PARADIGM pathway analysis of mRNASeq expression and copy number data
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C17S7N0P
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C17S7N0P
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 45 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Nephrin/Neph1 signaling in the kidney podocyte 424
EGFR-dependent Endothelin signaling events 278
FOXA2 and FOXA3 transcription factor networks 209
PDGFR-alpha signaling pathway 202
HIF-1-alpha transcription factor network 180
TCR signaling in naïve CD8+ T cells 158
Glypican 1 network 144
TCGA08_p53 143
Angiopoietin receptor Tie2-mediated signaling 140
TCGA08_retinoblastoma 135
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 889 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 889 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Nephrin/Neph1 signaling in the kidney podocyte 0.4769 424 14433 34 -0.5 0.028 1000 -1000 -0.046 -1000
EGFR-dependent Endothelin signaling events 0.3127 278 5850 21 -0.54 0.037 1000 -1000 -0.056 -1000
FOXA2 and FOXA3 transcription factor networks 0.2351 209 9644 46 -1 0.031 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.2272 202 8901 44 -0.24 0.036 1000 -1000 -0.045 -1000
HIF-1-alpha transcription factor network 0.2025 180 13726 76 -0.65 0.043 1000 -1000 -0.16 -1000
TCR signaling in naïve CD8+ T cells 0.1777 158 14718 93 -0.35 0.15 1000 -1000 -0.068 -1000
Glypican 1 network 0.1620 144 6921 48 -0.41 0.048 1000 -1000 -0.049 -1000
TCGA08_p53 0.1609 143 1003 7 -0.26 0.15 1000 -1000 -0.011 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1575 140 12327 88 -0.46 0.032 1000 -1000 -0.074 -1000
TCGA08_retinoblastoma 0.1519 135 1087 8 -0.37 0.098 1000 -1000 -0.005 -1000
Aurora B signaling 0.1282 114 7651 67 -0.26 0.036 1000 -1000 -0.05 -1000
BMP receptor signaling 0.1271 113 9208 81 -0.45 0.055 1000 -1000 -0.088 -1000
Glypican 2 network 0.1249 111 447 4 -0.023 -0.02 1000 -1000 -0.003 -1000
amb2 Integrin signaling 0.1136 101 8349 82 -0.44 0.034 1000 -1000 -0.056 -1000
IL12-mediated signaling events 0.1069 95 8338 87 -0.22 0.071 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.0990 88 4525 51 -0.36 0.027 1000 -1000 -0.13 -1000
IL4-mediated signaling events 0.0956 85 7763 91 -0.7 0.5 1000 -1000 -0.12 -1000
Syndecan-4-mediated signaling events 0.0934 83 5592 67 -0.3 0.1 1000 -1000 -0.065 -1000
Effects of Botulinum toxin 0.0922 82 2154 26 -0.2 0.028 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0821 73 5724 78 -0.28 0.05 1000 -1000 -0.075 -1000
Thromboxane A2 receptor signaling 0.0765 68 7225 105 -0.54 0.034 1000 -1000 -0.059 -1000
Syndecan-1-mediated signaling events 0.0754 67 2289 34 -0.14 0.028 1000 -1000 -0.064 -1000
Signaling mediated by p38-alpha and p38-beta 0.0754 67 2962 44 -0.087 0.027 1000 -1000 -0.039 -1000
Arf6 signaling events 0.0742 66 4110 62 -0.54 0.06 1000 -1000 -0.047 -1000
Endothelins 0.0731 65 6329 96 -0.49 0.027 1000 -1000 -0.066 -1000
LPA4-mediated signaling events 0.0697 62 745 12 -0.079 0.009 1000 -1000 -0.028 -1000
S1P1 pathway 0.0675 60 2186 36 -0.11 0.026 1000 -1000 -0.051 -1000
Coregulation of Androgen receptor activity 0.0652 58 4481 76 -0.77 0.054 1000 -1000 -0.032 -1000
JNK signaling in the CD4+ TCR pathway 0.0630 56 965 17 -0.09 0.027 1000 -1000 -0.043 -1000
Reelin signaling pathway 0.0619 55 3091 56 -0.12 0.072 1000 -1000 -0.063 -1000
Calcium signaling in the CD4+ TCR pathway 0.0619 55 1726 31 -0.22 0.027 1000 -1000 -0.052 -1000
Ephrin A reverse signaling 0.0607 54 384 7 -0.021 0 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0607 54 3739 68 -0.33 0.067 1000 -1000 -0.1 -1000
Signaling events mediated by the Hedgehog family 0.0596 53 2767 52 -0.12 0.043 1000 -1000 -0.061 -1000
Aurora C signaling 0.0596 53 373 7 -0.15 0.024 1000 -1000 -0.019 -1000
Caspase cascade in apoptosis 0.0574 51 3835 74 -0.32 0.038 1000 -1000 -0.042 -1000
Integrins in angiogenesis 0.0574 51 4310 84 -0.32 0.06 1000 -1000 -0.071 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0562 50 1651 33 -0.37 0.065 1000 -1000 -0.031 -1000
IL23-mediated signaling events 0.0540 48 2907 60 -0.19 0.028 1000 -1000 -0.091 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0529 47 3485 74 -0.54 0.068 1000 -1000 -0.081 -1000
p75(NTR)-mediated signaling 0.0517 46 5780 125 -0.32 0.076 1000 -1000 -0.084 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0517 46 5856 125 -0.13 0.04 1000 -1000 -0.081 -1000
Signaling events mediated by PTP1B 0.0506 45 3438 76 -0.54 0.055 1000 -1000 -0.056 -1000
Fc-epsilon receptor I signaling in mast cells 0.0506 45 4374 97 -0.13 0.047 1000 -1000 -0.076 -1000
PLK1 signaling events 0.0506 45 3892 85 -0.16 0.038 1000 -1000 -0.04 -1000
Ceramide signaling pathway 0.0495 44 3383 76 -0.54 0.19 1000 -1000 -0.047 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0484 43 2354 54 -0.32 0.041 1000 -1000 -0.08 -1000
FoxO family signaling 0.0484 43 2762 64 -0.62 0.072 1000 -1000 -0.063 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0461 41 4986 120 -0.18 0.1 1000 -1000 -0.071 -1000
IL2 signaling events mediated by PI3K 0.0439 39 2286 58 -0.14 0.048 1000 -1000 -0.052 -1000
IL2 signaling events mediated by STAT5 0.0439 39 859 22 -0.14 0.03 1000 -1000 -0.057 -1000
IL27-mediated signaling events 0.0427 38 1944 51 -0.7 0.086 1000 -1000 -0.058 -1000
Glucocorticoid receptor regulatory network 0.0405 36 4124 114 -0.32 0.15 1000 -1000 -0.069 -1000
Plasma membrane estrogen receptor signaling 0.0405 36 3099 86 -0.083 0.048 1000 -1000 -0.081 -1000
HIF-2-alpha transcription factor network 0.0394 35 1511 43 -0.22 0.072 1000 -1000 -0.066 -1000
Wnt signaling 0.0394 35 250 7 -0.047 0.027 1000 -1000 -0.036 -1000
Nongenotropic Androgen signaling 0.0382 34 1774 52 -0.055 0.044 1000 -1000 -0.042 -1000
PLK2 and PLK4 events 0.0360 32 97 3 0.003 0.025 1000 -1000 -0.017 -1000
Syndecan-2-mediated signaling events 0.0360 32 2234 69 -0.44 0.054 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 0.0360 32 2697 82 -0.039 0.028 1000 -1000 -0.082 -1000
BCR signaling pathway 0.0360 32 3221 99 -0.09 0.055 1000 -1000 -0.083 -1000
Noncanonical Wnt signaling pathway 0.0349 31 808 26 -0.13 0.027 1000 -1000 -0.067 -1000
Regulation of Telomerase 0.0337 30 3077 102 -0.54 0.068 1000 -1000 -0.082 -1000
ceramide signaling pathway 0.0326 29 1463 49 -0.023 0.041 1000 -1000 -0.051 -1000
VEGFR1 specific signals 0.0326 29 1663 56 -0.12 0.028 1000 -1000 -0.058 -1000
Visual signal transduction: Rods 0.0326 29 1529 52 -0.12 0.043 1000 -1000 -0.062 -1000
IFN-gamma pathway 0.0315 28 1943 68 -0.19 0.04 1000 -1000 -0.078 -1000
S1P3 pathway 0.0315 28 1176 42 -0.11 0.034 1000 -1000 -0.055 -1000
Regulation of Androgen receptor activity 0.0315 28 2015 70 -0.85 0.043 1000 -1000 -0.076 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0304 27 778 28 -0.042 0.036 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0304 27 1236 45 -0.17 0.075 1000 -1000 -0.074 -1000
Presenilin action in Notch and Wnt signaling 0.0281 25 1567 61 -0.14 0.076 1000 -1000 -0.066 -1000
LPA receptor mediated events 0.0281 25 2566 102 -0.14 0.046 1000 -1000 -0.07 -1000
IL6-mediated signaling events 0.0270 24 1818 75 -0.17 0.05 1000 -1000 -0.056 -1000
E-cadherin signaling events 0.0270 24 120 5 -0.005 0.026 1000 -1000 -0.008 -1000
ErbB4 signaling events 0.0259 23 1601 69 -0.14 0.095 1000 -1000 -0.055 -1000
Syndecan-3-mediated signaling events 0.0259 23 812 35 -0.027 0.076 1000 -1000 -0.056 -1000
TCGA08_rtk_signaling 0.0247 22 596 26 -0.24 0.059 1000 -1000 -0.027 -1000
E-cadherin signaling in keratinocytes 0.0247 22 972 43 -0.23 0.039 1000 -1000 -0.055 -1000
Regulation of nuclear SMAD2/3 signaling 0.0236 21 2933 136 -0.33 0.096 1000 -1000 -0.054 -1000
Ephrin B reverse signaling 0.0236 21 1049 48 -0.038 0.037 1000 -1000 -0.048 -1000
Regulation of p38-alpha and p38-beta 0.0236 21 1178 54 -0.044 0.06 1000 -1000 -0.071 -1000
Ras signaling in the CD4+ TCR pathway 0.0236 21 363 17 0 0.047 1000 -1000 -0.028 -1000
EPO signaling pathway 0.0225 20 1151 55 -0.067 0.043 1000 -1000 -0.067 -1000
Canonical Wnt signaling pathway 0.0225 20 1066 51 -0.14 0.068 1000 -1000 -0.064 -1000
Class IB PI3K non-lipid kinase events 0.0225 20 60 3 -0.014 0.014 1000 -1000 0 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0214 19 1617 85 -0.052 0.062 1000 -1000 -0.074 -1000
Aurora A signaling 0.0214 19 1146 60 -0.1 0.065 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 0.0214 19 915 47 -0.14 0.041 1000 -1000 -0.053 -1000
Class I PI3K signaling events 0.0214 19 1431 73 -0.12 0.051 1000 -1000 -0.067 -1000
ErbB2/ErbB3 signaling events 0.0202 18 1201 65 -0.077 0.037 1000 -1000 -0.075 -1000
Insulin-mediated glucose transport 0.0202 18 576 32 -0.072 0.049 1000 -1000 -0.038 -1000
S1P5 pathway 0.0202 18 319 17 -0.036 0.027 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 0.0191 17 87 5 0.012 0.028 1000 -1000 -0.008 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0191 17 634 37 -0.077 0.052 1000 -1000 -0.05 -1000
EPHB forward signaling 0.0191 17 1517 85 -0.046 0.058 1000 -1000 -0.089 -1000
PDGFR-beta signaling pathway 0.0180 16 1636 97 -0.039 0.065 1000 -1000 -0.066 -1000
Osteopontin-mediated events 0.0169 15 578 38 -0.014 0.053 1000 -1000 -0.07 -1000
IL1-mediated signaling events 0.0169 15 988 62 -0.11 0.063 1000 -1000 -0.064 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0169 15 830 52 -0.068 0.088 1000 -1000 -0.043 -1000
E-cadherin signaling in the nascent adherens junction 0.0169 15 1205 76 -0.027 0.047 1000 -1000 -0.079 -1000
S1P4 pathway 0.0169 15 392 25 -0.036 0.039 1000 -1000 -0.039 -1000
Cellular roles of Anthrax toxin 0.0157 14 569 39 -0.06 0.034 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0146 13 720 53 -0.018 0.051 1000 -1000 -0.051 -1000
Arf6 trafficking events 0.0146 13 969 71 -0.15 0.047 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 0.0146 13 454 34 -0.043 0.039 1000 -1000 -0.058 -1000
Visual signal transduction: Cones 0.0135 12 464 38 -0.029 0.04 1000 -1000 -0.026 -1000
Hedgehog signaling events mediated by Gli proteins 0.0135 12 838 65 -0.004 0.05 1000 -1000 -0.061 -1000
BARD1 signaling events 0.0124 11 640 57 -0.066 0.063 1000 -1000 -0.059 -1000
Nectin adhesion pathway 0.0124 11 736 63 -0.005 0.061 1000 -1000 -0.068 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0124 11 977 83 -0.072 0.055 1000 -1000 -0.064 -1000
p38 MAPK signaling pathway 0.0124 11 496 44 -0.059 0.05 1000 -1000 -0.047 -1000
Canonical NF-kappaB pathway 0.0112 10 398 39 -0.053 0.063 1000 -1000 -0.062 -1000
Signaling mediated by p38-gamma and p38-delta 0.0112 10 159 15 0 0.028 1000 -1000 -0.043 -1000
Insulin Pathway 0.0090 8 635 74 -0.033 0.069 1000 -1000 -0.067 -1000
Class I PI3K signaling events mediated by Akt 0.0079 7 503 68 -0.072 0.054 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class I 0.0079 7 746 104 -0.053 0.066 1000 -1000 -0.053 -1000
IGF1 pathway 0.0079 7 411 57 -0.034 0.061 1000 -1000 -0.066 -1000
Retinoic acid receptors-mediated signaling 0.0067 6 391 58 -0.023 0.054 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class III 0.0056 5 208 40 -0.049 0.049 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 0.0045 4 373 75 -0.034 0.069 1000 -1000 -0.035 -1000
Circadian rhythm pathway 0.0045 4 103 22 -0.012 0.055 1000 -1000 -0.037 -1000
Paxillin-dependent events mediated by a4b1 0.0045 4 169 36 -0.046 0.05 1000 -1000 -0.053 -1000
TRAIL signaling pathway 0.0034 3 160 48 -0.006 0.069 1000 -1000 -0.053 -1000
Atypical NF-kappaB pathway 0.0034 3 112 31 0 0.039 1000 -1000 -0.049 -1000
Rapid glucocorticoid signaling 0.0034 3 76 20 -0.016 0.035 1000 -1000 -0.012 -1000
Arf1 pathway 0.0034 3 210 54 0 0.042 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0022 2 60 23 -0.008 0.052 1000 -1000 -0.044 -1000
Arf6 downstream pathway 0.0022 2 97 43 -0.043 0.044 1000 -1000 -0.029 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0011 1 34 27 0 0.064 1000 -1000 -0.046 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.068 1000 -1000 -0.015 -1000
Total NA 6016 329166 7203 -25 7.3 131000 -131000 -7.3 -131000
Nephrin/Neph1 signaling in the kidney podocyte

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.4 0.26 0.55 643 -10000 0 643
KIRREL -0.081 0.15 -10000 0 -0.66 46 46
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.4 0.26 -10000 0 -0.55 643 643
PLCG1 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.024 0.03 -10000 0 -0.46 3 3
WASL 0.025 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.42 0.29 -10000 0 -0.55 692 692
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.35 0.25 -10000 0 -0.47 647 647
FYN -0.4 0.26 0.26 1 -0.52 693 694
mol:Ca2+ -0.41 0.29 -10000 0 -0.54 673 673
mol:DAG -0.41 0.29 -10000 0 -0.55 673 673
NPHS2 -0.32 0.33 -10000 0 -0.7 374 374
mol:IP3 -0.41 0.29 -10000 0 -0.55 673 673
regulation of endocytosis -0.37 0.26 -10000 0 -0.49 674 674
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.29 -10000 0 -0.55 693 693
establishment of cell polarity -0.4 0.26 -10000 0 -0.55 643 643
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.28 -10000 0 -0.51 680 680
Nephrin/NEPH1/beta Arrestin2 -0.38 0.26 -10000 0 -0.5 674 674
NPHS1 -0.5 0.31 -10000 0 -0.69 639 639
Nephrin/NEPH1/podocin -0.4 0.28 -10000 0 -0.52 693 693
TJP1 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.027 0.006 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.41 0.29 -10000 0 -0.55 673 673
CD2AP 0.026 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.29 -10000 0 -0.55 671 671
GRB2 0.025 0.009 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.44 0.28 0.27 1 -0.54 711 712
cytoskeleton organization -0.43 0.3 -10000 0 -0.58 635 635
Nephrin/NEPH1 -0.3 0.19 -10000 0 -0.41 643 643
Nephrin/NEPH1/ZO-1 -0.33 0.22 -10000 0 -0.45 642 642
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.027 0.015 -9999 0 -0.42 1 1
EGFR 0.017 0.061 -9999 0 -0.45 14 14
EGF/EGFR -0.29 0.16 -9999 0 -0.37 635 635
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.17 -9999 0 -0.37 601 601
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.007 0.11 -9999 0 -0.6 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.54 0.25 -9999 0 -0.65 731 731
EGF/EGFR dimer/SHC -0.32 0.18 -9999 0 -0.42 616 616
mol:GDP -0.26 0.17 -9999 0 -0.36 601 601
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.1 -9999 0 -0.46 38 38
GRB2/SOS1 0.037 0.014 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.15 -9999 0 -0.34 599 599
SHC1 0.026 0.016 -9999 0 -0.42 1 1
HRAS/GDP -0.25 0.16 -9999 0 -0.34 593 593
FRAP1 -0.26 0.15 -9999 0 -0.35 601 601
EGF/EGFR dimer -0.38 0.2 -9999 0 -0.46 727 727
SOS1 0.027 0.006 -9999 0 -10000 0 0
GRB2 0.025 0.009 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.007 0.12 -9999 0 -0.39 63 63
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.42 -10000 0 -1 222 222
PCK1 -0.97 0.71 -10000 0 -1.5 507 507
HNF4A -0.54 0.53 -10000 0 -1.3 216 216
KCNJ11 -0.48 0.46 -10000 0 -1.1 218 218
AKT1 -0.22 0.18 -10000 0 -0.48 105 105
response to starvation -0.008 0.018 -10000 0 -10000 0 0
DLK1 -0.53 0.49 -10000 0 -1.2 265 265
NKX2-1 -0.1 0.17 0.34 5 -0.49 27 32
ACADM -0.45 0.42 -10000 0 -1.1 218 218
TAT -0.46 0.29 -10000 0 -0.8 279 279
CEBPB -0.029 0.084 -10000 0 -0.47 22 22
CEBPA -0.039 0.1 -10000 0 -0.46 43 43
TTR -0.75 0.44 -10000 0 -1 525 525
PKLR -0.53 0.53 -10000 0 -1.3 245 245
APOA1 -0.53 0.5 -10000 0 -1.3 211 211
CPT1C -0.46 0.43 -10000 0 -1.1 227 227
ALAS1 -0.2 0.2 -10000 0 -0.68 42 42
TFRC -0.61 0.39 -10000 0 -0.93 410 410
FOXF1 0.016 0.07 -10000 0 -0.46 18 18
NF1 0.031 0.011 -10000 0 -10000 0 0
HNF1A (dimer) -0.033 0.11 -10000 0 -0.61 20 20
CPT1A -0.45 0.42 -10000 0 -1 217 217
HMGCS1 -0.45 0.42 -10000 0 -1 223 223
NR3C1 0.012 0.053 -10000 0 -0.37 2 2
CPT1B -0.46 0.44 -10000 0 -1.1 216 216
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.01 -10000 0 -10000 0 0
GCK -0.44 0.43 -10000 0 -1 222 222
CREB1 -0.054 0.085 -10000 0 -0.32 9 9
IGFBP1 -0.25 0.33 -10000 0 -1.1 71 71
PDX1 -0.23 0.23 -10000 0 -0.87 43 43
UCP2 -0.46 0.42 -10000 0 -1.1 219 219
ALDOB -0.98 0.55 -10000 0 -1.2 693 693
AFP -0.55 0.4 -10000 0 -0.84 413 413
BDH1 -0.53 0.48 -10000 0 -1.1 286 286
HADH -0.47 0.44 -10000 0 -1.1 226 226
F2 -0.56 0.5 -10000 0 -1.3 221 221
HNF1A -0.033 0.11 -10000 0 -0.61 20 20
G6PC -0.83 0.64 -10000 0 -1.4 448 448
SLC2A2 -0.4 0.54 -10000 0 -1.6 121 121
INS -0.005 0.061 0.28 1 -0.43 3 4
FOXA1 -0.25 0.19 -10000 0 -0.47 272 272
FOXA3 -0.52 0.29 -10000 0 -0.62 673 673
FOXA2 -0.54 0.5 -10000 0 -1.2 260 260
ABCC8 -0.48 0.44 -10000 0 -1.1 226 226
ALB -1 0.45 -10000 0 -1.2 734 734
PDGFR-alpha 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
PDGFRA -0.24 0.34 -10000 0 -0.66 348 348
PDGF/PDGFRA/CRKL -0.16 0.25 -10000 0 -0.48 344 344
positive regulation of JUN kinase activity -0.097 0.2 -10000 0 -0.36 304 304
CRKL 0.027 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.17 0.25 -10000 0 -0.47 350 350
AP1 -0.17 0.31 0.33 1 -1.2 56 57
mol:IP3 -0.17 0.25 -10000 0 -0.49 333 333
PLCG1 -0.17 0.25 -10000 0 -0.49 333 333
PDGF/PDGFRA/alphaV Integrin -0.16 0.25 -10000 0 -0.48 343 343
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.25 -10000 0 -0.49 333 333
CAV3 -0.007 0.031 -10000 0 -0.42 3 3
CAV1 0.002 0.097 -10000 0 -0.42 44 44
SHC/Grb2/SOS1 -0.096 0.2 -10000 0 -0.37 304 304
PDGF/PDGFRA/Shf -0.16 0.25 -10000 0 -0.48 344 344
FOS -0.18 0.3 0.32 1 -1.1 56 57
JUN -0.026 0.024 -10000 0 -10000 0 0
oligodendrocyte development -0.16 0.25 -10000 0 -0.48 343 343
GRB2 0.025 0.009 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:DAG -0.17 0.25 -10000 0 -0.49 333 333
PDGF/PDGFRA -0.24 0.34 -10000 0 -0.66 348 348
actin cytoskeleton reorganization -0.16 0.25 -10000 0 -0.48 344 344
SRF 0.021 0.011 -10000 0 -10000 0 0
SHC1 0.026 0.016 -10000 0 -0.42 1 1
PI3K -0.12 0.22 -10000 0 -0.41 317 317
PDGF/PDGFRA/Crk/C3G -0.12 0.22 -10000 0 -0.41 312 312
JAK1 -0.18 0.24 -10000 0 -0.48 343 343
ELK1/SRF -0.12 0.19 -10000 0 -0.38 314 314
SHB 0.028 0.004 -10000 0 -10000 0 0
SHF 0.028 0.003 -10000 0 -10000 0 0
CSNK2A1 0.036 0.019 -10000 0 -10000 0 0
GO:0007205 -0.19 0.25 -10000 0 -0.5 348 348
SOS1 0.027 0.006 -10000 0 -10000 0 0
Ras protein signal transduction -0.097 0.2 -10000 0 -0.36 304 304
PDGF/PDGFRA/SHB -0.16 0.25 -10000 0 -0.48 344 344
PDGF/PDGFRA/Caveolin-1 -0.17 0.24 -10000 0 -0.44 373 373
ITGAV 0.026 0.028 -10000 0 -0.54 2 2
ELK1 -0.17 0.22 -10000 0 -0.44 345 345
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.16 0.25 -10000 0 -0.46 346 346
JAK-STAT cascade -0.18 0.24 -10000 0 -0.48 343 343
cell proliferation -0.16 0.25 -10000 0 -0.48 344 344
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.53 0.48 -10000 0 -1.1 287 287
HDAC7 0.026 0.008 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.37 0.37 -10000 0 -0.84 199 199
SMAD4 0.029 0.005 -10000 0 -10000 0 0
ID2 -0.52 0.48 -10000 0 -1.1 265 265
AP1 0.007 0.12 -10000 0 -0.48 53 53
ABCG2 -0.52 0.48 -10000 0 -1.1 277 277
HIF1A -0.076 0.085 -10000 0 -0.77 2 2
TFF3 -0.56 0.49 -10000 0 -1.1 287 287
GATA2 -0.028 0.18 -10000 0 -0.64 71 71
AKT1 -0.07 0.079 -10000 0 -10000 0 0
response to hypoxia -0.08 0.072 -10000 0 -0.28 4 4
MCL1 -0.51 0.48 -10000 0 -1.1 265 265
NDRG1 -0.52 0.48 -10000 0 -1.1 261 261
SERPINE1 -0.54 0.48 -10000 0 -1.1 259 259
FECH -0.52 0.48 -10000 0 -1.1 250 250
FURIN -0.52 0.48 -10000 0 -1.1 271 271
NCOA2 -0.005 0.14 -10000 0 -0.65 40 40
EP300 -0.061 0.094 0.26 1 -0.35 9 10
HMOX1 -0.53 0.49 -10000 0 -1.1 282 282
BHLHE40 -0.52 0.48 -10000 0 -1.1 262 262
BHLHE41 -0.56 0.52 -10000 0 -1.2 291 291
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.06 0.11 -10000 0 -0.54 2 2
ENG -0.054 0.11 0.51 4 -0.5 2 6
JUN 0.027 0.009 -10000 0 -10000 0 0
RORA -0.52 0.48 -10000 0 -1.1 263 263
ABCB1 -0.25 0.41 -10000 0 -1.2 127 127
TFRC -0.52 0.48 -10000 0 -1.1 269 269
CXCR4 -0.56 0.52 -10000 0 -1.1 303 303
TF -0.54 0.51 -10000 0 -1.1 280 280
CITED2 -0.52 0.48 -10000 0 -1.1 272 272
HIF1A/ARNT -0.6 0.56 -10000 0 -1.2 309 309
LDHA -0.063 0.13 -10000 0 -0.73 22 22
ETS1 -0.52 0.48 -10000 0 -1.1 273 273
PGK1 -0.52 0.48 -10000 0 -1.1 265 265
NOS2 -0.53 0.48 -10000 0 -1.1 273 273
ITGB2 -0.55 0.5 -10000 0 -1.1 292 292
ALDOA -0.52 0.48 -10000 0 -1.1 261 261
Cbp/p300/CITED2 -0.5 0.48 -10000 0 -1.1 246 246
FOS -0.015 0.16 -10000 0 -0.62 57 57
HK2 -0.62 0.53 -10000 0 -1.2 336 336
SP1 0.014 0.053 -10000 0 -0.3 2 2
GCK -0.12 0.18 -10000 0 -0.98 10 10
HK1 -0.52 0.48 -10000 0 -1.1 264 264
NPM1 -0.51 0.48 -10000 0 -1.1 246 246
EGLN1 -0.52 0.48 -10000 0 -1.1 271 271
CREB1 0.033 0.009 -10000 0 -10000 0 0
PGM1 -0.52 0.48 -10000 0 -1.1 265 265
SMAD3 0.029 0.003 -10000 0 -10000 0 0
EDN1 -0.1 0.22 -10000 0 -0.92 32 32
IGFBP1 -0.56 0.49 -10000 0 -1.2 267 267
VEGFA -0.39 0.38 0.54 5 -0.85 234 239
HIF1A/JAB1 -0.039 0.067 -10000 0 -0.6 2 2
CP -0.62 0.52 -10000 0 -1.2 345 345
CXCL12 -0.54 0.49 -10000 0 -1.1 299 299
COPS5 0.026 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.043 0.009 -10000 0 -10000 0 0
BNIP3 -0.52 0.48 -10000 0 -1.1 271 271
EGLN3 -0.61 0.53 -10000 0 -1.2 344 344
CA9 -0.65 0.52 -10000 0 -1.1 375 375
TERT -0.54 0.49 -10000 0 -1.1 269 269
ENO1 -0.52 0.48 -10000 0 -1.1 265 265
PFKL -0.52 0.48 -10000 0 -1.1 264 264
NCOA1 0.027 0.006 -10000 0 -10000 0 0
ADM -0.54 0.5 -10000 0 -1.1 281 281
ARNT -0.072 0.079 -10000 0 -0.35 1 1
HNF4A -0.062 0.23 -10000 0 -0.65 118 118
ADFP -0.53 0.48 -10000 0 -1.1 287 287
SLC2A1 -0.34 0.36 0.54 5 -0.81 169 174
LEP -0.54 0.47 -10000 0 -1.1 268 268
HIF1A/ARNT/Cbp/p300 -0.39 0.37 -10000 0 -0.85 208 208
EPO -0.31 0.29 -10000 0 -0.79 113 113
CREBBP -0.059 0.089 -10000 0 -0.35 7 7
HIF1A/ARNT/Cbp/p300/HDAC7 -0.4 0.39 -10000 0 -0.88 217 217
PFKFB3 -0.52 0.49 -10000 0 -1.1 277 277
NT5E -0.52 0.49 -10000 0 -1.1 253 253
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.22 0.38 5 -0.47 186 191
FYN -0.14 0.27 0.44 22 -0.53 231 253
LAT/GRAP2/SLP76 -0.15 0.26 0.28 3 -0.55 210 213
IKBKB 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.1 0.24 0.44 47 -0.42 210 257
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.037 0.07 0.14 16 -0.16 72 88
MAP3K8 0.026 0.022 -10000 0 -0.42 2 2
mol:Ca2+ -0.078 0.054 0.072 5 -0.12 529 534
integrin-mediated signaling pathway 0.025 0.053 -10000 0 -0.24 32 32
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.16 0.31 0.47 35 -0.58 237 272
TRPV6 -0.35 0.47 0.74 97 -0.66 574 671
CD28 -0.008 0.12 -10000 0 -0.42 66 66
SHC1 -0.16 0.26 0.38 12 -0.53 250 262
receptor internalization -0.16 0.26 -10000 0 -0.52 262 262
PRF1 -0.16 0.3 0.41 2 -0.68 184 186
KRAS 0.027 0.007 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
COT/AKT1 -0.073 0.2 0.41 44 -0.34 183 227
LAT -0.18 0.29 0.37 12 -0.57 262 274
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D -0.12 0.21 -10000 0 -0.43 287 287
CD3E -0.11 0.21 -10000 0 -0.43 266 266
CD3G -0.099 0.2 -10000 0 -0.42 247 247
RASGRP2 -0.01 0.025 0.11 1 -0.17 4 5
RASGRP1 -0.096 0.24 0.48 43 -0.42 185 228
HLA-A -0.002 0.007 0.067 2 -10000 0 2
RASSF5 0.01 0.083 -10000 0 -0.42 32 32
RAP1A/GTP/RAPL 0.025 0.053 -10000 0 -0.24 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.14 0.33 70 -0.14 6 76
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.084 0.098 -10000 0 -0.26 141 141
PRKCA -0.073 0.13 0.2 9 -0.28 149 158
GRAP2 -0.001 0.11 -10000 0 -0.42 56 56
mol:IP3 -0.045 0.26 0.24 280 -0.42 179 459
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.22 -10000 0 -0.46 241 241
ORAI1 0.15 0.29 0.67 9 -0.57 92 101
CSK -0.16 0.26 0.31 9 -0.53 254 263
B7 family/CD28 -0.18 0.32 0.29 2 -0.66 220 222
CHUK 0.027 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.18 0.28 0.27 1 -0.58 264 265
PTPN6 -0.16 0.26 0.3 2 -0.52 250 252
VAV1 -0.19 0.3 0.39 13 -0.59 267 280
Monovalent TCR/CD3 -0.11 0.19 -10000 0 -0.4 248 248
CBL 0.027 0.023 -10000 0 -0.65 1 1
LCK -0.15 0.28 0.44 21 -0.54 245 266
PAG1 -0.16 0.26 0.27 10 -0.53 249 259
RAP1A 0.027 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.28 0.26 8 -0.57 257 265
CD80 -0.059 0.18 -10000 0 -0.42 167 167
CD86 -0.053 0.17 -10000 0 -0.42 156 156
PDK1/CARD11/BCL10/MALT1 -0.092 0.13 -10000 0 -0.3 161 161
HRAS 0.027 0.015 -10000 0 -0.42 1 1
GO:0035030 -0.16 0.26 0.43 6 -0.55 223 229
CD8A -0.11 0.21 -10000 0 -0.42 267 267
CD8B -0.09 0.2 -10000 0 -0.43 226 226
PTPRC -0.009 0.12 -10000 0 -0.43 67 67
PDK1/PKC theta -0.13 0.29 0.53 51 -0.51 216 267
CSK/PAG1 -0.15 0.26 0.34 7 -0.55 210 217
SOS1 0.027 0.006 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.16 0.28 0.27 2 -0.57 236 238
STIM1 0.088 0.14 1 2 -0.78 12 14
RAS family/GTP -0.011 0.13 0.34 50 -0.2 8 58
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.17 0.27 -10000 0 -0.55 262 262
mol:DAG -0.1 0.19 0.14 12 -0.38 201 213
RAP1A/GDP 0.01 0.086 0.23 54 -10000 0 54
PLCG1 0.027 0.007 -10000 0 -10000 0 0
CD247 -0.08 0.19 -10000 0 -0.42 207 207
cytotoxic T cell degranulation -0.16 0.29 0.41 2 -0.65 184 186
RAP1A/GTP -0.003 0.01 -10000 0 -0.06 4 4
mol:PI-3-4-5-P3 -0.13 0.26 0.45 36 -0.48 228 264
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.09 0.32 0.27 214 -0.56 195 409
NRAS 0.027 0.007 -10000 0 -10000 0 0
ZAP70 -0.12 0.21 -10000 0 -0.42 299 299
GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.17 0.26 0.26 3 -0.56 216 219
MALT1 0.027 0.005 -10000 0 -10000 0 0
TRAF6 0.028 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.13 0.26 -10000 0 -0.49 279 279
CARD11 -0.061 0.17 -10000 0 -0.42 169 169
PRKCB -0.077 0.13 0.2 6 -0.29 155 161
PRKCE -0.073 0.13 0.2 10 -0.28 147 157
PRKCQ -0.16 0.3 0.49 38 -0.56 246 284
LCP2 -0.006 0.12 -10000 0 -0.42 64 64
BCL10 0.027 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.083 0.21 0.42 49 -0.36 208 257
IKK complex 0.015 0.16 0.36 91 -0.12 10 101
RAS family/GDP -0.008 0.012 -10000 0 -10000 0 0
MAP3K14 -0.061 0.14 0.38 17 -0.27 137 154
PDPK1 -0.092 0.24 0.48 50 -0.4 197 247
TCR/CD3/MHC I/CD8/Fyn -0.16 0.28 -10000 0 -0.59 218 218
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.042 0.066 -10000 0 -0.42 15 15
fibroblast growth factor receptor signaling pathway 0.042 0.066 -10000 0 -0.42 15 15
LAMA1 0.006 0.12 -10000 0 -0.57 32 32
PRNP 0.027 0.007 -10000 0 -10000 0 0
GPC1/SLIT2 -0.042 0.19 -10000 0 -0.47 137 137
SMAD2 0.025 0.03 -10000 0 -0.38 1 1
GPC1/PrPc/Cu2+ 0.034 0.019 -10000 0 -0.42 1 1
GPC1/Laminin alpha1 0.021 0.092 -10000 0 -0.44 31 31
TDGF1 -0.41 0.31 -10000 0 -0.63 574 574
CRIPTO/GPC1 -0.3 0.24 -10000 0 -0.49 531 531
APP/GPC1 0.037 0.024 -10000 0 -0.39 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.26 0.2 -10000 0 -0.42 523 523
FLT1 0.018 0.067 -10000 0 -0.48 15 15
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.027 -10000 0 -0.42 1 1
SERPINC1 -0.015 0.15 -10000 0 -0.6 52 52
FYN -0.25 0.21 -10000 0 -0.42 526 526
FGR -0.26 0.21 -10000 0 -0.42 527 527
positive regulation of MAPKKK cascade -0.28 0.24 0.41 11 -0.46 524 535
SLIT2 -0.075 0.24 -10000 0 -0.62 139 139
GPC1/NRG 0.016 0.1 -10000 0 -0.47 35 35
NRG1 -0.001 0.13 -10000 0 -0.6 39 39
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.046 0.15 -10000 0 -0.45 18 18
LYN -0.25 0.21 -10000 0 -0.42 519 519
mol:Spermine 0.009 0.02 -10000 0 -0.39 2 2
cell growth 0.042 0.066 -10000 0 -0.42 15 15
BMP signaling pathway -0.025 0.028 0.53 2 -10000 0 2
SRC -0.25 0.2 -10000 0 -0.42 511 511
TGFBR1 0.028 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.032 0.13 -10000 0 -0.42 82 82
GPC1 0.025 0.028 -10000 0 -0.54 2 2
TGFBR1 (dimer) 0.028 0.004 -10000 0 -10000 0 0
VEGFA -0.11 0.2 -10000 0 -0.42 269 269
BLK -0.27 0.22 -10000 0 -0.44 523 523
HCK -0.27 0.21 -10000 0 -0.43 514 514
FGF2 0.016 0.087 -10000 0 -0.62 16 16
FGFR1 0.026 0.016 -10000 0 -0.42 1 1
VEGFR1 homodimer 0.018 0.067 -10000 0 -0.48 15 15
TGFBR2 0.026 0.008 -10000 0 -10000 0 0
cell death 0.037 0.024 -10000 0 -0.39 2 2
ATIII/GPC1 0.008 0.12 -10000 0 -0.45 52 52
PLA2G2A/GPC1 0.004 0.098 -10000 0 -0.3 82 82
LCK -0.27 0.21 -10000 0 -0.43 530 530
neuron differentiation 0.016 0.1 -10000 0 -0.47 35 35
PrPc/Cu2+ 0.02 0.005 -10000 0 -10000 0 0
APP 0.027 0.007 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.026 0.008 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.26 0.1 0.2 1 -0.3 773 774
TP53 -0.072 0.066 -10000 0 -0.29 56 56
Senescence -0.072 0.065 -10000 0 -0.29 56 56
Apoptosis -0.072 0.065 -10000 0 -0.29 56 56
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.15 0.097 0.42 61 -10000 0 61
MDM4 0.027 0.007 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.26 0.46 -10000 0 -1 224 224
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.43 222 222
NCK1/Dok-R -0.28 0.61 -10000 0 -1.3 224 224
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.032 0.087 0.24 124 -10000 0 124
RELA 0.028 0.003 -10000 0 -10000 0 0
SHC1 0.025 0.016 -10000 0 -0.42 1 1
Rac/GDP 0.018 0.007 -10000 0 -10000 0 0
F2 -0.06 0.23 0.27 89 -0.42 228 317
TNIP2 0.028 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.23 0.56 -10000 0 -1.2 223 223
FN1 -0.01 0.12 -10000 0 -0.42 72 72
PLD2 -0.3 0.63 -10000 0 -1.3 224 224
PTPN11 0.027 0.006 -10000 0 -10000 0 0
GRB14 -0.01 0.16 -10000 0 -0.65 48 48
ELK1 -0.24 0.54 0.48 4 -1.1 224 228
GRB7 0.018 0.069 -10000 0 -0.65 9 9
PAK1 0.028 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.28 0.59 -10000 0 -1.2 224 224
CDKN1A -0.18 0.31 -10000 0 -0.68 214 214
ITGA5 0.004 0.098 -10000 0 -0.42 45 45
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.29 0.61 -10000 0 -1.3 225 225
CRK 0.025 0.009 -10000 0 -10000 0 0
mol:NO -0.17 0.33 0.45 7 -0.69 223 230
PLG -0.46 0.63 -10000 0 -1.5 224 224
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.23 0.43 -10000 0 -0.94 224 224
GRB2 0.025 0.009 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ANGPT2 -0.16 0.27 -10000 0 -0.76 89 89
BMX -0.33 0.64 -10000 0 -1.4 224 224
ANGPT1 -0.18 0.5 -10000 0 -1.4 124 124
tube development -0.21 0.35 -10000 0 -0.78 222 222
ANGPT4 0.01 0.062 -10000 0 -0.42 17 17
response to hypoxia -0.018 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.33 0.68 -10000 0 -1.4 224 224
alpha5/beta1 Integrin 0.021 0.074 -10000 0 -0.29 45 45
FGF2 0.019 0.088 -10000 0 -0.62 16 16
STAT5A (dimer) -0.24 0.41 -10000 0 -0.89 219 219
mol:L-citrulline -0.17 0.33 0.45 7 -0.69 223 230
AGTR1 -0.081 0.23 -10000 0 -0.65 127 127
MAPK14 -0.34 0.63 -10000 0 -1.4 229 229
Tie2/SHP2 -0.26 0.55 -10000 0 -1.2 212 212
TEK -0.31 0.62 -10000 0 -1.4 213 213
RPS6KB1 -0.23 0.44 -10000 0 -0.95 224 224
Angiotensin II/AT1 -0.068 0.17 -10000 0 -0.49 127 127
Tie2/Ang1/GRB2 -0.31 0.67 -10000 0 -1.4 224 224
MAPK3 -0.26 0.55 -10000 0 -1.2 223 223
MAPK1 -0.26 0.55 -10000 0 -1.2 224 224
Tie2/Ang1/GRB7 -0.31 0.67 -10000 0 -1.4 224 224
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 -0.31 0.64 -10000 0 -1.4 224 224
PI3K -0.31 0.56 -10000 0 -1.2 224 224
FES -0.32 0.63 -10000 0 -1.4 225 225
Crk/Dok-R -0.28 0.6 -10000 0 -1.3 223 223
Tie2/Ang1/ABIN2 -0.32 0.68 -10000 0 -1.4 224 224
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.22 0.4 -10000 0 -0.89 224 224
STAT5A 0.025 0.009 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.24 0.44 0.45 4 -0.97 224 228
Tie2/Ang2 -0.32 0.52 -10000 0 -1.2 222 222
Tie2/Ang1 -0.36 0.74 -10000 0 -1.6 224 224
FOXO1 -0.23 0.41 -10000 0 -0.9 224 224
ELF1 0.001 0.065 -10000 0 -0.65 1 1
ELF2 -0.31 0.65 -10000 0 -1.4 224 224
mol:Choline -0.28 0.58 -10000 0 -1.2 224 224
cell migration -0.079 0.1 -10000 0 -0.25 203 203
FYN -0.25 0.41 -10000 0 -0.91 222 222
DOK2 -0.004 0.11 -10000 0 -0.42 59 59
negative regulation of cell cycle -0.16 0.28 -10000 0 -0.61 214 214
ETS1 -0.008 0.096 -10000 0 -0.25 112 112
PXN -0.18 0.36 0.59 5 -0.77 222 227
ITGB1 0.027 0.007 -10000 0 -10000 0 0
NOS3 -0.2 0.38 0.49 5 -0.8 223 228
RAC1 0.025 0.01 -10000 0 -10000 0 0
TNF -0.025 0.13 -10000 0 -0.4 50 50
MAPKKK cascade -0.28 0.58 -10000 0 -1.2 224 224
RASA1 0.027 0.023 -10000 0 -0.65 1 1
Tie2/Ang1/Shc -0.32 0.68 -10000 0 -1.4 224 224
NCK1 0.027 0.006 -10000 0 -10000 0 0
vasculogenesis -0.14 0.29 0.44 7 -0.62 223 230
mol:Phosphatidic acid -0.28 0.58 -10000 0 -1.2 224 224
mol:Angiotensin II -0.006 0.009 -10000 0 -10000 0 0
mol:NADP -0.17 0.33 0.45 7 -0.69 223 230
Rac1/GTP -0.21 0.4 -10000 0 -0.86 224 224
MMP2 -0.31 0.63 -10000 0 -1.3 224 224
TCGA08_retinoblastoma

