PARADIGM pathway analysis of mRNA expression and copy number data
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1F76BZG
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 mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1F76BZG
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 82 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
Glypican 2 network 228
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 115
PLK2 and PLK4 events 107
Effects of Botulinum toxin 91
TCGA08_rtk_signaling 88
Ceramide signaling pathway 85
S1P5 pathway 83
TCGA08_p53 81
Arf6 signaling events 76
Signaling events regulated by Ret tyrosine kinase 71
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 528 . 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 ( 528 ).

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
Glypican 2 network 0.4318 228 912 4 0 0.01 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2178 115 7845 68 -0.3 0.13 1000 -1000 -0.045 -1000
PLK2 and PLK4 events 0.2027 107 323 3 -0.023 0.033 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 0.1723 91 2390 26 0 0.051 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 0.1667 88 2295 26 -0.054 0.15 1000 -1000 -0.015 -1000
Ceramide signaling pathway 0.1610 85 6493 76 -0.12 0.064 1000 -1000 -0.027 -1000
S1P5 pathway 0.1572 83 1423 17 -0.038 0.037 1000 -1000 -0.009 -1000
TCGA08_p53 0.1534 81 571 7 -0.012 0.029 1000 -1000 -0.015 -1000
Arf6 signaling events 0.1439 76 4715 62 -0.002 0.087 1000 -1000 -0.009 -1000
Signaling events regulated by Ret tyrosine kinase 0.1345 71 5886 82 -0.073 0.042 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1345 71 2364 33 -0.068 0.063 1000 -1000 -0.014 -1000
S1P4 pathway 0.1269 67 1679 25 -0.037 0.052 1000 -1000 -0.019 -1000
Syndecan-1-mediated signaling events 0.1061 56 1915 34 -0.017 0.033 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.1023 54 2009 37 -0.041 0.072 1000 -1000 -0.019 -1000
EPO signaling pathway 0.0985 52 2867 55 -0.026 0.051 1000 -1000 -0.034 -1000
Wnt signaling 0.0966 51 361 7 0.001 0.033 1000 -1000 -0.005 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0947 50 2704 54 -0.034 0.047 1000 -1000 -0.032 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0928 49 1398 28 -0.03 0.033 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 0.0928 49 2526 51 -0.019 0.12 1000 -1000 -0.029 -1000
Syndecan-4-mediated signaling events 0.0928 49 3302 67 -0.039 0.033 1000 -1000 -0.03 -1000
JNK signaling in the CD4+ TCR pathway 0.0890 47 809 17 -0.14 0.059 1000 -1000 -0.017 -1000
BMP receptor signaling 0.0852 45 3673 81 -0.034 0.056 1000 -1000 -0.016 -1000
Syndecan-3-mediated signaling events 0.0852 45 1579 35 -0.011 0.074 1000 -1000 -0.023 -1000
Arf6 trafficking events 0.0852 45 3226 71 -0.034 0.042 1000 -1000 -0.03 -1000
Plasma membrane estrogen receptor signaling 0.0852 45 3906 86 -0.44 0.052 1000 -1000 -0.04 -1000
Osteopontin-mediated events 0.0833 44 1687 38 -0.074 0.047 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 0.0833 44 4667 105 -0.04 0.042 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 0.0833 44 1601 36 -0.036 0.047 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0833 44 3452 78 -0.043 0.05 1000 -1000 -0.048 -1000
BARD1 signaling events 0.0814 43 2498 57 -0.057 0.069 1000 -1000 -0.05 -1000
Regulation of p38-alpha and p38-beta 0.0814 43 2351 54 -0.021 0.042 1000 -1000 -0.031 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0795 42 1901 45 -0.079 0.058 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0795 42 5157 120 -0.045 0.082 1000 -1000 -0.036 -1000
EPHB forward signaling 0.0777 41 3530 85 -0.065 0.083 1000 -1000 -0.046 -1000
Nongenotropic Androgen signaling 0.0758 40 2090 52 -0.075 0.053 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0758 40 532 13 0 0.048 1000 -1000 0 -1000
Signaling events mediated by the Hedgehog family 0.0739 39 2060 52 -0.02 0.077 1000 -1000 -0.028 -1000
amb2 Integrin signaling 0.0739 39 3200 82 -0.047 0.065 1000 -1000 -0.019 -1000
E-cadherin signaling in keratinocytes 0.0739 39 1695 43 -0.022 0.06 1000 -1000 -0.022 -1000
EGFR-dependent Endothelin signaling events 0.0720 38 809 21 -0.013 0.033 1000 -1000 -0.031 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0701 37 3210 85 -0.032 0.14 1000 -1000 -0.028 -1000
Presenilin action in Notch and Wnt signaling 0.0701 37 2317 61 0 0.074 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.0701 37 2105 56 -0.022 0.054 1000 -1000 -0.019 -1000
FAS signaling pathway (CD95) 0.0701 37 1746 47 -0.17 0.046 1000 -1000 -0.029 -1000
LPA receptor mediated events 0.0701 37 3810 102 -0.038 0.057 1000 -1000 -0.052 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0701 37 2806 74 -0.24 0.074 1000 -1000 -0.046 -1000
Caspase cascade in apoptosis 0.0682 36 2664 74 -0.07 0.063 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0682 36 1404 38 -0.019 0.053 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 0.0682 36 1182 32 -0.048 0.042 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0682 36 3000 83 -0.062 0.062 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0682 36 4574 125 -0.049 0.046 1000 -1000 -0.042 -1000
Hedgehog signaling events mediated by Gli proteins 0.0663 35 2295 65 -0.011 0.051 1000 -1000 -0.022 -1000
PLK1 signaling events 0.0663 35 3027 85 -0.034 0.058 1000 -1000 -0.026 -1000
mTOR signaling pathway 0.0663 35 1903 53 -0.03 0.059 1000 -1000 -0.027 -1000
Endothelins 0.0663 35 3409 96 -0.46 0.042 1000 -1000 -0.042 -1000
Class I PI3K signaling events 0.0663 35 2620 73 -0.025 0.071 1000 -1000 -0.022 -1000
VEGFR1 specific signals 0.0663 35 2008 56 -0.048 0.048 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 0.0644 34 2314 68 -0.034 0.059 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0644 34 2885 84 -0.065 0.08 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 0.0625 33 2516 76 -0.027 0.068 1000 -1000 -0.019 -1000
Nectin adhesion pathway 0.0625 33 2090 63 -0.021 0.071 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 0.0625 33 1469 44 0 0.057 1000 -1000 -0.012 -1000
a4b1 and a4b7 Integrin signaling 0.0606 32 162 5 0.025 0.047 1000 -1000 0.029 -1000
p75(NTR)-mediated signaling 0.0606 32 4058 125 -0.067 0.074 1000 -1000 -0.047 -1000
TCGA08_retinoblastoma 0.0606 32 261 8 -0.039 0.065 1000 -1000 -0.002 -1000
Glypican 1 network 0.0587 31 1512 48 -0.037 0.061 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 0.0587 31 2411 76 -0.048 0.085 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 0.0587 31 3065 97 -0.056 0.093 1000 -1000 -0.043 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0568 30 706 23 -0.026 0.041 1000 -1000 -0.01 -1000
LPA4-mediated signaling events 0.0549 29 357 12 -0.026 0.005 1000 -1000 -0.022 -1000
IFN-gamma pathway 0.0549 29 2003 68 -0.093 0.06 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 0.0549 29 1437 48 -0.019 0.065 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 0.0549 29 644 22 -0.027 0.04 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0549 29 1013 34 -0.031 0.048 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.0549 29 499 17 0 0.036 1000 -1000 -0.015 -1000
FOXA2 and FOXA3 transcription factor networks 0.0530 28 1290 46 -0.027 0.076 1000 -1000 -0.079 -1000
PDGFR-alpha signaling pathway 0.0530 28 1251 44 -0.033 0.051 1000 -1000 -0.027 -1000
S1P1 pathway 0.0530 28 1021 36 -0.051 0.036 1000 -1000 -0.029 -1000
TCR signaling in naïve CD8+ T cells 0.0530 28 2639 93 -0.43 0.5 1000 -1000 -0.027 -1000
Arf1 pathway 0.0530 28 1539 54 -0.076 0.041 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0511 27 1619 58 -0.024 0.057 1000 -1000 -0.028 -1000
BCR signaling pathway 0.0511 27 2687 99 -0.057 0.073 1000 -1000 -0.042 -1000
HIF-2-alpha transcription factor network 0.0492 26 1156 43 -0.053 0.043 1000 -1000 -0.029 -1000
Aurora B signaling 0.0492 26 1742 67 -0.034 0.065 1000 -1000 -0.029 -1000
Arf6 downstream pathway 0.0473 25 1085 43 -0.028 0.051 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 0.0473 25 1009 40 -0.031 0.035 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class I 0.0473 25 2677 104 -0.04 0.06 1000 -1000 -0.035 -1000
Insulin Pathway 0.0473 25 1857 74 -0.047 0.081 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 0.0455 24 938 39 -0.041 0.065 1000 -1000 -0.021 -1000
TRAIL signaling pathway 0.0455 24 1185 48 -0.05 0.082 1000 -1000 -0.027 -1000
IL6-mediated signaling events 0.0455 24 1800 75 -0.019 0.11 1000 -1000 -0.065 -1000
S1P3 pathway 0.0455 24 1024 42 -0.037 0.033 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 0.0436 23 1756 76 -0.03 0.056 1000 -1000 -0.024 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0436 23 806 34 -0.048 0.09 1000 -1000 -0.041 -1000
Noncanonical Wnt signaling pathway 0.0436 23 602 26 -0.029 0.033 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 0.0436 23 1607 69 -0.036 0.055 1000 -1000 -0.025 -1000
Fc-epsilon receptor I signaling in mast cells 0.0436 23 2290 97 -0.12 0.058 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0436 23 1381 58 -0.21 0.042 1000 -1000 -0.028 -1000
IL1-mediated signaling events 0.0417 22 1385 62 -0.062 0.076 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 0.0417 22 701 31 -0.055 0.034 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.0398 21 2898 136 -0.22 0.074 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class II 0.0398 21 1646 75 -0.036 0.076 1000 -1000 -0.028 -1000
FoxO family signaling 0.0398 21 1358 64 -0.084 0.055 1000 -1000 -0.062 -1000
Atypical NF-kappaB pathway 0.0398 21 656 31 -0.039 0.041 1000 -1000 -0.031 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0398 21 571 27 -0.041 0.069 1000 -1000 -0.029 -1000
Aurora A signaling 0.0379 20 1228 60 -0.02 0.069 1000 -1000 -0.027 -1000
ceramide signaling pathway 0.0379 20 994 49 -0.024 0.045 1000 -1000 -0.026 -1000
Signaling mediated by p38-alpha and p38-beta 0.0360 19 871 44 -0.045 0.078 1000 -1000 -0.022 -1000
Rapid glucocorticoid signaling 0.0360 19 380 20 -0.016 0.032 1000 -1000 -0.015 -1000
Cellular roles of Anthrax toxin 0.0322 17 667 39 -0.031 0.033 1000 -1000 -0.017 -1000
Aurora C signaling 0.0322 17 122 7 0 0.05 1000 -1000 -0.004 -1000
Signaling mediated by p38-gamma and p38-delta 0.0322 17 260 15 -0.037 0.033 1000 -1000 -0.029 -1000
ErbB4 signaling events 0.0303 16 1151 69 -0.035 0.059 1000 -1000 -0.026 -1000
IGF1 pathway 0.0303 16 967 57 -0.055 0.066 1000 -1000 -0.032 -1000
E-cadherin signaling events 0.0303 16 84 5 0.032 0.059 1000 -1000 0.029 -1000
Regulation of Androgen receptor activity 0.0303 16 1150 70 -0.057 0.058 1000 -1000 -0.027 -1000
ErbB2/ErbB3 signaling events 0.0284 15 1024 65 -0.049 0.04 1000 -1000 -0.045 -1000
IL12-mediated signaling events 0.0284 15 1370 87 -0.073 0.064 1000 -1000 -0.079 -1000
Glucocorticoid receptor regulatory network 0.0284 15 1746 114 -0.081 0.12 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 0.0284 15 45 3 -0.032 0.032 1000 -1000 -0.03 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0265 14 1300 88 -0.041 0.037 1000 -1000 -0.046 -1000
HIF-1-alpha transcription factor network 0.0246 13 1005 76 -0.034 0.075 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0246 13 1395 102 -0.033 0.074 1000 -1000 -0.042 -1000
IL27-mediated signaling events 0.0227 12 619 51 -0.025 0.059 1000 -1000 -0.049 -1000
IL4-mediated signaling events 0.0208 11 1022 91 -0.17 0.057 1000 -1000 -0.14 -1000
Visual signal transduction: Rods 0.0208 11 609 52 -0.054 0.073 1000 -1000 -0.037 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0189 10 523 52 -0.019 0.092 1000 -1000 -0.023 -1000
FOXM1 transcription factor network 0.0170 9 467 51 -0.026 0.038 1000 -1000 -0.13 -1000
IL23-mediated signaling events 0.0133 7 453 60 -0.013 0.078 1000 -1000 -0.11 -1000
Circadian rhythm pathway 0.0114 6 142 22 -0.003 0.061 1000 -1000 -0.029 -1000
Ephrin A reverse signaling 0.0076 4 34 7 -0.03 0.043 1000 -1000 -0.015 -1000
Total NA 4686 241687 7203 -7.2 8.1 131000 -131000 -4 -131000
Glypican 2 network

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
MDK 0.013 0.016 -9999 0 0 304 304
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.01 0.012 -9999 0 0 304 304
neuron projection morphogenesis 0.01 0.012 -9999 0 0 304 304
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.034 0.003 -10000 0 -0.034 1 1
NFATC2 -0.047 0.1 -10000 0 -0.16 207 207
NFATC3 -0.066 0.12 -10000 0 -0.19 236 236
CD40LG -0.18 0.19 -10000 0 -0.39 223 223
ITCH -0.022 0.012 -10000 0 -10000 0 0
CBLB -0.025 0.01 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.17 0.18 -10000 0 -0.34 211 211
JUNB 0.031 0.009 -10000 0 0 42 42
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.014 -10000 0 -0.012 14 14
T cell anergy -0.016 0.032 0.17 5 -0.13 3 8
TLE4 -0.037 0.062 -10000 0 -0.11 197 197
Jun/NFAT1-c-4/p21SNFT -0.14 0.23 -10000 0 -0.39 236 236
AP-1/NFAT1-c-4 -0.15 0.24 -10000 0 -0.41 230 230
IKZF1 -0.02 0.051 -10000 0 -0.11 116 116
T-helper 2 cell differentiation -0.16 0.19 -10000 0 -0.5 85 85
AP-1/NFAT1 -0.023 0.077 -10000 0 -0.11 121 121
CALM1 0.031 0.012 -10000 0 -10000 0 0
EGR2 -0.17 0.22 -10000 0 -0.42 215 215
EGR3 -0.24 0.32 -10000 0 -0.64 196 196
NFAT1/FOXP3 -0.023 0.085 -10000 0 -0.11 229 229
EGR1 0.031 0.008 -10000 0 0 29 29
JUN 0.032 0.007 -10000 0 -10000 0 0
EGR4 0.033 0.001 -10000 0 0 1 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
GBP3 -0.033 0.055 -10000 0 -0.099 206 206
FOSL1 0.032 0.007 -10000 0 0 21 21
NFAT1-c-4/MAF/IRF4 -0.14 0.24 -10000 0 -0.4 237 237
DGKA -0.037 0.062 -10000 0 -0.11 198 198
CREM 0.025 0.014 -10000 0 0 129 129
NFAT1-c-4/PPARG -0.15 0.24 -10000 0 -0.41 235 235
CTLA4 -0.059 0.041 -10000 0 -0.1 203 203
NFAT1-c-4 (dimer)/EGR1 -0.15 0.24 -10000 0 -0.41 238 238
NFAT1-c-4 (dimer)/EGR4 -0.15 0.25 -10000 0 -0.41 238 238
FOS 0.022 0.016 -10000 0 -10000 0 0
IFNG -0.071 0.099 -10000 0 -0.29 32 32
T cell activation -0.1 0.12 -10000 0 -10000 0 0
MAF 0.032 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.13 0.19 0.37 197 -10000 0 197
TNF -0.18 0.2 -10000 0 -0.39 239 239
FASLG -0.3 0.31 -10000 0 -0.61 244 244
TBX21 0.034 0.005 -10000 0 -0.032 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.015 -10000 0 -10000 0 0
PTPN1 -0.034 0.06 -10000 0 -0.11 184 184
NFAT1-c-4/ICER1 -0.16 0.24 -10000 0 -0.41 238 238
GATA3 0.024 0.015 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.07 0.098 -10000 0 -0.29 32 32
IL2RA -0.16 0.2 -10000 0 -0.34 217 217
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.039 0.061 -10000 0 -0.11 201 201
E2F1 -0.009 0.031 -10000 0 -10000 0 0
PPARG 0.032 0.006 -10000 0 -10000 0 0
SLC3A2 -0.038 0.062 -10000 0 -0.11 202 202
IRF4 0.033 0.005 -10000 0 -10000 0 0
PTGS2 -0.18 0.18 -10000 0 -0.38 220 220
CSF2 -0.18 0.19 -10000 0 -0.39 224 224
JunB/Fra1/NFAT1-c-4 -0.14 0.24 -10000 0 -0.4 224 224
IL4 -0.17 0.2 -10000 0 -0.52 85 85
IL5 -0.18 0.19 -10000 0 -0.39 223 223
IL2 -0.1 0.12 -10000 0 -10000 0 0
IL3 -0.019 0.087 -10000 0 -0.6 8 8
RNF128 -0.025 0.01 -10000 0 -10000 0 0
NFATC1 -0.13 0.19 -10000 0 -0.37 196 196
CDK4 0.078 0.13 0.27 161 -10000 0 161
PTPRK -0.036 0.061 -10000 0 -0.11 191 191
IL8 -0.19 0.18 -10000 0 -0.38 224 224
POU2F1 0.034 0.005 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.023 0.015 -9999 0 0 154 154
PLK4 0.033 0.004 -9999 0 0 9 9
regulation of centriole replication -0.023 0.015 0 160 -9999 0 160
Effects of Botulinum toxin

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
STX1A 0 0.002 0 499 -10000 0 499
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.043 0.017 -10000 0 -10000 0 0
STXBP1 0.003 0.009 -10000 0 0 466 466
ACh/CHRNA1 0.034 0.031 0.082 54 -0.049 38 92
RAB3GAP2/RIMS1/UNC13B 0.051 0.038 -10000 0 -0.047 57 57
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.032 0.007 -10000 0 0 24 24
mol:ACh 0.022 0.041 0.1 58 -0.068 7 65
RAB3GAP2 0.032 0.006 -10000 0 0 17 17
STX1A/SNAP25/VAMP2 0.002 0.013 0.15 2 -10000 0 2
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.034 0.031 0.082 54 -0.049 38 92
UNC13B 0.03 0.01 -10000 0 0 55 55
CHRNA1 0.033 0.004 -10000 0 0 7 7
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.01 0.074 5 -10000 0 5
SNAP25 0 0.001 -10000 0 0 467 467
VAMP2 0.002 0.001 -10000 0 0 60 60
SYT1 0.002 0.008 -10000 0 0 480 480
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0 0.003 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.002 0.013 0.15 2 -10000 0 2
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.027 0.013 -10000 0 0 92 92
HRAS 0.032 0.007 -10000 0 0 24 24
EGFR 0.012 0.016 -10000 0 0 329 329
AKT 0.13 0.12 0.24 251 -0.16 1 252
FOXO3 0.031 0.009 -10000 0 0 36 36
AKT1 0.031 0.009 -10000 0 0 39 39
FOXO1 0.03 0.01 -10000 0 0 53 53
AKT3 0.032 0.007 -10000 0 0 27 27
FOXO4 0.033 0.002 -10000 0 0 2 2
MET 0.019 0.017 -10000 0 0 222 222
PIK3CA 0.031 0.009 -10000 0 0 41 41
PIK3CB 0.032 0.006 -10000 0 0 17 17
NRAS 0.025 0.015 -10000 0 0 134 134
PIK3CG 0.019 0.016 -10000 0 0 213 213
PIK3R3 0.032 0.005 -10000 0 0 12 12
PIK3R2 0.031 0.009 -10000 0 0 37 37
NF1 0.032 0.006 -10000 0 0 16 16
RAS 0.017 0.032 0.13 8 -0.081 7 15
ERBB2 0.033 0.004 -10000 0 0 6 6
proliferation/survival/translation -0.054 0.077 0.27 9 -0.22 28 37
PI3K 0.093 0.11 0.24 163 -0.1 1 164
PIK3R1 0.03 0.01 -10000 0 0 47 47
KRAS 0.031 0.009 -10000 0 0 37 37
FOXO 0.15 0.097 0.24 221 -10000 0 221
AKT2 0.031 0.008 -10000 0 0 34 34
PTEN 0.021 0.016 -10000 0 0 188 188
Ceramide 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
SPHK2 -0.018 0.017 0 226 -10000 0 226
MAP4K4 -0.015 0.039 -10000 0 -0.24 7 7
BAG4 0.033 0.004 -10000 0 0 9 9
PKC zeta/ceramide -0.08 0.14 -10000 0 -0.21 209 209
NFKBIA 0.031 0.009 -10000 0 0 40 40
BIRC3 0.031 0.009 -10000 0 0 40 40
BAX -0.037 0.093 -10000 0 -0.35 32 32
RIPK1 0.032 0.006 -10000 0 0 20 20
AKT1 -0.001 0.091 0.8 6 -10000 0 6
BAD -0.089 0.14 0.19 2 -0.22 209 211
SMPD1 -0.006 0.04 0.12 7 -0.18 15 22
RB1 -0.09 0.14 0.2 1 -0.22 209 210
FADD/Caspase 8 -0.008 0.041 -10000 0 -0.26 6 6
MAP2K4 -0.089 0.13 0.18 4 -0.22 197 201
NSMAF 0.033 0.005 -10000 0 0 11 11
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.091 0.13 0.18 5 -0.22 203 208
EGF 0.033 0.004 -10000 0 0 8 8
mol:ceramide -0.084 0.14 -10000 0 -0.22 209 209
MADD 0.032 0.007 -10000 0 0 22 22
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.019 0.016 0 218 -10000 0 218
ASAH1 0.032 0.006 -10000 0 0 17 17
negative regulation of cell cycle -0.089 0.13 0.2 1 -0.22 209 210
cell proliferation -0.089 0.11 -10000 0 -0.21 166 166
BID -0.032 0.16 -10000 0 -0.68 25 25
MAP3K1 -0.088 0.14 0.21 1 -0.22 206 207
EIF2A -0.089 0.12 0.16 4 -0.21 207 211
TRADD 0.033 0.004 -10000 0 0 9 9
CRADD 0.033 0.005 -10000 0 0 11 11
MAPK3 -0.083 0.12 0.18 3 -0.22 161 164
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.091 0.12 0.18 3 -0.23 170 173
Cathepsin D/ceramide -0.072 0.15 -10000 0 -0.22 207 207
FADD -0.013 0.034 -10000 0 -0.23 4 4
KSR1 -0.089 0.14 0.2 1 -0.22 207 208
MAPK8 -0.12 0.17 0.16 1 -0.27 232 233
PRKRA -0.089 0.14 0.2 1 -0.22 208 209
PDGFA 0.019 0.016 -10000 0 0 213 213
TRAF2 0.032 0.006 -10000 0 0 20 20
IGF1 0.032 0.005 -10000 0 0 12 12
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.084 0.14 -10000 0 -0.22 209 209
CTSD 0.031 0.009 -10000 0 0 36 36
regulation of nitric oxide biosynthetic process 0.047 0.011 -10000 0 -0.016 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.094 0.12 -10000 0 -0.23 166 166
PRKCD 0.032 0.006 -10000 0 0 16 16
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.019 0.016 0 218 -10000 0 218
RelA/NF kappa B1 0.047 0.011 -10000 0 -0.016 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.032 0.006 -10000 0 0 20 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.042 -10000 0 -0.24 7 7
TNFR1A/BAG4/TNF-alpha 0.032 0.045 -10000 0 -0.046 11 11
mol:Sphingosine-1-phosphate -0.018 0.016 0 226 -10000 0 226
MAP2K1 -0.093 0.12 0.18 4 -0.22 196 200
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.033 0.004 -10000 0 0 9 9
CYCS -0.021 0.074 0.12 1 -0.25 35 36
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
NFKB1 0.032 0.005 -10000 0 0 13 13
TNFR1A/BAG4 0.026 0.031 -10000 0 -0.016 160 160
EIF2AK2 -0.094 0.13 0.17 4 -0.22 208 212
TNF-alpha/TNFR1A/FAN 0.032 0.045 -10000 0 -0.046 10 10
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.048 -10000 0 -0.31 7 7
MAP2K2 -0.084 0.12 0.16 11 -0.21 185 196
SMPD3 0 0.042 0.12 1 -0.25 10 11
TNF 0.033 0.004 -10000 0 0 7 7
PKC zeta/PAR4 0.024 0.005 -10000 0 0 20 20
mol:PHOSPHOCHOLINE -0.045 0.077 0.13 2 -0.13 188 190
NF kappa B1/RelA/I kappa B alpha 0.064 0.039 -10000 0 -0.049 45 45
AIFM1 -0.058 0.092 -10000 0 -0.28 38 38
BCL2 0.032 0.007 -10000 0 0 21 21
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.037 0.046 0.14 30 -10000 0 30
GNAI2 0.032 0.006 -10000 0 0 17 17
S1P/S1P5/G12 0.013 0.011 -10000 0 0 203 203
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 0 465 465
RhoA/GTP -0.038 0.047 -10000 0 -0.14 30 30
negative regulation of cAMP metabolic process 0.002 0.015 0.082 12 -0.1 2 14
GNAZ 0.027 0.013 -10000 0 0 94 94
GNAI3 0.029 0.011 -10000 0 0 67 67
GNA12 0.02 0.016 -10000 0 0 203 203
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.015 0.083 12 -0.11 2 14
RhoA/GDP 0.024 0.005 -10000 0 0 19 19
RHOA 0.032 0.006 -10000 0 0 19 19
GNAI1 0.017 0.017 -10000 0 0 248 248
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.004 0.007 0 373 -10000 0 373
TP53 -0.006 0.04 -10000 0 -0.18 25 25
Senescence -0.012 0.05 -10000 0 -0.18 42 42
Apoptosis -0.012 0.05 -10000 0 -0.18 42 42
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.009 0.064 0.3 23 -10000 0 23
MDM4 0.029 0.011 -10000 0 0 66 66
Arf6 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
CENTA1/KIF3B 0.022 0.004 -10000 0 0 14 14
ARNO/beta Arrestin1-2 0.039 0.021 -10000 0 -0.071 12 12
EGFR 0.012 0.016 -10000 0 0 329 329
EPHA2 0.031 0.008 -10000 0 0 28 28
USP6 0.032 0.005 -10000 0 0 13 13
IQSEC1 0.032 0.007 -10000 0 0 22 22
EGFR/EGFR/EGF/EGF 0.017 0.024 -10000 0 -0.016 6 6
ARRB2 0.01 0.002 -10000 0 -10000 0 0
mol:GTP -0.002 0.013 0.12 3 -0.071 5 8
ARRB1 0.033 0.005 -10000 0 0 10 10
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.031 0.009 -10000 0 0 43 43
EGF 0.033 0.004 -10000 0 0 8 8
somatostatin receptor activity 0 0 0.001 198 0 11 209
ARAP2 0 0 0 192 0 5 197
mol:GDP 0.069 0.073 0.15 187 -0.14 7 194
mol:PI-3-4-5-P3 0 0 0 190 0 11 201
ITGA2B 0.033 0.003 -10000 0 0 5 5
ARF6 0.031 0.008 -10000 0 0 31 31
Ephrin A1/EPHA2/NCK1/GIT1 0.072 0.034 -10000 0 -0.053 15 15
ADAP1 0 0 0 74 0 4 78
KIF13B 0.032 0.005 -10000 0 0 14 14
HGF/MET 0.026 0.025 -10000 0 -0.016 3 3
PXN 0.033 0.004 -10000 0 0 7 7
ARF6/GTP 0.08 0.098 0.18 189 -0.19 11 200
EGFR/EGFR/EGF/EGF/ARFGEP100 0.021 0.032 -10000 0 -0.046 3 3
ADRB2 0.033 0.005 -10000 0 0 11 11
receptor agonist activity 0 0 0 190 0 11 201
actin filament binding 0 0 0 192 0 11 203
SRC 0.029 0.011 -10000 0 0 65 65
ITGB3 0.033 0.004 -10000 0 0 6 6
GNAQ 0.032 0.007 -10000 0 0 21 21
EFA6/PI-4-5-P2 0.001 0.001 0.001 208 -0.001 6 214
ARF6/GDP 0.023 0.071 0.13 32 -0.22 27 59
ARF6/GDP/GULP/ACAP1 0.087 0.07 0.16 178 -0.15 6 184
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.019 -10000 0 -0.057 5 5
ACAP1 0 0 0 70 -10000 0 70
ACAP2 0 0 0 135 0 8 143
LHCGR/beta Arrestin2 0.027 0.017 -10000 0 -0.085 12 12
EFNA1 0.031 0.009 -10000 0 0 36 36
HGF 0.019 0.016 -10000 0 0 213 213
CYTH3 0 0 0.001 191 0 11 202
CYTH2 0 0.001 0.002 3 -0.003 15 18
NCK1 0.031 0.008 -10000 0 0 28 28
fibronectin binding 0 0 0 189 0 12 201
endosomal lumen acidification 0 0 0 197 0 12 209
microtubule-based process 0 0 -10000 0 0 5 5
GULP1 0.033 0.004 -10000 0 0 7 7
GNAQ/ARNO 0.025 0.007 0.038 17 0 21 38
mol:Phosphatidic acid 0 0 0 135 0 8 143
PIP3-E 0 0 0 178 0 11 189
MET 0.019 0.017 -10000 0 0 222 222
GNA14 0.032 0.007 -10000 0 0 23 23
GNA15 0.031 0.009 -10000 0 0 44 44
GIT1 0.033 0.004 -10000 0 0 8 8
mol:PI-4-5-P2 0 0 0.001 200 -0.001 11 211
GNA11 0.031 0.009 -10000 0 0 37 37
LHCGR 0.033 0.002 -10000 0 0 1 1
AGTR1 0.032 0.006 -10000 0 0 17 17
desensitization of G-protein coupled receptor protein signaling pathway 0.027 0.017 -10000 0 -0.085 12 12
IPCEF1/ARNO 0.013 0.019 -10000 0 -0.015 7 7
alphaIIb/beta3 Integrin 0.049 0.005 -10000 0 -10000 0 0
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 0.005 0.06 -10000 0 -0.35 13 13
Crk/p130 Cas/Paxillin -0.073 0.071 -10000 0 -0.2 118 118
JUN -0.022 0.032 -10000 0 -0.2 5 5
HRAS 0.032 0.007 -10000 0 0 24 24
RET51/GFRalpha1/GDNF/GRB10 0.035 0.051 -10000 0 -0.056 54 54
RAP1A 0.032 0.005 -10000 0 0 12 12
FRS2 0.031 0.008 -10000 0 0 31 31
RAP1A/GDP 0.024 0.004 -10000 0 0 12 12
RET51/GFRalpha1/GDNF/DOK1 0.04 0.066 -10000 0 -0.057 155 155
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.033 0.005 -10000 0 0 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.005 -10000 0 0 10 10
RET9/GFRalpha1/GDNF/Enigma 0.03 0.049 -10000 0 -0.041 159 159
RHOA 0.032 0.006 -10000 0 0 19 19
RAP1A/GTP 0.035 0.065 -10000 0 -0.061 154 154
GRB7 0.033 0.004 -10000 0 0 7 7
RET51/GFRalpha1/GDNF 0.042 0.062 -10000 0 -0.057 128 128
MAPKKK cascade -0.072 0.053 0.062 9 -0.15 137 146
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.031 0.049 -10000 0 -0.041 154 154
lamellipodium assembly -0.035 0.055 -10000 0 -0.18 46 46
RET51/GFRalpha1/GDNF/SHC 0.037 0.064 -10000 0 -0.057 150 150
PIK3CA 0.031 0.009 -10000 0 0 41 41
RET9/GFRalpha1/GDNF/SHC 0.025 0.049 -10000 0 -0.041 149 149
RET9/GFRalpha1/GDNF/Shank3 0.02 0.033 -10000 0 -0.029 157 157
MAPK3 -0.055 0.037 0.24 2 -10000 0 2
DOK1 0.033 0.003 -10000 0 0 3 3
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.033 0.004 -10000 0 0 7 7
neurite development -0.045 0.047 0.2 5 -0.19 17 22
DOK5 0.027 0.013 -10000 0 0 98 98
GFRA1 0.023 0.015 -10000 0 0 158 158
MAPK8 -0.016 0.032 0.076 9 -0.13 28 37
HRAS/GTP 0.008 0.11 -10000 0 -0.16 148 148
tube development -0.028 0.033 0.17 13 -10000 0 13
MAPK1 -0.05 0.039 0.17 7 -10000 0 7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.02 0.059 -10000 0 -0.12 136 136
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
SRC 0.029 0.011 -10000 0 0 65 65
PDLIM7 0.032 0.005 -10000 0 0 13 13
RET51/GFRalpha1/GDNF/Dok6 0.041 0.055 -10000 0 -0.053 106 106
SHC1 0.03 0.01 -10000 0 0 55 55
RET51/GFRalpha1/GDNF/Dok4 0.04 0.066 -10000 0 -0.057 157 157
RET51/GFRalpha1/GDNF/Dok5 0.041 0.058 -10000 0 -0.057 97 97
PRKCA 0.033 0.005 -10000 0 0 10 10
HRAS/GDP 0.023 0.005 -10000 0 0 24 24
CREB1 -0.048 0.1 -10000 0 -0.21 141 141
PIK3R1 0.03 0.01 -10000 0 0 47 47
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.023 0.059 -10000 0 -0.12 140 140
RET51/GFRalpha1/GDNF/Grb7 0.04 0.066 -10000 0 -0.057 156 156
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.015 -10000 0 0 130 130
DOK4 0.033 0.005 -10000 0 0 11 11
JNK cascade -0.021 0.033 0.16 1 -0.2 5 6
RET9/GFRalpha1/GDNF/FRS2 0.03 0.048 -10000 0 -0.041 148 148
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 0 18 18
NCK1 0.031 0.008 -10000 0 0 28 28
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.055 -10000 0 -0.11 136 136
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.1 -10000 0 -0.2 139 139
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.047 0.1 -10000 0 -0.2 154 154
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.002 0.035 -10000 0 -0.13 29 29
PI3K -0.072 0.11 -10000 0 -0.24 133 133
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.028 0.044 -10000 0 -0.038 147 147
GRB10 0.019 0.016 -10000 0 0 213 213
activation of MAPKK activity -0.03 0.075 0.1 10 -0.16 112 122
RET51/GFRalpha1/GDNF/FRS2 0.039 0.065 -10000 0 -0.057 149 149
GAB1 0.032 0.005 -10000 0 0 12 12
IRS1 0.033 0.003 -10000 0 0 5 5
IRS2 0.031 0.009 -10000 0 0 41 41
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.004 0.037 -10000 0 -0.13 31 31
RET51/GFRalpha1/GDNF/PKC alpha 0.04 0.066 -10000 0 -0.057 153 153
GRB2 0.032 0.007 -10000 0 0 22 22
PRKACA 0.031 0.009 -10000 0 0 36 36
GDNF 0.033 0.005 -10000 0 0 11 11
RAC1 0.02 0.016 -10000 0 0 204 204
RET51/GFRalpha1/GDNF/IRS1 0.04 0.066 -10000 0 -0.057 157 157
Rac1/GTP -0.039 0.065 -10000 0 -0.21 45 45
RET9/GFRalpha1/GDNF 0.03 0.022 -10000 0 -0.035 5 5
GFRalpha1/GDNF 0.033 0.023 -10000 0 -0.016 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.031 0.009 -10000 0 0 40 40
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.033 0.004 -10000 0 0 6 6
TCEB1 0.032 0.006 -10000 0 0 15 15
HIF1A/p53 -0.061 0.14 0.16 2 -0.27 141 143
HIF1A -0.057 0.13 -10000 0 -0.33 92 92
COPS5 0.033 0.005 -10000 0 0 11 11
VHL/Elongin B/Elongin C/RBX1/CUL2 0.042 0.057 -10000 0 -0.05 136 136
FIH (dimer) 0.024 0.015 -10000 0 0 148 148
CDKN2A 0.009 0.015 -10000 0 0 373 373
ARNT/IPAS 0.044 0.015 -10000 0 -10000 0 0
HIF1AN 0.024 0.015 -10000 0 0 148 148
GNB2L1 0.032 0.005 -10000 0 0 12 12
HIF1A/ARNT -0.059 0.14 0.16 2 -0.28 136 138
CUL2 0.025 0.014 -10000 0 0 129 129
OS9 0.028 0.012 -10000 0 0 83 83
RACK1/Elongin B/Elongin C 0.063 0.02 -10000 0 -0.048 10 10
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.057 0.14 0.16 3 -0.28 140 143
PHD1-3/OS9 0.057 0.046 -10000 0 -0.053 36 36
HIF1A/RACK1/Elongin B/Elongin C -0.038 0.16 -10000 0 -0.28 139 139
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.031 0.009 -10000 0 0 37 37
HIF1A/JAB1 -0.059 0.14 0.16 2 -0.28 140 142
EGLN3 0.031 0.009 -10000 0 0 42 42
EGLN2 0.031 0.009 -10000 0 0 37 37
EGLN1 0.032 0.006 -10000 0 0 17 17
TP53 0.028 0.012 -10000 0 0 85 85
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.006 0.076 -10000 0 -0.57 4 4
ARNT 0.032 0.005 -10000 0 0 14 14
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.031 0.009 -10000 0 0 42 42
HIF1A/p19ARF -0.068 0.14 0.16 3 -0.28 139 142
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 0 465 465
CDC42/GTP -0.037 0.047 -10000 0 -0.14 28 28
PLCG1 -0.001 0.017 0.069 8 -0.13 6 14
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 0 17 17
GNAI3 0.029 0.011 -10000 0 0 67 67
G12/G13 0.029 0.024 -10000 0 -10000 0 0
cell migration -0.037 0.046 -10000 0 -0.14 28 28
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.024 0.069 12 -0.15 10 22
MAPK1 0 0.015 0.069 12 -0.12 3 15
S1P/S1P5/Gi 0.002 0.015 0.083 12 -0.11 2 14
GNAI1 0.017 0.017 -10000 0 0 248 248
CDC42/GDP 0.024 0.005 -10000 0 0 19 19
S1P/S1P5/G12 0.013 0.011 -10000 0 0 203 203
RHOA 0.052 0.1 0.18 197 -10000 0 197
S1P/S1P4/Gi 0.002 0.015 0.083 12 -0.11 2 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 0 94 94
S1P/S1P4/G12/G13 0.025 0.021 -10000 0 -0.029 2 2
GNA12 0.02 0.016 -10000 0 0 203 203
GNA13 0.033 0.005 -10000 0 0 10 10
CDC42 0.032 0.006 -10000 0 0 19 19
Syndecan-1-mediated signaling events

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
TGFB1 0.029 0.011 -10000 0 0 61 61
CCL5 0.031 0.008 -10000 0 0 32 32
SDCBP 0.033 0.005 -10000 0 0 11 11
FGFR/FGF2/Syndecan-1 0.004 0.052 0.18 12 -0.22 8 20
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.007 0.047 0.17 7 -0.22 10 17
Syndecan-1/Syntenin 0.025 0.066 0.2 28 -0.23 9 37
MAPK3 -0.017 0.047 0.16 8 -0.22 8 16
HGF/MET 0.026 0.025 -10000 0 -0.016 3 3
TGFB1/TGF beta receptor Type II 0.029 0.011 -10000 0 0 61 61
BSG 0.031 0.009 -10000 0 0 39 39
keratinocyte migration 0.007 0.046 0.17 7 -0.22 10 17
Syndecan-1/RANTES 0.025 0.067 0.2 29 -0.22 10 39
Syndecan-1/CD147 0.003 0.049 0.19 3 -0.22 9 12
Syndecan-1/Syntenin/PIP2 0.023 0.063 0.19 28 -0.22 9 37
LAMA5 0.028 0.012 -10000 0 0 79 79
positive regulation of cell-cell adhesion 0.023 0.062 0.19 28 -0.22 9 37
MMP7 0.028 0.012 -10000 0 0 85 85
HGF 0.019 0.016 -10000 0 0 213 213
Syndecan-1/CASK -0.003 0.041 -10000 0 -0.21 10 10
Syndecan-1/HGF/MET 0.017 0.049 0.23 7 -0.24 6 13
regulation of cell adhesion -0.011 0.079 0.23 33 -0.23 8 41
HPSE 0.03 0.01 -10000 0 0 52 52
positive regulation of cell migration 0.004 0.052 0.18 12 -0.22 8 20
SDC1 0 0.039 0.1 3 -0.21 5 8
Syndecan-1/Collagen 0.004 0.052 0.18 12 -0.22 8 20
PPIB 0.009 0.015 -10000 0 0 365 365
MET 0.019 0.017 -10000 0 0 222 222
PRKACA 0.031 0.009 -10000 0 0 36 36
MMP9 0.019 0.017 -10000 0 0 223 223
MAPK1 -0.016 0.047 0.16 7 -0.22 8 15
homophilic cell adhesion 0.006 0.054 0.18 18 -0.22 8 26
MMP1 0.03 0.01 -10000 0 0 48 48
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.035 0.039 0.12 9 -0.096 119 128
CRKL 0.031 0.008 -10000 0 0 29 29
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
DOCK1 0.023 0.016 -10000 0 0 163 163
ITGA4 0.033 0.004 -10000 0 0 8 8
alpha4/beta7 Integrin/MAdCAM1 0.072 0.034 -10000 0 -0.053 11 11
EPO 0.019 0.016 -10000 0 0 214 214
alpha4/beta7 Integrin 0.047 0.01 -10000 0 -0.016 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.005 -10000 0 0 10 10
alpha4/beta1 Integrin 0.036 0.022 -10000 0 -0.016 4 4
EPO/EPOR (dimer) 0.028 0.025 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.082 -10000 0 -0.29 31 31
PIK3CA 0.031 0.009 -10000 0 0 41 41
PI3K 0.041 0.019 -10000 0 -0.016 15 15
ARF6 0.031 0.008 -10000 0 0 31 31
JAK2 0.005 0.024 -10000 0 -0.1 20 20
PXN 0.033 0.004 -10000 0 0 7 7
PIK3R1 0.03 0.01 -10000 0 0 47 47
MADCAM1 0.031 0.009 -10000 0 0 40 40
cell adhesion 0.07 0.033 -10000 0 -0.053 11 11
CRKL/CBL 0.046 0.013 -10000 0 -10000 0 0
ITGB1 0.025 0.015 -10000 0 0 131 131
SRC -0.032 0.026 0.17 6 -10000 0 6
ITGB7 0.032 0.006 -10000 0 0 17 17
RAC1 0.02 0.016 -10000 0 0 204 204
alpha4/beta1 Integrin/VCAM1 0 0.04 -10000 0 -0.046 44 44
p130Cas/Crk/Dock1 -0.041 0.038 0.16 10 -10000 0 10
VCAM1 0.011 0.016 -10000 0 0 341 341
RHOA 0.032 0.006 -10000 0 0 19 19
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.06 -10000 0 -0.052 126 126
BCAR1 -0.029 0.024 0.16 6 -10000 0 6
EPOR 0.031 0.009 -10000 0 0 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.033 0.005 -10000 0 0 11 11
GIT1 0.033 0.004 -10000 0 0 8 8
Rac1/GTP -0.011 0.085 -10000 0 -0.3 31 31
EPO signaling pathway

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
BCL2L1 0.034 0.052 0.22 10 -0.24 1 11
CRKL 0.037 0.1 0.25 47 -10000 0 47
mol:DAG -0.008 0.027 0.12 14 -0.15 1 15
HRAS 0.028 0.11 0.25 60 -10000 0 60
MAPK8 0.016 0.085 0.16 119 -10000 0 119
RAP1A 0.04 0.11 0.25 49 -10000 0 49
GAB1 0.039 0.11 0.26 47 -10000 0 47
MAPK14 0.051 0.11 0.17 223 -10000 0 223
EPO 0.018 0.02 -10000 0 -0.036 19 19
PLCG1 -0.009 0.027 0.12 14 -0.16 1 15
EPOR/TRPC2/IP3 Receptors 0.034 0.02 0.093 4 -0.036 20 24
RAPGEF1 0.032 0.007 -10000 0 0 23 23
EPO/EPOR (dimer)/SOCS3 0.038 0.035 -10000 0 -0.052 1 1
GAB1/SHC/GRB2/SOS1 0.025 0.1 0.16 166 -10000 0 166
EPO/EPOR (dimer) 0.026 0.029 -10000 0 -0.043 19 19
IRS2 0.038 0.1 0.26 47 -10000 0 47
STAT1 -0.005 0.032 0.13 9 -0.16 1 10
STAT5B -0.009 0.028 0.12 14 -0.16 1 15
cell proliferation 0.009 0.083 0.15 118 -10000 0 118
GAB1/SHIP/PIK3R1/SHP2/SHC -0.003 0.075 0.1 126 -10000 0 126
TEC 0.04 0.11 0.26 48 -10000 0 48
SOCS3 0.033 0.004 -10000 0 0 9 9
STAT1 (dimer) -0.004 0.033 0.13 9 -0.15 1 10
JAK2 0.035 0.018 0.094 5 -0.036 2 7
PIK3R1 0.03 0.01 -10000 0 0 47 47
EPO/EPOR (dimer)/JAK2 0.042 0.051 0.23 7 -10000 0 7
EPO/EPOR 0.026 0.029 -10000 0 -0.043 19 19
LYN 0.029 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.017 0.097 0.15 165 -10000 0 165
elevation of cytosolic calcium ion concentration 0.034 0.02 0.093 4 -0.036 20 24
SHC1 0.03 0.01 -10000 0 0 55 55
EPO/EPOR (dimer)/LYN 0.03 0.038 -10000 0 -10000 0 0
mol:IP3 -0.008 0.027 0.12 14 -0.15 1 15
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.031 0.1 0.24 44 -10000 0 44
SH2B3 0.037 0.019 0.094 2 -0.036 19 21
NFKB1 0.05 0.11 0.17 222 -10000 0 222
EPO/EPOR (dimer)/JAK2/SOCS3 0.004 0.028 -10000 0 -0.13 18 18
PTPN6 0.043 0.1 0.17 174 -10000 0 174
TEC/VAV2/GRB2 0.025 0.11 0.16 167 -10000 0 167
EPOR 0.034 0.02 0.093 4 -0.036 20 24
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.1 0.16 166 -10000 0 166
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.032 0.007 -10000 0 0 26 26
CRKL/CBL/C3G 0.023 0.11 0.16 168 -10000 0 168
VAV2 0.036 0.1 0.25 46 -10000 0 46
CBL 0.04 0.11 0.26 49 -10000 0 49
SHC/Grb2/SOS1 -0.026 0.034 0.086 12 -10000 0 12
STAT5A -0.009 0.028 0.12 14 -0.16 1 15
GRB2 0.032 0.007 -10000 0 0 22 22
STAT5 (dimer) 0.016 0.037 0.16 7 -10000 0 7
LYN/PLCgamma2 0.04 0.022 -10000 0 -0.016 52 52
PTPN11 0.033 0.005 -10000 0 0 10 10
BTK 0.041 0.11 0.25 53 -10000 0 53
BCL2 0.038 0.057 0.22 8 -0.25 3 11
Wnt 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
Noncanonical Wnts/FZD 0.001 0.034 -9999 0 -0.13 24 24
FZD6 0.026 0.014 -9999 0 0 106 106
WNT6 0.033 0.002 -9999 0 0 2 2
WNT4 0.032 0.006 -9999 0 0 19 19
FZD3 0.031 0.008 -9999 0 0 28 28
WNT5A 0.022 0.016 -9999 0 0 168 168
WNT11 0.032 0.005 -9999 0 0 14 14
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.01 -10000 0 0 47 47
VLDLR 0.029 0.011 -10000 0 0 66 66
LRPAP1 0.033 0.004 -10000 0 0 7 7
NUDC 0.032 0.006 -10000 0 0 15 15
RELN/LRP8 0.017 0.03 -10000 0 -0.046 5 5
CaM/Ca2+ 0.022 0.008 -10000 0 0 61 61
KATNA1 0.03 0.009 -10000 0 0 43 43
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.019 0.075 0.17 91 -10000 0 91
IQGAP1/CaM 0.029 0.029 -10000 0 -0.016 109 109
DAB1 0.032 0.006 -10000 0 0 17 17
IQGAP1 0.025 0.015 -10000 0 0 131 131
PLA2G7 0.032 0.006 -10000 0 0 18 18
CALM1 0.029 0.011 -10000 0 0 61 61
DYNLT1 0.026 0.014 -10000 0 0 110 110
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.033 0.004 -10000 0 0 8 8
CDK5R1 0.027 0.013 -10000 0 0 102 102
LIS1/Poliovirus Protein 3A -0.022 0.01 0 80 -10000 0 80
CDK5R2 0.013 0.016 -10000 0 0 313 313
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.015 0.031 -10000 0 -0.047 13 13
YWHAE 0.032 0.005 -10000 0 0 12 12
NDEL1/14-3-3 E 0.031 0.12 0.29 76 -10000 0 76
MAP1B 0.003 0.002 -10000 0 -10000 0 0
RAC1 -0.001 0.022 -10000 0 -0.28 3 3
p35/CDK5 0.001 0.041 0.16 7 -10000 0 7
RELN 0.009 0.015 -10000 0 0 372 372
PAFAH/LIS1 -0.033 0.014 0 76 -10000 0 76
LIS1/CLIP170 -0.034 0.014 0 75 -10000 0 75
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.008 0.073 0.2 39 -10000 0 39
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.006 0.052 0.12 6 -0.23 22 28
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.038 0.1 0.28 74 -10000 0 74
LIS1/IQGAP1 -0.031 0.014 0 78 -10000 0 78
RHOA -0.001 0.027 -10000 0 -0.26 5 5
PAFAH1B1 -0.028 0.012 0 80 -10000 0 80
PAFAH1B3 0.031 0.009 -10000 0 0 39 39
PAFAH1B2 0.033 0.004 -10000 0 0 9 9
MAP1B/LIS1/Dynein heavy chain -0.024 0.026 0.11 6 -0.17 5 11
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.12 0.3 67 -10000 0 67
LRP8 0.032 0.005 -10000 0 0 14 14
NDEL1/Katanin 60 0.027 0.11 0.29 69 -10000 0 69
P39/CDK5 -0.001 0.029 0.16 5 -10000 0 5
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.033 0.014 0 79 -10000 0 79
CDK5 0.001 0.04 0.17 13 -10000 0 13
PPP2R5D 0.033 0.004 -10000 0 0 6 6
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.028 0.011 0 74 -10000 0 74
CSNK2A1 0.029 0.011 -10000 0 0 66 66
RELN/VLDLR/DAB1/LIS1 0.015 0.037 0.17 9 -10000 0 9
RELN/VLDLR 0.019 0.038 -10000 0 -0.052 13 13
CDC42 -0.002 0.033 -10000 0 -0.26 8 8
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.031 0.009 -10000 0 0 39 39
SPHK1 0.032 0.007 -10000 0 0 27 27
GNAI2 0.032 0.006 -10000 0 0 17 17
mol:S1P 0.005 0.003 -10000 0 -0.014 2 2
GNAO1 0.003 0.009 -10000 0 0 465 465
mol:Sphinganine-1-P -0.03 0.01 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.025 0.033 -10000 0 -0.12 12 12
GNAI3 0.029 0.011 -10000 0 0 67 67
G12/G13 0.029 0.024 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.024 -10000 0 -0.11 23 23
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.017 0.017 -10000 0 0 248 248
S1P/S1P5/G12 0.014 0.026 -10000 0 -0.11 12 12
S1P/S1P3/Gq 0.016 0.046 0.15 10 -0.29 8 18
S1P/S1P4/Gi -0.007 0.048 0.13 1 -0.22 23 24
GNAQ 0.032 0.007 -10000 0 0 21 21
GNAZ 0.027 0.013 -10000 0 0 94 94
GNA14 0.032 0.007 -10000 0 0 23 23
GNA15 0.03 0.009 -10000 0 0 44 44
GNA12 0.02 0.016 -10000 0 0 203 203
GNA13 0.033 0.005 -10000 0 0 10 10
GNA11 0.031 0.009 -10000 0 0 37 37
ABCC1 0.032 0.005 -10000 0 0 12 12
Canonical Wnt signaling pathway

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
HDAC1 0.029 0.012 -10000 0 -10000 0 0
AES 0.031 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 0 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.025 -10000 0 -0.016 4 4
SMAD4 0.025 0.015 -10000 0 0 134 134
DKK2 0.032 0.006 -10000 0 0 17 17
TLE1 0.032 0.007 -10000 0 -10000 0 0
MACF1 0.033 0.006 -10000 0 0 15 15
CTNNB1 0.11 0.11 0.25 120 -0.29 5 125
WIF1 0.004 0.01 -10000 0 0 452 452
beta catenin/RanBP3 0.086 0.079 0.23 37 -0.33 2 39
KREMEN2 0.033 0.003 -10000 0 0 5 5
DKK1 0.018 0.017 -10000 0 0 242 242
beta catenin/beta TrCP1 0.12 0.1 0.26 115 -0.26 6 121
FZD1 0.019 0.016 -10000 0 0 218 218
AXIN2 -0.005 0.018 -10000 0 -0.1 2 2
AXIN1 0.034 0.004 -10000 0 0 5 5
RAN 0.033 0.005 -10000 0 0 12 12
Axin1/APC/GSK3/beta catenin 0.041 0.089 -10000 0 -0.45 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.069 0.076 0.23 39 -0.25 5 44
Axin1/APC/GSK3 0.038 0.068 0.15 94 -0.29 3 97
Axin1/APC/GSK3/beta catenin/Macf1 0.066 0.1 0.19 153 -0.28 5 158
HNF1A 0.033 0.004 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 0 18 18
MYC -0.004 0.11 0.53 18 -10000 0 18
RANBP3 0.031 0.008 -10000 0 0 34 34
DKK2/LRP6/Kremen 2 0.059 0.026 -10000 0 -0.046 15 15
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.032 0.008 -10000 0 -10000 0 0
TCF3 0.031 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.044 -10000 0 -0.055 3 3
Ran/GTP 0.024 0.004 -10000 0 0 12 12
CtBP/CBP/TCF/TLE1/AES 0.009 0.038 -10000 0 -0.2 3 3
LEF1 0.033 0.005 -10000 0 -10000 0 0
DVL1 0.016 0.02 -10000 0 -0.15 1 1
CSNK2A1 0.029 0.011 -10000 0 0 66 66
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.072 0.074 0.24 41 -0.29 2 43
DKK1/LRP6/Kremen 2 0.017 0.051 -10000 0 -0.044 136 136
LRP6 0.032 0.008 -10000 0 0 31 31
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
NLK 0.033 0.005 -10000 0 -10000 0 0
CCND1 -0.019 0.046 0.51 3 -10000 0 3
WNT1 0.033 0.007 -10000 0 0 21 21
GSK3A 0.032 0.009 -10000 0 0 39 39
GSK3B 0.033 0.007 -10000 0 0 20 20
FRAT1 0.023 0.015 -10000 0 0 147 147
PPP2R5D 0.029 0.039 -10000 0 -0.25 5 5
APC 0.045 0.12 0.18 197 -10000 0 197
WNT1/LRP6/FZD1 0 0.02 -10000 0 -0.42 1 1
CREBBP 0.033 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.059 -10000 0 -0.35 9 9
Syndecan-4/Syndesmos -0.026 0.11 -10000 0 -0.52 14 14
positive regulation of JNK cascade -0.016 0.11 -10000 0 -0.41 19 19
Syndecan-4/ADAM12 -0.011 0.11 -10000 0 -0.48 17 17
CCL5 0.031 0.008 -10000 0 0 32 32
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
DNM2 0.031 0.009 -10000 0 0 41 41
ITGA5 0.027 0.013 -10000 0 0 90 90
SDCBP 0.033 0.005 -10000 0 0 11 11
PLG 0.02 0.029 -10000 0 -0.062 15 15
ADAM12 0.023 0.016 -10000 0 0 163 163
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.039 0.024 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.026 0.11 -10000 0 -0.52 14 14
Syndecan-4/CXCL12/CXCR4 -0.017 0.11 -10000 0 -0.44 19 19
Syndecan-4/Laminin alpha3 0 0.12 -10000 0 -0.43 21 21
MDK 0.013 0.016 -10000 0 0 304 304
Syndecan-4/FZD7 -0.016 0.12 -10000 0 -0.53 14 14
Syndecan-4/Midkine -0.02 0.11 -10000 0 -0.44 20 20
FZD7 0.018 0.017 -10000 0 0 239 239
Syndecan-4/FGFR1/FGF 0.027 0.12 -10000 0 -0.44 18 18
THBS1 0.029 0.011 -10000 0 0 60 60
integrin-mediated signaling pathway -0.027 0.097 -10000 0 -0.49 14 14
positive regulation of MAPKKK cascade -0.016 0.11 -10000 0 -0.41 19 19
Syndecan-4/TACI 0.002 0.12 -10000 0 -0.53 14 14
CXCR4 0.016 0.017 -10000 0 0 264 264
cell adhesion -0.011 0.029 0.19 5 -0.1 8 13
Syndecan-4/Dynamin -0.005 0.12 -10000 0 -0.55 13 13
Syndecan-4/TSP1 0 0.12 -10000 0 -0.51 15 15
Syndecan-4/GIPC -0.004 0.12 -10000 0 -0.54 13 13
Syndecan-4/RANTES 0.001 0.12 -10000 0 -0.51 15 15
ITGB1 0.025 0.015 -10000 0 0 131 131
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.031 0.008 -10000 0 0 30 30
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCA -0.002 0.11 0.8 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.001 0.12 -10000 0 -0.5 16 16
TFPI 0.026 0.014 -10000 0 0 115 115
F2 0.03 0.025 0.081 1 -0.064 6 7
alpha5/beta1 Integrin 0.027 0.027 -10000 0 -0.016 61 61
positive regulation of cell adhesion -0.016 0.11 -10000 0 -0.41 21 21
ACTN1 0.028 0.012 -10000 0 0 80 80
TNC 0.002 0.007 -10000 0 0 485 485
Syndecan-4/CXCL12 -0.01 0.12 -10000 0 -0.48 17 17
FGF6 0.031 0.008 -10000 0 0 32 32
RHOA 0.032 0.006 -10000 0 0 19 19
CXCL12 0.024 0.015 -10000 0 0 144 144
TNFRSF13B 0.033 0.005 -10000 0 0 10 10
FGF2 0.033 0.004 -10000 0 0 9 9
FGFR1 0.032 0.005 -10000 0 0 12 12
Syndecan-4/PI-4-5-P2 -0.026 0.11 -10000 0 -0.52 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.016 0.03 -10000 0 -0.063 11 11
cell migration -0.02 0.015 -10000 0 -10000 0 0
PRKCD 0.021 0.03 -10000 0 -0.063 14 14
vasculogenesis 0.001 0.12 -10000 0 -0.49 15 15
SDC4 -0.024 0.11 -10000 0 -0.47 19 19
Syndecan-4/Tenascin C -0.028 0.1 -10000 0 -0.51 14 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.032 0.02 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.001 0.12 -10000 0 -0.51 15 15
MMP9 0.013 0.024 -10000 0 -0.066 8 8
Rac1/GTP -0.011 0.029 0.19 5 -0.093 16 21
cytoskeleton organization -0.025 0.1 -10000 0 -0.48 15 15
GIPC1 0.031 0.009 -10000 0 0 36 36
Syndecan-4/TFPI -0.004 0.12 -10000 0 -0.52 14 14
JNK signaling in the CD4+ TCR pathway

