PARADIGM pathway analysis of mRNASeq expression and copy number data
Brain Lower Grade Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18051NC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C18051NC
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 57 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
Ephrin A reverse signaling 95
IL23-mediated signaling events 89
Signaling mediated by p38-alpha and p38-beta 68
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 64
Aurora B signaling 63
IL12-mediated signaling events 61
FOXM1 transcription factor network 61
TCR signaling in naïve CD8+ T cells 58
Signaling events regulated by Ret tyrosine kinase 55
Thromboxane A2 receptor signaling 52
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 516 . 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 ( 516 ).

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
Ephrin A reverse signaling 0.1841 95 670 7 -0.063 0 1000 -1000 -0.008 -1000
IL23-mediated signaling events 0.1725 89 5349 60 -0.49 0.026 1000 -1000 -0.068 -1000
Signaling mediated by p38-alpha and p38-beta 0.1318 68 3031 44 -0.1 0.026 1000 -1000 -0.017 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1240 64 4357 68 -0.3 0.18 1000 -1000 -0.068 -1000
Aurora B signaling 0.1221 63 4233 67 -0.26 0.046 1000 -1000 -0.029 -1000
IL12-mediated signaling events 0.1182 61 5391 87 -0.4 0.073 1000 -1000 -0.065 -1000
FOXM1 transcription factor network 0.1182 61 3155 51 -0.27 0.026 1000 -1000 -0.096 -1000
TCR signaling in naïve CD8+ T cells 0.1124 58 5431 93 -0.18 0.21 1000 -1000 -0.035 -1000
Signaling events regulated by Ret tyrosine kinase 0.1066 55 4571 82 -0.074 0.026 1000 -1000 -0.041 -1000
Thromboxane A2 receptor signaling 0.1008 52 5490 105 -0.13 0.034 1000 -1000 -0.03 -1000
Endothelins 0.0988 51 4914 96 -0.13 0.026 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 0.0969 50 1720 34 -0.075 0.026 1000 -1000 -0.032 -1000
Reelin signaling pathway 0.0969 50 2840 56 -0.1 0.059 1000 -1000 -0.025 -1000
E-cadherin signaling events 0.0969 50 251 5 -0.046 0.026 1000 -1000 0.007 -1000
Signaling events mediated by the Hedgehog family 0.0911 47 2487 52 -0.093 0.048 1000 -1000 -0.03 -1000
TCGA08_retinoblastoma 0.0891 46 371 8 -0.023 0.042 1000 -1000 -0.001 -1000
Effects of Botulinum toxin 0.0872 45 1178 26 -0.088 0.026 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0.0853 44 2904 65 -0.1 0.037 1000 -1000 -0.039 -1000
Syndecan-4-mediated signaling events 0.0853 44 3013 67 -0.094 0.035 1000 -1000 -0.033 -1000
FOXA2 and FOXA3 transcription factor networks 0.0833 43 1980 46 -0.22 0.03 1000 -1000 -0.09 -1000
Syndecan-3-mediated signaling events 0.0795 41 1465 35 -0.061 0.063 1000 -1000 -0.015 -1000
Aurora C signaling 0.0756 39 273 7 -0.072 0.011 1000 -1000 -0.014 -1000
IL4-mediated signaling events 0.0756 39 3575 91 -0.42 0.27 1000 -1000 -0.098 -1000
BCR signaling pathway 0.0756 39 3877 99 -0.095 0.044 1000 -1000 -0.036 -1000
Arf6 signaling events 0.0736 38 2415 62 -0.14 0.054 1000 -1000 -0.039 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0736 38 2813 74 -0.063 0.059 1000 -1000 -0.045 -1000
Caspase cascade in apoptosis 0.0717 37 2739 74 -0.13 0.05 1000 -1000 -0.041 -1000
HIF-1-alpha transcription factor network 0.0717 37 2866 76 -0.11 0.056 1000 -1000 -0.052 -1000
a4b1 and a4b7 Integrin signaling 0.0717 37 187 5 -0.008 0.012 1000 -1000 0.005 -1000
p75(NTR)-mediated signaling 0.0698 36 4568 125 -0.073 0.063 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.0698 36 762 21 -0.034 0.037 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.0698 36 1902 52 -0.1 0.026 1000 -1000 -0.023 -1000
amb2 Integrin signaling 0.0678 35 2949 82 -0.15 0.028 1000 -1000 -0.03 -1000
Nongenotropic Androgen signaling 0.0678 35 1827 52 -0.075 0.036 1000 -1000 -0.021 -1000
LPA receptor mediated events 0.0678 35 3612 102 -0.1 0.03 1000 -1000 -0.07 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0659 34 2891 85 -0.17 0.038 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.0640 33 1265 38 -0.05 0.027 1000 -1000 -0.034 -1000
Ceramide signaling pathway 0.0640 33 2510 76 -0.068 0.045 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 0.0620 32 1435 44 -0.1 0.032 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0601 31 1178 38 -0.055 0.034 1000 -1000 -0.006 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0601 31 1723 54 -0.072 0.033 1000 -1000 -0.03 -1000
Fc-epsilon receptor I signaling in mast cells 0.0601 31 3067 97 -0.06 0.042 1000 -1000 -0.052 -1000
IL1-mediated signaling events 0.0601 31 1978 62 -0.073 0.045 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.0601 31 541 17 -0.054 0.034 1000 -1000 -0.029 -1000
PLK1 signaling events 0.0581 30 2610 85 -0.078 0.038 1000 -1000 -0.028 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0581 30 2664 88 -0.087 0.029 1000 -1000 -0.056 -1000
JNK signaling in the CD4+ TCR pathway 0.0562 29 495 17 -0.025 0.026 1000 -1000 -0.03 -1000
Glypican 1 network 0.0562 29 1417 48 -0.08 0.05 1000 -1000 -0.021 -1000
Glypican 2 network 0.0562 29 116 4 -0.002 0.004 1000 -1000 0.006 -1000
Noncanonical Wnt signaling pathway 0.0543 28 728 26 -0.048 0.026 1000 -1000 -0.028 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0543 28 1472 52 -0.15 0.067 1000 -1000 -0.036 -1000
BMP receptor signaling 0.0523 27 2196 81 -0.079 0.044 1000 -1000 -0.033 -1000
Calcium signaling in the CD4+ TCR pathway 0.0523 27 846 31 -0.094 0.025 1000 -1000 -0.049 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0504 26 907 34 -0.017 0.04 1000 -1000 -0.017 -1000
S1P5 pathway 0.0504 26 457 17 -0.053 0.026 1000 -1000 -0.01 -1000
IL6-mediated signaling events 0.0504 26 1999 75 -0.1 0.04 1000 -1000 -0.042 -1000
E-cadherin signaling in the nascent adherens junction 0.0504 26 2018 76 -0.046 0.048 1000 -1000 -0.042 -1000
Glucocorticoid receptor regulatory network 0.0484 25 2936 114 -0.27 0.14 1000 -1000 -0.051 -1000
Retinoic acid receptors-mediated signaling 0.0484 25 1465 58 -0.088 0.051 1000 -1000 -0.044 -1000
Rapid glucocorticoid signaling 0.0484 25 515 20 -0.075 0.027 1000 -1000 -0.003 -1000
Ephrin B reverse signaling 0.0465 24 1182 48 -0.027 0.027 1000 -1000 -0.017 -1000
EPHB forward signaling 0.0465 24 2097 85 -0.029 0.054 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 0.0446 23 3249 136 -0.18 0.16 1000 -1000 -0.041 -1000
FAS signaling pathway (CD95) 0.0446 23 1105 47 -0.099 0.039 1000 -1000 -0.035 -1000
Wnt signaling 0.0446 23 161 7 -0.007 0.01 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 0.0426 22 1714 76 -0.082 0.05 1000 -1000 -0.023 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0426 22 821 37 -0.034 0.046 1000 -1000 -0.02 -1000
E-cadherin signaling in keratinocytes 0.0426 22 953 43 -0.046 0.027 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 0.0407 21 843 39 -0.13 0.029 1000 -1000 -0.017 -1000
IL2 signaling events mediated by PI3K 0.0407 21 1226 58 -0.075 0.041 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 0.0407 21 1083 51 -0.13 0.066 1000 -1000 -0.045 -1000
TCGA08_rtk_signaling 0.0407 21 563 26 -0.047 0.061 1000 -1000 -0.006 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0407 21 2628 120 -0.11 0.074 1000 -1000 -0.032 -1000
Syndecan-2-mediated signaling events 0.0388 20 1447 69 -0.061 0.038 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0388 20 1544 76 -0.072 0.04 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0388 20 1154 55 -0.029 0.07 1000 -1000 -0.029 -1000
TCGA08_p53 0.0388 20 140 7 -0.017 0.025 1000 -1000 -0.007 -1000
PLK2 and PLK4 events 0.0368 19 57 3 0.001 -1000 1000 -1000 -0.008 -1000
Presenilin action in Notch and Wnt signaling 0.0349 18 1154 61 -0.13 0.063 1000 -1000 -0.038 -1000
S1P1 pathway 0.0349 18 675 36 -0.095 0.026 1000 -1000 -0.026 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0349 18 1453 78 -0.017 0.037 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class III 0.0329 17 713 40 -0.064 0.05 1000 -1000 -0.019 -1000
ceramide signaling pathway 0.0329 17 856 49 -0.06 0.037 1000 -1000 -0.033 -1000
Class I PI3K signaling events 0.0329 17 1245 73 -0.074 0.048 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 0.0310 16 878 54 -0.055 0.056 1000 -1000 -0.045 -1000
IL27-mediated signaling events 0.0310 16 844 51 -0.085 0.026 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 0.0310 16 354 22 -0.028 0.027 1000 -1000 -0.033 -1000
Plasma membrane estrogen receptor signaling 0.0310 16 1408 86 -0.039 0.038 1000 -1000 -0.042 -1000
LPA4-mediated signaling events 0.0291 15 181 12 -0.031 0.005 1000 -1000 -0.019 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0291 15 691 45 -0.06 0.061 1000 -1000 -0.041 -1000
S1P4 pathway 0.0291 15 394 25 -0.053 0.045 1000 -1000 -0.019 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0271 14 414 28 -0.053 0.032 1000 -1000 -0.015 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0271 14 1233 83 -0.094 0.051 1000 -1000 -0.034 -1000
Paxillin-dependent events mediated by a4b1 0.0271 14 519 36 -0.038 0.047 1000 -1000 -0.026 -1000
VEGFR1 specific signals 0.0271 14 800 56 -0.038 0.055 1000 -1000 -0.034 -1000
BARD1 signaling events 0.0252 13 761 57 -0.041 0.051 1000 -1000 -0.031 -1000
Integrins in angiogenesis 0.0252 13 1139 84 -0.024 0.057 1000 -1000 -0.03 -1000
Regulation of Androgen receptor activity 0.0252 13 951 70 -0.066 0.036 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 0.0233 12 407 32 -0.04 0.051 1000 -1000 -0.029 -1000
Regulation of Telomerase 0.0233 12 1321 102 -0.13 0.065 1000 -1000 -0.035 -1000
Signaling events mediated by PRL 0.0233 12 419 34 -0.059 0.033 1000 -1000 -0.034 -1000
ErbB4 signaling events 0.0213 11 782 69 -0.071 0.045 1000 -1000 -0.033 -1000
TRAIL signaling pathway 0.0213 11 562 48 -0.001 0.063 1000 -1000 -0.025 -1000
Insulin Pathway 0.0213 11 833 74 -0.071 0.062 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 0.0213 11 1087 97 -0.072 0.072 1000 -1000 -0.036 -1000
Aurora A signaling 0.0194 10 656 60 -0.058 0.058 1000 -1000 -0.018 -1000
IFN-gamma pathway 0.0194 10 696 68 -0.099 0.056 1000 -1000 -0.041 -1000
Nectin adhesion pathway 0.0194 10 634 63 -0.046 0.066 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class I 0.0174 9 1023 104 -0.06 0.059 1000 -1000 -0.028 -1000
Signaling mediated by p38-gamma and p38-delta 0.0174 9 146 15 -0.016 0.025 1000 -1000 -0.024 -1000
Atypical NF-kappaB pathway 0.0174 9 309 31 -0.019 0.038 1000 -1000 -0.013 -1000
S1P3 pathway 0.0174 9 389 42 0 0.038 1000 -1000 -0.026 -1000
p38 MAPK signaling pathway 0.0174 9 409 44 -0.018 0.042 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 0.0155 8 352 43 -0.058 0.059 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0155 8 264 33 -0.029 0.065 1000 -1000 -0.031 -1000
Canonical NF-kappaB pathway 0.0136 7 295 39 -0.06 0.059 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 0.0136 7 542 68 -0.032 0.048 1000 -1000 -0.032 -1000
FoxO family signaling 0.0136 7 486 64 -0.033 0.079 1000 -1000 -0.041 -1000
IGF1 pathway 0.0136 7 407 57 -0.014 0.064 1000 -1000 -0.029 -1000
Hedgehog signaling events mediated by Gli proteins 0.0116 6 447 65 -0.006 0.059 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0097 5 116 22 -0.007 0.038 1000 -1000 -0.04 -1000
Arf6 downstream pathway 0.0097 5 239 43 -0.043 0.049 1000 -1000 -0.024 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0097 5 646 125 -0.02 0.065 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0097 5 397 71 -0.05 0.048 1000 -1000 -0.024 -1000
Class IB PI3K non-lipid kinase events 0.0097 5 15 3 -0.02 0.02 1000 -1000 -0.008 -1000
Signaling events mediated by HDAC Class II 0.0078 4 372 75 -0.094 0.071 1000 -1000 -0.018 -1000
mTOR signaling pathway 0.0078 4 256 53 -0.018 0.041 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0039 2 46 23 -0.001 0.05 1000 -1000 -0.026 -1000
Arf1 pathway 0.0019 1 78 54 -0.001 0.039 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0019 1 14 13 0 0.059 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.061 1000 -1000 -0.027 -1000
Total NA 3355 191886 7203 -10 -990 131000 -131000 -4.1 -131000
Ephrin A reverse signaling

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.052 0.14 -10000 0 -0.28 126 126
EFNA5 -0.029 0.14 -10000 0 -0.43 48 48
FYN -0.056 0.13 0.18 6 -0.29 100 106
neuron projection morphogenesis -0.052 0.14 -10000 0 -0.28 126 126
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.052 0.14 -10000 0 -0.28 126 126
EPHA5 -0.063 0.16 -10000 0 -0.3 138 138
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.42 0.54 -9999 0 -1.2 138 138
IL23A -0.44 0.55 -9999 0 -1.2 146 146
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.53 -9999 0 -1.1 139 139
positive regulation of T cell mediated cytotoxicity -0.45 0.6 -9999 0 -1.3 145 145
ITGA3 -0.39 0.5 -9999 0 -1.2 120 120
IL17F -0.26 0.32 -9999 0 -0.7 138 138
IL12B -0.02 0.045 -9999 0 -0.16 6 6
STAT1 (dimer) -0.43 0.57 -9999 0 -1.2 145 145
CD4 -0.37 0.49 -9999 0 -1.1 118 118
IL23 -0.42 0.53 -9999 0 -1.1 150 150
IL23R -0.2 0.38 -9999 0 -1 83 83
IL1B -0.46 0.59 -9999 0 -1.3 140 140
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.38 0.49 -9999 0 -1.1 121 121
TYK2 -0.007 0.035 -9999 0 -10000 0 0
STAT4 -0.064 0.16 -9999 0 -0.43 69 69
STAT3 0.026 0.003 -9999 0 -10000 0 0
IL18RAP -0.023 0.13 -9999 0 -0.43 41 41
IL12RB1 -0.032 0.1 -9999 0 -0.39 31 31
PIK3CA 0.025 0.02 -9999 0 -0.43 1 1
IL12Rbeta1/TYK2 -0.022 0.082 -9999 0 -0.32 24 24
IL23R/JAK2 -0.19 0.36 -9999 0 -1.1 65 65
positive regulation of chronic inflammatory response -0.45 0.6 -9999 0 -1.3 145 145
natural killer cell activation 0.005 0.007 -9999 0 -10000 0 0
JAK2 -0.008 0.042 -9999 0 -10000 0 0
PIK3R1 0.026 0.003 -9999 0 -10000 0 0
NFKB1 0.024 0.005 -9999 0 -10000 0 0
RELA 0.023 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.49 -9999 0 -1.1 150 150
ALOX12B -0.45 0.55 -9999 0 -1.2 153 153
CXCL1 -0.43 0.54 -9999 0 -1.2 138 138
T cell proliferation -0.45 0.6 -9999 0 -1.3 145 145
NFKBIA 0.024 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.25 -9999 0 -0.55 123 123
PI3K -0.4 0.54 -9999 0 -1.2 140 140
IFNG -0.018 0.031 -9999 0 -0.11 20 20
STAT3 (dimer) -0.38 0.51 -9999 0 -1.1 137 137
IL18R1 -0.006 0.11 -9999 0 -0.27 58 58
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.36 -9999 0 -0.79 109 109
IL18/IL18R -0.004 0.13 -9999 0 -0.3 73 73
macrophage activation -0.019 0.02 -9999 0 -0.044 141 141
TNF -0.46 0.59 -9999 0 -1.3 139 139
STAT3/STAT4 -0.43 0.55 -9999 0 -1.2 150 150
STAT4 (dimer) -0.45 0.58 -9999 0 -1.2 150 150
IL18 0.002 0.093 -9999 0 -0.43 21 21
IL19 -0.38 0.48 -9999 0 -1.1 121 121
STAT5A (dimer) -0.43 0.57 -9999 0 -1.2 145 145
STAT1 0.021 0.028 -9999 0 -10000 0 0
SOCS3 -0.029 0.12 -9999 0 -0.21 118 118
CXCL9 -0.45 0.55 -9999 0 -1.2 152 152
MPO -0.45 0.56 -9999 0 -1.2 154 154
positive regulation of humoral immune response -0.45 0.6 -9999 0 -1.3 145 145
IL23/IL23R/JAK2/TYK2 -0.49 0.69 -9999 0 -1.4 145 145
IL6 -0.4 0.54 -9999 0 -1.2 130 130
STAT5A 0.016 0.066 -9999 0 -0.43 11 11
IL2 0.01 0.019 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.007 -9999 0 -10000 0 0
CD3E -0.43 0.55 -9999 0 -1.2 141 141
keratinocyte proliferation -0.45 0.6 -9999 0 -1.3 145 145
NOS2 -0.4 0.51 -9999 0 -1.2 130 130
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.33 0.3 1 -0.86 75 76
MKNK1 0.022 0.01 -10000 0 -10000 0 0
MAPK14 -0.015 0.12 -10000 0 -0.29 76 76
ATF2/c-Jun -0.021 0.1 -10000 0 -0.42 11 11
MAPK11 -0.024 0.13 -10000 0 -0.31 83 83
MITF -0.026 0.14 0.3 1 -0.33 83 84
MAPKAPK5 -0.027 0.14 -10000 0 -0.34 83 83
KRT8 -0.064 0.18 -10000 0 -0.37 114 114
MAPKAPK3 0.025 0.021 -10000 0 -0.43 1 1
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.03 0.18 -10000 0 -0.42 83 83
CEBPB -0.034 0.16 -10000 0 -0.37 84 84
SLC9A1 -0.04 0.16 0.3 1 -0.39 81 82
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.023 0.15 -10000 0 -0.33 85 85
p38alpha-beta/MNK1 -0.011 0.14 -10000 0 -0.33 81 81
JUN -0.019 0.097 -10000 0 -0.42 11 11
PPARGC1A -0.04 0.17 -10000 0 -0.38 91 91
USF1 -0.025 0.14 0.3 1 -0.34 81 82
RAB5/GDP/GDI1 -0.012 0.11 -10000 0 -0.25 83 83
NOS2 -0.054 0.23 -10000 0 -0.52 77 77
DDIT3 -0.026 0.14 0.22 1 -0.34 82 83
RAB5A 0.026 0.004 -10000 0 -10000 0 0
HSPB1 0.007 0.15 0.28 68 -0.28 75 143
p38alpha-beta/HBP1 -0.008 0.14 -10000 0 -0.33 71 71
CREB1 -0.03 0.15 -10000 0 -0.36 82 82
RAB5/GDP 0.019 0.003 -10000 0 -10000 0 0
EIF4E -0.033 0.12 0.24 4 -0.29 81 85
RPS6KA4 -0.025 0.14 -10000 0 -0.34 80 80
PLA2G4A -0.04 0.13 0.2 1 -0.32 82 83
GDI1 -0.026 0.14 -10000 0 -0.34 83 83
TP53 -0.053 0.17 -10000 0 -0.42 82 82
RPS6KA5 -0.033 0.15 -10000 0 -0.35 89 89
ESR1 -0.035 0.15 -10000 0 -0.35 89 89
HBP1 0.02 0.011 -10000 0 -10000 0 0
MEF2C -0.028 0.14 -10000 0 -0.34 82 82
MEF2A -0.028 0.14 -10000 0 -0.35 82 82
EIF4EBP1 -0.034 0.15 -10000 0 -0.36 83 83
KRT19 -0.062 0.18 -10000 0 -0.37 116 116
ELK4 -0.025 0.14 0.3 1 -0.34 81 82
ATF6 -0.025 0.14 0.3 1 -0.34 81 82
ATF1 -0.033 0.15 -10000 0 -0.37 84 84
p38alpha-beta/MAPKAPK2 0 0.15 -10000 0 -0.33 81 81
p38alpha-beta/MAPKAPK3 -0.002 0.15 -10000 0 -0.34 82 82
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.004 0.075 -10000 0 -0.24 32 32
NFATC2 -0.083 0.23 -10000 0 -0.54 71 71
NFATC3 -0.036 0.11 -10000 0 -0.27 65 65
CD40LG -0.24 0.4 -10000 0 -0.94 106 106
ITCH -0.024 0.091 -10000 0 -0.22 86 86
CBLB -0.023 0.093 -10000 0 -0.22 83 83
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.36 -10000 0 -0.88 84 84
JUNB 0.007 0.071 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.11 -10000 0 -0.26 89 89
T cell anergy -0.066 0.16 0.26 1 -0.39 88 89
TLE4 -0.06 0.17 -10000 0 -0.5 44 44
Jun/NFAT1-c-4/p21SNFT -0.2 0.43 -10000 0 -0.98 106 106
AP-1/NFAT1-c-4 -0.24 0.5 -10000 0 -1.1 106 106
IKZF1 -0.063 0.18 -10000 0 -0.55 44 44
T-helper 2 cell differentiation -0.14 0.28 -10000 0 -0.8 50 50
AP-1/NFAT1 -0.063 0.18 -10000 0 -0.41 75 75
CALM1 -0.01 0.072 -10000 0 -0.2 2 2
EGR2 -0.24 0.51 -10000 0 -1.1 105 105
EGR3 -0.26 0.55 -10000 0 -1.3 95 95
NFAT1/FOXP3 -0.054 0.19 -10000 0 -0.45 63 63
EGR1 -0.043 0.14 -10000 0 -0.27 111 111
JUN 0.009 0.031 -10000 0 -0.14 9 9
EGR4 -0.088 0.17 -10000 0 -0.38 108 108
mol:Ca2+ -0.025 0.06 -10000 0 -0.15 88 88
GBP3 -0.079 0.22 0.25 1 -0.61 65 66
FOSL1 -0.028 0.13 -10000 0 -0.43 40 40
NFAT1-c-4/MAF/IRF4 -0.19 0.43 -10000 0 -0.96 106 106
DGKA -0.057 0.16 -10000 0 -0.46 41 41
CREM 0.023 0.022 -10000 0 -0.28 2 2
NFAT1-c-4/PPARG -0.2 0.44 -10000 0 -0.99 106 106
CTLA4 -0.079 0.19 -10000 0 -0.49 70 70
NFAT1-c-4 (dimer)/EGR1 -0.23 0.47 -10000 0 -1.1 106 106
NFAT1-c-4 (dimer)/EGR4 -0.24 0.46 -10000 0 -1 108 108
FOS -0.041 0.14 -10000 0 -0.32 80 80
IFNG -0.1 0.21 -10000 0 -0.62 42 42
T cell activation -0.11 0.23 -10000 0 -0.66 45 45
MAF 0.024 0.035 -10000 0 -0.43 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.18 0.38 0.84 106 -10000 0 106
TNF -0.3 0.44 -10000 0 -0.98 128 128
FASLG -0.26 0.55 -10000 0 -1.3 102 102
TBX21 -0.004 0.099 -10000 0 -0.39 27 27
BATF3 0.001 0.091 -10000 0 -0.43 19 19
PRKCQ 0.015 0.061 -10000 0 -0.37 11 11
PTPN1 -0.058 0.16 -10000 0 -0.45 46 46
NFAT1-c-4/ICER1 -0.19 0.43 -10000 0 -0.97 105 105
GATA3 -0.038 0.14 -10000 0 -0.43 49 49
T-helper 1 cell differentiation -0.1 0.2 -10000 0 -0.61 42 42
IL2RA -0.17 0.32 -10000 0 -0.8 73 73
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 0.16 -10000 0 -0.45 44 44
E2F1 0.017 0.057 -10000 0 -0.42 6 6
PPARG 0.009 0.081 -10000 0 -0.43 16 16
SLC3A2 -0.054 0.16 -10000 0 -0.46 42 42
IRF4 -0.006 0.1 -10000 0 -0.28 53 53
PTGS2 -0.26 0.43 -10000 0 -1 109 109
CSF2 -0.24 0.39 -10000 0 -0.95 106 106
JunB/Fra1/NFAT1-c-4 -0.2 0.43 -10000 0 -0.96 107 107
IL4 -0.15 0.3 -10000 0 -0.86 47 47
IL5 -0.24 0.4 -10000 0 -0.94 106 106
IL2 -0.12 0.23 -10000 0 -0.67 43 43
IL3 -0.024 0.082 -10000 0 -0.65 4 4
RNF128 -0.085 0.2 -10000 0 -0.52 88 88
NFATC1 -0.18 0.38 -10000 0 -0.85 106 106
CDK4 0.11 0.21 0.59 46 -10000 0 46
PTPRK -0.057 0.16 -10000 0 -0.47 45 45
IL8 -0.26 0.42 -10000 0 -0.97 115 115
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
Aurora B 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
Condensin I complex -0.071 0.19 -10000 0 -0.44 89 89
STMN1 -0.047 0.12 0.18 3 -0.31 76 79
Aurora B/RasGAP/Survivin -0.057 0.19 -10000 0 -0.34 133 133
Chromosomal passenger complex/Cul3 protein complex -0.069 0.15 -10000 0 -0.33 98 98
BIRC5 -0.064 0.17 -10000 0 -0.32 126 126
DES -0.26 0.45 -10000 0 -0.86 167 167
Aurora C/Aurora B/INCENP -0.013 0.11 -10000 0 -0.24 94 94
Aurora B/TACC1 -0.027 0.11 -10000 0 -0.26 87 87
Aurora B/PP2A -0.034 0.13 -10000 0 -0.31 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.019 0.059 -10000 0 -0.14 91 91
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.095 0.19 0.19 6 -0.36 145 151
Cul3 protein complex 0.046 0.027 -10000 0 -0.26 2 2
KIF2C -0.093 0.25 -10000 0 -0.47 106 106
PEBP1 0.015 0.04 -10000 0 -0.44 3 3
KIF20A -0.079 0.17 -10000 0 -0.3 163 163
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.035 0.13 -10000 0 -0.31 88 88
SEPT1 0.024 0.024 -10000 0 -0.19 5 5
SMC2 0.026 0.004 -10000 0 -10000 0 0
SMC4 0.017 0.036 -10000 0 -0.13 28 28
NSUN2/NPM1/Nucleolin -0.12 0.3 0.24 1 -0.76 90 91
PSMA3 0.026 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.043 0.12 0.12 1 -0.3 88 89
AURKB -0.074 0.18 -10000 0 -0.32 149 149
AURKC 0.011 0.051 -10000 0 -0.18 26 26
CDCA8 -0.01 0.075 -10000 0 -0.19 46 46
cytokinesis -0.16 0.32 0.22 2 -0.73 108 110
Aurora B/Septin1 -0.13 0.32 0.26 2 -0.71 104 106
AURKA 0.018 0.038 -10000 0 -0.15 22 22
INCENP 0.015 0.029 -10000 0 -0.44 1 1
KLHL13 0.025 0.028 -10000 0 -0.43 2 2
BUB1 -0.043 0.15 -10000 0 -0.29 110 110
hSgo1/Aurora B/Survivin -0.083 0.22 -10000 0 -0.36 164 164
EVI5 0.021 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.11 0.29 -10000 0 -0.62 105 105
SGOL1 -0.047 0.15 -10000 0 -0.28 122 122
CENPA -0.1 0.25 0.23 1 -0.56 102 103
NCAPG -0.061 0.16 -10000 0 -0.3 137 137
Aurora B/HC8 Proteasome -0.035 0.13 -10000 0 -0.31 88 88
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.035 0.13 -10000 0 -0.31 88 88
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH -0.015 0.12 -10000 0 -0.26 73 73
NPM1 -0.083 0.2 -10000 0 -0.51 92 92
RASA1 0.026 0.003 -10000 0 -10000 0 0
KLHL9 0.024 0.008 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.13 -10000 0 -0.31 88 88
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin -0.13 0.31 0.2 1 -0.66 109 110
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.082 0.2 -10000 0 -0.51 91 91
MYLK -0.049 0.12 -10000 0 -0.29 98 98
KIF23 -0.036 0.13 -10000 0 -0.44 41 41
VIM -0.081 0.15 0.18 6 -0.32 128 134
RACGAP1 0.017 0.022 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.085 0.21 -10000 0 -0.51 96 96
Chromosomal passenger complex -0.13 0.29 0.19 1 -0.61 114 115
Chromosomal passenger complex/EVI5 -0.043 0.19 -10000 0 -0.32 139 139
TACC1 0.025 0.005 -10000 0 -10000 0 0
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.073 0.13 -10000 0 -0.35 62 62
TBX21 -0.33 0.46 -10000 0 -1 124 124
B2M 0.025 0.016 -10000 0 -0.13 5 5
TYK2 -0.002 0.034 -10000 0 -10000 0 0
IL12RB1 -0.027 0.1 -10000 0 -0.38 31 31
GADD45B -0.24 0.36 -10000 0 -0.82 95 95
IL12RB2 -0.049 0.12 -10000 0 -0.3 68 68
GADD45G -0.25 0.38 -10000 0 -0.89 96 96
natural killer cell activation -0.012 0.02 -10000 0 -0.04 111 111
RELB 0.02 0.025 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
IL18 -0.005 0.095 -10000 0 -0.39 25 25
IL2RA -0.015 0.071 -10000 0 -0.17 67 67
IFNG -0.008 0.021 -10000 0 -0.13 5 5
STAT3 (dimer) -0.24 0.33 -10000 0 -0.72 134 134
HLA-DRB5 -0.002 0.006 -10000 0 -0.02 43 43
FASLG -0.3 0.42 -10000 0 -0.97 116 116
NF kappa B2 p52/RelB -0.3 0.43 -10000 0 -0.88 143 143
CD4 0.017 0.035 -10000 0 -0.23 6 6
SOCS1 0.008 0.068 -10000 0 -0.18 45 45
EntrezGene:6955 -0.001 0.007 -10000 0 -0.023 44 44
CD3D -0.033 0.12 -10000 0 -0.23 105 105
CD3E -0.052 0.14 -10000 0 -0.26 130 130
CD3G 0.004 0.044 -10000 0 -0.14 41 41
IL12Rbeta2/JAK2 -0.029 0.095 -10000 0 -0.3 37 37
CCL3 -0.4 0.55 -10000 0 -1.2 140 140
CCL4 -0.39 0.56 -10000 0 -1.3 130 130
HLA-A 0 0.003 -10000 0 -0.049 1 1
IL18/IL18R -0.021 0.14 -10000 0 -0.32 74 74
NOS2 -0.28 0.41 -10000 0 -0.87 134 134
IL12/IL12R/TYK2/JAK2/SPHK2 -0.068 0.13 -10000 0 -0.36 58 58
IL1R1 -0.32 0.44 -10000 0 -1 115 115
IL4 0.017 0.034 -10000 0 -10000 0 0
JAK2 -0.003 0.034 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -0.021 44 44
TCR/CD3/MHC I/CD8 -0.046 0.12 -10000 0 -0.4 36 36
RAB7A -0.19 0.3 0.52 1 -0.78 52 53
lysosomal transport -0.18 0.28 0.51 1 -0.72 55 56
FOS -0.23 0.44 -10000 0 -1.2 70 70
STAT4 (dimer) -0.28 0.38 0.5 1 -0.81 135 136
STAT5A (dimer) -0.3 0.43 -10000 0 -0.88 148 148
GZMA -0.37 0.5 -10000 0 -1.1 147 147
GZMB -0.36 0.49 -10000 0 -1.1 137 137
HLX 0.018 0.046 -10000 0 -0.21 16 16
LCK -0.34 0.47 -10000 0 -0.95 153 153
TCR/CD3/MHC II/CD4 -0.038 0.1 -10000 0 -0.22 98 98
IL2/IL2R 0.002 0.11 -10000 0 -0.24 69 69
MAPK14 -0.24 0.36 -10000 0 -0.79 110 110
CCR5 -0.28 0.42 -10000 0 -0.98 101 101
IL1B -0.094 0.16 -10000 0 -0.28 169 169
STAT6 -0.072 0.11 -10000 0 -0.41 6 6
STAT4 -0.064 0.16 -10000 0 -0.43 69 69
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.028 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.03 -10000 0 -0.43 2 2
IL12B -0.012 0.038 -10000 0 -0.15 6 6
CD8A -0.024 0.13 -10000 0 -0.33 66 66
CD8B -0.002 0.1 -10000 0 -0.32 42 42
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.073 0.13 0.35 62 -10000 0 62
IL2RB -0.028 0.13 -10000 0 -0.25 101 101
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.34 0.49 1 -0.73 136 137
IL2RG 0.001 0.087 -10000 0 -0.43 16 16
IL12 -0.019 0.084 -10000 0 -0.32 24 24
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
CD247 0.008 0.065 -10000 0 -0.43 8 8
IL2 -0.014 0.009 -10000 0 -10000 0 0
SPHK2 0.021 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.024 0.1 -10000 0 -0.43 25 25
IL12/IL12R/TYK2/JAK2 -0.36 0.52 -10000 0 -1 148 148
MAP2K3 -0.24 0.36 -10000 0 -0.77 120 120
RIPK2 0.024 0.007 -10000 0 -10000 0 0
MAP2K6 -0.24 0.36 -10000 0 -0.76 123 123
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.007 -10000 0 -0.023 44 44
IL18RAP -0.032 0.13 -10000 0 -0.37 53 53
IL12Rbeta1/TYK2 -0.017 0.086 -10000 0 -0.34 24 24
EOMES 0.022 0.097 -10000 0 -0.8 5 5
STAT1 (dimer) -0.24 0.32 -10000 0 -0.72 127 127
T cell proliferation -0.2 0.27 0.49 1 -0.57 138 139
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.014 0.11 -10000 0 -0.28 58 58
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.23 0.3 -10000 0 -0.64 136 136
ATF2 -0.22 0.33 0.51 1 -0.74 109 110
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.18 0.49 -9999 0 -1.2 79 79
PLK1 0.006 0.15 -9999 0 -1.3 6 6
BIRC5 -0.19 0.51 -9999 0 -1.4 75 75
HSPA1B -0.19 0.5 -9999 0 -1.2 82 82
MAP2K1 0.01 0.045 -9999 0 -0.18 1 1
BRCA2 -0.19 0.51 -9999 0 -1.2 83 83
FOXM1 -0.27 0.7 -9999 0 -1.6 87 87
XRCC1 -0.18 0.49 -9999 0 -1.2 77 77
FOXM1B/p19 -0.19 0.5 -9999 0 -1.2 83 83
Cyclin D1/CDK4 -0.17 0.45 -9999 0 -1 86 86
CDC2 -0.19 0.52 -9999 0 -1.2 85 85
TGFA -0.16 0.44 -9999 0 -0.99 87 87
SKP2 -0.19 0.5 -9999 0 -1.2 81 81
CCNE1 0.016 0.022 -9999 0 -10000 0 0
CKS1B -0.18 0.49 -9999 0 -1.1 87 87
RB1 -0.11 0.32 -9999 0 -0.9 50 50
FOXM1C/SP1 -0.22 0.59 -9999 0 -1.4 87 87
AURKB -0.23 0.56 -9999 0 -1.4 90 90
CENPF -0.2 0.52 -9999 0 -1.3 77 77
CDK4 0.014 0.026 -9999 0 -10000 0 0
MYC -0.16 0.43 -9999 0 -0.99 88 88
CHEK2 0.004 0.066 -9999 0 -0.26 12 12
ONECUT1 -0.18 0.47 -9999 0 -1.1 87 87
CDKN2A -0.012 0.11 -9999 0 -0.3 55 55
LAMA4 -0.18 0.49 -9999 0 -1.2 79 79
FOXM1B/HNF6 -0.23 0.58 -9999 0 -1.4 88 88
FOS -0.26 0.56 -9999 0 -1.2 124 124
SP1 0.025 0.009 -9999 0 -10000 0 0
CDC25B -0.18 0.49 -9999 0 -1.2 78 78
response to radiation 0 0.026 -9999 0 -10000 0 0
CENPB -0.18 0.49 -9999 0 -1.2 77 77
CENPA -0.21 0.53 -9999 0 -1.3 83 83
NEK2 -0.23 0.56 -9999 0 -1.3 93 93
HIST1H2BA -0.18 0.48 -9999 0 -1.2 77 77
CCNA2 -0.012 0.1 -9999 0 -0.33 35 35
EP300 0.022 0.04 -9999 0 -0.43 4 4
CCNB1/CDK1 -0.22 0.59 -9999 0 -1.5 78 78
CCNB2 -0.23 0.57 -9999 0 -1.4 89 89
CCNB1 -0.19 0.52 -9999 0 -1.3 79 79
ETV5 -0.19 0.49 -9999 0 -1.2 84 84
ESR1 -0.2 0.5 -9999 0 -1.2 87 87
CCND1 -0.18 0.46 -9999 0 -1 88 88
GSK3A 0.012 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.012 0.091 -9999 0 -0.3 26 26
CDK2 0.014 0.049 -9999 0 -0.24 12 12
G2/M transition of mitotic cell cycle -0.003 0.03 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.2 0.55 -9999 0 -1.3 86 86
GAS1 -0.18 0.49 -9999 0 -1.2 78 78
MMP2 -0.19 0.5 -9999 0 -1.2 80 80
RB1/FOXM1C -0.19 0.48 -9999 0 -1.1 85 85
CREBBP 0.026 0.003 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.046 0.17 0.24 11 -0.36 80 91
FYN -0.072 0.2 0.25 19 -0.42 96 115
LAT/GRAP2/SLP76 -0.074 0.17 0.23 5 -0.37 95 100
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.15 0.22 19 -0.33 87 106
B2M 0.021 0.021 -10000 0 -0.14 5 5
IKBKG -0.013 0.051 0.089 21 -0.12 33 54
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
mol:Ca2+ -0.016 0.027 0.089 12 -0.07 41 53
integrin-mediated signaling pathway 0.022 0.039 -10000 0 -0.24 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.081 0.2 0.25 16 -0.44 89 105
TRPV6 0.21 0.52 1.1 116 -0.45 39 155
CD28 -0.023 0.12 -10000 0 -0.29 76 76
SHC1 -0.074 0.19 0.24 22 -0.41 95 117
receptor internalization -0.059 0.15 0.24 2 -0.38 68 70
PRF1 -0.11 0.33 -10000 0 -0.95 56 56
KRAS 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.13 0.21 17 -0.28 76 93
LAT -0.084 0.19 0.23 16 -0.4 102 118
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.035 0.12 -10000 0 -0.23 105 105
CD3E -0.052 0.15 -10000 0 -0.27 127 127
CD3G 0.001 0.044 -10000 0 -0.13 41 41
RASGRP2 -0.003 0.019 0.13 1 -0.16 2 3
RASGRP1 -0.065 0.16 0.26 17 -0.35 87 104
HLA-A -0.002 0.006 -10000 0 -10000 0 0
RASSF5 0.016 0.062 -10000 0 -0.43 9 9
RAP1A/GTP/RAPL 0.023 0.039 -10000 0 -0.24 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.065 0.16 33 -0.12 18 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.067 -10000 0 -0.18 68 68
PRKCA -0.045 0.088 0.15 5 -0.21 68 73
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
mol:IP3 -0.063 0.14 0.19 17 -0.3 92 109
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.055 0.14 -10000 0 -0.38 56 56
ORAI1 -0.18 0.43 0.59 5 -0.95 114 119
CSK -0.076 0.19 0.22 17 -0.41 98 115
B7 family/CD28 -0.065 0.21 0.26 8 -0.44 91 99
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.09 0.2 0.26 1 -0.44 99 100
PTPN6 -0.085 0.19 0.22 4 -0.42 95 99
VAV1 -0.078 0.2 0.22 22 -0.42 100 122
Monovalent TCR/CD3 -0.044 0.11 -10000 0 -0.27 88 88
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.089 0.22 0.25 19 -0.45 104 123
PAG1 -0.073 0.19 0.22 20 -0.41 95 115
RAP1A 0.021 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.089 0.2 0.26 1 -0.44 96 97
CD80 -0.001 0.073 -10000 0 -0.18 55 55
CD86 0 0.1 -10000 0 -0.34 36 36
PDK1/CARD11/BCL10/MALT1 -0.04 0.084 -10000 0 -0.21 70 70
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.078 0.17 0.21 17 -0.37 94 111
CD8A -0.027 0.13 -10000 0 -0.35 59 59
CD8B -0.006 0.1 -10000 0 -0.33 42 42
PTPRC -0.004 0.1 -10000 0 -0.28 49 49
PDK1/PKC theta -0.065 0.18 0.3 14 -0.39 85 99
CSK/PAG1 -0.074 0.18 0.25 8 -0.4 92 100
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.019 -10000 0 -0.089 5 5
GRAP2/SLP76 -0.073 0.19 0.24 6 -0.4 100 106
STIM1 -0.008 0.2 1.2 10 -0.89 2 12
RAS family/GTP -0.011 0.08 0.18 22 -0.16 40 62
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.063 0.16 -10000 0 -0.4 68 68
mol:DAG -0.07 0.11 0.13 2 -0.26 103 105
RAP1A/GDP 0.004 0.027 0.08 20 -0.062 5 25
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.008 0.065 -10000 0 -0.43 8 8
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.9 56 56
RAP1A/GTP 0 0.007 -10000 0 -0.054 3 3
mol:PI-3-4-5-P3 -0.067 0.17 0.24 17 -0.37 89 106
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.078 0.17 0.23 8 -0.38 90 98
NRAS 0.021 0.01 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.25 56 56
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.088 0.16 0.2 1 -0.37 97 98
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
CD8 heterodimer -0.023 0.13 -10000 0 -0.3 79 79
CARD11 0.012 0.067 -10000 0 -0.43 11 11
PRKCB -0.053 0.093 0.15 6 -0.22 79 85
PRKCE -0.047 0.09 0.15 6 -0.21 73 79
PRKCQ -0.074 0.2 0.28 14 -0.42 88 102
LCP2 0.02 0.033 -10000 0 -0.15 15 15
BCL10 0.021 0.01 -10000 0 -10000 0 0
regulation of survival gene product expression -0.048 0.13 0.21 21 -0.28 86 107
IKK complex -0.003 0.057 0.16 23 -0.11 12 35
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.034 0.1 0.17 19 -0.22 66 85
PDPK1 -0.055 0.14 0.23 19 -0.32 81 100
TCR/CD3/MHC I/CD8/Fyn -0.09 0.22 0.23 1 -0.52 85 86
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.008 0.071 -10000 0 -0.39 11 11
Crk/p130 Cas/Paxillin -0.051 0.12 -10000 0 -0.28 76 76
JUN -0.061 0.14 -10000 0 -0.4 46 46
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.15 -10000 0 -0.28 109 109
RAP1A 0.021 0.01 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.025 0.16 -10000 0 -0.28 131 131
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.004 0.12 -10000 0 -0.26 86 86
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.038 0.15 -10000 0 -0.26 135 135
GRB7 0.001 0.044 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.019 0.15 -10000 0 -0.28 119 119
MAPKKK cascade -0.049 0.14 -10000 0 -0.28 125 125
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.003 0.12 -10000 0 -0.26 84 84
lamellipodium assembly -0.036 0.1 -10000 0 -0.26 66 66
RET51/GFRalpha1/GDNF/SHC -0.023 0.16 -10000 0 -0.28 127 127
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC -0.003 0.12 -10000 0 -0.26 82 82
RET9/GFRalpha1/GDNF/Shank3 -0.006 0.12 -10000 0 -0.26 88 88
MAPK3 -0.074 0.12 -10000 0 -0.26 123 123
DOK1 0.025 0.021 -10000 0 -0.28 2 2
DOK6 -0.017 0.13 -10000 0 -0.38 54 54
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.067 0.13 -10000 0 -0.36 52 52
DOK5 0.016 0.066 -10000 0 -0.43 11 11
GFRA1 -0.015 0.12 -10000 0 -0.43 36 36
MAPK8 -0.062 0.14 -10000 0 -0.28 133 133
HRAS/GTP -0.035 0.17 -10000 0 -0.3 131 131
tube development 0 0.12 0.2 14 -0.25 82 96
MAPK1 -0.074 0.12 -10000 0 -0.34 50 50
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.11 -10000 0 -0.25 82 82
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
PDLIM7 0.023 0.021 -10000 0 -0.13 9 9
RET51/GFRalpha1/GDNF/Dok6 -0.028 0.18 -10000 0 -0.31 133 133
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RET51/GFRalpha1/GDNF/Dok4 -0.032 0.17 -10000 0 -0.29 136 136
RET51/GFRalpha1/GDNF/Dok5 -0.026 0.16 -10000 0 -0.28 131 131
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
CREB1 -0.041 0.14 -10000 0 -0.31 85 85
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.11 -10000 0 -0.26 81 81
RET51/GFRalpha1/GDNF/Grb7 -0.028 0.16 -10000 0 -0.29 129 129
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.043 0.15 -10000 0 -0.3 107 107
DOK4 0.012 0.079 -10000 0 -0.43 16 16
JNK cascade -0.062 0.13 0.19 1 -0.4 44 45
RET9/GFRalpha1/GDNF/FRS2 -0.003 0.12 -10000 0 -0.26 85 85
SHANK3 0.021 0.035 -10000 0 -0.19 10 10
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.1 -10000 0 -0.25 81 81
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.15 -10000 0 -0.28 130 130
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.15 -10000 0 -0.28 134 134
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.15 -10000 0 -0.28 123 123
PI3K -0.06 0.16 0.23 1 -0.38 81 82
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.006 0.12 -10000 0 -0.25 82 82
GRB10 0.021 0.03 -10000 0 -0.43 2 2
activation of MAPKK activity -0.052 0.14 -10000 0 -0.34 83 83
RET51/GFRalpha1/GDNF/FRS2 -0.025 0.16 -10000 0 -0.28 132 132
GAB1 0.025 0.02 -10000 0 -0.43 1 1
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.15 -10000 0 -0.29 123 123
RET51/GFRalpha1/GDNF/PKC alpha -0.025 0.16 -10000 0 -0.28 129 129
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GDNF -0.034 0.15 -10000 0 -0.38 73 73
RAC1 0.023 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.023 0.16 -10000 0 -0.28 129 129
Rac1/GTP -0.037 0.12 -10000 0 -0.3 64 64
RET9/GFRalpha1/GDNF -0.028 0.12 -10000 0 -0.28 86 86
GFRalpha1/GDNF -0.035 0.14 -10000 0 -0.34 86 86
Thromboxane A2 receptor signaling

