PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1862DSN
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1862DSN
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 33 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 211
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 89
LPA receptor mediated events 79
amb2 Integrin signaling 72
Endothelins 72
Ceramide signaling pathway 67
TCGA08_retinoblastoma 65
BARD1 signaling events 59
EPO signaling pathway 55
HIF-2-alpha transcription factor network 54
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 0.3996 211 846 4 -0.023 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1686 89 6108 68 -0.24 0.054 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.1496 79 8075 102 -0.039 0.046 1000 -1000 -0.057 -1000
amb2 Integrin signaling 0.1364 72 5958 82 -0.043 0.045 1000 -1000 -0.013 -1000
Endothelins 0.1364 72 6934 96 -0.47 0.032 1000 -1000 -0.035 -1000
Ceramide signaling pathway 0.1269 67 5101 76 -0.093 0.065 1000 -1000 -0.02 -1000
TCGA08_retinoblastoma 0.1231 65 522 8 -0.073 0.08 1000 -1000 -0.002 -1000
BARD1 signaling events 0.1117 59 3415 57 -0.044 0.063 1000 -1000 -0.047 -1000
EPO signaling pathway 0.1042 55 3047 55 -0.005 0.062 1000 -1000 -0.022 -1000
HIF-2-alpha transcription factor network 0.1023 54 2339 43 -0.077 0.043 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0890 47 2683 56 -0.037 0.053 1000 -1000 -0.024 -1000
Arf6 signaling events 0.0871 46 2880 62 -0.001 0.081 1000 -1000 -0.006 -1000
Wnt signaling 0.0777 41 292 7 0 0.032 1000 -1000 0.002 -1000
Aurora B signaling 0.0777 41 2767 67 -0.04 0.049 1000 -1000 -0.03 -1000
Osteopontin-mediated events 0.0758 40 1544 38 -0.084 0.044 1000 -1000 -0.022 -1000
Syndecan-1-mediated signaling events 0.0720 38 1295 34 -0.036 0.032 1000 -1000 -0.017 -1000
HIF-1-alpha transcription factor network 0.0720 38 2925 76 -0.096 0.035 1000 -1000 -0.033 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0720 38 3015 78 -0.036 0.039 1000 -1000 -0.031 -1000
Syndecan-4-mediated signaling events 0.0701 37 2515 67 -0.058 0.032 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.0682 36 618 17 -0.003 0.031 1000 -1000 -0.011 -1000
S1P1 pathway 0.0663 35 1285 36 -0.055 0.035 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 0.0625 33 2474 74 -0.055 0.054 1000 -1000 -0.022 -1000
PLK1 signaling events 0.0606 32 2736 85 -0.039 0.056 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0587 31 3927 125 -0.048 0.044 1000 -1000 -0.032 -1000
PDGFR-alpha signaling pathway 0.0568 30 1339 44 -0.04 0.049 1000 -1000 -0.023 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0568 30 1010 33 -0.059 0.063 1000 -1000 -0.01 -1000
Glypican 1 network 0.0549 29 1404 48 -0.031 0.061 1000 -1000 -0.027 -1000
FAS signaling pathway (CD95) 0.0530 28 1333 47 -0.14 0.045 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0530 28 1271 45 -0.059 0.054 1000 -1000 -0.024 -1000
Effects of Botulinum toxin 0.0530 28 742 26 0 0.056 1000 -1000 -0.011 -1000
Arf6 trafficking events 0.0530 28 2007 71 -0.034 0.041 1000 -1000 -0.031 -1000
IL1-mediated signaling events 0.0511 27 1696 62 -0.052 0.056 1000 -1000 -0.035 -1000
Signaling mediated by p38-alpha and p38-beta 0.0511 27 1214 44 -0.037 0.06 1000 -1000 -0.013 -1000
Visual signal transduction: Cones 0.0492 26 996 38 -0.02 0.053 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 0.0492 26 457 17 -0.12 0.057 1000 -1000 -0.016 -1000
Signaling events regulated by Ret tyrosine kinase 0.0492 26 2157 82 -0.042 0.048 1000 -1000 -0.017 -1000
S1P5 pathway 0.0492 26 444 17 -0.032 0.032 1000 -1000 -0.005 -1000
TCGA08_rtk_signaling 0.0492 26 695 26 -0.044 0.13 1000 -1000 -0.009 -1000
Fc-epsilon receptor I signaling in mast cells 0.0473 25 2482 97 -0.1 0.056 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0473 25 931 37 -0.048 0.074 1000 -1000 -0.016 -1000
Plasma membrane estrogen receptor signaling 0.0473 25 2220 86 -0.43 0.052 1000 -1000 -0.031 -1000
Integrins in angiogenesis 0.0455 24 2028 84 -0.049 0.079 1000 -1000 -0.036 -1000
S1P3 pathway 0.0455 24 1041 42 -0.031 0.034 1000 -1000 -0.009 -1000
Regulation of nuclear SMAD2/3 signaling 0.0436 23 3210 136 -0.21 0.06 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0436 23 533 23 -0.021 0.037 1000 -1000 -0.012 -1000
Canonical Wnt signaling pathway 0.0436 23 1215 51 -0.034 0.11 1000 -1000 -0.02 -1000
E-cadherin signaling in keratinocytes 0.0436 23 1025 43 -0.012 0.075 1000 -1000 -0.013 -1000
Signaling events mediated by the Hedgehog family 0.0398 21 1116 52 -0.015 0.066 1000 -1000 -0.02 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0398 21 1854 85 -0.023 0.12 1000 -1000 -0.04 -1000
Signaling events mediated by PTP1B 0.0398 21 1645 76 -0.026 0.06 1000 -1000 -0.016 -1000
BMP receptor signaling 0.0398 21 1746 81 -0.028 0.059 1000 -1000 -0.008 -1000
IL2 signaling events mediated by STAT5 0.0398 21 473 22 -0.018 0.033 1000 -1000 -0.018 -1000
FOXM1 transcription factor network 0.0398 21 1088 51 -0.19 0.032 1000 -1000 -0.13 -1000
TRAIL signaling pathway 0.0379 20 965 48 -0.033 0.071 1000 -1000 -0.021 -1000
EGFR-dependent Endothelin signaling events 0.0379 20 420 21 -0.012 0.032 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0360 19 1463 76 -0.048 0.059 1000 -1000 -0.018 -1000
Noncanonical Wnt signaling pathway 0.0360 19 515 26 -0.023 0.032 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0360 19 826 43 -0.024 0.047 1000 -1000 -0.023 -1000
FOXA2 and FOXA3 transcription factor networks 0.0360 19 878 46 0 0.091 1000 -1000 -0.06 -1000
mTOR signaling pathway 0.0360 19 1050 53 -0.033 0.067 1000 -1000 -0.021 -1000
Nectin adhesion pathway 0.0360 19 1205 63 -0.015 0.075 1000 -1000 -0.024 -1000
ceramide signaling pathway 0.0360 19 937 49 -0.016 0.045 1000 -1000 -0.023 -1000
Aurora A signaling 0.0341 18 1112 60 -0.035 0.065 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class I 0.0341 18 1893 104 -0.041 0.053 1000 -1000 -0.034 -1000
IL2 signaling events mediated by PI3K 0.0341 18 1050 58 -0.18 0.042 1000 -1000 -0.027 -1000
E-cadherin signaling in the nascent adherens junction 0.0341 18 1436 76 -0.036 0.082 1000 -1000 -0.029 -1000
BCR signaling pathway 0.0341 18 1825 99 -0.048 0.051 1000 -1000 -0.035 -1000
S1P4 pathway 0.0341 18 468 25 -0.032 0.04 1000 -1000 -0.008 -1000
Class I PI3K signaling events mediated by Akt 0.0322 17 1172 68 -0.026 0.06 1000 -1000 -0.021 -1000
TCR signaling in naïve CD8+ T cells 0.0322 17 1631 93 -0.33 0.38 1000 -1000 -0.025 -1000
Class I PI3K signaling events 0.0322 17 1256 73 -0.025 0.057 1000 -1000 -0.016 -1000
Regulation of Telomerase 0.0322 17 1742 102 -0.025 0.075 1000 -1000 -0.033 -1000
Thromboxane A2 receptor signaling 0.0303 16 1691 105 -0.034 0.042 1000 -1000 -0.035 -1000
TCGA08_p53 0.0303 16 113 7 -0.007 0.029 1000 -1000 -0.011 -1000
EPHB forward signaling 0.0303 16 1378 85 -0.05 0.078 1000 -1000 -0.036 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0303 16 1201 74 -0.22 0.069 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 0.0303 16 1602 97 -0.042 0.066 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 0.0284 15 926 58 -0.013 0.059 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0284 15 565 36 -0.042 0.049 1000 -1000 -0.035 -1000
Syndecan-3-mediated signaling events 0.0284 15 530 35 -0.008 0.071 1000 -1000 -0.021 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0265 14 799 54 -0.02 0.047 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 0.0265 14 1010 69 -0.021 0.054 1000 -1000 -0.021 -1000
IL6-mediated signaling events 0.0265 14 1096 75 -0.021 0.071 1000 -1000 -0.059 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0265 14 404 27 -0.028 0.07 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0246 13 371 28 -0.022 0.034 1000 -1000 -0.02 -1000
Hedgehog signaling events mediated by Gli proteins 0.0246 13 858 65 -0.005 0.052 1000 -1000 -0.017 -1000
Presenilin action in Notch and Wnt signaling 0.0246 13 845 61 -0.006 0.071 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 0.0246 13 1723 125 -0.049 0.071 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0246 13 901 68 -0.056 0.063 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 0.0246 13 522 40 -0.037 0.041 1000 -1000 -0.041 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0246 13 1093 83 -0.045 0.062 1000 -1000 -0.016 -1000
FoxO family signaling 0.0246 13 835 64 -0.093 0.043 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0246 13 1655 120 -0.038 0.083 1000 -1000 -0.031 -1000
Signaling events mediated by PRL 0.0246 13 444 34 -0.026 0.047 1000 -1000 -0.025 -1000
Canonical NF-kappaB pathway 0.0227 12 506 39 -0.028 0.065 1000 -1000 -0.015 -1000
Cellular roles of Anthrax toxin 0.0227 12 470 39 -0.027 0.032 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 0.0227 12 692 54 -0.019 0.042 1000 -1000 -0.025 -1000
Arf1 pathway 0.0227 12 692 54 -0.063 0.042 1000 -1000 -0.011 -1000
ErbB2/ErbB3 signaling events 0.0208 11 765 65 -0.033 0.039 1000 -1000 -0.051 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0208 11 378 34 -0.049 0.091 1000 -1000 -0.038 -1000
Aurora C signaling 0.0208 11 82 7 0 0.05 1000 -1000 0 -1000
Nongenotropic Androgen signaling 0.0189 10 524 52 -0.065 0.055 1000 -1000 -0.017 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0189 10 912 88 -0.063 0.037 1000 -1000 -0.047 -1000
E-cadherin signaling events 0.0189 10 52 5 0.029 0.058 1000 -1000 0.028 -1000
IL12-mediated signaling events 0.0170 9 861 87 -0.067 0.058 1000 -1000 -0.063 -1000
Glucocorticoid receptor regulatory network 0.0170 9 1129 114 -0.073 0.12 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class II 0.0152 8 643 75 -0.032 0.077 1000 -1000 -0.022 -1000
Circadian rhythm pathway 0.0152 8 177 22 -0.01 0.046 1000 -1000 -0.018 -1000
IL4-mediated signaling events 0.0152 8 793 91 -0.17 0.069 1000 -1000 -0.14 -1000
Atypical NF-kappaB pathway 0.0152 8 249 31 -0.022 0.039 1000 -1000 -0.02 -1000
Insulin-mediated glucose transport 0.0133 7 229 32 -0.03 0.042 1000 -1000 -0.02 -1000
Reelin signaling pathway 0.0133 7 414 56 -0.015 0.061 1000 -1000 -0.014 -1000
Signaling mediated by p38-gamma and p38-delta 0.0133 7 105 15 -0.026 0.032 1000 -1000 -0.022 -1000
IGF1 pathway 0.0133 7 441 57 -0.037 0.062 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 0.0133 7 337 44 0 0.052 1000 -1000 -0.006 -1000
Regulation of Androgen receptor activity 0.0133 7 501 70 -0.036 0.058 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 0.0114 6 295 48 -0.011 0.05 1000 -1000 -0.039 -1000
Calcium signaling in the CD4+ TCR pathway 0.0114 6 198 31 -0.04 0.034 1000 -1000 -0.01 -1000
Insulin Pathway 0.0114 6 500 74 -0.041 0.078 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 0.0095 5 61 12 -0.018 0.008 1000 -1000 -0.016 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0095 5 291 52 -0.059 0.091 1000 -1000 -0.003 -1000
ErbB4 signaling events 0.0076 4 344 69 -0.027 0.065 1000 -1000 -0.024 -1000
IL27-mediated signaling events 0.0076 4 221 51 -0.02 0.056 1000 -1000 -0.052 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 16 5 0.025 0.046 1000 -1000 0.028 -1000
IL23-mediated signaling events 0.0057 3 184 60 -0.021 0.057 1000 -1000 -0.098 -1000
Rapid glucocorticoid signaling 0.0057 3 61 20 -0.011 0.032 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0057 3 44 13 0 0.054 1000 -1000 0 -1000
Ephrin A reverse signaling 0.0019 1 12 7 -0.02 0.043 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0019 1 81 52 -0.034 0.074 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.015 0.032 1000 -1000 -0.02 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.032 0.032 1000 -1000 -0.028 -1000
Total NA 2995 168339 7203 -6.7 7.5 131000 -131000 -3.3 -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 -0.023 0.047 -9999 0 -0.065 282 282
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.012 0.031 -9999 0 -0.04 282 282
neuron projection morphogenesis -0.012 0.031 -9999 0 -0.04 282 282
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 0.033 0.007 -10000 0 -0.028 6 6
NFATC2 -0.029 0.096 -10000 0 -0.14 199 199
NFATC3 -0.043 0.11 -10000 0 -0.16 215 215
CD40LG -0.14 0.17 0.26 1 -0.32 206 207
ITCH -0.015 0.009 -10000 0 -10000 0 0
CBLB -0.016 0.008 -10000 0 -0.059 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.13 0.17 -10000 0 -0.37 108 108
JUNB 0.03 0.014 -10000 0 -0.065 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.019 -10000 0 -0.052 14 14
T cell anergy -0.008 0.027 0.17 2 -0.1 5 7
TLE4 -0.021 0.059 0.097 1 -0.097 123 124
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.33 225 225
AP-1/NFAT1-c-4 -0.12 0.21 -10000 0 -0.34 210 210
IKZF1 -0.013 0.05 0.097 1 -0.097 79 80
T-helper 2 cell differentiation -0.13 0.17 -10000 0 -0.47 71 71
AP-1/NFAT1 -0.02 0.071 -10000 0 -0.11 20 20
CALM1 0.03 0.017 -10000 0 -0.045 14 14
EGR2 -0.092 0.18 -10000 0 -0.34 166 166
EGR3 0.014 0.097 -10000 0 -0.61 10 10
NFAT1/FOXP3 -0.006 0.08 -10000 0 -0.11 89 89
EGR1 0.029 0.017 -10000 0 -0.065 15 15
JUN 0.03 0.013 -10000 0 -10000 0 0
EGR4 0.033 0 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.006 -10000 0 -10000 0 0
GBP3 -0.02 0.053 0.089 1 -0.082 199 200
FOSL1 0.03 0.015 -10000 0 -0.065 12 12
NFAT1-c-4/MAF/IRF4 -0.098 0.22 -10000 0 -0.33 229 229
DGKA -0.021 0.06 0.097 1 -0.096 134 135
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.34 228 228
CTLA4 -0.023 0.054 0.082 1 -0.092 89 90
NFAT1-c-4 (dimer)/EGR1 -0.11 0.22 -10000 0 -0.34 230 230
NFAT1-c-4 (dimer)/EGR4 -0.11 0.22 -10000 0 -0.34 232 232
FOS 0.005 0.042 -10000 0 -0.066 122 122
IFNG -0.05 0.094 -10000 0 -0.26 35 35
T cell activation -0.079 0.11 -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 0.054 0.16 0.33 126 -10000 0 126
TNF -0.13 0.19 -10000 0 -0.33 231 231
FASLG -0.24 0.29 -10000 0 -0.53 241 241
TBX21 0.034 0.005 -10000 0 -0.041 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.014 -10000 0 -10000 0 0
PTPN1 -0.021 0.059 0.097 1 -0.1 98 99
NFAT1-c-4/ICER1 -0.12 0.21 -10000 0 -0.35 232 232
GATA3 0.025 0.015 -10000 0 -0.064 2 2
T-helper 1 cell differentiation -0.05 0.093 -10000 0 -0.26 32 32
IL2RA -0.12 0.17 -10000 0 -0.37 111 111
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.064 0.097 1 -0.1 136 137
E2F1 -0.019 0.04 -10000 0 -0.058 44 44
PPARG 0.031 0.01 -10000 0 -0.065 4 4
SLC3A2 -0.022 0.061 0.097 1 -0.1 117 118
IRF4 0.032 0.006 -10000 0 -0.064 1 1
PTGS2 -0.14 0.17 0.26 1 -0.33 204 205
CSF2 -0.14 0.17 0.26 1 -0.32 206 207
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.33 222 222
IL4 -0.13 0.18 -10000 0 -0.48 71 71
IL5 -0.14 0.17 0.26 1 -0.32 204 205
IL2 -0.079 0.11 -10000 0 -10000 0 0
IL3 -0.009 0.072 -10000 0 -0.54 6 6
RNF128 -0.017 0.012 -10000 0 -0.08 14 14
NFATC1 -0.048 0.16 -10000 0 -0.33 116 116
CDK4 0.011 0.11 0.27 66 -10000 0 66
PTPRK -0.02 0.059 0.097 1 -0.099 107 108
IL8 -0.15 0.17 0.26 1 -0.33 206 207
POU2F1 0.035 0.005 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.006 0.03 -10000 0 -0.035 258 258
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.061 0.21 6 -0.18 27 33
AP1 -0.017 0.03 -10000 0 -0.041 290 290
mol:PIP3 -0.013 0.019 -10000 0 -0.057 13 13
AKT1 0.009 0.072 0.18 31 -0.24 7 38
PTK2B -0.009 0.027 0.11 2 -0.2 6 8
RHOA 0.01 0.06 0.15 9 -0.3 10 19
PIK3CB 0.031 0.006 -10000 0 -0.03 1 1
mol:Ca2+ -0.013 0.019 0.17 2 -0.12 7 9
MAGI3 0 0 -10000 0 -0.004 2 2
RELA 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.015 0.026 -10000 0 -0.038 272 272
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.039 0.17 11 -0.19 6 17
NF kappa B1 p50/RelA -0.038 0.02 -10000 0 -0.12 11 11
endothelial cell migration -0.026 0.041 -10000 0 -0.069 242 242
ADCY4 -0.001 0.007 -10000 0 -0.093 1 1
ADCY5 -0.001 0.007 -10000 0 -0.093 1 1
ADCY6 -0.001 0.01 0.086 2 -0.1 2 4
ADCY7 -0.001 0.01 0.086 3 -0.079 2 5
ADCY1 -0.001 0.007 -10000 0 -0.089 1 1
ADCY2 -0.001 0.01 0.086 3 -0.089 1 4
ADCY3 -0.001 0.007 -10000 0 -0.093 1 1
ADCY8 -0.001 0.009 0.086 2 -0.089 1 3
ADCY9 -0.001 0.01 0.086 3 -0.089 1 4
GSK3B -0.013 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.002 0.014 0.077 3 -0.11 5 8
GNG2 0 0.001 -10000 0 -0.004 27 27
TRIP6 -0.008 0.025 -10000 0 -0.042 166 166
GNAO1 0 0.008 -10000 0 -0.04 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.021 0.05 0.18 8 -0.18 26 34
GAB1 0.031 0.008 -10000 0 -0.065 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.17 -10000 0 -0.7 25 25
JUN 0.032 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.002 0.022 -10000 0 -0.021 243 243
TIAM1 -0.003 0.2 -10000 0 -0.84 27 27
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.012 0.016 0.17 2 -0.12 2 4
PLCB3 -0.019 0.017 0.18 3 -10000 0 3
FOS 0.007 0.041 -10000 0 -0.065 120 120
positive regulation of mitosis -0.002 0.014 0.077 3 -0.11 5 8
LPA/LPA1-2-3 -0.012 0.016 -10000 0 -0.028 247 247
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 0.004 0.023 0.13 1 -0.14 1 2
GNAZ -0.011 0.025 -10000 0 -0.04 202 202
EGFR/PI3K-beta/Gab1 -0.013 0.019 0.023 2 -0.064 7 9
positive regulation of dendritic cell cytokine production -0.012 0.016 -10000 0 -0.027 247 247
LPA/LPA2/MAGI-3 -0.005 0.007 -10000 0 -0.012 249 249
ARHGEF1 0.026 0.094 0.17 141 -10000 0 141
GNAI2 -0.013 0.026 -10000 0 -0.04 239 239
GNAI3 -0.017 0.028 -10000 0 -0.042 269 269
GNAI1 -0.008 0.022 -10000 0 -0.04 154 154
LPA/LPA3 -0.007 0.008 -10000 0 -0.016 247 247
LPA/LPA2 -0.007 0.008 -10000 0 -0.015 246 246
LPA/LPA1 -0.017 0.022 -10000 0 -0.039 247 247
HB-EGF/EGFR -0.001 0.025 -10000 0 -0.049 83 83
HBEGF -0.03 0.016 0 45 -0.051 165 210
mol:DAG -0.012 0.016 0.17 2 -0.12 2 4
cAMP biosynthetic process 0.046 0.061 0.14 113 -10000 0 113
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
SRC 0.03 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
LYN -0.017 0.038 0.18 8 -0.16 1 9
GNAQ -0.001 0.013 -10000 0 -0.015 235 235
LPAR2 0 0 -10000 0 -0.004 2 2
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.012 0.013 -10000 0 -0.026 246 246
IL8 -0.039 0.055 0.2 2 -0.29 4 6
PTK2 -0.006 0.026 -10000 0 -0.033 239 239
Rac1/GDP 0.017 0.011 -10000 0 0 153 153
CASP3 -0.015 0.026 -10000 0 -0.038 272 272
EGFR 0.012 0.018 -10000 0 -0.065 6 6
PLCG1 0.002 0.008 -10000 0 -0.03 8 8
PLD2 -0.006 0.026 -10000 0 -0.032 243 243
G12/G13 0.002 0.037 -10000 0 -0.042 172 172
PI3K-beta -0.011 0.041 -10000 0 -0.22 11 11
cell migration -0.003 0.048 -10000 0 -0.22 18 18
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
PXN 0.004 0.024 0.13 1 -0.14 1 2
HRAS/GTP -0.001 0.012 0.077 3 -0.1 4 7
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
PRKCE 0.032 0.005 -10000 0 -0.027 3 3
PRKCD -0.013 0.036 0.21 9 -0.12 5 14
Gi(beta/gamma) 0 0.014 0.086 3 -0.14 3 6
mol:LPA -0.012 0.013 -10000 0 -0.026 247 247
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.024 -10000 0 -0.13 3 3
MAPKKK cascade -0.002 0.014 0.077 3 -0.11 5 8
contractile ring contraction involved in cytokinesis 0.013 0.062 0.14 13 -0.29 10 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.002 0.013 -10000 0 -0.016 238 238
GNA15 -0.002 0.014 -10000 0 -0.016 232 232
GNA12 0.023 0.015 -10000 0 0 152 152
GNA13 0.032 0.007 -10000 0 -0.065 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.001 0.013 -10000 0 -0.015 232 232
Rac1/GTP 0.002 0.18 -10000 0 -0.77 21 21
MMP2 -0.026 0.042 -10000 0 -0.069 242 242
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.018 0.057 -10000 0 -0.057 339 339
alphaM/beta2 Integrin/GPIbA 0.016 0.057 -10000 0 -0.05 212 212
alphaM/beta2 Integrin/proMMP-9 -0.006 0.059 -10000 0 -0.058 273 273
PLAUR 0.022 0.028 -10000 0 -0.065 44 44
HMGB1 0.029 0.012 -10000 0 -0.03 12 12
alphaM/beta2 Integrin/Talin 0.007 0.057 -10000 0 -0.052 229 229
AGER 0.03 0.014 -10000 0 -0.039 18 18
RAP1A 0.032 0.004 -10000 0 -10000 0 0
SELPLG 0.032 0.004 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.072 -10000 0 -0.085 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
CYR61 0.003 0.044 -10000 0 -0.065 150 150
TLN1 0.021 0.028 -10000 0 -0.065 43 43
Rap1/GTP 0.01 0.037 -10000 0 -0.15 4 4
RHOA 0.032 0.006 -10000 0 -10000 0 0
P-selectin oligomer 0.032 0.006 -10000 0 -0.065 1 1
MYH2 0 0.038 0.14 5 -0.16 3 8
MST1R 0.031 0.008 -10000 0 -0.065 2 2
leukocyte activation during inflammatory response 0.012 0.058 -10000 0 -0.048 213 213
APOB 0.031 0.008 -10000 0 -0.019 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.014 0.048 -10000 0 -0.065 241 241
JAM3 0.03 0.009 -10000 0 -0.065 1 1
GP1BA 0.032 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.008 0.057 -10000 0 -0.052 226 226
alphaM/beta2 Integrin 0.001 0.036 -10000 0 -0.15 6 6
JAM3 homodimer 0.03 0.009 -10000 0 -0.065 1 1
ICAM2 0.032 0.008 -10000 0 -0.065 3 3
ICAM1 0.028 0.018 -10000 0 -0.065 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor 0.001 0.036 -10000 0 -0.15 5 5
cell adhesion 0.015 0.057 -10000 0 -0.05 212 212
NFKB1 -0.042 0.032 0.18 6 -10000 0 6
THY1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.04 0.013 -10000 0 -0.043 3 3
alphaM/beta2 Integrin/LRP/tPA -0.012 0.065 -10000 0 -0.07 135 135
IL6 -0.033 0.038 0.16 4 -0.15 2 6
ITGB2 -0.009 0.048 -10000 0 -0.064 214 214
elevation of cytosolic calcium ion concentration -0.01 0.064 -10000 0 -0.074 120 120
alphaM/beta2 Integrin/JAM2/JAM3 0.009 0.067 -10000 0 -0.065 60 60
JAM2 0.018 0.034 -10000 0 -0.065 72 72
alphaM/beta2 Integrin/ICAM1 0.023 0.074 -10000 0 -0.076 12 12
alphaM/beta2 Integrin/uPA/Plg -0.008 0.065 -10000 0 -0.068 116 116
RhoA/GTP 0.005 0.037 0.14 1 -0.15 5 6
positive regulation of phagocytosis -0.002 0.053 0.14 7 -0.14 6 13
Ron/MSP 0.045 0.015 -10000 0 -0.051 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.009 0.066 -10000 0 -0.075 116 116
alphaM/beta2 Integrin/uPAR 0.011 0.059 -10000 0 -0.054 214 214
PLAU 0.007 0.037 -10000 0 -0.065 94 94
PLAT -0.012 0.048 -10000 0 -0.065 232 232
actin filament polymerization 0.001 0.039 0.15 6 -0.16 3 9
MST1 0.03 0.012 -10000 0 -0.065 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.062 -10000 0 -0.048 213 213
TNF -0.043 0.031 0.16 6 -0.14 1 7
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.056 -10000 0 -0.058 231 231
fibrinolysis -0.009 0.063 -10000 0 -0.068 116 116
HCK 0.014 0.036 -10000 0 -0.045 121 121
dendritic cell antigen processing and presentation 0.001 0.036 -10000 0 -0.15 5 5
VTN 0.032 0.007 -10000 0 -0.065 2 2
alphaM/beta2 Integrin/CYR61 -0.001 0.061 -10000 0 -0.058 267 267
LPA 0.03 0.008 -10000 0 0 34 34
LRP1 0.029 0.017 -10000 0 -0.065 13 13
cell migration -0.033 0.05 -10000 0 -0.066 339 339
FN1 0.014 0.038 -10000 0 -0.065 96 96
alphaM/beta2 Integrin/Thy1 0.007 0.05 -10000 0 -0.05 178 178
MPO 0.032 0.004 -10000 0 -10000 0 0
KNG1 0.031 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.022 0.003 -10000 0 -10000 0 0
ROCK1 0 0.041 0.17 7 -0.16 3 10
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
CTGF 0.023 0.026 -10000 0 -0.065 36 36
alphaM/beta2 Integrin/Hck 0.009 0.06 -10000 0 -0.059 208 208
ITGAM 0.031 0.01 -10000 0 -0.03 14 14
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.024 0.066 -10000 0 -0.056 67 67
HP 0.017 0.035 -10000 0 -0.065 77 77
leukocyte adhesion -0.008 0.055 -10000 0 -0.1 12 12
SELP 0.032 0.006 -10000 0 -0.065 1 1
Endothelins

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
AKT1 -0.067 0.034 -10000 0 -0.12 47 47
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.17 0.36 1 -0.41 95 96
EDN1 -0.036 0.044 -10000 0 -0.062 363 363
EDN3 0.029 0.012 -10000 0 -0.065 3 3
EDN2 0.032 0.007 -10000 0 -0.065 1 1
HRAS/GDP -0.028 0.08 0.23 14 -0.28 17 31
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.015 0.041 -10000 0 -0.16 14 14
ADCY4 -0.054 0.024 0.011 1 -0.075 255 256
ADCY5 -0.054 0.024 0.011 1 -0.075 255 256
ADCY6 -0.058 0.033 0.18 1 -10000 0 1
ADCY7 -0.058 0.036 0.18 1 -10000 0 1
ADCY1 -0.043 0.038 -10000 0 -10000 0 0
ADCY2 -0.057 0.036 0.18 1 -10000 0 1
ADCY3 -0.054 0.024 0.011 1 -0.075 255 256
ADCY8 -0.057 0.037 0.18 1 -10000 0 1
ADCY9 -0.058 0.036 0.18 1 -10000 0 1
arachidonic acid secretion -0.048 0.093 0.28 9 -0.32 19 28
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.034 -10000 0 -0.15 15 15
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.033 0.054 -10000 0 -0.087 179 179
ETA receptor/Endothelin-1/Gs/GTP -0.039 0.058 -10000 0 -0.081 235 235
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.09 0.042 -10000 0 -0.13 213 213
EDNRB -0.009 0.036 -10000 0 -0.042 257 257
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.064 0.036 -10000 0 -0.12 11 11
CYSLTR1 -0.061 0.031 0.04 1 -0.079 346 347
SLC9A1 -0.031 0.031 -10000 0 -0.054 258 258
mol:GDP -0.032 0.078 0.22 14 -0.28 17 31
SLC9A3 -0.074 0.19 -10000 0 -0.63 41 41
RAF1 -0.032 0.082 0.26 11 -0.3 15 26
JUN -0.097 0.19 0.35 1 -0.45 97 98
JAK2 -0.064 0.037 -10000 0 -0.11 80 80
mol:IP3 -0.015 0.046 -10000 0 -0.19 18 18
ETA receptor/Endothelin-1 -0.058 0.068 -10000 0 -0.097 356 356
PLCB1 0.03 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.006 -10000 0 -0.029 1 1
ETA receptor/Endothelin-3 -0.028 0.046 -10000 0 -0.058 331 331
FOS -0.039 0.097 0.33 9 -0.32 16 25
Gai/GDP -0.47 0.17 -10000 0 -0.52 454 454
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.045 0.051 -10000 0 -0.18 26 26
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.016 0.046 -10000 0 -0.2 17 17
GNAQ 0.031 0.007 -10000 0 -0.027 2 2
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
Gs family/GDP -0.03 0.074 0.2 13 -0.27 15 28
ETA receptor/Endothelin-1/Gq/GTP -0.021 0.036 -10000 0 -0.13 16 16
MAPK14 -0.011 0.035 -10000 0 -0.18 10 10
TRPC6 -0.091 0.18 0.36 1 -0.43 95 96
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.038 -10000 0 -0.15 19 19
ETB receptor/Endothelin-2 0.023 0.033 -10000 0 -0.043 83 83
ETB receptor/Endothelin-3 0.021 0.033 -10000 0 -0.043 81 81
ETB receptor/Endothelin-1 -0.033 0.048 -10000 0 -0.066 297 297
MAPK3 -0.034 0.096 0.32 11 -0.34 12 23
MAPK1 -0.043 0.1 0.32 10 -0.34 19 29
Rac1/GDP -0.026 0.059 0.2 4 -0.26 11 15
cAMP biosynthetic process -0.02 0.043 0.2 4 -10000 0 4
MAPK8 -0.11 0.22 0.37 1 -0.5 112 113
SRC 0.031 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.024 -10000 0 -0.13 17 17
p130Cas/CRK/Src/PYK2 -0.026 0.084 0.27 13 -0.31 13 26
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.026 0.059 0.2 4 -0.26 11 15
COL1A2 -0.055 0.063 -10000 0 -0.13 183 183
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.047 -10000 0 -0.058 349 349
mol:DAG -0.015 0.046 -10000 0 -0.19 18 18
MAP2K2 -0.035 0.099 0.33 16 -0.31 15 31
MAP2K1 -0.041 0.083 0.26 9 -0.32 14 23
EDNRA -0.048 0.05 -10000 0 -0.076 356 356
positive regulation of muscle contraction -0.009 0.096 0.15 124 -0.12 2 126
Gq family/GDP 0.005 0.08 0.25 3 -0.25 14 17
HRAS/GTP -0.025 0.076 0.21 15 -0.3 16 31
PRKCH -0.021 0.048 0.21 1 -0.23 14 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.023 0.053 0.19 2 -0.23 19 21
PRKCB -0.016 0.046 -10000 0 -0.2 17 17
PRKCE -0.025 0.052 -10000 0 -0.23 19 19
PRKCD -0.022 0.05 0.17 2 -0.23 16 18
PRKCG -0.024 0.053 0.21 1 -0.23 19 20
regulation of vascular smooth muscle contraction -0.042 0.11 0.36 9 -0.38 12 21
PRKCQ -0.017 0.041 0.19 3 -0.24 8 11
PLA2G4A -0.051 0.098 0.32 7 -0.34 19 26
GNA14 0.031 0.009 -10000 0 -0.046 4 4
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.033 0.054 -10000 0 -0.087 181 181
MMP1 0.022 0.045 0.07 109 -0.089 22 131
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 -0.015 0.011 0 177 -0.051 2 179
MAP4K4 -0.007 0.038 -10000 0 -0.2 8 8
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.059 0.11 -10000 0 -0.2 159 159
NFKBIA 0.03 0.009 -10000 0 -0.065 1 1
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BAX -0.027 0.087 -10000 0 -0.36 24 24
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
AKT1 0 0.07 0.75 4 -10000 0 4
BAD -0.064 0.11 0.19 2 -0.21 159 161
SMPD1 -0.005 0.037 0.11 10 -0.17 14 24
RB1 -0.065 0.11 0.2 1 -0.21 159 160
FADD/Caspase 8 -0.002 0.04 -10000 0 -0.25 6 6
MAP2K4 -0.064 0.11 0.19 4 -0.2 151 155
NSMAF 0.032 0.006 -10000 0 -0.065 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.066 0.11 0.18 5 -0.2 156 161
EGF 0.032 0.007 -10000 0 -0.065 2 2
mol:ceramide -0.062 0.12 -10000 0 -0.21 159 159
MADD 0.031 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.015 0.011 0 170 -0.051 2 172
ASAH1 0.032 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.064 0.11 0.2 1 -0.2 159 160
cell proliferation -0.036 0.1 -10000 0 -0.19 142 142
BID -0.027 0.15 -10000 0 -0.65 26 26
MAP3K1 -0.064 0.11 0.2 1 -0.21 158 159
EIF2A -0.065 0.1 0.17 1 -0.19 159 160
TRADD 0.032 0.004 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.059 0.095 0.18 4 -0.19 144 148
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.1 0.18 4 -0.21 147 151
Cathepsin D/ceramide -0.046 0.12 -10000 0 -0.21 158 158
FADD -0.006 0.033 -10000 0 -0.19 5 5
KSR1 -0.065 0.11 0.2 1 -0.21 159 160
MAPK8 -0.093 0.15 0.15 3 -0.25 189 192
PRKRA -0.065 0.11 -10000 0 -0.21 159 159
PDGFA 0.022 0.016 -10000 0 -0.065 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.061 0.12 -10000 0 -0.21 159 159
CTSD 0.028 0.017 -10000 0 -0.065 15 15
regulation of nitric oxide biosynthetic process 0.046 0.012 -10000 0 -0.051 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.11 -10000 0 -0.2 142 142
PRKCD 0.032 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.015 0.011 0 170 -0.051 2 172
RelA/NF kappa B1 0.046 0.012 -10000 0 -0.051 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.031 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.039 -10000 0 -0.18 11 11
TNFR1A/BAG4/TNF-alpha 0.025 0.053 -10000 0 -0.049 163 163
mol:Sphingosine-1-phosphate -0.015 0.011 0 177 -0.051 2 179
MAP2K1 -0.067 0.1 0.18 5 -0.2 151 156
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
CYCS -0.016 0.064 0.12 1 -0.23 29 30
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 162 162
EIF2AK2 -0.068 0.11 0.18 1 -0.2 159 160
TNF-alpha/TNFR1A/FAN 0.025 0.053 -10000 0 -0.049 163 163
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.048 -10000 0 -0.29 8 8
MAP2K2 -0.064 0.094 0.17 8 -0.2 149 157
SMPD3 0 0.04 0.1 2 -0.24 9 11
TNF 0.032 0.007 -10000 0 -0.065 2 2
PKC zeta/PAR4 0.023 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.035 0.066 0.13 3 -0.13 151 154
NF kappa B1/RelA/I kappa B alpha 0.065 0.034 -10000 0 -0.052 2 2
AIFM1 -0.043 0.081 0.12 1 -0.23 37 38
BCL2 0.031 0.006 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.019 -10000 0 -0.037 6 6
CDKN2C -0.006 0.029 -10000 0 -0.055 106 106
CDKN2A 0.006 0.026 -10000 0 -0.051 51 51
CCND2 0.002 0.01 0.079 2 -10000 0 2
RB1 -0.073 0.1 0.1 1 -0.22 168 169
CDK4 0.002 0.01 0.09 2 -10000 0 2
CDK6 0.004 0.016 0.11 6 -10000 0 6
G1/S progression 0.08 0.1 0.22 179 -0.1 1 180
BARD1 signaling events

