -10000 0 16
LYN -0.001 0.047 0.13 14 -0.12 1 15
GNAQ 0.003 0.004 -10000 0 -0.008 3 3
LPAR2 0 0 -10000 0 -0.002 2 2
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0 0.001 -10000 0 -0.004 4 4
IL8 -0.006 0.06 0.2 1 -0.29 5 6
PTK2 0.006 0.007 -10000 0 -0.01 20 20
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
CASP3 0.003 0.004 -10000 0 -0.008 4 4
EGFR -0.016 0.006 0 20 -10000 0 20
PLCG1 0.001 0.001 0.003 1 -0.003 3 4
PLD2 0.007 0.007 -10000 0 -0.01 25 25
G12/G13 0.018 0.012 -10000 0 -0.021 11 11
PI3K-beta -0.036 0.051 -10000 0 -0.19 15 15
cell migration 0.005 0.041 -10000 0 -0.23 4 4
SLC9A3R2 -0.018 0.002 0 3 -10000 0 3
PXN 0.006 0.028 -10000 0 -0.12 2 2
HRAS/GTP -0.012 0.007 -10000 0 -10000 0 0
RAC1 -0.017 0.004 0 10 -10000 0 10
MMP9 -0.017 0.005 0 11 -10000 0 11
PRKCE -0.015 0.01 0.014 16 -10000 0 16
PRKCD -0.011 0.037 0.17 6 -10000 0 6
Gi(beta/gamma) -0.005 0.02 0.077 9 -10000 0 9
mol:LPA 0 0.001 -10000 0 -0.004 5 5
TRIP6/p130 Cas/FAK1/Paxillin 0.012 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.015 0.058 6 -10000 0 6
contractile ring contraction involved in cytokinesis -0.041 0.096 0.12 1 -0.27 23 24
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.003 0.004 -10000 0 -0.007 4 4
GNA15 0.003 0.004 -10000 0 -0.007 4 4
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA13 -0.019 0.001 -10000 0 -10000 0 0
MAPT 0 0.066 0.16 18 -0.17 7 25
GNA11 0.003 0.004 -10000 0 -0.008 3 3
Rac1/GTP 0.004 0.15 -10000 0 -0.82 5 5
MMP2 -0.007 0.004 0.003 19 -0.015 1 20
IL2 signaling events mediated by STAT5

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
GAB2 -0.017 0.005 0 15 -10000 0 15
ELF1 -0.017 0.005 0 11 -10000 0 11
CCNA2 -0.018 0.004 0 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
JAK3 -0.018 0.001 0 1 -10000 0 1
PIK3R1 -0.018 0.004 0 8 -10000 0 8
JAK1 -0.018 0.002 0 3 -10000 0 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0 0.054 0.12 4 -0.22 5 9
SHC1 -0.018 0.004 0 7 -10000 0 7
SP1 -0.018 0.001 0 1 -10000 0 1
IL2RA -0.02 0.006 0 14 -10000 0 14
IL2RB -0.018 0.002 0 2 -10000 0 2
SOS1 -0.018 0.002 0 3 -10000 0 3
IL2RG -0.018 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.006 0.064 0.15 14 -0.22 5 19
PTPN11 -0.018 0.001 0 1 -10000 0 1
CCND2 -0.02 0.007 0 16 -10000 0 16
LCK -0.018 0.003 0 4 -10000 0 4
GRB2 -0.018 0.001 0 1 -10000 0 1
IL2 -0.018 0.004 0 7 -10000 0 7
CDK6 -0.017 0.004 0 10 -10000 0 10
CCND3 0 0.058 0.15 7 -0.23 4 11
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.021 0.037 0.13 8 -10000 0 8
DAPP1 0.011 0.079 0.17 11 -0.25 7 18
Src family/SYK family/BLNK-LAT/BTK-ITK 0.008 0.08 0.19 4 -0.34 5 9
mol:DAG -0.004 0.051 0.15 9 -0.14 3 12
HRAS -0.017 0.013 0.026 12 -10000 0 12
RAP1A -0.017 0.013 0.026 13 -10000 0 13
ARF5/GDP 0.004 0.045 -10000 0 -0.18 4 4
PLCG2 -0.017 0.005 0 11 -10000 0 11
PLCG1 -0.017 0.005 0 11 -10000 0 11
ARF5 -0.018 0.003 0 6 -10000 0 6
mol:GTP -0.018 0.036 0.13 8 -10000 0 8
ARF1/GTP -0.011 0.031 0.13 8 -10000 0 8
RHOA -0.016 0.006 0 23 -10000 0 23
YES1 -0.017 0.006 0 17 -10000 0 17
RAP1A/GTP -0.018 0.038 0.14 8 -10000 0 8
ADAP1 -0.019 0.031 0.12 7 -10000 0 7
ARAP3 -0.018 0.035 0.13 8 -10000 0 8
INPPL1 -0.016 0.007 0 26 -10000 0 26
PREX1 -0.017 0.005 0 11 -10000 0 11
ARHGEF6 -0.018 0 -10000 0 -10000 0 0
ARHGEF7 -0.018 0.003 0 6 -10000 0 6
ARF1 -0.018 0.003 0 5 -10000 0 5
NRAS -0.016 0.013 0.027 13 -10000 0 13
FYN -0.018 0.003 0 6 -10000 0 6
ARF6 -0.017 0.004 0 9 -10000 0 9
FGR -0.018 0.003 0 4 -10000 0 4
mol:Ca2+ -0.004 0.036 0.12 7 -10000 0 7
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.018 0.003 0 4 -10000 0 4
ZAP70 -0.018 0.003 0 6 -10000 0 6
mol:IP3 -0.007 0.045 0.15 7 -0.12 2 9
LYN -0.016 0.006 0 18 -10000 0 18
ARF1/GDP 0.003 0.045 -10000 0 -0.17 5 5
RhoA/GDP -0.016 0.041 0.14 8 -10000 0 8
PDK1/Src/Hsp90 0.021 0.007 -10000 0 0 16 16
BLNK -0.018 0.002 0 3 -10000 0 3
actin cytoskeleton reorganization -0.018 0.057 0.15 9 -0.16 6 15
SRC -0.017 0.005 0 14 -10000 0 14
PLEKHA2 -0.02 0.011 0 39 -10000 0 39
RAC1 -0.017 0.004 0 10 -10000 0 10
PTEN 0.013 0.015 -10000 0 -0.029 8 8
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.033 0.13 6 -10000 0 6
RhoA/GTP -0.02 0.037 0.14 8 -10000 0 8
Src family/SYK family/BLNK-LAT 0 0.039 -10000 0 -0.23 2 2
BLK -0.017 0.004 0 9 -10000 0 9
PDPK1 -0.018 0.002 0 3 -10000 0 3
CYTH1 -0.019 0.031 0.12 7 -10000 0 7
HCK -0.016 0.006 0 21 -10000 0 21
CYTH3 -0.019 0.031 0.12 7 -10000 0 7
CYTH2 -0.019 0.031 0.12 7 -10000 0 7
KRAS -0.018 0.01 0.025 6 -10000 0 6
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.008 0.031 0.086 7 -0.14 5 12
SGK1 -0.009 0.032 0.088 7 -0.15 5 12
INPP5D -0.018 0.004 0 8 -10000 0 8
mol:GDP -0.006 0.044 0.11 1 -0.17 5 6
SOS1 -0.018 0.002 0 3 -10000 0 3
SYK -0.018 0.001 0 1 -10000 0 1
ARF6/GDP -0.021 0.035 0.14 6 -10000 0 6
mol:PI-3-4-5-P3 -0.02 0.032 0.13 7 -10000 0 7
ARAP3/RAP1A/GTP -0.018 0.038 0.15 8 -10000 0 8
VAV1 -0.018 0.002 0 3 -10000 0 3
mol:PI-3-4-P2 -0.018 0.009 0 31 -10000 0 31
RAS family/GTP/PI3K Class I -0.022 0.025 0.17 2 -10000 0 2
PLEKHA1 -0.021 0.01 0 31 -10000 0 31
Rac1/GDP 0.004 0.043 -10000 0 -0.18 4 4
LAT -0.018 0.003 0 4 -10000 0 4
Rac1/GTP -0.001 0.037 -10000 0 -0.19 5 5
ITK -0.023 0.034 0.12 8 -10000 0 8
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.007 0.059 0.17 8 -0.18 4 12
LCK -0.018 0.003 0 4 -10000 0 4
BTK -0.024 0.034 0.12 8 -10000 0 8
Regulation of Telomerase

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
Telomerase catalytic core complex 0.006 0.06 0.12 7 -0.19 8 15
RAD9A -0.017 0.006 0 17 -10000 0 17
AP1 0.024 0.006 -10000 0 0 11 11
IFNAR2 -0.018 0.003 0 4 -10000 0 4
AKT1 0.005 0.002 -10000 0 -10000 0 0
ER alpha/Oestrogen 0.012 0.002 -10000 0 0 5 5
NFX1/SIN3/HDAC complex -0.011 0.041 -10000 0 -0.17 8 8
EGF -0.018 0.003 0 5 -10000 0 5
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.023 0.007 -10000 0 0 12 12
TERT/c-Abl 0.008 0.064 0.14 3 -0.19 11 14
SAP18 -0.018 0.004 0 7 -10000 0 7
MRN complex 0.026 0.015 -10000 0 0 39 39
WT1 -0.018 0.003 0 4 -10000 0 4
WRN -0.017 0.005 0 11 -10000 0 11
SP1 -0.018 0.001 0 1 -10000 0 1
SP3 -0.018 0.004 0 7 -10000 0 7
TERF2IP -0.018 0.004 0 7 -10000 0 7
Telomerase/Nucleolin 0.015 0.059 0.14 1 -0.18 9 10
Mad/Max 0.024 0.006 -10000 0 0 11 11
TERT 0.006 0.061 0.12 7 -0.18 9 16
CCND1 0.05 0.094 0.2 39 -0.2 3 42
MAX -0.017 0.004 0 9 -10000 0 9
RBBP7 -0.018 0 -10000 0 -10000 0 0
RBBP4 -0.018 0.003 0 4 -10000 0 4
TERF2 -0.014 0.026 0.062 17 -10000 0 17
PTGES3 -0.018 0.001 0 1 -10000 0 1
SIN3A -0.018 0.002 0 3 -10000 0 3
Telomerase/911 0.016 0.04 0.16 2 -0.2 2 4
CDKN1B -0.022 0.01 0 26 -10000 0 26
RAD1 -0.016 0.006 0 19 -10000 0 19
XRCC5 -0.018 0.004 0 8 -10000 0 8
XRCC6 -0.018 0.002 0 2 -10000 0 2
SAP30 -0.018 0.003 0 5 -10000 0 5
TRF2/PARP2 -0.016 0.027 0.063 16 -10000 0 16
UBE3A -0.018 0.003 0 5 -10000 0 5
JUN -0.018 0.003 0 4 -10000 0 4
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.002 -10000 0 0 5 5
FOS -0.018 0.004 0 8 -10000 0 8
IFN-gamma/IRF1 0.023 0.007 -10000 0 0 15 15
PARP2 -0.018 0.003 0 6 -10000 0 6
BLM -0.018 0.003 0 4 -10000 0 4
Telomerase 0.004 0.022 -10000 0 -0.14 2 2
IRF1 -0.017 0.004 0 9 -10000 0 9
ESR1 -0.018 0.003 0 5 -10000 0 5
KU/TER 0.024 0.006 -10000 0 0 10 10
ATM/TRF2 0.021 0.009 -10000 0 0 27 27
ubiquitin-dependent protein catabolic process -0.017 0.052 0.07 1 -0.22 8 9
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.017 0.053 -10000 0 -0.22 8 8
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC2 -0.018 0.003 0 6 -10000 0 6
ATM 0.007 0.007 0.064 2 -10000 0 2
SMAD3 -0.021 0.004 0 5 -10000 0 5
ABL1 -0.018 0.002 0 2 -10000 0 2
MXD1 -0.018 0.002 0 2 -10000 0 2
MRE11A -0.016 0.006 0 21 -10000 0 21
HUS1 -0.018 0.004 0 8 -10000 0 8
RPS6KB1 -0.018 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.018 0.078 0.17 2 -0.21 12 14
NR2F2 -0.018 0.003 0 4 -10000 0 4
MAPK3 -0.021 0.005 0 9 -10000 0 9
MAPK1 -0.02 0.006 0 13 -10000 0 13
TGFB1/TGF beta receptor Type II -0.018 0.001 0 1 -10000 0 1
NFKB1 -0.018 0.003 0 6 -10000 0 6
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.007 0.007 0.064 2 -10000 0 2
NBN -0.016 0.006 0 18 -10000 0 18
EGFR -0.016 0.006 0 20 -10000 0 20
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.021 0.009 -10000 0 0 25 25
MYC -0.015 0.007 0 31 -10000 0 31
IL2 -0.018 0.004 0 7 -10000 0 7
KU 0.024 0.006 -10000 0 0 10 10
RAD50 -0.017 0.004 0 9 -10000 0 9
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 -0.018 0.001 0 1 -10000 0 1
TRF2/BLM -0.016 0.027 0.063 16 -10000 0 16
FRAP1 -0.018 0.004 0 7 -10000 0 7
KU/TERT 0.019 0.063 0.16 2 -0.18 9 11
SP1/HDAC2 0.024 0.005 -10000 0 0 7 7
PINX1 -0.017 0.004 0 9 -10000 0 9
Telomerase/EST1A 0.01 0.055 0.094 1 -0.17 10 11
Smad3/Myc -0.021 0.01 0 33 -10000 0 33
911 complex 0.026 0.015 -10000 0 0 39 39
IFNG -0.018 0.003 0 6 -10000 0 6
Telomerase/PinX1 0.016 0.058 0.14 1 -0.17 9 10
Telomerase/AKT1/mTOR/p70S6K 0 0.049 -10000 0 -0.28 4 4
SIN3B -0.018 0.001 0 1 -10000 0 1
YWHAE -0.018 0.002 0 2 -10000 0 2
Telomerase/EST1B 0.01 0.055 0.094 1 -0.17 10 11
response to DNA damage stimulus -0.01 0.034 0.045 1 -0.088 24 25
MRN complex/TRF2/Rap1 0.037 0.023 -10000 0 -0.013 5 5
TRF2/WRN -0.016 0.026 0.063 15 -10000 0 15
Telomerase/hnRNP C1/C2 0.01 0.055 0.094 1 -0.17 10 11
E2F1 -0.016 0.006 0 22 -10000 0 22
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL -0.018 0.004 0 8 -10000 0 8
DKC1 -0.018 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS -0.018 0.003 0 5 -9999 0 5
EGFR -0.016 0.006 0 20 -9999 0 20
EGF/EGFR 0.026 0.014 -10000 0 0 37 37
EGF/EGFR dimer/SHC/GRB2/SOS1 0.04 0.021 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
EDNRA -0.018 0.004 0 8 -9999 0 8
response to oxidative stress 0 0 -10000 0 -9999 0 0
EGF -0.018 0.003 0 5 -9999 0 5
EGF/EGFR dimer/SHC 0.028 0.013 -10000 0 0 30 30
mol:GDP 0.037 0.019 -10000 0 -9999 0 0
mol:Ca2+ 0 0 -10000 0 -9999 0 0
EDN1 -0.017 0.005 0 12 -9999 0 12
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
HRAS/GTP -0.031 0.015 -10000 0 -9999 0 0
SHC1 -0.018 0.004 0 7 -9999 0 7
HRAS/GDP 0.035 0.019 -10000 0 -9999 0 0
FRAP1 -0.006 0.074 0.16 27 -9999 0 27
EGF/EGFR dimer 0.021 0.009 -10000 0 0 25 25
SOS1 -0.018 0.002 0 3 -9999 0 3
GRB2 -0.018 0.001 0 1 -9999 0 1
ETA receptor/Endothelin-1 0.023 0.008 -10000 0 0 17 17
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.016 0.062 -10000 0 -0.26 8 8
IL23A -0.006 0.044 0.14 6 -0.14 5 11
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.055 -10000 0 -0.19 8 8
positive regulation of T cell mediated cytotoxicity -0.011 0.065 -10000 0 -0.25 9 9
ITGA3 -0.013 0.05 0.12 1 -0.19 9 10
IL17F 0.014 0.083 0.14 38 -0.2 7 45
IL12B -0.012 0.014 0.026 2 -10000 0 2
STAT1 (dimer) 0.001 0.066 -10000 0 -0.23 10 10
CD4 -0.005 0.074 0.19 8 -0.26 7 15
IL23 -0.008 0.034 0.12 6 -0.13 2 8
IL23R 0 0.09 -10000 0 -0.65 3 3
IL1B -0.009 0.043 0.12 2 -0.16 8 10
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.01 0.07 0.17 5 -0.24 9 14
TYK2 -0.011 0.017 0.028 8 -10000 0 8
STAT4 -0.018 0.004 0 7 -10000 0 7
STAT3 -0.018 0.002 0 3 -10000 0 3
IL18RAP -0.017 0.007 0.018 6 -10000 0 6
IL12RB1 -0.011 0.017 0.026 9 -10000 0 9
PIK3CA -0.013 0.008 0 49 -10000 0 49
IL12Rbeta1/TYK2 -0.007 0.026 0.046 7 -10000 0 7
IL23R/JAK2 0.007 0.076 -10000 0 -0.54 3 3
positive regulation of chronic inflammatory response -0.011 0.065 -10000 0 -0.25 9 9
natural killer cell activation 0 0.001 0.005 2 -0.007 2 4
JAK2 -0.012 0.013 0.025 3 -10000 0 3
PIK3R1 -0.018 0.004 0 8 -10000 0 8
NFKB1 -0.011 0.015 0.019 32 -10000 0 32
RELA -0.013 0.013 0.019 21 -10000 0 21
positive regulation of dendritic cell antigen processing and presentation -0.008 0.034 0.12 6 -0.13 2 8
ALOX12B -0.015 0.061 -10000 0 -0.24 9 9
CXCL1 -0.013 0.062 0.16 1 -0.25 8 9
T cell proliferation -0.011 0.065 -10000 0 -0.25 9 9
NFKBIA -0.012 0.013 0.019 24 -10000 0 24
IL17A -0.012 0.031 0.069 1 -0.15 6 7
PI3K 0.007 0.06 -10000 0 -0.24 8 8
IFNG -0.001 0.022 0.067 3 -0.079 8 11
STAT3 (dimer) 0.012 0.061 -10000 0 -0.23 8 8
IL18R1 -0.017 0.007 0.018 6 -10000 0 6
IL23/IL23R/JAK2/TYK2/SOCS3 -0.009 0.075 0.13 1 -0.26 10 11
IL18/IL18R 0.029 0.014 -10000 0 -0.03 1 1
macrophage activation -0.002 0.002 -10000 0 -0.011 4 4
TNF -0.008 0.048 0.16 4 -0.16 8 12
STAT3/STAT4 0.009 0.067 -10000 0 -0.23 10 10
STAT4 (dimer) 0.001 0.066 -10000 0 -0.23 10 10
IL18 -0.015 0.008 0.018 4 -10000 0 4
IL19 -0.01 0.07 0.17 5 -0.26 8 13
STAT5A (dimer) 0 0.067 -10000 0 -0.23 11 11
STAT1 -0.018 0.004 0 7 -10000 0 7
SOCS3 -0.018 0.001 0 1 -10000 0 1
CXCL9 -0.014 0.061 -10000 0 -0.25 8 8
MPO -0.015 0.062 -10000 0 -0.24 9 9
positive regulation of humoral immune response -0.011 0.065 -10000 0 -0.25 9 9
IL23/IL23R/JAK2/TYK2 -0.012 0.065 -10000 0 -0.24 11 11
IL6 -0.009 0.055 0.15 4 -0.2 8 12
STAT5A -0.018 0.002 0 3 -10000 0 3
IL2 -0.015 0.01 0.02 11 -10000 0 11
positive regulation of tyrosine phosphorylation of STAT protein 0 0.001 0.005 2 -0.007 2 4
CD3E -0.012 0.06 0.2 1 -0.24 8 9
keratinocyte proliferation -0.011 0.065 -10000 0 -0.25 9 9
NOS2 -0.009 0.062 -10000 0 -0.24 9 9
Insulin Pathway