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
TGM2 0.023 0.016 -10000 0 -0.13 5 5
GNB1/GNG2 -0.055 0.077 -10000 0 -0.18 125 125
AKT1 -0.032 0.12 0.29 9 -0.24 48 57
EGF -0.01 0.11 -10000 0 -0.31 54 54
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.074 0.33 18 -0.25 1 19
mol:Ca2+ -0.051 0.16 0.33 7 -0.29 129 136
LYN 0.009 0.081 0.32 19 -0.24 4 23
RhoA/GTP -0.025 0.062 -10000 0 -0.13 111 111
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.18 0.31 11 -0.35 128 139
GNG2 0.022 0.04 -10000 0 -0.43 4 4
ARRB2 0.026 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.001 0.099 -10000 0 -0.39 22 22
G beta5/gamma2 -0.065 0.1 -10000 0 -0.24 123 123
PRKCH -0.064 0.17 0.33 7 -0.34 125 132
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
TXA2/TP beta/beta Arrestin3 -0.008 0.045 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.003 0.063 -10000 0 -0.16 52 52
G12 family/GTP -0.067 0.14 -10000 0 -0.3 117 117
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
ADRBK2 0.024 0.029 -10000 0 -0.33 3 3
RhoA/GTP/ROCK1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP 0.023 0.11 0.28 23 -0.3 10 33
mol:NADP 0.017 0.034 -10000 0 -0.43 2 2
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
mol:IP3 -0.068 0.19 0.35 7 -0.36 128 135
cell morphogenesis 0.033 0.007 -10000 0 -10000 0 0
PLCB2 -0.1 0.25 0.39 6 -0.49 128 134
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.088 0.31 16 -0.21 12 28
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.071 0.3 9 -0.25 9 18
RHOA 0.026 0.004 -10000 0 -10000 0 0
PTGIR 0.012 0.049 -10000 0 -0.43 4 4
PRKCB1 -0.07 0.18 0.33 6 -0.36 130 136
GNAQ 0.026 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.034 -10000 0 -0.43 2 2
TXA2/TXA2-R family -0.11 0.25 0.39 6 -0.52 129 135
LCK -0.001 0.085 0.34 16 -0.22 3 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.048 -10000 0 -0.2 9 9
TXA2-R family/G12 family/GDP/G beta/gamma -0.048 0.17 -10000 0 -0.43 80 80
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.009 0.049 -10000 0 -0.2 9 9
MAPK14 -0.041 0.12 0.26 11 -0.23 125 136
TGM2/GTP -0.081 0.2 0.38 3 -0.41 126 129
MAPK11 -0.043 0.12 0.26 11 -0.23 126 137
ARHGEF1 -0.036 0.083 0.14 1 -0.18 113 114
GNAI2 0.025 0.005 -10000 0 -10000 0 0
JNK cascade -0.076 0.19 0.35 7 -0.38 130 137
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.054 0.15 0.3 6 -0.28 131 137
cAMP biosynthetic process -0.066 0.18 0.35 7 -0.34 127 134
Gq family/GTP/EBP50 0.005 0.07 0.24 8 -0.22 34 42
actin cytoskeleton reorganization 0.033 0.007 -10000 0 -10000 0 0
SRC 0.004 0.063 0.3 9 -0.23 2 11
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.011 0.12 0.3 31 -0.26 33 64
VCAM1 -0.076 0.18 0.3 6 -0.36 131 137
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.099 -10000 0 -0.39 22 22
platelet activation -0.053 0.16 0.31 13 -0.3 130 143
PGI2/IP 0.01 0.034 -10000 0 -0.3 4 4
PRKACA 0.004 0.037 -10000 0 -0.23 8 8
Gq family/GDP/G beta5/gamma2 -0.001 0.094 -10000 0 -0.37 22 22
TXA2/TP beta/beta Arrestin2 -0.021 0.12 -10000 0 -0.48 33 33
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.036 -10000 0 -0.22 9 9
mol:DAG -0.078 0.21 0.37 6 -0.4 129 135
EGFR -0.016 0.12 -10000 0 -0.43 42 42
TXA2/TP alpha -0.093 0.23 0.41 6 -0.46 127 133
Gq family/GTP -0.002 0.063 0.21 5 -0.21 35 40
YES1 0.009 0.078 0.34 16 -0.23 4 20
GNAI2/GTP 0.003 0.045 -10000 0 -0.2 7 7
PGD2/DP 0.005 0.043 -10000 0 -0.1 52 52
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
FYN 0.01 0.077 0.32 18 -0.22 2 20
mol:NO 0.017 0.034 -10000 0 -0.43 2 2
GNA15 0.013 0.07 -10000 0 -0.34 17 17
PGK/cGMP 0.007 0.069 -10000 0 -0.25 31 31
RhoA/GDP 0.025 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.055 -10000 0 -0.29 2 2
NOS3 0.017 0.034 -10000 0 -0.43 2 2
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.061 0.18 0.3 10 -0.34 124 134
PRKCB -0.075 0.18 0.35 5 -0.36 131 136
PRKCE -0.066 0.18 0.32 8 -0.35 126 134
PRKCD -0.077 0.2 0.31 8 -0.38 131 139
PRKCG -0.086 0.19 0.35 8 -0.38 130 138
muscle contraction -0.1 0.24 0.39 5 -0.48 131 136
PRKCZ -0.07 0.17 0.33 7 -0.34 132 139
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
TXA2/TP beta 0.01 0.052 -10000 0 -0.21 11 11
PRKCQ -0.063 0.18 0.29 11 -0.35 125 136
MAPKKK cascade -0.088 0.22 0.37 6 -0.44 129 135
SELE -0.066 0.16 0.3 6 -0.32 132 138
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.053 -10000 0 -0.28 2 2
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
chemotaxis -0.13 0.29 0.39 5 -0.61 131 136
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.016 0.007 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.056 0.13 0.24 1 -0.27 112 113
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
mol:Ca2+ -0.045 0.22 -10000 0 -0.74 36 36
EDN1 -0.036 0.11 0.21 1 -0.3 48 49
EDN3 0.006 0.09 -10000 0 -0.4 23 23
EDN2 -0.006 0.031 -10000 0 -10000 0 0
HRAS/GDP -0.051 0.17 0.26 9 -0.43 51 60
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.13 0.17 2 -0.33 51 53
ADCY4 -0.069 0.14 -10000 0 -0.29 98 98
ADCY5 -0.073 0.14 -10000 0 -0.31 97 97
ADCY6 -0.067 0.13 -10000 0 -0.28 107 107
ADCY7 -0.067 0.13 -10000 0 -0.29 93 93
ADCY1 -0.072 0.14 -10000 0 -0.31 102 102
ADCY2 -0.071 0.14 -10000 0 -0.29 101 101
ADCY3 -0.067 0.13 -10000 0 -0.28 107 107
ADCY8 -0.081 0.15 -10000 0 -0.3 120 120
ADCY9 -0.067 0.14 -10000 0 -0.3 87 87
arachidonic acid secretion -0.066 0.2 0.28 11 -0.46 82 93
ETB receptor/Endothelin-1/Gq/GTP -0.026 0.12 -10000 0 -0.28 66 66
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.013 0.13 -10000 0 -0.25 102 102
ETA receptor/Endothelin-1/Gs/GTP -0.041 0.16 -10000 0 -0.26 156 156
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.099 0.2 0.23 1 -0.45 106 107
EDNRB -0.014 0.12 -10000 0 -0.41 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.065 0.16 0.24 1 -0.46 43 44
CYSLTR1 -0.064 0.15 0.24 1 -0.47 37 38
SLC9A1 -0.034 0.098 0.17 1 -0.25 61 62
mol:GDP -0.063 0.18 0.27 10 -0.44 56 66
SLC9A3 -0.075 0.25 -10000 0 -0.68 56 56
RAF1 -0.072 0.19 0.26 10 -0.44 76 86
JUN -0.037 0.19 -10000 0 -0.6 34 34
JAK2 -0.055 0.13 0.24 1 -0.27 109 110
mol:IP3 -0.042 0.14 -10000 0 -0.36 53 53
ETA receptor/Endothelin-1 -0.04 0.17 0.41 1 -0.32 116 117
PLCB1 0.01 0.081 -10000 0 -0.43 17 17
PLCB2 0.011 0.073 -10000 0 -0.36 17 17
ETA receptor/Endothelin-3 -0.018 0.11 -10000 0 -0.31 45 45
FOS -0.11 0.31 0.35 5 -0.87 65 70
Gai/GDP 0.002 0.14 -10000 0 -0.71 15 15
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca ++ -0.071 0.17 0.22 1 -0.42 66 67
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
PRKCB1 -0.042 0.14 -10000 0 -0.37 47 47
GNAQ 0.024 0.011 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.028 0.15 -10000 0 -0.42 61 61
Gs family/GDP -0.073 0.18 0.26 5 -0.42 68 73
ETA receptor/Endothelin-1/Gq/GTP -0.029 0.12 0.19 1 -0.3 51 52
MAPK14 -0.033 0.12 -10000 0 -0.37 37 37
TRPC6 -0.049 0.24 -10000 0 -0.8 35 35
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.032 0.13 0.16 1 -0.34 52 53
ETB receptor/Endothelin-2 -0.004 0.09 -10000 0 -0.3 37 37
ETB receptor/Endothelin-3 -0.003 0.11 -10000 0 -0.34 49 49
ETB receptor/Endothelin-1 -0.027 0.13 -10000 0 -0.31 69 69
MAPK3 -0.1 0.27 0.33 9 -0.74 67 76
MAPK1 -0.1 0.28 0.34 7 -0.75 66 73
Rac1/GDP -0.053 0.16 0.28 2 -0.44 45 47
cAMP biosynthetic process -0.073 0.16 0.22 1 -0.37 79 80
MAPK8 -0.049 0.22 0.32 1 -0.65 44 45
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.022 0.098 0.16 1 -0.3 38 39
p130Cas/CRK/Src/PYK2 -0.049 0.18 0.31 12 -0.52 39 51
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.053 0.16 0.34 1 -0.44 45 46
COL1A2 -0.058 0.16 -10000 0 -0.45 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.018 0.089 -10000 0 -0.27 31 31
mol:DAG -0.042 0.14 -10000 0 -0.36 54 54
MAP2K2 -0.081 0.22 0.34 14 -0.57 69 83
MAP2K1 -0.089 0.23 0.27 7 -0.59 69 76
EDNRA -0.033 0.12 0.21 1 -0.33 40 41
positive regulation of muscle contraction -0.024 0.13 0.21 38 -0.28 55 93
Gq family/GDP -0.043 0.17 -10000 0 -0.45 46 46
HRAS/GTP -0.061 0.17 0.25 11 -0.43 55 66
PRKCH -0.042 0.13 -10000 0 -0.38 43 43
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.039 0.14 0.23 8 -0.41 37 45
PRKCB -0.052 0.14 -10000 0 -0.4 45 45
PRKCE -0.043 0.14 0.22 1 -0.4 40 41
PRKCD -0.052 0.15 -10000 0 -0.43 47 47
PRKCG -0.075 0.15 -10000 0 -0.38 64 64
regulation of vascular smooth muscle contraction -0.13 0.36 0.4 4 -1 64 68
PRKCQ -0.035 0.15 0.22 21 -0.41 41 62
PLA2G4A -0.073 0.22 0.29 10 -0.5 82 92
GNA14 0.008 0.081 -10000 0 -0.34 23 23
GNA15 0.012 0.071 -10000 0 -0.34 17 17
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA11 0.016 0.06 -10000 0 -0.43 9 9
Rac1/GTP -0.012 0.13 -10000 0 -0.25 102 102
MMP1 0.017 0.1 0.42 12 -0.83 1 13
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CCL5 -0.025 0.12 -10000 0 -0.43 39 39
SDCBP 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.065 0.14 0.24 6 -0.34 65 71
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 -0.056 0.14 0.2 12 -0.37 48 60
Syndecan-1/Syntenin -0.048 0.14 0.24 16 -0.38 45 61
MAPK3 -0.051 0.13 0.19 14 -0.37 39 53
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
TGFB1/TGF beta receptor Type II 0.021 0.022 -10000 0 -0.43 1 1
BSG 0.025 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.055 0.14 0.2 12 -0.37 48 60
Syndecan-1/RANTES -0.068 0.16 0.24 16 -0.4 59 75
Syndecan-1/CD147 -0.043 0.14 0.24 4 -0.39 40 44
Syndecan-1/Syntenin/PIP2 -0.047 0.14 0.23 14 -0.37 45 59
LAMA5 0.024 0.022 -10000 0 -0.28 2 2
positive regulation of cell-cell adhesion -0.047 0.14 0.22 14 -0.36 45 59
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
HGF -0.009 0.091 -10000 0 -0.2 69 69
Syndecan-1/CASK -0.069 0.13 -10000 0 -0.31 74 74
Syndecan-1/HGF/MET -0.075 0.16 0.24 4 -0.38 72 76
regulation of cell adhesion -0.043 0.14 0.29 18 -0.36 39 57
HPSE -0.014 0.12 -10000 0 -0.43 39 39
positive regulation of cell migration -0.065 0.14 0.24 6 -0.34 65 71
SDC1 -0.063 0.14 0.19 2 -0.32 78 80
Syndecan-1/Collagen -0.065 0.14 0.24 6 -0.34 65 71
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.047 0.14 -10000 0 -0.43 52 52
PRKACA 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
MAPK1 -0.051 0.13 0.2 13 -0.37 39 52
homophilic cell adhesion -0.061 0.14 0.22 15 -0.33 65 80
MMP1 -0.008 0.048 -10000 0 -0.14 48 48
Reelin signaling pathway

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
CDK5R1/CDK5 0.015 0.07 -10000 0 -0.3 22 22
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
CRKL 0.025 0.008 -10000 0 -0.13 1 1
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ITGA3 0.017 0.046 -10000 0 -0.17 23 23
RELN/VLDLR/Fyn 0 0.1 -10000 0 -0.25 68 68
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.055 -10000 0 -0.22 15 15
AKT1 -0.047 0.11 -10000 0 -0.26 98 98
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
DAB1 -0.039 0.15 -10000 0 -0.36 80 80
RELN/LRP8/DAB1 -0.024 0.12 -10000 0 -0.24 103 103
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
RELN/LRP8/DAB1/Fyn -0.017 0.11 -10000 0 -0.23 96 96
DAB1/alpha3/beta1 Integrin -0.02 0.11 -10000 0 -0.23 92 92
long-term memory -0.1 0.17 -10000 0 -0.3 168 168
DAB1/LIS1 -0.014 0.12 -10000 0 -0.23 100 100
DAB1/CRLK/C3G -0.02 0.11 -10000 0 -0.23 95 95
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DAB1/NCK2 -0.014 0.12 -10000 0 -0.23 100 100
ARHGEF2 0.025 0.02 -10000 0 -0.43 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.071 0.17 -10000 0 -0.43 85 85
CDK5R1 0 0.1 -10000 0 -0.43 29 29
RELN -0.046 0.14 -10000 0 -0.29 107 107
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.001 0.095 -10000 0 -0.25 58 58
GRIN2A/RELN/LRP8/DAB1/Fyn -0.052 0.16 -10000 0 -0.28 134 134
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
RELN/VLDLR/DAB1 -0.031 0.12 -10000 0 -0.24 109 109
ITGB1 0.023 0.012 -10000 0 -10000 0 0
MAP1B -0.032 0.12 0.16 60 -0.25 102 162
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
GRIN2B/RELN/LRP8/DAB1/Fyn -0.057 0.15 -10000 0 -0.28 140 140
PI3K 0.038 0.007 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.037 -10000 0 -0.27 4 4
RAP1A -0.022 0.12 0.31 9 -0.32 18 27
PAFAH1B1 0.026 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.04 -10000 0 -0.43 4 4
CRLK/C3G 0.037 0.01 -10000 0 -10000 0 0
GRIN2B -0.077 0.16 -10000 0 -0.28 172 172
NCK2 0.026 0.002 -10000 0 -10000 0 0
neuron differentiation -0.028 0.13 -10000 0 -0.34 51 51
neuron adhesion -0.014 0.13 0.34 12 -0.37 10 22
LRP8 0.02 0.03 -10000 0 -0.43 2 2
GSK3B -0.052 0.11 -10000 0 -0.25 94 94
RELN/VLDLR/DAB1/Fyn -0.024 0.12 -10000 0 -0.24 102 102
MAP3K11 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.049 0.12 -10000 0 -0.27 103 103
CDK5 0.02 0.011 -10000 0 -10000 0 0
MAPT 0.006 0.098 0.77 6 -0.39 8 14
neuron migration -0.042 0.16 0.23 56 -0.31 96 152
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.13 -10000 0 -0.34 52 52
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 67 67
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 63 63
E-cadherin/beta catenin -0.017 0.11 -9999 0 -0.3 59 59
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
JUP 0.02 0.049 -9999 0 -0.39 7 7
CDH1 -0.046 0.15 -9999 0 -0.28 122 122
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.19 -10000 0 -0.58 53 53
IHH 0.012 0.056 0.18 1 -0.2 7 8
SHH Np/Cholesterol/GAS1 -0.011 0.084 0.16 12 -0.23 54 66
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.011 0.083 0.23 54 -0.15 12 66
SMO/beta Arrestin2 -0.005 0.12 -10000 0 -0.39 20 20
SMO -0.02 0.11 -10000 0 -0.37 33 33
AKT1 -0.003 0.11 -10000 0 -0.48 17 17
ARRB2 0.026 0.002 -10000 0 -10000 0 0
BOC 0.023 0.036 -10000 0 -0.31 5 5
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
heart looping -0.019 0.11 -10000 0 -0.36 33 33
STIL -0.012 0.13 0.23 3 -0.27 62 65
DHH N/PTCH2 0.004 0.085 -10000 0 -0.31 31 31
DHH N/PTCH1 -0.02 0.12 -10000 0 -0.28 79 79
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DHH -0.007 0.1 -10000 0 -0.28 53 53
PTHLH -0.061 0.26 -10000 0 -0.78 53 53
determination of left/right symmetry -0.019 0.11 -10000 0 -0.36 33 33
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
skeletal system development -0.06 0.25 -10000 0 -0.77 53 53
IHH N/Hhip -0.04 0.14 -10000 0 -0.33 78 78
DHH N/Hhip -0.049 0.14 -10000 0 -0.31 101 101
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.019 0.11 -10000 0 -0.36 33 33
pancreas development -0.058 0.16 -10000 0 -0.29 135 135
HHAT 0.012 0.077 -10000 0 -0.39 17 17
PI3K 0.038 0.007 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.016 0.047 -10000 0 -0.17 26 26
somite specification -0.019 0.11 -10000 0 -0.36 33 33
SHH Np/Cholesterol/PTCH1 -0.036 0.11 -10000 0 -0.28 68 68
SHH Np/Cholesterol/PTCH2 -0.016 0.082 0.15 2 -0.24 56 58
SHH Np/Cholesterol/Megalin -0.059 0.12 0.15 8 -0.27 115 123
SHH -0.03 0.097 -10000 0 -0.31 52 52
catabolic process -0.018 0.12 -10000 0 -0.34 52 52
SMO/Vitamin D3 -0.032 0.12 0.29 2 -0.33 38 40
SHH Np/Cholesterol/Hhip -0.048 0.12 0.15 8 -0.26 102 110
LRP2 -0.093 0.18 -10000 0 -0.43 108 108
receptor-mediated endocytosis -0.066 0.14 -10000 0 -0.4 47 47
SHH Np/Cholesterol/BOC -0.014 0.08 -10000 0 -0.24 54 54
SHH Np/Cholesterol/CDO -0.02 0.089 0.17 1 -0.25 59 60
mesenchymal cell differentiation 0.048 0.12 0.26 102 -0.15 8 110
mol:Vitamin D3 -0.001 0.14 0.32 3 -0.28 68 71
IHH N/PTCH2 0.023 0.051 -10000 0 -0.37 5 5
CDON 0.001 0.095 -10000 0 -0.34 32 32
IHH N/PTCH1 -0.011 0.12 -10000 0 -0.34 52 52
Megalin/LRPAP1 -0.052 0.14 -10000 0 -0.3 108 108
PTCH2 0.016 0.048 -10000 0 -0.43 5 5
SHH Np/Cholesterol -0.019 0.075 0.2 1 -0.23 52 53
PTCH1 -0.019 0.12 -10000 0 -0.34 52 52
HHIP -0.058 0.16 -10000 0 -0.29 135 135
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.078 -10000 0 -0.31 25 25
CDKN2C 0.01 0.042 -10000 0 -0.14 16 16
CDKN2A -0.014 0.1 -10000 0 -0.31 48 48
CCND2 0.016 0.068 0.21 47 -0.13 3 50
RB1 -0.023 0.079 0.12 1 -0.24 50 51
CDK4 0.021 0.077 0.24 48 -0.17 1 49
CDK6 0.017 0.081 0.25 44 -0.16 10 54
G1/S progression 0.042 0.099 0.26 75 -0.25 3 78
Effects of Botulinum toxin

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
STX1A -0.011 0.046 -10000 0 -0.3 7 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.019 0.12 -10000 0 -0.31 69 69
STXBP1 0.016 0.044 -10000 0 -0.43 2 2
ACh/CHRNA1 -0.042 0.11 0.13 8 -0.24 92 100
RAB3GAP2/RIMS1/UNC13B 0.01 0.11 -10000 0 -0.26 67 67
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 -0.049 0.16 -10000 0 -0.32 112 112
mol:ACh -0.008 0.057 0.099 59 -0.12 71 130
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.031 0.12 -10000 0 -0.23 110 110
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.11 0.13 8 -0.24 92 100
UNC13B 0.025 0.021 -10000 0 -0.43 1 1
CHRNA1 -0.065 0.15 -10000 0 -0.43 68 68
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.056 0.13 0.13 2 -0.31 90 92
SNAP25 -0.043 0.098 -10000 0 -0.26 86 86
VAMP2 0.005 0 -10000 0 -10000 0 0
SYT1 -0.088 0.17 -10000 0 -0.43 92 92
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0 0.052 -10000 0 -0.16 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.031 0.12 -10000 0 -0.23 110 110
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.12 -10000 0 -0.24 100 100
NFATC4 -0.057 0.089 0.22 2 -0.23 49 51
ERBB2IP 0.026 0.02 -10000 0 -0.42 1 1
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.047 0.11 0.2 1 -0.24 115 116
JUN -0.022 0.083 0.19 4 -0.36 10 14
HRAS 0.024 0.006 -10000 0 -10000 0 0
DOCK7 -0.064 0.098 -10000 0 -0.24 105 105
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.035 0.13 -10000 0 -0.25 119 119
AKT1 0.003 0.007 -10000 0 -10000 0 0
BAD -0.006 0.004 -10000 0 -10000 0 0
MAPK10 -0.03 0.065 0.17 2 -0.2 9 11
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.12 0.21 1 -0.26 115 116
RAF1 -0.044 0.12 0.23 11 -0.32 46 57
ErbB2/ErbB3/neuregulin 2 -0.003 0.08 0.16 2 -0.25 40 42
STAT3 0.028 0.043 -10000 0 -0.91 1 1
cell migration -0.022 0.077 0.22 13 -0.2 11 24
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.1 0.25 0.35 2 -0.61 83 85
FOS -0.083 0.2 0.28 3 -0.41 118 121
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.11 0.2 1 -0.24 115 116
MAPK3 -0.08 0.21 0.34 3 -0.51 70 73
MAPK1 -0.083 0.21 0.34 3 -0.51 70 73
JAK2 -0.067 0.097 0.15 1 -0.24 114 115
NF2 0.005 0.033 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.052 0.12 0.17 2 -0.26 118 120
NRG1 -0.081 0.18 -10000 0 -0.32 154 154
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
MAPK8 -0.054 0.12 -10000 0 -0.27 112 112
MAPK9 -0.029 0.063 0.17 3 -0.21 5 8
ERBB2 -0.022 0.017 -10000 0 -0.32 1 1
ERBB3 -0.017 0.12 -10000 0 -0.35 57 57
SHC1 0.024 0.014 -10000 0 -0.13 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
apoptosis 0.003 0.013 -10000 0 -0.2 1 1
STAT3 (dimer) 0.029 0.042 -10000 0 -0.89 1 1
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.004 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.041 0.074 -10000 0 -0.18 96 96
ErbB2/ErbB2/HSP90 (dimer) 0 0.025 -10000 0 -0.27 1 1
CHRNA1 -0.091 0.24 0.31 3 -0.63 71 74
myelination -0.054 0.089 0.23 3 -0.26 24 27
PPP3CB -0.065 0.091 -10000 0 -0.22 114 114
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.11 -10000 0 -0.23 106 106
NRG2 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.053 0.12 0.17 2 -0.26 119 121
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.048 0.13 0.23 12 -0.34 42 54
SRC 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.068 0.097 -10000 0 -0.24 115 115
MAP2K1 -0.088 0.2 -10000 0 -0.54 51 51
heart morphogenesis -0.047 0.11 0.2 1 -0.24 115 116
RAS family/GDP -0.026 0.12 0.22 2 -0.24 99 101
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.035 -10000 0 -0.74 1 1
CHRNE -0.002 0.031 0.1 1 -0.17 10 11
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.007 -10000 0 -10000 0 0
nervous system development -0.047 0.11 0.2 1 -0.24 115 116
CDC42 0.022 0.01 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.069 0.25 1 -0.43 5 6
Syndecan-4/Syndesmos -0.059 0.2 0.32 1 -0.46 91 92
positive regulation of JNK cascade -0.053 0.2 0.31 1 -0.44 92 93
Syndecan-4/ADAM12 -0.068 0.2 0.34 1 -0.46 92 93
CCL5 -0.025 0.12 -10000 0 -0.43 39 39
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.025 0.006 -10000 0 -10000 0 0
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
SDCBP 0.025 0.006 -10000 0 -10000 0 0
PLG 0.001 0.026 -10000 0 -0.14 4 4
ADAM12 -0.001 0.077 -10000 0 -0.43 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.22 0.32 1 -0.49 95 96
Syndecan-4/CXCL12/CXCR4 -0.056 0.21 0.32 1 -0.46 92 93
Syndecan-4/Laminin alpha3 -0.07 0.21 0.32 1 -0.48 93 94
MDK -0.002 0.097 -10000 0 -0.43 22 22
Syndecan-4/FZD7 -0.078 0.22 -10000 0 -0.5 95 95
Syndecan-4/Midkine -0.067 0.21 0.32 1 -0.47 90 91
FZD7 -0.018 0.13 -10000 0 -0.4 54 54
Syndecan-4/FGFR1/FGF -0.044 0.19 -10000 0 -0.44 85 85
THBS1 -0.018 0.1 -10000 0 -0.2 100 100
integrin-mediated signaling pathway -0.066 0.2 0.31 1 -0.47 91 92
positive regulation of MAPKKK cascade -0.053 0.2 0.31 1 -0.44 92 93
Syndecan-4/TACI -0.063 0.2 0.31 1 -0.46 92 93
CXCR4 0.012 0.072 -10000 0 -0.27 25 25
cell adhesion 0.017 0.036 0.2 14 -0.2 1 15
Syndecan-4/Dynamin -0.063 0.2 -10000 0 -0.46 92 92
Syndecan-4/TSP1 -0.071 0.21 0.32 1 -0.48 93 94
Syndecan-4/GIPC -0.063 0.2 -10000 0 -0.46 92 92
Syndecan-4/RANTES -0.077 0.21 0.32 1 -0.48 93 94
ITGB1 0.023 0.012 -10000 0 -10000 0 0
LAMA1 -0.024 0.14 -10000 0 -0.37 64 64
LAMA3 -0.004 0.1 -10000 0 -0.43 26 26
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.035 0.16 0.85 18 -0.4 1 19
Syndecan-4/alpha-Actinin -0.061 0.2 0.32 1 -0.46 92 93
TFPI -0.024 0.12 -10000 0 -0.43 33 33
F2 0.006 0.031 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
positive regulation of cell adhesion -0.094 0.22 0.31 1 -0.49 103 104
ACTN1 0.014 0.044 -10000 0 -0.43 1 1
TNC -0.005 0.1 -10000 0 -0.43 24 24
Syndecan-4/CXCL12 -0.062 0.2 0.32 1 -0.46 92 93
FGF6 -0.013 0.01 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CXCL12 0.021 0.038 -10000 0 -0.43 3 3
TNFRSF13B -0.003 0.028 -10000 0 -0.13 11 11
FGF2 0.024 0.029 -10000 0 -0.43 2 2
FGFR1 0.025 0.005 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.079 0.19 -10000 0 -0.46 93 93
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.034 -10000 0 -0.15 6 6
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.001 0.096 -10000 0 -0.41 26 26
vasculogenesis -0.068 0.2 0.31 1 -0.46 93 94
SDC4 -0.077 0.2 -10000 0 -0.48 93 93
Syndecan-4/Tenascin C -0.069 0.21 0.32 1 -0.48 91 92
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.058 0.2 0.32 1 -0.46 88 89
MMP9 -0.045 0.13 -10000 0 -0.34 60 60
Rac1/GTP 0.017 0.036 0.2 14 -0.2 1 15
cytoskeleton organization -0.056 0.2 0.31 1 -0.44 92 93
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
Syndecan-4/TFPI -0.074 0.21 0.34 1 -0.48 93 94
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.3 -10000 0 -0.8 58 58
PCK1 -0.18 0.39 -10000 0 -1.2 54 54
HNF4A -0.15 0.33 -10000 0 -0.9 57 57
KCNJ11 -0.18 0.4 -10000 0 -0.99 77 77
AKT1 -0.067 0.18 -10000 0 -0.41 57 57
response to starvation -0.003 0.026 -10000 0 -0.31 2 2
DLK1 -0.16 0.35 -10000 0 -0.9 70 70
NKX2-1 -0.058 0.15 0.3 3 -0.37 44 47
ACADM -0.13 0.3 -10000 0 -0.79 59 59
TAT -0.19 0.39 -10000 0 -1.1 55 55
CEBPB 0.013 0.073 -10000 0 -0.43 13 13
CEBPA 0.015 0.05 -10000 0 -0.28 10 10
TTR -0.12 0.27 0.53 3 -0.84 38 41
PKLR -0.14 0.3 -10000 0 -0.81 56 56
APOA1 -0.18 0.4 -10000 0 -1.1 62 62
CPT1C -0.13 0.3 -10000 0 -0.81 56 56
ALAS1 -0.06 0.18 -10000 0 -0.76 3 3
TFRC -0.14 0.3 -10000 0 -0.93 38 38
FOXF1 0.019 0.042 -10000 0 -0.19 16 16
NF1 0.03 0.02 -10000 0 -0.42 1 1
HNF1A (dimer) 0.025 0.026 -10000 0 -0.44 1 1
CPT1A -0.13 0.3 -10000 0 -0.8 59 59
HMGCS1 -0.13 0.3 -10000 0 -0.8 60 60
NR3C1 -0.018 0.089 -10000 0 -0.2 83 83
CPT1B -0.15 0.32 -10000 0 -0.8 74 74
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.024 0.013 -10000 0 -10000 0 0
GCK -0.16 0.37 0.5 1 -0.88 85 86
CREB1 0.008 0.058 -10000 0 -0.19 29 29
IGFBP1 -0.22 0.48 -10000 0 -1.2 85 85
PDX1 -0.058 0.17 -10000 0 -0.57 10 10
UCP2 -0.14 0.32 -10000 0 -0.8 70 70
ALDOB -0.14 0.35 -10000 0 -0.89 62 62
AFP -0.035 0.1 -10000 0 -0.44 8 8
BDH1 -0.16 0.35 -10000 0 -0.92 67 67
HADH -0.13 0.32 -10000 0 -0.83 60 60
F2 -0.15 0.35 -10000 0 -1 43 43
HNF1A 0.025 0.026 -10000 0 -0.44 1 1
G6PC -0.034 0.16 -10000 0 -1.1 6 6
SLC2A2 -0.064 0.19 -10000 0 -0.67 4 4
INS 0.008 0.086 0.21 56 -0.4 4 60
FOXA1 -0.007 0.087 -10000 0 -0.29 30 30
FOXA3 -0.041 0.14 -10000 0 -0.37 61 61
FOXA2 -0.15 0.37 -10000 0 -0.89 71 71
ABCC8 -0.19 0.41 -10000 0 -0.98 86 86
ALB -0.07 0.23 -10000 0 -0.91 32 32
Syndecan-3-mediated 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
CTTN 0.025 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.012 0.14 -10000 0 -0.35 64 64
Syndecan-3/Neurocan -0.042 0.15 -10000 0 -0.37 77 77
POMC 0.015 0.063 -10000 0 -0.43 9 9
EGFR -0.016 0.12 -10000 0 -0.43 42 42
Syndecan-3/EGFR -0.051 0.15 -10000 0 -0.38 74 74
AGRP 0.012 0.024 -10000 0 -10000 0 0
NCSTN 0.026 0.004 -10000 0 -10000 0 0
PSENEN 0.022 0.01 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
NCAN -0.001 0.1 -10000 0 -0.4 31 31
long-term memory -0.013 0.14 -10000 0 -0.35 72 72
Syndecan-3/IL8 -0.054 0.16 -10000 0 -0.4 77 77
PSEN1 0.025 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.036 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
limb bud formation -0.046 0.14 -10000 0 -0.38 77 77
MC4R -0.051 0.16 -10000 0 -0.33 106 106
SRC 0.025 0.005 -10000 0 -10000 0 0
PTN 0.019 0.03 -10000 0 -0.43 2 2
FGFR/FGF/Syndecan-3 -0.046 0.14 -10000 0 -0.38 77 77
neuron projection morphogenesis -0.015 0.15 0.26 1 -0.35 65 66
Syndecan-3/AgRP -0.03 0.14 -10000 0 -0.37 77 77
Syndecan-3/AgRP/MC4R -0.045 0.16 -10000 0 -0.38 77 77
Fyn/Cortactin 0.036 0.01 -10000 0 -10000 0 0
SDC3 -0.047 0.14 -10000 0 -0.39 77 77
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.053 0.16 -10000 0 -0.39 77 77
IL8 -0.061 0.15 -10000 0 -0.25 158 158
Syndecan-3/Fyn/Cortactin -0.013 0.14 -10000 0 -0.36 72 72
Syndecan-3/CASK -0.045 0.14 -10000 0 -0.36 77 77
alpha-MSH/MC4R -0.025 0.13 -10000 0 -0.32 76 76
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
Aurora C signaling

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.021 -9999 0 -0.43 1 1
Aurora C/Aurora B/INCENP -0.011 0.11 -9999 0 -0.23 94 94
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.031 -9999 0 -10000 0 0
AURKB -0.072 0.17 -9999 0 -0.3 152 152
AURKC 0.011 0.051 -9999 0 -0.18 26 26
IL4-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.36 -10000 0 -1.1 39 39
STAT6 (cleaved dimer) -0.28 0.39 -10000 0 -0.99 83 83
IGHG1 -0.1 0.2 -10000 0 -0.98 13 13
IGHG3 -0.24 0.34 -10000 0 -0.93 61 61
AKT1 -0.18 0.31 -10000 0 -0.88 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.31 -10000 0 -0.91 52 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.94 61 61
THY1 -0.26 0.39 -10000 0 -1.2 44 44
MYB -0.016 0.12 -10000 0 -0.28 67 67
HMGA1 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.31 -10000 0 -0.8 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.33 -10000 0 -0.94 63 63
SP1 0.025 0.019 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
SOCS5 0.033 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.38 -10000 0 -1 70 70
SOCS1 -0.21 0.28 -10000 0 -0.72 63 63
SOCS3 -0.23 0.36 -10000 0 -1 63 63
FCER2 -0.26 0.4 -10000 0 -1.1 59 59
PARP14 0.017 0.046 -10000 0 -0.37 5 5
CCL17 -0.25 0.36 -10000 0 -1.1 39 39
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.24 -10000 0 -0.7 49 49
T cell proliferation -0.27 0.38 -10000 0 -1 64 64
IL4R/JAK1 -0.25 0.36 -10000 0 -1 49 49
EGR2 -0.34 0.5 -10000 0 -1.3 76 76
JAK2 -0.008 0.041 -10000 0 -10000 0 0
JAK3 -0.011 0.1 -10000 0 -0.24 65 65
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.022 -10000 0 -10000 0 0
COL1A2 -0.088 0.2 -10000 0 -1.3 7 7
CCL26 -0.22 0.37 -10000 0 -1.1 37 37
IL4R -0.26 0.38 -10000 0 -1.1 47 47
PTPN6 0.019 0.065 -10000 0 -0.42 10 10
IL13RA2 -0.42 0.55 -10000 0 -1.3 129 129
IL13RA1 -0.013 0.07 -10000 0 -0.42 9 9
IRF4 -0.12 0.32 -10000 0 -1.3 30 30
ARG1 -0.09 0.21 -10000 0 -0.95 18 18
CBL -0.19 0.29 -10000 0 -0.75 74 74
GTF3A 0.003 0.052 -10000 0 -0.15 21 21
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL13RA1/JAK2 -0.01 0.07 -10000 0 -0.32 8 8
IRF4/BCL6 -0.099 0.3 -10000 0 -1.2 30 30
CD40LG 0.003 0.054 -10000 0 -0.14 9 9
MAPK14 -0.22 0.32 -10000 0 -0.81 79 79
mitosis -0.17 0.29 -10000 0 -0.82 59 59
STAT6 -0.28 0.4 -10000 0 -1.1 57 57
SPI1 0.015 0.064 -10000 0 -0.4 10 10
RPS6KB1 -0.16 0.28 -10000 0 -0.78 58 58
STAT6 (dimer) -0.28 0.4 -10000 0 -1.1 57 57
STAT6 (dimer)/PARP14 -0.26 0.38 -10000 0 -1 61 61
mast cell activation 0.007 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.31 -10000 0 -0.86 61 61
FRAP1 -0.18 0.31 -10000 0 -0.88 59 59
LTA -0.28 0.42 -10000 0 -1.2 57 57
FES 0.024 0.024 -10000 0 -0.21 4 4
T-helper 1 cell differentiation 0.27 0.39 1.1 57 -10000 0 57
CCL11 -0.25 0.34 -10000 0 -1 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.3 -10000 0 -0.86 53 53
IL2RG -0.002 0.087 -10000 0 -0.38 18 18
IL10 -0.33 0.5 -10000 0 -1.4 78 78
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
IL4 -0.064 0.12 -10000 0 -1 3 3
IL5 -0.25 0.36 -10000 0 -1.1 43 43
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.32 -10000 0 -0.89 50 50
COL1A1 -0.26 0.49 -10000 0 -1.4 77 77
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.36 -10000 0 -1.1 37 37
IL2R gamma/JAK3 -0.009 0.1 -10000 0 -0.27 53 53
TFF3 -0.26 0.36 -10000 0 -1.1 42 42
ALOX15 -0.26 0.36 -10000 0 -1 46 46
MYBL1 0.024 0.011 -10000 0 -0.13 2 2
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.91 71 71
SHC1 0.024 0.014 -10000 0 -0.13 4 4
CEBPB 0.013 0.074 -10000 0 -0.41 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.33 -10000 0 -0.93 62 62
mol:PI-3-4-5-P3 -0.18 0.31 -10000 0 -0.88 59 59
PI3K -0.19 0.34 -10000 0 -0.97 59 59
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
ETS1 0.022 0.052 -10000 0 -0.41 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.65 50 50
ITGB3 -0.27 0.39 -10000 0 -1.2 45 45
PIGR -0.34 0.51 -10000 0 -1.3 82 82
IGHE 0.011 0.058 0.16 9 -0.2 13 22
MAPKKK cascade -0.13 0.22 -10000 0 -0.64 50 50
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.26 0.36 -10000 0 -1.1 39 39
RETNLB -0.26 0.36 -10000 0 -1.1 39 39
SELP -0.25 0.36 -10000 0 -1 43 43
AICDA -0.24 0.35 -10000 0 -1 38 38
BCR signaling pathway

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
JUN -0.058 0.18 0.3 5 -0.41 85 90
IKBKB 0.016 0.09 0.25 18 -0.27 5 23
AKT1 -0.022 0.1 0.27 23 -0.22 34 57
IKBKG 0.004 0.093 0.24 12 -0.27 14 26
CALM1 -0.04 0.14 0.22 3 -0.37 58 61
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.033 0.18 0.31 14 -0.48 50 64
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.15 0.22 4 -0.4 58 62
DOK1 0.025 0.021 -10000 0 -0.28 2 2
AP-1 -0.044 0.12 0.24 3 -0.27 75 78
LYN 0.021 0.035 -10000 0 -0.19 10 10
BLNK -0.021 0.13 -10000 0 -0.38 59 59
SHC1 0.024 0.014 -10000 0 -0.13 4 4
BCR complex -0.006 0.096 -10000 0 -0.27 51 51
CD22 -0.065 0.15 -10000 0 -0.42 54 54
CAMK2G -0.037 0.14 0.26 4 -0.43 36 40
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
SHC/GRB2/SOS1 -0.027 0.11 -10000 0 -0.24 77 77
GO:0007205 -0.042 0.16 0.22 3 -0.4 58 61
SYK 0.009 0.083 -10000 0 -0.35 23 23
ELK1 -0.039 0.15 0.22 2 -0.38 58 60
NFATC1 -0.043 0.14 0.27 6 -0.42 48 54
B-cell antigen/BCR complex -0.006 0.096 -10000 0 -0.27 51 51
PAG1/CSK 0.036 0.01 -10000 0 -10000 0 0
NFKBIB 0.017 0.046 0.13 21 -0.13 13 34
HRAS -0.031 0.14 0.25 7 -0.35 52 59
NFKBIA 0.016 0.047 0.13 20 -0.13 13 33
NF-kappa-B/RelA/I kappa B beta 0.022 0.041 0.13 21 -10000 0 21
RasGAP/Csk -0.002 0.12 -10000 0 -0.24 96 96
mol:GDP -0.037 0.15 0.22 3 -0.39 58 61
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.005 0.099 -10000 0 -0.43 23 23
NF-kappa-B/RelA/I kappa B alpha 0.022 0.041 0.13 20 -10000 0 20
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.059 0.18 0.34 4 -0.5 53 57
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.044 0.16 0.22 3 -0.4 59 62
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.059 0.16 0.22 2 -0.4 57 59
CHUK -0.006 0.098 0.24 13 -0.27 27 40
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.002 0.15 0.24 11 -0.44 31 42
PTPN6 -0.068 0.15 0.22 2 -0.45 52 54
RELA 0.025 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.038 0.12 5 -0.12 2 7
VAV2 -0.053 0.15 0.22 1 -0.47 47 48
ubiquitin-dependent protein catabolic process 0.019 0.046 0.13 21 -0.13 13 34
BTK -0.018 0.21 -10000 0 -1.1 18 18
CD19 -0.056 0.14 -10000 0 -0.39 60 60
MAP4K1 0.013 0.061 -10000 0 -0.34 13 13
CD72 0.017 0.048 -10000 0 -0.19 20 20
PAG1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.026 0.16 0.28 18 -0.41 49 67
SH3BP5 0.024 0.029 -10000 0 -0.33 3 3
PIK3AP1 -0.041 0.16 -10000 0 -0.43 56 56
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.06 0.23 -10000 0 -0.56 61 61
RAF1 -0.028 0.13 0.24 7 -0.35 45 52
RasGAP/p62DOK/SHIP -0.002 0.12 -10000 0 -0.24 89 89
CD79A -0.001 0.086 -10000 0 -0.25 42 42
re-entry into mitotic cell cycle -0.044 0.12 0.24 3 -0.26 75 78
RASA1 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.11 0.24 6 -0.36 28 34
MAPK1 -0.023 0.11 0.23 6 -0.36 27 33
CD72/SHP1 -0.056 0.16 0.27 12 -0.41 58 70
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.031 0.16 0.28 16 -0.4 53 69
actin cytoskeleton organization -0.027 0.15 0.3 19 -0.42 40 59
NF-kappa-B/RelA 0.044 0.079 0.23 26 -0.2 11 37
Calcineurin -0.012 0.13 0.22 1 -0.41 33 34
PI3K -0.067 0.13 -10000 0 -0.37 56 56
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.17 -10000 0 -0.44 57 57
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.068 0.27 -10000 0 -0.79 56 56
DAPP1 -0.095 0.31 -10000 0 -0.91 56 56
cytokine secretion -0.04 0.14 0.26 6 -0.39 49 55
mol:DAG -0.044 0.16 0.22 3 -0.4 59 62
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
MAP2K1 -0.026 0.12 0.24 6 -0.39 29 35
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.13 -10000 0 -0.25 116 116
mol:PI-3-4-5-P3 -0.056 0.094 0.18 1 -0.29 46 47
ETS1 -0.026 0.13 0.26 9 -0.4 33 42
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.13 -10000 0 -0.26 89 89
B-cell antigen/BCR complex/LYN -0.048 0.15 -10000 0 -0.42 56 56
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 -0.033 0.15 0.28 15 -0.44 42 57
B-cell antigen/BCR complex/LYN/SYK -0.049 0.17 0.27 1 -0.43 61 62
CARD11 -0.022 0.18 0.25 23 -0.42 55 78
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
PPP3CA 0.025 0.011 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
IKK complex 0.01 0.051 0.15 23 -0.12 5 28
PTPRC -0.003 0.1 -10000 0 -0.28 49 49
PDPK1 -0.035 0.079 0.19 14 -0.21 36 50
PPP3CB 0.024 0.013 -10000 0 -0.13 3 3
PPP3CC 0.025 0.005 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.15 18 -10000 0 18
Arf6 signaling events

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
CENTA1/KIF3B 0.024 0.036 -10000 0 -0.26 6 6
ARNO/beta Arrestin1-2 -0.099 0.31 -10000 0 -0.81 81 81
EGFR -0.016 0.12 -10000 0 -0.43 42 42
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
USP6 0.023 0.022 -10000 0 -0.13 10 10
IQSEC1 0.023 0.027 -10000 0 -0.17 8 8
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.32 69 69
ARRB2 0.011 0.007 -10000 0 -10000 0 0
mol:GTP 0.007 0.042 0.18 5 -0.17 11 16
ARRB1 0.012 0.076 -10000 0 -0.43 15 15
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR -0.084 0.17 -10000 0 -0.43 90 90
EGF -0.01 0.11 -10000 0 -0.31 54 54
somatostatin receptor activity 0 0 0.001 60 -0.001 28 88
ARAP2 0.012 0.079 -10000 0 -0.43 16 16
mol:GDP -0.016 0.13 0.19 46 -0.28 48 94
mol:PI-3-4-5-P3 0 0 0.001 74 -0.001 12 86
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.036 -10000 0 -0.25 3 3
ADAP1 0.014 0.054 -10000 0 -0.24 17 17
KIF13B 0.025 0.005 -10000 0 -10000 0 0
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.13 0.25 56 -0.26 33 89
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.005 0.11 -10000 0 -0.27 70 70
ADRB2 0.005 0.094 -10000 0 -0.43 23 23
receptor agonist activity 0 0 0 32 0 27 59
actin filament binding 0 0 0.001 61 0 31 92
SRC 0.025 0.005 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
GNAQ 0.026 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 76 -0.001 19 95
ARF6/GDP -0.026 0.14 0.23 5 -0.44 34 39
ARF6/GDP/GULP/ACAP1 -0.012 0.16 0.22 29 -0.36 45 74
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.094 -10000 0 -0.24 51 51
ACAP1 0.01 0.06 -10000 0 -0.17 43 43
ACAP2 0.026 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.023 0.007 -10000 0 -10000 0 0
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
HGF -0.009 0.091 -10000 0 -0.2 69 69
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.14 0.38 -10000 0 -1 81 81
NCK1 0.025 0.02 -10000 0 -0.43 1 1
fibronectin binding 0 0 0.001 66 0 25 91
endosomal lumen acidification 0 0 0.001 61 0 39 100
microtubule-based process 0 0 -10000 0 0 12 12
GULP1 -0.016 0.13 -10000 0 -0.43 44 44
GNAQ/ARNO -0.12 0.35 -10000 0 -0.93 81 81
mol:Phosphatidic acid 0 0 0 20 -10000 0 20
PIP3-E 0 0 0 42 0 17 59
MET -0.047 0.14 -10000 0 -0.43 52 52
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.34 17 17
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 64 -0.001 21 85
GNA11 0.017 0.06 -10000 0 -0.43 9 9
LHCGR 0.009 0.031 -10000 0 -10000 0 0
AGTR1 0.001 0.093 -10000 0 -0.29 39 39
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.007 -10000 0 -10000 0 0
IPCEF1/ARNO -0.13 0.33 -10000 0 -0.88 81 81
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.084 -10000 0 -0.23 62 62
epithelial cell differentiation 0.024 0.086 -10000 0 -0.22 55 55
CYFIP2 0.022 0.037 -10000 0 -0.43 3 3
ENAH -0.024 0.061 0.27 3 -10000 0 3
EGFR -0.016 0.12 -10000 0 -0.43 42 42
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
MYO6 -0.014 0.08 0.18 21 -0.21 55 76
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.045 0.028 -10000 0 -0.23 3 3
AQP5 -0.063 0.16 0.22 4 -0.44 69 73
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.077 0.18 20 -0.21 53 73
regulation of calcium-dependent cell-cell adhesion -0.015 0.081 0.18 20 -0.21 58 78
EGF -0.01 0.11 -10000 0 -0.31 54 54
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.019 0.1 -10000 0 -0.45 17 17
cortical microtubule organization 0.024 0.086 -10000 0 -0.22 55 55
GO:0000145 -0.026 0.07 0.16 20 -0.2 53 73
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.088 -10000 0 -0.22 55 55
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GDP -0.038 0.056 -10000 0 -0.2 35 35
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.036 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.085 0.17 8 -0.34 18 26
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
ZYX -0.013 0.069 0.18 11 -0.21 44 55
ARF6/GTP 0.059 0.038 -10000 0 -0.24 3 3
CDH1 -0.046 0.15 -10000 0 -0.28 122 122
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.24 105 105
RhoA/GDP 0.026 0.083 -10000 0 -0.21 55 55
actin cytoskeleton organization -0.028 0.075 0.17 21 -0.21 56 77
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
IGF1R 0.026 0.004 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
DIAPH1 0.02 0.12 -10000 0 -0.55 14 14
Wnt receptor signaling pathway -0.024 0.086 0.22 55 -10000 0 55
RHOA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.038 0.056 -10000 0 -0.2 35 35
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.029 0.077 0.17 21 -0.21 56 77
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
LPP -0.036 0.077 0.17 19 -0.21 61 80
Ephrin A1/EPHA2 0.013 0.079 -10000 0 -0.2 54 54
SEC6/SEC8 -0.015 0.06 -10000 0 -0.21 26 26
MGAT3 -0.016 0.082 0.18 20 -0.21 58 78
HGF/MET -0.025 0.12 -10000 0 -0.25 95 95
HGF -0.009 0.091 -10000 0 -0.2 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.085 -10000 0 -0.23 62 62
actin cable formation -0.004 0.096 0.28 18 -0.26 11 29
KIAA1543 -0.032 0.076 0.16 15 -0.22 58 73
KIFC3 -0.016 0.079 0.18 16 -0.21 55 71
NCK1 0.025 0.02 -10000 0 -0.43 1 1
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.019 0.08 0.18 19 -0.21 56 75
NCK1/GIT1 0.038 0.016 -10000 0 -0.3 1 1
mol:GDP 0.024 0.086 -10000 0 -0.22 55 55
EXOC4 0.02 0.011 -10000 0 -10000 0 0
STX4 -0.014 0.079 0.18 20 -0.21 55 75
PIP5K1C -0.013 0.078 0.18 20 -0.21 53 73
LIMA1 0.019 0.056 -10000 0 -0.43 8 8
ABI1 0.023 0.008 -10000 0 -10000 0 0
ROCK1 -0.021 0.082 0.4 6 -10000 0 6
adherens junction assembly -0.01 0.089 0.26 11 -0.34 8 19
IGF-1R heterotetramer/IGF1 0.014 0.09 -10000 0 -0.22 62 62
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
MET -0.047 0.14 -10000 0 -0.43 52 52
PLEKHA7 -0.019 0.085 0.18 16 -0.22 58 74
mol:GTP 0.052 0.036 -10000 0 -0.25 3 3
establishment of epithelial cell apical/basal polarity 0.02 0.12 0.33 27 -0.28 3 30
cortical actin cytoskeleton stabilization -0.01 0.084 -10000 0 -0.23 62 62
regulation of cell-cell adhesion -0.028 0.075 0.17 21 -0.21 56 77
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.085 -10000 0 -0.23 62 62
Caspase cascade in apoptosis