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
BARD1/CSTF1 0.022 0.041 -10000 0 -0.051 114 114
ATM 0.027 0.021 -10000 0 -0.065 25 25
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
ATR 0.032 0.005 -10000 0 -10000 0 0
UBE2L3 0.031 0.007 -10000 0 -10000 0 0
FANCD2 0.01 0.011 -10000 0 -0.037 25 25
protein ubiquitination 0.043 0.065 -10000 0 -0.08 25 25
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.063 0.015 -10000 0 -0.044 1 1
MRE11A 0.032 0.005 -10000 0 -10000 0 0
DNA-PK 0.056 0.029 -10000 0 -0.051 22 22
FA complex/FANCD2/Ubiquitin -0.005 0.08 -10000 0 -0.25 37 37
FANCF 0.031 0.008 -10000 0 -0.065 2 2
BRCA1 0.031 0.01 -10000 0 -0.065 5 5
CCNE1 0.03 0.011 -10000 0 -0.065 4 4
CDK2/Cyclin E1 0.04 0.024 -10000 0 -0.054 23 23
FANCG 0.019 0.031 -10000 0 -0.065 57 57
BRCA1/BACH1/BARD1 0.024 0.042 -10000 0 -0.052 120 120
FANCE 0.032 0.005 -10000 0 -0.065 1 1
FANCC 0.031 0.006 -10000 0 -10000 0 0
NBN 0.032 0.004 -10000 0 -10000 0 0
FANCA 0.031 0.006 -10000 0 -10000 0 0
DNA repair -0.03 0.066 0.18 16 -0.22 26 42
BRCA1/BARD1/ubiquitin 0.024 0.042 -10000 0 -0.052 120 120
BARD1/DNA-PK 0.042 0.062 -10000 0 -0.065 25 25
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.041 0.051 114 -10000 0 114
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.042 0.11 5 -0.18 16 21
BRCA1/BACH1/BARD1/TopBP1 0.036 0.05 -10000 0 -0.05 122 122
BRCA1/BARD1/P53 0.035 0.065 -10000 0 -0.071 33 33
BARD1/CSTF1/BRCA1 0.034 0.049 -10000 0 -0.05 115 115
BRCA1/BACH1 0.031 0.01 -10000 0 -0.065 5 5
BARD1 0.009 0.041 -10000 0 -0.064 123 123
PCNA -0.027 0.046 -10000 0 -0.065 298 298
BRCA1/BARD1/UbcH5C 0.037 0.05 -10000 0 -0.05 123 123
BRCA1/BARD1/UbcH7 0.036 0.05 -10000 0 -0.051 122 122
BRCA1/BARD1/RAD51/PCNA -0.01 0.064 -10000 0 -0.071 105 105
BARD1/DNA-PK/P53 0.038 0.075 -10000 0 -0.078 35 35
BRCA1/BARD1/Ubiquitin 0.024 0.042 -10000 0 -0.052 120 120
BRCA1/BARD1/CTIP -0.035 0.044 -10000 0 -0.058 392 392
FA complex 0.012 0.034 -10000 0 -0.15 16 16
BARD1/EWS 0.024 0.04 -10000 0 -0.051 107 107
RBBP8 -0.044 0.016 -10000 0 -0.052 378 378
TP53 0.019 0.033 -10000 0 -0.052 81 81
TOPBP1 0.032 0.006 -10000 0 -0.065 1 1
G1/S transition of mitotic cell cycle -0.033 0.064 0.055 158 -10000 0 158
BRCA1/BARD1 0.048 0.07 -10000 0 -0.092 10 10
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0.027 -10000 0 -0.04 123 123
CDK2 0.027 0.021 -10000 0 -0.065 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.032 0.006 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.024 0.042 -10000 0 -0.052 120 120
EWSR1 0.03 0.008 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.036 0.047 0.18 20 -0.16 2 22
CRKL 0.027 0.093 0.16 134 -10000 0 134
mol:DAG 0.011 0.028 0.14 4 -0.14 2 6
HRAS 0.02 0.095 0.23 44 -10000 0 44
MAPK8 0.006 0.068 0.15 86 -10000 0 86
RAP1A 0.028 0.093 0.16 141 -10000 0 141
GAB1 0.028 0.094 0.16 141 -10000 0 141
MAPK14 0.021 0.084 0.15 147 -10000 0 147
EPO 0.023 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.028 0.14 4 -0.14 2 6
EPOR/TRPC2/IP3 Receptors 0.036 0.011 0.084 5 -10000 0 5
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -0.039 1 1
GAB1/SHC/GRB2/SOS1 0.014 0.086 0.15 143 -10000 0 143
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.028 0.092 0.16 137 -10000 0 137
STAT1 0.012 0.031 0.15 4 -0.14 2 6
STAT5B 0.012 0.03 0.15 4 -0.14 2 6
cell proliferation 0.005 0.074 0.16 90 -10000 0 90
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.064 0.11 116 -10000 0 116
TEC 0.028 0.093 0.16 137 -10000 0 137
SOCS3 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.031 0.15 4 -0.14 2 6
JAK2 0.034 0.015 0.085 6 -10000 0 6
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.051 0.05 0.23 5 -10000 0 5
EPO/EPOR 0.034 0.024 -10000 0 -10000 0 0
LYN 0.021 0.031 -10000 0 -0.064 60 60
TEC/VAV2 0.005 0.07 0.13 109 -10000 0 109
elevation of cytosolic calcium ion concentration 0.036 0.011 0.084 5 -10000 0 5
SHC1 0.024 0.026 -10000 0 -0.065 40 40
EPO/EPOR (dimer)/LYN 0.035 0.043 -10000 0 -0.052 49 49
mol:IP3 0.011 0.028 0.14 4 -0.14 2 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.022 0.09 0.15 147 -10000 0 147
SH2B3 0.036 0.016 0.093 1 -0.065 8 9
NFKB1 0.021 0.083 0.15 147 -10000 0 147
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 0.076 2 -10000 0 2
PTPN6 0.029 0.089 0.16 151 -10000 0 151
TEC/VAV2/GRB2 0.062 0.068 0.16 118 -10000 0 118
EPOR 0.036 0.011 0.084 5 -10000 0 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.087 0.15 143 -10000 0 143
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
CRKL/CBL/C3G 0.06 0.069 0.16 115 -10000 0 115
VAV2 0.026 0.091 0.16 133 -10000 0 133
CBL 0.029 0.094 0.16 143 -10000 0 143
SHC/Grb2/SOS1 0.02 0.036 -10000 0 -0.081 1 1
STAT5A 0.012 0.03 0.15 4 -0.14 2 6
GRB2 0.032 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.041 0.18 4 -10000 0 4
LYN/PLCgamma2 0.034 0.034 -10000 0 -0.054 61 61
PTPN11 0.032 0.003 -10000 0 -10000 0 0
BTK 0.029 0.095 0.15 170 -10000 0 170
BCL2 0.037 0.051 0.18 22 -0.19 6 28
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.16 -10000 0 -0.64 32 32
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.023 0.075 -10000 0 -0.16 60 60
EPO -0.031 0.071 -10000 0 -0.2 46 46
FIH (dimer) 0.02 0.018 -10000 0 -0.027 29 29
APEX1 0.023 0.021 -10000 0 -0.029 61 61
SERPINE1 -0.045 0.07 -10000 0 -0.18 67 67
FLT1 -0.015 0.16 -10000 0 -0.61 35 35
ADORA2A -0.069 0.065 -10000 0 -0.17 107 107
germ cell development -0.062 0.068 -10000 0 -0.16 119 119
SLC11A2 -0.065 0.074 -10000 0 -0.17 108 108
BHLHE40 -0.064 0.069 -10000 0 -0.16 119 119
HIF1AN 0.02 0.018 -10000 0 -0.027 29 29
HIF2A/ARNT/SIRT1 -0.03 0.086 0.17 1 -0.16 100 101
ETS1 0.034 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 39 39
KDR 0.016 0.076 -10000 0 -0.54 8 8
PGK1 -0.065 0.074 -10000 0 -0.17 108 108
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.033 0.11 -10000 0 -0.19 92 92
EPAS1 -0.031 0.049 0.12 1 -0.13 87 88
SP1 0.034 0.006 -10000 0 -0.038 1 1
ABCG2 -0.066 0.074 -10000 0 -0.17 108 108
EFNA1 -0.066 0.074 -10000 0 -0.17 109 109
FXN -0.068 0.065 -10000 0 -0.17 104 104
POU5F1 -0.064 0.069 -10000 0 -0.16 119 119
neuron apoptosis 0.033 0.11 0.19 96 -10000 0 96
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.024 0.019 -10000 0 -0.032 42 42
EGLN2 0.026 0.015 -10000 0 -0.027 30 30
EGLN1 0.025 0.016 -10000 0 -0.028 38 38
VHL/Elongin B/Elongin C 0.043 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.026 0.018 -10000 0 -0.029 43 43
SLC2A1 -0.068 0.065 -10000 0 -0.16 116 116
TWIST1 -0.04 0.056 -10000 0 -0.17 50 50
ELK1 0.033 0.012 -10000 0 -0.038 13 13
HIF2A/ARNT/Cbp/p300 -0.024 0.094 0.19 1 -0.16 98 99
VEGFA -0.077 0.08 -10000 0 -0.18 123 123
CREBBP 0.032 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.028 0.017 -10000 0 -0.036 23 23
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.017 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.011 0.035 -10000 0 -0.042 274 274
CaM/Ca2+ -0.027 0.019 0.18 2 -10000 0 2
HIF1A 0.035 0.011 -10000 0 -0.063 2 2
GAB1 0.031 0.008 -10000 0 -0.065 3 3
AKT1 -0.023 0.034 0.13 15 -0.19 1 16
PLCG1 -0.024 0.017 0.18 2 -10000 0 2
NOS3 -0.007 0.042 0.19 4 -0.21 14 18
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.006 0.055 0.15 19 -0.21 14 33
FLT1 -0.016 0.006 -10000 0 -10000 0 0
PGF 0.027 0.02 -10000 0 -0.065 19 19
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.05 -10000 0 -0.049 278 278
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
eNOS/Hsp90 0.023 0.074 0.19 13 -0.21 24 37
endothelial cell proliferation -0.011 0.048 0.12 34 -0.14 19 53
mol:Ca2+ -0.024 0.017 0.18 2 -10000 0 2
MAPK3 -0.035 0.017 0.15 2 -10000 0 2
MAPK1 -0.032 0.019 0.15 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PLGF homodimer 0.026 0.02 -10000 0 -0.065 19 19
PRKACA 0.031 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.019 0.041 -10000 0 -0.065 217 217
VEGFA homodimer -0.02 0.048 -10000 0 -0.065 275 275
VEGFR1 homodimer/VEGFA homodimer -0.012 0.039 -10000 0 -0.046 279 279
platelet activating factor biosynthetic process -0.037 0.02 0.14 2 -10000 0 2
PI3K 0.044 0.047 0.17 1 -0.077 1 2
PRKCA -0.028 0.018 0.17 2 -10000 0 2
PRKCB -0.022 0.016 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.027 0.019 -10000 0 -0.046 21 21
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
VEGFB 0.032 0.004 -10000 0 -10000 0 0
mol:IP3 -0.024 0.017 0.18 2 -10000 0 2
RASA1 -0.026 0.015 0.18 2 -10000 0 2
NRP2 0.032 0.004 -10000 0 -0.065 1 1
VEGFR1 homodimer -0.016 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.032 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
eNOS/Caveolin-1 -0.014 0.05 0.17 1 -0.22 16 17
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.046 0.16 1 -0.077 1 2
mol:L-citrulline 0.006 0.055 0.15 19 -0.21 14 33
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.009 0.06 -10000 0 -0.071 27 27
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.009 0.049 -10000 0 -0.049 280 280
CD2AP 0.023 0.029 -10000 0 -0.065 48 48
PI3K/GAB1 0.053 0.055 0.18 1 -0.087 1 2
PDPK1 -0.031 0.035 0.15 16 -10000 0 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.049 -10000 0 -0.049 277 277
mol:NADP 0.006 0.055 0.15 19 -0.21 14 33
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.01 0.058 -10000 0 -0.07 27 27
VEGFR1 homodimer/NRP2 0.028 0.017 -10000 0 -0.037 26 26
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.021 0.005 -10000 0 -0.032 2 2
ARNO/beta Arrestin1-2 0.04 0.017 -10000 0 -0.063 11 11
EGFR 0.012 0.018 -10000 0 -0.065 6 6
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
USP6 0.032 0.005 -10000 0 -10000 0 0
IQSEC1 0.032 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.018 0.025 -10000 0 -0.051 8 8
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP -0.001 0.012 0.1 3 -0.061 7 10
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -0.065 4 4
EGF 0.032 0.007 -10000 0 -0.065 2 2
somatostatin receptor activity 0 0 0 154 0 16 170
ARAP2 0 0 0 149 0 11 160
mol:GDP 0.06 0.064 0.14 143 -0.14 9 152
mol:PI-3-4-5-P3 0 0 0 144 0 14 158
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.073 7 7
ADAP1 0 0 0 89 0 6 95
KIF13B 0.031 0.008 -10000 0 -0.065 2 2
HGF/MET 0.031 0.024 -10000 0 -0.051 3 3
PXN 0.032 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.073 0.087 0.18 146 -0.18 14 160
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.048 9 9
ADRB2 0.032 0.006 -10000 0 -0.065 1 1
receptor agonist activity 0 0 0 143 0 15 158
actin filament binding 0 0 0 147 0 17 164
SRC 0.031 0.008 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
GNAQ 0.032 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 159 -0.001 12 171
ARF6/GDP 0.024 0.068 0.13 27 -0.2 29 56
ARF6/GDP/GULP/ACAP1 0.08 0.063 0.16 130 -0.15 7 137
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.017 -10000 0 -0.054 2 2
ACAP1 0 0 0 47 -10000 0 47
ACAP2 0 0 0 147 0 10 157
LHCGR/beta Arrestin2 0.028 0.016 -10000 0 -0.079 11 11
EFNA1 0.028 0.02 -10000 0 -0.065 21 21
HGF 0.022 0.016 -10000 0 -0.065 1 1
CYTH3 0 0 0.001 144 0 14 158
CYTH2 0 0.001 0.002 3 -0.003 18 21
NCK1 0.03 0.015 -10000 0 -0.065 11 11
fibronectin binding 0 0 0 140 0 17 157
endosomal lumen acidification 0 0 0 151 0 19 170
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 0.032 0.009 -10000 0 -0.065 4 4
GNAQ/ARNO 0.024 0.006 0.043 1 -10000 0 1
mol:Phosphatidic acid 0 0 0 147 0 10 157
PIP3-E 0 0 0 84 0 15 99
MET 0.022 0.016 -10000 0 -0.065 2 2
GNA14 0.031 0.009 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GIT1 0.032 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 154 -0.001 12 166
GNA11 0.031 0.007 -10000 0 -10000 0 0
LHCGR 0.033 0 -10000 0 -10000 0 0
AGTR1 0.032 0.008 -10000 0 -0.065 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.027 0.016 -10000 0 -0.079 11 11
IPCEF1/ARNO 0.014 0.02 -10000 0 -0.029 8 8
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0 0.039 -9999 0 -0.12 23 23
FZD6 0.014 0.038 -9999 0 -0.065 93 93
WNT6 0.032 0.001 -9999 0 -10000 0 0
WNT4 0.031 0.008 -9999 0 -0.065 2 2
FZD3 0.03 0.01 -9999 0 -0.065 3 3
WNT5A 0.002 0.044 -9999 0 -0.059 169 169
WNT11 0.032 0.007 -9999 0 -0.065 2 2
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.029 0.047 -10000 0 -0.12 74 74
STMN1 -0.023 0.008 -10000 0 -0.051 24 24
Aurora B/RasGAP/Survivin 0.017 0.058 -10000 0 -0.054 196 196
Chromosomal passenger complex/Cul3 protein complex -0.034 0.056 -10000 0 -0.1 163 163
BIRC5 -0.008 0.049 -10000 0 -0.068 201 201
DES 0.016 0.11 -10000 0 -0.68 11 11
Aurora C/Aurora B/INCENP 0.049 0.033 -10000 0 -0.042 48 48
Aurora B/TACC1 0.038 0.019 -10000 0 -0.041 23 23
Aurora B/PP2A 0.041 0.023 -10000 0 -0.051 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.005 -10000 0 -0.014 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.022 1 -10000 0 1
NDC80 -0.032 0.018 -10000 0 -0.056 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.005 0.042 -10000 0 -0.18 13 13
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.003 0.047 -10000 0 -0.066 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.023 -10000 0 -0.052 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.021 0.031 -10000 0 -0.065 56 56
SMC4 -0.04 0.041 -10000 0 -0.065 377 377
NSUN2/NPM1/Nucleolin -0.009 0.087 -10000 0 -0.55 11 11
PSMA3 0.031 0.008 -10000 0 0 31 31
G2/M transition of mitotic cell cycle -0.001 0.002 0.015 1 -10000 0 1
H3F3B 0.01 0.011 -10000 0 -0.037 25 25
AURKB 0.026 0.023 -10000 0 -0.064 29 29
AURKC 0.03 0.01 -10000 0 -0.065 2 2
CDCA8 0.028 0.018 -10000 0 -0.067 16 16
cytokinesis -0.02 0.065 0.15 1 -0.21 31 32
Aurora B/Septin1 -0.013 0.069 0.14 1 -0.21 28 29
AURKA 0.027 0.019 -10000 0 -0.064 16 16
INCENP 0.031 0.005 -10000 0 -0.026 1 1
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.032 0.009 -10000 0 -0.064 4 4
hSgo1/Aurora B/Survivin 0.007 0.039 -10000 0 -0.04 202 202
EVI5 0.031 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.073 0.16 1 -0.16 32 33
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0 0.044 -10000 0 -0.17 22 22
NCAPG 0.011 0.04 -10000 0 -0.065 111 111
Aurora B/HC8 Proteasome 0.04 0.023 -10000 0 -0.051 21 21
NCAPD2 0.013 0.038 -10000 0 -0.065 94 94
Aurora B/PP1-gamma 0.041 0.023 -10000 0 -0.051 25 25
RHOA 0.032 0.006 -10000 0 -10000 0 0
NCAPH 0.03 0.017 -10000 0 -0.065 15 15
NPM1 -0.003 0.084 -10000 0 -0.39 17 17
RASA1 0.031 0.006 -10000 0 -10000 0 0
KLHL9 0.021 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.023 -10000 0 -0.051 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0.002 0.069 0.16 1 -0.16 34 35
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.004 0.048 -10000 0 -0.31 11 11
MYLK 0.009 0.013 -10000 0 -0.038 34 34
KIF23 0.017 0.036 -10000 0 -0.068 77 77
VIM -0.019 0.013 0.021 1 -0.051 33 34
RACGAP1 0.002 0.046 -10000 0 -0.067 155 155
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.048 -10000 0 -0.29 12 12
Chromosomal passenger complex -0.009 0.043 0.086 1 -0.15 29 30
Chromosomal passenger complex/EVI5 0.028 0.075 -10000 0 -0.092 19 19
TACC1 0.032 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
CUL3 0.033 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.036 0.035 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.05 0.18 3 -0.19 16 19
alphaV/beta3 Integrin/Osteopontin/Src 0.009 0.051 -10000 0 -0.058 179 179
AP1 -0.062 0.066 -10000 0 -0.14 48 48
ILK -0.041 0.025 0.16 4 -10000 0 4
bone resorption -0.063 0.03 0.15 4 -10000 0 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.01 0.062 0.16 4 -0.087 18 22
ITGAV 0.029 0.017 -10000 0 -0.068 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.039 -10000 0 -0.051 394 394
alphaV/beta3 Integrin/Osteopontin 0.02 0.061 -10000 0 -0.071 75 75
MAP3K1 -0.042 0.026 0.17 5 -10000 0 5
JUN 0.031 0.004 -10000 0 -10000 0 0
MAPK3 -0.048 0.033 0.16 5 -10000 0 5
MAPK1 -0.045 0.035 0.16 5 -10000 0 5
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.037 0.033 0.16 4 -10000 0 4
ITGB3 0.031 0.004 -10000 0 -10000 0 0
NFKBIA -0.047 0.043 0.16 5 -0.17 16 21
FOS 0.006 0.041 -10000 0 -0.066 120 120
CD44 -0.044 0.039 -10000 0 -0.065 396 396
CHUK 0.024 0.015 -10000 0 -0.065 1 1
PLAU -0.07 0.066 -10000 0 -0.35 2 2
NF kappa B1 p50/RelA -0.066 0.048 0.16 6 -10000 0 6
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.044 0.019 -10000 0 -0.056 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.028 0.17 5 -10000 0 5
VAV3 -0.045 0.029 0.16 5 -10000 0 5
MAP3K14 -0.043 0.028 0.17 5 -10000 0 5
ROCK2 0.032 0.003 -10000 0 -10000 0 0
SPP1 -0.003 0.047 -10000 0 -0.068 175 175
RAC1 0.023 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.033 0.16 3 -10000 0 3
MMP2 -0.084 0.045 0.26 1 -0.17 1 2
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.022 -10000 0 -0.065 26 26
CCL5 0.027 0.021 -10000 0 -0.065 25 25
SDCBP 0.032 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.011 0.046 0.1 17 -0.13 32 49
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 -0.009 0.053 0.17 2 -0.2 13 15
Syndecan-1/Syntenin 0.003 0.067 0.2 17 -0.21 10 27
MAPK3 -0.034 0.052 0.16 4 -0.16 28 32
HGF/MET 0.031 0.024 -10000 0 -0.051 3 3
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.065 26 26
BSG 0.031 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.008 0.052 0.17 2 -0.2 13 15
Syndecan-1/RANTES 0.001 0.069 0.2 17 -0.19 16 33
Syndecan-1/CD147 -0.027 0.058 0.19 4 -0.21 14 18
Syndecan-1/Syntenin/PIP2 0.003 0.063 0.19 17 -0.2 10 27
LAMA5 0.027 0.017 -10000 0 -0.065 13 13
positive regulation of cell-cell adhesion 0.002 0.062 0.19 17 -0.2 10 27
MMP7 0.018 0.034 -10000 0 -0.065 75 75
HGF 0.022 0.016 -10000 0 -0.065 1 1
Syndecan-1/CASK -0.013 0.045 0.09 17 -0.19 14 31
Syndecan-1/HGF/MET 0.003 0.058 0.22 4 -0.21 10 14
regulation of cell adhesion -0.034 0.071 0.23 20 -0.21 13 33
HPSE 0.024 0.027 -10000 0 -0.065 44 44
positive regulation of cell migration -0.011 0.046 0.1 17 -0.13 32 49
SDC1 -0.009 0.042 0.098 26 -0.11 27 53
Syndecan-1/Collagen -0.011 0.046 0.1 17 -0.13 32 49
PPIB -0.036 0.044 -10000 0 -0.065 354 354
MET 0.022 0.016 -10000 0 -0.065 2 2
PRKACA 0.031 0.006 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 165 165
MAPK1 -0.033 0.052 0.16 4 -0.16 27 31
homophilic cell adhesion -0.009 0.053 0.18 7 -0.19 13 20
MMP1 0.025 0.026 -10000 0 -0.065 38 38
HIF-1-alpha transcription factor network

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
PKM2 -0.057 0.17 0.5 10 -0.3 13 23
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.078 0.11 -10000 0 -0.25 69 69
SMAD4 0.009 0.041 -10000 0 -0.065 116 116
ID2 -0.057 0.17 0.53 9 -0.3 13 22
AP1 0.021 0.042 -10000 0 -0.051 117 117
ABCG2 -0.061 0.16 0.48 13 -0.3 14 27
HIF1A -0.014 0.054 0.15 7 -0.094 9 16
TFF3 -0.058 0.17 0.51 10 -0.3 13 23
GATA2 0.031 0.009 -10000 0 -0.027 9 9
AKT1 -0.01 0.055 0.17 6 -0.097 1 7
response to hypoxia -0.019 0.025 0.091 7 -0.067 8 15
MCL1 -0.059 0.17 0.47 12 -0.29 17 29
NDRG1 -0.068 0.15 0.54 4 -0.3 13 17
SERPINE1 -0.054 0.15 0.51 7 -0.3 16 23
FECH -0.053 0.17 0.51 11 -0.3 15 26
FURIN -0.056 0.17 0.53 9 -0.3 13 22
NCOA2 0.033 0.004 -10000 0 -10000 0 0
EP300 0.001 0.056 0.25 9 -0.2 2 11
HMOX1 -0.077 0.16 0.53 7 -0.3 22 29
BHLHE40 -0.096 0.092 -10000 0 -0.21 157 157
BHLHE41 -0.096 0.092 -10000 0 -0.21 157 157
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.01 0.094 0.23 6 -0.11 68 74
ENG -0.035 0.079 0.27 10 -0.16 1 11
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.057 0.17 0.5 12 -0.29 17 29
ABCB1 -0.012 0.046 -10000 0 -0.34 5 5
TFRC -0.059 0.16 0.53 9 -0.3 13 22
CXCR4 -0.076 0.16 0.51 7 -0.3 26 33
TF -0.084 0.11 0.4 1 -0.3 13 14
CITED2 -0.061 0.16 0.55 6 -0.3 15 21
HIF1A/ARNT -0.072 0.14 0.27 8 -0.26 101 109
LDHA 0.002 0.057 -10000 0 -0.46 6 6
ETS1 -0.055 0.17 0.48 14 -0.3 15 29
PGK1 -0.056 0.17 0.51 11 -0.3 13 24
NOS2 -0.096 0.092 -10000 0 -0.21 157 157
ITGB2 -0.064 0.17 0.48 15 -0.3 24 39
ALDOA -0.056 0.17 0.46 13 -0.29 17 30
Cbp/p300/CITED2 -0.096 0.1 -10000 0 -0.25 103 103
FOS 0.007 0.041 -10000 0 -0.065 120 120
HK2 -0.056 0.17 0.51 11 -0.3 13 24
SP1 0.034 0.007 -10000 0 -0.041 2 2
GCK 0.003 0.089 0.41 4 -0.37 3 7
HK1 -0.078 0.14 0.46 5 -0.29 19 24
NPM1 -0.06 0.16 0.56 6 -0.3 13 19
EGLN1 -0.06 0.16 0.51 8 -0.3 13 21
CREB1 0.035 0.008 -10000 0 -0.084 2 2
PGM1 -0.057 0.17 0.53 9 -0.3 13 22
SMAD3 0.032 0.005 -10000 0 -10000 0 0
EDN1 -0.018 0.082 0.28 2 -0.33 14 16
IGFBP1 -0.047 0.15 0.51 8 -0.3 12 20
VEGFA -0.079 0.13 0.36 12 -0.28 34 46
HIF1A/JAB1 0.009 0.052 0.15 3 -0.054 156 159
CP -0.066 0.16 0.49 9 -0.3 23 32
CXCL12 -0.068 0.15 0.52 5 -0.3 19 24
COPS5 0.032 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.041 -10000 0 -0.051 112 112
BNIP3 -0.075 0.13 0.47 1 -0.3 15 16
EGLN3 -0.059 0.17 0.52 8 -0.3 14 22
CA9 -0.06 0.16 0.51 10 -0.3 14 24
TERT -0.054 0.17 0.48 14 -0.29 18 32
ENO1 -0.059 0.16 0.52 8 -0.3 14 22
PFKL -0.054 0.17 0.51 11 -0.3 13 24
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.075 0.16 0.47 11 -0.3 24 35
ARNT -0.015 0.056 0.15 7 -0.085 18 25
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.096 0.092 -10000 0 -0.21 157 157
SLC2A1 -0.065 0.13 0.37 13 -0.29 20 33
LEP -0.048 0.14 0.52 6 -0.3 10 16
HIF1A/ARNT/Cbp/p300 -0.079 0.11 -10000 0 -0.25 70 70
EPO -0.033 0.11 0.35 9 -0.37 19 28
CREBBP 0.002 0.056 0.25 9 -0.2 2 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.084 0.11 -10000 0 -0.24 96 96
PFKFB3 -0.067 0.15 0.52 5 -0.3 14 19
NT5E -0.064 0.16 0.5 8 -0.3 16 24
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.021 0.095 0.19 15 -0.3 46 61
CRKL -0.021 0.094 0.18 1 -0.3 47 48
HRAS -0.005 0.095 0.17 1 -0.26 49 50
mol:PIP3 0.038 0.12 0.25 33 -0.28 38 71
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.002 -10000 0 -10000 0 0
GAB1 -0.014 0.098 -10000 0 -0.31 47 47
FOXO3 0.026 0.14 0.24 29 -0.3 40 69
AKT1 0.031 0.14 0.24 28 -0.32 40 68
BAD 0.025 0.13 0.23 29 -0.3 40 69
megakaryocyte differentiation -0.012 0.089 -10000 0 -0.3 43 43
GSK3B 0.027 0.13 0.25 25 -0.3 40 65
RAF1 -0.011 0.082 0.16 7 -0.23 48 55
SHC1 0.024 0.026 -10000 0 -0.05 52 52
STAT3 -0.016 0.098 -10000 0 -0.31 47 47
STAT1 -0.033 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.008 0.081 0.14 2 -0.22 48 50
cell proliferation -0.019 0.095 -10000 0 -0.31 47 47
PIK3CA 0.028 0.018 -10000 0 -0.064 17 17
TEC 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 0.017 0.11 0.19 4 -0.29 41 45
HRAS/SPRED2 0.007 0.092 0.19 3 -0.23 47 50
LYN/TEC/p62DOK 0.024 0.12 -10000 0 -0.31 47 47
MAPK3 -0.006 0.07 0.18 17 -0.17 44 61
STAP1 -0.015 0.098 -10000 0 -0.31 47 47
GRAP2 0.03 0.008 -10000 0 -10000 0 0
JAK2 -0.028 0.16 -10000 0 -0.5 48 48
STAT1 (dimer) -0.031 0.17 -10000 0 -0.55 47 47
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.032 0.12 -10000 0 -0.31 46 46
actin filament polymerization -0.009 0.096 -10000 0 -0.3 47 47
LYN 0.021 0.031 -10000 0 -0.058 67 67
STAP1/STAT5A (dimer) -0.024 0.13 0.21 1 -0.39 49 50
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.1 0.2 3 -0.29 47 50
PI3K 0.039 0.12 0.22 3 -0.28 42 45
PTEN 0.023 0.016 -10000 0 -0.065 2 2
SCF/KIT/EPO/EPOR -0.016 0.18 -10000 0 -0.56 47 47
MAPK8 -0.019 0.096 -10000 0 -0.31 47 47
STAT3 (dimer) -0.015 0.097 -10000 0 -0.31 47 47
positive regulation of transcription -0.004 0.061 0.17 17 -0.14 35 52
mol:GDP 0.001 0.099 -10000 0 -0.28 46 46
PIK3C2B -0.016 0.096 -10000 0 -0.31 45 45
CBL/CRKL -0.004 0.1 0.2 4 -0.3 47 51
FER -0.015 0.098 -10000 0 -0.31 46 46
SH2B3 -0.015 0.097 -10000 0 -0.31 47 47
PDPK1 0.032 0.11 0.23 33 -0.26 37 70
SNAI2 -0.021 0.098 -10000 0 -0.32 47 47
positive regulation of cell proliferation -0.028 0.15 -10000 0 -0.47 48 48
KITLG 0.027 0.023 -10000 0 -0.044 45 45
cell motility -0.028 0.15 -10000 0 -0.47 48 48
PTPN6 0.028 0.018 -10000 0 -0.048 19 19
EPOR 0.015 0.077 -10000 0 -0.46 4 4
STAT5A (dimer) -0.018 0.13 -10000 0 -0.4 48 48
SOCS1 0.032 0.004 -10000 0 -10000 0 0
cell migration 0.015 0.095 0.31 45 -10000 0 45
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.02 0.02 -10000 0 -0.033 29 29
VAV1 0.031 0.007 -10000 0 -0.065 1 1
GRB10 -0.01 0.075 -10000 0 -0.32 27 27
PTPN11 0.031 0.01 -10000 0 -0.028 11 11
SCF/KIT -0.008 0.1 -10000 0 -0.32 47 47
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.069 0.15 9 -0.19 46 55
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.036 0.2 -10000 0 -0.63 51 51
MAP2K2 -0.014 0.076 0.2 17 -0.19 46 63
SHC/Grb2/SOS1 0.013 0.11 -10000 0 -0.3 47 47
STAT5A -0.017 0.13 -10000 0 -0.41 47 47
GRB2 0.032 0.006 -10000 0 -10000 0 0
response to radiation -0.02 0.097 -10000 0 -0.31 47 47
SHC/GRAP2 0.037 0.028 -10000 0 -0.051 38 38
PTPRO -0.012 0.091 -10000 0 -0.3 43 43
SH2B2 -0.01 0.098 -10000 0 -0.31 47 47
DOK1 0.032 0.001 -10000 0 -10000 0 0
MATK -0.015 0.096 -10000 0 -0.31 45 45
CREBBP 0.026 0.043 -10000 0 -0.1 47 47
BCL2 0.007 0.12 -10000 0 -0.6 11 11
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0 0.059 -10000 0 -0.31 11 11
Syndecan-4/Syndesmos -0.031 0.11 -10000 0 -0.48 17 17
positive regulation of JNK cascade -0.036 0.11 -10000 0 -0.38 24 24
Syndecan-4/ADAM12 -0.022 0.12 -10000 0 -0.45 20 20
CCL5 0.027 0.021 -10000 0 -0.065 25 25
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DNM2 0.031 0.007 -10000 0 -10000 0 0
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.025 0.022 -10000 0 -0.056 8 8
ADAM12 0.023 0.015 -10000 0 -10000 0 0
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 -0.037 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.031 0.11 -10000 0 -0.48 17 17
Syndecan-4/CXCL12/CXCR4 -0.038 0.11 -10000 0 -0.44 20 20
Syndecan-4/Laminin alpha3 -0.016 0.12 -10000 0 -0.48 17 17
MDK -0.023 0.047 -10000 0 -0.065 282 282
Syndecan-4/FZD7 -0.034 0.12 -10000 0 -0.43 22 22
Syndecan-4/Midkine -0.037 0.11 -10000 0 -0.42 23 23
FZD7 -0.013 0.048 -10000 0 -0.065 238 238
Syndecan-4/FGFR1/FGF -0.005 0.12 -10000 0 -0.42 20 20
THBS1 0.024 0.026 -10000 0 -0.065 39 39
integrin-mediated signaling pathway -0.048 0.1 -10000 0 -0.38 27 27
positive regulation of MAPKKK cascade -0.036 0.11 -10000 0 -0.38 24 24
Syndecan-4/TACI -0.015 0.12 -10000 0 -0.48 17 17
CXCR4 -0.018 0.049 -10000 0 -0.065 263 263
cell adhesion -0.007 0.03 0.2 3 -0.085 14 17
Syndecan-4/Dynamin -0.018 0.12 -10000 0 -0.42 22 22
Syndecan-4/TSP1 -0.018 0.12 -10000 0 -0.48 17 17
Syndecan-4/GIPC -0.018 0.12 -10000 0 -0.47 17 17
Syndecan-4/RANTES -0.016 0.12 -10000 0 -0.48 17 17
ITGB1 0.025 0.014 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.029 0.017 -10000 0 -0.065 15 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.002 0.081 0.8 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.018 0.12 -10000 0 -0.43 22 22
TFPI 0.011 0.04 -10000 0 -0.065 112 112
F2 0.029 0.02 -10000 0 -0.045 14 14
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.051 61 61
positive regulation of cell adhesion -0.026 0.11 -10000 0 -0.46 17 17
ACTN1 0.023 0.027 -10000 0 -0.065 40 40
TNC -0.058 0.023 -10000 0 -0.065 469 469
Syndecan-4/CXCL12 -0.022 0.12 -10000 0 -0.47 18 18
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CXCL12 0.023 0.019 -10000 0 -0.065 12 12
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.065 2 2
FGFR1 0.032 0.006 -10000 0 -0.065 1 1
Syndecan-4/PI-4-5-P2 -0.031 0.11 -10000 0 -0.48 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.039 -10000 0 -0.059 105 105
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.021 -10000 0 -0.053 10 10
vasculogenesis -0.017 0.12 -10000 0 -0.41 22 22
SDC4 -0.029 0.11 -10000 0 -0.48 19 19
Syndecan-4/Tenascin C -0.049 0.11 -10000 0 -0.39 27 27
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.014 0.12 -10000 0 -0.48 17 17
MMP9 -0.005 0.045 -10000 0 -0.061 182 182
Rac1/GTP -0.007 0.031 0.2 3 -0.087 14 17
cytoskeleton organization -0.03 0.1 -10000 0 -0.46 17 17
GIPC1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.023 0.12 -10000 0 -0.42 22 22
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.019 0.07 -10000 0 -0.24 14 14
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
FOS 0.01 0.061 0.19 1 -0.24 13 14
PRKCA 0.031 0.004 -10000 0 -10000 0 0
PTPN7 0.03 0.008 0.066 1 -0.045 2 3
HRAS 0.031 0.007 -10000 0 -10000 0 0
PRKCB -0.001 0.002 0.018 1 -0.003 119 120
NRAS 0.008 0.042 -10000 0 -0.06 134 134
RAS family/GTP 0.03 0.046 -10000 0 -0.044 121 121
MAPK3 0.026 0.031 -10000 0 -0.34 2 2
MAP2K1 -0.003 0.026 0.12 1 -0.16 3 4
ELK1 0.031 0.005 -10000 0 -0.022 2 2
BRAF 0.004 0.017 0.098 1 -0.23 2 3
mol:GTP 0 0 0.003 1 -0.001 124 125
MAPK1 0 0.1 -10000 0 -0.35 36 36
RAF1 0.006 0.016 0.098 1 -0.22 2 3
KRAS 0.03 0.008 -10000 0 -10000 0 0
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.047 -10000 0 -0.05 259 259
PDGFRB 0.032 0.007 -10000 0 -0.066 2 2
SPHK1 0.011 0.018 -10000 0 -10000 0 0
mol:S1P 0.005 0.023 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.069 -10000 0 -0.22 32 32
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.079 0.19 16 -0.24 18 34
PLCG1 -0.04 0.062 -10000 0 -0.2 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.066 2 2
GNAI2 0.035 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.064 59 59
GNAI1 0.019 0.016 -10000 0 -0.062 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.014 0.011 2 -0.039 244 246
S1P1/S1P -0.003 0.032 0.18 1 -10000 0 1
negative regulation of cAMP metabolic process -0.04 0.067 -10000 0 -0.22 30 30
MAPK3 -0.049 0.069 -10000 0 -0.24 29 29
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 0 153 153
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
KDR 0.028 0.018 -10000 0 -0.064 14 14
PLCB2 0.001 0.051 0.16 21 -10000 0 21
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.032 -10000 0 -10000 0 0
receptor internalization -0.003 0.031 0.18 1 -10000 0 1
PTGS2 -0.055 0.072 -10000 0 -0.31 14 14
Rac1/GTP -0.007 0.025 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.019 0.048 -10000 0 -0.063 275 275
negative regulation of T cell proliferation -0.04 0.067 -10000 0 -0.22 30 30
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
MAPK1 -0.047 0.069 -10000 0 -0.26 23 23
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.053 0.17 17 -10000 0 17
ABCC1 0.031 0.012 -10000 0 -0.065 8 8
Caspase cascade in apoptosis

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
TOP1 -0.016 0.096 -10000 0 -0.32 27 27
ACTA1 -0.045 0.086 -10000 0 -0.24 55 55
NUMA1 -0.014 0.084 -10000 0 -0.3 27 27
SPTAN1 -0.046 0.088 0.18 7 -0.31 32 39
LIMK1 -0.002 0.1 0.18 77 -0.26 29 106
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.065 6 6
CASP10 -0.02 0.013 -10000 0 -0.051 19 19
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 2 -0.001 9 11
PTK2 -0.015 0.085 -10000 0 -0.32 24 24
DIABLO 0.032 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.041 0.091 0.18 7 -0.31 32 39
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.048 0.089 0.18 7 -0.26 47 54
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.03 0.09 -10000 0 -0.62 8 8
BID -0.004 0.014 -10000 0 -0.13 5 5
MAP3K1 -0.009 0.056 -10000 0 -0.38 7 7
TRADD 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.051 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.048 0.09 0.18 10 -0.3 36 46
CASP9 0.031 0.009 -10000 0 -0.065 3 3
DNA repair 0.026 0.06 0.15 57 -10000 0 57
neuron apoptosis 0.02 0.068 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.035 0.091 0.2 2 -0.33 31 33
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.013 0.1 -10000 0 -0.92 4 4
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.089 0.27 5 -0.29 37 42
CASP7 -0.055 0.1 -10000 0 -0.22 134 134
KRT18 0.013 0.058 -10000 0 -0.48 5 5
apoptosis -0.049 0.096 -10000 0 -0.34 29 29
DFFA -0.049 0.087 0.18 3 -0.26 45 48
DFFB -0.05 0.087 0.18 3 -0.25 50 53
PARP1 -0.026 0.06 -10000 0 -0.15 57 57
actin filament polymerization -0.007 0.1 0.25 27 -0.17 76 103
TNF 0.032 0.007 -10000 0 -0.065 2 2
CYCS 0 0.026 -10000 0 -0.22 2 2
SATB1 0.017 0.1 0.31 1 -0.83 4 5
SLK -0.052 0.087 -10000 0 -0.27 46 46
p15 BID/BAX -0.012 0.065 -10000 0 -0.2 39 39
CASP2 0.043 0.088 0.2 119 -0.18 3 122
JNK cascade 0.009 0.055 0.38 7 -10000 0 7
CASP3 -0.047 0.09 -10000 0 -0.24 60 60
LMNB2 0.048 0.081 0.24 11 -0.31 3 14
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
CASP4 0.013 0.039 -10000 0 -0.065 101 101
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.043 37 37
negative regulation of DNA binding 0.03 0.089 -10000 0 -0.61 8 8
stress fiber formation -0.052 0.086 -10000 0 -0.27 45 45
GZMB -0.018 0.012 0 136 -0.054 19 155
CASP1 -0.012 0.034 -10000 0 -0.054 187 187
LMNB1 0.038 0.099 0.23 13 -0.37 10 23
APP 0.02 0.069 -10000 0 -0.63 5 5
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
response to stress 0 0 0.001 6 -0.001 21 27
CASP8 -0.012 0.004 -10000 0 -0.04 10 10
VIM -0.042 0.097 -10000 0 -0.34 29 29
LMNA 0.05 0.081 0.24 12 -0.31 3 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.037 -10000 0 -0.17 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.05 0.085 0.18 1 -0.3 35 36
APAF-1/Caspase 9 0.021 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.013 0.083 -10000 0 -0.3 27 27
CFL2 0.007 0.1 0.17 76 -0.26 27 103
GAS2 -0.052 0.086 0.18 1 -0.28 41 42
positive regulation of apoptosis 0.05 0.089 0.2 38 -0.32 7 45
PRF1 0.022 0.019 -10000 0 -0.065 12 12
PLK1 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
regulation of centriole-centriole cohesion 0 0.009 -10000 0 -0.029 26 26
BUB1B -0.013 0.035 0.1 5 -0.14 15 20
PLK1 0.006 0.022 0.069 34 -0.092 4 38
PLK1S1 0.002 0.013 0.042 33 -0.047 4 37
KIF2A -0.001 0.025 0.2 3 -0.1 2 5
regulation of mitotic centrosome separation 0.006 0.022 0.069 34 -0.092 4 38
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.028 0.1 3 -0.08 9 12
WEE1 -0.019 0.066 -10000 0 -0.34 15 15
cytokinesis -0.011 0.04 0.17 2 -0.16 11 13
PP2A-alpha B56 0.056 0.077 -10000 0 -0.56 7 7
AURKA 0.007 0.017 0.087 3 -0.18 1 4
PICH/PLK1 -0.032 0.021 0.13 1 -0.088 12 13
CENPE -0.004 0.026 0.14 6 -0.12 3 9
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.026 0.2 3 -0.11 1 4
PPP2CA 0.032 0.005 -10000 0 -10000 0 0
FZR1 0.031 0.006 -10000 0 -10000 0 0
TPX2 -0.01 0.025 0.1 3 -0.086 2 5
PAK1 0.032 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
CLSPN 0.009 0.031 -10000 0 -0.23 7 7
GORASP1 0.032 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 3 -0.011 3 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.042 33 -0.047 4 37
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -10000 0 8
STAG2 0.027 0.022 -10000 0 -0.065 26 26
GRASP65/GM130/RAB1/GTP 0.01 0.067 -10000 0 -0.51 8 8
spindle elongation 0.006 0.022 0.069 34 -0.092 4 38
ODF2 0.032 0.006 -10000 0 -10000 0 0
BUB1 0.023 0.074 -10000 0 -0.59 7 7
TPT1 -0.005 0.055 -10000 0 -0.19 39 39
CDC25C 0.011 0.031 -10000 0 -0.25 6 6
CDC25B 0.026 0.018 -10000 0 -0.061 16 16
SGOL1 0 0.009 0.029 26 -10000 0 26
RHOA 0.032 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 -0.012 0.047 -10000 0 -0.084 48 48
CDC14B -0.011 0.004 0.009 12 -10000 0 12
CDC20 -0.023 0.048 -10000 0 -0.065 287 287
PLK1/PBIP1 -0.018 0.015 0.052 2 -0.07 12 14
mitosis -0.003 0.003 0.015 5 -10000 0 5
FBXO5 -0.014 0.032 0.084 12 -0.095 35 47
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 -0.001 0.045 -10000 0 -0.065 169 169
metaphase plate congression 0.009 0.033 -10000 0 -0.23 8 8
ERCC6L -0.025 0.036 -10000 0 -0.097 34 34
NLP/gamma Tubulin 0.004 0.016 0.065 9 -0.067 6 15
microtubule cytoskeleton organization -0.005 0.055 -10000 0 -0.19 39 39
G2/M transition DNA damage checkpoint 0 0.002 0.011 5 -10000 0 5
PPP1R12A 0.032 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.011 5 -10000 0 5
PLK1/PRC1-2 0.006 0.048 0.12 3 -0.079 24 27
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.029 0.14 1 -0.086 5 6
RAB1A 0.032 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.005 0.022 0.068 39 -0.06 4 43
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.097 0.13 4 -0.23 99 103
microtubule-based process 0.009 0.031 0.11 3 -0.082 10 13
Golgi organization 0.006 0.022 0.069 34 -0.092 4 38
Cohesin/SA2 0.021 0.022 0.096 3 -0.071 6 9
PPP1CB/MYPT1 0.047 0.01 -10000 0 -0.047 1 1
KIF20A -0.002 0.046 -10000 0 -0.065 178 178
APC/C/CDC20 -0.002 0.031 0.11 2 -0.077 13 15
PPP2R1A 0.03 0.009 -10000 0 -10000 0 0
chromosome segregation -0.018 0.014 0.051 2 -0.069 12 14
PRC1 -0.009 0.048 -10000 0 -0.065 213 213
ECT2 -0.005 0.035 0.16 13 -0.12 3 16
C13orf34 0.005 0.02 0.063 34 -0.068 4 38
NUDC 0.009 0.033 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.013 0.034 0.1 5 -0.14 15 20
spindle assembly 0.004 0.019 0.063 24 -0.079 4 28
spindle stabilization 0.002 0.013 0.042 33 -0.047 4 37
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.031 0.11 3 -0.082 10 13
CCNB1 -0.021 0.049 -10000 0 -0.065 280 280
PPP1CB 0.032 0.007 -10000 0 -0.06 2 2
BTRC 0.024 0.014 -10000 0 -10000 0 0
ROCK2 0.016 0.025 -10000 0 -0.22 2 2
TUBG1 0.008 0.022 0.087 1 -0.16 5 6
G2/M transition of mitotic cell cycle -0.025 0.03 -10000 0 -0.089 38 38
MLF1IP -0.035 0.012 -10000 0 -0.041 419 419
INCENP 0.032 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.051 15 15
AKT1 -0.024 0.073 0.22 5 -0.29 13 18
PTK2B -0.034 0.057 0.16 37 -10000 0 37
VEGFR2 homodimer/Frs2 0.025 0.024 -10000 0 -0.09 13 13
CAV1 -0.019 0.041 -10000 0 -0.065 217 217
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.005 0.051 -10000 0 -0.079 33 33
endothelial cell proliferation -0.005 0.079 0.21 21 -0.25 10 31
mol:Ca2+ -0.03 0.051 0.15 32 -0.13 2 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.002 0.059 0.17 12 -0.1 13 25
RP11-342D11.1 -0.032 0.037 0.16 14 -0.1 11 25
CDH5 0.027 0.023 -10000 0 -0.065 29 29
VEGFA homodimer 0.001 0.052 -10000 0 -0.044 286 286
SHC1 0.024 0.026 -10000 0 -0.065 40 40
SHC2 0.031 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.018 0.053 -10000 0 -0.098 30 30
SH2D2A 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.007 0.06 0.2 2 -0.2 4 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.005 0.051 -10000 0 -0.084 30 30
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.004 0.068 0.16 13 -0.098 29 42
GRB10 -0.021 0.047 0.16 24 -0.12 1 25
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.006 0.077 0.18 12 -0.11 27 39
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.046 0.13 11 -0.15 22 33
HIF1A 0.03 0.01 -10000 0 -0.065 2 2
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.003 0.058 0.17 12 -0.1 13 25
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.004 -10000 0 -10000 0 0
Nck/Pak 0.044 0.017 -10000 0 -0.051 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.008 0.05 -10000 0 -0.073 49 49
mol:GDP -0.012 0.056 -10000 0 -0.092 35 35
mol:NADP 0.004 0.058 0.26 3 -0.2 1 4
eNOS/Hsp90 0.014 0.06 0.27 3 -0.2 1 4
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.03 0.052 0.15 32 -0.13 2 34
HIF1A/ARNT 0.044 0.015 -10000 0 -0.051 2 2
SHB 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.021 0.049 -10000 0 -0.066 275 275
VEGFC 0.029 0.015 -10000 0 -0.065 11 11
FAK1/Vinculin -0.004 0.059 0.2 11 -0.21 8 19
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.002 0.068 0.17 13 -0.1 14 27
PTPN6 0.029 0.015 -10000 0 -0.065 11 11
EPAS1 0.034 0.02 -10000 0 -0.073 16 16
mol:L-citrulline 0.004 0.058 0.26 3 -0.2 1 4
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.003 0.065 0.17 13 -0.1 12 25
VEGFR2 homodimer/VEGFA homodimer -0.006 0.055 -10000 0 -0.082 46 46
VEGFR2/3 heterodimer 0.026 0.025 -10000 0 -0.09 14 14
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.031 0.059 0.16 26 -0.17 13 39
VEGFR2 homodimer -0.02 0.015 -10000 0 -0.1 14 14
FLT1 0.03 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.019 -10000 0 -0.045 29 29
MAPK3 -0.019 0.064 0.28 4 -10000 0 4
MAPK1 -0.021 0.062 0.32 3 -10000 0 3
VEGFA145/NRP2 -0.006 0.049 -10000 0 -0.051 276 276
VEGFR1/2 heterodimer 0.025 0.025 -10000 0 -0.09 14 14
KDR -0.02 0.015 -10000 0 -0.1 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.003 0.06 0.16 14 -0.089 31 45
SRC 0.03 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.019 0.066 0.3 4 -10000 0 4
PI3K -0.02 0.064 0.17 7 -0.17 19 26
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.007 0.051 -10000 0 -0.078 38 38
FES -0.033 0.054 0.16 35 -0.13 2 37
GAB1 -0.019 0.067 0.16 10 -0.18 36 46
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.051 -10000 0 -0.081 32 32
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.008 0.047 0.27 3 -0.19 1 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.014 0.052 -10000 0 -0.064 129 129
PI3K/GAB1 -0.021 0.075 0.2 2 -0.23 20 22
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.005 0.073 0.18 12 -0.11 11 23
PRKACA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.031 -10000 0 -0.072 24 24
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
CDC42 -0.032 0.052 0.15 33 -0.13 2 35
actin cytoskeleton reorganization -0.005 0.051 -10000 0 -0.083 30 30
PTK2 -0.011 0.057 0.17 13 -0.2 9 22
EDG1 -0.032 0.037 0.16 14 -0.1 11 25
mol:DAG -0.03 0.052 0.15 32 -0.13 2 34
CaM/Ca2+ -0.032 0.05 0.15 29 -0.13 1 30
MAP2K3 -0.037 0.05 0.14 32 -10000 0 32
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.044 0.096 0.18 134 -0.099 18 152
PLCG1 -0.031 0.052 0.15 32 -0.13 2 34
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.002 0.064 0.17 10 -0.1 14 24
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
YES1 0.017 0.034 -10000 0 -0.065 74 74
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.006 0.052 -10000 0 -0.078 36 36
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.051 -10000 0 -0.061 107 107
cell migration -0.008 0.074 0.2 11 -0.22 17 28
mol:PI-3-4-5-P3 -0.019 0.061 0.17 7 -0.16 18 25
FYN 0.029 0.011 -10000 0 -0.065 1 1
VEGFB/NRP1 -0.031 0.051 0.15 34 -0.12 2 36
mol:NO 0.004 0.058 0.26 3 -0.2 1 4
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.023 -10000 0 -0.097 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.04 -10000 0 -0.091 23 23
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
NOS3 0.004 0.06 0.27 3 -0.22 1 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.005 0.051 -10000 0 -0.083 30 30
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.034 0.05 0.14 33 -0.13 1 34
PRKCB -0.029 0.047 0.14 32 -0.13 1 33
VCL 0.025 0.014 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.032 0.041 0.17 16 -0.12 2 18
VEGFR1/2 heterodimer/VEGFA homodimer -0.007 0.051 -10000 0 -0.074 47 47
VEGFA165/NRP2 -0.006 0.049 -10000 0 -0.051 276 276
MAPKKK cascade -0.033 0.039 0.15 9 -10000 0 9
NRP2 0.032 0.004 -10000 0 -0.065 1 1
VEGFC homodimer 0.029 0.015 -10000 0 -0.065 11 11
NCK1 0.03 0.015 -10000 0 -0.065 11 11
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.068 0.2 14 -0.23 5 19
MAP3K13 -0.033 0.051 0.15 31 -0.13 2 33
PDPK1 -0.034 0.053 0.15 8 -0.16 14 22
PDGFR-alpha signaling pathway