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
CBL/APS/CAP -0.024 0.019 0.049 7 -10000 0 7
TC10/GTP -0.027 0.01 0 8 -10000 0 8
Insulin Receptor/Insulin/IRS1/Shp2 0.041 0.016 0.087 5 -10000 0 5
HRAS -0.018 0.003 0 5 -10000 0 5
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.018 0.003 0 4 -10000 0 4
FOXO3 -0.006 0.005 0.006 3 -10000 0 3
AKT1 0.009 0.081 0.14 45 -10000 0 45
INSR -0.016 0.017 0.033 16 -10000 0 16
Insulin Receptor/Insulin 0.029 0.019 0.17 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 -0.018 0.004 0 8 -10000 0 8
SORBS1 -0.018 0.002 0 3 -10000 0 3
CRK -0.018 0.002 0 2 -10000 0 2
PTPN1 -0.017 0.025 0.14 4 -10000 0 4
CAV1 -0.024 0.013 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.034 0.015 -10000 0 0 27 27
Insulin Receptor/Insulin/IRS1/NCK2 0.041 0.016 0.087 5 -10000 0 5
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.019 0.07 2 -0.022 2 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.005 0.051 0.16 3 -0.32 3 6
RPS6KB1 0.003 0.076 0.12 45 -10000 0 45
PARD6A -0.017 0.004 0 9 -10000 0 9
CBL -0.016 0.006 0 24 -10000 0 24
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.005 -10000 0 -10000 0 0
PIK3R1 -0.018 0.004 0 8 -10000 0 8
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.07 0.11 39 -10000 0 39
HRAS/GTP -0.04 0.018 0.023 3 -10000 0 3
Insulin Receptor -0.016 0.017 0.033 16 -10000 0 16
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.045 0.021 0.1 3 -0.013 4 7
PRKCI 0.008 0.024 -10000 0 -0.28 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.027 0.023 0.036 4 -10000 0 4
SHC1 -0.018 0.004 0 7 -10000 0 7
negative regulation of MAPKKK cascade 0.024 0.018 -10000 0 -10000 0 0
PI3K 0.029 0.022 0.085 2 -0.011 2 4
NCK2 -0.018 0.002 0 3 -10000 0 3
RHOQ -0.018 0.003 0 4 -10000 0 4
mol:H2O2 -0.003 0.004 0.015 7 -10000 0 7
HRAS/GDP 0.012 0.002 -10000 0 0 5 5
AKT2 0.013 0.085 0.14 50 -10000 0 50
PRKCZ 0.005 0.038 -10000 0 -0.26 3 3
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.026 0.019 -10000 0 -10000 0 0
F2RL2 -0.018 0.004 0 8 -10000 0 8
TRIP10 -0.018 0.002 0 3 -10000 0 3
Insulin Receptor/Insulin/Shc 0.032 0.013 0.076 5 0 15 20
TC10/GTP/CIP4/Exocyst 0.022 0.005 -10000 0 0 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.019 0.1 3 -0.012 5 8
RAPGEF1 -0.018 0.002 0 2 -10000 0 2
RASA1 -0.018 0.004 0 8 -10000 0 8
NCK1 -0.015 0.007 0 27 -10000 0 27
CBL/APS/CAP/Crk-II 0.028 0.012 -10000 0 0 25 25
TC10/GDP 0.012 0.002 -10000 0 0 4 4
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.018 0.087 5 0 22 27
INPP5D -0.024 0.014 -10000 0 -10000 0 0
SOS1 -0.018 0.002 0 3 -10000 0 3
SGK1 -0.003 0.003 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 -0.018 0.001 0 1 -10000 0 1
IRS1 -0.018 0.004 0 8 -10000 0 8
p62DOK/RasGAP 0.024 0.018 -10000 0 -10000 0 0
INS -0.017 0.015 0.037 11 -10000 0 11
mol:PI-3-4-P2 -0.023 0.014 -10000 0 -10000 0 0
GRB2 -0.018 0.001 0 1 -10000 0 1
EIF4EBP1 -0.002 0.07 0.12 37 -10000 0 37
PTPRA -0.018 0.011 0.028 6 -10000 0 6
PIK3CA -0.013 0.008 0 49 -10000 0 49
TC10/GTP/CIP4 0.022 0.005 -10000 0 0 7 7
PDPK1 -0.018 0.002 0 3 -10000 0 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.009 0.02 0.046 3 -0.12 4 7
Insulin Receptor/Insulin/IRS1 0.032 0.013 0.076 5 0 15 20
Insulin Receptor/Insulin/IRS3 0.026 0.013 0.064 9 -0.004 11 20
Par3/Par6 0.035 0.013 -10000 0 0 21 21
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.016 0.07 0.17 10 -0.25 7 17
PDGFB-D/PDGFRB/SLAP 0.02 0.012 -10000 0 -0.025 4 4
PDGFB-D/PDGFRB/APS/CBL 0.02 0.009 -10000 0 0 26 26
AKT1 0.017 0.097 0.22 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.08 0.18 10 -0.29 7 17
PIK3CA -0.013 0.008 0 49 -10000 0 49
FGR -0.003 0.069 0.16 7 -0.51 2 9
mol:Ca2+ 0 0.086 0.18 10 -0.33 7 17
MYC 0.033 0.1 0.2 35 -0.2 6 41
SHC1 -0.018 0.004 0 7 -10000 0 7
HRAS/GDP -0.018 0.045 0.14 11 -10000 0 11
LRP1/PDGFRB/PDGFB 0.033 0.008 -10000 0 0 10 10
GRB10 -0.018 0.004 0 8 -10000 0 8
PTPN11 -0.018 0.001 0 1 -10000 0 1
GO:0007205 0 0.087 0.18 10 -0.34 7 17
PTEN -0.018 0.003 0 5 -10000 0 5
GRB2 -0.018 0.001 0 1 -10000 0 1
GRB7 -0.018 0.003 0 6 -10000 0 6
PDGFB-D/PDGFRB/SHP2 0.023 0.01 -10000 0 -0.024 6 6
PDGFB-D/PDGFRB/GRB10 0.022 0.01 -10000 0 -0.024 4 4
cell cycle arrest 0.019 0.012 -10000 0 -0.025 4 4
HRAS -0.018 0.003 0 5 -10000 0 5
HIF1A 0.008 0.086 0.2 11 -10000 0 11
GAB1 0.003 0.076 0.19 6 -0.26 8 14
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0 0.071 0.2 7 -0.23 7 14
PDGFB-D/PDGFRB 0.028 0.014 -10000 0 -0.028 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.023 0.01 -10000 0 -0.024 6 6
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.016 0.043 0.18 1 -0.2 4 5
positive regulation of MAPKKK cascade 0.023 0.01 -10000 0 -0.024 6 6
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:IP3 0 0.088 0.18 10 -0.34 7 17
E5 0 0.001 -10000 0 -10000 0 0
CSK -0.017 0.008 0.018 7 -10000 0 7
PDGFB-D/PDGFRB/GRB7 0.022 0.011 -10000 0 -0.024 5 5
SHB -0.017 0.005 0 13 -10000 0 13
BLK -0.009 0.077 0.16 5 -0.39 5 10
PTPN2 -0.016 0.009 0.021 7 -10000 0 7
PDGFB-D/PDGFRB/SNX15 0.022 0.011 -10000 0 -0.024 6 6
BCAR1 -0.018 0.004 0 7 -10000 0 7
VAV2 0.006 0.076 0.21 7 -0.25 7 14
CBL -0.016 0.006 0 24 -10000 0 24
PDGFB-D/PDGFRB/DEP1 0.023 0.011 -10000 0 -0.024 6 6
LCK -0.003 0.069 0.16 7 -0.39 3 10
PDGFRB -0.013 0.014 0.023 14 -10000 0 14
ACP1 -0.018 0.001 0 1 -10000 0 1
HCK 0.003 0.033 0.15 4 -10000 0 4
ABL1 0.003 0.072 0.17 10 -0.21 10 20
PDGFB-D/PDGFRB/CBL 0.001 0.086 0.23 3 -0.33 7 10
PTPN1 -0.015 0.011 0.02 11 -10000 0 11
SNX15 -0.018 0.004 0 8 -10000 0 8
STAT3 -0.018 0.002 0 3 -10000 0 3
STAT1 -0.018 0.004 0 7 -10000 0 7
cell proliferation 0.033 0.099 0.2 35 -0.19 6 41
SLA -0.015 0.007 0 27 -10000 0 27
actin cytoskeleton reorganization 0.004 0.088 0.17 33 -10000 0 33
SRC -0.006 0.088 0.15 7 -0.49 4 11
PI3K -0.03 0.024 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.031 0.011 -10000 0 0 18 18
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.009 0.082 0.19 10 -0.3 7 17
LYN 0.001 0.041 0.15 6 -0.29 1 7
LRP1 -0.018 0.002 0 2 -10000 0 2
SOS1 -0.018 0.002 0 3 -10000 0 3
STAT5B -0.018 0.002 0 3 -10000 0 3
STAT5A -0.018 0.002 0 3 -10000 0 3
NCK1-2/p130 Cas 0.036 0.024 -10000 0 -0.022 2 2
SPHK1 -0.013 0.015 0.023 14 -10000 0 14
EDG1 -0.013 0.015 0.023 14 -10000 0 14
mol:DAG 0 0.088 0.18 10 -0.34 7 17
PLCG1 0 0.089 0.18 10 -0.35 7 17
NHERF/PDGFRB 0.033 0.008 -10000 0 0 9 9
YES1 -0.004 0.031 0.17 1 -0.29 1 2
cell migration 0.033 0.008 -10000 0 0 9 9
SHC/Grb2/SOS1 0.041 0.022 -10000 0 -0.022 6 6
SLC9A3R2 -0.018 0.002 0 3 -10000 0 3
SLC9A3R1 -0.018 0.001 0 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.041 0.012 -10000 0 0 12 12
FYN -0.009 0.078 0.15 6 -0.35 6 12
DOK1 -0.025 0.017 0.15 1 -10000 0 1
HRAS/GTP 0.012 0.002 -10000 0 0 5 5
PDGFB -0.018 0.002 0 3 -10000 0 3
RAC1 0.008 0.08 0.19 13 -0.24 7 20
PRKCD -0.022 0.019 0.16 1 -10000 0 1
FER -0.024 0.022 0.16 2 -10000 0 2
MAPKKK cascade -0.013 0.079 0.2 17 -10000 0 17
RASA1 -0.024 0.023 0.16 2 -10000 0 2
NCK1 -0.015 0.007 0 27 -10000 0 27
NCK2 -0.018 0.002 0 3 -10000 0 3
p62DOK/Csk -0.02 0.046 0.15 11 -10000 0 11
PDGFB-D/PDGFRB/SHB 0.022 0.011 -10000 0 -0.025 4 4
chemotaxis 0.003 0.071 0.17 10 -0.2 10 20
STAT1-3-5/STAT1-3-5 -0.037 0.018 0.05 2 -10000 0 2
Bovine Papilomavirus E5/PDGFRB 0.012 0.006 -10000 0 -0.015 2 2
PTPRJ -0.018 0.002 0 2 -10000 0 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.008 0.045 0.18 6 -10000 0 6
CRKL -0.005 0.023 -10000 0 -0.1 3 3
HRAS -0.014 0.036 -10000 0 -0.16 4 4
mol:PIP3 0.018 0.055 0.2 2 -0.32 1 3
SPRED1 -0.018 0.002 0 3 -10000 0 3
SPRED2 -0.018 0.002 0 3 -10000 0 3
GAB1 0.002 0.022 0.075 5 -0.1 2 7
FOXO3 -0.005 0.087 0.17 4 -0.31 9 13
AKT1 -0.006 0.093 0.18 4 -0.33 9 13
BAD -0.005 0.093 0.17 8 -0.32 9 17
megakaryocyte differentiation -0.001 0.03 0.074 6 -0.12 6 12
GSK3B 0.009 0.095 0.21 14 -0.32 6 20
RAF1 -0.01 0.034 0.18 2 -10000 0 2
SHC1 -0.018 0.004 0 7 -10000 0 7
STAT3 -0.002 0.03 0.075 5 -0.12 6 11
STAT1 -0.007 0.046 0.17 2 -0.2 6 8
HRAS/SPRED1 -0.012 0.041 0.21 1 -0.14 3 4
cell proliferation 0 0.029 0.074 6 -0.12 5 11
PIK3CA -0.013 0.009 0.001 51 -10000 0 51
TEC -0.017 0.005 0 12 -10000 0 12
RPS6KB1 0.004 0.051 0.13 1 -0.17 3 4
HRAS/SPRED2 -0.015 0.037 -10000 0 -0.15 3 3
LYN/TEC/p62DOK 0.026 0.039 -10000 0 -0.12 4 4
MAPK3 -0.013 0.044 0.2 2 -0.18 5 7
STAP1 0.007 0.027 0.082 5 -0.1 5 10
GRAP2 -0.018 0.002 0 2 -10000 0 2
JAK2 -0.003 0.047 0.13 2 -0.22 6 8
STAT1 (dimer) -0.011 0.052 0.17 2 -0.21 8 10
mol:Gleevec 0 0.002 -10000 0 -0.008 6 6
GRB2/SOCS1/VAV1 0.026 0.046 -10000 0 -0.11 8 8
actin filament polymerization 0.006 0.03 0.081 5 -0.11 6 11
LYN -0.016 0.006 0 18 -10000 0 18
STAP1/STAT5A (dimer) -0.004 0.045 0.098 1 -0.16 10 11
PIK3R1 -0.013 0.012 0.013 29 -10000 0 29
CBL/CRKL/GRB2 -0.008 0.045 0.2 3 -10000 0 3
PI3K 0.013 0.04 -10000 0 -0.13 1 1
PTEN -0.018 0.003 0 5 -10000 0 5
SCF/KIT/EPO/EPOR 0.008 0.049 0.15 3 -0.17 8 11
MAPK8 0 0.029 0.076 5 -0.12 5 10
STAT3 (dimer) 0 0.035 0.1 6 -0.12 6 12
positive regulation of transcription -0.011 0.039 0.18 2 -0.15 5 7
mol:GDP -0.016 0.037 0.078 5 -0.12 2 7
PIK3C2B 0 0.027 0.076 6 -0.11 5 11
CBL/CRKL -0.004 0.04 0.2 3 -10000 0 3
FER 0 0.029 0.075 6 -0.12 5 11
SH2B3 0.007 0.027 0.082 5 -0.1 5 10
PDPK1 0.014 0.052 0.19 2 -0.28 1 3
SNAI2 -0.001 0.028 0.076 5 -0.13 4 9
positive regulation of cell proliferation -0.005 0.059 0.13 6 -0.19 10 16
KITLG -0.01 0.017 0.026 10 -10000 0 10
cell motility -0.005 0.059 0.13 6 -0.19 10 16
PTPN6 -0.016 0.01 0.019 8 -10000 0 8
EPOR 0.003 0.086 -10000 0 -0.47 5 5
STAT5A (dimer) -0.003 0.055 -10000 0 -0.18 9 9
SOCS1 -0.018 0.003 0 4 -10000 0 4
cell migration 0.001 0.03 0.12 6 -0.075 5 11
SOS1 -0.018 0.002 0 3 -10000 0 3
EPO -0.012 0.014 0.026 3 -10000 0 3
VAV1 -0.018 0.002 0 3 -10000 0 3
GRB10 -0.002 0.03 0.076 5 -0.12 6 11
PTPN11 -0.017 0.009 0.019 8 -10000 0 8
SCF/KIT 0.009 0.029 0.086 5 -0.11 5 10
GO:0007205 0 0.002 -10000 0 -0.008 8 8
MAP2K1 -0.013 0.03 0.16 2 -10000 0 2
CBL -0.016 0.006 0 24 -10000 0 24
KIT -0.009 0.1 -10000 0 -0.43 9 9
MAP2K2 -0.011 0.038 0.2 3 -10000 0 3
SHC/Grb2/SOS1 0.026 0.043 -10000 0 -0.11 8 8
STAT5A -0.006 0.047 -10000 0 -0.2 6 6
GRB2 -0.018 0.001 0 1 -10000 0 1
response to radiation -0.001 0.027 0.075 5 -0.13 4 9
SHC/GRAP2 0.024 0.005 -10000 0 0 8 8
PTPRO -0.001 0.031 0.075 6 -0.12 6 12
SH2B2 0.007 0.027 0.082 5 -0.1 5 10
DOK1 -0.018 0.002 0 2 -10000 0 2
MATK -0.001 0.03 0.076 5 -0.12 6 11
CREBBP -0.009 0.018 0.027 19 -10000 0 19
BCL2 -0.041 0.16 -10000 0 -0.47 20 20
p38 MAPK signaling 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
TRAF6/ASK1 0.009 0.017 -10000 0 -0.071 7 7
TRAF2/ASK1 0.022 0.005 -10000 0 0 9 9
ATM -0.016 0.007 0 25 -10000 0 25
MAP2K3 -0.044 0.12 -10000 0 -0.27 29 29
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.037 0.088 0.18 1 -0.21 27 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.018 0.001 0 1 -10000 0 1
TXN -0.002 0 -10000 0 -10000 0 0
CALM1 -0.017 0.005 0 14 -10000 0 14
GADD45A -0.018 0.002 0 3 -10000 0 3
GADD45B -0.018 0.003 0 4 -10000 0 4
MAP3K1 -0.017 0.004 0 9 -10000 0 9
MAP3K6 -0.018 0.003 0 4 -10000 0 4
MAP3K7 -0.018 0.003 0 6 -10000 0 6
MAP3K4 -0.018 0.003 0 5 -10000 0 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.024 0.006 -10000 0 0 10 10
TAK1/TAB family 0.006 0.019 -10000 0 -0.14 2 2
RAC1/OSM/MEKK3 0.03 0.009 -10000 0 0 12 12
TRAF2 -0.018 0.002 0 3 -10000 0 3
RAC1/OSM/MEKK3/MKK3 -0.023 0.099 -10000 0 -0.23 27 27
TRAF6 -0.004 0.001 0 11 -10000 0 11
RAC1 -0.017 0.004 0 10 -10000 0 10
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.018 0.003 0 6 -10000 0 6
CCM2 -0.018 0.003 0 6 -10000 0 6
CaM/Ca2+/CAMKIIB 0.02 0.007 -10000 0 0 19 19
MAPK11 -0.018 0.004 0 7 -10000 0 7
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.028 0.011 -10000 0 0 23 23
OSM/MEKK3 0.024 0.005 -10000 0 0 6 6
TAOK1 -0.003 0.002 0 27 -10000 0 27
TAOK2 -0.003 0.002 0 27 -10000 0 27
TAOK3 -0.004 0.001 0 25 -10000 0 25
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
MAPK14 -0.018 0.004 0 8 -10000 0 8
MAP3K7IP2 -0.018 0.003 0 5 -10000 0 5
MAP3K5 -0.018 0.003 0 6 -10000 0 6
MAP3K10 -0.018 0.002 0 3 -10000 0 3
MAP3K3 -0.018 0 -10000 0 -10000 0 0
TRX/ASK1 0.013 0.003 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.037 0.011 -10000 0 0 13 13
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.016 0.006 0.001 18 -10000 0 18
RAS family/GTP -0.013 0.035 0.12 1 -10000 0 1
NFATC4 -0.025 0.044 0.21 1 -10000 0 1
ERBB2IP -0.017 0.007 0.006 12 -10000 0 12
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.027 0.14 3 -10000 0 3
JUN 0.002 0.031 0.12 4 -0.085 5 9
HRAS -0.018 0.003 0 5 -10000 0 5
DOCK7 -0.026 0.048 0.12 14 -10000 0 14
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.026 0.02 0.045 7 -10000 0 7
AKT1 -0.011 0.004 0.001 15 -10000 0 15
BAD -0.016 0.006 0 20 -10000 0 20
MAPK10 -0.023 0.037 0.16 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.031 0.029 0.15 3 -10000 0 3
RAF1 -0.013 0.046 0.16 7 -10000 0 7
ErbB2/ErbB3/neuregulin 2 -0.024 0.017 0.029 11 -10000 0 11
STAT3 -0.004 0.13 -10000 0 -0.84 4 4
cell migration -0.015 0.05 0.2 5 -10000 0 5
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.025 0.11 0.2 3 -0.3 17 20
FOS -0.014 0.075 0.18 5 -0.19 17 22
NRAS -0.017 0.004 0 9 -10000 0 9
mol:Ca2+ -0.03 0.027 0.14 3 -10000 0 3
MAPK3 -0.027 0.11 0.19 3 -0.29 16 19
MAPK1 -0.02 0.084 0.18 3 -0.24 14 17
JAK2 -0.026 0.035 0.12 5 -10000 0 5
NF2 -0.005 0.048 -10000 0 -0.62 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.024 0.086 10 -0.068 1 11
NRG1 -0.014 0.012 0.02 17 -10000 0 17
GRB2/SOS1 0.025 0.003 -10000 0 0 3 3
MAPK8 -0.016 0.043 0.16 4 -0.16 4 8
MAPK9 -0.024 0.035 0.15 2 -10000 0 2
ERBB2 -0.02 0.007 0.001 14 -10000 0 14
ERBB3 -0.014 0.013 0.02 15 -10000 0 15
SHC1 -0.018 0.004 0 7 -10000 0 7
RAC1 -0.017 0.004 0 10 -10000 0 10
apoptosis 0.011 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.003 0.13 -10000 0 -0.82 4 4
RNF41 -0.021 0.008 0 18 -10000 0 18
FRAP1 -0.016 0.006 0 19 -10000 0 19
RAC1-CDC42/GTP -0.036 0.017 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.016 0.005 0.001 14 -10000 0 14
CHRNA1 -0.014 0.074 0.17 3 -0.2 15 18
myelination -0.02 0.061 0.27 3 -10000 0 3
PPP3CB -0.025 0.045 0.11 14 -10000 0 14
KRAS -0.017 0.005 0 11 -10000 0 11
RAC1-CDC42/GDP -0.009 0.036 0.13 1 -10000 0 1
NRG2 -0.018 0.003 0 5 -10000 0 5
mol:GDP -0.004 0.024 0.086 10 -0.068 1 11
SOS1 -0.018 0.002 0 3 -10000 0 3
MAP2K2 -0.017 0.044 0.15 7 -10000 0 7
SRC -0.017 0.005 0 14 -10000 0 14
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.025 0.049 0.13 12 -10000 0 12
MAP2K1 -0.034 0.14 0.22 1 -0.4 17 18
heart morphogenesis -0.03 0.027 0.14 3 -10000 0 3
RAS family/GDP 0.029 0.028 0.14 1 -0.077 4 5
GRB2 -0.018 0.001 0 1 -10000 0 1
PRKACA 0.003 0.051 -10000 0 -0.65 1 1
CHRNE 0 0.008 0.039 3 -0.021 2 5
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.011 0.004 -10000 0 -0.001 15 15
nervous system development -0.03 0.027 0.14 3 -10000 0 3
CDC42 -0.018 0.003 0 5 -10000 0 5
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 -0.018 0.002 0 2 -10000 0 2
HSPA8 -0.016 0.006 0 23 -10000 0 23
SMAD3/SMAD4/ER alpha 0.029 0.015 0.084 1 -0.028 2 3
AKT1 -0.017 0.005 0 13 -10000 0 13
GSC -0.004 0.091 0.28 2 -0.36 8 10
NKX2-5 -0.017 0.004 0 9 -10000 0 9
muscle cell differentiation -0.011 0.053 0.2 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.038 0.018 0.091 1 -0.032 2 3
SMAD4 -0.018 0.011 0.038 4 -10000 0 4
CBFB -0.017 0.004 0 9 -10000 0 9
SAP18 -0.018 0.004 0 7 -10000 0 7
Cbp/p300/MSG1 0.034 0.006 -10000 0 0 5 5
SMAD3/SMAD4/VDR 0.042 0.027 -10000 0 -0.041 2 2
MYC -0.015 0.007 0 31 -10000 0 31
CDKN2B -0.12 0.19 -10000 0 -0.38 48 48
AP1 -0.019 0.017 0.12 2 -10000 0 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.006 0.073 -10000 0 -0.23 11 11
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.017 0.053 -10000 0 -0.18 14 14
SP3 -0.018 0.004 0 7 -10000 0 7
CREB1 -0.018 0.003 0 6 -10000 0 6
FOXH1 -0.015 0.007 0 31 -10000 0 31
SMAD3/SMAD4/GR 0.03 0.014 0.084 1 -0.028 1 2
GATA3 -0.018 0.003 0 5 -10000 0 5
SKI/SIN3/HDAC complex/NCoR1 -0.016 0.076 -10000 0 -0.19 16 16
MEF2C/TIF2 -0.014 0.062 0.18 14 -10000 0 14
endothelial cell migration -0.003 0.071 0.6 2 -10000 0 2
MAX -0.017 0.004 0 9 -10000 0 9
RBBP7 -0.018 0 -10000 0 -10000 0 0
RBBP4 -0.018 0.003 0 4 -10000 0 4
RUNX2 -0.017 0.004 0 10 -10000 0 10
RUNX3 -0.018 0.003 0 5 -10000 0 5
RUNX1 -0.018 0.003 0 4 -10000 0 4
CTBP1 -0.017 0.005 0 15 -10000 0 15
NR3C1 -0.018 0.003 0 5 -10000 0 5
VDR -0.018 0.002 0 2 -10000 0 2
CDKN1A -0.016 0.069 -10000 0 -0.44 4 4
KAT2B 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.026 0.015 -10000 0 0 40 40
DCP1A -0.016 0.006 0 24 -10000 0 24
SKI -0.018 0.003 0 5 -10000 0 5
SERPINE1 0.003 0.072 -10000 0 -0.6 2 2
SMAD3/SMAD4/ATF2 0.028 0.015 -10000 0 -0.028 2 2
SMAD3/SMAD4/ATF3 0.029 0.015 0.084 1 -0.028 2 3
SAP30 -0.018 0.003 0 5 -10000 0 5
Cbp/p300/PIAS3 0.033 0.008 -10000 0 0 10 10
JUN -0.017 0.026 0.13 5 -10000 0 5
SMAD3/SMAD4/IRF7 0.03 0.014 0.084 1 -0.028 1 2
TFE3 -0.018 0 -10000 0 -10000 0 0
COL1A2 0.009 0.005 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.028 0.015 0.028 2 -0.083 1 3
DLX1 -0.017 0.004 0 9 -10000 0 9
TCF3 -0.018 0.003 0 4 -10000 0 4
FOS -0.02 0.01 0.039 3 -10000 0 3
SMAD3/SMAD4/Max 0.029 0.014 0.084 1 -0.028 1 2
Cbp/p300/SNIP1 0.033 0.007 -10000 0 0 7 7
ZBTB17 -0.018 0.004 0 8 -10000 0 8
LAMC1 -0.024 0.022 0.13 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.015 0.084 1 -0.028 1 2
IRF7 -0.018 0.003 0 5 -10000 0 5
ESR1 -0.018 0.003 0 5 -10000 0 5
HNF4A -0.017 0.005 0 12 -10000 0 12
MEF2C -0.002 0.073 0.17 23 -10000 0 23
SMAD2-3/SMAD4 0.03 0.014 0.084 1 -0.028 2 3
Cbp/p300/Src-1 0.033 0.007 -10000 0 0 7 7
IGHV3OR16-13 -0.013 0.053 -10000 0 -0.35 4 4
TGIF2/HDAC complex -0.017 0.005 0 16 -10000 0 16
CREBBP -0.018 0.002 0 3 -10000 0 3
SKIL -0.013 0.008 0 47 -10000 0 47
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC2 -0.018 0.003 0 6 -10000 0 6
SNIP1 -0.018 0.002 0 2 -10000 0 2
GCN5L2 -0.018 0.002 0 3 -10000 0 3
SMAD3/SMAD4/TFE3 0.03 0.014 0.084 1 -0.028 2 3
MSG1/HSC70 0.022 0.009 -10000 0 0 23 23
SMAD2 -0.017 0.005 0 15 -10000 0 15
SMAD3 -0.019 0.012 0.035 7 -10000 0 7
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.012 0.025 0.036 1 -0.12 8 9
SMAD2/SMAD2/SMAD4 -0.009 0.047 0.12 3 -0.15 13 16
NCOR1 -0.018 0.002 0 3 -10000 0 3
NCOA2 -0.016 0.006 0 19 -10000 0 19
NCOA1 -0.018 0.002 0 2 -10000 0 2
MYOD/E2A 0.024 0.005 -10000 0 0 7 7
SMAD2-3/SMAD4/SP1/MIZ-1 0.042 0.023 0.095 1 -0.023 7 8
IFNB1 -0.022 0.022 0.13 2 -10000 0 2
SMAD3/SMAD4/MEF2C -0.008 0.065 0.16 20 -10000 0 20
CITED1 -0.018 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.028 0.014 0.08 1 -0.024 2 3
RBL1 -0.017 0.005 0 15 -10000 0 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.016 0.059 0.074 4 -0.18 15 19
RUNX1-3/PEBPB2 0.031 0.011 -10000 0 0 17 17
SMAD7 -0.018 0.028 -10000 0 -0.14 8 8
MYC/MIZ-1 0.02 0.01 -10000 0 0 34 34
SMAD3/SMAD4 -0.008 0.04 -10000 0 -0.13 11 11
IL10 -0.022 0.026 0.14 3 -10000 0 3
PIASy/HDAC complex -0.018 0.003 0 4 -10000 0 4
PIAS3 -0.018 0.003 0 6 -10000 0 6
CDK2 -0.018 0.001 0 1 -10000 0 1
IL5 -0.023 0.024 0.15 2 -10000 0 2
CDK4 -0.018 0.002 0 2 -10000 0 2
PIAS4 -0.018 0.003 0 4 -10000 0 4
ATF3 -0.018 0.003 0 5 -10000 0 5
SMAD3/SMAD4/SP1 0.03 0.014 0.084 1 -0.028 2 3
FOXG1 0 0 -10000 0 -10000 0 0
FOXO3 -0.01 0.003 0 13 -10000 0 13
FOXO1 -0.01 0.003 0 13 -10000 0 13
FOXO4 -0.01 0.003 0 13 -10000 0 13
heart looping -0.002 0.072 0.17 23 -10000 0 23
CEBPB -0.017 0.005 0 11 -10000 0 11
SMAD3/SMAD4/DLX1 0.028 0.015 -10000 0 -0.028 2 2
MYOD1 -0.018 0.002 0 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.029 0.015 0.084 1 -0.028 1 2
SMAD3/SMAD4/GATA3 0.03 0.014 0.084 1 -0.028 1 2
SnoN/SIN3/HDAC complex/NCoR1 -0.013 0.008 0 47 -10000 0 47
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.041 0.024 0.095 1 -0.019 9 10
SMAD3/SMAD4/SP1-3 0.036 0.018 -10000 0 -0.032 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 -0.018 0.001 0 1 -10000 0 1
SIN3B -0.018 0.001 0 1 -10000 0 1
SIN3A -0.018 0.002 0 3 -10000 0 3
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.02 -10000 0 0 46 46
ITGB5 -0.021 0.039 0.15 7 -10000 0 7
TGIF/SIN3/HDAC complex/CtBP -0.014 0.055 -10000 0 -0.14 19 19
SMAD3/SMAD4/AR 0.03 0.014 0.084 1 -0.028 2 3
AR -0.018 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.011 0.039 0.064 2 -0.19 7 9
SMAD3/SMAD4/MYOD 0.03 0.014 0.084 1 -0.028 1 2
E2F5 -0.017 0.006 0 17 -10000 0 17
E2F4 -0.017 0.004 0 10 -10000 0 10
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.034 0.025 -10000 0 -0.009 15 15
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.019 -10000 0 -0.12 4 4
TFDP1 -0.018 0.004 0 7 -10000 0 7
SMAD3/SMAD4/AP1 0.027 0.016 0.16 1 -10000 0 1
SMAD3/SMAD4/RUNX2 0.029 0.015 0.084 1 -0.028 2 3
TGIF2 -0.017 0.005 0 16 -10000 0 16
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.018 0.004 0 8 -10000 0 8
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.024 0.006 -10000 0 0 9 9
Necdin/E2F1 0.021 0.009 -10000 0 0 27 27
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.039 0.008 -10000 0 0 6 6
NGF (dimer)/p75(NTR)/BEX1 0.023 0 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR) 0.013 0 -10000 0 -10000 0 0
IKBKB -0.016 0.006 0 18 -10000 0 18
AKT1 0.022 0.081 0.16 40 -10000 0 40
IKBKG -0.018 0 -10000 0 -10000 0 0
BDNF -0.018 0.003 0 4 -10000 0 4
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.005 -10000 0 0 9 9
FURIN -0.018 0.002 0 3 -10000 0 3
proBDNF (dimer)/p75(NTR)/Sortilin 0.033 0.007 -10000 0 0 7 7
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.043 0.016 -10000 0 -10000 0 0
proBDNF (dimer) -0.018 0.003 0 4 -10000 0 4
NTRK1 -0.018 0.004 0 7 -10000 0 7
RTN4R -0.017 0.004 0 9 -10000 0 9
neuron apoptosis -0.016 0.053 -10000 0 -0.23 6 6
IRAK1 -0.018 0 -10000 0 -10000 0 0
SHC1 -0.017 0.004 0 7 -10000 0 7
ARHGDIA -0.018 0.002 0 3 -10000 0 3
RhoA/GTP 0.011 0.004 -10000 0 0 23 23
Gamma Secretase 0.045 0.017 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.032 0.005 -10000 0 0 4 4
MAGEH1 -0.018 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.031 0.007 -10000 0 0 8 8
Mammalian IAPs/DIABLO 0.027 0.013 -10000 0 0 30 30
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.018 0 -10000 0 -10000 0 0
APP -0.018 0.003 0 5 -10000 0 5
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 -0.018 0.003 0 6 -10000 0 6
RhoA/GDP/RHOGDI -0.018 0.008 0 25 -10000 0 25
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.025 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.007 0.013 -10000 0 -0.17 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.022 0.004 -10000 0 0 6 6
NCSTN -0.018 0.004 0 7 -10000 0 7
mol:GTP 0.022 0.004 -10000 0 0 5 5
PSENEN -0.018 0.002 0 3 -10000 0 3
mol:ceramide -0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.005 0.015 -10000 0 -0.087 5 5
p75(NTR)/beta APP 0.024 0.004 -10000 0 0 5 5
BEX1 -0.018 0 -10000 0 -10000 0 0
mol:GDP -0.009 0 -10000 0 -10000 0 0
NGF (dimer) 0.026 0.013 -10000 0 0 35 35
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.03 0.009 -10000 0 0 12 12
PIK3R1 -0.018 0.004 0 8 -10000 0 8
RAC1/GTP 0.019 0.005 -10000 0 0 10 10
MYD88 -0.016 0.006 0 22 -10000 0 22
CHUK -0.018 0.002 0 3 -10000 0 3
NGF (dimer)/p75(NTR)/PKA 0.022 0.004 -10000 0 0 5 5
RHOB -0.018 0.002 0 2 -10000 0 2
RHOA -0.016 0.006 0 23 -10000 0 23
MAGE-G1/E2F1 0.021 0.009 -10000 0 0 26 26
NT3 (dimer) -0.017 0.005 0 13 -10000 0 13
TP53 -0.032 0.031 0.15 4 -10000 0 4
PRDM4 -0.022 0.004 -10000 0 -10000 0 0
BDNF (dimer) 0.034 0.018 -10000 0 0 36 36
PIK3CA -0.013 0.008 0 49 -10000 0 49
SORT1 -0.018 0.003 0 4 -10000 0 4
activation of caspase activity 0.035 0.007 -10000 0 0 6 6
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.031 0.007 -10000 0 0 9 9
RHOC -0.018 0.004 0 7 -10000 0 7
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.022 0.034 0.12 8 -10000 0 8
DIABLO -0.018 0.001 0 1 -10000 0 1
SMPD2 -0.022 0.005 -10000 0 -10000 0 0
APH1B -0.018 0.002 0 3 -10000 0 3
APH1A -0.018 0.004 0 7 -10000 0 7
proNGF (dimer)/p75(NTR)/Sortilin 0.023 0.004 -10000 0 0 4 4
PSEN1 -0.018 0.004 0 7 -10000 0 7
APAF-1/Pro-Caspase 9 0.024 0.005 -10000 0 0 7 7
NT3 (dimer)/p75(NTR) 0.023 0.007 -10000 0 0 13 13
MAPK8 -0.022 0.034 0.12 8 -10000 0 8
MAPK9 -0.021 0.034 0.12 8 -10000 0 8
APAF1 -0.018 0.002 0 2 -10000 0 2
NTF3 -0.017 0.005 0 13 -10000 0 13
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.018 0.003 0 6 -10000 0 6
RAC1/GDP 0.012 0.003 -10000 0 0 10 10
RhoA-B-C/GDP 0.031 0.015 -10000 0 -0.008 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.04 0.013 -10000 0 0 15 15
RhoA-B-C/GTP 0.022 0.004 -10000 0 0 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.046 0.016 -10000 0 -0.008 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.041 0.01 -10000 0 0 10 10
PRKACB -0.018 0.003 0 5 -10000 0 5
proBDNF (dimer)/p75 ECD 0.024 0.005 -10000 0 0 6 6
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.015 0.007 0 30 -10000 0 30
BIRC2 -0.015 0.007 0 30 -10000 0 30
neuron projection morphogenesis -0.016 0.007 -10000 0 -10000 0 0
BAD -0.025 0.038 -10000 0 -10000 0 0
RIPK2 -0.016 0.006 0 18 -10000 0 18
NGFR -0.018 0 -10000 0 -10000 0 0
CYCS -0.027 0.007 -10000 0 -10000 0 0
ADAM17 -0.018 0.002 0 2 -10000 0 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.028 0.011 -10000 0 0 23 23
BCL2L11 -0.027 0.039 -10000 0 -10000 0 0
BDNF (dimer)/p75(NTR) 0.025 0.004 -10000 0 0 4 4
PI3K 0.022 0.015 -10000 0 0 53 53
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.031 0.007 -10000 0 0 7 7
NDNL2 -0.018 0.003 0 5 -10000 0 5
YWHAE -0.018 0.002 0 2 -10000 0 2
PRKCI -0.013 0.008 0 47 -10000 0 47
NGF (dimer)/p75(NTR) 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.032 0.005 -10000 0 0 4 4
TRAF6 -0.018 0.003 0 6 -10000 0 6
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCZ -0.018 0.003 0 5 -10000 0 5
PLG -0.018 0.003 0 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.02 0.005 0 8 -10000 0 8
SQSTM1 -0.018 0.004 0 8 -10000 0 8
NGFRAP1 -0.018 0 -10000 0 -10000 0 0
CASP3 -0.026 0.038 -10000 0 -0.16 1 1
E2F1 -0.016 0.006 0 22 -10000 0 22
CASP9 -0.018 0.004 0 7 -10000 0 7
IKK complex 0.001 0.047 -10000 0 -0.12 1 1
NGF (dimer)/TRKA 0.012 0.003 -10000 0 0 7 7
MMP7 -0.015 0.007 0 30 -10000 0 30
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.037 0.011 -10000 0 0 14 14
MMP3 -0.015 0.007 0 29 -10000 0 29
APAF-1/Caspase 9 -0.041 0.02 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.017 0.045 0.13 21 -0.099 1 22
BUB1B -0.009 0.025 0.063 1 -0.11 6 7
PLK1 -0.005 0.017 0.058 1 -0.056 9 10
PLK1S1 -0.003 0.01 0.033 2 -0.029 8 10
KIF2A -0.004 0.015 0.051 1 -0.05 9 10
regulation of mitotic centrosome separation -0.004 0.017 0.058 1 -0.056 9 10
GOLGA2 -0.018 0.002 0 2 -10000 0 2
Hec1/SPC24 -0.006 0.011 -10000 0 -0.044 11 11
WEE1 -0.004 0.045 -10000 0 -0.26 4 4
cytokinesis -0.01 0.037 -10000 0 -0.17 6 6
PP2A-alpha B56 0.036 0.011 -10000 0 -10000 0 0
AURKA -0.003 0.01 0.037 2 -0.037 2 4
PICH/PLK1 -0.019 0.013 0.027 2 -0.057 8 10
CENPE -0.01 0.014 -10000 0 -10000 0 0
RhoA/GTP 0.011 0.004 -10000 0 0 23 23
positive regulation of microtubule depolymerization -0.004 0.015 0.051 1 -0.05 9 10
PPP2CA -0.018 0.003 0 6 -10000 0 6
FZR1 -0.018 0.003 0 5 -10000 0 5
TPX2 0.003 0.015 0.071 2 -10000 0 2
PAK1 -0.014 0.011 0.028 1 -10000 0 1
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 -0.018 0.004 0 8 -10000 0 8
CLSPN -0.001 0.03 -10000 0 -0.26 2 2
GORASP1 -0.016 0.006 0 22 -10000 0 22
metaphase 0 0.003 0.016 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.01 0.033 2 -0.029 8 10
G2 phase of mitotic cell cycle 0 0.002 0.009 3 -10000 0 3
STAG2 -0.018 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.058 0.17 -10000 0 -0.5 22 22
spindle elongation -0.004 0.017 0.058 1 -0.056 9 10
ODF2 -0.012 0.014 0.027 2 -10000 0 2
BUB1 0.017 0.007 -10000 0 -10000 0 0
TPT1 -0.013 0.049 -10000 0 -0.18 12 12
CDC25C -0.006 0.049 -10000 0 -0.28 5 5
CDC25B -0.016 0.01 0.021 1 -10000 0 1
SGOL1 -0.017 0.045 0.099 1 -0.13 21 22
RHOA -0.016 0.006 0 23 -10000 0 23
CCNB1/CDK1 0.027 0.031 -10000 0 -0.086 8 8
CDC14B -0.012 0.002 0.002 3 -10000 0 3
CDC20 -0.018 0.002 0 2 -10000 0 2
PLK1/PBIP1 -0.009 0.013 0.037 2 -0.046 9 11
mitosis -0.001 0.003 0.011 6 -10000 0 6
FBXO5 -0.007 0.02 0.088 2 -0.074 5 7
CDC2 -0.016 0.011 0.02 5 -10000 0 5
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression -0.004 0.038 -10000 0 -0.24 4 4
ERCC6L -0.014 0.018 0.035 1 -0.086 7 8
NLP/gamma Tubulin -0.002 0.014 0.039 2 -0.079 2 4
microtubule cytoskeleton organization -0.013 0.049 -10000 0 -0.18 12 12
G2/M transition DNA damage checkpoint 0 0.003 0.01 12 -10000 0 12
PPP1R12A -0.015 0.012 0.019 17 -10000 0 17
interphase 0 0.003 0.01 12 -10000 0 12
PLK1/PRC1-2 0.016 0.021 -10000 0 -0.058 9 9
GRASP65/GM130/RAB1/GTP/PLK1 0.021 0.021 -10000 0 -0.06 5 5
RAB1A -0.018 0.002 0 2 -10000 0 2
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.003 0.013 0.04 6 -0.044 2 8
mitotic prometaphase 0 0.003 0.018 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.037 0.13 1 -0.19 6 7
microtubule-based process -0.009 0.018 0.058 1 -0.058 7 8
Golgi organization -0.004 0.017 0.058 1 -0.056 9 10
Cohesin/SA2 -0.009 0.017 0.051 3 -0.05 7 10
PPP1CB/MYPT1 0.025 0.006 -10000 0 -0.005 5 5
KIF20A -0.018 0.003 0 5 -10000 0 5
APC/C/CDC20 -0.009 0.018 0.058 1 -0.054 6 7
PPP2R1A -0.018 0.001 0 1 -10000 0 1
chromosome segregation -0.009 0.013 0.037 2 -0.046 9 11
PRC1 -0.018 0.002 0 3 -10000 0 3
ECT2 0.049 0.096 0.2 47 -10000 0 47
C13orf34 -0.003 0.014 0.042 5 -0.042 9 14
NUDC -0.004 0.038 -10000 0 -0.24 4 4
regulation of attachment of spindle microtubules to kinetochore -0.009 0.025 0.063 1 -0.11 6 7
spindle assembly -0.005 0.016 0.052 3 -0.05 8 11
spindle stabilization -0.003 0.01 0.033 2 -0.029 8 10
APC/C/HCDH1 -0.017 0.005 0.016 2 -10000 0 2
MKLP2/PLK1 -0.009 0.019 0.058 1 -0.059 7 8
CCNB1 -0.015 0.011 0.02 11 -10000 0 11
PPP1CB -0.015 0.011 0.019 15 -10000 0 15
BTRC -0.018 0.002 0 2 -10000 0 2
ROCK2 -0.013 0.046 -10000 0 -0.13 21 21
TUBG1 -0.001 0.02 -10000 0 -0.22 1 1
G2/M transition of mitotic cell cycle -0.014 0.016 0.036 1 -0.088 5 6
MLF1IP -0.011 0.003 0 9 -0.017 1 10
INCENP -0.014 0.012 0.019 19 -10000 0 19
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.007 0.003 -10000 0 0 24 24
SMARCC2 -0.018 0.001 0 1 -10000 0 1
SMARCC1 -0.016 0.006 0 21 -10000 0 21
TBX21 -0.018 0.003 0 5 -10000 0 5
SUMO2 -0.018 0.001 0 1 -10000 0 1
STAT1 (dimer) -0.018 0.004 0 7 -10000 0 7
FKBP4 -0.017 0.005 0 14 -10000 0 14
FKBP5 -0.018 0.004 0 8 -10000 0 8
GR alpha/HSP90/FKBP51/HSP90 0.021 0.006 -10000 0 0 12 12
PRL -0.001 0 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.02 0.008 -10000 0 0 23 23
RELA -0.017 0.005 0 11 -10000 0 11
FGG -0.016 0.005 0 12 -10000 0 12
GR beta/TIF2 0.022 0.009 -10000 0 0 23 23
IFNG -0.003 0.001 -10000 0 -10000 0 0
apoptosis -0.008 0.051 -10000 0 -0.17 9 9
CREB1 -0.018 0.003 0 6 -10000 0 6
histone acetylation -0.005 0.001 0 10 -10000 0 10
BGLAP -0.005 0.002 0 18 -10000 0 18
GR/PKAc 0.04 0.012 -10000 0 0 14 14
NF kappa B1 p50/RelA 0.023 0.008 -10000 0 0 17 17
SMARCD1 -0.018 0.001 0 1 -10000 0 1
MDM2 -0.002 0 -10000 0 -10000 0 0
GATA3 -0.018 0.003 0 5 -10000 0 5
AKT1 -0.017 0.005 0 13 -10000 0 13
CSF2 -0.011 0.005 -10000 0 -10000 0 0
GSK3B -0.016 0.006 0 20 -10000 0 20
NR1I3 -0.002 0.058 0.15 8 -0.2 5 13
CSN2 -0.014 0.003 0 9 -10000 0 9
BRG1/BAF155/BAF170/BAF60A 0.036 0.017 -10000 0 0 29 29
NFATC1 -0.016 0.006 0 23 -10000 0 23
POU2F1 -0.018 0.003 0 5 -10000 0 5
CDKN1A -0.004 0.04 0.16 3 -0.16 7 10
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
SFN -0.018 0.003 0 4 -10000 0 4
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.03 0.009 -10000 0 0 15 15
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.005 0.042 0.12 2 -0.19 3 5
JUN -0.021 0.006 0 11 -10000 0 11
IL4 -0.004 0.002 0 28 -10000 0 28
CDK5R1 -0.018 0.001 0 1 -10000 0 1
PRKACA -0.018 0.003 0 4 -10000 0 4
cortisol/GR alpha (monomer)/AP-1 -0.03 0.01 0 12 -10000 0 12
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.03 0.009 -10000 0 0 14 14
cortisol/GR alpha (monomer) 0.012 0.002 -10000 0 0 5 5
NCOA2 -0.016 0.006 0 19 -10000 0 19
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.018 0.004 0 8 -10000 0 8
AP-1/NFAT1-c-4 -0.021 0.025 0.18 2 -10000 0 2
AFP -0.011 0.032 0.18 4 -10000 0 4
SUV420H1 -0.016 0.006 0 18 -10000 0 18
IRF1 0.005 0.002 -10000 0 0 16 16
TP53 -0.018 0.003 0 4 -10000 0 4
PPP5C -0.018 0.002 0 2 -10000 0 2
KRT17 -0.003 0.001 -10000 0 -10000 0 0
KRT14 -0.002 0.001 -10000 0 -10000 0 0
TBP -0.018 0.004 0 7 -10000 0 7
CREBBP -0.018 0.002 0 3 -10000 0 3
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC2 -0.018 0.003 0 6 -10000 0 6
AP-1 -0.021 0.025 0.18 2 -10000 0 2
MAPK14 -0.018 0.004 0 8 -10000 0 8
MAPK10 -0.018 0.003 0 5 -10000 0 5
MAPK11 -0.018 0.004 0 7 -10000 0 7
KRT5 -0.003 0.001 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 -0.018 0.002 0 2 -10000 0 2
STAT1 -0.018 0.004 0 7 -10000 0 7
CGA -0.005 0.002 0 15 -10000 0 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.01 0.024 -10000 0 -0.093 12 12
MAPK3 -0.018 0.003 0 4 -10000 0 4
MAPK1 -0.018 0.003 0 6 -10000 0 6
ICAM1 -0.005 0.002 0 22 -10000 0 22
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAPK8 -0.018 0.004 0 7 -10000 0 7
MAPK9 -0.018 0.004 0 8 -10000 0 8
cortisol/GR alpha (dimer) -0.008 0.052 -10000 0 -0.18 9 9
BAX -0.002 0.032 0.16 2 -0.17 4 6
POMC -0.004 0.022 0.21 1 -10000 0 1
EP300 -0.018 0.002 0 2 -10000 0 2
cortisol/GR alpha (dimer)/p53 0.022 0.005 -10000 0 0 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.002 0 9 -10000 0 9
SGK1 -0.008 0.03 -10000 0 -0.17 5 5
IL13 -0.005 0.002 -10000 0 -10000 0 0
IL6 -0.005 0.002 0 25 -10000 0 25
PRKACG -0.018 0.001 0 1 -10000 0 1
IL5 -0.005 0.027 0.074 2 -0.14 6 8
IL2 -0.01 0.04 -10000 0 -0.26 4 4
CDK5 -0.018 0.004 0 8 -10000 0 8
PRKACB -0.018 0.003 0 5 -10000 0 5
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.005 0.002 0 21 -10000 0 21
CDK5R1/CDK5 0.024 0.005 -10000 0 0 8 8
NF kappa B1 p50/RelA/PKAc 0.042 0.019 -10000 0 -0.008 10 10
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.019 0.007 -10000 0 0 19 19
SMARCA4 -0.017 0.004 0 9 -10000 0 9
chromatin remodeling -0.007 0.013 -10000 0 -0.17 1 1
NF kappa B1 p50/RelA/Cbp 0.039 0.014 -10000 0 0 19 19
JUN (dimer) -0.021 0.006 0 11 -10000 0 11
YWHAH -0.018 0.002 0 2 -10000 0 2
VIPR1 -0.016 0.006 0 23 -10000 0 23
NR3C1 -0.018 0.003 0 5 -10000 0 5
NR4A1 -0.018 0.001 0 1 -10000 0 1
TIF2/SUV420H1 0.02 0.01 -10000 0 0 33 33
MAPKKK cascade -0.008 0.051 -10000 0 -0.17 9 9
cortisol/GR alpha (dimer)/Src-1 0.022 0.005 -10000 0 0 7 7
PBX1 -0.018 0.003 0 5 -10000 0 5
POU1F1 -0.016 0.006 0 23 -10000 0 23
SELE -0.005 0.002 0 23 -10000 0 23
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.007 0.013 -10000 0 -0.17 1 1
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.019 0.007 -10000 0 0 19 19
mol:cortisol 0 0 -10000 0 -10000 0 0
MMP1 -0.032 0.13 -10000 0 -0.45 14 14
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.002 0.037 0.099 13 -0.073 7 20
GNAI2 -0.016 0.006 0 23 -10000 0 23
S1P/S1P5/G12 0.011 0.003 -10000 0 0 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.004 0 10 -10000 0 10
RhoA/GTP 0.003 0.038 0.075 7 -0.1 13 20
negative regulation of cAMP metabolic process -0.004 0.002 -10000 0 -10000 0 0
GNAZ -0.018 0.003 0 6 -10000 0 6
GNAI3 -0.018 0.003 0 4 -10000 0 4
GNA12 -0.017 0.004 0 9 -10000 0 9
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.011 0.004 -10000 0 0 23 23
RHOA -0.016 0.006 0 23 -10000 0 23
GNAI1 -0.018 0.003 0 4 -10000 0 4
Signaling events mediated by HDAC Class I