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
TOP1 -0.026 0.11 -10000 0 -0.36 25 25
ACTA1 -0.054 0.13 0.22 2 -0.33 70 72
NUMA1 -0.027 0.11 -10000 0 -0.36 25 25
SPTAN1 -0.049 0.13 0.26 2 -0.33 66 68
LIMK1 -0.028 0.14 0.2 36 -0.33 62 98
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
CASP10 -0.055 0.097 0.16 1 -0.28 71 72
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
PTK2 -0.03 0.12 -10000 0 -0.36 27 27
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.048 0.13 0.26 2 -0.33 66 68
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
GSN -0.054 0.13 0.22 4 -0.33 70 74
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.13 0.29 -10000 0 -0.59 136 136
BID -0.024 0.065 0.11 1 -0.18 70 71
MAP3K1 -0.011 0.065 -10000 0 -0.44 5 5
TRADD 0.025 0.02 -10000 0 -0.43 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.016 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.048 0.13 0.18 11 -0.33 68 79
CASP9 0.022 0.012 -10000 0 -10000 0 0
DNA repair 0.011 0.056 0.24 8 -0.15 9 17
neuron apoptosis 0.016 0.064 -10000 0 -0.62 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.037 0.13 0.21 2 -0.31 71 73
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.013 0.16 -10000 0 -0.92 12 12
TRAF2 0.025 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.13 0.31 8 -0.31 70 78
CASP7 -0.009 0.096 0.24 21 -0.35 11 32
KRT18 -0.067 0.21 -10000 0 -0.57 73 73
apoptosis -0.051 0.14 0.29 2 -0.43 35 37
DFFA -0.049 0.13 0.2 2 -0.32 70 72
DFFB -0.049 0.13 0.19 7 -0.32 70 77
PARP1 -0.011 0.056 0.15 8 -0.24 8 16
actin filament polymerization 0.025 0.13 0.31 62 -0.23 13 75
TNF -0.06 0.16 -10000 0 -0.26 151 151
CYCS -0.011 0.056 0.19 4 -0.2 10 14
SATB1 -0.014 0.16 -10000 0 -0.86 12 12
SLK -0.052 0.13 0.33 1 -0.33 70 71
p15 BID/BAX -0.011 0.063 -10000 0 -0.27 8 8
CASP2 0.024 0.11 0.21 86 -0.32 14 100
JNK cascade 0.011 0.065 0.43 5 -10000 0 5
CASP3 -0.055 0.13 0.19 2 -0.34 71 73
LMNB2 0.025 0.11 0.24 8 -0.45 10 18
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CASP4 0.016 0.044 -10000 0 -0.16 26 26
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.24 23 23
negative regulation of DNA binding -0.13 0.29 -10000 0 -0.58 136 136
stress fiber formation -0.052 0.13 0.33 1 -0.32 70 71
GZMB -0.052 0.12 -10000 0 -0.28 98 98
CASP1 0.003 0.049 -10000 0 -0.29 13 13
LMNB1 0.019 0.13 0.24 5 -0.49 11 16
APP 0.016 0.065 -10000 0 -0.63 4 4
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.02 -10000 0 -0.099 15 15
VIM -0.049 0.15 0.32 1 -0.43 36 37
LMNA 0.027 0.11 0.24 8 -0.44 8 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.094 -10000 0 -0.35 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.059 0.13 -10000 0 -0.32 76 76
APAF-1/Caspase 9 -0.072 0.22 -10000 0 -0.62 70 70
nuclear fragmentation during apoptosis -0.026 0.11 -10000 0 -0.35 26 26
CFL2 -0.026 0.14 0.25 11 -0.31 62 73
GAS2 -0.054 0.13 0.19 1 -0.32 75 76
positive regulation of apoptosis 0.028 0.12 0.24 11 -0.44 11 22
PRF1 -0.014 0.12 -10000 0 -0.43 33 33
HIF-1-alpha transcription factor network

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
PKM2 -0.078 0.3 -10000 0 -0.79 46 46
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.041 0.34 -10000 0 -0.74 57 57
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.065 0.31 -10000 0 -0.81 44 44
AP1 -0.011 0.1 -10000 0 -0.28 56 56
ABCG2 -0.067 0.32 -10000 0 -0.81 45 45
HIF1A 0.005 0.071 -10000 0 -0.35 2 2
TFF3 -0.069 0.32 -10000 0 -0.79 47 47
GATA2 0.014 0.066 -10000 0 -0.33 15 15
AKT1 -0.005 0.086 -10000 0 -0.22 20 20
response to hypoxia -0.021 0.075 -10000 0 -0.18 43 43
MCL1 -0.065 0.31 -10000 0 -0.81 44 44
NDRG1 -0.076 0.31 -10000 0 -0.81 46 46
SERPINE1 -0.092 0.32 -10000 0 -0.78 57 57
FECH -0.066 0.31 -10000 0 -0.8 44 44
FURIN -0.064 0.31 -10000 0 -0.8 44 44
NCOA2 -0.004 0.11 -10000 0 -0.43 34 34
EP300 -0.015 0.13 -10000 0 -0.32 54 54
HMOX1 -0.069 0.32 -10000 0 -0.8 47 47
BHLHE40 -0.07 0.32 -10000 0 -0.81 46 46
BHLHE41 -0.07 0.32 -10000 0 -0.84 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.056 0.1 -10000 0 -0.31 1 1
ENG 0.013 0.078 0.26 4 -0.29 1 5
JUN 0.018 0.024 -10000 0 -0.13 9 9
RORA -0.065 0.31 -10000 0 -0.79 46 46
ABCB1 -0.021 0.12 -10000 0 -0.69 10 10
TFRC -0.065 0.31 -10000 0 -0.81 44 44
CXCR4 -0.07 0.32 -10000 0 -0.82 47 47
TF -0.083 0.34 -10000 0 -0.82 53 53
CITED2 -0.065 0.31 -10000 0 -0.81 44 44
HIF1A/ARNT -0.034 0.39 -10000 0 -0.92 44 44
LDHA -0.012 0.14 -10000 0 -0.92 8 8
ETS1 -0.07 0.31 -10000 0 -0.81 43 43
PGK1 -0.065 0.31 -10000 0 -0.8 44 44
NOS2 -0.074 0.32 -10000 0 -0.82 48 48
ITGB2 -0.072 0.33 -10000 0 -0.85 46 46
ALDOA -0.064 0.31 -10000 0 -0.8 45 45
Cbp/p300/CITED2 -0.087 0.37 -10000 0 -0.85 61 61
FOS -0.032 0.14 -10000 0 -0.29 93 93
HK2 -0.072 0.33 -10000 0 -0.83 47 47
SP1 0.031 0.007 -10000 0 -10000 0 0
GCK -0.1 0.42 -10000 0 -1.3 51 51
HK1 -0.064 0.31 -10000 0 -0.81 44 44
NPM1 -0.064 0.31 -10000 0 -0.81 43 43
EGLN1 -0.065 0.31 -10000 0 -0.81 44 44
CREB1 0.03 0.008 -10000 0 -10000 0 0
PGM1 -0.067 0.31 -10000 0 -0.79 45 45
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.075 0.27 -10000 0 -0.8 45 45
IGFBP1 -0.099 0.33 -10000 0 -0.78 61 61
VEGFA -0.053 0.28 -10000 0 -0.65 54 54
HIF1A/JAB1 0.02 0.057 -10000 0 -0.36 1 1
CP -0.11 0.35 -10000 0 -0.84 57 57
CXCL12 -0.067 0.31 -10000 0 -0.79 47 47
COPS5 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.009 -10000 0 -10000 0 0
BNIP3 -0.066 0.31 -10000 0 -0.8 45 45
EGLN3 -0.069 0.32 -10000 0 -0.82 47 47
CA9 -0.08 0.32 -10000 0 -0.81 49 49
TERT -0.089 0.33 -10000 0 -0.82 51 51
ENO1 -0.065 0.31 -10000 0 -0.79 45 45
PFKL -0.064 0.31 -10000 0 -0.8 45 45
NCOA1 0.026 0.003 -10000 0 -10000 0 0
ADM -0.075 0.32 -10000 0 -0.79 51 51
ARNT 0.005 0.068 -10000 0 -0.27 1 1
HNF4A -0.004 0.055 -10000 0 -0.13 51 51
ADFP -0.078 0.3 -10000 0 -0.79 46 46
SLC2A1 -0.056 0.27 -10000 0 -0.65 51 51
LEP -0.067 0.29 -10000 0 -0.79 42 42
HIF1A/ARNT/Cbp/p300 -0.051 0.34 -10000 0 -0.76 60 60
EPO -0.047 0.24 -10000 0 -0.78 19 19
CREBBP -0.013 0.12 -10000 0 -0.31 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.038 0.34 -10000 0 -0.75 55 55
PFKFB3 -0.07 0.31 -10000 0 -0.83 42 42
NT5E -0.067 0.32 -10000 0 -0.8 47 47
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.012 -9999 0 -10000 0 0
ITGB7 0.001 0.091 -9999 0 -0.26 44 44
ITGA4 -0.008 0.1 -9999 0 -0.26 61 61
alpha4/beta7 Integrin -0.005 0.1 -9999 0 -0.28 56 56
alpha4/beta1 Integrin 0.012 0.077 -9999 0 -0.29 26 26
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.029 0.025 -10000 0 -0.28 2 2
Necdin/E2F1 0.013 0.082 -10000 0 -0.31 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.015 0.11 -10000 0 -0.24 73 73
NGF (dimer)/p75(NTR)/BEX1 -0.018 0.13 -10000 0 -0.28 92 92
NT-4/5 (dimer)/p75(NTR) -0.005 0.089 -10000 0 -0.29 40 40
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.092 0.18 9 -0.24 71 80
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.43 14 14
MGDIs/NGR/p75(NTR)/LINGO1 -0.002 0.13 -10000 0 -0.3 78 78
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.01 0.098 -10000 0 -0.26 53 53
LINGO1 0.001 0.1 -10000 0 -0.43 28 28
Sortilin/TRAF6/NRIF 0.025 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.01 0.089 -10000 0 -0.43 14 14
NTRK1 0.016 0.055 -10000 0 -0.43 6 6
RTN4R -0.006 0.11 -10000 0 -0.43 31 31
neuron apoptosis -0.066 0.16 0.29 8 -0.46 36 44
IRAK1 0.026 0.003 -10000 0 -10000 0 0
SHC1 -0.038 0.1 0.19 1 -0.27 76 77
ARHGDIA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.001 0.12 -10000 0 -0.25 81 81
MAGEH1 0.018 0.06 -10000 0 -0.43 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.14 -10000 0 -0.27 101 101
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.23 23 23
proNGF (dimer) -0.025 0.13 -10000 0 -0.35 63 63
MAGED1 0.026 0.002 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.16 12 12
ZNF274 0.021 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.017 0.094 -10000 0 -0.24 69 69
NGF -0.025 0.13 -10000 0 -0.35 63 63
cell cycle arrest -0.037 0.089 0.24 11 -0.21 72 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.099 -10000 0 -0.25 71 71
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.012 0.081 -10000 0 -0.24 40 40
NCSTN 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.017 0.12 -10000 0 -0.27 76 76
PSENEN 0.022 0.01 -10000 0 -10000 0 0
mol:ceramide -0.032 0.097 0.18 7 -0.25 73 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.021 0.094 -10000 0 -0.21 86 86
p75(NTR)/beta APP 0.005 0.09 -10000 0 -0.3 35 35
BEX1 0.01 0.084 -10000 0 -0.43 18 18
mol:GDP -0.044 0.1 -10000 0 -0.27 76 76
NGF (dimer) -0.025 0.13 -10000 0 -0.25 119 119
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.12 -10000 0 -0.27 76 76
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.006 0.094 -10000 0 -0.23 68 68
MYD88 0.019 0.054 -10000 0 -0.36 9 9
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.007 0.12 -10000 0 -0.27 76 76
RHOB 0.025 0.012 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.028 0.044 -10000 0 -0.3 6 6
NT3 (dimer) 0.006 0.032 -10000 0 -0.13 17 17
TP53 -0.021 0.1 0.22 32 -0.28 22 54
PRDM4 -0.032 0.099 0.18 7 -0.25 74 81
BDNF (dimer) -0.017 0.12 -10000 0 -0.25 97 97
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SORT1 0.02 0.022 -10000 0 -0.43 1 1
activation of caspase activity 0.011 0.11 -10000 0 -0.24 73 73
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.005 0.11 -10000 0 -0.25 77 77
RHOC 0.02 0.023 -10000 0 -0.28 2 2
XIAP 0.026 0.001 -10000 0 -10000 0 0
MAPK10 -0.017 0.13 0.3 25 -0.32 42 67
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.032 0.098 0.18 7 -0.25 73 80
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.007 0.12 -10000 0 -0.27 77 77
PSEN1 0.025 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.032 0.016 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.002 0.091 -10000 0 -0.3 38 38
MAPK8 -0.026 0.13 0.31 14 -0.32 43 57
MAPK9 -0.015 0.13 0.3 26 -0.32 39 65
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.032 -10000 0 -0.13 17 17
NTF4 -0.003 0.033 -10000 0 -0.16 12 12
NDN -0.003 0.11 -10000 0 -0.43 33 33
RAC1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.011 0.1 -10000 0 -0.22 74 74
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.045 -10000 0 -0.24 6 6
RhoA-B-C/GTP -0.017 0.12 -10000 0 -0.27 76 76
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.095 -10000 0 -0.24 46 46
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.097 -10000 0 -0.25 47 47
PRKACB 0.021 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.007 0.077 -10000 0 -0.32 18 18
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.1 0.14 7 -0.27 77 84
BAD -0.018 0.14 0.29 28 -0.32 41 69
RIPK2 0.024 0.007 -10000 0 -10000 0 0
NGFR -0.017 0.12 -10000 0 -0.28 72 72
CYCS -0.026 0.09 0.22 8 -0.24 64 72
ADAM17 0.022 0.045 -10000 0 -0.43 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.005 0.11 -10000 0 -0.25 69 69
BCL2L11 -0.021 0.13 0.28 25 -0.32 41 66
BDNF (dimer)/p75(NTR) -0.02 0.11 -10000 0 -0.3 53 53
PI3K 0.007 0.11 -10000 0 -0.25 74 74
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.006 0.11 -10000 0 -0.25 77 77
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.034 0.13 -10000 0 -0.23 126 126
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.006 0.11 -10000 0 -0.25 76 76
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
PLG -0.01 0.019 -10000 0 -0.13 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.044 0.11 0.19 4 -0.28 81 85
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.002 -10000 0 -10000 0 0
CASP3 -0.018 0.13 0.28 26 -0.31 41 67
E2F1 0.014 0.056 -10000 0 -0.43 6 6
CASP9 0.022 0.012 -10000 0 -10000 0 0
IKK complex -0.021 0.13 -10000 0 -0.31 45 45
NGF (dimer)/TRKA -0.012 0.1 -10000 0 -0.3 53 53
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.11 -10000 0 -0.24 71 71
MMP3 -0.005 0.047 -10000 0 -0.14 42 42
APAF-1/Caspase 9 -0.029 0.082 -10000 0 -0.28 19 19
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.43 42 42
EGF/EGFR -0.008 0.11 -10000 0 -0.24 88 88
EGF/EGFR dimer/SHC/GRB2/SOS1 0.022 0.1 -10000 0 -0.24 64 64
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.006 0.083 -10000 0 -0.28 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.01 0.11 -10000 0 -0.31 54 54
EGF/EGFR dimer/SHC 0 0.11 -10000 0 -0.27 67 67
mol:GDP 0.016 0.1 -10000 0 -0.23 64 64
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.002 0.086 -10000 0 -0.23 47 47
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.087 -10000 0 -0.22 63 63
SHC1 0.024 0.014 -10000 0 -0.13 4 4
HRAS/GDP 0.015 0.096 -10000 0 -0.22 63 63
FRAP1 -0.034 0.075 0.11 7 -0.22 64 71
EGF/EGFR dimer -0.02 0.12 -10000 0 -0.32 69 69
SOS1 0.026 0.002 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.005 0.088 -10000 0 -0.3 34 34
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.031 -10000 0 -0.3 2 2
Metarhodopsin II/Arrestin 0.013 0.05 -10000 0 -0.26 12 12
PDE6G/GNAT1/GTP 0.009 0.07 -10000 0 -0.26 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.047 -10000 0 -0.43 2 2
GRK1 0.021 0.015 -10000 0 -0.13 1 1
CNG Channel -0.047 0.14 -10000 0 -0.25 139 139
mol:Na + -0.068 0.13 -10000 0 -0.24 157 157
mol:ADP 0.021 0.015 -10000 0 -0.13 1 1
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.26 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.058 0.14 -10000 0 -0.25 157 157
CNGB1 -0.072 0.14 -10000 0 -0.43 61 61
RDH5 0.016 0.038 -10000 0 -0.13 31 31
SAG -0.009 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.11 0.31 3 -0.31 44 47
Na + (4 Units) -0.079 0.12 -10000 0 -0.24 147 147
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
GNB1/GNGT1 0.02 0.016 -10000 0 -10000 0 0
GNAT1/GDP 0.026 0.081 -10000 0 -0.23 40 40
GUCY2D 0.007 0.032 -10000 0 -10000 0 0
GNGT1 -0.012 0.011 -10000 0 -0.13 2 2
GUCY2F 0.011 0.024 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.087 0.15 2 -0.24 59 61
mol:11-cis-retinal 0.016 0.038 -10000 0 -0.13 31 31
mol:cGMP -0.006 0.11 -10000 0 -0.24 80 80
GNB1 0.022 0.01 -10000 0 -10000 0 0
Rhodopsin 0.013 0.063 -10000 0 -0.29 12 12
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.018 0.12 -10000 0 -0.43 40 40
Metarhodopsin II 0.018 0.045 -10000 0 -0.23 12 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.003 0.12 -10000 0 -0.25 82 82
RGS9BP 0.017 0.05 -10000 0 -0.39 7 7
Metarhodopsin II/Transducin -0.001 0.043 -10000 0 -0.25 11 11
GCAP Family/Ca ++ -0.007 0.11 -10000 0 -0.23 93 93
PDE6A/B 0.001 0.095 -10000 0 -0.3 38 38
mol:Pi 0.017 0.088 -10000 0 -0.26 41 41
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.023 0.03 -10000 0 -0.18 2 2
PDE6B 0.002 0.092 -10000 0 -0.28 40 40
PDE6A 0 0.088 -10000 0 -0.43 17 17
PDE6G -0.001 0.1 -10000 0 -0.32 39 39
RHO -0.003 0.077 -10000 0 -0.21 46 46
PDE6 0.009 0.12 -10000 0 -0.24 88 88
GUCA1A -0.061 0.15 -10000 0 -0.28 137 137
GC2/GCAP Family 0.006 0.12 -10000 0 -0.25 82 82
GUCA1C -0.007 0.029 -10000 0 -0.13 16 16
GUCA1B 0.012 0.079 -10000 0 -0.41 17 17
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.01 0.13 -10000 0 -0.34 51 51
alphaM/beta2 Integrin/GPIbA -0.011 0.12 -10000 0 -0.33 54 54
alphaM/beta2 Integrin/proMMP-9 -0.035 0.14 -10000 0 -0.32 85 85
PLAUR 0.011 0.042 -10000 0 -0.43 1 1
HMGB1 0.009 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.003 0.12 -10000 0 -0.35 40 40
AGER -0.008 0.091 -10000 0 -0.4 22 22
RAP1A 0.021 0.01 -10000 0 -10000 0 0
SELPLG -0.001 0.1 -10000 0 -0.4 32 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.16 -10000 0 -0.28 129 129
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
CYR61 -0.015 0.1 -10000 0 -0.43 26 26
TLN1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.024 0.12 -10000 0 -0.36 31 31
RHOA 0.026 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.003 0.042 -10000 0 -0.13 37 37
MYH2 -0.039 0.11 -10000 0 -0.38 26 26
MST1R 0.02 0.049 -10000 0 -0.39 7 7
leukocyte activation during inflammatory response -0.021 0.13 -10000 0 -0.3 71 71
APOB -0.025 0.13 -10000 0 -0.29 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.013 0.067 -10000 0 -0.43 10 10
JAM3 0.024 0.007 -10000 0 -10000 0 0
GP1BA 0.014 0.072 -10000 0 -0.43 13 13
alphaM/beta2 Integrin/CTGF -0.016 0.13 -10000 0 -0.33 58 58
alphaM/beta2 Integrin -0.045 0.13 -10000 0 -0.42 32 32
JAM3 homodimer 0.024 0.007 -10000 0 -10000 0 0
ICAM2 0.025 0.005 -10000 0 -10000 0 0
ICAM1 0.011 0.062 -10000 0 -0.2 32 32
phagocytosis triggered by activation of immune response cell surface activating receptor -0.044 0.13 -10000 0 -0.42 32 32
cell adhesion -0.011 0.12 -10000 0 -0.33 54 54
NFKB1 -0.1 0.19 -10000 0 -0.42 109 109
THY1 0.015 0.061 -10000 0 -0.32 14 14
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.005 0.083 -10000 0 -0.25 44 44
alphaM/beta2 Integrin/LRP/tPA 0.007 0.12 -10000 0 -0.34 40 40
IL6 -0.12 0.23 -10000 0 -0.52 93 93
ITGB2 -0.014 0.097 -10000 0 -0.33 33 33
elevation of cytosolic calcium ion concentration -0.008 0.12 -10000 0 -0.31 55 55
alphaM/beta2 Integrin/JAM2/JAM3 0.012 0.11 -10000 0 -0.33 38 38
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.002 0.13 -10000 0 -0.28 73 73
alphaM/beta2 Integrin/uPA/Plg -0.012 0.12 -10000 0 -0.32 53 53
RhoA/GTP -0.037 0.12 -10000 0 -0.38 30 30
positive regulation of phagocytosis -0.04 0.14 -10000 0 -0.39 52 52
Ron/MSP 0.015 0.083 -10000 0 -0.3 31 31
alphaM/beta2 Integrin/uPAR/uPA -0.006 0.12 -10000 0 -0.31 55 55
alphaM/beta2 Integrin/uPAR -0.011 0.12 -10000 0 -0.34 44 44
PLAU -0.001 0.081 -10000 0 -0.43 12 12
PLAT 0.005 0.058 -10000 0 -0.14 62 62
actin filament polymerization -0.036 0.11 0.19 2 -0.39 23 25
MST1 0.001 0.099 -10000 0 -0.36 32 32
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.14 -10000 0 -0.3 71 71
TNF -0.15 0.27 -10000 0 -0.63 101 101
RAP1B 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.02 0.13 -10000 0 -0.33 56 56
fibrinolysis -0.013 0.12 -10000 0 -0.32 53 53
HCK 0.014 0.063 -10000 0 -0.43 9 9
dendritic cell antigen processing and presentation -0.044 0.13 -10000 0 -0.42 32 32
VTN 0.012 0.075 -10000 0 -0.35 19 19
alphaM/beta2 Integrin/CYR61 -0.03 0.13 -10000 0 -0.33 66 66
LPA 0.005 0.039 -10000 0 -10000 0 0
LRP1 0.026 0.004 -10000 0 -10000 0 0
cell migration -0.05 0.13 -10000 0 -0.3 91 91
FN1 0.02 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.007 0.12 -10000 0 -0.33 51 51
MPO -0.05 0.15 -10000 0 -0.29 121 121
KNG1 -0.009 0.032 -10000 0 -10000 0 0
RAP1/GDP 0.028 0.015 -10000 0 -10000 0 0
ROCK1 -0.034 0.12 -10000 0 -0.41 22 22
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.01 0.019 -10000 0 -0.13 4 4
CTGF 0.004 0.086 -10000 0 -0.26 38 38
alphaM/beta2 Integrin/Hck -0.009 0.14 -10000 0 -0.37 47 47
ITGAM -0.02 0.12 -10000 0 -0.44 33 33
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.005 0.15 -10000 0 -0.4 50 50
HP -0.034 0.13 -10000 0 -0.43 43 43
leukocyte adhesion -0.031 0.14 -10000 0 -0.35 57 57
SELP 0.003 0.042 -10000 0 -0.13 37 37
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.004 0.097 -10000 0 -0.22 75 75
regulation of S phase of mitotic cell cycle -0.01 0.083 -10000 0 -0.22 69 69
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.012 0.036 -10000 0 -0.25 9 9
PELP1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.035 0.096 0.17 31 -0.22 68 99
T-DHT/AR -0.033 0.11 -10000 0 -0.29 75 75
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 55 55
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
mol:GDP -0.05 0.13 -10000 0 -0.38 71 71
cell proliferation -0.043 0.16 0.29 7 -0.42 53 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FOS -0.075 0.26 0.27 1 -0.78 56 57
mol:Ca2+ -0.007 0.019 -10000 0 -0.054 50 50
MAPK3 -0.036 0.13 0.26 9 -0.31 54 63
MAPK1 -0.015 0.089 0.22 1 -0.3 17 18
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 55 55
cAMP biosynthetic process -0.001 0.036 0.23 1 -0.24 9 10
GNG2 0.022 0.04 -10000 0 -0.43 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 55 55
HRAS/GTP 0 0.095 -10000 0 -0.22 70 70
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 55 55
PI3K 0.034 0.007 -10000 0 -10000 0 0
apoptosis 0.033 0.15 0.42 55 -0.24 6 61
T-DHT/AR/PELP1 -0.014 0.1 -10000 0 -0.26 71 71
HRAS/GDP -0.036 0.13 -10000 0 -0.36 71 71
CREB1 -0.037 0.16 0.25 6 -0.45 55 61
RAC1-CDC42/GTP 0.036 0.024 -10000 0 -10000 0 0
AR -0.048 0.16 -10000 0 -0.41 75 75
GNB1 0.022 0.01 -10000 0 -10000 0 0
RAF1 -0.02 0.098 0.18 28 -0.22 70 98
RAC1-CDC42/GDP -0.021 0.13 -10000 0 -0.34 67 67
T-DHT/AR/PELP1/Src 0.006 0.099 -10000 0 -0.24 71 71
MAP2K2 -0.036 0.092 0.18 26 -0.22 67 93
T-DHT/AR/PELP1/Src/PI3K -0.011 0.084 -10000 0 -0.22 69 69
GNAZ 0.026 0.004 -10000 0 -10000 0 0
SHBG 0.017 0.06 -10000 0 -0.43 9 9
Gi family/GNB1/GNG2/GDP -0.03 0.12 -10000 0 -0.35 38 38
mol:T-DHT 0 0.001 -10000 0 -0.002 35 35
RAC1 0.023 0.009 -10000 0 -10000 0 0
GNRH1 0.002 0.035 -10000 0 -0.19 12 12
Gi family/GTP -0.021 0.068 -10000 0 -0.2 37 37
CDC42 0.022 0.01 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.013 0.089 -10000 0 -0.22 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.11 0.24 15 -0.31 33 48
AP1 -0.03 0.1 -10000 0 -0.22 98 98
mol:PIP3 -0.036 0.088 -10000 0 -0.22 82 82
AKT1 0 0.1 0.27 17 -0.34 5 22
PTK2B -0.005 0.09 0.17 12 -0.22 51 63
RHOA 0.004 0.079 0.22 16 -0.36 7 23
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.071 0.21 20 -0.28 10 30
MAGI3 0.02 0.022 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.021 0.087 -10000 0 -0.27 52 52
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.088 0.21 9 -0.27 18 27
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.29 50 50
endothelial cell migration -0.022 0.11 -10000 0 -0.3 57 57
ADCY4 -0.015 0.12 -10000 0 -0.35 52 52
ADCY5 -0.015 0.12 -10000 0 -0.34 52 52
ADCY6 -0.013 0.12 -10000 0 -0.34 52 52
ADCY7 -0.014 0.12 -10000 0 -0.34 52 52
ADCY1 -0.032 0.12 -10000 0 -0.36 50 50
ADCY2 -0.018 0.12 -10000 0 -0.35 54 54
ADCY3 -0.013 0.12 -10000 0 -0.34 52 52
ADCY8 -0.035 0.14 -10000 0 -0.39 59 59
ADCY9 -0.014 0.12 -10000 0 -0.34 52 52
GSK3B -0.006 0.087 0.18 7 -0.27 20 27
arachidonic acid secretion -0.02 0.12 -10000 0 -0.32 60 60
GNG2 0.022 0.04 -10000 0 -0.43 4 4
TRIP6 0.012 0.031 -10000 0 -0.34 2 2
GNAO1 -0.018 0.089 -10000 0 -0.25 61 61
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA -0.019 0.12 0.24 17 -0.34 35 52
GAB1 0.025 0.02 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.11 -10000 0 -0.84 7 7
JUN 0.019 0.023 -10000 0 -0.13 9 9
LPA/LPA2/NHERF2 0.028 0.039 -10000 0 -0.25 7 7
TIAM1 0.017 0.13 -10000 0 -1 7 7
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 -0.008 0.066 0.2 13 -0.29 10 23
PLCB3 0.017 0.048 0.18 24 -0.23 7 31
FOS -0.031 0.14 -10000 0 -0.42 49 49
positive regulation of mitosis -0.02 0.12 -10000 0 -0.32 60 60
LPA/LPA1-2-3 0.007 0.094 -10000 0 -0.23 63 63
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
stress fiber formation 0.002 0.097 0.2 10 -0.27 21 31
GNAZ -0.014 0.084 -10000 0 -0.25 54 54
EGFR/PI3K-beta/Gab1 -0.03 0.095 -10000 0 -0.23 82 82
positive regulation of dendritic cell cytokine production 0.006 0.093 -10000 0 -0.23 63 63
LPA/LPA2/MAGI-3 0.021 0.042 -10000 0 -0.25 8 8
ARHGEF1 0.015 0.097 0.2 60 -0.2 47 107
GNAI2 -0.015 0.085 -10000 0 -0.25 55 55
GNAI3 -0.003 0.062 -10000 0 -0.26 26 26
GNAI1 -0.015 0.083 -10000 0 -0.25 53 53
LPA/LPA3 0.002 0.036 -10000 0 -0.14 13 13
LPA/LPA2 0.013 0.042 -10000 0 -0.19 16 16
LPA/LPA1 -0.017 0.1 -10000 0 -0.3 57 57
HB-EGF/EGFR -0.035 0.11 -10000 0 -0.27 78 78
HBEGF -0.033 0.09 -10000 0 -0.29 48 48
mol:DAG -0.008 0.066 0.2 13 -0.29 10 23
cAMP biosynthetic process -0.016 0.14 0.3 10 -0.34 59 69
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
LYN -0.015 0.12 0.24 22 -0.35 33 55
GNAQ 0.002 0.037 -10000 0 -0.18 14 14
LPAR2 0.018 0.054 -10000 0 -0.34 10 10
LPAR3 -0.009 0.044 -10000 0 -0.13 48 48
LPAR1 -0.025 0.14 -10000 0 -0.39 57 57
IL8 -0.1 0.21 0.35 9 -0.45 108 117
PTK2 -0.014 0.09 0.19 24 -0.22 60 84
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.021 0.087 -10000 0 -0.27 52 52
EGFR -0.017 0.12 -10000 0 -0.43 42 42
PLCG1 -0.013 0.059 0.15 6 -0.22 23 29
PLD2 -0.013 0.094 0.19 29 -0.22 63 92
G12/G13 0.018 0.084 -10000 0 -0.23 48 48
PI3K-beta -0.022 0.085 -10000 0 -0.27 28 28
cell migration 0.009 0.052 0.24 1 -0.25 4 5
SLC9A3R2 0.025 0.01 -10000 0 -10000 0 0
PXN 0.002 0.098 0.2 10 -0.28 21 31
HRAS/GTP -0.02 0.12 -10000 0 -0.33 60 60
RAC1 0.023 0.009 -10000 0 -10000 0 0
MMP9 -0.042 0.13 -10000 0 -0.23 133 133
PRKCE 0.022 0.034 -10000 0 -0.28 4 4
PRKCD -0.008 0.097 0.23 24 -0.29 27 51
Gi(beta/gamma) -0.019 0.13 -10000 0 -0.35 59 59
mol:LPA -0.001 0.022 -10000 0 -0.16 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.094 0.33 1 -0.35 9 10
MAPKKK cascade -0.02 0.12 -10000 0 -0.32 60 60
contractile ring contraction involved in cytokinesis 0.001 0.087 0.22 21 -0.37 8 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.007 0.06 0.12 1 -0.26 23 24
GNA15 -0.005 0.057 -10000 0 -0.27 19 19
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.008 0.09 0.21 8 -0.27 19 27
GNA11 -0.002 0.049 -10000 0 -0.25 15 15
Rac1/GTP 0.03 0.11 -10000 0 -0.9 7 7
MMP2 -0.023 0.11 -10000 0 -0.3 57 57
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.022 0.1 -10000 0 -0.3 52 52
CRKL 0.011 0.14 0.25 21 -0.45 21 42
mol:PIP3 0.001 0.039 -10000 0 -0.84 1 1
AKT1 -0.003 0.043 0.28 1 -0.73 1 2
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
RAPGEF1 0.014 0.14 0.29 15 -0.44 20 35
RANBP10 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
HGF/MET/SHIP2 -0.004 0.11 -10000 0 -0.28 58 58
MAP3K5 -0.008 0.16 0.25 20 -0.45 32 52
HGF/MET/CIN85/CBL/ENDOPHILINS 0.007 0.11 -10000 0 -0.26 55 55
AP1 -0.01 0.1 0.15 7 -0.24 56 63
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
apoptosis -0.17 0.38 -10000 0 -0.8 130 130
STAT3 (dimer) -0.006 0.09 0.22 4 -0.23 51 55
GAB1/CRKL/SHP2/PI3K 0.038 0.14 0.29 5 -0.42 20 25
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
CBL/CRK 0.02 0.14 0.27 15 -0.43 21 36
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
ELK1 0.038 0.16 0.31 119 -0.27 2 121
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.066 -10000 0 -0.3 12 12
PAK1 -0.004 0.059 -10000 0 -0.7 1 1
HGF/MET/RANBP10 -0.004 0.11 -10000 0 -0.28 60 60
HRAS -0.047 0.2 -10000 0 -0.6 53 53
DOCK1 0.008 0.14 0.26 19 -0.43 21 40
GAB1 0 0.14 0.23 10 -0.49 19 29
CRK 0.01 0.14 0.25 27 -0.45 21 48
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.045 0.19 -10000 0 -0.53 63 63
JUN 0.019 0.023 -10000 0 -0.13 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.082 -10000 0 -0.24 60 60
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.019 0.14 0.31 30 -0.45 11 41
GRB2/SHC 0.005 0.088 0.19 8 -0.22 57 65
FOS -0.031 0.14 -10000 0 -0.43 48 48
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.037 0.16 0.31 119 -0.27 2 121
HGF/MET/MUC20 -0.032 0.1 -10000 0 -0.24 83 83
cell migration 0.005 0.087 0.19 8 -0.21 57 65
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.022 0.1 -10000 0 -0.3 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.084 -10000 0 -0.24 53 53
MET/MUC20 -0.031 0.097 -10000 0 -0.3 52 52
RAP1B 0.015 0.14 0.29 17 -0.41 20 37
RAP1A 0.013 0.13 0.29 16 -0.4 20 36
HGF/MET/RANBP9 -0.004 0.11 -10000 0 -0.24 83 83
RAF1 -0.024 0.2 0.35 2 -0.56 53 55
STAT3 -0.006 0.09 0.22 4 -0.24 51 55
cell proliferation 0.001 0.15 0.29 15 -0.36 54 69
RPS6KB1 -0.005 0.043 -10000 0 -0.23 5 5
MAPK3 0.025 0.15 0.48 9 -10000 0 9
MAPK1 0.031 0.16 0.61 11 -10000 0 11
RANBP9 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.01 0.15 0.3 6 -0.41 36 42
SRC -0.018 0.078 0.16 1 -0.23 53 54
PI3K 0.005 0.09 0.19 9 -0.22 58 67
MET/Glomulin -0.038 0.092 -10000 0 -0.28 52 52
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 -0.022 0.19 0.33 4 -0.52 53 57
MET -0.047 0.14 -10000 0 -0.43 52 52
MAP4K1 -0.006 0.17 0.26 22 -0.47 31 53
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.015 0.2 0.33 17 -0.52 53 70
BAD 0 0.051 0.25 1 -0.7 1 2
MAP2K4 -0.006 0.15 0.27 16 -0.41 32 48
SHP2/GRB2/SOS1/GAB1 -0.006 0.13 -10000 0 -0.35 55 55
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.025 0.074 0.17 2 -0.22 57 59
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.009 0.091 -10000 0 -0.2 69 69
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.005 0.094 0.19 10 -0.22 62 72
PDPK1 -0.002 0.045 0.32 1 -0.78 1 2
HGF/MET/SHIP -0.007 0.11 -10000 0 -0.28 64 64
Osteopontin-mediated events

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
IKK alpha homodimer -0.006 0.085 -10000 0 -0.21 52 52
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.092 0.3 5 -0.52 1 6
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.095 -10000 0 -0.3 39 39
AP1 -0.023 0.12 -10000 0 -0.36 24 24
ILK -0.015 0.08 -10000 0 -0.22 47 47
bone resorption -0.032 0.13 0.32 2 -0.34 44 46
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
PYK2/p130Cas 0.02 0.11 -10000 0 -0.25 55 55
ITGAV 0.027 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.005 0.11 -10000 0 -0.31 53 53
alphaV/beta3 Integrin/Osteopontin 0.018 0.1 -10000 0 -0.24 53 53
MAP3K1 -0.018 0.083 0.19 6 -0.22 51 57
JUN 0.019 0.023 -10000 0 -0.13 9 9
MAPK3 -0.026 0.081 0.19 4 -0.21 62 66
MAPK1 -0.026 0.079 0.19 3 -0.21 61 64
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.029 0.084 0.19 4 -0.23 56 60
ITGB3 0 0.082 -10000 0 -0.42 12 12
NFKBIA -0.025 0.08 0.19 2 -0.27 15 17
FOS -0.031 0.14 -10000 0 -0.28 93 93
CD44 -0.015 0.12 -10000 0 -0.31 62 62
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU -0.044 0.18 -10000 0 -1.1 12 12
NF kappa B1 p50/RelA 0.004 0.098 -10000 0 -0.34 11 11
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.02 0.064 -10000 0 -0.3 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.025 0.1 0.19 7 -0.27 55 62
VAV3 -0.05 0.098 0.19 4 -0.24 76 80
MAP3K14 -0.019 0.084 0.19 4 -0.22 52 56
ROCK2 0.008 0.088 -10000 0 -0.43 20 20
SPP1 -0.023 0.12 -10000 0 -0.26 87 87
RAC1 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.092 0.18 3 -0.23 60 63
MMP2 -0.046 0.11 -10000 0 -0.4 24 24
Ceramide signaling pathway

