PARADIGM pathway analysis of mRNASeq expression data
Liver Hepatocellular Carcinoma
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
doi:10.7908/C1348JWP
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 data. Broad Institute of MIT and Harvard. doi:10.7908/C1348JWP
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 50 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
Wnt signaling 83
Reelin signaling pathway 71
Noncanonical Wnt signaling pathway 67
HIF-1-alpha transcription factor network 66
Glypican 1 network 66
PDGFR-alpha signaling pathway 66
FOXA2 and FOXA3 transcription factor networks 64
Ephrin A reverse signaling 61
Syndecan-1-mediated signaling events 57
Signaling events regulated by Ret tyrosine kinase 57
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 423 . 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 ( 423 ).

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
Wnt signaling 0.1962 83 581 7 -0.23 -0.014 1000 -1000 -0.021 -1000
Reelin signaling pathway 0.1678 71 3988 56 -0.27 0.021 1000 -1000 -0.064 -1000
Noncanonical Wnt signaling pathway 0.1584 67 1764 26 -0.23 0.014 1000 -1000 -0.036 -1000
HIF-1-alpha transcription factor network 0.1560 66 5068 76 -0.44 0.022 1000 -1000 -0.082 -1000
Glypican 1 network 0.1560 66 3208 48 -0.29 0.056 1000 -1000 -0.028 -1000
PDGFR-alpha signaling pathway 0.1560 66 2911 44 -0.18 0.027 1000 -1000 -0.036 -1000
FOXA2 and FOXA3 transcription factor networks 0.1513 64 2947 46 -0.58 0.02 1000 -1000 -0.055 -1000
Ephrin A reverse signaling 0.1442 61 433 7 -0.16 0 1000 -1000 -0.015 -1000
Syndecan-1-mediated signaling events 0.1348 57 1955 34 -0.2 0.014 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.1348 57 4744 82 -0.2 0.014 1000 -1000 -0.077 -1000
IL6-mediated signaling events 0.1182 50 3799 75 -0.46 0.055 1000 -1000 -0.056 -1000
Signaling events mediated by the Hedgehog family 0.1111 47 2450 52 -0.2 0.079 1000 -1000 -0.038 -1000
FOXM1 transcription factor network 0.1017 43 2200 51 -0.28 0.025 1000 -1000 -0.15 -1000
Osteopontin-mediated events 0.0993 42 1622 38 -0.21 0.014 1000 -1000 -0.073 -1000
Nongenotropic Androgen signaling 0.0993 42 2226 52 -0.15 0.047 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 0.0969 41 3535 86 -0.2 0.14 1000 -1000 -0.071 -1000
IL4-mediated signaling events 0.0946 40 3692 91 -0.52 0.37 1000 -1000 -0.14 -1000
LPA receptor mediated events 0.0946 40 4095 102 -0.19 0.014 1000 -1000 -0.069 -1000
Syndecan-4-mediated signaling events 0.0922 39 2621 67 -0.16 0.03 1000 -1000 -0.064 -1000
Endothelins 0.0898 38 3703 96 -0.17 0.014 1000 -1000 -0.066 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0827 35 1909 54 -0.28 0.028 1000 -1000 -0.079 -1000
Signaling mediated by p38-alpha and p38-beta 0.0827 35 1583 44 -0.14 0.014 1000 -1000 -0.033 -1000
Glypican 2 network 0.0827 35 141 4 -0.059 -0.007 1000 -1000 -0.015 -1000
TCGA08_retinoblastoma 0.0827 35 283 8 -0.064 0.027 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 0.0804 34 3603 105 -0.094 0.027 1000 -1000 -0.053 -1000
IL23-mediated signaling events 0.0804 34 2053 60 -0.42 0.014 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 0.0780 33 3138 93 -0.12 0.071 1000 -1000 -0.067 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0780 33 2308 68 -0.34 0.094 1000 -1000 -0.092 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0757 32 1111 34 -0.097 0.014 1000 -1000 -0.031 -1000
S1P1 pathway 0.0757 32 1171 36 -0.16 0.014 1000 -1000 -0.052 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0757 32 2822 88 -0.13 0.02 1000 -1000 -0.089 -1000
Ephrin B reverse signaling 0.0733 31 1529 48 -0.1 0.085 1000 -1000 -0.054 -1000
p75(NTR)-mediated signaling 0.0709 30 3781 125 -0.2 0.038 1000 -1000 -0.075 -1000
amb2 Integrin signaling 0.0709 30 2484 82 -0.11 0.019 1000 -1000 -0.058 -1000
Calcium signaling in the CD4+ TCR pathway 0.0709 30 930 31 -0.15 0.014 1000 -1000 -0.048 -1000
IL12-mediated signaling events 0.0686 29 2528 87 -0.16 0.019 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0686 29 3351 114 -0.35 0.2 1000 -1000 -0.059 -1000
Signaling mediated by p38-gamma and p38-delta 0.0686 29 440 15 -0.084 0.015 1000 -1000 -0.018 -1000
EPO signaling pathway 0.0662 28 1557 55 -0.18 0.014 1000 -1000 -0.078 -1000
IGF1 pathway 0.0662 28 1639 57 -0.099 0.029 1000 -1000 -0.082 -1000
Integrins in angiogenesis 0.0638 27 2282 84 -0.22 0.021 1000 -1000 -0.064 -1000
Nectin adhesion pathway 0.0615 26 1668 63 -0.084 0.026 1000 -1000 -0.057 -1000
EPHB forward signaling 0.0615 26 2213 85 -0.16 0.081 1000 -1000 -0.077 -1000
S1P5 pathway 0.0591 25 440 17 -0.15 0.069 1000 -1000 -0.032 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0567 24 681 28 -0.15 0.021 1000 -1000 -0.03 -1000
ErbB2/ErbB3 signaling events 0.0544 23 1543 65 -0.2 0.021 1000 -1000 -0.055 -1000
BMP receptor signaling 0.0544 23 1910 81 -0.14 0.04 1000 -1000 -0.072 -1000
BCR signaling pathway 0.0544 23 2320 99 -0.14 0.028 1000 -1000 -0.071 -1000
ErbB4 signaling events 0.0520 22 1581 69 -0.14 0.03 1000 -1000 -0.077 -1000
S1P3 pathway 0.0520 22 955 42 -0.15 0.024 1000 -1000 -0.035 -1000
Arf6 signaling events 0.0496 21 1360 62 -0.15 0.025 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 0.0496 21 547 26 -0.2 0.018 1000 -1000 -0.052 -1000
S1P4 pathway 0.0496 21 532 25 -0.15 0.026 1000 -1000 -0.03 -1000
Syndecan-2-mediated signaling events 0.0473 20 1417 69 -0.18 0.025 1000 -1000 -0.025 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0473 20 761 37 -0.18 0.027 1000 -1000 -0.04 -1000
IL2 signaling events mediated by PI3K 0.0473 20 1168 58 -0.14 0.029 1000 -1000 -0.06 -1000
Canonical Wnt signaling pathway 0.0473 20 1069 51 -0.2 0.11 1000 -1000 -0.052 -1000
Regulation of Androgen receptor activity 0.0473 20 1423 70 -0.19 0.03 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 0.0449 19 1514 76 -0.13 0.035 1000 -1000 -0.031 -1000
IL27-mediated signaling events 0.0449 19 1000 51 -0.15 0.089 1000 -1000 -0.076 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0449 19 1455 74 -0.092 0.043 1000 -1000 -0.069 -1000
JNK signaling in the CD4+ TCR pathway 0.0426 18 321 17 -0.054 0.014 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0426 18 1149 61 -0.16 0.074 1000 -1000 -0.061 -1000
TCGA08_p53 0.0426 18 127 7 -0.046 0.033 1000 -1000 -0.012 -1000
Fc-epsilon receptor I signaling in mast cells 0.0402 17 1736 97 -0.12 0.033 1000 -1000 -0.07 -1000
E-cadherin signaling events 0.0402 17 85 5 -0.034 0.014 1000 -1000 -0.012 -1000
p38 MAPK signaling pathway 0.0402 17 785 44 -0.2 0.028 1000 -1000 -0.054 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0378 16 845 52 -0.11 0.024 1000 -1000 -0.046 -1000
EGFR-dependent Endothelin signaling events 0.0378 16 343 21 -0.077 0.021 1000 -1000 -0.054 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0378 16 1976 120 -0.16 0.064 1000 -1000 -0.058 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0378 16 1262 78 -0.18 0.034 1000 -1000 -0.063 -1000
Aurora B signaling 0.0378 16 1085 67 -0.12 0.014 1000 -1000 -0.055 -1000
Cellular roles of Anthrax toxin 0.0355 15 602 39 -0.057 0.014 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0355 15 655 43 -0.16 0.027 1000 -1000 -0.059 -1000
Visual signal transduction: Rods 0.0355 15 817 52 -0.11 0.014 1000 -1000 -0.063 -1000
Ras signaling in the CD4+ TCR pathway 0.0355 15 266 17 -0.027 0.024 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 0.0331 14 174 12 -0.078 0.013 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 0.0331 14 571 40 -0.21 0.027 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0331 14 524 35 -0.18 0.038 1000 -1000 -0.034 -1000
IL2 signaling events mediated by STAT5 0.0331 14 321 22 -0.067 0.021 1000 -1000 -0.033 -1000
Regulation of Telomerase 0.0331 14 1479 102 -0.22 0.04 1000 -1000 -0.092 -1000
BARD1 signaling events 0.0307 13 750 57 -0.049 0.04 1000 -1000 -0.044 -1000
FAS signaling pathway (CD95) 0.0307 13 619 47 -0.086 0.018 1000 -1000 -0.033 -1000
E-cadherin signaling in the nascent adherens junction 0.0307 13 1026 76 -0.05 0.026 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 0.0307 13 39 3 -0.008 -1000 1000 -1000 -0.015 -1000
a4b1 and a4b7 Integrin signaling 0.0284 12 63 5 -0.011 0.006 1000 -1000 -0.016 -1000
Ceramide signaling pathway 0.0284 12 937 76 -0.092 0.031 1000 -1000 -0.039 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0284 12 570 45 -0.069 0.022 1000 -1000 -0.073 -1000
E-cadherin signaling in keratinocytes 0.0284 12 548 43 -0.035 0.029 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0260 11 876 76 -0.088 0.025 1000 -1000 -0.064 -1000
FoxO family signaling 0.0260 11 717 64 -0.16 0.074 1000 -1000 -0.058 -1000
Retinoic acid receptors-mediated signaling 0.0260 11 640 58 -0.11 0.042 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0260 11 223 20 -0.049 0.015 1000 -1000 -0.015 -1000
Signaling events mediated by PRL 0.0260 11 397 34 -0.14 0.021 1000 -1000 -0.033 -1000
Caspase cascade in apoptosis 0.0236 10 794 74 -0.042 0.035 1000 -1000 -0.03 -1000
Regulation of nuclear SMAD2/3 signaling 0.0236 10 1436 136 -0.14 0.14 1000 -1000 -0.05 -1000
PLK2 and PLK4 events 0.0236 10 32 3 0.001 0.01 1000 -1000 -0.01 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0236 10 893 85 -0.084 0.017 1000 -1000 -0.059 -1000
PLK1 signaling events 0.0236 10 929 85 -0.067 0.028 1000 -1000 -0.033 -1000
IL1-mediated signaling events 0.0236 10 656 62 -0.037 0.055 1000 -1000 -0.07 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0236 10 1363 125 -0.056 0.05 1000 -1000 -0.071 -1000
TCGA08_rtk_signaling 0.0236 10 277 26 -0.17 0.032 1000 -1000 -0.016 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0236 10 346 33 -0.11 0.039 1000 -1000 -0.024 -1000
Visual signal transduction: Cones 0.0213 9 363 38 -0.065 0.01 1000 -1000 -0.048 -1000
Hedgehog signaling events mediated by Gli proteins 0.0213 9 643 65 -0.15 0.053 1000 -1000 -0.05 -1000
Regulation of p38-alpha and p38-beta 0.0213 9 523 54 -0.062 0.037 1000 -1000 -0.049 -1000
PDGFR-beta signaling pathway 0.0213 9 942 97 -0.11 0.038 1000 -1000 -0.063 -1000
Aurora C signaling 0.0189 8 56 7 -0.019 0.002 1000 -1000 -0.03 -1000
Insulin-mediated glucose transport 0.0189 8 284 32 -0.16 0.03 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 0.0189 8 298 36 -0.067 0.031 1000 -1000 -0.063 -1000
Atypical NF-kappaB pathway 0.0189 8 276 31 -0.033 0.028 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0189 8 622 73 -0.062 0.037 1000 -1000 -0.05 -1000
TRAIL signaling pathway 0.0165 7 373 48 -0.014 0.036 1000 -1000 -0.049 -1000
VEGFR1 specific signals 0.0165 7 406 56 -0.056 0.046 1000 -1000 -0.037 -1000
Arf6 downstream pathway 0.0142 6 287 43 -0.018 0.023 1000 -1000 -0.029 -1000
IFN-gamma pathway 0.0142 6 439 68 -0.2 0.066 1000 -1000 -0.076 -1000
Class I PI3K signaling events mediated by Akt 0.0142 6 460 68 -0.16 0.043 1000 -1000 -0.033 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0142 6 558 83 -0.16 0.036 1000 -1000 -0.061 -1000
mTOR signaling pathway 0.0118 5 283 53 -0.056 0.031 1000 -1000 -0.05 -1000
Insulin Pathway 0.0118 5 397 74 -0.085 0.036 1000 -1000 -0.079 -1000
Signaling events mediated by HDAC Class II 0.0095 4 324 75 -0.13 0.041 1000 -1000 -0.035 -1000
Aurora A signaling 0.0095 4 251 60 -0.038 0.04 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0071 3 85 23 -0.045 0.045 1000 -1000 -0.038 -1000
ceramide signaling pathway 0.0071 3 168 49 -0.031 0.036 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class I 0.0047 2 265 104 -0.028 0.047 1000 -1000 -0.057 -1000
Arf6 trafficking events 0.0047 2 200 71 -0.04 0.043 1000 -1000 -0.059 -1000
Canonical NF-kappaB pathway 0.0024 1 71 39 -0.023 0.081 1000 -1000 -0.058 -1000
Circadian rhythm pathway 0.0024 1 39 22 -0.014 0.045 1000 -1000 -0.024 -1000
Arf1 pathway 0.0024 1 59 54 -0.004 0.03 1000 -1000 -0.025 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 0 0.037 1000 -1000 -0.042 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.04 1000 -1000 -0.027 -1000
Total NA 2880 161680 7203 -18 -1000 131000 -131000 -6.6 -131000
Wnt signaling

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
Noncanonical Wnts/FZD -0.23 0.28 -9999 0 -0.44 193 193
FZD6 -0.027 0.16 -9999 0 -0.62 24 24
WNT6 -0.014 0.11 -9999 0 -0.4 24 24
WNT4 -0.2 0.27 -9999 0 -0.51 151 151
FZD3 -0.025 0.15 -9999 0 -0.62 23 23
WNT5A -0.097 0.24 -9999 0 -0.58 69 69
WNT11 -0.14 0.26 -9999 0 -0.57 97 97
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.013 0.059 -9999 0 -0.4 7 7
VLDLR -0.16 0.26 -9999 0 -0.51 120 120
CRKL 0.014 0 -9999 0 -10000 0 0
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.013 0.018 -9999 0 -0.34 1 1
ITGA3 -0.022 0.12 -9999 0 -0.38 34 34
RELN/VLDLR/Fyn -0.23 0.26 -9999 0 -0.49 163 163
MAPK8IP1/MKK7/MAP3K11/JNK1 0.008 0.11 -9999 0 -0.33 32 32
AKT1 -0.18 0.2 -9999 0 -0.48 82 82
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.083 0.22 -9999 0 -0.54 64 64
RELN/LRP8/DAB1 -0.2 0.23 -9999 0 -0.43 162 162
LRPAP1/LRP8 -0.016 0.1 -9999 0 -0.46 9 9
RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.4 162 162
DAB1/alpha3/beta1 Integrin -0.26 0.24 -9999 0 -0.6 98 98
long-term memory -0.21 0.23 -9999 0 -0.42 173 173
DAB1/LIS1 -0.26 0.24 -9999 0 -0.44 189 189
DAB1/CRLK/C3G -0.24 0.23 -9999 0 -0.58 91 91
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
DAB1/NCK2 -0.27 0.25 -9999 0 -0.46 193 193
ARHGEF2 0.009 0.05 -9999 0 -0.4 5 5
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.087 0.18 -9999 0 -0.4 87 87
CDK5R1 0.004 0.079 -9999 0 -0.55 7 7
RELN -0.23 0.3 -9999 0 -0.57 157 157
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
RELN/LRP8/Fyn -0.16 0.21 -9999 0 -0.43 125 125
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.24 -9999 0 -0.43 183 183
MAPK8 -0.028 0.16 -9999 0 -0.63 24 24
RELN/VLDLR/DAB1 -0.26 0.26 -9999 0 -0.48 193 193
ITGB1 0.014 0 -9999 0 -10000 0 0
MAP1B -0.26 0.26 -9999 0 -0.46 200 200
RELN/LRP8 -0.16 0.21 -9999 0 -0.42 125 125
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.4 162 162
PI3K 0.015 0.062 -9999 0 -0.56 4 4
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.004 0.085 -9999 0 -0.46 5 5
RAP1A -0.21 0.23 -9999 0 -0.54 91 91
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 -0.001 0.095 -9999 0 -0.6 9 9
CRLK/C3G 0.021 0 -9999 0 -10000 0 0
GRIN2B 0.005 0.019 -9999 0 -0.34 1 1
NCK2 -0.01 0.11 -9999 0 -0.49 18 18
neuron differentiation -0.11 0.16 -9999 0 -0.41 46 46
neuron adhesion -0.2 0.23 -9999 0 -0.53 98 98
LRP8 -0.038 0.14 -9999 0 -0.4 47 47
GSK3B -0.16 0.2 -9999 0 -0.45 82 82
RELN/VLDLR/DAB1/Fyn -0.24 0.25 -9999 0 -0.45 193 193
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.2 0.22 -9999 0 -0.38 189 189
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT 0.004 0.13 -9999 0 -0.39 29 29
neuron migration -0.2 0.23 -9999 0 -0.5 102 102
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.11 0.16 -9999 0 -0.42 46 46
RELN/VLDLR -0.23 0.25 -9999 0 -0.46 175 175
Noncanonical Wnt signaling pathway

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
NFATC2 -0.1 0.24 -9999 0 -0.6 70 70
GNB1/GNG2 -0.2 0.26 -9999 0 -0.55 97 97
mol:DAG -0.17 0.23 -9999 0 -0.56 74 74
PLCG1 -0.18 0.24 -9999 0 -0.58 74 74
YES1 -0.21 0.26 -9999 0 -0.57 95 95
FZD3 -0.025 0.15 -9999 0 -0.62 23 23
FZD6 -0.027 0.16 -9999 0 -0.62 24 24
G protein -0.18 0.25 -9999 0 -0.59 74 74
MAP3K7 -0.16 0.21 -9999 0 -0.47 80 80
mol:Ca2+ -0.17 0.22 -9999 0 -0.54 74 74
mol:IP3 -0.17 0.23 -9999 0 -0.56 74 74
NLK -0.007 0.011 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.17 0.23 -9999 0 -0.49 94 94
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.28 -9999 0 -0.44 193 193
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.21 0.26 -9999 0 -0.57 97 97
GO:0007205 -0.17 0.23 -9999 0 -0.55 73 73
WNT6 -0.014 0.11 -9999 0 -0.4 24 24
WNT4 -0.2 0.27 -9999 0 -0.51 151 151
NFAT1/CK1 alpha -0.22 0.27 -9999 0 -0.58 107 107
GNG2 0.007 0.063 -9999 0 -0.52 5 5
WNT5A -0.097 0.24 -9999 0 -0.58 69 69
WNT11 -0.14 0.26 -9999 0 -0.57 97 97
CDC42 -0.19 0.25 -9999 0 -0.54 95 95
HIF-1-alpha transcription factor network

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
PKM2 -0.33 0.56 -9999 0 -1.2 89 89
HDAC7 0.012 0.039 -9999 0 -0.49 2 2
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.39 -9999 0 -0.87 99 99
SMAD4 0.012 0.047 -9999 0 -0.63 2 2
ID2 -0.32 0.54 -9999 0 -1.1 88 88
AP1 -0.034 0.14 -9999 0 -0.37 53 53
ABCG2 -0.36 0.58 -9999 0 -1.2 97 97
HIF1A -0.037 0.11 -9999 0 -0.57 7 7
TFF3 -0.36 0.57 -9999 0 -1.1 103 103
GATA2 -0.002 0.097 -9999 0 -0.51 12 12
AKT1 -0.048 0.091 -9999 0 -10000 0 0
response to hypoxia -0.066 0.096 -9999 0 -0.22 34 34
MCL1 -0.32 0.54 -9999 0 -1.1 89 89
NDRG1 -0.33 0.55 -9999 0 -1.1 88 88
SERPINE1 -0.36 0.56 -9999 0 -1.1 99 99
FECH -0.32 0.54 -9999 0 -1.1 88 88
FURIN -0.33 0.55 -9999 0 -1.1 92 92
NCOA2 -0.1 0.24 -9999 0 -0.64 64 64
EP300 -0.062 0.15 -9999 0 -0.33 42 42
HMOX1 -0.33 0.55 -9999 0 -1.1 91 91
BHLHE40 -0.32 0.54 -9999 0 -1.1 88 88
BHLHE41 -0.35 0.57 -9999 0 -1.2 96 96
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.039 0.09 -9999 0 -0.45 8 8
ENG 0.007 0.13 -9999 0 -0.55 6 6
JUN 0.011 0.047 -9999 0 -0.63 2 2
RORA -0.32 0.54 -9999 0 -1.1 89 89
ABCB1 -0.24 0.44 -9999 0 -1.3 56 56
TFRC -0.32 0.54 -9999 0 -1.1 89 89
CXCR4 -0.33 0.55 -9999 0 -1.1 91 91
TF -0.34 0.57 -9999 0 -1.2 90 90
CITED2 -0.32 0.54 -9999 0 -1.1 89 89
HIF1A/ARNT -0.44 0.62 -9999 0 -1.3 95 95
LDHA -0.045 0.051 -9999 0 -10000 0 0
ETS1 -0.32 0.54 -9999 0 -1.1 89 89
PGK1 -0.32 0.54 -9999 0 -1.1 88 88
NOS2 -0.34 0.55 -9999 0 -1.1 94 94
ITGB2 -0.33 0.55 -9999 0 -1.1 90 90
ALDOA -0.32 0.54 -9999 0 -1.1 89 89
Cbp/p300/CITED2 -0.39 0.55 -9999 0 -1.2 97 97
FOS -0.058 0.19 -9999 0 -0.51 51 51
HK2 -0.36 0.57 -9999 0 -1.1 103 103
SP1 0.012 0.034 -9999 0 -10000 0 0
GCK -0.24 0.5 -9999 0 -1.4 47 47
HK1 -0.33 0.55 -9999 0 -1.1 88 88
NPM1 -0.32 0.54 -9999 0 -1.1 88 88
EGLN1 -0.32 0.54 -9999 0 -1.1 88 88
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.32 0.54 -9999 0 -1.1 89 89
SMAD3 0.014 0.034 -9999 0 -0.63 1 1
EDN1 -0.12 0.28 -9999 0 -1.1 14 14
IGFBP1 -0.37 0.57 -9999 0 -1.2 98 98
VEGFA -0.23 0.39 -9999 0 -0.76 88 88
HIF1A/JAB1 -0.029 0.064 -9999 0 -0.41 7 7
CP -0.35 0.57 -9999 0 -1.2 94 94
CXCL12 -0.36 0.57 -9999 0 -1.2 100 100
COPS5 0.009 0.01 -9999 0 -10000 0 0
SMAD3/SMAD4 0.02 0.043 -9999 0 -0.46 3 3
BNIP3 -0.32 0.54 -9999 0 -1.1 89 89
EGLN3 -0.38 0.58 -9999 0 -1.1 108 108
CA9 -0.43 0.57 -9999 0 -1.1 120 120
TERT -0.39 0.57 -9999 0 -1.2 104 104
ENO1 -0.32 0.54 -9999 0 -1.1 88 88
PFKL -0.32 0.54 -9999 0 -1.1 89 89
NCOA1 0.013 0.005 -9999 0 -10000 0 0
ADM -0.32 0.54 -9999 0 -1.1 90 90
ARNT -0.024 0.075 -9999 0 -10000 0 0
HNF4A -0.02 0.11 -9999 0 -0.63 11 11
ADFP -0.33 0.53 -9999 0 -1.1 95 95
SLC2A1 -0.25 0.42 -9999 0 -0.82 92 92
LEP -0.34 0.54 -9999 0 -1.1 93 93
HIF1A/ARNT/Cbp/p300 -0.34 0.4 -9999 0 -0.89 99 99
EPO -0.42 0.52 -9999 0 -1.1 123 123
CREBBP -0.062 0.15 -9999 0 -0.34 40 40
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.4 -9999 0 -0.88 100 100
PFKFB3 -0.34 0.56 -9999 0 -1.2 92 92
NT5E -0.33 0.55 -9999 0 -1.1 91 91
Glypican 1 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
GPC1/FGF2 dimer/FGFR1 dimer -0.079 0.2 -10000 0 -0.46 63 63
fibroblast growth factor receptor signaling pathway -0.079 0.2 -10000 0 -0.46 63 63
LAMA1 -0.079 0.2 -10000 0 -0.47 69 69
PRNP -0.037 0.17 -10000 0 -0.62 30 30
GPC1/SLIT2 -0.11 0.21 -10000 0 -0.39 120 120
SMAD2 -0.011 0.12 -10000 0 -0.35 42 42
GPC1/PrPc/Cu2+ -0.057 0.19 -10000 0 -0.47 58 58
GPC1/Laminin alpha1 -0.098 0.2 -10000 0 -0.49 69 69
TDGF1 -0.17 0.25 -10000 0 -0.46 142 142
CRIPTO/GPC1 -0.16 0.23 -10000 0 -0.51 96 96
APP/GPC1 -0.05 0.18 -10000 0 -0.48 52 52
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.13 0.2 -10000 0 -0.43 96 96
FLT1 0.011 0.042 -10000 0 -0.44 3 3
GPC1/TGFB/TGFBR1/TGFBR2 -0.02 0.13 -10000 0 -0.39 42 42
SERPINC1 -0.083 0.23 -10000 0 -0.63 56 56
FYN -0.13 0.2 -10000 0 -0.43 96 96
FGR -0.13 0.2 -10000 0 -0.43 98 98
positive regulation of MAPKKK cascade -0.15 0.24 -10000 0 -0.48 106 106
SLIT2 -0.1 0.22 -10000 0 -0.48 86 86
GPC1/NRG -0.18 0.25 -10000 0 -0.5 130 130
NRG1 -0.2 0.28 -10000 0 -0.55 137 137
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.02 0.13 -10000 0 -0.39 42 42
LYN -0.13 0.2 -10000 0 -0.43 97 97
mol:Spermine -0.041 0.15 -10000 0 -0.47 41 41
cell growth -0.079 0.2 -10000 0 -0.46 63 63
BMP signaling pathway 0.056 0.2 0.62 41 -10000 0 41
SRC -0.15 0.22 -10000 0 -0.45 110 110
TGFBR1 0.012 0.026 -10000 0 -0.34 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.29 0.27 -10000 0 -0.5 219 219
GPC1 -0.056 0.2 -10000 0 -0.62 41 41
TGFBR1 (dimer) 0.012 0.026 -10000 0 -0.34 2 2
VEGFA 0.013 0.033 -10000 0 -0.63 1 1
BLK -0.17 0.23 -10000 0 -0.46 125 125
HCK -0.14 0.21 -10000 0 -0.44 103 103
FGF2 -0.06 0.18 -10000 0 -0.45 59 59
FGFR1 -0.018 0.12 -10000 0 -0.41 28 28
VEGFR1 homodimer 0.011 0.042 -10000 0 -0.44 3 3
TGFBR2 0.011 0.047 -10000 0 -0.63 2 2
cell death -0.05 0.18 -10000 0 -0.48 52 52
ATIII/GPC1 -0.1 0.22 -10000 0 -0.48 92 92
PLA2G2A/GPC1 -0.25 0.24 -10000 0 -0.51 141 141
LCK -0.16 0.22 -10000 0 -0.45 113 113
neuron differentiation -0.18 0.25 -10000 0 -0.5 130 130
PrPc/Cu2+ -0.028 0.13 -10000 0 -0.46 30 30
APP -0.011 0.12 -10000 0 -0.61 15 15
TGFBR2 (dimer) 0.011 0.047 -10000 0 -0.63 2 2
PDGFR-alpha signaling pathway

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.18 0.28 -9999 0 -0.58 118 118
PDGF/PDGFRA/CRKL -0.12 0.21 -9999 0 -0.44 99 99
positive regulation of JUN kinase activity -0.07 0.16 -9999 0 -0.34 93 93
CRKL 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.12 0.21 -9999 0 -0.42 112 112
AP1 -0.18 0.32 -9999 0 -0.98 41 41
mol:IP3 -0.12 0.22 -9999 0 -0.42 118 118
PLCG1 -0.12 0.22 -9999 0 -0.42 118 118
PDGF/PDGFRA/alphaV Integrin -0.12 0.21 -9999 0 -0.44 102 102
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.013 0.018 -9999 0 -0.34 1 1
mol:Ca2+ -0.12 0.21 -9999 0 -0.42 118 118
CAV3 0.001 0.018 -9999 0 -0.34 1 1
CAV1 0.01 0.051 -9999 0 -0.54 3 3
SHC/Grb2/SOS1 -0.07 0.16 -9999 0 -0.34 93 93
PDGF/PDGFRA/Shf -0.15 0.23 -9999 0 -0.47 119 119
FOS -0.15 0.34 -9999 0 -0.96 41 41
JUN -0.017 0.041 -9999 0 -0.49 2 2
oligodendrocyte development -0.12 0.21 -9999 0 -0.4 121 121
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
mol:DAG -0.12 0.22 -9999 0 -0.42 118 118
PDGF/PDGFRA -0.18 0.28 -9999 0 -0.58 118 118
actin cytoskeleton reorganization -0.12 0.21 -9999 0 -0.44 100 100
SRF 0.027 0.009 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
PI3K -0.092 0.19 -9999 0 -0.39 95 95
PDGF/PDGFRA/Crk/C3G -0.088 0.18 -9999 0 -0.38 93 93
JAK1 -0.11 0.21 -9999 0 -0.4 118 118
ELK1/SRF -0.069 0.16 -9999 0 -0.34 93 93
SHB 0.013 0.033 -9999 0 -0.63 1 1
SHF -0.03 0.16 -9999 0 -0.62 26 26
CSNK2A1 0.016 0.022 -9999 0 -10000 0 0
GO:0007205 -0.12 0.22 -9999 0 -0.48 99 99
SOS1 0.013 0.018 -9999 0 -0.34 1 1
Ras protein signal transduction -0.07 0.16 -9999 0 -0.34 93 93
PDGF/PDGFRA/SHB -0.12 0.21 -9999 0 -0.44 100 100
PDGF/PDGFRA/Caveolin-1 -0.12 0.21 -9999 0 -0.41 118 118
ITGAV 0.01 0.037 -9999 0 -0.34 4 4
ELK1 -0.1 0.2 -9999 0 -0.43 93 93
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
PDGF/PDGFRA/Crk -0.12 0.21 -9999 0 -0.44 99 99
JAK-STAT cascade -0.11 0.21 -9999 0 -0.4 118 118
cell proliferation -0.15 0.23 -9999 0 -0.47 119 119
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.34 0.53 -10000 0 -1.1 100 100
PCK1 -0.49 0.73 -10000 0 -1.5 115 115
HNF4A -0.39 0.63 -10000 0 -1.3 88 88
KCNJ11 -0.42 0.6 -10000 0 -1.1 121 121
AKT1 -0.14 0.19 -10000 0 -0.43 66 66
response to starvation -0.002 0.021 -10000 0 -10000 0 0
DLK1 -0.47 0.6 -10000 0 -1.2 133 133
NKX2-1 -0.11 0.2 0.56 1 -10000 0 1
ACADM -0.34 0.54 -10000 0 -1.1 92 92
TAT -0.58 0.77 -10000 0 -1.5 136 136
CEBPB 0.01 0.021 -10000 0 -10000 0 0
CEBPA -0.009 0.12 -10000 0 -0.62 12 12
TTR -0.34 0.57 -10000 0 -1.4 72 72
PKLR -0.38 0.59 -10000 0 -1.2 107 107
APOA1 -0.44 0.69 -10000 0 -1.4 102 102
CPT1C -0.35 0.54 -10000 0 -1.1 102 102
ALAS1 -0.12 0.21 -10000 0 -10000 0 0
TFRC -0.31 0.46 -10000 0 -0.91 99 99
FOXF1 -0.024 0.15 -10000 0 -0.55 25 25
NF1 0.02 0.034 -10000 0 -0.63 1 1
HNF1A (dimer) -0.023 0.1 -10000 0 -0.6 5 5
CPT1A -0.34 0.53 -10000 0 -1.1 94 94
HMGCS1 -0.34 0.53 -10000 0 -1.1 100 100
NR3C1 -0.034 0.085 -10000 0 -0.28 8 8
CPT1B -0.35 0.54 -10000 0 -1.1 94 94
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.011 0.061 -10000 0 -10000 0 0
GCK -0.44 0.57 -10000 0 -1.2 118 118
CREB1 -0.009 0.059 -10000 0 -10000 0 0
IGFBP1 -0.32 0.56 -10000 0 -1.6 57 57
PDX1 -0.33 0.52 -10000 0 -1.3 69 69
UCP2 -0.35 0.54 -10000 0 -1.1 92 92
ALDOB -0.43 0.65 -10000 0 -1.3 108 108
AFP -0.21 0.37 -10000 0 -0.98 54 54
BDH1 -0.37 0.58 -10000 0 -1.2 94 94
HADH -0.35 0.55 -10000 0 -1.1 93 93
F2 -0.4 0.64 -10000 0 -1.4 88 88
HNF1A -0.023 0.1 -10000 0 -0.6 5 5
G6PC -0.22 0.51 -10000 0 -1.5 50 50
SLC2A2 -0.3 0.55 -10000 0 -1.5 50 50
INS 0.005 0.071 -10000 0 -0.43 4 4
FOXA1 -0.045 0.14 -10000 0 -0.37 37 37
FOXA3 -0.15 0.25 -10000 0 -0.44 122 122
FOXA2 -0.42 0.67 -10000 0 -1.3 105 105
ABCC8 -0.37 0.56 -10000 0 -1.2 93 93
ALB -0.16 0.37 -10000 0 -1.2 35 35
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.1 0.16 -9999 0 -0.4 72 72
EFNA5 -0.16 0.25 -9999 0 -0.48 131 131
FYN -0.086 0.15 -9999 0 -0.36 72 72
neuron projection morphogenesis -0.1 0.16 -9999 0 -0.4 72 72
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.1 0.17 -9999 0 -0.41 72 72
EPHA5 -0.01 0.066 -9999 0 -0.34 14 14
Syndecan-1-mediated signaling events