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.063 0.045 -10000 0 -0.053 49 49
MAP4K1 0.031 0.009 -10000 0 0 36 36
MAP3K8 0.022 0.016 -10000 0 0 172 172
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.008 -10000 0 0 29 29
MAP3K1 -0.014 0.037 0.18 1 -0.27 3 4
JUN -0.14 0.24 0.24 1 -0.53 138 139
MAP3K7 -0.013 0.035 -10000 0 -0.14 20 20
GRAP2 0.031 0.009 -10000 0 0 39 39
CRK 0.033 0.005 -10000 0 0 10 10
MAP2K4 -0.031 0.064 0.16 3 -0.23 33 36
LAT 0.033 0.004 -10000 0 0 7 7
LCP2 0.03 0.009 -10000 0 0 44 44
MAPK8 -0.14 0.26 -10000 0 -0.55 138 138
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.043 -10000 0 -0.13 37 37
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.042 -10000 0 -0.049 49 49
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.049 0.066 -10000 0 -0.059 106 106
SMAD6-7/SMURF1 0.036 0.036 -10000 0 -0.047 12 12
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.033 0.16 -10000 0 -0.49 54 54
SMAD4 0.025 0.015 -10000 0 0 134 134
SMAD5 -0.034 0.092 -10000 0 -0.33 35 35
BMP7/USAG1 0.026 0.025 -10000 0 -0.016 5 5
SMAD5/SKI -0.026 0.099 -10000 0 -0.31 40 40
SMAD1 -0.013 0.072 -10000 0 -0.26 24 24
BMP2 0.026 0.014 -10000 0 0 112 112
SMAD1/SMAD1/SMAD4 -0.003 0.063 -10000 0 -0.26 11 11
BMPR1A 0.023 0.015 -10000 0 0 160 160
BMPR1B 0.033 0.004 -10000 0 0 9 9
BMPR1A-1B/BAMBI 0.026 0.054 -10000 0 -0.052 145 145
AHSG 0.032 0.007 -10000 0 0 26 26
CER1 0.029 0.012 -10000 0 0 71 71
BMP2-4/CER1 0.04 0.042 -10000 0 -0.047 46 46
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.008 0.061 -10000 0 -0.21 36 36
BMP2-4 (homodimer) 0.034 0.025 -10000 0 -0.016 46 46
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.041 0.064 -10000 0 -0.052 158 158
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.019 0.016 -10000 0 0 214 214
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.018 0.057 -10000 0 -0.12 100 100
BMP2-4/USAG1 0.028 0.037 -10000 0 -0.048 10 10
SMAD6/SMURF1/SMAD5 -0.013 0.085 -10000 0 -0.3 34 34
SOSTDC1 0.019 0.016 -10000 0 0 211 211
BMP7/BMPR2/BMPR1A-1B 0.044 0.058 -10000 0 -0.052 107 107
SKI 0.032 0.007 -10000 0 0 26 26
BMP6 (homodimer) 0.032 0.005 -10000 0 0 12 12
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.032 0.006 -10000 0 0 18 18
MAP3K7 0.031 0.008 -10000 0 0 29 29
BMP2-4/CHRD 0.042 0.039 -10000 0 -0.047 22 22
SMAD5/SMAD5/SMAD4 -0.028 0.096 -10000 0 -0.31 40 40
MAPK1 0.031 0.009 -10000 0 0 42 42
TAK1/TAB family 0.007 0.052 -10000 0 -0.15 39 39
BMP7 (homodimer) 0.029 0.011 -10000 0 0 70 70
NUP214 0.032 0.007 -10000 0 0 23 23
BMP6/FETUA 0.046 0.013 -10000 0 -0.016 4 4
SMAD1/SKI -0.004 0.08 0.22 1 -0.26 25 26
SMAD6 0.032 0.005 -10000 0 0 14 14
CTDSP2 0.028 0.012 -10000 0 0 79 79
BMP2-4/FETUA 0.043 0.039 -10000 0 -0.047 23 23
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.03 0.009 -10000 0 0 43 43
BMPR2 (homodimer) 0.033 0.003 -10000 0 0 3 3
GADD34/PP1CA 0.056 0.031 -10000 0 -0.047 29 29
BMPR1A-1B (homodimer) 0.033 0.023 -10000 0 -0.016 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.006 0.081 0.22 1 -0.26 26 27
SMAD6-7/SMURF1/SMAD1 0.014 0.07 0.24 1 -0.27 12 13
SMAD6/SMURF1 0.019 0.016 -10000 0 0 214 214
BAMBI 0.023 0.016 -10000 0 0 163 163
SMURF2 0.033 0.004 -10000 0 0 8 8
BMP2-4/CHRDL1 0.031 0.023 -10000 0 -0.014 49 49
BMP2-4/GREM1 0.039 0.042 -10000 0 -0.048 34 34
SMAD7 0.032 0.007 -10000 0 0 23 23
SMAD8A/SMAD8A/SMAD4 -0.03 0.16 -10000 0 -0.45 62 62
SMAD1/SMAD6 -0.002 0.06 0.22 1 -0.26 13 14
TAK1/SMAD6 0.028 0.025 -10000 0 -0.016 1 1
BMP7 0.029 0.011 -10000 0 0 70 70
BMP6 0.032 0.005 -10000 0 0 12 12
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.006 0.05 -10000 0 -0.23 17 17
PPM1A 0.031 0.008 -10000 0 0 34 34
SMAD1/SMURF2 -0.005 0.082 0.22 1 -0.26 26 27
SMAD7/SMURF1 0.027 0.025 -10000 0 -0.016 1 1
CTDSPL 0.032 0.005 -10000 0 0 14 14
PPP1CA 0.033 0.004 -10000 0 0 7 7
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.033 0.003 -10000 0 0 4 4
PPP1R15A 0.031 0.009 -10000 0 0 39 39
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.019 0.061 -10000 0 -0.13 103 103
CHRD 0.032 0.007 -10000 0 0 27 27
BMPR2 0.033 0.003 -10000 0 0 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.022 0.059 -10000 0 -0.13 106 106
BMP4 0.031 0.009 -10000 0 0 39 39
FST 0.032 0.007 -10000 0 0 26 26
BMP2-4/NOG 0.031 0.023 -10000 0 -0.014 49 49
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.042 0.055 -10000 0 -0.06 34 34
Syndecan-3-mediated signaling events

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
CTTN 0.033 0.005 -10000 0 0 10 10
Syndecan-3/Src/Cortactin 0.021 0.073 -10000 0 -0.27 21 21
Syndecan-3/Neurocan 0.008 0.074 -10000 0 -0.32 22 22
POMC 0.033 0.004 -10000 0 0 9 9
EGFR 0.012 0.016 -10000 0 0 329 329
Syndecan-3/EGFR -0.003 0.065 -10000 0 -0.28 23 23
AGRP 0.033 0.004 -10000 0 0 8 8
NCSTN 0.031 0.009 -10000 0 0 39 39
PSENEN 0.031 0.009 -10000 0 0 40 40
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.006 -10000 0 0 15 15
APH1A 0.032 0.006 -10000 0 0 19 19
NCAN 0.026 0.014 -10000 0 0 118 118
long-term memory 0.028 0.082 0.19 1 -0.32 23 24
Syndecan-3/IL8 0.006 0.085 -10000 0 -0.37 23 23
PSEN1 0.031 0.009 -10000 0 0 42 42
Src/Cortactin 0.042 0.018 -10000 0 -10000 0 0
FYN 0.03 0.01 -10000 0 0 53 53
limb bud formation -0.011 0.08 -10000 0 -0.38 22 22
MC4R 0.032 0.007 -10000 0 0 22 22
SRC 0.029 0.011 -10000 0 0 65 65
PTN 0.018 0.017 -10000 0 0 230 230
FGFR/FGF/Syndecan-3 -0.011 0.081 -10000 0 -0.39 22 22
neuron projection morphogenesis 0.028 0.11 0.17 151 -0.26 15 166
Syndecan-3/AgRP 0.012 0.086 -10000 0 -0.37 23 23
Syndecan-3/AgRP/MC4R 0.029 0.091 0.2 1 -0.37 23 24
Fyn/Cortactin 0.044 0.016 -10000 0 -0.016 1 1
SDC3 -0.011 0.081 -10000 0 -0.39 22 22
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.006 0.084 -10000 0 -0.36 23 23
IL8 0.026 0.014 -10000 0 0 116 116
Syndecan-3/Fyn/Cortactin 0.029 0.084 0.2 1 -0.33 23 24
Syndecan-3/CASK -0.011 0.078 -10000 0 -0.36 23 23
alpha-MSH/MC4R 0.046 0.012 -10000 0 -0.016 1 1
Gamma Secretase 0.074 0.051 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.032 0.005 -10000 0 0 14 14
CLTC 0.01 0.095 -10000 0 -0.34 31 31
calcium ion-dependent exocytosis 0.024 0.05 0.097 9 -0.2 7 16
Dynamin 2/GTP 0.019 0.013 -10000 0 -0.029 29 29
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.003 0.08 -10000 0 -0.29 29 29
CPE -0.022 0.01 0 83 -10000 0 83
CTNNB1 0.032 0.006 -10000 0 0 15 15
membrane fusion 0.029 0.049 0.091 170 -0.12 11 181
CTNND1 -0.017 0.05 0.16 38 -10000 0 38
DNM2 0.031 0.009 -10000 0 0 41 41
mol:PI-4-5-P2 0.02 0.068 0.16 41 -0.17 28 69
TSHR -0.024 0.007 0 43 -10000 0 43
INS 0.006 0.097 -10000 0 -0.46 19 19
BIN1 0.03 0.009 -10000 0 0 43 43
mol:Choline 0.029 0.049 0.091 170 -0.12 11 181
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 0 31 31
mol:Ca2+ 0.019 0.013 -10000 0 -0.029 29 29
JUP 0.005 0.076 -10000 0 -0.28 29 29
ASAP2/amphiphysin II 0.035 0.02 -10000 0 -0.029 29 29
ARF6/GTP 0.023 0.006 -10000 0 0 31 31
CDH1 0.005 0.076 -10000 0 -0.28 29 29
clathrin-independent pinocytosis 0.023 0.006 -10000 0 0 31 31
MAPK8IP3 0.033 0.004 -10000 0 0 6 6
positive regulation of endocytosis 0.023 0.006 -10000 0 0 31 31
EXOC2 0.033 0.004 -10000 0 0 9 9
substrate adhesion-dependent cell spreading -0.003 0.039 -10000 0 -0.14 35 35
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.033 0.004 -10000 0 0 8 8
regulation of calcium-dependent cell-cell adhesion -0.029 0.08 0.28 29 -10000 0 29
positive regulation of phagocytosis -0.023 0.009 0 67 -10000 0 67
ARF6/GTP/JIP3 0.042 0.012 -10000 0 -10000 0 0
ACAP1 0.029 0.049 0.09 170 -0.18 7 177
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0 0.067 -10000 0 -0.3 19 19
clathrin heavy chain/ACAP1 0.021 0.084 0.18 22 -0.26 29 51
JIP4/KLC1 0.041 0.034 -10000 0 -0.043 24 24
EXOC1 0.031 0.009 -10000 0 0 36 36
exocyst -0.003 0.04 -10000 0 -0.14 35 35
RALA/GTP 0.014 0.012 -10000 0 0 217 217
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.012 -10000 0 -0.013 1 1
receptor recycling 0.023 0.006 -10000 0 0 31 31
CTNNA1 -0.017 0.05 0.16 39 -10000 0 39
NME1 -0.012 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.094 0.18 1 -0.33 31 32
IL2RA -0.008 0.087 -10000 0 -0.34 28 28
VAMP3 -0.023 0.009 0 67 -10000 0 67
GLUT4/clathrin heavy chain/ACAP1 0.034 0.08 -10000 0 -0.25 30 30
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.029 0.041 0.092 148 -0.059 10 158
PLD2 0.03 0.041 0.092 151 -0.059 8 159
EXOC5 0.03 0.01 -10000 0 0 49 49
PIP5K1C 0.009 0.055 0.12 10 -0.17 27 37
SDC1 0.005 0.079 -10000 0 -0.29 29 29
ARF6/GDP 0.023 0.006 -10000 0 0 31 31
EXOC7 0.033 0.005 -10000 0 0 11 11
E-cadherin/beta catenin 0.031 0.082 -10000 0 -0.28 29 29
mol:Phosphatidic acid 0.029 0.049 0.091 170 -0.12 11 181
endocytosis -0.034 0.019 0.029 29 -10000 0 29
SCAMP2 0.032 0.005 -10000 0 0 13 13
ADRB2 0.002 0.092 0.24 3 -0.33 31 34
EXOC3 0.032 0.006 -10000 0 0 18 18
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.022 0.007 -10000 0 -10000 0 0
KLC1 0.023 0.015 -10000 0 0 153 153
AVPR2 0.002 0.09 0.2 3 -0.33 30 33
RALA 0.019 0.016 -10000 0 0 217 217
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.079 0.21 5 -0.29 27 32
Plasma membrane estrogen 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
GNB1/GNG2 0.044 0.035 -10000 0 -0.039 69 69
ER alpha/Gai/GDP/Gbeta gamma -0.1 0.13 -10000 0 -0.38 61 61
AKT1 -0.037 0.18 -10000 0 -0.7 35 35
PIK3CA 0.031 0.009 -10000 0 0 41 41
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.032 0.19 -10000 0 -0.71 35 35
mol:Ca2+ -0.009 0.054 0.16 34 -0.24 8 42
IGF1R 0.033 0.005 -10000 0 0 11 11
E2/ER alpha (dimer)/Striatin 0.042 0.012 -10000 0 -10000 0 0
SHC1 0.03 0.01 -10000 0 0 55 55
apoptosis 0.036 0.17 0.67 35 -10000 0 35
RhoA/GTP -0.049 0.018 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.063 0.12 0.17 22 -0.3 56 78
regulation of stress fiber formation 0.04 0.049 -10000 0 -0.27 2 2
E2/ERA-ERB (dimer) 0.039 0.018 -10000 0 -0.04 13 13
KRAS 0.031 0.009 -10000 0 0 37 37
G13/GTP 0.037 0.019 -10000 0 -0.029 35 35
pseudopodium formation -0.04 0.049 0.27 2 -10000 0 2
E2/ER alpha (dimer)/PELP1 0.041 0.014 -10000 0 -0.04 3 3
GRB2 0.032 0.007 -10000 0 0 22 22
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 0 465 465
HRAS 0.032 0.007 -10000 0 0 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.054 0.14 0.2 1 -0.45 40 41
E2/ER beta (dimer) 0.023 0.006 -10000 0 0 38 38
mol:GDP -0.035 0.051 0.13 5 -0.18 49 54
mol:NADP -0.054 0.14 0.2 1 -0.45 40 41
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:IP3 -0.009 0.055 0.16 34 -0.25 8 42
IGF-1R heterotetramer 0.033 0.005 -10000 0 0 11 11
PLCB1 -0.012 0.023 -10000 0 -0.22 5 5
PLCB2 -0.013 0.026 -10000 0 -0.23 6 6
IGF1 0.032 0.005 -10000 0 0 12 12
mol:L-citrulline -0.054 0.14 0.2 1 -0.45 40 41
RHOA 0.032 0.006 -10000 0 0 19 19
Gai/GDP -0.44 0.16 -10000 0 -0.49 443 443
JNK cascade 0.023 0.006 -10000 0 0 38 38
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.031 0.009 -10000 0 0 38 38
GNAQ 0.032 0.007 -10000 0 0 21 21
ESR1 0.031 0.009 -10000 0 0 36 36
Gq family/GDP/Gbeta gamma 0.012 0.073 -10000 0 -0.27 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.007 0.069 -10000 0 -0.6 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.061 0.13 0.2 24 -0.31 55 79
GNAZ 0.027 0.013 -10000 0 0 94 94
E2/ER alpha (dimer) 0.023 0.006 -10000 0 0 36 36
STRN 0.033 0.003 -10000 0 0 4 4
GNAL 0.032 0.006 -10000 0 0 19 19
PELP1 0.032 0.005 -10000 0 0 13 13
MAPK11 -0.022 0.009 0 76 -10000 0 76
GNAI2 0.032 0.006 -10000 0 0 17 17
GNAI3 0.029 0.011 -10000 0 0 67 67
GNAI1 0.017 0.017 -10000 0 0 248 248
HBEGF -0.089 0.14 0.24 29 -0.34 56 85
cAMP biosynthetic process 0.029 0.025 -10000 0 -0.037 61 61
SRC -0.099 0.12 -10000 0 -0.38 48 48
PI3K 0.041 0.019 -10000 0 -0.016 15 15
GNB1 0.031 0.008 -10000 0 0 31 31
G13/GDP/Gbeta gamma 0.02 0.065 -10000 0 -0.16 50 50
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.089 0.088 -10000 0 -0.27 56 56
Gs family/GTP 0.037 0.029 -10000 0 -0.038 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.04 -10000 0 -0.041 16 16
vasodilation -0.052 0.13 0.2 1 -0.43 40 41
mol:DAG -0.009 0.055 0.16 34 -0.25 8 42
Gs family/GDP/Gbeta gamma -0.047 0.044 -10000 0 -0.17 50 50
MSN -0.042 0.051 0.28 2 -10000 0 2
Gq family/GTP 0.016 0.019 -10000 0 -0.25 1 1
mol:PI-3-4-5-P3 -0.03 0.18 -10000 0 -0.68 35 35
NRAS 0.025 0.015 -10000 0 0 134 134
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.13 0.43 40 -0.2 1 41
GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
RhoA/GDP 0.014 0.067 0.14 5 -0.18 49 54
NOS3 -0.057 0.14 0.21 1 -0.47 40 41
GNA11 0.031 0.009 -10000 0 0 37 37
MAPKKK cascade -0.036 0.14 -10000 0 -0.48 38 38
E2/ER alpha (dimer)/PELP1/Src -0.061 0.13 0.2 24 -0.32 54 78
ruffle organization -0.04 0.049 0.27 2 -10000 0 2
ROCK2 -0.041 0.061 0.3 3 -10000 0 3
GNA14 0.032 0.007 -10000 0 0 23 23
GNA15 0.03 0.009 -10000 0 0 44 44
GNA13 0.033 0.005 -10000 0 0 10 10
MMP9 -0.11 0.11 -10000 0 -0.35 54 54
MMP2 -0.1 0.11 0.24 1 -0.35 55 56
Osteopontin-mediated events

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.032 0.034 0.18 6 -10000 0 6
NF kappa B1 p50/RelA/I kappa B alpha -0.067 0.046 -10000 0 -0.22 7 7
alphaV/beta3 Integrin/Osteopontin/Src 0.025 0.032 -10000 0 -0.023 1 1
AP1 -0.062 0.03 0.15 5 -10000 0 5
ILK -0.037 0.025 0.17 6 -10000 0 6
bone resorption -0.048 0.031 0.16 2 -10000 0 2
PTK2B 0.032 0.005 -10000 0 0 13 13
PYK2/p130Cas 0.022 0.052 0.16 7 -10000 0 7
ITGAV 0.032 0.008 -10000 0 -0.032 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.025 -10000 0 -0.016 391 391
alphaV/beta3 Integrin/Osteopontin 0.033 0.048 -10000 0 -10000 0 0
MAP3K1 -0.039 0.027 0.17 7 -10000 0 7
JUN 0.033 0.005 -10000 0 0 10 10
MAPK3 -0.047 0.026 0.16 6 -10000 0 6
MAPK1 -0.043 0.027 0.16 5 -10000 0 5
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
NFKB1 0.032 0.005 -10000 0 0 13 13
MAPK8 -0.032 0.03 0.16 5 -10000 0 5
ITGB3 0.033 0.005 -10000 0 -0.032 2 2
NFKBIA -0.049 0.038 0.15 4 -0.18 20 24
FOS 0.023 0.016 -10000 0 0 163 163
CD44 0.006 0.013 -10000 0 0 410 410
CHUK 0.024 0.015 -10000 0 0 148 148
PLAU -0.06 0.049 0.27 1 -0.34 2 3
NF kappa B1 p50/RelA -0.074 0.04 0.19 1 -10000 0 1
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.033 0.004 -10000 0 0 9 9
alphaV beta3 Integrin 0.047 0.013 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.037 0.027 0.17 7 -10000 0 7
VAV3 -0.043 0.028 0.16 7 -10000 0 7
MAP3K14 -0.04 0.025 0.17 6 -10000 0 6
ROCK2 0.033 0.004 -10000 0 0 6 6
SPP1 0.021 0.016 -10000 0 -0.032 2 2
RAC1 0.02 0.016 -10000 0 0 204 204
Rac1/GTP -0.029 0.032 0.15 4 -10000 0 4
MMP2 -0.058 0.03 0.26 1 -10000 0 1
Thromboxane A2 receptor signaling

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
TGM2 0.029 0.011 -10000 0 0 68 68
GNB1/GNG2 -0.025 0.022 -10000 0 -0.13 5 5
AKT1 0.015 0.092 0.24 21 -0.27 23 44
EGF 0.033 0.004 -10000 0 0 8 8
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.024 0.084 0.27 29 -0.17 2 31
mol:Ca2+ 0.02 0.084 0.26 21 -0.26 16 37
LYN -0.023 0.086 0.27 31 -0.17 2 33
RhoA/GTP 0.007 0.046 0.087 37 -0.12 7 44
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.009 0.083 0.26 22 -0.26 11 33
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 0 13 13
TP alpha/Gq family/GDP/G beta5/gamma2 0 0.052 0.14 8 -0.25 11 19
G beta5/gamma2 -0.028 0.028 -10000 0 -0.16 5 5
PRKCH 0.013 0.083 0.26 20 -0.28 16 36
DNM1 0.006 0.013 -10000 0 0 419 419
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 29 -0.002 8 37
PTGDR 0.031 0.008 -10000 0 0 31 31
G12 family/GTP -0.011 0.043 -10000 0 -0.24 7 7
ADRBK1 0.033 0.004 -10000 0 0 7 7
ADRBK2 0.031 0.008 -10000 0 0 33 33
RhoA/GTP/ROCK1 0.042 0.011 -10000 0 -10000 0 0
mol:GDP -0.014 0.087 0.32 11 -0.25 22 33
mol:NADP 0.019 0.016 -10000 0 0 213 213
RAB11A 0.032 0.005 -10000 0 0 14 14
PRKG1 0.024 0.015 -10000 0 0 149 149
mol:IP3 0.02 0.095 0.28 20 -0.32 16 36
cell morphogenesis 0.042 0.011 -10000 0 -10000 0 0
PLCB2 0.018 0.11 0.33 12 -0.42 16 28
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.023 0.086 0.27 31 -0.17 2 33
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.031 0.059 0.25 13 -0.18 1 14
RHOA 0.032 0.006 -10000 0 0 19 19
PTGIR 0.031 0.009 -10000 0 0 40 40
PRKCB1 0.016 0.086 0.26 19 -0.29 15 34
GNAQ 0.032 0.007 -10000 0 0 21 21
mol:L-citrulline 0.019 0.016 -10000 0 0 213 213
TXA2/TXA2-R family 0.012 0.1 0.31 16 -0.36 13 29
LCK -0.024 0.085 0.27 30 -0.17 2 32
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.031 0.043 0.17 8 -0.17 3 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.001 0.078 -10000 0 -0.42 16 16
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.031 0.042 0.17 8 -0.17 3 11
MAPK14 0.003 0.065 0.2 25 -0.18 10 35
TGM2/GTP 0.013 0.097 0.32 9 -0.36 14 23
MAPK11 0.003 0.064 0.2 24 -0.19 7 31
ARHGEF1 0.02 0.066 0.13 48 -0.15 7 55
GNAI2 0.032 0.006 -10000 0 0 17 17
JNK cascade 0.014 0.086 0.28 20 -0.28 13 33
RAB11/GDP 0.028 0.017 -10000 0 -0.024 44 44
ICAM1 0.011 0.067 0.22 21 -0.2 14 35
cAMP biosynthetic process 0.017 0.091 0.28 20 -0.3 15 35
Gq family/GTP/EBP50 0.008 0.043 0.22 11 -0.21 8 19
actin cytoskeleton reorganization 0.042 0.011 -10000 0 -10000 0 0
SRC -0.032 0.06 0.25 13 -0.18 1 14
GNB5 0.032 0.006 -10000 0 0 20 20
GNB1 0.031 0.008 -10000 0 0 31 31
EGF/EGFR 0.018 0.098 0.29 42 -0.18 6 48
VCAM1 0.017 0.065 0.23 20 -0.2 13 33
TP beta/Gq family/GDP/G beta5/gamma2 0 0.052 0.14 8 -0.25 11 19
platelet activation 0.007 0.085 0.27 22 -0.25 11 33
PGI2/IP 0.023 0.007 -10000 0 0 40 40
PRKACA 0.004 0.031 -10000 0 -0.099 39 39
Gq family/GDP/G beta5/gamma2 0.001 0.048 0.14 9 -0.21 15 24
TXA2/TP beta/beta Arrestin2 -0.01 0.063 -10000 0 -0.36 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.022 0.024 -10000 0 -0.1 39 39
mol:DAG 0.019 0.095 0.29 18 -0.32 15 33
EGFR 0.012 0.016 -10000 0 0 329 329
TXA2/TP alpha 0.019 0.11 0.32 19 -0.4 15 34
Gq family/GTP 0.005 0.035 0.21 12 -0.19 3 15
YES1 -0.026 0.077 0.28 23 -0.17 2 25
GNAI2/GTP -0.04 0.028 0.071 8 -0.14 7 15
PGD2/DP 0.023 0.006 -10000 0 0 31 31
SLC9A3R1 0.032 0.005 -10000 0 0 13 13
FYN -0.02 0.084 0.28 27 -0.17 2 29
mol:NO 0.019 0.016 -10000 0 0 213 213
GNA15 0.03 0.009 -10000 0 0 44 44
PGK/cGMP 0.022 0.023 -10000 0 -0.036 4 4
RhoA/GDP 0.028 0.017 -10000 0 -0.021 48 48
TP alpha/TGM2/GDP/G beta/gamma -0.028 0.042 0.18 9 -0.18 3 12
NOS3 0.019 0.016 -10000 0 0 213 213
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCA 0.016 0.083 0.26 22 -0.28 14 36
PRKCB 0.018 0.081 0.26 20 -0.26 13 33
PRKCE 0.013 0.082 0.25 19 -0.27 13 32
PRKCD 0.014 0.084 0.25 22 -0.28 13 35
PRKCG 0.016 0.09 0.29 21 -0.29 16 37
muscle contraction 0.009 0.099 0.31 15 -0.35 13 28
PRKCZ 0.013 0.079 0.26 20 -0.25 13 33
ARR3 0.033 0.002 -10000 0 0 2 2
TXA2/TP beta -0.001 0.055 0.19 11 -0.18 3 14
PRKCQ 0.003 0.075 0.27 12 -0.27 15 27
MAPKKK cascade 0.014 0.099 0.3 16 -0.36 14 30
SELE 0.011 0.068 0.23 20 -0.2 14 34
TP beta/GNAI2/GDP/G beta/gamma -0.028 0.044 0.18 11 -0.17 2 13
ROCK1 0.032 0.006 -10000 0 0 17 17
GNA14 0.032 0.007 -10000 0 0 23 23
chemotaxis 0.01 0.099 0.32 13 -0.37 6 19
GNA12 0.02 0.016 -10000 0 0 203 203
GNA13 0.033 0.005 -10000 0 0 10 10
GNA11 0.031 0.009 -10000 0 0 37 37
Rac1/GTP 0.015 0.012 -10000 0 0 204 204
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.008 -10000 0 0 29 29
Rac1/GDP 0.022 0.022 -10000 0 -0.034 7 7
DOCK1 0.023 0.016 -10000 0 0 163 163
ITGA4 0.033 0.004 -10000 0 0 8 8
RAC1 0.02 0.016 -10000 0 0 204 204
alpha4/beta7 Integrin 0.047 0.01 -10000 0 -0.016 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.005 -10000 0 0 10 10
alpha4/beta1 Integrin 0.039 0.047 -10000 0 -0.046 102 102
alpha4/beta7 Integrin/Paxillin 0.041 0.016 -10000 0 -0.052 2 2
lamellipodium assembly -0.016 0.081 -10000 0 -0.29 29 29
PIK3CA 0.031 0.009 -10000 0 0 41 41
PI3K 0.041 0.019 -10000 0 -0.016 15 15
ARF6 0.031 0.008 -10000 0 0 31 31
TLN1 0.027 0.013 -10000 0 0 102 102
PXN -0.031 0.009 0 42 -10000 0 42
PIK3R1 0.03 0.01 -10000 0 0 47 47
ARF6/GTP 0.034 0.057 0.15 12 -10000 0 12
cell adhesion 0.027 0.056 0.17 10 -10000 0 10
CRKL/CBL 0.046 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.022 0.04 -10000 0 -0.052 101 101
ITGB1 0.025 0.015 -10000 0 0 131 131
ITGB7 0.032 0.006 -10000 0 0 17 17
ARF6/GDP 0.033 0.019 -10000 0 -0.034 12 12
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.014 0.05 0.17 5 -10000 0 5
p130Cas/Crk/Dock1 0.03 0.023 -10000 0 -0.04 8 8
VCAM1 0.011 0.016 -10000 0 0 341 341
alpha4/beta1 Integrin/Paxillin/Talin 0.029 0.057 0.17 10 -10000 0 10
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.055 0.17 13 -10000 0 13
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.054 -10000 0 -0.17 13 13
CBL 0.033 0.005 -10000 0 0 11 11
PRKACA 0.031 0.009 -10000 0 0 36 36
GIT1 0.033 0.004 -10000 0 0 8 8
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.029 0.057 0.17 10 -10000 0 10
Rac1/GTP -0.018 0.089 -10000 0 -0.32 29 29
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.024 0.11 0.2 28 -0.31 47 75
CRKL -0.027 0.098 0.19 2 -0.32 48 50
HRAS -0.009 0.098 0.17 2 -0.28 47 49
mol:PIP3 0.05 0.13 0.27 34 -0.3 30 64
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.033 0.004 -10000 0 0 6 6
GAB1 -0.017 0.1 -10000 0 -0.32 48 48
FOXO3 0.035 0.14 0.27 19 -0.33 30 49
AKT1 0.043 0.15 0.26 23 -0.34 32 55
BAD 0.034 0.14 0.25 16 -0.33 30 46
megakaryocyte differentiation -0.015 0.093 -10000 0 -0.31 44 44
GSK3B 0.036 0.14 0.27 21 -0.32 32 53
RAF1 -0.019 0.086 0.18 11 -0.24 46 57
SHC1 0.03 0.01 -10000 0 0 55 55
STAT3 -0.019 0.1 -10000 0 -0.32 48 48
STAT1 -0.041 0.19 -10000 0 -0.6 47 47
HRAS/SPRED1 -0.011 0.084 0.13 7 -0.23 47 54
cell proliferation -0.024 0.098 -10000 0 -0.32 48 48
PIK3CA 0.031 0.009 -10000 0 0 41 41
TEC 0.032 0.007 -10000 0 0 21 21
RPS6KB1 0.022 0.12 0.22 3 -0.32 29 32
HRAS/SPRED2 0.007 0.096 0.21 5 -0.24 46 51
LYN/TEC/p62DOK 0.025 0.12 -10000 0 -0.32 48 48
MAPK3 -0.01 0.078 0.19 21 -0.19 31 52
STAP1 -0.019 0.1 -10000 0 -0.32 48 48
GRAP2 0.031 0.009 -10000 0 0 39 39
JAK2 -0.035 0.17 -10000 0 -0.53 49 49
STAT1 (dimer) -0.039 0.18 -10000 0 -0.59 47 47
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.028 0.12 -10000 0 -0.32 44 44
actin filament polymerization -0.01 0.1 -10000 0 -0.31 48 48
LYN 0.029 0.011 -10000 0 0 69 69
STAP1/STAT5A (dimer) -0.032 0.13 0.2 1 -0.42 49 50
PIK3R1 0.031 0.01 -10000 0 0 47 47
CBL/CRKL/GRB2 0.002 0.11 0.25 4 -0.31 46 50
PI3K 0.045 0.12 0.25 3 -0.3 38 41
PTEN 0.021 0.016 -10000 0 0 188 188
SCF/KIT/EPO/EPOR -0.029 0.19 -10000 0 -0.6 47 47
MAPK8 -0.024 0.1 -10000 0 -0.32 48 48
STAT3 (dimer) -0.018 0.1 -10000 0 -0.32 48 48
positive regulation of transcription -0.007 0.069 0.18 23 -0.18 9 32
mol:GDP -0.004 0.1 -10000 0 -0.29 44 44
PIK3C2B -0.02 0.099 -10000 0 -0.33 44 44
CBL/CRKL -0.018 0.1 0.24 5 -0.31 47 52
FER -0.018 0.1 -10000 0 -0.33 46 46
SH2B3 -0.018 0.1 -10000 0 -0.32 47 47
PDPK1 0.04 0.12 0.25 33 -0.28 28 61
SNAI2 -0.017 0.1 -10000 0 -0.32 48 48
positive regulation of cell proliferation -0.035 0.16 -10000 0 -0.49 48 48
KITLG 0.024 0.029 -10000 0 -0.054 45 45
cell motility -0.035 0.16 -10000 0 -0.49 48 48
PTPN6 0.021 0.026 -10000 0 -0.032 55 55
EPOR 0.01 0.082 -10000 0 -0.52 2 2
STAT5A (dimer) -0.024 0.14 -10000 0 -0.41 49 49
SOCS1 0.033 0.005 -10000 0 0 10 10
cell migration 0.018 0.097 0.32 45 -10000 0 45
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.016 0.022 -10000 0 -0.042 27 27
VAV1 0.031 0.008 -10000 0 0 33 33
GRB10 -0.016 0.076 -10000 0 -0.33 25 25
PTPN11 0.02 0.028 -10000 0 -0.033 105 105
SCF/KIT -0.008 0.11 -10000 0 -0.33 48 48
GO:0007205 0.002 0.006 -10000 0 -10000 0 0
MAP2K1 -0.024 0.072 0.17 8 -0.2 43 51
CBL 0.033 0.005 -10000 0 0 11 11
KIT -0.043 0.22 -10000 0 -0.66 53 53
MAP2K2 -0.016 0.088 0.23 25 -0.2 43 68
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.31 46 46
STAT5A -0.022 0.14 -10000 0 -0.42 48 48
GRB2 0.032 0.007 -10000 0 0 22 22
response to radiation -0.017 0.1 -10000 0 -0.32 48 48
SHC/GRAP2 0.04 0.022 -10000 0 -0.016 37 37
PTPRO -0.016 0.094 -10000 0 -0.31 44 44
SH2B2 -0.01 0.1 -10000 0 -0.31 48 48
DOK1 0.033 0.003 -10000 0 0 3 3
MATK -0.018 0.099 -10000 0 -0.32 45 45
CREBBP 0.024 0.046 -10000 0 -0.12 47 47
BCL2 0 0.13 -10000 0 -0.71 11 11
BARD1 signaling events

