PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1J67FNN
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1J67FNN
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 35 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 212
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 90
LPA receptor mediated events 76
Endothelins 75
amb2 Integrin signaling 66
TCGA08_retinoblastoma 65
TCGA08_p53 61
BARD1 signaling events 59
Ceramide signaling pathway 58
HIF-2-alpha transcription factor network 57
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 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 0.4015 212 849 4 -0.023 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1705 90 6154 68 -0.24 0.056 1000 -1000 -0.04 -1000
LPA receptor mediated events 0.1439 76 7785 102 -0.039 0.046 1000 -1000 -0.046 -1000
Endothelins 0.1420 75 7201 96 -0.47 0.032 1000 -1000 -0.027 -1000
amb2 Integrin signaling 0.1250 66 5412 82 -0.044 0.045 1000 -1000 -0.011 -1000
TCGA08_retinoblastoma 0.1231 65 521 8 -0.072 0.08 1000 -1000 -0.003 -1000
TCGA08_p53 0.1155 61 431 7 -0.007 0.028 1000 -1000 -0.012 -1000
BARD1 signaling events 0.1117 59 3394 57 -0.044 0.062 1000 -1000 -0.047 -1000
Ceramide signaling pathway 0.1098 58 4439 76 -0.092 0.065 1000 -1000 -0.02 -1000
HIF-2-alpha transcription factor network 0.1080 57 2473 43 -0.077 0.042 1000 -1000 -0.022 -1000
EPO signaling pathway 0.1004 53 2937 55 -0.004 0.05 1000 -1000 -0.018 -1000
HIF-1-alpha transcription factor network 0.0890 47 3573 76 -0.097 0.034 1000 -1000 -0.031 -1000
Arf6 signaling events 0.0871 46 2903 62 0 0.08 1000 -1000 -0.006 -1000
VEGFR1 specific signals 0.0871 46 2590 56 -0.037 0.053 1000 -1000 -0.023 -1000
Osteopontin-mediated events 0.0795 42 1621 38 -0.084 0.043 1000 -1000 -0.019 -1000
Aurora B signaling 0.0758 40 2737 67 -0.041 0.048 1000 -1000 -0.023 -1000
Wnt signaling 0.0739 39 276 7 -0.001 0.032 1000 -1000 0.002 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0739 39 3111 78 -0.038 0.042 1000 -1000 -0.035 -1000
Syndecan-1-mediated signaling events 0.0720 38 1318 34 -0.036 0.032 1000 -1000 -0.015 -1000
Syndecan-4-mediated signaling events 0.0720 38 2593 67 -0.059 0.032 1000 -1000 -0.03 -1000
PLK1 signaling events 0.0625 33 2884 85 -0.037 0.053 1000 -1000 -0.022 -1000
Ras signaling in the CD4+ TCR pathway 0.0625 33 575 17 -0.003 0.031 1000 -1000 -0.009 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0606 32 4035 125 -0.048 0.044 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 0.0587 31 2326 74 -0.054 0.054 1000 -1000 -0.034 -1000
PDGFR-alpha signaling pathway 0.0568 30 1352 44 -0.04 0.05 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0568 30 1385 45 -0.059 0.054 1000 -1000 -0.025 -1000
Glypican 1 network 0.0549 29 1403 48 -0.031 0.06 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 0.0549 29 2418 82 -0.042 0.048 1000 -1000 -0.018 -1000
FAS signaling pathway (CD95) 0.0549 29 1379 47 -0.14 0.044 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0549 29 959 33 -0.056 0.063 1000 -1000 -0.003 -1000
Fc-epsilon receptor I signaling in mast cells 0.0530 28 2790 97 -0.1 0.056 1000 -1000 -0.042 -1000
S1P1 pathway 0.0530 28 1020 36 -0.055 0.035 1000 -1000 -0.016 -1000
Signaling events mediated by the Hedgehog family 0.0511 27 1454 52 -0.015 0.066 1000 -1000 -0.02 -1000
IL1-mediated signaling events 0.0511 27 1718 62 -0.052 0.056 1000 -1000 -0.034 -1000
TCGA08_rtk_signaling 0.0511 27 704 26 -0.047 0.13 1000 -1000 -0.005 -1000
JNK signaling in the CD4+ TCR pathway 0.0492 26 447 17 -0.11 0.056 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 0.0492 26 1180 44 -0.037 0.06 1000 -1000 -0.015 -1000
Plasma membrane estrogen receptor signaling 0.0492 26 2274 86 -0.43 0.052 1000 -1000 -0.03 -1000
Regulation of nuclear SMAD2/3 signaling 0.0473 25 3488 136 -0.21 0.06 1000 -1000 -0.035 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0473 25 928 37 -0.048 0.074 1000 -1000 -0.017 -1000
Integrins in angiogenesis 0.0455 24 2037 84 -0.05 0.078 1000 -1000 -0.036 -1000
E-cadherin signaling in keratinocytes 0.0455 24 1033 43 -0.013 0.075 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0436 23 1971 85 -0.021 0.11 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0436 23 1211 51 -0.034 0.11 1000 -1000 -0.02 -1000
Arf6 trafficking events 0.0436 23 1654 71 -0.035 0.041 1000 -1000 -0.03 -1000
FOXM1 transcription factor network 0.0436 23 1192 51 -0.19 0.032 1000 -1000 -0.12 -1000
EGFR-dependent Endothelin signaling events 0.0417 22 479 21 -0.011 0.031 1000 -1000 -0.024 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0398 21 504 23 -0.02 0.037 1000 -1000 -0.009 -1000
Signaling events mediated by PTP1B 0.0379 20 1564 76 -0.026 0.059 1000 -1000 -0.017 -1000
BMP receptor signaling 0.0379 20 1621 81 -0.024 0.058 1000 -1000 -0.008 -1000
Visual signal transduction: Cones 0.0360 19 753 38 -0.02 0.052 1000 -1000 -0.015 -1000
Noncanonical Wnt signaling pathway 0.0360 19 519 26 -0.023 0.032 1000 -1000 -0.028 -1000
Nectin adhesion pathway 0.0360 19 1228 63 -0.016 0.072 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0360 19 2062 104 -0.041 0.052 1000 -1000 -0.033 -1000
FOXA2 and FOXA3 transcription factor networks 0.0341 18 866 46 0 0.091 1000 -1000 -0.068 -1000
TRAIL signaling pathway 0.0341 18 903 48 -0.032 0.07 1000 -1000 -0.021 -1000
ceramide signaling pathway 0.0341 18 923 49 -0.016 0.044 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 0.0341 18 1086 58 -0.013 0.059 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 0.0341 18 660 35 -0.009 0.072 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 0.0341 18 1396 76 -0.036 0.082 1000 -1000 -0.028 -1000
Coregulation of Androgen receptor activity 0.0322 17 1300 76 -0.049 0.059 1000 -1000 -0.019 -1000
Thromboxane A2 receptor signaling 0.0322 17 1823 105 -0.034 0.041 1000 -1000 -0.027 -1000
Aurora A signaling 0.0322 17 1078 60 -0.035 0.065 1000 -1000 -0.021 -1000
Arf6 downstream pathway 0.0322 17 758 43 -0.024 0.046 1000 -1000 -0.023 -1000
mTOR signaling pathway 0.0322 17 948 53 -0.034 0.055 1000 -1000 -0.029 -1000
S1P5 pathway 0.0322 17 298 17 -0.033 0.032 1000 -1000 -0.007 -1000
TCR signaling in naïve CD8+ T cells 0.0322 17 1587 93 -0.33 0.38 1000 -1000 -0.025 -1000
Class I PI3K signaling events 0.0322 17 1265 73 -0.024 0.062 1000 -1000 -0.016 -1000
Regulation of Telomerase 0.0322 17 1734 102 -0.025 0.075 1000 -1000 -0.025 -1000
BCR signaling pathway 0.0322 17 1710 99 -0.048 0.05 1000 -1000 -0.033 -1000
S1P3 pathway 0.0322 17 733 42 -0.031 0.033 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0322 17 2050 120 -0.038 0.082 1000 -1000 -0.036 -1000
Class I PI3K signaling events mediated by Akt 0.0303 16 1106 68 -0.025 0.06 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 0.0303 16 660 40 -0.037 0.041 1000 -1000 -0.043 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0303 16 1250 74 -0.21 0.069 1000 -1000 -0.041 -1000
PDGFR-beta signaling pathway 0.0303 16 1563 97 -0.043 0.065 1000 -1000 -0.036 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0284 15 845 54 -0.02 0.046 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 0.0284 15 1072 69 -0.021 0.053 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 0.0284 15 550 36 -0.043 0.049 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0284 15 906 58 -0.18 0.044 1000 -1000 -0.033 -1000
EPHB forward signaling 0.0284 15 1353 85 -0.05 0.077 1000 -1000 -0.037 -1000
Hedgehog signaling events mediated by Gli proteins 0.0265 14 914 65 -0.005 0.052 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 0.0265 14 885 61 -0.007 0.071 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0265 14 954 68 -0.056 0.063 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 0.0246 13 513 39 -0.028 0.065 1000 -1000 -0.016 -1000
p75(NTR)-mediated signaling 0.0246 13 1690 125 -0.049 0.072 1000 -1000 -0.036 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0246 13 1101 83 -0.045 0.062 1000 -1000 -0.016 -1000
FoxO family signaling 0.0246 13 853 64 -0.092 0.043 1000 -1000 -0.044 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0246 13 355 27 -0.029 0.069 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 0.0246 13 298 22 -0.018 0.033 1000 -1000 -0.018 -1000
Signaling events mediated by PRL 0.0246 13 460 34 -0.026 0.046 1000 -1000 -0.025 -1000
S1P4 pathway 0.0246 13 342 25 -0.033 0.04 1000 -1000 -0.007 -1000
IL6-mediated signaling events 0.0227 12 905 75 -0.019 0.07 1000 -1000 -0.061 -1000
ErbB2/ErbB3 signaling events 0.0208 11 739 65 -0.033 0.038 1000 -1000 -0.051 -1000
Cellular roles of Anthrax toxin 0.0189 10 420 39 -0.026 0.032 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 0.0189 10 591 54 -0.019 0.042 1000 -1000 -0.027 -1000
Nongenotropic Androgen signaling 0.0189 10 557 52 -0.064 0.055 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0189 10 955 88 -0.063 0.037 1000 -1000 -0.042 -1000
E-cadherin signaling events 0.0189 10 52 5 0.029 0.057 1000 -1000 0.028 -1000
LPA4-mediated signaling events 0.0170 9 119 12 -0.018 0.007 1000 -1000 -0.017 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0170 9 308 34 -0.049 0.089 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0170 9 859 87 -0.068 0.058 1000 -1000 -0.056 -1000
Glucocorticoid receptor regulatory network 0.0170 9 1129 114 -0.073 0.12 1000 -1000 -0.04 -1000
Effects of Botulinum toxin 0.0170 9 254 26 0 0.056 1000 -1000 -0.011 -1000
Arf1 pathway 0.0170 9 514 54 -0.061 0.042 1000 -1000 -0.011 -1000
Signaling events mediated by HDAC Class II 0.0152 8 641 75 -0.032 0.075 1000 -1000 -0.023 -1000
Aurora C signaling 0.0152 8 61 7 0 0.049 1000 -1000 -0.001 -1000
Signaling mediated by p38-gamma and p38-delta 0.0152 8 129 15 -0.026 0.032 1000 -1000 -0.022 -1000
Atypical NF-kappaB pathway 0.0152 8 266 31 -0.022 0.039 1000 -1000 -0.02 -1000
Insulin Pathway 0.0152 8 600 74 -0.041 0.077 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 0.0152 8 570 70 -0.036 0.057 1000 -1000 -0.026 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0133 7 221 28 -0.022 0.033 1000 -1000 -0.02 -1000
IL4-mediated signaling events 0.0133 7 678 91 -0.17 0.07 1000 -1000 -0.15 -1000
Reelin signaling pathway 0.0133 7 440 56 -0.015 0.061 1000 -1000 -0.017 -1000
Calcium signaling in the CD4+ TCR pathway 0.0133 7 222 31 -0.04 0.034 1000 -1000 -0.016 -1000
IGF1 pathway 0.0133 7 433 57 -0.038 0.061 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 0.0114 6 207 32 -0.03 0.041 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 0.0114 6 271 44 0 0.051 1000 -1000 -0.012 -1000
ErbB4 signaling events 0.0095 5 354 69 -0.027 0.064 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0095 5 284 52 -0.06 0.09 1000 -1000 -0.005 -1000
Ephrin B reverse signaling 0.0095 5 284 48 -0.011 0.049 1000 -1000 -0.038 -1000
Circadian rhythm pathway 0.0057 3 72 22 -0.01 0.045 1000 -1000 -0.016 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 18 5 0.025 0.046 1000 -1000 0.027 -1000
IL27-mediated signaling events 0.0057 3 199 51 -0.021 0.055 1000 -1000 -0.033 -1000
IL23-mediated signaling events 0.0038 2 167 60 -0.021 0.056 1000 -1000 -0.086 -1000
Rapid glucocorticoid signaling 0.0038 2 43 20 -0.011 0.032 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0038 2 38 13 0 0.055 1000 -1000 0 -1000
Visual signal transduction: Rods 0.0019 1 55 52 -0.034 0.074 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.016 0.032 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 0.0000 0 3 7 -0.02 0.042 1000 -1000 -0.013 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.031 0.032 1000 -1000 -0.027 -1000
Total NA 2966 167311 7203 -6.6 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 -0.065 283 283
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.013 0.031 -9999 0 -0.04 283 283
neuron projection morphogenesis -0.013 0.031 -9999 0 -0.04 283 283
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 -0.028 0.096 -10000 0 -0.14 198 198
NFATC3 -0.043 0.11 -10000 0 -0.16 214 214
CD40LG -0.14 0.17 -10000 0 -0.33 206 206
ITCH -0.015 0.009 -10000 0 -10000 0 0
CBLB -0.016 0.008 -10000 0 -0.058 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.16 -10000 0 -0.38 97 97
JUNB 0.03 0.013 -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 0.15 3 -0.12 3 6
TLE4 -0.021 0.059 0.097 1 -0.098 117 118
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.33 227 227
AP-1/NFAT1-c-4 -0.12 0.22 -10000 0 -0.34 219 219
IKZF1 -0.013 0.05 0.097 1 -0.1 61 62
T-helper 2 cell differentiation -0.12 0.17 -10000 0 -0.48 61 61
AP-1/NFAT1 -0.02 0.071 -10000 0 -0.11 20 20
CALM1 0.03 0.017 -10000 0 -0.046 14 14
EGR2 -0.092 0.18 -10000 0 -0.34 167 167
EGR3 0.006 0.12 -10000 0 -0.61 17 17
NFAT1/FOXP3 -0.006 0.08 -10000 0 -0.11 87 87
EGR1 0.029 0.017 -10000 0 -0.065 15 15
JUN 0.029 0.013 -10000 0 -0.034 2 2
EGR4 0.032 0.003 -10000 0 -0.026 1 1
mol:Ca2+ 0.003 0.006 -10000 0 -10000 0 0
GBP3 -0.02 0.054 0.089 1 -0.082 198 199
FOSL1 0.029 0.015 -10000 0 -0.065 12 12
NFAT1-c-4/MAF/IRF4 -0.099 0.22 -10000 0 -0.33 231 231
DGKA -0.021 0.06 0.097 1 -0.097 130 131
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.34 229 229
CTLA4 -0.023 0.054 0.082 1 -0.09 101 102
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 -0.067 122 122
IFNG -0.049 0.092 -10000 0 -0.25 32 32
T cell activation -0.079 0.11 -10000 0 -10000 0 0
MAF 0.031 0.005 -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 0.056 0.16 0.33 130 -10000 0 130
TNF -0.13 0.19 -10000 0 -0.32 234 234
FASLG -0.24 0.29 -10000 0 -0.53 242 242
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 -0.02 0.059 0.097 1 -0.1 84 85
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 -0.049 0.091 -10000 0 -0.28 19 19
IL2RA -0.12 0.17 -10000 0 -0.38 102 102
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.064 0.097 1 -0.11 124 125
E2F1 -0.02 0.04 -10000 0 -0.056 170 170
PPARG 0.031 0.01 -10000 0 -0.065 4 4
SLC3A2 -0.022 0.061 0.097 1 -0.1 101 102
IRF4 0.032 0.006 -10000 0 -0.065 1 1
PTGS2 -0.14 0.17 0.26 1 -0.33 207 208
CSF2 -0.14 0.17 0.26 1 -0.33 207 208
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.33 226 226
IL4 -0.13 0.18 -10000 0 -0.5 60 60
IL5 -0.14 0.17 0.26 1 -0.33 206 207
IL2 -0.08 0.11 -10000 0 -10000 0 0
IL3 -0.01 0.072 -10000 0 -0.54 6 6
RNF128 -0.017 0.012 -10000 0 -0.081 14 14
NFATC1 -0.049 0.16 -10000 0 -0.33 118 118
CDK4 0.011 0.11 0.27 67 -10000 0 67
PTPRK -0.02 0.059 0.097 1 -0.1 100 101
IL8 -0.15 0.17 0.26 1 -0.33 209 210
POU2F1 0.034 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 -0.035 260 260
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.06 0.21 6 -0.18 25 31
AP1 -0.017 0.03 -10000 0 -0.041 290 290
mol:PIP3 -0.013 0.019 -10000 0 -0.057 12 12
AKT1 0.01 0.073 0.2 22 -0.24 7 29
PTK2B -0.009 0.027 0.11 2 -0.2 6 8
RHOA 0.011 0.06 0.16 9 -0.31 9 18
PIK3CB 0.031 0.006 -10000 0 -0.031 1 1
mol:Ca2+ -0.013 0.018 0.17 2 -0.12 6 8
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 -0.012 0.039 0.17 11 -0.19 6 17
NF kappa B1 p50/RelA -0.038 0.02 0.069 1 -0.11 10 11
endothelial cell migration -0.026 0.042 -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 0.011 0.085 3 -0.091 3 6
ADCY7 -0.001 0.011 0.085 4 -0.089 1 5
ADCY1 -0.001 0.007 -10000 0 -0.089 1 1
ADCY2 -0.001 0.011 0.085 4 -0.08 2 6
ADCY3 -0.001 0.007 -10000 0 -0.093 1 1
ADCY8 -0.001 0.01 0.085 3 -0.089 1 4
ADCY9 -0.001 0.011 0.085 4 -0.089 1 5
GSK3B -0.013 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.001 0.013 0.076 4 -0.1 4 8
GNG2 0 0.001 -10000 0 -0.004 27 27
TRIP6 -0.008 0.025 -10000 0 -0.042 164 164
GNAO1 -0.001 0.008 -10000 0 -0.04 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.021 0.049 0.18 8 -0.18 24 32
GAB1 0.031 0.008 -10000 0 -0.065 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.18 -10000 0 -0.7 32 32
JUN 0.032 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.002 0.022 -10000 0 -0.021 243 243
TIAM1 -0.013 0.22 -10000 0 -0.85 32 32
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 -0.012 0.017 0.17 2 -0.12 3 5
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 -0.001 0.013 0.076 4 -0.1 4 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 -10000 0 -10000 0 0
GNAZ -0.011 0.025 -10000 0 -0.04 201 201
EGFR/PI3K-beta/Gab1 -0.013 0.019 0.023 2 -0.064 6 8
positive regulation of dendritic cell cytokine production -0.012 0.016 -10000 0 -0.028 247 247
LPA/LPA2/MAGI-3 -0.005 0.007 -10000 0 -0.012 249 249
ARHGEF1 0.026 0.094 0.17 143 -10000 0 143
GNAI2 -0.013 0.026 -10000 0 -0.04 240 240
GNAI3 -0.017 0.028 -10000 0 -0.042 269 269
GNAI1 -0.009 0.022 -10000 0 -0.04 153 153
LPA/LPA3 -0.007 0.008 -10000 0 -0.016 247 247
LPA/LPA2 -0.007 0.008 -10000 0 -0.016 246 246
LPA/LPA1 -0.017 0.022 -10000 0 -0.04 247 247
HB-EGF/EGFR -0.003 0.024 -10000 0 -0.05 77 77
HBEGF -0.03 0.016 0 45 -0.052 165 210
mol:DAG -0.012 0.017 0.17 2 -0.12 3 5
cAMP biosynthetic process 0.046 0.062 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 -0.002 0.013 -10000 0 -0.016 235 235
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 -0.033 242 242
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
CASP3 -0.015 0.026 -10000 0 -0.038 272 272
EGFR 0.012 0.017 -10000 0 -0.065 5 5
PLCG1 0.002 0.008 -10000 0 -0.03 8 8
PLD2 -0.006 0.026 -10000 0 -0.032 246 246
G12/G13 0.002 0.037 -10000 0 -0.043 172 172
PI3K-beta -0.011 0.041 -10000 0 -0.22 10 10
cell migration -0.005 0.052 -10000 0 -0.22 23 23
SLC9A3R2 0.032 0.003 -10000 0 -10000 0 0
PXN 0.004 0.024 -10000 0 -10000 0 0
HRAS/GTP -0.001 0.013 0.077 4 -0.1 4 8
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 166 166
PRKCE 0.031 0.006 -10000 0 -0.027 3 3
PRKCD -0.014 0.036 0.21 9 -0.12 4 13
Gi(beta/gamma) 0 0.015 0.085 4 -0.14 3 7
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 -0.001 0.013 0.076 4 -0.1 4 8
contractile ring contraction involved in cytokinesis 0.014 0.062 0.15 14 -0.31 9 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 -0.016 231 231
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA13 0.031 0.007 -10000 0 -0.066 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.001 0.013 -10000 0 -0.016 232 232
Rac1/GTP -0.007 0.19 -10000 0 -0.74 32 32
MMP2 -0.026 0.042 -10000 0 -0.069 242 242
Endothelins

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
AKT1 -0.068 0.035 -10000 0 -0.11 91 91
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.087 0.17 0.36 1 -0.4 98 99
EDN1 -0.037 0.044 -10000 0 -0.062 364 364
EDN3 0.029 0.012 -10000 0 -0.065 3 3
EDN2 0.031 0.006 -10000 0 -0.065 1 1
HRAS/GDP -0.031 0.08 0.23 13 -0.27 18 31
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.015 0.041 -10000 0 -0.17 11 11
ADCY4 -0.055 0.024 0.011 1 -0.075 253 254
ADCY5 -0.055 0.024 0.011 1 -0.075 253 254
ADCY6 -0.058 0.033 0.16 3 -10000 0 3
ADCY7 -0.058 0.036 0.16 4 -10000 0 4
ADCY1 -0.043 0.038 0.15 2 -10000 0 2
ADCY2 -0.057 0.037 0.16 4 -10000 0 4
ADCY3 -0.055 0.024 0.011 1 -0.075 253 254
ADCY8 -0.057 0.037 0.16 4 -10000 0 4
ADCY9 -0.058 0.036 0.16 4 -10000 0 4
arachidonic acid secretion -0.048 0.093 0.28 9 -0.32 19 28
ETB receptor/Endothelin-1/Gq/GTP -0.008 0.034 -10000 0 -0.16 14 14
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 -0.087 186 186
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 -0.091 0.042 -10000 0 -0.12 247 247
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 -0.11 87 87
CYSLTR1 -0.062 0.031 0.04 1 -0.085 285 286
SLC9A1 -0.032 0.032 -10000 0 -0.056 259 259
mol:GDP -0.033 0.078 0.22 14 -0.28 18 32
SLC9A3 -0.074 0.19 -10000 0 -0.58 48 48
RAF1 -0.032 0.082 0.26 11 -0.31 15 26
JUN -0.095 0.19 0.35 1 -0.44 100 101
JAK2 -0.064 0.037 -10000 0 -0.11 84 84
mol:IP3 -0.016 0.046 -10000 0 -0.22 14 14
ETA receptor/Endothelin-1 -0.059 0.068 -10000 0 -0.098 357 357
PLCB1 0.029 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.006 -10000 0 -0.029 1 1
ETA receptor/Endothelin-3 -0.03 0.045 -10000 0 -0.058 342 342
FOS -0.04 0.097 0.31 10 -0.32 16 26
Gai/GDP -0.47 0.17 -10000 0 -0.52 454 454
CRK 0.032 0.004 -10000 0 -10000 0 0
mol:Ca ++ -0.046 0.051 -10000 0 -0.19 21 21
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.017 0.046 -10000 0 -0.22 13 13
GNAQ 0.031 0.008 -10000 0 -0.027 3 3
GNAZ 0.026 0.012 -10000 0 -10000 0 0
GNAL 0.031 0.005 -10000 0 -10000 0 0
Gs family/GDP -0.031 0.074 0.2 13 -0.26 16 29
ETA receptor/Endothelin-1/Gq/GTP -0.022 0.036 -10000 0 -0.14 14 14
MAPK14 -0.012 0.035 -10000 0 -0.21 7 7
TRPC6 -0.09 0.18 0.36 1 -0.42 98 99
GNAI2 0.031 0.005 -10000 0 -10000 0 0
GNAI3 0.02 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 -0.005 0.039 -10000 0 -0.16 16 16
ETB receptor/Endothelin-2 0.013 0.037 -10000 0 -0.039 151 151
ETB receptor/Endothelin-3 0.012 0.037 -10000 0 -0.039 146 146
ETB receptor/Endothelin-1 -0.034 0.048 -10000 0 -0.067 293 293
MAPK3 -0.035 0.097 0.32 11 -0.34 13 24
MAPK1 -0.043 0.1 0.32 10 -0.34 18 28
Rac1/GDP -0.028 0.059 0.2 4 -0.26 12 16
cAMP biosynthetic process -0.02 0.043 0.17 8 -0.15 1 9
MAPK8 -0.11 0.22 0.37 1 -0.5 110 111
SRC 0.03 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.022 -10000 0 -0.12 16 16
p130Cas/CRK/Src/PYK2 -0.027 0.084 0.28 12 -0.31 13 25
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.028 0.059 0.2 4 -0.26 12 16
COL1A2 -0.055 0.063 -10000 0 -0.13 192 192
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.031 0.046 -10000 0 -0.058 355 355
mol:DAG -0.016 0.046 -10000 0 -0.22 14 14
MAP2K2 -0.036 0.099 0.33 16 -0.32 14 30
MAP2K1 -0.042 0.083 0.26 9 -0.32 14 23
EDNRA -0.049 0.05 -10000 0 -0.075 365 365
positive regulation of muscle contraction -0.009 0.096 0.15 125 -0.12 4 129
Gq family/GDP 0.004 0.08 0.25 3 -0.25 14 17
HRAS/GTP -0.025 0.076 0.21 14 -0.3 16 30
PRKCH -0.022 0.049 0.21 1 -0.25 12 13
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.024 0.054 0.18 3 -0.25 16 19
PRKCB -0.017 0.046 -10000 0 -0.22 13 13
PRKCE -0.025 0.052 -10000 0 -0.24 17 17
PRKCD -0.024 0.052 0.17 2 -0.25 15 17
PRKCG -0.024 0.053 0.21 1 -0.25 16 17
regulation of vascular smooth muscle contraction -0.043 0.11 0.36 9 -0.38 13 22
PRKCQ -0.018 0.041 0.19 3 -0.26 7 10
PLA2G4A -0.051 0.097 0.29 9 -0.33 20 29
GNA14 0.031 0.01 -10000 0 -0.042 5 5
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.054 -10000 0 -0.088 181 181
MMP1 0.022 0.045 0.07 110 -0.089 22 132
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.051 211 211
alphaM/beta2 Integrin/proMMP-9 -0.006 0.059 -10000 0 -0.058 272 272
PLAUR 0.022 0.028 -10000 0 -0.065 44 44
HMGB1 0.028 0.014 -10000 0 -0.029 19 19
alphaM/beta2 Integrin/Talin 0.006 0.057 -10000 0 -0.053 228 228
AGER 0.029 0.015 -10000 0 -0.036 25 25
RAP1A 0.032 0.004 -10000 0 -10000 0 0
SELPLG 0.032 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.016 0.072 -10000 0 -0.086 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.045 -10000 0 -0.065 166 166
CYR61 0.003 0.044 -10000 0 -0.065 150 150
TLN1 0.021 0.028 -10000 0 -0.065 43 43
Rap1/GTP 0.009 0.038 0.11 2 -0.15 4 6
RHOA 0.031 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.031 0.006 -10000 0 -0.065 1 1
MYH2 0 0.037 0.14 4 -0.16 3 7
MST1R 0.031 0.008 -10000 0 -0.065 2 2
leukocyte activation during inflammatory response 0.012 0.058 -10000 0 -0.056 37 37
APOB 0.031 0.008 -10000 0 -0.065 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.015 0.048 -10000 0 -0.065 241 241
JAM3 0.03 0.009 -10000 0 -0.065 1 1
GP1BA 0.032 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.007 0.057 -10000 0 -0.053 225 225
alphaM/beta2 Integrin 0 0.036 -10000 0 -0.14 8 8
JAM3 homodimer 0.03 0.009 -10000 0 -0.065 1 1
ICAM2 0.031 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 0.036 -10000 0 -0.14 8 8
cell adhesion 0.015 0.056 -10000 0 -0.05 211 211
NFKB1 -0.043 0.033 0.18 6 -10000 0 6
THY1 0.023 0.014 -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 -0.013 0.065 -10000 0 -0.071 133 133
IL6 -0.033 0.038 0.16 4 -0.16 2 6
ITGB2 -0.01 0.048 -10000 0 -0.064 221 221
elevation of cytosolic calcium ion concentration -0.009 0.065 -10000 0 -0.075 116 116
alphaM/beta2 Integrin/JAM2/JAM3 0.008 0.066 -10000 0 -0.066 56 56
JAM2 0.017 0.034 -10000 0 -0.065 72 72
alphaM/beta2 Integrin/ICAM1 0.023 0.074 -10000 0 -0.077 12 12
alphaM/beta2 Integrin/uPA/Plg -0.008 0.064 -10000 0 -0.07 109 109
RhoA/GTP 0.004 0.037 0.1 16 -0.13 10 26
positive regulation of phagocytosis -0.002 0.053 0.14 8 -0.13 9 17
Ron/MSP 0.045 0.014 -10000 0 -0.051 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.009 0.066 -10000 0 -0.076 116 116
alphaM/beta2 Integrin/uPAR 0.011 0.059 -10000 0 -0.055 213 213
PLAU 0.007 0.037 -10000 0 -0.065 94 94
PLAT -0.013 0.048 -10000 0 -0.065 232 232
actin filament polymerization 0.001 0.038 0.15 6 -0.16 3 9
MST1 0.03 0.012 -10000 0 -0.065 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.015 0.062 -10000 0 -0.056 37 37
TNF -0.044 0.031 0.16 6 -10000 0 6
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.056 -10000 0 -0.059 229 229
fibrinolysis -0.009 0.063 -10000 0 -0.07 109 109
HCK 0.014 0.036 -10000 0 -0.065 84 84
dendritic cell antigen processing and presentation 0 0.036 -10000 0 -0.14 8 8
VTN 0.032 0.007 -10000 0 -0.065 2 2
alphaM/beta2 Integrin/CYR61 -0.002 0.061 -10000 0 -0.058 267 267
LPA 0.03 0.008 -10000 0 -10000 0 0
LRP1 0.028 0.017 -10000 0 -0.065 13 13
cell migration -0.034 0.05 -10000 0 -0.074 228 228
FN1 0.014 0.038 -10000 0 -0.065 96 96
alphaM/beta2 Integrin/Thy1 0.006 0.05 -10000 0 -0.051 178 178
MPO 0.032 0.003 -10000 0 -10000 0 0
KNG1 0.031 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0 0.043 0.18 9 -0.15 5 14
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 -0.059 207 207
ITGAM 0.03 0.012 -10000 0 -0.029 21 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.023 0.066 -10000 0 -0.062 34 34
HP 0.017 0.035 -10000 0 -0.065 77 77
leukocyte adhesion -0.008 0.055 -10000 0 -0.1 8 8
SELP 0.031 0.006 -10000 0 -0.065 1 1
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.018 -10000 0 -0.038 5 5
CDKN2C -0.007 0.029 -10000 0 -0.056 106 106
CDKN2A 0.005 0.026 -10000 0 -0.051 52 52
CCND2 0.002 0.011 0.088 3 -10000 0 3
RB1 -0.072 0.1 0.1 1 -0.22 166 167
CDK4 0.002 0.011 0.1 3 -10000 0 3
CDK6 0.005 0.017 0.11 7 -10000 0 7
G1/S progression 0.08 0.11 0.22 177 -0.1 1 178
TCGA08_p53