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
PDGFRA 0.015 0.028 -10000 0 -0.032 103 103
PDGF/PDGFRA/CRKL 0.037 0.021 -10000 0 -0.052 5 5
positive regulation of JUN kinase activity 0.039 0.035 -10000 0 -0.044 42 42
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.052 5 5
AP1 -0.027 0.073 0.14 58 -0.15 3 61
mol:IP3 -0.022 0.014 0.034 3 -0.067 2 5
PLCG1 -0.022 0.014 0.034 3 -0.067 2 5
PDGF/PDGFRA/alphaV Integrin 0.036 0.026 -10000 0 -0.054 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.014 0.034 3 -0.067 2 5
CAV3 0.032 0.004 -10000 0 0 9 9
CAV1 -0.019 0.041 -10000 0 -0.065 217 217
SHC/Grb2/SOS1 0.04 0.036 -10000 0 -0.044 42 42
PDGF/PDGFRA/Shf 0.019 0.012 -10000 0 -0.041 6 6
FOS -0.04 0.048 0.17 4 -0.13 98 102
JUN -0.026 0.021 0.032 11 -10000 0 11
oligodendrocyte development 0.036 0.026 -10000 0 -0.054 20 20
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.014 0.034 3 -0.067 2 5
PDGF/PDGFRA 0.015 0.028 -10000 0 -0.032 103 103
actin cytoskeleton reorganization 0.035 0.022 -10000 0 -0.051 4 4
SRF -0.021 0.007 0.02 1 -10000 0 1
SHC1 0.024 0.026 -10000 0 -0.05 52 52
PI3K 0.045 0.034 -10000 0 -0.053 19 19
PDGF/PDGFRA/Crk/C3G 0.049 0.031 -10000 0 -0.04 18 18
JAK1 -0.018 0.014 0.022 26 -0.056 2 28
ELK1/SRF -0.009 0.059 0.13 72 -10000 0 72
SHB 0.03 0.009 -10000 0 -10000 0 0
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.024 -10000 0 -0.03 64 64
GO:0007205 -0.016 0.011 0.024 3 -0.058 5 8
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.039 0.035 -10000 0 -0.044 42 42
PDGF/PDGFRA/SHB 0.036 0.022 -10000 0 -0.051 4 4
PDGF/PDGFRA/Caveolin-1 -0.01 0.039 -10000 0 -0.055 185 185
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
ELK1 -0.021 0.015 0.026 3 -0.071 2 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.051 5 5
JAK-STAT cascade -0.018 0.014 0.022 26 -0.056 2 28
cell proliferation 0.019 0.011 -10000 0 -0.041 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.031 0.007 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.049 0.14 0.16 1 -0.26 130 131
HIF1A -0.048 0.13 -10000 0 -0.32 89 89
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.049 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.014 -10000 0 -10000 0 0
CDKN2A 0.002 0.027 -10000 0 -0.065 53 53
ARNT/IPAS 0.045 0.012 -10000 0 -10000 0 0
HIF1AN 0.024 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 0 9 9
HIF1A/ARNT -0.044 0.13 0.16 1 -0.26 125 126
CUL2 0.025 0.014 -10000 0 -10000 0 0
OS9 0.028 0.012 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.063 0.014 -10000 0 -0.052 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.043 0.14 0.16 2 -0.26 127 129
PHD1-3/OS9 0.06 0.042 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.023 0.15 0.18 1 -0.26 126 127
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.045 0.14 0.16 1 -0.26 126 127
EGLN3 0.03 0.011 -10000 0 -0.065 4 4
EGLN2 0.031 0.006 -10000 0 -10000 0 0
EGLN1 0.031 0.007 -10000 0 -0.065 1 1
TP53 0.019 0.033 -10000 0 -0.052 81 81
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.002 0.07 -10000 0 -0.57 3 3
ARNT 0.032 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF -0.059 0.13 0.16 2 -0.27 127 129
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.062 0.02 -10000 0 -0.049 10 10
fibroblast growth factor receptor signaling pathway 0.061 0.019 -10000 0 -0.049 10 10
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.028 0.011 -10000 0 -10000 0 0
GPC1/SLIT2 0.03 0.024 -10000 0 -0.051 5 5
SMAD2 -0.027 0.029 0.17 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.037 0.018 -10000 0 -0.04 7 7
GPC1/Laminin alpha1 0.023 0.008 -10000 0 -0.04 7 7
TDGF1 0.031 0.008 -10000 0 -0.065 2 2
CRIPTO/GPC1 0.045 0.016 -10000 0 -0.051 9 9
APP/GPC1 0.045 0.014 -10000 0 -0.051 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.012 -10000 0 -0.05 76 76
FLT1 0.03 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.023 -10000 0 -0.049 14 14
SERPINC1 0.032 0.006 -10000 0 -0.065 1 1
FYN -0.023 0.009 -10000 0 -0.049 7 7
FGR -0.026 0.008 -10000 0 -0.049 24 24
positive regulation of MAPKKK cascade -0.007 0.06 0.18 33 -0.2 6 39
SLIT2 0.021 0.017 -10000 0 -0.065 3 3
GPC1/NRG 0.046 0.014 -10000 0 -0.051 7 7
NRG1 0.032 0.005 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0 0.056 -10000 0 -0.05 277 277
LYN -0.028 0.01 -10000 0 -0.049 67 67
mol:Spermine -0.012 0.003 -10000 0 -0.04 7 7
cell growth 0.061 0.019 -10000 0 -0.049 10 10
BMP signaling pathway -0.031 0.012 0.065 7 -10000 0 7
SRC -0.024 0.008 -10000 0 -0.049 8 8
TGFBR1 0.032 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.003 0.046 -10000 0 -0.065 179 179
GPC1 0.031 0.012 -10000 0 -0.065 7 7
TGFBR1 (dimer) 0.032 0.005 -10000 0 -10000 0 0
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
BLK -0.025 0.007 -10000 0 -0.049 8 8
HCK -0.028 0.013 -10000 0 -0.049 91 91
FGF2 0.032 0.007 -10000 0 -0.065 2 2
FGFR1 0.032 0.006 -10000 0 -0.065 1 1
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.011 -10000 0 -0.065 6 6
cell death 0.045 0.014 -10000 0 -0.051 7 7
ATIII/GPC1 0.045 0.014 -10000 0 -0.051 8 8
PLA2G2A/GPC1 0.011 0.047 -10000 0 -0.051 182 182
LCK -0.025 0.007 -10000 0 -0.051 11 11
neuron differentiation 0.045 0.014 -10000 0 -0.051 7 7
PrPc/Cu2+ 0.021 0.008 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.031 0.011 -10000 0 -0.065 6 6
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.042 0.21 8 -0.19 12 20
RFC1 -0.022 0.035 0.17 2 -0.19 14 16
PRKDC -0.023 0.037 0.19 3 -0.19 14 17
RIPK1 0.03 0.013 -10000 0 -0.064 9 9
CASP7 -0.14 0.26 -10000 0 -0.59 131 131
FASLG/FAS/FADD/FAF1 -0.021 0.057 0.11 1 -0.12 122 123
MAP2K4 -0.059 0.11 0.19 1 -0.24 125 126
mol:ceramide -0.014 0.061 -10000 0 -0.16 18 18
GSN -0.019 0.043 0.21 8 -0.19 13 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.062 0.14 1 -0.12 126 127
FAS 0.013 0.031 -10000 0 -0.065 55 55
BID -0.031 0.014 0.2 1 -10000 0 1
MAP3K1 -0.1 0.18 -10000 0 -0.39 134 134
MAP3K7 0.031 0.008 -10000 0 -0.064 1 1
RB1 -0.021 0.034 0.17 2 -0.19 13 15
CFLAR 0.032 0.009 -10000 0 -0.063 5 5
HGF/MET 0.037 0.037 -10000 0 -0.05 23 23
ARHGDIB -0.019 0.045 0.21 10 -0.2 11 21
FADD 0.032 0.006 -10000 0 -0.064 1 1
actin filament polymerization 0.019 0.043 0.19 13 -0.21 8 21
NFKB1 0.014 0.073 -10000 0 -0.62 6 6
MAPK8 -0.065 0.11 0.17 1 -0.24 112 113
DFFA -0.02 0.038 0.2 4 -0.2 13 17
DNA fragmentation during apoptosis -0.021 0.036 0.19 3 -0.2 13 16
FAS/FADD/MET 0.026 0.04 -10000 0 -0.049 52 52
CFLAR/RIP1 0.045 0.017 -10000 0 -0.049 14 14
FAIM3 0.031 0.007 -10000 0 -0.065 1 1
FAF1 0.031 0.006 -10000 0 -10000 0 0
PARP1 -0.023 0.037 0.22 2 -0.19 15 17
DFFB -0.021 0.036 0.19 3 -0.2 13 16
CHUK 0.005 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.034 -10000 0 -0.052 56 56
HGF 0.022 0.016 -10000 0 -0.065 1 1
LMNA -0.028 0.034 0.19 2 -0.18 13 15
CASP6 -0.023 0.033 0.17 2 -0.19 12 14
CASP10 0.032 0.001 -10000 0 -10000 0 0
CASP3 -0.016 0.034 0.16 1 -0.22 9 10
PTPN13 0.027 0.022 -10000 0 -0.065 26 26
CASP8 -0.03 0.007 0.053 1 -0.06 3 4
IL6 -0.026 0.092 -10000 0 -0.52 7 7
MET 0.022 0.016 -10000 0 -0.065 2 2
ICAD/CAD -0.026 0.04 0.25 4 -0.19 13 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.014 0.061 -10000 0 -0.17 18 18
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.02 0.041 0.21 7 -0.19 12 19
BCL2 0.031 0.006 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.004 0.078 0.15 3 -0.17 34 37
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.036 27 27
BIRC3 -0.033 0.021 0.17 3 -10000 0 3
CYCS 0.005 0.068 0.17 63 -0.12 3 66
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
CD247 0.033 0.008 -10000 0 -0.065 2 2
MAP2K7 -0.007 0.087 -10000 0 -0.42 6 6
protein ubiquitination 0.002 0.05 0.2 7 -0.24 8 15
CRADD 0.032 0.004 -10000 0 -10000 0 0
DAXX 0.032 0.005 -10000 0 -0.065 1 1
FAS 0.013 0.031 -10000 0 -0.065 55 55
BID -0.018 0.044 0.16 3 -0.1 94 97
NF-kappa-B/RelA/I kappa B alpha 0.054 0.042 -10000 0 -0.06 41 41
TRADD 0.032 0.004 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
CFLAR 0.032 0.01 -10000 0 -0.065 5 5
FADD 0.032 0.006 -10000 0 -0.065 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.042 -10000 0 -0.06 41 41
MAPK8 -0.005 0.081 -10000 0 -0.39 7 7
APAF1 0.032 0.004 -10000 0 -10000 0 0
TRAF1 0.031 0.008 -10000 0 -0.065 1 1
TRAF2 0.031 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.025 0.15 4 -0.13 6 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.051 -10000 0 -0.25 8 8
CHUK 0.003 0.05 0.2 7 -0.25 7 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.071 -10000 0 -0.073 4 4
TCRz/NEF 0.028 0.006 -10000 0 -0.04 2 2
TNF 0.032 0.007 -10000 0 -0.065 2 2
FASLG -0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.038 32 32
TNFR1A/BAG4/TNF-alpha 0.025 0.053 -10000 0 -0.049 163 163
CASP6 0.008 0.085 -10000 0 -0.44 5 5
CASP7 -0.059 0.11 0.18 5 -0.24 129 134
RELA 0.029 0.016 -10000 0 -0.034 30 30
CASP2 0.022 0.015 -10000 0 -10000 0 0
CASP3 -0.029 0.071 0.2 3 -0.26 19 22
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 162 162
CASP8 0.031 0.013 -10000 0 -0.065 10 10
CASP9 0.031 0.009 -10000 0 -0.065 3 3
MAP3K14 0.01 0.053 0.18 1 -0.25 10 11
APAF-1/Caspase 9 -0.015 0.071 0.13 68 -0.16 5 73
BCL2 -0.016 0.082 0.24 2 -0.38 6 8
Effects of Botulinum toxin

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
STX1A 0 0.002 0 498 -10000 0 498
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.043 0.015 -10000 0 -10000 0 0
STXBP1 0.003 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 0.034 0.027 0.081 29 -0.052 7 36
RAB3GAP2/RIMS1/UNC13B 0.056 0.025 -10000 0 -0.044 6 6
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 0.031 0.006 -10000 0 -10000 0 0
mol:ACh 0.019 0.035 0.066 150 -0.058 7 157
RAB3GAP2 0.032 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.001 0.01 0.14 1 -10000 0 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.034 0.027 0.081 29 -0.052 7 36
UNC13B 0.03 0.009 -10000 0 -10000 0 0
CHRNA1 0.032 0.008 -10000 0 -0.065 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.01 0.074 4 -10000 0 4
SNAP25 0 0.001 -10000 0 -10000 0 0
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.002 0.007 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.004 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.01 0.14 1 -10000 0 1
Arf6 trafficking events

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
SLC2A4 0.032 0.005 -10000 0 -10000 0 0
CLTC 0.009 0.088 -10000 0 -0.34 28 28
calcium ion-dependent exocytosis 0.022 0.045 0.091 112 -0.13 15 127
Dynamin 2/GTP 0.022 0.012 -10000 0 -0.023 27 27
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.007 0.074 -10000 0 -0.29 27 27
CPE -0.015 0.006 0 80 -10000 0 80
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
membrane fusion 0.026 0.044 0.093 130 -0.1 13 143
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.013 0.055 0.13 10 -0.17 28 38
TSHR -0.017 0.005 -10000 0 -0.04 4 4
INS 0.004 0.095 -10000 0 -0.46 19 19
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.026 0.044 0.093 130 -0.1 13 143
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.002 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.012 -10000 0 -0.023 27 27
JUP 0.006 0.072 -10000 0 -0.28 26 26
ASAP2/amphiphysin II 0.035 0.018 -10000 0 -0.023 26 26
ARF6/GTP 0.023 0.005 -10000 0 0 28 28
CDH1 0.007 0.071 -10000 0 -0.28 26 26
clathrin-independent pinocytosis 0.023 0.005 -10000 0 0 28 28
MAPK8IP3 0.032 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.005 -10000 0 0 28 28
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.003 0.04 -10000 0 -0.13 33 33
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.005 -10000 0 -0.065 1 1
regulation of calcium-dependent cell-cell adhesion -0.033 0.075 0.27 27 -10000 0 27
positive regulation of phagocytosis -0.015 0.006 0 62 -10000 0 62
ARF6/GTP/JIP3 0.041 0.011 -10000 0 -10000 0 0
ACAP1 0.027 0.042 0.091 130 -0.091 13 143
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.065 -10000 0 -0.29 21 21
clathrin heavy chain/ACAP1 0.018 0.077 0.16 16 -0.25 27 43
JIP4/KLC1 0.041 0.033 -10000 0 -0.034 25 25
EXOC1 0.03 0.009 -10000 0 -0.065 1 1
exocyst 0.003 0.04 -10000 0 -0.13 33 33
RALA/GTP 0.015 0.014 -10000 0 -0.003 169 169
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.04 1 1
receptor recycling 0.023 0.005 -10000 0 0 28 28
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.008 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.088 0.18 1 -0.33 28 29
IL2RA -0.002 0.079 -10000 0 -0.33 25 25
VAMP3 -0.016 0.006 0 62 -10000 0 62
GLUT4/clathrin heavy chain/ACAP1 0.035 0.074 -10000 0 -0.25 27 27
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.012 -10000 0 -0.052 14 14
PLD2 0.006 0.011 -10000 0 -0.054 11 11
EXOC5 0.028 0.018 -10000 0 -0.065 15 15
PIP5K1C 0.012 0.051 0.12 5 -0.17 26 31
SDC1 0.004 0.074 -10000 0 -0.29 27 27
ARF6/GDP 0.023 0.005 -10000 0 0 28 28
EXOC7 0.032 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.035 0.078 -10000 0 -0.28 27 27
mol:Phosphatidic acid 0.026 0.044 0.093 130 -0.1 13 143
endocytosis -0.034 0.017 0.023 26 -10000 0 26
SCAMP2 0.032 0.005 -10000 0 -10000 0 0
ADRB2 0.004 0.084 0.22 2 -0.32 28 30
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.011 -10000 0 -0.023 27 27
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.005 0.085 0.2 5 -0.32 28 33
RALA 0.02 0.02 -10000 0 -0.065 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.075 0.22 2 -0.28 27 29
IL1-mediated signaling events

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
UBC13/UEV1A 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.054 -10000 0 -0.18 29 29
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.031 4 4
IKBKB 0.032 0.003 -10000 0 0 5 5
IKBKG 0.032 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.027 -10000 0 -0.051 40 40
IL1A 0.032 0.008 -10000 0 -0.065 3 3
IL1B -0.032 0.015 -10000 0 -0.052 172 172
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.025 0.17 4 -10000 0 4
IL1R2 0.025 0.025 -10000 0 -0.065 37 37
IL1R1 0.032 0.008 -10000 0 -0.065 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.01 0.047 -10000 0 -0.17 22 22
TOLLIP 0.031 0.006 -10000 0 0 20 20
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.005 -10000 0 -0.032 1 1
IKK complex/ELKS -0.025 0.095 -10000 0 -0.19 118 118
JUN -0.025 0.022 0.14 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.018 0.068 0.18 2 -0.093 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.057 -10000 0 -0.071 11 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.056 0.066 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.008 0.05 -10000 0 -0.054 194 194
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.022 0.023 0.16 5 -10000 0 5
IRAK1 -0.017 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.048 0.008 -10000 0 -0.051 3 3
IRAK4 0.031 0.007 -10000 0 -0.065 1 1
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.047 0.13 1 -0.18 22 23
CHUK 0.024 0.015 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.008 0.05 -10000 0 -0.054 194 194
IL1 beta/IL1R2 0.004 0.044 -10000 0 -0.052 193 193
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.023 0.16 4 -10000 0 4
NF kappa B1 p50/RelA 0.006 0.065 -10000 0 -0.099 8 8
IRAK3 0.031 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.014 0.058 0.16 2 -0.071 33 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.041 -10000 0 -0.12 37 37
IL1 alpha/IL1R1/IL1RAP 0.053 0.035 -10000 0 -0.05 46 46
RELA 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
MYD88 0.019 0.033 -10000 0 -0.065 66 66
IRAK/TRAF6/MEKK3 0.05 0.018 0.18 4 -10000 0 4
IL1RAP 0.024 0.027 -10000 0 -0.046 57 57
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.052 0.016 0.035 1 -0.094 4 5
CASP1 0 0.045 -10000 0 -0.065 167 167
IL1RN/IL1R2 0.041 0.026 -10000 0 -0.051 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.01 0.064 0.17 2 -0.076 67 69
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.048 -10000 0 -0.22 12 12
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL1RN 0.032 0.001 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.02 -10000 0 -0.035 5 5
MAP2K6 -0.023 0.025 0.17 8 -10000 0 8
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.026 0.076 3 -0.094 25 28
MKNK1 0.032 0.005 -10000 0 -10000 0 0
MAPK14 0.032 0.024 0.093 3 -0.067 26 29
ATF2/c-Jun 0.004 0.041 -10000 0 -0.11 51 51
MAPK11 0.029 0.025 0.091 2 -0.067 25 27
MITF 0.016 0.017 0.082 4 -0.043 28 32
MAPKAPK5 0.016 0.016 0.082 3 -0.044 26 29
KRT8 0.013 0.021 0.082 3 -0.045 45 48
MAPKAPK3 0.031 0.007 -10000 0 -0.065 1 1
MAPKAPK2 0.032 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.033 -10000 0 -0.083 26 26
CEBPB 0.014 0.019 0.073 2 -0.05 30 32
SLC9A1 0.016 0.016 0.1 1 -0.044 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.019 0.1 8 -0.046 25 33
p38alpha-beta/MNK1 0.053 0.036 -10000 0 -0.071 25 25
JUN -0.001 0.039 -10000 0 -0.11 51 51
PPARGC1A 0.016 0.017 0.082 4 -0.045 28 32
USF1 0.012 0.015 0.077 4 -0.045 26 30
RAB5/GDP/GDI1 0.013 0.048 -10000 0 -0.12 49 49
NOS2 0.012 0.015 0.077 4 -0.045 26 30
DDIT3 0.014 0.018 0.083 2 -0.046 28 30
RAB5A 0.032 0.004 -10000 0 -10000 0 0
HSPB1 0.06 0.12 0.27 123 -10000 0 123
p38alpha-beta/HBP1 0.038 0.04 -10000 0 -0.071 20 20
CREB1 0.004 0.057 -10000 0 -0.2 36 36
RAB5/GDP 0.024 0.003 -10000 0 -10000 0 0
EIF4E -0.031 0.027 0.22 5 -10000 0 5
RPS6KA4 0.016 0.017 0.082 4 -0.044 26 30
PLA2G4A -0.037 0.024 0.21 3 -10000 0 3
GDI1 0.016 0.015 0.082 4 -0.044 17 21
TP53 -0.015 0.017 0.062 5 -0.072 25 30
RPS6KA5 0.016 0.017 0.082 4 -0.044 26 30
ESR1 0.016 0.017 0.082 4 -0.044 25 29
HBP1 0.022 0.015 -10000 0 -10000 0 0
MEF2C 0.014 0.015 0.073 2 -0.044 17 19
MEF2A 0.016 0.017 0.082 4 -0.044 26 30
EIF4EBP1 -0.009 0.058 -10000 0 -0.21 35 35
KRT19 0.014 0.021 0.082 4 -0.044 45 49
ELK4 0.016 0.016 0.076 3 -0.044 25 28
ATF6 0.016 0.016 0.076 3 -0.044 25 28
ATF1 0.001 0.058 -10000 0 -0.19 38 38
p38alpha-beta/MAPKAPK2 0.053 0.036 -10000 0 -0.07 24 24
p38alpha-beta/MAPKAPK3 0.052 0.037 -10000 0 -0.07 26 26
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.011 -10000 0 -0.021 9 9
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 + 0.013 0.04 -10000 0 -0.04 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.032 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.032 0.004 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.024 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.032 0.18 10 -10000 0 10
Cone PDE6 0.044 0.05 -10000 0 -10000 0 0
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.014 0.051 -10000 0 -0.042 229 229
GNAT2/GDP 0.053 0.018 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.032 0.18 12 -10000 0 12
Cone Transducin 0.039 0.012 -10000 0 -0.023 9 9
SLC24A2 0.027 0.013 -10000 0 0 93 93
GNB3/GNGT2 0.023 0.005 -10000 0 -10000 0 0
GNB3 0.031 0.007 -10000 0 -10000 0 0
GNAT2/GTP 0.024 0.003 -10000 0 -10000 0 0
CNGA3 -0.002 0.046 -10000 0 -0.065 179 179
ARR3 0.032 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.013 0.04 -10000 0 -0.04 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.064 -10000 0 -0.065 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.013 -10000 0 0 93 93
RGS9 0.032 0.004 -10000 0 -10000 0 0
PDE6C 0.024 0.014 -10000 0 -10000 0 0
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.007 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.061 0.047 -10000 0 -0.058 1 1
MAP4K1 0.031 0.008 -10000 0 -0.065 1 1
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
MAP3K1 0.001 0.034 0.076 13 -0.11 28 41
JUN -0.12 0.23 0.23 2 -0.52 121 123
MAP3K7 0.001 0.033 0.076 13 -0.12 24 37
GRAP2 0.03 0.008 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
MAP2K4 -0.02 0.063 0.15 4 -0.22 32 36
LAT 0.032 0.005 -10000 0 -0.065 1 1
LCP2 0.026 0.023 -10000 0 -0.065 29 29
MAPK8 -0.12 0.24 -10000 0 -0.55 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.035 0.087 13 -0.14 16 29
LAT/GRAP2/SLP76/HPK1/HIP-55 0.057 0.044 -10000 0 -0.054 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.013 0.052 -10000 0 -0.35 10 10
Crk/p130 Cas/Paxillin -0.036 0.08 -10000 0 -0.18 116 116
JUN -0.012 0.029 0.075 5 -0.18 7 12
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.043 0.049 -10000 0 -0.058 1 1
RAP1A 0.032 0.004 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.048 0.057 -10000 0 -0.058 1 1
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.037 0.042 -10000 0 -0.041 9 9
RHOA 0.032 0.006 -10000 0 -10000 0 0
RAP1A/GTP 0.044 0.056 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
RET51/GFRalpha1/GDNF 0.048 0.056 -10000 0 -0.058 1 1
MAPKKK cascade -0.005 0.076 -10000 0 -0.13 125 125
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.037 0.042 -10000 0 -0.032 137 137
lamellipodium assembly -0.012 0.06 -10000 0 -0.17 48 48
RET51/GFRalpha1/GDNF/SHC 0.039 0.061 -10000 0 -0.061 7 7
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RET9/GFRalpha1/GDNF/SHC 0.029 0.045 -10000 0 -0.034 164 164
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.023 136 136
MAPK3 -0.038 0.03 0.17 9 -10000 0 9
DOK1 0.032 0.001 -10000 0 -10000 0 0
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
neurite development -0.026 0.029 0.19 6 -10000 0 6
DOK5 0.028 0.011 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.065 1 1
MAPK8 0.001 0.03 -10000 0 -0.12 24 24
HRAS/GTP 0.02 0.096 -10000 0 -0.14 130 130
tube development 0.02 0.035 0.16 10 -10000 0 10
MAPK1 -0.034 0.031 0.19 6 -10000 0 6
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.055 -10000 0 -0.11 120 120
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
PDLIM7 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.047 0.05 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.05 52 52
RET51/GFRalpha1/GDNF/Dok4 0.048 0.058 -10000 0 -0.055 7 7
RET51/GFRalpha1/GDNF/Dok5 0.047 0.053 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
CREB1 -0.035 0.095 -10000 0 -0.2 124 124
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.055 -10000 0 -0.11 123 123
RET51/GFRalpha1/GDNF/Grb7 0.048 0.057 -10000 0 -0.062 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.014 -10000 0 -0.065 1 1
DOK4 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.012 0.029 -10000 0 -0.18 7 7
RET9/GFRalpha1/GDNF/FRS2 0.036 0.041 -10000 0 -0.039 5 5
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.015 0.052 -10000 0 -0.1 124 124
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.095 -10000 0 -0.19 123 123
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.098 -10000 0 -0.19 135 135
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.033 -10000 0 -0.12 25 25
PI3K -0.042 0.11 -10000 0 -0.22 121 121
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.038 -10000 0 -0.037 4 4
GRB10 0.022 0.017 -10000 0 -0.065 4 4
activation of MAPKK activity -0.013 0.068 0.1 7 -0.15 101 108
RET51/GFRalpha1/GDNF/FRS2 0.047 0.056 -10000 0 -0.058 1 1
GAB1 0.031 0.008 -10000 0 -0.065 3 3
IRS1 0.032 0.009 -10000 0 -0.065 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.036 -10000 0 -0.12 27 27
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.057 -10000 0 -0.058 1 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GDNF 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.048 0.058 -10000 0 -0.061 4 4
Rac1/GTP -0.012 0.07 -10000 0 -0.2 48 48
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.04 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.051 1 1
S1P5 pathway