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
BARD1/CSTF1 0.03 0.028 -10000 0 -0.016 101 101
ATM 0.031 0.008 -10000 0 0 35 35
UBE2D3 0.033 0.005 -10000 0 0 10 10
PRKDC 0.031 0.008 -10000 0 0 31 31
ATR 0.032 0.006 -10000 0 0 19 19
UBE2L3 0.031 0.008 -10000 0 0 29 29
FANCD2 0.008 0.004 -10000 0 -10000 0 0
protein ubiquitination 0.063 0.042 -10000 0 -0.059 8 8
XRCC5 0.033 0.002 -10000 0 0 2 2
XRCC6 0.03 0.009 -10000 0 0 43 43
M/R/N Complex 0.062 0.022 -10000 0 -0.047 14 14
MRE11A 0.033 0.005 -10000 0 0 11 11
DNA-PK 0.054 0.035 -10000 0 -0.047 39 39
FA complex/FANCD2/Ubiquitin -0.012 0.082 -10000 0 -0.25 42 42
FANCF 0.032 0.006 -10000 0 0 19 19
BRCA1 0.032 0.005 -10000 0 0 14 14
CCNE1 0.03 0.01 -10000 0 0 49 49
CDK2/Cyclin E1 0.041 0.02 -10000 0 -0.016 20 20
FANCG 0.026 0.014 -10000 0 0 111 111
BRCA1/BACH1/BARD1 0.033 0.028 -10000 0 -0.016 116 116
FANCE 0.033 0.003 -10000 0 0 5 5
FANCC 0.032 0.006 -10000 0 0 18 18
NBN 0.032 0.005 -10000 0 0 12 12
FANCA 0.032 0.006 -10000 0 0 18 18
DNA repair -0.016 0.072 0.2 19 -0.26 7 26
BRCA1/BARD1/ubiquitin 0.033 0.028 -10000 0 -0.016 116 116
BARD1/DNA-PK 0.061 0.041 -10000 0 -0.048 41 41
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.03 0.028 0.016 101 -10000 0 101
BRCA1/BARD1/CTIP/M/R/N Complex -0.002 0.039 0.1 12 -0.19 12 24
BRCA1/BACH1/BARD1/TopBP1 0.042 0.041 -10000 0 -0.046 5 5
BRCA1/BARD1/P53 0.06 0.039 -10000 0 -0.052 16 16
BARD1/CSTF1/BRCA1 0.04 0.04 -10000 0 -0.05 2 2
BRCA1/BACH1 0.032 0.005 -10000 0 0 14 14
BARD1 0.025 0.014 -10000 0 0 124 124
PCNA 0.011 0.016 -10000 0 0 338 338
BRCA1/BARD1/UbcH5C 0.043 0.041 -10000 0 -0.047 6 6
BRCA1/BARD1/UbcH7 0.041 0.042 -10000 0 -0.046 14 14
BRCA1/BARD1/RAD51/PCNA 0.036 0.04 -10000 0 -0.044 12 12
BARD1/DNA-PK/P53 0.064 0.053 -10000 0 -0.059 33 33
BRCA1/BARD1/Ubiquitin 0.033 0.028 -10000 0 -0.016 116 116
BRCA1/BARD1/CTIP 0.024 0.027 -10000 0 -0.043 4 4
FA complex 0.001 0.044 -10000 0 -0.12 42 42
BARD1/EWS 0.032 0.028 -10000 0 -0.016 108 108
RBBP8 -0.018 0.009 0 48 -10000 0 48
TP53 0.028 0.012 -10000 0 0 85 85
TOPBP1 0.032 0.006 -10000 0 0 16 16
G1/S transition of mitotic cell cycle -0.057 0.038 0.052 16 -10000 0 16
BRCA1/BARD1 0.069 0.046 -10000 0 -0.059 8 8
CSTF1 0.029 0.011 -10000 0 0 65 65
BARD1/EWS-Fli1 0.019 0.011 -10000 0 0 124 124
CDK2 0.03 0.009 -10000 0 0 44 44
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.032 0.006 -10000 0 0 20 20
RAD50 0.032 0.005 -10000 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.028 -10000 0 -0.016 116 116
EWSR1 0.031 0.009 -10000 0 0 36 36
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.042 0.011 -10000 0 -0.013 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.032 0.006 -10000 0 0 20 20
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.033 0.004 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.031 0.008 -10000 0 0 30 30
RAC1-CDC42/GTP/PAK family -0.001 0.013 -10000 0 -0.12 6 6
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.013 -10000 0 0 96 96
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.033 0.004 -10000 0 0 6 6
FYN 0.03 0.01 -10000 0 0 53 53
MAP3K12 0.032 0.006 -10000 0 0 15 15
FGR 0.031 0.008 -10000 0 0 32 32
p38 alpha/TAB1 -0.021 0.053 -10000 0 -0.23 20 20
PRKG1 0.024 0.015 -10000 0 0 149 149
DUSP8 0.024 0.015 -10000 0 0 142 142
PGK/cGMP/p38 alpha 0 0.071 0.14 3 -0.25 16 19
apoptosis -0.02 0.051 -10000 0 -0.22 20 20
RAL/GTP 0.025 0.023 -10000 0 -0.013 10 10
LYN 0.029 0.011 -10000 0 0 69 69
DUSP1 0.031 0.008 -10000 0 0 28 28
PAK1 0.033 0.005 -10000 0 0 11 11
SRC 0.029 0.011 -10000 0 0 65 65
RAC1/OSM/MEKK3/MKK3 0.037 0.033 -10000 0 -0.042 8 8
TRAF6 0.032 0.006 -10000 0 0 16 16
RAC1 0.02 0.016 -10000 0 0 204 204
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0.022 -10000 0 -10000 0 0
MAPK11 0.01 0.087 0.19 23 -0.27 13 36
BLK 0.032 0.006 -10000 0 0 15 15
HCK 0.023 0.015 -10000 0 0 152 152
MAP2K3 0.033 0.005 -10000 0 0 11 11
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.032 0.007 -10000 0 0 23 23
TRAF6/MEKK3 0.04 0.012 -10000 0 -0.029 11 11
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.013 0.083 0.16 28 -0.27 16 44
positive regulation of innate immune response 0.009 0.099 0.2 21 -0.32 14 35
LCK 0.032 0.006 -10000 0 0 16 16
p38alpha-beta/MKP7 0.005 0.095 0.18 22 -0.31 14 36
p38alpha-beta/MKP5 0.017 0.1 0.2 21 -0.31 13 34
PGK/cGMP 0.017 0.011 -10000 0 0 149 149
PAK2 0.03 0.009 -10000 0 0 45 45
p38alpha-beta/MKP1 0.015 0.1 0.2 21 -0.31 15 36
CDC42 0.032 0.006 -10000 0 0 19 19
RALB 0.033 0.003 -10000 0 0 3 3
RALA 0.019 0.016 -10000 0 0 217 217
PAK3 0.005 0.012 -10000 0 0 433 433
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.033 0.004 -10000 0 0 9 9
Caspase 8 (4 units) -0.01 0.085 -10000 0 -0.13 149 149
NEF 0.001 0.001 -10000 0 -10000 0 0
NFKBIA 0.031 0.009 -10000 0 -0.001 41 41
BIRC3 -0.043 0.023 0.17 5 -10000 0 5
CYCS 0.006 0.077 0.16 91 -10000 0 91
RIPK1 0.032 0.006 -10000 0 0 20 20
CD247 0.033 0.006 -10000 0 0 14 14
MAP2K7 -0.015 0.092 -10000 0 -0.44 5 5
protein ubiquitination -0.003 0.055 0.19 8 -0.26 9 17
CRADD 0.033 0.005 -10000 0 0 11 11
DAXX 0.033 0.003 -10000 0 0 5 5
FAS 0.019 0.016 -10000 0 0 211 211
BID -0.034 0.047 0.15 5 -0.12 102 107
NF-kappa-B/RelA/I kappa B alpha 0.058 0.035 -10000 0 -0.051 42 42
TRADD 0.033 0.004 -10000 0 0 9 9
MAP3K5 0.03 0.01 -10000 0 0 46 46
CFLAR 0.033 0.004 -10000 0 0 6 6
FADD 0.033 0.005 -10000 0 0 11 11
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.058 0.035 -10000 0 -0.051 42 42
MAPK8 -0.015 0.086 -10000 0 -0.39 7 7
APAF1 0.033 0.005 -10000 0 0 11 11
TRAF1 0.032 0.007 -10000 0 0 24 24
TRAF2 0.032 0.006 -10000 0 0 20 20
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.021 0.053 0.17 4 -0.11 118 122
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.018 0.057 0.14 1 -0.26 10 11
CHUK -0.003 0.057 0.19 8 -0.28 9 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.042 0.072 -10000 0 -0.07 2 2
TCRz/NEF 0.028 0.005 -10000 0 0 14 14
TNF 0.033 0.004 -10000 0 0 7 7
FASLG -0.025 0.005 -10000 0 -10000 0 0
NFKB1 0.032 0.006 -10000 0 -0.002 14 14
TNFR1A/BAG4/TNF-alpha 0.032 0.045 -10000 0 -0.046 11 11
CASP6 0.001 0.086 -10000 0 -0.46 4 4
CASP7 -0.079 0.12 0.23 3 -0.26 140 143
RELA 0.033 0.004 -10000 0 0 9 9
CASP2 0.019 0.016 -10000 0 0 212 212
CASP3 -0.041 0.071 0.26 2 -0.26 20 22
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
TNFR1A/BAG4 0.026 0.031 -10000 0 -0.016 160 160
CASP8 0.033 0.005 -10000 0 0 11 11
CASP9 0.032 0.006 -10000 0 0 17 17
MAP3K14 0.008 0.061 0.19 3 -0.27 11 14
APAF-1/Caspase 9 -0.019 0.084 0.17 5 -0.18 6 11
BCL2 -0.029 0.086 0.24 2 -0.36 8 10
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.031 0.008 -10000 0 0 29 29
RAS family/GTP/Tiam1 0 0.036 -10000 0 -0.14 24 24
NT3 (dimer)/TRKC 0.045 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.051 0.032 -10000 0 -0.046 11 11
SHC/Grb2/SOS1/GAB1/PI3K 0.009 0.022 -10000 0 -0.12 10 10
RAPGEF1 0.032 0.007 -10000 0 0 23 23
BDNF 0.01 0.015 -10000 0 0 363 363
PIK3CA 0.031 0.009 -10000 0 0 41 41
DYNLT1 0.026 0.014 -10000 0 0 110 110
NTRK1 0.032 0.006 -10000 0 0 15 15
NTRK2 0.029 0.011 -10000 0 0 66 66
NTRK3 0.032 0.007 -10000 0 0 23 23
NT-4/5 (dimer)/TRKB 0.037 0.018 -10000 0 -0.013 18 18
neuron apoptosis 0.036 0.067 0.21 7 -0.2 4 11
SHC 2-3/Grb2 -0.038 0.071 0.21 4 -0.22 7 11
SHC1 0.03 0.01 -10000 0 0 55 55
SHC2 -0.04 0.05 -10000 0 -0.29 4 4
SHC3 -0.045 0.067 -10000 0 -0.31 18 18
STAT3 (dimer) 0.025 0.025 -10000 0 -0.023 107 107
NT3 (dimer)/TRKA 0.057 0.027 -10000 0 -0.046 6 6
RIN/GDP -0.007 0.045 0.36 1 -0.18 10 11
GIPC1 0.031 0.009 -10000 0 0 36 36
KRAS 0.031 0.009 -10000 0 0 37 37
DNAJA3 -0.014 0.021 0.071 20 -0.16 2 22
RIN/GTP 0.013 0.012 -10000 0 0 237 237
CCND1 -0.029 0.006 0 22 -10000 0 22
MAGED1 0.033 0.003 -10000 0 0 4 4
PTPN11 0.033 0.005 -10000 0 0 10 10
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.037 0.018 -10000 0 -0.013 38 38
GRB2 0.032 0.007 -10000 0 0 22 22
NGF (dimer)/TRKA/MATK 0.041 0.013 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.046 0.013 -10000 0 -10000 0 0
ELMO1 0.013 0.016 -10000 0 0 302 302
RhoG/GTP/ELMO1/DOCK1 0.015 0.021 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.032 0.007 -10000 0 0 24 24
DOCK1 0.023 0.016 -10000 0 0 163 163
GAB2 0.032 0.006 -10000 0 0 16 16
RIT2 0.018 0.017 -10000 0 0 237 237
RIT1 0.023 0.015 -10000 0 0 161 161
FRS2 0.031 0.008 -10000 0 0 31 31
DNM1 0.006 0.013 -10000 0 0 419 419
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.005 -10000 0 0 10 10
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.022 -10000 0 -10000 0 0
mol:GDP -0.013 0.078 0.26 11 -0.23 20 31
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.01 0.012 -10000 0 0 302 302
RIT1/GDP -0.011 0.056 0.22 7 -0.17 18 25
TIAM1 0.031 0.009 -10000 0 0 37 37
PIK3R1 0.03 0.01 -10000 0 0 47 47
BDNF (dimer)/TRKB 0.012 0.028 -10000 0 -0.046 6 6
KIDINS220/CRKL/C3G 0.045 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.042 0.02 -10000 0 -0.016 38 38
FRS2 family/SHP2 0.062 0.021 -10000 0 -0.049 9 9
SHC/GRB2/SOS1/GAB1 0.051 0.029 -10000 0 -0.041 4 4
RIT1/GTP 0.017 0.011 -10000 0 0 161 161
NT3 (dimer) 0.031 0.007 -10000 0 0 27 27
RAP1/GDP -0.014 0.043 0.091 2 -0.14 21 23
KIDINS220/CRKL 0.031 0.008 -10000 0 0 29 29
BDNF (dimer) 0.009 0.015 -10000 0 0 363 363
ubiquitin-dependent protein catabolic process 0.041 0.012 -10000 0 -10000 0 0
Schwann cell development -0.004 0.007 -10000 0 -10000 0 0
EHD4 0.03 0.01 -10000 0 0 54 54
FRS2 family/GRB2/SOS1 0.057 0.022 -10000 0 -0.042 7 7
FRS2 family/SHP2/CRK family/C3G/GAB2 0.008 0.047 -10000 0 -0.22 9 9
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 0 12 12
CDC42/GTP -0.011 0.029 0.15 3 -10000 0 3
ABL1 0.032 0.007 -10000 0 0 27 27
SH2B family/GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
Rap1/GTP -0.008 0.049 -10000 0 -0.2 28 28
STAT3 0.025 0.025 -10000 0 -0.023 107 107
axon guidance -0.011 0.027 0.11 3 -10000 0 3
MAPK3 -0.015 0.063 0.19 44 -10000 0 44
MAPK1 -0.016 0.058 0.19 36 -10000 0 36
CDC42/GDP -0.009 0.06 0.2 9 -0.17 17 26
NTF3 0.032 0.007 -10000 0 0 27 27
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.04 0.015 -10000 0 -0.013 18 18
PI3K 0.041 0.019 -10000 0 -0.016 15 15
FRS3 0.033 0.003 -10000 0 0 3 3
FAIM 0.031 0.008 -10000 0 0 35 35
GAB1 0.032 0.005 -10000 0 0 12 12
RASGRF1 -0.014 0.02 0.071 18 -0.16 2 20
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.029 0.017 -10000 0 -10000 0 0
RGS19 0.029 0.012 -10000 0 0 71 71
CDC42 0.032 0.006 -10000 0 0 19 19
RAS family/GTP 0.007 0.06 0.22 3 -0.27 12 15
Rac1/GDP -0.006 0.045 0.22 4 -0.16 7 11
NGF (dimer)/TRKA/GRIT 0.022 0.004 -10000 0 0 15 15
neuron projection morphogenesis 0.015 0.075 -10000 0 -0.66 5 5
NGF (dimer)/TRKA/NEDD4-2 0.042 0.012 -10000 0 -10000 0 0
MAP2K1 -0.026 0.052 0.17 33 -10000 0 33
NGFR 0.031 0.008 -10000 0 0 28 28
NGF (dimer)/TRKA/GIPC/GAIP -0.005 0.034 -10000 0 -0.16 23 23
RAS family/GTP/PI3K 0.002 0.032 -10000 0 -0.12 27 27
FRS2 family/SHP2/GRB2/SOS1 0.07 0.027 -10000 0 -0.05 8 8
NRAS 0.025 0.015 -10000 0 0 134 134
GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
PRKCI 0.032 0.006 -10000 0 0 17 17
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.023 0.048 -10000 0 -0.39 5 5
RASA1 0.032 0.006 -10000 0 0 18 18
TRKA/c-Abl 0.045 0.014 -10000 0 -0.016 1 1
SQSTM1 0.032 0.006 -10000 0 0 16 16
BDNF (dimer)/TRKB/GIPC 0.014 0.033 -10000 0 -0.052 9 9
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.021 -10000 0 -0.038 13 13
MATK 0.031 0.008 -10000 0 0 34 34
NEDD4L 0.032 0.007 -10000 0 0 23 23
RAS family/GDP -0.029 0.032 -10000 0 -0.12 34 34
NGF (dimer)/TRKA 0.01 0.015 -10000 0 -0.16 2 2
Rac1/GTP -0.016 0.028 -10000 0 -0.15 6 6
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.065 7 7
EPHB forward 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
Ephrin A5/EPHB2 0.042 0.011 -10000 0 -0.013 1 1
cell-cell adhesion 0.034 0.036 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.076 0.051 -10000 0 -0.06 43 43
ITSN1 0.032 0.005 -10000 0 0 13 13
PIK3CA 0.031 0.009 -10000 0 0 41 41
SHC1 0.03 0.01 -10000 0 0 55 55
Ephrin B1/EPHB3 0.042 0.012 -10000 0 -0.013 7 7
Ephrin B1/EPHB1 0.043 0.011 -10000 0 -0.013 8 8
HRAS/GDP 0.015 0.056 0.19 5 -0.16 26 31
Ephrin B/EPHB1/GRB7 0.078 0.048 -10000 0 -0.059 35 35
Endophilin/SYNJ1 -0.036 0.043 0.17 16 -10000 0 16
KRAS 0.031 0.009 -10000 0 0 37 37
Ephrin B/EPHB1/Src 0.069 0.051 -10000 0 -0.059 27 27
endothelial cell migration 0.031 0.038 -10000 0 -0.049 15 15
GRB2 0.032 0.007 -10000 0 0 22 22
GRB7 0.033 0.004 -10000 0 0 7 7
PAK1 -0.045 0.053 0.18 18 -10000 0 18
HRAS 0.032 0.007 -10000 0 0 24 24
RRAS -0.035 0.047 0.18 17 -10000 0 17
DNM1 0.006 0.013 -10000 0 0 419 419
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.039 0.042 0.16 15 -10000 0 15
lamellipodium assembly -0.034 0.036 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.041 -10000 0 -0.12 21 21
PIK3R1 0.03 0.01 -10000 0 0 47 47
EPHB2 0.032 0.007 -10000 0 0 22 22
EPHB3 0.031 0.008 -10000 0 0 35 35
EPHB1 0.032 0.007 -10000 0 0 25 25
EPHB4 0.019 0.016 -10000 0 0 214 214
mol:GDP 0.037 0.11 0.18 167 -0.17 23 190
Ephrin B/EPHB2 0.062 0.04 -10000 0 -0.049 42 42
Ephrin B/EPHB3 0.061 0.039 -10000 0 -0.049 31 31
JNK cascade -0.039 0.063 0.25 21 -10000 0 21
Ephrin B/EPHB1 0.063 0.039 -10000 0 -0.049 36 36
RAP1/GDP 0.041 0.11 0.18 175 -0.18 14 189
EFNB2 0.03 0.01 -10000 0 0 52 52
EFNB3 0.032 0.006 -10000 0 0 19 19
EFNB1 0.033 0.002 -10000 0 0 2 2
Ephrin B2/EPHB1-2 0.049 0.033 -10000 0 -0.041 37 37
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 0 12 12
CDC42/GTP 0.058 0.05 -10000 0 -0.13 15 15
Rap1/GTP -0.063 0.024 -10000 0 -10000 0 0
axon guidance 0.042 0.011 -10000 0 -0.013 1 1
MAPK3 -0.012 0.04 0.18 3 -0.21 1 4
MAPK1 -0.012 0.038 0.18 2 -0.21 1 3
Rac1/GDP -0.011 0.072 0.22 29 -0.18 12 41
actin cytoskeleton reorganization -0.039 0.042 -10000 0 -0.16 13 13
CDC42/GDP 0.044 0.12 0.2 173 -0.18 14 187
PI3K 0.034 0.041 -10000 0 -0.049 15 15
EFNA5 0.033 0.005 -10000 0 0 11 11
Ephrin B2/EPHB4 0.023 0.023 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.006 0.029 -10000 0 -0.13 18 18
CDC42 0.032 0.006 -10000 0 0 19 19
RAS family/GTP -0.065 0.029 -10000 0 -10000 0 0
PTK2 -0.012 0.092 0.56 13 -10000 0 13
MAP4K4 -0.04 0.063 0.25 21 -10000 0 21
SRC 0.029 0.011 -10000 0 0 65 65
KALRN 0.032 0.006 -10000 0 0 19 19
Intersectin/N-WASP 0.028 0.024 -10000 0 -10000 0 0
neuron projection morphogenesis 0.074 0.18 0.3 179 -0.2 1 180
MAP2K1 -0.005 0.036 -10000 0 -0.21 1 1
WASL 0.019 0.016 -10000 0 0 211 211
Ephrin B1/EPHB1-2/NCK1 0.075 0.031 -10000 0 -0.054 18 18
cell migration -0.008 0.058 0.19 5 -0.23 6 11
NRAS 0.025 0.015 -10000 0 0 134 134
SYNJ1 -0.036 0.043 0.17 16 -10000 0 16
PXN 0.033 0.004 -10000 0 0 7 7
TF -0.026 0.039 0.16 8 -10000 0 8
HRAS/GTP -0.053 0.039 0.12 16 -10000 0 16
Ephrin B1/EPHB1-2 0.057 0.025 -10000 0 -0.041 17 17
cell adhesion mediated by integrin 0.022 0.041 -10000 0 -0.19 10 10
RAC1 0.02 0.016 -10000 0 0 204 204
mol:GTP 0.05 0.042 0.14 15 -10000 0 15
RAC1-CDC42/GTP -0.041 0.04 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 0 18 18
RAC1-CDC42/GDP -0.016 0.072 0.21 28 -0.19 12 40
ruffle organization 0.083 0.17 0.3 179 -10000 0 179
NCK1 0.031 0.008 -10000 0 0 28 28
receptor internalization -0.008 0.028 0.2 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.075 0.052 -10000 0 -0.06 46 46
ROCK1 -0.023 0.046 0.18 25 -10000 0 25
RAS family/GDP -0.04 0.043 -10000 0 -0.15 21 21
Rac1/GTP -0.035 0.037 0.045 2 -10000 0 2
Ephrin B/EPHB1/Src/Paxillin 0.008 0.034 -10000 0 -0.12 29 29
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.016 0.003 0 22 -10000 0 22
GNB1/GNG2 0.038 0.016 -10000 0 -0.024 27 27
regulation of S phase of mitotic cell cycle 0.01 0.02 -10000 0 -0.11 11 11
GNAO1 0.003 0.009 -10000 0 0 465 465
HRAS 0.031 0.008 -10000 0 -0.003 26 26
SHBG/T-DHT 0.022 0.004 -10000 0 0 19 19
PELP1 0.032 0.006 -10000 0 -0.003 14 14
AKT1 -0.015 0.004 0 39 -10000 0 39
MAP2K1 -0.028 0.065 0.13 66 -0.16 1 67
T-DHT/AR 0.024 0.005 -10000 0 -0.004 12 12
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -0.007 2 2
GNAI2 0.032 0.006 -10000 0 0 17 17
GNAI3 0.029 0.011 -10000 0 0 67 67
GNAI1 0.017 0.017 -10000 0 0 248 248
mol:GDP -0.017 0.01 -10000 0 -10000 0 0
cell proliferation -0.016 0.08 0.23 22 -0.36 1 23
PIK3CA 0.031 0.009 -10000 0 0 41 41
FOS -0.009 0.07 0.28 4 -0.4 2 6
mol:Ca2+ 0 0.002 -10000 0 -0.032 2 2
MAPK3 -0.016 0.077 0.22 23 -0.27 1 24
MAPK1 -0.018 0.1 -10000 0 -0.36 34 34
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:IP3 0 0 -10000 0 -0.004 2 2
cAMP biosynthetic process -0.001 0.004 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0 -10000 0 -0.004 2 2
HRAS/GTP 0.049 0.032 -10000 0 -0.049 23 23
actin cytoskeleton reorganization 0.025 0.029 -10000 0 -0.046 12 12
SRC 0.029 0.011 -10000 0 0 66 66
voltage-gated calcium channel activity 0 0 -10000 0 -0.004 2 2
PI3K 0.037 0.018 -10000 0 -0.013 15 15
apoptosis 0.005 0.071 0.23 6 -0.2 14 20
T-DHT/AR/PELP1 0.043 0.011 -10000 0 -0.02 9 9
HRAS/GDP -0.007 0.046 0.095 72 -10000 0 72
CREB1 -0.005 0.072 0.2 13 -0.22 5 18
RAC1-CDC42/GTP 0.032 0.035 -10000 0 -0.047 12 12
AR 0.032 0.006 -10000 0 -0.006 12 12
GNB1 0.031 0.008 -10000 0 0 31 31
RAF1 -0.02 0.07 0.16 69 -10000 0 69
RAC1-CDC42/GDP -0.012 0.039 0.12 11 -10000 0 11
T-DHT/AR/PELP1/Src 0.053 0.026 -10000 0 -0.044 7 7
MAP2K2 -0.034 0.056 0.13 46 -0.16 1 47
T-DHT/AR/PELP1/Src/PI3K 0.01 0.02 -10000 0 -0.11 11 11
GNAZ 0.027 0.013 -10000 0 0 94 94
SHBG 0.032 0.006 -10000 0 0 19 19
Gi family/GNB1/GNG2/GDP -0.075 0.1 -10000 0 -0.25 71 71
mol:T-DHT 0 0 -10000 0 -0.004 1 1
RAC1 0.02 0.016 -10000 0 0 204 204
GNRH1 -0.016 0.003 0 14 -10000 0 14
Gi family/GTP 0.001 0.013 0.072 12 -0.11 2 14
CDC42 0.032 0.006 -10000 0 0 19 19
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.035 0.023 -9999 0 -0.016 3 3
FBXW11 0.032 0.005 -9999 0 0 13 13
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -9999 0 0 13 13
CHUK 0.024 0.015 -9999 0 0 148 148
NF kappa B2 p100/RelB 0.048 0.073 -9999 0 -0.065 128 128
NFKB1 0.032 0.005 -9999 0 0 13 13
MAP3K14 0.033 0.004 -9999 0 0 7 7
NF kappa B1 p50/RelB 0.044 0.015 -9999 0 -0.016 5 5
RELB 0.031 0.009 -9999 0 0 39 39
NFKB2 0.024 0.015 -9999 0 0 147 147
NF kappa B2 p52/RelB 0.03 0.022 -9999 0 -0.037 8 8
regulation of B cell activation 0.03 0.022 -9999 0 -0.037 8 8
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.019 0.026 0.15 10 -10000 0 10
IHH 0.039 0.018 0.12 19 -0.035 8 27
SHH Np/Cholesterol/GAS1 -0.019 0.017 -10000 0 -10000 0 0
LRPAP1 0.033 0.004 -10000 0 0 7 7
dorsoventral neural tube patterning 0.019 0.017 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.077 0.066 0.25 10 -10000 0 10
SMO 0.005 0.017 0.13 3 -0.15 2 5
AKT1 -0.002 0.082 -10000 0 -0.35 19 19
ARRB2 0.032 0.005 -10000 0 0 13 13
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.033 0.004 -10000 0 0 7 7
heart looping 0.005 0.017 0.13 3 -0.15 2 5
STIL 0.033 0.097 0.16 170 -10000 0 170
DHH N/PTCH2 0.024 0.004 -10000 0 0 11 11
DHH N/PTCH1 0.012 0.009 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
DHH 0 0 -10000 0 -10000 0 0
PTHLH -0.007 0.02 0.15 8 -10000 0 8
determination of left/right symmetry 0.005 0.017 0.13 3 -0.15 2 5
PIK3R1 0.03 0.01 -10000 0 0 47 47
skeletal system development -0.007 0.02 0.15 8 -10000 0 8
IHH N/Hhip 0.026 0.009 0.073 19 -10000 0 19
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.005 0.017 0.13 3 -0.15 2 5
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.032 0.006 -10000 0 0 19 19
PI3K 0.041 0.019 -10000 0 -0.016 15 15
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.029 0.012 -10000 0 0 71 71
somite specification 0.005 0.017 0.13 3 -0.15 2 5
SHH Np/Cholesterol/PTCH1 -0.019 0.016 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 -0.02 0.017 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin -0.02 0.017 -10000 0 -10000 0 0
SHH -0.019 0.016 0 219 -10000 0 219
catabolic process 0.015 0.011 0.088 2 -10000 0 2
SMO/Vitamin D3 -0.011 0.03 0.17 11 -10000 0 11
SHH Np/Cholesterol/Hhip -0.013 0.012 0 214 -10000 0 214
LRP2 0.033 0.003 -10000 0 0 4 4
receptor-mediated endocytosis -0.009 0.03 0.14 11 -10000 0 11
SHH Np/Cholesterol/BOC -0.013 0.012 0 214 -10000 0 214
SHH Np/Cholesterol/CDO -0.02 0.017 0 218 -10000 0 218
mesenchymal cell differentiation 0.013 0.011 -10000 0 0 214 214
mol:Vitamin D3 0.052 0.11 0.18 193 -10000 0 193
IHH N/PTCH2 0.051 0.012 0.1 12 -10000 0 12
CDON 0.033 0.004 -10000 0 0 9 9
IHH N/PTCH1 0.033 0.013 0.14 1 -10000 0 1
Megalin/LRPAP1 0.048 0.007 -10000 0 -0.016 1 1
PTCH2 0.033 0.005 -10000 0 0 11 11
SHH Np/Cholesterol 0.06 0.1 0.19 197 -10000 0 197
PTCH1 0.015 0.011 0.089 2 -10000 0 2
HHIP 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.007 0.041 -10000 0 -0.053 1 1
alphaM/beta2 Integrin/GPIbA 0.026 0.047 -10000 0 -0.053 4 4
alphaM/beta2 Integrin/proMMP-9 0.013 0.041 -10000 0 -10000 0 0
PLAUR 0.028 0.013 -10000 0 0 87 87
HMGB1 0.031 0.009 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.017 0.046 -10000 0 -0.047 31 31
AGER 0.033 0.004 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 0 12 12
SELPLG 0.033 0.004 -10000 0 0 9 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.052 0.047 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.019 0.017 -10000 0 0 223 223
CYR61 0.023 0.016 -10000 0 0 163 163
TLN1 0.027 0.013 -10000 0 0 102 102
Rap1/GTP 0.019 0.034 -10000 0 -0.17 4 4
RHOA 0.032 0.006 -10000 0 0 19 19
P-selectin oligomer 0.032 0.005 -10000 0 0 14 14
MYH2 -0.001 0.038 0.14 7 -0.17 4 11
MST1R 0.032 0.006 -10000 0 0 19 19
leukocyte activation during inflammatory response 0.044 0.035 -10000 0 -0.048 38 38
APOB 0.032 0.005 -10000 0 0 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.017 -10000 0 0 252 252
JAM3 0.031 0.008 -10000 0 0 32 32
GP1BA 0.032 0.005 -10000 0 0 13 13
alphaM/beta2 Integrin/CTGF 0.017 0.047 -10000 0 -0.053 1 1
alphaM/beta2 Integrin 0.009 0.033 -10000 0 -0.18 4 4
JAM3 homodimer 0.031 0.008 -10000 0 0 32 32
ICAM2 0.033 0.004 -10000 0 0 9 9
ICAM1 0.03 0.01 -10000 0 0 56 56
phagocytosis triggered by activation of immune response cell surface activating receptor 0.009 0.032 -10000 0 -0.18 4 4
cell adhesion 0.025 0.046 -10000 0 -0.053 4 4
NFKB1 -0.043 0.03 0.17 9 -10000 0 9
THY1 0.024 0.015 -10000 0 0 142 142
RhoA/GDP 0.024 0.005 -10000 0 0 19 19
Lipoprotein(a) 0.041 0.013 -10000 0 -0.013 2 2
alphaM/beta2 Integrin/LRP/tPA 0.035 0.042 -10000 0 -0.052 7 7
IL6 -0.027 0.032 0.15 6 -10000 0 6
ITGB2 0.019 0.017 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.016 0.052 -10000 0 -0.053 99 99
alphaM/beta2 Integrin/JAM2/JAM3 0.05 0.037 -10000 0 -0.054 13 13
JAM2 0.027 0.013 -10000 0 0 92 92
alphaM/beta2 Integrin/ICAM1 0.065 0.041 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.015 0.055 -10000 0 -0.054 115 115
RhoA/GTP 0.008 0.036 0.13 1 -0.17 4 5
positive regulation of phagocytosis 0.008 0.041 0.16 5 -0.18 3 8
Ron/MSP 0.047 0.012 -10000 0 -0.016 8 8
alphaM/beta2 Integrin/uPAR/uPA 0.017 0.053 -10000 0 -0.053 99 99
alphaM/beta2 Integrin/uPAR 0.022 0.045 -10000 0 -0.053 1 1
PLAU 0.018 0.017 -10000 0 0 240 240
PLAT 0.018 0.017 -10000 0 0 239 239
actin filament polymerization 0.001 0.041 0.15 12 -0.16 4 16
MST1 0.032 0.007 -10000 0 0 22 22
alphaM/beta2 Integrin/lipoprotein(a) 0.049 0.037 -10000 0 -0.049 38 38
TNF -0.047 0.029 0.14 10 -10000 0 10
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.045 -10000 0 -0.047 87 87
fibrinolysis 0.014 0.054 -10000 0 -0.053 115 115
HCK 0.023 0.015 -10000 0 0 152 152
dendritic cell antigen processing and presentation 0.009 0.032 -10000 0 -0.18 4 4
VTN 0.033 0.004 -10000 0 0 8 8
alphaM/beta2 Integrin/CYR61 0.018 0.044 -10000 0 -0.048 1 1
LPA 0.031 0.009 -10000 0 0 38 38
LRP1 0.03 0.009 -10000 0 0 44 44
cell migration 0.007 0.032 -10000 0 -10000 0 0
FN1 0.027 0.013 -10000 0 0 100 100
alphaM/beta2 Integrin/Thy1 0.015 0.041 -10000 0 -0.053 1 1
MPO 0.033 0.004 -10000 0 0 7 7
KNG1 0.032 0.007 -10000 0 0 23 23
RAP1/GDP 0.022 0.003 -10000 0 0 12 12
ROCK1 0.001 0.047 0.18 16 -0.17 4 20
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.009 -10000 0 0 43 43
CTGF 0.028 0.012 -10000 0 0 77 77
alphaM/beta2 Integrin/Hck 0.023 0.042 -10000 0 -0.046 5 5
ITGAM 0.033 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.061 0.03 -10000 0 -0.053 6 6
HP 0.027 0.013 -10000 0 0 91 91
leukocyte adhesion 0 0.049 -10000 0 -0.12 6 6
SELP 0.032 0.005 -10000 0 0 14 14
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.01 0.039 0.14 16 -0.19 8 24
adherens junction organization 0.001 0.046 0.13 9 -0.25 6 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.081 0.16 107 -0.2 1 108
FMN1 0.009 0.041 0.14 9 -0.17 12 21
mol:IP3 -0.018 0.032 0.13 9 -0.15 6 15
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.014 0.043 0.14 8 -0.18 12 20
CTNNB1 0.033 0.007 -10000 0 -0.002 16 16
AKT1 -0.013 0.042 0.092 44 -0.17 6 50
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.023 0.063 0.17 3 -0.26 13 16
CTNND1 0.033 0.007 -10000 0 0 19 19
mol:PI-4-5-P2 -0.005 0.043 0.13 10 -0.18 12 22
VASP -0.006 0.04 0.13 8 -0.17 11 19
ZYX -0.004 0.031 0.13 5 -0.18 6 11
JUB 0.009 0.041 0.14 9 -0.17 12 21
EGFR(dimer) 0.008 0.034 0.15 2 -0.18 7 9
E-cadherin/beta catenin-gamma catenin 0.06 0.024 -10000 0 -0.035 9 9
mol:PI-3-4-5-P3 0.042 0.054 0.16 49 -0.16 7 56
PIK3CA 0.03 0.014 -10000 0 -0.034 11 11
PI3K 0.043 0.055 0.16 49 -0.17 7 56
FYN -0.022 0.055 0.14 14 -0.21 26 40
mol:Ca2+ -0.017 0.033 0.14 10 -0.15 6 16
JUP 0.032 0.008 -10000 0 -0.001 25 25
PIK3R1 0.031 0.012 -10000 0 -0.034 5 5
mol:DAG -0.018 0.032 0.13 9 -0.15 6 15
CDH1 0.032 0.007 -10000 0 -0.002 20 20
RhoA/GDP 0.06 0.096 0.16 233 -0.2 1 234
establishment of polarity of embryonic epithelium -0.006 0.04 0.13 8 -0.17 11 19
SRC 0.029 0.011 -10000 0 0 65 65
RAC1 0.02 0.016 -10000 0 0 204 204
RHOA 0.032 0.006 -10000 0 0 19 19
EGFR 0.012 0.016 -10000 0 0 329 329
CASR -0.022 0.036 0.14 14 -0.16 5 19
RhoA/GTP -0.021 0.038 0.14 15 -0.16 4 19
AKT2 -0.016 0.041 0.092 36 -0.17 6 42
actin cable formation -0.004 0.044 0.14 16 -0.17 11 27
apoptosis 0.003 0.048 0.18 10 -0.15 18 28
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
mol:GDP -0.011 0.027 0.17 3 -0.16 4 7
PIP5K1A -0.005 0.043 0.13 10 -0.18 12 22
PLCG1 -0.018 0.032 0.13 9 -0.16 6 15
Rac1/GTP 0.011 0.037 -10000 0 -0.17 7 7
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.032 0.007 -9999 0 0 24 24
EGFR 0.012 0.016 -9999 0 0 329 329
EGF/EGFR 0.017 0.028 -9999 0 -0.049 4 4
EGF/EGFR dimer/SHC/GRB2/SOS1 0.023 0.036 -9999 0 -0.048 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.023 0.015 -9999 0 0 158 158
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.033 0.004 -9999 0 0 8 8
EGF/EGFR dimer/SHC 0.018 0.032 -9999 0 -0.046 2 2
mol:GDP 0.021 0.032 -9999 0 -0.048 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.032 0.006 -9999 0 0 17 17
GRB2/SOS1 0.024 0.005 -9999 0 0 22 22
HRAS/GTP 0.01 0.028 -9999 0 -0.059 2 2
SHC1 0.03 0.01 -9999 0 0 55 55
HRAS/GDP 0.019 0.035 -9999 0 -0.056 13 13
FRAP1 -0.013 0.018 -9999 0 -10000 0 0
EGF/EGFR dimer 0.017 0.024 -9999 0 -0.016 6 6
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.032 0.007 -9999 0 0 22 22
ETA receptor/Endothelin-1 0.029 0.03 -9999 0 -0.016 143 143
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.028 0.025 -10000 0 -0.016 2 2
CRKL 0.065 0.091 0.26 13 -0.44 4 17
mol:PIP3 0.024 0.04 -10000 0 -0.71 1 1
AKT1 0.004 0.044 -10000 0 -0.63 1 1
PTK2B 0.032 0.005 -10000 0 0 13 13
RAPGEF1 0.058 0.095 0.31 17 -0.38 4 21
RANBP10 0.033 0.005 -10000 0 0 10 10
PIK3CA 0.031 0.009 -10000 0 0 41 41
HGF/MET/SHIP2 0.035 0.035 -10000 0 -0.047 6 6
MAP3K5 0.057 0.089 0.25 9 -0.4 4 13
HGF/MET/CIN85/CBL/ENDOPHILINS 0.033 0.033 -10000 0 -0.041 7 7
AP1 0.024 0.079 0.14 151 -10000 0 151
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.03 0.01 -10000 0 0 55 55
apoptosis -0.011 0.23 -10000 0 -0.72 44 44
STAT3 (dimer) 0.009 0.032 0.13 15 -0.19 1 16
GAB1/CRKL/SHP2/PI3K 0.089 0.088 0.3 4 -0.37 4 8
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.08 0.089 0.26 7 -0.43 4 11
PTPN11 0.033 0.005 -10000 0 0 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.029 0.011 -10000 0 0 66 66
PTEN 0.021 0.016 -10000 0 0 188 188
ELK1 0.14 0.19 0.35 216 -10000 0 216
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.029 0.16 1 -0.16 10 11
PAK1 -0.004 0.046 -10000 0 -0.61 1 1
HGF/MET/RANBP10 0.035 0.035 -10000 0 -0.046 6 6
HRAS 0.011 0.035 -10000 0 -0.34 2 2
DOCK1 0.047 0.086 0.25 10 -0.43 4 14
GAB1 0.057 0.084 0.23 4 -0.45 4 8
CRK 0.066 0.09 0.25 9 -0.44 4 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.035 -10000 0 -0.37 3 3
JUN 0.033 0.005 -10000 0 0 10 10
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.004 0.016 0.084 8 -0.057 17 25
PIK3R1 0.03 0.01 -10000 0 0 47 47
cell morphogenesis 0.052 0.11 0.27 61 -0.31 2 63
GRB2/SHC 0.071 0.069 0.17 122 -0.12 10 132
FOS 0.023 0.016 -10000 0 0 163 163
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.14 0.19 0.34 216 -10000 0 216
HGF/MET/MUC20 0.024 0.023 -10000 0 -0.013 3 3
cell migration 0.07 0.067 0.16 122 -0.12 10 132
GRB2 0.032 0.007 -10000 0 0 22 22
CBL 0.033 0.005 -10000 0 0 11 11
MET/RANBP10 0.027 0.025 -10000 0 -0.016 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.008 0.021 -10000 0 -0.13 8 8
MET/MUC20 0.014 0.012 -10000 0 0 222 222
RAP1B 0.057 0.091 0.3 17 -0.36 4 21
RAP1A 0.05 0.093 0.3 18 -0.37 4 22
HGF/MET/RANBP9 0.036 0.034 -10000 0 -0.046 3 3
RAF1 0.047 0.069 0.26 3 -0.3 3 6
STAT3 0.005 0.025 -10000 0 -0.2 1 1
cell proliferation 0.034 0.076 0.22 28 -0.21 2 30
RPS6KB1 0.008 0.018 0.13 1 -10000 0 1
MAPK3 0.11 0.17 0.47 9 -10000 0 9
MAPK1 0.14 0.21 0.62 42 -10000 0 42
RANBP9 0.033 0.004 -10000 0 0 7 7
MAPK8 -0.032 0.14 0.27 4 -0.34 37 41
SRC -0.005 0.024 -10000 0 -0.16 1 1
PI3K 0.072 0.068 0.17 121 -0.12 9 130
MET/Glomulin 0.01 0.028 0.09 1 -0.091 24 25
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.042 0.073 0.26 7 -0.27 3 10
MET 0.019 0.017 -10000 0 0 222 222
MAP4K1 0.068 0.095 0.24 18 -0.41 5 23
PTK2 0.032 0.007 -10000 0 0 22 22
MAP2K2 0.055 0.091 0.29 29 -0.29 3 32
BAD -0.006 0.043 -10000 0 -0.61 1 1
MAP2K4 0.048 0.086 0.24 13 -0.35 4 17
SHP2/GRB2/SOS1/GAB1 0.022 0.05 -10000 0 -0.38 4 4
INPPL1 0.033 0.005 -10000 0 0 10 10
PXN 0.033 0.004 -10000 0 0 7 7
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.009 0.021 0.069 7 -0.11 11 18
PLCgamma1/PKC 0.021 0.008 -10000 0 0 66 66
HGF 0.019 0.016 -10000 0 0 213 213
RASA1 0.032 0.006 -10000 0 0 18 18
NCK1 0.031 0.008 -10000 0 0 28 28
PTPRJ 0.032 0.006 -10000 0 0 16 16
NCK/PLCgamma1 0.07 0.066 0.16 137 -0.12 11 148
PDPK1 0.013 0.042 0.32 1 -0.66 1 2
HGF/MET/SHIP 0.024 0.023 -10000 0 -0.013 3 3
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.009 0.088 -10000 0 -0.4 21 21
HDAC1 0.028 0.012 -10000 0 0 74 74
AES 0.031 0.009 -10000 0 0 38 38
FBXW11 0.032 0.005 -10000 0 0 13 13
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.025 -10000 0 -0.016 4 4
TLE1 0.032 0.007 -10000 0 0 21 21
AP1 0.003 0.019 -10000 0 -0.14 5 5
NCSTN 0.031 0.009 -10000 0 0 39 39
ADAM10 0.031 0.008 -10000 0 0 34 34
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.053 -10000 0 -0.49 4 4
NICD/RBPSUH 0.027 0.094 -10000 0 -0.4 21 21
WIF1 0.004 0.01 -10000 0 0 452 452
NOTCH1 0.009 0.088 -10000 0 -0.45 17 17
PSENEN 0.031 0.009 -10000 0 0 40 40
KREMEN2 0.033 0.003 -10000 0 0 5 5
DKK1 0.017 0.017 -10000 0 0 242 242
beta catenin/beta TrCP1 0.072 0.084 0.22 64 -0.26 3 67
APH1B 0.032 0.006 -10000 0 0 15 15
APH1A 0.032 0.006 -10000 0 0 19 19
AXIN1 0.031 0.05 0.26 5 -10000 0 5
CtBP/CBP/TCF1/TLE1/AES 0.009 0.031 -10000 0 -0.12 19 19
PSEN1 0.031 0.009 -10000 0 0 42 42
FOS 0.023 0.016 -10000 0 0 163 163
JUN 0.033 0.005 -10000 0 0 10 10
MAP3K7 0.031 0.008 -10000 0 0 29 29
CTNNB1 0.057 0.087 0.21 74 -0.26 3 77
MAPK3 0.033 0.003 -10000 0 0 4 4
DKK2/LRP6/Kremen 2 0.059 0.026 -10000 0 -0.047 15 15
HNF1A 0.033 0.004 -10000 0 0 7 7
CTBP1 0.032 0.006 -10000 0 0 18 18
MYC 0.016 0.052 -10000 0 -0.76 2 2
NKD1 0 0 -10000 0 -10000 0 0
FZD1 0.019 0.016 -10000 0 0 218 218
NOTCH1 precursor/Deltex homolog 1 0.005 0.087 -10000 0 -0.4 21 21
apoptosis 0.003 0.019 -10000 0 -0.14 5 5
Delta 1/NOTCHprecursor 0.005 0.087 -10000 0 -0.4 21 21
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.021 0.062 -10000 0 -0.76 3 3
Gamma Secretase 0.074 0.051 -10000 0 -0.065 1 1
APC 0.013 0.094 0.27 4 -0.35 21 25
DVL1 0.01 0.019 -10000 0 -0.21 2 2
CSNK2A1 0.029 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.016 0.052 -10000 0 -0.047 136 136
LRP6 0.031 0.008 -10000 0 0 31 31
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
NLK 0.009 0.003 -10000 0 -0.01 1 1
CCND1 0.012 0.093 -10000 0 -0.77 7 7
WNT1 0.032 0.007 -10000 0 0 21 21
Axin1/APC/beta catenin 0.048 0.093 0.26 25 -0.39 5 30
DKK2 0.032 0.006 -10000 0 0 17 17
NOTCH1 precursor/DVL1 0.03 0.096 0.29 2 -0.4 16 18
GSK3B 0.032 0.006 -10000 0 0 20 20
FRAT1 0.024 0.015 -10000 0 0 146 146
NOTCH/Deltex homolog 1 0.009 0.088 -10000 0 -0.4 21 21
PPP2R5D 0.023 0.034 -10000 0 -0.39 2 2
MAPK1 0.031 0.009 -10000 0 0 42 42
WNT1/LRP6/FZD1 0.007 0.024 -10000 0 -0.052 1 1
RBPJ 0.033 0.004 -10000 0 0 6 6
CREBBP 0.033 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.021 0.024 -10000 0 -10000 0 0
VLDLR 0.029 0.011 -10000 0 0 66 66
CRKL 0.031 0.008 -10000 0 0 29 29
LRPAP1 0.033 0.004 -10000 0 0 7 7
FYN 0.03 0.01 -10000 0 0 53 53
ITGA3 0.032 0.007 -10000 0 0 24 24
RELN/VLDLR/Fyn 0.014 0.03 -10000 0 -0.048 11 11
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.067 -10000 0 -0.067 7 7
AKT1 -0.011 0.035 0.075 1 -0.16 25 26
MAP2K7 0.031 0.008 -10000 0 0 35 35
RAPGEF1 0.032 0.007 -10000 0 0 23 23
DAB1 0.032 0.006 -10000 0 0 17 17
RELN/LRP8/DAB1 0.016 0.029 -10000 0 -0.043 6 6
LRPAP1/LRP8 0.047 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.017 0.035 -10000 0 -0.05 10 10
DAB1/alpha3/beta1 Integrin 0.013 0.038 -10000 0 -10000 0 0
long-term memory 0.014 0.037 0.18 7 -10000 0 7
DAB1/LIS1 0.021 0.044 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.015 0.038 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
DAB1/NCK2 0.022 0.045 -10000 0 -10000 0 0
ARHGEF2 0.032 0.006 -10000 0 0 16 16
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.022 0.016 -10000 0 0 177 177
CDK5R1 0.027 0.013 -10000 0 0 102 102
RELN 0.009 0.015 -10000 0 0 372 372
PIK3R1 0.03 0.01 -10000 0 0 47 47
RELN/LRP8/Fyn 0.015 0.03 -10000 0 -0.046 8 8
GRIN2A/RELN/LRP8/DAB1/Fyn 0.017 0.039 -10000 0 -0.06 8 8
MAPK8 0.024 0.015 -10000 0 0 138 138
RELN/VLDLR/DAB1 0.014 0.029 -10000 0 -0.041 13 13
ITGB1 0.025 0.015 -10000 0 0 131 131
MAP1B 0.013 0.061 0.14 81 -10000 0 81
RELN/LRP8 0.017 0.03 -10000 0 -0.046 5 5
GRIN2B/RELN/LRP8/DAB1/Fyn 0.02 0.042 -10000 0 -0.061 12 12
PI3K 0.041 0.019 -10000 0 -0.016 15 15
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.023 -10000 0 -0.016 15 15
RAP1A 0.048 0.099 0.32 19 -10000 0 19
PAFAH1B1 0.032 0.006 -10000 0 0 17 17
MAPK8IP1 0.032 0.006 -10000 0 0 19 19
CRLK/C3G 0.045 0.015 -10000 0 -10000 0 0
GRIN2B 0.031 0.008 -10000 0 0 32 32
NCK2 0.033 0.003 -10000 0 0 5 5
neuron differentiation -0.019 0.068 0.14 2 -0.2 38 40
neuron adhesion 0.024 0.1 0.34 17 -10000 0 17
LRP8 0.032 0.005 -10000 0 0 14 14
GSK3B -0.019 0.053 -10000 0 -0.18 19 19
RELN/VLDLR/DAB1/Fyn 0.016 0.035 -10000 0 -0.05 14 14
MAP3K11 0.033 0.004 -10000 0 0 9 9
RELN/VLDLR/DAB1/P13K -0.004 0.034 -10000 0 -0.14 27 27
CDK5 0.018 0.017 -10000 0 0 240 240
MAPT 0 0.061 0.7 2 -10000 0 2
neuron migration -0.022 0.096 0.17 65 -0.19 15 80
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.019 0.066 -10000 0 -0.2 36 36
RELN/VLDLR 0.019 0.038 -10000 0 -0.052 13 13
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.043 0.22 8 -0.2 14 22
RFC1 -0.023 0.037 0.21 2 -0.2 17 19
PRKDC -0.021 0.041 0.22 5 -0.2 17 22
RIPK1 0.032 0.006 -10000 0 0 20 20
CASP7 -0.17 0.28 -10000 0 -0.6 152 152
FASLG/FAS/FADD/FAF1 -0.028 0.061 0.1 1 -0.12 134 135
MAP2K4 -0.078 0.12 0.18 1 -0.25 149 150
mol:ceramide -0.026 0.072 -10000 0 -0.2 31 31
GSN -0.019 0.046 0.21 9 -0.2 16 25
FASLG/FAS/FADD/FAF1/Caspase 8 -0.04 0.07 -10000 0 -0.21 28 28
FAS 0.02 0.016 -10000 0 -10000 0 0
BID -0.038 0.016 0.2 1 -10000 0 1
MAP3K1 -0.13 0.19 -10000 0 -0.41 153 153
MAP3K7 0.031 0.008 -10000 0 0 29 29
RB1 -0.021 0.035 0.22 1 -0.2 16 17
CFLAR 0.033 0.004 -10000 0 0 6 6
HGF/MET 0.032 0.036 -10000 0 -0.046 5 5
ARHGDIB -0.015 0.049 0.22 13 -0.2 14 27
FADD 0.033 0.005 -10000 0 -10000 0 0
actin filament polymerization 0.019 0.045 0.2 16 -0.21 9 25
NFKB1 0.015 0.073 -10000 0 -0.62 6 6
MAPK8 -0.085 0.12 -10000 0 -0.29 73 73
DFFA -0.021 0.038 0.22 3 -0.2 16 19
DNA fragmentation during apoptosis -0.021 0.035 0.22 2 -0.2 15 17
FAS/FADD/MET 0.019 0.04 -10000 0 -0.047 47 47
CFLAR/RIP1 0.046 0.013 -10000 0 -0.016 14 14
FAIM3 0.032 0.006 -10000 0 0 19 19
FAF1 0.031 0.008 -10000 0 -10000 0 0
PARP1 -0.023 0.038 0.22 2 -0.2 18 20
DFFB -0.021 0.036 0.22 2 -0.2 15 17
CHUK 0.004 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.027 0.027 -10000 0 -0.017 15 15
HGF 0.019 0.016 -10000 0 0 213 213
LMNA -0.028 0.038 0.19 5 -0.19 16 21
CASP6 -0.022 0.033 0.22 1 -0.2 15 16
CASP10 0.033 0.002 -10000 0 -10000 0 0
CASP3 -0.015 0.038 -10000 0 -0.22 17 17
PTPN13 0.031 0.008 -10000 0 0 33 33
CASP8 -0.035 0.007 0.014 1 -10000 0 1
IL6 -0.025 0.082 -10000 0 -0.51 7 7
MET 0.019 0.017 -10000 0 0 222 222
ICAD/CAD -0.03 0.041 0.24 4 -0.2 16 20
FASLG/FAS/FADD/FAF1/Caspase 10 -0.026 0.073 -10000 0 -0.2 31 31
activation of caspase activity by cytochrome c -0.038 0.016 0.2 1 -10000 0 1
PAK2 -0.018 0.044 0.22 8 -0.2 15 23
BCL2 0.032 0.007 -10000 0 0 21 21
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.016 -10000 0 -0.022 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.029 0.062 0.2 8 -0.18 32 40
AP1 0 0.018 -10000 0 -0.028 10 10
mol:PIP3 -0.011 0.016 -10000 0 -10000 0 0
AKT1 0.021 0.079 0.23 19 -0.24 7 26
PTK2B 0.001 0.027 0.12 2 -0.19 7 9
RHOA 0.027 0.064 0.15 25 -0.31 8 33
PIK3CB 0.03 0.012 -10000 0 -0.015 31 31
mol:Ca2+ -0.015 0.02 0.17 3 -0.12 1 4
MAGI3 0 0 -10000 0 -0.005 1 1
RELA 0.033 0.004 -10000 0 0 9 9
apoptosis 0.007 0.005 -10000 0 -0.009 21 21
HRAS/GDP 0.023 0.005 -10000 0 0 24 24
positive regulation of microtubule depolymerization -0.009 0.039 0.18 11 -0.19 7 18
NF kappa B1 p50/RelA -0.038 0.019 0.082 1 -0.12 7 8
endothelial cell migration 0.003 0.01 -10000 0 -0.024 2 2
ADCY4 0 0.01 0.076 7 -10000 0 7
ADCY5 0 0.01 0.076 7 -10000 0 7
ADCY6 0.001 0.012 0.078 10 -10000 0 10
ADCY7 0.001 0.013 0.078 12 -10000 0 12
ADCY1 -0.001 0.005 -10000 0 -10000 0 0
ADCY2 0.001 0.013 0.078 12 -10000 0 12
ADCY3 0 0.01 0.076 7 -10000 0 7
ADCY8 0.001 0.012 0.078 10 -10000 0 10
ADCY9 0.001 0.013 0.078 11 -10000 0 11
GSK3B -0.006 0.034 0.18 7 -0.19 7 14
arachidonic acid secretion 0 0.014 0.068 12 -0.12 2 14
GNG2 0 0.001 -10000 0 -0.004 22 22
TRIP6 0.003 0.01 -10000 0 -0.008 123 123
GNAO1 0 0.004 0.013 16 -10000 0 16
HRAS 0.032 0.007 -10000 0 0 24 24
NFKBIA -0.021 0.054 0.17 10 -0.18 32 42
GAB1 0.032 0.005 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.012 0.18 -10000 0 -0.69 33 33
JUN 0.033 0.005 -10000 0 0 10 10
LPA/LPA2/NHERF2 0.021 0.004 -10000 0 -0.003 8 8
TIAM1 -0.016 0.22 -10000 0 -0.86 33 33
PIK3R1 0.03 0.011 -10000 0 -0.003 51 51
mol:IP3 -0.015 0.02 0.17 3 -0.12 6 9
PLCB3 -0.02 0.019 0.19 4 -10000 0 4
FOS 0.023 0.016 -10000 0 0 163 163
positive regulation of mitosis 0 0.014 0.068 12 -0.12 2 14
LPA/LPA1-2-3 0.002 0.003 -10000 0 -0.008 9 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.014 0.024 0.13 1 -10000 0 1
GNAZ -0.001 0.013 0.013 199 -0.027 1 200
EGFR/PI3K-beta/Gab1 -0.012 0.017 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production 0.001 0.003 -10000 0 -0.008 9 9
LPA/LPA2/MAGI-3 0.001 0.002 -10000 0 -0.006 10 10
ARHGEF1 0.049 0.1 0.18 180 -10000 0 180
GNAI2 -0.001 0.014 0.013 234 -0.027 1 235
GNAI3 -0.001 0.013 0.013 208 -10000 0 208
GNAI1 0 0.01 0.013 132 -10000 0 132
LPA/LPA3 0 0.001 -10000 0 -0.004 11 11
LPA/LPA2 0 0.001 -10000 0 -0.007 5 5
LPA/LPA1 0.001 0.003 -10000 0 -0.008 16 16
HB-EGF/EGFR -0.012 0.017 -10000 0 -10000 0 0
HBEGF -0.023 0.012 0 76 -10000 0 76
mol:DAG -0.015 0.02 0.17 3 -0.12 6 9
cAMP biosynthetic process 0.057 0.063 0.14 148 -10000 0 148
NFKB1 0.032 0.005 -10000 0 0 13 13
SRC 0.029 0.011 -10000 0 0 65 65
GNB1 0.029 0.013 -10000 0 -0.009 44 44
LYN -0.011 0.041 0.17 11 -0.17 1 12
GNAQ 0.01 0.003 -10000 0 -0.01 5 5
LPAR2 0 0 -10000 0 -0.005 1 1
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0 0.001 -10000 0 -0.006 12 12
IL8 -0.005 0.035 0.23 1 -0.29 4 5
PTK2 0.02 0.008 -10000 0 -0.017 13 13
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
CASP3 0.007 0.005 -10000 0 -0.01 21 21
EGFR 0.012 0.016 -10000 0 0 329 329
PLCG1 0.005 0.005 -10000 0 -0.084 1 1
PLD2 0.02 0.008 -10000 0 -0.017 13 13
G12/G13 0.021 0.02 -10000 0 -0.029 5 5
PI3K-beta -0.017 0.036 -10000 0 -0.24 9 9
cell migration 0 0.053 -10000 0 -0.22 20 20
SLC9A3R2 0.033 0.004 -10000 0 0 7 7
PXN 0.014 0.024 0.13 1 -10000 0 1
HRAS/GTP 0 0.013 0.069 12 -0.091 1 13
RAC1 0.02 0.016 -10000 0 0 204 204
MMP9 0.019 0.017 -10000 0 0 223 223
PRKCE 0.029 0.015 -10000 0 -0.032 27 27
PRKCD -0.017 0.039 0.19 11 -10000 0 11
Gi(beta/gamma) 0.001 0.015 0.081 11 -0.18 1 12
mol:LPA 0 0.002 -10000 0 -0.006 12 12
TRIP6/p130 Cas/FAK1/Paxillin 0.007 0.018 -10000 0 -0.14 3 3
MAPKKK cascade 0 0.014 0.068 12 -0.12 2 14
contractile ring contraction involved in cytokinesis 0.031 0.065 0.14 36 -0.3 8 44
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.01 0.003 -10000 0 -0.01 5 5
GNA15 0.009 0.003 -10000 0 -0.009 4 4
GNA12 0.02 0.016 -10000 0 0 203 203
GNA13 0.032 0.005 -10000 0 0 10 10
MAPT -0.011 0.038 0.19 9 -0.2 7 16
GNA11 0.01 0.003 -10000 0 -0.009 4 4
Rac1/GTP -0.013 0.19 -10000 0 -0.72 33 33
MMP2 0.002 0.01 -10000 0 -0.024 2 2
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.026 -10000 0 -0.12 23 23
epithelial cell differentiation 0.063 0.028 -10000 0 -0.049 24 24
CYFIP2 0.019 0.017 -10000 0 0 223 223
ENAH -0.062 0.059 0.38 5 -10000 0 5
EGFR 0.012 0.016 -10000 0 0 329 329
EPHA2 0.031 0.008 -10000 0 0 28 28
MYO6 -0.042 0.035 0.16 12 -10000 0 12
CTNNB1 0.032 0.006 -10000 0 0 15 15
ABI1/Sra1/Nap1 0.021 0.042 -10000 0 -0.046 76 76
AQP5 -0.026 0.05 -10000 0 -0.33 8 8
CTNND1 0.032 0.006 -10000 0 0 19 19
mol:PI-4-5-P2 -0.041 0.03 0.16 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.04 0.035 0.16 13 -10000 0 13
EGF 0.033 0.004 -10000 0 0 8 8
NCKAP1 0.033 0.003 -10000 0 0 3 3
AQP3 -0.047 0.089 -10000 0 -0.34 40 40
cortical microtubule organization 0.063 0.028 -10000 0 -0.049 24 24
GO:0000145 -0.039 0.028 0.14 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.069 0.03 -10000 0 -0.049 24 24
MLLT4 0.03 0.009 -10000 0 0 45 45
ARF6/GDP -0.073 0.023 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 0 31 31
Ephrin A1/EPHA2/NCK1/GIT1 0.072 0.034 -10000 0 -0.053 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.019 0.025 0.14 2 -0.2 2 4
PVRL2 0.031 0.009 -10000 0 0 37 37
ZYX -0.026 0.031 0.16 5 -10000 0 5
ARF6/GTP 0.074 0.046 -10000 0 -0.059 34 34
CDH1 0.032 0.006 -10000 0 0 19 19
EGFR/EGFR/EGF/EGF 0.018 0.034 -10000 0 -10000 0 0
RhoA/GDP 0.064 0.031 -10000 0 -0.057 24 24
actin cytoskeleton organization -0.033 0.033 0.14 8 -10000 0 8
IGF-1R heterotetramer 0.033 0.005 -10000 0 0 11 11
GIT1 0.033 0.004 -10000 0 0 8 8
IGF1R 0.033 0.005 -10000 0 0 11 11
IGF1 0.032 0.005 -10000 0 0 12 12
DIAPH1 -0.24 0.27 -10000 0 -0.48 265 265
Wnt receptor signaling pathway -0.063 0.028 0.049 24 -10000 0 24
RHOA 0.032 0.006 -10000 0 0 19 19
RhoA/GTP -0.072 0.024 -10000 0 -10000 0 0
CTNNA1 0.033 0.005 -10000 0 0 10 10
VCL -0.034 0.034 0.14 8 -10000 0 8
EFNA1 0.031 0.009 -10000 0 0 36 36
LPP -0.047 0.03 0.14 7 -10000 0 7
Ephrin A1/EPHA2 0.047 0.042 -10000 0 -10000 0 0
SEC6/SEC8 -0.059 0.019 -10000 0 -10000 0 0
MGAT3 -0.041 0.036 0.16 13 -10000 0 13
HGF/MET 0.029 0.038 -10000 0 -10000 0 0
HGF 0.019 0.016 -10000 0 0 213 213
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.026 -10000 0 -0.12 23 23
actin cable formation -0.051 0.081 0.36 10 -0.25 7 17
KIAA1543 -0.034 0.028 0.14 13 -10000 0 13
KIFC3 -0.044 0.031 0.16 10 -10000 0 10
NCK1 0.031 0.008 -10000 0 0 28 28
EXOC3 0.032 0.006 -10000 0 0 18 18
ACTN1 -0.041 0.033 0.16 10 -10000 0 10
NCK1/GIT1 0.046 0.014 -10000 0 -0.016 10 10
mol:GDP 0.063 0.028 -10000 0 -0.049 24 24
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.044 0.034 0.16 12 -10000 0 12
PIP5K1C -0.041 0.031 0.16 8 -10000 0 8
LIMA1 0.005 0.012 -10000 0 0 437 437
ABI1 0.024 0.015 -10000 0 0 138 138
ROCK1 -0.059 0.074 0.4 8 -10000 0 8
adherens junction assembly -0.033 0.048 0.26 3 -0.22 7 10
IGF-1R heterotetramer/IGF1 0.051 0.039 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.017 -10000 0 -10000 0 0
MET 0.019 0.017 -10000 0 0 222 222
PLEKHA7 -0.039 0.007 -10000 0 -10000 0 0
mol:GTP 0.07 0.033 -10000 0 -0.052 15 15
establishment of epithelial cell apical/basal polarity -0.055 0.055 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.01 0.026 -10000 0 -0.12 23 23
regulation of cell-cell adhesion -0.033 0.033 0.14 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.026 -10000 0 -0.12 23 23
Caspase cascade in apoptosis

