PARADIGM pathway analysis of mRNASeq expression and copy number data
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1RV0N3Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1RV0N3Q
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 43 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 217
PDGFR-alpha signaling pathway 202
HIF-1-alpha transcription factor network 187
TCR signaling in naïve CD8+ T cells 167
Glypican 1 network 150
TCGA08_p53 142
Angiopoietin receptor Tie2-mediated signaling 140
TCGA08_retinoblastoma 133
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 14421 34 -0.5 0.028 1000 -1000 -0.043 -1000
EGFR-dependent Endothelin signaling events 0.3127 278 5858 21 -0.54 0.037 1000 -1000 -0.054 -1000
FOXA2 and FOXA3 transcription factor networks 0.2441 217 10005 46 -1 0.031 1000 -1000 -0.092 -1000
PDGFR-alpha signaling pathway 0.2272 202 8888 44 -0.24 0.036 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.2103 187 14282 76 -0.65 0.043 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 0.1879 167 15614 93 -0.35 0.16 1000 -1000 -0.058 -1000
Glypican 1 network 0.1687 150 7230 48 -0.41 0.048 1000 -1000 -0.041 -1000
TCGA08_p53 0.1597 142 996 7 -0.26 0.15 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1575 140 12330 88 -0.46 0.032 1000 -1000 -0.077 -1000
TCGA08_retinoblastoma 0.1496 133 1067 8 -0.37 0.097 1000 -1000 -0.007 -1000
BMP receptor signaling 0.1271 113 9205 81 -0.45 0.055 1000 -1000 -0.078 -1000
Glypican 2 network 0.1260 112 450 4 -0.023 -1000 1000 -1000 -0.005 -1000
Aurora B signaling 0.1260 112 7544 67 -0.26 0.036 1000 -1000 -0.057 -1000
amb2 Integrin signaling 0.1249 111 9114 82 -0.44 0.034 1000 -1000 -0.06 -1000
IL12-mediated signaling events 0.1080 96 8367 87 -0.22 0.07 1000 -1000 -0.1 -1000
IL4-mediated signaling events 0.0979 87 7987 91 -0.7 0.5 1000 -1000 -0.13 -1000
Syndecan-4-mediated signaling events 0.0945 84 5673 67 -0.3 0.1 1000 -1000 -0.064 -1000
Effects of Botulinum toxin 0.0900 80 2103 26 -0.2 0.028 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0832 74 5772 78 -0.27 0.05 1000 -1000 -0.066 -1000
Arf6 signaling events 0.0776 69 4308 62 -0.54 0.06 1000 -1000 -0.049 -1000
Thromboxane A2 receptor signaling 0.0742 66 6936 105 -0.54 0.034 1000 -1000 -0.061 -1000
Endothelins 0.0731 65 6262 96 -0.49 0.027 1000 -1000 -0.069 -1000
FOXM1 transcription factor network 0.0731 65 3353 51 -0.36 0.027 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.0697 62 2132 34 -0.14 0.028 1000 -1000 -0.064 -1000
Signaling mediated by p38-alpha and p38-beta 0.0697 62 2745 44 -0.087 0.027 1000 -1000 -0.041 -1000
LPA4-mediated signaling events 0.0686 61 742 12 -0.079 0.009 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 0.0675 60 1030 17 -0.09 0.027 1000 -1000 -0.044 -1000
S1P1 pathway 0.0675 60 2161 36 -0.11 0.026 1000 -1000 -0.05 -1000
Coregulation of Androgen receptor activity 0.0664 59 4491 76 -0.77 0.054 1000 -1000 -0.033 -1000
Signaling events mediated by the Hedgehog family 0.0630 56 2921 52 -0.12 0.042 1000 -1000 -0.058 -1000
Ephrin A reverse signaling 0.0607 54 384 7 -0.021 0 1000 -1000 -0.028 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0607 54 3705 68 -0.33 0.067 1000 -1000 -0.093 -1000
Caspase cascade in apoptosis 0.0596 53 3952 74 -0.32 0.038 1000 -1000 -0.049 -1000
Aurora C signaling 0.0596 53 375 7 -0.15 0.024 1000 -1000 -0.022 -1000
Reelin signaling pathway 0.0596 53 2981 56 -0.12 0.072 1000 -1000 -0.061 -1000
Calcium signaling in the CD4+ TCR pathway 0.0596 53 1654 31 -0.21 0.027 1000 -1000 -0.06 -1000
Integrins in angiogenesis 0.0574 51 4305 84 -0.32 0.06 1000 -1000 -0.069 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0540 48 1606 33 -0.37 0.065 1000 -1000 -0.05 -1000
Fc-epsilon receptor I signaling in mast cells 0.0529 47 4646 97 -0.13 0.047 1000 -1000 -0.071 -1000
PLK1 signaling events 0.0529 47 4030 85 -0.16 0.038 1000 -1000 -0.037 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0529 47 5914 125 -0.14 0.04 1000 -1000 -0.069 -1000
p75(NTR)-mediated signaling 0.0517 46 5784 125 -0.31 0.076 1000 -1000 -0.091 -1000
IL2 signaling events mediated by STAT5 0.0506 45 992 22 -0.14 0.03 1000 -1000 -0.053 -1000
Signaling events mediated by PTP1B 0.0495 44 3409 76 -0.54 0.055 1000 -1000 -0.054 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0495 44 3303 74 -0.54 0.067 1000 -1000 -0.085 -1000
Ceramide signaling pathway 0.0484 43 3268 76 -0.54 0.19 1000 -1000 -0.059 -1000
FoxO family signaling 0.0484 43 2764 64 -0.62 0.072 1000 -1000 -0.065 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0461 41 2240 54 -0.32 0.04 1000 -1000 -0.09 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0461 41 4941 120 -0.18 0.1 1000 -1000 -0.068 -1000
IL27-mediated signaling events 0.0450 40 2045 51 -0.7 0.087 1000 -1000 -0.065 -1000
Visual signal transduction: Rods 0.0450 40 2124 52 -0.12 0.043 1000 -1000 -0.053 -1000
IL23-mediated signaling events 0.0439 39 2358 60 -0.19 0.028 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0416 37 4298 114 -0.32 0.15 1000 -1000 -0.069 -1000
IL2 signaling events mediated by PI3K 0.0416 37 2191 58 -0.14 0.048 1000 -1000 -0.051 -1000
Wnt signaling 0.0405 36 252 7 -0.047 0.027 1000 -1000 -0.034 -1000
Signaling events regulated by Ret tyrosine kinase 0.0394 35 2881 82 -0.039 0.028 1000 -1000 -0.088 -1000
Plasma membrane estrogen receptor signaling 0.0394 35 3062 86 -0.083 0.048 1000 -1000 -0.078 -1000
Noncanonical Wnt signaling pathway 0.0371 33 859 26 -0.13 0.027 1000 -1000 -0.063 -1000
Nongenotropic Androgen signaling 0.0371 33 1738 52 -0.055 0.044 1000 -1000 -0.049 -1000
Syndecan-2-mediated signaling events 0.0360 32 2229 69 -0.44 0.054 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 0.0360 32 1394 43 -0.22 0.072 1000 -1000 -0.064 -1000
BCR signaling pathway 0.0360 32 3222 99 -0.09 0.055 1000 -1000 -0.074 -1000
PLK2 and PLK4 events 0.0349 31 94 3 0.003 0.025 1000 -1000 -0.023 -1000
Regulation of Telomerase 0.0337 30 3074 102 -0.54 0.069 1000 -1000 -0.078 -1000
VEGFR1 specific signals 0.0337 30 1684 56 -0.12 0.028 1000 -1000 -0.064 -1000
ceramide signaling pathway 0.0326 29 1457 49 -0.023 0.041 1000 -1000 -0.06 -1000
Regulation of Androgen receptor activity 0.0326 29 2044 70 -0.85 0.043 1000 -1000 -0.061 -1000
IFN-gamma pathway 0.0304 27 1857 68 -0.19 0.04 1000 -1000 -0.087 -1000
S1P3 pathway 0.0304 27 1135 42 -0.11 0.034 1000 -1000 -0.043 -1000
Regulation of nuclear SMAD2/3 signaling 0.0292 26 3618 136 -0.33 0.096 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0292 26 738 28 -0.042 0.036 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0292 26 1588 61 -0.14 0.076 1000 -1000 -0.071 -1000
Syndecan-3-mediated signaling events 0.0292 26 936 35 -0.028 0.076 1000 -1000 -0.043 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0292 26 1210 45 -0.17 0.075 1000 -1000 -0.073 -1000
LPA receptor mediated events 0.0270 24 2463 102 -0.14 0.045 1000 -1000 -0.086 -1000
E-cadherin signaling events 0.0270 24 120 5 -0.005 0.026 1000 -1000 -0.004 -1000
TCGA08_rtk_signaling 0.0259 23 602 26 -0.24 0.059 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 0.0247 22 1100 48 -0.039 0.037 1000 -1000 -0.043 -1000
Regulation of p38-alpha and p38-beta 0.0247 22 1215 54 -0.044 0.059 1000 -1000 -0.061 -1000
E-cadherin signaling in keratinocytes 0.0247 22 956 43 -0.23 0.038 1000 -1000 -0.054 -1000
ErbB4 signaling events 0.0236 21 1495 69 -0.14 0.095 1000 -1000 -0.061 -1000
IL6-mediated signaling events 0.0236 21 1591 75 -0.17 0.05 1000 -1000 -0.066 -1000
Ras signaling in the CD4+ TCR pathway 0.0236 21 358 17 0 0.048 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0225 20 1736 85 -0.052 0.061 1000 -1000 -0.064 -1000
EPO signaling pathway 0.0225 20 1144 55 -0.067 0.043 1000 -1000 -0.067 -1000
Canonical Wnt signaling pathway 0.0225 20 1058 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 -0.009 -1000
Aurora A signaling 0.0214 19 1148 60 -0.1 0.065 1000 -1000 -0.032 -1000
FAS signaling pathway (CD95) 0.0214 19 908 47 -0.14 0.041 1000 -1000 -0.052 -1000
Class I PI3K signaling events 0.0214 19 1421 73 -0.12 0.051 1000 -1000 -0.058 -1000
Signaling events mediated by PRL 0.0214 19 667 34 -0.043 0.039 1000 -1000 -0.046 -1000
Insulin-mediated glucose transport 0.0202 18 595 32 -0.072 0.049 1000 -1000 -0.041 -1000
S1P5 pathway 0.0202 18 319 17 -0.036 0.027 1000 -1000 -0.029 -1000
EPHB forward signaling 0.0202 18 1568 85 -0.046 0.058 1000 -1000 -0.084 -1000
Osteopontin-mediated events 0.0191 17 650 38 -0.014 0.052 1000 -1000 -0.06 -1000
a4b1 and a4b7 Integrin signaling 0.0191 17 87 5 0.012 0.028 1000 -1000 -0.01 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0191 17 638 37 -0.076 0.052 1000 -1000 -0.051 -1000
Visual signal transduction: Cones 0.0180 16 641 38 -0.029 0.04 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 0.0180 16 1559 97 -0.04 0.065 1000 -1000 -0.069 -1000
ErbB2/ErbB3 signaling events 0.0169 15 1013 65 -0.078 0.037 1000 -1000 -0.066 -1000
IL1-mediated signaling events 0.0169 15 984 62 -0.11 0.063 1000 -1000 -0.071 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0169 15 781 52 -0.068 0.088 1000 -1000 -0.054 -1000
E-cadherin signaling in the nascent adherens junction 0.0169 15 1195 76 -0.027 0.048 1000 -1000 -0.081 -1000
S1P4 pathway 0.0169 15 394 25 -0.036 0.038 1000 -1000 -0.037 -1000
Cellular roles of Anthrax toxin 0.0157 14 565 39 -0.059 0.034 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0146 13 849 65 -0.004 0.049 1000 -1000 -0.056 -1000
mTOR signaling pathway 0.0146 13 705 53 -0.018 0.05 1000 -1000 -0.05 -1000
Nectin adhesion pathway 0.0146 13 851 63 -0.006 0.061 1000 -1000 -0.054 -1000
BARD1 signaling events 0.0124 11 636 57 -0.066 0.063 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0124 11 956 83 -0.072 0.054 1000 -1000 -0.052 -1000
p38 MAPK signaling pathway 0.0124 11 491 44 -0.059 0.05 1000 -1000 -0.045 -1000
Canonical NF-kappaB pathway 0.0112 10 394 39 -0.053 0.062 1000 -1000 -0.053 -1000
Signaling mediated by p38-gamma and p38-delta 0.0101 9 143 15 0 0.028 1000 -1000 -0.036 -1000
Class I PI3K signaling events mediated by Akt 0.0090 8 571 68 -0.072 0.054 1000 -1000 -0.048 -1000
Retinoic acid receptors-mediated signaling 0.0090 8 481 58 -0.023 0.054 1000 -1000 -0.052 -1000
Arf6 trafficking events 0.0090 8 578 71 -0.15 0.047 1000 -1000 -0.049 -1000
Insulin Pathway 0.0090 8 633 74 -0.033 0.069 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class I 0.0079 7 743 104 -0.053 0.066 1000 -1000 -0.061 -1000
IGF1 pathway 0.0079 7 453 57 -0.034 0.062 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class III 0.0056 5 211 40 -0.049 0.049 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0045 4 369 75 -0.034 0.069 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0045 4 103 22 -0.012 0.055 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0045 4 169 36 -0.046 0.05 1000 -1000 -0.052 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0034 3 75 23 -0.008 0.052 1000 -1000 -0.04 -1000
TRAIL signaling pathway 0.0034 3 161 48 -0.006 0.069 1000 -1000 -0.053 -1000
Atypical NF-kappaB pathway 0.0034 3 118 31 0 0.039 1000 -1000 -0.048 -1000
Rapid glucocorticoid signaling 0.0034 3 76 20 -0.016 0.035 1000 -1000 -0.007 -1000
Arf1 pathway 0.0034 3 215 54 0 0.042 1000 -1000 -0.024 -1000
Arf6 downstream pathway 0.0022 2 92 43 -0.043 0.044 1000 -1000 -0.035 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0011 1 34 27 0 0.064 1000 -1000 -0.043 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.069 1000 -1000 -0.009 -1000
Total NA 6049 331470 7203 -25 -990 131000 -131000 -7.2 -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 0.55 647 -10000 0 647
KIRREL -0.081 0.15 -10000 0 -0.66 46 46
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.4 0.26 -10000 0 -0.55 647 647
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 -0.54 692 692
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 -0.54 674 674
mol:DAG -0.41 0.29 -10000 0 -0.54 674 674
NPHS2 -0.32 0.33 -10000 0 -0.7 374 374
mol:IP3 -0.41 0.29 -10000 0 -0.54 674 674
regulation of endocytosis -0.37 0.26 -10000 0 -0.49 659 659
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.29 -10000 0 -0.55 695 695
establishment of cell polarity -0.4 0.26 -10000 0 -0.55 647 647
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.28 -10000 0 -0.51 681 681
Nephrin/NEPH1/beta Arrestin2 -0.38 0.26 -10000 0 -0.5 659 659
NPHS1 -0.5 0.31 -10000 0 -0.69 638 638
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 -0.55 674 674
CD2AP 0.026 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.29 -10000 0 -0.55 673 673
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 -0.41 642 642
Nephrin/NEPH1/ZO-1 -0.32 0.22 -10000 0 -0.45 641 641
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 -0.37 637 637
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.17 -9999 0 -0.37 603 603
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 -0.42 618 618
mol:GDP -0.26 0.16 -9999 0 -0.36 603 603
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 -0.34 595 595
SHC1 0.026 0.016 -9999 0 -0.42 1 1
HRAS/GDP -0.25 0.16 -9999 0 -0.34 595 595
FRAP1 -0.26 0.15 -9999 0 -0.35 603 603
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 -1.5 496 496
HNF4A -0.53 0.52 -10000 0 -1.3 232 232
KCNJ11 -0.48 0.46 -10000 0 -1.1 228 228
AKT1 -0.22 0.18 -10000 0 -0.46 151 151
response to starvation -0.008 0.018 -10000 0 -10000 0 0
DLK1 -0.52 0.49 -10000 0 -1.1 286 286
NKX2-1 -0.1 0.17 0.32 7 -0.42 53 60
ACADM -0.45 0.42 -10000 0 -1 232 232
TAT -0.46 0.29 -10000 0 -0.77 325 325
CEBPB -0.029 0.084 -10000 0 -0.47 22 22
CEBPA -0.038 0.1 -10000 0 -0.46 43 43
TTR -0.75 0.44 -10000 0 -1 509 509
PKLR -0.53 0.53 -10000 0 -1.2 252 252
APOA1 -0.53 0.5 -10000 0 -1.2 230 230
CPT1C -0.46 0.43 -10000 0 -1 244 244
ALAS1 -0.2 0.2 -10000 0 -0.68 41 41
TFRC -0.61 0.39 -10000 0 -0.95 387 387
FOXF1 0.016 0.07 -10000 0 -0.46 18 18
NF1 0.031 0.01 -10000 0 -10000 0 0
HNF1A (dimer) -0.034 0.11 -10000 0 -0.58 22 22
CPT1A -0.45 0.42 -10000 0 -1 224 224
HMGCS1 -0.45 0.42 -10000 0 -1 231 231
NR3C1 0.013 0.053 -10000 0 -0.28 4 4
CPT1B -0.46 0.44 -10000 0 -1.1 230 230
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 -1 231 231
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 -0.74 74 74
UCP2 -0.45 0.42 -10000 0 -1 235 235
ALDOB -0.98 0.55 -10000 0 -1.2 702 702
AFP -0.54 0.4 -10000 0 -0.79 460 460
BDH1 -0.53 0.48 -10000 0 -1.1 307 307
HADH -0.47 0.44 -10000 0 -1.1 226 226
F2 -0.56 0.5 -10000 0 -1.2 261 261
HNF1A -0.033 0.11 -10000 0 -0.58 22 22
G6PC -0.83 0.64 -10000 0 -1.4 444 444
SLC2A2 -0.4 0.54 -10000 0 -1.6 129 129
INS -0.005 0.06 0.24 2 -0.43 3 5
FOXA1 -0.25 0.19 -10000 0 -0.53 206 206
FOXA3 -0.52 0.29 -10000 0 -0.62 678 678
FOXA2 -0.54 0.5 -10000 0 -1.1 279 279
ABCC8 -0.47 0.44 -10000 0 -1.1 240 240
ALB -1 0.45 -10000 0 -1.2 737 737
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 -0.66 347 347
PDGF/PDGFRA/CRKL -0.16 0.25 -10000 0 -0.48 343 343
positive regulation of JUN kinase activity -0.097 0.2 -10000 0 -0.36 305 305
CRKL 0.027 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.17 0.25 -10000 0 -0.48 346 346
AP1 -0.17 0.31 0.33 2 -1.2 56 58
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 -0.48 345 345
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 -0.37 305 305
PDGF/PDGFRA/Shf -0.16 0.25 -10000 0 -0.48 345 345
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 -0.47 345 345
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 0.33 -10000 0 -0.65 347 347
actin cytoskeleton reorganization -0.16 0.25 -10000 0 -0.48 343 343
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 -0.41 313 313
JAK1 -0.18 0.24 -10000 0 -0.48 342 342
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 0.004 -10000 0 -10000 0 0
CSNK2A1 0.036 0.019 -10000 0 -10000 0 0
GO:0007205 -0.19 0.25 -10000 0 -0.5 347 347
SOS1 0.027 0.006 -10000 0 -10000 0 0
Ras protein signal transduction -0.097 0.2 -10000 0 -0.36 305 305
PDGF/PDGFRA/SHB -0.16 0.25 -10000 0 -0.48 343 343
PDGF/PDGFRA/Caveolin-1 -0.17 0.24 -10000 0 -0.43 383 383
ITGAV 0.026 0.028 -10000 0 -0.53 2 2
ELK1 -0.17 0.22 -10000 0 -0.44 344 344
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.16 0.25 -10000 0 -0.47 325 325
JAK-STAT cascade -0.17 0.24 -10000 0 -0.48 342 342
cell proliferation -0.16 0.25 -10000 0 -0.48 345 345
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 -1 309 309
HDAC7 0.026 0.008 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.37 0.37 -10000 0 -0.83 212 212
SMAD4 0.029 0.005 -10000 0 -10000 0 0
ID2 -0.52 0.48 -10000 0 -1.1 273 273
AP1 0.007 0.12 -10000 0 -0.48 53 53
ABCG2 -0.52 0.48 -10000 0 -1.1 281 281
HIF1A -0.075 0.085 -10000 0 -0.77 2 2
TFF3 -0.56 0.49 -10000 0 -1.1 303 303
GATA2 -0.028 0.18 -10000 0 -0.64 72 72
AKT1 -0.07 0.079 -10000 0 -10000 0 0
response to hypoxia -0.08 0.072 -10000 0 -0.26 7 7
MCL1 -0.51 0.48 -10000 0 -1.1 275 275
NDRG1 -0.52 0.48 -10000 0 -1.1 273 273
SERPINE1 -0.54 0.48 -10000 0 -1.1 281 281
FECH -0.52 0.48 -10000 0 -1.1 278 278
FURIN -0.52 0.48 -10000 0 -1.1 278 278
NCOA2 -0.005 0.14 -10000 0 -0.65 40 40
EP300 -0.06 0.094 0.26 1 -0.35 9 10
HMOX1 -0.53 0.49 -10000 0 -1.1 288 288
BHLHE40 -0.52 0.48 -10000 0 -1.1 275 275
BHLHE41 -0.56 0.52 -10000 0 -1.1 307 307
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.059 0.11 -10000 0 -0.54 2 2
ENG -0.055 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 -1.1 277 277
ABCB1 -0.25 0.41 -10000 0 -1.2 126 126
TFRC -0.52 0.48 -10000 0 -1.1 275 275
CXCR4 -0.56 0.52 -10000 0 -1.1 315 315
TF -0.54 0.51 -10000 0 -1.1 287 287
CITED2 -0.52 0.48 -10000 0 -1.1 273 273
HIF1A/ARNT -0.6 0.56 -10000 0 -1.2 316 316
LDHA -0.063 0.13 -10000 0 -0.7 26 26
ETS1 -0.52 0.48 -10000 0 -1.1 277 277
PGK1 -0.52 0.48 -10000 0 -1.1 277 277
NOS2 -0.53 0.48 -10000 0 -1.1 276 276
ITGB2 -0.55 0.5 -10000 0 -1.1 311 311
ALDOA -0.52 0.48 -10000 0 -1.1 270 270
Cbp/p300/CITED2 -0.5 0.48 -10000 0 -1.1 256 256
FOS -0.015 0.16 -10000 0 -0.62 57 57
HK2 -0.62 0.53 -10000 0 -1.1 362 362
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 -1.1 273 273
NPM1 -0.51 0.48 -10000 0 -1.1 269 269
EGLN1 -0.52 0.48 -10000 0 -1.1 275 275
CREB1 0.033 0.009 -10000 0 -10000 0 0
PGM1 -0.52 0.48 -10000 0 -1.1 277 277
SMAD3 0.029 0.003 -10000 0 -10000 0 0
EDN1 -0.1 0.22 -10000 0 -0.91 34 34
IGFBP1 -0.56 0.49 -10000 0 -1.1 284 284
VEGFA -0.39 0.38 0.55 2 -0.85 235 237
HIF1A/JAB1 -0.039 0.067 -10000 0 -0.6 2 2
CP -0.62 0.52 -10000 0 -1.1 355 355
CXCL12 -0.54 0.49 -10000 0 -1.1 300 300
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 -1.1 277 277
EGLN3 -0.61 0.53 -10000 0 -1.1 356 356
CA9 -0.65 0.52 -10000 0 -1.1 388 388
TERT -0.54 0.49 -10000 0 -1.1 290 290
ENO1 -0.52 0.48 -10000 0 -1.1 277 277
PFKL -0.52 0.48 -10000 0 -1.1 274 274
NCOA1 0.027 0.006 -10000 0 -10000 0 0
ADM -0.54 0.5 -10000 0 -1.1 291 291
ARNT -0.072 0.078 -10000 0 -0.31 2 2
HNF4A -0.061 0.23 -10000 0 -0.65 117 117
ADFP -0.53 0.48 -10000 0 -1 309 309
SLC2A1 -0.34 0.35 0.55 2 -0.82 165 167
LEP -0.54 0.47 -10000 0 -1.1 277 277
HIF1A/ARNT/Cbp/p300 -0.39 0.37 -10000 0 -0.85 217 217
EPO -0.31 0.29 -10000 0 -0.77 135 135
CREBBP -0.058 0.088 -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 -1.1 283 283
NT5E -0.52 0.49 -10000 0 -1.1 274 274
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 0.37 6 -0.46 201 207
FYN -0.14 0.27 0.47 22 -0.51 250 272
LAT/GRAP2/SLP76 -0.15 0.26 0.29 4 -0.52 243 247
IKBKB 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.1 0.24 0.45 49 -0.4 252 301
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.037 0.07 0.15 14 -0.16 80 94
MAP3K8 0.026 0.022 -10000 0 -0.42 2 2
mol:Ca2+ -0.078 0.053 0.072 5 -0.12 533 538
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 0.48 36 -0.55 269 305
TRPV6 -0.35 0.47 0.74 94 -0.65 578 672
CD28 -0.008 0.12 -10000 0 -0.42 66 66
SHC1 -0.16 0.27 0.41 13 -0.52 261 274
receptor internalization -0.16 0.26 0.22 1 -0.51 274 275
PRF1 -0.16 0.3 0.43 3 -0.68 184 187
KRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
COT/AKT1 -0.072 0.2 0.42 46 -0.33 205 251
LAT -0.18 0.29 0.42 13 -0.56 274 287
EntrezGene:6955 -0.001 0.005 0.048 1 -10000 0 1
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 0.09 2 -0.17 4 6
RASGRP1 -0.095 0.24 0.52 42 -0.4 208 250
HLA-A -0.002 0.008 0.076 3 -10000 0 3
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 0.011 0.15 0.35 70 -0.13 8 78
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.084 0.098 -10000 0 -0.25 162 162
PRKCA -0.073 0.13 0.18 19 -0.27 173 192
GRAP2 -0.001 0.11 -10000 0 -0.42 56 56
mol:IP3 -0.045 0.26 0.24 291 -0.41 199 490
EntrezGene:6957 -0.002 0.006 0.058 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.12 0.22 -10000 0 -0.45 245 245
ORAI1 0.16 0.29 0.67 9 -0.58 89 98
CSK -0.16 0.26 0.32 8 -0.52 261 269
B7 family/CD28 -0.18 0.32 0.29 1 -0.66 223 224
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 -0.57 272 273
PTPN6 -0.16 0.26 0.3 2 -0.52 260 262
VAV1 -0.19 0.3 0.45 13 -0.58 283 296
Monovalent TCR/CD3 -0.11 0.19 -10000 0 -0.38 276 276
CBL 0.027 0.023 -10000 0 -0.65 1 1
LCK -0.15 0.28 0.46 22 -0.53 253 275
PAG1 -0.16 0.26 0.32 11 -0.52 263 274
RAP1A 0.027 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.28 0.27 7 -0.55 273 280
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 -0.3 171 171
HRAS 0.027 0.015 -10000 0 -0.42 1 1
GO:0035030 -0.16 0.26 0.48 7 -0.54 233 240
CD8A -0.11 0.21 -10000 0 -0.42 267 267
CD8B -0.09 0.2 -10000 0 -0.43 226 226
PTPRC -0.008 0.12 -10000 0 -0.43 67 67
PDK1/PKC theta -0.13 0.3 0.55 52 -0.49 245 297
CSK/PAG1 -0.15 0.26 0.4 9 -0.54 223 232
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 0.28 1 -0.55 254 255
STIM1 0.09 0.14 1 2 -0.77 11 13
RAS family/GTP -0.01 0.14 0.37 47 -0.2 9 56
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.17 0.27 0.22 1 -0.54 274 275
mol:DAG -0.1 0.19 0.14 12 -0.36 242 254
RAP1A/GDP 0.011 0.098 0.23 61 -10000 0 61
PLCG1 0.027 0.007 -10000 0 -10000 0 0
CD247 -0.079 0.19 -10000 0 -0.42 207 207
cytotoxic T cell degranulation -0.16 0.29 0.43 3 -0.65 184 187
RAP1A/GTP -0.003 0.01 -10000 0 -0.06 4 4
mol:PI-3-4-5-P3 -0.13 0.27 0.46 38 -0.46 259 297
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.09 0.32 0.27 217 -0.54 213 430
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 0.27 4 -0.52 257 261
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 0.17 13 -0.28 177 190
PRKCE -0.073 0.13 0.18 20 -0.28 161 181
PRKCQ -0.16 0.31 0.51 38 -0.55 257 295
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 -0.082 0.22 0.42 52 -0.34 249 301
IKK complex 0.016 0.17 0.37 92 -0.12 14 106
RAS family/GDP -0.008 0.012 -10000 0 -10000 0 0
MAP3K14 -0.059 0.15 0.39 20 -0.27 164 184
PDPK1 -0.091 0.24 0.48 53 -0.39 223 276
TCR/CD3/MHC I/CD8/Fyn -0.16 0.28 -10000 0 -0.55 260 260
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 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.042 0.19 -10000 0 -0.47 137 137
SMAD2 0.025 0.031 -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 -0.47 570 570
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 -0.42 530 530
positive regulation of MAPKKK cascade -0.28 0.24 0.4 11 -0.45 539 550
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 -0.26 268 268
LYN -0.25 0.21 -10000 0 -0.42 520 520
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 -0.53 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 -0.26 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 -0.44 53 53
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 2 -0.3 772 774
TP53 -0.071 0.062 -10000 0 -0.28 54 54
Senescence -0.071 0.062 -10000 0 -0.28 54 54
Apoptosis -0.071 0.062 -10000 0 -0.28 54 54
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.15 0.095 0.41 60 -10000 0 60
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 -0.44 216 216
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 0.26 121 -0.42 228 349
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 0.15 -10000 0 -0.65 48 48
ELK1 -0.24 0.54 0.48 4 -1.1 223 227
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 -1.3 222 222
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 -1.3 224 224
CRK 0.025 0.009 -10000 0 -10000 0 0
mol:NO -0.17 0.33 0.49 6 -0.69 223 229
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 -0.75 95 95
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 -1.4 223 223
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 -0.9 213 213
mol:L-citrulline -0.17 0.33 0.49 6 -0.69 223 229
AGTR1 -0.081 0.24 -10000 0 -0.65 128 128
MAPK14 -0.34 0.63 -10000 0 -1.4 226 226
Tie2/SHP2 -0.26 0.55 -10000 0 -1.2 212 212
TEK -0.31 0.62 -10000 0 -1.4 212 212
RPS6KB1 -0.23 0.44 -10000 0 -0.95 224 224
Angiotensin II/AT1 -0.068 0.18 -10000 0 -0.49 128 128
Tie2/Ang1/GRB2 -0.31 0.67 -10000 0 -1.4 224 224
MAPK3 -0.26 0.55 -10000 0 -1.2 222 222
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 -1.4 224 224
Crk/Dok-R -0.28 0.61 -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 0.026 0.009 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.24 0.44 0.46 3 -0.97 224 227
Tie2/Ang2 -0.32 0.52 -10000 0 -1.2 221 221
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 0.064 -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 -0.24 220 220
FYN -0.25 0.41 -10000 0 -0.92 221 221
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 -0.25 108 108
PXN -0.18 0.36 0.56 6 -0.77 222 228
ITGB1 0.027 0.007 -10000 0 -10000 0 0
NOS3 -0.2 0.38 0.5 6 -0.8 223 229
RAC1 0.025 0.01 -10000 0 -10000 0 0
TNF -0.025 0.13 -10000 0 -0.51 26 26
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 0.45 8 -0.62 223 231
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 0.49 6 -0.69 223 229
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 -0.43 772 772
CCND2 0.081 0.048 0.21 41 -10000 0 41
RB1 -0.093 0.057 -10000 0 -0.26 38 38
CDK4 0.097 0.058 0.22 79 -10000 0 79
CDK6 0.093 0.057 0.22 68 -0.16 1 69
G1/S progression 0.097 0.057 0.24 54 -10000 0 54
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.43 0.3 -10000 0 -0.56 676 676
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 -0.076 0.18 -10000 0 -0.61 75 75
SMAD4 0.028 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 0.32 7 -0.45 54 61
SMAD1 -0.018 0.068 -10000 0 -0.49 6 6
BMP2 0.025 0.033 -10000 0 -0.65 2 2
SMAD1/SMAD1/SMAD4 -0.01 0.062 -10000 0 -0.45 3 3
BMPR1A 0.026 0.024 -10000 0 -0.65 1 1
BMPR1B -0.38 0.33 -10000 0 -0.64 535 535
BMPR1A-1B/BAMBI -0.24 0.23 -10000 0 -0.42 526 526
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 -0.42 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.13 -10000 0 -0.44 33 33
BMP2-4 (homodimer) 0.034 0.049 -10000 0 -0.49 7 7
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 72 72
BMP2-4/USAG1 -0.18 0.23 -10000 0 -0.42 412 412
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.34 2 -0.44 58 60
SOSTDC1 -0.3 0.33 -10000 0 -0.64 426 426
BMP7/BMPR2/BMPR1A-1B -0.4 0.29 -10000 0 -0.54 657 657
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 -0.45 30 30
SMAD5/SMAD5/SMAD4 -0.16 0.16 0.31 4 -0.43 66 70
MAPK1 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.37 33 33
BMP7 (homodimer) -0.34 0.33 -10000 0 -0.65 462 462
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 0.084 0.41 6 -0.47 6 12
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 -0.64 277 277
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 -0.48 533 533
CHRDL1 -0.31 0.34 -10000 0 -0.65 430 430
ENDOFIN/SMAD1 -0.008 0.082 0.41 4 -0.48 6 10
SMAD6-7/SMURF1/SMAD1 -0.005 0.075 -10000 0 -0.47 5 5
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 -0.42 408 408
BMP2-4/GREM1 -0.091 0.22 -10000 0 -0.42 244 244
SMAD7 0.028 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.068 0.18 -10000 0 -0.58 79 79
SMAD1/SMAD6 -0.013 0.07 -10000 0 -0.49 6 6
TAK1/SMAD6 0.034 0.017 -10000 0 -10000 0 0
BMP7 -0.34 0.33 -10000 0 -0.65 462 462
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 -0.11 0.12 -10000 0 -0.38 48 48
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.01 0.079 0.41 6 -0.49 6 12
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 -0.56 158 158
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 -0.4 75 75
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 -0.41 19 19
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.37 0.28 -10000 0 -0.52 609 609
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.02 0.14 -9999 0 -0.42 94 94
GPC2 -0.02 0.13 -9999 0 -0.42 88 88
GPC2/Midkine -0.023 0.14 -9999 0 -0.34 134 134
neuron projection morphogenesis -0.023 0.14 -9999 0 -0.34 134 134
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.064 0.13 -10000 0 -0.3 135 135
STMN1 -0.099 0.16 0.21 1 -0.29 353 354
Aurora B/RasGAP/Survivin -0.12 0.22 -10000 0 -0.45 239 239
Chromosomal passenger complex/Cul3 protein complex -0.055 0.12 0.2 7 -0.39 48 55
BIRC5 -0.11 0.2 -10000 0 -0.43 256 256
DES -0.26 0.34 -10000 0 -0.67 326 326
Aurora C/Aurora B/INCENP -0.058 0.13 -10000 0 -0.32 9 9
Aurora B/TACC1 -0.076 0.14 -10000 0 -0.24 351 351
Aurora B/PP2A -0.091 0.16 -10000 0 -0.29 348 348
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 -10000 0 -0.41 365 365
Cul3 protein complex 0.036 0.089 -10000 0 -0.42 31 31
KIF2C -0.069 0.14 -10000 0 -0.38 101 101
PEBP1 0.023 0.009 -10000 0 -10000 0 0
KIF20A -0.16 0.22 -10000 0 -0.42 358 358
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.09 0.16 -10000 0 -0.29 344 344
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 -0.054 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 -0.42 353 353
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 81 81
Aurora B/Septin1 -0.1 0.19 0.33 1 -0.47 92 93
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 -0.44 250 250
EVI5 0.027 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.079 0.16 -10000 0 -0.42 59 59
SGOL1 0.003 0.098 -10000 0 -0.42 44 44
CENPA -0.086 0.15 0.22 13 -0.3 202 215
NCAPG -0.12 0.21 -10000 0 -0.42 301 301
Aurora B/HC8 Proteasome -0.092 0.16 -10000 0 -0.29 352 352
NCAPD2 0.027 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.089 0.16 -10000 0 -0.29 342 342
RHOA 0.026 0.008 -10000 0 -10000 0 0
NCAPH -0.042 0.16 -10000 0 -0.42 136 136
NPM1 -0.055 0.12 -10000 0 -0.57 15 15
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 -0.29 352 352
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 -0.39 43 43
MYLK -0.056 0.1 -10000 0 -0.38 27 27
KIF23 0.022 0.046 -10000 0 -0.43 9 9
VIM -0.12 0.19 -10000 0 -0.33 359 359
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 -0.82 40 40
Chromosomal passenger complex -0.11 0.16 0.21 3 -0.34 244 247
Chromosomal passenger complex/EVI5 -0.093 0.23 -10000 0 -0.43 243 243
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
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 73 73
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 -0.5 144 144
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 -0.43 71 71
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 -0.42 332 332
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 -0.43 179 179
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 -0.47 287 287
MST1R 0.006 0.098 -10000 0 -0.46 35 35
leukocyte activation during inflammatory response -0.093 0.18 -10000 0 -0.44 122 122
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 -0.45 85 85
alphaM/beta2 Integrin -0.21 0.2 -10000 0 -0.39 366 366
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 -0.38 366 366
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 -0.43 104 104
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 -0.43 70 70
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 -0.48 311 311
positive regulation of phagocytosis -0.17 0.18 -10000 0 -0.46 176 176
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 81 81
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 -0.46 280 280
MST1 0.02 0.054 -10000 0 -0.5 9 9
alphaM/beta2 Integrin/lipoprotein(a) -0.092 0.18 -10000 0 -0.44 122 122
TNF -0.092 0.2 0.39 1 -0.64 48 49
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.052 0.17 -10000 0 -0.43 101 101
fibrinolysis -0.23 0.25 -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 -0.38 366 366
VTN -0.078 0.23 -10000 0 -0.58 148 148
alphaM/beta2 Integrin/CYR61 -0.051 0.17 -10000 0 -0.44 93 93
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 -0.5 127 127
FN1 -0.01 0.12 -10000 0 -0.42 72 72
alphaM/beta2 Integrin/Thy1 -0.07 0.19 -10000 0 -0.43 137 137
MPO 0.006 0.085 -10000 0 -0.42 33 33
KNG1 -0.44 0.3 -10000 0 -0.65 587 587
RAP1/GDP 0.034 0.012 -10000 0 -10000 0 0
ROCK1 -0.24 0.21 -10000 0 -0.47 278 278
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.31 0.32 -10000 0 -0.63 441 441
CTGF 0.008 0.11 -10000 0 -0.56 28 28
alphaM/beta2 Integrin/Hck -0.05 0.19 -10000 0 -0.53 88 88
ITGAM -0.018 0.12 -10000 0 -0.42 71 71
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.21 -10000 0 -0.47 142 142
HP -0.067 0.18 -10000 0 -0.42 181 181
leukocyte adhesion -0.08 0.19 -10000 0 -0.56 58 58
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 -0.36 58 58
TBX21 -0.2 0.37 0.6 2 -0.85 137 139
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 -0.65 53 53
IL12RB2 -0.11 0.2 -10000 0 -0.43 233 233
GADD45G -0.13 0.28 -10000 0 -0.73 46 46
natural killer cell activation -0.005 0.023 0.042 3 -0.038 123 126
RELB 0.028 0.003 -10000 0 -10000 0 0
RELA 0.028 0.003 -10000 0 -10000 0 0
IL18 0.006 0.095 -10000 0 -0.42 40 40
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 -0.63 183 183
HLA-DRB5 -0.001 0.006 -10000 0 -0.024 43 43
FASLG -0.22 0.37 -10000 0 -0.83 170 170
NF kappa B2 p52/RelB -0.17 0.33 -10000 0 -0.71 164 164
CD4 0.01 0.081 -10000 0 -0.42 30 30
SOCS1 0.018 0.068 -10000 0 -0.52 13 13
EntrezGene:6955 -0.003 0.009 -10000 0 -0.025 52 52
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 -0.34 127 127
CCL3 -0.18 0.36 0.6 2 -0.85 119 121
CCL4 -0.19 0.37 0.6 2 -0.86 137 139
HLA-A -0.003 0.007 -10000 0 -0.022 19 19
IL18/IL18R -0.02 0.15 -10000 0 -0.3 83 83
NOS2 -0.17 0.34 -10000 0 -0.82 111 111
IL12/IL12R/TYK2/JAK2/SPHK2 -0.068 0.13 -10000 0 -0.36 50 50
IL1R1 -0.18 0.34 0.6 2 -0.77 139 141
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 -0.023 45 45
TCR/CD3/MHC I/CD8 -0.17 0.27 -10000 0 -0.58 236 236
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 -0.93 118 118
STAT4 (dimer) -0.16 0.33 0.58 5 -0.71 152 157
STAT5A (dimer) -0.22 0.37 -10000 0 -0.8 203 203
GZMA -0.21 0.37 -10000 0 -0.82 173 173
GZMB -0.2 0.36 -10000 0 -0.82 158 158
HLX -0.01 0.12 -10000 0 -0.42 71 71
LCK -0.2 0.36 -10000 0 -0.79 175 175
TCR/CD3/MHC II/CD4 -0.1 0.16 -10000 0 -0.33 270 270
IL2/IL2R -0.098 0.2 -10000 0 -0.48 129 129
MAPK14 -0.12 0.29 0.51 3 -0.68 80 83
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 -0.037 0.14 -10000 0 -0.44 90 90
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 0.07 0.13 0.36 58 -10000 0 58
IL2RB -0.14 0.22 -10000 0 -0.42 328 328
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.31 0.57 5 -0.65 151 156
IL2RG 0.003 0.11 -10000 0 -0.44 47 47
IL12 -0.019 0.11 -10000 0 -0.32 88 88
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 -0.78 185 185
MAP2K3 -0.12 0.29 0.5 3 -0.67 86 89
RIPK2 0.027 0.016 -10000 0 -0.42 1 1
MAP2K6 -0.12 0.29 0.5 3 -0.67 86 89
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 44 44
IL18RAP -0.058 0.18 -10000 0 -0.42 164 164
IL12Rbeta1/TYK2 -0.053 0.16 -10000 0 -0.34 189 189
EOMES -0.099 0.17 -10000 0 -0.72 20 20
STAT1 (dimer) -0.18 0.32 -10000 0 -0.68 170 170
T cell proliferation -0.12 0.26 0.46 5 -0.54 132 137
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 -0.62 103 103
ATF2 -0.11 0.28 0.64 4 -0.66 63 67
IL4-mediated signaling events