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.03 0.033 -10000 0 -0.09 8 8
Ran/GTP/Exportin 1/HDAC1 -0.023 0.006 0 10 -10000 0 10
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.046 0.15 1 -0.15 9 10
SUMO1 -0.018 0.004 0 7 -10000 0 7
ZFPM1 -0.017 0.005 0 12 -10000 0 12
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.001 -10000 0 -10000 0 0
FKBP3 -0.018 0.004 0 8 -10000 0 8
Histones 0.029 0.042 -10000 0 -0.15 6 6
YY1/LSF 0.004 0.04 0.086 5 -0.11 16 21
SMG5 0 0 -10000 0 -10000 0 0
RAN -0.018 0.001 0 1 -10000 0 1
I kappa B alpha/HDAC3 -0.01 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.012 0.037 0.087 10 -0.15 6 16
SAP18 -0.018 0.004 0 7 -10000 0 7
RELA 0.006 0.027 0.11 9 -0.08 3 12
HDAC1/Smad7 0.029 0.013 -10000 0 0 28 28
RANGAP1 -0.018 0.002 0 2 -10000 0 2
HDAC3/TR2 0.013 0.039 0.087 12 -0.16 6 18
NuRD/MBD3 Complex -0.002 0.019 -10000 0 -0.085 8 8
NF kappa B1 p50/RelA 0.014 0.046 0.16 3 -0.16 5 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.016 0.006 0 20 -10000 0 20
GATA1 -0.018 0 -10000 0 -10000 0 0
Mad/Max 0.024 0.006 -10000 0 0 11 11
NuRD/MBD3 Complex/GATA1/Fog1 -0.011 0.05 -10000 0 -0.21 6 6
RBBP7 -0.018 0 -10000 0 -10000 0 0
NPC 0.01 0.001 -10000 0 0 2 2
RBBP4 -0.018 0.003 0 4 -10000 0 4
MAX -0.017 0.004 0 9 -10000 0 9
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 -0.018 0.004 0 8 -10000 0 8
NFKBIA -0.006 0.003 0 31 -10000 0 31
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.01 0.022 -10000 0 -0.096 9 9
SIN3 complex 0.041 0.01 -10000 0 0 10 10
SMURF1 -0.017 0.005 0 13 -10000 0 13
CHD3 -0.018 0.002 0 2 -10000 0 2
SAP30 -0.018 0.003 0 5 -10000 0 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 -0.018 0.002 0 3 -10000 0 3
YY1/HDAC3 -0.014 0.03 0.075 3 -0.1 15 18
YY1/HDAC2 0.005 0.037 0.086 5 -0.11 13 18
YY1/HDAC1 0.004 0.039 0.086 5 -0.11 15 20
NuRD/MBD2 Complex (MeCP1) -0.009 0.031 -10000 0 -0.094 18 18
PPARG 0.003 0.035 0.12 11 -0.1 3 14
HDAC8/hEST1B 0.023 0.004 -10000 0 0 4 4
UBE2I -0.018 0.002 0 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex -0.017 0.004 0 8 -10000 0 8
TNFRSF1A -0.017 0.005 0 13 -10000 0 13
HDAC3/SMRT (N-CoR2) 0.013 0.039 0.087 12 -0.16 6 18
MBD3L2 -0.018 0.002 0 3 -10000 0 3
ubiquitin-dependent protein catabolic process 0.028 0.013 -10000 0 0 28 28
CREBBP -0.018 0.002 0 3 -10000 0 3
NuRD/MBD3/MBD3L2 Complex -0.01 0.045 -10000 0 -0.19 7 7
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC3 -0.006 0.003 0 26 -10000 0 26
HDAC2 -0.018 0.003 0 6 -10000 0 6
YY1 -0.002 0.001 -10000 0 -10000 0 0
HDAC8 -0.018 0 -10000 0 -10000 0 0
SMAD7 -0.017 0.005 0 15 -10000 0 15
NCOR2 -0.018 0.003 0 4 -10000 0 4
MXD1 -0.018 0.002 0 2 -10000 0 2
STAT3 -0.006 0.001 0 8 -10000 0 8
NFKB1 -0.018 0.003 0 6 -10000 0 6
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.018 0.002 0 2 -10000 0 2
YY1/LSF/HDAC1 0.013 0.041 -10000 0 -0.1 16 16
YY1/SAP30/HDAC1 0.013 0.04 -10000 0 -0.1 15 15
EP300 -0.018 0.002 0 2 -10000 0 2
STAT3 (dimer non-phopshorylated) -0.006 0.001 0 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.003 0 31 -10000 0 31
histone deacetylation -0.003 0.037 -10000 0 -0.17 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 -0.014 0.022 -10000 0 -0.11 8 8
nuclear export -0.022 0.004 0 4 -10000 0 4
PRKACA -0.018 0.003 0 4 -10000 0 4
GATAD2B -0.018 0.004 0 7 -10000 0 7
GATAD2A -0.018 0.001 0 1 -10000 0 1
GATA2/HDAC3 0.013 0.035 0.087 12 -0.15 4 16
GATA1/HDAC1 0.025 0.004 -10000 0 0 4 4
GATA1/HDAC3 0.013 0.039 0.087 12 -0.16 6 18
CHD4 -0.017 0.005 0 12 -10000 0 12
TNF-alpha/TNFR1A 0.022 0.008 -10000 0 0 20 20
SIN3/HDAC complex/Mad/Max -0.005 0.033 -10000 0 -0.26 2 2
NuRD Complex -0.017 0.052 -10000 0 -0.2 7 7
positive regulation of chromatin silencing 0.028 0.041 -10000 0 -0.12 9 9
SIN3B -0.018 0.001 0 1 -10000 0 1
MTA2 -0.018 0.003 0 5 -10000 0 5
SIN3A -0.018 0.002 0 3 -10000 0 3
XPO1 -0.018 0.003 0 4 -10000 0 4
SUMO1/HDAC1 0.016 0.026 -10000 0 -0.1 7 7
HDAC complex 0.041 0.01 -10000 0 0 10 10
GATA1/Fog1 0.023 0.007 -10000 0 0 12 12
FKBP25/HDAC1/HDAC2 0.031 0.01 -10000 0 0 15 15
TNF -0.018 0.004 0 8 -10000 0 8
negative regulation of cell growth -0.003 0.035 -10000 0 -0.26 2 2
NuRD/MBD2/PRMT5 Complex -0.009 0.031 -10000 0 -0.094 18 18
Ran/GTP/Exportin 1 0.017 0.026 -10000 0 -0.097 7 7
NF kappa B/RelA/I kappa B alpha -0.01 0.031 -10000 0 -0.16 5 5
SIN3/HDAC complex/NCoR1 -0.013 0.058 -10000 0 -0.25 7 7
TFCP2 -0.018 0.001 0 1 -10000 0 1
NR2C1 -0.018 0.002 0 3 -10000 0 3
MBD3 -0.018 0.003 0 4 -10000 0 4
MBD2 -0.016 0.006 0 19 -10000 0 19
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.013 0.028 0.2 1 -0.15 1 2
PLK1 -0.019 0.056 0.17 2 -0.19 10 12
CDKN1B -0.004 0.066 0.16 3 -0.21 10 13
FOXO3 -0.004 0.033 0.082 11 -0.086 14 25
KAT2B 0 0.001 0.002 2 -0.002 8 10
FOXO1/SIRT1 -0.013 0.025 0.084 3 -0.11 4 7
CAT -0.016 0.062 0.18 5 -0.18 10 15
CTNNB1 -0.015 0.007 0 28 -10000 0 28
AKT1 -0.016 0.008 0.018 6 -10000 0 6
FOXO1 -0.008 0.026 0.12 1 -0.11 4 5
MAPK10 -0.016 0.036 0.23 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.017 0.043 0.22 3 -10000 0 3
response to oxidative stress 0 0.001 0.002 2 -0.002 10 12
FOXO3A/SIRT1 -0.004 0.058 0.093 10 -0.12 24 34
XPO1 -0.018 0.003 0 4 -10000 0 4
EP300 -0.017 0.007 0.013 7 -10000 0 7
BCL2L11 0.012 0.007 -10000 0 -10000 0 0
FOXO1/SKP2 -0.012 0.023 0.085 3 -0.11 3 6
mol:GDP 0 0.001 0.002 2 -0.002 10 12
RAN -0.018 0.001 0 1 -10000 0 1
GADD45A -0.011 0.095 -10000 0 -0.57 4 4
YWHAQ -0.018 0.002 0 2 -10000 0 2
FOXO1/14-3-3 family -0.007 0.067 -10000 0 -0.24 9 9
MST1 -0.016 0.006 0 23 -10000 0 23
CSNK1D -0.018 0.003 0 4 -10000 0 4
CSNK1E -0.018 0.002 0 2 -10000 0 2
FOXO4/14-3-3 family 0.003 0.05 -10000 0 -0.23 6 6
YWHAB -0.017 0.005 0 12 -10000 0 12
MAPK8 -0.016 0.036 0.23 3 -10000 0 3
MAPK9 -0.015 0.036 0.23 3 -10000 0 3
YWHAG -0.018 0.003 0 5 -10000 0 5
YWHAE -0.018 0.002 0 2 -10000 0 2
YWHAZ -0.016 0.006 0 21 -10000 0 21
SIRT1 -0.014 0.012 0.019 19 -10000 0 19
SOD2 -0.023 0.056 0.17 1 -0.17 15 16
RBL2 -0.037 0.17 -10000 0 -0.74 8 8
RAL/GDP 0.022 0.004 -10000 0 0 4 4
CHUK -0.018 0.003 0 3 -10000 0 3
Ran/GTP 0.013 0.001 -10000 0 0 1 1
CSNK1G2 -0.018 0.003 0 4 -10000 0 4
RAL/GTP 0.021 0.003 -10000 0 0 4 4
CSNK1G1 -0.018 0.002 0 3 -10000 0 3
FASLG 0.012 0.007 -10000 0 -10000 0 0
SKP2 -0.016 0.006 0 19 -10000 0 19
USP7 -0.018 0.002 0 3 -10000 0 3
IKBKB -0.016 0.006 0.001 19 -10000 0 19
CCNB1 -0.019 0.053 0.15 1 -0.18 10 11
FOXO1-3a-4/beta catenin -0.018 0.047 0.14 2 -0.16 11 13
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.023 0.085 3 -0.11 3 6
CSNK1A1 -0.018 0.003 0 5 -10000 0 5
SGK1 0 0.001 0.002 2 -0.002 8 10
CSNK1G3 -0.018 0.003 0 6 -10000 0 6
Ran/GTP/Exportin 1 0.022 0.004 -10000 0 0 5 5
ZFAND5 -0.016 0.043 0.2 3 -0.27 1 4
SFN -0.018 0.003 0 4 -10000 0 4
CDK2 -0.017 0.007 0.016 7 -10000 0 7
FOXO3A/14-3-3 -0.001 0.055 -10000 0 -0.22 8 8
CREBBP -0.017 0.007 0.012 9 -10000 0 9
FBXO32 0.008 0.084 0.18 22 -0.2 7 29
BCL6 -0.016 0.054 -10000 0 -0.26 2 2
RALB -0.018 0.001 0 1 -10000 0 1
RALA -0.018 0.003 0 4 -10000 0 4
YWHAH -0.018 0.002 0 2 -10000 0 2
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.024 0.007 0 13 -10000 0 13
SNTA1 -0.016 0.006 0 23 -10000 0 23
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.024 0.007 0 12 -10000 0 12
MAPK12 -0.016 0.006 0 18 -10000 0 18
CCND1 -0.007 0.05 -10000 0 -0.36 3 3
p38 gamma/SNTA1 -0.01 0.041 0.2 4 -10000 0 4
MAP2K3 -0.018 0.003 0 4 -10000 0 4
PKN1 -0.018 0.002 0 3 -10000 0 3
G2/M transition checkpoint -0.015 0.017 0.19 1 -10000 0 1
MAP2K6 -0.011 0.003 0 12 -10000 0 12
MAPT -0.006 0.032 0.12 5 -0.21 1 6
MAPK13 -0.021 0.006 0 11 -10000 0 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.004 0.001 0 11 -10000 0 11
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL -0.018 0.004 0 7 -10000 0 7
Rac1/GDP 0.019 0.01 -9999 0 -0.02 7 7
DOCK1 -0.018 0.002 0 2 -10000 0 2
ITGA4 -0.018 0.002 0 3 -10000 0 3
RAC1 -0.017 0.004 0 10 -10000 0 10
alpha4/beta7 Integrin 0.025 0.004 -9999 0 0 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.018 0.002 0 2 -10000 0 2
alpha4/beta1 Integrin 0.032 0.009 -9999 0 0 12 12
alpha4/beta7 Integrin/Paxillin -0.029 0.007 -9999 0 -10000 0 0
lamellipodium assembly -0.017 0.042 -9999 0 -0.22 5 5
PIK3CA -0.013 0.008 0 49 -10000 0 49
PI3K 0.017 0.012 -9999 0 0 53 53
ARF6 -0.017 0.004 0 9 -10000 0 9
TLN1 -0.016 0.006 0 18 -10000 0 18
PXN -0.021 0.004 0 5 -10000 0 5
PIK3R1 -0.018 0.004 0 8 -10000 0 8
ARF6/GTP -0.034 0.012 -9999 0 -10000 0 0
cell adhesion -0.03 0.012 -9999 0 -10000 0 0
CRKL/CBL 0.021 0.009 -9999 0 0 28 28
alpha4/beta1 Integrin/Paxillin -0.028 0.008 -9999 0 -10000 0 0
ITGB1 -0.018 0.003 0 5 -10000 0 5
ITGB7 -0.018 0.001 0 1 -10000 0 1
ARF6/GDP 0.019 0.01 -9999 0 -0.02 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.032 0.01 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0.033 0.008 -9999 0 0 9 9
VCAM1 -0.018 0.003 0 4 -10000 0 4
alpha4/beta1 Integrin/Paxillin/Talin -0.03 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.032 0.01 -9999 0 -10000 0 0
BCAR1 -0.018 0.004 0 7 -10000 0 7
mol:GDP 0.032 0.01 -9999 0 -10000 0 0
CBL -0.016 0.006 0 24 -10000 0 24
PRKACA -0.018 0.003 0 4 -10000 0 4
GIT1 -0.018 0.002 0 2 -10000 0 2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.03 0.012 -9999 0 -10000 0 0
Rac1/GTP -0.019 0.046 -9999 0 -0.24 5 5
Effects of Botulinum toxin