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
TOP1 -0.022 0.096 -10000 0 -0.32 26 26
ACTA1 -0.058 0.088 0.14 1 -0.32 35 36
NUMA1 -0.019 0.086 -10000 0 -0.29 33 33
SPTAN1 -0.057 0.091 0.17 8 -0.33 34 42
LIMK1 0.002 0.1 0.17 96 -0.28 25 121
BIRC3 0.031 0.009 -10000 0 0 40 40
BIRC2 0.033 0.005 -10000 0 0 10 10
BAX 0.03 0.009 -10000 0 0 43 43
CASP10 -0.027 0.018 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 0.001 2 -0.001 8 10
PTK2 -0.02 0.086 -10000 0 -0.32 25 25
DIABLO 0.033 0.004 -10000 0 0 8 8
apoptotic nuclear changes -0.056 0.09 0.17 8 -0.33 33 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.033 0.005 -10000 0 0 11 11
GSN -0.061 0.091 0.17 7 -0.33 35 42
MADD 0.032 0.007 -10000 0 0 22 22
TFAP2A 0.03 0.096 -10000 0 -0.63 9 9
BID -0.008 0.01 -10000 0 -0.15 2 2
MAP3K1 -0.014 0.056 -10000 0 -0.39 7 7
TRADD 0.033 0.004 -10000 0 0 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.047 0.012 -10000 0 -0.016 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.058 0.093 0.17 12 -0.33 34 46
CASP9 0.032 0.006 -10000 0 0 17 17
DNA repair 0.032 0.061 0.17 35 -10000 0 35
neuron apoptosis 0.017 0.085 -10000 0 -0.63 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.047 0.091 0.19 2 -0.32 38 40
APAF1 0.033 0.005 -10000 0 0 11 11
CASP6 0.017 0.1 -10000 0 -0.93 4 4
TRAF2 0.032 0.006 -10000 0 0 20 20
ICAD/CAD -0.07 0.087 0.3 2 -0.34 33 35
CASP7 -0.061 0.1 -10000 0 -0.22 149 149
KRT18 0.016 0.055 -10000 0 -0.47 5 5
apoptosis -0.06 0.096 -10000 0 -0.34 33 33
DFFA -0.063 0.087 0.17 2 -0.34 33 35
DFFB -0.063 0.087 0.17 2 -0.34 33 35
PARP1 -0.033 0.061 -10000 0 -0.17 35 35
actin filament polymerization -0.013 0.1 0.26 25 -0.16 95 120
TNF 0.033 0.004 -10000 0 0 7 7
CYCS 0.001 0.03 -10000 0 -0.24 2 2
SATB1 0.019 0.1 0.3 1 -0.79 4 5
SLK -0.066 0.088 -10000 0 -0.34 34 34
p15 BID/BAX -0.041 0.057 0.094 1 -0.22 38 39
CASP2 0.055 0.097 0.19 167 -0.19 4 171
JNK cascade 0.014 0.055 0.38 7 -10000 0 7
CASP3 -0.058 0.091 -10000 0 -0.34 35 35
LMNB2 0.059 0.086 0.24 14 -0.34 2 16
RIPK1 0.032 0.006 -10000 0 0 20 20
CASP4 0.026 0.014 -10000 0 0 111 111
Mammalian IAPs/DIABLO 0.056 0.026 -10000 0 -0.049 9 9
negative regulation of DNA binding 0.031 0.095 -10000 0 -0.62 9 9
stress fiber formation -0.065 0.087 -10000 0 -0.33 34 34
GZMB -0.022 0.015 0 160 -10000 0 160
CASP1 0.004 0.008 -10000 0 -0.009 105 105
LMNB1 0.053 0.1 0.23 17 -0.37 10 27
APP 0.017 0.086 -10000 0 -0.64 8 8
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
response to stress 0 0 0.001 7 -0.001 18 25
CASP8 -0.016 0.002 0 11 -10000 0 11
VIM -0.05 0.098 0.2 1 -0.33 34 35
LMNA 0.062 0.087 0.24 14 -0.3 3 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.04 -10000 0 -0.23 7 7
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.064 0.087 0.17 1 -0.33 35 36
APAF-1/Caspase 9 0.026 0.08 -10000 0 -0.62 7 7
nuclear fragmentation during apoptosis -0.019 0.085 -10000 0 -0.29 33 33
CFL2 0.013 0.1 0.16 95 -0.26 25 120
GAS2 -0.063 0.087 0.17 2 -0.33 34 36
positive regulation of apoptosis 0.063 0.094 0.23 19 -0.35 5 24
PRF1 0.023 0.015 -10000 0 0 159 159
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.012 -10000 0 -0.027 8 8
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.023 0.027 -10000 0 -0.013 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.033 0.004 -10000 0 0 9 9
RGS9-1/Gbeta5/R9AP 0.043 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.042 0.012 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.033 0.005 -10000 0 0 11 11
Cone Metarhodopsin II/X-Arrestin 0.025 0.002 -10000 0 0 2 2
mol:Ca2+ -0.019 0.033 0.18 12 -10000 0 12
Cone PDE6 0.037 0.058 -10000 0 -0.049 149 149
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.019 0.045 -10000 0 -0.041 58 58
GNAT2/GDP 0.053 0.021 -10000 0 -0.038 18 18
GNB5 0.032 0.006 -10000 0 0 20 20
mol:GMP (4 units) -0.017 0.041 0.19 16 -10000 0 16
Cone Transducin 0.04 0.013 -10000 0 -0.029 8 8
SLC24A2 0.026 0.014 -10000 0 0 114 114
GNB3/GNGT2 0.023 0.005 -10000 0 0 25 25
GNB3 0.032 0.007 -10000 0 0 25 25
GNAT2/GTP 0.024 0.003 -10000 0 0 9 9
CNGA3 0.021 0.016 -10000 0 0 183 183
ARR3 0.033 0.002 -10000 0 0 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.028 -10000 0 -0.013 179 179
mol:Pi 0.042 0.01 -10000 0 -10000 0 0
Cone CNG Channel 0.032 0.057 -10000 0 -0.057 73 73
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.026 0.014 -10000 0 0 114 114
RGS9 0.033 0.004 -10000 0 0 9 9
PDE6C 0.023 0.015 -10000 0 0 151 151
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.008 -10000 0 0 30 30
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.025 0.098 -9999 0 -0.24 60 60
CaM/Ca2+ 0.022 0.008 -9999 0 0 61 61
AKT1 0.031 0.009 -9999 0 0 39 39
AKT2 0.031 0.008 -9999 0 0 34 34
STXBP4 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.044 0.092 -9999 0 -0.25 63 63
YWHAZ 0.032 0.006 -9999 0 0 19 19
CALM1 0.029 0.011 -9999 0 0 61 61
YWHAQ 0.033 0.004 -9999 0 0 7 7
TBC1D4 -0.029 0.011 0 69 -10000 0 69
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.015 0.017 -9999 0 0 278 278
YWHAB 0.029 0.011 -9999 0 0 67 67
SNARE/Synip 0.039 0.015 -9999 0 -0.04 1 1
YWHAG 0 0 -9999 0 -10000 0 0
ASIP 0.029 0.011 -9999 0 0 66 66
PRKCI 0.032 0.006 -9999 0 0 17 17
AS160/CaM/Ca2+ 0.022 0.008 -9999 0 0 61 61
RHOQ 0.033 0.002 -9999 0 0 2 2
GYS1 -0.018 0.028 -9999 0 -0.14 24 24
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.031 0.009 -9999 0 0 37 37
TC10/GTP/CIP4/Exocyst 0.042 0.012 -9999 0 -0.013 6 6
AS160/14-3-3 -0.031 0.047 -9999 0 -0.2 12 12
VAMP2 0.029 0.011 -9999 0 0 60 60
SLC2A4 -0.048 0.1 -9999 0 -0.27 64 64
STX4 0.033 0.003 -9999 0 0 3 3
GSK3B 0.012 0.005 -9999 0 -10000 0 0
SFN 0.03 0.01 -9999 0 0 46 46
LNPEP 0.032 0.005 -9999 0 0 13 13
YWHAE 0.032 0.005 -9999 0 0 12 12
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.011 -10000 0 0 67 67
NFATC1 0.013 0.057 0.22 4 -0.32 5 9
NFATC2 -0.044 0.08 0.14 2 -0.17 127 129
NFATC3 0.003 0.016 -10000 0 -0.061 30 30
YWHAE 0.032 0.005 -10000 0 0 12 12
Calcineurin A alpha-beta B1/CABIN1 -0.032 0.076 0.15 3 -0.24 39 42
Exportin 1/Ran/NUP214 0.062 0.022 -10000 0 -0.046 13 13
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.004 0.094 0.16 1 -0.23 38 39
BCL2/BAX 0.043 0.016 -10000 0 -0.016 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.008 -10000 0 0 61 61
CaM/Ca2+ 0.021 0.008 -10000 0 0 61 61
BAX 0.03 0.009 -10000 0 0 43 43
MAPK14 0.033 0.003 -10000 0 0 5 5
BAD 0.033 0.004 -10000 0 0 8 8
CABIN1/MEF2D -0.018 0.083 0.15 4 -0.23 41 45
Calcineurin A alpha-beta B1/BCL2 0.032 0.007 -10000 0 0 21 21
FKBP8 0.031 0.009 -10000 0 0 39 39
activation-induced cell death of T cells 0.018 0.082 0.22 41 -0.15 4 45
KPNB1 0.033 0.003 -10000 0 0 5 5
KPNA2 0.032 0.006 -10000 0 0 18 18
XPO1 0.033 0.001 -10000 0 0 1 1
SFN 0.03 0.01 -10000 0 0 46 46
MAP3K8 0.022 0.016 -10000 0 0 172 172
NFAT4/CK1 alpha -0.035 0.018 -10000 0 -0.095 29 29
MEF2D/NFAT1/Cbp/p300 -0.004 0.11 0.19 1 -0.18 120 121
CABIN1 -0.031 0.075 0.15 3 -0.23 40 43
CALM1 0.029 0.011 -10000 0 0 61 61
RAN 0.032 0.005 -10000 0 0 12 12
MAP3K1 0.033 0.005 -10000 0 0 11 11
CAMK4 0.033 0.004 -10000 0 0 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 0.033 0.003 -10000 0 0 4 4
YWHAH 0.015 0.017 -10000 0 0 278 278
Calcineurin A alpha-beta B1/AKAP79/PKA 0.043 0.017 -10000 0 -10000 0 0
YWHAB 0.029 0.011 -10000 0 0 67 67
MAPK8 0.024 0.015 -10000 0 0 138 138
MAPK9 0.032 0.005 -10000 0 0 14 14
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.029 0.011 -10000 0 0 66 66
NFAT1-c-4/YWHAQ -0.002 0.074 0.22 2 -0.24 21 23
PRKCH 0.031 0.009 -10000 0 0 41 41
CABIN1/Cbp/p300 0.045 0.014 -10000 0 -10000 0 0
CASP3 0.026 0.014 -10000 0 0 110 110
PIM1 0.033 0.003 -10000 0 0 5 5
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.008 -10000 0 0 66 66
apoptosis 0.015 0.023 -10000 0 -0.11 13 13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.048 -10000 0 -0.19 16 16
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.033 0.004 -10000 0 0 6 6
JNK2/NFAT4 0.019 0.034 0.1 2 -0.088 36 38
BAD/BCL-XL 0.042 0.018 -10000 0 -10000 0 0
PRKCD 0.032 0.006 -10000 0 0 16 16
NUP214 0.032 0.007 -10000 0 0 23 23
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.033 0.005 -10000 0 0 10 10
PRKCG 0.031 0.009 -10000 0 0 42 42
PRKCQ 0.024 0.015 -10000 0 0 141 141
FKBP38/BCL2 0.044 0.016 -10000 0 -10000 0 0
EP300 0.031 0.009 -10000 0 0 41 41
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.011 -10000 0 0 66 66
NFATc/JNK1 0.018 0.051 0.28 1 -0.26 8 9
CaM/Ca2+/FKBP38 0.037 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.021 0.008 -10000 0 0 66 66
CSNK1A1 -0.023 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.039 0.015 -10000 0 -10000 0 0
NFATc/ERK1 0.03 0.06 0.23 3 -0.31 5 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.003 0.095 0.16 1 -0.23 41 42
NR4A1 -0.062 0.071 0.14 12 -0.18 97 109
GSK3B 0.032 0.006 -10000 0 0 20 20
positive T cell selection 0.003 0.016 -10000 0 -0.061 30 30
NFAT1/CK1 alpha -0.04 0.055 0.064 3 -0.13 124 127
RCH1/ KPNB1 0.047 0.011 -10000 0 -0.016 11 11
YWHAQ 0.033 0.004 -10000 0 0 7 7
PRKACA 0.031 0.009 -10000 0 0 36 36
AKAP5 0.031 0.009 -10000 0 0 37 37
MEF2D 0.032 0.006 -10000 0 0 17 17
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 0 19 19
NFATc/p38 alpha 0.03 0.06 0.23 4 -0.31 5 9
CREBBP 0.033 0.004 -10000 0 0 7 7
BCL2 0.032 0.007 -10000 0 0 21 21
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.046 0.013 -10000 0 -0.016 15 15
AKT1 -0.02 0.078 0.22 10 -0.27 15 25
PTK2B -0.035 0.06 0.16 41 -10000 0 41
VEGFR2 homodimer/Frs2 -0.032 0.016 0.037 11 -10000 0 11
CAV1 0.007 0.014 -10000 0 0 400 400
CALM1 0.029 0.011 -10000 0 0 61 61
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.007 0.047 0.16 14 -0.061 1 15
endothelial cell proliferation 0.006 0.092 0.21 47 -0.29 6 53
mol:Ca2+ -0.027 0.052 0.16 32 -10000 0 32
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.004 0.047 0.18 13 -10000 0 13
RP11-342D11.1 -0.028 0.033 0.15 15 -10000 0 15
CDH5 0.031 0.009 -10000 0 0 38 38
VEGFA homodimer 0.013 0.043 -10000 0 -0.042 16 16
SHC1 0.03 0.01 -10000 0 0 55 55
SHC2 0.031 0.009 -10000 0 0 41 41
HRAS/GDP -0.049 0.023 -10000 0 -10000 0 0
SH2D2A 0.032 0.005 -10000 0 0 13 13
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.021 0.071 0.28 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.008 0.048 0.16 16 -10000 0 16
VEGFR1 homodimer 0.031 0.009 -10000 0 0 38 38
SHC/GRB2/SOS1 0.004 0.06 0.16 14 -10000 0 14
GRB10 -0.018 0.044 0.16 21 -10000 0 21
PTPN11 0.033 0.005 -10000 0 0 10 10
GRB2 0.032 0.007 -10000 0 0 22 22
PAK1 0.033 0.005 -10000 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.009 0.07 0.18 13 -10000 0 13
HRAS 0.032 0.007 -10000 0 0 24 24
VEGF/Rho/ROCK1/Integrin Complex 0.003 0.052 0.12 13 -0.27 7 20
HIF1A 0.031 0.009 -10000 0 0 40 40
FRS2 0.031 0.008 -10000 0 0 31 31
oxygen and reactive oxygen species metabolic process 0.004 0.046 0.17 13 -10000 0 13
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.005 -10000 0 0 13 13
Nck/Pak 0.045 0.014 -10000 0 -0.016 10 10
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.005 0.047 0.16 14 -0.061 3 17
mol:GDP -0.017 0.05 0.13 14 -10000 0 14
mol:NADP 0.017 0.069 0.28 8 -10000 0 8
eNOS/Hsp90 0.021 0.071 0.27 7 -10000 0 7
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:IP3 -0.027 0.053 0.16 32 -10000 0 32
HIF1A/ARNT 0.044 0.015 -10000 0 -0.016 2 2
SHB 0.03 0.01 -10000 0 0 46 46
VEGFA 0.015 0.017 -10000 0 0 282 282
VEGFC 0.032 0.007 -10000 0 0 27 27
FAK1/Vinculin -0.01 0.059 0.17 23 -0.25 4 27
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 0 19 19
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.01 0.059 0.18 14 -10000 0 14
PTPN6 0.031 0.009 -10000 0 0 36 36
EPAS1 0.035 0.011 -10000 0 -0.022 18 18
mol:L-citrulline 0.017 0.069 0.28 8 -10000 0 8
ITGAV 0.032 0.006 -10000 0 0 20 20
PIK3CA 0.031 0.009 -10000 0 0 41 41
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.01 0.057 0.18 14 -10000 0 14
VEGFR2 homodimer/VEGFA homodimer 0.009 0.05 0.17 15 -10000 0 15
VEGFR2/3 heterodimer -0.033 0.015 0.037 11 -10000 0 11
VEGFB 0.033 0.004 -10000 0 0 7 7
MAPK11 -0.028 0.058 0.16 30 -0.18 6 36
VEGFR2 homodimer -0.028 0.011 0.017 11 -10000 0 11
FLT1 0.031 0.009 -10000 0 0 38 38
NEDD4 0.032 0.008 -10000 0 0 28 28
MAPK3 -0.01 0.074 0.23 11 -10000 0 11
MAPK1 -0.012 0.071 0.23 10 -10000 0 10
VEGFA145/NRP2 0.013 0.032 -10000 0 -0.016 274 274
VEGFR1/2 heterodimer -0.032 0.016 0.037 8 -10000 0 8
KDR -0.028 0.011 0.017 11 -10000 0 11
VEGFA165/NRP1/VEGFR2 homodimer -0.036 0.037 0.16 16 -10000 0 16
SRC 0.029 0.011 -10000 0 0 65 65
platelet activating factor biosynthetic process -0.01 0.075 0.24 11 -10000 0 11
PI3K -0.03 0.059 0.13 22 -0.21 6 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.006 0.048 0.16 16 -0.061 1 17
FES -0.031 0.054 0.16 35 -10000 0 35
GAB1 -0.022 0.062 0.14 27 -0.19 29 56
VEGFR2 homodimer/VEGFA homodimer/Src 0.007 0.045 0.16 12 -10000 0 12
CTNNB1 0.032 0.006 -10000 0 0 15 15
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.005 -10000 0 0 14 14
eNOS/Caveolin-1 -0.003 0.044 0.28 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Yes 0.002 0.046 0.16 14 -0.061 1 15
PI3K/GAB1 -0.015 0.074 0.21 5 -0.25 15 20
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.014 0.071 0.18 12 -10000 0 12
PRKACA 0.031 0.009 -10000 0 0 36 36
VEGFR2/3 heterodimer/VEGFC homodimer 0.046 0.039 0.16 28 -0.058 3 31
HSP90AA1 0.031 0.009 -10000 0 0 37 37
CDC42 -0.031 0.054 0.16 34 -10000 0 34
actin cytoskeleton reorganization 0.008 0.048 0.16 16 -10000 0 16
PTK2 -0.004 0.061 0.15 35 -0.19 11 46
EDG1 -0.028 0.033 0.15 15 -10000 0 15
mol:DAG -0.027 0.053 0.16 32 -10000 0 32
CaM/Ca2+ -0.03 0.052 0.16 28 -10000 0 28
MAP2K3 -0.037 0.052 0.14 35 -10000 0 35
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.042 0.11 0.19 174 -10000 0 174
PLCG1 -0.028 0.053 0.16 32 -10000 0 32
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.008 0.054 0.18 9 -10000 0 9
IQGAP1 0.025 0.015 -10000 0 0 131 131
YES1 0.027 0.013 -10000 0 0 96 96
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.007 0.049 0.16 16 -10000 0 16
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.004 0.046 0.16 12 -10000 0 12
cell migration 0 0.076 0.2 20 -0.24 12 32
mol:PI-3-4-5-P3 -0.029 0.057 0.13 22 -0.2 6 28
FYN 0.03 0.01 -10000 0 0 53 53
VEGFB/NRP1 -0.028 0.054 0.16 37 -10000 0 37
mol:NO 0.017 0.069 0.28 8 -10000 0 8
PXN 0.033 0.004 -10000 0 0 7 7
HRAS/GTP -0.048 0.023 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.001 0.07 0.14 90 -10000 0 90
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.033 0.004 -10000 0 0 6 6
NOS3 0.017 0.072 0.28 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.007 0.048 0.16 16 -10000 0 16
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCA -0.033 0.051 0.14 33 -10000 0 33
PRKCB -0.025 0.049 0.15 34 -10000 0 34
VCL 0.024 0.015 -10000 0 0 149 149
VEGFA165/NRP1 -0.027 0.039 0.17 17 -10000 0 17
VEGFR1/2 heterodimer/VEGFA homodimer 0.006 0.048 0.16 14 -0.061 1 15
VEGFA165/NRP2 0.013 0.032 -10000 0 -0.016 274 274
MAPKKK cascade -0.007 0.076 0.22 19 -10000 0 19
NRP2 0.033 0.003 -10000 0 0 3 3
VEGFC homodimer 0.031 0.007 -10000 0 0 27 27
NCK1 0.031 0.008 -10000 0 0 28 28
ROCK1 0.032 0.006 -10000 0 0 17 17
FAK1/Paxillin -0.003 0.072 0.18 34 -0.26 3 37
MAP3K13 -0.031 0.053 0.16 32 -10000 0 32
PDPK1 -0.032 0.058 0.16 10 -0.19 6 16
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.012 -10000 0 0 74 74
HDAC2 0.031 0.009 -10000 0 0 40 40
GNB1/GNG2 0.025 0.022 -10000 0 -10000 0 0
forebrain development 0.027 0.059 0.21 15 -10000 0 15
GNAO1 0.003 0.009 -10000 0 0 465 465
SMO/beta Arrestin2 0.027 0.025 -10000 0 -10000 0 0
SMO 0.019 0.017 -10000 0 -10000 0 0
ARRB2 0.033 0.005 -10000 0 0 13 13
GLI3/SPOP 0.003 0.074 -10000 0 -0.24 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 0 20 20
GNAI2 0.032 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.051 0.032 -10000 0 -0.042 39 39
GNAI1 0.017 0.017 -10000 0 0 248 248
XPO1 0.033 0.004 -10000 0 -0.031 2 2
GLI1/Su(fu) 0 0.024 -10000 0 -0.22 1 1
SAP30 0.032 0.006 -10000 0 0 16 16
mol:GDP 0.019 0.017 -10000 0 -10000 0 0
MIM/GLI2A 0.033 0.008 -10000 0 -0.032 3 3
IFT88 0.031 0.008 -10000 0 0 34 34
GNAI3 0.029 0.011 -10000 0 -10000 0 0
GLI2 0.006 0.055 0.16 21 -0.22 10 31
GLI3 -0.011 0.066 0.16 2 -0.25 12 14
CSNK1D 0.033 0.005 -10000 0 0 11 11
CSNK1E 0.031 0.009 -10000 0 0 39 39
SAP18 0.031 0.009 -10000 0 0 36 36
embryonic digit morphogenesis 0.031 0.008 -10000 0 0 34 34
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.001 0.016 -10000 0 -0.15 4 4
SIN3B 0.031 0.009 -10000 0 0 40 40
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.009 0.045 0.15 1 -0.22 10 11
GLI2/Su(fu) -0.001 0.035 0.12 5 -0.2 7 12
FOXA2 0.031 0.056 -10000 0 -0.5 5 5
neural tube patterning 0.027 0.059 0.21 15 -10000 0 15
SPOP 0.033 0.004 -10000 0 0 8 8
Su(fu)/PIAS1 0.051 0.038 0.094 209 -0.069 7 216
GNB1 0.031 0.008 -10000 0 0 31 31
CSNK1G2 0.031 0.009 -10000 0 0 36 36
CSNK1G3 0.033 0.005 -10000 0 0 10 10
MTSS1 0.033 0.008 -10000 0 -0.032 3 3
embryonic limb morphogenesis 0.027 0.059 0.21 15 -10000 0 15
SUFU -0.004 0.004 -10000 0 -10000 0 0
LGALS3 0.027 0.013 -10000 0 0 103 103
catabolic process 0.019 0.083 0.21 12 -0.3 13 25
GLI3A/CBP 0.037 0.008 -10000 0 -0.018 8 8
KIF3A 0.03 0.01 -10000 0 0 55 55
GLI1 0.027 0.06 0.21 15 -10000 0 15
RAB23 0.033 0.004 -10000 0 0 9 9
CSNK1A1 0.033 0.004 -10000 0 0 9 9
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.033 0.002 -10000 0 0 2 2
Su(fu)/Galectin3 0.042 0.039 0.095 173 -0.069 3 176
GNAZ 0.027 0.013 -10000 0 0 94 94
RBBP4 0.026 0.013 -10000 0 0 105 105
CSNK1G1 0.032 0.005 -10000 0 0 13 13
PIAS1 0.033 0.005 -10000 0 0 11 11
PRKACA 0.031 0.009 -10000 0 0 36 36
GLI2/SPOP 0.024 0.058 0.19 5 -0.22 10 15
STK36 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.001 0.019 -10000 0 -0.17 6 6
PTCH1 0.023 0.066 0.3 10 -10000 0 10
MIM/GLI1 0.033 0.068 0.22 14 -10000 0 14
CREBBP 0.037 0.008 -10000 0 -0.018 8 8
Su(fu)/SIN3/HDAC complex 0.008 0.056 0.15 2 -0.19 26 28
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.011 0.028 1 -0.03 36 37
BUB1B 0.001 0.036 0.1 12 -0.12 17 29
PLK1 0.008 0.028 0.071 58 -0.085 5 63
PLK1S1 0.004 0.016 0.041 58 -0.044 5 63
KIF2A -0.002 0.036 0.26 5 -10000 0 5
regulation of mitotic centrosome separation 0.008 0.028 0.07 58 -0.084 5 63
GOLGA2 0.032 0.007 -10000 0 0 22 22
Hec1/SPC24 0.015 0.023 0.094 5 -0.074 4 9
WEE1 -0.002 0.063 -10000 0 -0.32 16 16
cytokinesis 0.004 0.032 0.15 3 -0.15 6 9
PP2A-alpha B56 0.058 0.081 -10000 0 -0.55 8 8
AURKA 0.01 0.02 0.092 3 -0.19 1 4
PICH/PLK1 -0.016 0.037 0.14 20 -0.11 1 21
CENPE -0.002 0.029 0.17 4 -10000 0 4
RhoA/GTP 0.024 0.005 -10000 0 0 19 19
positive regulation of microtubule depolymerization -0.001 0.036 0.26 5 -10000 0 5
PPP2CA 0.032 0.005 -10000 0 0 14 14
FZR1 0.031 0.008 -10000 0 0 35 35
TPX2 0.004 0.026 0.11 3 -0.2 1 4
PAK1 0.034 0.005 -10000 0 0 11 11
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 0 13 13
CLSPN 0.01 0.033 0.1 1 -0.23 7 8
GORASP1 0.032 0.006 -10000 0 0 15 15
metaphase 0 0.002 0.014 3 -0.011 6 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.016 0.041 58 -0.044 5 63
G2 phase of mitotic cell cycle 0 0.003 0.013 9 -10000 0 9
STAG2 0.031 0.008 -10000 0 0 31 31
GRASP65/GM130/RAB1/GTP 0.012 0.056 -10000 0 -0.45 7 7
spindle elongation 0.008 0.028 0.07 58 -0.084 5 63
ODF2 0.033 0.009 -10000 0 -0.03 2 2
BUB1 0.023 0.077 -10000 0 -0.57 8 8
TPT1 -0.005 0.057 -10000 0 -0.19 41 41
CDC25C 0.011 0.034 -10000 0 -0.24 7 7
CDC25B 0.028 0.013 -10000 0 -0.036 2 2
SGOL1 0.001 0.011 0.03 36 -0.028 1 37
RHOA 0.032 0.006 -10000 0 0 19 19
CCNB1/CDK1 0.009 0.035 -10000 0 -0.089 17 17
CDC14B -0.017 0.004 0.001 19 -10000 0 19
CDC20 0.014 0.016 -10000 0 0 297 297
PLK1/PBIP1 -0.003 0.011 0.057 2 -0.067 4 6
mitosis -0.003 0.003 0.017 4 -10000 0 4
FBXO5 -0.003 0.034 0.099 13 -0.095 25 38
CDC2 0 0.001 -10000 0 -0.01 3 3
NDC80 0.021 0.016 -10000 0 0 189 189
metaphase plate congression 0.01 0.037 -10000 0 -0.23 9 9
ERCC6L -0.02 0.019 -10000 0 -0.1 12 12
NLP/gamma Tubulin 0.005 0.018 0.064 14 -0.064 5 19
microtubule cytoskeleton organization -0.005 0.057 -10000 0 -0.19 41 41
G2/M transition DNA damage checkpoint 0 0.002 0.011 6 -10000 0 6
PPP1R12A 0.033 0.007 -10000 0 -0.032 1 1
interphase 0 0.002 0.011 6 -10000 0 6
PLK1/PRC1-2 0.023 0.033 0.12 3 -0.076 3 6
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.035 0.14 1 -0.098 4 5
RAB1A 0.033 0.004 -10000 0 0 6 6
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.027 0.069 69 -0.057 3 72
mitotic prometaphase -0.001 0.003 0.019 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process -0.034 0.094 0.14 6 -0.22 94 100
microtubule-based process 0.017 0.026 0.099 7 -0.079 4 11
Golgi organization 0.008 0.028 0.07 58 -0.084 5 63
Cohesin/SA2 0.024 0.024 0.088 9 -0.09 2 11
PPP1CB/MYPT1 0.048 0.011 -10000 0 -0.013 1 1
KIF20A 0.021 0.016 -10000 0 0 185 185
APC/C/CDC20 0.01 0.022 0.1 4 -0.079 4 8
PPP2R1A 0.029 0.011 -10000 0 0 59 59
chromosome segregation -0.003 0.011 0.056 2 -0.066 4 6
PRC1 0.019 0.017 -10000 0 0 224 224
ECT2 0.005 0.042 0.21 14 -10000 0 14
C13orf34 0.007 0.025 0.065 58 -0.062 5 63
NUDC 0.01 0.037 -10000 0 -0.23 9 9
regulation of attachment of spindle microtubules to kinetochore 0.001 0.036 0.1 12 -0.12 17 29
spindle assembly 0.005 0.024 0.08 17 -0.073 5 22
spindle stabilization 0.004 0.016 0.041 58 -0.044 5 63
APC/C/HCDH1 -0.018 0.019 0.035 1 -10000 0 1
MKLP2/PLK1 0.017 0.026 0.099 7 -0.079 4 11
CCNB1 0.015 0.017 -10000 0 -10000 0 0
PPP1CB 0.033 0.008 -10000 0 -0.031 6 6
BTRC 0.024 0.015 -10000 0 0 147 147
ROCK2 0.016 0.026 -10000 0 -0.29 1 1
TUBG1 0.009 0.023 -10000 0 -0.16 4 4
G2/M transition of mitotic cell cycle -0.013 0.017 -10000 0 -0.097 13 13
MLF1IP -0.003 0.006 0 435 -10000 0 435
INCENP 0.033 0.005 -10000 0 -0.032 1 1
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.033 0.005 -10000 0 0 11 11
mol:PIP3 -0.012 0.015 -10000 0 -10000 0 0
FRAP1 0.05 0.066 0.22 8 -0.46 2 10
AKT1 0.038 0.086 0.16 160 -0.16 3 163
INSR 0.031 0.008 -10000 0 0 34 34
Insulin Receptor/Insulin 0.04 0.014 -10000 0 -10000 0 0
mol:GTP 0.046 0.097 0.18 128 -10000 0 128
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.009 0.028 -10000 0 -0.17 2 2
TSC2 0.033 0.004 -10000 0 0 8 8
RHEB/GDP -0.009 0.046 0.11 45 -0.15 3 48
TSC1 0.032 0.008 -10000 0 0 32 32
Insulin Receptor/IRS1 0.03 0.01 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.026 0.058 0.14 6 -0.21 1 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.023 0.015 -10000 0 0 158 158
RPS6KB1 0.059 0.076 0.24 16 -0.29 1 17
MAP3K5 -0.016 0.059 0.18 3 -0.2 43 46
PIK3R1 0.031 0.01 -10000 0 0 47 47
apoptosis -0.017 0.058 0.18 3 -0.2 43 46
mol:LY294002 0 0 0.001 1 -0.001 2 3
EIF4B 0.051 0.077 0.24 22 -0.26 1 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.05 0.22 4 -0.19 1 5
eIF4E/eIF4G1/eIF4A1 0.009 0.047 -10000 0 -0.26 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.049 0.025 0.14 1 -10000 0 1
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.046 0.15 27 -10000 0 27
FKBP1A 0.029 0.011 -10000 0 0 66 66
RHEB/GTP 0.001 0.065 0.17 28 -10000 0 28
mol:Amino Acids 0 0 0.001 1 -0.001 2 3
FKBP12/Rapamycin 0.022 0.009 -10000 0 0 66 66
PDPK1 -0.013 0.033 0.15 14 -10000 0 14
EIF4E 0.032 0.005 -10000 0 0 12 12
ASK1/PP5C 0.013 0.17 -10000 0 -0.52 44 44
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.037 -10000 0 -0.24 4 4
TSC1/TSC2 0.05 0.1 0.2 128 -10000 0 128
tumor necrosis factor receptor activity 0 0 0.001 2 -0.001 1 3
RPS6 0.028 0.012 -10000 0 0 78 78
PPP5C 0.031 0.009 -10000 0 0 39 39
EIF4G1 0.032 0.007 -10000 0 0 27 27
IRS1 0.01 0.006 -10000 0 -10000 0 0
INS 0.032 0.007 -10000 0 0 21 21
PTEN 0.02 0.017 -10000 0 -0.001 194 194
PDK2 -0.013 0.031 0.15 13 -10000 0 13
EIF4EBP1 -0.011 0.094 -10000 0 -0.97 4 4
PIK3CA 0.031 0.009 -10000 0 0 41 41
PPP2R5D 0.039 0.063 0.22 9 -0.42 2 11
peptide biosynthetic process -0.03 0.024 0.18 6 -10000 0 6
RHEB 0.019 0.016 -10000 0 0 216 216
EIF4A1 0.032 0.007 -10000 0 0 26 26
mol:Rapamycin 0 0.001 0.004 29 -0.003 1 30
EEF2 -0.03 0.024 0.18 6 -10000 0 6
eIF4E/4E-BP1 -0.006 0.094 -10000 0 -0.91 4 4
Endothelins

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
AKT1 -0.026 0.019 -10000 0 -10000 0 0
PTK2B 0.033 0.005 -10000 0 0 13 13
mol:Ca2+ -0.081 0.18 0.36 1 -0.42 78 79
EDN1 0.007 0.028 -10000 0 -10000 0 0
EDN3 0.029 0.012 -10000 0 0 73 73
EDN2 0.032 0.005 -10000 0 0 14 14
HRAS/GDP -0.014 0.086 0.23 24 -0.29 15 39
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.006 0.036 -10000 0 -0.22 6 6
ADCY4 -0.024 0.011 -10000 0 -10000 0 0
ADCY5 -0.024 0.011 -10000 0 -10000 0 0
ADCY6 -0.028 0.031 0.18 8 -10000 0 8
ADCY7 -0.027 0.035 0.18 11 -10000 0 11
ADCY1 -0.018 0.028 0.18 5 -10000 0 5
ADCY2 -0.027 0.034 0.18 10 -10000 0 10
ADCY3 -0.024 0.011 -10000 0 -10000 0 0
ADCY8 -0.027 0.035 0.18 11 -10000 0 11
ADCY9 -0.027 0.035 0.18 11 -10000 0 11
arachidonic acid secretion -0.023 0.099 0.27 18 -0.33 16 34
ETB receptor/Endothelin-1/Gq/GTP 0.004 0.033 -10000 0 -0.21 6 6
GNAO1 0.003 0.009 -10000 0 0 465 465
HRAS 0.032 0.008 -10000 0 -0.001 25 25
ETA receptor/Endothelin-1/G12/GTP 0.014 0.031 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/Gs/GTP 0.023 0.036 -10000 0 -0.056 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.022 0.018 -10000 0 -10000 0 0
EDNRB 0.026 0.013 -10000 0 -0.031 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.025 0.019 -10000 0 -10000 0 0
CYSLTR1 -0.018 0.012 0.011 8 -10000 0 8
SLC9A1 -0.006 0.013 -10000 0 -0.069 12 12
mol:GDP -0.009 0.084 0.22 26 -0.3 15 41
SLC9A3 -0.057 0.19 -10000 0 -0.61 43 43
RAF1 -0.01 0.087 0.24 22 -0.31 14 36
JUN -0.091 0.19 0.35 1 -0.45 87 88
JAK2 -0.025 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.043 -10000 0 -0.26 8 8
ETA receptor/Endothelin-1 0.012 0.033 -10000 0 -0.042 2 2
PLCB1 0.028 0.012 -10000 0 -0.032 1 1
PLCB2 0.032 0.007 -10000 0 -0.037 1 1
ETA receptor/Endothelin-3 0.024 0.028 -10000 0 -10000 0 0
FOS -0.012 0.1 0.31 21 -0.38 10 31
Gai/GDP -0.46 0.17 -10000 0 -0.52 421 421
CRK 0.033 0.005 -10000 0 0 10 10
mol:Ca ++ -0.009 0.038 -10000 0 -0.23 8 8
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.002 0.05 -10000 0 -0.26 13 13
GNAQ 0.032 0.008 -10000 0 -0.035 2 2
GNAZ 0.027 0.013 -10000 0 0 94 94
GNAL 0.032 0.006 -10000 0 0 19 19
Gs family/GDP -0.013 0.081 0.21 25 -0.29 13 38
ETA receptor/Endothelin-1/Gq/GTP 0.005 0.023 -10000 0 -0.23 2 2
MAPK14 -0.006 0.041 0.12 10 -0.22 7 17
TRPC6 -0.084 0.18 0.36 1 -0.44 77 78
GNAI2 0.032 0.006 -10000 0 0 17 17
GNAI3 0.029 0.011 -10000 0 0 67 67
GNAI1 0.017 0.017 -10000 0 0 248 248
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.003 0.043 -10000 0 -0.23 9 9
ETB receptor/Endothelin-2 0.037 0.023 -10000 0 -0.016 36 36
ETB receptor/Endothelin-3 0.033 0.024 -10000 0 -0.016 32 32
ETB receptor/Endothelin-1 0.012 0.035 -10000 0 -0.036 1 1
MAPK3 -0.008 0.1 0.32 22 -0.36 10 32
MAPK1 -0.015 0.11 0.31 21 -0.4 11 32
Rac1/GDP -0.015 0.059 0.21 10 -0.26 11 21
cAMP biosynthetic process 0.011 0.042 0.22 6 -10000 0 6
MAPK8 -0.1 0.22 0.38 1 -0.49 107 108
SRC 0.029 0.011 -10000 0 0 65 65
ETB receptor/Endothelin-1/Gi/GTP -0.001 0.019 -10000 0 -0.15 4 4
p130Cas/CRK/Src/PYK2 -0.007 0.098 0.29 22 -0.32 11 33
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.014 0.06 0.22 11 -0.26 11 22
COL1A2 -0.013 0.02 0.12 1 -10000 0 1
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.027 0.028 -10000 0 -10000 0 0
mol:DAG 0.002 0.043 -10000 0 -0.26 8 8
MAP2K2 -0.008 0.11 0.32 35 -0.32 13 48
MAP2K1 -0.018 0.086 0.26 13 -0.33 13 26
EDNRA 0.015 0.021 -10000 0 -10000 0 0
positive regulation of muscle contraction 0.042 0.1 0.18 171 -10000 0 171
Gq family/GDP 0.024 0.074 0.26 4 -0.26 13 17
HRAS/GTP -0.003 0.083 0.22 25 -0.29 17 42
PRKCH -0.009 0.046 0.2 1 -0.26 11 12
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCA -0.01 0.054 0.18 4 -0.26 15 19
PRKCB -0.001 0.05 -10000 0 -0.26 13 13
PRKCE -0.012 0.051 -10000 0 -0.26 15 15
PRKCD -0.011 0.051 0.18 2 -0.26 14 16
PRKCG -0.009 0.054 0.2 4 -0.26 14 18
regulation of vascular smooth muscle contraction -0.013 0.12 0.34 21 -0.47 7 28
PRKCQ -0.007 0.038 0.19 3 -0.26 7 10
PLA2G4A -0.025 0.1 0.28 17 -0.35 16 33
GNA14 0.032 0.008 -10000 0 -0.035 2 2
GNA15 0.03 0.01 -10000 0 -0.032 2 2
GNA12 0.02 0.016 -10000 0 0 203 203
GNA11 0.031 0.01 -10000 0 -0.032 2 2
Rac1/GTP 0.013 0.031 -10000 0 -10000 0 0
MMP1 -0.015 0.021 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.018 0.038 0.17 10 -10000 0 10
DAPP1 0.01 0.069 0.18 10 -0.23 14 24
Src family/SYK family/BLNK-LAT/BTK-ITK 0 0.073 0.28 4 -0.29 15 19
mol:DAG 0.007 0.068 0.17 45 -0.16 2 47
HRAS 0.036 0.013 0.08 2 -0.034 4 6
RAP1A 0.036 0.013 -10000 0 -0.034 10 10
ARF5/GDP 0.013 0.054 0.16 2 -0.23 14 16
PLCG2 0.032 0.007 -10000 0 0 26 26
PLCG1 0.029 0.011 -10000 0 0 66 66
ARF5 0.019 0.016 -10000 0 0 216 216
mol:GTP -0.02 0.046 0.17 17 -10000 0 17
ARF1/GTP -0.013 0.033 0.14 14 -0.12 1 15
RHOA 0.032 0.006 -10000 0 0 19 19
YES1 0.027 0.013 -10000 0 0 96 96
RAP1A/GTP -0.021 0.037 0.15 14 -10000 0 14
ADAP1 -0.02 0.043 0.16 17 -10000 0 17
ARAP3 -0.02 0.045 0.17 17 -10000 0 17
INPPL1 0.033 0.005 -10000 0 0 10 10
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.032 0.007 -10000 0 0 22 22
ARHGEF7 0.031 0.008 -10000 0 0 33 33
ARF1 0.032 0.006 -10000 0 0 19 19
NRAS 0.027 0.02 -10000 0 -0.034 8 8
FYN 0.03 0.01 -10000 0 0 53 53
ARF6 0.031 0.008 -10000 0 0 31 31
FGR 0.031 0.008 -10000 0 0 32 32
mol:Ca2+ 0.007 0.052 0.15 37 -10000 0 37
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.031 0.009 -10000 0 0 37 37
ZAP70 0.033 0.002 -10000 0 0 2 2
mol:IP3 -0.003 0.051 0.21 11 -10000 0 11
LYN 0.029 0.011 -10000 0 0 69 69
ARF1/GDP 0.029 0.07 0.22 2 -0.22 23 25
RhoA/GDP 0.019 0.084 0.16 53 -10000 0 53
PDK1/Src/Hsp90 0.051 0.034 -10000 0 -0.047 32 32
BLNK 0.02 0.016 -10000 0 0 209 209
actin cytoskeleton reorganization 0.035 0.086 0.2 50 -0.22 3 53
SRC 0.029 0.011 -10000 0 0 65 65
PLEKHA2 -0.025 0.005 0 20 -10000 0 20
RAC1 0.02 0.016 -10000 0 0 204 204
PTEN 0.02 0.022 -10000 0 -0.059 4 4
HSP90AA1 0.031 0.009 -10000 0 0 37 37
ARF6/GTP -0.024 0.048 0.18 16 -10000 0 16
RhoA/GTP -0.023 0.049 0.18 18 -10000 0 18
Src family/SYK family/BLNK-LAT -0.02 0.069 -10000 0 -0.23 35 35
BLK 0.032 0.006 -10000 0 0 15 15
PDPK1 0.033 0.004 -10000 0 0 7 7
CYTH1 -0.02 0.043 0.16 17 -10000 0 17
HCK 0.023 0.015 -10000 0 0 152 152
CYTH3 -0.02 0.043 0.16 17 -10000 0 17
CYTH2 -0.02 0.043 0.16 17 -10000 0 17
KRAS 0.034 0.015 0.081 1 -0.034 9 10
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.008 0.033 0.21 3 -0.18 10 13
SGK1 -0.002 0.034 0.26 2 -0.18 10 12
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.068 0.16 9 -0.22 23 32
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.03 0.01 -10000 0 0 53 53
ARF6/GDP -0.018 0.05 0.18 16 -10000 0 16
mol:PI-3-4-5-P3 -0.021 0.043 0.16 16 -10000 0 16
ARAP3/RAP1A/GTP -0.021 0.037 0.15 14 -10000 0 14
VAV1 0.031 0.008 -10000 0 0 33 33
mol:PI-3-4-P2 -0.016 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.071 0.085 0.2 119 -10000 0 119
PLEKHA1 -0.016 0.013 0 201 -10000 0 201
Rac1/GDP 0.015 0.056 0.26 1 -0.22 15 16
LAT 0.033 0.004 -10000 0 0 7 7
Rac1/GTP 0.025 0.064 0.16 3 -0.26 15 18
ITK -0.025 0.044 0.16 15 -10000 0 15
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.006 0.066 0.25 13 -0.19 4 17
LCK 0.032 0.006 -10000 0 0 16 16
BTK -0.025 0.046 0.16 17 -10000 0 17
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.036 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.021 0.008 -10000 0 -10000 0 0
mol:DAG -0.033 0.024 0.17 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.026 0.008 0 16 -0.056 1 17
CaM/Ca2+ -0.038 0.027 0.18 3 -10000 0 3
HIF1A 0.035 0.01 -10000 0 0 40 40
GAB1 0.032 0.005 -10000 0 0 12 12
AKT1 -0.038 0.044 0.17 6 -0.19 3 9
PLCG1 -0.033 0.024 0.18 3 -10000 0 3
NOS3 0.001 0.057 0.22 3 -0.23 10 13
CBL 0.033 0.005 -10000 0 0 11 11
mol:NO 0.005 0.062 0.21 4 -0.22 10 14
FLT1 -0.026 0.01 0 67 -10000 0 67
PGF 0.029 0.011 -10000 0 0 61 61
VEGFR1 homodimer/NRP2/VEGFR121 0 0.042 0.16 2 -0.067 1 3
CALM1 0.029 0.011 -10000 0 0 61 61
PIK3CA 0.031 0.009 -10000 0 0 41 41
eNOS/Hsp90 0.008 0.088 0.2 17 -0.23 20 37
endothelial cell proliferation -0.016 0.057 0.14 7 -0.14 23 30
mol:Ca2+ -0.033 0.024 0.17 3 -10000 0 3
MAPK3 -0.048 0.026 0.13 3 -10000 0 3
MAPK1 -0.045 0.028 0.13 3 -10000 0 3
PIK3R1 0.03 0.01 -10000 0 0 47 47
PLGF homodimer 0.029 0.011 -10000 0 0 61 61
PRKACA 0.031 0.009 -10000 0 0 36 36
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.007 0.014 -10000 0 0 400 400
VEGFA homodimer 0.015 0.017 -10000 0 0 282 282
VEGFR1 homodimer/VEGFA homodimer -0.027 0.011 0 49 -10000 0 49
platelet activating factor biosynthetic process -0.039 0.058 0.11 58 -10000 0 58
PI3K 0.04 0.048 0.17 1 -0.078 1 2
PRKCA -0.042 0.025 0.15 3 -10000 0 3
PRKCB -0.031 0.022 0.16 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer -0.033 0.011 0 46 -10000 0 46
VEGFA 0.015 0.017 -10000 0 0 282 282
VEGFB 0.033 0.004 -10000 0 0 7 7
mol:IP3 -0.033 0.024 0.17 3 -10000 0 3
RASA1 -0.04 0.022 0.18 4 -10000 0 4
NRP2 0.033 0.003 -10000 0 0 3 3
VEGFR1 homodimer -0.026 0.01 0 67 -10000 0 67
VEGFB homodimer 0.033 0.004 -10000 0 0 7 7
NCK1 0.031 0.008 -10000 0 0 28 28
eNOS/Caveolin-1 -0.016 0.048 0.21 1 -0.23 10 11
PTPN11 0.033 0.005 -10000 0 0 10 10
mol:PI-3-4-5-P3 0.039 0.047 0.17 1 -0.078 1 2
mol:L-citrulline 0.005 0.062 0.21 4 -0.22 10 14
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.003 0.053 0.18 2 -0.078 1 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.042 0.16 2 -0.063 5 7
CD2AP 0.029 0.011 -10000 0 0 58 58
PI3K/GAB1 0.048 0.057 0.18 1 -10000 0 1
PDPK1 -0.044 0.047 0.16 22 -10000 0 22
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.001 0.042 0.16 1 -0.063 3 4
mol:NADP 0.005 0.062 0.21 4 -0.22 10 14
HSP90AA1 0.031 0.009 -10000 0 0 37 37
ubiquitin-dependent protein catabolic process -0.003 0.052 0.17 2 -0.078 1 3
VEGFR1 homodimer/NRP2 -0.037 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.028 0.012 0 84 -10000 0 84
BAD/BCL-XL/YWHAZ 0.036 0.022 -10000 0 -0.053 8 8
CDKN1B -0.011 0.094 0.2 13 -0.33 34 47
CDKN1A -0.013 0.087 0.24 1 -0.33 33 34
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.008 -10000 0 0 31 31
FOXO3 -0.013 0.088 0.19 4 -0.33 33 37
AKT1 -0.005 0.092 -10000 0 -0.34 33 33
BAD 0.033 0.004 -10000 0 0 8 8
AKT3 0.009 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.015 0.088 -10000 0 -0.33 34 34
AKT1/ASK1 0.012 0.095 0.22 2 -0.32 36 38
BAD/YWHAZ 0.059 0.025 -10000 0 -0.046 8 8
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.032 0.005 -10000 0 0 13 13
JNK cascade -0.011 0.092 0.31 36 -0.21 2 38
TSC1 -0.011 0.094 0.23 12 -0.33 33 45
YWHAZ 0.032 0.006 -10000 0 0 19 19
AKT1/RAF1 0.015 0.098 0.23 2 -0.32 36 38
EP300 0.031 0.009 -10000 0 0 41 41
mol:GDP -0.005 0.091 -10000 0 -0.34 33 33
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.015 0.092 0.26 3 -0.33 36 39
YWHAQ 0.033 0.004 -10000 0 0 7 7
TBC1D4 -0.011 0.019 0.23 3 -10000 0 3
MAP3K5 0.03 0.01 -10000 0 0 46 46
MAPKAP1 0.032 0.007 -10000 0 0 24 24
negative regulation of cell cycle 0.017 0.061 0.21 23 -0.14 1 24
YWHAH 0.015 0.017 -10000 0 0 278 278
AKT1S1 -0.005 0.088 -10000 0 -0.33 33 33
CASP9 -0.014 0.089 0.19 3 -0.33 34 37
YWHAB 0.029 0.011 -10000 0 0 67 67
p27Kip1/KPNA1 0.009 0.099 0.22 16 -0.32 35 51
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.051 0.034 -10000 0 -0.047 32 32
YWHAE 0.032 0.005 -10000 0 0 12 12
SRC 0.029 0.011 -10000 0 0 65 65
AKT2/p21CIP1 -0.016 0.081 0.23 1 -0.3 35 36
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.002 0.027 -10000 0 -10000 0 0
CHUK -0.02 0.084 -10000 0 -0.34 32 32
BAD/BCL-XL 0.003 0.09 -10000 0 -0.33 32 32
mTORC2 0.02 0.006 -10000 0 -0.018 10 10
AKT2 0.009 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.034 0.087 0.18 1 -0.3 34 35
PDPK1 0.033 0.004 -10000 0 0 7 7
MDM2 0.002 0.1 0.19 44 -0.33 32 76
MAPKKK cascade -0.015 0.096 0.32 36 -0.23 2 38
MDM2/Cbp/p300 0.033 0.11 0.26 7 -0.32 33 40
TSC1/TSC2 -0.019 0.096 0.22 16 -0.33 35 51
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.11 0.25 7 -0.31 33 40
glucose import -0.021 0.024 0.19 4 -0.13 7 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.059 -10000 0 -0.18 35 35
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.021 0.024 0.19 4 -0.13 7 11
GSK3A -0.008 0.1 0.23 21 -0.33 34 55
FOXO1 -0.016 0.087 -10000 0 -0.33 34 34
GSK3B -0.013 0.088 0.2 5 -0.33 33 38
SFN 0.03 0.01 -10000 0 0 46 46
G1/S transition of mitotic cell cycle -0.014 0.099 0.21 27 -0.33 33 60
p27Kip1/14-3-3 family 0.004 0.037 0.14 1 -0.29 5 6
PRKACA 0.031 0.009 -10000 0 0 36 36
KPNA1 0.032 0.006 -10000 0 0 18 18
HSP90AA1 0.031 0.009 -10000 0 0 37 37
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.019 0.016 -10000 0 0 216 216
CREBBP 0.033 0.004 -10000 0 0 7 7
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.031 -10000 0 -0.016 248 248
alphaV beta3 Integrin 0.061 0.024 -10000 0 -0.046 10 10
PTK2 -0.006 0.071 0.26 14 -0.28 5 19
IGF1R 0.033 0.005 -10000 0 0 11 11
PI4KB 0.032 0.006 -10000 0 0 16 16
MFGE8 0.032 0.005 -10000 0 0 12 12
SRC 0.029 0.011 -10000 0 0 65 65
CDKN1B 0.009 0.053 -10000 0 -0.27 17 17
VEGFA 0.015 0.017 -10000 0 0 282 282
ILK 0.009 0.053 -10000 0 -0.27 17 17
ROCK1 0.032 0.006 -10000 0 0 17 17
AKT1 -0.016 0.045 0.19 3 -0.26 14 17
PTK2B -0.028 0.06 0.17 42 -10000 0 42
alphaV/beta3 Integrin/JAM-A 0.06 0.03 0.17 9 -10000 0 9
CBL 0.033 0.005 -10000 0 0 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.061 0.024 -10000 0 -0.046 9 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.08 0.025 -10000 0 -0.053 11 11
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.048 -10000 0 -0.29 6 6
alphaV/beta3 Integrin/Syndecan-1 0.054 0.032 -10000 0 -0.046 8 8
PI4KA 0.012 0.016 -10000 0 0 329 329
IGF-1R heterotetramer/IGF1/IRS1 0.043 0.06 -10000 0 -10000 0 0
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
alphaV/beta3 Integrin/Osteopontin 0.031 0.045 -10000 0 -0.046 9 9
RPS6KB1 -0.065 0.041 0.48 1 -10000 0 1
TLN1 0.027 0.013 -10000 0 0 102 102
MAPK3 -0.014 0.042 0.16 5 -0.3 8 13
GPR124 0.033 0.005 -10000 0 0 11 11
MAPK1 -0.014 0.04 0.16 3 -0.3 7 10
PXN 0.033 0.004 -10000 0 0 7 7
PIK3R1 0.03 0.01 -10000 0 0 47 47
alphaV/beta3 Integrin/Tumstatin 0.063 0.02 -10000 0 -0.046 5 5
cell adhesion 0.044 0.031 -10000 0 -0.083 20 20
ANGPTL3 0.033 0.005 -10000 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/Src 0.014 0.042 -10000 0 -0.046 6 6
IGF-1R heterotetramer 0.033 0.005 -10000 0 0 11 11
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
TGFBR2 0.032 0.006 -10000 0 0 18 18
ITGB3 0.033 0.004 -10000 0 0 6 6
IGF1 0.032 0.005 -10000 0 0 12 12
RAC1 0.02 0.016 -10000 0 0 204 204
regulation of cell-matrix adhesion 0.06 0.023 -10000 0 -0.047 8 8
apoptosis 0.032 0.006 -10000 0 0 20 20
CD47 0.032 0.006 -10000 0 0 16 16
alphaV/beta3 Integrin/CD47 0.06 0.025 -10000 0 -0.046 10 10
VCL 0.024 0.015 -10000 0 0 149 149
alphaV/beta3 Integrin/Del1 0.062 0.023 -10000 0 -0.046 9 9
CSF1 0.033 0.004 -10000 0 0 9 9
PIK3C2A -0.008 0.012 -10000 0 -0.26 1 1
PI4 Kinase/Pyk2 -0.026 0.039 0.11 10 -10000 0 10
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.034 -10000 0 -0.053 8 8
FAK1/Vinculin -0.012 0.059 0.25 10 -0.24 5 15
alphaV beta3/Integrin/ppsTEM5 0.061 0.024 -10000 0 -0.047 8 8
RHOA 0.032 0.006 -10000 0 0 19 19
VTN 0.033 0.004 -10000 0 0 8 8
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.033 0.004 -10000 0 0 9 9
F11R -0.031 0.007 0 16 -10000 0 16
alphaV/beta3 Integrin/Lactadherin 0.061 0.025 -10000 0 -0.046 12 12
alphaV/beta3 Integrin/TGFBR2 0.06 0.025 -10000 0 -0.046 9 9
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.022 -10000 0 -0.041 10 10
HSP90AA1 0.031 0.009 -10000 0 0 37 37
alphaV/beta3 Integrin/Talin 0.044 0.038 -10000 0 -0.041 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.027 0.013 -10000 0 0 100 100
alphaV/beta3 Integrin/Pyk2 0.011 0.066 0.18 35 -10000 0 35
SDC1 0.03 0.01 -10000 0 0 55 55
VAV3 -0.038 0.025 0.17 7 -10000 0 7
PTPN11 0.033 0.005 -10000 0 0 10 10
IRS1 0.033 0.003 -10000 0 0 5 5
FAK1/Paxillin -0.006 0.071 0.25 15 -0.24 5 20
cell migration -0.017 0.055 0.24 10 -0.23 5 15
ITGAV 0.032 0.006 -10000 0 0 20 20
PI3K 0.062 0.046 0.17 4 -10000 0 4
SPP1 0.021 0.016 -10000 0 0 189 189
KDR 0.03 0.01 -10000 0 0 53 53
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.032 0.006 -10000 0 0 20 20
COL4A3 0.033 0.001 -10000 0 0 1 1
angiogenesis -0.011 0.048 0.23 2 -0.33 7 9
Rac1/GTP -0.026 0.032 0.17 6 -10000 0 6
EDIL3 0.033 0.005 -10000 0 0 10 10
cell proliferation 0.059 0.025 -10000 0 -0.046 9 9
Signaling events mediated by PTP1B