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
TGFB1 -0.005 0.09 -9999 0 -0.39 18 18
CCL5 -0.024 0.13 -9999 0 -0.44 31 31
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.16 0.2 -9999 0 -0.41 104 104
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.15 0.2 -9999 0 -0.46 77 77
Syndecan-1/Syntenin -0.14 0.19 -9999 0 -0.45 75 75
MAPK3 -0.12 0.18 -9999 0 -0.48 49 49
HGF/MET -0.055 0.16 -9999 0 -0.46 39 39
TGFB1/TGF beta receptor Type II -0.005 0.09 -9999 0 -0.39 18 18
BSG 0.012 0.026 -9999 0 -0.34 2 2
keratinocyte migration -0.15 0.19 -9999 0 -0.45 77 77
Syndecan-1/RANTES -0.16 0.22 -9999 0 -0.48 83 83
Syndecan-1/CD147 -0.13 0.19 -9999 0 -0.51 49 49
Syndecan-1/Syntenin/PIP2 -0.14 0.19 -9999 0 -0.43 75 75
LAMA5 0.003 0.078 -9999 0 -0.47 9 9
positive regulation of cell-cell adhesion -0.14 0.18 -9999 0 -0.42 75 75
MMP7 -0.2 0.27 -9999 0 -0.51 153 153
HGF -0.084 0.21 -9999 0 -0.48 74 74
Syndecan-1/CASK -0.15 0.19 -9999 0 -0.4 104 104
Syndecan-1/HGF/MET -0.18 0.22 -9999 0 -0.46 110 110
regulation of cell adhesion -0.11 0.17 -9999 0 -0.47 46 46
HPSE -0.044 0.18 -9999 0 -0.56 38 38
positive regulation of cell migration -0.16 0.2 -9999 0 -0.41 104 104
SDC1 -0.16 0.2 -9999 0 -0.42 104 104
Syndecan-1/Collagen -0.16 0.2 -9999 0 -0.41 104 104
PPIB 0.014 0 -9999 0 -10000 0 0
MET 0.008 0.061 -9999 0 -0.56 4 4
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
MMP9 -0.11 0.22 -9999 0 -0.46 100 100
MAPK1 -0.12 0.18 -9999 0 -0.48 49 49
homophilic cell adhesion -0.16 0.2 -9999 0 -0.41 104 104
MMP1 -0.086 0.2 -9999 0 -0.45 79 79
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.034 0.057 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.11 0.14 -9999 0 -0.41 33 33
JUN -0.11 0.2 -9999 0 -0.49 43 43
HRAS 0.012 0.026 -9999 0 -0.34 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.21 -9999 0 -0.41 133 133
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.014 0 -9999 0 -10000 0 0
RAP1A/GDP 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.21 -9999 0 -0.41 133 133
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.018 -9999 0 -0.34 1 1
RET9/GFRalpha1/GDNF/Enigma -0.099 0.18 -9999 0 -0.38 104 104
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.14 0.18 -9999 0 -0.36 133 133
GRB7 -0.011 0.11 -9999 0 -0.48 19 19
RET51/GFRalpha1/GDNF -0.15 0.21 -9999 0 -0.41 133 133
MAPKKK cascade -0.13 0.17 -9999 0 -0.5 33 33
BCAR1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.1 0.18 -9999 0 -0.38 107 107
lamellipodium assembly -0.11 0.14 -9999 0 -0.3 105 105
RET51/GFRalpha1/GDNF/SHC -0.15 0.21 -9999 0 -0.41 133 133
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
RET9/GFRalpha1/GDNF/SHC -0.099 0.18 -9999 0 -0.37 104 104
RET9/GFRalpha1/GDNF/Shank3 -0.099 0.18 -9999 0 -0.37 104 104
MAPK3 -0.12 0.18 -9999 0 -0.34 125 125
DOK1 0.014 0 -9999 0 -10000 0 0
DOK6 -0.071 0.19 -9999 0 -0.45 67 67
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.12 0.18 -9999 0 -0.43 55 55
DOK5 -0.03 0.15 -9999 0 -0.51 31 31
GFRA1 -0.17 0.29 -9999 0 -0.62 106 106
MAPK8 -0.12 0.2 -9999 0 -0.48 53 53
HRAS/GTP -0.15 0.2 -9999 0 -0.4 125 125
tube development -0.086 0.17 -9999 0 -0.34 104 104
MAPK1 -0.12 0.18 -9999 0 -0.34 126 126
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.064 0.14 -9999 0 -0.28 102 102
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
SRC -0.021 0.14 -9999 0 -0.6 21 21
PDLIM7 0.013 0.018 -9999 0 -0.34 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.2 0.24 -9999 0 -0.42 166 166
SHC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.21 -9999 0 -0.41 133 133
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.23 -9999 0 -0.43 142 142
PRKCA 0.014 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.018 -9999 0 -0.23 2 2
CREB1 -0.09 0.17 -9999 0 -0.34 102 102
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.14 -9999 0 -0.29 102 102
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.22 -9999 0 -0.42 141 141
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.094 0.21 -9999 0 -0.45 85 85
DOK4 0.014 0 -9999 0 -10000 0 0
JNK cascade -0.1 0.19 -9999 0 -0.47 43 43
RET9/GFRalpha1/GDNF/FRS2 -0.099 0.18 -9999 0 -0.37 104 104
SHANK3 0.013 0.018 -9999 0 -0.34 1 1
RASA1 0.002 0.088 -9999 0 -0.63 7 7
NCK1 0.011 0.047 -9999 0 -0.63 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.065 0.14 -9999 0 -0.28 102 102
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.17 -9999 0 -0.33 87 87
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.11 0.18 -9999 0 -0.5 32 32
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.18 -9999 0 -0.33 125 125
PI3K -0.13 0.24 -9999 0 -0.46 107 107
SOS1 0.013 0.018 -9999 0 -0.34 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.086 0.17 -9999 0 -0.34 104 104
GRB10 0.014 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.088 0.15 -9999 0 -0.41 28 28
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.21 -9999 0 -0.41 133 133
GAB1 0.013 0.033 -9999 0 -0.63 1 1
IRS1 0.006 0.074 -9999 0 -0.63 5 5
IRS2 -0.005 0.11 -9999 0 -0.63 11 11
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.19 -9999 0 -0.33 125 125
RET51/GFRalpha1/GDNF/PKC alpha -0.15 0.21 -9999 0 -0.41 133 133
GRB2 0.014 0 -9999 0 -10000 0 0
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
GDNF -0.022 0.1 -9999 0 -0.36 29 29
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.15 0.22 -9999 0 -0.41 136 136
Rac1/GTP -0.13 0.16 -9999 0 -0.36 105 105
RET9/GFRalpha1/GDNF -0.12 0.19 -9999 0 -0.42 104 104
GFRalpha1/GDNF -0.14 0.22 -9999 0 -0.48 104 104
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.33 -10000 0 -0.76 69 69
CRP -0.46 0.52 -10000 0 -1 144 144
cell cycle arrest -0.29 0.4 -10000 0 -0.81 103 103
TIMP1 -0.26 0.37 -10000 0 -0.83 81 81
IL6ST -0.14 0.27 -10000 0 -0.63 86 86
Rac1/GDP -0.15 0.24 -10000 0 -0.48 94 94
AP1 -0.005 0.13 -10000 0 -0.38 20 20
GAB2 0.018 0.008 -10000 0 -10000 0 0
TNFSF11 -0.34 0.45 -10000 0 -0.99 98 98
HSP90B1 -0.008 0.056 -10000 0 -10000 0 0
GAB1 0.015 0.034 -10000 0 -0.63 1 1
MAPK14 -0.14 0.25 -10000 0 -0.6 62 62
AKT1 0.05 0.052 -10000 0 -0.76 1 1
FOXO1 0.053 0.051 -10000 0 -0.72 1 1
MAP2K6 -0.15 0.25 -10000 0 -0.47 110 110
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.17 0.26 -10000 0 -0.53 91 91
MITF -0.14 0.22 -10000 0 -0.46 90 90
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.014 0 -10000 0 -10000 0 0
A2M -0.19 0.51 -10000 0 -1.4 52 52
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.003 0.092 0.24 1 -0.26 1 2
STAT3 -0.31 0.43 -10000 0 -0.87 103 103
STAT1 -0.012 0.026 -10000 0 -10000 0 0
CEBPD -0.25 0.35 -10000 0 -0.8 69 69
PIK3CA 0.012 0.047 -10000 0 -0.63 2 2
PI3K 0.018 0.063 -10000 0 -0.56 4 4
JUN 0.011 0.047 -10000 0 -0.63 2 2
PIAS3/MITF -0.12 0.21 -10000 0 -0.49 65 65
MAPK11 -0.14 0.26 -10000 0 -0.6 63 63
STAT3 (dimer)/FOXO1 -0.22 0.36 -10000 0 -0.71 91 91
GRB2/SOS1/GAB family -0.082 0.18 0.2 1 -0.5 36 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.22 -10000 0 -0.42 95 95
GRB2 0.017 0.005 -10000 0 -10000 0 0
JAK2 0.011 0.042 -10000 0 -0.44 3 3
LBP -0.2 0.34 -10000 0 -0.84 53 53
PIK3R1 0.01 0.058 -10000 0 -0.63 3 3
JAK1 0.012 0.008 -10000 0 -10000 0 0
MYC -0.29 0.41 -10000 0 -0.89 89 89
FGG -0.27 0.39 -10000 0 -0.88 76 76
macrophage differentiation -0.29 0.4 -10000 0 -0.81 103 103
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.13 0.23 -10000 0 -0.44 111 111
JUNB -0.24 0.34 -10000 0 -0.74 79 79
FOS -0.058 0.19 -10000 0 -0.51 51 51
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.23 -10000 0 -0.47 97 97
STAT1/PIAS1 -0.14 0.22 -10000 0 -0.45 86 86
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.055 -10000 0 -0.55 2 2
STAT3 (dimer) -0.31 0.43 -10000 0 -0.86 103 103
PRKCD -0.2 0.29 -10000 0 -0.6 86 86
IL6R -0.034 0.16 -10000 0 -0.61 28 28
SOCS3 -0.14 0.3 -10000 0 -0.74 51 51
gp130 (dimer)/JAK1/JAK1/LMO4 -0.084 0.19 -10000 0 -0.41 87 87
Rac1/GTP -0.16 0.25 -10000 0 -0.51 94 94
HCK -0.001 0.097 -10000 0 -0.57 10 10
MAPKKK cascade 0.022 0.079 -10000 0 -0.48 1 1
bone resorption -0.31 0.41 -10000 0 -0.9 98 98
IRF1 -0.24 0.33 -10000 0 -0.76 70 70
mol:GDP -0.15 0.25 -10000 0 -0.49 98 98
SOS1 0.017 0.02 -10000 0 -0.34 1 1
VAV1 -0.16 0.25 -10000 0 -0.5 98 98
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.12 0.25 -10000 0 -0.61 54 54
PTPN11 -0.009 0.022 -10000 0 -10000 0 0
IL6/IL6RA -0.075 0.18 -10000 0 -0.4 77 77
gp130 (dimer)/TYK2/TYK2/LMO4 -0.083 0.18 -10000 0 -0.41 87 87
gp130 (dimer)/JAK2/JAK2/LMO4 -0.085 0.19 -10000 0 -0.41 87 87
IL6 -0.067 0.18 -10000 0 -0.47 58 58
PIAS3 0.014 0 -10000 0 -10000 0 0
PTPRE 0.009 0.082 -10000 0 -0.45 10 10
PIAS1 0.014 0 -10000 0 -10000 0 0
RAC1 0.013 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.2 0.24 1 -0.39 108 109
LMO4 0 0.077 -10000 0 -0.65 5 5
STAT3 (dimer)/PIAS3 -0.29 0.38 -10000 0 -0.8 97 97
MCL1 0.055 0.046 -10000 0 -0.66 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.31 -10000 0 -0.69 75 75
IHH -0.097 0.22 -10000 0 -0.58 56 56
SHH Np/Cholesterol/GAS1 -0.044 0.15 -10000 0 -0.37 56 56
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.044 0.14 0.37 56 -10000 0 56
SMO/beta Arrestin2 -0.1 0.26 -10000 0 -0.69 45 45
SMO -0.12 0.28 -10000 0 -0.64 63 63
AKT1 -0.033 0.14 -10000 0 -0.46 14 14
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC 0.002 0.069 -10000 0 -0.36 12 12
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.12 0.27 -10000 0 -0.62 63 63
STIL -0.096 0.23 -10000 0 -0.56 53 53
DHH N/PTCH2 -0.017 0.12 -10000 0 -0.39 33 33
DHH N/PTCH1 -0.12 0.24 -10000 0 -0.57 59 59
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
DHH -0.022 0.14 -10000 0 -0.59 21 21
PTHLH -0.2 0.38 -10000 0 -0.85 74 74
determination of left/right symmetry -0.12 0.27 -10000 0 -0.62 63 63
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
skeletal system development -0.2 0.37 -10000 0 -0.83 75 75
IHH N/Hhip -0.15 0.23 -10000 0 -0.45 119 119
DHH N/Hhip -0.1 0.21 -10000 0 -0.4 104 104
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.12 0.27 -10000 0 -0.62 63 63
pancreas development -0.12 0.24 -10000 0 -0.51 91 91
HHAT 0.004 0.074 -10000 0 -0.51 7 7
PI3K 0.015 0.062 -10000 0 -0.56 4 4
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.058 0.19 -10000 0 -0.53 49 49
somite specification -0.12 0.27 -10000 0 -0.62 63 63
SHH Np/Cholesterol/PTCH1 -0.1 0.24 -10000 0 -0.59 54 54
SHH Np/Cholesterol/PTCH2 -0.012 0.11 -10000 0 -0.37 29 29
SHH Np/Cholesterol/Megalin -0.087 0.17 -10000 0 -0.39 74 74
SHH -0.013 0.13 -10000 0 -0.45 28 28
catabolic process -0.12 0.25 -10000 0 -0.54 74 74
SMO/Vitamin D3 -0.11 0.26 -10000 0 -0.66 53 53
SHH Np/Cholesterol/Hhip -0.079 0.17 -10000 0 -0.38 76 76
LRP2 -0.14 0.24 -10000 0 -0.48 111 111
receptor-mediated endocytosis -0.16 0.28 -10000 0 -0.66 66 66
SHH Np/Cholesterol/BOC -0.009 0.11 -10000 0 -0.38 26 26
SHH Np/Cholesterol/CDO -0.005 0.1 -10000 0 -0.37 26 26
mesenchymal cell differentiation 0.079 0.17 0.38 76 -10000 0 76
mol:Vitamin D3 -0.1 0.24 -10000 0 -0.6 54 54
IHH N/PTCH2 -0.056 0.16 -10000 0 -0.44 48 48
CDON 0.011 0.042 -10000 0 -0.44 3 3
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.54 74 74
Megalin/LRPAP1 -0.088 0.18 -10000 0 -0.46 52 52
PTCH2 -0.002 0.086 -10000 0 -0.43 13 13
SHH Np/Cholesterol -0.012 0.1 -10000 0 -0.38 25 25
PTCH1 -0.12 0.25 -10000 0 -0.54 74 74
HHIP -0.12 0.24 -10000 0 -0.51 91 91
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.1 0.52 -10000 0 -1.1 52 52
PLK1 -0.06 0.38 -10000 0 -1.5 23 23
BIRC5 -0.046 0.33 -10000 0 -1.5 16 16
HSPA1B -0.13 0.55 -10000 0 -1.1 60 60
MAP2K1 0.025 0.041 -10000 0 -10000 0 0
BRCA2 -0.13 0.56 -10000 0 -1.2 60 60
FOXM1 -0.2 0.76 -10000 0 -1.7 56 56
XRCC1 -0.1 0.52 -10000 0 -1.1 51 51
FOXM1B/p19 -0.28 0.45 0.4 1 -1.1 64 65
Cyclin D1/CDK4 -0.15 0.53 -10000 0 -1 73 73
CDC2 -0.12 0.55 -10000 0 -1.2 56 56
TGFA -0.16 0.53 -10000 0 -1 73 73
SKP2 -0.11 0.53 -10000 0 -1.1 52 52
CCNE1 -0.022 0.12 -10000 0 -0.39 35 35
CKS1B -0.1 0.52 -10000 0 -1.1 51 51
RB1 -0.12 0.22 -10000 0 -0.79 16 16
FOXM1C/SP1 -0.16 0.6 -10000 0 -1.3 59 59
AURKB -0.018 0.28 -10000 0 -1.5 11 11
CENPF -0.12 0.54 -10000 0 -1.2 52 52
CDK4 0.018 0.016 -10000 0 -10000 0 0
MYC -0.12 0.51 -10000 0 -1 67 67
CHEK2 0.013 0.089 -10000 0 -0.45 10 10
ONECUT1 -0.15 0.55 -10000 0 -1.1 69 69
CDKN2A -0.066 0.2 -10000 0 -0.55 51 51
LAMA4 -0.11 0.52 -10000 0 -1.1 54 54
FOXM1B/HNF6 -0.2 0.66 -10000 0 -1.4 69 69
FOS -0.16 0.59 -10000 0 -1.3 64 64
SP1 0.014 0.008 -10000 0 -10000 0 0
CDC25B -0.1 0.52 -10000 0 -1.1 51 51
response to radiation 0.009 0.037 -10000 0 -10000 0 0
CENPB -0.1 0.52 -10000 0 -1.1 52 52
CENPA -0.12 0.56 -10000 0 -1.2 56 56
NEK2 -0.13 0.57 -10000 0 -1.2 59 59
HIST1H2BA -0.11 0.52 -10000 0 -1.1 51 51
CCNA2 -0.003 0.097 -10000 0 -0.43 16 16
EP300 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.15 0.61 -10000 0 -1.4 54 54
CCNB2 -0.13 0.56 -10000 0 -1.2 56 56
CCNB1 -0.12 0.56 -10000 0 -1.2 54 54
ETV5 -0.11 0.52 -10000 0 -1.1 52 52
ESR1 -0.24 0.66 -10000 0 -1.2 101 101
CCND1 -0.15 0.55 -10000 0 -1.1 74 74
GSK3A 0.025 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.003 0.11 -10000 0 -0.41 11 11
CDK2 0.016 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.044 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.45 -10000 0 -1.2 63 63
GAS1 -0.16 0.6 -10000 0 -1.2 73 73
MMP2 -0.15 0.58 -10000 0 -1.2 64 64
RB1/FOXM1C -0.15 0.55 -10000 0 -1.1 68 68
CREBBP 0.014 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.1 0.17 -9999 0 -0.33 104 104
NF kappa B1 p50/RelA/I kappa B alpha -0.066 0.16 -9999 0 -0.43 19 19
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.19 -9999 0 -0.45 80 80
AP1 -0.14 0.25 -9999 0 -0.63 52 52
ILK -0.12 0.18 -9999 0 -0.47 25 25
bone resorption -0.12 0.2 -9999 0 -0.55 39 39
PTK2B 0.014 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.1 0.17 -9999 0 -0.5 19 19
ITGAV 0.014 0.036 -9999 0 -0.33 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.046 0.16 -9999 0 -0.37 63 63
alphaV/beta3 Integrin/Osteopontin -0.14 0.2 -9999 0 -0.41 107 107
MAP3K1 -0.12 0.18 -9999 0 -0.36 107 107
JUN 0.011 0.047 -9999 0 -0.63 2 2
MAPK3 -0.098 0.17 -9999 0 -0.33 103 103
MAPK1 -0.099 0.17 -9999 0 -0.34 104 104
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.13 0.2 -9999 0 -0.55 39 39
ITGB3 -0.045 0.18 -9999 0 -0.55 41 41
NFKBIA -0.086 0.17 -9999 0 -0.46 22 22
FOS -0.058 0.19 -9999 0 -0.51 51 51
CD44 -0.025 0.13 -9999 0 -0.43 33 33
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.075 0.16 -9999 0 -0.55 8 8
NF kappa B1 p50/RelA -0.095 0.12 -9999 0 -0.42 18 18
BCAR1 0.014 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.14 -9999 0 -0.46 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.13 0.18 -9999 0 -0.37 116 116
VAV3 -0.12 0.18 -9999 0 -0.45 38 38
MAP3K14 -0.12 0.18 -9999 0 -0.36 107 107
ROCK2 -0.038 0.18 -9999 0 -0.61 31 31
SPP1 -0.21 0.26 -9999 0 -0.46 178 178
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.11 0.17 -9999 0 -0.48 25 25
MMP2 -0.14 0.25 -9999 0 -0.61 57 57
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.055 0.16 -10000 0 -0.36 74 74
regulation of S phase of mitotic cell cycle -0.049 0.14 -10000 0 -0.28 93 93
GNAO1 -0.15 0.27 -10000 0 -0.56 108 108
HRAS 0.012 0.026 -10000 0 -0.34 2 2
SHBG/T-DHT -0.089 0.17 -10000 0 -0.36 100 100
PELP1 0.014 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.047 0.14 -10000 0 -0.37 9 9
T-DHT/AR -0.089 0.19 -10000 0 -0.45 80 80
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 48 48
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.007 0.067 -10000 0 -0.63 4 4
mol:GDP -0.11 0.19 -10000 0 -0.48 75 75
cell proliferation -0.065 0.17 -10000 0 -0.4 35 35
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
FOS -0.076 0.24 -10000 0 -0.8 33 33
mol:Ca2+ -0.032 0.037 -10000 0 -0.077 126 126
MAPK3 -0.058 0.15 -10000 0 -0.43 11 11
MAPK1 -0.025 0.085 -10000 0 -0.3 7 7
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
mol:IP3 0 0.001 -10000 0 -0.004 51 51
cAMP biosynthetic process -0.065 0.16 -10000 0 -0.32 98 98
GNG2 0.007 0.063 -10000 0 -0.52 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 51 51
HRAS/GTP -0.084 0.14 -10000 0 -0.32 91 91
actin cytoskeleton reorganization -0.004 0.043 -10000 0 -0.39 4 4
SRC -0.021 0.14 -10000 0 -0.6 21 21
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 51 51
PI3K 0.014 0.055 -10000 0 -0.49 4 4
apoptosis 0.047 0.14 0.41 33 -10000 0 33
T-DHT/AR/PELP1 -0.067 0.16 -10000 0 -0.4 72 72
HRAS/GDP -0.099 0.18 -10000 0 -0.45 75 75
CREB1 -0.051 0.15 -10000 0 -0.44 33 33
RAC1-CDC42/GTP -0.003 0.044 -10000 0 -0.4 4 4
AR -0.12 0.26 -10000 0 -0.6 80 80
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.055 0.14 -10000 0 -0.3 91 91
RAC1-CDC42/GDP -0.092 0.18 -10000 0 -0.44 73 73
T-DHT/AR/PELP1/Src -0.073 0.17 -10000 0 -0.36 91 91
MAP2K2 -0.048 0.14 -10000 0 -0.37 9 9
T-DHT/AR/PELP1/Src/PI3K -0.05 0.14 -10000 0 -0.28 93 93
GNAZ -0.086 0.22 -10000 0 -0.55 66 66
SHBG -0.14 0.26 -10000 0 -0.56 100 100
Gi family/GNB1/GNG2/GDP -0.11 0.2 -10000 0 -0.44 82 82
mol:T-DHT 0 0.001 0.001 4 -0.002 38 42
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 0.004 0.057 -10000 0 -0.43 6 6
Gi family/GTP -0.11 0.17 -10000 0 -0.35 90 90
CDC42 0.014 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.051 0.14 -10000 0 -0.33 67 67
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.28 -10000 0 -0.59 81 81
AKT1 -0.15 0.34 -10000 0 -0.88 64 64
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.15 0.35 -10000 0 -0.9 64 64
mol:Ca2+ -0.065 0.18 -10000 0 -0.48 46 46
IGF1R -0.036 0.14 -10000 0 -0.41 44 44
E2/ER alpha (dimer)/Striatin -0.099 0.19 -10000 0 -0.43 82 82
SHC1 0.014 0 -10000 0 -10000 0 0
apoptosis 0.14 0.32 0.83 64 -10000 0 64
RhoA/GTP -0.06 0.11 -10000 0 -0.29 63 63
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.17 0.23 -10000 0 -0.55 80 80
regulation of stress fiber formation 0.032 0.14 0.45 16 -10000 0 16
E2/ERA-ERB (dimer) -0.074 0.16 -10000 0 -0.32 103 103
KRAS 0.013 0.018 -10000 0 -0.34 1 1
G13/GTP -0.064 0.14 -10000 0 -0.36 63 63
pseudopodium formation -0.032 0.14 -10000 0 -0.45 16 16
E2/ER alpha (dimer)/PELP1 -0.071 0.16 -10000 0 -0.4 63 63
GRB2 0.014 0 -10000 0 -10000 0 0
GNG2 0.007 0.063 -10000 0 -0.52 5 5
GNAO1 -0.15 0.27 -10000 0 -0.56 108 108
HRAS 0.012 0.026 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.13 0.26 -10000 0 -0.63 67 67
E2/ER beta (dimer) 0.007 0.028 -10000 0 -0.23 5 5
mol:GDP -0.085 0.16 -10000 0 -0.44 63 63
mol:NADP -0.13 0.26 -10000 0 -0.63 67 67
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
mol:IP3 -0.068 0.19 -10000 0 -0.5 46 46
IGF-1R heterotetramer -0.036 0.14 -10000 0 -0.41 44 44
PLCB1 -0.067 0.18 -10000 0 -0.44 58 58
PLCB2 -0.058 0.19 -10000 0 -0.5 45 45
IGF1 -0.092 0.23 -10000 0 -0.57 68 68
mol:L-citrulline -0.13 0.26 -10000 0 -0.63 67 67
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.19 0.34 -10000 0 -0.79 81 81
JNK cascade 0.007 0.028 -10000 0 -0.23 5 5
BCAR1 0.014 0 -10000 0 -10000 0 0
ESR2 0.009 0.041 -10000 0 -0.34 5 5
GNAQ 0.013 0.033 -10000 0 -0.63 1 1
ESR1 -0.13 0.25 -10000 0 -0.53 98 98
Gq family/GDP/Gbeta gamma -0.028 0.16 -10000 0 -0.5 31 31
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.042 0.12 -10000 0 -0.32 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.17 0.23 -10000 0 -0.55 80 80
GNAZ -0.086 0.22 -10000 0 -0.55 66 66
E2/ER alpha (dimer) -0.094 0.18 -10000 0 -0.39 98 98
STRN -0.031 0.16 -10000 0 -0.63 26 26
GNAL -0.049 0.17 -10000 0 -0.46 50 50
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.01 0.046 -10000 0 -0.22 13 13
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.007 0.067 -10000 0 -0.63 4 4
HBEGF -0.19 0.27 -10000 0 -0.6 85 85
cAMP biosynthetic process -0.098 0.15 -10000 0 -0.34 85 85
SRC -0.16 0.28 -10000 0 -0.57 85 85
PI3K 0.015 0.062 -10000 0 -0.56 4 4
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.076 0.14 -10000 0 -0.38 63 63
SOS1 0.013 0.018 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1 -0.18 0.22 -10000 0 -0.5 97 97
Gs family/GTP -0.099 0.15 -10000 0 -0.35 85 85
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.017 -10000 0 -10000 0 0
vasodilation -0.12 0.24 -10000 0 -0.59 67 67
mol:DAG -0.068 0.19 -10000 0 -0.5 46 46
Gs family/GDP/Gbeta gamma -0.092 0.15 -10000 0 -0.38 66 66
MSN -0.036 0.15 -10000 0 -0.49 16 16
Gq family/GTP -0.058 0.18 -10000 0 -0.52 38 38
mol:PI-3-4-5-P3 -0.14 0.33 -10000 0 -0.86 64 64
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.24 0.59 67 -10000 0 67
GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
RhoA/GDP -0.079 0.15 -10000 0 -0.41 63 63
NOS3 -0.14 0.28 -10000 0 -0.67 67 67
GNA11 -0.028 0.16 -10000 0 -0.63 24 24
MAPKKK cascade -0.14 0.28 -10000 0 -0.63 82 82
E2/ER alpha (dimer)/PELP1/Src -0.18 0.25 -10000 0 -0.58 81 81
ruffle organization -0.032 0.14 -10000 0 -0.45 16 16
ROCK2 -0.045 0.16 -10000 0 -0.55 14 14
GNA14 -0.027 0.16 -10000 0 -0.62 24 24
GNA15 -0.002 0.092 -10000 0 -0.49 12 12
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.2 0.28 -10000 0 -0.64 84 84
MMP2 -0.18 0.28 -10000 0 -0.68 65 65
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.33 0.51 -10000 0 -1.2 61 61
STAT6 (cleaved dimer) -0.42 0.48 -10000 0 -1.1 98 98
IGHG1 -0.11 0.2 -10000 0 -0.42 47 47
IGHG3 -0.32 0.48 -10000 0 -1 84 84
AKT1 -0.18 0.33 -10000 0 -0.86 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.34 -10000 0 -1 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.18 0.34 -10000 0 -0.89 36 36
THY1 -0.33 0.52 -10000 0 -1.2 66 66
MYB -0.036 0.14 -10000 0 -0.41 44 44
HMGA1 0.004 0.071 -10000 0 -0.45 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.25 0.42 -10000 0 -0.86 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.18 0.34 -10000 0 -0.93 33 33
SP1 0.019 0.014 -10000 0 -10000 0 0
INPP5D 0.009 0.054 -10000 0 -0.49 4 4
SOCS5 0.024 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.36 0.53 -10000 0 -1.2 82 82
SOCS1 -0.23 0.36 -10000 0 -0.77 67 67
SOCS3 -0.22 0.39 -10000 0 -1 42 42
FCER2 -0.3 0.48 -10000 0 -1.1 62 62
PARP14 0.013 0.034 -10000 0 -0.63 1 1
CCL17 -0.34 0.51 -10000 0 -1.2 67 67
GRB2 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.28 -10000 0 -0.85 23 23
T cell proliferation -0.35 0.53 -10000 0 -1.2 68 68
IL4R/JAK1 -0.34 0.51 -10000 0 -1.2 64 64
EGR2 -0.39 0.6 -10000 0 -1.4 75 75
JAK2 -0.002 0.058 -10000 0 -0.49 3 3
JAK3 -0.009 0.11 -10000 0 -0.46 19 19
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
JAK1 0.011 0.016 -10000 0 -10000 0 0
COL1A2 -0.16 0.38 -10000 0 -1.3 26 26
CCL26 -0.35 0.52 -10000 0 -1.2 69 69
IL4R -0.36 0.55 -10000 0 -1.3 63 63
PTPN6 0.021 0.013 -10000 0 -10000 0 0
IL13RA2 -0.37 0.56 -10000 0 -1.3 74 74
IL13RA1 0.001 0.036 -10000 0 -10000 0 0
IRF4 -0.23 0.5 -10000 0 -1.4 49 49
ARG1 -0.26 0.56 -10000 0 -1.5 59 59
CBL -0.23 0.39 -10000 0 -0.84 65 65
GTF3A 0.018 0.015 -10000 0 -10000 0 0
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
IL13RA1/JAK2 0.002 0.064 -10000 0 -0.37 3 3
IRF4/BCL6 -0.21 0.46 -10000 0 -1.3 48 48
CD40LG -0.043 0.18 -10000 0 -0.61 35 35
MAPK14 -0.23 0.4 -10000 0 -0.88 64 64
mitosis -0.17 0.31 -10000 0 -0.79 39 39
STAT6 -0.38 0.6 -10000 0 -1.3 81 81
SPI1 -0.01 0.093 -10000 0 -0.57 7 7
RPS6KB1 -0.15 0.3 -10000 0 -0.78 36 36
STAT6 (dimer) -0.38 0.61 -10000 0 -1.3 81 81
STAT6 (dimer)/PARP14 -0.36 0.54 -10000 0 -1.2 76 76
mast cell activation 0.007 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.19 0.37 -10000 0 -1 35 35
FRAP1 -0.18 0.33 -10000 0 -0.86 39 39
LTA -0.36 0.54 -10000 0 -1.2 71 71
FES -0.011 0.12 -10000 0 -0.5 18 18
T-helper 1 cell differentiation 0.37 0.58 1.2 81 -10000 0 81
CCL11 -0.37 0.54 -10000 0 -1.2 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.37 -10000 0 -0.97 40 40
IL2RG -0.038 0.16 -10000 0 -0.49 39 39
IL10 -0.36 0.54 -10000 0 -1.2 71 71
IRS1 0.006 0.074 -10000 0 -0.63 5 5
IRS2 -0.005 0.11 -10000 0 -0.63 11 11
IL4 -0.067 0.14 -10000 0 -10000 0 0
IL5 -0.33 0.5 -10000 0 -1.2 63 63
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.4 -10000 0 -0.87 65 65
COL1A1 -0.19 0.43 -10000 0 -1.5 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.52 -10000 0 -1.3 50 50
IL2R gamma/JAK3 -0.033 0.17 -10000 0 -0.52 33 33
TFF3 -0.4 0.59 -10000 0 -1.3 85 85
ALOX15 -0.34 0.51 -10000 0 -1.2 65 65
MYBL1 0.009 0.041 -10000 0 -0.34 5 5
T-helper 2 cell differentiation -0.3 0.45 -10000 0 -0.98 74 74
SHC1 0.014 0 -10000 0 -10000 0 0
CEBPB 0.001 0.048 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.34 -10000 0 -0.9 37 37
mol:PI-3-4-5-P3 -0.18 0.33 -10000 0 -0.86 39 39
PI3K -0.19 0.36 -10000 0 -0.95 39 39
DOK2 0.002 0.083 -10000 0 -0.5 9 9
ETS1 0.015 0.062 -10000 0 -0.48 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.26 -10000 0 -0.82 22 22
ITGB3 -0.39 0.59 -10000 0 -1.3 78 78
PIGR -0.52 0.7 -10000 0 -1.4 118 118
IGHE 0.015 0.046 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.26 -10000 0 -0.8 22 22
BCL6 0.014 0.003 -10000 0 -10000 0 0
OPRM1 -0.34 0.5 -10000 0 -1.2 67 67
RETNLB -0.34 0.5 -10000 0 -1.2 64 64
SELP -0.43 0.64 -10000 0 -1.4 94 94
AICDA -0.32 0.48 -10000 0 -1.1 63 63
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.058 0.18 -9999 0 -0.39 72 72
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.11 -9999 0 -0.4 13 13
AP1 -0.13 0.2 -9999 0 -0.44 90 90
mol:PIP3 -0.098 0.16 -9999 0 -0.48 34 34
AKT1 -0.014 0.13 -9999 0 -0.4 18 18
PTK2B -0.049 0.14 -9999 0 -0.36 37 37
RHOA -0.007 0.072 -9999 0 -0.37 4 4
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.021 0.11 -9999 0 -0.41 18 18
MAGI3 0.014 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.067 0.15 -9999 0 -0.37 63 63
HRAS/GDP 0.009 0.018 -9999 0 -0.23 2 2
positive regulation of microtubule depolymerization -0.046 0.14 -9999 0 -0.34 39 39
NF kappa B1 p50/RelA -0.092 0.15 -9999 0 -0.46 37 37
endothelial cell migration -0.1 0.26 -9999 0 -0.55 78 78
ADCY4 -0.15 0.25 -9999 0 -0.56 76 76
ADCY5 -0.18 0.29 -9999 0 -0.6 94 94
ADCY6 -0.14 0.25 -9999 0 -0.56 74 74
ADCY7 -0.14 0.25 -9999 0 -0.56 75 75
ADCY1 -0.19 0.3 -9999 0 -0.59 98 98
ADCY2 -0.15 0.25 -9999 0 -0.56 77 77
ADCY3 -0.14 0.25 -9999 0 -0.58 71 71
ADCY8 -0.16 0.26 -9999 0 -0.56 81 81
ADCY9 -0.14 0.25 -9999 0 -0.56 74 74
GSK3B -0.04 0.13 -9999 0 -0.34 37 37
arachidonic acid secretion -0.14 0.24 -9999 0 -0.54 77 77
GNG2 0.007 0.063 -9999 0 -0.51 5 5
TRIP6 -0.029 0.14 -9999 0 -0.48 30 30
GNAO1 -0.17 0.26 -9999 0 -0.49 124 124
HRAS 0.012 0.026 -9999 0 -0.34 2 2
NFKBIA -0.034 0.12 -9999 0 -0.43 18 18
GAB1 0.013 0.033 -9999 0 -0.63 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.015 0.19 -9999 0 -0.94 15 15
JUN 0.011 0.047 -9999 0 -0.63 2 2
LPA/LPA2/NHERF2 -0.015 0.1 -9999 0 -0.42 18 18
TIAM1 -0.042 0.22 -9999 0 -1.1 15 15
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
mol:IP3 -0.022 0.11 -9999 0 -0.42 18 18
PLCB3 -0.006 0.094 -9999 0 -0.38 17 17
FOS -0.058 0.19 -9999 0 -0.51 51 51
positive regulation of mitosis -0.14 0.24 -9999 0 -0.54 77 77
LPA/LPA1-2-3 -0.1 0.19 -9999 0 -0.43 78 78
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.014 0 -9999 0 -10000 0 0
stress fiber formation -0.055 0.15 -9999 0 -0.37 45 45
GNAZ -0.13 0.23 -9999 0 -0.44 108 108
EGFR/PI3K-beta/Gab1 -0.1 0.16 -9999 0 -0.5 34 34
positive regulation of dendritic cell cytokine production -0.1 0.19 -9999 0 -0.42 78 78
LPA/LPA2/MAGI-3 -0.009 0.086 -9999 0 -0.39 12 12
ARHGEF1 -0.044 0.16 -9999 0 -0.37 57 57
GNAI2 -0.069 0.18 -9999 0 -0.41 72 72
GNAI3 -0.069 0.18 -9999 0 -0.41 72 72
GNAI1 -0.073 0.19 -9999 0 -0.41 75 75
LPA/LPA3 -0.027 0.076 -9999 0 -0.24 36 36
LPA/LPA2 -0.023 0.1 -9999 0 -0.32 31 31
LPA/LPA1 -0.092 0.21 -9999 0 -0.43 89 89
HB-EGF/EGFR -0.07 0.16 -9999 0 -0.41 53 53
HBEGF -0.074 0.17 -9999 0 -0.47 43 43
mol:DAG -0.022 0.11 -9999 0 -0.42 18 18
cAMP biosynthetic process -0.18 0.28 -9999 0 -0.53 106 106
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC -0.021 0.14 -9999 0 -0.6 21 21
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN -0.034 0.13 -9999 0 -0.44 18 18
GNAQ -0.019 0.085 -9999 0 -0.33 17 17
LPAR2 -0.024 0.13 -9999 0 -0.44 31 31
LPAR3 -0.029 0.1 -9999 0 -0.34 36 36
LPAR1 -0.11 0.24 -9999 0 -0.57 74 74
IL8 -0.19 0.24 -9999 0 -0.51 115 115
PTK2 -0.085 0.18 -9999 0 -0.4 76 76
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
CASP3 -0.067 0.16 -9999 0 -0.37 63 63
EGFR -0.007 0.11 -9999 0 -0.59 13 13
PLCG1 -0.03 0.1 -9999 0 -0.33 23 23
PLD2 -0.085 0.18 -9999 0 -0.4 76 76
G12/G13 -0.054 0.17 -9999 0 -0.39 62 62
PI3K-beta -0.065 0.12 -9999 0 -0.46 19 19
cell migration -0.023 0.094 -9999 0 -0.25 31 31
SLC9A3R2 0.004 0.082 -9999 0 -0.63 6 6
PXN -0.056 0.15 -9999 0 -0.38 45 45
HRAS/GTP -0.14 0.25 -9999 0 -0.55 77 77
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.11 0.22 -9999 0 -0.46 100 100
PRKCE 0.004 0.067 -9999 0 -0.4 9 9
PRKCD -0.014 0.11 -9999 0 -0.41 15 15
Gi(beta/gamma) -0.14 0.24 -9999 0 -0.56 69 69
mol:LPA -0.01 0.045 -9999 0 -0.2 15 15
TRIP6/p130 Cas/FAK1/Paxillin -0.1 0.17 -9999 0 -0.54 31 31
MAPKKK cascade -0.14 0.24 -9999 0 -0.54 77 77
contractile ring contraction involved in cytokinesis -0.007 0.072 -9999 0 -0.37 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.04 0.12 -9999 0 -0.35 39 39
GNA15 -0.027 0.11 -9999 0 -0.41 19 19
GNA12 0.014 0 -9999 0 -10000 0 0
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.048 0.14 -9999 0 -0.35 39 39
GNA11 -0.041 0.12 -9999 0 -0.34 40 40
Rac1/GTP -0.017 0.2 -9999 0 -1 15 15
MMP2 -0.1 0.26 -9999 0 -0.56 78 78
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.05 -9999 0 -0.68 1 1
Syndecan-4/Syndesmos -0.095 0.27 -9999 0 -0.61 67 67
positive regulation of JNK cascade -0.13 0.26 -9999 0 -0.59 74 74
Syndecan-4/ADAM12 -0.13 0.29 -9999 0 -0.65 72 72
CCL5 -0.024 0.13 -9999 0 -0.44 31 31
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 0.012 0.026 -9999 0 -0.34 2 2
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG -0.046 0.18 -9999 0 -0.61 36 36
ADAM12 -0.062 0.18 -9999 0 -0.43 64 64
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.017 0.027 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.29 -9999 0 -0.66 73 73
Syndecan-4/CXCL12/CXCR4 -0.14 0.28 -9999 0 -0.64 74 74
Syndecan-4/Laminin alpha3 -0.14 0.28 -9999 0 -0.63 74 74
MDK -0.059 0.18 -9999 0 -0.48 55 55
Syndecan-4/FZD7 -0.13 0.29 -9999 0 -0.67 68 68
Syndecan-4/Midkine -0.13 0.29 -9999 0 -0.66 68 68
FZD7 -0.056 0.19 -9999 0 -0.52 49 49
Syndecan-4/FGFR1/FGF -0.16 0.25 -9999 0 -0.6 74 74
THBS1 -0.037 0.16 -9999 0 -0.52 36 36
integrin-mediated signaling pathway -0.12 0.28 -9999 0 -0.62 74 74
positive regulation of MAPKKK cascade -0.13 0.26 -9999 0 -0.59 74 74
Syndecan-4/TACI -0.11 0.27 -9999 0 -0.62 68 68
CXCR4 -0.003 0.1 -9999 0 -0.58 11 11
cell adhesion 0.03 0.019 -9999 0 -0.3 1 1
Syndecan-4/Dynamin -0.095 0.27 -9999 0 -0.61 67 67
Syndecan-4/TSP1 -0.12 0.28 -9999 0 -0.64 68 68
Syndecan-4/GIPC -0.096 0.27 -9999 0 -0.61 67 67
Syndecan-4/RANTES -0.11 0.28 -9999 0 -0.64 69 69
ITGB1 0.014 0 -9999 0 -10000 0 0
LAMA1 -0.079 0.2 -9999 0 -0.47 69 69
LAMA3 -0.071 0.19 -9999 0 -0.45 68 68
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.028 0.046 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.095 0.27 -9999 0 -0.61 67 67
TFPI -0.028 0.16 -9999 0 -0.62 25 25
F2 -0.031 0.16 -9999 0 -0.62 25 25
alpha5/beta1 Integrin 0.02 0.018 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.29 -9999 0 -0.65 80 80
ACTN1 0.013 0.018 -9999 0 -0.34 1 1
TNC -0.062 0.2 -9999 0 -0.57 49 49
Syndecan-4/CXCL12 -0.14 0.28 -9999 0 -0.65 71 71
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 -0.075 0.22 -9999 0 -0.58 56 56
TNFRSF13B -0.015 0.1 -9999 0 -0.39 23 23
FGF2 -0.06 0.18 -9999 0 -0.45 59 59
FGFR1 -0.018 0.12 -9999 0 -0.41 28 28
Syndecan-4/PI-4-5-P2 -0.1 0.27 -9999 0 -0.62 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.015 0.032 -9999 0 -0.59 1 1
cell migration -0.001 0.011 -9999 0 -10000 0 0
PRKCD 0.016 0.008 -9999 0 -10000 0 0
vasculogenesis -0.11 0.26 -9999 0 -0.6 69 69
SDC4 -0.11 0.29 -9999 0 -0.66 67 67
Syndecan-4/Tenascin C -0.13 0.3 -9999 0 -0.66 73 73
Syndecan-4/PI-4-5-P2/PKC alpha -0.013 0.022 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.095 0.27 -9999 0 -0.61 67 67
MMP9 -0.11 0.22 -9999 0 -0.46 100 100
Rac1/GTP 0.03 0.02 -9999 0 -0.31 1 1
cytoskeleton organization -0.09 0.25 -9999 0 -0.58 67 67
GIPC1 0.013 0.018 -9999 0 -0.34 1 1
Syndecan-4/TFPI -0.12 0.3 -9999 0 -0.65 70 70
Endothelins

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
AKT1 -0.041 0.25 0.28 25 -0.6 44 69
PTK2B 0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.031 0.25 -10000 0 -0.72 30 30
EDN1 -0.024 0.17 -10000 0 -0.46 33 33
EDN3 -0.006 0.062 -10000 0 -0.34 12 12
EDN2 -0.067 0.19 -10000 0 -0.49 58 58
HRAS/GDP -0.032 0.22 -10000 0 -0.58 35 35
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.041 0.21 -10000 0 -0.51 42 42
ADCY4 -0.067 0.23 -10000 0 -0.5 62 62
ADCY5 -0.11 0.27 -10000 0 -0.52 87 87
ADCY6 -0.063 0.22 -10000 0 -0.5 58 58
ADCY7 -0.065 0.22 -10000 0 -0.51 55 55
ADCY1 -0.14 0.27 -10000 0 -0.55 83 83
ADCY2 -0.072 0.22 -10000 0 -0.49 63 63
ADCY3 -0.066 0.22 -10000 0 -0.51 55 55
ADCY8 -0.089 0.23 -10000 0 -0.5 68 68
ADCY9 -0.065 0.22 -10000 0 -0.49 60 60
arachidonic acid secretion -0.046 0.25 -10000 0 -0.57 51 51
ETB receptor/Endothelin-1/Gq/GTP -0.026 0.16 -10000 0 -0.45 28 28
GNAO1 -0.15 0.27 -10000 0 -0.56 108 108
HRAS 0.012 0.026 -10000 0 -0.34 2 2
ETA receptor/Endothelin-1/G12/GTP -0.042 0.24 0.38 26 -0.56 44 70
ETA receptor/Endothelin-1/Gs/GTP -0.071 0.25 0.35 25 -0.51 63 88
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.082 0.33 -10000 0 -0.71 65 65
EDNRB -0.007 0.11 -10000 0 -0.63 11 11
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.3 -10000 0 -0.72 52 52
CYSLTR1 -0.057 0.28 -10000 0 -0.73 43 43
SLC9A1 -0.031 0.13 0.2 25 -0.34 30 55
mol:GDP -0.042 0.24 -10000 0 -0.61 38 38
SLC9A3 -0.041 0.22 -10000 0 -0.69 26 26
RAF1 -0.046 0.24 -10000 0 -0.57 43 43
JUN -0.028 0.25 -10000 0 -0.68 32 32
JAK2 -0.043 0.25 0.28 23 -0.59 46 69
mol:IP3 -0.044 0.21 -10000 0 -0.55 37 37
ETA receptor/Endothelin-1 -0.063 0.3 0.45 26 -0.68 46 72
PLCB1 -0.024 0.15 -10000 0 -0.62 22 22
PLCB2 -0.007 0.11 -10000 0 -0.55 14 14
ETA receptor/Endothelin-3 -0.03 0.15 -10000 0 -0.53 21 21
FOS -0.066 0.31 -10000 0 -0.87 40 40
Gai/GDP -0.17 0.33 -10000 0 -0.75 81 81
CRK 0.013 0.019 -10000 0 -0.34 1 1
mol:Ca ++ -0.074 0.3 -10000 0 -0.74 48 48
BCAR1 0.014 0.001 -10000 0 -10000 0 0
PRKCB1 -0.042 0.2 -10000 0 -0.53 37 37
GNAQ 0.014 0.034 -10000 0 -0.63 1 1
GNAZ -0.086 0.22 -10000 0 -0.55 66 66
GNAL -0.049 0.17 -10000 0 -0.46 50 50
Gs family/GDP -0.11 0.2 -10000 0 -0.54 48 48
ETA receptor/Endothelin-1/Gq/GTP -0.033 0.2 -10000 0 -0.49 40 40
MAPK14 -0.024 0.16 -10000 0 -0.45 26 26
TRPC6 -0.036 0.27 -10000 0 -0.78 29 29
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.007 0.067 -10000 0 -0.63 4 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.16 -10000 0 -0.44 33 33
ETB receptor/Endothelin-2 -0.053 0.16 -10000 0 -0.38 67 67
ETB receptor/Endothelin-3 -0.009 0.092 -10000 0 -0.47 11 11
ETB receptor/Endothelin-1 -0.021 0.16 -10000 0 -0.44 34 34
MAPK3 -0.062 0.3 -10000 0 -0.76 45 45
MAPK1 -0.062 0.3 -10000 0 -0.76 45 45
Rac1/GDP -0.03 0.22 -10000 0 -0.59 34 34
cAMP biosynthetic process -0.098 0.25 -10000 0 -0.55 66 66
MAPK8 -0.047 0.28 -10000 0 -0.76 37 37
SRC -0.021 0.14 -10000 0 -0.6 21 21
ETB receptor/Endothelin-1/Gi/GTP -0.084 0.17 -10000 0 -0.4 56 56
p130Cas/CRK/Src/PYK2 -0.027 0.24 -10000 0 -0.65 32 32
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.03 0.22 -10000 0 -0.6 32 32
COL1A2 -0.076 0.35 -10000 0 -0.87 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.069 0.2 -10000 0 -0.5 52 52
mol:DAG -0.044 0.21 -10000 0 -0.55 37 37
MAP2K2 -0.05 0.26 -10000 0 -0.63 46 46
MAP2K1 -0.049 0.26 -10000 0 -0.63 46 46
EDNRA -0.027 0.2 -10000 0 -0.6 28 28
positive regulation of muscle contraction -0.028 0.22 -10000 0 -0.57 37 37
Gq family/GDP -0.099 0.21 -10000 0 -0.61 39 39
HRAS/GTP -0.045 0.23 -10000 0 -0.55 42 42
PRKCH -0.036 0.2 -10000 0 -0.56 33 33
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.036 0.2 -10000 0 -0.55 33 33
PRKCB -0.056 0.24 -10000 0 -0.58 43 43
PRKCE -0.04 0.21 -10000 0 -0.56 35 35
PRKCD -0.036 0.2 -10000 0 -0.55 33 33
PRKCG -0.044 0.2 -10000 0 -0.54 36 36
regulation of vascular smooth muscle contraction -0.082 0.36 -10000 0 -1 40 40
PRKCQ -0.057 0.23 -10000 0 -0.59 42 42
PLA2G4A -0.055 0.28 -10000 0 -0.63 51 51
GNA14 -0.026 0.16 -10000 0 -0.62 24 24
GNA15 -0.001 0.093 -10000 0 -0.49 12 12
GNA12 0.014 0 -10000 0 -10000 0 0
GNA11 -0.026 0.16 -10000 0 -0.63 24 24
Rac1/GTP -0.043 0.24 0.38 26 -0.56 44 70
MMP1 -0.076 0.3 0.33 1 -0.68 54 55
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR -0.16 0.26 -9999 0 -0.51 120 120
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.21 -9999 0 -0.42 125 125
CaM/Ca2+ 0.011 0 -9999 0 -10000 0 0
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.14 0.19 -9999 0 -0.38 125 125
IQGAP1/CaM 0.019 0.025 -9999 0 -0.22 4 4
DAB1 -0.083 0.22 -9999 0 -0.54 64 64
IQGAP1 0.01 0.037 -9999 0 -0.34 4 4
PLA2G7 -0.025 0.14 -9999 0 -0.45 31 31
CALM1 0.014 0 -9999 0 -10000 0 0
DYNLT1 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.016 0.1 -9999 0 -0.46 9 9
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.014 0 -9999 0 -10000 0 0
CDK5R1 0.004 0.079 -9999 0 -0.55 7 7
LIS1/Poliovirus Protein 3A 0.017 0 -9999 0 -10000 0 0
CDK5R2 -0.006 0.056 -9999 0 -0.34 10 10
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.28 0.28 -9999 0 -0.52 193 193
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.09 0.16 -9999 0 -0.44 24 24
MAP1B -0.006 0.037 -9999 0 -0.33 4 4
RAC1 0.021 0.009 -9999 0 -10000 0 0
p35/CDK5 -0.11 0.18 -9999 0 -0.33 128 128
RELN -0.23 0.3 -9999 0 -0.57 157 157
PAFAH/LIS1 0.004 0.085 -9999 0 -0.39 12 12
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.088 0.11 -9999 0 -0.4 11 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.24 -9999 0 -0.46 117 117
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.1 0.17 -9999 0 -0.48 24 24
LIS1/IQGAP1 0.026 0.021 -9999 0 -10000 0 0
RHOA 0.021 0.009 -9999 0 -10000 0 0
PAFAH1B1 0.023 0 -9999 0 -10000 0 0
PAFAH1B3 -0.008 0.1 -9999 0 -0.45 18 18
PAFAH1B2 -0.001 0.099 -9999 0 -0.63 9 9
MAP1B/LIS1/Dynein heavy chain 0.022 0.026 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.081 0.16 -9999 0 -0.42 24 24
LRP8 -0.038 0.14 -9999 0 -0.4 47 47
NDEL1/Katanin 60 -0.09 0.16 -9999 0 -0.44 24 24
P39/CDK5 -0.12 0.18 -9999 0 -0.33 125 125
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.12 0.18 -9999 0 -0.35 125 125
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0 -9999 0 -10000 0 0
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.23 0.25 -9999 0 -0.44 193 193
RELN/VLDLR -0.23 0.25 -9999 0 -0.46 175 175
CDC42 0.021 0.009 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.092 0.36 -9999 0 -1.2 35 35
MKNK1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.015 0.11 -9999 0 -0.3 42 42
ATF2/c-Jun -0.01 0.13 -9999 0 -0.84 4 4
MAPK11 -0.024 0.13 -9999 0 -0.32 50 50
MITF -0.019 0.15 -9999 0 -0.37 45 45
MAPKAPK5 -0.012 0.14 -9999 0 -0.36 44 44
KRT8 -0.014 0.14 -9999 0 -0.36 46 46
MAPKAPK3 0.013 0.033 -9999 0 -0.63 1 1
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.026 0.17 -9999 0 -0.46 45 45
CEBPB -0.012 0.14 -9999 0 -0.36 44 44
SLC9A1 -0.014 0.14 -9999 0 -0.36 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.024 0.16 -9999 0 -0.36 59 59
p38alpha-beta/MNK1 -0.008 0.14 -9999 0 -0.36 44 44
JUN -0.01 0.13 -9999 0 -0.83 4 4
PPARGC1A -0.065 0.2 -9999 0 -0.39 82 82
USF1 -0.012 0.14 -9999 0 -0.36 44 44
RAB5/GDP/GDI1 -0.034 0.087 -9999 0 -0.39 6 6
NOS2 -0.042 0.24 -9999 0 -1 14 14
DDIT3 -0.014 0.14 -9999 0 -0.36 44 44
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.004 0.12 -9999 0 -0.43 8 8
p38alpha-beta/HBP1 -0.008 0.14 -9999 0 -0.36 44 44
CREB1 -0.016 0.14 -9999 0 -0.38 44 44
RAB5/GDP 0.011 0 -9999 0 -10000 0 0
EIF4E -0.005 0.12 -9999 0 -0.49 6 6
RPS6KA4 -0.012 0.14 -9999 0 -0.36 44 44
PLA2G4A -0.037 0.17 -9999 0 -0.48 31 31
GDI1 -0.012 0.14 -9999 0 -0.36 44 44
TP53 -0.032 0.18 -9999 0 -0.47 45 45
RPS6KA5 -0.025 0.15 -9999 0 -0.35 56 56
ESR1 -0.097 0.22 -9999 0 -0.42 95 95
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.014 0.14 -9999 0 -0.36 45 45
MEF2A -0.015 0.14 -9999 0 -0.37 45 45
EIF4EBP1 -0.016 0.14 -9999 0 -0.38 44 44
KRT19 -0.14 0.24 -9999 0 -0.43 113 113
ELK4 -0.014 0.14 -9999 0 -0.37 44 44
ATF6 -0.013 0.14 -9999 0 -0.36 45 45
ATF1 -0.016 0.14 -9999 0 -0.38 44 44
p38alpha-beta/MAPKAPK2 -0.008 0.14 -9999 0 -0.36 44 44
p38alpha-beta/MAPKAPK3 -0.009 0.14 -9999 0 -0.36 45 45
Glypican 2 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
MDK -0.059 0.18 -9999 0 -0.48 55 55
GPC2 -0.007 0.098 -9999 0 -0.42 18 18
GPC2/Midkine -0.047 0.15 -9999 0 -0.47 34 34
neuron projection morphogenesis -0.047 0.15 -9999 0 -0.47 34 34
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.069 -10000 0 -0.52 6 6
CDKN2C 0.01 0.053 -10000 0 -0.36 7 7
CDKN2A -0.064 0.2 -10000 0 -0.54 51 51
CCND2 0.015 0.071 0.2 38 -0.15 1 39
RB1 -0.004 0.081 -10000 0 -0.22 37 37
CDK4 0.027 0.079 0.24 39 -10000 0 39
CDK6 0.007 0.091 0.23 36 -0.17 31 67
G1/S progression 0.004 0.08 0.22 37 -10000 0 37
Thromboxane A2 receptor signaling

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
TGM2 -0.004 0.098 -10000 0 -0.5 13 13
GNB1/GNG2 -0.052 0.078 -10000 0 -0.19 79 79
AKT1 -0.014 0.11 -10000 0 -0.21 55 55
EGF -0.077 0.16 -10000 0 -0.36 84 84
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.002 0.11 -10000 0 -0.44 10 10
mol:Ca2+ -0.035 0.16 -10000 0 -0.31 80 80
LYN 0 0.11 -10000 0 -0.46 9 9
RhoA/GTP -0.03 0.051 -10000 0 -0.14 11 11
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.043 0.18 -10000 0 -0.35 79 79
GNG2 0.007 0.063 -10000 0 -0.52 5 5
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.018 0.14 -10000 0 -0.42 32 32
G beta5/gamma2 -0.068 0.1 -10000 0 -0.25 81 81
PRKCH -0.043 0.18 -10000 0 -0.36 78 78
DNM1 -0.057 0.18 -10000 0 -0.46 56 56
TXA2/TP beta/beta Arrestin3 -0.027 0.063 -10000 0 -0.26 20 20
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.019 0.14 -10000 0 -0.54 22 22
G12 family/GTP -0.076 0.12 -10000 0 -0.3 78 78
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 -0.025 0.13 -10000 0 -0.44 32 32
RhoA/GTP/ROCK1 0.019 0.001 -10000 0 -10000 0 0
mol:GDP 0.027 0.13 0.35 29 -10000 0 29
mol:NADP 0.005 0.071 -10000 0 -0.54 6 6
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.035 0.16 -10000 0 -0.53 33 33
mol:IP3 -0.05 0.19 -10000 0 -0.39 80 80
cell morphogenesis 0.019 0.001 -10000 0 -10000 0 0
PLCB2 -0.08 0.25 -10000 0 -0.53 80 80
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.035 0.13 -10000 0 -0.36 29 29
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.005 0.12 -10000 0 -0.45 15 15
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.033 0.17 -10000 0 -0.61 28 28
PRKCB1 -0.051 0.19 -10000 0 -0.38 79 79
GNAQ 0.013 0.033 -10000 0 -0.63 1 1
mol:L-citrulline 0.005 0.071 -10000 0 -0.54 6 6
TXA2/TXA2-R family -0.079 0.25 -10000 0 -0.54 78 78
LCK -0.019 0.14 -10000 0 -0.42 25 25
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.026 0.097 -10000 0 -0.55 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.021 0.038 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.007 0.1 -10000 0 -0.54 5 5
MAPK14 -0.017 0.12 -10000 0 -0.23 78 78
TGM2/GTP -0.058 0.21 -10000 0 -0.44 80 80
MAPK11 -0.02 0.12 -10000 0 -0.23 78 78
ARHGEF1 -0.01 0.095 -10000 0 -0.18 75 75
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.049 0.19 -10000 0 -0.39 78 78
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.03 0.15 -10000 0 -0.29 77 77
cAMP biosynthetic process -0.048 0.18 -10000 0 -0.36 80 80
Gq family/GTP/EBP50 -0.012 0.11 -10000 0 -0.26 52 52
actin cytoskeleton reorganization 0.019 0.001 -10000 0 -10000 0 0
SRC -0.014 0.13 -10000 0 -0.45 17 17
GNB5 0.01 0.046 -10000 0 -0.41 4 4
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.017 0.11 -10000 0 -0.3 32 32
VCAM1 -0.046 0.17 -10000 0 -0.36 77 77
TP beta/Gq family/GDP/G beta5/gamma2 -0.018 0.14 -10000 0 -0.42 32 32
platelet activation -0.025 0.16 -10000 0 -0.3 79 79
PGI2/IP -0.025 0.12 -10000 0 -0.46 28 28
PRKACA -0.018 0.12 -10000 0 -0.33 39 39
Gq family/GDP/G beta5/gamma2 -0.019 0.13 -10000 0 -0.39 32 32
TXA2/TP beta/beta Arrestin2 -0.043 0.13 -10000 0 -0.56 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.012 0.12 -10000 0 -0.32 40 40
mol:DAG -0.059 0.21 -10000 0 -0.44 79 79
EGFR -0.007 0.11 -10000 0 -0.59 13 13
TXA2/TP alpha -0.071 0.24 -10000 0 -0.49 80 80
Gq family/GTP -0.031 0.095 -10000 0 -0.25 52 52
YES1 0.001 0.1 -10000 0 -0.43 9 9
GNAI2/GTP -0.042 0.1 -10000 0 -0.45 12 12
PGD2/DP -0.014 0.1 -10000 0 -0.4 22 22
SLC9A3R1 0.013 0.033 -10000 0 -0.63 1 1
FYN 0.001 0.1 -10000 0 -0.43 9 9
mol:NO 0.005 0.071 -10000 0 -0.54 6 6
GNA15 -0.002 0.092 -10000 0 -0.49 12 12
PGK/cGMP -0.017 0.12 -10000 0 -0.41 25 25
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0 0.13 -10000 0 -0.58 10 10
NOS3 0.005 0.071 -10000 0 -0.54 6 6
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.042 0.18 -10000 0 -0.36 78 78
PRKCB -0.053 0.19 -10000 0 -0.38 81 81
PRKCE -0.044 0.18 -10000 0 -0.36 78 78
PRKCD -0.049 0.19 -10000 0 -0.39 78 78
PRKCG -0.053 0.19 -10000 0 -0.39 79 79
muscle contraction -0.069 0.24 -10000 0 -0.5 78 78
PRKCZ -0.05 0.18 -10000 0 -0.36 81 81
ARR3 -0.001 0.031 -10000 0 -0.34 3 3
TXA2/TP beta -0.019 0.13 -10000 0 -0.45 17 17
PRKCQ -0.054 0.19 -10000 0 -0.39 82 82
MAPKKK cascade -0.067 0.23 -10000 0 -0.47 80 80
SELE -0.05 0.18 -10000 0 -0.37 77 77
TP beta/GNAI2/GDP/G beta/gamma 0.008 0.11 -10000 0 -0.56 7 7
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.027 0.16 -10000 0 -0.62 24 24
chemotaxis -0.094 0.28 -10000 0 -0.62 77 77
GNA12 0.014 0 -10000 0 -10000 0 0
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 -0.028 0.16 -10000 0 -0.63 24 24
Rac1/GTP 0.009 0.005 -10000 0 -10000 0 0
IL23-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
CCL2 -0.24 0.47 -10000 0 -1.1 60 60
IL23A -0.23 0.47 -10000 0 -1.2 48 48
NF kappa B1 p50/RelA/I kappa B alpha -0.26 0.39 -10000 0 -1.1 50 50
positive regulation of T cell mediated cytotoxicity -0.24 0.5 -10000 0 -1.2 50 50
ITGA3 -0.22 0.44 -10000 0 -1.1 49 49
IL17F -0.13 0.3 -10000 0 -0.7 44 44
IL12B 0 0.051 -10000 0 -0.37 4 4
STAT1 (dimer) -0.23 0.47 -10000 0 -1.2 51 51
CD4 -0.21 0.44 -10000 0 -1.1 47 47
IL23 -0.23 0.45 -10000 0 -1.2 48 48
IL23R -0.02 0.091 -10000 0 -10000 0 0
IL1B -0.25 0.51 -10000 0 -1.3 53 53
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.42 -10000 0 -1.1 45 45
TYK2 0.01 0.021 -10000 0 -10000 0 0
STAT4 -0.035 0.16 -10000 0 -0.56 32 32
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.02 0.14 -10000 0 -0.59 21 21
IL12RB1 -0.032 0.15 -10000 0 -0.53 29 29
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
IL12Rbeta1/TYK2 -0.018 0.12 -10000 0 -0.39 29 29
IL23R/JAK2 -0.022 0.11 -10000 0 -0.52 1 1
positive regulation of chronic inflammatory response -0.24 0.5 -10000 0 -1.2 50 50
natural killer cell activation 0.002 0.008 0.035 3 -10000 0 3
JAK2 0.011 0.052 -10000 0 -0.47 3 3
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.43 -10000 0 -1.1 48 48
ALOX12B -0.21 0.42 -10000 0 -1.1 45 45
CXCL1 -0.42 0.62 -10000 0 -1.3 119 119
T cell proliferation -0.24 0.5 -10000 0 -1.2 50 50
NFKBIA 0.011 0.039 -10000 0 -0.49 2 2
IL17A -0.088 0.25 -10000 0 -0.57 31 31
PI3K -0.27 0.41 -10000 0 -1.1 50 50
IFNG -0.015 0.037 0.084 1 -0.1 15 16
STAT3 (dimer) -0.26 0.38 -10000 0 -1.1 48 48
IL18R1 -0.058 0.2 -10000 0 -0.62 42 42
IL23/IL23R/JAK2/TYK2/SOCS3 -0.12 0.3 -10000 0 -0.76 33 33
IL18/IL18R -0.059 0.21 -10000 0 -0.48 61 61
macrophage activation -0.015 0.017 -10000 0 -0.044 45 45
TNF -0.24 0.5 -10000 0 -1.3 51 51
STAT3/STAT4 -0.28 0.42 -10000 0 -1.2 51 51
STAT4 (dimer) -0.25 0.49 -10000 0 -1.2 51 51
IL18 -0.023 0.14 -10000 0 -0.54 25 25
IL19 -0.21 0.42 -10000 0 -1.1 47 47
STAT5A (dimer) -0.23 0.47 -10000 0 -1.2 49 49
STAT1 0.009 0.041 -10000 0 -0.34 5 5
SOCS3 -0.027 0.14 -10000 0 -0.47 32 32
CXCL9 -0.24 0.48 -10000 0 -1.2 54 54
MPO -0.21 0.43 -10000 0 -1.1 46 46
positive regulation of humoral immune response -0.24 0.5 -10000 0 -1.2 50 50
IL23/IL23R/JAK2/TYK2 -0.26 0.54 -10000 0 -1.3 50 50
IL6 -0.26 0.5 -10000 0 -1.2 65 65
STAT5A 0.011 0.042 -10000 0 -0.44 3 3
IL2 0.004 0.021 -10000 0 -0.36 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 0.035 3 -10000 0 3
CD3E -0.23 0.48 -10000 0 -1.2 54 54
keratinocyte proliferation -0.24 0.5 -10000 0 -1.2 50 50
NOS2 -0.23 0.46 -10000 0 -1.1 54 54
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.088 0.19 -10000 0 -0.54 47 47
FYN -0.075 0.28 -10000 0 -0.71 49 49
LAT/GRAP2/SLP76 -0.095 0.22 -10000 0 -0.58 53 53
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.038 0.18 -10000 0 -0.44 51 51
B2M 0.014 0.004 -10000 0 -10000 0 0
IKBKG -0.023 0.049 -10000 0 -0.15 34 34
MAP3K8 -0.012 0.12 -10000 0 -0.56 17 17
mol:Ca2+ -0.023 0.037 -10000 0 -0.091 62 62
integrin-mediated signaling pathway 0.014 0.048 -10000 0 -0.4 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.072 0.27 -10000 0 -0.67 52 52
TRPV6 -0.12 0.23 -10000 0 -0.51 87 87
CD28 -0.012 0.12 -10000 0 -0.58 16 16
SHC1 -0.074 0.27 -10000 0 -0.69 50 50
receptor internalization -0.08 0.28 -10000 0 -0.68 52 52
PRF1 -0.064 0.26 -10000 0 -0.82 30 30
KRAS 0.013 0.018 -10000 0 -0.34 1 1
GRB2 0.014 0 -10000 0 -10000 0 0
COT/AKT1 -0.03 0.16 -10000 0 -0.37 48 48
LAT -0.076 0.28 -10000 0 -0.7 49 49
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.06 0.19 -10000 0 -0.49 55 55
CD3E -0.036 0.17 -10000 0 -0.55 34 34
CD3G -0.055 0.18 -10000 0 -0.47 53 53
RASGRP2 -0.001 0.032 -10000 0 -0.18 7 7
RASGRP1 -0.038 0.2 -10000 0 -0.47 52 52
HLA-A 0.01 0.043 -10000 0 -0.44 3 3
RASSF5 0.006 0.074 -10000 0 -0.63 5 5
RAP1A/GTP/RAPL 0.014 0.048 -10000 0 -0.4 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.061 -10000 0 -0.13 34 34
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.045 0.086 -10000 0 -0.26 39 39
PRKCA -0.04 0.1 -10000 0 -0.28 41 41
GRAP2 -0.033 0.16 -10000 0 -0.53 32 32
mol:IP3 -0.041 0.19 0.22 53 -0.44 47 100
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.079 0.27 -10000 0 -0.66 49 49
ORAI1 0.071 0.12 0.28 87 -10000 0 87
CSK -0.078 0.28 -10000 0 -0.72 49 49
B7 family/CD28 -0.09 0.29 -10000 0 -0.68 55 55
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.099 0.33 -10000 0 -0.83 50 50
PTPN6 -0.081 0.28 -10000 0 -0.72 49 49
VAV1 -0.087 0.3 -10000 0 -0.73 53 53
Monovalent TCR/CD3 -0.063 0.22 -10000 0 -0.49 57 57
CBL 0.011 0.047 -10000 0 -0.63 2 2
LCK -0.089 0.31 -10000 0 -0.78 50 50
PAG1 -0.084 0.29 -10000 0 -0.71 53 53
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.099 0.32 -10000 0 -0.82 49 49
CD80 -0.033 0.16 -10000 0 -0.51 33 33
CD86 -0.012 0.12 -10000 0 -0.55 17 17
PDK1/CARD11/BCL10/MALT1 -0.055 0.1 -10000 0 -0.31 42 42
HRAS 0.012 0.026 -10000 0 -0.34 2 2
GO:0035030 -0.071 0.23 -10000 0 -0.55 55 55
CD8A -0.055 0.18 -10000 0 -0.46 55 55
CD8B -0.087 0.21 -10000 0 -0.46 80 80
PTPRC -0.026 0.14 -10000 0 -0.51 28 28
PDK1/PKC theta -0.05 0.23 -10000 0 -0.56 51 51
CSK/PAG1 -0.077 0.28 -10000 0 -0.72 48 48
SOS1 0.013 0.018 -10000 0 -0.34 1 1
peptide-MHC class I 0.018 0.032 -10000 0 -0.47 1 1
GRAP2/SLP76 -0.11 0.26 -10000 0 -0.68 54 54
STIM1 0.036 0.06 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.08 -10000 0 -0.18 34 34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.089 0.31 -10000 0 -0.75 51 51
mol:DAG -0.058 0.15 -10000 0 -0.39 51 51
RAP1A/GDP 0.006 0.027 -10000 0 -0.064 8 8
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 0.002 0.084 -10000 0 -0.51 9 9
cytotoxic T cell degranulation -0.06 0.25 -10000 0 -0.78 30 30
RAP1A/GTP -0.003 0.01 -10000 0 -0.069 4 4
mol:PI-3-4-5-P3 -0.052 0.22 -10000 0 -0.53 52 52
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.066 0.24 0.24 48 -0.58 49 97
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.017 0.12 -10000 0 -0.48 23 23
GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
LAT/GRAP2/SLP76/VAV1 -0.096 0.22 -10000 0 -0.57 53 53
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.033 -10000 0 -0.63 1 1
CD8 heterodimer -0.094 0.23 -10000 0 -0.52 73 73
CARD11 -0.037 0.16 -10000 0 -0.48 39 39
PRKCB -0.05 0.13 -10000 0 -0.35 45 45
PRKCE -0.043 0.1 -10000 0 -0.28 44 44
PRKCQ -0.067 0.26 -10000 0 -0.65 52 52
LCP2 0.005 0.071 -10000 0 -0.54 6 6
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.028 0.16 -10000 0 -0.37 51 51
IKK complex 0.017 0.059 -10000 0 -0.12 32 32
RAS family/GDP -0.005 0.009 -10000 0 -10000 0 0
MAP3K14 -0.015 0.12 -10000 0 -0.28 42 42
PDPK1 -0.033 0.18 -10000 0 -0.42 52 52
TCR/CD3/MHC I/CD8/Fyn -0.11 0.34 -10000 0 -0.83 55 55
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.079 0.2 -10000 0 -0.52 55 55
NFATC2 -0.12 0.3 -10000 0 -0.62 76 76
NFATC3 0.001 0.08 -10000 0 -0.28 4 4
CD40LG -0.25 0.45 -10000 0 -1.1 63 63
ITCH 0.045 0.034 -10000 0 -10000 0 0
CBLB 0.045 0.034 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.34 0.48 -10000 0 -1 101 101
JUNB 0 0.094 -10000 0 -0.63 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.035 -10000 0 -0.3 5 5
T cell anergy 0.015 0.074 -10000 0 -0.46 5 5
TLE4 -0.076 0.24 -10000 0 -0.65 31 31
Jun/NFAT1-c-4/p21SNFT -0.17 0.4 -10000 0 -1.1 47 47
AP-1/NFAT1-c-4 -0.27 0.54 -10000 0 -1.3 60 60
IKZF1 -0.083 0.26 -10000 0 -0.72 31 31
T-helper 2 cell differentiation -0.17 0.32 -10000 0 -0.84 52 52
AP-1/NFAT1 -0.12 0.25 -10000 0 -0.55 66 66
CALM1 0.027 0.022 -10000 0 -10000 0 0
EGR2 -0.17 0.5 -10000 0 -1.5 38 38
EGR3 -0.13 0.4 -10000 0 -1.1 40 40
NFAT1/FOXP3 -0.15 0.29 -10000 0 -0.67 65 65
EGR1 -0.028 0.16 -10000 0 -0.57 27 27
JUN 0 0.056 -10000 0 -0.7 2 2
EGR4 -0.003 0.064 -10000 0 -0.35 12 12
mol:Ca2+ 0.013 0.023 -10000 0 -10000 0 0
GBP3 -0.13 0.31 -10000 0 -0.76 57 57
FOSL1 -0.008 0.097 -10000 0 -0.4 20 20
NFAT1-c-4/MAF/IRF4 -0.17 0.41 -10000 0 -1.1 50 50
DGKA -0.081 0.25 -10000 0 -0.69 31 31
CREM 0.014 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.15 0.39 -10000 0 -1.1 44 44
CTLA4 -0.18 0.34 -10000 0 -0.76 70 70
NFAT1-c-4 (dimer)/EGR1 -0.16 0.42 -10000 0 -1.1 47 47
NFAT1-c-4 (dimer)/EGR4 -0.15 0.39 -10000 0 -1.1 45 45
FOS -0.07 0.19 -10000 0 -0.53 51 51
IFNG -0.15 0.29 -10000 0 -0.83 33 33
T cell activation -0.11 0.25 -10000 0 -0.75 28 28
MAF 0.013 0.033 -10000 0 -0.63 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.094 0.32 0.92 34 -10000 0 34
TNF -0.16 0.39 -10000 0 -1 49 49
FASLG -0.22 0.55 -10000 0 -1.5 52 52
TBX21 -0.009 0.12 -10000 0 -0.54 16 16
BATF3 -0.011 0.11 -10000 0 -0.48 19 19
PRKCQ -0.028 0.15 -10000 0 -0.55 28 28
PTPN1 -0.069 0.22 -10000 0 -0.63 26 26
NFAT1-c-4/ICER1 -0.14 0.39 -10000 0 -1.1 44 44
GATA3 -0.039 0.17 -10000 0 -0.55 35 35
T-helper 1 cell differentiation -0.14 0.29 -10000 0 -0.81 33 33
IL2RA -0.3 0.4 -10000 0 -0.92 88 88
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.071 0.22 -10000 0 -0.67 23 23
E2F1 -0.002 0.1 -10000 0 -0.45 18 18
PPARG 0.006 0.069 -10000 0 -0.57 5 5
SLC3A2 -0.069 0.22 -10000 0 -0.63 26 26
IRF4 -0.077 0.2 -10000 0 -0.48 69 69
PTGS2 -0.26 0.45 -10000 0 -1.1 68 68
CSF2 -0.23 0.41 -10000 0 -1 61 61
JunB/Fra1/NFAT1-c-4 -0.14 0.39 -10000 0 -1.1 43 43
IL4 -0.18 0.34 -10000 0 -0.9 51 51
IL5 -0.23 0.41 -10000 0 -1 60 60
IL2 -0.11 0.25 -10000 0 -0.76 28 28
IL3 -0.048 0.068 -10000 0 -0.88 1 1
RNF128 0.038 0.086 -10000 0 -0.7 5 5
NFATC1 -0.095 0.33 -10000 0 -0.94 33 33
CDK4 0.075 0.2 0.61 20 -10000 0 20
PTPRK -0.073 0.23 -10000 0 -0.65 28 28
IL8 -0.31 0.47 -10000 0 -1 78 78
POU2F1 0.013 0.038 -10000 0 -0.49 2 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.078 0.17 0.47 49 -10000 0 49
KIRREL -0.097 0.22 -10000 0 -0.52 76 76
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.079 0.17 -10000 0 -0.48 49 49
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.048 0.13 -10000 0 -0.36 48 48
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.037 0.13 -10000 0 -0.33 53 53
FYN -0.048 0.12 -10000 0 -0.34 49 49
mol:Ca2+ -0.049 0.13 -10000 0 -0.35 48 48
mol:DAG -0.048 0.13 -10000 0 -0.36 48 48
NPHS2 -0.014 0.051 -10000 0 -0.35 7 7
mol:IP3 -0.048 0.13 -10000 0 -0.36 48 48
regulation of endocytosis -0.037 0.12 -10000 0 -0.31 48 48
Nephrin/NEPH1/podocin/Cholesterol -0.057 0.13 -10000 0 -0.36 48 48
establishment of cell polarity -0.078 0.17 -10000 0 -0.47 49 49
Nephrin/NEPH1/podocin/NCK1-2 -0.05 0.15 -10000 0 -0.36 57 57
Nephrin/NEPH1/beta Arrestin2 -0.036 0.12 -10000 0 -0.32 48 48
NPHS1 -0.022 0.083 -10000 0 -0.35 21 21
Nephrin/NEPH1/podocin -0.049 0.12 -10000 0 -0.34 49 49
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.011 0.047 -10000 0 -0.63 2 2
NCK2 -0.01 0.11 -10000 0 -0.49 18 18
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.048 0.13 -10000 0 -0.36 48 48
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.048 0.13 -10000 0 -0.36 48 48
GRB2 0.014 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.052 0.13 -10000 0 -0.34 57 57
cytoskeleton organization -0.039 0.14 -10000 0 -0.37 49 49
Nephrin/NEPH1 -0.054 0.12 -10000 0 -0.35 47 47
Nephrin/NEPH1/ZO-1 -0.052 0.14 -10000 0 -0.38 47 47
S1P1 pathway