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
SPHK2 0.005 0.023 -10000 0 -0.3 1 1
MAP4K4 -0.01 0.094 -10000 0 -0.37 16 16
BAG4 0.014 0.071 -10000 0 -0.43 13 13
PKC zeta/ceramide -0.032 0.13 0.14 1 -0.29 74 75
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX -0.063 0.14 -10000 0 -0.35 93 93
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.003 0.046 0.68 2 -10000 0 2
BAD -0.036 0.12 0.18 14 -0.27 70 84
SMPD1 -0.009 0.076 0.16 7 -0.17 66 73
RB1 -0.041 0.12 0.15 2 -0.27 71 73
FADD/Caspase 8 -0.003 0.091 -10000 0 -0.38 13 13
MAP2K4 -0.04 0.11 0.24 1 -0.26 68 69
NSMAF 0.025 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.038 0.11 0.18 6 -0.26 65 71
EGF -0.01 0.11 -10000 0 -0.31 54 54
mol:ceramide -0.042 0.12 0.14 1 -0.28 73 74
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.007 0.024 -10000 0 -0.3 1 1
ASAH1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.12 0.15 2 -0.26 71 73
cell proliferation -0.02 0.11 0.18 3 -0.28 54 57
BID -0.006 0.11 -10000 0 -0.69 6 6
MAP3K1 -0.041 0.12 0.19 2 -0.27 70 72
EIF2A -0.04 0.11 0.34 1 -0.48 18 19
TRADD 0.025 0.02 -10000 0 -0.43 1 1
CRADD 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.029 0.093 0.17 7 -0.27 41 48
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.03 0.093 0.17 7 -0.28 38 45
Cathepsin D/ceramide -0.028 0.12 0.14 1 -0.27 71 72
FADD -0.01 0.091 -10000 0 -0.36 15 15
KSR1 -0.041 0.12 -10000 0 -0.27 70 70
MAPK8 -0.068 0.16 -10000 0 -0.36 66 66
PRKRA -0.041 0.12 -10000 0 -0.27 71 71
PDGFA 0.016 0.036 -10000 0 -0.43 1 1
TRAF2 0.026 0.005 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.042 0.12 0.14 1 -0.28 73 74
CTSD 0.025 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.037 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.021 0.12 0.19 5 -0.3 54 59
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.024 -10000 0 -0.3 1 1
RelA/NF kappa B1 0.037 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.003 0.087 -10000 0 -0.25 44 44
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.096 -10000 0 -0.34 21 21
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
mol:Sphingosine-1-phosphate 0.005 0.023 -10000 0 -0.3 1 1
MAP2K1 -0.037 0.11 0.18 6 -0.27 55 61
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
CYCS -0.033 0.084 -10000 0 -0.21 82 82
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
EIF2AK2 -0.041 0.11 0.17 2 -0.27 65 67
TNF-alpha/TNFR1A/FAN 0.008 0.11 -10000 0 -0.27 66 66
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.079 -10000 0 -0.51 6 6
MAP2K2 -0.032 0.088 0.17 8 -0.24 56 64
SMPD3 -0.02 0.1 0.19 1 -0.29 40 41
TNF -0.06 0.16 -10000 0 -0.26 151 151
PKC zeta/PAR4 0.004 0.085 -10000 0 -0.31 31 31
mol:PHOSPHOCHOLINE -0.009 0.089 0.2 32 -0.19 50 82
NF kappa B1/RelA/I kappa B alpha 0.045 0.073 -10000 0 -0.22 29 29
AIFM1 -0.044 0.095 -10000 0 -0.22 82 82
BCL2 0.021 0.045 -10000 0 -0.43 5 5
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.028 0.14 -10000 0 -0.41 55 55
PDGF/PDGFRA/CRKL -0.003 0.099 -10000 0 -0.3 50 50
positive regulation of JUN kinase activity 0.03 0.084 -10000 0 -0.23 46 46
CRKL 0.025 0.008 -10000 0 -0.13 1 1
PDGF/PDGFRA/Caveolin-3 -0.009 0.1 -10000 0 -0.3 51 51
AP1 -0.094 0.25 -10000 0 -0.79 54 54
mol:IP3 -0.024 0.091 -10000 0 -0.31 44 44
PLCG1 -0.024 0.092 -10000 0 -0.31 44 44
PDGF/PDGFRA/alphaV Integrin -0.003 0.1 -10000 0 -0.29 52 52
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.091 -10000 0 -0.31 44 44
CAV3 0.002 0.031 -10000 0 -10000 0 0
CAV1 0.006 0.051 -10000 0 -0.15 44 44
SHC/Grb2/SOS1 0.032 0.085 -10000 0 -0.23 46 46
PDGF/PDGFRA/Shf -0.005 0.11 -10000 0 -0.31 52 52
FOS -0.1 0.25 0.31 2 -0.78 54 56
JUN -0.02 0.025 0.16 1 -10000 0 1
oligodendrocyte development -0.003 0.1 -10000 0 -0.29 52 52
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:DAG -0.024 0.091 -10000 0 -0.31 44 44
PDGF/PDGFRA -0.028 0.14 -10000 0 -0.41 55 55
actin cytoskeleton reorganization -0.003 0.099 -10000 0 -0.3 50 50
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
PI3K 0.019 0.088 -10000 0 -0.25 48 48
PDGF/PDGFRA/Crk/C3G 0.017 0.09 -10000 0 -0.25 51 51
JAK1 -0.021 0.088 -10000 0 -0.3 46 46
ELK1/SRF -0.011 0.081 0.16 26 -0.25 41 67
SHB 0.026 0.004 -10000 0 -10000 0 0
SHF 0.022 0.04 -10000 0 -0.43 4 4
CSNK2A1 0.029 0.018 -10000 0 -10000 0 0
GO:0007205 -0.028 0.1 0.23 6 -0.34 43 49
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.03 0.084 -10000 0 -0.23 46 46
PDGF/PDGFRA/SHB -0.003 0.099 -10000 0 -0.3 50 50
PDGF/PDGFRA/Caveolin-1 -0.005 0.085 -10000 0 -0.31 31 31
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.034 0.087 0.2 5 -0.3 43 48
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PDGF/PDGFRA/Crk -0.003 0.1 -10000 0 -0.3 51 51
JAK-STAT cascade -0.021 0.088 -10000 0 -0.3 46 46
cell proliferation -0.005 0.11 -10000 0 -0.31 52 52
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.077 -10000 0 -0.22 50 50
RGS9BP 0.017 0.05 -10000 0 -0.39 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.021 0.015 -10000 0 -0.13 1 1
mol:Na + -0.019 0.088 -10000 0 -0.25 51 51
mol:ADP 0.005 0.016 -10000 0 -10000 0 0
GNAT2 0.015 0.018 -10000 0 -0.13 2 2
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.26 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.02 0.025 -10000 0 -0.13 1 1
GRK7 0.017 0.023 -10000 0 -0.13 6 6
CNGB3 0.004 0.032 -10000 0 -0.13 16 16
Cone Metarhodopsin II/X-Arrestin 0.013 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 0.18 20 -0.26 94 114
Cone PDE6 0.034 0.085 -10000 0 -0.23 40 40
Cone Metarhodopsin II 0.029 0.013 -10000 0 -10000 0 0
Na + (4 Units) -0.025 0.12 -10000 0 -0.24 109 109
GNAT2/GDP 0.024 0.078 -10000 0 -0.22 40 40
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.004 0.03 0.18 8 -10000 0 8
Cone Transducin 0.009 0.082 -10000 0 -0.23 50 50
SLC24A2 -0.042 0.15 -10000 0 -0.3 103 103
GNB3/GNGT2 -0.001 0.1 -10000 0 -0.31 51 51
GNB3 -0.007 0.12 -10000 0 -0.43 35 35
GNAT2/GTP 0.014 0.01 -10000 0 -0.084 2 2
CNGA3 -0.049 0.14 -10000 0 -0.24 143 143
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.089 -10000 0 -0.26 51 51
mol:Pi 0.017 0.088 -10000 0 -0.26 41 41
Cone CNG Channel 0.009 0.082 -10000 0 -0.21 47 47
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.042 0.15 -10000 0 -0.3 103 103
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
PDE6C 0.004 0.025 -10000 0 -0.13 5 5
GNGT2 0.008 0.082 -10000 0 -0.43 16 16
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.005 0.036 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.022 0.01 -10000 0 -10000 0 0
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
KATNA1 0.025 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.007 0.11 0.18 82 -0.23 53 135
IQGAP1/CaM 0.033 0.033 -10000 0 -0.28 4 4
DAB1 -0.039 0.15 -10000 0 -0.36 80 80
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
PLA2G7 -0.004 0.11 -10000 0 -0.31 46 46
CALM1 0.025 0.009 -10000 0 -10000 0 0
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0 0.1 -10000 0 -0.43 29 29
LIS1/Poliovirus Protein 3A 0.01 0.002 -10000 0 -10000 0 0
CDK5R2 -0.05 0.16 -10000 0 -0.36 102 102
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.035 0.13 -10000 0 -0.27 109 109
YWHAE 0.026 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.014 0.18 0.31 86 -0.41 32 118
MAP1B 0.005 0.012 -10000 0 -0.26 1 1
RAC1 0.011 0.016 -10000 0 -0.15 4 4
p35/CDK5 -0.021 0.092 0.18 8 -0.23 66 74
RELN -0.046 0.14 -10000 0 -0.29 107 107
PAFAH/LIS1 0.011 0.064 0.17 1 -0.26 25 26
LIS1/CLIP170 0.028 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.03 0.11 -10000 0 -0.36 28 28
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.072 0.16 -10000 0 -0.3 135 135
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.037 0.14 0.28 20 -0.43 32 52
LIS1/IQGAP1 0.025 0.029 0.17 2 -0.26 4 6
RHOA 0.012 0.016 -10000 0 -0.15 4 4
PAFAH1B1 0.013 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.01 -10000 0 -10000 0 0
PAFAH1B2 0.012 0.074 -10000 0 -0.43 14 14
MAP1B/LIS1/Dynein heavy chain 0.025 0.019 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.019 0.18 0.32 78 -0.4 31 109
LRP8 0.02 0.03 -10000 0 -0.43 2 2
NDEL1/Katanin 60 0.013 0.18 0.31 85 -0.41 32 117
P39/CDK5 -0.037 0.11 0.21 11 -0.24 91 102
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.029 0.072 0.18 10 -0.22 52 62
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.007 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.024 0.12 -10000 0 -0.24 100 100
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 67 67
CDC42 0.008 0.042 -10000 0 -0.46 4 4
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.008 -10000 0 -10000 0 0
LAT2 -0.023 0.12 0.17 5 -0.43 25 30
AP1 -0.015 0.17 0.25 1 -0.51 33 34
mol:PIP3 -0.009 0.17 0.3 37 -0.48 28 65
IKBKB 0.005 0.11 0.25 37 -0.27 20 57
AKT1 -0.03 0.11 0.31 22 -0.34 9 31
IKBKG 0.001 0.1 0.23 27 -0.26 22 49
MS4A2 -0.006 0.037 -10000 0 -0.14 25 25
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.007 0.13 0.32 10 -0.48 23 33
mol:Ca2+ -0.001 0.14 0.27 38 -0.35 28 66
LYN 0.021 0.036 -10000 0 -0.22 7 7
CBLB -0.019 0.1 0.14 1 -0.37 25 26
SHC1 0.024 0.014 -10000 0 -0.13 3 3
RasGAP/p62DOK 0.042 0.047 -10000 0 -0.23 14 14
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
PLD2 -0.041 0.1 0.27 17 -0.24 68 85
PTPN13 -0.007 0.13 -10000 0 -0.51 20 20
PTPN11 0.021 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.005 0.1 0.26 22 -0.3 17 39
SYK 0.009 0.085 -10000 0 -0.37 22 22
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.14 0.21 6 -0.48 29 35
LAT -0.029 0.11 0.14 1 -0.3 46 47
PAK2 -0.009 0.15 0.3 9 -0.54 23 32
NFATC2 -0.051 0.15 -10000 0 -0.53 43 43
HRAS -0.014 0.16 0.24 10 -0.55 27 37
GAB2 0.025 0.005 -10000 0 -10000 0 0
PLA2G1B 0.025 0.094 -10000 0 -0.82 5 5
Fc epsilon R1 -0.016 0.13 -10000 0 -0.27 87 87
Antigen/IgE/Fc epsilon R1 -0.008 0.12 -10000 0 -0.25 87 87
mol:GDP -0.016 0.16 0.22 8 -0.56 30 38
JUN 0.019 0.023 -10000 0 -0.13 9 9
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.43 48 48
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.27 55 55
CHUK 0 0.1 0.22 29 -0.26 22 51
KLRG1 -0.023 0.098 0.16 3 -0.24 66 69
VAV1 -0.026 0.13 0.17 2 -0.45 28 30
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.018 0.1 0.18 4 -0.38 23 27
negative regulation of mast cell degranulation -0.003 0.11 0.2 9 -0.4 18 27
BTK -0.022 0.17 -10000 0 -0.62 29 29
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.14 -10000 0 -0.29 106 106
GAB2/PI3K/SHP2 -0.046 0.081 -10000 0 -0.24 58 58
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 0.19 1 -0.26 75 76
RAF1 0.02 0.099 -10000 0 -0.93 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.02 0.16 -10000 0 -0.28 122 122
FCER1G 0.006 0.09 -10000 0 -0.35 27 27
FCER1A -0.06 0.15 -10000 0 -0.43 66 66
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.11 -10000 0 -0.24 76 76
MAPK3 0.024 0.093 -10000 0 -0.82 5 5
MAPK1 0.023 0.096 -10000 0 -0.85 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.003 0.14 -10000 0 -0.53 29 29
DUSP1 0.008 0.076 -10000 0 -0.25 32 32
NF-kappa-B/RelA 0.004 0.059 0.13 12 -0.17 16 28
actin cytoskeleton reorganization -0.005 0.13 -10000 0 -0.5 20 20
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.006 0.14 0.26 3 -0.49 26 29
FER -0.026 0.11 0.14 1 -0.32 40 41
RELA 0.025 0.005 -10000 0 -10000 0 0
ITK -0.024 0.092 -10000 0 -0.35 35 35
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.007 0.17 0.26 24 -0.57 28 52
cytokine secretion -0.002 0.038 -10000 0 -0.15 4 4
SPHK1 -0.028 0.12 0.2 1 -0.37 32 33
PTK2 -0.006 0.13 -10000 0 -0.53 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.15 0.25 10 -0.53 26 36
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.003 0.16 0.29 32 -0.46 27 59
MAP2K2 0.023 0.098 -10000 0 -0.82 5 5
MAP2K1 0.015 0.092 -10000 0 -0.87 5 5
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.1 0.18 21 -0.34 20 41
MAP2K4 0.032 0.063 -10000 0 -1.4 1 1
Fc epsilon R1/FcgammaRIIB -0.031 0.16 -10000 0 -0.29 121 121
mol:Choline -0.041 0.1 0.27 17 -0.24 68 85
SHC/Grb2/SOS1 0.019 0.12 -10000 0 -0.37 22 22
FYN 0.025 0.005 -10000 0 -10000 0 0
DOK1 0.025 0.021 -10000 0 -0.28 2 2
PXN -0.003 0.12 -10000 0 -0.49 20 20
HCLS1 -0.026 0.12 0.14 1 -0.42 29 30
PRKCB -0.005 0.13 0.27 24 -0.34 28 52
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.003 0.11 0.2 9 -0.41 18 27
LCP2 0.021 0.033 -10000 0 -0.15 15 15
PLA2G4A -0.027 0.12 -10000 0 -0.37 35 35
RASA1 0.026 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.041 0.1 0.27 17 -0.24 68 85
IKK complex 0.009 0.093 0.23 39 -0.21 17 56
WIPF1 0.026 0.002 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.024 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.098 -10000 0 -0.32 34 34
IRAK/TOLLIP 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
IKBKG 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.056 0.14 -10000 0 -0.31 101 101
IL1A -0.033 0.14 -10000 0 -0.43 48 48
IL1B -0.057 0.12 -10000 0 -0.32 76 76
IRAK/TRAF6/p62/Atypical PKCs 0.045 0.052 -10000 0 -0.2 15 15
IL1R2 -0.045 0.14 -10000 0 -0.25 127 127
IL1R1 0.006 0.077 -10000 0 -0.21 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.093 -10000 0 -0.34 23 23
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.016 0.064 -10000 0 -0.38 12 12
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.03 0.048 -10000 0 -0.27 1 1
JUN -0.009 0.036 0.16 6 -0.22 10 16
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.12 -10000 0 -0.25 82 82
IL1 alpha/IL1R1/IL1RAP/MYD88 0.02 0.12 -10000 0 -0.26 66 66
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.029 0.12 -10000 0 -0.24 66 66
IL1 beta fragment/IL1R1/IL1RAP -0.044 0.12 0.17 1 -0.26 90 91
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.009 0.042 0.17 10 -0.21 13 23
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -10000 0 -0.28 69 69
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.025 0.11 -10000 0 -0.36 30 30
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.044 0.12 0.17 1 -0.26 90 91
IL1 beta/IL1R2 -0.073 0.14 -10000 0 -0.3 113 113
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.015 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.24 78 78
IRAK3 0.022 0.041 -10000 0 -0.33 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.023 0.13 -10000 0 -0.25 95 95
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.099 -10000 0 -0.25 64 64
IL1 alpha/IL1R1/IL1RAP 0.009 0.11 -10000 0 -0.28 62 62
RELA 0.025 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.019 0.054 -10000 0 -0.36 9 9
IRAK/TRAF6/MEKK3 0.042 0.018 -10000 0 -0.22 1 1
IL1RAP 0.007 0.067 -10000 0 -0.18 47 47
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.04 0.1 -10000 0 -0.23 84 84
CASP1 0.01 0.071 -10000 0 -0.43 11 11
IL1RN/IL1R2 -0.056 0.14 -10000 0 -0.29 114 114
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.028 0.13 0.18 1 -0.26 93 94
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.1 -10000 0 -0.36 28 28
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL1RN -0.035 0.13 -10000 0 -0.24 117 117
TRAF6/TAK1/TAB1/TAB2 0.036 0.015 -10000 0 -0.21 1 1
MAP2K6 0.015 0.028 0.18 11 -0.2 2 13
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.042 0.2 -9999 0 -0.47 69 69
MAP3K8 0.015 0.047 -9999 0 -0.43 4 4
FOS -0.041 0.18 -9999 0 -0.44 70 70
PRKCA 0.02 0.024 -9999 0 -0.43 1 1
PTPN7 -0.054 0.15 -9999 0 -0.39 76 76
HRAS 0.024 0.006 -9999 0 -10000 0 0
PRKCB -0.011 0.098 -9999 0 -0.22 68 68
NRAS 0.021 0.01 -9999 0 -10000 0 0
RAS family/GTP 0.034 0.026 -9999 0 -10000 0 0
MAPK3 -0.032 0.16 -9999 0 -0.43 67 67
MAP2K1 0.003 0.1 -9999 0 -0.44 20 20
ELK1 0.021 0.017 -9999 0 -10000 0 0
BRAF -0.005 0.083 -9999 0 -0.39 21 21
mol:GTP 0 0.001 -9999 0 -0.004 58 58
MAPK1 -0.035 0.17 -9999 0 -0.43 68 68
RAF1 -0.001 0.086 -9999 0 -0.41 19 19
KRAS 0.025 0.005 -9999 0 -10000 0 0
PLK1 signaling 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
regulation of centriole-centriole cohesion 0.023 0.076 0.22 66 -0.092 6 72
BUB1B -0.03 0.1 0.12 2 -0.27 71 73
PLK1 0.003 0.031 0.091 12 -0.12 9 21
PLK1S1 0.007 0.029 0.11 3 -0.16 6 9
KIF2A 0 0.039 0.21 5 -0.2 5 10
regulation of mitotic centrosome separation 0.003 0.031 0.091 12 -0.12 9 21
GOLGA2 0.025 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.034 0.14 -10000 0 -0.27 113 113
WEE1 -0.003 0.084 -10000 0 -0.35 25 25
cytokinesis -0.067 0.16 0.2 2 -0.37 107 109
PP2A-alpha B56 -0.03 0.22 -10000 0 -0.63 61 61
AURKA 0.008 0.025 0.099 3 -0.34 1 4
PICH/PLK1 -0.008 0.062 0.16 6 -0.22 25 31
CENPE -0.018 0.061 0.11 1 -0.24 28 29
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.039 0.21 5 -0.2 5 10
PPP2CA 0.026 0.003 -10000 0 -10000 0 0
FZR1 0.025 0.006 -10000 0 -10000 0 0
TPX2 -0.006 0.071 0.11 11 -0.27 31 42
PAK1 0.009 0.061 -10000 0 -0.16 46 46
SPC24 -0.044 0.14 -10000 0 -0.28 114 114
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.05 0.12 0.13 2 -0.26 119 121
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 3 -0.017 5 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.018 0.047 23 -0.062 9 32
G2 phase of mitotic cell cycle 0 0.002 0.014 2 -0.01 1 3
STAG2 0.026 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.068 -10000 0 -0.52 8 8
spindle elongation 0.003 0.031 0.091 12 -0.12 9 21
ODF2 0.026 0.005 -10000 0 -10000 0 0
BUB1 -0.051 0.23 -10000 0 -0.68 60 60
TPT1 0 0.043 -10000 0 -0.18 22 22
CDC25C -0.028 0.12 0.15 1 -0.36 56 57
CDC25B 0.026 0.006 -10000 0 -10000 0 0
SGOL1 -0.023 0.076 0.092 6 -0.22 66 72
RHOA 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.041 -10000 0 -0.22 6 6
CDC14B 0.006 0.002 -10000 0 -10000 0 0
CDC20 -0.028 0.12 -10000 0 -0.25 93 93
PLK1/PBIP1 -0.013 0.06 0.087 1 -0.22 33 34
mitosis -0.002 0.004 0.023 2 -10000 0 2
FBXO5 0 0.031 0.11 2 -0.14 6 8
CDC2 0.001 0.002 0.011 1 -0.014 1 2
NDC80 -0.056 0.16 -10000 0 -0.3 128 128
metaphase plate congression -0.024 0.089 -10000 0 -0.23 76 76
ERCC6L -0.003 0.063 0.26 1 -0.22 25 26
NLP/gamma Tubulin 0.003 0.02 0.068 8 -0.087 6 14
microtubule cytoskeleton organization 0 0.043 -10000 0 -0.18 22 22
G2/M transition DNA damage checkpoint 0 0.002 0.012 3 -10000 0 3
PPP1R12A 0.026 0.02 -10000 0 -0.43 1 1
interphase 0 0.002 0.012 3 -10000 0 3
PLK1/PRC1-2 -0.016 0.11 0.14 2 -0.22 105 107
GRASP65/GM130/RAB1/GTP/PLK1 0.037 0.035 -10000 0 -0.17 1 1
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.026 0.075 30 -0.089 8 38
mitotic prometaphase 0.002 0.007 0.018 76 -0.012 3 79
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.06 0.21 1 -0.47 2 3
microtubule-based process -0.032 0.1 0.11 4 -0.24 95 99
Golgi organization 0.003 0.031 0.091 12 -0.12 9 21
Cohesin/SA2 0.017 0.028 0.1 1 -0.12 5 6
PPP1CB/MYPT1 0.038 0.016 -10000 0 -0.31 1 1
KIF20A -0.078 0.17 -10000 0 -0.3 163 163
APC/C/CDC20 -0.004 0.074 0.12 2 -0.23 40 42
PPP2R1A 0.021 0.01 -10000 0 -10000 0 0
chromosome segregation -0.013 0.059 0.086 1 -0.22 33 34
PRC1 0.019 0.032 -10000 0 -10000 0 0
ECT2 0.001 0.038 0.21 7 -0.17 3 10
C13orf34 0.003 0.027 0.072 24 -0.097 9 33
NUDC -0.024 0.089 -10000 0 -0.23 76 76
regulation of attachment of spindle microtubules to kinetochore -0.029 0.099 0.12 2 -0.26 71 73
spindle assembly 0.002 0.027 0.081 13 -0.1 8 21
spindle stabilization 0.007 0.029 0.11 3 -0.16 6 9
APC/C/HCDH1 0.023 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 -0.033 0.1 0.11 4 -0.24 95 99
CCNB1 0.017 0.038 -10000 0 -0.13 23 23
PPP1CB 0.027 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 -0.004 0.085 -10000 0 -0.38 22 22
TUBG1 0.008 0.021 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle -0.003 0.034 -10000 0 -0.21 6 6
MLF1IP -0.018 0.076 -10000 0 -0.31 30 30
INCENP 0.024 0.021 -10000 0 -0.43 1 1
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.06 0.25 -10000 0 -0.85 38 38
NCK1/PAK1/Dok-R -0.056 0.12 -10000 0 -0.4 41 41
NCK1/Dok-R -0.057 0.28 -10000 0 -1 36 36
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
mol:beta2-estradiol 0.011 0.058 0.23 31 -10000 0 31
RELA 0.025 0.005 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -0.13 4 4
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
F2 0.012 0.064 0.25 27 -10000 0 27
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.03 0.27 -10000 0 -0.96 36 36
FN1 0.02 0.029 -10000 0 -10000 0 0
PLD2 -0.064 0.28 -10000 0 -1.1 36 36
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 -0.071 0.16 -10000 0 -0.25 180 180
ELK1 -0.057 0.26 -10000 0 -0.95 36 36
GRB7 0.001 0.044 -10000 0 -10000 0 0
PAK1 0.008 0.061 -10000 0 -0.16 46 46
Tie2/Ang1/alpha5/beta1 Integrin -0.036 0.28 -10000 0 -0.99 36 36
CDKN1A -0.069 0.24 -10000 0 -0.66 66 66
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.057 0.28 -10000 0 -1 36 36
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:NO -0.01 0.21 0.34 2 -0.6 39 41
PLG -0.068 0.28 -10000 0 -1.1 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.052 0.23 -10000 0 -0.81 37 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ANGPT2 -0.066 0.24 -10000 0 -0.72 45 45
BMX -0.072 0.28 -10000 0 -1.1 36 36
ANGPT1 -0.083 0.3 -10000 0 -1.2 32 32
tube development -0.063 0.22 -10000 0 -0.66 53 53
ANGPT4 -0.008 0.1 -10000 0 -0.27 53 53
response to hypoxia -0.006 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.086 0.31 -10000 0 -1.2 36 36
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
FGF2 0.024 0.03 -10000 0 -0.43 2 2
STAT5A (dimer) -0.073 0.28 -10000 0 -0.73 67 67
mol:L-citrulline -0.01 0.21 0.34 2 -0.6 39 41
AGTR1 0 0.094 -10000 0 -0.29 39 39
MAPK14 -0.059 0.28 -10000 0 -1 37 37
Tie2/SHP2 -0.019 0.2 -10000 0 -1.1 14 14
TEK -0.022 0.21 -10000 0 -1.2 14 14
RPS6KB1 -0.047 0.24 -10000 0 -0.81 37 37
Angiotensin II/AT1 0 0.067 -10000 0 -0.22 35 35
Tie2/Ang1/GRB2 -0.056 0.29 -10000 0 -1.1 36 36
MAPK3 -0.061 0.26 -10000 0 -0.98 36 36
MAPK1 -0.061 0.26 -10000 0 -0.97 36 36
Tie2/Ang1/GRB7 -0.06 0.3 -10000 0 -1.1 36 36
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.068 0.29 -10000 0 -1.1 36 36
PI3K -0.063 0.28 -10000 0 -0.97 37 37
FES -0.062 0.29 -10000 0 -1 37 37
Crk/Dok-R -0.057 0.28 -10000 0 -1 36 36
Tie2/Ang1/ABIN2 -0.056 0.3 -10000 0 -1.1 36 36
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.052 0.23 -10000 0 -0.75 39 39
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.038 0.25 -10000 0 -0.81 37 37
Tie2/Ang2 -0.087 0.3 -10000 0 -0.9 53 53
Tie2/Ang1 -0.065 0.3 -10000 0 -1.1 36 36
FOXO1 -0.059 0.24 -10000 0 -0.72 53 53
ELF1 0.026 0.022 -10000 0 -10000 0 0
ELF2 -0.06 0.28 -10000 0 -1 36 36
mol:Choline -0.061 0.27 -10000 0 -1 36 36
cell migration -0.029 0.066 -10000 0 -0.23 39 39
FYN -0.074 0.25 -10000 0 -0.76 53 53
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
negative regulation of cell cycle -0.06 0.22 -10000 0 -0.59 67 67
ETS1 0.003 0.082 -10000 0 -0.28 35 35
PXN -0.023 0.22 0.41 3 -0.67 37 40
ITGB1 0.023 0.012 -10000 0 -10000 0 0
NOS3 -0.02 0.23 -10000 0 -0.69 38 38
RAC1 0.023 0.009 -10000 0 -10000 0 0
TNF -0.074 0.17 -10000 0 -0.41 91 91
MAPKKK cascade -0.061 0.27 -10000 0 -1 36 36
RASA1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.058 0.3 -10000 0 -1.1 36 36
NCK1 0.025 0.02 -10000 0 -0.43 1 1
vasculogenesis -0.005 0.19 0.34 2 -0.53 40 42
mol:Phosphatidic acid -0.061 0.27 -10000 0 -1 36 36
mol:Angiotensin II -0.001 0.006 -10000 0 -10000 0 0
mol:NADP -0.01 0.21 0.34 2 -0.6 39 41
Rac1/GTP -0.044 0.22 -10000 0 -0.75 37 37
MMP2 -0.07 0.28 -10000 0 -1.1 36 36
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.1 -10000 0 -0.24 62 62
MAP4K1 0.013 0.061 -10000 0 -0.34 13 13
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
DBNL 0.023 0.009 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -0.13 1 1
MAP3K1 -0.007 0.082 0.17 1 -0.26 24 25
JUN -0.025 0.17 -10000 0 -0.58 40 40
MAP3K7 -0.007 0.081 -10000 0 -0.26 24 24
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
CRK 0.026 0.002 -10000 0 -10000 0 0
MAP2K4 -0.002 0.091 0.21 9 -0.35 12 21
LAT 0.003 0.1 -10000 0 -0.42 27 27
LCP2 0.02 0.033 -10000 0 -0.15 15 15
MAPK8 -0.023 0.18 -10000 0 -0.6 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.002 0.089 -10000 0 -0.23 46 46
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.098 -10000 0 -0.24 48 48
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.025 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.046 0.027 -10000 0 -0.26 2 2
LAMA1 -0.024 0.14 -10000 0 -0.37 64 64
PRNP 0.025 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.016 0.11 -10000 0 -0.3 56 56
SMAD2 0.018 0.032 0.18 14 -0.23 1 15
GPC1/PrPc/Cu2+ 0.032 0.013 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.001 0.1 -10000 0 -0.3 51 51
TDGF1 -0.028 0.14 -10000 0 -0.34 74 74
CRIPTO/GPC1 -0.004 0.11 -10000 0 -0.31 53 53
APP/GPC1 0.036 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.088 -10000 0 -0.27 53 53
FLT1 0.024 0.021 -10000 0 -0.43 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.022 -10000 0 -0.2 2 2
SERPINC1 0.015 0.029 -10000 0 -0.13 14 14
FYN -0.015 0.082 -10000 0 -0.26 50 50
FGR -0.013 0.076 -10000 0 -0.26 42 42
positive regulation of MAPKKK cascade -0.05 0.15 0.22 19 -0.38 59 78
SLIT2 -0.044 0.14 -10000 0 -0.43 56 56
GPC1/NRG -0.043 0.13 -10000 0 -0.3 99 99
NRG1 -0.08 0.18 -10000 0 -0.32 156 156
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.018 -10000 0 -0.14 1 1
LYN -0.019 0.086 -10000 0 -0.26 53 53
mol:Spermine 0.006 0.008 -10000 0 -10000 0 0
cell growth 0.046 0.027 -10000 0 -0.26 2 2
BMP signaling pathway -0.024 0.015 0.13 4 -10000 0 4
SRC -0.014 0.08 -10000 0 -0.26 47 47
TGFBR1 0.024 0.022 -10000 0 -0.28 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.032 0.087 -10000 0 -0.19 84 84
GPC1 0.024 0.015 -10000 0 -0.13 4 4
TGFBR1 (dimer) 0.024 0.022 -10000 0 -0.28 2 2
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
BLK -0.048 0.11 -10000 0 -0.28 75 75
HCK -0.02 0.091 -10000 0 -0.28 52 52
FGF2 0.024 0.029 -10000 0 -0.43 2 2
FGFR1 0.025 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
TGFBR2 0.024 0.016 -10000 0 -0.13 5 5
cell death 0.036 0.014 -10000 0 -10000 0 0
ATIII/GPC1 0.032 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 0 0.07 -10000 0 -0.28 20 20
LCK -0.037 0.1 -10000 0 -0.28 69 69
neuron differentiation -0.043 0.13 -10000 0 -0.3 99 99
PrPc/Cu2+ 0.019 0.004 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.016 -10000 0 -0.13 5 5
Glypican 2 network

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
MDK -0.002 0.097 -9999 0 -0.43 22 22
GPC2 0.004 0.084 -9999 0 -0.37 22 22
GPC2/Midkine 0.002 0.091 -9999 0 -0.31 36 36
neuron projection morphogenesis 0.002 0.09 -9999 0 -0.31 36 36
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.023 0.13 -10000 0 -0.32 71 71
GNB1/GNG2 0.021 0.097 -10000 0 -0.27 33 33
mol:DAG 0.003 0.089 0.21 13 -0.26 25 38
PLCG1 0.003 0.091 0.21 13 -0.27 25 38
YES1 -0.013 0.082 -10000 0 -0.27 40 40
FZD3 0.023 0.035 -10000 0 -0.43 3 3
FZD6 0.015 0.04 -10000 0 -0.14 27 27
G protein 0.025 0.099 0.26 2 -0.27 26 28
MAP3K7 -0.048 0.1 0.21 14 -0.27 34 48
mol:Ca2+ 0.003 0.087 0.21 13 -0.26 25 38
mol:IP3 0.003 0.089 0.21 13 -0.26 25 38
NLK 0.01 0.044 -10000 0 -0.95 1 1
GNB1 0.022 0.01 -10000 0 -10000 0 0
CAMK2A -0.048 0.11 0.26 5 -0.27 47 52
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.007 0.087 -10000 0 -0.27 44 44
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
GNAS -0.013 0.079 0.16 1 -0.26 42 43
GO:0007205 -0.005 0.088 0.21 13 -0.27 25 38
WNT6 0.003 0.087 -10000 0 -0.43 17 17
WNT4 0.008 0.057 -10000 0 -0.18 35 35
NFAT1/CK1 alpha -0.002 0.12 0.33 3 -0.29 40 43
GNG2 0.022 0.04 -10000 0 -0.43 4 4
WNT5A 0.01 0.078 -10000 0 -0.33 22 22
WNT11 0.009 0.075 -10000 0 -0.43 13 13
CDC42 0.001 0.064 -10000 0 -0.27 14 14
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.17 -10000 0 -1.1 9 9
VDR -0.014 0.11 -10000 0 -0.43 31 31
FAM120B 0.025 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.33 90 90
RXRs/LXRs/DNA/Oxysterols -0.073 0.21 -10000 0 -0.5 85 85
MED1 0.026 0.003 -10000 0 -10000 0 0
mol:9cRA -0.006 0.02 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.023 0.041 -10000 0 -0.22 14 14
RXRs/NUR77 0.011 0.11 -10000 0 -0.25 57 57
RXRs/PPAR -0.013 0.098 -10000 0 -0.26 57 57
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RARs/VDR/DNA/Vit D3 0.042 0.071 -10000 0 -0.22 32 32
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.014 0.11 -10000 0 -0.43 31 31
RARs/RARs/DNA/9cRA 0.035 0.032 -10000 0 -0.22 3 3
RARG 0.025 0.008 -10000 0 -0.13 1 1
RPS6KB1 0.028 0.12 0.58 17 -0.43 9 26
RARs/THRs/DNA/SMRT 0.022 0.041 -10000 0 -0.22 14 14
THRA 0.023 0.035 -10000 0 -0.43 3 3
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.29 33 33
RXRs/PPAR/9cRA/PGJ2/DNA -0.004 0.11 -10000 0 -0.24 59 59
NR1H4 -0.042 0.13 -10000 0 -0.24 128 128
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.27 42 42
NR1H2 0.015 0.026 -10000 0 -10000 0 0
NR1H3 0.015 0.031 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.003 0.12 -10000 0 -0.24 77 77
NR4A1 0.012 0.062 -10000 0 -0.43 7 7
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.037 0.11 -10000 0 -0.26 82 82
RXRG -0.036 0.14 -10000 0 -0.4 63 63
RXR alpha/CCPG 0.027 0.028 -10000 0 -10000 0 0
RXRA 0.015 0.029 -10000 0 -10000 0 0
RXRB 0.015 0.031 -10000 0 -10000 0 0
THRB 0.015 0.059 -10000 0 -0.23 22 22
PPARG 0.009 0.081 -10000 0 -0.43 16 16
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF -0.15 0.37 -10000 0 -0.96 81 81
mol:Oxysterols -0.006 0.019 -10000 0 -10000 0 0
cholesterol transport -0.072 0.21 -10000 0 -0.49 85 85
PPARA 0.026 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.035 -10000 0 -0.43 3 3
RXRs/NUR77/BCL2 -0.016 0.094 -10000 0 -0.25 59 59
SREBF1 -0.085 0.24 -10000 0 -0.87 30 30
RXRs/RXRs/DNA/9cRA -0.004 0.11 -10000 0 -0.24 59 59
ABCA1 -0.086 0.24 -10000 0 -0.82 33 33
RARs/THRs 0.067 0.05 -10000 0 -0.22 13 13
RXRs/FXR -0.01 0.14 -10000 0 -0.27 89 89
BCL2 0.021 0.045 -10000 0 -0.43 5 5
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.034 0.1 -10000 0 -0.23 61 61
SMAD6-7/SMURF1 0.039 0.03 -10000 0 -0.26 2 2
NOG -0.029 0.14 -10000 0 -0.43 58 58
SMAD9 -0.047 0.18 -10000 0 -0.49 61 61
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.022 0.11 -10000 0 -0.39 22 22
BMP7/USAG1 -0.009 0.093 -10000 0 -0.3 37 37
SMAD5/SKI -0.013 0.11 -10000 0 -0.38 22 22
SMAD1 0.019 0.05 -10000 0 -0.36 3 3
BMP2 -0.033 0.15 -10000 0 -0.43 66 66
SMAD1/SMAD1/SMAD4 0.022 0.053 -10000 0 -0.31 3 3
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B 0.003 0.1 -10000 0 -0.43 26 26
BMPR1A-1B/BAMBI 0.031 0.069 -10000 0 -0.26 24 24
AHSG -0.029 0.14 -10000 0 -0.31 81 81
CER1 -0.001 0.033 -10000 0 -10000 0 0
BMP2-4/CER1 -0.005 0.13 -10000 0 -0.31 69 69
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.13 -10000 0 -0.43 33 33
BMP2-4 (homodimer) -0.017 0.14 -10000 0 -0.36 69 69
RGMB 0.02 0.047 -10000 0 -0.43 5 5
BMP6/BMPR2/BMPR1A-1B 0.044 0.074 -10000 0 -0.24 29 29
RGMA 0.016 0.066 -10000 0 -0.4 12 12
SMURF1 0.021 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.025 0.12 -10000 0 -0.39 38 38
BMP2-4/USAG1 -0.011 0.13 -10000 0 -0.3 82 82
SMAD6/SMURF1/SMAD5 -0.011 0.1 -10000 0 -0.38 19 19
SOSTDC1 -0.028 0.12 -10000 0 -0.23 102 102
BMP7/BMPR2/BMPR1A-1B 0.043 0.072 -10000 0 -0.23 30 30
SKI 0.022 0.01 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.054 -10000 0 -0.24 17 17
HFE2 0.012 0.025 -10000 0 -10000 0 0
ZFYVE16 0.026 0.003 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD -0.001 0.13 -10000 0 -0.3 72 72
SMAD5/SMAD5/SMAD4 -0.015 0.11 -10000 0 -0.38 23 23
MAPK1 0.026 0.003 -10000 0 -10000 0 0
TAK1/TAB family -0.011 0.1 -10000 0 -0.36 24 24
BMP7 (homodimer) 0.02 0.049 -10000 0 -0.43 6 6
NUP214 0.025 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.008 0.11 -10000 0 -0.32 52 52
SMAD1/SKI 0.025 0.057 -10000 0 -0.37 3 3
SMAD6 0.022 0.041 -10000 0 -0.33 6 6
CTDSP2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.023 0.15 -10000 0 -0.32 101 101
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.079 0.17 -10000 0 -0.3 162 162
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.023 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.02 0.074 -10000 0 -0.3 25 25
CHRDL1 -0.036 0.15 -10000 0 -0.37 80 80
ENDOFIN/SMAD1 0.029 0.06 0.3 1 -0.37 3 4
SMAD6-7/SMURF1/SMAD1 0.036 0.064 -10000 0 -0.35 4 4
SMAD6/SMURF1 0.021 0.011 -10000 0 -10000 0 0
BAMBI 0.022 0.019 -10000 0 -0.13 6 6
SMURF2 0.024 0.029 -10000 0 -0.43 2 2
BMP2-4/CHRDL1 -0.036 0.16 -10000 0 -0.3 125 125
BMP2-4/GREM1 -0.054 0.17 -10000 0 -0.3 153 153
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.038 0.18 -10000 0 -0.47 62 62
SMAD1/SMAD6 0.021 0.055 -10000 0 -0.36 3 3
TAK1/SMAD6 0.03 0.017 -10000 0 -10000 0 0
BMP7 0.02 0.049 -10000 0 -0.43 6 6
BMP6 0.017 0.054 -10000 0 -0.24 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.029 0.11 -10000 0 -0.38 31 31
PPM1A 0.025 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.029 0.061 0.3 1 -0.36 3 4
SMAD7/SMURF1 0.03 0.016 -10000 0 -10000 0 0
CTDSPL 0.025 0.02 -10000 0 -0.43 1 1
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.019 0.021 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 -10000 0 -0.42 46 46
CHRD 0.021 0.045 -10000 0 -0.43 5 5
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.13 -10000 0 -0.42 38 38
BMP4 0.007 0.088 -10000 0 -0.4 22 22
FST -0.016 0.12 -10000 0 -0.43 34 34
BMP2-4/NOG -0.024 0.17 -10000 0 -0.39 83 83
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.044 0.069 -10000 0 -0.22 25 25
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.009 0.057 -10000 0 -0.25 22 22
NFATC2 -0.022 0.074 -10000 0 -0.26 40 40
NFATC3 0.002 0.023 -10000 0 -0.14 1 1
CD40LG -0.073 0.14 0.31 3 -0.38 51 54
PTGS2 -0.094 0.18 0.36 1 -0.46 75 76
JUNB 0.007 0.071 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.018 -10000 0 -10000 0 0
CALM1 0.021 0.016 -10000 0 -10000 0 0
JUN 0.015 0.025 -10000 0 -0.14 9 9
mol:Ca2+ -0.003 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.005 -10000 0 -10000 0 0
FOSL1 -0.028 0.13 -10000 0 -0.43 40 40
CREM 0.023 0.022 -10000 0 -0.28 2 2
Jun/NFAT1-c-4/p21SNFT -0.029 0.12 -10000 0 -0.35 32 32
FOS -0.036 0.14 -10000 0 -0.33 74 74
IFNG -0.072 0.14 0.28 2 -0.38 49 51
AP-1/NFAT1-c-4 -0.057 0.17 -10000 0 -0.42 51 51
FASLG -0.073 0.14 0.36 1 -0.38 50 51
NFAT1-c-4/ICER1 -0.024 0.097 0.18 1 -0.25 57 58
IL2RA -0.074 0.15 0.31 3 -0.39 57 60
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.072 0.14 0.3 3 -0.38 48 51
JunB/Fra1/NFAT1-c-4 -0.039 0.13 0.2 1 -0.33 49 50
IL4 -0.071 0.14 0.33 2 -0.38 46 48
IL2 -0.011 0.14 -10000 0 -0.93 12 12
IL3 0.009 0.069 -10000 0 -0.66 5 5
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
BATF3 0.001 0.091 -10000 0 -0.43 19 19
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.003 0.095 0.32 38 -10000 0 38
KIRREL -0.009 0.12 -10000 0 -0.43 38 38
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.003 0.095 -10000 0 -0.32 38 38
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.002 -10000 0 -10000 0 0
WASL 0.02 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.029 0.08 -10000 0 -0.24 38 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.069 -10000 0 -0.24 32 32
FYN -0.009 0.076 0.18 23 -0.22 39 62
mol:Ca2+ 0.026 0.08 -10000 0 -0.24 39 39
mol:DAG 0.027 0.081 -10000 0 -0.24 39 39
NPHS2 0.001 0.033 -10000 0 -0.28 2 2
mol:IP3 0.027 0.081 -10000 0 -0.24 39 39
regulation of endocytosis 0.023 0.072 -10000 0 -0.21 39 39
Nephrin/NEPH1/podocin/Cholesterol 0.016 0.075 -10000 0 -0.23 39 39
establishment of cell polarity -0.003 0.095 -10000 0 -0.32 38 38
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.082 -10000 0 -0.22 38 38
Nephrin/NEPH1/beta Arrestin2 0.025 0.074 -10000 0 -0.22 39 39
NPHS1 -0.001 0.053 -10000 0 -0.15 40 40
Nephrin/NEPH1/podocin 0.018 0.073 -10000 0 -0.23 39 39
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.081 -10000 0 -0.24 39 39
CD2AP 0.026 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.027 0.08 -10000 0 -0.24 38 38
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.086 0.19 26 -0.23 46 72
cytoskeleton organization -0.017 0.083 0.2 12 -0.27 32 44
Nephrin/NEPH1 0.009 0.067 -10000 0 -0.22 38 38
Nephrin/NEPH1/ZO-1 0.021 0.081 -10000 0 -0.25 38 38
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.095 0.22 66 -10000 0 66
GNAI2 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.094 -10000 0 -0.26 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
RhoA/GTP -0.009 0.097 -10000 0 -0.22 66 66
negative regulation of cAMP metabolic process -0.019 0.099 -10000 0 -0.24 66 66
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNA12 0.022 0.009 -10000 0 -10000 0 0
S1PR5 -0.053 0.16 -10000 0 -0.3 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.019 0.1 -10000 0 -0.24 66 66
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
IL6-mediated signaling events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.009 0.2 0.48 7 -0.66 17 24
CRP -0.016 0.2 0.59 5 -0.69 15 20
cell cycle arrest -0.021 0.22 0.49 3 -0.64 32 35
TIMP1 -0.014 0.2 0.46 2 -0.67 21 23
IL6ST -0.008 0.11 -10000 0 -0.42 33 33
Rac1/GDP -0.05 0.16 -10000 0 -0.42 60 60
AP1 0.033 0.1 -10000 0 -0.58 2 2
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.018 0.2 0.5 2 -0.67 17 19
HSP90B1 0.012 0.16 -10000 0 -0.91 14 14
GAB1 0.025 0.021 -10000 0 -0.43 1 1
MAPK14 -0.073 0.19 -10000 0 -0.55 55 55
AKT1 0.035 0.049 -10000 0 -0.7 1 1
FOXO1 0.035 0.051 -10000 0 -0.66 1 1
MAP2K6 -0.059 0.16 0.2 2 -0.45 58 60
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.049 0.17 0.29 3 -0.44 55 58
MITF -0.05 0.15 -10000 0 -0.41 56 56
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.006 -10000 0 -10000 0 0
A2M 0.017 0.082 -10000 0 -1.2 2 2
CEBPB 0.017 0.073 -10000 0 -0.43 13 13
GRB2/SOS1/GAB family/SHP2 0.007 0.081 -10000 0 -0.43 6 6
STAT3 -0.028 0.24 0.5 3 -0.7 30 33
STAT1 0.017 0.045 -10000 0 -0.9 1 1
CEBPD -0.044 0.3 0.49 4 -1 35 39
PIK3CA 0.026 0.02 -10000 0 -0.43 1 1
PI3K 0.04 0.007 -10000 0 -10000 0 0
JUN 0.019 0.023 -10000 0 -0.13 9 9
PIAS3/MITF -0.032 0.16 -10000 0 -0.41 49 49
MAPK11 -0.076 0.19 -10000 0 -0.55 55 55
STAT3 (dimer)/FOXO1 -0.007 0.17 -10000 0 -0.56 19 19
GRB2/SOS1/GAB family -0.012 0.15 -10000 0 -0.41 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.046 0.15 -10000 0 -0.33 87 87
GRB2 0.025 0.006 -10000 0 -10000 0 0
JAK2 0.025 0.006 -10000 0 -10000 0 0
LBP 0.001 0.19 0.45 7 -0.62 20 27
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.016 -10000 0 -10000 0 0
MYC -0.022 0.28 0.49 4 -0.89 34 38
FGG -0.02 0.2 0.5 2 -0.66 18 20
macrophage differentiation -0.021 0.22 0.49 3 -0.64 32 35
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.12 -10000 0 -0.27 61 61
JUNB -0.021 0.24 0.45 10 -0.81 22 32
FOS -0.031 0.14 -10000 0 -0.42 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.16 0.23 1 -0.42 61 62
STAT1/PIAS1 -0.022 0.16 0.24 1 -0.42 42 43
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.049 -10000 0 -0.36 5 5
STAT3 (dimer) -0.025 0.24 0.5 3 -0.68 31 34
PRKCD -0.026 0.23 0.39 34 -0.54 51 85
IL6R 0.005 0.082 -10000 0 -0.34 23 23
SOCS3 -0.094 0.3 0.39 2 -1.1 38 40
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.078 -10000 0 -0.24 32 32
Rac1/GTP -0.05 0.17 -10000 0 -0.42 61 61
HCK 0.014 0.063 -10000 0 -0.43 9 9
MAPKKK cascade 0.032 0.08 -10000 0 -0.96 1 1
bone resorption -0.016 0.19 0.5 2 -0.63 17 19
IRF1 -0.016 0.2 0.51 3 -0.67 17 20
mol:GDP -0.058 0.16 0.2 1 -0.42 64 65
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.058 0.16 0.2 1 -0.43 64 65
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.25 -10000 0 -0.6 71 71
PTPN11 0.009 0.079 -10000 0 -0.69 6 6
IL6/IL6RA -0.024 0.11 -10000 0 -0.32 51 51
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.074 -10000 0 -0.25 30 30
gp130 (dimer)/JAK2/JAK2/LMO4 0.02 0.075 -10000 0 -0.25 31 31
IL6 -0.038 0.12 -10000 0 -0.3 67 67
PIAS3 0.024 0.008 -10000 0 -10000 0 0
PTPRE 0.023 0.024 -10000 0 -0.43 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.12 0.21 1 -0.3 68 69
LMO4 0.018 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.028 0.22 -10000 0 -0.66 29 29
MCL1 0.039 0.057 -10000 0 -0.62 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.14 -10000 0 -0.41 59 59
KLHL20 0.011 0.07 0.16 7 -0.22 6 13
CYFIP2 0.022 0.037 -10000 0 -0.43 3 3
Rac1/GDP -0.004 0.095 0.26 4 -0.26 48 52
ENAH -0.032 0.14 -10000 0 -0.42 62 62
AP1M1 0.025 0.006 -10000 0 -10000 0 0
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.004 0.065 -10000 0 -0.24 1 1
ABI1/Sra1/Nap1 -0.014 0.035 -10000 0 -0.15 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.021 0.12 -10000 0 -0.26 70 70
RAPGEF1 -0.02 0.14 0.24 5 -0.37 55 60
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.028 0.15 -10000 0 -0.42 65 65
CRK -0.03 0.14 0.22 1 -0.4 57 58
E-cadherin/gamma catenin/alpha catenin 0.014 0.1 -10000 0 -0.26 63 63
alphaE/beta7 Integrin 0.019 0.069 -10000 0 -0.3 19 19
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
DLG1 -0.031 0.14 -10000 0 -0.41 62 62
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.044 -10000 0 -0.18 1 1
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.012 -10000 0 -10000 0 0
PI3K -0.015 0.057 -10000 0 -0.23 1 1
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.12 -10000 0 -0.31 63 63
TIAM1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.029 0.088 -10000 0 -0.22 55 55
AKT1 -0.003 0.043 0.12 2 -0.14 1 3
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.28 122 122
RhoA/GDP 0.004 0.1 0.26 8 -0.26 52 60
actin cytoskeleton organization 0.014 0.06 0.16 19 -0.16 6 25
CDC42/GDP 0 0.099 0.25 5 -0.25 52 57
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.078 -10000 0 -0.22 60 60
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
RAC1 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.031 0.095 -10000 0 -0.23 55 55
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.085 -10000 0 -0.22 59 59
mol:GDP -0.011 0.11 0.26 9 -0.3 52 61
CDC42/GTP/IQGAP1 0.027 0.028 -10000 0 -0.23 4 4
JUP 0.02 0.049 -10000 0 -0.39 7 7
p120 catenin/RhoA/GDP 0.009 0.1 0.26 6 -0.26 51 57
RAC1/GTP/IQGAP1 0.027 0.029 -10000 0 -0.26 4 4
PIP5K1C/AP1M1 0.037 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.051 0.13 22 -0.16 14 36
NME1 0.026 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.031 0.15 -10000 0 -0.42 62 62
regulation of cell-cell adhesion -0.009 0.055 -10000 0 -0.21 1 1
WASF2 0.009 0.029 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.081 0.24 2 -0.26 1 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.12 -10000 0 -0.25 74 74
CCND1 0.012 0.06 0.15 19 -0.2 14 33
VAV2 -0.013 0.15 -10000 0 -0.41 49 49
RAP1/GDP 0.004 0.091 0.27 4 -0.23 22 26
adherens junction assembly -0.03 0.14 -10000 0 -0.4 62 62
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.023 0.008 -10000 0 -10000 0 0
PIP5K1C 0.025 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.016 0.11 0.2 3 -0.24 74 77
E-cadherin/beta catenin -0.028 0.1 -10000 0 -0.32 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.032 0.14 -10000 0 -0.4 64 64
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.016 0.084 -10000 0 -0.34 7 7
E-cadherin/beta catenin/alpha catenin 0.016 0.1 -10000 0 -0.26 59 59
ITGAE 0.026 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.029 0.15 -10000 0 -0.43 64 64
Glucocorticoid receptor regulatory network

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
PCK2 0.047 0.09 -10000 0 -0.84 3 3
SMARCC2 0.024 0.017 -10000 0 -0.13 1 1
SMARCC1 0.024 0.017 -10000 0 -10000 0 0
TBX21 -0.067 0.17 -10000 0 -0.68 31 31
SUMO2 0.023 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.033 -10000 0 -0.16 10 10
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 -0.037 0.15 -10000 0 -0.34 89 89
GR alpha/HSP90/FKBP51/HSP90 0.049 0.12 0.27 16 -0.23 47 63
PRL -0.034 0.068 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.11 0.19 0.48 54 -0.33 2 56
RELA -0.032 0.092 -10000 0 -0.23 34 34
FGG 0.09 0.14 0.4 43 -10000 0 43
GR beta/TIF2 0.056 0.12 0.26 36 -0.29 31 67
IFNG -0.13 0.18 -10000 0 -0.58 27 27
apoptosis 0.014 0.17 0.57 19 -0.53 6 25
CREB1 0.026 0.009 -10000 0 -10000 0 0
histone acetylation -0.048 0.1 -10000 0 -0.34 33 33
BGLAP -0.039 0.097 -10000 0 -1.2 1 1
GR/PKAc 0.076 0.068 0.27 12 -10000 0 12
NF kappa B1 p50/RelA -0.05 0.15 -10000 0 -0.3 111 111
SMARCD1 0.024 0.017 -10000 0 -10000 0 0
MDM2 0.047 0.063 0.19 45 -10000 0 45
GATA3 -0.032 0.14 -10000 0 -0.42 49 49
AKT1 0.022 0.013 0.18 3 -10000 0 3
CSF2 -0.056 0.084 -10000 0 -0.41 4 4
GSK3B 0.023 0.026 -10000 0 -0.43 1 1
NR1I3 0.021 0.17 0.57 17 -0.62 3 20
CSN2 0.074 0.12 0.34 35 -10000 0 35
BRG1/BAF155/BAF170/BAF60A 0.06 0.047 -10000 0 -0.22 11 11
NFATC1 0.005 0.095 -10000 0 -0.43 23 23
POU2F1 0.025 0.021 -10000 0 -0.43 1 1
CDKN1A -0.044 0.28 -10000 0 -1.4 20 20
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.01 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.43 28 28
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.032 0.12 0.28 8 -0.24 42 50
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.04 0.27 0.54 16 -0.76 53 69
JUN -0.078 0.13 -10000 0 -0.39 40 40
IL4 -0.062 0.12 -10000 0 -0.52 13 13
CDK5R1 0 0.1 -10000 0 -0.43 29 29
PRKACA 0.025 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.092 0.1 -10000 0 -0.29 76 76
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.11 0.28 11 -0.21 38 49
cortisol/GR alpha (monomer) 0.14 0.19 0.54 56 -10000 0 56
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.14 -10000 0 -0.4 62 62
AP-1/NFAT1-c-4 -0.17 0.23 -10000 0 -0.51 123 123
AFP -0.077 0.12 -10000 0 -10000 0 0
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.084 0.096 0.38 14 -10000 0 14
TP53 0.004 0.12 -10000 0 -0.47 32 32
PPP5C 0.022 0.01 -10000 0 -10000 0 0
KRT17 -0.27 0.42 -10000 0 -1.1 101 101
KRT14 -0.057 0.086 -10000 0 -10000 0 0
TBP 0.03 0.016 -10000 0 -0.29 1 1
CREBBP 0.025 0.046 -10000 0 -0.25 14 14
HDAC1 0.02 0.009 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
AP-1 -0.17 0.23 -10000 0 -0.52 123 123
MAPK14 0.024 0.015 -10000 0 -10000 0 0
MAPK10 0.021 0.038 -10000 0 -0.43 3 3
MAPK11 0.016 0.058 -10000 0 -0.43 8 8
KRT5 -0.24 0.39 -10000 0 -1.1 81 81
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.027 0.009 -10000 0 -10000 0 0
STAT1 0.024 0.033 -10000 0 -0.16 10 10
CGA -0.048 0.085 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.044 0.091 0.32 6 -0.38 4 10
MAPK3 0.024 0.016 -10000 0 -10000 0 0
MAPK1 0.024 0.015 -10000 0 -10000 0 0
ICAM1 -0.098 0.19 -10000 0 -0.59 39 39
NFKB1 -0.031 0.089 -10000 0 -0.22 36 36
MAPK8 -0.079 0.12 0.31 1 -0.35 51 52
MAPK9 0.023 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.012 0.18 0.57 19 -0.56 6 25
BAX -0.024 0.11 -10000 0 -0.6 1 1
POMC -0.086 0.22 -10000 0 -1.5 9 9
EP300 0.021 0.061 -10000 0 -0.29 18 18
cortisol/GR alpha (dimer)/p53 0.12 0.18 0.48 48 -0.46 1 49
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.053 0.2 17 -10000 0 17
SGK1 0.002 0.24 -10000 0 -1.4 14 14
IL13 -0.13 0.19 -10000 0 -0.67 21 21
IL6 -0.14 0.29 -10000 0 -0.89 52 52
PRKACG 0.01 0.024 -10000 0 -0.13 4 4
IL5 -0.1 0.15 -10000 0 -0.55 21 21
IL2 -0.13 0.18 -10000 0 -0.56 29 29
CDK5 0.02 0.012 -10000 0 -10000 0 0
PRKACB 0.021 0.01 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
IL8 -0.19 0.35 -10000 0 -0.92 83 83
CDK5R1/CDK5 0.015 0.07 -10000 0 -0.3 22 22
NF kappa B1 p50/RelA/PKAc -0.007 0.12 -10000 0 -0.28 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.47 46 -10000 0 46
SMARCA4 0.024 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.079 0.12 0.34 32 -0.35 8 40
NF kappa B1 p50/RelA/Cbp -0.014 0.15 -10000 0 -0.38 35 35
JUN (dimer) -0.077 0.13 -10000 0 -0.38 40 40
YWHAH 0.019 0.033 -10000 0 -10000 0 0
VIPR1 -0.071 0.18 -10000 0 -0.69 33 33
NR3C1 0.083 0.12 0.35 44 -10000 0 44
NR4A1 0.008 0.087 -10000 0 -0.45 15 15
TIF2/SUV420H1 0.015 0.083 -10000 0 -0.3 32 32
MAPKKK cascade 0.014 0.17 0.57 19 -0.53 6 25
cortisol/GR alpha (dimer)/Src-1 0.14 0.17 0.48 55 -10000 0 55
PBX1 0.025 0.021 -10000 0 -0.43 1 1
POU1F1 0 0.021 -10000 0 -10000 0 0
SELE -0.15 0.28 -10000 0 -0.77 69 69
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.078 0.12 0.35 27 -0.35 8 35
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.47 46 -10000 0 46
mol:cortisol 0.066 0.11 0.31 52 -10000 0 52
MMP1 -0.041 0.09 -10000 0 -0.94 2 2
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR -0.014 0.11 -10000 0 -0.43 31 31
Cbp/p300/PCAF 0.048 0.03 -10000 0 -0.26 4 4
EP300 0.022 0.04 -10000 0 -0.43 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.073 -10000 0 -0.37 10 10
KAT2B 0.025 0.008 -10000 0 -0.13 1 1
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.012 0.075 0.19 7 -0.35 9 16
RAR alpha/9cRA/Cyclin H -0.008 0.11 0.22 1 -0.38 11 12
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.062 0.18 1 -0.31 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.026 0.1 -10000 0 -0.4 18 18
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RXRs/RARs/NRIP1/9cRA -0.075 0.19 0.28 1 -0.44 78 79
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA3 0.025 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.014 0.11 -10000 0 -0.43 31 31
RARG 0.026 0.008 -10000 0 -0.13 1 1
RAR gamma1/9cRA 0.034 0.009 -10000 0 -10000 0 0
MAPK3 0.027 0.002 -10000 0 -10000 0 0
MAPK1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.087 0.2 -10000 0 -0.45 94 94
RARA -0.026 0.097 -10000 0 -0.24 75 75
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.089 0.18 1 -0.34 20 21
PRKCA 0.026 0.021 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.08 0.2 -10000 0 -0.54 45 45
RXRG -0.061 0.16 -10000 0 -0.38 93 93
RXRA -0.022 0.088 -10000 0 -0.21 72 72
RXRB -0.027 0.099 -10000 0 -0.28 65 65
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.29 33 33
RBP1 -0.006 0.082 -10000 0 -0.17 85 85
CRBP1/9-cic-RA -0.002 0.056 -10000 0 -0.11 87 87
RARB 0.024 0.035 -10000 0 -0.43 3 3
PRKCG -0.065 0.15 -10000 0 -0.43 67 67
MNAT1 0.025 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.08 0.19 -10000 0 -0.45 82 82
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.059 0.16 -10000 0 -0.38 70 70
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.096 0.21 2 -0.34 18 20
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.076 0.19 -10000 0 -0.55 40 40
positive regulation of DNA binding -0.014 0.1 -10000 0 -0.36 11 11
NRIP1 -0.066 0.18 -10000 0 -0.57 26 26
RXRs/RARs -0.076 0.2 -10000 0 -0.45 81 81
RXRs/RXRs/DNA/9cRA -0.088 0.18 -10000 0 -0.44 87 87
PRKACA 0.025 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.003 -10000 0 -10000 0 0
TFIIH 0.051 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.007 0.092 -10000 0 -0.31 9 9
CCNH 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.017 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.008 0.086 -10000 0 -0.22 58 58
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.058 0.11 -10000 0 -0.3 79 79
GNB1/GNG2 0.027 0.028 -10000 0 -0.26 4 4
GNB1 0.022 0.01 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.012 0.079 -10000 0 -0.23 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.008 0.02 0.063 60 -10000 0 60
GNAL -0.028 0.15 -10000 0 -0.42 61 61
GNG2 0.022 0.04 -10000 0 -0.43 4 4
CRH -0.075 0.16 -10000 0 -0.27 167 167
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.047 -10000 0 -0.3 13 13
MAPK11 0.002 0.037 -10000 0 -0.3 8 8
Ephrin B reverse signaling

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
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EPHB2 0.017 0.04 -10000 0 -0.22 10 10
EFNB1 -0.023 0.082 -10000 0 -0.31 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.095 -10000 0 -0.25 46 46
Ephrin B2/EPHB1-2 0.016 0.082 -10000 0 -0.25 41 41
neuron projection morphogenesis -0.009 0.085 -10000 0 -0.24 46 46
Ephrin B1/EPHB1-2/Tiam1 -0.008 0.11 -10000 0 -0.26 61 61
DNM1 -0.027 0.12 -10000 0 -0.22 107 107
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.085 0.22 1 -0.51 13 14
YES1 -0.005 0.13 -10000 0 -0.77 13 13
Ephrin B1/EPHB1-2/NCK2 -0.008 0.11 -10000 0 -0.26 62 62
PI3K 0.027 0.091 -10000 0 -0.52 13 13
mol:GDP -0.009 0.1 -10000 0 -0.26 61 61
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
endothelial cell proliferation 0.025 0.022 -10000 0 -0.26 1 1
FYN -0.003 0.12 -10000 0 -0.75 13 13
MAP3K7 -0.01 0.089 0.22 1 -0.54 13 14
FGR -0.008 0.13 -10000 0 -0.76 13 13
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RGS3 0.025 0.013 -10000 0 -0.13 3 3
cell adhesion -0.012 0.11 -10000 0 -0.41 20 20
LYN -0.002 0.12 -10000 0 -0.75 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.11 -10000 0 -0.69 13 13
Ephrin B1/EPHB1-2 -0.01 0.095 -10000 0 -0.58 13 13
SRC -0.004 0.12 -10000 0 -0.74 13 13
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
EPHB1 -0.009 0.12 -10000 0 -0.43 39 39
EPHB4 0.021 0.011 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
BLK -0.01 0.13 -10000 0 -0.74 13 13
HCK -0.004 0.13 -10000 0 -0.76 13 13
regulation of stress fiber formation 0.009 0.1 0.26 62 -10000 0 62
MAPK8 -0.014 0.09 -10000 0 -0.5 13 13
Ephrin B1/EPHB1-2/RGS3 -0.008 0.11 -10000 0 -0.26 62 62
endothelial cell migration 0.026 0.11 0.22 28 -0.41 13 41
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTPN13 0.023 0.052 -10000 0 -0.56 4 4
regulation of focal adhesion formation 0.009 0.1 0.26 62 -10000 0 62
chemotaxis 0.009 0.11 0.26 62 -10000 0 62
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.004 0.09 -10000 0 -0.24 46 46
angiogenesis -0.009 0.095 -10000 0 -0.58 13 13
LCK -0.019 0.13 -10000 0 -0.76 13 13
EPHB forward 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
Ephrin A5/EPHB2 -0.007 0.089 -10000 0 -0.26 49 49
cell-cell adhesion 0.02 0.05 0.22 26 -10000 0 26
Ephrin B/EPHB2/RasGAP 0.054 0.058 -10000 0 -0.24 12 12
ITSN1 0.026 0.003 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Ephrin B1/EPHB3 0.033 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.012 0.077 -10000 0 -0.26 38 38
HRAS/GDP 0.018 0.064 -10000 0 -0.27 10 10
Ephrin B/EPHB1/GRB7 0.042 0.098 -10000 0 -0.26 45 45
Endophilin/SYNJ1 0.012 0.056 0.18 26 -0.22 13 39
KRAS 0.025 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.045 0.088 -10000 0 -0.24 38 38
endothelial cell migration 0.042 0.028 -10000 0 -0.22 1 1
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.001 0.044 -10000 0 -10000 0 0
PAK1 -0.012 0.065 0.19 21 -0.22 15 36
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS 0.01 0.054 0.18 24 -0.23 11 35
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.005 0.08 0.19 16 -0.23 45 61
lamellipodium assembly -0.02 0.05 -10000 0 -0.22 26 26
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.074 -10000 0 -0.24 31 31
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPHB2 0.017 0.04 -10000 0 -0.22 10 10
EPHB3 0.025 0.011 -10000 0 -0.13 2 2
EPHB1 -0.009 0.12 -10000 0 -0.43 39 39
EPHB4 0.021 0.011 -10000 0 -10000 0 0
mol:GDP -0.002 0.057 0.23 3 -0.3 7 10
Ephrin B/EPHB2 0.042 0.053 -10000 0 -0.23 14 14
Ephrin B/EPHB3 0.052 0.045 -10000 0 -0.23 11 11
JNK cascade -0.003 0.078 0.22 15 -0.23 40 55
Ephrin B/EPHB1 0.031 0.089 -10000 0 -0.24 45 45
RAP1/GDP 0.044 0.095 0.23 64 -0.28 8 72
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EFNB3 0.016 0.064 -10000 0 -0.36 13 13
EFNB1 0.025 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.017 0.082 -10000 0 -0.25 41 41
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.077 -10000 0 -0.24 28 28
Rap1/GTP -0.001 0.073 -10000 0 -0.22 44 44
axon guidance -0.007 0.088 -10000 0 -0.26 49 49
MAPK3 0.001 0.066 0.19 1 -0.28 10 11
MAPK1 0.002 0.065 0.19 1 -0.28 10 11
Rac1/GDP 0.024 0.084 0.23 40 -0.28 8 48
actin cytoskeleton reorganization -0.004 0.047 -10000 0 -0.25 9 9
CDC42/GDP 0.04 0.098 0.23 71 -0.28 8 79
PI3K 0.046 0.03 -10000 0 -0.22 1 1
EFNA5 -0.029 0.14 -10000 0 -0.43 48 48
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.045 -10000 0 -0.29 8 8
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.07 -10000 0 -0.22 43 43
PTK2 0.054 0.16 0.54 52 -10000 0 52
MAP4K4 -0.003 0.079 0.22 15 -0.23 40 55
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.02 0.038 -10000 0 -0.17 16 16
Intersectin/N-WASP 0.03 0.017 -10000 0 -10000 0 0
neuron projection morphogenesis 0.031 0.12 0.3 69 -0.32 5 74
MAP2K1 0.005 0.069 -10000 0 -0.23 30 30
WASL 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.03 0.086 -10000 0 -0.25 40 40
cell migration 0.004 0.087 0.3 2 -0.3 16 18
NRAS 0.021 0.01 -10000 0 -10000 0 0
SYNJ1 0.012 0.056 0.18 26 -0.22 13 39
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.022 0.075 0.17 20 -0.22 45 65
HRAS/GTP 0.016 0.082 -10000 0 -0.22 44 44
Ephrin B1/EPHB1-2 0.018 0.08 -10000 0 -0.24 40 40
cell adhesion mediated by integrin 0.002 0.048 0.21 11 -0.19 16 27
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0.02 0.087 0.17 1 -0.23 45 46
RAC1-CDC42/GTP -0.004 0.059 -10000 0 -0.22 28 28
RASA1 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.08 0.23 35 -0.27 8 43
ruffle organization 0.039 0.13 0.35 52 -0.35 5 57
NCK1 0.025 0.02 -10000 0 -0.43 1 1
receptor internalization -0.025 0.075 0.17 20 -0.23 37 57
Ephrin B/EPHB2/KALRN 0.053 0.061 -10000 0 -0.24 14 14
ROCK1 0.02 0.031 0.18 17 -10000 0 17
RAS family/GDP -0.007 0.044 -10000 0 -0.28 7 7
Rac1/GTP -0.001 0.058 -10000 0 -0.23 26 26
Ephrin B/EPHB1/Src/Paxillin 0.006 0.074 -10000 0 -0.24 39 39
Regulation of nuclear SMAD2/3 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
EP300 0.017 0.048 -10000 0 -0.43 4 4
HSPA8 0.023 0.022 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.017 0.091 0.21 2 -0.27 19 21
AKT1 0.015 0.034 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 69 69
NKX2-5 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.062 0.17 0.37 98 -10000 0 98
SMAD2-3/SMAD4/SP1 0.02 0.12 -10000 0 -0.3 25 25
SMAD4 -0.009 0.069 -10000 0 -0.23 13 13
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.028 0.08 -10000 0 -0.26 23 23
SMAD3/SMAD4/VDR 0.037 0.11 -10000 0 -0.28 19 19
MYC 0.009 0.087 -10000 0 -0.41 20 20
CDKN2B -0.18 0.49 -10000 0 -1.5 59 59
AP1 0.001 0.092 -10000 0 -0.26 29 29
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.004 0.083 -10000 0 -0.32 16 16
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.038 0.14 -10000 0 -0.38 61 61
SP3 0.027 0.01 -10000 0 -10000 0 0
CREB1 0.026 0.002 -10000 0 -10000 0 0
FOXH1 -0.003 0.076 -10000 0 -0.24 29 29
SMAD3/SMAD4/GR 0.038 0.084 0.21 4 -0.23 7 11
GATA3 -0.053 0.14 -10000 0 -0.4 62 62
SKI/SIN3/HDAC complex/NCoR1 0.014 0.061 -10000 0 -0.3 15 15
MEF2C/TIF2 -0.02 0.13 0.31 3 -0.32 33 36
endothelial cell migration 0.16 0.46 1.3 73 -10000 0 73
MAX 0.032 0.019 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
RUNX2 0.017 0.057 -10000 0 -0.25 18 18
RUNX3 -0.001 0.091 -10000 0 -0.43 20 20
RUNX1 -0.007 0.1 -10000 0 -0.24 62 62
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.033 0.019 -10000 0 -10000 0 0
VDR -0.014 0.11 -10000 0 -0.43 31 31
CDKN1A -0.041 0.25 -10000 0 -1.3 20 20
KAT2B 0.021 0.018 -10000 0 -0.13 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.011 0.13 -10000 0 -0.3 71 71
DCP1A 0.026 0.004 -10000 0 -10000 0 0
SKI 0.022 0.01 -10000 0 -10000 0 0
SERPINE1 -0.17 0.47 -10000 0 -1.3 73 73
SMAD3/SMAD4/ATF2 0.019 0.086 -10000 0 -0.25 18 18
SMAD3/SMAD4/ATF3 0.014 0.091 -10000 0 -0.28 16 16
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.061 0.2 4 -0.26 4 8
JUN -0.014 0.082 -10000 0 -0.27 25 25
SMAD3/SMAD4/IRF7 0.019 0.084 -10000 0 -0.26 12 12
TFE3 0.014 0.035 -10000 0 -10000 0 0
COL1A2 0.005 0.093 -10000 0 -0.88 5 5
mesenchymal cell differentiation -0.02 0.087 0.26 17 -10000 0 17
DLX1 -0.066 0.16 -10000 0 -0.28 157 157
TCF3 0.023 0.029 -10000 0 -0.43 2 2
FOS -0.03 0.14 -10000 0 -0.39 57 57
SMAD3/SMAD4/Max 0.038 0.084 0.21 2 -0.25 6 8
Cbp/p300/SNIP1 0.036 0.043 -10000 0 -0.26 4 4
ZBTB17 0.023 0.014 -10000 0 -10000 0 0
LAMC1 -0.01 0.061 0.21 1 -0.31 2 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.082 -10000 0 -0.3 10 10
IRF7 0.016 0.052 -10000 0 -0.21 20 20
ESR1 0.009 0.071 -10000 0 -0.39 13 13
HNF4A -0.007 0.042 -10000 0 -0.13 40 40
MEF2C -0.01 0.12 0.28 5 -0.31 36 41
SMAD2-3/SMAD4 0.008 0.1 -10000 0 -0.26 25 25
Cbp/p300/Src-1 0.042 0.049 -10000 0 -0.26 4 4
IGHV3OR16-13 0.001 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.02 0.045 -10000 0 -0.43 5 5
CREBBP 0.021 0.023 -10000 0 -10000 0 0
SKIL 0.021 0.049 -10000 0 -0.43 6 6
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
SNIP1 0.022 0.011 -10000 0 -10000 0 0
GCN5L2 0 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.083 -10000 0 -0.23 8 8
MSG1/HSC70 0.015 0.072 -10000 0 -0.3 20 20
SMAD2 0 0.059 -10000 0 -0.18 15 15
SMAD3 0.006 0.056 -10000 0 -0.21 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.06 -10000 0 -0.26 13 13
SMAD2/SMAD2/SMAD4 -0.005 0.044 0.18 1 -0.21 3 4
NCOR1 0.024 0.028 -10000 0 -0.43 2 2
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA1 0.026 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.045 0.13 -10000 0 -0.3 91 91
SMAD2-3/SMAD4/SP1/MIZ-1 0.019 0.12 -10000 0 -0.29 26 26
IFNB1 -0.01 0.06 0.19 1 -0.3 5 6
SMAD3/SMAD4/MEF2C 0.005 0.13 -10000 0 -0.32 32 32
CITED1 -0.001 0.092 -10000 0 -0.43 19 19
SMAD2-3/SMAD4/ARC105 0.022 0.1 -10000 0 -0.24 20 20
RBL1 0.012 0.077 -10000 0 -0.43 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.049 0.19 -10000 0 -0.55 58 58
RUNX1-3/PEBPB2 0.02 0.086 -10000 0 -0.24 48 48
SMAD7 -0.017 0.11 -10000 0 -0.42 13 13
MYC/MIZ-1 0.02 0.067 0.18 8 -0.29 18 26
SMAD3/SMAD4 -0.024 0.18 0.28 38 -0.44 66 104
IL10 -0.062 0.19 0.25 3 -0.5 63 66
PIASy/HDAC complex 0.021 0.023 -10000 0 -10000 0 0
PIAS3 0.02 0.017 -10000 0 -10000 0 0
CDK2 0.015 0.049 -10000 0 -0.23 12 12
IL5 -0.039 0.13 0.21 22 -0.3 65 87
CDK4 0.02 0.024 -10000 0 -10000 0 0
PIAS4 0.022 0.023 -10000 0 -10000 0 0
ATF3 0.006 0.072 -10000 0 -0.43 9 9
SMAD3/SMAD4/SP1 0.024 0.099 -10000 0 -0.31 11 11
FOXG1 -0.001 0.11 -10000 0 -0.43 30 30
FOXO3 0.002 0.037 -10000 0 -0.14 1 1
FOXO1 0.002 0.038 -10000 0 -0.3 1 1
FOXO4 0.001 0.041 -10000 0 -0.19 5 5
heart looping -0.01 0.12 0.28 5 -0.3 36 41
CEBPB 0.007 0.076 -10000 0 -0.44 13 13
SMAD3/SMAD4/DLX1 -0.026 0.14 -10000 0 -0.28 86 86
MYOD1 -0.09 0.17 -10000 0 -0.3 167 167
SMAD3/SMAD4/HNF4 0.021 0.079 -10000 0 -0.22 12 12
SMAD3/SMAD4/GATA3 -0.026 0.15 -10000 0 -0.32 83 83
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.049 -10000 0 -0.43 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.11 -10000 0 -0.25 38 38
SMAD3/SMAD4/SP1-3 0.042 0.096 -10000 0 -0.28 11 11
MED15 0.026 0.004 -10000 0 -10000 0 0
SP1 0.013 0.038 -10000 0 -0.23 1 1
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.006 0.12 -10000 0 -0.27 72 72
ITGB5 -0.007 0.08 -10000 0 -0.44 7 7
TGIF/SIN3/HDAC complex/CtBP 0.012 0.074 -10000 0 -0.46 10 10
SMAD3/SMAD4/AR -0.019 0.13 -10000 0 -0.29 76 76
AR -0.047 0.16 -10000 0 -0.43 71 71
negative regulation of cell growth -0.002 0.094 -10000 0 -0.39 17 17
SMAD3/SMAD4/MYOD -0.037 0.14 -10000 0 -0.29 101 101
E2F5 0.023 0.029 -10000 0 -0.43 2 2
E2F4 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.25 48 48
SMAD2-3/SMAD4/FOXO1-3a-4 -0.029 0.14 -10000 0 -0.4 54 54
TFDP1 0.025 0.021 -10000 0 -0.43 1 1
SMAD3/SMAD4/AP1 0.022 0.1 -10000 0 -0.27 25 25
SMAD3/SMAD4/RUNX2 0.021 0.087 -10000 0 -0.26 17 17
TGIF2 0.021 0.045 -10000 0 -0.43 5 5
TGIF1 0.016 0.06 -10000 0 -0.27 17 17
ATF2 0.016 0.069 -10000 0 -0.43 12 12
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.052 0.2 30 -0.2 2 32
RFC1 0 0.037 0.18 18 -0.2 2 20
PRKDC 0.007 0.054 0.2 35 -0.2 2 37
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP7 -0.016 0.14 -10000 0 -0.57 29 29
FASLG/FAS/FADD/FAF1 0.004 0.054 0.19 14 -0.26 8 22
MAP2K4 -0.028 0.11 0.22 1 -0.32 40 41
mol:ceramide 0.003 0.068 -10000 0 -0.26 19 19
GSN -0.001 0.062 0.19 26 -0.3 9 35
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.054 -10000 0 -0.27 5 5
FAS 0.011 0.064 -10000 0 -0.3 16 16
BID -0.01 0.052 0.26 17 -10000 0 17
MAP3K1 -0.024 0.11 0.22 1 -0.35 33 34
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
RB1 0.001 0.039 0.18 19 -0.2 2 21
CFLAR 0.026 0.008 -10000 0 -0.13 1 1
HGF/MET -0.006 0.12 -10000 0 -0.24 85 85
ARHGDIB 0.006 0.052 0.2 32 -0.22 1 33
FADD 0.022 0.014 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.066 0.24 19 -0.19 26 45
NFKB1 -0.011 0.12 -10000 0 -0.74 11 11
MAPK8 -0.045 0.15 -10000 0 -0.46 44 44
DFFA 0 0.034 0.17 16 -0.2 2 18
DNA fragmentation during apoptosis -0.003 0.045 0.18 17 -0.18 12 29
FAS/FADD/MET -0.004 0.1 -10000 0 -0.28 52 52
CFLAR/RIP1 0.039 0.009 -10000 0 -10000 0 0
FAIM3 0.004 0.088 -10000 0 -0.27 39 39
FAF1 0.019 0.016 -10000 0 -10000 0 0
PARP1 0.001 0.039 0.18 19 -0.2 2 21
DFFB 0 0.034 0.17 16 -0.2 2 18
CHUK -0.012 0.12 -10000 0 -0.7 11 11
FASLG 0.007 0.04 -10000 0 -0.13 32 32
FAS/FADD 0.024 0.049 -10000 0 -0.31 8 8
HGF -0.009 0.091 -10000 0 -0.2 69 69
LMNA -0.001 0.047 0.2 12 -0.21 1 13
CASP6 0 0.041 0.18 20 -0.22 3 23
CASP10 0.022 0.015 -10000 0 -0.13 1 1
CASP3 0.003 0.046 0.22 18 -0.22 2 20
PTPN13 0.022 0.041 -10000 0 -0.37 5 5
CASP8 -0.01 0.066 0.34 17 -10000 0 17
IL6 -0.099 0.36 -10000 0 -1.2 46 46
MET -0.047 0.14 -10000 0 -0.43 52 52
ICAD/CAD 0.001 0.044 0.2 18 -0.18 2 20
FASLG/FAS/FADD/FAF1/Caspase 10 0.003 0.069 -10000 0 -0.26 19 19
activation of caspase activity by cytochrome c -0.01 0.051 0.26 17 -10000 0 17
PAK2 0.002 0.041 0.18 22 -0.22 1 23
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Wnt signaling

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
Noncanonical Wnts/FZD -0.007 0.087 -9999 0 -0.27 44 44
FZD6 0.015 0.04 -9999 0 -0.14 27 27
WNT6 0.003 0.087 -9999 0 -0.43 17 17
WNT4 0.008 0.057 -9999 0 -0.18 35 35
FZD3 0.023 0.035 -9999 0 -0.43 3 3
WNT5A 0.01 0.078 -9999 0 -0.33 22 22
WNT11 0.009 0.075 -9999 0 -0.43 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0.026 0.004 -9999 0 -10000 0 0
SVIL 0.015 0.042 -9999 0 -0.16 23 23
ZNF318 0.026 0.003 -9999 0 -10000 0 0
JMJD2C 0 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.02 0.11 -9999 0 -0.26 75 75
CARM1 0.025 0.006 -9999 0 -10000 0 0
PRDX1 0.012 0.066 -9999 0 -0.43 11 11
PELP1 0.026 0.002 -9999 0 -10000 0 0
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
AKT1 0.025 0.005 -9999 0 -10000 0 0
PTK2B 0.018 0.032 -9999 0 -0.13 22 22
MED1 0.026 0.003 -9999 0 -10000 0 0
MAK 0.007 0.063 -9999 0 -0.16 51 51
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.011 0.069 -9999 0 -0.43 12 12
GSN 0.017 0.06 -9999 0 -0.37 11 11
NCOA2 -0.005 0.11 -9999 0 -0.43 34 34
NCOA6 0.025 0.005 -9999 0 -10000 0 0
DNA-PK 0.05 0.014 -9999 0 -10000 0 0
NCOA4 0.025 0.005 -9999 0 -10000 0 0
PIAS3 0.023 0.008 -9999 0 -10000 0 0
cell proliferation -0.005 0.079 -9999 0 -0.52 10 10
XRCC5 0.026 0.003 -9999 0 -10000 0 0
UBE3A 0.026 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.03 0.12 -9999 0 -0.27 89 89
FHL2 -0.02 0.16 -9999 0 -0.98 12 12
RANBP9 0.026 0.003 -9999 0 -10000 0 0
JMJD1A -0.009 0.038 -9999 0 -0.13 42 42
CDK6 0.004 0.083 -9999 0 -0.43 17 17
TGFB1I1 0.022 0.038 -9999 0 -0.43 3 3
T-DHT/AR/CyclinD1 -0.029 0.12 -9999 0 -0.27 86 86
XRCC6 0.026 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.026 0.12 -9999 0 -0.25 106 106
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
BRCA1 0.025 0.012 -9999 0 -0.13 3 3
TCF4 0.025 0.02 -9999 0 -0.43 1 1
CDKN2A -0.012 0.11 -9999 0 -0.3 55 55
SRF 0.024 0.027 -9999 0 -10000 0 0
NKX3-1 -0.035 0.077 -9999 0 -0.17 104 104
KLK3 0.003 0.046 -9999 0 -10000 0 0
TMF1 0.025 0.02 -9999 0 -0.43 1 1
HNRNPA1 0.026 0.004 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.024 0.11 -9999 0 -0.26 80 80
AR -0.056 0.16 -9999 0 -0.41 80 80
UBA3 0.026 0.004 -9999 0 -10000 0 0
PATZ1 0.026 0.004 -9999 0 -10000 0 0
PAWR 0.003 0.087 -9999 0 -0.25 44 44
PRKDC 0.025 0.005 -9999 0 -10000 0 0
PA2G4 0.026 0.003 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.099 -9999 0 -0.24 76 76
RPS6KA3 0.025 0.02 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.021 0.11 -9999 0 -0.26 77 77
LATS2 0.018 0.046 -9999 0 -0.43 4 4
T-DHT/AR/PRX1 -0.026 0.1 -9999 0 -0.24 86 86
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -10000 0 0
VAV3 -0.031 0.11 -9999 0 -0.2 115 115
KLK2 -0.044 0.12 -9999 0 -0.43 36 36
CASP8 0.021 0.033 -9999 0 -0.15 15 15
T-DHT/AR/TIF2/CARM1 -0.017 0.12 -9999 0 -0.27 86 86
TMPRSS2 -0.082 0.25 -9999 0 -0.89 43 43
CCND1 0.011 0.07 -9999 0 -0.26 25 25
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
mol:T-DHT -0.006 0.019 -9999 0 -0.065 41 41
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.025 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.029 0.12 -9999 0 -0.28 79 79
CMTM2 0.013 0.073 -9999 0 -0.33 19 19
SNURF 0.011 0.079 -9999 0 -0.4 18 18
ZMIZ1 0.016 0.029 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -10000 0 0
TGIF1 0.016 0.06 -9999 0 -0.27 17 17
FKBP4 0.024 0.007 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.086 -10000 0 -0.29 41 41
CRKL 0.025 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.26 61 61
alpha4/beta7 Integrin/MAdCAM1 0.01 0.12 -10000 0 -0.25 80 80
EPO 0.013 0.03 -10000 0 -0.18 7 7
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.012 0.077 -10000 0 -0.29 26 26
EPO/EPOR (dimer) 0.027 0.025 -10000 0 -0.3 1 1
lamellipodium assembly 0.014 0.035 -10000 0 -0.26 4 4
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.006 0.051 -10000 0 -0.22 22 22
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
MADCAM1 -0.034 0.13 -10000 0 -0.43 42 42
cell adhesion 0.008 0.12 -10000 0 -0.25 80 80
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
ITGB1 0.023 0.012 -10000 0 -10000 0 0
SRC -0.024 0.099 0.18 29 -0.24 67 96
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.009 0.11 -10000 0 -0.26 74 74
p130Cas/Crk/Dock1 -0.007 0.099 0.35 1 -0.26 11 12
VCAM1 -0.033 0.13 -10000 0 -0.43 48 48
RHOA 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.046 0.066 -10000 0 -0.23 23 23
BCAR1 -0.034 0.092 0.19 28 -0.23 67 95
EPOR 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.036 -10000 0 -0.27 4 4
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.053 0.19 1 -0.29 3 4
adherens junction organization -0.019 0.09 -10000 0 -0.25 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.082 -10000 0 -0.29 8 8
FMN1 -0.032 0.11 -10000 0 -0.27 60 60
mol:IP3 0.004 0.052 -10000 0 -0.23 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.09 -10000 0 -0.24 56 56
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.008 0.064 0.18 2 -0.27 4 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.36 55 55
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.083 -10000 0 -0.23 55 55
VASP -0.011 0.081 -10000 0 -0.24 40 40
ZYX -0.012 0.078 -10000 0 -0.24 48 48
JUB -0.009 0.085 -10000 0 -0.23 56 56
EGFR(dimer) -0.017 0.1 -10000 0 -0.25 56 56
E-cadherin/beta catenin-gamma catenin -0.001 0.1 -10000 0 -0.25 63 63
mol:PI-3-4-5-P3 0.024 0.074 0.21 2 -0.28 4 6
PIK3CA 0.026 0.02 -10000 0 -0.41 1 1
PI3K 0.024 0.075 0.21 2 -0.29 4 6
FYN 0.002 0.05 -10000 0 -0.26 4 4
mol:Ca2+ 0.004 0.052 -10000 0 -0.23 4 4
JUP 0.021 0.05 -10000 0 -0.38 7 7
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG 0.004 0.052 -10000 0 -0.23 4 4
CDH1 -0.046 0.15 -10000 0 -0.28 118 118
RhoA/GDP 0.011 0.094 0.23 3 -0.29 8 11
establishment of polarity of embryonic epithelium -0.011 0.08 -10000 0 -0.23 40 40
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.43 42 42
CASR -0.005 0.049 -10000 0 -0.3 1 1
RhoA/GTP 0.016 0.053 -10000 0 -0.3 1 1
AKT2 0.01 0.056 0.18 2 -0.26 4 6
actin cable formation -0.03 0.098 0.18 1 -0.28 45 46
apoptosis -0.003 0.064 0.28 5 -0.2 4 9
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.017 0.076 -10000 0 -0.3 9 9
PIP5K1A -0.01 0.084 -10000 0 -0.23 55 55
PLCG1 0.004 0.053 -10000 0 -0.24 4 4
Rac1/GTP -0.007 0.1 -10000 0 -0.33 12 12
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.04 -10000 0 -0.43 4 4
ANTXR2 0.021 0.035 -10000 0 -0.43 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.006 -10000 0 -0.058 6 6
monocyte activation -0.13 0.23 -10000 0 -0.42 176 176
MAP2K2 0.013 0.039 -10000 0 -0.61 2 2
MAP2K1 -0.003 0.007 -10000 0 -0.11 1 1
MAP2K7 -0.003 0.006 -10000 0 -10000 0 0
MAP2K6 -0.003 0.011 -10000 0 -0.22 1 1
CYAA -0.007 0.023 -10000 0 -0.21 6 6
MAP2K4 -0.003 0.008 -10000 0 -0.11 2 2
IL1B -0.043 0.079 0.17 2 -0.22 76 78
Channel 0.028 0.031 -10000 0 -0.23 6 6
NLRP1 -0.004 0.014 -10000 0 -0.22 2 2
CALM1 0.025 0.009 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.078 -10000 0 -0.39 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.006 0.058 6 -10000 0 6
MAPK3 -0.003 0.006 -10000 0 -10000 0 0
MAPK1 -0.003 0.006 -10000 0 -10000 0 0
PGR -0.022 0.061 -10000 0 -0.22 46 46
PA/Cellular Receptors 0.029 0.034 -10000 0 -0.25 6 6
apoptosis -0.001 0.006 -10000 0 -0.058 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.027 -10000 0 -0.22 6 6
macrophage activation -0.005 0.005 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.26 151 151
VCAM1 -0.13 0.23 -10000 0 -0.43 174 174
platelet activation -0.004 0.078 -10000 0 -0.39 20 20
MAPKKK cascade -0.005 0.024 0.091 1 -0.077 41 42
IL18 -0.012 0.051 0.16 3 -0.23 21 24
negative regulation of macrophage activation -0.001 0.006 -10000 0 -0.058 6 6
LEF -0.001 0.006 -10000 0 -0.058 6 6
CASP1 -0.001 0.018 -10000 0 -0.098 12 12
mol:cAMP -0.005 0.079 -10000 0 -0.39 20 20
necrosis -0.001 0.006 -10000 0 -0.058 6 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.028 0.029 -10000 0 -0.21 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.032 0.13 -10000 0 -0.49 18 18
UGCG -0.018 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.037 0.15 0.23 2 -0.4 38 40
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.018 0.14 -10000 0 -0.66 23 23
mol:DAG -0.016 0.16 -10000 0 -0.82 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.15 0.25 1 -0.42 36 37
FRAP1 -0.028 0.17 0.27 2 -0.47 38 40
FOXO3 -0.027 0.15 0.27 2 -0.42 42 44
AKT1 -0.029 0.16 0.28 1 -0.45 42 43
GAB2 0.025 0.006 -10000 0 -10000 0 0
SMPD1 -0.013 0.12 -10000 0 -0.58 21 21
SGMS1 -0.008 0.11 -10000 0 -0.56 18 18
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 0.005 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
cell proliferation -0.011 0.14 0.25 3 -0.4 27 30
EIF3A 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.012 -10000 0 -10000 0 0
RPS6KB1 0.002 0.076 -10000 0 -1.1 1 1
mol:sphingomyelin -0.016 0.16 -10000 0 -0.82 18 18
natural killer cell activation 0 0.002 -10000 0 -0.011 16 16
JAK3 -0.008 0.1 -10000 0 -0.24 65 65
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.023 0.011 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.025 0.24 0.35 3 -0.88 26 29
MYB -0.075 0.33 -10000 0 -1.1 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.027 0.14 -10000 0 -0.37 41 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.078 -10000 0 -1 1 1
mol:PI-3-4-5-P3 -0.026 0.13 -10000 0 -0.36 41 41
Rac1/GDP 0.019 0.013 -10000 0 -10000 0 0
T cell proliferation -0.018 0.12 0.22 1 -0.36 34 35
SHC1 0.024 0.015 -10000 0 -0.13 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.018 -10000 0 -0.064 38 38
PRKCZ -0.015 0.12 0.22 1 -0.38 31 32
NF kappa B1 p50/RelA -0.009 0.15 0.27 2 -0.42 35 37
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.033 0.14 -10000 0 -0.42 44 44
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
IL2RA -0.007 0.072 -10000 0 -0.17 67 67
IL2RB -0.027 0.13 -10000 0 -0.24 101 101
TERT -0.042 0.13 -10000 0 -0.32 74 74
E2F1 -0.014 0.13 -10000 0 -0.45 42 42
SOS1 0.026 0.004 -10000 0 -10000 0 0
RPS6 0.024 0.01 -10000 0 -0.13 1 1
mol:cAMP 0.001 0.009 0.031 38 -10000 0 38
PTPN11 0.025 0.008 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.41 17 17
actin cytoskeleton organization -0.018 0.12 0.22 1 -0.36 34 35
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL2 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.021 -10000 0 -0.43 1 1
Rac1/GTP 0.041 0.025 -10000 0 -10000 0 0
LCK -0.019 0.11 -10000 0 -0.43 30 30
BCL2 -0.023 0.16 -10000 0 -0.57 22 22
Canonical Wnt signaling 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
HDAC1 0.024 0.024 0.19 4 -10000 0 4
AES 0.026 0.019 0.17 3 -10000 0 3
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
SMAD4 0.026 0.004 -10000 0 -10000 0 0
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
TLE1 0.025 0.035 0.18 4 -0.43 2 6
MACF1 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.044 0.099 0.28 29 -0.31 4 33
WIF1 -0.13 0.18 -10000 0 -0.43 121 121
beta catenin/RanBP3 0.016 0.1 0.4 27 -0.3 1 28
KREMEN2 -0.007 0.1 -10000 0 -0.43 23 23
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.053 0.097 0.28 27 -0.28 4 31
FZD1 0.021 0.01 -10000 0 -10000 0 0
AXIN2 0.003 0.16 0.58 18 -0.89 5 23
AXIN1 0.027 0.002 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.075 -10000 0 -0.55 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.09 0.3 15 -0.58 3 18
Axin1/APC/GSK3 0.03 0.073 0.25 12 -0.29 1 13
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.075 0.28 6 -0.42 2 8
HNF1A 0.027 0.029 0.19 4 -0.43 1 5
CTBP1 0.027 0.021 0.19 4 -10000 0 4
MYC 0.008 0.36 0.55 62 -1.5 21 83
RANBP3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.005 0.11 -10000 0 -0.27 67 67
NKD1 0.016 0.059 -10000 0 -0.28 16 16
TCF4 0.026 0.027 0.18 4 -0.38 1 5
TCF3 0.025 0.031 0.18 3 -0.37 2 5
WNT1/LRP6/FZD1/Axin1 0.052 0.03 -10000 0 -10000 0 0
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.13 0.5 29 -0.36 1 30
LEF1 0.026 0.026 0.18 4 -10000 0 4
DVL1 0.027 0.037 -10000 0 -0.26 1 1
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.062 0.11 0.3 16 -0.73 3 19
DKK1/LRP6/Kremen 2 0.002 0.11 -10000 0 -0.25 71 71
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.028 0.022 0.19 4 -10000 0 4
NLK 0.024 0.013 -10000 0 -0.16 1 1
CCND1 -0.018 0.25 0.56 19 -1.5 11 30
WNT1 0.01 0.04 -10000 0 -10000 0 0
GSK3A 0.022 0.01 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.28 4 4
PPP2R5D 0.027 0.055 0.28 8 -0.25 2 10
APC 0.038 0.079 0.19 101 -10000 0 101
WNT1/LRP6/FZD1 0.042 0.079 0.2 75 -0.21 1 76
CREBBP 0.028 0.021 0.19 4 -10000 0 4
TCGA08_rtk_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
PDGFRA -0.022 0.14 -10000 0 -0.41 55 55
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.43 42 42
AKT 0.038 0.11 0.27 47 -0.24 8 55
FOXO3 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.022 -10000 0 -0.43 1 1
AKT3 0.022 0.04 -10000 0 -0.43 4 4
FOXO4 0.025 0.02 -10000 0 -0.43 1 1
MET -0.047 0.14 -10000 0 -0.43 52 52
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
PIK3CG -0.01 0.1 -10000 0 -0.27 53 53
PIK3R3 0.02 0.024 -10000 0 -0.23 3 3
PIK3R2 0.025 0.005 -10000 0 -10000 0 0
NF1 0.025 0.02 -10000 0 -0.43 1 1
RAS -0.008 0.07 0.16 3 -0.15 73 76
ERBB2 0.023 0.027 -10000 0 -0.43 1 1
proliferation/survival/translation -0.025 0.081 0.33 14 -0.22 12 26
PI3K 0.021 0.11 0.25 61 -0.15 53 114
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
FOXO 0.061 0.087 0.22 78 -10000 0 78
AKT2 0.022 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.025 0.008 -10000 0 -0.13 1 1
RAS family/GTP/Tiam1 0.016 0.023 -10000 0 -0.26 2 2
NT3 (dimer)/TRKC 0.028 0.033 -10000 0 -0.34 2 2
NT3 (dimer)/TRKB 0.01 0.098 -10000 0 -0.26 55 55
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.026 -10000 0 -0.48 1 1
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.43 14 14
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
NTRK1 0.016 0.055 -10000 0 -0.43 6 6
NTRK2 0.006 0.092 -10000 0 -0.43 22 22
NTRK3 0.022 0.04 -10000 0 -0.43 4 4
NT-4/5 (dimer)/TRKB 0.004 0.093 -10000 0 -0.25 54 54
neuron apoptosis 0.057 0.15 0.36 80 -10000 0 80
SHC 2-3/Grb2 -0.062 0.16 -10000 0 -0.38 80 80
SHC1 0.024 0.014 -10000 0 -0.13 4 4
SHC2 -0.029 0.1 -10000 0 -0.36 19 19
SHC3 -0.099 0.21 -10000 0 -0.5 91 91
STAT3 (dimer) 0.021 0.055 -10000 0 -0.33 11 11
NT3 (dimer)/TRKA 0.018 0.087 -10000 0 -0.25 46 46
RIN/GDP -0.004 0.081 0.23 6 -0.3 2 8
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
KRAS 0.025 0.005 -10000 0 -10000 0 0
DNAJA3 -0.047 0.099 -10000 0 -0.26 76 76
RIN/GTP -0.072 0.13 -10000 0 -0.3 119 119
CCND1 0.002 0.11 0.2 4 -0.7 11 15
MAGED1 0.026 0.002 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.16 12 12
SHC/GRB2/SOS1 0.05 0.014 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.014 0.12 -10000 0 -0.28 83 83
TRKA/NEDD4-2 0.025 0.054 -10000 0 -0.31 10 10
ELMO1 0.017 0.049 -10000 0 -0.43 6 6
RhoG/GTP/ELMO1/DOCK1 0.024 0.038 -10000 0 -0.25 8 8
NGF -0.025 0.13 -10000 0 -0.35 63 63
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
GAB2 0.025 0.005 -10000 0 -10000 0 0
RIT2 -0.11 0.19 -10000 0 -0.43 119 119
RIT1 0.026 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.032 0.1 -10000 0 -0.25 71 71
mol:GDP 0.03 0.073 0.28 7 -0.62 1 8
NGF (dimer) -0.025 0.13 -10000 0 -0.35 63 63
RhoG/GDP 0.013 0.035 -10000 0 -0.3 6 6
RIT1/GDP 0.027 0.053 0.2 4 -0.37 1 5
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.03 0.083 -10000 0 -0.26 36 36
KIDINS220/CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.024 -10000 0 -0.24 1 1
RIT1/GTP 0.019 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.032 -10000 0 -0.13 17 17
RAP1/GDP 0.023 0.04 -10000 0 -0.31 1 1
KIDINS220/CRKL 0.025 0.008 -10000 0 -0.13 1 1
BDNF (dimer) -0.01 0.089 -10000 0 -0.43 14 14
ubiquitin-dependent protein catabolic process -0.001 0.098 -10000 0 -0.25 59 59
Schwann cell development -0.014 0.019 -10000 0 -10000 0 0
EHD4 0.024 0.019 -10000 0 -0.13 7 7
FRS2 family/GRB2/SOS1 0.063 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.03 -10000 0 -0.42 1 1
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.016 0.069 -10000 0 -0.22 27 27
ABL1 0.025 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.089 -10000 0 -0.32 9 9
STAT3 0.021 0.055 -10000 0 -0.33 11 11
axon guidance -0.002 0.064 -10000 0 -0.22 27 27
MAPK3 -0.037 0.11 0.18 11 -0.26 78 89
MAPK1 -0.036 0.11 0.18 11 -0.26 77 88
CDC42/GDP 0.032 0.052 0.22 6 -0.37 1 7
NTF3 0.006 0.032 -10000 0 -0.13 17 17
NTF4 -0.003 0.033 -10000 0 -0.16 12 12
NGF (dimer)/TRKA/FAIM 0.008 0.096 -10000 0 -0.26 55 55
PI3K 0.038 0.007 -10000 0 -10000 0 0
FRS3 0.026 0.002 -10000 0 -10000 0 0
FAIM 0.022 0.04 -10000 0 -0.43 4 4
GAB1 0.025 0.02 -10000 0 -0.43 1 1
RASGRF1 -0.069 0.12 -10000 0 -0.25 120 120
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L 0.002 0.028 -10000 0 -0.28 3 3
RGS19 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.069 -10000 0 -0.61 2 2
Rac1/GDP 0.025 0.053 0.22 5 -0.36 1 6
NGF (dimer)/TRKA/GRIT -0.008 0.088 -10000 0 -0.25 53 53
neuron projection morphogenesis -0.029 0.12 0.35 1 -0.53 7 8
NGF (dimer)/TRKA/NEDD4-2 0.006 0.098 -10000 0 -0.25 59 59
MAP2K1 0.024 0.05 0.2 35 -0.23 1 36
NGFR -0.017 0.12 -10000 0 -0.28 72 72
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.096 -10000 0 -0.24 73 73
RAS family/GTP/PI3K 0.019 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.072 0.022 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
MAPKKK cascade -0.11 0.23 -10000 0 -0.47 138 138
RASA1 0.026 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.042 -10000 0 -0.3 6 6
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.043 0.075 -10000 0 -0.25 27 27
NGF (dimer)/TRKA/p62/Atypical PKCs 0.022 0.1 -10000 0 -0.24 58 58
MATK -0.027 0.13 -10000 0 -0.43 46 46
NEDD4L 0.02 0.044 -10000 0 -0.23 12 12
RAS family/GDP -0.006 0.02 -10000 0 -0.28 1 1
NGF (dimer)/TRKA -0.035 0.1 -10000 0 -0.26 78 78
Rac1/GTP -0.04 0.077 -10000 0 -0.22 44 44
FRS2 family/SHP2/CRK family 0.074 0.018 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.015 0.048 0.16 1 -0.25 13 14
EPHB2 0.017 0.04 -10000 0 -0.22 10 10
Syndecan-2/TACI 0.012 0.046 -10000 0 -0.24 14 14
LAMA1 -0.024 0.14 -10000 0 -0.37 64 64
Syndecan-2/alpha2 ITGB1 0.021 0.093 -10000 0 -0.26 43 43
HRAS 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.041 -10000 0 -0.25 13 13
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
BAX -0.001 0.037 -10000 0 -10000 0 0
EPB41 0.021 0.023 -10000 0 -0.43 1 1
positive regulation of cell-cell adhesion 0.016 0.04 -10000 0 -0.22 13 13
LAMA3 -0.004 0.1 -10000 0 -0.43 26 26
EZR 0.017 0.06 -10000 0 -0.43 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.041 -10000 0 -0.43 2 2
Syndecan-2/MMP2 0.01 0.06 -10000 0 -0.25 23 23
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.068 -10000 0 -0.3 19 19
dendrite morphogenesis 0.011 0.049 -10000 0 -0.24 17 17
Syndecan-2/GM-CSF 0.011 0.044 -10000 0 -0.25 13 13
determination of left/right symmetry 0.002 0.049 -10000 0 -0.3 13 13
Syndecan-2/PKC delta 0.005 0.081 -10000 0 -0.29 32 32
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.02 0.066 0.19 49 -0.23 13 62
MAPK1 0.02 0.063 0.19 46 -0.23 11 57
Syndecan-2/RACK1 0.028 0.043 -10000 0 -0.21 13 13
NF1 0.025 0.02 -10000 0 -0.43 1 1
FGFR/FGF/Syndecan-2 0.002 0.049 -10000 0 -0.3 13 13
ITGA2 0.002 0.09 -10000 0 -0.27 41 41
MAPK8 -0.003 0.056 -10000 0 -0.25 25 25
Syndecan-2/alpha2/beta1 Integrin 0.008 0.11 0.19 1 -0.26 62 63
Syndecan-2/Kininogen 0.009 0.047 -10000 0 -0.25 13 13
ITGB1 0.023 0.012 -10000 0 -10000 0 0
SRC 0.025 0.064 0.19 50 -0.2 13 63
Syndecan-2/CASK/Protein 4.1 0.012 0.041 -10000 0 -0.21 15 15
extracellular matrix organization 0.013 0.045 -10000 0 -0.24 14 14
actin cytoskeleton reorganization 0.015 0.048 0.16 1 -0.25 13 14
Syndecan-2/Caveolin-2/Ras 0.023 0.046 -10000 0 -0.23 13 13
Syndecan-2/Laminin alpha3 0.002 0.077 0.16 1 -0.28 31 32
Syndecan-2/RasGAP 0.038 0.045 -10000 0 -0.2 13 13
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
Syndecan-2 dimer 0.011 0.049 -10000 0 -0.24 17 17
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.045 0.18 9 -0.2 13 22
RHOA 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.025 0.006 -10000 0 -10000 0 0
TNFRSF13B -0.003 0.028 -10000 0 -0.13 11 11
RASA1 0.026 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.068 -10000 0 -0.3 19 19
Syndecan-2/Synbindin 0.016 0.045 -10000 0 -0.25 13 13
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CASP3 0.013 0.089 0.19 46 -0.27 30 76
FN1 0.02 0.029 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.028 0.099 0.17 4 -0.26 68 72
SDC2 0.002 0.049 -10000 0 -0.3 13 13
KNG1 -0.009 0.032 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.018 0.045 -10000 0 -0.25 13 13
TRAPPC4 0.025 0.007 -10000 0 -10000 0 0
CSF2 -0.014 0.009 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.013 0.045 -10000 0 -0.24 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.041 -10000 0 -0.22 13 13
Syndecan-2/Ezrin 0.026 0.063 -10000 0 -0.29 17 17
PRKACA 0.025 0.066 0.19 48 -0.23 13 61
angiogenesis -0.028 0.099 0.17 4 -0.26 68 72
MMP2 0.013 0.067 -10000 0 -0.43 10 10
IL8 -0.061 0.15 -10000 0 -0.25 158 158
calcineurin-NFAT signaling pathway 0.012 0.046 -10000 0 -0.24 14 14
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
Jak2/Leptin Receptor 0.006 0.12 0.24 3 -0.39 29 32
PTP1B/AKT1 0.014 0.091 0.19 7 -0.26 22 29
FYN 0.025 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.094 0.18 13 -0.28 22 35
EGFR -0.019 0.13 -10000 0 -0.44 42 42
EGF/EGFR -0.018 0.12 -10000 0 -0.28 70 70
CSF1 0.017 0.045 -10000 0 -0.43 5 5
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.025 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.013 0.096 0.2 5 -0.27 22 27
Insulin Receptor/Insulin 0.018 0.086 0.2 1 -0.31 10 11
HCK 0.014 0.063 -10000 0 -0.43 9 9
CRK 0.026 0.002 -10000 0 -10000 0 0
TYK2 0.008 0.1 0.3 21 -0.3 15 36
EGF -0.012 0.12 -10000 0 -0.36 43 43
YES1 0.022 0.04 -10000 0 -0.43 4 4
CAV1 0.017 0.12 0.23 49 -0.29 25 74
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.021 0.093 0.21 2 -0.29 15 17
cell migration -0.003 0.094 0.28 22 -0.18 13 35
STAT3 0.026 0.003 -10000 0 -10000 0 0
PRLR 0.007 0.088 -10000 0 -0.43 19 19
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
CSF1R 0.002 0.099 -10000 0 -0.37 31 31
Prolactin Receptor/Prolactin 0.02 0.066 -10000 0 -0.31 18 18
FGR 0.021 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.012 0.095 0.2 5 -0.26 23 28
Crk/p130 Cas 0.023 0.097 0.22 2 -0.29 15 17
DOK1 0.008 0.092 0.21 10 -0.35 10 20
JAK2 0.001 0.12 -10000 0 -0.4 30 30
Jak2/Leptin Receptor/Leptin -0.019 0.1 -10000 0 -0.32 23 23
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PTPN1 0.003 0.095 0.18 13 -0.28 22 35
LYN 0.021 0.035 -10000 0 -0.19 10 10
CDH2 0.025 0.02 -10000 0 -0.43 1 1
SRC 0.024 0.052 -10000 0 -0.37 4 4
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
CAT1/PTP1B -0.015 0.16 0.28 37 -0.37 41 78
CAPN1 0.025 0.021 -10000 0 -0.43 1 1
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.084 -10000 0 -0.36 6 6
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.02 0.099 -10000 0 -0.34 22 22
negative regulation of transcription 0.001 0.12 -10000 0 -0.4 30 30
FCGR2A 0.001 0.092 -10000 0 -0.27 42 42
FER 0.008 0.09 -10000 0 -0.42 21 21
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
BLK -0.03 0.11 -10000 0 -0.21 108 108
Insulin Receptor/Insulin/Shc 0.039 0.031 -10000 0 -0.26 4 4
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.017 0.04 -10000 0 -0.21 11 11
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
p210 bcr-abl/Grb2 0.025 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.032 0.17 0.26 19 -0.43 44 63
PRL 0.003 0.02 -10000 0 -10000 0 0
SOCS3 -0.072 0.31 -10000 0 -1.3 33 33
SPRY2 0.024 0.028 -10000 0 -0.17 8 8
Insulin Receptor/Insulin/IRS1 0.04 0.03 -10000 0 -0.26 4 4
CSF1/CSF1R 0.005 0.11 0.2 4 -0.29 31 35
Ras protein signal transduction 0.018 0.11 0.5 25 -10000 0 25
IRS1 0.026 0.003 -10000 0 -10000 0 0
INS 0.005 0.042 -10000 0 -0.37 5 5
LEP 0.007 0.02 -10000 0 -0.13 4 4
STAT5B 0.009 0.1 0.2 5 -0.3 20 25
STAT5A 0.005 0.11 0.21 4 -0.32 20 24
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.094 0.2 4 -0.27 21 25
CSN2 -0.01 0.06 -10000 0 -0.56 2 2
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
LAT -0.015 0.14 -10000 0 -0.45 47 47
YBX1 0.026 0.031 -10000 0 -0.42 2 2
LCK -0.019 0.11 -10000 0 -0.43 30 30
SHC1 0.024 0.014 -10000 0 -0.13 4 4
NOX4 -0.009 0.1 -10000 0 -0.22 70 70
EPO 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
BCL2L1 0.06 0.08 0.36 1 -0.48 4 5
CRKL 0.052 0.081 0.23 41 -0.38 1 42
mol:DAG 0.028 0.049 -10000 0 -0.35 3 3
HRAS 0.049 0.086 0.27 36 -0.3 1 37
MAPK8 0.032 0.071 0.16 79 -0.24 12 91
RAP1A 0.047 0.08 0.24 39 -0.36 1 40
GAB1 0.051 0.083 0.23 42 -0.35 2 44
MAPK14 0.04 0.063 0.16 88 -0.26 2 90
EPO 0.018 0.03 -10000 0 -0.46 1 1
PLCG1 0.028 0.05 -10000 0 -0.36 3 3
EPOR/TRPC2/IP3 Receptors 0.029 0.013 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.075 -10000 0 -0.27 24 24
GAB1/SHC/GRB2/SOS1 0.07 0.073 0.26 21 -0.33 2 23
EPO/EPOR (dimer) 0.031 0.03 -10000 0 -0.34 1 1
IRS2 0.049 0.081 0.23 35 -0.35 2 37
STAT1 0.035 0.059 -10000 0 -0.35 5 5
STAT5B 0.03 0.053 -10000 0 -0.34 4 4
cell proliferation 0.028 0.095 0.2 100 -0.23 11 111
GAB1/SHIP/PIK3R1/SHP2/SHC 0.047 0.056 0.22 1 -0.33 3 4
TEC 0.047 0.085 0.24 36 -0.24 6 42
SOCS3 -0.029 0.12 -10000 0 -0.21 118 118
STAT1 (dimer) 0.035 0.058 -10000 0 -0.34 5 5
JAK2 0.03 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.06 -10000 0 -0.21 7 7
EPO/EPOR 0.031 0.03 -10000 0 -0.34 1 1
LYN 0.022 0.036 -10000 0 -0.19 10 10
TEC/VAV2 0.047 0.071 0.21 20 -0.23 6 26
elevation of cytosolic calcium ion concentration 0.029 0.013 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -0.13 4 4
EPO/EPOR (dimer)/LYN 0.045 0.037 -10000 0 -0.29 2 2
mol:IP3 0.028 0.049 -10000 0 -0.35 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.069 0.08 0.28 18 -0.33 3 21
SH2B3 0.03 0.016 -10000 0 -0.13 2 2
NFKB1 0.039 0.062 0.16 86 -0.26 2 88
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.05 -10000 0 -0.21 24 24
PTPN6 0.048 0.081 0.29 20 -0.39 1 21
TEC/VAV2/GRB2 0.055 0.072 0.27 7 -0.29 2 9
EPOR 0.029 0.013 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
mol:GDP 0.07 0.073 0.26 21 -0.33 2 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
CRKL/CBL/C3G 0.059 0.065 0.27 7 -10000 0 7
VAV2 0.05 0.081 0.24 38 -0.38 1 39
CBL 0.05 0.079 0.28 22 -0.21 1 23
SHC/Grb2/SOS1 0.028 0.04 -10000 0 -0.36 1 1
STAT5A 0.025 0.073 -10000 0 -0.36 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.079 -10000 0 -0.39 9 9
LYN/PLCgamma2 0.029 0.051 -10000 0 -0.28 11 11
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK 0.046 0.096 0.23 40 -0.28 14 54
BCL2 0.056 0.12 0.36 1 -0.74 9 10
TCGA08_p53

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
CDKN2A -0.017 0.075 -10000 0 -0.3 31 31
TP53 -0.015 0.07 -10000 0 -0.29 25 25
Senescence -0.015 0.07 -10000 0 -0.29 25 25
Apoptosis -0.015 0.07 -10000 0 -0.29 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.056 0.21 34 -10000 0 34
MDM4 0.025 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.017 0.044 -9999 0 -0.15 27 27
PLK4 0.016 0.05 -9999 0 -0.18 24 24
regulation of centriole replication 0.001 0.042 -9999 0 -0.28 6 6
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.14 -10000 0 -0.55 26 26
HDAC1 0.022 0.014 -10000 0 -10000 0 0
AES 0.025 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.019 0.053 -10000 0 -0.43 7 7
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
TLE1 0.024 0.029 -10000 0 -0.43 2 2
AP1 -0.027 0.091 -10000 0 -0.25 60 60
NCSTN 0.026 0.004 -10000 0 -10000 0 0
ADAM10 0.015 0.069 -10000 0 -0.43 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.065 -10000 0 -10000 0 0
NICD/RBPSUH 0.016 0.12 -10000 0 -0.49 26 26
WIF1 -0.13 0.18 -10000 0 -0.43 121 121
NOTCH1 0 0.12 -10000 0 -0.52 26 26
PSENEN 0.022 0.01 -10000 0 -10000 0 0
KREMEN2 -0.007 0.1 -10000 0 -0.43 23 23
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.011 0.072 0.31 4 -0.31 2 6
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
AXIN1 0.007 0.049 0.34 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.02 0.049 0.29 4 -0.26 3 7
PSEN1 0.025 0.005 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.43 48 48
JUN 0.019 0.023 -10000 0 -0.13 9 9
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.002 0.072 0.29 7 -0.3 3 10
MAPK3 0.026 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.27 68 68
HNF1A 0.025 0.021 -10000 0 -0.43 1 1
CTBP1 0.026 0.006 -10000 0 -10000 0 0
MYC -0.033 0.28 -10000 0 -1.4 21 21
NKD1 0.016 0.059 -10000 0 -0.28 16 16
FZD1 0.021 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.013 0.12 -10000 0 -0.5 26 26
apoptosis -0.027 0.09 -10000 0 -0.25 60 60
Delta 1/NOTCHprecursor -0.001 0.14 -10000 0 -0.55 26 26
DLL1 -0.008 0.12 -10000 0 -0.43 38 38
PPARD 0.022 0.058 -10000 0 -1.1 1 1
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
APC 0.003 0.069 0.34 1 -0.47 4 5
DVL1 -0.012 0.07 -10000 0 -0.26 31 31
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.25 71 71
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
NLK 0.014 0.011 -10000 0 -10000 0 0
CCND1 -0.008 0.21 -10000 0 -1.4 12 12
WNT1 0.007 0.04 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.004 0.094 0.3 6 -0.42 3 9
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
NOTCH1 precursor/DVL1 -0.019 0.14 -10000 0 -0.53 24 24
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.28 4 4
NOTCH/Deltex homolog 1 0.015 0.13 -10000 0 -0.51 26 26
PPP2R5D 0.01 0.051 0.25 8 -0.3 3 11
MAPK1 0.026 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.011 0.12 -10000 0 -0.24 95 95
RBPJ 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.023 0.042 -10000 0 -0.25 5 5
PDGFRB 0.025 0.013 -10000 0 -0.14 3 3
SPHK1 -0.02 0.14 -10000 0 -0.72 19 19
mol:S1P -0.019 0.13 -10000 0 -0.63 19 19
S1P1/S1P/Gi -0.028 0.13 -10000 0 -0.35 59 59
GNAO1 0.017 0.047 -10000 0 -0.43 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.014 0.13 0.28 10 -0.34 52 62
PLCG1 -0.027 0.12 -10000 0 -0.34 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.14 3 3
GNAI2 0.021 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.038 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.028 -10000 0 -0.2 5 5
S1P1/S1P -0.016 0.1 0.18 1 -0.47 18 19
negative regulation of cAMP metabolic process -0.027 0.13 -10000 0 -0.34 59 59
MAPK3 -0.05 0.18 -10000 0 -0.53 59 59
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
KDR 0.017 0.04 -10000 0 -0.43 3 3
PLCB2 -0.012 0.11 0.31 3 -0.44 19 22
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.087 -10000 0 -0.4 18 18
receptor internalization -0.016 0.096 -10000 0 -0.42 19 19
PTGS2 -0.095 0.33 -10000 0 -1 58 58
Rac1/GTP -0.015 0.083 -10000 0 -0.38 17 17
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.034 -10000 0 -0.13 22 22
negative regulation of T cell proliferation -0.027 0.13 -10000 0 -0.34 59 59
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.016 -10000 0 -10000 0 0
MAPK1 -0.051 0.18 -10000 0 -0.53 60 60
S1P1/S1P/PDGFB-D/PDGFRB -0.006 0.1 0.22 1 -0.4 18 19
ABCC1 0.025 0.015 -10000 0 -0.14 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.002 0.099 0.23 7 -0.41 18 25
CRKL 0 0.098 -10000 0 -0.43 20 20
HRAS 0.007 0.11 -10000 0 -0.38 20 20
mol:PIP3 0.012 0.1 0.31 7 -0.38 18 25
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.012 -10000 0 -0.13 3 3
GAB1 0.002 0.1 -10000 0 -0.45 20 20
FOXO3 0.017 0.13 0.29 8 -0.4 26 34
AKT1 0.018 0.14 0.3 10 -0.43 29 39
BAD 0.021 0.14 0.31 12 -0.4 28 40
megakaryocyte differentiation 0 0.1 -10000 0 -0.42 21 21
GSK3B 0.017 0.13 0.3 11 -0.41 26 37
RAF1 0.006 0.093 0.25 1 -0.32 17 18
SHC1 0.024 0.014 -10000 0 -0.13 4 4
STAT3 0.004 0.1 -10000 0 -0.44 20 20
STAT1 -0.013 0.22 -10000 0 -0.95 24 24
HRAS/SPRED1 0.018 0.099 0.25 1 -0.31 19 20
cell proliferation -0.003 0.11 -10000 0 -0.46 21 21
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TEC 0.015 0.063 -10000 0 -0.43 9 9
RPS6KB1 0.014 0.12 0.26 3 -0.44 23 26
HRAS/SPRED2 0.018 0.099 0.25 1 -0.31 20 21
LYN/TEC/p62DOK 0.029 0.12 -10000 0 -0.43 23 23
MAPK3 0.014 0.082 0.22 19 -0.27 8 27
STAP1 -0.001 0.1 -10000 0 -0.44 21 21
GRAP2 -0.007 0.1 -10000 0 -0.26 58 58
JAK2 -0.014 0.2 -10000 0 -0.86 22 22
STAT1 (dimer) -0.011 0.22 -10000 0 -0.93 24 24
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.023 0.12 -10000 0 -0.42 25 25
actin filament polymerization -0.005 0.099 0.34 4 -0.44 16 20
LYN 0.021 0.035 -10000 0 -0.19 10 10
STAP1/STAT5A (dimer) -0.011 0.16 -10000 0 -0.63 25 25
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.021 0.099 -10000 0 -0.4 19 19
PI3K 0.036 0.12 0.27 2 -0.42 20 22
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.007 0.25 -10000 0 -1.2 20 20
MAPK8 -0.003 0.11 -10000 0 -0.47 21 21
STAT3 (dimer) 0.004 0.1 -10000 0 -0.43 20 20
positive regulation of transcription 0.015 0.071 0.2 20 -0.22 8 28
mol:GDP 0.003 0.11 -10000 0 -0.39 22 22
PIK3C2B 0.002 0.1 -10000 0 -0.45 18 18
CBL/CRKL 0.011 0.099 -10000 0 -0.41 19 19
FER -0.005 0.12 -10000 0 -0.46 23 23
SH2B3 0.003 0.1 -10000 0 -0.44 20 20
PDPK1 0.011 0.1 0.32 8 -0.39 15 23
SNAI2 -0.003 0.11 0.38 1 -0.42 24 25
positive regulation of cell proliferation -0.007 0.18 -10000 0 -0.74 25 25
KITLG 0.017 0.066 -10000 0 -0.44 10 10
cell motility -0.007 0.18 -10000 0 -0.74 25 25
PTPN6 0.013 0.063 -10000 0 -0.42 10 10
EPOR 0.031 0.084 -10000 0 -1.2 1 1
STAT5A (dimer) -0.004 0.16 -10000 0 -0.62 26 26
SOCS1 0.008 0.068 -10000 0 -0.18 45 45
cell migration 0.017 0.11 0.44 23 -10000 0 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.016 0.03 -10000 0 -0.24 3 3
VAV1 0.005 0.09 -10000 0 -0.34 29 29
GRB10 -0.001 0.094 0.24 1 -0.45 16 17
PTPN11 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT 0.006 0.11 -10000 0 -0.46 20 20
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.008 0.081 0.22 5 -0.26 16 21
CBL 0.025 0.007 -10000 0 -10000 0 0
KIT -0.012 0.26 -10000 0 -1.3 19 19
MAP2K2 0.013 0.086 0.26 16 -0.26 15 31
SHC/Grb2/SOS1 0.037 0.11 -10000 0 -0.42 19 19
STAT5A -0.004 0.16 -10000 0 -0.66 24 24
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.002 0.1 0.37 1 -0.42 24 25
SHC/GRAP2 0.012 0.079 -10000 0 -0.3 26 26
PTPRO 0 0.1 -10000 0 -0.43 21 21
SH2B2 -0.007 0.096 0.25 1 -0.45 16 17
DOK1 0.025 0.021 -10000 0 -0.28 2 2
MATK -0.017 0.11 -10000 0 -0.45 23 23
CREBBP 0.034 0.033 -10000 0 -10000 0 0
BCL2 0.012 0.19 -10000 0 -1.4 8 8
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.04 -10000 0 -0.43 4 4
HDAC4 0.025 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.025 -10000 0 -0.13 18 18
CDKN1A -0.034 0.13 -10000 0 -0.65 20 20
KAT2B 0.025 0.008 -10000 0 -0.13 1 1
BAX 0.021 0.01 -10000 0 -10000 0 0
FOXO3 -0.003 0.033 0.36 4 -10000 0 4
FOXO1 0.024 0.022 -10000 0 -0.43 1 1
FOXO4 0.013 0.026 -10000 0 -0.25 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
TAT -0.025 0.12 -10000 0 -0.26 88 88
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.064 0.12 -10000 0 -0.3 93 93
PPARGC1A 0.009 0.082 -10000 0 -0.37 21 21
FHL2 0.006 0.077 -10000 0 -0.43 12 12
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.025 0.16 18 -10000 0 18
HIST2H4A 0.012 0.025 0.13 18 -10000 0 18
SIRT1/FOXO3a 0.02 0.038 0.26 4 -0.19 4 8
SIRT1 0.03 0.033 0.2 18 -10000 0 18
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.028 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.022 0.057 0.23 1 -0.22 19 20
apoptosis -0.045 0.031 -10000 0 -10000 0 0
SIRT1/PGC1A 0.025 0.057 -10000 0 -0.25 17 17
p53/SIRT1 0.037 0.085 0.38 18 -0.31 12 30
SIRT1/FOXO4 0.031 0.037 -10000 0 -0.22 5 5
FOXO1/FHL2/SIRT1 0.042 0.05 -10000 0 -0.23 13 13
HIST1H1E 0.004 0.05 -10000 0 -0.25 18 18
SIRT1/p300 0.037 0.039 -10000 0 -0.31 4 4
muscle cell differentiation 0.03 0.12 0.25 93 -0.22 10 103
TP53 0.02 0.077 0.2 18 -0.43 12 30
KU70/SIRT1/BAX 0.045 0.031 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
MEF2D 0.025 0.011 -10000 0 -0.13 2 2
HIV-1 Tat/SIRT1 0.003 0.097 0.18 1 -0.3 38 39
ACSS2 0.013 0.024 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.03 0.12 0.22 10 -0.25 93 103
ceramide signaling pathway

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.008 0.11 0.23 1 -0.47 17 18
BAG4 0.014 0.071 -10000 0 -0.43 13 13
BAD 0.005 0.058 0.24 15 -0.14 14 29
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX 0.007 0.05 0.19 15 -0.16 4 19
EnzymeConsortium:3.1.4.12 0 0.03 0.076 2 -0.099 18 20
IKBKB -0.002 0.12 0.24 5 -0.46 16 21
MAP2K2 0.003 0.057 0.18 23 -0.2 1 24
MAP2K1 -0.001 0.051 0.18 9 -0.19 2 11
SMPD1 0.001 0.038 0.12 8 -0.13 10 18
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.12 0.3 7 -0.44 17 24
MAP2K4 -0.001 0.048 0.21 5 -0.17 5 10
protein ubiquitination -0.005 0.11 -10000 0 -0.46 16 16
EnzymeConsortium:2.7.1.37 -0.001 0.058 0.19 10 -0.19 4 14
response to UV 0 0.001 0.002 6 -0.002 4 10
RAF1 0 0.051 0.18 9 -0.18 3 12
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.002 0.046 0.12 7 -0.14 19 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.008 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 0.001 0.048 0.16 8 -0.15 16 24
TRADD 0.025 0.02 -10000 0 -0.43 1 1
RELA/p50 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.005 0.055 0.18 10 -0.19 3 13
MAPK1 0.004 0.056 0.18 10 -0.23 2 12
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD -0.005 0.12 0.26 7 -0.46 16 23
KSR1 0 0.047 0.15 5 -0.15 11 16
MAPK8 -0.006 0.05 0.19 4 -0.19 10 14
TRAF2 0.025 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.007 0.11 0.23 2 -0.46 16 18
TNF R/SODD 0.023 0.063 -10000 0 -0.31 17 17
TNF -0.06 0.16 -10000 0 -0.27 151 151
CYCS 0.016 0.061 0.18 29 -0.14 3 32
IKBKG -0.007 0.11 0.22 1 -0.46 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.006 0.12 -10000 0 -0.44 22 22
RELA 0.025 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AIFM1 0.008 0.052 0.16 26 -0.15 4 30
TNF/TNF R/SODD 0 0.12 -10000 0 -0.27 77 77
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.023 0.078 -10000 0 -0.85 3 3
NSMAF -0.002 0.12 0.22 13 -0.45 17 30
response to hydrogen peroxide 0 0.001 0.002 6 -0.002 4 10
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Class I PI3K signaling events

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
ARF5/GTP 0 0.04 0.2 8 -10000 0 8
DAPP1 -0.033 0.14 0.25 7 -0.4 38 45
Src family/SYK family/BLNK-LAT/BTK-ITK -0.074 0.22 0.32 7 -0.51 64 71
mol:DAG -0.02 0.099 0.29 13 -0.26 25 38
HRAS 0.025 0.008 -10000 0 -10000 0 0
RAP1A 0.022 0.011 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.06 0.19 4 -0.31 6 10
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.051 0.18 30 -10000 0 30
ARF1/GTP 0.003 0.035 0.2 7 -10000 0 7
RHOA 0.026 0.004 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
RAP1A/GTP -0.004 0.041 0.17 19 -10000 0 19
ADAP1 -0.006 0.046 0.16 26 -0.21 5 31
ARAP3 0 0.05 0.18 30 -10000 0 30
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PREX1 0.016 0.063 -10000 0 -0.43 10 10
ARHGEF6 0.023 0.04 -10000 0 -0.43 4 4
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
ARF1 0.026 0.004 -10000 0 -10000 0 0
NRAS 0.022 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.059 0.23 11 -0.14 14 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.004 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.25 56 56
mol:IP3 -0.017 0.076 0.23 15 -0.19 20 35
LYN 0.021 0.035 -10000 0 -0.19 10 10
ARF1/GDP 0.033 0.07 0.2 6 -0.3 9 15
RhoA/GDP 0.037 0.06 0.24 14 -0.2 1 15
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
BLNK -0.021 0.13 -10000 0 -0.38 59 59
actin cytoskeleton reorganization 0.022 0.1 0.27 27 -0.38 9 36
SRC 0.025 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.02 -10000 0 -0.26 3 3
RAC1 0.023 0.009 -10000 0 -10000 0 0
PTEN 0.022 0.013 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.043 0.22 7 -10000 0 7
RhoA/GTP 0.005 0.054 0.18 29 -10000 0 29
Src family/SYK family/BLNK-LAT -0.067 0.17 -10000 0 -0.42 63 63
BLK -0.03 0.11 -10000 0 -0.21 108 108
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
CYTH1 -0.004 0.043 0.16 31 -10000 0 31
HCK 0.014 0.063 -10000 0 -0.43 9 9
CYTH3 -0.003 0.041 0.18 13 -10000 0 13
CYTH2 -0.004 0.043 0.18 16 -10000 0 16
KRAS 0.026 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.008 0.08 0.21 2 -0.4 16 18
SGK1 -0.001 0.1 -10000 0 -0.38 30 30
INPP5D 0.022 0.037 -10000 0 -0.43 3 3
mol:GDP 0.022 0.072 0.2 11 -0.31 9 20
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.009 0.083 -10000 0 -0.35 23 23
ARF6/GDP 0.033 0.064 0.24 22 -0.22 1 23
mol:PI-3-4-5-P3 -0.011 0.027 0.18 7 -10000 0 7
ARAP3/RAP1A/GTP -0.004 0.041 0.17 19 -10000 0 19
VAV1 0.005 0.09 -10000 0 -0.34 29 29
mol:PI-3-4-P2 0.01 0.026 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.031 0.04 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.021 -10000 0 -0.26 3 3
Rac1/GDP 0.024 0.063 0.2 3 -0.3 7 10
LAT 0.003 0.1 -10000 0 -0.42 27 27
Rac1/GTP 0.019 0.075 0.17 1 -0.4 10 11
ITK -0.022 0.064 0.16 22 -0.21 28 50
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.035 0.12 0.31 10 -0.35 29 39
LCK -0.019 0.11 -10000 0 -0.43 30 30
BTK -0.01 0.055 0.16 31 -0.19 15 46
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -0.13 2 2
RAC1-CDC42/GTP/PAK family -0.02 0.069 -10000 0 -0.19 61 61
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.004 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.034 0.071 -10000 0 -0.28 21 21
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
DUSP8 0.02 0.039 -10000 0 -0.22 10 10
PGK/cGMP/p38 alpha -0.011 0.11 0.16 2 -0.3 27 29
apoptosis -0.033 0.068 -10000 0 -0.27 21 21
RAL/GTP 0.031 0.012 -10000 0 -10000 0 0
LYN 0.021 0.035 -10000 0 -0.19 10 10
DUSP1 0.008 0.076 -10000 0 -0.25 32 32
PAK1 0.008 0.061 -10000 0 -0.16 46 46
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.056 0.026 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -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 0.022 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0.016 -10000 0 -10000 0 0
MAPK11 0 0.13 0.28 26 -0.33 23 49
BLK -0.03 0.11 -10000 0 -0.21 108 108
HCK 0.014 0.063 -10000 0 -0.43 9 9
MAP2K3 0.025 0.01 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.015 0.065 -10000 0 -0.32 16 16
TRAF6/MEKK3 0.031 0.015 -10000 0 -0.23 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.11 0.24 26 -0.33 17 43
positive regulation of innate immune response 0.003 0.14 0.3 27 -0.38 22 49
LCK -0.019 0.11 -10000 0 -0.43 30 30
p38alpha-beta/MKP7 0.013 0.14 0.31 26 -0.36 21 47
p38alpha-beta/MKP5 0.006 0.14 0.29 23 -0.36 26 49
PGK/cGMP -0.005 0.082 -10000 0 -0.3 36 36
PAK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.007 0.15 0.31 24 -0.37 23 47
CDC42 0.022 0.01 -10000 0 -10000 0 0
RALB 0.026 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
PAK3 -0.055 0.16 -10000 0 -0.34 113 113
IL27-mediated signaling events

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
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.001 0.088 0.4 2 -0.48 2 4
IL27/IL27R/JAK1 0.022 0.12 0.88 2 -10000 0 2
TBX21 -0.019 0.16 0.45 15 -0.4 19 34
IL12B -0.001 0.024 -10000 0 -0.13 6 6
IL12A -0.008 0.065 -10000 0 -0.3 23 23
IL6ST -0.002 0.11 -10000 0 -0.42 33 33
IL27RA/JAK1 0.024 0.051 -10000 0 -10000 0 0
IL27 0.014 0.038 -10000 0 -0.13 24 24
TYK2 0.025 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.01 0.12 0.43 1 -0.5 3 4
T-helper 2 cell differentiation 0.001 0.088 0.4 2 -0.48 2 4
T cell proliferation during immune response 0.001 0.088 0.4 2 -0.48 2 4
MAPKKK cascade -0.001 0.088 0.48 2 -0.4 2 4
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT2 0.025 0.014 -10000 0 -0.13 4 4
STAT1 0.021 0.029 -10000 0 -0.14 1 1
IL12RB1 -0.001 0.098 -10000 0 -0.31 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.034 0.16 0.45 13 -0.4 27 40
IL27/IL27R/JAK2/TYK2 -0.001 0.089 0.48 2 -0.4 2 4
positive regulation of T cell mediated cytotoxicity -0.001 0.088 0.48 2 -0.4 2 4
STAT1 (dimer) 0.009 0.19 0.55 27 -0.48 4 31
JAK2 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.021 0.012 -10000 0 -10000 0 0
STAT2 (dimer) 0.018 0.097 0.39 3 -0.39 2 5
T cell proliferation -0.021 0.1 0.44 2 -0.4 6 8
IL12/IL12R/TYK2/JAK2 0.001 0.13 -10000 0 -0.78 10 10
IL17A -0.009 0.11 0.43 1 -0.47 2 3
mast cell activation 0.001 0.088 0.4 2 -0.48 2 4
IFNG 0.005 0.026 0.12 4 -0.1 6 10
T cell differentiation -0.002 0.004 -10000 0 -0.015 4 4
STAT3 (dimer) 0.018 0.098 0.39 3 -0.39 2 5
STAT5A (dimer) 0.013 0.11 0.39 3 -0.47 4 7
STAT4 (dimer) -0.011 0.13 0.39 3 -0.42 8 11
STAT4 -0.064 0.16 -10000 0 -0.43 69 69
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.025 0.074 -10000 0 -10000 0 0
GATA3 -0.085 0.44 0.61 40 -1.3 49 89
IL18 -0.009 0.063 -10000 0 -0.3 21 21
positive regulation of mast cell cytokine production 0.018 0.096 0.39 3 -0.38 2 5
IL27/EBI3 0.019 0.067 0.24 2 -0.28 18 20
IL27RA 0.009 0.033 -10000 0 -10000 0 0
IL6 -0.035 0.12 -10000 0 -0.43 37 37
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.015 0.023 -10000 0 -10000 0 0
IL1B -0.056 0.11 -10000 0 -0.18 173 173
EBI3 0.011 0.078 -10000 0 -0.38 18 18
TNF -0.049 0.1 -10000 0 -0.3 68 68
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.013 0.052 -10000 0 -0.33 8 8
CCNA2 -0.007 0.099 -10000 0 -0.43 22 22
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
JAK3 -0.009 0.1 -10000 0 -0.25 65 65
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.01 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.017 0.13 -10000 0 -0.42 22 22
SHC1 0.025 0.015 -10000 0 -0.13 4 4
SP1 0.027 0.034 -10000 0 -0.33 4 4
IL2RA -0.015 0.093 -10000 0 -0.7 8 8
IL2RB -0.028 0.13 -10000 0 -0.25 101 101
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.43 16 16
G1/S transition of mitotic cell cycle 0.004 0.17 0.28 5 -0.48 40 45
PTPN11 0.026 0.004 -10000 0 -10000 0 0
CCND2 0.013 0.066 -10000 0 -0.7 4 4
LCK -0.019 0.11 -10000 0 -0.43 30 30
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.016 0.004 -10000 0 -10000 0 0
CDK6 0.004 0.083 -10000 0 -0.43 17 17
CCND3 -0.012 0.12 -10000 0 -0.46 7 7
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.036 0.064 -10000 0 -0.22 25 25
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.12 -10000 0 -0.42 14 14
AKT1 -0.009 0.17 -10000 0 -0.67 30 30
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.005 0.18 -10000 0 -0.69 30 30
mol:Ca2+ -0.018 0.093 -10000 0 -0.38 23 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.076 -10000 0 -0.26 34 34
SHC1 0.024 0.014 -10000 0 -0.13 4 4
apoptosis 0.008 0.16 0.64 30 -10000 0 30
RhoA/GTP 0.012 0.032 -10000 0 -0.2 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0 0.12 -10000 0 -0.4 14 14
regulation of stress fiber formation 0.003 0.066 0.39 2 -0.17 16 18
E2/ERA-ERB (dimer) 0.018 0.06 -10000 0 -0.24 23 23
KRAS 0.025 0.005 -10000 0 -10000 0 0
G13/GTP 0.024 0.041 -10000 0 -0.23 11 11
pseudopodium formation -0.003 0.066 0.17 16 -0.39 2 18
E2/ER alpha (dimer)/PELP1 0.025 0.045 -10000 0 -0.26 11 11
GRB2 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.022 0.04 -10000 0 -0.43 4 4
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.004 0.13 0.28 2 -0.38 28 30
E2/ER beta (dimer) 0.012 0.045 -10000 0 -0.3 10 10
mol:GDP 0 0.068 -10000 0 -0.3 19 19
mol:NADP 0.004 0.13 0.28 2 -0.38 28 30
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.019 0.097 -10000 0 -0.4 23 23
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
PLCB1 -0.01 0.09 -10000 0 -0.38 20 20
PLCB2 -0.01 0.095 -10000 0 -0.4 22 22
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:L-citrulline 0.004 0.13 0.28 2 -0.38 28 30
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP 0.008 0.11 -10000 0 -0.6 15 15
JNK cascade 0.011 0.045 -10000 0 -0.3 10 10
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
ESR2 0.015 0.065 -10000 0 -0.43 10 10
GNAQ 0.026 0.004 -10000 0 -10000 0 0
ESR1 0.011 0.07 -10000 0 -0.43 11 11
Gq family/GDP/Gbeta gamma -0.024 0.17 -10000 0 -0.57 30 30
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.029 0.071 -10000 0 -1.2 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.001 0.11 -10000 0 -0.4 13 13
GNAZ 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.009 0.049 -10000 0 -0.3 11 11
STRN 0.005 0.096 -10000 0 -0.42 25 25
GNAL -0.028 0.15 -10000 0 -0.42 61 61
PELP1 0.026 0.002 -10000 0 -10000 0 0
MAPK11 0.003 0.05 -10000 0 -0.26 18 18
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
HBEGF -0.019 0.14 0.35 21 -0.37 17 38
cAMP biosynthetic process -0.011 0.089 -10000 0 -0.22 76 76
SRC -0.025 0.12 0.21 1 -0.37 19 20
PI3K 0.038 0.007 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.022 0.072 -10000 0 -0.27 19 19
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.09 -10000 0 -0.31 21 21
Gs family/GTP -0.005 0.093 -10000 0 -0.22 76 76
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.022 -10000 0 -10000 0 0
vasodilation 0.005 0.12 0.25 4 -0.37 28 32
mol:DAG -0.019 0.097 -10000 0 -0.4 23 23
Gs family/GDP/Gbeta gamma -0.014 0.088 -10000 0 -0.3 22 22
MSN -0.003 0.069 0.18 16 -0.42 2 18
Gq family/GTP 0.001 0.089 -10000 0 -0.36 22 22
mol:PI-3-4-5-P3 -0.004 0.17 -10000 0 -0.66 30 30
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 0.37 28 -0.25 4 32
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.073 -10000 0 -0.29 19 19
NOS3 0.003 0.14 0.29 2 -0.4 28 30
GNA11 0.017 0.06 -10000 0 -0.43 9 9
MAPKKK cascade -0.006 0.15 0.37 3 -0.44 40 43
E2/ER alpha (dimer)/PELP1/Src 0.003 0.12 0.26 9 -0.39 16 25
ruffle organization -0.003 0.066 0.17 16 -0.39 2 18
ROCK2 0.002 0.07 0.19 16 -0.36 1 17
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.34 17 17
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.039 0.13 0.33 4 -0.36 25 29
MMP2 -0.014 0.13 0.27 14 -0.36 18 32
LPA4-mediated signaling events