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
CDKN2A -0.007 0.012 0 312 -0.04 53 365
TP53 -0.002 0.025 -10000 0 -0.2 7 7
Senescence -0.003 0.027 -10000 0 -0.2 8 8
Apoptosis -0.003 0.027 -10000 0 -0.2 8 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.009 0.022 43 -10000 0 43
MDM4 0.028 0.01 -10000 0 -10000 0 0
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 -0.051 113 113
ATM 0.027 0.021 -10000 0 -0.065 25 25
UBE2D3 0.032 0.004 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
ATR 0.031 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 24 24
protein ubiquitination 0.042 0.065 -10000 0 -0.08 25 25
XRCC5 0.032 0.001 -10000 0 -10000 0 0
XRCC6 0.03 0.008 -10000 0 -10000 0 0
M/R/N Complex 0.062 0.014 -10000 0 -10000 0 0
MRE11A 0.032 0.004 -10000 0 -10000 0 0
DNA-PK 0.056 0.028 -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 0.039 0.024 -10000 0 -0.055 23 23
FANCG 0.018 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 0.067 0.18 15 -0.22 26 41
BRCA1/BARD1/ubiquitin 0.024 0.042 -10000 0 -0.052 120 120
BARD1/DNA-PK 0.041 0.062 -10000 0 -0.054 131 131
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.041 0.051 113 -10000 0 113
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.039 0.1 6 -0.16 16 22
BRCA1/BACH1/BARD1/TopBP1 0.036 0.05 -10000 0 -0.051 122 122
BRCA1/BARD1/P53 0.034 0.065 -10000 0 -0.072 34 34
BARD1/CSTF1/BRCA1 0.034 0.049 -10000 0 -0.05 114 114
BRCA1/BACH1 0.031 0.01 -10000 0 -0.065 5 5
BARD1 0.009 0.042 -10000 0 -0.065 122 122
PCNA -0.027 0.046 -10000 0 -0.065 297 297
BRCA1/BARD1/UbcH5C 0.036 0.05 -10000 0 -0.05 123 123
BRCA1/BARD1/UbcH7 0.035 0.05 -10000 0 -0.051 122 122
BRCA1/BARD1/RAD51/PCNA -0.011 0.064 -10000 0 -0.071 103 103
BARD1/DNA-PK/P53 0.037 0.075 -10000 0 -0.077 37 37
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 0.011 0.034 -10000 0 -0.15 16 16
BARD1/EWS 0.023 0.041 -10000 0 -0.051 110 110
RBBP8 -0.044 0.016 -10000 0 -0.053 379 379
TP53 0.019 0.033 -10000 0 -0.065 65 65
TOPBP1 0.031 0.006 -10000 0 -0.065 1 1
G1/S transition of mitotic cell cycle -0.033 0.064 0.071 35 -10000 0 35
BRCA1/BARD1 0.047 0.069 -10000 0 -0.081 25 25
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.008 0.027 -10000 0 -0.04 122 122
CDK2 0.027 0.021 -10000 0 -0.065 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.031 0.005 -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
Ceramide 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
SPHK2 -0.015 0.011 -10000 0 -0.051 2 2
MAP4K4 -0.008 0.039 -10000 0 -0.2 9 9
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.059 0.11 -10000 0 -0.2 160 160
NFKBIA 0.03 0.008 -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 0.014 -10000 0 -0.065 9 9
AKT1 0 0.07 0.75 4 -10000 0 4
BAD -0.065 0.11 0.19 2 -0.21 160 162
SMPD1 -0.006 0.037 0.11 5 -0.17 15 20
RB1 -0.065 0.11 0.2 1 -0.21 160 161
FADD/Caspase 8 -0.002 0.041 -10000 0 -0.24 7 7
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 0.17 6 -0.2 157 163
EGF 0.031 0.007 -10000 0 -0.065 2 2
mol:ceramide -0.062 0.12 -10000 0 -0.21 160 160
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 -10000 0 -0.051 2 2
ASAH1 0.031 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.065 0.11 0.2 1 -0.2 160 161
cell proliferation -0.037 0.1 0.16 1 -0.19 144 145
BID -0.024 0.15 -10000 0 -0.65 23 23
MAP3K1 -0.065 0.11 0.2 1 -0.21 159 160
EIF2A -0.065 0.1 0.17 1 -0.19 160 161
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 -0.19 145 149
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.1 0.18 4 -0.21 148 152
Cathepsin D/ceramide -0.047 0.12 -10000 0 -0.21 159 159
FADD -0.007 0.034 -10000 0 -0.17 8 8
KSR1 -0.065 0.11 0.19 2 -0.21 160 162
MAPK8 -0.092 0.15 0.15 3 -0.25 189 192
PRKRA -0.065 0.11 -10000 0 -0.21 160 160
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 -0.062 0.12 -10000 0 -0.21 160 160
CTSD 0.028 0.017 -10000 0 -0.065 15 15
regulation of nitric oxide biosynthetic process 0.045 0.012 -10000 0 -0.051 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.039 0.11 0.18 1 -0.2 144 145
PRKCD 0.031 0.005 -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 -10000 0 -0.051 2 2
RelA/NF kappa B1 0.045 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 -0.002 0.04 -10000 0 -0.19 11 11
TNFR1A/BAG4/TNF-alpha 0.025 0.053 -10000 0 -0.049 164 164
mol:Sphingosine-1-phosphate -0.015 0.011 -10000 0 -0.051 2 2
MAP2K1 -0.067 0.1 0.17 6 -0.2 152 158
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
CYCS -0.017 0.064 0.12 1 -0.23 29 30
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 163 163
EIF2AK2 -0.068 0.11 0.18 1 -0.2 160 161
TNF-alpha/TNFR1A/FAN 0.024 0.053 -10000 0 -0.049 164 164
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.048 -10000 0 -0.29 8 8
MAP2K2 -0.064 0.094 0.17 9 -0.2 150 159
SMPD3 0 0.04 -10000 0 -0.24 9 9
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 -0.036 0.067 0.13 3 -0.13 151 154
NF kappa B1/RelA/I kappa B alpha 0.065 0.034 -10000 0 -0.049 6 6
AIFM1 -0.043 0.081 0.12 1 -0.23 38 39
BCL2 0.031 0.006 -10000 0 -10000 0 0
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 -0.012 0.16 -10000 0 -0.65 31 31
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.003 -10000 0 -10000 0 0
TCEB1 0.031 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.023 0.074 -10000 0 -0.14 90 90
EPO -0.031 0.071 -10000 0 -0.2 46 46
FIH (dimer) 0.019 0.018 -10000 0 -0.027 30 30
APEX1 0.022 0.022 -10000 0 -0.029 65 65
SERPINE1 -0.045 0.07 -10000 0 -0.18 67 67
FLT1 -0.015 0.16 -10000 0 -0.6 35 35
ADORA2A -0.069 0.066 0.18 1 -0.16 116 117
germ cell development -0.062 0.068 -10000 0 -0.16 118 118
SLC11A2 -0.065 0.074 -10000 0 -0.17 117 117
BHLHE40 -0.064 0.069 -10000 0 -0.16 118 118
HIF1AN 0.019 0.018 -10000 0 -0.027 30 30
HIF2A/ARNT/SIRT1 -0.03 0.085 0.17 1 -0.16 98 99
ETS1 0.034 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 38 38
KDR 0.014 0.08 -10000 0 -0.55 9 9
PGK1 -0.065 0.074 -10000 0 -0.17 117 117
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.035 0.11 -10000 0 -0.19 98 98
EPAS1 -0.031 0.049 0.12 1 -0.12 100 101
SP1 0.034 0.006 -10000 0 -0.038 1 1
ABCG2 -0.066 0.074 -10000 0 -0.17 117 117
EFNA1 -0.066 0.074 -10000 0 -0.17 116 116
FXN -0.068 0.065 -10000 0 -0.16 113 113
POU5F1 -0.064 0.069 -10000 0 -0.16 118 118
neuron apoptosis 0.035 0.11 0.18 100 -10000 0 100
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.023 0.019 -10000 0 -0.032 42 42
EGLN2 0.025 0.015 -10000 0 -0.027 31 31
EGLN1 0.025 0.016 -10000 0 -0.028 39 39
VHL/Elongin B/Elongin C 0.042 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.024 0.021 -10000 0 -0.029 62 62
SLC2A1 -0.068 0.066 0.18 1 -0.16 114 115
TWIST1 -0.04 0.055 -10000 0 -0.16 53 53
ELK1 0.033 0.012 -10000 0 -0.038 13 13
HIF2A/ARNT/Cbp/p300 -0.024 0.094 0.19 1 -0.16 97 98
VEGFA -0.077 0.08 -10000 0 -0.18 123 123
CREBBP 0.032 0.003 -10000 0 0 6 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.036 0.047 0.18 19 -0.16 2 21
CRKL 0.026 0.09 0.16 131 -10000 0 131
mol:DAG 0.011 0.029 0.13 6 -0.14 2 8
HRAS 0.019 0.094 0.26 30 -10000 0 30
MAPK8 0.006 0.068 0.15 87 -10000 0 87
RAP1A 0.028 0.091 0.16 139 -10000 0 139
GAB1 0.028 0.091 0.16 137 -10000 0 137
MAPK14 0.021 0.083 0.15 146 -10000 0 146
EPO 0.023 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.029 0.14 6 -0.14 2 8
EPOR/TRPC2/IP3 Receptors 0.036 0.011 0.093 2 -10000 0 2
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.013 0.086 0.15 124 -10000 0 124
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.027 0.089 0.16 135 -10000 0 135
STAT1 0.012 0.032 0.15 4 -0.14 2 6
STAT5B 0.012 0.03 0.14 6 -0.14 2 8
cell proliferation 0.005 0.074 0.16 91 -10000 0 91
GAB1/SHIP/PIK3R1/SHP2/SHC -0.004 0.065 0.11 120 -10000 0 120
TEC 0.027 0.091 0.16 136 -10000 0 136
SOCS3 0.032 0.003 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.032 0.15 4 -0.14 2 6
JAK2 0.034 0.015 0.092 3 -10000 0 3
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.05 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 -0.065 60 60
TEC/VAV2 0.006 0.071 0.13 114 -10000 0 114
elevation of cytosolic calcium ion concentration 0.036 0.011 0.092 2 -10000 0 2
SHC1 0.024 0.026 -10000 0 -0.065 40 40
EPO/EPOR (dimer)/LYN 0.035 0.043 -10000 0 -0.053 47 47
mol:IP3 0.011 0.029 0.13 6 -0.14 2 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.088 0.16 124 -10000 0 124
SH2B3 0.036 0.016 0.092 1 -0.066 8 9
NFKB1 0.021 0.083 0.15 146 -10000 0 146
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 0.076 2 -10000 0 2
PTPN6 0.03 0.089 0.16 155 -10000 0 155
TEC/VAV2/GRB2 0.015 0.088 0.16 122 -10000 0 122
EPOR 0.036 0.011 0.093 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.086 0.15 124 -10000 0 124
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.029 0.014 -10000 0 -0.065 10 10
CRKL/CBL/C3G 0.013 0.088 0.16 120 -10000 0 120
VAV2 0.025 0.088 0.16 131 -10000 0 131
CBL 0.028 0.092 0.16 138 -10000 0 138
SHC/Grb2/SOS1 0.019 0.036 -10000 0 -0.082 1 1
STAT5A 0.012 0.03 0.14 6 -0.14 2 8
GRB2 0.031 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 -0.055 61 61
PTPN11 0.032 0.004 -10000 0 -10000 0 0
BTK 0.029 0.093 0.16 141 -10000 0 141
BCL2 0.035 0.05 0.17 19 -0.19 6 25
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.057 0.17 0.47 14 -0.29 21 35
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.078 0.11 -10000 0 -0.24 85 85
SMAD4 0.009 0.041 -10000 0 -0.065 114 114
ID2 -0.058 0.17 0.5 12 -0.29 20 32
AP1 0.021 0.042 -10000 0 -0.051 117 117
ABCG2 -0.061 0.16 0.48 13 -0.29 21 34
HIF1A -0.014 0.055 0.15 7 -0.086 25 32
TFF3 -0.059 0.17 0.48 14 -0.29 20 34
GATA2 0.031 0.009 -10000 0 -0.028 9 9
AKT1 -0.01 0.055 0.17 6 -0.097 1 7
response to hypoxia -0.019 0.025 0.091 6 -0.058 44 50
MCL1 -0.06 0.17 0.48 11 -0.29 21 32
NDRG1 -0.069 0.15 0.49 6 -0.29 21 27
SERPINE1 -0.055 0.15 0.46 12 -0.29 34 46
FECH -0.054 0.17 0.48 15 -0.29 19 34
FURIN -0.056 0.17 0.48 15 -0.29 22 37
NCOA2 0.032 0.004 -10000 0 -10000 0 0
EP300 0.001 0.055 0.24 9 -0.2 2 11
HMOX1 -0.078 0.16 0.47 13 -0.29 43 56
BHLHE40 -0.096 0.092 -10000 0 -0.21 170 170
BHLHE41 -0.096 0.092 -10000 0 -0.21 170 170
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.008 0.093 0.23 6 -0.1 93 99
ENG -0.034 0.08 0.27 10 -0.16 1 11
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.058 0.17 0.49 13 -0.29 20 33
ABCB1 -0.011 0.043 -10000 0 -0.3 5 5
TFRC -0.06 0.16 0.48 14 -0.29 20 34
CXCR4 -0.076 0.16 0.48 9 -0.29 42 51
TF -0.084 0.11 -10000 0 -0.29 18 18
CITED2 -0.062 0.16 0.48 11 -0.29 20 31
HIF1A/ARNT -0.073 0.14 0.26 23 -0.25 124 147
LDHA 0.002 0.057 -10000 0 -0.46 6 6
ETS1 -0.056 0.17 0.48 14 -0.29 21 35
PGK1 -0.056 0.17 0.51 11 -0.29 20 31
NOS2 -0.096 0.092 -10000 0 -0.21 170 170
ITGB2 -0.065 0.17 0.49 13 -0.29 40 53
ALDOA -0.057 0.17 0.49 9 -0.29 20 29
Cbp/p300/CITED2 -0.097 0.1 -10000 0 -0.24 121 121
FOS 0.007 0.041 -10000 0 -0.065 120 120
HK2 -0.056 0.17 0.5 12 -0.29 20 32
SP1 0.034 0.007 -10000 0 -0.04 2 2
GCK 0.004 0.088 0.39 5 -0.37 3 8
HK1 -0.078 0.14 0.46 5 -0.29 21 26
NPM1 -0.061 0.16 0.47 13 -0.29 21 34
EGLN1 -0.06 0.16 0.47 12 -0.29 21 33
CREB1 0.034 0.008 -10000 0 -0.084 2 2
PGM1 -0.057 0.17 0.48 15 -0.29 20 35
SMAD3 0.031 0.004 -10000 0 -10000 0 0
EDN1 -0.017 0.081 0.28 2 -0.3 21 23
IGFBP1 -0.047 0.15 0.53 7 -0.29 17 24
VEGFA -0.079 0.13 0.36 12 -0.27 43 55
HIF1A/JAB1 0.007 0.053 0.14 5 -0.054 160 165
CP -0.067 0.16 0.48 11 -0.29 36 47
CXCL12 -0.069 0.15 0.49 7 -0.29 22 29
COPS5 0.032 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.041 -10000 0 -0.052 110 110
BNIP3 -0.075 0.13 0.42 3 -0.29 21 24
EGLN3 -0.059 0.17 0.47 13 -0.29 21 34
CA9 -0.061 0.16 0.49 12 -0.29 24 36
TERT -0.055 0.17 0.48 14 -0.29 21 35
ENO1 -0.06 0.16 0.5 10 -0.29 17 27
PFKL -0.055 0.17 0.51 11 -0.29 19 30
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.076 0.16 0.47 11 -0.29 41 52
ARNT -0.015 0.056 0.15 7 -0.085 20 27
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.096 0.092 -10000 0 -0.21 170 170
SLC2A1 -0.065 0.13 0.37 13 -0.27 30 43
LEP -0.047 0.15 0.46 11 -0.29 16 27
HIF1A/ARNT/Cbp/p300 -0.081 0.11 -10000 0 -0.23 105 105
EPO -0.032 0.11 0.33 11 -0.37 18 29
CREBBP 0.001 0.056 0.24 10 -0.2 2 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.084 0.11 -10000 0 -0.23 107 107
PFKFB3 -0.066 0.15 0.49 8 -0.29 21 29
NT5E -0.065 0.16 0.49 9 -0.29 26 35
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.021 0.005 -10000 0 -0.005 12 12
ARNO/beta Arrestin1-2 0.04 0.016 -10000 0 -0.062 9 9
EGFR 0.012 0.017 -10000 0 -0.065 5 5
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
USP6 0.032 0.004 -10000 0 -10000 0 0
IQSEC1 0.031 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.017 0.024 -10000 0 -0.051 7 7
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0.013 0.1 4 -0.064 6 10
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.029 0.012 -10000 0 -0.065 4 4
EGF 0.032 0.007 -10000 0 -0.065 2 2
somatostatin receptor activity 0 0 0 155 0 12 167
ARAP2 0 0 0 149 0 7 156
mol:GDP 0.06 0.064 0.14 141 -0.13 9 150
mol:PI-3-4-5-P3 0 0 0 145 0 12 157
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 0.066 0.042 -10000 0 -0.056 33 33
ADAP1 0 0 0 88 0 6 94
KIF13B 0.031 0.008 -10000 0 -0.011 12 12
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 0.086 0.18 149 -0.19 11 160
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.049 7 7
ADRB2 0.032 0.006 -10000 0 -0.065 1 1
receptor agonist activity 0 0 0 144 0 12 156
actin filament binding 0 0 0 145 0 12 157
SRC 0.03 0.008 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 159 -0.001 9 168
ARF6/GDP 0.026 0.065 0.13 27 -0.2 26 53
ARF6/GDP/GULP/ACAP1 0.08 0.063 0.16 129 -0.15 6 135
alphaIIb/beta3 Integrin/paxillin/GIT1 0.08 0.016 -10000 0 -10000 0 0
ACAP1 0 0 0 45 -10000 0 45
ACAP2 0 0 0 146 0 10 156
LHCGR/beta Arrestin2 0.028 0.014 -10000 0 -0.079 9 9
EFNA1 0.027 0.02 -10000 0 -0.065 21 21
HGF 0.022 0.015 -10000 0 -0.065 1 1
CYTH3 0 0 0.001 149 0 12 161
CYTH2 0 0.001 0.002 3 -0.003 15 18
NCK1 0.029 0.015 -10000 0 -0.065 11 11
fibronectin binding 0 0 0 140 0 15 155
endosomal lumen acidification 0 0 0 155 0 16 171
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 0.031 0.009 -10000 0 -0.065 4 4
GNAQ/ARNO 0.024 0.006 0.038 5 0 18 23
mol:Phosphatidic acid 0 0 0 146 0 10 156
PIP3-E 0 0 0 85 0 13 98
MET 0.021 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 0.001 157 -0.001 11 168
GNA11 0.031 0.006 -10000 0 -10000 0 0
LHCGR 0.032 0 -10000 0 -10000 0 0
AGTR1 0.031 0.008 -10000 0 -0.065 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.028 0.014 -10000 0 -0.079 9 9
IPCEF1/ARNO 0.014 0.019 -10000 0 -0.029 7 7
alphaIIb/beta3 Integrin 0.047 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.028 0.016 -10000 0 -0.036 21 21
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.019 0.18 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.011 0.035 -10000 0 -0.042 274 274
CaM/Ca2+ -0.027 0.021 0.18 3 -10000 0 3
HIF1A 0.035 0.011 -10000 0 -0.064 2 2
GAB1 0.031 0.008 -10000 0 -0.065 3 3
AKT1 -0.023 0.033 0.13 15 -0.19 1 16
PLCG1 -0.024 0.019 0.18 3 -10000 0 3
NOS3 -0.006 0.042 0.19 4 -0.21 13 17
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.007 0.055 0.2 3 -0.21 13 16
FLT1 -0.017 0.006 -10000 0 -10000 0 0
PGF 0.026 0.02 -10000 0 -0.065 19 19
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.049 -10000 0 -0.049 277 277
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
eNOS/Hsp90 0.024 0.073 0.19 11 -0.22 22 33
endothelial cell proliferation -0.01 0.048 0.13 37 -0.14 18 55
mol:Ca2+ -0.024 0.019 0.18 3 -10000 0 3
MAPK3 -0.035 0.019 0.15 3 -10000 0 3
MAPK1 -0.032 0.021 0.15 3 -10000 0 3
PIK3R1 0.029 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 0.042 -10000 0 -0.065 218 218
VEGFA homodimer -0.021 0.048 -10000 0 -0.065 275 275
VEGFR1 homodimer/VEGFA homodimer -0.012 0.039 -10000 0 -0.047 279 279
platelet activating factor biosynthetic process -0.037 0.021 0.14 3 -10000 0 3
PI3K 0.044 0.047 0.17 2 -0.076 1 3
PRKCA -0.028 0.02 0.17 3 -10000 0 3
PRKCB -0.022 0.018 0.17 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer 0.027 0.019 -10000 0 -0.046 22 22
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 0.019 0.18 3 -10000 0 3
RASA1 -0.026 0.018 0.18 3 -10000 0 3
NRP2 0.032 0.005 -10000 0 -0.065 1 1
VEGFR1 homodimer -0.017 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.032 0.004 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
eNOS/Caveolin-1 -0.014 0.05 -10000 0 -0.22 16 16
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.046 0.16 2 -0.076 1 3
mol:L-citrulline 0.007 0.055 0.2 3 -0.21 13 16
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.009 0.06 0.17 1 -0.076 1 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.009 0.049 -10000 0 -0.05 280 280
CD2AP 0.022 0.029 -10000 0 -0.065 48 48
PI3K/GAB1 0.053 0.055 0.18 2 -0.085 1 3
PDPK1 -0.031 0.036 0.15 17 -10000 0 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.049 -10000 0 -0.049 277 277
mol:NADP 0.007 0.055 0.2 3 -0.21 13 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.009 0.058 0.17 1 -0.076 1 2
VEGFR1 homodimer/NRP2 0.028 0.017 -10000 0 -0.036 24 24
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 -0.058 0.049 0.18 2 -0.2 9 11
alphaV/beta3 Integrin/Osteopontin/Src 0.009 0.051 -10000 0 -0.058 179 179
AP1 -0.062 0.066 -10000 0 -0.14 65 65
ILK -0.041 0.025 0.16 4 -10000 0 4
bone resorption -0.064 0.03 0.16 3 -10000 0 3
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.009 0.062 0.16 4 -0.087 18 22
ITGAV 0.026 0.021 -10000 0 -0.044 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.031 0.039 -10000 0 -0.051 396 396
alphaV/beta3 Integrin/Osteopontin 0.02 0.061 -10000 0 -0.071 76 76
MAP3K1 -0.042 0.027 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 -0.046 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 0.029 0.013 -10000 0 -0.028 23 23
NFKBIA -0.047 0.042 0.16 5 -0.17 14 19
FOS 0.006 0.041 -10000 0 -0.066 120 120
CD44 -0.045 0.039 -10000 0 -0.065 398 398
CHUK 0.024 0.014 -10000 0 -0.065 1 1
PLAU -0.07 0.066 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA -0.067 0.048 0.18 3 -10000 0 3
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.043 0.019 -10000 0 -0.057 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 -0.006 0.047 -10000 0 -0.064 197 197
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
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.029 0.046 -10000 0 -0.12 76 76
STMN1 -0.024 0.008 -10000 0 -0.052 24 24
Aurora B/RasGAP/Survivin 0.016 0.057 -10000 0 -0.054 196 196
Chromosomal passenger complex/Cul3 protein complex -0.034 0.056 -10000 0 -0.1 165 165
BIRC5 -0.008 0.049 -10000 0 -0.068 201 201
DES 0.018 0.097 -10000 0 -0.68 9 9
Aurora C/Aurora B/INCENP 0.048 0.033 -10000 0 -0.043 44 44
Aurora B/TACC1 0.038 0.019 -10000 0 -0.041 23 23
Aurora B/PP2A 0.041 0.023 -10000 0 -0.052 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.005 0.005 -10000 0 -0.015 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.02 2 -10000 0 2
NDC80 -0.033 0.018 -10000 0 -0.056 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.005 0.04 -10000 0 -0.17 12 12
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.003 0.047 -10000 0 -0.067 178 178
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 -0.041 0.042 -10000 0 -0.065 377 377
NSUN2/NPM1/Nucleolin -0.007 0.078 -10000 0 -0.54 9 9
PSMA3 0.03 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 0.015 1 -10000 0 1
H3F3B 0.01 0.011 -10000 0 -0.038 25 25
AURKB 0.026 0.023 -10000 0 -0.063 30 30
AURKC 0.03 0.01 -10000 0 -0.065 2 2
CDCA8 0.028 0.018 -10000 0 -0.068 16 16
cytokinesis -0.021 0.063 0.15 1 -0.2 31 32
Aurora B/Septin1 -0.013 0.067 0.14 1 -0.21 26 27
AURKA 0.026 0.019 -10000 0 -0.065 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 -0.04 201 201
EVI5 0.031 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.007 0.072 0.16 1 -0.16 30 31
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0 0.043 -10000 0 -0.16 21 21
NCAPG 0.011 0.04 -10000 0 -0.065 111 111
Aurora B/HC8 Proteasome 0.04 0.023 -10000 0 -0.052 21 21
NCAPD2 0.013 0.038 -10000 0 -0.065 94 94
Aurora B/PP1-gamma 0.041 0.023 -10000 0 -0.052 25 25
RHOA 0.031 0.005 -10000 0 -10000 0 0
NCAPH 0.029 0.017 -10000 0 -0.065 15 15
NPM1 -0.002 0.074 -10000 0 -0.36 16 16
RASA1 0.031 0.006 -10000 0 -10000 0 0
KLHL9 0.02 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 -0.052 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0.001 0.069 0.16 1 -0.16 31 32
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.003 0.044 -10000 0 -0.31 9 9
MYLK 0.008 0.013 -10000 0 -0.039 34 34
KIF23 0.016 0.036 -10000 0 -0.068 77 77
VIM -0.019 0.013 0.021 1 -0.052 32 33
RACGAP1 0.001 0.046 -10000 0 -0.068 155 155
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.044 -10000 0 -0.29 10 10
Chromosomal passenger complex -0.009 0.041 0.086 1 -0.13 33 34
Chromosomal passenger complex/EVI5 0.027 0.075 -10000 0 -0.086 34 34
TACC1 0.032 0.004 -10000 0 -10000 0 0
PPP2R5D 0.032 0.003 -10000 0 -10000 0 0
CUL3 0.032 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.001 0.039 -9999 0 -0.13 21 21
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 0.045 -9999 0 -0.065 155 155
WNT11 0.031 0.008 -9999 0 -0.065 2 2
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 -0.022 0.096 0.19 14 -0.3 47 61
CRKL -0.021 0.095 0.18 1 -0.3 48 49
HRAS -0.006 0.096 0.16 5 -0.26 51 56
mol:PIP3 0.042 0.12 0.25 36 -0.28 37 73
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.003 -10000 0 -10000 0 0
GAB1 -0.014 0.099 -10000 0 -0.31 48 48
FOXO3 0.029 0.14 0.24 30 -0.3 43 73
AKT1 0.034 0.14 0.23 50 -0.31 43 93
BAD 0.028 0.13 0.22 32 -0.3 43 75
megakaryocyte differentiation -0.013 0.09 -10000 0 -0.3 44 44
GSK3B 0.029 0.14 0.24 34 -0.3 43 77
RAF1 -0.012 0.083 0.15 10 -0.23 51 61
SHC1 0.024 0.026 -10000 0 -0.065 40 40
STAT3 -0.016 0.099 -10000 0 -0.31 48 48
STAT1 -0.034 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.008 0.081 0.14 4 -0.22 51 55
cell proliferation -0.019 0.096 -10000 0 -0.31 48 48
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
TEC 0.031 0.006 -10000 0 -10000 0 0
RPS6KB1 0.018 0.11 0.2 2 -0.31 33 35
HRAS/SPRED2 0.006 0.092 0.18 4 -0.23 50 54
LYN/TEC/p62DOK 0.022 0.12 -10000 0 -0.31 48 48
MAPK3 -0.007 0.071 0.18 17 -0.17 47 64
STAP1 -0.015 0.099 -10000 0 -0.31 48 48
GRAP2 0.03 0.008 -10000 0 -10000 0 0
JAK2 -0.028 0.16 -10000 0 -0.49 49 49
STAT1 (dimer) -0.032 0.17 -10000 0 -0.55 47 47
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.031 0.12 -10000 0 -0.31 47 47
actin filament polymerization -0.01 0.097 -10000 0 -0.3 48 48
LYN 0.02 0.031 -10000 0 -0.065 60 60
STAP1/STAT5A (dimer) -0.025 0.13 0.21 1 -0.39 50 51
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.11 0.21 3 -0.29 48 51
PI3K 0.04 0.12 0.23 2 -0.28 42 44
PTEN 0.022 0.016 -10000 0 -0.065 2 2
SCF/KIT/EPO/EPOR -0.017 0.18 -10000 0 -0.57 47 47
MAPK8 -0.019 0.097 -10000 0 -0.31 48 48
STAT3 (dimer) -0.016 0.098 -10000 0 -0.31 48 48
positive regulation of transcription -0.004 0.062 0.17 18 -0.14 47 65
mol:GDP 0.001 0.1 -10000 0 -0.28 48 48
PIK3C2B -0.017 0.097 -10000 0 -0.31 46 46
CBL/CRKL -0.005 0.1 0.2 5 -0.3 48 53
FER -0.015 0.099 -10000 0 -0.31 47 47
SH2B3 -0.016 0.098 -10000 0 -0.31 48 48
PDPK1 0.035 0.12 0.24 33 -0.27 35 68
SNAI2 -0.021 0.099 -10000 0 -0.32 48 48
positive regulation of cell proliferation -0.029 0.15 -10000 0 -0.47 48 48
KITLG 0.026 0.023 -10000 0 -0.044 45 45
cell motility -0.029 0.15 -10000 0 -0.47 48 48
PTPN6 0.028 0.018 -10000 0 -0.046 22 22
EPOR 0.015 0.078 -10000 0 -0.48 4 4
STAT5A (dimer) -0.019 0.13 -10000 0 -0.4 49 49
SOCS1 0.032 0.003 -10000 0 -10000 0 0
cell migration 0.015 0.096 0.31 46 -10000 0 46
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.019 0.02 -10000 0 -0.033 27 27
VAV1 0.031 0.007 -10000 0 -0.065 1 1
GRB10 -0.011 0.077 -10000 0 -0.32 29 29
PTPN11 0.031 0.01 -10000 0 -0.029 10 10
SCF/KIT -0.009 0.1 -10000 0 -0.32 48 48
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.069 0.15 10 -0.19 47 57
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.038 0.2 -10000 0 -0.62 54 54
MAP2K2 -0.014 0.077 0.2 18 -0.19 48 66
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.3 48 48
STAT5A -0.018 0.13 -10000 0 -0.41 48 48
GRB2 0.031 0.006 -10000 0 -10000 0 0
response to radiation -0.02 0.097 -10000 0 -0.31 48 48
SHC/GRAP2 0.036 0.028 -10000 0 -0.051 38 38
PTPRO -0.013 0.092 -10000 0 -0.3 44 44
SH2B2 -0.01 0.099 -10000 0 -0.31 48 48
DOK1 0.032 0.001 -10000 0 -10000 0 0
MATK -0.015 0.097 -10000 0 -0.31 46 46
CREBBP 0.026 0.043 -10000 0 -0.1 47 47
BCL2 0.005 0.12 -10000 0 -0.63 12 12
Syndecan-1-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
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 0.047 0.1 17 -0.14 28 45
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 0.052 0.17 2 -0.18 16 18
Syndecan-1/Syntenin 0.003 0.065 0.2 15 -0.19 11 26
MAPK3 -0.035 0.052 0.16 4 -0.15 31 35
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 -0.009 0.052 0.17 2 -0.17 16 18
Syndecan-1/RANTES 0.001 0.068 0.2 16 -0.17 18 34
Syndecan-1/CD147 -0.027 0.057 0.19 4 -0.16 28 32
Syndecan-1/Syntenin/PIP2 0.002 0.062 0.19 15 -0.18 11 26
LAMA5 0.027 0.017 -10000 0 -0.065 13 13
positive regulation of cell-cell adhesion 0.002 0.061 0.19 15 -0.18 11 26
MMP7 0.017 0.035 -10000 0 -0.065 75 75
HGF 0.022 0.015 -10000 0 -0.065 1 1
Syndecan-1/CASK -0.013 0.044 0.09 17 -0.18 14 31
Syndecan-1/HGF/MET 0.004 0.056 0.2 5 -0.18 11 16
regulation of cell adhesion -0.034 0.071 0.23 19 -0.2 13 32
HPSE 0.023 0.028 -10000 0 -0.065 44 44
positive regulation of cell migration -0.011 0.047 0.1 17 -0.14 28 45
SDC1 -0.01 0.042 0.1 17 -0.11 28 45
Syndecan-1/Collagen -0.011 0.047 0.1 17 -0.14 28 45
PPIB -0.036 0.044 -10000 0 -0.065 354 354
MET 0.021 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 -0.065 166 166
MAPK1 -0.034 0.051 0.16 4 -0.16 30 34
homophilic cell adhesion -0.01 0.053 0.12 23 -0.18 14 37
MMP1 0.024 0.026 -10000 0 -0.065 38 38
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0 0.058 -10000 0 -0.32 10 10
Syndecan-4/Syndesmos -0.03 0.098 -10000 0 -0.38 21 21
positive regulation of JNK cascade -0.036 0.098 -10000 0 -0.34 24 24
Syndecan-4/ADAM12 -0.02 0.1 -10000 0 -0.38 21 21
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 0.006 -10000 0 -10000 0 0
ITGA5 0.018 0.033 -10000 0 -0.065 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.024 0.023 -10000 0 -0.052 14 14
ADAM12 0.023 0.014 -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 -0.036 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.03 0.098 -10000 0 -0.38 21 21
Syndecan-4/CXCL12/CXCR4 -0.037 0.1 -10000 0 -0.36 23 23
Syndecan-4/Laminin alpha3 -0.015 0.11 -10000 0 -0.38 21 21
MDK -0.023 0.047 -10000 0 -0.065 283 283
Syndecan-4/FZD7 -0.032 0.11 -10000 0 -0.39 21 21
Syndecan-4/Midkine -0.036 0.1 -10000 0 -0.38 22 22
FZD7 -0.013 0.049 -10000 0 -0.065 238 238
Syndecan-4/FGFR1/FGF -0.004 0.12 -10000 0 -0.34 26 26
THBS1 0.024 0.026 -10000 0 -0.065 39 39
integrin-mediated signaling pathway -0.047 0.091 -10000 0 -0.34 26 26
positive regulation of MAPKKK cascade -0.036 0.098 -10000 0 -0.34 24 24
Syndecan-4/TACI -0.013 0.11 -10000 0 -0.43 16 16
CXCR4 -0.018 0.049 -10000 0 -0.065 263 263
cell adhesion -0.006 0.031 0.2 4 -0.084 15 19
Syndecan-4/Dynamin -0.016 0.11 -10000 0 -0.38 21 21
Syndecan-4/TSP1 -0.017 0.11 -10000 0 -0.43 16 16
Syndecan-4/GIPC -0.017 0.11 -10000 0 -0.37 21 21
Syndecan-4/RANTES -0.015 0.11 -10000 0 -0.38 21 21
ITGB1 0.025 0.013 -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 0.001 0.095 0.8 7 -10000 0 7
Syndecan-4/alpha-Actinin -0.017 0.11 -10000 0 -0.38 21 21
TFPI 0.011 0.04 -10000 0 -0.065 112 112
F2 0.028 0.02 0.074 1 -0.037 30 31
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
positive regulation of cell adhesion -0.024 0.1 -10000 0 -0.36 21 21
ACTN1 0.022 0.027 -10000 0 -0.065 40 40
TNC -0.059 0.023 -10000 0 -0.065 469 469
Syndecan-4/CXCL12 -0.02 0.1 -10000 0 -0.38 21 21
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.031 0.005 -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 0.031 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 -0.03 0.098 -10000 0 -0.38 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.04 -10000 0 -0.058 113 113
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -0.054 11 11
vasculogenesis -0.016 0.11 -10000 0 -0.37 21 21
SDC4 -0.028 0.1 -10000 0 -0.36 25 25
Syndecan-4/Tenascin C -0.048 0.095 -10000 0 -0.36 26 26
Syndecan-4/PI-4-5-P2/PKC alpha -0.029 0.017 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.013 0.11 -10000 0 -0.38 21 21
MMP9 -0.005 0.045 -10000 0 -0.063 177 177
Rac1/GTP -0.007 0.032 0.2 4 -0.085 15 19
cytoskeleton organization -0.029 0.094 -10000 0 -0.36 21 21
GIPC1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.022 0.11 -10000 0 -0.38 21 21
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.009 -10000 0 -0.028 29 29
BUB1B -0.013 0.035 0.09 7 -0.11 23 30
PLK1 0.006 0.023 0.069 35 -0.086 5 40
PLK1S1 0.002 0.013 0.041 35 -0.044 5 40
KIF2A -0.001 0.025 0.14 6 -0.097 3 9
regulation of mitotic centrosome separation 0.006 0.023 0.069 35 -0.085 5 40
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.028 0.11 2 -0.078 10 12
WEE1 -0.019 0.066 -10000 0 -0.34 15 15
cytokinesis -0.012 0.04 0.16 2 -0.16 10 12
PP2A-alpha B56 0.053 0.081 -10000 0 -0.55 8 8
AURKA 0.007 0.017 0.088 3 -0.14 2 5
PICH/PLK1 -0.032 0.022 0.13 1 -0.089 11 12
CENPE -0.004 0.026 0.17 4 -0.12 3 7
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.025 0.13 8 -0.097 3 11
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 0.13 1 -0.091 1 2
PAK1 0.032 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.004 -10000 0 0 10 10
CLSPN 0.009 0.032 0.089 2 -0.23 7 9
GORASP1 0.031 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.013 4 -0.011 4 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.041 35 -0.044 5 40
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 0.011 0.061 -10000 0 -0.5 7 7
spindle elongation 0.006 0.023 0.069 35 -0.085 5 40
ODF2 0.032 0.007 -10000 0 -10000 0 0
BUB1 0.021 0.08 -10000 0 -0.57 9 9
TPT1 -0.004 0.053 0.087 1 -0.19 35 36
CDC25C 0.011 0.031 -10000 0 -0.24 6 6
CDC25B 0.026 0.018 -10000 0 -0.061 16 16
SGOL1 0.001 0.009 0.028 29 -10000 0 29
RHOA 0.031 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.012 0.048 -10000 0 -0.065 137 137
CDC14B -0.011 0.004 0.009 11 -10000 0 11
CDC20 -0.023 0.048 -10000 0 -0.065 287 287
PLK1/PBIP1 -0.019 0.015 0.045 2 -0.07 14 16
mitosis -0.003 0.003 0.015 5 -10000 0 5
FBXO5 -0.014 0.032 0.11 6 -0.095 35 41
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 -0.001 0.045 -10000 0 -0.065 168 168
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 0.061 11 -0.068 6 17
microtubule cytoskeleton organization -0.004 0.052 0.087 1 -0.19 35 36
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 0.005 0.048 0.13 2 -0.081 25 27
GRASP65/GM130/RAB1/GTP/PLK1 0.052 0.029 0.14 1 -0.091 4 5
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 0.067 42 -0.06 4 46
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.094 0.13 3 -0.22 96 99
microtubule-based process 0.008 0.031 0.11 3 -0.078 12 15
Golgi organization 0.006 0.023 0.069 35 -0.085 5 40
Cohesin/SA2 0.02 0.023 0.095 3 -0.071 6 9
PPP1CB/MYPT1 0.046 0.01 -10000 0 -0.048 1 1
KIF20A -0.002 0.046 -10000 0 -0.065 178 178
APC/C/CDC20 -0.002 0.031 0.12 1 -0.076 14 15
PPP2R1A 0.029 0.009 -10000 0 -10000 0 0
chromosome segregation -0.018 0.015 0.044 2 -0.069 14 16
PRC1 -0.009 0.048 -10000 0 -0.065 213 213
ECT2 -0.005 0.037 0.2 10 -0.12 3 13
C13orf34 0.005 0.02 0.063 35 -0.069 4 39
NUDC 0.009 0.034 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.013 0.034 0.09 7 -0.11 23 30
spindle assembly 0.004 0.02 0.062 27 -0.074 5 32
spindle stabilization 0.002 0.013 0.041 35 -0.044 5 40
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.008 0.031 0.11 3 -0.079 12 15
CCNB1 -0.022 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 0.024 -10000 0 -0.29 1 1
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 -0.036 0.012 -10000 0 -0.041 419 419
INCENP 0.032 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.02 0.068 -9999 0 -0.23 14 14
MAP3K8 0.018 0.027 -9999 0 -0.066 37 37
FOS 0.011 0.058 -9999 0 -0.23 13 13
PRKCA 0.031 0.004 -9999 0 -10000 0 0
PTPN7 0.03 0.007 -9999 0 -0.045 2 2
HRAS 0.031 0.007 -9999 0 -10000 0 0
PRKCB -0.001 0.001 -9999 0 -0.003 82 82
NRAS 0.008 0.042 -9999 0 -0.065 125 125
RAS family/GTP 0.029 0.046 -9999 0 -0.043 136 136
MAPK3 0.026 0.031 -9999 0 -0.36 2 2
MAP2K1 -0.003 0.025 -9999 0 -0.16 3 3
ELK1 0.031 0.005 -9999 0 -0.021 3 3
BRAF 0.003 0.016 -9999 0 -0.23 2 2
mol:GTP 0 0 -9999 0 -0.001 121 121
MAPK1 0.002 0.097 -9999 0 -0.35 33 33
RAF1 0.005 0.016 -9999 0 -0.22 2 2
KRAS 0.03 0.008 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.051 15 15
AKT1 -0.024 0.073 0.22 5 -0.28 14 19
PTK2B -0.035 0.057 0.16 37 -10000 0 37
VEGFR2 homodimer/Frs2 0.024 0.024 -10000 0 -0.091 13 13
CAV1 -0.019 0.042 -10000 0 -0.065 218 218
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.005 0.051 -10000 0 -0.084 29 29
endothelial cell proliferation -0.005 0.078 0.2 25 -0.25 10 35
mol:Ca2+ -0.031 0.051 0.15 32 -0.13 2 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.003 0.059 0.17 12 -0.1 14 26
RP11-342D11.1 -0.033 0.037 0.16 14 -0.1 11 25
CDH5 0.026 0.023 -10000 0 -0.065 29 29
VEGFA homodimer 0.001 0.052 -10000 0 -0.044 274 274
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 -0.095 35 35
SH2D2A 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.007 0.06 0.2 1 -0.22 1 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.006 0.051 -10000 0 -0.079 36 36
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.004 0.068 0.16 13 -0.099 29 42
GRB10 -0.021 0.046 0.16 23 -0.12 1 24
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB2 0.031 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 -0.007 0.077 0.18 12 -0.11 27 39
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.005 0.051 0.13 11 -0.17 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 14 26
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.005 -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 51 51
mol:GDP -0.013 0.056 -10000 0 -0.096 31 31
mol:NADP 0.004 0.057 0.26 3 -10000 0 3
eNOS/Hsp90 0.013 0.06 0.27 3 -0.2 1 4
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 -0.031 0.052 0.15 32 -0.13 2 34
HIF1A/ARNT 0.044 0.014 -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 0.06 0.2 11 -0.21 8 19
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.031 0.005 -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 -0.071 17 17
mol:L-citrulline 0.004 0.057 0.26 3 -10000 0 3
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 0.002 0.065 0.17 13 -0.1 12 25
VEGFR2 homodimer/VEGFA homodimer -0.006 0.055 -10000 0 -0.084 45 45
VEGFR2/3 heterodimer 0.025 0.025 -10000 0 -0.091 14 14
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.031 0.058 0.16 26 -0.16 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 0.25 5 -10000 0 5
MAPK1 -0.021 0.063 0.2 10 -10000 0 10
VEGFA145/NRP2 -0.007 0.049 -10000 0 -0.052 275 275
VEGFR1/2 heterodimer 0.024 0.024 -10000 0 -0.091 14 14
KDR -0.02 0.015 -10000 0 -0.1 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.003 0.06 0.16 14 -0.092 28 42
SRC 0.03 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.019 0.066 0.25 6 -10000 0 6
PI3K -0.02 0.064 0.17 7 -0.16 21 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.007 0.051 -10000 0 -0.061 108 108
FES -0.033 0.054 0.16 35 -0.13 2 37
GAB1 -0.018 0.066 0.16 10 -0.18 30 40
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.05 -10000 0 -0.078 37 37
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.048 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.014 0.052 -10000 0 -0.063 142 142
PI3K/GAB1 -0.021 0.074 0.2 2 -0.25 16 18
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.004 0.073 0.18 12 -0.1 13 25
PRKACA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.031 -10000 0 -0.073 24 24
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
CDC42 -0.033 0.052 0.15 33 -0.13 2 35
actin cytoskeleton reorganization -0.006 0.051 -10000 0 -0.079 36 36
PTK2 -0.012 0.057 0.14 28 -0.19 10 38
EDG1 -0.033 0.037 0.16 14 -0.1 11 25
mol:DAG -0.031 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 30 -10000 0 30
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.044 0.096 0.18 138 -0.11 16 154
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 -0.06 109 109
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.051 -10000 0 -0.083 33 33
cell migration -0.007 0.074 0.2 11 -0.2 24 35
mol:PI-3-4-5-P3 -0.019 0.061 0.17 7 -0.16 19 26
FYN 0.029 0.01 -10000 0 -0.065 1 1
VEGFB/NRP1 -0.031 0.051 0.15 34 -0.12 2 36
mol:NO 0.004 0.057 0.26 3 -10000 0 3
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.023 -10000 0 -0.098 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.04 -10000 0 -0.093 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 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.005 0.051 -10000 0 -0.079 35 35
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 0.024 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 -0.077 43 43
VEGFA165/NRP2 -0.007 0.049 -10000 0 -0.052 275 275
MAPKKK cascade -0.033 0.04 0.18 6 -10000 0 6
NRP2 0.032 0.005 -10000 0 -0.065 1 1
VEGFC homodimer 0.029 0.015 -10000 0 -0.065 11 11
NCK1 0.029 0.015 -10000 0 -0.065 11 11
ROCK1 0.031 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.068 0.2 14 -0.21 8 22
MAP3K13 -0.034 0.051 0.15 31 -0.13 2 33
PDPK1 -0.034 0.053 0.15 8 -0.16 14 22
Caspase cascade in apoptosis