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
PDGFRB 0.032 0.005 -10000 0 0 12 12
Jak2/Leptin Receptor 0.009 0.13 -10000 0 -0.3 61 61
PTP1B/AKT1 0.04 0.064 0.18 8 -0.25 10 18
FYN 0.03 0.01 -10000 0 0 53 53
p210 bcr-abl/PTP1B 0.027 0.065 0.16 15 -0.26 9 24
EGFR 0.011 0.017 -10000 0 -0.035 8 8
EGF/EGFR 0.008 0.041 0.17 1 -0.21 9 10
CSF1 0.033 0.004 -10000 0 0 9 9
AKT1 0.029 0.015 -10000 0 -0.032 19 19
INSR 0.026 0.02 -10000 0 -0.032 47 47
PTP1B/N-cadherin 0.039 0.065 0.18 6 -0.25 10 16
Insulin Receptor/Insulin 0.05 0.069 0.2 2 -0.21 14 16
HCK 0.023 0.015 -10000 0 0 152 152
CRK 0.033 0.005 -10000 0 0 10 10
TYK2 0.031 0.094 0.27 43 -0.26 9 52
EGF 0.035 0.009 -10000 0 -0.035 6 6
YES1 0.027 0.013 -10000 0 0 96 96
CAV1 0.068 0.095 0.21 87 -0.26 9 96
TXN 0.033 0.01 -10000 0 -0.032 4 4
PTP1B/IRS1/GRB2 0.055 0.071 0.2 5 -0.26 9 14
cell migration -0.027 0.065 0.26 9 -0.16 15 24
STAT3 0.032 0.007 -10000 0 -0.002 19 19
PRLR 0.034 0.005 -10000 0 -10000 0 0
ITGA2B 0.033 0.003 -10000 0 0 5 5
CSF1R 0.03 0.01 -10000 0 0 50 50
Prolactin Receptor/Prolactin 0.049 0.012 -10000 0 -10000 0 0
FGR 0.031 0.008 -10000 0 0 32 32
PTP1B/p130 Cas 0.023 0.059 0.13 24 -0.23 11 35
Crk/p130 Cas 0.038 0.064 0.17 7 -0.24 10 17
DOK1 0.02 0.068 0.17 25 -0.26 11 36
JAK2 -0.004 0.13 0.2 1 -0.31 62 63
Jak2/Leptin Receptor/Leptin 0.014 0.078 -10000 0 -0.25 17 17
PIK3R1 0.03 0.01 -10000 0 0 47 47
PTPN1 0.027 0.065 0.15 23 -0.25 10 33
LYN 0.029 0.011 -10000 0 0 69 69
CDH2 0.031 0.008 -10000 0 0 33 33
SRC 0.032 0.065 -10000 0 -0.4 9 9
ITGB3 0.033 0.004 -10000 0 0 6 6
CAT1/PTP1B 0.06 0.11 0.25 72 -0.3 11 83
CAPN1 0.032 0.008 -10000 0 -0.012 14 14
CSK 0.032 0.005 -10000 0 0 12 12
PI3K 0.049 0.074 0.2 1 -0.23 11 12
mol:H2O2 0.003 0.004 0.034 1 -10000 0 1
STAT3 (dimer) 0.013 0.072 -10000 0 -0.23 17 17
negative regulation of transcription -0.004 0.12 0.2 1 -0.31 62 63
FCGR2A 0.016 0.017 -10000 0 0 262 262
FER 0.034 0.007 -10000 0 -0.032 3 3
alphaIIb/beta3 Integrin 0.049 0.006 -10000 0 -10000 0 0
BLK 0.032 0.006 -10000 0 0 15 15
Insulin Receptor/Insulin/Shc 0.05 0.036 -10000 0 -0.051 18 18
RHOA 0.031 0.01 -10000 0 -0.009 26 26
LEPR 0.032 0.006 -10000 0 0 16 16
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.007 -10000 0 0 22 22
mol:NADPH 0.002 0.002 -10000 0 -10000 0 0
TRPV6 0.045 0.089 0.2 52 -0.26 13 65
PRL 0.034 0.005 -10000 0 -10000 0 0
SOCS3 0.018 0.016 -10000 0 -10000 0 0
SPRY2 0.033 0.012 -10000 0 -0.001 52 52
Insulin Receptor/Insulin/IRS1 0.058 0.028 -10000 0 -0.051 19 19
CSF1/CSF1R 0.052 0.072 0.2 5 -0.25 10 15
Ras protein signal transduction -0.012 0.1 0.53 17 -10000 0 17
IRS1 0.033 0.003 -10000 0 0 5 5
INS 0.029 0.016 -10000 0 -0.031 29 29
LEP 0.019 0.017 -10000 0 0 218 218
STAT5B 0.019 0.081 0.18 6 -0.26 21 27
STAT5A 0.019 0.081 0.18 6 -0.26 21 27
GRB2 0.032 0.007 -10000 0 0 22 22
PDGFB-D/PDGFRB 0.041 0.066 0.18 7 -0.25 10 17
CSN2 -0.005 0.035 -10000 0 -0.29 5 5
PIK3CA 0.031 0.009 -10000 0 0 41 41
LAT 0.021 0.044 -10000 0 -0.32 3 3
YBX1 0.038 0.009 -10000 0 0 21 21
LCK 0.032 0.006 -10000 0 0 16 16
SHC1 0.03 0.01 -10000 0 0 55 55
NOX4 0.031 0.014 -10000 0 0 80 80
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.005 -10000 0 0 12 12
alphaV beta3 Integrin 0.046 0.013 -10000 0 -0.016 15 15
PTK2 0.005 0.089 0.22 1 -0.25 49 50
positive regulation of JNK cascade 0.013 0.09 -10000 0 -0.25 43 43
CDC42/GDP 0.024 0.12 0.35 2 -0.33 44 46
Rac1/GDP 0.01 0.094 0.3 1 -0.31 22 23
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 0 12 12
CTNNB1 0.032 0.006 -10000 0 0 15 15
CDC42/GTP 0.02 0.11 0.32 1 -0.3 43 44
nectin-3/I-afadin 0.044 0.016 -10000 0 -0.016 1 1
RAPGEF1 -0.006 0.12 0.26 4 -0.35 44 48
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.12 -10000 0 -0.38 45 45
PDGFB-D/PDGFRB 0.032 0.005 -10000 0 0 12 12
TLN1 -0.012 0.047 0.17 27 -0.18 2 29
Rap1/GTP -0.008 0.083 -10000 0 -0.26 45 45
IQGAP1 0.025 0.015 -10000 0 0 131 131
Rap1/GTP/I-afadin 0.035 0.022 -10000 0 -0.029 48 48
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.016 -10000 0 -0.016 1 1
PVR 0.031 0.009 -10000 0 0 39 39
Necl-5(dimer) 0.031 0.009 -10000 0 0 39 39
mol:GDP 0.007 0.14 0.33 3 -0.39 45 48
MLLT4 0.03 0.009 -10000 0 0 45 45
PIK3CA 0.031 0.009 -10000 0 0 41 41
PI3K 0.07 0.054 -10000 0 -0.065 5 5
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.005 0.077 -10000 0 -0.26 22 22
PVRL1 0.033 0.005 -10000 0 0 10 10
PVRL3 0.032 0.006 -10000 0 0 18 18
PVRL2 0.031 0.009 -10000 0 0 37 37
PIK3R1 0.03 0.01 -10000 0 0 47 47
CDH1 0.032 0.006 -10000 0 0 19 19
CLDN1 0.031 0.008 -10000 0 0 32 32
JAM-A/CLDN1 0.063 0.046 -10000 0 -0.053 51 51
SRC -0.003 0.13 -10000 0 -0.4 45 45
ITGB3 0.033 0.004 -10000 0 0 6 6
nectin-1(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -10000 0 0
FARP2 0.015 0.14 0.37 1 -0.4 35 36
RAC1 0.02 0.016 -10000 0 0 204 204
CTNNA1 0.033 0.005 -10000 0 0 10 10
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.051 0.037 -10000 0 -0.047 51 51
nectin-1/I-afadin 0.044 0.015 -10000 0 -10000 0 0
nectin-2/I-afadin 0.042 0.017 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.017 0.024 -10000 0 -0.013 84 84
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.053 0.036 -10000 0 -0.046 54 54
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.025 -10000 0 -0.013 116 116
F11R 0.031 0.009 -10000 0 0 40 40
positive regulation of filopodium formation 0.013 0.09 -10000 0 -0.25 43 43
alphaV/beta3 Integrin/Talin -0.021 0.078 0.2 43 -0.19 6 49
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.017 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.042 0.017 -10000 0 -10000 0 0
PIP5K1C -0.02 0.022 -10000 0 -0.084 40 40
VAV2 0.008 0.15 0.32 2 -0.43 34 36
RAP1/GDP 0.014 0.11 0.31 2 -0.31 44 46
ITGAV 0.032 0.006 -10000 0 0 20 20
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.051 0.037 -10000 0 -0.047 51 51
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.016 -10000 0 -0.016 1 1
Rac1/GTP 0.008 0.093 0.26 1 -0.32 21 22
PTPRM 0.001 0.021 -10000 0 -0.067 42 42
E-cadherin/beta catenin/alpha catenin 0.071 0.059 -10000 0 -0.079 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.032 0.006 -10000 0 0 19 19
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.019 -10000 0 -0.11 10 10
TRAF2/ASK1 0.039 0.016 -10000 0 -0.04 4 4
ATM 0.031 0.008 -10000 0 0 35 35
MAP2K3 0.024 0.065 0.17 6 -0.26 12 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.018 0.059 0.18 8 -0.21 13 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.031 0.008 -10000 0 0 30 30
TXN 0.005 0.001 -10000 0 0 22 22
CALM1 0.029 0.011 -10000 0 0 61 61
GADD45A 0.03 0.01 -10000 0 0 51 51
GADD45B 0.03 0.009 -10000 0 0 45 45
MAP3K1 0.033 0.005 -10000 0 0 11 11
MAP3K6 0.032 0.006 -10000 0 0 16 16
MAP3K7 0.031 0.008 -10000 0 0 29 29
MAP3K4 0.031 0.009 -10000 0 0 42 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.043 0.016 -10000 0 -0.016 2 2
TAK1/TAB family 0.009 0.024 0.075 45 -0.075 10 55
RAC1/OSM/MEKK3 0.025 0.021 -10000 0 -0.029 3 3
TRAF2 0.032 0.006 -10000 0 0 20 20
RAC1/OSM/MEKK3/MKK3 0.015 0.049 -10000 0 -0.23 12 12
TRAF6 0.005 0.001 -10000 0 0 16 16
RAC1 0.02 0.016 -10000 0 0 204 204
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.002 0.008 -10000 0 0 474 474
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.011 -10000 0 -10000 0 0
MAPK11 0.03 0.01 -10000 0 0 53 53
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.004 0.016 -10000 0 -0.041 2 2
OSM/MEKK3 0.024 0.003 -10000 0 0 6 6
TAOK1 0.004 0.001 -10000 0 0 35 35
TAOK2 0.008 0.004 -10000 0 -0.009 25 25
TAOK3 0.008 0.004 -10000 0 -0.009 25 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.033 0.003 -10000 0 0 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.01 -10000 0 0 46 46
MAP3K10 0.031 0.008 -10000 0 0 33 33
MAP3K3 0.033 0.004 -10000 0 0 6 6
TRX/ASK1 0.026 0.021 0.095 12 -0.12 6 18
GADD45/MTK1/MTK1 0.057 0.04 -10000 0 -0.049 34 34
a4b1 and a4b7 Integrin 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
ITGB1 0.025 0.015 -9999 0 0 131 131
ITGB7 0.032 0.006 -9999 0 0 17 17
ITGA4 0.033 0.004 -9999 0 0 8 8
alpha4/beta7 Integrin 0.047 0.01 -9999 0 -0.016 2 2
alpha4/beta1 Integrin 0.036 0.022 -9999 0 -0.016 4 4
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.047 0.011 -10000 0 -10000 0 0
Necdin/E2F1 0.027 0.025 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.071 0.026 -10000 0 -0.049 12 12
NGF (dimer)/p75(NTR)/BEX1 0.029 0.022 -10000 0 -0.013 16 16
NT-4/5 (dimer)/p75(NTR) 0.023 0.006 -10000 0 0 28 28
IKBKB 0.033 0.004 -10000 0 0 7 7
AKT1 -0.022 0.055 0.19 27 -10000 0 27
IKBKG 0.033 0.003 -10000 0 0 5 5
BDNF 0.01 0.015 -10000 0 0 363 363
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.005 -10000 0 0 28 28
FURIN 0.032 0.005 -10000 0 0 14 14
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.046 1 1
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.067 0.025 -10000 0 -10000 0 0
proBDNF (dimer) 0.009 0.015 -10000 0 0 363 363
NTRK1 0.032 0.006 -10000 0 0 15 15
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.013 0.086 0.23 8 -0.33 18 26
IRAK1 0.033 0.003 -10000 0 0 5 5
SHC1 -0.024 0.007 0 24 -10000 0 24
ARHGDIA 0.033 0.004 -10000 0 0 8 8
RhoA/GTP 0.024 0.005 -10000 0 0 19 19
Gamma Secretase 0.074 0.051 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.054 0.026 -10000 0 -0.041 6 6
MAGEH1 0.031 0.009 -10000 0 0 41 41
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.034 0.034 -10000 0 -0.041 11 11
Mammalian IAPs/DIABLO 0.056 0.026 -10000 0 -0.046 9 9
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.033 0.003 -10000 0 0 4 4
APP 0.032 0.006 -10000 0 0 18 18
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.03 0.01 -10000 0 0 56 56
RhoA/GDP/RHOGDI 0.038 0.014 0.17 1 -10000 0 1
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.025 0.028 0.19 5 -10000 0 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.025 -10000 0 -0.12 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.041 0.014 -10000 0 -0.013 21 21
NCSTN 0.031 0.009 -10000 0 0 39 39
mol:GTP 0.037 0.018 -10000 0 -0.013 19 19
PSENEN 0.031 0.009 -10000 0 0 40 40
mol:ceramide -0.029 0.027 0.18 8 -10000 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.024 -10000 0 -0.11 20 20
p75(NTR)/beta APP 0.044 0.016 -10000 0 -0.016 20 20
BEX1 0.023 0.015 -10000 0 0 150 150
mol:GDP -0.013 0.003 -10000 0 -10000 0 0
NGF (dimer) 0.039 0.041 -10000 0 -0.041 53 53
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.04 0.012 -10000 0 -0.029 1 1
PIK3R1 0.03 0.01 -10000 0 0 47 47
RAC1/GTP 0.022 0.02 -10000 0 -0.027 3 3
MYD88 0.028 0.012 -10000 0 0 79 79
CHUK 0.024 0.015 -10000 0 0 148 148
NGF (dimer)/p75(NTR)/PKA 0.037 0.018 -10000 0 -0.013 19 19
RHOB 0.031 0.008 -10000 0 0 33 33
RHOA 0.032 0.006 -10000 0 0 19 19
MAGE-G1/E2F1 0.021 0.008 -10000 0 0 66 66
NT3 (dimer) 0.031 0.007 -10000 0 0 27 27
TP53 0.021 0.069 0.24 25 -10000 0 25
PRDM4 -0.03 0.027 0.18 8 -10000 0 8
BDNF (dimer) 0.017 0.036 -10000 0 -0.053 13 13
PIK3CA 0.031 0.009 -10000 0 0 41 41
SORT1 0.033 0.004 -10000 0 0 9 9
activation of caspase activity 0.065 0.024 -10000 0 -0.049 12 12
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.056 0.027 -10000 0 -0.041 17 17
RHOC 0.023 0.016 -10000 0 0 164 164
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.036 0.081 0.2 79 -10000 0 79
DIABLO 0.033 0.004 -10000 0 0 8 8
SMPD2 -0.029 0.028 0.18 8 -10000 0 8
APH1B 0.032 0.006 -10000 0 0 15 15
APH1A 0.032 0.006 -10000 0 0 19 19
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.013 -10000 0 -0.013 20 20
PSEN1 0.031 0.009 -10000 0 0 42 42
APAF-1/Pro-Caspase 9 0.047 0.012 -10000 0 -0.016 3 3
NT3 (dimer)/p75(NTR) 0.044 0.017 -10000 0 -0.016 20 20
MAPK8 0.028 0.071 0.18 69 -10000 0 69
MAPK9 0.062 0.096 0.2 133 -0.18 1 134
APAF1 0.033 0.005 -10000 0 0 11 11
NTF3 0.032 0.007 -10000 0 0 27 27
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.016 -10000 0 0 201 201
RAC1/GDP 0.015 0.012 -10000 0 0 204 204
RhoA-B-C/GDP 0.048 0.034 -10000 0 -0.056 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.038 -10000 0 -0.054 27 27
RhoA-B-C/GTP 0.036 0.018 -10000 0 -0.012 19 19
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.042 -10000 0 -0.065 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.038 -10000 0 -0.052 1 1
PRKACB 0.029 0.011 -10000 0 0 60 60
proBDNF (dimer)/p75 ECD 0.014 0.022 -10000 0 -0.016 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.031 0.009 -10000 0 0 40 40
BIRC2 0.033 0.005 -10000 0 0 10 10
neuron projection morphogenesis -0.014 0.025 0.14 1 -0.15 1 2
BAD 0.04 0.089 0.24 37 -0.18 2 39
RIPK2 0.032 0.005 -10000 0 0 13 13
NGFR 0.031 0.008 -10000 0 0 28 28
CYCS -0.022 0.03 0.17 6 -10000 0 6
ADAM17 0.032 0.005 -10000 0 0 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.056 0.026 -10000 0 -0.041 12 12
BCL2L11 0.04 0.089 0.24 38 -0.18 2 40
BDNF (dimer)/p75(NTR) 0.013 0.022 -10000 0 -0.016 9 9
PI3K 0.049 0.03 -10000 0 -0.041 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.014 -10000 0 -0.029 6 6
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 0 12 12
PRKCI 0.032 0.006 -10000 0 0 17 17
NGF (dimer)/p75(NTR) 0.023 0.006 -10000 0 0 28 28
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.058 0.022 -10000 0 -0.041 6 6
TRAF6 0.032 0.006 -10000 0 0 16 16
RAC1 0.02 0.016 -10000 0 0 204 204
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.03 0.009 -10000 0 0 43 43
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.008 0.016 0.14 2 -0.087 1 3
SQSTM1 0.032 0.006 -10000 0 0 16 16
NGFRAP1 0.033 0.004 -10000 0 0 6 6
CASP3 0.039 0.087 0.24 36 -0.18 2 38
E2F1 0.029 0.011 -10000 0 0 66 66
CASP9 0.032 0.006 -10000 0 0 17 17
IKK complex 0.026 0.057 -10000 0 -0.16 7 7
NGF (dimer)/TRKA 0.024 0.004 -10000 0 0 15 15
MMP7 0.028 0.012 -10000 0 0 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.063 0.036 -10000 0 -0.05 27 27
MMP3 0.032 0.006 -10000 0 0 17 17
APAF-1/Caspase 9 -0.043 0.038 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.02 -10000 0 -0.047 3 3
CDKN2C 0.005 0.017 -10000 0 -0.091 1 1
CDKN2A 0.009 0.019 -10000 0 -0.067 3 3
CCND2 0.001 0.008 0.083 4 -10000 0 4
RB1 -0.039 0.082 0.1 1 -0.21 92 93
CDK4 0.001 0.008 0.092 4 -10000 0 4
CDK6 0.002 0.009 0.1 4 -10000 0 4
G1/S progression 0.065 0.1 0.22 148 -0.1 1 149
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.061 0.024 -10000 0 -0.046 14 14
fibroblast growth factor receptor signaling pathway 0.061 0.024 -10000 0 -0.046 14 14
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.027 0.013 -10000 0 0 97 97
GPC1/SLIT2 0.031 0.024 -10000 0 -0.016 5 5
SMAD2 -0.037 0.04 0.18 15 -10000 0 15
GPC1/PrPc/Cu2+ 0.035 0.019 -10000 0 -0.013 6 6
GPC1/Laminin alpha1 0.024 0.004 -10000 0 0 14 14
TDGF1 0.032 0.006 -10000 0 0 17 17
CRIPTO/GPC1 0.046 0.013 -10000 0 -0.016 9 9
APP/GPC1 0.046 0.013 -10000 0 -0.016 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.034 0.012 -10000 0 -10000 0 0
FLT1 0.031 0.009 -10000 0 0 38 38
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.028 -10000 0 -0.046 18 18
SERPINC1 0.032 0.005 -10000 0 0 14 14
FYN -0.034 0.014 -10000 0 -10000 0 0
FGR -0.036 0.011 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.002 0.074 0.17 57 -0.24 4 61
SLIT2 0.021 0.016 -10000 0 0 182 182
GPC1/NRG 0.047 0.012 -10000 0 -0.016 7 7
NRG1 0.032 0.005 -10000 0 0 12 12
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.013 0.046 -10000 0 -0.047 18 18
LYN -0.035 0.01 -10000 0 -10000 0 0
mol:Spermine -0.016 0.003 -10000 0 -10000 0 0
cell growth 0.061 0.024 -10000 0 -0.046 14 14
BMP signaling pathway -0.032 0.005 0 14 -10000 0 14
SRC -0.033 0.015 -10000 0 -10000 0 0
TGFBR1 0.032 0.006 -10000 0 0 18 18
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.021 0.016 -10000 0 0 193 193
GPC1 0.032 0.005 -10000 0 0 14 14
TGFBR1 (dimer) 0.032 0.006 -10000 0 0 18 18
VEGFA 0.015 0.017 -10000 0 0 282 282
BLK -0.036 0.01 -10000 0 -10000 0 0
HCK -0.03 0.015 -10000 0 -10000 0 0
FGF2 0.033 0.004 -10000 0 0 9 9
FGFR1 0.032 0.005 -10000 0 0 12 12
VEGFR1 homodimer 0.031 0.009 -10000 0 0 38 38
TGFBR2 0.032 0.006 -10000 0 0 18 18
cell death 0.046 0.013 -10000 0 -0.016 7 7
ATIII/GPC1 0.047 0.012 -10000 0 -0.016 8 8
PLA2G2A/GPC1 0.024 0.031 -10000 0 -0.016 179 179
LCK -0.037 0.01 -10000 0 -10000 0 0
neuron differentiation 0.046 0.012 -10000 0 -0.016 7 7
PrPc/Cu2+ 0.02 0.01 -10000 0 0 97 97
APP 0.032 0.006 -10000 0 0 18 18
TGFBR2 (dimer) 0.032 0.006 -10000 0 0 18 18
E-cadherin signaling in the nascent adherens junction

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
CTTN 0 0.053 -10000 0 -0.31 13 13
KLHL20 0.031 0.079 0.17 58 -0.19 13 71
CYFIP2 0.019 0.017 -10000 0 0 223 223
Rac1/GDP -0.011 0.047 0.22 1 -0.19 3 4
ENAH -0.002 0.056 -10000 0 -0.31 15 15
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 0 12 12
CTNNB1 0.032 0.006 -10000 0 0 15 15
CDC42/GTP -0.035 0.051 0.11 46 -0.15 4 50
ABI1/Sra1/Nap1 -0.012 0.024 -10000 0 -0.12 15 15
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.074 0.035 -10000 0 -0.053 25 25
RAPGEF1 -0.002 0.073 0.27 4 -0.29 9 13
CTNND1 0.032 0.006 -10000 0 0 19 19
regulation of calcium-dependent cell-cell adhesion 0.016 0.057 -10000 0 -0.31 14 14
CRK 0.001 0.072 0.16 54 -0.3 11 65
E-cadherin/gamma catenin/alpha catenin 0.059 0.027 -10000 0 -0.047 18 18
alphaE/beta7 Integrin 0.047 0.012 -10000 0 -0.016 2 2
IQGAP1 0.025 0.015 -10000 0 0 131 131
NCKAP1 0.033 0.003 -10000 0 0 3 3
Rap1/GTP/I-afadin 0.035 0.022 -10000 0 -0.029 48 48
DLG1 -0.002 0.056 -10000 0 -0.31 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.039 0.025 -10000 0 -0.11 11 11
MLLT4 0.03 0.009 -10000 0 0 45 45
ARF6/GTP/NME1/Tiam1 0.036 0.02 -10000 0 -0.029 33 33
PI3K -0.048 0.032 -10000 0 -0.14 11 11
ARF6 0.031 0.008 -10000 0 0 31 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.046 0.014 -10000 0 -0.016 13 13
TIAM1 0.031 0.009 -10000 0 0 37 37
E-cadherin(dimer)/Ca2+ 0.069 0.03 -10000 0 -0.049 24 24
AKT1 -0.022 0.046 0.14 12 -10000 0 12
PIK3R1 0.03 0.01 -10000 0 0 47 47
CDH1 0.032 0.006 -10000 0 0 19 19
RhoA/GDP -0.009 0.072 0.26 4 -0.2 5 9
actin cytoskeleton organization 0.027 0.063 0.14 59 -0.14 13 72
CDC42/GDP -0.01 0.07 0.24 4 -0.2 5 9
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.027 -10000 0 -0.12 21 21
ITGB7 0.032 0.006 -10000 0 0 17 17
RAC1 0.02 0.016 -10000 0 0 204 204
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.075 0.033 -10000 0 -0.053 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin 0.053 0.023 -10000 0 -0.038 21 21
mol:GDP -0.006 0.072 0.26 5 -0.21 8 13
CDC42/GTP/IQGAP1 0.029 0.025 -10000 0 -0.013 116 116
JUP 0.032 0.007 -10000 0 0 24 24
p120 catenin/RhoA/GDP -0.011 0.078 0.25 4 -0.2 8 12
RAC1/GTP/IQGAP1 0.017 0.024 -10000 0 -0.013 84 84
PIP5K1C/AP1M1 0.022 0.008 -10000 0 0 54 54
RHOA 0.032 0.006 -10000 0 0 19 19
CDC42 0.032 0.006 -10000 0 0 19 19
CTNNA1 0.033 0.005 -10000 0 0 10 10
positive regulation of S phase of mitotic cell cycle 0.016 0.043 0.1 50 -0.094 12 62
NME1 0 0 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.002 0.056 -10000 0 -0.31 15 15
regulation of cell-cell adhesion -0.04 0.024 -10000 0 -0.12 12 12
WASF2 -0.007 0.013 -10000 0 -0.068 15 15
Rap1/GTP -0.027 0.062 0.14 55 -0.18 2 57
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.085 0.04 -10000 0 -0.065 7 7
CCND1 0.018 0.05 0.12 50 -0.11 12 62
VAV2 0.011 0.13 -10000 0 -0.55 18 18
RAP1/GDP -0.016 0.064 0.15 45 -0.19 2 47
adherens junction assembly -0.001 0.055 -10000 0 -0.3 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.015 -10000 0 0 138 138
PIP5K1C 0.03 0.01 -10000 0 0 54 54
regulation of heterotypic cell-cell adhesion 0.052 0.036 0.19 4 -10000 0 4
E-cadherin/beta catenin -0.002 0.024 -10000 0 -0.16 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.001 0.051 -10000 0 -0.31 12 12
PIK3CA 0.031 0.009 -10000 0 0 41 41
Rac1/GTP -0.008 0.055 -10000 0 -0.29 14 14
E-cadherin/beta catenin/alpha catenin 0.06 0.027 -10000 0 -0.047 21 21
ITGAE 0.032 0.005 -10000 0 0 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.016 0.058 -10000 0 -0.31 14 14
PDGFR-beta signaling pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.041 0.087 0.24 55 -0.31 6 61
PDGFB-D/PDGFRB/SLAP 0.043 0.02 -10000 0 -0.016 33 33
PDGFB-D/PDGFRB/APS/CBL 0.044 0.011 -10000 0 -0.021 3 3
AKT1 -0.028 0.091 0.29 15 -10000 0 15
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.048 0.091 0.26 52 -0.34 6 58
PIK3CA 0.031 0.009 -10000 0 0 41 41
FGR 0.013 0.075 0.35 2 -0.39 8 10
mol:Ca2+ 0.035 0.088 0.23 51 -0.37 6 57
MYC 0.086 0.13 0.3 82 -0.27 3 85
SHC1 0.03 0.01 -10000 0 0 55 55
HRAS/GDP -0.02 0.071 0.16 64 -10000 0 64
LRP1/PDGFRB/PDGFB 0.053 0.035 -10000 0 -0.046 36 36
GRB10 0.019 0.016 -10000 0 0 213 213
PTPN11 0.033 0.005 -10000 0 0 10 10
GO:0007205 0.034 0.088 0.23 51 -0.38 6 57
PTEN 0.021 0.016 -10000 0 0 188 188
GRB2 0.032 0.007 -10000 0 0 22 22
GRB7 0.033 0.004 -10000 0 0 7 7
PDGFB-D/PDGFRB/SHP2 0.048 0.011 -10000 0 -0.017 2 2
PDGFB-D/PDGFRB/GRB10 0.028 0.025 -10000 0 -0.016 4 4
cell cycle arrest 0.043 0.02 -10000 0 -0.016 33 33
HRAS 0.032 0.007 -10000 0 0 24 24
HIF1A -0.036 0.082 0.24 17 -10000 0 17
GAB1 0.033 0.091 0.29 26 -0.33 9 35
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.032 0.1 0.26 64 -0.29 8 72
PDGFB-D/PDGFRB 0.055 0.03 -10000 0 -0.056 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.011 -10000 0 -0.017 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.053 0.19 16 -0.27 5 21
positive regulation of MAPKKK cascade 0.048 0.011 -10000 0 -0.017 2 2
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:IP3 0.035 0.089 0.24 51 -0.38 6 57
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.023 0.024 -10000 0 -0.036 68 68
PDGFB-D/PDGFRB/GRB7 0.048 0.01 -10000 0 -0.017 2 2
SHB 0.03 0.01 -10000 0 0 46 46
BLK 0.016 0.069 0.3 3 -0.34 7 10
PTPN2 0.033 0.01 -10000 0 -0.032 5 5
PDGFB-D/PDGFRB/SNX15 0.048 0.011 -10000 0 -0.017 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.035 0.097 0.26 46 -0.34 8 54
CBL 0.033 0.005 -10000 0 0 11 11
PDGFB-D/PDGFRB/DEP1 0.048 0.012 -10000 0 -0.017 2 2
LCK 0.017 0.065 0.31 3 -0.34 5 8
PDGFRB 0.033 0.01 -10000 0 -0.033 6 6
ACP1 0.032 0.005 -10000 0 0 12 12
HCK 0.003 0.036 0.2 1 -0.36 1 2
ABL1 0.033 0.088 0.23 52 -0.29 7 59
PDGFB-D/PDGFRB/CBL 0.037 0.093 0.27 25 -0.39 8 33
PTPN1 0.029 0.014 -10000 0 -0.032 8 8
SNX15 0.033 0.004 -10000 0 0 9 9
STAT3 0.032 0.006 -10000 0 0 18 18
STAT1 0.032 0.006 -10000 0 0 20 20
cell proliferation 0.084 0.12 0.29 86 -0.25 3 89
SLA 0.03 0.01 -10000 0 0 52 52
actin cytoskeleton reorganization -0.024 0.082 0.18 62 -10000 0 62
SRC 0.007 0.044 -10000 0 -0.72 1 1
PI3K -0.056 0.032 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.057 0.03 -10000 0 -0.047 7 7
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.048 0.092 0.26 52 -0.35 6 58
LYN 0.016 0.057 0.34 2 -0.36 1 3
LRP1 0.03 0.009 -10000 0 0 44 44
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.033 0.004 -10000 0 0 8 8
STAT5A 0.033 0.004 -10000 0 0 9 9
NCK1-2/p130 Cas 0.065 0.04 -10000 0 -0.064 6 6
SPHK1 0.032 0.011 -10000 0 -0.032 6 6
EDG1 0.001 0.004 0.022 3 -10000 0 3
mol:DAG 0.035 0.089 0.24 51 -0.38 6 57
PLCG1 0.035 0.09 0.24 50 -0.39 6 56
NHERF/PDGFRB 0.063 0.021 -10000 0 -0.047 8 8
YES1 -0.002 0.099 0.29 2 -0.53 13 15
cell migration 0.063 0.021 -10000 0 -0.047 8 8
SHC/Grb2/SOS1 0.063 0.038 -10000 0 -0.065 5 5
SLC9A3R2 0.033 0.004 -10000 0 0 7 7
SLC9A3R1 0.032 0.005 -10000 0 0 13 13
NHERF1-2/PDGFRB/PTEN 0.034 0.065 -10000 0 -0.051 165 165
FYN -0.013 0.12 0.34 2 -0.36 46 48
DOK1 -0.017 0.071 0.17 64 -10000 0 64
HRAS/GTP 0.023 0.005 -10000 0 0 24 24
PDGFB 0.031 0.009 -10000 0 0 39 39
RAC1 0.093 0.14 0.32 83 -0.33 5 88
PRKCD -0.014 0.077 0.18 66 -10000 0 66
FER -0.016 0.075 0.18 64 -10000 0 64
MAPKKK cascade -0.009 0.085 0.2 30 -10000 0 30
RASA1 -0.015 0.075 0.18 64 -10000 0 64
NCK1 0.031 0.008 -10000 0 0 28 28
NCK2 0.033 0.003 -10000 0 0 5 5
p62DOK/Csk -0.023 0.073 0.16 64 -10000 0 64
PDGFB-D/PDGFRB/SHB 0.045 0.016 -10000 0 -0.017 2 2
chemotaxis 0.033 0.087 0.23 52 -0.28 7 59
STAT1-3-5/STAT1-3-5 0.065 0.042 -10000 0 -0.11 1 1
Bovine Papilomavirus E5/PDGFRB 0.024 0.006 0.05 3 -0.021 2 5
PTPRJ 0.032 0.006 -10000 0 0 16 16
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.015 -10000 0 0 134 134
SMAD2 -0.026 0.06 0.14 2 -0.22 30 32
SMAD3 0.001 0.055 0.26 1 -0.2 12 13
SMAD3/SMAD4 0.023 0.053 -10000 0 -0.48 4 4
SMAD4/Ubc9/PIASy 0.041 0.04 -10000 0 -0.046 7 7
SMAD2/SMAD2/SMAD4 0.016 0.085 -10000 0 -0.21 27 27
PPM1A 0.031 0.008 -10000 0 0 34 34
CALM1 0.029 0.011 -10000 0 0 61 61
SMAD2/SMAD4 -0.012 0.061 0.14 1 -0.2 28 29
MAP3K1 0.033 0.005 -10000 0 0 11 11
TRAP-1/SMAD4 0.033 0.028 -10000 0 -0.016 114 114
MAPK3 0.033 0.003 -10000 0 0 4 4
MAPK1 0.031 0.009 -10000 0 0 42 42
NUP214 0.032 0.007 -10000 0 0 23 23
CTDSP1 0.033 0.003 -10000 0 0 4 4
CTDSP2 0.028 0.012 -10000 0 0 79 79
CTDSPL 0.032 0.005 -10000 0 0 14 14
KPNB1 0.033 0.003 -10000 0 0 5 5
TGFBRAP1 0.033 0.003 -10000 0 0 3 3
UBE2I 0.033 0.003 -10000 0 0 5 5
NUP153 0.033 0.004 -10000 0 0 8 8
KPNA2 0.032 0.006 -10000 0 0 18 18
PIAS4 0.031 0.008 -10000 0 0 35 35
LPA4-mediated signaling events

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
ADCY4 -0.013 0.001 0 6 -10000 0 6
ADCY5 -0.013 0.001 0 6 -10000 0 6
ADCY6 -0.025 0.006 0 27 -10000 0 27
ADCY7 -0.025 0.005 0 20 -10000 0 20
ADCY1 -0.016 0.013 0 204 -10000 0 204
ADCY2 -0.025 0.006 0 24 -10000 0 24
ADCY3 -0.013 0.001 0 6 -10000 0 6
ADCY8 -0.025 0.006 0 26 -10000 0 26
PRKCE -0.017 0.002 0 6 -10000 0 6
ADCY9 -0.026 0.004 0 13 -10000 0 13
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.005 0.045 0.16 16 -0.13 3 19
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.047 0.057 -10000 0 -0.07 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.008 -10000 0 0 29 29
STAT1 (dimer)/Cbp/p300 -0.055 0.057 0.27 7 -10000 0 7
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.05 0.16 2 -0.057 86 88
antigen processing and presentation of peptide antigen via MHC class I -0.041 0.036 -10000 0 -0.12 20 20
CaM/Ca2+ 0.045 0.061 -10000 0 -0.077 29 29
RAP1A 0.032 0.005 -10000 0 0 12 12
STAT1 (dimer)/SHP2 -0.045 0.041 0.14 20 -10000 0 20
AKT1 -0.036 0.07 0.26 11 -10000 0 11
MAP2K1 -0.048 0.046 0.23 5 -10000 0 5
MAP3K11 -0.041 0.054 0.26 8 -10000 0 8
IFNGR1 -0.008 0.032 0.079 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.093 0.11 -10000 0 -0.24 160 160
Rap1/GTP -0.063 0.023 -10000 0 -10000 0 0
CRKL/C3G 0.045 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.06 0.066 -10000 0 -0.072 18 18
CEBPB -0.023 0.1 0.36 5 -0.35 20 25
STAT3 0.032 0.006 -10000 0 0 18 18
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.051 0.093 -10000 0 -0.76 4 4
STAT1 -0.041 0.054 0.26 8 -10000 0 8
CALM1 0.029 0.011 -10000 0 0 61 61
IFN-gamma (dimer) -0.011 0.031 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
STAT1 (dimer)/PIAS1 -0.047 0.058 0.27 8 -10000 0 8
CEBPB/PTGES2/Cbp/p300 -0.034 0.072 0.17 2 -0.24 32 34
mol:Ca2+ 0.044 0.055 -10000 0 -0.069 19 19
MAPK3 -0.016 0.078 0.43 2 -0.64 4 6
STAT1 (dimer) -0.052 0.047 0.092 1 -0.16 16 17
MAPK1 -0.063 0.19 0.43 2 -0.69 39 41
JAK2 -0.006 0.032 0.079 3 -10000 0 3
PIK3R1 0.03 0.01 -10000 0 0 47 47
JAK1 -0.01 0.033 0.071 2 -10000 0 2
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.015 0.077 0.32 8 -0.22 21 29
SMAD7 -0.019 0.04 0.14 16 -10000 0 16
CBL/CRKL/C3G -0.053 0.06 0.26 8 -10000 0 8
PI3K 0.038 0.062 -10000 0 -10000 0 0
IFNG -0.011 0.031 -10000 0 -10000 0 0
apoptosis -0.005 0.073 0.33 6 -0.42 4 10
CAMK2G 0.012 0.016 -10000 0 0 329 329
STAT3 (dimer) 0.032 0.006 -10000 0 0 18 18
CAMK2A 0.031 0.008 -10000 0 0 30 30
CAMK2B 0.002 0.008 -10000 0 0 474 474
FRAP1 -0.036 0.064 0.25 11 -10000 0 11
PRKCD -0.039 0.073 0.28 11 -10000 0 11
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.041 0.036 -10000 0 -0.12 20 20
PTPN2 0.032 0.007 -10000 0 0 21 21
EP300 0.031 0.009 -10000 0 0 41 41
IRF1 -0.055 0.041 0.22 5 -10000 0 5
STAT1 (dimer)/PIASy -0.045 0.055 0.25 7 -10000 0 7
SOCS1 0.016 0.094 -10000 0 -1 4 4
mol:GDP -0.052 0.057 0.26 7 -10000 0 7
CASP1 -0.018 0.037 0.13 15 -10000 0 15
PTGES2 0.032 0.007 -10000 0 0 24 24
IRF9 -0.017 0.041 0.17 7 -0.12 12 19
mol:PI-3-4-5-P3 0.024 0.052 -10000 0 -10000 0 0
RAP1/GDP -0.06 0.037 0.097 17 -10000 0 17
CBL -0.04 0.054 0.26 8 -10000 0 8
MAP3K1 -0.043 0.047 0.24 5 -10000 0 5
PIAS1 0.033 0.005 -10000 0 0 11 11
PIAS4 0.031 0.008 -10000 0 0 35 35
antigen processing and presentation of peptide antigen via MHC class II -0.041 0.036 -10000 0 -0.12 20 20
PTPN11 -0.035 0.047 0.16 24 -10000 0 24
CREBBP 0.033 0.004 -10000 0 -10000 0 0
RAPGEF1 0.032 0.007 -10000 0 0 23 23
Ephrin B reverse 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
EFNB2 0.03 0.01 -10000 0 0 52 52
EPHB2 0.032 0.007 0.054 1 0 22 23
EFNB1 -0.006 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.023 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.049 0.033 -10000 0 -0.042 36 36
neuron projection morphogenesis -0.007 0.019 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.027 0.17 3 -10000 0 3
DNM1 0.006 0.013 -10000 0 0 420 420
cell-cell signaling -0.001 0.002 0.022 1 -10000 0 1
MAP2K4 -0.011 0.031 -10000 0 -0.38 3 3
YES1 0.014 0.052 -10000 0 -0.6 3 3
Ephrin B1/EPHB1-2/NCK2 0.011 0.027 0.17 3 -10000 0 3
PI3K 0.041 0.042 -10000 0 -0.34 3 3
mol:GDP 0.01 0.026 0.16 3 -10000 0 3
ITGA2B 0.033 0.003 -10000 0 0 5 5
endothelial cell proliferation 0.023 0.022 -10000 0 -10000 0 0
FYN 0.013 0.055 -10000 0 -0.6 3 3
MAP3K7 -0.004 0.031 -10000 0 -0.39 3 3
FGR 0.015 0.048 -10000 0 -0.58 3 3
TIAM1 0.031 0.009 -10000 0 0 37 37
PIK3R1 0.03 0.01 -10000 0 0 47 47
RGS3 0.032 0.006 -10000 0 0 19 19
cell adhesion -0.019 0.038 -10000 0 -0.33 3 3
LYN 0.015 0.049 -10000 0 -0.6 3 3
Ephrin B1/EPHB1-2/Src Family Kinases 0.007 0.046 -10000 0 -0.57 3 3
Ephrin B1/EPHB1-2 0.006 0.028 -10000 0 -0.42 2 2
SRC 0.015 0.048 -10000 0 -0.58 3 3
ITGB3 0.033 0.004 -10000 0 0 6 6
EPHB1 0.032 0.007 -10000 0 0 25 25
EPHB4 0.019 0.016 -10000 0 0 214 214
RAC1 0.02 0.016 -10000 0 0 204 204
Ephrin B2/EPHB4 0.023 0.022 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.049 0.005 -10000 0 -10000 0 0
BLK 0.013 0.056 -10000 0 -0.57 4 4
HCK 0.012 0.054 -10000 0 -0.57 4 4
regulation of stress fiber formation -0.011 0.026 -10000 0 -0.16 3 3
MAPK8 -0.015 0.034 -10000 0 -0.37 3 3
Ephrin B1/EPHB1-2/RGS3 0.011 0.026 0.17 2 -10000 0 2
endothelial cell migration 0.065 0.1 0.19 193 -0.32 2 195
NCK2 0.033 0.003 -10000 0 0 5 5
PTPN13 0.031 0.011 -10000 0 0 38 38
regulation of focal adhesion formation -0.011 0.026 -10000 0 -0.16 3 3
chemotaxis -0.01 0.025 -10000 0 -0.16 2 2
PIK3CA 0.031 0.009 -10000 0 0 41 41
Rac1/GTP 0.007 0.02 -10000 0 -10000 0 0
angiogenesis 0.005 0.033 -10000 0 -0.42 3 3
LCK 0.014 0.055 -10000 0 -0.59 4 4
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.006 -10000 0 -10000 0 0
ELF1 0.034 0.013 -10000 0 -0.028 5 5
CCNA2 0.024 0.015 -10000 0 0 142 142
PIK3CA 0.031 0.009 -10000 0 -10000 0 0
JAK3 0.031 0.009 -10000 0 -10000 0 0
PIK3R1 0.03 0.01 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.002 0.059 0.16 3 -0.25 7 10
SHC1 0.03 0.01 -10000 0 -10000 0 0
SP1 0.034 0.013 -10000 0 -0.023 14 14
IL2RA -0.021 0.014 0 158 -10000 0 158
IL2RB 0.031 0.009 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.033 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.04 0.1 0.3 20 -0.33 15 35
PTPN11 0.033 0.005 -10000 0 -10000 0 0
CCND2 -0.027 0.009 0 53 -10000 0 53
LCK 0.032 0.006 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
IL2 0.033 0.004 -10000 0 -10000 0 0
CDK6 0.019 0.017 -10000 0 0 222 222
CCND3 -0.006 0.059 0.2 2 -0.29 3 5
Signaling events mediated by PRL

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
CCNE1 0.03 0.01 -10000 0 0 49 49
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.014 0.062 -10000 0 -0.34 10 10
PRL-3/alpha Tubulin 0.042 0.019 -10000 0 -0.016 28 28
mol:Ca2+ -0.029 0.016 0.014 27 -10000 0 27
AGT 0.029 0.011 -10000 0 0 58 58
CCNA2 -0.015 0.057 0.16 46 -10000 0 46
TUBA1B 0.032 0.006 -10000 0 0 19 19
EGR1 -0.014 0.004 0 29 -10000 0 29
CDK2/Cyclin E1 0.038 0.063 -10000 0 -0.32 9 9
MAPK3 -0.031 0.008 0 24 -10000 0 24
PRL-2 /Rab GGTase beta 0.048 0.009 -10000 0 -10000 0 0
MAPK1 -0.028 0.011 0 62 -10000 0 62
PTP4A1 -0.025 0.012 -10000 0 -10000 0 0
PTP4A3 0.03 0.01 -10000 0 0 50 50
PTP4A2 0.032 0.005 -10000 0 0 14 14
ITGB1 -0.023 0.015 0 145 -10000 0 145
SRC 0.029 0.011 -10000 0 0 65 65
RAC1 0.007 0.039 -10000 0 -0.34 4 4
Rab GGTase beta/Rab GGTase alpha 0.045 0.014 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.013 0.065 0.18 51 -10000 0 51
RABGGTA 0.031 0.009 -10000 0 0 36 36
BCAR1 -0.018 0.006 0 50 -10000 0 50
RHOC 0.005 0.053 -10000 0 -0.34 7 7
RHOA 0.015 0.064 -10000 0 -0.33 11 11
cell motility 0.018 0.06 -10000 0 -0.31 6 6
PRL-1/alpha Tubulin -0.01 0.07 0.18 62 -10000 0 62
PRL-3/alpha1 Integrin 0.022 0.007 -10000 0 0 50 50
ROCK1 0.018 0.06 -10000 0 -0.31 6 6
RABGGTB 0.033 0.005 -10000 0 0 11 11
CDK2 0.03 0.009 -10000 0 0 44 44
mitosis -0.025 0.012 -10000 0 -10000 0 0
ATF5 0.031 0.009 -10000 0 0 40 40
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.031 0.067 -10000 0 -0.24 11 11
MAP3K8 0.022 0.016 -10000 0 0 172 172
FOS 0.018 0.061 -10000 0 -0.24 10 10
PRKCA 0.033 0.005 -10000 0 0 10 10
PTPN7 0.032 0.007 0.061 1 -0.002 20 21
HRAS 0.032 0.007 -10000 0 0 24 24
PRKCB 0 0.001 0.003 8 -0.002 1 9
NRAS 0.025 0.015 -10000 0 0 134 134
RAS family/GTP 0.036 0.04 -10000 0 -0.041 16 16
MAPK3 0.029 0.039 -10000 0 -0.34 4 4
MAP2K1 0.008 0.031 -10000 0 -0.19 1 1
ELK1 0.033 0.004 -10000 0 -0.01 3 3
BRAF 0.002 0.015 0.095 1 -0.23 2 3
mol:GTP 0 0 0.001 2 0 1 3
MAPK1 0.005 0.1 -10000 0 -0.35 37 37
RAF1 0.004 0.019 0.095 1 -0.22 3 4
KRAS 0.031 0.009 -10000 0 0 37 37
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.028 0.068 0.21 61 -10000 0 61
PCK1 0.021 0.027 -10000 0 -10000 0 0
HNF4A 0.013 0.036 0.23 2 -10000 0 2
KCNJ11 0.047 0.071 0.23 59 -10000 0 59
AKT1 0.063 0.03 -10000 0 -10000 0 0
response to starvation 0.001 0.001 -10000 0 -10000 0 0
DLK1 0.038 0.072 0.23 56 -10000 0 56
NKX2-1 0.028 0.044 0.15 54 -10000 0 54
ACADM 0.028 0.067 0.21 59 -10000 0 59
TAT 0.031 0.046 -10000 0 -10000 0 0
CEBPB 0.029 0.012 -10000 0 -10000 0 0
CEBPA 0.031 0.011 -10000 0 -10000 0 0
TTR 0.056 0.12 0.35 57 -0.48 1 58
PKLR 0.033 0.074 0.21 72 -10000 0 72
APOA1 0.06 0.11 0.38 45 -10000 0 45
CPT1C 0.036 0.066 0.21 59 -10000 0 59
ALAS1 0.034 0.065 -10000 0 -0.76 1 1
TFRC 0.043 0.067 -10000 0 -0.57 2 2
FOXF1 0.03 0.01 -10000 0 -10000 0 0
NF1 0.034 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.037 0.005 -10000 0 -10000 0 0
CPT1A 0.029 0.068 0.21 62 -10000 0 62
HMGCS1 0.03 0.07 0.21 65 -10000 0 65
NR3C1 0.034 0.012 -10000 0 -10000 0 0
CPT1B 0.022 0.06 0.21 45 -10000 0 45
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.006 -10000 0 -10000 0 0
GCK 0.068 0.1 0.22 154 -10000 0 154
CREB1 0.035 0.007 -10000 0 -10000 0 0
IGFBP1 0.043 0.049 -10000 0 -10000 0 0
PDX1 0.031 0.056 -10000 0 -0.31 1 1
UCP2 0.028 0.068 0.21 61 -10000 0 61
ALDOB 0.047 0.078 0.23 70 -10000 0 70
AFP 0.007 0.005 -10000 0 -0.07 2 2
BDH1 0.033 0.073 0.21 71 -10000 0 71
HADH 0.045 0.075 0.23 66 -10000 0 66
F2 0.058 0.11 0.38 45 -10000 0 45
HNF1A 0.037 0.005 -10000 0 -10000 0 0
G6PC 0.015 0.036 -10000 0 -10000 0 0
SLC2A2 0.05 0.055 -10000 0 -10000 0 0
INS -0.027 0.016 0.15 1 -10000 0 1
FOXA1 0.006 0.001 -10000 0 -10000 0 0
FOXA3 0.011 0.009 -10000 0 -0.12 2 2
FOXA2 0.076 0.071 0.26 52 -10000 0 52
ABCC8 0.044 0.074 0.23 63 -10000 0 63
ALB 0.007 0.005 -10000 0 -0.07 2 2
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.016 0.028 -10000 0 -0.033 100 100
PDGF/PDGFRA/CRKL 0.039 0.022 -10000 0 -0.019 4 4
positive regulation of JUN kinase activity 0.042 0.032 -10000 0 -0.043 1 1
CRKL 0.031 0.008 -10000 0 0 29 29
PDGF/PDGFRA/Caveolin-3 0.04 0.021 -10000 0 -0.019 4 4
AP1 -0.019 0.063 0.27 3 -10000 0 3
mol:IP3 -0.026 0.018 -10000 0 -10000 0 0
PLCG1 -0.026 0.018 -10000 0 -10000 0 0
PDGF/PDGFRA/alphaV Integrin 0.039 0.023 -10000 0 -0.018 19 19
RAPGEF1 0.032 0.007 -10000 0 0 23 23
CRK 0.033 0.005 -10000 0 0 10 10
mol:Ca2+ -0.026 0.018 -10000 0 -10000 0 0
CAV3 0.032 0.005 -10000 0 0 13 13
CAV1 0.007 0.014 -10000 0 0 400 400
SHC/Grb2/SOS1 0.043 0.033 -10000 0 -0.043 1 1
PDGF/PDGFRA/Shf 0.021 0.011 0.048 6 -10000 0 6
FOS -0.033 0.032 0.17 3 -10000 0 3
JUN -0.027 0.024 0.051 3 -10000 0 3
oligodendrocyte development 0.038 0.022 -10000 0 -0.018 19 19
GRB2 0.032 0.007 -10000 0 0 22 22
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:DAG -0.026 0.018 -10000 0 -10000 0 0
PDGF/PDGFRA 0.016 0.028 -10000 0 -0.033 100 100
actin cytoskeleton reorganization 0.037 0.022 -10000 0 -0.019 3 3
SRF -0.029 0.012 0.016 1 -10000 0 1
SHC1 0.03 0.01 -10000 0 0 55 55
PI3K 0.047 0.034 -10000 0 -0.047 5 5
PDGF/PDGFRA/Crk/C3G 0.051 0.033 -10000 0 -0.046 17 17
JAK1 -0.027 0.015 0.029 4 -10000 0 4
ELK1/SRF -0.018 0.065 0.13 76 -10000 0 76
SHB 0.03 0.01 -10000 0 0 46 46
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.028 -10000 0 -0.051 4 4
GO:0007205 -0.02 0.013 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.042 0.032 -10000 0 -0.043 1 1
PDGF/PDGFRA/SHB 0.037 0.022 -10000 0 -0.019 3 3
PDGF/PDGFRA/Caveolin-1 0.003 0.022 -10000 0 -0.018 153 153
ITGAV 0.032 0.006 -10000 0 0 20 20
ELK1 -0.026 0.021 0.23 1 -10000 0 1
PIK3CA 0.031 0.009 -10000 0 0 41 41
PDGF/PDGFRA/Crk 0.04 0.021 -10000 0 -0.019 4 4
JAK-STAT cascade -0.027 0.015 0.029 4 -10000 0 4
cell proliferation 0.02 0.011 0.048 6 -10000 0 6
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.031 -10000 0 -0.014 222 222
PDGFRB 0.032 0.011 -10000 0 -0.032 12 12
SPHK1 0.011 0.013 -10000 0 -10000 0 0
mol:S1P 0.004 0.021 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.036 0.063 -10000 0 -0.34 10 10
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.031 0.089 0.19 30 -0.31 7 37
PLCG1 -0.045 0.061 -10000 0 -0.32 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.011 -10000 0 -0.032 12 12
GNAI2 0.036 0.007 -10000 0 -10000 0 0
GNAI3 0.028 0.013 -10000 0 -0.031 7 7
GNAI1 0.016 0.017 -10000 0 -0.031 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.009 0 60 -10000 0 60
S1P1/S1P 0.005 0.035 0.15 2 -10000 0 2
negative regulation of cAMP metabolic process -0.037 0.062 -10000 0 -0.33 10 10
MAPK3 -0.051 0.067 -10000 0 -0.37 8 8
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
RhoA/GDP 0.024 0.005 -10000 0 0 19 19
KDR 0.031 0.01 -10000 0 0 53 53
PLCB2 0.01 0.054 0.17 24 -10000 0 24
RAC1 0.02 0.016 -10000 0 0 204 204
RhoA/GTP 0.001 0.034 0.13 1 -10000 0 1
receptor internalization 0.005 0.034 0.14 2 -10000 0 2
PTGS2 -0.05 0.071 0.24 1 -0.36 7 8
Rac1/GTP -0.008 0.023 0.13 1 -10000 0 1
RHOA 0.032 0.006 -10000 0 0 19 19
VEGFA 0.015 0.017 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.037 0.062 -10000 0 -0.33 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.014 -10000 0 -0.031 6 6
MAPK1 -0.048 0.066 -10000 0 -0.37 8 8
S1P1/S1P/PDGFB-D/PDGFRB 0.025 0.068 0.16 60 -10000 0 60
ABCC1 0.032 0.01 -10000 0 -0.033 8 8
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.005 0.056 0.2 16 -0.28 6 22
FYN -0.009 0.057 0.19 8 -0.29 7 15
LAT/GRAP2/SLP76 -0.018 0.052 0.22 3 -0.3 6 9
IKBKB 0.033 0.004 -10000 0 0 7 7
AKT1 -0.011 0.059 0.17 9 -0.22 14 23
B2M 0.032 0.009 -10000 0 -0.007 23 23
IKBKG -0.017 0.028 0.098 10 -0.094 5 15
MAP3K8 0.022 0.016 -10000 0 0 172 172
mol:Ca2+ -0.012 0.012 -10000 0 -0.044 2 2
integrin-mediated signaling pathway 0.022 0.003 -10000 0 0 12 12
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.008 0.066 0.2 8 -0.29 10 18
TRPV6 0.5 0.61 1.2 211 -10000 0 211
CD28 0.033 0.002 -10000 0 0 2 2
SHC1 -0.004 0.059 0.22 15 -0.34 5 20
receptor internalization 0.003 0.053 0.12 1 -0.38 7 8
PRF1 -0.16 0.29 -10000 0 -0.61 147 147
KRAS 0.031 0.009 -10000 0 0 37 37
GRB2 0.032 0.007 -10000 0 0 22 22
COT/AKT1 -0.012 0.047 0.18 7 -0.2 12 19
LAT -0.008 0.052 0.18 7 -0.34 6 13
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.032 0.008 -10000 0 0 30 30
CD3E 0.033 0.005 -10000 0 0 11 11
CD3G 0.033 0.005 -10000 0 0 11 11
RASGRP2 0.002 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.056 0.094 0.18 22 -0.26 19 41
HLA-A 0 0.001 -10000 0 -10000 0 0
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.022 0.003 -10000 0 0 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.046 0.12 29 -0.098 10 39
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.027 0.023 -10000 0 -0.12 10 10
PRKCA -0.016 0.054 0.18 12 -0.18 5 17
GRAP2 0.031 0.009 -10000 0 0 39 39
mol:IP3 -0.035 0.039 0.1 1 -0.24 6 7
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.002 0.036 0.076 1 -0.15 20 21
ORAI1 -0.43 0.51 -10000 0 -1 210 210
CSK -0.006 0.051 0.18 9 -0.33 6 15
B7 family/CD28 0.046 0.059 0.23 5 -0.25 8 13
CHUK 0.024 0.015 -10000 0 0 148 148
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.049 0.14 2 -0.36 6 8
PTPN6 -0.01 0.048 0.15 12 -0.32 6 18
VAV1 0.002 0.064 0.17 34 -0.31 6 40
Monovalent TCR/CD3 0.009 0.031 -10000 0 -0.26 6 6
CBL 0.033 0.005 -10000 0 0 11 11
LCK -0.004 0.055 0.2 9 -0.29 6 15
PAG1 -0.003 0.048 0.21 3 -0.33 6 9
RAP1A 0.032 0.005 -10000 0 0 12 12
TCR/CD3/MHC I/CD8/LCK -0.003 0.048 0.13 5 -0.35 6 11
CD80 0.032 0.006 -10000 0 0 18 18
CD86 0.031 0.009 -10000 0 0 41 41
PDK1/CARD11/BCL10/MALT1 -0.023 0.031 -10000 0 -0.15 9 9
HRAS 0.032 0.007 -10000 0 0 24 24
GO:0035030 -0.019 0.041 0.16 7 -0.22 8 15
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.033 0.007 -10000 0 -0.018 9 9
PTPRC 0.024 0.016 -10000 0 -0.001 141 141
PDK1/PKC theta -0.015 0.066 0.22 8 -0.26 9 17
CSK/PAG1 -0.009 0.048 0.18 6 -0.31 6 12
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.023 0.007 -10000 0 -0.022 5 5
GRAP2/SLP76 0.024 0.057 0.22 5 -0.34 6 11
STIM1 -0.086 0.14 1 4 -10000 0 4
RAS family/GTP -0.011 0.05 0.14 8 -0.16 22 30
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.003 0.054 0.12 1 -0.4 7 8
mol:DAG -0.033 0.03 -10000 0 -0.22 6 6
RAP1A/GDP -0.002 0.023 0.056 25 -0.049 9 34
PLCG1 0.029 0.011 -10000 0 0 66 66
CD247 0.032 0.005 -10000 0 0 14 14
cytotoxic T cell degranulation -0.15 0.28 -10000 0 -0.59 147 147
RAP1A/GTP 0 0.009 -10000 0 -0.059 4 4
mol:PI-3-4-5-P3 -0.007 0.061 0.2 8 -0.25 10 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.037 0.048 0.16 3 -0.29 6 9
NRAS 0.025 0.015 -10000 0 0 134 134
ZAP70 0.033 0.002 -10000 0 0 2 2
GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
LAT/GRAP2/SLP76/VAV1 -0.02 0.057 0.17 18 -0.28 6 24
MALT1 0.031 0.009 -10000 0 0 42 42
TRAF6 0.032 0.006 -10000 0 0 16 16
CD8 heterodimer 0.024 0.005 -10000 0 -0.022 5 5
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.026 0.022 -10000 0 -0.16 6 6
PRKCE -0.016 0.055 0.18 14 -0.18 5 19
PRKCQ -0.011 0.068 0.21 9 -0.27 10 19
LCP2 0.03 0.009 -10000 0 0 44 44
BCL10 0.032 0.006 -10000 0 0 19 19
regulation of survival gene product expression -0.01 0.054 0.16 9 -0.19 14 23
IKK complex -0.011 0.034 0.17 6 -0.085 5 11
RAS family/GDP -0.01 0.009 -10000 0 -0.031 8 8
MAP3K14 -0.019 0.039 0.14 7 -0.16 14 21
PDPK1 -0.013 0.054 0.17 10 -0.22 10 20
TCR/CD3/MHC I/CD8/Fyn 0.003 0.055 -10000 0 -0.4 6 6
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.007 0.047 0.14 53 -0.17 4 57
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.011 0.044 0.12 6 -0.13 14 20
AP2 0.023 0.007 -10000 0 0 40 40
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.025 0.025 -10000 0 -0.04 10 10
CLTB 0.032 0.005 -10000 0 0 14 14
coatomer protein complex/ARF1/GTP/ER cargo protein 0.003 0.032 -10000 0 -0.11 35 35
CD4 0.03 0.009 -10000 0 0 44 44
CLTA 0.03 0.01 -10000 0 0 50 50
mol:GTP -0.004 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.014 0.006 0 70 -10000 0 70
mol:PI-4-5-P2 -0.004 0.008 0.073 5 -10000 0 5
ARF1/GTP -0.02 0.008 0.037 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.004 0.054 0.16 51 -0.098 23 74
mol:Choline -0.004 0.008 0.074 5 -10000 0 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.033 0.007 -10000 0 0 19 19
DDEF1 -0.002 0.008 0.073 5 -10000 0 5
ARF1/GDP 0.002 0.016 -10000 0 -0.089 12 12
AP2M1 0.031 0.009 -10000 0 0 40 40
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.014 0.013 0.022 2 -10000 0 2
Rac/GTP 0.015 0.012 0.046 1 -0.019 1 2
ARF1/GTP/GGA3/ARF-GAP1 0.034 0.018 -10000 0 -0.037 4 4
ARFIP2 0.027 0.019 -10000 0 -0.049 12 12
COPA 0.032 0.005 -10000 0 0 12 12
RAC1 0.02 0.016 -10000 0 0 204 204
ARF1/GTP/coatomer protein complex -0.002 0.042 0.12 2 -0.15 31 33
ARF1/GTP/ARHGAP10 0.021 0.004 -10000 0 0 19 19
GGA3 0.032 0.005 -10000 0 0 14 14
ARF1/GTP/Membrin 0.023 0.024 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.002 0.03 -10000 0 -0.11 27 27
ARF1/GDP/Membrin 0.026 0.028 -10000 0 -0.3 3 3
Arfaptin 2/Rac/GDP 0.024 0.025 -10000 0 -0.037 14 14
CYTH2 -0.004 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.041 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.015 0.012 -10000 0 0 204 204
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.001 0.031 0.081 1 -0.1 31 32
PLD2 -0.004 0.008 0.074 5 -10000 0 5
ARF-GAP1/v-SNARE -0.014 0.006 0 70 -10000 0 70
PIP5K1A -0.004 0.008 0.074 5 -10000 0 5
ARF1/GTP/Membrin/GBF1/p115 -0.003 0.037 -10000 0 -0.064 132 132
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.008 0.074 5 -10000 0 5
KDEL Receptor/Ligand/ARF-GAP1 -0.014 0.006 0 70 -10000 0 70
GOSR2 0.009 0.029 -10000 0 -0.36 3 3
USO1 0.01 0.02 -10000 0 -0.29 2 2
GBF1 -0.076 0.15 -10000 0 -0.33 131 131
ARF1/GTP/Arfaptin 2 0.041 0.017 -10000 0 -0.041 11 11
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.018 -10000 0 -0.013 19 19
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.012 -10000 0 0 74 74
HDAC3 0.033 0.004 -10000 0 0 9 9
VDR 0.032 0.007 -10000 0 0 24 24
Cbp/p300/PCAF 0.041 0.013 -10000 0 -10000 0 0
EP300 0.031 0.009 -10000 0 0 41 41
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.01 0.055 0.13 1 -0.19 30 31
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.033 0.003 -10000 0 0 5 5
AKT1 -0.01 0.052 0.16 1 -0.17 25 26
RAR alpha/9cRA/Cyclin H -0.005 0.094 0.17 1 -0.23 20 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.011 0.05 0.12 2 -0.16 39 41
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.014 0.045 -10000 0 -0.16 22 22
NCOR2 0.033 0.005 -10000 0 0 11 11
VDR/VDR/Vit D3 0.023 0.005 -10000 0 0 24 24
RXRs/RARs/NRIP1/9cRA -0.016 0.073 0.24 3 -0.33 11 14
NCOA2 0.032 0.005 -10000 0 0 12 12
NCOA3 0.029 0.011 -10000 0 0 68 68
NCOA1 0.031 0.008 -10000 0 0 28 28
VDR/VDR/DNA 0.032 0.007 -10000 0 0 24 24
RARG 0.032 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.041 0.013 -10000 0 -10000 0 0
MAPK3 0.033 0.003 -10000 0 -10000 0 0
MAPK1 0.031 0.009 -10000 0 0 42 42
MAPK8 0.024 0.015 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.001 0.074 -10000 0 -0.3 16 16
RARA -0.024 0.058 -10000 0 -0.13 124 124
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.01 0.049 0.12 2 -0.16 38 40
PRKCA 0.033 0.007 -10000 0 -0.031 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.007 0.069 -10000 0 -0.33 9 9
RXRG 0.014 0.005 -10000 0 -10000 0 0
RXRA -0.02 0.046 0.097 10 -0.11 5 15
RXRB 0.014 0.005 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 0 24 24
RBP1 0.017 0.017 -10000 0 0 246 246
CRBP1/9-cic-RA 0.013 0.012 -10000 0 0 246 246
RARB 0.033 0.005 -10000 0 -10000 0 0
PRKCG 0.031 0.01 -10000 0 -0.031 3 3
MNAT1 0.031 0.009 -10000 0 0 37 37
RAR alpha/RXRs -0.016 0.08 -10000 0 -0.33 17 17
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.011 0.067 0.21 2 -0.29 14 16
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.063 0.16 4 -0.23 16 20
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.007 0.067 -10000 0 -0.34 7 7
positive regulation of DNA binding -0.01 0.086 -10000 0 -0.22 20 20
NRIP1 -0.001 0.069 0.27 1 -0.37 4 5
RXRs/RARs 0 0.067 -10000 0 -0.32 11 11
RXRs/RXRs/DNA/9cRA -0.014 0.065 -10000 0 -0.3 17 17
PRKACA 0.031 0.009 -10000 0 0 36 36
CDK7 0.032 0.005 -10000 0 0 14 14
TFIIH 0.057 0.032 -10000 0 -0.047 40 40
RAR alpha/9cRA 0.017 0.087 -10000 0 -0.13 118 118
CCNH 0.033 0.005 -10000 0 0 11 11
CREBBP 0.033 0.004 -10000 0 0 7 7
RAR gamma2/9cRA 0.052 0.038 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.003 0.09 0.23 9 -0.24 28 37
IKBKB 0.017 0.064 0.24 7 -0.26 8 15
AKT1 0.019 0.086 0.24 42 -10000 0 42
IKBKG 0.011 0.054 0.28 3 -0.24 8 11
CALM1 -0.01 0.049 0.2 3 -0.25 2 5
PIK3CA 0.031 0.009 -10000 0 0 41 41
MAP3K1 0.043 0.097 0.26 27 -0.4 6 33
MAP3K7 0.031 0.008 -10000 0 0 29 29
mol:Ca2+ -0.004 0.053 0.23 1 -0.24 3 4
DOK1 0.033 0.003 -10000 0 0 3 3
AP-1 -0.014 0.067 0.21 4 -0.19 20 24
LYN 0.029 0.011 -10000 0 0 69 69
BLNK 0.02 0.016 -10000 0 0 209 209
SHC1 0.03 0.01 -10000 0 0 55 55
BCR complex 0.045 0.014 -10000 0 -10000 0 0
CD22 -0.013 0.025 -10000 0 -0.34 1 1
CAMK2G -0.002 0.03 0.18 2 -0.29 1 3
CSNK2A1 0.029 0.011 -10000 0 0 66 66
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.054 0.024 -10000 0 -10000 0 0
GO:0007205 -0.005 0.054 0.23 1 -0.24 3 4
SYK 0.03 0.01 -10000 0 0 53 53
ELK1 -0.014 0.053 0.21 1 -0.24 3 4
NFATC1 -0.02 0.068 0.25 8 -0.25 17 25
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -10000 0 0
PAG1/CSK 0.024 0.004 -10000 0 0 12 12
NFKBIB 0.02 0.033 0.15 3 -0.13 14 17
HRAS -0.014 0.053 0.19 4 -0.19 10 14
NFKBIA 0.02 0.032 0.14 4 -0.12 14 18
NF-kappa-B/RelA/I kappa B beta 0.023 0.03 0.13 5 -0.098 14 19
RasGAP/Csk 0.073 0.042 -10000 0 -0.064 3 3
mol:GDP -0.004 0.054 0.22 1 -0.25 2 3
PTEN 0.021 0.016 -10000 0 0 188 188
CD79B 0.033 0.004 -10000 0 0 8 8
NF-kappa-B/RelA/I kappa B alpha 0.023 0.029 0.13 5 -0.094 14 19
GRB2 0.032 0.007 -10000 0 0 22 22
PI3K/BCAP/CD19 -0.005 0.08 0.35 3 -0.33 2 5
PIK3R1 0.03 0.01 -10000 0 0 47 47
mol:IP3 -0.004 0.053 0.23 1 -0.24 3 4
CSK 0.033 0.005 -10000 0 0 12 12
FOS -0.017 0.051 0.21 2 -0.25 2 4
CHUK -0.057 0.13 0.28 3 -0.26 121 124
IBTK 0.032 0.007 -10000 0 0 26 26
CARD11/BCL10/MALT1/TAK1 0.021 0.073 -10000 0 -0.22 5 5
PTPN6 -0.016 0.038 0.15 15 -0.33 1 16
RELA 0.033 0.004 -10000 0 0 9 9
BCL2A1 0.013 0.02 0.085 5 -0.071 13 18
VAV2 -0.015 0.062 0.15 1 -0.29 18 19
ubiquitin-dependent protein catabolic process 0.021 0.033 0.15 3 -0.12 14 17
BTK 0.015 0.012 -10000 0 -10000 0 0
CD19 -0.011 0.033 -10000 0 -0.34 1 1
MAP4K1 0.031 0.009 -10000 0 0 36 36
CD72 0.03 0.011 -10000 0 0 57 57
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.033 0.089 0.24 27 -0.35 6 33
SH3BP5 0.03 0.01 -10000 0 0 54 54
PIK3AP1 -0.004 0.052 0.23 1 -0.22 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.06 -10000 0 -0.29 17 17
RAF1 -0.019 0.051 0.19 4 -0.22 5 9
RasGAP/p62DOK/SHIP 0.062 0.035 -10000 0 -0.056 16 16
CD79A 0.031 0.009 -10000 0 0 42 42
re-entry into mitotic cell cycle -0.014 0.066 0.2 4 -0.19 19 23
RASA1 0.032 0.006 -10000 0 0 18 18
MAPK3 -0.032 0.05 0.2 3 -0.23 3 6
MAPK1 -0.029 0.05 0.2 5 -0.23 2 7
CD72/SHP1 -0.004 0.078 0.22 45 -0.33 1 46
NFKB1 0.032 0.005 -10000 0 0 13 13
MAPK8 0.026 0.085 0.23 25 -0.35 6 31
actin cytoskeleton organization 0.045 0.095 0.25 24 -0.27 6 30
NF-kappa-B/RelA 0.045 0.057 0.25 4 -0.2 13 17
Calcineurin 0.006 0.069 0.2 1 -0.23 3 4
PI3K -0.049 0.044 0.1 9 -0.23 3 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.043 -10000 0 -0.22 4 4
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.043 0.076 -10000 0 -0.57 6 6
DAPP1 0.028 0.074 -10000 0 -0.62 5 5
cytokine secretion -0.019 0.065 0.24 8 -0.23 17 25
mol:DAG -0.004 0.053 0.23 1 -0.24 3 4
PLCG2 0.032 0.007 -10000 0 0 26 26
MAP2K1 -0.027 0.05 0.22 3 -0.24 3 6
B-cell antigen/BCR complex/FcgammaRIIB 0.038 0.043 -10000 0 -0.046 14 14
mol:PI-3-4-5-P3 -0.016 0.069 0.27 14 -10000 0 14
ETS1 0.014 0.064 0.18 12 -0.24 2 14
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.036 0.068 -10000 0 -0.064 10 10
B-cell antigen/BCR complex/LYN 0.012 0.029 -10000 0 -0.34 1 1
MALT1 0.031 0.009 -10000 0 0 42 42
TRAF6 0.032 0.006 -10000 0 0 16 16
RAC1 0.042 0.094 0.24 22 -0.28 6 28
B-cell antigen/BCR complex/LYN/SYK 0.045 0.059 0.22 24 -0.32 1 25
CARD11 -0.005 0.053 0.22 1 -0.23 3 4
FCGR2B 0.025 0.014 -10000 0 0 129 129
PPP3CA 0.027 0.013 -10000 0 0 100 100
BCL10 0.032 0.006 -10000 0 0 19 19
IKK complex 0.001 0.038 0.15 9 -0.12 9 18
PTPRC 0.024 0.015 -10000 0 0 137 137
PDPK1 -0.013 0.064 0.24 19 -10000 0 19
PPP3CB 0.023 0.015 -10000 0 0 151 151
PPP3CC 0.032 0.006 -10000 0 0 16 16
POU2F2 0.014 0.021 0.12 6 -0.07 10 16
HIF-2-alpha transcription factor network