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.011 0.002 0 4 -10000 0 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.021 0.01 -10000 0 0 29 29
STXBP1 -0.018 0.002 0 2 -10000 0 2
ACh/CHRNA1 0.009 0.018 0.058 10 -0.048 5 15
RAB3GAP2/RIMS1/UNC13B 0.027 0.014 -10000 0 0 34 34
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.017 0.005 0 14 -10000 0 14
mol:ACh 0.001 0.025 0.079 12 -0.053 5 17
RAB3GAP2 -0.018 0.003 0 5 -10000 0 5
STX1A/SNAP25/VAMP2 -0.022 0.022 0.069 5 -0.079 4 9
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.018 0.057 10 -0.048 5 15
UNC13B -0.016 0.006 0 18 -10000 0 18
CHRNA1 -0.018 0.004 0 8 -10000 0 8
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.01 0.019 0.058 11 -0.048 5 16
SNAP25 -0.001 0 0 14 -10000 0 14
VAMP2 0 0 -10000 0 0 2 2
SYT1 -0.018 0.002 0 2 -10000 0 2
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.017 0.003 0 6 -10000 0 6
STX1A/SNAP25 fragment 1/VAMP2 -0.022 0.022 0.069 5 -0.079 4 9
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.014 0.007 0 31 -10000 0 31
NFATC2 -0.015 0.006 0 24 -10000 0 24
NFATC3 -0.016 0.006 0 19 -10000 0 19
CD40LG -0.024 0.048 0.15 10 -10000 0 10
PTGS2 -0.024 0.046 0.15 9 -10000 0 9
JUNB -0.018 0.002 0 3 -10000 0 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.004 -10000 0 0 14 14
CaM/Ca2+ 0.012 0.004 -10000 0 0 14 14
CALM1 -0.017 0.005 0 14 -10000 0 14
JUN -0.018 0.003 0 4 -10000 0 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.003 -10000 0 0 12 12
FOSL1 -0.017 0.005 0 12 -10000 0 12
CREM -0.018 0.003 0 5 -10000 0 5
Jun/NFAT1-c-4/p21SNFT -0.025 0.013 -10000 0 -10000 0 0
FOS -0.018 0.004 0 8 -10000 0 8
IFNG -0.025 0.041 0.14 9 -10000 0 9
AP-1/NFAT1-c-4 -0.03 0.015 -10000 0 -10000 0 0
FASLG -0.024 0.046 0.15 9 -10000 0 9
NFAT1-c-4/ICER1 -0.025 0.015 -10000 0 -10000 0 0
IL2RA -0.024 0.046 0.15 9 -10000 0 9
FKBP12/FK506 0.012 0.003 -10000 0 0 12 12
CSF2 -0.024 0.046 0.15 9 -10000 0 9
JunB/Fra1/NFAT1-c-4 -0.029 0.016 -10000 0 -10000 0 0
IL4 -0.024 0.046 0.15 9 -10000 0 9
IL2 -0.017 0.16 -10000 0 -0.84 6 6
IL3 -0.011 0.12 -10000 0 -0.55 8 8
FKBP1A -0.017 0.005 0 12 -10000 0 12
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 -0.018 0.003 0 5 -10000 0 5
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.007 0.071 0.16 21 -0.14 2 23
CRP -0.009 0.07 0.26 8 -0.14 2 10
cell cycle arrest -0.012 0.048 0.19 3 -0.15 2 5
TIMP1 0.002 0.042 0.21 1 -10000 0 1
IL6ST -0.018 0.004 0 8 -10000 0 8
Rac1/GDP -0.019 0.029 -10000 0 -0.14 2 2
AP1 0.017 0.09 -10000 0 -0.32 8 8
GAB2 -0.017 0.005 0 15 -10000 0 15
TNFSF11 -0.014 0.044 0.21 2 -0.14 1 3
HSP90B1 -0.011 0.1 -10000 0 -0.57 5 5
GAB1 -0.018 0.004 0 7 -10000 0 7
MAPK14 -0.022 0.021 -10000 0 -0.1 9 9
AKT1 0.008 0.058 0.16 4 -0.34 3 7
FOXO1 0.007 0.058 0.16 5 -0.33 3 8
MAP2K6 -0.018 0.022 -10000 0 -0.099 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.025 0.027 -10000 0 -0.16 1 1
MITF -0.013 0.014 -10000 0 -0.092 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 -0.018 0.002 0 3 -10000 0 3
A2M -0.002 0.12 -10000 0 -1.1 2 2
CEBPB -0.017 0.005 0 11 -10000 0 11
GRB2/SOS1/GAB family/SHP2 0 0.081 -10000 0 -0.34 8 8
STAT3 -0.009 0.04 0.18 2 -10000 0 2
STAT1 0.004 0.077 -10000 0 -0.68 2 2
CEBPD 0.002 0.067 0.17 16 -0.14 2 18
PIK3CA -0.013 0.008 0 49 -10000 0 49
PI3K 0.017 0.012 -10000 0 0 53 53
JUN -0.018 0.003 0 4 -10000 0 4
PIAS3/MITF -0.02 0.026 -10000 0 -0.14 1 1
MAPK11 -0.021 0.019 -10000 0 -0.094 9 9
STAT3 (dimer)/FOXO1 -0.002 0.062 0.15 11 -0.21 4 15
GRB2/SOS1/GAB family 0.033 0.037 -10000 0 -0.11 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.017 -10000 0 -0.091 7 7
GRB2 -0.018 0.001 0 1 -10000 0 1
JAK2 -0.015 0.007 0 28 -10000 0 28
LBP -0.011 0.093 0.18 6 -0.37 6 12
PIK3R1 -0.018 0.004 0 8 -10000 0 8
JAK1 -0.018 0.002 0 3 -10000 0 3
MYC 0.013 0.078 0.18 23 -0.14 2 25
FGG -0.015 0.045 0.19 3 -0.14 1 4
macrophage differentiation -0.012 0.048 0.19 3 -0.15 2 5
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.037 0.023 -10000 0 -10000 0 0
JUNB -0.013 0.047 0.17 4 -0.14 2 6
FOS -0.018 0.004 0 8 -10000 0 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.013 0.023 -10000 0 -0.099 10 10
STAT1/PIAS1 0.012 0.037 -10000 0 -0.13 3 3
GRB2/SOS1/GAB family/SHP2/PI3K 0.012 0.059 0.14 2 -0.31 4 6
STAT3 (dimer) -0.011 0.048 0.19 3 -0.15 1 4
PRKCD -0.019 0.042 0.18 5 -0.13 1 6
IL6R -0.018 0.004 0 7 -10000 0 7
SOCS3 -0.011 0.041 0.15 1 -0.14 3 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.009 -10000 0 0 13 13
Rac1/GTP -0.019 0.028 -10000 0 -0.14 2 2
HCK -0.016 0.006 0 21 -10000 0 21
MAPKKK cascade 0.004 0.089 -10000 0 -0.37 7 7
bone resorption -0.014 0.044 0.21 2 -0.14 1 3
IRF1 -0.013 0.043 0.21 2 -0.14 1 3
mol:GDP -0.017 0.021 -10000 0 -0.099 9 9
SOS1 -0.018 0.002 0 3 -10000 0 3
VAV1 -0.017 0.021 -10000 0 -0.1 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.006 0.031 -10000 0 -0.31 1 1
PTPN11 0.013 0.007 -10000 0 -10000 0 0
IL6/IL6RA 0.023 0.007 -10000 0 0 14 14
gp130 (dimer)/TYK2/TYK2/LMO4 0.032 0.01 -10000 0 0 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.028 0.014 -10000 0 0 32 32
IL6 -0.018 0.004 0 8 -10000 0 8
PIAS3 -0.018 0.003 0 6 -10000 0 6
PTPRE -0.018 0.002 0 2 -10000 0 2
PIAS1 -0.018 0.002 0 3 -10000 0 3
RAC1 -0.017 0.004 0 10 -10000 0 10
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.012 0.023 -10000 0 -0.099 10 10
LMO4 -0.018 0.003 0 5 -10000 0 5
STAT3 (dimer)/PIAS3 -0.021 0.043 0.19 2 -0.16 2 4
MCL1 0.005 0.06 0.18 8 -0.27 3 11
FOXM1 transcription factor network

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.004 0.047 0.17 7 -0.15 1 8
PLK1 0.007 0.098 -10000 0 -0.71 3 3
BIRC5 0.02 0.011 -10000 0 -10000 0 0
HSPA1B 0.005 0.048 0.16 9 -10000 0 9
MAP2K1 -0.006 0.019 0.033 5 -10000 0 5
BRCA2 0.001 0.041 0.15 5 -0.15 1 6
FOXM1 0.007 0.044 0.16 5 -0.16 1 6
XRCC1 0.002 0.045 0.17 5 -0.15 1 6
FOXM1B/p19 -0.002 0.033 0.17 2 -10000 0 2
Cyclin D1/CDK4 -0.015 0.024 -10000 0 -0.15 1 1
CDC2 0.005 0.045 0.18 5 -10000 0 5
TGFA 0.004 0.049 0.15 6 -0.15 1 7
SKP2 0.02 0.067 0.18 21 -10000 0 21
CCNE1 -0.008 0.017 0.021 2 -10000 0 2
CKS1B 0.008 0.055 0.18 11 -0.15 1 12
RB1 0.015 0.066 -10000 0 -0.25 7 7
FOXM1C/SP1 0.005 0.046 0.16 4 -0.16 1 5
AURKB 0.012 0.078 -10000 0 -0.68 2 2
CENPF 0.006 0.052 0.18 9 -0.15 1 10
CDK4 -0.004 0.021 0.024 45 -10000 0 45
MYC -0.005 0.034 0.14 2 -0.15 1 3
CHEK2 -0.006 0.019 0.033 3 -10000 0 3
ONECUT1 0.011 0.052 0.15 7 -0.15 1 8
CDKN2A -0.014 0.008 0 44 -10000 0 44
LAMA4 0.001 0.04 0.15 5 -10000 0 5
FOXM1B/HNF6 0.011 0.054 0.15 7 -0.16 1 8
FOS 0.005 0.051 0.17 9 -0.15 1 10
SP1 -0.018 0.001 0 1 -10000 0 1
CDC25B 0.011 0.057 0.17 14 -0.15 1 15
response to radiation 0.001 0.004 0.015 5 -10000 0 5
CENPB 0.011 0.057 0.17 14 -0.15 1 15
CENPA 0.003 0.047 0.17 7 -0.15 1 8
NEK2 0.006 0.052 0.18 9 -0.15 1 10
HIST1H2BA 0.004 0.045 0.15 8 -10000 0 8
CCNA2 -0.007 0.017 0.021 2 -10000 0 2
EP300 -0.018 0.002 0 2 -10000 0 2
CCNB1/CDK1 0.003 0.045 0.18 5 -10000 0 5
CCNB2 0.001 0.04 0.15 5 -0.15 1 6
CCNB1 0.004 0.043 0.16 5 -10000 0 5
ETV5 0.05 0.096 0.19 47 -0.15 1 48
ESR1 0.002 0.044 0.16 6 -10000 0 6
CCND1 -0.014 0.023 0.088 2 -0.15 1 3
GSK3A -0.005 0.02 0.031 7 -10000 0 7
Cyclin A-E1/CDK1-2 0.033 0.01 -10000 0 -10000 0 0
CDK2 -0.008 0.017 0.021 2 -10000 0 2
G2/M transition of mitotic cell cycle -0.001 0.004 0.015 5 -10000 0 5
FOXM1B/Cbp/p300 0.006 0.052 0.16 5 -10000 0 5
GAS1 0.001 0.041 0.15 5 -0.15 1 6
MMP2 0.004 0.046 0.16 7 -0.15 1 8
RB1/FOXM1C 0.015 0.062 0.12 39 -0.17 1 40
CREBBP -0.018 0.002 0 3 -10000 0 3
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.021 0.006 -10000 0 0 12 12
EFNA5 -0.018 0.003 0 6 -9999 0 6
FYN -0.019 0.016 0.17 1 -9999 0 1
neuron projection morphogenesis 0.021 0.006 -10000 0 0 12 12
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.021 0.006 -10000 0 0 12 12
EPHA5 -0.018 0.003 0 6 -9999 0 6
Hedgehog signaling events mediated by Gli proteins

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC2 -0.018 0.003 0 6 -10000 0 6
GNB1/GNG2 0.031 0.01 -10000 0 0 15 15
forebrain development -0.011 0.077 -10000 0 -0.34 7 7
GNAO1 -0.017 0.004 0 10 -10000 0 10
SMO/beta Arrestin2 0.024 0.005 -10000 0 0 7 7
SMO -0.018 0.003 0 5 -10000 0 5
ARRB2 -0.018 0.002 0 2 -10000 0 2
GLI3/SPOP 0.01 0.06 0.16 3 -0.17 9 12
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B -0.016 0.006 0 20 -10000 0 20
GNAI2 -0.016 0.006 0 23 -10000 0 23
SIN3/HDAC complex 0.041 0.01 -10000 0 0 10 10
GNAI1 -0.018 0.003 0 4 -10000 0 4
XPO1 -0.018 0.003 0 4 -10000 0 4
GLI1/Su(fu) -0.009 0.091 -10000 0 -0.38 8 8
SAP30 -0.018 0.003 0 5 -10000 0 5
mol:GDP -0.018 0.003 0 5 -10000 0 5
MIM/GLI2A -0.015 0.007 0 28 -10000 0 28
IFT88 -0.018 0.004 0 7 -10000 0 7
GNAI3 -0.018 0.003 0 4 -10000 0 4
GLI2 0 0.044 0.17 2 -0.2 3 5
GLI3 0.002 0.059 0.16 3 -0.17 9 12
CSNK1D -0.018 0.003 0 4 -10000 0 4
CSNK1E -0.018 0.002 0 2 -10000 0 2
SAP18 -0.018 0.004 0 7 -10000 0 7
embryonic digit morphogenesis -0.018 0.004 0 7 -10000 0 7
GNG2 -0.018 0.004 0 7 -10000 0 7
Gi family/GTP -0.007 0.033 0.078 6 -0.17 5 11
SIN3B -0.018 0.001 0 1 -10000 0 1
SIN3A -0.018 0.002 0 3 -10000 0 3
GLI3/Su(fu) 0 0.055 0.12 2 -0.18 8 10
GLI2/Su(fu) -0.008 0.042 0.16 1 -0.16 6 7
FOXA2 0.015 0.016 -10000 0 -10000 0 0
neural tube patterning -0.011 0.077 -10000 0 -0.34 7 7
SPOP -0.018 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.005 0.042 -10000 0 -0.15 11 11
GNB1 -0.018 0.003 0 5 -10000 0 5
CSNK1G2 -0.018 0.003 0 4 -10000 0 4
CSNK1G3 -0.018 0.003 0 6 -10000 0 6
MTSS1 -0.015 0.007 0 28 -10000 0 28
embryonic limb morphogenesis -0.011 0.077 -10000 0 -0.34 7 7
SUFU -0.007 0.002 -10000 0 -10000 0 0
LGALS3 -0.018 0.004 0 8 -10000 0 8
catabolic process 0.003 0.069 0.22 2 -0.2 10 12
GLI3A/CBP -0.018 0.002 0 3 -10000 0 3
KIF3A -0.018 0.004 0 8 -10000 0 8
GLI1 -0.011 0.078 -10000 0 -0.35 7 7
RAB23 -0.017 0.004 0 9 -10000 0 9
CSNK1A1 -0.018 0.003 0 5 -10000 0 5
IFT172 -0.018 0.002 0 2 -10000 0 2
RBBP7 -0.018 0 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.005 0.041 -10000 0 -0.15 10 10
GNAZ -0.018 0.003 0 6 -10000 0 6
RBBP4 -0.018 0.003 0 4 -10000 0 4
CSNK1G1 -0.018 0.002 0 3 -10000 0 3
PIAS1 -0.018 0.002 0 3 -10000 0 3
PRKACA -0.018 0.003 0 4 -10000 0 4
GLI2/SPOP 0.008 0.046 0.16 2 -0.19 4 6
STK36 -0.018 0.004 0 8 -10000 0 8
Gi family/GNB1/GNG2/GDP -0.014 0.04 -10000 0 -0.12 14 14
PTCH1 -0.01 0.071 -10000 0 -0.32 7 7
MIM/GLI1 0 0.065 -10000 0 -0.3 6 6
CREBBP -0.018 0.002 0 3 -10000 0 3
Su(fu)/SIN3/HDAC complex -0.016 0.079 -10000 0 -0.27 10 10
Retinoic acid receptors-mediated signaling

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.018 0.003 0 4 -10000 0 4
HDAC3 -0.018 0.003 0 6 -10000 0 6
VDR -0.018 0.002 0 2 -10000 0 2
Cbp/p300/PCAF 0.022 0.004 -10000 0 0 5 5
EP300 -0.018 0.002 0 2 -10000 0 2
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.027 0.077 2 -0.15 4 6
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 -0.018 0.004 0 8 -10000 0 8
AKT1 -0.02 0.049 0.1 3 -0.13 12 15
RAR alpha/9cRA/Cyclin H -0.018 0.027 0.09 3 -0.17 1 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.005 0.03 -10000 0 -0.19 4 4
CDC2 -0.018 0.002 0 3 -10000 0 3
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.014 0.014 0.074 6 -0.084 1 7
NCOR2 -0.018 0.003 0 4 -10000 0 4
VDR/VDR/Vit D3 0.012 0.001 -10000 0 0 2 2
RXRs/RARs/NRIP1/9cRA -0.018 0.05 0.17 1 -0.16 11 12
NCOA2 -0.016 0.006 0 19 -10000 0 19
NCOA3 -0.017 0.005 0 11 -10000 0 11
NCOA1 -0.018 0.002 0 2 -10000 0 2
VDR/VDR/DNA -0.018 0.002 0 2 -10000 0 2
RARG -0.018 0.001 0 1 -10000 0 1
RAR gamma1/9cRA 0.022 0.004 -10000 0 0 5 5
MAPK3 -0.018 0.003 0 4 -10000 0 4
MAPK1 -0.018 0.003 0 6 -10000 0 6
MAPK8 -0.018 0.002 0 3 -10000 0 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.014 0.023 -10000 0 -0.17 1 1
RARA 0.001 0 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.027 -10000 0 -0.19 3 3
PRKCA -0.018 0.001 0 1 -10000 0 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.018 0.062 -10000 0 -0.17 21 21
RXRG -0.006 0.001 0 7 -10000 0 7
RXRA -0.004 0.014 0.098 3 -10000 0 3
RXRB -0.005 0.001 0 10 -10000 0 10
VDR/Vit D3/DNA 0.012 0.001 -10000 0 0 2 2
RBP1 -0.015 0.007 0 27 -10000 0 27
CRBP1/9-cic-RA 0.011 0.005 -10000 0 0 27 27
RARB -0.016 0.006 0 23 -10000 0 23
PRKCG -0.018 0.001 0 1 -10000 0 1
MNAT1 -0.018 0.004 0 8 -10000 0 8
RAR alpha/RXRs -0.02 0.042 -10000 0 -0.23 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.011 0.043 0.1 1 -0.14 10 11
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.059 0.13 1 -0.22 8 9
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.019 0.063 -10000 0 -0.17 21 21
positive regulation of DNA binding -0.018 0.024 0.074 3 -0.17 1 4
NRIP1 -0.023 0.079 0.19 2 -0.2 23 25
RXRs/RARs -0.02 0.082 -10000 0 -0.22 23 23
RXRs/RXRs/DNA/9cRA -0.005 0.016 -10000 0 -0.17 1 1
PRKACA -0.018 0.003 0 4 -10000 0 4
CDK7 -0.018 0.004 0 8 -10000 0 8
TFIIH 0.031 0.01 -10000 0 0 16 16
RAR alpha/9cRA 0.03 0.021 -10000 0 -0.1 2 2
CCNH -0.018 0.004 0 7 -10000 0 7
CREBBP -0.018 0.002 0 3 -10000 0 3
RAR gamma2/9cRA -0.033 0.013 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.022 0.006 -10000 0 0 10 10
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 -0.017 0.004 0 10 -10000 0 10
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.018 0.001 0 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.018 0.002 0 3 -10000 0 3
RAC1-CDC42/GTP/PAK family -0.002 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 -0.017 0.006 0 17 -10000 0 17
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 -0.018 0 -10000 0 -10000 0 0
FYN -0.018 0.003 0 6 -10000 0 6
MAP3K12 -0.018 0.001 0 1 -10000 0 1
FGR -0.018 0.003 0 4 -10000 0 4
p38 alpha/TAB1 0.015 0.064 0.13 5 -0.2 7 12
PRKG1 -0.018 0.003 0 6 -10000 0 6
DUSP8 -0.018 0.003 0 5 -10000 0 5
PGK/cGMP/p38 alpha 0.013 0.054 0.12 5 -0.18 7 12
apoptosis 0.014 0.061 0.13 5 -0.2 7 12
RAL/GTP 0.023 0.004 -10000 0 0 4 4
LYN -0.016 0.006 0 18 -10000 0 18
DUSP1 -0.018 0.004 0 8 -10000 0 8
PAK1 -0.017 0.005 0 15 -10000 0 15
SRC -0.017 0.005 0 14 -10000 0 14
RAC1/OSM/MEKK3/MKK3 0.04 0.013 -10000 0 -10000 0 0
TRAF6 -0.018 0.003 0 6 -10000 0 6
RAC1 -0.017 0.004 0 10 -10000 0 10
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 -0.018 0.003 0 6 -10000 0 6
RAC1-CDC42/GTP 0.021 0.006 -10000 0 0 14 14
MAPK11 0.009 0.062 0.14 9 -0.19 7 16
BLK -0.017 0.004 0 9 -10000 0 9
HCK -0.016 0.006 0 21 -10000 0 21
MAP2K3 -0.018 0.003 0 4 -10000 0 4
DUSP16 -0.017 0.005 0 11 -10000 0 11
DUSP10 -0.018 0.003 0 5 -10000 0 5
TRAF6/MEKK3 0.021 0.004 -10000 0 0 6 6
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
MAPK14 0.007 0.066 0.12 9 -0.21 7 16
positive regulation of innate immune response 0.009 0.075 0.15 10 -0.25 7 17
LCK -0.018 0.003 0 4 -10000 0 4
p38alpha-beta/MKP7 0.013 0.073 0.15 7 -0.24 7 14
p38alpha-beta/MKP5 0.017 0.074 0.15 10 -0.24 7 17
PGK/cGMP 0.012 0.002 -10000 0 0 6 6
PAK2 -0.013 0.008 0 45 -10000 0 45
p38alpha-beta/MKP1 0.016 0.074 0.15 8 -0.24 7 15
CDC42 -0.018 0.003 0 5 -10000 0 5
RALB -0.018 0.001 0 1 -10000 0 1
RALA -0.018 0.003 0 4 -10000 0 4
PAK3 -0.018 0 -10000 0 -10000 0 0
BCR signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.013 0.069 -10000 0 -0.23 11 11
IKBKB 0.005 0.075 0.2 3 -0.27 7 10
AKT1 0.021 0.072 0.19 16 -10000 0 16
IKBKG 0.015 0.044 0.15 3 -0.18 2 5
CALM1 0.02 0.046 0.18 7 -10000 0 7
PIK3CA -0.013 0.008 0 49 -10000 0 49
MAP3K1 -0.005 0.057 -10000 0 -0.26 4 4
MAP3K7 -0.018 0.003 0 6 -10000 0 6
mol:Ca2+ 0.024 0.044 0.16 8 -10000 0 8
DOK1 -0.018 0.002 0 2 -10000 0 2
AP-1 -0.002 0.053 0.15 2 -0.17 9 11
LYN -0.016 0.006 0 18 -10000 0 18
BLNK -0.018 0.002 0 3 -10000 0 3
SHC1 -0.018 0.004 0 7 -10000 0 7
BCR complex 0.025 0.002 -10000 0 0 1 1
CD22 -0.012 0.008 -10000 0 -10000 0 0
CAMK2G 0.017 0.047 0.16 9 -10000 0 9
CSNK2A1 -0.017 0.005 0 13 -10000 0 13
INPP5D -0.017 0.004 0 8 -10000 0 8
SHC/GRB2/SOS1 -0.041 0.019 -10000 0 -10000 0 0
GO:0007205 0.024 0.044 0.17 7 -10000 0 7
SYK -0.018 0.001 0 1 -10000 0 1
ELK1 0.018 0.045 0.19 4 -10000 0 4
NFATC1 -0.009 0.044 0.18 3 -10000 0 3
B-cell antigen/BCR complex 0.025 0.002 -10000 0 0 1 1
PAG1/CSK 0.022 0.008 -10000 0 0 19 19
NFKBIB 0.011 0.033 0.092 1 -0.12 7 8
HRAS 0.013 0.042 0.17 3 -0.14 1 4
NFKBIA 0.011 0.033 0.092 1 -0.11 7 8
NF-kappa-B/RelA/I kappa B beta 0.013 0.028 0.074 4 -0.082 8 12
RasGAP/Csk 0.043 0.018 -10000 0 -0.008 13 13
mol:GDP 0.026 0.043 0.18 4 -10000 0 4
PTEN -0.018 0.003 0 5 -10000 0 5
CD79B -0.018 0 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.013 0.027 0.074 4 -0.081 8 12
GRB2 -0.018 0.001 0 1 -10000 0 1
PI3K/BCAP/CD19 0.005 0.048 -10000 0 -10000 0 0
PIK3R1 -0.018 0.004 0 8 -10000 0 8
mol:IP3 0.023 0.043 0.16 9 -10000 0 9
CSK -0.018 0.002 0 3 -10000 0 3
FOS 0.015 0.048 0.17 8 -10000 0 8
CHUK 0.01 0.062 0.15 3 -0.28 4 7
IBTK -0.018 0.003 0 4 -10000 0 4
CARD11/BCL10/MALT1/TAK1 0.026 0.038 0.17 5 -10000 0 5
PTPN6 -0.015 0.012 0.081 1 -10000 0 1
RELA -0.017 0.005 0 11 -10000 0 11
BCL2A1 0.007 0.02 0.055 2 -0.064 7 9
VAV2 -0.002 0.031 0.14 6 -10000 0 6
ubiquitin-dependent protein catabolic process 0.011 0.033 0.091 1 -0.12 7 8
BTK 0.022 0.009 -10000 0 -10000 0 0
CD19 -0.011 0.008 -10000 0 -10000 0 0
MAP4K1 -0.018 0.003 0 4 -10000 0 4
CD72 -0.016 0.006 0 18 -10000 0 18
PAG1 -0.016 0.006 0 18 -10000 0 18
MAPK14 -0.005 0.057 0.16 4 -0.23 4 8
SH3BP5 -0.016 0.006 0 20 -10000 0 20
PIK3AP1 0.017 0.037 -10000 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.012 0.027 -10000 0 -0.24 1 1
RAF1 0.005 0.042 0.16 5 -10000 0 5
RasGAP/p62DOK/SHIP 0.04 0.022 -10000 0 -0.015 6 6
CD79A -0.018 0.001 0 1 -10000 0 1
re-entry into mitotic cell cycle -0.002 0.052 0.15 2 -0.16 9 11
RASA1 -0.018 0.004 0 8 -10000 0 8
MAPK3 -0.001 0.041 0.18 2 -10000 0 2
MAPK1 0.003 0.051 0.17 7 -10000 0 7
CD72/SHP1 -0.006 0.052 0.17 11 -10000 0 11
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAPK8 -0.009 0.053 0.15 1 -0.23 4 5
actin cytoskeleton organization -0.001 0.045 0.17 6 -10000 0 6
NF-kappa-B/RelA 0.025 0.058 0.16 2 -0.18 7 9
Calcineurin 0.037 0.038 0.17 6 -10000 0 6
PI3K -0.025 0.022 -10000 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.021 0.032 0.14 4 -10000 0 4
SOS1 -0.018 0.002 0 3 -10000 0 3
Bam32/HPK1 0.003 0.11 -10000 0 -0.56 6 6
DAPP1 -0.006 0.12 -10000 0 -0.61 6 6
cytokine secretion -0.009 0.043 0.18 3 -10000 0 3
mol:DAG 0.023 0.043 0.16 9 -10000 0 9
PLCG2 -0.017 0.005 0 11 -10000 0 11
MAP2K1 0.002 0.041 0.15 4 -10000 0 4
B-cell antigen/BCR complex/FcgammaRIIB 0.032 0.008 -10000 0 0 10 10
mol:PI-3-4-5-P3 0.008 0.067 0.19 8 -10000 0 8
ETS1 0.007 0.043 0.16 8 -10000 0 8
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.043 0.018 -10000 0 -0.009 1 1
B-cell antigen/BCR complex/LYN 0.009 0.008 -10000 0 -10000 0 0
MALT1 -0.016 0.006 0 21 -10000 0 21
TRAF6 -0.018 0.003 0 6 -10000 0 6
RAC1 -0.002 0.046 0.18 6 -10000 0 6
B-cell antigen/BCR complex/LYN/SYK -0.018 0.045 0.18 7 -10000 0 7
CARD11 0.026 0.058 0.2 11 -10000 0 11
FCGR2B -0.017 0.004 0 9 -10000 0 9
PPP3CA -0.018 0.003 0 6 -10000 0 6
BCL10 -0.018 0.003 0 4 -10000 0 4
IKK complex 0.008 0.037 0.11 7 -0.12 3 10
PTPRC -0.018 0.003 0 5 -10000 0 5
PDPK1 0.012 0.067 0.18 14 -10000 0 14
PPP3CB -0.018 0.002 0 2 -10000 0 2
PPP3CC -0.017 0.004 0 9 -10000 0 9
POU2F2 0.007 0.02 0.052 3 -0.063 8 11
S1P3 pathway

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.018 0.003 0 5 -10000 0 5
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.025 0.056 0.078 1 -0.15 23 24
GNAO1 -0.017 0.004 0 10 -10000 0 10
S1P/S1P3/G12/G13 0.021 0.005 -10000 0 0 9 9
AKT1 -0.008 0.09 -10000 0 -0.4 8 8
AKT3 0 0.045 -10000 0 -0.22 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.018 0.003 0 5 -10000 0 5
GNAI2 -0.016 0.006 0 23 -10000 0 23
GNAI3 -0.018 0.003 0 4 -10000 0 4
GNAI1 -0.018 0.003 0 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.003 0 4 -10000 0 4
mol:Ca2+ -0.004 0.002 -10000 0 -10000 0 0
MAPK3 -0.01 0.029 0.069 7 -0.16 4 11
MAPK1 -0.011 0.027 0.069 4 -0.16 4 8
JAK2 -0.009 0.03 0.069 5 -0.12 9 14
CXCR4 -0.011 0.031 0.069 7 -0.16 5 12
FLT1 -0.018 0.004 0 7 -10000 0 7
RhoA/GDP 0.011 0.004 -10000 0 0 23 23
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
SRC -0.01 0.029 0.069 7 -0.16 4 11
S1P/S1P3/Gi -0.004 0.002 -10000 0 -10000 0 0
RAC1 -0.017 0.004 0 10 -10000 0 10
RhoA/GTP 0.003 0.038 0.075 7 -0.1 13 20
VEGFA 0 0 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.004 0.002 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.012 0.003 -10000 0 0 7 7
RHOA -0.016 0.006 0 23 -10000 0 23
S1P/S1P3/Gq -0.006 0.001 -10000 0 -10000 0 0
GNAQ -0.018 0 -10000 0 -10000 0 0
GNAZ -0.018 0.003 0 6 -10000 0 6
G12/G13 0.024 0.006 -10000 0 0 9 9
GNA14 -0.018 0 -10000 0 -10000 0 0
GNA15 -0.018 0.003 0 5 -10000 0 5
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA13 -0.018 0 -10000 0 -10000 0 0
GNA11 -0.018 0.003 0 5 -10000 0 5
Rac1/GTP 0 0.042 0.075 6 -0.1 22 28
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.018 0.002 0 2 -10000 0 2
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 -0.018 0.002 0 3 -10000 0 3
TCEB1 -0.016 0.006 0 19 -10000 0 19
HIF1A/p53 -0.007 0.043 0.15 4 -0.25 2 6
HIF1A -0.007 0.033 -10000 0 -0.27 2 2
COPS5 -0.017 0.006 0 17 -10000 0 17
VHL/Elongin B/Elongin C/RBX1/CUL2 0.039 0.022 -10000 0 -10000 0 0
FIH (dimer) -0.018 0.002 0 2 -10000 0 2
CDKN2A -0.014 0.008 0 44 -10000 0 44
ARNT/IPAS 0.024 0.005 -10000 0 0 8 8
HIF1AN -0.018 0.002 0 2 -10000 0 2
GNB2L1 -0.017 0.004 0 10 -10000 0 10
HIF1A/ARNT -0.009 0.043 0.15 4 -0.27 2 6
CUL2 -0.018 0.003 0 5 -10000 0 5
OS9 -0.018 0.002 0 2 -10000 0 2
RACK1/Elongin B/Elongin C 0.029 0.013 -10000 0 0 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.007 0.032 -10000 0 -0.26 2 2
PHD1-3/OS9 0.04 0.013 -10000 0 0 16 16
HIF1A/RACK1/Elongin B/Elongin C -0.017 0.04 0.12 3 -0.25 2 5
VHL -0.016 0.006 0 19 -10000 0 19
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 -0.008 0.04 0.15 2 -0.27 2 4
EGLN3 -0.018 0.004 0 8 -10000 0 8
EGLN2 -0.018 0.002 0 2 -10000 0 2
EGLN1 -0.018 0.003 0 5 -10000 0 5
TP53 -0.018 0.003 0 4 -10000 0 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.04 0.16 -10000 0 -0.48 19 19
ARNT -0.018 0.003 0 6 -10000 0 6
ARD1A -0.018 0 -10000 0 -10000 0 0
RBX1 -0.018 0.002 0 2 -10000 0 2
HIF1A/p19ARF -0.009 0.034 0.15 1 -0.24 2 3
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.027 0.01 -9999 0 0 20 20
MAPK9 -0.002 0 0 8 -9999 0 8
adrenocorticotropin secretion -0.01 0.003 0 17 -9999 0 17
GNB1/GNG2 0.022 0.006 -9999 0 0 11 11
GNB1 -0.018 0.003 0 5 -9999 0 5
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 -0.002 0 0 8 -9999 0 8
Gs family/GTP 0.01 0.003 -9999 0 0 13 13
EntrezGene:2778 0 0 -9999 0 -9999 0 0
vasopressin secretion 0 0 -9999 0 -9999 0 0
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
glutamate secretion 0.002 0.001 -9999 0 0 13 13
GNAL -0.017 0.005 0 13 -9999 0 13
GNG2 -0.018 0.004 0 7 -9999 0 7
CRH -0.017 0.006 0 17 -9999 0 17
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 -0.002 0 0 3 -9999 0 3
MAPK11 -0.002 0 0 7 -9999 0 7
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.004 0 10 -10000 0 10
CDC42/GTP 0 0.044 0.075 7 -0.1 21 28
PLCG1 -0.01 0.029 0.069 7 -0.16 4 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 -0.016 0.006 0 23 -10000 0 23
GNAI3 -0.018 0.003 0 4 -10000 0 4
G12/G13 0.024 0.006 -10000 0 0 9 9
cell migration 0 0.043 0.073 7 -0.1 21 28
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.01 0.029 0.069 7 -0.16 4 11
MAPK1 -0.011 0.027 0.069 4 -0.16 4 8
S1P/S1P5/Gi -0.004 0.002 -10000 0 -10000 0 0
GNAI1 -0.018 0.003 0 4 -10000 0 4
CDC42/GDP 0.012 0.002 -10000 0 0 5 5
S1P/S1P5/G12 0.011 0.003 -10000 0 0 9 9
RHOA -0.013 0.033 0.17 5 -10000 0 5
S1P/S1P4/Gi -0.004 0.002 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.018 0.003 0 6 -10000 0 6
S1P/S1P4/G12/G13 0.021 0.005 -10000 0 0 9 9
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA13 -0.018 0 -10000 0 -10000 0 0
CDC42 -0.018 0.003 0 5 -10000 0 5
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.022 0.003 0 4 -10000 0 4
SMARCC1 -0.003 0.002 -10000 0 -10000 0 0
REL -0.018 0.002 0 3 -10000 0 3
HDAC7 -0.021 0.039 0.13 5 -10000 0 5
JUN -0.018 0.003 0 4 -10000 0 4
EP300 -0.018 0.002 0 2 -10000 0 2
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.008 0.003 12 -10000 0 12
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.017 0.048 0.16 5 -10000 0 5
MAP2K6 -0.012 0.015 0.021 29 -10000 0 29
BRM/BAF57 0.022 0.009 -10000 0 0 24 24
MAP2K4 -0.012 0.015 0.021 29 -10000 0 29
SMARCA2 -0.016 0.006 0 21 -10000 0 21
PDE9A 0 0.055 -10000 0 -0.48 2 2
NCOA2 -0.016 0.006 0 19 -10000 0 19
CEBPA -0.018 0.003 0 4 -10000 0 4
EHMT2 -0.018 0.004 0 7 -10000 0 7
cell proliferation -0.001 0.073 0.2 10 -0.16 3 13
NR0B1 -0.018 0 -10000 0 -10000 0 0
EGR1 -0.018 0.003 0 5 -10000 0 5
RXRs/9cRA 0.03 0.009 -10000 0 0 14 14
AR/RACK1/Src -0.011 0.057 0.16 13 -10000 0 13
AR/GR -0.004 0.039 0.1 11 -10000 0 11
GNB2L1 -0.017 0.004 0 10 -10000 0 10
PKN1 -0.018 0.002 0 3 -10000 0 3
RCHY1 -0.018 0.003 0 6 -10000 0 6
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.02 0.007 0.005 9 -10000 0 9
T-DHT/AR/TIF2/CARM1 -0.017 0.045 0.16 6 -10000 0 6
SRC -0.029 0.014 -10000 0 -10000 0 0
NR3C1 -0.018 0.003 0 5 -10000 0 5
KLK3 0.007 0.069 0.19 15 -0.21 4 19
APPBP2 -0.012 0.016 0.02 31 -10000 0 31
TRIM24 -0.018 0.004 0 7 -10000 0 7
T-DHT/AR/TIP60 -0.021 0.012 0.009 2 -10000 0 2
TMPRSS2 0 0.055 -10000 0 -0.48 2 2
RXRG -0.018 0.003 0 5 -10000 0 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA -0.018 0.001 0 1 -10000 0 1
RXRB -0.018 0.004 0 8 -10000 0 8
CARM1 -0.018 0.002 0 3 -10000 0 3
NR2C2 -0.016 0.006 0 20 -10000 0 20
KLK2 -0.01 0.041 0.15 6 -10000 0 6
AR -0.011 0.007 0.005 2 -10000 0 2
SENP1 -0.018 0.001 0 1 -10000 0 1
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 -0.018 0.004 0 7 -10000 0 7
SRY -0.018 0 -10000 0 -10000 0 0
GATA2 -0.016 0.006 0 20 -10000 0 20
MYST2 -0.018 0 -10000 0 -10000 0 0
HOXB13 -0.018 0 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.011 0.06 0.17 13 -10000 0 13
positive regulation of transcription -0.016 0.006 0 20 -10000 0 20
DNAJA1 -0.013 0.013 0.02 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.001 -10000 0 -10000 0 0
NCOA1 -0.003 0.033 0.082 21 -10000 0 21
SPDEF -0.018 0.004 0 8 -10000 0 8
T-DHT/AR/TIF2 0 0.039 0.12 5 -10000 0 5
T-DHT/AR/Hsp90 -0.021 0.012 0.009 2 -10000 0 2
GSK3B -0.012 0.013 0.019 21 -10000 0 21
NR2C1 -0.018 0.002 0 3 -10000 0 3
mol:T-DHT -0.027 0.012 0.009 2 -10000 0 2
SIRT1 -0.018 0.002 0 2 -10000 0 2
ZMIZ2 0 0 -10000 0 -10000 0 0
POU2F1 -0.018 0.003 0 5 -10000 0 5
T-DHT/AR/DAX-1 -0.014 0.044 0.16 6 -10000 0 6
CREBBP -0.018 0.002 0 3 -10000 0 3
SMARCE1 -0.018 0.003 0 4 -10000 0 4
Ras signaling in the CD4+ TCR pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.008 0.051 -9999 0 -0.25 4 4
MAP3K8 -0.018 0.003 0 5 -10000 0 5
FOS -0.001 0.049 -9999 0 -0.25 4 4
PRKCA -0.018 0.001 0 1 -10000 0 1
PTPN7 -0.018 0.003 0 6 -10000 0 6
HRAS -0.018 0.003 0 5 -10000 0 5
PRKCB 0 0 -9999 0 -10000 0 0
NRAS -0.017 0.004 0 9 -10000 0 9
RAS family/GTP 0.028 0.011 -9999 0 0 22 22
MAPK3 -0.002 0.066 -9999 0 -0.4 4 4
MAP2K1 -0.007 0.029 -9999 0 -0.099 11 11
ELK1 -0.018 0 -9999 0 -10000 0 0
BRAF -0.002 0.001 0 17 -10000 0 17
mol:GTP 0 0 -9999 0 -10000 0 0
MAPK1 0.005 0.033 -9999 0 -0.35 1 1
RAF1 -0.002 0.001 0 27 -10000 0 27
KRAS -0.017 0.005 0 11 -10000 0 11
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.016 0.013 0.079 1 -10000 0 1
CLOCK -0.018 0.004 0 7 -10000 0 7
TIMELESS/CRY2 -0.007 0.015 0.058 8 -10000 0 8
DEC1/BMAL1 0.024 0.005 -10000 0 0 6 6
ATR -0.015 0.007 0 28 -10000 0 28
NR1D1 -0.003 0.001 0 16 -10000 0 16
ARNTL -0.018 0.003 0 5 -10000 0 5
TIMELESS -0.003 0.001 0 14 -10000 0 14
NPAS2 -0.018 0.002 0 3 -10000 0 3
CRY2 -0.018 0.004 0 7 -10000 0 7
mol:CO 0 0 -10000 0 -10000 0 0
CHEK1 -0.016 0.006 0 22 -10000 0 22
mol:HEME 0 0 -10000 0 -10000 0 0
PER1 -0.018 0.002 0 2 -10000 0 2
BMAL/CLOCK/NPAS2 0.032 0.009 -10000 0 0 13 13
BMAL1/CLOCK -0.002 0.044 -10000 0 -0.21 6 6
S phase of mitotic cell cycle 0.016 0.013 0.079 1 -10000 0 1
TIMELESS/CHEK1/ATR 0.016 0.013 0.08 1 -10000 0 1
mol:NADPH 0 0 -10000 0 -10000 0 0
PER1/TIMELESS -0.007 0.015 0.058 8 -10000 0 8
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.018 0.001 0 1 -10000 0 1
Presenilin action in Notch and Wnt signaling

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.014 0.07 -10000 0 -0.38 5 5
HDAC1 -0.018 0.003 0 4 -10000 0 4
AES -0.018 0.003 0 5 -10000 0 5
FBXW11 -0.018 0.004 0 8 -10000 0 8
DTX1 -0.018 0.001 0 1 -10000 0 1
LRP6/FZD1 0.023 0.008 -10000 0 0 17 17
TLE1 -0.018 0 -10000 0 -10000 0 0
AP1 -0.008 0.029 0.064 2 -0.17 4 6
NCSTN -0.018 0.004 0 7 -10000 0 7
ADAM10 -0.018 0.002 0 3 -10000 0 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.002 0.093 -10000 0 -0.68 3 3
NICD/RBPSUH -0.003 0.066 -10000 0 -0.38 5 5
WIF1 -0.018 0.004 0 8 -10000 0 8
NOTCH1 -0.002 0.07 -10000 0 -0.4 5 5
PSENEN -0.018 0.002 0 3 -10000 0 3
KREMEN2 -0.018 0.002 0 3 -10000 0 3
DKK1 -0.018 0.003 0 4 -10000 0 4
beta catenin/beta TrCP1 -0.011 0.089 0.15 1 -0.21 20 21
APH1B -0.018 0.002 0 3 -10000 0 3
APH1A -0.018 0.004 0 7 -10000 0 7
AXIN1 0.003 0.066 -10000 0 -0.42 3 3
CtBP/CBP/TCF1/TLE1/AES -0.01 0.025 -10000 0 -0.17 4 4
PSEN1 -0.018 0.004 0 7 -10000 0 7
FOS -0.018 0.004 0 8 -10000 0 8
JUN -0.018 0.003 0 4 -10000 0 4
MAP3K7 -0.018 0.003 0 6 -10000 0 6
CTNNB1 -0.021 0.091 0.15 1 -0.23 18 19
MAPK3 -0.018 0.003 0 4 -10000 0 4
DKK2/LRP6/Kremen 2 0.031 0.011 -10000 0 0 17 17
HNF1A 0 0 -10000 0 -10000 0 0
CTBP1 -0.017 0.005 0 15 -10000 0 15
MYC 0.007 0.063 -10000 0 -0.78 1 1
NKD1 -0.017 0.005 0 11 -10000 0 11
FZD1 -0.018 0.004 0 8 -10000 0 8
NOTCH1 precursor/Deltex homolog 1 0.01 0.07 -10000 0 -0.38 5 5
apoptosis -0.008 0.029 0.064 2 -0.17 4 6
Delta 1/NOTCHprecursor 0.01 0.069 -10000 0 -0.38 5 5
DLL1 -0.018 0.003 0 6 -10000 0 6
PPARD -0.008 0.15 -10000 0 -0.92 4 4
Gamma Secretase 0.045 0.017 -10000 0 -10000 0 0
APC -0.002 0.075 -10000 0 -0.34 6 6
DVL1 -0.002 0.001 -10000 0 -10000 0 0
CSNK2A1 -0.017 0.005 0 13 -10000 0 13
MAP3K7IP1 -0.018 0.002 0 2 -10000 0 2
DKK1/LRP6/Kremen 2 0.031 0.011 -10000 0 0 17 17
LRP6 -0.017 0.005 0 11 -10000 0 11
CSNK1A1 -0.018 0.003 0 5 -10000 0 5
NLK -0.006 0.001 -10000 0 -10000 0 0
CCND1 -0.004 0.11 -10000 0 -0.78 3 3
WNT1 -0.018 0.002 0 2 -10000 0 2
Axin1/APC/beta catenin -0.01 0.096 -10000 0 -0.37 8 8
DKK2 -0.018 0.003 0 6 -10000 0 6
NOTCH1 precursor/DVL1 -0.004 0.08 -10000 0 -0.34 7 7
GSK3B -0.016 0.006 0 20 -10000 0 20
FRAT1 -0.018 0.002 0 3 -10000 0 3
NOTCH/Deltex homolog 1 0.015 0.071 -10000 0 -0.38 5 5
PPP2R5D 0.006 0.05 -10000 0 -0.34 3 3
MAPK1 -0.018 0.003 0 6 -10000 0 6
WNT1/LRP6/FZD1 0.037 0.016 -10000 0 0 26 26
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP -0.018 0.002 0 3 -10000 0 3
RXR and RAR heterodimerization with other nuclear receptor

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.019 0.026 0.3 1 -10000 0 1
VDR -0.018 0.002 0 2 -10000 0 2
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.006 0.002 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols -0.004 0.002 -10000 0 -10000 0 0
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.029 0.055 -10000 0 -0.17 22 22
RXRs/NUR77 0.04 0.013 -10000 0 -10000 0 0
RXRs/PPAR -0.017 0.028 -10000 0 -0.096 17 17
NCOR2 -0.018 0.003 0 4 -10000 0 4
VDR/VDR/Vit D3 0.012 0.001 -10000 0 0 2 2
RARs/VDR/DNA/Vit D3 0.034 0.015 -10000 0 0 26 26
RARA -0.018 0.003 0 5 -10000 0 5
NCOA1 -0.018 0.002 0 2 -10000 0 2
VDR/VDR/DNA -0.018 0.002 0 2 -10000 0 2
RARs/RARs/DNA/9cRA 0.026 0.011 -10000 0 0 26 26
RARG -0.018 0.001 0 1 -10000 0 1
RPS6KB1 -0.018 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.028 0.054 -10000 0 -0.17 21 21
THRA -0.018 0.003 0 4 -10000 0 4
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.012 0.001 -10000 0 0 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.03 0.009 -10000 0 0 14 14
NR1H4 -0.018 0.002 0 2 -10000 0 2
RXRs/LXRs/DNA 0.045 0.017 -10000 0 -10000 0 0
NR1H2 -0.018 0.001 0 1 -10000 0 1
NR1H3 -0.018 0.003 0 4 -10000 0 4
RXRs/VDR/DNA/Vit D3 0.037 0.012 -10000 0 0 16 16
NR4A1 -0.018 0.001 0 1 -10000 0 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.004 0.001 -10000 0 -10000 0 0
RXRG -0.018 0.003 0 5 -10000 0 5
RXR alpha/CCPG 0.013 0.001 -10000 0 0 1 1
RXRA -0.018 0.001 0 1 -10000 0 1
RXRB -0.018 0.004 0 8 -10000 0 8
THRB -0.016 0.006 0 24 -10000 0 24
PPARG -0.016 0.006 0 20 -10000 0 20
PPARD -0.018 0.004 0 8 -10000 0 8
TNF -0.007 0.016 0.068 7 -10000 0 7
mol:Oxysterols 0 0 -10000 0 -10000 0 0
cholesterol transport -0.004 0.002 -10000 0 -10000 0 0
PPARA -0.018 0.003 0 4 -10000 0 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.016 0.006 0 23 -10000 0 23
RXRs/NUR77/BCL2 -0.008 0.018 -10000 0 -0.17 2 2
SREBF1 -0.007 0.016 0.068 7 -10000 0 7
RXRs/RXRs/DNA/9cRA 0.03 0.009 -10000 0 0 14 14
ABCA1 -0.008 0.014 0.068 5 -10000 0 5
RARs/THRs 0.042 0.019 -10000 0 -0.008 1 1
RXRs/FXR 0.04 0.013 -10000 0 0 15 15
BCL2 -0.016 0.006 0 22 -10000 0 22
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.01 0.062 -10000 0 -0.55 2 2
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 -0.018 0.002 0 3 -10000 0 3
TCEB1 -0.016 0.006 0 19 -10000 0 19
VHL/Elongin B/Elongin C/HIF2A 0.025 0.028 -10000 0 -0.097 2 2
EPO -0.013 0.019 0.081 4 -0.11 1 5
FIH (dimer) -0.018 0.002 0 2 -10000 0 2
APEX1 -0.018 0.003 0 6 -10000 0 6
SERPINE1 -0.02 0.021 0.079 4 -0.12 1 5
FLT1 -0.051 0.18 -10000 0 -0.55 20 20
ADORA2A -0.02 0.02 0.067 5 -0.11 1 6
germ cell development -0.018 0.022 0.078 6 -10000 0 6
SLC11A2 -0.02 0.023 0.079 6 -0.12 1 7
BHLHE40 -0.015 0.021 0.075 6 -0.11 1 7
HIF1AN -0.018 0.002 0 2 -10000 0 2
HIF2A/ARNT/SIRT1 -0.012 0.031 0.096 11 -10000 0 11
ETS1 -0.016 0.006 0 22 -10000 0 22
CITED2 0.002 0.08 -10000 0 -0.5 4 4
KDR -0.05 0.18 -10000 0 -0.53 20 20
PGK1 -0.02 0.023 0.079 6 -0.12 1 7
SIRT1 -0.018 0.002 0 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.016 0.027 0.1 6 -0.12 1 7
EPAS1 -0.006 0.002 -10000 0 -10000 0 0
SP1 -0.018 0.001 0 1 -10000 0 1
ABCG2 -0.019 0.021 0.079 5 -10000 0 5
EFNA1 -0.021 0.022 0.079 5 -0.12 1 6
FXN -0.02 0.021 0.068 6 -0.11 1 7
POU5F1 -0.018 0.023 0.079 6 -10000 0 6
neuron apoptosis 0.015 0.026 0.12 1 -0.1 6 7
EP300 -0.018 0.002 0 2 -10000 0 2
EGLN3 -0.018 0.004 0 8 -10000 0 8
EGLN2 -0.018 0.002 0 2 -10000 0 2
EGLN1 -0.018 0.003 0 5 -10000 0 5
VHL/Elongin B/Elongin C 0.028 0.014 -10000 0 0 32 32
VHL -0.016 0.006 0 19 -10000 0 19
ARNT -0.018 0.003 0 6 -10000 0 6
SLC2A1 -0.02 0.021 0.068 6 -0.11 1 7
TWIST1 -0.02 0.021 0.068 5 -0.11 1 6
ELK1 -0.018 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.027 0.03 -10000 0 -0.1 4 4
VEGFA -0.015 0.021 0.075 6 -0.11 1 7
CREBBP -0.018 0.002 0 3 -10000 0 3
Arf6 trafficking events

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.018 0.002 0 2 -10000 0 2
CLTC 0.004 0.047 -10000 0 -0.3 3 3
calcium ion-dependent exocytosis 0 0.025 0.11 5 -0.12 2 7
Dynamin 2/GTP -0.021 0.006 0 12 -10000 0 12
EXOC4 -0.018 0.003 0 4 -10000 0 4
CD59 -0.003 0.031 -10000 0 -0.26 2 2
CPE -0.016 0.005 0 14 -10000 0 14
CTNNB1 -0.015 0.007 0 28 -10000 0 28
membrane fusion -0.003 0.007 -10000 0 -0.068 2 2
CTNND1 -0.021 0.033 0.16 5 -10000 0 5
DNM2 -0.018 0.002 0 3 -10000 0 3
mol:PI-4-5-P2 -0.002 0.034 0.13 6 -0.14 3 9
TSHR -0.016 0.005 0 14 -10000 0 14
INS -0.005 0.087 -10000 0 -0.45 6 6
BIN1 -0.018 0.002 0 2 -10000 0 2
mol:Choline -0.003 0.007 -10000 0 -0.068 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.004 0 9 -10000 0 9
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 -0.017 0.004 0 9 -10000 0 9
mol:Ca2+ -0.021 0.006 0 12 -10000 0 12
JUP -0.003 0.031 -10000 0 -0.26 2 2
ASAP2/amphiphysin II 0.021 0.005 -10000 0 0 10 10
ARF6/GTP 0.012 0.003 -10000 0 0 9 9
CDH1 -0.003 0.031 -10000 0 -0.26 2 2
clathrin-independent pinocytosis 0.012 0.003 -10000 0 0 9 9
MAPK8IP3 -0.018 0.002 0 3 -10000 0 3
positive regulation of endocytosis 0.012 0.003 -10000 0 0 9 9
EXOC2 -0.017 0.004 0 10 -10000 0 10
substrate adhesion-dependent cell spreading -0.009 0.03 0.073 1 -0.14 8 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 -0.018 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.014 0.033 0.24 2 -10000 0 2
positive regulation of phagocytosis -0.016 0.005 0 14 -10000 0 14
ARF6/GTP/JIP3 0.021 0.006 -10000 0 0 12 12
ACAP1 0 0.019 0.088 4 -0.16 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.004 0.03 -10000 0 -0.26 2 2
clathrin heavy chain/ACAP1 -0.005 0.033 0.14 1 -0.24 2 3
JIP4/KLC1 0.021 0.005 -10000 0 0 9 9
EXOC1 -0.018 0.004 0 7 -10000 0 7
exocyst -0.009 0.03 0.073 1 -0.14 8 9
RALA/GTP 0.012 0.002 -10000 0 0 4 4
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.022 0.005 -10000 0 0 9 9
receptor recycling 0.012 0.003 -10000 0 0 9 9
CTNNA1 -0.02 0.036 0.16 6 -10000 0 6
NME1 -0.017 0.004 0 9 -10000 0 9
clathrin coat assembly 0.005 0.048 -10000 0 -0.3 3 3
IL2RA -0.003 0.031 -10000 0 -0.26 2 2
VAMP3 -0.016 0.005 0 14 -10000 0 14
GLUT4/clathrin heavy chain/ACAP1 0.015 0.037 -10000 0 -0.2 3 3
EXOC6 -0.018 0.002 0 3 -10000 0 3
PLD1 -0.002 0.005 -10000 0 -0.047 2 2
PLD2 -0.002 0.006 -10000 0 -0.047 3 3
EXOC5 -0.018 0.004 0 7 -10000 0 7
PIP5K1C -0.002 0.027 0.12 4 -0.16 2 6
SDC1 -0.003 0.031 -10000 0 -0.26 2 2
ARF6/GDP -0.017 0.004 0 9 -10000 0 9
EXOC7 -0.018 0.001 0 1 -10000 0 1
E-cadherin/beta catenin 0.015 0.034 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.003 0.007 -10000 0 -0.068 2 2
endocytosis -0.02 0.005 0 10 -10000 0 10
SCAMP2 -0.018 0.002 0 3 -10000 0 3
ADRB2 -0.002 0.045 -10000 0 -0.29 3 3
EXOC3 -0.015 0.007 0 27 -10000 0 27
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.021 0.006 0 12 -10000 0 12
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.002 0.046 -10000 0 -0.29 3 3
RALA -0.018 0.003 0 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.039 0.16 2 -0.25 2 4
TCGA08_retinoblastoma

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.012 0.012 0.024 7 -10000 0 7
CDKN2C 0.008 0.018 -10000 0 -0.032 6 6
CDKN2A 0.013 0.012 -10000 0 -0.024 8 8
CCND2 0.002 0.001 -10000 0 -10000 0 0
RB1 -0.005 0.011 -10000 0 -0.084 3 3
CDK4 0.002 0.002 -10000 0 -10000 0 0
CDK6 0.003 0.002 -10000 0 -10000 0 0
G1/S progression 0.032 0.063 0.16 29 -10000 0 29
Class IB PI3K non-lipid kinase events

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.018 0.003 -9999 0 0 6 6
PI3K Class IB/PDE3B -0.018 0.003 0 6 -9999 0 6
PDE3B -0.018 0.003 0 6 -9999 0 6
Arf1 pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.004 0.025 0.13 4 -0.11 2 6
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.006 0.021 0.12 3 -0.11 1 4
AP2 0.018 0.011 -10000 0 0 46 46
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.021 0.008 -10000 0 -0.028 1 1
CLTB -0.018 0.004 0 7 -10000 0 7
coatomer protein complex/ARF1/GTP/ER cargo protein -0.006 0.003 0.017 1 -10000 0 1
CD4 -0.017 0.005 0 12 -10000 0 12
CLTA -0.017 0.005 0 16 -10000 0 16
mol:GTP -0.003 0.001 0.002 5 -10000 0 5
ARFGAP1 -0.01 0.003 0 10 -10000 0 10
mol:PI-4-5-P2 -0.004 0.006 0.072 1 -10000 0 1
ARF1/GTP -0.013 0.005 0.024 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.009 0.011 -10000 0 -0.081 3 3
mol:Choline -0.004 0.006 0.073 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.018 0.009 0.022 7 -10000 0 7
DDEF1 -0.002 0.006 0.073 1 -10000 0 1
ARF1/GDP -0.002 0.008 -10000 0 -0.088 1 1
AP2M1 -0.014 0.008 0 44 -10000 0 44
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.015 0.006 0.016 2 -10000 0 2
Rac/GTP -0.01 0.009 0.02 11 -10000 0 11
ARF1/GTP/GGA3/ARF-GAP1 -0.019 0.01 0.027 4 -10000 0 4
ARFIP2 -0.02 0.004 -10000 0 -0.04 1 1
COPA -0.018 0.004 0 7 -10000 0 7
RAC1 -0.017 0.004 0 10 -10000 0 10
ARF1/GTP/coatomer protein complex -0.002 0.033 0.075 8 -0.14 7 15
ARF1/GTP/ARHGAP10 0.01 0.002 -10000 0 0 7 7
GGA3 -0.018 0.001 0 1 -10000 0 1
ARF1/GTP/Membrin 0.012 0.005 -10000 0 -10000 0 0
AP2A1 -0.018 0.002 0 2 -10000 0 2
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.009 0.028 -10000 0 -0.16 5 5
ARF1/GDP/Membrin 0.015 0.007 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.02 0.011 -10000 0 -0.023 7 7
CYTH2 -0.003 0.001 0.002 5 -10000 0 5
ARF1/GTP/GGA3 0.022 0.004 -10000 0 0 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.012 0.003 -10000 0 0 10 10
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.002 0.023 0.064 7 -0.094 6 13
PLD2 -0.004 0.006 0.073 1 -10000 0 1
ARF-GAP1/v-SNARE -0.01 0.003 0 10 -10000 0 10
PIP5K1A -0.004 0.006 0.072 1 -10000 0 1
ARF1/GTP/Membrin/GBF1/p115 -0.008 0.01 0.04 4 -0.079 1 5
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.006 0.073 1 -10000 0 1
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 0 10 -10000 0 10
GOSR2 0.005 0.003 -10000 0 -10000 0 0
USO1 -0.001 0 -10000 0 -10000 0 0
GBF1 0.005 0.003 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.022 0.007 -10000 0 -0.003 10 10
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.023 0.016 -10000 0 0 54 54
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.002 0.009 -10000 0 -0.086 2 2
STMN1 -0.022 0.004 0 5 -10000 0 5
Aurora B/RasGAP/Survivin 0.032 0.01 -10000 0 -0.03 1 1
Chromosomal passenger complex/Cul3 protein complex -0.009 0.027 0.064 2 -0.086 13 15
BIRC5 -0.017 0.01 0.025 2 -10000 0 2
DES -0.014 0.13 -10000 0 -0.52 10 10
Aurora C/Aurora B/INCENP 0.031 0.008 -10000 0 0 9 9
Aurora B/TACC1 0.021 0.008 -10000 0 -0.02 1 1
Aurora B/PP2A 0.023 0.01 -10000 0 -0.024 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0 0.001 0.004 1 -10000 0 1
mitotic metaphase/anaphase transition 0 0.002 0.006 7 -10000 0 7
NDC80 -0.011 0.002 0.003 3 -10000 0 3
Cul3 protein complex 0.029 0.013 -10000 0 0 26 26
KIF2C 0.001 0.01 -10000 0 -0.086 1 1
PEBP1 -0.001 0.001 0.004 3 -10000 0 3
KIF20A -0.016 0.011 0.026 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.023 0.009 -10000 0 -0.024 3 3
SEPT1 -0.018 0.003 0 4 -10000 0 4
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0 0.064 -10000 0 -0.49 2 2
PSMA3 -0.018 0.003 0 6 -10000 0 6
G2/M transition of mitotic cell cycle -0.001 0.001 0.007 2 -10000 0 2
H3F3B -0.003 0.003 0.007 12 -10000 0 12
AURKB -0.015 0.013 0.025 12 -10000 0 12
AURKC -0.018 0.003 0 4 -10000 0 4
CDCA8 -0.016 0.011 0.025 3 -10000 0 3
cytokinesis -0.009 0.021 0.084 3 -0.12 3 6
Aurora B/Septin1 0.012 0.037 -10000 0 -0.2 3 3
AURKA -0.001 0.001 0.007 2 -10000 0 2
INCENP -0.017 0.01 0.024 2 -10000 0 2
KLHL13 -0.018 0 -10000 0 -10000 0 0
BUB1 -0.015 0.012 0.024 7 -10000 0 7
hSgo1/Aurora B/Survivin 0.028 0.012 -10000 0 0 23 23
EVI5 -0.016 0.01 0.02 9 -10000 0 9
RhoA/GTP 0.022 0.025 -10000 0 -0.12 2 2
SGOL1 -0.016 0.006 0 22 -10000 0 22
CENPA -0.001 0.021 -10000 0 -0.18 2 2
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.024 0.009 -10000 0 -0.024 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.025 0.008 -10000 0 -0.024 3 3
RHOA -0.016 0.006 0 23 -10000 0 23
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.01 0.057 -10000 0 -0.23 10 10
RASA1 -0.018 0.004 0 8 -10000 0 8
KLHL9 -0.016 0.006 0 20 -10000 0 20
mitotic prometaphase -0.001 0.001 0.004 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.009 -10000 0 -0.024 3 3
PPP1CC -0.018 0.001 0 1 -10000 0 1
Centraspindlin 0.019 0.028 0.1 1 -0.12 3 4
RhoA/GDP 0.011 0.004 -10000 0 0 23 23
NSUN2 0.007 0.044 -10000 0 -0.26 3 3
MYLK -0.003 0.003 0.007 6 -10000 0 6
KIF23 -0.016 0.01 0.02 11 -10000 0 11
VIM -0.021 0.005 0 7 -10000 0 7
RACGAP1 -0.016 0.01 0.021 9 -10000 0 9
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.001 0.035 -10000 0 -0.26 3 3
Chromosomal passenger complex -0.005 0.021 0.068 1 -0.088 7 8
Chromosomal passenger complex/EVI5 0.048 0.018 0.11 6 -0.02 1 7
TACC1 -0.017 0.005 0 15 -10000 0 15
PPP2R5D -0.017 0.004 0 10 -10000 0 10
CUL3 -0.018 0.004 0 8 -10000 0 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.03 0.027 0.16 3 -9999 0 3
NF kappa B1 p50/RelA/I kappa B alpha -0.027 0.042 0.17 5 -9999 0 5
alphaV/beta3 Integrin/Osteopontin/Src 0.023 0.007 -10000 0 0 12 12
AP1 -0.04 0.031 0.14 4 -9999 0 4
ILK -0.025 0.027 0.16 3 -9999 0 3
bone resorption -0.039 0.033 0.13 5 -9999 0 5
PTK2B -0.017 0.004 0 10 -9999 0 10
PYK2/p130Cas -0.036 0.012 0 10 -9999 0 10
ITGAV -0.018 0.003 0 5 -9999 0 5
mol:GTP 0 0 -10000 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.006 -10000 0 0 9 9
alphaV/beta3 Integrin/Osteopontin 0.032 0.009 -10000 0 0 12 12
MAP3K1 -0.024 0.027 0.16 3 -9999 0 3
JUN -0.018 0.003 0 4 -9999 0 4
MAPK3 -0.03 0.023 0.16 2 -9999 0 2
MAPK1 -0.03 0.023 0.16 2 -9999 0 2
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
NFKB1 -0.018 0.003 0 6 -9999 0 6
MAPK8 -0.028 0.028 0.16 3 -9999 0 3
ITGB3 -0.018 0 -10000 0 -9999 0 0
NFKBIA -0.025 0.017 0.15 1 -9999 0 1
FOS -0.018 0.004 0 8 -9999 0 8
CD44 -0.018 0.004 0 7 -9999 0 7
CHUK -0.018 0.002 0 3 -9999 0 3
PLAU -0.023 0.038 0.18 3 -9999 0 3
NF kappa B1 p50/RelA -0.042 0.038 0.15 5 -9999 0 5
BCAR1 -0.018 0.004 0 7 -9999 0 7
RELA -0.017 0.005 0 11 -9999 0 11
alphaV beta3 Integrin 0.024 0.004 -10000 0 0 5 5
mol:GDP 0 0 -10000 0 -9999 0 0
SYK -0.025 0.027 0.16 3 -9999 0 3
VAV3 -0.029 0.023 0.16 2 -9999 0 2
MAP3K14 -0.025 0.027 0.16 3 -9999 0 3
ROCK2 -0.018 0.002 0 2 -9999 0 2
SPP1 -0.018 0.004 0 7 -9999 0 7
RAC1 -0.017 0.004 0 10 -9999 0 10
Rac1/GTP -0.032 0.023 0.15 2 -9999 0 2
MMP2 -0.036 0.038 0.12 4 -9999 0 4
JNK signaling in the CD4+ TCR pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.039 0.013 -10000 0 0 17 17
MAP4K1 -0.018 0.003 0 4 -10000 0 4
MAP3K8 -0.018 0.003 0 5 -10000 0 5
PRKCB 0 0 -10000 0 -10000 0 0
DBNL -0.018 0.003 0 6 -10000 0 6
CRKL -0.018 0.004 0 7 -10000 0 7
MAP3K1 -0.01 0.024 0.068 7 -0.11 4 11
JUN -0.008 0.062 0.19 1 -0.54 2 3
MAP3K7 -0.01 0.023 0.068 7 -0.11 4 11
GRAP2 -0.018 0.002 0 2 -10000 0 2
CRK -0.018 0.002 0 2 -10000 0 2
MAP2K4 -0.012 0.035 0.14 1 -0.15 3 4
LAT -0.018 0.003 0 4 -10000 0 4
LCP2 -0.017 0.004 0 9 -10000 0 9
MAPK8 -0.002 0.064 -10000 0 -0.56 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.005 0.029 0.078 8 -0.12 5 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.043 0.019 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.018 0.002 0 2 -10000 0 2
ANTXR2 -0.018 0.003 0 4 -10000 0 4
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.001 0 6 -10000 0 6
monocyte activation -0.004 0.066 -10000 0 -0.32 7 7
MAP2K2 -0.003 0.076 -10000 0 -0.56 3 3
MAP2K1 -0.01 0.002 0 5 -10000 0 5
MAP2K7 -0.01 0.002 0 5 -10000 0 5
MAP2K6 -0.01 0.001 0 2 -10000 0 2
CYAA -0.014 0.003 0 6 -10000 0 6
MAP2K4 -0.01 0.002 0 5 -10000 0 5
IL1B -0.006 0.006 -10000 0 -10000 0 0
Channel 0.021 0.004 -10000 0 0 6 6
NLRP1 -0.003 0.001 0 6 -10000 0 6
CALM1 -0.017 0.005 0 14 -10000 0 14
negative regulation of phagocytosis -0.023 0.097 -10000 0 -0.39 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.001 -10000 0 0 6 6
MAPK3 -0.01 0.002 0 6 -10000 0 6
MAPK1 -0.01 0.002 0 8 -10000 0 8
PGR -0.008 0.004 0 34 -10000 0 34
PA/Cellular Receptors 0.022 0.004 -10000 0 0 6 6
apoptosis -0.003 0.001 0 6 -10000 0 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.004 -10000 0 0 6 6
macrophage activation -0.015 0.004 0 12 -10000 0 12
TNF -0.018 0.004 0 8 -10000 0 8
VCAM1 -0.002 0.059 -10000 0 -0.31 6 6
platelet activation -0.023 0.097 -10000 0 -0.39 11 11
MAPKKK cascade 0.01 0.012 0.057 1 -0.12 1 2
IL18 -0.006 0.006 -10000 0 -10000 0 0
negative regulation of macrophage activation -0.003 0.001 0 6 -10000 0 6
LEF -0.003 0.001 0 6 -10000 0 6
CASP1 -0.001 0.001 -10000 0 -10000 0 0
mol:cAMP -0.023 0.098 -10000 0 -0.39 11 11
necrosis -0.003 0.001 0 6 -10000 0 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.004 -10000 0 0 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Arf6 downstream pathway

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.006 0.013 0.042 4 -0.11 1 5
regulation of axonogenesis 0.008 0.02 0.25 1 -10000 0 1
myoblast fusion -0.02 0.027 -10000 0 -0.094 17 17
mol:GTP 0.014 0.016 -10000 0 -0.16 1 1
regulation of calcium-dependent cell-cell adhesion -0.031 0.019 0.064 3 -10000 0 3
ARF1/GTP 0.023 0.015 -10000 0 -0.1 1 1
mol:GM1 0.005 0.012 -10000 0 -0.11 1 1
mol:Choline -0.012 0.011 -10000 0 -0.11 1 1
lamellipodium assembly 0.004 0.028 -10000 0 -0.34 1 1
MAPK3 -0.009 0.013 -10000 0 -0.1 1 1
ARF6/GTP/NME1/Tiam1 0.032 0.019 -10000 0 -0.064 3 3
ARF1 -0.018 0.003 0 5 -10000 0 5
ARF6/GDP 0.02 0.027 0.094 17 -10000 0 17
ARF1/GDP 0.022 0.023 -10000 0 -0.1 1 1
ARF6 0.024 0.013 0.052 17 -0.019 5 22
RAB11A -0.018 0.002 0 3 -10000 0 3
TIAM1 -0.012 0.015 0.021 29 -10000 0 29
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.008 0.013 -10000 0 -0.1 1 1
actin filament bundle formation -0.017 0.027 0.16 2 -10000 0 2
KALRN 0.003 0.003 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.024 0.005 -10000 0 0 6 6
RhoA/GDP 0.017 0.027 -10000 0 -0.16 2 2
NME1 -0.012 0.015 0.021 29 -10000 0 29
Rac1/GDP 0.021 0.025 -10000 0 -0.2 1 1
substrate adhesion-dependent cell spreading 0.014 0.016 -10000 0 -0.16 1 1
cortical actin cytoskeleton organization 0.004 0.029 -10000 0 -0.34 1 1
RAC1 -0.017 0.004 0 10 -10000 0 10
liver development 0.014 0.016 -10000 0 -0.16 1 1
ARF6/GTP 0.014 0.016 -10000 0 -0.16 1 1
RhoA/GTP 0.019 0.019 -10000 0 -0.087 3 3
mol:GDP 0.002 0.017 -10000 0 -0.21 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.029 0.023 -10000 0 -0.1 3 3
RHOA -0.016 0.006 0 23 -10000 0 23
PLD1 -0.008 0.01 -10000 0 -0.12 1 1
RAB11FIP3 -0.018 0.002 0 3 -10000 0 3
tube morphogenesis 0.004 0.028 -10000 0 -0.34 1 1
ruffle organization -0.008 0.02 -10000 0 -0.25 1 1
regulation of epithelial cell migration 0.014 0.016 -10000 0 -0.16 1 1
PLD2 -0.008 0.019 0.03 15 -0.11 3 18
PIP5K1A -0.008 0.02 -10000 0 -0.25 1 1
mol:Phosphatidic acid -0.012 0.011 -10000 0 -0.11 1 1
Rac1/GTP 0.004 0.029 -10000 0 -0.34 1 1
Signaling events mediated by HDAC Class III

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 -0.018 0.002 0 2 -10000 0 2
HDAC4 -0.017 0.004 0 10 -10000 0 10
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.011 0.001 -10000 0 0 2 2
CDKN1A -0.014 0.004 0 13 -10000 0 13
KAT2B 0 0 -10000 0 -10000 0 0
BAX -0.018 0.002 0 2 -10000 0 2
FOXO3 0.005 0.001 0.014 1 0 3 4
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 -0.002 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 -0.018 0.002 0 2 -10000 0 2
TAT -0.018 0.004 0 8 -10000 0 8
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.001 0 3 -10000 0 3
PPARGC1A -0.017 0.005 0 15 -10000 0 15
FHL2 -0.018 0.002 0 2 -10000 0 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.025 0.004 -10000 0 0 4 4
HIST2H4A -0.011 0.001 0 2 -10000 0 2
SIRT1/FOXO3a 0.017 0.01 0.11 2 -10000 0 2
SIRT1 -0.018 0.002 0 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.031 0.011 -10000 0 0 19 19
SIRT1/Histone H1b 0.008 0.034 0.086 3 -0.13 8 11
apoptosis -0.033 0.006 0 6 -10000 0 6
SIRT1/PGC1A 0.021 0.007 -10000 0 0 16 16
p53/SIRT1 0.024 0.004 -10000 0 0 5 5
SIRT1/FOXO4 0.01 0.02 -10000 0 -0.1 5 5
FOXO1/FHL2/SIRT1 0.021 0.003 -10000 0 0 4 4
HIST1H1E -0.003 0.001 0 11 -10000 0 11
SIRT1/p300 0.025 0.004 -10000 0 0 4 4
muscle cell differentiation 0.017 0.006 -10000 0 -0.031 2 2
TP53 -0.018 0.003 0 4 -10000 0 4
KU70/SIRT1/BAX 0.033 0.006 -10000 0 0 6 6
CREBBP -0.018 0.002 0 3 -10000 0 3
MEF2D -0.018 0.004 0 7 -10000 0 7
HIV-1 Tat/SIRT1 0.024 0.006 -10000 0 0 10 10
ACSS2 -0.019 0.007 0 21 -10000 0 21
SIRT1/PCAF/MYOD -0.017 0.006 0.031 2 -10000 0 2
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.018 0.003 0 4 -10000 0 4
Ran/GTP/Exportin 1/HDAC4 -0.025 0.009 -10000 0 -0.051 4 4
MDM2/SUMO1 0.016 0.026 -10000 0 -0.1 7 7
HDAC4 -0.017 0.004 0 10 -10000 0 10
Ran/GTP/Exportin 1/HDAC1 -0.026 0.008 -10000 0 -0.051 4 4
SUMO1 -0.018 0.004 0 7 -10000 0 7
NPC/RanGAP1/SUMO1 -0.004 0.011 -10000 0 -0.085 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.013 0.019 -10000 0 -0.097 7 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN -0.018 0.001 0 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.018 0.002 0 2 -10000 0 2
SUMO1/HDAC4 0.017 0.022 0.084 1 -0.098 5 6
SUMO1/HDAC1 0.016 0.026 -10000 0 -0.1 7 7
RANGAP1 -0.018 0.002 0 2 -10000 0 2
MDM2/SUMO1/SUMO1 0.037 0.016 -10000 0 0 27 27
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.002 0.001 -10000 0 -10000 0 0
Ran/GTP 0.009 0.024 0.074 4 -0.093 7 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 -0.018 0.004 0 7 -10000 0 7
UBE2I -0.018 0.002 0 3 -10000 0 3
Ran/GTP/Exportin 1 -0.012 0.038 0.18 4 -0.16 1 5
NPC 0.01 0.001 -10000 0 0 2 2
PIAS2 -0.017 0.005 0 15 -10000 0 15
PIAS1 -0.018 0.002 0 3 -10000 0 3
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.019 0.11 -10000 0 -0.3 18 18
Syndecan-4/Syndesmos -0.016 0.14 -10000 0 -0.77 5 5
positive regulation of JNK cascade -0.01 0.13 -10000 0 -0.7 5 5
Syndecan-4/ADAM12 -0.017 0.14 -10000 0 -0.77 5 5
CCL5 -0.018 0.001 0 1 -10000 0 1
Rac1/GDP 0.012 0.003 -10000 0 0 10 10
DNM2 -0.018 0.002 0 3 -10000 0 3
ITGA5 -0.018 0 -10000 0 -10000 0 0
SDCBP -0.017 0.006 0 17 -10000 0 17
PLG 0.015 0.014 -10000 0 -0.041 7 7
ADAM12 -0.018 0.002 0 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 -0.018 0.003 0 4 -10000 0 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.017 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.019 0.14 -10000 0 -0.77 5 5
Syndecan-4/CXCL12/CXCR4 -0.01 0.14 -10000 0 -0.75 5 5
Syndecan-4/Laminin alpha3 -0.018 0.14 -10000 0 -0.78 5 5
MDK -0.018 0.003 0 6 -10000 0 6
Syndecan-4/FZD7 -0.016 0.14 -10000 0 -0.77 5 5
Syndecan-4/Midkine -0.018 0.14 -10000 0 -0.74 5 5
FZD7 -0.018 0.003 0 6 -10000 0 6
Syndecan-4/FGFR1/FGF -0.008 0.13 -10000 0 -0.72 5 5
THBS1 -0.018 0.002 0 3 -10000 0 3
integrin-mediated signaling pathway -0.017 0.14 -10000 0 -0.74 5 5
positive regulation of MAPKKK cascade -0.01 0.13 -10000 0 -0.7 5 5
Syndecan-4/TACI -0.017 0.14 -10000 0 -0.77 5 5
CXCR4 -0.018 0.001 0 1 -10000 0 1
cell adhesion -0.009 0.017 0.18 1 -0.077 1 2
Syndecan-4/Dynamin -0.017 0.14 -10000 0 -0.78 5 5
Syndecan-4/TSP1 -0.017 0.14 -10000 0 -0.77 5 5
Syndecan-4/GIPC -0.017 0.14 -10000 0 -0.78 5 5
Syndecan-4/RANTES -0.017 0.14 -10000 0 -0.78 5 5
ITGB1 -0.018 0.003 0 5 -10000 0 5
LAMA1 -0.017 0.005 0 13 -10000 0 13
LAMA3 -0.017 0.005 0 11 -10000 0 11
RAC1 -0.017 0.004 0 10 -10000 0 10
PRKCA -0.007 0.061 0.77 1 -10000 0 1
Syndecan-4/alpha-Actinin -0.017 0.14 -10000 0 -0.78 5 5
TFPI -0.018 0.002 0 3 -10000 0 3
F2 0.016 0.013 0.053 6 -0.044 5 11
alpha5/beta1 Integrin 0.024 0.004 -10000 0 0 5 5
positive regulation of cell adhesion -0.039 0.13 0.14 1 -0.75 5 6
ACTN1 -0.018 0.004 0 7 -10000 0 7
TNC -0.018 0.001 0 1 -10000 0 1
Syndecan-4/CXCL12 -0.018 0.14 -10000 0 -0.77 5 5
FGF6 -0.017 0.005 0 15 -10000 0 15
RHOA -0.016 0.006 0 23 -10000 0 23
CXCL12 -0.018 0.003 0 4 -10000 0 4
TNFRSF13B -0.018 0.003 0 4 -10000 0 4
FGF2 -0.018 0.004 0 7 -10000 0 7
FGFR1 -0.016 0.006 0 21 -10000 0 21
Syndecan-4/PI-4-5-P2 -0.032 0.13 -10000 0 -0.77 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.016 -10000 0 -0.041 9 9
cell migration -0.016 0.009 -10000 0 -10000 0 0
PRKCD 0.012 0.014 -10000 0 -0.041 7 7
vasculogenesis -0.015 0.13 -10000 0 -0.73 5 5
SDC4 -0.02 0.12 -10000 0 -0.88 3 3
Syndecan-4/Tenascin C -0.018 0.14 -10000 0 -0.78 5 5
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.017 0.13 -10000 0 -0.72 5 5
MMP9 0.016 0.007 -10000 0 -0.029 2 2
Rac1/GTP -0.009 0.017 0.18 1 -0.078 1 2
cytoskeleton organization -0.015 0.13 -10000 0 -0.73 5 5
GIPC1 -0.018 0.002 0 3 -10000 0 3
Syndecan-4/TFPI -0.017 0.14 -10000 0 -0.78 5 5
Nephrin/Neph1 signaling in the kidney podocyte

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.026 0.009 -10000 0 -0.061 6 6
KIRREL -0.019 0.012 0.033 8 -10000 0 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.026 0.009 0.061 6 -10000 0 6
PLCG1 -0.017 0.005 0 11 -10000 0 11
ARRB2 -0.018 0.002 0 2 -10000 0 2
WASL -0.018 0.004 0 7 -10000 0 7
Nephrin/NEPH1/podocin/CD2AP 0.04 0.017 0.11 4 -10000 0 4
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.007 0.007 -10000 0 -10000 0 0
FYN -0.011 0.052 0.21 8 -10000 0 8
mol:Ca2+ 0.038 0.017 0.11 4 -10000 0 4
mol:DAG 0.039 0.017 0.11 4 -10000 0 4
NPHS2 -0.019 0.012 0.033 8 -10000 0 8
mol:IP3 0.039 0.017 0.11 4 -10000 0 4
regulation of endocytosis 0.031 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.032 0.015 0.1 6 -10000 0 6
establishment of cell polarity 0.026 0.009 0.061 6 -10000 0 6
Nephrin/NEPH1/podocin/NCK1-2 0.042 0.024 0.12 5 -10000 0 5
Nephrin/NEPH1/beta Arrestin2 0.032 0.01 -10000 0 -10000 0 0
NPHS1 -0.017 0.018 0.042 13 -10000 0 13
Nephrin/NEPH1/podocin 0.031 0.007 -10000 0 -10000 0 0
TJP1 -0.018 0.003 0 5 -10000 0 5
NCK1 -0.015 0.007 0 27 -10000 0 27
NCK2 -0.018 0.002 0 3 -10000 0 3
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.04 0.017 0.11 4 -10000 0 4
CD2AP -0.018 0.004 0 8 -10000 0 8
Nephrin/NEPH1/podocin/GRB2 0.043 0.016 0.11 6 -10000 0 6
GRB2 -0.018 0.001 0 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.049 0.22 6 -10000 0 6
cytoskeleton organization -0.019 0.012 -10000 0 -10000 0 0
Nephrin/NEPH1 0.022 0.007 0.051 6 -10000 0 6
Nephrin/NEPH1/ZO-1 0.033 0.011 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 -0.018 0.003 0 5 -9999 0 5
ITGB7 -0.018 0.001 0 1 -9999 0 1
ITGA4 -0.018 0.002 0 3 -9999 0 3
alpha4/beta7 Integrin 0.025 0.004 -9999 0 0 4 4
alpha4/beta1 Integrin 0.024 0.005 -9999 0 0 8 8
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.013 0.006 -10000 0 -10000 0 0
BIRC5 -0.018 0.001 0 1 -10000 0 1
NFKBIA -0.012 0.006 -10000 0 -10000 0 0
CPEB1 -0.018 0.002 0 3 -10000 0 3
AKT1 -0.012 0.006 -10000 0 -10000 0 0
NDEL1 -0.018 0.002 0 3 -10000 0 3
Aurora A/BRCA1 -0.011 0.006 -10000 0 -10000 0 0
NDEL1/TACC3 0.025 0.018 0.076 16 -10000 0 16
GADD45A -0.018 0.002 0 3 -10000 0 3
GSK3B -0.017 0.008 0.016 4 -10000 0 4
PAK1/Aurora A -0.012 0.006 -10000 0 -10000 0 0
MDM2 -0.018 0.004 0 7 -10000 0 7
JUB -0.018 0.004 0 8 -10000 0 8
TPX2 -0.019 0.008 0 24 -10000 0 24
TP53 0.004 0.002 -10000 0 -10000 0 0
DLG7 -0.012 0.006 -10000 0 -10000 0 0
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 -0.018 0.003 0 6 -10000 0 6
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.026 0.019 0.081 16 -10000 0 16
G2/M transition of mitotic cell cycle -0.011 0.006 -10000 0 -10000 0 0
AURKA -0.007 0.003 -10000 0 -10000 0 0
AURKB 0.005 0.002 -10000 0 -10000 0 0
CDC25B -0.003 0.003 -10000 0 -0.03 1 1
G2/M transition checkpoint -0.011 0.006 -10000 0 -10000 0 0
mRNA polyadenylation -0.011 0.006 -10000 0 -10000 0 0
Aurora A/CPEB -0.011 0.006 -10000 0 -10000 0 0
Aurora A/TACC1/TRAP/chTOG 0.035 0.021 0.09 1 -10000 0 1
BRCA1 -0.018 0.002 0 3 -10000 0 3
centrosome duplication -0.012 0.006 -10000 0 -10000 0 0
regulation of centrosome cycle 0.017 0.009 -10000 0 -10000 0 0
spindle assembly 0.034 0.021 0.087 1 -10000 0 1
TDRD7 -0.018 0.001 0 1 -10000 0 1
Aurora A/RasGAP/Survivin 0.034 0.018 -10000 0 -10000 0 0
CENPA 0.006 0.003 -10000 0 -10000 0 0
Aurora A/PP2A -0.012 0.006 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.003 0.03 0.12 9 -10000 0 9
negative regulation of DNA binding 0 0.027 -10000 0 -0.2 3 3
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.024 0.005 -10000 0 0 8 8
RASA1 -0.018 0.004 0 8 -10000 0 8
Ajuba/Aurora A -0.011 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.008 0.067 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.003 -10000 0 -10000 0 0
TACC1 -0.017 0.005 0 15 -10000 0 15
TACC3 -0.017 0.005 0 15 -10000 0 15
Aurora A/Antizyme1 -0.011 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP -0.012 0.006 -10000 0 -10000 0 0
OAZ1 -0.018 0.003 0 4 -10000 0 4
RAN -0.018 0.001 0 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.012 0.015 19 -10000 0 19
GIT1 -0.018 0.002 0 2 -10000 0 2
GIT1/beta-PIX/PAK1 0.03 0.011 -10000 0 0 20 20
Importin alpha/Importin beta/TPX2 -0.019 0.008 0 24 -10000 0 24
PPP2R5D -0.017 0.004 0 10 -10000 0 10
Aurora A/TPX2 -0.015 0.009 -10000 0 -10000 0 0
PAK1 -0.017 0.005 0 15 -10000 0 15
CKAP5 -0.018 0.003 0 6 -10000 0 6
Signaling mediated by p38-alpha and p38-beta

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.006 0.009 0.057 2 -10000 0 2
MKNK1 -0.018 0.001 0 1 -10000 0 1
MAPK14 -0.018 0.015 0.053 4 -10000 0 4
ATF2/c-Jun -0.014 0.017 -10000 0 -0.12 4 4
MAPK11 -0.018 0.015 0.05 4 -10000 0 4
MITF -0.006 0.008 0.076 1 -10000 0 1
MAPKAPK5 -0.006 0.009 0.057 2 -10000 0 2
KRT8 -0.006 0.009 0.057 2 -10000 0 2
MAPKAPK3 -0.016 0.006 0 23 -10000 0 23
MAPKAPK2 -0.018 0.003 0 5 -10000 0 5
p38alpha-beta/CK2 -0.023 0.013 0.065 2 -10000 0 2
CEBPB -0.006 0.01 0.051 3 -10000 0 3
SLC9A1 -0.007 0.008 0.076 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.008 0.01 0.078 2 -10000 0 2
p38alpha-beta/MNK1 0.029 0.011 0.069 1 -10000 0 1
JUN -0.01 0.025 0.061 11 -0.12 4 15
PPARGC1A -0.006 0.009 0.057 2 -10000 0 2
USF1 -0.007 0.006 0.038 1 -10000 0 1
RAB5/GDP/GDI1 -0.012 0.015 0.054 1 -0.093 4 5
NOS2 -0.004 0.009 0.05 3 -10000 0 3
DDIT3 -0.006 0.009 0.051 3 -10000 0 3
RAB5A -0.016 0.006 0 22 -10000 0 22
HSPB1 -0.009 0.036 0.25 3 -10000 0 3
p38alpha-beta/HBP1 0.028 0.013 0.069 2 -10000 0 2
CREB1 0.003 0.007 0.055 2 -10000 0 2
RAB5/GDP 0.011 0.004 -10000 0 0 22 22
EIF4E -0.027 0.015 0.057 1 -10000 0 1
RPS6KA4 -0.006 0.01 0.051 3 -10000 0 3
PLA2G4A -0.027 0.015 0.057 1 -10000 0 1
GDI1 -0.006 0.009 0.051 3 -10000 0 3
TP53 -0.016 0.012 0.056 2 -10000 0 2
RPS6KA5 -0.006 0.009 0.057 2 -10000 0 2
ESR1 -0.006 0.009 0.051 3 -10000 0 3
HBP1 -0.017 0.005 0 11 -10000 0 11
MEF2C -0.006 0.01 0.051 3 -10000 0 3
MEF2A -0.006 0.009 0.057 2 -10000 0 2
EIF4EBP1 0.003 0.006 0.073 1 -10000 0 1
KRT19 -0.006 0.009 0.057 2 -10000 0 2
ELK4 -0.006 0.009 0.057 2 -10000 0 2
ATF6 -0.006 0.009 0.057 2 -10000 0 2
ATF1 0.003 0.006 0.073 1 -10000 0 1
p38alpha-beta/MAPKAPK2 0.029 0.011 0.069 1 -10000 0 1
p38alpha-beta/MAPKAPK3 0.026 0.013 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.025 0.003 -9999 0 0 3 3
FBXW11 -0.018 0.004 0 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex -0.017 0.004 0 8 -10000 0 8
CHUK -0.018 0.002 0 3 -10000 0 3
NF kappa B2 p100/RelB 0.046 0.015 -9999 0 -0.008 8 8
NFKB1 -0.018 0.003 0 6 -10000 0 6
MAP3K14 -0.018 0.001 0 1 -10000 0 1
NF kappa B1 p50/RelB 0.024 0.006 -9999 0 0 9 9
RELB -0.018 0.002 0 3 -10000 0 3
NFKB2 -0.018 0.002 0 2 -10000 0 2
NF kappa B2 p52/RelB 0.022 0.004 -9999 0 0 5 5
regulation of B cell activation 0.022 0.004 -9999 0 0 5 5
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.018 0.002 0 2 -10000 0 2
SPHK1 -0.018 0.001 0 1 -10000 0 1
GNAI2 -0.016 0.006 0 23 -10000 0 23
mol:S1P -0.003 0.001 -10000 0 -10000 0 0
GNAO1 -0.017 0.004 0 10 -10000 0 10
mol:Sphinganine-1-P -0.022 0.003 0 3 -10000 0 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.021 0.017 -10000 0 -0.086 3 3
GNAI3 -0.018 0.003 0 4 -10000 0 4
G12/G13 0.024 0.006 -10000 0 0 9 9
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.003 0 4 -10000 0 4
S1P1/S1P 0.013 0.016 0.086 3 -0.1 2 5
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.018 0.003 0 4 -10000 0 4
S1P/S1P5/G12 0.011 0.016 -10000 0 -0.084 3 3
S1P/S1P3/Gq 0.007 0.011 -10000 0 -10000 0 0
S1P/S1P4/Gi 0 0.025 0.077 7 -0.23 1 8
GNAQ -0.018 0 -10000 0 -10000 0 0
GNAZ -0.018 0.003 0 6 -10000 0 6
GNA14 -0.018 0 -10000 0 -10000 0 0
GNA15 -0.018 0.003 0 5 -10000 0 5
GNA12 -0.017 0.004 0 9 -10000 0 9
GNA13 -0.018 0 -10000 0 -10000 0 0
GNA11 -0.018 0.003 0 5 -10000 0 5
ABCC1 -0.018 0.002 0 3 -10000 0 3
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP -0.018 0.002 0 3 -9999 0 3
Aurora C/Aurora B/INCENP 0.031 0.007 -9999 0 0 9 9
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B -0.004 0.001 -9999 0 -9999 0 0
AURKB -0.018 0.002 0 2 -9999 0 2
AURKC -0.018 0.003 0 4 -9999 0 4
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • Expression File Used = Expression data was not used in this analysis.

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/HNSC/718215/1.GetReducedSegments.Finished/HNSC.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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