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
CDKN2B 0.025 0.054 -10000 0 -0.42 12 12
CDKN2C 0.06 0.031 -10000 0 -0.38 2 2
CDKN2A -0.37 0.15 -10000 0 -0.43 773 773
CCND2 0.081 0.048 0.21 44 -10000 0 44
RB1 -0.093 0.057 -10000 0 -0.24 52 52
CDK4 0.097 0.058 0.22 79 -10000 0 79
CDK6 0.093 0.058 0.22 68 -0.16 1 69
G1/S progression 0.098 0.057 0.24 56 -10000 0 56
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.064 0.13 -10000 0 -0.31 135 135
STMN1 -0.098 0.16 -10000 0 -0.29 351 351
Aurora B/RasGAP/Survivin -0.12 0.22 -10000 0 -0.45 238 238
Chromosomal passenger complex/Cul3 protein complex -0.054 0.13 0.2 9 -0.37 57 66
BIRC5 -0.11 0.2 -10000 0 -0.43 255 255
DES -0.26 0.34 -10000 0 -0.67 330 330
Aurora C/Aurora B/INCENP -0.058 0.13 -10000 0 -0.24 43 43
Aurora B/TACC1 -0.075 0.14 -10000 0 -0.24 349 349
Aurora B/PP2A -0.09 0.16 -10000 0 -0.29 346 346
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.015 0.038 -10000 0 -0.17 7 7
mitotic metaphase/anaphase transition 0.002 0.004 -10000 0 -10000 0 0
NDC80 -0.15 0.23 0.21 7 -0.41 365 372
Cul3 protein complex 0.036 0.089 -10000 0 -0.42 31 31
KIF2C -0.069 0.14 -10000 0 -0.38 103 103
PEBP1 0.023 0.009 -10000 0 -10000 0 0
KIF20A -0.15 0.22 -10000 0 -0.42 357 357
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.089 0.16 -10000 0 -0.29 342 342
SEPT1 -0.004 0.11 -10000 0 -0.42 60 60
SMC2 0.028 0.004 -10000 0 -10000 0 0
SMC4 0.027 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.053 0.18 0.39 1 -0.74 44 45
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.049 0.085 -10000 0 -0.36 7 7
AURKB -0.15 0.22 -10000 0 -0.42 351 351
AURKC 0.024 0.042 -10000 0 -0.42 8 8
CDCA8 -0.007 0.11 -10000 0 -0.43 53 53
cytokinesis -0.12 0.16 -10000 0 -0.46 82 82
Aurora B/Septin1 -0.1 0.19 0.33 1 -0.46 96 97
AURKA 0.022 0.05 -10000 0 -0.42 11 11
INCENP 0.019 0.018 -10000 0 -10000 0 0
KLHL13 0.004 0.13 -10000 0 -0.65 32 32
BUB1 -0.18 0.22 -10000 0 -0.42 400 400
hSgo1/Aurora B/Survivin -0.12 0.22 -10000 0 -0.44 249 249
EVI5 0.027 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.079 0.16 -10000 0 -0.4 76 76
SGOL1 0.003 0.098 -10000 0 -0.42 44 44
CENPA -0.085 0.15 0.22 17 -0.28 249 266
NCAPG -0.12 0.21 -10000 0 -0.42 301 301
Aurora B/HC8 Proteasome -0.092 0.16 -10000 0 -0.29 350 350
NCAPD2 0.027 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.089 0.16 -10000 0 -0.29 340 340
RHOA 0.026 0.008 -10000 0 -10000 0 0
NCAPH -0.042 0.16 -10000 0 -0.42 136 136
NPM1 -0.054 0.12 -10000 0 -0.51 20 20
RASA1 0.027 0.023 -10000 0 -0.65 1 1
KLHL9 0.027 0.013 -10000 0 -0.35 1 1
mitotic prometaphase -0.004 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.092 0.16 -10000 0 -0.29 350 350
PPP1CC 0.027 0.006 -10000 0 -10000 0 0
Centraspindlin -0.091 0.17 -10000 0 -0.42 83 83
RhoA/GDP 0.019 0.006 -10000 0 -10000 0 0
NSUN2 -0.055 0.11 -10000 0 -0.48 23 23
MYLK -0.055 0.1 -10000 0 -0.37 27 27
KIF23 0.022 0.046 -10000 0 -0.43 9 9
VIM -0.12 0.19 0.21 1 -0.33 371 372
RACGAP1 0.024 0.023 -10000 0 -0.43 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.077 0.19 -10000 0 -0.73 48 48
Chromosomal passenger complex -0.11 0.16 0.22 3 -0.34 236 239
Chromosomal passenger complex/EVI5 -0.092 0.24 -10000 0 -0.43 242 242
TACC1 0.026 0.024 -10000 0 -0.65 1 1
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
CUL3 0.027 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.43 0.3 -10000 0 -0.56 674 674
SMAD6-7/SMURF1 0.048 0.031 -10000 0 -0.42 2 2
NOG -0.026 0.14 -10000 0 -0.45 90 90
SMAD9 -0.077 0.18 -10000 0 -0.61 76 76
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.16 0.16 -10000 0 -0.44 69 69
BMP7/USAG1 -0.45 0.35 -10000 0 -0.64 624 624
SMAD5/SKI -0.15 0.17 0.34 6 -0.46 49 55
SMAD1 -0.018 0.069 -10000 0 -0.52 5 5
BMP2 0.025 0.033 -10000 0 -0.65 2 2
SMAD1/SMAD1/SMAD4 -0.01 0.061 -10000 0 -0.47 2 2
BMPR1A 0.026 0.024 -10000 0 -0.65 1 1
BMPR1B -0.38 0.33 -10000 0 -0.65 535 535
BMPR1A-1B/BAMBI -0.24 0.23 -10000 0 -0.42 527 527
AHSG -0.006 0.063 -10000 0 -0.42 18 18
CER1 -0.004 0.025 -10000 0 -0.42 1 1
BMP2-4/CER1 0.043 0.047 -10000 0 -0.38 9 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.13 -10000 0 -0.42 36 36
BMP2-4 (homodimer) 0.034 0.049 -10000 0 -0.46 8 8
RGMB 0.026 0.022 -10000 0 -0.42 2 2
BMP6/BMPR2/BMPR1A-1B -0.21 0.22 -10000 0 -0.39 522 522
RGMA -0.001 0.14 -10000 0 -0.64 38 38
SMURF1 0.025 0.01 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.14 0.14 -10000 0 -0.38 74 74
BMP2-4/USAG1 -0.18 0.23 -10000 0 -0.42 425 425
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.34 2 -0.47 46 48
SOSTDC1 -0.3 0.33 -10000 0 -0.64 426 426
BMP7/BMPR2/BMPR1A-1B -0.4 0.29 -10000 0 -0.54 656 656
SKI 0.026 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.012 0.098 -10000 0 -0.62 20 20
HFE2 0.004 0.072 -10000 0 -0.42 23 23
ZFYVE16 0.028 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.033 0.097 -10000 0 -0.43 33 33
SMAD5/SMAD5/SMAD4 -0.16 0.16 0.31 4 -0.46 53 57
MAPK1 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.37 34 34
BMP7 (homodimer) -0.34 0.33 -10000 0 -0.65 463 463
NUP214 0.028 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.016 0.088 -10000 0 -0.39 37 37
SMAD1/SKI -0.005 0.083 0.41 5 -0.49 5 10
SMAD6 0.027 0.033 -10000 0 -0.65 2 2
CTDSP2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.038 0.061 -10000 0 -0.43 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.18 0.31 -10000 0 -0.64 278 278
BMPR2 (homodimer) 0.027 0.006 -10000 0 -10000 0 0
GADD34/PP1CA 0.055 0.012 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.28 0.25 -10000 0 -0.48 536 536
CHRDL1 -0.31 0.34 -10000 0 -0.65 430 430
ENDOFIN/SMAD1 -0.008 0.083 0.41 4 -0.5 5 9
SMAD6-7/SMURF1/SMAD1 -0.005 0.075 -10000 0 -0.5 3 3
SMAD6/SMURF1 0.025 0.01 -10000 0 -10000 0 0
BAMBI 0.018 0.075 -10000 0 -0.58 13 13
SMURF2 0.024 0.025 -10000 0 -0.65 1 1
BMP2-4/CHRDL1 -0.18 0.24 -10000 0 -0.42 407 407
BMP2-4/GREM1 -0.091 0.22 -10000 0 -0.43 242 242
SMAD7 0.028 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.068 0.18 -10000 0 -0.58 80 80
SMAD1/SMAD6 -0.013 0.069 -10000 0 -0.51 5 5
TAK1/SMAD6 0.034 0.017 -10000 0 -10000 0 0
BMP7 -0.34 0.33 -10000 0 -0.65 463 463
BMP6 0.012 0.098 -10000 0 -0.62 20 20
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.12 -10000 0 -0.35 64 64
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.01 0.078 0.41 5 -0.51 5 10
SMAD7/SMURF1 0.036 0.015 -10000 0 -10000 0 0
CTDSPL 0.026 0.008 -10000 0 -10000 0 0
PPP1CA 0.028 0.003 -10000 0 -10000 0 0
XIAP 0.028 0.001 -10000 0 -10000 0 0
CTDSP1 0.027 0.007 -10000 0 -10000 0 0
PPP1R15A 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.22 -10000 0 -0.56 157 157
CHRD 0.005 0.12 -10000 0 -0.63 30 30
BMPR2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.14 0.14 -10000 0 -0.39 76 76
BMP4 0.023 0.056 -10000 0 -0.65 6 6
FST -0.079 0.24 -10000 0 -0.61 139 139
BMP2-4/NOG 0.012 0.1 -10000 0 -0.42 19 19
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.37 0.28 -10000 0 -0.52 609 609
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 -0.02 0.14 -9999 0 -0.42 94 94
GPC2 -0.02 0.13 -9999 0 -0.42 87 87
GPC2/Midkine -0.023 0.14 -9999 0 -0.34 133 133
neuron projection morphogenesis -0.023 0.14 -9999 0 -0.34 133 133
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.036 0.16 -10000 0 -0.44 72 72
alphaM/beta2 Integrin/GPIbA -0.037 0.16 -10000 0 -0.44 71 71
alphaM/beta2 Integrin/proMMP-9 -0.13 0.21 -10000 0 -0.47 166 166
PLAUR 0.006 0.096 -10000 0 -0.42 43 43
HMGB1 0.018 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.034 0.15 -10000 0 -0.44 70 70
AGER -0.03 0.14 -10000 0 -0.42 92 92
RAP1A 0.027 0.007 -10000 0 -10000 0 0
SELPLG -0.014 0.13 -10000 0 -0.42 82 82
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.061 0.18 -10000 0 -0.42 107 107
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.14 0.22 -10000 0 -0.42 331 331
CYR61 -0.002 0.13 -10000 0 -0.54 45 45
TLN1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.18 0.17 -10000 0 -0.47 139 139
RHOA 0.026 0.008 -10000 0 -10000 0 0
P-selectin oligomer -0.025 0.18 -10000 0 -0.61 72 72
MYH2 -0.25 0.21 -10000 0 -0.53 208 208
MST1R 0.006 0.098 -10000 0 -0.46 35 35
leukocyte activation during inflammatory response -0.093 0.18 -10000 0 -0.44 119 119
APOB -0.1 0.21 -10000 0 -0.45 234 234
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.048 -10000 0 -0.44 9 9
JAM3 0.026 0.04 -10000 0 -0.65 3 3
GP1BA 0.023 0.037 -10000 0 -0.57 3 3
alphaM/beta2 Integrin/CTGF -0.046 0.16 -10000 0 -0.44 89 89
alphaM/beta2 Integrin -0.21 0.2 -10000 0 -0.47 224 224
JAM3 homodimer 0.026 0.04 -10000 0 -0.65 3 3
ICAM2 0.025 0.009 -10000 0 -10000 0 0
ICAM1 0.021 0.058 -10000 0 -0.42 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.21 0.19 -10000 0 -0.46 224 224
cell adhesion -0.037 0.15 -10000 0 -0.44 71 71
NFKB1 -0.094 0.2 0.37 3 -0.66 41 44
THY1 -0.035 0.2 -10000 0 -0.64 82 82
RhoA/GDP 0.019 0.006 -10000 0 -10000 0 0
Lipoprotein(a) -0.053 0.14 -10000 0 -0.28 238 238
alphaM/beta2 Integrin/LRP/tPA -0.044 0.18 -10000 0 -0.43 101 101
IL6 -0.13 0.27 -10000 0 -0.76 107 107
ITGB2 -0.063 0.17 -10000 0 -0.42 158 158
elevation of cytosolic calcium ion concentration -0.046 0.18 -10000 0 -0.46 88 88
alphaM/beta2 Integrin/JAM2/JAM3 -0.022 0.16 -10000 0 -0.44 67 67
JAM2 0.018 0.077 -10000 0 -0.63 12 12
alphaM/beta2 Integrin/ICAM1 -0.025 0.16 -10000 0 -0.42 70 70
alphaM/beta2 Integrin/uPA/Plg -0.23 0.26 -10000 0 -0.46 432 432
RhoA/GTP -0.26 0.22 -10000 0 -0.51 267 267
positive regulation of phagocytosis -0.17 0.18 -10000 0 -0.46 174 174
Ron/MSP 0.02 0.084 -10000 0 -0.34 43 43
alphaM/beta2 Integrin/uPAR/uPA -0.045 0.18 -10000 0 -0.46 88 88
alphaM/beta2 Integrin/uPAR -0.046 0.17 -10000 0 -0.46 80 80
PLAU -0.004 0.13 -10000 0 -0.55 47 47
PLAT -0.022 0.18 -10000 0 -0.63 66 66
actin filament polymerization -0.24 0.2 -10000 0 -0.5 208 208
MST1 0.021 0.054 -10000 0 -0.5 9 9
alphaM/beta2 Integrin/lipoprotein(a) -0.092 0.18 -10000 0 -0.45 119 119
TNF -0.093 0.2 0.37 3 -0.63 50 53
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.052 0.17 -10000 0 -0.45 89 89
fibrinolysis -0.23 0.26 -10000 0 -0.46 432 432
HCK -0.006 0.12 -10000 0 -0.42 63 63
dendritic cell antigen processing and presentation -0.21 0.19 -10000 0 -0.46 224 224
VTN -0.078 0.23 -10000 0 -0.58 148 148
alphaM/beta2 Integrin/CYR61 -0.051 0.17 -10000 0 -0.45 91 91
LPA -0.003 0.049 -10000 0 -0.43 9 9
LRP1 0.027 0.006 -10000 0 -10000 0 0
cell migration -0.12 0.2 -10000 0 -0.5 128 128
FN1 -0.01 0.12 -10000 0 -0.42 72 72
alphaM/beta2 Integrin/Thy1 -0.07 0.19 -10000 0 -0.44 130 130
MPO 0.006 0.085 -10000 0 -0.42 33 33
KNG1 -0.44 0.3 -10000 0 -0.65 586 586
RAP1/GDP 0.034 0.012 -10000 0 -10000 0 0
ROCK1 -0.24 0.21 -10000 0 -0.54 187 187
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.32 0.32 -10000 0 -0.63 441 441
CTGF 0.008 0.11 -10000 0 -0.57 28 28
alphaM/beta2 Integrin/Hck -0.05 0.19 -10000 0 -0.52 91 91
ITGAM -0.018 0.12 -10000 0 -0.42 71 71
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.21 -10000 0 -0.48 137 137
HP -0.066 0.18 -10000 0 -0.42 180 180
leukocyte adhesion -0.08 0.19 -10000 0 -0.56 57 57
SELP -0.025 0.18 -10000 0 -0.61 72 72
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.071 0.13 -10000 0 -0.35 72 72
TBX21 -0.2 0.37 0.6 2 -0.89 114 116
B2M 0.023 0.013 -10000 0 -10000 0 0
TYK2 0.009 0.035 -10000 0 -10000 0 0
IL12RB1 -0.087 0.2 -10000 0 -0.45 200 200
GADD45B -0.12 0.26 -10000 0 -0.63 62 62
IL12RB2 -0.11 0.2 -10000 0 -0.43 233 233
GADD45G -0.13 0.28 -10000 0 -0.75 39 39
natural killer cell activation -0.005 0.023 0.042 3 -0.038 120 123
RELB 0.028 0.003 -10000 0 -10000 0 0
RELA 0.028 0.003 -10000 0 -10000 0 0
IL18 0.006 0.096 -10000 0 -0.42 41 41
IL2RA -0.045 0.16 -10000 0 -0.42 140 140
IFNG -0.11 0.2 -10000 0 -0.42 257 257
STAT3 (dimer) -0.17 0.3 -10000 0 -0.64 169 169
HLA-DRB5 -0.001 0.006 -10000 0 -0.023 47 47
FASLG -0.22 0.37 -10000 0 -0.85 156 156
NF kappa B2 p52/RelB -0.17 0.33 -10000 0 -0.73 152 152
CD4 0.01 0.081 -10000 0 -0.42 30 30
SOCS1 0.018 0.069 -10000 0 -0.53 13 13
EntrezGene:6955 -0.003 0.009 -10000 0 -0.024 62 62
CD3D -0.12 0.21 -10000 0 -0.43 287 287
CD3E -0.12 0.21 -10000 0 -0.43 266 266
CD3G -0.1 0.2 -10000 0 -0.43 247 247
IL12Rbeta2/JAK2 -0.073 0.15 -10000 0 -0.31 223 223
CCL3 -0.18 0.36 0.6 2 -0.85 118 120
CCL4 -0.19 0.37 0.6 2 -0.87 133 135
HLA-A -0.003 0.007 -10000 0 -0.021 25 25
IL18/IL18R -0.021 0.15 -10000 0 -0.3 87 87
NOS2 -0.17 0.34 -10000 0 -0.82 114 114
IL12/IL12R/TYK2/JAK2/SPHK2 -0.068 0.13 -10000 0 -0.35 63 63
IL1R1 -0.18 0.34 0.6 2 -0.82 107 109
IL4 0.01 0.038 -10000 0 -10000 0 0
JAK2 0.008 0.034 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.008 -10000 0 -0.022 58 58
TCR/CD3/MHC I/CD8 -0.17 0.27 -10000 0 -0.59 224 224
RAB7A -0.093 0.26 0.59 4 -0.78 14 18
lysosomal transport -0.088 0.25 0.59 4 -0.72 15 19
FOS -0.18 0.38 -10000 0 -0.86 139 139
STAT4 (dimer) -0.16 0.33 0.58 5 -0.71 146 151
STAT5A (dimer) -0.22 0.37 -10000 0 -0.8 208 208
GZMA -0.21 0.37 -10000 0 -0.83 169 169
GZMB -0.2 0.36 -10000 0 -0.85 143 143
HLX -0.01 0.12 -10000 0 -0.42 71 71
LCK -0.2 0.36 -10000 0 -0.8 167 167
TCR/CD3/MHC II/CD4 -0.1 0.16 -10000 0 -0.35 228 228
IL2/IL2R -0.098 0.2 -10000 0 -0.48 129 129
MAPK14 -0.12 0.29 0.51 3 -0.7 66 69
CCR5 -0.18 0.33 0.61 2 -0.72 150 152
IL1B -0.003 0.086 -10000 0 -0.54 18 18
STAT6 -0.038 0.1 -10000 0 -10000 0 0
STAT4 0.003 0.1 -10000 0 -0.42 47 47
STAT3 0.025 0.009 -10000 0 -10000 0 0
STAT1 0.026 0.022 -10000 0 -0.42 2 2
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
NFKB2 0.027 0.007 -10000 0 -10000 0 0
IL12B -0.038 0.14 -10000 0 -0.44 91 91
CD8A -0.11 0.21 -10000 0 -0.43 267 267
CD8B -0.093 0.2 -10000 0 -0.43 226 226
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.071 0.13 0.35 72 -10000 0 72
IL2RB -0.14 0.22 -10000 0 -0.42 329 329
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.31 0.57 5 -0.66 146 151
IL2RG 0.003 0.11 -10000 0 -0.44 47 47
IL12 -0.02 0.11 -10000 0 -0.32 84 84
STAT5A 0.025 0.009 -10000 0 -10000 0 0
CD247 -0.085 0.19 -10000 0 -0.43 207 207
IL2 -0.004 0.061 -10000 0 -0.42 16 16
SPHK2 0.027 0.033 -10000 0 -0.65 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.034 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.2 0.36 -10000 0 -0.79 176 176
MAP2K3 -0.12 0.29 0.52 2 -0.68 82 84
RIPK2 0.027 0.016 -10000 0 -0.42 1 1
MAP2K6 -0.12 0.29 0.5 3 -0.68 82 85
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.027 46 46
IL18RAP -0.058 0.18 -10000 0 -0.42 164 164
IL12Rbeta1/TYK2 -0.053 0.16 -10000 0 -0.34 200 200
EOMES -0.099 0.17 -10000 0 -0.72 20 20
STAT1 (dimer) -0.18 0.32 -10000 0 -0.67 178 178
T cell proliferation -0.12 0.26 0.46 5 -0.55 118 123
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.019 0.06 -10000 0 -0.48 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.16 0.26 -10000 0 -0.63 92 92
ATF2 -0.11 0.28 0.64 4 -0.66 61 65
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.12 0.44 0.84 4 -0.98 91 95
PLK1 -0.029 0.18 -10000 0 -1.2 2 2
BIRC5 -0.084 0.24 -10000 0 -0.87 28 28
HSPA1B -0.13 0.44 0.78 2 -1 83 85
MAP2K1 0.019 0.048 -10000 0 -10000 0 0
BRCA2 -0.13 0.45 0.74 3 -1 96 99
FOXM1 -0.17 0.51 0.88 2 -1.2 112 114
XRCC1 -0.13 0.44 0.9 2 -0.98 92 94
FOXM1B/p19 -0.21 0.43 0.66 2 -1 105 107
Cyclin D1/CDK4 -0.13 0.41 -10000 0 -0.94 75 75
CDC2 -0.14 0.46 0.82 2 -1 111 113
TGFA -0.14 0.43 0.87 1 -0.99 76 77
SKP2 -0.12 0.44 0.78 2 -0.98 89 91
CCNE1 0.017 0.072 -10000 0 -0.43 22 22
CKS1B -0.13 0.44 0.78 2 -0.95 112 114
RB1 -0.041 0.25 -10000 0 -0.88 23 23
FOXM1C/SP1 -0.15 0.47 -10000 0 -1.1 106 106
AURKB -0.12 0.26 -10000 0 -0.94 39 39
CENPF -0.15 0.47 0.78 2 -1 123 125
CDK4 0.02 0.024 -10000 0 -10000 0 0
MYC -0.12 0.4 -10000 0 -0.88 88 88
CHEK2 0.017 0.058 -10000 0 -0.44 5 5
ONECUT1 -0.13 0.44 0.75 1 -0.96 99 100
CDKN2A -0.36 0.14 -10000 0 -0.42 773 773
LAMA4 -0.16 0.45 0.78 2 -1 88 90
FOXM1B/HNF6 -0.16 0.49 0.75 1 -1.1 101 102
FOS -0.17 0.5 0.9 3 -1.1 135 138
SP1 0.027 0.008 -10000 0 -10000 0 0
CDC25B -0.12 0.44 0.91 3 -1 77 80
response to radiation 0.002 0.031 -10000 0 -10000 0 0
CENPB -0.12 0.44 0.91 3 -0.98 88 91
CENPA -0.17 0.48 0.82 3 -1 148 151
NEK2 -0.16 0.48 0.78 2 -1 145 147
HIST1H2BA -0.13 0.44 0.77 2 -0.98 93 95
CCNA2 -0.057 0.18 -10000 0 -0.43 166 166
EP300 0.027 0.024 -10000 0 -0.65 1 1
CCNB1/CDK1 -0.15 0.48 0.79 2 -1.1 99 101
CCNB2 -0.16 0.48 0.91 2 -1 138 140
CCNB1 -0.14 0.46 0.82 2 -1 99 101
ETV5 -0.12 0.44 0.72 4 -0.97 95 99
ESR1 -0.15 0.48 0.78 2 -1.1 113 115
CCND1 -0.13 0.42 -10000 0 -0.94 90 90
GSK3A 0.02 0.042 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.009 0.15 -10000 0 -0.48 22 22
CDK2 0.027 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.001 0.036 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.14 0.46 -10000 0 -1 102 102
GAS1 -0.17 0.49 0.78 2 -1.1 125 127
MMP2 -0.12 0.45 0.84 4 -1 86 90
RB1/FOXM1C -0.14 0.44 -10000 0 -0.99 102 102
CREBBP 0.027 0.007 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.44 0.43 -10000 0 -1.2 130 130
STAT6 (cleaved dimer) -0.47 0.44 -10000 0 -1.1 197 197
IGHG1 -0.16 0.15 -10000 0 -0.42 25 25
IGHG3 -0.43 0.42 -10000 0 -1.1 177 177
AKT1 -0.22 0.25 0.56 2 -0.74 58 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.18 -10000 0 -0.74 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.89 57 57
THY1 -0.51 0.53 -10000 0 -1.4 173 173
MYB -0.093 0.2 -10000 0 -0.42 233 233
HMGA1 0.022 0.043 -10000 0 -0.42 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.29 0.26 -10000 0 -0.69 124 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.91 51 51
SP1 0.025 0.026 -10000 0 -10000 0 0
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
SOCS5 0.038 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.44 -10000 0 -1.1 183 183
SOCS1 -0.31 0.29 -10000 0 -0.77 97 97
SOCS3 -0.24 0.24 -10000 0 -0.83 26 26
FCER2 -0.36 0.35 -10000 0 -0.94 114 114
PARP14 0.027 0.008 -10000 0 -10000 0 0
CCL17 -0.45 0.44 -10000 0 -1.2 133 133
GRB2 0.025 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.24 -10000 0 -0.79 61 61
T cell proliferation -0.45 0.44 -10000 0 -1.2 148 148
IL4R/JAK1 -0.44 0.43 -10000 0 -1.2 133 133
EGR2 -0.48 0.48 -10000 0 -1.3 147 147
JAK2 -0.024 0.039 -10000 0 -10000 0 0
JAK3 -0.054 0.18 -10000 0 -0.42 165 165
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
JAK1 0.006 0.021 -10000 0 -10000 0 0
COL1A2 -0.15 0.17 -10000 0 -0.63 2 2
CCL26 -0.43 0.44 -10000 0 -1.2 125 125
IL4R -0.47 0.46 -10000 0 -1.3 134 134
PTPN6 0.038 0.014 -10000 0 -10000 0 0
IL13RA2 -0.64 0.62 -10000 0 -1.4 277 277
IL13RA1 -0.024 0.04 -10000 0 -10000 0 0
IRF4 -0.15 0.22 -10000 0 -0.77 46 46
ARG1 -0.14 0.17 -10000 0 -0.8 7 7
CBL -0.27 0.25 -10000 0 -0.68 98 98
GTF3A 0.011 0.04 -10000 0 -0.41 1 1
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.028 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.14 0.21 -10000 0 -0.74 42 42
CD40LG -0.029 0.15 -10000 0 -0.45 101 101
MAPK14 -0.27 0.25 -10000 0 -0.69 92 92
mitosis -0.21 0.23 0.56 2 -0.7 58 60
STAT6 -0.51 0.51 -10000 0 -1.3 164 164
SPI1 -0.036 0.16 -10000 0 -0.41 130 130
RPS6KB1 -0.19 0.23 0.54 2 -0.71 44 46
STAT6 (dimer) -0.51 0.51 -10000 0 -1.3 164 164
STAT6 (dimer)/PARP14 -0.46 0.47 -10000 0 -1.2 163 163
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.22 -10000 0 -0.67 55 55
FRAP1 -0.22 0.24 0.56 2 -0.74 58 60
LTA -0.48 0.44 -10000 0 -1.2 158 158
FES 0.026 0.04 -10000 0 -0.65 3 3
T-helper 1 cell differentiation 0.5 0.49 1.3 165 -10000 0 165
CCL11 -0.61 0.58 -10000 0 -1.4 278 278
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.22 -10000 0 -0.67 45 45
IL2RG 0.006 0.11 -10000 0 -0.45 47 47
IL10 -0.46 0.44 -10000 0 -1.2 146 146
IRS1 0.019 0.072 -10000 0 -0.65 10 10
IRS2 0.018 0.064 -10000 0 -0.42 18 18
IL4 -0.11 0.13 -10000 0 -0.96 7 7
IL5 -0.45 0.44 -10000 0 -1.2 136 136
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.93 142 142
COL1A1 -0.24 0.27 -10000 0 -1.1 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.45 -10000 0 -1.2 119 119
IL2R gamma/JAK3 -0.039 0.17 -10000 0 -0.36 176 176
TFF3 -0.53 0.55 -10000 0 -1.4 176 176
ALOX15 -0.44 0.43 -10000 0 -1.2 133 133
MYBL1 -0.001 0.11 -10000 0 -0.42 56 56
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.95 173 173
SHC1 0.026 0.016 -10000 0 -0.42 1 1
CEBPB 0.018 0.071 -10000 0 -0.42 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.26 0.44 1 -0.87 57 58
mol:PI-3-4-5-P3 -0.22 0.24 0.57 2 -0.74 58 60
PI3K -0.23 0.26 0.57 2 -0.8 58 60
DOK2 -0.004 0.11 -10000 0 -0.42 59 59
ETS1 0.038 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.24 -10000 0 -0.8 63 63
ITGB3 -0.46 0.46 -10000 0 -1.2 140 140
PIGR -0.7 0.64 -10000 0 -1.4 350 350
IGHE 0.034 0.063 0.23 15 -0.27 1 16
MAPKKK cascade -0.19 0.24 -10000 0 -0.77 64 64
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.46 0.43 -10000 0 -1.2 137 137
RETNLB -0.45 0.43 -10000 0 -1.2 133 133
SELP -0.5 0.52 -10000 0 -1.4 152 152
AICDA -0.47 0.43 -10000 0 -1.1 184 184
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.042 0.11 -10000 0 -0.65 12 12
Syndecan-4/Syndesmos -0.2 0.2 -10000 0 -0.53 107 107
positive regulation of JNK cascade -0.25 0.22 -10000 0 -0.55 181 181
Syndecan-4/ADAM12 -0.24 0.23 -10000 0 -0.61 145 145
CCL5 -0.1 0.2 -10000 0 -0.42 253 253
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
DNM2 0.028 0.003 -10000 0 -10000 0 0
ITGA5 0.004 0.098 -10000 0 -0.42 45 45
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG -0.3 0.32 -10000 0 -0.62 442 442
ADAM12 -0.068 0.18 -10000 0 -0.42 187 187
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.075 0.054 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.21 0.21 -10000 0 -0.55 123 123
Syndecan-4/CXCL12/CXCR4 -0.26 0.23 -10000 0 -0.58 180 180
Syndecan-4/Laminin alpha3 -0.22 0.2 -10000 0 -0.54 123 123
MDK -0.02 0.14 -10000 0 -0.42 94 94
Syndecan-4/FZD7 -0.21 0.2 -10000 0 -0.54 111 111
Syndecan-4/Midkine -0.22 0.21 0.41 1 -0.56 122 123
FZD7 0.015 0.086 -10000 0 -0.61 16 16
Syndecan-4/FGFR1/FGF -0.19 0.19 -10000 0 -0.6 37 37
THBS1 0.005 0.12 -10000 0 -0.64 30 30
integrin-mediated signaling pathway -0.2 0.2 -10000 0 -0.53 119 119
positive regulation of MAPKKK cascade -0.25 0.22 -10000 0 -0.55 181 181
Syndecan-4/TACI -0.21 0.2 -10000 0 -0.55 119 119
CXCR4 -0.086 0.19 -10000 0 -0.42 223 223
cell adhesion 0.018 0.055 0.22 11 -0.25 1 12
Syndecan-4/Dynamin -0.2 0.2 -10000 0 -0.53 106 106
Syndecan-4/TSP1 -0.21 0.2 -10000 0 -0.55 119 119
Syndecan-4/GIPC -0.2 0.2 -10000 0 -0.53 108 108
Syndecan-4/RANTES -0.25 0.22 -10000 0 -0.6 155 155
ITGB1 0.027 0.007 -10000 0 -10000 0 0
LAMA1 0.006 0.12 -10000 0 -0.57 32 32
LAMA3 -0.011 0.13 -10000 0 -0.42 75 75
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA 0.1 0.19 0.83 54 -10000 0 54
Syndecan-4/alpha-Actinin -0.2 0.2 -10000 0 -0.54 107 107
TFPI 0.012 0.092 -10000 0 -0.5 26 26
F2 -0.1 0.2 -10000 0 -0.41 251 251
alpha5/beta1 Integrin 0.021 0.074 -10000 0 -0.29 45 45
positive regulation of cell adhesion -0.22 0.2 -10000 0 -0.53 140 140
ACTN1 0.027 0.024 -10000 0 -0.65 1 1
TNC 0.003 0.12 -10000 0 -0.58 35 35
Syndecan-4/CXCL12 -0.22 0.21 -10000 0 -0.56 132 132
FGF6 -0.016 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
CXCL12 -0.025 0.17 -10000 0 -0.57 77 77
TNFRSF13B -0.007 0.1 -10000 0 -0.42 48 48
FGF2 0.016 0.087 -10000 0 -0.62 16 16
FGFR1 0.026 0.016 -10000 0 -0.42 1 1
Syndecan-4/PI-4-5-P2 -0.21 0.19 -10000 0 -0.53 108 108
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.005 0.12 -10000 0 -0.4 72 72
cell migration -0.027 0.018 -10000 0 -10000 0 0
PRKCD 0.027 0.049 -10000 0 -0.41 9 9
vasculogenesis -0.2 0.2 -10000 0 -0.53 119 119
SDC4 -0.21 0.2 -10000 0 -0.56 106 106
Syndecan-4/Tenascin C -0.21 0.2 -10000 0 -0.55 119 119
Syndecan-4/PI-4-5-P2/PKC alpha -0.06 0.042 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.2 0.2 -10000 0 -0.54 105 105
MMP9 -0.14 0.21 -10000 0 -0.41 331 331
Rac1/GTP 0.018 0.056 0.22 9 -0.25 1 10
cytoskeleton organization -0.19 0.19 -10000 0 -0.51 107 107
GIPC1 0.027 0.023 -10000 0 -0.65 1 1
Syndecan-4/TFPI -0.21 0.2 -10000 0 -0.54 114 114
Effects of Botulinum toxin

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
STX1A 0.008 0.029 0.2 4 -0.33 5 9
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.01 0.1 -10000 0 -0.34 66 66
STXBP1 0.027 0.023 -10000 0 -0.65 1 1
ACh/CHRNA1 -0.12 0.14 -10000 0 -0.26 424 424
RAB3GAP2/RIMS1/UNC13B 0.028 0.088 -10000 0 -0.32 32 32
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 -0.023 0.13 -10000 0 -0.47 67 67
mol:ACh 0.005 0.055 0.13 85 -0.14 16 101
RAB3GAP2 0.027 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.005 0.092 -10000 0 -0.32 32 32
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.12 0.14 -10000 0 -0.26 424 424
UNC13B 0.028 0.004 -10000 0 -10000 0 0
CHRNA1 -0.2 0.22 -10000 0 -0.42 430 430
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.076 0.18 -10000 0 -0.44 174 174
SNAP25 -0.024 0.064 -10000 0 -0.14 182 182
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 -0.11 0.27 -10000 0 -0.65 174 174
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.022 0.03 -10000 0 -0.3 6 6
STX1A/SNAP25 fragment 1/VAMP2 0.005 0.092 -10000 0 -0.32 32 32
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.08 0.17 0.43 2 -0.47 93 95
CRKL -0.033 0.16 -10000 0 -0.47 94 94
HRAS -0.034 0.15 -10000 0 -0.48 39 39
mol:PIP3 -0.024 0.16 0.26 2 -0.43 90 92
SPRED1 0.028 0.004 -10000 0 -10000 0 0
SPRED2 0.026 0.024 -10000 0 -0.65 1 1
GAB1 -0.035 0.18 -10000 0 -0.49 96 96
FOXO3 -0.009 0.17 0.36 1 -0.44 79 80
AKT1 -0.013 0.18 0.3 7 -0.47 87 94
BAD -0.009 0.17 0.33 4 -0.44 79 83
megakaryocyte differentiation -0.097 0.22 -10000 0 -0.43 233 233
GSK3B -0.003 0.17 0.39 18 -0.43 79 97
RAF1 -0.024 0.12 0.28 9 -0.4 27 36
SHC1 0.026 0.016 -10000 0 -0.42 1 1
STAT3 -0.033 0.17 -10000 0 -0.49 87 87
STAT1 -0.085 0.34 -10000 0 -1 96 96
HRAS/SPRED1 -0.019 0.13 -10000 0 -0.4 29 29
cell proliferation -0.035 0.17 -10000 0 -0.48 97 97
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
TEC 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.03 0.18 -10000 0 -0.48 96 96
HRAS/SPRED2 -0.018 0.13 -10000 0 -0.39 32 32
LYN/TEC/p62DOK -0.001 0.18 -10000 0 -0.46 93 93
MAPK3 0 0.12 0.37 29 -0.3 14 43
STAP1 -0.28 0.23 -10000 0 -0.4 560 560
GRAP2 -0.002 0.11 -10000 0 -0.42 56 56
JAK2 -0.074 0.3 -10000 0 -0.89 96 96
STAT1 (dimer) -0.082 0.33 -10000 0 -1 96 96
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.051 0.18 -10000 0 -0.49 82 82
actin filament polymerization -0.037 0.16 -10000 0 -0.49 83 83
LYN 0.026 0.024 -10000 0 -0.65 1 1
STAP1/STAT5A (dimer) -0.27 0.26 -10000 0 -0.75 129 129
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.006 0.15 0.4 1 -0.43 73 74
PI3K -0.006 0.18 -10000 0 -0.47 79 79
PTEN 0.026 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.4 -10000 0 -1.2 96 96
MAPK8 -0.036 0.18 -10000 0 -0.5 97 97
STAT3 (dimer) -0.032 0.16 -10000 0 -0.48 87 87
positive regulation of transcription 0.004 0.1 0.34 30 -0.27 5 35
mol:GDP -0.045 0.16 -10000 0 -0.5 40 40
PIK3C2B -0.033 0.17 -10000 0 -0.49 93 93
CBL/CRKL -0.017 0.16 0.4 1 -0.44 90 91
FER -0.036 0.17 -10000 0 -0.49 96 96
SH2B3 -0.034 0.17 -10000 0 -0.48 96 96
PDPK1 -0.013 0.14 0.32 12 -0.4 77 89
SNAI2 -0.054 0.2 -10000 0 -0.54 106 106
positive regulation of cell proliferation -0.055 0.26 -10000 0 -0.76 97 97
KITLG 0.013 0.092 -10000 0 -0.67 15 15
cell motility -0.055 0.26 -10000 0 -0.76 97 97
PTPN6 0.027 0.011 -10000 0 -10000 0 0
EPOR 0.013 0.12 -10000 0 -1 4 4
STAT5A (dimer) -0.048 0.23 -10000 0 -0.64 97 97
SOCS1 0.018 0.069 -10000 0 -0.53 13 13
cell migration 0.05 0.18 0.5 97 -10000 0 97
SOS1 0.027 0.006 -10000 0 -10000 0 0
EPO -0.073 0.18 -10000 0 -0.41 184 184
VAV1 -0.069 0.18 -10000 0 -0.42 191 191
GRB10 -0.038 0.16 -10000 0 -0.49 84 84
PTPN11 0.027 0.009 -10000 0 -10000 0 0
SCF/KIT -0.038 0.19 -10000 0 -0.5 103 103
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 -0.008 0.12 0.36 24 -0.33 15 39
CBL 0.027 0.023 -10000 0 -0.65 1 1
KIT -0.11 0.43 -10000 0 -1.3 98 98
MAP2K2 -0.009 0.12 0.35 26 -0.33 16 42
SHC/Grb2/SOS1 0.001 0.17 -10000 0 -0.46 80 80
STAT5A -0.051 0.23 -10000 0 -0.67 97 97
GRB2 0.025 0.009 -10000 0 -10000 0 0
response to radiation -0.052 0.2 -10000 0 -0.52 107 107
SHC/GRAP2 0.016 0.084 -10000 0 -0.3 57 57
PTPRO -0.099 0.22 -10000 0 -0.44 232 232
SH2B2 -0.039 0.17 -10000 0 -0.5 83 83
DOK1 0.026 0.022 -10000 0 -0.42 2 2
MATK -0.052 0.19 -10000 0 -0.52 97 97
CREBBP 0.031 0.045 -10000 0 -10000 0 0
BCL2 0.005 0.16 -10000 0 -1 11 11
Thromboxane A2 receptor signaling

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
TGM2 0.015 0.07 -10000 0 -0.42 22 22
GNB1/GNG2 -0.055 0.076 -10000 0 -0.19 159 159
AKT1 -0.017 0.13 0.36 17 -0.35 13 30
EGF -0.54 0.25 -10000 0 -0.65 731 731
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.012 0.083 0.52 7 -0.69 1 8
mol:Ca2+ -0.042 0.16 0.44 8 -0.31 168 176
LYN 0.011 0.064 0.36 3 -0.37 2 5
RhoA/GTP -0.014 0.063 -10000 0 -10000 0 0
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.053 0.18 0.47 9 -0.34 189 198
GNG2 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.024 0.03 -10000 0 -0.46 3 3
TP alpha/Gq family/GDP/G beta5/gamma2 -0.001 0.09 -10000 0 -0.48 13 13
G beta5/gamma2 -0.071 0.1 -10000 0 -0.26 122 122
PRKCH -0.056 0.18 0.46 7 -0.36 178 185
DNM1 -0.039 0.16 -10000 0 -0.42 129 129
TXA2/TP beta/beta Arrestin3 -0.008 0.053 -10000 0 -0.3 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.012 0.13 -10000 0 -0.42 78 78
G12 family/GTP -0.049 0.14 -10000 0 -0.3 135 135
ADRBK1 0.028 0.003 -10000 0 -10000 0 0
ADRBK2 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.034 0.012 -10000 0 -10000 0 0
mol:GDP 0.019 0.13 0.43 33 -0.38 8 41
mol:NADP 0.017 0.072 -10000 0 -0.65 10 10
RAB11A 0.028 0.003 -10000 0 -10000 0 0
PRKG1 -0.044 0.21 -10000 0 -0.64 92 92
mol:IP3 -0.059 0.2 0.49 7 -0.38 168 175
cell morphogenesis 0.033 0.012 -10000 0 -10000 0 0
PLCB2 -0.092 0.25 0.48 5 -0.52 173 178
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.001 0.078 0.37 4 -0.45 1 5
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK -0.004 0.078 0.38 2 -0.59 2 4
RHOA 0.026 0.008 -10000 0 -10000 0 0
PTGIR 0.024 0.053 -10000 0 -0.61 6 6
PRKCB1 -0.06 0.2 0.48 8 -0.37 203 211
GNAQ 0.028 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.072 -10000 0 -0.65 10 10
TXA2/TXA2-R family -0.094 0.26 0.55 8 -0.52 212 220
LCK 0.005 0.094 0.52 7 -0.42 5 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.016 0.071 -10000 0 -0.33 18 18
TXA2-R family/G12 family/GDP/G beta/gamma -0.001 0.12 -10000 0 -0.44 58 58
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.016 0.067 -10000 0 -0.32 12 12
MAPK14 -0.03 0.13 0.37 11 -0.24 42 53
TGM2/GTP -0.069 0.21 0.4 4 -0.44 122 126
MAPK11 -0.028 0.13 0.43 10 -0.26 12 22
ARHGEF1 -0.022 0.087 -10000 0 -0.2 3 3
GNAI2 0.026 0.008 -10000 0 -10000 0 0
JNK cascade -0.062 0.2 0.52 8 -0.38 210 218
RAB11/GDP 0.028 0.005 -10000 0 -10000 0 0
ICAM1 -0.039 0.15 0.45 8 -0.28 170 178
cAMP biosynthetic process -0.056 0.18 0.48 9 -0.37 129 138
Gq family/GTP/EBP50 -0.006 0.076 0.24 1 -0.3 16 17
actin cytoskeleton reorganization 0.033 0.012 -10000 0 -10000 0 0
SRC 0.009 0.057 0.38 2 -0.45 1 3
GNB5 0.028 0.003 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.09 0.11 0.56 9 -0.34 13 22
VCAM1 -0.049 0.17 0.45 8 -0.31 205 213
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.09 -10000 0 -0.48 13 13
platelet activation -0.038 0.17 0.44 14 -0.31 117 131
PGI2/IP 0.017 0.04 -10000 0 -0.46 6 6
PRKACA 0.008 0.05 -10000 0 -0.31 5 5
Gq family/GDP/G beta5/gamma2 -0.001 0.085 -10000 0 -0.44 13 13
TXA2/TP beta/beta Arrestin2 -0.011 0.072 -10000 0 -0.46 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.003 0.07 -10000 0 -0.36 22 22
mol:DAG -0.07 0.22 0.49 7 -0.43 192 199
EGFR 0.017 0.061 -10000 0 -0.45 14 14
TXA2/TP alpha -0.081 0.24 0.56 8 -0.5 131 139
Gq family/GTP -0.017 0.09 -10000 0 -0.26 99 99
YES1 0.012 0.067 0.41 4 -0.45 1 5
GNAI2/GTP 0.009 0.063 -10000 0 -0.32 12 12
PGD2/DP -0.008 0.089 -10000 0 -0.29 78 78
SLC9A3R1 0.025 0.009 -10000 0 -10000 0 0
FYN 0.014 0.078 0.52 7 -0.45 1 8
mol:NO 0.017 0.072 -10000 0 -0.65 10 10
GNA15 0.011 0.088 -10000 0 -0.42 34 34
PGK/cGMP -0.012 0.13 -10000 0 -0.36 97 97
RhoA/GDP 0.026 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.082 -10000 0 -0.73 1 1
NOS3 0.017 0.073 -10000 0 -0.65 10 10
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.05 0.18 0.42 13 -0.36 144 157
PRKCB -0.052 0.19 0.42 13 -0.36 168 181
PRKCE -0.055 0.18 0.47 8 -0.36 160 168
PRKCD -0.064 0.2 0.48 9 -0.38 199 208
PRKCG -0.073 0.21 0.49 8 -0.42 193 201
muscle contraction -0.084 0.24 0.56 8 -0.48 208 216
PRKCZ -0.054 0.18 0.49 8 -0.34 187 195
ARR3 -0.007 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.021 0.073 -10000 0 -0.34 18 18
PRKCQ -0.067 0.19 0.44 7 -0.38 189 196
MAPKKK cascade -0.076 0.23 0.53 8 -0.45 178 186
SELE -0.071 0.2 0.45 8 -0.41 219 227
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.076 -10000 0 -0.56 1 1
ROCK1 0.028 0.005 -10000 0 -10000 0 0
GNA14 -0.042 0.21 -10000 0 -0.64 92 92
chemotaxis -0.12 0.3 0.58 7 -0.61 218 225
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.025 0.009 -10000 0 -10000 0 0
GNA11 0.022 0.065 -10000 0 -0.65 8 8
Rac1/GTP 0.018 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.03 -10000 0 -0.42 4 4
CCL5 -0.1 0.2 -10000 0 -0.42 253 253
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.094 0.15 0.26 3 -0.42 84 87
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 -0.087 0.14 0.27 1 -0.42 69 70
Syndecan-1/Syntenin -0.085 0.15 0.28 2 -0.42 71 73
MAPK3 -0.075 0.13 -10000 0 -0.43 47 47
HGF/MET 0.01 0.11 -10000 0 -0.46 46 46
TGFB1/TGF beta receptor Type II 0.026 0.03 -10000 0 -0.42 4 4
BSG 0.027 0.021 -10000 0 -0.42 2 2
keratinocyte migration -0.086 0.14 0.27 1 -0.42 69 70
Syndecan-1/RANTES -0.14 0.16 0.33 3 -0.42 115 118
Syndecan-1/CD147 -0.075 0.15 -10000 0 -0.46 49 49
Syndecan-1/Syntenin/PIP2 -0.082 0.14 0.24 1 -0.4 71 72
LAMA5 0.025 0.028 -10000 0 -0.54 2 2
positive regulation of cell-cell adhesion -0.081 0.14 0.23 1 -0.4 71 72
MMP7 -0.069 0.23 -10000 0 -0.58 140 140
HGF -0.007 0.14 -10000 0 -0.6 45 45
Syndecan-1/CASK -0.096 0.14 0.2 1 -0.4 87 88
Syndecan-1/HGF/MET -0.084 0.16 -10000 0 -0.49 65 65
regulation of cell adhesion -0.074 0.13 0.32 1 -0.47 25 26
HPSE 0.007 0.11 -10000 0 -0.6 29 29
positive regulation of cell migration -0.094 0.15 0.26 3 -0.42 84 87
SDC1 -0.095 0.15 0.25 2 -0.38 120 122
Syndecan-1/Collagen -0.094 0.15 0.26 3 -0.42 84 87
PPIB 0.028 0.003 -10000 0 -10000 0 0
MET 0.021 0.04 -10000 0 -0.42 7 7
PRKACA 0.028 0.002 -10000 0 -10000 0 0
MMP9 -0.14 0.22 -10000 0 -0.42 331 331
MAPK1 -0.077 0.14 -10000 0 -0.46 36 36
homophilic cell adhesion -0.094 0.15 0.26 3 -0.41 85 88
MMP1 -0.08 0.22 -10000 0 -0.52 169 169
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.087 0.37 -10000 0 -1.2 90 90
MKNK1 0.027 0.007 -10000 0 -10000 0 0
MAPK14 0.001 0.12 -10000 0 -0.33 82 82
ATF2/c-Jun 0.001 0.095 -10000 0 -0.43 12 12
MAPK11 0.004 0.12 -10000 0 -0.33 82 82
MITF -0.004 0.13 -10000 0 -0.38 89 89
MAPKAPK5 0 0.13 -10000 0 -0.38 83 83
KRT8 -0.001 0.13 -10000 0 -0.38 77 77
MAPKAPK3 0.026 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.004 0.18 -10000 0 -0.5 87 87
CEBPB -0.006 0.13 -10000 0 -0.38 85 85
SLC9A1 -0.006 0.14 -10000 0 -0.38 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0 0.13 -10000 0 -0.37 90 90
p38alpha-beta/MNK1 0.015 0.15 -10000 0 -0.41 81 81
JUN 0 0.094 -10000 0 -0.43 12 12
PPARGC1A -0.028 0.16 -10000 0 -0.38 134 134
USF1 -0.006 0.14 -10000 0 -0.38 97 97
RAB5/GDP/GDI1 0.001 0.1 -10000 0 -0.46 8 8
NOS2 -0.018 0.22 -10000 0 -1.1 25 25
DDIT3 -0.005 0.13 -10000 0 -0.39 82 82
RAB5A 0.026 0.008 -10000 0 -10000 0 0
HSPB1 0.02 0.12 0.29 60 -0.47 13 73
p38alpha-beta/HBP1 0.018 0.13 -10000 0 -0.42 57 57
CREB1 -0.008 0.15 -10000 0 -0.4 100 100
RAB5/GDP 0.019 0.006 -10000 0 -10000 0 0
EIF4E -0.008 0.13 -10000 0 -0.67 11 11
RPS6KA4 -0.006 0.14 -10000 0 -0.37 98 98
PLA2G4A -0.016 0.15 -10000 0 -0.62 28 28
GDI1 -0.006 0.14 -10000 0 -0.38 89 89
TP53 -0.013 0.15 -10000 0 -0.49 69 69
RPS6KA5 -0.009 0.14 -10000 0 -0.39 99 99
ESR1 -0.018 0.17 -10000 0 -0.44 106 106
HBP1 0.025 0.01 -10000 0 -10000 0 0
MEF2C -0.005 0.13 -10000 0 -0.37 95 95
MEF2A -0.006 0.14 -10000 0 -0.37 99 99
EIF4EBP1 -0.009 0.15 -10000 0 -0.4 100 100
KRT19 -0.065 0.21 -10000 0 -0.42 190 190
ELK4 -0.006 0.14 -10000 0 -0.38 91 91
ATF6 -0.006 0.14 -10000 0 -0.38 95 95
ATF1 -0.007 0.14 -10000 0 -0.4 100 100
p38alpha-beta/MAPKAPK2 0.015 0.15 -10000 0 -0.41 82 82
p38alpha-beta/MAPKAPK3 0.015 0.14 -10000 0 -0.4 75 75
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.029 0.037 -10000 0 -0.42 5 5
ARNO/beta Arrestin1-2 0.021 0.066 -10000 0 -0.82 2 2
EGFR 0.017 0.061 -10000 0 -0.45 14 14
EPHA2 0.026 0.024 -10000 0 -0.65 1 1
USP6 0.02 0.05 -10000 0 -0.42 11 11
IQSEC1 0.026 0.008 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.38 0.2 -10000 0 -0.46 727 727
ARRB2 -0.002 0.048 -10000 0 -0.5 1 1
mol:GTP 0.017 0.065 0.2 59 -0.22 8 67
ARRB1 0.027 0.023 -10000 0 -0.65 1 1
FBXO8 0.028 0.004 -10000 0 -10000 0 0
TSHR -0.015 0.13 -10000 0 -0.42 78 78
EGF -0.54 0.25 -10000 0 -0.65 731 731
somatostatin receptor activity 0 0 0.001 34 -0.001 67 101
ARAP2 0.026 0.033 -10000 0 -0.65 2 2
mol:GDP -0.049 0.11 0.25 16 -0.31 57 73
mol:PI-3-4-5-P3 0 0 0.001 28 -0.001 34 62
ITGA2B 0.015 0.068 -10000 0 -0.46 17 17
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.033 -10000 0 -0.38 1 1
ADAP1 0.021 0.052 -10000 0 -0.65 5 5
KIF13B 0.027 0.007 -10000 0 -10000 0 0
HGF/MET 0.01 0.11 -10000 0 -0.46 46 46
PXN 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.077 0.13 0.31 32 -0.32 71 103
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.32 0.18 -10000 0 -0.42 621 621
ADRB2 0.017 0.067 -10000 0 -0.43 19 19
receptor agonist activity 0 0 0.001 35 0 60 95
actin filament binding 0 0 0.001 35 -0.001 76 111
SRC 0.027 0.007 -10000 0 -10000 0 0
ITGB3 0.008 0.1 -10000 0 -0.61 24 24
GNAQ 0.028 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 55 -0.001 37 92
ARF6/GDP -0.03 0.11 0.31 5 -0.39 33 38
ARF6/GDP/GULP/ACAP1 -0.077 0.14 0.24 1 -0.42 48 49
alphaIIb/beta3 Integrin/paxillin/GIT1 0.046 0.082 -10000 0 -0.4 19 19
ACAP1 -0.088 0.19 -10000 0 -0.42 224 224
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.068 -10000 0 -0.45 1 1
EFNA1 0.026 0.016 -10000 0 -0.42 1 1
HGF -0.007 0.14 -10000 0 -0.6 45 45
CYTH3 0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.016 0.049 -10000 0 -1 2 2
NCK1 0.027 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 56 0 42 98
endosomal lumen acidification 0 0 0.001 23 -0.001 80 103
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 0.017 0.08 -10000 0 -0.63 13 13
GNAQ/ARNO 0.032 0.047 -10000 0 -0.93 2 2
mol:Phosphatidic acid 0 0 0.001 9 -10000 0 9
PIP3-E 0 0 0.001 8 0 3 11
MET 0.021 0.04 -10000 0 -0.42 7 7
GNA14 -0.042 0.21 -10000 0 -0.64 92 92
GNA15 0.011 0.088 -10000 0 -0.42 34 34
GIT1 0.025 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 48 -0.001 40 88
GNA11 0.022 0.065 -10000 0 -0.65 8 8
LHCGR -0.03 0.12 -10000 0 -0.42 69 69
AGTR1 -0.071 0.24 -10000 0 -0.65 127 127
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.068 -10000 0 -0.44 1 1
IPCEF1/ARNO -0.24 0.14 -10000 0 -0.57 13 13
alphaIIb/beta3 Integrin 0.017 0.097 -10000 0 -0.41 39 39
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.025 0.17 -10000 0 -0.52 39 39
PTK2B 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.38 0.61 3 -0.94 135 138
EDN1 -0.008 0.14 0.47 1 -0.47 39 40
EDN3 0 0.065 -10000 0 -0.43 17 17
EDN2 -0.04 0.18 -10000 0 -0.5 111 111
HRAS/GDP -0.051 0.21 0.33 10 -0.54 84 94
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.056 0.19 0.25 2 -0.46 107 109
ADCY4 -0.028 0.16 0.34 1 -0.57 33 34
ADCY5 -0.038 0.17 0.42 3 -0.55 43 46
ADCY6 -0.021 0.14 -10000 0 -0.52 24 24
ADCY7 -0.027 0.14 0.34 1 -0.49 24 25
ADCY1 -0.059 0.17 0.45 1 -0.5 60 61
ADCY2 -0.091 0.18 0.34 2 -0.55 48 50
ADCY3 -0.019 0.14 0.35 3 -0.52 24 27
ADCY8 -0.061 0.16 0.34 1 -0.46 55 56
ADCY9 -0.02 0.13 -10000 0 -0.5 21 21
arachidonic acid secretion -0.07 0.25 0.44 12 -0.59 120 132
ETB receptor/Endothelin-1/Gq/GTP -0.024 0.13 -10000 0 -0.35 83 83
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
HRAS 0.027 0.015 -10000 0 -0.42 1 1
ETA receptor/Endothelin-1/G12/GTP 0.008 0.18 0.37 39 -0.5 29 68
ETA receptor/Endothelin-1/Gs/GTP 0.009 0.18 0.34 50 -0.49 35 85
mol:GTP 0 0.006 -10000 0 -10000 0 0
COL3A1 -0.044 0.21 -10000 0 -0.55 85 85
EDNRB 0.015 0.068 -10000 0 -0.57 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.075 0.24 0.52 1 -0.7 69 70
CYSLTR1 -0.025 0.18 0.52 1 -0.64 24 25
SLC9A1 -0.006 0.11 0.37 1 -0.4 24 25
mol:GDP -0.062 0.22 0.38 15 -0.55 95 110
SLC9A3 -0.49 0.39 -10000 0 -0.81 402 402
RAF1 -0.063 0.21 0.42 11 -0.55 93 104
JUN -0.065 0.26 0.51 2 -0.68 83 85
JAK2 -0.024 0.17 0.52 1 -0.53 39 40
mol:IP3 -0.062 0.19 0.23 2 -0.48 113 115
ETA receptor/Endothelin-1 -0.008 0.23 0.43 57 -0.58 44 101
PLCB1 -0.042 0.2 -10000 0 -0.65 90 90
PLCB2 -0.018 0.13 -10000 0 -0.42 89 89
ETA receptor/Endothelin-3 0.002 0.13 -10000 0 -0.44 40 40
FOS -0.068 0.28 0.47 10 -0.82 82 92
Gai/GDP -0.027 0.21 -10000 0 -0.71 57 57
CRK 0.025 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.076 0.22 0.3 2 -0.62 77 79
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
PRKCB1 -0.062 0.19 -10000 0 -0.47 111 111
GNAQ 0.025 0.016 -10000 0 -10000 0 0
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
GNAL 0.026 0.028 -10000 0 -0.54 2 2
Gs family/GDP -0.05 0.2 0.33 10 -0.52 84 94
ETA receptor/Endothelin-1/Gq/GTP -0.036 0.19 0.52 1 -0.52 73 74
MAPK14 -0.041 0.14 -10000 0 -0.44 63 63
TRPC6 -0.14 0.41 0.61 3 -1 132 135
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.048 0.16 -10000 0 -0.41 93 93
ETB receptor/Endothelin-2 -0.022 0.15 -10000 0 -0.4 97 97
ETB receptor/Endothelin-3 0.019 0.07 -10000 0 -0.34 26 26
ETB receptor/Endothelin-1 0.005 0.13 0.34 1 -0.49 21 22
MAPK3 -0.068 0.26 0.47 10 -0.75 85 95
MAPK1 -0.072 0.28 0.46 11 -0.77 86 97
Rac1/GDP -0.045 0.19 0.52 2 -0.53 70 72
cAMP biosynthetic process -0.059 0.17 0.42 14 -0.5 51 65
MAPK8 -0.087 0.31 0.55 2 -0.77 113 115
SRC 0.027 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.006 0.086 -10000 0 -0.36 27 27
p130Cas/CRK/Src/PYK2 -0.072 0.25 0.44 16 -0.62 101 117
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.046 0.19 0.52 2 -0.52 73 75
COL1A2 -0.032 0.19 0.5 1 -0.51 65 66
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.038 0.18 -10000 0 -0.49 85 85
mol:DAG -0.062 0.19 0.23 2 -0.48 113 115
MAP2K2 -0.063 0.23 0.45 11 -0.61 90 101
MAP2K1 -0.062 0.23 0.46 11 -0.62 89 100
EDNRA -0.008 0.16 -10000 0 -0.62 32 32
positive regulation of muscle contraction 0.002 0.16 0.35 20 -0.57 17 37
Gq family/GDP -0.053 0.22 0.31 4 -0.57 92 96
HRAS/GTP -0.065 0.21 0.36 11 -0.51 108 119
PRKCH -0.061 0.19 -10000 0 -0.49 100 100
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.048 0.18 0.28 14 -0.5 81 95
PRKCB -0.054 0.19 0.28 9 -0.5 92 101
PRKCE -0.057 0.18 0.24 1 -0.49 98 99
PRKCD -0.061 0.18 0.25 1 -0.5 95 96
PRKCG -0.085 0.21 -10000 0 -0.54 114 114
regulation of vascular smooth muscle contraction -0.085 0.32 0.5 10 -0.97 80 90
PRKCQ -0.073 0.21 -10000 0 -0.5 129 129
PLA2G4A -0.08 0.28 0.46 11 -0.65 120 131
GNA14 -0.045 0.21 -10000 0 -0.65 92 92
GNA15 0.009 0.088 -10000 0 -0.42 34 34
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA11 0.02 0.066 -10000 0 -0.66 8 8
Rac1/GTP 0.008 0.18 0.37 39 -0.52 27 66
MMP1 -0.1 0.3 0.51 2 -0.73 132 134
LPA4-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
ADCY4 -0.002 0.064 -10000 0 -0.42 20 20
ADCY5 -0.018 0.1 -10000 0 -0.42 52 52
ADCY6 0.007 0.027 -10000 0 -0.79 1 1
ADCY7 -0.002 0.05 0.19 1 -0.25 33 34
ADCY1 -0.039 0.13 0.19 3 -0.4 101 104
ADCY2 -0.079 0.13 0.19 12 -0.26 295 307
ADCY3 0.007 0.017 -10000 0 -0.33 2 2
ADCY8 -0.044 0.1 0.19 5 -0.25 170 175
PRKCE 0.009 0.017 -10000 0 -0.49 1 1
ADCY9 0.007 0.015 -10000 0 -0.42 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.046 0.11 0.34 26 -0.3 22 48
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.1 0.18 -10000 0 -0.33 331 331
PDGFRB 0.017 0.081 -10000 0 -0.64 13 13
SPHK1 -0.027 0.13 -10000 0 -0.62 35 35
mol:S1P -0.02 0.11 0.29 1 -0.53 34 35
S1P1/S1P/Gi -0.049 0.15 0.24 1 -0.46 67 68
GNAO1 0.01 0.096 -10000 0 -0.56 23 23
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.14 0.38 5 -0.48 46 51
PLCG1 -0.042 0.14 0.26 1 -0.44 60 61
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.081 -10000 0 -0.64 13 13
GNAI2 0.024 0.014 -10000 0 -10000 0 0
GNAI3 0.024 0.014 -10000 0 -10000 0 0
GNAI1 0.021 0.041 -10000 0 -0.65 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.1 0.14 -10000 0 -0.28 331 331
S1P1/S1P -0.082 0.13 -10000 0 -0.38 79 79
negative regulation of cAMP metabolic process -0.047 0.14 0.23 1 -0.45 67 68
MAPK3 -0.056 0.18 0.32 2 -0.57 74 76
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.006 -10000 0 -10000 0 0
KDR -0.023 0.18 -10000 0 -0.65 64 64
PLCB2 -0.082 0.14 0.35 13 -0.34 107 120
RAC1 0.025 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.073 0.11 -10000 0 -0.33 74 74
receptor internalization -0.079 0.12 -10000 0 -0.36 79 79
PTGS2 -0.098 0.33 0.52 19 -0.96 99 118
Rac1/GTP -0.068 0.11 -10000 0 -0.32 62 62
RHOA 0.026 0.008 -10000 0 -10000 0 0
VEGFA -0.11 0.2 -10000 0 -0.42 269 269
negative regulation of T cell proliferation -0.047 0.14 0.23 1 -0.45 67 68
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.042 -10000 0 -0.65 3 3
MAPK1 -0.072 0.21 -10000 0 -0.62 93 93
S1P1/S1P/PDGFB-D/PDGFRB -0.077 0.15 0.42 1 -0.45 48 49
ABCC1 0.026 0.007 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.023 0.015 -9999 0 -10000 0 0
SVIL 0.024 0.014 -9999 0 -10000 0 0
ZNF318 0.029 0.015 -9999 0 -10000 0 0
JMJD2C -0.004 0.02 -9999 0 -0.067 79 79
T-DHT/AR/Ubc9 -0.083 0.11 -9999 0 -0.45 52 52
CARM1 0.028 0.003 -9999 0 -10000 0 0
PRDX1 0.027 0.007 -9999 0 -10000 0 0
PELP1 0.026 0.009 -9999 0 -10000 0 0
CTNNB1 0.023 0.013 -9999 0 -10000 0 0
AKT1 0.029 0.007 -9999 0 -10000 0 0
PTK2B 0.026 0.008 -9999 0 -10000 0 0
MED1 0.026 0.01 -9999 0 -10000 0 0
MAK 0.023 0.051 -9999 0 -0.41 11 11
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.017 0.053 -9999 0 -0.66 5 5
GSN 0.023 0.016 -9999 0 -10000 0 0
NCOA2 -0.004 0.14 -9999 0 -0.65 40 40
NCOA6 0.022 0.015 -9999 0 -10000 0 0
DNA-PK 0.054 0.023 -9999 0 -10000 0 0
NCOA4 0.027 0.007 -9999 0 -10000 0 0
PIAS3 0.024 0.013 -9999 0 -10000 0 0
cell proliferation -0.054 0.12 -9999 0 -0.51 51 51
XRCC5 0.028 0.007 -9999 0 -10000 0 0
UBE3A 0.022 0.02 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.14 -9999 0 -0.48 85 85
FHL2 -0.057 0.14 -9999 0 -0.77 24 24
RANBP9 0.024 0.014 -9999 0 -10000 0 0
JMJD1A -0.11 0.066 -9999 0 -0.14 652 652
CDK6 0.024 0.025 -9999 0 -0.65 1 1
TGFB1I1 0.018 0.055 -9999 0 -0.61 6 6
T-DHT/AR/CyclinD1 -0.096 0.12 -9999 0 -0.41 86 86
XRCC6 0.028 0.006 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.42 77 77
CTDSP1 0.026 0.007 -9999 0 -10000 0 0
CTDSP2 0.03 0.013 -9999 0 -10000 0 0
BRCA1 0.02 0.033 -9999 0 -0.42 4 4
TCF4 0.026 0.049 -9999 0 -0.6 5 5
CDKN2A -0.36 0.15 -9999 0 -0.42 773 773
SRF 0.032 0.019 -9999 0 -10000 0 0
NKX3-1 -0.19 0.1 -9999 0 -0.24 683 683
KLK3 0.001 0.088 -9999 0 -10000 0 0
TMF1 0.025 0.024 -9999 0 -0.65 1 1
HNRNPA1 0.028 0.008 -9999 0 -10000 0 0
AOF2 -0.002 0.006 -9999 0 -10000 0 0
APPL1 0.02 0.012 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.084 0.11 -9999 0 -0.45 53 53
AR -0.088 0.15 -9999 0 -0.67 53 53
UBA3 0.026 0.007 -9999 0 -10000 0 0
PATZ1 0.029 0.007 -9999 0 -10000 0 0
PAWR 0.026 0.024 -9999 0 -0.65 1 1
PRKDC 0.028 0.007 -9999 0 -10000 0 0
PA2G4 0.029 0.009 -9999 0 -10000 0 0
UBE2I 0.027 0.007 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.075 0.099 -9999 0 -0.42 53 53
RPS6KA3 0.023 0.017 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.086 0.11 -9999 0 -0.46 52 52
LATS2 0.028 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.075 0.099 -9999 0 -0.42 51 51
Cyclin D3/CDK11 p58 0.02 0.005 -9999 0 -10000 0 0
VAV3 0.015 0.08 -9999 0 -0.65 12 12
KLK2 -0.087 0.1 -9999 0 -0.43 35 35
CASP8 0.027 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.09 0.14 -9999 0 -0.48 80 80
TMPRSS2 -0.77 0.44 -9999 0 -1 655 655
CCND1 0.01 0.088 -9999 0 -0.42 34 34
PIAS1 0.022 0.02 -9999 0 -10000 0 0
mol:T-DHT -0.054 0.03 -9999 0 -0.071 648 648
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.02 0.025 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.45 53 53
CMTM2 0.012 0.078 -9999 0 -0.42 28 28
SNURF -0.004 0.13 -9999 0 -0.63 38 38
ZMIZ1 -0.045 0.04 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -10000 0 0
TGIF1 0.029 0.007 -9999 0 -10000 0 0
FKBP4 0.022 0.015 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.077 0.23 -10000 0 -0.58 118 118
MAP4K1 -0.09 0.2 -10000 0 -0.42 234 234
MAP3K8 0.026 0.022 -10000 0 -0.42 2 2
PRKCB 0.019 0.066 -10000 0 -0.58 10 10
DBNL 0.025 0.009 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 -0.022 0.1 -10000 0 -0.35 32 32
JUN -0.003 0.16 0.33 1 -0.6 51 52
MAP3K7 -0.02 0.1 -10000 0 -0.35 32 32
GRAP2 -0.002 0.11 -10000 0 -0.42 56 56
CRK 0.025 0.009 -10000 0 -10000 0 0
MAP2K4 -0.001 0.11 0.3 24 -0.45 1 25
LAT -0.047 0.16 -10000 0 -0.42 145 145
LCP2 -0.006 0.12 -10000 0 -0.42 64 64
MAPK8 -0.009 0.17 -10000 0 -0.64 51 51
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.023 0.11 -10000 0 -0.37 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.064 0.22 -10000 0 -0.56 112 112
Reelin signaling pathway