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.04 0.13 32 -10000 0 32
GNAI2 0.032 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 0 152 152
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.04 -10000 0 -0.13 32 32
negative regulation of cAMP metabolic process 0.002 0.012 0.082 6 -0.11 2 8
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNA12 0.023 0.015 -10000 0 0 152 152
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.012 0.083 6 -0.11 2 8
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
TCGA08_rtk_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
PDGFRA 0.026 0.016 -10000 0 -0.065 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
AKT 0.12 0.093 0.22 195 -0.14 1 196
FOXO3 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
AKT3 0.031 0.006 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.065 2 2
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PIK3CB 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.06 134 134
PIK3CG 0.022 0.015 -10000 0 -10000 0 0
PIK3R3 0.032 0.006 -10000 0 -0.065 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.032 0.003 -10000 0 -10000 0 0
RAS 0.006 0.024 -10000 0 -0.084 9 9
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.044 0.071 0.3 9 -0.21 16 25
PI3K 0.049 0.073 0.17 94 -10000 0 94
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
FOXO 0.13 0.083 0.22 174 -10000 0 174
AKT2 0.031 0.006 -10000 0 0 18 18
PTEN 0.023 0.016 -10000 0 -0.065 2 2
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.032 0.007 -10000 0 -0.065 1 1
LAT2 -0.014 0.03 0.12 4 -0.13 6 10
AP1 -0.031 0.11 0.22 1 -0.29 30 31
mol:PIP3 0.026 0.097 0.25 38 -0.18 1 39
IKBKB 0.016 0.072 0.2 35 -0.14 1 36
AKT1 -0.032 0.075 0.27 13 -10000 0 13
IKBKG 0.016 0.07 0.19 35 -0.14 1 36
MS4A2 0.035 0.005 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
MAP3K1 -0.01 0.059 0.18 21 -0.2 6 27
mol:Ca2+ 0.025 0.086 0.22 41 -0.14 1 42
LYN 0.02 0.033 -10000 0 -0.066 62 62
CBLB -0.015 0.036 0.14 7 -0.13 8 15
SHC1 0.024 0.026 -10000 0 -0.05 52 52
RasGAP/p62DOK 0.056 0.024 -10000 0 -0.042 21 21
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.058 0.29 11 -10000 0 11
PTPN13 0.005 0.073 -10000 0 -0.57 5 5
PTPN11 0.032 0.01 -10000 0 -0.029 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.07 0.29 8 -0.28 5 13
SYK 0.024 0.026 -10000 0 -0.066 36 36
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.013 0.067 0.18 19 -0.16 5 24
LAT -0.015 0.037 0.14 7 -0.13 8 15
PAK2 -0.006 0.06 0.17 29 -0.2 7 36
NFATC2 -0.013 0.005 -10000 0 -10000 0 0
HRAS -0.002 0.056 0.17 22 -0.2 8 30
GAB2 0.032 0.006 -10000 0 -10000 0 0
PLA2G1B 0.022 0.064 -10000 0 -0.81 2 2
Fc epsilon R1 0.009 0.059 -10000 0 -0.051 235 235
Antigen/IgE/Fc epsilon R1 0.01 0.055 -10000 0 -0.046 233 233
mol:GDP 0.004 0.052 0.18 17 -0.19 1 18
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.007 0.036 0.12 3 -0.12 6 9
CHUK 0.006 0.062 0.18 31 -0.14 1 32
KLRG1 -0.012 0.027 0.082 3 -0.096 3 6
VAV1 -0.015 0.037 0.12 9 -0.13 8 17
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.036 0.14 7 -0.13 6 13
negative regulation of mast cell degranulation -0.013 0.027 0.076 2 -0.11 3 5
BTK 0.007 0.041 0.18 3 -10000 0 3
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.008 0.029 -10000 0 -0.1 8 8
GAB2/PI3K/SHP2 -0.052 0.024 0.025 2 -10000 0 2
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.031 -10000 0 -0.085 32 32
RAF1 0.025 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.066 -10000 0 -0.067 96 96
FCER1G -0.015 0.05 -10000 0 -0.067 241 241
FCER1A 0.03 0.015 -10000 0 -0.062 12 12
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.062 -10000 0 -0.07 6 6
MAPK3 0.024 0.063 -10000 0 -0.82 2 2
MAPK1 0.014 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.1 0.25 -10000 0 -0.52 124 124
DUSP1 0.029 0.017 -10000 0 -0.065 16 16
NF-kappa-B/RelA 0.007 0.052 0.13 31 -0.099 1 32
actin cytoskeleton reorganization 0.012 0.075 -10000 0 -0.59 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.067 0.2 17 -0.18 7 24
FER -0.014 0.037 0.14 7 -0.13 7 14
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.025 -10000 0 -0.23 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.073 0.23 27 -0.19 1 28
cytokine secretion 0.001 0.033 0.072 28 -0.068 2 30
SPHK1 -0.016 0.036 0.13 6 -0.13 8 14
PTK2 0.011 0.078 -10000 0 -0.62 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.02 0.08 0.22 24 -0.16 5 29
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.02 0.089 0.24 34 -0.24 2 36
MAP2K2 0.021 0.071 -10000 0 -0.84 2 2
MAP2K1 0.016 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.045 0.2 11 -0.1 1 12
MAP2K4 0 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.006 0.071 -10000 0 -0.073 96 96
mol:Choline -0.031 0.057 0.29 11 -10000 0 11
SHC/Grb2/SOS1 0.009 0.058 0.17 4 -0.13 4 8
FYN 0.029 0.011 -10000 0 -0.065 1 1
DOK1 0.032 0.001 -10000 0 -10000 0 0
PXN 0.007 0.076 0.33 3 -0.57 5 8
HCLS1 -0.018 0.04 0.14 7 -0.13 9 16
PRKCB 0.021 0.081 0.21 39 -0.18 1 40
FCGR2B 0.009 0.041 -10000 0 -0.065 120 120
IGHE -0.001 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.013 0.028 0.077 2 -0.11 3 5
LCP2 0.027 0.023 -10000 0 -0.065 29 29
PLA2G4A -0.02 0.038 0.14 7 -0.14 8 15
RASA1 0.031 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.031 0.057 0.29 11 -10000 0 11
IKK complex 0.008 0.063 0.19 26 -10000 0 26
WIPF1 0.03 0.014 -10000 0 -0.065 11 11
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.004 0.043 -10000 0 -0.084 113 113
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.065 5 5
alpha4/beta7 Integrin/MAdCAM1 0.074 0.03 -10000 0 -0.071 2 2
EPO 0.022 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.062 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.022 -10000 0 -0.051 4 4
EPO/EPOR (dimer) 0.033 0.023 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.082 -10000 0 -0.3 29 29
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.039 0.023 -10000 0 -0.051 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
JAK2 0.009 0.028 -10000 0 -0.091 30 30
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
MADCAM1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0.071 0.03 -10000 0 -0.07 2 2
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.042 0.02 0.17 2 -10000 0 2
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.017 0.05 -10000 0 -0.051 335 335
p130Cas/Crk/Dock1 -0.048 0.024 0.18 3 -10000 0 3
VCAM1 -0.032 0.046 -10000 0 -0.065 333 333
RHOA 0.032 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.052 -10000 0 -0.058 1 1
BCAR1 -0.038 0.02 0.16 3 -10000 0 3
EPOR 0.031 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.084 -10000 0 -0.31 29 29
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.045 0.03 -10000 0 -0.037 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.088 0.13 -10000 0 -0.38 59 59
AKT1 -0.03 0.17 -10000 0 -0.71 30 30
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.026 0.18 -10000 0 -0.72 30 30
mol:Ca2+ -0.004 0.045 0.17 18 -0.23 9 27
IGF1R 0.032 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.041 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.05 52 52
apoptosis 0.028 0.17 0.68 30 -10000 0 30
RhoA/GTP -0.039 0.014 -10000 0 -0.077 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.07 0.11 0.18 9 -0.29 60 69
regulation of stress fiber formation 0.045 0.044 -10000 0 -0.26 2 2
E2/ERA-ERB (dimer) 0.039 0.013 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
G13/GTP 0.037 0.016 -10000 0 -0.025 31 31
pseudopodium formation -0.045 0.044 0.26 2 -10000 0 2
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.054 0.13 0.2 1 -0.46 36 37
E2/ER beta (dimer) 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.004 0.057 0.13 5 -0.17 44 49
mol:NADP -0.054 0.13 0.2 1 -0.46 36 37
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.01 0.032 -10000 0 -0.24 9 9
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
PLCB1 0.009 0.015 -10000 0 -0.23 1 1
PLCB2 0.009 0.015 -10000 0 -0.23 1 1
IGF1 0.031 0.009 -10000 0 -0.065 4 4
mol:L-citrulline -0.054 0.13 0.2 1 -0.46 36 37
RHOA 0.032 0.006 -10000 0 -10000 0 0
Gai/GDP -0.43 0.16 -10000 0 -0.48 455 455
JNK cascade 0.022 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.03 0.008 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 0.031 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.015 0.071 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.071 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.069 0.12 0.2 10 -0.3 59 69
GNAZ 0.027 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.023 0.006 -10000 0 -10000 0 0
STRN 0.032 0.001 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
HBEGF -0.11 0.13 0.24 15 -0.34 61 76
cAMP biosynthetic process 0.031 0.021 -10000 0 -0.029 53 53
SRC -0.096 0.12 0.2 1 -0.35 60 61
PI3K 0.039 0.023 -10000 0 -0.051 16 16
GNB1 0.031 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.059 -10000 0 -0.15 45 45
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.077 0.09 -10000 0 -0.25 67 67
Gs family/GTP 0.039 0.024 -10000 0 -0.034 17 17
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.047 -10000 0 -0.044 119 119
vasodilation -0.052 0.13 0.2 1 -0.44 36 37
mol:DAG -0.01 0.032 -10000 0 -0.24 9 9
Gs family/GDP/Gbeta gamma -0.004 0.056 -10000 0 -0.16 45 45
MSN -0.051 0.039 0.27 2 -10000 0 2
Gq family/GTP 0.023 0.019 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.025 0.17 -10000 0 -0.7 30 30
NRAS 0.008 0.042 -10000 0 -0.06 134 134
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.13 0.44 36 -0.2 1 37
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.062 0.14 5 -0.17 45 50
NOS3 -0.057 0.14 0.2 1 -0.48 36 37
GNA11 0.031 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.035 0.13 -10000 0 -0.49 34 34
E2/ER alpha (dimer)/PELP1/Src -0.069 0.12 0.21 10 -0.31 58 68
ruffle organization -0.045 0.044 0.26 2 -10000 0 2
ROCK2 -0.032 0.052 0.31 2 -10000 0 2
GNA14 0.031 0.009 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA13 0.032 0.007 -10000 0 -0.065 2 2
MMP9 -0.11 0.11 0.37 1 -0.35 58 59
MMP2 -0.11 0.11 0.19 1 -0.36 58 59
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.007 0.048 -10000 0 -0.052 259 259
alphaV beta3 Integrin 0.06 0.023 -10000 0 -0.049 17 17
PTK2 -0.011 0.063 0.27 7 -0.26 6 13
IGF1R 0.032 0.004 -10000 0 -10000 0 0
PI4KB 0.032 0.005 -10000 0 -10000 0 0
MFGE8 0.032 0.007 -10000 0 -0.065 2 2
SRC 0.03 0.008 -10000 0 -10000 0 0
CDKN1B 0.013 0.051 -10000 0 -0.26 17 17
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0 0.041 -10000 0 -0.25 13 13
PTK2B -0.03 0.058 0.16 39 -10000 0 39
alphaV/beta3 Integrin/JAM-A 0.054 0.041 0.17 6 -10000 0 6
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.06 0.022 -10000 0 -0.049 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.079 0.023 -10000 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.044 -10000 0 -0.16 23 23
alphaV/beta3 Integrin/Syndecan-1 0.051 0.037 -10000 0 -0.051 55 55
PI4KA 0.012 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.042 0.06 -10000 0 -0.096 2 2
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
alphaV/beta3 Integrin/Osteopontin 0.023 0.055 -10000 0 -0.05 178 178
RPS6KB1 -0.049 0.03 -10000 0 -10000 0 0
TLN1 0.021 0.028 -10000 0 -0.065 43 43
MAPK3 0 0.039 -10000 0 -0.28 8 8
GPR124 0.032 0.007 -10000 0 -0.065 2 2
MAPK1 -0.001 0.039 -10000 0 -0.28 8 8
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.062 0.021 -10000 0 -0.049 15 15
cell adhesion 0.047 0.03 -10000 0 -0.081 4 4
ANGPTL3 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.002 0.054 -10000 0 -0.05 237 237
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
TGFBR2 0.031 0.011 -10000 0 -0.065 6 6
ITGB3 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.06 0.023 -10000 0 -0.049 18 18
apoptosis 0.029 0.017 -10000 0 -0.064 15 15
CD47 0.031 0.008 -10000 0 -0.065 2 2
alphaV/beta3 Integrin/CD47 0.06 0.024 -10000 0 -0.049 17 17
VCL 0.025 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.061 0.022 -10000 0 -0.049 15 15
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.009 0.013 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.022 0.031 -10000 0 -0.1 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.005 0.064 -10000 0 -0.07 20 20
FAK1/Vinculin -0.005 0.057 0.26 7 -0.23 6 13
alphaV beta3/Integrin/ppsTEM5 0.06 0.023 -10000 0 -0.049 18 18
RHOA 0.032 0.006 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -0.065 2 2
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.065 2 2
F11R -0.024 0.008 -10000 0 -0.051 33 33
alphaV/beta3 Integrin/Lactadherin 0.06 0.023 -10000 0 -0.049 17 17
alphaV/beta3 Integrin/TGFBR2 0.059 0.026 -10000 0 -0.049 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.023 -10000 0 -0.043 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.04 -10000 0 -0.045 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.038 -10000 0 -0.065 96 96
alphaV/beta3 Integrin/Pyk2 0.001 0.067 0.17 34 -0.073 18 52
SDC1 0.023 0.028 -10000 0 -0.065 45 45
VAV3 -0.028 0.022 0.18 5 -10000 0 5
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.065 4 4
FAK1/Paxillin -0.003 0.063 0.25 8 -0.22 6 14
cell migration -0.015 0.052 0.25 7 -0.21 6 13
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
PI3K 0.061 0.049 0.16 5 -10000 0 5
SPP1 -0.002 0.046 -10000 0 -0.065 175 175
KDR 0.027 0.018 -10000 0 -0.065 14 14
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.017 -10000 0 -0.065 15 15
COL4A3 0.033 0 -10000 0 -10000 0 0
angiogenesis 0.002 0.044 0.18 3 -0.31 8 11
Rac1/GTP -0.022 0.024 0.18 4 -10000 0 4
EDIL3 0.032 0.004 -10000 0 -10000 0 0
cell proliferation 0.058 0.025 -10000 0 -0.049 21 21
S1P3 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
PDGFRB 0.032 0.007 -9999 0 -0.065 2 2
mol:S1P 0 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.018 0.027 -9999 0 -0.078 31 31
GNAO1 0.003 0.009 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.03 0.02 -9999 0 -0.023 2 2
AKT1 -0.008 0.069 -9999 0 -0.43 13 13
AKT3 -0.008 0.046 -9999 0 -0.24 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -9999 0 -0.065 2 2
GNAI2 0.032 0.006 -9999 0 -0.028 1 1
GNAI3 0.021 0.031 -9999 0 -0.064 59 59
GNAI1 0.02 0.017 -9999 0 -0.064 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0 -9999 0 -0.009 1 1
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.013 -9999 0 -0.12 1 1
MAPK3 0.001 0.013 -9999 0 -0.14 2 2
MAPK1 0.001 0.01 -9999 0 -10000 0 0
JAK2 -0.005 0.031 -9999 0 -0.16 14 14
CXCR4 0 0.009 -9999 0 -0.12 1 1
FLT1 0.031 0.009 -9999 0 -0.028 1 1
RhoA/GDP 0.023 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.017 0.011 -9999 0 0 153 153
SRC 0.001 0.013 -9999 0 -0.14 2 2
S1P/S1P3/Gi 0.002 0.013 -9999 0 -0.12 1 1
RAC1 0.023 0.015 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.04 -9999 0 -0.13 24 24
VEGFA -0.02 0.048 -9999 0 -0.064 276 276
S1P/S1P2/Gi 0.002 0.013 -9999 0 -0.11 2 2
VEGFR1 homodimer/VEGFA homodimer -0.004 0.048 -9999 0 -0.05 255 255
RHOA 0.032 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.017 0.009 -9999 0 -0.1 1 1
GNAQ 0.031 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.013 -9999 0 -10000 0 0
G12/G13 0.034 0.022 -9999 0 -10000 0 0
GNA14 0.031 0.009 -9999 0 -0.065 2 2
GNA15 0.03 0.013 -9999 0 -0.065 7 7
GNA12 0.023 0.015 -9999 0 0 152 152
GNA13 0.032 0.007 -9999 0 -0.065 2 2
GNA11 0.031 0.006 -9999 0 -10000 0 0
Rac1/GTP -0.027 0.036 -9999 0 -0.13 17 17
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.022 0.019 -10000 0 -0.026 53 53
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.061 -10000 0 -0.089 5 5
AKT1 0.031 0.008 -10000 0 -10000 0 0
GSC 0.007 0.027 0.091 25 -10000 0 25
NKX2-5 0.036 0.012 0.089 9 -10000 0 9
muscle cell differentiation -0.013 0.07 0.25 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.016 0.077 0.2 1 -0.12 5 6
SMAD4 -0.008 0.051 0.11 2 -0.084 98 100
CBFB 0.031 0.009 -10000 0 -0.065 4 4
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.05 0.031 -10000 0 -0.049 34 34
SMAD3/SMAD4/VDR 0.041 0.076 -10000 0 -10000 0 0
MYC 0.008 0.041 -10000 0 -0.066 119 119
CDKN2B -0.21 0.19 -10000 0 -0.36 285 285
AP1 -0.003 0.048 0.15 5 -0.087 12 17
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.071 -10000 0 -0.22 31 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.061 0.16 2 -0.25 22 24
SP3 0.017 0.035 -10000 0 -0.062 81 81
CREB1 0.033 0 -10000 0 -10000 0 0
FOXH1 0.035 0.011 0.1 5 -10000 0 5
SMAD3/SMAD4/GR 0.032 0.06 -10000 0 -0.083 16 16
GATA3 0.025 0.015 -10000 0 -0.065 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.068 -10000 0 -0.2 33 33
MEF2C/TIF2 -0.034 0.039 0.22 8 -10000 0 8
endothelial cell migration 0.035 0.068 0.46 2 -10000 0 2
MAX 0.034 0.01 -10000 0 -10000 0 0
RBBP7 0.033 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.064 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.009 -10000 0 -0.065 3 3
RUNX1 0.032 0.005 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 0.035 0.006 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
CDKN1A -0.016 0.053 0.33 3 -10000 0 3
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.029 0.05 0.26 1 -0.066 7 8
DCP1A 0.032 0.006 -10000 0 -10000 0 0
SKI 0.031 0.007 -10000 0 -10000 0 0
SERPINE1 -0.033 0.068 -10000 0 -0.46 2 2
SMAD3/SMAD4/ATF2 0.024 0.061 -10000 0 -0.08 29 29
SMAD3/SMAD4/ATF3 0.008 0.065 -10000 0 -0.083 63 63
SAP30 0.032 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.052 0.023 -10000 0 -0.042 12 12
JUN -0.027 0.038 0.14 9 -10000 0 9
SMAD3/SMAD4/IRF7 0.024 0.064 -10000 0 -0.088 22 22
TFE3 -0.006 0.037 -10000 0 -0.044 187 187
COL1A2 -0.025 0.052 -10000 0 -0.11 32 32
mesenchymal cell differentiation -0.022 0.061 0.082 23 -10000 0 23
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.006 -10000 0 -10000 0 0
FOS 0.003 0.045 -10000 0 -0.064 143 143
SMAD3/SMAD4/Max 0.031 0.061 -10000 0 -0.084 18 18
Cbp/p300/SNIP1 0.057 0.022 -10000 0 -0.039 10 10
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.051 0.043 0.14 4 -0.13 10 14
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.059 -10000 0 -0.083 22 22
IRF7 0.029 0.016 -10000 0 -0.066 12 12
ESR1 0.037 0.014 0.13 3 -10000 0 3
HNF4A 0.03 0.009 -10000 0 -10000 0 0
MEF2C -0.03 0.04 0.2 10 -10000 0 10
SMAD2-3/SMAD4 0.026 0.061 0.18 1 -0.09 8 9
Cbp/p300/Src-1 0.053 0.024 -10000 0 -0.041 12 12
IGHV3OR16-13 0.006 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.029 0.012 -10000 0 -0.065 4 4
CREBBP 0.03 0.005 -10000 0 -0.026 2 2
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.02 0.032 -10000 0 -0.064 61 61
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
SNIP1 0.032 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.001 0.073 -10000 0 -0.092 85 85
MSG1/HSC70 0.043 0.022 -10000 0 -0.05 24 24
SMAD2 0.036 0.012 0.13 3 -10000 0 3
SMAD3 0.001 0.04 -10000 0 -0.067 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.042 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.01 0.039 0.12 9 -0.18 10 19
NCOR1 0.032 0.004 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
MYOD/E2A 0.046 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.081 0.21 1 -0.12 1 2
IFNB1 -0.021 0.034 0.14 9 -10000 0 9
SMAD3/SMAD4/MEF2C -0.009 0.054 0.2 3 -10000 0 3
CITED1 0.028 0.021 -10000 0 -0.065 24 24
SMAD2-3/SMAD4/ARC105 0.04 0.067 0.19 1 -0.092 3 4
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.051 0.19 1 -0.25 12 13
RUNX1-3/PEBPB2 0.06 0.021 -10000 0 -0.049 8 8
SMAD7 -0.024 0.065 -10000 0 -0.19 33 33
MYC/MIZ-1 0.022 0.042 -10000 0 -0.052 116 116
SMAD3/SMAD4 -0.045 0.066 -10000 0 -0.24 31 31
IL10 -0.032 0.04 0.16 13 -10000 0 13
PIASy/HDAC complex 0.033 0.007 -10000 0 -10000 0 0
PIAS3 0.031 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.021 -10000 0 -0.066 24 24
IL5 -0.033 0.039 0.16 12 -10000 0 12
CDK4 -0.022 0.045 -10000 0 -0.066 250 250
PIAS4 0.033 0.007 -10000 0 -10000 0 0
ATF3 0.012 0.039 -10000 0 -0.065 103 103
SMAD3/SMAD4/SP1 -0.004 0.07 -10000 0 -0.11 28 28
FOXG1 0.027 0.012 -10000 0 -10000 0 0
FOXO3 -0.019 0.007 -10000 0 -10000 0 0
FOXO1 -0.019 0.008 -10000 0 -10000 0 0
FOXO4 -0.02 0.005 -10000 0 -10000 0 0
heart looping -0.03 0.04 0.2 10 -10000 0 10
CEBPB 0.028 0.016 -10000 0 -0.064 11 11
SMAD3/SMAD4/DLX1 0.007 0.048 -10000 0 -0.07 31 31
MYOD1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.023 0.058 -10000 0 -0.083 19 19
SMAD3/SMAD4/GATA3 0.016 0.065 -10000 0 -0.09 22 22
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.051 0.071 -10000 0 -0.092 1 1
SMAD3/SMAD4/SP1-3 0.007 0.082 -10000 0 -0.12 21 21
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.004 0.037 -10000 0 -0.052 49 49
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.04 0.06 -10000 0 -10000 0 0
ITGB5 -0.044 0.051 0.23 9 -10000 0 9
TGIF/SIN3/HDAC complex/CtBP -0.02 0.06 -10000 0 -0.18 40 40
SMAD3/SMAD4/AR 0.023 0.061 -10000 0 -0.083 27 27
AR 0.031 0.012 -10000 0 -0.065 8 8
negative regulation of cell growth -0.004 0.048 -10000 0 -0.23 13 13
SMAD3/SMAD4/MYOD 0.023 0.061 -10000 0 -0.083 20 20
E2F5 0.032 0.004 -10000 0 -10000 0 0
E2F4 0.032 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.042 0.066 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.042 0.15 1 -0.22 9 10
TFDP1 0.029 0.016 -10000 0 -0.065 11 11
SMAD3/SMAD4/AP1 0.012 0.065 -10000 0 -0.087 14 14
SMAD3/SMAD4/RUNX2 0.023 0.061 -10000 0 -0.081 24 24
TGIF2 0.03 0.012 -10000 0 -0.065 4 4
TGIF1 -0.034 0.044 -10000 0 -0.065 342 342
ATF2 0.032 0.002 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.009 0.041 -10000 0 -0.065 116 116
SMAD2 -0.021 0.057 0.14 1 -0.21 27 28
SMAD3 0.013 0.042 0.1 31 -0.096 36 67
SMAD3/SMAD4 0.026 0.056 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.037 0.048 -10000 0 -0.049 108 108
SMAD2/SMAD2/SMAD4 0.017 0.083 -10000 0 -0.18 38 38
PPM1A 0.031 0.008 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.014 0.062 -10000 0 -0.18 39 39
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
TRAP-1/SMAD4 0.024 0.042 -10000 0 -0.051 116 116
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.065 3 3
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
KPNB1 0.032 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.032 0.002 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
NUP153 0.032 0.007 -10000 0 -0.065 2 2
KPNA2 0.03 0.015 -10000 0 -0.065 11 11
PIAS4 0.031 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.032 -10000 0 -0.059 61 61
AES 0.034 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.024 -10000 0 -0.051 4 4
SMAD4 0.009 0.041 -10000 0 -0.065 116 116
DKK2 0.03 0.013 -10000 0 -0.065 8 8
TLE1 0.034 0.008 -10000 0 -10000 0 0
MACF1 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.095 0.098 0.21 153 -0.28 6 159
WIF1 0.004 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.097 0.079 0.26 30 -0.31 3 33
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.005 0.037 -10000 0 -0.064 101 101
beta catenin/beta TrCP1 0.11 0.094 0.22 148 -0.27 6 154
FZD1 0.022 0.017 -10000 0 -0.065 4 4
AXIN2 -0.014 0.022 -10000 0 -0.16 1 1
AXIN1 0.034 0.004 -10000 0 0 5 5
RAN 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.045 0.085 -10000 0 -0.45 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.07 0.23 19 -0.25 5 24
Axin1/APC/GSK3 0.041 0.064 0.16 75 -0.21 6 81
Axin1/APC/GSK3/beta catenin/Macf1 0.066 0.094 0.2 125 -0.23 9 134
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.034 0.008 -10000 0 -10000 0 0
MYC -0.026 0.098 0.45 15 -10000 0 15
RANBP3 0.032 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.023 -10000 0 -0.045 12 12
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.034 0.009 -10000 0 -10000 0 0
TCF3 0.034 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.053 0.042 -10000 0 -0.056 2 2
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.035 0.05 0.22 1 -0.2 2 3
LEF1 0.034 0.01 -10000 0 -0.06 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.061 0.24 16 -0.22 2 18
DKK1/LRP6/Kremen 2 0.025 0.047 -10000 0 -0.048 105 105
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.008 -10000 0 -10000 0 0
NLK 0.031 0.004 -10000 0 -10000 0 0
CCND1 -0.034 0.056 0.37 3 -10000 0 3
WNT1 0.032 0.006 -10000 0 -10000 0 0
GSK3A 0.032 0.007 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.024 0.014 -10000 0 -10000 0 0
PPP2R5D 0.032 0.036 -10000 0 -0.25 4 4
APC 0.032 0.1 0.18 152 -10000 0 152
WNT1/LRP6/FZD1 0 0.026 -10000 0 -0.29 3 3
CREBBP 0.035 0.007 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.038 0.15 15 -0.17 9 24
adherens junction organization 0.007 0.041 0.13 7 -0.15 20 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.07 0.16 128 -0.15 5 133
FMN1 0.013 0.038 0.13 7 -0.14 16 23
mol:IP3 0.004 0.025 0.086 1 -0.13 10 11
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.018 0.04 0.14 7 -0.15 16 23
CTNNB1 0.032 0.006 -10000 0 -10000 0 0
AKT1 0.012 0.035 0.1 30 -0.14 8 38
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.06 0.17 3 -0.25 16 19
CTNND1 0.031 0.015 -10000 0 -0.066 10 10
mol:PI-4-5-P2 0.007 0.037 0.13 7 -0.15 16 23
VASP 0.007 0.034 0.13 7 -0.14 14 21
ZYX 0.001 0.03 0.13 2 -0.17 9 11
JUB 0.013 0.038 0.13 7 -0.14 16 23
EGFR(dimer) 0.011 0.035 0.15 2 -0.16 9 11
E-cadherin/beta catenin-gamma catenin 0.058 0.027 -10000 0 -0.053 19 19
mol:PI-3-4-5-P3 0.041 0.05 0.16 32 -0.15 8 40
PIK3CA 0.028 0.02 -10000 0 -0.059 21 21
PI3K 0.042 0.051 0.16 32 -0.15 8 40
FYN -0.011 0.054 0.15 11 -0.2 28 39
mol:Ca2+ 0.004 0.025 0.085 1 -0.13 10 11
JUP 0.03 0.017 -10000 0 -0.064 16 16
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.025 0.086 1 -0.13 10 11
CDH1 0.031 0.013 -10000 0 -0.063 8 8
RhoA/GDP 0.075 0.077 0.16 221 -0.14 6 227
establishment of polarity of embryonic epithelium 0.006 0.035 0.13 7 -0.14 16 23
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
CASR -0.012 0.033 0.15 12 -0.14 7 19
RhoA/GTP 0.02 0.037 0.14 12 -0.13 8 20
AKT2 0.011 0.034 0.1 23 -0.14 9 32
actin cable formation 0.004 0.034 0.12 7 -0.14 16 23
apoptosis -0.011 0.043 0.17 9 -0.17 12 21
CTNNA1 0.033 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.021 0.14 1 -0.14 6 7
PIP5K1A 0.007 0.038 0.13 7 -0.15 16 23
PLCG1 0.004 0.026 0.086 1 -0.13 10 11
Rac1/GTP 0.015 0.039 0.15 2 -0.16 9 11
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.16 9 -0.084 14 23
IHH 0.038 0.021 0.11 15 -0.045 7 22
SHH Np/Cholesterol/GAS1 0.014 0.02 -10000 0 -0.042 37 37
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.013 0.02 0.042 37 -10000 0 37
SMO/beta Arrestin2 0.066 0.056 -10000 0 -10000 0 0
SMO 0.013 0.019 0.14 3 -10000 0 3
AKT1 0.002 0.083 -10000 0 -0.33 21 21
ARRB2 0.032 0.005 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
heart looping 0.014 0.019 0.14 3 -10000 0 3
STIL 0.024 0.085 0.17 125 -10000 0 125
DHH N/PTCH2 0.024 0.003 -10000 0 -10000 0 0
DHH N/PTCH1 0.017 0.014 -10000 0 -0.066 1 1
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.015 0.025 0.16 7 -0.095 6 13
determination of left/right symmetry 0.014 0.019 0.14 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
skeletal system development 0.015 0.024 0.16 7 -0.094 6 13
IHH N/Hhip 0.025 0.012 0.071 17 -0.023 1 18
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.014 0.019 0.14 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.03 -10000 0 -0.065 55 55
somite specification 0.014 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.017 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.018 0.014 -10000 0 -0.031 4 4
SHH Np/Cholesterol/Megalin 0.018 0.014 -10000 0 -0.033 5 5
SHH -0.015 0.01 -10000 0 -10000 0 0
catabolic process 0.02 0.017 -10000 0 -0.077 1 1
SMO/Vitamin D3 0.016 0.031 0.18 13 -10000 0 13
SHH Np/Cholesterol/Hhip -0.011 0.007 0 162 -10000 0 162
LRP2 0.032 0.005 -10000 0 -0.065 1 1
receptor-mediated endocytosis 0.012 0.027 0.15 12 -10000 0 12
SHH Np/Cholesterol/BOC -0.011 0.007 0 162 -10000 0 162
SHH Np/Cholesterol/CDO 0.018 0.014 -10000 0 -0.031 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 162 162
mol:Vitamin D3 0.064 0.082 0.19 146 -10000 0 146
IHH N/PTCH2 0.05 0.012 0.1 8 -0.036 1 9
CDON 0.032 0.004 -10000 0 0 7 7
IHH N/PTCH1 0.036 0.021 -10000 0 -0.064 13 13
Megalin/LRPAP1 0.047 0.007 -10000 0 -0.051 1 1
PTCH2 0.032 0.004 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.011 0.007 -10000 0 -10000 0 0
PTCH1 0.02 0.017 -10000 0 -0.077 1 1
HHIP 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.023 -10000 0 -0.051 2 2
CRKL 0.05 0.083 0.27 5 -0.43 5 10
mol:PIP3 0.013 0.019 -10000 0 -10000 0 0
AKT1 0.005 0.03 -10000 0 -10000 0 0
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.047 0.084 0.3 12 -0.38 5 17
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
HGF/MET/SHIP2 0.042 0.032 -10000 0 -0.048 4 4
MAP3K5 0.049 0.08 0.24 7 -0.38 5 12
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.031 -10000 0 -0.043 3 3
AP1 0.013 0.075 0.14 116 -10000 0 116
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.05 52 52
apoptosis -0.021 0.22 -10000 0 -0.72 41 41
STAT3 (dimer) 0.011 0.027 -10000 0 -0.2 2 2
GAB1/CRKL/SHP2/PI3K 0.079 0.082 0.3 2 -0.4 5 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.068 0.081 0.25 4 -0.38 6 10
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.03 0.009 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.065 2 2
ELK1 0.11 0.18 0.34 183 -10000 0 183
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.029 0.16 1 -0.16 10 11
PAK1 0 0.035 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.042 0.032 -10000 0 -0.049 3 3
HRAS 0.016 0.035 -10000 0 -0.28 3 3
DOCK1 0.036 0.077 0.26 4 -0.41 5 9
GAB1 0.05 0.077 0.22 1 -0.47 4 5
CRK 0.053 0.081 0.24 5 -0.43 5 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.034 -10000 0 -0.35 3 3
JUN 0.032 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.016 0.081 8 -0.051 16 24
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.044 0.089 0.27 32 -0.36 2 34
GRB2/SHC 0.059 0.062 0.16 105 -0.11 10 115
FOS 0.007 0.041 -10000 0 -0.065 120 120
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.11 0.18 0.34 183 -10000 0 183
HGF/MET/MUC20 0.028 0.022 -10000 0 -0.04 3 3
cell migration 0.058 0.061 0.15 105 -0.11 10 115
GRB2 0.032 0.006 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.032 0.023 -10000 0 -0.051 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.04 2 2
RAP1B 0.046 0.08 0.29 12 -0.36 5 17
RAP1A 0.042 0.082 0.29 14 -0.38 4 18
HGF/MET/RANBP9 0.042 0.032 -10000 0 -0.049 3 3
RAF1 0.039 0.06 0.22 2 -0.26 5 7
STAT3 0.011 0.027 -10000 0 -0.2 2 2
cell proliferation 0.03 0.061 0.21 15 -0.25 2 17
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.076 0.16 0.32 115 -10000 0 115
MAPK1 0.12 0.21 0.4 156 -10000 0 156
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.14 0.26 3 -0.33 50 53
SRC 0.005 0.017 -10000 0 -0.12 7 7
PI3K 0.057 0.059 0.16 96 -0.11 9 105
MET/Glomulin 0.015 0.025 0.084 1 -0.086 19 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.061 0.25 5 -0.28 2 7
MET 0.022 0.016 -10000 0 -0.065 2 2
MAP4K1 0.057 0.085 0.27 4 -0.44 5 9
PTK2 0.031 0.006 -10000 0 -10000 0 0
MAP2K2 0.041 0.073 0.28 13 -0.25 5 18
BAD -0.002 0.031 -10000 0 -10000 0 0
MAP2K4 0.043 0.078 0.23 14 -0.34 5 19
SHP2/GRB2/SOS1/GAB1 0.028 0.052 -10000 0 -0.36 5 5
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.004 0.014 0.071 8 -0.11 2 10
PLCgamma1/PKC 0.022 0.006 -10000 0 -10000 0 0
HGF 0.022 0.016 -10000 0 -0.065 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.15 112 -0.11 10 122
PDPK1 0.012 0.027 0.27 1 -10000 0 1
HGF/MET/SHIP 0.028 0.022 -10000 0 -0.04 3 3
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
Jak2/Leptin Receptor 0.019 0.12 -10000 0 -0.29 54 54
PTP1B/AKT1 0.039 0.059 0.16 9 -0.23 10 19
FYN 0.029 0.011 -10000 0 -0.065 1 1
p210 bcr-abl/PTP1B 0.026 0.059 0.16 10 -0.23 11 21
EGFR 0.012 0.019 -10000 0 -0.053 9 9
EGF/EGFR 0.01 0.041 -10000 0 -0.19 10 10
CSF1 0.032 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.009 -10000 0 -0.026 2 2
INSR 0.031 0.008 -10000 0 -0.026 5 5
PTP1B/N-cadherin 0.038 0.06 0.16 5 -0.23 11 16
Insulin Receptor/Insulin 0.054 0.063 0.18 2 -0.2 15 17
HCK 0.014 0.036 -10000 0 -0.045 121 121
CRK 0.032 0.005 -10000 0 -10000 0 0
TYK2 0.026 0.077 0.27 25 -0.25 9 34
EGF 0.033 0.008 -10000 0 -0.054 3 3
YES1 0.017 0.034 -10000 0 -0.065 74 74
CAV1 0.05 0.085 0.17 110 -0.25 10 120
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.065 0.18 7 -0.23 11 18
cell migration -0.026 0.059 0.23 11 -0.16 10 21
STAT3 0.031 0.014 -10000 0 -0.064 10 10
PRLR 0.033 0.005 -10000 0 -10000 0 0
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
CSF1R 0.024 0.026 -10000 0 -0.065 40 40
Prolactin Receptor/Prolactin 0.049 0.014 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
PTP1B/p130 Cas 0.022 0.055 0.12 24 -0.2 13 37
Crk/p130 Cas 0.038 0.059 0.16 7 -0.22 11 18
DOK1 0.022 0.061 0.17 13 -0.25 12 25
JAK2 0.005 0.12 0.2 1 -0.3 54 55
Jak2/Leptin Receptor/Leptin 0.026 0.076 -10000 0 -0.25 16 16
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.059 0.15 16 -0.23 11 27
LYN 0.021 0.031 -10000 0 -0.058 67 67
CDH2 0.03 0.009 -10000 0 -0.065 2 2
SRC 0.033 0.059 -10000 0 -0.41 7 7
ITGB3 0.032 0.003 -10000 0 -10000 0 0
CAT1/PTP1B 0.045 0.094 0.24 39 -0.29 11 50
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.053 0.069 -10000 0 -0.2 15 15
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.025 0.07 -10000 0 -0.23 16 16
negative regulation of transcription 0.005 0.11 0.2 1 -0.3 54 55
FCGR2A -0.016 0.048 -10000 0 -0.065 253 253
FER 0.034 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.032 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.05 0.038 -10000 0 -0.046 56 56
RHOA 0.032 0.006 -10000 0 -10000 0 0
LEPR 0.031 0.009 -10000 0 -0.065 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.031 0.081 0.2 28 -0.28 11 39
PRL 0.033 0.011 -10000 0 -0.062 6 6
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.031 0.015 -10000 0 -0.063 8 8
Insulin Receptor/Insulin/IRS1 0.06 0.024 -10000 0 -0.041 20 20
CSF1/CSF1R 0.051 0.067 0.2 3 -0.23 11 14
Ras protein signal transduction -0.011 0.082 0.51 11 -10000 0 11
IRS1 0.032 0.009 -10000 0 -0.065 4 4
INS 0.032 0.007 -10000 0 -0.026 1 1
LEP 0.022 0.015 -10000 0 -10000 0 0
STAT5B 0.022 0.074 0.19 3 -0.25 20 23
STAT5A 0.022 0.074 0.19 3 -0.24 21 24
GRB2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.04 0.061 0.17 7 -0.23 11 18
CSN2 0.001 0.034 -10000 0 -0.28 5 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
LAT 0.009 0.043 -10000 0 -0.29 2 2
YBX1 0.037 0.017 -10000 0 -0.063 12 12
LCK 0.031 0.01 -10000 0 -0.065 4 4
SHC1 0.024 0.026 -10000 0 -0.05 52 52
NOX4 0.022 0.034 -10000 0 -0.062 70 70
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.054 0.063 -10000 0 -0.068 1 1
SMAD6-7/SMURF1 0.044 0.032 -10000 0 -0.046 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.028 0.16 -10000 0 -0.48 52 52
SMAD4 0.009 0.041 -10000 0 -0.065 116 116
SMAD5 -0.027 0.09 0.12 2 -0.3 38 40
BMP7/USAG1 0.031 0.024 -10000 0 -0.051 6 6
SMAD5/SKI -0.015 0.096 -10000 0 -0.3 39 39
SMAD1 -0.009 0.072 0.14 1 -0.25 26 27
BMP2 0.021 0.028 -10000 0 -0.065 44 44
SMAD1/SMAD1/SMAD4 0 0.071 -10000 0 -0.25 19 19
BMPR1A 0.023 0.017 -10000 0 -0.065 6 6
BMPR1B 0.032 0.006 -10000 0 -0.065 1 1
BMPR1A-1B/BAMBI 0.031 0.05 -10000 0 -0.046 133 133
AHSG 0.031 0.008 -10000 0 -0.065 2 2
CER1 0.029 0.01 -10000 0 -10000 0 0
BMP2-4/CER1 0.042 0.041 -10000 0 -0.051 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.003 0.06 -10000 0 -0.19 39 39
BMP2-4 (homodimer) 0.033 0.031 -10000 0 -0.051 47 47
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.049 0.056 -10000 0 -0.054 10 10
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.022 0.015 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.057 -10000 0 -0.12 99 99
BMP2-4/USAG1 0.032 0.041 -10000 0 -0.05 49 49
SMAD6/SMURF1/SMAD5 -0.007 0.085 -10000 0 -0.29 33 33
SOSTDC1 0.022 0.018 -10000 0 -0.065 6 6
BMP7/BMPR2/BMPR1A-1B 0.051 0.052 -10000 0 -0.053 9 9
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.032 0.007 -10000 0 -0.065 2 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.031 0.011 -10000 0 -0.065 5 5
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
BMP2-4/CHRD 0.045 0.039 -10000 0 -0.049 52 52
SMAD5/SMAD5/SMAD4 -0.021 0.097 -10000 0 -0.3 41 41
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.011 0.052 -10000 0 -0.13 47 47
BMP7 (homodimer) 0.03 0.01 -10000 0 -0.065 1 1
NUP214 0.031 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.014 -10000 0 -0.051 4 4
SMAD1/SKI 0.004 0.081 -10000 0 -0.25 28 28
SMAD6 0.032 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
BMP2-4/FETUA 0.045 0.039 -10000 0 -0.049 54 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.02 -10000 0 -0.065 22 22
BMPR2 (homodimer) 0.032 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.059 0.022 -10000 0 -0.05 7 7
BMPR1A-1B (homodimer) 0.034 0.023 -10000 0 -0.051 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.002 0.082 -10000 0 -0.25 30 30
SMAD6-7/SMURF1/SMAD1 0.016 0.078 -10000 0 -0.25 18 18
SMAD6/SMURF1 0.022 0.015 -10000 0 -10000 0 0
BAMBI 0.019 0.024 -10000 0 -0.065 27 27
SMURF2 0.032 0.006 -10000 0 -0.065 1 1
BMP2-4/CHRDL1 0.03 0.028 -10000 0 -0.041 50 50
BMP2-4/GREM1 0.041 0.043 -10000 0 -0.05 74 74
SMAD7 0.031 0.007 -10000 0 -0.065 1 1
SMAD8A/SMAD8A/SMAD4 -0.026 0.16 -10000 0 -0.46 58 58
SMAD1/SMAD6 0.002 0.068 -10000 0 -0.25 20 20
TAK1/SMAD6 0.032 0.023 -10000 0 -0.051 1 1
BMP7 0.03 0.01 -10000 0 -0.065 1 1
BMP6 0.032 0.007 -10000 0 -0.065 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.004 0.05 -10000 0 -0.14 46 46
PPM1A 0.031 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.082 -10000 0 -0.25 28 28
SMAD7/SMURF1 0.032 0.023 -10000 0 -0.051 1 1
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
PPP1CA 0.032 0.004 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.065 3 3
PPP1R15A 0.031 0.009 -10000 0 -0.065 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.014 0.058 -10000 0 -0.12 100 100
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.033 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.058 -10000 0 -0.12 106 106
BMP4 0.029 0.014 -10000 0 -0.065 8 8
FST 0.029 0.017 -10000 0 -0.065 16 16
BMP2-4/NOG 0.03 0.028 -10000 0 -0.041 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.051 0.054 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.006 -10000 0 -10000 0 0
ELF1 0.033 0.018 -10000 0 -0.066 11 11
CCNA2 0.006 0.043 -10000 0 -0.065 135 135
PIK3CA 0.028 0.018 -10000 0 -0.064 17 17
JAK3 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -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 0.01 0.057 0.16 1 -0.2 16 17
SHC1 0.024 0.026 -10000 0 -0.064 40 40
SP1 0.033 0.02 -10000 0 -0.073 14 14
IL2RA -0.014 0.012 -10000 0 -0.072 10 10
IL2RB 0.03 0.012 -10000 0 -0.064 4 4
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.064 9 9
G1/S transition of mitotic cell cycle 0.024 0.092 0.26 14 -0.32 17 31
PTPN11 0.032 0.003 -10000 0 -10000 0 0
CCND2 -0.018 0.011 -10000 0 -0.098 8 8
LCK 0.031 0.01 -10000 0 -0.064 4 4
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
CDK6 0.022 0.015 -10000 0 0 166 166
CCND3 0.006 0.055 0.19 2 -0.25 5 7
FOXM1 transcription factor network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.17 0.2 -9999 0 -0.71 14 14
PLK1 0 0.11 -9999 0 -0.86 7 7
BIRC5 -0.028 0.073 -9999 0 -10000 0 0
HSPA1B -0.16 0.2 -9999 0 -0.68 18 18
MAP2K1 -0.013 0.038 -9999 0 -10000 0 0
BRCA2 -0.17 0.2 -9999 0 -0.71 13 13
FOXM1 -0.18 0.22 -9999 0 -0.74 23 23
XRCC1 -0.16 0.2 -9999 0 -0.7 13 13
FOXM1B/p19 -0.17 0.2 -9999 0 -0.7 19 19
Cyclin D1/CDK4 -0.16 0.19 -9999 0 -0.66 15 15
CDC2 -0.17 0.21 -9999 0 -0.73 15 15
TGFA -0.16 0.19 -9999 0 -0.62 20 20
SKP2 -0.16 0.2 -9999 0 -0.71 15 15
CCNE1 0.015 0.026 -9999 0 -0.074 4 4
CKS1B -0.17 0.21 -9999 0 -0.72 16 16
RB1 -0.11 0.19 -9999 0 -0.6 46 46
FOXM1C/SP1 -0.18 0.22 -9999 0 -0.72 21 21
AURKB -0.009 0.14 -9999 0 -0.92 11 11
CENPF -0.18 0.21 -9999 0 -0.7 19 19
CDK4 -0.029 0.047 -9999 0 -0.075 232 232
MYC -0.16 0.19 -9999 0 -0.62 20 20
CHEK2 -0.012 0.04 -9999 0 -0.1 15 15
ONECUT1 -0.16 0.2 -9999 0 -0.67 17 17
CDKN2A 0.003 0.027 -9999 0 -0.063 53 53
LAMA4 -0.17 0.2 -9999 0 -0.7 14 14
FOXM1B/HNF6 -0.17 0.22 -9999 0 -0.73 18 18
FOS -0.18 0.2 -9999 0 -0.74 14 14
SP1 0.031 0.006 -9999 0 -0.025 2 2
CDC25B -0.16 0.2 -9999 0 -0.7 13 13
response to radiation -0.011 0.013 -9999 0 -10000 0 0
CENPB -0.16 0.2 -9999 0 -0.71 12 12
CENPA -0.17 0.21 -9999 0 -0.71 20 20
NEK2 -0.16 0.2 -9999 0 -0.72 14 14
HIST1H2BA -0.16 0.2 -9999 0 -0.68 18 18
CCNA2 0 0.046 -9999 0 -0.073 135 135
EP300 0.03 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.18 0.22 -9999 0 -0.77 15 15
CCNB2 -0.19 0.21 -9999 0 -0.72 18 18
CCNB1 -0.18 0.21 -9999 0 -0.73 16 16
ETV5 -0.16 0.2 -9999 0 -0.7 14 14
ESR1 -0.17 0.2 -9999 0 -0.7 14 14
CCND1 -0.16 0.2 -9999 0 -0.66 18 18
GSK3A -0.009 0.036 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.013 0.061 -9999 0 -0.1 9 9
CDK2 0.014 0.031 -9999 0 -0.075 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.22 -9999 0 -0.72 18 18
GAS1 -0.17 0.2 -9999 0 -0.71 15 15
MMP2 -0.18 0.21 -9999 0 -0.71 18 18
RB1/FOXM1C -0.18 0.21 -9999 0 -0.68 23 23
CREBBP 0.032 0.004 -9999 0 -10000 0 0
TRAIL 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
TNFSF10 0.023 0.028 -10000 0 -0.065 45 45
positive regulation of NF-kappaB transcription factor activity 0.038 0.029 -10000 0 -0.051 44 44
MAP2K4 0.008 0.037 0.2 2 -0.16 11 13
IKBKB 0.032 0.003 -10000 0 0 5 5
TNFRSF10B 0.031 0.011 -10000 0 -0.065 6 6
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.007 0.013 -10000 0 -0.056 8 8
IKBKG 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.052 48 48
TRAIL/TRAILR3 0.038 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1 0.018 0.018 -10000 0 -0.04 45 45
TRAIL/TRAILR4 0.038 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.023 -10000 0 -0.035 46 46
IKK complex -0.033 0.11 -10000 0 -0.23 121 121
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.009 -10000 0 -0.051 45 45
MAP3K1 0.014 0.035 -10000 0 -0.14 20 20
TRAILR4 (trimer) 0.032 0.005 -10000 0 -10000 0 0
TRADD 0.032 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.029 -10000 0 -0.11 20 20
CFLAR 0.032 0.01 -10000 0 -0.065 5 5
MAPK1 -0.022 0.011 -10000 0 -0.051 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.043 -10000 0 -0.048 52 52
mol:ceramide 0.007 0.013 -10000 0 -0.056 8 8
FADD 0.032 0.006 -10000 0 -0.065 1 1
MAPK8 -0.001 0.031 0.19 1 -0.24 2 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.032 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.065 1 1
TRAIL/TRAILR1/FADD 0.035 0.025 -10000 0 -0.041 45 45
DAP3 0.032 0.005 -10000 0 -10000 0 0
CASP10 -0.013 0.026 0.14 10 -0.092 7 17
JNK cascade 0.038 0.029 -10000 0 -0.051 44 44
TRAIL (trimer) 0.023 0.028 -10000 0 -0.065 45 45
TNFRSF10C 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.031 -10000 0 -0.039 51 51
TRAIL/TRAILR2/FADD 0.051 0.036 -10000 0 -0.05 49 49
cell death 0.007 0.013 -10000 0 -0.056 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.033 -10000 0 -0.11 22 22
TRAILR2 (trimer) 0.031 0.011 -10000 0 -0.065 6 6
CASP8 0.016 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.071 0.055 -10000 0 -0.073 5 5
EGFR-dependent Endothelin signaling events