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
MMP14 -0.017 0.18 -10000 0 -0.64 37 37
oxygen homeostasis 0 0.002 0.025 1 -10000 0 1
TCEB2 0.033 0.004 -10000 0 0 6 6
TCEB1 0.032 0.006 -10000 0 0 15 15
VHL/Elongin B/Elongin C/HIF2A -0.008 0.081 -10000 0 -0.2 30 30
EPO -0.008 0.058 -10000 0 -0.24 22 22
FIH (dimer) 0.023 0.016 -10000 0 -0.032 4 4
APEX1 0.032 0.009 -10000 0 -10000 0 0
SERPINE1 -0.025 0.046 -10000 0 -0.21 19 19
FLT1 -0.017 0.17 -10000 0 -0.6 39 39
ADORA2A -0.051 0.061 0.16 6 -0.2 35 41
germ cell development -0.047 0.056 0.08 3 -0.19 38 41
SLC11A2 -0.051 0.061 0.16 2 -0.2 34 36
BHLHE40 -0.047 0.057 0.081 3 -0.19 38 41
HIF1AN 0.023 0.016 -10000 0 -0.032 4 4
HIF2A/ARNT/SIRT1 -0.007 0.086 -10000 0 -0.17 72 72
ETS1 0.034 0.013 -10000 0 -10000 0 0
CITED2 -0.023 0.16 -10000 0 -0.57 41 41
KDR 0.017 0.082 -10000 0 -0.55 10 10
PGK1 -0.053 0.061 0.16 2 -0.21 34 36
SIRT1 0.024 0.015 -10000 0 0 145 145
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.006 0.096 -10000 0 -0.22 34 34
EPAS1 -0.023 0.045 0.099 1 -0.12 86 87
SP1 0.034 0.007 -10000 0 -0.032 1 1
ABCG2 -0.053 0.062 0.16 2 -0.2 35 37
EFNA1 -0.053 0.06 -10000 0 -0.21 34 34
FXN -0.052 0.058 0.15 3 -0.2 33 36
POU5F1 -0.047 0.057 0.081 3 -0.19 38 41
neuron apoptosis -0.006 0.094 0.21 34 -10000 0 34
EP300 0.031 0.009 -10000 0 0 41 41
EGLN3 0.03 0.011 -10000 0 -0.031 3 3
EGLN2 0.03 0.011 -10000 0 -0.032 7 7
EGLN1 0.032 0.009 -10000 0 -0.031 6 6
VHL/Elongin B/Elongin C 0.043 0.009 -10000 0 -0.04 1 1
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.033 0.009 -10000 0 -0.032 5 5
SLC2A1 -0.051 0.061 0.16 6 -0.2 34 40
TWIST1 -0.025 0.043 0.17 2 -0.19 14 16
ELK1 0.033 0.011 -10000 0 -0.032 13 13
HIF2A/ARNT/Cbp/p300 0.005 0.096 -10000 0 -0.2 38 38
VEGFA -0.052 0.058 0.16 2 -0.2 33 35
CREBBP 0.033 0.004 -10000 0 0 7 7
Aurora B signaling

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
Condensin I complex -0.008 0.026 -10000 0 -0.13 16 16
STMN1 -0.031 0.008 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.029 0.044 -10000 0 -0.05 3 3
Chromosomal passenger complex/Cul3 protein complex -0.034 0.051 -10000 0 -0.096 181 181
BIRC5 0.019 0.017 -10000 0 -0.032 6 6
DES 0.02 0.1 -10000 0 -0.65 11 11
Aurora C/Aurora B/INCENP 0.05 0.032 -10000 0 -0.042 29 29
Aurora B/TACC1 0.04 0.016 -10000 0 -0.015 25 25
Aurora B/PP2A 0.044 0.017 -10000 0 -0.017 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.002 0.013 -10000 0 -0.15 4 4
mitotic metaphase/anaphase transition -0.001 0.002 0.015 4 -10000 0 4
NDC80 -0.026 0.012 -10000 0 -10000 0 0
Cul3 protein complex 0.027 0.022 -10000 0 -10000 0 0
KIF2C 0.002 0.032 -10000 0 -0.24 6 6
PEBP1 0.032 0.009 -10000 0 -0.031 7 7
KIF20A 0.021 0.016 -10000 0 -0.031 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.044 0.017 -10000 0 -0.017 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.028 0.012 -10000 0 0 75 75
SMC4 0.008 0.014 -10000 0 0 389 389
NSUN2/NPM1/Nucleolin -0.005 0.082 -10000 0 -0.53 11 11
PSMA3 0.031 0.008 -10000 0 0 34 34
G2/M transition of mitotic cell cycle -0.001 0.002 0.017 1 -10000 0 1
H3F3B 0.008 0.005 0.021 1 -0.01 28 29
AURKB 0.028 0.015 -10000 0 -0.033 20 20
AURKC 0.03 0.01 -10000 0 0 50 50
CDCA8 0.03 0.012 -10000 0 -0.032 10 10
cytokinesis -0.007 0.044 0.15 3 -0.24 8 11
Aurora B/Septin1 0.006 0.052 0.18 3 -0.25 8 11
AURKA 0.028 0.013 -10000 0 -0.031 2 2
INCENP 0.032 0.009 -10000 0 -0.031 9 9
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.033 0.007 -10000 0 -0.031 4 4
hSgo1/Aurora B/Survivin 0.019 0.026 -10000 0 -0.023 9 9
EVI5 0.031 0.009 -10000 0 -0.031 6 6
RhoA/GTP 0.028 0.05 0.16 1 -0.18 4 5
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0.008 0.037 0.13 1 -0.19 10 11
NCAPG 0.026 0.014 -10000 0 0 116 116
Aurora B/HC8 Proteasome 0.043 0.018 -10000 0 -0.017 20 20
NCAPD2 0.025 0.014 -10000 0 0 119 119
Aurora B/PP1-gamma 0.044 0.017 -10000 0 -0.017 24 24
RHOA 0.032 0.006 -10000 0 0 19 19
NCAPH 0.032 0.006 -10000 0 0 18 18
NPM1 -0.002 0.081 -10000 0 -0.38 16 16
RASA1 0.032 0.006 -10000 0 0 18 18
KLHL9 0.02 0.016 -10000 0 0 200 200
mitotic prometaphase -0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.018 -10000 0 -0.017 20 20
PPP1CC 0.033 0.005 -10000 0 0 11 11
Centraspindlin 0.022 0.044 0.16 1 -0.17 6 7
RhoA/GDP 0.024 0.005 -10000 0 0 19 19
NSUN2 -0.002 0.046 -10000 0 -0.3 11 11
MYLK 0.008 0.005 0.021 1 -0.009 35 36
KIF23 0.027 0.014 -10000 0 -0.032 6 6
VIM -0.023 0.015 -10000 0 -10000 0 0
RACGAP1 0.022 0.017 -10000 0 -0.033 5 5
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.046 -10000 0 -0.28 13 13
Chromosomal passenger complex 0 0.029 0.083 1 -0.16 9 10
Chromosomal passenger complex/EVI5 0.065 0.044 -10000 0 -0.077 6 6
TACC1 0.032 0.005 -10000 0 0 12 12
PPP2R5D 0.033 0.004 -10000 0 0 6 6
CUL3 0.033 0.001 -10000 0 0 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.006 0.042 0.066 1 -0.16 30 31
regulation of axonogenesis 0.023 0.06 0.27 27 -10000 0 27
myoblast fusion -0.017 0.034 0.35 3 -10000 0 3
mol:GTP 0.015 0.05 -10000 0 -0.18 31 31
regulation of calcium-dependent cell-cell adhesion -0.027 0.038 0.12 26 -10000 0 26
ARF1/GTP 0.034 0.046 -10000 0 -0.15 29 29
mol:GM1 -0.001 0.034 -10000 0 -0.13 31 31
mol:Choline -0.028 0.026 -10000 0 -0.14 25 25
lamellipodium assembly -0.005 0.059 -10000 0 -0.39 11 11
MAPK3 0.004 0.036 -10000 0 -0.12 31 31
ARF6/GTP/NME1/Tiam1 0.028 0.038 -10000 0 -0.12 26 26
ARF1 0.032 0.006 -10000 0 0 19 19
ARF6/GDP 0.017 0.035 -10000 0 -0.35 3 3
ARF1/GDP 0.007 0.068 -10000 0 -0.25 29 29
ARF6 0.042 0.012 0.09 1 -10000 0 1
RAB11A 0.032 0.005 -10000 0 0 14 14
TIAM1 0.026 0.019 -10000 0 -0.035 37 37
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.031 -10000 0 -0.12 21 21
actin filament bundle formation -0.019 0.07 0.25 29 -10000 0 29
KALRN -0.001 0.044 -10000 0 -0.26 13 13
RAB11FIP3/RAB11A 0.048 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.071 -10000 0 -0.25 29 29
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.051 -10000 0 -0.25 13 13
substrate adhesion-dependent cell spreading 0.014 0.05 -10000 0 -0.18 31 31
cortical actin cytoskeleton organization -0.005 0.06 -10000 0 -0.39 11 11
RAC1 0.02 0.016 -10000 0 0 204 204
liver development 0.014 0.05 -10000 0 -0.18 31 31
ARF6/GTP 0.015 0.05 -10000 0 -0.18 31 31
RhoA/GTP 0.033 0.046 -10000 0 -0.15 29 29
mol:GDP -0.009 0.061 -10000 0 -0.26 27 27
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.051 -10000 0 -0.14 31 31
RHOA 0.032 0.006 -10000 0 0 19 19
PLD1 0.003 0.039 -10000 0 -0.15 29 29
RAB11FIP3 0.033 0.003 -10000 0 0 5 5
tube morphogenesis -0.005 0.059 -10000 0 -0.39 11 11
ruffle organization -0.023 0.06 -10000 0 -0.27 27 27
regulation of epithelial cell migration 0.014 0.05 -10000 0 -0.18 31 31
PLD2 0.004 0.037 -10000 0 -0.15 26 26
PIP5K1A -0.023 0.06 -10000 0 -0.28 27 27
mol:Phosphatidic acid -0.028 0.026 -10000 0 -0.14 25 25
Rac1/GTP -0.005 0.06 -10000 0 -0.4 11 11
Signaling events mediated by HDAC Class III

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
EP300 0.031 0.009 -10000 0 0 41 41
HDAC4 0.033 0.004 -10000 0 0 6 6
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.011 0.01 -10000 0 -10000 0 0
CDKN1A 0.002 0.036 0.06 135 -10000 0 135
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.009 -10000 0 0 43 43
FOXO3 0.008 0.011 -10000 0 -10000 0 0
FOXO1 0.03 0.01 -10000 0 0 53 53
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 0 43 43
TAT 0.032 0.005 -10000 0 0 13 13
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.003 0 14 -10000 0 14
PPARGC1A 0.033 0.004 -10000 0 0 9 9
FHL2 0.032 0.007 -10000 0 0 26 26
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.034 0.023 -10000 0 -10000 0 0
HIST2H4A -0.011 0.01 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.019 0.023 0.15 5 -0.2 1 6
SIRT1 0.023 0.016 -10000 0 -0.034 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.032 0.052 -10000 0 -0.048 134 134
SIRT1/Histone H1b 0.019 0.026 -10000 0 -0.14 8 8
apoptosis -0.031 0.052 0.05 135 -10000 0 135
SIRT1/PGC1A 0.031 0.022 -10000 0 -0.031 9 9
p53/SIRT1 0.029 0.026 -10000 0 -0.021 29 29
SIRT1/FOXO4 0.02 0.022 -10000 0 -0.13 6 6
FOXO1/FHL2/SIRT1 0.028 0.049 -10000 0 -0.043 134 134
HIST1H1E 0.006 0.002 -10000 0 -0.007 1 1
SIRT1/p300 0.035 0.023 -10000 0 -10000 0 0
muscle cell differentiation 0.019 0.013 -10000 0 -10000 0 0
TP53 0.027 0.013 -10000 0 -0.034 2 2
KU70/SIRT1/BAX 0.031 0.053 -10000 0 -0.05 135 135
CREBBP 0.033 0.004 -10000 0 0 7 7
MEF2D 0.032 0.006 -10000 0 0 17 17
HIV-1 Tat/SIRT1 0.035 0.022 -10000 0 -10000 0 0
ACSS2 -0.011 0.01 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.019 0.013 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.044 0.06 -10000 0 -0.15 16 16
Ran/GTP/Exportin 1/HDAC1 -0.035 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.062 0.16 1 -0.19 26 27
SUMO1 0.033 0.001 -10000 0 0 1 1
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.03 -10000 0 -0.1 42 42
FKBP3 0.031 0.009 -10000 0 0 37 37
Histones 0.035 0.044 -10000 0 -0.2 8 8
YY1/LSF 0.007 0.064 -10000 0 -0.16 61 61
SMG5 0.032 0.006 -10000 0 0 17 17
RAN 0.032 0.005 -10000 0 0 12 12
I kappa B alpha/HDAC3 -0.002 0.035 -10000 0 -0.11 36 36
I kappa B alpha/HDAC1 0.015 0.062 -10000 0 -0.19 39 39
SAP18 0.031 0.009 -10000 0 0 36 36
RELA 0 0.051 0.11 16 -0.15 39 55
HDAC1/Smad7 0.032 0.037 -10000 0 -0.046 8 8
RANGAP1 0.031 0.009 -10000 0 0 40 40
HDAC3/TR2 0.031 0.038 -10000 0 -0.21 9 9
NuRD/MBD3 Complex 0.001 0.047 -10000 0 -0.21 14 14
NF kappa B1 p50/RelA 0.017 0.062 0.17 2 -0.21 14 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.006 -10000 0 0 17 17
GATA1 0.033 0.002 -10000 0 0 2 2
Mad/Max 0.046 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.046 -10000 0 -0.19 15 15
RBBP7 0.033 0.002 -10000 0 0 2 2
NPC 0.019 0.003 -10000 0 -0.008 4 4
RBBP4 0.026 0.013 -10000 0 0 105 105
MAX 0.031 0.009 -10000 0 0 39 39
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 0 13 13
NFKBIA 0.001 0.049 -10000 0 -0.19 30 30
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.055 -10000 0 -0.16 36 36
SIN3 complex 0.051 0.032 -10000 0 -0.042 39 39
SMURF1 0.019 0.016 -10000 0 0 214 214
CHD3 0.032 0.005 -10000 0 0 12 12
SAP30 0.032 0.006 -10000 0 0 16 16
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.033 0.005 -10000 0 0 10 10
YY1/HDAC3 -0.002 0.053 -10000 0 -0.21 19 19
YY1/HDAC2 0.008 0.063 -10000 0 -0.16 56 56
YY1/HDAC1 0.006 0.061 -10000 0 -0.15 57 57
NuRD/MBD2 Complex (MeCP1) 0.002 0.053 -10000 0 -0.23 14 14
PPARG 0.006 0.044 0.12 15 -0.21 13 28
HDAC8/hEST1B 0.041 0.013 -10000 0 -10000 0 0
UBE2I 0.033 0.003 -10000 0 0 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 0 13 13
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
HDAC3/SMRT (N-CoR2) 0.031 0.038 -10000 0 -0.21 9 9
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.031 0.036 -10000 0 -0.046 8 8
CREBBP 0.033 0.004 -10000 0 0 7 7
NuRD/MBD3/MBD3L2 Complex 0.005 0.045 0.15 1 -0.19 12 13
HDAC1 0.028 0.012 -10000 0 0 74 74
HDAC3 0.011 0.021 -10000 0 -0.19 4 4
HDAC2 0.031 0.009 -10000 0 0 40 40
YY1 0.006 0.002 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.032 0.007 -10000 0 0 23 23
NCOR2 0.033 0.005 -10000 0 0 11 11
MXD1 0.033 0.001 -10000 0 0 1 1
STAT3 0.013 0.005 -10000 0 -0.011 8 8
NFKB1 0.032 0.005 -10000 0 0 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.033 0.003 -10000 0 0 4 4
YY1/LSF/HDAC1 0.019 0.067 -10000 0 -0.15 59 59
YY1/SAP30/HDAC1 0.019 0.067 -10000 0 -0.15 60 60
EP300 0.031 0.009 -10000 0 0 41 41
STAT3 (dimer non-phopshorylated) 0.013 0.005 -10000 0 -0.01 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.049 -10000 0 -0.19 30 30
histone deacetylation 0.002 0.052 -10000 0 -0.23 14 14
STAT3 (dimer non-phopshorylated)/HDAC3 0.01 0.045 -10000 0 -0.12 45 45
nuclear export -0.04 0.013 -10000 0 -10000 0 0
PRKACA 0.031 0.009 -10000 0 0 36 36
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.028 0.012 -10000 0 0 77 77
GATA2/HDAC3 0.031 0.038 -10000 0 -0.22 9 9
GATA1/HDAC1 0.04 0.022 -10000 0 -0.016 61 61
GATA1/HDAC3 0.032 0.038 -10000 0 -0.22 9 9
CHD4 0.032 0.007 -10000 0 0 27 27
TNF-alpha/TNFR1A 0.026 0.031 -10000 0 -0.016 163 163
SIN3/HDAC complex/Mad/Max -0.007 0.063 -10000 0 -0.23 24 24
NuRD Complex 0.004 0.05 -10000 0 -0.22 13 13
positive regulation of chromatin silencing 0.033 0.042 -10000 0 -0.2 8 8
SIN3B 0.031 0.009 -10000 0 0 40 40
MTA2 0.033 0.004 -10000 0 0 9 9
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.033 0.001 -10000 0 0 1 1
SUMO1/HDAC1 0.029 0.043 -10000 0 -0.11 39 39
HDAC complex 0.06 0.042 -10000 0 -0.054 26 26
GATA1/Fog1 0.025 0.002 -10000 0 0 2 2
FKBP25/HDAC1/HDAC2 0.043 0.043 -10000 0 -0.047 52 52
TNF 0.033 0.004 -10000 0 0 7 7
negative regulation of cell growth -0.006 0.063 -10000 0 -0.23 24 24
NuRD/MBD2/PRMT5 Complex 0.002 0.053 -10000 0 -0.23 14 14
Ran/GTP/Exportin 1 0.033 0.043 -10000 0 -0.11 41 41
NF kappa B/RelA/I kappa B alpha -0.007 0.048 -10000 0 -0.2 21 21
SIN3/HDAC complex/NCoR1 0 0.053 -10000 0 -0.25 13 13
TFCP2 0.032 0.006 -10000 0 0 17 17
NR2C1 0.033 0.005 -10000 0 0 10 10
MBD3 0.031 0.008 -10000 0 0 35 35
MBD2 0.032 0.006 -10000 0 0 20 20
Insulin Pathway

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
CBL/APS/CAP 0.028 0.047 -10000 0 -0.062 12 12
TC10/GTP 0.019 0.049 -10000 0 -0.059 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.04 -10000 0 -0.056 21 21
HRAS 0.032 0.007 -10000 0 0 24 24
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.032 0.007 -10000 0 0 21 21
FOXO3 -0.025 0.14 -10000 0 -0.57 31 31
AKT1 -0.034 0.071 0.25 8 -10000 0 8
INSR 0.032 0.019 0.071 35 -0.035 20 55
Insulin Receptor/Insulin 0.051 0.037 0.21 5 -0.063 2 7
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.016 -10000 0 0 213 213
SORBS1 0.023 0.015 -10000 0 0 154 154
CRK 0.033 0.005 -10000 0 0 10 10
PTPN1 -0.023 0.04 0.14 24 -10000 0 24
CAV1 -0.016 0.03 0.17 7 -10000 0 7
CBL/APS/CAP/Crk-II/C3G 0.038 0.059 -10000 0 -0.049 152 152
Insulin Receptor/Insulin/IRS1/NCK2 0.078 0.039 -10000 0 -0.056 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.041 -10000 0 -0.064 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.051 0.17 29 -0.21 3 32
RPS6KB1 -0.042 0.066 0.22 8 -10000 0 8
PARD6A 0.033 0.004 -10000 0 0 8 8
CBL 0.033 0.005 -10000 0 0 11 11
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.016 -10000 0 -10000 0 0
PIK3R1 0.03 0.01 -10000 0 0 47 47
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.069 0.15 25 -10000 0 25
HRAS/GTP -0.041 0.026 0.03 31 -10000 0 31
Insulin Receptor 0.032 0.019 0.071 35 -0.035 20 55
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.081 0.047 -10000 0 -0.062 17 17
PRKCI 0.03 0.035 -10000 0 -0.33 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.044 0.041 0.064 40 -10000 0 40
SHC1 0.03 0.01 -10000 0 0 55 55
negative regulation of MAPKKK cascade 0.022 0.05 -10000 0 -10000 0 0
PI3K 0.066 0.045 -10000 0 -0.059 17 17
NCK2 0.033 0.003 -10000 0 0 5 5
RHOQ 0.033 0.002 -10000 0 0 2 2
mol:H2O2 -0.004 0.005 0.03 1 -10000 0 1
HRAS/GDP 0.023 0.005 -10000 0 0 24 24
AKT2 -0.041 0.064 0.23 6 -10000 0 6
PRKCZ 0.013 0.008 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.018 0.053 0.15 35 -10000 0 35
F2RL2 0.033 0.005 -10000 0 0 10 10
TRIP10 0.031 0.009 -10000 0 0 37 37
Insulin Receptor/Insulin/Shc 0.052 0.037 -10000 0 -0.044 18 18
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.013 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.065 0.039 -10000 0 -0.051 17 17
RAPGEF1 0.032 0.007 -10000 0 0 23 23
RASA1 0.032 0.006 -10000 0 0 18 18
NCK1 0.031 0.008 -10000 0 0 28 28
CBL/APS/CAP/Crk-II 0.031 0.049 -10000 0 -0.041 155 155
TC10/GDP 0.025 0.002 -10000 0 0 2 2
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.046 -10000 0 -0.056 15 15
INPP5D -0.025 0.018 0.03 34 -10000 0 34
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.006 0.003 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.033 0.005 -10000 0 0 10 10
IRS1 0.033 0.003 -10000 0 0 5 5
p62DOK/RasGAP 0.023 0.051 -10000 0 -10000 0 0
INS 0.038 0.017 0.079 55 -0.035 1 56
mol:PI-3-4-P2 -0.025 0.018 0.03 34 -10000 0 34
GRB2 0.032 0.007 -10000 0 0 22 22
EIF4EBP1 -0.039 0.063 0.22 8 -10000 0 8
PTPRA 0.028 0.017 0.072 2 -0.035 17 19
PIK3CA 0.031 0.009 -10000 0 0 41 41
TC10/GTP/CIP4 0.042 0.012 -10000 0 -0.013 6 6
PDPK1 0.033 0.004 -10000 0 0 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.011 0.028 -10000 0 -0.12 17 17
Insulin Receptor/Insulin/IRS1 0.06 0.031 -10000 0 -0.044 19 19
Insulin Receptor/Insulin/IRS3 0.05 0.024 0.11 34 -0.042 1 35
Par3/Par6 0.07 0.028 -10000 0 -0.048 12 12
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.032 0.005 -10000 0 0 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.076 0.19 3 -0.26 19 22
ERC1 0.032 0.007 -10000 0 0 26 26
RIP2/NOD2 0.046 0.013 -10000 0 -0.016 9 9
NFKBIA -0.041 0.025 0.19 4 -10000 0 4
BIRC2 0.033 0.005 -10000 0 0 10 10
IKBKB 0.033 0.004 -10000 0 0 7 7
RIPK2 0.032 0.005 -10000 0 0 13 13
IKBKG 0.007 0.06 -10000 0 -0.39 9 9
IKK complex/A20 0.04 0.07 -10000 0 -0.38 9 9
NEMO/A20/RIP2 0.032 0.005 -10000 0 0 13 13
XPO1 0.033 0.001 -10000 0 0 1 1
NEMO/ATM 0.025 0.063 -10000 0 -0.38 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.005 -10000 0 0 12 12
Exportin 1/RanGTP 0.044 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.024 0.071 -10000 0 -0.37 9 9
BCL10/MALT1/TRAF6 0.055 0.033 -10000 0 -0.047 28 28
NOD2 0.032 0.006 -10000 0 0 19 19
NFKB1 0.032 0.005 -10000 0 0 13 13
RELA 0.033 0.004 -10000 0 0 9 9
MALT1 0.031 0.009 -10000 0 0 42 42
cIAP1/UbcH5C 0.047 0.01 -10000 0 -10000 0 0
ATM 0.031 0.008 -10000 0 0 35 35
TNF/TNFR1A 0.026 0.031 -10000 0 -0.016 163 163
TRAF6 0.032 0.006 -10000 0 0 16 16
PRKCA 0.033 0.005 -10000 0 0 10 10
CHUK 0.024 0.015 -10000 0 0 148 148
UBE2D3 0.033 0.005 -10000 0 0 10 10
TNF 0.033 0.004 -10000 0 0 7 7
NF kappa B1 p50/RelA 0.065 0.026 -10000 0 -0.051 20 20
BCL10 0.032 0.006 -10000 0 0 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.04 0.025 0.19 4 -10000 0 4
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 0 13 13
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
IKK complex 0.03 0.07 -10000 0 -0.38 9 9
CYLD 0.033 0.005 -10000 0 0 11 11
IKK complex/PKC alpha 0.038 0.076 -10000 0 -0.38 9 9
TRAIL signaling pathway

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
TNFSF10 0.029 0.011 -10000 0 0 60 60
positive regulation of NF-kappaB transcription factor activity 0.041 0.021 -10000 0 -0.016 43 43
MAP2K4 -0.001 0.041 0.2 2 -0.18 12 14
IKBKB 0.033 0.004 -10000 0 0 7 7
TNFRSF10B 0.032 0.006 -10000 0 0 19 19
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.005 0.01 -10000 0 -0.067 8 8
IKBKG 0.033 0.003 -10000 0 0 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.005 -10000 0 0 13 13
TRAIL/TRAILR2 0.041 0.021 -10000 0 -0.016 44 44
TRAIL/TRAILR3 0.041 0.021 -10000 0 -0.016 43 43
TRAIL/TRAILR1 0.022 0.008 -10000 0 0 60 60
TRAIL/TRAILR4 0.041 0.021 -10000 0 -0.016 43 43
TRAIL/TRAILR1/DAP3/GTP 0.036 0.018 -10000 0 -0.029 2 2
IKK complex -0.05 0.12 -10000 0 -0.24 138 138
RIPK1 0.032 0.006 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.004 -10000 0 0 15 15
MAPK3 -0.03 0.008 0 20 -10000 0 20
MAP3K1 0.01 0.036 -10000 0 -0.18 11 11
TRAILR4 (trimer) 0.032 0.005 -10000 0 0 13 13
TRADD 0.033 0.004 -10000 0 0 9 9
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.028 -10000 0 -0.12 20 20
CFLAR 0.033 0.004 -10000 0 0 6 6
MAPK1 -0.028 0.011 0 57 -10000 0 57
TRAIL/TRAILR1/FADD/TRADD/RIP 0.067 0.031 -10000 0 -0.049 18 18
mol:ceramide 0.005 0.01 -10000 0 -0.067 8 8
FADD 0.033 0.005 -10000 0 0 11 11
MAPK8 -0.01 0.037 0.17 2 -0.26 4 6
TRAF2 0.032 0.006 -10000 0 0 20 20
TRAILR3 (trimer) 0.032 0.005 -10000 0 0 13 13
CHUK 0.024 0.015 -10000 0 0 148 148
TRAIL/TRAILR1/FADD 0.038 0.018 -10000 0 -0.013 43 43
DAP3 0.032 0.006 -10000 0 0 15 15
CASP10 -0.017 0.029 0.14 14 -0.1 8 22
JNK cascade 0.041 0.021 -10000 0 -0.016 43 43
TRAIL (trimer) 0.029 0.011 -10000 0 0 60 60
TNFRSF10C 0.032 0.005 -10000 0 0 13 13
TRAIL/TRAILR1/DAP3/GTP/FADD 0.048 0.027 -10000 0 -0.038 7 7
TRAIL/TRAILR2/FADD 0.053 0.034 -10000 0 -0.047 15 15
cell death 0.005 0.01 -10000 0 -0.067 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.033 -10000 0 -0.13 23 23
TRAILR2 (trimer) 0.032 0.006 -10000 0 0 19 19
CASP8 0.015 0.025 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.082 0.041 -10000 0 -0.06 23 23
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.1 0.14 0.4 59 -10000 0 59
CRP 0.082 0.12 0.36 28 -10000 0 28
cell cycle arrest 0.088 0.11 0.34 30 -10000 0 30
TIMP1 0.081 0.1 0.4 9 -0.53 1 10
IL6ST 0.034 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.058 0.25 16 -0.21 3 19
AP1 0.051 0.074 -10000 0 -0.36 6 6
GAB2 0.033 0.006 -10000 0 -10000 0 0
TNFSF11 0.077 0.1 0.38 13 -10000 0 13
HSP90B1 0.052 0.048 -10000 0 -0.44 2 2
GAB1 0.033 0.005 -10000 0 0 12 12
MAPK14 0.036 0.075 0.17 91 -10000 0 91
AKT1 0.017 0.047 0.22 3 -0.39 3 6
FOXO1 0.008 0.048 0.21 3 -0.38 3 6
MAP2K6 0.014 0.047 0.19 1 -0.22 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.004 0.062 0.26 18 -10000 0 18
MITF 0.015 0.045 -10000 0 -0.21 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.009 -10000 0 0 43 43
A2M -0.019 0.18 -10000 0 -0.95 18 18
CEBPB 0.03 0.013 -10000 0 -0.032 1 1
GRB2/SOS1/GAB family/SHP2 0.036 0.05 0.22 1 -0.28 5 6
STAT3 0.086 0.11 0.36 25 -10000 0 25
STAT1 0.017 0.019 -10000 0 -10000 0 0
CEBPD 0.08 0.11 0.37 17 -10000 0 17
PIK3CA 0.031 0.009 -10000 0 0 41 41
PI3K 0.041 0.02 -10000 0 -0.016 15 15
JUN 0.033 0.005 -10000 0 0 10 10
PIAS3/MITF 0.067 0.079 0.19 103 -0.22 2 105
MAPK11 0.028 0.07 0.17 71 -10000 0 71
STAT3 (dimer)/FOXO1 0.01 0.054 0.28 3 -10000 0 3
GRB2/SOS1/GAB family 0.073 0.055 0.21 3 -0.21 3 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.006 0.027 -10000 0 -0.22 3 3
GRB2 0.032 0.007 -10000 0 0 22 22
JAK2 0.029 0.011 -10000 0 0 70 70
LBP 0.097 0.12 0.36 53 -0.51 1 54
PIK3R1 0.03 0.01 -10000 0 0 47 47
JAK1 0.033 0.006 -10000 0 -10000 0 0
MYC 0.082 0.11 0.39 19 -10000 0 19
FGG 0.077 0.1 0.39 12 -10000 0 12
macrophage differentiation 0.088 0.11 0.34 30 -10000 0 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.044 0.055 -10000 0 -10000 0 0
JUNB 0.087 0.12 0.39 42 -10000 0 42
FOS 0.023 0.016 -10000 0 0 163 163
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.038 0.12 13 -0.22 3 16
STAT1/PIAS1 0.084 0.068 0.2 87 -10000 0 87
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.048 -10000 0 -0.4 3 3
STAT3 (dimer) 0.087 0.11 0.34 29 -10000 0 29
PRKCD 0.11 0.16 0.29 196 -10000 0 196
IL6R 0.033 0.005 -10000 0 -10000 0 0
SOCS3 0.048 0.085 0.36 9 -10000 0 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.063 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.054 0.24 14 -0.22 1 15
HCK 0.023 0.015 -10000 0 0 152 152
MAPKKK cascade 0.05 0.068 0.27 3 -0.38 6 9
bone resorption 0.077 0.1 0.36 15 -10000 0 15
IRF1 0.078 0.11 0.35 22 -10000 0 22
mol:GDP 0.014 0.046 0.19 1 -0.21 3 4
SOS1 0 0.002 0.021 5 -10000 0 5
VAV1 0.014 0.046 0.19 1 -0.22 3 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.012 0.044 0.19 1 -0.33 4 5
PTPN11 0.013 0.061 -10000 0 -0.64 4 4
IL6/IL6RA 0.025 0.027 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.058 0.029 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.051 0.041 -10000 0 -10000 0 0
IL6 0.018 0.017 -10000 0 -10000 0 0
PIAS3 0.032 0.006 -10000 0 0 15 15
PTPRE 0.018 0.019 -10000 0 -0.031 29 29
PIAS1 0.033 0.005 -10000 0 0 11 11
RAC1 0.02 0.016 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.03 0.11 32 -10000 0 32
LMO4 0.033 0.007 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.082 0.089 0.32 2 -10000 0 2
MCL1 0.015 0.056 0.25 5 -0.41 2 7
S1P3 pathway

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
PDGFRB 0.032 0.005 -10000 0 0 12 12
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.021 0.032 -10000 0 -0.15 10 10
GNAO1 0.003 0.009 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.026 0.021 -10000 0 -0.029 2 2
AKT1 -0.014 0.085 -10000 0 -0.43 20 20
AKT3 -0.006 0.046 -10000 0 -0.33 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.005 -10000 0 0 12 12
GNAI2 0.033 0.006 -10000 0 -10000 0 0
GNAI3 0.029 0.011 -10000 0 -10000 0 0
GNAI1 0.017 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.015 -10000 0 -0.1 2 2
MAPK3 -0.002 0.024 -10000 0 -0.16 7 7
MAPK1 0 0.015 -10000 0 -0.15 1 1
JAK2 -0.024 0.048 -10000 0 -0.18 13 13
CXCR4 -0.001 0.023 0.078 7 -0.17 5 12
FLT1 0.031 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.005 -10000 0 0 19 19
Rac1/GDP 0.015 0.012 -10000 0 0 204 204
SRC -0.001 0.017 -10000 0 -0.15 3 3
S1P/S1P3/Gi 0.002 0.015 -10000 0 -0.1 2 2
RAC1 0.02 0.016 -10000 0 0 204 204
RhoA/GTP -0.037 0.047 -10000 0 -0.16 20 20
VEGFA 0.015 0.017 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.002 0.015 0.084 12 -0.1 2 14
VEGFR1 homodimer/VEGFA homodimer 0.014 0.032 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 0 19 19
S1P/S1P3/Gq 0.012 0.007 -10000 0 -0.11 1 1
GNAQ 0.032 0.007 -10000 0 0 21 21
GNAZ 0.027 0.013 -10000 0 0 94 94
G12/G13 0.029 0.024 -10000 0 -10000 0 0
GNA14 0.032 0.007 -10000 0 0 23 23
GNA15 0.03 0.009 -10000 0 0 44 44
GNA12 0.02 0.016 -10000 0 0 203 203
GNA13 0.033 0.005 -10000 0 0 10 10
GNA11 0.031 0.009 -10000 0 0 37 37
Rac1/GTP -0.03 0.041 -10000 0 -0.15 11 11
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.007 -9999 0 -10000 0 0
SVIL 0.023 0.016 -9999 0 -10000 0 0
ZNF318 0.032 0.004 -9999 0 -10000 0 0
JMJD2C 0.002 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.043 0.014 -9999 0 -0.03 11 11
CARM1 0.031 0.009 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 0 12 12
PELP1 0.032 0.005 -9999 0 0 13 13
CTNNB1 0.033 0.006 -9999 0 -10000 0 0
AKT1 0.031 0.009 -9999 0 0 39 39
PTK2B 0.033 0.005 -9999 0 -10000 0 0
MED1 0.033 0.004 -9999 0 0 8 8
MAK 0.032 0.006 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.017 -9999 0 -10000 0 0
GSN 0.031 0.009 -9999 0 -10000 0 0
NCOA2 0.033 0.005 -9999 0 -10000 0 0
NCOA6 0.029 0.011 -9999 0 -10000 0 0
DNA-PK 0.054 0.035 -9999 0 -0.047 39 39
NCOA4 0.024 0.015 -9999 0 0 143 143
PIAS3 0.033 0.006 -9999 0 -10000 0 0
cell proliferation 0.003 0.054 -9999 0 -0.43 7 7
XRCC5 0.033 0.002 -9999 0 0 2 2
UBE3A 0.033 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.023 0.007 -9999 0 -0.017 11 11
FHL2 0.006 0.03 -9999 0 -0.27 3 3
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.002 0 -9999 0 -10000 0 0
CDK6 0.019 0.016 -9999 0 0 222 222
TGFB1I1 0.005 0.012 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.034 0.024 -9999 0 -0.03 5 5
XRCC6 0.03 0.009 -9999 0 0 43 43
T-DHT/AR 0.031 0.03 -9999 0 -0.035 38 38
CTDSP1 0.033 0.003 -9999 0 -10000 0 0
CTDSP2 0.028 0.012 -9999 0 -10000 0 0
BRCA1 0.033 0.006 -9999 0 -10000 0 0
TCF4 0.031 0.008 -9999 0 0 30 30
CDKN2A 0.009 0.015 -9999 0 0 373 373
SRF 0.03 0.025 -9999 0 -0.084 23 23
NKX3-1 -0.013 0.011 -9999 0 -0.032 139 139
KLK3 0.023 0.038 -9999 0 -10000 0 0
TMF1 0.032 0.006 -9999 0 -10000 0 0
HNRNPA1 0.032 0.006 -9999 0 0 18 18
AOF2 0 0 -9999 0 -10000 0 0
APPL1 -0.03 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.042 0.016 -9999 0 -0.03 11 11
AR 0.032 0.01 -9999 0 -0.031 11 11
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.03 0.009 -9999 0 0 39 39
PAWR 0.032 0.006 -9999 0 -10000 0 0
PRKDC 0.031 0.008 -9999 0 0 31 31
PA2G4 0.031 0.007 -9999 0 0 24 24
UBE2I 0.033 0.003 -9999 0 0 5 5
T-DHT/AR/Cyclin D3/CDK11 p58 0.041 0.013 -9999 0 -0.027 12 12
RPS6KA3 0.033 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.032 0.023 -9999 0 -0.03 12 12
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.04 0.014 -9999 0 -0.027 12 12
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 0 5 5
VAV3 0.031 0.01 -9999 0 -10000 0 0
KLK2 -0.006 0.038 -9999 0 -0.25 10 10
CASP8 0.032 0.005 -9999 0 0 11 11
T-DHT/AR/TIF2/CARM1 0.056 0.026 -9999 0 -10000 0 0
TMPRSS2 -0.005 0.027 -9999 0 -0.25 4 4
CCND1 0.027 0.013 -9999 0 -10000 0 0
PIAS1 0.033 0.005 -9999 0 -10000 0 0
mol:T-DHT 0 0.001 -9999 0 -10000 0 0
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.032 0.009 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.025 0.024 -9999 0 -0.03 8 8
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.021 0.018 -9999 0 -0.031 11 11
CCND3 0.033 0.003 -9999 0 0 5 5
TGIF1 0.009 0.015 -9999 0 0 366 366
FKBP4 0.032 0.007 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.048 0.02 0.022 1 -0.12 4 5
KIRREL 0.036 0.012 0.086 1 -0.041 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.02 0.12 4 -0.022 1 5
PLCG1 0.029 0.011 -10000 0 0 66 66
ARRB2 0.032 0.005 -10000 0 0 13 13
WASL 0.019 0.016 -10000 0 0 211 211
Nephrin/NEPH1/podocin/CD2AP 0.073 0.039 0.18 7 -10000 0 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.028 0.11 25 -0.13 5 30
FYN -0.013 0.057 0.16 44 -10000 0 44
mol:Ca2+ 0.069 0.042 0.17 18 -10000 0 18
mol:DAG 0.071 0.043 0.18 18 -10000 0 18
NPHS2 0.036 0.012 0.086 1 -0.041 5 6
mol:IP3 0.071 0.043 0.18 18 -10000 0 18
regulation of endocytosis 0.052 0.034 0.14 2 -0.072 5 7
Nephrin/NEPH1/podocin/Cholesterol 0.061 0.032 0.16 19 -0.049 5 24
establishment of cell polarity 0.048 0.02 0.12 4 -0.022 1 5
Nephrin/NEPH1/podocin/NCK1-2 0.09 0.043 0.19 10 -10000 0 10
Nephrin/NEPH1/beta Arrestin2 0.054 0.035 0.15 2 -0.072 5 7
NPHS1 0.034 0.013 0.077 7 -10000 0 7
Nephrin/NEPH1/podocin 0.057 0.026 0.17 4 -0.066 5 9
TJP1 0.032 0.006 -10000 0 0 19 19
NCK1 0.031 0.008 -10000 0 0 28 28
NCK2 0.033 0.003 -10000 0 0 5 5
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.072 0.044 0.18 18 -10000 0 18
CD2AP 0.029 0.011 -10000 0 0 58 58
Nephrin/NEPH1/podocin/GRB2 0.076 0.04 0.18 16 -0.061 5 21
GRB2 0.032 0.007 -10000 0 0 22 22
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.019 0.063 0.17 46 -10000 0 46
cytoskeleton organization -0.006 0.055 0.15 40 -0.16 4 44
Nephrin/NEPH1 0.041 0.018 0.098 4 -0.034 5 9
Nephrin/NEPH1/ZO-1 0.06 0.032 -10000 0 -0.05 20 20
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.021 0.043 -10000 0 -0.16 12 12
mol:DAG -0.02 0.037 0.18 6 -0.21 4 10
PLCG1 -0.02 0.038 0.18 6 -0.21 4 10
YES1 -0.019 0.029 -10000 0 -0.18 7 7
FZD3 0.031 0.008 -10000 0 0 28 28
FZD6 0.026 0.014 -10000 0 0 106 106
G protein -0.004 0.068 0.17 54 -0.21 5 59
MAP3K7 -0.029 0.038 0.15 8 -0.2 4 12
mol:Ca2+ -0.02 0.037 0.17 6 -0.2 4 10
mol:IP3 -0.02 0.037 0.18 6 -0.21 4 10
NLK 0.003 0.094 -10000 0 -0.74 8 8
GNB1 0.031 0.008 -10000 0 0 31 31
CAMK2A -0.024 0.04 0.17 9 -0.2 4 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.001 0.034 -10000 0 -0.13 24 24
CSNK1A1 0.033 0.004 -10000 0 0 9 9
GNAS -0.017 0.028 -10000 0 -0.18 8 8
GO:0007205 -0.013 0.04 0.17 11 -0.19 5 16
WNT6 0.033 0.002 -10000 0 0 2 2
WNT4 0.032 0.006 -10000 0 0 19 19
NFAT1/CK1 alpha -0.028 0.048 0.19 11 -0.21 5 16
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.022 0.016 -10000 0 0 168 168
WNT11 0.032 0.005 -10000 0 0 14 14
CDC42 -0.021 0.035 0.16 8 -0.2 2 10
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.019 0.016 -10000 0 -10000 0 0
EPHB2 0.032 0.007 -10000 0 0 22 22
Syndecan-2/TACI 0.025 0.008 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.023 0.053 0.17 4 -10000 0 4
HRAS 0.032 0.007 -10000 0 0 24 24
Syndecan-2/CASK -0.012 0.003 -10000 0 -10000 0 0
ITGA5 0.027 0.013 -10000 0 0 90 90
BAX -0.02 0.014 -10000 0 -0.05 1 1
EPB41 0.032 0.005 -10000 0 0 14 14
positive regulation of cell-cell adhesion 0.023 0.008 -10000 0 -10000 0 0
LAMA3 0.031 0.008 -10000 0 0 30 30
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.017 0.017 -10000 0 0 252 252
Syndecan-2/MMP2 0.008 0.019 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.028 0.027 -10000 0 -0.016 63 63
dendrite morphogenesis 0.025 0.009 -10000 0 -10000 0 0
Syndecan-2/GM-CSF 0.025 0.008 -10000 0 -10000 0 0
determination of left/right symmetry -0.015 0.003 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.009 -10000 0 -10000 0 0
GNB2L1 0.032 0.005 -10000 0 0 12 12
MAPK3 -0.028 0.032 0.18 11 -10000 0 11
MAPK1 -0.025 0.033 0.18 11 -10000 0 11
Syndecan-2/RACK1 0.04 0.019 -10000 0 -10000 0 0
NF1 0.032 0.006 -10000 0 0 16 16
FGFR/FGF/Syndecan-2 -0.015 0.003 -10000 0 -10000 0 0
ITGA2 0.027 0.013 -10000 0 0 100 100
MAPK8 -0.017 0.011 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.015 0.036 -10000 0 -10000 0 0
Syndecan-2/Kininogen 0.025 0.009 -10000 0 -10000 0 0
ITGB1 0.025 0.015 -10000 0 0 131 131
SRC -0.028 0.037 0.16 15 -10000 0 15
Syndecan-2/CASK/Protein 4.1 0.023 0.008 -10000 0 -10000 0 0
extracellular matrix organization 0.022 0.012 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.019 0.016 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.02 0.026 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.024 0.01 -10000 0 -10000 0 0
Syndecan-2/RasGAP 0.055 0.028 0.16 8 -10000 0 8
alpha5/beta1 Integrin 0.027 0.027 -10000 0 -0.016 61 61
PRKCD 0.032 0.006 -10000 0 0 16 16
Syndecan-2 dimer 0.025 0.009 -10000 0 -10000 0 0
GO:0007205 0.001 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.036 0.031 0.18 7 -10000 0 7
RHOA 0.032 0.006 -10000 0 0 19 19
SDCBP 0.033 0.005 -10000 0 0 11 11
TNFRSF13B 0.033 0.005 -10000 0 0 10 10
RASA1 0.032 0.006 -10000 0 0 18 18
alpha2/beta1 Integrin 0.028 0.027 -10000 0 -0.016 63 63
Syndecan-2/Synbindin 0.025 0.008 -10000 0 -10000 0 0
TGFB1 0.029 0.011 -10000 0 0 61 61
CASP3 -0.025 0.029 0.18 9 -10000 0 9
FN1 0.027 0.013 -10000 0 0 100 100
Syndecan-2/IL8 0.017 0.017 -10000 0 -10000 0 0
SDC2 -0.015 0.003 -10000 0 -10000 0 0
KNG1 0.032 0.007 -10000 0 0 23 23
Syndecan-2/Neurofibromin 0.025 0.009 -10000 0 -10000 0 0
TRAPPC4 0.032 0.005 -10000 0 0 12 12
CSF2 0.032 0.005 -10000 0 0 13 13
Syndecan-2/TGFB1 0.022 0.012 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.023 0.008 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.023 0.009 -10000 0 -10000 0 0
PRKACA -0.025 0.034 0.18 12 -10000 0 12
angiogenesis 0.017 0.017 -10000 0 -10000 0 0
MMP2 0.017 0.017 -10000 0 0 252 252
IL8 0.026 0.014 -10000 0 0 116 116
calcineurin-NFAT signaling pathway 0.025 0.008 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.006 -10000 0 0 16 16
LAT2 -0.009 0.035 0.14 15 -0.16 5 20
AP1 -0.026 0.12 0.28 1 -0.31 24 25
mol:PIP3 0.046 0.11 0.27 54 -0.2 1 55
IKBKB 0.028 0.082 0.21 48 -0.15 1 49
AKT1 -0.041 0.08 0.29 14 -10000 0 14
IKBKG 0.027 0.081 0.21 46 -0.15 1 47
MS4A2 0.032 0.016 -10000 0 -0.034 25 25
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
MAP3K1 -0.005 0.069 0.22 18 -0.23 5 23
mol:Ca2+ 0.043 0.097 0.24 55 -10000 0 55
LYN 0.028 0.014 -10000 0 -0.035 7 7
CBLB -0.014 0.033 0.11 15 -0.16 7 22
SHC1 0.03 0.01 -10000 0 0 55 55
RasGAP/p62DOK 0.058 0.023 -10000 0 -0.044 9 9
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.032 0.062 0.32 12 -10000 0 12
PTPN13 0.011 0.083 -10000 0 -0.59 7 7
PTPN11 0.032 0.012 -10000 0 -0.036 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.012 0.081 0.34 9 -0.3 7 16
SYK 0.029 0.013 -10000 0 -0.034 6 6
GRB2 0.032 0.007 -10000 0 0 22 22
LAT/PLCgamma1/GRB2/SLP76/GADs 0.025 0.071 0.18 36 -0.18 4 40
LAT -0.013 0.035 0.11 16 -0.16 7 23
PAK2 0.002 0.069 0.22 18 -0.24 5 23
NFATC2 -0.011 0.004 -10000 0 -10000 0 0
HRAS 0.006 0.064 0.2 17 -0.22 8 25
GAB2 0.032 0.006 -10000 0 0 16 16
PLA2G1B 0.02 0.079 -10000 0 -0.81 3 3
Fc epsilon R1 0.024 0.048 -10000 0 -0.03 149 149
Antigen/IgE/Fc epsilon R1 0.029 0.044 -10000 0 -0.035 8 8
mol:GDP 0.013 0.059 0.21 15 -0.2 2 17
JUN 0.033 0.005 -10000 0 0 10 10
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.01 -10000 0 0 47 47
FOS 0.023 0.016 -10000 0 0 163 163
Antigen/IgE/Fc epsilon R1/LYN/SYK 0 0.034 0.12 8 -0.16 7 15
CHUK 0.017 0.075 0.2 43 -0.16 1 44
KLRG1 -0.012 0.021 0.078 3 -0.16 2 5
VAV1 -0.012 0.037 0.12 18 -0.16 7 25
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.013 0.033 0.12 11 -0.16 5 16
negative regulation of mast cell degranulation -0.013 0.023 0.07 3 -0.14 3 6
BTK 0.014 0.039 0.19 1 -10000 0 1
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.001 0.02 0.11 2 -0.13 4 6
GAB2/PI3K/SHP2 -0.059 0.029 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.006 0.019 -10000 0 -0.11 6 6
RAF1 0.022 0.073 -10000 0 -0.89 3 3
Fc epsilon R1/FcgammaRIIB/SHIP 0.041 0.043 -10000 0 -10000 0 0
FCER1G 0.014 0.02 -10000 0 -0.035 24 24
FCER1A 0.03 0.013 0.07 1 -0.033 14 15
Antigen/IgE/Fc epsilon R1/Fyn 0.03 0.054 -10000 0 -0.053 18 18
MAPK3 0.022 0.079 -10000 0 -0.82 3 3
MAPK1 0.013 0.083 -10000 0 -0.82 3 3
NFKB1 0.032 0.005 -10000 0 0 13 13
MAPK8 -0.12 0.26 -10000 0 -0.52 138 138
DUSP1 0.031 0.008 -10000 0 0 28 28
NF-kappa-B/RelA 0.015 0.059 0.14 46 -0.11 1 47
actin cytoskeleton reorganization 0.02 0.085 0.31 1 -0.6 7 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.01 0.072 0.2 27 -0.22 6 33
FER -0.013 0.033 0.11 15 -0.16 6 21
RELA 0.033 0.004 -10000 0 0 9 9
ITK 0.002 0.025 -10000 0 -0.23 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.085 0.26 38 -0.19 4 42
cytokine secretion 0.006 0.038 0.08 41 -0.082 1 42
SPHK1 -0.013 0.036 0.12 17 -0.16 7 24
PTK2 0.02 0.089 -10000 0 -0.63 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.037 0.088 0.22 45 -0.18 4 49
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.038 0.1 0.26 46 -0.29 1 47
MAP2K2 0.023 0.091 -10000 0 -0.84 3 3
MAP2K1 0.008 0.069 -10000 0 -0.84 3 3
MAP2K7 0.031 0.008 -10000 0 0 35 35
KLRG1/SHP2 -0.001 0.045 0.19 15 -0.22 1 16
MAP2K4 -0.003 0.18 -10000 0 -0.77 27 27
Fc epsilon R1/FcgammaRIIB 0.044 0.047 -10000 0 -10000 0 0
mol:Choline -0.032 0.062 0.32 12 -10000 0 12
SHC/Grb2/SOS1 0.033 0.048 0.17 6 -0.15 7 13
FYN 0.03 0.01 -10000 0 0 53 53
DOK1 0.033 0.003 -10000 0 0 3 3
PXN 0.012 0.088 0.38 4 -0.59 7 11
HCLS1 -0.012 0.033 0.11 15 -0.16 7 22
PRKCB 0.037 0.092 0.23 51 -0.2 1 52
FCGR2B 0.025 0.014 -10000 0 0 129 129
IGHE -0.001 0.004 0.025 5 -10000 0 5
KLRG1/SHIP -0.014 0.023 0.071 3 -0.14 3 6
LCP2 0.031 0.01 -10000 0 0 44 44
PLA2G4A -0.011 0.032 0.11 14 -0.15 6 20
RASA1 0.032 0.006 -10000 0 0 18 18
mol:Phosphatidic acid -0.032 0.062 0.32 12 -10000 0 12
IKK complex 0.013 0.071 0.21 28 -10000 0 28
WIPF1 0.032 0.006 -10000 0 0 15 15
IL2 signaling events mediated by PI3K

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
BCL2L1 0.008 0.06 0.19 30 -0.22 4 34
UGCG 0.006 0.075 -10000 0 -0.57 8 8
AKT1/mTOR/p70S6K/Hsp90/TERT -0.004 0.09 0.2 3 -0.3 26 29
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.006 0.074 -10000 0 -0.56 8 8
mol:DAG -0.21 0.37 -10000 0 -0.8 142 142
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.071 0.22 2 -0.26 3 5
FRAP1 -0.006 0.071 0.23 2 -0.28 3 5
FOXO3 -0.014 0.071 0.21 4 -0.26 8 12
AKT1 -0.008 0.073 0.22 3 -0.26 10 13
GAB2 0.032 0.006 -10000 0 -10000 0 0
SMPD1 -0.003 0.1 -10000 0 -0.57 16 16
SGMS1 -0.15 0.28 -10000 0 -0.59 141 141
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 -0.022 0.009 -10000 0 -10000 0 0
CALM1 0.029 0.011 -10000 0 0 61 61
cell proliferation -0.071 0.16 0.22 2 -0.34 127 129
EIF3A 0.023 0.015 -10000 0 0 158 158
PI3K 0.042 0.02 -10000 0 -10000 0 0
RPS6KB1 0.02 0.035 -10000 0 -0.73 1 1
mol:sphingomyelin -0.21 0.37 -10000 0 -0.8 142 142
natural killer cell activation 0 0 -10000 0 -10000 0 0
JAK3 0.031 0.009 -10000 0 -10000 0 0
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
JAK1 0.033 0.006 -10000 0 -10000 0 0
NFKB1 0.032 0.005 -10000 0 0 13 13
MYC -0.007 0.074 0.25 4 -0.29 2 6
MYB 0.012 0.027 -10000 0 -0.35 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.012 0.067 -10000 0 -0.21 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.046 -10000 0 -0.7 1 1
mol:PI-3-4-5-P3 -0.012 0.066 -10000 0 -0.21 17 17
Rac1/GDP -0.018 0.017 -10000 0 -10000 0 0
T cell proliferation -0.012 0.064 0.18 3 -0.21 13 16
SHC1 0.03 0.01 -10000 0 -10000 0 0
RAC1 0.02 0.016 -10000 0 0 204 204
positive regulation of cyclin-dependent protein kinase activity 0.001 0.001 -10000 0 -10000 0 0
PRKCZ -0.013 0.064 0.17 1 -0.21 13 14
NF kappa B1 p50/RelA 0.014 0.085 0.24 2 -0.27 3 5
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.008 0.046 -10000 0 -0.2 10 10
HSP90AA1 0.031 0.009 -10000 0 0 37 37
RELA 0.033 0.004 -10000 0 0 9 9
IL2RA 0.024 0.015 -10000 0 -10000 0 0
IL2RB 0.031 0.009 -10000 0 -10000 0 0
TERT 0.032 0.007 -10000 0 0 21 21
E2F1 0.021 0.03 -10000 0 -0.39 2 2
SOS1 0 0 -10000 0 -10000 0 0
RPS6 0.028 0.012 -10000 0 0 78 78
mol:cAMP -0.001 0 -10000 0 -10000 0 0
PTPN11 0.033 0.005 -10000 0 -10000 0 0
IL2RG 0.033 0.005 -10000 0 -10000 0 0
actin cytoskeleton organization -0.012 0.064 0.18 3 -0.21 13 16
GRB2 0.032 0.007 -10000 0 -10000 0 0
IL2 0.033 0.004 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.03 0.032 -10000 0 -10000 0 0
LCK 0.033 0.006 -10000 0 -10000 0 0
BCL2 -0.007 0.068 0.27 5 -0.26 1 6
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.024 0.004 -10000 0 0 11 11
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.032 0.007 -10000 0 0 26 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.003 0.051 -10000 0 -0.19 27 27
IRAK/TOLLIP -0.031 0.024 0.18 6 -10000 0 6
IKBKB 0.033 0.004 -10000 0 0 7 7
IKBKG 0.033 0.003 -10000 0 0 5 5
IL1 alpha/IL1R2 0.044 0.018 -10000 0 -0.016 40 40
IL1A 0.033 0.003 -10000 0 0 4 4
IL1B -0.026 0.01 0 19 -10000 0 19
IRAK/TRAF6/p62/Atypical PKCs 0.052 0.031 0.18 6 -10000 0 6
IL1R2 0.031 0.009 -10000 0 0 39 39
IL1R1 0.033 0.003 -10000 0 0 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.047 -10000 0 -0.24 10 10
TOLLIP 0.032 0.007 -10000 0 0 21 21
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.033 0.004 -10000 0 0 6 6
TAK1/TAB1/TAB2 0.021 0.005 -10000 0 0 29 29
IKK complex/ELKS -0.046 0.099 -10000 0 -0.21 130 130
JUN -0.037 0.028 0.12 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 0 29 29
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.051 0.049 0.18 2 -10000 0 2
IL1 alpha/IL1R1/IL1RAP/MYD88 0.068 0.034 -10000 0 -0.052 16 16
PIK3R1 0.03 0.01 -10000 0 0 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.076 0.044 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP 0.034 0.026 -10000 0 -0.052 14 14
NFKB1 0.032 0.005 -10000 0 0 13 13
MAPK8 -0.032 0.028 0.14 5 -10000 0 5
IRAK1 -0.026 0.005 0 16 -10000 0 16
IL1RN/IL1R1 0.049 0.006 -10000 0 -0.016 3 3
IRAK4 0.032 0.007 -10000 0 0 24 24
PRKCI 0.032 0.006 -10000 0 0 17 17
TRAF6 0.032 0.006 -10000 0 0 16 16
PI3K 0.041 0.019 -10000 0 -0.016 15 15
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.047 0.12 1 -0.2 18 19
CHUK 0.024 0.015 -10000 0 0 148 148
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.034 0.026 -10000 0 -0.052 14 14
IL1 beta/IL1R2 -0.032 0.012 -10000 0 -10000 0 0
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.026 0.16 5 -0.049 4 9
NF kappa B1 p50/RelA -0.06 0.028 0.069 6 -10000 0 6
IRAK3 0.031 0.008 -10000 0 0 33 33
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.037 0.16 2 -10000 0 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.039 -10000 0 -0.13 35 35
IL1 alpha/IL1R1/IL1RAP 0.055 0.031 -10000 0 -0.046 9 9
RELA 0.033 0.004 -10000 0 0 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.006 -10000 0 0 16 16
MYD88 0.028 0.012 -10000 0 0 79 79
IRAK/TRAF6/MEKK3 0.047 0.022 0.19 5 -10000 0 5
IL1RAP 0.029 0.011 -10000 0 0 63 63
UBE2N 0.033 0.005 -10000 0 0 11 11
IRAK/TRAF6 -0.062 0.02 0.095 1 -10000 0 1
CASP1 0.022 0.016 -10000 0 0 176 176
IL1RN/IL1R2 0.044 0.017 -10000 0 -0.016 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.038 0.045 0.17 2 -10000 0 2
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.047 -10000 0 -0.26 10 10
PIK3CA 0.031 0.009 -10000 0 0 41 41
IL1RN 0.033 0.001 -10000 0 0 1 1
TRAF6/TAK1/TAB1/TAB2 0.042 0.023 -10000 0 -0.036 36 36
MAP2K6 -0.034 0.029 0.16 10 -10000 0 10
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.025 0.011 -10000 0 -10000 0 0
NFATC2 -0.015 0.006 -10000 0 -10000 0 0
NFATC3 -0.026 0.01 -10000 0 -10000 0 0
CD40LG -0.055 0.046 0.29 3 -10000 0 3
PTGS2 -0.055 0.043 0.27 2 -10000 0 2
JUNB 0.031 0.009 -10000 0 0 42 42
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.009 -10000 0 -0.023 4 4
CaM/Ca2+ 0.021 0.009 -10000 0 -0.023 4 4
CALM1 0.029 0.011 -10000 0 -0.001 63 63
JUN 0.032 0.007 -10000 0 -0.007 13 13
mol:Ca2+ -0.002 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.007 -10000 0 0 66 66
FOSL1 0.032 0.007 -10000 0 0 21 21
CREM 0.025 0.014 -10000 0 0 129 129
Jun/NFAT1-c-4/p21SNFT -0.044 0.029 0.14 9 -10000 0 9
FOS 0.022 0.016 -10000 0 0 165 165
IFNG -0.053 0.044 0.29 2 -10000 0 2
AP-1/NFAT1-c-4 0.022 0.067 0.18 5 -0.095 3 8
FASLG -0.055 0.043 0.27 2 -10000 0 2
NFAT1-c-4/ICER1 -0.045 0.029 0.14 9 -10000 0 9
IL2RA -0.039 0.045 0.3 2 -10000 0 2
FKBP12/FK506 0.021 0.008 -10000 0 0 66 66
CSF2 -0.055 0.044 0.27 2 -10000 0 2
JunB/Fra1/NFAT1-c-4 -0.046 0.032 0.15 7 -10000 0 7
IL4 -0.055 0.044 0.27 2 -10000 0 2
IL2 0.016 0.089 -10000 0 -0.87 5 5
IL3 0.022 0.083 -10000 0 -0.59 9 9
FKBP1A 0.029 0.011 -10000 0 0 66 66
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.034 0.005 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.03 0.009 -10000 0 -10000 0 0
HSPA8 0.033 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.041 0.046 -10000 0 -0.07 2 2
AKT1 0.031 0.009 -10000 0 -10000 0 0
GSC 0.002 0.027 0.097 23 -0.044 1 24
NKX2-5 -0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.022 0.067 0.24 21 -10000 0 21
SMAD2-3/SMAD4/SP1 0.061 0.046 -10000 0 -10000 0 0
SMAD4 0.008 0.033 0.083 2 -10000 0 2
CBFB 0.032 0.005 -10000 0 0 13 13
SAP18 0.031 0.009 -10000 0 0 36 36
Cbp/p300/MSG1 0.052 0.036 -10000 0 -0.047 41 41
SMAD3/SMAD4/VDR 0.067 0.059 -10000 0 -10000 0 0
MYC 0.024 0.015 -10000 0 0 138 138
CDKN2B -0.22 0.19 -10000 0 -0.37 273 273
AP1 0.002 0.039 0.14 6 -10000 0 6
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.067 -10000 0 -0.25 23 23
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.025 0.064 0.13 5 -0.26 26 31
SP3 0.028 0.012 -10000 0 0 78 78
CREB1 0.033 0.001 -10000 0 0 1 1
FOXH1 0.034 0.011 0.079 7 -0.001 22 29
SMAD3/SMAD4/GR 0.043 0.045 -10000 0 -0.077 1 1
GATA3 0.023 0.016 -10000 0 -0.036 6 6
SKI/SIN3/HDAC complex/NCoR1 -0.006 0.068 -10000 0 -0.29 17 17
MEF2C/TIF2 -0.033 0.046 0.22 12 -10000 0 12
endothelial cell migration -0.007 0.032 0.54 1 -10000 0 1
MAX 0.031 0.009 -10000 0 0 39 39
RBBP7 0.033 0.002 -10000 0 0 2 2
RBBP4 0.026 0.013 -10000 0 0 105 105
RUNX2 0.033 0.004 -10000 0 0 7 7
RUNX3 0.032 0.006 -10000 0 0 20 20
RUNX1 0.032 0.006 -10000 0 0 16 16
CTBP1 0.032 0.006 -10000 0 0 18 18
NR3C1 0.033 0.005 -10000 0 0 9 9
VDR 0.032 0.007 -10000 0 0 24 24
CDKN1A 0.003 0.04 0.31 4 -10000 0 4
KAT2B 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.034 0.044 -10000 0 -0.06 6 6
DCP1A 0.032 0.006 -10000 0 0 16 16
SKI 0.032 0.007 -10000 0 0 26 26
SERPINE1 0.008 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/ATF2 0.041 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.03 0.046 -10000 0 -0.076 1 1
SAP30 0.032 0.006 -10000 0 0 16 16
Cbp/p300/PIAS3 0.054 0.033 -10000 0 -0.047 45 45
JUN -0.022 0.036 0.15 13 -10000 0 13
SMAD3/SMAD4/IRF7 0.042 0.049 -10000 0 -0.077 1 1
TFE3 0.029 0.016 -10000 0 -0.032 32 32
COL1A2 0.001 0.021 -10000 0 -0.31 1 1
mesenchymal cell differentiation -0.041 0.045 -10000 0 -10000 0 0
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.008 -10000 0 0 35 35
FOS 0.018 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.042 0.046 -10000 0 -0.072 1 1
Cbp/p300/SNIP1 0.056 0.033 -10000 0 -0.046 44 44
ZBTB17 0.032 0.006 -10000 0 0 15 15
LAMC1 -0.032 0.026 0.13 6 -10000 0 6
TGIF2/HDAC complex/SMAD3/SMAD4 0.038 0.044 -10000 0 -0.069 1 1
IRF7 0.03 0.011 -10000 0 -0.005 40 40
ESR1 0.029 0.022 0.13 3 -0.032 40 43
HNF4A 0.029 0.011 -10000 0 0 66 66
MEF2C -0.026 0.047 0.2 17 -10000 0 17
SMAD2-3/SMAD4 0.042 0.047 -10000 0 -0.078 1 1
Cbp/p300/Src-1 0.053 0.034 -10000 0 -0.048 12 12
IGHV3OR16-13 0.005 0.007 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.029 0.011 -10000 0 0 69 69
CREBBP 0.032 0.004 -10000 0 -10000 0 0
SKIL 0.032 0.006 -10000 0 0 16 16
HDAC1 0.028 0.012 -10000 0 0 74 74
HDAC2 0.031 0.009 -10000 0 0 40 40
SNIP1 0.033 0.005 -10000 0 -10000 0 0
GCN5L2 0 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.044 -10000 0 -10000 0 0
MSG1/HSC70 0.045 0.016 -10000 0 -0.016 24 24
SMAD2 0.035 0.011 0.1 3 -10000 0 3
SMAD3 0.008 0.037 0.089 2 -10000 0 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.039 -10000 0 -0.13 36 36
SMAD2/SMAD2/SMAD4 -0.004 0.037 0.13 11 -0.18 9 20
NCOR1 0.033 0.005 -10000 0 0 10 10
NCOA2 0.032 0.005 -10000 0 0 12 12
NCOA1 0.031 0.008 -10000 0 0 28 28
MYOD/E2A 0.045 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.073 0.052 -10000 0 -10000 0 0
IFNB1 -0.023 0.033 0.14 10 -10000 0 10
SMAD3/SMAD4/MEF2C -0.029 0.041 0.19 8 -10000 0 8
CITED1 0.032 0.007 -10000 0 0 25 25
SMAD2-3/SMAD4/ARC105 0.059 0.05 -10000 0 -0.078 1 1
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.006 0.054 0.19 1 -0.26 12 13
RUNX1-3/PEBPB2 0.059 0.027 -10000 0 -0.047 22 22
SMAD7 -0.009 0.055 0.2 1 -0.21 17 18
MYC/MIZ-1 0.031 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.018 0.06 -10000 0 -0.24 20 20
IL10 -0.034 0.042 0.16 19 -10000 0 19
PIASy/HDAC complex 0.031 0.009 -10000 0 -10000 0 0
PIAS3 0.032 0.006 -10000 0 0 15 15
CDK2 0.03 0.009 -10000 0 -10000 0 0
IL5 -0.035 0.04 0.16 17 -10000 0 17
CDK4 0.011 0.016 -10000 0 -10000 0 0
PIAS4 0.031 0.009 -10000 0 -10000 0 0
ATF3 0.026 0.014 -10000 0 0 118 118
SMAD3/SMAD4/SP1 0.039 0.045 -10000 0 -10000 0 0
FOXG1 0.028 0.013 -10000 0 0 87 87
FOXO3 -0.028 0.011 -10000 0 -10000 0 0
FOXO1 -0.028 0.011 -10000 0 -10000 0 0
FOXO4 -0.03 0.009 -10000 0 -10000 0 0
heart looping -0.026 0.047 0.2 17 -10000 0 17
CEBPB 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.029 0.03 -10000 0 -0.052 4 4
MYOD1 0.032 0.005 -10000 0 0 14 14
SMAD3/SMAD4/HNF4 0.038 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.03 0.055 -10000 0 -0.076 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.006 -10000 0 0 16 16
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.074 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.058 0.048 -10000 0 -10000 0 0
MED15 0.031 0.008 -10000 0 0 29 29
SP1 0.027 0.019 -10000 0 -0.032 43 43
SIN3B 0.031 0.009 -10000 0 0 40 40
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.034 0.042 -10000 0 -0.058 3 3
ITGB5 -0.033 0.052 0.21 15 -10000 0 15
TGIF/SIN3/HDAC complex/CtBP -0.01 0.061 -10000 0 -0.24 21 21
SMAD3/SMAD4/AR 0.042 0.045 -10000 0 -0.069 1 1
AR 0.033 0.005 -10000 0 0 10 10
negative regulation of cell growth 0.003 0.043 -10000 0 -0.22 12 12
SMAD3/SMAD4/MYOD 0.041 0.046 -10000 0 -0.076 1 1
E2F5 0.033 0.005 -10000 0 0 11 11
E2F4 0.033 0.004 -10000 0 0 8 8
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.064 0.052 -10000 0 -0.073 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 -0.012 0.041 0.13 3 -0.22 10 13
TFDP1 0.031 0.009 -10000 0 0 41 41
SMAD3/SMAD4/AP1 0.026 0.052 0.16 2 -0.079 5 7
SMAD3/SMAD4/RUNX2 0.042 0.046 -10000 0 -10000 0 0
TGIF2 0.029 0.011 -10000 0 0 69 69
TGIF1 0.009 0.015 -10000 0 0 366 366
ATF2 0.033 0.003 -10000 0 0 3 3
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.057 0.025 -10000 0 -0.042 26 26
HDAC3 0.033 0.004 -10000 0 0 9 9
Ran/GTP/Exportin 1/HDAC4 -0.036 0.005 -10000 0 -10000 0 0
GATA1/HDAC4 0.049 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.049 0.007 -10000 0 -10000 0 0
GATA2/HDAC5 0.047 0.01 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.058 0.028 -10000 0 -0.047 14 14
HDAC9 0.02 0.016 -10000 0 0 210 210
Glucocorticoid receptor/Hsp90/HDAC6 0.058 0.031 -10000 0 -0.047 38 38
HDAC4/ANKRA2 0.048 0.009 -10000 0 -0.016 1 1
HDAC5/YWHAB 0.042 0.017 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.002 0.03 -10000 0 -0.1 42 42
GATA2 0.032 0.006 -10000 0 0 17 17
HDAC4/RFXANK 0.04 0.021 -10000 0 -0.016 37 37
BCOR 0.033 0.004 -10000 0 0 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.033 0.004 -10000 0 0 7 7
GNB1/GNG2 0.023 0.006 -10000 0 0 31 31
Histones 0.038 0.037 0.083 196 -0.1 4 200
ADRBK1 0.033 0.004 -10000 0 0 7 7
HDAC4 0.033 0.004 -10000 0 0 6 6
XPO1 0.033 0.001 -10000 0 0 1 1
HDAC5/ANKRA2 0.048 0.009 -10000 0 -0.016 1 1
HDAC4/Ubc9 0.048 0.007 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.048 0.009 -10000 0 -10000 0 0
TUBA1B 0.032 0.006 -10000 0 0 19 19
HDAC6 0.033 0.002 -10000 0 0 2 2
HDAC5/RFXANK 0.041 0.021 -10000 0 -0.016 35 35
CAMK4 0.033 0.004 -10000 0 0 8 8
Tubulin/HDAC6 0.059 0.025 -10000 0 -0.047 12 12
SUMO1 0.033 0.001 -10000 0 0 1 1
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.011 -10000 0 0 67 67
GATA1 0.033 0.002 -10000 0 0 2 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 0 12 12
NR3C1 0.033 0.004 -10000 0 0 9 9
SUMO1/HDAC4 0.034 0.043 -10000 0 -0.11 41 41
SRF 0.033 0.004 -10000 0 0 6 6
HDAC4/YWHAB 0.042 0.017 -10000 0 -10000 0 0
Tubulin 0.044 0.016 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.048 0.009 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 0 31 31
RANGAP1 0.031 0.009 -10000 0 0 40 40
BCL6/BCoR 0.044 0.016 -10000 0 -0.016 18 18
HDAC4/HDAC3/SMRT (N-CoR2) 0.063 0.02 -10000 0 -0.046 13 13
HDAC4/SRF 0.064 0.02 -10000 0 -0.046 15 15
HDAC4/ER alpha 0.045 0.013 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.038 0.037 0.082 196 -0.1 4 200
cell motility 0.058 0.025 -10000 0 -0.047 12 12
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.033 0.003 -10000 0 0 5 5
HDAC7/HDAC3 0.024 0.003 -10000 0 0 9 9
BCL6 0.031 0.009 -10000 0 0 42 42
HDAC4/CaMK II delta B 0.033 0.004 -10000 0 0 6 6
Hsp90/HDAC6 0.046 0.013 -10000 0 -10000 0 0
ESR1 0.031 0.009 -10000 0 0 36 36
HDAC6/HDAC11 0.048 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0.043 -10000 0 -0.11 41 41
NPC 0.019 0.003 -10000 0 -0.016 2 2
MEF2C 0.027 0.013 -10000 0 0 93 93
RAN 0.032 0.005 -10000 0 0 12 12
HDAC4/MEF2C 0.076 0.044 -10000 0 -0.065 3 3
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.033 0.005 -10000 0 0 11 11
TUBB2A 0.031 0.009 -10000 0 0 41 41
HDAC11 0.033 0.005 -10000 0 0 11 11
HSP90AA1 0.031 0.009 -10000 0 0 37 37
RANBP2 0.033 0.003 -10000 0 0 4 4
ANKRA2 0.033 0.005 -10000 0 0 10 10
RFXANK 0.028 0.012 -10000 0 0 75 75
nuclear import -0.027 0.026 0.13 11 -10000 0 11
FoxO family signaling

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
G6PC -0.022 0.05 -10000 0 -10000 0 0
PLK1 -0.036 0.066 -10000 0 -10000 0 0
CDKN1B -0.084 0.16 0.22 4 -0.33 143 147
FOXO3 -0.028 0.065 -10000 0 -0.32 3 3
KAT2B 0.001 0.002 -10000 0 -10000 0 0
FOXO1/SIRT1 0.002 0.054 -10000 0 -0.25 7 7
CAT -0.034 0.067 -10000 0 -10000 0 0
CTNNB1 0.032 0.006 -10000 0 0 15 15
AKT1 0.031 0.012 -10000 0 -10000 0 0
FOXO1 -0.017 0.056 -10000 0 -0.28 6 6
MAPK10 0.028 0.08 0.18 109 -10000 0 109
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.08 0.24 7 -0.24 1 8
response to oxidative stress 0.002 0.002 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.004 0.072 -10000 0 -0.3 7 7
XPO1 0.033 0.001 -10000 0 -10000 0 0
EP300 0.031 0.009 -10000 0 -10000 0 0
BCL2L11 0.023 0.01 -10000 0 -10000 0 0
FOXO1/SKP2 0.001 0.06 -10000 0 -0.26 6 6
mol:GDP 0.002 0.002 -10000 0 -10000 0 0
RAN 0.033 0.005 -10000 0 -10000 0 0
GADD45A -0.058 0.15 -10000 0 -0.46 15 15
YWHAQ 0.033 0.004 -10000 0 0 7 7
FOXO1/14-3-3 family -0.029 0.082 -10000 0 -0.28 27 27
MST1 0.031 0.012 -10000 0 -10000 0 0
CSNK1D 0.033 0.005 -10000 0 0 11 11
CSNK1E 0.031 0.009 -10000 0 0 39 39
FOXO4/14-3-3 family -0.05 0.091 -10000 0 -0.32 21 21
YWHAB 0.029 0.011 -10000 0 0 67 67
MAPK8 0.022 0.083 0.18 106 -10000 0 106
MAPK9 0.055 0.1 0.18 202 -10000 0 202
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 0 12 12
YWHAZ 0.032 0.006 -10000 0 0 19 19
SIRT1 0.022 0.017 -10000 0 -0.032 14 14
SOD2 -0.052 0.12 0.23 1 -0.43 30 31
RBL2 -0.015 0.11 -10000 0 -0.68 10 10
RAL/GDP 0.026 0.023 -10000 0 -10000 0 0
CHUK 0.022 0.017 -10000 0 -10000 0 0
Ran/GTP 0.024 0.004 -10000 0 -10000 0 0
CSNK1G2 0.031 0.009 -10000 0 0 36 36
RAL/GTP 0.025 0.023 -10000 0 -10000 0 0
CSNK1G1 0.032 0.005 -10000 0 0 13 13
FASLG 0.02 0.031 -10000 0 -0.62 1 1
SKP2 0.032 0.005 -10000 0 0 14 14
USP7 0.033 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.011 -10000 0 -10000 0 0
CCNB1 -0.034 0.071 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.001 0.079 0.22 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.06 -10000 0 -0.26 6 6
CSNK1A1 0.033 0.004 -10000 0 0 9 9
SGK1 0.001 0.002 -10000 0 -10000 0 0
CSNK1G3 0.033 0.005 -10000 0 0 10 10
Ran/GTP/Exportin 1 0.045 0.007 -10000 0 -10000 0 0
ZFAND5 0.008 0.08 0.27 12 -10000 0 12
SFN 0.03 0.01 -10000 0 0 46 46
CDK2 0.031 0.01 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.047 0.078 -10000 0 -0.26 25 25
CREBBP 0.034 0.004 -10000 0 -10000 0 0
FBXO32 -0.028 0.066 -10000 0 -0.29 6 6
BCL6 -0.018 0.11 -10000 0 -0.65 10 10
RALB 0.033 0.003 -10000 0 -10000 0 0
RALA 0.019 0.017 -10000 0 -10000 0 0
YWHAH 0.015 0.017 -10000 0 0 278 278
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.045 0.014 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 0 13 13
NF kappa B1 p50/c-Rel -0.039 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.058 0.11 55 -0.23 6 61
NFKBIA 0.005 0.043 0.1 52 -0.1 31 83
MAPK14 0.033 0.003 -10000 0 0 5 5
NF kappa B1 p105/p50 -0.038 0.007 -10000 0 -10000 0 0
ARRB2 0.009 0.002 -10000 0 -10000 0 0
REL 0.033 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.036 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.038 0.007 0 16 -10000 0 16
PIK3CA 0.031 0.009 -10000 0 0 41 41
NF kappa B1 p50 dimer -0.031 0.019 0.26 2 -10000 0 2
PIK3R1 0.03 0.01 -10000 0 0 47 47
NFKB1 -0.032 0.006 0 15 -10000 0 15
RELA 0.033 0.004 -10000 0 0 9 9
positive regulation of anti-apoptosis 0.003 0.034 0.097 4 -0.15 6 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.023 0.059 0.11 53 -0.21 10 63
SRC 0.029 0.011 -10000 0 0 65 65
PI3K 0.041 0.019 -10000 0 -0.016 15 15
NF kappa B1 p50/RelA 0.003 0.034 0.097 4 -0.15 6 10
IKBKB 0.033 0.004 -10000 0 0 7 7
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 0 13 13
SYK 0.03 0.01 -10000 0 0 53 53
I kappa B alpha/PIK3R1 0.02 0.052 0.18 3 -0.22 6 9
cell death -0.022 0.057 0.1 53 -0.2 10 63
NF kappa B1 p105/c-Rel -0.039 0.005 -10000 0 -10000 0 0
LCK 0.032 0.006 -10000 0 0 16 16
BCL3 0.031 0.009 -10000 0 0 38 38
Sumoylation by RanBP2 regulates transcriptional repression

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 0.028 0.012 -9999 0 0 74 74
Ran/GTP/Exportin 1/HDAC4 -0.041 0.013 -9999 0 -0.078 41 41
MDM2/SUMO1 0.03 0.043 -9999 0 -0.11 37 37
HDAC4 0.033 0.004 -9999 0 0 6 6
Ran/GTP/Exportin 1/HDAC1 -0.04 0.014 -9999 0 -0.079 31 31
SUMO1 0.033 0.001 -9999 0 0 1 1
NPC/RanGAP1/SUMO1 0.006 0.01 -9999 0 -0.15 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.018 0.027 -9999 0 -0.11 42 42
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.005 -9999 0 0 12 12
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.033 0.003 -9999 0 0 4 4
SUMO1/HDAC4 0.034 0.043 -9999 0 -0.11 41 41
SUMO1/HDAC1 0.029 0.043 -9999 0 -0.11 39 39
RANGAP1 0.031 0.009 -9999 0 0 40 40
MDM2/SUMO1/SUMO1 0.069 0.038 -9999 0 -0.053 19 19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.002 0.03 -9999 0 -0.1 42 42
Ran/GTP 0.017 0.036 -9999 0 -0.1 41 41
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.03 0.01 -9999 0 0 56 56
UBE2I 0.033 0.003 -9999 0 0 5 5
Ran/GTP/Exportin 1 -0.024 0.028 -9999 0 -0.19 1 1
NPC 0.019 0.003 -9999 0 -0.016 2 2
PIAS2 0.032 0.007 -9999 0 0 24 24
PIAS1 0.033 0.005 -9999 0 0 11 11
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.032 0.031 -10000 0 -0.14 6 6
BIRC5 0.02 0.016 -10000 0 0 209 209
NFKBIA -0.015 0.017 0.24 1 -0.14 2 3
CPEB1 0.024 0.015 -10000 0 0 137 137
AKT1 -0.014 0.02 0.24 2 -0.14 2 4
NDEL1 0.031 0.008 -10000 0 0 31 31
Aurora A/BRCA1 0.031 0.028 -10000 0 -0.12 6 6
NDEL1/TACC3 0.037 0.036 -10000 0 -0.12 6 6
GADD45A 0.03 0.01 -10000 0 0 51 51
GSK3B 0.031 0.009 0.083 2 -0.031 4 6
PAK1/Aurora A 0.035 0.031 -10000 0 -0.14 6 6
MDM2 0.03 0.01 -10000 0 0 56 56
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.02 0.012 0 76 -10000 0 76
TP53 0.004 0.037 -10000 0 -0.2 14 14
DLG7 -0.004 0.009 0.091 2 -10000 0 2
AURKAIP1 0.032 0.007 -10000 0 0 26 26
ARHGEF7 0.031 0.008 -10000 0 0 33 33
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.038 -10000 0 -0.13 6 6
G2/M transition of mitotic cell cycle 0.031 0.028 -10000 0 -0.12 6 6
AURKA -0.004 0.013 0.13 2 -10000 0 2
AURKB 0.008 0.019 -10000 0 -0.15 6 6
CDC25B 0.006 0.019 0.092 2 -0.16 5 7
G2/M transition checkpoint -0.005 0.015 0.073 2 -0.11 6 8
mRNA polyadenylation 0.023 0.027 -10000 0 -0.12 6 6
Aurora A/CPEB 0.023 0.027 -10000 0 -0.12 6 6
Aurora A/TACC1/TRAP/chTOG 0.069 0.045 0.19 15 -0.14 5 20
BRCA1 0.032 0.005 -10000 0 0 14 14
centrosome duplication 0.035 0.031 -10000 0 -0.14 6 6
regulation of centrosome cycle 0.036 0.035 -10000 0 -0.12 6 6
spindle assembly 0.067 0.044 0.18 15 -0.13 5 20
TDRD7 0.032 0.007 -10000 0 0 22 22
Aurora A/RasGAP/Survivin 0.041 0.05 0.18 12 -0.12 4 16
CENPA 0.01 0.019 -10000 0 -0.24 2 2
Aurora A/PP2A 0.036 0.029 -10000 0 -0.14 4 4
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.002 0.032 -10000 0 -0.17 7 7
negative regulation of DNA binding 0.003 0.037 -10000 0 -0.2 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.046 0.013 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 0 18 18
Ajuba/Aurora A -0.005 0.015 0.074 2 -0.11 6 8
mitotic prometaphase -0.003 0.011 0.072 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.013 0.13 2 -10000 0 2
TACC1 0.032 0.005 -10000 0 0 12 12
TACC3 0.026 0.013 -10000 0 0 105 105
Aurora A/Antizyme1 0.048 0.034 -10000 0 -0.13 7 7
Aurora A/RasGAP 0.035 0.03 -10000 0 -0.14 5 5
OAZ1 0.031 0.009 -10000 0 0 37 37
RAN 0.032 0.005 -10000 0 0 12 12
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.03 0.011 0.083 2 -0.031 4 6
GIT1 0.033 0.004 -10000 0 0 8 8
GIT1/beta-PIX/PAK1 0.059 0.03 -10000 0 -0.047 32 32
Importin alpha/Importin beta/TPX2 -0.02 0.012 0 76 -10000 0 76
PPP2R5D 0.033 0.004 -10000 0 0 6 6
Aurora A/TPX2 -0.019 0.02 0.076 1 -0.12 3 4
PAK1 0.033 0.005 -10000 0 0 11 11
CKAP5 0.032 0.006 -10000 0 0 18 18
ceramide 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
MAP4K4 -0.006 0.055 0.17 3 -0.3 7 10
BAG4 0.033 0.004 -10000 0 0 9 9
BAD -0.013 0.026 0.13 3 -0.13 7 10
NFKBIA 0.031 0.009 -10000 0 0 40 40
BIRC3 0.031 0.009 -10000 0 0 40 40
BAX -0.007 0.045 0.18 21 -0.13 8 29
EnzymeConsortium:3.1.4.12 -0.001 0.016 0.067 3 -0.073 8 11
IKBKB -0.015 0.056 0.19 5 -0.3 7 12
MAP2K2 -0.017 0.056 0.15 39 -0.16 5 44
MAP2K1 -0.024 0.038 0.17 9 -0.16 5 14
SMPD1 -0.004 0.025 0.1 3 -0.11 16 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.004 0.058 0.21 3 -0.3 9 12
MAP2K4 -0.02 0.032 0.19 5 -0.15 5 10
protein ubiquitination -0.017 0.056 -10000 0 -0.31 7 7
EnzymeConsortium:2.7.1.37 -0.024 0.048 0.18 7 -0.17 5 12
response to UV 0 0 0.002 8 -0.002 2 10
RAF1 -0.019 0.036 0.16 9 -0.15 5 14
CRADD 0.032 0.005 -10000 0 0 11 11
mol:ceramide -0.005 0.026 0.095 4 -0.11 12 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.014 -10000 0 -0.033 4 4
MADD 0.032 0.007 -10000 0 0 22 22
MAP3K1 -0.013 0.031 0.18 5 -0.14 5 10
TRADD 0.032 0.004 -10000 0 0 9 9
RELA/p50 0.033 0.004 -10000 0 0 9 9
MAPK3 -0.016 0.048 0.18 9 -0.16 3 12
MAPK1 -0.022 0.054 0.18 8 -0.19 10 18
p50/RELA/I-kappa-B-alpha 0.045 0.014 -10000 0 -0.016 1 1
FADD -0.005 0.052 0.2 3 -0.3 5 8
KSR1 -0.013 0.028 0.12 4 -0.13 8 12
MAPK8 -0.02 0.033 0.18 5 -0.15 5 10
TRAF2 0.032 0.006 -10000 0 0 20 20
response to radiation 0 0 0.001 2 -10000 0 2
CHUK -0.015 0.05 -10000 0 -0.3 7 7
TNF R/SODD 0.026 0.031 -10000 0 -0.016 160 160
TNF 0.033 0.004 -10000 0 0 7 7
CYCS 0.015 0.05 0.14 25 -0.13 4 29
IKBKG -0.016 0.055 0.18 4 -0.3 7 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.053 0.15 1 -0.29 8 9
RELA 0.033 0.004 -10000 0 0 9 9
RIPK1 0.032 0.006 -10000 0 0 20 20
AIFM1 -0.013 0.035 0.12 16 -0.14 5 21
TNF/TNF R/SODD 0.032 0.045 -10000 0 -0.047 11 11
TNFRSF1A 0.021 0.016 -10000 0 0 187 187
response to heat 0 0 0.001 2 -10000 0 2
CASP8 0.028 0.073 -10000 0 -0.62 6 6
NSMAF -0.004 0.059 0.19 10 -0.3 7 17
response to hydrogen peroxide 0 0 0.002 8 -0.002 2 10
BCL2 0.032 0.007 -10000 0 0 21 21
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.012 0.01 0.073 2 -0.024 23 25
MKNK1 0.033 0.005 -10000 0 0 11 11
MAPK14 0.033 0.018 0.098 2 -0.041 25 27
ATF2/c-Jun -0.026 0.035 -10000 0 -0.13 53 53
MAPK11 0.029 0.02 -10000 0 -0.041 25 25
MITF 0.011 0.01 0.074 4 -10000 0 4
MAPKAPK5 0.012 0.01 0.074 3 -10000 0 3
KRT8 0.01 0.011 0.074 3 -10000 0 3
MAPKAPK3 0.032 0.006 -10000 0 0 17 17
MAPKAPK2 0.032 0.006 -10000 0 0 18 18
p38alpha-beta/CK2 0.041 0.027 -10000 0 -10000 0 0
CEBPB 0.01 0.01 0.065 2 -10000 0 2
SLC9A1 0.011 0.009 0.091 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.011 0.016 0.15 4 -10000 0 4
p38alpha-beta/MNK1 0.048 0.044 -10000 0 -10000 0 0
JUN -0.025 0.035 -10000 0 -0.12 53 53
PPARGC1A 0.012 0.01 0.074 4 -10000 0 4
USF1 0.009 0.009 0.071 4 -10000 0 4
RAB5/GDP/GDI1 0.01 0.051 -10000 0 -0.13 50 50
NOS2 0.009 0.009 0.07 4 -10000 0 4
DDIT3 0.01 0.01 0.075 2 -10000 0 2
RAB5A 0.033 0.005 -10000 0 0 10 10
HSPB1 0.078 0.13 0.26 172 -0.15 1 173
p38alpha-beta/HBP1 0.03 0.041 -10000 0 -10000 0 0
CREB1 -0.002 0.058 -10000 0 -0.21 37 37
RAB5/GDP 0.024 0.003 -10000 0 0 10 10
EIF4E -0.045 0.028 0.2 6 -10000 0 6
RPS6KA4 0.012 0.01 0.074 4 -10000 0 4
PLA2G4A -0.042 0.025 0.19 4 -10000 0 4
GDI1 0.011 0.01 0.074 4 -10000 0 4
TP53 -0.021 0.013 0.068 3 -10000 0 3
RPS6KA5 0.011 0.01 0.074 4 -10000 0 4
ESR1 0.011 0.01 0.079 3 -10000 0 3
HBP1 0.019 0.016 -10000 0 0 213 213
MEF2C 0.01 0.009 0.065 2 -10000 0 2
MEF2A 0.012 0.01 0.074 4 -10000 0 4
EIF4EBP1 -0.01 0.057 -10000 0 -0.21 37 37
KRT19 0.011 0.011 0.074 4 -10000 0 4
ELK4 0.011 0.009 0.068 3 -10000 0 3
ATF6 0.011 0.009 0.068 3 -10000 0 3
ATF1 -0.003 0.056 -10000 0 -0.2 37 37
p38alpha-beta/MAPKAPK2 0.048 0.044 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.047 0.045 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.034 0.017 -10000 0 -0.028 27 27
MAPK9 0.005 0.001 -10000 0 0 14 14
adrenocorticotropin secretion -0.016 0.003 0 12 -10000 0 12
GNB1/GNG2 0.021 0.005 -10000 0 0 31 31
GNB1 0.031 0.008 -10000 0 0 31 31
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 0.005 0 -10000 0 0 5 5
Gs family/GTP 0.02 0.006 -10000 0 -0.009 19 19
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 0.004 0.001 0.006 10 0 9 19
GNAL 0.032 0.006 -10000 0 0 19 19
GNG2 0 0 -10000 0 -10000 0 0
CRH 0.032 0.005 -10000 0 0 12 12
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.002 -10000 0 0 138 138
MAPK11 0.004 0.001 -10000 0 0 53 53
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.004 -10000 0 0 6 6
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.001 -10000 0 -0.011 2 2
monocyte activation -0.001 0.042 -10000 0 -0.32 8 8
MAP2K2 0.016 0.026 -10000 0 -0.57 1 1
MAP2K1 -0.013 0.003 0 24 -10000 0 24
MAP2K7 -0.012 0.003 0 36 -10000 0 36
MAP2K6 -0.013 0.002 0 9 -10000 0 9
CYAA -0.011 0.001 0 4 -0.016 2 6
MAP2K4 -0.012 0.003 0 31 -10000 0 31
IL1B -0.017 0.015 0.13 3 -10000 0 3
Channel 0.021 0.003 -10000 0 -0.006 6 6
NLRP1 -0.013 0.002 0 16 -10000 0 16
CALM1 0.029 0.011 -10000 0 0 61 61
negative regulation of phagocytosis -0.031 0.12 -10000 0 -0.38 57 57
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.001 0.011 2 -10000 0 2
MAPK3 -0.013 0.001 0 5 -10000 0 5
MAPK1 -0.012 0.004 0 43 -10000 0 43
PGR -0.013 0.002 0 11 -10000 0 11
PA/Cellular Receptors 0.022 0.002 -10000 0 0 6 6
apoptosis -0.003 0.001 -10000 0 -0.011 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.004 -10000 0 -0.029 2 2
macrophage activation -0.021 0.006 -10000 0 -10000 0 0
TNF 0.033 0.004 -10000 0 0 7 7
VCAM1 -0.001 0.042 -10000 0 -0.32 8 8
platelet activation -0.031 0.12 -10000 0 -0.38 57 57
MAPKKK cascade 0.007 0.022 -10000 0 -0.069 26 26
IL18 -0.016 0.01 0.1 2 -10000 0 2
negative regulation of macrophage activation -0.003 0.001 -10000 0 -0.011 2 2
LEF -0.003 0.001 -10000 0 -0.011 2 2
CASP1 -0.007 0.004 -10000 0 -0.013 165 165
mol:cAMP -0.028 0.12 -10000 0 -0.38 53 53
necrosis -0.003 0.001 -10000 0 -0.011 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.003 -10000 0 -0.005 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.033 0.004 -9999 0 0 7 7
Aurora C/Aurora B/INCENP 0.05 0.032 -9999 0 -0.042 27 27
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.007 0.005 -9999 0 -10000 0 0
AURKB 0.031 0.009 -9999 0 0 38 38
AURKC 0.03 0.01 -9999 0 0 50 50
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.025 0.005 0 14 -10000 0 14
SNTA1 0.029 0.011 -10000 0 0 69 69
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.037 0.009 -10000 0 -10000 0 0
MAPK12 -0.02 0.009 -10000 0 -10000 0 0
CCND1 -0.007 0.043 -10000 0 -0.35 7 7
p38 gamma/SNTA1 -0.023 0.031 0.18 5 -10000 0 5
MAP2K3 0.033 0.005 -10000 0 0 11 11
PKN1 0.03 0.009 -10000 0 0 43 43
G2/M transition checkpoint -0.018 0.021 0.19 4 -10000 0 4
MAP2K6 -0.013 0.004 0 44 -10000 0 44
MAPT -0.033 0.049 0.15 4 -0.34 2 6
MAPK13 -0.032 0.006 0 14 -10000 0 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.004 0.001 -10000 0 0 43 43
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.028 0.033 -10000 0 -10000 0 0
epithelial cell differentiation -0.016 0.077 -10000 0 -10000 0 0
ITCH 0.03 0.015 -10000 0 -0.036 6 6
WWP1 -0.001 0.027 0.2 7 -10000 0 7
FYN 0.03 0.01 -10000 0 0 53 53
EGFR 0.012 0.016 -10000 0 0 329 329
PRL 0.032 0.005 -10000 0 0 12 12
neuron projection morphogenesis -0.035 0.059 0.22 10 -10000 0 10
PTPRZ1 0.018 0.017 -10000 0 0 240 240
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.05 0.05 0.23 3 -10000 0 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.01 0.024 -10000 0 -10000 0 0
ADAM17 0.027 0.023 -10000 0 -0.045 1 1
ErbB4/ErbB4 0.005 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.019 -10000 0 -10000 0 0
NCOR1 0.033 0.005 -10000 0 0 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.024 0.029 -10000 0 -10000 0 0
GRIN2B -0.021 0.033 0.23 3 -10000 0 3
ErbB4/ErbB2/betacellulin 0.025 0.031 -10000 0 -10000 0 0
STAT1 0.032 0.006 -10000 0 0 20 20
HBEGF 0.032 0.005 -10000 0 0 13 13
PRLR 0.032 0.005 -10000 0 0 13 13
E4ICDs/ETO2 0.029 0.033 -10000 0 -10000 0 0
axon guidance -0.026 0.053 0.22 3 -0.25 1 4
NEDD4 0.025 0.024 -10000 0 -0.045 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.047 0.012 -10000 0 -0.016 6 6
CBFA2T3 0.032 0.006 -10000 0 0 18 18
ErbB4/ErbB2/HBEGF 0.025 0.03 -10000 0 -10000 0 0
MAPK3 -0.027 0.062 0.24 10 -10000 0 10
STAT1 (dimer) 0.028 0.034 -10000 0 -10000 0 0
MAPK1 -0.025 0.061 0.24 10 -10000 0 10
JAK2 0.029 0.011 -10000 0 0 70 70
ErbB4/ErbB2/neuregulin 1 beta -0.018 0.027 0.17 2 -10000 0 2
NRG1 -0.032 0.009 0.025 3 -10000 0 3
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.033 0.005 -10000 0 0 11 11
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.026 0.053 0.22 3 -0.25 1 4
neural crest cell migration -0.018 0.027 0.17 2 -10000 0 2
ERBB2 -0.033 0.008 0.022 3 -10000 0 3
WWOX/E4ICDs 0.029 0.033 -10000 0 -10000 0 0
SHC1 0.03 0.01 -10000 0 0 55 55
ErbB4/EGFR/neuregulin 4 0.009 0.021 -10000 0 -10000 0 0
apoptosis -0.012 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.029 0.033 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.025 0.031 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.028 0.034 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.059 0.058 -10000 0 -0.16 1 1
MDM2 0.014 0.071 0.24 43 -10000 0 43
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.02 0.022 -10000 0 -10000 0 0
STAT5A -0.035 0.052 0.21 2 -0.25 1 3
ErbB4/EGFR/neuregulin 1 beta 0.008 0.02 -10000 0 -10000 0 0
DLG4 0.032 0.005 -10000 0 0 14 14
GRB2/SHC 0.041 0.021 -10000 0 -0.016 38 38
E4ICDs/TAB2/NCoR1 0.026 0.031 -10000 0 -10000 0 0
STAT5A (dimer) -0.012 0.086 0.22 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.017 0.067 0.26 2 -0.25 1 3
LRIG1 0.031 0.009 -10000 0 0 41 41
EREG 0.032 0.006 -10000 0 0 15 15
BTC 0.033 0.004 -10000 0 0 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.027 0.052 0.2 2 -0.25 1 3
ERBB4 0.005 0.021 -10000 0 -10000 0 0
STAT5B 0.033 0.004 -10000 0 0 8 8
YAP1 0.012 0.062 -10000 0 -0.46 8 8
GRB2 0.032 0.007 -10000 0 0 22 22
ErbB4/ErbB2/neuregulin 4 -0.009 0.023 -10000 0 -10000 0 0
glial cell differentiation -0.025 0.031 -10000 0 -10000 0 0
WWOX 0.032 0.006 -10000 0 0 20 20
cell proliferation -0.015 0.037 0.21 3 -0.26 2 5
IGF1 pathway

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
NCK2 0.033 0.003 -10000 0 0 5 5
PTK2 0.032 0.007 -10000 0 0 22 22
CRKL -0.031 0.014 0.16 1 -10000 0 1
GRB2/SOS1/SHC 0.037 0.018 -10000 0 -0.013 38 38
HRAS 0.032 0.007 -10000 0 0 24 24
IRS1/Crk -0.033 0.009 -10000 0 -0.082 7 7
IGF-1R heterotetramer/IGF1/PTP1B 0.053 0.029 0.15 1 -0.056 11 12
AKT1 -0.035 0.052 0.16 23 -10000 0 23
BAD -0.043 0.05 0.14 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.032 0.012 0.16 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.032 0.02 0.19 3 -10000 0 3
RAF1 -0.019 0.064 0.26 4 -0.46 4 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.052 0.023 0.17 1 -0.077 8 9
YWHAZ 0.032 0.006 -10000 0 0 19 19
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.019 0.17 1 -0.078 9 10
PIK3CA 0.031 0.009 -10000 0 0 41 41
RPS6KB1 -0.038 0.053 0.15 25 -10000 0 25
GNB2L1 0.032 0.005 -10000 0 0 12 12
positive regulation of MAPKKK cascade -0.023 0.061 0.22 5 -0.38 4 9
PXN 0.033 0.004 -10000 0 0 7 7
PIK3R1 0.03 0.01 -10000 0 0 47 47
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
HRAS/GTP -0.042 0.016 0.038 2 -0.089 7 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.066 0.029 -10000 0 -0.056 7 7
IGF-1R heterotetramer 0.034 0.008 0.088 1 -0.049 2 3
IGF-1R heterotetramer/IGF1/IRS/Nck 0.057 0.024 0.18 1 -0.082 9 10
Crk/p130 Cas/Paxillin 0.043 0.024 0.18 2 -0.085 9 11
IGF1R 0.034 0.008 0.089 1 -0.049 2 3
IGF1 0.034 0.012 0.089 1 -0.049 7 8
IRS2/Crk -0.037 0.016 0.15 1 -10000 0 1
PI3K 0.063 0.037 0.19 1 -0.087 7 8
apoptosis 0.044 0.058 -10000 0 -0.22 7 7
HRAS/GDP 0.023 0.005 -10000 0 0 24 24
PRKCD -0.004 0.033 0.18 6 -0.15 6 12
RAF1/14-3-3 E -0.019 0.068 0.24 6 -0.41 4 10
BAD/14-3-3 -0.045 0.061 0.23 7 -10000 0 7
PRKCZ -0.029 0.053 0.16 27 -10000 0 27
Crk/p130 Cas/Paxillin/FAK1 -0.055 0.053 0.12 22 -10000 0 22
PTPN1 0.029 0.011 -10000 0 0 63 63
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.024 -10000 0 -0.16 7 7
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.042 0.042 -10000 0 -0.062 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.031 0.024 0.13 10 -10000 0 10
GRB10 0.019 0.016 -10000 0 0 213 213
PTPN11 -0.033 0.012 0.16 1 -10000 0 1
IRS1 -0.023 0.022 0.12 10 -10000 0 10
IRS2 -0.03 0.014 0.16 1 -10000 0 1
IGF-1R heterotetramer/IGF1 0.046 0.012 0.14 1 -10000 0 1
GRB2 0.032 0.007 -10000 0 0 22 22
PDPK1 -0.03 0.057 0.18 27 -10000 0 27
YWHAE 0.032 0.005 -10000 0 0 12 12
PRKD1 -0.005 0.024 -10000 0 -0.16 3 3
SHC1 0.03 0.01 -10000 0 0 55 55
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.059 0.028 -9999 0 -0.047 18 18
E-cadherin/beta catenin 0.046 0.013 -9999 0 -0.016 8 8
CTNNB1 0.032 0.006 -9999 0 0 15 15
JUP 0.032 0.007 -9999 0 0 24 24
CDH1 0.032 0.006 -9999 0 0 19 19
Regulation of Androgen receptor activity