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.002 0.093 -9999 0 -0.45 15 15
PDGFRB 0 0.083 -9999 0 -0.51 9 9
SPHK1 -0.11 0.26 -9999 0 -0.9 35 35
mol:S1P -0.11 0.24 -9999 0 -0.75 42 42
S1P1/S1P/Gi -0.14 0.24 -9999 0 -0.51 82 82
GNAO1 -0.15 0.27 -9999 0 -0.56 108 108
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.22 -9999 0 -0.53 55 55
PLCG1 -0.12 0.23 -9999 0 -0.53 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0 0.083 -9999 0 -0.5 9 9
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.012 0.005 -9999 0 -10000 0 0
GNAI1 0.005 0.067 -9999 0 -0.64 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.001 0.079 -9999 0 -0.39 14 14
S1P1/S1P -0.08 0.2 -9999 0 -0.53 52 52
negative regulation of cAMP metabolic process -0.13 0.24 -9999 0 -0.49 82 82
MAPK3 -0.14 0.27 -9999 0 -0.63 62 62
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
KDR -0.01 0.12 -9999 0 -0.61 14 14
PLCB2 -0.072 0.2 -9999 0 -0.52 49 49
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.08 0.16 -9999 0 -0.46 46 46
receptor internalization -0.089 0.18 -9999 0 -0.49 52 52
PTGS2 -0.16 0.34 -9999 0 -1 42 42
Rac1/GTP -0.08 0.16 -9999 0 -0.45 49 49
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA 0.012 0.034 -9999 0 -0.64 1 1
negative regulation of T cell proliferation -0.13 0.24 -9999 0 -0.49 82 82
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.088 0.22 -9999 0 -0.55 66 66
MAPK1 -0.14 0.27 -9999 0 -0.63 63 63
S1P1/S1P/PDGFB-D/PDGFRB -0.079 0.2 -9999 0 -0.51 53 53
ABCC1 -0.018 0.13 -9999 0 -0.48 23 23
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.058 0.37 -10000 0 -0.94 52 52
NCK1/PAK1/Dok-R -0.069 0.15 -10000 0 -0.43 52 52
NCK1/Dok-R -0.1 0.41 -10000 0 -1.1 52 52
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
mol:beta2-estradiol 0.004 0.054 0.24 17 -10000 0 17
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0.002 -10000 0 -10000 0 0
Rac/GDP 0.011 0 -10000 0 -10000 0 0
F2 -0.025 0.17 0.26 15 -0.62 25 40
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.086 0.38 -10000 0 -1 52 52
FN1 0.013 0.033 -10000 0 -0.63 1 1
PLD2 -0.099 0.43 -10000 0 -1.1 52 52
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.003 0.1 -10000 0 -0.63 10 10
ELK1 -0.076 0.38 -10000 0 -1 52 52
GRB7 -0.011 0.11 -10000 0 -0.48 19 19
PAK1 0.009 0.058 -10000 0 -0.63 3 3
Tie2/Ang1/alpha5/beta1 Integrin -0.093 0.4 -10000 0 -1.1 52 52
CDKN1A -0.035 0.3 -10000 0 -0.71 53 53
ITGA5 0.012 0.026 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.11 0.42 -10000 0 -1.1 52 52
CRK 0.013 0.018 -10000 0 -0.34 1 1
mol:NO -0.022 0.28 -10000 0 -0.68 52 52
PLG -0.13 0.43 -10000 0 -1.2 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.054 0.35 -10000 0 -0.88 52 52
GRB2 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.058 -10000 0 -0.64 3 3
ANGPT2 0.004 0.17 -10000 0 -1.1 4 4
BMX -0.13 0.45 -10000 0 -1.2 52 52
ANGPT1 -0.042 0.3 -10000 0 -1.4 17 17
tube development -0.031 0.3 -10000 0 -0.71 54 54
ANGPT4 -0.003 0.057 -10000 0 -0.34 10 10
response to hypoxia -0.006 0.025 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.11 0.44 -10000 0 -1.2 52 52
alpha5/beta1 Integrin 0.02 0.018 -10000 0 -10000 0 0
FGF2 -0.06 0.18 -10000 0 -0.45 59 59
STAT5A (dimer) -0.048 0.35 -10000 0 -0.82 54 54
mol:L-citrulline -0.022 0.28 -10000 0 -0.68 52 52
AGTR1 -0.017 0.14 -10000 0 -0.63 19 19
MAPK14 -0.1 0.45 -10000 0 -1.2 52 52
Tie2/SHP2 -0.097 0.38 -10000 0 -1.2 40 40
TEK -0.11 0.42 -10000 0 -1.3 40 40
RPS6KB1 -0.052 0.35 -10000 0 -0.89 52 52
Angiotensin II/AT1 -0.01 0.11 -10000 0 -0.47 19 19
Tie2/Ang1/GRB2 -0.1 0.44 -10000 0 -1.2 52 52
MAPK3 -0.082 0.39 -10000 0 -1 52 52
MAPK1 -0.083 0.39 -10000 0 -1 52 52
Tie2/Ang1/GRB7 -0.12 0.44 -10000 0 -1.2 53 53
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.12 0.44 -10000 0 -1.2 52 52
PI3K -0.082 0.42 -10000 0 -1.1 52 52
FES -0.11 0.45 -10000 0 -1.2 52 52
Crk/Dok-R -0.1 0.41 -10000 0 -1.1 52 52
Tie2/Ang1/ABIN2 -0.1 0.44 -10000 0 -1.2 52 52
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.043 0.33 -10000 0 -0.82 52 52
STAT5A 0.011 0.042 -10000 0 -0.44 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.052 0.35 -10000 0 -0.89 52 52
Tie2/Ang2 -0.075 0.4 -10000 0 -1 54 54
Tie2/Ang1 -0.12 0.47 -10000 0 -1.2 52 52
FOXO1 -0.043 0.33 -10000 0 -0.82 55 55
ELF1 0.007 0.069 -10000 0 -0.66 3 3
ELF2 -0.1 0.43 -10000 0 -1.1 52 52
mol:Choline -0.092 0.4 -10000 0 -1.1 52 52
cell migration -0.037 0.083 -10000 0 -0.24 52 52
FYN -0.045 0.33 -10000 0 -0.81 54 54
DOK2 0.002 0.083 -10000 0 -0.5 9 9
negative regulation of cell cycle -0.025 0.28 -10000 0 -0.64 53 53
ETS1 0.003 0.087 -10000 0 -0.4 10 10
PXN -0.026 0.29 -10000 0 -0.73 52 52
ITGB1 0.014 0 -10000 0 -10000 0 0
NOS3 -0.035 0.32 -10000 0 -0.79 52 52
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.027 0.15 -10000 0 -0.56 24 24
MAPKKK cascade -0.092 0.4 -10000 0 -1.1 52 52
RASA1 0.002 0.088 -10000 0 -0.63 7 7
Tie2/Ang1/Shc -0.1 0.44 -10000 0 -1.2 52 52
NCK1 0.011 0.047 -10000 0 -0.63 2 2
vasculogenesis -0.012 0.25 -10000 0 -0.61 52 52
mol:Phosphatidic acid -0.092 0.4 -10000 0 -1.1 52 52
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP -0.022 0.28 -10000 0 -0.68 52 52
Rac1/GTP -0.13 0.29 -10000 0 -0.83 52 52
MMP2 -0.13 0.46 -10000 0 -1.2 52 52
Ephrin B reverse signaling

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0.038 -10000 0 -0.49 2 2
EPHB2 -0.095 0.2 -10000 0 -0.43 92 92
EFNB1 -0.031 0.13 -10000 0 -0.46 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.18 -10000 0 -0.41 65 65
Ephrin B2/EPHB1-2 -0.056 0.15 -10000 0 -0.4 43 43
neuron projection morphogenesis -0.098 0.16 -10000 0 -0.39 65 65
Ephrin B1/EPHB1-2/Tiam1 -0.088 0.2 -10000 0 -0.42 74 74
DNM1 -0.057 0.18 -10000 0 -0.46 56 56
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.025 0.16 -10000 0 -0.69 19 19
YES1 -0.053 0.2 -10000 0 -0.92 19 19
Ephrin B1/EPHB1-2/NCK2 -0.085 0.19 -10000 0 -0.41 75 75
PI3K -0.028 0.17 -10000 0 -0.67 22 22
mol:GDP -0.088 0.19 -10000 0 -0.42 74 74
ITGA2B -0.011 0.087 -10000 0 -0.34 24 24
endothelial cell proliferation 0.012 0.049 -10000 0 -0.4 4 4
FYN -0.053 0.2 -10000 0 -0.92 19 19
MAP3K7 -0.035 0.17 -10000 0 -0.73 19 19
FGR -0.054 0.2 -10000 0 -0.92 19 19
TIAM1 -0.015 0.13 -10000 0 -0.53 20 20
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
RGS3 0.013 0.033 -10000 0 -0.63 1 1
cell adhesion -0.054 0.2 -10000 0 -0.76 21 21
LYN -0.054 0.2 -10000 0 -0.92 19 19
Ephrin B1/EPHB1-2/Src Family Kinases -0.053 0.19 -10000 0 -0.87 19 19
Ephrin B1/EPHB1-2 -0.052 0.18 -10000 0 -0.79 19 19
SRC -0.062 0.21 -10000 0 -0.94 19 19
ITGB3 -0.049 0.18 -10000 0 -0.55 41 41
EPHB1 -0.025 0.14 -10000 0 -0.51 27 27
EPHB4 0.005 0.068 -10000 0 -0.47 7 7
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.012 0.049 -10000 0 -0.4 4 4
alphaIIb/beta3 Integrin -0.043 0.15 -10000 0 -0.34 64 64
BLK -0.069 0.21 -10000 0 -0.94 19 19
HCK -0.056 0.2 -10000 0 -0.92 19 19
regulation of stress fiber formation 0.085 0.19 0.41 75 -10000 0 75
MAPK8 -0.039 0.17 -10000 0 -0.65 21 21
Ephrin B1/EPHB1-2/RGS3 -0.074 0.18 -10000 0 -0.39 70 70
endothelial cell migration -0.029 0.15 -10000 0 -0.6 22 22
NCK2 -0.01 0.11 -10000 0 -0.49 18 18
PTPN13 -0.058 0.19 -10000 0 -0.46 57 57
regulation of focal adhesion formation 0.085 0.19 0.41 75 -10000 0 75
chemotaxis 0.074 0.17 0.38 70 -10000 0 70
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
Rac1/GTP -0.1 0.16 -10000 0 -0.4 65 65
angiogenesis -0.052 0.17 -10000 0 -0.78 19 19
LCK -0.063 0.21 -10000 0 -0.92 19 19
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.007 0.082 -10000 0 -0.46 11 11
Necdin/E2F1 -0.03 0.13 -10000 0 -0.47 19 19
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.083 0.21 -10000 0 -0.4 93 93
NGF (dimer)/p75(NTR)/BEX1 -0.13 0.21 -10000 0 -0.45 92 92
NT-4/5 (dimer)/p75(NTR) -0.058 0.15 -10000 0 -0.47 37 37
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.027 0.15 -10000 0 -0.38 47 47
IKBKG 0.013 0.018 -10000 0 -0.34 1 1
BDNF -0.01 0.09 -10000 0 -0.35 23 23
MGDIs/NGR/p75(NTR)/LINGO1 -0.088 0.19 -10000 0 -0.45 66 66
FURIN -0.011 0.12 -10000 0 -0.61 15 15
proBDNF (dimer)/p75(NTR)/Sortilin -0.052 0.16 -10000 0 -0.41 52 52
LINGO1 -0.051 0.15 -10000 0 -0.38 61 61
Sortilin/TRAF6/NRIF -0.011 0.058 -10000 0 -0.58 1 1
proBDNF (dimer) -0.01 0.09 -10000 0 -0.35 23 23
NTRK1 0.002 0.051 -10000 0 -0.34 8 8
RTN4R -0.022 0.15 -10000 0 -0.6 22 22
neuron apoptosis -0.038 0.17 -10000 0 -0.52 21 21
IRAK1 0.014 0 -10000 0 -10000 0 0
SHC1 -0.044 0.16 -10000 0 -0.44 44 44
ARHGDIA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP 0.011 0 -10000 0 -10000 0 0
Gamma Secretase 0.038 0.039 -10000 0 -0.32 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.065 0.2 -10000 0 -0.43 69 69
MAGEH1 -0.03 0.16 -10000 0 -0.62 26 26
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.066 0.2 -10000 0 -0.45 59 59
Mammalian IAPs/DIABLO 0.011 0.085 -10000 0 -0.35 15 15
proNGF (dimer) -0.011 0.12 -10000 0 -0.58 16 16
MAGED1 0.002 0.088 -10000 0 -0.63 7 7
APP -0.011 0.12 -10000 0 -0.61 15 15
NT-4/5 (dimer) -0.004 0.047 -10000 0 -0.34 7 7
ZNF274 0.014 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.029 0.14 -10000 0 -0.37 44 44
NGF -0.011 0.12 -10000 0 -0.58 16 16
cell cycle arrest -0.028 0.16 -10000 0 -0.36 52 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.012 0.12 -10000 0 -0.3 45 45
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.041 0.13 -10000 0 -0.4 38 38
NCSTN 0.013 0.033 -10000 0 -0.63 1 1
mol:GTP -0.044 0.16 -10000 0 -0.44 45 45
PSENEN 0.013 0.018 -10000 0 -0.34 1 1
mol:ceramide -0.042 0.16 -10000 0 -0.4 52 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.018 0.13 -10000 0 -0.47 13 13
p75(NTR)/beta APP -0.063 0.18 -10000 0 -0.49 48 48
BEX1 -0.12 0.23 -10000 0 -0.48 102 102
mol:GDP -0.054 0.16 -10000 0 -0.45 44 44
NGF (dimer) -0.15 0.22 -10000 0 -0.42 132 132
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.071 0.18 -10000 0 -0.4 66 66
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
RAC1/GTP -0.037 0.14 -10000 0 -0.38 44 44
MYD88 0.014 0 -10000 0 -10000 0 0
CHUK 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.044 0.16 -10000 0 -0.44 45 45
RHOB 0.009 0.058 -10000 0 -0.63 3 3
RHOA 0.014 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.077 -10000 0 -0.46 7 7
NT3 (dimer) -0.052 0.18 -10000 0 -0.54 44 44
TP53 -0.035 0.14 -10000 0 -0.33 59 59
PRDM4 -0.042 0.16 -10000 0 -0.4 52 52
BDNF (dimer) -0.16 0.2 -10000 0 -0.41 132 132
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
SORT1 -0.003 0.1 -10000 0 -0.63 10 10
activation of caspase activity -0.085 0.21 -10000 0 -0.4 93 93
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.16 -10000 0 -0.4 53 53
RHOC 0.014 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
MAPK10 -0.041 0.18 -10000 0 -0.55 23 23
DIABLO 0.014 0 -10000 0 -10000 0 0
SMPD2 -0.042 0.16 -10000 0 -0.4 52 52
APH1B 0.009 0.058 -10000 0 -0.63 3 3
APH1A 0.014 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.054 0.18 -10000 0 -0.45 52 52
PSEN1 0.014 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.018 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.092 0.21 -10000 0 -0.51 64 64
MAPK8 -0.038 0.17 -10000 0 -0.52 20 20
MAPK9 -0.02 0.15 -10000 0 -0.39 38 38
APAF1 0.014 0 -10000 0 -10000 0 0
NTF3 -0.052 0.18 -10000 0 -0.54 44 44
NTF4 -0.004 0.047 -10000 0 -0.34 7 7
NDN -0.034 0.14 -10000 0 -0.43 41 41
RAC1/GDP 0.011 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.053 0.12 -10000 0 -0.34 47 47
p75 CTF/Sortilin/TRAF6/NRIF 0.021 0.08 -10000 0 -0.37 14 14
RhoA-B-C/GTP -0.044 0.16 -10000 0 -0.44 45 45
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.029 0.14 -10000 0 -0.34 53 53
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.039 0.15 -10000 0 -0.37 53 53
PRKACB 0.013 0.033 -10000 0 -0.63 1 1
proBDNF (dimer)/p75 ECD -0.001 0.08 -10000 0 -0.27 27 27
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.031 0.15 -10000 0 -0.47 35 35
BIRC2 0.014 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.2 0.21 36 -0.45 50 86
BAD -0.031 0.16 -10000 0 -0.5 22 22
RIPK2 0.014 0 -10000 0 -10000 0 0
NGFR -0.076 0.21 -10000 0 -0.51 64 64
CYCS -0.039 0.16 -10000 0 -0.37 58 58
ADAM17 0.007 0.067 -10000 0 -0.63 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.031 0.15 -10000 0 -0.4 45 45
BCL2L11 -0.031 0.16 -10000 0 -0.5 22 22
BDNF (dimer)/p75(NTR) -0.06 0.17 -10000 0 -0.47 45 45
PI3K -0.035 0.16 -10000 0 -0.41 47 47
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.16 -10000 0 -0.4 52 52
NDNL2 0.014 0 -10000 0 -10000 0 0
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.062 0.18 -10000 0 -0.52 44 44
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.047 0.17 -10000 0 -0.4 58 58
TRAF6 0.013 0.033 -10000 0 -0.63 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.029 0.16 -10000 0 -0.63 25 25
PLG -0.048 0.19 -10000 0 -0.63 36 36
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.047 0.17 -10000 0 -0.42 53 53
SQSTM1 0.009 0.045 -10000 0 -0.34 6 6
NGFRAP1 -0.083 0.23 -10000 0 -0.62 57 57
CASP3 -0.027 0.15 -10000 0 -0.46 22 22
E2F1 -0.008 0.1 -10000 0 -0.45 18 18
CASP9 0.012 0.026 -10000 0 -0.34 2 2
IKK complex -0.046 0.11 -10000 0 -0.46 16 16
NGF (dimer)/TRKA -0.006 0.098 -10000 0 -0.37 23 23
MMP7 -0.2 0.27 -10000 0 -0.51 153 153
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.031 0.16 -10000 0 -0.37 53 53
MMP3 -0.029 0.1 -10000 0 -0.34 37 37
APAF-1/Caspase 9 -0.062 0.12 -10000 0 -0.49 13 13
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.052 0.17 -9999 0 -0.45 49 49
alphaM/beta2 Integrin/GPIbA -0.034 0.14 -9999 0 -0.42 39 39
alphaM/beta2 Integrin/proMMP-9 -0.091 0.19 -9999 0 -0.46 64 64
PLAUR -0.001 0.081 -9999 0 -0.41 13 13
HMGB1 0.009 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.014 0.12 -9999 0 -0.42 26 26
AGER 0.004 0.057 -9999 0 -0.5 4 4
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG 0.004 0.071 -9999 0 -0.45 8 8
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.022 0.14 -9999 0 -0.4 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.11 0.22 -9999 0 -0.46 100 100
CYR61 -0.003 0.094 -9999 0 -0.48 13 13
TLN1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP -0.074 0.15 -9999 0 -0.47 38 38
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.088 0.22 -9999 0 -0.55 67 67
MYH2 -0.079 0.24 -9999 0 -0.65 43 43
MST1R -0.091 0.2 -9999 0 -0.43 89 89
leukocyte activation during inflammatory response -0.083 0.16 -9999 0 -0.4 66 66
APOB -0.014 0.13 -9999 0 -0.63 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.047 0.18 -9999 0 -0.53 42 42
JAM3 0.012 0.026 -9999 0 -0.34 2 2
GP1BA -0.017 0.13 -9999 0 -0.5 22 22
alphaM/beta2 Integrin/CTGF -0.032 0.15 -9999 0 -0.44 36 36
alphaM/beta2 Integrin -0.064 0.19 -9999 0 -0.52 43 43
JAM3 homodimer 0.012 0.026 -9999 0 -0.34 2 2
ICAM2 0.012 0.038 -9999 0 -0.49 2 2
ICAM1 0.001 0.085 -9999 0 -0.49 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.063 0.19 -9999 0 -0.52 43 43
cell adhesion -0.034 0.14 -9999 0 -0.42 39 39
NFKB1 -0.032 0.18 -9999 0 -0.57 15 15
THY1 0.003 0.076 -9999 0 -0.49 8 8
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.048 0.16 -9999 0 -0.46 44 44
alphaM/beta2 Integrin/LRP/tPA -0.024 0.15 -9999 0 -0.42 38 38
IL6 -0.066 0.26 -9999 0 -0.77 33 33
ITGB2 -0.006 0.092 -9999 0 -0.51 11 11
elevation of cytosolic calcium ion concentration -0.014 0.13 -9999 0 -0.41 29 29
alphaM/beta2 Integrin/JAM2/JAM3 -0.035 0.16 -9999 0 -0.4 52 52
JAM2 -0.04 0.18 -9999 0 -0.6 33 33
alphaM/beta2 Integrin/ICAM1 -0.083 0.19 -9999 0 -0.4 82 82
alphaM/beta2 Integrin/uPA/Plg -0.042 0.17 -9999 0 -0.41 57 57
RhoA/GTP -0.082 0.26 -9999 0 -0.7 42 42
positive regulation of phagocytosis -0.076 0.16 -9999 0 -0.46 47 47
Ron/MSP -0.088 0.2 -9999 0 -0.52 53 53
alphaM/beta2 Integrin/uPAR/uPA -0.013 0.13 -9999 0 -0.41 29 29
alphaM/beta2 Integrin/uPAR -0.023 0.14 -9999 0 -0.44 28 28
PLAU 0.009 0.045 -9999 0 -0.34 6 6
PLAT -0.021 0.14 -9999 0 -0.54 24 24
actin filament polymerization -0.073 0.23 -9999 0 -0.61 43 43
MST1 -0.034 0.17 -9999 0 -0.63 28 28
alphaM/beta2 Integrin/lipoprotein(a) -0.061 0.18 -9999 0 -0.4 66 66
TNF -0.046 0.23 -9999 0 -0.77 24 24
RAP1B 0.014 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.018 0.13 -9999 0 -0.43 26 26
fibrinolysis -0.042 0.17 -9999 0 -0.41 57 57
HCK -0.002 0.097 -9999 0 -0.57 10 10
dendritic cell antigen processing and presentation -0.063 0.19 -9999 0 -0.52 43 43
VTN -0.022 0.15 -9999 0 -0.63 21 21
alphaM/beta2 Integrin/CYR61 -0.024 0.14 -9999 0 -0.46 29 29
LPA -0.066 0.2 -9999 0 -0.53 55 55
LRP1 0.011 0.047 -9999 0 -0.63 2 2
cell migration -0.11 0.22 -9999 0 -0.45 82 82
FN1 0.013 0.033 -9999 0 -0.63 1 1
alphaM/beta2 Integrin/Thy1 -0.021 0.13 -9999 0 -0.43 29 29
MPO -0.001 0.068 -9999 0 -0.36 12 12
KNG1 -0.048 0.19 -9999 0 -0.63 36 36
RAP1/GDP 0.019 0 -9999 0 -10000 0 0
ROCK1 -0.068 0.24 -9999 0 -0.66 40 40
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.048 0.19 -9999 0 -0.63 36 36
CTGF -0.015 0.13 -9999 0 -0.53 20 20
alphaM/beta2 Integrin/Hck -0.023 0.16 -9999 0 -0.49 29 29
ITGAM -0.035 0.15 -9999 0 -0.51 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.067 0.18 -9999 0 -0.4 73 73
HP -0.11 0.25 -9999 0 -0.62 71 71
leukocyte adhesion -0.074 0.14 -9999 0 -0.54 16 16
SELP -0.088 0.22 -9999 0 -0.55 67 67
Calcium signaling in the CD4+ TCR 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
NFATC1 0.002 0.07 -9999 0 -0.42 8 8
NFATC2 -0.064 0.16 -9999 0 -0.4 66 66
NFATC3 0.012 0.028 -9999 0 -10000 0 0
CD40LG -0.14 0.31 -9999 0 -0.65 80 80
PTGS2 -0.15 0.31 -9999 0 -0.65 83 83
JUNB 0 0.094 -9999 0 -0.63 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.015 -9999 0 -10000 0 0
CaM/Ca2+ 0.001 0.015 -9999 0 -10000 0 0
CALM1 0.012 0.008 -9999 0 -10000 0 0
JUN 0.009 0.05 -9999 0 -0.65 2 2
mol:Ca2+ -0.005 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.005 -9999 0 -10000 0 0
FOSL1 -0.008 0.097 -9999 0 -0.4 20 20
CREM 0.014 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.072 0.21 -9999 0 -0.49 44 44
FOS -0.061 0.19 -9999 0 -0.52 51 51
IFNG -0.14 0.28 -9999 0 -0.59 80 80
AP-1/NFAT1-c-4 -0.14 0.32 -9999 0 -0.66 79 79
FASLG -0.14 0.3 -9999 0 -0.63 79 79
NFAT1-c-4/ICER1 -0.061 0.16 -9999 0 -0.42 36 36
IL2RA -0.15 0.31 -9999 0 -0.62 86 86
FKBP12/FK506 0.011 0 -9999 0 -10000 0 0
CSF2 -0.12 0.27 -9999 0 -0.57 74 74
JunB/Fra1/NFAT1-c-4 -0.063 0.18 -9999 0 -0.44 38 38
IL4 -0.12 0.26 -9999 0 -0.57 74 74
IL2 -0.004 0.021 -9999 0 -10000 0 0
IL3 -0.017 0.044 -9999 0 -0.77 1 1
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 -0.011 0.11 -9999 0 -0.48 19 19
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.038 -9999 0 -0.49 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.01 0.15 -10000 0 -0.4 29 29
TBX21 -0.055 0.38 -10000 0 -1 36 36
B2M 0.013 0.01 -10000 0 -10000 0 0
TYK2 0.019 0.019 -10000 0 -10000 0 0
IL12RB1 -0.021 0.15 -10000 0 -0.53 29 29
GADD45B -0.065 0.37 -10000 0 -0.95 40 40
IL12RB2 -0.038 0.17 -10000 0 -0.49 42 42
GADD45G -0.1 0.44 -10000 0 -1.1 51 51
natural killer cell activation 0.006 0.022 -10000 0 -10000 0 0
RELB 0.011 0.042 -10000 0 -0.44 3 3
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.021 0.14 -10000 0 -0.54 25 25
IL2RA -0.059 0.18 -10000 0 -0.45 58 58
IFNG -0.029 0.11 -10000 0 -0.34 42 42
STAT3 (dimer) -0.046 0.31 -10000 0 -0.7 48 48
HLA-DRB5 -0.047 0.17 -10000 0 -0.47 47 47
FASLG -0.078 0.42 -10000 0 -1.1 44 44
NF kappa B2 p52/RelB -0.14 0.29 -10000 0 -0.78 47 47
CD4 -0.001 0.096 -10000 0 -0.6 9 9
SOCS1 -0.014 0.12 -10000 0 -0.46 22 22
EntrezGene:6955 -0.002 0.013 -10000 0 -10000 0 0
CD3D -0.062 0.19 -10000 0 -0.49 55 55
CD3E -0.038 0.17 -10000 0 -0.55 34 34
CD3G -0.057 0.18 -10000 0 -0.47 53 53
IL12Rbeta2/JAK2 -0.014 0.13 -10000 0 -0.39 35 35
CCL3 -0.058 0.39 -10000 0 -0.96 42 42
CCL4 -0.055 0.39 -10000 0 -0.98 39 39
HLA-A 0.009 0.043 -10000 0 -0.44 3 3
IL18/IL18R -0.038 0.22 -10000 0 -0.49 61 61
NOS2 -0.071 0.39 -10000 0 -0.98 42 42
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.14 -10000 0 -0.38 23 23
IL1R1 -0.046 0.36 -10000 0 -0.94 36 36
IL4 -0.006 0.034 -10000 0 -0.36 2 2
JAK2 0.016 0.049 -10000 0 -0.46 3 3
EntrezGene:6957 -0.002 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.14 0.4 -10000 0 -0.85 63 63
RAB7A -0.045 0.31 -10000 0 -0.78 31 31
lysosomal transport -0.039 0.3 -10000 0 -0.72 33 33
FOS -0.13 0.44 -10000 0 -1.1 54 54
STAT4 (dimer) -0.063 0.36 -10000 0 -0.78 55 55
STAT5A (dimer) -0.15 0.3 -10000 0 -0.81 48 48
GZMA -0.064 0.4 -10000 0 -1.1 35 35
GZMB -0.065 0.39 -10000 0 -0.96 43 43
HLX 0.011 0.047 -10000 0 -0.63 2 2
LCK -0.07 0.41 -10000 0 -0.95 49 49
TCR/CD3/MHC II/CD4 -0.091 0.28 -10000 0 -0.62 53 53
IL2/IL2R -0.053 0.18 -10000 0 -0.46 52 52
MAPK14 -0.077 0.38 -10000 0 -0.8 62 62
CCR5 -0.081 0.41 -10000 0 -1.1 42 42
IL1B -0.038 0.18 -10000 0 -0.53 39 39
STAT6 0.006 0.12 -10000 0 -0.34 15 15
STAT4 -0.035 0.16 -10000 0 -0.56 32 32
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 0.009 0.041 -10000 0 -0.34 5 5
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.014 0 -10000 0 -10000 0 0
IL12B 0.011 0.046 -10000 0 -0.36 4 4
CD8A -0.056 0.18 -10000 0 -0.46 55 55
CD8B -0.088 0.2 -10000 0 -0.46 80 80
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.01 0.15 0.4 29 -10000 0 29
IL2RB -0.009 0.11 -10000 0 -0.52 16 16
proteasomal ubiquitin-dependent protein catabolic process -0.051 0.33 -10000 0 -0.7 55 55
IL2RG -0.039 0.16 -10000 0 -0.49 39 39
IL12 0.013 0.074 -10000 0 -0.36 5 5
STAT5A 0.011 0.042 -10000 0 -0.44 3 3
CD247 0 0.084 -10000 0 -0.51 9 9
IL2 0.003 0.019 -10000 0 -0.34 1 1
SPHK2 0.013 0.018 -10000 0 -0.34 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.001 0.082 -10000 0 -0.36 16 16
IL12/IL12R/TYK2/JAK2 -0.071 0.45 -10000 0 -0.94 51 51
MAP2K3 -0.071 0.38 -10000 0 -0.81 56 56
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.09 0.39 -10000 0 -0.84 57 57
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.013 0.12 -10000 0 -0.5 19 19
IL18RAP -0.018 0.14 -10000 0 -0.6 21 21
IL12Rbeta1/TYK2 -0.003 0.12 -10000 0 -0.4 28 28
EOMES -0.1 0.34 -10000 0 -1.4 23 23
STAT1 (dimer) -0.047 0.31 -10000 0 -0.76 39 39
T cell proliferation -0.038 0.28 -10000 0 -0.58 56 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.056 0.2 -10000 0 -0.63 42 42
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 -0.68 59 59
ATF2 -0.074 0.35 -10000 0 -0.79 51 51
Glucocorticoid receptor regulatory network

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
PCK2 -0.047 0.27 0.33 1 -0.99 26 27
SMARCC2 0.014 0.011 -10000 0 -10000 0 0
SMARCC1 0.014 0.011 -10000 0 -10000 0 0
TBX21 -0.065 0.19 -10000 0 -0.64 26 26
SUMO2 0.01 0.009 -10000 0 -10000 0 0
STAT1 (dimer) 0.018 0.047 -10000 0 -0.38 5 5
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 -0.001 0.091 -10000 0 -0.5 11 11
GR alpha/HSP90/FKBP51/HSP90 0.075 0.1 0.28 23 -0.33 6 29
PRL -0.065 0.12 -10000 0 -0.56 6 6
cortisol/GR alpha (dimer)/TIF2 0.097 0.27 0.51 56 -0.45 25 81
RELA -0.055 0.093 -10000 0 -0.25 23 23
FGG 0.11 0.25 0.46 36 -0.62 25 61
GR beta/TIF2 -0.002 0.21 0.31 22 -0.43 64 86
IFNG -0.2 0.2 -10000 0 -0.67 25 25
apoptosis -0.14 0.28 0.49 10 -0.58 77 87
CREB1 0.007 0.037 -10000 0 -10000 0 0
histone acetylation -0.037 0.11 -10000 0 -0.34 27 27
BGLAP -0.04 0.14 -10000 0 -1 3 3
GR/PKAc 0.081 0.081 0.28 19 -0.31 1 20
NF kappa B1 p50/RelA -0.095 0.17 -10000 0 -0.4 45 45
SMARCD1 0.014 0.011 -10000 0 -10000 0 0
MDM2 0.066 0.075 0.25 23 -10000 0 23
GATA3 -0.037 0.17 -10000 0 -0.55 35 35
AKT1 0.017 0.044 0.23 4 -10000 0 4
CSF2 -0.048 0.094 -10000 0 -0.5 2 2
GSK3B 0.01 0.009 -10000 0 -10000 0 0
NR1I3 -0.21 0.42 0.5 8 -0.9 87 95
CSN2 0.11 0.15 0.39 21 -0.51 3 24
BRG1/BAF155/BAF170/BAF60A 0.037 0.043 -10000 0 -0.34 1 1
NFATC1 -0.001 0.096 -10000 0 -0.6 9 9
POU2F1 0.011 0.039 -10000 0 -0.49 2 2
CDKN1A -0.034 0.33 -10000 0 -1.5 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.004 0.009 -10000 0 -10000 0 0
SFN -0.16 0.25 -10000 0 -0.48 132 132
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.017 0.18 0.28 16 -0.35 56 72
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.13 0.3 0.48 8 -0.64 61 69
JUN -0.18 0.21 -10000 0 -0.51 79 79
IL4 -0.06 0.13 -10000 0 -0.56 8 8
CDK5R1 0.002 0.079 -10000 0 -0.55 7 7
PRKACA 0.013 0.018 -10000 0 -0.34 1 1
cortisol/GR alpha (monomer)/AP-1 -0.12 0.2 0.23 21 -0.44 65 86
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.081 0.094 0.29 19 -0.32 4 23
cortisol/GR alpha (monomer) 0.2 0.25 0.6 67 -0.48 1 68
NCOA2 -0.097 0.24 -10000 0 -0.63 64 64
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.087 0.19 -10000 0 -0.53 51 51
AP-1/NFAT1-c-4 -0.26 0.26 -10000 0 -0.63 85 85
AFP -0.29 0.44 -10000 0 -1.2 53 53
SUV420H1 0.013 0.018 -10000 0 -0.34 1 1
IRF1 0.12 0.12 0.45 8 -10000 0 8
TP53 -0.007 0.16 -10000 0 -0.59 26 26
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.33 0.43 -10000 0 -0.96 92 92
KRT14 -0.1 0.14 -10000 0 -0.58 3 3
TBP 0.021 0.028 -10000 0 -0.34 1 1
CREBBP 0.023 0.056 -10000 0 -10000 0 0
HDAC1 0.013 0.003 -10000 0 -10000 0 0
HDAC2 0.013 0.002 -10000 0 -10000 0 0
AP-1 -0.26 0.26 -10000 0 -0.63 85 85
MAPK14 0.01 0.008 -10000 0 -10000 0 0
MAPK10 -0.051 0.17 -10000 0 -0.49 46 46
MAPK11 0.001 0.065 -10000 0 -0.42 8 8
KRT5 -0.21 0.22 -10000 0 -0.66 33 33
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.011 0.025 -10000 0 -10000 0 0
STAT1 0.018 0.047 -10000 0 -0.38 5 5
CGA -0.065 0.14 -10000 0 -0.63 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.063 0.11 0.33 11 -0.34 3 14
MAPK3 0.01 0.009 -10000 0 -10000 0 0
MAPK1 0.009 0.034 -10000 0 -0.63 1 1
ICAM1 -0.15 0.23 -10000 0 -0.59 50 50
NFKB1 -0.055 0.093 -10000 0 -0.26 13 13
MAPK8 -0.16 0.2 -10000 0 -0.52 60 60
MAPK9 0.01 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.16 0.29 0.5 10 -0.62 77 87
BAX 0.017 0.1 -10000 0 -10000 0 0
POMC -0.1 0.28 -10000 0 -1.3 14 14
EP300 0.023 0.056 -10000 0 -0.24 9 9
cortisol/GR alpha (dimer)/p53 0.16 0.22 0.5 60 -0.44 6 66
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.059 0.23 3 -10000 0 3
SGK1 0.037 0.26 -10000 0 -1.4 11 11
IL13 -0.18 0.22 -10000 0 -0.66 36 36
IL6 -0.21 0.34 -10000 0 -0.82 63 63
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.16 0.17 -10000 0 -0.67 16 16
IL2 -0.18 0.19 -10000 0 -0.58 31 31
CDK5 0.012 0.004 -10000 0 -10000 0 0
PRKACB 0.013 0.033 -10000 0 -0.63 1 1
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.35 0.48 -10000 0 -1.1 97 97
CDK5R1/CDK5 0.005 0.059 -10000 0 -0.4 7 7
NF kappa B1 p50/RelA/PKAc -0.049 0.13 -10000 0 -0.37 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.19 0.5 61 -10000 0 61
SMARCA4 0.013 0.035 -10000 0 -0.63 1 1
chromatin remodeling 0.12 0.14 0.37 33 -0.42 8 41
NF kappa B1 p50/RelA/Cbp -0.046 0.16 -10000 0 -0.41 20 20
JUN (dimer) -0.18 0.21 -10000 0 -0.51 79 79
YWHAH 0.014 0 -10000 0 -10000 0 0
VIPR1 -0.15 0.33 -10000 0 -0.79 67 67
NR3C1 0.11 0.14 0.4 42 -10000 0 42
NR4A1 -0.012 0.12 -10000 0 -0.45 25 25
TIF2/SUV420H1 -0.063 0.18 -10000 0 -0.46 64 64
MAPKKK cascade -0.14 0.28 0.49 10 -0.58 77 87
cortisol/GR alpha (dimer)/Src-1 0.17 0.21 0.51 63 -0.41 3 66
PBX1 -0.047 0.17 -10000 0 -0.5 44 44
POU1F1 0.001 0.021 -10000 0 -0.34 1 1
SELE -0.26 0.42 -10000 0 -1 67 67
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.14 0.38 32 -0.42 8 40
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.19 0.5 61 -10000 0 61
mol:cortisol 0.1 0.14 0.34 67 -0.23 4 71
MMP1 -0.19 0.36 -10000 0 -1.2 35 35
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.062 0.15 -9999 0 -0.39 45 45
SNTA1 0.012 0.026 -9999 0 -0.34 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 -0.063 0.15 -9999 0 -0.39 45 45
MAPK12 -0.026 0.13 -9999 0 -0.37 36 36
CCND1 -0.031 0.13 -9999 0 -0.5 23 23
p38 gamma/SNTA1 -0.018 0.12 -9999 0 -0.34 36 36
MAP2K3 0.014 0 -9999 0 -10000 0 0
PKN1 0.01 0.051 -9999 0 -0.54 3 3
G2/M transition checkpoint -0.026 0.12 -9999 0 -0.37 36 36
MAP2K6 -0.017 0.12 -9999 0 -0.38 34 34
MAPT -0.061 0.13 -9999 0 -0.31 61 61
MAPK13 -0.084 0.17 -9999 0 -0.32 117 117
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.029 -9999 0 -0.37 2 2
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.025 0.16 -9999 0 -0.55 1 1
CRKL -0.046 0.13 -9999 0 -0.38 3 3
mol:DAG -0.051 0.16 -9999 0 -0.34 79 79
HRAS -0.017 0.12 -9999 0 -0.58 2 2
MAPK8 -0.094 0.18 -9999 0 -0.36 98 98
RAP1A -0.046 0.13 -9999 0 -0.38 3 3
GAB1 -0.047 0.14 -9999 0 -0.49 3 3
MAPK14 -0.069 0.15 -9999 0 -0.33 79 79
EPO -0.18 0.26 -9999 0 -0.5 141 141
PLCG1 -0.052 0.16 -9999 0 -0.34 79 79
EPOR/TRPC2/IP3 Receptors 0.005 0.041 -9999 0 -0.49 2 2
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.11 0.19 -9999 0 -0.41 90 90
GAB1/SHC/GRB2/SOS1 -0.062 0.096 -9999 0 -0.49 2 2
EPO/EPOR (dimer) -0.12 0.2 -9999 0 -0.46 81 81
IRS2 -0.056 0.14 -9999 0 -0.46 7 7
STAT1 -0.046 0.16 -9999 0 -0.51 4 4
STAT5B -0.048 0.16 -9999 0 -0.34 79 79
cell proliferation -0.08 0.17 -9999 0 -0.33 98 98
GAB1/SHIP/PIK3R1/SHP2/SHC -0.062 0.1 -9999 0 -0.48 5 5
TEC -0.053 0.14 -9999 0 -0.37 10 10
SOCS3 -0.027 0.14 -9999 0 -0.47 32 32
STAT1 (dimer) -0.045 0.16 -9999 0 -0.49 4 4
JAK2 0.004 0.044 -9999 0 -0.44 3 3
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
EPO/EPOR (dimer)/JAK2 -0.046 0.15 -9999 0 -0.3 80 80
EPO/EPOR -0.12 0.2 -9999 0 -0.46 81 81
LYN 0.014 0.034 -9999 0 -0.63 1 1
TEC/VAV2 -0.043 0.14 -9999 0 -0.44 4 4
elevation of cytosolic calcium ion concentration 0.005 0.041 -9999 0 -0.49 2 2
SHC1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.083 0.17 -9999 0 -0.38 79 79
mol:IP3 -0.051 0.16 -9999 0 -0.34 79 79
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.043 0.14 -9999 0 -0.51 8 8
SH2B3 0.007 0.014 -9999 0 -10000 0 0
NFKB1 -0.069 0.15 -9999 0 -0.33 79 79
EPO/EPOR (dimer)/JAK2/SOCS3 -0.094 0.13 -9999 0 -0.32 88 88
PTPN6 -0.056 0.14 -9999 0 -0.3 80 80
TEC/VAV2/GRB2 -0.035 0.13 -9999 0 -0.43 4 4
EPOR 0.005 0.041 -9999 0 -0.49 2 2
INPP5D 0.009 0.054 -9999 0 -0.49 4 4
mol:GDP -0.063 0.098 -9999 0 -0.51 2 2
SOS1 0.013 0.018 -9999 0 -0.34 1 1
PLCG2 -0.004 0.11 -9999 0 -0.6 11 11
CRKL/CBL/C3G -0.03 0.13 -9999 0 -0.53 2 2
VAV2 -0.046 0.13 -9999 0 -0.38 3 3
CBL -0.048 0.14 -9999 0 -0.49 3 3
SHC/Grb2/SOS1 -0.067 0.1 -9999 0 -0.38 2 2
STAT5A -0.05 0.16 -9999 0 -0.44 5 5
GRB2 0.014 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.027 0.15 -9999 0 -0.46 4 4
LYN/PLCgamma2 0.007 0.083 -9999 0 -0.44 12 12
PTPN11 0.014 0 -9999 0 -10000 0 0
BTK -0.058 0.14 -9999 0 -0.41 8 8
BCL2 -0.031 0.18 -9999 0 -0.77 5 5
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 -0.01 0.11 -10000 0 -0.49 18 18
PTK2 0.014 0 -10000 0 -10000 0 0
CRKL -0.052 0.15 -10000 0 -0.36 61 61
GRB2/SOS1/SHC 0.029 0.011 -10000 0 -10000 0 0
HRAS 0.012 0.026 -10000 0 -0.34 2 2
IRS1/Crk -0.052 0.15 -10000 0 -0.36 62 62
IGF-1R heterotetramer/IGF1/PTP1B -0.063 0.17 -10000 0 -0.42 60 60
AKT1 -0.03 0.14 -10000 0 -0.48 17 17
BAD -0.021 0.14 -10000 0 -0.44 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.052 0.15 -10000 0 -0.36 62 62
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.052 0.15 -10000 0 -0.36 61 61
RAF1 -0.014 0.13 -10000 0 -0.53 7 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.04 0.14 -10000 0 -0.34 61 61
YWHAZ 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.064 0.16 -10000 0 -0.39 64 64
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
RPS6KB1 -0.03 0.14 -10000 0 -0.48 17 17
GNB2L1 0.014 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.014 0.11 -10000 0 -0.44 7 7
PXN 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
HRAS/GTP -0.058 0.12 -10000 0 -0.42 17 17
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.033 0.14 -10000 0 -0.32 60 60
IGF-1R heterotetramer -0.049 0.15 -10000 0 -0.44 44 44
IGF-1R heterotetramer/IGF1/IRS/Nck -0.063 0.17 -10000 0 -0.4 68 68
Crk/p130 Cas/Paxillin -0.032 0.14 -10000 0 -0.45 16 16
IGF1R -0.049 0.15 -10000 0 -0.44 44 44
IGF1 -0.099 0.24 -10000 0 -0.58 68 68
IRS2/Crk -0.052 0.16 -10000 0 -0.36 69 69
PI3K -0.044 0.16 -10000 0 -0.36 63 63
apoptosis 0.01 0.12 0.37 17 -10000 0 17
HRAS/GDP 0.009 0.018 -10000 0 -0.23 2 2
PRKCD -0.043 0.17 -10000 0 -0.42 60 60
RAF1/14-3-3 E -0.003 0.12 -10000 0 -0.45 7 7
BAD/14-3-3 -0.011 0.13 -10000 0 -0.4 17 17
PRKCZ -0.052 0.17 -10000 0 -0.5 27 27
Crk/p130 Cas/Paxillin/FAK1 -0.049 0.11 -10000 0 -0.52 7 7
PTPN1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.053 0.18 -10000 0 -0.45 60 60
BCAR1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.045 0.15 -10000 0 -0.36 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0.018 -10000 0 -0.34 1 1
IRS1/NCK2 -0.064 0.17 -10000 0 -0.39 68 68
GRB10 0.014 0 -10000 0 -10000 0 0
PTPN11 -0.052 0.15 -10000 0 -0.36 61 61
IRS1 -0.065 0.16 -10000 0 -0.39 64 64
IRS2 -0.063 0.17 -10000 0 -0.38 69 69
IGF-1R heterotetramer/IGF1 -0.095 0.21 -10000 0 -0.53 61 61
GRB2 0.014 0 -10000 0 -10000 0 0
PDPK1 -0.039 0.15 -10000 0 -0.48 20 20
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKD1 -0.066 0.2 -10000 0 -0.46 67 67
SHC1 0.014 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.002 0.093 -9999 0 -0.45 15 15
alphaV beta3 Integrin -0.057 0.17 -9999 0 -0.45 47 47
PTK2 -0.065 0.2 -9999 0 -0.48 44 44
IGF1R -0.036 0.14 -9999 0 -0.41 44 44
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.008 0.057 -9999 0 -0.46 5 5
SRC -0.021 0.14 -9999 0 -0.6 21 21
CDKN1B -0.035 0.15 -9999 0 -0.58 21 21
VEGFA 0.013 0.033 -9999 0 -0.63 1 1
ILK -0.035 0.15 -9999 0 -0.58 21 21
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 -0.025 0.14 -9999 0 -0.54 21 21
PTK2B -0.011 0.13 -9999 0 -0.37 38 38
alphaV/beta3 Integrin/JAM-A -0.056 0.18 -9999 0 -0.41 66 66
CBL 0.011 0.047 -9999 0 -0.63 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.055 0.18 -9999 0 -0.43 63 63
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.057 0.17 -9999 0 -0.4 64 64
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.11 -9999 0 -0.42 9 9
alphaV/beta3 Integrin/Syndecan-1 -0.018 0.12 -9999 0 -0.39 34 34
PI4KA 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.2 -9999 0 -0.6 41 41
PI4 Kinase 0.021 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
alphaV/beta3 Integrin/Osteopontin -0.15 0.2 -9999 0 -0.42 107 107
RPS6KB1 -0.088 0.21 -9999 0 -0.56 41 41
TLN1 0.014 0 -9999 0 -10000 0 0
MAPK3 -0.084 0.24 -9999 0 -0.61 52 52
GPR124 -0.005 0.11 -9999 0 -0.58 12 12
MAPK1 -0.085 0.24 -9999 0 -0.61 52 52
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
alphaV/beta3 Integrin/Tumstatin -0.067 0.18 -9999 0 -0.45 52 52
cell adhesion -0.045 0.17 -9999 0 -0.37 69 69
ANGPTL3 -0.052 0.2 -9999 0 -0.63 38 38
VEGFR2 homodimer/VEGFA homodimer/Src -0.01 0.12 -9999 0 -0.4 32 32
IGF-1R heterotetramer -0.036 0.14 -9999 0 -0.41 44 44
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.047 -9999 0 -0.63 2 2
ITGB3 -0.049 0.18 -9999 0 -0.55 41 41
IGF1 -0.092 0.23 -9999 0 -0.57 68 68
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.025 0.14 -9999 0 -0.41 38 38
apoptosis 0.01 0.037 -9999 0 -0.34 4 4
CD47 0.006 0.074 -9999 0 -0.63 5 5
alphaV/beta3 Integrin/CD47 -0.019 0.13 -9999 0 -0.4 34 34
VCL 0.013 0.018 -9999 0 -0.34 1 1
alphaV/beta3 Integrin/Del1 -0.074 0.18 -9999 0 -0.42 66 66
CSF1 -0.013 0.12 -9999 0 -0.55 18 18
PIK3C2A -0.037 0.16 -9999 0 -0.59 22 22
PI4 Kinase/Pyk2 -0.077 0.15 -9999 0 -0.53 22 22
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.016 0.14 -9999 0 -0.4 38 38
FAK1/Vinculin -0.044 0.16 -9999 0 -0.44 26 26
alphaV beta3/Integrin/ppsTEM5 -0.025 0.14 -9999 0 -0.41 38 38
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.022 0.15 -9999 0 -0.63 21 21
BCAR1 0.014 0 -9999 0 -10000 0 0
FGF2 -0.06 0.18 -9999 0 -0.45 59 59
F11R -0.036 0.14 -9999 0 -0.47 26 26
alphaV/beta3 Integrin/Lactadherin -0.017 0.12 -9999 0 -0.39 32 32
alphaV/beta3 Integrin/TGFBR2 -0.015 0.12 -9999 0 -0.4 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.017 0.084 -9999 0 -0.37 14 14
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.011 0.11 -9999 0 -0.36 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.013 0.033 -9999 0 -0.63 1 1
alphaV/beta3 Integrin/Pyk2 -0.009 0.13 -9999 0 -0.38 38 38
SDC1 0.007 0.067 -9999 0 -0.63 4 4
VAV3 0.009 0.09 -9999 0 -0.34 17 17
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.006 0.074 -9999 0 -0.63 5 5
FAK1/Paxillin -0.043 0.16 -9999 0 -0.45 24 24
cell migration -0.032 0.14 -9999 0 -0.41 23 23
ITGAV 0.01 0.037 -9999 0 -0.34 4 4
PI3K -0.08 0.16 -9999 0 -0.57 23 23
SPP1 -0.22 0.26 -9999 0 -0.47 178 178
KDR -0.009 0.12 -9999 0 -0.61 14 14
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.037 -9999 0 -0.34 4 4
COL4A3 -0.076 0.19 -9999 0 -0.45 71 71
angiogenesis -0.083 0.24 -9999 0 -0.6 59 59
Rac1/GTP 0.015 0.083 -9999 0 -0.31 16 16
EDIL3 -0.085 0.21 -9999 0 -0.48 73 73
cell proliferation -0.015 0.12 -9999 0 -0.4 31 31
Nectin adhesion pathway