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
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.018 -9999 0 -0.065 6 6
EGF/EGFR 0.007 0.036 -9999 0 -0.059 7 7
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.04 -9999 0 -0.06 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.004 0.044 -9999 0 -0.065 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.032 0.007 -9999 0 -0.065 2 2
EGF/EGFR dimer/SHC 0.018 0.035 -9999 0 -0.05 33 33
mol:GDP 0.019 0.037 -9999 0 -0.059 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.03 0.013 -9999 0 -0.065 9 9
GRB2/SOS1 0.023 0.004 -9999 0 -10000 0 0
HRAS/GTP 0.011 0.03 -9999 0 -0.066 1 1
SHC1 0.024 0.026 -9999 0 -0.05 52 52
HRAS/GDP 0.017 0.038 -9999 0 -0.068 1 1
FRAP1 -0.012 0.015 -9999 0 -0.056 2 2
EGF/EGFR dimer 0.018 0.025 -9999 0 -0.051 8 8
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.032 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.017 0.045 -9999 0 -0.052 149 149
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.008 -9999 0 -0.064 2 2
SVIL 0.023 0.02 -9999 0 -0.064 14 14
ZNF318 0.031 0.003 -9999 0 -10000 0 0
JMJD2C 0.003 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.044 0.016 -9999 0 -0.04 9 9
CARM1 0.031 0.006 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 -10000 0 0
PELP1 0.032 0.005 -9999 0 -10000 0 0
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
AKT1 0.03 0.008 -9999 0 -10000 0 0
PTK2B 0.032 0.005 -9999 0 -10000 0 0
MED1 0.032 0.003 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -0.066 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.017 0.026 -9999 0 -0.064 31 31
GSN 0.029 0.018 -9999 0 -0.064 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.031 0.008 -9999 0 -10000 0 0
DNA-PK 0.053 0.034 -9999 0 -0.051 22 22
NCOA4 0.025 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.004 -9999 0 -10000 0 0
cell proliferation 0.006 0.053 -9999 0 -0.42 7 7
XRCC5 0.032 0.001 -9999 0 -10000 0 0
UBE3A 0.032 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.024 0.01 -9999 0 -0.027 14 14
FHL2 0.013 0.028 -9999 0 -0.22 4 4
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.006 0.002 -9999 0 -0.024 3 3
CDK6 0.022 0.015 -9999 0 0 166 166
TGFB1I1 -0.048 0.036 -9999 0 -0.064 425 425
T-DHT/AR/CyclinD1 0.03 0.035 -9999 0 -0.04 87 87
XRCC6 0.03 0.009 -9999 0 -10000 0 0
T-DHT/AR 0.039 0.03 -9999 0 -0.048 9 9
CTDSP1 0.032 0.007 -9999 0 -0.064 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.032 0.01 -9999 0 -0.064 5 5
TCF4 0.03 0.007 -9999 0 -10000 0 0
CDKN2A 0.002 0.027 -9999 0 -0.065 53 53
SRF 0.033 0.01 -9999 0 -0.046 3 3
NKX3-1 0.005 0.019 -9999 0 -0.14 2 2
KLK3 0.02 0.033 -9999 0 -10000 0 0
TMF1 0.031 0.01 -9999 0 -0.065 4 4
HNRNPA1 0.031 0.005 -9999 0 -10000 0 0
AOF2 0.001 0 -9999 0 -10000 0 0
APPL1 -0.021 0.007 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.043 0.019 -9999 0 -0.042 18 18
AR 0.031 0.014 -9999 0 -0.052 12 12
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.03 0.008 -9999 0 -10000 0 0
PAWR 0.031 0.006 -9999 0 -10000 0 0
PRKDC 0.028 0.02 -9999 0 -0.065 21 21
PA2G4 0.031 0.006 -9999 0 -10000 0 0
UBE2I 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.042 0.014 -9999 0 -0.035 8 8
RPS6KA3 0.033 0.005 -9999 0 -0.064 1 1
T-DHT/AR/ARA70 0.034 0.025 -9999 0 -0.043 10 10
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.041 0.015 -9999 0 -0.036 8 8
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.025 0.025 -9999 0 -0.064 36 36
KLK2 0.004 0.023 -9999 0 -0.28 2 2
CASP8 0.03 0.014 -9999 0 -0.065 10 10
T-DHT/AR/TIF2/CARM1 0.059 0.024 -9999 0 -10000 0 0
TMPRSS2 0.004 0.026 -9999 0 -0.17 6 6
CCND1 0.015 0.037 -9999 0 -0.064 90 90
PIAS1 0.033 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.009 6 6
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.032 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.03 0.025 -9999 0 -0.04 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.024 0.016 -9999 0 -0.029 3 3
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 -0.035 0.044 -9999 0 -0.065 342 342
FKBP4 0.032 0.007 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.007 0.048 -10000 0 -0.14 11 11
mol:DAG -0.005 0.04 0.15 5 -0.14 9 14
PLCG1 -0.005 0.041 0.15 5 -0.15 9 14
YES1 -0.014 0.034 -10000 0 -0.12 24 24
FZD3 0.03 0.01 -10000 0 -0.065 3 3
FZD6 0.014 0.038 -10000 0 -0.065 93 93
G protein 0.01 0.06 0.17 35 -0.14 10 45
MAP3K7 -0.023 0.034 0.14 7 -0.14 9 16
mol:Ca2+ -0.005 0.039 0.14 5 -0.14 9 14
mol:IP3 -0.005 0.04 0.15 5 -0.14 9 14
NLK 0.007 0.08 -10000 0 -0.72 6 6
GNB1 0.031 0.008 -10000 0 -10000 0 0
CAMK2A -0.02 0.037 0.16 8 -0.14 7 15
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.039 -10000 0 -0.12 23 23
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
GNAS -0.009 0.03 -10000 0 -0.13 16 16
GO:0007205 -0.009 0.035 0.14 5 -0.13 11 16
WNT6 0.032 0.001 -10000 0 -10000 0 0
WNT4 0.031 0.008 -10000 0 -0.065 2 2
NFAT1/CK1 alpha -0.006 0.053 0.2 7 -0.15 13 20
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.002 0.044 -10000 0 -0.065 155 155
WNT11 0.032 0.007 -10000 0 -0.065 2 2
CDC42 -0.023 0.031 0.14 5 -0.15 7 12
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0 0.037 -10000 0 -0.1 59 59
regulation of axonogenesis 0.01 0.059 0.26 26 -10000 0 26
myoblast fusion -0.013 0.038 0.35 3 -10000 0 3
mol:GTP 0.01 0.049 -10000 0 -0.18 28 28
regulation of calcium-dependent cell-cell adhesion -0.024 0.04 0.12 23 -10000 0 23
ARF1/GTP 0.027 0.047 -10000 0 -0.14 27 27
mol:GM1 -0.001 0.033 -10000 0 -0.13 28 28
mol:Choline -0.02 0.025 0.033 1 -0.13 24 25
lamellipodium assembly -0.006 0.064 -10000 0 -0.38 13 13
MAPK3 0.006 0.038 -10000 0 -0.12 28 28
ARF6/GTP/NME1/Tiam1 0.025 0.041 -10000 0 -0.12 23 23
ARF1 0.031 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.013 0.039 -10000 0 -0.35 3 3
ARF1/GDP 0.008 0.067 -10000 0 -0.24 27 27
ARF6 0.033 0.024 -10000 0 -0.039 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.029 0.011 -10000 0 -0.03 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.12 18 18
actin filament bundle formation -0.016 0.07 0.25 27 -10000 0 27
KALRN 0 0.045 -10000 0 -0.26 13 13
RAB11FIP3/RAB11A 0.047 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.07 -10000 0 -0.25 27 27
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.055 -10000 0 -0.24 15 15
substrate adhesion-dependent cell spreading 0.01 0.049 -10000 0 -0.18 28 28
cortical actin cytoskeleton organization -0.006 0.065 -10000 0 -0.38 13 13
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.01 0.049 -10000 0 -0.18 28 28
ARF6/GTP 0.01 0.049 -10000 0 -0.18 28 28
RhoA/GTP 0.027 0.047 -10000 0 -0.14 27 27
mol:GDP -0.009 0.061 -10000 0 -0.26 26 26
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.051 -10000 0 -0.13 28 28
RHOA 0.032 0.006 -10000 0 -10000 0 0
PLD1 0.005 0.039 -10000 0 -0.14 27 27
RAB11FIP3 0.032 0.003 -10000 0 -10000 0 0
tube morphogenesis -0.006 0.064 -10000 0 -0.38 13 13
ruffle organization -0.01 0.059 -10000 0 -0.26 26 26
regulation of epithelial cell migration 0.01 0.049 -10000 0 -0.18 28 28
PLD2 0.006 0.037 -10000 0 -0.14 25 25
PIP5K1A -0.011 0.06 -10000 0 -0.26 26 26
mol:Phosphatidic acid -0.02 0.025 0.033 1 -0.13 24 25
Rac1/GTP -0.006 0.065 -10000 0 -0.38 13 13
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.042 0.061 0.23 36 -10000 0 36
PCK1 0.037 0.031 -10000 0 -10000 0 0
HNF4A 0.036 0.043 0.24 8 -0.28 1 9
KCNJ11 0.056 0.062 0.26 29 -10000 0 29
AKT1 0.068 0.042 -10000 0 -0.25 1 1
response to starvation 0.002 0.004 -10000 0 -0.076 1 1
DLK1 0.05 0.072 0.26 33 -0.24 1 34
NKX2-1 0.04 0.049 0.21 4 -10000 0 4
ACADM 0.043 0.061 0.23 36 -10000 0 36
TAT 0.044 0.043 -10000 0 -10000 0 0
CEBPB 0.029 0.017 -10000 0 -0.063 11 11
CEBPA 0.03 0.019 -10000 0 -0.063 15 15
TTR 0.054 0.093 0.35 35 -0.43 1 36
PKLR 0.046 0.066 0.23 44 -10000 0 44
APOA1 0.06 0.072 0.39 12 -10000 0 12
CPT1C 0.044 0.057 0.24 30 -10000 0 30
ALAS1 0.047 0.058 -10000 0 -0.62 1 1
TFRC 0.056 0.052 0.2 31 -10000 0 31
FOXF1 0.023 0.025 -10000 0 -0.065 35 35
NF1 0.034 0.01 -10000 0 -0.17 1 1
HNF1A (dimer) 0.039 0.005 -10000 0 -10000 0 0
CPT1A 0.043 0.061 0.23 37 -10000 0 37
HMGCS1 0.043 0.062 0.23 38 -10000 0 38
NR3C1 0.035 0.014 -10000 0 -10000 0 0
CPT1B 0.036 0.054 0.23 25 -10000 0 25
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.005 -10000 0 -10000 0 0
GCK 0.078 0.099 0.25 121 -10000 0 121
CREB1 0.035 0.008 -10000 0 -10000 0 0
IGFBP1 0.051 0.047 -10000 0 -10000 0 0
PDX1 0.045 0.052 -10000 0 -0.31 1 1
UCP2 0.037 0.067 0.23 36 -10000 0 36
ALDOB 0.062 0.071 0.26 44 -10000 0 44
AFP 0.01 0.009 -10000 0 -0.082 4 4
BDH1 0.047 0.067 0.24 46 -10000 0 46
HADH 0.06 0.069 0.26 40 -10000 0 40
F2 0.059 0.074 0.41 10 -10000 0 10
HNF1A 0.039 0.005 -10000 0 -10000 0 0
G6PC 0.021 0.03 -10000 0 -10000 0 0
SLC2A2 0.062 0.052 0.2 35 -10000 0 35
INS 0.028 0.01 0.18 1 -10000 0 1
FOXA1 0.006 0.006 -10000 0 -0.088 1 1
FOXA3 0.015 0.011 -10000 0 -0.12 2 2
FOXA2 0.091 0.071 0.29 29 -10000 0 29
ABCC8 0.059 0.066 0.25 38 -10000 0 38
ALB 0.01 0.009 -10000 0 -0.082 4 4
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.008 0.015 0.055 1 -10000 0 1
FRAP1 0.041 0.06 0.22 5 -0.44 2 7
AKT1 0.033 0.08 0.16 123 -0.13 10 133
INSR 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.011 -10000 0 -10000 0 0
mol:GTP 0.036 0.089 0.18 124 -0.14 2 126
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.023 -10000 0 -0.17 2 2
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.042 0.11 40 -0.13 6 46
TSC1 0.031 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.03 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.042 0.043 0.13 9 -0.18 2 11
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.014 -10000 0 0 137 137
RPS6KB1 0.05 0.071 0.2 35 -0.25 2 37
MAP3K5 -0.012 0.056 0.16 2 -0.2 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
apoptosis -0.012 0.056 0.16 2 -0.2 40 42
mol:LY294002 0 0 0.001 1 -0.001 1 2
EIF4B 0.044 0.069 0.19 39 -0.23 2 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.045 0.23 4 -0.23 1 5
eIF4E/eIF4G1/eIF4A1 0.025 0.032 -10000 0 -0.24 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.025 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.046 0.12 54 -10000 0 54
FKBP1A 0.03 0.01 -10000 0 -0.065 1 1
RHEB/GTP 0.033 0.051 0.15 49 -0.13 6 55
mol:Amino Acids 0 0 0.001 1 -0.001 1 2
FKBP12/Rapamycin 0.023 0.007 -10000 0 -0.041 1 1
PDPK1 -0.013 0.022 0.16 5 -10000 0 5
EIF4E 0.031 0.01 -10000 0 -0.065 5 5
ASK1/PP5C 0.013 0.16 -10000 0 -0.52 42 42
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.032 -10000 0 -0.24 4 4
TSC1/TSC2 0.067 0.081 0.19 123 -0.14 8 131
tumor necrosis factor receptor activity 0 0 0.001 1 -0.001 1 2
RPS6 0.028 0.011 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
EIF4G1 0.031 0.006 -10000 0 -10000 0 0
IRS1 0.01 0.006 -10000 0 -10000 0 0
INS 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.064 2 2
PDK2 -0.013 0.021 0.16 5 -10000 0 5
EIF4EBP1 -0.033 0.094 -10000 0 -0.97 3 3
PIK3CA 0.029 0.018 -10000 0 -0.065 17 17
PPP2R5D 0.033 0.058 0.22 6 -0.4 2 8
peptide biosynthetic process -0.021 0.016 0.18 3 -10000 0 3
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.03 0.015 -10000 0 -0.065 10 10
mol:Rapamycin 0 0.001 0.003 58 -0.003 1 59
EEF2 -0.022 0.016 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.023 0.094 -10000 0 -0.91 3 3
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 0.007 -10000 0 -0.065 2 2
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.051 15 15
PTK2 0.016 0.078 -10000 0 -0.23 42 42
positive regulation of JNK cascade 0.021 0.081 -10000 0 -0.24 36 36
CDC42/GDP 0.036 0.11 0.35 2 -0.33 37 39
Rac1/GDP 0.024 0.092 0.29 1 -0.32 21 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.099 -10000 0 -0.3 36 36
nectin-3/I-afadin 0.044 0.015 -10000 0 -0.051 1 1
RAPGEF1 0.006 0.11 0.24 5 -0.34 38 43
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.004 0.11 -10000 0 -0.37 39 39
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.065 2 2
TLN1 -0.015 0.015 -10000 0 -0.14 3 3
Rap1/GTP 0.001 0.077 -10000 0 -0.26 39 39
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.023 40 40
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.051 1 1
PVR 0.031 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.021 0.13 0.33 3 -0.39 38 41
MLLT4 0.03 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.07 0.052 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.015 0.075 -10000 0 -0.27 22 22
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.032 0.007 -10000 0 -0.065 1 1
PVRL2 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
CLDN1 0.03 0.014 -10000 0 -0.065 9 9
JAM-A/CLDN1 0.062 0.048 -10000 0 -0.057 33 33
SRC 0.011 0.12 -10000 0 -0.4 39 39
ITGB3 0.032 0.003 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
FARP2 0.026 0.12 0.37 1 -0.39 31 32
RAC1 0.023 0.015 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.025 -10000 0 -0.044 10 10
nectin-1/I-afadin 0.044 0.014 -10000 0 -10000 0 0
nectin-2/I-afadin 0.043 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.016 0.032 -10000 0 -0.04 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.058 0.022 -10000 0 -0.046 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.022 0.036 -10000 0 -0.041 119 119
F11R 0.026 0.024 -10000 0 -0.065 32 32
positive regulation of filopodium formation 0.021 0.081 -10000 0 -0.24 36 36
alphaV/beta3 Integrin/Talin 0.024 0.065 0.2 28 -0.17 9 37
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
PIP5K1C -0.01 0.014 -10000 0 -0.062 32 32
VAV2 0.021 0.14 0.31 2 -0.41 41 43
RAP1/GDP 0.025 0.1 0.32 2 -0.31 37 39
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.057 0.025 -10000 0 -0.044 10 10
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.051 1 1
Rac1/GTP 0.021 0.091 0.25 1 -0.32 22 23
PTPRM 0.006 0.019 -10000 0 -0.061 35 35
E-cadherin/beta catenin/alpha catenin 0.075 0.052 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
ceramide 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
MAP4K4 -0.003 0.051 -10000 0 -0.28 8 8
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.007 0.025 0.15 2 -0.12 8 10
NFKBIA 0.03 0.009 -10000 0 -0.065 1 1
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BAX -0.005 0.037 0.19 11 -0.12 8 19
EnzymeConsortium:3.1.4.12 0 0.016 0.056 3 -0.066 9 12
IKBKB -0.007 0.054 0.19 4 -0.27 8 12
MAP2K2 -0.012 0.046 0.17 24 -0.14 5 29
MAP2K1 -0.016 0.034 0.16 9 -0.14 6 15
SMPD1 -0.002 0.024 0.13 1 -0.1 17 18
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.001 0.057 0.29 1 -0.28 10 11
MAP2K4 -0.012 0.027 0.17 4 -0.14 5 9
protein ubiquitination -0.011 0.055 -10000 0 -0.28 8 8
EnzymeConsortium:2.7.1.37 -0.015 0.042 0.16 10 -0.15 6 16
response to UV 0 0 0.002 12 -0.002 2 14
RAF1 -0.011 0.033 0.16 9 -0.13 7 16
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.002 0.025 0.089 3 -0.1 13 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.012 -10000 0 -0.04 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.027 0.16 3 -0.12 8 11
TRADD 0.032 0.004 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.008 0.04 0.17 10 -0.14 5 15
MAPK1 -0.015 0.047 0.17 9 -0.16 13 22
p50/RELA/I-kappa-B-alpha 0.045 0.013 -10000 0 -0.051 1 1
FADD -0.002 0.049 0.24 1 -0.27 6 7
KSR1 -0.008 0.026 0.12 3 -0.11 13 16
MAPK8 -0.012 0.029 0.15 4 -0.14 5 9
TRAF2 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.049 -10000 0 -0.27 8 8
TNF R/SODD 0.014 0.046 -10000 0 -0.051 162 162
TNF 0.032 0.007 -10000 0 -0.065 2 2
CYCS 0.012 0.044 0.13 22 -0.12 5 27
IKBKG -0.008 0.054 0.19 3 -0.27 8 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.054 -10000 0 -0.27 9 9
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
AIFM1 -0.009 0.031 0.13 12 -0.12 6 18
TNF/TNF R/SODD 0.025 0.053 -10000 0 -0.049 165 165
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.001 0.055 0.19 6 -0.27 8 14
response to hydrogen peroxide 0 0 0.002 12 -0.002 2 14
BCL2 0.031 0.006 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.028 0.033 -10000 0 -0.12 8 8
BIRC5 -0.006 0.047 -10000 0 -0.065 201 201
NFKBIA -0.006 0.015 0.17 2 -10000 0 2
CPEB1 0.024 0.014 -10000 0 -10000 0 0
AKT1 -0.006 0.015 0.14 3 -10000 0 3
NDEL1 0.031 0.008 -10000 0 0 31 31
Aurora A/BRCA1 0.025 0.024 0.099 2 -0.12 8 10
NDEL1/TACC3 0.033 0.04 -10000 0 -0.12 8 8
GADD45A 0.024 0.026 -10000 0 -0.065 39 39
GSK3B 0.032 0.007 0.082 2 -10000 0 2
PAK1/Aurora A 0.034 0.029 -10000 0 -0.12 8 8
MDM2 0.029 0.011 -10000 0 -0.065 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.035 0.017 -10000 0 -0.051 253 253
TP53 0.009 0.034 -10000 0 -0.2 10 10
DLG7 0.006 0.009 0.096 2 -10000 0 2
AURKAIP1 0.031 0.007 -10000 0 -10000 0 0
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.035 0.042 -10000 0 -0.13 8 8
G2/M transition of mitotic cell cycle 0.024 0.024 0.098 2 -0.11 8 10
AURKA 0.014 0.013 0.13 2 -0.042 1 3
AURKB 0.007 0.025 -10000 0 -0.1 18 18
CDC25B 0.012 0.019 0.097 2 -0.21 2 4
G2/M transition checkpoint 0.007 0.017 0.076 2 -0.1 8 10
mRNA polyadenylation 0.019 0.021 0.098 1 -0.11 5 6
Aurora A/CPEB 0.019 0.021 0.099 1 -0.11 5 6
Aurora A/TACC1/TRAP/chTOG 0.065 0.037 -10000 0 -0.12 7 7
BRCA1 0.031 0.01 -10000 0 -0.065 5 5
centrosome duplication 0.034 0.029 -10000 0 -0.12 8 8
regulation of centrosome cycle 0.032 0.039 -10000 0 -0.12 8 8
spindle assembly 0.063 0.036 -10000 0 -0.12 7 7
TDRD7 0.031 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.024 0.054 -10000 0 -0.13 8 8
CENPA 0.01 0.024 -10000 0 -0.24 2 2
Aurora A/PP2A 0.035 0.027 -10000 0 -0.12 5 5
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.03 0.089 5 -0.19 8 13
negative regulation of DNA binding 0.009 0.034 -10000 0 -0.2 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.012 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.007 0.017 0.076 2 -0.1 8 10
mitotic prometaphase -0.002 0.012 0.071 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.013 0.13 2 -0.042 1 3
TACC1 0.032 0.005 -10000 0 -10000 0 0
TACC3 0.014 0.037 -10000 0 -0.065 92 92
Aurora A/Antizyme1 0.049 0.031 -10000 0 -0.12 8 8
Aurora A/RasGAP 0.033 0.029 -10000 0 -0.13 7 7
OAZ1 0.031 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.008 0.082 2 -10000 0 2
GIT1 0.032 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.061 0.018 -10000 0 -0.044 2 2
Importin alpha/Importin beta/TPX2 -0.035 0.017 -10000 0 -0.051 253 253
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.025 0.02 -10000 0 -0.14 8 8
PAK1 0.032 0.004 -10000 0 -10000 0 0
CKAP5 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.022 0.071 -10000 0 -0.14 21 21
Ran/GTP/Exportin 1/HDAC1 -0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.061 -10000 0 -0.18 26 26
SUMO1 0.033 0 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.028 -10000 0 -0.095 39 39
FKBP3 0.03 0.008 -10000 0 -10000 0 0
Histones 0.032 0.044 -10000 0 -0.2 7 7
YY1/LSF 0.012 0.06 -10000 0 -0.14 59 59
SMG5 0.032 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0 0.036 -10000 0 -0.1 30 30
I kappa B alpha/HDAC1 0 0.059 -10000 0 -0.18 33 33
SAP18 0.03 0.008 -10000 0 -10000 0 0
RELA 0 0.049 0.11 13 -0.15 36 49
HDAC1/Smad7 0.035 0.039 -10000 0 -0.05 39 39
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.044 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.048 -10000 0 -0.16 28 28
NF kappa B1 p50/RelA 0.016 0.058 -10000 0 -0.15 43 43
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.048 -10000 0 -0.18 18 18
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.065 89 89
MAX 0.03 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.019 -10000 0 -0.055 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.007 0.052 -10000 0 -0.13 59 59
SIN3 complex 0.053 0.028 -10000 0 -0.039 5 5
SMURF1 0.022 0.015 -10000 0 -10000 0 0
CHD3 0.032 0.005 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
YY1/HDAC3 -0.002 0.05 -10000 0 -0.18 22 22
YY1/HDAC2 0.012 0.059 -10000 0 -0.15 54 54
YY1/HDAC1 0.007 0.061 -10000 0 -0.15 55 55
NuRD/MBD2 Complex (MeCP1) 0.002 0.052 -10000 0 -0.19 21 21
PPARG 0.004 0.038 0.12 10 -0.15 14 24
HDAC8/hEST1B 0.041 0.01 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
HDAC3/SMRT (N-CoR2) 0.016 0.044 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.039 -10000 0 -0.05 39 39
CREBBP 0.032 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.047 -10000 0 -0.17 17 17
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC3 0.007 0.02 -10000 0 -0.059 7 7
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
YY1 0.01 0.004 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.031 0.007 -10000 0 -0.065 1 1
NCOR2 0.032 0.004 -10000 0 -10000 0 0
MXD1 0.033 0 -10000 0 -10000 0 0
STAT3 0.017 0.009 -10000 0 -0.035 8 8
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.066 -10000 0 -0.14 58 58
YY1/SAP30/HDAC1 0.02 0.067 -10000 0 -0.14 59 59
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.009 -10000 0 -0.035 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.019 -10000 0 -0.055 5 5
histone deacetylation 0.002 0.052 -10000 0 -0.19 21 21
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.041 -10000 0 -0.11 41 41
nuclear export -0.041 0.01 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.023 0.027 -10000 0 -0.065 43 43
GATA2/HDAC3 0.016 0.044 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.033 -10000 0 -0.051 61 61
GATA1/HDAC3 0.016 0.045 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.014 0.046 -10000 0 -0.051 165 165
SIN3/HDAC complex/Mad/Max -0.006 0.067 -10000 0 -0.18 47 47
NuRD Complex 0.004 0.051 -10000 0 -0.18 18 18
positive regulation of chromatin silencing 0.031 0.042 -10000 0 -0.2 7 7
SIN3B 0.031 0.007 -10000 0 -10000 0 0
MTA2 0.032 0.004 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.033 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.044 -10000 0 -0.1 38 38
HDAC complex 0.039 0.063 -10000 0 -0.067 28 28
GATA1/Fog1 0.024 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.043 0.042 -10000 0 -0.05 69 69
TNF 0.032 0.007 -10000 0 -0.065 2 2
negative regulation of cell growth -0.006 0.067 -10000 0 -0.18 47 47
NuRD/MBD2/PRMT5 Complex 0.002 0.052 -10000 0 -0.19 21 21
Ran/GTP/Exportin 1 0.038 0.039 -10000 0 -0.096 38 38
NF kappa B/RelA/I kappa B alpha -0.005 0.048 -10000 0 -0.17 25 25
SIN3/HDAC complex/NCoR1 0.006 0.044 -10000 0 -0.17 21 21
TFCP2 0.032 0.005 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 0 8 8
MBD3 0.031 0.006 -10000 0 -10000 0 0
MBD2 0.031 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.048 0.2 11 -0.19 8 19
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.003 0.09 0.22 1 -0.31 22 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.071 -10000 0 -0.57 7 7
mol:DAG -0.18 0.35 -10000 0 -0.8 122 122
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.076 0.24 1 -0.25 10 11
FRAP1 -0.008 0.078 0.25 1 -0.28 11 12
FOXO3 -0.014 0.078 0.23 2 -0.27 17 19
AKT1 -0.01 0.08 0.26 1 -0.27 18 19
GAB2 0.031 0.006 -10000 0 -10000 0 0
SMPD1 -0.001 0.1 -10000 0 -0.59 15 15
SGMS1 -0.13 0.26 -10000 0 -0.6 121 121
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 -0.016 0.008 -10000 0 -0.041 16 16
CALM1 0.029 0.01 -10000 0 -10000 0 0
cell proliferation -0.063 0.16 -10000 0 -0.35 107 107
EIF3A 0.024 0.014 -10000 0 0 137 137
PI3K 0.04 0.023 -10000 0 -0.051 16 16
RPS6KB1 0.02 0.037 -10000 0 -0.74 1 1
mol:sphingomyelin -0.18 0.35 -10000 0 -0.8 122 122
natural killer cell activation 0 0.001 -10000 0 -0.005 1 1
JAK3 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MYC -0.015 0.084 0.24 1 -0.29 11 12
MYB 0.015 0.026 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.009 0.071 0.14 3 -0.21 27 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.047 -10000 0 -0.71 1 1
mol:PI-3-4-5-P3 -0.008 0.07 0.14 3 -0.21 26 29
Rac1/GDP 0.005 0.019 -10000 0 -0.046 5 5
T cell proliferation -0.009 0.066 -10000 0 -0.2 23 23
SHC1 0.024 0.027 -10000 0 -0.065 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.002 -10000 0 -10000 0 0
PRKCZ -0.01 0.067 -10000 0 -0.2 26 26
NF kappa B1 p50/RelA 0.008 0.09 0.26 1 -0.26 12 13
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.015 0.042 -10000 0 -0.19 9 9
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL2RA 0.023 0.017 -10000 0 -0.065 6 6
IL2RB 0.03 0.012 -10000 0 -0.066 4 4
TERT 0.031 0.006 -10000 0 -10000 0 0
E2F1 0.023 0.024 -10000 0 -0.38 1 1
SOS1 0 0.001 -10000 0 -10000 0 0
RPS6 0.028 0.011 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.066 9 9
actin cytoskeleton organization -0.009 0.066 -10000 0 -0.2 23 23
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP 0.031 0.032 -10000 0 -0.043 5 5
LCK 0.031 0.01 -10000 0 -0.065 4 4
BCL2 -0.005 0.073 0.26 6 -0.24 7 13
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.053 -10000 0 -0.3 14 14
KLHL20 0.028 0.068 0.17 34 -0.18 15 49
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.039 0.17 9 -0.16 9 18
ENAH 0.005 0.055 -10000 0 -0.3 15 15
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.033 0.11 20 -0.12 9 29
ABI1/Sra1/Nap1 -0.01 0.022 -10000 0 -0.12 15 15
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.072 0.035 -10000 0 -0.053 10 10
RAPGEF1 -0.002 0.06 0.16 31 -0.28 11 42
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
regulation of calcium-dependent cell-cell adhesion 0.02 0.056 -10000 0 -0.3 14 14
CRK 0.005 0.061 0.17 25 -0.29 13 38
E-cadherin/gamma catenin/alpha catenin 0.059 0.026 -10000 0 -0.055 20 20
alphaE/beta7 Integrin 0.046 0.012 -10000 0 -0.051 2 2
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.023 40 40
DLG1 0.006 0.055 -10000 0 -0.29 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.018 -10000 0 -0.093 12 12
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.017 -10000 0 -0.023 29 29
PI3K -0.036 0.022 -10000 0 -0.12 12 12
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.043 0.022 -10000 0 -0.058 19 19
TIAM1 0.031 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.066 0.034 -10000 0 -0.048 9 9
AKT1 -0.016 0.037 0.14 9 -0.1 2 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
RhoA/GDP 0.012 0.06 0.18 27 -0.17 16 43
actin cytoskeleton organization 0.024 0.054 0.14 35 -0.13 15 50
CDC42/GDP 0.011 0.057 0.18 23 -0.17 16 39
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.027 -10000 0 -0.11 19 19
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.072 0.036 -10000 0 -0.051 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.022 -10000 0 -0.032 28 28
mol:GDP -0.002 0.061 0.18 26 -0.18 16 42
CDC42/GTP/IQGAP1 0.022 0.036 -10000 0 -0.041 119 119
JUP 0.029 0.017 -10000 0 -0.065 16 16
p120 catenin/RhoA/GDP 0.025 0.063 0.19 26 -0.17 18 44
RAC1/GTP/IQGAP1 0.016 0.032 -10000 0 -0.04 89 89
PIP5K1C/AP1M1 0.022 0.006 -10000 0 0 37 37
RHOA 0.032 0.006 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.04 0.11 30 -0.094 14 44
NME1 0 0 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.006 0.055 -10000 0 -0.3 15 15
regulation of cell-cell adhesion -0.029 0.017 0.043 1 -0.099 13 14
WASF2 -0.006 0.012 -10000 0 -0.064 15 15
Rap1/GTP -0.022 0.045 0.14 29 -0.14 4 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.082 0.043 -10000 0 -0.076 5 5
CCND1 0.017 0.047 0.12 30 -0.11 14 44
VAV2 0.014 0.11 -10000 0 -0.58 13 13
RAP1/GDP -0.011 0.052 0.16 31 -0.17 3 34
adherens junction assembly 0.006 0.053 -10000 0 -0.29 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.014 -10000 0 -10000 0 0
PIP5K1C 0.03 0.008 -10000 0 0 37 37
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 2 -0.082 3 5
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.13 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.005 0.053 -10000 0 -0.3 14 14
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP -0.007 0.055 -10000 0 -0.26 16 16
E-cadherin/beta catenin/alpha catenin 0.06 0.021 -10000 0 -0.05 9 9
ITGAE 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.057 -10000 0 -0.3 14 14
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.01 0.075 0.23 7 -0.24 15 22
IKBKB 0.016 0.057 0.26 4 -0.25 7 11
AKT1 0.012 0.073 0.22 34 -10000 0 34
IKBKG 0.012 0.048 0.28 2 -0.22 7 9
CALM1 -0.009 0.048 0.2 2 -0.18 14 16
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
MAP3K1 0.034 0.09 0.27 16 -0.37 8 24
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
mol:Ca2+ -0.006 0.053 0.21 1 -0.18 19 20
DOK1 0.032 0.001 -10000 0 -10000 0 0
AP-1 -0.007 0.057 0.17 5 -0.19 12 17
LYN 0.021 0.031 -10000 0 -0.058 67 67
BLNK 0.013 0.032 -10000 0 -0.065 60 60
SHC1 0.024 0.026 -10000 0 -0.05 52 52
BCR complex 0.045 0.014 -10000 0 -0.064 2 2
CD22 -0.007 0.031 -10000 0 -0.24 2 2
CAMK2G -0.001 0.029 0.18 2 -0.2 5 7
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.048 0.02 -10000 0 -0.098 25 25
GO:0007205 -0.007 0.054 0.21 1 -0.18 19 20
SYK 0.025 0.025 -10000 0 -0.065 35 35
ELK1 -0.013 0.052 0.2 1 -0.18 17 18
NFATC1 -0.015 0.061 0.22 9 -0.24 13 22
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -0.064 2 2
PAG1/CSK 0.024 0.003 -10000 0 -10000 0 0
NFKBIB 0.02 0.032 0.14 3 -0.12 14 17
HRAS -0.013 0.052 0.17 6 -0.17 21 27
NFKBIA 0.021 0.031 0.14 3 -0.12 14 17
NF-kappa-B/RelA/I kappa B beta 0.024 0.028 0.13 4 -0.096 14 18
RasGAP/Csk 0.051 0.066 -10000 0 -0.092 2 2
mol:GDP -0.006 0.054 0.22 1 -0.18 17 18
PTEN 0.023 0.016 -10000 0 -0.065 2 2
CD79B 0.032 0.006 -10000 0 -0.064 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.028 0.13 4 -0.093 14 18
GRB2 0.032 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.006 0.076 0.29 3 -0.3 4 7
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.006 0.053 0.22 1 -0.18 19 20
CSK 0.032 0.005 -10000 0 -10000 0 0
FOS -0.02 0.05 0.17 2 -0.18 16 18
CHUK -0.048 0.12 0.24 3 -0.25 120 123
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.071 -10000 0 -0.18 17 17
PTPN6 -0.018 0.031 0.14 4 -0.23 2 6
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.012 0.02 0.091 4 -0.069 14 18
VAV2 -0.011 0.055 0.16 3 -0.28 13 16
ubiquitin-dependent protein catabolic process 0.022 0.032 0.14 3 -0.13 13 16
BTK 0.016 0.011 -10000 0 -10000 0 0
CD19 -0.008 0.032 -10000 0 -0.24 2 2
MAP4K1 0.031 0.008 -10000 0 -0.065 1 1
CD72 0.03 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.083 0.25 16 -0.32 8 24
SH3BP5 0.029 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.007 0.052 -10000 0 -0.18 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.06 -10000 0 -0.28 15 15
RAF1 -0.017 0.05 0.18 6 -0.19 10 16
RasGAP/p62DOK/SHIP 0.042 0.058 -10000 0 -0.081 2 2
CD79A 0.03 0.009 -10000 0 -0.005 28 28
re-entry into mitotic cell cycle -0.007 0.056 0.17 5 -0.19 11 16
RASA1 0.031 0.006 -10000 0 -10000 0 0
MAPK3 -0.024 0.05 0.17 6 -0.21 5 11
MAPK1 -0.021 0.05 0.2 7 -0.21 4 11
CD72/SHP1 0.007 0.064 0.21 28 -0.23 2 30
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 0.025 0.081 0.24 16 -0.33 8 24
actin cytoskeleton organization 0.033 0.088 0.2 50 -0.26 4 54
NF-kappa-B/RelA 0.047 0.055 0.24 4 -0.19 13 17
Calcineurin 0.009 0.065 0.2 1 -0.18 12 13
PI3K -0.025 0.048 -10000 0 -0.16 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0 0.043 -10000 0 -0.21 6 6
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.036 0.078 -10000 0 -0.57 6 6
DAPP1 0.019 0.074 -10000 0 -0.64 5 5
cytokine secretion -0.014 0.059 0.22 9 -0.22 13 22
mol:DAG -0.006 0.053 0.22 1 -0.18 19 20
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
MAP2K1 -0.021 0.049 0.18 6 -0.2 7 13
B-cell antigen/BCR complex/FcgammaRIIB 0.034 0.049 -10000 0 -0.05 119 119
mol:PI-3-4-5-P3 -0.02 0.051 0.19 13 -10000 0 13
ETS1 0.02 0.065 0.17 23 -0.19 6 29
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.026 0.073 -10000 0 -0.083 35 35
B-cell antigen/BCR complex/LYN 0.005 0.036 -10000 0 -0.24 2 2
MALT1 0.028 0.02 -10000 0 -0.065 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.085 0.19 47 -0.28 4 51
B-cell antigen/BCR complex/LYN/SYK 0.042 0.064 0.22 18 -0.22 2 20
CARD11 -0.007 0.052 0.21 1 -0.18 18 19
FCGR2B 0.009 0.041 -10000 0 -0.065 120 120
PPP3CA 0.026 0.013 -10000 0 -10000 0 0
BCL10 0.031 0.01 -10000 0 -0.065 4 4
IKK complex 0.003 0.036 0.14 8 -0.12 10 18
PTPRC 0.009 0.041 -10000 0 -0.065 122 122
PDPK1 -0.015 0.052 0.19 17 -10000 0 17
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.032 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.02 0.11 5 -0.068 10 15
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.032 0.04 -10000 0 -0.13 31 31
PLCG1 0 0.013 0.073 5 -0.13 3 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
G12/G13 0.034 0.022 -10000 0 -10000 0 0
cell migration -0.032 0.04 -10000 0 -0.12 32 32
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 0 0.013 0.073 6 -0.13 3 9
MAPK1 0.001 0.01 0.073 6 -0.095 1 7
S1P/S1P5/Gi 0.002 0.012 0.083 6 -0.11 2 8
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
CDC42/GDP 0.023 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
RHOA 0.04 0.095 0.18 149 -10000 0 149
S1P/S1P4/Gi 0.002 0.012 0.083 6 -0.11 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.029 0.019 -10000 0 -0.023 2 2
GNA12 0.023 0.015 -10000 0 0 152 152
GNA13 0.032 0.007 -10000 0 -0.065 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.02 0.006 0 43 -10000 0 43
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.004 0.083 0.2 8 -0.33 28 36
CDKN1A -0.011 0.084 -10000 0 -0.33 31 31
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
FOXO3 -0.004 0.078 0.2 4 -0.33 25 29
AKT1 -0.001 0.087 -10000 0 -0.34 30 30
BAD 0.032 0.004 -10000 0 -10000 0 0
AKT3 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.008 0.083 -10000 0 -0.33 30 30
AKT1/ASK1 0.014 0.088 -10000 0 -0.32 32 32
BAD/YWHAZ 0.06 0.019 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.032 0.004 -10000 0 -10000 0 0
JNK cascade -0.013 0.086 0.31 32 -10000 0 32
TSC1 -0.009 0.084 0.19 1 -0.33 31 32
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.092 -10000 0 -0.33 32 32
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.001 0.086 -10000 0 -0.34 30 30
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.01 0.084 -10000 0 -0.33 32 32
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAPKAP1 0.031 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle 0.013 0.053 0.19 23 -0.14 1 24
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.002 0.083 -10000 0 -0.32 30 30
CASP9 -0.008 0.086 0.2 4 -0.33 31 35
YWHAB 0.03 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.013 0.092 0.22 10 -0.32 31 41
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.057 0.023 -10000 0 -0.044 2 2
YWHAE 0.032 0.005 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.009 0.078 0.23 1 -0.3 32 33
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.029 -10000 0 -10000 0 0
CHUK -0.004 0.064 -10000 0 -0.34 17 17
BAD/BCL-XL 0.014 0.088 -10000 0 -0.32 30 30
mTORC2 0.02 0.006 -10000 0 -0.016 8 8
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.026 0.079 -10000 0 -0.27 34 34
PDPK1 0.032 0.003 -10000 0 -10000 0 0
MDM2 0.007 0.098 0.2 42 -0.33 29 71
MAPKKK cascade -0.016 0.09 0.32 32 -10000 0 32
MDM2/Cbp/p300 0.039 0.1 0.22 44 -0.31 30 74
TSC1/TSC2 -0.011 0.09 0.23 11 -0.32 32 43
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.21 44 -0.3 30 74
glucose import -0.01 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.053 -10000 0 -0.19 32 32
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.017 0.2 3 -10000 0 3
GSK3A -0.006 0.08 0.2 4 -0.33 27 31
FOXO1 -0.006 0.075 -10000 0 -0.33 25 25
GSK3B -0.007 0.085 0.2 4 -0.33 31 35
SFN 0.026 0.024 -10000 0 -0.065 31 31
G1/S transition of mitotic cell cycle -0.01 0.092 0.22 16 -0.33 32 48
p27Kip1/14-3-3 family 0.006 0.033 -10000 0 -0.26 5 5
PRKACA 0.031 0.006 -10000 0 -10000 0 0
KPNA1 0.032 0.005 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.022 0.015 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.05 0.21 10 -0.23 7 17
FYN 0.002 0.054 0.18 6 -0.25 9 15
LAT/GRAP2/SLP76 0.023 0.051 0.2 3 -0.26 6 9
IKBKB 0.032 0.003 -10000 0 0 5 5
AKT1 0.001 0.054 0.16 9 -0.22 11 20
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.01 0.023 0.09 9 -0.087 5 14
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.039 2 2
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.003 0.062 0.18 9 -0.27 10 19
TRPV6 0.38 0.59 1.3 157 -10000 0 157
CD28 0.033 0.001 -10000 0 -10000 0 0
SHC1 0.008 0.052 0.24 9 -0.27 6 15
receptor internalization 0.014 0.05 -10000 0 -0.36 6 6
PRF1 -0.13 0.27 -10000 0 -0.6 125 125
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
COT/AKT1 0.007 0.049 0.17 5 -0.19 11 16
LAT 0.008 0.049 0.19 5 -0.28 7 12
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.028 0.02 -10000 0 -0.066 20 20
CD3E 0.032 0.006 -10000 0 -0.066 1 1
CD3G 0.032 0.006 -10000 0 -0.07 1 1
RASGRP2 0.004 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.045 0.084 0.21 11 -0.23 24 35
HLA-A 0.032 0.005 -10000 0 -0.065 1 1
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.022 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.04 0.13 17 -0.092 12 29
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.027 -10000 0 -0.11 13 13
PRKCA -0.011 0.04 0.18 4 -0.16 5 9
GRAP2 0.03 0.008 -10000 0 -10000 0 0
mol:IP3 0.005 0.043 -10000 0 -0.2 8 8
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.011 0.035 -10000 0 -0.26 5 5
ORAI1 -0.33 0.5 -10000 0 -1.1 157 157
CSK 0.009 0.047 0.19 5 -0.27 7 12
B7 family/CD28 0.05 0.058 0.22 4 -0.27 5 9
CHUK 0.024 0.015 -10000 0 -0.065 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.013 0.048 -10000 0 -0.3 7 7
PTPN6 0.005 0.048 0.17 10 -0.26 7 17
VAV1 0.012 0.056 0.19 17 -0.28 7 24
Monovalent TCR/CD3 0.014 0.029 -10000 0 -0.2 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.005 0.052 0.19 7 -0.25 7 14
PAG1 0.01 0.045 0.24 1 -0.27 7 8
RAP1A 0.032 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.012 0.047 0.14 1 -0.29 7 8
CD80 0.032 0.007 -10000 0 -0.066 1 1
CD86 0.027 0.021 -10000 0 -0.065 24 24
PDK1/CARD11/BCL10/MALT1 0.002 0.032 -10000 0 -0.13 12 12
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 0 0.041 0.14 7 -0.22 6 13
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.066 2 2
PTPRC 0.009 0.041 -10000 0 -0.065 122 122
PDK1/PKC theta -0.003 0.061 0.2 11 -0.27 7 18
CSK/PAG1 0.006 0.044 0.16 2 -0.26 7 9
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.046 0.011 -10000 0 -0.051 1 1
GRAP2/SLP76 0.034 0.057 0.2 4 -0.27 7 11
STIM1 -0.066 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.007 0.047 0.14 9 -0.15 20 29
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.014 0.051 -10000 0 -0.38 6 6
mol:DAG -0.02 0.026 -10000 0 -0.18 8 8
RAP1A/GDP 0.001 0.021 0.063 15 -0.045 11 26
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.032 0.008 -10000 0 -0.07 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 125 125
RAP1A/GTP 0.003 0.007 -10000 0 -0.056 4 4
mol:PI-3-4-5-P3 0.004 0.057 0.17 9 -0.24 9 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.013 0.052 -10000 0 -0.25 7 7
NRAS 0.008 0.042 -10000 0 -0.06 134 134
ZAP70 0.032 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.011 0.052 0.19 8 -0.26 6 14
MALT1 0.028 0.02 -10000 0 -0.065 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.022 13 13
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.02 -10000 0 -0.14 8 8
PRKCE -0.011 0.04 0.18 4 -0.16 5 9
PRKCQ -0.001 0.063 0.2 12 -0.28 8 20
LCP2 0.026 0.023 -10000 0 -0.065 29 29
BCL10 0.031 0.01 -10000 0 -0.065 4 4
regulation of survival gene product expression 0.001 0.05 0.15 9 -0.2 10 19
IKK complex -0.006 0.03 0.15 5 -0.085 5 10
RAS family/GDP -0.006 0.01 -10000 0 -0.03 11 11
MAP3K14 -0.003 0.038 0.13 6 -0.16 10 16
PDPK1 -0.001 0.05 0.15 10 -0.21 9 19
TCR/CD3/MHC I/CD8/Fyn 0.014 0.054 -10000 0 -0.39 5 5
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.02 0.032 0.16 7 -10000 0 7
DAPP1 0.005 0.061 0.15 24 -0.22 11 35
Src family/SYK family/BLNK-LAT/BTK-ITK -0.004 0.071 0.32 1 -0.25 19 20
mol:DAG -0.005 0.054 0.22 12 -0.13 4 16
HRAS 0.035 0.01 0.078 2 -10000 0 2
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.055 0.14 1 -0.24 16 17
PLCG2 0.03 0.014 -10000 0 -0.065 10 10
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARF5 0.022 0.015 -10000 0 -10000 0 0
mol:GTP -0.021 0.041 0.18 13 -10000 0 13
ARF1/GTP -0.014 0.032 0.15 11 -0.11 1 12
RHOA 0.032 0.006 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.065 74 74
RAP1A/GTP -0.022 0.033 0.15 11 -10000 0 11
ADAP1 -0.021 0.036 0.16 12 -10000 0 12
ARAP3 -0.021 0.041 0.18 13 -10000 0 13
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.03 0.012 -10000 0 -0.065 7 7
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.031 0.006 -10000 0 -10000 0 0
NRAS 0.012 0.043 -10000 0 -0.061 125 125
FYN 0.029 0.011 -10000 0 -0.065 1 1
ARF6 0.031 0.007 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
mol:Ca2+ -0.004 0.037 0.13 23 -10000 0 23
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.031 0.008 -10000 0 -10000 0 0
ZAP70 0.032 0.002 -10000 0 -10000 0 0
mol:IP3 -0.009 0.042 0.14 22 -10000 0 22
LYN 0.021 0.031 -10000 0 -0.058 67 67
ARF1/GDP 0.028 0.066 0.26 1 -0.22 23 24
RhoA/GDP 0.037 0.065 0.17 28 -0.12 5 33
PDK1/Src/Hsp90 0.057 0.023 -10000 0 -0.044 2 2
BLNK 0.013 0.032 -10000 0 -0.065 60 60
actin cytoskeleton reorganization 0.026 0.079 0.16 82 -0.18 6 88
SRC 0.03 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.003 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PTEN 0.023 0.02 -10000 0 -0.038 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.042 0.18 13 -10000 0 13
RhoA/GTP -0.023 0.044 0.18 14 -10000 0 14
Src family/SYK family/BLNK-LAT -0.019 0.067 -10000 0 -0.19 40 40
BLK 0.032 0.005 -10000 0 -10000 0 0
PDPK1 0.032 0.003 -10000 0 -10000 0 0
CYTH1 -0.021 0.036 0.16 12 -10000 0 12
HCK 0.014 0.036 -10000 0 -0.045 121 121
CYTH3 -0.021 0.036 0.16 12 -10000 0 12
CYTH2 -0.021 0.036 0.16 12 -10000 0 12
KRAS 0.034 0.011 0.079 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.029 0.3 1 -0.17 8 9
SGK1 0.001 0.03 -10000 0 -0.17 12 12
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.065 0.15 9 -0.22 24 33
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.025 -10000 0 -0.065 35 35
ARF6/GDP -0.018 0.043 0.2 11 -0.13 3 14
mol:PI-3-4-5-P3 -0.023 0.032 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.022 0.033 0.15 11 -10000 0 11
VAV1 0.031 0.007 -10000 0 -0.065 1 1
mol:PI-3-4-P2 -0.011 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.081 0.2 94 -0.07 3 97
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.057 0.2 2 -0.24 17 19
LAT 0.032 0.005 -10000 0 -0.065 1 1
Rac1/GTP 0.022 0.061 0.14 2 -0.24 18 20
ITK -0.025 0.038 0.16 11 -10000 0 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.059 0.26 8 -0.16 6 14
LCK 0.031 0.01 -10000 0 -0.065 4 4
BTK -0.025 0.041 0.16 14 -10000 0 14
Regulation of Telomerase

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
Telomerase catalytic core complex 0.021 0.086 0.25 1 -0.38 8 9
RAD9A 0.032 0.006 -10000 0 -0.065 1 1
AP1 0.021 0.042 -10000 0 -0.051 117 117
IFNAR2 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.015 -10000 0 -0.054 19 19
ER alpha/Oestrogen 0.023 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.051 -10000 0 -0.14 46 46
EGF 0.032 0.007 -10000 0 -0.064 2 2
SMG5 0.032 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.035 -10000 0 -0.053 65 65
TERT/c-Abl 0.033 0.088 -10000 0 -0.36 8 8
SAP18 0.03 0.008 -10000 0 -10000 0 0
MRN complex 0.063 0.015 -10000 0 -0.044 1 1
WT1 0.031 0.011 -10000 0 -0.066 5 5
WRN 0.031 0.01 -10000 0 -0.065 4 4
SP1 0.032 0.006 -10000 0 -0.026 1 1
SP3 0.018 0.034 -10000 0 -0.065 74 74
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.37 7 7
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
TERT 0.02 0.087 0.25 1 -0.39 8 9
CCND1 0.01 0.088 -10000 0 -0.4 7 7
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.065 89 89
TERF2 -0.02 0.019 0.047 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.044 0.062 -10000 0 -0.41 4 4
CDKN1B -0.025 0.012 -10000 0 -0.058 1 1
RAD1 0.031 0.008 -10000 0 -0.065 2 2
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.039 0.018 0.088 5 -10000 0 5
UBE3A 0.032 0.005 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.023 0.004 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
IFN-gamma/IRF1 0.037 0.036 -10000 0 -0.051 62 62
PARP2 0.031 0.008 -10000 0 0 31 31
BLM 0.009 0.041 -10000 0 -0.065 119 119
Telomerase 0.007 0.065 -10000 0 -0.24 30 30
IRF1 0.021 0.033 -10000 0 -0.065 66 66
ESR1 0.031 0.008 -10000 0 -10000 0 0
KU/TER 0.045 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.029 -10000 0 -0.061 30 30
ubiquitin-dependent protein catabolic process -0.003 0.053 -10000 0 -0.16 34 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.002 0.053 -10000 0 -0.16 33 33
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.03 0.012 -10000 0 -0.067 4 4
ATM 0.012 0.018 0.091 6 -0.053 25 31
SMAD3 -0.022 0.008 -10000 0 -0.05 26 26
ABL1 0.031 0.008 -10000 0 -0.065 1 1
MXD1 0.033 0.001 -10000 0 -10000 0 0
MRE11A 0.032 0.005 -10000 0 -10000 0 0
HUS1 0.023 0.015 -10000 0 -10000 0 0
RPS6KB1 0.032 0.006 -10000 0 -0.065 1 1
TERT/NF kappa B1/14-3-3 0.041 0.11 -10000 0 -0.4 13 13
NR2F2 0.031 0.009 -10000 0 -0.062 4 4
MAPK3 -0.022 0.003 -10000 0 -10000 0 0
MAPK1 -0.02 0.007 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.064 26 26
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
HNRNPC 0.031 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.018 0.091 6 -0.053 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.025 -10000 0 -0.051 8 8
MYC 0.009 0.041 -10000 0 -0.065 119 119
IL2 0.032 0.005 -10000 0 -10000 0 0
KU 0.045 0.013 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.064 26 26
TRF2/BLM 0.018 0.042 -10000 0 -0.054 114 114
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.097 -10000 0 -0.38 8 8
SP1/HDAC2 0.043 0.017 -10000 0 -0.054 4 4
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.047 0.097 -10000 0 -0.38 7 7
Smad3/Myc 0.007 0.036 -10000 0 -0.051 137 137
911 complex 0.044 0.032 -10000 0 -0.046 4 4
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.036 0.09 -10000 0 -0.37 7 7
Telomerase/AKT1/mTOR/p70S6K 0.01 0.093 0.17 1 -0.3 33 34
SIN3B 0.031 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.095 -10000 0 -0.37 7 7
response to DNA damage stimulus 0.003 0.014 -10000 0 -0.1 6 6
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.04 0.018 0.088 4 -0.053 4 8
Telomerase/hnRNP C1/C2 0.046 0.098 -10000 0 -0.38 7 7
E2F1 0.03 0.009 -10000 0 -10000 0 0
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.032 0.002 -10000 0 -10000 0 0
DKC1 0.031 0.012 -10000 0 -0.065 7 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.03 0.011 -10000 0 -0.065 3 3
GNB1/GNG2 -0.031 0.026 -10000 0 -0.12 12 12
AKT1 -0.006 0.083 0.23 14 -0.25 27 41
EGF 0.032 0.007 -10000 0 -0.065 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.021 0.063 0.28 17 -0.15 4 21
mol:Ca2+ -0.008 0.075 0.27 9 -0.27 14 23
LYN -0.022 0.066 0.27 19 -0.15 4 23
RhoA/GTP -0.006 0.036 -10000 0 -0.11 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.019 0.078 0.28 11 -0.26 11 22
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.051 0.14 6 -0.24 11 17
G beta5/gamma2 -0.034 0.036 -10000 0 -0.16 6 6
PRKCH -0.014 0.076 0.27 9 -0.28 14 23
DNM1 0.006 0.012 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 14 -0.002 11 25
PTGDR 0.031 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.023 0.051 -10000 0 -0.25 7 7
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
ADRBK2 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0.003 0.082 0.29 19 -0.26 10 29
mol:NADP 0.022 0.015 -10000 0 -10000 0 0
RAB11A 0.032 0.005 -10000 0 -10000 0 0
PRKG1 0.025 0.014 -10000 0 -10000 0 0
mol:IP3 -0.011 0.087 0.29 9 -0.33 14 23
cell morphogenesis 0.041 0.01 -10000 0 -10000 0 0
PLCB2 -0.017 0.1 0.34 6 -0.44 14 20
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.02 0.066 0.27 19 -0.15 4 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.028 0.046 0.24 10 -0.16 3 13
RHOA 0.032 0.006 -10000 0 -10000 0 0
PTGIR 0.031 0.007 -10000 0 -10000 0 0
PRKCB1 -0.014 0.079 0.27 8 -0.3 14 22
GNAQ 0.031 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.022 0.015 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.024 0.094 0.33 6 -0.38 12 18
LCK -0.021 0.065 0.28 18 -0.15 4 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.027 0.038 0.19 2 -0.1 27 29
TXA2-R family/G12 family/GDP/G beta/gamma 0.003 0.087 -10000 0 -0.42 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.026 0.039 0.19 2 -0.1 28 30
MAPK14 -0.017 0.059 0.23 11 -0.19 10 21
TGM2/GTP -0.011 0.092 0.34 4 -0.36 14 18
MAPK11 -0.015 0.058 0.23 10 -0.19 10 20
ARHGEF1 -0.018 0.032 -10000 0 -0.15 7 7
GNAI2 0.032 0.006 -10000 0 -10000 0 0
JNK cascade -0.018 0.079 0.28 9 -0.29 12 21
RAB11/GDP 0.031 0.009 -10000 0 -0.03 8 8
ICAM1 -0.014 0.062 0.22 10 -0.21 14 24
cAMP biosynthetic process -0.012 0.082 0.29 9 -0.31 14 23
Gq family/GTP/EBP50 0.013 0.039 0.22 8 -0.2 8 16
actin cytoskeleton reorganization 0.041 0.01 -10000 0 -10000 0 0
SRC -0.026 0.046 0.24 10 -0.15 4 14
GNB5 0.031 0.006 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.078 0.24 32 -0.16 11 43
VCAM1 -0.021 0.065 0.23 9 -0.21 14 23
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.051 0.14 6 -0.24 11 17
platelet activation -0.018 0.077 0.3 11 -0.25 11 22
PGI2/IP 0.023 0.005 -10000 0 0 27 27
PRKACA 0.009 0.028 -10000 0 -0.089 37 37
Gq family/GDP/G beta5/gamma2 0.009 0.045 0.14 7 -0.2 16 23
TXA2/TP beta/beta Arrestin2 -0.007 0.057 -10000 0 -0.33 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.024 -10000 0 -0.094 38 38
mol:DAG -0.014 0.088 0.29 9 -0.34 14 23
EGFR 0.012 0.018 -10000 0 -0.065 6 6
TXA2/TP alpha -0.016 0.1 0.33 9 -0.41 14 23
Gq family/GTP 0.008 0.026 0.21 6 -0.21 2 8
YES1 -0.024 0.06 0.27 15 -0.16 4 19
GNAI2/GTP 0.016 0.038 -10000 0 -0.1 35 35
PGD2/DP 0.023 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.065 2 2
FYN -0.017 0.065 0.27 19 -0.15 4 23
mol:NO 0.022 0.015 -10000 0 -10000 0 0
GNA15 0.03 0.013 -10000 0 -0.065 7 7
PGK/cGMP 0.026 0.022 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.009 -10000 0 -0.03 7 7
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.038 0.18 1 -0.1 27 28
NOS3 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.014 0.077 0.26 11 -0.28 14 25
PRKCB -0.012 0.075 0.26 9 -0.27 13 22
PRKCE -0.015 0.075 0.26 9 -0.28 12 21
PRKCD -0.017 0.078 0.26 11 -0.28 13 24
PRKCG -0.016 0.082 0.29 10 -0.3 14 24
muscle contraction -0.025 0.093 0.33 6 -0.36 14 20
PRKCZ -0.016 0.073 0.26 9 -0.26 12 21
ARR3 0.032 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.027 0.041 0.18 1 -0.1 37 38
PRKCQ -0.018 0.069 0.3 5 -0.28 14 19
MAPKKK cascade -0.019 0.092 0.29 9 -0.37 14 23
SELE -0.015 0.062 0.23 9 -0.21 14 23
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.039 0.18 2 -0.1 25 27
ROCK1 0.032 0.005 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.065 2 2
chemotaxis -0.029 0.095 0.33 6 -0.38 11 17
GNA12 0.023 0.015 -10000 0 0 152 152
GNA13 0.032 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.011 -10000 0 0 153 153
TCGA08_p53