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
BCL2L1 -0.44 0.43 -10000 0 -1.2 133 133
STAT6 (cleaved dimer) -0.47 0.44 -10000 0 -1.1 211 211
IGHG1 -0.16 0.15 -10000 0 -0.42 23 23
IGHG3 -0.43 0.42 -10000 0 -1 191 191
AKT1 -0.22 0.24 0.56 2 -0.78 47 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.18 -10000 0 -0.8 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.93 51 51
THY1 -0.51 0.53 -10000 0 -1.4 175 175
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 -0.69 127 127
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.96 44 44
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 -1.1 188 188
SOCS1 -0.31 0.29 -10000 0 -0.76 110 110
SOCS3 -0.24 0.24 -10000 0 -0.84 24 24
FCER2 -0.36 0.34 -10000 0 -0.97 92 92
PARP14 0.027 0.008 -10000 0 -10000 0 0
CCL17 -0.45 0.44 -10000 0 -1.1 154 154
GRB2 0.025 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.24 -10000 0 -0.86 50 50
T cell proliferation -0.45 0.44 -10000 0 -1.2 157 157
IL4R/JAK1 -0.44 0.43 -10000 0 -1.1 145 145
EGR2 -0.48 0.48 -10000 0 -1.3 151 151
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 -0.56 13 13
CCL26 -0.43 0.44 -10000 0 -1.1 147 147
IL4R -0.47 0.46 -10000 0 -1.2 140 140
PTPN6 0.038 0.014 -10000 0 -10000 0 0
IL13RA2 -0.64 0.61 -10000 0 -1.4 282 282
IL13RA1 -0.024 0.039 -10000 0 -10000 0 0
IRF4 -0.15 0.22 -10000 0 -0.72 58 58
ARG1 -0.14 0.17 -10000 0 -0.84 6 6
CBL -0.27 0.25 -10000 0 -0.68 104 104
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 -0.72 46 46
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 -0.73 47 49
STAT6 -0.5 0.5 -10000 0 -1.3 179 179
SPI1 -0.036 0.16 -10000 0 -0.41 130 130
RPS6KB1 -0.19 0.23 0.54 2 -0.74 38 40
STAT6 (dimer) -0.5 0.51 -10000 0 -1.3 179 179
STAT6 (dimer)/PARP14 -0.46 0.46 -10000 0 -1.2 167 167
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.22 -10000 0 -0.71 42 42
FRAP1 -0.22 0.24 0.56 2 -0.78 47 49
LTA -0.48 0.44 -10000 0 -1.1 179 179
FES 0.026 0.04 -10000 0 -0.65 3 3
T-helper 1 cell differentiation 0.5 0.49 1.2 179 -10000 0 179
CCL11 -0.61 0.58 -10000 0 -1.3 294 294
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.22 -10000 0 -0.72 32 32
IL2RG 0.006 0.11 -10000 0 -0.45 47 47
IL10 -0.46 0.44 -10000 0 -1.2 150 150
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 -0.44 0.44 -10000 0 -1.1 150 150
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.93 145 145
COL1A1 -0.24 0.27 -10000 0 -0.82 71 71
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.44 -10000 0 -1.2 117 117
IL2R gamma/JAK3 -0.039 0.17 -10000 0 -0.36 176 176
TFF3 -0.53 0.55 -10000 0 -1.4 194 194
ALOX15 -0.44 0.43 -10000 0 -1.2 132 132
MYBL1 -0.001 0.11 -10000 0 -0.42 56 56
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.94 174 174
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 -0.9 53 54
mol:PI-3-4-5-P3 -0.22 0.24 0.57 2 -0.78 47 49
PI3K -0.23 0.26 0.57 2 -0.84 47 49
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 -0.82 59 59
ITGB3 -0.46 0.46 -10000 0 -1.2 140 140
PIGR -0.7 0.64 -10000 0 -1.4 358 358
IGHE 0.034 0.062 0.23 15 -0.27 1 16
MAPKKK cascade -0.19 0.24 -10000 0 -0.8 59 59
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.46 0.43 -10000 0 -1.1 158 158
RETNLB -0.45 0.43 -10000 0 -1.2 136 136
SELP -0.5 0.52 -10000 0 -1.3 178 178
AICDA -0.47 0.43 -10000 0 -1.1 184 184
Syndecan-4-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
PTK2 -0.042 0.11 -10000 0 -0.65 12 12
Syndecan-4/Syndesmos -0.2 0.19 -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 0.2 -10000 0 -0.55 123 123
Syndecan-4/CXCL12/CXCR4 -0.26 0.23 -10000 0 -0.58 181 181
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 -0.54 112 112
Syndecan-4/Midkine -0.22 0.21 0.41 1 -0.56 123 124
FZD7 0.015 0.086 -10000 0 -0.61 16 16
Syndecan-4/FGFR1/FGF -0.19 0.19 -10000 0 -0.52 106 106
THBS1 0.006 0.12 -10000 0 -0.64 29 29
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 -0.55 121 121
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 -0.53 107 107
Syndecan-4/TSP1 -0.21 0.2 -10000 0 -0.55 120 120
Syndecan-4/GIPC -0.2 0.2 -10000 0 -0.53 108 108
Syndecan-4/RANTES -0.25 0.22 -10000 0 -0.6 156 156
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 52 -10000 0 52
Syndecan-4/alpha-Actinin -0.2 0.2 -10000 0 -0.53 108 108
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 -0.55 133 133
FGF6 -0.016 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.008 -10000 0 -10000 0 0
CXCL12 -0.024 0.17 -10000 0 -0.56 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 -0.004 0.12 -10000 0 -0.4 72 72
cell migration -0.027 0.018 -10000 0 -10000 0 0
PRKCD 0.028 0.049 -10000 0 -0.41 9 9
vasculogenesis -0.2 0.2 -10000 0 -0.52 120 120
SDC4 -0.21 0.2 -10000 0 -0.56 107 107
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 -0.53 106 106
MMP9 -0.14 0.21 -10000 0 -0.41 332 332
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 -0.54 115 115
Effects of Botulinum toxin

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
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 -0.26 421 421
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 0.004 0.054 0.13 83 -0.14 16 99
RAB3GAP2 0.027 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.005 0.092 -10000 0 -0.36 10 10
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.12 0.14 -10000 0 -0.26 421 421
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 -0.077 0.18 -10000 0 -0.44 174 174
SNAP25 -0.024 0.064 -10000 0 -0.14 183 183
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 -0.36 10 10
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.079 0.17 0.43 2 -0.47 93 95
CRKL -0.033 0.16 -10000 0 -0.47 93 93
HRAS -0.034 0.15 -10000 0 -0.48 39 39
mol:PIP3 -0.024 0.16 -10000 0 -0.44 84 84
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 0.29 7 -0.43 82 89
AKT1 -0.013 0.18 0.3 7 -0.46 88 95
BAD -0.009 0.17 0.3 10 -0.44 82 92
megakaryocyte differentiation -0.096 0.22 -10000 0 -0.43 232 232
GSK3B -0.003 0.17 0.39 19 -0.43 81 100
RAF1 -0.024 0.12 0.28 8 -0.39 29 37
SHC1 0.026 0.016 -10000 0 -0.42 1 1
STAT3 -0.033 0.17 -10000 0 -0.49 87 87
STAT1 -0.084 0.34 -10000 0 -1 96 96
HRAS/SPRED1 -0.018 0.13 -10000 0 -0.39 33 33
cell proliferation -0.034 0.17 -10000 0 -0.48 98 98
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
TEC 0.028 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.03 0.18 -10000 0 -0.48 97 97
HRAS/SPRED2 -0.017 0.13 -10000 0 -0.39 32 32
LYN/TEC/p62DOK 0 0.18 -10000 0 -0.46 93 93
MAPK3 0 0.12 0.37 28 -0.3 12 40
STAP1 -0.27 0.23 -10000 0 -0.39 603 603
GRAP2 -0.002 0.11 -10000 0 -0.42 56 56
JAK2 -0.073 0.3 -10000 0 -0.89 96 96
STAT1 (dimer) -0.082 0.33 -10000 0 -1 97 97
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.05 0.18 -10000 0 -0.49 82 82
actin filament polymerization -0.037 0.16 0.24 1 -0.49 83 84
LYN 0.026 0.024 -10000 0 -0.65 1 1
STAP1/STAT5A (dimer) -0.27 0.26 -10000 0 -0.74 133 133
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.005 0.15 0.4 1 -0.44 62 63
PI3K -0.005 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 -0.035 0.18 -10000 0 -0.49 98 98
STAT3 (dimer) -0.031 0.16 -10000 0 -0.48 87 87
positive regulation of transcription 0.005 0.1 0.35 30 -0.27 5 35
mol:GDP -0.045 0.16 -10000 0 -0.5 41 41
PIK3C2B -0.032 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 -0.033 0.17 -10000 0 -0.48 96 96
PDPK1 -0.012 0.14 0.33 11 -0.4 77 88
SNAI2 -0.053 0.2 -10000 0 -0.54 106 106
positive regulation of cell proliferation -0.054 0.26 -10000 0 -0.76 97 97
KITLG 0.013 0.092 -10000 0 -0.67 15 15
cell motility -0.054 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 0.068 -10000 0 -0.52 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 -0.037 0.16 -10000 0 -0.49 84 84
PTPN11 0.027 0.008 -10000 0 -10000 0 0
SCF/KIT -0.037 0.18 -10000 0 -0.51 102 102
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 -0.008 0.12 0.37 22 -0.33 14 36
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 25 -0.33 16 41
SHC/Grb2/SOS1 0.002 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 -0.098 0.22 -10000 0 -0.44 231 231
SH2B2 -0.038 0.17 -10000 0 -0.5 83 83
DOK1 0.026 0.022 -10000 0 -0.42 2 2
MATK -0.051 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 -1.1 10 10
Arf6 signaling events