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
PDGFRB 0.002 0.083 -9999 0 -0.5 9 9
alphaV beta3 Integrin -0.028 0.14 -9999 0 -0.38 45 45
PTK2 -0.084 0.2 -9999 0 -0.53 52 52
positive regulation of JNK cascade -0.059 0.12 -9999 0 -0.33 54 54
CDC42/GDP -0.031 0.18 -9999 0 -0.44 52 52
Rac1/GDP -0.028 0.18 -9999 0 -0.43 54 54
RAP1B 0.014 0 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.072 0.15 -9999 0 -0.41 54 54
nectin-3/I-afadin -0.046 0.17 -9999 0 -0.47 51 51
RAPGEF1 -0.043 0.2 -9999 0 -0.49 54 54
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.06 0.23 -9999 0 -0.57 55 55
PDGFB-D/PDGFRB 0.002 0.083 -9999 0 -0.5 9 9
TLN1 -0.01 0.11 -9999 0 -0.47 12 12
Rap1/GTP -0.06 0.12 -9999 0 -0.34 52 52
IQGAP1 0.01 0.037 -9999 0 -0.34 4 4
Rap1/GTP/I-afadin 0.026 0.028 -9999 0 -0.36 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.046 0.17 -9999 0 -0.47 51 51
PVR 0.014 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0 -9999 0 -10000 0 0
mol:GDP -0.049 0.22 -9999 0 -0.55 55 55
MLLT4 0.011 0.047 -9999 0 -0.63 2 2
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
PI3K -0.02 0.15 -9999 0 -0.35 57 57
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.015 0.056 -9999 0 -0.46 5 5
positive regulation of lamellipodium assembly -0.06 0.12 -9999 0 -0.34 55 55
PVRL1 0.009 0.058 -9999 0 -0.63 3 3
PVRL3 -0.073 0.22 -9999 0 -0.63 50 50
PVRL2 0.013 0.018 -9999 0 -0.34 1 1
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
CDH1 -0.034 0.17 -9999 0 -0.63 28 28
CLDN1 0.006 0.074 -9999 0 -0.63 5 5
JAM-A/CLDN1 -0.026 0.15 -9999 0 -0.38 56 56
SRC -0.076 0.26 -9999 0 -0.64 55 55
ITGB3 -0.049 0.18 -9999 0 -0.55 41 41
nectin-1(dimer)/I-afadin/I-afadin 0.015 0.056 -9999 0 -0.46 5 5
FARP2 -0.055 0.23 -9999 0 -0.55 54 54
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.03 0.15 -9999 0 -0.4 51 51
nectin-1/I-afadin 0.015 0.056 -9999 0 -0.46 5 5
nectin-2/I-afadin 0.018 0.038 -9999 0 -0.46 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.017 0.021 -9999 0 -0.18 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.033 0.15 -9999 0 -0.4 54 54
CDC42/GTP/IQGAP1/filamentous actin 0.017 0.021 -9999 0 -0.18 4 4
F11R 0.007 0.067 -9999 0 -0.63 4 4
positive regulation of filopodium formation -0.059 0.12 -9999 0 -0.33 54 54
alphaV/beta3 Integrin/Talin -0.026 0.17 -9999 0 -0.48 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.038 -9999 0 -0.46 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.018 0.038 -9999 0 -0.46 2 2
PIP5K1C -0.018 0.12 -9999 0 -0.51 12 12
VAV2 -0.053 0.22 -9999 0 -0.55 54 54
RAP1/GDP -0.07 0.15 -9999 0 -0.41 52 52
ITGAV 0.01 0.037 -9999 0 -0.34 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.03 0.15 -9999 0 -0.4 51 51
nectin-3(dimer)/I-afadin/I-afadin -0.046 0.17 -9999 0 -0.47 51 51
Rac1/GTP -0.072 0.15 -9999 0 -0.41 54 54
PTPRM -0.029 0.13 -9999 0 -0.3 56 56
E-cadherin/beta catenin/alpha catenin -0.027 0.09 -9999 0 -0.31 32 32
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.15 0.21 -10000 0 -0.48 88 88
cell-cell adhesion 0.081 0.14 0.47 24 -10000 0 24
Ephrin B/EPHB2/RasGAP -0.054 0.16 -10000 0 -0.37 56 56
ITSN1 0.013 0.033 -10000 0 -0.63 1 1
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
SHC1 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.041 0.14 -10000 0 -0.4 42 42
Ephrin B1/EPHB1 -0.005 0.091 -10000 0 -0.4 16 16
HRAS/GDP -0.039 0.11 -10000 0 -0.43 13 13
Ephrin B/EPHB1/GRB7 -0.024 0.15 -10000 0 -0.37 49 49
Endophilin/SYNJ1 -0.047 0.14 -10000 0 -0.34 51 51
KRAS 0.013 0.018 -10000 0 -0.34 1 1
Ephrin B/EPHB1/Src -0.03 0.16 -10000 0 -0.39 52 52
endothelial cell migration 0.02 0.071 -10000 0 -0.42 7 7
GRB2 0.014 0 -10000 0 -10000 0 0
GRB7 -0.011 0.11 -10000 0 -0.48 19 19
PAK1 -0.046 0.15 -10000 0 -0.35 56 56
HRAS 0.012 0.026 -10000 0 -0.34 2 2
RRAS -0.048 0.14 -10000 0 -0.34 56 56
DNM1 -0.057 0.18 -10000 0 -0.46 56 56
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.13 -10000 0 -0.36 37 37
lamellipodium assembly -0.081 0.14 -10000 0 -0.47 24 24
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.011 0.12 -10000 0 -0.39 20 20
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
EPHB2 -0.095 0.2 -10000 0 -0.43 92 92
EPHB3 -0.079 0.21 -10000 0 -0.53 64 64
EPHB1 -0.024 0.14 -10000 0 -0.5 27 27
EPHB4 0.005 0.068 -10000 0 -0.47 7 7
mol:GDP -0.004 0.13 -10000 0 -0.37 25 25
Ephrin B/EPHB2 -0.056 0.15 -10000 0 -0.36 56 56
Ephrin B/EPHB3 -0.05 0.16 -10000 0 -0.37 63 63
JNK cascade -0.039 0.14 -10000 0 -0.36 45 45
Ephrin B/EPHB1 -0.019 0.13 -10000 0 -0.38 37 37
RAP1/GDP 0.011 0.12 -10000 0 -0.38 9 9
EFNB2 0.012 0.038 -10000 0 -0.49 2 2
EFNB3 -0.042 0.17 -10000 0 -0.53 38 38
EFNB1 0.013 0.033 -10000 0 -0.63 1 1
Ephrin B2/EPHB1-2 -0.055 0.15 -10000 0 -0.4 43 43
RAP1B 0.014 0 -10000 0 -10000 0 0
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.083 0.15 -10000 0 -0.53 22 22
Rap1/GTP -0.077 0.14 -10000 0 -0.49 22 22
axon guidance -0.15 0.21 -10000 0 -0.48 88 88
MAPK3 0.005 0.11 -10000 0 -0.47 9 9
MAPK1 0.004 0.11 -10000 0 -0.45 10 10
Rac1/GDP 0.004 0.12 -10000 0 -0.38 13 13
actin cytoskeleton reorganization -0.058 0.1 -10000 0 -0.4 17 17
CDC42/GDP 0.004 0.12 -10000 0 -0.38 12 12
PI3K 0.023 0.072 -10000 0 -0.42 7 7
EFNA5 -0.16 0.25 -10000 0 -0.48 131 131
Ephrin B2/EPHB4 0.012 0.049 -10000 0 -0.4 4 4
Ephrin B/EPHB2/Intersectin/N-WASP -0.029 0.12 -10000 0 -0.42 9 9
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.076 0.13 -10000 0 -0.47 23 23
PTK2 0.019 0.032 -10000 0 -10000 0 0
MAP4K4 -0.04 0.14 -10000 0 -0.36 45 45
SRC -0.021 0.14 -10000 0 -0.6 21 21
KALRN 0.009 0.058 -10000 0 -0.63 3 3
Intersectin/N-WASP 0.02 0.025 -10000 0 -0.46 1 1
neuron projection morphogenesis -0.021 0.14 -10000 0 -0.42 19 19
MAP2K1 -0.003 0.12 -10000 0 -0.45 12 12
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.048 0.15 -10000 0 -0.39 45 45
cell migration 0.002 0.13 -10000 0 -0.48 12 12
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 -0.048 0.14 -10000 0 -0.35 51 51
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.061 0.16 -10000 0 -0.5 17 17
HRAS/GTP -0.085 0.14 -10000 0 -0.52 22 22
Ephrin B1/EPHB1-2 -0.055 0.15 -10000 0 -0.4 43 43
cell adhesion mediated by integrin 0.046 0.11 0.34 36 -10000 0 36
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.063 0.17 -10000 0 -0.55 23 23
RAC1-CDC42/GTP -0.11 0.18 -10000 0 -0.53 40 40
RASA1 0.002 0.088 -10000 0 -0.63 7 7
RAC1-CDC42/GDP 0.011 0.12 -10000 0 -0.39 8 8
ruffle organization -0.043 0.16 -10000 0 -0.48 24 24
NCK1 0.011 0.047 -10000 0 -0.63 2 2
receptor internalization -0.073 0.17 -10000 0 -0.43 38 38
Ephrin B/EPHB2/KALRN -0.05 0.15 -10000 0 -0.36 58 58
ROCK1 -0.029 0.12 -10000 0 -0.36 42 42
RAS family/GDP -0.058 0.1 -10000 0 -0.39 17 17
Rac1/GTP -0.085 0.14 -10000 0 -0.5 24 24
Ephrin B/EPHB1/Src/Paxillin -0.021 0.14 -10000 0 -0.33 52 52
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.069 0.14 0.38 28 -10000 0 28
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.062 -10000 0 -0.4 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.15 0.27 -10000 0 -0.56 108 108
RhoA/GTP -0.07 0.15 -10000 0 -0.39 28 28
negative regulation of cAMP metabolic process -0.084 0.16 -10000 0 -0.31 93 93
GNAZ -0.086 0.22 -10000 0 -0.55 66 66
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.014 0 -10000 0 -10000 0 0
S1PR5 -0.004 0.098 -10000 0 -0.5 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.085 0.16 -10000 0 -0.32 93 93
RhoA/GDP 0.011 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 0.007 0.067 -10000 0 -0.63 4 4
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0.018 -9999 0 -0.34 1 1
SPHK1 -0.11 0.22 -9999 0 -0.44 98 98
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P -0.043 0.13 -9999 0 -0.32 51 51
GNAO1 -0.15 0.27 -9999 0 -0.56 108 108
mol:Sphinganine-1-P -0.065 0.16 -9999 0 -0.46 36 36
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.029 0.14 -9999 0 -0.44 25 25
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 0.021 0 -9999 0 -10000 0 0
S1PR3 -0.019 0.14 -9999 0 -0.55 22 22
S1PR2 -0.023 0.15 -9999 0 -0.62 22 22
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.04 0.11 -9999 0 -0.3 42 42
S1PR5 -0.004 0.098 -9999 0 -0.5 13 13
S1PR4 0.002 0.075 -9999 0 -0.43 10 10
GNAI1 0.007 0.067 -9999 0 -0.63 4 4
S1P/S1P5/G12 -0.028 0.12 -9999 0 -0.48 12 12
S1P/S1P3/Gq -0.053 0.16 -9999 0 -0.48 27 27
S1P/S1P4/Gi -0.098 0.17 -9999 0 -0.4 60 60
GNAQ 0.013 0.033 -9999 0 -0.63 1 1
GNAZ -0.086 0.22 -9999 0 -0.55 66 66
GNA14 -0.027 0.16 -9999 0 -0.62 24 24
GNA15 -0.002 0.092 -9999 0 -0.49 12 12
GNA12 0.014 0 -9999 0 -10000 0 0
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 -0.028 0.16 -9999 0 -0.63 24 24
ABCC1 -0.016 0.12 -9999 0 -0.48 23 23
ErbB2/ErbB3 signaling events

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
USP8 0.016 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.043 0.13 -10000 0 -0.35 10 10
NFATC4 -0.058 0.13 -10000 0 -0.39 15 15
ERBB2IP 0.014 0.033 -10000 0 -0.63 1 1
HSP90 (dimer) 0.014 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.083 0.16 -10000 0 -0.31 102 102
JUN -0.006 0.097 -10000 0 -0.38 11 11
HRAS 0.012 0.026 -10000 0 -0.34 2 2
DOCK7 -0.073 0.15 -10000 0 -0.51 9 9
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.11 0.18 0.24 1 -0.36 113 114
AKT1 0.01 0.004 -10000 0 -10000 0 0
BAD 0.018 0.003 -10000 0 -10000 0 0
MAPK10 -0.044 0.1 -10000 0 -0.28 27 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.088 0.17 -10000 0 -0.34 102 102
RAF1 -0.03 0.12 -10000 0 -0.36 6 6
ErbB2/ErbB3/neuregulin 2 -0.064 0.14 0.25 1 -0.4 41 42
STAT3 -0.048 0.23 -10000 0 -1 19 19
cell migration -0.037 0.098 -10000 0 -0.25 23 23
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.025 0.16 -10000 0 -0.48 12 12
FOS -0.032 0.18 -10000 0 -0.47 38 38
NRAS 0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.083 0.16 -10000 0 -0.31 102 102
MAPK3 -0.019 0.14 -10000 0 -0.4 11 11
MAPK1 -0.02 0.14 -10000 0 -0.42 8 8
JAK2 -0.074 0.15 -10000 0 -0.5 10 10
NF2 -0.003 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.077 0.15 -10000 0 -0.3 102 102
NRG1 -0.2 0.28 -10000 0 -0.55 137 137
GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
MAPK8 -0.082 0.16 -10000 0 -0.33 54 54
MAPK9 -0.024 0.086 -10000 0 -0.24 9 9
ERBB2 -0.024 0.11 0.41 1 -0.47 20 21
ERBB3 0.008 0.058 -10000 0 -0.64 3 3
SHC1 0.014 0.001 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
apoptosis -0.001 0.012 -10000 0 -10000 0 0
STAT3 (dimer) -0.034 0.22 -10000 0 -0.99 19 19
RNF41 0.02 0.009 -10000 0 -10000 0 0
FRAP1 0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.069 0.096 -10000 0 -0.35 9 9
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.093 0.27 1 -0.4 19 20
CHRNA1 -0.009 0.12 -10000 0 -0.36 4 4
myelination -0.055 0.13 -10000 0 -0.37 15 15
PPP3CB -0.068 0.14 -10000 0 -0.47 9 9
KRAS 0.013 0.018 -10000 0 -0.34 1 1
RAC1-CDC42/GDP -0.052 0.13 -10000 0 -0.39 9 9
NRG2 -0.091 0.19 -10000 0 -0.4 92 92
mol:GDP -0.077 0.15 -10000 0 -0.3 102 102
SOS1 0.013 0.018 -10000 0 -0.34 1 1
MAP2K2 -0.02 0.12 -10000 0 -0.4 3 3
SRC -0.021 0.14 -10000 0 -0.6 21 21
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.072 0.15 -10000 0 -0.51 9 9
MAP2K1 -0.04 0.16 -10000 0 -0.45 11 11
heart morphogenesis -0.083 0.16 -10000 0 -0.31 102 102
RAS family/GDP -0.044 0.13 -10000 0 -0.37 9 9
GRB2 0.014 0 -10000 0 -10000 0 0
PRKACA -0.006 0.01 -10000 0 -10000 0 0
CHRNE 0.004 0.043 -10000 0 -0.19 14 14
HSP90AA1 0.014 0 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.004 -10000 0 -10000 0 0
nervous system development -0.083 0.16 -10000 0 -0.31 102 102
CDC42 0.014 0 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.073 0.17 -9999 0 -0.38 77 77
SMAD6-7/SMURF1 0.013 0.089 -9999 0 -0.45 12 12
NOG -0.004 0.059 -9999 0 -0.34 11 11
SMAD9 -0.015 0.086 -9999 0 -0.52 5 5
SMAD4 0.011 0.047 -9999 0 -0.63 2 2
SMAD5 -0.029 0.13 -9999 0 -0.38 19 19
BMP7/USAG1 -0.072 0.15 -9999 0 -0.3 102 102
SMAD5/SKI -0.021 0.12 -9999 0 -0.38 18 18
SMAD1 0.033 0.044 -9999 0 -0.38 3 3
BMP2 -0.005 0.097 -9999 0 -0.46 15 15
SMAD1/SMAD1/SMAD4 -0.012 0.063 -9999 0 -0.51 3 3
BMPR1A 0.014 0 -9999 0 -10000 0 0
BMPR1B -0.065 0.2 -9999 0 -0.54 51 51
BMPR1A-1B/BAMBI -0.062 0.18 -9999 0 -0.45 60 60
AHSG -0.08 0.23 -9999 0 -0.63 54 54
CER1 -0.005 0.043 -9999 0 -0.34 6 6
BMP2-4/CER1 -0.021 0.1 -9999 0 -0.41 13 13
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.039 0.15 -9999 0 -0.4 28 28
BMP2-4 (homodimer) -0.024 0.12 -9999 0 -0.28 55 55
RGMB -0.002 0.08 -9999 0 -0.38 15 15
BMP6/BMPR2/BMPR1A-1B -0.021 0.13 -9999 0 -0.36 39 39
RGMA -0.01 0.11 -9999 0 -0.46 19 19
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.05 0.15 -9999 0 -0.37 37 37
BMP2-4/USAG1 -0.058 0.15 -9999 0 -0.41 39 39
SMAD6/SMURF1/SMAD5 -0.02 0.12 -9999 0 -0.37 16 16
SOSTDC1 -0.068 0.18 -9999 0 -0.42 68 68
BMP7/BMPR2/BMPR1A-1B -0.037 0.13 -9999 0 -0.37 40 40
SKI 0.011 0.047 -9999 0 -0.63 2 2
BMP6 (homodimer) -0.007 0.093 -9999 0 -0.38 20 20
HFE2 -0.075 0.22 -9999 0 -0.63 52 52
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.022 0.12 -9999 0 -0.4 23 23
SMAD5/SMAD5/SMAD4 -0.021 0.12 -9999 0 -0.38 14 14
MAPK1 0.013 0.033 -9999 0 -0.63 1 1
TAK1/TAB family -0.062 0.11 -9999 0 -0.44 11 11
BMP7 (homodimer) -0.038 0.12 -9999 0 -0.35 46 46
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.063 0.19 -9999 0 -0.5 57 57
SMAD1/SKI 0.038 0.055 -9999 0 -0.46 3 3
SMAD6 0.001 0.09 -9999 0 -0.6 8 8
CTDSP2 0.014 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.07 0.17 -9999 0 -0.41 67 67
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.14 0.25 -9999 0 -0.53 102 102
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.029 0.011 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.037 0.14 -9999 0 -0.46 34 34
CHRDL1 -0.12 0.23 -9999 0 -0.51 90 90
ENDOFIN/SMAD1 0.04 0.043 -9999 0 -0.35 3 3
SMAD6-7/SMURF1/SMAD1 0.038 0.081 -9999 0 -0.47 5 5
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI -0.052 0.19 -9999 0 -0.59 41 41
SMURF2 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.09 0.18 -9999 0 -0.43 64 64
BMP2-4/GREM1 -0.1 0.19 -9999 0 -0.44 79 79
SMAD7 0.002 0.088 -9999 0 -0.63 7 7
SMAD8A/SMAD8A/SMAD4 -0.008 0.083 -9999 0 -0.44 7 7
SMAD1/SMAD6 0.04 0.043 -9999 0 -0.35 3 3
TAK1/SMAD6 0.021 0 -9999 0 -10000 0 0
BMP7 -0.038 0.12 -9999 0 -0.35 46 46
BMP6 -0.007 0.093 -9999 0 -0.38 20 20
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.039 0.13 -9999 0 -0.32 39 39
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.04 0.043 -9999 0 -0.35 3 3
SMAD7/SMURF1 0.012 0.066 -9999 0 -0.46 7 7
CTDSPL 0.014 0 -9999 0 -10000 0 0
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.018 -9999 0 -0.34 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.076 0.17 -9999 0 -0.42 49 49
CHRD -0.005 0.11 -9999 0 -0.58 12 12
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.054 0.15 -9999 0 -0.38 37 37
BMP4 -0.03 0.13 -9999 0 -0.39 41 41
FST -0.07 0.21 -9999 0 -0.56 54 54
BMP2-4/NOG -0.021 0.11 -9999 0 -0.4 15 15
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.027 0.12 -9999 0 -0.34 40 40
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.038 0.12 -10000 0 -0.32 25 25
IKBKB -0.009 0.071 -10000 0 -0.25 7 7
AKT1 -0.034 0.097 -10000 0 -0.24 28 28
IKBKG -0.009 0.075 -10000 0 -0.26 10 10
CALM1 -0.037 0.11 -10000 0 -0.45 13 13
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
MAP3K1 -0.057 0.16 -10000 0 -0.44 31 31
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.046 0.12 0.22 2 -0.45 15 17
DOK1 0.014 0 -10000 0 -10000 0 0
AP-1 -0.025 0.085 0.18 1 -0.23 22 23
LYN 0.013 0.033 -10000 0 -0.63 1 1
BLNK -0.003 0.1 -10000 0 -0.63 10 10
SHC1 0.014 0 -10000 0 -10000 0 0
BCR complex -0.089 0.18 -10000 0 -0.36 106 106
CD22 -0.12 0.19 -10000 0 -0.41 84 84
CAMK2G -0.028 0.1 -10000 0 -0.41 13 13
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.009 0.054 -10000 0 -0.49 4 4
SHC/GRB2/SOS1 -0.073 0.13 -10000 0 -0.57 9 9
GO:0007205 -0.046 0.12 0.22 2 -0.46 15 17
SYK -0.006 0.099 -10000 0 -0.45 16 16
ELK1 -0.037 0.11 -10000 0 -0.45 13 13
NFATC1 -0.058 0.15 -10000 0 -0.5 20 20
B-cell antigen/BCR complex -0.089 0.18 -10000 0 -0.36 106 106
PAG1/CSK 0.004 0.086 -10000 0 -0.46 11 11
NFKBIB 0.007 0.027 0.081 1 -0.12 1 2
HRAS -0.033 0.11 -10000 0 -0.43 14 14
NFKBIA 0.007 0.026 0.081 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.012 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.11 0.21 -10000 0 -0.4 107 107
mol:GDP -0.042 0.11 0.22 2 -0.43 15 17
PTEN 0.007 0.067 -10000 0 -0.63 4 4
CD79B 0.008 0.053 -10000 0 -0.39 6 6
NF-kappa-B/RelA/I kappa B alpha 0.013 0.022 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.078 0.18 -10000 0 -0.42 62 62
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
mol:IP3 -0.047 0.12 0.22 2 -0.46 15 17
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.062 0.14 -10000 0 -0.39 41 41
CHUK -0.008 0.075 -10000 0 -0.27 8 8
IBTK 0.013 0.034 -10000 0 -0.63 1 1
CARD11/BCL10/MALT1/TAK1 -0.059 0.12 -10000 0 -0.47 18 18
PTPN6 -0.088 0.19 -10000 0 -0.45 53 53
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 0.004 0.035 -10000 0 -0.1 23 23
VAV2 -0.089 0.18 -10000 0 -0.46 39 39
ubiquitin-dependent protein catabolic process 0.011 0.027 0.084 1 -0.11 1 2
BTK -0.027 0.17 0.38 1 -1.1 8 9
CD19 -0.11 0.17 -10000 0 -0.39 79 79
MAP4K1 -0.028 0.15 -10000 0 -0.51 30 30
CD72 -0.01 0.11 -10000 0 -0.46 19 19
PAG1 -0.01 0.12 -10000 0 -0.54 16 16
MAPK14 -0.042 0.14 -10000 0 -0.39 26 26
SH3BP5 0.008 0.061 -10000 0 -0.56 4 4
PIK3AP1 -0.04 0.12 0.24 2 -0.47 17 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.071 0.2 -10000 0 -0.45 62 62
RAF1 -0.025 0.11 -10000 0 -0.41 13 13
RasGAP/p62DOK/SHIP -0.13 0.19 -10000 0 -0.6 32 32
CD79A -0.13 0.24 -10000 0 -0.5 104 104
re-entry into mitotic cell cycle -0.025 0.084 0.18 1 -0.23 21 22
RASA1 0.002 0.088 -10000 0 -0.63 7 7
MAPK3 -0.007 0.092 -10000 0 -0.36 10 10
MAPK1 -0.008 0.093 -10000 0 -0.36 10 10
CD72/SHP1 -0.086 0.19 -10000 0 -0.49 45 45
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.061 0.15 -10000 0 -0.4 32 32
actin cytoskeleton organization -0.068 0.16 -10000 0 -0.4 38 38
NF-kappa-B/RelA 0.028 0.048 0.16 1 -0.38 1 2
Calcineurin -0.017 0.093 -10000 0 -0.36 14 14
PI3K -0.11 0.16 -10000 0 -0.43 49 49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.044 0.12 0.25 2 -0.47 15 17
SOS1 0.013 0.018 -10000 0 -0.34 1 1
Bam32/HPK1 -0.092 0.24 -10000 0 -0.78 28 28
DAPP1 -0.11 0.24 -10000 0 -0.95 20 20
cytokine secretion -0.054 0.14 -10000 0 -0.46 20 20
mol:DAG -0.047 0.12 0.22 2 -0.46 15 17
PLCG2 -0.004 0.11 -10000 0 -0.6 11 11
MAP2K1 -0.016 0.1 -10000 0 -0.41 10 10
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.23 -10000 0 -0.47 102 102
mol:PI-3-4-5-P3 -0.08 0.11 0.23 1 -0.32 36 37
ETS1 -0.022 0.1 -10000 0 -0.38 15 15
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.06 0.17 -10000 0 -0.36 73 73
B-cell antigen/BCR complex/LYN -0.094 0.16 -10000 0 -0.39 68 68
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.033 -10000 0 -0.63 1 1
RAC1 -0.073 0.17 -10000 0 -0.42 37 37
B-cell antigen/BCR complex/LYN/SYK -0.12 0.19 -10000 0 -0.52 48 48
CARD11 -0.062 0.15 -10000 0 -0.47 30 30
FCGR2B -0.11 0.24 -10000 0 -0.54 82 82
PPP3CA 0.014 0 -10000 0 -10000 0 0
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.004 0.034 -10000 0 -0.11 3 3
PTPRC -0.025 0.14 -10000 0 -0.51 28 28
PDPK1 -0.035 0.093 -10000 0 -0.23 31 31
PPP3CB 0.014 0 -10000 0 -10000 0 0
PPP3CC 0.013 0.018 -10000 0 -0.34 1 1
POU2F2 0.01 0.03 -10000 0 -0.11 14 14
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.024 0.076 -10000 0 -0.56 4 4
epithelial cell differentiation -0.036 0.088 -10000 0 -0.53 6 6
ITCH 0.017 0.008 -10000 0 -10000 0 0
WWP1 0.025 0.091 -10000 0 -1.6 1 1
FYN 0.013 0.018 -10000 0 -0.34 1 1
EGFR -0.007 0.11 -10000 0 -0.59 13 13
PRL -0.004 0.043 -10000 0 -0.34 6 6
neuron projection morphogenesis -0.045 0.15 -10000 0 -0.45 6 6
PTPRZ1 -0.016 0.096 -10000 0 -0.36 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.062 0.16 -10000 0 -0.45 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.095 0.18 -10000 0 -0.36 105 105
ADAM17 0.009 0.066 -10000 0 -0.62 4 4
ErbB4/ErbB4 0.025 0.077 -10000 0 -0.83 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.007 0.1 -10000 0 -0.43 12 12
NCOR1 0.009 0.058 -10000 0 -0.63 3 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.083 0.17 -10000 0 -0.33 105 105
GRIN2B -0.076 0.16 -10000 0 -0.42 12 12
ErbB4/ErbB2/betacellulin -0.006 0.13 -10000 0 -0.39 33 33
STAT1 0.009 0.041 -10000 0 -0.34 5 5
HBEGF 0.01 0.051 -10000 0 -0.54 3 3
PRLR -0.013 0.13 -10000 0 -0.61 16 16
E4ICDs/ETO2 0.015 0.094 -10000 0 -0.43 11 11
axon guidance -0.014 0.083 -10000 0 -0.81 1 1
NEDD4 0.004 0.089 -10000 0 -0.64 7 7
Prolactin receptor/Prolactin receptor/Prolactin -0.012 0.1 -10000 0 -0.48 16 16
CBFA2T3 -0.006 0.1 -10000 0 -0.5 15 15
ErbB4/ErbB2/HBEGF 0.012 0.11 -10000 0 -0.39 19 19
MAPK3 -0.053 0.15 -10000 0 -0.48 5 5
STAT1 (dimer) 0.025 0.073 -10000 0 -0.75 2 2
MAPK1 -0.054 0.15 -10000 0 -0.47 6 6
JAK2 0.011 0.042 -10000 0 -0.44 3 3
ErbB4/ErbB2/neuregulin 1 beta -0.1 0.19 -10000 0 -0.36 115 115
NRG1 -0.14 0.22 -10000 0 -0.4 141 141
NRG3 -0.034 0.13 -10000 0 -0.41 39 39
NRG2 -0.091 0.19 -10000 0 -0.4 92 92
NRG4 -0.093 0.21 -10000 0 -0.48 80 80
heart development -0.014 0.083 -10000 0 -0.81 1 1
neural crest cell migration -0.1 0.19 -10000 0 -0.36 115 115
ERBB2 -0.006 0.12 -10000 0 -0.47 23 23
WWOX/E4ICDs 0.027 0.07 -10000 0 -0.76 2 2
SHC1 0.014 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.036 0.15 -10000 0 -0.36 48 48
apoptosis 0.021 0.089 0.42 11 -10000 0 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.034 0.13 -10000 0 -0.4 23 23
ErbB4/ErbB2/epiregulin -0.018 0.13 -10000 0 -0.39 27 27
ErbB4/ErbB4/betacellulin/betacellulin 0.001 0.1 -10000 0 -0.43 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.018 0.11 -10000 0 -0.63 5 5
MDM2 0.03 0.07 -10000 0 -0.76 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.089 0.17 -10000 0 -0.34 105 105
STAT5A -0.008 0.086 -10000 0 -0.68 2 2
ErbB4/EGFR/neuregulin 1 beta -0.094 0.18 -10000 0 -0.35 83 83
DLG4 0.012 0.026 -10000 0 -0.34 2 2
GRB2/SHC 0.021 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.021 0.074 -10000 0 -0.49 5 5
STAT5A (dimer) -0.038 0.096 -10000 0 -0.62 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.006 0.078 -10000 0 -0.77 1 1
LRIG1 0.013 0.018 -10000 0 -0.34 1 1
EREG -0.046 0.14 -10000 0 -0.36 55 55
BTC -0.021 0.13 -10000 0 -0.49 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.015 0.084 -10000 0 -0.82 1 1
ERBB4 0.025 0.077 -10000 0 -0.84 2 2
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 0.017 0.016 -10000 0 -0.19 1 1
GRB2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.043 0.16 -10000 0 -0.38 56 56
glial cell differentiation -0.021 0.072 0.48 5 -10000 0 5
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.11 0.21 -10000 0 -0.54 40 40
S1P3 pathway

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
PDGFRB 0.002 0.083 -9999 0 -0.5 9 9
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.076 0.15 -9999 0 -0.32 65 65
GNAO1 -0.15 0.27 -9999 0 -0.56 108 108
S1P/S1P3/G12/G13 0.01 0.082 -9999 0 -0.36 16 16
AKT1 -0.024 0.1 -9999 0 -0.64 5 5
AKT3 -0.047 0.2 -9999 0 -1.3 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.002 0.083 -9999 0 -0.5 9 9
GNAI2 0.015 0.003 -9999 0 -10000 0 0
GNAI3 0.015 0.003 -9999 0 -10000 0 0
GNAI1 0.008 0.067 -9999 0 -0.63 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.018 0.14 -9999 0 -0.55 22 22
S1PR2 -0.023 0.15 -9999 0 -0.62 22 22
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.091 0.2 -9999 0 -0.51 41 41
MAPK3 -0.08 0.19 -9999 0 -0.48 41 41
MAPK1 -0.081 0.19 -9999 0 -0.49 41 41
JAK2 -0.092 0.21 -9999 0 -0.49 49 49
CXCR4 -0.089 0.2 -9999 0 -0.49 47 47
FLT1 0.013 0.043 -9999 0 -0.44 3 3
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
SRC -0.099 0.21 -9999 0 -0.46 59 59
S1P/S1P3/Gi -0.092 0.2 -9999 0 -0.52 41 41
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.078 0.18 -9999 0 -0.5 35 35
VEGFA 0.015 0.034 -9999 0 -0.63 1 1
S1P/S1P2/Gi -0.095 0.2 -9999 0 -0.37 97 97
VEGFR1 homodimer/VEGFA homodimer 0.024 0.041 -9999 0 -0.46 2 2
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.031 0.15 -9999 0 -0.32 63 63
GNAQ 0.013 0.033 -9999 0 -0.63 1 1
GNAZ -0.085 0.22 -9999 0 -0.55 66 66
G12/G13 0.021 0 -9999 0 -10000 0 0
GNA14 -0.027 0.16 -9999 0 -0.62 24 24
GNA15 -0.002 0.092 -9999 0 -0.49 12 12
GNA12 0.014 0 -9999 0 -10000 0 0
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 -0.028 0.16 -9999 0 -0.63 24 24
Rac1/GTP -0.078 0.18 -9999 0 -0.47 41 41
Arf6 signaling events

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.017 0.096 -9999 0 -0.4 13 13
ARNO/beta Arrestin1-2 -0.02 0.11 -9999 0 -10000 0 0
EGFR -0.007 0.11 -9999 0 -0.59 13 13
EPHA2 0.003 0.083 -9999 0 -0.59 7 7
USP6 0.013 0.034 -9999 0 -0.63 1 1
IQSEC1 0.014 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.058 0.14 -9999 0 -0.47 19 19
ARRB2 0.008 0.01 -9999 0 -10000 0 0
mol:GTP -0.007 0.058 -9999 0 -0.2 20 20
ARRB1 -0.001 0.093 -9999 0 -0.55 10 10
FBXO8 0.013 0.033 -9999 0 -0.63 1 1
TSHR 0.005 0.045 -9999 0 -0.34 6 6
EGF -0.077 0.16 -9999 0 -0.36 84 84
somatostatin receptor activity 0 0 -9999 0 -0.001 38 38
ARAP2 -0.009 0.12 -9999 0 -0.61 14 14
mol:GDP -0.03 0.096 -9999 0 -0.29 30 30
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 30 30
ITGA2B -0.011 0.087 -9999 0 -0.34 24 24
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.066 -9999 0 -0.35 11 11
ADAP1 -0.046 0.16 -9999 0 -0.41 52 52
KIF13B 0.014 0 -9999 0 -10000 0 0
HGF/MET -0.055 0.16 -9999 0 -0.46 39 39
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.035 0.11 -9999 0 -0.28 37 37
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.039 0.12 -9999 0 -0.4 19 19
ADRB2 -0.063 0.21 -9999 0 -0.62 45 45
receptor agonist activity 0 0 -9999 0 0 39 39
actin filament binding 0 0 -9999 0 -0.001 39 39
SRC -0.021 0.14 -9999 0 -0.6 21 21
ITGB3 -0.049 0.18 -9999 0 -0.55 41 41
GNAQ 0.012 0.034 -9999 0 -0.63 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 37 37
ARF6/GDP -0.008 0.12 -9999 0 -0.34 33 33
ARF6/GDP/GULP/ACAP1 -0.11 0.18 -9999 0 -0.38 90 90
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.014 0.12 -9999 0 -0.36 30 30
ACAP1 -0.051 0.19 -9999 0 -0.55 43 43
ACAP2 0.011 0.047 -9999 0 -0.63 2 2
LHCGR/beta Arrestin2 0 0.014 -9999 0 -10000 0 0
EFNA1 0.009 0.058 -9999 0 -0.63 3 3
HGF -0.084 0.21 -9999 0 -0.48 74 74
CYTH3 0.007 0.04 -9999 0 -0.35 4 4
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.011 0.047 -9999 0 -0.63 2 2
fibronectin binding 0 0 -9999 0 0 33 33
endosomal lumen acidification 0 0 -9999 0 0 30 30
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.15 0.24 -9999 0 -0.45 129 129
GNAQ/ARNO 0.016 0.019 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 8 8
MET 0.008 0.061 -9999 0 -0.56 4 4
GNA14 -0.027 0.16 -9999 0 -0.62 24 24
GNA15 -0.002 0.092 -9999 0 -0.49 12 12
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 38 38
GNA11 -0.028 0.16 -9999 0 -0.63 24 24
LHCGR -0.001 0.025 -9999 0 -0.34 2 2
AGTR1 -0.019 0.14 -9999 0 -0.63 19 19
desensitization of G-protein coupled receptor protein signaling pathway 0 0.014 -9999 0 -10000 0 0
IPCEF1/ARNO -0.028 0.089 -9999 0 -0.45 1 1
alphaIIb/beta3 Integrin -0.043 0.15 -9999 0 -0.34 64 64
Effects of Botulinum toxin

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
STX1A 0.006 0.036 -9999 0 -0.23 8 8
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.009 0.038 -9999 0 -0.23 3 3
STXBP1 -0.002 0.097 -9999 0 -0.57 10 10
ACh/CHRNA1 -0.024 0.064 -9999 0 -0.22 21 21
RAB3GAP2/RIMS1/UNC13B 0.018 0.032 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0 0.044 -9999 0 -0.34 6 6
mol:ACh -0.024 0.054 -9999 0 -0.13 69 69
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.043 0.079 -9999 0 -0.32 12 12
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.024 0.064 -9999 0 -0.22 21 21
UNC13B 0.011 0.032 -9999 0 -0.34 3 3
CHRNA1 -0.01 0.081 -9999 0 -0.34 21 21
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.15 0.19 -9999 0 -0.37 144 144
SNAP25 -0.066 0.13 -9999 0 -0.33 65 65
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.2 0.28 -9999 0 -0.53 144 144
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.005 0.068 -9999 0 -0.4 8 8
STX1A/SNAP25 fragment 1/VAMP2 -0.043 0.079 -9999 0 -0.32 12 12
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.15 0.27 -9999 0 -0.56 108 108
CDC42/GTP -0.067 0.14 -9999 0 -0.38 27 27
PLCG1 -0.07 0.15 -9999 0 -0.39 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 0.021 0 -9999 0 -10000 0 0
cell migration -0.066 0.14 -9999 0 -0.37 27 27
S1PR5 -0.004 0.098 -9999 0 -0.5 13 13
S1PR4 0.002 0.075 -9999 0 -0.43 10 10
MAPK3 -0.07 0.15 -9999 0 -0.39 27 27
MAPK1 -0.071 0.15 -9999 0 -0.4 28 28
S1P/S1P5/Gi -0.085 0.16 -9999 0 -0.32 93 93
GNAI1 0.007 0.067 -9999 0 -0.63 4 4
CDC42/GDP 0.011 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.008 0.062 -9999 0 -0.4 7 7
RHOA 0.026 0.039 -9999 0 -0.33 3 3
S1P/S1P4/Gi -0.082 0.16 -9999 0 -0.31 89 89
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.086 0.22 -9999 0 -0.55 66 66
S1P/S1P4/G12/G13 0.021 0.042 -9999 0 -0.36 3 3
GNA12 0.014 0 -9999 0 -10000 0 0
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.018 0.056 -9999 0 -0.39 7 7
EPHB2 -0.095 0.2 -9999 0 -0.43 92 92
Syndecan-2/TACI 0.001 0.079 -9999 0 -0.39 10 10
LAMA1 -0.079 0.2 -9999 0 -0.47 69 69
Syndecan-2/alpha2 ITGB1 -0.041 0.15 -9999 0 -0.35 56 56
HRAS 0.012 0.026 -9999 0 -0.34 2 2
Syndecan-2/CASK 0.008 0.052 -9999 0 -0.4 6 6
ITGA5 0.012 0.026 -9999 0 -0.34 2 2
BAX 0.009 0.1 -9999 0 -10000 0 0
EPB41 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.047 -9999 0 -0.35 6 6
LAMA3 -0.071 0.19 -9999 0 -0.45 68 68
EZR 0.009 0.058 -9999 0 -0.63 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.024 0.15 -9999 0 -0.61 23 23
Syndecan-2/MMP2 -0.02 0.12 -9999 0 -0.4 33 33
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.021 0.12 -9999 0 -0.3 50 50
dendrite morphogenesis -0.047 0.14 -9999 0 -0.41 33 33
Syndecan-2/GM-CSF 0.012 0.053 -9999 0 -0.39 6 6
determination of left/right symmetry 0.012 0.061 -9999 0 -0.46 6 6
Syndecan-2/PKC delta 0.019 0.052 -9999 0 -0.39 6 6
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.02 0.048 -9999 0 -0.35 6 6
MAPK1 0.019 0.052 -9999 0 -0.35 7 7
Syndecan-2/RACK1 0.025 0.047 -9999 0 -0.33 6 6
NF1 0.013 0.033 -9999 0 -0.63 1 1
FGFR/FGF/Syndecan-2 0.012 0.061 -9999 0 -0.46 6 6
ITGA2 -0.045 0.16 -9999 0 -0.43 50 50
MAPK8 0 0.11 -9999 0 -0.38 30 30
Syndecan-2/alpha2/beta1 Integrin -0.046 0.15 -9999 0 -0.35 60 60
Syndecan-2/Kininogen -0.021 0.14 -9999 0 -0.44 37 37
ITGB1 0.014 0 -9999 0 -10000 0 0
SRC 0.011 0.088 -9999 0 -0.31 25 25
Syndecan-2/CASK/Protein 4.1 0.017 0.048 -9999 0 -0.36 6 6
extracellular matrix organization 0.007 0.081 -9999 0 -0.44 9 9
actin cytoskeleton reorganization 0.018 0.056 -9999 0 -0.39 7 7
Syndecan-2/Caveolin-2/Ras 0.003 0.1 -9999 0 -0.35 28 28
Syndecan-2/Laminin alpha3 -0.033 0.13 -9999 0 -0.41 31 31
Syndecan-2/RasGAP 0.024 0.067 -9999 0 -0.32 13 13
alpha5/beta1 Integrin 0.02 0.018 -9999 0 -10000 0 0
PRKCD 0.014 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.047 0.14 -9999 0 -0.41 33 33
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.014 0.097 -9999 0 -0.3 32 32
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.015 0.1 -9999 0 -0.39 23 23
RASA1 0.002 0.088 -9999 0 -0.63 7 7
alpha2/beta1 Integrin -0.021 0.12 -9999 0 -0.3 50 50
Syndecan-2/Synbindin 0.019 0.052 -9999 0 -0.39 6 6
TGFB1 -0.005 0.09 -9999 0 -0.39 18 18
CASP3 0.025 0.052 -9999 0 -0.35 7 7
FN1 0.013 0.033 -9999 0 -0.63 1 1
Syndecan-2/IL8 -0.1 0.18 -9999 0 -0.4 87 87
SDC2 0.012 0.061 -9999 0 -0.46 6 6
KNG1 -0.048 0.19 -9999 0 -0.63 36 36
Syndecan-2/Neurofibromin 0.018 0.056 -9999 0 -0.39 7 7
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 0.005 0.019 -9999 0 -0.34 1 1
Syndecan-2/TGFB1 0.008 0.081 -9999 0 -0.45 9 9
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.048 -9999 0 -0.36 6 6
Syndecan-2/Ezrin 0.024 0.059 -9999 0 -0.35 9 9
PRKACA 0.025 0.052 -9999 0 -0.35 7 7
angiogenesis -0.1 0.18 -9999 0 -0.39 87 87
MMP2 -0.047 0.18 -9999 0 -0.53 42 42
IL8 -0.18 0.27 -9999 0 -0.52 133 133
calcineurin-NFAT signaling pathway 0.001 0.079 -9999 0 -0.39 10 10
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.1 -9999 0 -0.38 22 22
CRKL 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
DOCK1 -0.01 0.12 -9999 0 -0.63 14 14
ITGA4 -0.006 0.11 -9999 0 -0.53 14 14
alpha4/beta7 Integrin/MAdCAM1 -0.015 0.13 -9999 0 -0.38 33 33
EPO -0.18 0.26 -9999 0 -0.5 141 141
alpha4/beta7 Integrin -0.011 0.12 -9999 0 -0.44 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.018 -9999 0 -0.34 1 1
alpha4/beta1 Integrin 0.006 0.079 -9999 0 -0.46 9 9
EPO/EPOR (dimer) -0.13 0.2 -9999 0 -0.46 79 79
lamellipodium assembly 0.027 0.058 -9999 0 -0.46 4 4
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
PI3K 0.015 0.062 -9999 0 -0.56 4 4
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 -0.068 0.15 -9999 0 -0.31 86 86
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
MADCAM1 -0.033 0.14 -9999 0 -0.43 38 38
cell adhesion -0.016 0.13 -9999 0 -0.38 33 33
CRKL/CBL 0.019 0.035 -9999 0 -0.46 2 2
ITGB1 0.014 0 -9999 0 -10000 0 0
SRC -0.044 0.17 -9999 0 -0.41 53 53
ITGB7 -0.009 0.12 -9999 0 -0.61 14 14
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.034 0.15 -9999 0 -0.42 39 39
p130Cas/Crk/Dock1 -0.028 0.16 -9999 0 -0.58 16 16
VCAM1 -0.067 0.2 -9999 0 -0.51 58 58
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.025 0.063 -9999 0 -0.35 9 9
BCAR1 -0.034 0.16 -9999 0 -0.38 53 53
EPOR 0.012 0.038 -9999 0 -0.49 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0.047 -9999 0 -0.63 2 2
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.057 -9999 0 -0.48 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.005 0.16 -10000 0 -0.74 12 12
UGCG -0.071 0.24 -10000 0 -0.73 41 41
AKT1/mTOR/p70S6K/Hsp90/TERT -0.035 0.17 -10000 0 -0.38 50 50
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.068 0.24 -10000 0 -0.72 41 41
mol:DAG -0.001 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.068 0.16 -10000 0 -0.42 51 51
FRAP1 -0.014 0.22 -10000 0 -0.49 51 51
FOXO3 -0.009 0.21 -10000 0 -0.47 51 51
AKT1 -0.02 0.22 -10000 0 -0.52 52 52
GAB2 0.014 0.004 -10000 0 -10000 0 0
SMPD1 0.01 0.037 -10000 0 -10000 0 0
SGMS1 0.01 0.037 -10000 0 -10000 0 0
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 0.015 0.055 -10000 0 -0.49 4 4
CALM1 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.048 0.22 -10000 0 -0.4 70 70
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.018 0.063 -10000 0 -0.56 4 4
RPS6KB1 0.007 0.049 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 26 26
JAK3 -0.009 0.11 -10000 0 -0.46 19 19
PIK3R1 0.011 0.058 -10000 0 -0.63 3 3
JAK1 0.016 0.005 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC -0.062 0.34 -10000 0 -0.88 48 48
MYB -0.038 0.23 -10000 0 -0.92 17 17
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.014 0.2 -10000 0 -0.6 29 29
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.047 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.013 0.2 -10000 0 -0.58 29 29
Rac1/GDP 0.022 0.051 -10000 0 -0.44 4 4
T cell proliferation -0.024 0.2 -10000 0 -0.52 35 35
SHC1 0.014 0.004 -10000 0 -10000 0 0
RAC1 0.014 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0 0.015 -10000 0 -0.038 44 44
PRKCZ -0.027 0.21 -10000 0 -0.55 35 35
NF kappa B1 p50/RelA -0.06 0.16 -10000 0 -0.49 31 31
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.005 0.18 -10000 0 -0.6 25 25
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.059 0.18 -10000 0 -0.45 58 58
IL2RB -0.007 0.11 -10000 0 -0.52 16 16
TERT -0.14 0.23 -10000 0 -0.45 122 122
E2F1 -0.012 0.11 -10000 0 -0.46 17 17
SOS1 0.013 0.019 -10000 0 -0.34 1 1
RPS6 0.013 0.018 -10000 0 -0.34 1 1
mol:cAMP 0 0.007 0.018 44 -10000 0 44
PTPN11 0.014 0.004 -10000 0 -10000 0 0
IL2RG -0.037 0.16 -10000 0 -0.49 39 39
actin cytoskeleton organization -0.024 0.2 -10000 0 -0.52 35 35
GRB2 0.014 0.004 -10000 0 -10000 0 0
IL2 0.005 0.019 -10000 0 -0.34 1 1
PIK3CA 0.012 0.048 -10000 0 -0.63 2 2
Rac1/GTP 0.029 0.051 -10000 0 -0.42 4 4
LCK -0.031 0.16 -10000 0 -0.52 33 33
BCL2 0.002 0.18 -10000 0 -0.53 23 23
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.051 0.23 12 -10000 0 12
AES 0.032 0.045 0.24 4 -10000 0 4
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.003 0.083 -10000 0 -0.46 9 9
SMAD4 0.011 0.047 -10000 0 -0.63 2 2
DKK2 -0.078 0.2 -10000 0 -0.48 69 69
TLE1 0.028 0.052 0.23 3 -0.64 1 4
MACF1 0.015 0.001 -10000 0 -10000 0 0
CTNNB1 0.04 0.08 0.3 4 -0.35 2 6
WIF1 -0.025 0.096 -10000 0 -0.34 31 31
beta catenin/RanBP3 0.099 0.19 0.45 65 -10000 0 65
KREMEN2 -0.023 0.1 -10000 0 -0.34 36 36
DKK1 -0.16 0.23 -10000 0 -0.44 141 141
beta catenin/beta TrCP1 0.047 0.076 0.29 4 -10000 0 4
FZD1 -0.01 0.11 -10000 0 -0.49 18 18
AXIN2 -0.2 0.45 -10000 0 -1.5 37 37
AXIN1 0.01 0.058 -10000 0 -0.63 3 3
RAN 0.015 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.023 0.067 -10000 0 -0.56 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.1 0.3 2 -0.48 3 5
Axin1/APC/GSK3 0.052 0.068 0.26 4 -0.39 1 5
Axin1/APC/GSK3/beta catenin/Macf1 0.044 0.081 -10000 0 -0.54 2 2
HNF1A 0.023 0.079 0.25 2 -0.62 4 6
CTBP1 0.03 0.041 0.24 3 -10000 0 3
MYC -0.16 0.47 -10000 0 -1.5 36 36
RANBP3 0.015 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.049 0.14 -10000 0 -0.39 34 34
NKD1 -0.14 0.23 -10000 0 -0.44 127 127
TCF4 0.028 0.069 0.27 3 -0.52 3 6
TCF3 0.03 0.04 0.24 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.014 0.083 -10000 0 -0.38 12 12
Ran/GTP 0.012 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.11 0.24 0.58 58 -0.44 2 60
LEF1 -0.07 0.22 0.25 2 -0.5 69 71
DVL1 0.044 0.034 -10000 0 -10000 0 0
CSNK2A1 0.015 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.017 0.14 -10000 0 -0.44 18 18
DKK1/LRP6/Kremen 2 -0.097 0.16 -10000 0 -0.39 63 63
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.035 0.051 0.24 12 -10000 0 12
NLK 0.012 0.006 -10000 0 -10000 0 0
CCND1 -0.12 0.39 -10000 0 -1.5 25 25
WNT1 0.002 0.051 -10000 0 -0.34 8 8
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.047 -10000 0 -0.63 2 2
PPP2R5D 0.092 0.1 0.24 105 -10000 0 105
APC 0.018 0.077 -10000 0 -0.35 12 12
WNT1/LRP6/FZD1 0.032 0.06 -10000 0 -0.28 7 7
CREBBP 0.03 0.04 0.24 3 -10000 0 3
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.002 -9999 0 -10000 0 0
SMARCC1 0.008 0.01 -9999 0 -10000 0 0
REL -0.003 0.11 -9999 0 -0.6 11 11
HDAC7 -0.051 0.17 -9999 0 -0.49 25 25
JUN 0.01 0.047 -9999 0 -0.63 2 2
EP300 0.014 0 -9999 0 -10000 0 0
KAT2B 0.007 0.067 -9999 0 -0.63 4 4
KAT5 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.14 -9999 0 -0.45 34 34
FOXO1 0.01 0.037 -9999 0 -0.34 4 4
T-DHT/AR -0.056 0.18 -9999 0 -0.51 26 26
MAP2K6 -0.05 0.19 -9999 0 -0.58 39 39
BRM/BAF57 0.004 0.083 -9999 0 -0.46 11 11
MAP2K4 0.012 0.007 -9999 0 -10000 0 0
SMARCA2 -0.007 0.11 -9999 0 -0.61 12 12
PDE9A -0.19 0.41 -9999 0 -1.1 59 59
NCOA2 -0.098 0.24 -9999 0 -0.63 64 64
CEBPA -0.006 0.11 -9999 0 -0.61 12 12
EHMT2 0.014 0.002 -9999 0 -10000 0 0
cell proliferation -0.061 0.2 -9999 0 -0.49 34 34
NR0B1 -0.059 0.17 -9999 0 -0.46 50 50
EGR1 -0.029 0.16 -9999 0 -0.57 27 27
RXRs/9cRA -0.047 0.12 -9999 0 -0.36 37 37
AR/RACK1/Src -0.064 0.17 -9999 0 -0.47 38 38
AR/GR -0.062 0.16 -9999 0 -0.4 41 41
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.01 0.051 -9999 0 -0.54 3 3
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 -0.013 0.12 -9999 0 -0.47 24 24
T-DHT/AR/TIF2/CARM1 -0.1 0.24 -9999 0 -0.57 57 57
SRC -0.047 0.17 -9999 0 -0.38 66 66
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.069 0.21 -9999 0 -1.1 10 10
APPBP2 0.012 0.007 -9999 0 -10000 0 0
TRIM24 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.051 0.16 -9999 0 -0.41 52 52
TMPRSS2 -0.088 0.28 -9999 0 -1.2 20 20
RXRG -0.11 0.22 -9999 0 -0.44 101 101
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.012 0.033 -9999 0 -0.63 1 1
RXRB 0.014 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.002 -9999 0 -10000 0 0
NR2C2 -0.019 0.14 -9999 0 -0.63 19 19
KLK2 -0.095 0.21 -9999 0 -0.53 48 48
AR -0.075 0.18 -9999 0 -0.36 81 81
SENP1 0.014 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.016 0.005 -9999 0 -10000 0 0
SRY 0 0.026 -9999 0 -0.34 2 2
GATA2 -0.003 0.096 -9999 0 -0.51 12 12
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.073 0.18 -9999 0 -0.44 64 64
T-DHT/AR/RACK1/Src -0.063 0.18 -9999 0 -0.48 38 38
positive regulation of transcription -0.003 0.096 -9999 0 -0.51 12 12
DNAJA1 0.012 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.002 -9999 0 -10000 0 0
NCOA1 0.019 0.005 -9999 0 -10000 0 0
SPDEF -0.053 0.14 -9999 0 -0.34 66 66
T-DHT/AR/TIF2 -0.058 0.19 -9999 0 -0.49 44 44
T-DHT/AR/Hsp90 -0.051 0.16 -9999 0 -0.41 52 52
GSK3B 0.014 0.003 -9999 0 -10000 0 0
NR2C1 0.015 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.037 0.15 -9999 0 -0.38 52 52
SIRT1 0.009 0.058 -9999 0 -0.63 3 3
ZMIZ2 0.016 0.005 -9999 0 -10000 0 0
POU2F1 0.011 0.054 -9999 0 -0.48 2 2
T-DHT/AR/DAX-1 -0.09 0.18 -9999 0 -0.42 64 64
CREBBP 0.014 0 -9999 0 -10000 0 0
SMARCE1 0.014 0.003 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.035 -10000 0 -0.63 1 1
SVIL 0.003 0.075 -10000 0 -0.64 5 5
ZNF318 0.021 0.027 0.21 1 -10000 0 1
JMJD2C -0.004 0.022 -10000 0 -0.066 36 36
T-DHT/AR/Ubc9 -0.081 0.18 -10000 0 -0.43 73 73
CARM1 0.014 0.001 -10000 0 -10000 0 0
PRDX1 0.015 0.001 -10000 0 -10000 0 0
PELP1 0.015 0.004 -10000 0 -10000 0 0
CTNNB1 0.012 0.009 -10000 0 -10000 0 0
AKT1 0.016 0.007 -10000 0 -10000 0 0
PTK2B 0.013 0.006 -10000 0 -10000 0 0
MED1 0.016 0.007 -10000 0 -10000 0 0
MAK 0.018 0.028 0.21 2 -10000 0 2
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 -0.018 0.14 -10000 0 -0.63 17 17
GSN 0.009 0.04 -10000 0 -0.5 2 2
NCOA2 -0.097 0.24 -10000 0 -0.63 64 64
NCOA6 0.012 0.01 -10000 0 -10000 0 0
DNA-PK 0.035 0.025 -10000 0 -10000 0 0
NCOA4 0.014 0.001 -10000 0 -10000 0 0
PIAS3 0.012 0.009 -10000 0 -10000 0 0
cell proliferation -0.015 0.038 -10000 0 -10000 0 0
XRCC5 0.016 0.006 -10000 0 -10000 0 0
UBE3A 0.011 0.017 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.12 0.22 -10000 0 -0.46 96 96
FHL2 -0.09 0.31 -10000 0 -1.1 30 30
RANBP9 0.012 0.01 -10000 0 -10000 0 0
JMJD1A -0.007 0.053 -10000 0 -0.13 57 57
CDK6 -0.067 0.21 -10000 0 -0.61 48 48
TGFB1I1 0 0.081 -10000 0 -0.52 8 8
T-DHT/AR/CyclinD1 -0.11 0.2 -10000 0 -0.44 91 91
XRCC6 0.016 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.091 0.21 -10000 0 -0.44 81 81
CTDSP1 0.014 0.003 -10000 0 -10000 0 0
CTDSP2 0.018 0.018 -10000 0 -10000 0 0
BRCA1 0.011 0.021 -10000 0 -0.34 1 1
TCF4 0.013 0.052 -10000 0 -0.54 3 3
CDKN2A -0.061 0.2 -10000 0 -0.55 51 51
SRF 0.012 0.038 -10000 0 -10000 0 0
NKX3-1 -0.13 0.36 -10000 0 -1.1 40 40
KLK3 -0.045 0.22 -10000 0 -1.5 8 8
TMF1 0.014 0.002 -10000 0 -10000 0 0
HNRNPA1 0.017 0.011 -10000 0 -10000 0 0
AOF2 -0.003 0.011 -10000 0 -0.073 8 8
APPL1 0.025 0.03 -10000 0 -0.46 1 1
T-DHT/AR/Caspase 8 -0.079 0.18 -10000 0 -0.43 72 72
AR -0.13 0.26 -10000 0 -0.62 80 80
UBA3 0.014 0.003 -10000 0 -10000 0 0
PATZ1 0.017 0.011 -10000 0 -10000 0 0
PAWR 0.014 0.002 -10000 0 -10000 0 0
PRKDC 0.016 0.006 -10000 0 -10000 0 0
PA2G4 0.017 0.012 -10000 0 -10000 0 0
UBE2I 0.014 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.072 0.17 -10000 0 -0.39 73 73
RPS6KA3 -0.004 0.1 -10000 0 -0.63 9 9
T-DHT/AR/ARA70 -0.081 0.18 -10000 0 -0.43 73 73
LATS2 0.016 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.07 0.17 -10000 0 -0.39 73 73
Cyclin D3/CDK11 p58 0.011 0.002 -10000 0 -10000 0 0
VAV3 -0.011 0.095 -10000 0 -0.37 23 23
KLK2 -0.068 0.13 -10000 0 -0.52 12 12
CASP8 0.015 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.13 0.24 -10000 0 -0.46 111 111
TMPRSS2 -0.086 0.28 -10000 0 -1.2 19 19
CCND1 -0.031 0.16 -10000 0 -0.57 28 28
PIAS1 0.011 0.017 -10000 0 -10000 0 0
mol:T-DHT -0.011 0.032 -10000 0 -0.077 58 58
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.008 0.026 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.22 -10000 0 -0.45 110 110
CMTM2 0.001 0.063 -10000 0 -0.34 12 12
SNURF -0.046 0.18 -10000 0 -0.58 36 36
ZMIZ1 0.004 0.035 -10000 0 -0.37 1 1
CCND3 0.014 0.001 -10000 0 -10000 0 0
TGIF1 0.017 0.011 -10000 0 -10000 0 0
FKBP4 0.012 0.01 -10000 0 -10000 0 0
IL27-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
TGFB1 -0.005 0.091 -10000 0 -0.39 18 18
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.089 0.19 0.59 23 -10000 0 23
IL27/IL27R/JAK1 -0.1 0.22 -10000 0 -0.67 19 19
TBX21 -0.088 0.22 -10000 0 -0.57 33 33
IL12B 0.004 0.037 -10000 0 -0.34 4 4
IL12A -0.001 0.054 -10000 0 -0.25 16 16
IL6ST -0.14 0.27 -10000 0 -0.63 86 86
IL27RA/JAK1 0.011 0.034 -10000 0 -10000 0 0
IL27 -0.072 0.22 -10000 0 -0.63 49 49
TYK2 0.014 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.028 0.099 -10000 0 -0.57 1 1
T-helper 2 cell differentiation 0.089 0.19 0.59 23 -10000 0 23
T cell proliferation during immune response 0.089 0.19 0.59 23 -10000 0 23
MAPKKK cascade -0.089 0.19 -10000 0 -0.59 23 23
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.014 0 -10000 0 -10000 0 0
STAT1 0.01 0.041 -10000 0 -0.34 5 5
IL12RB1 -0.026 0.14 -10000 0 -0.5 29 29
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.23 -10000 0 -0.6 39 39
IL27/IL27R/JAK2/TYK2 -0.09 0.2 -10000 0 -0.61 22 22
positive regulation of T cell mediated cytotoxicity -0.089 0.19 -10000 0 -0.59 23 23
STAT1 (dimer) -0.15 0.25 0.52 8 -0.74 28 36
JAK2 0.01 0.044 -10000 0 -0.45 3 3
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.079 0.18 -10000 0 -0.59 21 21
T cell proliferation -0.12 0.2 -10000 0 -0.57 33 33
IL12/IL12R/TYK2/JAK2 -0.001 0.084 -10000 0 -10000 0 0
IL17A -0.03 0.099 -10000 0 -0.57 1 1
mast cell activation 0.089 0.19 0.59 23 -10000 0 23
IFNG -0.012 0.034 -10000 0 -0.084 32 32
T cell differentiation -0.005 0.007 -10000 0 -0.022 18 18
STAT3 (dimer) -0.079 0.18 -10000 0 -0.61 19 19
STAT5A (dimer) -0.081 0.19 -10000 0 -0.57 23 23
STAT4 (dimer) -0.1 0.21 -10000 0 -0.6 33 33
STAT4 -0.035 0.16 -10000 0 -0.56 32 32
T cell activation -0.012 0.009 0.044 2 -10000 0 2
IL27R/JAK2/TYK2 -0.055 0.17 -10000 0 -0.73 1 1
GATA3 -0.066 0.36 -10000 0 -1.4 25 25
IL18 -0.016 0.11 -10000 0 -0.4 25 25
positive regulation of mast cell cytokine production -0.078 0.18 -10000 0 -0.59 20 20
IL27/EBI3 -0.071 0.19 -10000 0 -0.46 70 70
IL27RA 0.001 0.035 -10000 0 -10000 0 0
IL6 -0.061 0.18 -10000 0 -0.46 58 58
STAT5A 0.011 0.042 -10000 0 -0.44 3 3
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.007 0.022 -10000 0 -10000 0 0
IL1B -0.03 0.13 -10000 0 -0.38 39 39
EBI3 -0.024 0.15 -10000 0 -0.58 23 23
TNF -0.016 0.1 -10000 0 -0.4 24 24
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.008 0.082 -10000 0 -0.27 29 29
epithelial cell differentiation 0.004 0.094 -10000 0 -0.33 28 28
CYFIP2 -0.045 0.18 -10000 0 -0.55 39 39
ENAH 0.034 0.086 -10000 0 -0.37 4 4
EGFR -0.007 0.11 -10000 0 -0.59 13 13
EPHA2 0.003 0.083 -10000 0 -0.59 7 7
MYO6 0.004 0.11 -10000 0 -0.34 33 33
CTNNB1 0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.009 0.11 -10000 0 -0.39 28 28
AQP5 -0.024 0.072 -10000 0 -0.36 2 2
CTNND1 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.011 0.09 -10000 0 -0.3 28 28
regulation of calcium-dependent cell-cell adhesion -0.002 0.1 -10000 0 -0.31 33 33
EGF -0.077 0.16 -10000 0 -0.36 84 84
NCKAP1 0.014 0 -10000 0 -10000 0 0
AQP3 -0.04 0.13 -10000 0 -0.6 15 15
cortical microtubule organization 0.004 0.094 -10000 0 -0.33 28 28
GO:0000145 0.01 0.086 -10000 0 -0.29 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.007 0.096 -10000 0 -0.33 28 28
MLLT4 0.011 0.047 -10000 0 -0.63 2 2
ARF6/GDP -0.027 0.086 -10000 0 -0.53 4 4
ARF6 0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.066 -10000 0 -0.35 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.021 0.092 -10000 0 -0.45 2 2
PVRL2 0.013 0.018 -10000 0 -0.34 1 1
ZYX 0.01 0.097 -10000 0 -0.32 29 29
ARF6/GTP 0.029 0.061 -10000 0 -0.32 11 11
CDH1 -0.034 0.17 -10000 0 -0.63 28 28
EGFR/EGFR/EGF/EGF -0.062 0.12 -10000 0 -0.34 42 42
RhoA/GDP -0.023 0.08 -10000 0 -0.3 28 28
actin cytoskeleton organization 0.01 0.11 -10000 0 -0.32 33 33
IGF-1R heterotetramer -0.036 0.14 -10000 0 -0.41 44 44
GIT1 0.014 0 -10000 0 -10000 0 0
IGF1R -0.036 0.14 -10000 0 -0.41 44 44
IGF1 -0.092 0.23 -10000 0 -0.57 68 68
DIAPH1 -0.052 0.18 -10000 0 -0.66 29 29
Wnt receptor signaling pathway -0.004 0.094 0.33 28 -10000 0 28
RHOA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.027 0.087 -10000 0 -0.53 4 4
CTNNA1 0.014 0 -10000 0 -10000 0 0
VCL 0.01 0.11 -10000 0 -0.34 28 28
EFNA1 0.009 0.058 -10000 0 -0.63 3 3
LPP 0.017 0.09 -10000 0 -0.36 2 2
Ephrin A1/EPHA2 -0.03 0.099 -10000 0 -0.33 33 33
SEC6/SEC8 -0.022 0.072 -10000 0 -10000 0 0
MGAT3 -0.002 0.1 -10000 0 -0.31 33 33
HGF/MET -0.065 0.13 -10000 0 -0.32 61 61
HGF -0.084 0.21 -10000 0 -0.48 74 74
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.008 0.083 -10000 0 -0.28 29 29
actin cable formation 0.043 0.089 -10000 0 -0.3 5 5
KIAA1543 0.008 0.11 -10000 0 -0.32 36 36
KIFC3 0.012 0.091 -10000 0 -0.31 28 28
NCK1 0.011 0.047 -10000 0 -0.63 2 2
EXOC3 0.014 0 -10000 0 -10000 0 0
ACTN1 0.011 0.093 -10000 0 -0.31 28 28
NCK1/GIT1 0.019 0.035 -10000 0 -0.46 2 2
mol:GDP 0.004 0.094 -10000 0 -0.33 28 28
EXOC4 0.014 0 -10000 0 -10000 0 0
STX4 0.012 0.091 -10000 0 -0.31 28 28
PIP5K1C 0.011 0.091 -10000 0 -0.31 28 28
LIMA1 0.012 0.038 -10000 0 -0.49 2 2
ABI1 0.014 0 -10000 0 -10000 0 0
ROCK1 0.032 0.092 -10000 0 -0.45 4 4
adherens junction assembly 0.021 0.12 -10000 0 -0.64 4 4
IGF-1R heterotetramer/IGF1 -0.089 0.15 -10000 0 -0.5 20 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.038 -10000 0 -0.46 2 2
MET 0.008 0.061 -10000 0 -0.56 4 4
PLEKHA7 0.006 0.099 -10000 0 -0.31 34 34
mol:GTP 0.024 0.066 -10000 0 -0.35 11 11
establishment of epithelial cell apical/basal polarity 0.035 0.084 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.008 0.082 -10000 0 -0.27 29 29
regulation of cell-cell adhesion 0.01 0.11 -10000 0 -0.32 33 33
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.008 0.083 -10000 0 -0.28 29 29
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.022 0.17 -9999 0 -0.47 37 37
MAP4K1 -0.028 0.15 -9999 0 -0.51 30 30
MAP3K8 -0.012 0.12 -9999 0 -0.56 17 17
PRKCB -0.027 0.15 -9999 0 -0.53 28 28
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.006 0.12 -9999 0 -0.57 10 10
JUN -0.046 0.22 -9999 0 -0.61 44 44
MAP3K7 0.006 0.12 -9999 0 -0.57 10 10
GRAP2 -0.033 0.16 -9999 0 -0.53 32 32
CRK 0.013 0.018 -9999 0 -0.34 1 1
MAP2K4 0.008 0.13 -9999 0 -0.53 12 12
LAT 0.008 0.057 -9999 0 -0.46 5 5
LCP2 0.005 0.071 -9999 0 -0.54 6 6
MAPK8 -0.054 0.23 -9999 0 -0.67 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.001 0.13 -9999 0 -0.6 10 10
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.013 0.16 -9999 0 -0.44 37 37
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.034 0.12 -10000 0 -0.71 8 8
HDAC1 0.016 0.017 -10000 0 -10000 0 0
AES 0.015 0.007 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 -0.11 0.25 -10000 0 -0.6 75 75
LRP6/FZD1 0.004 0.083 -10000 0 -0.46 9 9
TLE1 0.013 0.034 -10000 0 -0.63 1 1
AP1 -0.075 0.16 -10000 0 -0.37 67 67
NCSTN 0.013 0.033 -10000 0 -0.63 1 1
ADAM10 0.002 0.088 -10000 0 -0.63 7 7
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.11 -10000 0 -0.51 2 2
NICD/RBPSUH 0.022 0.095 -10000 0 -0.65 7 7
WIF1 -0.025 0.096 -10000 0 -0.34 31 31
NOTCH1 -0.013 0.095 -10000 0 -0.69 7 7
PSENEN 0.013 0.018 -10000 0 -0.34 1 1
KREMEN2 -0.023 0.1 -10000 0 -0.34 36 36
DKK1 -0.16 0.23 -10000 0 -0.44 141 141
beta catenin/beta TrCP1 0.059 0.071 0.28 5 -10000 0 5
APH1B 0.009 0.058 -10000 0 -0.63 3 3
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 -0.014 0.056 0.24 1 -0.34 7 8
CtBP/CBP/TCF1/TLE1/AES 0.039 0.071 0.29 10 -0.38 3 13
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.058 0.19 -10000 0 -0.51 51 51
JUN 0.011 0.047 -10000 0 -0.63 2 2
MAP3K7 0.015 0.007 -10000 0 -10000 0 0
CTNNB1 0.054 0.075 0.22 31 -10000 0 31
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.05 0.14 -10000 0 -0.4 34 34
HNF1A 0.008 0.067 -10000 0 -0.63 4 4
CTBP1 0.015 0.007 -10000 0 -10000 0 0
MYC -0.12 0.44 -10000 0 -1.5 35 35
NKD1 -0.14 0.23 -10000 0 -0.44 127 127
FZD1 -0.01 0.11 -10000 0 -0.49 18 18
NOTCH1 precursor/Deltex homolog 1 -0.044 0.16 -10000 0 -0.6 10 10
apoptosis -0.074 0.16 -10000 0 -0.37 67 67
Delta 1/NOTCHprecursor -0.002 0.13 -10000 0 -0.7 8 8
DLL1 -0.032 0.16 -10000 0 -0.51 33 33
PPARD 0.013 0.038 -10000 0 -10000 0 0
Gamma Secretase 0.038 0.039 -10000 0 -0.32 4 4
APC -0.01 0.04 0.24 1 -0.24 6 7
DVL1 0.022 0.022 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0.007 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.097 0.16 -10000 0 -0.39 63 63
LRP6 0.014 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.019 0.017 -10000 0 -10000 0 0
CCND1 -0.073 0.36 -10000 0 -1.5 22 22
WNT1 0.002 0.051 -10000 0 -0.34 8 8
Axin1/APC/beta catenin 0.046 0.054 0.33 1 -10000 0 1
DKK2 -0.078 0.2 -10000 0 -0.48 69 69
NOTCH1 precursor/DVL1 -0.005 0.082 -10000 0 -0.58 7 7
GSK3B 0.014 0.002 -10000 0 -10000 0 0
FRAT1 0.011 0.047 -10000 0 -0.63 2 2
NOTCH/Deltex homolog 1 -0.072 0.15 -10000 0 -0.61 10 10
PPP2R5D 0.074 0.11 0.24 99 -10000 0 99
MAPK1 0.013 0.033 -10000 0 -0.63 1 1
WNT1/LRP6/FZD1 -0.007 0.086 -10000 0 -0.35 13 13
RBPJ 0.013 0.018 -10000 0 -0.34 1 1
CREBBP 0.016 0.006 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.046 0.15 -10000 0 -0.41 51 51
TP53 -0.031 0.083 -10000 0 -0.38 13 13
Senescence -0.031 0.082 -10000 0 -0.38 13 13
Apoptosis -0.031 0.082 -10000 0 -0.38 13 13
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.086 0.28 37 -10000 0 37
MDM4 0.014 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.038 -9999 0 -0.49 2 2
LAT2 -0.024 0.13 -9999 0 -0.41 23 23
AP1 -0.08 0.16 -9999 0 -0.55 25 25
mol:PIP3 -0.024 0.17 -9999 0 -0.56 20 20
IKBKB -0.004 0.1 -9999 0 -0.3 23 23
AKT1 -0.006 0.12 -9999 0 -0.42 10 10
IKBKG -0.004 0.11 -9999 0 -0.29 28 28
MS4A2 -0.029 0.13 -9999 0 -0.43 32 32
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.048 -9999 0 -0.64 2 2
MAP3K1 -0.003 0.13 -9999 0 -0.51 15 15
mol:Ca2+ -0.013 0.13 -9999 0 -0.4 20 20
LYN 0.012 0.034 -9999 0 -0.64 1 1
CBLB -0.016 0.11 -9999 0 -0.36 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.008 0.088 -9999 0 -0.38 18 18
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.054 -9999 0 -0.49 4 4
PLD2 -0.03 0.13 -9999 0 -0.33 48 48
PTPN13 -0.037 0.14 -9999 0 -0.51 12 12
PTPN11 0.013 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.015 0.1 -9999 0 -0.33 10 10
SYK -0.006 0.1 -9999 0 -0.46 16 16
GRB2 0.014 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.07 0.15 -9999 0 -0.55 22 22
LAT -0.019 0.12 -9999 0 -0.41 16 16
PAK2 -0.013 0.15 -9999 0 -0.57 16 16
NFATC2 -0.12 0.23 -9999 0 -0.62 63 63
HRAS -0.023 0.16 -9999 0 -0.62 17 17
GAB2 0.014 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.024 -9999 0 -10000 0 0
Fc epsilon R1 -0.074 0.15 -9999 0 -0.42 48 48
Antigen/IgE/Fc epsilon R1 -0.053 0.14 -9999 0 -0.39 48 48
mol:GDP -0.031 0.18 -9999 0 -0.59 22 22
JUN 0.011 0.047 -9999 0 -0.63 2 2
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
FOS -0.058 0.19 -9999 0 -0.51 51 51
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.025 0.12 -9999 0 -0.39 19 19
CHUK -0.004 0.1 -9999 0 -0.3 23 23
KLRG1 -0.025 0.12 -9999 0 -0.38 22 22
VAV1 -0.036 0.16 -9999 0 -0.43 35 35
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.018 0.11 -9999 0 -0.4 15 15
negative regulation of mast cell degranulation -0.018 0.12 -9999 0 -0.45 13 13
BTK -0.029 0.17 -9999 0 -0.68 16 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.08 0.2 -9999 0 -0.55 36 36
GAB2/PI3K/SHP2 -0.052 0.11 -9999 0 -0.44 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.13 -9999 0 -0.42 20 20
RAF1 0.024 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.21 -9999 0 -0.42 90 90
FCER1G 0 0.082 -9999 0 -0.45 11 11
FCER1A -0.069 0.2 -9999 0 -0.5 59 59
Antigen/IgE/Fc epsilon R1/Fyn -0.043 0.14 -9999 0 -0.36 48 48
MAPK3 0.033 0.021 -9999 0 -10000 0 0
MAPK1 0.033 0.022 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.019 0.15 -9999 0 -0.56 24 24
DUSP1 -0.007 0.11 -9999 0 -0.63 12 12
NF-kappa-B/RelA -0.023 0.05 -9999 0 -0.22 6 6
actin cytoskeleton reorganization -0.012 0.11 -9999 0 -0.47 8 8
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.14 -9999 0 -0.58 18 18
FER -0.016 0.11 -9999 0 -0.41 13 13
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.049 0.13 -9999 0 -0.48 29 29
SOS1 0.013 0.018 -9999 0 -0.34 1 1
PLCG1 -0.027 0.17 -9999 0 -0.61 20 20
cytokine secretion -0.017 0.036 -9999 0 -10000 0 0
SPHK1 -0.076 0.17 -9999 0 -0.4 55 55
PTK2 -0.014 0.11 -9999 0 -0.49 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.073 0.16 -9999 0 -0.61 20 20
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.019 0.16 -9999 0 -0.53 20 20
MAP2K2 0.029 0.023 -9999 0 -10000 0 0
MAP2K1 0.029 0.022 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.023 0.12 -9999 0 -0.38 18 18
MAP2K4 0.021 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.44 90 90
mol:Choline -0.03 0.13 -9999 0 -0.33 48 48
SHC/Grb2/SOS1 -0.003 0.11 -9999 0 -0.43 9 9
FYN 0.013 0.018 -9999 0 -0.34 1 1
DOK1 0.014 0 -9999 0 -10000 0 0
PXN -0.005 0.11 -9999 0 -0.48 6 6
HCLS1 -0.019 0.12 -9999 0 -0.41 17 17
PRKCB -0.019 0.14 -9999 0 -0.41 29 29
FCGR2B -0.11 0.24 -9999 0 -0.54 82 82
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.12 -9999 0 -0.46 13 13
LCP2 0.005 0.072 -9999 0 -0.54 6 6
PLA2G4A -0.044 0.16 -9999 0 -0.4 44 44
RASA1 0.002 0.088 -9999 0 -0.63 7 7
mol:Phosphatidic acid -0.03 0.13 -9999 0 -0.33 48 48
IKK complex 0.012 0.083 -9999 0 -0.22 21 21
WIPF1 0.003 0.076 -9999 0 -0.49 8 8
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.003 0.12 -9999 0 -0.4 28 28
E-cadherin/beta catenin -0.015 0.13 -9999 0 -0.46 28 28
CTNNB1 0.014 0 -9999 0 -10000 0 0
JUP 0.013 0.033 -9999 0 -0.63 1 1
CDH1 -0.034 0.17 -9999 0 -0.63 28 28
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.032 0.12 -10000 0 -0.34 49 49
TRAF2/ASK1 -0.034 0.14 -10000 0 -0.4 47 47
ATM 0.013 0.033 -10000 0 -0.63 1 1
MAP2K3 -0.017 0.086 -10000 0 -0.44 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.052 0.16 -10000 0 -0.39 53 53
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.036 0.17 -10000 0 -0.55 33 33
TXN 0.009 0 -10000 0 -10000 0 0
CALM1 0.014 0 -10000 0 -10000 0 0
GADD45A 0.004 0.081 -10000 0 -0.63 6 6
GADD45B -0.008 0.11 -10000 0 -0.57 14 14
MAP3K1 0.014 0 -10000 0 -10000 0 0
MAP3K6 0.011 0.042 -10000 0 -0.44 3 3
MAP3K7 0.014 0 -10000 0 -10000 0 0
MAP3K4 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.043 0.16 -10000 0 -0.45 51 51
TAK1/TAB family 0.002 0.02 0.19 2 -0.18 1 3
RAC1/OSM/MEKK3 0.028 0 -10000 0 -10000 0 0
TRAF2 0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.024 0.055 -10000 0 -0.33 2 2
TRAF6 0.008 0.02 -10000 0 -0.38 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.2 0.28 -10000 0 -0.53 148 148
CCM2 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.12 0.18 -10000 0 -0.4 94 94
MAPK11 0.005 0.065 -10000 0 -0.41 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.14 0.21 -10000 0 -0.41 126 126
OSM/MEKK3 0.021 0 -10000 0 -10000 0 0
TAOK1 0.01 0.051 -10000 0 -0.37 6 6
TAOK2 0.017 0.02 -10000 0 -0.37 1 1
TAOK3 0.017 0.02 -10000 0 -0.37 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.069 0.22 -10000 0 -0.63 48 48
MAP3K10 0.011 0.047 -10000 0 -0.63 2 2
MAP3K3 0.014 0 -10000 0 -10000 0 0
TRX/ASK1 -0.035 0.14 -10000 0 -0.39 48 48
GADD45/MTK1/MTK1 -0.012 0.12 -10000 0 -0.36 38 38
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.005 0.13 -10000 0 -1.3 3 3
VDR -0.04 0.17 -10000 0 -0.53 37 37
FAM120B 0.013 0.033 -10000 0 -0.63 1 1
RXRs/LXRs/DNA/9cRA -0.004 0.12 -10000 0 -0.38 11 11
RXRs/LXRs/DNA/Oxysterols 0.003 0.14 -10000 0 -0.45 21 21
MED1 0.014 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.062 -10000 0 -0.26 15 15
RXRs/NUR77 -0.036 0.14 -10000 0 -0.35 42 42
RXRs/PPAR -0.014 0.11 -10000 0 -0.28 44 44
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.029 0.12 -10000 0 -0.39 37 37
RARs/VDR/DNA/Vit D3 -0.009 0.11 -10000 0 -0.33 36 36
RARA 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.04 0.17 -10000 0 -0.53 37 37
RARs/RARs/DNA/9cRA 0.014 0.065 -10000 0 -0.33 11 11
RARG 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.013 0.06 -10000 0 -0.42 3 3
RARs/THRs/DNA/SMRT 0.024 0.062 -10000 0 -0.26 15 15
THRA 0.011 0.042 -10000 0 -0.44 3 3
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.029 0.12 -10000 0 -0.39 37 37
RXRs/PPAR/9cRA/PGJ2/DNA -0.03 0.14 0.29 3 -0.35 41 44
NR1H4 -0.005 0.11 -10000 0 -0.63 11 11
RXRs/LXRs/DNA -0.009 0.13 -10000 0 -0.46 4 4
NR1H2 0.018 0.011 -10000 0 -10000 0 0
NR1H3 0.018 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.054 0.16 -10000 0 -0.36 62 62
NR4A1 -0.004 0.093 -10000 0 -0.44 15 15
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.015 0.1 -10000 0 -0.32 15 15
RXRG -0.11 0.22 -10000 0 -0.44 101 101
RXR alpha/CCPG 0.022 0.036 -10000 0 -0.46 2 2
RXRA 0.016 0.035 -10000 0 -0.63 1 1
RXRB 0.018 0.012 -10000 0 -10000 0 0
THRB 0.009 0.058 -10000 0 -0.63 3 3
PPARG 0.006 0.069 -10000 0 -0.57 5 5
PPARD 0.014 0 -10000 0 -10000 0 0
TNF -0.026 0.26 -10000 0 -1.1 19 19
mol:Oxysterols 0.004 0.012 -10000 0 -10000 0 0
cholesterol transport 0.003 0.14 -10000 0 -0.45 21 21
PPARA 0.006 0.074 -10000 0 -0.63 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.011 0.12 -10000 0 -0.53 17 17
RXRs/NUR77/BCL2 -0.026 0.1 -10000 0 -0.28 44 44
SREBF1 0.007 0.15 -10000 0 -0.78 6 6
RXRs/RXRs/DNA/9cRA -0.03 0.14 0.29 3 -0.35 41 44
ABCA1 0.008 0.15 -10000 0 -0.84 5 5
RARs/THRs 0.024 0.077 -10000 0 -0.32 16 16
RXRs/FXR -0.037 0.15 -10000 0 -0.37 46 46
BCL2 0.006 0.066 -10000 0 -0.49 6 6
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.026 -9999 0 -0.34 2 2
EGFR -0.007 0.11 -9999 0 -0.59 13 13
EGF/EGFR -0.071 0.12 -9999 0 -0.34 45 45
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.016 0.1 -9999 0 -0.33 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.014 0.13 -9999 0 -0.54 19 19
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.077 0.16 -9999 0 -0.36 84 84
EGF/EGFR dimer/SHC -0.038 0.12 -9999 0 -0.4 19 19
mol:GDP -0.018 0.1 -9999 0 -0.33 20 20
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.014 0.12 -9999 0 -0.48 21 21
GRB2/SOS1 0.021 0.013 -9999 0 -0.22 1 1
HRAS/GTP -0.04 0.077 -9999 0 -0.3 18 18
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.041 0.079 -9999 0 -0.31 18 18
FRAP1 -0.019 0.095 -9999 0 -0.31 20 20
EGF/EGFR dimer -0.058 0.14 -9999 0 -0.47 19 19
SOS1 0.013 0.018 -9999 0 -0.34 1 1
GRB2 0.014 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.02 0.13 -9999 0 -0.48 23 23
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.014 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.006 0.09 -10000 0 -0.31 15 15
NT3 (dimer)/TRKC -0.046 0.16 -10000 0 -0.4 57 57
NT3 (dimer)/TRKB -0.16 0.26 -10000 0 -0.5 116 116
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.061 -10000 0 -0.45 4 4
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.01 0.09 -10000 0 -0.35 23 23
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
DYNLT1 0.014 0 -10000 0 -10000 0 0
NTRK1 0.002 0.051 -10000 0 -0.34 8 8
NTRK2 -0.13 0.25 -10000 0 -0.54 96 96
NTRK3 -0.012 0.1 -10000 0 -0.43 20 20
NT-4/5 (dimer)/TRKB -0.13 0.22 -10000 0 -0.46 97 97
neuron apoptosis 0.064 0.17 0.43 42 -0.22 3 45
SHC 2-3/Grb2 -0.07 0.18 0.23 3 -0.47 42 45
SHC1 0.014 0 -10000 0 -10000 0 0
SHC2 -0.089 0.18 0.22 4 -0.49 46 50
SHC3 -0.081 0.15 0.22 4 -0.49 33 37
STAT3 (dimer) -0.002 0.091 -10000 0 -0.36 22 22
NT3 (dimer)/TRKA -0.076 0.18 -10000 0 -0.44 65 65
RIN/GDP 0.017 0.065 -10000 0 -0.22 2 2
GIPC1 0.013 0.018 -10000 0 -0.34 1 1
KRAS 0.013 0.018 -10000 0 -0.34 1 1
DNAJA3 -0.03 0.14 0.25 6 -0.37 44 50
RIN/GTP 0.001 0.004 -10000 0 -10000 0 0
CCND1 -0.027 0.21 -10000 0 -0.86 22 22
MAGED1 0.002 0.088 -10000 0 -0.63 7 7
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.047 -10000 0 -0.34 7 7
SHC/GRB2/SOS1 0.029 0.011 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.005 0.1 -10000 0 -0.39 20 20
TRKA/NEDD4-2 0.013 0.036 -10000 0 -10000 0 0
ELMO1 0.006 0.069 -10000 0 -0.57 5 5
RhoG/GTP/ELMO1/DOCK1 -0.001 0.098 -10000 0 -0.44 16 16
NGF -0.011 0.12 -10000 0 -0.58 16 16
HRAS 0.012 0.026 -10000 0 -0.34 2 2
DOCK1 -0.01 0.12 -10000 0 -0.63 14 14
GAB2 0.014 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.014 0 -10000 0 -10000 0 0
DNM1 -0.057 0.18 -10000 0 -0.46 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0.018 -10000 0 -0.34 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.033 0.14 0.24 6 -0.38 41 47
mol:GDP 0.021 0.091 -10000 0 -0.31 4 4
NGF (dimer) -0.011 0.12 -10000 0 -0.58 16 16
RhoG/GDP 0.005 0.051 -10000 0 -0.42 5 5
RIT1/GDP 0.023 0.066 -10000 0 -0.22 2 2
TIAM1 -0.015 0.13 -10000 0 -0.53 20 20
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
BDNF (dimer)/TRKB -0.076 0.17 -10000 0 -0.4 75 75
KIDINS220/CRKL/C3G 0.021 0 -10000 0 -10000 0 0
SHC/RasGAP 0.012 0.066 -10000 0 -0.46 7 7
FRS2 family/SHP2 0.029 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.035 0.022 -10000 0 -0.35 1 1
RIT1/GTP 0.011 0 -10000 0 -10000 0 0
NT3 (dimer) -0.052 0.18 -10000 0 -0.54 44 44
RAP1/GDP -0.015 0.038 -10000 0 -10000 0 0
KIDINS220/CRKL 0.014 0 -10000 0 -10000 0 0
BDNF (dimer) -0.01 0.09 -10000 0 -0.35 23 23
ubiquitin-dependent protein catabolic process 0.005 0.084 -10000 0 -0.39 14 14
Schwann cell development -0.025 0.032 -10000 0 -10000 0 0
EHD4 0.014 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.036 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.041 0.005 -10000 0 -10000 0 0
RAP1B 0.014 0 -10000 0 -10000 0 0
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.17 -10000 0 -0.41 63 63
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
Rap1/GTP 0.008 0.074 -10000 0 -10000 0 0
STAT3 -0.002 0.091 -10000 0 -0.36 22 22
axon guidance -0.1 0.16 -10000 0 -0.36 87 87
MAPK3 0.003 0.091 -10000 0 -0.35 20 20
MAPK1 0.002 0.093 -10000 0 -0.35 21 21
CDC42/GDP 0.023 0.066 -10000 0 -0.22 2 2
NTF3 -0.052 0.18 -10000 0 -0.54 44 44
NTF4 -0.004 0.047 -10000 0 -0.34 7 7
NGF (dimer)/TRKA/FAIM 0.005 0.087 -10000 0 -0.4 14 14
PI3K 0.015 0.062 -10000 0 -0.56 4 4
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.013 0.018 -10000 0 -0.34 1 1
GAB1 0.013 0.033 -10000 0 -0.63 1 1
RASGRF1 -0.068 0.16 0.25 5 -0.4 52 57
SOS1 0.013 0.018 -10000 0 -0.34 1 1
MCF2L -0.032 0.14 -10000 0 -0.41 41 41
RGS19 0.013 0.033 -10000 0 -0.63 1 1
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.062 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.066 -10000 0 -0.22 2 2
NGF (dimer)/TRKA/GRIT -0.004 0.084 -10000 0 -0.4 14 14
neuron projection morphogenesis -0.029 0.15 -10000 0 -0.57 12 12
NGF (dimer)/TRKA/NEDD4-2 0.005 0.085 -10000 0 -0.39 14 14
MAP2K1 0.038 0.021 -10000 0 -0.32 1 1
NGFR -0.076 0.21 -10000 0 -0.51 64 64
NGF (dimer)/TRKA/GIPC/GAIP -0.006 0.098 -10000 0 -0.28 35 35
RAS family/GTP/PI3K 0.027 0.046 -10000 0 -0.37 4 4
FRS2 family/SHP2/GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 0.021 0.013 -10000 0 -0.22 1 1
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.029 0.16 -10000 0 -0.63 25 25
MAPKKK cascade -0.031 0.13 -10000 0 -0.64 13 13
RASA1 0.002 0.088 -10000 0 -0.63 7 7
TRKA/c-Abl 0.013 0.036 -10000 0 -10000 0 0
SQSTM1 0.009 0.045 -10000 0 -0.34 6 6
BDNF (dimer)/TRKB/GIPC -0.06 0.16 -10000 0 -0.35 75 75
NGF (dimer)/TRKA/p62/Atypical PKCs -0.005 0.12 -10000 0 -0.35 38 38
MATK -0.002 0.09 -10000 0 -0.45 13 13
NEDD4L 0.014 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.039 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.054 0.14 0.27 6 -0.4 44 50
Rac1/GTP -0.064 0.1 -10000 0 -0.32 32 32
FRS2 family/SHP2/CRK family 0.042 0.009 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.01 0.12 -10000 0 -0.42 20 20
CRKL 0.003 0.1 -10000 0 -0.43 14 14
HRAS -0.008 0.14 -10000 0 -0.42 25 25
mol:PIP3 -0.008 0.095 -10000 0 -0.4 15 15
SPRED1 0.01 0.051 -10000 0 -0.54 3 3
SPRED2 0.011 0.047 -10000 0 -0.63 2 2
GAB1 -0.004 0.1 -10000 0 -0.43 16 16
FOXO3 0.011 0.091 -10000 0 -0.39 13 13
AKT1 0.004 0.097 -10000 0 -0.42 13 13
BAD 0.011 0.091 -10000 0 -0.39 13 13
megakaryocyte differentiation -0.022 0.13 -10000 0 -0.38 33 33
GSK3B 0.011 0.091 -10000 0 -0.39 13 13
RAF1 0.003 0.12 -10000 0 -0.38 15 15
SHC1 0.014 0 -10000 0 -10000 0 0
STAT3 -0.003 0.1 -10000 0 -0.42 16 16
STAT1 -0.033 0.23 -10000 0 -0.99 16 16
HRAS/SPRED1 0 0.12 -10000 0 -0.4 17 17
cell proliferation -0.024 0.14 -10000 0 -0.39 37 37
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
TEC 0.002 0.085 -10000 0 -0.56 8 8
RPS6KB1 -0.001 0.1 -10000 0 -0.42 16 16
HRAS/SPRED2 0 0.12 -10000 0 -0.38 16 16
LYN/TEC/p62DOK 0.007 0.11 -10000 0 -0.41 15 15
MAPK3 0.016 0.087 -10000 0 -0.27 13 13
STAP1 -0.013 0.11 -10000 0 -0.41 18 18
GRAP2 -0.033 0.16 -10000 0 -0.53 32 32
JAK2 -0.028 0.19 -10000 0 -0.8 17 17
STAT1 (dimer) -0.031 0.22 -10000 0 -0.96 16 16
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.019 0.14 -10000 0 -0.44 25 25
actin filament polymerization -0.007 0.11 -10000 0 -0.43 17 17
LYN 0.013 0.033 -10000 0 -0.63 1 1
STAP1/STAT5A (dimer) -0.011 0.14 -10000 0 -0.59 15 15
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
CBL/CRKL/GRB2 0.018 0.1 -10000 0 -0.42 14 14
PI3K 0.009 0.11 -10000 0 -0.44 16 16
PTEN 0.007 0.067 -10000 0 -0.63 4 4
SCF/KIT/EPO/EPOR -0.099 0.31 -10000 0 -1.4 15 15
MAPK8 -0.025 0.14 -10000 0 -0.4 37 37
STAT3 (dimer) -0.003 0.1 -10000 0 -0.42 16 16
positive regulation of transcription 0.017 0.074 -10000 0 -0.22 13 13
mol:GDP -0.018 0.15 -10000 0 -0.46 27 27
PIK3C2B -0.003 0.1 -10000 0 -0.42 16 16
CBL/CRKL 0.01 0.1 -10000 0 -0.44 14 14
FER -0.003 0.1 -10000 0 -0.42 16 16
SH2B3 -0.003 0.1 -10000 0 -0.43 15 15
PDPK1 -0.002 0.092 -10000 0 -0.37 15 15
SNAI2 -0.025 0.13 -10000 0 -0.41 31 31
positive regulation of cell proliferation -0.014 0.17 -10000 0 -0.71 16 16
KITLG -0.001 0.085 -10000 0 -0.44 12 12
cell motility -0.014 0.17 -10000 0 -0.71 16 16
PTPN6 0.014 0.006 -10000 0 -10000 0 0
EPOR 0.019 0.1 -10000 0 -1.4 1 1
STAT5A (dimer) -0.009 0.14 -10000 0 -0.58 16 16
SOCS1 -0.014 0.12 -10000 0 -0.46 22 22
cell migration 0.011 0.11 0.4 21 -10000 0 21
SOS1 0.013 0.018 -10000 0 -0.34 1 1
EPO -0.18 0.27 -10000 0 -0.5 141 141
VAV1 -0.027 0.15 -10000 0 -0.53 28 28
GRB10 -0.003 0.1 -10000 0 -0.42 16 16
PTPN11 0.014 0.004 -10000 0 -10000 0 0
SCF/KIT -0.011 0.11 -10000 0 -0.42 19 19
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.012 0.095 -10000 0 -0.3 13 13
CBL 0.011 0.047 -10000 0 -0.63 2 2
KIT -0.023 0.27 -10000 0 -1.4 13 13
MAP2K2 0.012 0.095 -10000 0 -0.3 14 14
SHC/Grb2/SOS1 0.013 0.098 -10000 0 -0.42 13 13
STAT5A -0.01 0.15 -10000 0 -0.6 16 16
GRB2 0.014 0 -10000 0 -10000 0 0
response to radiation -0.024 0.13 -10000 0 -0.39 32 32
SHC/GRAP2 -0.014 0.12 -10000 0 -0.38 32 32
PTPRO -0.023 0.13 -10000 0 -0.39 33 33
SH2B2 -0.007 0.11 -10000 0 -0.44 17 17
DOK1 0.014 0 -10000 0 -10000 0 0
MATK -0.011 0.12 -10000 0 -0.41 21 21
CREBBP 0.034 0.011 -10000 0 -10000 0 0
BCL2 0.014 0.15 -10000 0 -1.4 3 3
Aurora B 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
Condensin I complex 0 0.12 -9999 0 -0.4 24 24
STMN1 -0.002 0.097 -9999 0 -0.32 28 28
Aurora B/RasGAP/Survivin -0.028 0.16 -9999 0 -0.49 37 37
Chromosomal passenger complex/Cul3 protein complex -0.02 0.13 -9999 0 -0.32 44 44
BIRC5 -0.039 0.16 -9999 0 -0.46 42 42
DES -0.12 0.28 -9999 0 -0.7 60 60
Aurora C/Aurora B/INCENP 0.001 0.098 -9999 0 -0.38 19 19
Aurora B/TACC1 -0.003 0.089 -9999 0 -0.35 18 18
Aurora B/PP2A -0.002 0.095 -9999 0 -0.41 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.008 0.035 -9999 0 -0.18 11 11
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -10000 0 0
NDC80 -0.023 0.16 -9999 0 -0.56 24 24
Cul3 protein complex -0.006 0.11 -9999 0 -0.39 27 27
KIF2C -0.045 0.23 -9999 0 -0.69 31 31
PEBP1 0.004 0.076 -9999 0 -0.64 5 5
KIF20A -0.041 0.18 -9999 0 -0.58 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.011 0.12 -9999 0 -0.49 18 18
SEPT1 0.008 0.053 -9999 0 -0.39 6 6
SMC2 0.013 0.018 -9999 0 -0.34 1 1
SMC4 0.011 0.032 -9999 0 -0.34 3 3
NSUN2/NPM1/Nucleolin -0.006 0.16 -9999 0 -0.88 11 11
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0.001 0.072 -9999 0 -0.38 11 11
AURKB -0.018 0.13 -9999 0 -0.48 26 26
AURKC 0.002 0.083 -9999 0 -0.5 9 9
CDCA8 -0.005 0.11 -9999 0 -0.59 12 12
cytokinesis -0.052 0.25 -9999 0 -0.74 35 35
Aurora B/Septin1 -0.062 0.23 -9999 0 -0.67 36 36
AURKA 0.007 0.057 -9999 0 -0.46 5 5
INCENP 0.01 0.049 -9999 0 -0.65 2 2
KLHL13 -0.033 0.16 -9999 0 -0.56 31 31
BUB1 -0.042 0.18 -9999 0 -0.59 35 35
hSgo1/Aurora B/Survivin -0.039 0.17 -9999 0 -0.47 42 42
EVI5 0.014 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.076 0.22 -9999 0 -0.74 31 31
SGOL1 -0.023 0.14 -9999 0 -0.5 27 27
CENPA -0.032 0.2 -9999 0 -0.61 29 29
NCAPG -0.016 0.13 -9999 0 -0.57 19 19
Aurora B/HC8 Proteasome -0.002 0.095 -9999 0 -0.47 11 11
NCAPD2 0.01 0.037 -9999 0 -0.34 4 4
Aurora B/PP1-gamma -0.002 0.095 -9999 0 -0.47 11 11
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH -0.011 0.12 -9999 0 -0.5 18 18
NPM1 -0.007 0.12 -9999 0 -0.65 11 11
RASA1 0.002 0.088 -9999 0 -0.63 7 7
KLHL9 0.007 0.067 -9999 0 -0.63 4 4
mitotic prometaphase -0.001 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.095 -9999 0 -0.47 11 11
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.056 0.26 -9999 0 -0.75 36 36
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
NSUN2 -0.007 0.12 -9999 0 -0.65 11 11
MYLK -0.008 0.097 -9999 0 -0.41 19 19
KIF23 -0.035 0.16 -9999 0 -0.52 35 35
VIM -0.002 0.1 -9999 0 -0.48 12 12
RACGAP1 0.013 0.019 -9999 0 -0.35 1 1
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.007 0.12 -9999 0 -0.65 11 11
Chromosomal passenger complex -0.043 0.23 -9999 0 -0.65 35 35
Chromosomal passenger complex/EVI5 -0.032 0.17 -9999 0 -0.48 36 36
TACC1 0.009 0.054 -9999 0 -0.49 4 4
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.038 0.16 -10000 0 -0.49 38 38
ANTXR2 0.009 0.058 -10000 0 -0.63 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.021 -10000 0 -0.082 23 23
monocyte activation -0.055 0.19 -10000 0 -0.53 43 43
MAP2K2 -0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.006 0.017 -10000 0 -10000 0 0
MAP2K7 -0.006 0.017 -10000 0 -10000 0 0
MAP2K6 -0.039 0.1 -10000 0 -0.32 39 39
CYAA -0.016 0.091 -10000 0 -0.34 23 23
MAP2K4 -0.006 0.017 -10000 0 -10000 0 0
IL1B -0.025 0.1 -10000 0 -0.28 42 42
Channel -0.014 0.098 -10000 0 -0.36 23 23
NLRP1 -0.014 0.046 -10000 0 -0.2 17 17
CALM1 0.014 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.008 0.023 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.021 0.082 23 -10000 0 23
MAPK3 -0.006 0.017 -10000 0 -10000 0 0
MAPK1 -0.007 0.027 -10000 0 -0.42 1 1
PGR -0.057 0.12 -10000 0 -0.28 69 69
PA/Cellular Receptors -0.016 0.11 -10000 0 -0.4 23 23
apoptosis -0.007 0.021 -10000 0 -0.082 23 23
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.012 0.092 -10000 0 -0.34 23 23
macrophage activation 0.011 0.029 -10000 0 -0.4 1 1
TNF -0.023 0.14 -10000 0 -0.55 24 24
VCAM1 -0.056 0.19 -10000 0 -0.54 43 43
platelet activation -0.008 0.023 -10000 0 -10000 0 0
MAPKKK cascade 0 0.034 0.16 3 -10000 0 3
IL18 -0.015 0.093 -10000 0 -0.35 21 21
negative regulation of macrophage activation -0.007 0.021 -10000 0 -0.082 23 23
LEF -0.007 0.021 -10000 0 -0.082 23 23
CASP1 -0.012 0.041 -10000 0 -0.27 5 5
mol:cAMP -0.008 0.023 -10000 0 -10000 0 0
necrosis -0.007 0.021 -10000 0 -0.082 23 23
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.093 -10000 0 -0.34 23 23
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.012 0.051 -10000 0 -10000 0 0
oxygen homeostasis 0.002 0.016 -10000 0 -10000 0 0
TCEB2 0.012 0.026 -10000 0 -0.34 2 2
TCEB1 0.014 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.044 0.1 -10000 0 -0.35 16 16
EPO -0.16 0.37 -10000 0 -0.66 97 97
FIH (dimer) 0.017 0.015 -10000 0 -10000 0 0
APEX1 0.014 0.017 -10000 0 -10000 0 0
SERPINE1 -0.061 0.33 -10000 0 -0.78 38 38
FLT1 -0.019 0.13 -10000 0 -1.1 4 4
ADORA2A -0.034 0.27 -10000 0 -0.7 18 18
germ cell development -0.046 0.3 -10000 0 -0.72 30 30
SLC11A2 -0.021 0.26 -10000 0 -0.72 16 16
BHLHE40 -0.025 0.27 -10000 0 -0.73 19 19
HIF1AN 0.017 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.052 0.2 -10000 0 -0.48 21 21
ETS1 0.021 0.068 -10000 0 -0.54 5 5
CITED2 -0.012 0.091 -10000 0 -1.2 2 2
KDR -0.05 0.25 -10000 0 -1.3 14 14
PGK1 -0.021 0.27 -10000 0 -0.73 16 16
SIRT1 0.007 0.059 -10000 0 -0.64 3 3
response to hypoxia -0.004 0.006 -10000 0 -10000 0 0
HIF2A/ARNT -0.028 0.31 -10000 0 -0.82 20 20
EPAS1 -0.012 0.15 -10000 0 -0.38 23 23
SP1 0.022 0.004 -10000 0 -10000 0 0
ABCG2 -0.066 0.33 -10000 0 -0.76 45 45
EFNA1 -0.023 0.27 -10000 0 -0.78 16 16
FXN -0.033 0.27 -10000 0 -0.71 17 17
POU5F1 -0.05 0.31 -10000 0 -0.75 30 30
neuron apoptosis 0.027 0.3 0.79 20 -10000 0 20
EP300 0.014 0 -10000 0 -10000 0 0
EGLN3 -0.11 0.23 -10000 0 -0.5 89 89
EGLN2 0.016 0.025 -10000 0 -0.37 1 1
EGLN1 0.017 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.025 0.04 -10000 0 -0.39 3 3
VHL 0.009 0.058 -10000 0 -0.63 3 3
ARNT 0.013 0.017 -10000 0 -10000 0 0
SLC2A1 -0.057 0.3 -10000 0 -0.75 32 32
TWIST1 -0.046 0.28 -10000 0 -0.74 21 21
ELK1 0.022 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.009 0.18 -10000 0 -0.44 15 15
VEGFA -0.022 0.27 -10000 0 -0.71 19 19
CREBBP 0.014 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP 0.001 0.054 -9999 0 -0.3 10 10
Metarhodopsin II/Arrestin 0 0.037 -9999 0 -0.19 12 12
PDE6G/GNAT1/GTP -0.003 0.087 -9999 0 -0.4 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.075 -9999 0 -0.43 10 10
GRK1 0 0.018 -9999 0 -0.34 1 1
CNG Channel -0.098 0.16 -9999 0 -0.39 67 67
mol:Na + -0.084 0.13 -9999 0 -0.34 39 39
mol:ADP 0 0.018 -9999 0 -0.34 1 1
RGS9-1/Gbeta5/R9AP -0.028 0.13 -9999 0 -0.39 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.085 0.13 -9999 0 -0.35 39 39
CNGB1 -0.007 0.071 -9999 0 -0.34 16 16
RDH5 -0.022 0.15 -9999 0 -0.6 22 22
SAG 0 0.026 -9999 0 -0.34 2 2
mol:Ca2+ -0.058 0.14 -9999 0 -0.44 8 8
Na + (4 Units) -0.078 0.12 -9999 0 -0.43 8 8
RGS9 -0.065 0.19 -9999 0 -0.48 59 59
GNB1/GNGT1 0.004 0.062 -9999 0 -0.46 5 5
GNAT1/GDP -0.022 0.12 -9999 0 -0.34 35 35
GUCY2D -0.027 0.11 -9999 0 -0.35 38 38
GNGT1 -0.01 0.085 -9999 0 -0.47 11 11
GUCY2F 0.001 0.026 -9999 0 -0.34 2 2
GNB5 0.01 0.046 -9999 0 -0.41 4 4
mol:GMP (4 units) -0.017 0.11 -9999 0 -0.36 25 25
mol:11-cis-retinal -0.022 0.15 -9999 0 -0.6 22 22
mol:cGMP -0.011 0.076 -9999 0 -0.34 9 9
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.017 0.12 -9999 0 -0.46 20 20
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.11 0.24 -9999 0 -0.58 75 75
Metarhodopsin II 0.001 0.032 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.012 0.08 -9999 0 -0.36 9 9
RGS9BP 0.007 0.041 -9999 0 -0.34 5 5
Metarhodopsin II/Transducin 0.005 0.055 -9999 0 -0.31 8 8
GCAP Family/Ca ++ 0.001 0.059 -9999 0 -0.37 8 8
PDE6A/B -0.021 0.11 -9999 0 -0.4 14 14
mol:Pi -0.028 0.13 -9999 0 -0.39 33 33
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.006 0.066 -9999 0 -0.38 8 8
PDE6B -0.029 0.14 -9999 0 -0.42 37 37
PDE6A -0.002 0.065 -9999 0 -0.34 13 13
PDE6G -0.009 0.12 -9999 0 -0.59 14 14
RHO -0.001 0.06 -9999 0 -0.34 11 11
PDE6 -0.071 0.13 -9999 0 -0.36 48 48
GUCA1A 0.001 0.026 -9999 0 -0.34 2 2
GC2/GCAP Family 0.002 0.06 -9999 0 -0.37 8 8
GUCA1C 0 0.002 -9999 0 -10000 0 0
GUCA1B -0.003 0.099 -9999 0 -0.55 11 11
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.016 0.19 -9999 0 -0.49 39 39
MAP3K8 -0.013 0.12 -9999 0 -0.56 17 17
FOS -0.011 0.16 -9999 0 -0.57 20 20
PRKCA 0.013 0.005 -9999 0 -10000 0 0
PTPN7 -0.017 0.13 -9999 0 -0.48 24 24
HRAS 0.012 0.026 -9999 0 -0.34 2 2
PRKCB -0.027 0.15 -9999 0 -0.53 28 28
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.024 0.02 -9999 0 -10000 0 0
MAPK3 -0.005 0.13 -9999 0 -0.54 16 16
MAP2K1 0.001 0.12 -9999 0 -0.49 18 18
ELK1 0.013 0.007 -9999 0 -10000 0 0
BRAF 0.003 0.11 -9999 0 -0.45 18 18
mol:GTP 0 0.002 -9999 0 -0.004 51 51
MAPK1 -0.006 0.14 -9999 0 -0.61 14 14
RAF1 0.003 0.11 -9999 0 -0.45 18 18
KRAS 0.013 0.019 -9999 0 -0.34 1 1
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.009 0.059 -9999 0 -0.28 13 13
ADCY5 -0.05 0.14 -9999 0 -0.41 45 45
ADCY6 0.013 0.041 -9999 0 -0.4 2 2
ADCY7 0.01 0.05 -9999 0 -0.4 3 3
ADCY1 -0.078 0.16 -9999 0 -0.41 57 57
ADCY2 0.003 0.05 -9999 0 -0.21 17 17
ADCY3 0.01 0.051 -9999 0 -0.4 3 3
ADCY8 -0.019 0.082 -9999 0 -0.28 12 12
PRKCE 0.004 0.048 -9999 0 -0.29 9 9
ADCY9 0.011 0.051 -9999 0 -0.4 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.023 0.079 -9999 0 -0.32 9 9
Signaling events mediated by HDAC Class III

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
EP300 0.014 0 -10000 0 -10000 0 0
HDAC4 0.013 0.018 -10000 0 -0.34 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.015 0.06 0.32 9 -10000 0 9
CDKN1A -0.031 0.17 -10000 0 -0.82 16 16
KAT2B 0.007 0.067 -10000 0 -0.63 4 4
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.001 0.011 -10000 0 -10000 0 0
FOXO1 0.01 0.037 -10000 0 -0.34 4 4
FOXO4 0.023 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.21 0.3 -10000 0 -0.6 133 133
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.002 0.06 -10000 0 -0.31 12 12
PPARGC1A -0.072 0.21 -10000 0 -0.58 54 54
FHL2 -0.042 0.18 -10000 0 -0.58 35 35
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.018 0.048 -10000 0 -0.43 3 3
HIST2H4A 0.015 0.06 -10000 0 -0.32 9 9
SIRT1/FOXO3a 0.002 0.042 -10000 0 -0.37 3 3
SIRT1 0.011 0.065 -10000 0 -0.6 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.026 0.043 -10000 0 -0.36 3 3
SIRT1/Histone H1b 0.022 0.044 -10000 0 -0.35 3 3
apoptosis -0.026 0.041 0.36 3 -10000 0 3
SIRT1/PGC1A -0.051 0.14 -10000 0 -0.4 46 46
p53/SIRT1 -0.005 0.12 0.41 12 -0.43 16 28
SIRT1/FOXO4 0.025 0.042 -10000 0 -0.35 3 3
FOXO1/FHL2/SIRT1 -0.01 0.11 -10000 0 -0.36 31 31
HIST1H1E 0.02 0.018 -10000 0 -10000 0 0
SIRT1/p300 0.018 0.048 -10000 0 -0.43 3 3
muscle cell differentiation -0.01 0.07 0.44 6 -10000 0 6
TP53 -0.006 0.12 0.2 12 -0.61 13 25
KU70/SIRT1/BAX 0.027 0.042 -10000 0 -0.36 3 3
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.014 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.15 0.23 -10000 0 -0.46 122 122
ACSS2 0.018 0.056 -10000 0 -0.5 3 3
SIRT1/PCAF/MYOD 0.01 0.07 -10000 0 -0.44 6 6
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.015 0.14 -9999 0 -0.61 9 9
Syndecan-3/Neurocan 0.007 0.068 -9999 0 -0.61 3 3
POMC -0.01 0.11 -9999 0 -0.51 17 17
EGFR -0.007 0.11 -9999 0 -0.59 13 13
Syndecan-3/EGFR 0.01 0.091 -9999 0 -0.42 12 12
AGRP -0.014 0.084 -9999 0 -0.34 23 23
NCSTN 0.013 0.033 -9999 0 -0.63 1 1
PSENEN 0.013 0.018 -9999 0 -0.34 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.009 0.058 -9999 0 -0.63 3 3
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.003 0.07 -9999 0 -0.36 13 13
long-term memory 0.028 0.056 -9999 0 -0.69 2 2
Syndecan-3/IL8 -0.078 0.16 -9999 0 -0.34 81 81
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin -0.005 0.11 -9999 0 -0.46 19 19
FYN 0.013 0.018 -9999 0 -0.34 1 1
limb bud formation -0.005 0.057 -9999 0 -0.77 2 2
MC4R 0 0.026 -9999 0 -0.34 2 2
SRC -0.021 0.14 -9999 0 -0.6 21 21
PTN -0.053 0.19 -9999 0 -0.58 42 42
FGFR/FGF/Syndecan-3 -0.005 0.058 -9999 0 -0.78 2 2
neuron projection morphogenesis -0.027 0.14 -9999 0 -0.6 9 9
Syndecan-3/AgRP -0.001 0.069 -9999 0 -0.75 2 2
Syndecan-3/AgRP/MC4R -0.012 0.065 -9999 0 -0.73 2 2
Fyn/Cortactin 0.021 0.013 -9999 0 -0.22 1 1
SDC3 -0.005 0.059 -9999 0 -0.79 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.077 0.16 -9999 0 -0.34 81 81
IL8 -0.18 0.27 -9999 0 -0.52 133 133
Syndecan-3/Fyn/Cortactin 0.029 0.058 -9999 0 -0.72 2 2
Syndecan-3/CASK -0.005 0.056 -9999 0 -0.75 2 2
alpha-MSH/MC4R -0.007 0.086 -9999 0 -0.36 19 19
Gamma Secretase 0.038 0.039 -9999 0 -0.32 4 4
IL2 signaling events mediated by STAT5

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
GAB2 0.015 0 -9999 0 -10000 0 0
ELF1 -0.022 0.12 -9999 0 -0.4 25 25
CCNA2 -0.005 0.095 -9999 0 -0.43 16 16
PIK3CA 0.012 0.047 -9999 0 -0.63 2 2
JAK3 -0.009 0.11 -9999 0 -0.46 19 19
PIK3R1 0.01 0.058 -9999 0 -0.63 3 3
JAK1 0.015 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.005 0.18 -9999 0 -0.65 21 21
SHC1 0.015 0 -9999 0 -10000 0 0
SP1 0.018 0.034 -9999 0 -0.36 1 1
IL2RA -0.056 0.23 -9999 0 -0.83 25 25
IL2RB -0.008 0.11 -9999 0 -0.52 16 16
SOS1 0.014 0.018 -9999 0 -0.34 1 1
IL2RG -0.038 0.16 -9999 0 -0.49 39 39
G1/S transition of mitotic cell cycle -0.034 0.18 -9999 0 -0.46 51 51
PTPN11 0.015 0 -9999 0 -10000 0 0
CCND2 0.021 0.067 -9999 0 -0.86 1 1
LCK -0.032 0.16 -9999 0 -0.52 33 33
GRB2 0.015 0 -9999 0 -10000 0 0
IL2 0.003 0.019 -9999 0 -0.34 1 1
CDK6 -0.067 0.21 -9999 0 -0.61 48 48
CCND3 0.018 0.16 -9999 0 -0.56 19 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.21 0.42 -9999 0 -1.1 62 62
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.04 0.14 -9999 0 -0.37 53 53
IFNAR2 0.01 0.008 -9999 0 -10000 0 0
AKT1 -0.046 0.097 -9999 0 -0.24 63 63
ER alpha/Oestrogen -0.098 0.18 -9999 0 -0.39 98 98
NFX1/SIN3/HDAC complex 0.029 0.037 -9999 0 -0.27 1 1
EGF -0.08 0.16 -9999 0 -0.37 84 84
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.014 0.015 -9999 0 -10000 0 0
TERT/c-Abl -0.19 0.38 -9999 0 -1 59 59
SAP18 0.013 0.002 -9999 0 -10000 0 0
MRN complex 0.027 0.041 -9999 0 -0.75 1 1
WT1 -0.041 0.12 -9999 0 -0.36 46 46
WRN 0.013 0.018 -9999 0 -0.34 1 1
SP1 0.009 0.012 -9999 0 -10000 0 0
SP3 0.011 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.19 0.32 -9999 0 -0.88 58 58
Mad/Max 0.014 0.017 -9999 0 -10000 0 0
TERT -0.22 0.44 -9999 0 -1.2 59 59
CCND1 -0.21 0.42 -9999 0 -1.1 68 68
MAX 0.011 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.002 -9999 0 -10000 0 0
RBBP4 0.005 0.074 -9999 0 -0.63 5 5
TERF2 0.013 0.004 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.013 0.002 -9999 0 -10000 0 0
Telomerase/911 0.019 0.042 -9999 0 -10000 0 0
CDKN1B 0.007 0.067 -9999 0 -10000 0 0
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.011 0.034 -9999 0 -0.64 1 1
TRF2/PARP2 0.021 0.003 -9999 0 -10000 0 0
UBE3A 0.012 0.005 -9999 0 -10000 0 0
JUN 0.008 0.048 -9999 0 -0.64 2 2
E6 -0.003 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.007 0.008 -9999 0 -10000 0 0
FOS -0.061 0.19 -9999 0 -0.52 51 51
IFN-gamma/IRF1 -0.008 0.079 -9999 0 -0.42 2 2
PARP2 0.014 0 -9999 0 -10000 0 0
BLM -0.021 0.14 -9999 0 -0.5 25 25
Telomerase -0.025 0.1 -9999 0 -0.5 12 12
IRF1 0.014 0.026 -9999 0 -0.33 2 2
ESR1 -0.13 0.25 -9999 0 -0.53 98 98
KU/TER 0.021 0 -9999 0 -10000 0 0
ATM/TRF2 0.021 0.022 -9999 0 -0.41 1 1
ubiquitin-dependent protein catabolic process 0.037 0.036 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.037 -9999 0 -10000 0 0
HDAC1 0.013 0.002 -9999 0 -10000 0 0
HDAC2 0.009 0.012 -9999 0 -10000 0 0
ATM -0.001 0.024 -9999 0 -0.47 1 1
SMAD3 0.011 0.069 -9999 0 -0.3 13 13
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.011 0.019 -9999 0 -0.34 1 1
MRE11A 0.013 0.033 -9999 0 -0.63 1 1
HUS1 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.2 0.37 -9999 0 -0.97 59 59
NR2F2 0.019 0.022 -9999 0 -0.34 1 1
MAPK3 0.009 0.016 -9999 0 -0.22 1 1
MAPK1 0.008 0.03 -9999 0 -0.35 2 2
TGFB1/TGF beta receptor Type II -0.004 0.089 -9999 0 -0.39 18 18
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.024 -9999 0 -0.47 1 1
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.009 0.11 -9999 0 -0.59 13 13
mol:Oestrogen -0.002 0.004 -9999 0 -10000 0 0
EGF/EGFR -0.063 0.14 -9999 0 -0.38 33 33
MYC -0.051 0.19 -9999 0 -0.63 36 36
IL2 -0.004 0.024 -9999 0 -0.34 1 1
KU 0.021 0 -9999 0 -10000 0 0
RAD50 0.013 0.033 -9999 0 -0.63 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 -0.004 0.09 -9999 0 -0.39 18 18
TRF2/BLM -0.002 0.093 -9999 0 -0.43 14 14
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.18 0.38 -9999 0 -1 59 59
SP1/HDAC2 0.014 0.021 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.19 0.32 -9999 0 -0.88 58 58
Smad3/Myc -0.022 0.14 -9999 0 -0.4 38 38
911 complex 0.029 0 -9999 0 -10000 0 0
IFNG -0.026 0.11 -9999 0 -0.33 42 42
Telomerase/PinX1 -0.19 0.32 -9999 0 -0.88 58 58
Telomerase/AKT1/mTOR/p70S6K -0.025 0.084 -9999 0 -10000 0 0
SIN3B 0.013 0.002 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.19 0.32 -9999 0 -0.88 58 58
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.04 0.035 -9999 0 -0.64 1 1
TRF2/WRN 0.021 0.012 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.19 0.32 -9999 0 -0.88 58 58
E2F1 -0.012 0.11 -9999 0 -0.46 18 18
ZNFX1 0.013 0.002 -9999 0 -10000 0 0
PIF1 -0.017 0.13 -9999 0 -0.49 23 23
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
BARD1 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
BARD1/CSTF1 -0.025 0.13 -10000 0 -0.46 27 27
ATM 0.013 0.033 -10000 0 -0.63 1 1
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.021 0.043 -10000 0 -0.36 4 4
protein ubiquitination -0.016 0.12 -10000 0 -0.32 34 34
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0.027 0.041 -10000 0 -0.75 1 1
MRE11A 0.013 0.033 -10000 0 -0.63 1 1
DNA-PK 0.029 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.04 0.039 -10000 0 -0.38 1 1
FANCF 0.014 0 -10000 0 -10000 0 0
BRCA1 0.013 0.018 -10000 0 -0.34 1 1
CCNE1 -0.024 0.12 -10000 0 -0.39 35 35
CDK2/Cyclin E1 -0.006 0.088 -10000 0 -0.46 6 6
FANCG 0.013 0.018 -10000 0 -0.34 1 1
BRCA1/BACH1/BARD1 -0.026 0.13 -10000 0 -0.46 27 27
FANCE 0.011 0.032 -10000 0 -0.34 3 3
FANCC 0.012 0.038 -10000 0 -0.49 2 2
NBN 0.014 0 -10000 0 -10000 0 0
FANCA 0.013 0.033 -10000 0 -0.63 1 1
DNA repair 0.026 0.1 -10000 0 -0.36 2 2
BRCA1/BARD1/ubiquitin -0.026 0.13 -10000 0 -0.46 27 27
BARD1/DNA-PK 0 0.1 -10000 0 -0.35 27 27
FANCL 0.014 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.025 0.13 0.46 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.1 -10000 0 -0.81 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.011 0.11 -10000 0 -0.39 27 27
BRCA1/BARD1/P53 -0.014 0.13 -10000 0 -0.37 39 39
BARD1/CSTF1/BRCA1 -0.011 0.11 -10000 0 -0.39 27 27
BRCA1/BACH1 0.013 0.018 -10000 0 -0.34 1 1
BARD1 -0.049 0.18 -10000 0 -0.52 43 43
PCNA 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.011 0.11 -10000 0 -0.39 27 27
BRCA1/BARD1/UbcH7 -0.011 0.11 -10000 0 -0.39 27 27
BRCA1/BARD1/RAD51/PCNA -0.011 0.12 -10000 0 -0.35 35 35
BARD1/DNA-PK/P53 -0.005 0.12 -10000 0 -0.34 39 39
BRCA1/BARD1/Ubiquitin -0.026 0.13 -10000 0 -0.46 27 27
BRCA1/BARD1/CTIP -0.004 0.11 -10000 0 -0.36 28 28
FA complex 0.038 0.024 -10000 0 -0.26 1 1
BARD1/EWS -0.025 0.13 -10000 0 -0.46 27 27
RBBP8 0.02 0.036 -10000 0 -0.46 2 2
TP53 -0.008 0.12 -10000 0 -0.63 13 13
TOPBP1 0.014 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.014 0.13 0.36 39 -10000 0 39
BRCA1/BARD1 -0.013 0.12 -10000 0 -0.33 34 34
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.036 0.13 -10000 0 -0.38 43 43
CDK2 0.014 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.004 0.098 -10000 0 -0.5 13 13
RAD50 0.013 0.033 -10000 0 -0.63 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.026 0.13 -10000 0 -0.46 27 27
EWSR1 0.014 0 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.041 0.26 6 -0.33 1 7
RFC1 0.006 0.041 0.26 6 -0.33 1 7
PRKDC 0.006 0.041 0.26 6 -0.33 1 7
RIPK1 0.015 0.003 -10000 0 -10000 0 0
CASP7 -0.008 0.049 0.26 3 -0.57 1 4
FASLG/FAS/FADD/FAF1 -0.008 0.12 0.26 19 -0.32 28 47
MAP2K4 0.003 0.12 -10000 0 -0.4 9 9
mol:ceramide -0.006 0.12 -10000 0 -0.4 20 20
GSN 0.004 0.047 0.26 6 -0.36 2 8
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.12 0.32 2 -0.38 19 21
FAS -0.014 0.13 -10000 0 -0.62 16 16
BID 0.003 0.046 0.31 4 -0.41 2 6
MAP3K1 0.012 0.074 0.21 3 -0.26 6 9
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.005 0.046 0.26 6 -0.36 2 8
CFLAR 0.015 0.003 -10000 0 -10000 0 0
HGF/MET -0.076 0.19 -10000 0 -0.45 60 60
ARHGDIB 0.005 0.04 0.26 6 -0.33 1 7
FADD 0.012 0.02 -10000 0 -0.35 1 1
actin filament polymerization -0.004 0.046 0.35 2 -0.26 6 8
NFKB1 -0.027 0.057 -10000 0 -0.27 4 4
MAPK8 -0.024 0.16 -10000 0 -0.43 32 32
DFFA 0.006 0.041 0.26 6 -0.33 1 7
DNA fragmentation during apoptosis 0.005 0.045 0.26 6 -0.35 2 8
FAS/FADD/MET 0.004 0.096 -10000 0 -0.41 18 18
CFLAR/RIP1 0.017 0.007 -10000 0 -10000 0 0
FAIM3 0 0.084 -10000 0 -0.44 12 12
FAF1 0.013 0.006 -10000 0 -10000 0 0
PARP1 0.006 0.041 0.26 6 -0.33 1 7
DFFB 0.005 0.046 0.26 6 -0.36 2 8
CHUK -0.022 0.049 -10000 0 -10000 0 0
FASLG -0.036 0.16 -10000 0 -0.48 37 37
FAS/FADD -0.002 0.097 -10000 0 -0.47 15 15
HGF -0.084 0.21 -10000 0 -0.48 74 74
LMNA 0.018 0.037 0.28 3 -0.3 1 4
CASP6 0.006 0.041 0.26 6 -0.33 1 7
CASP10 0.013 0.005 -10000 0 -10000 0 0
CASP3 0.007 0.049 0.3 7 -0.38 1 8
PTPN13 -0.055 0.17 -10000 0 -0.44 57 57
CASP8 0.008 0.048 0.41 4 -10000 0 4
IL6 -0.086 0.34 -10000 0 -1.3 24 24
MET 0.008 0.061 -10000 0 -0.56 4 4
ICAD/CAD 0.004 0.042 0.29 3 -0.32 2 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.12 -10000 0 -0.4 20 20
activation of caspase activity by cytochrome c 0.003 0.046 0.3 4 -0.41 2 6
PAK2 0.006 0.041 0.26 6 -0.33 1 7
BCL2 0.006 0.066 -10000 0 -0.49 6 6
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.002 0.14 -9999 0 -0.48 28 28
KLHL20 -0.032 0.065 -9999 0 -0.25 11 11
CYFIP2 -0.045 0.18 -9999 0 -0.55 39 39
Rac1/GDP 0.02 0.11 -9999 0 -0.3 28 28
ENAH -0.003 0.14 -9999 0 -0.48 28 28
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.014 0 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.027 0.073 -9999 0 -0.38 3 3
ABI1/Sra1/Nap1 -0.03 0.056 -9999 0 -0.19 24 24
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.011 0.12 -9999 0 -0.35 41 41
RAPGEF1 0.001 0.14 -9999 0 -0.42 29 29
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.007 0.14 -9999 0 -0.5 28 28
CRK -0.008 0.15 -9999 0 -0.46 29 29
E-cadherin/gamma catenin/alpha catenin -0.003 0.12 -9999 0 -0.4 28 28
alphaE/beta7 Integrin -0.002 0.096 -9999 0 -0.36 23 23
IQGAP1 0.01 0.037 -9999 0 -0.34 4 4
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0.028 -9999 0 -0.36 2 2
DLG1 0.002 0.14 -9999 0 -0.48 28 28
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.056 -9999 0 -0.28 4 4
MLLT4 0.011 0.047 -9999 0 -0.63 2 2
ARF6/GTP/NME1/Tiam1 0.011 0.074 -9999 0 -0.36 13 13
PI3K -0.027 0.072 -9999 0 -0.38 4 4
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.016 0.13 -9999 0 -0.48 28 28
TIAM1 -0.015 0.13 -9999 0 -0.53 20 20
E-cadherin(dimer)/Ca2+ 0.007 0.096 -9999 0 -0.33 28 28
AKT1 -0.016 0.04 -9999 0 -0.21 3 3
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
CDH1 -0.034 0.17 -9999 0 -0.63 28 28
RhoA/GDP 0.02 0.11 -9999 0 -0.48 2 2
actin cytoskeleton organization 0.012 0.066 -9999 0 -0.18 11 11
CDC42/GDP 0.02 0.11 -9999 0 -0.42 3 3
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.002 0.084 -9999 0 -0.29 28 28
ITGB7 -0.009 0.12 -9999 0 -0.61 14 14
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.006 0.1 -9999 0 -0.35 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin -0.002 0.096 -9999 0 -0.34 28 28
mol:GDP 0.011 0.12 -9999 0 -0.35 28 28
CDC42/GTP/IQGAP1 0.017 0.021 -9999 0 -0.18 4 4
JUP 0.013 0.033 -9999 0 -0.63 1 1
p120 catenin/RhoA/GDP 0.015 0.11 -9999 0 -0.49 2 2
RAC1/GTP/IQGAP1 0.017 0.021 -9999 0 -0.18 4 4
PIP5K1C/AP1M1 0.021 0.013 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.003 0.073 -9999 0 -0.22 28 28
NME1 0.014 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.002 0.14 -9999 0 -0.48 28 28
regulation of cell-cell adhesion -0.024 0.064 -9999 0 -0.33 3 3
WASF2 -0.015 0.029 -9999 0 -10000 0 0
Rap1/GTP -0.031 0.084 -9999 0 -0.45 3 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.003 0.12 -9999 0 -0.33 41 41
CCND1 0.002 0.09 -9999 0 -0.27 28 28
VAV2 -0.004 0.15 -9999 0 -0.46 28 28
RAP1/GDP 0.015 0.1 -9999 0 -0.43 3 3
adherens junction assembly 0.003 0.14 -9999 0 -0.47 28 28
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0.018 -9999 0 -0.34 1 1
regulation of heterotypic cell-cell adhesion 0.004 0.12 -9999 0 -0.31 41 41
E-cadherin/beta catenin -0.03 0.11 -9999 0 -0.41 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.017 0.16 -9999 0 -0.5 29 29
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
Rac1/GTP -0.05 0.1 -9999 0 -0.41 11 11
E-cadherin/beta catenin/alpha catenin -0.003 0.11 -9999 0 -0.39 28 28
ITGAE 0.006 0.055 -9999 0 -0.34 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.008 0.15 -9999 0 -0.52 28 28
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.008 0.12 0.61 13 -10000 0 13
PI3K Class IB/PDE3B -0.008 0.12 -10000 0 -0.61 13 13
PDE3B -0.008 0.12 -10000 0 -0.61 13 13
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.014 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.12 -9999 0 -0.61 14 14
ITGA4 -0.006 0.11 -9999 0 -0.53 14 14
alpha4/beta7 Integrin -0.011 0.12 -9999 0 -0.44 26 26
alpha4/beta1 Integrin 0.006 0.079 -9999 0 -0.46 9 9
Ceramide signaling pathway

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
SPHK2 -0.006 0.11 -10000 0 -0.46 21 21
MAP4K4 0.021 0.073 -10000 0 -0.29 2 2
BAG4 -0.008 0.12 -10000 0 -0.63 13 13
PKC zeta/ceramide -0.025 0.096 0.16 15 -0.34 25 40
NFKBIA 0.012 0.038 -10000 0 -0.49 2 2
BIRC3 -0.031 0.15 -10000 0 -0.47 35 35
BAX 0.004 0.024 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.023 0.018 -10000 0 -10000 0 0
BAD -0.002 0.045 0.17 17 -10000 0 17
SMPD1 0.011 0.055 -10000 0 -0.2 20 20
RB1 -0.003 0.049 0.17 17 -0.35 1 18
FADD/Caspase 8 0.031 0.07 -10000 0 -10000 0 0
MAP2K4 0.005 0.043 0.17 11 -10000 0 11
NSMAF 0.006 0.074 -10000 0 -0.63 5 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.045 -10000 0 -10000 0 0
EGF -0.077 0.16 -10000 0 -0.36 84 84
mol:ceramide -0.01 0.049 0.18 17 -10000 0 17
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.008 0.12 -10000 0 -0.46 21 21
ASAH1 0.011 0.032 -10000 0 -0.34 3 3
negative regulation of cell cycle -0.003 0.049 0.17 17 -0.35 1 18
cell proliferation -0.028 0.1 -10000 0 -0.28 48 48
BID 0.016 0.07 -10000 0 -0.61 2 2
MAP3K1 -0.002 0.045 0.17 17 -10000 0 17
EIF2A 0.012 0.041 -10000 0 -10000 0 0
TRADD 0.013 0.033 -10000 0 -0.63 1 1
CRADD 0.013 0.033 -10000 0 -0.63 1 1
MAPK3 0.015 0.043 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.043 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.001 0.044 0.16 17 -10000 0 17
FADD 0.02 0.073 -10000 0 -0.29 2 2
KSR1 -0.003 0.047 0.17 17 -0.17 2 19
MAPK8 -0.025 0.11 0.17 14 -0.28 43 57
PRKRA -0.002 0.045 0.17 17 -10000 0 17
PDGFA -0.024 0.15 -10000 0 -0.61 23 23
TRAF2 0.014 0 -10000 0 -10000 0 0
IGF1 -0.092 0.23 -10000 0 -0.57 68 68
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.01 0.049 0.17 17 -10000 0 17
CTSD 0.014 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.021 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.029 0.11 -10000 0 -0.29 48 48
PRKCD 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.029 0.16 -10000 0 -0.63 25 25
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.008 0.12 -10000 0 -0.46 21 21
RelA/NF kappa B1 0.021 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.077 -10000 0 -0.32 2 2
TNFR1A/BAG4/TNF-alpha -0.009 0.12 -10000 0 -0.39 30 30
mol:Sphingosine-1-phosphate -0.006 0.11 -10000 0 -0.46 21 21
MAP2K1 0.011 0.043 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS 0.004 0.038 0.23 3 -10000 0 3
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.004 0.089 -10000 0 -0.46 13 13
EIF2AK2 0.005 0.043 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0 0.1 -10000 0 -0.39 22 22
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.046 -10000 0 -10000 0 0
MAP2K2 0.01 0.044 -10000 0 -10000 0 0
SMPD3 0.006 0.075 -10000 0 -0.24 23 23
TNF -0.023 0.14 -10000 0 -0.55 24 24
PKC zeta/PAR4 -0.011 0.12 -10000 0 -0.46 25 25
mol:PHOSPHOCHOLINE 0.026 0.068 0.19 29 -10000 0 29
NF kappa B1/RelA/I kappa B alpha 0.017 0.093 -10000 0 -0.32 26 26
AIFM1 0.004 0.038 0.23 3 -10000 0 3
BCL2 0.006 0.066 -10000 0 -0.49 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.008 0.12 -9999 0 -0.63 13 13
Caspase 8 (4 units) -0.022 0.15 -9999 0 -0.6 13 13
NEF -0.01 0.048 -9999 0 -0.2 16 16
NFKBIA 0.006 0.047 -9999 0 -0.48 2 2
BIRC3 -0.004 0.16 -9999 0 -0.63 16 16
CYCS -0.019 0.15 -9999 0 -0.59 13 13
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.008 0.1 -9999 0 -0.59 9 9
MAP2K7 -0.014 0.14 -9999 0 -0.54 12 12
protein ubiquitination 0.022 0.091 -9999 0 -0.37 6 6
CRADD 0.013 0.033 -9999 0 -0.63 1 1
DAXX 0.014 0 -9999 0 -10000 0 0
FAS -0.013 0.13 -9999 0 -0.61 16 16
BID -0.027 0.16 -9999 0 -0.59 15 15
NF-kappa-B/RelA/I kappa B alpha 0.015 0.082 -9999 0 -0.3 16 16
TRADD 0.013 0.033 -9999 0 -0.63 1 1
MAP3K5 -0.069 0.22 -9999 0 -0.63 48 48
CFLAR 0.014 0 -9999 0 -10000 0 0
FADD 0.013 0.018 -9999 0 -0.34 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.015 0.082 -9999 0 -0.3 16 16
MAPK8 -0.026 0.16 -9999 0 -0.52 20 20
APAF1 0.014 0 -9999 0 -10000 0 0
TRAF1 0.012 0.038 -9999 0 -0.49 2 2
TRAF2 0.014 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.034 0.16 -9999 0 -0.48 25 25
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.008 0.11 -9999 0 -0.5 6 6
CHUK 0.022 0.096 -9999 0 -0.41 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.019 0.15 -9999 0 -0.36 55 55
TCRz/NEF -0.015 0.11 -9999 0 -0.4 25 25
TNF -0.023 0.14 -9999 0 -0.55 24 24
FASLG -0.032 0.19 -9999 0 -0.54 40 40
NFKB1 0.009 0.028 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.009 0.12 -9999 0 -0.39 30 30
CASP6 -0.04 0.1 -9999 0 -0.56 7 7
CASP7 -0.004 0.16 -9999 0 -0.52 23 23
RELA 0.009 0.028 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 -0.004 0.16 -9999 0 -0.52 23 23
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.004 0.089 -9999 0 -0.46 13 13
CASP8 0.014 0 -9999 0 -10000 0 0
CASP9 0.012 0.026 -9999 0 -0.34 2 2
MAP3K14 0.015 0.1 -9999 0 -0.46 6 6
APAF-1/Caspase 9 -0.059 0.11 -9999 0 -0.4 28 28
BCL2 -0.02 0.15 -9999 0 -0.48 21 21
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.031 0.069 -10000 0 -0.4 5 5
adherens junction organization 0.015 0.088 -10000 0 -0.27 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.09 -10000 0 -0.45 7 7
FMN1 0.005 0.096 -10000 0 -0.28 28 28
mol:IP3 0.024 0.066 -10000 0 -0.37 5 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.013 0.088 -10000 0 -0.28 28 28
CTNNB1 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.029 0.072 -10000 0 -0.37 5 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.021 0.17 -10000 0 -0.46 45 45
CTNND1 0.015 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.09 -10000 0 -0.27 32 32
VASP 0.019 0.084 -10000 0 -0.26 28 28
ZYX 0.018 0.09 -10000 0 -0.28 29 29
JUB 0.017 0.089 -10000 0 -0.38 4 4
EGFR(dimer) 0.01 0.11 -10000 0 -0.31 35 35
E-cadherin/beta catenin-gamma catenin -0.004 0.11 -10000 0 -0.39 28 28
mol:PI-3-4-5-P3 0.022 0.075 -10000 0 -0.4 5 5
PIK3CA 0.011 0.048 -10000 0 -0.64 2 2
PI3K 0.022 0.077 -10000 0 -0.41 5 5
FYN 0 0.1 -10000 0 -0.43 6 6
mol:Ca2+ 0.024 0.065 -10000 0 -0.36 5 5
JUP 0.013 0.033 -10000 0 -0.63 1 1
PIK3R1 0.01 0.058 -10000 0 -0.64 3 3
mol:DAG 0.024 0.066 -10000 0 -0.37 5 5
CDH1 -0.035 0.17 -10000 0 -0.63 28 28
RhoA/GDP 0.028 0.09 -10000 0 -0.45 7 7
establishment of polarity of embryonic epithelium 0.019 0.083 -10000 0 -0.26 28 28
SRC -0.021 0.14 -10000 0 -0.6 21 21
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.007 0.11 -10000 0 -0.59 13 13
CASR -0.014 0.12 -10000 0 -0.32 33 33
RhoA/GTP 0.029 0.06 -10000 0 -0.44 2 2
AKT2 0.028 0.073 -10000 0 -0.37 5 5
actin cable formation 0.012 0.094 -10000 0 -0.5 3 3
apoptosis -0.027 0.071 0.38 5 -10000 0 5
CTNNA1 0.015 0.002 -10000 0 -10000 0 0
mol:GDP 0.021 0.095 -10000 0 -0.38 15 15
PIP5K1A 0.016 0.092 -10000 0 -0.27 32 32
PLCG1 0.024 0.068 -10000 0 -0.38 5 5
Rac1/GTP -0.028 0.089 -10000 0 -0.39 12 12
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.002 0.083 -10000 0 -0.5 9 9
Jak2/Leptin Receptor -0.036 0.14 0.2 2 -0.33 54 56
PTP1B/AKT1 0.02 0.052 0.26 1 -0.25 2 3
FYN 0.013 0.018 -10000 0 -0.34 1 1
p210 bcr-abl/PTP1B 0.014 0.059 0.27 2 -0.28 3 5
EGFR -0.007 0.11 -10000 0 -0.59 13 13
EGF/EGFR -0.031 0.1 0.2 2 -0.38 18 20
CSF1 -0.013 0.12 -10000 0 -0.55 18 18
AKT1 0.015 0.001 -10000 0 -10000 0 0
INSR 0.015 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.009 0.088 0.24 2 -0.34 15 17
Insulin Receptor/Insulin -0.004 0.033 -10000 0 -10000 0 0
HCK -0.002 0.097 -10000 0 -0.57 10 10
CRK 0.013 0.018 -10000 0 -0.34 1 1
TYK2 0.02 0.056 0.26 2 -0.26 3 5
EGF -0.076 0.16 -10000 0 -0.36 84 84
YES1 0.014 0 -10000 0 -10000 0 0
CAV1 0.008 0.072 0.24 1 -0.28 3 4
TXN 0.014 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.021 0.065 -10000 0 -0.34 5 5
cell migration -0.014 0.059 0.28 3 -0.27 2 5
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.014 0.13 -10000 0 -0.61 16 16
ITGA2B -0.012 0.087 -10000 0 -0.34 24 24
CSF1R -0.004 0.1 -10000 0 -0.56 12 12
Prolactin Receptor/Prolactin -0.014 0.11 -10000 0 -0.47 17 17
FGR 0.007 0.06 -10000 0 -0.44 6 6
PTP1B/p130 Cas 0.021 0.055 0.24 2 -0.26 3 5
Crk/p130 Cas 0.025 0.051 -10000 0 -10000 0 0
DOK1 0.023 0.06 0.28 1 -0.3 2 3
JAK2 0.009 0.073 -10000 0 -0.3 10 10
Jak2/Leptin Receptor/Leptin -0.049 0.11 -10000 0 -0.42 20 20
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
PTPN1 0.014 0.059 0.27 2 -0.28 3 5
LYN 0.013 0.033 -10000 0 -0.63 1 1
CDH2 -0.008 0.12 -10000 0 -0.63 13 13
SRC -0.002 0.11 -10000 0 -0.46 19 19
ITGB3 -0.049 0.18 -10000 0 -0.56 41 41
CAT1/PTP1B -0.028 0.12 0.28 1 -0.39 16 17
CAPN1 0.015 0.003 -10000 0 -10000 0 0
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.008 0.052 -10000 0 -0.47 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.043 0.11 -10000 0 -0.44 20 20
negative regulation of transcription 0.01 0.072 -10000 0 -0.3 10 10
FCGR2A 0.003 0.078 -10000 0 -0.47 9 9
FER 0.014 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.043 0.15 -10000 0 -0.34 63 63
BLK -0.062 0.19 -10000 0 -0.51 52 52
Insulin Receptor/Insulin/Shc 0.018 0.027 -10000 0 -0.37 1 1
RHOA 0.015 0.003 -10000 0 -10000 0 0
LEPR -0.088 0.23 -10000 0 -0.6 62 62
BCAR1 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.014 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.052 0.15 -10000 0 -0.42 29 29
PRL -0.005 0.046 -10000 0 -0.34 6 6
SOCS3 -0.054 0.27 -10000 0 -1.4 14 14
SPRY2 0.012 0.034 -10000 0 -0.64 1 1
Insulin Receptor/Insulin/IRS1 0.013 0.056 -10000 0 -0.4 6 6
CSF1/CSF1R 0.002 0.11 -10000 0 -0.36 24 24
Ras protein signal transduction 0.01 0.02 -10000 0 -10000 0 0
IRS1 0.006 0.074 -10000 0 -0.63 5 5
INS -0.003 0.045 -10000 0 -0.41 4 4
LEP -0.008 0.066 -10000 0 -0.34 14 14
STAT5B 0.016 0.057 0.2 2 -0.23 5 7
STAT5A 0.016 0.058 0.2 2 -0.23 4 6
GRB2 0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.071 0.24 2 -0.31 8 10
CSN2 -0.016 0.12 -10000 0 -1.5 2 2
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
LAT 0.014 0.066 -10000 0 -0.45 6 6
YBX1 0.023 0.002 -10000 0 -10000 0 0
LCK -0.033 0.16 -10000 0 -0.52 33 33
SHC1 0.014 0 -10000 0 -10000 0 0
NOX4 -0.011 0.11 -10000 0 -0.47 19 19
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.13 0.46 -9999 0 -1.4 46 46
PLK1 -0.037 0.38 -9999 0 -1.2 31 31
CDKN1B 0.074 0.14 -9999 0 -0.37 2 2
FOXO3 0.01 0.24 -9999 0 -0.7 26 26
KAT2B 0.012 0.07 -9999 0 -0.64 4 4
FOXO1/SIRT1 -0.038 0.14 -9999 0 -0.39 47 47
CAT 0.004 0.28 -9999 0 -0.96 20 20
CTNNB1 0.014 0 -9999 0 -10000 0 0
AKT1 0.016 0.029 -9999 0 -10000 0 0
FOXO1 -0.012 0.16 -9999 0 -0.42 46 46
MAPK10 0.001 0.097 -9999 0 -0.33 22 22
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.057 0.11 -9999 0 -0.42 8 8
response to oxidative stress 0.001 0.032 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.057 0.2 -9999 0 -0.72 20 20
XPO1 0.015 0.001 -9999 0 -10000 0 0
EP300 0.01 0.02 -9999 0 -10000 0 0
BCL2L11 0.022 0.09 -9999 0 -1.5 1 1
FOXO1/SKP2 -0.012 0.15 -9999 0 -0.38 51 51
mol:GDP 0.001 0.032 -9999 0 -10000 0 0
RAN 0.016 0.001 -9999 0 -10000 0 0
GADD45A 0.052 0.18 -9999 0 -0.84 9 9
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.021 0.08 -9999 0 -10000 0 0
MST1 -0.029 0.18 -9999 0 -0.64 28 28
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.013 0.018 -9999 0 -0.34 1 1
FOXO4/14-3-3 family -0.015 0.12 -9999 0 -0.33 4 4
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.011 0.095 -9999 0 -0.34 24 24
MAPK9 0.034 0.017 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.01 0.059 -9999 0 -0.63 3 3
SOD2 0.056 0.2 -9999 0 -0.74 7 7
RBL2 0.02 0.25 -9999 0 -1 13 13
RAL/GDP 0.026 0.02 -9999 0 -10000 0 0
CHUK 0.02 0.018 -9999 0 -10000 0 0
Ran/GTP 0.014 0.004 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.033 0.021 -9999 0 -10000 0 0
CSNK1G1 0.014 0 -9999 0 -10000 0 0
FASLG -0.054 0.33 -9999 0 -1.5 18 18
SKP2 0.004 0.079 -9999 0 -0.55 7 7
USP7 0.016 0.001 -9999 0 -10000 0 0
IKBKB 0.02 0.018 -9999 0 -10000 0 0
CCNB1 0.003 0.28 -9999 0 -0.94 21 21
FOXO1-3a-4/beta catenin 0.069 0.17 -9999 0 -0.41 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.15 -9999 0 -0.37 51 51
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.003 0.12 -9999 0 -0.57 14 14
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.006 -9999 0 -10000 0 0
ZFAND5 0.061 0.096 -9999 0 -10000 0 0
SFN -0.16 0.25 -9999 0 -0.48 132 132
CDK2 0.006 0.03 -9999 0 -10000 0 0
FOXO3A/14-3-3 -0.004 0.12 -9999 0 -0.36 16 16
CREBBP 0.006 0.03 -9999 0 -10000 0 0
FBXO32 -0.007 0.29 -9999 0 -0.88 26 26
BCL6 0.043 0.17 -9999 0 -0.61 7 7
RALB 0.015 0.001 -9999 0 -10000 0 0
RALA 0.015 0.001 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.014 0 -10000 0 -10000 0 0
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR -0.04 0.17 -10000 0 -0.53 37 37
Cbp/p300/PCAF 0.025 0.043 -10000 0 -0.39 4 4
EP300 0.014 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.029 0.051 -10000 0 -0.27 1 1
KAT2B 0.007 0.067 -10000 0 -0.63 4 4
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.042 0.092 0.22 48 -0.28 8 56
RAR alpha/9cRA/Cyclin H -0.015 0.054 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.024 0.059 -10000 0 -0.3 2 2
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.013 0.13 -10000 0 -0.51 24 24
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.029 0.12 -10000 0 -0.39 37 37
RXRs/RARs/NRIP1/9cRA 0.025 0.079 -10000 0 -0.53 1 1
NCOA2 -0.097 0.24 -10000 0 -0.63 64 64
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.04 0.17 -10000 0 -0.53 37 37
RARG 0.015 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.02 0.011 -10000 0 -10000 0 0
MAPK3 0.015 0.001 -10000 0 -10000 0 0
MAPK1 0.013 0.033 -10000 0 -0.63 1 1
MAPK8 -0.026 0.16 -10000 0 -0.63 24 24
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.017 0.1 -10000 0 -0.41 4 4
RARA 0.006 0.072 -10000 0 -0.26 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.019 0.13 -10000 0 -0.34 32 32
PRKCA 0.018 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.076 -10000 0 -0.58 1 1
RXRG -0.042 0.12 -10000 0 -0.36 36 36
RXRA 0.014 0.067 -10000 0 -0.26 1 1
RXRB 0.022 0.02 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.029 0.12 -10000 0 -0.39 37 37
RBP1 -0.11 0.24 -10000 0 -0.51 91 91
CRBP1/9-cic-RA -0.083 0.18 -10000 0 -0.37 91 91
RARB -0.008 0.12 -10000 0 -0.53 17 17
PRKCG 0.001 0.047 -10000 0 -0.34 7 7
MNAT1 0.014 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.037 0.096 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.03 0.073 -10000 0 -0.33 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.067 -10000 0 -0.36 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 0.01 0.076 -10000 0 -0.58 1 1
positive regulation of DNA binding -0.014 0.051 -10000 0 -10000 0 0
NRIP1 0.011 0.091 -10000 0 -1.3 1 1
RXRs/RARs 0.005 0.072 -10000 0 -0.37 2 2
RXRs/RXRs/DNA/9cRA -0.013 0.058 -10000 0 -10000 0 0
PRKACA 0.013 0.018 -10000 0 -0.34 1 1
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH 0.029 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.01 0.038 -10000 0 -10000 0 0
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0.006 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.012 0.097 -10000 0 -0.34 23 23
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.028 -10000 0 -0.23 5 5
GNB1/GNG2 0.015 0.04 -10000 0 -0.4 3 3
GNB1 0.014 0 -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 -10000 0 -10000 0 0
Gs family/GTP -0.026 0.096 -10000 0 -0.25 50 50
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 0.009 0.024 0.067 50 -10000 0 50
GNAL -0.049 0.17 -10000 0 -0.46 50 50
GNG2 0.007 0.063 -10000 0 -0.52 5 5
CRH -0.002 0.04 -10000 0 -0.34 5 5
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.016 0.096 -10000 0 -0.38 24 24
MAPK11 0.004 0.034 -10000 0 -0.2 8 8
Signaling events mediated by PRL

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
CCNE1 -0.024 0.12 -10000 0 -0.39 35 35
mol:Halofuginone 0.004 0.017 -10000 0 -0.23 2 2
ITGA1 0.009 0.058 -10000 0 -0.63 3 3
CDKN1A -0.008 0.12 -10000 0 -0.46 18 18
PRL-3/alpha Tubulin -0.001 0.081 -10000 0 -0.46 5 5
mol:Ca2+ 0.008 0.087 0.41 5 -0.48 6 11
AGT 0.004 0.081 -10000 0 -0.63 6 6
CCNA2 -0.016 0.14 -10000 0 -0.84 3 3
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 -0.009 0.12 -10000 0 -0.4 29 29
CDK2/Cyclin E1 -0.01 0.12 -10000 0 -0.42 22 22
MAPK3 0 0.081 -10000 0 -0.26 29 29
PRL-2 /Rab GGTase beta 0.021 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.085 -10000 0 -0.46 6 6
PTP4A1 -0.014 0.14 -10000 0 -0.89 3 3
PTP4A3 -0.017 0.11 -10000 0 -0.39 29 29
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0 0.081 -10000 0 -0.46 5 5
SRC -0.021 0.14 -10000 0 -0.6 21 21
RAC1 0 0.095 -10000 0 -0.49 8 8
Rab GGTase beta/Rab GGTase alpha 0.021 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.091 0.2 -10000 0 -0.67 16 16
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.016 0.06 0.41 5 -10000 0 5
RHOC 0 0.095 -10000 0 -0.49 8 8
RHOA 0 0.095 -10000 0 -0.52 7 7
cell motility 0.004 0.097 -10000 0 -0.49 8 8
PRL-1/alpha Tubulin -0.006 0.13 -10000 0 -0.84 3 3
PRL-3/alpha1 Integrin -0.005 0.091 -10000 0 -0.46 8 8
ROCK1 0.004 0.098 -10000 0 -0.5 8 8
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0.014 0 -10000 0 -10000 0 0
mitosis -0.013 0.14 -10000 0 -0.88 3 3
ATF5 -0.14 0.27 -10000 0 -0.59 96 96
Caspase cascade in apoptosis

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
TOP1 0.017 0.085 0.24 1 -0.32 13 14
ACTA1 0.004 0.11 0.21 11 -0.38 18 29
NUMA1 0.017 0.085 0.24 1 -0.32 13 14
SPTAN1 0.009 0.11 0.28 1 -0.37 18 19
LIMK1 0.007 0.11 0.28 1 -0.38 19 20
BIRC3 -0.031 0.15 -10000 0 -0.47 35 35
BIRC2 0.014 0 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.005 0.11 -10000 0 -0.4 20 20
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 0.017 0.085 0.24 1 -0.32 13 14
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.01 0.1 0.28 1 -0.37 18 19
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0.033 -10000 0 -0.63 1 1
GSN 0.008 0.11 0.28 1 -0.36 20 21
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A -0.042 0.18 -10000 0 -0.58 34 34
BID 0.005 0.061 -10000 0 -0.24 15 15
MAP3K1 0.012 0.042 0.16 1 -0.22 1 2
TRADD 0.013 0.033 -10000 0 -0.63 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.018 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.11 0.28 1 -0.37 19 20
CASP9 0.012 0.026 -10000 0 -0.34 2 2
DNA repair -0.014 0.049 0.16 1 -0.2 15 16
neuron apoptosis -0.002 0.13 -10000 0 -0.66 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.1 0.27 1 -0.39 14 15
APAF1 0.014 0 -10000 0 -10000 0 0
CASP6 0.026 0.052 -10000 0 -10000 0 0
TRAF2 0.014 0 -10000 0 -10000 0 0
ICAD/CAD 0.015 0.1 0.27 1 -0.39 14 15
CASP7 0.009 0.073 0.28 16 -0.52 1 17
KRT18 0.018 0.016 -10000 0 -10000 0 0
apoptosis 0.023 0.097 0.23 15 -0.35 13 28
DFFA 0.009 0.11 0.28 1 -0.37 18 19
DFFB 0.009 0.11 0.28 1 -0.37 19 20
PARP1 0.014 0.049 0.2 15 -0.16 1 16
actin filament polymerization -0.013 0.1 0.37 17 -0.27 1 18
TNF -0.023 0.14 -10000 0 -0.55 24 24
CYCS 0.007 0.044 -10000 0 -0.19 3 3
SATB1 0.002 0.1 -10000 0 -0.36 4 4
SLK 0.009 0.11 0.28 1 -0.42 13 14
p15 BID/BAX 0.012 0.054 -10000 0 -0.28 3 3
CASP2 0.025 0.068 -10000 0 -10000 0 0
JNK cascade -0.012 0.042 0.22 1 -0.16 1 2
CASP3 0.003 0.11 0.22 15 -0.4 18 33
LMNB2 0.032 0.047 -10000 0 -0.26 1 1
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 0.009 0.058 -10000 0 -0.63 3 3
Mammalian IAPs/DIABLO 0.011 0.085 -10000 0 -0.35 15 15
negative regulation of DNA binding -0.041 0.18 -10000 0 -0.58 34 34
stress fiber formation 0.01 0.1 0.28 1 -0.41 13 14
GZMB -0.017 0.12 -10000 0 -0.35 40 40
CASP1 0.007 0.072 -10000 0 -0.44 8 8
LMNB1 0.032 0.046 -10000 0 -0.26 1 1
APP -0.002 0.13 -10000 0 -0.67 14 14
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.018 0.096 0.23 15 -0.35 13 28
LMNA 0.032 0.046 -10000 0 -0.26 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.019 0.072 -10000 0 -0.28 2 2
LRDD 0.014 0 -10000 0 -10000 0 0
SREBF1 0.007 0.11 0.28 1 -0.4 15 16
APAF-1/Caspase 9 0.004 0.035 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.017 0.084 0.24 1 -0.32 13 14
CFL2 0.012 0.11 0.27 1 -0.38 17 18
GAS2 -0.007 0.13 0.28 1 -0.38 29 30
positive regulation of apoptosis 0.035 0.047 -10000 0 -0.25 1 1
PRF1 -0.001 0.086 -10000 0 -0.43 13 13
Regulation of nuclear SMAD2/3 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
EP300 0.012 0.01 -10000 0 -10000 0 0
HSPA8 0.013 0.034 -10000 0 -0.63 1 1
SMAD3/SMAD4/ER alpha -0.078 0.17 0.21 4 -0.4 70 74
AKT1 0.016 0.009 -10000 0 -10000 0 0
GSC 0.006 0.068 -10000 0 -10000 0 0
NKX2-5 -0.015 0.081 -10000 0 -0.34 22 22
muscle cell differentiation 0.011 0.055 0.38 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.044 0.096 -10000 0 -0.37 5 5
SMAD4 0.012 0.06 -10000 0 -0.58 2 2
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.046 -10000 0 -0.38 1 1
SMAD3/SMAD4/VDR -0.007 0.096 -10000 0 -0.34 8 8
MYC -0.05 0.19 -10000 0 -0.62 36 36
CDKN2B 0.036 0.16 -10000 0 -1.4 4 4
AP1 0.014 0.13 -10000 0 -0.37 27 27
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.054 0.057 -10000 0 -0.54 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.04 0.054 -10000 0 -0.36 4 4
SP3 0.017 0 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 0.001 0.071 -10000 0 -0.34 15 15
SMAD3/SMAD4/GR 0.026 0.056 -10000 0 -0.29 4 4
GATA3 -0.041 0.17 -10000 0 -0.56 35 35
SKI/SIN3/HDAC complex/NCoR1 0.044 0.044 -10000 0 -0.48 1 1
MEF2C/TIF2 -0.026 0.16 -10000 0 -0.5 14 14
endothelial cell migration 0.14 0.42 1.4 36 -10000 0 36
MAX 0.018 0.016 -10000 0 -10000 0 0
RBBP7 0.015 0.001 -10000 0 -10000 0 0
RBBP4 0.006 0.075 -10000 0 -0.63 5 5
RUNX2 -0.033 0.16 -10000 0 -0.53 32 32
RUNX3 -0.008 0.11 -10000 0 -0.54 15 15
RUNX1 0 0.094 -10000 0 -0.63 8 8
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.018 0.016 -10000 0 -10000 0 0
VDR -0.04 0.17 -10000 0 -0.53 37 37
CDKN1A -0.008 0.29 -10000 0 -1.4 16 16
KAT2B 0.006 0.067 -10000 0 -0.64 4 4
SMAD2/SMAD2/SMAD4/FOXH1 0.027 0.061 -10000 0 -0.31 2 2
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.011 0.047 -10000 0 -0.63 2 2
SERPINE1 -0.14 0.43 -10000 0 -1.4 36 36
SMAD3/SMAD4/ATF2 0.011 0.11 -10000 0 -0.4 20 20
SMAD3/SMAD4/ATF3 0.025 0.068 -10000 0 -0.32 5 5
SAP30 0.013 0.034 -10000 0 -0.63 1 1
Cbp/p300/PIAS3 0.025 0.02 -10000 0 -10000 0 0
JUN 0.012 0.12 -10000 0 -0.38 21 21
SMAD3/SMAD4/IRF7 0.019 0.09 -10000 0 -0.4 10 10
TFE3 0.014 0.021 -10000 0 -10000 0 0
COL1A2 -0.043 0.26 -10000 0 -1.1 20 20
mesenchymal cell differentiation 0.003 0.13 0.41 26 -10000 0 26
DLX1 -0.015 0.09 -10000 0 -0.34 26 26
TCF3 0.014 0 -10000 0 -10000 0 0
FOS -0.053 0.19 -10000 0 -0.51 51 51
SMAD3/SMAD4/Max 0.026 0.056 -10000 0 -0.3 3 3
Cbp/p300/SNIP1 0.026 0.01 -10000 0 -10000 0 0
ZBTB17 0.013 0.005 -10000 0 -10000 0 0
LAMC1 0.033 0.08 -10000 0 -0.66 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.064 -10000 0 -0.31 6 6
IRF7 -0.001 0.097 -10000 0 -0.57 10 10
ESR1 -0.13 0.25 -10000 0 -0.52 98 98
HNF4A -0.005 0.11 -10000 0 -0.63 11 11
MEF2C 0.027 0.076 -10000 0 -0.49 2 2
SMAD2-3/SMAD4 0.034 0.063 -10000 0 -0.29 4 4
Cbp/p300/Src-1 0.026 0.014 -10000 0 -10000 0 0
IGHV3OR16-13 -0.005 0.021 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0.038 -10000 0 -0.49 2 2
CREBBP 0.012 0.007 -10000 0 -10000 0 0
SKIL 0.004 0.081 -10000 0 -0.63 6 6
HDAC1 0.015 0.001 -10000 0 -10000 0 0
HDAC2 0.015 0.001 -10000 0 -10000 0 0
SNIP1 0.015 0.002 -10000 0 -10000 0 0
GCN5L2 -0.002 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.037 0.071 -10000 0 -0.32 4 4
MSG1/HSC70 0.01 0.061 -10000 0 -0.56 2 2
SMAD2 0.018 0.012 -10000 0 -10000 0 0
SMAD3 0.012 0.052 -10000 0 -0.4 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.077 -10000 0 -0.31 3 3
SMAD2/SMAD2/SMAD4 0.006 0.051 -10000 0 -0.35 6 6
NCOR1 0.009 0.058 -10000 0 -0.63 3 3
NCOA2 -0.097 0.24 -10000 0 -0.63 64 64
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A 0.006 0.034 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.051 0.092 -10000 0 -0.34 5 5
IFNB1 0.019 0.08 -10000 0 -0.37 8 8
SMAD3/SMAD4/MEF2C 0.036 0.085 -10000 0 -0.58 1 1
CITED1 -0.001 0.073 -10000 0 -0.36 14 14
SMAD2-3/SMAD4/ARC105 0.042 0.058 -10000 0 -0.29 1 1
RBL1 -0.014 0.12 -10000 0 -0.46 22 22
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.051 0.08 -10000 0 -0.63 4 4
RUNX1-3/PEBPB2 0.006 0.1 -10000 0 -0.44 16 16
SMAD7 0.023 0.19 -10000 0 -0.78 13 13
MYC/MIZ-1 -0.029 0.14 -10000 0 -0.46 35 35
SMAD3/SMAD4 -0.029 0.14 -10000 0 -0.42 36 36
IL10 -0.015 0.18 -10000 0 -0.55 27 27
PIASy/HDAC complex 0.017 0.009 -10000 0 -10000 0 0
PIAS3 0.013 0.004 -10000 0 -10000 0 0
CDK2 0.013 0.006 -10000 0 -10000 0 0
IL5 -0.004 0.13 -10000 0 -0.39 19 19
CDK4 0.013 0.006 -10000 0 -10000 0 0
PIAS4 0.017 0.009 -10000 0 -10000 0 0
ATF3 0.007 0.056 -10000 0 -0.38 7 7
SMAD3/SMAD4/SP1 0.024 0.1 -10000 0 -0.39 7 7
FOXG1 -0.008 0.055 -10000 0 -0.34 10 10
FOXO3 0.026 0.012 -10000 0 -10000 0 0
FOXO1 0.023 0.028 -10000 0 -10000 0 0
FOXO4 0.026 0.012 -10000 0 -10000 0 0
heart looping 0.027 0.076 -10000 0 -0.48 2 2
CEBPB 0.015 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.012 0.082 -10000 0 -0.34 7 7
MYOD1 -0.006 0.05 -10000 0 -0.34 8 8
SMAD3/SMAD4/HNF4 0.016 0.098 -10000 0 -0.4 14 14
SMAD3/SMAD4/GATA3 -0.011 0.15 -10000 0 -0.4 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.004 0.081 -10000 0 -0.63 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.022 0.11 -10000 0 -0.41 16 16
SMAD3/SMAD4/SP1-3 0.04 0.09 -10000 0 -0.37 4 4
MED15 0.014 0 -10000 0 -10000 0 0
SP1 0.008 0.045 -10000 0 -10000 0 0
SIN3B 0.015 0.001 -10000 0 -10000 0 0
SIN3A 0.015 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.022 0.076 -10000 0 -0.37 1 1
ITGB5 0.043 0.079 -10000 0 -0.39 1 1
TGIF/SIN3/HDAC complex/CtBP 0.046 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.061 0.19 -10000 0 -0.42 75 75
AR -0.12 0.26 -10000 0 -0.6 80 80
negative regulation of cell growth 0.026 0.071 -10000 0 -0.31 4 4
SMAD3/SMAD4/MYOD 0.016 0.066 -10000 0 -0.29 6 6
E2F5 -0.009 0.1 -10000 0 -0.43 19 19
E2F4 0.013 0.033 -10000 0 -0.63 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.038 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.043 0.066 -10000 0 -0.43 4 4
TFDP1 0.008 0.057 -10000 0 -0.46 5 5
SMAD3/SMAD4/AP1 0.014 0.13 -10000 0 -0.39 21 21
SMAD3/SMAD4/RUNX2 -0.003 0.13 -10000 0 -0.41 26 26
TGIF2 0.012 0.038 -10000 0 -0.49 2 2
TGIF1 0.014 0 -10000 0 -10000 0 0
ATF2 -0.014 0.13 -10000 0 -0.63 16 16
PLK2 and PLK4 events

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
PLK2 0.01 0.051 -9999 0 -0.54 3 3
PLK4 0.001 0.071 -9999 0 -0.36 13 13
regulation of centriole replication 0.01 0.062 -9999 0 -0.27 16 16
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.017 0.045 -10000 0 -0.4 4 4
CRKL -0.004 0.09 -10000 0 -0.35 6 6
mol:PIP3 -0.012 0.059 0.55 4 -10000 0 4
AKT1 0.005 0.048 0.38 4 -0.35 2 6
PTK2B 0.014 0 -10000 0 -10000 0 0
RAPGEF1 0.003 0.086 -10000 0 -0.4 3 3
RANBP10 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
HGF/MET/SHIP2 -0.036 0.14 -10000 0 -0.39 39 39
MAP3K5 -0.042 0.16 -10000 0 -0.45 31 31
HGF/MET/CIN85/CBL/ENDOPHILINS -0.028 0.13 -10000 0 -0.36 43 43
AP1 -0.031 0.13 -10000 0 -0.32 53 53
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
apoptosis -0.063 0.24 -10000 0 -0.84 32 32
STAT3 (dimer) -0.013 0.11 -10000 0 -0.44 4 4
GAB1/CRKL/SHP2/PI3K 0.012 0.1 -10000 0 -0.57 4 4
INPP5D 0.009 0.054 -10000 0 -0.49 4 4
CBL/CRK 0.002 0.099 -10000 0 -0.71 2 2
PTPN11 0.014 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
PTEN 0.007 0.067 -10000 0 -0.63 4 4
ELK1 -0.003 0.026 0.24 1 -0.2 4 5
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.02 0.048 -10000 0 -10000 0 0
PAK1 0.008 0.054 0.36 4 -0.33 5 9
HGF/MET/RANBP10 -0.036 0.14 -10000 0 -0.39 39 39
HRAS -0.012 0.12 -10000 0 -0.5 6 6
DOCK1 -0.009 0.12 -10000 0 -0.53 10 10
GAB1 -0.012 0.094 -10000 0 -0.36 7 7
CRK -0.005 0.093 -10000 0 -0.47 3 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.16 -10000 0 -0.5 38 38
JUN 0.011 0.047 -10000 0 -0.63 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.017 0.074 -10000 0 -0.22 38 38
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
cell morphogenesis 0.006 0.13 -10000 0 -0.55 5 5
GRB2/SHC 0.002 0.067 -10000 0 -0.25 3 3
FOS -0.058 0.19 -10000 0 -0.51 51 51
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.026 0.24 1 -0.2 4 5
HGF/MET/MUC20 -0.045 0.14 -10000 0 -0.4 39 39
cell migration 0.001 0.066 -10000 0 -0.25 3 3
GRB2 0.014 0 -10000 0 -10000 0 0
CBL 0.011 0.047 -10000 0 -0.63 2 2
MET/RANBP10 0.017 0.045 -10000 0 -0.4 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.1 -10000 0 -0.48 3 3
MET/MUC20 0.006 0.045 -10000 0 -0.41 4 4
RAP1B 0.01 0.082 -10000 0 -0.59 1 1
RAP1A 0.01 0.082 -10000 0 -0.59 1 1
HGF/MET/RANBP9 -0.036 0.14 -10000 0 -0.39 39 39
RAF1 -0.004 0.12 -10000 0 -0.54 4 4
STAT3 -0.013 0.11 -10000 0 -0.44 4 4
cell proliferation -0.01 0.13 -10000 0 -0.36 38 38
RPS6KB1 0.002 0.029 -10000 0 -10000 0 0
MAPK3 -0.009 0.021 -10000 0 -0.21 3 3
MAPK1 -0.006 0.047 0.79 1 -0.21 3 4
RANBP9 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.18 -10000 0 -0.47 42 42
SRC -0.021 0.12 -10000 0 -0.33 23 23
PI3K -0.003 0.085 -10000 0 -0.38 7 7
MET/Glomulin 0.009 0.04 -10000 0 -0.36 4 4
SOS1 0.013 0.018 -10000 0 -0.34 1 1
MAP2K1 0.004 0.11 -10000 0 -0.5 4 4
MET 0.008 0.061 -10000 0 -0.56 4 4
MAP4K1 -0.009 0.11 -10000 0 -0.45 10 10
PTK2 0.014 0 -10000 0 -10000 0 0
MAP2K2 0.003 0.11 -10000 0 -0.48 5 5
BAD 0.011 0.044 0.36 4 -0.33 2 6
MAP2K4 -0.031 0.15 -10000 0 -0.41 30 30
SHP2/GRB2/SOS1/GAB1 -0.029 0.07 -10000 0 -0.43 4 4
INPPL1 0.014 0 -10000 0 -10000 0 0
PXN 0.014 0 -10000 0 -10000 0 0
SH3KBP1 0.009 0.058 -10000 0 -0.63 3 3
HGS -0.008 0.069 -10000 0 -0.27 3 3
PLCgamma1/PKC 0.011 0 -10000 0 -10000 0 0
HGF -0.084 0.21 -10000 0 -0.48 74 74
RASA1 0.002 0.088 -10000 0 -0.63 7 7
NCK1 0.011 0.047 -10000 0 -0.63 2 2
PTPRJ 0.014 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.001 0.079 -10000 0 -0.29 5 5
PDPK1 -0.004 0.054 0.43 4 -0.39 2 6
HGF/MET/SHIP -0.039 0.14 -10000 0 -0.41 39 39
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.005 0.059 0.26 17 -10000 0 17
BUB1B -0.012 0.12 -10000 0 -0.4 25 25
PLK1 0.007 0.038 -10000 0 -0.13 20 20
PLK1S1 0.009 0.025 -10000 0 -0.26 1 1
KIF2A 0.014 0.035 -10000 0 -0.2 1 1
regulation of mitotic centrosome separation 0.007 0.038 -10000 0 -0.13 20 20
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.019 0.15 -10000 0 -0.45 32 32
WEE1 0.015 0.04 -10000 0 -0.21 6 6
cytokinesis -0.036 0.18 -10000 0 -0.55 31 31
PP2A-alpha B56 -0.026 0.22 -10000 0 -0.75 30 30
AURKA 0.008 0.033 -10000 0 -0.33 2 2
PICH/PLK1 0.008 0.1 -10000 0 -0.38 19 19
CENPE -0.001 0.085 -10000 0 -0.28 24 24
RhoA/GTP 0.011 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.034 -10000 0 -0.2 1 1
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 0.003 0.057 -10000 0 -0.34 9 9
PAK1 0.009 0.059 -10000 0 -0.64 3 3
SPC24 -0.032 0.16 -10000 0 -0.57 29 29
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN -0.011 0.073 -10000 0 -0.33 15 15
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase -0.001 0.005 -10000 0 -0.021 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.02 -10000 0 -0.071 19 19
G2 phase of mitotic cell cycle 0 0.001 -10000 0 -0.012 2 2
STAG2 0.013 0.033 -10000 0 -0.63 1 1
GRASP65/GM130/RAB1/GTP 0.001 0.01 -10000 0 -10000 0 0
spindle elongation 0.007 0.038 -10000 0 -0.13 20 20
ODF2 0.014 0.001 -10000 0 -10000 0 0
BUB1 -0.067 0.23 -10000 0 -0.82 30 30
TPT1 0.01 0.02 -10000 0 -10000 0 0
CDC25C -0.033 0.14 -10000 0 -0.44 39 39
CDC25B 0.012 0.039 -10000 0 -0.49 2 2
SGOL1 -0.005 0.059 -10000 0 -0.26 17 17
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.014 0.07 -10000 0 -0.47 8 8
CDC14B -0.003 0.083 -10000 0 -0.48 11 11
CDC20 -0.035 0.15 -10000 0 -0.46 38 38
PLK1/PBIP1 0.006 0.049 -10000 0 -0.19 13 13
mitosis 0 0.004 0.041 2 -10000 0 2
FBXO5 0.012 0.036 -10000 0 -0.17 8 8
CDC2 0.001 0.003 -10000 0 -0.02 8 8
NDC80 -0.019 0.14 -10000 0 -0.54 22 22
metaphase plate congression 0.009 0.026 -10000 0 -0.14 1 1
ERCC6L 0.007 0.1 -10000 0 -0.4 19 19
NLP/gamma Tubulin 0.007 0.023 -10000 0 -0.081 16 16
microtubule cytoskeleton organization 0.01 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 0.01 3 -10000 0 3
PPP1R12A 0.014 0 -10000 0 -10000 0 0
interphase 0 0.001 0.01 3 -10000 0 3
PLK1/PRC1-2 -0.011 0.14 -10000 0 -0.44 28 28
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.03 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.025 -10000 0 -0.18 1 1
mitotic prometaphase -0.001 0.003 -10000 0 -0.014 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.06 -10000 0 -0.28 1 1
microtubule-based process -0.016 0.12 -10000 0 -0.38 34 34
Golgi organization 0.007 0.038 -10000 0 -0.13 20 20
Cohesin/SA2 0.01 0.04 -10000 0 -0.18 8 8
PPP1CB/MYPT1 0.021 0.002 -10000 0 -10000 0 0
KIF20A -0.04 0.18 -10000 0 -0.58 34 34
APC/C/CDC20 -0.011 0.11 -10000 0 -0.36 25 25
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation 0.006 0.048 -10000 0 -0.19 13 13
PRC1 0.003 0.076 -10000 0 -0.49 8 8
ECT2 0.005 0.064 -10000 0 -0.34 7 7
C13orf34 0.013 0.028 -10000 0 -0.18 1 1
NUDC 0.009 0.026 -10000 0 -0.14 1 1
regulation of attachment of spindle microtubules to kinetochore -0.011 0.11 -10000 0 -0.4 25 25
spindle assembly 0.009 0.031 -10000 0 -0.11 16 16
spindle stabilization 0.009 0.025 -10000 0 -0.26 1 1
APC/C/HCDH1 0.007 0.071 -10000 0 -0.4 11 11
MKLP2/PLK1 -0.016 0.12 -10000 0 -0.38 34 34
CCNB1 0 0.095 -10000 0 -0.55 10 10
PPP1CB 0.014 0 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 -0.02 0.13 -10000 0 -0.45 29 29
TUBG1 0.01 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.014 0.069 -10000 0 -0.46 8 8
MLF1IP 0.006 0.044 -10000 0 -0.32 6 6
INCENP 0.01 0.048 -10000 0 -0.64 2 2
IL1-mediated 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
UBC13/UEV1A 0.013 0.004 -10000 0 -10000 0 0
PRKCZ -0.029 0.16 -10000 0 -0.63 25 25
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.069 -10000 0 -0.26 7 7
IRAK/TOLLIP 0.028 0.003 -10000 0 -10000 0 0
IKBKB 0.014 0 -10000 0 -10000 0 0
IKBKG 0.013 0.018 -10000 0 -0.34 1 1
IL1 alpha/IL1R2 -0.003 0.088 -10000 0 -0.47 11 11
IL1A 0.003 0.037 -10000 0 -0.34 4 4
IL1B -0.027 0.14 -10000 0 -0.4 44 44
IRAK/TRAF6/p62/Atypical PKCs 0.019 0.091 -10000 0 -0.44 2 2
IL1R2 -0.008 0.11 -10000 0 -0.57 14 14
IL1R1 0.007 0.067 -10000 0 -0.63 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.02 0.068 0.22 4 -0.26 5 9
TOLLIP 0.014 0 -10000 0 -10000 0 0
TICAM2 0.005 0.074 -10000 0 -0.63 5 5
MAP3K3 0.014 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.01 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.055 0.034 -10000 0 -10000 0 0
JUN -0.01 0.12 -10000 0 -0.6 5 5
MAP3K7 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.001 0.13 -10000 0 -0.34 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88 0.02 0.064 -10000 0 -0.35 9 9
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.027 0.06 -10000 0 -0.33 9 9
IL1 beta fragment/IL1R1/IL1RAP -0.014 0.13 -10000 0 -0.37 38 38
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.016 0.13 -10000 0 -0.32 52 52
IRAK1 0.021 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.14 -10000 0 -0.45 34 34
IRAK4 0.014 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.033 -10000 0 -0.63 1 1
PI3K 0.015 0.062 -10000 0 -0.56 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.082 -10000 0 -0.29 10 10
CHUK 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.014 0.13 -10000 0 -0.37 38 38
IL1 beta/IL1R2 -0.028 0.15 -10000 0 -0.43 38 38
IRAK/TRAF6/TAK1/TAB1/TAB2 0.022 0.021 -10000 0 -0.31 1 1
NF kappa B1 p50/RelA -0.037 0.1 -10000 0 -0.74 3 3
IRAK3 -0.007 0.11 -10000 0 -0.49 16 16
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.002 0.12 -10000 0 -0.33 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.026 0.048 -10000 0 -0.27 9 9
IL1 alpha/IL1R1/IL1RAP 0.011 0.069 -10000 0 -0.4 9 9
RELA 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.009 0.045 -10000 0 -0.34 6 6
MYD88 0.014 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.035 0.019 -10000 0 -0.33 1 1
IL1RAP 0.004 0.079 -10000 0 -0.55 7 7
UBE2N 0.014 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.034 0.093 -10000 0 -0.61 3 3
CASP1 0.003 0.083 -10000 0 -0.59 7 7
IL1RN/IL1R2 -0.033 0.15 -10000 0 -0.47 38 38
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.004 0.12 -10000 0 -0.34 38 38
TMEM189-UBE2V1 0.003 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.033 0.048 -10000 0 -0.34 4 4
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
IL1RN -0.036 0.17 -10000 0 -0.61 30 30
TRAF6/TAK1/TAB1/TAB2 -0.001 0.017 -10000 0 -0.32 1 1
MAP2K6 -0.002 0.1 -10000 0 -0.32 32 32
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.028 0.14 -9999 0 -0.38 45 45
AKT1 0.036 0.16 -9999 0 -0.65 14 14
PTK2B -0.002 0.17 -9999 0 -0.76 13 13
VEGFR2 homodimer/Frs2 0.009 0.15 -9999 0 -0.76 13 13
CAV1 0.01 0.051 -9999 0 -0.54 3 3
CALM1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.02 0.14 -9999 0 -0.67 14 14
endothelial cell proliferation 0.046 0.14 -9999 0 -0.59 14 14
mol:Ca2+ 0.025 0.15 -9999 0 -0.7 13 13
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.026 0.13 -9999 0 -0.66 13 13
RP11-342D11.1 0.016 0.14 -9999 0 -0.7 13 13
CDH5 0.007 0.067 -9999 0 -0.63 4 4
VEGFA homodimer 0.029 0.056 -9999 0 -0.35 7 7
SHC1 0.014 0 -9999 0 -10000 0 0
SHC2 -0.006 0.11 -9999 0 -0.61 12 12
HRAS/GDP -0.025 0.12 -9999 0 -0.6 13 13
SH2D2A -0.032 0.16 -9999 0 -0.54 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.026 0.13 -9999 0 -0.66 13 13
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.006 0.17 -9999 0 -0.51 33 33
VEGFR1 homodimer 0.011 0.042 -9999 0 -0.44 3 3
SHC/GRB2/SOS1 -0.028 0.13 -9999 0 -0.66 13 13
GRB10 0.025 0.15 -9999 0 -0.7 13 13
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PAK1 0.009 0.058 -9999 0 -0.63 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.028 0.15 -9999 0 -0.73 13 13
HRAS 0.012 0.026 -9999 0 -0.34 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.015 0.11 -9999 0 -0.45 13 13
HIF1A 0.005 0.068 -9999 0 -0.47 7 7
FRS2 0.014 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.025 0.13 -9999 0 -0.65 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.007 0.067 -9999 0 -0.63 4 4
Nck/Pak 0.015 0.056 -9999 0 -0.46 5 5
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.02 0.14 -9999 0 -0.67 14 14
mol:GDP -0.027 0.12 -9999 0 -0.64 13 13
mol:NADP 0.045 0.13 -9999 0 -0.57 13 13
eNOS/Hsp90 0.05 0.12 -9999 0 -0.52 13 13
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
mol:IP3 0.025 0.15 -9999 0 -0.71 13 13
HIF1A/ARNT 0.015 0.05 -9999 0 -0.33 7 7
SHB 0.013 0.033 -9999 0 -0.63 1 1
VEGFA 0.015 0.033 -9999 0 -0.63 1 1
VEGFC 0.005 0.071 -9999 0 -0.54 6 6
FAK1/Vinculin 0.012 0.17 -9999 0 -0.72 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.008 0.18 -9999 0 -0.81 13 13
PTPN6 0.014 0 -9999 0 -10000 0 0
EPAS1 0.011 0.07 -9999 0 -0.35 13 13
mol:L-citrulline 0.045 0.13 -9999 0 -0.57 13 13
ITGAV 0.01 0.037 -9999 0 -0.34 4 4
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.028 0.13 -9999 0 -0.66 13 13
VEGFR2 homodimer/VEGFA homodimer 0.019 0.16 -9999 0 -0.77 13 13
VEGFR2/3 heterodimer 0.006 0.16 -9999 0 -0.8 14 14
VEGFB -0.056 0.2 -9999 0 -0.62 41 41
MAPK11 0.02 0.16 -9999 0 -0.71 14 14
VEGFR2 homodimer 0.005 0.16 -9999 0 -0.85 13 13
FLT1 0.011 0.042 -9999 0 -0.44 3 3
NEDD4 0.004 0.088 -9999 0 -0.63 7 7
MAPK3 0.024 0.14 -9999 0 -0.64 13 13
MAPK1 0.024 0.14 -9999 0 -0.64 13 13
VEGFA145/NRP2 0.015 0.058 -9999 0 -0.46 5 5
VEGFR1/2 heterodimer 0.007 0.15 -9999 0 -0.76 14 14
KDR 0.005 0.16 -9999 0 -0.86 13 13
VEGFA165/NRP1/VEGFR2 homodimer 0.021 0.16 -9999 0 -0.73 13 13
SRC -0.021 0.14 -9999 0 -0.6 21 21
platelet activating factor biosynthetic process 0.025 0.14 -9999 0 -0.66 13 13
PI3K 0.02 0.18 -9999 0 -0.79 14 14
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.018 0.15 -9999 0 -0.67 15 15
FES 0.011 0.16 -9999 0 -0.75 13 13
GAB1 -0.029 0.14 -9999 0 -0.75 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0 0.16 -9999 0 -0.49 32 32
CTNNB1 0.014 0 -9999 0 -10000 0 0
SOS1 0.013 0.018 -9999 0 -0.34 1 1
ARNT 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.049 0.12 -9999 0 -0.55 13 13
VEGFR2 homodimer/VEGFA homodimer/Yes 0.02 0.14 -9999 0 -0.67 14 14
PI3K/GAB1 0.038 0.16 -9999 0 -0.65 14 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.029 0.14 -9999 0 -0.68 13 13
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
VEGFR2/3 heterodimer/VEGFC homodimer 0.009 0.17 -9999 0 -0.78 15 15
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.025 0.15 -9999 0 -0.72 13 13
actin cytoskeleton reorganization -0.006 0.17 -9999 0 -0.5 33 33
PTK2 0.004 0.18 -9999 0 -0.79 15 15
EDG1 0.016 0.14 -9999 0 -0.7 13 13
mol:DAG 0.025 0.15 -9999 0 -0.71 13 13
CaM/Ca2+ 0.029 0.14 -9999 0 -0.65 13 13
MAP2K3 0.012 0.17 -9999 0 -0.71 14 14
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.027 0.15 -9999 0 -0.73 13 13
PLCG1 0.025 0.15 -9999 0 -0.72 13 13
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.008 0.16 -9999 0 -0.68 14 14
IQGAP1 0.01 0.037 -9999 0 -0.34 4 4
YES1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.02 0.14 -9999 0 -0.67 14 14
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.02 0.14 -9999 0 -0.67 14 14
cell migration 0.037 0.15 -9999 0 -0.65 13 13
mol:PI-3-4-5-P3 0.022 0.16 -9999 0 -0.7 14 14
FYN 0.013 0.018 -9999 0 -0.34 1 1
VEGFB/NRP1 -0.014 0.17 -9999 0 -0.63 15 15
mol:NO 0.045 0.13 -9999 0 -0.57 13 13
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.025 0.12 -9999 0 -0.6 13 13
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.026 0.15 -9999 0 -0.73 13 13
VHL 0.009 0.058 -9999 0 -0.63 3 3
ITGB3 -0.049 0.18 -9999 0 -0.55 41 41
NOS3 0.043 0.15 -9999 0 -0.67 13 13
VEGFR2 homodimer/VEGFA homodimer/Sck 0.008 0.15 -9999 0 -0.52 25 25
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.031 0.14 -9999 0 -0.66 13 13
PRKCB 0.01 0.16 -9999 0 -0.68 13 13
VCL 0.013 0.018 -9999 0 -0.34 1 1
VEGFA165/NRP1 0.017 0.15 -9999 0 -0.68 14 14
VEGFR1/2 heterodimer/VEGFA homodimer 0.018 0.15 -9999 0 -0.68 15 15
VEGFA165/NRP2 0.015 0.058 -9999 0 -0.46 5 5
MAPKKK cascade 0.048 0.13 -9999 0 -0.6 13 13
NRP2 0.005 0.071 -9999 0 -0.54 6 6
VEGFC homodimer 0.005 0.071 -9999 0 -0.53 6 6
NCK1 0.011 0.047 -9999 0 -0.63 2 2
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.013 0.17 -9999 0 -0.72 15 15
MAP3K13 0.005 0.18 -9999 0 -0.76 14 14
PDPK1 0.029 0.15 -9999 0 -0.63 14 14
TCGA08_rtk_signaling