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
TOP1 -0.015 0.095 -10000 0 -0.34 23 23
ACTA1 -0.044 0.083 -10000 0 -0.24 47 47
NUMA1 -0.013 0.083 -10000 0 -0.31 24 24
SPTAN1 -0.044 0.086 0.18 7 -0.29 33 40
LIMK1 0 0.1 0.18 79 -0.28 23 102
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.029 0.013 -10000 0 -0.065 6 6
CASP10 -0.021 0.013 -10000 0 -0.052 19 19
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0 1 -0.001 8 9
PTK2 -0.014 0.083 -10000 0 -0.32 22 22
DIABLO 0.032 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.04 0.088 0.17 7 -0.3 31 38
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.047 0.086 0.18 7 -0.28 35 42
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.029 0.096 -10000 0 -0.68 8 8
BID -0.004 0.014 -10000 0 -0.13 5 5
MAP3K1 -0.009 0.055 -10000 0 -0.42 6 6
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 0.011 -10000 0 -0.051 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.047 0.088 0.18 11 -0.25 46 57
CASP9 0.031 0.009 -10000 0 -0.065 3 3
DNA repair 0.025 0.058 0.16 39 -10000 0 39
neuron apoptosis 0.019 0.076 -10000 0 -0.64 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.033 0.089 0.2 2 -0.33 29 31
APAF1 0.032 0.003 -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 -0.051 0.086 0.27 5 -0.31 29 34
CASP7 -0.054 0.1 -10000 0 -0.22 132 132
KRT18 0.014 0.052 -10000 0 -0.47 4 4
apoptosis -0.047 0.094 -10000 0 -0.34 27 27
DFFA -0.048 0.084 0.18 3 -0.29 34 37
DFFB -0.048 0.084 0.18 3 -0.29 35 38
PARP1 -0.026 0.059 -10000 0 -0.16 39 39
actin filament polymerization -0.008 0.099 0.26 23 -0.17 78 101
TNF 0.032 0.007 -10000 0 -0.065 2 2
CYCS 0 0.026 -10000 0 -0.22 2 2
SATB1 0.016 0.1 -10000 0 -0.83 4 4
SLK -0.051 0.084 -10000 0 -0.26 43 43
p15 BID/BAX -0.01 0.062 -10000 0 -0.19 36 36
CASP2 0.041 0.088 0.2 116 -0.15 7 123
JNK cascade 0.008 0.055 0.42 6 -10000 0 6
CASP3 -0.045 0.087 -10000 0 -0.24 51 51
LMNB2 0.047 0.081 0.22 11 -0.28 4 15
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
CASP4 0.012 0.039 -10000 0 -0.065 101 101
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.043 36 36
negative regulation of DNA binding 0.029 0.095 -10000 0 -0.67 8 8
stress fiber formation -0.05 0.083 -10000 0 -0.27 40 40
GZMB -0.018 0.012 0 132 -0.054 19 151
CASP1 -0.012 0.034 -10000 0 -0.054 187 187
LMNB1 0.037 0.098 0.22 13 -0.35 11 24
APP 0.019 0.077 -10000 0 -0.65 6 6
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
response to stress 0 0 0.001 6 -0.001 19 25
CASP8 -0.012 0.004 -10000 0 -0.04 10 10
VIM -0.04 0.095 -10000 0 -0.34 27 27
LMNA 0.049 0.08 0.24 9 -0.31 3 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.038 -10000 0 -0.18 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.049 0.083 0.18 1 -0.3 33 34
APAF-1/Caspase 9 0.022 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.013 0.081 -10000 0 -0.31 24 24
CFL2 0.008 0.1 0.17 78 -0.27 23 101
GAS2 -0.05 0.083 0.18 2 -0.28 37 39
positive regulation of apoptosis 0.048 0.089 0.2 34 -0.36 5 39
PRF1 0.022 0.019 -10000 0 -0.065 12 12
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 0.027 -10000 0 -0.033 100 100
PDGF/PDGFRA/CRKL 0.036 0.021 -10000 0 -0.053 5 5
positive regulation of JUN kinase activity 0.038 0.035 -10000 0 -0.045 42 42
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.053 5 5
AP1 -0.027 0.073 0.14 58 -0.13 94 152
mol:IP3 -0.022 0.015 0.034 3 -0.067 2 5
PLCG1 -0.022 0.015 0.034 3 -0.067 2 5
PDGF/PDGFRA/alphaV Integrin 0.035 0.026 -10000 0 -0.054 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.015 0.034 3 -0.067 2 5
CAV3 0.032 0.004 -10000 0 -10000 0 0
CAV1 -0.019 0.042 -10000 0 -0.065 218 218
SHC/Grb2/SOS1 0.04 0.036 -10000 0 -0.045 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 95 99
JUN -0.026 0.021 0.032 11 -10000 0 11
oligodendrocyte development 0.035 0.026 -10000 0 -0.054 20 20
GRB2 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.015 0.034 3 -0.067 2 5
PDGF/PDGFRA 0.015 0.027 -10000 0 -0.033 100 100
actin cytoskeleton reorganization 0.035 0.022 -10000 0 -0.051 4 4
SRF -0.021 0.007 0.023 1 -10000 0 1
SHC1 0.024 0.026 -10000 0 -0.065 40 40
PI3K 0.045 0.034 -10000 0 -0.053 19 19
PDGF/PDGFRA/Crk/C3G 0.05 0.029 -10000 0 -0.044 9 9
JAK1 -0.018 0.014 0.021 26 -0.054 5 31
ELK1/SRF -0.009 0.06 0.13 74 -10000 0 74
SHB 0.03 0.009 -10000 0 -10000 0 0
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.024 -10000 0 -0.034 16 16
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 0.038 0.035 -10000 0 -0.045 42 42
PDGF/PDGFRA/SHB 0.035 0.022 -10000 0 -0.052 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 -0.072 2 5
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.052 5 5
JAK-STAT cascade -0.018 0.014 0.021 26 -0.054 5 31
cell proliferation 0.018 0.011 -10000 0 -0.041 6 6
HIV-1 Nef: Negative effector of Fas and TNF-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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.004 0.078 0.15 3 -0.12 137 140
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.036 28 28
BIRC3 -0.033 0.023 0.17 4 -10000 0 4
CYCS 0.004 0.068 0.17 62 -0.12 3 65
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
CD247 0.033 0.008 -10000 0 -0.065 2 2
MAP2K7 -0.008 0.087 -10000 0 -0.39 8 8
protein ubiquitination 0.001 0.052 0.2 7 -0.24 10 17
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 -0.019 0.044 0.16 3 -0.1 95 98
NF-kappa-B/RelA/I kappa B alpha 0.054 0.041 -10000 0 -0.062 37 37
TRADD 0.032 0.004 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
CFLAR 0.031 0.01 -10000 0 -0.065 5 5
FADD 0.031 0.006 -10000 0 -0.065 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.041 -10000 0 -0.062 37 37
MAPK8 -0.006 0.081 -10000 0 -0.38 8 8
APAF1 0.032 0.003 -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 0.012 0.053 -10000 0 -0.26 9 9
CHUK 0.002 0.052 0.2 7 -0.25 9 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.07 -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 -0.049 164 164
CASP6 0.008 0.085 -10000 0 -0.47 4 4
CASP7 -0.059 0.11 0.18 5 -0.24 127 132
RELA 0.028 0.016 -10000 0 -0.034 30 30
CASP2 0.022 0.015 -10000 0 -10000 0 0
CASP3 -0.029 0.069 0.18 4 -0.23 26 30
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
TNFR1A/BAG4 0.014 0.046 -10000 0 -0.051 163 163
CASP8 0.03 0.014 -10000 0 -0.065 10 10
CASP9 0.031 0.009 -10000 0 -0.065 3 3
MAP3K14 0.009 0.056 0.17 1 -0.26 11 12
APAF-1/Caspase 9 -0.016 0.071 0.13 66 -0.16 5 71
BCL2 -0.017 0.082 0.24 2 -0.35 8 10
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 0.061 0.02 -10000 0 -0.049 10 10
fibroblast growth factor receptor signaling pathway 0.06 0.02 -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+ 0.036 0.018 -10000 0 -0.041 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 0.015 -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 -0.029 0.012 -10000 0 -0.051 77 77
FLT1 0.03 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.023 -10000 0 -0.049 13 13
SERPINC1 0.031 0.006 -10000 0 -0.065 1 1
FYN -0.024 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 0.059 0.17 34 -0.19 5 39
SLIT2 0.02 0.017 -10000 0 -0.065 3 3
GPC1/NRG 0.045 0.014 -10000 0 -0.051 7 7
NRG1 0.032 0.004 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0 0.056 -10000 0 -0.05 277 277
LYN -0.029 0.01 -10000 0 -0.05 67 67
mol:Spermine -0.012 0.004 -10000 0 -0.04 7 7
cell growth 0.06 0.02 -10000 0 -0.049 10 10
BMP signaling pathway -0.031 0.012 0.065 7 -10000 0 7
SRC -0.024 0.009 -10000 0 -0.049 8 8
TGFBR1 0.031 0.005 -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) 0.031 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 -0.05 90 90
FGF2 0.031 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 0.03 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 -0.026 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) 0.03 0.011 -10000 0 -0.065 6 6
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.014 0.049 -10000 0 -0.35 9 9
Crk/p130 Cas/Paxillin -0.036 0.08 -10000 0 -0.18 116 116
JUN -0.012 0.029 -10000 0 -0.18 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.042 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 0.023 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.048 0.057 -10000 0 -0.055 2 2
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.036 0.042 -10000 0 -0.04 9 9
RHOA 0.031 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.044 0.055 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
RET51/GFRalpha1/GDNF 0.048 0.055 -10000 0 -0.058 1 1
MAPKKK cascade -0.006 0.075 -10000 0 -0.13 124 124
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.036 0.042 -10000 0 -0.031 136 136
lamellipodium assembly -0.012 0.06 -10000 0 -0.17 48 48
RET51/GFRalpha1/GDNF/SHC 0.039 0.061 -10000 0 -0.053 42 42
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RET9/GFRalpha1/GDNF/SHC 0.029 0.045 -10000 0 -0.034 163 163
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.023 135 135
MAPK3 -0.038 0.032 0.17 11 -10000 0 11
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 0.03 0.18 6 -10000 0 6
DOK5 0.027 0.011 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.065 1 1
MAPK8 0 0.03 -10000 0 -0.12 26 26
HRAS/GTP 0.019 0.096 -10000 0 -0.14 129 129
tube development 0.02 0.035 0.17 11 -10000 0 11
MAPK1 -0.034 0.033 0.17 11 -10000 0 11
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.055 -10000 0 -0.11 118 118
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 0.046 0.049 -10000 0 -0.049 1 1
SHC1 0.024 0.026 -10000 0 -0.065 40 40
RET51/GFRalpha1/GDNF/Dok4 0.048 0.057 -10000 0 -0.058 1 1
RET51/GFRalpha1/GDNF/Dok5 0.047 0.052 -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 -0.2 123 123
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.056 -10000 0 -0.11 122 122
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 0.028 -10000 0 -0.18 6 6
RET9/GFRalpha1/GDNF/FRS2 0.036 0.041 -10000 0 -0.031 127 127
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.053 -10000 0 -0.1 123 123
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.095 -10000 0 -0.19 122 122
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.098 -10000 0 -0.19 136 136
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.034 -10000 0 -0.12 25 25
PI3K -0.042 0.11 -10000 0 -0.23 120 120
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.038 -10000 0 -0.029 129 129
GRB10 0.021 0.018 -10000 0 -0.065 6 6
activation of MAPKK activity -0.014 0.069 0.1 7 -0.15 100 107
RET51/GFRalpha1/GDNF/FRS2 0.047 0.056 -10000 0 -0.054 4 4
GAB1 0.031 0.008 -10000 0 -0.065 3 3
IRS1 0.031 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 0.037 -10000 0 -0.12 27 27
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.056 -10000 0 -0.058 1 1
GRB2 0.031 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 0.057 -10000 0 -0.06 4 4
Rac1/GTP -0.013 0.07 -10000 0 -0.2 48 48
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.041 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.051 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.043 0.21 8 -0.19 13 21
RFC1 -0.023 0.036 0.17 2 -0.19 15 17
PRKDC -0.023 0.038 0.19 3 -0.19 15 18
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
CASP7 -0.14 0.26 -10000 0 -0.6 128 128
FASLG/FAS/FADD/FAF1 -0.022 0.056 0.11 1 -0.12 122 123
MAP2K4 -0.063 0.12 0.19 1 -0.24 126 127
mol:ceramide -0.018 0.066 -10000 0 -0.17 33 33
GSN -0.02 0.044 0.21 8 -0.19 14 22
FASLG/FAS/FADD/FAF1/Caspase 8 -0.028 0.065 0.14 1 -0.13 125 126
FAS 0.013 0.031 -10000 0 -0.066 55 55
BID -0.031 0.014 0.2 1 -10000 0 1
MAP3K1 -0.11 0.18 -10000 0 -0.39 133 133
MAP3K7 0.03 0.008 -10000 0 -0.065 1 1
RB1 -0.021 0.036 0.17 2 -0.19 15 17
CFLAR 0.031 0.009 -10000 0 -0.063 5 5
HGF/MET 0.037 0.036 -10000 0 -0.05 23 23
ARHGDIB -0.02 0.044 0.21 9 -0.2 12 21
FADD 0.031 0.006 -10000 0 -0.065 1 1
actin filament polymerization 0.02 0.044 0.19 14 -0.21 8 22
NFKB1 0.013 0.073 -10000 0 -0.62 6 6
MAPK8 -0.069 0.11 0.17 1 -0.25 119 120
DFFA -0.021 0.038 0.2 4 -0.2 14 18
DNA fragmentation during apoptosis -0.021 0.037 0.19 3 -0.19 14 17
FAS/FADD/MET 0.025 0.04 -10000 0 -0.049 54 54
CFLAR/RIP1 0.044 0.017 -10000 0 -0.05 14 14
FAIM3 0.031 0.007 -10000 0 -0.065 1 1
FAF1 0.03 0.008 -10000 0 -10000 0 0
PARP1 -0.023 0.037 0.22 2 -0.19 16 18
DFFB -0.021 0.037 0.19 3 -0.2 14 17
CHUK 0.004 0.067 -10000 0 -0.59 6 6
FASLG 0.031 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.034 -10000 0 -0.052 56 56
HGF 0.022 0.015 -10000 0 -0.065 1 1
LMNA -0.028 0.035 0.19 2 -0.18 14 16
CASP6 -0.023 0.034 0.17 2 -0.19 13 15
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 0.008 0.054 1 -10000 0 1
IL6 -0.026 0.089 -10000 0 -0.51 6 6
MET 0.021 0.016 -10000 0 -0.065 2 2
ICAD/CAD -0.027 0.04 0.25 4 -0.19 14 18
FASLG/FAS/FADD/FAF1/Caspase 10 -0.018 0.066 -10000 0 -0.17 33 33
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.02 0.042 0.21 7 -0.19 13 20
BCL2 0.031 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
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 0.031 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.047 0.13 0.16 1 -0.26 127 128
HIF1A -0.045 0.13 -10000 0 -0.32 86 86
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.049 0.048 -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 0.044 0.012 -10000 0 -10000 0 0
HIF1AN 0.024 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.041 0.13 0.16 1 -0.26 121 122
CUL2 0.025 0.013 -10000 0 -10000 0 0
OS9 0.027 0.011 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.063 0.014 -10000 0 -0.051 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.041 0.13 0.16 2 -0.26 123 125
PHD1-3/OS9 0.059 0.042 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.02 0.14 0.18 1 -0.26 123 124
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.042 0.13 0.16 1 -0.26 122 123
EGLN3 0.03 0.011 -10000 0 -0.065 4 4
EGLN2 0.031 0.007 -10000 0 -10000 0 0
EGLN1 0.031 0.007 -10000 0 -0.065 1 1
TP53 0.019 0.033 -10000 0 -0.065 65 65
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.002 0.07 -10000 0 -0.58 3 3
ARNT 0.032 0.004 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF -0.056 0.13 0.16 2 -0.27 122 124
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.031 0.007 -10000 0 -0.065 1 1
LAT2 -0.015 0.031 0.12 4 -0.13 7 11
AP1 -0.03 0.11 0.22 1 -0.26 51 52
mol:PIP3 0.025 0.097 0.24 40 -10000 0 40
IKBKB 0.015 0.071 0.19 37 -10000 0 37
AKT1 -0.033 0.076 0.28 13 -10000 0 13
IKBKG 0.016 0.07 0.18 38 -10000 0 38
MS4A2 0.034 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 -0.066 17 17
MAP3K1 -0.011 0.059 0.2 15 -0.21 5 20
mol:Ca2+ 0.024 0.086 0.22 40 -10000 0 40
LYN 0.019 0.033 -10000 0 -0.066 64 64
CBLB -0.016 0.037 0.14 7 -0.13 9 16
SHC1 0.024 0.026 -10000 0 -0.065 40 40
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 -0.032 0.058 0.31 10 -10000 0 10
PTPN13 0.004 0.073 -10000 0 -0.58 5 5
PTPN11 0.031 0.01 -10000 0 -0.029 8 8
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.07 0.28 7 -0.28 5 12
SYK 0.024 0.026 -10000 0 -0.065 37 37
GRB2 0.031 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.013 0.066 0.18 18 -0.15 4 22
LAT -0.016 0.037 0.14 7 -0.13 9 16
PAK2 -0.007 0.06 0.2 17 -0.21 6 23
NFATC2 -0.013 0.005 -10000 0 -10000 0 0
HRAS -0.003 0.056 0.17 21 -0.21 7 28
GAB2 0.031 0.005 -10000 0 -10000 0 0
PLA2G1B 0.022 0.064 -10000 0 -0.81 2 2
Fc epsilon R1 0.008 0.059 -10000 0 -0.051 242 242
Antigen/IgE/Fc epsilon R1 0.01 0.055 -10000 0 -0.046 240 240
mol:GDP 0.003 0.052 0.18 17 -0.19 2 19
JUN 0.032 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.029 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 0.11 5 -0.11 8 13
CHUK 0.006 0.062 0.18 31 -10000 0 31
KLRG1 -0.013 0.029 0.082 3 -0.1 8 11
VAV1 -0.016 0.037 0.11 11 -0.14 9 20
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.015 0.036 0.14 7 -0.13 7 14
negative regulation of mast cell degranulation -0.014 0.028 0.076 2 -0.12 5 7
BTK 0.007 0.041 0.19 2 -0.22 1 3
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.008 0.029 -10000 0 -0.091 8 8
GAB2/PI3K/SHP2 -0.052 0.024 0.027 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.01 0.031 -10000 0 -0.086 35 35
RAF1 0.024 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.066 -10000 0 -0.062 145 145
FCER1G -0.016 0.05 -10000 0 -0.068 242 242
FCER1A 0.029 0.016 -10000 0 -0.058 14 14
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.062 -10000 0 -0.051 182 182
MAPK3 0.024 0.063 -10000 0 -0.82 2 2
MAPK1 0.015 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 -0.1 0.24 -10000 0 -0.51 125 125
DUSP1 0.029 0.017 -10000 0 -0.065 16 16
NF-kappa-B/RelA 0.007 0.051 0.13 31 -10000 0 31
actin cytoskeleton reorganization 0.011 0.075 -10000 0 -0.59 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.066 0.2 17 -0.19 6 23
FER -0.016 0.037 0.14 7 -0.13 9 16
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.024 -10000 0 -0.21 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.015 0.072 0.24 23 -0.18 4 27
cytokine secretion 0.001 0.033 0.073 26 -0.063 1 27
SPHK1 -0.017 0.036 0.13 6 -0.13 9 15
PTK2 0.011 0.077 -10000 0 -0.62 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.02 0.08 0.21 25 -0.16 4 29
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.02 0.088 0.24 34 -0.2 1 35
MAP2K2 0.021 0.071 -10000 0 -0.84 2 2
MAP2K1 0.015 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.046 0.2 11 -0.13 4 15
MAP2K4 0 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.006 0.071 -10000 0 -0.067 150 150
mol:Choline -0.032 0.057 0.31 10 -10000 0 10
SHC/Grb2/SOS1 0.008 0.058 0.17 4 -0.13 7 11
FYN 0.029 0.01 -10000 0 -0.065 1 1
DOK1 0.032 0.001 -10000 0 -10000 0 0
PXN 0.005 0.075 0.34 2 -0.58 5 7
HCLS1 -0.019 0.04 0.14 7 -0.13 10 17
PRKCB 0.021 0.08 0.21 38 -10000 0 38
FCGR2B 0.009 0.041 -10000 0 -0.065 120 120
IGHE -0.001 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.014 0.029 0.077 2 -0.13 5 7
LCP2 0.026 0.023 -10000 0 -0.065 29 29
PLA2G4A -0.021 0.038 0.14 7 -0.13 10 17
RASA1 0.031 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.032 0.057 0.31 10 -10000 0 10
IKK complex 0.007 0.063 0.19 28 -10000 0 28
WIPF1 0.03 0.014 -10000 0 -0.065 11 11
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.006 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 0.004 0.023 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.067 -10000 0 -0.27 20 20
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.079 0.19 14 -0.28 11 25
PLCG1 -0.04 0.061 -10000 0 -0.24 19 19
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 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.031 -10000 0 -0.064 59 59
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.026 0.014 0.011 1 -0.039 230 231
S1P1/S1P -0.004 0.033 0.18 1 -10000 0 1
negative regulation of cAMP metabolic process -0.04 0.066 -10000 0 -0.26 20 20
MAPK3 -0.05 0.068 -10000 0 -0.31 14 14
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
KDR 0.028 0.018 -10000 0 -0.064 14 14
PLCB2 0 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 -0.004 0.031 0.17 1 -10000 0 1
PTGS2 -0.055 0.071 -10000 0 -0.38 7 7
Rac1/GTP -0.007 0.026 -10000 0 -10000 0 0
RHOA 0.031 0.005 -10000 0 -10000 0 0
VEGFA -0.02 0.048 -10000 0 -0.064 275 275
negative regulation of T cell proliferation -0.04 0.066 -10000 0 -0.26 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.012 -10000 0 -10000 0 0
MAPK1 -0.047 0.067 -10000 0 -0.36 10 10
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.053 0.18 11 -10000 0 11
ABCC1 0.031 0.012 -10000 0 -0.065 8 8
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.15 9 -0.079 19 28
IHH 0.037 0.021 0.11 15 -0.046 6 21
SHH Np/Cholesterol/GAS1 0.013 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 0.16 120 -10000 0 120
SMO 0.013 0.019 0.14 3 -10000 0 3
AKT1 0.003 0.082 -10000 0 -0.37 16 16
ARRB2 0.032 0.004 -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 0.013 0.019 0.14 3 -10000 0 3
STIL 0.024 0.085 0.17 126 -10000 0 126
DHH N/PTCH2 0.023 0.003 -10000 0 0 10 10
DHH N/PTCH1 0.017 0.014 -10000 0 -0.058 6 6
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 0.013 0.019 0.14 3 -10000 0 3
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
skeletal system development 0.015 0.024 0.16 7 -0.095 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 0.013 0.019 0.14 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.031 0.006 -10000 0 0 16 16
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 0.013 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.017 -10000 0 -0.062 5 5
SHH Np/Cholesterol/PTCH2 0.018 0.013 -10000 0 -0.031 4 4
SHH Np/Cholesterol/Megalin 0.018 0.014 -10000 0 -0.033 5 5
SHH -0.015 0.011 0 168 -10000 0 168
catabolic process 0.02 0.017 -10000 0 -0.067 7 7
SMO/Vitamin D3 0.016 0.032 0.18 14 -10000 0 14
SHH Np/Cholesterol/Hhip -0.011 0.007 0 164 -10000 0 164
LRP2 0.032 0.005 -10000 0 -0.065 1 1
receptor-mediated endocytosis 0.012 0.027 0.15 13 -10000 0 13
SHH Np/Cholesterol/BOC -0.011 0.007 0 164 -10000 0 164
SHH Np/Cholesterol/CDO 0.018 0.013 -10000 0 -0.031 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 164 164
mol:Vitamin D3 0.041 0.096 0.19 147 -10000 0 147
IHH N/PTCH2 0.05 0.012 0.1 8 -0.036 1 9
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.036 0.021 -10000 0 -0.065 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 -0.068 7 7
HHIP 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.023 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 0.051 -10000 0 -0.18 25 25
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.031 4 4
IKBKB 0.032 0.003 -10000 0 -10000 0 0
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 0.055 0.025 0.17 3 -10000 0 3
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 0.046 -10000 0 -0.18 20 20
TOLLIP 0.031 0.006 -10000 0 -10000 0 0
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 -0.024 0.092 -10000 0 -0.19 113 113
JUN -0.026 0.022 0.14 4 -10000 0 4
MAP3K7 0.03 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.018 0.068 0.18 2 -0.094 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.057 -10000 0 -0.053 101 101
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.056 0.065 -10000 0 -0.073 11 11
IL1 beta fragment/IL1R1/IL1RAP 0.008 0.05 -10000 0 -0.055 187 187
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 0.047 0.008 -10000 0 -0.051 3 3
IRAK4 0.031 0.007 -10000 0 -0.065 1 1
PRKCI 0.031 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 -0.004 0.046 0.13 1 -0.18 20 21
CHUK 0.024 0.014 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.008 0.05 -10000 0 -0.055 187 187
IL1 beta/IL1R2 0.004 0.044 -10000 0 -0.052 193 193
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.021 0.16 3 -10000 0 3
NF kappa B1 p50/RelA 0.006 0.065 -10000 0 -0.099 8 8
IRAK3 0.03 0.008 -10000 0 -0.065 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.014 0.057 0.16 2 -0.072 32 34
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.04 -10000 0 -0.12 33 33
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 0.031 0.007 -10000 0 -0.065 1 1
MYD88 0.019 0.033 -10000 0 -0.065 66 66
IRAK/TRAF6/MEKK3 0.05 0.016 0.18 3 -10000 0 3
IL1RAP 0.023 0.027 -10000 0 -0.065 41 41
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.052 0.016 0.035 1 -0.095 4 5
CASP1 0 0.046 -10000 0 -0.065 167 167
IL1RN/IL1R2 0.04 0.026 -10000 0 -0.051 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.01 0.064 0.17 2 -0.077 67 69
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.046 -10000 0 -0.23 11 11
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 -0.034 5 5
MAP2K6 -0.024 0.022 0.17 6 -10000 0 6
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.026 0.016 -10000 0 -0.065 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.017 -10000 0 -0.065 5 5
AKT 0.12 0.093 0.22 203 -0.14 1 204
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 0.007 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.021 0.016 -10000 0 -0.065 2 2
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PIK3CB 0.031 0.005 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.065 125 125
PIK3CG 0.022 0.015 -10000 0 -10000 0 0
PIK3R3 0.031 0.006 -10000 0 -0.065 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.031 0.005 -10000 0 -10000 0 0
RAS 0.007 0.024 0.1 1 -0.083 8 9
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.047 0.068 0.29 7 -0.21 17 24
PI3K 0.053 0.076 0.18 101 -10000 0 101
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
KRAS 0.03 0.008 -10000 0 -10000 0 0
FOXO 0.13 0.082 0.21 197 -10000 0 197
AKT2 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -0.065 2 2
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.03 0.076 12 -0.1 29 41
JUN -0.11 0.22 0.23 2 -0.52 118 120
MAP3K7 0.001 0.028 0.076 12 -0.11 24 36
GRAP2 0.03 0.008 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
MAP2K4 -0.019 0.057 0.15 4 -0.21 30 34
LAT 0.032 0.005 -10000 0 -0.065 1 1
LCP2 0.026 0.023 -10000 0 -0.065 29 29
MAPK8 -0.11 0.24 -10000 0 -0.54 118 118
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.03 0.087 12 -0.12 16 28
LAT/GRAP2/SLP76/HPK1/HIP-55 0.056 0.043 -10000 0 -0.054 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.026 0.076 3 -0.092 26 29
MKNK1 0.032 0.004 -10000 0 -10000 0 0
MAPK14 0.032 0.024 0.092 4 -0.068 26 30
ATF2/c-Jun 0.004 0.041 -10000 0 -0.11 49 49
MAPK11 0.029 0.025 0.091 3 -0.067 25 28
MITF 0.016 0.017 0.076 4 -0.044 28 32
MAPKAPK5 0.016 0.016 0.075 3 -0.044 26 29
KRT8 0.013 0.021 0.075 3 -0.046 45 48
MAPKAPK3 0.031 0.007 -10000 0 -0.065 1 1
MAPKAPK2 0.031 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.033 -10000 0 -0.084 25 25
CEBPB 0.014 0.019 0.073 2 -0.051 30 32
SLC9A1 0.015 0.016 0.081 1 -0.044 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.02 0.11 9 -0.054 1 10
p38alpha-beta/MNK1 0.053 0.036 -10000 0 -0.071 25 25
JUN 0 0.039 -10000 0 -0.11 49 49
PPARGC1A 0.016 0.017 0.076 4 -0.045 28 32
USF1 0.011 0.015 0.071 4 -0.046 26 30
RAB5/GDP/GDI1 0.013 0.047 -10000 0 -0.12 44 44
NOS2 0.011 0.015 0.071 4 -0.045 26 30
DDIT3 0.014 0.018 0.073 2 -0.047 28 30
RAB5A 0.032 0.004 -10000 0 -10000 0 0
HSPB1 0.06 0.12 0.27 124 -10000 0 124
p38alpha-beta/HBP1 0.037 0.039 -10000 0 -0.071 20 20
CREB1 0.004 0.056 -10000 0 -0.2 34 34
RAB5/GDP 0.023 0.003 -10000 0 -10000 0 0
EIF4E -0.032 0.026 0.21 5 -10000 0 5
RPS6KA4 0.016 0.016 0.076 4 -0.044 26 30
PLA2G4A -0.037 0.024 0.21 3 -10000 0 3
GDI1 0.016 0.015 0.076 4 -0.045 17 21
TP53 -0.016 0.017 0.054 5 -0.072 25 30
RPS6KA5 0.015 0.017 0.076 4 -0.044 26 30
ESR1 0.015 0.017 0.076 4 -0.044 25 29
HBP1 0.022 0.015 -10000 0 -10000 0 0
MEF2C 0.014 0.015 0.073 2 -0.045 17 19
MEF2A 0.016 0.017 0.076 4 -0.044 26 30
EIF4EBP1 -0.009 0.057 -10000 0 -0.21 33 33
KRT19 0.013 0.021 0.076 4 -0.045 45 49
ELK4 0.015 0.016 0.075 3 -0.044 25 28
ATF6 0.016 0.016 0.075 3 -0.044 25 28
ATF1 0.001 0.057 -10000 0 -0.19 38 38
p38alpha-beta/MAPKAPK2 0.053 0.036 -10000 0 -0.071 24 24
p38alpha-beta/MAPKAPK3 0.052 0.037 -10000 0 -0.071 25 25
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.045 0.03 -10000 0 -0.036 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.088 0.13 -10000 0 -0.38 59 59
AKT1 -0.032 0.18 -10000 0 -0.71 31 31
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.028 0.18 -10000 0 -0.72 31 31
mol:Ca2+ -0.004 0.046 0.17 19 -0.23 9 28
IGF1R 0.032 0.003 -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 -0.065 40 40
apoptosis 0.03 0.17 0.68 31 -10000 0 31
RhoA/GTP -0.039 0.014 -10000 0 -0.077 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.07 0.11 0.17 10 -0.28 68 78
regulation of stress fiber formation 0.046 0.043 -10000 0 -0.14 9 9
E2/ERA-ERB (dimer) 0.039 0.013 -10000 0 -10000 0 0
KRAS 0.03 0.008 -10000 0 -10000 0 0
G13/GTP 0.037 0.017 -10000 0 -0.024 32 32
pseudopodium formation -0.046 0.043 0.14 9 -10000 0 9
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.031 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 -0.055 0.13 0.2 1 -0.45 38 39
E2/ER beta (dimer) 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.005 0.057 0.13 5 -0.17 43 48
mol:NADP -0.055 0.13 0.2 1 -0.45 38 39
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 -0.01 0.032 -10000 0 -0.24 9 9
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
PLCB1 0.008 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 -0.055 0.13 0.2 1 -0.45 38 39
RHOA 0.031 0.005 -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 0.03 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.014 0.071 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.07 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.068 0.12 0.2 12 -0.28 68 80
GNAZ 0.026 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.022 0.006 -10000 0 -10000 0 0
STRN 0.032 0.002 -10000 0 -10000 0 0
GNAL 0.031 0.005 -10000 0 -10000 0 0
PELP1 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.031 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.031 -10000 0 -0.065 59 59
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
HBEGF -0.11 0.12 0.24 16 -0.33 67 83
cAMP biosynthetic process 0.031 0.02 -10000 0 -0.034 15 15
SRC -0.097 0.12 0.2 1 -0.35 59 60
PI3K 0.039 0.023 -10000 0 -0.051 16 16
GNB1 0.03 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.058 -10000 0 -0.15 44 44
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.077 0.09 -10000 0 -0.24 73 73
Gs family/GTP 0.039 0.023 -10000 0 -0.034 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.046 -10000 0 -0.042 136 136
vasodilation -0.052 0.13 0.2 1 -0.43 38 39
mol:DAG -0.01 0.032 -10000 0 -0.24 9 9
Gs family/GDP/Gbeta gamma -0.005 0.056 -10000 0 -0.16 44 44
MSN -0.051 0.038 0.15 9 -10000 0 9
Gq family/GTP 0.022 0.019 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.026 0.17 -10000 0 -0.7 31 31
NRAS 0.008 0.042 -10000 0 -0.065 125 125
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.13 0.43 38 -0.2 1 39
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.062 0.14 5 -0.17 44 49
NOS3 -0.057 0.14 0.2 1 -0.47 38 39
GNA11 0.031 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.036 0.13 -10000 0 -0.48 36 36
E2/ER alpha (dimer)/PELP1/Src -0.069 0.12 0.2 12 -0.28 68 80
ruffle organization -0.046 0.043 0.14 9 -10000 0 9
ROCK2 -0.032 0.053 0.31 2 -10000 0 2
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA13 0.031 0.007 -10000 0 -0.065 2 2
MMP9 -0.11 0.11 0.37 1 -0.33 62 63
MMP2 -0.11 0.11 0.19 1 -0.34 64 65
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.021 0.02 -10000 0 -0.026 67 67
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.037 0.061 -10000 0 -0.079 16 16
AKT1 0.031 0.008 -10000 0 -10000 0 0
GSC 0.008 0.028 0.075 41 -10000 0 41
NKX2-5 0.035 0.012 0.089 10 -10000 0 10
muscle cell differentiation -0.012 0.07 0.25 20 -10000 0 20
SMAD2-3/SMAD4/SP1 0.014 0.077 0.2 1 -0.11 15 16
SMAD4 -0.009 0.051 0.1 2 -0.084 101 103
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 -0.05 33 33
SMAD3/SMAD4/VDR 0.038 0.076 -10000 0 -0.094 1 1
MYC 0.008 0.041 -10000 0 -0.066 119 119
CDKN2B -0.21 0.19 -10000 0 -0.36 287 287
AP1 -0.003 0.049 0.14 7 -0.085 16 23
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.069 -10000 0 -0.21 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.058 0.14 3 -0.24 22 25
SP3 0.017 0.035 -10000 0 -0.063 81 81
CREB1 0.032 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 -0.08 26 26
GATA3 0.025 0.015 -10000 0 -0.066 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.002 0.066 -10000 0 -0.17 42 42
MEF2C/TIF2 -0.033 0.04 0.2 10 -10000 0 10
endothelial cell migration 0.035 0.068 0.46 2 -10000 0 2
MAX 0.034 0.01 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.037 -10000 0 -0.065 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.009 -10000 0 -0.065 3 3
RUNX1 0.031 0.005 -10000 0 -10000 0 0
CTBP1 0.031 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 0.056 0.32 3 -0.42 1 4
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.028 0.05 0.26 1 -0.06 36 37
DCP1A 0.031 0.005 -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 0.023 0.061 -10000 0 -0.078 38 38
SMAD3/SMAD4/ATF3 0.007 0.065 -10000 0 -0.082 70 70
SAP30 0.031 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.05 0.024 -10000 0 -0.042 12 12
JUN -0.026 0.039 0.14 11 -10000 0 11
SMAD3/SMAD4/IRF7 0.023 0.064 -10000 0 -0.085 29 29
TFE3 -0.006 0.037 -10000 0 -0.044 187 187
COL1A2 -0.025 0.053 -10000 0 -0.18 3 3
mesenchymal cell differentiation -0.022 0.06 0.079 34 -10000 0 34
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 -0.063 151 151
SMAD3/SMAD4/Max 0.031 0.061 -10000 0 -0.084 19 19
Cbp/p300/SNIP1 0.056 0.021 -10000 0 -0.039 9 9
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.05 0.044 0.13 6 -0.12 15 21
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.058 -10000 0 -0.079 35 35
IRF7 0.029 0.016 -10000 0 -0.066 12 12
ESR1 0.037 0.015 0.13 3 -0.028 1 4
HNF4A 0.03 0.008 -10000 0 -10000 0 0
MEF2C -0.029 0.041 0.19 13 -10000 0 13
SMAD2-3/SMAD4 0.025 0.061 0.18 1 -0.085 16 17
Cbp/p300/Src-1 0.053 0.024 -10000 0 -0.041 11 11
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 -0.027 2 2
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.029 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 -0.093 87 87
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 0.04 -10000 0 -0.066 9 9
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.042 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.009 0.039 0.13 10 -0.17 11 21
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 0.045 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.034 0.081 0.21 1 -0.12 5 6
IFNB1 -0.021 0.035 0.14 10 -10000 0 10
SMAD3/SMAD4/MEF2C -0.009 0.054 0.19 4 -10000 0 4
CITED1 0.028 0.021 -10000 0 -0.065 24 24
SMAD2-3/SMAD4/ARC105 0.039 0.067 0.19 1 -0.087 8 9
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.049 0.19 1 -0.25 10 11
RUNX1-3/PEBPB2 0.06 0.021 -10000 0 -0.05 8 8
SMAD7 -0.024 0.064 -10000 0 -0.18 36 36
MYC/MIZ-1 0.021 0.042 -10000 0 -0.052 116 116
SMAD3/SMAD4 -0.045 0.063 -10000 0 -0.23 29 29
IL10 -0.032 0.042 0.15 15 -10000 0 15
PIASy/HDAC complex 0.033 0.007 -10000 0 -10000 0 0
PIAS3 0.03 0.005 -10000 0 -10000 0 0
CDK2 0.025 0.021 -10000 0 -0.066 24 24
IL5 -0.032 0.04 0.15 14 -10000 0 14
CDK4 -0.023 0.045 -10000 0 -0.067 252 252
PIAS4 0.033 0.007 -10000 0 -10000 0 0
ATF3 0.012 0.039 -10000 0 -0.065 103 103
SMAD3/SMAD4/SP1 -0.006 0.07 -10000 0 -0.11 34 34
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 -0.029 0.041 0.19 13 -10000 0 13
CEBPB 0.028 0.016 -10000 0 -0.065 11 11
SMAD3/SMAD4/DLX1 0.006 0.048 -10000 0 -0.069 37 37
MYOD1 0.032 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.023 0.058 -10000 0 -0.078 33 33
SMAD3/SMAD4/GATA3 0.017 0.065 -10000 0 -0.088 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.031 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.05 0.071 -10000 0 -0.091 2 2
SMAD3/SMAD4/SP1-3 0.006 0.081 -10000 0 -0.12 32 32
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.005 0.037 -10000 0 -0.054 45 45
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.039 0.059 -10000 0 -10000 0 0
ITGB5 -0.044 0.05 0.22 8 -10000 0 8
TGIF/SIN3/HDAC complex/CtBP -0.02 0.06 -10000 0 -0.17 51 51
SMAD3/SMAD4/AR 0.022 0.061 -10000 0 -0.079 42 42
AR 0.031 0.012 -10000 0 -0.065 8 8
negative regulation of cell growth -0.004 0.047 -10000 0 -0.24 11 11
SMAD3/SMAD4/MYOD 0.022 0.061 -10000 0 -0.08 31 31
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 0.041 0.066 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.041 0.15 1 -0.2 10 11
TFDP1 0.028 0.016 -10000 0 -0.065 11 11
SMAD3/SMAD4/AP1 0.012 0.064 -10000 0 -0.086 16 16
SMAD3/SMAD4/RUNX2 0.023 0.061 -10000 0 -0.079 34 34
TGIF2 0.029 0.012 -10000 0 -0.065 4 4
TGIF1 -0.035 0.044 -10000 0 -0.065 343 343
ATF2 0.032 0.001 -10000 0 -10000 0 0
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 -0.003 0.042 -10000 0 -0.083 108 108
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.014 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.047 7 7
alpha4/beta7 Integrin/MAdCAM1 0.074 0.03 -10000 0 -0.059 5 5
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 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.021 -10000 0 -0.051 4 4
EPO/EPOR (dimer) 0.033 0.022 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.076 0.16 1 -0.29 26 27
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 0.027 -10000 0 -0.091 28 28
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
MADCAM1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0.071 0.029 -10000 0 -0.059 5 5
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.013 -10000 0 -10000 0 0
SRC -0.042 0.02 0.17 2 -10000 0 2
ITGB7 0.031 0.007 -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 0.031 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.051 -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 -0.004 0.078 0.16 1 -0.3 26 27
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.007 0.048 -10000 0 -0.052 259 259
alphaV beta3 Integrin 0.06 0.023 -10000 0 -0.049 17 17
PTK2 -0.011 0.064 0.27 8 -0.26 6 14
IGF1R 0.032 0.003 -10000 0 -10000 0 0
PI4KB 0.032 0.005 -10000 0 -10000 0 0
MFGE8 0.031 0.007 -10000 0 -0.065 2 2
SRC 0.03 0.008 -10000 0 -10000 0 0
CDKN1B 0.013 0.048 -10000 0 -0.26 15 15
VEGFA -0.021 0.048 -10000 0 -0.065 275 275
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.031 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 0.053 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 0.023 -10000 0 -0.049 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.078 0.024 -10000 0 -0.051 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.045 -10000 0 -0.16 21 21
alphaV/beta3 Integrin/Syndecan-1 0.051 0.037 -10000 0 -0.051 55 55
PI4KA 0.011 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.041 0.061 -10000 0 -0.097 2 2
PI4 Kinase 0.016 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
alphaV/beta3 Integrin/Osteopontin 0.022 0.055 -10000 0 -0.051 178 178
RPS6KB1 -0.05 0.029 -10000 0 -10000 0 0
TLN1 0.021 0.028 -10000 0 -0.065 43 43
MAPK3 -0.002 0.04 -10000 0 -0.28 9 9
GPR124 0.031 0.007 -10000 0 -0.065 2 2
MAPK1 -0.002 0.038 -10000 0 -0.28 8 8
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.021 -10000 0 -0.049 15 15
cell adhesion 0.046 0.031 -10000 0 -0.079 6 6
ANGPTL3 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.002 0.053 -10000 0 -0.05 237 237
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
TGFBR2 0.03 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 0.059 0.023 -10000 0 -0.049 18 18
apoptosis 0.029 0.017 -10000 0 -0.065 15 15
CD47 0.031 0.008 -10000 0 -0.065 2 2
alphaV/beta3 Integrin/CD47 0.059 0.024 -10000 0 -0.049 17 17
VCL 0.024 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.06 0.022 -10000 0 -0.049 15 15
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.008 0.014 -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 0.004 0.064 -10000 0 -0.071 20 20
FAK1/Vinculin -0.006 0.057 0.26 7 -0.23 6 13
alphaV beta3/Integrin/ppsTEM5 0.06 0.023 -10000 0 -0.049 18 18
RHOA 0.031 0.005 -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 0.031 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 0.058 0.025 -10000 0 -0.049 21 21
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.022 -10000 0 -0.043 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.039 -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 -0.074 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 0.004 -10000 0 -10000 0 0
IRS1 0.031 0.009 -10000 0 -0.065 4 4
FAK1/Paxillin -0.003 0.064 0.25 9 -0.22 6 15
cell migration -0.016 0.052 0.25 7 -0.21 6 13
ITGAV 0.029 0.017 -10000 0 -0.065 15 15
PI3K 0.06 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 0.032 0 -10000 0 -10000 0 0
angiogenesis 0.001 0.045 0.18 3 -0.31 8 11
Rac1/GTP -0.023 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
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.036 0.14 14 -0.16 9 23
adherens junction organization 0.007 0.042 0.13 8 -0.15 21 29
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.07 0.16 126 -0.14 5 131
FMN1 0.012 0.038 0.13 8 -0.14 16 24
mol:IP3 0.004 0.024 -10000 0 -0.12 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.017 0.04 0.14 8 -0.15 16 24
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.012 0.034 0.1 30 -0.14 8 38
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.059 0.17 3 -0.24 16 19
CTNND1 0.031 0.014 -10000 0 -0.067 10 10
mol:PI-4-5-P2 0.007 0.038 0.12 8 -0.15 16 24
VASP 0.007 0.034 0.12 8 -0.14 14 22
ZYX 0 0.031 0.12 3 -0.16 10 13
JUB 0.012 0.038 0.13 8 -0.14 16 24
EGFR(dimer) 0.01 0.034 0.15 2 -0.16 8 10
E-cadherin/beta catenin-gamma catenin 0.057 0.026 -10000 0 -0.053 19 19
mol:PI-3-4-5-P3 0.041 0.049 0.16 32 -0.13 10 42
PIK3CA 0.028 0.02 -10000 0 -0.059 21 21
PI3K 0.042 0.05 0.16 32 -0.13 10 42
FYN -0.011 0.054 0.16 12 -0.19 29 41
mol:Ca2+ 0.004 0.024 -10000 0 -0.12 10 10
JUP 0.029 0.017 -10000 0 -0.064 16 16
PIK3R1 0.03 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.024 -10000 0 -0.12 10 10
CDH1 0.03 0.013 -10000 0 -0.064 8 8
RhoA/GDP 0.075 0.076 0.16 222 -0.14 6 228
establishment of polarity of embryonic epithelium 0.006 0.035 0.12 8 -0.14 16 24
SRC 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.031 0.005 -10000 0 -10000 0 0
EGFR 0.012 0.017 -10000 0 -0.065 5 5
CASR -0.013 0.032 0.15 12 -0.13 7 19
RhoA/GTP 0.019 0.036 0.14 12 -0.13 8 20
AKT2 0.01 0.033 0.1 23 -0.13 9 32
actin cable formation 0.003 0.034 0.12 8 -0.14 16 24
apoptosis -0.01 0.041 0.16 9 -0.17 11 20
CTNNA1 0.032 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.019 -10000 0 -0.13 8 8
PIP5K1A 0.007 0.038 0.12 8 -0.15 16 24
PLCG1 0.004 0.024 -10000 0 -0.12 9 9
Rac1/GTP 0.014 0.038 0.15 2 -0.16 8 10
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.023 -10000 0 -0.051 2 2
CRKL 0.05 0.082 0.22 21 -0.41 5 26
mol:PIP3 0.013 0.037 -10000 0 -0.7 1 1
AKT1 0.005 0.041 -10000 0 -0.62 1 1
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.047 0.084 0.27 17 -0.34 6 23
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
HGF/MET/SHIP2 0.041 0.032 -10000 0 -0.048 4 4
MAP3K5 0.049 0.079 0.25 8 -0.41 4 12
HGF/MET/CIN85/CBL/ENDOPHILINS 0.039 0.031 -10000 0 -0.044 3 3
AP1 0.012 0.074 0.14 116 -10000 0 116
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
apoptosis -0.019 0.21 -10000 0 -0.71 40 40
STAT3 (dimer) 0.011 0.027 -10000 0 -0.17 3 3
GAB1/CRKL/SHP2/PI3K 0.079 0.081 0.3 4 -0.38 5 9
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.067 0.08 0.23 7 -0.4 5 12
PTPN11 0.032 0.004 -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 0.022 0.016 -10000 0 -0.065 2 2
ELK1 0.11 0.18 0.34 184 -10000 0 184
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.028 0.16 1 -0.15 9 10
PAK1 -0.001 0.043 -10000 0 -0.6 1 1
HGF/MET/RANBP10 0.041 0.032 -10000 0 -0.049 3 3
HRAS 0.014 0.042 -10000 0 -0.32 5 5
DOCK1 0.037 0.078 0.25 8 -0.37 6 14
GAB1 0.051 0.078 0.22 1 -0.47 4 5
CRK 0.052 0.08 0.2 21 -0.46 4 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.036 -10000 0 -0.35 3 3
JUN 0.032 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.016 0.081 9 -0.05 17 26
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.045 0.089 0.25 43 -0.31 3 46
GRB2/SHC 0.059 0.061 0.16 104 -0.11 8 112
FOS 0.007 0.041 -10000 0 -0.065 120 120
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.1 0.18 0.33 184 -10000 0 184
HGF/MET/MUC20 0.028 0.021 -10000 0 -0.041 3 3
cell migration 0.058 0.06 0.15 104 -0.11 8 112
GRB2 0.031 0.006 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.031 0.023 -10000 0 -0.051 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.04 2 2
RAP1B 0.047 0.081 0.28 15 -0.32 6 21
RAP1A 0.043 0.083 0.28 17 -0.35 5 22
HGF/MET/RANBP9 0.042 0.032 -10000 0 -0.049 3 3
RAF1 0.038 0.064 0.21 4 -0.3 6 10
STAT3 0.011 0.027 -10000 0 -0.14 7 7
cell proliferation 0.031 0.062 0.22 15 -0.25 2 17
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.076 0.16 0.32 134 -10000 0 134
MAPK1 0.11 0.21 0.39 151 -10000 0 151
RANBP9 0.032 0.003 -10000 0 -10000 0 0
MAPK8 -0.021 0.14 0.26 3 -0.32 55 58
SRC 0.004 0.017 -10000 0 -0.12 7 7
PI3K 0.057 0.059 0.16 96 -0.11 7 103
MET/Glomulin 0.014 0.025 -10000 0 -0.085 20 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.034 0.064 0.25 4 -0.31 3 7
MET 0.021 0.016 -10000 0 -0.065 2 2
MAP4K1 0.057 0.085 0.24 13 -0.42 5 18
PTK2 0.031 0.006 -10000 0 -10000 0 0
MAP2K2 0.04 0.075 0.28 12 -0.29 6 18
BAD -0.002 0.04 -10000 0 -0.6 1 1
MAP2K4 0.043 0.077 0.23 16 -0.36 4 20
SHP2/GRB2/SOS1/GAB1 0.028 0.051 -10000 0 -0.35 5 5
INPPL1 0.032 0.004 -10000 0 0 8 8
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 9 -0.054 17 26
PLCgamma1/PKC 0.022 0.006 -10000 0 -10000 0 0
HGF 0.022 0.015 -10000 0 -0.065 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
PTPRJ 0.031 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.16 112 -0.11 9 121
PDPK1 0.012 0.04 0.26 2 -0.65 1 3
HGF/MET/SHIP 0.028 0.021 -10000 0 -0.041 3 3
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.032 -10000 0 -0.06 61 61
AES 0.033 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.004 -10000 0 0 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.024 -10000 0 -0.052 4 4
SMAD4 0.009 0.04 -10000 0 -0.065 114 114
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 0.097 0.21 150 -0.29 6 156
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 -0.065 101 101
beta catenin/beta TrCP1 0.11 0.093 0.22 143 -0.26 7 150
FZD1 0.021 0.017 -10000 0 -0.066 4 4
AXIN2 -0.014 0.022 -10000 0 -0.17 1 1
AXIN1 0.033 0.004 -10000 0 -10000 0 0
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 0.063 0.068 0.22 22 -0.22 10 32
Axin1/APC/GSK3 0.041 0.065 0.16 75 -0.26 4 79
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.094 0.2 123 -0.25 7 130
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.034 0.009 -10000 0 -10000 0 0
MYC -0.025 0.099 0.45 15 -10000 0 15
RANBP3 0.031 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.021 -10000 0 -0.047 9 9
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.033 0.01 -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 -0.061 1 1
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.034 0.051 0.22 1 -0.2 1 2
LEF1 0.034 0.01 -10000 0 -0.061 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.03 0.009 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.065 0.061 0.23 20 -0.22 2 22
DKK1/LRP6/Kremen 2 0.025 0.046 -10000 0 -0.048 103 103
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.036 0.008 -10000 0 -10000 0 0
NLK 0.031 0.005 -10000 0 -10000 0 0
CCND1 -0.034 0.057 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 0.18 153 -10000 0 153
WNT1/LRP6/FZD1 0 0.026 -10000 0 -0.29 3 3
CREBBP 0.035 0.007 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.031 0.005 -10000 0 -10000 0 0
CLTC 0.012 0.084 -10000 0 -0.34 25 25
calcium ion-dependent exocytosis 0.023 0.044 0.093 92 -0.2 5 97
Dynamin 2/GTP 0.022 0.011 -10000 0 -0.023 24 24
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.009 0.07 -10000 0 -0.28 24 24
CPE -0.015 0.006 0 78 -10000 0 78
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
membrane fusion 0.027 0.044 0.093 132 -0.11 12 144
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.053 0.14 10 -0.17 24 34
TSHR -0.017 0.005 0 37 -0.041 4 41
INS 0.006 0.093 -10000 0 -0.46 18 18
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.027 0.044 0.093 132 -0.11 12 144
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 0.011 -10000 0 -0.023 24 24
JUP 0.008 0.068 -10000 0 -0.28 23 23
ASAP2/amphiphysin II 0.035 0.017 -10000 0 -0.023 23 23
ARF6/GTP 0.023 0.005 -10000 0 -10000 0 0
CDH1 0.009 0.067 -10000 0 -0.28 23 23
clathrin-independent pinocytosis 0.023 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.005 -10000 0 -10000 0 0
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.004 0.039 -10000 0 -0.14 31 31
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 -0.035 0.071 0.27 24 -10000 0 24
positive regulation of phagocytosis -0.016 0.006 0 59 -10000 0 59
ARF6/GTP/JIP3 0.041 0.01 -10000 0 -10000 0 0
ACAP1 0.028 0.042 0.091 132 -0.093 12 144
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.002 0.062 -10000 0 -0.29 19 19
clathrin heavy chain/ACAP1 0.02 0.073 0.18 11 -0.25 24 35
JIP4/KLC1 0.041 0.032 -10000 0 -0.034 23 23
EXOC1 0.03 0.009 -10000 0 -0.065 1 1
exocyst 0.004 0.039 -10000 0 -0.14 31 31
RALA/GTP 0.015 0.014 -10000 0 -0.04 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.041 1 1
receptor recycling 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.008 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.013 0.083 0.18 1 -0.33 25 26
IL2RA 0 0.075 -10000 0 -0.33 22 22
VAMP3 -0.016 0.006 0 59 -10000 0 59
GLUT4/clathrin heavy chain/ACAP1 0.037 0.07 -10000 0 -0.24 24 24
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.011 -10000 0 -0.052 12 12
PLD2 0.006 0.01 -10000 0 -0.054 10 10
EXOC5 0.028 0.018 -10000 0 -0.065 15 15
PIP5K1C 0.013 0.048 0.12 4 -0.17 22 26
SDC1 0.006 0.07 -10000 0 -0.28 24 24
ARF6/GDP 0.023 0.005 -10000 0 0 25 25
EXOC7 0.032 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.073 -10000 0 -0.27 24 24
mol:Phosphatidic acid 0.027 0.044 0.093 132 -0.11 12 144
endocytosis -0.034 0.016 0.023 23 -10000 0 23
SCAMP2 0.032 0.004 -10000 0 -10000 0 0
ADRB2 0.006 0.08 0.22 2 -0.32 25 27
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.01 -10000 0 -0.023 24 24
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.007 0.081 0.2 5 -0.32 25 30
RALA 0.02 0.02 -10000 0 -0.065 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.071 0.22 2 -0.27 24 26
FOXM1 transcription factor network

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
NFATC3 -0.17 0.2 -9999 0 -0.71 15 15
PLK1 -0.002 0.12 -9999 0 -0.9 8 8
BIRC5 -0.029 0.073 -9999 0 -10000 0 0
HSPA1B -0.16 0.2 -9999 0 -0.68 20 20
MAP2K1 -0.013 0.038 -9999 0 -10000 0 0
BRCA2 -0.17 0.2 -9999 0 -0.69 16 16
FOXM1 -0.18 0.22 -9999 0 -0.74 24 24
XRCC1 -0.16 0.2 -9999 0 -0.7 14 14
FOXM1B/p19 -0.17 0.2 -9999 0 -0.71 18 18
Cyclin D1/CDK4 -0.16 0.19 -9999 0 -0.65 17 17
CDC2 -0.17 0.21 -9999 0 -0.7 20 20
TGFA -0.16 0.19 -9999 0 -0.62 22 22
SKP2 -0.17 0.2 -9999 0 -0.7 17 17
CCNE1 0.014 0.027 -9999 0 -0.074 4 4
CKS1B -0.17 0.2 -9999 0 -0.71 19 19
RB1 -0.11 0.19 -9999 0 -0.59 49 49
FOXM1C/SP1 -0.18 0.22 -9999 0 -0.71 24 24
AURKB -0.006 0.13 -9999 0 -0.93 9 9
CENPF -0.18 0.21 -9999 0 -0.7 20 20
CDK4 -0.03 0.047 -9999 0 -0.074 250 250
MYC -0.16 0.19 -9999 0 -0.62 23 23
CHEK2 -0.013 0.04 -9999 0 -0.1 15 15
ONECUT1 -0.16 0.2 -9999 0 -0.66 22 22
CDKN2A 0.002 0.027 -9999 0 -0.063 53 53
LAMA4 -0.17 0.2 -9999 0 -0.7 15 15
FOXM1B/HNF6 -0.17 0.22 -9999 0 -0.72 22 22
FOS -0.18 0.2 -9999 0 -0.72 17 17
SP1 0.031 0.006 -9999 0 -0.025 2 2
CDC25B -0.16 0.2 -9999 0 -0.69 15 15
response to radiation -0.011 0.013 -9999 0 -0.039 1 1
CENPB -0.16 0.2 -9999 0 -0.69 15 15
CENPA -0.17 0.21 -9999 0 -0.71 21 21
NEK2 -0.16 0.2 -9999 0 -0.72 14 14
HIST1H2BA -0.16 0.2 -9999 0 -0.68 20 20
CCNA2 -0.001 0.046 -9999 0 -0.074 135 135
EP300 0.03 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.18 0.22 -9999 0 -0.75 19 19
CCNB2 -0.19 0.21 -9999 0 -0.7 22 22
CCNB1 -0.18 0.21 -9999 0 -0.71 20 20
ETV5 -0.16 0.2 -9999 0 -0.69 16 16
ESR1 -0.17 0.2 -9999 0 -0.69 16 16
CCND1 -0.17 0.2 -9999 0 -0.65 20 20
GSK3A -0.01 0.035 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.012 0.061 -9999 0 -0.099 18 18
CDK2 0.013 0.031 -9999 0 -0.075 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -9999 0 -0.047 1 1
FOXM1B/Cbp/p300 -0.17 0.22 -9999 0 -0.71 20 20
GAS1 -0.17 0.2 -9999 0 -0.71 17 17
MMP2 -0.19 0.21 -9999 0 -0.71 18 18
RB1/FOXM1C -0.18 0.21 -9999 0 -0.67 25 25
CREBBP 0.032 0.003 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.017 -9999 0 -0.065 5 5
EGF/EGFR 0.007 0.035 -9999 0 -0.046 79 79
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.039 -9999 0 -0.06 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.003 0.044 -9999 0 -0.065 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.031 0.007 -9999 0 -0.065 2 2
EGF/EGFR dimer/SHC 0.018 0.035 -9999 0 -0.05 32 32
mol:GDP 0.018 0.036 -9999 0 -0.06 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 0.029 -9999 0 -0.059 3 3
SHC1 0.024 0.026 -9999 0 -0.065 40 40
HRAS/GDP 0.016 0.038 -9999 0 -0.069 1 1
FRAP1 -0.011 0.015 -9999 0 -0.057 2 2
EGF/EGFR dimer 0.017 0.024 -9999 0 -0.051 7 7
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.031 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.017 0.045 -9999 0 -0.052 149 149
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.009 0.04 -10000 0 -0.065 114 114
SMAD2 -0.02 0.054 -10000 0 -0.21 24 24
SMAD3 0.014 0.042 0.1 32 -0.099 26 58
SMAD3/SMAD4 0.026 0.055 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.037 0.047 -10000 0 -0.05 106 106
SMAD2/SMAD2/SMAD4 0.017 0.081 -10000 0 -0.18 33 33
PPM1A 0.03 0.007 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.013 0.06 -10000 0 -0.18 34 34
MAP3K1 0.032 0.006 -10000 0 -0.065 1 1
TRAP-1/SMAD4 0.024 0.041 -10000 0 -0.051 114 114
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 0.031 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
Signaling events mediated by PTP1B

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
PDGFRB 0.031 0.007 -10000 0 -0.065 2 2
Jak2/Leptin Receptor 0.018 0.11 -10000 0 -0.29 53 53
PTP1B/AKT1 0.039 0.058 0.17 7 -0.27 7 14
FYN 0.029 0.01 -10000 0 -0.065 1 1
p210 bcr-abl/PTP1B 0.026 0.057 0.16 10 -0.26 8 18
EGFR 0.012 0.018 -10000 0 -0.051 8 8
EGF/EGFR 0.01 0.039 -10000 0 -0.2 8 8
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 0.059 0.16 5 -0.24 9 14
Insulin Receptor/Insulin 0.054 0.061 0.18 1 -0.2 13 14
HCK 0.014 0.036 -10000 0 -0.065 84 84
CRK 0.032 0.004 -10000 0 -10000 0 0
TYK2 0.026 0.076 0.27 25 -0.25 8 33
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 0.083 0.16 110 -0.26 8 118
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.063 0.18 7 -0.24 9 16
cell migration -0.026 0.057 0.26 8 -0.16 10 18
STAT3 0.03 0.014 -10000 0 -0.065 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 0.028 0.017 -10000 0 -0.065 15 15
PTP1B/p130 Cas 0.023 0.053 0.11 31 -0.2 12 43
Crk/p130 Cas 0.038 0.057 0.16 7 -0.23 9 16
DOK1 0.023 0.059 0.17 13 -0.26 10 23
JAK2 0.004 0.12 0.2 1 -0.3 54 55
Jak2/Leptin Receptor/Leptin 0.026 0.074 -10000 0 -0.25 14 14
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.058 0.14 26 -0.24 9 35
LYN 0.02 0.031 -10000 0 -0.065 60 60
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 0.092 0.23 43 -0.29 11 54
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.004 -10000 0 -10000 0 0
PI3K 0.053 0.067 -10000 0 -0.2 12 12
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.025 0.068 -10000 0 -0.23 14 14
negative regulation of transcription 0.004 0.11 0.2 1 -0.3 54 55
FCGR2A -0.017 0.048 -10000 0 -0.065 253 253
FER 0.033 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.047 0.005 -10000 0 -10000 0 0
BLK 0.031 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.049 0.037 -10000 0 -0.047 54 54
RHOA 0.031 0.006 -10000 0 -10000 0 0
LEPR 0.03 0.009 -10000 0 -0.065 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.031 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.03 0.08 0.2 25 -0.28 11 36
PRL 0.032 0.011 -10000 0 -0.063 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 0.059 0.023 -10000 0 -0.041 18 18
CSF1/CSF1R 0.052 0.065 0.18 6 -0.24 9 15
Ras protein signal transduction -0.011 0.085 0.51 12 -10000 0 12
IRS1 0.031 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 0.023 0.072 0.19 3 -0.24 20 23
STAT5A 0.022 0.073 0.16 7 -0.24 20 27
GRB2 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.041 0.059 0.17 7 -0.24 9 16
CSN2 0 0.034 -10000 0 -0.3 1 1
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
LAT 0.008 0.045 -10000 0 -0.3 3 3
YBX1 0.036 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 -0.065 40 40
NOX4 0.021 0.034 -10000 0 -0.063 70 70
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.054 0.062 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.043 0.031 -10000 0 -0.046 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.023 0.15 -10000 0 -0.48 47 47
SMAD4 0.009 0.04 -10000 0 -0.065 114 114
SMAD5 -0.024 0.088 0.12 3 -0.31 33 36
BMP7/USAG1 0.03 0.024 -10000 0 -0.051 6 6
SMAD5/SKI -0.012 0.093 -10000 0 -0.31 34 34
SMAD1 -0.007 0.065 -10000 0 -0.24 22 22
BMP2 0.021 0.028 -10000 0 -0.065 44 44
SMAD1/SMAD1/SMAD4 0.001 0.066 -10000 0 -0.23 16 16
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 0.032 0.049 -10000 0 -0.045 130 130
AHSG 0.031 0.008 -10000 0 -0.065 2 2
CER1 0.028 0.01 -10000 0 -10000 0 0
BMP2-4/CER1 0.042 0.04 -10000 0 -0.051 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.002 0.059 -10000 0 -0.2 33 33
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 0.055 -10000 0 -0.058 4 4
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 -0.014 0.056 -10000 0 -0.12 95 95
BMP2-4/USAG1 0.032 0.041 -10000 0 -0.051 49 49
SMAD6/SMURF1/SMAD5 -0.006 0.083 -10000 0 -0.3 29 29
SOSTDC1 0.021 0.018 -10000 0 -0.065 6 6
BMP7/BMPR2/BMPR1A-1B 0.051 0.051 -10000 0 -0.058 2 2
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.031 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 0.03 0.008 -10000 0 -0.065 1 1
BMP2-4/CHRD 0.044 0.039 -10000 0 -0.05 52 52
SMAD5/SMAD5/SMAD4 -0.019 0.094 -10000 0 -0.3 36 36
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.011 0.052 -10000 0 -0.19 17 17
BMP7 (homodimer) 0.029 0.01 -10000 0 -0.065 1 1
NUP214 0.031 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.013 -10000 0 -0.051 4 4
SMAD1/SKI 0.006 0.075 -10000 0 -0.24 24 24
SMAD6 0.031 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 -0.05 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 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.058 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 0.004 0.077 -10000 0 -0.24 25 25
SMAD6-7/SMURF1/SMAD1 0.017 0.072 -10000 0 -0.24 15 15
SMAD6/SMURF1 0.022 0.015 -10000 0 -10000 0 0
BAMBI 0.02 0.024 -10000 0 -0.065 27 27
SMURF2 0.032 0.006 -10000 0 -0.065 1 1
BMP2-4/CHRDL1 0.03 0.027 -10000 0 -0.041 50 50
BMP2-4/GREM1 0.041 0.043 -10000 0 -0.05 73 73
SMAD7 0.031 0.007 -10000 0 -0.065 1 1
SMAD8A/SMAD8A/SMAD4 -0.021 0.16 -10000 0 -0.46 53 53
SMAD1/SMAD6 0.004 0.061 -10000 0 -0.24 16 16
TAK1/SMAD6 0.032 0.023 -10000 0 -0.051 1 1
BMP7 0.029 0.01 -10000 0 -0.065 1 1
BMP6 0.031 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 0.049 -10000 0 -0.13 45 45
PPM1A 0.03 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.005 0.077 -10000 0 -0.24 25 25
SMAD7/SMURF1 0.032 0.023 -10000 0 -0.051 1 1
CTDSPL 0.031 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 0.03 0.008 -10000 0 -0.065 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.013 0.057 -10000 0 -0.12 96 96
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.032 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.016 0.057 -10000 0 -0.12 101 101
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 0.027 -10000 0 -0.041 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.049 0.054 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.01 -10000 0 -0.021 8 8
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.04 -10000 0 -0.041 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.032 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.041 0.009 -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 0.001 -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) 0.012 0.051 -10000 0 -0.045 178 178
GNAT2/GDP 0.052 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 0.011 -10000 0 -0.023 8 8
SLC24A2 0.026 0.013 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.005 -10000 0 -10000 0 0
GNB3 0.031 0.006 -10000 0 -10000 0 0
GNAT2/GTP 0.023 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 -0.041 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.064 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.026 0.013 -10000 0 -10000 0 0
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
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.007 0.049 -10000 0 -0.15 12 12
mol:DAG -0.006 0.041 0.15 5 -0.15 10 15
PLCG1 -0.006 0.041 0.15 5 -0.15 10 15
YES1 -0.015 0.035 -10000 0 -0.13 23 23
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 0.061 0.17 36 -0.16 10 46
MAP3K7 -0.023 0.035 0.14 7 -0.15 9 16
mol:Ca2+ -0.006 0.04 0.14 5 -0.15 10 15
mol:IP3 -0.006 0.041 0.15 5 -0.15 10 15
NLK 0.006 0.087 -10000 0 -0.73 7 7
GNB1 0.03 0.008 -10000 0 -10000 0 0
CAMK2A -0.02 0.037 0.16 8 -0.15 9 17
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.001 0.039 -10000 0 -0.13 21 21
CSNK1A1 0.032 0.003 -10000 0 -10000 0 0
GNAS -0.01 0.031 -10000 0 -0.13 18 18
GO:0007205 -0.01 0.036 0.14 5 -0.15 10 15
WNT6 0.032 0.001 -10000 0 -10000 0 0
WNT4 0.031 0.008 -10000 0 -0.065 2 2
NFAT1/CK1 alpha -0.007 0.054 0.19 7 -0.16 13 20
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.002 0.045 -10000 0 -0.065 155 155
WNT11 0.031 0.008 -10000 0 -0.065 2 2
CDC42 -0.023 0.031 0.18 3 -0.15 6 9
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.031 0.007 -10000 0 -0.065 2 2
alphaV beta3 Integrin 0.044 0.018 -10000 0 -0.051 15 15
PTK2 0.014 0.081 -10000 0 -0.23 45 45
positive regulation of JNK cascade 0.019 0.083 -10000 0 -0.25 35 35
CDC42/GDP 0.032 0.12 0.35 2 -0.33 41 43
Rac1/GDP 0.022 0.093 0.29 1 -0.32 20 21
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.1 -10000 0 -0.3 35 35
nectin-3/I-afadin 0.043 0.015 -10000 0 -0.051 1 1
RAPGEF1 0.003 0.11 0.24 5 -0.34 42 47
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.001 0.12 -10000 0 -0.37 42 42
PDGFB-D/PDGFRB 0.031 0.007 -10000 0 -0.065 2 2
TLN1 -0.016 0.016 -10000 0 -0.073 22 22
Rap1/GTP -0.001 0.08 -10000 0 -0.26 42 42
IQGAP1 0.009 0.041 -10000 0 -0.065 120 120
Rap1/GTP/I-afadin 0.035 0.018 -10000 0 -0.023 43 43
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 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 0.017 0.13 0.33 3 -0.38 42 45
MLLT4 0.03 0.009 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PI3K 0.068 0.052 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.043 0.014 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.013 0.077 -10000 0 -0.27 20 20
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.031 0.007 -10000 0 -0.065 1 1
PVRL2 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
CLDN1 0.029 0.014 -10000 0 -0.065 9 9
JAM-A/CLDN1 0.06 0.048 -10000 0 -0.068 11 11
SRC 0.007 0.13 -10000 0 -0.4 43 43
ITGB3 0.032 0.003 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.043 0.014 -10000 0 -10000 0 0
FARP2 0.023 0.13 0.37 1 -0.38 34 35
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) 0.056 0.025 -10000 0 -0.044 9 9
nectin-1/I-afadin 0.043 0.014 -10000 0 -10000 0 0
nectin-2/I-afadin 0.042 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.015 0.032 -10000 0 -0.041 90 90
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.057 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 0.019 0.083 -10000 0 -0.25 35 35
alphaV/beta3 Integrin/Talin 0.024 0.066 0.2 28 -0.17 8 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.042 0.015 -10000 0 -10000 0 0
PIP5K1C -0.011 0.014 -10000 0 -0.062 35 35
VAV2 0.015 0.14 0.31 2 -0.42 36 38
RAP1/GDP 0.022 0.11 0.32 2 -0.3 41 43
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 0.056 0.025 -10000 0 -0.044 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -0.051 1 1
Rac1/GTP 0.017 0.093 0.25 1 -0.33 20 21
PTPRM 0.006 0.019 -10000 0 -0.061 38 38
E-cadherin/beta catenin/alpha catenin 0.072 0.053 -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
Signaling events mediated by HDAC Class I

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
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 0.001 0.06 -10000 0 -0.17 25 25
SUMO1 0.032 0 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.029 -10000 0 -0.097 37 37
FKBP3 0.03 0.007 -10000 0 -10000 0 0
Histones 0.032 0.044 -10000 0 -0.2 7 7
YY1/LSF 0.012 0.059 -10000 0 -0.14 57 57
SMG5 0.031 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.001 0.035 -10000 0 -0.1 30 30
I kappa B alpha/HDAC1 0 0.058 -10000 0 -0.18 32 32
SAP18 0.03 0.008 -10000 0 -10000 0 0
RELA 0 0.049 0.11 12 -0.15 35 47
HDAC1/Smad7 0.035 0.039 -10000 0 -0.05 38 38
RANGAP1 0.03 0.008 -10000 0 -10000 0 0
HDAC3/TR2 0.015 0.044 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.047 -10000 0 -0.16 27 27
NF kappa B1 p50/RelA 0.016 0.058 -10000 0 -0.21 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.031 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
Mad/Max 0.045 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.047 -10000 0 -0.16 24 24
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.002 -10000 0 -0.014 1 1
RBBP4 0.014 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 0.004 -10000 0 0 10 10
NFKBIA 0.006 0.019 -10000 0 -0.056 6 6
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 58 58
SIN3 complex 0.052 0.027 -10000 0 -0.031 37 37
SMURF1 0.022 0.015 -10000 0 -10000 0 0
CHD3 0.032 0.004 -10000 0 0 10 10
SAP30 0.031 0.005 -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 -0.003 0.05 -10000 0 -0.18 22 22
YY1/HDAC2 0.013 0.058 -10000 0 -0.15 51 51
YY1/HDAC1 0.007 0.06 -10000 0 -0.15 52 52
NuRD/MBD2 Complex (MeCP1) 0.002 0.051 -10000 0 -0.16 28 28
PPARG 0.003 0.038 0.12 10 -0.16 13 23
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 0.004 -10000 0 0 10 10
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
HDAC3/SMRT (N-CoR2) 0.015 0.044 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.038 -10000 0 -0.05 38 38
CREBBP 0.032 0.003 -10000 0 0 6 6
NuRD/MBD3/MBD3L2 Complex 0.003 0.046 -10000 0 -0.15 24 24
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC3 0.007 0.02 -10000 0 -0.059 7 7
HDAC2 0.029 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 0.032 0 -10000 0 -10000 0 0
STAT3 0.016 0.009 -10000 0 -0.036 9 9
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 0.065 -10000 0 -0.14 55 55
YY1/SAP30/HDAC1 0.02 0.066 -10000 0 -0.14 56 56
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.009 -10000 0 -0.036 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.019 -10000 0 -0.056 6 6
histone deacetylation 0.002 0.051 -10000 0 -0.16 28 28
STAT3 (dimer non-phopshorylated)/HDAC3 0.004 0.042 -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 42 42
GATA2/HDAC3 0.015 0.044 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.033 -10000 0 -0.051 61 61
GATA1/HDAC3 0.016 0.044 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.013 0.046 -10000 0 -0.051 166 166
SIN3/HDAC complex/Mad/Max -0.006 0.067 -10000 0 -0.18 45 45
NuRD Complex 0.004 0.05 -10000 0 -0.18 18 18
positive regulation of chromatin silencing 0.03 0.042 -10000 0 -0.2 7 7
SIN3B 0.031 0.007 -10000 0 0 22 22
MTA2 0.032 0.004 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.032 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.043 -10000 0 -0.1 36 36
HDAC complex 0.038 0.063 -10000 0 -0.055 136 136
GATA1/Fog1 0.024 0.001 -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 -0.005 0.066 -10000 0 -0.18 45 45
NuRD/MBD2/PRMT5 Complex 0.002 0.051 -10000 0 -0.16 28 28
Ran/GTP/Exportin 1 0.037 0.039 -10000 0 -0.098 37 37
NF kappa B/RelA/I kappa B alpha -0.006 0.048 -10000 0 -0.17 26 26
SIN3/HDAC complex/NCoR1 0.006 0.043 -10000 0 -0.17 19 19
TFCP2 0.031 0.005 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
MBD3 0.031 0.006 -10000 0 -10000 0 0
MBD2 0.031 0.006 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.043 0.062 0.23 37 -10000 0 37
PCK1 0.037 0.031 -10000 0 -10000 0 0
HNF4A 0.036 0.044 0.24 8 -10000 0 8
KCNJ11 0.056 0.061 0.26 28 -10000 0 28
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 -10000 0 33
NKX2-1 0.041 0.048 0.21 4 -10000 0 4
ACADM 0.043 0.06 0.23 35 -10000 0 35
TAT 0.044 0.043 -10000 0 -10000 0 0
CEBPB 0.029 0.017 -10000 0 -0.063 11 11
CEBPA 0.029 0.019 -10000 0 -0.064 15 15
TTR 0.055 0.093 0.35 35 -0.44 1 36
PKLR 0.047 0.066 0.23 45 -10000 0 45
APOA1 0.061 0.072 0.41 10 -10000 0 10
CPT1C 0.044 0.055 0.24 28 -10000 0 28
ALAS1 0.047 0.051 -10000 0 -10000 0 0
TFRC 0.056 0.051 0.2 30 -10000 0 30
FOXF1 0.022 0.025 -10000 0 -0.065 35 35
NF1 0.034 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.038 0.005 -10000 0 -10000 0 0
CPT1A 0.043 0.061 0.23 38 -10000 0 38
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 0.25 122 -10000 0 122
CREB1 0.035 0.008 -10000 0 -10000 0 0
IGFBP1 0.05 0.047 -10000 0 -10000 0 0
PDX1 0.046 0.05 -10000 0 -10000 0 0
UCP2 0.037 0.067 0.23 35 -10000 0 35
ALDOB 0.062 0.071 0.26 45 -10000 0 45
AFP 0.01 0.009 -10000 0 -0.083 4 4
BDH1 0.047 0.067 0.24 46 -10000 0 46
HADH 0.06 0.068 0.26 40 -10000 0 40
F2 0.059 0.074 0.41 10 -10000 0 10
HNF1A 0.038 0.005 -10000 0 -10000 0 0
G6PC 0.021 0.03 -10000 0 -10000 0 0
SLC2A2 0.062 0.052 0.21 31 -10000 0 31
INS 0.028 0.009 0.15 1 -10000 0 1
FOXA1 0.006 0.006 -10000 0 -0.088 1 1
FOXA3 0.015 0.011 -10000 0 -0.11 3 3
FOXA2 0.091 0.071 0.29 28 -10000 0 28
ABCC8 0.059 0.066 0.25 38 -10000 0 38
ALB 0.01 0.009 -10000 0 -0.083 4 4
TRAIL signaling pathway

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
TNFSF10 0.023 0.028 -10000 0 -0.065 45 45
positive regulation of NF-kappaB transcription factor activity 0.037 0.029 -10000 0 -0.051 44 44
MAP2K4 0.007 0.039 0.2 2 -0.18 11 13
IKBKB 0.032 0.003 -10000 0 -10000 0 0
TNFRSF10B 0.03 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 47 47
TRAIL/TRAILR3 0.037 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1 0.018 0.018 -10000 0 -0.04 45 45
TRAIL/TRAILR4 0.037 0.029 -10000 0 -0.051 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.023 -10000 0 -0.035 46 46
IKK complex -0.032 0.11 -10000 0 -0.23 117 117
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.023 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.009 -10000 0 -0.051 45 45
MAP3K1 0.013 0.037 -10000 0 -0.14 21 21
TRAILR4 (trimer) 0.031 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 0.011 0.031 -10000 0 -0.11 21 21
CFLAR 0.031 0.01 -10000 0 -0.065 5 5
MAPK1 -0.023 0.011 -10000 0 -0.051 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.057 0.043 -10000 0 -0.066 3 3
mol:ceramide 0.007 0.013 -10000 0 -0.056 8 8
FADD 0.031 0.006 -10000 0 -0.065 1 1
MAPK8 -0.002 0.034 0.19 1 -0.26 3 4
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.031 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.014 -10000 0 -0.065 1 1
TRAIL/TRAILR1/FADD 0.034 0.025 -10000 0 -0.041 45 45
DAP3 0.032 0.004 -10000 0 -10000 0 0
CASP10 -0.013 0.027 0.14 11 -0.092 7 18
JNK cascade 0.037 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 0.045 0.031 -10000 0 -0.041 44 44
TRAIL/TRAILR2/FADD 0.051 0.036 -10000 0 -0.051 48 48
cell death 0.007 0.013 -10000 0 -0.056 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.034 -10000 0 -0.12 23 23
TRAILR2 (trimer) 0.03 0.011 -10000 0 -0.065 6 6
CASP8 0.015 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.07 0.055 -10000 0 -0.073 5 5
ceramide 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
MAP4K4 -0.004 0.052 -10000 0 -0.26 10 10
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.008 0.024 0.2 1 -0.12 7 8
NFKBIA 0.03 0.008 -10000 0 -0.065 1 1
BIRC3 0.026 0.023 -10000 0 -0.065 30 30
BAX -0.005 0.036 0.2 10 -0.12 8 18
EnzymeConsortium:3.1.4.12 0 0.015 0.05 3 -0.066 10 13
IKBKB -0.008 0.054 0.19 4 -0.26 9 13
MAP2K2 -0.012 0.045 0.17 23 -0.14 5 28
MAP2K1 -0.016 0.033 0.16 8 -0.14 5 13
SMPD1 -0.002 0.024 0.082 2 -0.1 18 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.056 0.29 1 -0.27 11 12
MAP2K4 -0.013 0.027 0.17 4 -0.14 5 9
protein ubiquitination -0.011 0.054 -10000 0 -0.28 9 9
EnzymeConsortium:2.7.1.37 -0.016 0.041 0.18 7 -0.15 5 12
response to UV 0 0 0.002 10 -0.002 2 12
RAF1 -0.012 0.032 0.17 7 -0.14 6 13
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.002 0.024 0.079 2 -0.11 12 14
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.011 -10000 0 -0.041 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.026 0.19 2 -0.12 8 10
TRADD 0.032 0.004 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.009 0.04 0.17 10 -0.14 5 15
MAPK1 -0.015 0.046 0.17 9 -0.17 11 20
p50/RELA/I-kappa-B-alpha 0.044 0.013 -10000 0 -0.051 1 1
FADD -0.002 0.05 0.24 1 -0.23 11 12
KSR1 -0.008 0.025 0.11 2 -0.12 8 10
MAPK8 -0.013 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 -0.01 0.05 -10000 0 -0.27 9 9
TNF R/SODD 0.014 0.046 -10000 0 -0.051 163 163
TNF 0.031 0.007 -10000 0 -0.065 2 2
CYCS 0.011 0.044 0.14 18 -0.12 4 22
IKBKG -0.009 0.053 0.19 3 -0.26 9 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.004 0.054 0.15 1 -0.27 10 11
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
AIFM1 -0.01 0.031 0.12 12 -0.13 5 17
TNF/TNF R/SODD 0.024 0.053 -10000 0 -0.05 164 164
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.002 0.054 0.18 6 -0.26 10 16
response to hydrogen peroxide 0 0 0.002 10 -0.002 2 12
BCL2 0.031 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 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 -0.001 0.054 -10000 0 -0.16 35 35
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
AKT1 0.005 0.051 0.14 6 -0.19 14 20
RAR alpha/9cRA/Cyclin H 0.008 0.086 0.18 2 -0.17 34 36
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.002 0.048 0.091 7 -0.14 39 46
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 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.002 0.07 0.25 2 -0.29 16 18
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA3 0.029 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 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.032 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 0.071 -10000 0 -0.29 17 17
RARA 0.011 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 0.048 0.091 7 -0.15 37 44
PRKCA 0.032 0.007 -10000 0 -0.033 3 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.066 -10000 0 -0.3 11 11
RXRG 0.018 0.007 -10000 0 -0.034 2 2
RXRA -0.013 0.045 0.1 9 -0.094 111 120
RXRB 0.019 0.006 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.004 -10000 0 -10000 0 0
RBP1 -0.012 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 0.079 0.2 1 -0.34 16 17
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.065 0.17 2 -0.26 17 19
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.062 0.16 2 -0.18 31 33
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.065 -10000 0 -0.31 9 9
positive regulation of DNA binding 0.002 0.078 0.15 2 -0.16 34 36
NRIP1 0.008 0.065 0.27 1 -0.35 4 5
RXRs/RARs 0.008 0.066 -10000 0 -0.29 13 13
RXRs/RXRs/DNA/9cRA -0.004 0.064 -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 0.021 -10000 0 -0.046 8 8
RAR alpha/9cRA 0.024 0.08 -10000 0 -0.14 29 29
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.003 -10000 0 0 6 6
RAR gamma2/9cRA 0.054 0.032 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.032 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.029 0.071 -10000 0 -0.25 21 21
Syndecan-3/Neurocan 0.01 0.071 -10000 0 -0.3 22 22
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.017 -10000 0 -0.065 5 5
Syndecan-3/EGFR 0 0.064 -10000 0 -0.26 23 23
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.026 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 0.004 -10000 0 -10000 0 0
APH1A 0.03 0.012 -10000 0 -0.065 7 7
NCAN 0.026 0.014 -10000 0 -0.001 102 102
long-term memory 0.028 0.078 -10000 0 -0.3 23 23
Syndecan-3/IL8 0.002 0.084 -10000 0 -0.36 23 23
PSEN1 0.03 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.044 0.013 -10000 0 -10000 0 0
FYN 0.029 0.01 -10000 0 -0.065 1 1
limb bud formation -0.007 0.076 -10000 0 -0.36 21 21
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 -0.007 0.077 -10000 0 -0.37 21 21
neuron projection morphogenesis 0.015 0.087 0.16 107 -0.29 6 113
Syndecan-3/AgRP 0.013 0.083 -10000 0 -0.35 23 23
Syndecan-3/AgRP/MC4R 0.029 0.087 -10000 0 -0.35 23 23
Fyn/Cortactin 0.042 0.016 -10000 0 -0.051 1 1
SDC3 -0.007 0.077 -10000 0 -0.37 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.002 0.083 -10000 0 -0.35 23 23
IL8 0.011 0.04 -10000 0 -0.065 110 110
Syndecan-3/Fyn/Cortactin 0.029 0.08 -10000 0 -0.31 23 23
Syndecan-3/CASK -0.009 0.075 -10000 0 -0.34 23 23
alpha-MSH/MC4R 0.045 0.011 -10000 0 -0.051 1 1
Gamma Secretase 0.072 0.052 -10000 0 -0.08 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.008 0.049 -10000 0 -0.29 12 12
KLHL20 0.027 0.07 0.17 31 -0.18 17 48
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.005 0.041 0.16 12 -0.16 8 20
ENAH 0.006 0.052 -10000 0 -0.29 13 13
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 0.031 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.033 0.11 19 -0.12 7 26
ABI1/Sra1/Nap1 -0.011 0.024 -10000 0 -0.12 16 16
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.073 0.033 -10000 0 -0.053 11 11
RAPGEF1 -0.001 0.059 0.16 33 -0.27 10 43
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
regulation of calcium-dependent cell-cell adhesion 0.02 0.055 -10000 0 -0.3 13 13
CRK 0.005 0.06 0.17 25 -0.28 12 37
E-cadherin/gamma catenin/alpha catenin 0.058 0.026 -10000 0 -0.055 20 20
alphaE/beta7 Integrin 0.046 0.011 -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 0.035 0.018 -10000 0 -0.023 43 43
DLG1 0.006 0.052 -10000 0 -0.29 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.018 -10000 0 -0.084 17 17
MLLT4 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.017 -10000 0 -0.023 27 27
PI3K -0.036 0.022 -10000 0 -0.11 11 11
ARF6 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.042 0.022 -10000 0 -0.058 19 19
TIAM1 0.03 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.066 0.033 -10000 0 -0.048 18 18
AKT1 -0.016 0.036 0.15 7 -0.098 1 8
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.065 8 8
RhoA/GDP 0.011 0.06 0.17 28 -0.16 15 43
actin cytoskeleton organization 0.023 0.055 0.14 31 -0.14 17 48
CDC42/GDP 0.011 0.058 0.17 23 -0.16 15 38
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.026 -10000 0 -0.1 20 20
ITGB7 0.031 0.007 -10000 0 -0.065 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.071 0.036 -10000 0 -0.051 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.021 -10000 0 -0.032 27 27
mol:GDP -0.002 0.062 0.17 28 -0.18 15 43
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 0.024 0.064 0.18 33 -0.17 16 49
RAC1/GTP/IQGAP1 0.015 0.032 -10000 0 -0.041 90 90
PIP5K1C/AP1M1 0.022 0.006 -10000 0 -10000 0 0
RHOA 0.031 0.005 -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 0.014 0.04 0.11 27 -0.095 16 43
NME1 0 0 -10000 0 0 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.007 0.051 -10000 0 -0.29 13 13
regulation of cell-cell adhesion -0.029 0.017 0.043 2 -0.098 11 13
WASF2 -0.006 0.013 -10000 0 -0.065 18 18
Rap1/GTP -0.022 0.044 0.14 30 -0.13 3 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.082 0.043 -10000 0 -0.077 5 5
CCND1 0.016 0.047 0.13 26 -0.11 16 42
VAV2 0.01 0.12 -10000 0 -0.55 17 17
RAP1/GDP -0.011 0.051 0.16 32 -0.18 1 33
adherens junction assembly 0.006 0.052 -10000 0 -0.29 14 14
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 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 3 -0.08 5 8
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.15 6 6
mol:GTP 0 0 -10000 0 0 1 1
SRC 0.006 0.05 -10000 0 -0.29 12 12
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
Rac1/GTP -0.009 0.06 -10000 0 -0.28 18 18
E-cadherin/beta catenin/alpha catenin 0.06 0.021 -10000 0 -0.05 9 9
ITGAE 0.031 0.005 -10000 0 0 12 12
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.056 -10000 0 -0.3 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0.031 0.008 -9999 0 -0.065 2 2
SVIL 0.022 0.02 -9999 0 -0.065 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 0.031 0.005 -9999 0 -10000 0 0
PELP1 0.031 0.004 -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 0.031 0.004 -9999 0 -10000 0 0
MAK 0.029 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 -0.065 31 31
GSN 0.029 0.018 -9999 0 -0.065 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.03 0.008 -9999 0 -10000 0 0
DNA-PK 0.054 0.029 -9999 0 -0.052 22 22
NCOA4 0.024 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.005 -9999 0 -10000 0 0
cell proliferation 0.007 0.049 -9999 0 -0.42 6 6
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 0.012 0.028 -9999 0 -0.22 4 4
RANBP9 0.032 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 -10000 0 0
TGFB1I1 -0.049 0.036 -9999 0 -0.065 425 425
T-DHT/AR/CyclinD1 0.03 0.035 -9999 0 -0.041 87 87
XRCC6 0.03 0.008 -9999 0 -10000 0 0
T-DHT/AR 0.039 0.03 -9999 0 -0.045 13 13
CTDSP1 0.032 0.007 -9999 0 -0.065 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.031 0.01 -9999 0 -0.065 5 5
TCF4 0.03 0.007 -9999 0 -10000 0 0
CDKN2A 0.002 0.027 -9999 0 -0.066 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 0.042 0.019 -9999 0 -0.042 18 18
AR 0.031 0.015 -9999 0 -0.051 13 13
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 -0.036 8 8
RPS6KA3 0.032 0.005 -9999 0 -0.065 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 0.04 0.015 -9999 0 -0.037 1 1
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.025 0.025 -9999 0 -0.065 36 36
KLK2 0.004 0.019 -9999 0 -0.063 8 8
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 0.024 -9999 0 -0.16 5 5
CCND1 0.015 0.037 -9999 0 -0.065 90 90
PIAS1 0.032 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.01 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 0.024 -9999 0 -0.04 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.023 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 -0.066 343 343
FKBP4 0.032 0.006 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.029 0.011 -10000 0 -0.065 3 3
GNB1/GNG2 -0.031 0.025 -10000 0 -0.12 11 11
AKT1 -0.006 0.082 0.23 14 -0.25 26 40
EGF 0.031 0.007 -10000 0 -0.065 2 2
mol:TXA2 0 0 0.002 1 -10000 0 1
FGR -0.021 0.064 0.26 19 -0.15 4 23
mol:Ca2+ -0.008 0.075 0.26 10 -0.26 15 25
LYN -0.022 0.067 0.26 21 -0.15 4 25
RhoA/GTP -0.006 0.036 0.084 2 -0.11 9 11
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.019 0.077 0.28 11 -0.26 13 24
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.032 0.004 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.05 0.14 6 -0.26 9 15
G beta5/gamma2 -0.034 0.035 -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 0 418 418
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 14 -0.002 15 29
PTGDR 0.031 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.023 0.05 -10000 0 -0.23 9 9
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
ADRBK2 0.03 0.007 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.041 0.01 -10000 0 -10000 0 0
mol:GDP 0.003 0.08 0.28 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 0.024 0.014 -10000 0 -10000 0 0
mol:IP3 -0.012 0.086 0.29 9 -0.32 15 24
cell morphogenesis 0.041 0.01 -10000 0 -10000 0 0
PLCB2 -0.018 0.1 0.32 8 -0.43 15 23
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.019 0.066 0.26 21 -0.15 4 25
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.028 0.047 0.22 12 -0.16 3 15
RHOA 0.031 0.005 -10000 0 -10000 0 0
PTGIR 0.03 0.007 -10000 0 -10000 0 0
PRKCB1 -0.015 0.079 0.26 9 -0.3 14 23
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 0.31 9 -0.36 14 23
LCK -0.02 0.065 0.26 20 -0.15 4 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.028 0.038 0.19 3 -0.1 26 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 0.027 0.038 0.17 4 -0.1 27 31
MAPK14 -0.017 0.059 0.23 11 -0.18 12 23
TGM2/GTP -0.011 0.091 0.34 4 -0.35 15 19
MAPK11 -0.016 0.058 0.23 10 -0.18 13 23
ARHGEF1 -0.018 0.031 -10000 0 -0.15 8 8
GNAI2 0.031 0.005 -10000 0 -10000 0 0
JNK cascade -0.018 0.079 0.28 9 -0.28 14 23
RAB11/GDP 0.03 0.009 -10000 0 -0.03 8 8
ICAM1 -0.015 0.062 0.22 10 -0.2 17 27
cAMP biosynthetic process -0.012 0.082 0.29 9 -0.3 16 25
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 -0.025 0.047 0.22 12 -0.15 3 15
GNB5 0.031 0.006 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.078 0.26 29 -0.16 9 38
VCAM1 -0.021 0.064 0.23 9 -0.21 15 24
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.05 0.14 6 -0.26 9 15
platelet activation -0.018 0.077 0.3 11 -0.24 13 24
PGI2/IP 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.01 0.025 -10000 0 -0.085 32 32
Gq family/GDP/G beta5/gamma2 0.01 0.044 0.14 7 -0.2 15 22
TXA2/TP beta/beta Arrestin2 -0.005 0.049 -10000 0 -0.32 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.023 -10000 0 -0.095 35 35
mol:DAG -0.014 0.088 0.29 9 -0.33 15 24
EGFR 0.012 0.017 -10000 0 -0.065 5 5
TXA2/TP alpha -0.016 0.1 0.33 9 -0.39 16 25
Gq family/GTP 0.008 0.026 0.21 6 -0.21 2 8
YES1 -0.023 0.06 0.26 17 -0.16 4 21
GNAI2/GTP 0.016 0.036 0.083 1 -0.1 32 33
PGD2/DP 0.023 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.031 0.007 -10000 0 -0.065 2 2
FYN -0.017 0.065 0.26 21 -0.15 4 25
mol:NO 0.022 0.015 -10000 0 -10000 0 0
GNA15 0.03 0.013 -10000 0 -0.065 7 7
PGK/cGMP 0.025 0.021 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.009 -10000 0 -0.03 7 7
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.038 0.16 3 -0.1 26 29
NOS3 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.014 0.076 0.26 11 -0.28 13 24
PRKCB -0.013 0.075 0.26 9 -0.27 14 23
PRKCE -0.015 0.075 0.26 9 -0.27 14 23
PRKCD -0.017 0.078 0.26 11 -0.28 14 25
PRKCG -0.015 0.081 0.29 10 -0.3 14 24
muscle contraction -0.025 0.093 0.31 8 -0.35 15 23
PRKCZ -0.016 0.072 0.27 9 -0.25 14 23
ARR3 0.032 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.027 0.04 0.16 3 -0.1 33 36
PRKCQ -0.019 0.068 0.3 5 -0.28 14 19
MAPKKK cascade -0.02 0.091 0.29 9 -0.36 15 24
SELE -0.015 0.062 0.22 11 -0.2 16 27
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.038 0.18 3 -0.1 24 27
ROCK1 0.031 0.005 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
chemotaxis -0.03 0.094 0.33 6 -0.38 10 16
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA13 0.031 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 -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 -0.007 0.047 -10000 0 -0.065 201 201
NFKBIA -0.007 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 0.03 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.024 0.098 2 -0.11 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 0.031 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 0.007 0.038 -10000 0 -0.2 13 13
DLG7 0.005 0.009 0.095 2 -0.034 1 3
AURKAIP1 0.031 0.007 -10000 0 -10000 0 0
ARHGEF7 0.03 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 0.097 2 -0.11 8 10
AURKA 0.014 0.013 0.13 2 -0.042 1 3
AURKB 0.007 0.024 -10000 0 -0.097 17 17
CDC25B 0.011 0.019 0.097 2 -0.21 2 4
G2/M transition checkpoint 0.006 0.017 0.075 2 -0.1 8 10
mRNA polyadenylation 0.019 0.021 0.097 1 -0.11 5 6
Aurora A/CPEB 0.019 0.021 0.098 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 -10000 0 -0.19 8 8
negative regulation of DNA binding 0.007 0.038 -10000 0 -0.2 13 13
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 0.011 0.071 9 -10000 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.013 0.13 2 -0.042 1 3
TACC1 0.032 0.004 -10000 0 -10000 0 0
TACC3 0.014 0.037 -10000 0 -0.065 90 90
Aurora A/Antizyme1 0.048 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 0.06 0.018 -10000 0 -0.043 2 2
Importin alpha/Importin beta/TPX2 -0.035 0.017 -10000 0 -0.051 253 253
PPP2R5D 0.032 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 -0.025 0.021 -10000 0 -0.14 8 8
PAK1 0.032 0.004 -10000 0 -10000 0 0
CKAP5 0.031 0.005 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0 0.037 0.073 1 -0.1 58 59
regulation of axonogenesis 0.009 0.056 0.26 23 -10000 0 23
myoblast fusion -0.014 0.038 0.35 3 -10000 0 3
mol:GTP 0.011 0.047 -10000 0 -0.18 25 25
regulation of calcium-dependent cell-cell adhesion -0.024 0.039 0.12 21 -10000 0 21
ARF1/GTP 0.028 0.045 -10000 0 -0.14 24 24
mol:GM1 0 0.032 -10000 0 -0.13 25 25
mol:Choline -0.02 0.025 0.033 1 -0.13 22 23
lamellipodium assembly -0.004 0.059 -10000 0 -0.38 11 11
MAPK3 0.007 0.037 -10000 0 -0.12 25 25
ARF6/GTP/NME1/Tiam1 0.025 0.039 -10000 0 -0.12 21 21
ARF1 0.031 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.039 -10000 0 -0.35 3 3
ARF1/GDP 0.01 0.064 -10000 0 -0.24 24 24
ARF6 0.033 0.024 -10000 0 -0.039 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.028 0.013 -10000 0 -0.029 17 17
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.12 17 17
actin filament bundle formation -0.018 0.067 0.24 24 -10000 0 24
KALRN 0.001 0.043 -10000 0 -0.26 11 11
RAB11FIP3/RAB11A 0.046 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.067 -10000 0 -0.25 24 24
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.052 -10000 0 -0.24 13 13
substrate adhesion-dependent cell spreading 0.011 0.047 -10000 0 -0.18 25 25
cortical actin cytoskeleton organization -0.004 0.06 -10000 0 -0.38 11 11
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.011 0.047 -10000 0 -0.18 25 25
ARF6/GTP 0.011 0.047 -10000 0 -0.18 25 25
RhoA/GTP 0.028 0.045 -10000 0 -0.14 24 24
mol:GDP -0.007 0.057 -10000 0 -0.25 23 23
ARF6/GTP/RAB11FIP3/RAB11A 0.044 0.05 -10000 0 -0.13 25 25
RHOA 0.031 0.005 -10000 0 -10000 0 0
PLD1 0.006 0.037 -10000 0 -0.14 24 24
RAB11FIP3 0.032 0.003 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.059 -10000 0 -0.38 11 11
ruffle organization -0.009 0.056 -10000 0 -0.26 23 23
regulation of epithelial cell migration 0.011 0.047 -10000 0 -0.18 25 25
PLD2 0.007 0.036 -10000 0 -0.14 23 23
PIP5K1A -0.009 0.056 -10000 0 -0.26 23 23
mol:Phosphatidic acid -0.02 0.025 0.033 1 -0.13 22 23
Rac1/GTP -0.004 0.06 -10000 0 -0.38 11 11
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.007 0.014 -10000 0 -10000 0 0
FRAP1 0.043 0.061 0.22 5 -0.44 2 7
AKT1 0.038 0.083 0.16 138 -0.13 6 144
INSR 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.04 0.011 -10000 0 -10000 0 0
mol:GTP 0.041 0.09 0.17 139 -0.14 2 141
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.021 -10000 0 -0.17 1 1
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.004 0.044 0.11 51 -0.13 4 55
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 0.045 0.042 0.14 4 -0.19 1 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.014 -10000 0 -10000 0 0
RPS6KB1 0.055 0.071 0.2 35 -0.26 1 36
MAP3K5 -0.013 0.056 0.16 2 -0.2 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
apoptosis -0.013 0.056 0.16 2 -0.2 40 42
mol:LY294002 0 0 0.001 1 -0.001 2 3
EIF4B 0.048 0.069 0.19 40 -0.24 1 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.04 0.046 0.22 5 -10000 0 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 0.012 0.048 0.12 69 -10000 0 69
FKBP1A 0.03 0.01 -10000 0 -0.066 1 1
RHEB/GTP 0.036 0.053 0.18 21 -0.13 4 25
mol:Amino Acids 0 0 0.001 1 -0.001 2 3
FKBP12/Rapamycin 0.023 0.008 -10000 0 -0.041 1 1
PDPK1 -0.012 0.02 0.16 4 -10000 0 4
EIF4E 0.031 0.01 -10000 0 -0.065 5 5
ASK1/PP5C 0.014 0.16 -10000 0 -0.52 42 42
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.031 -10000 0 -0.24 4 4
TSC1/TSC2 0.046 0.098 0.19 140 -0.15 2 142
tumor necrosis factor receptor activity 0 0 0.001 2 -0.001 1 3
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 0.021 0.016 -10000 0 -0.064 2 2
PDK2 -0.012 0.02 0.16 4 -10000 0 4
EIF4EBP1 -0.034 0.094 -10000 0 -0.97 3 3
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
PPP2R5D 0.036 0.059 0.22 6 -0.4 2 8
peptide biosynthetic process -0.022 0.013 0.18 2 -10000 0 2
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.029 0.014 -10000 0 -0.065 10 10
mol:Rapamycin 0 0.001 0.003 72 -0.003 1 73
EEF2 -0.022 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.024 0.095 -10000 0 -0.91 3 3
S1P5 pathway

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.04 0.13 33 -10000 0 33
GNAI2 0.031 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 0 154 154
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.041 -10000 0 -0.13 33 33
negative regulation of cAMP metabolic process 0.002 0.013 0.082 7 -0.11 2 9
GNAZ 0.026 0.012 -10000 0 -10000 0 0
GNAI3 0.02 0.031 -10000 0 -0.065 59 59
GNA12 0.022 0.015 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.013 0.083 7 -0.11 2 9
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.031 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.048 0.21 10 -0.22 6 16
FYN 0.002 0.052 0.19 5 -0.24 8 13
LAT/GRAP2/SLP76 0.023 0.049 0.2 3 -0.24 6 9
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.053 0.16 9 -0.22 10 19
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.009 0.024 0.086 13 -0.087 4 17
MAP3K8 0.018 0.027 -10000 0 -0.065 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.039 1 1
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.003 0.061 0.18 9 -0.26 10 19
TRPV6 0.38 0.59 1.3 155 -10000 0 155
CD28 0.032 0.001 -10000 0 -10000 0 0
SHC1 0.008 0.05 0.24 9 -0.26 5 14
receptor internalization 0.015 0.046 -10000 0 -0.36 5 5
PRF1 -0.12 0.27 -10000 0 -0.6 122 122
KRAS 0.03 0.008 -10000 0 -10000 0 0
GRB2 0.031 0.006 -10000 0 -10000 0 0
COT/AKT1 0.008 0.049 0.17 5 -0.19 10 15
LAT 0.008 0.046 0.19 5 -0.27 6 11
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 -0.067 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 0.083 0.21 11 -0.24 17 28
HLA-A 0.032 0.005 -10000 0 -0.066 1 1
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.039 0.13 17 -0.093 10 27
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.026 -10000 0 -0.11 12 12
PRKCA -0.011 0.039 0.16 5 -0.16 4 9
GRAP2 0.03 0.008 -10000 0 -10000 0 0
mol:IP3 0.005 0.041 -10000 0 -0.2 7 7
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.011 0.032 -10000 0 -0.25 4 4
ORAI1 -0.33 0.5 -10000 0 -1.1 155 155
CSK 0.009 0.045 0.19 5 -0.27 6 11
B7 family/CD28 0.05 0.056 0.22 4 -0.27 4 8
CHUK 0.024 0.014 -10000 0 -0.065 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.013 0.045 -10000 0 -0.29 6 6
PTPN6 0.004 0.045 0.17 10 -0.26 6 16
VAV1 0.012 0.054 0.19 17 -0.27 6 23
Monovalent TCR/CD3 0.014 0.026 -10000 0 -0.18 6 6
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.005 0.05 0.19 7 -0.24 6 13
PAG1 0.011 0.044 0.21 2 -0.26 6 8
RAP1A 0.032 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.012 0.044 0.14 1 -0.28 6 7
CD80 0.031 0.007 -10000 0 -0.067 1 1
CD86 0.027 0.021 -10000 0 -0.066 24 24
PDK1/CARD11/BCL10/MALT1 0.002 0.031 -10000 0 -0.12 11 11
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 0 0.039 0.15 6 -0.24 4 10
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.066 2 2
PTPRC 0.008 0.042 -10000 0 -0.065 122 122
PDK1/PKC theta -0.003 0.059 0.19 13 -0.27 6 19
CSK/PAG1 0.006 0.041 0.16 2 -0.25 6 8
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.046 0.01 -10000 0 -0.051 1 1
GRAP2/SLP76 0.034 0.054 0.2 4 -0.27 6 10
STIM1 -0.066 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.008 0.046 0.14 9 -0.15 19 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.015 0.048 -10000 0 -0.37 5 5
mol:DAG -0.02 0.025 -10000 0 -0.18 7 7
RAP1A/GDP 0 0.021 0.063 15 -0.046 8 23
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.031 0.008 -10000 0 -0.07 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 122 122
RAP1A/GTP 0.003 0.007 -10000 0 -0.056 4 4
mol:PI-3-4-5-P3 0.004 0.055 0.17 9 -0.24 8 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.013 0.05 -10000 0 -0.24 6 6
NRAS 0.008 0.042 -10000 0 -0.065 125 125
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 0.05 0.18 10 -0.24 6 16
MALT1 0.027 0.02 -10000 0 -0.035 37 37
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.022 14 14
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.018 -10000 0 -0.13 7 7
PRKCE -0.011 0.039 0.16 5 -0.16 4 9
PRKCQ 0 0.061 0.2 12 -0.26 9 21
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 0.049 0.15 9 -0.2 10 19
IKK complex -0.006 0.03 0.14 6 -0.085 4 10
RAS family/GDP -0.006 0.01 -10000 0 -0.031 8 8
MAP3K14 -0.002 0.037 0.12 7 -0.16 10 17
PDPK1 -0.001 0.049 0.15 10 -0.2 10 20
TCR/CD3/MHC I/CD8/Fyn 0.015 0.051 -10000 0 -0.36 5 5
Class I PI3K signaling events

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
ARF5/GTP -0.019 0.032 0.15 9 -10000 0 9
DAPP1 0.004 0.061 0.15 24 -0.24 10 34
Src family/SYK family/BLNK-LAT/BTK-ITK -0.002 0.07 0.32 1 -0.27 14 15
mol:DAG -0.001 0.057 0.22 13 -0.15 2 15
HRAS 0.035 0.01 0.078 2 -10000 0 2
RAP1A 0.035 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.017 0.056 0.15 2 -0.22 18 20
PLCG2 0.029 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 -0.02 0.041 0.17 14 -10000 0 14
ARF1/GTP -0.013 0.032 0.15 11 -0.11 1 12
RHOA 0.031 0.005 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.065 74 74
RAP1A/GTP -0.021 0.032 0.15 10 -10000 0 10
ADAP1 -0.02 0.036 0.16 12 -10000 0 12
ARAP3 -0.02 0.041 0.17 14 -10000 0 14
INPPL1 0.032 0.004 -10000 0 0 8 8
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.03 0.012 -10000 0 -0.065 7 7
ARHGEF7 0.03 0.007 -10000 0 -10000 0 0
ARF1 0.031 0.006 -10000 0 -10000 0 0
NRAS 0.012 0.042 0.063 1 -0.06 124 125
FYN 0.029 0.01 -10000 0 -0.065 1 1
ARF6 0.031 0.007 -10000 0 -10000 0 0
FGR 0.028 0.017 -10000 0 -0.065 15 15
mol:Ca2+ 0.001 0.043 0.13 35 -10000 0 35
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.03 0.008 -10000 0 -10000 0 0
ZAP70 0.032 0.002 -10000 0 -10000 0 0
mol:IP3 -0.003 0.049 0.15 31 -10000 0 31
LYN 0.02 0.031 -10000 0 -0.065 60 60
ARF1/GDP 0.029 0.066 0.2 2 -0.21 23 25
RhoA/GDP 0.04 0.066 0.17 28 -0.12 5 33
PDK1/Src/Hsp90 0.057 0.022 -10000 0 -0.043 2 2
BLNK 0.013 0.032 -10000 0 -0.065 60 60
actin cytoskeleton reorganization 0.031 0.081 0.16 94 -0.16 7 101
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 0.022 0.02 -10000 0 -0.038 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.043 0.18 14 -10000 0 14
RhoA/GTP -0.022 0.043 0.18 14 -10000 0 14
Src family/SYK family/BLNK-LAT -0.02 0.068 -10000 0 -0.2 39 39
BLK 0.031 0.005 -10000 0 -10000 0 0
PDPK1 0.032 0.003 -10000 0 -10000 0 0
CYTH1 -0.02 0.036 0.16 12 -10000 0 12
HCK 0.014 0.036 -10000 0 -0.065 84 84
CYTH3 -0.02 0.036 0.16 12 -10000 0 12
CYTH2 -0.02 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 0.028 0.3 1 -0.17 7 8
SGK1 0.001 0.028 -10000 0 -0.17 10 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.065 0.15 10 -0.22 23 33
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.025 -10000 0 -0.065 35 35
ARF6/GDP -0.017 0.043 0.19 13 -0.13 2 15
mol:PI-3-4-5-P3 -0.022 0.032 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.021 0.032 0.15 10 -10000 0 10
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 0.062 0.083 0.2 104 -0.071 4 108
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.057 0.17 4 -0.22 19 23
LAT 0.032 0.005 -10000 0 -0.065 1 1
Rac1/GTP 0.023 0.061 0.16 1 -0.24 18 19
ITK -0.024 0.038 0.16 12 -10000 0 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.006 0.062 0.25 9 -0.17 4 13
LCK 0.031 0.01 -10000 0 -0.065 4 4
BTK -0.023 0.041 0.16 14 -10000 0 14
Regulation of Telomerase

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
Telomerase catalytic core complex 0.02 0.085 0.25 1 -0.39 7 8
RAD9A 0.032 0.006 -10000 0 -0.065 1 1
AP1 0.021 0.042 -10000 0 -0.051 117 117
IFNAR2 0.031 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.015 -10000 0 -0.054 20 20
ER alpha/Oestrogen 0.022 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.051 -10000 0 -0.15 45 45
EGF 0.031 0.007 -10000 0 -0.065 2 2
SMG5 0.031 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.004 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.035 -10000 0 -0.053 66 66
TERT/c-Abl 0.033 0.087 -10000 0 -0.37 7 7
SAP18 0.03 0.008 -10000 0 -10000 0 0
MRN complex 0.062 0.014 -10000 0 -10000 0 0
WT1 0.031 0.011 -10000 0 -0.067 5 5
WRN 0.031 0.01 -10000 0 -0.065 4 4
SP1 0.031 0.006 -10000 0 -0.026 1 1
SP3 0.018 0.035 -10000 0 -0.066 74 74
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.34 9 9
Mad/Max 0.045 0.011 -10000 0 -10000 0 0
TERT 0.02 0.086 0.25 1 -0.4 7 8
CCND1 0.01 0.087 -10000 0 -0.41 6 6
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.037 -10000 0 -0.065 89 89
TERF2 -0.02 0.019 0.046 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.043 0.061 -10000 0 -0.33 6 6
CDKN1B -0.025 0.011 -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 0.008 -10000 0 -10000 0 0
SAP30 0.031 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.018 -10000 0 -10000 0 0
UBE3A 0.031 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 0.036 0.035 -10000 0 -0.051 62 62
PARP2 0.03 0.008 -10000 0 -10000 0 0
BLM 0.009 0.041 -10000 0 -0.065 119 119
Telomerase 0.007 0.064 -10000 0 -0.24 29 29
IRF1 0.02 0.033 -10000 0 -0.065 66 66
ESR1 0.03 0.008 -10000 0 -10000 0 0
KU/TER 0.044 0.012 -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 35 35
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.003 0.053 -10000 0 -0.16 34 34
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.029 0.012 -10000 0 -0.059 5 5
ATM 0.012 0.018 0.091 6 -0.054 25 31
SMAD3 -0.023 0.008 -10000 0 -0.051 26 26
ABL1 0.031 0.008 -10000 0 -0.065 1 1
MXD1 0.032 0.001 -10000 0 -10000 0 0
MRE11A 0.032 0.004 -10000 0 -10000 0 0
HUS1 0.022 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 -0.38 15 15
NR2F2 0.031 0.009 -10000 0 -0.063 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 -0.065 26 26
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
HNRNPC 0.03 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 -0.054 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.017 -10000 0 -0.065 5 5
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.017 0.024 -10000 0 -0.051 7 7
MYC 0.008 0.041 -10000 0 -0.065 119 119
IL2 0.032 0.005 -10000 0 -0.026 1 1
KU 0.044 0.012 -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 -0.065 26 26
TRF2/BLM 0.017 0.042 -10000 0 -0.055 114 114
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.096 -10000 0 -0.38 7 7
SP1/HDAC2 0.043 0.017 -10000 0 -0.055 4 4
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.097 -10000 0 -0.34 10 10
Smad3/Myc 0.006 0.036 -10000 0 -0.051 137 137
911 complex 0.044 0.031 -10000 0 -0.046 4 4
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.035 0.089 -10000 0 -0.34 9 9
Telomerase/AKT1/mTOR/p70S6K 0.01 0.092 0.17 1 -0.3 33 34
SIN3B 0.031 0.007 -10000 0 0 22 22
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.046 0.095 -10000 0 -0.34 9 9
response to DNA damage stimulus 0.003 0.013 -10000 0 -0.1 5 5
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.039 0.018 -10000 0 -0.053 4 4
Telomerase/hnRNP C1/C2 0.045 0.097 -10000 0 -0.35 9 9
E2F1 0.03 0.008 -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
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.009 0.076 0.23 7 -0.26 12 19
IKBKB 0.016 0.057 0.25 5 -0.26 6 11
AKT1 0.015 0.074 0.22 36 -0.16 1 37
IKBKG 0.013 0.048 0.22 5 -0.22 6 11
CALM1 -0.009 0.048 0.2 2 -0.19 10 12
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
MAP3K1 0.032 0.091 0.27 16 -0.39 7 23
MAP3K7 0.03 0.008 -10000 0 -0.065 1 1
mol:Ca2+ -0.006 0.053 0.22 1 -0.18 17 18
DOK1 0.032 0.001 -10000 0 -10000 0 0
AP-1 -0.007 0.057 0.17 5 -0.19 11 16
LYN 0.02 0.031 -10000 0 -0.065 60 60
BLNK 0.013 0.032 -10000 0 -0.065 60 60
SHC1 0.024 0.026 -10000 0 -0.065 40 40
BCR complex 0.044 0.014 -10000 0 -0.065 2 2
CD22 -0.008 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 -0.099 25 25
GO:0007205 -0.006 0.054 0.22 1 -0.18 17 18
SYK 0.025 0.025 -10000 0 -0.065 35 35
ELK1 -0.013 0.052 0.2 1 -0.19 12 13
NFATC1 -0.017 0.061 0.22 8 -0.21 17 25
B-cell antigen/BCR complex 0.044 0.014 -10000 0 -0.065 2 2
PAG1/CSK 0.023 0.003 -10000 0 -10000 0 0
NFKBIB 0.02 0.032 0.14 3 -0.12 14 17
HRAS -0.013 0.052 0.19 4 -0.17 17 21
NFKBIA 0.021 0.031 0.13 4 -0.12 14 18
NF-kappa-B/RelA/I kappa B beta 0.024 0.028 0.13 4 -0.096 14 18
RasGAP/Csk 0.05 0.066 -10000 0 -0.092 2 2
mol:GDP -0.005 0.054 0.22 1 -0.18 17 18
PTEN 0.022 0.016 -10000 0 -0.065 2 2
CD79B 0.032 0.006 -10000 0 -0.065 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.028 0.13 4 -0.093 14 18
GRB2 0.031 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.007 0.077 0.3 3 -0.3 4 7
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 -0.006 0.053 0.22 1 -0.18 18 19
CSK 0.032 0.004 -10000 0 -10000 0 0
FOS -0.02 0.051 0.17 2 -0.2 9 11
CHUK -0.044 0.12 0.23 4 -0.25 115 119
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.071 -10000 0 -0.18 13 13
PTPN6 -0.019 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 -0.014 0.059 0.16 3 -0.27 17 20
ubiquitin-dependent protein catabolic process 0.022 0.032 0.14 3 -0.12 14 17
BTK 0.015 0.012 -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 0.029 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.083 0.25 16 -0.34 7 23
SH3BP5 0.029 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.006 0.052 -10000 0 -0.18 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.059 -10000 0 -0.27 15 15
RAF1 -0.017 0.051 0.2 4 -0.19 9 13
RasGAP/p62DOK/SHIP 0.041 0.057 -10000 0 -0.081 2 2
CD79A 0.03 0.009 -10000 0 -0.065 2 2
re-entry into mitotic cell cycle -0.007 0.057 0.17 4 -0.19 11 15
RASA1 0.031 0.006 -10000 0 -10000 0 0
MAPK3 -0.024 0.05 0.18 5 -0.21 5 10
MAPK1 -0.022 0.05 0.2 7 -0.21 4 11
CD72/SHP1 0.006 0.064 0.22 27 -0.3 1 28
NFKB1 0.031 0.01 -10000 0 -0.065 4 4
MAPK8 0.023 0.081 0.25 15 -0.34 7 22
actin cytoskeleton organization 0.029 0.091 0.2 50 -0.25 9 59
NF-kappa-B/RelA 0.047 0.055 0.24 4 -0.19 13 17
Calcineurin 0.009 0.065 0.2 1 -0.19 10 11
PI3K -0.029 0.048 -10000 0 -0.19 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0 0.043 -10000 0 -0.22 5 5
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.035 0.078 -10000 0 -0.57 6 6
DAPP1 0.018 0.074 -10000 0 -0.64 5 5
cytokine secretion -0.016 0.058 0.21 9 -0.2 17 26
mol:DAG -0.006 0.053 0.22 1 -0.18 18 19
PLCG2 0.029 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 0.2 11 -0.21 1 12
ETS1 0.02 0.065 0.18 13 -0.21 3 16
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.027 0.073 -10000 0 -0.093 18 18
B-cell antigen/BCR complex/LYN 0.005 0.036 -10000 0 -0.24 2 2
MALT1 0.027 0.02 -10000 0 -0.065 20 20
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.089 0.19 47 -0.26 9 56
B-cell antigen/BCR complex/LYN/SYK 0.042 0.063 0.22 17 -0.3 1 18
CARD11 -0.007 0.052 0.21 1 -0.18 17 18
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 0.004 0.035 0.14 7 -0.12 8 15
PTPRC 0.008 0.041 -10000 0 -0.065 122 122
PDPK1 -0.015 0.052 0.2 15 -0.16 1 16
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.031 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.02 0.13 4 -0.068 10 14
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.031 0.007 -10000 0 -0.065 2 2
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.019 0.027 -10000 0 -0.079 32 32
GNAO1 0.003 0.009 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.029 0.02 -10000 0 -0.023 2 2
AKT1 -0.007 0.068 -10000 0 -0.44 12 12
AKT3 -0.007 0.044 -10000 0 -0.28 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.031 0.007 -10000 0 -0.065 2 2
GNAI2 0.032 0.006 -10000 0 -0.028 1 1
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 0 -10000 0 -10000 0 0
S1PR3 0.001 0 -10000 0 -0.009 1 1
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.013 -10000 0 -0.12 1 1
MAPK3 0.001 0.012 -10000 0 -0.12 1 1
MAPK1 0.001 0.01 -10000 0 -10000 0 0
JAK2 -0.004 0.03 -10000 0 -0.16 16 16
CXCR4 0 0.009 -10000 0 -0.12 1 1
FLT1 0.031 0.009 -10000 0 -0.029 1 1
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.001 0.011 -10000 0 -0.11 2 2
S1P/S1P3/Gi 0.002 0.013 -10000 0 -0.12 1 1
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.041 -10000 0 -0.14 24 24
VEGFA -0.02 0.048 -10000 0 -0.064 276 276
S1P/S1P2/Gi 0.002 0.013 0.085 7 -0.11 2 9
VEGFR1 homodimer/VEGFA homodimer -0.004 0.048 -10000 0 -0.05 256 256
RHOA 0.031 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.016 0.009 -10000 0 -0.1 1 1
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
G12/G13 0.033 0.022 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA13 0.031 0.007 -10000 0 -0.065 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.036 -10000 0 -0.13 16 16
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.004 0.034 -10000 0 -0.12 21 21
NT3 (dimer)/TRKC 0.044 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.05 0.031 -10000 0 -0.05 18 18
SHC/Grb2/SOS1/GAB1/PI3K 0.012 0.024 -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 0.016 0.034 -10000 0 -0.065 72 72
NTRK1 0.031 0.005 -10000 0 -10000 0 0
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 -0.041 18 18
neuron apoptosis 0.03 0.055 0.18 9 -0.15 1 10
SHC 2-3/Grb2 -0.031 0.058 -10000 0 -0.2 9 9
SHC1 0.024 0.026 -10000 0 -0.065 40 40
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 -0.07 99 99
NT3 (dimer)/TRKA 0.057 0.027 -10000 0 -0.05 19 19
RIN/GDP 0.004 0.04 0.13 5 -0.15 10 15
GIPC1 0.031 0.006 -10000 0 -10000 0 0
KRAS 0.03 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 -0.096 93 93
MAGED1 0.032 0.003 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -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 -0.041 40 40
GRB2 0.031 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.041 0.01 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.045 0.011 -10000 0 -10000 0 0
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 0.014 -10000 0 -10000 0 0
GAB2 0.031 0.005 -10000 0 -10000 0 0
RIT2 0.017 0.017 -10000 0 -0.065 2 2
RIT1 0.003 0.044 -10000 0 -0.065 151 151
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 0.006 0.012 -10000 0 0 418 418
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.022 -10000 0 -10000 0 0
mol:GDP -0.003 0.068 0.21 11 -0.21 18 29
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.012 -10000 0 -10000 0 0
RIT1/GDP -0.002 0.052 0.15 10 -0.15 20 30
TIAM1 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.029 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 0.061 0.016 -10000 0 -0.043 2 2
SHC/GRB2/SOS1/GAB1 0.049 0.033 -10000 0 -0.043 47 47
RIT1/GTP 0.004 0.029 -10000 0 -0.04 151 151
NT3 (dimer) 0.031 0.006 -10000 0 -10000 0 0
RAP1/GDP -0.002 0.039 -10000 0 -0.12 22 22
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 -10000 0 0
Schwann cell development -0.002 0.006 -10000 0 -0.033 1 1
EHD4 0.025 0.024 -10000 0 -0.065 31 31
FRS2 family/GRB2/SOS1 0.057 0.019 -10000 0 -0.038 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.036 0.09 25 -0.12 22 47
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 0.036 -10000 0 -0.21 12 12
STAT3 0.016 0.043 -10000 0 -0.07 99 99
axon guidance -0.008 0.018 0.039 2 -10000 0 2
MAPK3 -0.012 0.046 0.18 28 -10000 0 28
MAPK1 -0.013 0.041 0.18 22 -10000 0 22
CDC42/GDP 0.006 0.053 0.15 9 -0.15 16 25
NTF3 0.031 0.006 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.018 -10000 0 -0.041 19 19
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 -0.009 0.017 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 0.029 0.009 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.01 0.056 0.21 2 -0.26 11 13
Rac1/GDP 0.005 0.043 0.17 8 -0.14 9 17
NGF (dimer)/TRKA/GRIT 0.021 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis 0.013 0.08 -10000 0 -0.72 5 5
NGF (dimer)/TRKA/NEDD4-2 0.041 0.01 -10000 0 -10000 0 0
MAP2K1 -0.02 0.043 0.17 23 -10000 0 23
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 0.002 0.035 -10000 0 -0.12 26 26
FRS2 family/SHP2/GRB2/SOS1 0.069 0.024 -10000 0 -10000 0 0
NRAS 0.008 0.042 -10000 0 -0.065 125 125
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
PRKCI 0.031 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 0.044 0.013 -10000 0 -0.051 1 1
SQSTM1 0.031 0.007 -10000 0 -0.065 1 1
BDNF (dimer)/TRKB/GIPC 0.013 0.034 -10000 0 -10000 0 0
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.018 -10000 0 -0.04 2 2
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 -0.1 33 33
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 0.082 0.04 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.021 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.005 0.083 0.2 7 -0.32 28 35
CDKN1A -0.011 0.082 -10000 0 -0.33 30 30
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.02 -10000 0 -0.065 21 21
FOXO3 -0.004 0.077 0.2 4 -0.33 24 28
AKT1 -0.001 0.086 -10000 0 -0.34 29 29
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 0.081 -10000 0 -0.33 29 29
AKT1/ASK1 0.014 0.087 -10000 0 -0.31 32 32
BAD/YWHAZ 0.06 0.018 -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 0.085 0.3 32 -10000 0 32
TSC1 -0.01 0.084 0.19 2 -0.33 31 33
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.091 -10000 0 -0.32 32 32
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.001 0.085 -10000 0 -0.33 29 29
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.01 0.083 -10000 0 -0.32 31 31
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 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle 0.013 0.052 0.19 20 -0.14 1 21
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.002 0.081 -10000 0 -0.32 29 29
CASP9 -0.008 0.085 0.2 4 -0.33 31 35
YWHAB 0.03 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.013 0.09 0.22 9 -0.31 31 40
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.057 0.022 -10000 0 -0.043 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 0.077 0.23 1 -0.29 32 33
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.029 -10000 0 -0.14 2 2
CHUK -0.004 0.063 -10000 0 -0.34 17 17
BAD/BCL-XL 0.013 0.087 -10000 0 -0.32 30 30
mTORC2 0.02 0.004 -10000 0 -10000 0 0
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.025 0.078 -10000 0 -0.28 30 30
PDPK1 0.032 0.003 -10000 0 -10000 0 0
MDM2 0.007 0.096 0.2 41 -0.32 28 69
MAPKKK cascade -0.016 0.089 0.32 32 -10000 0 32
MDM2/Cbp/p300 0.039 0.1 0.22 44 -0.31 29 73
TSC1/TSC2 -0.01 0.09 0.23 13 -0.32 31 44
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.099 0.21 44 -0.3 29 73
glucose import -0.01 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.052 -10000 0 -0.18 31 31
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 0.074 -10000 0 -0.32 24 24
GSK3B -0.007 0.084 0.2 4 -0.32 30 34
SFN 0.025 0.024 -10000 0 -0.065 31 31
G1/S transition of mitotic cell cycle -0.01 0.091 0.22 16 -0.32 31 47
p27Kip1/14-3-3 family 0.007 0.03 -10000 0 -0.25 4 4
PRKACA 0.031 0.006 -10000 0 -10000 0 0
KPNA1 0.031 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 0.003 -10000 0 0 6 6
Signaling events mediated by HDAC Class III

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
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 0.041 0.065 119 -0.074 46 165
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.029 0.013 -10000 0 -0.065 6 6
FOXO3 0 0.011 0.027 75 -10000 0 75
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 0.008 -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 0.031 0.008 -10000 0 -0.024 8 8
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 -0.037 114 114
SIRT1/Histone H1b 0.023 0.027 -10000 0 -0.13 9 9
apoptosis -0.037 0.046 0.046 38 -10000 0 38
SIRT1/PGC1A 0.033 0.02 -10000 0 -0.042 3 3
p53/SIRT1 0.031 0.035 0.1 37 -0.057 30 67
SIRT1/FOXO4 0.024 0.023 -10000 0 -0.12 7 7
FOXO1/FHL2/SIRT1 0.035 0.043 -10000 0 -0.043 28 28
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 0.019 0.033 -10000 0 -0.064 65 65
KU70/SIRT1/BAX 0.038 0.046 -10000 0 -0.046 38 38
CREBBP 0.032 0.003 -10000 0 0 6 6
MEF2D 0.031 0.005 -10000 0 0 12 12
HIV-1 Tat/SIRT1 0.037 0.021 -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
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.023 0.03 -10000 0 -0.13 23 23
epithelial cell differentiation 0.06 0.031 -10000 0 -0.047 18 18
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
ENAH -0.045 0.052 0.41 4 -10000 0 4
EGFR 0.012 0.017 -10000 0 -0.065 5 5
EPHA2 0.029 0.016 -10000 0 -0.065 12 12
MYO6 -0.03 0.029 0.16 10 -10000 0 10
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.029 0.032 -10000 0 -10000 0 0
AQP5 -0.013 0.043 -10000 0 -0.31 7 7
CTNND1 0.03 0.014 -10000 0 -0.065 10 10
mol:PI-4-5-P2 -0.03 0.023 0.16 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.028 0.029 0.16 10 -10000 0 10
EGF 0.031 0.007 -10000 0 -0.065 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.078 -10000 0 -0.32 32 32
cortical microtubule organization 0.06 0.031 -10000 0 -0.047 18 18
GO:0000145 -0.028 0.021 0.15 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.066 0.033 -10000 0 -0.047 18 18
MLLT4 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP -0.053 0.016 -10000 0 -0.1 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.066 0.042 -10000 0 -0.056 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.023 0.16 2 -0.19 1 3
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.025 0.027 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.05 -10000 0 -0.075 7 7
CDH1 0.03 0.013 -10000 0 -0.065 8 8
EGFR/EGFR/EGF/EGF 0.019 0.034 -10000 0 -10000 0 0
RhoA/GDP 0.061 0.033 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.026 0.14 8 -10000 0 8
IGF-1R heterotetramer 0.032 0.003 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
IGF1R 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.031 0.009 -10000 0 -0.065 4 4
DIAPH1 -0.21 0.26 -10000 0 -0.45 267 267
Wnt receptor signaling pathway -0.06 0.031 0.047 18 -10000 0 18
RHOA 0.031 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.016 -10000 0 -0.1 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.027 0.14 8 -10000 0 8
EFNA1 0.027 0.02 -10000 0 -0.065 21 21
LPP -0.035 0.023 0.15 5 -10000 0 5
Ephrin A1/EPHA2 0.046 0.041 -10000 0 -0.073 8 8
SEC6/SEC8 -0.043 0.011 -10000 0 -10000 0 0
MGAT3 -0.029 0.029 0.16 10 -10000 0 10
HGF/MET 0.035 0.037 -10000 0 -0.073 1 1
HGF 0.022 0.015 -10000 0 -0.065 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.023 0.03 -10000 0 -0.13 23 23
actin cable formation -0.038 0.075 0.34 10 -0.22 10 20
KIAA1543 -0.024 0.022 0.15 8 -10000 0 8
KIFC3 -0.031 0.024 0.16 7 -10000 0 7
NCK1 0.029 0.015 -10000 0 -0.065 11 11
EXOC3 0.031 0.006 -10000 0 -10000 0 0
ACTN1 -0.031 0.027 0.16 8 -10000 0 8
NCK1/GIT1 0.044 0.017 -10000 0 -0.051 11 11
mol:GDP 0.06 0.031 -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 -0.03 0.023 0.16 6 -10000 0 6
LIMA1 -0.05 0.035 -10000 0 -0.065 425 425
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.041 0.066 0.41 7 -10000 0 7
adherens junction assembly -0.023 0.042 0.21 5 -0.2 9 14
IGF-1R heterotetramer/IGF1 0.052 0.034 -10000 0 -0.073 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.015 -10000 0 -10000 0 0
MET 0.021 0.016 -10000 0 -0.065 2 2
PLEKHA7 -0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0.064 0.041 -10000 0 -0.056 33 33
establishment of epithelial cell apical/basal polarity -0.04 0.042 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.023 0.03 -10000 0 -0.13 23 23
regulation of cell-cell adhesion -0.024 0.026 0.14 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.023 0.03 -10000 0 -0.13 23 23
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.07 0.22 32 -0.3 5 37
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -0.053 34 34
PDGFB-D/PDGFRB/APS/CBL 0.042 0.009 -10000 0 -0.041 2 2
AKT1 -0.019 0.079 0.3 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.074 0.23 34 -0.34 5 39
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FGR 0.009 0.063 0.35 1 -0.37 7 8
mol:Ca2+ 0.024 0.071 0.22 30 -0.38 5 35
MYC 0.046 0.12 0.3 42 -0.34 3 45
SHC1 0.024 0.026 -10000 0 -0.065 40 40
HRAS/GDP -0.016 0.054 0.17 37 -10000 0 37
LRP1/PDGFRB/PDGFB 0.054 0.029 -10000 0 -0.047 22 22
GRB10 0.021 0.018 -10000 0 -0.065 6 6
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.22 30 -0.38 5 35
PTEN 0.022 0.016 -10000 0 -0.065 2 2
GRB2 0.031 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PDGFB-D/PDGFRB/SHP2 0.046 0.01 -10000 0 -0.051 2 2
PDGFB-D/PDGFRB/GRB10 0.03 0.025 -10000 0 -0.052 8 8
cell cycle arrest 0.039 0.027 -10000 0 -0.053 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.023 0.072 0.28 13 -10000 0 13
GAB1 0.019 0.076 0.24 23 -0.31 9 32
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.083 0.24 37 -0.26 9 46
PDGFB-D/PDGFRB 0.054 0.026 -10000 0 -0.051 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.046 0.011 -10000 0 -0.051 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.053 0.2 10 -0.25 5 15
positive regulation of MAPKKK cascade 0.046 0.01 -10000 0 -0.051 2 2
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.072 0.22 30 -0.38 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 0.046 0.011 -10000 0 -0.051 3 3
SHB 0.03 0.009 -10000 0 -10000 0 0
BLK 0.009 0.058 0.34 1 -0.37 7 8
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.046 0.01 -10000 0 -0.051 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.016 0.084 0.25 25 -0.31 9 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 0.2 18 -0.35 5 23
PDGFRB 0.032 0.009 -10000 0 -0.047 4 4
ACP1 0.031 0.005 -10000 0 -10000 0 0
HCK 0 0.035 0.17 5 -10000 0 5
ABL1 0.02 0.073 0.21 32 -0.25 9 41
PDGFB-D/PDGFRB/CBL 0.023 0.079 0.26 13 -0.35 9 22
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 0.045 0.11 0.29 43 -0.31 3 46
SLA 0.025 0.024 -10000 0 -0.065 33 33
actin cytoskeleton reorganization -0.017 0.066 0.2 40 -10000 0 40
SRC 0.01 0.043 0.18 1 -0.73 1 2
PI3K -0.043 0.021 -10000 0 -0.092 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.053 0.035 -10000 0 -0.05 46 46
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.076 0.23 34 -0.35 5 39
LYN 0.004 0.041 0.18 3 -0.35 1 4
LRP1 0.028 0.017 -10000 0 -0.065 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.003 -10000 0 -10000 0 0
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
NCK1-2/p130 Cas 0.065 0.038 -10000 0 -10000 0 0
SPHK1 0.029 0.019 -10000 0 -0.066 18 18
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.024 0.072 0.22 30 -0.38 5 35
PLCG1 0.024 0.073 0.22 30 -0.39 5 35
NHERF/PDGFRB 0.062 0.018 -10000 0 -0.043 9 9
YES1 -0.005 0.09 0.19 9 -0.55 10 19
cell migration 0.061 0.017 -10000 0 -0.043 9 9
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.074 2 2
SLC9A3R2 0.032 0.003 -10000 0 -10000 0 0
SLC9A3R1 0.031 0.007 -10000 0 -0.065 2 2
NHERF1-2/PDGFRB/PTEN 0.041 0.057 -10000 0 -0.057 2 2
FYN -0.02 0.11 -10000 0 -0.37 44 44
DOK1 -0.015 0.053 0.17 39 -10000 0 39
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.056 0.12 0.25 102 -0.4 4 106
PRKCD -0.015 0.054 0.17 38 -10000 0 38
FER -0.016 0.054 0.17 37 -10000 0 37
MAPKKK cascade -0.011 0.072 0.18 57 -10000 0 57
RASA1 -0.015 0.054 0.17 37 -10000 0 37
NCK1 0.029 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.004 -10000 0 -10000 0 0
p62DOK/Csk -0.02 0.053 0.16 38 -10000 0 38
PDGFB-D/PDGFRB/SHB 0.043 0.015 -10000 0 -0.051 2 2
chemotaxis 0.02 0.072 0.21 32 -0.25 9 41
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 -0.033 3 5
PTPRJ 0.031 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.028 0.012 -10000 0 -0.065 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.031 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 0.011 0.062 0.17 62 -10000 0 62
IQGAP1/CaM 0.02 0.041 -10000 0 -0.051 111 111
DAB1 0.031 0.006 -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 0.016 0.034 -10000 0 -0.065 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.046 0.009 -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 0.03 -10000 0 -0.048 4 4
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.096 0.3 48 -10000 0 48
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.001 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.009 0.044 0.17 5 -10000 0 5
RELN 0.01 0.016 -10000 0 -0.065 2 2
PAFAH/LIS1 0.024 0.015 -10000 0 -0.041 18 18
LIS1/CLIP170 0.026 0.013 -10000 0 -0.035 12 12
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.038 0.12 3 -10000 0 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0 0.044 0.13 5 -0.21 19 24
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.019 0.076 0.32 28 -10000 0 28
LIS1/IQGAP1 0.008 0.033 -10000 0 -0.048 126 126
RHOA 0 0.028 -10000 0 -0.26 5 5
PAFAH1B1 -0.02 0.007 0 53 -10000 0 53
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 0.019 0.029 0.1 1 -0.14 7 8
NDEL1/Katanin 60/Dynein heavy chain 0.028 0.098 0.31 45 -10000 0 45
LRP8 0.031 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.092 0.3 43 -10000 0 43
P39/CDK5 0.002 0.029 0.17 2 -10000 0 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.013 -10000 0 -0.035 11 11
CDK5 0.011 0.043 0.18 10 -10000 0 10
PPP2R5D 0.032 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.011 -10000 0 -10000 0 0
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.018 0.036 0.17 6 -10000 0 6
RELN/VLDLR 0.023 0.039 -10000 0 -10000 0 0
CDC42 -0.002 0.035 -10000 0 -0.26 8 8
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.015 0.028 -10000 0 -0.06 6 6
EPHB2 0.031 0.007 -10000 0 -0.065 1 1
Syndecan-2/TACI 0.027 0.011 -10000 0 -0.053 5 5
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.052 -10000 0 -0.068 9 9
HRAS 0.031 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.005 -10000 0 -0.064 1 1
ITGA5 0.018 0.033 -10000 0 -0.065 68 68
BAX -0.013 0.012 -10000 0 -0.13 3 3
EPB41 0.031 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.01 -10000 0 -0.047 5 5
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 65 65
dendrite morphogenesis 0.026 0.012 -10000 0 -0.053 5 5
Syndecan-2/GM-CSF 0.027 0.011 -10000 0 -0.053 5 5
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 -0.053 5 5
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.018 0.028 0.18 9 -10000 0 9
MAPK1 -0.016 0.028 0.18 9 -10000 0 9
Syndecan-2/RACK1 0.04 0.02 -10000 0 -0.066 1 1
NF1 0.031 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.006 -10000 0 -0.079 1 1
ITGA2 0.014 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 -0.057 4 4
Syndecan-2/Kininogen 0.027 0.011 -10000 0 -0.055 4 4
ITGB1 0.025 0.013 -10000 0 -10000 0 0
SRC -0.02 0.028 0.17 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.024 0.011 -10000 0 -0.047 5 5
extracellular matrix organization 0.023 0.019 -10000 0 -0.054 6 6
actin cytoskeleton reorganization 0.015 0.028 -10000 0 -0.06 6 6
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 -0.058 5 5
Syndecan-2/RasGAP 0.053 0.026 -10000 0 -0.07 1 1
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
PRKCD 0.031 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.026 0.012 -10000 0 -0.053 5 5
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 0.031 0.005 -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 65 65
Syndecan-2/Synbindin 0.027 0.011 -10000 0 -0.053 5 5
TGFB1 0.026 0.022 -10000 0 -0.065 26 26
CASP3 -0.021 0.028 0.19 8 -10000 0 8
FN1 0.014 0.038 -10000 0 -0.065 96 96
Syndecan-2/IL8 0.012 0.029 -10000 0 -0.054 6 6
SDC2 -0.009 0.006 -10000 0 -0.08 1 1
KNG1 0.031 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.027 0.011 -10000 0 -0.053 5 5
TRAPPC4 0.032 0.004 -10000 0 -10000 0 0
CSF2 0.032 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.019 -10000 0 -0.054 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.025 0.01 -10000 0 -0.047 5 5
Syndecan-2/Ezrin 0.024 0.011 -10000 0 -0.047 5 5
PRKACA -0.016 0.029 0.19 10 -10000 0 10
angiogenesis 0.012 0.029 -10000 0 -0.054 6 6
MMP2 -0.015 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 -0.053 5 5
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 -0.026 5 5
DOCK1 0.023 0.014 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.047 7 7
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 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.029 -10000 0 -0.051 5 5
alpha4/beta7 Integrin/Paxillin 0.045 0.015 -10000 0 -0.059 5 5
lamellipodium assembly -0.01 0.081 -10000 0 -0.34 18 18
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 -0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.041 0.049 0.14 9 -10000 0 9
cell adhesion 0.032 0.053 0.16 8 -0.07 2 10
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.036 0.023 -10000 0 -0.053 5 5
ITGB1 0.025 0.013 -10000 0 -10000 0 0
ITGB7 0.031 0.007 -10000 0 -0.065 2 2
ARF6/GDP 0.033 0.013 -10000 0 -0.026 9 9
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 0.034 0.054 0.17 8 -0.07 2 10
alpha4/beta1 Integrin/Paxillin/GIT1 0.045 0.048 0.17 9 -10000 0 9
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.043 0.047 -10000 0 -0.16 9 9
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 0.034 0.054 0.17 8 -0.07 2 10
Rac1/GTP -0.011 0.088 -10000 0 -0.38 18 18
IL2 signaling events mediated by PI3K

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
BCL2L1 0.011 0.047 0.2 11 -0.19 7 18
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.002 0.091 0.22 1 -0.31 24 25
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 0.004 0.075 0.24 1 -0.26 9 10
FRAP1 -0.006 0.078 0.25 1 -0.27 12 13
FOXO3 -0.013 0.078 0.22 3 -0.27 17 20
AKT1 -0.009 0.08 0.26 1 -0.27 17 18
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 -0.34 115 115
EIF3A 0.024 0.014 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.051 16 16
RPS6KB1 0.022 0.015 -10000 0 -10000 0 0
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 0.006 -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 -0.014 0.084 0.24 1 -0.3 10 11
MYB 0.015 0.025 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.008 0.07 0.14 3 -0.21 25 28
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.044 0.033 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.069 0.14 3 -0.2 25 28
Rac1/GDP 0.005 0.019 -10000 0 -0.046 5 5
T cell proliferation -0.008 0.065 -10000 0 -0.2 21 21
SHC1 0.024 0.027 -10000 0 -0.066 40 40
RAC1 0.022 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 -0.009 0.066 0.13 3 -0.2 24 27
NF kappa B1 p50/RelA 0.009 0.09 0.26 1 -0.26 11 12
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.015 0.04 -10000 0 -0.19 8 8
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 -0.066 6 6
IL2RB 0.03 0.011 -10000 0 -0.066 4 4
TERT 0.031 0.006 -10000 0 -10000 0 0
E2F1 0.024 0.023 -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 0.031 0.004 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.067 9 9
actin cytoskeleton organization -0.008 0.065 -10000 0 -0.2 21 21
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 -10000 0 0
LCK 0.031 0.01 -10000 0 -0.066 4 4
BCL2 -0.004 0.073 0.25 7 -0.25 6 13
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.041 0.01 -10000 0 -0.041 1 1
cell-cell adhesion 0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.077 0.044 -10000 0 -10000 0 0
ITSN1 0.032 0.004 -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 0.04 0.013 -10000 0 -0.041 7 7
Ephrin B1/EPHB1 0.041 0.013 -10000 0 -0.041 9 9
HRAS/GDP 0.021 0.05 -10000 0 -0.15 24 24
Ephrin B/EPHB1/GRB7 0.077 0.045 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.023 0.039 0.18 14 -10000 0 14
KRAS 0.03 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.072 0.047 -10000 0 -0.074 1 1
endothelial cell migration 0.037 0.038 -10000 0 -0.054 1 1
GRB2 0.031 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.065 1 1
PAK1 -0.028 0.047 0.18 18 -10000 0 18
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.045 0.19 16 -10000 0 16
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 -0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.035 0.09 34 -0.16 8 42
PIK3R1 0.029 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 -10000 0 0
Ephrin B/EPHB3 0.061 0.035 -10000 0 -10000 0 0
JNK cascade -0.027 0.054 0.24 18 -10000 0 18
Ephrin B/EPHB1 0.062 0.036 -10000 0 -0.057 2 2
RAP1/GDP 0.03 0.099 0.19 129 -0.17 13 142
EFNB2 0.029 0.009 -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 0.049 0.03 -10000 0 -0.043 13 13
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.057 0.047 0.14 1 -0.11 18 19
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.041 1 1
MAPK3 -0.007 0.036 0.17 3 -0.19 4 7
MAPK1 -0.007 0.033 0.16 2 -0.19 4 6
Rac1/GDP -0.007 0.064 0.2 28 -0.18 13 41
actin cytoskeleton reorganization -0.035 0.033 0.034 1 -0.13 19 20
CDC42/GDP 0.036 0.11 0.2 132 -0.18 13 145
PI3K 0.04 0.041 -10000 0 -0.054 1 1
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 0.03 -10000 0 -0.12 20 20
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 0.054 0.24 18 -10000 0 18
SRC 0.03 0.008 -10000 0 -10000 0 0
KALRN 0.031 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.022 -10000 0 -10000 0 0
neuron projection morphogenesis 0.058 0.16 0.32 129 -0.17 2 131
MAP2K1 0.004 0.036 0.078 33 -0.12 21 54
WASL 0.022 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.071 0.036 -10000 0 -10000 0 0
cell migration -0.001 0.055 0.17 10 -0.21 8 18
NRAS 0.008 0.042 -10000 0 -0.065 125 125
SYNJ1 -0.023 0.04 0.18 14 -10000 0 14
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.033 0.18 7 -10000 0 7
HRAS/GTP 0.045 0.04 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.055 0.024 -10000 0 -0.044 10 10
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 0.038 0.14 5 -10000 0 5
RAC1-CDC42/GTP -0.034 0.028 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.018 0.063 0.22 22 -0.17 15 37
ruffle organization 0.067 0.16 0.32 132 -10000 0 132
NCK1 0.029 0.015 -10000 0 -0.065 11 11
receptor internalization -0.005 0.024 0.21 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.076 0.045 -10000 0 -10000 0 0
ROCK1 -0.015 0.039 0.18 20 -10000 0 20
RAS family/GDP -0.035 0.034 -10000 0 -0.14 23 23
Rac1/GTP -0.029 0.026 0.046 4 -10000 0 4
Ephrin B/EPHB1/Src/Paxillin 0.014 0.037 -10000 0 -0.12 31 31
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.02 0.032 -10000 0 -0.065 61 61
HDAC2 0.029 0.012 -10000 0 -0.065 4 4
GNB1/GNG2 0.028 0.021 -10000 0 -10000 0 0
forebrain development 0.026 0.052 0.21 11 -10000 0 11
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 0.009 0.069 -10000 0 -0.19 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.031 0.006 -10000 0 -10000 0 0
GNAI2 0.031 0.006 -10000 0 -0.027 2 2
SIN3/HDAC complex 0.052 0.027 -10000 0 -0.032 37 37
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
XPO1 0.032 0.007 -10000 0 -0.027 6 6
GLI1/Su(fu) 0.006 0.022 -10000 0 -0.24 1 1
SAP30 0.031 0.005 -10000 0 -10000 0 0
mol:GDP 0.022 0.015 -10000 0 -10000 0 0
MIM/GLI2A 0.033 0.008 -10000 0 -0.04 3 3
IFT88 0.03 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.031 -10000 0 -0.065 59 59
GLI2 0.012 0.048 0.16 11 -0.22 9 20
GLI3 -0.005 0.062 -10000 0 -0.19 26 26
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 0.007 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.01 0.088 1 -0.12 2 3
SIN3B 0.031 0.007 -10000 0 0 22 22
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.004 0.045 0.1 1 -0.17 22 23
GLI2/Su(fu) 0.006 0.034 0.12 3 -0.19 7 10
FOXA2 0.035 0.044 -10000 0 -0.49 3 3
neural tube patterning 0.026 0.052 0.21 11 -10000 0 11
SPOP 0.032 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.033 0.093 152 -0.063 6 158
GNB1 0.03 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 0.026 0.052 0.21 11 -10000 0 11
SUFU -0.002 0.002 -10000 0 -10000 0 0
LGALS3 0.018 0.032 -10000 0 -0.065 61 61
catabolic process 0.027 0.077 0.2 7 -0.27 16 23
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 0.21 11 -10000 0 11
RAB23 0.031 0.01 -10000 0 -0.041 8 8
CSNK1A1 0.032 0.003 -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 0.093 127 -0.062 5 132
GNAZ 0.027 0.012 -10000 0 -10000 0 0
RBBP4 0.014 0.037 -10000 0 -0.065 89 89
CSNK1G1 0.032 0.004 -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 11 -0.21 9 20
STK36 0.001 0.001 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0 0.012 -10000 0 -0.14 3 3
PTCH1 0.024 0.058 0.31 5 -10000 0 5
MIM/GLI1 0.043 0.055 0.22 9 -10000 0 9
CREBBP 0.036 0.016 -10000 0 -0.085 8 8
Su(fu)/SIN3/HDAC complex 0.007 0.057 0.13 4 -0.18 30 34
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.012 0.081 -10000 0 -0.39 18 18
HDAC1 0.021 0.031 -10000 0 -0.061 61 61
AES 0.031 0.007 -10000 0 -10000 0 0
FBXW11 0.032 0.004 -10000 0 0 10 10
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 0.026 0.023 -10000 0 -0.065 28 28
ADAM10 0.028 0.018 -10000 0 -0.065 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.057 -10000 0 -0.5 4 4
NICD/RBPSUH 0.029 0.086 -10000 0 -0.39 18 18
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.08 -10000 0 -0.44 14 14
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 0.062 0.078 0.2 77 -0.22 7 84
APH1B 0.032 0.004 -10000 0 -10000 0 0
APH1A 0.03 0.012 -10000 0 -0.065 7 7
AXIN1 0.025 0.048 0.26 5 -0.25 1 6
CtBP/CBP/TCF1/TLE1/AES 0.021 0.033 -10000 0 -0.12 14 14
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.065 120 120
JUN 0.032 0.004 -10000 0 -10000 0 0
MAP3K7 0.031 0.009 -10000 0 -0.066 1 1
CTNNB1 0.046 0.081 0.19 87 -0.23 6 93
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.021 -10000 0 -0.05 8 8
HNF1A 0.032 0.003 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 0 16 16
MYC -0.006 0.066 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.021 0.017 -10000 0 -0.065 4 4
NOTCH1 precursor/Deltex homolog 1 0.006 0.079 -10000 0 -0.39 18 18
apoptosis 0.002 0.022 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.006 0.079 -10000 0 -0.39 18 18
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.018 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.071 0.052 -10000 0 -0.077 2 2
APC 0.008 0.091 0.26 4 -0.34 22 26
DVL1 0.017 0.021 -10000 0 -0.21 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 0.046 -10000 0 -0.049 101 101
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.013 0.006 -10000 0 -0.039 1 1
CCND1 -0.007 0.11 -10000 0 -0.81 7 7
WNT1 0.031 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.041 0.087 0.25 18 -0.37 6 24
DKK2 0.03 0.013 -10000 0 -0.065 8 8
NOTCH1 precursor/DVL1 0.034 0.09 0.25 1 -0.38 15 16
GSK3B 0.031 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.014 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.012 0.081 -10000 0 -0.39 18 18
PPP2R5D 0.014 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 0.003 -10000 0 -10000 0 0
CREBBP 0.03 0.005 -10000 0 -0.022 1 1
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.05 -10000 0 -0.068 6 6
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 -0.042 0.054 0.2 20 -10000 0 20
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.038 0.16 1 -0.049 48 49
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.033 -10000 0 -0.094 69 69
CaM/Ca2+ 0.047 0.054 -10000 0 -0.076 1 1
RAP1A 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.034 0.037 0.14 18 -10000 0 18
AKT1 -0.022 0.063 0.26 9 -10000 0 9
MAP2K1 -0.033 0.041 0.14 19 -10000 0 19
MAP3K11 -0.028 0.048 0.27 6 -10000 0 6
IFNGR1 0.028 0.018 0.081 2 -0.066 12 14
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.087 -10000 0 -0.22 92 92
Rap1/GTP -0.045 0.018 -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 0.058 -10000 0 -10000 0 0
CEBPB -0.009 0.089 0.34 4 -0.29 28 32
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 -0.03 0.049 0.17 22 -10000 0 22
CALM1 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.029 0.011 -10000 0 -0.028 8 8
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
STAT1 (dimer)/PIAS1 -0.034 0.052 0.18 21 -10000 0 21
CEBPB/PTGES2/Cbp/p300 0.007 0.071 -10000 0 -0.22 31 31
mol:Ca2+ 0.047 0.048 -10000 0 -0.068 6 6
MAPK3 -0.001 0.059 0.51 1 -0.57 2 3
STAT1 (dimer) -0.047 0.044 0.079 3 -0.14 35 38
MAPK1 -0.047 0.18 0.51 1 -0.67 37 38
JAK2 0.029 0.012 0.092 1 -0.027 3 4
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.01 0.067 2 -0.028 8 10
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.003 0.066 0.27 6 -0.19 30 36
SMAD7 -0.016 0.038 0.13 14 -0.084 3 17
CBL/CRKL/C3G -0.035 0.054 0.19 22 -10000 0 22
PI3K 0.041 0.055 -10000 0 -0.081 1 1
IFNG 0.029 0.011 -10000 0 -0.028 8 8
apoptosis 0.001 0.062 0.28 4 -0.34 4 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 -0.022 0.058 0.25 9 -10000 0 9
PRKCD -0.024 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 -0.094 69 69
PTPN2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
IRF1 -0.043 0.043 0.23 5 -10000 0 5
STAT1 (dimer)/PIASy -0.034 0.048 0.25 5 -10000 0 5
SOCS1 0.016 0.093 -10000 0 -1 4 4
mol:GDP -0.035 0.051 0.18 22 -10000 0 22
CASP1 -0.02 0.042 0.14 15 -0.092 9 24
PTGES2 0.031 0.006 -10000 0 -10000 0 0
IRF9 -0.008 0.037 0.15 7 -0.11 12 19
mol:PI-3-4-5-P3 0.028 0.046 -10000 0 -0.075 8 8
RAP1/GDP -0.042 0.031 0.098 17 -10000 0 17
CBL -0.028 0.048 0.18 16 -10000 0 16
MAP3K1 -0.029 0.042 0.24 4 -10000 0 4
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 -0.094 69 69
PTPN11 -0.024 0.045 0.16 24 -10000 0 24
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
Canonical NF-kappaB 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
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 0.07 0.18 5 -0.25 16 21
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 0.019 0.2 3 -10000 0 3
BIRC2 0.032 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.003 -10000 0 -10000 0 0
RIPK2 0.031 0.006 -10000 0 -0.065 1 1
IKBKG 0.017 0.051 -10000 0 -0.28 10 10
IKK complex/A20 0.034 0.068 -10000 0 -0.37 6 6
NEMO/A20/RIP2 0.031 0.006 -10000 0 -0.065 1 1
XPO1 0.032 0 -10000 0 -10000 0 0
NEMO/ATM 0.034 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 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.058 -10000 0 -0.36 6 6
BCL10/MALT1/TRAF6 0.055 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 -0.06 5 5
RELA 0.032 0.005 -10000 0 -0.034 1 1
MALT1 0.027 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 0.013 0.046 -10000 0 -0.051 166 166
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.014 -10000 0 -0.065 1 1
UBE2D3 0.032 0.004 -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 -0.049 10 10
BCL10 0.031 0.01 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.019 0.2 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -0.034 1 1
TNFRSF1A -0.001 0.045 -10000 0 -0.065 165 165
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 0.065 -10000 0 -0.37 6 6
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.027 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.067 0.031 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 0.028 0.023 -10000 0 -0.041 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 -10000 0 0
AKT1 -0.013 0.047 0.18 22 -10000 0 22
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 0.019 0.011 -10000 0 -0.032 21 21
FURIN 0.032 0.004 -10000 0 -10000 0 0
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 -10000 0 0
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.031 0.005 -10000 0 -10000 0 0
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.079 0.22 5 -0.31 18 23
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 0.072 0.052 -10000 0 -0.08 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.027 -10000 0 -0.044 18 18
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.033 0.034 -10000 0 -0.044 14 14
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.043 36 36
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 0.036 0.018 -10000 0 -0.04 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.018 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.027 -10000 0 -0.11 12 12
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.018 -10000 0 -0.041 21 21
NCSTN 0.026 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 -0.097 17 17
p75(NTR)/beta APP 0.042 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 -10000 0 0
NGF (dimer) 0.038 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 0.029 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 0.014 -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 0.031 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.031 0.006 -10000 0 -10000 0 0
TP53 0.032 0.062 0.22 24 -10000 0 24
PRDM4 -0.021 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.013 0.038 -10000 0 -0.068 4 4
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 0.029 -10000 0 -0.054 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.054 0.026 -10000 0 -0.044 20 20
RHOC 0.002 0.045 -10000 0 -0.065 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.037 0.072 0.19 80 -10000 0 80
DIABLO 0.032 0.003 -10000 0 -10000 0 0
SMPD2 -0.02 0.023 0.18 6 -10000 0 6
APH1B 0.032 0.004 -10000 0 -10000 0 0
APH1A 0.03 0.012 -10000 0 -0.065 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.018 -10000 0 -0.041 20 20
PSEN1 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.011 -10000 0 -0.051 3 3
NT3 (dimer)/p75(NTR) 0.042 0.021 -10000 0 -0.051 20 20
MAPK8 0.035 0.066 0.18 72 -0.14 1 73
MAPK9 0.064 0.084 0.19 136 -10000 0 136
APAF1 0.032 0.003 -10000 0 -10000 0 0
NTF3 0.031 0.006 -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 0.022 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 0.034 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 0.047 0.079 0.2 63 -0.16 2 65
RIPK2 0.031 0.006 -10000 0 -0.065 1 1
NGFR 0.028 0.02 -10000 0 -0.065 21 21
CYCS -0.018 0.023 0.17 4 -10000 0 4
ADAM17 0.031 0.01 -10000 0 -0.065 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.054 0.026 -10000 0 -0.043 22 22
BCL2L11 0.047 0.079 0.21 63 -0.16 2 65
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 0.031 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 -0.044 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 -0.006 0.012 0.14 1 -0.074 1 2
SQSTM1 0.031 0.007 -10000 0 -0.065 1 1
NGFRAP1 0.032 0.003 -10000 0 -10000 0 0
CASP3 0.045 0.077 0.2 61 -0.17 3 64
E2F1 0.03 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -0.065 3 3
IKK complex 0.036 0.048 -10000 0 -0.14 4 4
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -10000 0 0
MMP7 0.017 0.035 -10000 0 -0.065 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.038 -10000 0 -0.054 1 1
MMP3 0.03 0.012 -10000 0 -0.065 7 7
APAF-1/Caspase 9 -0.036 0.026 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.03 0.008 -10000 0 -10000 0 0
NFATC1 0.017 0.051 0.23 2 -0.23 11 13
NFATC2 -0.035 0.078 0.11 1 -0.17 117 118
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 -0.022 0.074 0.15 2 -0.23 40 42
Exportin 1/Ran/NUP214 0.062 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.01 0.088 0.15 2 -0.22 38 40
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 0.029 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 -0.007 0.08 0.15 2 -0.22 38 40
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 0.007 0.079 0.22 38 -0.15 2 40
KPNB1 0.032 0.003 -10000 0 -10000 0 0
KPNA2 0.03 0.015 -10000 0 -0.065 11 11
XPO1 0.032 0 -10000 0 -10000 0 0
SFN 0.025 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 -0.077 36 36
MEF2D/NFAT1/Cbp/p300 0.011 0.1 -10000 0 -0.16 110 110
CABIN1 -0.022 0.074 0.15 2 -0.23 38 40
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 -10000 0 0
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 0.014 -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 0.031 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 0.007 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 0.013 -10000 0 -10000 0 0
CASP3 0.013 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 -0.001 38 38
apoptosis 0.017 0.024 -10000 0 -0.097 17 17
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.034 -10000 0 -0.19 10 10
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.032 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.031 0.099 1 -0.16 7 8
BAD/BCL-XL 0.044 0.013 -10000 0 -10000 0 0
PRKCD 0.031 0.005 -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 0.03 0.008 -10000 0 -10000 0 0
PRKCQ 0.025 0.014 -10000 0 -10000 0 0
FKBP38/BCL2 0.044 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 0.025 0.049 0.27 1 -0.23 11 12
CaM/Ca2+/FKBP38 0.037 0.015 -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 0.034 0.054 0.23 2 -0.23 11 13
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.01 0.088 0.15 2 -0.21 39 41
NR4A1 -0.045 0.066 0.14 7 -0.16 100 107
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 -0.023 0.058 0.063 6 -0.12 115 121
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 0 12 12
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.034 0.054 0.23 2 -0.23 11 13
CREBBP 0.032 0.003 -10000 0 0 6 6
BCL2 0.031 0.006 -10000 0 -10000 0 0
FoxO family 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
G6PC -0.014 0.046 -10000 0 -0.26 4 4
PLK1 -0.051 0.079 -10000 0 -0.35 8 8
CDKN1B -0.089 0.15 0.23 2 -0.33 125 127
FOXO3 -0.049 0.081 -10000 0 -0.33 12 12
KAT2B -0.003 0.005 -10000 0 -10000 0 0
FOXO1/SIRT1 0.006 0.05 -10000 0 -0.19 20 20
CAT -0.049 0.076 -10000 0 -0.39 2 2
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
AKT1 0.015 0.026 -10000 0 -10000 0 0
FOXO1 -0.012 0.053 -10000 0 -0.2 20 20
MAPK10 0.023 0.073 0.18 89 -10000 0 89
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 0 0.075 0.19 12 -0.23 2 14
response to oxidative stress -0.002 0.005 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.036 0.083 -10000 0 -0.32 11 11
XPO1 0.032 0 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
BCL2L11 0.019 0.012 -10000 0 -10000 0 0
FOXO1/SKP2 0.006 0.056 -10000 0 -0.19 19 19
mol:GDP -0.002 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
GADD45A -0.064 0.14 -10000 0 -0.46 20 20
YWHAQ 0.032 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.02 0.076 -10000 0 -0.26 25 25
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 0.088 -10000 0 -0.29 24 24
YWHAB 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.013 0.073 0.18 78 -10000 0 78
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 0.022 0.015 -10000 0 -0.025 12 12
SOD2 -0.092 0.12 -10000 0 -0.42 35 35
RBL2 -0.026 0.097 -10000 0 -0.7 6 6
RAL/GDP 0.026 0.023 -10000 0 -10000 0 0
CHUK 0.009 0.025 -10000 0 -0.062 1 1
Ran/GTP 0.023 0.003 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
RAL/GTP 0.023 0.023 -10000 0 -10000 0 0
CSNK1G1 0.032 0.004 -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 0.015 0.027 -10000 0 -10000 0 0
CCNB1 -0.073 0.089 -10000 0 -0.37 9 9
FOXO1-3a-4/beta catenin -0.026 0.08 0.21 1 -0.3 3 4
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.056 -10000 0 -0.19 19 19
CSNK1A1 0.032 0.003 -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 0.075 0.26 9 -10000 0 9
SFN 0.025 0.024 -10000 0 -0.065 31 31
CDK2 0.028 0.021 -10000 0 -0.063 24 24
FOXO3A/14-3-3 -0.047 0.074 -10000 0 -0.22 33 33
CREBBP 0.033 0.004 -10000 0 -10000 0 0
FBXO32 -0.046 0.075 -10000 0 -0.32 10 10
BCL6 -0.033 0.1 -10000 0 -0.67 8 8
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
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.02 0.032 -9999 0 -0.065 61 61
Ran/GTP/Exportin 1/HDAC4 -0.027 0.011 -9999 0 -0.063 37 37
MDM2/SUMO1 0.034 0.039 -9999 0 -0.099 34 34
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.029 0.013 -9999 0 -0.067 36 36
SUMO1 0.032 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.009 -9999 0 -0.19 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.026 -9999 0 -0.098 37 37
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 0.037 0.039 -9999 0 -0.099 37 37
SUMO1/HDAC1 0.03 0.043 -9999 0 -0.1 36 36
RANGAP1 0.03 0.008 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.069 0.033 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.029 -9999 0 -0.097 37 37
Ran/GTP 0.021 0.033 -9999 0 -0.094 37 37
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 -0.18 1 1
NPC 0.019 0.002 -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
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.005 -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 -0.065 17 17
JAK3 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.011 0.055 0.16 1 -0.25 6 7
SHC1 0.024 0.026 -10000 0 -0.065 40 40
SP1 0.033 0.02 -10000 0 -0.074 14 14
IL2RA -0.014 0.012 -10000 0 -0.073 10 10
IL2RB 0.03 0.011 -10000 0 -0.065 4 4
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.065 9 9
G1/S transition of mitotic cell cycle 0.024 0.092 0.24 17 -0.32 17 34
PTPN11 0.032 0.004 -10000 0 -10000 0 0
CCND2 -0.018 0.011 -10000 0 -0.099 8 8
LCK 0.031 0.01 -10000 0 -0.065 4 4
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
CDK6 0.022 0.015 -10000 0 -10000 0 0
CCND3 0.007 0.054 0.19 2 -0.27 3 5
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.03 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 0.024 -10000 0 -0.051 28 28
mol:Ca2+ -0.022 0.021 0.054 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 0.031 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 0 18 -0.051 30 48
PRL-2 /Rab GGTase beta 0.046 0.009 -10000 0 -10000 0 0
MAPK1 -0.022 0.01 0 55 -0.051 30 85
PTP4A1 -0.017 0.008 -10000 0 -0.1 1 1
PTP4A3 0.025 0.023 -10000 0 -0.065 30 30
PTP4A2 0.031 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 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.014 0.044 0.18 23 -10000 0 23
RABGGTA 0.03 0.007 -10000 0 -10000 0 0
BCAR1 -0.015 0.017 0.05 30 -10000 0 30
RHOC -0.007 0.046 -10000 0 -0.34 6 6
RHOA 0.006 0.049 -10000 0 -0.32 10 10
cell motility 0.012 0.052 -10000 0 -0.29 5 5
PRL-1/alpha Tubulin -0.011 0.05 0.18 31 -10000 0 31
PRL-3/alpha1 Integrin 0.019 0.015 -10000 0 -0.04 30 30
ROCK1 0.012 0.05 -10000 0 -0.28 5 5
RABGGTB 0.032 0.004 -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 0.03 0.009 -10000 0 -0.065 1 1
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.033 0.041 -10000 0 -0.13 33 33
PLCG1 0.001 0.011 0.073 6 -0.11 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.031 0.005 -10000 0 -10000 0 0
GNAI3 0.02 0.031 -10000 0 -0.065 59 59
G12/G13 0.033 0.022 -10000 0 -10000 0 0
cell migration -0.032 0.04 -10000 0 -0.13 33 33
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 0.001 0.012 0.073 7 -0.11 2 9
MAPK1 0.001 0.01 0.073 7 -0.096 1 8
S1P/S1P5/Gi 0.002 0.013 0.083 7 -0.11 2 9
GNAI1 0.019 0.016 -10000 0 -0.065 1 1
CDC42/GDP 0.023 0.004 -10000 0 0 18 18
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
RHOA 0.04 0.095 0.18 151 -10000 0 151
S1P/S1P4/Gi 0.002 0.013 0.083 7 -0.11 2 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.029 0.019 -10000 0 -0.023 2 2
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA13 0.031 0.007 -10000 0 -0.065 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.057 0.13 0.4 29 -10000 0 29
CRP 0.048 0.12 0.46 9 -10000 0 9
cell cycle arrest 0.05 0.12 0.45 7 -10000 0 7
TIMP1 0.013 0.11 0.38 6 -0.53 1 7
IL6ST 0.03 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.055 0.24 8 -0.22 3 11
AP1 0.031 0.067 -10000 0 -0.35 6 6
GAB2 0.031 0.006 -10000 0 -0.026 1 1
TNFSF11 0.044 0.11 0.44 6 -10000 0 6
HSP90B1 0.042 0.051 -10000 0 -0.55 1 1
GAB1 0.031 0.009 -10000 0 -0.055 4 4
MAPK14 0.009 0.044 0.18 2 -0.21 3 5
AKT1 0.02 0.043 -10000 0 -0.39 3 3
FOXO1 0.014 0.045 0.2 3 -0.38 3 6
MAP2K6 0.006 0.038 0.12 9 -0.22 3 12
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.007 0.061 0.27 10 -0.26 1 11
MITF 0.005 0.037 0.11 21 -0.21 2 23
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 -0.019 0.18 -10000 0 -0.93 17 17
CEBPB 0.03 0.017 -10000 0 -0.062 12 12
GRB2/SOS1/GAB family/SHP2 0.02 0.046 0.23 1 -0.26 5 6
STAT3 0.049 0.12 0.45 7 -10000 0 7
STAT1 0.017 0.022 -10000 0 -10000 0 0
CEBPD 0.046 0.11 0.4 10 -10000 0 10
PIK3CA 0.028 0.019 -10000 0 -0.063 18 18
PI3K 0.039 0.023 -10000 0 -0.05 17 17
JUN 0.031 0.004 -10000 0 -10000 0 0
PIAS3/MITF 0.054 0.076 0.19 76 -0.21 2 78
MAPK11 0.007 0.042 0.18 2 -0.21 3 5
STAT3 (dimer)/FOXO1 -0.005 0.066 0.33 1 -0.4 1 2
GRB2/SOS1/GAB family 0.057 0.058 0.19 2 -0.21 3 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.003 0.033 -10000 0 -0.18 5 5
GRB2 0.031 0.006 -10000 0 -0.027 1 1
JAK2 0.029 0.01 -10000 0 -10000 0 0
LBP 0.059 0.12 0.38 20 -0.62 1 21
PIK3R1 0.03 0.01 -10000 0 -0.027 1 1
JAK1 0.031 0.008 -10000 0 -10000 0 0
MYC 0.04 0.12 0.43 10 -10000 0 10
FGG 0.044 0.11 0.44 6 -10000 0 6
macrophage differentiation 0.05 0.12 0.45 7 -10000 0 7
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.058 -10000 0 -10000 0 0
JUNB 0.049 0.12 0.4 20 -10000 0 20
FOS 0.006 0.041 -10000 0 -0.065 120 120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.011 0.04 0.13 9 -0.23 3 12
STAT1/PIAS1 0.039 0.063 0.2 16 -10000 0 16
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.044 -10000 0 -0.36 4 4
STAT3 (dimer) 0.05 0.12 0.45 7 -10000 0 7
PRKCD 0.07 0.15 0.3 123 -10000 0 123
IL6R 0.032 0.007 -10000 0 -10000 0 0
SOCS3 0.047 0.083 0.38 8 -10000 0 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.06 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.012 0.05 0.19 3 -0.22 3 6
HCK 0.014 0.036 -10000 0 -0.065 84 84
MAPKKK cascade 0.04 0.062 0.28 1 -0.37 6 7
bone resorption 0.044 0.11 0.44 6 -10000 0 6
IRF1 0.04 0.11 0.41 8 -10000 0 8
mol:GDP 0.004 0.039 0.12 10 -0.22 3 13
SOS1 0 0.002 -10000 0 -10000 0 0
VAV1 0.004 0.039 0.12 11 -0.22 3 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.018 0.046 -10000 0 -0.32 4 4
PTPN11 0.015 0.056 -10000 0 -0.68 3 3
IL6/IL6RA 0.026 0.031 -10000 0 -0.06 1 1
gp130 (dimer)/TYK2/TYK2/LMO4 0.058 0.022 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.053 0.03 -10000 0 -10000 0 0
IL6 0.015 0.027 -10000 0 -0.067 36 36
PIAS3 0.031 0.005 -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 0.022 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.015 0.034 0.11 36 -0.11 4 40
LMO4 0.03 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.021 0.078 -10000 0 -10000 0 0
MCL1 0.02 0.051 0.26 2 -0.41 2 4
ErbB2/ErbB3 signaling events

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
USP8 -0.017 0.008 0.017 10 -10000 0 10
RAS family/GTP 0.014 0.056 -10000 0 -0.12 7 7
NFATC4 -0.025 0.042 0.26 6 -10000 0 6
ERBB2IP 0.026 0.023 -10000 0 -0.062 32 32
HSP90 (dimer) 0.03 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.03 0.032 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 0.038 0.045 0.17 3 -0.068 2 5
AKT1 -0.01 0.007 0.016 15 -10000 0 15
BAD -0.017 0.006 0.015 3 -10000 0 3
MAPK10 0.004 0.051 0.18 17 -10000 0 17
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 18 -10000 0 18
ErbB2/ErbB3/neuregulin 2 0.032 0.03 -10000 0 -0.058 27 27
STAT3 0.025 0.099 -10000 0 -0.93 5 5
cell migration -0.013 0.048 0.21 10 -0.13 2 12
mol:PI-3-4-5-P3 -0.001 0.001 0.004 8 -10000 0 8
cell proliferation -0.004 0.096 0.43 2 -0.44 10 12
FOS -0.007 0.073 0.3 4 -0.27 11 15
NRAS 0.008 0.042 -10000 0 -0.065 125 125
mol:Ca2+ -0.03 0.032 0.14 5 -10000 0 5
MAPK3 0.008 0.064 0.37 3 -10000 0 3
MAPK1 -0.015 0.12 0.42 2 -0.48 15 17
JAK2 -0.03 0.035 0.13 6 -10000 0 6
NF2 0.009 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.021 0.1 12 -0.057 1 13
NRG1 0.031 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.016 0.055 0.17 2 -0.18 28 30
MAPK9 0.006 0.066 0.17 30 -10000 0 30
ERBB2 -0.025 0.021 0.051 32 -10000 0 32
ERBB3 0.022 0.024 -10000 0 -0.066 28 28
SHC1 0.024 0.026 -10000 0 -0.065 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
apoptosis 0.009 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.096 -10000 0 -0.91 5 5
RNF41 -0.022 0.009 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 0.007 14 -10000 0 14
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 0.006 0.066 0.34 3 -0.24 8 11
myelination -0.028 0.057 0.29 11 -10000 0 11
PPP3CB -0.026 0.03 0.12 4 -10000 0 4
KRAS 0.03 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.04 -10000 0 -0.11 3 3
NRG2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.021 0.1 12 -0.057 1 13
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.024 0.054 0.19 16 -10000 0 16
SRC 0.03 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 0.003 3 -10000 0 3
PTPN11 -0.033 0.037 0.12 8 -10000 0 8
MAP2K1 -0.011 0.12 0.42 2 -0.53 21 23
heart morphogenesis -0.03 0.032 0.14 5 -10000 0 5
RAS family/GDP 0.018 0.06 -10000 0 -0.12 7 7
GRB2 0.031 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 15 15
nervous system development -0.03 0.032 0.14 5 -10000 0 5
CDC42 0.031 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
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 -0.018 0.047 -10000 0 -0.32 8 8
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 -10000 0 -10000 0 0
CYAA -0.007 0.001 -10000 0 -0.026 3 3
MAP2K4 -0.008 0.002 -10000 0 -0.017 1 1
IL1B -0.013 0.015 0.13 3 -0.079 5 8
Channel 0.02 0.004 -10000 0 -0.028 3 3
NLRP1 -0.009 0.002 -10000 0 -0.017 1 1
CALM1 0.029 0.01 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.026 0.12 -10000 0 -0.37 53 53
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 -10000 0 -10000 0 0
PGR -0.009 0.001 -10000 0 -10000 0 0
PA/Cellular Receptors 0.021 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 -0.019 0.047 -10000 0 -0.33 8 8
platelet activation -0.026 0.12 -10000 0 -0.37 53 53
MAPKKK cascade 0.004 0.018 0.064 1 -0.068 25 26
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 -0.007 0.007 -10000 0 -0.016 165 165
mol:cAMP -0.026 0.12 -10000 0 -0.37 53 53
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 -0.026 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.013 -10000 0 -0.041 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.03 0.014 -10000 0 -0.065 9 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.03 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.013 -10000 0 -0.11 6 6
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 0.01 -10000 0 -0.065 1 1
MAP3K12 0.032 0.004 -10000 0 -10000 0 0
FGR 0.028 0.017 -10000 0 -0.065 15 15
p38 alpha/TAB1 -0.019 0.048 -10000 0 -0.22 17 17
PRKG1 0.024 0.014 -10000 0 -10000 0 0
DUSP8 0.023 0.014 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.001 0.064 0.14 2 -0.23 15 17
apoptosis -0.019 0.046 -10000 0 -0.21 17 17
RAL/GTP 0.028 0.023 -10000 0 -0.041 12 12
LYN 0.02 0.031 -10000 0 -0.065 60 60
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 -0.038 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 0.079 0.17 23 -0.27 12 35
BLK 0.031 0.005 -10000 0 -10000 0 0
HCK 0.014 0.036 -10000 0 -0.065 84 84
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 0.009 -10000 0 -0.023 8 8
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.074 0.16 18 -0.25 15 33
positive regulation of innate immune response 0.004 0.09 0.18 20 -0.31 13 33
LCK 0.031 0.01 -10000 0 -0.065 4 4
p38alpha-beta/MKP7 0.001 0.085 0.17 24 -0.3 13 37
p38alpha-beta/MKP5 0.012 0.093 0.2 19 -0.29 12 31
PGK/cGMP 0.018 0.01 -10000 0 -10000 0 0
PAK2 0.027 0.02 -10000 0 -0.065 22 22
p38alpha-beta/MKP1 0.011 0.095 0.2 19 -0.3 13 32
CDC42 0.031 0.006 -10000 0 -10000 0 0
RALB 0.032 0.005 -10000 0 -0.065 1 1
RALA 0.02 0.02 -10000 0 -0.065 11 11
PAK3 0.005 0.011 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.002 0 18 -10000 0 18
GNB1/GNG2 0.037 0.016 -10000 0 -0.027 27 27
regulation of S phase of mitotic cell cycle 0.014 0.021 -10000 0 -0.11 10 10
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 -10000 0 0
PELP1 0.031 0.004 -10000 0 -10000 0 0
AKT1 -0.011 0.003 0 33 -10000 0 33
MAP2K1 -0.028 0.05 0.14 35 -0.14 2 37
T-DHT/AR 0.023 0.008 -10000 0 -0.041 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 0.031 0.005 -10000 0 -10000 0 0
GNAI3 0.02 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 0.21 15 -0.25 4 19
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
FOS -0.023 0.068 0.2 5 -0.32 4 9
mol:Ca2+ 0 0.002 -10000 0 -0.033 2 2
MAPK3 -0.02 0.062 0.19 22 -0.24 2 24
MAPK1 -0.023 0.094 0.16 4 -0.34 35 39
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.002 7 7
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 7 7
HRAS/GTP 0.049 0.03 -10000 0 -0.061 6 6
actin cytoskeleton reorganization 0.028 0.028 -10000 0 -0.045 11 11
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.002 7 7
PI3K 0.036 0.02 -10000 0 -0.041 16 16
apoptosis 0.014 0.065 0.25 6 -0.2 5 11
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 -0.26 6 10
RAC1-CDC42/GTP 0.036 0.034 -10000 0 -0.046 11 11
AR 0.03 0.012 -10000 0 -0.066 8 8
GNB1 0.03 0.008 -10000 0 -10000 0 0
RAF1 -0.022 0.053 0.16 37 -10000 0 37
RAC1-CDC42/GDP 0.027 0.031 0.15 1 -10000 0 1
T-DHT/AR/PELP1/Src 0.055 0.022 -10000 0 -0.044 9 9
MAP2K2 -0.031 0.044 0.14 26 -0.14 2 28
T-DHT/AR/PELP1/Src/PI3K 0.014 0.021 -10000 0 -0.11 10 10
GNAZ 0.026 0.012 -10000 0 -10000 0 0
SHBG 0.031 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.064 0.099 -10000 0 -0.36 35 35
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 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
AKT1 -0.051 0.072 -10000 0 -0.35 1 1
NCK1/PAK1/Dok-R -0.031 0.039 -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 0.023 0.027 -10000 0 -0.066 40 40
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
F2 0.037 0.019 -10000 0 -0.067 2 2
TNIP2 0.03 0.015 -10000 0 -0.065 11 11
NF kappa B/RelA 0.014 0.08 -10000 0 -10000 0 0
FN1 0.014 0.038 -10000 0 -0.065 96 96
PLD2 -0.013 0.039 -10000 0 -0.24 1 1
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.065 18 18
ELK1 -0.024 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 -0.011 0.078 -10000 0 -10000 0 0
CDKN1A -0.057 0.077 -10000 0 -0.34 3 3
ITGA5 0.018 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 0.004 -10000 0 -10000 0 0
mol:NO -0.006 0.094 0.3 3 -0.3 1 4
PLG -0.011 0.036 -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 0.031 0.006 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ANGPT2 -0.05 0.068 -10000 0 -0.31 2 2
BMX -0.013 0.039 -10000 0 -0.24 1 1
ANGPT1 -0.008 0.038 -10000 0 -0.2 1 1
tube development -0.061 0.072 -10000 0 -0.32 1 1
ANGPT4 0.028 0.008 -10000 0 -10000 0 0
response to hypoxia -0.003 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.006 0.063 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.024 0.034 -10000 0 -0.051 61 61
FGF2 0.033 0.008 -10000 0 -0.063 2 2
STAT5A (dimer) -0.061 0.09 -10000 0 -0.34 1 1
mol:L-citrulline -0.006 0.094 0.3 3 -0.3 1 4
AGTR1 0.018 0.023 -10000 0 -0.027 97 97
MAPK14 -0.02 0.072 -10000 0 -0.56 3 3
Tie2/SHP2 -0.027 0.12 -10000 0 -0.27 95 95
TEK -0.035 0.12 -10000 0 -0.29 90 90
RPS6KB1 -0.047 0.071 -10000 0 -0.37 1 1
Angiotensin II/AT1 0 0.023 -10000 0 -0.022 267 267
Tie2/Ang1/GRB2 -0.004 0.063 -10000 0 -10000 0 0
MAPK3 -0.029 0.045 -10000 0 -0.24 1 1
MAPK1 -0.026 0.043 -10000 0 -0.24 1 1
Tie2/Ang1/GRB7 -0.005 0.063 -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 -0.041 0.073 -10000 0 -0.39 1 1
FES -0.022 0.072 -10000 0 -0.44 3 3
Crk/Dok-R -0.005 0.06 -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 -0.05 0.07 -10000 0 -0.33 1 1
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.044 0.076 0.3 2 -10000 0 2
Tie2/Ang2 -0.059 0.082 -10000 0 -0.33 3 3
Tie2/Ang1 -0.004 0.042 -10000 0 -0.25 1 1
FOXO1 -0.059 0.073 -10000 0 -10000 0 0
ELF1 0.035 0.017 -10000 0 -0.065 6 6
ELF2 -0.008 0.036 -10000 0 -0.21 1 1
mol:Choline -0.013 0.04 -10000 0 -0.24 1 1
cell migration -0.022 0.029 -10000 0 -0.12 2 2
FYN -0.063 0.076 -10000 0 -0.34 1 1
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.054 0.073 -10000 0 -0.32 3 3
ETS1 0.022 0.031 -10000 0 -10000 0 0
PXN -0.044 0.074 0.27 3 -10000 0 3
ITGB1 0.025 0.013 -10000 0 -10000 0 0
NOS3 -0.019 0.089 0.31 3 -0.32 1 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
TNF 0.021 0.032 -10000 0 -0.065 2 2
MAPKKK cascade -0.013 0.04 -10000 0 -0.24 1 1
RASA1 0.031 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.011 0.062 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
vasculogenesis -0.002 0.092 0.28 4 -0.28 1 5
mol:Phosphatidic acid -0.013 0.04 -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 -0.3 1 4
Rac1/GTP -0.026 0.064 -10000 0 -0.36 1 1
MMP2 -0.02 0.04 -10000 0 -0.26 1 1
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.057 0.027 -9999 0 -0.055 20 20
E-cadherin/beta catenin 0.044 0.015 -9999 0 -0.051 8 8
CTNNB1 0.031 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
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.001 0 6 -10000 0 6
ADCY5 -0.009 0.001 0 6 -10000 0 6
ADCY6 -0.017 0.003 0 20 -10000 0 20
ADCY7 -0.018 0.004 0 15 -0.041 5 20
ADCY1 -0.012 0.008 -10000 0 -10000 0 0
ADCY2 -0.017 0.004 0 21 -10000 0 21
ADCY3 -0.009 0.001 0 6 -10000 0 6
ADCY8 -0.017 0.004 -10000 0 -0.041 5 5
PRKCE -0.011 0.001 0 6 -10000 0 6
ADCY9 -0.017 0.003 0 13 -10000 0 13
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.007 0.041 0.16 11 -0.12 5 16
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.018 0.055 1 -0.12 4 5
KIRREL 0.035 0.011 0.083 1 -0.038 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.018 0.12 4 -0.055 1 5
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.004 -10000 0 -10000 0 0
WASL 0.022 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.068 0.045 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+ 0.073 0.036 0.17 19 -10000 0 19
mol:DAG 0.075 0.037 0.17 19 -10000 0 19
NPHS2 0.035 0.01 0.083 1 -0.03 4 5
mol:IP3 0.075 0.037 0.17 19 -10000 0 19
regulation of endocytosis 0.055 0.029 0.13 1 -10000 0 1
Nephrin/NEPH1/podocin/Cholesterol 0.061 0.029 0.16 19 -10000 0 19
establishment of cell polarity 0.049 0.018 0.12 4 -0.055 1 5
Nephrin/NEPH1/podocin/NCK1-2 0.089 0.039 0.19 10 -10000 0 10
Nephrin/NEPH1/beta Arrestin2 0.057 0.03 0.14 1 -10000 0 1
NPHS1 0.034 0.011 0.093 1 -10000 0 1
Nephrin/NEPH1/podocin 0.058 0.024 0.17 4 -0.057 2 6
TJP1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
NCK2 0.032 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.076 0.038 0.18 19 -10000 0 19
CD2AP 0.022 0.029 -10000 0 -0.065 48 48
Nephrin/NEPH1/podocin/GRB2 0.078 0.035 0.18 16 -10000 0 16
GRB2 0.031 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 -0.008 0.032 0.17 11 -0.15 3 14
Nephrin/NEPH1 0.041 0.016 0.097 4 -0.029 5 9
Nephrin/NEPH1/ZO-1 0.062 0.024 -10000 0 -0.05 1 1
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.002 0.056 -10000 0 -0.17 23 23
TBX21 -0.02 0.12 -10000 0 -0.39 4 4
B2M 0.031 0.005 -10000 0 -10000 0 0
TYK2 0.02 0.029 -10000 0 -0.052 2 2
IL12RB1 0.02 0.029 -10000 0 -0.052 1 1
GADD45B 0.002 0.095 -10000 0 -0.44 1 1
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 -0.033 2 2
RELB 0.03 0.008 -10000 0 -0.065 1 1
RELA 0.032 0.004 -10000 0 -10000 0 0
IL18 0.024 0.028 -10000 0 -0.065 43 43
IL2RA 0.024 0.017 -10000 0 -0.065 6 6
IFNG 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.006 0.11 -10000 0 -0.38 6 6
HLA-DRB5 -0.001 0.002 -10000 0 -10000 0 0
FASLG -0.018 0.12 0.28 1 -0.4 3 4
NF kappa B2 p52/RelB -0.008 0.13 -10000 0 -0.35 15 15
CD4 0.026 0.02 -10000 0 -0.064 21 21
SOCS1 0.032 0.003 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.003 -10000 0 -10000 0 0
CD3D 0.027 0.02 -10000 0 -0.064 22 22
CD3E 0.03 0.007 -10000 0 -0.045 3 3
CD3G 0.03 0.008 -10000 0 -0.048 3 3
IL12Rbeta2/JAK2 0.03 0.04 -10000 0 -10000 0 0
CCL3 -0.019 0.12 -10000 0 -0.35 15 15
CCL4 -0.068 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 0.11 -10000 0 -0.37 5 5
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.058 -10000 0 -0.18 24 24
IL1R1 -0.021 0.12 -10000 0 -0.39 4 4
IL4 0.033 0.014 -10000 0 -0.028 8 8
JAK2 0.019 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.009 0.032 -10000 0 -0.12 21 21
RAB7A 0.013 0.098 0.34 2 -0.41 2 4
lysosomal transport 0.013 0.096 0.31 4 -0.4 2 6
FOS -0.056 0.17 -10000 0 -0.57 39 39
STAT4 (dimer) -0.016 0.12 0.38 1 -0.43 5 6
STAT5A (dimer) 0 0.13 -10000 0 -0.35 13 13
GZMA -0.025 0.12 0.28 1 -0.4 3 4
GZMB -0.026 0.12 -10000 0 -0.41 2 2
HLX 0.031 0.009 -10000 0 -0.065 3 3
LCK -0.026 0.12 0.28 2 -0.37 15 17
TCR/CD3/MHC II/CD4 -0.01 0.031 -10000 0 -0.099 10 10
IL2/IL2R 0.05 0.055 -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 0.065 -10000 0 -0.39 7 7
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 0.02 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 -0.002 0.056 0.17 23 -10000 0 23
IL2RB 0.03 0.011 -10000 0 -0.065 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.11 0.37 1 -0.41 5 6
IL2RG 0.03 0.013 -10000 0 -0.065 9 9
IL12 0.031 0.042 -10000 0 -0.069 1 1
STAT5A 0.032 0.006 -10000 0 -0.065 1 1
CD247 0.03 0.009 -10000 0 -0.046 5 5
IL2 0.032 0.004 -10000 0 -10000 0 0
SPHK2 0.03 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.02 0.03 -10000 0 -0.052 2 2
IL12/IL12R/TYK2/JAK2 -0.018 0.12 -10000 0 -0.38 16 16
MAP2K3 0.008 0.1 -10000 0 -0.53 2 2
RIPK2 0.031 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 -0.065 2 2
EOMES 0.004 0.019 0.069 5 -0.07 4 9
STAT1 (dimer) 0 0.11 -10000 0 -0.41 2 2
T cell proliferation -0.019 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 -0.028 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.013 0.12 -10000 0 -0.41 3 3
ATF2 0.006 0.099 -10000 0 -0.45 2 2
Glucocorticoid receptor regulatory network

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
PCK2 -0.006 0.028 -10000 0 -0.25 5 5
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 0.006 -10000 0 -0.025 2 2
STAT1 (dimer) 0.021 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 0.079 0.053 -10000 0 -0.078 3 3
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 0.014 0.039 -10000 0 -0.07 39 39
FGG 0.11 0.14 0.27 25 -10000 0 25
GR beta/TIF2 -0.005 0.037 -10000 0 -10000 0 0
IFNG -0.061 0.093 -10000 0 -0.22 25 25
apoptosis 0.021 0.088 -10000 0 -0.36 8 8
CREB1 0.035 0.011 -10000 0 -0.068 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 0.091 0.055 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.061 -10000 0 -0.1 38 38
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 -10000 0 -10000 0 0
CSF2 -0.072 0.072 -10000 0 -0.24 2 2
GSK3B 0.031 0.006 -10000 0 -0.027 1 1
NR1I3 0.024 0.089 -10000 0 -0.35 6 6
CSN2 0.12 0.14 0.27 26 -10000 0 26
BRG1/BAF155/BAF170/BAF60A 0.069 0.036 -10000 0 -0.065 1 1
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.033 0.01 -10000 0 -10000 0 0
CDKN1A -0.016 0.053 -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 0.025 0.024 -10000 0 -0.065 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.086 0.062 -10000 0 -0.085 5 5
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.026 0.088 -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 3 3
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.092 0.057 -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 -0.076 10 10
AP-1/NFAT1-c-4 -0.015 0.042 0.24 1 -0.2 1 2
AFP -0.053 0.057 -10000 0 -0.37 1 1
SUV420H1 0.031 0.005 -10000 0 -10000 0 0
IRF1 -0.005 0.033 0.17 6 -0.13 8 14
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 12 -0.14 14 26
TBP 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.029 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 -0.066 4 4
AP-1 -0.015 0.042 0.24 1 -0.2 1 2
MAPK14 0.032 0.006 -10000 0 -0.039 3 3
MAPK10 0.018 0.016 -10000 0 -10000 0 0
MAPK11 0.029 0.01 -10000 0 -0.025 2 2
KRT5 -0.061 0.092 -10000 0 -0.22 16 16
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.03 0.01 -10000 0 -0.032 8 8
STAT1 0.021 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 0.079 0.14 7 -0.15 20 27
MAPK3 0.032 0.005 -10000 0 -0.026 3 3
MAPK1 0.03 0.009 -10000 0 -0.026 2 2
ICAM1 -0.017 0.07 0.14 2 -0.18 74 76
NFKB1 0.014 0.04 -10000 0 -0.071 41 41
MAPK8 0.005 0.018 -10000 0 -10000 0 0
MAPK9 0.031 0.006 -10000 0 -0.026 2 2
cortisol/GR alpha (dimer) 0.017 0.088 -10000 0 -0.37 8 8
BAX -0.013 0.058 -10000 0 -0.37 3 3
POMC -0.073 0.079 0.27 1 -10000 0 1
EP300 0.028 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.016 0.041 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.22 2 -10000 0 2
SGK1 0.019 0.048 -10000 0 -0.15 17 17
IL13 -0.043 0.068 -10000 0 -0.24 3 3
IL6 -0.016 0.067 0.14 2 -0.18 62 64
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 -0.049 0.069 -10000 0 -0.28 1 1
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 0.085 0.14 2 -0.2 82 84
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.066 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 0.073 0.079 0.17 23 -0.2 2 25
NF kappa B1 p50/RelA/Cbp 0.039 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 0.009 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 0.021 0.088 -10000 0 -0.36 8 8
cortisol/GR alpha (dimer)/Src-1 -0.013 0.038 -10000 0 -10000 0 0
PBX1 0.033 0.01 -10000 0 -10000 0 0
POU1F1 0.033 0.011 -10000 0 -10000 0 0
SELE -0.016 0.069 0.14 2 -0.17 77 79
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.079 0.17 23 -0.2 2 25
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 0.001 0.046 -10000 0 -0.48 3 3
Effects of Botulinum toxin