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
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 -0.51 1 1
mol:GTP 0.017 0.065 0.2 58 -0.22 8 66
ARRB1 0.027 0.023 -10000 0 -0.65 1 1
FBXO8 0.028 0.005 -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 33 -0.001 71 104
ARAP2 0.026 0.033 -10000 0 -0.65 2 2
mol:GDP -0.049 0.11 0.26 16 -0.29 71 87
mol:PI-3-4-5-P3 0 0 0.001 27 -0.001 37 64
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 0.032 -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 0.33 31 -0.32 78 109
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.32 0.18 -10000 0 -0.42 624 624
ADRB2 0.016 0.069 -10000 0 -0.43 20 20
receptor agonist activity 0 0 0.001 33 0 59 92
actin filament binding 0 0 0.001 31 -0.001 77 108
SRC 0.027 0.007 -10000 0 -10000 0 0
ITGB3 0.007 0.11 -10000 0 -0.61 25 25
GNAQ 0.028 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 54 -0.001 40 94
ARF6/GDP -0.03 0.11 0.34 6 -0.45 19 25
ARF6/GDP/GULP/ACAP1 -0.078 0.14 -10000 0 -0.42 48 48
alphaIIb/beta3 Integrin/paxillin/GIT1 0.046 0.083 -10000 0 -0.4 20 20
ACAP1 -0.089 0.19 -10000 0 -0.42 225 225
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.068 -10000 0 -0.23 69 69
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 47 103
endosomal lumen acidification 0 0 0.001 23 -0.001 114 137
microtubule-based process 0 0 -10000 0 -0.001 8 8
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 10 -10000 0 10
PIP3-E 0 0 0.001 9 0 2 11
MET 0.021 0.04 -10000 0 -0.42 7 7
GNA14 -0.042 0.21 -10000 0 -0.64 92 92
GNA15 0.01 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 0.002 47 -0.001 47 94
GNA11 0.022 0.065 -10000 0 -0.65 8 8
LHCGR -0.03 0.12 -10000 0 -0.42 69 69
AGTR1 -0.072 0.24 -10000 0 -0.65 128 128
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.068 -10000 0 -0.23 69 69
IPCEF1/ARNO -0.24 0.14 -10000 0 -0.57 13 13
alphaIIb/beta3 Integrin 0.016 0.098 -10000 0 -0.42 40 40
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 -0.19 117 117
AKT1 -0.017 0.13 0.35 18 -0.35 13 31
EGF -0.54 0.25 -10000 0 -0.65 731 731
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.087 0.55 8 -0.69 1 9
mol:Ca2+ -0.042 0.16 0.42 9 -0.31 160 169
LYN 0.012 0.069 0.47 4 -0.45 1 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 0.44 11 -0.34 186 197
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 -0.26 116 116
PRKCH -0.056 0.18 0.46 7 -0.36 167 174
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 32 -0.34 11 43
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 0.46 8 -0.38 167 175
cell morphogenesis 0.033 0.012 -10000 0 -10000 0 0
PLCB2 -0.091 0.25 0.46 6 -0.52 170 176
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.002 0.083 0.45 5 -0.45 1 6
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK -0.004 0.079 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 -0.38 182 190
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 -0.52 209 217
LCK 0.007 0.097 0.55 8 -0.49 3 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.016 0.071 -10000 0 -0.33 16 16
TXA2-R family/G12 family/GDP/G beta/gamma -0.001 0.12 -10000 0 -0.44 54 54
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.016 0.067 -10000 0 -0.42 1 1
MAPK14 -0.029 0.13 0.36 12 -0.26 8 20
TGM2/GTP -0.069 0.21 0.4 4 -0.44 117 121
MAPK11 -0.027 0.13 0.41 12 -0.26 19 31
ARHGEF1 -0.022 0.087 -10000 0 -0.2 4 4
GNAI2 0.026 0.008 -10000 0 -10000 0 0
JNK cascade -0.061 0.2 0.49 9 -0.38 208 217
RAB11/GDP 0.028 0.005 -10000 0 -10000 0 0
ICAM1 -0.038 0.15 0.42 9 -0.28 113 122
cAMP biosynthetic process -0.056 0.18 0.48 9 -0.37 125 134
Gq family/GTP/EBP50 -0.005 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 -0.089 0.11 0.6 10 -0.34 13 23
VCAM1 -0.049 0.17 0.43 9 -0.31 187 196
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.09 -10000 0 -0.48 13 13
platelet activation -0.037 0.17 0.42 17 -0.31 99 116
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 0.085 -10000 0 -0.41 16 16
TXA2/TP beta/beta Arrestin2 -0.012 0.072 -10000 0 -0.42 13 13
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 -0.43 180 187
EGFR 0.017 0.061 -10000 0 -0.45 14 14
TXA2/TP alpha -0.081 0.24 0.56 8 -0.5 128 136
Gq family/GTP -0.016 0.09 -10000 0 -0.26 99 99
YES1 0.013 0.072 0.49 5 -0.45 1 6
GNAI2/GTP 0.009 0.063 -10000 0 -0.52 1 1
PGD2/DP -0.008 0.089 -10000 0 -0.29 78 78
SLC9A3R1 0.025 0.009 -10000 0 -10000 0 0
FYN 0.015 0.083 0.55 8 -0.45 1 9
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 0.072 -10000 0 -0.65 10 10
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.049 0.18 0.4 15 -0.36 143 158
PRKCB -0.051 0.19 0.4 14 -0.37 157 171
PRKCE -0.055 0.18 0.47 8 -0.36 154 162
PRKCD -0.063 0.2 0.46 10 -0.38 196 206
PRKCG -0.072 0.21 0.49 8 -0.42 190 198
muscle contraction -0.083 0.24 0.56 8 -0.48 207 215
PRKCZ -0.053 0.18 0.44 10 -0.34 184 194
ARR3 -0.007 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.021 0.073 -10000 0 -0.58 1 1
PRKCQ -0.067 0.19 0.42 8 -0.38 187 195
MAPKKK cascade -0.075 0.23 0.5 9 -0.45 172 181
SELE -0.071 0.2 0.43 9 -0.41 218 227
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 0.56 8 -0.61 217 225
GNA12 0.025 0.009 -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
Endothelins

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
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 0.62 4 -0.93 136 140
EDN1 -0.008 0.14 0.47 1 -0.46 40 41
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 0.32 9 -0.55 76 85
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.056 0.19 0.25 2 -0.47 104 106
ADCY4 -0.027 0.16 0.34 1 -0.6 30 31
ADCY5 -0.038 0.17 0.42 3 -0.56 40 43
ADCY6 -0.021 0.14 -10000 0 -0.52 24 24
ADCY7 -0.027 0.14 0.34 1 -0.51 21 22
ADCY1 -0.059 0.17 0.45 1 -0.51 58 59
ADCY2 -0.09 0.18 0.34 2 -0.54 49 51
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 -0.069 0.26 0.48 12 -0.59 117 129
ETB receptor/Endothelin-1/Gq/GTP -0.024 0.13 -10000 0 -0.36 76 76
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 -0.49 32 71
ETA receptor/Endothelin-1/Gs/GTP 0.009 0.18 0.34 48 -0.51 31 79
mol:GTP 0 0.006 -10000 0 -10000 0 0
COL3A1 -0.043 0.21 -10000 0 -0.56 73 73
EDNRB 0.015 0.068 -10000 0 -0.57 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.24 0.52 1 -0.69 69 70
CYSLTR1 -0.025 0.18 0.52 1 -0.64 24 25
SLC9A1 -0.005 0.11 0.37 1 -0.37 33 34
mol:GDP -0.062 0.22 0.41 14 -0.56 91 105
SLC9A3 -0.49 0.39 -10000 0 -0.81 400 400
RAF1 -0.062 0.21 0.45 11 -0.55 93 104
JUN -0.065 0.26 0.51 3 -0.67 87 90
JAK2 -0.024 0.17 0.52 1 -0.53 39 40
mol:IP3 -0.062 0.19 0.23 1 -0.48 114 115
ETA receptor/Endothelin-1 -0.008 0.23 0.43 55 -0.59 42 97
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 -0.5 30 30
FOS -0.067 0.28 0.5 11 -0.85 75 86
Gai/GDP -0.027 0.21 -10000 0 -0.74 51 51
CRK 0.025 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.076 0.22 0.3 2 -0.62 76 78
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
PRKCB1 -0.062 0.19 -10000 0 -0.47 113 113
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 -0.53 2 2
Gs family/GDP -0.05 0.2 0.33 9 -0.53 76 85
ETA receptor/Endothelin-1/Gq/GTP -0.036 0.19 0.52 1 -0.53 71 72
MAPK14 -0.041 0.14 -10000 0 -0.44 63 63
TRPC6 -0.14 0.41 0.63 4 -1 136 140
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 -0.43 84 84
ETB receptor/Endothelin-2 -0.021 0.15 -10000 0 -0.39 106 106
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 -0.067 0.27 0.5 11 -0.76 82 93
MAPK1 -0.071 0.28 0.49 12 -0.78 85 97
Rac1/GDP -0.045 0.19 0.52 2 -0.53 71 73
cAMP biosynthetic process -0.059 0.17 0.42 14 -0.51 49 63
MAPK8 -0.087 0.31 0.54 3 -0.77 113 116
SRC 0.027 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.006 0.086 -10000 0 -0.36 26 26
p130Cas/CRK/Src/PYK2 -0.071 0.25 0.48 15 -0.62 98 113
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.046 0.19 0.52 2 -0.52 73 75
COL1A2 -0.031 0.19 0.5 1 -0.5 69 70
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.038 0.18 -10000 0 -0.44 108 108
mol:DAG -0.062 0.19 0.23 1 -0.48 114 115
MAP2K2 -0.062 0.23 0.48 12 -0.62 87 99
MAP2K1 -0.061 0.23 0.5 11 -0.62 86 97
EDNRA -0.008 0.16 -10000 0 -0.61 33 33
positive regulation of muscle contraction 0.002 0.16 0.35 21 -0.5 24 45
Gq family/GDP -0.053 0.22 0.31 5 -0.58 89 94
HRAS/GTP -0.064 0.21 0.4 11 -0.51 107 118
PRKCH -0.061 0.19 -10000 0 -0.49 99 99
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.048 0.18 0.31 6 -0.49 82 88
PRKCB -0.054 0.19 0.28 9 -0.5 92 101
PRKCE -0.057 0.18 -10000 0 -0.49 96 96
PRKCD -0.06 0.18 0.25 1 -0.5 93 94
PRKCG -0.085 0.21 -10000 0 -0.54 115 115
regulation of vascular smooth muscle contraction -0.084 0.32 0.53 11 -1 73 84
PRKCQ -0.073 0.21 -10000 0 -0.5 126 126
PLA2G4A -0.079 0.28 0.51 11 -0.66 117 128
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 0.009 -10000 0 -10000 0 0
GNA11 0.02 0.066 -10000 0 -0.65 8 8
Rac1/GTP 0.008 0.18 0.37 39 -0.49 32 71
MMP1 -0.1 0.3 0.51 2 -0.73 131 133
FOXM1 transcription factor network

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
NFATC3 -0.12 0.45 0.94 5 -1.1 53 58
PLK1 -0.029 0.18 -10000 0 -1.2 2 2
BIRC5 -0.084 0.24 -10000 0 -0.98 19 19
HSPA1B -0.13 0.44 0.85 3 -1.1 56 59
MAP2K1 0.019 0.048 -10000 0 -10000 0 0
BRCA2 -0.13 0.45 0.8 4 -1.1 62 66
FOXM1 -0.16 0.51 0.97 3 -1.2 88 91
XRCC1 -0.13 0.44 1 3 -1.1 53 56
FOXM1B/p19 -0.21 0.43 0.66 2 -1.1 67 69
Cyclin D1/CDK4 -0.13 0.41 -10000 0 -1 44 44
CDC2 -0.14 0.46 0.91 3 -1.1 83 86
TGFA -0.14 0.43 0.93 2 -1 56 58
SKP2 -0.12 0.44 0.95 3 -1.1 45 48
CCNE1 0.017 0.072 -10000 0 -0.43 22 22
CKS1B -0.13 0.44 0.84 3 -1 85 88
RB1 -0.039 0.25 -10000 0 -0.9 22 22
FOXM1C/SP1 -0.15 0.47 -10000 0 -1.1 80 80
AURKB -0.12 0.26 -10000 0 -0.94 39 39
CENPF -0.14 0.47 0.85 3 -1.1 85 88
CDK4 0.02 0.024 -10000 0 -10000 0 0
MYC -0.12 0.4 -10000 0 -0.94 55 55
CHEK2 0.017 0.058 -10000 0 -0.44 5 5
ONECUT1 -0.13 0.43 0.74 1 -1 61 62
CDKN2A -0.36 0.14 -10000 0 -0.42 772 772
LAMA4 -0.16 0.45 0.85 3 -1.1 73 76
FOXM1B/HNF6 -0.16 0.49 0.75 1 -1.3 62 63
FOS -0.17 0.5 1.1 3 -1.2 96 99
SP1 0.027 0.008 -10000 0 -10000 0 0
CDC25B -0.12 0.44 1 4 -1.1 53 57
response to radiation 0.002 0.031 -10000 0 -10000 0 0
CENPB -0.12 0.44 1 4 -1.1 47 51
CENPA -0.17 0.48 0.86 4 -1.1 86 90
NEK2 -0.16 0.48 0.85 3 -1.1 84 87
HIST1H2BA -0.13 0.44 0.84 3 -1.1 57 60
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 0.9 3 -1.2 57 60
CCNB2 -0.16 0.49 1 3 -1.1 98 101
CCNB1 -0.14 0.46 0.95 3 -1.1 55 58
ETV5 -0.12 0.44 0.77 5 -1.1 55 60
ESR1 -0.15 0.48 0.85 3 -1.2 74 77
CCND1 -0.13 0.42 -10000 0 -1 45 45
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 0.037 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.14 0.46 -10000 0 -1.1 77 77
GAS1 -0.17 0.5 0.95 3 -1.1 92 95
MMP2 -0.12 0.45 1 4 -1.1 53 57
RB1/FOXM1C -0.14 0.44 -10000 0 -1.1 62 62
CREBBP 0.027 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated 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
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 81 84
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 -0.46 51 52
Syndecan-1/Syntenin -0.084 0.15 0.28 2 -0.46 51 53
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 -0.45 51 52
Syndecan-1/RANTES -0.14 0.16 0.33 3 -0.43 99 102
Syndecan-1/CD147 -0.075 0.15 -10000 0 -0.46 49 49
Syndecan-1/Syntenin/PIP2 -0.082 0.14 -10000 0 -0.44 51 51
LAMA5 0.025 0.028 -10000 0 -0.53 2 2
positive regulation of cell-cell adhesion -0.081 0.14 -10000 0 -0.43 51 51
MMP7 -0.068 0.22 -10000 0 -0.58 139 139
HGF -0.007 0.14 -10000 0 -0.59 45 45
Syndecan-1/CASK -0.096 0.14 0.2 1 -0.4 82 83
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 81 84
SDC1 -0.095 0.15 0.25 2 -0.43 81 83
Syndecan-1/Collagen -0.094 0.15 0.26 3 -0.42 81 84
PPIB 0.028 0.003 -10000 0 -10000 0 0
MET 0.021 0.04 -10000 0 -0.42 7 7
PRKACA 0.028 0.003 -10000 0 -10000 0 0
MMP9 -0.14 0.22 -10000 0 -0.42 332 332
MAPK1 -0.077 0.14 0.24 1 -0.43 49 50
homophilic cell adhesion -0.094 0.15 0.25 3 -0.42 81 84
MMP1 -0.08 0.22 -10000 0 -0.52 169 169
Signaling mediated by p38-alpha and p38-beta

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
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 -0.52 12 12
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 83 83
MAPKAPK5 0 0.13 -10000 0 -0.38 80 80
KRT8 -0.001 0.13 -10000 0 -0.38 75 75
MAPKAPK3 0.026 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.005 0.18 -10000 0 -0.5 87 87
CEBPB -0.006 0.13 -10000 0 -0.39 78 78
SLC9A1 -0.006 0.14 -10000 0 -0.38 91 91
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0 0.13 -10000 0 -0.37 89 89
p38alpha-beta/MNK1 0.015 0.15 -10000 0 -0.68 13 13
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 0.099 -10000 0 -0.4 12 12
NOS2 -0.019 0.22 -10000 0 -1.1 25 25
DDIT3 -0.004 0.13 -10000 0 -0.39 82 82
RAB5A 0.026 0.008 -10000 0 -10000 0 0
HSPB1 0.019 0.12 0.29 58 -0.47 13 71
p38alpha-beta/HBP1 0.018 0.13 -10000 0 -0.42 56 56
CREB1 -0.008 0.15 -10000 0 -0.4 95 95
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 -0.38 90 90
PLA2G4A -0.016 0.15 -10000 0 -0.63 27 27
GDI1 -0.006 0.14 -10000 0 -0.38 92 92
TP53 -0.013 0.15 -10000 0 -0.49 69 69
RPS6KA5 -0.009 0.14 -10000 0 -0.39 92 92
ESR1 -0.018 0.17 -10000 0 -0.44 99 99
HBP1 0.025 0.01 -10000 0 -10000 0 0
MEF2C -0.005 0.13 -10000 0 -0.38 89 89
MEF2A -0.006 0.14 -10000 0 -0.38 89 89
EIF4EBP1 -0.009 0.15 -10000 0 -0.41 96 96
KRT19 -0.066 0.21 -10000 0 -0.42 184 184
ELK4 -0.006 0.14 -10000 0 -0.38 90 90
ATF6 -0.006 0.14 -10000 0 -0.38 91 91
ATF1 -0.007 0.14 -10000 0 -0.4 95 95
p38alpha-beta/MAPKAPK2 0.015 0.15 -10000 0 -0.41 81 81
p38alpha-beta/MAPKAPK3 0.015 0.14 -10000 0 -0.4 74 74
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 32 33
ADCY1 -0.038 0.13 0.19 4 -0.4 101 105
ADCY2 -0.079 0.13 0.19 12 -0.26 297 309
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 0.35 25 -0.32 18 43
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.077 0.23 -10000 0 -0.57 119 119
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 0.36 2 -0.6 51 53
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 -0.002 0.11 0.3 26 -0.33 33 59
LAT -0.047 0.16 -10000 0 -0.42 145 145
LCP2 -0.006 0.12 -10000 0 -0.42 64 64
MAPK8 -0.01 0.17 -10000 0 -0.64 52 52
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.023 0.11 -10000 0 -0.33 60 60
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.065 0.22 -10000 0 -0.56 112 112
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.019 0.11 0.29 1 -0.53 34 35
S1P1/S1P/Gi -0.049 0.15 -10000 0 -0.46 65 65
GNAO1 0.01 0.096 -10000 0 -0.56 23 23
PDGFB-D/PDGFRB/PLCgamma1 -0.036 0.15 0.39 7 -0.48 45 52
PLCG1 -0.043 0.14 0.26 1 -0.48 44 45
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 0.16 1 -0.28 331 332
S1P1/S1P -0.082 0.13 -10000 0 -0.38 79 79
negative regulation of cAMP metabolic process -0.047 0.14 -10000 0 -0.45 65 65
MAPK3 -0.057 0.18 0.32 2 -0.58 71 73
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 -0.083 0.14 0.36 11 -0.34 107 118
RAC1 0.025 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.073 0.11 -10000 0 -0.33 72 72
receptor internalization -0.079 0.12 -10000 0 -0.35 84 84
PTGS2 -0.098 0.33 0.56 17 -0.97 96 113
Rac1/GTP -0.068 0.11 -10000 0 -0.32 67 67
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 -10000 0 -0.45 65 65
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 91 91
S1P1/S1P/PDGFB-D/PDGFRB -0.076 0.15 0.29 3 -0.45 48 51
ABCC1 0.026 0.008 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
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 -0.066 82 82
T-DHT/AR/Ubc9 -0.083 0.11 -9999 0 -0.44 53 53
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 0.023 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 -0.4 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 -0.42 772 772
SRF 0.032 0.019 -9999 0 -10000 0 0
NKX3-1 -0.19 0.1 -9999 0 -0.24 684 684
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 -0.087 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 0.026 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 0.016 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.085 0.11 -9999 0 -0.47 50 50
LATS2 0.028 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.075 0.099 -9999 0 -0.42 53 53
Cyclin D3/CDK11 p58 0.02 0.005 -9999 0 -10000 0 0
VAV3 0.015 0.079 -9999 0 -0.65 12 12
KLK2 -0.087 0.1 -9999 0 -0.42 40 40
CASP8 0.027 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.089 0.14 -9999 0 -0.48 80 80
TMPRSS2 -0.77 0.44 -9999 0 -1 657 657
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 52 52
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
Signaling events mediated by the Hedgehog family

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
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 -0.01 0.12 -10000 0 -0.38 68 68
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.01 0.11 0.38 68 -10000 0 68
SMO/beta Arrestin2 -0.046 0.14 -10000 0 -0.51 37 37
SMO -0.058 0.14 -10000 0 -0.47 66 66
AKT1 -0.011 0.098 -10000 0 -0.57 11 11
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 -0.47 66 66
STIL -0.032 0.14 -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 -0.44 72 72
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 -0.72 38 38
determination of left/right symmetry -0.057 0.14 -10000 0 -0.47 66 66
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
skeletal system development -0.12 0.21 -10000 0 -0.72 38 38
IHH N/Hhip -0.095 0.22 -10000 0 -0.5 187 187
DHH N/Hhip -0.055 0.2 -10000 0 -0.47 160 160
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.057 0.14 -10000 0 -0.47 66 66
pancreas development -0.067 0.22 -10000 0 -0.61 125 125
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 -0.47 66 66
SHH Np/Cholesterol/PTCH1 -0.054 0.13 -10000 0 -0.44 48 48
SHH Np/Cholesterol/PTCH2 0.005 0.086 -10000 0 -0.37 35 35
SHH Np/Cholesterol/Megalin -0.036 0.16 -10000 0 -0.46 102 102
SHH -0.005 0.1 0.21 2 -0.46 39 41
catabolic process -0.058 0.14 -10000 0 -0.42 71 71
SMO/Vitamin D3 -0.057 0.14 -10000 0 -0.49 50 50
SHH Np/Cholesterol/Hhip -0.042 0.16 -10000 0 -0.42 117 117
LRP2 -0.055 0.21 -10000 0 -0.57 121 121
receptor-mediated endocytosis -0.085 0.19 -10000 0 -0.57 76 76
SHH Np/Cholesterol/BOC 0.009 0.081 -10000 0 -0.38 35 35
SHH Np/Cholesterol/CDO -0.014 0.1 -10000 0 -0.38 35 35
mesenchymal cell differentiation 0.042 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 88 88
CDON -0.016 0.13 -10000 0 -0.42 87 87
IHH N/PTCH1 -0.056 0.14 -10000 0 -0.43 71 71
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 -0.001 0.079 -10000 0 -0.38 35 35
PTCH1 -0.058 0.14 -10000 0 -0.43 71 71
HHIP -0.067 0.23 -10000 0 -0.61 125 125
Ephrin A reverse signaling

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.007 0.12 -9999 0 -0.39 80 80
EFNA5 -0.021 0.17 -9999 0 -0.64 63 63
FYN -0.018 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 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
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 -0.33 19 19
CD40LG -0.17 0.34 0.52 1 -0.92 84 85
ITCH 0.019 0.08 -10000 0 -0.46 1 1
CBLB 0.019 0.079 -10000 0 -0.46 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.31 -10000 0 -0.79 107 107
JUNB 0.027 0.032 -10000 0 -0.65 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.095 -10000 0 -0.31 64 64
T cell anergy 0.002 0.12 -10000 0 -0.42 64 64
TLE4 -0.022 0.12 -10000 0 -0.49 8 8
Jun/NFAT1-c-4/p21SNFT -0.1 0.29 -10000 0 -0.95 48 48
AP-1/NFAT1-c-4 -0.17 0.38 -10000 0 -1.1 66 66
IKZF1 -0.061 0.18 -10000 0 -0.47 59 59
T-helper 2 cell differentiation -0.32 0.29 0.46 1 -0.75 147 148
AP-1/NFAT1 -0.048 0.17 -10000 0 -0.49 44 44
CALM1 0.024 0.058 -10000 0 -0.28 1 1
EGR2 -0.12 0.37 -10000 0 -1.4 52 52
EGR3 -0.14 0.41 -10000 0 -1.5 68 68
NFAT1/FOXP3 -0.081 0.22 -10000 0 -0.6 85 85
EGR1 -0.01 0.15 -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 0.056 -10000 0 -0.28 6 6
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 -0.87 57 57
DGKA -0.024 0.13 -10000 0 -0.52 15 15
CREM 0.026 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.086 0.28 -10000 0 -0.9 55 55
CTLA4 -0.13 0.26 -10000 0 -0.6 152 152
NFAT1-c-4 (dimer)/EGR1 -0.099 0.32 -10000 0 -1 61 61
NFAT1-c-4 (dimer)/EGR4 -0.088 0.28 -10000 0 -0.92 56 56
FOS -0.031 0.16 -10000 0 -0.64 57 57
IFNG -0.13 0.22 -10000 0 -0.71 12 12
T cell activation -0.049 0.19 0.57 2 -0.72 16 18
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 0.75 52 -10000 0 52
TNF -0.1 0.28 -10000 0 -0.98 49 49
FASLG -0.19 0.43 -10000 0 -1.4 76 76
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 7 7
NFAT1-c-4/ICER1 -0.088 0.28 -10000 0 -0.91 56 56
GATA3 -0.32 0.34 -10000 0 -0.65 458 458
T-helper 1 cell differentiation -0.13 0.22 -10000 0 -0.69 13 13
IL2RA -0.14 0.28 -10000 0 -0.71 100 100
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.023 0.12 -10000 0 -0.49 8 8
E2F1 -0.051 0.17 -10000 0 -0.41 163 163
PPARG 0.025 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 -10000 0 -0.97 66 66
JunB/Fra1/NFAT1-c-4 -0.078 0.28 -10000 0 -0.89 55 55
IL4 -0.33 0.3 -10000 0 -0.8 135 135
IL5 -0.16 0.32 -10000 0 -0.96 63 63
IL2 -0.05 0.19 0.57 2 -0.73 16 18
IL3 -0.039 0.13 -10000 0 -0.81 18 18
RNF128 -0.017 0.2 -10000 0 -0.68 73 73
NFATC1 -0.067 0.21 -10000 0 -0.76 51 51
CDK4 0.035 0.15 0.65 7 -10000 0 7
PTPRK -0.024 0.12 -10000 0 -0.54 9 9
IL8 -0.17 0.34 -10000 0 -0.96 79 79
POU2F1 0.027 0.007 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.027 0.12 -10000 0 -0.39 12 12
ACTA1 -0.057 0.13 -10000 0 -0.33 100 100
NUMA1 -0.027 0.12 -10000 0 -0.48 10 10
SPTAN1 -0.056 0.13 0.27 2 -0.33 100 102
LIMK1 -0.035 0.15 0.3 17 -0.33 100 117
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 -0.43 19 19
DIABLO 0.027 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.055 0.12 0.27 2 -0.33 100 102
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 0.27 2 -0.33 100 102
MADD 0.028 0.004 -10000 0 -10000 0 0
TFAP2A -0.32 0.29 -10000 0 -0.55 464 464
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 -0.048 0.14 0.3 14 -0.33 102 116
CASP9 0.027 0.007 -10000 0 -10000 0 0
DNA repair 0.019 0.088 0.34 45 -10000 0 45
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 -0.94 10 10
TRAF2 0.028 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.052 0.12 -10000 0 -0.32 100 100
CASP7 0.005 0.091 -10000 0 -0.29 36 36
KRT18 0.018 0.038 -10000 0 -0.48 1 1
apoptosis -0.053 0.14 0.49 4 -0.46 25 29
DFFA -0.053 0.13 -10000 0 -0.33 100 100
DFFB -0.052 0.13 -10000 0 -0.33 100 100
PARP1 -0.019 0.088 -10000 0 -0.34 45 45
actin filament polymerization 0.029 0.15 0.39 5 -0.35 18 23
TNF 0.012 0.082 -10000 0 -0.46 25 25
CYCS -0.018 0.078 0.21 16 -0.2 1 17
SATB1 0.006 0.14 0.42 15 -0.87 10 25
SLK -0.052 0.13 0.33 4 -0.33 101 105
p15 BID/BAX -0.021 0.085 -10000 0 -0.27 2 2
CASP2 0.006 0.06 -10000 0 -0.36 7 7
JNK cascade 0.011 0.061 0.46 5 -10000 0 5
CASP3 -0.06 0.13 0.25 1 -0.35 101 102
LMNB2 0.038 0.11 0.35 31 -0.59 7 38
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 -0.55 465 465
stress fiber formation -0.054 0.13 0.33 4 -0.33 101 105
GZMB -0.1 0.21 0.21 1 -0.43 237 238
CASP1 0.018 0.012 -10000 0 -10000 0 0
LMNB1 0.036 0.11 0.31 46 -0.42 11 57
APP -0.007 0.15 -10000 0 -0.65 41 41
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.002 -10000 0 -10000 0 0
VIM -0.053 0.14 0.33 4 -0.44 31 35
LMNA 0.025 0.14 0.32 46 -0.46 41 87
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.016 0.053 -10000 0 -0.42 3 3
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 -10000 0 -0.46 10 10
CFL2 -0.03 0.15 0.35 18 -0.4 5 23
GAS2 -0.063 0.14 0.34 4 -0.34 115 119
positive regulation of apoptosis 0.037 0.12 0.32 46 -0.47 16 62
PRF1 -0.056 0.17 -10000 0 -0.42 163 163
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.42 353 353
AURKC 0.024 0.042 -9999 0 -0.42 8 8
Reelin signaling pathway