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
PDGFRA -0.17 0.28 -10000 0 -0.57 118 118
HRAS 0.012 0.026 -10000 0 -0.34 2 2
EGFR -0.007 0.11 -10000 0 -0.59 13 13
AKT 0.016 0.072 -10000 0 -0.37 9 9
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
FOXO1 0.01 0.037 -10000 0 -0.34 4 4
AKT3 -0.007 0.1 -10000 0 -0.44 17 17
FOXO4 0.014 0 -10000 0 -10000 0 0
MET 0.008 0.061 -10000 0 -0.56 4 4
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
PIK3CB 0.014 0 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
PIK3CG -0.027 0.15 -10000 0 -0.51 29 29
PIK3R3 0.013 0.018 -10000 0 -0.34 1 1
PIK3R2 0.013 0.018 -10000 0 -0.34 1 1
NF1 0.013 0.033 -10000 0 -0.63 1 1
RAS -0.037 0.1 0.23 1 -0.33 16 17
ERBB2 -0.02 0.14 -10000 0 -0.62 20 20
proliferation/survival/translation -0.028 0.037 0.24 2 -10000 0 2
PI3K -0.03 0.11 0.2 1 -0.31 25 26
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
KRAS 0.013 0.018 -10000 0 -0.34 1 1
FOXO 0.032 0.033 0.18 1 -0.14 1 2
AKT2 0.013 0.018 -10000 0 -0.34 1 1
PTEN 0.007 0.067 -10000 0 -0.63 4 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.041 0.16 -9999 0 -0.46 43 43
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.026 -9999 0 -0.34 2 2
TCEB1 0.014 0 -9999 0 -10000 0 0
HIF1A/p53 -0.002 0.078 -9999 0 -0.32 16 16
HIF1A 0.001 0.049 -9999 0 -0.29 3 3
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.039 0.035 -9999 0 -0.32 3 3
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.064 0.2 -9999 0 -0.55 51 51
ARNT/IPAS -0.019 0.12 -9999 0 -0.46 18 18
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.01 0.047 -9999 0 -0.27 3 3
CUL2 0.014 0 -9999 0 -10000 0 0
OS9 0.014 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.028 0.015 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.01 0.047 -9999 0 -0.27 3 3
PHD1-3/OS9 -0.034 0.14 -9999 0 -0.35 49 49
HIF1A/RACK1/Elongin B/Elongin C 0.021 0.048 -9999 0 -0.33 2 2
VHL 0.009 0.058 -9999 0 -0.63 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.01 0.047 -9999 0 -0.27 3 3
EGLN3 -0.11 0.23 -9999 0 -0.5 89 89
EGLN2 0.013 0.018 -9999 0 -0.34 1 1
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 -0.008 0.12 -9999 0 -0.63 13 13
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.053 -9999 0 -0.54 3 3
ARNT 0.014 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.029 0.11 -9999 0 -0.31 41 41
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.004 0.071 -9999 0 -0.34 11 11
RGS9BP 0.007 0.041 -9999 0 -0.34 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0.018 -9999 0 -0.34 1 1
mol:Na + -0.01 0.055 -9999 0 -0.37 2 2
mol:ADP 0.003 0.018 -9999 0 -0.22 2 2
GNAT2 0.002 0.067 -9999 0 -0.41 9 9
RGS9-1/Gbeta5/R9AP -0.028 0.13 -9999 0 -0.39 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.003 0.041 -9999 0 -0.41 2 2
GRK7 0.003 0.019 -9999 0 -0.34 1 1
CNGB3 -0.017 0.084 -9999 0 -0.34 23 23
Cone Metarhodopsin II/X-Arrestin 0 0.021 -9999 0 -0.23 3 3
mol:Ca2+ -0.009 0.05 -9999 0 -0.33 2 2
Cone PDE6 -0.027 0.11 -9999 0 -0.33 34 34
Cone Metarhodopsin II 0.002 0.013 -9999 0 -10000 0 0
Na + (4 Units) -0.009 0.05 -9999 0 -0.33 2 2
GNAT2/GDP -0.021 0.12 -9999 0 -0.34 35 35
GNB5 0.01 0.046 -9999 0 -0.41 4 4
mol:GMP (4 units) -0.002 0.057 -9999 0 -0.45 2 2
Cone Transducin 0.004 0.075 -9999 0 -0.36 11 11
SLC24A2 0 0.018 -9999 0 -0.34 1 1
GNB3/GNGT2 0 0.085 -9999 0 -0.33 21 21
GNB3 0.002 0.06 -9999 0 -0.34 11 11
GNAT2/GTP 0.002 0.048 -9999 0 -0.29 9 9
CNGA3 -0.003 0.04 -9999 0 -0.34 5 5
ARR3 -0.001 0.031 -9999 0 -0.34 3 3
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.01 0.055 -9999 0 -0.37 2 2
mol:Pi -0.028 0.13 -9999 0 -0.39 33 33
Cone CNG Channel -0.023 0.062 -9999 0 -0.34 5 5
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0 0.018 -9999 0 -0.34 1 1
RGS9 -0.065 0.19 -9999 0 -0.48 59 59
PDE6C -0.011 0.079 -9999 0 -0.34 20 20
GNGT2 -0.003 0.099 -9999 0 -0.55 11 11
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.004 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.014 0.076 -9999 0 -0.39 12 12
forebrain development -0.027 0.15 -9999 0 -0.47 33 33
GNAO1 -0.15 0.27 -9999 0 -0.56 108 108
SMO/beta Arrestin2 0.012 0.075 -9999 0 -0.46 9 9
SMO -0.001 0.1 -9999 0 -0.63 9 9
ARRB2 0.015 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.042 0.049 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.014 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.036 0.02 -9999 0 -0.35 1 1
GNAI1 0.007 0.067 -9999 0 -0.63 4 4
XPO1 0.017 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.046 0.13 -9999 0 -0.46 22 22
SAP30 0.012 0.034 -9999 0 -0.63 1 1
mol:GDP -0.001 0.1 -9999 0 -0.63 9 9
MIM/GLI2A 0.014 0.076 -9999 0 -0.64 5 5
IFT88 0.013 0.018 -9999 0 -0.34 1 1
GNAI3 0.014 0.003 -9999 0 -10000 0 0
GLI2 0.017 0.069 -9999 0 -10000 0 0
GLI3 0.036 0.052 -9999 0 -10000 0 0
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.013 0.018 -9999 0 -0.34 1 1
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0.018 -9999 0 -0.34 1 1
GNG2 0.007 0.063 -9999 0 -0.52 5 5
Gi family/GTP -0.085 0.17 -9999 0 -0.33 93 93
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.053 0.041 -9999 0 -10000 0 0
GLI2/Su(fu) 0.031 0.071 -9999 0 -0.33 2 2
FOXA2 -0.014 0.14 -9999 0 -0.98 7 7
neural tube patterning -0.027 0.15 -9999 0 -0.47 33 33
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.029 0.037 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.014 0.076 -9999 0 -0.64 5 5
embryonic limb morphogenesis -0.027 0.15 -9999 0 -0.47 33 33
SUFU 0.024 0.04 -9999 0 -10000 0 0
LGALS3 -0.023 0.12 -9999 0 -0.4 33 33
catabolic process 0.047 0.069 -9999 0 -0.33 2 2
GLI3A/CBP 0.004 0.073 -9999 0 -0.36 11 11
KIF3A 0.013 0.033 -9999 0 -0.63 1 1
GLI1 -0.028 0.16 -9999 0 -0.48 33 33
RAB23 0.014 0 -9999 0 -10000 0 0
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.014 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.009 0.078 -9999 0 -0.35 9 9
GNAZ -0.086 0.22 -9999 0 -0.55 66 66
RBBP4 0.006 0.074 -9999 0 -0.63 5 5
CSNK1G1 0.014 0 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
GLI2/SPOP 0.023 0.065 -9999 0 -10000 0 0
STK36 0.017 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.066 0.15 -9999 0 -0.41 28 28
PTCH1 -0.06 0.3 -9999 0 -1.2 23 23
MIM/GLI1 -0.017 0.16 -9999 0 -0.5 25 25
CREBBP 0.004 0.073 -9999 0 -0.35 11 11
Su(fu)/SIN3/HDAC complex 0.045 0.035 -9999 0 -0.29 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.019 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.048 0.19 -9999 0 -0.58 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.035 -9999 0 -0.23 3 3
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.013 0.018 -9999 0 -0.34 1 1
MAP3K12 0.011 0.032 -9999 0 -0.34 3 3
FGR 0.007 0.06 -9999 0 -0.44 6 6
p38 alpha/TAB1 -0.039 0.08 -9999 0 -0.3 21 21
PRKG1 -0.035 0.16 -9999 0 -0.53 33 33
DUSP8 -0.011 0.12 -9999 0 -0.61 15 15
PGK/cGMP/p38 alpha -0.054 0.099 -9999 0 -0.3 37 37
apoptosis -0.037 0.077 -9999 0 -0.29 21 21
RAL/GTP 0.019 0 -9999 0 -10000 0 0
LYN 0.013 0.033 -9999 0 -0.63 1 1
DUSP1 -0.007 0.11 -9999 0 -0.63 12 12
PAK1 0.009 0.058 -9999 0 -0.63 3 3
SRC -0.021 0.14 -9999 0 -0.6 21 21
RAC1/OSM/MEKK3/MKK3 0.037 0 -9999 0 -10000 0 0
TRAF6 0.013 0.033 -9999 0 -0.63 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.019 0 -9999 0 -10000 0 0
MAPK11 -0.016 0.13 -9999 0 -0.39 24 24
BLK -0.062 0.19 -9999 0 -0.51 52 52
HCK -0.002 0.097 -9999 0 -0.57 10 10
MAP2K3 0.014 0 -9999 0 -10000 0 0
DUSP16 0.013 0.033 -9999 0 -0.63 1 1
DUSP10 0.007 0.067 -9999 0 -0.63 4 4
TRAF6/MEKK3 0.017 0.02 -9999 0 -0.36 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.002 0.11 -9999 0 -0.33 21 21
positive regulation of innate immune response -0.013 0.15 -9999 0 -0.42 24 24
LCK -0.033 0.16 -9999 0 -0.52 33 33
p38alpha-beta/MKP7 -0.006 0.14 -9999 0 -0.42 20 20
p38alpha-beta/MKP5 -0.008 0.14 -9999 0 -0.42 20 20
PGK/cGMP -0.025 0.12 -9999 0 -0.38 33 33
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.014 0.15 -9999 0 -0.45 23 23
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.03 0.11 -9999 0 -0.34 40 40
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.039 0.14 -9999 0 -0.39 39 39
PDGFB-D/PDGFRB/SLAP -0.011 0.11 -9999 0 -0.37 28 28
PDGFB-D/PDGFRB/APS/CBL 0.011 0.072 -9999 0 -0.39 10 10
AKT1 0.037 0.074 -9999 0 -0.51 1 1
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.04 0.14 -9999 0 -0.44 28 28
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
FGR -0.016 0.075 -9999 0 -0.5 7 7
mol:Ca2+ -0.002 0.089 -9999 0 -0.62 5 5
MYC -0.059 0.26 -9999 0 -0.82 37 37
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP 0.02 0.071 -9999 0 -0.36 11 11
LRP1/PDGFRB/PDGFB 0.014 0.073 -9999 0 -0.44 8 8
GRB10 0.014 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 -0.002 0.091 -9999 0 -0.64 5 5
PTEN 0.007 0.067 -9999 0 -0.63 4 4
GRB2 0.014 0 -9999 0 -10000 0 0
GRB7 -0.011 0.11 -9999 0 -0.48 19 19
PDGFB-D/PDGFRB/SHP2 0.01 0.061 -9999 0 -0.46 5 5
PDGFB-D/PDGFRB/GRB10 0.01 0.061 -9999 0 -0.46 5 5
cell cycle arrest -0.011 0.11 -9999 0 -0.37 28 28
HRAS 0.012 0.026 -9999 0 -0.34 2 2
HIF1A 0.038 0.08 -9999 0 -0.59 2 2
GAB1 -0.022 0.12 -9999 0 -0.45 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.021 0.12 -9999 0 -0.44 14 14
PDGFB-D/PDGFRB 0.018 0.054 -9999 0 -0.4 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.01 0.061 -9999 0 -0.46 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.069 0.14 -9999 0 -0.43 39 39
positive regulation of MAPKKK cascade 0.01 0.061 -9999 0 -0.46 5 5
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
mol:IP3 -0.002 0.091 -9999 0 -0.64 5 5
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.009 0.11 -9999 0 -0.49 14 14
SHB 0.013 0.033 -9999 0 -0.63 1 1
BLK -0.066 0.18 -9999 0 -0.59 35 35
PTPN2 0.013 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.01 0.061 -9999 0 -0.46 5 5
BCAR1 0.014 0 -9999 0 -10000 0 0
VAV2 -0.026 0.14 -9999 0 -0.47 19 19
CBL 0.011 0.047 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/DEP1 0.01 0.061 -9999 0 -0.46 5 5
LCK -0.048 0.16 -9999 0 -0.62 24 24
PDGFRB 0 0.083 -9999 0 -0.5 9 9
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.023 0.11 -9999 0 -0.56 13 13
ABL1 -0.015 0.1 -9999 0 -0.46 9 9
PDGFB-D/PDGFRB/CBL -0.022 0.12 -9999 0 -0.48 13 13
PTPN1 0.013 0.004 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 0.009 0.041 -9999 0 -0.34 5 5
cell proliferation -0.048 0.23 -9999 0 -0.71 37 37
SLA -0.013 0.12 -9999 0 -0.52 19 19
actin cytoskeleton reorganization 0.023 0.084 -9999 0 -0.61 2 2
SRC -0.044 0.16 -9999 0 -0.64 23 23
PI3K -0.017 0.068 -9999 0 -0.57 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.003 0.091 -9999 0 -0.42 14 14
SH2B2 0.006 0.062 -9999 0 -0.42 7 7
PLCgamma1/SPHK1 -0.042 0.15 -9999 0 -0.45 28 28
LYN -0.012 0.064 -9999 0 -0.46 6 6
LRP1 0.011 0.047 -9999 0 -0.63 2 2
SOS1 0.013 0.018 -9999 0 -0.34 1 1
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.011 0.042 -9999 0 -0.44 3 3
NCK1-2/p130 Cas -0.008 0.08 -9999 0 -0.36 14 14
SPHK1 -0.11 0.22 -9999 0 -0.44 98 98
EDG1 -0.001 0.003 -9999 0 -10000 0 0
mol:DAG -0.002 0.091 -9999 0 -0.64 5 5
PLCG1 -0.003 0.094 -9999 0 -0.66 5 5
NHERF/PDGFRB 0.011 0.077 -9999 0 -0.39 12 12
YES1 -0.011 0.053 -9999 0 -0.41 5 5
cell migration 0.01 0.076 -9999 0 -0.39 12 12
SHC/Grb2/SOS1 0.005 0.044 -9999 0 -0.31 5 5
SLC9A3R2 0.004 0.081 -9999 0 -0.63 6 6
SLC9A3R1 0.013 0.033 -9999 0 -0.63 1 1
NHERF1-2/PDGFRB/PTEN 0.017 0.08 -9999 0 -0.35 16 16
FYN -0.01 0.053 -9999 0 -0.41 5 5
DOK1 0.023 0.048 -9999 0 -0.35 5 5
HRAS/GTP 0.009 0.018 -9999 0 -0.23 2 2
PDGFB 0.01 0.051 -9999 0 -0.54 3 3
RAC1 -0.034 0.18 -9999 0 -0.48 41 41
PRKCD 0.022 0.049 -9999 0 -0.36 5 5
FER 0.022 0.049 -9999 0 -0.36 5 5
MAPKKK cascade -0.003 0.041 -9999 0 -0.3 4 4
RASA1 0.015 0.076 -9999 0 -0.39 11 11
NCK1 0.011 0.047 -9999 0 -0.63 2 2
NCK2 -0.01 0.11 -9999 0 -0.49 18 18
p62DOK/Csk 0.034 0.045 -9999 0 -0.32 5 5
PDGFB-D/PDGFRB/SHB 0.008 0.066 -9999 0 -0.46 6 6
chemotaxis -0.015 0.099 -9999 0 -0.44 9 9
STAT1-3-5/STAT1-3-5 -0.008 0.041 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.001 0.061 -9999 0 -0.37 9 9
PTPRJ 0.014 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.011 0.047 -9999 0 -0.63 2 2
Aurora C/Aurora B/INCENP 0 0.095 -9999 0 -0.37 19 19
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.025 -9999 0 -10000 0 0
AURKB -0.019 0.13 -9999 0 -0.46 26 26
AURKC 0.002 0.083 -9999 0 -0.5 9 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.013 0.11 -9999 0 -0.35 25 25
CaM/Ca2+ 0.011 0 -9999 0 -10000 0 0
AKT1 0.014 0 -9999 0 -10000 0 0
AKT2 0.013 0.018 -9999 0 -0.34 1 1
STXBP4 0.01 0.046 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.016 0.13 -9999 0 -0.36 31 31
YWHAZ 0.014 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
YWHAQ 0.014 0 -9999 0 -10000 0 0
TBC1D4 0.005 0.091 -9999 0 -0.46 13 13
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
SNARE/Synip 0.026 0.028 -9999 0 -0.39 1 1
YWHAG 0.014 0 -9999 0 -10000 0 0
ASIP -0.001 0.071 -9999 0 -0.36 13 13
PRKCI 0.014 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.011 0 -9999 0 -10000 0 0
RHOQ 0.012 0.038 -9999 0 -0.49 2 2
GYS1 0.03 0.016 -9999 0 -10000 0 0
PRKCZ -0.029 0.16 -9999 0 -0.63 25 25
TRIP10 0.014 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.018 0.024 -9999 0 -0.29 2 2
AS160/14-3-3 -0.019 0.099 -9999 0 -0.38 1 1
VAMP2 0.014 0 -9999 0 -10000 0 0
SLC2A4 -0.019 0.14 -9999 0 -0.4 31 31
STX4 0.014 0 -9999 0 -10000 0 0
GSK3B 0.026 0.008 -9999 0 -10000 0 0
SFN -0.16 0.25 -9999 0 -0.48 132 132
LNPEP 0.011 0.042 -9999 0 -0.44 3 3
YWHAE 0.014 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.014 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.01 -10000 0 -10000 0 0
DOCK1 -0.01 0.12 -10000 0 -0.63 14 14
ITGA4 -0.006 0.11 -10000 0 -0.53 14 14
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.011 0.12 -10000 0 -0.44 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0.018 -10000 0 -0.34 1 1
alpha4/beta1 Integrin 0.016 0.069 -10000 0 -0.39 9 9
alpha4/beta7 Integrin/Paxillin 0.009 0.098 -10000 0 -0.36 22 22
lamellipodium assembly -0.014 0.087 -10000 0 -0.61 5 5
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
PI3K 0.015 0.062 -10000 0 -0.56 4 4
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.014 0 -10000 0 -10000 0 0
PXN 0.022 0.013 -10000 0 -10000 0 0
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
ARF6/GTP -0.009 0.047 -10000 0 -0.29 9 9
cell adhesion 0.03 0.059 -10000 0 -0.32 9 9
CRKL/CBL 0.019 0.035 -10000 0 -0.46 2 2
alpha4/beta1 Integrin/Paxillin 0.023 0.063 -10000 0 -0.35 9 9
ITGB1 0.014 0 -10000 0 -10000 0 0
ITGB7 -0.009 0.12 -10000 0 -0.61 14 14
ARF6/GDP 0.002 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.013 0.13 -10000 0 -0.36 39 39
p130Cas/Crk/Dock1 0.013 0.083 -10000 0 -0.4 14 14
VCAM1 -0.067 0.2 -10000 0 -0.51 58 58
alpha4/beta1 Integrin/Paxillin/Talin 0.031 0.06 -10000 0 -0.32 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.031 0.06 -10000 0 -0.32 9 9
BCAR1 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.059 0.32 9 -10000 0 9
CBL 0.011 0.047 -10000 0 -0.63 2 2
PRKACA 0.013 0.018 -10000 0 -0.34 1 1
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.031 0.06 -10000 0 -0.32 9 9
Rac1/GTP -0.016 0.1 -10000 0 -0.72 5 5
Atypical NF-kappaB 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
BCL3/RelA 0.02 0.025 -9999 0 -0.46 1 1
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.016 0.068 -9999 0 -0.39 10 10
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.1 -9999 0 -0.5 8 8
NFKBIA -0.013 0.12 -9999 0 -0.32 38 38
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.004 0.11 -9999 0 -0.6 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.022 -9999 0 -0.39 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
NF kappa B1 p50 dimer 0.021 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
NFKB1 0.023 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.001 0.1 -9999 0 -0.28 37 37
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.019 0.093 -9999 0 -0.46 8 8
SRC -0.021 0.14 -9999 0 -0.6 21 21
PI3K 0.015 0.062 -9999 0 -0.56 4 4
NF kappa B1 p50/RelA -0.001 0.1 -9999 0 -0.29 37 37
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK -0.006 0.099 -9999 0 -0.45 16 16
I kappa B alpha/PIK3R1 -0.007 0.12 -9999 0 -0.36 27 27
cell death 0.018 0.089 -9999 0 -0.43 8 8
NF kappa B1 p105/c-Rel 0.016 0.068 -9999 0 -0.39 10 10
LCK -0.033 0.16 -9999 0 -0.52 33 33
BCL3 0.013 0.033 -9999 0 -0.63 1 1
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.048 0.27 4 -0.56 1 5
DAPP1 -0.019 0.14 -10000 0 -0.46 22 22
Src family/SYK family/BLNK-LAT/BTK-ITK -0.028 0.21 -10000 0 -0.65 25 25
mol:DAG 0.011 0.093 0.2 1 -0.28 17 18
HRAS 0.013 0.026 -10000 0 -0.34 2 2
RAP1A 0.015 0.002 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.076 -10000 0 -0.37 7 7
PLCG2 -0.004 0.11 -10000 0 -0.6 11 11
PLCG1 0.014 0 -10000 0 -10000 0 0
ARF5 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.037 0.24 4 -0.28 3 7
ARF1/GTP 0.037 0.044 0.25 4 -0.46 1 5
RHOA 0.014 0 -10000 0 -10000 0 0
YES1 0.014 0 -10000 0 -10000 0 0
RAP1A/GTP 0.026 0.037 0.23 4 -0.28 3 7
ADAP1 -0.024 0.078 0.24 4 -0.32 13 17
ARAP3 -0.001 0.037 0.24 4 -0.28 3 7
INPPL1 0.014 0 -10000 0 -10000 0 0
PREX1 0.011 0.047 -10000 0 -0.63 2 2
ARHGEF6 0.008 0.061 -10000 0 -0.56 4 4
ARHGEF7 0.014 0 -10000 0 -10000 0 0
ARF1 0.014 0 -10000 0 -10000 0 0
NRAS 0.015 0.002 -10000 0 -10000 0 0
FYN 0.013 0.018 -10000 0 -0.34 1 1
ARF6 0.014 0 -10000 0 -10000 0 0
FGR 0.007 0.06 -10000 0 -0.44 6 6
mol:Ca2+ 0.015 0.051 -10000 0 -0.18 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.015 0.13 -10000 0 -0.53 20 20
ZAP70 -0.016 0.12 -10000 0 -0.48 23 23
mol:IP3 0.015 0.069 -10000 0 -0.22 10 10
LYN 0.013 0.033 -10000 0 -0.63 1 1
ARF1/GDP 0.023 0.076 -10000 0 -0.37 7 7
RhoA/GDP -0.005 0.044 0.26 3 -0.33 2 5
PDK1/Src/Hsp90 0.004 0.098 -10000 0 -0.39 21 21
BLNK -0.003 0.1 -10000 0 -0.63 10 10
actin cytoskeleton reorganization 0.043 0.073 0.25 3 -0.4 3 6
SRC -0.021 0.14 -10000 0 -0.6 21 21
PLEKHA2 0.023 0.062 -10000 0 -0.62 3 3
RAC1 0.014 0 -10000 0 -10000 0 0
PTEN 0.004 0.064 -10000 0 -0.61 4 4
HSP90AA1 0.014 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.037 0.27 4 -10000 0 4
RhoA/GTP 0.033 0.036 0.24 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.027 0.18 -10000 0 -0.59 22 22
BLK -0.062 0.19 -10000 0 -0.51 52 52
PDPK1 0.011 0.047 -10000 0 -0.63 2 2
CYTH1 0 0.035 0.24 4 -10000 0 4
HCK -0.002 0.097 -10000 0 -0.57 10 10
CYTH3 -0.003 0.048 0.24 4 -0.44 2 6
CYTH2 0 0.035 0.24 4 -10000 0 4
KRAS 0.014 0.018 -10000 0 -0.34 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.11 -10000 0 -0.52 11 11
SGK1 -0.028 0.11 0.21 4 -0.58 11 15
INPP5D 0.009 0.054 -10000 0 -0.49 4 4
mol:GDP 0.016 0.08 -10000 0 -0.28 15 15
SOS1 0.013 0.018 -10000 0 -0.34 1 1
SYK -0.006 0.099 -10000 0 -0.45 16 16
ARF6/GDP -0.005 0.045 0.26 3 -0.32 3 6
mol:PI-3-4-5-P3 0 0.042 0.31 4 -10000 0 4
ARAP3/RAP1A/GTP 0.026 0.037 0.23 4 -0.28 3 7
VAV1 -0.027 0.15 -10000 0 -0.53 28 28
mol:PI-3-4-P2 0.019 0.04 -10000 0 -0.46 2 2
RAS family/GTP/PI3K Class I 0.029 0.031 -10000 0 -0.28 3 3
PLEKHA1 0.026 0.034 -10000 0 -0.39 2 2
Rac1/GDP 0.023 0.076 -10000 0 -0.37 7 7
LAT 0.008 0.057 -10000 0 -0.46 5 5
Rac1/GTP 0.011 0.11 -10000 0 -0.4 16 16
ITK -0.029 0.089 0.24 3 -0.3 29 32
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.006 0.12 0.23 1 -0.4 17 18
LCK -0.033 0.16 -10000 0 -0.52 33 33
BTK -0.01 0.056 0.24 3 -0.3 7 10
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.002 0.095 -10000 0 -0.53 11 11
positive regulation of NF-kappaB transcription factor activity 0.007 0.075 -10000 0 -0.37 13 13
MAP2K4 0.036 0.05 -10000 0 -0.27 1 1
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.014 0 -10000 0 -10000 0 0
TNFRSF10A -0.004 0.11 -10000 0 -0.6 11 11
SMPD1 0.014 0.036 -10000 0 -0.23 7 7
IKBKG 0.013 0.018 -10000 0 -0.34 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.038 -10000 0 -0.49 2 2
TRAIL/TRAILR2 0.009 0.07 -10000 0 -0.38 11 11
TRAIL/TRAILR3 -0.006 0.097 -10000 0 -0.31 31 31
TRAIL/TRAILR1 -0.004 0.1 -10000 0 -0.41 22 22
TRAIL/TRAILR4 0.008 0.075 -10000 0 -0.37 13 13
TRAIL/TRAILR1/DAP3/GTP 0.008 0.083 -10000 0 -0.36 17 17
IKK complex -0.006 0.024 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.011 0 -10000 0 -10000 0 0
MAPK3 0.011 0.07 -10000 0 -0.38 11 11
MAP3K1 0.03 0.052 -10000 0 -0.27 8 8
TRAILR4 (trimer) 0.012 0.038 -10000 0 -0.49 2 2
TRADD 0.013 0.033 -10000 0 -0.63 1 1
TRAILR1 (trimer) -0.004 0.11 -10000 0 -0.6 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.066 -10000 0 -0.26 18 18
CFLAR 0.014 0 -10000 0 -10000 0 0
MAPK1 0.01 0.075 -10000 0 -0.38 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP 0.022 0.081 -10000 0 -0.32 18 18
mol:ceramide 0.014 0.036 -10000 0 -0.23 7 7
FADD 0.013 0.018 -10000 0 -0.34 1 1
MAPK8 0.02 0.1 -10000 0 -0.45 8 8
TRAF2 0.014 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.008 0.097 -10000 0 -0.4 20 20
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.007 0.091 -10000 0 -0.39 17 17
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.014 0.065 0.28 1 -0.38 7 8
JNK cascade 0.007 0.075 -10000 0 -0.37 13 13
TRAIL (trimer) -0.002 0.095 -10000 0 -0.52 11 11
TNFRSF10C -0.008 0.097 -10000 0 -0.4 20 20
TRAIL/TRAILR1/DAP3/GTP/FADD 0.015 0.079 -10000 0 -0.33 17 17
TRAIL/TRAILR2/FADD 0.018 0.061 -10000 0 -0.39 7 7
cell death 0.014 0.036 -10000 0 -0.23 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.045 -10000 0 -0.26 8 8
TRAILR2 (trimer) 0.014 0 -10000 0 -10000 0 0
CASP8 0.003 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.032 0.056 -10000 0 -0.32 8 8
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.02 0.14 -9999 0 -0.39 43 43
VEGFR1 homodimer/NRP1 0.014 0.061 -9999 0 -0.48 4 4
mol:DAG 0.021 0.081 -9999 0 -0.37 13 13
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.06 -9999 0 -0.42 5 5
CaM/Ca2+ 0.028 0.077 -9999 0 -0.5 2 2
HIF1A 0.012 0.071 -9999 0 -0.44 8 8
GAB1 0.013 0.033 -9999 0 -0.63 1 1
AKT1 0.035 0.11 -9999 0 -0.98 2 2
PLCG1 0.021 0.082 -9999 0 -0.37 13 13
NOS3 0.04 0.096 -9999 0 -0.66 3 3
CBL 0.011 0.047 -9999 0 -0.63 2 2
mol:NO 0.04 0.092 -9999 0 -0.62 3 3
FLT1 0.021 0.071 -9999 0 -0.55 4 4
PGF -0.004 0.1 -9999 0 -0.52 13 13
VEGFR1 homodimer/NRP2/VEGFR121 0.027 0.082 -9999 0 -0.43 8 8
CALM1 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
eNOS/Hsp90 0.046 0.09 -9999 0 -0.59 3 3
endothelial cell proliferation 0.018 0.1 -9999 0 -0.66 2 2
mol:Ca2+ 0.021 0.081 -9999 0 -0.36 13 13
MAPK3 0.033 0.072 -9999 0 -0.61 1 1
MAPK1 0.032 0.078 -9999 0 -0.61 2 2
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
PLGF homodimer -0.004 0.1 -9999 0 -0.52 13 13
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.01 0.051 -9999 0 -0.54 3 3
VEGFA homodimer 0.013 0.033 -9999 0 -0.63 1 1
VEGFR1 homodimer/VEGFA homodimer 0.024 0.065 -9999 0 -0.46 5 5
platelet activating factor biosynthetic process 0.038 0.076 -9999 0 -0.58 2 2
PI3K 0.025 0.097 -9999 0 -0.66 3 3
PRKCA 0.027 0.076 -9999 0 -0.49 2 2
PRKCB 0.005 0.11 -9999 0 -0.35 19 19
VEGFR1 homodimer/PLGF homodimer 0.013 0.09 -9999 0 -0.41 13 13
VEGFA 0.013 0.033 -9999 0 -0.63 1 1
VEGFB -0.056 0.2 -9999 0 -0.62 41 41
mol:IP3 0.021 0.081 -9999 0 -0.37 13 13
RASA1 -0.016 0.14 -9999 0 -0.37 47 47
NRP2 0.005 0.071 -9999 0 -0.54 6 6
VEGFR1 homodimer 0.021 0.071 -9999 0 -0.55 4 4
VEGFB homodimer -0.055 0.2 -9999 0 -0.62 41 41
NCK1 0.011 0.047 -9999 0 -0.63 2 2
eNOS/Caveolin-1 0.044 0.096 -9999 0 -0.59 4 4
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.024 0.095 -9999 0 -0.64 3 3
mol:L-citrulline 0.04 0.092 -9999 0 -0.62 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0.068 -9999 0 -0.66 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.03 0.075 -9999 0 -0.55 5 5
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 0.03 0.1 -9999 0 -0.92 2 2
PDPK1 0.027 0.1 -9999 0 -0.9 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.031 0.06 -9999 0 -0.41 5 5
mol:NADP 0.04 0.092 -9999 0 -0.62 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.067 -9999 0 -0.65 2 2
VEGFR1 homodimer/NRP2 0.02 0.085 -9999 0 -0.47 8 8
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.023 0.12 -10000 0 -1.1 3 3
regulation of axonogenesis -0.005 0.076 0.24 30 -10000 0 30
myoblast fusion -0.014 0.05 0.42 3 -10000 0 3
mol:GTP 0.007 0.028 -10000 0 -0.23 3 3
regulation of calcium-dependent cell-cell adhesion -0.015 0.083 0.37 13 -10000 0 13
ARF1/GTP 0.016 0.022 -10000 0 -10000 0 0
mol:GM1 0.007 0.021 -10000 0 -0.18 3 3
mol:Choline -0.002 0.11 -10000 0 -0.38 26 26
lamellipodium assembly -0.003 0.052 -10000 0 -0.45 3 3
MAPK3 0.022 0.041 -10000 0 -0.34 3 3
ARF6/GTP/NME1/Tiam1 0.015 0.083 -10000 0 -0.37 13 13
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.05 -10000 0 -0.42 3 3
ARF1/GDP 0.023 0.047 -10000 0 -0.38 3 3
ARF6 0.011 0.016 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 -0.014 0.13 -10000 0 -0.53 20 20
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.047 -10000 0 -0.36 4 4
actin filament bundle formation -0.018 0.045 0.38 3 -10000 0 3
KALRN -0.004 0.049 -10000 0 -0.34 6 6
RAB11FIP3/RAB11A 0.019 0.035 -10000 0 -0.46 2 2
RhoA/GDP 0.019 0.045 -10000 0 -0.38 3 3
NME1 0.016 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.045 -10000 0 -0.38 3 3
substrate adhesion-dependent cell spreading 0.007 0.028 -10000 0 -0.23 3 3
cortical actin cytoskeleton organization -0.003 0.052 -10000 0 -0.45 3 3
RAC1 0.014 0 -10000 0 -10000 0 0
liver development 0.007 0.028 -10000 0 -0.23 3 3
ARF6/GTP 0.007 0.028 -10000 0 -0.23 3 3
RhoA/GTP 0.016 0.022 -10000 0 -10000 0 0
mol:GDP -0.003 0.05 -10000 0 -0.42 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.023 0.035 -10000 0 -0.37 2 2
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 -0.013 0.12 -10000 0 -0.44 26 26
RAB11FIP3 0.011 0.047 -10000 0 -0.63 2 2
tube morphogenesis -0.003 0.052 -10000 0 -0.45 3 3
ruffle organization 0.005 0.076 -10000 0 -0.24 30 30
regulation of epithelial cell migration 0.007 0.028 -10000 0 -0.23 3 3
PLD2 0.018 0.021 -10000 0 -10000 0 0
PIP5K1A 0.005 0.076 -10000 0 -0.24 30 30
mol:Phosphatidic acid -0.002 0.11 -10000 0 -0.38 26 26
Rac1/GTP -0.003 0.053 -10000 0 -0.46 3 3
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.057 -9999 0 -0.3 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.048 0.062 -9999 0 -0.41 2 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.024 0.035 -9999 0 -0.39 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.029 0.071 -9999 0 -0.32 10 10
CaM/Ca2+ 0.021 0.051 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.028 0.061 -9999 0 -0.32 2 2
AKT1 0.034 0.07 -9999 0 -0.59 2 2
MAP2K1 0.035 0.051 -9999 0 -10000 0 0
MAP3K11 0.027 0.053 -9999 0 -10000 0 0
IFNGR1 0.012 0.032 -9999 0 -0.33 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.096 0.15 -9999 0 -0.41 31 31
Rap1/GTP -0.009 0.034 -9999 0 -0.45 1 1
CRKL/C3G 0.021 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.022 0.061 -9999 0 -0.31 1 1
CEBPB 0.066 0.059 -9999 0 -0.38 2 2
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.008 0.2 -9999 0 -1.2 9 9
STAT1 0.026 0.061 -9999 0 -0.32 2 2
CALM1 0.014 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.026 0.11 -9999 0 -0.34 42 42
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
STAT1 (dimer)/PIAS1 0.034 0.059 -9999 0 -0.32 1 1
CEBPB/PTGES2/Cbp/p300 -0.002 0.023 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.056 -9999 0 -0.3 1 1
MAPK3 0.048 0.048 -9999 0 -10000 0 0
STAT1 (dimer) -0.037 0.1 -9999 0 -0.48 10 10
MAPK1 0.046 0.064 -9999 0 -0.78 1 1
JAK2 0.011 0.043 -9999 0 -0.45 3 3
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
JAK1 0.015 0.005 -9999 0 -10000 0 0
CAMK2D 0.014 0 -9999 0 -10000 0 0
DAPK1 0.061 0.064 -9999 0 -0.63 2 2
SMAD7 0.013 0.07 -9999 0 -0.34 7 7
CBL/CRKL/C3G 0.037 0.058 -9999 0 -0.55 1 1
PI3K -0.016 0.063 -9999 0 -0.66 2 2
IFNG -0.026 0.11 -9999 0 -0.34 42 42
apoptosis 0.042 0.051 -9999 0 -0.44 2 2
CAMK2G 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.042 0.14 -9999 0 -0.38 51 51
CAMK2B -0.2 0.28 -9999 0 -0.53 148 148
FRAP1 0.032 0.065 -9999 0 -0.54 2 2
PRKCD 0.035 0.071 -9999 0 -0.61 2 2
RAP1B 0.014 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.029 0.071 -9999 0 -0.32 10 10
PTPN2 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.001 -9999 0 -10000 0 0
IRF1 0.045 0.079 -9999 0 -0.5 2 2
STAT1 (dimer)/PIASy 0.033 0.063 -9999 0 -0.32 1 1
SOCS1 -0.041 0.23 -9999 0 -1.4 9 9
mol:GDP -0.002 0.047 -9999 0 -0.52 1 1
CASP1 0.013 0.068 -9999 0 -0.28 10 10
PTGES2 0.013 0.018 -9999 0 -0.34 1 1
IRF9 0.053 0.023 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.06 -9999 0 -0.63 2 2
RAP1/GDP -0.009 0.034 -9999 0 -0.45 1 1
CBL 0.024 0.062 -9999 0 -0.46 2 2
MAP3K1 0.028 0.053 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.029 0.071 -9999 0 -0.32 10 10
PTPN11 0.019 0.055 -9999 0 -0.3 1 1
CREBBP 0.015 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0.013 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0.01 -10000 0 -10000 0 0
CDKN1B 0.029 0.033 -10000 0 -10000 0 0
CDKN1A 0.014 0.076 -10000 0 -0.3 16 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
FOXO3 0.029 0.033 -10000 0 -10000 0 0
AKT1 0.023 0.035 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
AKT3 0.005 0.061 -10000 0 -0.37 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.029 0.033 -10000 0 -10000 0 0
AKT1/ASK1 -0.014 0.12 -10000 0 -0.3 47 47
BAD/YWHAZ 0.029 0.011 -10000 0 -10000 0 0
RICTOR 0.014 0 -10000 0 -10000 0 0
RAF1 0.014 0 -10000 0 -10000 0 0
JNK cascade 0.014 0.11 0.3 47 -10000 0 47
TSC1 0.027 0.041 -10000 0 -0.3 2 2
YWHAZ 0.014 0 -10000 0 -10000 0 0
AKT1/RAF1 0.03 0.034 -10000 0 -10000 0 0
EP300 0.014 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.035 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.026 0.045 -10000 0 -0.3 3 3
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.006 0.08 -10000 0 -0.38 15 15
MAP3K5 -0.069 0.22 -10000 0 -0.63 48 48
MAPKAP1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.002 0.065 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
AKT1S1 0.029 0.033 -10000 0 -10000 0 0
CASP9 0.028 0.037 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.032 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.004 0.098 -10000 0 -0.39 21 21
YWHAE 0.014 0 -10000 0 -10000 0 0
SRC -0.021 0.14 -10000 0 -0.6 21 21
AKT2/p21CIP1 0.017 0.078 -10000 0 -0.3 16 16
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.011 -10000 0 -10000 0 0
CHUK 0.029 0.033 -10000 0 -10000 0 0
BAD/BCL-XL 0.043 0.033 -10000 0 -10000 0 0
mTORC2 0.018 0 -10000 0 -10000 0 0
AKT2 0.015 0.029 -10000 0 -0.37 2 2
FOXO1-3a-4/14-3-3 family 0.01 0.078 -10000 0 -10000 0 0
PDPK1 0.011 0.047 -10000 0 -0.63 2 2
MDM2 0.029 0.033 -10000 0 -10000 0 0
MAPKKK cascade -0.029 0.033 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.043 0.032 -10000 0 -10000 0 0
TSC1/TSC2 0.03 0.049 -10000 0 -0.29 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.031 -10000 0 -10000 0 0
glucose import -0.017 0.12 -10000 0 -0.34 37 37
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.022 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.017 0.12 -10000 0 -0.34 37 37
GSK3A 0.029 0.033 -10000 0 -10000 0 0
FOXO1 0.027 0.037 -10000 0 -10000 0 0
GSK3B 0.029 0.033 -10000 0 -10000 0 0
SFN -0.16 0.25 -10000 0 -0.48 132 132
G1/S transition of mitotic cell cycle 0.035 0.032 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.008 0.089 -10000 0 -10000 0 0
PRKACA 0.013 0.018 -10000 0 -0.34 1 1
KPNA1 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
RHEB 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.014 0 -10000 0 -10000 0 0
NFATC1 0.029 0.094 -10000 0 -0.42 3 3
NFATC2 -0.017 0.1 -10000 0 -0.33 19 19
NFATC3 -0.006 0.11 -10000 0 -0.43 25 25
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.005 0.097 -10000 0 -0.49 9 9
Exportin 1/Ran/NUP214 0.029 0.004 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.029 0.086 -10000 0 -0.43 10 10
BCL2/BAX 0.015 0.048 -10000 0 -0.34 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.003 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.002 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.012 0.093 -10000 0 -0.49 8 8
Calcineurin A alpha-beta B1/BCL2 0.006 0.066 -10000 0 -0.49 6 6
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.012 0.092 0.48 8 -10000 0 8
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SFN -0.16 0.25 -10000 0 -0.48 132 132
MAP3K8 -0.012 0.12 -10000 0 -0.56 17 17
NFAT4/CK1 alpha 0.015 0.073 -10000 0 -0.25 25 25
MEF2D/NFAT1/Cbp/p300 0.01 0.1 -10000 0 -0.44 5 5
CABIN1 0.005 0.098 -10000 0 -0.49 9 9
CALM1 0.015 0.001 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.014 0 -10000 0 -10000 0 0
CAMK4 -0.01 0.11 -10000 0 -0.48 17 17
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.013 0.05 -10000 0 -0.27 10 10
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.027 0.16 -10000 0 -0.63 24 24
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.024 0.12 -10000 0 -0.41 10 10
PRKCH 0.013 0.033 -10000 0 -0.63 1 1
CABIN1/Cbp/p300 0.022 0.004 -10000 0 -10000 0 0
CASP3 0.013 0.034 -10000 0 -0.63 1 1
PIM1 0.012 0.026 -10000 0 -0.34 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.002 -10000 0 -10000 0 0
apoptosis -0.002 0.014 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.082 -10000 0 -10000 0 0
PRKCB -0.027 0.15 -10000 0 -0.53 28 28
PRKCE 0.004 0.067 -10000 0 -0.41 9 9
JNK2/NFAT4 0.002 0.1 -10000 0 -0.38 25 25
BAD/BCL-XL 0.021 0 -10000 0 -10000 0 0
PRKCD 0.014 0 -10000 0 -10000 0 0
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.029 0.16 -10000 0 -0.63 25 25
PRKCA 0.014 0 -10000 0 -10000 0 0
PRKCG -0.002 0.047 -10000 0 -0.34 7 7
PRKCQ -0.028 0.15 -10000 0 -0.54 28 28
FKBP38/BCL2 0.015 0.048 -10000 0 -0.34 6 6
EP300 0.015 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.014 0.12 -10000 0 -0.54 4 4
CaM/Ca2+/FKBP38 0.02 0.004 -10000 0 -10000 0 0
FKBP12/FK506 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.005 0.068 -10000 0 -0.4 8 8
NFATc/ERK1 0.036 0.09 -10000 0 -0.43 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.029 0.086 -10000 0 -0.43 10 10
NR4A1 0.008 0.12 -10000 0 -0.5 10 10
GSK3B 0.014 0.002 -10000 0 -10000 0 0
positive T cell selection -0.006 0.11 -10000 0 -0.42 25 25
NFAT1/CK1 alpha -0.032 0.065 -10000 0 -0.34 6 6
RCH1/ KPNB1 0.021 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.013 0.018 -10000 0 -0.34 1 1
AKAP5 0.004 0.067 -10000 0 -0.41 9 9
MEF2D 0.015 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.034 0.09 -10000 0 -0.43 2 2
CREBBP 0.015 0.002 -10000 0 -10000 0 0
BCL2 0.006 0.066 -10000 0 -0.49 6 6
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.014 0 -10000 0 -10000 0 0
mol:PIP3 -0.005 0.071 0.29 4 -0.39 8 12
FRAP1 0.015 0.028 -10000 0 -10000 0 0
AKT1 0.02 0.07 0.23 4 -0.35 8 12
INSR 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0.028 -10000 0 -0.4 1 1
mol:GTP 0.025 0.061 -10000 0 -0.32 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.015 -10000 0 -0.22 1 1
TSC2 0.009 0.058 -10000 0 -0.63 3 3
RHEB/GDP -0.009 0.048 -10000 0 -0.61 1 1
TSC1 0.011 0.047 -10000 0 -0.63 2 2
Insulin Receptor/IRS1 0.012 0.045 -10000 0 -0.37 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.018 -10000 0 -0.26 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.026 0.042 -10000 0 -0.45 1 1
MAP3K5 -0.042 0.14 -10000 0 -0.39 48 48
PIK3R1 0.009 0.058 -10000 0 -0.63 3 3
apoptosis -0.042 0.14 -10000 0 -0.39 48 48
mol:LY294002 0 0 0.001 1 -0.002 4 5
EIF4B 0.031 0.038 -10000 0 -0.38 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.033 -10000 0 -0.36 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.071 -10000 0 -0.41 8 8
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.035 0.17 4 -0.22 3 7
FKBP1A 0.014 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.009 0.048 -10000 0 -0.6 1 1
mol:Amino Acids 0 0 0.001 1 -0.002 4 5
FKBP12/Rapamycin 0.011 0.002 -10000 0 -10000 0 0
PDPK1 -0.007 0.075 0.24 4 -0.38 9 13
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C -0.056 0.21 -10000 0 -0.61 47 47
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.002 -10000 0 -10000 0 0
TSC1/TSC2 0.028 0.067 -10000 0 -0.35 6 6
tumor necrosis factor receptor activity 0 0 0.002 4 -0.001 1 5
RPS6 0.013 0.018 -10000 0 -0.34 1 1
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.003 0.048 -10000 0 -0.4 5 5
INS -0.004 0.045 -10000 0 -0.41 4 4
PTEN 0.007 0.067 -10000 0 -0.63 4 4
PDK2 -0.007 0.067 0.24 4 -0.34 10 14
EIF4EBP1 0.014 0.006 -10000 0 -10000 0 0
PIK3CA 0.011 0.047 -10000 0 -0.63 2 2
PPP2R5D 0.021 0.026 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.025 -10000 0 -0.35 1 1
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 4 -0.003 4 8
EEF2 0.016 0.025 -10000 0 -0.36 1 1
eIF4E/4E-BP1 0.021 0.005 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.014 0.067 -9999 0 -0.35 12 12
TC10/GTP -0.009 0.055 -9999 0 -0.34 9 9
Insulin Receptor/Insulin/IRS1/Shp2 0.024 0.051 -9999 0 -0.36 6 6
HRAS 0.012 0.026 -9999 0 -0.34 2 2
APS homodimer 0.006 0.062 -9999 0 -0.42 7 7
GRB14 -0.003 0.1 -9999 0 -0.63 10 10
FOXO3 0.004 0.12 -9999 0 -0.67 11 11
AKT1 0.03 0.087 -9999 0 -0.97 1 1
INSR 0.016 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.036 0.022 -9999 0 -0.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.014 0 -9999 0 -10000 0 0
SORBS1 0.007 0.067 -9999 0 -0.63 4 4
CRK 0.013 0.018 -9999 0 -0.34 1 1
PTPN1 0.032 0.021 -9999 0 -10000 0 0
CAV1 0.018 0.055 -9999 0 -0.33 8 8
CBL/APS/CAP/Crk-II/C3G 0.032 0.064 -9999 0 -0.38 8 8
Insulin Receptor/Insulin/IRS1/NCK2 0.01 0.087 -9999 0 -0.38 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.066 -9999 0 -0.38 9 9
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.035 0.036 -9999 0 -10000 0 0
RPS6KB1 0.036 0.079 -9999 0 -0.83 1 1
PARD6A 0.008 0.061 -9999 0 -0.56 4 4
CBL 0.011 0.047 -9999 0 -0.63 2 2
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 0.009 0.058 -9999 0 -0.63 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.015 0.068 -9999 0 -0.87 1 1
HRAS/GTP -0.008 0.045 -9999 0 -0.39 2 2
Insulin Receptor 0.016 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.031 0.048 -9999 0 -0.33 6 6
PRKCI -0.005 0.031 -9999 0 -0.5 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.018 0.085 -9999 0 -1.1 1 1
SHC1 0.014 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.017 0.066 -9999 0 -0.67 2 2
PI3K -0.01 0.068 -9999 0 -0.38 9 9
NCK2 -0.01 0.11 -9999 0 -0.49 18 18
RHOQ 0.012 0.038 -9999 0 -0.49 2 2
mol:H2O2 0 0.002 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.018 -9999 0 -0.23 2 2
AKT2 0.03 0.087 -9999 0 -0.97 1 1
PRKCZ -0.042 0.14 -9999 0 -0.55 26 26
SH2B2 0.006 0.062 -9999 0 -0.42 7 7
SHC/SHIP 0.026 0.053 -9999 0 -0.31 8 8
F2RL2 -0.085 0.22 -9999 0 -0.52 68 68
TRIP10 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.02 0.023 -9999 0 -0.33 1 1
TC10/GTP/CIP4/Exocyst 0.018 0.024 -9999 0 -0.29 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.035 0.029 -9999 0 -0.46 1 1
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.002 0.088 -9999 0 -0.63 7 7
NCK1 0.011 0.047 -9999 0 -0.63 2 2
CBL/APS/CAP/Crk-II 0.026 0.068 -9999 0 -0.41 8 8
TC10/GDP 0.009 0.028 -9999 0 -0.35 2 2
Insulin Receptor/Insulin/SHC/GRB10 0.029 0.024 -9999 0 -0.32 1 1
INPP5D 0.018 0.055 -9999 0 -0.33 8 8
SOS1 0.013 0.018 -9999 0 -0.34 1 1
SGK1 -0.03 0.16 -9999 0 -0.96 11 11
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.006 0.074 -9999 0 -0.63 5 5
p62DOK/RasGAP 0.019 0.066 -9999 0 -0.68 2 2
INS -0.001 0.045 -9999 0 -0.41 4 4
mol:PI-3-4-P2 0.018 0.055 -9999 0 -0.33 8 8
GRB2 0.014 0 -9999 0 -10000 0 0
EIF4EBP1 0.036 0.079 -9999 0 -0.83 1 1
PTPRA 0.016 0.002 -9999 0 -10000 0 0
PIK3CA 0.011 0.047 -9999 0 -0.63 2 2
TC10/GTP/CIP4 0.018 0.024 -9999 0 -0.29 2 2
PDPK1 0.011 0.047 -9999 0 -0.63 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.029 0.042 -9999 0 -0.29 6 6
Insulin Receptor/Insulin/IRS1 0.014 0.051 -9999 0 -0.36 6 6
Insulin Receptor/Insulin/IRS3 0.012 0.032 -9999 0 -0.46 1 1
Par3/Par6 -0.025 0.12 -9999 0 -0.33 47 47
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 0.033 0.037 -9999 0 -0.35 3 3
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.006 -9999 0 -10000 0 0
GATA1/HDAC4 0.01 0.037 -9999 0 -10000 0 0
GATA1/HDAC5 0.01 0.035 -9999 0 -10000 0 0
GATA2/HDAC5 0.009 0.071 -9999 0 -0.46 7 7
HDAC5/BCL6/BCoR 0.027 0.031 -9999 0 -0.39 2 2
HDAC9 -0.024 0.14 -9999 0 -0.49 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.029 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.019 0.028 -9999 0 -0.46 1 1
HDAC5/YWHAB 0.021 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.022 0 -9999 0 -10000 0 0
GATA2 -0.003 0.096 -9999 0 -0.51 12 12
HDAC4/RFXANK 0.019 0.022 -9999 0 -10000 0 0
BCOR 0.011 0.047 -9999 0 -0.63 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 0.016 0.047 -9999 0 -0.46 3 3
Histones 0.026 0.058 -9999 0 -0.5 1 1
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.013 0.018 -9999 0 -0.34 1 1
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.02 0.025 -9999 0 -0.46 1 1
HDAC4/Ubc9 0.021 0.013 -9999 0 -10000 0 0
HDAC7 0.012 0.038 -9999 0 -0.49 2 2
HDAC5/14-3-3 E 0.021 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.02 0.018 -9999 0 -10000 0 0
CAMK4 -0.01 0.11 -9999 0 -0.48 17 17
Tubulin/HDAC6 0.026 0.038 -9999 0 -0.39 3 3
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 -0.001 0.051 -9999 0 -0.34 8 8
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0.009 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.021 0.013 -9999 0 -0.22 1 1
Tubulin 0.017 0.043 -9999 0 -0.46 3 3
HDAC4/14-3-3 E 0.021 0.013 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR 0.019 0.035 -9999 0 -0.46 2 2
HDAC4/HDAC3/SMRT (N-CoR2) 0.029 0.011 -9999 0 -10000 0 0
HDAC4/SRF 0.013 0.069 -9999 0 -0.39 8 8
HDAC4/ER alpha -0.085 0.19 -9999 0 -0.38 98 98
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.026 0.058 -9999 0 -0.49 1 1
cell motility 0.025 0.037 -9999 0 -0.39 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.019 0.028 -9999 0 -0.46 1 1
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.013 0.018 -9999 0 -0.34 1 1
Hsp90/HDAC6 0.021 0 -9999 0 -10000 0 0
ESR1 -0.13 0.25 -9999 0 -0.53 98 98
HDAC6/HDAC11 0.019 0.022 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0 -9999 0 -10000 0 0
NPC 0.008 0 -9999 0 -10000 0 0
MEF2C 0.012 0.038 -9999 0 -0.49 2 2
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.041 0.023 -9999 0 -0.32 1 1
GNG2 0.007 0.063 -9999 0 -0.52 5 5
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.009 0.058 -9999 0 -0.63 3 3
HDAC11 0.011 0.032 -9999 0 -0.34 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.013 0.033 -9999 0 -0.63 1 1
RFXANK 0.012 0.026 -9999 0 -0.34 2 2
nuclear import -0.03 0.008 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.022 0.059 -9999 0 -0.39 6 6
BIRC5 -0.038 0.16 -9999 0 -0.45 42 42
NFKBIA 0.029 0.038 -9999 0 -0.39 1 1
CPEB1 -0.016 0.084 -9999 0 -0.34 23 23
AKT1 0.031 0.029 -9999 0 -10000 0 0
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.025 0.026 -9999 0 -10000 0 0
NDEL1/TACC3 0.031 0.033 -9999 0 -10000 0 0
GADD45A 0.004 0.081 -9999 0 -0.63 6 6
GSK3B 0.016 0.012 -9999 0 -10000 0 0
PAK1/Aurora A 0.025 0.046 -9999 0 -0.39 3 3
MDM2 0.014 0 -9999 0 -10000 0 0
JUB 0.009 0.058 -9999 0 -0.63 3 3
TPX2 0.01 0.077 -9999 0 -0.46 9 9
TP53 0.019 0.068 -9999 0 -0.32 13 13
DLG7 0.021 0.029 -9999 0 -0.23 2 2
AURKAIP1 0.014 0 -9999 0 -10000 0 0
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.032 0.035 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.026 -9999 0 -10000 0 0
AURKA 0.027 0.036 -9999 0 -0.27 2 2
AURKB -0.007 0.085 -9999 0 -0.29 23 23
CDC25B 0.029 0.038 -9999 0 -0.39 1 1
G2/M transition checkpoint 0.022 0.044 -9999 0 -0.39 3 3
mRNA polyadenylation 0.001 0.05 -9999 0 -0.25 1 1
Aurora A/CPEB 0.001 0.05 -9999 0 -0.25 1 1
Aurora A/TACC1/TRAP/chTOG 0.04 0.038 -9999 0 -0.32 2 2
BRCA1 0.013 0.018 -9999 0 -0.34 1 1
centrosome duplication 0.025 0.046 -9999 0 -0.39 3 3
regulation of centrosome cycle 0.03 0.032 -9999 0 -10000 0 0
spindle assembly 0.039 0.037 -9999 0 -0.32 2 2
TDRD7 0.014 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.006 0.1 -9999 0 -0.38 15 15
CENPA -0.007 0.094 -9999 0 -0.36 21 21
Aurora A/PP2A 0.029 0.027 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.031 0.038 -9999 0 -10000 0 0
negative regulation of DNA binding 0.019 0.068 -9999 0 -0.32 13 13
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.021 0 -9999 0 -10000 0 0
RASA1 0.002 0.088 -9999 0 -0.63 7 7
Ajuba/Aurora A 0.023 0.044 -9999 0 -0.39 3 3
mitotic prometaphase 0.003 0.016 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.036 -9999 0 -0.27 2 2
TACC1 0.009 0.054 -9999 0 -0.49 4 4
TACC3 0.009 0.045 -9999 0 -0.34 6 6
Aurora A/Antizyme1 0.035 0.026 -9999 0 -10000 0 0
Aurora A/RasGAP 0.021 0.062 -9999 0 -0.38 7 7
OAZ1 0.013 0.018 -9999 0 -0.34 1 1
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.015 0.022 -9999 0 -0.34 1 1
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.026 0.038 -9999 0 -0.39 3 3
Importin alpha/Importin beta/TPX2 0.01 0.077 -9999 0 -0.46 9 9
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.025 0.062 -9999 0 -0.32 9 9
PAK1 0.009 0.058 -9999 0 -0.63 3 3
CKAP5 0.014 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.011 0.047 -9999 0 -0.63 2 2
SMAD2 0.013 0.014 -9999 0 -0.26 1 1
SMAD3 0.04 0.021 -9999 0 -0.26 1 1
SMAD3/SMAD4 0.045 0.03 -9999 0 -0.37 1 1
SMAD4/Ubc9/PIASy 0.027 0.031 -9999 0 -0.39 2 2
SMAD2/SMAD2/SMAD4 0.039 0.032 -9999 0 -0.29 3 3
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.019 0.03 -9999 0 -0.31 3 3
MAP3K1 0.014 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.026 0.14 -9999 0 -0.46 36 36
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.013 0.033 -9999 0 -0.63 1 1
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.045 0.19 -9999 0 -0.63 34 34
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.013 0.033 -9999 0 -0.63 1 1
KPNA2 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.024 0.081 -10000 0 -10000 0 0
BAG4 -0.008 0.12 -10000 0 -0.63 13 13
BAD 0.022 0.031 -10000 0 -10000 0 0
NFKBIA 0.012 0.038 -10000 0 -0.49 2 2
BIRC3 -0.031 0.15 -10000 0 -0.47 35 35
BAX 0.022 0.031 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.009 0.023 -10000 0 -0.074 3 3
IKBKB 0.03 0.078 -10000 0 -10000 0 0
MAP2K2 0.032 0.036 -10000 0 -10000 0 0
MAP2K1 0.032 0.036 -10000 0 -10000 0 0
SMPD1 0.014 0.023 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.03 0.08 -10000 0 -10000 0 0
MAP2K4 0.028 0.031 -10000 0 -10000 0 0
protein ubiquitination 0.031 0.079 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.036 0.038 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.027 0.036 -10000 0 -10000 0 0
CRADD 0.013 0.034 -10000 0 -0.63 1 1
mol:ceramide 0.016 0.033 -10000 0 -0.12 3 3
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0.024 -10000 0 -0.4 1 1
MADD 0.015 0 -10000 0 -10000 0 0
MAP3K1 0.022 0.032 -10000 0 -10000 0 0
TRADD 0.013 0.034 -10000 0 -0.63 1 1
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.034 0.036 -10000 0 -10000 0 0
MAPK1 0.034 0.036 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.019 0.028 -10000 0 -0.34 2 2
FADD 0.023 0.082 -10000 0 -10000 0 0
KSR1 0.021 0.036 -10000 0 -0.22 1 1
MAPK8 0.013 0.083 -10000 0 -0.28 24 24
TRAF2 0.014 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.03 0.078 -10000 0 -10000 0 0
TNF R/SODD 0.004 0.089 -10000 0 -0.46 13 13
TNF -0.023 0.14 -10000 0 -0.55 24 24
CYCS 0.024 0.031 0.14 1 -10000 0 1
IKBKG 0.029 0.078 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.085 -10000 0 -0.31 4 4
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.024 0.031 0.14 1 -10000 0 1
TNF/TNF R/SODD -0.009 0.12 -10000 0 -0.39 30 30
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.025 0.023 -10000 0 -10000 0 0
NSMAF 0.02 0.096 -10000 0 -0.58 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0.006 0.066 -10000 0 -0.49 6 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.019 0.078 -9999 0 -0.37 17 17
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.081 -9999 0 -0.33 17 17
SUMO1 0.014 0 -9999 0 -10000 0 0
ZFPM1 0.004 0.081 -9999 0 -0.63 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.022 0 -9999 0 -10000 0 0
FKBP3 0.014 0 -9999 0 -10000 0 0
Histones 0.037 0.045 -9999 0 -10000 0 0
YY1/LSF 0.024 0.055 -9999 0 -0.32 9 9
SMG5 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.017 0.071 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.02 0.053 -9999 0 -0.38 1 1
SAP18 0.014 0 -9999 0 -10000 0 0
RELA 0.023 0.063 -9999 0 -0.26 17 17
HDAC1/Smad7 0.021 0.057 -9999 0 -0.39 7 7
RANGAP1 0.014 0 -9999 0 -10000 0 0
HDAC3/TR2 0.022 0.049 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.04 0.041 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.028 0.058 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.003 0.096 -9999 0 -0.51 12 12
GATA1 -0.001 0.051 -9999 0 -0.34 8 8
Mad/Max 0.021 0.013 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.042 0.056 -9999 0 -0.4 1 1
RBBP7 0.014 0 -9999 0 -10000 0 0
NPC 0.008 0 -9999 0 -10000 0 0
RBBP4 0.006 0.074 -9999 0 -0.63 5 5
MAX 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
NFKBIA 0.014 0.059 -9999 0 -0.42 1 1
KAT2B 0.007 0.067 -9999 0 -0.63 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.04 0.032 -9999 0 -10000 0 0
SIN3 complex 0.036 0.02 -9999 0 -0.35 1 1
SMURF1 0.014 0 -9999 0 -10000 0 0
CHD3 -0.006 0.1 -9999 0 -0.5 15 15
SAP30 0.013 0.033 -9999 0 -0.63 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.009 0.058 -9999 0 -0.63 3 3
YY1/HDAC3 0.031 0.054 -9999 0 -0.4 1 1
YY1/HDAC2 0.029 0.029 -9999 0 -0.25 4 4
YY1/HDAC1 0.029 0.029 -9999 0 -0.25 4 4
NuRD/MBD2 Complex (MeCP1) 0.04 0.041 -9999 0 -10000 0 0
PPARG 0.012 0.1 -9999 0 -0.36 23 23
HDAC8/hEST1B 0.029 0.011 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.022 0.049 -9999 0 -10000 0 0
MBD3L2 0 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.057 -9999 0 -0.39 7 7
CREBBP 0.014 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.042 0.044 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC3 0.016 0.054 -9999 0 -10000 0 0
HDAC2 0.014 0 -9999 0 -10000 0 0
YY1 0.027 0.034 -9999 0 -0.3 4 4
HDAC8 0.014 0 -9999 0 -10000 0 0
SMAD7 0.002 0.088 -9999 0 -0.63 7 7
NCOR2 0.014 0 -9999 0 -10000 0 0
MXD1 0.013 0.018 -9999 0 -0.34 1 1
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.031 0.051 -9999 0 -0.34 5 5
YY1/SAP30/HDAC1 0.035 0.033 -9999 0 -0.34 1 1
EP300 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.026 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.059 -9999 0 -0.42 1 1
histone deacetylation 0.039 0.041 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.031 0.045 -9999 0 -10000 0 0
nuclear export -0.028 0.011 -9999 0 -10000 0 0
PRKACA 0.013 0.018 -9999 0 -0.34 1 1
GATAD2B 0.014 0 -9999 0 -10000 0 0
GATAD2A 0.014 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.012 0.072 -9999 0 -0.34 7 7
GATA1/HDAC1 0.01 0.035 -9999 0 -10000 0 0
GATA1/HDAC3 0.012 0.054 -9999 0 -10000 0 0
CHD4 0.014 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.006 0.11 -9999 0 -0.46 17 17
SIN3/HDAC complex/Mad/Max 0.045 0.028 -9999 0 -10000 0 0
NuRD Complex 0.047 0.044 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.044 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
MTA2 0.014 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex 0.032 0.045 -9999 0 -0.35 5 5
GATA1/Fog1 0.002 0.07 -9999 0 -0.47 6 6
FKBP25/HDAC1/HDAC2 0.029 0 -9999 0 -10000 0 0
TNF -0.023 0.14 -9999 0 -0.55 24 24
negative regulation of cell growth 0.045 0.028 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.04 0.041 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.022 0.084 -9999 0 -0.35 17 17
SIN3/HDAC complex/NCoR1 0.041 0.037 -9999 0 -10000 0 0
TFCP2 0.006 0.074 -9999 0 -0.63 5 5
NR2C1 0.014 0 -9999 0 -10000 0 0
MBD3 0.014 0 -9999 0 -10000 0 0
MBD2 0.014 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.04 0.17 -10000 0 -0.5 39 39
CLTC 0.029 0.015 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.014 0.047 -10000 0 -10000 0 0
Dynamin 2/GTP 0.025 0 -10000 0 -10000 0 0
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.024 0.021 -10000 0 -10000 0 0
CPE 0.01 0.051 -10000 0 -0.4 3 3
CTNNB1 0.014 0 -10000 0 -10000 0 0
membrane fusion 0.013 0.05 -10000 0 -10000 0 0
CTNND1 0.032 0 -10000 0 -10000 0 0
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.026 -10000 0 -10000 0 0
TSHR 0.013 0.026 -10000 0 -10000 0 0
INS 0.008 0.031 -10000 0 -0.54 1 1
BIN1 0.005 0.077 -10000 0 -0.58 6 6
mol:Choline 0.013 0.05 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0 -10000 0 -10000 0 0
JUP 0.023 0.024 -10000 0 -0.22 1 1
ASAP2/amphiphysin II 0.02 0.049 -10000 0 -0.36 5 5
ARF6/GTP 0.011 0 -10000 0 -10000 0 0
CDH1 0.005 0.076 -10000 0 -0.31 10 10
clathrin-independent pinocytosis 0.011 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.033 -10000 0 -0.63 1 1
positive regulation of endocytosis 0.011 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.043 0.013 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.014 0.046 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.019 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.018 0.022 -10000 0 -0.4 1 1
ACAP1 0.003 0.06 -10000 0 -0.3 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.028 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.027 0.033 -10000 0 -10000 0 0
JIP4/KLC1 0.028 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.043 0.013 -10000 0 -10000 0 0
RALA/GTP 0.011 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.019 0 -10000 0 -10000 0 0
receptor recycling 0.011 0 -10000 0 -10000 0 0
CTNNA1 0.032 0 -10000 0 -10000 0 0
NME1 0.019 0 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.015 -10000 0 -10000 0 0
IL2RA -0.001 0.067 -10000 0 -0.23 22 22
VAMP3 0.019 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.027 0.072 -10000 0 -0.28 22 22
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 0 0.081 -10000 0 -0.3 26 26
PLD2 0.023 0 -10000 0 -10000 0 0
EXOC5 0.013 0.033 -10000 0 -0.63 1 1
PIP5K1C 0.026 0.026 -10000 0 -10000 0 0
SDC1 0.021 0.033 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.014 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.014 0.047 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.013 0.05 -10000 0 -10000 0 0
endocytosis -0.019 0.049 0.35 5 -10000 0 5
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 -0.006 0.11 -10000 0 -0.3 43 43
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.01 0.037 -10000 0 -0.34 4 4
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.022 0.051 -10000 0 -0.3 4 4
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.042 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.081 0.033 -9999 0 -0.27 1 1
ERC1 0.014 0 -9999 0 -10000 0 0
RIP2/NOD2 0.009 0.075 -9999 0 -0.44 10 10
NFKBIA 0.042 0.04 -9999 0 -0.65 1 1
BIRC2 0.014 0 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG 0.04 0.041 -9999 0 -10000 0 0
IKK complex/A20 0.036 0.083 -9999 0 -0.48 2 2
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.045 0.045 -9999 0 -0.42 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.019 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.004 0.026 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.028 0.022 -9999 0 -0.39 1 1
NOD2 -0.002 0.1 -9999 0 -0.6 10 10
NFKB1 0.017 0.007 -9999 0 -10000 0 0
RELA 0.017 0.007 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.021 0 -9999 0 -10000 0 0
ATM 0.013 0.033 -9999 0 -0.63 1 1
TNF/TNFR1A -0.006 0.11 -9999 0 -0.46 17 17
TRAF6 0.013 0.033 -9999 0 -0.63 1 1
PRKCA 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.023 0.14 -9999 0 -0.55 24 24
NF kappa B1 p50/RelA 0.039 0.02 -9999 0 -0.3 1 1
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.04 -9999 0 -0.64 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0.007 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
IKK complex 0.053 0.038 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.057 0.037 -9999 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.044 0.039 -10000 0 -10000 0 0
CLOCK 0.001 0.1 -10000 0 -0.6 10 10
TIMELESS/CRY2 0.041 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.012 0.031 -10000 0 -0.47 1 1
ATR 0.014 0 -10000 0 -10000 0 0
NR1D1 0.036 0.076 -10000 0 -1.4 1 1
ARNTL 0.016 0.034 -10000 0 -0.63 1 1
TIMELESS 0.039 0.029 -10000 0 -10000 0 0
NPAS2 0.012 0.058 -10000 0 -0.63 3 3
CRY2 0.014 0 -10000 0 -10000 0 0
mol:CO -0.014 0.009 0.14 1 -10000 0 1
CHEK1 0.009 0.054 -10000 0 -0.49 4 4
mol:HEME 0.014 0.009 -10000 0 -0.14 1 1
PER1 0.014 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.031 0.084 -10000 0 -0.41 12 12
BMAL1/CLOCK 0.038 0.087 -10000 0 -0.81 2 2
S phase of mitotic cell cycle 0.044 0.039 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.039 -10000 0 -10000 0 0
mol:NADPH 0.014 0.009 -10000 0 -0.14 1 1
PER1/TIMELESS 0.041 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0.026 -10000 0 -0.34 2 2
Arf1 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
coatomer protein complex 0 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.019 0.025 -9999 0 -0.21 4 4
AP2 0.021 0.013 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.021 0.003 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.026 0 -9999 0 -10000 0 0
CD4 -0.001 0.095 -9999 0 -0.6 9 9
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ARFGAP1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0.036 -9999 0 -0.35 4 4
ARF1/GTP -0.002 0.017 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.027 0 -9999 0 -10000 0 0
mol:Choline -0.004 0.035 -9999 0 -0.34 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
DDEF1 -0.004 0.036 -9999 0 -0.35 4 4
ARF1/GDP 0.007 0.011 -9999 0 -10000 0 0
AP2M1 0.013 0.018 -9999 0 -0.34 1 1
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.017 0 -9999 0 -10000 0 0
Rac/GTP 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.001 -9999 0 -10000 0 0
ARFIP2 0.013 0.006 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.01 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.01 0.001 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.018 0.013 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.028 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0.014 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.019 0.004 -9999 0 -10000 0 0
CYTH2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.02 0.001 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.011 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.03 0.038 -9999 0 -0.22 8 8
PLD2 -0.004 0.036 -9999 0 -0.34 4 4
ARF-GAP1/v-SNARE 0.011 0 -9999 0 -10000 0 0
PIP5K1A -0.004 0.036 -9999 0 -0.35 4 4
ARF1/GTP/Membrin/GBF1/p115 0.02 0.024 -9999 0 -0.21 4 4
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.035 -9999 0 -0.34 4 4
KDEL Receptor/Ligand/ARF-GAP1 0.011 0 -9999 0 -10000 0 0
GOSR2 -0.002 0.015 -9999 0 -10000 0 0
USO1 -0.003 0.04 -9999 0 -0.74 1 1
GBF1 -0.002 0.015 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.021 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.019 0.063 -9999 0 -0.39 8 8
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 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.006 -9999 0 -10000 0 0
MDM2/SUMO1 0.032 0 -9999 0 -10000 0 0
HDAC4 0.013 0.018 -9999 0 -0.34 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0.009 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.037 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.022 0 -9999 0 -10000 0 0
Ran/GTP 0.028 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.014 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0 -9999 0 -10000 0 0
NPC 0.008 0 -9999 0 -10000 0 0
PIAS2 0.014 0 -9999 0 -10000 0 0
PIAS1 0.014 0 -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 0.02 0.018 -9999 0 -0.22 2 2
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.04 0.026 -9999 0 -0.32 1 1
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.012 0.026 -9999 0 -0.34 2 2
NF kappa B1 p50/RelB 0.019 0.031 -9999 0 -0.46 1 1
RELB 0.011 0.042 -9999 0 -0.44 3 3
NFKB2 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.017 0.026 -9999 0 -0.4 1 1
regulation of B cell activation 0.017 0.026 -9999 0 -0.4 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 371 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZS.A9CG TCGA.ZS.A9CF TCGA.ZS.A9CE TCGA.ZS.A9CD
109_MAP3K5 0.055 0.055 0.055 0.055
47_PPARGC1A 0.014 0.014 0.014 0.014
105_BMP4 0.014 -0.63 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0 0.014 7.1e-15
105_BMP2 0.014 0.014 0.014 0.014
131_RELN/VLDLR -0.15 -0.7 -0.36 0.037
30_TGFB1/TGF beta receptor Type II 0.022 0.015 0.014 0.014
84_STAT5B 0.12 0.012 -0.13 0.043
84_STAT5A 0.12 0.012 -0.13 0.043
Methods & Data
Input

  • Expression Data Normalization = Tumor samples 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/LIHC/26848775/LIHC.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

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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