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
CDK5R1/CDK5 0.033 0.027 -10000 0 -0.32 3 3
VLDLR 0.027 0.016 -10000 0 -0.42 1 1
CRKL 0.027 0.005 -10000 0 -10000 0 0
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
FYN 0.026 0.007 -10000 0 -10000 0 0
ITGA3 0.02 0.048 -10000 0 -0.42 10 10
RELN/VLDLR/Fyn -0.053 0.18 -10000 0 -0.42 163 163
MAPK8IP1/MKK7/MAP3K11/JNK1 0.072 0.056 -10000 0 -0.4 9 9
AKT1 -0.038 0.12 -10000 0 -0.36 13 13
MAP2K7 0.028 0.003 -10000 0 -10000 0 0
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
DAB1 -0.003 0.07 -10000 0 -0.42 22 22
RELN/LRP8/DAB1 -0.056 0.17 -10000 0 -0.37 180 180
LRPAP1/LRP8 0.037 0.025 -10000 0 -0.29 4 4
RELN/LRP8/DAB1/Fyn -0.044 0.17 -10000 0 -0.37 162 162
DAB1/alpha3/beta1 Integrin -0.04 0.16 -10000 0 -0.52 2 2
long-term memory -0.093 0.2 -10000 0 -0.4 202 202
DAB1/LIS1 -0.029 0.17 -10000 0 -0.36 77 77
DAB1/CRLK/C3G -0.038 0.16 -10000 0 -0.52 2 2
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DAB1/NCK2 -0.025 0.17 -10000 0 -0.36 77 77
ARHGEF2 0.027 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.085 0.23 -10000 0 -0.53 175 175
CDK5R1 0.023 0.036 -10000 0 -0.44 5 5
RELN -0.12 0.27 -10000 0 -0.61 195 195
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.053 0.18 -10000 0 -0.42 162 162
GRIN2A/RELN/LRP8/DAB1/Fyn -0.092 0.21 -10000 0 -0.41 216 216
MAPK8 0.022 0.058 -10000 0 -0.61 7 7
RELN/VLDLR/DAB1 -0.056 0.17 -10000 0 -0.39 163 163
ITGB1 0.027 0.007 -10000 0 -10000 0 0
MAP1B -0.063 0.16 -10000 0 -0.37 160 160
RELN/LRP8 -0.053 0.18 -10000 0 -0.42 161 161
GRIN2B/RELN/LRP8/DAB1/Fyn -0.034 0.18 -10000 0 -0.37 160 160
PI3K 0.039 0.011 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.038 -10000 0 -0.29 10 10
RAP1A -0.033 0.16 0.44 9 -0.49 2 11
PAFAH1B1 0.025 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.04 -10000 0 -0.65 3 3
CRLK/C3G 0.04 0.009 -10000 0 -10000 0 0
GRIN2B 0.005 0.05 -10000 0 -0.42 10 10
NCK2 0.027 0.006 -10000 0 -10000 0 0
neuron differentiation -0.027 0.15 -10000 0 -0.47 50 50
neuron adhesion -0.02 0.17 0.37 38 -0.47 2 40
LRP8 0.025 0.031 -10000 0 -0.42 4 4
GSK3B -0.038 0.11 -10000 0 -0.34 12 12
RELN/VLDLR/DAB1/Fyn -0.044 0.17 -10000 0 -0.37 163 163
MAP3K11 0.027 0.023 -10000 0 -0.65 1 1
RELN/VLDLR/DAB1/P13K -0.04 0.13 -10000 0 -0.29 162 162
CDK5 0.025 0.01 -10000 0 -10000 0 0
MAPT 0.03 0.16 0.66 44 -0.58 14 58
neuron migration -0.039 0.16 0.3 17 -0.4 11 28
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.027 0.15 -10000 0 -0.49 47 47
RELN/VLDLR -0.037 0.18 -10000 0 -0.38 161 161
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.013 0.041 -10000 0 -10000 0 0
NFATC2 -0.024 0.078 -10000 0 -0.42 24 24
NFATC3 -0.012 0.04 -10000 0 -10000 0 0
CD40LG -0.17 0.28 0.4 4 -0.63 158 162
PTGS2 -0.19 0.28 0.39 5 -0.61 186 191
JUNB 0.027 0.033 -10000 0 -0.65 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.03 -10000 0 -10000 0 0
CaM/Ca2+ -0.005 0.03 -10000 0 -10000 0 0
CALM1 0.01 0.026 -10000 0 -10000 0 0
JUN 0.009 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.012 -10000 0 -10000 0 0
FOSL1 0.012 0.084 -10000 0 -0.42 31 31
CREM 0.027 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.079 0.16 -10000 0 -0.46 28 28
FOS -0.033 0.16 -10000 0 -0.63 57 57
IFNG -0.2 0.3 0.4 3 -0.61 259 262
AP-1/NFAT1-c-4 -0.18 0.29 -10000 0 -0.68 141 141
FASLG -0.22 0.31 0.4 4 -0.6 279 283
NFAT1-c-4/ICER1 -0.042 0.1 -10000 0 -0.42 10 10
IL2RA -0.18 0.28 0.4 3 -0.65 156 159
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.16 0.25 0.4 4 -0.58 138 142
JunB/Fra1/NFAT1-c-4 -0.039 0.12 -10000 0 -0.41 18 18
IL4 -0.16 0.24 0.39 4 -0.57 134 138
IL2 -0.003 0.1 -10000 0 -0.88 9 9
IL3 -0.023 0.14 -10000 0 -0.6 36 36
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
BATF3 0.01 0.085 -10000 0 -0.42 33 33
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.007 -10000 0 -10000 0 0
Ephrin A reverse 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
MAPKKK cascade -0.007 0.12 -9999 0 -0.39 80 80
EFNA5 -0.021 0.17 -9999 0 -0.64 63 63
FYN -0.015 0.11 -9999 0 -0.4 61 61
neuron projection morphogenesis -0.007 0.12 -9999 0 -0.39 80 80
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.007 0.12 -9999 0 -0.39 80 80
EPHA5 -0.013 0.066 -9999 0 -0.42 20 20
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.052 0.16 -10000 0 -0.54 76 76
NFATC2 -0.049 0.18 -10000 0 -0.57 29 29
NFATC3 -0.017 0.083 -10000 0 -0.32 20 20
CD40LG -0.17 0.34 0.52 1 -0.94 76 77
ITCH 0.018 0.08 -10000 0 -0.46 1 1
CBLB 0.019 0.08 -10000 0 -0.46 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.31 -10000 0 -0.82 90 90
JUNB 0.027 0.033 -10000 0 -0.65 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.095 -10000 0 -0.31 65 65
T cell anergy 0.002 0.12 -10000 0 -0.42 65 65
TLE4 -0.022 0.12 -10000 0 -0.5 7 7
Jun/NFAT1-c-4/p21SNFT -0.1 0.29 -10000 0 -0.97 42 42
AP-1/NFAT1-c-4 -0.16 0.38 -10000 0 -1.1 61 61
IKZF1 -0.061 0.18 -10000 0 -0.49 32 32
T-helper 2 cell differentiation -0.32 0.29 0.46 1 -0.68 218 219
AP-1/NFAT1 -0.048 0.17 -10000 0 -0.5 41 41
CALM1 0.024 0.059 -10000 0 -10000 0 0
EGR2 -0.12 0.36 -10000 0 -1.4 51 51
EGR3 -0.14 0.41 -10000 0 -1.4 68 68
NFAT1/FOXP3 -0.081 0.22 -10000 0 -0.6 84 84
EGR1 -0.01 0.16 -10000 0 -0.65 48 48
JUN 0.01 0.032 -10000 0 -10000 0 0
EGR4 0.019 0.046 -10000 0 -0.41 9 9
mol:Ca2+ -0.003 0.055 -10000 0 -0.28 5 5
GBP3 -0.03 0.14 -10000 0 -0.6 17 17
FOSL1 0.012 0.084 -10000 0 -0.42 31 31
NFAT1-c-4/MAF/IRF4 -0.11 0.29 -10000 0 -0.95 40 40
DGKA -0.025 0.13 -10000 0 -0.53 14 14
CREM 0.026 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.085 0.27 -10000 0 -0.96 43 43
CTLA4 -0.13 0.26 -10000 0 -0.6 152 152
NFAT1-c-4 (dimer)/EGR1 -0.099 0.31 -10000 0 -1.1 52 52
NFAT1-c-4 (dimer)/EGR4 -0.088 0.28 -10000 0 -0.94 50 50
FOS -0.031 0.16 -10000 0 -0.64 57 57
IFNG -0.13 0.22 -10000 0 -0.58 54 54
T cell activation -0.049 0.19 0.57 2 -0.69 21 23
MAF 0.026 0.007 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.067 0.21 0.84 35 -10000 0 35
TNF -0.1 0.28 -10000 0 -1 46 46
FASLG -0.19 0.43 -10000 0 -1.4 70 70
TBX21 -0.094 0.2 -10000 0 -0.46 200 200
BATF3 0.01 0.085 -10000 0 -0.42 33 33
PRKCQ -0.028 0.14 -10000 0 -0.55 51 51
PTPN1 -0.022 0.12 -10000 0 -0.5 8 8
NFAT1-c-4/ICER1 -0.088 0.28 -10000 0 -0.93 50 50
GATA3 -0.32 0.34 -10000 0 -0.65 458 458
T-helper 1 cell differentiation -0.13 0.22 -10000 0 -0.57 63 63
IL2RA -0.14 0.28 -10000 0 -0.74 80 80
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.023 0.12 -10000 0 -0.5 7 7
E2F1 -0.051 0.17 -10000 0 -0.41 163 163
PPARG 0.026 0.017 -10000 0 -0.42 1 1
SLC3A2 -0.022 0.12 -10000 0 -0.5 7 7
IRF4 -0.051 0.17 -10000 0 -0.42 152 152
PTGS2 -0.18 0.36 0.52 1 -1 83 84
CSF2 -0.16 0.32 0.51 1 -0.99 61 62
JunB/Fra1/NFAT1-c-4 -0.077 0.28 -10000 0 -0.92 46 46
IL4 -0.33 0.3 0.46 1 -0.72 200 201
IL5 -0.15 0.32 0.51 1 -0.97 60 61
IL2 -0.05 0.19 0.57 2 -0.7 20 22
IL3 -0.039 0.13 -10000 0 -0.81 18 18
RNF128 -0.017 0.2 -10000 0 -0.69 72 72
NFATC1 -0.067 0.21 -10000 0 -0.84 35 35
CDK4 0.035 0.15 0.65 7 -10000 0 7
PTPRK -0.025 0.12 -10000 0 -0.55 8 8
IL8 -0.17 0.34 -10000 0 -0.98 73 73
POU2F1 0.027 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.08 0.16 -10000 0 -0.56 32 32
IHH -0.056 0.2 -10000 0 -0.66 78 78
SHH Np/Cholesterol/GAS1 -0.011 0.12 -10000 0 -0.39 68 68
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.011 0.12 0.38 68 -10000 0 68
SMO/beta Arrestin2 -0.047 0.14 -10000 0 -0.51 37 37
SMO -0.058 0.14 -10000 0 -0.53 38 38
AKT1 -0.011 0.097 -10000 0 -0.58 10 10
ARRB2 0.024 0.03 -10000 0 -0.46 3 3
BOC 0.026 0.024 -10000 0 -0.65 1 1
ADRBK1 0.028 0.003 -10000 0 -10000 0 0
heart looping -0.057 0.14 -10000 0 -0.52 38 38
STIL -0.032 0.15 -10000 0 -0.43 43 43
DHH N/PTCH2 0.007 0.12 -10000 0 -0.43 57 57
DHH N/PTCH1 -0.063 0.15 -10000 0 -0.45 68 68
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DHH -0.006 0.14 -10000 0 -0.65 41 41
PTHLH -0.12 0.21 -10000 0 -0.73 37 37
determination of left/right symmetry -0.057 0.14 -10000 0 -0.52 38 38
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
skeletal system development -0.12 0.21 -10000 0 -0.72 37 37
IHH N/Hhip -0.096 0.22 -10000 0 -0.5 188 188
DHH N/Hhip -0.055 0.2 -10000 0 -0.48 158 158
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.057 0.14 -10000 0 -0.52 38 38
pancreas development -0.068 0.23 -10000 0 -0.61 126 126
HHAT 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.011 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.01 0.16 -10000 0 -0.64 50 50
somite specification -0.057 0.14 -10000 0 -0.52 38 38
SHH Np/Cholesterol/PTCH1 -0.054 0.13 -10000 0 -0.44 48 48
SHH Np/Cholesterol/PTCH2 0.004 0.087 -10000 0 -0.37 36 36
SHH Np/Cholesterol/Megalin -0.037 0.16 -10000 0 -0.46 103 103
SHH -0.006 0.1 -10000 0 -0.46 40 40
catabolic process -0.058 0.14 -10000 0 -0.43 69 69
SMO/Vitamin D3 -0.057 0.14 -10000 0 -0.49 48 48
SHH Np/Cholesterol/Hhip -0.043 0.16 -10000 0 -0.43 117 117
LRP2 -0.055 0.21 -10000 0 -0.58 121 121
receptor-mediated endocytosis -0.086 0.19 -10000 0 -0.58 76 76
SHH Np/Cholesterol/BOC 0.009 0.083 -10000 0 -0.38 36 36
SHH Np/Cholesterol/CDO -0.014 0.1 -10000 0 -0.38 36 36
mesenchymal cell differentiation 0.043 0.16 0.42 117 -10000 0 117
mol:Vitamin D3 -0.035 0.15 -10000 0 -0.44 48 48
IHH N/PTCH2 -0.029 0.14 -10000 0 -0.42 85 85
CDON -0.016 0.13 -10000 0 -0.42 87 87
IHH N/PTCH1 -0.056 0.14 -10000 0 -0.43 69 69
Megalin/LRPAP1 -0.022 0.16 -10000 0 -0.47 92 92
PTCH2 0.018 0.062 -10000 0 -0.42 17 17
SHH Np/Cholesterol -0.002 0.08 -10000 0 -0.38 36 36
PTCH1 -0.058 0.14 -10000 0 -0.43 68 68
HHIP -0.068 0.23 -10000 0 -0.62 126 126
Aurora C signaling

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
INCENP 0.028 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.063 0.13 -9999 0 -0.31 9 9
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.016 0.05 -9999 0 -0.47 5 5
AURKB -0.15 0.22 -9999 0 -0.42 351 351
AURKC 0.024 0.042 -9999 0 -0.42 8 8
Caspase cascade in apoptosis

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
TOP1 -0.027 0.12 -10000 0 -0.39 12 12
ACTA1 -0.058 0.13 -10000 0 -0.33 100 100
NUMA1 -0.027 0.12 0.22 1 -0.46 11 12
SPTAN1 -0.056 0.13 0.28 1 -0.33 100 101
LIMK1 -0.035 0.15 0.3 16 -0.33 99 115
BIRC3 -0.023 0.14 -10000 0 -0.42 100 100
BIRC2 0.028 0.004 -10000 0 -10000 0 0
BAX 0.028 0.015 -10000 0 -0.42 1 1
CASP10 -0.091 0.18 -10000 0 -0.46 134 134
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.001 -10000 0 -10000 0 0
PTK2 -0.029 0.13 -10000 0 -0.47 15 15
DIABLO 0.027 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.056 0.12 0.28 1 -0.33 100 101
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.006 -10000 0 -10000 0 0
GSN -0.056 0.13 0.28 1 -0.33 100 101
MADD 0.028 0.004 -10000 0 -10000 0 0
TFAP2A -0.32 0.29 -10000 0 -0.54 507 507
BID -0.034 0.082 -10000 0 -0.2 134 134
MAP3K1 -0.011 0.061 -10000 0 -0.46 5 5
TRADD 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.014 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.047 0.14 0.3 13 -0.33 102 115
CASP9 0.027 0.007 -10000 0 -10000 0 0
DNA repair 0.019 0.088 0.34 44 -10000 0 44
neuron apoptosis -0.007 0.15 -10000 0 -0.64 41 41
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.041 0.13 -10000 0 -0.46 9 9
APAF1 0.027 0.006 -10000 0 -10000 0 0
CASP6 0.001 0.14 -10000 0 -0.93 10 10
TRAF2 0.028 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.12 -10000 0 -0.43 4 4
CASP7 0.006 0.09 -10000 0 -0.34 6 6
KRT18 0.018 0.038 -10000 0 -0.48 1 1
apoptosis -0.053 0.14 0.49 4 -0.46 26 30
DFFA -0.053 0.13 -10000 0 -0.4 6 6
DFFB -0.053 0.13 -10000 0 -0.33 100 100
PARP1 -0.019 0.088 -10000 0 -0.34 44 44
actin filament polymerization 0.029 0.14 0.4 4 -0.37 13 17
TNF 0.012 0.082 -10000 0 -0.46 25 25
CYCS -0.018 0.077 0.21 16 -0.18 5 21
SATB1 0.007 0.14 0.4 20 -0.86 10 30
SLK -0.052 0.13 0.33 4 -0.33 101 105
p15 BID/BAX -0.022 0.085 0.19 3 -0.27 2 5
CASP2 0.006 0.06 -10000 0 -0.36 7 7
JNK cascade 0.011 0.061 0.46 5 -10000 0 5
CASP3 -0.061 0.13 0.25 1 -0.35 100 101
LMNB2 0.038 0.11 0.31 50 -0.58 7 57
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP4 0.028 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.035 0.093 -10000 0 -0.39 1 1
negative regulation of DNA binding -0.31 0.29 -10000 0 -0.53 507 507
stress fiber formation -0.054 0.13 0.32 4 -0.33 101 105
GZMB -0.1 0.21 -10000 0 -0.43 237 237
CASP1 0.018 0.012 -10000 0 -10000 0 0
LMNB1 0.036 0.11 0.31 49 -0.41 11 60
APP -0.007 0.15 -10000 0 -0.65 41 41
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.002 -10000 0 -10000 0 0
VIM -0.053 0.14 0.33 4 -0.44 31 35
LMNA 0.025 0.14 0.31 50 -0.46 42 92
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.016 0.051 -10000 0 -0.47 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.043 0.14 0.29 8 -0.33 100 108
APAF-1/Caspase 9 -0.024 0.15 -10000 0 -0.6 52 52
nuclear fragmentation during apoptosis -0.026 0.12 0.22 1 -0.45 11 12
CFL2 -0.03 0.15 0.38 12 -0.41 4 16
GAS2 -0.064 0.14 0.34 4 -0.34 109 113
positive regulation of apoptosis 0.037 0.12 0.32 50 -0.43 20 70
PRF1 -0.056 0.17 -10000 0 -0.42 163 163
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.1 0.18 -10000 0 -0.33 331 331
alphaV beta3 Integrin 0.029 0.098 -10000 0 -0.43 34 34
PTK2 -0.09 0.2 0.42 20 -0.56 56 76
IGF1R 0.028 0.003 -10000 0 -10000 0 0
PI4KB 0.027 0.007 -10000 0 -10000 0 0
MFGE8 0.027 0.028 -10000 0 -0.54 2 2
SRC 0.027 0.007 -10000 0 -10000 0 0
CDKN1B -0.058 0.19 -10000 0 -0.51 127 127
VEGFA -0.11 0.2 -10000 0 -0.42 269 269
ILK -0.059 0.19 -10000 0 -0.51 129 129
ROCK1 0.028 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.18 -10000 0 -0.48 126 126
PTK2B -0.07 0.14 0.36 4 -0.37 61 65
alphaV/beta3 Integrin/JAM-A -0.02 0.16 -10000 0 -0.38 133 133
CBL 0.027 0.023 -10000 0 -0.65 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.19 0.23 -10000 0 -0.43 396 396
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.081 -10000 0 -0.38 19 19
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.072 0.15 -10000 0 -0.42 98 98
alphaV/beta3 Integrin/Syndecan-1 0.034 0.089 -10000 0 -0.43 28 28
PI4KA 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.009 0.12 -10000 0 -0.53 15 15
PI4 Kinase 0.038 0.012 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.03 0.1 -10000 0 -0.47 28 28
RPS6KB1 -0.011 0.12 0.49 7 -0.55 11 18
TLN1 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.03 0.14 -10000 0 -0.58 37 37
GPR124 0.025 0.032 -10000 0 -0.5 3 3
MAPK1 -0.032 0.14 -10000 0 -0.59 36 36
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.001 0.15 -10000 0 -0.45 82 82
cell adhesion -0.14 0.19 -10000 0 -0.35 381 381
ANGPTL3 -0.32 0.33 -10000 0 -0.62 467 467
VEGFR2 homodimer/VEGFA homodimer/Src -0.071 0.16 -10000 0 -0.42 50 50
IGF-1R heterotetramer 0.028 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
TGFBR2 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.008 0.1 -10000 0 -0.61 24 24
IGF1 0.008 0.098 -10000 0 -0.48 32 32
RAC1 0.025 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.035 0.077 -10000 0 -0.41 21 21
apoptosis 0.026 0.028 -10000 0 -0.53 2 2
CD47 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.037 0.075 -10000 0 -0.42 19 19
VCL 0.027 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.003 0.15 -10000 0 -0.45 74 74
CSF1 0.023 0.049 -10000 0 -0.6 5 5
PIK3C2A -0.06 0.2 -10000 0 -0.52 130 130
PI4 Kinase/Pyk2 -0.11 0.17 -10000 0 -0.53 62 62
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.065 0.16 -10000 0 -0.4 63 63
FAK1/Vinculin -0.065 0.17 0.41 22 -0.46 42 64
alphaV beta3/Integrin/ppsTEM5 0.035 0.077 -10000 0 -0.41 21 21
RHOA 0.026 0.008 -10000 0 -10000 0 0
VTN -0.078 0.23 -10000 0 -0.58 148 148
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
FGF2 0.016 0.087 -10000 0 -0.62 16 16
F11R 0.009 0.065 -10000 0 -0.47 15 15
alphaV/beta3 Integrin/Lactadherin 0.037 0.078 -10000 0 -0.41 22 22
alphaV/beta3 Integrin/TGFBR2 0.035 0.075 -10000 0 -0.42 19 19
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.06 0.049 -10000 0 -0.47 4 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.07 -10000 0 -0.38 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.01 0.12 -10000 0 -0.42 72 72
alphaV/beta3 Integrin/Pyk2 -0.066 0.14 -10000 0 -0.38 61 61
SDC1 0.021 0.062 -10000 0 -0.62 8 8
VAV3 0.027 0.077 0.38 10 -0.39 14 24
PTPN11 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.019 0.072 -10000 0 -0.65 10 10
FAK1/Paxillin -0.07 0.16 0.35 15 -0.45 42 57
cell migration -0.064 0.14 0.35 14 -0.42 34 48
ITGAV 0.026 0.028 -10000 0 -0.54 2 2
PI3K -0.006 0.16 -10000 0 -0.55 12 12
SPP1 0.016 0.086 -10000 0 -0.58 17 17
KDR -0.021 0.18 -10000 0 -0.64 64 64
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.028 -10000 0 -0.53 2 2
COL4A3 -0.028 0.18 -10000 0 -0.64 72 72
angiogenesis -0.037 0.17 0.3 2 -0.6 37 39
Rac1/GTP 0.028 0.057 -10000 0 -0.64 1 1
EDIL3 -0.036 0.19 -10000 0 -0.6 89 89
cell proliferation 0.034 0.075 -10000 0 -0.42 19 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.021 0.18 -10000 0 -0.63 66 66
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.038 -10000 0 -0.46 5 5
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.025 0.077 0.31 5 -0.34 15 20
HIF1A -0.035 0.07 -10000 0 -0.28 50 50
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.042 -10000 0 -0.36 1 1
FIH (dimer) 0.027 0.007 -10000 0 -10000 0 0
CDKN2A -0.37 0.15 -10000 0 -0.42 773 773
ARNT/IPAS 0.001 0.14 -10000 0 -0.47 65 65
HIF1AN 0.027 0.007 -10000 0 -10000 0 0
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
HIF1A/ARNT -0.021 0.08 0.31 5 -0.39 10 15
CUL2 0.027 0.007 -10000 0 -10000 0 0
OS9 0.027 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.048 0.032 -10000 0 -0.28 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.022 0.076 -10000 0 -0.39 10 10
PHD1-3/OS9 -0.095 0.14 -10000 0 -0.33 10 10
HIF1A/RACK1/Elongin B/Elongin C -0.015 0.08 -10000 0 -0.4 9 9
VHL 0.026 0.008 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 -0.022 0.077 -10000 0 -0.39 10 10
EGLN3 -0.22 0.22 -10000 0 -0.42 484 484
EGLN2 0.028 0.003 -10000 0 -10000 0 0
EGLN1 0.027 0.007 -10000 0 -10000 0 0
TP53 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.006 0.15 -10000 0 -0.55 62 62
ARNT 0.027 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF -0.2 0.11 0.3 3 -0.41 63 66
IL23-mediated signaling events

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
CCL2 -0.14 0.36 -10000 0 -1.1 54 54
IL23A -0.14 0.34 -10000 0 -1.1 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.34 -10000 0 -0.95 60 60
positive regulation of T cell mediated cytotoxicity -0.15 0.36 -10000 0 -1 68 68
ITGA3 -0.13 0.33 -10000 0 -0.98 44 44
IL17F -0.084 0.25 0.51 11 -0.68 36 47
IL12B -0.038 0.14 -10000 0 -0.43 91 91
STAT1 (dimer) -0.15 0.35 -10000 0 -0.99 66 66
CD4 -0.13 0.33 -10000 0 -0.98 45 45
IL23 -0.15 0.34 -10000 0 -1 48 48
IL23R -0.042 0.2 -10000 0 -0.87 35 35
IL1B -0.15 0.35 -10000 0 -1.1 52 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.14 0.33 -10000 0 -0.95 56 56
TYK2 0.011 0.033 -10000 0 -10000 0 0
STAT4 0.003 0.1 -10000 0 -0.42 47 47
STAT3 0.025 0.009 -10000 0 -10000 0 0
IL18RAP -0.06 0.18 -10000 0 -0.42 164 164
IL12RB1 -0.085 0.19 -10000 0 -0.44 200 200
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.051 0.15 -10000 0 -0.32 200 200
IL23R/JAK2 -0.036 0.19 -10000 0 -0.84 28 28
positive regulation of chronic inflammatory response -0.15 0.36 -10000 0 -1 68 68
natural killer cell activation 0.002 0.009 0.039 13 -0.037 1 14
JAK2 0.01 0.042 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
RELA 0.028 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.32 -10000 0 -0.96 49 49
ALOX12B -0.14 0.34 -10000 0 -0.97 48 48
CXCL1 -0.19 0.4 -10000 0 -1.1 94 94
T cell proliferation -0.15 0.36 -10000 0 -1 68 68
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.059 0.21 0.4 10 -0.56 21 31
PI3K -0.13 0.34 -10000 0 -0.98 56 56
IFNG -0.02 0.043 0.11 2 -0.11 13 15
STAT3 (dimer) -0.12 0.32 -10000 0 -0.96 45 45
IL18R1 0.018 0.059 -10000 0 -0.48 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.25 -10000 0 -0.78 29 29
IL18/IL18R -0.036 0.14 -10000 0 -0.29 104 104
macrophage activation -0.01 0.017 -10000 0 -0.045 20 20
TNF -0.15 0.35 -10000 0 -1.1 53 53
STAT3/STAT4 -0.15 0.34 -10000 0 -0.97 59 59
STAT4 (dimer) -0.16 0.36 -10000 0 -0.98 72 72
IL18 0.004 0.096 -10000 0 -0.42 41 41
IL19 -0.14 0.33 -10000 0 -0.97 49 49
STAT5A (dimer) -0.15 0.34 -10000 0 -1 56 56
STAT1 0.026 0.022 -10000 0 -0.42 2 2
SOCS3 0.02 0.052 -10000 0 -0.44 10 10
CXCL9 -0.18 0.36 -10000 0 -0.96 65 65
MPO -0.13 0.33 -10000 0 -0.99 40 40
positive regulation of humoral immune response -0.15 0.36 -10000 0 -1 68 68
IL23/IL23R/JAK2/TYK2 -0.16 0.37 -10000 0 -1.1 68 68
IL6 -0.19 0.46 -10000 0 -1.2 110 110
STAT5A 0.025 0.009 -10000 0 -10000 0 0
IL2 -0.003 0.062 -10000 0 -0.42 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.009 0.039 13 -0.037 1 14
CD3E -0.18 0.36 -10000 0 -1 54 54
keratinocyte proliferation -0.15 0.36 -10000 0 -1 68 68
NOS2 -0.15 0.37 -10000 0 -1.1 61 61
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.066 -10000 0 -0.28 39 39
epithelial cell differentiation 0.032 0.088 -10000 0 -0.36 39 39
CYFIP2 0.018 0.076 -10000 0 -0.65 11 11
ENAH 0.04 0.13 0.5 46 -10000 0 46
EGFR 0.017 0.061 -10000 0 -0.45 14 14
EPHA2 0.026 0.024 -10000 0 -0.65 1 1
MYO6 0.027 0.11 0.36 31 -0.36 39 70
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.044 0.056 -10000 0 -0.42 11 11
AQP5 -0.12 0.24 0.34 1 -0.54 202 203
CTNND1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.11 0.36 29 -0.34 39 68
regulation of calcium-dependent cell-cell adhesion 0.01 0.12 0.35 20 -0.37 54 74
EGF -0.54 0.25 -10000 0 -0.65 731 731
NCKAP1 0.027 0.006 -10000 0 -10000 0 0
AQP3 -0.073 0.22 0.34 1 -0.56 142 143
cortical microtubule organization 0.032 0.088 -10000 0 -0.36 39 39
GO:0000145 0.018 0.1 0.35 29 -0.32 39 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.09 -10000 0 -0.36 39 39
MLLT4 0.026 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.06 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.033 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.012 0.079 0.35 4 -10000 0 4
PVRL2 0.028 0.003 -10000 0 -10000 0 0
ZYX 0.014 0.087 0.34 6 -0.34 36 42
ARF6/GTP 0.065 0.036 -10000 0 -0.36 1 1
CDH1 -0.005 0.14 -10000 0 -0.65 40 40
EGFR/EGFR/EGF/EGF -0.26 0.17 -10000 0 -0.36 557 557
RhoA/GDP 0.034 0.085 -10000 0 -0.34 39 39
actin cytoskeleton organization 0.021 0.11 0.35 28 -0.35 39 67
IGF-1R heterotetramer 0.028 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.009 -10000 0 -10000 0 0
IGF1R 0.028 0.003 -10000 0 -10000 0 0
IGF1 0.008 0.098 -10000 0 -0.48 32 32
DIAPH1 0.017 0.14 -10000 0 -0.68 10 10
Wnt receptor signaling pathway -0.032 0.088 0.36 39 -10000 0 39
RHOA 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.061 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
VCL 0.021 0.11 0.36 28 -0.36 39 67
EFNA1 0.026 0.016 -10000 0 -0.42 1 1
LPP 0.012 0.086 0.34 6 -10000 0 6
Ephrin A1/EPHA2 0.025 0.083 -10000 0 -0.34 37 37
SEC6/SEC8 -0.002 0.066 -10000 0 -10000 0 0
MGAT3 0.01 0.12 0.35 20 -0.38 54 74
HGF/MET 0.009 0.11 -10000 0 -0.4 32 32
HGF -0.007 0.14 -10000 0 -0.6 45 45
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.067 -10000 0 -0.29 39 39
actin cable formation 0.068 0.16 0.5 72 -10000 0 72
KIAA1543 0.016 0.11 0.36 28 -0.36 41 69
KIFC3 0.011 0.091 0.35 2 -0.34 44 46
NCK1 0.027 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ACTN1 0.027 0.1 0.35 26 -0.34 38 64
NCK1/GIT1 0.037 0.014 -10000 0 -10000 0 0
mol:GDP 0.032 0.088 -10000 0 -0.36 39 39
EXOC4 0.025 0.01 -10000 0 -10000 0 0
STX4 0.014 0.087 0.35 3 -0.34 39 42
PIP5K1C 0.029 0.11 0.36 29 -0.34 39 68
LIMA1 0.027 0.006 -10000 0 -10000 0 0
ABI1 0.027 0.007 -10000 0 -10000 0 0
ROCK1 0.049 0.14 0.51 49 -10000 0 49
adherens junction assembly 0.034 0.14 0.43 44 -0.53 10 54
IGF-1R heterotetramer/IGF1 0.018 0.095 -10000 0 -0.38 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.012 -10000 0 -10000 0 0
MET 0.021 0.04 -10000 0 -0.42 7 7
PLEKHA7 0.026 0.12 0.36 28 -0.38 41 69
mol:GTP 0.058 0.032 -10000 0 -0.38 1 1
establishment of epithelial cell apical/basal polarity 0.035 0.11 0.4 24 -10000 0 24
cortical actin cytoskeleton stabilization 0.013 0.066 -10000 0 -0.28 39 39
regulation of cell-cell adhesion 0.021 0.11 0.35 28 -0.35 39 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.067 -10000 0 -0.29 39 39
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.039 0.021 -10000 0 -0.49 1 1
Necdin/E2F1 -0.035 0.15 -10000 0 -0.32 185 185
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.026 0.12 -10000 0 -0.39 31 31
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.22 -10000 0 -0.44 241 241
NT-4/5 (dimer)/p75(NTR) -0.004 0.11 -10000 0 -0.33 89 89
IKBKB 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.004 0.12 0.37 20 -0.4 24 44
IKBKG 0.028 0.002 -10000 0 -10000 0 0
BDNF -0.039 0.16 -10000 0 -0.42 130 130
MGDIs/NGR/p75(NTR)/LINGO1 0.007 0.12 -10000 0 -0.38 32 32
FURIN 0.028 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.02 0.14 -10000 0 -0.42 44 44
LINGO1 0.008 0.096 -10000 0 -0.45 36 36
Sortilin/TRAF6/NRIF 0.035 0.024 -10000 0 -10000 0 0
proBDNF (dimer) -0.039 0.16 -10000 0 -0.42 130 130
NTRK1 -0.032 0.18 -10000 0 -0.61 74 74
RTN4R 0.022 0.053 -10000 0 -0.44 11 11
neuron apoptosis -0.02 0.15 0.41 9 -0.52 25 34
IRAK1 0.028 0.002 -10000 0 -10000 0 0
SHC1 -0.024 0.12 -10000 0 -0.45 29 29
ARHGDIA 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.076 0.033 -10000 0 -0.36 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.015 0.12 -10000 0 -0.42 29 29
MAGEH1 0.028 0.015 -10000 0 -0.42 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.005 0.14 -10000 0 -0.45 42 42
Mammalian IAPs/DIABLO 0.036 0.093 -10000 0 -0.38 1 1
proNGF (dimer) -0.011 0.13 -10000 0 -0.46 67 67
MAGED1 0.028 0.002 -10000 0 -10000 0 0
APP 0.027 0.007 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.011 0.074 -10000 0 -0.42 25 25
ZNF274 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.002 0.1 -10000 0 -0.39 27 27
NGF -0.011 0.13 -10000 0 -0.46 67 67
cell cycle arrest 0.01 0.14 0.34 9 -0.41 29 38
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.003 0.082 -10000 0 -0.36 19 19
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.014 0.1 -10000 0 -0.37 24 24
NCSTN 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.13 -10000 0 -0.4 44 44
PSENEN 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide -0.008 0.12 -10000 0 -0.41 29 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.005 0.085 -10000 0 -0.46 19 19
p75(NTR)/beta APP 0.006 0.1 -10000 0 -0.33 72 72
BEX1 -0.14 0.29 -10000 0 -0.64 216 216
mol:GDP -0.035 0.11 -10000 0 -0.4 45 45
NGF (dimer) -0.23 0.25 -10000 0 -0.44 473 473
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.022 0.11 -10000 0 -0.4 16 16
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
RAC1/GTP 0 0.1 -10000 0 -0.34 40 40
MYD88 0.026 0.008 -10000 0 -10000 0 0
CHUK 0.027 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.001 0.13 -10000 0 -0.4 44 44
RHOB 0.027 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.022 0.13 -10000 0 -0.29 162 162
NT3 (dimer) -0.006 0.14 -10000 0 -0.64 42 42
TP53 -0.025 0.12 0.42 5 -0.41 22 27
PRDM4 -0.011 0.12 -10000 0 -0.41 29 29
BDNF (dimer) -0.27 0.26 -10000 0 -0.47 479 479
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
SORT1 0.026 0.024 -10000 0 -0.65 1 1
activation of caspase activity 0.021 0.12 -10000 0 -0.39 31 31
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.015 0.12 -10000 0 -0.42 29 29
RHOC 0.027 0.007 -10000 0 -10000 0 0
XIAP 0.028 0.001 -10000 0 -10000 0 0
MAPK10 -0.008 0.14 0.31 39 -0.47 14 53
DIABLO 0.027 0.006 -10000 0 -10000 0 0
SMPD2 -0.008 0.12 -10000 0 -0.41 29 29
APH1B 0.026 0.033 -10000 0 -0.65 2 2
APH1A 0.027 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0 0.13 -10000 0 -0.4 45 45
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.013 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.016 0.15 -10000 0 -0.39 109 109
MAPK8 -0.005 0.13 0.32 36 -0.48 7 43
MAPK9 -0.004 0.13 0.32 39 -0.48 7 46
APAF1 0.027 0.006 -10000 0 -10000 0 0
NTF3 -0.006 0.14 -10000 0 -0.64 42 42
NTF4 -0.011 0.074 -10000 0 -0.42 25 25
NDN 0.008 0.11 -10000 0 -0.62 27 27
RAC1/GDP 0.018 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.02 0.11 -10000 0 -0.4 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.066 0.026 -10000 0 -0.38 1 1
RhoA-B-C/GTP 0 0.13 -10000 0 -0.4 44 44
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.007 0.14 -10000 0 -0.41 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.14 -10000 0 -0.44 29 29
PRKACB 0.027 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.011 0.12 -10000 0 -0.3 130 130
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.023 0.14 -10000 0 -0.42 100 100
BIRC2 0.028 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.01 0.14 0.36 5 -0.42 30 35
BAD -0.001 0.14 0.33 42 -0.47 10 52
RIPK2 0.027 0.016 -10000 0 -0.42 1 1
NGFR -0.015 0.14 -10000 0 -0.47 73 73
CYCS -0.012 0.1 0.36 2 -0.39 26 28
ADAM17 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.015 0.12 -10000 0 -0.42 28 28
BCL2L11 -0.002 0.14 0.33 43 -0.46 14 57
BDNF (dimer)/p75(NTR) -0.04 0.16 -10000 0 -0.34 180 180
PI3K 0.015 0.12 -10000 0 -0.42 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.015 0.12 -10000 0 -0.42 29 29
NDNL2 0.028 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
PRKCI 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.019 0.14 -10000 0 -0.36 120 120
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.015 0.12 -10000 0 -0.42 29 29
TRAF6 0.028 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCZ 0.024 0.04 -10000 0 -0.65 3 3
PLG -0.32 0.32 -10000 0 -0.63 441 441
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.037 0.12 -10000 0 -0.39 51 51
SQSTM1 0.024 0.034 -10000 0 -0.42 5 5
NGFRAP1 0.027 0.032 -10000 0 -0.65 2 2
CASP3 0.001 0.14 0.32 44 -0.45 10 54
E2F1 -0.056 0.17 -10000 0 -0.42 163 163
CASP9 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.005 0.15 -10000 0 -0.5 19 19
NGF (dimer)/TRKA -0.03 0.17 -10000 0 -0.41 128 128
MMP7 -0.069 0.23 -10000 0 -0.58 140 140
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.12 -10000 0 -0.4 28 28
MMP3 -0.031 0.11 -10000 0 -0.42 68 68
APAF-1/Caspase 9 -0.03 0.091 -10000 0 -0.43 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.023 0.084 -10000 0 -0.45 25 25
AKT1 -0.022 0.17 0.37 13 -0.56 57 70
PTK2B -0.081 0.19 -10000 0 -0.65 58 58
VEGFR2 homodimer/Frs2 -0.018 0.21 -10000 0 -0.78 60 60
CAV1 0.002 0.097 -10000 0 -0.42 44 44
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.081 0.21 -10000 0 -0.71 61 61
endothelial cell proliferation 0.008 0.2 0.54 44 -0.52 49 93
mol:Ca2+ -0.08 0.18 -10000 0 -0.64 60 60
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.065 0.2 -10000 0 -0.63 60 60
RP11-342D11.1 -0.088 0.19 -10000 0 -0.67 60 60
CDH5 0.025 0.032 -10000 0 -0.5 3 3
VEGFA homodimer -0.025 0.13 -10000 0 -0.38 2 2
SHC1 0.026 0.016 -10000 0 -0.42 1 1
SHC2 0.017 0.075 -10000 0 -0.46 20 20
HRAS/GDP -0.059 0.16 -10000 0 -0.56 59 59
SH2D2A -0.071 0.18 -10000 0 -0.42 193 193
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.18 0.36 2 -0.59 50 52
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.13 0.23 -10000 0 -0.56 134 134
VEGFR1 homodimer 0.018 0.067 -10000 0 -0.48 15 15
SHC/GRB2/SOS1 -0.05 0.19 -10000 0 -0.61 58 58
GRB10 -0.077 0.18 0.36 1 -0.6 59 60
PTPN11 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
PAK1 0.028 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.057 0.2 -10000 0 -0.66 58 58
HRAS 0.027 0.015 -10000 0 -0.42 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.031 0.11 -10000 0 -0.38 49 49
HIF1A 0.026 0.033 -10000 0 -0.65 2 2
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.065 0.19 -10000 0 -0.62 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.02 0.069 -10000 0 -0.65 9 9
Nck/Pak 0.04 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.082 0.22 -10000 0 -0.74 60 60
mol:GDP -0.056 0.18 -10000 0 -0.59 58 58
mol:NADP -0.014 0.16 0.47 16 -0.5 52 68
eNOS/Hsp90 -0.007 0.15 0.37 9 -0.47 48 57
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.081 0.19 -10000 0 -0.65 60 60
HIF1A/ARNT 0.037 0.028 -10000 0 -0.49 2 2
SHB 0.028 0.004 -10000 0 -10000 0 0
VEGFA -0.11 0.2 -10000 0 -0.41 269 269
VEGFC 0.026 0.03 -10000 0 -0.42 4 4
FAK1/Vinculin -0.054 0.2 0.46 6 -0.64 68 74
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.077 0.21 -10000 0 -0.67 60 60
PTPN6 0.027 0.007 -10000 0 -10000 0 0
EPAS1 0.005 0.11 -10000 0 -0.4 61 61
mol:L-citrulline -0.014 0.16 0.47 16 -0.5 52 68
ITGAV 0.026 0.028 -10000 0 -0.54 2 2
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.066 0.2 -10000 0 -0.66 56 56
VEGFR2 homodimer/VEGFA homodimer -0.078 0.22 -10000 0 -0.73 60 60
VEGFR2/3 heterodimer -0.024 0.22 -10000 0 -0.79 66 66
VEGFB 0.028 0.003 -10000 0 -10000 0 0
MAPK11 -0.077 0.19 0.44 3 -0.68 60 63
VEGFR2 homodimer -0.036 0.23 -10000 0 -0.85 64 64
FLT1 0.018 0.067 -10000 0 -0.48 15 15
NEDD4 0.029 0.023 -10000 0 -0.65 1 1
MAPK3 -0.073 0.17 0.53 2 -0.56 59 61
MAPK1 -0.073 0.17 0.47 3 -0.56 60 63
VEGFA145/NRP2 -0.069 0.16 -10000 0 -0.3 282 282
VEGFR1/2 heterodimer -0.024 0.22 -10000 0 -0.79 64 64
KDR -0.037 0.23 -10000 0 -0.86 64 64
VEGFA165/NRP1/VEGFR2 homodimer -0.07 0.2 -10000 0 -0.68 61 61
SRC 0.027 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.058 0.19 0.45 22 -0.58 59 81
PI3K -0.046 0.19 -10000 0 -0.68 57 57
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.081 0.21 -10000 0 -0.71 61 61
FES -0.083 0.2 0.37 1 -0.69 61 62
GAB1 -0.056 0.19 -10000 0 -0.69 59 59
VEGFR2 homodimer/VEGFA homodimer/Src -0.08 0.21 -10000 0 -0.71 60 60
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
ARNT 0.027 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.024 0.14 0.42 4 -0.48 34 38
VEGFR2 homodimer/VEGFA homodimer/Yes -0.082 0.21 -10000 0 -0.73 60 60
PI3K/GAB1 -0.021 0.17 -10000 0 -0.58 53 53
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.057 0.2 -10000 0 -0.65 59 59
PRKACA 0.028 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.01 0.21 -10000 0 -0.76 63 63
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 -0.083 0.2 0.37 1 -0.69 60 61
actin cytoskeleton reorganization -0.13 0.22 -10000 0 -0.56 134 134
PTK2 -0.064 0.2 0.33 1 -0.7 63 64
EDG1 -0.088 0.19 -10000 0 -0.67 60 60
mol:DAG -0.081 0.19 -10000 0 -0.65 60 60
CaM/Ca2+ -0.066 0.18 -10000 0 -0.6 60 60
MAP2K3 -0.076 0.18 0.37 4 -0.62 58 62
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.051 0.2 -10000 0 -0.63 59 59
PLCG1 -0.082 0.19 -10000 0 -0.66 60 60
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.066 0.2 -10000 0 -0.67 60 60
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
YES1 0.028 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.081 0.21 -10000 0 -0.72 60 60
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.081 0.21 -10000 0 -0.72 60 60
cell migration -0.037 0.17 0.33 6 -0.56 49 55
mol:PI-3-4-5-P3 -0.041 0.18 -10000 0 -0.62 57 57
FYN 0.026 0.007 -10000 0 -10000 0 0
VEGFB/NRP1 -0.074 0.18 -10000 0 -0.64 60 60
mol:NO -0.014 0.16 0.47 16 -0.5 52 68
PXN 0.027 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.56 59 59
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.07 0.19 -10000 0 -0.63 59 59
VHL 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.008 0.1 -10000 0 -0.61 24 24
NOS3 -0.02 0.18 0.51 14 -0.57 52 66
VEGFR2 homodimer/VEGFA homodimer/Sck -0.087 0.22 -10000 0 -0.76 62 62
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.074 0.17 0.37 1 -0.59 55 56
PRKCB -0.079 0.17 -10000 0 -0.6 56 56
VCL 0.027 0.007 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.08 0.19 -10000 0 -0.67 60 60
VEGFR1/2 heterodimer/VEGFA homodimer -0.086 0.22 -10000 0 -0.71 70 70
VEGFA165/NRP2 -0.069 0.16 -10000 0 -0.3 282 282
MAPKKK cascade -0.05 0.16 0.36 2 -0.6 29 31
NRP2 0.017 0.069 -10000 0 -0.43 20 20
VEGFC homodimer 0.026 0.03 -10000 0 -0.42 4 4
NCK1 0.027 0.006 -10000 0 -10000 0 0
ROCK1 0.028 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.058 0.2 0.45 3 -0.63 66 69
MAP3K13 -0.082 0.19 0.37 1 -0.68 60 61
PDPK1 -0.043 0.15 0.28 1 -0.55 53 54
Signaling events mediated by PTP1B