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
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 -0.42 162 162
MAPK8IP1/MKK7/MAP3K11/JNK1 0.072 0.056 -10000 0 -0.4 9 9
AKT1 -0.039 0.12 -10000 0 -0.28 90 90
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 -0.39 161 161
LRPAP1/LRP8 0.037 0.025 -10000 0 -0.29 3 3
RELN/LRP8/DAB1/Fyn -0.044 0.17 -10000 0 -0.37 161 161
DAB1/alpha3/beta1 Integrin -0.04 0.16 -10000 0 -0.51 2 2
long-term memory -0.092 0.2 -10000 0 -0.4 201 201
DAB1/LIS1 -0.029 0.17 -10000 0 -0.53 2 2
DAB1/CRLK/C3G -0.037 0.16 -10000 0 -0.51 2 2
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
DAB1/NCK2 -0.025 0.17 -10000 0 -0.53 2 2
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 -0.084 0.22 -10000 0 -0.52 174 174
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 -0.42 161 161
GRIN2A/RELN/LRP8/DAB1/Fyn -0.092 0.21 -10000 0 -0.41 215 215
MAPK8 0.022 0.058 -10000 0 -0.61 7 7
RELN/VLDLR/DAB1 -0.055 0.17 -10000 0 -0.39 162 162
ITGB1 0.027 0.007 -10000 0 -10000 0 0
MAP1B -0.063 0.16 -10000 0 -0.37 159 159
RELN/LRP8 -0.053 0.18 -10000 0 -0.42 160 160
GRIN2B/RELN/LRP8/DAB1/Fyn -0.034 0.18 -10000 0 -0.37 159 159
PI3K 0.039 0.011 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.037 -10000 0 -0.29 10 10
RAP1A -0.032 0.16 0.46 11 -0.48 2 13
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 -0.019 0.17 0.36 48 -0.47 2 50
LRP8 0.025 0.031 -10000 0 -0.42 4 4
GSK3B -0.038 0.11 -10000 0 -0.34 13 13
RELN/VLDLR/DAB1/Fyn -0.044 0.17 -10000 0 -0.37 162 162
MAP3K11 0.027 0.023 -10000 0 -0.65 1 1
RELN/VLDLR/DAB1/P13K -0.039 0.13 -10000 0 -0.29 161 161
CDK5 0.025 0.01 -10000 0 -10000 0 0
MAPT 0.028 0.16 0.66 42 -0.58 14 56
neuron migration -0.038 0.16 0.35 8 -0.42 5 13
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 -0.38 160 160
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.013 0.041 -10000 0 -10000 0 0
NFATC2 -0.023 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 3 -0.63 155 158
PTGS2 -0.19 0.28 0.39 4 -0.61 187 191
JUNB 0.027 0.032 -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 0.025 -10000 0 -10000 0 0
JUN 0.009 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.014 -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 -0.65 187 190
AP-1/NFAT1-c-4 -0.18 0.29 -10000 0 -0.68 140 140
FASLG -0.21 0.31 0.4 5 -0.6 280 285
NFAT1-c-4/ICER1 -0.042 0.1 -10000 0 -0.44 10 10
IL2RA -0.18 0.28 0.39 3 -0.64 158 161
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.16 0.25 0.39 3 -0.58 139 142
JunB/Fra1/NFAT1-c-4 -0.039 0.12 -10000 0 -0.42 16 16
IL4 -0.16 0.24 0.39 3 -0.57 133 136
IL2 -0.003 0.1 -10000 0 -0.88 9 9
IL3 -0.023 0.14 -10000 0 -0.59 41 41
FKBP1A 0.027 0.006 -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
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 0.099 -10000 0 -0.43 34 34
PTK2 -0.091 0.2 0.45 17 -0.56 56 73
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 -0.53 2 2
SRC 0.027 0.007 -10000 0 -10000 0 0
CDKN1B -0.058 0.19 -10000 0 -0.51 124 124
VEGFA -0.11 0.2 -10000 0 -0.42 269 269
ILK -0.059 0.19 -10000 0 -0.52 126 126
ROCK1 0.028 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.18 -10000 0 -0.48 125 125
PTK2B -0.07 0.15 0.36 4 -0.37 63 67
alphaV/beta3 Integrin/JAM-A -0.02 0.16 -10000 0 -0.38 132 132
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 -0.43 397 397
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.081 -10000 0 -0.38 19 19
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.073 0.15 -10000 0 -0.42 98 98
alphaV/beta3 Integrin/Syndecan-1 0.034 0.09 -10000 0 -0.44 28 28
PI4KA 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.008 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 0.029 0.1 -10000 0 -0.46 29 29
RPS6KB1 -0.011 0.12 0.5 8 -0.55 11 19
TLN1 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.03 0.14 -10000 0 -0.59 35 35
GPR124 0.025 0.032 -10000 0 -0.5 3 3
MAPK1 -0.031 0.14 -10000 0 -0.61 32 32
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 0.15 -10000 0 -0.44 83 83
cell adhesion -0.14 0.19 -10000 0 -0.35 382 382
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 0.007 0.11 -10000 0 -0.61 25 25
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 0.078 -10000 0 -0.42 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 0.076 -10000 0 -0.42 20 20
VCL 0.027 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.004 0.15 -10000 0 -0.46 73 73
CSF1 0.023 0.049 -10000 0 -0.6 5 5
PIK3C2A -0.06 0.2 -10000 0 -0.52 127 127
PI4 Kinase/Pyk2 -0.11 0.17 -10000 0 -0.53 62 62
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.066 0.16 -10000 0 -0.4 65 65
FAK1/Vinculin -0.065 0.17 0.43 20 -0.46 42 62
alphaV beta3/Integrin/ppsTEM5 0.035 0.079 -10000 0 -0.42 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 0.01 0.065 -10000 0 -0.47 15 15
alphaV/beta3 Integrin/Lactadherin 0.036 0.08 -10000 0 -0.42 22 22
alphaV/beta3 Integrin/TGFBR2 0.034 0.076 -10000 0 -0.42 20 20
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 0.035 0.071 -10000 0 -0.38 21 21
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 -0.37 63 63
SDC1 0.021 0.062 -10000 0 -0.62 8 8
VAV3 0.027 0.077 0.38 11 -0.39 14 25
PTPN11 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.019 0.072 -10000 0 -0.65 10 10
FAK1/Paxillin -0.071 0.16 0.35 14 -0.45 42 56
cell migration -0.064 0.14 0.35 13 -0.43 28 41
ITGAV 0.026 0.028 -10000 0 -0.53 2 2
PI3K -0.006 0.16 -10000 0 -0.57 11 11
SPP1 0.016 0.085 -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 -0.038 0.17 -10000 0 -0.6 36 36
Rac1/GTP 0.028 0.057 -10000 0 -0.36 14 14
EDIL3 -0.036 0.19 -10000 0 -0.6 89 89
cell proliferation 0.034 0.076 -10000 0 -0.42 20 20
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 -0.024 0.078 0.32 6 -0.41 9 15
HIF1A -0.035 0.07 -10000 0 -0.35 16 16
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 -0.42 772 772
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 0.081 0.32 6 -0.41 9 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 -0.41 9 9
PHD1-3/OS9 -0.094 0.14 -10000 0 -0.33 10 10
HIF1A/RACK1/Elongin B/Elongin C -0.015 0.08 -10000 0 -0.42 8 8
VHL 0.026 0.008 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 -0.022 0.078 0.35 1 -0.41 9 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 -0.19 0.11 0.3 3 -0.41 60 63
Fc-epsilon receptor I signaling in mast cells

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
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 -10000 0 -0.54 53 53
mol:PIP3 -0.061 0.24 0.49 57 -0.5 88 145
IKBKB -0.012 0.16 0.4 66 -0.27 40 106
AKT1 -0.065 0.14 0.37 16 -0.49 5 21
IKBKG -0.014 0.16 0.4 63 -0.28 35 98
MS4A2 -0.087 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 -0.036 0.15 0.36 44 -0.4 15 59
mol:Ca2+ -0.039 0.2 0.45 59 -0.37 87 146
LYN 0.024 0.025 -10000 0 -0.68 1 1
CBLB -0.042 0.093 -10000 0 -0.41 15 15
SHC1 0.026 0.016 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.047 0.032 -10000 0 -0.38 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 -0.085 0.14 0.32 10 -0.4 64 74
PTPN13 -0.021 0.15 0.44 8 -0.66 26 34
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 0.5 43 -0.38 10 53
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 -0.48 117 117
LAT -0.071 0.13 0.23 2 -0.33 109 111
PAK2 -0.045 0.16 0.36 38 -0.39 29 67
NFATC2 -0.044 0.12 -10000 0 -0.64 25 25
HRAS -0.06 0.15 0.28 15 -0.39 42 57
GAB2 0.027 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 -0.42 96 96
Antigen/IgE/Fc epsilon R1 -0.096 0.17 -10000 0 -0.34 138 138
mol:GDP -0.074 0.15 -10000 0 -0.41 49 49
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 -0.37 25 25
CHUK -0.013 0.16 0.41 62 -0.28 35 97
KLRG1 -0.044 0.095 -10000 0 -0.4 16 16
VAV1 -0.083 0.14 -10000 0 -0.32 163 163
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.043 0.095 -10000 0 -0.42 16 16
negative regulation of mast cell degranulation -0.035 0.1 -10000 0 -0.42 14 14
BTK -0.046 0.11 -10000 0 -0.44 21 21
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.062 0.12 -10000 0 -0.35 72 72
GAB2/PI3K/SHP2 -0.089 0.13 -10000 0 -0.4 44 44
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.043 0.099 -10000 0 -0.34 33 33
RAF1 -0.024 0.22 -10000 0 -0.91 52 52
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.21 -10000 0 -0.45 184 184
FCER1G -0.07 0.19 -10000 0 -0.42 189 189
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 -0.018 0.21 -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 -0.025 0.22 -10000 0 -0.84 54 54
DUSP1 0.025 0.036 -10000 0 -0.57 3 3
NF-kappa-B/RelA -0.022 0.07 -10000 0 -0.23 1 1
actin cytoskeleton reorganization -0.016 0.14 0.42 2 -0.76 16 18
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.068 0.16 -10000 0 -0.42 37 37
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 -0.057 0.18 0.37 29 -0.39 65 94
cytokine secretion -0.022 0.045 -10000 0 -10000 0 0
SPHK1 -0.06 0.13 0.23 7 -0.36 60 67
PTK2 -0.017 0.15 0.42 2 -0.81 16 18
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 -0.049 0.22 0.45 57 -0.45 77 134
MAP2K2 -0.023 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 -10000 0 -0.45 9 9
MAP2K4 -0.012 0.2 -10000 0 -0.86 46 46
Fc epsilon R1/FcgammaRIIB -0.13 0.22 -10000 0 -0.47 183 183
mol:Choline -0.084 0.14 0.32 10 -0.39 64 74
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 0.42 22 -0.75 15 37
HCLS1 -0.048 0.1 -10000 0 -0.35 42 42
PRKCB -0.031 0.2 0.44 62 -0.35 82 144
FCGR2B -0.065 0.18 -10000 0 -0.42 180 180
IGHE -0.003 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.036 0.1 -10000 0 -0.43 14 14
LCP2 -0.006 0.12 -10000 0 -0.42 64 64
PLA2G4A -0.043 0.1 -10000 0 -0.43 27 27
RASA1 0.027 0.023 -10000 0 -0.65 1 1
mol:Phosphatidic acid -0.084 0.14 0.32 10 -0.39 64 74
IKK complex 0.001 0.14 0.39 66 -0.28 1 67
WIPF1 0.026 0.016 -10000 0 -0.42 1 1
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.004 0.049 0.13 90 -0.13 22 112
BUB1B -0.001 0.064 0.2 20 -0.19 48 68
PLK1 0.002 0.042 0.14 30 -0.12 16 46
PLK1S1 0.01 0.033 0.14 24 -0.23 2 26
KIF2A 0.006 0.056 0.23 27 -0.23 7 34
regulation of mitotic centrosome separation 0.002 0.042 0.14 30 -0.12 16 46
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 0.057 0.26 5 -0.38 9 14
cytokinesis -0.048 0.12 0.26 19 -0.33 21 40
PP2A-alpha B56 -0.009 0.13 -10000 0 -0.58 34 34
AURKA 0.008 0.031 0.15 12 -0.22 2 14
PICH/PLK1 -0.012 0.08 -10000 0 -0.38 22 22
CENPE -0.02 0.097 0.36 10 -0.25 99 109
RhoA/GTP 0.019 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.006 0.056 0.23 27 -0.22 7 34
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 0.14 33 -0.18 5 38
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 0.15 5 -0.26 57 62
GORASP1 0.026 0.008 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.017 54 -0.017 2 56
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.024 0.081 32 -0.061 16 48
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 0.042 0.14 30 -0.12 16 46
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 0.13 15 -0.22 39 54
CDC25C -0.022 0.068 0.18 7 -0.28 9 16
CDC25B 0.025 0.034 -10000 0 -0.42 5 5
SGOL1 -0.004 0.049 0.13 22 -0.13 90 112
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 0.064 0.12 6 -0.23 53 59
mitosis -0.002 0.003 0.019 3 -10000 0 3
FBXO5 0.001 0.044 0.17 15 -0.17 5 20
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 0.073 0.16 5 -0.26 56 61
ERCC6L -0.001 0.078 -10000 0 -0.38 21 21
NLP/gamma Tubulin 0.002 0.037 0.11 34 -0.12 35 69
microtubule cytoskeleton organization 0 0.053 0.13 15 -0.22 39 54
G2/M transition DNA damage checkpoint 0 0.002 0.014 7 -10000 0 7
PPP1R12A 0.027 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.014 7 -10000 0 7
PLK1/PRC1-2 -0.068 0.14 0.2 2 -0.26 169 171
GRASP65/GM130/RAB1/GTP/PLK1 0.032 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 0.005 0.033 0.12 39 -0.1 10 49
mitotic prometaphase -0.001 0.005 0.017 46 -10000 0 46
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.05 -10000 0 -0.46 5 5
microtubule-based process -0.078 0.13 0.16 9 -0.23 356 365
Golgi organization 0.002 0.042 0.14 30 -0.12 16 46
Cohesin/SA2 0.014 0.038 0.18 5 -10000 0 5
PPP1CB/MYPT1 0.038 0.012 -10000 0 -10000 0 0
KIF20A -0.16 0.22 -10000 0 -0.42 358 358
APC/C/CDC20 -0.002 0.087 0.2 5 -0.26 76 81
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 0.011 0.065 0.26 42 -0.27 1 43
C13orf34 0.003 0.033 0.12 31 -0.099 13 44
NUDC -0.006 0.073 0.16 5 -0.26 56 61
regulation of attachment of spindle microtubules to kinetochore 0 0.063 0.2 20 -0.19 48 68
spindle assembly 0.005 0.044 0.14 53 -0.12 8 61
spindle stabilization 0.01 0.033 0.16 18 -0.23 2 20
APC/C/HCDH1 0.027 0.016 -10000 0 -0.42 1 1
MKLP2/PLK1 -0.078 0.13 0.17 9 -0.23 356 365
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 0.091 0.26 7 -0.35 42 49
TUBG1 0.002 0.054 0.14 16 -0.23 35 51
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 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.022 0.085 -10000 0 -0.45 26 26
AKT1 -0.023 0.17 0.37 13 -0.56 58 71
PTK2B -0.081 0.19 -10000 0 -0.65 58 58
VEGFR2 homodimer/Frs2 -0.018 0.21 -10000 0 -0.77 61 61
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 -0.72 61 61
endothelial cell proliferation 0.008 0.2 0.56 42 -0.52 49 91
mol:Ca2+ -0.079 0.18 -10000 0 -0.64 60 60
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.065 0.2 -10000 0 -0.64 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 -0.55 59 59
SH2D2A -0.071 0.18 -10000 0 -0.42 193 193
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.18 0.33 4 -0.58 53 57
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.14 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 -0.61 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 -0.058 0.2 -10000 0 -0.66 59 59
HRAS 0.027 0.015 -10000 0 -0.42 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.031 0.12 -10000 0 -0.39 48 48
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 -0.63 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 -0.73 61 61
mol:GDP -0.056 0.18 -10000 0 -0.59 58 58
mol:NADP -0.013 0.17 0.5 17 -0.5 52 69
eNOS/Hsp90 -0.008 0.15 0.37 9 -0.47 49 58
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.08 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 0.44 7 -0.64 68 75
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 -0.68 59 59
PTPN6 0.027 0.006 -10000 0 -10000 0 0
EPAS1 0.005 0.11 -10000 0 -0.4 61 61
mol:L-citrulline -0.013 0.17 0.5 17 -0.5 52 69
ITGAV 0.026 0.028 -10000 0 -0.53 2 2
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.066 0.2 -10000 0 -0.64 60 60
VEGFR2 homodimer/VEGFA homodimer -0.078 0.22 -10000 0 -0.72 61 61
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 -0.67 61 64
VEGFR2 homodimer -0.036 0.23 -10000 0 -0.84 66 66
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 0.16 0.53 2 -0.56 60 62
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 -0.78 65 65
KDR -0.036 0.23 -10000 0 -0.84 66 66
VEGFA165/NRP1/VEGFR2 homodimer -0.07 0.2 -10000 0 -0.66 65 65
SRC 0.027 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.058 0.19 0.46 22 -0.57 60 82
PI3K -0.045 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 -0.055 0.19 -10000 0 -0.68 60 60
VEGFR2 homodimer/VEGFA homodimer/Src -0.08 0.21 -10000 0 -0.7 61 61
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 -0.025 0.14 0.42 4 -0.48 35 39
VEGFR2 homodimer/VEGFA homodimer/Yes -0.082 0.21 -10000 0 -0.73 61 61
PI3K/GAB1 -0.021 0.17 -10000 0 -0.57 59 59
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.057 0.2 -10000 0 -0.66 59 59
PRKACA 0.028 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.009 0.21 -10000 0 -0.76 63 63
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 -0.082 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 2 -0.7 63 65
EDG1 -0.088 0.19 -10000 0 -0.67 60 60
mol:DAG -0.08 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 5 -0.62 58 63
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.051 0.21 -10000 0 -0.63 59 59
PLCG1 -0.081 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 61 61
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.081 0.21 -10000 0 -0.72 61 61
cell migration -0.037 0.18 0.39 2 -0.54 57 59
mol:PI-3-4-5-P3 -0.041 0.18 -10000 0 -0.62 58 58
FYN 0.026 0.007 -10000 0 -10000 0 0
VEGFB/NRP1 -0.073 0.18 -10000 0 -0.64 60 60
mol:NO -0.013 0.17 0.5 17 -0.5 52 69
PXN 0.027 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.55 59 59
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.071 0.19 -10000 0 -0.64 59 59
VHL 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.007 0.11 -10000 0 -0.61 25 25
NOS3 -0.019 0.18 0.53 15 -0.57 52 67
VEGFR2 homodimer/VEGFA homodimer/Sck -0.087 0.22 -10000 0 -0.73 66 66
RAC1 0.025 0.01 -10000 0 -10000 0 0
PRKCA -0.073 0.17 0.37 1 -0.58 55 56
PRKCB -0.078 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 71 71
VEGFA165/NRP2 -0.069 0.16 -10000 0 -0.3 282 282
MAPKKK cascade -0.05 0.16 0.36 1 -0.58 33 34
NRP2 0.016 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 -0.059 0.2 0.45 3 -0.63 67 70
MAP3K13 -0.082 0.19 0.37 1 -0.68 60 61
PDPK1 -0.042 0.15 0.28 1 -0.55 53 54
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.039 0.021 -10000 0 -0.49 1 1
Necdin/E2F1 -0.035 0.15 -10000 0 -0.32 183 183
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.026 0.12 -10000 0 -0.39 30 30
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.22 -10000 0 -0.44 241 241
NT-4/5 (dimer)/p75(NTR) -0.005 0.11 -10000 0 -0.33 90 90
IKBKB 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.003 0.12 0.37 19 -0.4 24 43
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 -0.43 42 42
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 75 75
RTN4R 0.022 0.05 -10000 0 -0.44 10 10
neuron apoptosis -0.02 0.15 0.43 10 -0.53 22 32
IRAK1 0.028 0.002 -10000 0 -10000 0 0
SHC1 -0.024 0.12 -10000 0 -0.4 44 44
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 0.035 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 10 -0.41 28 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 0.013 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 0.003 -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 0.006 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 -0.3 120 120
NGF (dimer) -0.23 0.25 -10000 0 -0.44 472 472
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.023 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) -0.007 0.15 -10000 0 -0.64 44 44
TP53 -0.024 0.12 0.44 6 -0.41 22 28
PRDM4 -0.012 0.12 -10000 0 -0.41 29 29
BDNF (dimer) -0.26 0.26 -10000 0 -0.47 477 477
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 30 30
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 -0.007 0.14 0.32 37 -0.46 14 51
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) -0.017 0.15 -10000 0 -0.39 111 111
MAPK8 -0.004 0.13 0.33 35 -0.48 7 42
MAPK9 -0.003 0.13 0.47 12 -0.47 7 19
APAF1 0.027 0.006 -10000 0 -10000 0 0
NTF3 -0.007 0.15 -10000 0 -0.64 44 44
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 0.13 -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 -0.3 128 128
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 0.011 0.14 0.34 6 -0.42 30 36
BAD -0.001 0.14 0.42 20 -0.47 10 30
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 25 27
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 -0.001 0.14 0.41 23 -0.44 19 42
BDNF (dimer)/p75(NTR) -0.04 0.16 -10000 0 -0.34 178 178
PI3K 0.015 0.12 -10000 0 -0.42 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.016 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 -0.35 125 125
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.016 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 -0.31 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 -0.42 34 34
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 0.33 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 -0.49 20 20
NGF (dimer)/TRKA -0.031 0.17 -10000 0 -0.41 129 129
MMP7 -0.068 0.22 -10000 0 -0.58 139 139
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
IL2 signaling events mediated by STAT5

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
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 -0.35 141 141
IL2RB -0.14 0.22 -10000 0 -0.42 328 328
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 0.02 0.11 0.41 24 -0.46 3 27
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 0.37 1 -0.54 7 8
Signaling events mediated by PTP1B

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
PDGFRB 0.017 0.08 -10000 0 -0.63 13 13
Jak2/Leptin Receptor -0.072 0.14 -10000 0 -0.5 36 36
PTP1B/AKT1 -0.046 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 0.098 0.28 13 -0.38 29 42
EGFR -0.015 0.061 -10000 0 -0.47 14 14
EGF/EGFR -0.28 0.16 -10000 0 -0.37 614 614
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 -0.45 82 85
Insulin Receptor/Insulin -0.026 0.088 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 0.098 0.36 10 -0.46 13 23
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 0.34 20 -0.39 34 54
TXN 0.022 0.016 -10000 0 -0.42 1 1
PTP1B/IRS1/GRB2 -0.055 0.094 0.3 6 -0.48 19 25
cell migration 0.055 0.098 0.38 29 -0.28 13 42
STAT3 0.025 0.009 -10000 0 -10000 0 0
PRLR -0.083 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 0.084 0.27 1 -0.42 18 19
Crk/p130 Cas -0.051 0.081 0.27 1 -0.45 13 14
DOK1 -0.038 0.11 0.34 17 -0.41 23 40
JAK2 -0.073 0.15 0.3 4 -0.48 48 52
Jak2/Leptin Receptor/Leptin -0.058 0.097 -10000 0 -0.52 11 11
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
PTPN1 -0.055 0.099 0.29 12 -0.38 29 41
LYN 0.026 0.024 -10000 0 -0.65 1 1
CDH2 -0.033 0.19 -10000 0 -0.64 80 80
SRC 0.003 0.067 0.31 3 -0.58 7 10
ITGB3 0.006 0.11 -10000 0 -0.61 25 25
CAT1/PTP1B -0.19 0.19 0.38 27 -0.44 136 163
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 -0.44 4 4
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 0.3 4 -0.47 48 52
FCGR2A 0.002 0.1 -10000 0 -0.42 48 48
FER 0.02 0.033 -10000 0 -0.66 2 2
alphaIIb/beta3 Integrin 0.014 0.098 -10000 0 -0.42 40 40
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 0.025 0.008 -10000 0 -10000 0 0
LEPR 0.025 0.032 -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 0.31 14 -0.44 142 156
PRL -0.002 0.021 -10000 0 -10000 0 0
SOCS3 -0.014 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 0.1 0.28 5 -0.51 16 21
Ras protein signal transduction 0.051 0.12 0.46 63 -10000 0 63
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 0.28 11 -0.42 36 47
STAT5A -0.06 0.11 0.28 12 -0.42 36 48
GRB2 0.025 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.055 0.099 0.28 5 -0.42 28 33
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 0.29 2 -0.48 41 43
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
Stabilization and expansion of the E-cadherin adherens junction

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
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 0.039 0.13 0.5 44 -10000 0 44
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 0.37 29 -0.36 38 67
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 -0.53 211 212
CTNND1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.1 0.36 26 -0.34 38 64
regulation of calcium-dependent cell-cell adhesion 0.01 0.12 0.35 18 -0.38 50 68
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 -0.55 144 145
cortical microtubule organization 0.032 0.088 -10000 0 -0.36 39 39
GO:0000145 0.017 0.1 0.35 26 -0.32 38 64
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 -0.007 0.06 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.032 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.013 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 -0.36 559 559
RhoA/GDP 0.034 0.084 -10000 0 -0.34 39 39
actin cytoskeleton organization 0.021 0.11 0.36 27 -0.63 2 29
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 -0.69 9 9
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 27 -0.65 2 29
EFNA1 0.026 0.016 -10000 0 -0.42 1 1
LPP 0.013 0.087 0.35 6 -10000 0 6
Ephrin A1/EPHA2 0.025 0.082 -10000 0 -10000 0 0
SEC6/SEC8 -0.002 0.066 -10000 0 -10000 0 0
MGAT3 0.009 0.12 0.35 18 -0.38 50 68
HGF/MET 0.009 0.11 -10000 0 -0.37 59 59
HGF -0.007 0.14 -10000 0 -0.59 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 0.067 0.16 0.55 60 -10000 0 60
KIAA1543 0.015 0.11 0.36 25 -0.36 41 66
KIFC3 0.011 0.089 -10000 0 -0.34 44 44
NCK1 0.027 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ACTN1 0.026 0.1 0.35 23 -0.34 38 61
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 0.013 0.086 0.35 1 -0.34 39 40
PIP5K1C 0.028 0.11 0.36 26 -0.34 38 64
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 47 -10000 0 47
adherens junction assembly 0.034 0.14 0.49 33 -0.56 8 41
IGF-1R heterotetramer/IGF1 0.018 0.094 -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 0.37 25 -0.38 41 66
mol:GTP 0.058 0.032 -10000 0 -0.38 1 1
establishment of epithelial cell apical/basal polarity 0.035 0.1 0.38 23 -10000 0 23
cortical actin cytoskeleton stabilization 0.013 0.066 -10000 0 -0.28 39 39
regulation of cell-cell adhesion 0.021 0.11 0.36 27 -0.63 2 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.067 -10000 0 -0.29 39 39
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 0.049 -10000 0 -0.4 3 3
BAG4 0.025 0.033 -10000 0 -0.65 2 2
PKC zeta/ceramide -0.099 0.086 0.17 1 -0.29 111 112
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 0.029 0.088 0.83 10 -10000 0 10
BAD -0.1 0.079 0.17 1 -0.28 110 111
SMPD1 0.018 0.06 0.23 22 -0.28 7 29
RB1 -0.1 0.08 -10000 0 -0.29 99 99
FADD/Caspase 8 0.015 0.084 -10000 0 -0.46 7 7
MAP2K4 -0.079 0.071 0.2 2 -0.27 62 64
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.079 0.077 0.2 2 -0.28 67 69
EGF -0.54 0.25 -10000 0 -0.65 731 731
mol:ceramide -0.11 0.086 0.18 2 -0.3 109 111
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 0.079 -10000 0 -0.28 99 99
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 0.19 3 -0.28 104 107
EIF2A -0.079 0.075 0.25 7 -0.46 5 12
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 16 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.072 0.074 -10000 0 -0.31 19 19
Cathepsin D/ceramide -0.098 0.084 -10000 0 -0.28 111 111
FADD 0.01 0.055 -10000 0 -0.41 3 3
KSR1 -0.092 0.077 0.19 5 -0.29 75 80
MAPK8 -0.09 0.078 -10000 0 -0.26 110 110
PRKRA -0.099 0.081 0.18 3 -0.28 102 105
PDGFA 0.023 0.029 -10000 0 -0.53 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 -0.3 109 111
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 0.04 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 0.051 -10000 0 -0.48 3 3
TNFR1A/BAG4/TNF-alpha 0.04 0.06 -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 17 17
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 -0.26 9 10
TNFRSF1A 0.027 0.006 -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 0.08 0.32 2 -0.28 92 94
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 0.018 0.1 -10000 0 -0.45 33 33
MAP2K2 -0.076 0.072 -10000 0 -0.31 16 16
SMPD3 0.012 0.048 -10000 0 -0.33 6 6
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 0.25 639 -0.27 5 644
NF kappa B1/RelA/I kappa B alpha 0.071 0.04 -10000 0 -0.36 3 3
AIFM1 -0.06 0.054 0.17 1 -0.2 37 38
BCL2 0.027 0.023 -10000 0 -0.65 1 1
FoxO family signaling

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
G6PC -0.62 0.68 0.58 6 -1.3 438 444
PLK1 -0.027 0.18 0.53 1 -0.64 6 7
CDKN1B -0.02 0.16 0.5 13 -0.38 3 16
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 0.35 3 -0.44 413 416
CAT -0.011 0.15 -10000 0 -1.2 4 4
CTNNB1 0.026 0.008 -10000 0 -10000 0 0
AKT1 -0.015 0.052 -10000 0 -0.31 2 2
FOXO1 -0.22 0.3 0.44 10 -0.48 420 430
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 0.096 0.4 29 -0.4 2 31
response to oxidative stress -0.028 0.041 -10000 0 -0.24 5 5
FOXO3A/SIRT1 0.032 0.14 -10000 0 -0.55 7 7
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 0.39 4 -0.45 399 403
mol:GDP -0.028 0.041 -10000 0 -0.23 5 5
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.048 0.2 0.43 4 -0.67 48 52
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 -0.004 0.15 -10000 0 -0.59 37 37
YWHAB 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.033 0.064 0.27 11 -10000 0 11
MAPK9 0.033 0.058 0.33 5 -10000 0 5
YWHAG 0.025 0.009 -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 -0.048 0.19 0.53 8 -0.52 45 53
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 -0.67 2 2
FOXO1-3a-4/beta catenin -0.028 0.15 0.35 8 -0.43 1 9
proteasomal ubiquitin-dependent protein catabolic process -0.19 0.27 0.39 4 -0.44 399 403
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 0.092 0.48 16 -10000 0 16
SFN -0.072 0.2 -10000 0 -0.44 185 185
CDK2 -0.029 0.065 -10000 0 -0.29 4 4
FOXO3A/14-3-3 -0.007 0.14 -10000 0 -0.55 41 41
CREBBP -0.028 0.061 -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 -0.79 7 7
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
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.027 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 -0.42 160 160
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 -0.38 160 160
IQGAP1/CaM 0.04 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 3 3
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 -0.43 162 162
YWHAE 0.025 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.03 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 -0.037 0.12 -10000 0 -10000 0 0
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 -0.43 18 26
LIS1/IQGAP1 0.031 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 -0.53 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 0.33 31 -0.47 1 32
LRP8 0.025 0.031 -10000 0 -0.42 4 4
NDEL1/Katanin 60 -0.03 0.17 0.33 53 -0.49 1 54
P39/CDK5 -0.073 0.16 0.35 1 -0.47 22 23
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 -0.36 144 145
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 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.042 0.16 -10000 0 -0.37 158 158
RELN/VLDLR -0.037 0.18 -10000 0 -0.38 160 160
CDC42 0.017 0.008 -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 0.002 0.08 -10000 0 -0.31 16 16
NT3 (dimer)/TRKC -0.03 0.18 -10000 0 -0.5 114 114
NT3 (dimer)/TRKB -0.12 0.24 -10000 0 -0.47 244 244
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.016 -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 75 75
NTRK2 -0.18 0.31 -10000 0 -0.64 268 268
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 0.49 125 -10000 0 125
SHC 2-3/Grb2 -0.11 0.22 -10000 0 -0.58 105 105
SHC1 0.026 0.016 -10000 0 -0.42 1 1
SHC2 -0.082 0.18 -10000 0 -0.52 87 87
SHC3 -0.13 0.25 -10000 0 -0.64 133 133
STAT3 (dimer) 0.023 0.045 -10000 0 -0.37 1 1
NT3 (dimer)/TRKA -0.033 0.18 -10000 0 -0.45 108 108
RIN/GDP 0.018 0.12 0.34 35 -0.32 37 72
GIPC1 0.027 0.023 -10000 0 -0.65 1 1
KRAS 0.027 0.006 -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 -0.89 1 1
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 0.05 0.022 -10000 0 -10000 0 0
GRB2 0.025 0.009 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.033 0.17 -10000 0 -0.44 80 80
TRKA/NEDD4-2 -0.005 0.14 -10000 0 -0.49 67 67
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 0.027 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 0.013 0.17 0.41 41 -0.49 44 85
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 41 -0.31 37 78
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 -0.44 258 258
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 0.062 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.007 0.15 -10000 0 -0.64 44 44
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 74 74
Schwann cell development -0.028 0.032 -10000 0 -10000 0 0
EHD4 0.028 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.027 -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 -0.62 88 88
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 41 41
STAT3 0.023 0.045 -10000 0 -0.37 1 1
axon guidance -0.13 0.21 -10000 0 -0.59 88 88
MAPK3 -0.046 0.14 -10000 0 -0.4 74 74
MAPK1 -0.047 0.14 -10000 0 -0.4 80 80
CDC42/GDP 0.027 0.12 0.34 44 -0.31 37 81
NTF3 -0.007 0.15 -10000 0 -0.64 44 44
NTF4 -0.011 0.074 -10000 0 -0.42 25 25
NGF (dimer)/TRKA/FAIM -0.01 0.15 -10000 0 -0.44 69 69
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 -0.44 105 105
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 3 -0.56 36 39
Rac1/GDP 0.012 0.1 0.26 14 -0.32 37 51
NGF (dimer)/TRKA/GRIT -0.024 0.14 -10000 0 -0.35 129 129
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 74 74
MAP2K1 0.039 0.058 0.38 11 -10000 0 11
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 0.032 -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 -0.69 125 125
RASA1 0.027 0.023 -10000 0 -0.65 1 1
TRKA/c-Abl -0.004 0.14 -10000 0 -0.48 66 66
SQSTM1 0.024 0.034 -10000 0 -0.42 5 5
BDNF (dimer)/TRKB/GIPC -0.11 0.21 -10000 0 -0.4 259 259
NGF (dimer)/TRKA/p62/Atypical PKCs 0.012 0.14 -10000 0 -0.38 69 69
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 0.13 -10000 0 -0.36 90 90
Rac1/GTP -0.03 0.087 -10000 0 -0.32 26 26
FRS2 family/SHP2/CRK family 0.07 0.033 -10000 0 -10000 0 0
IL27-mediated signaling events

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
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 0.028 0.12 0.43 10 -0.37 1 11
IL27/IL27R/JAK1 0.018 0.23 0.71 4 -0.55 37 41
TBX21 -0.071 0.24 0.6 9 -0.55 74 83
IL12B -0.026 0.13 -10000 0 -0.42 90 90
IL12A 0.006 0.006 -10000 0 -10000 0 0
IL6ST -0.032 0.19 -10000 0 -0.66 71 71
IL27RA/JAK1 0.019 0.05 -10000 0 -10000 0 0
IL27 -0.008 0.11 -10000 0 -0.43 51 51
TYK2 0.017 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.12 -10000 0 -0.49 9 9
T-helper 2 cell differentiation 0.028 0.12 0.43 10 -0.37 1 11
T cell proliferation during immune response 0.028 0.12 0.43 10 -0.37 1 11
MAPKKK cascade -0.028 0.12 0.37 1 -0.43 10 11
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 -0.079 0.24 0.56 13 -0.53 72 85
IL27/IL27R/JAK2/TYK2 -0.028 0.12 0.37 1 -0.44 9 10
positive regulation of T cell mediated cytotoxicity -0.028 0.12 0.37 1 -0.43 10 11
STAT1 (dimer) 0.087 0.36 0.52 209 -0.65 35 244
JAK2 0.021 0.017 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
STAT2 (dimer) -0.012 0.12 0.4 1 -0.43 7 8
T cell proliferation -0.061 0.14 0.54 1 -0.51 24 25
IL12/IL12R/TYK2/JAK2 -0.024 0.12 -10000 0 -0.71 8 8
IL17A -0.017 0.11 -10000 0 -0.49 9 9
mast cell activation 0.028 0.12 0.43 10 -0.37 1 11
IFNG -0.009 0.039 0.13 4 -0.095 1 5
T cell differentiation -0.004 0.008 0.016 2 -0.022 31 33
STAT3 (dimer) -0.014 0.12 0.37 2 -0.44 6 8
STAT5A (dimer) -0.014 0.12 0.37 2 -0.47 4 6
STAT4 (dimer) -0.024 0.14 0.38 3 -0.46 19 22
STAT4 0.003 0.1 -10000 0 -0.42 47 47
T cell activation -0.008 0.005 0.048 1 -10000 0 1
IL27R/JAK2/TYK2 -0.005 0.13 -10000 0 -0.47 1 1
GATA3 -0.7 0.69 0.6 4 -1.4 458 462
IL18 -0.004 0.067 0.2 5 -0.3 40 45
positive regulation of mast cell cytokine production -0.014 0.12 0.37 2 -0.43 6 8
IL27/EBI3 -0.025 0.15 -10000 0 -0.36 131 131
IL27RA 0.003 0.036 -10000 0 -10000 0 0
IL6 -0.053 0.2 -10000 0 -0.55 117 117
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
Visual signal transduction: Rods

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
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 -0.37 172 172
mol:Na + -0.061 0.17 -10000 0 -0.38 157 157
mol:ADP -0.009 0.032 -10000 0 -0.46 3 3
RGS9-1/Gbeta5/R9AP 0.025 0.1 -10000 0 -0.36 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.056 0.18 -10000 0 -0.39 157 157
CNGB1 -0.012 0.098 -10000 0 -0.42 46 46
RDH5 -0.003 0.12 -10000 0 -0.45 55 55
SAG -0.012 0.02 -10000 0 -0.42 1 1
mol:Ca2+ -0.075 0.17 0.41 21 -0.51 29 50
Na + (4 Units) -0.06 0.16 -10000 0 -0.47 35 35
RGS9 0.001 0.11 -10000 0 -0.49 41 41
GNB1/GNGT1 -0.05 0.14 -10000 0 -0.29 221 221
GNAT1/GDP 0.027 0.094 -10000 0 -0.37 32 32
GUCY2D -0.011 0.11 -10000 0 -0.42 54 54
GNGT1 -0.096 0.19 -10000 0 -0.42 221 221
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 -0.42 24 24
mol:11-cis-retinal -0.003 0.12 -10000 0 -0.45 55 55
mol:cGMP 0.021 0.079 -10000 0 -0.41 3 3
GNB1 0.026 0.007 -10000 0 -10000 0 0
Rhodopsin 0.009 0.093 -10000 0 -0.31 65 65
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 -0.36 6 6
RGS9BP 0.014 0.093 -10000 0 -0.63 18 18
Metarhodopsin II/Transducin -0.022 0.077 -10000 0 -0.25 38 38
GCAP Family/Ca ++ 0.033 0.048 -10000 0 -0.36 2 2
PDE6A/B 0.022 0.079 -10000 0 -0.34 37 37
mol:Pi 0.025 0.1 -10000 0 -0.36 48 48
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.032 0.12 -10000 0 -0.24 115 115
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 0.061 -10000 0 -0.42 16 16
PDE6 0.03 0.13 -10000 0 -0.43 45 45
GUCA1A -0.009 0.064 -10000 0 -0.42 18 18
GC2/GCAP Family 0.043 0.052 -10000 0 -0.37 2 2
GUCA1C -0.004 0.029 -10000 0 -0.42 2 2
GUCA1B 0.024 0.034 -10000 0 -0.42 5 5
IL23-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
CCL2 -0.14 0.36 -10000 0 -1.2 36 36
IL23A -0.14 0.34 -10000 0 -1.2 29 29
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.34 -10000 0 -1 46 46
positive regulation of T cell mediated cytotoxicity -0.15 0.36 -10000 0 -1.1 56 56
ITGA3 -0.13 0.33 -10000 0 -1.1 29 29
IL17F -0.085 0.25 0.51 10 -0.72 24 34
IL12B -0.038 0.14 -10000 0 -0.43 90 90
STAT1 (dimer) -0.15 0.35 -10000 0 -1 52 52
CD4 -0.13 0.33 -10000 0 -1 34 34
IL23 -0.14 0.34 -10000 0 -1.1 33 33
IL23R -0.042 0.2 -10000 0 -0.91 31 31
IL1B -0.15 0.35 -10000 0 -1.3 29 29
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.14 0.33 -10000 0 -1.1 28 28
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 -0.32 187 187
IL23R/JAK2 -0.036 0.19 -10000 0 -0.84 28 28
positive regulation of chronic inflammatory response -0.15 0.36 -10000 0 -1.1 56 56
natural killer cell activation 0.002 0.009 0.039 11 -0.037 1 12
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 -1 33 33
ALOX12B -0.14 0.33 -10000 0 -1.1 27 27
CXCL1 -0.19 0.4 -10000 0 -1.2 70 70
T cell proliferation -0.15 0.36 -10000 0 -1.1 56 56
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.059 0.21 0.4 9 -0.57 17 26
PI3K -0.13 0.34 -10000 0 -1 42 42
IFNG -0.02 0.043 0.11 2 -0.12 6 8
STAT3 (dimer) -0.12 0.32 -10000 0 -1 35 35
IL18R1 0.018 0.059 -10000 0 -0.48 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.25 -10000 0 -0.88 20 20
IL18/IL18R -0.036 0.14 -10000 0 -0.29 104 104
macrophage activation -0.01 0.017 -10000 0 -0.045 18 18
TNF -0.15 0.35 -10000 0 -1.2 30 30
STAT3/STAT4 -0.14 0.34 -10000 0 -1.1 41 41
STAT4 (dimer) -0.16 0.36 -10000 0 -1 54 54
IL18 0.004 0.094 -10000 0 -0.42 40 40
IL19 -0.14 0.33 -10000 0 -1.1 29 29
STAT5A (dimer) -0.15 0.34 -10000 0 -1.1 43 43
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 0.35 -10000 0 -1.1 35 35
MPO -0.13 0.33 -10000 0 -1.1 24 24
positive regulation of humoral immune response -0.15 0.36 -10000 0 -1.1 56 56
IL23/IL23R/JAK2/TYK2 -0.16 0.37 -10000 0 -1.1 55 55
IL6 -0.19 0.46 -10000 0 -1.2 103 103
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 11 -0.037 1 12
CD3E -0.18 0.36 -10000 0 -1.1 34 34
keratinocyte proliferation -0.15 0.36 -10000 0 -1.1 56 56
NOS2 -0.15 0.37 -10000 0 -1.2 46 46
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 -0.44 73 74
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 0.006 -10000 0 -10000 0 0
FKBP5 0.012 0.087 -10000 0 -0.49 24 24
GR alpha/HSP90/FKBP51/HSP90 0.072 0.098 0.32 9 -0.34 14 23
PRL -0.025 0.079 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.12 0.21 0.51 50 -0.43 8 58
RELA -0.034 0.11 -10000 0 -0.31 29 29
FGG 0.028 0.22 0.51 17 -0.43 26 43
GR beta/TIF2 0.047 0.14 0.32 11 -0.43 40 51
IFNG -0.18 0.2 -10000 0 -0.74 17 17
apoptosis -0.071 0.22 0.62 3 -0.58 81 84
CREB1 0.01 0.08 -10000 0 -0.36 36 36
histone acetylation -0.012 0.088 0.26 1 -0.4 8 9
BGLAP -0.026 0.086 -10000 0 -0.53 2 2
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 82 82
SMARCD1 0.028 0.01 -10000 0 -10000 0 0
MDM2 0.043 0.065 0.28 14 -10000 0 14
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 -0.48 2 2
GSK3B 0.022 0.013 -10000 0 -10000 0 0
NR1I3 -0.046 0.22 0.57 4 -0.72 32 36
CSN2 0.061 0.13 0.41 18 -10000 0 18
BRG1/BAF155/BAF170/BAF60A 0.069 0.032 -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 -0.35 27 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.063 0.27 0.55 4 -0.79 61 65
JUN -0.14 0.18 0.31 1 -0.51 102 103
IL4 -0.038 0.083 -10000 0 -10000 0 0
CDK5R1 0.021 0.037 -10000 0 -0.45 5 5
PRKACA 0.028 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.19 0.22 46 -0.44 135 181
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.084 0.097 0.35 5 -0.33 9 14
cortisol/GR alpha (monomer) 0.15 0.22 0.57 69 -10000 0 69
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 -1.4 137 137
SUV420H1 0.028 0.004 -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 87 87
KRT14 -0.078 0.13 -10000 0 -0.53 5 5
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 -0.71 17 17
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 -0.093 0.19 -10000 0 -0.58 50 50
NFKB1 -0.034 0.11 -10000 0 -0.34 18 18
MAPK8 -0.11 0.14 -10000 0 -0.41 62 62
MAPK9 0.023 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.075 0.23 0.63 3 -0.6 85 88
BAX 0.028 0.042 -10000 0 -10000 0 0
POMC -0.097 0.22 0.56 1 -1.1 18 19
EP300 0.042 0.049 -10000 0 -0.43 2 2
cortisol/GR alpha (dimer)/p53 0.14 0.19 0.52 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.063 0.35 14 -10000 0 14
SGK1 0.058 0.13 0.59 2 -1.4 4 6
IL13 -0.32 0.27 -10000 0 -0.68 230 230
IL6 -0.17 0.38 -10000 0 -1.2 101 101
PRKACG -0.007 0.024 -10000 0 -0.42 1 1
IL5 -0.26 0.22 -10000 0 -0.6 140 140
IL2 -0.13 0.17 -10000 0 -0.72 14 14
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 -0.71 89 89
CDK5R1/CDK5 0.03 0.027 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA/PKAc -0.017 0.17 -10000 0 -0.47 31 31
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.5 48 -10000 0 48
SMARCA4 0.029 0.008 -10000 0 -10000 0 0
chromatin remodeling 0.084 0.11 0.37 22 -0.4 2 24
NF kappa B1 p50/RelA/Cbp 0.001 0.18 -10000 0 -0.53 23 23
JUN (dimer) -0.14 0.18 0.31 1 -0.51 101 102
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 0.39 34 -0.43 1 35
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 0.62 3 -0.58 81 84
cortisol/GR alpha (dimer)/Src-1 0.14 0.19 0.52 58 -10000 0 58
PBX1 0.018 0.085 -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 21 -0.4 2 23
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.5 48 -10000 0 48
mol:cortisol 0.059 0.12 0.31 72 -0.25 7 79
MMP1 -0.17 0.37 -10000 0 -1.2 84 84
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.016 0.1 -10000 0 -0.5 1 1
UGCG 0 0.11 -10000 0 -0.68 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.008 0.16 0.34 14 -0.51 43 57
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 0.13 0.29 7 -0.46 17 24
FRAP1 -0.002 0.15 0.36 13 -0.46 38 51
FOXO3 -0.002 0.15 0.35 14 -0.46 38 52
AKT1 -0.007 0.15 0.32 8 -0.5 40 48
GAB2 0.028 0.015 -10000 0 -0.42 1 1
SMPD1 0.007 0.078 -10000 0 -0.69 9 9
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 8 -0.61 50 58
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 0.002 0.15 0.48 9 -0.55 14 23
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 -0.48 45 45
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 -0.46 45 45
Rac1/GDP 0.027 0.012 -10000 0 -10000 0 0
T cell proliferation -0.011 0.13 0.29 4 -0.44 39 43
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 0.13 -10000 0 -0.46 39 39
NF kappa B1 p50/RelA 0.016 0.14 0.31 7 -0.48 14 21
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.024 0.1 -10000 0 -0.36 34 34
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 -0.42 328 328
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 0.005 0.11 -10000 0 -0.44 47 47
actin cytoskeleton organization -0.011 0.13 0.29 4 -0.44 39 43
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 0.48 5 -0.54 8 13
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.031 0.14 -9999 0 -0.46 40 40
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
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.005 0.098 -10000 0 -0.52 14 14
Crk/p130 Cas/Paxillin -0.039 0.094 -10000 0 -0.4 11 11
JUN -0.009 0.094 -10000 0 -0.41 17 17
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 0.14 -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 55 55
RHOA 0.026 0.008 -10000 0 -10000 0 0
RAP1A/GTP 0.011 0.12 -10000 0 -0.36 71 71
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 -0.001 0.12 -10000 0 -0.36 60 60
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
RET9/GFRalpha1/GDNF/IRS1 0.003 0.13 -10000 0 -0.41 62 62
lamellipodium assembly -0.01 0.1 -10000 0 -0.31 51 51
RET51/GFRalpha1/GDNF/SHC 0.008 0.14 -10000 0 -0.4 81 81
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.008 0.12 -10000 0 -0.39 55 55
RET9/GFRalpha1/GDNF/Shank3 0.008 0.11 -10000 0 -0.39 52 52
MAPK3 -0.015 0.11 0.41 2 -0.35 63 65
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 -0.024 0.12 0.33 1 -0.47 18 19
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 -0.42 18 18
HRAS/GTP 0.005 0.14 -10000 0 -0.39 74 74
tube development 0.019 0.11 -10000 0 -0.37 45 45
MAPK1 -0.009 0.12 0.39 9 -0.35 47 56
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.002 0.087 -10000 0 -0.29 60 60
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 0.18 -10000 0 -0.43 127 127
SHC1 0.026 0.016 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 0.009 0.14 -10000 0 -0.4 71 71
RET51/GFRalpha1/GDNF/Dok5 -0.005 0.17 -10000 0 -0.44 95 95
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 -0.35 59 59
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 0.026 0.007 -10000 0 -10000 0 0
JNK cascade -0.005 0.094 -10000 0 -0.4 17 17
RET9/GFRalpha1/GDNF/FRS2 0.008 0.11 -10000 0 -0.39 51 51
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 73 73
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.11 -10000 0 -0.35 29 29
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.011 0.12 -10000 0 -0.32 100 100
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.013 0.12 -10000 0 -0.34 92 92
PI3K -0.016 0.15 -10000 0 -0.45 62 62
SOS1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.02 0.11 -10000 0 -0.37 45 45
GRB10 0.025 0.009 -10000 0 -10000 0 0
activation of MAPKK activity -0.007 0.095 -10000 0 -0.35 21 21
RET51/GFRalpha1/GDNF/FRS2 0.009 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 -0.013 0.12 -10000 0 -0.34 92 92
RET51/GFRalpha1/GDNF/PKC alpha 0.009 0.14 -10000 0 -0.4 68 68
GRB2 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -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 -0.37 51 51
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
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.045 0.075 -10000 0 -0.36 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.19 -10000 0 -0.58 75 75
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 -0.51 103 103
IGF1R 0.028 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.016 0.092 -10000 0 -0.42 34 34
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 0.004 0.16 -10000 0 -0.58 39 39
regulation of stress fiber formation -0.026 0.08 -10000 0 -0.35 24 24
E2/ERA-ERB (dimer) 0.019 0.079 -10000 0 -0.38 29 29
KRAS 0.027 0.006 -10000 0 -10000 0 0
G13/GTP 0.02 0.062 -10000 0 -0.32 23 23
pseudopodium formation 0.026 0.08 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 0.21 0.35 20 -0.58 78 98
E2/ER beta (dimer) 0.018 0.031 -10000 0 -0.31 7 7
mol:GDP 0.008 0.079 -10000 0 -0.38 29 29
mol:NADP 0 0.21 0.35 20 -0.58 78 98
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.083 0.2 -10000 0 -0.53 103 103
IGF-1R heterotetramer 0.028 0.003 -10000 0 -10000 0 0
PLCB1 -0.064 0.2 -10000 0 -0.46 150 150
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 0.21 0.35 20 -0.58 78 98
RHOA 0.026 0.008 -10000 0 -10000 0 0
Gai/GDP -0.015 0.19 -10000 0 -0.61 72 72
JNK cascade 0.018 0.031 -10000 0 -0.31 7 7
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
ESR2 0.023 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 -0.015 0.25 -10000 0 -1.1 44 44
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.005 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 -0.53 2 2
PELP1 0.025 0.009 -10000 0 -10000 0 0
MAPK11 0.016 0.027 -10000 0 -0.26 8 8
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 -0.032 0.2 0.4 37 -0.57 64 101
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 0.032 0.081 -10000 0 -0.41 13 13
SOS1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.044 0.12 -10000 0 -0.48 44 44
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 0.34 21 -0.55 78 99
mol:DAG -0.083 0.2 -10000 0 -0.53 103 103
Gs family/GDP/Gbeta gamma 0.012 0.073 -10000 0 -0.39 12 12
MSN 0.026 0.083 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 -0.34 21 99
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 0.36 19 -0.63 77 96
GNA11 0.022 0.065 -10000 0 -0.65 8 8
MAPKKK cascade 0.001 0.23 0.42 23 -0.67 74 97
E2/ER alpha (dimer)/PELP1/Src 0.002 0.17 0.26 1 -0.52 63 64
ruffle organization 0.026 0.08 0.35 24 -10000 0 24
ROCK2 0.031 0.087 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 -0.009 0.18 0.3 16 -0.58 55 71
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.008 0.11 -10000 0 -0.63 24 24
GNB1/GNG2 -0.012 0.14 -10000 0 -0.47 29 29
mol:DAG -0.024 0.12 -10000 0 -0.43 28 28
PLCG1 -0.025 0.12 -10000 0 -0.45 28 28
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 -0.45 28 30
MAP3K7 -0.12 0.18 -10000 0 -0.45 106 106
mol:Ca2+ -0.023 0.12 -10000 0 -0.42 28 28
mol:IP3 -0.024 0.12 -10000 0 -0.43 28 28
NLK -0.029 0.17 -10000 0 -0.85 37 37
GNB1 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.13 0.19 -10000 0 -0.48 111 111
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.031 0.14 -10000 0 -0.46 40 40
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
GNAS -0.031 0.13 -10000 0 -0.45 38 38
GO:0007205 -0.03 0.12 -10000 0 -0.42 29 29
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 -0.45 32 32
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.025 0.1 -10000 0 -0.38 49 49
regulation of S phase of mitotic cell cycle 0.011 0.075 -10000 0 -0.3 44 44
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 0.095 0.35 7 -0.42 7 14
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 -0.016 0.12 -10000 0 -0.5 48 48
cell proliferation 0.012 0.15 0.43 29 -0.46 35 64
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
FOS -0.02 0.23 0.43 17 -0.8 58 75
mol:Ca2+ 0 0.019 -10000 0 -0.072 31 31
MAPK3 0.017 0.13 0.4 36 -0.47 12 48
MAPK1 0.009 0.1 0.29 18 -0.43 24 42
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 0.25 11 -0.39 55 66
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 0.024 0.094 -10000 0 -0.35 46 46
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 24 70
T-DHT/AR/PELP1 0.008 0.11 -10000 0 -0.41 53 53
HRAS/GDP -0.001 0.12 -10000 0 -0.47 48 48
CREB1 0.004 0.16 0.4 19 -0.51 46 65
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 0.099 0.35 9 -0.34 43 52
RAC1-CDC42/GDP 0.015 0.12 -10000 0 -0.46 45 45
T-DHT/AR/PELP1/Src 0.023 0.1 -10000 0 -0.38 46 46
MAP2K2 0.006 0.095 0.35 7 -0.42 7 14
T-DHT/AR/PELP1/Src/PI3K 0.011 0.075 -10000 0 -0.3 44 44
GNAZ 0.025 0.04 -10000 0 -0.65 3 3
SHBG -0.017 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 0.002 1 -0.007 50 51
RAC1 0.025 0.01 -10000 0 -10000 0 0
GNRH1 -0.055 0.13 0.19 2 -0.3 184 186
Gi family/GTP -0.001 0.068 -10000 0 -0.28 28 28
CDC42 0.027 0.007 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
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 -10000 0 0
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 -0.42 570 570
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 0.037 0.042 -10000 0 -0.42 1 1
Syndecan-2/Laminin alpha3 0.009 0.077 -10000 0 -0.24 72 72
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 -0.24 1 1
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 0.005 0.092 -10000 0 -0.28 77 77
SDC2 0.016 0.011 -10000 0 -0.28 1 1
KNG1 -0.44 0.3 -10000 0 -0.65 587 587
Syndecan-2/Neurofibromin 0.029 0.015 -10000 0 -10000 0 0
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 -10000 0 0
Syndecan-2/Ezrin 0.042 0.021 -10000 0 -10000 0 0
PRKACA 0.024 0.024 -10000 0 -10000 0 0
angiogenesis 0.005 0.092 -10000 0 -0.28 77 77
MMP2 0.022 0.048 -10000 0 -0.44 9 9
IL8 -0.016 0.14 -10000 0 -0.48 77 77
calcineurin-NFAT signaling pathway 0.013 0.062 -10000 0 -0.24 49 49
HIF-2-alpha transcription factor network

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
MMP14 0.001 0.093 -10000 0 -0.68 10 10
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 -0.43 3 3
EPO -0.1 0.24 -10000 0 -0.58 73 73
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 -0.67 59 59
FLT1 -0.018 0.15 -10000 0 -0.66 31 31
ADORA2A -0.083 0.23 0.46 3 -0.62 38 41
germ cell development -0.11 0.27 -10000 0 -0.65 60 60
SLC11A2 -0.073 0.23 -10000 0 -0.71 13 13
BHLHE40 -0.073 0.23 -10000 0 -0.62 31 31
HIF1AN 0.023 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.061 0.18 -10000 0 -0.46 9 9
ETS1 0.03 0.037 -10000 0 -10000 0 0
CITED2 -0.023 0.14 -10000 0 -0.66 23 23
KDR -0.07 0.31 -10000 0 -1.1 67 67
PGK1 -0.071 0.23 -10000 0 -0.62 34 34
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 -0.72 35 35
EPAS1 -0.057 0.12 -10000 0 -0.39 10 10
SP1 0.031 0.015 -10000 0 -10000 0 0
ABCG2 -0.075 0.24 -10000 0 -0.65 38 38
EFNA1 -0.071 0.23 -10000 0 -0.62 33 33
FXN -0.077 0.23 0.49 8 -0.62 35 43
POU5F1 -0.12 0.28 -10000 0 -0.68 60 60
neuron apoptosis 0.072 0.26 0.69 35 -10000 0 35
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 0.022 0.024 -10000 0 -10000 0 0
SLC2A1 -0.084 0.24 0.5 7 -0.66 50 57
TWIST1 -0.088 0.22 0.52 3 -0.63 33 36
ELK1 0.035 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.046 0.16 -10000 0 -0.47 4 4
VEGFA -0.12 0.28 -10000 0 -0.63 98 98
CREBBP 0.027 0.007 -10000 0 -10000 0 0
BCR 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
JUN -0.016 0.15 0.34 19 -0.51 42 61
IKBKB 0.007 0.1 0.32 33 -0.3 13 46
AKT1 -0.001 0.12 0.36 56 -0.24 3 59
IKBKG 0.017 0.094 0.32 29 -0.3 4 33
CALM1 -0.004 0.087 0.31 6 -0.43 12 18
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.016 0.16 0.39 19 -0.49 38 57
MAP3K7 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.09 0.32 3 -0.42 16 19
DOK1 0.026 0.022 -10000 0 -0.42 2 2
AP-1 -0.005 0.1 0.3 19 -0.28 41 60
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 0.084 0.32 6 -0.4 11 17
CSNK2A1 0.027 0.006 -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 -0.43 7 7
GO:0007205 -0.008 0.091 0.32 3 -0.42 16 19
SYK 0.024 0.048 -10000 0 -0.59 5 5
ELK1 -0.005 0.088 0.3 3 -0.44 12 15
NFATC1 -0.022 0.11 0.38 10 -0.43 7 17
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 0.049 0.16 40 -0.13 11 51
HRAS 0.002 0.083 0.32 6 -0.49 3 9
NFKBIA 0.022 0.048 0.16 40 -0.13 8 48
NF-kappa-B/RelA/I kappa B beta 0.025 0.044 0.16 33 -0.18 1 34
RasGAP/Csk -0.037 0.16 -10000 0 -0.41 68 68
mol:GDP -0.005 0.09 0.31 3 -0.4 18 21
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 0.045 0.16 34 -0.18 1 35
GRB2 0.025 0.009 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.016 0.14 0.4 11 -0.46 20 31
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
mol:IP3 -0.006 0.09 0.32 3 -0.43 16 19
CSK 0.028 0.003 -10000 0 -10000 0 0
FOS -0.023 0.12 0.31 8 -0.48 28 36
CHUK 0.003 0.12 0.31 30 -0.33 43 73
IBTK 0.027 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.007 0.12 0.29 3 -0.43 4 7
PTPN6 -0.055 0.12 -10000 0 -0.47 27 27
RELA 0.028 0.003 -10000 0 -10000 0 0
BCL2A1 0.007 0.048 0.17 16 -0.13 1 17
VAV2 -0.047 0.12 -10000 0 -0.44 25 25
ubiquitin-dependent protein catabolic process 0.025 0.048 0.16 40 -0.13 9 49
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 -0.009 0.15 0.34 26 -0.41 35 61
SH3BP5 0.012 0.097 -10000 0 -0.64 19 19
PIK3AP1 -0.002 0.097 0.34 3 -0.47 17 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.022 0.11 -10000 0 -0.5 22 22
RAF1 0.006 0.084 0.31 12 -0.45 3 15
RasGAP/p62DOK/SHIP -0.037 0.16 -10000 0 -0.4 74 74
CD79A -0.06 0.18 -10000 0 -0.42 172 172
re-entry into mitotic cell cycle -0.005 0.1 0.3 19 -0.28 38 57
RASA1 0.027 0.023 -10000 0 -0.65 1 1
MAPK3 0.022 0.1 0.38 36 -0.4 1 37
MAPK1 0.014 0.087 0.42 13 -0.4 2 15
CD72/SHP1 -0.065 0.16 0.34 2 -0.46 49 51
NFKB1 0.027 0.023 -10000 0 -0.65 1 1
MAPK8 -0.011 0.15 0.37 25 -0.41 37 62
actin cytoskeleton organization -0.022 0.13 0.35 7 -0.45 9 16
NF-kappa-B/RelA 0.055 0.082 0.29 37 -10000 0 37
Calcineurin 0.02 0.082 0.3 1 -0.42 4 5
PI3K -0.056 0.12 -10000 0 -0.44 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 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 0.36 11 -0.4 7 18
mol:DAG -0.006 0.09 0.32 3 -0.43 16 19
PLCG2 0.005 0.11 -10000 0 -0.51 35 35
MAP2K1 0.011 0.084 0.34 13 -0.42 3 16
B-cell antigen/BCR complex/FcgammaRIIB -0.066 0.17 -10000 0 -0.47 69 69
mol:PI-3-4-5-P3 -0.044 0.085 -10000 0 -0.31 17 17
ETS1 0.001 0.085 0.41 8 -0.38 9 17
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 -0.48 9 11
B-cell antigen/BCR complex/LYN/SYK -0.043 0.14 -10000 0 -0.44 34 34
CARD11 -0.022 0.14 0.36 19 -0.41 15 34
FCGR2B -0.065 0.18 -10000 0 -0.42 180 180
PPP3CA 0.028 0.004 -10000 0 -10000 0 0
BCL10 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.016 0.067 0.2 58 -0.13 3 61
PTPRC -0.007 0.12 -10000 0 -0.42 67 67
PDPK1 -0.024 0.076 0.32 10 -0.23 4 14
PPP3CB 0.027 0.007 -10000 0 -10000 0 0
PPP3CC 0.027 0.007 -10000 0 -10000 0 0
POU2F2 0.016 0.045 0.18 16 -10000 0 16
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.006 0.095 -9999 0 -0.42 42 42
PLK4 0.025 0.034 -9999 0 -0.42 5 5
regulation of centriole replication 0.003 0.071 -9999 0 -0.29 47 47
Regulation of Telomerase

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
Telomerase catalytic core complex -0.16 0.17 0.53 6 -0.61 26 32
RAD9A 0.027 0.021 -10000 0 -0.42 2 2
AP1 0.005 0.12 -10000 0 -0.46 57 57
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 -0.6 19 24
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 -0.62 8 8
Mad/Max 0.037 0.017 -10000 0 -0.29 1 1
TERT -0.17 0.18 0.54 6 -0.65 20 26
CCND1 -0.16 0.18 0.69 6 -0.75 9 15
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 0.008 -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 0.11 -10000 0 -0.42 62 62
TRF2/PARP2 0.037 0.012 -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 0.027 0.005 -10000 0 -10000 0 0
BLM 0.012 0.082 -10000 0 -0.42 31 31
Telomerase -0.007 0.085 0.29 1 -0.74 5 6
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 -0.4 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.03 0.062 -10000 0 -0.41 6 6
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 0.22 1 -0.29 4 5
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 -0.12 0.16 -10000 0 -0.65 10 10
NR2F2 0.028 0.024 -10000 0 -0.65 1 1
MAPK3 0.005 0.042 -10000 0 -0.29 16 16
MAPK1 0.006 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 0.01 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 -0.46 728 728
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 -0.61 17 17
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 -10000 0 0
IFNG -0.1 0.2 -10000 0 -0.41 257 257
Telomerase/PinX1 -0.14 0.15 -10000 0 -0.62 8 8
Telomerase/AKT1/mTOR/p70S6K -0.015 0.075 -10000 0 -0.54 5 5
SIN3B 0.028 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.009 -10000 0 -10000 0 0
Telomerase/EST1B -0.14 0.15 -10000 0 -0.6 8 8
response to DNA damage stimulus 0.004 0.015 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.069 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 10 10
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
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 -0.52 15 15
VEGFR1 homodimer/NRP1/VEGFR 121 -0.052 0.13 -10000 0 -0.52 17 17
CaM/Ca2+ -0.049 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 -0.59 6 8
FLT1 0.014 0.078 -10000 0 -0.49 17 17
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 -0.003 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 0.003 -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 -0.54 19 19
platelet activating factor biosynthetic process -0.058 0.1 0.35 2 -0.44 12 14
PI3K -0.034 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 -0.52 15 15
RASA1 0.017 0.069 -10000 0 -0.68 6 6
NRP2 0.016 0.069 -10000 0 -0.43 20 20
VEGFR1 homodimer 0.014 0.077 -10000 0 -0.49 17 17
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 -0.59 6 8
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 -0.048 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 -0.59 6 8
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
ceramide signaling pathway

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
MAP4K4 0.016 0.083 0.28 1 -0.45 16 17
BAG4 0.025 0.033 -10000 0 -0.65 2 2
BAD 0.02 0.061 0.26 28 -0.26 2 30
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.023 0.14 -10000 0 -0.42 100 100
BAX 0.021 0.059 0.27 24 -0.2 1 25
EnzymeConsortium:3.1.4.12 0.012 0.036 0.13 42 -0.1 13 55
IKBKB 0.022 0.089 0.29 8 -0.46 10 18
MAP2K2 0.032 0.09 0.31 59 -0.3 1 60
MAP2K1 0.033 0.089 0.31 59 -10000 0 59
SMPD1 0.016 0.042 0.17 27 -0.18 5 32
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.019 0.099 0.32 1 -0.49 13 14
MAP2K4 0.035 0.08 0.28 69 -10000 0 69
protein ubiquitination 0.029 0.11 0.38 21 -0.44 15 36
EnzymeConsortium:2.7.1.37 0.038 0.1 0.36 61 -10000 0 61
response to UV 0 0.002 0.005 72 -10000 0 72
RAF1 0.032 0.089 0.29 67 -10000 0 67
CRADD 0.027 0.006 -10000 0 -10000 0 0
mol:ceramide 0.019 0.053 0.19 41 -0.18 8 49
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 0.061 0.23 43 -0.2 1 44
TRADD 0.027 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 63 -10000 0 63
MAPK1 0.034 0.09 0.3 64 -10000 0 64
p50/RELA/I-kappa-B-alpha 0.041 0.008 -10000 0 -10000 0 0
FADD 0.011 0.089 0.32 1 -0.45 14 15
KSR1 0.029 0.075 0.26 62 -0.19 2 64
MAPK8 0.033 0.08 0.28 66 -0.26 3 69
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 0.084 0.3 10 -0.45 11 21
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 0.071 0.25 46 -10000 0 46
IKBKG 0.021 0.092 0.29 10 -0.44 12 22
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.092 -10000 0 -0.47 16 16
RELA 0.028 0.003 -10000 0 -10000 0 0
RIPK1 0.027 0.007 -10000 0 -10000 0 0
AIFM1 0.02 0.06 0.24 31 -10000 0 31
TNF/TNF R/SODD 0.04 0.06 -10000 0 -0.42 7 7
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 39 -10000 0 39
CASP8 0.007 0.14 -10000 0 -0.67 36 36
NSMAF 0.014 0.089 -10000 0 -0.44 15 15
response to hydrogen peroxide 0 0.002 0.005 72 -10000 0 72
BCL2 0.027 0.023 -10000 0 -0.65 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.017 0.006 -10000 0 -10000 0 0
SMARCC1 0.009 0.048 -10000 0 -0.66 4 4
REL 0.02 0.071 -10000 0 -0.6 11 11
HDAC7 -0.12 0.1 -10000 0 -0.53 6 6
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 -0.5 12 12
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 41 41
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 -0.13 0.19 0.51 34 -0.5 56 90
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 -0.29 3 3
AR/RACK1/Src -0.047 0.086 0.34 2 -0.44 7 9
AR/GR -0.023 0.12 0.26 24 -0.37 48 72
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 -0.001 0.002 -10000 0 -0.019 7 7
MAPK8 -0.019 0.041 -10000 0 -0.4 7 7
T-DHT/AR/TIF2/CARM1 -0.059 0.13 0.36 8 -0.49 39 47
SRC -0.039 0.042 0.21 1 -0.39 3 4
NR3C1 0.026 0.016 -10000 0 -0.42 1 1
KLK3 -0.06 0.19 0.4 1 -0.59 51 52
APPBP2 -0.005 0.02 -10000 0 -10000 0 0
TRIM24 0.024 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.046 0.095 0.35 11 -0.47 9 20
TMPRSS2 -0.85 0.47 -10000 0 -1.1 685 685
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 23 -0.51 41 64
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 -0.028 0.18 -10000 0 -0.64 72 72
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 0.099 0.4 12 -0.44 7 19
positive regulation of transcription -0.028 0.18 -10000 0 -0.64 72 72
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 0.098 0.3 11 -0.46 16 27
T-DHT/AR/Hsp90 -0.046 0.095 0.35 11 -0.45 10 21
GSK3B 0.023 0.007 -10000 0 -10000 0 0
NR2C1 0.027 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.044 0.046 -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 -0.072 0.11 0.35 9 -0.49 14 23
CREBBP 0.026 0.007 -10000 0 -10000 0 0
SMARCE1 0.025 0.009 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.006 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 0.006 0.1 0.31 1 -0.54 1 2
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 30 -10000 0 30
MAP2K1 -0.017 0.1 0.3 29 -10000 0 29
MAP3K11 -0.018 0.11 0.3 30 -0.5 1 31
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 -0.51 254 254
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 0.13 0.42 26 -0.54 5 31
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 -0.006 0.11 0.3 27 -0.42 1 28
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 0.094 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 -0.68 20 22
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 0.37 31 -0.62 22 53
SMAD7 -0.006 0.08 0.25 33 -10000 0 33
CBL/CRKL/C3G 0.003 0.11 0.3 27 -10000 0 27
PI3K -0.004 0.1 -10000 0 -10000 0 0
IFNG -0.1 0.2 -10000 0 -0.41 257 257
apoptosis -0.015 0.13 0.37 18 -0.41 51 69
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 -0.01 0.1 0.34 31 -10000 0 31
PRKCD -0.012 0.1 0.32 24 -10000 0 24
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 -0.008 0.11 0.3 28 -0.42 1 29
SOCS1 0.016 0.14 -10000 0 -1.3 9 9
mol:GDP 0.001 0.1 0.28 27 -10000 0 27
CASP1 -0.007 0.081 0.26 32 -0.26 4 36
PTGES2 0.026 0.033 -10000 0 -0.65 2 2
IRF9 0.029 0.062 0.25 31 -10000 0 31
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 30 -0.35 1 31
MAP3K1 -0.017 0.11 0.3 30 -10000 0 30
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 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
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 -0.28 18 18
GNAO1 0.013 0.095 -9999 0 -0.56 23 23
S1P/S1P3/G12/G13 0.03 0.08 -9999 0 -0.38 24 24
AKT1 0.012 0.11 -9999 0 -0.55 25 25
AKT3 -0.008 0.12 -9999 0 -0.62 13 13
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 0.024 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 -0.46 15 15
MAPK3 0.014 0.087 -9999 0 -0.46 13 13
MAPK1 0.014 0.086 -9999 0 -0.46 13 13
JAK2 -0.011 0.1 -9999 0 -0.46 17 17
CXCR4 -0.04 0.12 -9999 0 -0.44 16 16
FLT1 0.021 0.067 -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 0.013 0.086 -9999 0 -0.46 13 13
S1P/S1P3/Gi 0.016 0.094 -9999 0 -0.46 15 15
RAC1 0.025 0.01 -9999 0 -10000 0 0
RhoA/GTP 0.022 0.093 -9999 0 -0.45 13 13
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 0.009 -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 nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.067 -10000 0 -10000 0 0
SMAD4 0.035 0.033 -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 -0.57 1 1
AP1 0.039 0.093 -10000 0 -0.32 24 24
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 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 -0.52 21 23
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 -0.51 1 1
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 -0.43 21 21
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 0.03 0.09 0.3 6 -0.32 13 19
SMAD3/SMAD4/IRF7 0.064 0.057 -10000 0 -0.44 1 1
TFE3 0.027 0.023 -10000 0 -10000 0 0
COL1A2 0.001 0.11 0.48 4 -10000 0 4
mesenchymal cell differentiation -0.05 0.075 0.33 8 -10000 0 8
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 -0.064 0.23 -10000 0 -0.65 117 117
MEF2C 0.026 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 0.049 -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 0.043 0.029 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.054 0.29 3 -0.44 3 6
NCOR1 0.026 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 2 2
IFNB1 0.028 0.05 -10000 0 -0.38 3 3
SMAD3/SMAD4/MEF2C 0.059 0.079 -10000 0 -10000 0 0
CITED1 0.023 0.045 -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 0.046 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 -0.43 28 28
IL10 -0.19 0.22 -10000 0 -0.4 325 325
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 -0.38 404 404
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 0.066 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 0.026 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 -0.31 47 47
MYOD1 -0.017 0.071 -10000 0 -0.42 25 25
SMAD3/SMAD4/HNF4 -0.001 0.17 -10000 0 -0.44 114 114
SMAD3/SMAD4/GATA3 -0.19 0.24 -10000 0 -0.42 446 446
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 27 27
SMAD3/SMAD4/SP1-3 0.081 0.067 -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 -0.31 3 3
ITGB5 0.046 0.064 0.41 5 -10000 0 5
TGIF/SIN3/HDAC complex/CtBP 0.031 0.054 -10000 0 -0.54 5 5
SMAD3/SMAD4/AR 0.039 0.12 -10000 0 -0.44 49 49
AR -0.012 0.16 -10000 0 -0.64 53 53
negative regulation of cell growth 0.04 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.052 0.068 -10000 0 -0.31 6 6
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 0.061 0.088 -10000 0 -0.61 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.046 0.026 -10000 0 -10000 0 0
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.062 0.097 -10000 0 -0.33 13 13
SMAD3/SMAD4/RUNX2 0.05 0.076 -10000 0 -0.33 8 8
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
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.033 -10000 0 -0.65 2 2
SPHK1 -0.041 0.16 -10000 0 -0.42 131 131
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 -0.02 0.12 -10000 0 -0.3 131 131
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 -0.024 0.15 -10000 0 -0.44 74 74
S1P/S1P4/Gi 0.014 0.078 0.24 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 0.009 -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
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 0.018 0.044 -10000 0 -0.45 7 7
NOTCH1 0.028 0.055 -10000 0 -0.68 1 1
PSENEN 0.028 0.003 -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 0.055 0.11 0.3 21 -0.41 5 26
APH1B 0.026 0.033 -10000 0 -0.65 2 2
APH1A 0.027 0.007 -10000 0 -10000 0 0
AXIN1 0.005 0.054 0.3 6 -10000 0 6
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 0.049 0.12 0.29 35 -0.4 8 43
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 -0.53 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 0.067 0.3 6 -0.44 6 12
DVL1 0.02 0.029 -10000 0 -0.45 2 2
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.008 0.11 -10000 0 -0.42 8 8
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 -0.004 0.11 -10000 0 -0.42 58 58
Axin1/APC/beta catenin 0.067 0.11 0.38 37 -0.45 5 42
DKK2 0.002 0.11 -10000 0 -0.49 42 42
NOTCH1 precursor/DVL1 0.033 0.086 -10000 0 -0.59 3 3
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 0.34 192 -0.45 33 225
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
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.004 0.14 -9999 0 -0.49 19 19
Syndecan-3/Neurocan 0 0.1 -9999 0 -0.35 55 55
POMC 0.02 0.065 -9999 0 -0.6 9 9
EGFR 0.017 0.061 -9999 0 -0.45 14 14
Syndecan-3/EGFR 0.003 0.097 -9999 0 -0.35 54 54
AGRP 0.011 0.03 -9999 0 -0.42 2 2
NCSTN 0.027 0.007 -9999 0 -10000 0 0
PSENEN 0.028 0.003 -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 -0.32 53 53
Syndecan-3/IL8 -0.011 0.12 -9999 0 -0.37 70 70
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 -0.028 0.18 -9999 0 -0.63 70 70
FGFR/FGF/Syndecan-3 -0.005 0.092 -9999 0 -0.36 53 53
neuron projection morphogenesis -0.008 0.14 -9999 0 -0.54 17 17
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 45 45
Fyn/Cortactin 0.039 0.012 -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 -0.011 0.12 -9999 0 -0.36 70 70
IL8 -0.016 0.14 -9999 0 -0.48 77 77
Syndecan-3/Fyn/Cortactin 0.028 0.093 -9999 0 -0.33 51 51
Syndecan-3/CASK -0.007 0.088 -9999 0 -0.35 55 55
alpha-MSH/MC4R 0.025 0.06 -9999 0 -0.38 17 17
Gamma Secretase 0.076 0.033 -9999 0 -0.36 2 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
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 99 99
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 0.34 1 -0.71 41 42
protein ubiquitination 0.05 0.12 0.38 54 -0.42 7 61
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 -0.4 2 2
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 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.032 0.09 -10000 0 -0.41 2 2
MAPK8 -0.025 0.16 0.34 3 -0.64 41 44
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 0.007 0.098 -10000 0 -0.5 13 13
CHUK 0.041 0.096 0.32 33 -0.46 6 39
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 0.06 -10000 0 -0.42 7 7
CASP6 -0.013 0.14 -10000 0 -0.55 37 37
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 0.006 -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 -0.047 0.12 -10000 0 -0.47 2 2
BCL2 -0.021 0.15 0.38 6 -0.58 41 47
LPA receptor mediated 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
GNB1/GNG2 0.04 0.076 -10000 0 -0.38 23 23
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.082 0.32 8 -10000 0 8
AP1 0.007 0.12 -10000 0 -0.36 69 69
mol:PIP3 0.001 0.062 -10000 0 -0.4 2 2
AKT1 0.042 0.096 0.38 23 -0.4 2 25
PTK2B 0.009 0.072 0.3 4 -0.38 10 14
RHOA 0.009 0.077 0.26 4 -0.36 8 12
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 0.35 30 -0.34 20 50
NF kappa B1 p50/RelA 0.016 0.079 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 -0.47 25 25
ADCY5 0 0.11 -10000 0 -0.44 35 35
ADCY6 0.012 0.089 -10000 0 -0.46 23 23
ADCY7 0.009 0.09 -10000 0 -0.45 24 24
ADCY1 -0.017 0.12 -10000 0 -0.47 36 36
ADCY2 -0.012 0.1 -10000 0 -0.45 31 31
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 23 23
GSK3B 0.016 0.079 0.27 22 -0.36 10 32
arachidonic acid secretion 0.011 0.088 -10000 0 -0.42 25 25
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 -0.4 35 35
HRAS 0.027 0.015 -10000 0 -0.42 1 1
NFKBIA 0.017 0.091 0.41 14 -0.42 2 16
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 -0.87 53 53
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 60 60
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.009 0.063 0.38 4 -0.37 2 6
PLCB3 0.031 0.04 -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 -0.42 25 25
LPA/LPA1-2-3 0.036 0.082 -10000 0 -0.38 25 25
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.024 -10000 0 -0.65 1 1
stress fiber formation 0.019 0.076 0.38 4 -0.38 9 13
GNAZ 0.01 0.08 -10000 0 -0.41 28 28
EGFR/PI3K-beta/Gab1 0.011 0.068 -10000 0 -0.42 2 2
positive regulation of dendritic cell cytokine production 0.035 0.081 -10000 0 -0.38 25 25
LPA/LPA2/MAGI-3 0.036 0.03 -10000 0 -0.36 3 3
ARHGEF1 0.045 0.1 0.36 37 -0.35 20 57
GNAI2 0.011 0.072 -10000 0 -0.4 22 22
GNAI3 0.011 0.076 -10000 0 -0.4 26 26
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 -0.46 27 27
HB-EGF/EGFR -0.07 0.14 -10000 0 -0.48 11 11
HBEGF -0.097 0.15 -10000 0 -0.3 322 322
mol:DAG 0.009 0.063 0.38 4 -0.37 2 6
cAMP biosynthetic process 0.015 0.13 0.38 39 -0.43 31 70
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 0.018 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 0.015 0.049 -10000 0 -0.43 10 10
LPAR1 0.012 0.11 -10000 0 -0.59 26 26
IL8 -0.033 0.13 0.37 3 -0.51 24 27
PTK2 0.012 0.07 0.3 1 -0.36 21 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 -0.31 7 7
PLD2 0.011 0.07 0.3 1 -0.36 22 23
G12/G13 0.036 0.073 -10000 0 -0.38 20 20
PI3K-beta 0.006 0.066 -10000 0 -0.46 2 2
cell migration 0.017 0.076 -10000 0 -0.27 25 25
SLC9A3R2 0.026 0.024 -10000 0 -0.65 1 1
PXN 0.019 0.077 0.39 4 -0.38 9 13
HRAS/GTP 0.004 0.086 -10000 0 -0.43 25 25
RAC1 0.025 0.01 -10000 0 -10000 0 0
MMP9 -0.14 0.22 -10000 0 -0.42 332 332
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 -10000 0 0
MAPKKK cascade 0.011 0.088 -10000 0 -0.42 25 25
contractile ring contraction involved in cytokinesis 0.013 0.083 0.26 12 -0.34 9 21
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 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.009 -10000 0 -10000 0 0
MAPT 0.023 0.1 0.36 29 -0.35 20 49
GNA11 0.014 0.043 -10000 0 -0.34 10 10
Rac1/GTP -0.019 0.24 -10000 0 -0.93 53 53
MMP2 0.009 0.082 -10000 0 -0.41 30 30
E-cadherin 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
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 0.04 -9999 0 -0.65 3 3
CDH1 -0.005 0.14 -9999 0 -0.65 40 40
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.24 0.33 -10000 0 -0.65 347 347
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 60 -0.39 1 61
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 -0.032 0.081 -10000 0 -0.27 9 9
ERBB2 0.025 0.024 -10000 0 -0.65 1 1
proliferation/survival/translation -0.044 0.048 0.24 5 -0.24 11 16
PI3K -0.001 0.11 0.29 52 -0.23 12 64
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
FOXO 0.059 0.082 0.27 67 -10000 0 67
AKT2 0.028 0.003 -10000 0 -10000 0 0
PTEN 0.027 0.007 -10000 0 -10000 0 0
Ephrin B reverse 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
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 -0.3 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.095 -10000 0 -0.39 14 14
Ephrin B2/EPHB1-2 0.037 0.066 -10000 0 -0.43 11 11
neuron projection morphogenesis 0.013 0.084 -10000 0 -0.37 14 14
Ephrin B1/EPHB1-2/Tiam1 0.013 0.11 -10000 0 -0.43 18 18
DNM1 -0.039 0.16 -10000 0 -0.42 129 129
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0 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 -0.43 17 17
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 -0.59 27 27
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 0.15 -10000 0 -0.79 32 32
ITGB3 0.007 0.11 -10000 0 -0.61 25 25
EPHB1 0.015 0.083 -10000 0 -0.53 19 19
EPHB4 0.025 0.009 -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 0.016 0.098 -10000 0 -0.42 40 40
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 0.42 17 -10000 0 17
MAPK8 0.001 0.12 0.37 3 -0.54 31 34
Ephrin B1/EPHB1-2/RGS3 0.014 0.11 -10000 0 -0.43 17 17
endothelial cell migration 0.009 0.12 0.4 2 -0.54 28 30
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 0.42 17 -10000 0 17
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 -0.38 14 14
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 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
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 0.2 -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 62 62
apoptosis -0.036 0.13 -10000 0 -0.55 46 46
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 0.4 77 -0.47 44 121
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 0.033 0.19 0.35 74 -0.64 46 120
positive regulation of innate immune response 0.051 0.21 0.44 79 -0.63 44 123
LCK 0.003 0.1 -10000 0 -0.44 44 44
p38alpha-beta/MKP7 0.043 0.18 0.4 48 -0.61 41 89
p38alpha-beta/MKP5 0.059 0.2 0.45 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 0.44 66 -0.61 41 107
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
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.026 0.055 -10000 0 -0.44 1 1
adherens junction organization 0.004 0.091 0.25 8 -0.38 10 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.027 0.062 -10000 0 -0.5 1 1
FMN1 -0.011 0.11 -10000 0 -0.37 37 37
mol:IP3 0.02 0.049 -10000 0 -0.51 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.006 0.082 -10000 0 -0.42 5 5
CTNNB1 0.026 0.009 -10000 0 -10000 0 0
AKT1 0.026 0.061 0.28 3 -0.4 1 4
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 0.009 0.073 -10000 0 -0.48 3 3
VASP 0.005 0.079 -10000 0 -0.58 2 2
ZYX 0.003 0.076 -10000 0 -0.58 2 2
JUB 0.004 0.079 -10000 0 -0.4 5 5
EGFR(dimer) 0.013 0.088 -10000 0 -0.47 5 5
E-cadherin/beta catenin-gamma catenin 0.024 0.097 -10000 0 -0.41 37 37
mol:PI-3-4-5-P3 0.037 0.069 0.26 6 -0.44 2 8
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.038 0.071 0.26 6 -0.46 2 8
FYN -0.2 0.14 -10000 0 -0.42 91 91
mol:Ca2+ 0.02 0.049 -10000 0 -0.5 1 1
JUP 0.024 0.041 -10000 0 -0.65 3 3
PIK3R1 0.03 0.008 -10000 0 -10000 0 0
mol:DAG 0.02 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 0.006 0.078 -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 -0.33 577 579
RhoA/GTP 0.031 0.049 -10000 0 -0.46 1 1
AKT2 0.027 0.064 0.27 5 -0.55 1 6
actin cable formation -0.009 0.11 -10000 0 -0.5 10 10
apoptosis -0.032 0.081 0.48 1 -0.4 20 21
CTNNA1 0.029 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.056 -10000 0 -0.41 3 3
PIP5K1A 0.009 0.075 -10000 0 -0.49 3 3
PLCG1 0.02 0.05 -10000 0 -0.53 1 1
Rac1/GTP 0.022 0.086 -10000 0 -0.47 4 4
homophilic cell adhesion 0.002 0.007 -10000 0 -10000 0 0
ErbB4 signaling events

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
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 22 22
ITCH 0.057 0.023 -10000 0 -10000 0 0
WWP1 -0.083 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 -0.004 0.02 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.096 0.34 6 -0.5 2 8
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 -0.45 31 31
ADAM17 0.057 0.023 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.11 0.098 -10000 0 -0.45 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.11 -10000 0 -0.42 32 32
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 0.28 1 -0.45 19 20
ErbB4/ErbB2/betacellulin -0.095 0.13 -10000 0 -0.46 67 67
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 -0.046 0.064 -10000 0 -10000 0 0
NEDD4 0.058 0.031 -10000 0 -0.63 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.053 0.19 -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 -0.43 9 9
STAT1 (dimer) -0.093 0.092 -10000 0 -0.43 2 2
MAPK1 -0.059 0.085 -10000 0 -0.43 9 9
JAK2 0.028 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.07 0.098 -10000 0 -0.46 21 21
NRG1 0.015 0.1 -10000 0 -0.47 33 33
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 -0.046 0.064 -10000 0 -10000 0 0
neural crest cell migration -0.069 0.097 -10000 0 -0.46 21 21
ERBB2 0.034 0.024 -10000 0 -0.48 1 1
WWOX/E4ICDs -0.094 0.089 -10000 0 -0.38 2 2
SHC1 0.026 0.016 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.099 0.12 -10000 0 -0.48 27 27
apoptosis 0.095 0.11 0.51 30 -10000 0 30
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.1 -10000 0 -0.37 30 30
ErbB4/ErbB2/epiregulin -0.088 0.1 -10000 0 -0.44 2 2
ErbB4/ErbB4/betacellulin/betacellulin -0.14 0.15 -10000 0 -0.5 94 94
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.16 -10000 0 -0.47 104 104
MDM2 -0.09 0.087 -10000 0 -0.4 1 1
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 21 21
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 0.082 -10000 0 -0.37 1 1
STAT5A (dimer) -0.076 0.14 -10000 0 -0.49 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.035 0.068 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 -0.046 0.063 -10000 0 -10000 0 0
ERBB4 -0.11 0.098 -10000 0 -0.45 1 1
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 26 26
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 -0.61 26 28
IL6-mediated signaling events

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
BCL2L1 -0.049 0.19 0.58 4 -0.64 3 7
CRP -0.075 0.21 -10000 0 -0.67 9 9
cell cycle arrest -0.07 0.19 -10000 0 -0.66 8 8
TIMP1 -0.057 0.2 -10000 0 -0.59 10 10
IL6ST -0.028 0.18 -10000 0 -0.65 71 71
Rac1/GDP -0.068 0.15 -10000 0 -0.45 41 41
AP1 -0.001 0.16 -10000 0 -0.65 20 20
GAB2 0.027 0.015 -10000 0 -0.42 1 1
TNFSF11 -0.071 0.2 0.63 1 -0.68 8 9
HSP90B1 0.026 0.049 -10000 0 -10000 0 0
GAB1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.016 0.11 -10000 0 -0.6 10 10
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 -0.49 21 21
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.071 0.15 -10000 0 -0.49 24 24
MITF -0.038 0.12 -10000 0 -0.45 31 31
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 0.003 0.11 -10000 0 -0.63 17 17
STAT3 -0.081 0.19 -10000 0 -0.69 8 8
STAT1 -0.01 0.13 -10000 0 -0.68 30 30
CEBPD -0.053 0.18 0.48 4 -0.61 5 9
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.011 -10000 0 -10000 0 0
JUN 0.026 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.02 0.13 -10000 0 -0.5 17 17
MAPK11 -0.018 0.11 -10000 0 -0.54 16 16
STAT3 (dimer)/FOXO1 -0.039 0.16 -10000 0 -0.57 2 2
GRB2/SOS1/GAB family 0.001 0.14 -10000 0 -0.5 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.035 0.14 -10000 0 -0.5 37 37
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 0.48 8 -0.88 155 163
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 0.5 2 -0.72 6 8
FGG -0.089 0.22 -10000 0 -0.7 5 5
macrophage differentiation -0.07 0.19 -10000 0 -0.66 8 8
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.16 -10000 0 -0.42 46 46
JUNB -0.055 0.18 -10000 0 -0.8 5 5
FOS -0.015 0.16 -10000 0 -0.62 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.13 -10000 0 -0.45 36 36
STAT1/PIAS1 -0.032 0.13 -10000 0 -0.46 18 18
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.027 -10000 0 -10000 0 0
STAT3 (dimer) -0.076 0.19 -10000 0 -0.68 8 8
PRKCD -0.066 0.17 0.4 11 -0.52 17 28
IL6R 0.026 0.033 -10000 0 -0.65 2 2
SOCS3 -0.005 0.14 -10000 0 -0.83 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 0.015 0.13 -10000 0 -0.41 71 71
Rac1/GTP -0.071 0.15 -10000 0 -0.46 36 36
HCK -0.006 0.12 -10000 0 -0.42 63 63
MAPKKK cascade 0.009 0.13 -10000 0 -0.57 30 30
bone resorption -0.067 0.2 0.52 3 -0.64 8 11
IRF1 -0.049 0.19 0.63 1 -0.64 3 4
mol:GDP -0.083 0.15 -10000 0 -0.44 56 56
SOS1 0.027 0.006 -10000 0 -10000 0 0
VAV1 -0.084 0.15 -10000 0 -0.45 56 56
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.028 0.17 -10000 0 -0.65 32 32
PTPN11 0.013 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.026 0.16 -10000 0 -0.44 89 89
gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.13 -10000 0 -0.42 70 70
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.13 -10000 0 -0.42 71 71
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 -0.035 0.12 -10000 0 -0.4 35 35
LMO4 0.026 0.013 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.075 0.19 -10000 0 -0.67 8 8
MCL1 0.05 0.04 -10000 0 -10000 0 0
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 0.32 11 -0.59 50 61
MAP3K8 0.025 0.023 -10000 0 -0.42 2 2
FOS 0.019 0.16 0.31 15 -0.57 45 60
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 0.048 0.023 -10000 0 -10000 0 0
MAPK3 0.007 0.15 -10000 0 -0.59 43 43
MAP2K1 0.026 0.087 -10000 0 -0.6 12 12
ELK1 0.026 0.014 -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 0.019 0.067 -10000 0 -0.67 7 7
KRAS 0.027 0.006 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.034 -10000 0 -0.29 7 7
CRKL 0.035 0.095 0.32 12 -0.46 9 21
mol:PIP3 -0.008 0.049 -10000 0 -0.65 5 5
AKT1 0.005 0.061 0.36 2 -0.5 5 7
PTK2B 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.039 0.097 0.35 18 -0.44 8 26
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.025 0.1 -10000 0 -0.43 38 38
MAP3K5 0.036 0.11 0.37 38 -0.47 6 44
HGF/MET/CIN85/CBL/ENDOPHILINS 0.039 0.1 -10000 0 -0.4 37 37
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 0.075 -10000 0 -0.43 10 10
GAB1/CRKL/SHP2/PI3K 0.061 0.086 0.35 2 -0.53 3 5
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
CBL/CRK 0.061 0.11 0.36 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 0.039 0.14 0.35 120 -10000 0 120
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.013 0.049 -10000 0 -0.27 9 9
PAK1 0.008 0.071 0.5 7 -0.47 5 12
HGF/MET/RANBP10 0.026 0.099 -10000 0 -0.43 32 32
HRAS -0.002 0.13 -10000 0 -0.46 42 42
DOCK1 0.039 0.1 0.39 17 -0.5 7 24
GAB1 0.028 0.09 0.26 2 -0.43 14 16
CRK 0.044 0.11 0.38 41 -0.47 9 50
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.14 -10000 0 -0.55 36 36
JUN 0.027 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.003 0.051 -10000 0 -0.23 37 37
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.045 0.12 0.4 40 -0.53 4 44
GRB2/SHC 0.031 0.057 -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 0.038 0.14 0.35 120 -10000 0 120
HGF/MET/MUC20 0.01 0.098 -10000 0 -0.4 46 46
cell migration 0.03 0.056 -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 0.072 -10000 0 -0.32 30 30
MET/MUC20 0.016 0.029 -10000 0 -0.29 7 7
RAP1B 0.05 0.12 0.44 39 -0.46 5 44
RAP1A 0.042 0.1 0.44 17 -0.48 4 21
HGF/MET/RANBP9 0.023 0.1 -10000 0 -0.42 38 38
RAF1 0.005 0.13 0.35 1 -0.54 16 17
STAT3 0.012 0.072 -10000 0 -0.44 10 10
cell proliferation 0.022 0.093 0.28 4 -0.4 28 32
RPS6KB1 0.008 0.046 -10000 0 -0.39 9 9
MAPK3 0.024 0.12 0.48 33 -10000 0 33
MAPK1 0.035 0.16 0.56 49 -10000 0 49
RANBP9 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.046 0.15 0.43 62 -0.47 12 74
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 0.021 0.13 0.38 13 -0.51 14 27
MET 0.021 0.04 -10000 0 -0.42 7 7
MAP4K1 0.036 0.11 0.35 36 -0.47 8 44
PTK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K2 0.02 0.13 0.36 12 -0.51 14 26
BAD 0.008 0.072 0.5 7 -0.45 6 13
MAP2K4 0.047 0.13 0.42 63 -0.44 5 68
SHP2/GRB2/SOS1/GAB1 0.033 0.074 -10000 0 -0.46 5 5
INPPL1 0.028 0.004 -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 0.046 -10000 0 -0.28 4 4
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF -0.007 0.14 -10000 0 -0.59 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 0.035 0.059 -10000 0 -0.33 1 1
PDPK1 0.002 0.06 -10000 0 -0.53 5 5
HGF/MET/SHIP 0.02 0.11 -10000 0 -0.43 37 37
EPO 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
BCL2L1 0.041 0.068 0.36 1 -10000 0 1
CRKL 0.016 0.12 0.37 33 -10000 0 33
mol:DAG 0.01 0.067 -10000 0 -0.36 1 1
HRAS 0.029 0.12 0.36 59 -10000 0 59
MAPK8 -0.006 0.11 0.25 1 -0.39 2 3
RAP1A 0.019 0.12 0.38 40 -10000 0 40
GAB1 0.017 0.12 0.38 33 -10000 0 33
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 -0.36 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 -0.39 7 7
GAB1/SHC/GRB2/SOS1 0.022 0.094 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.029 0.13 -10000 0 -0.29 183 183
IRS2 0.014 0.12 0.38 37 -0.35 1 38
STAT1 0.015 0.071 -10000 0 -0.35 2 2
STAT5B 0.012 0.069 -10000 0 -0.4 1 1
cell proliferation -0.003 0.12 0.39 12 -0.35 2 14
GAB1/SHIP/PIK3R1/SHP2/SHC 0.003 0.079 -10000 0 -10000 0 0
TEC 0.018 0.12 0.37 34 -10000 0 34
SOCS3 0.02 0.052 -10000 0 -0.44 10 10
STAT1 (dimer) 0.017 0.072 -10000 0 -0.34 2 2
JAK2 0.022 0.026 -10000 0 -10000 0 0
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.024 0.1 -10000 0 -10000 0 0
EPO/EPOR -0.029 0.13 -10000 0 -0.29 183 183
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 0.35 27 -10000 0 27
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 0.058 -10000 0 -0.26 3 3
PTPN6 0.003 0.097 0.3 4 -10000 0 4
TEC/VAV2/GRB2 0.02 0.096 -10000 0 -10000 0 0
EPOR 0.023 0.026 -10000 0 -10000 0 0
INPP5D 0.022 0.048 -10000 0 -0.42 10 10
mol:GDP 0.022 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 10 -0.47 1 11
VAV2 0.02 0.12 0.38 38 -10000 0 38
CBL 0.018 0.12 0.38 35 -0.5 1 36
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) 0.028 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 -0.029 0.16 0.39 36 -0.35 55 91
BCL2 0.043 0.08 0.42 4 -0.75 1 5
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.01 -10000 0 -10000 0 0
AES 0.025 0.008 -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 0.028 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 0.41 44 -0.35 1 45
WIF1 0.006 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 0.007 0.093 -10000 0 -0.44 36 36
beta catenin/beta TrCP1 0.06 0.11 0.39 38 -10000 0 38
FZD1 0.024 0.029 -10000 0 -0.53 2 2
AXIN2 0.035 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 -0.53 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.093 0.28 2 -0.5 7 9
Axin1/APC/GSK3 0.055 0.075 0.3 16 -0.36 1 17
Axin1/APC/GSK3/beta catenin/Macf1 0.046 0.088 0.38 18 -10000 0 18
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 0.56 13 -1.4 1 14
RANBP3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.43 14 14
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 -0.44 2 7
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 0.33 9 -0.55 5 14
DKK1/LRP6/Kremen 2 0.008 0.11 -10000 0 -0.42 8 8
LRP6 0.027 0.006 -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 0.74 2 -1.5 1 3
WNT1 -0.004 0.11 -10000 0 -0.42 58 58
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 0.33 194 -0.39 35 229
APC 0.034 0.095 0.36 29 -0.36 1 30
WNT1/LRP6/FZD1 0.023 0.038 0.25 1 -0.28 1 2
CREBBP 0.024 0.01 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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
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 -0.42 256 256
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 -0.27 1 1
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 0.018 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 -0.027 0.062 -10000 0 -0.32 13 13
CDC25B 0.026 0.024 -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 -0.27 1 1
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 -0.35 9 9
Aurora A/PP2A 0.035 0.025 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.022 0.024 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.025 -10000 0 -0.28 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 -0.34 2 2
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 0.03 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 0.003 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 -0.057 0.21 0.34 5 -0.77 50 55
mol:ceramide -0.032 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 0.3 6 -0.58 50 56
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 55 55
ARHGDIB 0.002 0.022 0.26 2 -10000 0 2
FADD 0.023 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 -0.58 115 123
DFFA 0.003 0.017 0.25 1 -10000 0 1
DNA fragmentation during apoptosis 0.003 0.02 0.23 2 -10000 0 2
FAS/FADD/MET 0.041 0.037 -10000 0 -0.26 2 2
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 0.003 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 -0.51 1 1
HGF -0.007 0.14 -10000 0 -0.59 45 45
LMNA 0.003 0.021 -10000 0 -10000 0 0
CASP6 0.003 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 0.22 1 -10000 0 1
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 0.003 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 0.021 0.034 0.29 2 -10000 0 2
DAPP1 0.005 0.13 0.34 17 -0.41 41 58
Src family/SYK family/BLNK-LAT/BTK-ITK -0.042 0.17 0.32 6 -0.53 51 57
mol:DAG -0.011 0.12 0.33 46 -0.28 4 50
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 0.046 0.3 4 -10000 0 4
ARF1/GTP 0.012 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 0.044 0.3 3 -0.32 6 9
ADAP1 0.009 0.049 0.28 3 -0.35 3 6
ARAP3 0.001 0.046 0.3 4 -0.32 6 10
INPPL1 0.028 0.004 -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 0.076 0.33 24 -10000 0 24
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 0.089 0.34 26 -10000 0 26
LYN 0.026 0.024 -10000 0 -0.65 1 1
ARF1/GDP 0.027 0.084 0.27 10 -0.37 15 25
RhoA/GDP 0.034 0.062 0.33 8 -10000 0 8
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 0.1 0.38 26 -0.39 2 28
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 0.013 -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 47 47
BLK -0.001 0.1 -10000 0 -0.42 48 48
PDPK1 0.027 0.007 -10000 0 -10000 0 0
CYTH1 0.014 0.051 0.3 9 -10000 0 9
HCK -0.006 0.12 -10000 0 -0.42 63 63
CYTH3 0.01 0.043 0.28 3 -10000 0 3
CYTH2 0.015 0.053 0.29 7 -10000 0 7
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 0.086 0.26 13 -0.38 19 32
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 0.062 0.29 12 -10000 0 12
mol:PI-3-4-5-P3 0.009 0.04 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.023 0.044 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 -10000 0 -0.29 10 10
RAS family/GTP/PI3K Class I 0.047 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 -0.37 17 19
LAT -0.047 0.16 -10000 0 -0.42 145 145
Rac1/GTP 0.017 0.056 -10000 0 -0.57 1 1
ITK -0.03 0.09 0.28 4 -10000 0 4
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.03 0.13 0.32 32 -0.34 16 48
LCK 0.003 0.1 -10000 0 -0.44 44 44
BTK -0.033 0.11 0.3 12 -10000 0 12
Signaling events mediated by PRL

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
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 0.01 0.083 -10000 0 -0.42 22 22
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 -0.04 0.11 -10000 0 -0.4 36 36
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 -0.39 45 45
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 -0.004 0.081 -10000 0 -0.37 41 41
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 0.048 -10000 0 -0.45 4 4
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 -0.35 41 41
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 -0.43 18 18
RHOA 0.001 0.085 -10000 0 -0.58 5 5
cell motility 0.02 0.09 0.29 9 -0.39 17 26
PRL-1/alpha Tubulin 0.021 0.089 -10000 0 -0.35 32 32
PRL-3/alpha1 Integrin 0.03 0.065 -10000 0 -0.37 21 21
ROCK1 0.019 0.081 0.28 5 -0.44 10 15
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 -0.36 41 41
ATF5 0.026 0.03 -10000 0 -0.42 4 4
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 0.032 0.16 0.28 5 -0.53 48 53
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 0.015 -10000 0 -0.35 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.033 0.18 0.33 48 -0.57 51 99
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 0.009 -10000 0 -10000 0 0
ASIP -0.054 0.16 -10000 0 -0.42 142 142
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 0.02 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 0.007 0.075 -10000 0 -0.4 12 12
VAMP2 0.025 0.009 -10000 0 -10000 0 0
SLC2A4 0.029 0.2 0.35 43 -0.66 51 94
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 0.073 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 0.01 0.075 -10000 0 -0.37 5 5
negative regulation of cAMP metabolic process 0.002 0.075 -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 0.009 -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
EPHB forward 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
Ephrin A5/EPHB2 -0.002 0.12 -10000 0 -0.39 74 74
cell-cell adhesion 0.002 0.059 0.5 2 -10000 0 2
Ephrin B/EPHB2/RasGAP 0.058 0.08 -10000 0 -0.36 21 21
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 -0.013 0.14 -10000 0 -0.42 95 95
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 0.052 0.092 -10000 0 -0.37 28 28
Endophilin/SYNJ1 0.019 0.074 0.35 5 -0.34 21 26
KRAS 0.027 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.054 0.085 -10000 0 -0.36 22 22
endothelial cell migration 0.049 0.024 -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 0.029 0.091 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 0.068 -10000 0 -0.34 19 19
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 95 95
EPHB1 0.015 0.083 -10000 0 -0.53 19 19
EPHB4 0.025 0.009 -10000 0 -10000 0 0
mol:GDP 0.026 0.096 0.4 25 -0.38 12 37
Ephrin B/EPHB2 0.044 0.074 -10000 0 -0.36 21 21
Ephrin B/EPHB3 0.006 0.15 -10000 0 -0.4 88 88
JNK cascade 0.023 0.079 0.36 23 -0.41 11 34
Ephrin B/EPHB1 0.041 0.08 -10000 0 -0.36 22 22
RAP1/GDP 0.049 0.1 0.38 22 -0.39 3 25
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 -0.43 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 -0.47 4 4
Rap1/GTP 0.015 0.067 -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 0.018 0.056 -10000 0 -0.41 1 1
Rac1/GDP 0.022 0.085 0.34 3 -0.42 3 6
actin cytoskeleton reorganization 0 0.053 -10000 0 -0.4 3 3
CDC42/GDP 0.045 0.11 0.4 26 -0.41 3 29
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 -0.3 21 21
CDC42 0.027 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.066 -10000 0 -0.48 3 3
PTK2 0.016 0.072 0.52 17 -10000 0 17
MAP4K4 0.023 0.079 0.36 23 -0.41 11 34
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 55 -0.43 2 57
MAP2K1 0.021 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 39 -0.43 2 41
NRAS 0.027 0.007 -10000 0 -10000 0 0
SYNJ1 0.019 0.075 0.35 5 -0.34 21 26
PXN 0.027 0.006 -10000 0 -10000 0 0
TF -0.021 0.098 -10000 0 -0.41 5 5
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 0.015 0.082 0.4 21 -10000 0 21
RAC1 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0.039 0.083 -10000 0 -0.36 24 24
RAC1-CDC42/GTP -0.024 0.12 -10000 0 -0.55 15 15
RASA1 0.027 0.023 -10000 0 -0.65 1 1
RAC1-CDC42/GDP 0.033 0.084 0.33 3 -0.4 3 6
ruffle organization 0.037 0.12 0.36 63 -0.5 2 65
NCK1 0.027 0.006 -10000 0 -10000 0 0
receptor internalization -0.016 0.095 0.34 5 -0.39 10 15
Ephrin B/EPHB2/KALRN 0.058 0.078 -10000 0 -0.36 19 19
ROCK1 -0.022 0.12 -10000 0 -0.38 92 92
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 0.059 -10000 0 -0.34 3 3
Osteopontin-mediated events