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
CDKN2A -0.007 0.012 -10000 0 -0.04 53 53
TP53 -0.002 0.022 -10000 0 -0.2 5 5
Senescence -0.002 0.024 -10000 0 -0.2 6 6
Apoptosis -0.002 0.024 -10000 0 -0.2 6 6
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.009 0.022 43 -10000 0 43
MDM4 0.029 0.01 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.042 0.01 -10000 0 -0.04 1 1
cell-cell adhesion 0.028 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.077 0.045 -10000 0 -10000 0 0
ITSN1 0.032 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
SHC1 0.024 0.026 -10000 0 -0.065 40 40
Ephrin B1/EPHB3 0.041 0.013 -10000 0 -0.04 7 7
Ephrin B1/EPHB1 0.041 0.013 -10000 0 -0.04 9 9
HRAS/GDP 0.021 0.051 -10000 0 -0.15 25 25
Ephrin B/EPHB1/GRB7 0.078 0.046 -10000 0 -0.075 1 1
Endophilin/SYNJ1 -0.023 0.038 0.18 13 -10000 0 13
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.073 0.048 -10000 0 -0.075 1 1
endothelial cell migration 0.037 0.038 -10000 0 -0.046 14 14
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PAK1 -0.029 0.046 0.19 13 -10000 0 13
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.044 0.19 15 -10000 0 15
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.038 0.17 13 -10000 0 13
lamellipodium assembly -0.028 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.035 -10000 0 -0.15 9 9
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.065 1 1
EPHB3 0.03 0.013 -10000 0 -0.065 7 7
EPHB1 0.03 0.014 -10000 0 -0.065 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
mol:GDP -0.011 0.043 0.15 13 -0.16 19 32
Ephrin B/EPHB2 0.063 0.035 -10000 0 -0.047 1 1
Ephrin B/EPHB3 0.062 0.036 -10000 0 -0.049 7 7
JNK cascade -0.027 0.053 0.24 17 -10000 0 17
Ephrin B/EPHB1 0.062 0.037 -10000 0 -0.049 9 9
RAP1/GDP 0.03 0.1 0.19 130 -0.17 13 143
EFNB2 0.029 0.01 -10000 0 -10000 0 0
EFNB3 0.031 0.006 -10000 0 -10000 0 0
EFNB1 0.032 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.035 41 41
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.058 0.048 0.14 1 -0.11 21 22
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.04 1 1
MAPK3 -0.006 0.035 0.17 3 -0.19 4 7
MAPK1 -0.007 0.033 0.16 2 -0.19 4 6
Rac1/GDP -0.006 0.065 0.21 29 -0.18 12 41
actin cytoskeleton reorganization -0.035 0.033 -10000 0 -0.13 20 20
CDC42/GDP 0.037 0.11 0.2 136 -0.18 13 149
PI3K 0.04 0.042 -10000 0 -0.048 11 11
EFNA5 0.032 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.021 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.032 -10000 0 -0.11 23 23
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.022 -10000 0 -0.096 1 1
PTK2 -0.006 0.086 0.55 12 -10000 0 12
MAP4K4 -0.027 0.053 0.24 17 -10000 0 17
SRC 0.03 0.008 -10000 0 -10000 0 0
KALRN 0.032 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.022 -10000 0 -10000 0 0
neuron projection morphogenesis 0.061 0.17 0.33 131 -0.17 2 133
MAP2K1 0.004 0.035 -10000 0 -0.2 4 4
WASL 0.023 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.072 0.035 -10000 0 -0.051 21 21
cell migration -0.001 0.055 0.17 9 -0.22 8 17
NRAS 0.008 0.042 -10000 0 -0.065 125 125
SYNJ1 -0.023 0.039 0.18 13 -10000 0 13
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.034 0.18 8 -10000 0 8
HRAS/GTP 0.046 0.04 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.056 0.023 -10000 0 -0.037 22 22
cell adhesion mediated by integrin 0.013 0.039 -10000 0 -0.2 9 9
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0.051 0.039 0.14 5 -10000 0 5
RAC1-CDC42/GTP -0.034 0.027 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.019 0.064 0.22 23 -0.17 14 37
ruffle organization 0.067 0.16 0.32 133 -10000 0 133
NCK1 0.03 0.015 -10000 0 -0.065 11 11
receptor internalization -0.005 0.024 0.22 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.077 0.045 -10000 0 -10000 0 0
ROCK1 -0.015 0.04 0.18 21 -10000 0 21
RAS family/GDP -0.035 0.034 -10000 0 -0.13 24 24
Rac1/GTP -0.029 0.026 0.047 4 -10000 0 4
Ephrin B/EPHB1/Src/Paxillin 0.015 0.037 -10000 0 -0.12 32 32
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.022 0.03 -10000 0 -0.13 24 24
epithelial cell differentiation 0.06 0.032 -10000 0 -0.047 18 18
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
ENAH -0.045 0.051 0.41 4 -10000 0 4
EGFR 0.012 0.018 -10000 0 -0.065 6 6
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
MYO6 -0.029 0.029 0.16 10 -10000 0 10
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.028 0.033 -10000 0 -10000 0 0
AQP5 -0.014 0.045 0.16 7 -0.31 8 15
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
mol:PI-4-5-P2 -0.029 0.024 0.16 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.028 0.029 0.16 10 -10000 0 10
EGF 0.032 0.007 -10000 0 -0.065 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.076 0.16 4 -0.32 31 35
cortical microtubule organization 0.06 0.032 -10000 0 -0.047 18 18
GO:0000145 -0.028 0.023 0.15 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.066 0.034 -10000 0 -10000 0 0
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.053 0.015 -10000 0 -0.1 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.073 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.022 0.16 2 -0.19 1 3
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.024 0.026 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.051 -10000 0 -0.074 7 7
CDH1 0.03 0.013 -10000 0 -0.065 8 8
EGFR/EGFR/EGF/EGF 0.019 0.035 -10000 0 -10000 0 0
RhoA/GDP 0.061 0.034 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.025 0.14 7 -10000 0 7
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
IGF1R 0.032 0.004 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
DIAPH1 -0.22 0.26 -10000 0 -0.45 271 271
Wnt receptor signaling pathway -0.06 0.032 0.047 18 -10000 0 18
RHOA 0.032 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.015 -10000 0 -0.1 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.026 0.14 7 -10000 0 7
EFNA1 0.028 0.02 -10000 0 -0.065 21 21
LPP -0.035 0.021 0.15 4 -10000 0 4
Ephrin A1/EPHA2 0.046 0.041 -10000 0 -0.072 8 8
SEC6/SEC8 -0.042 0.011 -10000 0 -10000 0 0
MGAT3 -0.028 0.029 0.16 10 -10000 0 10
HGF/MET 0.035 0.038 -10000 0 -0.073 1 1
HGF 0.022 0.016 -10000 0 -0.065 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.022 0.03 -10000 0 -0.13 24 24
actin cable formation -0.04 0.074 0.32 11 -0.23 10 21
KIAA1543 -0.024 0.022 0.15 8 -10000 0 8
KIFC3 -0.031 0.024 0.16 7 -10000 0 7
NCK1 0.03 0.015 -10000 0 -0.065 11 11
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ACTN1 -0.031 0.026 0.16 7 -10000 0 7
NCK1/GIT1 0.044 0.017 -10000 0 -0.051 11 11
mol:GDP 0.06 0.032 -10000 0 -0.047 18 18
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.031 0.027 0.16 9 -10000 0 9
PIP5K1C -0.029 0.025 0.16 7 -10000 0 7
LIMA1 -0.05 0.034 -10000 0 -0.065 425 425
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.042 0.065 0.41 7 -10000 0 7
adherens junction assembly -0.023 0.042 0.2 6 -0.2 10 16
IGF-1R heterotetramer/IGF1 0.053 0.035 -10000 0 -0.073 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.065 2 2
PLEKHA7 -0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0.065 0.041 -10000 0 -0.073 7 7
establishment of epithelial cell apical/basal polarity -0.04 0.041 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.022 0.03 -10000 0 -0.13 24 24
regulation of cell-cell adhesion -0.024 0.025 0.14 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.022 0.03 -10000 0 -0.13 24 24
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.027 0.071 0.22 32 -0.32 5 37
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -0.052 34 34
PDGFB-D/PDGFRB/APS/CBL 0.043 0.009 -10000 0 -0.04 2 2
AKT1 -0.019 0.077 0.3 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.075 0.23 35 -0.36 5 40
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FGR 0.009 0.062 0.19 21 -0.37 7 28
mol:Ca2+ 0.024 0.072 0.22 32 -0.39 5 37
MYC 0.046 0.12 0.3 42 -0.31 4 46
SHC1 0.024 0.026 -10000 0 -0.05 52 52
HRAS/GDP -0.016 0.053 0.17 36 -10000 0 36
LRP1/PDGFRB/PDGFB 0.054 0.03 -10000 0 -0.045 28 28
GRB10 0.022 0.017 -10000 0 -0.065 4 4
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.22 30 -0.4 5 35
PTEN 0.023 0.016 -10000 0 -0.065 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.01 -10000 0 -0.051 2 2
PDGFB-D/PDGFRB/GRB10 0.032 0.024 -10000 0 -0.051 6 6
cell cycle arrest 0.04 0.026 -10000 0 -0.052 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.024 0.07 0.27 12 -10000 0 12
GAB1 0.019 0.077 0.23 26 -0.34 8 34
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.016 0.085 0.25 37 -0.28 8 45
PDGFB-D/PDGFRB 0.055 0.026 -10000 0 -0.055 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.011 -10000 0 -0.051 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.053 0.2 10 -0.26 5 15
positive regulation of MAPKKK cascade 0.047 0.01 -10000 0 -0.051 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.073 0.22 30 -0.4 5 35
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.03 0.01 -10000 0 -0.032 11 11
PDGFB-D/PDGFRB/GRB7 0.047 0.011 -10000 0 -0.051 3 3
SHB 0.03 0.009 -10000 0 -10000 0 0
BLK 0.009 0.057 0.34 1 -0.36 7 8
PTPN2 0.032 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -0.051 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.016 0.085 0.25 26 -0.34 8 34
CBL 0.032 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.046 0.011 -10000 0 -0.051 2 2
LCK 0.013 0.057 0.19 22 -0.35 5 27
PDGFRB 0.032 0.008 -10000 0 -0.054 3 3
ACP1 0.032 0.005 -10000 0 -10000 0 0
HCK 0 0.035 0.18 1 -10000 0 1
ABL1 0.02 0.074 0.21 34 -0.27 8 42
PDGFB-D/PDGFRB/CBL 0.024 0.08 0.24 19 -0.38 8 27
PTPN1 0.03 0.009 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT1 0.029 0.018 -10000 0 -0.065 18 18
cell proliferation 0.046 0.11 0.3 42 -0.29 4 46
SLA 0.025 0.024 -10000 0 -0.065 33 33
actin cytoskeleton reorganization -0.016 0.067 0.2 40 -10000 0 40
SRC 0.01 0.043 -10000 0 -0.73 1 1
PI3K -0.042 0.021 -10000 0 -0.093 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.035 -10000 0 -0.049 46 46
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.036 0.077 0.24 35 -0.37 5 40
LYN 0.004 0.041 0.18 4 -0.27 2 6
LRP1 0.029 0.017 -10000 0 -0.065 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.004 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
NCK1-2/p130 Cas 0.066 0.037 -10000 0 -10000 0 0
SPHK1 0.029 0.019 -10000 0 -0.065 18 18
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.024 0.073 0.22 30 -0.4 5 35
PLCG1 0.025 0.074 0.22 30 -0.41 5 35
NHERF/PDGFRB 0.063 0.018 -10000 0 -0.043 9 9
YES1 -0.006 0.095 0.19 11 -0.57 11 22
cell migration 0.062 0.018 -10000 0 -0.043 9 9
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.078 1 1
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.065 2 2
NHERF1-2/PDGFRB/PTEN 0.047 0.056 -10000 0 -0.061 1 1
FYN -0.02 0.11 0.18 3 -0.36 44 47
DOK1 -0.015 0.053 0.17 38 -10000 0 38
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.057 0.12 0.25 101 -0.42 4 105
PRKCD -0.015 0.054 0.17 37 -10000 0 37
FER -0.016 0.053 0.18 36 -10000 0 36
MAPKKK cascade -0.011 0.072 0.18 56 -10000 0 56
RASA1 -0.015 0.053 0.18 36 -10000 0 36
NCK1 0.03 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.003 -10000 0 -10000 0 0
p62DOK/Csk -0.02 0.052 0.17 37 -10000 0 37
PDGFB-D/PDGFRB/SHB 0.044 0.015 -10000 0 -0.051 2 2
chemotaxis 0.02 0.073 0.21 34 -0.27 8 42
STAT1-3-5/STAT1-3-5 0.063 0.043 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.023 0.006 0.052 2 -0.041 2 4
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC3 0.032 0.004 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.057 -10000 0 -0.18 32 32
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
AKT1 0.004 0.053 0.14 5 -0.19 16 21
RAR alpha/9cRA/Cyclin H 0.007 0.087 0.18 2 -0.22 16 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.052 0.091 7 -0.15 43 50
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.045 0.15 1 -0.16 22 23
NCOR2 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.003 0.071 0.25 2 -0.3 13 15
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA3 0.03 0.011 -10000 0 -0.065 2 2
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 -10000 0 0
RARG 0.032 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.033 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -0.027 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.072 -10000 0 -0.29 17 17
RARA 0.012 0.007 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.05 0.091 7 -0.15 40 47
PRKCA 0.033 0.006 -10000 0 -0.032 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.068 -10000 0 -0.3 12 12
RXRG 0.019 0.007 -10000 0 -0.034 2 2
RXRA -0.013 0.044 0.1 8 -0.099 4 12
RXRB 0.019 0.006 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 -10000 0 0
RBP1 -0.011 0.047 -10000 0 -0.065 222 222
CRBP1/9-cic-RA -0.005 0.031 -10000 0 -0.04 222 222
RARB 0.032 0.006 -10000 0 -0.025 3 3
PRKCG 0.031 0.009 -10000 0 -0.032 3 3
MNAT1 0.03 0.009 -10000 0 -0.065 1 1
RAR alpha/RXRs 0.004 0.08 0.2 1 -0.33 17 18
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.066 0.2 1 -0.27 16 17
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.063 0.16 2 -0.18 35 37
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.067 -10000 0 -0.31 10 10
positive regulation of DNA binding 0.001 0.08 0.15 2 -0.2 18 20
NRIP1 0.008 0.066 0.27 1 -0.34 5 6
RXRs/RARs 0.008 0.067 -10000 0 -0.3 14 14
RXRs/RXRs/DNA/9cRA -0.004 0.065 -10000 0 -0.28 18 18
PRKACA 0.031 0.006 -10000 0 -10000 0 0
CDK7 0.031 0.008 -10000 0 -0.065 2 2
TFIIH 0.059 0.022 -10000 0 -0.048 8 8
RAR alpha/9cRA 0.024 0.081 -10000 0 -0.21 8 8
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.053 0.033 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.018 -10000 0 -0.025 4 4
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.065 5 5
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.062 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.03 -10000 0 -0.051 5 5
alpha4/beta7 Integrin/Paxillin 0.046 0.016 -10000 0 -0.059 5 5
lamellipodium assembly -0.011 0.081 -10000 0 -0.25 35 35
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.039 0.023 -10000 0 -0.051 16 16
ARF6 0.031 0.007 -10000 0 -10000 0 0
TLN1 0.021 0.028 -10000 0 -0.065 43 43
PXN -0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.05 0.14 7 -10000 0 7
cell adhesion 0.031 0.053 0.16 6 -0.07 2 8
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.023 -10000 0 -0.052 5 5
ITGB1 0.025 0.014 -10000 0 -10000 0 0
ITGB7 0.031 0.008 -10000 0 -0.065 2 2
ARF6/GDP 0.033 0.013 -10000 0 -0.025 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.021 0.054 0.17 3 -0.073 2 5
p130Cas/Crk/Dock1 0.031 0.02 -10000 0 -10000 0 0
VCAM1 -0.032 0.046 -10000 0 -0.065 333 333
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.054 0.17 6 -0.073 1 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.048 0.17 7 -10000 0 7
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.047 -10000 0 -0.16 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.054 0.17 6 -0.073 1 7
Rac1/GTP -0.012 0.088 -10000 0 -0.28 35 35
Syndecan-3-mediated signaling events

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
CTTN 0.032 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.069 -10000 0 -0.27 15 15
Syndecan-3/Neurocan 0.011 0.068 -10000 0 -0.29 21 21
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.065 6 6
Syndecan-3/EGFR 0 0.063 -10000 0 -0.33 13 13
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.027 0.022 -10000 0 -0.065 28 28
PSENEN 0.031 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.065 7 7
NCAN 0.026 0.014 -10000 0 -0.065 2 2
long-term memory 0.03 0.076 -10000 0 -0.3 22 22
Syndecan-3/IL8 0.003 0.082 -10000 0 -0.35 22 22
PSEN1 0.03 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.044 0.013 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
limb bud formation -0.006 0.074 -10000 0 -0.36 20 20
MC4R 0.031 0.007 -10000 0 -0.065 1 1
SRC 0.03 0.008 -10000 0 -10000 0 0
PTN 0.021 0.015 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.006 0.074 -10000 0 -0.36 20 20
neuron projection morphogenesis 0.015 0.085 0.16 104 -0.3 5 109
Syndecan-3/AgRP 0.015 0.081 -10000 0 -0.35 22 22
Syndecan-3/AgRP/MC4R 0.031 0.084 -10000 0 -0.34 22 22
Fyn/Cortactin 0.043 0.016 -10000 0 -0.051 1 1
SDC3 -0.006 0.075 -10000 0 -0.37 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.081 -10000 0 -0.35 22 22
IL8 0.011 0.04 -10000 0 -0.065 110 110
Syndecan-3/Fyn/Cortactin 0.031 0.077 -10000 0 -0.3 22 22
Syndecan-3/CASK -0.008 0.073 -10000 0 -0.35 21 21
alpha-MSH/MC4R 0.046 0.011 -10000 0 -0.051 1 1
Gamma Secretase 0.071 0.053 -10000 0 -0.076 2 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.065 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.031 -10000 0 -0.049 2 2
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
KATNA1 0.029 0.012 -10000 0 -0.065 5 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.012 0.063 0.18 64 -10000 0 64
IQGAP1/CaM 0.021 0.041 -10000 0 -0.051 111 111
DAB1 0.032 0.005 -10000 0 -10000 0 0
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
PLA2G7 0.03 0.013 -10000 0 -0.065 8 8
CALM1 0.029 0.01 -10000 0 -10000 0 0
DYNLT1 0.017 0.034 -10000 0 -0.065 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.008 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.003 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.016 0.005 -10000 0 -10000 0 0
CDK5R2 0.012 0.016 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.019 0.031 -10000 0 -0.049 3 3
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.026 0.095 0.29 50 -10000 0 50
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.001 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.01 0.044 0.18 5 -10000 0 5
RELN 0.01 0.016 -10000 0 -0.065 2 2
PAFAH/LIS1 0.025 0.015 -10000 0 -0.042 16 16
LIS1/CLIP170 0.026 0.012 -10000 0 -0.035 10 10
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.005 0.039 0.14 4 -10000 0 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.046 0.13 4 -0.21 20 24
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.02 0.075 0.3 30 -10000 0 30
LIS1/IQGAP1 0.008 0.033 -10000 0 -0.048 124 124
RHOA 0 0.031 -10000 0 -0.26 6 6
PAFAH1B1 -0.02 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.032 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.02 0.027 0.11 1 -0.15 5 6
NDEL1/Katanin 60/Dynein heavy chain 0.028 0.097 0.3 46 -10000 0 46
LRP8 0.032 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.091 0.29 44 -10000 0 44
P39/CDK5 0.003 0.03 0.17 3 -10000 0 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -0.035 9 9
CDK5 0.011 0.042 0.18 9 -10000 0 9
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.01 -10000 0 -0.029 10 10
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.035 0.17 5 -10000 0 5
RELN/VLDLR 0.024 0.039 -10000 0 -10000 0 0
CDC42 -0.001 0.033 -10000 0 -0.26 7 7
Syndecan-2-mediated signaling events

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.015 0.028 -10000 0 -0.066 4 4
EPHB2 0.031 0.007 -10000 0 -0.065 1 1
Syndecan-2/TACI 0.027 0.011 -10000 0 -0.057 3 3
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.053 -10000 0 -0.072 4 4
HRAS 0.031 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.005 -10000 0 -0.063 1 1
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
BAX -0.012 0.012 -10000 0 -0.12 3 3
EPB41 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.025 0.01 -10000 0 -0.063 1 1
LAMA3 0.029 0.017 -10000 0 -0.065 15 15
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.029 -10000 0 -0.065 49 49
Syndecan-2/MMP2 -0.004 0.034 -10000 0 -0.068 7 7
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.035 -10000 0 -0.051 64 64
dendrite morphogenesis 0.027 0.012 -10000 0 -0.057 3 3
Syndecan-2/GM-CSF 0.027 0.011 -10000 0 -0.072 1 1
determination of left/right symmetry -0.009 0.006 -10000 0 -0.079 1 1
Syndecan-2/PKC delta 0.027 0.012 -10000 0 -0.057 3 3
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.018 0.026 0.19 8 -10000 0 8
MAPK1 -0.017 0.027 0.19 8 -10000 0 8
Syndecan-2/RACK1 0.041 0.02 -10000 0 -0.066 1 1
NF1 0.032 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.006 -10000 0 -0.079 1 1
ITGA2 0.015 0.037 -10000 0 -0.065 90 90
MAPK8 -0.011 0.009 -10000 0 -0.1 1 1
Syndecan-2/alpha2/beta1 Integrin 0.016 0.039 -10000 0 -0.061 2 2
Syndecan-2/Kininogen 0.027 0.011 -10000 0 -0.057 3 3
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.02 0.028 0.17 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.025 0.011 -10000 0 -0.064 1 1
extracellular matrix organization 0.023 0.019 -10000 0 -0.058 4 4
actin cytoskeleton reorganization 0.015 0.028 -10000 0 -0.066 4 4
Syndecan-2/Caveolin-2/Ras 0.023 0.031 -10000 0 -0.066 2 2
Syndecan-2/Laminin alpha3 0.025 0.015 -10000 0 -0.064 3 3
Syndecan-2/RasGAP 0.054 0.027 -10000 0 -0.069 1 1
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.051 61 61
PRKCD 0.032 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.027 0.012 -10000 0 -0.057 3 3
GO:0007205 0.001 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.023 0.18 3 -10000 0 3
RHOA 0.032 0.006 -10000 0 -10000 0 0
SDCBP 0.032 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.024 0.035 -10000 0 -0.051 64 64
Syndecan-2/Synbindin 0.027 0.011 -10000 0 -0.057 3 3
TGFB1 0.026 0.022 -10000 0 -0.065 26 26
CASP3 -0.021 0.027 0.19 7 -10000 0 7
FN1 0.014 0.038 -10000 0 -0.065 96 96
Syndecan-2/IL8 0.013 0.029 -10000 0 -0.058 4 4
SDC2 -0.009 0.006 -10000 0 -0.079 1 1
KNG1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.028 0.011 -10000 0 -0.057 3 3
TRAPPC4 0.032 0.005 -10000 0 -10000 0 0
CSF2 0.032 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.019 -10000 0 -0.058 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.025 0.01 -10000 0 -0.064 1 1
Syndecan-2/Ezrin 0.024 0.011 -10000 0 -0.064 1 1
PRKACA -0.017 0.028 0.19 9 -10000 0 9
angiogenesis 0.013 0.029 -10000 0 -0.058 4 4
MMP2 -0.014 0.048 -10000 0 -0.065 241 241
IL8 0.011 0.04 -10000 0 -0.065 110 110
calcineurin-NFAT signaling pathway 0.027 0.011 -10000 0 -0.057 3 3
IL6-mediated signaling events

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
BCL2L1 0.059 0.13 0.39 33 -10000 0 33
CRP 0.049 0.12 0.38 16 -10000 0 16
cell cycle arrest 0.052 0.12 0.31 34 -10000 0 34
TIMP1 0.015 0.11 0.38 6 -0.53 1 7
IL6ST 0.031 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.056 0.22 10 -0.22 3 13
AP1 0.033 0.065 -10000 0 -0.35 5 5
GAB2 0.032 0.007 -10000 0 -0.026 1 1
TNFSF11 0.046 0.11 0.35 13 -10000 0 13
HSP90B1 0.042 0.051 -10000 0 -0.55 1 1
GAB1 0.032 0.009 -10000 0 -0.055 4 4
MAPK14 0.01 0.045 0.18 2 -0.21 3 5
AKT1 0.022 0.041 0.23 1 -0.45 2 3
FOXO1 0.016 0.043 0.21 3 -0.44 2 5
MAP2K6 0.007 0.038 0.12 10 -0.22 3 13
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.008 0.062 0.26 11 -0.26 1 12
MITF 0.006 0.038 0.11 28 -0.21 2 30
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -10000 0 0
A2M -0.021 0.18 -10000 0 -0.94 18 18
CEBPB 0.03 0.017 -10000 0 -0.063 11 11
GRB2/SOS1/GAB family/SHP2 0.021 0.044 0.23 1 -0.27 4 5
STAT3 0.05 0.12 0.35 18 -10000 0 18
STAT1 0.017 0.023 -10000 0 -10000 0 0
CEBPD 0.048 0.11 0.37 13 -10000 0 13
PIK3CA 0.028 0.019 -10000 0 -0.062 18 18
PI3K 0.04 0.023 -10000 0 -0.05 17 17
JUN 0.032 0.004 -10000 0 -10000 0 0
PIAS3/MITF 0.056 0.076 0.19 78 -0.21 2 80
MAPK11 0.008 0.042 0.18 2 -0.21 3 5
STAT3 (dimer)/FOXO1 -0.005 0.065 0.27 1 -0.4 1 2
GRB2/SOS1/GAB family 0.058 0.058 0.17 6 -0.21 3 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.033 -10000 0 -0.2 4 4
GRB2 0.032 0.006 -10000 0 -0.027 1 1
JAK2 0.029 0.01 -10000 0 -10000 0 0
LBP 0.06 0.12 0.36 24 -0.62 1 25
PIK3R1 0.03 0.01 -10000 0 -0.026 1 1
JAK1 0.031 0.008 -10000 0 -10000 0 0
MYC 0.042 0.12 0.38 14 -10000 0 14
FGG 0.046 0.11 0.35 13 -10000 0 13
macrophage differentiation 0.052 0.12 0.31 34 -10000 0 34
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.058 -10000 0 -10000 0 0
JUNB 0.051 0.12 0.37 26 -10000 0 26
FOS 0.007 0.041 -10000 0 -0.065 120 120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.041 0.13 14 -0.23 3 17
STAT1/PIAS1 0.04 0.063 0.2 16 -10000 0 16
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.04 -10000 0 -0.47 2 2
STAT3 (dimer) 0.052 0.12 0.32 25 -10000 0 25
PRKCD 0.071 0.15 0.3 129 -10000 0 129
IL6R 0.032 0.006 -10000 0 -10000 0 0
SOCS3 0.048 0.083 0.38 8 -10000 0 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.06 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.051 0.19 3 -0.22 3 6
HCK 0.014 0.036 -10000 0 -0.065 85 85
MAPKKK cascade 0.042 0.059 0.28 1 -0.38 5 6
bone resorption 0.046 0.11 0.33 16 -10000 0 16
IRF1 0.042 0.11 0.34 14 -10000 0 14
mol:GDP 0.004 0.039 0.11 20 -0.22 3 23
SOS1 0 0.002 -10000 0 -10000 0 0
VAV1 0.004 0.04 0.11 20 -0.22 3 23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.018 0.046 0.2 1 -0.3 5 6
PTPN11 0.017 0.044 -10000 0 -0.63 2 2
IL6/IL6RA 0.026 0.031 -10000 0 -0.059 8 8
gp130 (dimer)/TYK2/TYK2/LMO4 0.059 0.022 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.03 -10000 0 -0.05 1 1
IL6 0.015 0.027 -10000 0 -0.067 36 36
PIAS3 0.032 0.004 -10000 0 -10000 0 0
PTPRE 0.023 0.015 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.035 0.11 39 -0.12 1 40
LMO4 0.03 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.022 0.077 0.29 1 -10000 0 1
MCL1 0.021 0.048 0.25 1 -0.41 2 3
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.02 0.032 -9999 0 -0.065 61 61
Ran/GTP/Exportin 1/HDAC4 -0.027 0.01 -9999 0 -0.062 38 38
MDM2/SUMO1 0.034 0.039 -9999 0 -0.097 35 35
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.028 0.012 -9999 0 -0.066 37 37
SUMO1 0.033 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.026 -9999 0 -0.096 39 39
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.039 -9999 0 -0.097 39 39
SUMO1/HDAC1 0.03 0.044 -9999 0 -0.1 38 38
RANGAP1 0.03 0.008 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.07 0.034 -9999 0 -0.051 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.028 -9999 0 -0.095 39 39
Ran/GTP 0.022 0.033 -9999 0 -0.092 38 38
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.011 -9999 0 -0.065 1 1
UBE2I 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 -9999 0 -0.096 38 38
NPC 0.019 0.001 -9999 0 -10000 0 0
PIAS2 0.031 0.006 -9999 0 -10000 0 0
PIAS1 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.031 0.008 -10000 0 -10000 0 0
SPHK1 0.029 0.018 -10000 0 -0.065 18 18
GNAI2 0.032 0.006 -10000 0 -10000 0 0
mol:S1P 0.009 0.01 -10000 0 -0.032 23 23
GNAO1 0.003 0.009 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.022 0.008 -10000 0 -0.051 18 18
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.035 -10000 0 -0.11 14 14
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
G12/G13 0.034 0.022 -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 0.002 0.024 -10000 0 -0.11 21 21
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
S1P/S1P5/G12 0.016 0.027 -10000 0 -0.11 14 14
S1P/S1P3/Gq 0.019 0.044 0.15 8 -0.28 8 16
S1P/S1P4/Gi -0.005 0.041 -10000 0 -0.22 16 16
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.023 0.015 -10000 0 0 152 152
GNA13 0.032 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
ABCC1 0.031 0.012 -10000 0 -0.065 8 8
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
GNB1/GNG2 0.028 0.021 -10000 0 -10000 0 0
forebrain development 0.025 0.052 0.2 17 -10000 0 17
GNAO1 0.003 0.009 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.033 0.023 -10000 0 -10000 0 0
SMO 0.022 0.015 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
GLI3/SPOP 0.01 0.069 -10000 0 -0.21 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.031 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -0.026 1 1
SIN3/HDAC complex 0.052 0.028 -10000 0 -0.039 5 5
GNAI1 0.019 0.016 -10000 0 -0.064 1 1
XPO1 0.033 0.007 -10000 0 -0.027 6 6
GLI1/Su(fu) 0.006 0.024 -10000 0 -0.24 1 1
SAP30 0.032 0.005 -10000 0 -10000 0 0
mol:GDP 0.022 0.015 -10000 0 -10000 0 0
MIM/GLI2A 0.034 0.008 -10000 0 -0.04 3 3
IFT88 0.031 0.008 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GLI2 0.012 0.049 0.15 12 -0.22 9 21
GLI3 -0.005 0.062 -10000 0 -0.22 15 15
CSNK1D 0.032 0.007 -10000 0 -0.065 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
SAP18 0.03 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.03 0.008 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.01 0.089 1 -0.12 2 3
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.004 0.045 0.1 1 -0.19 17 18
GLI2/Su(fu) 0.006 0.035 0.12 3 -0.19 8 11
FOXA2 0.037 0.037 -10000 0 -0.47 2 2
neural tube patterning 0.025 0.052 0.2 17 -10000 0 17
SPOP 0.032 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.034 0.093 152 -0.063 7 159
GNB1 0.031 0.008 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
MTSS1 0.034 0.008 -10000 0 -0.04 3 3
embryonic limb morphogenesis 0.025 0.052 0.2 17 -10000 0 17
SUFU 0.001 0.002 -10000 0 -10000 0 0
LGALS3 0.018 0.032 -10000 0 -0.065 61 61
catabolic process 0.027 0.078 0.2 8 -0.29 14 22
GLI3A/CBP 0.036 0.016 -10000 0 -0.085 8 8
KIF3A 0.029 0.01 -10000 0 -10000 0 0
GLI1 0.026 0.052 0.2 14 -10000 0 14
RAB23 0.031 0.01 -10000 0 -0.065 5 5
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.034 0.038 0.093 126 -0.062 5 131
GNAZ 0.027 0.013 -10000 0 -10000 0 0
RBBP4 0.015 0.037 -10000 0 -0.065 89 89
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.029 0.051 0.16 12 -0.22 9 21
STK36 0.001 0.001 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0 0.014 -10000 0 -0.14 4 4
PTCH1 0.024 0.058 0.3 6 -10000 0 6
MIM/GLI1 0.043 0.055 0.21 12 -10000 0 12
CREBBP 0.036 0.016 -10000 0 -0.085 8 8
Su(fu)/SIN3/HDAC complex 0.007 0.057 0.13 3 -0.18 31 34
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.083 -10000 0 -0.39 19 19
HDAC1 0.022 0.031 -10000 0 -0.061 61 61
AES 0.032 0.007 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.024 -10000 0 -0.051 4 4
TLE1 0.032 0.006 -10000 0 -10000 0 0
AP1 0.002 0.022 -10000 0 -0.14 4 4
NCSTN 0.027 0.022 -10000 0 -0.065 28 28
ADAM10 0.028 0.019 -10000 0 -0.064 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.058 -10000 0 -0.51 4 4
NICD/RBPSUH 0.028 0.088 -10000 0 -0.39 19 19
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.082 -10000 0 -0.44 15 15
PSENEN 0.031 0.007 -10000 0 -10000 0 0
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.005 0.037 -10000 0 -0.065 101 101
beta catenin/beta TrCP1 0.063 0.078 0.2 71 -0.23 6 77
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.065 7 7
AXIN1 0.026 0.047 0.26 4 -0.25 1 5
CtBP/CBP/TCF1/TLE1/AES 0.022 0.031 -10000 0 -0.12 11 11
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
JUN 0.032 0.005 -10000 0 -10000 0 0
MAP3K7 0.031 0.009 -10000 0 -0.065 1 1
CTNNB1 0.048 0.081 0.19 79 -0.23 6 85
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.022 -10000 0 -0.049 9 9
HNF1A 0.033 0.003 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.006 0.066 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.022 0.017 -10000 0 -0.065 4 4
NOTCH1 precursor/Deltex homolog 1 0.005 0.081 -10000 0 -0.39 19 19
apoptosis 0.002 0.022 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.005 0.081 -10000 0 -0.39 19 19
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.018 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.071 0.053 -10000 0 -0.077 2 2
APC 0.01 0.084 0.26 3 -0.33 20 23
DVL1 0.018 0.021 -10000 0 -0.2 2 2
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.025 0.047 -10000 0 -0.048 105 105
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -0.038 1 1
CCND1 -0.006 0.11 -10000 0 -0.8 7 7
WNT1 0.031 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.085 0.26 17 -0.4 4 21
DKK2 0.03 0.013 -10000 0 -0.065 8 8
NOTCH1 precursor/DVL1 0.034 0.091 0.25 1 -0.39 15 16
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.014 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.083 -10000 0 -0.39 19 19
PPP2R5D 0.015 0.03 -10000 0 -0.39 2 2
MAPK1 0.03 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.007 0.024 -10000 0 -10000 0 0
RBPJ 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.005 -10000 0 -0.022 1 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.01 -10000 0 -10000 0 0
Necdin/E2F1 0.028 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.068 0.032 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 0.028 0.024 -10000 0 -0.04 16 16
NT-4/5 (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.04 21 21
IKBKB 0.032 0.003 -10000 0 0 5 5
AKT1 -0.013 0.046 0.18 21 -10000 0 21
IKBKG 0.032 0.003 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.02 0.011 -10000 0 -0.032 21 21
FURIN 0.032 0.004 -10000 0 0 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.049 8 8
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.049 0.015 -10000 0 -0.089 1 1
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.032 0.006 -10000 0 -0.065 1 1
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.078 0.22 6 -0.31 18 24
IRAK1 0.032 0.003 -10000 0 -10000 0 0
SHC1 -0.02 0.008 -10000 0 -0.041 59 59
ARHGDIA 0.032 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.071 0.053 -10000 0 -0.076 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.027 -10000 0 -0.043 18 18
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.034 0.034 -10000 0 -0.043 14 14
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.003 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.029 0.012 -10000 0 -0.065 4 4
RhoA/GDP/RHOGDI 0.037 0.018 -10000 0 -0.039 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.027 -10000 0 -0.11 14 14
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.018 -10000 0 -0.04 21 21
NCSTN 0.027 0.022 -10000 0 -0.065 28 28
mol:GTP 0.035 0.021 -10000 0 -0.041 20 20
PSENEN 0.031 0.007 -10000 0 -10000 0 0
mol:ceramide -0.02 0.023 0.18 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.022 -10000 0 -0.1 15 15
p75(NTR)/beta APP 0.043 0.021 -10000 0 -0.051 20 20
BEX1 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.005 -10000 0 -0.032 21 21
NGF (dimer) 0.039 0.043 -10000 0 -0.044 75 75
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.016 -10000 0 -0.035 22 22
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.021 -10000 0 -0.031 21 21
MYD88 0.019 0.033 -10000 0 -0.065 66 66
CHUK 0.024 0.015 -10000 0 -0.065 1 1
NGF (dimer)/p75(NTR)/PKA 0.035 0.021 -10000 0 -0.041 20 20
RHOB 0.03 0.011 -10000 0 -0.065 4 4
RHOA 0.032 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
TP53 0.033 0.064 0.23 25 -10000 0 25
PRDM4 -0.021 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.014 0.038 -10000 0 -0.071 3 3
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
SORT1 0.032 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.061 0.03 -10000 0 -0.054 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.055 0.027 -10000 0 -0.043 20 20
RHOC 0.002 0.045 -10000 0 -0.065 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.038 0.075 0.19 78 -10000 0 78
DIABLO 0.032 0.004 -10000 0 -10000 0 0
SMPD2 -0.02 0.023 0.18 6 -10000 0 6
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.065 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.018 -10000 0 -0.04 20 20
PSEN1 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.051 3 3
NT3 (dimer)/p75(NTR) 0.042 0.022 -10000 0 -0.051 20 20
MAPK8 0.036 0.066 0.18 69 -0.14 1 70
MAPK9 0.066 0.087 0.19 137 -10000 0 137
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.016 -10000 0 -10000 0 0
RAC1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.023 0.056 -10000 0 -0.067 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.036 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.035 0.021 -10000 0 -0.041 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.022 0.043 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.038 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.022 -10000 0 -0.051 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.024 -10000 0 -0.12 2 2
BAD 0.049 0.081 0.21 62 -0.16 2 64
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
NGFR 0.028 0.02 -10000 0 -0.065 21 21
CYCS -0.018 0.022 0.17 4 -10000 0 4
ADAM17 0.031 0.01 -10000 0 -0.065 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.055 0.026 -10000 0 -0.043 22 22
BCL2L11 0.049 0.081 0.21 62 -0.16 2 64
BDNF (dimer)/p75(NTR) 0.012 0.023 -10000 0 -0.051 9 9
PI3K 0.047 0.033 -10000 0 -0.045 32 32
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.017 -10000 0 -0.033 25 25
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
NGF (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.04 21 21
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.024 -10000 0 -0.043 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.012 0.14 1 -0.075 1 2
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.047 0.079 0.21 60 -0.17 3 63
E2F1 0.03 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -0.065 3 3
IKK complex 0.037 0.048 -10000 0 -0.15 5 5
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -0.04 1 1
MMP7 0.018 0.034 -10000 0 -0.065 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.038 -10000 0 -0.054 1 1
MMP3 0.031 0.012 -10000 0 -0.065 7 7
APAF-1/Caspase 9 -0.035 0.026 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.051 -10000 0 -0.074 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.041 0.054 0.2 18 -10000 0 18
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.046 0.042 0.16 2 -0.047 78 80
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.033 -10000 0 -0.1 37 37
CaM/Ca2+ 0.047 0.055 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.034 0.035 0.15 16 -10000 0 16
AKT1 -0.023 0.063 0.27 9 -10000 0 9
MAP2K1 -0.032 0.043 0.15 20 -10000 0 20
MAP3K11 -0.028 0.049 0.18 21 -10000 0 21
IFNGR1 0.029 0.018 0.077 3 -0.069 11 14
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.088 -10000 0 -0.22 89 89
Rap1/GTP -0.045 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.044 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.059 -10000 0 -10000 0 0
CEBPB -0.01 0.092 0.34 5 -0.3 23 28
STAT3 0.03 0.014 -10000 0 -0.065 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.057 0.087 -10000 0 -0.74 4 4
STAT1 -0.031 0.049 0.18 21 -10000 0 21
CALM1 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.03 0.01 -10000 0 -0.028 5 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
STAT1 (dimer)/PIAS1 -0.034 0.052 0.19 21 -10000 0 21
CEBPB/PTGES2/Cbp/p300 0.006 0.073 -10000 0 -0.21 34 34
mol:Ca2+ 0.047 0.049 -10000 0 -0.073 1 1
MAPK3 -0.001 0.06 0.51 1 -0.57 2 3
STAT1 (dimer) -0.048 0.044 -10000 0 -0.14 24 24
MAPK1 -0.051 0.19 0.51 1 -0.67 40 41
JAK2 0.03 0.011 0.077 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.01 0.07 2 -0.029 6 8
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.004 0.068 0.26 8 -0.18 34 42
SMAD7 -0.016 0.038 0.12 17 -0.084 3 20
CBL/CRKL/C3G -0.036 0.054 0.2 21 -10000 0 21
PI3K 0.041 0.056 -10000 0 -10000 0 0
IFNG 0.03 0.01 -10000 0 -0.028 5 5
apoptosis 0.001 0.064 0.28 5 -0.38 3 8
CAMK2G 0.012 0.016 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.014 -10000 0 -0.065 10 10
CAMK2A 0.031 0.007 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
FRAP1 -0.023 0.057 0.22 12 -10000 0 12
PRKCD -0.025 0.066 0.27 10 -10000 0 10
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.038 0.033 -10000 0 -0.1 37 37
PTPN2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
IRF1 -0.043 0.042 0.23 5 -10000 0 5
STAT1 (dimer)/PIASy -0.034 0.049 0.18 19 -10000 0 19
SOCS1 0.017 0.093 -10000 0 -1 4 4
mol:GDP -0.035 0.051 0.18 21 -10000 0 21
CASP1 -0.02 0.042 0.13 17 -0.091 9 26
PTGES2 0.031 0.006 -10000 0 -10000 0 0
IRF9 -0.008 0.037 0.15 7 -0.11 14 21
mol:PI-3-4-5-P3 0.028 0.047 -10000 0 -0.08 1 1
RAP1/GDP -0.043 0.029 0.099 14 -10000 0 14
CBL -0.028 0.049 0.18 21 -10000 0 21
MAP3K1 -0.029 0.043 0.16 19 -10000 0 19
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PIAS4 0.031 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.038 0.033 -10000 0 -0.1 37 37
PTPN11 -0.024 0.044 0.16 23 -10000 0 23
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.03 0.008 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.007 0.011 -10000 0 -10000 0 0
CDKN1A 0 0.04 0.065 117 -0.074 45 162
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.065 6 6
FOXO3 0 0.012 0.027 76 -10000 0 76
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
TAT 0.032 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.002 -10000 0 -10000 0 0
PPARGC1A 0.032 0.008 -10000 0 -0.065 3 3
FHL2 0.03 0.01 -10000 0 -0.065 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.022 -10000 0 -10000 0 0
HIST2H4A -0.007 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.019 0.019 0.15 4 -10000 0 4
SIRT1 0.026 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.044 -10000 0 -0.039 2 2
SIRT1/Histone H1b 0.023 0.027 -10000 0 -0.13 9 9
apoptosis -0.037 0.047 0.047 36 -10000 0 36
SIRT1/PGC1A 0.033 0.021 -10000 0 -0.042 3 3
p53/SIRT1 0.032 0.035 0.1 37 -0.056 30 67
SIRT1/FOXO4 0.024 0.023 -10000 0 -0.12 7 7
FOXO1/FHL2/SIRT1 0.035 0.044 -10000 0 -0.043 31 31
HIST1H1E 0.011 0.004 -10000 0 -0.029 1 1
SIRT1/p300 0.037 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.01 0.016 -10000 0 -10000 0 0
TP53 0.02 0.033 -10000 0 -0.063 65 65
KU70/SIRT1/BAX 0.038 0.047 -10000 0 -0.047 36 36
CREBBP 0.032 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.037 0.022 -10000 0 -10000 0 0
ACSS2 -0.007 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.01 0.016 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.03 0.008 -10000 0 -10000 0 0
NFATC1 0.018 0.05 0.23 2 -0.24 10 12
NFATC2 -0.036 0.078 0.1 2 -0.16 121 123
NFATC3 0.009 0.004 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.023 0.075 0.15 2 -0.22 43 45
Exportin 1/Ran/NUP214 0.062 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.009 0.089 0.15 2 -0.21 41 43
BCL2/BAX 0.043 0.017 -10000 0 -0.051 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.065 6 6
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
BAD 0.032 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.008 0.081 0.15 2 -0.22 41 43
Calcineurin A alpha-beta B1/BCL2 0.031 0.006 -10000 0 -10000 0 0
FKBP8 0.031 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.008 0.08 0.22 41 -0.15 2 43
KPNB1 0.032 0.003 -10000 0 -10000 0 0
KPNA2 0.03 0.015 -10000 0 -0.065 11 11
XPO1 0.033 0 -10000 0 -10000 0 0
SFN 0.026 0.024 -10000 0 -0.065 31 31
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
NFAT4/CK1 alpha 0.022 0.029 -10000 0 -0.078 36 36
MEF2D/NFAT1/Cbp/p300 0.009 0.1 -10000 0 -0.17 110 110
CABIN1 -0.023 0.075 0.15 2 -0.23 41 43
CALM1 0.029 0.01 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
CAMK4 0.032 0.004 -10000 0 0 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 0.032 0.002 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.043 0.015 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
MAPK9 0.032 0.005 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.03 0.009 -10000 0 -0.065 1 1
NFAT1-c-4/YWHAQ 0.008 0.071 0.26 1 -0.23 20 21
PRKCH 0.03 0.01 -10000 0 -0.065 2 2
CABIN1/Cbp/p300 0.044 0.014 -10000 0 -10000 0 0
CASP3 0.014 0.038 -10000 0 -0.065 94 94
PIM1 0.032 0.005 -10000 0 -0.065 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.032 1 1
apoptosis 0.017 0.024 -10000 0 -0.097 17 17
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.036 -10000 0 -0.12 29 29
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.032 0.001 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.03 0.099 1 -0.16 6 7
BAD/BCL-XL 0.044 0.013 -10000 0 -10000 0 0
PRKCD 0.032 0.006 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
PRKCG 0.031 0.008 -10000 0 -10000 0 0
PRKCQ 0.024 0.014 -10000 0 -10000 0 0
FKBP38/BCL2 0.045 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.049 0.27 1 -0.24 10 11
CaM/Ca2+/FKBP38 0.037 0.016 -10000 0 -10000 0 0
FKBP12/FK506 0.022 0.007 -10000 0 -0.04 1 1
CSNK1A1 -0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.038 0.014 -10000 0 -10000 0 0
NFATc/ERK1 0.035 0.053 0.23 2 -0.23 10 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.009 0.089 0.15 2 -0.21 40 42
NR4A1 -0.045 0.066 0.14 7 -0.16 106 113
GSK3B 0.031 0.006 -10000 0 -10000 0 0
positive T cell selection 0.009 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.024 0.058 0.069 3 -0.12 117 120
RCH1/ KPNB1 0.045 0.015 -10000 0 -0.051 11 11
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
AKAP5 0.03 0.008 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.054 0.23 2 -0.24 10 12
CREBBP 0.032 0.004 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.014 0.049 -10000 0 -10000 0 0
PLK1 -0.052 0.08 -10000 0 -0.43 2 2
CDKN1B -0.09 0.15 0.23 2 -0.33 128 130
FOXO3 -0.05 0.082 -10000 0 -0.32 15 15
KAT2B -0.003 0.005 -10000 0 -10000 0 0
FOXO1/SIRT1 0.005 0.053 -10000 0 -0.22 12 12
CAT -0.049 0.077 -10000 0 -0.37 3 3
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.026 -10000 0 -10000 0 0
FOXO1 -0.013 0.055 -10000 0 -0.24 10 10
MAPK10 0.021 0.072 0.18 85 -10000 0 85
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 0 0.075 0.2 9 -0.24 1 10
response to oxidative stress -0.002 0.005 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.036 0.084 -10000 0 -0.32 13 13
XPO1 0.032 0 -10000 0 -10000 0 0
EP300 0.03 0.009 -10000 0 -10000 0 0
BCL2L11 0.019 0.012 -10000 0 -10000 0 0
FOXO1/SKP2 0.006 0.058 -10000 0 -0.23 10 10
mol:GDP -0.002 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
GADD45A -0.065 0.14 -10000 0 -0.44 24 24
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.02 0.078 -10000 0 -0.24 32 32
MST1 0.014 0.028 -10000 0 -0.068 6 6
CSNK1D 0.032 0.007 -10000 0 -0.065 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.046 0.09 -10000 0 -0.23 41 41
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.012 0.072 0.18 75 -10000 0 75
MAPK9 0.04 0.095 0.18 156 -10000 0 156
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
SIRT1 0.023 0.015 -10000 0 -0.025 10 10
SOD2 -0.093 0.12 -10000 0 -0.43 33 33
RBL2 -0.028 0.1 -10000 0 -0.7 7 7
RAL/GDP 0.027 0.023 -10000 0 -10000 0 0
CHUK 0.009 0.025 -10000 0 -0.061 1 1
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
RAL/GTP 0.024 0.023 -10000 0 -10000 0 0
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
FASLG 0.016 0.032 -10000 0 -0.61 1 1
SKP2 0.031 0.008 -10000 0 -0.065 2 2
USP7 0.032 0.003 -10000 0 -10000 0 0
IKBKB 0.016 0.027 -10000 0 -10000 0 0
CCNB1 -0.073 0.09 -10000 0 -0.37 9 9
FOXO1-3a-4/beta catenin -0.026 0.081 0.21 1 -0.3 2 3
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.058 -10000 0 -0.23 10 10
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
SGK1 -0.003 0.005 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.006 -10000 0 -10000 0 0
ZFAND5 0.003 0.074 0.27 9 -10000 0 9
SFN 0.026 0.024 -10000 0 -0.065 31 31
CDK2 0.028 0.021 -10000 0 -0.062 24 24
FOXO3A/14-3-3 -0.047 0.076 -10000 0 -0.22 39 39
CREBBP 0.033 0.004 -10000 0 -10000 0 0
FBXO32 -0.047 0.076 -10000 0 -0.32 11 11
BCL6 -0.032 0.1 -10000 0 -0.67 7 7
RALB 0.032 0.005 -10000 0 -0.064 1 1
RALA 0.02 0.02 -10000 0 -0.065 11 11
YWHAH 0.015 0.016 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.004 0.035 -10000 0 -0.13 21 21
NT3 (dimer)/TRKC 0.044 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.051 0.031 -10000 0 -0.05 18 18
SHC/Grb2/SOS1/GAB1/PI3K 0.013 0.025 -10000 0 -0.12 10 10
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DYNLT1 0.017 0.034 -10000 0 -0.065 72 72
NTRK1 0.032 0.006 -10000 0 -0.065 1 1
NTRK2 0.028 0.011 -10000 0 -10000 0 0
NTRK3 0.031 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.035 0.021 -10000 0 -0.04 18 18
neuron apoptosis 0.03 0.055 0.19 8 -10000 0 8
SHC 2-3/Grb2 -0.031 0.059 -10000 0 -0.2 8 8
SHC1 0.024 0.026 -10000 0 -0.05 52 52
SHC2 -0.033 0.045 -10000 0 -0.29 3 3
SHC3 -0.038 0.062 -10000 0 -0.3 16 16
STAT3 (dimer) 0.016 0.043 -10000 0 -0.069 99 99
NT3 (dimer)/TRKA 0.057 0.028 -10000 0 -0.051 20 20
RIN/GDP 0.004 0.039 0.13 6 -0.16 10 16
GIPC1 0.031 0.006 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
DNAJA3 -0.008 0.018 0.074 15 -0.15 1 16
RIN/GTP 0.013 0.012 -10000 0 -0.04 2 2
CCND1 -0.032 0.031 -10000 0 -0.099 87 87
MAGED1 0.032 0.003 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.035 0.024 -10000 0 -0.04 40 40
GRB2 0.032 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.041 0.011 -10000 0 -0.04 1 1
TRKA/NEDD4-2 0.046 0.011 -10000 0 -0.051 1 1
ELMO1 0.015 0.016 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.017 0.021 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
GAB2 0.032 0.006 -10000 0 -10000 0 0
RIT2 0.017 0.017 -10000 0 -0.065 2 2
RIT1 0.003 0.044 -10000 0 -0.065 152 152
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 0.006 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.023 -10000 0 -10000 0 0
mol:GDP -0.003 0.071 0.21 13 -0.22 17 30
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.012 -10000 0 -10000 0 0
RIT1/GDP -0.001 0.054 0.15 13 -0.16 19 32
TIAM1 0.031 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.012 0.028 -10000 0 -0.049 11 11
KIDINS220/CRKL/C3G 0.044 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.028 -10000 0 -0.051 40 40
FRS2 family/SHP2 0.062 0.015 -10000 0 -0.044 1 1
SHC/GRB2/SOS1/GAB1 0.049 0.033 -10000 0 -0.042 47 47
RIT1/GTP 0.005 0.029 -10000 0 -0.04 152 152
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
RAP1/GDP -0.002 0.039 -10000 0 -0.13 20 20
KIDINS220/CRKL 0.031 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.01 -10000 0 -0.04 1 1
Schwann cell development -0.002 0.006 -10000 0 -10000 0 0
EHD4 0.026 0.024 -10000 0 -0.065 31 31
FRS2 family/GRB2/SOS1 0.058 0.018 -10000 0 -0.039 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.038 -10000 0 -0.13 22 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.027 0.15 4 -10000 0 4
ABL1 0.031 0.008 -10000 0 -0.065 1 1
SH2B family/GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.034 -10000 0 -0.19 13 13
STAT3 0.016 0.043 -10000 0 -0.069 99 99
axon guidance -0.008 0.018 0.04 2 -10000 0 2
MAPK3 -0.013 0.045 0.18 26 -10000 0 26
MAPK1 -0.013 0.04 0.18 20 -10000 0 20
CDC42/GDP 0.007 0.054 0.14 16 -0.16 16 32
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.018 -10000 0 -0.04 20 20
PI3K 0.039 0.023 -10000 0 -0.051 16 16
FRS3 0.032 0.002 -10000 0 -10000 0 0
FAIM 0.028 0.019 -10000 0 -0.065 19 19
GAB1 0.031 0.008 -10000 0 -0.065 3 3
RASGRF1 -0.008 0.018 0.074 13 -0.15 1 14
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.02 0.011 -10000 0 -10000 0 0
RGS19 0.03 0.009 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.056 0.22 3 -0.26 11 14
Rac1/GDP 0.005 0.044 0.17 8 -0.15 10 18
NGF (dimer)/TRKA/GRIT 0.021 0.004 -10000 0 -0.032 1 1
neuron projection morphogenesis 0.014 0.072 -10000 0 -0.72 4 4
NGF (dimer)/TRKA/NEDD4-2 0.042 0.01 -10000 0 -0.04 1 1
MAP2K1 -0.02 0.042 0.17 22 -10000 0 22
NGFR 0.028 0.02 -10000 0 -0.065 21 21
NGF (dimer)/TRKA/GIPC/GAIP 0.002 0.014 -10000 0 -0.13 3 3
RAS family/GTP/PI3K 0.003 0.035 -10000 0 -0.12 27 27
FRS2 family/SHP2/GRB2/SOS1 0.071 0.023 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.06 134 134
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.048 -10000 0 -0.39 5 5
RASA1 0.031 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.045 0.013 -10000 0 -0.051 2 2
SQSTM1 0.032 0.006 -10000 0 -0.065 1 1
BDNF (dimer)/TRKB/GIPC 0.013 0.034 -10000 0 -0.051 13 13
NGF (dimer)/TRKA/p62/Atypical PKCs 0.054 0.017 -10000 0 -0.031 12 12
MATK 0.031 0.006 -10000 0 -10000 0 0
NEDD4L 0.031 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.013 0.034 -10000 0 -0.11 30 30
NGF (dimer)/TRKA 0.01 0.016 -10000 0 -0.16 1 1
Rac1/GTP -0.003 0.028 -10000 0 -0.13 8 8
FRS2 family/SHP2/CRK family 0.083 0.039 -10000 0 -10000 0 0
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.03 0.011 -10000 0 -0.065 4 4
mol:Halofuginone 0.002 0.004 -10000 0 -0.038 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.004 0.051 -10000 0 -0.34 10 10
PRL-3/alpha Tubulin 0.04 0.025 -10000 0 -0.051 28 28
mol:Ca2+ -0.022 0.021 0.053 27 -10000 0 27
AGT 0.029 0.01 -10000 0 -10000 0 0
CCNA2 -0.026 0.013 -10000 0 -0.073 5 5
TUBA1B 0.032 0.005 -10000 0 -10000 0 0
EGR1 0.008 0.009 -10000 0 -0.039 16 16
CDK2/Cyclin E1 0.035 0.062 -10000 0 -0.32 9 9
MAPK3 -0.023 0.008 -10000 0 -0.051 30 30
PRL-2 /Rab GGTase beta 0.047 0.009 -10000 0 -10000 0 0
MAPK1 -0.021 0.01 0 58 -0.051 30 88
PTP4A1 -0.017 0.008 -10000 0 -0.1 1 1
PTP4A3 0.026 0.023 -10000 0 -0.065 30 30
PTP4A2 0.032 0.005 -10000 0 -10000 0 0
ITGB1 -0.018 0.012 -10000 0 -0.051 23 23
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.007 0.033 -10000 0 -0.33 4 4
Rab GGTase beta/Rab GGTase alpha 0.044 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.013 0.044 0.18 23 -10000 0 23
RABGGTA 0.031 0.008 -10000 0 -10000 0 0
BCAR1 -0.015 0.016 0.049 30 -10000 0 30
RHOC -0.007 0.046 -10000 0 -0.34 6 6
RHOA 0.006 0.051 -10000 0 -0.33 11 11
cell motility 0.012 0.052 -10000 0 -0.29 5 5
PRL-1/alpha Tubulin -0.011 0.049 0.18 30 -10000 0 30
PRL-3/alpha1 Integrin 0.02 0.015 -10000 0 -0.04 30 30
ROCK1 0.012 0.05 -10000 0 -0.3 4 4
RABGGTB 0.032 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.021 -10000 0 -0.065 24 24
mitosis -0.017 0.008 -10000 0 -0.1 1 1
ATF5 0.031 0.009 -10000 0 -0.065 1 1
Canonical NF-kappaB 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
FBXW11 0.032 0.005 -10000 0 -0.034 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.071 0.18 6 -0.25 16 22
ERC1 0.031 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.045 0.015 -10000 0 -0.051 9 9
NFKBIA -0.028 0.017 0.2 2 -10000 0 2
BIRC2 0.032 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.003 -10000 0 -10000 0 0
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
IKBKG 0.018 0.051 -10000 0 -0.28 10 10
IKK complex/A20 0.035 0.068 -10000 0 -0.37 6 6
NEMO/A20/RIP2 0.032 0.006 -10000 0 -0.065 1 1
XPO1 0.033 0 -10000 0 -10000 0 0
NEMO/ATM 0.035 0.054 0.18 2 -0.38 6 8
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.043 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.058 -10000 0 -0.36 6 6
BCL10/MALT1/TRAF6 0.056 0.029 -10000 0 -0.05 24 24
NOD2 0.03 0.013 -10000 0 -0.065 8 8
NFKB1 0.031 0.01 -10000 0 -0.059 5 5
RELA 0.032 0.005 -10000 0 -0.034 1 1
MALT1 0.028 0.02 -10000 0 -0.065 20 20
cIAP1/UbcH5C 0.046 0.009 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.065 25 25
TNF/TNFR1A 0.014 0.046 -10000 0 -0.051 165 165
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.065 1 1
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.065 2 2
NF kappa B1 p50/RelA 0.065 0.025 -10000 0 -0.054 6 6
BCL10 0.031 0.01 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.017 0.2 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -0.034 1 1
TNFRSF1A 0 0.045 -10000 0 -0.065 164 164
IKK complex 0.04 0.061 -10000 0 -0.38 6 6
CYLD 0.032 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.049 0.066 -10000 0 -0.37 6 6
Cellular roles of Anthrax toxin