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
ADCY4 -0.009 0.027 -10000 0 -0.26 5 5
ADCY5 -0.014 0.046 -10000 0 -0.27 15 15
ADCY6 -0.007 0.017 -10000 0 -0.26 2 2
ADCY7 -0.007 0.017 -10000 0 -0.26 2 2
ADCY1 -0.03 0.069 -10000 0 -0.24 46 46
ADCY2 -0.012 0.04 -10000 0 -0.26 13 13
ADCY3 -0.007 0.017 -10000 0 -0.26 2 2
ADCY8 -0.031 0.075 -10000 0 -0.26 51 51
PRKCE 0.005 0.022 -10000 0 -0.3 2 2
ADCY9 -0.008 0.023 -10000 0 -0.26 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.076 0.18 22 -0.22 17 39
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.071 -10000 0 -0.43 13 13
Caspase 8 (4 units) 0.031 0.059 -10000 0 -0.26 7 7
NEF -0.001 0.011 -10000 0 -10000 0 0
NFKBIA 0.02 0.029 -10000 0 -0.14 1 1
BIRC3 -0.005 0.1 -10000 0 -0.45 24 24
CYCS 0.007 0.048 0.18 9 -0.33 2 11
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CD247 0.01 0.068 -10000 0 -0.25 25 25
MAP2K7 0.025 0.086 -10000 0 -0.61 4 4
protein ubiquitination 0.018 0.089 0.22 14 -0.32 10 24
CRADD 0.026 0.003 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.014 0.063 -10000 0 -0.43 9 9
BID 0.01 0.048 0.18 6 -0.26 5 11
NF-kappa-B/RelA/I kappa B alpha 0.038 0.069 -10000 0 -0.24 24 24
TRADD 0.025 0.02 -10000 0 -0.43 1 1
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
CFLAR 0.026 0.007 -10000 0 -0.13 1 1
FADD 0.025 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.038 0.069 -10000 0 -0.25 24 24
MAPK8 0.019 0.082 -10000 0 -0.55 4 4
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.019 0.053 -10000 0 -0.43 7 7
TRAF2 0.026 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.047 -10000 0 -0.23 11 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.088 -10000 0 -0.4 11 11
CHUK 0.017 0.094 0.23 12 -0.35 10 22
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.061 0.054 -10000 0 -0.22 13 13
TCRz/NEF 0.009 0.052 -10000 0 -0.19 25 25
TNF -0.06 0.16 -10000 0 -0.26 151 151
FASLG -0.006 0.051 -10000 0 -0.26 8 8
NFKB1 0.021 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
CASP6 0.027 0.099 -10000 0 -0.54 10 10
CASP7 0.007 0.13 0.29 14 -0.47 26 40
RELA 0.019 0.03 -10000 0 -0.14 1 1
CASP2 0.02 0.011 -10000 0 -10000 0 0
CASP3 0.007 0.13 0.29 14 -0.46 29 43
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
CASP8 0.021 0.033 -10000 0 -0.15 15 15
CASP9 0.022 0.012 -10000 0 -10000 0 0
MAP3K14 0.014 0.094 0.21 5 -0.39 10 15
APAF-1/Caspase 9 0.004 0.083 -10000 0 -0.32 22 22
BCL2 0.016 0.082 0.27 1 -0.58 3 4
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
CDC42/GTP 0.026 0.051 -10000 0 -0.24 7 7
PLCG1 0.005 0.054 -10000 0 -0.24 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
G12/G13 0.032 0.015 -10000 0 -10000 0 0
cell migration 0.025 0.05 -10000 0 -0.24 7 7
S1PR5 -0.053 0.16 -10000 0 -0.3 124 124
S1PR4 0.019 0.042 -10000 0 -0.43 3 3
MAPK3 0.006 0.055 -10000 0 -0.24 8 8
MAPK1 0.007 0.05 -10000 0 -0.21 7 7
S1P/S1P5/Gi -0.019 0.1 -10000 0 -0.24 66 66
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
CDC42/GDP 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.094 -10000 0 -0.26 61 61
RHOA 0.045 0.087 0.22 81 -0.22 3 84
S1P/S1P4/Gi 0.011 0.058 -10000 0 -0.26 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.04 0.029 -10000 0 -0.23 3 3
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.021 0.01 -9999 0 -10000 0 0
SPHK1 0.004 0.086 -9999 0 -0.43 17 17
GNAI2 0.025 0.005 -9999 0 -10000 0 0
mol:S1P 0 0.064 -9999 0 -0.34 16 16
GNAO1 0.022 0.045 -9999 0 -0.43 5 5
mol:Sphinganine-1-P 0.003 0.041 -9999 0 -0.3 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.022 0.074 -9999 0 -0.31 11 11
GNAI3 0.021 0.01 -9999 0 -10000 0 0
G12/G13 0.032 0.015 -9999 0 -10000 0 0
S1PR3 0.005 0.075 -9999 0 -0.2 45 45
S1PR2 0.022 0.036 -9999 0 -0.43 3 3
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.062 -9999 0 -0.29 17 17
S1PR5 -0.053 0.16 -9999 0 -0.3 124 124
S1PR4 0.019 0.042 -9999 0 -0.43 3 3
GNAI1 0.019 0.036 -9999 0 -0.43 3 3
S1P/S1P5/G12 -0.016 0.11 -9999 0 -0.26 71 71
S1P/S1P3/Gq -0.006 0.11 -9999 0 -0.38 29 29
S1P/S1P4/Gi 0.003 0.084 -9999 0 -0.3 14 14
GNAQ 0.026 0.004 -9999 0 -10000 0 0
GNAZ 0.026 0.004 -9999 0 -10000 0 0
GNA14 0.009 0.081 -9999 0 -0.34 23 23
GNA15 0.013 0.07 -9999 0 -0.34 17 17
GNA12 0.022 0.009 -9999 0 -10000 0 0
GNA13 0.025 0.005 -9999 0 -10000 0 0
GNA11 0.017 0.06 -9999 0 -0.43 9 9
ABCC1 0.025 0.014 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.025 0.009 -10000 0 -0.13 1 1
NFATC1 0.002 0.11 0.25 4 -0.37 22 26
NFATC2 -0.011 0.082 0.14 2 -0.24 38 40
NFATC3 0.007 0.059 -10000 0 -0.34 14 14
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.044 0.15 0.17 3 -0.42 47 50
Exportin 1/Ran/NUP214 0.051 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.064 0.17 -10000 0 -0.37 73 73
BCL2/BAX 0.029 0.034 -10000 0 -0.28 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.018 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
BAD 0.025 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D -0.031 0.15 -10000 0 -0.4 46 46
Calcineurin A alpha-beta B1/BCL2 0.021 0.045 -10000 0 -0.43 5 5
FKBP8 0.025 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.03 0.14 0.39 46 -10000 0 46
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.43 28 28
MAP3K8 0.016 0.047 -10000 0 -0.43 4 4
NFAT4/CK1 alpha 0.016 0.042 -10000 0 -0.19 13 13
MEF2D/NFAT1/Cbp/p300 0.019 0.1 -10000 0 -0.29 22 22
CABIN1 -0.044 0.15 0.17 3 -0.42 47 50
CALM1 0.025 0.009 -10000 0 -0.14 1 1
RAN 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.019 -10000 0 -0.13 7 7
CAMK4 -0.094 0.19 -10000 0 -0.35 162 162
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.002 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.024 0.043 -10000 0 -0.3 3 3
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.13 0.26 1 -0.36 32 33
PRKCH 0.025 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.035 0.032 -10000 0 -0.3 4 4
CASP3 0.025 0.009 -10000 0 -0.13 1 1
PIM1 0.024 0.017 -10000 0 -0.13 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.004 -10000 0 -10000 0 0
apoptosis 0.015 0.019 -10000 0 -0.31 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.046 -10000 0 -0.22 2 2
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
JNK2/NFAT4 -0.001 0.078 -10000 0 -0.31 14 14
BAD/BCL-XL 0.036 0.01 -10000 0 -10000 0 0
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
NUP214 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
PRKCG -0.066 0.15 -10000 0 -0.43 67 67
PRKCQ 0.015 0.061 -10000 0 -0.37 11 11
FKBP38/BCL2 0.033 0.034 -10000 0 -0.3 5 5
EP300 0.022 0.04 -10000 0 -0.43 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.008 0.11 0.26 1 -0.35 23 24
CaM/Ca2+/FKBP38 0.032 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.012 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.044 0.12 -10000 0 -0.25 122 122
NFATc/ERK1 0.015 0.11 0.26 3 -0.35 21 24
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.067 0.17 -10000 0 -0.37 78 78
NR4A1 -0.001 0.099 0.22 3 -0.38 15 18
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
positive T cell selection 0.007 0.059 -10000 0 -0.34 14 14
NFAT1/CK1 alpha -0.003 0.06 -10000 0 -0.2 21 21
RCH1/ KPNB1 0.037 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
AKAP5 0.009 0.058 -10000 0 -0.43 4 4
MEF2D 0.024 0.012 -10000 0 -0.14 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha 0.014 0.11 0.26 3 -0.35 22 25
CREBBP 0.026 0.006 -10000 0 -10000 0 0
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.022 0.014 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.26 61 61
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.067 -10000 0 -0.25 25 25
alpha4/beta7 Integrin/Paxillin 0.009 0.083 0.18 3 -0.24 42 45
lamellipodium assembly 0.023 0.049 0.27 1 -0.43 3 4
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.013 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.037 0.057 -10000 0 -0.21 22 22
cell adhesion 0.036 0.06 -10000 0 -0.22 22 22
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.02 0.062 0.17 1 -0.23 22 23
ITGB1 0.023 0.012 -10000 0 -10000 0 0
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
ARF6/GDP 0.024 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0 0.097 -10000 0 -0.23 67 67
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.26 4 4
VCAM1 -0.033 0.13 -10000 0 -0.43 48 48
alpha4/beta1 Integrin/Paxillin/Talin 0.038 0.061 -10000 0 -0.22 22 22
alpha4/beta1 Integrin/Paxillin/GIT1 0.039 0.061 -10000 0 -0.22 22 22
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.038 0.06 0.22 22 -10000 0 22
CBL 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.038 0.061 -10000 0 -0.22 22 22
Rac1/GTP 0.023 0.054 0.28 1 -0.48 3 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0.023 -10000 0 -0.3 2 2
VEGFR1 homodimer/NRP1 0.012 0.02 -10000 0 -0.3 2 2
mol:DAG -0.014 0.074 0.19 3 -0.23 49 52
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.027 -10000 0 -0.27 2 2
CaM/Ca2+ 0 0.076 -10000 0 -0.26 2 2
HIF1A 0.03 0.021 -10000 0 -0.42 1 1
GAB1 0.025 0.02 -10000 0 -0.43 1 1
AKT1 -0.015 0.082 -10000 0 -0.49 1 1
PLCG1 -0.014 0.075 0.19 3 -0.23 49 52
NOS3 -0.009 0.07 -10000 0 -0.32 1 1
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.005 0.081 0.28 1 -0.31 1 2
FLT1 0.017 0.024 -10000 0 -0.35 2 2
PGF -0.034 0.14 -10000 0 -0.31 90 90
VEGFR1 homodimer/NRP2/VEGFR121 0.042 0.035 -10000 0 -0.23 6 6
CALM1 0.025 0.009 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Hsp90 0.021 0.089 0.28 3 -0.3 1 4
endothelial cell proliferation -0.026 0.097 0.27 1 -0.32 15 16
mol:Ca2+ -0.014 0.074 0.19 3 -0.23 49 52
MAPK3 -0.027 0.061 0.17 3 -0.26 1 4
MAPK1 -0.027 0.061 0.17 3 -0.26 1 4
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PLGF homodimer -0.034 0.14 -10000 0 -0.31 90 90
PRKACA 0.025 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.006 0.051 -10000 0 -0.15 44 44
VEGFA homodimer 0.019 0.032 -10000 0 -0.13 22 22
VEGFR1 homodimer/VEGFA homodimer 0.027 0.03 -10000 0 -0.3 2 2
platelet activating factor biosynthetic process -0.027 0.059 -10000 0 -0.26 1 1
PI3K 0.028 0.088 -10000 0 -0.22 55 55
PRKCA -0.027 0.064 0.18 3 -0.27 1 4
PRKCB -0.038 0.073 0.18 3 -0.28 11 14
VEGFR1 homodimer/PLGF homodimer -0.007 0.091 -10000 0 -0.26 57 57
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
VEGFB 0.025 0.005 -10000 0 -10000 0 0
mol:IP3 -0.014 0.074 0.19 3 -0.23 49 52
RASA1 0.014 0.021 0.19 3 -0.32 1 4
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFR1 homodimer 0.017 0.024 -10000 0 -0.35 2 2
VEGFB homodimer 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Caveolin-1 0.002 0.076 -10000 0 -0.3 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.026 0.087 -10000 0 -0.22 55 55
mol:L-citrulline 0.005 0.081 0.28 1 -0.31 1 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.055 0.031 -10000 0 -0.26 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.044 0.021 -10000 0 -0.23 1 1
CD2AP 0.026 0.002 -10000 0 -10000 0 0
PI3K/GAB1 0.036 0.089 -10000 0 -0.21 54 54
PDPK1 -0.012 0.075 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.025 -10000 0 -0.27 2 2
mol:NADP 0.005 0.081 0.28 1 -0.31 1 2
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.053 0.03 -10000 0 -0.26 2 2
VEGFR1 homodimer/NRP2 0.027 0.034 -10000 0 -0.25 6 6
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.019 0.076 -10000 0 -0.3 26 26
ATM 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
UBE2L3 0.026 0.004 -10000 0 -10000 0 0
FANCD2 0.016 0.029 -10000 0 -0.29 4 4
protein ubiquitination 0.04 0.07 -10000 0 -0.22 27 27
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.018 -10000 0 -10000 0 0
MRE11A 0.025 0.006 -10000 0 -10000 0 0
DNA-PK 0.05 0.014 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.024 0.062 -10000 0 -0.48 4 4
FANCF 0.025 0.005 -10000 0 -10000 0 0
BRCA1 0.025 0.012 -10000 0 -0.13 3 3
CCNE1 0.021 0.014 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.027 0.037 -10000 0 -0.28 5 5
FANCG 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.02 0.076 -10000 0 -0.3 27 27
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.024 0.022 -10000 0 -0.28 2 2
NBN 0.024 0.007 -10000 0 -10000 0 0
FANCA 0.009 0.069 -10000 0 -0.43 9 9
DNA repair 0.01 0.09 0.27 9 -0.4 7 16
BRCA1/BARD1/ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BARD1/DNA-PK 0.049 0.065 -10000 0 -0.23 24 24
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.019 0.075 0.3 26 -10000 0 26
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.058 -10000 0 -0.22 23 23
BRCA1/BACH1/BARD1/TopBP1 0.035 0.072 -10000 0 -0.26 27 27
BRCA1/BARD1/P53 0.043 0.083 -10000 0 -0.25 37 37
BARD1/CSTF1/BRCA1 0.035 0.069 -10000 0 -0.26 26 26
BRCA1/BACH1 0.025 0.012 -10000 0 -0.13 3 3
BARD1 0.002 0.1 -10000 0 -0.41 28 28
PCNA 0.025 0.011 -10000 0 -0.13 2 2
BRCA1/BARD1/UbcH5C 0.035 0.069 -10000 0 -0.25 27 27
BRCA1/BARD1/UbcH7 0.036 0.068 -10000 0 -0.25 26 26
BRCA1/BARD1/RAD51/PCNA 0.04 0.085 -10000 0 -0.24 39 39
BARD1/DNA-PK/P53 0.051 0.08 -10000 0 -0.23 34 34
BRCA1/BARD1/Ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BRCA1/BARD1/CTIP 0.028 0.06 0.21 1 -0.23 24 25
FA complex 0.024 0.037 -10000 0 -0.21 8 8
BARD1/EWS 0.021 0.074 -10000 0 -0.3 25 25
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.43 13 13
TOPBP1 0.025 0.02 -10000 0 -0.43 1 1
G1/S transition of mitotic cell cycle -0.041 0.082 0.24 37 -10000 0 37
BRCA1/BARD1 0.045 0.073 -10000 0 -0.22 27 27
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.071 -10000 0 -0.3 26 26
CDK2 0.02 0.044 -10000 0 -0.23 12 12
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.001 0.085 -10000 0 -0.2 61 61
RAD50 0.026 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.02 0.076 -10000 0 -0.3 27 27
EWSR1 0.026 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.039 -10000 0 -0.25 5 5
alphaV beta3 Integrin 0.044 0.053 -10000 0 -0.26 14 14
PTK2 0.01 0.11 0.34 7 -0.37 16 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.035 -10000 0 -0.43 3 3
SRC 0.025 0.005 -10000 0 -10000 0 0
CDKN1B 0.005 0.08 -10000 0 -0.41 17 17
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
ILK 0.005 0.078 -10000 0 -0.38 18 18
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.002 0.072 0.18 1 -0.37 17 18
PTK2B 0 0.061 0.18 21 -0.22 14 35
alphaV/beta3 Integrin/JAM-A 0.04 0.069 0.2 1 -0.23 27 28
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.029 0.054 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.057 0.048 -10000 0 -0.23 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.056 -10000 0 -0.32 4 4
alphaV/beta3 Integrin/Syndecan-1 0.035 0.071 -10000 0 -0.21 38 38
PI4KA 0.023 0.021 -10000 0 -0.13 9 9
IGF-1R heterotetramer/IGF1/IRS1 0.038 0.068 -10000 0 -0.21 26 26
PI4 Kinase 0.035 0.018 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
alphaV/beta3 Integrin/Osteopontin 0.014 0.099 -10000 0 -0.22 74 74
RPS6KB1 -0.021 0.062 0.38 3 -0.25 2 5
TLN1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.002 0.085 -10000 0 -0.38 17 17
GPR124 0.024 0.015 -10000 0 -10000 0 0
MAPK1 -0.001 0.084 -10000 0 -0.39 17 17
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.031 0.086 -10000 0 -0.25 40 40
cell adhesion 0.028 0.056 -10000 0 -0.25 15 15
ANGPTL3 0.002 0.02 -10000 0 -0.13 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.028 -10000 0 -0.2 4 4
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
TGFBR2 0.024 0.016 -10000 0 -0.13 5 5
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
IGF1 0.012 0.076 -10000 0 -0.34 20 20
RAC1 0.023 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.03 0.059 -10000 0 -0.26 12 12
apoptosis 0.026 0.002 -10000 0 -10000 0 0
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.047 0.048 -10000 0 -0.26 12 12
VCL 0.022 0.032 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/Del1 0.015 0.11 -10000 0 -0.28 59 59
CSF1 0.017 0.045 -10000 0 -0.43 5 5
PIK3C2A 0.003 0.084 -10000 0 -0.4 19 19
PI4 Kinase/Pyk2 0.006 0.069 -10000 0 -0.26 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.061 -10000 0 -0.23 15 15
FAK1/Vinculin 0.019 0.095 0.26 14 -0.32 15 29
alphaV beta3/Integrin/ppsTEM5 0.044 0.05 -10000 0 -0.24 14 14
RHOA 0.026 0.004 -10000 0 -10000 0 0
VTN 0.012 0.075 -10000 0 -0.35 19 19
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
FGF2 0.024 0.029 -10000 0 -0.43 2 2
F11R 0.01 0.024 -10000 0 -0.3 2 2
alphaV/beta3 Integrin/Lactadherin 0.045 0.054 -10000 0 -0.26 15 15
alphaV/beta3 Integrin/TGFBR2 0.045 0.051 -10000 0 -0.23 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.042 -10000 0 -0.23 5 5
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.044 0.045 -10000 0 -0.23 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.029 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.032 0.064 -10000 0 -0.22 14 14
SDC1 0.007 0.07 -10000 0 -0.43 9 9
VAV3 -0.008 0.074 0.18 26 -0.23 31 57
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.02 0.095 0.27 16 -0.3 15 31
cell migration 0.014 0.088 0.25 15 -0.31 11 26
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.05 0.067 -10000 0 -0.21 25 25
SPP1 -0.024 0.12 -10000 0 -0.26 87 87
KDR 0.021 0.039 -10000 0 -0.43 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.002 -10000 0 -10000 0 0
COL4A3 -0.011 0.1 -10000 0 -0.43 22 22
angiogenesis 0 0.097 -10000 0 -0.42 16 16
Rac1/GTP 0.003 0.068 -10000 0 -0.21 29 29
EDIL3 -0.024 0.14 -10000 0 -0.38 64 64
cell proliferation 0.03 0.06 -10000 0 -0.23 15 15
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.014 0.032 -10000 0 -0.69 1 1
REL 0.007 0.086 -10000 0 -0.43 18 18
HDAC7 -0.017 0.079 -10000 0 -0.29 16 16
JUN 0.019 0.023 -10000 0 -0.13 9 9
EP300 0.022 0.04 -10000 0 -0.43 4 4
KAT2B 0.025 0.008 -10000 0 -0.13 1 1
KAT5 0.025 0.005 -10000 0 -10000 0 0
MAPK14 0.007 0.02 -10000 0 -0.3 1 1
FOXO1 0.024 0.022 -10000 0 -0.43 1 1
T-DHT/AR 0.002 0.092 -10000 0 -0.3 17 17
MAP2K6 0.021 0.024 -10000 0 -0.43 1 1
BRM/BAF57 0.036 0.01 -10000 0 -10000 0 0
MAP2K4 0.022 0.018 -10000 0 -0.14 2 2
SMARCA2 0.025 0.006 -10000 0 -10000 0 0
PDE9A 0.008 0.092 -10000 0 -0.81 4 4
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
CEBPA 0.015 0.049 -10000 0 -0.25 13 13
EHMT2 0.026 0.003 -10000 0 -10000 0 0
cell proliferation 0.001 0.11 0.37 8 -0.39 10 18
NR0B1 -0.041 0.15 -10000 0 -0.31 102 102
EGR1 -0.038 0.14 -10000 0 -0.27 111 111
RXRs/9cRA 0.019 0.085 -10000 0 -0.23 52 52
AR/RACK1/Src 0.001 0.074 0.22 1 -0.28 8 9
AR/GR -0.012 0.1 0.23 2 -0.24 67 69
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
PKN1 0.025 0.005 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0 0.052 -10000 0 -0.3 13 13
T-DHT/AR/TIF2/CARM1 -0.002 0.1 0.35 1 -0.37 20 21
SRC -0.013 0.044 0.2 8 -0.22 12 20
NR3C1 0.026 0.004 -10000 0 -10000 0 0
KLK3 -0.042 0.1 -10000 0 -0.49 2 2
APPBP2 0.022 0.014 -10000 0 -10000 0 0
TRIM24 0.02 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.003 0.073 0.22 7 -0.3 10 17
TMPRSS2 -0.066 0.29 -10000 0 -0.99 45 45
RXRG -0.027 0.14 -10000 0 -0.4 63 63
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.025 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.025 0.006 -10000 0 -10000 0 0
NR2C2 0.018 0.06 -10000 0 -0.43 9 9
KLK2 -0.02 0.1 0.44 1 -0.39 14 15
AR -0.029 0.099 -10000 0 -0.26 67 67
SENP1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 0.015 0.064 -10000 0 -0.33 15 15
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.009 0.048 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.002 0.079 0.37 2 -0.27 10 12
positive regulation of transcription 0.015 0.064 -10000 0 -0.33 15 15
DNAJA1 0.022 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.03 0.011 -10000 0 -10000 0 0
SPDEF -0.005 0.1 -10000 0 -0.43 25 25
T-DHT/AR/TIF2 -0.003 0.1 0.23 3 -0.37 21 24
T-DHT/AR/Hsp90 -0.004 0.072 0.22 6 -0.3 11 17
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
NR2C1 0.026 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.04 -10000 0 -0.24 13 13
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.023 0.009 -10000 0 -10000 0 0
POU2F1 0.021 0.042 -10000 0 -0.43 1 1
T-DHT/AR/DAX-1 -0.032 0.1 0.22 7 -0.25 66 73
CREBBP 0.026 0.003 -10000 0 -10000 0 0
SMARCE1 0.026 0.003 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.004 0.15 0.24 5 -0.36 25 30
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
AKT2 0.022 0.01 -10000 0 -10000 0 0
STXBP4 0.025 0.02 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.013 0.15 0.22 31 -0.31 66 97
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
YWHAB 0.025 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.051 0.017 -10000 0 -0.26 1 1
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
ASIP -0.04 0.14 -10000 0 -0.32 94 94
PRKCI 0.026 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 1 -0.25 1 2
PRKCZ 0.007 0.076 -10000 0 -0.31 23 23
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
AS160/14-3-3 0.01 0.054 -10000 0 -0.51 1 1
VAMP2 0.026 0.002 -10000 0 -10000 0 0
SLC2A4 -0.018 0.16 0.23 24 -0.35 66 90
STX4 0.026 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.016 -10000 0 -0.29 1 1
SFN -0.023 0.11 -10000 0 -0.43 28 28
LNPEP 0.008 0.088 -10000 0 -0.43 20 20
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.37 -9999 0 -1.1 58 58
RAD9A 0.025 0.005 -9999 0 -10000 0 0
AP1 -0.016 0.1 -9999 0 -0.28 56 56
IFNAR2 0.02 0.018 -9999 0 -10000 0 0
AKT1 0.004 0.035 -9999 0 -0.18 11 11
ER alpha/Oestrogen 0.005 0.05 -9999 0 -0.25 15 15
NFX1/SIN3/HDAC complex -0.004 0.072 -9999 0 -0.23 13 13
EGF -0.014 0.11 -9999 0 -0.31 54 54
SMG5 0.025 0.005 -9999 0 -10000 0 0
SMG6 0.026 0.002 -9999 0 -10000 0 0
SP3/HDAC2 0.03 0.027 -9999 0 -10000 0 0
TERT/c-Abl -0.099 0.34 -9999 0 -1 58 58
SAP18 0.025 0.006 -9999 0 -10000 0 0
MRN complex 0.046 0.018 -9999 0 -10000 0 0
WT1 0 0.046 -9999 0 -0.14 45 45
WRN 0.023 0.035 -9999 0 -0.43 3 3
SP1 0.019 0.022 -9999 0 -10000 0 0
SP3 0.022 0.015 -9999 0 -10000 0 0
TERF2IP 0.026 0.003 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.072 0.31 -9999 0 -0.9 58 58
Mad/Max 0.03 0.023 -9999 0 -10000 0 0
TERT -0.13 0.39 -9999 0 -1.2 58 58
CCND1 -0.11 0.34 -9999 0 -0.99 63 63
MAX 0.021 0.015 -9999 0 -10000 0 0
RBBP7 0.025 0.004 -9999 0 -10000 0 0
RBBP4 0.021 0.022 -9999 0 -0.43 1 1
TERF2 0.021 0.006 -9999 0 -10000 0 0
PTGES3 0.026 0.003 -9999 0 -10000 0 0
SIN3A 0.025 0.003 -9999 0 -10000 0 0
Telomerase/911 0.031 0.056 -9999 0 -0.32 3 3
CDKN1B 0.009 0.024 -9999 0 -10000 0 0
RAD1 0.026 0.003 -9999 0 -10000 0 0
XRCC5 0.026 0.003 -9999 0 -10000 0 0
XRCC6 0.026 0.004 -9999 0 -10000 0 0
SAP30 0.025 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0.036 0.007 -9999 0 -10000 0 0
UBE3A 0.022 0.014 -9999 0 -10000 0 0
JUN 0.015 0.025 -9999 0 -0.13 9 9
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.015 -9999 0 -10000 0 0
FOS -0.035 0.13 -9999 0 -0.29 93 93
IFN-gamma/IRF1 0.025 0.035 -9999 0 -0.16 1 1
PARP2 0.026 0.004 -9999 0 -10000 0 0
BLM -0.008 0.1 -9999 0 -0.25 62 62
Telomerase -0.016 0.098 -9999 0 -0.33 32 32
IRF1 0.017 0.036 -9999 0 -0.14 1 1
ESR1 0.01 0.07 -9999 0 -0.35 15 15
KU/TER 0.038 0.007 -9999 0 -10000 0 0
ATM/TRF2 0.037 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.072 -9999 0 -0.27 7 7
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.001 0.074 -9999 0 -0.27 7 7
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC2 0.019 0.022 -9999 0 -10000 0 0
ATM 0.01 0.002 -9999 0 -10000 0 0
SMAD3 0.012 0.016 -9999 0 -0.3 1 1
ABL1 0.025 0.005 -9999 0 -10000 0 0
MXD1 0.021 0.015 -9999 0 -10000 0 0
MRE11A 0.025 0.006 -9999 0 -10000 0 0
HUS1 0.023 0.009 -9999 0 -10000 0 0
RPS6KB1 0.025 0.005 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.086 0.34 -9999 0 -1 54 54
NR2F2 0.017 0.06 -9999 0 -0.22 24 24
MAPK3 -0.014 0.01 -9999 0 -10000 0 0
MAPK1 -0.013 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.022 -9999 0 -0.42 1 1
NFKB1 0.026 0.004 -9999 0 -10000 0 0
HNRNPC 0.026 0.004 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -9999 0 -10000 0 0
NBN 0.024 0.007 -9999 0 -10000 0 0
EGFR -0.02 0.12 -9999 0 -0.41 45 45
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.025 0.12 -9999 0 -0.32 69 69
MYC 0.001 0.088 -9999 0 -0.43 20 20
IL2 0.007 0.024 -9999 0 -10000 0 0
KU 0.038 0.007 -9999 0 -10000 0 0
RAD50 0.026 0.003 -9999 0 -10000 0 0
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
TGFB1 0.021 0.022 -9999 0 -0.42 1 1
TRF2/BLM 0.012 0.072 -9999 0 -0.28 24 24
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.09 0.35 -9999 0 -1 58 58
SP1/HDAC2 0.029 0.032 -9999 0 -10000 0 0
PINX1 0.025 0.005 -9999 0 -10000 0 0
Telomerase/EST1A -0.071 0.31 -9999 0 -0.9 58 58
Smad3/Myc 0.01 0.058 -9999 0 -0.27 19 19
911 complex 0.044 0.021 -9999 0 -10000 0 0
IFNG 0.015 0.021 -9999 0 -0.14 2 2
Telomerase/PinX1 -0.073 0.31 -9999 0 -0.9 58 58
Telomerase/AKT1/mTOR/p70S6K -0.01 0.1 -9999 0 -0.48 8 8
SIN3B 0.025 0.006 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
Telomerase/EST1B -0.072 0.31 -9999 0 -0.9 58 58
response to DNA damage stimulus 0.006 0.009 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.065 0.026 -9999 0 -10000 0 0
TRF2/WRN 0.033 0.025 -9999 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.07 0.31 -9999 0 -0.9 58 58
E2F1 0.009 0.058 -9999 0 -0.36 8 8
ZNFX1 0.025 0.005 -9999 0 -10000 0 0
PIF1 -0.01 0.11 -9999 0 -0.43 29 29
NCL 0.026 0.004 -9999 0 -10000 0 0
DKC1 0.026 0.003 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.021 0.014 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.009 -10000 0 -0.2 1 1
ITGA1 0.015 0.059 -10000 0 -0.22 23 23
CDKN1A -0.059 0.16 -10000 0 -0.37 95 95
PRL-3/alpha Tubulin 0.033 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.06 -10000 0 -0.32 21 21
AGT 0.006 0.092 -10000 0 -0.43 22 22
CCNA2 -0.038 0.079 -10000 0 -0.58 1 1
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
EGR1 -0.027 0.095 -10000 0 -0.3 53 53
CDK2/Cyclin E1 -0.029 0.15 -10000 0 -0.38 50 50
MAPK3 0.012 0.008 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.032 0.015 -10000 0 -10000 0 0
MAPK1 0.012 0.008 -10000 0 -10000 0 0
PTP4A1 -0.025 0.074 -10000 0 -0.62 1 1
PTP4A3 0.023 0.013 -10000 0 -0.13 2 2
PTP4A2 0.022 0.01 -10000 0 -10000 0 0
ITGB1 0.01 0.01 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.006 0.036 -10000 0 -0.31 2 2
Rab GGTase beta/Rab GGTase alpha 0.032 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.008 0.079 -10000 0 -0.57 1 1
RABGGTA 0.026 0.004 -10000 0 -10000 0 0
BCAR1 -0.017 0.019 0.24 1 -0.32 1 2
RHOC -0.057 0.15 -10000 0 -0.36 95 95
RHOA 0.002 0.055 -10000 0 -0.32 10 10
cell motility -0.014 0.095 0.28 1 -0.34 9 10
PRL-1/alpha Tubulin -0.004 0.084 -10000 0 -0.58 1 1
PRL-3/alpha1 Integrin 0.027 0.042 -10000 0 -0.28 6 6
ROCK1 -0.017 0.093 0.28 1 -0.34 9 10
RABGGTB 0.022 0.01 -10000 0 -10000 0 0
CDK2 0.02 0.044 -10000 0 -0.23 12 12
mitosis -0.025 0.073 -10000 0 -0.61 1 1
ATF5 0.02 0.018 -10000 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.026 0.056 -10000 0 -10000 0 0
epithelial cell differentiation -0.014 0.086 -10000 0 -0.38 5 5
ITCH 0.03 0.013 -10000 0 -10000 0 0
WWP1 0.017 0.063 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.43 42 42
PRL -0.011 0.016 -10000 0 -0.13 2 2
neuron projection morphogenesis -0.019 0.11 0.28 19 -0.4 2 21
PTPRZ1 0.016 0.046 -10000 0 -0.38 6 6
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.11 -10000 0 -0.32 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.1 -10000 0 -0.32 14 14
ADAM17 0.025 0.046 -10000 0 -0.42 5 5
ErbB4/ErbB4 0.006 0.051 -10000 0 -0.36 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.013 0.082 -10000 0 -0.34 10 10
NCOR1 0.024 0.028 -10000 0 -0.43 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.1 -10000 0 -0.34 8 8
GRIN2B -0.068 0.13 0.24 10 -0.36 40 50
ErbB4/ErbB2/betacellulin -0.001 0.096 -10000 0 -0.34 12 12
STAT1 0.021 0.028 -10000 0 -10000 0 0
HBEGF 0.023 0.022 -10000 0 -0.13 10 10
PRLR 0.006 0.088 -10000 0 -0.32 30 30
E4ICDs/ETO2 0.022 0.065 -10000 0 -0.35 3 3
axon guidance -0.024 0.079 -10000 0 -0.4 6 6
NEDD4 0.025 0.041 -10000 0 -0.23 9 9
Prolactin receptor/Prolactin receptor/Prolactin 0.016 0.065 -10000 0 -0.31 18 18
CBFA2T3 0.02 0.053 -10000 0 -0.43 7 7
ErbB4/ErbB2/HBEGF 0.027 0.052 -10000 0 -0.28 3 3
MAPK3 -0.017 0.11 0.26 14 -0.33 5 19
STAT1 (dimer) 0.026 0.058 -10000 0 -0.32 1 1
MAPK1 -0.017 0.11 0.27 12 -0.41 2 14
JAK2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.099 -10000 0 -0.34 8 8
NRG1 -0.061 0.13 -10000 0 -0.31 101 101
NRG3 0.001 0.1 -10000 0 -0.43 27 27
NRG2 0.025 0.02 -10000 0 -0.43 1 1
NRG4 0.001 0.079 -10000 0 -0.43 12 12
heart development -0.024 0.079 -10000 0 -0.4 6 6
neural crest cell migration -0.036 0.099 -10000 0 -0.33 8 8
ERBB2 0.01 0.036 -10000 0 -0.29 6 6
WWOX/E4ICDs 0.025 0.057 -10000 0 -0.32 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
ErbB4/EGFR/neuregulin 4 0.004 0.1 -10000 0 -0.34 16 16
apoptosis -0.001 0.11 0.38 29 -10000 0 29
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.026 0.057 -10000 0 -0.37 1 1
ErbB4/ErbB2/epiregulin 0.025 0.056 -10000 0 -0.31 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.005 0.1 -10000 0 -0.38 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.076 -10000 0 -0.31 1 1
MDM2 0.01 0.055 0.25 4 -0.32 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.1 -10000 0 -0.32 8 8
STAT5A -0.028 0.084 -10000 0 -0.41 6 6
ErbB4/EGFR/neuregulin 1 beta -0.045 0.12 -10000 0 -0.38 22 22
DLG4 0.023 0.021 -10000 0 -10000 0 0
GRB2/SHC 0.036 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.022 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.007 0.097 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.012 0.083 -10000 0 -0.38 6 6
LRIG1 0.015 0.069 -10000 0 -0.43 12 12
EREG 0.008 0.036 -10000 0 -0.13 24 24
BTC -0.04 0.14 -10000 0 -0.33 87 87
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.075 -10000 0 -0.4 6 6
ERBB4 0.006 0.051 -10000 0 -0.36 1 1
STAT5B 0.026 0.003 -10000 0 -10000 0 0
YAP1 -0.015 0.13 -10000 0 -0.55 27 27
GRB2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.021 0.067 -10000 0 -0.31 5 5
glial cell differentiation -0.021 0.056 0.5 1 -10000 0 1
WWOX 0.026 0.003 -10000 0 -10000 0 0
cell proliferation -0.071 0.14 -10000 0 -0.43 26 26
TRAIL signaling pathway

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
TNFSF10 0.012 0.07 -10000 0 -0.26 25 25
positive regulation of NF-kappaB transcription factor activity 0.022 0.06 -10000 0 -0.3 13 13
MAP2K4 0.016 0.048 0.21 1 -0.24 2 3
IKBKB 0.025 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.022 0.036 -10000 0 -0.43 3 3
TNFRSF10A 0 0.098 -10000 0 -0.43 24 24
SMPD1 0.007 0.031 -10000 0 -0.18 13 13
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.038 -10000 0 -0.17 15 15
TRAIL/TRAILR2 0.024 0.061 -10000 0 -0.32 13 13
TRAIL/TRAILR3 0.015 0.08 -10000 0 -0.32 22 22
TRAIL/TRAILR1 0.008 0.089 -10000 0 -0.29 38 38
TRAIL/TRAILR4 0.022 0.06 -10000 0 -0.3 13 13
TRAIL/TRAILR1/DAP3/GTP 0.027 0.073 -10000 0 -0.23 35 35
IKK complex 0.014 0.044 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.003 -10000 0 -10000 0 0
MAPK3 0.004 0.048 -10000 0 -0.3 11 11
MAP3K1 0.02 0.049 -10000 0 -0.24 3 3
TRAILR4 (trimer) 0.019 0.038 -10000 0 -0.17 15 15
TRADD 0.025 0.02 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0 0.098 -10000 0 -0.43 24 24
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.059 -10000 0 -0.21 31 31
CFLAR 0.026 0.007 -10000 0 -0.13 1 1
MAPK1 0.004 0.048 -10000 0 -0.3 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP 0.05 0.077 -10000 0 -0.22 33 33
mol:ceramide 0.007 0.031 -10000 0 -0.18 13 13
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.059 0.2 2 -0.28 4 6
TRAF2 0.026 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.009 0.074 -10000 0 -0.43 12 12
CHUK 0.025 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.028 0.078 -10000 0 -0.26 33 33
DAP3 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.001 0.062 0.21 1 -0.27 11 12
JNK cascade 0.022 0.06 -10000 0 -0.3 13 13
TRAIL (trimer) 0.012 0.07 -10000 0 -0.26 25 25
TNFRSF10C 0.009 0.074 -10000 0 -0.43 12 12
TRAIL/TRAILR1/DAP3/GTP/FADD 0.037 0.072 -10000 0 -0.22 33 33
TRAIL/TRAILR2/FADD 0.042 0.051 -10000 0 -0.26 13 13
cell death 0.007 0.031 -10000 0 -0.18 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.22 13 13
TRAILR2 (trimer) 0.022 0.036 -10000 0 -0.43 3 3
CASP8 0.013 0.043 -10000 0 -0.77 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.063 0.053 -10000 0 -0.22 13 13
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.03 0.046 -10000 0 -0.2 14 14
TC10/GTP 0.031 0.04 -10000 0 -0.21 9 9
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.033 -10000 0 -0.22 4 4
HRAS 0.025 0.006 -10000 0 -10000 0 0
APS homodimer 0.014 0.057 -10000 0 -0.43 8 8
GRB14 -0.071 0.16 -10000 0 -0.25 180 180
FOXO3 -0.019 0.15 -10000 0 -0.61 31 31
AKT1 -0.034 0.089 0.34 7 -0.29 2 9
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.03 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
SORBS1 0.023 0.035 -10000 0 -0.43 3 3
CRK 0.026 0.002 -10000 0 -10000 0 0
PTPN1 0.01 0.035 0.16 1 -0.2 4 5
CAV1 0.005 0.039 0.18 11 -0.23 4 15
CBL/APS/CAP/Crk-II/C3G 0.049 0.052 -10000 0 -0.22 10 10
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.032 -10000 0 -0.22 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.028 -10000 0 -0.19 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.036 -10000 0 -0.42 1 1
RPS6KB1 -0.033 0.082 0.33 7 -0.33 1 8
PARD6A 0.026 0.002 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.04 -10000 0 -0.6 2 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.078 -10000 0 -0.27 2 2
HRAS/GTP 0.014 0.025 -10000 0 -0.19 6 6
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.061 0.037 -10000 0 -0.21 4 4
PRKCI 0.019 0.048 -10000 0 -0.44 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.084 -10000 0 -0.21 70 70
SHC1 0.024 0.014 -10000 0 -0.13 4 4
negative regulation of MAPKKK cascade 0.038 0.045 -10000 0 -0.5 2 2
PI3K 0.055 0.031 -10000 0 -0.2 4 4
NCK2 0.026 0.002 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
AKT2 -0.037 0.082 0.47 3 -0.36 1 4
PRKCZ -0.042 0.15 -10000 0 -0.36 88 88
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
SHC/SHIP 0.032 0.049 0.21 13 -0.21 7 20
F2RL2 -0.019 0.1 -10000 0 -0.19 104 104
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
Insulin Receptor/Insulin/Shc 0.039 0.029 -10000 0 -0.22 4 4
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.037 -10000 0 -0.21 4 4
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
CBL/APS/CAP/Crk-II 0.043 0.049 -10000 0 -0.23 10 10
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.038 -10000 0 -0.23 5 5
INPP5D 0.018 0.051 0.18 30 -0.22 7 37
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.034 0.18 -10000 0 -0.75 31 31
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
p62DOK/RasGAP 0.039 0.045 -10000 0 -0.51 2 2
INS 0.015 0.041 -10000 0 -0.37 5 5
mol:PI-3-4-P2 0.018 0.05 0.18 30 -0.22 7 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.035 0.085 0.33 7 -0.25 8 15
PTPRA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TC10/GTP/CIP4 0.032 0.024 -10000 0 -0.26 3 3
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.022 0.024 -10000 0 -0.21 4 4
Insulin Receptor/Insulin/IRS1 0.04 0.028 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS3 0.029 0.033 -10000 0 -0.31 4 4
Par3/Par6 0.047 0.061 -10000 0 -0.22 23 23
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.015 0.075 0.31 7 -0.29 12 19
PDGFB-D/PDGFRB/SLAP 0.021 0.06 -10000 0 -0.3 15 15
PDGFB-D/PDGFRB/APS/CBL 0.034 0.044 -10000 0 -0.26 8 8
AKT1 0.007 0.071 0.33 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.082 0.31 12 -0.3 12 24
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FGR -0.041 0.14 0.34 2 -0.37 74 76
mol:Ca2+ 0.019 0.073 0.28 17 -0.29 4 21
MYC 0.032 0.21 0.41 30 -0.75 22 52
SHC1 0.024 0.014 -10000 0 -0.13 4 4
HRAS/GDP 0.03 0.029 0.17 15 -10000 0 15
LRP1/PDGFRB/PDGFB 0.051 0.014 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.018 0.074 0.28 17 -0.3 4 21
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.001 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.038 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.031 0.027 -10000 0 -0.31 2 2
cell cycle arrest 0.021 0.06 -10000 0 -0.3 15 15
HRAS 0.025 0.006 -10000 0 -10000 0 0
HIF1A 0.005 0.066 0.31 11 -10000 0 11
GAB1 0.012 0.091 0.31 14 -0.31 11 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.014 0.096 0.33 20 -0.31 7 27
PDGFB-D/PDGFRB 0.049 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.011 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.015 0.079 0.2 6 -0.29 19 25
positive regulation of MAPKKK cascade 0.037 0.012 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.018 0.074 0.28 17 -0.3 4 21
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.025 0.036 -10000 0 -0.18 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
BLK -0.018 0.12 0.31 1 -0.47 31 32
PTPN2 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.012 -10000 0 -10000 0 0
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
VAV2 0.015 0.1 0.32 16 -0.34 13 29
CBL 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.012 -10000 0 -10000 0 0
LCK -0.072 0.18 0.34 2 -0.4 106 108
PDGFRB 0.025 0.014 -10000 0 -0.14 3 3
ACP1 0.026 0.004 -10000 0 -10000 0 0
HCK 0.003 0.083 0.31 1 -0.58 9 10
ABL1 0.006 0.094 0.29 17 -0.32 12 29
PDGFB-D/PDGFRB/CBL 0.015 0.093 0.3 13 -0.33 12 25
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.025 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.028 -10000 0 -10000 0 0
cell proliferation 0.035 0.19 0.39 32 -0.66 22 54
SLA 0.006 0.077 -10000 0 -0.28 28 28
actin cytoskeleton reorganization 0.033 0.047 0.33 4 -0.21 2 6
SRC 0.011 0.025 -10000 0 -10000 0 0
PI3K 0.006 0.024 -10000 0 -0.21 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.044 0.031 -10000 0 -0.21 1 1
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
PLCgamma1/SPHK1 0.02 0.084 0.31 12 -0.3 12 24
LYN 0.01 0.054 0.3 1 -0.5 4 5
LRP1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
STAT5B 0.026 0.003 -10000 0 -10000 0 0
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
NCK1-2/p130 Cas 0.072 0.032 -10000 0 -0.22 2 2
SPHK1 0.005 0.086 -10000 0 -0.43 17 17
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.018 0.074 0.28 17 -0.3 4 21
PLCG1 0.018 0.075 0.3 15 -0.3 4 19
NHERF/PDGFRB 0.048 0.031 -10000 0 -0.26 4 4
YES1 0.001 0.085 -10000 0 -0.49 13 13
cell migration 0.047 0.031 -10000 0 -0.26 4 4
SHC/Grb2/SOS1 0.07 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.025 0.01 -10000 0 -10000 0 0
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
NHERF1-2/PDGFRB/PTEN 0.059 0.034 -10000 0 -0.24 4 4
FYN 0.002 0.078 0.3 1 -0.4 15 16
DOK1 0.015 0.024 0.18 7 -0.24 1 8
HRAS/GTP 0.018 0.005 -10000 0 -10000 0 0
PDGFB 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.031 0.15 0.39 27 -0.43 22 49
PRKCD 0.006 0.066 0.18 17 -0.24 26 43
FER 0.009 0.06 0.19 16 -0.24 20 36
MAPKKK cascade 0.006 0.066 0.41 6 -10000 0 6
RASA1 0.019 0.033 0.19 16 -10000 0 16
NCK1 0.025 0.02 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.033 0.026 0.18 6 -0.22 1 7
PDGFB-D/PDGFRB/SHB 0.037 0.011 -10000 0 -10000 0 0
chemotaxis 0.006 0.093 0.29 17 -0.32 12 29
STAT1-3-5/STAT1-3-5 0.055 0.045 -10000 0 -0.21 11 11
Bovine Papilomavirus E5/PDGFRB 0.017 0.012 -10000 0 -0.087 3 3
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
Aurora A signaling

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.025 0.045 0.21 3 -0.27 3 6
BIRC5 -0.058 0.16 -10000 0 -0.3 129 129
NFKBIA 0.013 0.035 0.25 3 -0.24 2 5
CPEB1 0.013 0.074 -10000 0 -0.43 14 14
AKT1 0.013 0.033 0.23 2 -0.24 2 4
NDEL1 0.026 0.002 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.031 -10000 0 -0.22 2 2
NDEL1/TACC3 0.043 0.043 0.2 2 -0.31 2 4
GADD45A 0.012 0.042 -10000 0 -0.14 30 30
GSK3B 0.028 0.025 -10000 0 -0.44 1 1
PAK1/Aurora A 0.024 0.05 -10000 0 -0.25 7 7
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.013 0.077 -10000 0 -0.3 30 30
TP53 0.017 0.052 -10000 0 -0.25 15 15
DLG7 0.013 0.03 -10000 0 -0.24 2 2
AURKAIP1 0.022 0.01 -10000 0 -10000 0 0
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.043 0.048 0.21 2 -0.33 2 4
G2/M transition of mitotic cell cycle 0.028 0.031 -10000 0 -0.22 2 2
AURKA 0.022 0.039 -10000 0 -0.29 2 2
AURKB -0.043 0.13 -10000 0 -0.29 97 97
CDC25B 0.021 0.029 -10000 0 -0.23 2 2
G2/M transition checkpoint 0.012 0.026 -10000 0 -0.22 2 2
mRNA polyadenylation 0.022 0.051 -10000 0 -0.25 12 12
Aurora A/CPEB 0.023 0.051 -10000 0 -0.25 12 12
Aurora A/TACC1/TRAP/chTOG 0.058 0.039 -10000 0 -0.24 3 3
BRCA1 0.025 0.012 -10000 0 -0.13 3 3
centrosome duplication 0.024 0.05 -10000 0 -0.25 7 7
regulation of centrosome cycle 0.039 0.045 0.19 2 -0.31 2 4
spindle assembly 0.056 0.039 -10000 0 -0.24 3 3
TDRD7 0.025 0.021 -10000 0 -0.43 1 1
Aurora A/RasGAP/Survivin 0.018 0.09 0.2 3 -0.21 38 41
CENPA -0.03 0.12 -10000 0 -0.38 49 49
Aurora A/PP2A 0.032 0.034 -10000 0 -0.24 2 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.016 0.036 0.18 1 -0.23 2 3
negative regulation of DNA binding 0.017 0.053 -10000 0 -0.25 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
Ajuba/Aurora A 0.012 0.027 -10000 0 -0.22 2 2
mitotic prometaphase 0.011 0.035 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.039 -10000 0 -0.29 2 2
TACC1 0.025 0.005 -10000 0 -10000 0 0
TACC3 0.011 0.053 -10000 0 -0.15 40 40
Aurora A/Antizyme1 0.04 0.035 -10000 0 -0.22 2 2
Aurora A/RasGAP 0.033 0.032 -10000 0 -0.24 1 1
OAZ1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.028 0.015 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.032 -10000 0 -0.26 4 4
Importin alpha/Importin beta/TPX2 -0.013 0.077 -10000 0 -0.3 30 30
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.064 -10000 0 -0.24 17 17
PAK1 0.008 0.061 -10000 0 -0.16 46 46
CKAP5 0.025 0.005 -10000 0 -10000 0 0
IFN-gamma pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.033 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -0.13 1 1
STAT1 (dimer)/Cbp/p300 0.038 0.05 0.29 2 -0.23 1 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.025 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.074 -10000 0 -0.23 24 24
CaM/Ca2+ 0.046 0.034 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.019 0.033 -10000 0 -10000 0 0
AKT1 0.002 0.039 0.26 2 -10000 0 2
MAP2K1 -0.002 0.036 0.23 4 -10000 0 4
MAP3K11 0.011 0.032 0.28 2 -10000 0 2
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.059 0.19 -10000 0 -0.41 101 101
Rap1/GTP 0.012 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.056 0.035 -10000 0 -10000 0 0
CEBPB 0.016 0.11 0.29 2 -0.46 18 20
STAT3 0.026 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.031 0.15 -10000 0 -1.1 8 8
STAT1 0.01 0.036 0.26 3 -10000 0 3
CALM1 0.025 0.009 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.011 0.021 -10000 0 -0.13 5 5
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
STAT1 (dimer)/PIAS1 0.022 0.043 0.26 3 -0.2 4 7
CEBPB/PTGES2/Cbp/p300 0.028 0.074 -10000 0 -0.32 15 15
mol:Ca2+ 0.042 0.031 -10000 0 -10000 0 0
MAPK3 0.016 0.065 -10000 0 -0.74 2 2
STAT1 (dimer) -0.021 0.1 -10000 0 -0.32 22 22
MAPK1 0.011 0.089 -10000 0 -0.69 6 6
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.011 -10000 0 -10000 0 0
CAMK2D 0.025 0.02 -10000 0 -0.43 1 1
DAPK1 0.011 0.12 0.32 3 -0.59 18 21
SMAD7 -0.009 0.046 0.2 2 -0.17 3 5
CBL/CRKL/C3G 0.035 0.032 0.29 1 -10000 0 1
PI3K 0.044 0.035 -10000 0 -10000 0 0
IFNG 0.011 0.021 -10000 0 -0.13 5 5
apoptosis 0.007 0.11 0.26 4 -0.44 23 27
CAMK2G 0.024 0.021 -10000 0 -0.43 1 1
STAT3 (dimer) 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.099 0.17 -10000 0 -0.26 222 222
CAMK2B -0.018 0.12 -10000 0 -0.27 69 69
FRAP1 -0.002 0.036 0.21 4 -10000 0 4
PRKCD -0.008 0.055 0.24 3 -0.22 2 5
RAP1B 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.074 -10000 0 -0.23 24 24
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.022 0.04 -10000 0 -0.43 4 4
IRF1 -0.001 0.062 0.26 4 -0.31 7 11
STAT1 (dimer)/PIASy 0.022 0.041 0.28 3 -10000 0 3
SOCS1 0.001 0.17 -10000 0 -1.4 8 8
mol:GDP 0.032 0.03 0.27 1 -10000 0 1
CASP1 -0.012 0.058 0.2 3 -0.25 13 16
PTGES2 0.025 0.005 -10000 0 -10000 0 0
IRF9 0.022 0.04 0.16 7 -0.19 1 8
mol:PI-3-4-5-P3 0.031 0.028 -10000 0 -10000 0 0
RAP1/GDP 0.027 0.025 -10000 0 -10000 0 0
CBL 0.01 0.031 0.28 2 -10000 0 2
MAP3K1 0.01 0.033 0.28 2 -10000 0 2
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
PIAS4 0.025 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.074 -10000 0 -0.23 24 24
PTPN11 0.013 0.029 0.23 2 -10000 0 2
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
PTK2 0.009 0.088 -10000 0 -0.35 14 14
positive regulation of JNK cascade -0.007 0.092 -10000 0 -0.32 12 12
CDC42/GDP 0.02 0.12 -10000 0 -0.41 13 13
Rac1/GDP 0.004 0.12 -10000 0 -0.42 10 10
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.002 0.11 -10000 0 -0.4 12 12
nectin-3/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
RAPGEF1 0 0.12 0.28 2 -0.43 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.013 0.12 -10000 0 -0.48 8 8
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
TLN1 0.002 0.017 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.083 -10000 0 -0.31 9 9
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
PVR 0.022 0.01 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.01 -10000 0 -10000 0 0
mol:GDP -0.002 0.14 -10000 0 -0.5 13 13
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.066 0.043 -10000 0 -0.22 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
positive regulation of lamellipodium assembly -0.003 0.088 -10000 0 -0.31 12 12
PVRL1 0.011 0.076 -10000 0 -0.43 15 15
PVRL3 0.019 0.056 -10000 0 -0.43 8 8
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.28 122 122
CLDN1 0.01 0.073 -10000 0 -0.43 12 12
JAM-A/CLDN1 0.049 0.063 -10000 0 -0.24 20 20
SRC -0.014 0.12 -10000 0 -0.48 14 14
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
FARP2 -0.01 0.15 -10000 0 -0.56 12 12
RAC1 0.023 0.009 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.042 -10000 0 -0.26 7 7
nectin-1/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
nectin-2/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.027 0.029 -10000 0 -0.26 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.067 -10000 0 -0.27 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.028 -10000 0 -0.23 4 4
F11R 0.022 0.03 -10000 0 -0.16 11 11
positive regulation of filopodium formation -0.007 0.092 -10000 0 -0.32 12 12
alphaV/beta3 Integrin/Talin 0.035 0.062 0.21 4 -0.32 2 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
PIP5K1C 0.005 0.02 -10000 0 -0.16 7 7
VAV2 0.002 0.14 -10000 0 -0.52 10 10
RAP1/GDP 0.011 0.11 -10000 0 -0.37 12 12
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.044 -10000 0 -0.26 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
Rac1/GTP -0.001 0.11 -10000 0 -0.37 12 12
PTPRM 0.01 0.025 -10000 0 -0.17 9 9
E-cadherin/beta catenin/alpha catenin 0.022 0.1 -10000 0 -0.23 61 61
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.016 0.12 -9999 0 -0.28 70 70
Ran/GTP/Exportin 1/HDAC1 0.006 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.12 -9999 0 -0.28 65 65
SUMO1 0.026 0.002 -9999 0 -10000 0 0
ZFPM1 0.025 0.02 -9999 0 -0.43 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
FKBP3 0.026 0.004 -9999 0 -10000 0 0
Histones 0.026 0.075 -9999 0 -0.23 4 4
YY1/LSF 0.027 0.04 -9999 0 -0.24 6 6
SMG5 0.025 0.005 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.016 0.087 -9999 0 -0.23 67 67
I kappa B alpha/HDAC1 0.009 0.073 -9999 0 -0.31 9 9
SAP18 0.025 0.005 -9999 0 -10000 0 0
RELA -0.006 0.083 -9999 0 -0.21 64 64
HDAC1/Smad7 0.034 0.026 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
HDAC3/TR2 0.01 0.071 -9999 0 -0.25 5 5
NuRD/MBD3 Complex 0.019 0.023 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.009 0.088 -9999 0 -0.31 7 7
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.015 0.064 -9999 0 -0.33 15 15
GATA1 0.013 0.025 -9999 0 -0.13 7 7
Mad/Max 0.037 0.008 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.066 -9999 0 -0.36 1 1
RBBP7 0.026 0.003 -9999 0 -10000 0 0
NPC 0.016 0.001 -9999 0 -10000 0 0
RBBP4 0.021 0.022 -9999 0 -0.43 1 1
MAX 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
NFKBIA -0.013 0.075 -9999 0 -0.19 68 68
KAT2B 0.025 0.008 -9999 0 -0.13 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.021 0.017 -9999 0 -10000 0 0
SIN3 complex 0.059 0.023 -9999 0 -10000 0 0
SMURF1 0.021 0.011 -9999 0 -10000 0 0
CHD3 0.025 0.02 -9999 0 -0.43 1 1
SAP30 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.024 0.028 -9999 0 -0.43 2 2
YY1/HDAC3 0.002 0.062 -9999 0 -0.23 8 8
YY1/HDAC2 0.028 0.036 -9999 0 -0.2 7 7
YY1/HDAC1 0.022 0.038 -9999 0 -0.21 7 7
NuRD/MBD2 Complex (MeCP1) 0.019 0.029 -9999 0 -0.34 1 1
PPARG -0.026 0.12 -9999 0 -0.29 78 78
HDAC8/hEST1B 0.049 0.016 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.017 0.054 -9999 0 -0.34 10 10
HDAC3/SMRT (N-CoR2) 0.01 0.071 -9999 0 -0.27 4 4
MBD3L2 -0.015 0.005 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.026 -9999 0 -10000 0 0
CREBBP 0.026 0.003 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.014 0.063 -9999 0 -10000 0 0
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC3 -0.01 0.064 -9999 0 -0.17 68 68
HDAC2 0.025 0.005 -9999 0 -10000 0 0
YY1 0.017 0.024 -9999 0 -0.24 4 4
HDAC8 0.026 0.003 -9999 0 -10000 0 0
SMAD7 0.026 0.004 -9999 0 -10000 0 0
NCOR2 0.026 0.003 -9999 0 -10000 0 0
MXD1 0.026 0.002 -9999 0 -10000 0 0
STAT3 0.018 0.027 -9999 0 -0.28 4 4
NFKB1 0.026 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.034 0.042 -9999 0 -0.23 5 5
YY1/SAP30/HDAC1 0.034 0.039 -9999 0 -0.19 7 7
EP300 0.022 0.04 -9999 0 -0.43 4 4
STAT3 (dimer non-phopshorylated) 0.018 0.027 -9999 0 -0.28 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.075 -9999 0 -0.19 68 68
histone deacetylation 0.031 0.037 -9999 0 -0.33 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.06 -9999 0 -0.22 8 8
nuclear export -0.048 0.015 -9999 0 -10000 0 0
PRKACA 0.025 0.005 -9999 0 -10000 0 0
GATAD2B 0.026 0.004 -9999 0 -10000 0 0
GATAD2A 0.025 0.005 -9999 0 -10000 0 0
GATA2/HDAC3 0.006 0.08 -9999 0 -0.26 15 15
GATA1/HDAC1 0.029 0.02 -9999 0 -10000 0 0
GATA1/HDAC3 0.007 0.072 -9999 0 -0.25 6 6
CHD4 0.025 0.007 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.031 0.12 -9999 0 -0.32 69 69
SIN3/HDAC complex/Mad/Max 0.017 0.034 -9999 0 -10000 0 0
NuRD Complex 0.016 0.066 -9999 0 -0.22 6 6
positive regulation of chromatin silencing 0.024 0.073 -9999 0 -0.23 4 4
SIN3B 0.025 0.006 -9999 0 -10000 0 0
MTA2 0.025 0.005 -9999 0 -10000 0 0
SIN3A 0.026 0.003 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
HDAC complex 0.053 0.031 -9999 0 -0.23 1 1
GATA1/Fog1 0.034 0.022 -9999 0 -0.31 1 1
FKBP25/HDAC1/HDAC2 0.042 0.023 -9999 0 -10000 0 0
TNF -0.06 0.16 -9999 0 -0.26 151 151
negative regulation of cell growth 0.02 0.047 -9999 0 -0.24 6 6
NuRD/MBD2/PRMT5 Complex 0.019 0.029 -9999 0 -0.34 1 1
Ran/GTP/Exportin 1 0.043 0.019 -9999 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.019 0.11 -9999 0 -0.29 69 69
SIN3/HDAC complex/NCoR1 0.02 0.047 -9999 0 -0.25 9 9
TFCP2 0.025 0.02 -9999 0 -0.43 1 1
NR2C1 0.026 0.003 -9999 0 -10000 0 0
MBD3 0.025 0.006 -9999 0 -10000 0 0
MBD2 0.026 0.004 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.041 -10000 0 -0.26 13 13
SNTA1 -0.001 0.1 -10000 0 -0.43 27 27
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.012 0.032 -10000 0 -0.26 7 7
MAPK12 -0.003 0.017 -10000 0 -0.22 3 3
CCND1 0 0.061 -10000 0 -0.41 11 11
p38 gamma/SNTA1 0.013 0.062 0.19 18 -0.21 25 43
MAP2K3 0.025 0.01 -10000 0 -10000 0 0
PKN1 0.025 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.017 -10000 0 -0.22 3 3
MAP2K6 0.003 0.011 -10000 0 -0.24 1 1
MAPT 0.004 0.06 0.24 5 -0.23 19 24
MAPK13 0.001 0.053 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.028 0.023 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.016 0.054 -10000 0 -0.26 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.082 0.19 4 -0.28 15 19
NFKBIA -0.014 0.073 -10000 0 -0.23 46 46
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.008 -10000 0 -10000 0 0
ARRB2 0.014 0.002 -10000 0 -10000 0 0
REL 0.007 0.086 -10000 0 -0.43 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.019 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
NF kappa B1 p50 dimer 0.02 0.011 0.25 1 -10000 0 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.009 0.077 -10000 0 -0.22 41 41
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.009 0.082 0.19 2 -0.28 14 16
SRC 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.038 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.077 -10000 0 -0.22 41 41
IKBKB 0.025 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.009 0.083 -10000 0 -0.35 23 23
I kappa B alpha/PIK3R1 -0.001 0.087 0.19 4 -0.3 16 20
cell death 0.008 0.079 0.18 3 -0.27 14 17
NF kappa B1 p105/c-Rel 0.016 0.054 -10000 0 -0.26 18 18
LCK -0.019 0.11 -10000 0 -0.43 30 30
BCL3 0.018 0.024 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
mol:S1P 0.001 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.039 -10000 0 -0.25 8 8
GNAO1 0.022 0.046 -10000 0 -0.44 5 5
S1P/S1P3/G12/G13 0.038 0.043 -10000 0 -0.23 9 9
AKT1 0.015 0.074 -10000 0 -0.38 14 14
AKT3 0.013 0.13 -10000 0 -0.86 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.13 3 3
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.022 0.012 -10000 0 -10000 0 0
GNAI1 0.02 0.036 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.006 0.075 -10000 0 -0.2 45 45
S1PR2 0.022 0.036 -10000 0 -0.43 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.074 -10000 0 -0.27 20 20
MAPK3 0.006 0.07 -10000 0 -0.26 20 20
MAPK1 0.008 0.065 -10000 0 -0.25 17 17
JAK2 0.008 0.076 0.19 8 -0.29 14 22
CXCR4 0.001 0.078 -10000 0 -0.27 22 22
FLT1 0.026 0.024 -10000 0 -0.49 1 1
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.005 0.066 -10000 0 -0.27 16 16
S1P/S1P3/Gi 0.011 0.075 -10000 0 -0.27 20 20
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.073 -10000 0 -0.27 15 15
VEGFA 0.021 0.033 -10000 0 -0.13 22 22
S1P/S1P2/Gi 0.014 0.062 -10000 0 -0.27 9 9
VEGFR1 homodimer/VEGFA homodimer 0.036 0.034 -10000 0 -0.4 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.002 0.08 -10000 0 -0.25 41 41
GNAQ 0.026 0.004 -10000 0 -10000 0 0
GNAZ 0.026 0.008 -10000 0 -10000 0 0
G12/G13 0.032 0.015 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.34 17 17
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.012 0.068 -10000 0 -0.28 13 13
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.032 -10000 0 -0.21 8 8
TRAF2/ASK1 0.03 0.032 -10000 0 -0.26 6 6
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 0.011 0.072 -10000 0 -0.34 6 6
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.092 0.2 4 -0.31 17 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.002 0.09 -10000 0 -0.27 40 40
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -10000 0 0
GADD45A 0.012 0.042 -10000 0 -0.14 30 30
GADD45B 0.01 0.067 -10000 0 -0.21 33 33
MAP3K1 0.024 0.019 -10000 0 -0.13 7 7
MAP3K6 0.02 0.019 -10000 0 -0.13 6 6
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
MAP3K4 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.026 0.041 -10000 0 -0.3 6 6
TAK1/TAB family -0.002 0.025 0.16 7 -0.13 5 12
RAC1/OSM/MEKK3 0.042 0.02 -10000 0 -10000 0 0
TRAF2 0.026 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.059 -10000 0 -0.28 5 5
TRAF6 0.006 0.013 -10000 0 -0.3 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.018 0.12 -10000 0 -0.27 69 69
CCM2 0.022 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.073 -10000 0 -0.25 34 34
MAPK11 0.019 0.056 -10000 0 -0.43 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.021 0.08 -10000 0 -0.25 36 36
OSM/MEKK3 0.032 0.015 -10000 0 -10000 0 0
TAOK1 -0.012 0.085 -10000 0 -0.29 44 44
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
MAP3K10 0.019 0.023 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.021 0.028 -10000 0 -0.2 7 7
GADD45/MTK1/MTK1 0.027 0.068 -10000 0 -0.22 24 24
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.21 -10000 0 -0.94 22 22
oxygen homeostasis 0.002 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.035 0.09 -10000 0 -0.32 5 5
EPO 0.027 0.13 -10000 0 -0.5 6 6
FIH (dimer) 0.022 0.021 -10000 0 -10000 0 0
APEX1 0.022 0.024 -10000 0 -10000 0 0
SERPINE1 -0.011 0.19 -10000 0 -0.45 64 64
FLT1 0.013 0.14 -10000 0 -0.69 13 13
ADORA2A 0.017 0.15 0.32 5 -0.46 10 15
germ cell development 0.016 0.16 -10000 0 -0.47 20 20
SLC11A2 0.023 0.15 -10000 0 -0.5 7 7
BHLHE40 0.018 0.16 -10000 0 -0.54 14 14
HIF1AN 0.022 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.036 0.12 -10000 0 -0.36 8 8
ETS1 0.026 0.054 -10000 0 -0.43 6 6
CITED2 0.017 0.12 -10000 0 -0.66 9 9
KDR 0.016 0.14 -10000 0 -0.79 13 13
PGK1 0.023 0.15 -10000 0 -0.47 10 10
SIRT1 0.025 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.059 0.18 -10000 0 -0.51 12 12
EPAS1 0.012 0.073 -10000 0 -0.3 8 8
SP1 0.025 0.024 -10000 0 -10000 0 0
ABCG2 0.022 0.16 -10000 0 -0.55 8 8
EFNA1 0.023 0.15 -10000 0 -0.45 13 13
FXN 0.018 0.14 0.33 4 -0.49 6 10
POU5F1 0.015 0.17 -10000 0 -0.49 20 20
neuron apoptosis -0.058 0.18 0.5 12 -10000 0 12
EP300 0.022 0.04 -10000 0 -0.43 4 4
EGLN3 0.012 0.069 -10000 0 -0.43 11 11
EGLN2 0.018 0.022 -10000 0 -10000 0 0
EGLN1 0.022 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.049 0.015 -10000 0 -10000 0 0
VHL 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.021 0.025 -10000 0 -0.15 1 1
SLC2A1 0.015 0.14 0.35 2 -0.5 7 9
TWIST1 0.011 0.15 0.34 2 -0.5 13 15
ELK1 0.031 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.042 0.12 -10000 0 -0.36 7 7
VEGFA 0.022 0.15 -10000 0 -0.46 10 10
CREBBP 0.026 0.003 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.029 0.13 -10000 0 -0.31 78 78
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.058 -10000 0 -0.27 7 7
HIF1A 0.009 0.034 -10000 0 -0.25 6 6
COPS5 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.03 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A -0.013 0.11 -10000 0 -0.3 55 55
ARNT/IPAS -0.006 0.096 -10000 0 -0.3 43 43
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.018 0.047 -10000 0 -0.27 7 7
CUL2 0.024 0.007 -10000 0 -10000 0 0
OS9 0.025 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.049 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.021 0.047 -10000 0 -0.26 7 7
PHD1-3/OS9 0.047 0.046 -10000 0 -0.22 9 9
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.051 0.29 1 -0.26 6 7
VHL 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.047 -10000 0 -0.27 6 6
EGLN3 0.016 0.066 -10000 0 -0.43 11 11
EGLN2 0.022 0.01 -10000 0 -10000 0 0
EGLN1 0.026 0.004 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.43 13 13
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.065 -10000 0 -0.53 6 6
ARNT 0.025 0.008 -10000 0 -0.13 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.006 0.069 0.31 1 -0.29 7 8
Canonical NF-kappaB 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
FBXW11 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.061 0.21 7 -0.28 1 8
ERC1 0.024 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.051 -10000 0 -0.3 9 9
NFKBIA 0.019 0.034 0.21 15 -10000 0 15
BIRC2 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
RIPK2 0.024 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.033 -10000 0 -10000 0 0
IKK complex/A20 0.03 0.098 -10000 0 -0.39 4 4
NEMO/A20/RIP2 0.024 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.038 0.044 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.045 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.041 0.025 -10000 0 -0.23 1 1
NOD2 0.011 0.069 -10000 0 -0.43 10 10
NFKB1 0.028 0.004 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
MALT1 0.026 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.037 0.01 -10000 0 -10000 0 0
ATM 0.025 0.005 -10000 0 -10000 0 0
TNF/TNFR1A -0.031 0.12 -10000 0 -0.32 69 69
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
CHUK 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.26 151 151
NF kappa B1 p50/RelA 0.056 0.016 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.034 0.21 15 -10000 0 15
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
IKK complex 0.052 0.05 -10000 0 -10000 0 0
CYLD 0.026 0.003 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.054 -10000 0 -0.36 1 1
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.018 -10000 0 -10000 0 0
CDKN1B 0.014 0.063 -10000 0 -0.28 16 16
CDKN1A 0.002 0.066 -10000 0 -0.29 15 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
FOXO3 0.015 0.044 -10000 0 -0.28 9 9
AKT1 0.007 0.058 -10000 0 -0.3 18 18
BAD 0.025 0.005 -10000 0 -10000 0 0
AKT3 0.01 0.046 -10000 0 -0.48 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.062 -10000 0 -0.28 17 17
AKT1/ASK1 0.027 0.064 -10000 0 -0.27 18 18
BAD/YWHAZ 0.044 0.02 -10000 0 -10000 0 0
RICTOR 0.026 0.003 -10000 0 -10000 0 0
RAF1 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.062 0.26 18 -10000 0 18
TSC1 0.009 0.057 -10000 0 -0.28 17 17
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.06 -10000 0 -0.28 15 15
EP300 0.022 0.04 -10000 0 -0.43 4 4
mol:GDP 0.011 0.06 -10000 0 -0.29 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.01 0.059 -10000 0 -0.28 17 17
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.005 0.016 -10000 0 -0.25 2 2
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
MAPKAP1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.068 0.46 2 -0.19 7 9
YWHAH 0.019 0.033 -10000 0 -10000 0 0
AKT1S1 0.016 0.037 -10000 0 -0.28 4 4
CASP9 0.011 0.05 -10000 0 -0.28 11 11
YWHAB 0.025 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.065 0.24 2 -0.27 15 17
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
YWHAE 0.026 0.002 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.001 0.061 -10000 0 -0.31 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.018 -10000 0 -10000 0 0
CHUK 0.01 0.056 -10000 0 -0.28 16 16
BAD/BCL-XL 0.032 0.061 -10000 0 -0.27 17 17
mTORC2 0.032 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.02 -10000 0 -0.29 2 2
FOXO1-3a-4/14-3-3 family 0.023 0.08 0.23 1 -0.36 5 6
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
MDM2 0.013 0.061 0.26 1 -0.28 16 17
MAPKKK cascade -0.032 0.059 0.28 15 -10000 0 15
MDM2/Cbp/p300 0.043 0.064 0.26 1 -0.27 13 14
TSC1/TSC2 0.014 0.068 0.24 15 -0.28 17 32
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.062 0.25 1 -0.26 13 14
glucose import -0.016 0.064 0.21 2 -0.24 35 37
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.047 0.2 14 -10000 0 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.051 -10000 0 -0.22 27 27
GSK3A 0.017 0.041 -10000 0 -0.28 5 5
FOXO1 0.011 0.059 -10000 0 -0.28 16 16
GSK3B 0.011 0.057 -10000 0 -0.28 16 16
SFN -0.023 0.11 -10000 0 -0.43 28 28
G1/S transition of mitotic cell cycle 0.02 0.051 0.26 10 -0.28 4 14
p27Kip1/14-3-3 family 0.024 0.066 -10000 0 -0.93 1 1
PRKACA 0.025 0.005 -10000 0 -10000 0 0
KPNA1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
RHEB 0.02 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.002 0.14 -10000 0 -1.3 5 5
PLK1 0.024 0.16 -10000 0 -1.3 5 5
CDKN1B 0.052 0.11 -10000 0 -0.34 7 7
FOXO3 0.043 0.098 -10000 0 -0.52 5 5
KAT2B 0.03 0.014 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.076 -10000 0 -0.57 5 5
CAT 0.036 0.12 -10000 0 -0.69 4 4
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.016 -10000 0 -10000 0 0
FOXO1 0.008 0.08 -10000 0 -0.62 5 5
MAPK10 0.044 0.061 0.19 68 -0.21 2 70
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.06 0.065 0.29 2 -0.36 1 3
response to oxidative stress 0.008 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.044 0.1 -10000 0 -0.47 6 6
XPO1 0.027 0.002 -10000 0 -10000 0 0
EP300 0.023 0.041 -10000 0 -0.43 4 4
BCL2L11 0.024 0.12 -10000 0 -1.3 4 4
FOXO1/SKP2 0.018 0.082 -10000 0 -0.51 7 7
mol:GDP 0.008 0.01 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A -0.033 0.22 -10000 0 -0.49 80 80
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.035 0.071 -10000 0 -0.57 2 2
MST1 0.006 0.1 -10000 0 -0.36 32 32
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.001 0.094 -10000 0 -0.66 2 2
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.035 0.064 0.19 54 -0.22 11 65
MAPK9 0.046 0.059 0.19 71 -10000 0 71
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
YWHAE 0.026 0.002 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
SIRT1 0.024 0.007 -10000 0 -10000 0 0
SOD2 0.054 0.1 -10000 0 -0.95 1 1
RBL2 0.057 0.095 -10000 0 -1.1 1 1
RAL/GDP 0.037 0.018 -10000 0 -10000 0 0
CHUK 0.03 0.013 -10000 0 -10000 0 0
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
RAL/GTP 0.04 0.019 -10000 0 -10000 0 0
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
FASLG 0.025 0.023 -10000 0 -10000 0 0
SKP2 0.021 0.046 -10000 0 -0.32 8 8
USP7 0.027 0.002 -10000 0 -10000 0 0
IKBKB 0.03 0.013 -10000 0 -10000 0 0
CCNB1 0.032 0.1 -10000 0 -0.52 3 3
FOXO1-3a-4/beta catenin 0.079 0.092 -10000 0 -0.39 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.081 -10000 0 -0.5 7 7
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
SGK1 0.019 0.07 -10000 0 -0.4 13 13
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.006 -10000 0 -10000 0 0
ZFAND5 0.059 0.064 0.35 3 -10000 0 3
SFN -0.023 0.11 -10000 0 -0.43 28 28
CDK2 0.02 0.046 -10000 0 -0.22 13 13
FOXO3A/14-3-3 0.008 0.086 -10000 0 -0.68 2 2
CREBBP 0.026 0.014 -10000 0 -10000 0 0
FBXO32 0.051 0.15 -10000 0 -0.94 5 5
BCL6 0.052 0.11 -10000 0 -0.65 6 6
RALB 0.027 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTK2 0.023 0.008 -10000 0 -10000 0 0
CRKL 0.01 0.037 0.16 2 -0.22 11 13
GRB2/SOS1/SHC 0.05 0.014 -10000 0 -10000 0 0
HRAS 0.025 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.02 0.039 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.042 0.046 -10000 0 -0.24 12 12
AKT1 -0.009 0.041 0.17 7 -0.2 10 17
BAD -0.009 0.038 0.16 7 -0.22 1 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.038 0.16 2 -0.22 12 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.027 0.041 0.2 1 -0.22 12 13
RAF1 0.008 0.059 -10000 0 -0.42 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.052 0.045 -10000 0 -0.21 11 11
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.043 -10000 0 -0.24 12 12
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RPS6KB1 -0.008 0.043 0.19 7 -0.23 1 8
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.002 0.049 -10000 0 -0.34 4 4
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.034 -10000 0 -0.2 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.064 0.047 -10000 0 -0.19 12 12
IGF-1R heterotetramer 0.025 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.042 0.044 -10000 0 -0.22 12 12
Crk/p130 Cas/Paxillin 0.051 0.046 0.21 2 -0.2 13 15
IGF1R 0.025 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.077 -10000 0 -0.35 19 19
IRS2/Crk 0.019 0.039 0.16 2 -0.21 13 15
PI3K 0.054 0.045 -10000 0 -0.21 12 12
apoptosis -0.014 0.04 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
PRKCD -0.001 0.086 -10000 0 -0.42 16 16
RAF1/14-3-3 E 0.025 0.058 -10000 0 -0.37 5 5
BAD/14-3-3 0.015 0.041 -10000 0 -10000 0 0
PRKCZ -0.013 0.05 0.17 6 -0.21 17 23
Crk/p130 Cas/Paxillin/FAK1 0.028 0.041 -10000 0 -10000 0 0
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.012 0.062 -10000 0 -0.34 15 15
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.046 0.051 -10000 0 -0.21 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 0.027 0.042 -10000 0 -0.22 12 12
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.01 0.038 0.16 2 -0.22 12 14
IRS1 0.012 0.043 0.13 1 -0.24 12 13
IRS2 0.009 0.039 0.16 2 -0.22 13 15
IGF-1R heterotetramer/IGF1 0.027 0.058 -10000 0 -0.31 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDPK1 0.012 0.045 0.19 8 -0.2 13 21
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKD1 0.008 0.06 -10000 0 -0.32 15 15
SHC1 0.024 0.014 -10000 0 -0.13 4 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.038 -10000 0 -0.25 5 5
forebrain development 0.018 0.14 0.46 2 -0.43 30 32
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
SMO/beta Arrestin2 0.029 0.031 -10000 0 -0.3 3 3
SMO 0.018 0.036 -10000 0 -0.43 3 3
ARRB2 0.026 0.004 -10000 0 -10000 0 0
GLI3/SPOP 0.016 0.087 0.22 1 -0.36 12 13
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.023 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
XPO1 0.027 0.007 -10000 0 -10000 0 0
GLI1/Su(fu) 0.012 0.11 -10000 0 -0.76 5 5
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.036 -10000 0 -0.43 3 3
MIM/GLI2A 0.017 0.043 -10000 0 -0.37 5 5
IFT88 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.011 -10000 0 -10000 0 0
GLI2 0.031 0.048 0.24 3 -10000 0 3
GLI3 0.006 0.088 0.22 2 -0.36 14 16
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.04 -10000 0 -0.43 4 4
Gi family/GTP 0.002 0.055 -10000 0 -0.28 10 10
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.072 -10000 0 -0.44 5 5
GLI2/Su(fu) 0.027 0.049 -10000 0 -0.37 3 3
FOXA2 0.012 0.093 -10000 0 -0.75 5 5
neural tube patterning 0.018 0.14 0.46 2 -0.43 30 32
SPOP 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.046 -10000 0 -0.22 4 4
GNB1 0.022 0.01 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
MTSS1 0.017 0.043 -10000 0 -0.37 5 5
embryonic limb morphogenesis 0.018 0.14 0.46 2 -0.43 30 32
SUFU 0.018 0.018 -10000 0 -0.16 3 3
LGALS3 0.012 0.053 -10000 0 -0.16 39 39
catabolic process 0.042 0.09 0.29 1 -0.58 3 4
GLI3A/CBP 0.004 0.087 -10000 0 -0.32 31 31
KIF3A 0.025 0.02 -10000 0 -0.43 1 1
GLI1 0.018 0.14 0.46 2 -0.44 30 32
RAB23 0.025 0.02 -10000 0 -0.43 1 1
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.035 -10000 0 -0.43 3 3
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.045 0.047 -10000 0 -0.26 3 3
GNAZ 0.026 0.006 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.04 0.051 -10000 0 -0.52 1 1
STK36 0.026 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.011 0.053 -10000 0 -0.37 6 6
PTCH1 0.015 0.16 0.57 1 -1.1 7 8
MIM/GLI1 0.022 0.14 0.55 1 -0.63 8 9
CREBBP 0.004 0.087 -10000 0 -0.32 31 31
Su(fu)/SIN3/HDAC complex -0.006 0.11 0.24 2 -0.25 70 72
Circadian rhythm pathway

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
chromatin modification 0.037 0.05 -10000 0 -0.41 1 1
CLOCK 0.002 0.1 -10000 0 -0.42 28 28
TIMELESS/CRY2 0.026 0.047 -10000 0 -0.38 1 1
DEC1/BMAL1 0.031 0.022 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
NR1D1 0.009 0.1 -10000 0 -1.3 3 3
ARNTL 0.025 0.015 -10000 0 -0.14 1 1
TIMELESS 0.013 0.041 -10000 0 -0.42 1 1
NPAS2 0.021 0.052 -10000 0 -0.43 6 6
CRY2 0.023 0.035 -10000 0 -0.43 3 3
mol:CO -0.007 0.011 0.13 3 -10000 0 3
CHEK1 0.023 0.018 -10000 0 -0.13 6 6
mol:HEME 0.007 0.011 -10000 0 -0.13 3 3
PER1 0.018 0.06 -10000 0 -0.43 9 9
BMAL/CLOCK/NPAS2 0.037 0.078 -10000 0 -0.26 31 31
BMAL1/CLOCK 0.005 0.11 -10000 0 -0.86 3 3
S phase of mitotic cell cycle 0.037 0.05 -10000 0 -0.41 1 1
TIMELESS/CHEK1/ATR 0.038 0.05 -10000 0 -0.42 1 1
mol:NADPH 0.007 0.011 -10000 0 -0.13 3 3
PER1/TIMELESS 0.025 0.054 -10000 0 -0.38 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.008 0.029 -10000 0 -0.13 11 11
Arf6 downstream 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
PLAUR 0.013 0.066 -10000 0 -0.97 2 2
regulation of axonogenesis 0.002 0.055 0.28 9 -10000 0 9
myoblast fusion -0.008 0.041 0.35 4 -10000 0 4
mol:GTP 0.019 0.026 -10000 0 -0.17 6 6
regulation of calcium-dependent cell-cell adhesion -0.043 0.027 0.2 2 -10000 0 2
ARF1/GTP 0.034 0.024 -10000 0 -0.15 2 2
mol:GM1 0.008 0.018 -10000 0 -0.15 2 2
mol:Choline -0.009 0.065 -10000 0 -0.24 35 35
lamellipodium assembly 0.003 0.047 -10000 0 -0.37 6 6
MAPK3 0.02 0.026 -10000 0 -0.3 2 2
ARF6/GTP/NME1/Tiam1 0.044 0.027 -10000 0 -0.2 2 2
ARF1 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.008 0.041 -10000 0 -0.35 4 4
ARF1/GDP 0.012 0.048 -10000 0 -0.3 6 6
ARF6 0.032 0.012 -10000 0 -10000 0 0
RAB11A 0.026 0.003 -10000 0 -10000 0 0
TIAM1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.026 -10000 0 -0.3 2 2
actin filament bundle formation -0.016 0.047 0.31 5 -10000 0 5
KALRN 0.005 0.028 -10000 0 -0.25 4 4
RAB11FIP3/RAB11A 0.038 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.047 -10000 0 -0.31 5 5
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.045 -10000 0 -0.28 4 4
substrate adhesion-dependent cell spreading 0.019 0.026 -10000 0 -0.17 6 6
cortical actin cytoskeleton organization 0.003 0.048 -10000 0 -0.37 6 6
RAC1 0.023 0.009 -10000 0 -10000 0 0
liver development 0.019 0.026 -10000 0 -0.17 6 6
ARF6/GTP 0.019 0.026 -10000 0 -0.17 6 6
RhoA/GTP 0.035 0.023 -10000 0 -0.17 1 1
mol:GDP 0.008 0.032 -10000 0 -0.36 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.049 0.025 -10000 0 -0.15 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
PLD1 -0.004 0.075 -10000 0 -0.27 34 34
RAB11FIP3 0.026 0.002 -10000 0 -10000 0 0
tube morphogenesis 0.003 0.047 -10000 0 -0.37 6 6
ruffle organization -0.002 0.055 -10000 0 -0.28 9 9
regulation of epithelial cell migration 0.019 0.026 -10000 0 -0.17 6 6
PLD2 0.016 0.026 -10000 0 -0.19 3 3
PIP5K1A -0.002 0.055 -10000 0 -0.28 9 9
mol:Phosphatidic acid -0.009 0.065 -10000 0 -0.24 35 35
Rac1/GTP 0.003 0.048 -10000 0 -0.37 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
AKT1 0.034 0.078 0.32 5 -0.52 4 9
PTK2B 0.005 0.073 0.35 2 -0.52 3 5
VEGFR2 homodimer/Frs2 0.028 0.052 -10000 0 -0.61 3 3
CAV1 0.006 0.051 -10000 0 -0.15 44 44
CALM1 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.044 0.053 -10000 0 -0.57 3 3
endothelial cell proliferation 0.043 0.084 0.31 10 -0.45 4 14
mol:Ca2+ 0.019 0.06 0.36 1 -0.47 3 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.047 0.061 -10000 0 -0.54 3 3
RP11-342D11.1 0.008 0.058 -10000 0 -0.41 5 5
CDH5 0.025 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.063 0.024 -10000 0 -0.23 1 1
SHC1 0.024 0.014 -10000 0 -0.13 4 4
SHC2 0.025 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.049 -10000 0 -0.42 3 3
SH2D2A -0.02 0.12 -10000 0 -0.43 36 36
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.059 0.081 0.29 3 -0.42 5 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.089 -10000 0 -0.59 3 3
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
SHC/GRB2/SOS1 0.065 0.058 -10000 0 -0.45 3 3
GRB10 0.015 0.066 0.36 1 -0.52 5 6
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
PAK1 0.008 0.061 -10000 0 -0.16 46 46
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.063 0.062 -10000 0 -0.53 3 3
HRAS 0.025 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.019 0.052 -10000 0 -0.36 5 5
HIF1A 0.025 0.021 -10000 0 -0.43 1 1
FRS2 0.026 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.046 0.06 -10000 0 -0.54 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.039 -10000 0 -0.23 9 9
Nck/Pak 0.023 0.05 -10000 0 -0.3 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.053 -10000 0 -0.57 3 3
mol:GDP 0.051 0.054 -10000 0 -0.44 3 3
mol:NADP 0.042 0.071 0.3 3 -0.38 5 8
eNOS/Hsp90 0.053 0.068 0.29 3 -0.36 5 8
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.06 0.36 1 -0.47 3 4
HIF1A/ARNT 0.036 0.018 -10000 0 -0.3 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.02 0.033 -10000 0 -0.13 22 22
VEGFC 0.017 0.051 -10000 0 -0.21 18 18
FAK1/Vinculin 0.038 0.082 0.3 2 -0.53 5 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.072 -10000 0 -0.54 3 3
PTPN6 0.014 0.064 -10000 0 -0.43 10 10
EPAS1 0.03 0.029 -10000 0 -0.33 3 3
mol:L-citrulline 0.042 0.071 0.3 3 -0.38 5 8
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.055 0.051 -10000 0 -0.49 3 3
VEGFR2 homodimer/VEGFA homodimer 0.047 0.06 -10000 0 -0.45 5 5
VEGFR2/3 heterodimer 0.026 0.058 -10000 0 -0.47 5 5
VEGFB 0.025 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.072 0.32 5 -0.52 4 9
VEGFR2 homodimer 0.015 0.056 -10000 0 -0.69 3 3
FLT1 0.024 0.021 -10000 0 -0.43 1 1
NEDD4 0.022 0.04 -10000 0 -0.22 10 10
MAPK3 0.004 0.064 0.28 4 -0.38 4 8
MAPK1 0.005 0.064 0.27 5 -0.41 3 8
VEGFA145/NRP2 0.03 0.043 -10000 0 -0.28 6 6
VEGFR1/2 heterodimer 0.028 0.052 -10000 0 -0.61 3 3
KDR 0.015 0.056 -10000 0 -0.7 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.043 0.062 -10000 0 -0.41 5 5
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.006 0.068 0.28 5 -0.4 4 9
PI3K 0.041 0.063 -10000 0 -0.54 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.045 0.053 -10000 0 -0.57 3 3
FES 0.017 0.062 -10000 0 -0.54 3 3
GAB1 0.028 0.059 -10000 0 -0.5 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.05 -10000 0 -0.51 3 3
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.008 -10000 0 -0.13 1 1
eNOS/Caveolin-1 0.032 0.066 0.31 2 -0.39 5 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.055 -10000 0 -0.45 4 4
PI3K/GAB1 0.046 0.066 -10000 0 -0.47 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.063 0.063 -10000 0 -0.53 3 3
PRKACA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.063 -10000 0 -0.5 4 4
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.014 0.062 0.36 1 -0.54 3 4
actin cytoskeleton reorganization 0.023 0.088 -10000 0 -0.58 3 3
PTK2 0.016 0.065 -10000 0 -0.57 3 3
EDG1 0.008 0.058 -10000 0 -0.41 5 5
mol:DAG 0.019 0.06 0.36 1 -0.47 3 4
CaM/Ca2+ 0.028 0.055 -10000 0 -0.44 3 3
MAP2K3 0.005 0.069 0.36 1 -0.51 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.065 0.088 -10000 0 -0.53 5 5
PLCG1 0.019 0.061 0.36 1 -0.48 3 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.055 0.052 -10000 0 -0.49 3 3
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
YES1 0.022 0.04 -10000 0 -0.43 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.045 0.053 -10000 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.037 0.065 -10000 0 -0.57 3 3
cell migration 0.046 0.09 0.32 3 -0.51 6 9
mol:PI-3-4-5-P3 0.04 0.06 -10000 0 -0.5 3 3
FYN 0.025 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.022 0.058 -10000 0 -0.5 3 3
mol:NO 0.042 0.071 0.3 3 -0.38 5 8
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.046 -10000 0 -0.42 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.066 -10000 0 -0.53 5 5
VHL 0.026 0.004 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.43 12 12
NOS3 0.043 0.075 0.35 1 -0.43 5 6
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.054 -10000 0 -0.57 3 3
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.011 0.055 0.36 1 -0.39 3 4
PRKCB -0.001 0.071 0.36 2 -0.38 5 7
VCL 0.022 0.032 -10000 0 -0.23 6 6
VEGFA165/NRP1 0.029 0.059 -10000 0 -0.41 5 5
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.053 -10000 0 -0.57 3 3
VEGFA165/NRP2 0.03 0.043 -10000 0 -0.28 6 6
MAPKKK cascade 0.034 0.069 0.3 4 -0.42 5 9
NRP2 0.021 0.046 -10000 0 -0.43 5 5
VEGFC homodimer 0.017 0.051 -10000 0 -0.21 18 18
NCK1 0.025 0.02 -10000 0 -0.43 1 1
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.08 0.3 2 -0.56 4 6
MAP3K13 0.014 0.072 0.36 1 -0.47 4 5
PDPK1 0.026 0.061 0.27 2 -0.5 3 5
Arf6 trafficking 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
SLC2A4 -0.019 0.13 -10000 0 -0.43 41 41
CLTC 0.024 0.054 -10000 0 -0.36 6 6
calcium ion-dependent exocytosis 0.012 0.05 -10000 0 -0.26 3 3
Dynamin 2/GTP 0.025 0.008 -10000 0 -10000 0 0
EXOC4 0.02 0.011 -10000 0 -10000 0 0
CD59 0.015 0.047 -10000 0 -0.31 8 8
CPE 0.007 0.041 -10000 0 -0.26 12 12
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
membrane fusion 0.015 0.053 -10000 0 -0.26 3 3
CTNND1 0.014 0.024 0.18 10 -10000 0 10
DNM2 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.039 0.15 2 -0.25 2 4
TSHR -0.05 0.1 -10000 0 -0.26 90 90
INS -0.008 0.11 -10000 0 -0.45 27 27
BIN1 0.025 0.02 -10000 0 -0.43 1 1
mol:Choline 0.015 0.053 -10000 0 -0.26 3 3
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.007 -10000 0 -10000 0 0
JUP 0.012 0.055 -10000 0 -0.31 10 10
ASAP2/amphiphysin II 0.048 0.016 -10000 0 -0.23 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.008 0.079 -10000 0 -0.28 18 18
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.002 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.026 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.022 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.016 0.071 0.3 7 -10000 0 7
positive regulation of phagocytosis 0.012 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.006 -10000 0 -10000 0 0
ACAP1 0.02 0.05 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.01 0.07 -10000 0 -0.31 11 11
clathrin heavy chain/ACAP1 0.026 0.058 0.2 18 -0.28 6 24
JIP4/KLC1 0.048 0.012 -10000 0 -10000 0 0
EXOC1 0.025 0.006 -10000 0 -10000 0 0
exocyst 0.02 0.019 -10000 0 -10000 0 0
RALA/GTP 0.017 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.007 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.014 0.023 0.18 9 -10000 0 9
NME1 0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.057 0.25 2 -0.36 6 8
IL2RA 0.006 0.054 -10000 0 -0.31 9 9
VAMP3 0.012 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.07 -10000 0 -0.28 9 9
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.004 0.065 -10000 0 -0.26 31 31
PLD2 0.012 0.013 -10000 0 -0.25 1 1
EXOC5 0.026 0.004 -10000 0 -10000 0 0
PIP5K1C 0.016 0.037 -10000 0 -0.26 2 2
SDC1 0.011 0.053 -10000 0 -0.31 8 8
ARF6/GDP 0.024 0.005 -10000 0 -10000 0 0
EXOC7 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.018 0.073 -10000 0 -0.31 7 7
mol:Phosphatidic acid 0.015 0.053 -10000 0 -0.26 3 3
endocytosis -0.047 0.015 0.23 1 -10000 0 1
SCAMP2 0.026 0.003 -10000 0 -10000 0 0
ADRB2 0.015 0.074 0.27 3 -0.35 8 11
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ASAP2 0.026 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.009 -10000 0 -10000 0 0
KLC1 0.025 0.005 -10000 0 -10000 0 0
AVPR2 0.022 0.061 0.24 3 -0.34 7 10
RALA 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.073 -10000 0 -0.32 5 5
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.02 0.045 0.43 5 -10000 0 5
PI3K Class IB/PDE3B 0.02 0.045 -10000 0 -0.43 5 5
PDE3B 0.02 0.045 -10000 0 -0.43 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.052 0.037 -9999 0 -0.22 4 4
HDAC3 0.026 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.034 0.016 -9999 0 -10000 0 0
GATA1/HDAC5 0.035 0.016 -9999 0 -10000 0 0
GATA2/HDAC5 0.03 0.049 -9999 0 -0.3 10 10
HDAC5/BCL6/BCoR 0.051 0.01 -9999 0 -10000 0 0
HDAC9 0.015 0.055 -9999 0 -0.3 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.013 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.009 -9999 0 -10000 0 0
HDAC5/YWHAB 0.037 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
GATA2 0.015 0.064 -9999 0 -0.33 15 15
HDAC4/RFXANK 0.036 0.011 -9999 0 -10000 0 0
BCOR 0.026 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.004 -9999 0 -10000 0 0
HDAC5 0.026 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.03 0.033 -9999 0 -0.3 4 4
Histones 0.03 0.044 -9999 0 -0.23 2 2
ADRBK1 0.025 0.005 -9999 0 -10000 0 0
HDAC4 0.025 0.005 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.006 -9999 0 -10000 0 0
HDAC4/Ubc9 0.037 0.008 -9999 0 -10000 0 0
HDAC7 0.026 0.004 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.005 -9999 0 -10000 0 0
TUBA1B 0.026 0.004 -9999 0 -10000 0 0
HDAC6 0.026 0.002 -9999 0 -10000 0 0
HDAC5/RFXANK 0.037 0.011 -9999 0 -10000 0 0
CAMK4 -0.094 0.19 -9999 0 -0.35 162 162
Tubulin/HDAC6 0.051 0.012 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.025 0.005 -9999 0 -10000 0 0
GATA1 0.013 0.025 -9999 0 -0.13 7 7
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
NR3C1 0.026 0.004 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.021 -9999 0 -0.21 1 1
SRF 0.026 0.002 -9999 0 -10000 0 0
HDAC4/YWHAB 0.036 0.011 -9999 0 -10000 0 0
Tubulin 0.038 0.007 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.037 0.008 -9999 0 -10000 0 0
GNB1 0.022 0.01 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.038 0.007 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.014 -9999 0 -10000 0 0
HDAC4/SRF -0.019 0.13 -9999 0 -0.26 119 119
HDAC4/ER alpha 0.026 0.054 -9999 0 -0.3 11 11
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.03 0.044 -9999 0 -0.23 2 2
cell motility 0.05 0.012 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
HDAC7/HDAC3 0.038 0.007 -9999 0 -10000 0 0
BCL6 0.026 0.004 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.025 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.008 -9999 0 -10000 0 0
ESR1 0.011 0.07 -9999 0 -0.43 11 11
HDAC6/HDAC11 0.037 0.017 -9999 0 -0.3 1 1
Ran/GTP/Exportin 1 0.043 0.019 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
MEF2C 0.019 0.04 -9999 0 -0.43 2 2
RAN 0.026 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.071 0.029 -9999 0 -0.22 2 2
GNG2 0.022 0.04 -9999 0 -0.43 4 4
NCOR2 0.026 0.003 -9999 0 -10000 0 0
TUBB2A 0.026 0.004 -9999 0 -10000 0 0
HDAC11 0.025 0.02 -9999 0 -0.43 1 1
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
ANKRA2 0.026 0.003 -9999 0 -10000 0 0
RFXANK 0.025 0.009 -9999 0 -0.13 1 1
nuclear import -0.032 0.01 -9999 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.01 -10000 0 -10000 0 0
mol:PIP3 0.009 0.016 -10000 0 -0.16 3 3
FRAP1 0.021 0.044 0.27 2 -0.31 2 4
AKT1 0.009 0.034 0.17 15 -0.18 1 16
INSR 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.027 -10000 0 -0.26 4 4
mol:GTP 0.032 0.038 0.2 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.017 -10000 0 -10000 0 0
TSC2 0.026 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.015 0.025 -10000 0 -10000 0 0
TSC1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.017 -10000 0 -0.18 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.023 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.007 -10000 0 -10000 0 0
RPS6KB1 0.026 0.05 0.27 8 -0.32 1 9
MAP3K5 -0.005 0.051 -10000 0 -0.22 25 25
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
apoptosis -0.005 0.051 -10000 0 -0.22 25 25
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.024 0.048 0.26 9 -0.28 1 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.033 -10000 0 -0.25 1 1
eIF4E/eIF4G1/eIF4A1 0.016 0.023 -10000 0 -0.2 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.041 0.019 -10000 0 -0.17 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.022 0.14 3 -10000 0 3
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.032 0.18 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.003 0.022 0.18 2 -0.23 1 3
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.14 -10000 0 -0.56 27 27
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.045 -10000 0 -0.23 10 10
TSC1/TSC2 0.039 0.048 0.27 6 -10000 0 6
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.024 0.01 -10000 0 -0.13 1 1
PPP5C 0.022 0.01 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.008 0.018 -10000 0 -0.2 3 3
INS -0.018 0.037 -10000 0 -0.37 5 5
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.003 0.021 0.18 2 -0.17 3 5
EIF4EBP1 0.003 0.15 -10000 0 -1.1 9 9
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PPP2R5D 0.02 0.043 0.26 2 -0.28 2 4
peptide biosynthetic process -0.008 0.033 0.18 10 -0.23 4 14
RHEB 0.02 0.011 -10000 0 -10000 0 0
EIF4A1 0.026 0.003 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 25 -10000 0 25
EEF2 -0.008 0.033 0.18 10 -0.23 4 14
eIF4E/4E-BP1 0.016 0.14 -10000 0 -1 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.026 0.004 -9999 0 -10000 0 0
SMAD2 -0.001 0.035 -9999 0 -0.25 2 2
SMAD3 0.025 0.025 -9999 0 -0.18 1 1
SMAD3/SMAD4 0.038 0.044 -9999 0 -0.71 1 1
SMAD4/Ubc9/PIASy 0.05 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.047 0.044 -9999 0 -10000 0 0
PPM1A 0.025 0.005 -9999 0 -10000 0 0
CALM1 0.025 0.009 -9999 0 -10000 0 0
SMAD2/SMAD4 0.014 0.036 -9999 0 -0.23 2 2
MAP3K1 0.024 0.019 -9999 0 -0.13 7 7
TRAP-1/SMAD4 0.027 0.06 -9999 0 -0.3 16 16
MAPK3 0.026 0.002 -9999 0 -10000 0 0
MAPK1 0.026 0.003 -9999 0 -10000 0 0
NUP214 0.025 0.005 -9999 0 -10000 0 0
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
CTDSPL 0.025 0.02 -9999 0 -0.43 1 1
KPNB1 0.026 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.012 0.079 -9999 0 -0.43 16 16
UBE2I 0.026 0.002 -9999 0 -10000 0 0
NUP153 0.026 0.003 -9999 0 -10000 0 0
KPNA2 0.025 0.009 -9999 0 -10000 0 0
PIAS4 0.025 0.005 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.013 0.028 0.15 21 -10000 0 21
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.027 0.13 7 -10000 0 7
AP2 0.031 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.028 0.015 -10000 0 -10000 0 0
CLTB 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.007 -10000 0 -10000 0 0
CD4 0.022 0.032 -10000 0 -0.23 6 6
CLTA 0.026 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.007 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP 0.025 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.01 0.005 -10000 0 -10000 0 0
mol:Choline 0.004 0.017 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.015 -10000 0 -10000 0 0
DDEF1 0.003 0.017 -10000 0 -0.17 1 1
ARF1/GDP 0.002 0.018 -10000 0 -0.088 4 4
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.007 0.009 -10000 0 -10000 0 0
Rac/GTP 0.014 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.021 -10000 0 -10000 0 0
ARFIP2 0.023 0.008 -10000 0 -10000 0 0
COPA 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.023 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.014 0.011 -10000 0 -10000 0 0
GGA3 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.019 0.019 -10000 0 -0.16 1 1
AP2A1 0.021 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.014 0.015 -10000 0 -0.14 4 4
ARF1/GDP/Membrin 0.022 0.019 -10000 0 -0.21 1 1
Arfaptin 2/Rac/GDP 0.029 0.014 -10000 0 -10000 0 0
CYTH2 0.022 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.019 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.042 -10000 0 -0.19 7 7
PLD2 0.004 0.017 -10000 0 -0.17 1 1
ARF-GAP1/v-SNARE 0.007 0.004 -10000 0 -10000 0 0
PIP5K1A 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP/Membrin/GBF1/p115 0.014 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.017 -10000 0 -0.17 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.004 -10000 0 -10000 0 0
GOSR2 0.012 0.009 -10000 0 -10000 0 0
USO1 0.006 0.045 -10000 0 -0.33 9 9
GBF1 0.004 0.046 -10000 0 -0.32 10 10
ARF1/GTP/Arfaptin 2 0.027 0.021 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.029 -10000 0 -0.23 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.037 0.009 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
CHUK 0.025 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.04 -9999 0 -0.22 3 3
NFKB1 0.026 0.004 -9999 0 -10000 0 0
MAP3K14 0.026 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.018 -9999 0 -10000 0 0
RELB 0.02 0.025 -9999 0 -0.43 1 1
NFKB2 0.023 0.03 -9999 0 -0.43 2 2
NF kappa B2 p52/RelB 0.026 0.027 -9999 0 -0.22 4 4
regulation of B cell activation 0.026 0.027 -9999 0 -0.22 4 4
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.022 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.005 -9999 0 -10000 0 0
MDM2/SUMO1 0.041 0.02 -9999 0 -0.23 1 1
HDAC4 0.025 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.006 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.012 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.011 0.002 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.021 -9999 0 -0.21 1 1
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.033 -9999 0 -0.23 5 5
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.003 -9999 0 -10000 0 0
Ran/GTP 0.029 0.019 -9999 0 -0.24 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.026 0.004 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.017 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
PIAS2 0.025 0.02 -9999 0 -0.43 1 1
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.16 -0.16 0.064 -0.19
47_PPARGC1A 0.026 0.026 0.026 0.026
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0.026 0.026 0.026
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0 0.068 -0.23 0
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.027 0.026
84_STAT5B 0.097 0.033 0.066 0.033
84_STAT5A 0.097 0.033 0.066 0.033
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LGG-TP/14527214/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LGG-TP/15082616/GDAC_Gistic2Report_15086236/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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