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
HDAC1 -0.014 0.006 0 74 -10000 0 74
SMARCC1 -0.002 0.031 -10000 0 -0.64 1 1
REL 0.033 0.002 -10000 0 0 2 2
HDAC7 -0.057 0.03 0.14 2 -10000 0 2
JUN 0.033 0.005 -10000 0 0 10 10
EP300 0.031 0.009 -10000 0 0 41 41
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.033 0.008 0.024 5 -10000 0 5
FOXO1 0.03 0.01 -10000 0 0 53 53
T-DHT/AR -0.057 0.04 0.2 2 -10000 0 2
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
BRM/BAF57 0.043 0.017 -10000 0 -10000 0 0
MAP2K4 0.031 0.008 -10000 0 -10000 0 0
SMARCA2 0.029 0.011 -10000 0 -10000 0 0
PDE9A 0.007 0.067 -10000 0 -0.52 7 7
NCOA2 0.033 0.005 -10000 0 0 12 12
CEBPA 0.03 0.01 -10000 0 0 57 57
EHMT2 0.033 0.003 -10000 0 0 5 5
cell proliferation -0.04 0.077 0.26 5 -0.27 15 20
NR0B1 0.03 0.01 -10000 0 0 49 49
EGR1 0.032 0.008 -10000 0 -10000 0 0
RXRs/9cRA 0.058 0.023 -10000 0 -0.047 1 1
AR/RACK1/Src -0.032 0.066 0.16 17 -10000 0 17
AR/GR -0.034 0.039 0.13 3 -0.18 9 12
GNB2L1 0.033 0.005 -10000 0 0 12 12
PKN1 0.03 0.009 -10000 0 0 43 43
RCHY1 0.033 0.004 -10000 0 0 6 6
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.024 0.016 0.029 2 -10000 0 2
T-DHT/AR/TIF2/CARM1 -0.048 0.046 0.19 6 -10000 0 6
SRC -0.03 0.043 0.15 18 -10000 0 18
NR3C1 0.033 0.004 -10000 0 0 9 9
KLK3 -0.033 0.066 -10000 0 -0.38 5 5
APPBP2 0.033 0.004 -10000 0 -10000 0 0
TRIM24 0.019 0.017 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.045 0.021 0.043 2 -0.11 6 8
TMPRSS2 0.006 0.071 -10000 0 -0.53 8 8
RXRG 0.032 0.005 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.032 0.007 -10000 0 -10000 0 0
RXRB 0.033 0.003 -10000 0 -10000 0 0
CARM1 0.031 0.009 -10000 0 0 42 42
NR2C2 0.033 0.005 -10000 0 -10000 0 0
KLK2 -0.028 0.048 0.16 4 -0.2 11 15
AR -0.025 0.03 0.12 6 -0.15 4 10
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.031 0.009 -10000 0 0 37 37
MDM2 0.029 0.01 -10000 0 0 56 56
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.006 -10000 0 0 17 17
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.033 0.004 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.033 0.068 0.17 17 -10000 0 17
positive regulation of transcription 0.032 0.006 -10000 0 0 17 17
DNAJA1 0.03 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.02 -10000 0 -0.21 4 4
NCOA1 0.033 0.019 0.11 7 -10000 0 7
SPDEF 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.055 0.082 -10000 0 -0.27 43 43
T-DHT/AR/Hsp90 -0.046 0.037 0.17 5 -10000 0 5
GSK3B 0.032 0.007 -10000 0 0 20 20
NR2C1 0.033 0.005 -10000 0 0 10 10
mol:T-DHT -0.031 0.03 0.19 4 -10000 0 4
SIRT1 0.024 0.015 -10000 0 0 145 145
ZMIZ2 0.02 0.016 -10000 0 0 202 202
POU2F1 0.035 0.009 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.05 0.035 0.17 5 -10000 0 5
CREBBP 0.033 0.004 -10000 0 0 7 7
SMARCE1 0.033 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.024 0.01 0.024 5 -10000 0 5
RAS family/GTP 0.024 0.054 0.17 2 -0.13 4 6
NFATC4 -0.035 0.049 0.27 6 -10000 0 6
ERBB2IP 0.027 0.019 -10000 0 -0.031 37 37
HSP90 (dimer) 0.031 0.009 -10000 0 0 37 37
mammary gland morphogenesis -0.045 0.031 0.13 5 -10000 0 5
JUN -0.001 0.041 0.13 8 -10000 0 8
HRAS 0.032 0.008 -10000 0 -0.032 1 1
DOCK7 -0.044 0.029 0.1 4 -10000 0 4
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.04 0.042 0.18 4 -10000 0 4
AKT1 -0.016 0.007 0.015 14 -10000 0 14
BAD -0.025 0.008 0.013 1 -10000 0 1
MAPK10 0.005 0.059 0.18 25 -10000 0 25
mol:GTP 0 0 -10000 0 -0.005 1 1
ErbB2/ErbB3/neuregulin 1 beta -0.048 0.033 0.14 5 -10000 0 5
RAF1 -0.022 0.066 0.22 17 -10000 0 17
ErbB2/ErbB3/neuregulin 2 -0.032 0.033 -10000 0 -10000 0 0
STAT3 0.024 0.097 -10000 0 -0.92 5 5
cell migration -0.017 0.054 0.2 13 -0.15 1 14
mol:PI-3-4-5-P3 -0.001 0.001 0.005 9 -10000 0 9
cell proliferation -0.001 0.1 0.41 2 -0.47 9 11
FOS 0.001 0.073 0.28 5 -0.27 11 16
NRAS 0.025 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.045 0.031 0.13 5 -10000 0 5
MAPK3 0.009 0.071 0.36 3 -10000 0 3
MAPK1 -0.014 0.12 0.41 2 -0.56 11 13
JAK2 -0.044 0.044 0.22 2 -10000 0 2
NF2 0.007 0.017 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.021 0.1 15 -10000 0 15
NRG1 0.032 0.008 -10000 0 -0.03 4 4
GRB2/SOS1 0.024 0.005 -10000 0 0 22 22
MAPK8 -0.019 0.059 0.17 2 -0.19 28 30
MAPK9 0.01 0.078 0.19 39 -10000 0 39
ERBB2 -0.033 0.014 0.015 33 -10000 0 33
ERBB3 0.026 0.014 -10000 0 -0.03 3 3
SHC1 0.03 0.01 -10000 0 0 55 55
RAC1 0.02 0.016 -10000 0 0 204 204
apoptosis 0.015 0.013 -10000 0 -0.2 1 1
STAT3 (dimer) 0.027 0.095 -10000 0 -0.89 5 5
RNF41 -0.031 0.013 -10000 0 -10000 0 0
FRAP1 -0.013 0.005 0.002 44 -10000 0 44
RAC1-CDC42/GTP -0.031 0.031 0.064 3 -10000 0 3
ErbB2/ErbB2/HSP90 (dimer) -0.034 0.022 0.036 33 -10000 0 33
CHRNA1 0.008 0.07 0.32 3 -0.26 7 10
myelination -0.042 0.061 0.27 13 -10000 0 13
PPP3CB -0.037 0.035 -10000 0 -10000 0 0
KRAS 0.031 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.022 0.036 -10000 0 -0.13 2 2
NRG2 0.033 0.005 -10000 0 0 11 11
mol:GDP -0.005 0.021 0.1 15 -10000 0 15
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.028 0.059 0.19 15 -10000 0 15
SRC 0.029 0.011 -10000 0 0 65 65
mol:cAMP -0.001 0.001 0.003 6 -10000 0 6
PTPN11 -0.049 0.045 0.22 2 -10000 0 2
MAP2K1 -0.012 0.13 0.4 2 -0.54 24 26
heart morphogenesis -0.045 0.031 0.13 5 -10000 0 5
RAS family/GDP 0.027 0.057 0.19 2 -0.14 4 6
GRB2 0.032 0.007 -10000 0 0 22 22
PRKACA 0.016 0.006 -10000 0 -10000 0 0
CHRNE 0 0.011 0.041 6 -10000 0 6
HSP90AA1 0.031 0.009 -10000 0 0 37 37
activation of caspase activity 0.016 0.007 -10000 0 -0.015 14 14
nervous system development -0.045 0.031 0.13 5 -10000 0 5
CDC42 0.032 0.006 -10000 0 0 19 19
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.006 0.059 -10000 0 -0.19 24 24
TBX21 -0.027 0.12 -10000 0 -0.44 2 2
B2M 0.032 0.006 -10000 0 0 18 18
TYK2 0.021 0.03 -10000 0 -0.065 2 2
IL12RB1 0.02 0.031 -10000 0 -0.065 2 2
GADD45B -0.001 0.095 -10000 0 -0.43 1 1
IL12RB2 0.021 0.033 -10000 0 -0.066 2 2
GADD45G -0.006 0.1 -10000 0 -0.46 4 4
natural killer cell activation -0.002 0.01 -10000 0 -0.03 14 14
RELB 0.031 0.009 -10000 0 0 39 39
RELA 0.033 0.004 -10000 0 0 9 9
IL18 0.021 0.025 -10000 0 -10000 0 0
IL2RA 0.024 0.015 -10000 0 0 148 148
IFNG 0.031 0.009 -10000 0 0 36 36
STAT3 (dimer) -0.014 0.11 -10000 0 -0.41 6 6
HLA-DRB5 0 0.001 -10000 0 -10000 0 0
FASLG -0.024 0.12 -10000 0 -0.52 2 2
NF kappa B2 p52/RelB -0.013 0.13 -10000 0 -0.39 15 15
CD4 0.03 0.01 -10000 0 -0.045 1 1
SOCS1 0.033 0.005 -10000 0 0 10 10
EntrezGene:6955 0 0.001 -10000 0 -0.02 1 1
CD3D 0.031 0.009 -10000 0 -0.041 2 2
CD3E 0.032 0.007 -10000 0 -0.039 2 2
CD3G 0.032 0.007 -10000 0 -0.041 2 2
IL12Rbeta2/JAK2 0.031 0.042 -10000 0 -0.085 2 2
CCL3 -0.022 0.12 -10000 0 -0.38 16 16
CCL4 -0.073 0.23 -10000 0 -0.66 66 66
HLA-A 0 0 -10000 0 -10000 0 0
IL18/IL18R 0.064 0.027 -10000 0 -10000 0 0
NOS2 -0.021 0.11 -10000 0 -0.43 4 4
IL12/IL12R/TYK2/JAK2/SPHK2 -0.008 0.062 -10000 0 -0.2 26 26
IL1R1 -0.028 0.12 -10000 0 -0.52 2 2
IL4 0.031 0.021 -10000 0 -10000 0 0
JAK2 0.019 0.03 -10000 0 -0.065 2 2
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.002 0.036 -10000 0 -0.14 22 22
RAB7A 0.005 0.099 0.34 2 -10000 0 2
lysosomal transport 0.006 0.097 0.34 2 -10000 0 2
FOS -0.043 0.18 -10000 0 -0.58 43 43
STAT4 (dimer) -0.028 0.12 0.38 1 -0.51 4 5
STAT5A (dimer) -0.003 0.13 -10000 0 -0.38 13 13
GZMA -0.032 0.12 -10000 0 -0.52 2 2
GZMB -0.035 0.12 -10000 0 -0.52 2 2
HLX 0.032 0.006 -10000 0 0 20 20
LCK -0.034 0.12 0.26 3 -0.4 16 19
TCR/CD3/MHC II/CD4 0.008 0.02 -10000 0 -0.1 6 6
IL2/IL2R 0.044 0.062 -10000 0 -0.054 134 134
MAPK14 0.007 0.1 -10000 0 -0.5 1 1
CCR5 -0.009 0.11 -10000 0 -0.55 4 4
IL1B 0.02 0.033 -10000 0 -0.065 2 2
STAT6 -0.001 0.069 -10000 0 -0.37 10 10
STAT4 0.019 0.016 -10000 0 0 212 212
STAT3 0.032 0.006 -10000 0 0 18 18
STAT1 0.032 0.006 -10000 0 0 20 20
NFKB1 0.032 0.005 -10000 0 0 13 13
NFKB2 0.024 0.015 -10000 0 0 147 147
IL12B 0.021 0.033 -10000 0 -0.066 2 2
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.033 0.003 -10000 0 0 4 4
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.006 0.059 0.19 24 -10000 0 24
IL2RB 0.031 0.009 -10000 0 0 40 40
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.12 0.38 1 -0.48 4 5
IL2RG 0.033 0.005 -10000 0 0 11 11
IL12 0.032 0.044 -10000 0 -0.085 2 2
STAT5A 0.033 0.004 -10000 0 0 9 9
CD247 0.032 0.007 -10000 0 -0.039 2 2
IL2 0.033 0.004 -10000 0 0 8 8
SPHK2 0.031 0.009 -10000 0 0 39 39
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.02 0.033 -10000 0 -0.065 2 2
IL12/IL12R/TYK2/JAK2 -0.024 0.12 -10000 0 -0.41 17 17
MAP2K3 0.002 0.11 -10000 0 -0.53 2 2
RIPK2 0.032 0.005 -10000 0 0 13 13
MAP2K6 0.004 0.1 -10000 0 -0.44 2 2
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.001 -10000 0 -0.02 1 1
IL18RAP 0.024 0.025 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.032 0.04 -10000 0 -0.082 2 2
EOMES 0.003 0.021 0.07 7 -0.071 7 14
STAT1 (dimer) -0.009 0.12 -10000 0 -0.45 2 2
T cell proliferation -0.028 0.099 0.38 1 -0.4 5 6
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.024 0.025 -10000 0 -10000 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.007 0.12 -10000 0 -0.44 4 4
ATF2 -0.001 0.1 0.41 1 -0.48 1 2
Glucocorticoid receptor regulatory network

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
PCK2 0.05 0.069 -10000 0 -0.29 5 5
SMARCC2 0.032 0.007 -10000 0 0 24 24
SMARCC1 0.031 0.008 -10000 0 0 33 33
TBX21 -0.005 0.019 0.33 1 -10000 0 1
SUMO2 0.032 0.008 -10000 0 -0.034 5 5
STAT1 (dimer) 0.027 0.022 -10000 0 -0.031 56 56
FKBP4 0.032 0.007 -10000 0 0 25 25
FKBP5 0.031 0.008 -10000 0 0 31 31
GR alpha/HSP90/FKBP51/HSP90 0.083 0.056 -10000 0 -10000 0 0
PRL -0.049 0.059 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.021 0.032 -10000 0 -10000 0 0
RELA 0.031 0.016 -10000 0 -0.036 3 3
FGG 0.12 0.14 -10000 0 -10000 0 0
GR beta/TIF2 0.054 0.079 -10000 0 -10000 0 0
IFNG -0.071 0.093 -10000 0 -0.25 8 8
apoptosis 0.01 0.083 -10000 0 -0.39 6 6
CREB1 0.036 0.008 -10000 0 -10000 0 0
histone acetylation -0.001 0.035 -10000 0 -0.12 36 36
BGLAP 0.008 0.015 -10000 0 -0.11 2 2
GR/PKAc 0.094 0.06 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.049 0.026 -10000 0 -10000 0 0
SMARCD1 0.032 0.006 -10000 0 0 20 20
MDM2 0.043 0.048 0.11 7 -10000 0 7
GATA3 0.026 0.016 -10000 0 -10000 0 0
AKT1 0.03 0.009 -10000 0 0 39 39
CSF2 -0.081 0.071 -10000 0 -0.26 2 2
GSK3B 0.032 0.009 -10000 0 -0.034 4 4
NR1I3 0.009 0.087 -10000 0 -0.36 5 5
CSN2 0.12 0.13 0.3 13 -10000 0 13
BRG1/BAF155/BAF170/BAF60A 0.069 0.036 -10000 0 -0.053 14 14
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.033 0.009 -10000 0 -10000 0 0
CDKN1A -0.004 0.038 -10000 0 -0.36 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
SFN 0.03 0.01 -10000 0 0 46 46
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.098 0.059 -10000 0 -10000 0 0
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.01 0.088 -10000 0 -0.41 5 5
JUN -0.006 0.021 0.27 2 -10000 0 2
IL4 0.008 0.016 -10000 0 -0.12 1 1
CDK5R1 0.026 0.014 -10000 0 -0.032 1 1
PRKACA 0.031 0.009 -10000 0 0 36 36
cortisol/GR alpha (monomer)/AP-1 -0.029 0.042 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.058 -10000 0 -10000 0 0
cortisol/GR alpha (monomer) -0.021 0.031 -10000 0 -10000 0 0
NCOA2 0.032 0.005 -10000 0 0 12 12
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.025 0.019 -10000 0 -10000 0 0
AP-1/NFAT1-c-4 -0.024 0.034 0.22 1 -10000 0 1
AFP -0.069 0.057 -10000 0 -0.39 1 1
SUV420H1 0.032 0.006 -10000 0 0 15 15
IRF1 0.064 0.079 -10000 0 -10000 0 0
TP53 0.025 0.024 -10000 0 -10000 0 0
PPP5C 0.031 0.009 -10000 0 0 39 39
KRT17 -0.075 0.093 -10000 0 -0.23 7 7
KRT14 -0.049 0.069 0.17 15 -10000 0 15
TBP 0.034 0.01 -10000 0 -10000 0 0
CREBBP 0.031 0.005 -10000 0 -0.033 1 1
HDAC1 0.027 0.011 -10000 0 -10000 0 0
HDAC2 0.03 0.009 -10000 0 -10000 0 0
AP-1 -0.024 0.034 0.22 1 -10000 0 1
MAPK14 0.032 0.007 -10000 0 -0.033 5 5
MAPK10 0.019 0.017 -10000 0 -10000 0 0
MAPK11 0.029 0.012 -10000 0 -0.034 4 4
KRT5 -0.071 0.091 -10000 0 -0.22 5 5
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.032 0.008 -10000 0 0 28 28
STAT1 0.027 0.022 -10000 0 -0.031 56 56
CGA 0.007 0.018 -10000 0 -0.11 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.053 0.082 0.19 2 -0.31 3 5
MAPK3 0.032 0.007 -10000 0 -0.035 5 5
MAPK1 0.03 0.011 -10000 0 -0.034 4 4
ICAM1 -0.037 0.068 0.13 2 -0.13 163 165
NFKB1 0.031 0.016 -10000 0 -10000 0 0
MAPK8 -0.005 0.011 -10000 0 -10000 0 0
MAPK9 0.032 0.008 -10000 0 -0.033 5 5
cortisol/GR alpha (dimer) 0.012 0.084 -10000 0 -0.37 8 8
BAX -0.005 0.059 -10000 0 -0.37 2 2
POMC -0.076 0.09 0.8 1 -0.4 1 2
EP300 0.029 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.02 0.031 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.032 0.22 2 -10000 0 2
SGK1 0.017 0.051 0.18 1 -0.16 17 18
IL13 -0.058 0.071 -10000 0 -0.31 3 3
IL6 -0.022 0.056 0.13 2 -0.13 107 109
PRKACG 0.032 0.007 -10000 0 0 21 21
IL5 -0.078 0.09 -10000 0 -0.29 39 39
IL2 -0.073 0.093 -10000 0 -0.23 6 6
CDK5 0.017 0.017 -10000 0 -0.032 3 3
PRKACB 0.029 0.011 -10000 0 0 60 60
HSP90AA1 0.031 0.009 -10000 0 0 37 37
IL8 -0.043 0.07 0.13 2 -0.13 76 78
CDK5R1/CDK5 0.021 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.076 0.05 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.02 0.035 -10000 0 -10000 0 0
SMARCA4 0.03 0.01 -10000 0 0 47 47
chromatin remodeling 0.066 0.079 -10000 0 -0.19 2 2
NF kappa B1 p50/RelA/Cbp 0.07 0.047 -10000 0 -10000 0 0
JUN (dimer) -0.006 0.021 0.27 2 -10000 0 2
YWHAH 0.015 0.017 -10000 0 0 278 278
VIPR1 -0.004 0.028 0.33 3 -10000 0 3
NR3C1 0.04 0.085 -10000 0 -10000 0 0
NR4A1 0.034 0.007 -10000 0 -10000 0 0
TIF2/SUV420H1 0.047 0.011 -10000 0 -10000 0 0
MAPKKK cascade 0.01 0.083 -10000 0 -0.39 6 6
cortisol/GR alpha (dimer)/Src-1 -0.02 0.031 -10000 0 -10000 0 0
PBX1 0.033 0.009 -10000 0 -10000 0 0
POU1F1 0.033 0.009 -10000 0 -10000 0 0
SELE -0.041 0.071 0.13 2 -0.13 200 202
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.067 0.079 -10000 0 -0.19 2 2
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.02 0.035 -10000 0 -10000 0 0
mol:cortisol -0.01 0.015 -10000 0 -10000 0 0
MMP1 0 0.057 -10000 0 -0.51 6 6
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.032 0.006 0 15 -9999 0 15
PI3K Class IB/PDE3B 0.032 0.006 -9999 0 0 15 15
PDE3B 0.032 0.006 -9999 0 0 15 15
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.027 0.062 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.018 0.033 -10000 0 -0.22 1 1
NCK1/Dok-R -0.005 0.059 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
mol:beta2-estradiol 0.001 0.004 -10000 0 -10000 0 0
RELA 0.033 0.004 -10000 0 0 9 9
SHC1 0.029 0.01 -10000 0 -10000 0 0
Rac/GDP 0.015 0.012 -10000 0 0 204 204
F2 0.03 0.018 -10000 0 -10000 0 0
TNIP2 0.032 0.006 -10000 0 0 19 19
NF kappa B/RelA 0.022 0.08 -10000 0 -10000 0 0
FN1 0.027 0.013 -10000 0 0 100 100
PLD2 -0.025 0.044 -10000 0 -10000 0 0
PTPN11 0.033 0.005 -10000 0 0 10 10
GRB14 0.032 0.007 -10000 0 0 21 21
ELK1 -0.03 0.05 0.23 1 -10000 0 1
GRB7 0.033 0.004 -10000 0 0 7 7
PAK1 0.033 0.005 -10000 0 0 11 11
Tie2/Ang1/alpha5/beta1 Integrin 0 0.076 -10000 0 -10000 0 0
CDKN1A -0.025 0.059 -10000 0 -0.34 1 1
ITGA5 0.027 0.013 -10000 0 0 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.005 0.059 -10000 0 -10000 0 0
CRK 0.033 0.005 -10000 0 0 10 10
mol:NO 0.03 0.097 0.3 8 -10000 0 8
PLG -0.021 0.04 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.024 0.085 0.34 1 -10000 0 1
GRB2 0.032 0.007 -10000 0 0 22 22
PIK3R1 0.03 0.01 -10000 0 -10000 0 0
ANGPT2 -0.001 0.046 -10000 0 -10000 0 0
BMX -0.025 0.044 -10000 0 -10000 0 0
ANGPT1 -0.001 0.025 -10000 0 -10000 0 0
tube development -0.029 0.055 -10000 0 -10000 0 0
ANGPT4 0.029 0.011 -10000 0 -10000 0 0
response to hypoxia -0.002 0.003 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.005 0.061 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.027 0.027 -10000 0 -0.016 61 61
FGF2 0.033 0.005 -10000 0 0 9 9
STAT5A (dimer) -0.026 0.07 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.097 0.3 8 -10000 0 8
AGTR1 0.031 0.007 -10000 0 -0.03 1 1
MAPK14 -0.008 0.066 -10000 0 -0.55 2 2
Tie2/SHP2 -0.032 0.13 -10000 0 -0.27 108 108
TEK -0.041 0.13 -10000 0 -0.29 102 102
RPS6KB1 -0.027 0.063 -10000 0 -10000 0 0
Angiotensin II/AT1 0.021 0.009 -10000 0 -0.02 15 15
Tie2/Ang1/GRB2 -0.004 0.061 -10000 0 -10000 0 0
MAPK3 -0.034 0.043 -10000 0 -10000 0 0
MAPK1 -0.03 0.042 -10000 0 -10000 0 0
Tie2/Ang1/GRB7 -0.004 0.062 -10000 0 -10000 0 0
NFKB1 0.032 0.005 -10000 0 0 13 13
MAPK8 -0.014 0.031 -10000 0 -10000 0 0
PI3K -0.018 0.063 -10000 0 -10000 0 0
FES -0.011 0.068 -10000 0 -0.46 2 2
Crk/Dok-R -0.004 0.06 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 -0.005 0.061 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.027 0.061 -10000 0 -10000 0 0
STAT5A 0.033 0.004 -10000 0 0 9 9
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.023 0.071 0.3 5 -10000 0 5
Tie2/Ang2 -0.022 0.057 -10000 0 -10000 0 0
Tie2/Ang1 0.003 0.027 -10000 0 -10000 0 0
FOXO1 -0.031 0.058 -10000 0 -10000 0 0
ELF1 0.037 0.016 -10000 0 -10000 0 0
ELF2 -0.003 0.027 0.23 1 -10000 0 1
mol:Choline -0.026 0.044 -10000 0 -10000 0 0
cell migration -0.016 0.022 -10000 0 -10000 0 0
FYN -0.029 0.054 -10000 0 -10000 0 0
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.056 -10000 0 -0.32 1 1
ETS1 0.025 0.025 -10000 0 -10000 0 0
PXN -0.028 0.072 0.32 5 -10000 0 5
ITGB1 0.025 0.015 -10000 0 0 131 131
NOS3 0.024 0.098 0.33 5 -10000 0 5
RAC1 0.02 0.016 -10000 0 0 204 204
TNF 0.025 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.026 0.044 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 0 18 18
Tie2/Ang1/Shc -0.006 0.06 -10000 0 -10000 0 0
NCK1 0.031 0.008 -10000 0 0 28 28
vasculogenesis 0.032 0.094 0.29 8 -10000 0 8
mol:Phosphatidic acid -0.026 0.044 -10000 0 -10000 0 0
mol:Angiotensin II -0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.03 0.097 0.3 8 -10000 0 8
Rac1/GTP -0.004 0.053 -10000 0 -10000 0 0
MMP2 -0.013 0.036 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.034 0.045 -10000 0 -0.17 8 8
HDAC7 0 0 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.024 0.078 -10000 0 -0.27 15 15
SMAD4 0.024 0.015 -10000 0 0 134 134
ID2 0.023 0.13 0.45 15 -10000 0 15
AP1 0.03 0.029 -10000 0 -10000 0 0
ABCG2 0.02 0.13 0.46 14 -10000 0 14
HIF1A 0.016 0.045 0.16 7 -10000 0 7
TFF3 0.021 0.13 0.48 13 -10000 0 13
GATA2 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.021 0.045 0.15 8 -10000 0 8
response to hypoxia -0.003 0.015 0.081 9 -10000 0 9
MCL1 0.019 0.13 0.51 9 -10000 0 9
NDRG1 0.015 0.12 0.43 11 -10000 0 11
SERPINE1 0.001 0.093 0.49 7 -10000 0 7
FECH 0.026 0.14 0.45 19 -10000 0 19
FURIN 0.026 0.14 0.46 16 -10000 0 16
NCOA2 0.033 0.005 -10000 0 -10000 0 0
EP300 0.023 0.04 0.19 13 -10000 0 13
HMOX1 -0.007 0.11 0.45 10 -10000 0 10
BHLHE40 -0.034 0.045 -10000 0 -0.17 8 8
BHLHE41 -0.034 0.045 -10000 0 -0.17 8 8
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.075 0.063 0.24 5 -10000 0 5
ENG -0.018 0.079 0.3 11 -10000 0 11
JUN 0.033 0.005 -10000 0 -10000 0 0
RORA 0.024 0.13 0.48 13 -10000 0 13
ABCB1 0.011 0.028 -10000 0 -0.3 2 2
TFRC 0.018 0.13 0.46 11 -10000 0 11
CXCR4 -0.003 0.11 0.46 10 -10000 0 10
TF -0.031 0.062 -10000 0 -10000 0 0
CITED2 0.017 0.13 0.49 11 -10000 0 11
HIF1A/ARNT 0.054 0.08 -10000 0 -0.18 10 10
LDHA 0.018 0.072 -10000 0 -0.46 10 10
ETS1 0.026 0.14 0.45 18 -10000 0 18
PGK1 0.026 0.14 0.45 18 -10000 0 18
NOS2 -0.034 0.045 -10000 0 -0.17 8 8
ITGB2 0.013 0.13 0.46 17 -10000 0 17
ALDOA 0.024 0.14 0.47 13 -10000 0 13
Cbp/p300/CITED2 -0.02 0.075 0.18 7 -0.28 12 19
FOS 0.023 0.016 -10000 0 -10000 0 0
HK2 0.025 0.14 0.46 16 -10000 0 16
SP1 0.034 0.007 -10000 0 -0.031 2 2
GCK 0.034 0.078 0.36 5 -0.31 1 6
HK1 0.001 0.099 0.4 6 -10000 0 6
NPM1 0.019 0.13 0.45 13 -10000 0 13
EGLN1 0.021 0.13 0.44 16 -10000 0 16
CREB1 0.034 0.012 -10000 0 -0.082 5 5
PGM1 0.024 0.14 0.45 18 -10000 0 18
SMAD3 0.032 0.005 -10000 0 0 12 12
EDN1 -0.001 0.079 -10000 0 -0.37 7 7
IGFBP1 0.009 0.1 0.46 9 -10000 0 9
VEGFA -0.008 0.091 0.39 7 -0.28 6 13
HIF1A/JAB1 0.043 0.034 0.15 4 -10000 0 4
CP 0.01 0.12 0.44 13 -10000 0 13
CXCL12 0.009 0.11 0.43 8 -10000 0 8
COPS5 0.033 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.028 -10000 0 -0.017 109 109
BNIP3 0.003 0.098 0.42 5 -10000 0 5
EGLN3 0.024 0.13 0.47 13 -10000 0 13
CA9 0.013 0.12 0.51 8 -10000 0 8
TERT 0.025 0.14 0.46 17 -10000 0 17
ENO1 0.02 0.13 0.45 14 -10000 0 14
PFKL 0.027 0.14 0.46 16 -10000 0 16
NCOA1 0.031 0.008 -10000 0 0 28 28
ADM -0.005 0.11 0.48 9 -10000 0 9
ARNT 0.016 0.048 0.16 9 -10000 0 9
HNF4A 0.03 0.011 -10000 0 -10000 0 0
ADFP -0.034 0.045 -10000 0 -0.17 8 8
SLC2A1 0.01 0.11 0.37 11 -0.28 6 17
LEP 0.011 0.099 0.43 10 -10000 0 10
HIF1A/ARNT/Cbp/p300 0.013 0.074 -10000 0 -0.27 16 16
EPO 0.008 0.089 0.4 4 -0.32 20 24
CREBBP 0.024 0.043 0.19 16 -10000 0 16
HIF1A/ARNT/Cbp/p300/HDAC7 0.008 0.069 -10000 0 -0.26 16 16
PFKFB3 0.011 0.11 0.43 9 -10000 0 9
NT5E 0.011 0.12 0.44 13 -10000 0 13
Regulation of Telomerase

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
Telomerase catalytic core complex 0.025 0.082 0.26 1 -0.43 4 5
RAD9A 0.033 0.004 -10000 0 0 8 8
AP1 0.03 0.029 -10000 0 -10000 0 0
IFNAR2 0.032 0.006 -10000 0 -10000 0 0
AKT1 0.012 0.016 -10000 0 -0.061 22 22
ER alpha/Oestrogen 0.023 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.008 0.052 -10000 0 -0.22 18 18
EGF 0.033 0.004 -10000 0 -10000 0 0
SMG5 0.032 0.006 -10000 0 0 17 17
SMG6 0.033 0.005 -10000 0 0 10 10
SP3/HDAC2 0.038 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.038 0.084 -10000 0 -0.43 4 4
SAP18 0.031 0.009 -10000 0 -10000 0 0
MRN complex 0.062 0.022 -10000 0 -0.047 14 14
WT1 0.032 0.007 -10000 0 -10000 0 0
WRN 0.032 0.006 -10000 0 0 16 16
SP1 0.033 0.006 -10000 0 -10000 0 0
SP3 0.028 0.012 -10000 0 -10000 0 0
TERF2IP 0.029 0.011 -10000 0 0 59 59
Telomerase/Nucleolin 0.053 0.094 -10000 0 -0.39 6 6
Mad/Max 0.046 0.013 -10000 0 -10000 0 0
TERT 0.025 0.083 0.26 1 -0.44 4 5
CCND1 0.016 0.076 -10000 0 -0.47 2 2
MAX 0.031 0.009 -10000 0 -10000 0 0
RBBP7 0.033 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.014 -10000 0 -10000 0 0
TERF2 -0.029 0.023 0.042 31 -10000 0 31
PTGES3 0.032 0.007 -10000 0 0 26 26
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.045 0.068 -10000 0 -0.44 4 4
CDKN1B -0.033 0.012 -10000 0 -10000 0 0
RAD1 0.032 0.005 -10000 0 0 14 14
XRCC5 0.033 0.002 -10000 0 0 2 2
XRCC6 0.03 0.009 -10000 0 0 43 43
SAP30 0.032 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.019 0.089 5 -10000 0 5
UBE3A 0.032 0.006 -10000 0 -10000 0 0
JUN 0.033 0.005 -10000 0 -10000 0 0
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.004 -10000 0 -10000 0 0
FOS 0.023 0.016 -10000 0 -10000 0 0
IFN-gamma/IRF1 0.041 0.026 -10000 0 -10000 0 0
PARP2 0.031 0.009 -10000 0 0 36 36
BLM 0.025 0.015 -10000 0 0 132 132
Telomerase 0.004 0.068 0.13 1 -0.24 33 34
IRF1 0.028 0.015 -10000 0 -0.033 10 10
ESR1 0.031 0.009 -10000 0 -10000 0 0
KU/TER 0.045 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.027 -10000 0 -0.042 31 31
ubiquitin-dependent protein catabolic process -0.004 0.051 -10000 0 -0.21 17 17
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.005 0.052 -10000 0 -0.21 17 17
HDAC1 0.028 0.012 -10000 0 -10000 0 0
HDAC2 0.031 0.009 -10000 0 -10000 0 0
ATM 0.016 0.011 0.091 7 -10000 0 7
SMAD3 -0.03 0.01 0 44 -10000 0 44
ABL1 0.032 0.007 -10000 0 0 27 27
MXD1 0.033 0.001 -10000 0 -10000 0 0
MRE11A 0.033 0.005 -10000 0 0 11 11
HUS1 0.02 0.016 -10000 0 0 205 205
RPS6KB1 0.033 0.004 -10000 0 0 9 9
TERT/NF kappa B1/14-3-3 0.046 0.11 -10000 0 -0.43 9 9
NR2F2 0.032 0.006 -10000 0 0 16 16
MAPK3 -0.032 0.005 -10000 0 -10000 0 0
MAPK1 -0.03 0.01 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.029 0.011 -10000 0 0 61 61
NFKB1 0.032 0.005 -10000 0 0 13 13
HNRNPC 0.031 0.008 -10000 0 0 35 35
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.011 0.091 7 -10000 0 7
NBN 0.032 0.005 -10000 0 0 12 12
EGFR 0.012 0.016 -10000 0 -10000 0 0
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.024 -10000 0 -10000 0 0
MYC 0.024 0.015 -10000 0 -10000 0 0
IL2 0.033 0.004 -10000 0 -10000 0 0
KU 0.045 0.014 -10000 0 -10000 0 0
RAD50 0.032 0.005 -10000 0 0 12 12
HSP90AA1 0.031 0.009 -10000 0 0 37 37
TGFB1 0.029 0.011 -10000 0 0 61 61
TRF2/BLM 0.024 0.031 0.089 3 -0.025 111 114
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.048 0.093 -10000 0 -0.43 4 4
SP1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.053 0.094 -10000 0 -0.39 6 6
Smad3/Myc -0.032 0.013 -10000 0 -10000 0 0
911 complex 0.038 0.035 -10000 0 -0.048 8 8
IFNG 0.032 0.009 -10000 0 -0.033 1 1
Telomerase/PinX1 0.041 0.086 -10000 0 -0.38 6 6
Telomerase/AKT1/mTOR/p70S6K 0.003 0.093 0.17 1 -0.3 34 35
SIN3B 0.031 0.009 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 0 12 12
Telomerase/EST1B 0.053 0.092 -10000 0 -0.39 6 6
response to DNA damage stimulus 0.003 0.014 -10000 0 -0.1 7 7
MRN complex/TRF2/Rap1 0.074 0.044 -10000 0 -0.065 12 12
TRF2/WRN 0.04 0.018 0.089 5 -0.024 4 9
Telomerase/hnRNP C1/C2 0.052 0.095 -10000 0 -0.39 6 6
E2F1 0.029 0.011 -10000 0 -10000 0 0
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.033 0.003 -10000 0 0 4 4
DKC1 0.033 0.005 -10000 0 0 11 11
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.031 0.011 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.01 0.057 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.047 0.033 -10000 0 -10000 0 0
TBX21 -0.023 0.091 0.31 27 -10000 0 27
IL12B 0.033 0.005 -10000 0 -10000 0 0
IL12A -0.016 0.003 0 17 -10000 0 17
IL6ST 0.033 0.006 -10000 0 -10000 0 0
IL27RA/JAK1 0.028 0.055 -10000 0 -10000 0 0
IL27 -0.001 0.004 -10000 0 -10000 0 0
TYK2 0.03 0.01 -10000 0 -0.031 1 1
T-helper cell lineage commitment 0.059 0.09 0.38 1 -10000 0 1
T-helper 2 cell differentiation 0.01 0.057 -10000 0 -10000 0 0
T cell proliferation during immune response 0.01 0.057 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.057 -10000 0 -10000 0 0
STAT3 0.032 0.006 -10000 0 0 18 18
STAT2 0.032 0.007 -10000 0 0 24 24
STAT1 0.032 0.006 -10000 0 0 20 20
IL12RB1 0.031 0.009 -10000 0 0 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.025 0.087 0.31 25 -10000 0 25
IL27/IL27R/JAK2/TYK2 -0.01 0.058 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.01 0.057 -10000 0 -10000 0 0
STAT1 (dimer) 0.051 0.038 -10000 0 -10000 0 0
JAK2 0.028 0.012 -10000 0 -0.032 1 1
JAK1 0.032 0.006 -10000 0 0 16 16
STAT2 (dimer) 0.019 0.082 0.24 18 -10000 0 18
T cell proliferation -0.01 0.037 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.022 0.096 -10000 0 -0.66 9 9
IL17A 0.059 0.09 0.38 1 -10000 0 1
mast cell activation 0.01 0.057 -10000 0 -10000 0 0
IFNG 0.004 0.025 0.076 1 -0.087 13 14
T cell differentiation -0.002 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.084 0.24 19 -10000 0 19
STAT5A (dimer) 0.021 0.085 0.24 20 -10000 0 20
STAT4 (dimer) 0.013 0.058 0.24 8 -10000 0 8
STAT4 0.019 0.016 -10000 0 0 212 212
T cell activation -0.002 0.001 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.043 -10000 0 -10000 0 0
GATA3 0.003 0.098 0.69 10 -10000 0 10
IL18 -0.015 0.005 0 51 -10000 0 51
positive regulation of mast cell cytokine production 0.02 0.083 0.23 19 -10000 0 19
IL27/EBI3 0.023 0.009 -10000 0 -10000 0 0
IL27RA 0.001 0.039 0.25 11 -10000 0 11
IL6 0.018 0.018 -10000 0 -10000 0 0
STAT5A 0.033 0.004 -10000 0 0 9 9
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.009 0.027 0.32 3 -10000 0 3
IL1B -0.016 0.003 0 14 -10000 0 14
EBI3 0.031 0.012 -10000 0 -0.032 5 5
TNF -0.017 0.002 0 7 -10000 0 7
IL4-mediated signaling events

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
BCL2L1 -0.034 0.16 0.41 1 -0.74 1 2
STAT6 (cleaved dimer) -0.036 0.15 -10000 0 -0.67 2 2
IGHG1 -0.014 0.083 -10000 0 -0.49 1 1
IGHG3 -0.053 0.14 -10000 0 -0.71 1 1
AKT1 -0.021 0.12 -10000 0 -0.57 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.002 0.08 -10000 0 -0.5 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.01 0.1 -10000 0 -0.53 1 1
THY1 -0.17 0.33 -10000 0 -0.71 128 128
MYB 0.03 0.009 -10000 0 0 45 45
HMGA1 0.033 0.003 -10000 0 0 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.016 0.11 -10000 0 -0.52 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.014 0.1 -10000 0 -0.5 2 2
SP1 -0.001 0.035 -10000 0 -0.035 249 249
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.026 0.16 -10000 0 -10000 0 0
SOCS1 -0.036 0.13 -10000 0 -10000 0 0
SOCS3 -0.027 0.097 -10000 0 -10000 0 0
FCER2 -0.038 0.13 -10000 0 -0.64 1 1
PARP14 0 0 -10000 0 -10000 0 0
CCL17 -0.061 0.15 -10000 0 -0.74 1 1
GRB2 0.032 0.007 -10000 0 0 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.013 0.084 0.24 1 -0.5 1 2
T cell proliferation -0.051 0.15 -10000 0 -0.71 2 2
IL4R/JAK1 -0.046 0.16 -10000 0 -0.7 1 1
EGR2 -0.063 0.15 -10000 0 -0.74 1 1
JAK2 0.012 0.04 -10000 0 -10000 0 0
JAK3 0.029 0.018 -10000 0 -0.054 1 1
PIK3R1 0.03 0.01 -10000 0 0 47 47
JAK1 0.018 0.03 -10000 0 -10000 0 0
COL1A2 -0.02 0.1 -10000 0 -0.75 5 5
CCL26 -0.054 0.15 -10000 0 -0.73 1 1
IL4R -0.059 0.16 -10000 0 -0.74 1 1
PTPN6 0.019 0.028 -10000 0 -10000 0 0
IL13RA2 -0.066 0.15 -10000 0 -0.74 1 1
IL13RA1 0.015 0.042 -10000 0 -10000 0 0
IRF4 0.015 0.065 -10000 0 -0.44 4 4
ARG1 -0.017 0.093 -10000 0 -10000 0 0
CBL -0.025 0.1 -10000 0 -0.5 1 1
GTF3A 0.024 0.023 -10000 0 -0.034 63 63
PIK3CA 0.031 0.009 -10000 0 0 41 41
IL13RA1/JAK2 0.014 0.054 -10000 0 -10000 0 0
IRF4/BCL6 0.024 0.067 -10000 0 -0.41 3 3
CD40LG 0.035 0.004 -10000 0 -0.033 1 1
MAPK14 -0.025 0.1 -10000 0 -0.5 1 1
mitosis -0.018 0.11 -10000 0 -0.55 4 4
STAT6 -0.057 0.16 -10000 0 -0.74 2 2
SPI1 0.033 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.025 0.11 0.27 1 -0.54 4 5
STAT6 (dimer) -0.056 0.16 -10000 0 -0.73 2 2
STAT6 (dimer)/PARP14 -0.059 0.15 -10000 0 -0.76 1 1
mast cell activation 0.002 0.007 -10000 0 -0.018 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.01 0.09 -10000 0 -0.51 2 2
FRAP1 -0.019 0.12 -10000 0 -0.57 4 4
LTA -0.062 0.15 -10000 0 -0.74 1 1
FES 0.032 0.005 -10000 0 0 14 14
T-helper 1 cell differentiation 0.057 0.16 0.72 2 -10000 0 2
CCL11 -0.059 0.15 -10000 0 -0.72 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.008 0.095 -10000 0 -0.63 2 2
IL2RG 0.027 0.024 -10000 0 -0.055 4 4
IL10 -0.054 0.16 -10000 0 -0.74 1 1
IRS1 0.033 0.003 -10000 0 0 5 5
IRS2 0.031 0.009 -10000 0 0 41 41
IL4 -0.008 0.086 -10000 0 -0.53 7 7
IL5 -0.06 0.15 -10000 0 -0.74 1 1
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.058 0.16 -10000 0 -0.83 1 1
COL1A1 -0.029 0.12 -10000 0 -0.57 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.051 0.16 -10000 0 -0.69 1 1
IL2R gamma/JAK3 0.045 0.024 -10000 0 -0.051 14 14
TFF3 -0.06 0.15 -10000 0 -0.74 1 1
ALOX15 -0.061 0.15 -10000 0 -0.74 1 1
MYBL1 0.027 0.013 -10000 0 0 89 89
T-helper 2 cell differentiation -0.045 0.15 -10000 0 -0.7 3 3
SHC1 0.03 0.01 -10000 0 0 55 55
CEBPB 0.03 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.017 0.11 -10000 0 -0.52 5 5
mol:PI-3-4-5-P3 -0.019 0.12 -10000 0 -0.57 4 4
PI3K -0.02 0.12 -10000 0 -0.6 4 4
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.02 0.03 -10000 0 -0.056 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.011 0.083 0.26 1 -0.46 1 2
ITGB3 -0.061 0.15 -10000 0 -0.74 1 1
PIGR -0.054 0.16 -10000 0 -0.74 1 1
IGHE 0.013 0.046 0.14 33 -0.092 1 34
MAPKKK cascade -0.011 0.082 0.26 1 -0.45 1 2
BCL6 0.03 0.009 -10000 0 0 42 42
OPRM1 -0.061 0.15 -10000 0 -0.74 1 1
RETNLB -0.054 0.15 -10000 0 -0.73 1 1
SELP -0.057 0.15 -10000 0 -0.74 1 1
AICDA -0.053 0.15 0.37 1 -0.72 1 2
Visual signal transduction: Rods

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
mol:K + 0.032 0.005 -9999 0 0 12 12
GNAT1/GTP 0.024 0.004 -9999 0 0 16 16
Metarhodopsin II/Arrestin 0.043 0.01 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.043 0.009 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.032 0.006 -9999 0 0 16 16
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.058 0.03 -9999 0 -0.074 1 1
mol:Na + -0.047 0.007 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.043 0.01 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.043 0.024 -9999 0 -0.054 26 26
CNGB1 0.032 0.005 -9999 0 0 13 13
RDH5 0.032 0.007 -9999 0 0 21 21
SAG 0.033 0.005 -9999 0 0 10 10
mol:Ca2+ -0.051 0.028 -9999 0 -10000 0 0
Na + (4 Units) -0.054 0.009 -9999 0 -10000 0 0
RGS9 0.033 0.004 -9999 0 0 9 9
GNB1/GNGT1 0.027 0.025 -9999 0 -10000 0 0
GNAT1/GDP 0.052 0.022 -9999 0 -0.038 21 21
GUCY2D 0.032 0.005 -9999 0 0 13 13
GNGT1 0.019 0.016 -9999 0 0 216 216
GUCY2F 0.033 0.003 -9999 0 0 3 3
GNB5 0.032 0.006 -9999 0 0 20 20
mol:GMP (4 units) -0.04 0.01 -9999 0 -10000 0 0
mol:11-cis-retinal 0.032 0.007 -9999 0 0 21 21
mol:cGMP -0.032 0.003 0 4 -10000 0 4
GNB1 0.031 0.008 -9999 0 0 31 31
Rhodopsin 0.046 0.013 -9999 0 -0.016 1 1
SLC24A1 0.032 0.005 -9999 0 0 12 12
CNGA1 0.033 0.004 -9999 0 0 6 6
Metarhodopsin II 0.02 0.006 -9999 0 -0.008 17 17
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.04 0.013 -9999 0 -0.03 15 15
RGS9BP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Transducin 0.004 0.023 -9999 0 -0.12 14 14
GCAP Family/Ca ++ 0.021 0.004 -9999 0 -0.012 6 6
PDE6A/B 0.048 0.009 -9999 0 -10000 0 0
mol:Pi 0.042 0.01 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.034 0.034 -9999 0 -0.042 11 11
PDE6B 0.033 0.004 -9999 0 0 7 7
PDE6A 0.033 0.005 -9999 0 0 10 10
PDE6G 0.033 0.004 -9999 0 0 7 7
RHO 0.032 0.006 -9999 0 0 17 17
PDE6 0.073 0.032 -9999 0 -0.056 21 21
GUCA1A 0 0 -9999 0 -10000 0 0
GC2/GCAP Family 0.042 0.008 -9999 0 -0.029 6 6
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.033 0.004 -9999 0 0 6 6
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.009 0.09 0.36 24 -10000 0 24
VDR 0.032 0.007 -10000 0 0 24 24
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.008 0.033 -10000 0 -0.22 2 2
RXRs/LXRs/DNA/Oxysterols -0.003 0.036 -10000 0 -0.22 4 4
MED1 0.033 0.004 -10000 0 0 8 8
mol:9cRA -0.001 0.001 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.014 0.033 -10000 0 -0.16 16 16
RXRs/NUR77 0.072 0.034 -10000 0 -10000 0 0
RXRs/PPAR 0.002 0.049 -10000 0 -0.13 57 57
NCOR2 0.033 0.005 -10000 0 0 11 11
VDR/VDR/Vit D3 0.023 0.005 -10000 0 0 24 24
RARs/VDR/DNA/Vit D3 0.071 0.029 -10000 0 -0.05 19 19
RARA 0.033 0.004 -10000 0 0 7 7
NCOA1 0.031 0.008 -10000 0 0 28 28
VDR/VDR/DNA 0.032 0.007 -10000 0 0 24 24
RARs/RARs/DNA/9cRA 0.054 0.018 -10000 0 -10000 0 0
RARG 0.032 0.006 -10000 0 0 15 15
RPS6KB1 -0.019 0.064 0.56 6 -10000 0 6
RARs/THRs/DNA/SMRT 0.016 0.031 -10000 0 -0.16 13 13
THRA 0.033 0.004 -10000 0 0 7 7
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 0 24 24
RXRs/PPAR/9cRA/PGJ2/DNA 0.054 0.022 -10000 0 -10000 0 0
NR1H4 0.033 0.004 -10000 0 0 9 9
RXRs/LXRs/DNA 0.076 0.046 -10000 0 -10000 0 0
NR1H2 0.03 0.009 -10000 0 -10000 0 0
NR1H3 0.031 0.007 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.065 0.033 -10000 0 -10000 0 0
NR4A1 0.032 0.006 -10000 0 0 19 19
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.008 0.029 -10000 0 -0.12 17 17
RXRG 0.031 0.007 -10000 0 -10000 0 0
RXR alpha/CCPG 0.023 0.005 -10000 0 -10000 0 0
RXRA 0.031 0.008 -10000 0 -0.031 1 1
RXRB 0.031 0.009 -10000 0 -10000 0 0
THRB 0.033 0.005 -10000 0 0 11 11
PPARG 0.032 0.006 -10000 0 0 17 17
PPARD 0.033 0.003 -10000 0 0 4 4
TNF -0.011 0.036 -10000 0 -0.22 1 1
mol:Oxysterols 0 0.001 -10000 0 -10000 0 0
cholesterol transport -0.003 0.036 -10000 0 -0.21 4 4
PPARA 0.03 0.01 -10000 0 0 51 51
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.033 0.005 -10000 0 0 11 11
RXRs/NUR77/BCL2 0.008 0.033 -10000 0 -0.12 29 29
SREBF1 -0.011 0.036 -10000 0 -0.22 1 1
RXRs/RXRs/DNA/9cRA 0.054 0.022 -10000 0 -10000 0 0
ABCA1 -0.018 0.03 -10000 0 -0.22 2 2
RARs/THRs 0.092 0.031 -10000 0 -0.062 12 12
RXRs/FXR 0.073 0.032 -10000 0 -10000 0 0
BCL2 0.032 0.007 -10000 0 0 21 21
FOXM1 transcription factor network

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
NFATC3 -0.021 0.082 -10000 0 -10000 0 0
PLK1 0.018 0.11 -10000 0 -0.72 10 10
BIRC5 0.022 0.023 -10000 0 -10000 0 0
HSPA1B -0.015 0.08 -10000 0 -10000 0 0
MAP2K1 0.013 0.033 -10000 0 -10000 0 0
BRCA2 -0.021 0.08 -10000 0 -10000 0 0
FOXM1 -0.011 0.083 -10000 0 -10000 0 0
XRCC1 -0.011 0.096 0.42 1 -10000 0 1
FOXM1B/p19 -0.015 0.076 -10000 0 -10000 0 0
Cyclin D1/CDK4 -0.021 0.062 -10000 0 -10000 0 0
CDC2 -0.018 0.082 -10000 0 -10000 0 0
TGFA -0.019 0.073 -10000 0 -10000 0 0
SKP2 -0.019 0.085 -10000 0 -10000 0 0
CCNE1 0.027 0.017 -10000 0 -10000 0 0
CKS1B -0.015 0.08 -10000 0 -10000 0 0
RB1 -0.015 0.1 -10000 0 -0.55 2 2
FOXM1C/SP1 -0.012 0.088 -10000 0 -10000 0 0
AURKB 0.015 0.12 -10000 0 -0.77 11 11
CENPF -0.019 0.082 -10000 0 -10000 0 0
CDK4 0.01 0.017 -10000 0 -10000 0 0
MYC -0.025 0.074 -10000 0 -10000 0 0
CHEK2 0.016 0.031 -10000 0 -10000 0 0
ONECUT1 -0.011 0.077 -10000 0 -10000 0 0
CDKN2A 0.009 0.015 -10000 0 0 373 373
LAMA4 -0.02 0.082 -10000 0 -10000 0 0
FOXM1B/HNF6 -0.012 0.08 -10000 0 -10000 0 0
FOS -0.023 0.09 -10000 0 -0.72 1 1
SP1 0.032 0.006 -10000 0 0 16 16
CDC25B 0.001 0.099 0.42 1 -10000 0 1
response to radiation -0.001 0.006 -10000 0 -10000 0 0
CENPB 0.001 0.099 0.42 1 -10000 0 1
CENPA -0.022 0.08 -10000 0 -10000 0 0
NEK2 -0.017 0.081 -10000 0 -10000 0 0
HIST1H2BA -0.015 0.08 -10000 0 -10000 0 0
CCNA2 0.024 0.016 -10000 0 -10000 0 0
EP300 0.031 0.009 -10000 0 0 41 41
CCNB1/CDK1 -0.022 0.082 -10000 0 -10000 0 0
CCNB2 -0.026 0.083 -10000 0 -10000 0 0
CCNB1 -0.019 0.083 -10000 0 -10000 0 0
ETV5 -0.014 0.086 -10000 0 -10000 0 0
ESR1 -0.021 0.081 -10000 0 -10000 0 0
CCND1 -0.015 0.072 -10000 0 -10000 0 0
GSK3A 0.015 0.031 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.038 0.043 -10000 0 -10000 0 0
CDK2 0.029 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.007 0.037 1 -10000 0 1
FOXM1B/Cbp/p300 -0.002 0.1 -10000 0 -10000 0 0
GAS1 -0.018 0.087 0.44 2 -10000 0 2
MMP2 -0.024 0.083 -10000 0 -10000 0 0
RB1/FOXM1C -0.026 0.076 -10000 0 -10000 0 0
CREBBP 0.033 0.004 -10000 0 0 7 7
IL23-mediated signaling events

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
CCL2 -0.01 0.14 -10000 0 -0.7 12 12
IL23A 0.011 0.069 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.11 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.01 0.11 -10000 0 -10000 0 0
ITGA3 0.006 0.088 -10000 0 -10000 0 0
IL17F -0.013 0.08 0.29 1 -10000 0 1
IL12B 0.035 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.022 0.11 -10000 0 -10000 0 0
CD4 0.01 0.11 0.41 2 -10000 0 2
IL23 0.037 0.07 -10000 0 -10000 0 0
IL23R 0.006 0.025 0.092 3 -10000 0 3
IL1B 0.011 0.078 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.008 0.11 -10000 0 -10000 0 0
TYK2 0.026 0.022 -10000 0 -10000 0 0
STAT4 0.019 0.016 -10000 0 0 212 212
STAT3 0.032 0.006 -10000 0 0 18 18
IL18RAP 0.033 0.002 -10000 0 -10000 0 0
IL12RB1 0.026 0.022 -10000 0 -10000 0 0
PIK3CA 0.031 0.009 -10000 0 0 41 41
IL12Rbeta1/TYK2 0.044 0.022 -10000 0 -10000 0 0
IL23R/JAK2 0.035 0.031 0.14 1 -10000 0 1
positive regulation of chronic inflammatory response 0.01 0.11 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK2 0.032 0.022 -10000 0 -10000 0 0
PIK3R1 0.03 0.01 -10000 0 0 47 47
NFKB1 0.032 0.011 -10000 0 -10000 0 0
RELA 0.032 0.012 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.037 0.069 -10000 0 -10000 0 0
ALOX12B 0.003 0.1 -10000 0 -10000 0 0
CXCL1 0.003 0.1 -10000 0 -10000 0 0
T cell proliferation 0.01 0.11 -10000 0 -10000 0 0
NFKBIA 0.03 0.013 -10000 0 -10000 0 0
IL17A 0.003 0.073 0.22 2 -10000 0 2
PI3K 0.031 0.12 -10000 0 -10000 0 0
IFNG 0.003 0.017 0.072 2 -0.07 17 19
STAT3 (dimer) 0.041 0.12 -10000 0 -10000 0 0
IL18R1 0.033 0.002 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.011 0.089 0.3 2 -10000 0 2
IL18/IL18R 0.059 0.029 -10000 0 -10000 0 0
macrophage activation 0 0.004 -10000 0 -10000 0 0
TNF 0.011 0.079 -10000 0 -10000 0 0
STAT3/STAT4 0.013 0.1 -10000 0 -10000 0 0
STAT4 (dimer) 0.012 0.089 -10000 0 -10000 0 0
IL18 0.03 0.01 -10000 0 -10000 0 0
IL19 0.008 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.023 0.11 -10000 0 -10000 0 0
STAT1 0.032 0.006 -10000 0 0 20 20
SOCS3 0.033 0.004 -10000 0 0 9 9
CXCL9 0.002 0.1 -10000 0 -10000 0 0
MPO 0.005 0.1 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.01 0.11 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.011 0.11 -10000 0 -10000 0 0
IL6 0.078 0.13 0.37 13 -10000 0 13
STAT5A 0.033 0.004 -10000 0 0 9 9
IL2 0.028 0.019 -10000 0 -0.033 42 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0.002 -10000 0 -10000 0 0
CD3E 0.004 0.1 -10000 0 -10000 0 0
keratinocyte proliferation 0.01 0.11 -10000 0 -10000 0 0
NOS2 0.009 0.1 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.03 0.042 -9999 0 -10000 0 0
CLOCK 0.031 0.009 -9999 0 -10000 0 0
TIMELESS/CRY2 0.017 0.035 -9999 0 -10000 0 0
DEC1/BMAL1 0.046 0.013 -9999 0 -10000 0 0
ATR 0.032 0.006 -9999 0 0 19 19
NR1D1 -0.002 0.019 -9999 0 -10000 0 0
ARNTL 0.032 0.006 -9999 0 -10000 0 0
TIMELESS -0.003 0.021 -9999 0 -10000 0 0
NPAS2 0.033 0.003 -9999 0 -10000 0 0
CRY2 0.032 0.006 -9999 0 0 19 19
mol:CO -0.001 0.003 -9999 0 -10000 0 0
CHEK1 0.029 0.011 -9999 0 0 68 68
mol:HEME 0.001 0.003 -9999 0 -10000 0 0
PER1 0.032 0.006 -9999 0 0 15 15
BMAL/CLOCK/NPAS2 0.061 0.027 -9999 0 -10000 0 0
BMAL1/CLOCK 0.01 0.035 -9999 0 -0.3 1 1
S phase of mitotic cell cycle 0.03 0.042 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.03 0.042 -9999 0 -10000 0 0
mol:NADPH 0.001 0.003 -9999 0 -10000 0 0
PER1/TIMELESS 0.017 0.035 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.032 0.006 -9999 0 0 20 20
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.042 0.01 -10000 0 -0.04 2 2
EFNA5 0.033 0.005 -10000 0 0 11 11
FYN -0.03 0.021 0.18 4 -10000 0 4
neuron projection morphogenesis 0.042 0.01 -10000 0 -0.04 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.043 0.01 -10000 0 -0.04 2 2
EPHA5 0.032 0.005 -10000 0 0 13 13
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 508 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.18 0.04 -0.38 0.005
47_PPARGC1A 0.033 0.033 0.033 0.033
105_BMP4 0.033 0.033 0 0.033
105_BMP6 0.033 0.033 0 0.033
105_BMP7 0.033 0.033 0 0.033
105_BMP2 0.033 0.033 0 0.033
131_RELN/VLDLR 0 0 0.086 0
30_TGFB1/TGF beta receptor Type II 0 0.033 0 0
84_STAT5B 0.067 -0.018 -0.31 0.042
84_STAT5A 0.067 -0.018 -0.31 0.042
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBMLGG-TP/22217225/GDAC_MergeDataFiles_12184409/GBMLGG-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBMLGG-TP/22506578/GDAC_Gistic2Report_22534360/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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