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
STX1A 0 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.042 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 31 -0.046 9 40
RAB3GAP2/RIMS1/UNC13B 0.056 0.025 -10000 0 -0.043 7 7
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 0.007 -10000 0 -10000 0 0
mol:ACh 0.019 0.035 0.066 152 -0.058 6 158
RAB3GAP2 0.031 0.005 -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 0.026 0.081 31 -0.046 9 40
UNC13B 0.029 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
Arf1 pathway

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
coatomer protein complex 0.006 0.034 0.13 32 -0.14 3 35
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.005 0.04 0.12 4 -0.14 8 12
AP2 0.022 0.006 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.021 -10000 0 -0.039 1 1
CLTB 0.032 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.03 -10000 0 -0.1 34 34
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 0.008 -10000 0 -0.036 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.019 -10000 0 -0.09 23 23
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 0.03 0.008 -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 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.015 -10000 0 -0.03 1 1
ARFIP2 0.029 0.013 -10000 0 -0.04 9 9
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 0.038 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 0.023 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.004 0.028 -10000 0 -0.11 22 22
ARF1/GDP/Membrin 0.027 0.026 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.029 0.021 -10000 0 -0.032 2 2
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 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.028 -10000 0 -0.093 26 26
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 0.033 -10000 0 -0.056 113 113
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 0.011 0.02 -10000 0 -0.29 2 2
GBF1 -0.061 0.14 -10000 0 -0.32 112 112
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0.02 -10000 0 -0.041 19 19
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.056 0.023 -10000 0 -0.038 3 3
HDAC3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.025 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.047 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.047 0.006 -10000 0 -10000 0 0
GATA2/HDAC5 0.046 0.009 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.058 0.026 -10000 0 -0.05 20 20
HDAC9 0.022 0.016 -10000 0 -0.065 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.06 0.018 -10000 0 -0.043 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 0.029 -10000 0 -0.097 37 37
GATA2 0.031 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 0.022 0.006 -10000 0 -10000 0 0
Histones 0.035 0.032 0.083 152 -0.095 4 156
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
XPO1 0.032 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.046 0.009 -10000 0 -0.051 1 1
HDAC4/Ubc9 0.047 0.006 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.046 0.008 -10000 0 -10000 0 0
TUBA1B 0.031 0.005 -10000 0 -10000 0 0
HDAC6 0.032 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.037 0.029 -10000 0 -0.051 43 43
CAMK4 0.032 0.004 -10000 0 -10000 0 0
Tubulin/HDAC6 0.059 0.021 -10000 0 -0.043 2 2
SUMO1 0.032 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 0.037 0.039 -10000 0 -0.099 37 37
SRF 0.032 0.003 -10000 0 -10000 0 0
HDAC4/YWHAB 0.044 0.013 -10000 0 -10000 0 0
Tubulin 0.043 0.015 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.046 0.008 -10000 0 -10000 0 0
GNB1 0.03 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) 0.063 0.013 -10000 0 -10000 0 0
HDAC4/SRF 0.063 0.012 -10000 0 -10000 0 0
HDAC4/ER alpha 0.044 0.012 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.032 0.082 152 -0.094 4 156
cell motility 0.058 0.02 -10000 0 -0.043 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 0.03 0.008 -10000 0 -10000 0 0
HDAC6/HDAC11 0.047 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.039 -10000 0 -0.098 37 37
NPC 0.019 0.002 -10000 0 -0.014 1 1
MEF2C 0.026 0.012 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.075 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 0.022 0.028 -10000 0 -0.065 45 45
nuclear import -0.032 0.023 0.11 10 -10000 0 10
Aurora C signaling

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
INCENP 0.032 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.049 0.032 -9999 0 -0.044 32 32
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
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.005 0 12 -0.041 15 27
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 -0.008 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 0.029 0.013 -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 -0.039 8 8
MAPT -0.024 0.045 0.14 3 -0.14 16 19
MAPK13 -0.023 0.006 0 12 -0.051 15 27
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.007 -10000 0 -0.037 8 8
Atypical NF-kappaB pathway

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
BCL3/RelA 0.045 0.012 -10000 0 -10000 0 0
FBXW11 0.032 0.004 -10000 0 0 10 10
NF kappa B1 p50/c-Rel 0.028 0.011 -10000 0 -0.04 12 12
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.049 0.18 2 -0.18 10 12
NFKBIA 0.004 0.032 0.11 23 -0.097 25 48
MAPK14 0.032 0.005 -10000 0 -0.065 1 1
NF kappa B1 p105/p50 0.027 0.011 -10000 0 -0.039 11 11
ARRB2 0.012 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 10 10
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.012 -10000 0 -0.04 12 12
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 0.029 0.009 -10000 0 -10000 0 0
NFKB1 -0.022 0.005 -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 0.024 0.051 0.17 2 -0.2 9 11
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 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.004 -10000 0 0 10 10
SYK 0.025 0.025 -10000 0 -0.065 35 35
I kappa B alpha/PIK3R1 0.02 0.046 0.18 2 -0.2 7 9
cell death 0.023 0.049 0.17 2 -0.19 9 11
NF kappa B1 p105/c-Rel 0.028 0.011 -10000 0 -0.04 12 12
LCK 0.031 0.01 -10000 0 -0.065 4 4
BCL3 0.031 0.007 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.033 0.041 -10000 0 -0.056 1 1
TC10/GTP 0.026 0.04 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.033 -10000 0 -0.053 2 2
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 -0.021 0.14 -10000 0 -0.57 29 29
AKT1 -0.022 0.06 0.24 6 -10000 0 6
INSR 0.034 0.01 0.07 21 -10000 0 21
Insulin Receptor/Insulin 0.058 0.031 0.21 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.018 -10000 0 -0.065 6 6
SORBS1 0.024 0.014 -10000 0 -10000 0 0
CRK 0.032 0.004 -10000 0 -10000 0 0
PTPN1 -0.018 0.024 0.14 9 -10000 0 9
CAV1 -0.025 0.03 0.18 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.045 0.05 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.077 0.033 -10000 0 -0.053 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.037 -10000 0 -0.059 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.027 0.037 0.18 17 -0.19 3 20
RPS6KB1 -0.027 0.055 0.22 6 -10000 0 6
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 0.019 0.014 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.033 0.058 0.15 24 -10000 0 24
HRAS/GTP -0.032 0.018 0.029 22 -0.068 1 23
Insulin Receptor 0.034 0.01 0.07 21 -10000 0 21
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.074 0.054 -10000 0 -0.074 1 1
PRKCI 0.034 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 -0.065 40 40
negative regulation of MAPKKK cascade 0.031 0.044 -10000 0 -10000 0 0
PI3K 0.064 0.044 -10000 0 -10000 0 0
NCK2 0.032 0.004 -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 0.055 0.23 5 -10000 0 5
PRKCZ 0.016 0.017 -10000 0 -0.29 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.018 0.039 0.16 18 -10000 0 18
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 55 55
TC10/GTP/CIP4/Exocyst 0.041 0.012 -10000 0 -0.041 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.044 -10000 0 -0.048 37 37
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
RASA1 0.031 0.006 -10000 0 -10000 0 0
NCK1 0.029 0.015 -10000 0 -0.065 11 11
CBL/APS/CAP/Crk-II 0.037 0.041 -10000 0 -0.038 8 8
TC10/GDP 0.024 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.05 -10000 0 -0.053 36 36
INPP5D -0.018 0.013 0.032 27 -10000 0 27
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 0.004 -10000 0 -10000 0 0
IRS1 0.031 0.009 -10000 0 -0.065 4 4
p62DOK/RasGAP 0.032 0.044 -10000 0 -10000 0 0
INS 0.035 0.013 0.077 33 -10000 0 33
mol:PI-3-4-P2 -0.018 0.013 0.032 27 -10000 0 27
GRB2 0.031 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.041 0.042 0.24 2 -10000 0 2
PTPRA 0.031 0.01 0.07 1 -10000 0 1
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
TC10/GTP/CIP4 0.041 0.012 -10000 0 -0.041 6 6
PDPK1 0.032 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.027 -10000 0 -0.11 16 16
Insulin Receptor/Insulin/IRS1 0.059 0.025 -10000 0 -0.034 20 20
Insulin Receptor/Insulin/IRS3 0.049 0.019 0.11 21 -10000 0 21
Par3/Par6 0.069 0.025 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 -0.014 0.01 -10000 0 -0.04 61 61
SMARCC1 0.003 0.034 -10000 0 -0.6 1 1
REL 0.032 0.001 -10000 0 -10000 0 0
HDAC7 -0.036 0.031 0.14 3 -0.14 2 5
JUN 0.032 0.004 -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 0.02 28 -0.052 1 29
FOXO1 0.028 0.016 -10000 0 -0.065 11 11
T-DHT/AR -0.034 0.041 0.19 3 -0.16 1 4
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
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 0.032 0.003 -10000 0 -10000 0 0
cell proliferation -0.021 0.074 0.25 7 -0.24 21 28
NR0B1 0.023 0.028 -10000 0 -0.065 46 46
EGR1 0.029 0.017 -10000 0 -0.065 15 15
RXRs/9cRA 0.057 0.021 -10000 0 -0.043 3 3
AR/RACK1/Src -0.022 0.053 0.17 13 -0.15 1 14
AR/GR 0.003 0.044 0.14 3 -0.19 7 10
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.029 0.014 -10000 0 -0.065 8 8
RCHY1 0.032 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.016 0.012 0.019 15 -10000 0 15
T-DHT/AR/TIF2/CARM1 -0.029 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 0.061 -10000 0 -0.47 2 2
APPBP2 0.032 0.004 -10000 0 -10000 0 0
TRIM24 0.022 0.016 -10000 0 -0.065 2 2
T-DHT/AR/TIP60 -0.029 0.02 0.042 3 -0.1 7 10
TMPRSS2 0.013 0.068 -10000 0 -0.5 8 8
RXRG 0.031 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 0.006 -10000 0 -10000 0 0
NR2C2 0.032 0.004 -10000 0 -10000 0 0
KLK2 -0.015 0.045 0.17 6 -0.18 12 18
AR -0.003 0.017 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 0.028 0.01 -10000 0 -0.066 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.031 0.005 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.032 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.023 0.054 0.18 13 -0.16 1 14
positive regulation of transcription 0.031 0.005 -10000 0 -10000 0 0
DNAJA1 0.03 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.019 -10000 0 -0.2 3 3
NCOA1 0.032 0.019 0.11 4 -10000 0 4
SPDEF 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.034 0.079 0.13 4 -0.24 42 46
T-DHT/AR/Hsp90 -0.028 0.036 0.18 5 -0.16 1 6
GSK3B 0.031 0.006 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.015 -10000 0 -10000 0 0
SIRT1 0.025 0.014 -10000 0 -10000 0 0
ZMIZ2 0.022 0.015 -10000 0 0 152 152
POU2F1 0.036 0.009 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.032 0.036 0.18 5 -0.15 1 6
CREBBP 0.032 0.003 -10000 0 0 6 6
SMARCE1 0.032 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.03 0.007 -10000 0 -10000 0 0
SPHK1 0.028 0.018 -10000 0 -0.065 18 18
GNAI2 0.031 0.005 -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 0.027 0.034 -10000 0 -0.11 14 14
GNAI3 0.02 0.031 -10000 0 -0.065 59 59
G12/G13 0.033 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 0.001 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 0.042 -10000 0 -0.22 18 18
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.026 0.012 -10000 0 -10000 0 0
GNA14 0.031 0.008 -10000 0 -0.065 2 2
GNA15 0.03 0.013 -10000 0 -0.065 7 7
GNA12 0.022 0.015 -10000 0 -10000 0 0
GNA13 0.031 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
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.054 0.16 0.46 1 -0.7 1 2
STAT6 (cleaved dimer) -0.052 0.14 -10000 0 -0.7 2 2
IGHG1 -0.023 0.084 -10000 0 -0.49 1 1
IGHG3 -0.064 0.14 -10000 0 -0.66 2 2
AKT1 -0.023 0.11 -10000 0 -0.62 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.001 0.078 -10000 0 -0.6 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.015 0.1 -10000 0 -0.63 1 1
THY1 -0.17 0.31 -10000 0 -0.75 41 41
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 -0.046 202 202
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.025 0.025 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.045 0.15 -10000 0 -0.73 1 1
SOCS1 -0.044 0.13 0.29 1 -0.54 1 2
SOCS3 -0.029 0.095 -10000 0 -0.56 1 1
FCER2 -0.047 0.13 -10000 0 -0.65 1 1
PARP14 0.001 0 -10000 0 -10000 0 0
CCL17 -0.07 0.15 -10000 0 -0.7 1 1
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.018 0.086 -10000 0 -0.59 1 1
T cell proliferation -0.057 0.15 -10000 0 -0.85 1 1
IL4R/JAK1 -0.06 0.16 -10000 0 -0.69 1 1
EGR2 -0.071 0.15 -10000 0 -0.72 1 1
JAK2 0.007 0.038 -10000 0 -10000 0 0
JAK3 0.031 0.013 -10000 0 -0.042 1 1
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
JAK1 0.019 0.026 -10000 0 -10000 0 0
COL1A2 -0.054 0.11 -10000 0 -0.72 5 5
CCL26 -0.066 0.15 -10000 0 -0.68 2 2
IL4R -0.071 0.16 -10000 0 -0.72 1 1
PTPN6 0.03 0.018 -10000 0 -0.046 19 19
IL13RA2 -0.089 0.16 -10000 0 -0.7 1 1
IL13RA1 0 0.05 -10000 0 -0.1 5 5
IRF4 0.012 0.065 -10000 0 -0.44 3 3
ARG1 -0.021 0.09 -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 63 63
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
IL13RA1/JAK2 0.003 0.055 -10000 0 -10000 0 0
IRF4/BCL6 0.019 0.068 -10000 0 -0.42 3 3
CD40LG 0.035 0.004 -10000 0 -0.04 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 -0.07 0.17 -10000 0 -0.75 2 2
SPI1 0.032 0.013 -10000 0 -0.063 8 8
RPS6KB1 -0.023 0.11 -10000 0 -0.57 3 3
STAT6 (dimer) -0.069 0.17 -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 0.09 -10000 0 -0.63 1 1
FRAP1 -0.021 0.11 -10000 0 -0.61 3 3
LTA -0.07 0.15 -10000 0 -0.74 1 1
FES 0.032 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.07 0.16 0.74 2 -10000 0 2
CCL11 -0.067 0.15 -10000 0 -0.66 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.011 0.096 -10000 0 -0.88 1 1
IL2RG 0.03 0.019 -10000 0 -0.06 11 11
IL10 -0.065 0.16 -10000 0 -0.7 1 1
IRS1 0.031 0.009 -10000 0 -0.065 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
IL4 -0.011 0.085 -10000 0 -0.59 5 5
IL5 -0.07 0.15 -10000 0 -0.7 1 1
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.067 0.15 -10000 0 -0.72 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 -0.063 0.16 -10000 0 -0.71 1 1
IL2R gamma/JAK3 0.047 0.02 -10000 0 -0.047 14 14
TFF3 -0.07 0.15 -10000 0 -0.7 1 1
ALOX15 -0.07 0.15 -10000 0 -10000 0 0
MYBL1 0.017 0.035 -10000 0 -0.065 78 78
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 0.11 -10000 0 -0.9 1 1
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 0.032 0.014 -10000 0 -0.036 7 7
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 -0.7 1 1
PIGR -0.065 0.16 -10000 0 -0.7 1 1
IGHE 0.014 0.041 0.14 24 -0.095 3 27
MAPKKK cascade -0.016 0.083 -10000 0 -0.52 1 1
BCL6 0.028 0.017 -10000 0 -0.066 15 15
OPRM1 -0.07 0.15 -10000 0 -0.7 1 1
RETNLB -0.066 0.15 -10000 0 -0.68 2 2
SELP -0.067 0.16 -10000 0 -0.7 1 1
AICDA -0.063 0.15 0.41 1 -0.71 1 2
Reelin signaling 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
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
VLDLR 0.028 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 0.01 -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 -0.046 6 6
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.058 -10000 0 -10000 0 0
AKT1 -0.005 0.029 -10000 0 -0.13 25 25
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.031 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.019 0.029 -10000 0 -0.041 4 4
LRPAP1/LRP8 0.046 0.009 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.02 0.036 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin 0.016 0.038 -10000 0 -10000 0 0
long-term memory 0.016 0.036 0.17 5 -10000 0 5
DAB1/LIS1 0.025 0.045 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.019 0.038 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
DAB1/NCK2 0.026 0.046 -10000 0 -10000 0 0
ARHGEF2 0.031 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 0.029 0.009 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.018 0.03 -10000 0 -0.049 2 2
GRIN2A/RELN/LRP8/DAB1/Fyn 0.019 0.04 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.017 0.03 -10000 0 -0.042 4 4
ITGB1 0.025 0.013 -10000 0 -10000 0 0
MAP1B 0.008 0.051 0.15 57 -10000 0 57
RELN/LRP8 0.02 0.031 -10000 0 -0.049 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn 0.024 0.044 -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 0.054 0.094 0.32 19 -10000 0 19
PAFAH1B1 0.031 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.005 -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 0.004 -10000 0 -10000 0 0
neuron differentiation -0.015 0.059 -10000 0 -0.17 39 39
neuron adhesion 0.04 0.093 0.31 20 -10000 0 20
LRP8 0.031 0.005 -10000 0 -10000 0 0
GSK3B -0.004 0.041 0.077 47 -0.14 27 74
RELN/VLDLR/DAB1/Fyn 0.019 0.036 -10000 0 -10000 0 0
MAP3K11 0.032 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.003 0.019 -10000 0 -0.1 11 11
CDK5 0.02 0.016 -10000 0 -10000 0 0
MAPT 0.004 0.056 0.72 1 -10000 0 1
neuron migration -0.015 0.081 0.19 46 -0.16 15 61
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.059 -10000 0 -0.17 39 39
RELN/VLDLR 0.023 0.039 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.017 0.007 -10000 0 -10000 0 0
NFATC2 -0.01 0.004 -10000 0 -10000 0 0
NFATC3 -0.018 0.007 -10000 0 -10000 0 0
CD40LG -0.039 0.039 0.3 1 -10000 0 1
PTGS2 -0.04 0.039 0.19 4 -10000 0 4
JUNB 0.029 0.013 -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 0.008 -10000 0 -0.02 4 4
CALM1 0.028 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 -0.001 38 38
FOSL1 0.029 0.015 -10000 0 -0.065 12 12
CREM 0.025 0.013 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.023 0.032 -10000 0 -10000 0 0
FOS 0.007 0.041 -10000 0 -0.066 120 120
IFNG -0.038 0.036 -10000 0 -10000 0 0
AP-1/NFAT1-c-4 0.032 0.073 0.2 4 -0.11 3 7
FASLG -0.039 0.039 0.3 1 -10000 0 1
NFAT1-c-4/ICER1 0.004 0.036 -10000 0 -10000 0 0
IL2RA -0.03 0.038 0.3 1 -10000 0 1
FKBP12/FK506 0.022 0.007 -10000 0 -0.04 1 1
CSF2 -0.039 0.04 0.3 1 -10000 0 1
JunB/Fra1/NFAT1-c-4 0.032 0.041 0.15 6 -10000 0 6
IL4 -0.039 0.04 0.3 1 -10000 0 1
IL2 0.015 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
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.032 0.004 -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 -0.041 40 40
HRAS 0.031 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.024 0.014 -10000 0 -0.06 10 10
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.023 -10000 0 -0.048 10 10
AKT1 -0.022 0.046 0.17 18 -10000 0 18
BAD -0.027 0.044 0.16 18 -10000 0 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.032 0.018 0.21 1 -0.073 7 8
RAF1 -0.007 0.055 0.24 4 -0.43 3 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.053 0.02 -10000 0 -0.057 11 11
YWHAZ 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.015 -10000 0 -0.059 11 11
PIK3CA 0.028 0.018 -10000 0 -0.065 17 17
RPS6KB1 -0.024 0.046 0.16 21 -10000 0 21
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.012 0.053 0.21 7 -0.35 3 10
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.029 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 -0.068 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.059 0.039 -10000 0 -0.063 1 1
IGF-1R heterotetramer 0.033 0.008 -10000 0 -0.033 6 6
IGF-1R heterotetramer/IGF1/IRS/Nck 0.057 0.02 -10000 0 -0.071 7 7
Crk/p130 Cas/Paxillin 0.047 0.018 0.21 1 -0.071 7 8
IGF1R 0.033 0.008 -10000 0 -0.033 6 6
IGF1 0.032 0.012 -10000 0 -0.053 9 9
IRS2/Crk -0.026 0.009 -10000 0 -10000 0 0
PI3K 0.061 0.037 -10000 0 -0.073 5 5
apoptosis 0.028 0.049 -10000 0 -0.15 22 22
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
PRKCD 0.001 0.02 -10000 0 -0.14 5 5
RAF1/14-3-3 E -0.007 0.057 0.24 4 -0.38 3 7
BAD/14-3-3 -0.029 0.051 0.16 22 -10000 0 22
PRKCZ -0.018 0.045 0.17 20 -10000 0 20
Crk/p130 Cas/Paxillin/FAK1 -0.038 0.04 0.12 16 -10000 0 16
PTPN1 0.03 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.009 0.024 -10000 0 -0.12 13 13
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.042 0.047 -10000 0 -0.072 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.032 0.018 0.13 4 -0.07 7 11
GRB10 0.021 0.018 -10000 0 -0.065 6 6
PTPN11 -0.022 0.006 -10000 0 -10000 0 0
IRS1 -0.016 0.014 0.12 4 -10000 0 4
IRS2 -0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.045 0.011 -10000 0 -0.056 4 4
GRB2 0.031 0.006 -10000 0 -10000 0 0
PDPK1 -0.019 0.048 0.18 20 -10000 0 20
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKD1 -0.004 0.023 -10000 0 -0.14 9 9
SHC1 0.024 0.026 -10000 0 -0.065 40 40
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.009 0.079 -10000 0 -0.21 48 48
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 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.027 0.074 -10000 0 -0.22 48 48
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 0.038 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 0.031 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 0.041 0.012 -10000 0 -0.041 6 6
AS160/14-3-3 -0.021 0.043 0.1 1 -0.16 17 18
VAMP2 0.029 0.01 -10000 0 -10000 0 0
SLC2A4 -0.03 0.08 -10000 0 -0.24 48 48
STX4 0.032 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN 0.025 0.024 -10000 0 -0.065 31 31
LNPEP 0.031 0.006 -10000 0 -0.065 1 1
YWHAE 0.032 0.005 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0.021 0.016 -10000 0 -0.1 7 7
TRAF2/ASK1 0.039 0.014 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.065 25 25
MAP2K3 0.028 0.057 0.17 2 -0.27 8 10
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.054 0.16 8 -0.22 10 18
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 0.029 0.013 -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 0.03 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 0.042 0.016 -10000 0 -0.051 2 2
TAK1/TAB family 0.002 0.022 0.075 39 -0.069 6 45
RAC1/OSM/MEKK3 0.029 0.019 -10000 0 -0.023 3 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.022 0.046 -10000 0 -0.21 10 10
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 0.012 -10000 0 -10000 0 0
MAPK11 0.029 0.009 -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 0.051 0.047 -10000 0 -0.057 7 7
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.03 0.029 -10000 0 -10000 0 0
epithelial cell differentiation 0.009 0.064 -10000 0 -10000 0 0
ITCH 0.031 0.012 -10000 0 -0.054 2 2
WWP1 0.009 0.023 0.21 6 -10000 0 6
FYN 0.029 0.01 -10000 0 -0.065 1 1
EGFR 0.012 0.017 -10000 0 -0.065 5 5
PRL 0.031 0.011 -10000 0 -0.065 6 6
neuron projection morphogenesis -0.022 0.049 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 0.052 0.048 0.23 2 -10000 0 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.013 0.019 -10000 0 -10000 0 0
ADAM17 0.029 0.017 -10000 0 -0.061 4 4
ErbB4/ErbB4 0.013 0.014 0.12 6 -0.059 2 8
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 0.029 0.026 -10000 0 -10000 0 0
GRIN2B -0.012 0.024 0.24 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.03 0.027 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
HBEGF 0.031 0.007 -10000 0 -0.065 2 2
PRLR 0.032 0.005 -10000 0 -10000 0 0
E4ICDs/ETO2 0.03 0.029 -10000 0 -10000 0 0
axon guidance -0.007 0.044 0.21 2 -0.24 1 3
NEDD4 0.026 0.022 -10000 0 -0.067 13 13
Prolactin receptor/Prolactin receptor/Prolactin 0.045 0.013 -10000 0 -0.051 6 6
CBFA2T3 0.031 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.031 0.026 -10000 0 -10000 0 0
MAPK3 -0.017 0.051 0.23 8 -10000 0 8
STAT1 (dimer) 0.029 0.031 -10000 0 -10000 0 0
MAPK1 -0.016 0.049 0.19 19 -10000 0 19
JAK2 0.029 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.019 -10000 0 -10000 0 0
NRG1 -0.021 0.012 0.024 13 -10000 0 13
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 -0.007 0.044 0.21 2 -0.24 1 3
neural crest cell migration 0.012 0.019 -10000 0 -10000 0 0
ERBB2 -0.021 0.012 0.021 30 -10000 0 30
WWOX/E4ICDs 0.03 0.029 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.065 40 40
ErbB4/EGFR/neuregulin 4 0.011 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 0.03 0.029 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.03 0.028 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.03 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.064 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 0.028 0.018 -10000 0 -10000 0 0
STAT5A -0.015 0.046 0.21 2 -0.23 1 3
ErbB4/EGFR/neuregulin 1 beta 0.012 0.021 -10000 0 -10000 0 0
DLG4 0.031 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.037 0.028 -10000 0 -0.051 40 40
E4ICDs/TAB2/NCoR1 0.027 0.027 -10000 0 -10000 0 0
STAT5A (dimer) 0.017 0.073 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.002 0.058 0.23 1 -0.23 1 2
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 -0.008 0.044 0.21 2 -0.24 1 3
ERBB4 0.013 0.015 0.12 6 -0.059 2 8
STAT5B 0.032 0.003 -10000 0 -10000 0 0
YAP1 0.01 0.056 -10000 0 -0.44 6 6
GRB2 0.031 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 0.027 -10000 0 -10000 0 0
WWOX 0.031 0.006 -10000 0 -10000 0 0
cell proliferation -0.002 0.031 0.21 2 -0.22 2 4
RXR and RAR heterodimerization with other nuclear receptor

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
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 0.039 -10000 0 -0.15 15 15
RXRs/LXRs/DNA/Oxysterols -0.031 0.046 -10000 0 -0.17 17 17
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 0.02 0.034 -10000 0 -0.15 18 18
RXRs/NUR77 0.058 0.031 -10000 0 -10000 0 0
RXRs/PPAR 0.003 0.046 -10000 0 -0.12 54 54
NCOR2 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.004 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.07 0.025 -10000 0 -10000 0 0
RARA 0.032 0.003 -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 0.015 -10000 0 -10000 0 0
RARG 0.032 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.059 0.56 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.022 0.032 -10000 0 -0.16 14 14
THRA 0.032 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.004 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.012 0.053 -10000 0 -10000 0 0
NR1H4 0.032 0.003 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.017 0.073 -10000 0 -10000 0 0
NR1H2 -0.009 0.027 -10000 0 -10000 0 0
NR1H3 -0.011 0.028 -10000 0 -0.052 8 8
RXRs/VDR/DNA/Vit D3 0.052 0.03 -10000 0 -10000 0 0
NR4A1 0.031 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 17 17
RXRG -0.007 0.029 -10000 0 -0.062 4 4
RXR alpha/CCPG 0.018 0.007 -10000 0 -0.018 11 11
RXRA -0.007 0.028 -10000 0 -10000 0 0
RXRB -0.008 0.029 -10000 0 -0.036 1 1
THRB 0.032 0.004 -10000 0 -10000 0 0
PPARG 0.031 0.01 -10000 0 -0.02 13 13
PPARD 0.032 0.002 -10000 0 -10000 0 0
TNF -0.033 0.041 -10000 0 -0.16 16 16
mol:Oxysterols -0.005 0.004 -10000 0 -10000 0 0
cholesterol transport -0.031 0.045 -10000 0 -0.17 17 17
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 0.01 0.033 -10000 0 -0.12 29 29
SREBF1 -0.032 0.041 -10000 0 -0.16 16 16
RXRs/RXRs/DNA/9cRA -0.012 0.052 -10000 0 -10000 0 0
ABCA1 -0.06 0.056 -10000 0 -0.19 15 15
RARs/THRs 0.09 0.027 -10000 0 -10000 0 0
RXRs/FXR 0.059 0.03 -10000 0 -10000 0 0
BCL2 0.031 0.006 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.029 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.008 -10000 0 -0.067 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 0.025 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.049 0.03 -10000 0 -0.04 16 16
neuron projection morphogenesis 0.006 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.027 0.16 2 -10000 0 2
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.006 0.032 0.2 1 -0.37 3 4
YES1 0.008 0.061 -10000 0 -0.61 4 4
Ephrin B1/EPHB1-2/NCK2 0.011 0.027 0.16 2 -10000 0 2
PI3K 0.038 0.048 -10000 0 -0.36 4 4
mol:GDP 0.011 0.026 0.16 2 -10000 0 2
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 -0.39 3 3
FGR 0.012 0.058 -10000 0 -0.6 4 4
TIAM1 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
RGS3 0.031 0.007 -10000 0 -0.065 1 1
cell adhesion 0.019 0.042 -10000 0 -0.31 5 5
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 0.047 0.005 -10000 0 -10000 0 0
BLK 0.013 0.058 -10000 0 -0.58 4 4
HCK 0.01 0.057 -10000 0 -0.59 4 4
regulation of stress fiber formation -0.011 0.026 -10000 0 -0.16 2 2
MAPK8 -0.009 0.039 -10000 0 -0.38 4 4
Ephrin B1/EPHB1-2/RGS3 0.011 0.026 0.16 1 -10000 0 1
endothelial cell migration 0.047 0.095 0.19 137 -0.33 3 140
NCK2 0.032 0.004 -10000 0 -10000 0 0
PTPN13 0.026 0.024 -10000 0 -0.075 25 25
regulation of focal adhesion formation -0.011 0.026 -10000 0 -0.16 2 2
chemotaxis -0.011 0.025 -10000 0 -0.16 1 1
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 0.012 0.058 -10000 0 -0.6 4 4
Circadian rhythm pathway

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.019 0.064 -9999 0 -0.26 1 1
CLOCK 0.021 0.023 -9999 0 -10000 0 0
TIMELESS/CRY2 0.01 0.052 -9999 0 -0.26 1 1
DEC1/BMAL1 0.045 0.011 -9999 0 -10000 0 0
ATR 0.031 0.005 -9999 0 -10000 0 0
NR1D1 -0.002 0.029 -9999 0 -0.24 1 1
ARNTL 0.021 0.024 -9999 0 -0.034 1 1
TIMELESS -0.01 0.044 -9999 0 -0.27 1 1
NPAS2 0.021 0.024 -9999 0 -0.064 1 1
CRY2 0.031 0.005 -9999 0 -10000 0 0
mol:CO 0.001 0.011 -9999 0 -10000 0 0
CHEK1 0.02 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 0.045 0.046 -9999 0 -10000 0 0
BMAL1/CLOCK 0.011 0.042 -9999 0 -0.34 1 1
S phase of mitotic cell cycle 0.019 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 0.031 0.006 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.013 -9999 0 -10000 0 0
ITGB7 0.031 0.007 -9999 0 -0.065 2 2
ITGA4 0.031 0.01 -9999 0 -0.047 7 7
alpha4/beta7 Integrin 0.046 0.013 -9999 0 -0.062 5 5
alpha4/beta1 Integrin 0.036 0.021 -9999 0 -0.051 4 4
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 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 0.049 0.029 -10000 0 -10000 0 0
TBX21 -0.019 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 -10000 0 0
T-helper cell lineage commitment 0.046 0.083 -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 0.028 0.018 -10000 0 -0.066 18 18
IL12RB1 0.031 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.021 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) 0.055 0.035 -10000 0 -10000 0 0
JAK2 0.028 0.01 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.021 0.069 -10000 0 -10000 0 0
T cell proliferation -0.003 0.033 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.03 0.091 -10000 0 -0.66 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 -0.086 11 12
T cell differentiation -0.001 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.072 0.23 9 -10000 0 9
STAT5A (dimer) 0.021 0.072 -10000 0 -10000 0 0
STAT4 (dimer) 0.014 0.048 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 -0.014 0.008 0 6 -0.04 43 49
positive regulation of mast cell cytokine production 0.02 0.071 0.23 9 -10000 0 9
IL27/EBI3 0.023 0.009 -10000 0 -0.043 2 2
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 -10000 0 -0.04 13 13
EBI3 0.031 0.011 -10000 0 -0.065 3 3
TNF -0.011 0.002 0 4 -0.04 2 6
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 0.004 0.12 -10000 0 -10000 0 0
ITGA3 0.003 0.1 -10000 0 -10000 0 0
IL17F -0.011 0.085 -10000 0 -0.37 1 1
IL12B 0.026 0.03 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.12 -10000 0 -0.49 1 1
CD4 0.004 0.12 0.4 1 -10000 0 1
IL23 0.026 0.096 -10000 0 -10000 0 0
IL23R 0.003 0.031 0.098 1 -10000 0 1
IL1B 0.006 0.097 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.005 0.12 -10000 0 -10000 0 0
TYK2 0.021 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 0.032 0.003 -10000 0 -0.026 1 1
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 0.045 0.14 1 -10000 0 1
positive regulation of chronic inflammatory response 0.004 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 0.029 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.01 -10000 0 -0.069 4 4
RELA 0.032 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.026 0.095 -10000 0 -10000 0 0
ALOX12B 0 0.11 -10000 0 -10000 0 0
CXCL1 -0.001 0.12 -10000 0 -10000 0 0
T cell proliferation 0.004 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 0.021 0.12 -10000 0 -10000 0 0
IFNG 0.005 0.016 0.072 2 -0.068 15 17
STAT3 (dimer) 0.03 0.13 -10000 0 -10000 0 0
IL18R1 0.032 0.003 -10000 0 -0.026 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.008 0.092 0.27 2 -0.37 1 3
IL18/IL18R 0.056 0.033 -10000 0 -0.049 17 17
macrophage activation -0.001 0.006 -10000 0 -10000 0 0
TNF 0.006 0.096 -10000 0 -10000 0 0
STAT3/STAT4 0 0.11 -10000 0 -10000 0 0
STAT4 (dimer) -0.001 0.098 -10000 0 -10000 0 0
IL18 0.024 0.027 -10000 0 -0.063 44 44
IL19 0.005 0.12 -10000 0 -10000 0 0
STAT5A (dimer) 0.013 0.12 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.065 18 18
SOCS3 0.032 0.003 -10000 0 -10000 0 0
CXCL9 -0.004 0.12 -10000 0 -10000 0 0
MPO 0.002 0.11 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.004 0.12 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.005 0.12 -10000 0 -10000 0 0
IL6 0.055 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 0.001 0.11 -10000 0 -10000 0 0
keratinocyte proliferation 0.004 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 0.014 -9999 0 -0.022 25 25
MAPK9 0.006 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.002 0 8 -0.04 1 9
GNB1/GNG2 0.02 0.005 -9999 0 -10000 0 0
GNB1 0.03 0.008 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.006 0.002 -9999 0 -0.038 1 1
Gs family/GTP 0.02 0.003 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 0 7 7
GNAL 0.031 0.005 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.032 0.006 -9999 0 -0.065 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.005 0.003 -9999 0 -10000 0 0
MAPK11 0.006 0.002 -9999 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 0.004 -9999 0 0 10 10
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.004 -9999 0 0 10 10
CHUK 0.024 0.014 -9999 0 -0.065 1 1
NF kappa B2 p100/RelB 0.055 0.064 -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 0.03 0.008 -9999 0 -0.065 1 1
NFKB2 0.024 0.014 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.032 0.02 -9999 0 -0.041 1 1
regulation of B cell activation 0.031 0.019 -9999 0 -0.041 1 1
Visual signal transduction: Rods

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
mol:K + 0.032 0.004 -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 -10000 0 0
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 0.031 0.005 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.059 0.024 -10000 0 -10000 0 0
mol:Na + 0.037 0.017 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.041 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.046 0.019 -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 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.024 0.15 8 -10000 0 8
Na + (4 Units) 0.034 0.019 -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 0.004 -10000 0 -10000 0 0
GNGT1 0.022 0.015 -10000 0 -10000 0 0
GUCY2F 0.032 0.002 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.028 0.005 -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 -0.035 1 1
GNB1 0.03 0.008 -10000 0 -10000 0 0
Rhodopsin 0.045 0.012 -10000 0 -0.051 1 1
SLC24A1 0.032 0.004 -10000 0 -10000 0 0
CNGA1 0.032 0.003 -10000 0 -10000 0 0
Metarhodopsin II 0.02 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.01 -10000 0 -0.023 12 12
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 0.002 -10000 0 -10000 0 0
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 0.038 0.032 -10000 0 -0.038 2 2
PDE6B 0.032 0.003 -10000 0 -10000 0 0
PDE6A 0.032 0.003 -10000 0 -10000 0 0
PDE6G 0.032 0.003 -10000 0 -10000 0 0
RHO 0.031 0.005 -10000 0 -10000 0 0
PDE6 0.074 0.025 -10000 0 -10000 0 0
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.04 0.008 -10000 0 -0.023 6 6
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.032 0.003 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.023 0.015 -9999 0 -9999 0 0
PLK4 0.032 0.004 -9999 0 -9999 0 0
regulation of centriole replication -0.016 0.01 -9999 0 -9999 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.041 0.008 -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 0.041 0.008 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.042 0.008 -10000 0 -9999 0 0
EPHA5 0.031 0.005 -10000 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 -0.031 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.031 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 0.018 -0.36 0.018
47_PPARGC1A 0.032 0.032 0.032 0.032
105_BMP4 0.032 0.032 0 0.032
105_BMP6 0.032 0.032 0 0.032
105_BMP7 0.032 0.032 0 0.032
105_BMP2 0.032 0.032 -0.065 0.032
131_RELN/VLDLR 0 0 0.083 0
30_TGFB1/TGF beta receptor Type II 0 0.032 0 -0.065
84_STAT5B 0.044 0.034 -0.32 0.034
84_STAT5A 0.044 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/9825043/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/10005907/GDAC_Gistic2Report_10015626/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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