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
PDGFRB 0.017 0.08 -10000 0 -0.63 13 13
Jak2/Leptin Receptor -0.071 0.14 -10000 0 -0.5 36 36
PTP1B/AKT1 -0.045 0.089 0.25 4 -0.43 14 18
FYN 0.026 0.007 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.055 0.097 0.26 13 -0.37 30 43
EGFR -0.015 0.061 -10000 0 -0.47 14 14
EGF/EGFR -0.28 0.16 0.23 1 -0.38 613 614
CSF1 0.023 0.049 -10000 0 -0.6 5 5
AKT1 0.028 0.006 -10000 0 -10000 0 0
INSR 0.029 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.081 0.14 0.25 3 -0.44 88 91
Insulin Receptor/Insulin -0.025 0.089 0.27 1 -0.41 9 10
HCK -0.006 0.12 -10000 0 -0.42 63 63
CRK 0.025 0.009 -10000 0 -10000 0 0
TYK2 -0.051 0.096 0.34 9 -0.38 25 34
EGF -0.54 0.26 -10000 0 -0.65 731 731
YES1 0.028 0.005 -10000 0 -10000 0 0
CAV1 -0.12 0.13 0.32 19 -0.39 34 53
TXN 0.022 0.016 -10000 0 -0.42 1 1
PTP1B/IRS1/GRB2 -0.056 0.093 0.28 5 -0.48 19 24
cell migration 0.055 0.097 0.37 30 -0.26 13 43
STAT3 0.025 0.009 -10000 0 -10000 0 0
PRLR -0.084 0.25 -10000 0 -0.65 143 143
ITGA2B 0.014 0.068 -10000 0 -0.46 17 17
CSF1R 0.013 0.079 -10000 0 -0.44 26 26
Prolactin Receptor/Prolactin -0.054 0.19 -10000 0 -0.49 143 143
FGR 0.021 0.053 -10000 0 -0.44 11 11
PTP1B/p130 Cas -0.055 0.085 0.27 1 -0.37 26 27
Crk/p130 Cas -0.052 0.081 0.27 1 -0.44 14 15
DOK1 -0.038 0.11 0.34 15 -0.43 20 35
JAK2 -0.073 0.15 0.26 3 -0.46 53 56
Jak2/Leptin Receptor/Leptin -0.057 0.097 -10000 0 -0.51 12 12
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
PTPN1 -0.055 0.098 0.27 13 -0.38 30 43
LYN 0.026 0.024 -10000 0 -0.65 1 1
CDH2 -0.033 0.19 -10000 0 -0.64 80 80
SRC 0.002 0.066 0.28 2 -0.58 7 9
ITGB3 0.007 0.1 -10000 0 -0.61 24 24
CAT1/PTP1B -0.19 0.19 0.36 28 -0.44 136 164
CAPN1 0.027 0.004 -10000 0 -10000 0 0
CSK 0.028 0.003 -10000 0 -10000 0 0
PI3K 0.012 0.082 -10000 0 -0.49 2 2
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.046 0.093 -10000 0 -0.47 13 13
negative regulation of transcription -0.072 0.15 0.25 3 -0.46 53 56
FCGR2A 0.003 0.1 -10000 0 -0.42 47 47
FER 0.02 0.033 -10000 0 -0.66 2 2
alphaIIb/beta3 Integrin 0.014 0.097 -10000 0 -0.42 39 39
BLK -0.001 0.1 -10000 0 -0.42 48 48
Insulin Receptor/Insulin/Shc 0.046 0.024 -10000 0 -10000 0 0
RHOA 0.024 0.008 -10000 0 -10000 0 0
LEPR 0.025 0.033 -10000 0 -0.64 2 2
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
p210 bcr-abl/Grb2 0.025 0.009 -10000 0 -10000 0 0
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.17 0.19 0.32 11 -0.47 117 128
PRL -0.002 0.021 -10000 0 -10000 0 0
SOCS3 -0.015 0.23 -10000 0 -1.1 37 37
SPRY2 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.041 0.055 -10000 0 -0.43 10 10
CSF1/CSF1R -0.052 0.11 0.29 5 -0.5 17 22
Ras protein signal transduction 0.053 0.12 0.46 65 -10000 0 65
IRS1 0.019 0.072 -10000 0 -0.65 10 10
INS 0.012 0.029 -10000 0 -0.41 3 3
LEP -0.025 0.12 -10000 0 -0.42 78 78
STAT5B -0.06 0.11 0.26 11 -0.42 38 49
STAT5A -0.06 0.11 0.26 11 -0.36 55 66
GRB2 0.025 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.054 0.1 0.28 5 -0.38 36 41
CSN2 -0.016 0.085 -10000 0 -0.64 4 4
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
LAT -0.032 0.12 0.3 1 -0.48 41 42
YBX1 0.03 0.009 -10000 0 -10000 0 0
LCK 0.003 0.1 -10000 0 -0.44 44 44
SHC1 0.026 0.016 -10000 0 -0.42 1 1
NOX4 0.002 0.12 -10000 0 -0.66 29 29
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.005 -10000 0 -10000 0 0
LAT2 -0.056 0.12 -10000 0 -0.34 75 75
AP1 -0.047 0.17 0.27 1 -0.56 49 50
mol:PIP3 -0.06 0.24 0.48 59 -0.5 86 145
IKBKB -0.012 0.16 0.4 68 -0.28 32 100
AKT1 -0.064 0.15 0.37 17 -0.49 5 22
IKBKG -0.014 0.16 0.38 66 -0.27 39 105
MS4A2 -0.086 0.2 -10000 0 -0.42 224 224
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.035 0.15 0.36 41 -0.42 12 53
mol:Ca2+ -0.039 0.2 0.44 61 -0.37 85 146
LYN 0.024 0.025 -10000 0 -0.68 1 1
CBLB -0.042 0.094 -10000 0 -0.44 13 13
SHC1 0.026 0.016 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.047 0.032 -10000 0 -0.39 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
PLD2 -0.084 0.14 0.33 10 -0.4 64 74
PTPN13 -0.021 0.15 0.42 7 -0.68 25 32
PTPN11 0.025 0.012 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.008 0.16 0.44 52 -0.38 10 62
SYK 0.022 0.049 -10000 0 -0.6 5 5
GRB2 0.025 0.009 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.18 -10000 0 -0.49 111 111
LAT -0.071 0.13 0.23 2 -0.34 91 93
PAK2 -0.045 0.16 0.36 37 -0.45 15 52
NFATC2 -0.044 0.12 -10000 0 -0.64 25 25
HRAS -0.059 0.15 0.28 16 -0.4 39 55
GAB2 0.028 0.015 -10000 0 -0.42 1 1
PLA2G1B -0.017 0.2 -10000 0 -0.82 52 52
Fc epsilon R1 -0.11 0.18 -10000 0 -0.48 67 67
Antigen/IgE/Fc epsilon R1 -0.096 0.17 -10000 0 -0.45 67 67
mol:GDP -0.074 0.15 -10000 0 -0.42 45 45
JUN 0.027 0.007 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.015 0.16 -10000 0 -0.62 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.041 0.099 -10000 0 -0.38 24 24
CHUK -0.012 0.16 0.4 65 -0.28 33 98
KLRG1 -0.044 0.095 -10000 0 -0.4 16 16
VAV1 -0.083 0.14 -10000 0 -0.37 67 67
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.043 0.096 -10000 0 -0.44 14 14
negative regulation of mast cell degranulation -0.035 0.1 0.22 1 -0.4 17 18
BTK -0.046 0.11 -10000 0 -0.51 13 13
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.062 0.12 -10000 0 -0.36 68 68
GAB2/PI3K/SHP2 -0.089 0.13 -10000 0 -0.4 44 44
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.042 0.1 -10000 0 -0.4 19 19
RAF1 -0.024 0.22 -10000 0 -0.91 52 52
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.21 -10000 0 -0.45 183 183
FCER1G -0.069 0.18 -10000 0 -0.42 188 188
FCER1A -0.003 0.12 -10000 0 -0.55 41 41
Antigen/IgE/Fc epsilon R1/Fyn -0.082 0.16 -10000 0 -0.42 67 67
MAPK3 -0.019 0.2 -10000 0 -0.83 52 52
MAPK1 -0.02 0.21 -10000 0 -0.84 52 52
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 -0.024 0.22 -10000 0 -0.85 53 53
DUSP1 0.025 0.036 -10000 0 -0.57 3 3
NF-kappa-B/RelA -0.022 0.07 -10000 0 -0.23 2 2
actin cytoskeleton reorganization -0.015 0.14 0.43 1 -0.76 16 17
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.068 0.16 -10000 0 -0.42 35 35
FER -0.042 0.096 -10000 0 -0.43 16 16
RELA 0.028 0.003 -10000 0 -10000 0 0
ITK -0.025 0.062 -10000 0 -0.26 2 2
SOS1 0.027 0.006 -10000 0 -10000 0 0
PLCG1 -0.056 0.18 0.36 31 -0.39 65 96
cytokine secretion -0.022 0.045 -10000 0 -10000 0 0
SPHK1 -0.06 0.13 0.23 7 -0.38 50 57
PTK2 -0.017 0.15 0.43 1 -0.84 15 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.091 0.18 -10000 0 -0.47 97 97
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.048 0.22 0.44 59 -0.45 77 136
MAP2K2 -0.024 0.21 -10000 0 -0.85 52 52
MAP2K1 -0.023 0.21 -10000 0 -0.85 52 52
MAP2K7 0.028 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.044 0.097 0.22 1 -0.42 11 12
MAP2K4 -0.012 0.2 -10000 0 -0.85 46 46
Fc epsilon R1/FcgammaRIIB -0.13 0.22 -10000 0 -0.47 182 182
mol:Choline -0.083 0.14 0.32 11 -0.39 64 75
SHC/Grb2/SOS1 -0.018 0.11 -10000 0 -0.55 5 5
FYN 0.026 0.007 -10000 0 -10000 0 0
DOK1 0.026 0.022 -10000 0 -0.42 2 2
PXN -0.007 0.15 0.41 23 -0.77 14 37
HCLS1 -0.048 0.1 -10000 0 -0.36 38 38
PRKCB -0.03 0.19 0.43 65 -0.35 82 147
FCGR2B -0.065 0.18 -10000 0 -0.42 179 179
IGHE -0.003 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.036 0.1 0.22 1 -0.41 17 18
LCP2 -0.006 0.12 -10000 0 -0.42 64 64
PLA2G4A -0.042 0.1 -10000 0 -0.43 26 26
RASA1 0.027 0.023 -10000 0 -0.65 1 1
mol:Phosphatidic acid -0.083 0.14 0.32 11 -0.39 64 75
IKK complex 0.001 0.14 0.38 69 -0.28 1 70
WIPF1 0.026 0.016 -10000 0 -0.42 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.004 0.049 0.13 91 -0.12 24 115
BUB1B -0.001 0.063 0.18 19 -0.23 22 41
PLK1 0.002 0.041 0.14 30 -0.14 9 39
PLK1S1 0.01 0.032 0.13 28 -0.23 2 30
KIF2A 0.005 0.054 0.25 21 -0.27 4 25
regulation of mitotic centrosome separation 0.002 0.041 0.14 30 -0.14 9 39
GOLGA2 0.028 0.004 -10000 0 -10000 0 0
Hec1/SPC24 -0.047 0.16 0.19 1 -0.34 158 159
WEE1 0.012 0.056 0.24 4 -0.38 9 13
cytokinesis -0.048 0.12 0.25 17 -0.33 20 37
PP2A-alpha B56 -0.009 0.13 -10000 0 -0.58 34 34
AURKA 0.008 0.03 0.14 11 -0.22 2 13
PICH/PLK1 -0.012 0.08 -10000 0 -0.37 23 23
CENPE -0.02 0.096 0.34 9 -0.25 99 108
RhoA/GTP 0.019 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.005 0.054 0.25 21 -0.27 4 25
PPP2CA 0.027 0.007 -10000 0 -10000 0 0
FZR1 0.027 0.023 -10000 0 -0.65 1 1
TPX2 -0.009 0.055 0.13 37 -0.15 9 46
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 -0.033 0.15 -10000 0 -0.42 117 117
FBXW11 0.027 0.007 -10000 0 -10000 0 0
CLSPN -0.016 0.075 0.14 4 -0.26 57 61
GORASP1 0.026 0.008 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.017 52 -0.017 2 54
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.023 0.077 32 -0.067 10 42
G2 phase of mitotic cell cycle 0 0.002 0.013 14 -10000 0 14
STAG2 0.028 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.007 0.12 -10000 0 -0.48 55 55
spindle elongation 0.002 0.041 0.14 30 -0.14 9 39
ODF2 0.028 0.005 -10000 0 -10000 0 0
BUB1 -0.032 0.13 -10000 0 -0.63 34 34
TPT1 0 0.053 0.12 14 -0.22 39 53
CDC25C -0.022 0.067 0.17 5 -0.31 7 12
CDC25B 0.025 0.034 -10000 0 -0.42 5 5
SGOL1 -0.004 0.049 0.12 24 -0.13 91 115
RHOA 0.026 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.045 -10000 0 -0.39 3 3
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.015 0.13 -10000 0 -0.42 82 82
PLK1/PBIP1 -0.01 0.065 0.12 6 -0.23 53 59
mitosis -0.002 0.003 0.019 3 -10000 0 3
FBXO5 0.001 0.043 0.15 17 -0.17 5 22
CDC2 0 0.002 -10000 0 -0.014 5 5
NDC80 -0.07 0.18 -10000 0 -0.42 192 192
metaphase plate congression -0.006 0.072 0.15 4 -0.26 56 60
ERCC6L -0.001 0.078 -10000 0 -0.38 20 20
NLP/gamma Tubulin 0.002 0.037 0.11 37 -0.11 36 73
microtubule cytoskeleton organization 0 0.052 0.12 14 -0.22 39 53
G2/M transition DNA damage checkpoint 0 0.002 0.014 6 -10000 0 6
PPP1R12A 0.027 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 -0.068 0.14 0.22 1 -0.26 162 163
GRASP65/GM130/RAB1/GTP/PLK1 0.033 0.042 -10000 0 -10000 0 0
RAB1A 0.027 0.006 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.032 0.11 39 -0.1 10 49
mitotic prometaphase -0.001 0.005 0.017 46 -10000 0 46
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.05 -10000 0 -0.51 4 4
microtubule-based process -0.078 0.13 0.19 4 -0.23 343 347
Golgi organization 0.002 0.041 0.14 30 -0.14 9 39
Cohesin/SA2 0.014 0.038 0.17 4 -10000 0 4
PPP1CB/MYPT1 0.038 0.012 -10000 0 -10000 0 0
KIF20A -0.16 0.22 -10000 0 -0.42 357 357
APC/C/CDC20 -0.002 0.086 0.19 4 -0.26 75 79
PPP2R1A 0.028 0.003 -10000 0 -10000 0 0
chromosome segregation -0.009 0.064 0.12 6 -0.23 53 59
PRC1 0.02 0.058 -10000 0 -0.42 15 15
ECT2 0.012 0.066 0.26 43 -0.27 1 44
C13orf34 0.003 0.032 0.11 31 -0.12 5 36
NUDC -0.006 0.072 0.15 4 -0.26 56 60
regulation of attachment of spindle microtubules to kinetochore -0.001 0.062 0.18 19 -0.23 22 41
spindle assembly 0.005 0.044 0.13 55 -0.12 8 63
spindle stabilization 0.01 0.032 0.13 28 -0.23 2 30
APC/C/HCDH1 0.027 0.016 -10000 0 -0.42 1 1
MKLP2/PLK1 -0.078 0.13 0.19 4 -0.24 343 347
CCNB1 0.022 0.054 -10000 0 -0.42 13 13
PPP1CB 0.027 0.006 -10000 0 -10000 0 0
BTRC 0.027 0.007 -10000 0 -10000 0 0
ROCK2 -0.004 0.09 0.26 6 -0.34 44 50
TUBG1 0.002 0.054 0.13 22 -0.23 35 57
G2/M transition of mitotic cell cycle -0.003 0.04 -10000 0 -0.38 3 3
MLF1IP -0.01 0.074 -10000 0 -0.3 52 52
INCENP 0.027 0.003 -10000 0 -10000 0 0
Ceramide signaling 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
SPHK2 0.017 0.037 -10000 0 -0.44 4 4
MAP4K4 0.014 0.047 -10000 0 -0.43 2 2
BAG4 0.025 0.033 -10000 0 -0.65 2 2
PKC zeta/ceramide -0.099 0.086 0.17 1 -0.28 112 113
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.023 0.14 -10000 0 -0.42 100 100
BAX -0.036 0.039 -10000 0 -0.3 6 6
RIPK1 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.028 0.082 0.82 9 -10000 0 9
BAD -0.1 0.08 -10000 0 -0.28 108 108
SMPD1 0.018 0.059 0.22 22 -0.25 11 33
RB1 -0.099 0.08 0.17 1 -0.28 104 105
FADD/Caspase 8 0.015 0.083 -10000 0 -0.45 8 8
MAP2K4 -0.078 0.071 0.2 1 -0.28 58 59
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.079 0.076 0.2 1 -0.28 63 64
EGF -0.54 0.25 -10000 0 -0.65 731 731
mol:ceramide -0.11 0.085 0.18 2 -0.3 111 113
MADD 0.028 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.027 0.21 7 -0.39 2 9
ASAH1 0.027 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.099 0.078 0.17 1 -0.28 104 105
cell proliferation -0.067 0.076 -10000 0 -0.37 15 15
BID -0.015 0.12 -10000 0 -0.68 24 24
MAP3K1 -0.098 0.079 0.18 4 -0.28 104 108
EIF2A -0.078 0.074 0.25 7 -0.26 70 77
TRADD 0.026 0.007 -10000 0 -10000 0 0
CRADD 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.07 0.071 -10000 0 -0.31 15 15
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.072 0.074 -10000 0 -0.31 18 18
Cathepsin D/ceramide -0.098 0.084 0.18 1 -0.28 112 113
FADD 0.01 0.053 -10000 0 -0.44 2 2
KSR1 -0.092 0.076 0.19 4 -0.29 70 74
MAPK8 -0.089 0.078 -10000 0 -0.28 75 75
PRKRA -0.099 0.08 0.18 3 -0.28 103 106
PDGFA 0.023 0.029 -10000 0 -0.54 2 2
TRAF2 0.028 0.004 -10000 0 -10000 0 0
IGF1 0.008 0.098 -10000 0 -0.48 32 32
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.085 0.18 2 -0.3 111 113
CTSD 0.026 0.031 -10000 0 -0.5 3 3
regulation of nitric oxide biosynthetic process 0.04 0.019 -10000 0 -0.49 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.07 0.081 -10000 0 -0.4 15 15
PRKCD 0.021 0.045 -10000 0 -0.42 9 9
PRKCZ 0.024 0.04 -10000 0 -0.65 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.027 0.21 7 -0.39 2 9
RelA/NF kappa B1 0.041 0.019 -10000 0 -0.49 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.024 -10000 0 -0.65 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.05 -10000 0 -0.54 2 2
TNFR1A/BAG4/TNF-alpha 0.04 0.061 -10000 0 -0.42 7 7
mol:Sphingosine-1-phosphate 0.017 0.037 -10000 0 -0.44 4 4
MAP2K1 -0.075 0.074 -10000 0 -0.32 15 15
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.028 0.003 -10000 0 -10000 0 0
CYCS -0.051 0.04 0.17 1 -0.23 14 15
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
TNFR1A/BAG4 0.037 0.028 -10000 0 -0.49 2 2
EIF2AK2 -0.092 0.079 0.32 2 -0.27 98 100
TNF-alpha/TNFR1A/FAN 0.041 0.056 -10000 0 -0.42 5 5
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.017 0.1 -10000 0 -0.45 33 33
MAP2K2 -0.075 0.072 -10000 0 -0.32 14 14
SMPD3 0.012 0.046 -10000 0 -0.31 5 5
TNF 0.012 0.082 -10000 0 -0.46 25 25
PKC zeta/PAR4 0.035 0.038 -10000 0 -0.49 4 4
mol:PHOSPHOCHOLINE 0.19 0.11 0.25 655 -0.25 5 660
NF kappa B1/RelA/I kappa B alpha 0.071 0.041 -10000 0 -0.36 3 3
AIFM1 -0.06 0.054 0.17 1 -0.18 99 100
BCL2 0.027 0.023 -10000 0 -0.65 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR 0.027 0.016 -10000 0 -0.42 1 1
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.053 0.18 -10000 0 -0.42 161 161
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.007 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.042 0.18 -10000 0 -0.38 161 161
IQGAP1/CaM 0.041 0.008 -10000 0 -10000 0 0
DAB1 -0.003 0.07 -10000 0 -0.42 22 22
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
PLA2G7 -0.32 0.19 -10000 0 -0.42 683 683
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.037 0.025 -10000 0 -0.29 4 4
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.006 -10000 0 -10000 0 0
CDK5R1 0.023 0.036 -10000 0 -0.44 5 5
LIS1/Poliovirus Protein 3A 0.013 0.005 -10000 0 -10000 0 0
CDK5R2 -0.049 0.15 -10000 0 -0.42 128 128
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.062 0.19 -10000 0 -0.43 163 163
YWHAE 0.025 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.031 0.17 0.32 55 -0.41 14 69
MAP1B 0.006 0.013 -10000 0 -10000 0 0
RAC1 0.016 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.047 0.15 0.37 2 -10000 0 2
RELN -0.12 0.27 -10000 0 -0.61 195 195
PAFAH/LIS1 -0.17 0.12 -10000 0 -0.32 29 29
LIS1/CLIP170 0.03 0.013 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.038 0.12 -10000 0 -0.38 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.035 0.13 -10000 0 -0.46 14 14
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.059 0.14 0.31 8 -0.42 20 28
LIS1/IQGAP1 0.03 0.013 -10000 0 -10000 0 0
RHOA 0.016 0.008 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.028 -10000 0 -0.54 2 2
PAFAH1B2 0.026 0.035 -10000 0 -0.55 3 3
MAP1B/LIS1/Dynein heavy chain 0.029 0.021 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.025 0.16 0.32 47 -0.4 13 60
LRP8 0.025 0.031 -10000 0 -0.42 4 4
NDEL1/Katanin 60 -0.031 0.17 0.32 55 -0.41 14 69
P39/CDK5 -0.073 0.16 0.35 1 -0.39 70 71
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.013 -10000 0 -10000 0 0
CDK5 -0.061 0.15 0.38 1 -0.36 158 159
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.026 0.011 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.042 0.17 -10000 0 -0.37 159 159
RELN/VLDLR -0.037 0.18 -10000 0 -0.38 161 161
CDC42 0.017 0.008 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.62 0.68 0.54 8 -1.3 438 446
PLK1 -0.028 0.18 0.48 3 -0.62 8 11
CDKN1B -0.02 0.16 0.51 11 -0.38 3 14
FOXO3 0.001 0.13 -10000 0 -0.6 6 6
KAT2B 0.023 0.033 -10000 0 -0.69 1 1
FOXO1/SIRT1 -0.19 0.28 0.34 2 -0.45 415 417
CAT -0.011 0.15 -10000 0 -1.2 4 4
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
AKT1 -0.016 0.052 -10000 0 -0.31 2 2
FOXO1 -0.22 0.3 0.43 9 -0.48 429 438
MAPK10 0.028 0.076 0.33 5 -0.36 13 18
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.072 0.095 0.42 22 -0.4 1 23
response to oxidative stress -0.029 0.041 -10000 0 -0.24 5 5
FOXO3A/SIRT1 0.032 0.14 -10000 0 -0.54 8 8
XPO1 0.028 0.006 -10000 0 -10000 0 0
EP300 -0.018 0.056 -10000 0 -0.43 3 3
BCL2L11 -0.001 0.14 -10000 0 -0.74 32 32
FOXO1/SKP2 -0.19 0.28 0.33 8 -0.45 403 411
mol:GDP -0.029 0.041 -10000 0 -0.23 5 5
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.047 0.2 0.43 3 -0.67 48 51
YWHAQ 0.027 0.006 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.019 0.15 -10000 0 -0.57 43 43
MST1 0.018 0.058 -10000 0 -0.5 9 9
CSNK1D 0.025 0.009 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.005 0.15 -10000 0 -0.59 38 38
YWHAB 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.033 0.064 0.33 6 -10000 0 6
MAPK9 0.033 0.058 0.33 5 -10000 0 5
YWHAG 0.025 0.01 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.035 0.015 -10000 0 -10000 0 0
SOD2 -0.049 0.19 0.53 7 -0.55 29 36
RBL2 0.027 0.13 -10000 0 -0.91 6 6
RAL/GDP 0.017 0.031 -10000 0 -10000 0 0
CHUK 0.024 0.023 -10000 0 -10000 0 0
Ran/GTP 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.027 0.023 -10000 0 -0.65 1 1
RAL/GTP 0.022 0.031 -10000 0 -10000 0 0
CSNK1G1 0.028 0.003 -10000 0 -10000 0 0
FASLG -0.11 0.2 -10000 0 -0.73 41 41
SKP2 0.027 0.005 -10000 0 -10000 0 0
USP7 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.025 0.022 -10000 0 -10000 0 0
CCNB1 -0.008 0.14 -10000 0 -0.65 3 3
FOXO1-3a-4/beta catenin -0.029 0.15 0.35 9 -0.43 1 10
proteasomal ubiquitin-dependent protein catabolic process -0.19 0.28 0.32 8 -0.45 403 411
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
SGK1 0.021 0.043 -10000 0 -0.49 4 4
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.013 -10000 0 -10000 0 0
ZFAND5 0.07 0.09 0.47 15 -10000 0 15
SFN -0.072 0.2 -10000 0 -0.44 185 185
CDK2 -0.029 0.065 -10000 0 -0.34 2 2
FOXO3A/14-3-3 -0.007 0.14 -10000 0 -0.55 41 41
CREBBP -0.028 0.062 -10000 0 -0.24 1 1
FBXO32 -0.006 0.14 0.53 1 -0.71 3 4
BCL6 0.028 0.13 -10000 0 -0.84 6 6
RALB 0.028 0.006 -10000 0 -10000 0 0
RALA 0.026 0.01 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.003 0.079 -10000 0 -0.31 16 16
NT3 (dimer)/TRKC -0.029 0.18 -10000 0 -0.5 112 112
NT3 (dimer)/TRKB -0.12 0.24 -10000 0 -0.47 238 238
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.017 -10000 0 -10000 0 0
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
BDNF -0.039 0.16 -10000 0 -0.42 130 130
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DYNLT1 0.026 0.007 -10000 0 -10000 0 0
NTRK1 -0.032 0.18 -10000 0 -0.61 74 74
NTRK2 -0.18 0.31 -10000 0 -0.64 269 269
NTRK3 -0.033 0.19 -10000 0 -0.65 78 78
NT-4/5 (dimer)/TRKB -0.11 0.23 -10000 0 -0.46 230 230
neuron apoptosis 0.1 0.2 0.49 124 -10000 0 124
SHC 2-3/Grb2 -0.11 0.22 -10000 0 -0.55 124 124
SHC1 0.026 0.016 -10000 0 -0.42 1 1
SHC2 -0.082 0.18 -10000 0 -0.55 78 78
SHC3 -0.13 0.25 -10000 0 -0.63 139 139
STAT3 (dimer) 0.022 0.045 -10000 0 -0.37 1 1
NT3 (dimer)/TRKA -0.032 0.18 -10000 0 -0.45 105 105
RIN/GDP 0.019 0.12 0.32 36 -0.32 39 75
GIPC1 0.027 0.023 -10000 0 -0.65 1 1
KRAS 0.027 0.007 -10000 0 -10000 0 0
DNAJA3 -0.037 0.12 -10000 0 -0.45 34 34
RIN/GTP 0.013 0.018 -10000 0 -0.29 3 3
CCND1 0.008 0.077 -10000 0 -0.36 34 34
MAGED1 0.028 0.002 -10000 0 -10000 0 0
PTPN11 0.027 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.011 0.074 -10000 0 -0.42 25 25
SHC/GRB2/SOS1 0.049 0.022 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.032 0.17 -10000 0 -0.44 79 79
TRKA/NEDD4-2 -0.004 0.14 -10000 0 -0.49 66 66
ELMO1 0.023 0.031 -10000 0 -0.42 4 4
RhoG/GTP/ELMO1/DOCK1 0.03 0.028 -10000 0 -0.28 5 5
NGF -0.011 0.13 -10000 0 -0.46 67 67
HRAS 0.027 0.015 -10000 0 -0.42 1 1
DOCK1 0.026 0.024 -10000 0 -0.65 1 1
GAB2 0.028 0.015 -10000 0 -0.42 1 1
RIT2 -0.01 0.03 -10000 0 -0.42 3 3
RIT1 0.027 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 -0.039 0.16 -10000 0 -0.42 129 129
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.026 0.12 -10000 0 -0.43 34 34
mol:GDP 0.014 0.17 0.4 42 -0.48 48 90
NGF (dimer) -0.011 0.13 -10000 0 -0.46 67 67
RhoG/GDP 0.017 0.022 -10000 0 -0.29 4 4
RIT1/GDP 0.025 0.12 0.34 39 -0.31 37 76
TIAM1 0.026 0.024 -10000 0 -0.65 1 1
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.13 0.22 -10000 0 -0.44 259 259
KIDINS220/CRKL/C3G 0.04 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.024 -10000 0 -0.39 2 2
FRS2 family/SHP2 0.051 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.006 0.14 -10000 0 -0.64 42 42
RAP1/GDP 0.006 0.082 -10000 0 -0.26 36 36
KIDINS220/CRKL 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.039 0.16 -10000 0 -0.42 130 130
ubiquitin-dependent protein catabolic process -0.011 0.15 -10000 0 -0.44 73 73
Schwann cell development -0.027 0.032 -10000 0 -10000 0 0
EHD4 0.028 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.06 0.028 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.036 0.035 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.23 -10000 0 -0.59 95 95
ABL1 0.028 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
Rap1/GTP -0.039 0.13 -10000 0 -0.46 42 42
STAT3 0.023 0.045 -10000 0 -0.37 1 1
axon guidance -0.13 0.21 -10000 0 -0.56 95 95
MAPK3 -0.046 0.14 -10000 0 -0.4 73 73
MAPK1 -0.047 0.14 -10000 0 -0.4 79 79
CDC42/GDP 0.027 0.12 0.33 45 -0.31 38 83
NTF3 -0.006 0.14 -10000 0 -0.64 42 42
NTF4 -0.011 0.074 -10000 0 -0.42 25 25
NGF (dimer)/TRKA/FAIM -0.01 0.15 -10000 0 -0.44 68 68
PI3K 0.039 0.011 -10000 0 -10000 0 0
FRS3 0.026 0.007 -10000 0 -10000 0 0
FAIM 0.027 0.006 -10000 0 -10000 0 0
GAB1 0.028 0.004 -10000 0 -10000 0 0
RASGRF1 -0.043 0.12 -10000 0 -0.45 42 42
SOS1 0.027 0.006 -10000 0 -10000 0 0
MCF2L -0.036 0.16 -10000 0 -0.44 103 103
RGS19 0.025 0.027 -10000 0 -0.42 3 3
CDC42 0.027 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.14 0.31 4 -0.55 37 41
Rac1/GDP 0.012 0.1 0.27 14 -0.32 37 51
NGF (dimer)/TRKA/GRIT -0.024 0.14 -10000 0 -0.36 127 127
neuron projection morphogenesis -0.042 0.23 0.4 1 -1 39 40
NGF (dimer)/TRKA/NEDD4-2 -0.011 0.15 -10000 0 -0.44 73 73
MAP2K1 0.04 0.059 0.38 12 -10000 0 12
NGFR -0.015 0.14 -10000 0 -0.47 73 73
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.12 -10000 0 -0.43 33 33
RAS family/GTP/PI3K 0.028 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.07 0.033 -10000 0 -10000 0 0
NRAS 0.027 0.007 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
PRKCI 0.027 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCZ 0.024 0.04 -10000 0 -0.65 3 3
MAPKKK cascade -0.086 0.26 -10000 0 -0.69 123 123
RASA1 0.027 0.023 -10000 0 -0.65 1 1
TRKA/c-Abl -0.003 0.14 -10000 0 -0.48 65 65
SQSTM1 0.024 0.034 -10000 0 -0.42 5 5
BDNF (dimer)/TRKB/GIPC -0.11 0.21 -10000 0 -0.4 260 260
NGF (dimer)/TRKA/p62/Atypical PKCs 0.012 0.14 -10000 0 -0.38 66 66
MATK -0.008 0.12 -10000 0 -0.42 71 71
NEDD4L 0.026 0.033 -10000 0 -0.65 2 2
RAS family/GDP -0.023 0.058 -10000 0 -0.26 11 11
NGF (dimer)/TRKA -0.036 0.12 -10000 0 -0.36 88 88
Rac1/GTP -0.03 0.087 -10000 0 -0.31 29 29
FRS2 family/SHP2/CRK family 0.07 0.033 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.016 0.1 -10000 0 -0.48 2 2
UGCG 0 0.11 -10000 0 -0.68 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.008 0.16 0.33 13 -0.51 43 56
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.11 -10000 0 -0.67 19 19
mol:DAG -0.038 0.2 -10000 0 -0.86 47 47
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.14 0.29 8 -0.4 38 46
FRAP1 -0.002 0.15 0.34 13 -0.45 42 55
FOXO3 -0.002 0.15 0.33 14 -0.46 38 52
AKT1 -0.007 0.15 0.3 11 -0.48 44 55
GAB2 0.028 0.015 -10000 0 -0.42 1 1
SMPD1 0.008 0.075 -10000 0 -0.7 8 8
SGMS1 -0.026 0.18 -10000 0 -0.79 47 47
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 0.013 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.011 0.16 0.33 7 -0.61 50 57
EIF3A 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.043 0.012 -10000 0 -10000 0 0
RPS6KB1 -0.034 0.18 -10000 0 -0.9 35 35
mol:sphingomyelin -0.038 0.2 -10000 0 -0.86 47 47
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.053 0.17 -10000 0 -0.42 165 165
PIK3R1 0.03 0.005 -10000 0 -10000 0 0
JAK1 0.029 0.008 -10000 0 -10000 0 0
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MYC 0.001 0.15 0.49 8 -0.6 10 18
MYB -0.064 0.14 -10000 0 -0.5 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.023 0.14 -10000 0 -0.44 62 62
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.008 0.18 -10000 0 -0.82 35 35
mol:PI-3-4-5-P3 -0.022 0.14 -10000 0 -0.43 62 62
Rac1/GDP 0.027 0.012 -10000 0 -10000 0 0
T cell proliferation -0.01 0.14 0.27 12 -0.44 41 53
SHC1 0.027 0.016 -10000 0 -0.42 1 1
RAC1 0.025 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.005 0.015 -10000 0 -0.03 233 233
PRKCZ -0.015 0.14 0.23 2 -0.46 41 43
NF kappa B1 p50/RelA 0.016 0.14 0.31 8 -0.47 16 24
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.025 0.1 -10000 0 -0.36 36 36
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.028 0.003 -10000 0 -10000 0 0
IL2RA -0.044 0.16 -10000 0 -0.42 140 140
IL2RB -0.14 0.22 -10000 0 -0.42 329 329
TERT -0.057 0.15 -10000 0 -0.42 122 122
E2F1 -0.036 0.1 -10000 0 -0.46 3 3
SOS1 0.027 0.006 -10000 0 -10000 0 0
RPS6 0.027 0.022 -10000 0 -0.42 2 2
mol:cAMP 0.002 0.007 0.014 232 -10000 0 232
PTPN11 0.028 0.006 -10000 0 -10000 0 0
IL2RG 0.006 0.11 -10000 0 -0.44 47 47
actin cytoskeleton organization -0.01 0.14 0.27 12 -0.44 41 53
GRB2 0.026 0.009 -10000 0 -10000 0 0
IL2 0.016 0.059 -10000 0 -0.42 16 16
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.048 0.024 -10000 0 -10000 0 0
LCK 0.005 0.1 -10000 0 -0.44 44 44
BCL2 0.006 0.13 0.4 8 -0.51 10 18
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.015 -10000 0 -0.42 1 1
ELF1 -0.003 0.085 -10000 0 -0.44 3 3
CCNA2 -0.057 0.18 -10000 0 -0.42 166 166
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
JAK3 -0.055 0.17 -10000 0 -0.42 165 165
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.14 -10000 0 -0.5 42 42
SHC1 0.027 0.016 -10000 0 -0.42 1 1
SP1 0.03 0.032 -10000 0 -0.34 2 2
IL2RA -0.035 0.14 -10000 0 -0.5 3 3
IL2RB -0.14 0.22 -10000 0 -0.42 329 329
SOS1 0.028 0.006 -10000 0 -10000 0 0
IL2RG 0.004 0.11 -10000 0 -0.44 47 47
G1/S transition of mitotic cell cycle 0.021 0.11 0.4 26 -0.46 3 29
PTPN11 0.028 0.006 -10000 0 -10000 0 0
CCND2 0.02 0.043 -10000 0 -10000 0 0
LCK 0.004 0.1 -10000 0 -0.44 44 44
GRB2 0.026 0.009 -10000 0 -10000 0 0
IL2 0.015 0.059 -10000 0 -0.42 16 16
CDK6 0.024 0.025 -10000 0 -0.65 1 1
CCND3 -0.01 0.13 0.35 3 -0.54 7 10
IL27-mediated signaling events

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
TGFB1 0.027 0.03 -10000 0 -0.42 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.029 0.12 0.45 7 -0.37 1 8
IL27/IL27R/JAK1 0.017 0.23 0.79 3 -0.62 13 16
TBX21 -0.072 0.24 0.6 8 -0.56 70 78
IL12B -0.027 0.14 -10000 0 -0.42 91 91
IL12A 0.006 0.007 -10000 0 -10000 0 0
IL6ST -0.033 0.19 -10000 0 -0.66 72 72
IL27RA/JAK1 0.019 0.051 -10000 0 -10000 0 0
IL27 -0.008 0.11 -10000 0 -0.43 51 51
TYK2 0.017 0.022 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.12 -10000 0 -0.49 7 7
T-helper 2 cell differentiation 0.029 0.12 0.45 7 -0.37 1 8
T cell proliferation during immune response 0.029 0.12 0.45 7 -0.37 1 8
MAPKKK cascade -0.029 0.12 0.37 1 -0.45 7 8
STAT3 0.025 0.009 -10000 0 -10000 0 0
STAT2 0.027 0.006 -10000 0 -10000 0 0
STAT1 0.028 0.023 -10000 0 -0.42 2 2
IL12RB1 -0.074 0.19 -10000 0 -0.42 200 200
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.08 0.24 0.54 13 -0.55 56 69
IL27/IL27R/JAK2/TYK2 -0.029 0.12 0.37 1 -0.46 7 8
positive regulation of T cell mediated cytotoxicity -0.029 0.12 0.37 1 -0.45 7 8
STAT1 (dimer) 0.086 0.36 0.55 145 -0.71 18 163
JAK2 0.021 0.017 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
STAT2 (dimer) -0.013 0.12 0.4 1 -0.49 3 4
T cell proliferation -0.061 0.14 0.48 2 -0.54 18 20
IL12/IL12R/TYK2/JAK2 -0.024 0.12 -10000 0 -0.71 8 8
IL17A -0.017 0.12 -10000 0 -0.49 7 7
mast cell activation 0.029 0.12 0.45 7 -0.37 1 8
IFNG -0.009 0.039 0.11 6 -0.087 10 16
T cell differentiation -0.004 0.008 0.015 3 -0.02 92 95
STAT3 (dimer) -0.014 0.12 0.4 1 -0.49 3 4
STAT5A (dimer) -0.014 0.12 0.4 1 -0.49 3 4
STAT4 (dimer) -0.024 0.14 0.39 2 -0.48 15 17
STAT4 0.003 0.1 -10000 0 -0.42 47 47
T cell activation -0.009 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.005 0.13 -10000 0 -10000 0 0
GATA3 -0.7 0.69 0.6 4 -1.4 458 462
IL18 -0.004 0.067 0.2 4 -0.3 41 45
positive regulation of mast cell cytokine production -0.014 0.12 0.37 2 -0.48 3 5
IL27/EBI3 -0.025 0.15 -10000 0 -0.36 131 131
IL27RA 0.003 0.037 -10000 0 -10000 0 0
IL6 -0.053 0.2 -10000 0 -0.56 117 117
STAT5A 0.025 0.009 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.037 -10000 0 -10000 0 0
IL1B 0.001 0.057 -10000 0 -0.38 18 18
EBI3 -0.031 0.15 -10000 0 -0.43 110 110
TNF -0.001 0.058 -10000 0 -0.33 25 25
Glucocorticoid receptor regulatory network

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
PCK2 0.043 0.082 -10000 0 -1.1 2 2
SMARCC2 0.028 0.009 -10000 0 -10000 0 0
SMARCC1 0.027 0.011 -10000 0 -10000 0 0
TBX21 -0.1 0.16 0.5 1 -0.46 47 48
SUMO2 0.021 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.026 -10000 0 -0.48 2 2
FKBP4 0.027 0.007 -10000 0 -10000 0 0
FKBP5 0.012 0.088 -10000 0 -0.49 24 24
GR alpha/HSP90/FKBP51/HSP90 0.072 0.098 0.35 5 -0.37 9 14
PRL -0.025 0.079 -10000 0 -0.49 4 4
cortisol/GR alpha (dimer)/TIF2 0.12 0.21 0.5 62 -0.43 8 70
RELA -0.035 0.11 -10000 0 -0.32 24 24
FGG 0.028 0.22 0.46 28 -0.41 50 78
GR beta/TIF2 0.047 0.14 0.32 11 -0.43 40 51
IFNG -0.18 0.2 -10000 0 -0.58 57 57
apoptosis -0.071 0.22 0.58 4 -0.66 41 45
CREB1 0.01 0.08 -10000 0 -0.36 36 36
histone acetylation -0.012 0.088 -10000 0 -0.42 7 7
BGLAP -0.026 0.086 -10000 0 -0.5 3 3
GR/PKAc 0.088 0.079 0.35 4 -10000 0 4
NF kappa B1 p50/RelA -0.062 0.2 -10000 0 -0.51 83 83
SMARCD1 0.028 0.01 -10000 0 -10000 0 0
MDM2 0.043 0.066 0.28 15 -10000 0 15
GATA3 -0.32 0.34 -10000 0 -0.64 458 458
AKT1 0.021 0.008 -10000 0 -10000 0 0
CSF2 -0.028 0.074 -10000 0 -0.54 1 1
GSK3B 0.022 0.013 -10000 0 -10000 0 0
NR1I3 -0.045 0.22 0.57 4 -0.75 27 31
CSN2 0.061 0.13 0.4 22 -10000 0 22
BRG1/BAF155/BAF170/BAF60A 0.069 0.033 -10000 0 -10000 0 0
NFATC1 0.029 0.006 -10000 0 -10000 0 0
POU2F1 0.028 0.008 -10000 0 -10000 0 0
CDKN1A 0.022 0.061 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.007 -10000 0 -10000 0 0
SFN -0.072 0.2 -10000 0 -0.44 185 185
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.024 0.15 0.35 1 -0.4 13 14
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.062 0.27 0.55 4 -0.81 58 62
JUN -0.14 0.18 -10000 0 -0.53 89 89
IL4 -0.038 0.083 -10000 0 -0.45 1 1
CDK5R1 0.021 0.037 -10000 0 -0.45 5 5
PRKACA 0.028 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.19 0.22 44 -0.45 128 172
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.083 0.097 0.36 4 -0.38 3 7
cortisol/GR alpha (monomer) 0.15 0.22 0.58 67 -10000 0 67
NCOA2 -0.004 0.14 -10000 0 -0.65 40 40
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.063 0.16 -10000 0 -0.64 57 57
AP-1/NFAT1-c-4 -0.21 0.24 -10000 0 -0.66 102 102
AFP -0.28 0.5 -10000 0 -1.4 136 136
SUV420H1 0.028 0.003 -10000 0 -10000 0 0
IRF1 0.081 0.1 0.45 6 -10000 0 6
TP53 0.042 0.018 -10000 0 -10000 0 0
PPP5C 0.028 0.003 -10000 0 -10000 0 0
KRT17 -0.2 0.35 -10000 0 -1.1 91 91
KRT14 -0.078 0.13 -10000 0 -0.56 3 3
TBP 0.034 0.011 -10000 0 -10000 0 0
CREBBP 0.042 0.045 -10000 0 -10000 0 0
HDAC1 0.025 0.007 -10000 0 -10000 0 0
HDAC2 0.026 0.008 -10000 0 -10000 0 0
AP-1 -0.21 0.24 -10000 0 -0.66 103 103
MAPK14 0.023 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.086 -10000 0 -0.66 14 14
MAPK11 0.022 0.02 -10000 0 -0.43 1 1
KRT5 -0.16 0.2 -10000 0 -0.6 50 50
interleukin-1 receptor activity 0 0.004 -10000 0 -10000 0 0
NCOA1 0.029 0.008 -10000 0 -10000 0 0
STAT1 0.033 0.026 -10000 0 -0.48 2 2
CGA -0.095 0.26 -10000 0 -1.1 50 50
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.05 0.092 0.38 10 -0.46 2 12
MAPK3 0.023 0.011 -10000 0 -10000 0 0
MAPK1 0.024 0.011 -10000 0 -10000 0 0
ICAM1 -0.094 0.19 -10000 0 -0.59 49 49
NFKB1 -0.034 0.11 -10000 0 -0.33 24 24
MAPK8 -0.11 0.14 -10000 0 -0.46 36 36
MAPK9 0.023 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.075 0.23 0.58 4 -0.71 41 45
BAX 0.028 0.042 -10000 0 -10000 0 0
POMC -0.097 0.22 0.56 1 -1 20 21
EP300 0.042 0.049 -10000 0 -0.59 1 1
cortisol/GR alpha (dimer)/p53 0.14 0.19 0.51 60 -10000 0 60
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.063 0.35 14 -10000 0 14
SGK1 0.057 0.13 0.68 1 -1.4 4 5
IL13 -0.32 0.27 -10000 0 -0.72 171 171
IL6 -0.17 0.38 -10000 0 -1.1 104 104
PRKACG -0.007 0.024 -10000 0 -0.42 1 1
IL5 -0.26 0.22 -10000 0 -0.61 130 130
IL2 -0.13 0.17 -10000 0 -0.66 20 20
CDK5 0.023 0.01 -10000 0 -10000 0 0
PRKACB 0.027 0.007 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.12 0.26 -10000 0 -0.74 83 83
CDK5R1/CDK5 0.03 0.027 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA/PKAc -0.018 0.17 -10000 0 -0.46 35 35
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.5 52 -10000 0 52
SMARCA4 0.029 0.008 -10000 0 -10000 0 0
chromatin remodeling 0.084 0.11 0.38 21 -0.4 2 23
NF kappa B1 p50/RelA/Cbp 0 0.18 -10000 0 -0.54 22 22
JUN (dimer) -0.14 0.18 -10000 0 -0.53 89 89
YWHAH 0.027 0.005 -10000 0 -10000 0 0
VIPR1 -0.059 0.17 -10000 0 -0.85 27 27
NR3C1 0.08 0.13 0.42 25 -0.43 1 26
NR4A1 -0.065 0.24 -10000 0 -0.65 126 126
TIF2/SUV420H1 0.016 0.11 -10000 0 -0.49 40 40
MAPKKK cascade -0.071 0.22 0.58 4 -0.66 41 45
cortisol/GR alpha (dimer)/Src-1 0.14 0.19 0.51 66 -10000 0 66
PBX1 0.018 0.086 -10000 0 -0.65 14 14
POU1F1 0.006 0.023 -10000 0 -10000 0 0
SELE -0.29 0.51 -10000 0 -1.2 212 212
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.084 0.11 0.38 20 -0.4 2 22
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.5 52 -10000 0 52
mol:cortisol 0.059 0.12 0.32 64 -0.25 7 71
MMP1 -0.17 0.37 -10000 0 -1.2 87 87
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.046 0.076 -10000 0 -0.36 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.19 -10000 0 -0.57 78 78
AKT1 -0.038 0.25 -10000 0 -0.8 83 83
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.037 0.26 -10000 0 -0.82 83 83
mol:Ca2+ -0.079 0.19 -10000 0 -0.51 102 102
IGF1R 0.028 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.016 0.092 -10000 0 -0.4 38 38
SHC1 0.026 0.016 -10000 0 -0.42 1 1
apoptosis 0.034 0.24 0.76 83 -10000 0 83
RhoA/GTP 0.015 0.047 -10000 0 -0.33 10 10
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.005 0.16 -10000 0 -0.57 40 40
regulation of stress fiber formation -0.026 0.081 -10000 0 -0.35 24 24
E2/ERA-ERB (dimer) 0.019 0.079 -10000 0 -0.38 29 29
KRAS 0.027 0.007 -10000 0 -10000 0 0
G13/GTP 0.02 0.063 -10000 0 -0.32 23 23
pseudopodium formation 0.026 0.081 0.35 24 -10000 0 24
E2/ER alpha (dimer)/PELP1 0.021 0.068 -10000 0 -0.36 23 23
GRB2 0.025 0.009 -10000 0 -10000 0 0
GNG2 0.027 0.005 -10000 0 -10000 0 0
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
HRAS 0.027 0.015 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.001 0.2 0.32 27 -0.58 78 105
E2/ER beta (dimer) 0.018 0.031 -10000 0 -0.31 7 7
mol:GDP 0.007 0.079 -10000 0 -0.38 29 29
mol:NADP 0.001 0.2 0.32 27 -0.58 78 105
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.083 0.2 -10000 0 -0.53 102 102
IGF-1R heterotetramer 0.028 0.003 -10000 0 -10000 0 0
PLCB1 -0.064 0.2 -10000 0 -0.46 149 149
PLCB2 -0.052 0.17 -10000 0 -0.5 92 92
IGF1 0.008 0.098 -10000 0 -0.48 32 32
mol:L-citrulline 0.001 0.2 0.32 27 -0.58 78 105
RHOA 0.026 0.008 -10000 0 -10000 0 0
Gai/GDP -0.015 0.19 -10000 0 -0.62 71 71
JNK cascade 0.018 0.031 -10000 0 -0.31 7 7
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
ESR2 0.024 0.043 -10000 0 -0.44 7 7
GNAQ 0.028 0.004 -10000 0 -10000 0 0
ESR1 0.005 0.11 -10000 0 -0.56 32 32
Gq family/GDP/Gbeta gamma -0.013 0.13 -10000 0 -0.54 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.016 0.25 -10000 0 -1.1 44 44
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.006 0.16 -10000 0 -0.57 39 39
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
E2/ER alpha (dimer) 0.004 0.084 -10000 0 -0.41 32 32
STRN 0.018 0.079 -10000 0 -0.65 12 12
GNAL 0.026 0.028 -10000 0 -0.54 2 2
PELP1 0.025 0.009 -10000 0 -10000 0 0
MAPK11 0.015 0.027 -10000 0 -0.27 7 7
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
HBEGF -0.031 0.2 0.41 36 -0.57 62 98
cAMP biosynthetic process 0.016 0.066 -10000 0 -0.34 23 23
SRC -0.021 0.18 -10000 0 -0.58 64 64
PI3K 0.039 0.011 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.081 -10000 0 -0.42 12 12
SOS1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.043 0.12 -10000 0 -0.48 43 43
Gs family/GTP 0.023 0.069 -10000 0 -0.35 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.02 -10000 0 -10000 0 0
vasodilation 0.003 0.2 0.31 29 -0.55 78 107
mol:DAG -0.083 0.2 -10000 0 -0.53 102 102
Gs family/GDP/Gbeta gamma 0.011 0.073 -10000 0 -0.39 12 12
MSN 0.026 0.084 0.36 24 -10000 0 24
Gq family/GTP -0.031 0.17 -10000 0 -0.51 94 94
mol:PI-3-4-5-P3 -0.033 0.25 -10000 0 -0.78 83 83
NRAS 0.027 0.007 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.003 0.2 0.55 78 -0.31 29 107
GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.085 -10000 0 -0.38 20 20
NOS3 -0.003 0.22 0.32 27 -0.62 78 105
GNA11 0.022 0.065 -10000 0 -0.65 8 8
MAPKKK cascade 0.001 0.22 0.41 23 -0.66 75 98
E2/ER alpha (dimer)/PELP1/Src 0.002 0.17 -10000 0 -0.52 63 63
ruffle organization 0.026 0.081 0.35 24 -10000 0 24
ROCK2 0.031 0.088 0.37 24 -10000 0 24
GNA14 -0.042 0.21 -10000 0 -0.64 92 92
GNA15 0.011 0.088 -10000 0 -0.42 34 34
GNA13 0.025 0.009 -10000 0 -10000 0 0
MMP9 -0.078 0.19 0.38 14 -0.59 64 78
MMP2 -0.008 0.18 0.32 10 -0.58 55 65
HIF-2-alpha transcription factor network

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
MMP14 0.001 0.093 -10000 0 -0.7 9 9
oxygen homeostasis 0.001 0.014 -10000 0 -10000 0 0
TCEB2 0.024 0.038 -10000 0 -0.46 5 5
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.038 0.12 -10000 0 -0.41 4 4
EPO -0.1 0.24 -10000 0 -0.58 72 72
FIH (dimer) 0.023 0.022 -10000 0 -10000 0 0
APEX1 0.023 0.024 -10000 0 -10000 0 0
SERPINE1 -0.098 0.25 -10000 0 -0.69 51 51
FLT1 -0.018 0.15 -10000 0 -0.89 13 13
ADORA2A -0.083 0.23 0.46 3 -0.62 39 42
germ cell development -0.11 0.27 -10000 0 -0.61 89 89
SLC11A2 -0.073 0.23 -10000 0 -0.62 34 34
BHLHE40 -0.073 0.23 -10000 0 -0.62 31 31
HIF1AN 0.023 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.06 0.18 -10000 0 -0.42 26 26
ETS1 0.031 0.037 -10000 0 -10000 0 0
CITED2 -0.023 0.14 -10000 0 -0.57 46 46
KDR -0.07 0.31 -10000 0 -1.1 67 67
PGK1 -0.071 0.23 -10000 0 -0.62 35 35
SIRT1 0.026 0.007 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT -0.074 0.27 -10000 0 -0.71 37 37
EPAS1 -0.057 0.12 -10000 0 -0.34 20 20
SP1 0.031 0.015 -10000 0 -10000 0 0
ABCG2 -0.075 0.24 -10000 0 -0.65 40 40
EFNA1 -0.071 0.23 -10000 0 -0.62 35 35
FXN -0.077 0.23 0.49 8 -0.62 36 44
POU5F1 -0.12 0.28 -10000 0 -0.64 89 89
neuron apoptosis 0.072 0.26 0.69 37 -10000 0 37
EP300 0.027 0.024 -10000 0 -0.65 1 1
EGLN3 -0.22 0.23 -10000 0 -0.43 484 484
EGLN2 0.025 0.021 -10000 0 -10000 0 0
EGLN1 0.023 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.047 0.033 -10000 0 -0.42 1 1
VHL 0.026 0.008 -10000 0 -10000 0 0
ARNT 0.021 0.024 -10000 0 -10000 0 0
SLC2A1 -0.085 0.24 0.5 6 -0.65 53 59
TWIST1 -0.088 0.22 0.52 3 -0.62 34 37
ELK1 0.035 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.045 0.16 -10000 0 -0.47 4 4
VEGFA -0.12 0.28 -10000 0 -0.63 99 99
CREBBP 0.027 0.007 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.031 0.14 -9999 0 -0.48 38 38
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.016 0.067 -9999 0 -0.44 18 18
WNT4 -0.021 0.17 -9999 0 -0.62 64 64
FZD3 0.027 0.007 -9999 0 -10000 0 0
WNT5A 0.01 0.088 -9999 0 -0.46 29 29
WNT11 -0.047 0.21 -9999 0 -0.62 101 101
Nongenotropic Androgen signaling

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
PTK2 0.01 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.025 0.1 -10000 0 -0.38 50 50
regulation of S phase of mitotic cell cycle 0.01 0.075 -10000 0 -0.3 45 45
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
HRAS 0.027 0.016 -10000 0 -0.42 1 1
SHBG/T-DHT -0.01 0.1 -10000 0 -0.4 57 57
PELP1 0.025 0.009 -10000 0 -10000 0 0
AKT1 0.01 0.002 -10000 0 -10000 0 0
MAP2K1 0.007 0.097 0.34 10 -0.42 7 17
T-DHT/AR -0.01 0.12 -10000 0 -0.48 53 53
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -0.01 58 58
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
mol:GDP -0.017 0.12 -10000 0 -0.5 49 49
cell proliferation 0.012 0.15 0.44 29 -0.45 38 67
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
FOS -0.02 0.23 0.42 18 -0.78 60 78
mol:Ca2+ 0 0.019 -10000 0 -0.073 30 30
MAPK3 0.017 0.14 0.41 37 -0.47 12 49
MAPK1 0.009 0.1 0.29 20 -0.43 24 44
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 56 56
cAMP biosynthetic process -0.022 0.1 0.24 12 -0.39 55 67
GNG2 0.027 0.005 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 56 56
HRAS/GTP 0.023 0.095 -10000 0 -0.35 47 47
actin cytoskeleton reorganization 0.035 0.018 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 56 56
PI3K 0.036 0.01 -10000 0 -10000 0 0
apoptosis -0.006 0.15 0.47 46 -0.36 26 72
T-DHT/AR/PELP1 0.007 0.11 -10000 0 -0.41 53 53
HRAS/GDP -0.001 0.12 -10000 0 -0.47 49 49
CREB1 0.004 0.16 0.39 22 -0.51 46 68
RAC1-CDC42/GTP 0.044 0.023 -10000 0 -10000 0 0
AR -0.013 0.16 -10000 0 -0.64 53 53
GNB1 0.026 0.007 -10000 0 -10000 0 0
RAF1 0.011 0.1 0.35 12 -0.34 44 56
RAC1-CDC42/GDP 0.014 0.12 -10000 0 -0.46 46 46
T-DHT/AR/PELP1/Src 0.022 0.1 -10000 0 -0.39 47 47
MAP2K2 0.006 0.098 0.34 10 -0.41 8 18
T-DHT/AR/PELP1/Src/PI3K 0.01 0.076 -10000 0 -0.3 45 45
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
SHBG -0.018 0.16 -10000 0 -0.62 57 57
Gi family/GNB1/GNG2/GDP -0.002 0.12 -10000 0 -0.48 33 33
mol:T-DHT 0 0.002 0.001 5 -0.007 50 55
RAC1 0.025 0.01 -10000 0 -10000 0 0
GNRH1 -0.055 0.13 0.2 1 -0.3 184 185
Gi family/GTP -0.001 0.068 -10000 0 -0.28 28 28
CDC42 0.027 0.007 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.006 0.095 -10000 0 -0.42 42 42
PLK4 0.025 0.034 -10000 0 -0.42 5 5
regulation of centriole replication 0.003 0.071 0.21 3 -0.29 47 50
Syndecan-2-mediated signaling events

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.009 0.074 -10000 0 -0.24 70 70
EPHB2 0.02 0.058 -10000 0 -0.45 12 12
Syndecan-2/TACI 0.013 0.062 -10000 0 -0.24 49 49
LAMA1 0.006 0.12 -10000 0 -0.57 32 32
Syndecan-2/alpha2 ITGB1 0.032 0.085 -10000 0 -0.36 9 9
HRAS 0.027 0.015 -10000 0 -0.42 1 1
Syndecan-2/CASK 0.012 0.009 -10000 0 -0.24 1 1
ITGA5 0.004 0.098 -10000 0 -0.42 45 45
BAX 0.013 0.035 -10000 0 -10000 0 0
EPB41 0.027 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.029 0.011 -10000 0 -0.21 1 1
LAMA3 -0.011 0.13 -10000 0 -0.42 75 75
EZR 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.016 0.062 -10000 0 -0.42 17 17
Syndecan-2/MMP2 0.028 0.034 -10000 0 -0.29 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.054 -10000 0 -0.49 9 9
dendrite morphogenesis 0.027 0.038 -10000 0 -0.3 9 9
Syndecan-2/GM-CSF 0.021 0.04 -10000 0 -0.24 18 18
determination of left/right symmetry 0.016 0.011 -10000 0 -0.28 1 1
Syndecan-2/PKC delta 0.027 0.031 -10000 0 -0.24 10 10
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.015 0.039 -10000 0 -0.29 1 1
MAPK1 0.016 0.04 -10000 0 -0.29 1 1
Syndecan-2/RACK1 0.043 0.019 -10000 0 -10000 0 0
NF1 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.016 0.011 -10000 0 -0.28 1 1
ITGA2 0.021 0.069 -10000 0 -0.65 9 9
MAPK8 0.016 0.038 -10000 0 -0.41 6 6
Syndecan-2/alpha2/beta1 Integrin 0.042 0.08 -10000 0 -0.35 27 27
Syndecan-2/Kininogen -0.27 0.21 -10000 0 -0.42 569 569
ITGB1 0.027 0.007 -10000 0 -10000 0 0
SRC 0.032 0.037 0.34 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.028 0.012 -10000 0 -10000 0 0
extracellular matrix organization 0.031 0.022 -10000 0 -0.24 5 5
actin cytoskeleton reorganization 0.009 0.074 -10000 0 -0.24 70 70
Syndecan-2/Caveolin-2/Ras 0.036 0.042 -10000 0 -0.42 1 1
Syndecan-2/Laminin alpha3 0.009 0.077 -10000 0 -0.24 74 74
Syndecan-2/RasGAP 0.054 0.029 -10000 0 -0.53 1 1
alpha5/beta1 Integrin 0.021 0.074 -10000 0 -0.29 45 45
PRKCD 0.021 0.045 -10000 0 -0.42 9 9
Syndecan-2 dimer 0.027 0.038 -10000 0 -0.3 9 9
GO:0007205 0.003 0.002 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.046 0.034 -10000 0 -0.52 1 1
RHOA 0.026 0.008 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B -0.007 0.1 -10000 0 -0.42 48 48
RASA1 0.027 0.023 -10000 0 -0.65 1 1
alpha2/beta1 Integrin 0.033 0.054 -10000 0 -0.49 9 9
Syndecan-2/Synbindin 0.032 0.012 -10000 0 -10000 0 0
TGFB1 0.026 0.03 -10000 0 -0.42 4 4
CASP3 0.022 0.034 -10000 0 -10000 0 0
FN1 -0.01 0.12 -10000 0 -0.42 72 72
Syndecan-2/IL8 0.004 0.093 -10000 0 -0.28 78 78
SDC2 0.016 0.011 -10000 0 -0.28 1 1
KNG1 -0.44 0.3 -10000 0 -0.65 586 586
Syndecan-2/Neurofibromin 0.029 0.015 -10000 0 -0.22 1 1
TRAPPC4 0.028 0.004 -10000 0 -10000 0 0
CSF2 -0.006 0.063 -10000 0 -0.42 17 17
Syndecan-2/TGFB1 0.031 0.022 -10000 0 -0.24 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.029 0.011 -10000 0 -0.21 1 1
Syndecan-2/Ezrin 0.042 0.021 -10000 0 -10000 0 0
PRKACA 0.024 0.024 -10000 0 -10000 0 0
angiogenesis 0.004 0.093 -10000 0 -0.28 78 78
MMP2 0.022 0.048 -10000 0 -0.44 9 9
IL8 -0.017 0.15 -10000 0 -0.48 78 78
calcineurin-NFAT signaling pathway 0.013 0.062 -10000 0 -0.24 49 49
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.005 0.098 -10000 0 -0.52 14 14
Crk/p130 Cas/Paxillin -0.039 0.095 -10000 0 -0.38 14 14
JUN -0.009 0.094 -10000 0 -0.42 15 15
HRAS 0.027 0.015 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/GRB10 0.008 0.13 -10000 0 -0.4 63 63
RAP1A 0.027 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.008 0.15 -10000 0 -0.41 81 81
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.006 0.12 -10000 0 -0.39 56 56
RHOA 0.026 0.008 -10000 0 -10000 0 0
RAP1A/GTP 0.011 0.12 -10000 0 -0.36 72 72
GRB7 0.018 0.069 -10000 0 -0.65 9 9
RET51/GFRalpha1/GDNF 0.009 0.14 -10000 0 -0.4 79 79
MAPKKK cascade -0.002 0.12 -10000 0 -0.46 9 9
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
RET9/GFRalpha1/GDNF/IRS1 0.003 0.13 -10000 0 -0.41 63 63
lamellipodium assembly -0.011 0.1 -10000 0 -0.31 40 40
RET51/GFRalpha1/GDNF/SHC 0.008 0.14 -10000 0 -0.4 80 80
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.007 0.12 -10000 0 -0.39 55 55
RET9/GFRalpha1/GDNF/Shank3 0.008 0.11 -10000 0 -0.39 53 53
MAPK3 -0.016 0.11 0.41 2 -0.35 64 66
DOK1 0.026 0.022 -10000 0 -0.42 2 2
DOK6 -0.031 0.19 -10000 0 -0.63 78 78
PXN 0.027 0.006 -10000 0 -10000 0 0
neurite development -0.025 0.12 -10000 0 -0.47 18 18
DOK5 0.002 0.13 -10000 0 -0.64 32 32
GFRA1 -0.034 0.18 -10000 0 -0.54 95 95
MAPK8 -0.007 0.099 -10000 0 -0.43 17 17
HRAS/GTP 0.005 0.14 -10000 0 -0.4 73 73
tube development 0.019 0.11 -10000 0 -0.37 46 46
MAPK1 -0.009 0.12 0.39 9 -0.47 6 15
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.003 0.087 -10000 0 -0.29 66 66
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
PDLIM7 0.025 0.027 -10000 0 -0.42 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.012 0.19 -10000 0 -0.43 123 123
SHC1 0.026 0.016 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 0.009 0.14 -10000 0 -0.4 72 72
RET51/GFRalpha1/GDNF/Dok5 -0.005 0.17 -10000 0 -0.44 94 94
PRKCA 0.025 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.29 1 1
CREB1 -0.002 0.1 -10000 0 -0.36 48 48
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.1 -10000 0 -0.32 70 70
RET51/GFRalpha1/GDNF/Grb7 0.005 0.15 -10000 0 -0.43 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.002 0.12 -10000 0 -0.59 35 35
DOK4 0.027 0.007 -10000 0 -10000 0 0
JNK cascade -0.006 0.094 -10000 0 -0.46 10 10
RET9/GFRalpha1/GDNF/FRS2 0.008 0.11 -10000 0 -0.39 52 52
SHANK3 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.027 0.023 -10000 0 -0.65 1 1
NCK1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.008 0.1 -10000 0 -0.33 71 71
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.008 0.11 -10000 0 -0.31 72 72
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.011 0.12 -10000 0 -0.33 76 76
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.013 0.12 -10000 0 -0.43 36 36
PI3K -0.016 0.15 -10000 0 -0.46 56 56
SOS1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.019 0.11 -10000 0 -0.37 46 46
GRB10 0.025 0.009 -10000 0 -10000 0 0
activation of MAPKK activity -0.008 0.095 -10000 0 -0.34 27 27
RET51/GFRalpha1/GDNF/FRS2 0.008 0.14 -10000 0 -0.4 75 75
GAB1 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.019 0.072 -10000 0 -0.65 10 10
IRS2 0.018 0.064 -10000 0 -0.42 18 18
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.12 -10000 0 -0.34 92 92
RET51/GFRalpha1/GDNF/PKC alpha 0.008 0.14 -10000 0 -0.4 69 69
GRB2 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GDNF -0.005 0.035 -10000 0 -0.42 4 4
RAC1 0.025 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.003 0.15 -10000 0 -0.41 88 88
Rac1/GTP -0.008 0.12 -10000 0 -0.41 19 19
RET9/GFRalpha1/GDNF -0.009 0.12 -10000 0 -0.39 71 71
GFRalpha1/GDNF -0.013 0.14 -10000 0 -0.45 71 71
BCR signaling pathway

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
JUN -0.017 0.15 0.33 19 -0.51 42 61
IKBKB 0.007 0.1 0.3 35 -0.32 10 45
AKT1 -0.001 0.12 0.35 56 -0.25 1 57
IKBKG 0.017 0.092 0.3 32 -0.3 3 35
CALM1 -0.004 0.087 0.31 7 -0.44 11 18
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.016 0.16 0.35 26 -0.49 38 64
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.09 0.3 4 -0.42 16 20
DOK1 0.026 0.022 -10000 0 -0.42 2 2
AP-1 -0.006 0.1 0.26 26 -0.27 44 70
LYN 0.026 0.024 -10000 0 -0.65 1 1
BLNK 0.017 0.079 -10000 0 -0.65 12 12
SHC1 0.026 0.016 -10000 0 -0.42 1 1
BCR complex -0.031 0.14 -10000 0 -0.3 172 172
CD22 -0.057 0.12 -10000 0 -0.45 39 39
CAMK2G -0.001 0.083 0.3 6 -0.4 11 17
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
SHC/GRB2/SOS1 -0.016 0.097 -10000 0 -0.61 2 2
GO:0007205 -0.007 0.091 0.3 4 -0.43 16 20
SYK 0.024 0.048 -10000 0 -0.59 5 5
ELK1 -0.005 0.088 0.29 4 -0.45 11 15
NFATC1 -0.022 0.11 0.36 11 -0.43 7 18
B-cell antigen/BCR complex -0.031 0.14 -10000 0 -0.3 172 172
PAG1/CSK 0.039 0.024 -10000 0 -0.29 4 4
NFKBIB 0.022 0.048 0.15 42 -0.14 8 50
HRAS 0.002 0.083 0.31 6 -0.49 3 9
NFKBIA 0.022 0.047 0.15 42 -0.13 4 46
NF-kappa-B/RelA/I kappa B beta 0.025 0.043 0.15 36 -0.18 1 37
RasGAP/Csk -0.037 0.16 -10000 0 -0.41 68 68
mol:GDP -0.005 0.09 0.3 4 -0.4 18 22
PTEN 0.027 0.007 -10000 0 -10000 0 0
CD79B 0.022 0.045 -10000 0 -0.5 6 6
NF-kappa-B/RelA/I kappa B alpha 0.026 0.044 0.16 37 -0.18 1 38
GRB2 0.025 0.009 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.016 0.14 0.37 11 -0.5 13 24
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.006 0.09 0.31 4 -0.43 16 20
CSK 0.028 0.003 -10000 0 -10000 0 0
FOS -0.023 0.12 0.3 8 -0.48 28 36
CHUK 0.003 0.12 0.3 32 -0.34 37 69
IBTK 0.027 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.007 0.12 0.28 10 -0.43 4 14
PTPN6 -0.055 0.12 -10000 0 -0.47 27 27
RELA 0.028 0.003 -10000 0 -10000 0 0
BCL2A1 0.007 0.047 0.14 20 -0.13 1 21
VAV2 -0.047 0.12 -10000 0 -0.44 25 25
ubiquitin-dependent protein catabolic process 0.025 0.047 0.15 42 -0.13 8 50
BTK -0.01 0.092 -10000 0 -0.85 8 8
CD19 -0.058 0.13 -10000 0 -0.42 54 54
MAP4K1 -0.09 0.2 -10000 0 -0.42 234 234
CD72 -0.04 0.16 -10000 0 -0.42 134 134
PAG1 0.025 0.03 -10000 0 -0.42 4 4
MAPK14 -0.01 0.14 0.33 28 -0.41 33 61
SH3BP5 0.012 0.097 -10000 0 -0.64 19 19
PIK3AP1 -0.002 0.098 0.33 4 -0.47 17 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.022 0.11 -10000 0 -0.51 21 21
RAF1 0.006 0.083 0.31 11 -0.46 3 14
RasGAP/p62DOK/SHIP -0.037 0.16 -10000 0 -0.4 67 67
CD79A -0.06 0.18 -10000 0 -0.42 172 172
re-entry into mitotic cell cycle -0.006 0.098 0.26 26 -0.27 44 70
RASA1 0.027 0.023 -10000 0 -0.65 1 1
MAPK3 0.022 0.1 0.37 37 -0.37 2 39
MAPK1 0.013 0.085 0.39 13 -0.4 2 15
CD72/SHP1 -0.064 0.16 0.34 2 -0.46 48 50
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 -0.012 0.15 0.35 27 -0.46 17 44
actin cytoskeleton organization -0.022 0.13 0.35 6 -0.48 7 13
NF-kappa-B/RelA 0.055 0.081 0.26 51 -10000 0 51
Calcineurin 0.02 0.083 0.3 1 -0.42 4 5
PI3K -0.057 0.12 -10000 0 -0.44 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.006 0.099 0.28 11 -0.49 18 29
SOS1 0.027 0.006 -10000 0 -10000 0 0
Bam32/HPK1 -0.064 0.18 -10000 0 -0.67 20 20
DAPP1 -0.032 0.16 -10000 0 -0.75 20 20
cytokine secretion -0.02 0.11 0.35 11 -0.4 7 18
mol:DAG -0.006 0.09 0.31 4 -0.43 16 20
PLCG2 0.005 0.11 -10000 0 -0.51 35 35
MAP2K1 0.011 0.084 0.32 14 -0.42 3 17
B-cell antigen/BCR complex/FcgammaRIIB -0.066 0.17 -10000 0 -0.47 69 69
mol:PI-3-4-5-P3 -0.044 0.086 -10000 0 -0.31 17 17
ETS1 0.001 0.083 0.37 8 -0.41 6 14
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.006 0.12 -10000 0 -0.41 16 16
B-cell antigen/BCR complex/LYN -0.038 0.1 -10000 0 -0.48 9 9
MALT1 0.027 0.005 -10000 0 -10000 0 0
TRAF6 0.028 0.003 -10000 0 -10000 0 0
RAC1 -0.03 0.13 0.32 2 -0.51 7 9
B-cell antigen/BCR complex/LYN/SYK -0.043 0.14 -10000 0 -0.55 10 10
CARD11 -0.022 0.14 0.34 24 -0.41 15 39
FCGR2B -0.065 0.18 -10000 0 -0.42 179 179
PPP3CA 0.028 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.007 -10000 0 -10000 0 0
IKK complex 0.016 0.064 0.19 62 -0.13 3 65
PTPRC -0.008 0.12 -10000 0 -0.42 67 67
PDPK1 -0.024 0.076 0.32 10 -0.24 1 11
PPP3CB 0.027 0.007 -10000 0 -10000 0 0
PPP3CC 0.027 0.007 -10000 0 -10000 0 0
POU2F2 0.015 0.043 0.16 18 -10000 0 18
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.008 0.11 -10000 0 -0.63 24 24
GNB1/GNG2 -0.012 0.14 -10000 0 -0.47 28 28
mol:DAG -0.024 0.12 -10000 0 -0.44 26 26
PLCG1 -0.025 0.12 -10000 0 -0.46 26 26
YES1 -0.034 0.13 -10000 0 -0.46 36 36
FZD3 0.027 0.007 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.008 0.14 0.28 2 -0.48 22 24
MAP3K7 -0.12 0.18 -10000 0 -0.48 86 86
mol:Ca2+ -0.024 0.12 -10000 0 -0.43 26 26
mol:IP3 -0.024 0.12 -10000 0 -0.44 26 26
NLK -0.029 0.17 -10000 0 -0.85 37 37
GNB1 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.13 0.2 -10000 0 -0.49 109 109
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.031 0.14 -10000 0 -0.48 38 38
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
GNAS -0.031 0.13 -10000 0 -0.46 36 36
GO:0007205 -0.03 0.12 -10000 0 -0.45 22 22
WNT6 0.016 0.067 -10000 0 -0.44 18 18
WNT4 -0.021 0.17 -10000 0 -0.62 64 64
NFAT1/CK1 alpha -0.019 0.14 -10000 0 -0.48 23 23
GNG2 0.027 0.005 -10000 0 -10000 0 0
WNT5A 0.01 0.088 -10000 0 -0.46 29 29
WNT11 -0.047 0.21 -10000 0 -0.62 101 101
CDC42 -0.031 0.12 -10000 0 -0.46 29 29
Regulation of Telomerase

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
Telomerase catalytic core complex -0.16 0.17 0.51 5 -0.6 31 36
RAD9A 0.027 0.021 -10000 0 -0.42 2 2
AP1 0.006 0.12 -10000 0 -0.48 53 53
IFNAR2 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.051 -10000 0 -0.24 21 21
ER alpha/Oestrogen 0.003 0.084 -10000 0 -0.41 32 32
NFX1/SIN3/HDAC complex 0.013 0.091 -10000 0 -0.37 32 32
EGF -0.54 0.25 -10000 0 -0.65 731 731
SMG5 0.027 0.007 -10000 0 -10000 0 0
SMG6 0.025 0.009 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.015 -10000 0 -10000 0 0
TERT/c-Abl -0.15 0.16 0.5 5 -0.59 22 27
SAP18 0.027 0.006 -10000 0 -10000 0 0
MRN complex 0.051 0.024 -10000 0 -0.42 1 1
WT1 -0.3 0.34 -10000 0 -0.65 425 425
WRN 0.027 0.007 -10000 0 -10000 0 0
SP1 0.024 0.012 -10000 0 -10000 0 0
SP3 0.027 0.007 -10000 0 -10000 0 0
TERF2IP 0.026 0.007 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.15 -10000 0 -0.61 9 9
Mad/Max 0.037 0.017 -10000 0 -0.29 1 1
TERT -0.17 0.17 0.51 5 -0.64 22 27
CCND1 -0.16 0.17 0.67 5 -0.72 11 16
MAX 0.027 0.006 -10000 0 -10000 0 0
RBBP7 0.028 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.024 -10000 0 -0.65 1 1
TERF2 0.023 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.006 -10000 0 -10000 0 0
SIN3A 0.028 0.003 -10000 0 -10000 0 0
Telomerase/911 0.019 0.039 -10000 0 -10000 0 0
CDKN1B -0.046 0.12 -10000 0 -0.45 2 2
RAD1 0.027 0.005 -10000 0 -10000 0 0
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
SAP30 -0.004 0.12 -10000 0 -0.42 62 62
TRF2/PARP2 0.037 0.013 -10000 0 -10000 0 0
UBE3A 0.028 0.004 -10000 0 -10000 0 0
JUN 0.026 0.007 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.019 0.007 -10000 0 -10000 0 0
FOS -0.015 0.16 -10000 0 -0.62 57 57
IFN-gamma/IRF1 -0.049 0.15 -10000 0 -0.53 2 2
PARP2 0.028 0.005 -10000 0 -10000 0 0
BLM 0.012 0.082 -10000 0 -0.42 31 31
Telomerase -0.007 0.086 0.29 1 -0.68 6 7
IRF1 0.029 0.022 -10000 0 -0.41 2 2
ESR1 0.005 0.11 -10000 0 -0.56 32 32
KU/TER 0.039 0.012 -10000 0 -10000 0 0
ATM/TRF2 0.039 0.02 -10000 0 -0.44 1 1
ubiquitin-dependent protein catabolic process 0.03 0.061 -10000 0 -0.42 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.03 0.062 -10000 0 -0.43 5 5
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.024 0.012 -10000 0 -10000 0 0
ATM 0.01 0.017 -10000 0 -0.47 1 1
SMAD3 0.019 0.022 -10000 0 -0.29 2 2
ABL1 0.028 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.016 -10000 0 -0.42 1 1
MRE11A 0.028 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.009 -10000 0 -10000 0 0
RPS6KB1 0.025 0.009 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.16 -10000 0 -0.66 9 9
NR2F2 0.028 0.024 -10000 0 -0.65 1 1
MAPK3 0.005 0.042 -10000 0 -0.29 16 16
MAPK1 0.005 0.042 -10000 0 -0.29 16 16
TGFB1/TGF beta receptor Type II 0.026 0.03 -10000 0 -0.41 4 4
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.017 -10000 0 -0.47 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.017 0.061 -10000 0 -0.45 14 14
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.38 0.2 -10000 0 -0.46 727 727
MYC 0.014 0.076 -10000 0 -0.43 25 25
IL2 0.009 0.061 -10000 0 -0.42 16 16
KU 0.039 0.012 -10000 0 -10000 0 0
RAD50 0.026 0.024 -10000 0 -0.65 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.026 0.03 -10000 0 -0.42 4 4
TRF2/BLM 0.027 0.058 -10000 0 -0.27 29 29
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.15 0.16 -10000 0 -0.62 15 15
SP1/HDAC2 0.033 0.022 -10000 0 -10000 0 0
PINX1 0.027 0.007 -10000 0 -10000 0 0
Telomerase/EST1A -0.13 0.15 -10000 0 -0.62 8 8
Smad3/Myc 0.026 0.053 -10000 0 -0.44 2 2
911 complex 0.048 0.025 -10000 0 -0.24 2 2
IFNG -0.1 0.2 -10000 0 -0.41 257 257
Telomerase/PinX1 -0.14 0.15 -10000 0 -0.61 9 9
Telomerase/AKT1/mTOR/p70S6K -0.015 0.075 -10000 0 -0.49 7 7
SIN3B 0.028 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
Telomerase/EST1B -0.13 0.15 -10000 0 -0.59 9 9
response to DNA damage stimulus 0.004 0.014 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.068 0.033 -10000 0 -0.36 1 1
TRF2/WRN 0.036 0.014 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.15 -10000 0 -0.6 9 9
E2F1 -0.057 0.17 -10000 0 -0.42 163 163
ZNFX1 0.027 0.007 -10000 0 -10000 0 0
PIF1 -0.026 0.15 -10000 0 -0.42 107 107
NCL 0.027 0.006 -10000 0 -10000 0 0
DKC1 0.028 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.016 0.083 0.28 1 -0.45 15 16
BAG4 0.025 0.033 -10000 0 -0.65 2 2
BAD 0.02 0.059 0.28 20 -0.34 1 21
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.023 0.14 -10000 0 -0.42 100 100
BAX 0.02 0.057 0.22 33 -0.19 2 35
EnzymeConsortium:3.1.4.12 0.012 0.036 0.12 43 -0.098 15 58
IKBKB 0.022 0.089 0.3 7 -0.46 10 17
MAP2K2 0.033 0.09 0.3 62 -0.3 1 63
MAP2K1 0.033 0.089 0.3 62 -10000 0 62
SMPD1 0.016 0.041 0.16 28 -0.18 4 32
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.02 0.099 0.32 1 -0.48 14 15
MAP2K4 0.035 0.081 0.28 71 -10000 0 71
protein ubiquitination 0.029 0.11 0.38 20 -0.44 15 35
EnzymeConsortium:2.7.1.37 0.038 0.1 0.35 64 -10000 0 64
response to UV 0 0.002 0.005 73 -10000 0 73
RAF1 0.032 0.089 0.3 68 -10000 0 68
CRADD 0.027 0.006 -10000 0 -10000 0 0
mol:ceramide 0.019 0.053 0.19 36 -0.18 7 43
I-kappa-B-alpha/RELA/p50/ubiquitin 0.037 0.007 -10000 0 -10000 0 0
MADD 0.028 0.004 -10000 0 -10000 0 0
MAP3K1 0.024 0.06 0.22 45 -0.18 5 50
TRADD 0.026 0.007 -10000 0 -10000 0 0
RELA/p50 0.028 0.003 -10000 0 -10000 0 0
MAPK3 0.035 0.087 0.3 62 -10000 0 62
MAPK1 0.034 0.089 0.31 60 -10000 0 60
p50/RELA/I-kappa-B-alpha 0.041 0.008 -10000 0 -10000 0 0
FADD 0.011 0.089 0.32 1 -0.44 15 16
KSR1 0.03 0.076 0.26 64 -0.19 1 65
MAPK8 0.034 0.081 0.29 59 -0.27 1 60
TRAF2 0.028 0.004 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 39 -10000 0 39
CHUK 0.027 0.083 0.3 9 -0.43 13 22
TNF R/SODD 0.037 0.028 -10000 0 -0.49 2 2
TNF 0.013 0.082 -10000 0 -0.46 25 25
CYCS 0.028 0.069 0.24 47 -10000 0 47
IKBKG 0.021 0.092 0.29 10 -0.43 15 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.091 -10000 0 -0.48 15 15
RELA 0.028 0.003 -10000 0 -10000 0 0
RIPK1 0.027 0.007 -10000 0 -10000 0 0
AIFM1 0.02 0.058 0.22 32 -10000 0 32
TNF/TNF R/SODD 0.04 0.06 -10000 0 -0.42 7 7
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 39 -10000 0 39
CASP8 0.007 0.14 -10000 0 -0.68 34 34
NSMAF 0.014 0.089 -10000 0 -0.45 14 14
response to hydrogen peroxide 0 0.002 0.005 73 -10000 0 73
BCL2 0.027 0.023 -10000 0 -0.65 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0.071 -10000 0 -0.67 6 6
VEGFR1 homodimer/NRP1 0.01 0.068 -10000 0 -0.67 6 6
mol:DAG -0.064 0.13 -10000 0 -0.53 15 15
VEGFR1 homodimer/NRP1/VEGFR 121 -0.052 0.13 -10000 0 -0.52 17 17
CaM/Ca2+ -0.05 0.13 -10000 0 -0.5 15 15
HIF1A 0.028 0.049 -10000 0 -0.46 6 6
GAB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 -0.038 0.11 -10000 0 -0.6 6 6
PLCG1 -0.064 0.13 -10000 0 -0.53 15 15
NOS3 -0.034 0.1 0.46 1 -0.62 6 7
CBL 0.027 0.023 -10000 0 -0.65 1 1
mol:NO -0.022 0.11 0.44 2 -0.56 7 9
FLT1 0.014 0.078 -10000 0 -0.75 6 6
PGF -0.12 0.21 -10000 0 -0.42 298 298
VEGFR1 homodimer/NRP2/VEGFR121 -0.046 0.14 -10000 0 -0.49 23 23
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 -0.002 0.13 0.46 7 -0.57 6 13
endothelial cell proliferation -0.039 0.11 0.36 1 -0.56 6 7
mol:Ca2+ -0.063 0.13 -10000 0 -0.52 15 15
MAPK3 -0.06 0.11 0.36 2 -0.45 12 14
MAPK1 -0.06 0.11 0.36 2 -0.45 13 15
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.12 0.21 -10000 0 -0.42 298 298
PRKACA 0.028 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.002 0.097 -10000 0 -0.42 44 44
VEGFA homodimer -0.11 0.2 -10000 0 -0.42 269 269
VEGFR1 homodimer/VEGFA homodimer -0.057 0.14 -10000 0 -0.56 17 17
platelet activating factor biosynthetic process -0.059 0.1 0.35 2 -0.44 12 14
PI3K -0.035 0.14 -10000 0 -0.52 15 15
PRKCA -0.062 0.11 -10000 0 -0.46 15 15
PRKCB -0.066 0.12 -10000 0 -0.46 20 20
VEGFR1 homodimer/PLGF homodimer -0.066 0.15 -10000 0 -0.6 15 15
VEGFA -0.11 0.2 -10000 0 -0.42 269 269
VEGFB 0.028 0.003 -10000 0 -10000 0 0
mol:IP3 -0.064 0.13 -10000 0 -0.53 15 15
RASA1 0.017 0.069 -10000 0 -0.68 6 6
NRP2 0.017 0.069 -10000 0 -0.43 20 20
VEGFR1 homodimer 0.014 0.077 -10000 0 -0.75 6 6
VEGFB homodimer 0.028 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.031 0.12 0.43 2 -0.52 7 9
PTPN11 0.027 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.14 -10000 0 -0.52 15 15
mol:L-citrulline -0.022 0.11 0.44 2 -0.56 7 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.027 0.14 -10000 0 -0.52 16 16
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.041 0.14 -10000 0 -0.52 17 17
CD2AP 0.026 0.007 -10000 0 -10000 0 0
PI3K/GAB1 -0.025 0.14 -10000 0 -0.5 15 15
PDPK1 -0.049 0.12 0.34 2 -0.5 14 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.041 0.14 -10000 0 -0.51 17 17
mol:NADP -0.022 0.11 0.44 2 -0.56 7 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.028 0.14 -10000 0 -0.52 16 16
VEGFR1 homodimer/NRP2 0.022 0.081 -10000 0 -0.63 7 7
Visual signal transduction: Rods

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
mol:K + 0.028 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.033 -10000 0 -0.29 10 10
Metarhodopsin II/Arrestin 0.021 0.038 -10000 0 -0.25 16 16
PDE6G/GNAT1/GTP 0.017 0.063 -10000 0 -0.34 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.007 0.049 -10000 0 -0.42 10 10
GRK1 -0.009 0.032 -10000 0 -0.46 3 3
CNG Channel -0.063 0.17 -10000 0 -0.5 30 30
mol:Na + -0.061 0.17 -10000 0 -0.5 36 36
mol:ADP -0.009 0.032 -10000 0 -0.46 3 3
RGS9-1/Gbeta5/R9AP 0.025 0.1 -10000 0 -0.43 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.056 0.18 -10000 0 -0.52 35 35
CNGB1 -0.012 0.098 -10000 0 -0.42 46 46
RDH5 -0.002 0.12 -10000 0 -0.45 53 53
SAG -0.013 0.02 -10000 0 -0.42 1 1
mol:Ca2+ -0.075 0.17 0.4 22 -0.52 28 50
Na + (4 Units) -0.06 0.16 -10000 0 -0.5 29 29
RGS9 0.001 0.11 -10000 0 -0.49 41 41
GNB1/GNGT1 -0.05 0.14 -10000 0 -0.29 220 220
GNAT1/GDP 0.027 0.094 -10000 0 -0.38 32 32
GUCY2D -0.011 0.11 -10000 0 -0.42 53 53
GNGT1 -0.095 0.19 -10000 0 -0.42 220 220
GUCY2F -0.013 0.014 -10000 0 -10000 0 0
GNB5 0.028 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.005 0.085 -10000 0 -0.43 24 24
mol:11-cis-retinal -0.002 0.12 -10000 0 -0.45 53 53
mol:cGMP 0.021 0.079 -10000 0 -0.41 3 3
GNB1 0.026 0.007 -10000 0 -10000 0 0
Rhodopsin 0.01 0.092 -10000 0 -0.31 63 63
SLC24A1 0.028 0.003 -10000 0 -10000 0 0
CNGA1 -0.12 0.28 -10000 0 -0.64 199 199
Metarhodopsin II 0.02 0.04 -10000 0 -0.24 18 18
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.028 0.084 -10000 0 -0.43 3 3
RGS9BP 0.014 0.093 -10000 0 -0.63 18 18
Metarhodopsin II/Transducin -0.022 0.077 -10000 0 -0.28 23 23
GCAP Family/Ca ++ 0.033 0.048 -10000 0 -0.36 2 2
PDE6A/B 0.022 0.079 -10000 0 -0.34 36 36
mol:Pi 0.025 0.1 -10000 0 -0.43 31 31
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.032 0.12 -10000 0 -0.43 6 6
PDE6B 0.02 0.071 -10000 0 -0.6 11 11
PDE6A 0.006 0.076 -10000 0 -0.42 26 26
PDE6G 0.014 0.084 -10000 0 -0.58 16 16
RHO -0.001 0.061 -10000 0 -0.42 16 16
PDE6 0.03 0.13 -10000 0 -0.62 13 13
GUCA1A -0.009 0.064 -10000 0 -0.42 18 18
GC2/GCAP Family 0.043 0.052 -10000 0 -0.44 1 1
GUCA1C -0.004 0.029 -10000 0 -0.42 2 2
GUCA1B 0.024 0.034 -10000 0 -0.42 5 5
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.007 0.11 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.007 0.1 0.31 16 -0.54 1 17
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.028 0.053 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.05 0.088 -10000 0 -0.35 3 3
CaM/Ca2+ -0.003 0.1 -10000 0 -10000 0 0
RAP1A 0.027 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.019 0.095 -10000 0 -0.44 1 1
AKT1 -0.003 0.11 0.36 33 -10000 0 33
MAP2K1 -0.017 0.1 0.3 31 -10000 0 31
MAP3K11 -0.018 0.11 0.3 31 -0.5 1 32
IFNGR1 0.014 0.026 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.16 0.25 -10000 0 -0.5 271 271
Rap1/GTP -0.022 0.071 -10000 0 -10000 0 0
CRKL/C3G 0.04 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.007 0.12 -10000 0 -10000 0 0
CEBPB 0.015 0.14 0.39 33 -0.45 16 49
STAT3 0.025 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.005 0.15 -10000 0 -1 9 9
STAT1 -0.017 0.11 0.3 30 -0.44 1 31
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.2 -10000 0 -0.41 257 257
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.005 0.11 0.3 29 -0.42 1 30
CEBPB/PTGES2/Cbp/p300 0.013 0.076 -10000 0 -0.38 2 2
mol:Ca2+ -0.009 0.11 -10000 0 -10000 0 0
MAPK3 -0.002 0.095 0.42 1 -0.71 3 4
STAT1 (dimer) -0.062 0.12 -10000 0 -0.51 3 3
MAPK1 -0.01 0.14 0.42 2 -0.67 21 23
JAK2 0.015 0.026 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
JAK1 0.014 0.026 -10000 0 -10000 0 0
CAMK2D 0.028 0.004 -10000 0 -10000 0 0
DAPK1 0.013 0.14 0.34 34 -0.62 22 56
SMAD7 -0.005 0.081 0.25 37 -10000 0 37
CBL/CRKL/C3G 0.003 0.11 0.3 29 -10000 0 29
PI3K -0.004 0.1 -10000 0 -10000 0 0
IFNG -0.1 0.2 -10000 0 -0.41 257 257
apoptosis -0.017 0.13 0.34 17 -0.41 54 71
CAMK2G 0.027 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.009 -10000 0 -10000 0 0
CAMK2A -0.19 0.31 -10000 0 -0.65 275 275
CAMK2B -0.059 0.2 -10000 0 -0.54 129 129
FRAP1 -0.009 0.11 0.34 33 -10000 0 33
PRKCD -0.012 0.1 0.31 26 -10000 0 26
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.05 0.088 -10000 0 -0.35 3 3
PTPN2 0.028 0.005 -10000 0 -10000 0 0
EP300 0.027 0.024 -10000 0 -0.65 1 1
IRF1 0.007 0.11 0.49 18 -0.5 2 20
STAT1 (dimer)/PIASy -0.007 0.11 0.3 29 -0.43 1 30
SOCS1 0.016 0.14 -10000 0 -1.3 9 9
mol:GDP 0.001 0.1 0.28 29 -10000 0 29
CASP1 -0.006 0.082 0.26 35 -0.26 4 39
PTGES2 0.026 0.033 -10000 0 -0.65 2 2
IRF9 0.029 0.063 0.24 34 -10000 0 34
mol:PI-3-4-5-P3 -0.014 0.091 -10000 0 -10000 0 0
RAP1/GDP -0.008 0.082 -10000 0 -10000 0 0
CBL -0.019 0.11 0.3 32 -0.35 1 33
MAP3K1 -0.017 0.11 0.3 31 -10000 0 31
PIAS1 0.028 0.003 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.05 0.088 -10000 0 -0.35 3 3
PTPN11 -0.031 0.091 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.017 0.08 -9999 0 -0.63 13 13
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.015 0.054 -9999 0 -0.3 13 13
GNAO1 0.013 0.095 -9999 0 -0.56 23 23
S1P/S1P3/G12/G13 0.03 0.079 -9999 0 -0.38 23 23
AKT1 0.012 0.11 -9999 0 -0.5 32 32
AKT3 -0.008 0.12 -9999 0 -0.7 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.08 -9999 0 -0.63 13 13
GNAI2 0.027 0.009 -9999 0 -10000 0 0
GNAI3 0.028 0.008 -9999 0 -10000 0 0
GNAI1 0.023 0.041 -9999 0 -0.65 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.008 0.16 -9999 0 -0.64 49 49
S1PR2 0.028 0.015 -9999 0 -0.42 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.016 0.094 -9999 0 -0.35 35 35
MAPK3 0.014 0.086 -9999 0 -0.45 14 14
MAPK1 0.014 0.086 -9999 0 -0.44 14 14
JAK2 -0.011 0.1 -9999 0 -0.46 17 17
CXCR4 -0.04 0.12 -9999 0 -0.42 18 18
FLT1 0.021 0.068 -9999 0 -0.48 15 15
RhoA/GDP 0.019 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.018 0.007 -9999 0 -10000 0 0
SRC 0.014 0.084 -9999 0 -0.46 12 12
S1P/S1P3/Gi 0.016 0.094 -9999 0 -0.35 35 35
RAC1 0.025 0.01 -9999 0 -10000 0 0
RhoA/GTP 0.023 0.093 -9999 0 -0.42 15 15
VEGFA -0.11 0.2 -9999 0 -0.42 269 269
S1P/S1P2/Gi 0.026 0.063 -9999 0 -0.32 13 13
VEGFR1 homodimer/VEGFA homodimer -0.064 0.16 -9999 0 -0.3 273 273
RHOA 0.026 0.008 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.025 0.15 -9999 0 -0.37 119 119
GNAQ 0.028 0.004 -9999 0 -10000 0 0
GNAZ 0.026 0.04 -9999 0 -0.65 3 3
G12/G13 0.034 0.017 -9999 0 -10000 0 0
GNA14 -0.042 0.21 -9999 0 -0.64 92 92
GNA15 0.011 0.088 -9999 0 -0.42 34 34
GNA12 0.025 0.01 -9999 0 -10000 0 0
GNA13 0.025 0.009 -9999 0 -10000 0 0
GNA11 0.022 0.065 -9999 0 -0.65 8 8
Rac1/GTP 0.018 0.086 -9999 0 -0.44 12 12
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.006 -10000 0 -10000 0 0
SMARCC1 0.008 0.048 -10000 0 -0.66 4 4
REL 0.02 0.071 -10000 0 -0.6 11 11
HDAC7 -0.13 0.1 -10000 0 -0.58 4 4
JUN 0.026 0.007 -10000 0 -10000 0 0
EP300 0.027 0.024 -10000 0 -0.65 1 1
KAT2B 0.025 0.024 -10000 0 -0.65 1 1
KAT5 0.028 0.003 -10000 0 -10000 0 0
MAPK14 -0.017 0.036 0.24 1 -0.51 3 4
FOXO1 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.11 -10000 0 -0.56 7 7
MAP2K6 -0.008 0.045 -10000 0 -0.58 4 4
BRM/BAF57 0.036 0.015 -10000 0 -10000 0 0
MAP2K4 -0.005 0.02 -10000 0 -10000 0 0
SMARCA2 0.027 0.005 -10000 0 -10000 0 0
PDE9A -0.15 0.19 -10000 0 -0.78 40 40
NCOA2 -0.004 0.14 -10000 0 -0.65 40 40
CEBPA 0.007 0.095 -10000 0 -0.42 41 41
EHMT2 0.026 0.007 -10000 0 -10000 0 0
cell proliferation -0.12 0.2 0.5 39 -0.5 53 92
NR0B1 -0.044 0.13 -10000 0 -0.42 95 95
EGR1 -0.011 0.16 -10000 0 -0.65 48 48
RXRs/9cRA 0.043 0.036 -10000 0 -0.24 11 11
AR/RACK1/Src -0.048 0.085 0.34 2 -0.48 5 7
AR/GR -0.023 0.12 0.26 26 -0.44 30 56
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.028 0.003 -10000 0 -10000 0 0
RCHY1 0.028 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.018 6 6
MAPK8 -0.019 0.041 -10000 0 -0.42 6 6
T-DHT/AR/TIF2/CARM1 -0.058 0.13 0.35 11 -0.49 37 48
SRC -0.039 0.042 -10000 0 -0.42 2 2
NR3C1 0.026 0.016 -10000 0 -0.42 1 1
KLK3 -0.059 0.19 0.4 1 -0.61 44 45
APPBP2 -0.005 0.02 -10000 0 -10000 0 0
TRIM24 0.024 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.045 0.097 0.35 13 -0.47 9 22
TMPRSS2 -0.85 0.47 -10000 0 -1.1 670 670
RXRG 0.009 0.056 -10000 0 -0.45 11 11
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.028 0.004 -10000 0 -10000 0 0
RXRB 0.026 0.007 -10000 0 -10000 0 0
CARM1 0.028 0.003 -10000 0 -10000 0 0
NR2C2 0.023 0.046 -10000 0 -0.65 4 4
KLK2 -0.052 0.16 0.39 25 -0.52 38 63
AR -0.03 0.083 -10000 0 -0.37 44 44
SENP1 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.028 0.008 -10000 0 -10000 0 0
SRY 0.001 0.005 0.014 95 -10000 0 95
GATA2 -0.027 0.18 -10000 0 -0.64 71 71
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.073 0.17 -10000 0 -0.42 171 171
T-DHT/AR/RACK1/Src -0.039 0.1 0.41 15 -0.47 5 20
positive regulation of transcription -0.027 0.18 -10000 0 -0.64 71 71
DNAJA1 -0.005 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.009 -10000 0 -10000 0 0
NCOA1 0.036 0.02 -10000 0 -10000 0 0
SPDEF -0.034 0.15 -10000 0 -0.42 111 111
T-DHT/AR/TIF2 -0.018 0.099 0.27 19 -0.45 17 36
T-DHT/AR/Hsp90 -0.045 0.097 0.35 13 -0.47 9 22
GSK3B 0.023 0.007 -10000 0 -10000 0 0
NR2C1 0.027 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.045 0.047 -10000 0 -0.44 5 5
SIRT1 0.027 0.007 -10000 0 -10000 0 0
ZMIZ2 0.026 0.011 -10000 0 -10000 0 0
POU2F1 -0.061 0.06 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.071 0.11 0.35 11 -0.49 14 25
CREBBP 0.026 0.007 -10000 0 -10000 0 0
SMARCE1 0.025 0.009 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.033 -10000 0 -0.65 2 2
SPHK1 -0.04 0.16 -10000 0 -0.42 129 129
GNAI2 0.026 0.008 -10000 0 -10000 0 0
mol:S1P 0.002 0.055 -10000 0 -0.29 3 3
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
mol:Sphinganine-1-P -0.019 0.12 0.21 42 -0.3 130 172
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.036 0.056 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
G12/G13 0.034 0.017 -10000 0 -10000 0 0
S1PR3 -0.01 0.16 -10000 0 -0.65 49 49
S1PR2 0.028 0.015 -10000 0 -0.42 1 1
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.007 0.044 -10000 0 -0.24 4 4
S1PR5 -0.036 0.16 -10000 0 -0.42 125 125
S1PR4 0.014 0.077 -10000 0 -0.42 27 27
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
S1P/S1P5/G12 -0.01 0.098 -10000 0 -0.3 14 14
S1P/S1P3/Gq -0.023 0.15 -10000 0 -0.44 75 75
S1P/S1P4/Gi 0.014 0.078 0.29 1 -0.36 13 14
GNAQ 0.028 0.004 -10000 0 -10000 0 0
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
GNA14 -0.042 0.21 -10000 0 -0.64 92 92
GNA15 0.011 0.088 -10000 0 -0.42 34 34
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.025 0.009 -10000 0 -10000 0 0
GNA11 0.022 0.065 -10000 0 -0.65 8 8
ABCC1 0.026 0.007 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.025 0.033 -10000 0 -0.65 2 2
Caspase 8 (4 units) -0.023 0.095 -10000 0 -10000 0 0
NEF -0.032 0.053 -10000 0 -0.36 3 3
NFKBIA 0.018 0.036 -10000 0 -10000 0 0
BIRC3 -0.014 0.14 -10000 0 -0.38 100 100
CYCS -0.037 0.08 -10000 0 -0.35 1 1
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CD247 -0.12 0.23 -10000 0 -0.53 207 207
MAP2K7 -0.029 0.18 0.31 3 -0.68 46 49
protein ubiquitination 0.05 0.12 0.37 56 -0.42 7 63
CRADD 0.027 0.006 -10000 0 -10000 0 0
DAXX 0.027 0.007 -10000 0 -10000 0 0
FAS 0.026 0.024 -10000 0 -0.65 1 1
BID -0.035 0.087 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.032 0.09 -10000 0 -0.38 3 3
TRADD 0.026 0.007 -10000 0 -10000 0 0
MAP3K5 0.026 0.007 -10000 0 -10000 0 0
CFLAR 0.027 0.006 -10000 0 -10000 0 0
FADD 0.028 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.032 0.09 -10000 0 -0.38 3 3
MAPK8 -0.025 0.16 0.32 7 -0.63 43 50
APAF1 0.027 0.006 -10000 0 -10000 0 0
TRAF1 0.027 0.022 -10000 0 -0.42 2 2
TRAF2 0.028 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.036 0.092 -10000 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.006 0.098 -10000 0 -0.47 17 17
CHUK 0.042 0.098 0.32 36 -0.46 6 42
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.031 -10000 0 -0.36 1 1
TCRz/NEF -0.12 0.21 -10000 0 -0.47 207 207
TNF 0.012 0.082 -10000 0 -0.46 25 25
FASLG -0.17 0.26 -10000 0 -0.51 314 314
NFKB1 0.017 0.042 -10000 0 -0.65 1 1
TNFR1A/BAG4/TNF-alpha 0.04 0.061 -10000 0 -0.42 7 7
CASP6 -0.012 0.14 -10000 0 -0.56 35 35
CASP7 -0.03 0.14 0.42 4 -0.44 29 33
RELA 0.018 0.036 -10000 0 -10000 0 0
CASP2 0.025 0.01 -10000 0 -10000 0 0
CASP3 -0.022 0.12 0.34 2 -0.59 3 5
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.028 -10000 0 -0.49 2 2
CASP8 0.027 0.006 -10000 0 -10000 0 0
CASP9 0.026 0.007 -10000 0 -10000 0 0
MAP3K14 0.02 0.082 -10000 0 -0.47 11 11
APAF-1/Caspase 9 -0.048 0.12 -10000 0 -0.47 2 2
BCL2 -0.021 0.15 0.36 9 -0.58 41 50
Presenilin action in Notch and Wnt signaling

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.029 0.086 -10000 0 -0.59 2 2
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.027 0.003 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
DTX1 -0.029 0.19 -10000 0 -0.65 72 72
LRP6/FZD1 0.035 0.026 -10000 0 -0.39 2 2
TLE1 0.027 0.004 -10000 0 -10000 0 0
AP1 -0.079 0.18 -10000 0 -0.35 235 235
NCSTN 0.027 0.007 -10000 0 -10000 0 0
ADAM10 0.027 0.023 -10000 0 -0.65 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.064 -10000 0 -0.64 2 2
NICD/RBPSUH 0.042 0.06 -10000 0 -0.65 1 1
WIF1 0.015 0.045 -10000 0 -0.45 7 7
NOTCH1 0.028 0.055 -10000 0 -0.68 1 1
PSENEN 0.028 0.002 -10000 0 -10000 0 0
KREMEN2 -0.023 0.14 -10000 0 -0.42 92 92
DKK1 0.005 0.093 -10000 0 -0.44 36 36
beta catenin/beta TrCP1 0.056 0.11 0.32 16 -0.44 4 20
APH1B 0.027 0.033 -10000 0 -0.65 2 2
APH1A 0.027 0.007 -10000 0 -10000 0 0
AXIN1 0.005 0.053 0.28 5 -0.29 2 7
CtBP/CBP/TCF1/TLE1/AES 0.02 0.05 -10000 0 -0.32 15 15
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.015 0.16 -10000 0 -0.62 57 57
JUN 0.027 0.007 -10000 0 -10000 0 0
MAP3K7 0.025 0.007 -10000 0 -10000 0 0
CTNNB1 0.05 0.12 0.31 26 -0.43 6 32
MAPK3 0.026 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.42 15 15
HNF1A 0.014 0.091 -10000 0 -0.65 16 16
CTBP1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.018 0.1 -10000 0 -0.79 10 10
NKD1 -0.14 0.29 -10000 0 -0.65 213 213
FZD1 0.023 0.029 -10000 0 -0.54 2 2
NOTCH1 precursor/Deltex homolog 1 0.009 0.12 -10000 0 -0.66 2 2
apoptosis -0.078 0.18 -10000 0 -0.35 235 235
Delta 1/NOTCHprecursor 0.028 0.085 -10000 0 -0.58 2 2
DLL1 0.005 0.11 -10000 0 -0.57 31 31
PPARD -0.017 0.2 -10000 0 -0.76 58 58
Gamma Secretase 0.076 0.033 -10000 0 -0.36 2 2
APC 0.002 0.065 0.28 5 -0.42 7 12
DVL1 0.02 0.029 -10000 0 -0.45 2 2
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.008 0.1 -10000 0 -0.36 12 12
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.02 0.095 -10000 0 -0.85 6 6
WNT1 -0.005 0.11 -10000 0 -0.42 57 57
Axin1/APC/beta catenin 0.067 0.1 0.38 33 -0.44 6 39
DKK2 0.002 0.11 -10000 0 -0.49 42 42
NOTCH1 precursor/DVL1 0.033 0.086 -10000 0 -0.52 7 7
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.026 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.12 -10000 0 -0.67 2 2
PPP2R5D 0.068 0.17 0.34 187 -0.47 29 216
MAPK1 0.027 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.038 0.077 -10000 0 -0.39 2 2
RBPJ 0.028 0.004 -10000 0 -10000 0 0
CREBBP 0.029 0.009 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.04 0.076 -10000 0 -0.38 23 23
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.082 0.32 8 -0.37 2 10
AP1 0.007 0.12 -10000 0 -0.36 69 69
mol:PIP3 0.001 0.062 -10000 0 -0.47 1 1
AKT1 0.042 0.097 0.37 26 -0.4 2 28
PTK2B 0.009 0.073 0.3 4 -0.38 10 14
RHOA 0.01 0.077 0.21 24 -0.36 8 32
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.064 0.35 5 -0.36 2 7
MAGI3 0.025 0.033 -10000 0 -0.65 2 2
RELA 0.028 0.003 -10000 0 -10000 0 0
apoptosis 0.009 0.07 -10000 0 -0.34 30 30
HRAS/GDP 0.02 0.011 -10000 0 -0.29 1 1
positive regulation of microtubule depolymerization 0.024 0.1 0.34 33 -0.34 20 53
NF kappa B1 p50/RelA 0.016 0.08 0.24 3 -0.48 2 5
endothelial cell migration 0.009 0.081 -10000 0 -0.4 30 30
ADCY4 0.009 0.096 -10000 0 -0.46 26 26
ADCY5 0.001 0.11 -10000 0 -0.44 35 35
ADCY6 0.012 0.09 -10000 0 -0.45 24 24
ADCY7 0.009 0.09 -10000 0 -0.44 25 25
ADCY1 -0.017 0.12 -10000 0 -0.47 37 37
ADCY2 -0.012 0.1 -10000 0 -0.44 34 34
ADCY3 0.012 0.093 -10000 0 -0.47 24 24
ADCY8 -0.001 0.093 -10000 0 -0.45 25 25
ADCY9 0.012 0.089 -10000 0 -0.45 24 24
GSK3B 0.016 0.077 0.26 21 -0.36 10 31
arachidonic acid secretion 0.011 0.088 -10000 0 -0.41 26 26
GNG2 0.027 0.005 -10000 0 -10000 0 0
TRIP6 0.023 0.025 -10000 0 -0.44 2 2
GNAO1 0.002 0.091 -10000 0 -0.37 44 44
HRAS 0.027 0.015 -10000 0 -0.42 1 1
NFKBIA 0.017 0.091 0.41 14 -0.36 6 20
GAB1 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.017 0.23 -10000 0 -0.85 59 59
JUN 0.027 0.007 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.037 0.023 -10000 0 -0.33 2 2
TIAM1 -0.037 0.27 -10000 0 -1 61 61
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.009 0.063 0.38 4 -0.37 2 6
PLCB3 0.032 0.041 -10000 0 -0.38 1 1
FOS -0.015 0.16 -10000 0 -0.62 57 57
positive regulation of mitosis 0.011 0.088 -10000 0 -0.41 26 26
LPA/LPA1-2-3 0.036 0.082 -10000 0 -0.38 26 26
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
stress fiber formation 0.018 0.074 0.32 4 -0.38 9 13
GNAZ 0.01 0.08 -10000 0 -0.4 29 29
EGFR/PI3K-beta/Gab1 0.011 0.068 -10000 0 -0.49 1 1
positive regulation of dendritic cell cytokine production 0.035 0.081 -10000 0 -0.37 26 26
LPA/LPA2/MAGI-3 0.036 0.03 -10000 0 -0.36 3 3
ARHGEF1 0.046 0.1 0.36 39 -0.35 20 59
GNAI2 0.011 0.072 -10000 0 -0.4 23 23
GNAI3 0.011 0.076 -10000 0 -0.41 25 25
GNAI1 0.009 0.075 -10000 0 -0.4 24 24
LPA/LPA3 0.014 0.038 -10000 0 -0.28 12 12
LPA/LPA2 0.022 0.019 -10000 0 -0.23 3 3
LPA/LPA1 0.011 0.088 -10000 0 -0.45 29 29
HB-EGF/EGFR -0.07 0.14 -10000 0 -0.48 11 11
HBEGF -0.096 0.15 -10000 0 -0.3 320 320
mol:DAG 0.009 0.063 0.38 4 -0.37 2 6
cAMP biosynthetic process 0.014 0.13 0.37 40 -0.42 33 73
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
SRC 0.027 0.007 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN 0.017 0.091 0.39 15 -0.4 5 20
GNAQ 0.017 0.03 -10000 0 -0.3 4 4
LPAR2 0.028 0.015 -10000 0 -0.42 1 1
LPAR3 0.003 0.051 -10000 0 -0.43 10 10
LPAR1 0.012 0.11 -10000 0 -0.59 26 26
IL8 -0.034 0.13 0.37 3 -0.51 25 28
PTK2 0.012 0.069 -10000 0 -0.36 22 22
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
CASP3 0.009 0.07 -10000 0 -0.34 30 30
EGFR 0.017 0.061 -10000 0 -0.45 14 14
PLCG1 0.001 0.056 -10000 0 -0.3 9 9
PLD2 0.01 0.07 -10000 0 -0.36 22 22
G12/G13 0.036 0.073 -10000 0 -0.38 20 20
PI3K-beta 0.006 0.065 -10000 0 -0.46 2 2
cell migration 0.017 0.076 -10000 0 -0.26 44 44
SLC9A3R2 0.026 0.024 -10000 0 -0.65 1 1
PXN 0.018 0.075 0.32 4 -0.38 9 13
HRAS/GTP 0.004 0.086 -10000 0 -0.42 26 26
RAC1 0.025 0.01 -10000 0 -10000 0 0
MMP9 -0.14 0.22 -10000 0 -0.42 331 331
PRKCE 0.026 0.024 -10000 0 -0.65 1 1
PRKCD 0.013 0.084 0.37 21 -0.4 1 22
Gi(beta/gamma) 0.015 0.092 -10000 0 -0.44 27 27
mol:LPA 0.001 0.021 -10000 0 -0.25 4 4
TRIP6/p130 Cas/FAK1/Paxillin 0.035 0.079 -10000 0 -0.39 6 6
MAPKKK cascade 0.011 0.088 -10000 0 -0.41 26 26
contractile ring contraction involved in cytokinesis 0.013 0.083 0.25 16 -0.35 9 25
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.021 0.12 -10000 0 -0.35 95 95
GNA15 0.011 0.047 -10000 0 -0.32 7 7
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.025 0.009 -10000 0 -10000 0 0
MAPT 0.024 0.1 0.34 32 -0.35 20 52
GNA11 0.014 0.043 -10000 0 -0.34 10 10
Rac1/GTP -0.019 0.24 -10000 0 -0.91 58 58
MMP2 0.009 0.082 -10000 0 -0.41 30 30
IL6-mediated signaling 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
BCL2L1 -0.049 0.19 0.58 4 -0.61 5 9
CRP -0.074 0.21 -10000 0 -0.63 16 16
cell cycle arrest -0.07 0.19 -10000 0 -0.61 14 14
TIMP1 -0.057 0.2 -10000 0 -0.56 19 19
IL6ST -0.029 0.19 -10000 0 -0.65 72 72
Rac1/GDP -0.069 0.15 -10000 0 -0.45 40 40
AP1 -0.001 0.16 -10000 0 -0.67 19 19
GAB2 0.028 0.015 -10000 0 -0.42 1 1
TNFSF11 -0.071 0.2 0.63 1 -0.64 13 14
HSP90B1 0.027 0.049 -10000 0 -10000 0 0
GAB1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.017 0.11 -10000 0 -0.55 13 13
AKT1 0.041 0.027 -10000 0 -10000 0 0
FOXO1 0.045 0.032 -10000 0 -10000 0 0
MAP2K6 -0.026 0.12 -10000 0 -0.48 22 22
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.071 0.15 -10000 0 -0.52 18 18
MITF -0.039 0.12 -10000 0 -0.44 34 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.003 -10000 0 -10000 0 0
A2M 0.021 0.12 -10000 0 -1.2 7 7
CEBPB 0.019 0.07 -10000 0 -0.41 22 22
GRB2/SOS1/GAB family/SHP2 0.002 0.11 -10000 0 -0.65 16 16
STAT3 -0.081 0.19 -10000 0 -0.64 15 15
STAT1 -0.011 0.13 -10000 0 -0.68 30 30
CEBPD -0.053 0.18 0.52 1 -0.61 5 6
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.041 0.012 -10000 0 -10000 0 0
JUN 0.026 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.021 0.13 -10000 0 -0.45 25 25
MAPK11 -0.018 0.11 -10000 0 -0.54 16 16
STAT3 (dimer)/FOXO1 -0.039 0.16 -10000 0 -0.54 5 5
GRB2/SOS1/GAB family 0.001 0.14 -10000 0 -0.5 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.036 0.14 -10000 0 -0.48 42 42
GRB2 0.025 0.009 -10000 0 -10000 0 0
JAK2 0.028 0.005 -10000 0 -10000 0 0
LBP -0.17 0.37 0.52 3 -0.89 152 155
PIK3R1 0.029 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.009 -10000 0 -10000 0 0
MYC -0.057 0.19 0.52 1 -0.72 6 7
FGG -0.09 0.22 -10000 0 -0.6 24 24
macrophage differentiation -0.07 0.19 -10000 0 -0.61 14 14
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.16 -10000 0 -0.38 99 99
JUNB -0.055 0.18 0.44 1 -0.72 7 8
FOS -0.015 0.16 -10000 0 -0.62 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.13 -10000 0 -0.43 42 42
STAT1/PIAS1 -0.032 0.13 -10000 0 -0.45 21 21
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.028 -10000 0 -10000 0 0
STAT3 (dimer) -0.075 0.19 -10000 0 -0.64 14 14
PRKCD -0.067 0.17 0.39 8 -0.52 17 25
IL6R 0.026 0.033 -10000 0 -0.65 2 2
SOCS3 -0.006 0.14 -10000 0 -0.83 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 0.014 0.13 -10000 0 -0.42 72 72
Rac1/GTP -0.071 0.15 -10000 0 -0.48 32 32
HCK -0.006 0.12 -10000 0 -0.42 63 63
MAPKKK cascade 0.009 0.13 -10000 0 -0.58 30 30
bone resorption -0.067 0.2 0.55 2 -0.6 15 17
IRF1 -0.049 0.19 0.61 2 -0.64 3 5
mol:GDP -0.083 0.15 -10000 0 -0.43 63 63
SOS1 0.027 0.006 -10000 0 -10000 0 0
VAV1 -0.084 0.15 -10000 0 -0.44 63 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.028 0.17 -10000 0 -0.66 31 31
PTPN11 0.013 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.026 0.16 -10000 0 -0.41 119 119
gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.13 -10000 0 -0.42 71 71
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.13 -10000 0 -0.42 72 72
IL6 -0.054 0.2 -10000 0 -0.56 117 117
PIAS3 0.027 0.007 -10000 0 -10000 0 0
PTPRE 0.025 0.02 -10000 0 -0.39 1 1
PIAS1 0.028 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.036 0.12 -10000 0 -0.34 73 73
LMO4 0.026 0.013 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.075 0.19 -10000 0 -0.62 15 15
MCL1 0.05 0.041 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.024 0.1 -9999 0 -0.43 37 37
E-cadherin/beta catenin 0.012 0.11 -9999 0 -0.49 40 40
CTNNB1 0.026 0.008 -9999 0 -10000 0 0
JUP 0.023 0.041 -9999 0 -0.65 3 3
CDH1 -0.005 0.14 -9999 0 -0.65 40 40
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.095 0.094 -10000 0 -0.47 4 4
epithelial cell differentiation -0.076 0.12 -10000 0 -0.41 26 26
ITCH 0.057 0.023 -10000 0 -10000 0 0
WWP1 -0.082 0.077 -10000 0 -10000 0 0
FYN 0.026 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.061 -10000 0 -0.45 14 14
PRL -0.005 0.02 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.097 0.33 7 -0.42 11 18
PTPRZ1 -0.007 0.1 -10000 0 -0.58 26 26
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.096 -10000 0 -0.43 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.082 0.097 -10000 0 -0.44 32 32
ADAM17 0.057 0.023 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.11 0.098 -10000 0 -0.33 6 6
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.11 -10000 0 -0.42 33 33
NCOR1 0.025 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.074 0.096 -10000 0 -0.46 20 20
GRIN2B -0.073 0.092 -10000 0 -0.45 19 19
ErbB4/ErbB2/betacellulin -0.094 0.13 -10000 0 -0.44 80 80
STAT1 0.026 0.022 -10000 0 -0.42 2 2
HBEGF 0.023 0.048 -10000 0 -0.59 5 5
PRLR -0.083 0.25 -10000 0 -0.65 143 143
E4ICDs/ETO2 -0.096 0.09 -10000 0 -0.38 4 4
axon guidance -0.047 0.064 -10000 0 -10000 0 0
NEDD4 0.059 0.031 -10000 0 -0.63 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.053 0.2 -10000 0 -0.49 143 143
CBFA2T3 0.025 0.027 -10000 0 -0.42 3 3
ErbB4/ErbB2/HBEGF -0.055 0.073 -10000 0 -0.43 3 3
MAPK3 -0.059 0.085 -10000 0 -0.41 16 16
STAT1 (dimer) -0.093 0.092 -10000 0 -0.43 2 2
MAPK1 -0.059 0.086 -10000 0 -0.42 12 12
JAK2 0.028 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.069 0.098 -10000 0 -0.46 22 22
NRG1 0.015 0.1 -10000 0 -0.47 34 34
NRG3 -0.005 0.12 -10000 0 -0.48 55 55
NRG2 0.001 0.11 -10000 0 -0.43 49 49
NRG4 -0.015 0.14 -10000 0 -0.52 63 63
heart development -0.047 0.064 -10000 0 -10000 0 0
neural crest cell migration -0.069 0.097 -10000 0 -0.45 22 22
ERBB2 0.034 0.024 -10000 0 -0.48 1 1
WWOX/E4ICDs -0.094 0.089 -10000 0 -0.39 2 2
SHC1 0.026 0.016 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.099 0.12 -10000 0 -0.43 46 46
apoptosis 0.095 0.11 0.49 34 -10000 0 34
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.1 -10000 0 -0.37 30 30
ErbB4/ErbB2/epiregulin -0.087 0.1 -10000 0 -0.44 2 2
ErbB4/ErbB4/betacellulin/betacellulin -0.14 0.15 -10000 0 -0.51 94 94
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.16 -10000 0 -0.47 107 107
MDM2 -0.09 0.088 0.26 5 -0.4 1 6
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.056 0.087 -10000 0 -0.41 30 30
STAT5A -0.037 0.06 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.074 0.1 -10000 0 -0.48 22 22
DLG4 0.025 0.009 -10000 0 -10000 0 0
GRB2/SHC 0.036 0.018 -10000 0 -0.29 1 1
E4ICDs/TAB2/NCoR1 -0.085 0.081 -10000 0 -0.37 1 1
STAT5A (dimer) -0.076 0.14 -10000 0 -0.44 26 26
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.035 0.069 0.33 2 -10000 0 2
LRIG1 0.026 0.007 -10000 0 -10000 0 0
EREG -0.053 0.17 -10000 0 -0.42 153 153
BTC -0.045 0.21 -10000 0 -0.65 94 94
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.047 0.064 -10000 0 -10000 0 0
ERBB4 -0.11 0.098 -10000 0 -0.33 6 6
STAT5B 0.025 0.009 -10000 0 -10000 0 0
YAP1 -0.022 0.059 -10000 0 -0.53 9 9
GRB2 0.025 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.078 0.1 -10000 0 -0.46 27 27
glial cell differentiation 0.085 0.081 0.37 1 -10000 0 1
WWOX 0.026 0.017 -10000 0 -0.42 1 1
cell proliferation -0.085 0.16 0.54 2 -0.6 28 30
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.005 0.14 -9999 0 -0.59 12 12
Syndecan-3/Neurocan 0 0.1 -9999 0 -0.35 55 55
POMC 0.02 0.065 -9999 0 -0.61 9 9
EGFR 0.017 0.061 -9999 0 -0.45 14 14
Syndecan-3/EGFR 0.003 0.097 -9999 0 -0.35 52 52
AGRP 0.011 0.03 -9999 0 -0.42 2 2
NCSTN 0.027 0.007 -9999 0 -10000 0 0
PSENEN 0.028 0.002 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.033 -9999 0 -0.65 2 2
APH1A 0.027 0.007 -9999 0 -10000 0 0
NCAN -0.003 0.088 -9999 0 -0.42 35 35
long-term memory 0.027 0.091 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.012 0.12 -9999 0 -0.37 69 69
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.011 -9999 0 -10000 0 0
FYN 0.026 0.007 -9999 0 -10000 0 0
limb bud formation -0.005 0.091 -9999 0 -0.36 53 53
MC4R -0.009 0.046 -9999 0 -0.42 9 9
SRC 0.027 0.007 -9999 0 -10000 0 0
PTN -0.027 0.18 -9999 0 -0.63 69 69
FGFR/FGF/Syndecan-3 -0.006 0.092 -9999 0 -0.36 53 53
neuron projection morphogenesis -0.009 0.14 -9999 0 -0.56 15 15
Syndecan-3/AgRP 0.007 0.092 -9999 0 -0.35 51 51
Syndecan-3/AgRP/MC4R 0.016 0.096 -9999 0 -0.35 37 37
Fyn/Cortactin 0.039 0.011 -9999 0 -10000 0 0
SDC3 -0.006 0.092 -9999 0 -0.37 53 53
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.012 0.12 -9999 0 -0.36 69 69
IL8 -0.017 0.15 -9999 0 -0.48 78 78
Syndecan-3/Fyn/Cortactin 0.028 0.093 -9999 0 -10000 0 0
Syndecan-3/CASK -0.007 0.089 -9999 0 -0.35 55 55
alpha-MSH/MC4R 0.025 0.06 -9999 0 -0.38 18 18
Gamma Secretase 0.076 0.033 -9999 0 -0.36 2 2
TCGA08_rtk_signaling

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
PDGFRA -0.24 0.33 -10000 0 -0.65 348 348
HRAS 0.027 0.015 -10000 0 -0.42 1 1
EGFR 0.017 0.061 -10000 0 -0.45 14 14
AKT 0.03 0.1 0.28 57 -0.39 1 58
FOXO3 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.027 0.006 -10000 0 -10000 0 0
AKT3 0.026 0.024 -10000 0 -0.65 1 1
FOXO4 0.028 0.001 -10000 0 -10000 0 0
MET 0.021 0.04 -10000 0 -0.42 7 7
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
NRAS 0.027 0.007 -10000 0 -10000 0 0
PIK3CG 0.017 0.066 -10000 0 -0.51 13 13
PIK3R3 0.026 0.024 -10000 0 -0.65 1 1
PIK3R2 0.028 0.003 -10000 0 -10000 0 0
NF1 0.025 0.009 -10000 0 -10000 0 0
RAS -0.031 0.081 -10000 0 -0.27 9 9
ERBB2 0.024 0.025 -10000 0 -0.65 1 1
proliferation/survival/translation -0.044 0.048 0.25 4 -0.24 11 15
PI3K -0.001 0.11 0.29 52 -0.23 11 63
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.007 -10000 0 -10000 0 0
FOXO 0.059 0.082 0.27 65 -10000 0 65
AKT2 0.028 0.003 -10000 0 -10000 0 0
PTEN 0.027 0.007 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.026 0.054 -10000 0 -0.44 1 1
adherens junction organization 0.005 0.092 0.25 10 -0.37 11 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.063 -10000 0 -0.5 1 1
FMN1 -0.011 0.11 -10000 0 -0.37 37 37
mol:IP3 0.019 0.049 -10000 0 -0.51 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.005 0.082 -10000 0 -0.38 7 7
CTNNB1 0.026 0.009 -10000 0 -10000 0 0
AKT1 0.026 0.062 0.27 4 -0.4 1 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.021 0.13 -10000 0 -0.52 38 38
CTNND1 0.03 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.074 -10000 0 -0.48 3 3
VASP 0.005 0.079 -10000 0 -0.58 2 2
ZYX 0.002 0.076 -10000 0 -0.58 2 2
JUB 0.003 0.078 -10000 0 -0.37 7 7
EGFR(dimer) 0.013 0.088 -10000 0 -0.47 5 5
E-cadherin/beta catenin-gamma catenin 0.024 0.097 -10000 0 -0.42 37 37
mol:PI-3-4-5-P3 0.037 0.07 0.26 7 -0.44 2 9
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.072 0.26 7 -0.46 2 9
FYN -0.2 0.14 -10000 0 -0.42 92 92
mol:Ca2+ 0.019 0.049 -10000 0 -0.5 1 1
JUP 0.023 0.041 -10000 0 -0.65 3 3
PIK3R1 0.03 0.008 -10000 0 -10000 0 0
mol:DAG 0.019 0.049 -10000 0 -0.51 1 1
CDH1 -0.004 0.14 -10000 0 -0.65 40 40
RhoA/GDP 0.035 0.068 -10000 0 -0.5 1 1
establishment of polarity of embryonic epithelium 0.005 0.077 -10000 0 -0.56 2 2
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
EGFR 0.017 0.061 -10000 0 -0.45 14 14
CASR -0.23 0.15 0.23 2 -0.33 579 581
RhoA/GTP 0.03 0.049 -10000 0 -0.46 1 1
AKT2 0.027 0.065 0.26 6 -0.55 1 7
actin cable formation -0.01 0.11 -10000 0 -0.5 10 10
apoptosis -0.032 0.083 0.48 1 -0.39 22 23
CTNNA1 0.029 0.01 -10000 0 -10000 0 0
mol:GDP 0.012 0.056 -10000 0 -0.41 3 3
PIP5K1A 0.008 0.074 -10000 0 -0.49 3 3
PLCG1 0.02 0.05 -10000 0 -0.53 1 1
Rac1/GTP 0.021 0.086 -10000 0 -0.47 4 4
homophilic cell adhesion 0.002 0.007 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.029 -10000 0 -0.64 1 1
HSPA8 0.028 0.023 -10000 0 -0.63 1 1
SMAD3/SMAD4/ER alpha 0.053 0.094 -10000 0 -0.43 20 20
AKT1 0.029 0.009 -10000 0 -10000 0 0
GSC 0.001 0.093 -10000 0 -0.61 2 2
NKX2-5 0.002 0.002 -10000 0 -10000 0 0
muscle cell differentiation -0.054 0.057 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.092 0.068 -10000 0 -10000 0 0
SMAD4 0.035 0.034 -10000 0 -10000 0 0
CBFB 0.026 0.007 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.044 0.04 -10000 0 -0.41 1 1
SMAD3/SMAD4/VDR 0.079 0.056 -10000 0 -10000 0 0
MYC 0.012 0.076 -10000 0 -0.43 25 25
CDKN2B 0.024 0.093 -10000 0 -0.53 3 3
AP1 0.04 0.093 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.026 0.097 -10000 0 -0.38 30 30
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.036 0.037 -10000 0 -10000 0 0
SP3 0.029 0.007 -10000 0 -10000 0 0
CREB1 0.027 0.006 -10000 0 -10000 0 0
FOXH1 -0.006 0.12 -10000 0 -0.42 66 66
SMAD3/SMAD4/GR 0.068 0.049 -10000 0 -10000 0 0
GATA3 -0.33 0.33 -10000 0 -0.64 458 458
SKI/SIN3/HDAC complex/NCoR1 0.028 0.064 0.2 1 -0.43 13 14
MEF2C/TIF2 0.019 0.12 0.32 2 -0.51 23 25
endothelial cell migration 0.053 0.26 1.3 31 -10000 0 31
MAX 0.03 0.014 -10000 0 -10000 0 0
RBBP7 0.028 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.024 -10000 0 -0.65 1 1
RUNX2 0.009 0.088 -10000 0 -0.42 35 35
RUNX3 -0.11 0.2 -10000 0 -0.42 271 271
RUNX1 -0.006 0.12 -10000 0 -0.42 65 65
CTBP1 0.028 0.004 -10000 0 -10000 0 0
NR3C1 0.029 0.021 -10000 0 -0.42 1 1
VDR 0.024 0.046 -10000 0 -0.65 4 4
CDKN1A 0.04 0.087 -10000 0 -10000 0 0
KAT2B 0.024 0.025 -10000 0 -0.65 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.048 0.09 -10000 0 -0.33 10 10
DCP1A 0.026 0.008 -10000 0 -10000 0 0
SKI 0.027 0.007 -10000 0 -10000 0 0
SERPINE1 -0.054 0.27 -10000 0 -1.4 31 31
SMAD3/SMAD4/ATF2 0.063 0.048 -10000 0 -0.43 1 1
SMAD3/SMAD4/ATF3 0.051 0.088 -10000 0 -0.44 20 20
SAP30 -0.004 0.11 -10000 0 -0.42 62 62
Cbp/p300/PIAS3 0.041 0.037 -10000 0 -0.41 1 1
JUN 0.029 0.09 0.3 5 -0.38 1 6
SMAD3/SMAD4/IRF7 0.064 0.057 -10000 0 -0.44 1 1
TFE3 0.027 0.023 -10000 0 -10000 0 0
COL1A2 0 0.11 0.48 4 -10000 0 4
mesenchymal cell differentiation -0.05 0.075 0.35 4 -10000 0 4
DLX1 -0.16 0.22 -10000 0 -0.42 355 355
TCF3 0.028 0.003 -10000 0 -10000 0 0
FOS -0.008 0.16 -10000 0 -0.61 57 57
SMAD3/SMAD4/Max 0.071 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.046 0.028 -10000 0 -0.41 1 1
ZBTB17 0.023 0.032 -10000 0 -0.64 2 2
LAMC1 0.04 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.065 0.045 -10000 0 -10000 0 0
IRF7 0.023 0.051 -10000 0 -0.44 10 10
ESR1 0.006 0.11 -10000 0 -0.56 32 32
HNF4A -0.065 0.23 -10000 0 -0.65 118 118
MEF2C 0.025 0.076 0.44 5 -0.38 1 6
SMAD2-3/SMAD4 0.074 0.045 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.046 0.029 -10000 0 -0.41 1 1
IGHV3OR16-13 -0.008 0.049 -10000 0 -0.35 10 10
TGIF2/HDAC complex 0.027 0.007 -10000 0 -10000 0 0
CREBBP 0.024 0.012 -10000 0 -10000 0 0
SKIL 0.027 0.006 -10000 0 -10000 0 0
HDAC1 0.027 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.007 -10000 0 -10000 0 0
SNIP1 0.027 0.007 -10000 0 -10000 0 0
GCN5L2 -0.002 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.072 0.05 -10000 0 -10000 0 0
MSG1/HSC70 0.039 0.037 -10000 0 -0.31 9 9
SMAD2 0.031 0.017 -10000 0 -10000 0 0
SMAD3 0.035 0.033 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.042 0.03 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.054 0.29 3 -0.44 3 6
NCOR1 0.025 0.009 -10000 0 -10000 0 0
NCOA2 -0.004 0.14 -10000 0 -0.65 40 40
NCOA1 0.027 0.006 -10000 0 -10000 0 0
MYOD/E2A 0.026 0.055 -10000 0 -0.29 25 25
SMAD2-3/SMAD4/SP1/MIZ-1 0.096 0.073 -10000 0 -0.38 1 1
IFNB1 0.028 0.05 -10000 0 -0.39 2 2
SMAD3/SMAD4/MEF2C 0.059 0.079 -10000 0 -10000 0 0
CITED1 0.022 0.046 -10000 0 -0.42 9 9
SMAD2-3/SMAD4/ARC105 0.089 0.041 -10000 0 -10000 0 0
RBL1 0.027 0.007 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.045 0.04 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.062 0.15 -10000 0 -0.46 28 28
SMAD7 0.061 0.082 -10000 0 -10000 0 0
MYC/MIZ-1 0.024 0.062 -10000 0 -0.32 26 26
SMAD3/SMAD4 0.004 0.1 -10000 0 -0.45 24 24
IL10 -0.19 0.22 -10000 0 -0.52 64 64
PIASy/HDAC complex 0.03 0.009 -10000 0 -10000 0 0
PIAS3 0.025 0.011 -10000 0 -10000 0 0
CDK2 0.025 0.011 -10000 0 -10000 0 0
IL5 -0.18 0.2 -10000 0 -0.44 73 73
CDK4 0.024 0.012 -10000 0 -10000 0 0
PIAS4 0.03 0.009 -10000 0 -10000 0 0
ATF3 0.009 0.11 -10000 0 -0.61 24 24
SMAD3/SMAD4/SP1 0.065 0.07 -10000 0 -10000 0 0
FOXG1 -0.011 0.082 -10000 0 -0.42 32 32
FOXO3 0.021 0.01 -10000 0 -10000 0 0
FOXO1 0.021 0.009 -10000 0 -10000 0 0
FOXO4 0.022 0.008 -10000 0 -10000 0 0
heart looping 0.025 0.075 0.44 5 -0.38 1 6
CEBPB 0.016 0.07 -10000 0 -0.42 22 22
SMAD3/SMAD4/DLX1 -0.065 0.16 -10000 0 -0.34 18 18
MYOD1 -0.017 0.071 -10000 0 -0.42 25 25
SMAD3/SMAD4/HNF4 -0.001 0.18 -10000 0 -0.44 115 115
SMAD3/SMAD4/GATA3 -0.19 0.24 -10000 0 -0.42 445 445
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.025 0.15 -10000 0 -0.42 26 26
SMAD3/SMAD4/SP1-3 0.08 0.068 -10000 0 -10000 0 0
MED15 0.027 0.005 -10000 0 -10000 0 0
SP1 0.024 0.036 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.051 0.082 -10000 0 -0.3 4 4
ITGB5 0.046 0.063 0.42 4 -10000 0 4
TGIF/SIN3/HDAC complex/CtBP 0.031 0.054 -10000 0 -0.5 6 6
SMAD3/SMAD4/AR 0.039 0.13 -10000 0 -0.44 50 50
AR -0.012 0.16 -10000 0 -0.64 53 53
negative regulation of cell growth 0.039 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.052 0.068 -10000 0 -10000 0 0
E2F5 0.027 0.024 -10000 0 -0.65 1 1
E2F4 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.062 0.088 -10000 0 -0.62 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.046 0.026 -10000 0 -10000 0 0
TFDP1 0.027 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.062 0.098 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX2 0.05 0.076 -10000 0 -0.35 4 4
TGIF2 0.027 0.007 -10000 0 -10000 0 0
TGIF1 0.028 0.005 -10000 0 -10000 0 0
ATF2 0.026 0.024 -10000 0 -0.65 1 1
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.02 0.057 -10000 0 -0.45 12 12
EFNB1 -0.027 0.11 -10000 0 -0.3 96 96
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.095 -10000 0 -0.41 9 9
Ephrin B2/EPHB1-2 0.037 0.066 -10000 0 -0.43 11 11
neuron projection morphogenesis 0.013 0.084 -10000 0 -0.39 10 10
Ephrin B1/EPHB1-2/Tiam1 0.013 0.11 -10000 0 -0.44 18 18
DNM1 -0.038 0.16 -10000 0 -0.42 129 129
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.001 0.12 -10000 0 -0.56 32 32
YES1 -0.011 0.16 -10000 0 -0.81 32 32
Ephrin B1/EPHB1-2/NCK2 0.015 0.11 -10000 0 -0.44 16 16
PI3K 0.022 0.12 -10000 0 -0.59 30 30
mol:GDP 0.012 0.11 -10000 0 -0.43 18 18
ITGA2B 0.015 0.068 -10000 0 -0.46 17 17
endothelial cell proliferation 0.031 0.014 -10000 0 -10000 0 0
FYN -0.014 0.16 -10000 0 -0.83 32 32
MAP3K7 -0.012 0.12 -10000 0 -0.63 29 29
FGR -0.012 0.16 -10000 0 -0.82 32 32
TIAM1 0.026 0.024 -10000 0 -0.65 1 1
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
RGS3 0.028 0.004 -10000 0 -10000 0 0
cell adhesion 0.003 0.13 -10000 0 -0.58 28 28
LYN -0.01 0.16 -10000 0 -0.81 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.14 -10000 0 -0.75 32 32
Ephrin B1/EPHB1-2 -0.015 0.13 -10000 0 -0.67 31 31
SRC -0.009 0.16 -10000 0 -0.79 32 32
ITGB3 0.008 0.1 -10000 0 -0.61 24 24
EPHB1 0.015 0.083 -10000 0 -0.53 19 19
EPHB4 0.025 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.031 0.015 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.017 0.097 -10000 0 -0.41 39 39
BLK -0.012 0.16 -10000 0 -0.8 32 32
HCK -0.012 0.16 -10000 0 -0.8 32 32
regulation of stress fiber formation -0.013 0.11 0.43 16 -10000 0 16
MAPK8 0.001 0.12 0.37 3 -0.59 25 28
Ephrin B1/EPHB1-2/RGS3 0.014 0.11 -10000 0 -0.43 17 17
endothelial cell migration 0.011 0.12 0.42 6 -0.55 27 33
NCK2 0.027 0.006 -10000 0 -10000 0 0
PTPN13 0.008 0.13 -10000 0 -0.76 23 23
regulation of focal adhesion formation -0.013 0.11 0.43 16 -10000 0 16
chemotaxis -0.013 0.11 0.43 17 -10000 0 17
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.021 0.09 -10000 0 -0.4 10 10
angiogenesis -0.015 0.13 -10000 0 -0.66 32 32
LCK -0.014 0.16 -10000 0 -0.82 32 32
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.022 0.042 -10000 0 -0.58 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.016 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.028 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.009 -10000 0 -10000 0 0
FYN 0.026 0.007 -10000 0 -10000 0 0
MAP3K12 0.026 0.024 -10000 0 -0.65 1 1
FGR 0.021 0.053 -10000 0 -0.44 11 11
p38 alpha/TAB1 -0.038 0.14 -10000 0 -0.58 46 46
PRKG1 -0.044 0.21 -10000 0 -0.64 92 92
DUSP8 0.026 0.031 -10000 0 -0.5 3 3
PGK/cGMP/p38 alpha -0.016 0.16 -10000 0 -0.51 61 61
apoptosis -0.036 0.13 -10000 0 -0.55 45 45
RAL/GTP 0.032 0.014 -10000 0 -10000 0 0
LYN 0.026 0.024 -10000 0 -0.65 1 1
DUSP1 0.025 0.036 -10000 0 -0.57 3 3
PAK1 0.028 0.003 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.059 0.029 -10000 0 -10000 0 0
TRAF6 0.028 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
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 0.025 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.015 -10000 0 -10000 0 0
MAPK11 0.047 0.18 0.42 73 -0.48 42 115
BLK -0.001 0.1 -10000 0 -0.42 48 48
HCK -0.006 0.12 -10000 0 -0.42 63 63
MAP2K3 0.025 0.009 -10000 0 -10000 0 0
DUSP16 0.027 0.006 -10000 0 -10000 0 0
DUSP10 0.021 0.052 -10000 0 -0.42 12 12
TRAF6/MEKK3 0.032 0.012 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.19 0.37 69 -0.64 45 114
positive regulation of innate immune response 0.051 0.21 0.47 73 -0.65 41 114
LCK 0.003 0.1 -10000 0 -0.44 44 44
p38alpha-beta/MKP7 0.043 0.19 0.44 42 -0.62 40 82
p38alpha-beta/MKP5 0.06 0.2 0.46 71 -0.61 40 111
PGK/cGMP -0.033 0.15 -10000 0 -0.48 92 92
PAK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.054 0.2 0.47 60 -0.62 40 100
CDC42 0.027 0.007 -10000 0 -10000 0 0
RALB 0.027 0.006 -10000 0 -10000 0 0
RALA 0.025 0.009 -10000 0 -10000 0 0
PAK3 0.014 0.063 -10000 0 -0.43 16 16
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.023 0.18 0.31 10 -0.59 50 60
MAP3K8 0.025 0.023 -10000 0 -0.42 2 2
FOS 0.019 0.16 0.29 19 -0.56 47 66
PRKCA 0.024 0.012 -10000 0 -10000 0 0
PTPN7 0.004 0.099 -10000 0 -0.44 41 41
HRAS 0.027 0.016 -10000 0 -0.42 1 1
PRKCB 0.019 0.067 -10000 0 -0.59 10 10
NRAS 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.023 -10000 0 -10000 0 0
MAPK3 0.007 0.15 -10000 0 -0.59 43 43
MAP2K1 0.025 0.087 -10000 0 -0.6 12 12
ELK1 0.026 0.015 -10000 0 -10000 0 0
BRAF 0.019 0.065 -10000 0 -0.66 7 7
mol:GTP 0 0.003 -10000 0 -0.008 56 56
MAPK1 0.002 0.16 -10000 0 -0.54 58 58
RAF1 0.018 0.067 -10000 0 -0.67 7 7
KRAS 0.027 0.007 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.068 0.36 1 -10000 0 1
CRKL 0.017 0.12 0.37 34 -10000 0 34
mol:DAG 0.01 0.067 -10000 0 -0.36 1 1
HRAS 0.03 0.12 0.36 62 -10000 0 62
MAPK8 -0.006 0.11 -10000 0 -0.39 2 2
RAP1A 0.02 0.12 0.38 41 -10000 0 41
GAB1 0.018 0.12 0.38 34 -10000 0 34
MAPK14 -0.003 0.11 0.25 1 -0.38 1 2
EPO -0.067 0.18 -10000 0 -0.41 184 184
PLCG1 0.01 0.068 -10000 0 -0.37 1 1
EPOR/TRPC2/IP3 Receptors 0.023 0.026 -10000 0 -10000 0 0
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.014 0.12 -10000 0 -0.45 5 5
GAB1/SHC/GRB2/SOS1 0.022 0.094 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.029 0.13 -10000 0 -0.29 182 182
IRS2 0.014 0.12 0.38 38 -0.35 1 39
STAT1 0.015 0.071 -10000 0 -10000 0 0
STAT5B 0.012 0.069 -10000 0 -0.4 1 1
cell proliferation -0.003 0.12 0.4 11 -0.37 1 12
GAB1/SHIP/PIK3R1/SHP2/SHC 0.003 0.079 -10000 0 -10000 0 0
TEC 0.018 0.12 0.38 35 -10000 0 35
SOCS3 0.02 0.052 -10000 0 -0.44 10 10
STAT1 (dimer) 0.017 0.073 -10000 0 -10000 0 0
JAK2 0.022 0.026 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.023 0.1 -10000 0 -10000 0 0
EPO/EPOR -0.029 0.13 -10000 0 -0.29 182 182
LYN 0.028 0.024 -10000 0 -0.65 1 1
TEC/VAV2 0.019 0.097 0.28 10 -10000 0 10
elevation of cytosolic calcium ion concentration 0.023 0.026 -10000 0 -10000 0 0
SHC1 0.026 0.016 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/LYN -0.004 0.12 -10000 0 -0.44 1 1
mol:IP3 0.01 0.067 -10000 0 -0.36 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.028 0.12 0.36 28 -10000 0 28
SH2B3 0.02 0.023 -10000 0 -10000 0 0
NFKB1 -0.003 0.11 -10000 0 -0.48 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.016 0.059 -10000 0 -0.26 3 3
PTPN6 0.003 0.097 0.3 3 -10000 0 3
TEC/VAV2/GRB2 0.02 0.096 0.29 9 -10000 0 9
EPOR 0.023 0.026 -10000 0 -10000 0 0
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
mol:GDP 0.021 0.094 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
PLCG2 0.005 0.11 -10000 0 -0.51 35 35
CRKL/CBL/C3G 0.027 0.1 0.29 2 -0.47 1 3
VAV2 0.021 0.12 0.38 39 -10000 0 39
CBL 0.018 0.12 0.38 36 -0.5 1 37
SHC/Grb2/SOS1 0.002 0.08 -10000 0 -10000 0 0
STAT5A 0.012 0.069 -10000 0 -0.4 1 1
GRB2 0.025 0.009 -10000 0 -10000 0 0
STAT5 (dimer) 0.027 0.078 -10000 0 -10000 0 0
LYN/PLCgamma2 0.023 0.082 -10000 0 -0.36 36 36
PTPN11 0.027 0.006 -10000 0 -10000 0 0
BTK -0.028 0.16 0.39 37 -0.35 55 92
BCL2 0.043 0.079 0.36 10 -0.75 1 11
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.01 -10000 0 -10000 0 0
AES 0.026 0.007 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.026 -10000 0 -0.39 2 2
SMAD4 0.027 0.005 -10000 0 -10000 0 0
DKK2 0.002 0.11 -10000 0 -0.49 42 42
TLE1 0.025 0.008 -10000 0 -10000 0 0
MACF1 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.059 0.12 0.44 38 -10000 0 38
WIF1 0.005 0.047 -10000 0 -0.45 7 7
beta catenin/RanBP3 0.004 0.065 0.33 6 -10000 0 6
KREMEN2 -0.023 0.14 -10000 0 -0.42 92 92
DKK1 0.006 0.093 -10000 0 -0.44 36 36
beta catenin/beta TrCP1 0.061 0.11 0.42 32 -10000 0 32
FZD1 0.024 0.029 -10000 0 -0.53 2 2
AXIN2 0.037 0.16 0.56 52 -1.5 2 54
AXIN1 0.027 0.007 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.067 -10000 0 -0.51 11 11
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.046 0.093 0.3 1 -0.52 6 7
Axin1/APC/GSK3 0.055 0.076 0.3 18 -0.36 1 19
Axin1/APC/GSK3/beta catenin/Macf1 0.047 0.09 0.38 20 -10000 0 20
HNF1A 0.012 0.091 -10000 0 -0.66 16 16
CTBP1 0.025 0.008 -10000 0 -10000 0 0
MYC 0.002 0.1 0.57 12 -1.4 1 13
RANBP3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.42 15 15
NKD1 -0.14 0.29 -10000 0 -0.65 213 213
TCF4 0.021 0.049 -10000 0 -0.61 5 5
TCF3 0.025 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.043 0.072 -10000 0 -0.38 1 1
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.004 0.087 0.4 5 -0.4 5 10
LEF1 -0.015 0.15 -10000 0 -0.56 61 61
DVL1 0.019 0.043 -10000 0 -0.42 6 6
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.052 0.1 0.32 12 -0.55 5 17
DKK1/LRP6/Kremen 2 0.008 0.1 -10000 0 -0.3 24 24
LRP6 0.027 0.007 -10000 0 -10000 0 0
CSNK1A1 0.025 0.011 -10000 0 -10000 0 0
NLK 0.026 0.009 -10000 0 -10000 0 0
CCND1 -0.007 0.091 0.64 3 -1.5 1 4
WNT1 -0.004 0.11 -10000 0 -0.42 57 57
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.026 0.007 -10000 0 -10000 0 0
PPP2R5D 0.068 0.16 0.33 192 -0.41 31 223
APC 0.034 0.097 0.36 31 -0.36 1 32
WNT1/LRP6/FZD1 0.022 0.038 0.25 1 -10000 0 1
CREBBP 0.024 0.01 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.014 0.089 0.56 20 -10000 0 20
PI3K Class IB/PDE3B 0.014 0.089 -10000 0 -0.56 20 20
PDE3B 0.014 0.089 -10000 0 -0.56 20 20
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.034 -10000 0 -0.29 7 7
CRKL 0.036 0.095 0.31 13 -0.46 9 22
mol:PIP3 -0.008 0.05 -10000 0 -0.66 5 5
AKT1 0.004 0.061 0.36 2 -0.51 5 7
PTK2B 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.04 0.097 0.38 13 -0.5 5 18
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.026 0.1 -10000 0 -0.43 36 36
MAP3K5 0.036 0.11 0.38 32 -0.49 5 37
HGF/MET/CIN85/CBL/ENDOPHILINS 0.039 0.1 -10000 0 -0.4 36 36
AP1 0.015 0.11 -10000 0 -0.39 52 52
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.016 -10000 0 -0.42 1 1
apoptosis -0.052 0.28 -10000 0 -0.8 97 97
STAT3 (dimer) 0.016 0.074 -10000 0 -0.51 6 6
GAB1/CRKL/SHP2/PI3K 0.061 0.085 0.4 1 -0.53 3 4
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
CBL/CRK 0.062 0.12 0.37 48 -0.46 10 58
PTPN11 0.027 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.007 -10000 0 -10000 0 0
PTEN 0.027 0.007 -10000 0 -10000 0 0
ELK1 0.04 0.14 0.36 120 -10000 0 120
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.013 0.048 -10000 0 -0.29 6 6
PAK1 0.008 0.069 0.5 6 -0.56 3 9
HGF/MET/RANBP10 0.026 0.098 -10000 0 -0.43 32 32
HRAS -0.002 0.13 -10000 0 -0.59 14 14
DOCK1 0.039 0.1 0.39 15 -0.52 6 21
GAB1 0.028 0.09 0.26 1 -0.49 9 10
CRK 0.045 0.12 0.38 44 -0.47 9 53
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.14 -10000 0 -0.56 32 32
JUN 0.027 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.003 0.05 -10000 0 -0.23 36 36
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.046 0.12 0.44 32 -0.53 4 36
GRB2/SHC 0.031 0.056 -10000 0 -0.34 2 2
FOS -0.015 0.16 -10000 0 -0.62 57 57
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.04 0.14 0.36 120 -10000 0 120
HGF/MET/MUC20 0.01 0.097 -10000 0 -0.39 46 46
cell migration 0.03 0.055 -10000 0 -0.34 2 2
GRB2 0.025 0.009 -10000 0 -10000 0 0
CBL 0.027 0.023 -10000 0 -0.65 1 1
MET/RANBP10 0.033 0.033 -10000 0 -0.29 7 7
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.017 0.071 -10000 0 -0.49 6 6
MET/MUC20 0.016 0.029 -10000 0 -0.29 7 7
RAP1B 0.05 0.12 0.44 38 -0.51 3 41
RAP1A 0.041 0.099 0.44 14 -0.51 3 17
HGF/MET/RANBP9 0.023 0.1 -10000 0 -0.43 36 36
RAF1 0.005 0.13 0.35 1 -0.56 14 15
STAT3 0.012 0.072 -10000 0 -0.52 6 6
cell proliferation 0.022 0.094 0.32 4 -0.47 10 14
RPS6KB1 0.007 0.046 -10000 0 -0.39 9 9
MAPK3 0.025 0.13 0.38 77 -10000 0 77
MAPK1 0.036 0.16 0.56 51 -10000 0 51
RANBP9 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.046 0.15 0.46 52 -0.48 11 63
SRC 0.014 0.065 -10000 0 -0.46 6 6
PI3K 0.033 0.056 -10000 0 -0.3 1 1
MET/Glomulin 0.011 0.037 -10000 0 -0.25 7 7
SOS1 0.027 0.006 -10000 0 -10000 0 0
MAP2K1 0.022 0.14 0.38 12 -0.54 11 23
MET 0.021 0.04 -10000 0 -0.42 7 7
MAP4K1 0.036 0.12 0.36 36 -0.51 6 42
PTK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K2 0.021 0.13 0.37 10 -0.54 11 21
BAD 0.007 0.07 0.5 6 -0.48 5 11
MAP2K4 0.047 0.13 0.42 61 -0.5 3 64
SHP2/GRB2/SOS1/GAB1 0.033 0.073 -10000 0 -0.57 2 2
INPPL1 0.028 0.003 -10000 0 -10000 0 0
PXN 0.027 0.006 -10000 0 -10000 0 0
SH3KBP1 0.028 0.002 -10000 0 -10000 0 0
HGS 0.003 0.045 -10000 0 -0.28 3 3
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF -0.007 0.14 -10000 0 -0.6 45 45
RASA1 0.027 0.023 -10000 0 -0.65 1 1
NCK1 0.027 0.006 -10000 0 -10000 0 0
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.034 0.059 -10000 0 -0.33 1 1
PDPK1 0.002 0.061 -10000 0 -0.54 5 5
HGF/MET/SHIP 0.02 0.1 -10000 0 -0.43 36 36
Aurora A signaling

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
Aurora A/GADD45A 0.035 0.027 -10000 0 -10000 0 0
BIRC5 -0.1 0.2 -10000 0 -0.42 255 255
NFKBIA 0.02 0.026 0.26 2 -10000 0 2
CPEB1 -0.058 0.21 -10000 0 -0.57 120 120
AKT1 0.02 0.025 0.26 1 -10000 0 1
NDEL1 0.025 0.009 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.028 -10000 0 -0.32 1 1
NDEL1/TACC3 0.043 0.038 -10000 0 -0.3 4 4
GADD45A 0.027 0.007 -10000 0 -10000 0 0
GSK3B 0.029 0.012 -10000 0 -10000 0 0
PAK1/Aurora A 0.038 0.03 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.069 0.14 0.21 10 -0.29 251 261
TP53 0.025 0.024 -10000 0 -0.29 1 1
DLG7 0.017 0.025 -10000 0 -0.27 1 1
AURKAIP1 0.024 0.036 -10000 0 -0.57 3 3
ARHGEF7 0.027 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.04 -10000 0 -0.32 4 4
G2/M transition of mitotic cell cycle 0.027 0.028 -10000 0 -0.31 1 1
AURKA 0.027 0.032 -10000 0 -0.32 1 1
AURKB -0.026 0.062 -10000 0 -0.31 14 14
CDC25B 0.026 0.025 -10000 0 -10000 0 0
G2/M transition checkpoint 0.013 0.019 -10000 0 -0.24 1 1
mRNA polyadenylation -0.016 0.13 -10000 0 -0.38 80 80
Aurora A/CPEB -0.016 0.13 -10000 0 -0.38 80 80
Aurora A/TACC1/TRAP/chTOG 0.065 0.037 -10000 0 -0.35 1 1
BRCA1 0.023 0.031 -10000 0 -0.42 4 4
centrosome duplication 0.038 0.03 -10000 0 -10000 0 0
regulation of centrosome cycle 0.041 0.037 -10000 0 -0.29 4 4
spindle assembly 0.063 0.036 -10000 0 -0.35 1 1
TDRD7 0.028 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.016 0.12 -10000 0 -0.41 6 6
CENPA -0.016 0.056 -10000 0 -0.33 10 10
Aurora A/PP2A 0.035 0.025 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.024 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.025 -10000 0 -0.29 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.014 -10000 0 -10000 0 0
RASA1 0.027 0.023 -10000 0 -0.65 1 1
Ajuba/Aurora A 0.013 0.019 -10000 0 -0.24 1 1
mitotic prometaphase 0.013 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.032 -10000 0 -0.32 1 1
TACC1 0.026 0.024 -10000 0 -0.65 1 1
TACC3 0.024 0.04 -10000 0 -0.42 7 7
Aurora A/Antizyme1 0.049 0.037 -10000 0 -0.37 2 2
Aurora A/RasGAP 0.037 0.033 -10000 0 -0.41 1 1
OAZ1 0.028 0.015 -10000 0 -0.42 1 1
RAN 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.011 -10000 0 -10000 0 0
GIT1 0.025 0.009 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.02 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.069 0.14 0.21 10 -0.29 251 261
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
Aurora A/TPX2 -0.039 0.11 -10000 0 -0.31 13 13
PAK1 0.028 0.003 -10000 0 -10000 0 0
CKAP5 0.028 0.004 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.018 0.26 1 -10000 0 1
RFC1 0.002 0.017 0.25 1 -10000 0 1
PRKDC 0.003 0.02 0.26 2 -10000 0 2
RIPK1 0.027 0.008 -10000 0 -10000 0 0
CASP7 0.001 0.091 -10000 0 -0.63 15 15
FASLG/FAS/FADD/FAF1 -0.027 0.072 0.25 9 -10000 0 9
MAP2K4 -0.056 0.21 0.34 5 -0.73 56 61
mol:ceramide -0.033 0.087 -10000 0 -0.41 2 2
GSN 0.002 0.018 0.26 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.075 0.24 1 -10000 0 1
FAS 0.022 0.028 -10000 0 -0.67 1 1
BID -0.004 0.026 -10000 0 -10000 0 0
MAP3K1 -0.03 0.16 0.29 7 -0.57 51 58
MAP3K7 0.026 0.008 -10000 0 -10000 0 0
RB1 0.002 0.018 0.25 1 -10000 0 1
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET 0.014 0.12 -10000 0 -0.44 54 54
ARHGDIB 0.002 0.022 0.26 2 -10000 0 2
FADD 0.024 0.015 -10000 0 -10000 0 0
actin filament polymerization -0.003 0.022 -10000 0 -0.24 2 2
NFKB1 -0.016 0.088 -10000 0 -0.61 8 8
MAPK8 -0.074 0.23 0.34 8 -0.58 116 124
DFFA 0.002 0.017 0.25 1 -10000 0 1
DNA fragmentation during apoptosis 0.002 0.02 0.23 2 -10000 0 2
FAS/FADD/MET 0.041 0.037 -10000 0 -10000 0 0
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 -0.004 0.11 -10000 0 -0.42 62 62
FAF1 0.021 0.021 -10000 0 -0.35 1 1
PARP1 0.002 0.018 0.25 1 -10000 0 1
DFFB 0.002 0.017 0.25 1 -10000 0 1
CHUK -0.013 0.078 -10000 0 -0.56 7 7
FASLG -0.14 0.21 -10000 0 -0.42 314 314
FAS/FADD 0.032 0.029 -10000 0 -0.52 1 1
HGF -0.007 0.14 -10000 0 -0.6 45 45
LMNA 0.003 0.023 0.23 2 -10000 0 2
CASP6 0.002 0.017 0.25 1 -10000 0 1
CASP10 0.023 0.015 -10000 0 -10000 0 0
CASP3 0.003 0.023 0.31 1 -10000 0 1
PTPN13 0.01 0.11 -10000 0 -0.65 23 23
CASP8 -0.002 0.048 -10000 0 -10000 0 0
IL6 -0.14 0.41 -10000 0 -1.3 99 99
MET 0.021 0.04 -10000 0 -0.42 7 7
ICAD/CAD 0.005 0.018 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.033 0.088 -10000 0 -0.41 2 2
activation of caspase activity by cytochrome c -0.004 0.025 -10000 0 -10000 0 0
PAK2 0.002 0.018 0.25 1 -10000 0 1
BCL2 0.027 0.023 -10000 0 -0.65 1 1
Class I PI3K signaling events

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
ARF5/GTP 0.022 0.033 0.29 2 -10000 0 2
DAPP1 0.004 0.13 0.34 16 -0.52 21 37
Src family/SYK family/BLNK-LAT/BTK-ITK -0.042 0.17 0.32 6 -0.53 50 56
mol:DAG -0.011 0.12 0.32 50 -0.28 4 54
HRAS 0.029 0.017 -10000 0 -0.42 1 1
RAP1A 0.028 0.01 -10000 0 -10000 0 0
ARF5/GDP 0.015 0.078 0.27 2 -0.38 15 17
PLCG2 0.005 0.11 -10000 0 -0.51 35 35
PLCG1 0.027 0.007 -10000 0 -10000 0 0
ARF5 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0.001 0.047 0.3 4 -0.32 6 10
ARF1/GTP 0.011 0.038 0.38 1 -10000 0 1
RHOA 0.026 0.008 -10000 0 -10000 0 0
YES1 0.028 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.023 0.045 0.3 3 -0.32 6 9
ADAP1 0.001 0.05 0.28 3 -0.34 4 7
ARAP3 0.001 0.047 0.3 4 -0.32 6 10
INPPL1 0.028 0.003 -10000 0 -10000 0 0
PREX1 0.025 0.033 -10000 0 -0.65 2 2
ARHGEF6 0.028 0.001 -10000 0 -10000 0 0
ARHGEF7 0.027 0.006 -10000 0 -10000 0 0
ARF1 0.027 0.007 -10000 0 -10000 0 0
NRAS 0.028 0.01 -10000 0 -10000 0 0
FYN 0.026 0.007 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.021 0.053 -10000 0 -0.44 11 11
mol:Ca2+ 0.004 0.075 0.32 25 -10000 0 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.024 -10000 0 -0.65 1 1
ZAP70 -0.12 0.21 -10000 0 -0.42 299 299
mol:IP3 -0.001 0.088 0.33 28 -10000 0 28
LYN 0.026 0.024 -10000 0 -0.65 1 1
ARF1/GDP 0.027 0.083 0.26 9 -0.36 16 25
RhoA/GDP 0.034 0.063 0.32 10 -10000 0 10
PDK1/Src/Hsp90 0.051 0.019 -10000 0 -10000 0 0
BLNK 0.017 0.079 -10000 0 -0.65 12 12
actin cytoskeleton reorganization 0.034 0.099 0.34 34 -0.39 2 36
SRC 0.027 0.007 -10000 0 -10000 0 0
PLEKHA2 0.009 0.028 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
PTEN 0.022 0.014 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.04 0.29 1 -10000 0 1
RhoA/GTP 0.021 0.04 0.3 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.047 0.14 -10000 0 -0.44 46 46
BLK -0.001 0.1 -10000 0 -0.42 48 48
PDPK1 0.027 0.007 -10000 0 -10000 0 0
CYTH1 0.006 0.05 0.28 7 -10000 0 7
HCK -0.006 0.12 -10000 0 -0.42 63 63
CYTH3 0.003 0.044 0.28 3 -10000 0 3
CYTH2 0.008 0.056 0.29 8 -10000 0 8
KRAS 0.028 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.027 0.043 -10000 0 -0.51 2 2
SGK1 0.027 0.056 -10000 0 -0.55 2 2
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
mol:GDP 0.015 0.085 0.23 17 -0.38 19 36
SOS1 0.027 0.006 -10000 0 -10000 0 0
SYK 0.024 0.048 -10000 0 -0.59 5 5
ARF6/GDP 0.029 0.063 0.28 17 -10000 0 17
mol:PI-3-4-5-P3 0.009 0.04 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.023 0.045 0.3 3 -0.32 6 9
VAV1 -0.069 0.18 -10000 0 -0.42 191 191
mol:PI-3-4-P2 0.015 0.034 0.21 1 -0.29 10 11
RAS family/GTP/PI3K Class I 0.046 0.05 -10000 0 -0.32 6 6
PLEKHA1 0.009 0.028 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.078 0.27 2 -0.38 15 17
LAT -0.047 0.16 -10000 0 -0.42 145 145
Rac1/GTP 0.017 0.056 -10000 0 -0.57 1 1
ITK -0.036 0.089 0.28 4 -10000 0 4
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.029 0.13 0.33 34 -0.34 16 50
LCK 0.003 0.1 -10000 0 -0.44 44 44
BTK -0.038 0.1 0.29 12 -10000 0 12
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.008 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.12 -10000 0 -0.55 18 18
NFATC4 0.004 0.091 0.31 30 -0.38 5 35
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis 0.004 0.086 0.3 1 -0.35 40 41
JUN 0.019 0.075 0.28 24 -0.3 4 28
HRAS 0.027 0.015 -10000 0 -0.42 1 1
DOCK7 -0.001 0.083 0.29 2 -0.46 4 6
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.018 0.1 -10000 0 -0.4 44 44
AKT1 0.01 0.006 -10000 0 -10000 0 0
BAD 0.007 0.018 -10000 0 -0.34 2 2
MAPK10 0.006 0.064 0.21 14 -0.29 11 25
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.005 0.092 0.32 1 -0.37 40 41
RAF1 -0.016 0.11 0.44 8 -0.56 14 22
ErbB2/ErbB3/neuregulin 2 0.008 0.087 -10000 0 -0.43 19 19
STAT3 -0.004 0.18 -10000 0 -0.86 37 37
cell migration 0.031 0.11 0.33 67 -0.29 8 75
mol:PI-3-4-5-P3 0 0.003 -10000 0 -10000 0 0
cell proliferation -0.065 0.17 0.51 8 -0.54 22 30
FOS -0.05 0.16 0.46 10 -0.5 59 69
NRAS 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.086 0.3 1 -0.35 40 41
MAPK3 -0.047 0.15 0.47 9 -0.52 14 23
MAPK1 -0.053 0.16 0.48 9 -0.59 23 32
JAK2 -0.001 0.083 0.29 2 -0.51 3 5
NF2 0.013 0.037 -10000 0 -0.71 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.13 0.23 2 -0.41 62 64
NRG1 -0.001 0.13 -10000 0 -0.6 39 39
GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
MAPK8 0.001 0.084 0.3 2 -0.36 14 16
MAPK9 0.009 0.056 0.23 13 -0.26 2 15
ERBB2 -0.015 0.019 -10000 0 -0.5 1 1
ERBB3 0.013 0.094 -10000 0 -0.65 17 17
SHC1 0.026 0.016 -10000 0 -0.42 1 1
RAC1 0.025 0.01 -10000 0 -10000 0 0
apoptosis -0.004 0.017 0.32 1 -10000 0 1
STAT3 (dimer) -0.003 0.18 -10000 0 -0.84 37 37
RNF41 0.005 0.006 -10000 0 -10000 0 0
FRAP1 0.004 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.001 0.057 -10000 0 -0.35 3 3
ErbB2/ErbB2/HSP90 (dimer) 0.016 0.018 -10000 0 -0.43 1 1
CHRNA1 -0.077 0.16 0.45 9 -0.42 32 41
myelination 0.01 0.12 0.4 42 -0.39 4 46
PPP3CB 0 0.078 0.28 2 -0.42 4 6
KRAS 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.016 0.12 -10000 0 -0.56 18 18
NRG2 0.001 0.11 -10000 0 -0.43 49 49
mol:GDP -0.006 0.13 0.23 2 -0.4 62 64
SOS1 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.026 0.11 0.34 9 -0.52 14 23
SRC 0.027 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.001 0.084 0.29 2 -0.46 4 6
MAP2K1 -0.051 0.16 0.46 5 -0.56 22 27
heart morphogenesis 0.004 0.086 0.3 1 -0.35 40 41
RAS family/GDP 0.026 0.12 -10000 0 -0.56 17 17
GRB2 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.014 0.038 -10000 0 -0.75 2 2
CHRNE 0.013 0.031 0.14 24 -0.15 5 29
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.006 -10000 0 -10000 0 0
nervous system development 0.004 0.086 0.3 1 -0.35 40 41
CDC42 0.027 0.007 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.031 0.16 0.28 3 -0.56 43 46
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.028 0.003 -10000 0 -10000 0 0
STXBP4 0.025 0.016 -10000 0 -0.35 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.033 0.18 0.34 44 -0.58 50 94
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.006 -10000 0 -10000 0 0
TBC1D4 0.018 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
YWHAB 0.027 0.007 -10000 0 -10000 0 0
SNARE/Synip 0.049 0.022 -10000 0 -10000 0 0
YWHAG 0.025 0.01 -10000 0 -10000 0 0
ASIP -0.053 0.16 -10000 0 -0.42 140 140
PRKCI 0.027 0.006 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.006 -10000 0 -10000 0 0
GYS1 0.019 0.006 -10000 0 -10000 0 0
PRKCZ 0.024 0.04 -10000 0 -0.65 3 3
TRIP10 0.028 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.006 0.075 -10000 0 -0.4 12 12
VAMP2 0.025 0.009 -10000 0 -10000 0 0
SLC2A4 0.029 0.2 0.36 38 -0.66 51 89
STX4 0.026 0.007 -10000 0 -10000 0 0
GSK3B 0.026 0.008 -10000 0 -10000 0 0
SFN -0.072 0.2 -10000 0 -0.44 185 185
LNPEP 0.023 0.056 -10000 0 -0.65 6 6
YWHAE 0.025 0.009 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.01 0.074 0.36 5 -10000 0 5
GNAI2 0.026 0.008 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.007 0.098 -10000 0 -0.25 125 125
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
RhoA/GTP 0.011 0.075 -10000 0 -0.37 5 5
negative regulation of cAMP metabolic process 0.002 0.076 -10000 0 -0.32 15 15
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNA12 0.025 0.01 -10000 0 -10000 0 0
S1PR5 -0.036 0.16 -10000 0 -0.42 125 125
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.076 -10000 0 -0.32 15 15
RhoA/GDP 0.019 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.007 -9999 0 -10000 0 0
ITGB7 0.027 0.006 -9999 0 -10000 0 0
ITGA4 0.012 0.08 -9999 0 -0.42 29 29
alpha4/beta7 Integrin 0.027 0.06 -9999 0 -0.29 29 29
alpha4/beta1 Integrin 0.028 0.06 -9999 0 -0.29 29 29
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.021 0.041 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
DOCK1 0.026 0.024 -10000 0 -0.65 1 1
ITGA4 0.012 0.08 -10000 0 -0.42 29 29
alpha4/beta7 Integrin/MAdCAM1 0.036 0.082 -10000 0 -0.36 2 2
EPO -0.077 0.18 -10000 0 -0.42 184 184
alpha4/beta7 Integrin 0.027 0.06 -10000 0 -0.29 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.06 -10000 0 -0.29 29 29
EPO/EPOR (dimer) -0.035 0.13 -10000 0 -0.29 184 184
lamellipodium assembly 0.022 0.057 -10000 0 -0.62 2 2
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.011 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
JAK2 -0.008 0.069 -10000 0 -0.48 1 1
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
MADCAM1 -0.005 0.1 -10000 0 -0.42 52 52
cell adhesion 0.034 0.081 -10000 0 -0.36 2 2
CRKL/CBL 0.04 0.02 -10000 0 -0.49 1 1
ITGB1 0.027 0.007 -10000 0 -10000 0 0
SRC -0.005 0.087 -10000 0 -0.4 15 15
ITGB7 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.018 0.1 -10000 0 -0.43 17 17
p130Cas/Crk/Dock1 0.016 0.084 0.35 1 -0.68 1 2
VCAM1 -0.012 0.13 -10000 0 -0.43 74 74
RHOA 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.057 -10000 0 -10000 0 0
BCAR1 -0.01 0.081 0.38 1 -0.46 6 7
EPOR 0.028 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.023 -10000 0 -0.65 1 1
GIT1 0.025 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.022 0.059 -10000 0 -0.64 2 2
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.002 0.12 -10000 0 -0.4 71 71
cell-cell adhesion 0.002 0.059 0.5 2 -10000 0 2
Ephrin B/EPHB2/RasGAP 0.057 0.08 -10000 0 -0.36 20 20
ITSN1 0.027 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
SHC1 0.026 0.016 -10000 0 -0.42 1 1
Ephrin B1/EPHB3 -0.012 0.14 -10000 0 -0.42 93 93
Ephrin B1/EPHB1 0.029 0.054 -10000 0 -0.32 19 19
HRAS/GDP 0.016 0.076 -10000 0 -0.45 3 3
Ephrin B/EPHB1/GRB7 0.051 0.092 -10000 0 -0.37 29 29
Endophilin/SYNJ1 0.019 0.074 0.35 5 -0.34 20 25
KRAS 0.027 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.054 0.085 -10000 0 -0.36 22 22
endothelial cell migration 0.049 0.025 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
GRB7 0.018 0.069 -10000 0 -0.65 9 9
PAK1 0.03 0.092 0.41 19 -10000 0 19
HRAS 0.027 0.015 -10000 0 -0.42 1 1
RRAS 0.022 0.077 0.35 6 -0.34 19 25
DNM1 -0.039 0.16 -10000 0 -0.42 129 129
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.01 0.069 -10000 0 -0.34 22 22
lamellipodium assembly -0.002 0.059 -10000 0 -0.5 2 2
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.023 0.062 -10000 0 -0.38 4 4
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
EPHB2 0.02 0.058 -10000 0 -0.45 12 12
EPHB3 -0.046 0.21 -10000 0 -0.65 94 94
EPHB1 0.015 0.083 -10000 0 -0.53 19 19
EPHB4 0.025 0.01 -10000 0 -10000 0 0
mol:GDP 0.025 0.097 0.38 28 -0.38 13 41
Ephrin B/EPHB2 0.044 0.075 -10000 0 -0.36 21 21
Ephrin B/EPHB3 0.007 0.14 -10000 0 -0.4 86 86
JNK cascade 0.023 0.079 0.36 24 -0.41 11 35
Ephrin B/EPHB1 0.04 0.08 -10000 0 -0.36 22 22
RAP1/GDP 0.049 0.1 0.38 23 -0.39 3 26
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EFNB3 0.007 0.1 -10000 0 -0.57 27 27
EFNB1 0.028 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.038 0.067 -10000 0 -0.44 11 11
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.034 0.083 -10000 0 -0.57 2 2
Rap1/GTP 0.015 0.066 -10000 0 -0.5 2 2
axon guidance -0.002 0.12 -10000 0 -0.4 71 71
MAPK3 0.018 0.055 -10000 0 -0.41 1 1
MAPK1 0.017 0.056 -10000 0 -0.41 1 1
Rac1/GDP 0.022 0.086 0.33 4 -0.42 3 7
actin cytoskeleton reorganization 0 0.053 -10000 0 -0.4 3 3
CDC42/GDP 0.045 0.11 0.39 27 -0.41 3 30
PI3K 0.054 0.027 -10000 0 -10000 0 0
EFNA5 -0.021 0.17 -10000 0 -0.64 63 63
Ephrin B2/EPHB4 0.032 0.015 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.021 0.059 -10000 0 -0.41 3 3
CDC42 0.027 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.065 -10000 0 -0.48 3 3
PTK2 0.016 0.072 0.52 17 -10000 0 17
MAP4K4 0.023 0.08 0.36 24 -0.41 11 35
SRC 0.027 0.007 -10000 0 -10000 0 0
KALRN 0.027 0.014 -10000 0 -0.35 1 1
Intersectin/N-WASP 0.035 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis 0.043 0.11 0.38 54 -0.43 2 56
MAP2K1 0.02 0.059 -10000 0 -0.36 4 4
WASL 0.025 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.054 0.07 -10000 0 -0.44 10 10
cell migration 0.039 0.12 0.41 40 -0.43 2 42
NRAS 0.027 0.007 -10000 0 -10000 0 0
SYNJ1 0.019 0.075 0.35 5 -0.35 20 25
PXN 0.027 0.006 -10000 0 -10000 0 0
TF -0.021 0.099 -10000 0 -0.51 2 2
HRAS/GTP 0.035 0.08 -10000 0 -0.52 3 3
Ephrin B1/EPHB1-2 0.038 0.066 -10000 0 -0.44 10 10
cell adhesion mediated by integrin 0.014 0.082 0.41 20 -10000 0 20
RAC1 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0.039 0.084 -10000 0 -0.57 2 2
RAC1-CDC42/GTP -0.024 0.11 -10000 0 -0.56 15 15
RASA1 0.027 0.023 -10000 0 -0.65 1 1
RAC1-CDC42/GDP 0.033 0.084 0.33 4 -0.4 3 7
ruffle organization 0.036 0.11 0.36 62 -0.5 2 64
NCK1 0.027 0.006 -10000 0 -10000 0 0
receptor internalization -0.015 0.095 0.34 5 -0.43 6 11
Ephrin B/EPHB2/KALRN 0.058 0.078 -10000 0 -0.36 18 18
ROCK1 -0.017 0.13 -10000 0 -0.38 91 91
RAS family/GDP -0.013 0.05 -10000 0 -0.38 3 3
Rac1/GTP 0.005 0.065 -10000 0 -0.53 2 2
Ephrin B/EPHB1/Src/Paxillin 0.022 0.058 -10000 0 -0.36 2 2
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0 0.094 0.41 1 -0.48 13 14
PDGFB-D/PDGFRB/SLAP 0.014 0.097 -10000 0 -0.34 58 58
PDGFB-D/PDGFRB/APS/CBL 0.039 0.058 -10000 0 -0.42 7 7
AKT1 0.063 0.13 0.47 62 -10000 0 62
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.11 0.36 7 -0.48 18 25
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
FGR -0.01 0.13 0.34 1 -0.53 22 23
mol:Ca2+ 0.027 0.1 0.31 25 -0.51 18 43
MYC 0.05 0.13 0.46 36 -0.69 2 38
SHC1 0.026 0.016 -10000 0 -0.42 1 1
HRAS/GDP 0.035 0.054 -10000 0 -0.36 11 11
LRP1/PDGFRB/PDGFB 0.043 0.062 -10000 0 -0.42 14 14
GRB10 0.025 0.009 -10000 0 -10000 0 0
PTPN11 0.027 0.006 -10000 0 -10000 0 0
GO:0007205 0.027 0.1 0.31 25 -0.52 18 43
PTEN 0.027 0.007 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
GRB7 0.018 0.069 -10000 0 -0.65 9 9
PDGFB-D/PDGFRB/SHP2 0.031 0.063 -10000 0 -0.47 13 13
PDGFB-D/PDGFRB/GRB10 0.029 0.053 -10000 0 -0.37 13 13
cell cycle arrest 0.014 0.097 -10000 0 -0.34 58 58
HRAS 0.027 0.015 -10000 0 -0.42 1 1
HIF1A 0.056 0.13 0.46 62 -10000 0 62
GAB1 0.025 0.11 0.34 25 -0.48 18 43
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.11 0.36 29 -0.47 12 41
PDGFB-D/PDGFRB 0.045 0.057 -10000 0 -0.42 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.063 -10000 0 -0.47 13 13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.089 -10000 0 -0.51 8 8
positive regulation of MAPKKK cascade 0.031 0.063 -10000 0 -0.47 13 13
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 0.027 0.11 0.31 25 -0.52 18 43
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.023 0.079 -10000 0 -0.45 22 22
SHB 0.028 0.004 -10000 0 -10000 0 0
BLK -0.004 0.095 -10000 0 -0.4 22 22
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.032 0.063 -10000 0 -0.47 13 13
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
VAV2 0.028 0.12 0.36 25 -0.47 19 44
CBL 0.027 0.023 -10000 0 -0.65 1 1
PDGFB-D/PDGFRB/DEP1 0.032 0.063 -10000 0 -0.47 13 13
LCK -0.015 0.13 0.32 2 -0.44 56 58
PDGFRB 0.018 0.081 -10000 0 -0.64 13 13
ACP1 0.027 0.006 -10000 0 -10000 0 0
HCK 0.008 0.072 -10000 0 -0.44 14 14
ABL1 0.023 0.11 0.32 25 -0.46 19 44
PDGFB-D/PDGFRB/CBL 0.021 0.11 0.36 3 -0.53 21 24
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.028 0.003 -10000 0 -10000 0 0
STAT3 0.025 0.009 -10000 0 -10000 0 0
STAT1 0.026 0.022 -10000 0 -0.42 2 2
cell proliferation 0.05 0.13 0.44 38 -0.61 2 40
SLA 0.004 0.1 -10000 0 -0.42 47 47
actin cytoskeleton reorganization 0.045 0.068 0.35 18 -0.34 7 25
SRC 0.015 0.063 -10000 0 -0.43 9 9
PI3K 0.01 0.034 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.073 -10000 0 -0.41 19 19
SH2B2 0.021 0.038 -10000 0 -0.42 6 6
PLCgamma1/SPHK1 0.008 0.11 0.37 7 -0.5 18 25
LYN 0.01 0.079 -10000 0 -0.41 17 17
LRP1 0.027 0.006 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
STAT5B 0.025 0.009 -10000 0 -10000 0 0
STAT5A 0.025 0.009 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.065 0.056 -10000 0 -0.35 9 9
SPHK1 -0.039 0.16 -10000 0 -0.42 129 129
EDG1 0.001 0.004 -10000 0 -10000 0 0
mol:DAG 0.027 0.11 0.31 25 -0.52 18 43
PLCG1 0.027 0.11 0.32 23 -0.54 18 41
NHERF/PDGFRB 0.041 0.055 -10000 0 -0.42 9 9
YES1 0.008 0.099 0.32 2 -0.54 22 24
cell migration 0.04 0.055 -10000 0 -0.42 9 9
SHC/Grb2/SOS1 0.064 0.057 -10000 0 -0.35 7 7
SLC9A3R2 0.026 0.024 -10000 0 -0.65 1 1
SLC9A3R1 0.025 0.009 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.052 0.056 -10000 0 -0.38 9 9
FYN -0.01 0.12 -10000 0 -0.48 25 25
DOK1 0.023 0.057 -10000 0 -0.38 10 10
HRAS/GTP 0.02 0.011 -10000 0 -0.29 1 1
PDGFB 0.026 0.033 -10000 0 -0.65 2 2
RAC1 0.051 0.13 0.43 39 -0.51 7 46
PRKCD 0.021 0.06 -10000 0 -0.38 9 9
FER 0.022 0.058 -10000 0 -0.39 12 12
MAPKKK cascade 0.027 0.097 0.41 33 -10000 0 33
RASA1 0.024 0.058 -10000 0 -0.38 11 11
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.027 0.006 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.057 -10000 0 -0.36 10 10
PDGFB-D/PDGFRB/SHB 0.032 0.063 -10000 0 -0.47 13 13
chemotaxis 0.023 0.11 0.32 26 -0.44 19 45
STAT1-3-5/STAT1-3-5 0.053 0.05 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.012 0.06 -10000 0 -0.47 13 13
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.029 0.091 -10000 0 -0.55 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.13 0.4 20 -0.55 8 28
alphaV/beta3 Integrin/Osteopontin/Src 0.034 0.072 -10000 0 -0.49 13 13
AP1 0.044 0.14 -10000 0 -0.65 9 9
ILK 0.026 0.097 -10000 0 -0.55 8 8
bone resorption 0.024 0.11 -10000 0 -0.58 9 9
PTK2B 0.027 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.051 0.097 -10000 0 -0.55 6 6
ITGAV 0.028 0.03 -10000 0 -0.52 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.018 0.089 -10000 0 -0.33 51 51
alphaV/beta3 Integrin/Osteopontin 0.038 0.1 -10000 0 -0.46 28 28
MAP3K1 0.026 0.098 -10000 0 -0.42 28 28
JUN 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.089 0.35 1 -0.57 7 8
MAPK1 0.011 0.091 0.35 1 -0.58 8 9
Rac1/GDP 0.018 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 0.023 0.1 0.39 9 -0.55 9 18
ITGB3 0.01 0.1 -10000 0 -0.61 24 24
NFKBIA 0.011 0.093 0.35 1 -0.55 9 10
FOS -0.014 0.16 -10000 0 -0.62 57 57
CD44 0.006 0.098 -10000 0 -0.42 43 43
CHUK 0.027 0.007 -10000 0 -10000 0 0
PLAU -0.005 0.29 0.52 18 -1.1 46 64
NF kappa B1 p50/RelA 0.046 0.11 -10000 0 -0.56 8 8
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
RELA 0.028 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.085 -10000 0 -0.44 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.025 0.1 -10000 0 -0.42 31 31
VAV3 0.018 0.11 0.39 8 -0.53 10 18
MAP3K14 0.017 0.092 -10000 0 -0.43 27 27
ROCK2 0.02 0.066 -10000 0 -0.62 9 9
SPP1 0.018 0.086 -10000 0 -0.58 17 17
RAC1 0.025 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.091 -10000 0 -0.54 7 7
MMP2 0.017 0.12 0.39 3 -0.55 8 11
IL1-mediated signaling events

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
UBC13/UEV1A 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.024 0.04 -10000 0 -0.65 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.06 -10000 0 -0.34 5 5
IRAK/TOLLIP 0.034 0.009 -10000 0 -10000 0 0
IKBKB 0.027 0.006 -10000 0 -10000 0 0
IKBKG 0.028 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.078 0.21 -10000 0 -0.45 203 203
IL1A 0.002 0.093 -10000 0 -0.42 40 40
IL1B 0.009 0.062 -10000 0 -0.36 22 22
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.044 -10000 0 -10000 0 0
IL1R2 -0.11 0.26 -10000 0 -0.6 189 189
IL1R1 0.026 0.03 -10000 0 -0.45 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.016 0.046 -10000 0 -0.33 4 4
TOLLIP 0.028 0.003 -10000 0 -10000 0 0
TICAM2 0.026 0.024 -10000 0 -0.65 1 1
MAP3K3 0.025 0.009 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.041 0.062 -10000 0 -10000 0 0
JUN 0.012 0.038 0.33 3 -10000 0 3
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.06 0.06 -10000 0 -0.35 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88 0.046 0.07 -10000 0 -0.39 2 2
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.054 0.071 -10000 0 -0.37 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.036 0.06 -10000 0 -0.38 8 8
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 0.016 0.04 0.34 3 -0.33 3 6
IRAK1 0.018 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.024 0.081 -10000 0 -0.35 36 36
IRAK4 0.027 0.006 -10000 0 -10000 0 0
PRKCI 0.027 0.006 -10000 0 -10000 0 0
TRAF6 0.028 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.054 -10000 0 -0.3 5 5
CHUK 0.027 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.036 0.06 -10000 0 -0.38 8 8
IL1 beta/IL1R2 -0.058 0.18 -10000 0 -0.43 153 153
IRAK/TRAF6/TAK1/TAB1/TAB2 0.039 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.056 -10000 0 -0.64 1 1
IRAK3 0.026 0.022 -10000 0 -0.42 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.058 0.06 -10000 0 -0.35 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.025 0.039 -10000 0 -0.28 3 3
IL1 alpha/IL1R1/IL1RAP 0.035 0.071 -10000 0 -0.37 3 3
RELA 0.028 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.034 -10000 0 -0.42 5 5
MYD88 0.026 0.008 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.019 -10000 0 -10000 0 0
IL1RAP 0.024 0.041 -10000 0 -0.46 6 6
UBE2N 0.027 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 0.03 0.044 -10000 0 -10000 0 0
CASP1 0.026 0.03 -10000 0 -0.42 4 4
IL1RN/IL1R2 -0.077 0.21 -10000 0 -0.45 200 200
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.047 0.061 -10000 0 -0.36 8 8
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.08 -10000 0 -0.37 7 7
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
IL1RN 0.007 0.099 -10000 0 -0.46 36 36
TRAF6/TAK1/TAB1/TAB2 0.037 0.013 -10000 0 -10000 0 0
MAP2K6 0.023 0.039 0.34 3 -0.34 3 6
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.031 0.083 -10000 0 -10000 0 0
VDR 0.024 0.046 -10000 0 -0.65 4 4
FAM120B 0.026 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.045 0.055 -10000 0 -0.39 7 7
RXRs/LXRs/DNA/Oxysterols 0.047 0.067 -10000 0 -0.42 11 11
MED1 0.025 0.009 -10000 0 -10000 0 0
mol:9cRA 0.005 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.02 0.062 -10000 0 -10000 0 0
RXRs/NUR77 0.004 0.16 -10000 0 -0.38 122 122
RXRs/PPAR 0.034 0.041 -10000 0 -0.46 4 4
NCOR2 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.035 -10000 0 -0.49 4 4
RARs/VDR/DNA/Vit D3 0.051 0.042 -10000 0 -0.36 5 5
RARA 0.025 0.009 -10000 0 -10000 0 0
NCOA1 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.046 -10000 0 -0.65 4 4
RARs/RARs/DNA/9cRA 0.042 0.03 -10000 0 -0.36 2 2
RARG 0.026 0.016 -10000 0 -0.42 1 1
RPS6KB1 0.047 0.13 0.51 64 -10000 0 64
RARs/THRs/DNA/SMRT 0.019 0.063 -10000 0 -0.28 34 34
THRA 0.024 0.025 -10000 0 -0.65 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.035 -10000 0 -0.49 4 4
RXRs/PPAR/9cRA/PGJ2/DNA 0.057 0.047 -10000 0 -0.29 3 3
NR1H4 -0.017 0.17 -10000 0 -0.65 57 57
RXRs/LXRs/DNA 0.088 0.061 -10000 0 -0.39 2 2
NR1H2 0.031 0.026 -10000 0 -0.67 1 1
NR1H3 0.032 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.059 0.053 -10000 0 -0.32 7 7
NR4A1 -0.068 0.24 -10000 0 -0.65 123 123
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.005 0.13 -10000 0 -0.4 72 72
RXRG 0.021 0.055 -10000 0 -0.44 11 11
RXR alpha/CCPG 0.042 0.014 -10000 0 -10000 0 0
RXRA 0.031 0.012 -10000 0 -10000 0 0
RXRB 0.03 0.013 -10000 0 -10000 0 0
THRB -0.001 0.13 -10000 0 -0.64 35 35
PPARG 0.025 0.017 -10000 0 -0.42 1 1
PPARD 0.026 0.007 -10000 0 -10000 0 0
TNF 0.037 0.12 -10000 0 -0.97 9 9
mol:Oxysterols 0.005 0.006 -10000 0 -10000 0 0
cholesterol transport 0.047 0.067 -10000 0 -0.42 11 11
PPARA 0.027 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.024 0.033 -10000 0 -0.65 2 2
RXRs/NUR77/BCL2 -0.02 0.12 -10000 0 -0.31 125 125
SREBF1 0.041 0.065 -10000 0 -0.49 5 5
RXRs/RXRs/DNA/9cRA 0.058 0.047 -10000 0 -0.29 3 3
ABCA1 0.044 0.066 -10000 0 -0.47 5 5
RARs/THRs 0.05 0.091 -10000 0 -0.36 34 34
RXRs/FXR 0.04 0.12 -10000 0 -0.38 56 56
BCL2 0.027 0.023 -10000 0 -0.65 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.13 -10000 0 -0.51 39 39
KLHL20 0.023 0.069 0.19 5 -0.31 2 7
CYFIP2 0.018 0.076 -10000 0 -0.65 11 11
Rac1/GDP 0.023 0.092 0.33 11 -0.37 2 13
ENAH -0.005 0.12 -10000 0 -0.51 39 39
AP1M1 0.028 0.003 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.007 -10000 0 -10000 0 0
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.061 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.036 -10000 0 -0.2 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.037 0.095 -10000 0 -0.38 37 37
RAPGEF1 0.003 0.12 -10000 0 -0.44 34 34
CTNND1 0.028 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.006 0.13 -10000 0 -0.53 40 40
CRK -0.005 0.12 -10000 0 -0.48 35 35
E-cadherin/gamma catenin/alpha catenin 0.025 0.1 -10000 0 -0.43 36 36
alphaE/beta7 Integrin 0.036 0.015 -10000 0 -10000 0 0
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
NCKAP1 0.027 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.019 -10000 0 -10000 0 0
DLG1 -0.005 0.12 -10000 0 -0.51 40 40
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.036 -10000 0 -10000 0 0
MLLT4 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.027 -10000 0 -0.22 3 3
PI3K 0.004 0.051 -10000 0 -10000 0 0
ARF6 0.028 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.012 0.11 -10000 0 -0.5 37 37
TIAM1 0.026 0.024 -10000 0 -0.65 1 1
E-cadherin(dimer)/Ca2+ 0.036 0.09 -10000 0 -0.36 39 39
AKT1 0.014 0.035 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
CDH1 -0.005 0.14 -10000 0 -0.65 40 40
RhoA/GDP 0.04 0.1 0.34 30 -0.36 2 32
actin cytoskeleton organization 0.023 0.057 0.16 26 -0.22 2 28
CDC42/GDP 0.047 0.13 0.42 46 -0.36 2 48
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.069 -10000 0 -0.3 36 36
ITGB7 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.04 0.096 -10000 0 -0.38 39 39
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0.086 -10000 0 -0.36 39 39
mol:GDP 0.035 0.14 0.44 45 -0.4 5 50
CDC42/GTP/IQGAP1 0.036 0.01 -10000 0 -10000 0 0
JUP 0.023 0.041 -10000 0 -0.65 3 3
p120 catenin/RhoA/GDP 0.033 0.099 0.33 15 -0.37 2 17
RAC1/GTP/IQGAP1 0.033 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.042 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.027 0.007 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.027 0.069 0.21 48 -0.17 34 82
NME1 0.024 0.027 -10000 0 -0.42 3 3
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.13 -10000 0 -0.51 40 40
regulation of cell-cell adhesion 0.011 0.051 -10000 0 -10000 0 0
WASF2 0.012 0.029 -10000 0 -10000 0 0
Rap1/GTP 0.027 0.074 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.095 -10000 0 -0.37 36 36
CCND1 0.023 0.067 0.19 27 -0.21 34 61
VAV2 0.005 0.15 -10000 0 -0.56 17 17
RAP1/GDP 0.037 0.09 0.35 14 -0.35 1 15
adherens junction assembly -0.006 0.12 -10000 0 -0.5 40 40
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.007 -10000 0 -10000 0 0
PIP5K1C 0.028 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.04 0.092 -10000 0 -0.67 1 1
E-cadherin/beta catenin -0.005 0.092 -10000 0 -0.43 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.13 -10000 0 -0.51 38 38
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.073 -10000 0 -0.55 2 2
E-cadherin/beta catenin/alpha catenin 0.026 0.099 -10000 0 -0.42 39 39
ITGAE 0.025 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.13 -10000 0 -0.54 40 40
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
CDC42/GTP 0.026 0.066 -10000 0 -0.37 5 5
PLCG1 0.014 0.06 -10000 0 -0.37 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
G12/G13 0.034 0.017 -10000 0 -10000 0 0
cell migration 0.025 0.065 -10000 0 -0.36 5 5
S1PR5 -0.036 0.16 -10000 0 -0.42 125 125
S1PR4 0.014 0.077 -10000 0 -0.42 27 27
MAPK3 0.014 0.061 -10000 0 -0.37 6 6
MAPK1 0.016 0.059 -10000 0 -0.37 6 6
S1P/S1P5/Gi 0.002 0.076 -10000 0 -0.32 15 15
GNAI1 0.022 0.041 -10000 0 -0.65 3 3
CDC42/GDP 0.02 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.007 0.098 -10000 0 -0.25 125 125
RHOA 0.039 0.086 0.36 29 -10000 0 29
S1P/S1P4/Gi 0.017 0.065 -10000 0 -0.33 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
S1P/S1P4/G12/G13 0.036 0.05 -10000 0 -10000 0 0
GNA12 0.025 0.01 -10000 0 -10000 0 0
GNA13 0.025 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.007 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.027 0.016 -10000 0 -0.42 1 1
ANTXR2 0.026 0.036 -10000 0 -0.57 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation 0.001 0.005 -10000 0 -0.067 4 4
monocyte activation -0.024 0.14 -10000 0 -0.44 81 81
MAP2K2 0.014 0.052 -10000 0 -0.6 6 6
MAP2K1 0.002 0.004 -10000 0 -10000 0 0
MAP2K7 0.002 0.004 -10000 0 -10000 0 0
MAP2K6 0 0.023 0.16 1 -0.32 4 5
CYAA 0.002 0.02 -10000 0 -0.28 4 4
MAP2K4 0.002 0.004 -10000 0 -10000 0 0
IL1B 0.005 0.047 0.24 1 -0.26 17 18
Channel 0.033 0.025 -10000 0 -0.3 4 4
NLRP1 0 0.018 -10000 0 -0.21 6 6
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.004 0.063 -10000 0 -0.38 23 23
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation -0.001 0.005 0.067 4 -10000 0 4
MAPK3 0.002 0.006 0.14 1 -10000 0 1
MAPK1 0.002 0.004 -10000 0 -10000 0 0
PGR -0.06 0.14 -10000 0 -0.36 150 150
PA/Cellular Receptors 0.034 0.027 -10000 0 -0.33 4 4
apoptosis 0.001 0.005 -10000 0 -0.067 4 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.032 0.023 -10000 0 -0.27 4 4
macrophage activation 0.002 0.006 0.13 1 -10000 0 1
TNF 0.012 0.082 -10000 0 -0.46 25 25
VCAM1 -0.011 0.12 -10000 0 -0.46 54 54
platelet activation 0.004 0.063 -10000 0 -0.38 23 23
MAPKKK cascade -0.013 0.034 -10000 0 -0.13 59 59
IL18 0 0.053 -10000 0 -0.21 40 40
negative regulation of macrophage activation 0.001 0.005 -10000 0 -0.067 4 4
LEF 0.001 0.005 -10000 0 -0.067 4 4
CASP1 0.003 0.01 -10000 0 -0.11 6 6
mol:cAMP 0.004 0.063 -10000 0 -0.38 23 23
necrosis 0.001 0.005 -10000 0 -0.067 4 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.032 0.024 -10000 0 -0.28 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.007 -10000 0 -10000 0 0
mol:PIP3 0.008 0.042 -10000 0 -0.32 10 10
FRAP1 0.028 0.06 0.37 14 -0.3 1 15
AKT1 0.009 0.042 0.2 1 -0.28 9 10
INSR 0.028 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.03 0.017 -10000 0 -0.24 3 3
mol:GTP 0.036 0.047 0.24 1 -0.3 1 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.011 0.028 -10000 0 -10000 0 0
TSC2 0.026 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.032 -10000 0 -10000 0 0
TSC1 0.028 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.062 -10000 0 -0.36 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.023 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.007 -10000 0 -10000 0 0
RPS6KB1 0.034 0.089 0.38 26 -0.32 2 28
MAP3K5 -0.005 0.049 -10000 0 -0.18 61 61
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.005 0.049 -10000 0 -0.18 61 61
mol:LY294002 0 0 -10000 0 -0.001 51 51
EIF4B 0.041 0.1 0.39 43 -0.29 1 44
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.051 0.078 0.36 23 -0.4 1 24
eIF4E/eIF4G1/eIF4A1 0.02 0.018 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.031 0.06 -10000 0 -0.34 10 10
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.04 0.25 13 -10000 0 13
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.034 0.041 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 51 51
FKBP12/Rapamycin 0.02 0.005 -10000 0 -10000 0 0
PDPK1 0.005 0.038 -10000 0 -0.3 10 10
EIF4E 0.028 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.003 0.16 -10000 0 -0.54 63 63
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.027 -10000 0 -10000 0 0
TSC1/TSC2 0.041 0.052 0.27 2 -0.32 1 3
tumor necrosis factor receptor activity 0 0 0.001 51 -10000 0 51
RPS6 0.027 0.022 -10000 0 -0.42 2 2
PPP5C 0.028 0.003 -10000 0 -10000 0 0
EIF4G1 0.027 0.006 -10000 0 -10000 0 0
IRS1 -0.002 0.062 -10000 0 -0.24 51 51
INS -0.018 0.024 -10000 0 -0.42 3 3
PTEN 0.025 0.008 -10000 0 -10000 0 0
PDK2 0.005 0.038 0.22 3 -0.3 9 12
EIF4EBP1 -0.017 0.2 -10000 0 -1 33 33
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PPP2R5D 0.029 0.059 0.35 15 -10000 0 15
peptide biosynthetic process 0.014 0.018 -10000 0 -10000 0 0
RHEB 0.025 0.01 -10000 0 -10000 0 0
EIF4A1 0.025 0.009 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.006 50 -10000 0 50
EEF2 0.014 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0.19 -10000 0 -0.94 33 33
Arf6 trafficking events

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
SLC2A4 -0.005 0.12 -10000 0 -0.49 53 53
CLTC 0.023 0.063 -10000 0 -0.37 18 18
calcium ion-dependent exocytosis 0.022 0.029 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.027 0.019 -10000 0 -10000 0 0
EXOC4 0.025 0.01 -10000 0 -10000 0 0
CD59 0.017 0.051 -10000 0 -0.31 18 18
CPE 0.008 0.054 -10000 0 -0.26 33 33
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
membrane fusion 0.016 0.012 -10000 0 -10000 0 0
CTNND1 0.031 0.046 -10000 0 -10000 0 0
DNM2 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.043 0.26 4 -0.34 4 8
TSHR -0.006 0.075 -10000 0 -0.24 78 78
INS 0.014 0.054 -10000 0 -0.5 8 8
BIN1 0.025 0.036 -10000 0 -0.57 3 3
mol:Choline 0.016 0.012 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.017 -10000 0 -0.24 3 3
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.018 -10000 0 -10000 0 0
JUP 0.016 0.051 -10000 0 -0.3 18 18
ASAP2/amphiphysin II 0.047 0.04 -10000 0 -0.39 6 6
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.007 0.07 -10000 0 -0.32 18 18
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.01 0.083 -10000 0 -0.42 32 32
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.027 0.042 -10000 0 -0.35 7 7
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.009 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.07 0.41 4 -10000 0 4
positive regulation of phagocytosis 0.017 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.025 0.053 -10000 0 -0.24 32 32
ACAP1 0.021 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.01 0.048 -10000 0 -0.3 18 18
clathrin heavy chain/ACAP1 0.025 0.056 0.25 4 -0.38 5 9
JIP4/KLC1 0.047 0.02 -10000 0 -10000 0 0
EXOC1 0.028 0.004 -10000 0 -10000 0 0
exocyst 0.027 0.042 -10000 0 -0.35 7 7
RALA/GTP 0.018 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.014 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.029 0.045 -10000 0 -10000 0 0
NME1 0.015 0.017 -10000 0 -0.24 3 3
clathrin coat assembly 0.028 0.083 0.25 25 -0.36 18 43
IL2RA 0 0.066 -10000 0 -0.32 18 18
VAMP3 0.017 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.012 0.088 -10000 0 -0.34 34 34
EXOC6 0.027 0.007 -10000 0 -10000 0 0
PLD1 0.018 0.008 -10000 0 -10000 0 0
PLD2 0.017 0.009 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.04 -10000 0 -0.35 4 4
SDC1 0.016 0.054 -10000 0 -0.3 18 18
ARF6/GDP 0.023 0.019 -10000 0 -0.24 3 3
EXOC7 0.025 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.073 -10000 0 -0.42 4 4
mol:Phosphatidic acid 0.016 0.012 -10000 0 -10000 0 0
endocytosis -0.045 0.039 0.38 6 -10000 0 6
SCAMP2 0.028 0.003 -10000 0 -10000 0 0
ADRB2 0.039 0.1 0.28 53 -0.35 23 76
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ASAP2 0.024 0.046 -10000 0 -0.65 4 4
Dynamin 2/GDP 0.03 0.019 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 -0.15 0.18 0.28 7 -0.33 372 379
RALA 0.025 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.074 0.33 1 -0.53 1 2
Signaling events mediated by PRL

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
CCNE1 0.017 0.07 -10000 0 -0.42 22 22
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.021 0.065 -10000 0 -0.65 8 8
CDKN1A 0.009 0.083 -10000 0 -0.71 7 7
PRL-3/alpha Tubulin 0.034 0.043 -10000 0 -0.29 14 14
mol:Ca2+ -0.043 0.1 -10000 0 -0.35 80 80
AGT -0.02 0.15 -10000 0 -0.48 83 83
CCNA2 -0.041 0.11 -10000 0 -0.54 10 10
TUBA1B 0.027 0.006 -10000 0 -10000 0 0
EGR1 -0.007 0.11 -10000 0 -0.48 48 48
CDK2/Cyclin E1 0.021 0.12 -10000 0 -0.63 8 8
MAPK3 0.013 0.039 -10000 0 -0.29 14 14
PRL-2 /Rab GGTase beta 0.039 0.01 -10000 0 -10000 0 0
MAPK1 0.014 0.039 -10000 0 -0.29 14 14
PTP4A1 -0.005 0.081 -10000 0 -10000 0 0
PTP4A3 0.02 0.056 -10000 0 -0.42 14 14
PTP4A2 0.027 0.007 -10000 0 -10000 0 0
ITGB1 0.013 0.039 -10000 0 -0.29 14 14
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.014 0.049 -10000 0 -0.6 2 2
Rab GGTase beta/Rab GGTase alpha 0.037 0.028 -10000 0 -0.49 2 2
PRL-1/ATF-5 0.022 0.095 -10000 0 -0.54 1 1
RABGGTA 0.026 0.033 -10000 0 -0.65 2 2
BCAR1 -0.012 0.029 -10000 0 -0.5 1 1
RHOC 0.01 0.076 -10000 0 -0.6 8 8
RHOA 0.001 0.085 -10000 0 -0.33 42 42
cell motility 0.02 0.09 0.29 8 -0.41 14 22
PRL-1/alpha Tubulin 0.021 0.089 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.03 0.065 -10000 0 -0.37 21 21
ROCK1 0.019 0.081 0.28 4 -0.46 9 13
RABGGTB 0.027 0.007 -10000 0 -10000 0 0
CDK2 0.027 0.006 -10000 0 -10000 0 0
mitosis -0.004 0.08 -10000 0 -10000 0 0
ATF5 0.026 0.03 -10000 0 -0.42 4 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.032 0.052 -10000 0 -0.39 2 2
RGS9BP 0.014 0.093 -10000 0 -0.63 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.009 0.032 -10000 0 -0.46 3 3
mol:Na + 0.012 0.062 -10000 0 -0.26 23 23
mol:ADP -0.01 0.029 -10000 0 -0.32 6 6
GNAT2 0.02 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.025 0.1 -10000 0 -0.43 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.014 -10000 0 -0.24 1 1
GRK7 0.01 0.033 -10000 0 -0.42 3 3
CNGB3 -0.021 0.093 -10000 0 -0.42 42 42
Cone Metarhodopsin II/X-Arrestin 0.015 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.074 0.26 1 -0.42 15 16
Cone PDE6 0.04 0.095 -10000 0 -0.38 31 31
Cone Metarhodopsin II 0.024 0.024 -10000 0 -0.24 6 6
Na + (4 Units) 0.014 0.083 -10000 0 -0.42 15 15
GNAT2/GDP 0.034 0.09 -10000 0 -0.37 31 31
GNB5 0.028 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.003 0.03 -10000 0 -10000 0 0
Cone Transducin 0.035 0.056 -10000 0 -0.41 2 2
SLC24A2 -0.024 0.079 -10000 0 -0.42 33 33
GNB3/GNGT2 0.023 0.066 -10000 0 -0.31 31 31
GNB3 0.01 0.081 -10000 0 -0.42 30 30
GNAT2/GTP 0.019 0.006 -10000 0 -10000 0 0
CNGA3 -0.006 0.037 -10000 0 -0.42 5 5
ARR3 -0.007 0.02 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.012 0.063 -10000 0 -0.26 23 23
mol:Pi 0.025 0.1 -10000 0 -0.43 31 31
Cone CNG Channel 0.034 0.061 -10000 0 -0.4 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.024 0.079 -10000 0 -0.42 33 33
RGS9 0.001 0.11 -10000 0 -0.49 41 41
PDE6C 0 0.03 -10000 0 -0.42 2 2
GNGT2 0.023 0.032 -10000 0 -0.5 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.005 0.025 -10000 0 -0.42 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.044 0.037 -10000 0 -0.42 3 3
forebrain development 0.044 0.18 0.5 28 -0.57 36 64
GNAO1 0.012 0.096 -10000 0 -0.56 23 23
SMO/beta Arrestin2 0.032 0.044 -10000 0 -0.41 7 7
SMO 0.022 0.047 -10000 0 -0.65 4 4
ARRB2 0.024 0.03 -10000 0 -0.46 3 3
GLI3/SPOP 0.023 0.14 0.28 1 -0.57 34 35
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.047 0.076 -10000 0 -10000 0 0
GNAI1 0.023 0.041 -10000 0 -0.65 3 3
XPO1 0.029 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0.029 0.12 -10000 0 -0.85 12 12
SAP30 -0.004 0.12 -10000 0 -0.42 62 62
mol:GDP 0.022 0.047 -10000 0 -0.65 4 4
MIM/GLI2A 0.026 0.039 -10000 0 -0.65 2 2
IFT88 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GLI2 0.04 0.077 0.29 16 -0.33 5 21
GLI3 0.016 0.15 0.31 7 -0.56 41 48
CSNK1D 0.025 0.009 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.006 -10000 0 -10000 0 0
GNG2 0.027 0.005 -10000 0 -10000 0 0
Gi family/GTP 0.017 0.061 -10000 0 -0.33 18 18
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.15 -10000 0 -0.64 39 39
GLI2/Su(fu) 0.041 0.062 -10000 0 -0.48 5 5
FOXA2 0.015 0.12 -10000 0 -0.8 12 12
neural tube patterning 0.044 0.18 0.5 28 -0.57 36 64
SPOP 0.025 0.009 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.036 0.057 -10000 0 -0.46 2 2
GNB1 0.026 0.007 -10000 0 -10000 0 0
CSNK1G2 0.027 0.023 -10000 0 -0.65 1 1
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
MTSS1 0.026 0.039 -10000 0 -0.65 2 2
embryonic limb morphogenesis 0.044 0.18 0.5 28 -0.57 36 64
SUFU 0.023 0.033 -10000 0 -0.5 2 2
LGALS3 0 0.11 -10000 0 -0.42 53 53
catabolic process 0.045 0.14 0.35 6 -0.56 33 39
GLI3A/CBP 0.025 0.058 -10000 0 -0.39 13 13
KIF3A 0.027 0.007 -10000 0 -10000 0 0
GLI1 0.044 0.18 0.5 28 -0.59 36 64
RAB23 0.027 0.007 -10000 0 -10000 0 0
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
IFT172 0.027 0.006 -10000 0 -10000 0 0
RBBP7 0.028 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.094 -10000 0 -0.36 35 35
GNAZ 0.026 0.04 -10000 0 -0.65 3 3
RBBP4 0.026 0.024 -10000 0 -0.65 1 1
CSNK1G1 0.028 0.003 -10000 0 -10000 0 0
PIAS1 0.028 0.003 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GLI2/SPOP 0.045 0.06 0.33 3 -10000 0 3
STK36 0.029 0.009 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.023 0.058 -10000 0 -0.44 8 8
PTCH1 0.045 0.16 0.53 17 -0.83 9 26
MIM/GLI1 0.05 0.18 0.51 15 -0.79 14 29
CREBBP 0.025 0.057 -10000 0 -0.39 13 13
Su(fu)/SIN3/HDAC complex 0.006 0.16 0.27 4 -0.62 47 51
BARD1 signaling events

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
BARD1/CSTF1 0.03 0.064 -10000 0 -0.43 15 15
ATM 0.027 0.023 -10000 0 -0.65 1 1
UBE2D3 0.028 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.006 -10000 0 -10000 0 0
ATR 0.027 0.006 -10000 0 -10000 0 0
UBE2L3 0.027 0.005 -10000 0 -10000 0 0
FANCD2 0.024 0.018 -10000 0 -0.37 1 1
protein ubiquitination 0.051 0.072 -10000 0 -0.36 11 11
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.024 -10000 0 -0.42 1 1
MRE11A 0.028 0.004 -10000 0 -10000 0 0
DNA-PK 0.051 0.018 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.005 0.092 -10000 0 -0.5 13 13
FANCF 0.028 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.031 -10000 0 -0.42 4 4
CCNE1 0.017 0.07 -10000 0 -0.42 22 22
CDK2/Cyclin E1 0.032 0.053 -10000 0 -0.29 22 22
FANCG 0.028 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.069 -10000 0 -0.41 19 19
FANCE 0.026 0.017 -10000 0 -0.42 1 1
FANCC 0.028 0.004 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA -0.066 0.18 -10000 0 -0.42 182 182
DNA repair 0.029 0.13 0.45 36 -0.48 6 42
BRCA1/BARD1/ubiquitin 0.027 0.069 -10000 0 -0.41 19 19
BARD1/DNA-PK 0.057 0.063 -10000 0 -0.38 15 15
FANCL 0.027 0.006 -10000 0 -10000 0 0
mRNA polyadenylation -0.029 0.064 0.43 15 -10000 0 15
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.057 -10000 0 -0.5 2 2
BRCA1/BACH1/BARD1/TopBP1 0.041 0.062 -10000 0 -0.42 11 11
BRCA1/BARD1/P53 0.055 0.059 -10000 0 -0.38 11 11
BARD1/CSTF1/BRCA1 0.041 0.059 -10000 0 -0.42 9 9
BRCA1/BACH1 0.023 0.031 -10000 0 -0.42 4 4
BARD1 0.014 0.089 -10000 0 -0.63 16 16
PCNA 0.027 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.041 0.064 -10000 0 -0.42 12 12
BRCA1/BARD1/UbcH7 0.04 0.064 -10000 0 -0.42 12 12
BRCA1/BARD1/RAD51/PCNA 0.043 0.082 -10000 0 -0.39 15 15
BARD1/DNA-PK/P53 0.063 0.062 -10000 0 -0.36 12 12
BRCA1/BARD1/Ubiquitin 0.027 0.069 -10000 0 -0.41 19 19
BRCA1/BARD1/CTIP 0.035 0.065 -10000 0 -0.41 14 14
FA complex 0.008 0.064 -10000 0 -0.34 6 6
BARD1/EWS 0.029 0.07 -10000 0 -0.49 15 15
RBBP8 0.017 0.035 -10000 0 -0.68 2 2
TP53 0.025 0.009 -10000 0 -10000 0 0
TOPBP1 0.027 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.053 0.059 0.38 11 -10000 0 11
BRCA1/BARD1 0.057 0.074 -10000 0 -0.36 11 11
CSTF1 0.027 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.067 -10000 0 -0.47 16 16
CDK2 0.027 0.006 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.008 0.092 -10000 0 -0.42 39 39
RAD50 0.026 0.024 -10000 0 -0.65 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.069 -10000 0 -0.41 19 19
EWSR1 0.027 0.005 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.017 0.08 -10000 0 -0.63 13 13
alphaV beta3 Integrin 0.023 0.084 -10000 0 -0.45 25 25
PTK2 0.019 0.089 -10000 0 -0.51 10 10
positive regulation of JNK cascade 0.012 0.1 -10000 0 -0.36 38 38
CDC42/GDP 0.045 0.14 0.39 8 -0.44 44 52
Rac1/GDP 0.028 0.13 0.52 1 -0.45 42 43
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.007 -10000 0 -10000 0 0
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
CDC42/GTP 0.023 0.13 -10000 0 -0.45 38 38
nectin-3/I-afadin 0.032 0.052 -10000 0 -0.49 8 8
RAPGEF1 0.028 0.12 0.3 3 -0.5 8 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.12 -10000 0 -0.56 9 9
PDGFB-D/PDGFRB 0.017 0.08 -10000 0 -0.63 13 13
TLN1 0.01 0.021 -10000 0 -10000 0 0
Rap1/GTP 0.015 0.082 -10000 0 -0.36 6 6
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.019 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.032 0.052 -10000 0 -0.49 8 8
PVR 0.028 0.015 -10000 0 -0.42 1 1
Necl-5(dimer) 0.028 0.015 -10000 0 -0.42 1 1
mol:GDP 0.031 0.17 0.42 8 -0.55 47 55
MLLT4 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.061 0.07 -10000 0 -0.36 18 18
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.016 -10000 0 -0.28 1 1
positive regulation of lamellipodium assembly 0.016 0.099 -10000 0 -0.37 22 22
PVRL1 0.027 0.015 -10000 0 -0.42 1 1
PVRL3 0.02 0.066 -10000 0 -0.62 9 9
PVRL2 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
CDH1 -0.005 0.14 -10000 0 -0.65 40 40
CLDN1 -0.005 0.12 -10000 0 -0.46 58 58
JAM-A/CLDN1 0.038 0.093 -10000 0 -0.39 19 19
SRC 0.01 0.13 -10000 0 -0.6 11 11
ITGB3 0.008 0.1 -10000 0 -0.61 24 24
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.016 -10000 0 -0.28 1 1
FARP2 0.016 0.18 -10000 0 -0.68 40 40
RAC1 0.025 0.01 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.046 0.05 -10000 0 -0.42 8 8
nectin-1/I-afadin 0.038 0.016 -10000 0 -0.28 1 1
nectin-2/I-afadin 0.039 0.012 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.046 0.05 -10000 0 -0.42 8 8
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.01 -10000 0 -10000 0 0
F11R 0.027 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.012 0.1 -10000 0 -0.36 38 38
alphaV/beta3 Integrin/Talin 0.029 0.069 0.28 1 -0.35 17 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.012 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.012 -10000 0 -10000 0 0
PIP5K1C 0.012 0.023 -10000 0 -10000 0 0
VAV2 0.025 0.16 0.4 2 -0.62 24 26
RAP1/GDP 0.04 0.12 -10000 0 -0.43 14 14
ITGAV 0.026 0.028 -10000 0 -0.54 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.046 0.049 -10000 0 -0.42 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.032 0.052 -10000 0 -0.49 8 8
Rac1/GTP 0.021 0.12 -10000 0 -0.46 22 22
PTPRM 0.014 0.026 -10000 0 -0.24 8 8
E-cadherin/beta catenin/alpha catenin 0.046 0.093 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.007 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.007 -10000 0 -10000 0 0
NFATC1 0.041 0.11 0.34 28 -0.46 4 32
NFATC2 0.003 0.095 0.23 14 -0.29 52 66
NFATC3 0.02 0.028 -10000 0 -0.41 3 3
YWHAE 0.025 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.002 0.11 0.27 15 -0.35 39 54
Exportin 1/Ran/NUP214 0.051 0.018 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.017 0.1 0.27 1 -0.48 11 12
BCL2/BAX 0.04 0.023 -10000 0 -0.39 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.018 -10000 0 -10000 0 0
BAX 0.028 0.015 -10000 0 -0.42 1 1
MAPK14 0.025 0.008 -10000 0 -10000 0 0
BAD 0.027 0.028 -10000 0 -0.54 2 2
CABIN1/MEF2D 0.014 0.1 0.29 5 -0.39 23 28
Calcineurin A alpha-beta B1/BCL2 0.027 0.023 -10000 0 -0.65 1 1
FKBP8 0.027 0.023 -10000 0 -0.65 1 1
activation-induced cell death of T cells -0.014 0.1 0.39 23 -0.29 5 28
KPNB1 0.025 0.009 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.027 0.006 -10000 0 -10000 0 0
SFN -0.072 0.2 -10000 0 -0.44 185 185
MAP3K8 0.024 0.023 -10000 0 -0.42 2 2
NFAT4/CK1 alpha 0.027 0.031 -10000 0 -0.3 2 2
MEF2D/NFAT1/Cbp/p300 0.007 0.16 -10000 0 -0.45 32 32
CABIN1 0.001 0.1 0.25 12 -0.35 39 51
CALM1 0.025 0.01 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 0.028 0.005 -10000 0 -10000 0 0
CAMK4 0.018 0.074 -10000 0 -0.63 11 11
mol:Ca2+ -0.002 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.007 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.031 0.067 -10000 0 -0.49 14 14
YWHAB 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.02 0.058 -10000 0 -0.61 7 7
MAPK9 0.027 0.007 -10000 0 -10000 0 0
YWHAG 0.025 0.01 -10000 0 -10000 0 0
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.1 0.29 13 -0.42 7 20
PRKCH 0.027 0.024 -10000 0 -0.65 1 1
CABIN1/Cbp/p300 0.031 0.03 -10000 0 -0.49 1 1
CASP3 0.026 0.007 -10000 0 -10000 0 0
PIM1 0.025 0.022 -10000 0 -0.42 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.01 -10000 0 -10000 0 0
apoptosis 0.022 0.013 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.064 -10000 0 -0.37 11 11
PRKCB 0.019 0.066 -10000 0 -0.58 10 10
PRKCE 0.026 0.024 -10000 0 -0.65 1 1
JNK2/NFAT4 0.024 0.047 -10000 0 -0.37 3 3
BAD/BCL-XL 0.038 0.023 -10000 0 -0.39 2 2
PRKCD 0.021 0.045 -10000 0 -0.42 9 9
NUP214 0.028 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.041 -10000 0 -0.66 3 3
PRKCA 0.025 0.009 -10000 0 -10000 0 0
PRKCG -0.042 0.14 -10000 0 -0.42 98 98
PRKCQ -0.006 0.14 -10000 0 -0.55 51 51
FKBP38/BCL2 0.039 0.026 -10000 0 -0.49 2 2
EP300 0.021 0.029 -10000 0 -0.65 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.05 0.11 0.36 19 -0.45 3 22
CaM/Ca2+/FKBP38 0.03 0.026 -10000 0 -0.44 1 1
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.012 0.017 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.024 0.052 -10000 0 -0.41 10 10
NFATc/ERK1 0.042 0.094 0.31 5 -0.44 4 9
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.1 0.27 1 -0.49 11 12
NR4A1 -0.052 0.23 0.3 2 -0.59 121 123
GSK3B 0.026 0.008 -10000 0 -10000 0 0
positive T cell selection 0.02 0.028 -10000 0 -0.41 3 3
NFAT1/CK1 alpha 0.003 0.064 -10000 0 -0.28 6 6
RCH1/ KPNB1 0.037 0.013 -10000 0 -10000 0 0
YWHAQ 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.006 -10000 0 -10000 0 0
AKAP5 0.016 0.085 -10000 0 -0.65 14 14
MEF2D 0.02 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.055 0.11 0.35 24 -0.45 3 27
CREBBP 0.022 0.016 -10000 0 -10000 0 0
BCL2 0.027 0.023 -10000 0 -0.65 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.022 0.01 -10000 0 -10000 0 0
TRAF2/ASK1 0.035 0.011 -10000 0 -10000 0 0
ATM 0.027 0.023 -10000 0 -0.65 1 1
MAP2K3 0.033 0.084 0.28 37 -0.36 7 44
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.098 0.25 21 -0.34 35 56
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.005 0.1 -10000 0 -0.44 43 43
TXN 0.009 0.006 -10000 0 -0.16 1 1
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.007 -10000 0 -10000 0 0
GADD45B 0.027 0.023 -10000 0 -0.65 1 1
MAP3K1 0.028 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.007 -10000 0 -10000 0 0
MAP3K7 0.027 0.007 -10000 0 -10000 0 0
MAP3K4 0.026 0.015 -10000 0 -0.35 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.003 0.013 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.044 0.022 -10000 0 -10000 0 0
TRAF2 0.028 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.029 0.056 -10000 0 -0.33 1 1
TRAF6 0.009 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.059 0.2 -10000 0 -0.54 129 129
CCM2 0.025 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.023 0.14 -10000 0 -0.34 129 129
MAPK11 0.027 0.016 -10000 0 -0.42 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.008 0.13 -10000 0 -0.38 68 68
OSM/MEKK3 0.034 0.017 -10000 0 -10000 0 0
TAOK1 0.011 0.047 -10000 0 -0.37 13 13
TAOK2 0.017 0.014 -10000 0 -0.38 1 1
TAOK3 0.017 0.014 -10000 0 -0.38 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.007 -10000 0 -10000 0 0
MAP3K10 0.027 0.023 -10000 0 -0.65 1 1
MAP3K3 0.025 0.009 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.014 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.05 0.062 -10000 0 -0.34 5 5
Canonical NF-kappaB pathway

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
FBXW11 0.03 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.063 0.076 0.3 33 -10000 0 33
ERC1 0.027 0.007 -10000 0 -10000 0 0
RIP2/NOD2 -0.02 0.13 -10000 0 -0.3 151 151
NFKBIA 0.025 0.018 -10000 0 -0.37 1 1
BIRC2 0.028 0.004 -10000 0 -10000 0 0
IKBKB 0.027 0.006 -10000 0 -10000 0 0
RIPK2 0.027 0.016 -10000 0 -0.42 1 1
IKBKG 0.02 0.039 -10000 0 -10000 0 0
IKK complex/A20 0.043 0.078 -10000 0 -0.47 2 2
NEMO/A20/RIP2 0.027 0.016 -10000 0 -0.42 1 1
XPO1 0.027 0.006 -10000 0 -10000 0 0
NEMO/ATM 0.038 0.062 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.011 -10000 0 -10000 0 0
IKK complex/ELKS 0.035 0.056 -10000 0 -0.41 1 1
BCL10/MALT1/TRAF6 0.052 0.017 -10000 0 -10000 0 0
NOD2 -0.053 0.17 -10000 0 -0.42 155 155
NFKB1 0.03 0.023 -10000 0 -0.65 1 1
RELA 0.031 0.003 -10000 0 -10000 0 0
MALT1 0.027 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.041 0.008 -10000 0 -10000 0 0
ATM 0.027 0.023 -10000 0 -0.65 1 1
TNF/TNFR1A 0.028 0.061 -10000 0 -0.33 22 22
TRAF6 0.028 0.003 -10000 0 -10000 0 0
PRKCA 0.025 0.009 -10000 0 -10000 0 0
CHUK 0.027 0.007 -10000 0 -10000 0 0
UBE2D3 0.028 0.004 -10000 0 -10000 0 0
TNF 0.012 0.082 -10000 0 -0.46 25 25
NF kappa B1 p50/RelA 0.062 0.024 -10000 0 -0.41 1 1
BCL10 0.027 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.018 -10000 0 -0.37 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.03 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
IKK complex 0.047 0.066 -10000 0 -0.44 1 1
CYLD 0.027 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.046 0.066 -10000 0 -0.43 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.007 0.035 -10000 0 -0.42 4 4
SNTA1 0.023 0.051 -10000 0 -0.57 6 6
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.007 0.038 -10000 0 -0.42 6 6
MAPK12 0.002 0.037 0.17 1 -0.36 4 5
CCND1 0.007 0.035 -10000 0 -0.42 3 3
p38 gamma/SNTA1 0.026 0.061 -10000 0 -0.4 6 6
MAP2K3 0.025 0.009 -10000 0 -10000 0 0
PKN1 0.028 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.037 0.17 1 -0.35 4 5
MAP2K6 0.006 0.026 0.19 1 -0.41 3 4
MAPT 0.008 0.13 0.3 60 -0.39 54 114
MAPK13 0.013 0.044 -10000 0 -0.49 6 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.001 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP 0.039 0.054 -10000 0 -0.34 11 11
TC10/GTP 0.04 0.032 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.057 0.056 -10000 0 -0.4 10 10
HRAS 0.027 0.015 -10000 0 -0.42 1 1
APS homodimer 0.021 0.038 -10000 0 -0.42 6 6
GRB14 -0.01 0.16 -10000 0 -0.65 48 48
FOXO3 -0.016 0.16 -10000 0 -0.62 60 60
AKT1 0.02 0.12 0.43 29 -0.6 3 32
INSR 0.032 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.058 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.009 -10000 0 -10000 0 0
SORBS1 0.027 0.007 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
PTPN1 0.016 0.014 -10000 0 -10000 0 0
CAV1 0 0.068 0.5 1 -0.37 10 11
CBL/APS/CAP/Crk-II/C3G 0.063 0.044 -10000 0 -0.36 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.06 0.056 -10000 0 -0.4 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.048 -10000 0 -0.35 10 10
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.032 0.046 -10000 0 -10000 0 0
RPS6KB1 0.002 0.086 0.36 8 -0.5 3 11
PARD6A 0.024 0.04 -10000 0 -0.65 3 3
CBL 0.027 0.023 -10000 0 -0.65 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 -0.002 0.11 -10000 0 -0.52 35 35
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.026 0.084 -10000 0 -0.56 2 2
HRAS/GTP 0.012 0.045 -10000 0 -0.48 2 2
Insulin Receptor 0.032 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.064 0.057 -10000 0 -0.37 9 9
PRKCI 0.022 0.066 -10000 0 -0.5 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.009 0.093 -10000 0 -0.65 3 3
SHC1 0.026 0.016 -10000 0 -0.42 1 1
negative regulation of MAPKKK cascade 0.026 0.096 -10000 0 -0.43 33 33
PI3K 0.056 0.052 -10000 0 -0.36 10 10
NCK2 0.027 0.006 -10000 0 -10000 0 0
RHOQ 0.027 0.006 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.29 1 1
AKT2 0.021 0.12 0.42 31 -0.6 3 34
PRKCZ 0.022 0.073 -10000 0 -0.63 5 5
SH2B2 0.021 0.038 -10000 0 -0.42 6 6
SHC/SHIP 0.028 0.056 0.3 1 -0.39 10 11
F2RL2 -0.008 0.13 -10000 0 -0.47 62 62
TRIP10 0.028 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.048 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.069 0.034 -10000 0 -10000 0 0
RAPGEF1 0.028 0.004 -10000 0 -10000 0 0
RASA1 0.027 0.023 -10000 0 -0.65 1 1
NCK1 0.027 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.055 0.04 -10000 0 -0.38 1 1
TC10/GDP 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.056 0.032 -10000 0 -10000 0 0
INPP5D 0.013 0.056 0.31 1 -0.41 10 11
SOS1 0.027 0.006 -10000 0 -10000 0 0
SGK1 -0.033 0.17 -10000 0 -0.65 64 64
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.019 0.072 -10000 0 -0.65 10 10
p62DOK/RasGAP 0.027 0.097 -10000 0 -0.44 33 33
INS 0.021 0.025 -10000 0 -0.39 3 3
mol:PI-3-4-P2 0.013 0.055 0.31 1 -0.41 10 11
GRB2 0.025 0.009 -10000 0 -10000 0 0
EIF4EBP1 0.008 0.12 0.41 27 -0.52 7 34
PTPRA 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.036 0.009 -10000 0 -10000 0 0
PDPK1 0.027 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.028 0.036 -10000 0 -0.28 9 9
Insulin Receptor/Insulin/IRS1 0.043 0.052 -10000 0 -0.4 10 10
Insulin Receptor/Insulin/IRS3 0.039 0.022 -10000 0 -0.29 2 2
Par3/Par6 0.037 0.082 -10000 0 -0.36 15 15
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.019 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.046 0.023 -10000 0 -0.38 1 1
CDKN1B 0.022 0.073 -10000 0 -0.6 5 5
CDKN1A 0.023 0.061 -10000 0 -0.6 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.006 -10000 0 -10000 0 0
FOXO3 0.023 0.061 -10000 0 -0.6 3 3
AKT1 0.013 0.07 -10000 0 -0.63 5 5
BAD 0.027 0.028 -10000 0 -0.54 2 2
AKT3 0.016 0.015 -10000 0 -0.38 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.073 -10000 0 -0.6 5 5
AKT1/ASK1 0.034 0.075 -10000 0 -0.58 5 5
BAD/YWHAZ 0.054 0.022 -10000 0 -0.42 1 1
RICTOR 0.027 0.005 -10000 0 -10000 0 0
RAF1 0.026 0.008 -10000 0 -10000 0 0
JNK cascade -0.032 0.073 0.56 5 -10000 0 5
TSC1 0.022 0.065 -10000 0 -0.6 3 3
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.078 0.31 2 -0.6 5 7
EP300 0.027 0.024 -10000 0 -0.65 1 1
mol:GDP 0.012 0.071 -10000 0 -0.62 5 5
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.015 0.07 -10000 0 -0.6 5 5
YWHAQ 0.027 0.006 -10000 0 -10000 0 0
TBC1D4 0.013 0.005 -10000 0 -10000 0 0
MAP3K5 0.026 0.007 -10000 0 -10000 0 0
MAPKAP1 0.028 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.023 0.1 0.41 17 -0.28 22 39
YWHAH 0.027 0.005 -10000 0 -10000 0 0
AKT1S1 0.021 0.073 -10000 0 -0.6 5 5
CASP9 0.024 0.055 -10000 0 -0.6 2 2
YWHAB 0.027 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.041 0.082 0.35 7 -0.57 5 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.051 0.019 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.063 -10000 0 -0.55 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.021 -10000 0 -10000 0 0
CHUK 0.022 0.068 -10000 0 -0.6 5 5
BAD/BCL-XL 0.041 0.074 -10000 0 -0.57 5 5
mTORC2 0.035 0.008 -10000 0 -10000 0 0
AKT2 0.017 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.028 0.12 0.36 22 -0.54 15 37
PDPK1 0.027 0.007 -10000 0 -10000 0 0
MDM2 0.022 0.073 -10000 0 -0.6 5 5
MAPKKK cascade -0.034 0.077 0.59 5 -0.3 2 7
MDM2/Cbp/p300 0.049 0.078 0.31 2 -0.55 5 7
TSC1/TSC2 0.029 0.088 0.34 15 -0.58 5 20
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.075 0.3 2 -0.52 5 7
glucose import -0.004 0.063 0.21 1 -0.29 30 31
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.044 0.24 1 -0.33 5 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.004 0.063 -10000 0 -0.29 30 30
GSK3A 0.021 0.073 -10000 0 -0.6 5 5
FOXO1 0.023 0.058 -10000 0 -0.6 2 2
GSK3B 0.02 0.07 -10000 0 -0.6 5 5
SFN -0.072 0.2 -10000 0 -0.44 185 185
G1/S transition of mitotic cell cycle 0.029 0.083 0.34 14 -0.59 5 19
p27Kip1/14-3-3 family 0.022 0.083 -10000 0 -0.48 7 7
PRKACA 0.028 0.002 -10000 0 -10000 0 0
KPNA1 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.025 0.01 -10000 0 -10000 0 0
RHEB 0.025 0.01 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.051 0.062 -10000 0 -0.41 4 4
Ran/GTP/Exportin 1/HDAC1 0.007 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.038 0.065 -10000 0 -0.39 3 3
SUMO1 0.027 0.006 -10000 0 -10000 0 0
ZFPM1 0.024 0.043 -10000 0 -0.59 4 4
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.007 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.064 0.042 -10000 0 -10000 0 0
YY1/LSF 0.028 0.05 -10000 0 -0.67 1 1
SMG5 0.027 0.007 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.025 0.034 -10000 0 -0.3 3 3
I kappa B alpha/HDAC1 0.036 0.037 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
RELA 0.026 0.04 -10000 0 -10000 0 0
HDAC1/Smad7 0.046 0.023 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.033 0.036 -10000 0 -0.31 1 1
NuRD/MBD3 Complex 0.017 0.1 -10000 0 -0.44 37 37
NF kappa B1 p50/RelA 0.045 0.065 0.29 5 -0.57 1 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.027 0.18 -10000 0 -0.64 71 71
GATA1 -0.002 0.097 -10000 0 -0.42 44 44
Mad/Max 0.038 0.016 -10000 0 -0.29 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.02 0.093 -10000 0 -0.37 36 36
RBBP7 0.028 0.002 -10000 0 -10000 0 0
NPC 0.016 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.024 -10000 0 -0.65 1 1
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
NFKBIA 0.022 0.028 -10000 0 -10000 0 0
KAT2B 0.025 0.024 -10000 0 -0.65 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.033 -10000 0 -0.32 1 1
SIN3 complex 0.047 0.076 -10000 0 -10000 0 0
SMURF1 0.025 0.01 -10000 0 -10000 0 0
CHD3 0.025 0.009 -10000 0 -10000 0 0
SAP30 -0.004 0.12 -10000 0 -0.42 62 62
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.026 0.049 -10000 0 -0.59 1 1
YY1/HDAC2 0.03 0.048 -10000 0 -0.67 1 1
YY1/HDAC1 0.029 0.049 -10000 0 -0.67 1 1
NuRD/MBD2 Complex (MeCP1) 0.017 0.1 -10000 0 -0.45 36 36
PPARG 0.02 0.048 -10000 0 -0.38 7 7
HDAC8/hEST1B 0.054 0.015 -10000 0 -10000 0 0
UBE2I 0.027 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.033 0.036 -10000 0 -0.31 1 1
MBD3L2 -0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.023 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.028 0.093 -10000 0 -0.37 32 32
HDAC1 0.027 0.007 -10000 0 -10000 0 0
HDAC3 0.022 0.029 -10000 0 -0.34 1 1
HDAC2 0.026 0.007 -10000 0 -10000 0 0
YY1 0.023 0.028 -10000 0 -0.74 1 1
HDAC8 0.028 0.001 -10000 0 -10000 0 0
SMAD7 0.028 0.005 -10000 0 -10000 0 0
NCOR2 0.027 0.006 -10000 0 -10000 0 0
MXD1 0.027 0.016 -10000 0 -0.42 1 1
STAT3 0.023 0.017 -10000 0 -0.37 1 1
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.006 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.04 0.05 -10000 0 -0.63 1 1
YY1/SAP30/HDAC1 0.024 0.08 -10000 0 -0.46 3 3
EP300 0.027 0.024 -10000 0 -0.65 1 1
STAT3 (dimer non-phopshorylated) 0.023 0.017 -10000 0 -0.37 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.028 -10000 0 -10000 0 0
histone deacetylation 0.025 0.1 -10000 0 -0.45 36 36
STAT3 (dimer non-phopshorylated)/HDAC3 0.03 0.032 -10000 0 -10000 0 0
nuclear export -0.053 0.014 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GATAD2B 0.027 0.007 -10000 0 -10000 0 0
GATAD2A 0.028 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.003 0.12 -10000 0 -0.38 65 65
GATA1/HDAC1 0.021 0.073 -10000 0 -0.29 44 44
GATA1/HDAC3 0.024 0.063 -10000 0 -0.32 3 3
CHD4 0.027 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.028 0.061 -10000 0 -0.33 22 22
SIN3/HDAC complex/Mad/Max 0.017 0.091 -10000 0 -0.41 34 34
NuRD Complex 0.031 0.094 -10000 0 -0.37 32 32
positive regulation of chromatin silencing 0.061 0.041 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
MTA2 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.003 -10000 0 -10000 0 0
XPO1 0.027 0.006 -10000 0 -10000 0 0
SUMO1/HDAC1 0.041 0.042 -10000 0 -10000 0 0
HDAC complex 0.066 0.026 -10000 0 -0.38 1 1
GATA1/Fog1 0.02 0.076 -10000 0 -0.31 43 43
FKBP25/HDAC1/HDAC2 0.052 0.018 -10000 0 -10000 0 0
TNF 0.012 0.082 -10000 0 -0.46 25 25
negative regulation of cell growth 0.019 0.091 -10000 0 -0.4 34 34
NuRD/MBD2/PRMT5 Complex 0.017 0.1 -10000 0 -0.45 36 36
Ran/GTP/Exportin 1 0.041 0.043 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.028 0.046 -10000 0 -0.35 3 3
SIN3/HDAC complex/NCoR1 0.034 0.037 -10000 0 -10000 0 0
TFCP2 0.027 0.006 -10000 0 -10000 0 0
NR2C1 0.027 0.006 -10000 0 -10000 0 0
MBD3 0.027 0.028 -10000 0 -0.54 2 2
MBD2 0.028 0.005 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.006 -10000 0 -10000 0 0
PTK2 0.027 0.005 -10000 0 -10000 0 0
CRKL 0.012 0.054 -10000 0 -0.31 17 17
GRB2/SOS1/SHC 0.049 0.022 -10000 0 -10000 0 0
HRAS 0.027 0.015 -10000 0 -0.42 1 1
IRS1/Crk 0.019 0.053 -10000 0 -0.3 17 17
IGF-1R heterotetramer/IGF1/PTP1B 0.04 0.063 -10000 0 -0.4 8 8
AKT1 0.016 0.055 0.3 4 -10000 0 4
BAD 0.012 0.054 0.29 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.051 -10000 0 -0.3 17 17
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.024 0.057 -10000 0 -0.3 19 19
RAF1 0.002 0.11 0.34 1 -0.47 2 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.049 0.059 -10000 0 -0.32 6 6
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.023 0.061 -10000 0 -0.33 19 19
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 0.015 0.052 0.31 4 -10000 0 4
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.007 0.1 0.36 4 -10000 0 4
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.014 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.047 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.058 -10000 0 -0.32 5 5
IGF-1R heterotetramer 0.028 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.06 -10000 0 -0.3 18 18
Crk/p130 Cas/Paxillin 0.052 0.063 -10000 0 -0.32 7 7
IGF1R 0.028 0.021 -10000 0 -10000 0 0
IGF1 0.01 0.098 -10000 0 -0.48 32 32
IRS2/Crk 0.017 0.06 -10000 0 -0.32 9 9
PI3K 0.051 0.06 -10000 0 -0.33 7 7
apoptosis -0.034 0.066 -10000 0 -0.3 18 18
HRAS/GDP 0.02 0.011 -10000 0 -0.29 1 1
PRKCD 0.015 0.069 -10000 0 -0.42 13 13
RAF1/14-3-3 E 0.018 0.11 0.43 2 -0.43 1 3
BAD/14-3-3 0.039 0.079 0.35 26 -10000 0 26
PRKCZ 0.015 0.058 0.3 5 -0.33 2 7
Crk/p130 Cas/Paxillin/FAK1 0.032 0.046 -10000 0 -10000 0 0
PTPN1 0.027 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.017 0.06 -10000 0 -0.36 16 16
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.047 0.058 -10000 0 -0.35 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
IRS1/NCK2 0.029 0.058 -10000 0 -0.3 18 18
GRB10 0.025 0.009 -10000 0 -10000 0 0
PTPN11 0.013 0.055 -10000 0 -0.3 19 19
IRS1 0.014 0.061 0.22 2 -0.33 19 21
IRS2 0.007 0.062 -10000 0 -0.31 19 19
IGF-1R heterotetramer/IGF1 0.026 0.077 -10000 0 -0.37 23 23
GRB2 0.025 0.009 -10000 0 -10000 0 0
PDPK1 0.023 0.059 0.3 6 -10000 0 6
YWHAE 0.025 0.009 -10000 0 -10000 0 0
PRKD1 0.016 0.071 -10000 0 -0.44 13 13
SHC1 0.026 0.016 -10000 0 -0.42 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.007 -10000 0 -10000 0 0
HDAC3 0.027 0.007 -10000 0 -10000 0 0
VDR 0.024 0.046 -10000 0 -0.65 4 4
Cbp/p300/PCAF 0.048 0.035 -10000 0 -0.79 1 1
EP300 0.027 0.024 -10000 0 -0.65 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.018 0.076 -10000 0 -0.39 9 9
KAT2B 0.025 0.024 -10000 0 -0.65 1 1
MAPK14 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.011 0.06 0.26 3 -10000 0 3
RAR alpha/9cRA/Cyclin H 0.042 0.079 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.027 0.065 0.24 3 -0.41 5 8
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.01 0.088 -10000 0 -0.35 40 40
NCOR2 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.035 -10000 0 -0.49 4 4
RXRs/RARs/NRIP1/9cRA 0.018 0.099 -10000 0 -0.54 4 4
NCOA2 -0.004 0.14 -10000 0 -0.65 40 40
NCOA3 0.027 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.046 -10000 0 -0.65 4 4
RARG 0.027 0.016 -10000 0 -0.42 1 1
RAR gamma1/9cRA 0.037 0.013 -10000 0 -0.24 1 1
MAPK3 0.027 0.007 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.023 0.058 -10000 0 -0.61 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.024 0.079 -10000 0 -0.44 4 4
RARA 0.012 0.042 -10000 0 -0.28 8 8
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.017 0.081 0.24 2 -0.41 9 11
PRKCA 0.028 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.018 0.11 0.34 2 -0.64 5 7
RXRG 0.003 0.062 -10000 0 -0.41 7 7
RXRA 0.016 0.041 -10000 0 -0.3 3 3
RXRB 0.008 0.055 -10000 0 -0.38 5 5
VDR/Vit D3/DNA 0.018 0.035 -10000 0 -0.49 4 4
RBP1 0.026 0.027 -10000 0 -0.42 3 3
CRBP1/9-cic-RA 0.019 0.019 -10000 0 -0.29 3 3
RARB 0.026 0.034 -10000 0 -0.65 2 2
PRKCG -0.023 0.14 -10000 0 -0.42 98 98
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.013 0.089 -10000 0 -0.5 3 3
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.023 0.09 0.31 2 -0.43 6 8
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.12 0.31 42 -0.38 35 77
RXRs/RARs/NRIP1/9cRA/HDAC3 0.022 0.11 0.36 3 -0.6 5 8
positive regulation of DNA binding 0.026 0.068 -10000 0 -0.32 1 1
NRIP1 0.016 0.11 -10000 0 -0.72 2 2
RXRs/RARs 0.005 0.11 -10000 0 -0.61 6 6
RXRs/RXRs/DNA/9cRA 0.01 0.072 -10000 0 -0.48 3 3
PRKACA 0.028 0.002 -10000 0 -10000 0 0
CDK7 0.028 0.005 -10000 0 -10000 0 0
TFIIH 0.054 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.078 -10000 0 -10000 0 0
CCNH 0.028 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.022 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.024 -10000 0 -0.65 1 1
HDAC4 0.026 0.014 -10000 0 -0.35 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.015 0.016 0.29 2 -10000 0 2
CDKN1A -0.005 0.015 -10000 0 -10000 0 0
KAT2B 0.025 0.024 -10000 0 -0.65 1 1
BAX 0.028 0.015 -10000 0 -0.42 1 1
FOXO3 -0.006 0.017 0.48 1 -10000 0 1
FOXO1 0.027 0.006 -10000 0 -10000 0 0
FOXO4 0.02 0.013 -10000 0 -0.31 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
TAT 0.008 0.066 -10000 0 -0.42 19 19
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.01 0.052 -10000 0 -0.3 26 26
PPARGC1A -0.012 0.16 -10000 0 -0.65 52 52
FHL2 0.018 0.074 -10000 0 -0.5 16 16
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.012 -10000 0 -10000 0 0
HIST2H4A 0.015 0.016 -10000 0 -0.29 2 2
SIRT1/FOXO3a 0.012 0.027 0.32 1 -10000 0 1
SIRT1 0.023 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.028 0.035 -10000 0 -0.28 1 1
apoptosis -0.049 0.019 -10000 0 -10000 0 0
SIRT1/PGC1A 0.006 0.11 -10000 0 -0.42 51 51
p53/SIRT1 0.026 0.014 -10000 0 -10000 0 0
SIRT1/FOXO4 0.032 0.025 -10000 0 -0.27 1 1
FOXO1/FHL2/SIRT1 0.042 0.048 -10000 0 -0.38 8 8
HIST1H1E 0.018 0.014 -10000 0 -0.32 1 1
SIRT1/p300 0.035 0.021 -10000 0 -0.49 1 1
muscle cell differentiation -0.021 0.051 0.43 1 -10000 0 1
TP53 0.021 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.049 0.019 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
MEF2D 0.027 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.026 0.049 -10000 0 -0.29 19 19
ACSS2 0.016 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.021 0.051 -10000 0 -0.43 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.061 0.031 -10000 0 -0.38 1 1
HDAC3 0.027 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.022 0.073 -10000 0 -0.29 44 44
GATA1/HDAC5 0.021 0.07 -10000 0 -0.3 38 38
GATA2/HDAC5 -0.003 0.14 -10000 0 -0.46 70 70
HDAC5/BCL6/BCoR 0.049 0.026 -10000 0 -0.42 1 1
HDAC9 0.024 0.025 -10000 0 -0.65 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.052 0.02 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.015 -10000 0 -0.24 1 1
HDAC5/YWHAB 0.036 0.023 -10000 0 -0.49 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.007 -10000 0 -10000 0 0
GATA2 -0.027 0.18 -10000 0 -0.64 71 71
HDAC4/RFXANK 0.039 0.018 -10000 0 -0.29 1 1
BCOR 0.028 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.027 0.024 -10000 0 -0.65 1 1
HDAC5 0.024 0.025 -10000 0 -0.65 1 1
GNB1/GNG2 0.038 0.012 -10000 0 -10000 0 0
Histones 0.032 0.035 -10000 0 -10000 0 0
ADRBK1 0.028 0.003 -10000 0 -10000 0 0
HDAC4 0.026 0.014 -10000 0 -0.35 1 1
XPO1 0.027 0.006 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.023 -10000 0 -0.49 1 1
HDAC4/Ubc9 0.037 0.016 -10000 0 -10000 0 0
HDAC7 0.027 0.006 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.036 0.022 -10000 0 -0.49 1 1
TUBA1B 0.027 0.006 -10000 0 -10000 0 0
HDAC6 0.028 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.036 0.025 -10000 0 -0.39 2 2
CAMK4 0.018 0.074 -10000 0 -0.63 11 11
Tubulin/HDAC6 0.05 0.025 -10000 0 -0.42 1 1
SUMO1 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.027 0.007 -10000 0 -10000 0 0
GATA1 -0.002 0.097 -10000 0 -0.42 44 44
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
NR3C1 0.026 0.016 -10000 0 -0.42 1 1
SUMO1/HDAC4 0.041 0.042 -10000 0 -10000 0 0
SRF 0.026 0.007 -10000 0 -10000 0 0
HDAC4/YWHAB 0.037 0.016 -10000 0 -0.24 1 1
Tubulin 0.037 0.022 -10000 0 -0.49 1 1
HDAC4/14-3-3 E 0.036 0.017 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.04 0.01 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.049 0.022 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.055 -10000 0 -0.42 10 10
HDAC4/ER alpha 0.022 0.087 -10000 0 -0.43 28 28
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.035 -10000 0 -10000 0 0
cell motility 0.05 0.024 -10000 0 -0.42 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.013 -10000 0 -10000 0 0
BCL6 0.027 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.026 0.014 -10000 0 -0.35 1 1
Hsp90/HDAC6 0.04 0.008 -10000 0 -10000 0 0
ESR1 0.005 0.11 -10000 0 -0.56 32 32
HDAC6/HDAC11 0.038 0.016 -10000 0 -0.28 1 1
Ran/GTP/Exportin 1 0.041 0.043 -10000 0 -10000 0 0
NPC 0.016 0.004 -10000 0 -10000 0 0
MEF2C 0.027 0.016 -10000 0 -0.42 1 1
RAN 0.027 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.069 0.035 -10000 0 -10000 0 0
GNG2 0.027 0.005 -10000 0 -10000 0 0
NCOR2 0.027 0.006 -10000 0 -10000 0 0
TUBB2A 0.026 0.024 -10000 0 -0.65 1 1
HDAC11 0.025 0.024 -10000 0 -0.65 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RANBP2 0.027 0.006 -10000 0 -10000 0 0
ANKRA2 0.028 0.005 -10000 0 -10000 0 0
RFXANK 0.028 0.015 -10000 0 -0.42 1 1
nuclear import -0.034 0.022 0.36 1 -10000 0 1
Circadian rhythm pathway

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
chromatin modification 0.054 0.032 -9999 0 -10000 0 0
CLOCK 0.022 0.076 -9999 0 -0.65 11 11
TIMELESS/CRY2 0.045 0.03 -9999 0 -10000 0 0
DEC1/BMAL1 0.036 0.014 -9999 0 -0.29 1 1
ATR 0.027 0.006 -9999 0 -10000 0 0
NR1D1 0.02 0.05 -9999 0 -10000 0 0
ARNTL 0.031 0.005 -9999 0 -10000 0 0
TIMELESS 0.027 0.025 -9999 0 -10000 0 0
NPAS2 -0.002 0.14 -9999 0 -0.51 54 54
CRY2 0.028 0.004 -9999 0 -10000 0 0
mol:CO -0.012 0.004 -9999 0 -10000 0 0
CHEK1 0.028 0.004 -9999 0 -10000 0 0
mol:HEME 0.012 0.004 -9999 0 -10000 0 0
PER1 0.025 0.009 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.042 0.1 -9999 0 -0.41 36 36
BMAL1/CLOCK 0.034 0.078 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.054 0.032 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.055 0.032 -9999 0 -10000 0 0
mol:NADPH 0.012 0.004 -9999 0 -10000 0 0
PER1/TIMELESS 0.042 0.028 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.009 0.023 -9999 0 -0.42 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.012 -10000 0 -10000 0 0
DOCK1 0.026 0.024 -10000 0 -0.65 1 1
ITGA4 0.012 0.08 -10000 0 -0.42 29 29
RAC1 0.025 0.01 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.027 0.06 -10000 0 -0.29 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.043 0.055 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.038 0.05 -10000 0 -10000 0 0
lamellipodium assembly 0.033 0.051 0.27 1 -0.38 8 9
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.011 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.028 0.004 -10000 0 -10000 0 0
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.045 0.05 -10000 0 -10000 0 0
cell adhesion 0.048 0.051 -10000 0 -10000 0 0
CRKL/CBL 0.04 0.02 -10000 0 -0.49 1 1
alpha4/beta1 Integrin/Paxillin 0.037 0.05 -10000 0 -10000 0 0
ITGB1 0.027 0.007 -10000 0 -10000 0 0
ITGB7 0.027 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.092 -10000 0 -0.38 14 14
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.42 2 2
VCAM1 -0.012 0.13 -10000 0 -0.43 74 74
alpha4/beta1 Integrin/Paxillin/Talin 0.05 0.052 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.053 -10000 0 -10000 0 0
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
mol:GDP -0.046 0.052 -10000 0 -10000 0 0
CBL 0.027 0.023 -10000 0 -0.65 1 1
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GIT1 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.05 0.052 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.055 -10000 0 -0.42 8 8
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.025 0.033 -10000 0 -0.65 2 2
positive regulation of NF-kappaB transcription factor activity 0.036 0.033 -10000 0 -0.49 3 3
MAP2K4 0.036 0.044 -10000 0 -0.44 2 2
IKBKB 0.027 0.006 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.016 -10000 0 -0.42 1 1
TNFRSF10A 0.023 0.048 -10000 0 -0.59 5 5
SMPD1 0.017 0.014 -10000 0 -0.24 2 2
IKBKG 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.026 0.024 -10000 0 -0.65 1 1
TRAIL/TRAILR2 0.037 0.028 -10000 0 -0.49 2 2
TRAIL/TRAILR3 0.033 0.046 -10000 0 -0.35 11 11
TRAIL/TRAILR1 0.034 0.046 -10000 0 -0.49 6 6
TRAIL/TRAILR4 0.036 0.033 -10000 0 -0.49 3 3
TRAIL/TRAILR1/DAP3/GTP 0.044 0.04 -10000 0 -0.37 6 6
IKK complex 0.027 0.05 -10000 0 -0.45 1 1
RIPK1 0.027 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.025 -10000 0 -0.49 2 2
MAP3K1 0.033 0.042 -10000 0 -0.43 3 3
TRAILR4 (trimer) 0.026 0.024 -10000 0 -0.65 1 1
TRADD 0.026 0.007 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.048 -10000 0 -0.59 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.03 0.04 -10000 0 -0.4 6 6
CFLAR 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.017 0.026 -10000 0 -0.49 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.067 0.048 -10000 0 -0.35 6 6
mol:ceramide 0.017 0.014 -10000 0 -0.24 2 2
FADD 0.028 0.003 -10000 0 -10000 0 0
MAPK8 0.037 0.052 0.29 6 -0.38 1 7
TRAF2 0.028 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.021 0.053 -10000 0 -0.44 11 11
CHUK 0.027 0.007 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.043 -10000 0 -0.42 6 6
DAP3 0.027 0.007 -10000 0 -10000 0 0
CASP10 0.012 0.034 -10000 0 -0.43 4 4
JNK cascade 0.036 0.033 -10000 0 -0.49 3 3
TRAIL (trimer) 0.025 0.033 -10000 0 -0.65 2 2
TNFRSF10C 0.021 0.053 -10000 0 -0.44 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD 0.055 0.042 -10000 0 -0.35 6 6
TRAIL/TRAILR2/FADD 0.05 0.029 -10000 0 -0.42 2 2
cell death 0.017 0.014 -10000 0 -0.24 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.032 0.025 -10000 0 -0.37 2 2
TRAILR2 (trimer) 0.026 0.016 -10000 0 -0.42 1 1
CASP8 -0.006 0.11 -10000 0 -0.61 29 29
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.069 0.038 -10000 0 -0.36 2 2
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.041 0.017 -9999 0 -0.29 2 2
FBXW11 0.027 0.007 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.027 0.051 -9999 0 -0.42 10 10
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.066 -9999 0 -0.42 1 1
NFKBIA 0.012 0.037 -9999 0 -0.37 3 3
MAPK14 0.027 0.007 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0.019 -9999 0 -0.42 1 1
ARRB2 0.015 0.02 -9999 0 -0.5 1 1
REL 0.019 0.071 -9999 0 -0.6 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.032 0.022 -9999 0 -0.42 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.018 -9999 0 -0.42 1 1
PIK3CA 0.027 0.006 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0.024 -9999 0 -0.49 1 1
PIK3R1 0.028 0.005 -9999 0 -10000 0 0
NFKB1 0.018 0.018 -9999 0 -0.49 1 1
RELA 0.028 0.003 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.016 0.056 -9999 0 -0.35 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.029 0.074 -9999 0 -0.44 2 2
SRC 0.027 0.007 -9999 0 -10000 0 0
PI3K 0.039 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.016 0.056 -9999 0 -0.35 5 5
IKBKB 0.027 0.006 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -9999 0 -10000 0 0
SYK 0.024 0.048 -9999 0 -0.59 5 5
I kappa B alpha/PIK3R1 0.021 0.066 -9999 0 -0.36 4 4
cell death 0.027 0.071 -9999 0 -0.42 2 2
NF kappa B1 p105/c-Rel 0.027 0.051 -9999 0 -0.42 10 10
LCK 0.003 0.1 -9999 0 -0.44 44 44
BCL3 0.027 0.021 -9999 0 -0.42 2 2
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.044 0.023 -10000 0 -0.36 1 1
MAPK9 0.009 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.013 0.055 0.2 3 -0.3 29 32
GNB1/GNG2 0.035 0.011 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.017 0.016 -10000 0 -0.3 2 2
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0 0.004 0.079 2 -10000 0 2
GNAL 0.026 0.028 -10000 0 -0.54 2 2
GNG2 0.027 0.005 -10000 0 -10000 0 0
CRH -0.016 0.079 -10000 0 -0.42 29 29
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.034 -10000 0 -0.37 7 7
MAPK11 0.009 0.006 -10000 0 -0.16 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.022 0.044 0.3 6 -0.47 1 7
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.002 0.08 -10000 0 -0.35 38 38
AP2 0.04 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.016 -10000 0 -10000 0 0
CLTB 0.027 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0.009 -10000 0 -10000 0 0
CD4 0.012 0.081 -10000 0 -0.42 30 30
CLTA 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.009 0.017 -10000 0 -0.49 1 1
mol:PI-4-5-P2 0.008 0.013 -10000 0 -0.36 1 1
ARF1/GTP 0.031 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.016 -10000 0 -0.42 1 1
mol:Choline 0.008 0.013 -10000 0 -0.36 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.007 -10000 0 -10000 0 0
DDEF1 0.008 0.014 -10000 0 -0.36 1 1
ARF1/GDP 0.004 0.02 -10000 0 -0.4 1 1
AP2M1 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.007 -10000 0 -10000 0 0
Rac/GTP 0.019 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.021 -10000 0 -0.37 1 1
ARFIP2 0.023 0.012 -10000 0 -10000 0 0
COPA 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.01 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.009 0.064 -10000 0 -0.28 35 35
ARF1/GTP/ARHGAP10 0.019 0.005 -10000 0 -10000 0 0
GGA3 0.025 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.022 0.054 -10000 0 -0.24 33 33
AP2A1 0.028 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.025 -10000 0 -0.28 4 4
ARF1/GDP/Membrin 0.018 0.068 -10000 0 -0.32 33 33
Arfaptin 2/Rac/GDP 0.033 0.014 -10000 0 -10000 0 0
CYTH2 0.029 0.004 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.034 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.007 -10000 0 -10000 0 0
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 0.016 0.045 -10000 0 -0.35 1 1
PLD2 0.008 0.013 -10000 0 -0.36 1 1
ARF-GAP1/v-SNARE 0.009 0.017 -10000 0 -0.49 1 1
PIP5K1A 0.008 0.013 -10000 0 -0.36 1 1
ARF1/GTP/Membrin/GBF1/p115 0.025 0.031 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.013 -10000 0 -0.36 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.017 -10000 0 -0.49 1 1
GOSR2 0.014 0.009 -10000 0 -10000 0 0
USO1 0.013 0.025 -10000 0 -0.31 5 5
GBF1 0.01 0.038 -10000 0 -0.31 12 12
ARF1/GTP/Arfaptin 2 0.038 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.042 0.056 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD2 -0.008 0.05 -10000 0 -0.32 2 2
SMAD3 0.031 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4 0.015 0.13 0.35 2 -0.51 43 45
SMAD4/Ubc9/PIASy 0.052 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.043 0.057 -10000 0 -10000 0 0
PPM1A 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.053 -10000 0 -0.32 1 1
MAP3K1 0.028 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.036 0.045 -10000 0 -0.49 6 6
MAPK3 0.026 0.007 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.028 0.004 -10000 0 -10000 0 0
CTDSP1 0.027 0.007 -10000 0 -10000 0 0
CTDSP2 0.027 0.006 -10000 0 -10000 0 0
CTDSPL 0.026 0.008 -10000 0 -10000 0 0
KPNB1 0.025 0.009 -10000 0 -10000 0 0
TGFBRAP1 0.022 0.056 -10000 0 -0.65 6 6
UBE2I 0.027 0.007 -10000 0 -10000 0 0
NUP153 0.027 0.007 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.018 0.071 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.035 0.26 1 -10000 0 1
myoblast fusion -0.021 0.043 0.21 1 -10000 0 1
mol:GTP 0.012 0.038 -10000 0 -0.25 2 2
regulation of calcium-dependent cell-cell adhesion -0.043 0.046 -10000 0 -10000 0 0
ARF1/GTP 0.027 0.034 -10000 0 -0.24 1 1
mol:GM1 0.005 0.027 -10000 0 -0.24 1 1
mol:Choline 0.012 0.023 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.062 -10000 0 -0.34 17 17
MAPK3 0.02 0.042 -10000 0 -0.34 1 1
ARF6/GTP/NME1/Tiam1 0.043 0.047 -10000 0 -10000 0 0
ARF1 0.027 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.044 -10000 0 -0.21 1 1
ARF1/GDP 0.024 0.055 0.27 1 -0.26 1 2
ARF6 0.028 0.022 -10000 0 -10000 0 0
RAB11A 0.028 0.003 -10000 0 -10000 0 0
TIAM1 0.027 0.022 -10000 0 -0.59 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.04 -10000 0 -10000 0 0
actin filament bundle formation -0.027 0.054 0.24 1 -10000 0 1
KALRN 0.012 0.032 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.039 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.054 -10000 0 -0.24 1 1
NME1 0.024 0.028 -10000 0 -0.42 3 3
Rac1/GDP 0.025 0.052 -10000 0 -0.26 1 1
substrate adhesion-dependent cell spreading 0.012 0.038 -10000 0 -0.25 2 2
cortical actin cytoskeleton organization 0.007 0.062 -10000 0 -0.34 17 17
RAC1 0.025 0.01 -10000 0 -10000 0 0
liver development 0.012 0.038 -10000 0 -0.25 2 2
ARF6/GTP 0.012 0.038 -10000 0 -0.25 2 2
RhoA/GTP 0.027 0.034 -10000 0 -0.24 1 1
mol:GDP 0.01 0.044 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.044 0.035 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
PLD1 0.017 0.028 -10000 0 -10000 0 0
RAB11FIP3 0.027 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.062 -10000 0 -0.34 17 17
ruffle organization 0.012 0.035 -10000 0 -0.26 1 1
regulation of epithelial cell migration 0.012 0.038 -10000 0 -0.25 2 2
PLD2 0.015 0.03 -10000 0 -0.24 1 1
PIP5K1A 0.012 0.035 -10000 0 -0.26 1 1
mol:Phosphatidic acid 0.012 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.063 -10000 0 -0.34 17 17
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.007 -9999 0 -10000 0 0
MDM2/SUMO1 0.038 0.044 -9999 0 -10000 0 0
HDAC4 0.026 0.014 -9999 0 -0.35 1 1
Ran/GTP/Exportin 1/HDAC1 0.008 0.005 -9999 0 -10000 0 0
SUMO1 0.027 0.006 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.037 -9999 0 -0.18 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.017 0.01 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.027 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.041 0.042 -9999 0 -10000 0 0
SUMO1/HDAC1 0.041 0.042 -9999 0 -10000 0 0
RANGAP1 0.027 0.005 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.064 0.024 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.007 -9999 0 -10000 0 0
Ran/GTP 0.027 0.042 -9999 0 -0.24 2 2
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.006 -9999 0 -10000 0 0
UBE2I 0.027 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.039 -9999 0 -10000 0 0
NPC 0.016 0.004 -9999 0 -10000 0 0
PIAS2 0.028 0.005 -9999 0 -10000 0 0
PIAS1 0.028 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.018 -9999 0 -0.29 1 1
FBXW11 0.027 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -9999 0 -10000 0 0
CHUK 0.027 0.007 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.068 0.035 -9999 0 -10000 0 0
NFKB1 0.027 0.023 -9999 0 -0.65 1 1
MAP3K14 0.025 0.017 -9999 0 -0.42 1 1
NF kappa B1 p50/RelB 0.04 0.019 -9999 0 -0.49 1 1
RELB 0.028 0.003 -9999 0 -10000 0 0
NFKB2 0.027 0.007 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.036 0.01 -9999 0 -10000 0 0
regulation of B cell activation 0.035 0.01 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 879 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Y8.A8S1 TCGA.Y8.A8S0 TCGA.Y8.A8RZ TCGA.Y8.A8RY
109_MAP3K5 -0.02 0.17 0.055 0.17
47_PPARGC1A 0.028 0.028 0.028 0.028
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 -0.65 0.028
105_BMP7 0.028 0.028 -0.65 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR 0.073 0 0.073 0
30_TGFB1/TGF beta receptor Type II 0.028 0.028 0.028 0.028
84_STAT5B -0.034 -0.11 -0.22 -0.11
84_STAT5A -0.034 -0.11 -0.22 -0.11
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIPAN-TP/19438837/KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIPAN-TP/19775237/GDAC_Gistic2Report_19782144/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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