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
ANTXR1 0.032 0.008 -10000 0 -0.065 3 3
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -0.008 3 3
monocyte activation -0.017 0.045 -10000 0 -0.33 7 7
MAP2K2 0.017 0.027 -10000 0 -0.58 1 1
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.001 0 6 -0.017 1 7
CYAA -0.007 0.001 -10000 0 -0.026 3 3
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B -0.013 0.015 0.13 3 -0.079 6 9
Channel 0.021 0.004 -10000 0 -0.025 4 4
NLRP1 -0.008 0.002 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.027 0.12 -10000 0 -0.37 54 54
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 0.008 3 -10000 0 3
MAPK3 -0.009 0.001 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 0 42 -10000 0 42
PGR -0.009 0.001 -10000 0 -10000 0 0
PA/Cellular Receptors 0.022 0.004 -10000 0 -0.032 3 3
apoptosis -0.002 0 -10000 0 -0.008 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.004 -10000 0 -0.026 4 4
macrophage activation -0.014 0.004 -10000 0 -10000 0 0
TNF 0.032 0.007 -10000 0 -0.065 2 2
VCAM1 -0.017 0.045 -10000 0 -0.33 7 7
platelet activation -0.027 0.12 -10000 0 -0.37 54 54
MAPKKK cascade 0.004 0.017 0.064 1 -0.068 24 25
IL18 -0.014 0.013 0.11 2 -0.079 2 4
negative regulation of macrophage activation -0.002 0 -10000 0 -0.008 3 3
LEF -0.002 0 -10000 0 -0.008 3 3
CASP1 -0.006 0.007 -10000 0 -0.016 165 165
mol:cAMP -0.027 0.12 -10000 0 -0.37 54 54
necrosis -0.002 0 -10000 0 -0.008 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.004 -10000 0 -0.023 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.013 -10000 0 -0.04 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.065 9 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.004 -10000 0 0 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.031 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.013 -10000 0 -0.11 5 5
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.065 74 74
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
MAP3K12 0.032 0.005 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.065 15 15
p38 alpha/TAB1 -0.019 0.049 -10000 0 -0.22 19 19
PRKG1 0.024 0.014 -10000 0 -10000 0 0
DUSP8 0.023 0.015 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.001 0.065 0.14 3 -0.24 16 19
apoptosis -0.018 0.047 -10000 0 -0.21 19 19
RAL/GTP 0.028 0.023 -10000 0 -0.04 12 12
LYN 0.021 0.031 -10000 0 -0.058 67 67
DUSP1 0.029 0.017 -10000 0 -0.065 16 16
PAK1 0.032 0.004 -10000 0 -10000 0 0
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0.03 -10000 0 -0.039 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.03 0.02 -10000 0 -10000 0 0
MAPK11 0.004 0.08 0.17 24 -0.23 18 42
BLK 0.032 0.005 -10000 0 -10000 0 0
HCK 0.014 0.036 -10000 0 -0.045 121 121
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.03 0.012 -10000 0 -0.065 6 6
TRAF6/MEKK3 0.04 0.01 -10000 0 -0.023 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.075 0.15 17 -0.25 16 33
positive regulation of innate immune response 0.004 0.091 0.18 25 -0.29 17 42
LCK 0.031 0.01 -10000 0 -0.065 4 4
p38alpha-beta/MKP7 0.002 0.086 0.17 25 -0.28 17 42
p38alpha-beta/MKP5 0.013 0.094 0.19 20 -0.28 16 36
PGK/cGMP 0.018 0.01 -10000 0 -10000 0 0
PAK2 0.027 0.02 -10000 0 -0.039 36 36
p38alpha-beta/MKP1 0.011 0.096 0.19 19 -0.29 17 36
CDC42 0.031 0.006 -10000 0 -10000 0 0
RALB 0.032 0.005 -10000 0 -0.032 2 2
RALA 0.02 0.02 -10000 0 -0.065 11 11
PAK3 0.005 0.012 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.006 0.034 0.13 31 -0.14 3 34
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.041 0.12 4 -0.14 9 13
AP2 0.023 0.005 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.022 -10000 0 -0.039 1 1
CLTB 0.032 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.031 -10000 0 -0.1 35 35
CD4 0.027 0.019 -10000 0 -0.065 19 19
CLTA 0.03 0.009 -10000 0 -10000 0 0
mol:GTP -0.003 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.01 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.007 0.074 4 -0.035 1 5
ARF1/GTP 0.018 0.009 -10000 0 -0.036 10 10
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.02 -10000 0 -0.09 24 24
mol:Choline 0.004 0.007 0.075 4 -0.035 1 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
DDEF1 0.002 0.007 0.074 4 -0.034 1 5
ARF1/GDP 0.004 0.012 -10000 0 -0.082 7 7
AP2M1 0.031 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.017 0.011 0.047 1 -10000 0 1
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.015 -10000 0 -10000 0 0
ARFIP2 0.029 0.014 -10000 0 -0.035 17 17
COPA 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.039 0.1 1 -0.14 29 30
ARF1/GTP/ARHGAP10 0.02 0.004 -10000 0 -10000 0 0
GGA3 0.032 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.024 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.028 -10000 0 -0.1 27 27
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.03 0.021 -10000 0 -0.038 1 1
CYTH2 -0.003 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.041 0.009 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.011 -10000 0 0 153 153
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 0.008 0.028 -10000 0 -0.092 29 29
PLD2 0.004 0.007 0.075 4 -0.035 1 5
ARF-GAP1/v-SNARE -0.01 0.003 -10000 0 -10000 0 0
PIP5K1A 0.004 0.007 0.074 4 -0.035 1 5
ARF1/GTP/Membrin/GBF1/p115 0.003 0.034 -10000 0 -0.056 116 116
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.007 0.075 4 -0.035 1 5
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 -10000 0 -10000 0 0
GOSR2 0.011 0.029 -10000 0 -0.36 3 3
USO1 0.012 0.02 -10000 0 -0.29 2 2
GBF1 -0.063 0.14 -10000 0 -0.32 115 115
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.02 -10000 0 -0.04 19 19
ErbB2/ErbB3 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
USP8 -0.016 0.008 0.014 14 -10000 0 14
RAS family/GTP 0.015 0.056 -10000 0 -0.12 6 6
NFATC4 -0.025 0.039 0.22 6 -10000 0 6
ERBB2IP 0.027 0.023 -10000 0 -0.062 32 32
HSP90 (dimer) 0.03 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.031 0.14 5 -10000 0 5
JUN 0 0.042 0.14 5 -10000 0 5
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK7 -0.032 0.025 0.12 5 -10000 0 5
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.039 0.045 0.17 3 -0.069 1 4
AKT1 -0.01 0.007 0.016 16 -10000 0 16
BAD -0.017 0.006 0.015 3 -10000 0 3
MAPK10 0.003 0.05 0.18 15 -10000 0 15
mol:GTP 0 0 -10000 0 -0.004 1 1
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.034 0.15 5 -10000 0 5
RAF1 -0.019 0.059 0.21 19 -10000 0 19
ErbB2/ErbB3/neuregulin 2 0.032 0.03 -10000 0 -0.058 27 27
STAT3 0.027 0.091 -10000 0 -0.96 4 4
cell migration -0.014 0.047 0.21 9 -0.13 2 11
mol:PI-3-4-5-P3 -0.001 0.001 0.005 8 -10000 0 8
cell proliferation -0.004 0.097 0.43 2 -0.45 9 11
FOS -0.007 0.074 0.3 4 -0.27 11 15
NRAS 0.008 0.042 -10000 0 -0.06 134 134
mol:Ca2+ -0.031 0.031 0.14 5 -10000 0 5
MAPK3 0.008 0.064 0.37 3 -10000 0 3
MAPK1 -0.017 0.12 0.42 2 -0.47 17 19
JAK2 -0.03 0.034 0.12 7 -10000 0 7
NF2 0.009 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.021 0.1 11 -0.057 1 12
NRG1 0.032 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.016 0.056 0.17 2 -0.18 30 32
MAPK9 0.007 0.067 0.17 30 -10000 0 30
ERBB2 -0.025 0.021 0.051 32 -10000 0 32
ERBB3 0.023 0.024 -10000 0 -0.066 28 28
SHC1 0.024 0.026 -10000 0 -0.05 52 52
RAC1 0.023 0.015 -10000 0 -10000 0 0
apoptosis 0.009 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.088 -10000 0 -0.93 4 4
RNF41 -0.022 0.009 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 0.007 16 -10000 0 16
RAC1-CDC42/GTP -0.026 0.022 -10000 0 -0.085 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.026 0.05 47 -10000 0 47
CHRNA1 0.005 0.067 0.4 2 -0.25 7 9
myelination -0.028 0.054 0.29 10 -10000 0 10
PPP3CB -0.026 0.029 0.12 4 -10000 0 4
KRAS 0.031 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.04 -10000 0 -0.11 4 4
NRG2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.021 0.1 11 -0.057 1 12
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.024 0.054 0.18 18 -10000 0 18
SRC 0.03 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 0.003 4 -10000 0 4
PTPN11 -0.033 0.036 0.13 8 -10000 0 8
MAP2K1 -0.011 0.12 0.42 2 -0.53 21 23
heart morphogenesis -0.031 0.031 0.14 5 -10000 0 5
RAS family/GDP 0.018 0.061 -10000 0 -0.12 7 7
GRB2 0.032 0.006 -10000 0 -10000 0 0
PRKACA 0.017 0.006 -10000 0 -10000 0 0
CHRNE 0.001 0.012 0.047 5 -10000 0 5
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.007 -10000 0 -0.016 16 16
nervous system development -0.031 0.031 0.14 5 -10000 0 5
CDC42 0.031 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.018 0.055 1 -0.1 19 20
KIRREL 0.035 0.011 0.084 1 -0.038 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.019 0.1 19 -0.055 1 20
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
WASL 0.023 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.068 0.046 0.18 7 -10000 0 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.016 0.019 -10000 0 -0.12 4 4
FYN -0.01 0.044 0.16 28 -10000 0 28
mol:Ca2+ 0.074 0.036 0.17 19 -10000 0 19
mol:DAG 0.075 0.037 0.18 19 -10000 0 19
NPHS2 0.035 0.01 0.084 1 -0.03 4 5
mol:IP3 0.075 0.037 0.18 19 -10000 0 19
regulation of endocytosis 0.055 0.03 0.13 1 -10000 0 1
Nephrin/NEPH1/podocin/Cholesterol 0.062 0.029 0.16 19 -10000 0 19
establishment of cell polarity 0.049 0.018 0.1 19 -0.055 1 20
Nephrin/NEPH1/podocin/NCK1-2 0.091 0.039 0.19 10 -10000 0 10
Nephrin/NEPH1/beta Arrestin2 0.058 0.031 0.14 1 -10000 0 1
NPHS1 0.034 0.011 0.076 6 -10000 0 6
Nephrin/NEPH1/podocin 0.059 0.024 0.17 4 -0.056 4 8
TJP1 0.032 0.005 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.077 0.038 0.18 19 -10000 0 19
CD2AP 0.023 0.029 -10000 0 -0.065 48 48
Nephrin/NEPH1/podocin/GRB2 0.079 0.035 0.18 16 -10000 0 16
GRB2 0.032 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.05 0.17 30 -10000 0 30
cytoskeleton organization -0.007 0.032 0.18 10 -0.15 3 13
Nephrin/NEPH1 0.041 0.016 0.087 19 -0.029 5 24
Nephrin/NEPH1/ZO-1 0.063 0.024 -10000 0 -0.044 5 5
Aurora C 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
INCENP 0.032 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.05 0.033 -9999 0 -0.039 53 53
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.016 -9999 0 -0.33 1 1
AURKB 0.027 0.022 -9999 0 -0.065 26 26
AURKC 0.03 0.01 -9999 0 -0.065 2 2
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.017 -10000 0 -0.027 27 27
regulation of S phase of mitotic cell cycle 0.014 0.022 -10000 0 -0.1 12 12
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.004 -10000 0 0 17 17
PELP1 0.032 0.005 -10000 0 -10000 0 0
AKT1 -0.01 0.003 0 34 -10000 0 34
MAP2K1 -0.028 0.049 0.15 28 -10000 0 28
T-DHT/AR 0.023 0.008 -10000 0 -0.04 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.003 11 11
GNAI2 0.032 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
mol:GDP -0.012 0.009 -10000 0 -10000 0 0
cell proliferation -0.023 0.068 0.22 11 -0.28 3 14
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FOS -0.023 0.066 0.2 5 -0.28 4 9
mol:Ca2+ 0 0.002 -10000 0 -0.033 2 2
MAPK3 -0.02 0.062 0.21 13 -0.24 2 15
MAPK1 -0.025 0.098 0.16 1 -0.35 36 37
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.002 5 5
cAMP biosynthetic process -0.001 0.003 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.002 5 5
HRAS/GTP 0.049 0.03 -10000 0 -0.066 4 4
actin cytoskeleton reorganization 0.029 0.029 -10000 0 -0.044 13 13
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.002 5 5
PI3K 0.036 0.02 -10000 0 -0.04 16 16
apoptosis 0.015 0.065 0.23 9 -0.21 4 13
T-DHT/AR/PELP1 0.041 0.013 -10000 0 -0.042 9 9
HRAS/GDP 0.016 0.034 -10000 0 -10000 0 0
CREB1 -0.015 0.067 0.22 4 -0.23 8 12
RAC1-CDC42/GTP 0.036 0.035 -10000 0 -0.046 11 11
AR 0.031 0.012 -10000 0 -0.065 8 8
GNB1 0.031 0.008 -10000 0 -10000 0 0
RAF1 -0.022 0.052 0.16 32 -10000 0 32
RAC1-CDC42/GDP 0.027 0.03 0.13 1 -10000 0 1
T-DHT/AR/PELP1/Src 0.055 0.023 -10000 0 -0.044 9 9
MAP2K2 -0.031 0.044 0.15 21 -10000 0 21
T-DHT/AR/PELP1/Src/PI3K 0.014 0.022 -10000 0 -0.1 12 12
GNAZ 0.027 0.013 -10000 0 -10000 0 0
SHBG 0.031 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.065 0.1 -10000 0 -0.36 37 37
mol:T-DHT 0 0 -10000 0 -0.002 6 6
RAC1 0.023 0.015 -10000 0 -10000 0 0
GNRH1 -0.011 0.002 0 12 -10000 0 12
Gi family/GTP 0 0.008 -10000 0 -0.11 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.051 0.073 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.031 0.04 -10000 0 -0.24 1 1
NCK1/Dok-R -0.005 0.06 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
mol:beta2-estradiol 0.004 0.013 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
F2 0.037 0.019 -10000 0 -0.066 2 2
TNIP2 0.03 0.014 -10000 0 -0.065 11 11
NF kappa B/RelA 0.015 0.081 -10000 0 -10000 0 0
FN1 0.014 0.038 -10000 0 -0.065 96 96
PLD2 -0.013 0.04 -10000 0 -0.24 1 1
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.065 18 18
ELK1 -0.025 0.05 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PAK1 0.032 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.012 0.079 -10000 0 -10000 0 0
CDKN1A -0.057 0.078 -10000 0 -0.4 1 1
ITGA5 0.019 0.033 -10000 0 -0.065 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.005 0.06 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:NO -0.006 0.094 0.3 3 -10000 0 3
PLG -0.011 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.012 0.082 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ANGPT2 -0.05 0.07 -10000 0 -0.39 2 2
BMX -0.013 0.04 -10000 0 -0.24 1 1
ANGPT1 -0.007 0.037 -10000 0 -0.2 1 1
tube development -0.061 0.074 -10000 0 -10000 0 0
ANGPT4 0.029 0.008 -10000 0 -10000 0 0
response to hypoxia -0.003 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.006 0.064 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.051 61 61
FGF2 0.034 0.008 -10000 0 -0.063 2 2
STAT5A (dimer) -0.061 0.091 -10000 0 -10000 0 0
mol:L-citrulline -0.006 0.094 0.3 3 -10000 0 3
AGTR1 0.022 0.02 -10000 0 -0.028 68 68
MAPK14 -0.02 0.072 -10000 0 -0.56 3 3
Tie2/SHP2 -0.028 0.12 -10000 0 -0.27 98 98
TEK -0.036 0.12 -10000 0 -0.29 93 93
RPS6KB1 -0.046 0.072 -10000 0 -0.37 1 1
Angiotensin II/AT1 0 0.023 -10000 0 -0.022 266 266
Tie2/Ang1/GRB2 -0.004 0.063 -10000 0 -10000 0 0
MAPK3 -0.029 0.045 -10000 0 -10000 0 0
MAPK1 -0.026 0.044 -10000 0 -0.24 1 1
Tie2/Ang1/GRB7 -0.004 0.064 -10000 0 -10000 0 0
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.008 0.03 -10000 0 -0.24 1 1
PI3K -0.042 0.074 -10000 0 -0.39 1 1
FES -0.022 0.072 -10000 0 -0.47 2 2
Crk/Dok-R -0.005 0.061 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 -0.005 0.063 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.051 0.071 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.044 0.077 0.29 3 -10000 0 3
Tie2/Ang2 -0.06 0.084 -10000 0 -0.36 1 1
Tie2/Ang1 -0.004 0.043 -10000 0 -0.25 1 1
FOXO1 -0.059 0.074 -10000 0 -10000 0 0
ELF1 0.035 0.018 -10000 0 -0.065 6 6
ELF2 -0.007 0.037 -10000 0 -0.21 1 1
mol:Choline -0.013 0.041 -10000 0 -0.24 1 1
cell migration -0.022 0.03 -10000 0 -10000 0 0
FYN -0.063 0.078 -10000 0 -10000 0 0
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.054 0.074 -10000 0 -0.37 1 1
ETS1 0.023 0.031 -10000 0 -10000 0 0
PXN -0.044 0.075 0.27 3 -10000 0 3
ITGB1 0.025 0.014 -10000 0 -10000 0 0
NOS3 -0.019 0.089 0.31 3 -10000 0 3
RAC1 0.023 0.015 -10000 0 -10000 0 0
TNF 0.021 0.031 -10000 0 -0.065 2 2
MAPKKK cascade -0.013 0.041 -10000 0 -0.24 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.011 0.063 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
vasculogenesis -0.002 0.092 0.28 4 -10000 0 4
mol:Phosphatidic acid -0.013 0.041 -10000 0 -0.24 1 1
mol:Angiotensin II -0.004 0.004 -10000 0 -10000 0 0
mol:NADP -0.006 0.094 0.3 3 -10000 0 3
Rac1/GTP -0.026 0.064 -10000 0 -0.36 1 1
MMP2 -0.02 0.041 -10000 0 -0.26 1 1
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.058 0.027 -9999 0 -0.054 20 20
E-cadherin/beta catenin 0.045 0.016 -9999 0 -0.051 8 8
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
JUP 0.029 0.017 -9999 0 -0.065 16 16
CDH1 0.03 0.013 -9999 0 -0.065 8 8
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.003 0.056 -10000 0 -0.17 22 22
TBX21 -0.019 0.12 -10000 0 -0.4 2 2
B2M 0.031 0.006 -10000 0 -10000 0 0
TYK2 0.02 0.029 -10000 0 -10000 0 0
IL12RB1 0.02 0.029 -10000 0 -10000 0 0
GADD45B 0.003 0.095 -10000 0 -0.41 2 2
IL12RB2 0.02 0.03 -10000 0 -10000 0 0
GADD45G 0.001 0.1 -10000 0 -0.46 4 4
natural killer cell activation -0.002 0.01 -10000 0 -0.032 2 2
RELB 0.031 0.008 -10000 0 -0.002 27 27
RELA 0.032 0.004 -10000 0 -10000 0 0
IL18 0.024 0.028 -10000 0 -0.065 43 43
IL2RA 0.023 0.017 -10000 0 -0.065 6 6
IFNG 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.005 0.11 0.23 1 -0.38 6 7
HLA-DRB5 -0.001 0.002 -10000 0 -10000 0 0
FASLG -0.017 0.12 0.28 1 -0.4 2 3
NF kappa B2 p52/RelB -0.008 0.13 -10000 0 -0.35 15 15
CD4 0.027 0.02 -10000 0 -0.065 20 20
SOCS1 0.032 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.003 -10000 0 -10000 0 0
CD3D 0.027 0.02 -10000 0 -0.065 21 21
CD3E 0.031 0.007 -10000 0 -0.049 2 2
CD3G 0.031 0.007 -10000 0 -0.052 2 2
IL12Rbeta2/JAK2 0.031 0.04 -10000 0 -10000 0 0
CCL3 -0.018 0.12 -10000 0 -0.34 16 16
CCL4 -0.067 0.23 -10000 0 -0.61 72 72
HLA-A 0.032 0.005 -10000 0 -0.065 1 1
IL18/IL18R 0.058 0.042 -10000 0 -10000 0 0
NOS2 -0.013 0.1 -10000 0 -0.37 4 4
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.058 -10000 0 -0.18 24 24
IL1R1 -0.021 0.12 -10000 0 -0.4 2 2
IL4 0.033 0.014 -10000 0 -0.027 9 9
JAK2 0.019 0.028 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.008 0.034 -10000 0 -0.19 9 9
RAB7A 0.013 0.098 0.31 4 -0.41 2 6
lysosomal transport 0.013 0.095 0.31 4 -0.4 2 6
FOS -0.057 0.17 -10000 0 -0.58 39 39
STAT4 (dimer) -0.015 0.12 0.38 1 -0.45 4 5
STAT5A (dimer) 0 0.13 -10000 0 -0.34 14 14
GZMA -0.024 0.12 0.28 1 -0.4 2 3
GZMB -0.025 0.12 -10000 0 -0.41 1 1
HLX 0.031 0.009 -10000 0 -0.065 3 3
LCK -0.025 0.12 0.26 4 -0.36 16 20
TCR/CD3/MHC II/CD4 -0.009 0.031 -10000 0 -0.097 11 11
IL2/IL2R 0.049 0.056 -10000 0 -0.068 6 6
MAPK14 0.013 0.1 -10000 0 -0.47 2 2
CCR5 -0.002 0.11 -10000 0 -0.53 4 4
IL1B 0.018 0.033 -10000 0 -0.067 13 13
STAT6 0.003 0.066 -10000 0 -0.38 8 8
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT1 0.029 0.018 -10000 0 -0.065 18 18
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
NFKB2 0.024 0.014 -10000 0 -10000 0 0
IL12B 0.021 0.03 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.032 0.006 -10000 0 -0.065 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.003 0.056 0.17 22 -10000 0 22
IL2RB 0.03 0.012 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.11 0.37 1 -0.42 4 5
IL2RG 0.031 0.013 -10000 0 -0.065 9 9
IL12 0.032 0.042 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
CD247 0.031 0.008 -10000 0 -0.055 3 3
IL2 0.032 0.004 -10000 0 -10000 0 0
SPHK2 0.031 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.02 0.03 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.018 0.12 -10000 0 -0.36 19 19
MAP2K3 0.008 0.1 -10000 0 -0.53 2 2
RIPK2 0.032 0.006 -10000 0 -0.065 1 1
MAP2K6 0.01 0.1 -10000 0 -0.47 1 1
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.023 0.048 -10000 0 -0.066 281 281
IL18RAP 0.033 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.032 0.039 -10000 0 -10000 0 0
EOMES 0.004 0.02 0.069 5 -0.072 5 10
STAT1 (dimer) -0.001 0.11 -10000 0 -0.41 2 2
T cell proliferation -0.018 0.095 0.38 1 -0.39 4 5
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.033 0.006 -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 0.014 0.12 -10000 0 -0.41 3 3
ATF2 0.007 0.099 0.42 1 -0.45 2 3
Glucocorticoid receptor regulatory network