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
IKK alpha homodimer 0.029 0.092 -10000 0 -0.54 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.12 0.36 44 -0.55 8 52
alphaV/beta3 Integrin/Osteopontin/Src 0.034 0.072 -10000 0 -0.42 19 19
AP1 0.044 0.14 -10000 0 -0.55 20 20
ILK 0.025 0.097 -10000 0 -0.55 8 8
bone resorption 0.023 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 29 29
MAP3K1 0.025 0.099 -10000 0 -0.42 29 29
JUN 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.09 0.35 1 -0.55 8 9
MAPK1 0.011 0.092 0.35 1 -0.55 9 10
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 -0.5 12 21
ITGB3 0.009 0.11 -10000 0 -0.61 25 25
NFKBIA 0.011 0.094 0.35 1 -0.53 10 11
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 -0.006 0.29 0.5 23 -1.1 49 72
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 0.087 -10000 0 -0.47 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.024 0.1 -10000 0 -0.41 32 32
VAV3 0.017 0.11 0.39 8 -0.44 20 28
MAP3K14 0.017 0.093 -10000 0 -0.42 29 29
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 0.09 -10000 0 -0.51 8 8
MMP2 0.017 0.12 0.38 4 -0.53 9 13
a4b1 and a4b7 Integrin 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
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 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
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 -0.43 1 1
EPO -0.076 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 -0.52 3 3
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 0.035 0.081 -10000 0 -0.42 1 1
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 0.086 -10000 0 -0.4 14 14
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 0.017 0.083 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 -0.009 0.08 0.38 1 -0.41 12 13
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
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.032 0.052 -10000 0 -0.27 6 6
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 -0.25 47 47
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 -0.36 48 48
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 0.073 0.26 1 -0.3 42 43
Cone PDE6 0.04 0.095 -10000 0 -0.37 31 31
Cone Metarhodopsin II 0.024 0.024 -10000 0 -0.24 6 6
Na + (4 Units) 0.014 0.083 -10000 0 -0.29 49 49
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) 0.001 0.02 -10000 0 -0.22 3 3
Cone Transducin 0.035 0.056 -10000 0 -0.23 29 29
SLC24A2 -0.024 0.079 -10000 0 -0.42 33 33
GNB3/GNGT2 0.024 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 -0.25 47 47
mol:Pi 0.025 0.1 -10000 0 -0.36 48 48
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
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0 0.095 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 0.057 -10000 0 -0.34 12 12
AKT1 0.062 0.13 0.47 60 -10000 0 60
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.11 0.36 8 -0.48 18 26
PIK3CA 0.027 0.006 -10000 0 -10000 0 0
FGR -0.009 0.13 0.31 3 -0.44 52 55
mol:Ca2+ 0.027 0.1 0.34 17 -0.51 18 35
MYC 0.05 0.13 0.46 34 -0.69 2 36
SHC1 0.026 0.016 -10000 0 -0.42 1 1
HRAS/GDP 0.034 0.053 -10000 0 -0.36 11 11
LRP1/PDGFRB/PDGFB 0.043 0.062 -10000 0 -0.41 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 0.34 15 -0.52 18 33
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 -0.39 11 11
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 0.055 0.13 0.46 60 -10000 0 60
GAB1 0.025 0.11 0.34 23 -0.48 18 41
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.024 0.11 0.37 26 -0.47 12 38
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 0.35 15 -0.52 18 33
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.024 0.079 -10000 0 -0.45 22 22
SHB 0.028 0.004 -10000 0 -10000 0 0
BLK -0.003 0.095 -10000 0 -0.41 16 16
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 0.027 0.12 0.36 24 -0.48 18 42
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 -0.014 0.13 0.32 2 -0.53 25 27
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 -0.48 8 8
ABL1 0.023 0.11 0.33 24 -0.46 19 43
PDGFB-D/PDGFRB/CBL 0.02 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 -0.52 3 41
SLA 0.004 0.1 -10000 0 -0.42 47 47
actin cytoskeleton reorganization 0.044 0.065 0.35 13 -10000 0 13
SRC 0.015 0.062 -10000 0 -0.43 9 9
PI3K 0.01 0.034 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.037 0.073 -10000 0 -0.41 19 19
SH2B2 0.022 0.038 -10000 0 -0.42 6 6
PLCgamma1/SPHK1 0.009 0.11 0.37 8 -0.5 18 26
LYN 0.01 0.08 -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 2 2
SPHK1 -0.04 0.16 -10000 0 -0.42 131 131
EDG1 0.001 0.004 -10000 0 -10000 0 0
mol:DAG 0.027 0.11 0.35 15 -0.52 18 33
PLCG1 0.027 0.11 0.35 15 -0.54 18 33
NHERF/PDGFRB 0.041 0.055 -10000 0 -0.42 9 9
YES1 0.008 0.1 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 2 2
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 -0.009 0.12 -10000 0 -0.43 49 49
DOK1 0.023 0.056 -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 0.05 0.13 0.46 31 -0.51 7 38
PRKCD 0.021 0.059 -10000 0 -0.38 9 9
FER 0.022 0.058 -10000 0 -0.38 12 12
MAPKKK cascade 0.026 0.094 0.41 29 -10000 0 29
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 0.33 24 -0.44 19 43
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
ErbB2/ErbB3 signaling events

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
USP8 0.008 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.12 -10000 0 -0.57 16 16
NFATC4 0.004 0.089 0.31 29 -0.38 5 34
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 0.085 -10000 0 -0.38 13 13
JUN 0.019 0.078 0.37 15 -0.34 3 18
HRAS 0.027 0.015 -10000 0 -0.42 1 1
DOCK7 -0.001 0.083 0.29 2 -0.5 3 5
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.019 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 0.063 0.2 14 -0.29 10 24
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.005 0.092 0.32 1 -0.42 13 14
RAF1 -0.016 0.11 0.45 8 -0.57 13 21
ErbB2/ErbB3/neuregulin 2 0.008 0.087 -10000 0 -0.42 19 19
STAT3 -0.004 0.18 -10000 0 -0.86 37 37
cell migration 0.03 0.11 0.33 64 -0.28 8 72
mol:PI-3-4-5-P3 0 0.003 -10000 0 -10000 0 0
cell proliferation -0.065 0.17 0.53 8 -0.57 16 24
FOS -0.05 0.16 0.48 11 -0.5 57 68
NRAS 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.085 -10000 0 -0.38 13 13
MAPK3 -0.048 0.15 0.48 8 -0.55 10 18
MAPK1 -0.054 0.16 0.48 9 -0.61 21 30
JAK2 -0.001 0.082 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 0.013 -10000 0 -10000 0 0
MAPK8 0.002 0.084 0.3 2 -0.34 22 24
MAPK9 0.009 0.055 0.22 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 -0.16 2 3
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 -0.078 0.16 0.45 10 -0.46 19 29
myelination 0.01 0.12 0.41 41 -0.38 4 45
PPP3CB 0 0.078 0.28 2 -0.46 3 5
KRAS 0.026 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.016 0.12 -10000 0 -0.53 20 20
NRG2 0.001 0.11 -10000 0 -0.43 49 49
mol:GDP -0.006 0.12 0.23 2 -0.4 62 64
SOS1 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.026 0.11 0.38 6 -0.54 12 18
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 -0.51 3 5
MAP2K1 -0.052 0.16 0.48 4 -0.58 18 22
heart morphogenesis 0.004 0.085 -10000 0 -0.38 13 13
RAS family/GDP 0.026 0.12 -10000 0 -0.57 16 16
GRB2 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.014 0.038 -10000 0 -0.75 2 2
CHRNE 0.013 0.032 0.16 22 -0.15 5 27
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 0.085 -10000 0 -0.38 13 13
CDC42 0.027 0.007 -10000 0 -10000 0 0
IL1-mediated signaling events

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
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 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.06 -10000 0 -0.37 4 4
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 -0.37 21 21
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.044 -10000 0 -0.33 2 2
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 -0.38 2 2
TOLLIP 0.028 0.004 -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 0.013 0.039 0.33 4 -0.3 4 8
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 4 -0.32 4 8
IRAK1 0.018 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.024 0.081 -10000 0 -0.34 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 -0.31 4 4
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 -0.43 152 152
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 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.025 0.039 -10000 0 -0.28 2 2
IL1 alpha/IL1R1/IL1RAP 0.035 0.071 -10000 0 -0.43 2 2
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 0.04 0.34 4 -0.34 3 7
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.031 0.082 -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 -0.4 6 6
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 0.052 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 0.027 0.016 -10000 0 -0.42 1 1
RPS6KB1 0.046 0.13 0.51 62 -10000 0 62
RARs/THRs/DNA/SMRT 0.02 0.063 -10000 0 -10000 0 0
THRA 0.025 0.024 -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 -0.35 1 1
NR1H4 -0.017 0.16 -10000 0 -0.65 56 56
RXRs/LXRs/DNA 0.088 0.061 -10000 0 -0.43 1 1
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 -0.34 5 5
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 -0.41 71 71
RXRG 0.021 0.055 -10000 0 -0.44 11 11
RXR alpha/CCPG 0.041 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 -1 8 8
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 -0.35 1 1
ABCA1 0.044 0.066 -10000 0 -0.47 5 5
RARs/THRs 0.05 0.09 -10000 0 -0.36 34 34
RXRs/FXR 0.041 0.12 -10000 0 -0.38 54 54
BCL2 0.027 0.023 -10000 0 -0.65 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.005 0.13 -10000 0 -0.51 40 40
KLHL20 0.023 0.069 0.21 3 -0.31 2 5
CYFIP2 0.018 0.076 -10000 0 -0.65 11 11
Rac1/GDP 0.023 0.091 0.31 13 -0.37 2 15
ENAH -0.005 0.12 -10000 0 -0.51 40 40
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 0.021 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 0.094 -10000 0 -0.38 37 37
RAPGEF1 0.004 0.12 0.26 4 -0.44 34 38
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 0.026 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 0.13 -10000 0 -0.51 39 39
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 -10000 0 0
PI3K 0.004 0.051 -10000 0 -10000 0 0
ARF6 0.027 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 -0.47 42 42
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 0.036 -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 29 -0.36 2 31
actin cytoskeleton organization 0.022 0.057 0.17 17 -0.22 2 19
CDC42/GDP 0.047 0.13 0.4 51 -0.36 2 53
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 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 0.034 0.14 0.44 42 -0.4 5 47
CDC42/GTP/IQGAP1 0.036 0.01 -10000 0 -10000 0 0
JUP 0.023 0.04 -10000 0 -0.65 3 3
p120 catenin/RhoA/GDP 0.033 0.097 0.31 13 -0.37 2 15
RAC1/GTP/IQGAP1 0.033 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.042 0.005 -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 0.026 0.068 0.22 42 -0.17 33 75
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 0.24 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.048 0.095 -10000 0 -0.37 36 36
CCND1 0.023 0.067 0.19 24 -0.21 33 57
VAV2 0.005 0.15 -10000 0 -0.57 17 17
RAP1/GDP 0.037 0.09 0.32 16 -0.35 1 17
adherens junction assembly -0.005 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 0.12 -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 -0.006 0.13 -10000 0 -0.54 40 40
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.095 -10000 0 -0.56 23 23
CDC42/GTP 0.025 0.066 -10000 0 -0.35 6 6
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 0.064 -10000 0 -0.35 6 6
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 0.038 0.085 0.36 28 -10000 0 28
S1P/S1P4/Gi 0.017 0.065 -10000 0 -0.32 15 15
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 0.009 -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 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
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 0.004 0.046 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 -0.059 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 -0.45 54 54
platelet activation 0.004 0.063 -10000 0 -0.38 23 23
MAPKKK cascade -0.013 0.033 -10000 0 -0.13 56 56
IL18 0 0.052 -10000 0 -0.21 39 39
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
Hedgehog signaling events mediated by Gli proteins

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
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 0.49 28 -0.56 38 66
GNAO1 0.012 0.095 -10000 0 -0.56 23 23
SMO/beta Arrestin2 0.033 0.043 -10000 0 -0.43 6 6
SMO 0.022 0.047 -10000 0 -0.65 4 4
ARRB2 0.024 0.03 -10000 0 -0.46 3 3
GLI3/SPOP 0.024 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 0.046 0.076 -10000 0 -0.3 1 1
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 0.11 -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 0.039 0.077 0.29 15 -0.33 5 20
GLI3 0.016 0.15 0.31 7 -0.6 36 43
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 -0.32 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) 0.015 0.15 0.28 1 -0.64 39 40
GLI2/Su(fu) 0.042 0.064 0.42 1 -0.48 5 6
FOXA2 0.015 0.12 -10000 0 -0.8 12 12
neural tube patterning 0.044 0.18 0.49 28 -0.56 38 66
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 0.49 28 -0.56 38 66
SUFU 0.024 0.032 -10000 0 -0.5 2 2
LGALS3 0.001 0.11 -10000 0 -0.42 52 52
catabolic process 0.046 0.14 0.38 7 -0.56 33 40
GLI3A/CBP 0.025 0.057 -10000 0 -0.39 13 13
KIF3A 0.027 0.007 -10000 0 -10000 0 0
GLI1 0.044 0.18 0.5 28 -0.58 38 66
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 0.093 -10000 0 -0.36 34 34
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 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.045 0.061 0.36 4 -0.31 3 7
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 18 -0.83 9 27
MIM/GLI1 0.049 0.17 0.51 15 -0.77 15 30
CREBBP 0.025 0.057 -10000 0 -0.39 13 13
Su(fu)/SIN3/HDAC complex 0.006 0.16 0.27 4 -0.61 49 53
mTOR signaling pathway

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
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 0.027 0.06 0.38 14 -0.3 1 15
AKT1 0.009 0.042 0.2 2 -0.28 9 11
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 0.048 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 -0.26 1 1
TSC1 0.028 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.062 -10000 0 -0.38 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.024 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 0.033 0.088 0.39 24 -0.32 2 26
MAP3K5 -0.005 0.049 -10000 0 -0.18 63 63
PIK3R1 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.005 0.049 -10000 0 -0.18 63 63
mol:LY294002 0 0 -10000 0 -0.001 51 51
EIF4B 0.04 0.1 0.4 39 -0.28 2 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.05 0.077 0.37 20 -0.4 1 21
eIF4E/eIF4G1/eIF4A1 0.02 0.018 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.031 0.059 -10000 0 -0.34 10 10
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.042 0.26 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 0.002 0.16 0.3 1 -0.54 63 64
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 0.009 -10000 0 -10000 0 0
PDK2 0.005 0.038 0.21 2 -0.3 9 11
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 0.36 15 -10000 0 15
peptide biosynthetic process 0.014 0.015 -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 0.007 38 -10000 0 38
EEF2 0.014 0.014 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0.19 -10000 0 -0.94 33 33
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.017 0.08 -10000 0 -0.63 13 13
alphaV beta3 Integrin 0.022 0.085 -10000 0 -0.45 26 26
PTK2 0.019 0.089 -10000 0 -0.52 9 9
positive regulation of JNK cascade 0.012 0.1 -10000 0 -0.36 42 42
CDC42/GDP 0.045 0.14 0.4 9 -0.44 49 58
Rac1/GDP 0.028 0.13 0.52 1 -0.44 47 48
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 41 41
nectin-3/I-afadin 0.032 0.052 -10000 0 -0.49 8 8
RAPGEF1 0.028 0.12 0.29 7 -0.49 9 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.12 -10000 0 -0.52 12 12
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 7 7
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 9 -0.54 49 58
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 -0.36 27 27
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 -0.006 0.12 -10000 0 -0.46 59 59
JAM-A/CLDN1 0.038 0.092 -10000 0 -0.39 19 19
SRC 0.01 0.13 -10000 0 -0.5 25 25
ITGB3 0.007 0.11 -10000 0 -0.61 25 25
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.016 -10000 0 -0.28 1 1
FARP2 0.016 0.18 -10000 0 -0.66 43 43
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 42 42
alphaV/beta3 Integrin/Talin 0.029 0.071 0.35 1 -0.46 3 4
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 -0.6 26 28
RAP1/GDP 0.04 0.12 0.26 1 -0.38 42 43
ITGAV 0.026 0.028 -10000 0 -0.53 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 -0.44 26 26
PTPRM 0.015 0.026 -10000 0 -0.24 8 8
E-cadherin/beta catenin/alpha catenin 0.046 0.093 -10000 0 -0.35 36 36
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.007 -10000 0 -10000 0 0
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 -0.42 16 16
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 0.071 -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 0.027 0.13 0.46 31 -0.48 6 37
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 0.42 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.057 -10000 0 -0.72 1 1
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 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.041 0.063 -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 0.061 -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 0.058 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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.007 -10000 0 -10000 0 0
NFATC1 0.04 0.11 0.34 26 -0.46 4 30
NFATC2 0.004 0.095 0.25 14 -0.28 60 74
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 16 -0.41 25 41
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 0.017 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.017 -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 -0.53 2 2
CABIN1/MEF2D 0.015 0.1 0.29 6 -0.44 15 21
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 -0.015 0.1 0.44 15 -0.29 6 21
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 -0.44 33 33
CABIN1 0.001 0.1 0.24 12 -0.41 25 37
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 0.009 -10000 0 -10000 0 0
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.1 0.29 10 -0.42 7 17
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 0.006 -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 0.023 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 0.025 0.047 -10000 0 -0.42 2 2
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 0.027 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 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.049 0.11 0.34 25 -0.42 5 30
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 -0.4 11 11
NFATc/ERK1 0.042 0.093 0.31 3 -0.42 5 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.019 0.1 0.27 1 -0.48 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 -0.26 11 11
RCH1/ KPNB1 0.037 0.013 -10000 0 -10000 0 0
YWHAQ 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -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 0.054 0.11 0.34 27 -0.43 4 31
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 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
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 0.085 0.28 35 -0.36 7 42
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.099 0.26 21 -0.35 34 55
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 42 42
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 -0.007 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 0.061 -10000 0 -0.36 4 4
Canonical NF-kappaB 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
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 0.062 0.074 0.29 32 -10000 0 32
ERC1 0.027 0.006 -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 0.061 -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 0.004 -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 -0.34 19 19
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 -0.36 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.03 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.006 -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 0.047 0.066 -10000 0 -0.42 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.008 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 -10000 0 -0.36 4 4
CCND1 0.007 0.035 -10000 0 -0.42 3 3
p38 gamma/SNTA1 0.026 0.061 -10000 0 -0.42 5 5
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 -10000 0 -0.35 4 4
MAP2K6 0.006 0.026 0.19 1 -0.41 3 4
MAPT 0.007 0.12 0.32 47 -0.39 54 101
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
Class I PI3K signaling events mediated by Akt

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
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 -0.39 17 17
BAD 0.027 0.028 -10000 0 -0.53 2 2
AKT3 0.016 0.015 -10000 0 -0.38 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.021 0.073 -10000 0 -0.6 5 5
AKT1/ASK1 0.033 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 -0.38 19 19
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 -0.29 21 38
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 0.3 15 -0.57 5 20
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 0.042 0.074 -10000 0 -0.57 5 5
mTORC2 0.035 0.008 -10000 0 -10000 0 0
AKT2 0.018 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.028 0.12 0.36 23 -0.54 15 38
PDPK1 0.027 0.007 -10000 0 -10000 0 0
MDM2 0.022 0.074 -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 0.03 0.089 0.29 41 -0.58 5 46
proteasomal ubiquitin-dependent protein catabolic process 0.046 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 0.022 0.045 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 0.31 22 -0.59 5 27
p27Kip1/14-3-3 family 0.021 0.082 -10000 0 -0.48 7 7
PRKACA 0.028 0.003 -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 0.009 -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
Retinoic acid receptors-mediated signaling

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
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 0.22 7 -10000 0 7
RAR alpha/9cRA/Cyclin H 0.041 0.078 -10000 0 -0.34 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.027 0.065 0.24 2 -0.41 5 7
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 0.098 0.31 3 -0.5 6 9
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 1 -0.4 10 11
PRKCA 0.028 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.019 0.11 0.31 5 -0.43 33 38
RXRG 0.003 0.063 -10000 0 -0.41 7 7
RXRA 0.016 0.041 -10000 0 -0.28 4 4
RXRB 0.008 0.056 -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 0.089 0.28 5 -0.42 6 11
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.12 0.3 47 -0.37 37 84
RXRs/RARs/NRIP1/9cRA/HDAC3 0.023 0.11 0.34 6 -0.52 8 14
positive regulation of DNA binding 0.026 0.068 -10000 0 -0.32 1 1
NRIP1 0.016 0.11 0.39 1 -0.62 4 5
RXRs/RARs 0.006 0.11 0.29 1 -0.4 34 35
RXRs/RXRs/DNA/9cRA 0.01 0.072 -10000 0 -0.45 4 4
PRKACA 0.028 0.003 -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
Arf6 trafficking events

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
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 0.018 -10000 0 -10000 0 0
EXOC4 0.025 0.01 -10000 0 -10000 0 0
CD59 0.018 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 0.017 0.012 -10000 0 -10000 0 0
CTNND1 0.03 0.045 -10000 0 -10000 0 0
DNM2 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.043 0.25 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 0.017 0.012 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 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 -0.38 6 6
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.008 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 0.028 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 0.006 -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 0.27 3 -0.4 4 7
JIP4/KLC1 0.047 0.019 -10000 0 -10000 0 0
EXOC1 0.028 0.004 -10000 0 -10000 0 0
exocyst 0.028 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 0.013 -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 0.016 0.017 -10000 0 -0.24 3 3
clathrin coat assembly 0.028 0.082 0.25 23 -0.36 18 41
IL2RA 0 0.066 -10000 0 -0.32 18 18
VAMP3 0.017 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.013 0.088 -10000 0 -0.35 30 30
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 0.024 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 0.017 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 0.038 0.1 0.32 25 -0.4 10 35
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 0.29 6 -0.53 31 37
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
Insulin Pathway

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
CBL/APS/CAP 0.04 0.054 -10000 0 -0.34 11 11
TC10/GTP 0.04 0.033 -10000 0 -0.33 1 1
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 0.022 0.038 -10000 0 -0.42 6 6
GRB14 -0.01 0.15 -10000 0 -0.65 48 48
FOXO3 -0.016 0.17 -10000 0 -0.62 60 60
AKT1 0.019 0.12 0.44 27 -0.6 3 30
INSR 0.031 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 0.013 -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 0.055 -10000 0 -0.4 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.046 0.048 -10000 0 -0.35 10 10
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.033 0.046 -10000 0 -10000 0 0
RPS6KB1 0.002 0.086 0.36 7 -0.5 3 10
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 0.031 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 34 34
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 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.29 1 1
AKT2 0.02 0.12 0.43 29 -0.6 3 32
PRKCZ 0.022 0.073 -10000 0 -0.63 5 5
SH2B2 0.022 0.038 -10000 0 -0.42 6 6
SHC/SHIP 0.028 0.057 0.3 2 -0.39 10 12
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 0.041 -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 2 -0.41 10 12
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 -0.43 34 34
INS 0.021 0.025 -10000 0 -0.39 3 3
mol:PI-3-4-P2 0.013 0.056 0.31 2 -0.41 10 12
GRB2 0.025 0.009 -10000 0 -10000 0 0
EIF4EBP1 0.007 0.12 0.42 25 -0.52 7 32
PTPRA 0.028 0.007 -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 14 14
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.052 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 0.039 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 0.026 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 -10000 0 0
NuRD/MBD3 Complex 0.017 0.1 -10000 0 -0.44 37 37
NF kappa B1 p50/RelA 0.044 0.065 0.29 4 -0.57 1 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.028 0.18 -10000 0 -0.64 72 72
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 -0.3 1 1
SMURF1 0.025 0.01 -10000 0 -10000 0 0
CHD3 0.025 0.009 -10000 0 -10000 0 0
SAP30 -0.004 0.11 -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 0.027 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) 0.018 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 0.026 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 0.006 -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 0.041 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 0.031 0.032 -10000 0 -10000 0 0
nuclear export -0.053 0.014 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -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 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.028 0.061 -10000 0 -0.34 19 19
SIN3/HDAC complex/Mad/Max 0.017 0.091 -10000 0 -0.41 34 34
NuRD Complex 0.031 0.093 -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 0.018 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 -0.34 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 -0.53 2 2
MBD2 0.028 0.005 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.006 -10000 0 -10000 0 0
PTK2 0.027 0.005 -10000 0 -10000 0 0
CRKL 0.013 0.054 -10000 0 -0.3 17 17
GRB2/SOS1/SHC 0.05 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 0.054 0.3 4 -10000 0 4
BAD 0.012 0.053 0.29 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 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 -0.41 41 42
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 0.32 7 -0.35 1 8
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 0.023 0.046 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.062 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 -0.34 1 1
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 8 8
PI3K 0.051 0.06 -10000 0 -0.33 7 7
apoptosis -0.034 0.066 -10000 0 -0.3 17 17
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 0.34 5 -0.4 2 7
BAD/14-3-3 0.039 0.078 0.35 24 -10000 0 24
PRKCZ 0.015 0.057 0.3 5 -0.33 2 7
Crk/p130 Cas/Paxillin/FAK1 0.033 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 0.054 -10000 0 -0.3 19 19
IRS1 0.014 0.06 0.22 2 -0.33 19 21
IRS2 0.008 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 0.022 0.058 0.3 5 -0.31 6 11
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
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 -0.26 3 3
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 0.035 0.012 -10000 0 -10000 0 0
HIST2H4A 0.015 0.016 -10000 0 -0.29 2 2
SIRT1/FOXO3a 0.012 0.028 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 0.022 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 39 39
GATA2/HDAC5 -0.003 0.14 -10000 0 -0.46 71 71
HDAC5/BCL6/BCoR 0.05 0.025 -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 -10000 0 0
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 -0.028 0.18 -10000 0 -0.64 72 72
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 0.025 0.024 -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 0.037 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 0.024 -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 -10000 0 0
Tubulin 0.037 0.022 -10000 0 -0.49 1 1
HDAC4/14-3-3 E 0.037 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 0.009 -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 -0.47 23 23
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 0.026 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.012 -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 0.044 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 0.033 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 0.05 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 0.03 0.091 -10000 0 -0.38 13 13
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 0.003 -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 0.28 1 -0.41 8 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.028 0.005 -10000 0 -10000 0 0
SMAD2 -0.008 0.05 -10000 0 -0.27 10 10
SMAD3 0.031 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4 0.015 0.13 0.35 2 -0.49 49 51
SMAD4/Ubc9/PIASy 0.052 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.044 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 -0.29 2 2
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 0.026 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
TRAIL signaling 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
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 -0.45 7 7
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 -0.42 5 5
CFLAR 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.017 0.025 0.21 1 -0.49 2 3
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 0.004 -10000 0 -10000 0 0
MAPK8 0.037 0.051 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 0.033 -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 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
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 -0.38 2 2
NFKBIA 0.012 0.037 -9999 0 -0.29 8 8
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 0.025 0.025 -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 0.015 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 0.015 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 0.028 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 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
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 0.078 2 -10000 0 2
GNAL 0.026 0.028 -10000 0 -0.53 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 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
coatomer protein complex 0.022 0.044 0.3 5 -0.47 1 6
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 0.009 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 -0.41 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 -0.26 5 5
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 0.005 -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 0.017 0.045 -10000 0 -0.25 6 6
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 0.009 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 0.015 0.008 -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
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 0.07 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.035 0.26 1 -10000 0 1
myoblast fusion -0.021 0.043 -10000 0 -10000 0 0
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 0.043 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.055 0.27 1 -10000 0 1
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 -10000 0 -10000 0 0
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 -10000 0 0
NME1 0.025 0.028 -10000 0 -0.42 3 3
Rac1/GDP 0.025 0.053 -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 0.063 -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 0.026 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 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 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 0.069 0.034 -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/22311286/KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIPAN-TP/22506737/Gistic2_Analysis_22507383/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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