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
PCK2 -0.007 0.03 -10000 0 -0.26 6 6
SMARCC2 0.031 0.006 -10000 0 -10000 0 0
SMARCC1 0.028 0.018 -10000 0 -0.065 17 17
TBX21 0.006 0.016 -10000 0 -10000 0 0
SUMO2 0.032 0.005 -10000 0 -0.026 1 1
STAT1 (dimer) 0.022 0.036 -10000 0 -0.064 74 74
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 0.027 0.022 -10000 0 -0.065 26 26
GR alpha/HSP90/FKBP51/HSP90 0.08 0.054 -10000 0 -0.071 11 11
PRL -0.042 0.059 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.014 0.039 -10000 0 -10000 0 0
RELA 0.015 0.039 -10000 0 -0.069 41 41
FGG 0.11 0.14 0.27 24 -10000 0 24
GR beta/TIF2 -0.004 0.037 -10000 0 -10000 0 0
IFNG -0.06 0.092 -10000 0 -0.23 19 19
apoptosis 0.02 0.09 -10000 0 -0.35 9 9
CREB1 0.036 0.011 -10000 0 -0.067 6 6
histone acetylation 0.009 0.014 -10000 0 -10000 0 0
BGLAP 0.01 0.017 -10000 0 -10000 0 0
GR/PKAc 0.092 0.054 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.061 -10000 0 -0.1 39 39
SMARCD1 0.032 0.005 -10000 0 -10000 0 0
MDM2 0.003 0.027 0.11 26 -10000 0 26
GATA3 0.028 0.017 -10000 0 -10000 0 0
AKT1 0.029 0.009 0.064 4 -10000 0 4
CSF2 -0.072 0.072 -10000 0 -0.24 2 2
GSK3B 0.032 0.006 -10000 0 -0.026 1 1
NR1I3 0.023 0.09 -10000 0 -0.32 8 8
CSN2 0.12 0.14 0.26 35 -10000 0 35
BRG1/BAF155/BAF170/BAF60A 0.07 0.036 -10000 0 -0.066 1 1
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.034 0.01 -10000 0 -10000 0 0
CDKN1A -0.015 0.051 -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 0.026 0.024 -10000 0 -0.065 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.087 0.062 -10000 0 -0.074 14 14
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.026 0.089 -10000 0 -0.37 5 5
JUN 0.001 0.023 0.28 2 -10000 0 2
IL4 0.011 0.018 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.027 0.038 -10000 0 -0.12 4 4
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.093 0.056 -10000 0 -0.076 3 3
cortisol/GR alpha (monomer) -0.02 0.039 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.01 0.044 -10000 0 -0.086 3 3
AP-1/NFAT1-c-4 -0.014 0.042 0.24 1 -0.2 1 2
AFP -0.053 0.057 -10000 0 -0.37 1 1
SUV420H1 0.032 0.005 -10000 0 -10000 0 0
IRF1 -0.004 0.033 0.17 6 -0.15 3 9
TP53 0.015 0.045 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
KRT17 -0.062 0.093 0.17 1 -0.21 18 19
KRT14 -0.042 0.069 0.17 13 -0.15 8 21
TBP 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -10000 0 0
HDAC1 0.018 0.032 -10000 0 -0.067 61 61
HDAC2 0.029 0.012 -10000 0 -0.065 4 4
AP-1 -0.014 0.042 0.24 1 -0.2 1 2
MAPK14 0.032 0.006 -10000 0 -0.045 2 2
MAPK10 0.018 0.016 -10000 0 -10000 0 0
MAPK11 0.03 0.01 -10000 0 -0.026 1 1
KRT5 -0.06 0.092 -10000 0 -0.21 18 18
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.03 0.01 -10000 0 -0.032 8 8
STAT1 0.022 0.036 -10000 0 -0.064 74 74
CGA 0.01 0.019 -10000 0 -0.11 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.053 0.08 0.16 2 -0.23 6 8
MAPK3 0.032 0.005 -10000 0 -0.026 3 3
MAPK1 0.03 0.009 -10000 0 -0.026 1 1
ICAM1 -0.017 0.07 0.13 1 -0.17 74 75
NFKB1 0.014 0.04 -10000 0 -0.07 42 42
MAPK8 0.005 0.018 -10000 0 -10000 0 0
MAPK9 0.032 0.006 -10000 0 -0.026 1 1
cortisol/GR alpha (dimer) 0.017 0.09 0.24 3 -0.36 9 12
BAX -0.012 0.057 -10000 0 -0.37 3 3
POMC -0.073 0.08 0.26 2 -0.33 2 4
EP300 0.028 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.015 0.041 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.034 0.22 3 -10000 0 3
SGK1 0.018 0.05 -10000 0 -0.15 19 19
IL13 -0.044 0.068 -10000 0 -0.24 3 3
IL6 -0.016 0.067 0.13 1 -0.18 61 62
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 -0.051 0.07 -10000 0 -0.28 2 2
IL2 -0.06 0.092 0.17 1 -0.21 17 18
CDK5 0.021 0.016 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
IL8 -0.026 0.084 0.13 1 -0.21 80 81
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.067 0.062 -10000 0 -0.11 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
SMARCA4 0.031 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.072 0.079 0.17 23 -0.19 3 26
NF kappa B1 p50/RelA/Cbp 0.04 0.075 -10000 0 -0.13 5 5
JUN (dimer) 0.001 0.023 0.28 2 -10000 0 2
YWHAH 0.015 0.016 -10000 0 -10000 0 0
VIPR1 0.008 0.034 0.34 4 -10000 0 4
NR3C1 -0.016 0.03 -10000 0 -10000 0 0
NR4A1 0.034 0.006 -10000 0 -10000 0 0
TIF2/SUV420H1 0.046 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.09 -10000 0 -0.35 9 9
cortisol/GR alpha (dimer)/Src-1 -0.013 0.038 -10000 0 -10000 0 0
PBX1 0.034 0.01 -10000 0 -10000 0 0
POU1F1 0.033 0.011 -10000 0 -10000 0 0
SELE -0.016 0.068 0.13 1 -0.17 77 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.08 0.17 23 -0.19 3 26
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
mol:cortisol -0.011 0.02 -10000 0 -10000 0 0
MMP1 0.002 0.046 -10000 0 -0.48 3 3
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.056 0.023 -10000 0 -0.039 3 3
HDAC3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.024 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.048 0.005 -10000 0 -10000 0 0
GATA1/HDAC5 0.048 0.006 -10000 0 -10000 0 0
GATA2/HDAC5 0.047 0.009 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.058 0.026 -10000 0 -0.049 21 21
HDAC9 0.022 0.016 -10000 0 -0.065 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.061 0.019 -10000 0 -0.044 3 3
HDAC4/ANKRA2 0.047 0.008 -10000 0 -0.051 1 1
HDAC5/YWHAB 0.044 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.028 -10000 0 -0.095 39 39
GATA2 0.032 0.005 -10000 0 -10000 0 0
HDAC4/RFXANK 0.037 0.029 -10000 0 -0.051 45 45
BCOR 0.031 0.01 -10000 0 -0.065 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.032 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.006 -10000 0 -10000 0 0
Histones 0.036 0.032 0.083 148 -0.095 3 151
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
XPO1 0.033 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.047 0.009 -10000 0 -0.051 1 1
HDAC4/Ubc9 0.048 0.006 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.047 0.008 -10000 0 -10000 0 0
TUBA1B 0.032 0.005 -10000 0 -10000 0 0
HDAC6 0.032 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.029 -10000 0 -0.051 43 43
CAMK4 0.032 0.004 -10000 0 0 7 7
Tubulin/HDAC6 0.059 0.021 -10000 0 -0.044 2 2
SUMO1 0.033 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NR3C1 0.032 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.038 0.039 -10000 0 -0.097 39 39
SRF 0.032 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.044 0.014 -10000 0 -10000 0 0
Tubulin 0.043 0.015 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.047 0.008 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.021 -10000 0 -0.051 19 19
HDAC4/HDAC3/SMRT (N-CoR2) 0.064 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.064 0.012 -10000 0 -10000 0 0
HDAC4/ER alpha 0.045 0.012 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.031 0.082 148 -0.094 3 151
cell motility 0.058 0.021 -10000 0 -0.044 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.024 0.003 -10000 0 -10000 0 0
BCL6 0.028 0.017 -10000 0 -0.065 15 15
HDAC4/CaMK II delta B 0.032 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.045 0.012 -10000 0 -10000 0 0
ESR1 0.031 0.008 -10000 0 -10000 0 0
HDAC6/HDAC11 0.047 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.039 -10000 0 -0.096 38 38
NPC 0.019 0.001 -10000 0 -10000 0 0
MEF2C 0.027 0.012 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.077 0.041 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.032 0.004 -10000 0 -10000 0 0
TUBB2A 0.03 0.009 -10000 0 -10000 0 0
HDAC11 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
ANKRA2 0.032 0.006 -10000 0 -0.065 1 1
RFXANK 0.023 0.028 -10000 0 -0.065 45 45
nuclear import -0.032 0.023 0.11 10 -10000 0 10
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.02 0.064 -9999 0 -0.26 1 1
CLOCK 0.022 0.023 -9999 0 -10000 0 0
TIMELESS/CRY2 0.01 0.053 -9999 0 -0.26 1 1
DEC1/BMAL1 0.045 0.011 -9999 0 -10000 0 0
ATR 0.032 0.005 -9999 0 -10000 0 0
NR1D1 -0.002 0.029 -9999 0 -0.24 1 1
ARNTL 0.022 0.024 -9999 0 -0.031 13 13
TIMELESS -0.01 0.045 -9999 0 -0.27 1 1
NPAS2 0.022 0.024 -9999 0 -0.029 94 94
CRY2 0.031 0.006 -9999 0 -10000 0 0
mol:CO 0.001 0.011 -9999 0 -10000 0 0
CHEK1 0.021 0.031 -9999 0 -0.065 59 59
mol:HEME -0.001 0.011 -9999 0 -10000 0 0
PER1 0.031 0.009 -9999 0 -0.065 3 3
BMAL/CLOCK/NPAS2 0.046 0.046 -9999 0 -10000 0 0
BMAL1/CLOCK 0.011 0.041 -9999 0 -0.34 1 1
S phase of mitotic cell cycle 0.02 0.064 -9999 0 -0.26 1 1
TIMELESS/CHEK1/ATR 0.02 0.065 -9999 0 -0.27 1 1
mol:NADPH -0.001 0.011 -9999 0 -10000 0 0
PER1/TIMELESS 0.008 0.054 -9999 0 -0.27 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.032 0.006 -9999 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.054 0.16 0.45 1 -0.68 2 3
STAT6 (cleaved dimer) -0.052 0.14 -10000 0 -0.7 2 2
IGHG1 -0.022 0.084 -10000 0 -0.49 1 1
IGHG3 -0.064 0.14 -10000 0 -0.66 2 2
AKT1 -0.022 0.11 -10000 0 -0.62 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.001 0.08 0.26 1 -0.5 2 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.015 0.1 -10000 0 -0.63 1 1
THY1 -0.17 0.31 -10000 0 -0.7 90 90
MYB 0.029 0.014 -10000 0 -0.065 7 7
HMGA1 0.032 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.11 -10000 0 -0.64 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.019 0.1 -10000 0 -0.64 1 1
SP1 -0.005 0.04 -10000 0 -0.044 251 251
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.031 0.017 -10000 0 -0.032 2 2
STAT6 (dimer)/ETS1 -0.045 0.15 -10000 0 -0.73 1 1
SOCS1 -0.044 0.13 0.29 1 -0.53 1 2
SOCS3 -0.03 0.095 -10000 0 -0.56 1 1
FCER2 -0.047 0.13 -10000 0 -0.62 2 2
PARP14 0.001 0 -10000 0 -10000 0 0
CCL17 -0.069 0.15 -10000 0 -0.68 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.018 0.086 -10000 0 -0.58 1 1
T cell proliferation -0.057 0.15 -10000 0 -0.73 2 2
IL4R/JAK1 -0.06 0.16 -10000 0 -0.66 2 2
EGR2 -0.071 0.15 -10000 0 -0.69 2 2
JAK2 0.009 0.038 -10000 0 -10000 0 0
JAK3 0.032 0.013 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.019 0.026 -10000 0 -10000 0 0
COL1A2 -0.055 0.11 -10000 0 -0.72 5 5
CCL26 -0.066 0.15 -10000 0 -0.68 2 2
IL4R -0.07 0.16 -10000 0 -0.7 2 2
PTPN6 0.03 0.018 -10000 0 -0.047 18 18
IL13RA2 -0.088 0.15 -10000 0 -0.68 2 2
IL13RA1 0.001 0.05 -10000 0 -0.1 9 9
IRF4 0.012 0.065 -10000 0 -0.45 3 3
ARG1 -0.021 0.091 -10000 0 -0.41 2 2
CBL -0.03 0.1 0.29 1 -0.61 1 2
GTF3A 0.023 0.026 -10000 0 -0.043 57 57
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL13RA1/JAK2 0.004 0.056 -10000 0 -10000 0 0
IRF4/BCL6 0.02 0.068 -10000 0 -0.43 3 3
CD40LG 0.035 0.004 -10000 0 -0.039 1 1
MAPK14 -0.03 0.1 0.28 1 -0.61 1 2
mitosis -0.02 0.11 -10000 0 -0.58 3 3
STAT6 -0.069 0.16 -10000 0 -0.75 2 2
SPI1 0.032 0.014 -10000 0 -0.063 8 8
RPS6KB1 -0.023 0.11 -10000 0 -0.57 3 3
STAT6 (dimer) -0.068 0.16 -10000 0 -0.74 2 2
STAT6 (dimer)/PARP14 -0.07 0.15 -10000 0 -0.71 2 2
mast cell activation 0.003 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.092 -10000 0 -0.63 1 1
FRAP1 -0.021 0.11 -10000 0 -0.61 3 3
LTA -0.07 0.15 -10000 0 -0.7 2 2
FES 0.032 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.069 0.16 0.74 2 -10000 0 2
CCL11 -0.067 0.14 -10000 0 -0.66 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.011 0.097 -10000 0 -0.88 1 1
IL2RG 0.03 0.019 -10000 0 -0.062 10 10
IL10 -0.064 0.16 -10000 0 -0.68 2 2
IRS1 0.032 0.009 -10000 0 -0.065 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
IL4 -0.01 0.085 -10000 0 -0.56 6 6
IL5 -0.069 0.15 -10000 0 -0.68 2 2
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.066 0.15 -10000 0 -0.71 2 2
COL1A1 -0.04 0.12 -10000 0 -0.6 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.062 0.16 -10000 0 -0.71 1 1
IL2R gamma/JAK3 0.048 0.019 -10000 0 -0.048 11 11
TFF3 -0.069 0.15 -10000 0 -0.68 2 2
ALOX15 -0.07 0.15 -10000 0 -0.68 2 2
MYBL1 0.017 0.035 -10000 0 -0.065 77 77
T-helper 2 cell differentiation -0.053 0.14 -10000 0 -0.79 2 2
SHC1 0.024 0.026 -10000 0 -0.065 40 40
CEBPB 0.03 0.017 -10000 0 -0.063 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.021 0.1 -10000 0 -0.68 2 2
mol:PI-3-4-5-P3 -0.021 0.11 -10000 0 -0.61 3 3
PI3K -0.022 0.12 -10000 0 -0.65 3 3
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.033 0.013 -10000 0 -0.033 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.016 0.083 -10000 0 -0.53 1 1
ITGB3 -0.069 0.15 -10000 0 -0.68 2 2
PIGR -0.064 0.16 -10000 0 -0.68 2 2
IGHE 0.014 0.04 0.14 23 -0.096 3 26
MAPKKK cascade -0.016 0.082 -10000 0 -0.52 1 1
BCL6 0.028 0.017 -10000 0 -0.065 15 15
OPRM1 -0.069 0.15 -10000 0 -0.68 2 2
RETNLB -0.066 0.15 -10000 0 -0.68 2 2
SELP -0.066 0.15 -10000 0 -0.68 2 2
AICDA -0.063 0.15 0.41 1 -0.68 2 3
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.045 0.012 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.05 0.18 2 -0.21 7 9
NFKBIA 0.004 0.033 0.11 24 -0.097 28 52
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -0.039 10 10
ARRB2 0.013 0.003 -10000 0 -0.037 1 1
REL 0.032 0.001 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.012 -10000 0 -0.041 9 9
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.011 -10000 0 -0.04 11 11
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
NF kappa B1 p50 dimer -0.021 0.018 0.26 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 -0.022 0.004 -10000 0 -0.051 4 4
RELA 0.032 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.011 0.026 0.11 3 -0.14 6 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.053 0.18 2 -0.2 10 12
SRC 0.03 0.008 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
NF kappa B1 p50/RelA 0.011 0.026 0.11 3 -0.14 6 9
IKBKB 0.032 0.003 -10000 0 0 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
SYK 0.025 0.025 -10000 0 -0.065 35 35
I kappa B alpha/PIK3R1 0.02 0.047 0.18 2 -0.2 7 9
cell death 0.022 0.051 0.17 2 -0.19 10 12
NF kappa B1 p105/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
LCK 0.031 0.01 -10000 0 -0.065 4 4
BCL3 0.031 0.007 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.01 0.083 -10000 0 -0.22 49 49
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
AKT2 0.031 0.006 -10000 0 0 18 18
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.028 0.077 -10000 0 -0.23 49 49
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
TBC1D4 -0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.014 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.03 0.008 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.065 1 1
AS160/CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -10000 0 -10000 0 0
GYS1 -0.006 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.065 6 6
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.04 6 6
AS160/14-3-3 -0.021 0.045 0.1 1 -0.17 18 19
VAMP2 0.029 0.01 -10000 0 -10000 0 0
SLC2A4 -0.03 0.085 -10000 0 -0.25 49 49
STX4 0.032 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN 0.026 0.024 -10000 0 -0.065 31 31
LNPEP 0.032 0.006 -10000 0 -0.065 1 1
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.065 3 3
CRKL 0.031 0.007 -10000 0 -10000 0 0
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.065 1 1
ITGA3 0.029 0.018 -10000 0 -0.065 17 17
RELN/VLDLR/Fyn 0.018 0.03 -10000 0 -0.047 5 5
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.059 -10000 0 -10000 0 0
AKT1 -0.004 0.028 -10000 0 -0.13 23 23
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.019 0.03 -10000 0 -0.042 3 3
LRPAP1/LRP8 0.047 0.008 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.022 0.036 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin 0.017 0.038 -10000 0 -10000 0 0
long-term memory 0.017 0.035 0.17 2 -10000 0 2
DAB1/LIS1 0.026 0.045 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.02 0.038 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DAB1/NCK2 0.027 0.046 -10000 0 -10000 0 0
ARHGEF2 0.032 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.021 0.015 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
RELN 0.01 0.016 -10000 0 -0.065 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.019 0.03 -10000 0 -0.049 2 2
GRIN2A/RELN/LRP8/DAB1/Fyn 0.021 0.041 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.018 0.03 -10000 0 -0.043 3 3
ITGB1 0.025 0.014 -10000 0 -10000 0 0
MAP1B 0.008 0.05 0.15 55 -10000 0 55
RELN/LRP8 0.02 0.031 -10000 0 -0.049 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn 0.025 0.045 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.051 16 16
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.025 -10000 0 -0.051 15 15
RAP1A 0.053 0.092 0.31 17 -10000 0 17
PAFAH1B1 0.031 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.006 -10000 0 -10000 0 0
CRLK/C3G 0.044 0.014 -10000 0 -10000 0 0
GRIN2B 0.031 0.007 -10000 0 -10000 0 0
NCK2 0.032 0.003 -10000 0 -10000 0 0
neuron differentiation -0.015 0.058 -10000 0 -0.17 39 39
neuron adhesion 0.04 0.091 0.31 18 -10000 0 18
LRP8 0.032 0.005 -10000 0 -10000 0 0
GSK3B -0.003 0.039 0.077 46 -0.14 23 69
RELN/VLDLR/DAB1/Fyn 0.02 0.036 -10000 0 -10000 0 0
MAP3K11 0.032 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.004 0.017 -10000 0 -0.1 8 8
CDK5 0.02 0.016 -10000 0 -10000 0 0
MAPT 0.004 0.056 0.72 1 -10000 0 1
neuron migration -0.014 0.079 0.19 44 -0.16 13 57
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.058 -10000 0 -0.17 39 39
RELN/VLDLR 0.024 0.039 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.018 0.005 -10000 0 -0.04 15 15
SNTA1 0.03 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.026 0.007 -10000 0 -0.049 15 15
MAPK12 -0.011 0.017 0.2 3 -10000 0 3
CCND1 -0.007 0.046 -10000 0 -0.35 7 7
p38 gamma/SNTA1 -0.016 0.024 0.19 4 -10000 0 4
MAP2K3 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.014 -10000 0 -0.065 8 8
G2/M transition checkpoint -0.011 0.017 0.2 3 -10000 0 3
MAP2K6 -0.007 0.004 -10000 0 -0.038 8 8
MAPT -0.024 0.045 0.14 3 -0.14 16 19
MAPK13 -0.023 0.006 -10000 0 -0.051 15 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.007 -10000 0 -0.037 8 8
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 0.032 0.003 -10000 0 -10000 0 0
PTK2 0.031 0.006 -10000 0 -10000 0 0
CRKL -0.021 0.007 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.035 0.024 -10000 0 -0.04 40 40
HRAS 0.031 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.024 0.013 -10000 0 -0.058 9 9
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.022 -10000 0 -0.048 9 9
AKT1 -0.022 0.045 0.17 17 -10000 0 17
BAD -0.026 0.043 0.15 18 -10000 0 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.032 0.015 -10000 0 -0.072 6 6
RAF1 -0.007 0.054 0.24 3 -0.43 3 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.053 0.019 -10000 0 -0.067 6 6
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.015 -10000 0 -0.058 10 10
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RPS6KB1 -0.023 0.046 0.17 18 -10000 0 18
GNB2L1 0.032 0.004 -10000 0 0 9 9
positive regulation of MAPKKK cascade -0.012 0.053 0.22 6 -0.35 3 9
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.029 -10000 0 -0.071 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.06 0.039 -10000 0 -0.063 1 1
IGF-1R heterotetramer 0.034 0.008 -10000 0 -0.031 5 5
IGF-1R heterotetramer/IGF1/IRS/Nck 0.058 0.019 -10000 0 -0.071 6 6
Crk/p130 Cas/Paxillin 0.047 0.018 0.21 1 -0.071 6 7
IGF1R 0.034 0.008 -10000 0 -0.031 5 5
IGF1 0.033 0.012 -10000 0 -0.053 9 9
IRS2/Crk -0.025 0.009 -10000 0 -10000 0 0
PI3K 0.062 0.037 -10000 0 -0.073 4 4
apoptosis 0.027 0.049 -10000 0 -0.15 20 20
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
PRKCD 0.002 0.018 -10000 0 -0.14 4 4
RAF1/14-3-3 E -0.006 0.056 0.25 3 -0.38 3 6
BAD/14-3-3 -0.029 0.051 0.16 20 -10000 0 20
PRKCZ -0.018 0.044 0.16 19 -10000 0 19
Crk/p130 Cas/Paxillin/FAK1 -0.037 0.04 0.087 39 -10000 0 39
PTPN1 0.03 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.01 0.022 -10000 0 -0.15 5 5
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.047 -10000 0 -0.071 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.033 0.017 0.13 5 -0.071 6 11
GRB10 0.022 0.017 -10000 0 -0.065 4 4
PTPN11 -0.022 0.006 -10000 0 -10000 0 0
IRS1 -0.015 0.015 0.12 5 -0.07 6 11
IRS2 -0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.045 0.011 -10000 0 -0.055 4 4
GRB2 0.032 0.006 -10000 0 -10000 0 0
PDPK1 -0.018 0.047 0.18 19 -10000 0 19
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKD1 -0.003 0.021 -10000 0 -0.13 8 8
SHC1 0.024 0.026 -10000 0 -0.05 52 52
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.017 -10000 0 -0.1 8 8
TRAF2/ASK1 0.039 0.014 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.065 25 25
MAP2K3 0.029 0.059 0.18 3 -0.24 12 15
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.055 0.16 10 -0.19 16 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.029 0.016 -10000 0 -0.065 12 12
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
GADD45A 0.024 0.026 -10000 0 -0.065 39 39
GADD45B 0.03 0.014 -10000 0 -0.065 8 8
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
MAP3K6 0.031 0.008 -10000 0 -0.065 2 2
MAP3K7 0.031 0.008 -10000 0 -0.065 1 1
MAP3K4 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.043 0.016 -10000 0 -0.051 2 2
TAK1/TAB family 0.002 0.023 0.074 42 -0.069 7 49
RAC1/OSM/MEKK3 0.029 0.02 -10000 0 -0.023 3 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.021 0.048 -10000 0 -0.21 12 12
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.004 0.013 -10000 0 -10000 0 0
MAPK11 0.029 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.005 0.018 -10000 0 -10000 0 0
OSM/MEKK3 0.024 0.002 -10000 0 -10000 0 0
TAOK1 0.004 0.01 -10000 0 -0.038 25 25
TAOK2 0.01 0.011 -10000 0 -0.037 25 25
TAOK3 0.01 0.011 -10000 0 -0.037 25 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAP3K10 0.031 0.006 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.016 -10000 0 -0.11 5 5
GADD45/MTK1/MTK1 0.052 0.047 -10000 0 -0.048 53 53
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 0.01 0 12 -0.04 61 73
SMARCC1 0.004 0.02 -10000 0 -10000 0 0
REL 0.032 0.001 -10000 0 -10000 0 0
HDAC7 -0.036 0.03 0.16 2 -0.14 2 4
JUN 0.032 0.005 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.021 0.011 0.019 29 -0.052 1 30
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
T-DHT/AR 0.01 0.052 0.21 2 -0.15 2 4
MAP2K6 0.032 0.004 -10000 0 0 6 6
BRM/BAF57 0.043 0.015 -10000 0 -10000 0 0
MAP2K4 0.031 0.008 -10000 0 -10000 0 0
SMARCA2 0.029 0.01 -10000 0 -10000 0 0
PDE9A 0.014 0.063 -10000 0 -0.5 7 7
NCOA2 0.032 0.004 -10000 0 -10000 0 0
CEBPA 0.028 0.018 -10000 0 -0.065 15 15
EHMT2 0.033 0.003 -10000 0 -10000 0 0
cell proliferation -0.021 0.074 0.27 6 -0.24 20 26
NR0B1 0.024 0.028 -10000 0 -0.065 46 46
EGR1 0.029 0.017 -10000 0 -0.064 15 15
RXRs/9cRA 0.058 0.021 -10000 0 -0.043 3 3
AR/RACK1/Src -0.022 0.052 0.17 11 -0.15 1 12
AR/GR 0.003 0.044 0.14 3 -0.19 7 10
GNB2L1 0.032 0.004 -10000 0 0 9 9
PKN1 0.03 0.014 -10000 0 -0.065 8 8
RCHY1 0.032 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.015 0.012 0.02 15 -10000 0 15
T-DHT/AR/TIF2/CARM1 -0.03 0.043 0.2 6 -0.15 1 7
SRC -0.024 0.025 0.18 4 -10000 0 4
NR3C1 0.032 0.004 -10000 0 -10000 0 0
KLK3 -0.02 0.062 -10000 0 -0.41 3 3
APPBP2 0.033 0.004 -10000 0 -10000 0 0
TRIM24 0.022 0.016 -10000 0 -0.064 2 2
T-DHT/AR/TIP60 -0.029 0.02 0.042 3 -0.082 19 22
TMPRSS2 0.013 0.068 -10000 0 -0.5 8 8
RXRG 0.032 0.008 -10000 0 -0.065 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.031 0.007 -10000 0 -10000 0 0
RXRB 0.032 0.002 -10000 0 -10000 0 0
CARM1 0.031 0.007 -10000 0 -10000 0 0
NR2C2 0.032 0.004 -10000 0 -10000 0 0
KLK2 -0.016 0.044 0.17 6 -0.18 13 19
AR -0.003 0.018 0.14 4 -0.16 2 6
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.011 -10000 0 -0.065 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.023 0.053 0.18 11 -0.16 1 12
positive regulation of transcription 0.032 0.005 -10000 0 -10000 0 0
DNAJA1 0.03 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.019 -10000 0 -0.2 3 3
NCOA1 0.032 0.02 0.11 4 -10000 0 4
SPDEF 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.034 0.081 0.13 5 -0.18 96 101
T-DHT/AR/Hsp90 -0.028 0.036 0.19 5 -0.16 1 6
GSK3B 0.032 0.006 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.015 -10000 0 -10000 0 0
SIRT1 0.025 0.014 -10000 0 -10000 0 0
ZMIZ2 0.022 0.015 -10000 0 -10000 0 0
POU2F1 0.036 0.009 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.033 0.036 0.19 5 -0.15 1 6
CREBBP 0.032 0.004 -10000 0 -10000 0 0
SMARCE1 0.032 0.004 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.029 0.01 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.066 1 1
EFNB1 -0.004 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.026 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.036 34 34
neuron projection morphogenesis 0.006 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.026 0.16 1 -10000 0 1
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.007 0.037 0.2 1 -0.38 4 5
YES1 0.008 0.061 -10000 0 -0.61 4 4
Ephrin B1/EPHB1-2/NCK2 0.011 0.026 0.16 1 -10000 0 1
PI3K 0.038 0.048 -10000 0 -0.36 4 4
mol:GDP 0.01 0.025 0.16 1 -10000 0 1
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
endothelial cell proliferation 0.027 0.021 -10000 0 -10000 0 0
FYN 0.01 0.063 -10000 0 -0.61 4 4
MAP3K7 -0.002 0.032 -10000 0 -0.38 3 3
FGR 0.013 0.058 -10000 0 -0.6 4 4
TIAM1 0.031 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RGS3 0.031 0.007 -10000 0 -0.065 1 1
cell adhesion 0.02 0.042 -10000 0 -0.34 4 4
LYN 0.01 0.058 -10000 0 -0.6 4 4
Ephrin B1/EPHB1-2/Src Family Kinases 0.006 0.054 -10000 0 -0.57 4 4
Ephrin B1/EPHB1-2 0.006 0.036 -10000 0 -0.42 3 3
SRC 0.013 0.058 -10000 0 -0.6 4 4
ITGB3 0.032 0.003 -10000 0 -10000 0 0
EPHB1 0.03 0.014 -10000 0 -0.063 9 9
EPHB4 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.021 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.014 0.058 -10000 0 -0.58 4 4
HCK 0.01 0.057 -10000 0 -0.58 4 4
regulation of stress fiber formation -0.011 0.025 -10000 0 -0.16 1 1
MAPK8 -0.008 0.039 -10000 0 -0.38 4 4
Ephrin B1/EPHB1-2/RGS3 0.011 0.025 -10000 0 -10000 0 0
endothelial cell migration 0.048 0.095 0.19 137 -0.33 3 140
NCK2 0.032 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.024 -10000 0 -0.075 25 25
regulation of focal adhesion formation -0.011 0.025 -10000 0 -0.16 1 1
chemotaxis -0.01 0.025 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP 0.008 0.022 -10000 0 -10000 0 0
angiogenesis 0.005 0.041 -10000 0 -0.42 4 4
LCK 0.013 0.058 -10000 0 -0.6 4 4
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.017 0.007 -10000 0 -10000 0 0
NFATC2 -0.01 0.004 -10000 0 -10000 0 0
NFATC3 -0.017 0.007 -10000 0 -10000 0 0
CD40LG -0.039 0.039 0.19 4 -10000 0 4
PTGS2 -0.04 0.039 0.3 1 -10000 0 1
JUNB 0.03 0.014 -10000 0 -0.065 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.009 -10000 0 -0.02 4 4
CaM/Ca2+ 0.021 0.009 -10000 0 -0.02 4 4
CALM1 0.029 0.01 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.032 1 1
FOSL1 0.03 0.015 -10000 0 -0.065 12 12
CREM 0.025 0.013 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.024 0.032 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.066 120 120
IFNG -0.038 0.035 0.15 3 -10000 0 3
AP-1/NFAT1-c-4 0.032 0.073 0.2 4 -0.12 1 5
FASLG -0.039 0.039 0.19 4 -10000 0 4
NFAT1-c-4/ICER1 0.003 0.036 -10000 0 -10000 0 0
IL2RA -0.029 0.039 0.19 4 -10000 0 4
FKBP12/FK506 0.022 0.007 -10000 0 -0.04 1 1
CSF2 -0.039 0.04 0.19 4 -10000 0 4
JunB/Fra1/NFAT1-c-4 0.032 0.041 0.16 6 -10000 0 6
IL4 -0.039 0.04 0.19 4 -10000 0 4
IL2 0.016 0.088 -10000 0 -0.86 5 5
IL3 0.027 0.073 -10000 0 -0.59 7 7
FKBP1A 0.03 0.009 -10000 0 -0.065 1 1
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
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.033 0.041 -10000 0 -0.056 1 1
TC10/GTP 0.027 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.078 0.033 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.065 18 18
FOXO3 -0.02 0.14 -10000 0 -0.57 29 29
AKT1 -0.022 0.058 0.24 4 -10000 0 4
INSR 0.034 0.01 0.07 20 -10000 0 20
Insulin Receptor/Insulin 0.058 0.032 0.21 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.017 -10000 0 -0.065 4 4
SORBS1 0.024 0.014 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
PTPN1 -0.019 0.023 0.14 8 -10000 0 8
CAV1 -0.025 0.029 0.18 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.045 0.051 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.078 0.033 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.053 0.038 -10000 0 -0.059 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.037 0.18 16 -0.19 3 19
RPS6KB1 -0.027 0.053 0.22 4 -10000 0 4
PARD6A 0.032 0.004 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.02 0.014 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.033 0.058 0.15 25 -10000 0 25
HRAS/GTP -0.032 0.018 0.029 21 -10000 0 21
Insulin Receptor 0.034 0.01 0.07 20 -10000 0 20
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.054 -10000 0 -0.074 1 1
PRKCI 0.035 0.035 -10000 0 -0.32 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.03 0.033 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.05 52 52
negative regulation of MAPKKK cascade 0.032 0.044 -10000 0 -10000 0 0
PI3K 0.064 0.044 -10000 0 -10000 0 0
NCK2 0.032 0.003 -10000 0 -10000 0 0
RHOQ 0.032 0.001 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
AKT2 -0.027 0.054 0.24 4 -10000 0 4
PRKCZ 0.017 0.017 -10000 0 -0.29 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.018 0.038 0.16 17 -10000 0 17
F2RL2 0.032 0.004 -10000 0 -10000 0 0
TRIP10 0.03 0.012 -10000 0 -0.065 6 6
Insulin Receptor/Insulin/Shc 0.05 0.037 -10000 0 -0.041 56 56
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.04 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.044 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.065 11 11
CBL/APS/CAP/Crk-II 0.037 0.042 -10000 0 -0.039 10 10
TC10/GDP 0.024 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.051 -10000 0 -0.073 1 1
INPP5D -0.018 0.013 0.034 24 -10000 0 24
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.005 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.065 4 4
p62DOK/RasGAP 0.033 0.044 -10000 0 -10000 0 0
INS 0.035 0.013 0.078 32 -10000 0 32
mol:PI-3-4-P2 -0.018 0.013 0.034 24 -10000 0 24
GRB2 0.032 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.041 0.041 0.22 2 -10000 0 2
PTPRA 0.031 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
TC10/GTP/CIP4 0.042 0.012 -10000 0 -0.04 6 6
PDPK1 0.032 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.028 -10000 0 -0.11 17 17
Insulin Receptor/Insulin/IRS1 0.06 0.025 -10000 0 -0.045 2 2
Insulin Receptor/Insulin/IRS3 0.049 0.018 0.11 20 -10000 0 20
Par3/Par6 0.07 0.026 -10000 0 -10000 0 0
LPA4-mediated signaling 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
ADCY4 -0.009 0 0 1 -10000 0 1
ADCY5 -0.009 0 0 1 -10000 0 1
ADCY6 -0.017 0.003 0 16 -10000 0 16
ADCY7 -0.018 0.003 -10000 0 -0.04 5 5
ADCY1 -0.012 0.008 -10000 0 -10000 0 0
ADCY2 -0.017 0.003 -10000 0 -10000 0 0
ADCY3 -0.009 0 0 1 -10000 0 1
ADCY8 -0.017 0.004 -10000 0 -0.04 5 5
PRKCE -0.011 0 0 1 -10000 0 1
ADCY9 -0.017 0.002 0 7 -10000 0 7
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.008 0.039 0.13 23 -0.12 1 24
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.011 0.06 0.32 14 -10000 0 14
VDR 0.031 0.006 -10000 0 -10000 0 0
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.024 0.04 -10000 0 -0.15 17 17
RXRs/LXRs/DNA/Oxysterols -0.031 0.046 -10000 0 -0.17 19 19
MED1 0.032 0.004 -10000 0 -10000 0 0
mol:9cRA -0.006 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.035 -10000 0 -0.16 17 17
RXRs/NUR77 0.059 0.031 -10000 0 -10000 0 0
RXRs/PPAR 0.003 0.046 -10000 0 -0.12 56 56
NCOR2 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.07 0.026 -10000 0 -10000 0 0
RARA 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.051 0.016 -10000 0 -10000 0 0
RARG 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.059 0.56 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.023 0.032 -10000 0 -0.17 12 12
THRA 0.032 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.011 0.053 -10000 0 -10000 0 0
NR1H4 0.032 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.016 0.073 -10000 0 -10000 0 0
NR1H2 -0.008 0.027 -10000 0 -0.033 5 5
NR1H3 -0.01 0.028 -10000 0 -0.051 8 8
RXRs/VDR/DNA/Vit D3 0.053 0.031 -10000 0 -10000 0 0
NR4A1 0.032 0.005 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.004 0.028 -10000 0 -0.12 16 16
RXRG -0.007 0.029 -10000 0 -0.048 8 8
RXR alpha/CCPG 0.019 0.007 -10000 0 -0.018 9 9
RXRA -0.007 0.028 -10000 0 -10000 0 0
RXRB -0.008 0.029 -10000 0 -0.04 1 1
THRB 0.032 0.004 -10000 0 -10000 0 0
PPARG 0.031 0.01 -10000 0 -0.065 4 4
PPARD 0.032 0.002 -10000 0 -10000 0 0
TNF -0.032 0.041 -10000 0 -0.15 18 18
mol:Oxysterols -0.005 0.004 -10000 0 -10000 0 0
cholesterol transport -0.031 0.046 -10000 0 -0.17 19 19
PPARA 0.03 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.032 0.004 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 0.011 0.032 -10000 0 -0.12 27 27
SREBF1 -0.032 0.041 -10000 0 -0.16 17 17
RXRs/RXRs/DNA/9cRA -0.011 0.053 -10000 0 -10000 0 0
ABCA1 -0.059 0.056 -10000 0 -0.18 19 19
RARs/THRs 0.091 0.027 -10000 0 -10000 0 0
RXRs/FXR 0.06 0.029 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.031 0.028 -10000 0 -10000 0 0
epithelial cell differentiation 0.011 0.064 -10000 0 -10000 0 0
ITCH 0.031 0.012 -10000 0 -0.067 1 1
WWP1 0.009 0.023 0.21 6 -10000 0 6
FYN 0.029 0.011 -10000 0 -0.065 1 1
EGFR 0.012 0.018 -10000 0 -0.065 6 6
PRL 0.031 0.011 -10000 0 -0.065 6 6
neuron projection morphogenesis -0.022 0.048 0.24 7 -10000 0 7
PTPRZ1 0.018 0.022 -10000 0 -0.065 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.053 0.048 0.23 2 -10000 0 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.014 0.019 -10000 0 -10000 0 0
ADAM17 0.029 0.017 -10000 0 -0.056 5 5
ErbB4/ErbB4 0.014 0.014 0.12 6 -0.08 1 7
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.017 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.03 0.025 -10000 0 -10000 0 0
GRIN2B -0.012 0.024 0.24 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.032 0.025 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
HBEGF 0.032 0.007 -10000 0 -0.065 2 2
PRLR 0.032 0.005 -10000 0 -10000 0 0
E4ICDs/ETO2 0.031 0.028 -10000 0 -10000 0 0
axon guidance -0.006 0.043 0.21 2 -10000 0 2
NEDD4 0.027 0.021 -10000 0 -0.065 14 14
Prolactin receptor/Prolactin receptor/Prolactin 0.046 0.013 -10000 0 -0.051 6 6
CBFA2T3 0.031 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.032 0.025 -10000 0 -10000 0 0
MAPK3 -0.017 0.05 0.18 20 -10000 0 20
STAT1 (dimer) 0.03 0.03 -10000 0 -10000 0 0
MAPK1 -0.016 0.048 0.19 19 -10000 0 19
JAK2 0.029 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.013 0.019 -10000 0 -10000 0 0
NRG1 -0.021 0.012 0.024 12 -10000 0 12
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.032 0.004 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.006 0.043 0.21 2 -10000 0 2
neural crest cell migration 0.012 0.019 -10000 0 -10000 0 0
ERBB2 -0.021 0.011 0.024 12 -10000 0 12
WWOX/E4ICDs 0.031 0.028 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
ErbB4/EGFR/neuregulin 4 0.012 0.021 -10000 0 -10000 0 0
apoptosis -0.015 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.028 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.031 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.029 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.065 0.05 -10000 0 -10000 0 0
MDM2 0.023 0.071 0.25 43 -10000 0 43
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.029 0.018 -10000 0 -10000 0 0
STAT5A -0.014 0.046 0.2 3 -10000 0 3
ErbB4/EGFR/neuregulin 1 beta 0.013 0.022 -10000 0 -10000 0 0
DLG4 0.032 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.051 40 40
E4ICDs/TAB2/NCoR1 0.027 0.026 -10000 0 -10000 0 0
STAT5A (dimer) 0.019 0.073 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.003 0.057 0.23 1 -10000 0 1
LRIG1 0.027 0.02 -10000 0 -0.065 21 21
EREG 0.03 0.013 -10000 0 -0.065 9 9
BTC 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.044 0.21 2 -10000 0 2
ERBB4 0.014 0.015 0.12 6 -0.08 1 7
STAT5B 0.032 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.06 -10000 0 -0.45 7 7
GRB2 0.032 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.012 0.019 -10000 0 -10000 0 0
glial cell differentiation -0.027 0.026 -10000 0 -10000 0 0
WWOX 0.032 0.006 -10000 0 -10000 0 0
cell proliferation -0.001 0.031 0.21 2 -0.22 2 4
IL27-mediated signaling events

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
TGFB1 0.029 0.022 -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 0.002 0.054 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.05 0.028 -10000 0 -10000 0 0
TBX21 -0.018 0.069 0.32 14 -10000 0 14
IL12B 0.032 0.004 -10000 0 -10000 0 0
IL12A -0.011 0.002 0 13 -10000 0 13
IL6ST 0.032 0.005 -10000 0 -10000 0 0
IL27RA/JAK1 0.025 0.042 -10000 0 -10000 0 0
IL27 -0.001 0.003 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -0.026 1 1
T-helper cell lineage commitment 0.047 0.084 -10000 0 -0.29 1 1
T-helper 2 cell differentiation 0.002 0.054 -10000 0 -10000 0 0
T cell proliferation during immune response 0.002 0.054 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.054 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
STAT2 0.031 0.006 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
IL12RB1 0.031 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.02 0.064 0.32 13 -10000 0 13
IL27/IL27R/JAK2/TYK2 -0.002 0.055 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.002 0.054 -10000 0 -10000 0 0
STAT1 (dimer) 0.056 0.035 -10000 0 -10000 0 0
JAK2 0.029 0.01 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.022 0.069 0.23 9 -10000 0 9
T cell proliferation -0.002 0.032 -10000 0 -0.18 1 1
IL12/IL12R/TYK2/JAK2 0.03 0.092 -10000 0 -0.67 8 8
IL17A 0.046 0.083 -10000 0 -0.29 1 1
mast cell activation 0.002 0.054 -10000 0 -10000 0 0
IFNG 0.004 0.022 0.072 1 -0.083 14 15
T cell differentiation -0.001 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.072 0.23 10 -10000 0 10
STAT5A (dimer) 0.022 0.072 0.23 11 -10000 0 11
STAT4 (dimer) 0.014 0.049 0.23 2 -10000 0 2
STAT4 0.019 0.016 -10000 0 -10000 0 0
T cell activation -0.003 0.001 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.043 0.038 -10000 0 -10000 0 0
GATA3 0 0.072 0.64 6 -10000 0 6
IL18 -0.013 0.008 -10000 0 -0.04 43 43
positive regulation of mast cell cytokine production 0.021 0.071 0.23 10 -10000 0 10
IL27/EBI3 0.023 0.009 -10000 0 -0.04 3 3
IL27RA 0.003 0.029 0.25 6 -10000 0 6
IL6 0.017 0.027 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.027 0.32 3 -10000 0 3
IL1B -0.012 0.005 0 1 -0.04 13 14
EBI3 0.031 0.011 -10000 0 -0.065 3 3
TNF -0.011 0.002 0 3 -0.04 2 5
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.014 -9999 0 -10000 0 0
ITGB7 0.031 0.008 -9999 0 -0.065 2 2
ITGA4 0.031 0.01 -9999 0 -0.065 5 5
alpha4/beta7 Integrin 0.046 0.013 -9999 0 -0.062 5 5
alpha4/beta1 Integrin 0.036 0.022 -9999 0 -0.051 4 4
IL23-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
CCL2 -0.021 0.15 -10000 0 -0.63 14 14
IL23A 0.007 0.091 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.12 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.005 0.12 -10000 0 -10000 0 0
ITGA3 0.003 0.1 -10000 0 -10000 0 0
IL17F -0.011 0.085 -10000 0 -10000 0 0
IL12B 0.027 0.03 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.12 -10000 0 -10000 0 0
CD4 0.005 0.12 0.4 1 -10000 0 1
IL23 0.026 0.097 -10000 0 -10000 0 0
IL23R 0.003 0.031 0.09 2 -10000 0 2
IL1B 0.006 0.096 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.006 0.11 -10000 0 -10000 0 0
TYK2 0.022 0.027 -10000 0 -10000 0 0
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.065 10 10
IL18RAP 0.033 0.002 -10000 0 -10000 0 0
IL12RB1 0.022 0.027 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL12Rbeta1/TYK2 0.04 0.029 -10000 0 -10000 0 0
IL23R/JAK2 0.027 0.046 0.14 1 -10000 0 1
positive regulation of chronic inflammatory response 0.005 0.12 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK2 0.024 0.03 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.01 -10000 0 -0.068 4 4
RELA 0.033 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.026 0.096 -10000 0 -10000 0 0
ALOX12B 0.001 0.11 -10000 0 -10000 0 0
CXCL1 -0.001 0.11 -10000 0 -10000 0 0
T cell proliferation 0.005 0.12 -10000 0 -10000 0 0
NFKBIA 0.031 0.009 -10000 0 -0.069 1 1
IL17A 0.008 0.082 0.26 1 -0.34 1 2
PI3K 0.022 0.12 -10000 0 -10000 0 0
IFNG 0.005 0.016 0.072 2 -0.067 17 19
STAT3 (dimer) 0.031 0.13 -10000 0 -10000 0 0
IL18R1 0.033 0.002 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.009 0.091 0.27 2 -10000 0 2
IL18/IL18R 0.057 0.033 -10000 0 -0.047 37 37
macrophage activation -0.001 0.006 -10000 0 -10000 0 0
TNF 0.006 0.096 -10000 0 -10000 0 0
STAT3/STAT4 0 0.1 -10000 0 -10000 0 0
STAT4 (dimer) 0 0.097 -10000 0 -10000 0 0
IL18 0.024 0.027 -10000 0 -0.064 43 43
IL19 0.006 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.014 0.12 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
SOCS3 0.032 0.004 -10000 0 -10000 0 0
CXCL9 -0.004 0.12 -10000 0 -10000 0 0
MPO 0.003 0.11 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.005 0.12 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.005 0.12 -10000 0 -10000 0 0
IL6 0.056 0.13 0.4 10 -10000 0 10
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
IL2 0.032 0.006 -10000 0 -0.03 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0 0.003 -10000 0 -10000 0 0
CD3E 0.002 0.11 -10000 0 -10000 0 0
keratinocyte proliferation 0.005 0.12 -10000 0 -10000 0 0
NOS2 0.004 0.11 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.034 0.015 -10000 0 -0.022 26 26
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.002 0 9 -0.04 1 10
GNB1/GNG2 0.021 0.005 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.002 -10000 0 -0.038 1 1
Gs family/GTP 0.02 0.005 -10000 0 -0.016 8 8
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 0.003 0 0.005 8 0 7 15
GNAL 0.032 0.006 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
CRH 0.032 0.006 -10000 0 -0.065 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.003 -10000 0 -10000 0 0
MAPK11 0.006 0.002 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.035 0.022 -9999 0 -0.051 3 3
FBXW11 0.032 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -9999 0 -10000 0 0
CHUK 0.024 0.015 -9999 0 -0.065 1 1
NF kappa B2 p100/RelB 0.054 0.066 -9999 0 -10000 0 0
NFKB1 0.031 0.01 -9999 0 -0.065 4 4
MAP3K14 0.032 0.007 -9999 0 -0.065 2 2
NF kappa B1 p50/RelB 0.044 0.015 -9999 0 -0.051 5 5
RELB 0.031 0.008 -9999 0 -0.002 27 27
NFKB2 0.024 0.014 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.032 0.02 -9999 0 -0.04 1 1
regulation of B cell activation 0.031 0.02 -9999 0 -0.04 1 1
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.042 0.007 -10000 0 -9999 0 0
EFNA5 0.032 0.004 -10000 0 -9999 0 0
FYN -0.02 0.017 0.18 3 -9999 0 3
neuron projection morphogenesis 0.042 0.007 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.043 0.007 -10000 0 -9999 0 0
EPHA5 0.032 0.004 -10000 0 0 9 9
Visual signal transduction: Rods

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
mol:K + 0.032 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.023 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.042 0.009 -10000 0 -0.04 1 1
PDE6G/GNAT1/GTP 0.042 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.005 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.059 0.025 -10000 0 -10000 0 0
mol:Na + 0.037 0.018 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.047 0.02 -10000 0 -10000 0 0
CNGB1 0.032 0.005 -10000 0 -10000 0 0
RDH5 0.031 0.007 -10000 0 -0.065 1 1
SAG 0.032 0.006 -10000 0 -0.065 1 1
mol:Ca2+ -0.034 0.023 0.15 7 -10000 0 7
Na + (4 Units) 0.035 0.02 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
GNB1/GNGT1 0.031 0.023 -10000 0 -10000 0 0
GNAT1/GDP 0.052 0.019 -10000 0 -10000 0 0
GUCY2D 0.032 0.005 -10000 0 -10000 0 0
GNGT1 0.022 0.015 -10000 0 -10000 0 0
GUCY2F 0.032 0.001 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.028 0.006 -10000 0 -10000 0 0
mol:11-cis-retinal 0.031 0.007 -10000 0 -0.065 1 1
mol:cGMP 0.024 0.009 -10000 0 -0.029 15 15
GNB1 0.031 0.008 -10000 0 -10000 0 0
Rhodopsin 0.045 0.012 -10000 0 -0.051 1 1
SLC24A1 0.032 0.005 -10000 0 -10000 0 0
CNGA1 0.032 0.004 -10000 0 -10000 0 0
Metarhodopsin II 0.02 0.005 -10000 0 -0.016 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.011 -10000 0 -0.024 14 14
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.007 0.027 -10000 0 -0.11 23 23
GCAP Family/Ca ++ 0.02 0.003 -10000 0 -0.016 4 4
PDE6A/B 0.047 0.007 -10000 0 -10000 0 0
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.039 0.032 -10000 0 -0.039 2 2
PDE6B 0.032 0.004 -10000 0 -10000 0 0
PDE6A 0.032 0.004 -10000 0 -10000 0 0
PDE6G 0.032 0.003 -10000 0 -10000 0 0
RHO 0.032 0.005 -10000 0 -10000 0 0
PDE6 0.074 0.026 -10000 0 -10000 0 0
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.041 0.007 -10000 0 -0.023 5 5
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.032 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.023 0.015 -9999 0 -9999 0 0
PLK4 0.032 0.004 -9999 0 -9999 0 0
regulation of centriole replication -0.015 0.01 -9999 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.032 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.032 0.005 -9999 0 -9999 0 0
PDE3B 0.032 0.005 -9999 0 -9999 0 0
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 0.15 0.019 -0.36 0.019
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 -0.065 0.033
131_RELN/VLDLR 0 0 0.084 0
30_TGFB1/TGF beta receptor Type II 0 0.032 0 -0.065
84_STAT5B 0.045 0.034 -0.32 0.034
84_STAT5A 0.045 0.034 -0.32 0.034
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/GBM-TP/4392507/GDAC_MergeDataFiles_4396203/GBM-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/GBM-TP/4425502/GDAC_Gistic2Report_4431500/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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle