PARADIGM pathway analysis of mRNA expression and copy number data
Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1028QK3
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 mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1028QK3
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 104 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
HIF-1-alpha transcription factor network 121
FOXM1 transcription factor network 110
Endothelins 92
TCGA08_rtk_signaling 90
Angiopoietin receptor Tie2-mediated signaling 89
Effects of Botulinum toxin 80
Thromboxane A2 receptor signaling 78
TCGA08_p53 78
Syndecan-1-mediated signaling events 75
Syndecan-3-mediated signaling events 75
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 528 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 528 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 0.2292 121 9237 76 -0.058 0.17 1000 -1000 -0.017 -1000
FOXM1 transcription factor network 0.2083 110 5622 51 -0.29 0.075 1000 -1000 -0.039 -1000
Endothelins 0.1742 92 8881 96 -0.13 0.043 1000 -1000 -0.029 -1000
TCGA08_rtk_signaling 0.1705 90 2350 26 -0.046 0.12 1000 -1000 -0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1686 89 7878 88 -0.28 0.042 1000 -1000 -0.053 -1000
Effects of Botulinum toxin 0.1515 80 2102 26 -0.01 0.055 1000 -1000 -0.016 -1000
Thromboxane A2 receptor signaling 0.1477 78 8191 105 -0.062 0.047 1000 -1000 -0.035 -1000
TCGA08_p53 0.1477 78 547 7 -0.002 0.034 1000 -1000 -0.016 -1000
Syndecan-1-mediated signaling events 0.1420 75 2558 34 0 0.041 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 0.1420 75 2628 35 -0.066 0.078 1000 -1000 -0.016 -1000
IL23-mediated signaling events 0.1383 73 4407 60 -0.008 0.22 1000 -1000 -0.046 -1000
HIF-2-alpha transcription factor network 0.1364 72 3108 43 -0.07 0.051 1000 -1000 -0.035 -1000
Arf6 signaling events 0.1345 71 4438 62 -0.002 0.097 1000 -1000 -0.002 -1000
Ceramide signaling pathway 0.1326 70 5330 76 -0.12 0.072 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 0.1288 68 3015 44 -0.07 0.038 1000 -1000 -0.026 -1000
Wnt signaling 0.1288 68 478 7 -0.008 0.039 1000 -1000 -0.005 -1000
Canonical Wnt signaling pathway 0.1269 67 3423 51 -0.088 0.067 1000 -1000 -0.031 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1250 66 2188 33 -0.059 0.071 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.1231 65 3426 52 -0.073 0.053 1000 -1000 -0.029 -1000
LPA receptor mediated events 0.1193 63 6496 102 -0.11 0.049 1000 -1000 -0.072 -1000
S1P5 pathway 0.1174 62 1058 17 -0.012 0.038 1000 -1000 -0.01 -1000
Syndecan-4-mediated signaling events 0.1155 61 4121 67 -0.14 0.038 1000 -1000 -0.033 -1000
S1P4 pathway 0.1117 59 1483 25 -0.014 0.053 1000 -1000 -0.02 -1000
Arf6 downstream pathway 0.1080 57 2467 43 -0.029 0.053 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1080 57 7142 125 -0.058 0.053 1000 -1000 -0.053 -1000
EGFR-dependent Endothelin signaling events 0.1061 56 1194 21 -0.017 0.037 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.1061 56 954 17 -0.001 0.042 1000 -1000 -0.012 -1000
Syndecan-2-mediated signaling events 0.1042 55 3846 69 -0.04 0.04 1000 -1000 -0.024 -1000
IL2 signaling events mediated by PI3K 0.1042 55 3217 58 -0.22 0.046 1000 -1000 -0.025 -1000
amb2 Integrin signaling 0.1004 53 4409 82 -0.022 0.082 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 0.0985 52 5073 97 -0.12 0.052 1000 -1000 -0.052 -1000
Glypican 2 network 0.0985 52 208 4 0 0.011 1000 -1000 0 -1000
IL12-mediated signaling events 0.0966 51 4483 87 -0.071 0.13 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0947 50 3062 61 -0.067 0.078 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 0.0928 49 148 3 -0.019 0.038 1000 -1000 -0.023 -1000
JNK signaling in the CD4+ TCR pathway 0.0909 48 826 17 -0.14 0.064 1000 -1000 -0.019 -1000
FoxO family signaling 0.0909 48 3089 64 -0.17 0.058 1000 -1000 -0.024 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0890 47 2568 54 -0.041 0.08 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0890 47 1055 22 -0.1 0.044 1000 -1000 -0.031 -1000
Regulation of nuclear SMAD2/3 signaling 0.0871 46 6273 136 -0.22 0.17 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0871 46 3187 68 -0.11 0.049 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.0871 46 375 8 -0.04 0.048 1000 -1000 -0.006 -1000
BCR signaling pathway 0.0871 46 4606 99 -0.058 0.052 1000 -1000 -0.051 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0852 45 1271 28 -0.021 0.038 1000 -1000 -0.022 -1000
mTOR signaling pathway 0.0852 45 2434 53 -0.035 0.047 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 0.0833 44 1606 36 -0.053 0.059 1000 -1000 -0.042 -1000
BMP receptor signaling 0.0814 43 3550 81 -0.035 0.054 1000 -1000 -0.01 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0814 43 1627 37 -0.038 0.084 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 0.0814 43 2092 48 -0.065 0.067 1000 -1000 -0.042 -1000
FAS signaling pathway (CD95) 0.0814 43 2053 47 -0.16 0.043 1000 -1000 -0.037 -1000
EPHB forward signaling 0.0814 43 3711 85 -0.067 0.088 1000 -1000 -0.053 -1000
IL6-mediated signaling events 0.0814 43 3291 75 -0.076 0.13 1000 -1000 -0.036 -1000
Class I PI3K signaling events 0.0814 43 3178 73 -0.047 0.074 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 0.0814 43 4243 97 -0.059 0.066 1000 -1000 -0.051 -1000
Osteopontin-mediated events 0.0795 42 1631 38 -0.077 0.057 1000 -1000 -0.023 -1000
Glypican 1 network 0.0795 42 2048 48 -0.034 0.055 1000 -1000 -0.035 -1000
EPO signaling pathway 0.0795 42 2330 55 0 0.049 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 0.0795 42 2906 68 -0.037 0.065 1000 -1000 -0.024 -1000
Reelin signaling pathway 0.0777 41 2344 56 -0.01 0.067 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0777 41 2220 54 -0.034 0.05 1000 -1000 -0.035 -1000
ErbB2/ErbB3 signaling events 0.0758 40 2631 65 -0.042 0.038 1000 -1000 -0.033 -1000
Noncanonical Wnt signaling pathway 0.0758 40 1047 26 -0.041 0.039 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0758 40 3427 85 -0.12 0.14 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0758 40 3095 76 -0.032 0.06 1000 -1000 -0.028 -1000
PLK1 signaling events 0.0758 40 3458 85 -0.047 0.059 1000 -1000 -0.017 -1000
IL1-mediated signaling events 0.0758 40 2480 62 -0.054 0.079 1000 -1000 -0.05 -1000
Integrins in angiogenesis 0.0739 39 3323 84 -0.06 0.074 1000 -1000 -0.05 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0739 39 1779 45 -0.041 0.082 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0739 39 2940 74 -0.13 0.08 1000 -1000 -0.054 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0739 39 3093 78 -0.031 0.081 1000 -1000 -0.041 -1000
p38 MAPK signaling pathway 0.0739 39 1720 44 0 0.046 1000 -1000 -0.01 -1000
IFN-gamma pathway 0.0701 37 2528 68 -0.056 0.064 1000 -1000 -0.041 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0701 37 4508 120 -0.052 0.09 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0701 37 1612 43 -0.043 0.067 1000 -1000 -0.018 -1000
Plasma membrane estrogen receptor signaling 0.0682 36 3097 86 -0.07 0.055 1000 -1000 -0.041 -1000
IGF1 pathway 0.0663 35 2020 57 -0.064 0.07 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.0644 34 2869 82 -0.076 0.06 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 0.0644 34 524 15 -0.032 0.038 1000 -1000 -0.025 -1000
TCR signaling in naïve CD8+ T cells 0.0644 34 3210 93 -0.43 0.49 1000 -1000 -0.031 -1000
E-cadherin signaling in the nascent adherens junction 0.0644 34 2635 76 -0.054 0.094 1000 -1000 -0.043 -1000
S1P3 pathway 0.0644 34 1454 42 -0.025 0.039 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 0.0644 34 451 13 0 0.064 1000 -1000 0 -1000
p75(NTR)-mediated signaling 0.0625 33 4145 125 -0.075 0.089 1000 -1000 -0.053 -1000
IL4-mediated signaling events 0.0625 33 3037 91 -0.28 0.055 1000 -1000 -0.071 -1000
S1P1 pathway 0.0625 33 1223 36 -0.025 0.042 1000 -1000 -0.025 -1000
Aurora B signaling 0.0625 33 2242 67 -0.037 0.065 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0606 32 2237 69 -0.066 0.062 1000 -1000 -0.033 -1000
a4b1 and a4b7 Integrin signaling 0.0606 32 162 5 0.029 0.055 1000 -1000 0.034 -1000
Signaling events mediated by PRL 0.0606 32 1092 34 -0.027 0.051 1000 -1000 -0.028 -1000
Caspase cascade in apoptosis 0.0587 31 2317 74 -0.078 0.072 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0587 31 735 23 -0.026 0.057 1000 -1000 -0.012 -1000
Insulin-mediated glucose transport 0.0568 30 967 32 -0.025 0.044 1000 -1000 -0.023 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0568 30 2555 83 -0.054 0.071 1000 -1000 -0.023 -1000
BARD1 signaling events 0.0549 29 1680 57 -0.068 0.084 1000 -1000 -0.056 -1000
Glucocorticoid receptor regulatory network 0.0549 29 3389 114 -0.12 0.063 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class III 0.0549 29 1173 40 -0.047 0.048 1000 -1000 -0.043 -1000
Regulation of Telomerase 0.0549 29 3040 102 -0.035 0.079 1000 -1000 -0.029 -1000
Insulin Pathway 0.0549 29 2177 74 -0.051 0.083 1000 -1000 -0.044 -1000
Visual signal transduction: Cones 0.0530 28 1066 38 -0.019 0.062 1000 -1000 -0.014 -1000
Hedgehog signaling events mediated by Gli proteins 0.0530 28 1834 65 -0.02 0.08 1000 -1000 -0.021 -1000
Aurora A signaling 0.0530 28 1715 60 -0.034 0.06 1000 -1000 -0.023 -1000
Nectin adhesion pathway 0.0530 28 1773 63 -0.019 0.082 1000 -1000 -0.026 -1000
TRAIL signaling pathway 0.0511 27 1304 48 -0.038 0.091 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0511 27 1561 56 -0.045 0.043 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 0.0492 26 1552 58 -0.055 0.062 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 0.0492 26 807 31 -0.038 0.069 1000 -1000 -0.019 -1000
Circadian rhythm pathway 0.0473 25 570 22 -0.012 0.06 1000 -1000 -0.031 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0473 25 1340 52 -0.049 0.11 1000 -1000 -0.013 -1000
Signaling events mediated by HDAC Class I 0.0473 25 2703 104 -0.047 0.069 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0455 24 1746 70 -0.05 0.069 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class II 0.0436 23 1725 75 -0.042 0.095 1000 -1000 -0.034 -1000
Signaling events mediated by the Hedgehog family 0.0436 23 1218 52 -0.021 0.1 1000 -1000 -0.028 -1000
Signaling mediated by p38-alpha and p38-beta 0.0436 23 1013 44 -0.023 0.092 1000 -1000 -0.018 -1000
Arf6 trafficking events 0.0436 23 1689 71 -0.035 0.051 1000 -1000 -0.035 -1000
E-cadherin signaling events 0.0436 23 117 5 0.035 0.066 1000 -1000 0.034 -1000
Arf1 pathway 0.0436 23 1294 54 -0.07 0.046 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 0.0417 22 685 31 -0.04 0.039 1000 -1000 -0.033 -1000
Canonical NF-kappaB pathway 0.0398 21 849 39 -0.046 0.067 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0360 19 655 34 -0.056 0.098 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 0.0341 18 1432 76 -0.028 0.068 1000 -1000 -0.022 -1000
ceramide signaling pathway 0.0341 18 907 49 -0.026 0.056 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0341 18 505 27 -0.047 0.076 1000 -1000 -0.034 -1000
Rapid glucocorticoid signaling 0.0341 18 362 20 -0.017 0.038 1000 -1000 -0.016 -1000
Aurora C signaling 0.0322 17 124 7 0 0.06 1000 -1000 -0.007 -1000
Cellular roles of Anthrax toxin 0.0303 16 641 39 -0.074 0.038 1000 -1000 -0.012 -1000
Class IB PI3K non-lipid kinase events 0.0284 15 45 3 -0.038 0.038 1000 -1000 -0.035 -1000
FOXA2 and FOXA3 transcription factor networks 0.0246 13 640 46 -0.033 0.12 1000 -1000 -0.028 -1000
IL27-mediated signaling events 0.0227 12 659 51 -0.026 0.081 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 0.0189 10 121 12 -0.026 0.013 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 0.0189 10 555 52 -0.056 0.088 1000 -1000 -0.04 -1000
Ephrin A reverse signaling 0.0076 4 28 7 -0.028 0.05 1000 -1000 -0.016 -1000
Total NA 5500 312989 7203 -7.7 9.1 131000 -131000 -3.7 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.004 0.38 0.62 80 -0.66 63 143
HDAC7 -0.005 0.01 -10000 0 -0.05 13 13
HIF1A/ARNT/Cbp/p300/Src-1 0.002 0.37 0.62 55 -0.66 59 114
SMAD4 0.036 0.017 0.1 13 -10000 0 13
ID2 0.14 0.46 0.69 135 -0.7 55 190
AP1 0.019 0.076 0.14 5 -0.15 72 77
ABCG2 0.097 0.45 0.7 107 -0.71 56 163
HIF1A 0.068 0.14 0.26 116 -0.21 6 122
TFF3 0.13 0.46 0.7 127 -0.69 56 183
GATA2 0.043 0.02 0.1 33 -0.13 1 34
AKT1 0.084 0.15 0.3 115 -0.27 9 124
response to hypoxia 0.036 0.11 0.23 105 -0.15 7 112
MCL1 0.15 0.46 0.69 136 -0.7 56 192
NDRG1 0.082 0.44 0.67 103 -0.71 59 162
SERPINE1 -0.013 0.34 0.65 46 -0.74 46 92
FECH 0.14 0.46 0.69 127 -0.71 54 181
FURIN 0.15 0.46 0.7 131 -0.7 55 186
NCOA2 0.039 0.007 -10000 0 -10000 0 0
EP300 0.12 0.23 0.44 129 -0.29 26 155
HMOX1 0.065 0.44 0.69 96 -0.72 61 157
BHLHE40 0.004 0.38 0.62 80 -0.66 63 143
BHLHE41 0.004 0.38 0.62 80 -0.66 63 143
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.081 0.19 0.37 76 -0.28 13 89
ENG 0.054 0.18 0.34 65 -0.28 9 74
JUN 0.038 0.016 0.08 19 -0.08 1 20
RORA 0.11 0.45 0.69 114 -0.71 54 168
ABCB1 -0.034 0.17 0.3 1 -0.8 18 19
TFRC 0.12 0.46 0.69 123 -0.7 58 181
CXCR4 0.11 0.46 0.7 107 -0.71 62 169
TF -0.015 0.38 0.69 55 -0.69 61 116
CITED2 0.1 0.45 0.68 113 -0.71 56 169
HIF1A/ARNT -0.039 0.38 0.74 24 -0.77 54 78
LDHA -0.058 0.26 -10000 0 -0.94 38 38
ETS1 0.16 0.47 0.7 133 -0.7 55 188
PGK1 0.15 0.47 0.7 127 -0.71 58 185
NOS2 0.004 0.38 0.62 80 -0.66 63 143
ITGB2 0.094 0.45 0.68 111 -0.71 60 171
ALDOA 0.16 0.47 0.7 139 -0.71 56 195
Cbp/p300/CITED2 0.041 0.44 0.67 94 -0.72 69 163
FOS 0.028 0.02 0.081 5 -10000 0 5
HK2 0.16 0.47 0.7 142 -0.7 56 198
SP1 0.034 0.071 0.13 51 -0.18 38 89
GCK 0.17 0.3 0.67 88 -0.49 7 95
HK1 0.077 0.43 0.69 99 -0.71 55 154
NPM1 0.15 0.46 0.7 129 -0.71 54 183
EGLN1 0.15 0.46 0.69 138 -0.71 55 193
CREB1 0.033 0.037 -10000 0 -0.11 30 30
PGM1 0.15 0.47 0.7 137 -0.7 56 193
SMAD3 0.039 0.012 0.1 13 -10000 0 13
EDN1 0.094 0.25 0.59 42 -0.56 10 52
IGFBP1 0.053 0.39 0.68 76 -0.72 45 121
VEGFA 0.032 0.38 0.62 76 -0.64 63 139
HIF1A/JAB1 0.063 0.11 0.23 61 -0.19 11 72
CP 0.043 0.43 0.68 88 -0.7 65 153
CXCL12 0.035 0.4 0.67 77 -0.71 52 129
COPS5 0.039 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.043 0.052 0.17 12 -0.13 34 46
BNIP3 0.064 0.43 0.7 89 -0.71 55 144
EGLN3 0.087 0.44 0.69 100 -0.7 56 156
CA9 0.059 0.41 0.67 84 -0.71 53 137
TERT 0.15 0.47 0.7 137 -0.7 56 193
ENO1 0.14 0.46 0.7 131 -0.71 56 187
PFKL 0.16 0.47 0.7 134 -0.7 56 190
NCOA1 0.035 0.012 -10000 0 -10000 0 0
ADM 0.061 0.44 0.69 96 -0.7 63 159
ARNT 0.069 0.14 0.26 119 -0.17 6 125
HNF4A 0.037 0.017 0.11 10 -10000 0 10
ADFP 0.004 0.38 0.62 80 -0.66 63 143
SLC2A1 0.073 0.4 0.62 106 -0.61 63 169
LEP 0.07 0.4 0.68 88 -0.71 44 132
HIF1A/ARNT/Cbp/p300 -0.008 0.36 0.63 53 -0.67 60 113
EPO 0.056 0.32 0.62 56 -0.64 23 79
CREBBP 0.12 0.22 0.42 143 -0.26 25 168
HIF1A/ARNT/Cbp/p300/HDAC7 -0.038 0.34 0.59 36 -0.68 65 101
PFKFB3 0.085 0.44 0.69 107 -0.72 51 158
NT5E 0.044 0.42 0.68 83 -0.7 60 143
FOXM1 transcription factor network

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
NFATC3 -0.056 0.66 1 40 -1.2 96 136
PLK1 0.074 0.2 0.7 25 -0.82 7 32
BIRC5 -0.045 0.44 0.8 16 -1.2 59 75
HSPA1B -0.051 0.66 0.95 54 -1.1 98 152
MAP2K1 0.051 0.12 0.27 68 -10000 0 68
BRCA2 -0.052 0.66 1.1 41 -1.2 96 137
FOXM1 -0.15 0.91 1.2 51 -1.7 98 149
XRCC1 -0.04 0.68 1.1 46 -1.2 96 142
FOXM1B/p19 -0.29 0.53 -10000 0 -1.3 96 96
Cyclin D1/CDK4 -0.09 0.58 0.9 35 -1.1 98 133
CDC2 -0.052 0.72 1.1 56 -1.2 99 155
TGFA -0.04 0.59 0.9 53 -0.99 99 152
SKP2 -0.051 0.66 1.1 43 -1.2 95 138
CCNE1 0.019 0.046 0.12 19 -10000 0 19
CKS1B -0.051 0.66 0.95 54 -1.1 98 152
RB1 -0.072 0.37 0.52 29 -0.92 57 86
FOXM1C/SP1 -0.14 0.72 0.88 32 -1.4 99 131
AURKB 0.075 0.17 0.78 17 -0.82 2 19
CENPF -0.068 0.72 1.1 45 -1.2 110 155
CDK4 0.026 0.061 0.16 38 -10000 0 38
MYC -0.083 0.56 0.81 49 -0.99 103 152
CHEK2 0.039 0.1 0.24 58 -10000 0 58
ONECUT1 -0.056 0.64 0.92 54 -1.1 100 154
CDKN2A 0.003 0.024 0.096 1 -0.19 4 5
LAMA4 -0.057 0.66 1.1 40 -1.2 97 137
FOXM1B/HNF6 -0.12 0.76 0.94 52 -1.4 101 153
FOS -0.1 0.71 1.1 39 -1.2 121 160
SP1 0.035 0.022 0.09 5 -0.028 44 49
CDC25B -0.035 0.7 1.1 54 -1.2 98 152
response to radiation 0.03 0.08 0.15 108 -10000 0 108
CENPB -0.026 0.69 1.1 54 -1.2 97 151
CENPA -0.054 0.68 1.1 40 -1.2 96 136
NEK2 -0.041 0.68 1.1 44 -1.2 96 140
HIST1H2BA -0.051 0.66 0.95 54 -1.1 98 152
CCNA2 0.018 0.04 0.11 6 -10000 0 6
EP300 0.035 0.012 -10000 0 0 52 52
CCNB1/CDK1 -0.14 0.82 1.2 39 -1.5 106 145
CCNB2 -0.072 0.71 1.1 44 -1.2 101 145
CCNB1 -0.076 0.76 1.2 44 -1.3 106 150
ETV5 -0.079 0.69 1 47 -1.1 117 164
ESR1 -0.055 0.66 1 42 -1.2 96 138
CCND1 -0.08 0.61 0.95 45 -1.1 99 144
GSK3A 0.038 0.096 0.23 53 -10000 0 53
Cyclin A-E1/CDK1-2 0.045 0.11 0.27 37 -0.16 40 77
CDK2 0.019 0.047 0.12 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.034 0.095 0.19 95 -10000 0 95
FOXM1B/Cbp/p300 -0.13 0.67 0.83 29 -1.3 98 127
GAS1 -0.05 0.68 1.1 47 -1.2 98 145
MMP2 -0.08 0.7 1 44 -1.2 110 154
RB1/FOXM1C -0.14 0.59 0.86 32 -1.1 101 133
CREBBP 0.038 0.005 -10000 0 0 7 7
Endothelins

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
AKT1 -0.013 0.16 0.25 86 -0.27 59 145
PTK2B 0.038 0.007 -10000 0 0 18 18
mol:Ca2+ -0.086 0.25 0.49 5 -0.55 64 69
EDN1 0.007 0.1 0.18 47 -0.16 97 144
EDN3 0.033 0.014 -10000 0 0 82 82
EDN2 0.038 0.007 -10000 0 0 16 16
HRAS/GDP -0.005 0.19 0.34 31 -0.38 56 87
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.009 0.13 0.23 31 -0.27 47 78
ADCY4 -0.034 0.1 0.16 52 -0.19 91 143
ADCY5 -0.034 0.1 0.16 52 -0.19 91 143
ADCY6 -0.002 0.14 0.23 92 -0.23 48 140
ADCY7 -0.005 0.14 0.23 88 -0.23 50 138
ADCY1 0.008 0.12 0.23 68 -0.24 26 94
ADCY2 0 0.15 0.24 94 -0.23 50 144
ADCY3 -0.034 0.1 0.16 52 -0.19 91 143
ADCY8 -0.004 0.14 0.23 86 -0.23 43 129
ADCY9 -0.002 0.15 0.23 93 -0.23 50 143
arachidonic acid secretion -0.064 0.28 0.37 40 -0.51 101 141
ETB receptor/Endothelin-1/Gq/GTP -0.002 0.11 0.21 28 -0.26 43 71
GNAO1 0.032 0.015 -10000 0 0 88 88
HRAS 0.036 0.011 -10000 0 -0.002 41 41
ETA receptor/Endothelin-1/G12/GTP 0.015 0.11 0.25 27 -0.22 51 78
ETA receptor/Endothelin-1/Gs/GTP 0.012 0.13 0.23 28 -0.2 97 125
mol:GTP 0.001 0.008 0.035 7 -0.03 2 9
COL3A1 -0.071 0.14 0.22 12 -0.34 94 106
EDNRB 0.026 0.054 0.13 62 -0.073 61 123
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.013 0.15 0.27 74 -0.27 55 129
CYSLTR1 -0.028 0.13 0.21 64 -0.22 91 155
SLC9A1 -0.014 0.091 0.17 33 -0.18 64 97
mol:GDP -0.012 0.19 0.33 34 -0.39 55 89
SLC9A3 -0.12 0.3 0.38 1 -0.66 83 84
RAF1 -0.021 0.22 0.35 45 -0.43 77 122
JUN -0.13 0.33 0.46 5 -0.72 83 88
JAK2 -0.015 0.15 0.26 76 -0.26 65 141
mol:IP3 0.004 0.13 0.24 34 -0.3 33 67
ETA receptor/Endothelin-1 -0.02 0.14 0.27 1 -0.26 104 105
PLCB1 0.024 0.027 -10000 0 -0.015 147 147
PLCB2 0.027 0.03 -10000 0 -0.04 78 78
ETA receptor/Endothelin-3 0.007 0.086 0.16 9 -0.14 94 103
FOS -0.078 0.36 0.44 40 -0.81 84 124
Gai/GDP -0.07 0.26 -10000 0 -0.7 68 68
CRK 0.037 0.009 -10000 0 0 25 25
mol:Ca ++ -0.006 0.18 0.3 74 -0.33 66 140
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 0.002 0.13 0.25 34 -0.3 41 75
GNAQ 0.026 0.033 0.087 3 -0.043 84 87
GNAZ 0.033 0.014 -10000 0 0 83 83
GNAL 0.037 0.008 -10000 0 0 21 21
Gs family/GDP -0.004 0.18 0.32 29 -0.37 51 80
ETA receptor/Endothelin-1/Gq/GTP -0.002 0.13 0.23 29 -0.28 50 79
MAPK14 -0.009 0.1 0.2 18 -0.27 34 52
TRPC6 -0.091 0.26 0.5 5 -0.58 63 68
GNAI2 0.035 0.011 -10000 0 0 46 46
GNAI3 0.038 0.007 -10000 0 0 16 16
GNAI1 0.016 0.019 -10000 0 0 297 297
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.001 0.11 0.21 30 -0.28 35 65
ETB receptor/Endothelin-2 0.023 0.072 0.14 4 -0.1 94 98
ETB receptor/Endothelin-3 0.019 0.069 0.14 3 -0.11 87 90
ETB receptor/Endothelin-1 0.005 0.1 0.22 35 -0.17 90 125
MAPK3 -0.062 0.34 0.42 44 -0.72 84 128
MAPK1 -0.076 0.36 0.42 43 -0.77 87 130
Rac1/GDP -0.007 0.16 0.33 23 -0.39 35 58
cAMP biosynthetic process 0.028 0.13 0.24 83 -0.23 23 106
MAPK8 -0.12 0.31 0.42 8 -0.61 109 117
SRC 0.034 0.013 -10000 0 0 65 65
ETB receptor/Endothelin-1/Gi/GTP -0.018 0.13 0.17 16 -0.34 46 62
p130Cas/CRK/Src/PYK2 -0.009 0.2 0.38 29 -0.5 40 69
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.009 0.16 0.33 21 -0.38 39 60
COL1A2 -0.04 0.14 0.28 2 -0.44 42 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.009 0.092 0.16 9 -0.14 106 115
mol:DAG 0.003 0.13 0.24 34 -0.31 33 67
MAP2K2 -0.037 0.28 0.38 60 -0.56 81 141
MAP2K1 -0.052 0.28 0.37 46 -0.57 86 132
EDNRA 0.004 0.094 0.18 34 -0.17 83 117
positive regulation of muscle contraction 0.043 0.16 0.24 153 -0.27 27 180
Gq family/GDP -0.003 0.17 0.35 8 -0.37 51 59
HRAS/GTP -0.001 0.18 0.31 44 -0.36 55 99
PRKCH 0 0.13 0.27 29 -0.3 39 68
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCA -0.005 0.13 0.26 26 -0.32 37 63
PRKCB 0.002 0.13 0.25 34 -0.3 42 76
PRKCE -0.006 0.13 0.25 25 -0.32 37 62
PRKCD 0.001 0.14 0.3 30 -0.31 35 65
PRKCG -0.006 0.14 0.26 27 -0.32 38 65
regulation of vascular smooth muscle contraction -0.11 0.43 0.48 32 -0.99 83 115
PRKCQ 0 0.12 0.28 27 -0.32 29 56
PLA2G4A -0.075 0.3 0.39 36 -0.56 101 137
GNA14 0.026 0.033 0.086 2 -0.043 84 86
GNA15 0.025 0.03 -10000 0 -0.039 74 74
GNA12 0.022 0.019 -10000 0 0 227 227
GNA11 0.026 0.028 -10000 0 -0.039 63 63
Rac1/GTP 0.017 0.11 0.25 27 -0.22 48 75
MMP1 0.013 0.076 0.27 9 -10000 0 9
TCGA08_rtk_signaling

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.026 0.018 -10000 0 0 168 168
HRAS 0.036 0.01 -10000 0 0 39 39
EGFR 0.009 0.017 -10000 0 0 385 385
AKT 0.11 0.14 0.27 145 -0.2 8 153
FOXO3 0.034 0.013 -10000 0 0 63 63
AKT1 0.034 0.013 -10000 0 0 61 61
FOXO1 0.031 0.015 -10000 0 0 98 98
AKT3 0.037 0.009 -10000 0 0 27 27
FOXO4 0.039 0.002 -10000 0 0 2 2
MET 0.021 0.019 -10000 0 0 239 239
PIK3CA 0.033 0.014 -10000 0 0 79 79
PIK3CB 0.037 0.008 -10000 0 0 22 22
NRAS 0.034 0.013 -10000 0 0 66 66
PIK3CG 0.023 0.019 -10000 0 0 213 213
PIK3R3 0.038 0.007 -10000 0 0 18 18
PIK3R2 0.036 0.01 -10000 0 0 37 37
NF1 0.038 0.007 -10000 0 0 16 16
RAS 0.006 0.054 0.14 10 -0.23 9 19
ERBB2 0.038 0.005 -10000 0 0 8 8
proliferation/survival/translation -0.046 0.1 0.36 16 -0.25 19 35
PI3K 0.061 0.11 0.25 111 -0.15 10 121
PIK3R1 0.034 0.013 -10000 0 0 69 69
KRAS 0.036 0.011 -10000 0 0 40 40
FOXO 0.12 0.12 0.27 138 -0.12 4 142
AKT2 0.036 0.01 -10000 0 0 34 34
PTEN 0.024 0.019 -10000 0 0 196 196
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.22 0.41 -10000 0 -0.82 134 134
NCK1/PAK1/Dok-R -0.12 0.16 -10000 0 -0.39 119 119
NCK1/Dok-R -0.13 0.35 -10000 0 -0.84 96 96
PIK3CA 0.033 0.014 -10000 0 0 79 79
mol:beta2-estradiol 0.027 0.1 0.22 96 -0.091 79 175
RELA 0.038 0.006 -10000 0 0 12 12
SHC1 0.033 0.014 -10000 0 -0.003 61 61
Rac/GDP 0.016 0.019 -10000 0 -0.11 5 5
F2 0.042 0.12 0.27 86 -0.13 63 149
TNIP2 0.038 0.006 -10000 0 0 14 14
NF kappa B/RelA -0.11 0.35 -10000 0 -0.82 96 96
FN1 0.037 0.009 -10000 0 0 31 31
PLD2 -0.15 0.35 -10000 0 -0.87 96 96
PTPN11 0.038 0.007 -10000 0 0 17 17
GRB14 0.034 0.013 -10000 0 0 70 70
ELK1 -0.15 0.32 -10000 0 -0.81 96 96
GRB7 0.038 0.007 -10000 0 0 17 17
PAK1 0.037 0.008 -10000 0 0 20 20
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.36 -10000 0 -0.84 96 96
CDKN1A -0.18 0.36 0.48 7 -0.68 146 153
ITGA5 0.034 0.013 -10000 0 0 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.35 -10000 0 -0.84 96 96
CRK 0.037 0.008 -10000 0 0 25 25
mol:NO -0.11 0.32 0.44 10 -0.58 127 137
PLG -0.15 0.35 -10000 0 -0.87 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.36 0.44 2 -0.75 115 117
GRB2 0.037 0.009 -10000 0 0 26 26
PIK3R1 0.033 0.015 -10000 0 -0.002 74 74
ANGPT2 -0.21 0.45 0.41 7 -1 105 112
BMX -0.15 0.35 -10000 0 -0.87 96 96
ANGPT1 -0.15 0.42 -10000 0 -1 94 94
tube development -0.2 0.36 0.44 5 -0.7 157 162
ANGPT4 0.02 0.034 -10000 0 -0.045 94 94
response to hypoxia -0.012 0.026 -10000 0 -0.063 96 96
Tie2/Ang1/GRB14 -0.14 0.36 -10000 0 -0.87 96 96
alpha5/beta1 Integrin 0.032 0.041 -10000 0 -0.12 20 20
FGF2 0.035 0.023 -10000 0 -0.043 31 31
STAT5A (dimer) -0.23 0.45 0.55 3 -0.82 166 169
mol:L-citrulline -0.11 0.32 0.44 10 -0.58 127 137
AGTR1 0.021 0.04 0.075 3 -0.057 94 97
MAPK14 -0.16 0.37 -10000 0 -0.88 96 96
Tie2/SHP2 -0.085 0.25 -10000 0 -0.85 36 36
TEK -0.095 0.26 -10000 0 -0.94 35 35
RPS6KB1 -0.2 0.37 -10000 0 -0.77 131 131
Angiotensin II/AT1 0.015 0.042 0.098 30 -0.063 89 119
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -0.88 96 96
MAPK3 -0.16 0.33 -10000 0 -0.82 96 96
MAPK1 -0.16 0.33 -10000 0 -0.82 96 96
Tie2/Ang1/GRB7 -0.14 0.37 -10000 0 -0.88 96 96
NFKB1 0.038 0.007 -10000 0 0 18 18
MAPK8 -0.15 0.35 -10000 0 -0.86 96 96
PI3K -0.23 0.44 -10000 0 -0.91 126 126
FES -0.16 0.37 -10000 0 -0.89 95 95
Crk/Dok-R -0.14 0.35 -10000 0 -0.84 96 96
Tie2/Ang1/ABIN2 -0.14 0.37 -10000 0 -0.88 96 96
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.36 0.43 2 -0.73 136 138
STAT5A 0.037 0.011 -10000 0 -0.017 19 19
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.37 -10000 0 -0.77 129 129
Tie2/Ang2 -0.28 0.5 0.51 2 -0.97 156 158
Tie2/Ang1 -0.15 0.37 -10000 0 -0.91 96 96
FOXO1 -0.22 0.4 0.44 4 -0.76 160 164
ELF1 0.029 0.041 0.15 3 -0.056 77 80
ELF2 -0.14 0.35 -10000 0 -0.84 96 96
mol:Choline -0.15 0.34 -10000 0 -0.84 96 96
cell migration -0.066 0.095 -10000 0 -0.22 125 125
FYN -0.24 0.41 0.46 4 -0.81 157 161
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.16 0.32 0.47 7 -0.61 146 153
ETS1 0.003 0.13 0.15 17 -0.26 91 108
PXN -0.17 0.31 0.39 1 -0.65 128 129
ITGB1 0.029 0.017 -10000 0 0 131 131
NOS3 -0.13 0.36 0.48 6 -0.66 127 133
RAC1 0.023 0.019 -10000 0 0 209 209
TNF -0.005 0.13 0.15 5 -0.26 91 96
MAPKKK cascade -0.15 0.34 -10000 0 -0.84 96 96
RASA1 0.036 0.01 -10000 0 0 37 37
Tie2/Ang1/Shc -0.14 0.37 -10000 0 -0.88 96 96
NCK1 0.037 0.009 -10000 0 0 31 31
vasculogenesis -0.089 0.3 0.42 12 -0.52 127 139
mol:Phosphatidic acid -0.15 0.34 -10000 0 -0.84 96 96
mol:Angiotensin II -0.003 0.015 0.029 29 -0.033 73 102
mol:NADP -0.11 0.32 0.44 10 -0.58 127 137
Rac1/GTP -0.17 0.33 -10000 0 -0.7 120 120
MMP2 -0.15 0.36 -10000 0 -0.87 96 96
Effects of Botulinum toxin

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
STX1A -0.01 0.009 0 217 -10000 0 217
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.043 0.037 -10000 0 -0.13 15 15
STXBP1 0.031 0.016 -10000 0 0 107 107
ACh/CHRNA1 0.034 0.06 0.1 92 -0.078 88 180
RAB3GAP2/RIMS1/UNC13B 0.055 0.049 -10000 0 -0.12 22 22
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 0.037 0.009 -10000 0 0 28 28
mol:ACh 0.031 0.074 0.11 200 -0.088 81 281
RAB3GAP2 0.037 0.009 -10000 0 0 28 28
STX1A/SNAP25/VAMP2 0.038 0.11 0.19 51 -0.16 74 125
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.034 0.06 0.1 92 -0.078 88 180
UNC13B 0.033 0.014 -10000 0 0 80 80
CHRNA1 0.037 0.008 -10000 0 0 20 20
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.017 0.046 0.11 39 -0.085 40 79
SNAP25 0.001 0.002 -10000 0 0 297 297
VAMP2 0.003 0.001 -10000 0 0 50 50
SYT1 0.018 0.019 -10000 0 0 268 268
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.016 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.038 0.11 0.19 51 -0.16 74 125
Thromboxane A2 receptor signaling

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
TGM2 0.034 0.014 0.06 1 0 74 75
GNB1/GNG2 -0.051 0.073 -10000 0 -0.18 122 122
AKT1 0.008 0.18 0.33 55 -0.32 34 89
EGF 0.037 0.008 -10000 0 0 25 25
mol:TXA2 0 0.001 0.004 3 -10000 0 3
FGR -0.022 0.086 0.28 28 -10000 0 28
mol:Ca2+ 0.013 0.21 0.38 57 -0.28 75 132
LYN -0.023 0.086 0.28 25 -10000 0 25
RhoA/GTP 0.006 0.098 0.2 44 -0.13 70 114
mol:PGI2 0 0.001 0.003 3 -10000 0 3
SYK -0.003 0.23 0.39 57 -0.33 109 166
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.037 0.009 -10000 0 0 28 28
TP alpha/Gq family/GDP/G beta5/gamma2 -0.002 0.076 -10000 0 -0.25 30 30
G beta5/gamma2 -0.062 0.097 -10000 0 -0.23 117 117
PRKCH -0.002 0.23 0.39 51 -0.33 81 132
DNM1 0.037 0.009 -10000 0 0 30 30
TXA2/TP beta/beta Arrestin3 0.012 0.02 -10000 0 -10000 0 0
mol:GTP 0.001 0.003 0.008 66 -10000 0 66
PTGDR 0.037 0.009 -10000 0 0 31 31
G12 family/GTP -0.044 0.14 0.25 4 -0.29 77 81
ADRBK1 0.038 0.006 -10000 0 0 13 13
ADRBK2 0.036 0.01 -10000 0 0 34 34
RhoA/GTP/ROCK1 0.047 0.026 -10000 0 -0.11 10 10
mol:GDP -0.017 0.15 0.42 14 -0.33 32 46
mol:NADP 0.023 0.019 -10000 0 0 214 214
RAB11A 0.038 0.007 -10000 0 0 19 19
PRKG1 0.028 0.018 -10000 0 0 149 149
mol:IP3 0.002 0.24 0.42 47 -0.35 78 125
cell morphogenesis 0.046 0.026 -10000 0 -0.11 10 10
PLCB2 -0.02 0.29 0.52 27 -0.47 80 107
mol:cGMP 0 0.001 0.004 1 -10000 0 1
BLK -0.021 0.09 0.28 32 -10000 0 32
mol:PDG2 0 0.001 0.003 3 -10000 0 3
HCK -0.028 0.065 0.28 11 -0.19 1 12
RHOA 0.037 0.008 -10000 0 0 24 24
PTGIR 0.036 0.011 -10000 0 0 40 40
PRKCB1 -0.004 0.24 0.4 48 -0.35 85 133
GNAQ 0.036 0.01 -10000 0 0 37 37
mol:L-citrulline 0.023 0.019 -10000 0 0 214 214
TXA2/TXA2-R family -0.032 0.3 0.53 27 -0.48 119 146
LCK -0.022 0.088 0.27 31 -10000 0 31
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.015 0.055 0.19 12 -10000 0 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.032 0.15 -10000 0 -0.45 56 56
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.055 0.19 12 -10000 0 12
MAPK14 0.005 0.17 0.32 60 -0.23 92 152
TGM2/GTP -0.006 0.25 0.45 44 -0.39 71 115
MAPK11 0.004 0.17 0.32 58 -0.22 102 160
ARHGEF1 0.018 0.14 0.28 58 -0.18 70 128
GNAI2 0.035 0.011 -10000 0 0 46 46
JNK cascade -0.007 0.24 0.42 49 -0.36 114 163
RAB11/GDP 0.028 0.026 -10000 0 -0.03 77 77
ICAM1 0.01 0.2 0.37 57 -0.27 111 168
cAMP biosynthetic process 0.001 0.22 0.39 51 -0.33 75 126
Gq family/GTP/EBP50 0.01 0.056 0.19 14 -0.16 30 44
actin cytoskeleton reorganization 0.046 0.026 -10000 0 -0.11 10 10
SRC -0.03 0.066 0.25 15 -10000 0 15
GNB5 0.038 0.008 -10000 0 0 20 20
GNB1 0.035 0.011 -10000 0 0 46 46
EGF/EGFR -0.007 0.12 0.3 34 -0.24 33 67
VCAM1 -0.007 0.23 0.38 53 -0.32 133 186
TP beta/Gq family/GDP/G beta5/gamma2 -0.002 0.076 -10000 0 -0.25 30 30
platelet activation 0.003 0.21 0.38 59 -0.29 80 139
PGI2/IP 0.027 0.008 -10000 0 -10000 0 0
PRKACA 0.01 0.026 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.002 0.067 -10000 0 -0.22 29 29
TXA2/TP beta/beta Arrestin2 0 0.048 -10000 0 -0.32 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.02 0.024 0.1 2 -0.15 3 5
mol:DAG -0.006 0.26 0.43 47 -0.39 86 133
EGFR 0.009 0.017 -10000 0 0 385 385
TXA2/TP alpha -0.013 0.28 0.52 27 -0.44 76 103
Gq family/GTP 0.01 0.052 0.2 20 -0.12 27 47
YES1 -0.023 0.084 0.27 27 -10000 0 27
GNAI2/GTP -0.024 0.051 0.12 5 -0.16 2 7
PGD2/DP 0.027 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.036 0.01 -10000 0 0 37 37
FYN -0.021 0.087 0.28 27 -10000 0 27
mol:NO 0.023 0.019 -10000 0 0 214 214
GNA15 0.034 0.013 -10000 0 0 62 62
PGK/cGMP 0.026 0.027 -10000 0 -10000 0 0
RhoA/GDP 0.028 0.026 -10000 0 -0.028 82 82
TP alpha/TGM2/GDP/G beta/gamma 0.019 0.051 0.2 8 -0.14 2 10
NOS3 0.023 0.019 -10000 0 0 214 214
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCA -0.001 0.23 0.39 49 -0.34 82 131
PRKCB 0 0.23 0.4 48 -0.32 113 161
PRKCE -0.005 0.23 0.39 51 -0.33 109 160
PRKCD -0.004 0.24 0.4 55 -0.35 111 166
PRKCG -0.005 0.24 0.4 53 -0.36 111 164
muscle contraction -0.027 0.28 0.5 30 -0.44 117 147
PRKCZ -0.002 0.22 0.38 53 -0.32 114 167
ARR3 0.039 0.002 -10000 0 0 2 2
TXA2/TP beta 0.018 0.059 0.2 11 -0.15 3 14
PRKCQ -0.01 0.22 0.39 50 -0.33 96 146
MAPKKK cascade -0.017 0.26 0.49 29 -0.4 107 136
SELE 0.003 0.2 0.35 58 -0.28 121 179
TP beta/GNAI2/GDP/G beta/gamma 0.016 0.059 0.2 9 -0.15 14 23
ROCK1 0.037 0.008 -10000 0 0 22 22
GNA14 0.036 0.01 -10000 0 0 36 36
chemotaxis -0.052 0.34 0.58 23 -0.55 131 154
GNA12 0.022 0.019 -10000 0 0 227 227
GNA13 0.037 0.008 -10000 0 0 22 22
GNA11 0.034 0.013 -10000 0 0 63 63
Rac1/GTP 0.016 0.019 -10000 0 -0.11 5 5
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.002 0.006 0 449 -10000 0 449
TP53 0.006 0.038 -10000 0 -0.23 8 8
Senescence 0.006 0.038 -10000 0 -0.23 8 8
Apoptosis 0.006 0.038 -10000 0 -0.23 8 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.002 0.036 0.3 7 -10000 0 7
MDM4 0.034 0.013 -10000 0 0 67 67
Syndecan-1-mediated signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.013 -10000 0 0 70 70
CCL5 0.035 0.012 -10000 0 0 56 56
SDCBP 0.037 0.008 -10000 0 0 25 25
FGFR/FGF2/Syndecan-1 0.028 0.11 0.23 59 -0.22 11 70
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 0.024 0.11 0.23 43 -0.24 14 57
Syndecan-1/Syntenin 0.041 0.12 0.23 63 -0.24 17 80
MAPK3 0.003 0.11 0.19 54 -0.24 15 69
HGF/MET 0.029 0.029 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.034 0.013 -10000 0 0 70 70
BSG 0.033 0.014 -10000 0 0 73 73
keratinocyte migration 0.024 0.11 0.23 43 -0.23 14 57
Syndecan-1/RANTES 0.033 0.11 0.23 48 -0.23 14 62
Syndecan-1/CD147 0.036 0.12 0.24 40 -0.24 15 55
Syndecan-1/Syntenin/PIP2 0.037 0.12 0.22 63 -0.23 15 78
LAMA5 0.032 0.015 -10000 0 0 93 93
positive regulation of cell-cell adhesion 0.036 0.11 0.21 63 -0.23 15 78
MMP7 0.028 0.017 -10000 0 0 140 140
HGF 0.022 0.019 -10000 0 0 216 216
Syndecan-1/CASK 0.005 0.091 0.17 32 -0.22 14 46
Syndecan-1/HGF/MET 0.025 0.093 0.24 21 -0.25 8 29
regulation of cell adhesion 0.002 0.12 0.24 46 -0.25 13 59
HPSE 0.035 0.012 -10000 0 0 58 58
positive regulation of cell migration 0.028 0.11 0.23 59 -0.22 11 70
SDC1 0.018 0.1 0.21 42 -0.23 9 51
Syndecan-1/Collagen 0.028 0.11 0.23 59 -0.22 11 70
PPIB 0.036 0.01 -10000 0 0 37 37
MET 0.021 0.019 -10000 0 0 239 239
PRKACA 0.036 0.01 -10000 0 0 36 36
MMP9 0.016 0.019 -10000 0 0 296 296
MAPK1 0.003 0.11 0.19 53 -0.24 14 67
homophilic cell adhesion 0.03 0.12 0.23 64 -0.23 12 76
MMP1 0.033 0.014 -10000 0 0 75 75
Syndecan-3-mediated signaling events

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
CTTN 0.038 0.006 -10000 0 0 14 14
Syndecan-3/Src/Cortactin -0.027 0.17 -10000 0 -0.43 71 71
Syndecan-3/Neurocan -0.057 0.2 -10000 0 -0.51 77 77
POMC 0.038 0.006 -10000 0 0 14 14
EGFR 0.009 0.017 -10000 0 0 385 385
Syndecan-3/EGFR -0.053 0.16 -10000 0 -0.4 76 76
AGRP 0.038 0.005 -10000 0 0 8 8
NCSTN 0.037 0.009 -10000 0 0 31 31
PSENEN 0.035 0.011 -10000 0 0 48 48
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.038 0.007 -10000 0 0 18 18
APH1A 0.038 0.007 -10000 0 0 19 19
NCAN 0.024 0.019 -10000 0 0 197 197
long-term memory -0.029 0.2 -10000 0 -0.47 79 79
Syndecan-3/IL8 -0.052 0.18 -10000 0 -0.45 79 79
PSEN1 0.035 0.012 -10000 0 0 53 53
Src/Cortactin 0.049 0.022 -10000 0 -0.13 1 1
FYN 0.032 0.015 -10000 0 0 95 95
limb bud formation -0.065 0.18 -10000 0 -0.49 75 75
MC4R 0.037 0.008 -10000 0 0 22 22
SRC 0.034 0.013 -10000 0 0 65 65
PTN 0.02 0.019 -10000 0 0 250 250
FGFR/FGF/Syndecan-3 -0.066 0.18 -10000 0 -0.5 75 75
neuron projection morphogenesis -0.034 0.2 0.32 18 -0.47 67 85
Syndecan-3/AgRP -0.041 0.19 -10000 0 -0.47 80 80
Syndecan-3/AgRP/MC4R -0.021 0.19 -10000 0 -0.46 79 79
Fyn/Cortactin 0.033 0.058 -10000 0 -0.13 53 53
SDC3 -0.066 0.18 -10000 0 -0.5 75 75
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.051 0.17 -10000 0 -0.44 79 79
IL8 0.02 0.019 -10000 0 0 243 243
Syndecan-3/Fyn/Cortactin -0.029 0.2 -10000 0 -0.48 79 79
Syndecan-3/CASK -0.065 0.17 -10000 0 -0.48 75 75
alpha-MSH/MC4R 0.054 0.015 -10000 0 -10000 0 0
Gamma Secretase 0.078 0.076 -10000 0 -0.15 28 28
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.003 0.65 0.88 70 -1 122 192
IL23A 0.14 0.43 0.87 53 -1 19 72
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.39 0.7 57 -0.88 24 81
positive regulation of T cell mediated cytotoxicity 0.14 0.48 0.94 64 -0.99 24 88
ITGA3 0.13 0.42 0.86 50 -0.96 18 68
IL17F 0.056 0.3 0.59 53 -0.62 25 78
IL12B 0.079 0.11 0.23 124 -10000 0 124
STAT1 (dimer) 0.1 0.42 0.74 61 -0.94 25 86
CD4 0.12 0.48 0.88 57 -1.1 30 87
IL23 0.13 0.41 0.82 44 -0.97 20 64
IL23R 0.1 0.2 0.38 133 -0.16 2 135
IL1B 0.13 0.47 0.91 53 -1.2 22 75
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.13 0.42 0.83 53 -0.93 18 71
TYK2 0.052 0.079 0.19 73 -10000 0 73
STAT4 0.037 0.009 -10000 0 0 31 31
STAT3 0.036 0.011 -10000 0 0 42 42
IL18RAP 0.027 0.028 -10000 0 -0.04 71 71
IL12RB1 0.055 0.08 0.19 76 -10000 0 76
PIK3CA 0.033 0.014 -10000 0 0 79 79
IL12Rbeta1/TYK2 0.063 0.094 0.22 66 -0.13 6 72
IL23R/JAK2 0.14 0.22 0.44 128 -0.21 5 133
positive regulation of chronic inflammatory response 0.14 0.48 0.94 64 -0.99 24 88
natural killer cell activation -0.008 0.016 -10000 0 -0.039 70 70
JAK2 0.073 0.11 0.23 118 -10000 0 118
PIK3R1 0.034 0.013 -10000 0 0 69 69
NFKB1 0.038 0.024 0.09 2 -0.038 36 38
RELA 0.038 0.023 0.09 2 -0.038 36 38
positive regulation of dendritic cell antigen processing and presentation 0.14 0.4 0.78 54 -0.92 20 74
ALOX12B 0.13 0.42 0.84 52 -0.94 19 71
CXCL1 0.14 0.44 0.86 69 -0.92 20 89
T cell proliferation 0.14 0.48 0.94 64 -0.99 24 88
NFKBIA 0.035 0.024 0.09 2 -0.038 27 29
IL17A 0.093 0.29 0.55 69 -0.5 22 91
PI3K 0.073 0.39 0.71 49 -0.92 25 74
IFNG 0.023 0.043 0.12 48 -0.086 5 53
STAT3 (dimer) 0.075 0.39 0.69 49 -0.89 25 74
IL18R1 0.027 0.028 -10000 0 -0.04 73 73
IL23/IL23R/JAK2/TYK2/SOCS3 0.14 0.33 0.66 79 -0.55 18 97
IL18/IL18R 0.055 0.05 0.2 3 -0.098 13 16
macrophage activation -0.001 0.017 0.032 28 -0.043 14 42
TNF 0.14 0.43 0.86 53 -1 17 70
STAT3/STAT4 0.099 0.4 0.7 56 -0.9 26 82
STAT4 (dimer) 0.1 0.41 0.73 58 -0.94 25 83
IL18 0.026 0.025 -10000 0 -0.039 46 46
IL19 0.13 0.42 0.83 54 -0.93 18 72
STAT5A (dimer) 0.12 0.42 0.74 64 -0.94 25 89
STAT1 0.036 0.011 -10000 0 0 41 41
SOCS3 0.038 0.005 -10000 0 0 9 9
CXCL9 0.14 0.44 0.86 62 -0.94 19 81
MPO 0.13 0.42 0.83 54 -0.94 18 72
positive regulation of humoral immune response 0.14 0.48 0.94 64 -0.99 24 88
IL23/IL23R/JAK2/TYK2 0.14 0.48 0.95 63 -1 24 87
IL6 0.22 0.44 0.89 80 -1 13 93
STAT5A 0.038 0.005 -10000 0 0 10 10
IL2 0.003 0.045 0.1 3 -0.061 69 72
positive regulation of tyrosine phosphorylation of STAT protein -0.008 0.016 -10000 0 -0.039 70 70
CD3E 0.13 0.42 0.83 53 -0.94 19 72
keratinocyte proliferation 0.14 0.48 0.94 64 -0.99 24 88
NOS2 0.13 0.42 0.8 66 -0.86 26 92
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.019 0.16 -10000 0 -0.64 28 28
oxygen homeostasis 0.014 0.039 0.079 94 -0.032 3 97
TCEB2 0.039 0.004 -10000 0 0 6 6
TCEB1 0.037 0.008 -10000 0 0 25 25
VHL/Elongin B/Elongin C/HIF2A 0.03 0.18 0.36 61 -0.26 41 102
EPO -0.032 0.23 0.5 34 -0.46 49 83
FIH (dimer) 0.021 0.056 0.15 33 -0.057 12 45
APEX1 0.016 0.054 0.14 20 -0.063 25 45
SERPINE1 -0.068 0.2 0.42 14 -0.52 54 68
FLT1 -0.015 0.16 -10000 0 -0.71 23 23
ADORA2A -0.003 0.3 0.51 78 -0.48 54 132
germ cell development -0.025 0.28 0.5 61 -0.45 65 126
SLC11A2 -0.018 0.3 0.53 67 -0.49 60 127
BHLHE40 -0.027 0.28 0.51 61 -0.46 65 126
HIF1AN 0.021 0.056 0.15 33 -0.057 12 45
HIF2A/ARNT/SIRT1 -0.012 0.19 0.4 41 -0.34 38 79
ETS1 0.051 0.043 0.16 47 -0.12 11 58
CITED2 -0.061 0.26 -10000 0 -0.8 50 50
KDR -0.004 0.16 -10000 0 -0.8 16 16
PGK1 -0.022 0.3 0.53 68 -0.51 58 126
SIRT1 0.026 0.018 -10000 0 0 170 170
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.027 0.29 0.54 34 -0.52 65 99
EPAS1 0.025 0.2 0.43 62 -0.29 30 92
SP1 0.042 0.015 0.15 7 -10000 0 7
ABCG2 -0.028 0.3 0.54 63 -0.5 65 128
EFNA1 -0.028 0.29 0.51 62 -0.5 58 120
FXN -0.004 0.3 0.5 81 -0.47 61 142
POU5F1 -0.027 0.28 0.51 61 -0.46 65 126
neuron apoptosis 0.026 0.29 0.51 65 -0.53 34 99
EP300 0.035 0.012 -10000 0 0 52 52
EGLN3 0.023 0.057 0.15 32 -0.056 15 47
EGLN2 0.028 0.062 0.15 44 -0.055 17 61
EGLN1 0.029 0.06 0.15 39 -0.058 6 45
VHL/Elongin B/Elongin C 0.048 0.023 -10000 0 -0.1 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.016 0.054 0.13 20 -0.062 25 45
SLC2A1 -0.027 0.29 0.54 53 -0.5 57 110
TWIST1 -0.044 0.23 0.5 31 -0.49 54 85
ELK1 0.041 0.043 0.16 29 -0.11 25 54
HIF2A/ARNT/Cbp/p300 0.012 0.22 0.43 48 -0.35 41 89
VEGFA -0.07 0.26 0.46 41 -0.5 73 114
CREBBP 0.038 0.005 -10000 0 0 7 7
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.016 0.031 -10000 0 -0.091 37 37
ARNO/beta Arrestin1-2 0.042 0.028 -10000 0 -0.084 12 12
EGFR 0.009 0.017 -10000 0 0 385 385
EPHA2 0.035 0.012 -10000 0 0 57 57
USP6 0.037 0.008 -10000 0 0 21 21
IQSEC1 0.038 0.008 -10000 0 0 21 21
EGFR/EGFR/EGF/EGF -0.002 0.051 -10000 0 -0.13 58 58
ARRB2 0.009 0.024 -10000 0 -0.19 7 7
mol:GTP 0 0.016 0.11 3 -0.068 3 6
ARRB1 0.038 0.006 -10000 0 0 14 14
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.035 0.012 -10000 0 0 54 54
EGF 0.037 0.008 -10000 0 0 25 25
somatostatin receptor activity 0 0 0.001 175 -0.001 8 183
ARAP2 0 0 0 106 0 4 110
mol:GDP 0.075 0.079 0.19 83 -0.2 3 86
mol:PI-3-4-5-P3 0 0 0.001 102 0 8 110
ITGA2B 0.039 0.004 -10000 0 0 5 5
ARF6 0.037 0.01 -10000 0 0 33 33
Ephrin A1/EPHA2/NCK1/GIT1 0.077 0.058 -10000 0 -0.12 25 25
ADAP1 0 0 0 61 0 2 63
KIF13B 0.034 0.013 -10000 0 0 64 64
HGF/MET 0.029 0.029 -10000 0 -10000 0 0
PXN 0.038 0.006 -10000 0 0 11 11
ARF6/GTP 0.089 0.1 0.22 113 -0.22 8 121
EGFR/EGFR/EGF/EGF/ARFGEP100 0.003 0.053 -10000 0 -0.12 57 57
ADRB2 0.036 0.011 -10000 0 0 45 45
receptor agonist activity 0 0 0 142 0 9 151
actin filament binding 0 0 0 170 0 8 178
SRC 0.034 0.013 -10000 0 0 65 65
ITGB3 0.039 0.005 -10000 0 0 7 7
GNAQ 0.037 0.01 -10000 0 0 37 37
EFA6/PI-4-5-P2 0.001 0.001 0.001 193 -0.001 5 198
ARF6/GDP 0.032 0.076 0.16 23 -0.23 22 45
ARF6/GDP/GULP/ACAP1 0.06 0.081 0.22 24 -0.25 2 26
alphaIIb/beta3 Integrin/paxillin/GIT1 0.097 0.019 -10000 0 -10000 0 0
ACAP1 0 0 0 60 -10000 0 60
ACAP2 0 0 0 99 0 5 104
LHCGR/beta Arrestin2 0.031 0.026 0.082 8 -0.094 19 27
EFNA1 0.035 0.012 -10000 0 0 56 56
HGF 0.022 0.019 -10000 0 0 216 216
CYTH3 0 0 0.001 169 -0.001 8 177
CYTH2 0 0.001 0.002 3 -0.004 11 14
NCK1 0.037 0.009 -10000 0 0 31 31
fibronectin binding 0 0 0 102 0 9 111
endosomal lumen acidification 0 0 0 163 0 11 174
microtubule-based process 0 0 -10000 0 0 4 4
GULP1 0.026 0.018 -10000 0 0 170 170
GNAQ/ARNO 0.028 0.009 0.043 16 0 38 54
mol:Phosphatidic acid 0 0 0 99 0 5 104
PIP3-E 0 0 0 101 0 14 115
MET 0.021 0.019 -10000 0 0 239 239
GNA14 0.036 0.01 -10000 0 0 36 36
GNA15 0.034 0.013 -10000 0 0 62 62
GIT1 0.038 0.005 -10000 0 0 9 9
mol:PI-4-5-P2 0 0 0.001 177 -0.001 6 183
GNA11 0.034 0.013 -10000 0 0 63 63
LHCGR 0.039 0.002 -10000 0 0 1 1
AGTR1 0.037 0.009 -10000 0 0 26 26
desensitization of G-protein coupled receptor protein signaling pathway 0.031 0.026 0.082 8 -0.094 19 27
IPCEF1/ARNO 0.002 0.034 -10000 0 -0.077 58 58
alphaIIb/beta3 Integrin 0.057 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.012 0.028 0.12 14 -10000 0 14
MAP4K4 -0.013 0.061 -10000 0 -0.25 15 15
BAG4 0.038 0.006 -10000 0 0 13 13
PKC zeta/ceramide -0.077 0.14 -10000 0 -0.21 209 209
NFKBIA 0.034 0.013 -10000 0 0 61 61
BIRC3 0.032 0.015 -10000 0 0 85 85
BAX -0.036 0.11 -10000 0 -0.37 36 36
RIPK1 0.037 0.008 -10000 0 0 22 22
AKT1 -0.002 0.1 0.73 8 -10000 0 8
BAD -0.086 0.14 0.22 2 -0.22 207 209
SMPD1 -0.009 0.056 0.16 4 -0.23 14 18
RB1 -0.087 0.14 0.21 1 -0.22 208 209
FADD/Caspase 8 0.002 0.057 -10000 0 -0.24 11 11
MAP2K4 -0.087 0.14 0.21 4 -0.22 192 196
NSMAF 0.037 0.009 -10000 0 0 31 31
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.09 0.14 0.21 7 -0.22 201 208
EGF 0.037 0.008 -10000 0 0 25 25
mol:ceramide -0.081 0.15 -10000 0 -0.22 209 209
MADD 0.037 0.008 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.012 0.028 0.12 15 -10000 0 15
ASAH1 0.038 0.007 -10000 0 0 19 19
negative regulation of cell cycle -0.086 0.14 0.21 1 -0.22 208 209
cell proliferation -0.083 0.12 0.21 1 -0.29 54 55
BID -0.05 0.21 -10000 0 -0.66 48 48
MAP3K1 -0.083 0.14 0.18 2 -0.22 195 197
EIF2A -0.089 0.13 0.2 4 -0.21 201 205
TRADD 0.038 0.005 -10000 0 0 9 9
CRADD 0.038 0.007 -10000 0 0 18 18
MAPK3 -0.084 0.12 0.2 5 -0.22 157 162
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.091 0.13 0.2 5 -0.23 172 177
Cathepsin D/ceramide -0.069 0.15 -10000 0 -0.22 202 202
FADD -0.006 0.052 -10000 0 -0.23 8 8
KSR1 -0.086 0.14 0.2 1 -0.22 207 208
MAPK8 -0.12 0.18 0.17 1 -0.28 201 202
PRKRA -0.088 0.14 0.25 1 -0.22 207 208
PDGFA 0.017 0.019 -10000 0 0 282 282
TRAF2 0.037 0.008 -10000 0 0 20 20
IGF1 0.037 0.009 -10000 0 0 28 28
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.08 0.15 -10000 0 -0.22 209 209
CTSD 0.034 0.013 -10000 0 0 60 60
regulation of nitric oxide biosynthetic process 0.052 0.024 -10000 0 -0.13 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.087 0.13 0.22 1 -0.31 56 57
PRKCD 0.036 0.011 -10000 0 0 43 43
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.012 0.028 0.12 15 -10000 0 15
RelA/NF kappa B1 0.053 0.025 -10000 0 -0.13 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.037 0.008 -10000 0 0 20 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.01 0.061 -10000 0 -0.24 12 12
TNFR1A/BAG4/TNF-alpha 0.057 0.056 -10000 0 -0.12 40 40
mol:Sphingosine-1-phosphate -0.012 0.028 0.12 14 -10000 0 14
MAP2K1 -0.096 0.13 0.19 6 -0.23 196 202
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.038 0.006 -10000 0 0 12 12
CYCS -0.02 0.085 -10000 0 -0.29 30 30
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
NFKB1 0.038 0.007 -10000 0 0 18 18
TNFR1A/BAG4 0.039 0.052 -10000 0 -0.13 41 41
EIF2AK2 -0.093 0.14 0.21 4 -0.22 201 205
TNF-alpha/TNFR1A/FAN 0.051 0.065 -10000 0 -0.13 53 53
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.026 0.06 -10000 0 -0.31 7 7
MAP2K2 -0.085 0.12 0.18 13 -0.22 182 195
SMPD3 0 0.061 0.18 1 -0.25 13 14
TNF 0.038 0.005 -10000 0 0 8 8
PKC zeta/PAR4 0.028 0.006 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.043 0.085 0.15 3 -0.2 44 47
NF kappa B1/RelA/I kappa B alpha 0.072 0.052 -10000 0 -0.11 19 19
AIFM1 -0.055 0.1 -10000 0 -0.33 34 34
BCL2 0.037 0.008 -10000 0 0 21 21
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.018 0.037 0.11 6 -0.064 56 62
PDGF/PDGFRA/CRKL 0.011 0.066 0.12 1 -0.097 116 117
positive regulation of JUN kinase activity 0.028 0.061 -10000 0 -0.11 63 63
CRKL 0.037 0.009 -10000 0 0 32 32
PDGF/PDGFRA/Caveolin-3 0.012 0.068 -10000 0 -0.097 118 118
AP1 -0.069 0.24 0.28 46 -0.59 71 117
mol:IP3 -0.017 0.05 0.12 22 -0.18 7 29
PLCG1 -0.017 0.05 0.12 22 -0.18 7 29
PDGF/PDGFRA/alphaV Integrin 0.008 0.073 -10000 0 -0.11 120 120
RAPGEF1 0.037 0.008 -10000 0 0 23 23
CRK 0.037 0.008 -10000 0 0 25 25
mol:Ca2+ -0.017 0.05 0.12 22 -0.18 7 29
CAV3 0.038 0.006 -10000 0 0 14 14
CAV1 0.015 0.019 -10000 0 0 315 315
SHC/Grb2/SOS1 0.029 0.063 -10000 0 -0.11 63 63
PDGF/PDGFRA/Shf 0.001 0.049 0.076 6 -0.079 115 121
FOS -0.07 0.23 0.27 38 -0.61 65 103
JUN -0.022 0.05 0.19 7 -0.19 4 11
oligodendrocyte development 0.008 0.073 -10000 0 -0.11 120 120
GRB2 0.037 0.009 -10000 0 0 26 26
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:DAG -0.017 0.05 0.12 22 -0.18 7 29
PDGF/PDGFRA 0.018 0.037 0.11 6 -0.064 56 62
actin cytoskeleton reorganization 0.009 0.064 -10000 0 -0.097 110 110
SRF -0.023 0.025 -10000 0 -10000 0 0
SHC1 0.035 0.012 -10000 0 0 56 56
PI3K 0.013 0.087 -10000 0 -0.14 106 106
PDGF/PDGFRA/Crk/C3G 0.031 0.072 -10000 0 -0.12 76 76
JAK1 -0.013 0.036 0.1 28 -10000 0 28
ELK1/SRF -0.023 0.084 0.13 74 -0.21 10 84
SHB 0.035 0.012 -10000 0 0 58 58
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.019 0.042 -10000 0 -0.062 6 6
GO:0007205 -0.024 0.067 0.14 22 -0.18 43 65
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.028 0.061 -10000 0 -0.11 63 63
PDGF/PDGFRA/SHB 0.009 0.064 -10000 0 -0.097 110 110
PDGF/PDGFRA/Caveolin-1 -0.006 0.063 -10000 0 -0.13 82 82
ITGAV 0.036 0.01 -10000 0 0 34 34
ELK1 -0.017 0.094 0.2 45 -0.18 47 92
PIK3CA 0.033 0.014 -10000 0 0 79 79
PDGF/PDGFRA/Crk 0.009 0.071 -10000 0 -0.1 120 120
JAK-STAT cascade -0.013 0.036 0.1 28 -10000 0 28
cell proliferation 0.001 0.049 0.076 6 -0.079 115 121
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.008 0.089 -9999 0 -0.17 89 89
FZD6 0.029 0.017 -9999 0 0 133 133
WNT6 0.039 0.002 -9999 0 0 2 2
WNT4 0.037 0.008 -9999 0 0 21 21
FZD3 0.03 0.016 -9999 0 0 111 111
WNT5A 0.031 0.016 -9999 0 0 102 102
WNT11 0.037 0.008 -9999 0 0 20 20
Canonical Wnt signaling pathway

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
HDAC1 0.032 0.051 0.12 66 -0.056 83 149
AES 0.029 0.047 0.11 60 -0.052 82 142
FBXW11 0.037 0.009 -10000 0 0 27 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.029 -10000 0 -10000 0 0
SMAD4 0.034 0.013 -10000 0 0 62 62
DKK2 0.037 0.009 -10000 0 0 32 32
TLE1 0.03 0.046 0.11 64 -0.051 84 148
MACF1 0.035 0.012 -10000 0 0 52 52
CTNNB1 0.05 0.12 0.29 33 -0.37 11 44
WIF1 0.03 0.016 -10000 0 0 113 113
beta catenin/RanBP3 0.062 0.17 0.42 57 -0.37 12 69
KREMEN2 0.039 0.004 -10000 0 0 6 6
DKK1 0.018 0.019 -10000 0 0 272 272
beta catenin/beta TrCP1 0.063 0.12 0.29 34 -0.38 10 44
FZD1 0.022 0.019 -10000 0 0 220 220
AXIN2 -0.019 0.095 0.12 9 -0.23 66 75
AXIN1 0.04 0.004 -10000 0 0 5 5
RAN 0.038 0.007 -10000 0 0 16 16
Axin1/APC/GSK3/beta catenin 0.01 0.16 -10000 0 -0.59 28 28
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.023 0.13 0.28 11 -0.44 16 27
Axin1/APC/GSK3 0 0.094 0.26 9 -0.36 18 27
Axin1/APC/GSK3/beta catenin/Macf1 0.029 0.14 0.33 11 -0.37 29 40
HNF1A 0.032 0.048 0.12 66 -0.052 89 155
CTBP1 0.03 0.046 0.11 58 -0.053 83 141
MYC -0.088 0.41 0.79 16 -1.2 50 66
RANBP3 0.037 0.01 -10000 0 0 34 34
DKK2/LRP6/Kremen 2 0.067 0.029 -10000 0 -0.12 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
TCF4 0.029 0.043 0.11 58 -0.053 67 125
TCF3 0.03 0.047 0.12 61 -0.052 84 145
WNT1/LRP6/FZD1/Axin1 0.054 0.051 -10000 0 -10000 0 0
Ran/GTP 0.027 0.015 -10000 0 -0.095 6 6
CtBP/CBP/TCF/TLE1/AES 0.018 0.21 0.46 65 -0.38 35 100
LEF1 0.033 0.049 0.12 69 -0.053 85 154
DVL1 0.002 0.096 -10000 0 -0.39 20 20
CSNK2A1 0.033 0.014 -10000 0 0 81 81
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.014 0.16 0.29 11 -0.51 27 38
DKK1/LRP6/Kremen 2 0.033 0.039 -10000 0 -10000 0 0
LRP6 0.036 0.012 -10000 0 0 48 48
CSNK1A1 0.033 0.052 0.12 67 -0.056 85 152
NLK 0.026 0.028 -10000 0 -0.042 63 63
CCND1 -0.069 0.36 0.9 3 -1.2 38 41
WNT1 0.038 0.008 -10000 0 0 22 22
GSK3A 0.036 0.011 -10000 0 0 39 39
GSK3B 0.036 0.012 -10000 0 -0.002 42 42
FRAT1 0.027 0.018 -10000 0 0 157 157
PPP2R5D 0.02 0.054 -10000 0 -0.25 11 11
APC 0.046 0.12 0.31 24 -10000 0 24
WNT1/LRP6/FZD1 -0.002 0.046 -10000 0 -0.28 6 6
CREBBP 0.032 0.048 0.11 66 -0.052 88 154
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.035 0.011 -9999 0 0 47 47
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.039 0.004 -9999 0 0 6 6
TCEB1 0.037 0.008 -9999 0 0 25 25
HIF1A/p53 -0.051 0.13 -9999 0 -0.29 98 98
HIF1A -0.04 0.11 -9999 0 -0.3 75 75
COPS5 0.038 0.007 -9999 0 0 16 16
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.066 -9999 0 -0.12 22 22
FIH (dimer) 0.028 0.018 -9999 0 0 148 148
CDKN2A 0.005 0.012 -9999 0 0 449 449
ARNT/IPAS 0.051 0.019 -9999 0 -10000 0 0
HIF1AN 0.028 0.018 -9999 0 0 148 148
GNB2L1 0.038 0.006 -9999 0 0 13 13
HIF1A/ARNT -0.051 0.14 -9999 0 -0.3 98 98
CUL2 0.028 0.018 -9999 0 0 146 146
OS9 0.031 0.016 -9999 0 0 100 100
RACK1/Elongin B/Elongin C 0.071 0.032 -9999 0 -0.13 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.049 0.14 -9999 0 -0.3 101 101
PHD1-3/OS9 0.055 0.068 -9999 0 -0.13 29 29
HIF1A/RACK1/Elongin B/Elongin C -0.032 0.16 -9999 0 -0.3 103 103
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0.036 0.01 -9999 0 0 39 39
HIF1A/JAB1 -0.052 0.14 -9999 0 -0.3 104 104
EGLN3 0.031 0.015 -9999 0 0 99 99
EGLN2 0.036 0.01 -9999 0 0 37 37
EGLN1 0.036 0.01 -9999 0 0 34 34
TP53 0.033 0.014 -9999 0 0 73 73
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.012 0.11 -9999 0 -0.6 13 13
ARNT 0.038 0.006 -9999 0 0 14 14
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.035 0.012 -9999 0 0 49 49
HIF1A/p19ARF -0.059 0.12 -9999 0 -0.28 93 93
Nongenotropic Androgen signaling

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 -0.017 0.005 0 37 -10000 0 37
GNB1/GNG2 0.04 0.031 -10000 0 -0.094 20 20
regulation of S phase of mitotic cell cycle -0.008 0.076 -10000 0 -0.19 64 64
GNAO1 0.032 0.015 -10000 0 0 88 88
HRAS 0.03 0.023 -10000 0 -0.019 83 83
SHBG/T-DHT 0.025 0.005 -10000 0 -10000 0 0
PELP1 0.033 0.02 -10000 0 -0.023 55 55
AKT1 -0.016 0.006 0 61 -10000 0 61
MAP2K1 -0.031 0.099 0.16 57 -0.19 56 113
T-DHT/AR 0.025 0.014 -10000 0 -0.027 29 29
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 0.004 61 -0.006 77 138
GNAI2 0.035 0.011 -10000 0 0 46 46
GNAI3 0.038 0.007 -10000 0 0 16 16
GNAI1 0.016 0.019 -10000 0 0 297 297
mol:GDP -0.025 0.033 -10000 0 -0.14 9 9
cell proliferation -0.048 0.2 0.29 28 -0.42 83 111
PIK3CA 0.033 0.014 -10000 0 0 79 79
FOS -0.073 0.29 0.38 14 -0.68 83 97
mol:Ca2+ 0.001 0.023 0.04 23 -0.054 51 74
MAPK3 -0.035 0.15 0.27 31 -0.32 68 99
MAPK1 -0.03 0.17 0.29 7 -0.48 38 45
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:IP3 0 0.002 0.005 60 -0.004 70 130
cAMP biosynthetic process -0.009 0.017 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 0.005 60 -0.004 70 130
HRAS/GTP 0.039 0.072 -10000 0 -0.1 76 76
actin cytoskeleton reorganization 0.02 0.049 -10000 0 -0.12 33 33
SRC 0.029 0.022 -10000 0 -0.012 97 97
voltage-gated calcium channel activity 0 0.002 0.005 60 -0.004 70 130
PI3K 0.023 0.059 -10000 0 -0.11 72 72
apoptosis 0.036 0.2 0.42 85 -0.33 11 96
T-DHT/AR/PELP1 0.045 0.027 -10000 0 -0.071 18 18
HRAS/GDP -0.009 0.067 0.14 7 -0.2 7 14
CREB1 -0.062 0.2 0.29 18 -0.45 85 103
RAC1-CDC42/GTP 0.028 0.056 -10000 0 -0.12 33 33
AR 0.03 0.023 -10000 0 -0.025 71 71
GNB1 0.035 0.011 -10000 0 0 46 46
RAF1 -0.018 0.096 0.18 59 -0.24 8 67
RAC1-CDC42/GDP 0.018 0.054 0.19 3 -0.17 8 11
T-DHT/AR/PELP1/Src 0.053 0.045 -10000 0 -0.071 31 31
MAP2K2 -0.036 0.089 0.16 40 -0.19 51 91
T-DHT/AR/PELP1/Src/PI3K -0.008 0.076 -10000 0 -0.19 64 64
GNAZ 0.033 0.014 -10000 0 0 83 83
SHBG 0.038 0.007 -10000 0 0 19 19
Gi family/GNB1/GNG2/GDP -0.042 0.16 -10000 0 -0.47 48 48
mol:T-DHT 0 0.001 -10000 0 -0.004 23 23
RAC1 0.023 0.019 -10000 0 0 209 209
GNRH1 -0.017 0.003 0 14 -10000 0 14
Gi family/GTP -0.001 0.08 0.12 8 -0.2 52 60
CDC42 0.037 0.009 -10000 0 0 27 27
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.007 0.053 -10000 0 -0.13 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.11 0.22 20 -0.23 34 54
AP1 -0.002 0.075 0.11 72 -0.13 92 164
mol:PIP3 -0.023 0.045 -10000 0 -0.14 42 42
AKT1 0.009 0.1 0.23 29 -0.24 20 49
PTK2B -0.001 0.062 0.14 14 -0.14 58 72
RHOA 0.028 0.085 0.18 43 -0.34 12 55
PIK3CB 0.037 0.009 -10000 0 -0.003 24 24
mol:Ca2+ -0.014 0.042 0.16 5 -0.14 14 19
MAGI3 0 0 -10000 0 -0.006 1 1
RELA 0.038 0.006 -10000 0 0 12 12
apoptosis 0.005 0.064 0.14 37 -0.15 53 90
HRAS/GDP 0.023 0.025 -10000 0 -0.11 16 16
positive regulation of microtubule depolymerization -0.022 0.074 0.19 11 -0.21 31 42
NF kappa B1 p50/RelA -0.025 0.078 0.1 90 -0.18 49 139
endothelial cell migration -0.017 0.088 -10000 0 -0.27 54 54
ADCY4 0 0.088 0.16 29 -0.24 32 61
ADCY5 0 0.088 0.16 29 -0.24 32 61
ADCY6 0.007 0.089 0.17 31 -0.25 27 58
ADCY7 0.004 0.095 0.18 32 -0.25 32 64
ADCY1 -0.006 0.076 0.16 17 -0.25 26 43
ADCY2 0.007 0.093 0.18 34 -0.24 32 66
ADCY3 0 0.088 0.16 29 -0.24 32 61
ADCY8 0.005 0.09 0.18 33 -0.26 26 59
ADCY9 0.008 0.092 0.18 34 -0.24 32 66
GSK3B -0.01 0.067 0.17 11 -0.17 40 51
arachidonic acid secretion -0.014 0.11 0.15 36 -0.26 52 88
GNG2 0 0.001 -10000 0 -0.005 11 11
TRIP6 -0.014 0.075 -10000 0 -0.24 49 49
GNAO1 0.003 0.057 0.17 26 -0.14 43 69
HRAS 0.036 0.01 -10000 0 0 39 39
NFKBIA -0.02 0.09 0.19 17 -0.22 43 60
GAB1 0.035 0.012 -10000 0 0 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.21 -10000 0 -0.78 34 34
JUN 0.036 0.011 -10000 0 0 43 43
LPA/LPA2/NHERF2 0.022 0.031 0.071 38 -0.06 55 93
TIAM1 -0.022 0.26 -10000 0 -0.96 36 36
PIK3R1 0.033 0.014 -10000 0 -0.001 70 70
mol:IP3 -0.014 0.04 0.2 2 -0.14 16 18
PLCB3 -0.016 0.038 0.13 10 -10000 0 10
FOS 0.026 0.018 -10000 0 0 168 168
positive regulation of mitosis -0.014 0.11 0.15 36 -0.26 52 88
LPA/LPA1-2-3 -0.006 0.037 -10000 0 -0.11 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 0.002 1 -10000 0 1
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.012 0.071 0.17 6 -0.27 10 16
GNAZ 0.003 0.057 0.17 28 -0.14 39 67
EGFR/PI3K-beta/Gab1 -0.022 0.048 0.036 16 -0.15 41 57
positive regulation of dendritic cell cytokine production -0.006 0.037 -10000 0 -0.11 54 54
LPA/LPA2/MAGI-3 -0.003 0.015 -10000 0 -0.046 55 55
ARHGEF1 0.049 0.12 0.2 177 -0.19 11 188
GNAI2 0.007 0.064 0.17 41 -0.14 41 82
GNAI3 0.005 0.067 0.17 40 -0.14 51 91
GNAI1 0.001 0.044 0.17 15 -0.14 26 41
LPA/LPA3 -0.005 0.019 -10000 0 -0.059 54 54
LPA/LPA2 -0.005 0.019 -10000 0 -0.059 54 54
LPA/LPA1 -0.011 0.049 -10000 0 -0.15 54 54
HB-EGF/EGFR -0.008 0.049 0.12 25 -0.13 44 69
HBEGF 0.012 0.058 0.12 109 -10000 0 109
mol:DAG -0.014 0.04 0.2 2 -0.14 16 18
cAMP biosynthetic process 0.011 0.11 0.2 44 -0.25 38 82
NFKB1 0.038 0.007 -10000 0 0 18 18
SRC 0.034 0.013 -10000 0 0 65 65
GNB1 0.035 0.011 -10000 0 0 46 46
LYN -0.023 0.099 0.2 23 -0.22 59 82
GNAQ 0.01 0.029 0.076 39 -0.057 54 93
LPAR2 0 0.001 0.003 18 -0.005 4 22
LPAR3 0 0.001 0.003 8 -0.002 5 13
LPAR1 -0.009 0.029 -10000 0 -0.094 54 54
IL8 -0.11 0.2 0.35 20 -0.39 140 160
PTK2 0.018 0.061 0.16 39 -0.12 50 89
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
CASP3 0.005 0.065 0.14 37 -0.15 53 90
EGFR 0.009 0.017 -10000 0 0 385 385
PLCG1 0.003 0.038 0.079 24 -0.12 23 47
PLD2 0.018 0.059 0.16 39 -0.11 53 92
G12/G13 0.015 0.054 -10000 0 -0.14 40 40
PI3K-beta -0.026 0.059 -10000 0 -0.24 21 21
cell migration -0.003 0.074 -10000 0 -0.25 28 28
SLC9A3R2 0.039 0.005 -10000 0 0 7 7
PXN 0.011 0.071 0.18 5 -0.28 10 15
HRAS/GTP -0.016 0.11 0.15 29 -0.26 55 84
RAC1 0.023 0.019 -10000 0 0 209 209
MMP9 0.016 0.019 -10000 0 0 296 296
PRKCE 0.038 0.007 -10000 0 -0.009 9 9
PRKCD -0.01 0.062 0.19 18 -0.2 3 21
Gi(beta/gamma) -0.002 0.11 0.16 31 -0.26 45 76
mol:LPA -0.009 0.03 -10000 0 -0.094 54 54
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.076 0.14 16 -0.25 27 43
MAPKKK cascade -0.014 0.11 0.15 36 -0.26 52 88
contractile ring contraction involved in cytokinesis 0.031 0.086 0.18 45 -0.34 12 57
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.009 0.029 0.076 38 -0.057 54 92
GNA15 0.008 0.028 0.075 33 -0.057 51 84
GNA12 0.022 0.019 -10000 0 0 227 227
GNA13 0.037 0.008 -10000 0 0 22 22
MAPT -0.021 0.074 0.19 11 -0.21 31 42
GNA11 0.011 0.026 0.076 37 -0.058 34 71
Rac1/GTP -0.018 0.23 -10000 0 -0.83 33 33
MMP2 -0.017 0.088 -10000 0 -0.27 54 54
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.012 0.1 0.23 48 -0.16 3 51
GNAI2 0.035 0.011 -10000 0 0 46 46
S1P/S1P5/G12 0.01 0.026 -10000 0 -0.091 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.032 0.015 -10000 0 0 88 88
RhoA/GTP 0.013 0.1 0.16 3 -0.24 48 51
negative regulation of cAMP metabolic process 0.001 0.092 -10000 0 -0.19 72 72
GNAZ 0.033 0.014 -10000 0 0 83 83
GNAI3 0.038 0.007 -10000 0 0 16 16
GNA12 0.022 0.019 -10000 0 0 227 227
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0 0.093 -10000 0 -0.2 72 72
RhoA/GDP 0.026 0.017 -10000 0 -0.11 7 7
RHOA 0.037 0.008 -10000 0 0 24 24
GNAI1 0.016 0.019 -10000 0 0 297 297
Syndecan-4-mediated signaling events

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
PTK2 -0.03 0.15 -10000 0 -0.47 38 38
Syndecan-4/Syndesmos -0.14 0.28 -10000 0 -0.73 69 69
positive regulation of JNK cascade -0.13 0.26 -10000 0 -0.62 79 79
Syndecan-4/ADAM12 -0.13 0.29 -10000 0 -0.73 69 69
CCL5 0.035 0.012 -10000 0 0 56 56
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
DNM2 0.036 0.011 -10000 0 0 41 41
ITGA5 0.034 0.013 -10000 0 0 68 68
SDCBP 0.037 0.008 -10000 0 0 25 25
PLG 0.02 0.036 -10000 0 -0.069 13 13
ADAM12 0.026 0.018 -10000 0 0 171 171
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.027 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.28 -10000 0 -0.73 69 69
Syndecan-4/CXCL12/CXCR4 -0.14 0.28 -10000 0 -0.68 79 79
Syndecan-4/Laminin alpha3 -0.12 0.3 -10000 0 -0.74 67 67
MDK 0.032 0.015 -10000 0 0 96 96
Syndecan-4/FZD7 -0.13 0.3 -10000 0 -0.66 90 90
Syndecan-4/Midkine -0.13 0.3 -10000 0 -0.69 81 81
FZD7 0.028 0.018 -10000 0 0 143 143
Syndecan-4/FGFR1/FGF -0.095 0.29 -10000 0 -0.7 65 65
THBS1 0.032 0.015 -10000 0 0 95 95
integrin-mediated signaling pathway -0.12 0.28 -10000 0 -0.63 87 87
positive regulation of MAPKKK cascade -0.13 0.26 -10000 0 -0.62 79 79
Syndecan-4/TACI -0.12 0.3 -10000 0 -0.74 69 69
CXCR4 0.031 0.016 -10000 0 0 103 103
cell adhesion -0.015 0.05 0.2 5 -0.23 16 21
Syndecan-4/Dynamin -0.12 0.3 -10000 0 -0.73 69 69
Syndecan-4/TSP1 -0.13 0.29 -10000 0 -0.75 66 66
Syndecan-4/GIPC -0.12 0.3 -10000 0 -0.73 69 69
Syndecan-4/RANTES -0.13 0.29 -10000 0 -0.74 68 68
ITGB1 0.029 0.017 -10000 0 0 131 131
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.035 0.012 -10000 0 0 51 51
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCA 0.004 0.13 0.96 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.12 0.3 -10000 0 -0.68 83 83
TFPI 0.031 0.016 -10000 0 0 104 104
F2 0.009 0.05 -10000 0 -0.058 162 162
alpha5/beta1 Integrin 0.032 0.041 -10000 0 -0.12 20 20
positive regulation of cell adhesion -0.13 0.28 -10000 0 -0.71 67 67
ACTN1 0.03 0.017 -10000 0 0 123 123
TNC 0.029 0.017 -10000 0 0 125 125
Syndecan-4/CXCL12 -0.14 0.28 -10000 0 -0.73 68 68
FGF6 0.037 0.009 -10000 0 0 32 32
RHOA 0.037 0.008 -10000 0 0 24 24
CXCL12 0.024 0.019 -10000 0 0 199 199
TNFRSF13B 0.038 0.006 -10000 0 0 11 11
FGF2 0.037 0.008 -10000 0 0 25 25
FGFR1 0.038 0.006 -10000 0 0 12 12
Syndecan-4/PI-4-5-P2 -0.14 0.28 -10000 0 -0.73 69 69
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.036 -10000 0 -0.068 14 14
cell migration -0.012 0.017 -10000 0 -10000 0 0
PRKCD 0.023 0.034 -10000 0 -0.064 14 14
vasculogenesis -0.12 0.28 -10000 0 -0.71 66 66
SDC4 -0.14 0.3 -10000 0 -0.79 67 67
Syndecan-4/Tenascin C -0.13 0.3 -10000 0 -0.66 87 87
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.021 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.3 -10000 0 -0.74 69 69
MMP9 0.01 0.026 -10000 0 -0.053 35 35
Rac1/GTP -0.015 0.051 0.2 5 -0.23 16 21
cytoskeleton organization -0.13 0.27 -10000 0 -0.69 69 69
GIPC1 0.036 0.01 -10000 0 0 36 36
Syndecan-4/TFPI -0.13 0.3 -10000 0 -0.73 69 69
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.032 0.015 -10000 0 0 88 88
CDC42/GTP 0.012 0.1 0.16 3 -0.23 49 52
PLCG1 -0.014 0.087 0.1 10 -0.24 39 49
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 0 46 46
GNAI3 0.038 0.007 -10000 0 0 16 16
G12/G13 0.025 0.044 -10000 0 -0.13 24 24
cell migration 0.011 0.1 0.16 3 -0.23 49 52
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.014 0.093 0.1 9 -0.23 50 59
MAPK1 -0.007 0.086 0.11 16 -0.23 38 54
S1P/S1P5/Gi 0 0.093 -10000 0 -0.2 72 72
GNAI1 0.016 0.019 -10000 0 0 297 297
CDC42/GDP 0.027 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.026 -10000 0 -0.091 24 24
RHOA 0.053 0.11 0.19 195 -10000 0 195
S1P/S1P4/Gi 0 0.093 -10000 0 -0.2 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.014 -10000 0 0 83 83
S1P/S1P4/G12/G13 0.022 0.035 -10000 0 -0.093 24 24
GNA12 0.022 0.019 -10000 0 0 227 227
GNA13 0.037 0.008 -10000 0 0 22 22
CDC42 0.037 0.009 -10000 0 0 27 27
Arf6 downstream 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
PLAUR -0.012 0.19 0.29 39 -0.78 25 64
regulation of axonogenesis 0.018 0.073 0.23 41 -0.14 1 42
myoblast fusion -0.017 0.1 0.35 30 -0.19 40 70
mol:GTP 0.017 0.074 -10000 0 -0.18 55 55
regulation of calcium-dependent cell-cell adhesion -0.029 0.08 0.16 54 -0.17 38 92
ARF1/GTP 0.037 0.07 -10000 0 -0.14 58 58
mol:GM1 0.003 0.054 0.099 40 -0.13 55 95
mol:Choline -0.025 0.047 0.079 42 -0.14 46 88
lamellipodium assembly -0.01 0.11 0.21 1 -0.38 35 36
MAPK3 0.011 0.093 0.19 40 -0.29 27 67
ARF6/GTP/NME1/Tiam1 0.029 0.081 0.18 38 -0.16 54 92
ARF1 0.037 0.008 -10000 0 0 25 25
ARF6/GDP 0.017 0.1 0.19 40 -0.35 30 70
ARF1/GDP 0.012 0.11 0.2 3 -0.29 52 55
ARF6 0.045 0.046 0.12 1 -0.13 25 26
RAB11A 0.038 0.007 -10000 0 0 19 19
TIAM1 0.029 0.027 -10000 0 -0.05 42 42
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.089 0.19 40 -0.29 25 65
actin filament bundle formation -0.019 0.12 0.29 55 -0.2 2 57
KALRN 0.001 0.085 0.14 39 -0.26 40 79
RAB11FIP3/RAB11A 0.051 0.033 -10000 0 -0.14 12 12
RhoA/GDP 0.02 0.12 0.2 2 -0.29 55 57
NME1 -0.001 0.008 -10000 0 -0.03 24 24
Rac1/GDP 0.011 0.097 -10000 0 -0.3 31 31
substrate adhesion-dependent cell spreading 0.017 0.074 -10000 0 -0.18 55 55
cortical actin cytoskeleton organization -0.01 0.11 0.21 1 -0.38 35 36
RAC1 0.023 0.019 -10000 0 0 209 209
liver development 0.017 0.074 -10000 0 -0.18 55 55
ARF6/GTP 0.017 0.074 -10000 0 -0.18 55 55
RhoA/GTP 0.036 0.071 -10000 0 -0.15 58 58
mol:GDP -0.008 0.11 0.19 38 -0.3 51 89
ARF6/GTP/RAB11FIP3/RAB11A 0.053 0.077 -10000 0 -0.14 64 64
RHOA 0.037 0.008 -10000 0 0 24 24
PLD1 0.01 0.059 0.11 40 -0.15 54 94
RAB11FIP3 0.038 0.007 -10000 0 0 18 18
tube morphogenesis -0.01 0.11 0.21 1 -0.38 35 36
ruffle organization -0.018 0.073 0.14 1 -0.23 41 42
regulation of epithelial cell migration 0.017 0.074 -10000 0 -0.18 55 55
PLD2 0.011 0.059 0.11 40 -0.15 50 90
PIP5K1A -0.018 0.073 0.14 1 -0.23 41 42
mol:Phosphatidic acid -0.025 0.047 0.079 42 -0.14 46 88
Rac1/GTP -0.01 0.11 0.21 1 -0.38 35 36
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.047 0.04 -10000 0 -0.13 23 23
AKT1 -0.055 0.22 0.33 33 -0.39 103 136
PTK2B -0.016 0.14 0.28 43 -0.36 13 56
VEGFR2 homodimer/Frs2 -0.017 0.086 0.16 64 -0.38 10 74
CAV1 0.015 0.019 -10000 0 0 315 315
CALM1 0.034 0.013 -10000 0 0 62 62
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.017 0.11 0.23 12 -0.25 31 43
endothelial cell proliferation -0.005 0.19 0.34 51 -0.36 46 97
mol:Ca2+ -0.006 0.14 0.34 47 -0.33 12 59
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.015 0.1 0.26 4 -0.22 35 39
RP11-342D11.1 -0.024 0.11 0.18 66 -0.26 27 93
CDH5 0.032 0.015 -10000 0 0 92 92
VEGFA homodimer 0.018 0.076 -10000 0 -0.11 106 106
SHC1 0.035 0.012 -10000 0 0 56 56
SHC2 0.033 0.014 -10000 0 0 74 74
HRAS/GDP -0.048 0.088 0.11 37 -0.27 26 63
SH2D2A 0.038 0.006 -10000 0 0 14 14
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.016 0.14 0.34 15 -0.35 19 34
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.017 0.11 0.23 12 -0.25 30 42
VEGFR1 homodimer 0.036 0.01 -10000 0 0 40 40
SHC/GRB2/SOS1 0.021 0.11 -10000 0 -0.24 38 38
GRB10 -0.022 0.099 0.27 9 -0.3 29 38
PTPN11 0.038 0.007 -10000 0 0 17 17
GRB2 0.037 0.009 -10000 0 0 26 26
PAK1 0.037 0.008 -10000 0 0 20 20
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.021 0.14 0.3 3 -0.25 49 52
HRAS 0.036 0.01 -10000 0 0 39 39
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.14 0.22 19 -0.37 38 57
HIF1A 0.035 0.012 -10000 0 0 50 50
FRS2 0.037 0.009 -10000 0 0 31 31
oxygen and reactive oxygen species metabolic process 0.013 0.099 0.25 4 -0.22 35 39
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.038 0.006 -10000 0 0 13 13
Nck/Pak 0.051 0.025 -10000 0 -0.13 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.005 0.12 0.23 12 -0.25 42 54
mol:GDP 0.01 0.1 -10000 0 -0.23 38 38
mol:NADP 0.028 0.15 0.35 42 -0.34 13 55
eNOS/Hsp90 0.037 0.15 0.35 41 -0.33 14 55
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:IP3 -0.006 0.15 0.34 47 -0.33 12 59
HIF1A/ARNT 0.048 0.03 -10000 0 -0.13 10 10
SHB 0.035 0.012 -10000 0 0 58 58
VEGFA 0.025 0.027 0.095 21 -0.057 14 35
VEGFC 0.035 0.012 -10000 0 0 51 51
FAK1/Vinculin -0.035 0.16 0.28 24 -0.45 32 56
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.037 0.008 -10000 0 0 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.03 0.12 0.28 3 -0.25 36 39
PTPN6 0.035 0.012 -10000 0 0 58 58
EPAS1 0.039 0.058 0.15 6 -0.26 11 17
mol:L-citrulline 0.028 0.15 0.35 42 -0.34 13 55
ITGAV 0.036 0.01 -10000 0 0 34 34
PIK3CA 0.033 0.014 -10000 0 0 79 79
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.032 0.12 0.25 13 -0.25 33 46
VEGFR2 homodimer/VEGFA homodimer 0.012 0.11 -10000 0 -0.26 36 36
VEGFR2/3 heterodimer -0.018 0.087 0.16 66 -0.38 10 76
VEGFB 0.038 0.005 -10000 0 0 9 9
MAPK11 -0.008 0.16 0.33 53 -0.29 28 81
VEGFR2 homodimer -0.022 0.077 0.18 32 -0.44 8 40
FLT1 0.036 0.011 -10000 0 0 40 40
NEDD4 0.034 0.033 0.1 38 -0.054 38 76
MAPK3 0.016 0.16 0.33 66 -0.31 11 77
MAPK1 0.013 0.16 0.34 63 -0.32 12 75
VEGFA145/NRP2 0.008 0.077 -10000 0 -0.13 113 113
VEGFR1/2 heterodimer -0.019 0.085 0.16 61 -0.38 10 71
KDR -0.022 0.077 0.18 32 -0.44 8 40
VEGFA165/NRP1/VEGFR2 homodimer 0.021 0.12 0.27 15 -0.24 36 51
SRC 0.034 0.013 -10000 0 0 65 65
platelet activating factor biosynthetic process 0.016 0.16 0.33 66 -0.32 12 78
PI3K -0.048 0.17 0.28 34 -0.31 93 127
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.015 0.11 0.23 12 -0.24 31 43
FES -0.007 0.15 0.34 52 -0.34 13 65
GAB1 -0.038 0.16 0.25 34 -0.3 92 126
VEGFR2 homodimer/VEGFA homodimer/Src 0.012 0.11 0.23 10 -0.24 31 41
CTNNB1 0.038 0.007 -10000 0 0 18 18
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.038 0.006 -10000 0 0 14 14
eNOS/Caveolin-1 -0.006 0.1 0.3 10 -0.34 12 22
VEGFR2 homodimer/VEGFA homodimer/Yes 0.012 0.11 0.23 10 -0.24 36 46
PI3K/GAB1 -0.04 0.21 0.32 29 -0.38 98 127
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.044 0.12 0.29 5 -0.24 27 32
PRKACA 0.036 0.01 -10000 0 0 36 36
VEGFR2/3 heterodimer/VEGFC homodimer 0.053 0.083 0.23 5 -0.28 12 17
HSP90AA1 0.036 0.01 -10000 0 0 39 39
CDC42 -0.006 0.15 0.33 52 -0.34 13 65
actin cytoskeleton reorganization 0.016 0.11 0.22 11 -0.25 30 41
PTK2 -0.022 0.18 0.28 40 -0.42 43 83
EDG1 -0.024 0.11 0.18 66 -0.26 27 93
mol:DAG -0.006 0.15 0.34 47 -0.33 12 59
CaM/Ca2+ -0.017 0.13 0.29 40 -0.31 16 56
MAP2K3 -0.013 0.15 0.31 55 -0.32 11 66
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.051 0.14 0.34 17 -0.29 32 49
PLCG1 -0.007 0.15 0.34 47 -0.34 12 59
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.024 0.11 0.28 2 -0.23 29 31
IQGAP1 0.035 0.012 -10000 0 0 49 49
YES1 0.035 0.011 -10000 0 0 47 47
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.016 0.11 0.23 12 -0.24 35 47
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.014 0.11 0.23 12 -0.25 31 43
cell migration -0.031 0.18 0.3 28 -0.4 47 75
mol:PI-3-4-5-P3 -0.044 0.16 0.27 34 -0.3 93 127
FYN 0.032 0.015 -10000 0 0 95 95
VEGFB/NRP1 -0.012 0.13 0.28 45 -0.32 13 58
mol:NO 0.028 0.15 0.35 42 -0.34 13 55
PXN 0.038 0.006 -10000 0 0 11 11
HRAS/GTP -0.058 0.073 -10000 0 -0.24 38 38
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.007 0.11 0.16 110 -0.3 29 139
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.038 0.005 -10000 0 0 7 7
NOS3 0.026 0.16 0.37 37 -0.37 13 50
VEGFR2 homodimer/VEGFA homodimer/Sck 0.01 0.12 0.23 12 -0.26 35 47
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCA -0.012 0.14 0.31 50 -0.32 12 62
PRKCB -0.008 0.14 0.32 47 -0.31 12 59
VCL 0.027 0.018 -10000 0 0 151 151
VEGFA165/NRP1 -0.031 0.1 0.19 56 -0.33 13 69
VEGFR1/2 heterodimer/VEGFA homodimer 0.013 0.11 0.23 10 -0.24 32 42
VEGFA165/NRP2 0.008 0.077 -10000 0 -0.13 113 113
MAPKKK cascade -0.01 0.12 0.25 24 -0.31 25 49
NRP2 0.038 0.005 -10000 0 0 9 9
VEGFC homodimer 0.035 0.012 -10000 0 0 51 51
NCK1 0.037 0.009 -10000 0 0 31 31
ROCK1 0.037 0.008 -10000 0 0 22 22
FAK1/Paxillin -0.017 0.18 0.28 41 -0.44 33 74
MAP3K13 -0.007 0.15 0.33 51 -0.33 11 62
PDPK1 -0.04 0.16 0.29 41 -0.28 91 132
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.036 0.01 -10000 0 0 39 39
EGFR 0.009 0.017 -10000 0 0 385 385
EGF/EGFR 0.003 0.052 -10000 0 -0.11 60 60
EGF/EGFR dimer/SHC/GRB2/SOS1 0.008 0.056 -10000 0 -0.11 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.03 0.017 -10000 0 0 122 122
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.037 0.008 -10000 0 0 25 25
EGF/EGFR dimer/SHC 0.002 0.052 -10000 0 -0.12 55 55
mol:GDP 0.006 0.053 -10000 0 -0.11 55 55
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.035 0.012 -10000 0 0 54 54
GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
HRAS/GTP -0.003 0.049 -10000 0 -0.12 63 63
SHC1 0.035 0.012 -10000 0 0 56 56
HRAS/GDP 0.001 0.057 -10000 0 -0.12 62 62
FRAP1 -0.017 0.037 0.063 17 -0.16 3 20
EGF/EGFR dimer -0.002 0.051 -10000 0 -0.13 58 58
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.037 0.009 -10000 0 0 26 26
ETA receptor/Endothelin-1 0.027 0.057 -10000 0 -0.13 51 51
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.034 0.15 0.29 28 -0.38 18 46
MAP3K8 0.017 0.026 -10000 0 -0.037 51 51
FOS 0.028 0.11 0.25 29 -0.36 12 41
PRKCA 0.029 0.032 0.072 6 -0.041 78 84
PTPN7 0.03 0.036 0.086 54 -0.046 74 128
HRAS 0.036 0.011 -10000 0 -0.001 40 40
PRKCB 0.001 0.01 0.026 61 -0.013 62 123
NRAS 0.034 0.013 -10000 0 0 66 66
RAS family/GTP 0.042 0.069 -10000 0 -0.12 53 53
MAPK3 0.041 0.063 -10000 0 -0.33 3 3
MAP2K1 0.013 0.061 0.18 2 -0.22 10 12
ELK1 0.027 0.033 -10000 0 -0.049 80 80
BRAF 0.005 0.027 -10000 0 -0.21 1 1
mol:GTP 0 0.002 0.004 61 -0.003 78 139
MAPK1 0.017 0.13 -10000 0 -0.44 28 28
RAF1 -0.001 0.068 -10000 0 -0.32 18 18
KRAS 0.036 0.011 -10000 0 -0.001 41 41
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.016 0.057 0.11 27 -0.12 65 92
EPHB2 0.036 0.011 -10000 0 0 43 43
Syndecan-2/TACI 0.019 0.053 0.12 7 -0.11 62 69
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.021 0.076 -10000 0 -0.12 76 76
HRAS 0.036 0.01 -10000 0 0 39 39
Syndecan-2/CASK -0.021 0.031 0.089 3 -0.096 66 69
ITGA5 0.034 0.013 -10000 0 0 68 68
BAX -0.012 0.079 -10000 0 -0.88 3 3
EPB41 0.038 0.006 -10000 0 0 14 14
positive regulation of cell-cell adhesion 0.015 0.051 0.1 5 -0.1 69 74
LAMA3 0.035 0.012 -10000 0 0 51 51
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.017 0.019 -10000 0 0 283 283
Syndecan-2/MMP2 0.011 0.057 0.12 4 -0.12 63 67
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.022 0.052 -10000 0 -0.13 42 42
dendrite morphogenesis 0.017 0.051 0.12 7 -0.11 59 66
Syndecan-2/GM-CSF 0.019 0.052 0.12 9 -0.11 61 70
determination of left/right symmetry -0.012 0.022 0.12 5 -0.22 3 8
Syndecan-2/PKC delta 0.017 0.052 0.12 5 -0.11 60 65
GNB2L1 0.038 0.006 -10000 0 0 13 13
MAPK3 -0.031 0.055 0.13 39 -0.2 4 43
MAPK1 -0.026 0.052 0.13 37 -0.18 3 40
Syndecan-2/RACK1 0.032 0.062 0.18 2 -0.11 71 73
NF1 0.038 0.007 -10000 0 0 16 16
FGFR/FGF/Syndecan-2 -0.012 0.022 0.12 5 -0.22 3 8
ITGA2 0.03 0.016 -10000 0 0 115 115
MAPK8 -0.01 0.043 0.19 3 -0.39 3 6
Syndecan-2/alpha2/beta1 Integrin 0.009 0.061 0.18 1 -0.1 90 91
Syndecan-2/Kininogen 0.018 0.053 0.11 27 -0.11 62 89
ITGB1 0.029 0.017 -10000 0 0 131 131
SRC -0.029 0.06 0.17 21 -0.2 4 25
Syndecan-2/CASK/Protein 4.1 0.017 0.048 0.11 3 -0.097 65 68
extracellular matrix organization 0.016 0.049 0.11 21 -0.11 55 76
actin cytoskeleton reorganization 0.016 0.057 0.11 27 -0.12 65 92
Syndecan-2/Caveolin-2/Ras 0.006 0.06 0.19 1 -0.12 67 68
Syndecan-2/Laminin alpha3 0.017 0.05 0.11 24 -0.11 59 83
Syndecan-2/RasGAP 0.04 0.079 0.19 3 -0.12 78 81
alpha5/beta1 Integrin 0.032 0.041 -10000 0 -0.12 20 20
PRKCD 0.036 0.011 -10000 0 0 43 43
Syndecan-2 dimer 0.017 0.051 0.12 7 -0.11 59 66
GO:0007205 0.001 0.01 -10000 0 -0.11 4 4
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.04 0.062 0.17 15 -0.23 5 20
RHOA 0.037 0.008 -10000 0 0 24 24
SDCBP 0.037 0.008 -10000 0 0 25 25
TNFRSF13B 0.038 0.006 -10000 0 0 11 11
RASA1 0.036 0.01 -10000 0 0 37 37
alpha2/beta1 Integrin 0.022 0.052 -10000 0 -0.13 42 42
Syndecan-2/Synbindin 0.018 0.056 0.11 29 -0.12 62 91
TGFB1 0.034 0.013 -10000 0 0 70 70
CASP3 -0.022 0.059 0.12 58 -0.2 4 62
FN1 0.037 0.009 -10000 0 0 31 31
Syndecan-2/IL8 0 0.062 0.11 14 -0.15 59 73
SDC2 -0.012 0.022 0.12 5 -0.22 3 8
KNG1 0.037 0.008 -10000 0 0 23 23
Syndecan-2/Neurofibromin 0.018 0.053 0.11 27 -0.11 64 91
TRAPPC4 0.038 0.007 -10000 0 0 19 19
CSF2 0.038 0.006 -10000 0 0 13 13
Syndecan-2/TGFB1 0.016 0.049 0.11 21 -0.11 55 76
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.051 0.11 5 -0.1 69 74
Syndecan-2/Ezrin 0.015 0.051 0.11 5 -0.1 68 73
PRKACA -0.027 0.053 0.13 38 -0.18 3 41
angiogenesis 0 0.062 0.11 14 -0.15 59 73
MMP2 0.031 0.016 -10000 0 0 107 107
IL8 0.02 0.019 -10000 0 0 243 243
calcineurin-NFAT signaling pathway 0.019 0.053 0.12 7 -0.11 62 69
IL2 signaling events mediated by PI3K

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
BCL2L1 0.016 0.12 0.34 16 -0.36 5 21
UGCG -0.024 0.19 -10000 0 -0.72 31 31
AKT1/mTOR/p70S6K/Hsp90/TERT -0.007 0.16 0.33 12 -0.36 43 55
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.023 0.18 -10000 0 -0.7 31 31
mol:DAG -0.22 0.38 -10000 0 -0.82 144 144
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.18 0.35 12 -0.41 60 72
FRAP1 -0.026 0.2 0.36 14 -0.46 62 76
FOXO3 -0.038 0.2 0.35 13 -0.46 67 80
AKT1 -0.039 0.21 0.35 11 -0.49 64 75
GAB2 0.03 0.024 -10000 0 -0.039 42 42
SMPD1 0.003 0.098 -10000 0 -0.5 15 15
SGMS1 -0.15 0.29 -10000 0 -0.6 140 140
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 -0.033 0.04 0.054 23 -0.11 72 95
CALM1 0.034 0.013 -10000 0 0 62 62
cell proliferation -0.1 0.26 0.34 12 -0.44 129 141
EIF3A 0.026 0.018 -10000 0 0 170 170
PI3K 0.021 0.074 0.15 2 -0.14 72 74
RPS6KB1 0.032 0.049 -10000 0 -0.71 1 1
mol:sphingomyelin -0.22 0.38 -10000 0 -0.82 144 144
natural killer cell activation 0 0.004 0.011 30 -0.01 43 73
JAK3 0.033 0.025 0.092 3 -0.038 42 45
PIK3R1 0.03 0.025 0.089 2 -0.039 39 41
JAK1 0.033 0.025 0.09 3 -0.038 40 43
NFKB1 0.038 0.007 -10000 0 0 18 18
MYC -0.062 0.3 0.45 16 -0.81 57 73
MYB 0.034 0.062 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.16 0.3 15 -0.37 54 69
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.057 -10000 0 -0.66 1 1
mol:PI-3-4-5-P3 -0.022 0.16 0.3 16 -0.36 54 70
Rac1/GDP -0.018 0.043 0.093 23 -0.16 11 34
T cell proliferation -0.021 0.15 0.29 16 -0.35 49 65
SHC1 0.029 0.025 -10000 0 -0.039 45 45
RAC1 0.023 0.019 -10000 0 0 209 209
positive regulation of cyclin-dependent protein kinase activity 0.006 0.018 0.088 24 -10000 0 24
PRKCZ -0.023 0.16 0.29 16 -0.36 50 66
NF kappa B1 p50/RelA -0.004 0.19 0.37 12 -0.42 61 73
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.097 0.25 15 -0.28 24 39
HSP90AA1 0.036 0.01 -10000 0 0 39 39
RELA 0.038 0.006 -10000 0 0 12 12
IL2RA 0.021 0.025 -10000 0 -0.038 38 38
IL2RB 0.032 0.025 0.09 3 -0.038 41 44
TERT 0.037 0.008 -10000 0 0 21 21
E2F1 0.035 0.049 0.27 2 -0.38 1 3
SOS1 0 0.004 0.012 37 -0.009 42 79
RPS6 0.033 0.014 -10000 0 0 83 83
mol:cAMP -0.003 0.011 -10000 0 -0.05 25 25
PTPN11 0.032 0.023 -10000 0 -0.039 44 44
IL2RG 0.033 0.025 0.092 3 -0.039 44 47
actin cytoskeleton organization -0.021 0.15 0.29 16 -0.35 49 65
GRB2 0.032 0.023 -10000 0 -0.038 40 40
IL2 0.035 0.024 0.092 3 -0.039 43 46
PIK3CA 0.03 0.026 0.092 3 -0.039 38 41
Rac1/GTP 0.027 0.061 0.18 16 -0.11 34 50
LCK 0.034 0.025 0.09 3 -0.039 43 46
BCL2 -0.016 0.16 0.38 8 -0.44 29 37
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.035 0.086 0.18 1 -0.13 85 86
alphaM/beta2 Integrin/GPIbA 0.055 0.073 0.18 1 -0.12 62 63
alphaM/beta2 Integrin/proMMP-9 -0.002 0.085 0.18 1 -0.13 119 120
PLAUR 0.031 0.016 -10000 0 0 104 104
HMGB1 0.043 0.019 0.1 3 -10000 0 3
alphaM/beta2 Integrin/Talin 0.043 0.074 0.18 1 -0.12 55 56
AGER 0.046 0.016 0.1 5 -10000 0 5
RAP1A 0.038 0.006 -10000 0 0 13 13
SELPLG 0.038 0.007 -10000 0 0 15 15
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.082 0.1 0.26 25 -0.18 1 26
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.016 0.019 -10000 0 0 296 296
CYR61 0.026 0.018 -10000 0 0 167 167
TLN1 0.03 0.016 -10000 0 0 113 113
Rap1/GTP 0.026 0.076 -10000 0 -0.22 19 19
RHOA 0.037 0.008 -10000 0 0 24 24
P-selectin oligomer 0.038 0.007 -10000 0 0 17 17
MYH2 0.019 0.073 0.21 4 -0.29 7 11
MST1R 0.037 0.008 -10000 0 0 24 24
leukocyte activation during inflammatory response 0.059 0.071 -10000 0 -0.11 57 57
APOB 0.038 0.006 -10000 0 0 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.031 0.016 -10000 0 0 107 107
JAM3 0.035 0.012 -10000 0 0 56 56
GP1BA 0.038 0.006 -10000 0 0 13 13
alphaM/beta2 Integrin/CTGF 0.027 0.086 0.18 1 -0.13 96 97
alphaM/beta2 Integrin 0.023 0.081 0.17 11 -0.24 19 30
JAM3 homodimer 0.035 0.012 -10000 0 0 56 56
ICAM2 0.037 0.009 -10000 0 0 31 31
ICAM1 0.032 0.015 -10000 0 0 96 96
phagocytosis triggered by activation of immune response cell surface activating receptor 0.023 0.081 0.17 10 -0.24 19 29
cell adhesion 0.054 0.072 0.17 1 -0.12 62 63
NFKB1 -0.013 0.099 0.28 15 -10000 0 15
THY1 0.033 0.014 -10000 0 0 84 84
RhoA/GDP 0.026 0.017 -10000 0 -0.11 7 7
Lipoprotein(a) 0.048 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.044 0.1 -10000 0 -0.14 95 95
IL6 -0.022 0.044 -10000 0 -10000 0 0
ITGB2 0.036 0.023 0.1 1 -10000 0 1
elevation of cytosolic calcium ion concentration 0.032 0.09 -10000 0 -0.13 69 69
alphaM/beta2 Integrin/JAM2/JAM3 0.058 0.099 -10000 0 -0.14 85 85
JAM2 0.034 0.012 -10000 0 0 59 59
alphaM/beta2 Integrin/ICAM1 0.08 0.084 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.041 0.09 -10000 0 -0.13 55 55
RhoA/GTP 0.027 0.074 0.18 2 -0.25 12 14
positive regulation of phagocytosis 0.014 0.097 0.22 1 -0.25 37 38
Ron/MSP 0.054 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.034 0.092 -10000 0 -0.13 69 69
alphaM/beta2 Integrin/uPAR 0.042 0.077 0.18 1 -0.13 64 65
PLAU 0.021 0.019 -10000 0 0 233 233
PLAT 0.029 0.017 -10000 0 0 133 133
actin filament polymerization 0.019 0.073 0.22 5 -0.28 7 12
MST1 0.037 0.009 -10000 0 0 29 29
alphaM/beta2 Integrin/lipoprotein(a) 0.067 0.075 -10000 0 -0.11 57 57
TNF 0 0.12 0.28 45 -10000 0 45
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.023 0.074 -10000 0 -0.13 65 65
fibrinolysis 0.039 0.088 -10000 0 -0.13 55 55
HCK 0.026 0.018 -10000 0 0 170 170
dendritic cell antigen processing and presentation 0.023 0.081 0.17 10 -0.24 19 29
VTN 0.038 0.005 -10000 0 0 9 9
alphaM/beta2 Integrin/CYR61 0.017 0.093 0.18 1 -0.13 122 123
LPA 0.036 0.01 -10000 0 0 38 38
LRP1 0.033 0.014 -10000 0 0 79 79
cell migration 0.015 0.11 0.18 55 -0.14 129 184
FN1 0.037 0.009 -10000 0 0 31 31
alphaM/beta2 Integrin/Thy1 0.038 0.084 0.18 1 -0.13 85 86
MPO 0.038 0.005 -10000 0 0 7 7
KNG1 0.037 0.008 -10000 0 0 23 23
RAP1/GDP 0.025 0.007 -10000 0 -0.091 1 1
ROCK1 0.02 0.077 0.21 10 -0.28 9 19
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.036 0.011 -10000 0 0 43 43
CTGF 0.028 0.018 -10000 0 0 144 144
alphaM/beta2 Integrin/Hck 0.035 0.085 0.18 1 -0.16 60 61
ITGAM 0.046 0.015 0.1 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.076 0.078 -10000 0 -0.12 57 57
HP 0.028 0.017 -10000 0 0 137 137
leukocyte adhesion 0.023 0.12 0.22 22 -0.25 29 51
SELP 0.038 0.007 -10000 0 0 17 17
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.034 0.013 -10000 0 0 67 67
LAT2 0.022 0.12 0.18 129 -0.28 41 170
AP1 -0.057 0.18 -10000 0 -0.4 67 67
mol:PIP3 0.027 0.15 0.29 47 -0.31 31 78
IKBKB 0.014 0.1 0.22 48 -0.2 32 80
AKT1 -0.067 0.1 0.27 12 -0.29 26 38
IKBKG 0.014 0.1 0.23 43 -0.2 31 74
MS4A2 0.04 0.016 0.085 1 -0.04 15 16
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.014 -10000 0 0 79 79
MAP3K1 -0.024 0.13 0.24 24 -0.32 47 71
mol:Ca2+ 0.029 0.12 0.26 51 -0.24 30 81
LYN 0.031 0.018 -10000 0 -0.042 10 10
CBLB -0.03 0.11 0.18 8 -0.28 62 70
SHC1 0.035 0.012 -10000 0 0 56 56
RasGAP/p62DOK 0.052 0.052 -10000 0 -0.11 36 36
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.042 0.078 0.29 14 -0.18 1 15
PTPN13 -0.038 0.19 -10000 0 -0.62 34 34
PTPN11 0.03 0.028 -10000 0 -0.043 56 56
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.042 0.12 0.33 8 -0.35 28 36
SYK 0.031 0.017 -10000 0 -0.042 9 9
GRB2 0.037 0.009 -10000 0 0 26 26
LAT/PLCgamma1/GRB2/SLP76/GADs 0.016 0.12 0.21 14 -0.28 47 61
LAT -0.031 0.11 0.17 6 -0.28 63 69
PAK2 -0.022 0.14 0.23 24 -0.34 50 74
NFATC2 -0.016 0.011 -10000 0 -0.042 62 62
HRAS -0.023 0.14 0.23 14 -0.34 53 67
GAB2 0.035 0.012 -10000 0 0 52 52
PLA2G1B -0.007 0.19 -10000 0 -0.88 21 21
Fc epsilon R1 0.046 0.067 -10000 0 -0.11 69 69
Antigen/IgE/Fc epsilon R1 0.048 0.06 -10000 0 -0.09 67 67
mol:GDP -0.013 0.14 0.24 11 -0.37 44 55
JUN 0.036 0.011 -10000 0 0 43 43
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.013 -10000 0 0 69 69
FOS 0.026 0.018 -10000 0 0 168 168
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.12 0.19 1 -0.28 66 67
CHUK 0.009 0.1 0.22 44 -0.2 32 76
KLRG1 -0.026 0.093 0.15 10 -0.27 44 54
VAV1 -0.026 0.11 0.17 19 -0.29 55 74
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.032 0.11 0.16 4 -0.28 63 67
negative regulation of mast cell degranulation -0.033 0.085 0.11 1 -0.25 47 48
BTK -0.014 0.13 -10000 0 -0.37 42 42
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.19 116 116
GAB2/PI3K/SHP2 -0.082 0.068 -10000 0 -0.23 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.002 0.055 -10000 0 -0.2 19 19
RAF1 -0.006 0.2 -10000 0 -0.95 21 21
Fc epsilon R1/FcgammaRIIB/SHIP 0.033 0.095 -10000 0 -0.12 125 125
FCER1G 0.029 0.021 -10000 0 -0.04 15 15
FCER1A 0.034 0.018 0.082 1 -0.04 19 20
Antigen/IgE/Fc epsilon R1/Fyn 0.046 0.083 -10000 0 -0.11 93 93
MAPK3 -0.006 0.19 -10000 0 -0.88 21 21
MAPK1 -0.015 0.2 -10000 0 -0.92 21 21
NFKB1 0.038 0.007 -10000 0 0 18 18
MAPK8 -0.12 0.29 -10000 0 -0.56 139 139
DUSP1 0.033 0.014 -10000 0 0 80 80
NF-kappa-B/RelA 0.009 0.078 0.16 46 -0.14 23 69
actin cytoskeleton reorganization -0.026 0.19 -10000 0 -0.61 35 35
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.014 0.15 0.24 15 -0.32 65 80
FER -0.03 0.11 0.17 6 -0.28 66 72
RELA 0.038 0.006 -10000 0 0 12 12
ITK 0 0.038 -10000 0 -0.21 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.005 0.14 0.27 28 -0.35 41 69
cytokine secretion 0.002 0.051 0.097 40 -0.099 32 72
SPHK1 -0.025 0.11 0.18 10 -0.28 63 73
PTK2 -0.028 0.2 -10000 0 -0.65 34 34
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.039 0.13 0.26 30 -0.29 42 72
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.009 0.16 0.29 42 -0.34 41 83
MAP2K2 -0.005 0.2 -10000 0 -0.89 21 21
MAP2K1 -0.02 0.19 -10000 0 -0.91 21 21
MAP2K7 0.036 0.01 -10000 0 0 35 35
KLRG1/SHP2 -0.016 0.094 0.18 17 -0.24 44 61
MAP2K4 0.023 0.15 -10000 0 -0.86 14 14
Fc epsilon R1/FcgammaRIIB 0.036 0.1 -10000 0 -0.14 125 125
mol:Choline -0.041 0.078 0.29 14 -0.18 1 15
SHC/Grb2/SOS1 0.011 0.13 0.21 1 -0.28 64 65
FYN 0.032 0.015 -10000 0 0 95 95
DOK1 0.039 0.003 -10000 0 0 3 3
PXN -0.031 0.19 0.37 3 -0.6 34 37
HCLS1 -0.031 0.12 0.18 11 -0.31 62 73
PRKCB 0.019 0.12 0.25 47 -0.25 36 83
FCGR2B 0.022 0.019 -10000 0 0 221 221
IGHE -0.002 0.005 0.029 3 -10000 0 3
KLRG1/SHIP -0.033 0.087 0.12 2 -0.26 47 49
LCP2 0.033 0.014 -10000 0 0 80 80
PLA2G4A -0.021 0.12 0.17 14 -0.3 57 71
RASA1 0.036 0.01 -10000 0 0 37 37
mol:Phosphatidic acid -0.041 0.078 0.29 14 -0.18 1 15
IKK complex 0.007 0.089 0.23 28 -0.18 15 43
WIPF1 0.037 0.008 -10000 0 0 21 21
Glypican 2 network

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
MDK 0.032 0.015 -9999 0 0 96 96
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.011 0.044 -9999 0 -0.11 56 56
neuron projection morphogenesis 0.011 0.044 -9999 0 -0.11 56 56
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.054 0.12 0.29 48 -0.21 11 59
TBX21 0.098 0.25 0.62 36 -0.59 8 44
B2M 0.037 0.008 -10000 0 0 22 22
TYK2 0.042 0.053 0.15 38 -0.07 6 44
IL12RB1 0.043 0.054 0.15 40 -0.068 10 50
GADD45B 0.097 0.33 0.64 40 -0.95 25 65
IL12RB2 0.047 0.056 0.15 44 -0.067 12 56
GADD45G 0.13 0.24 0.59 53 -0.56 5 58
natural killer cell activation 0.02 0.038 0.086 91 -0.041 7 98
RELB 0.036 0.011 -10000 0 0 42 42
RELA 0.038 0.006 -10000 0 0 12 12
IL18 0.035 0.032 0.11 5 -0.045 38 43
IL2RA 0.026 0.018 -10000 0 0 168 168
IFNG 0.036 0.01 -10000 0 0 38 38
STAT3 (dimer) 0.09 0.26 0.52 55 -0.53 28 83
HLA-DRB5 0 0.011 0.025 8 -0.027 18 26
FASLG 0.1 0.25 0.62 36 -0.59 8 44
NF kappa B2 p52/RelB 0.071 0.22 0.52 32 -0.5 16 48
CD4 0.024 0.032 -10000 0 -0.05 63 63
SOCS1 0.038 0.005 -10000 0 0 10 10
EntrezGene:6955 0 0.013 0.025 30 -0.026 55 85
CD3D 0.025 0.035 0.071 1 -0.052 73 74
CD3E 0.027 0.034 -10000 0 -0.05 78 78
CD3G 0.027 0.035 0.071 1 -0.052 76 77
IL12Rbeta2/JAK2 0.065 0.08 0.23 41 -10000 0 41
CCL3 0.1 0.25 0.57 55 -0.5 16 71
CCL4 0.077 0.37 0.68 51 -1 32 83
HLA-A 0 0 -10000 0 -10000 0 0
IL18/IL18R 0.11 0.096 0.27 92 -0.13 6 98
NOS2 0.11 0.24 0.55 66 -0.49 11 77
IL12/IL12R/TYK2/JAK2/SPHK2 0.047 0.12 0.28 46 -0.22 12 58
IL1R1 0.1 0.25 0.65 35 -0.63 5 40
IL4 -0.031 0.06 0.087 1 -0.14 45 46
JAK2 0.038 0.052 0.15 33 -0.069 8 41
EntrezGene:6957 0 0.011 0.025 8 -0.027 18 26
TCR/CD3/MHC I/CD8 0.008 0.049 0.15 3 -0.22 10 13
RAB7A 0.11 0.3 0.6 41 -0.79 23 64
lysosomal transport 0.11 0.29 0.59 42 -0.74 23 65
FOS -0.071 0.5 0.56 52 -0.99 98 150
STAT4 (dimer) 0.12 0.26 0.58 51 -0.56 12 63
STAT5A (dimer) 0.099 0.23 0.52 38 -0.52 14 52
GZMA 0.1 0.26 0.64 41 -0.59 8 49
GZMB 0.099 0.25 0.63 38 -0.59 8 46
HLX 0.037 0.009 -10000 0 0 30 30
LCK 0.089 0.25 0.59 45 -0.53 15 60
TCR/CD3/MHC II/CD4 0.002 0.1 0.17 58 -0.22 67 125
IL2/IL2R 0.059 0.06 -10000 0 -10000 0 0
MAPK14 0.13 0.29 0.6 56 -0.71 21 77
CCR5 0.12 0.25 0.62 46 -0.68 7 53
IL1B 0.034 0.05 0.15 23 -0.067 8 31
STAT6 0.07 0.14 0.38 45 -0.38 5 50
STAT4 0.037 0.009 -10000 0 0 31 31
STAT3 0.036 0.011 -10000 0 0 42 42
STAT1 0.036 0.011 -10000 0 0 41 41
NFKB1 0.038 0.007 -10000 0 0 18 18
NFKB2 0.028 0.018 -10000 0 0 149 149
IL12B 0.047 0.056 0.16 43 -0.069 11 54
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.039 0.004 -10000 0 0 6 6
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.054 0.12 0.21 10 -0.29 48 58
IL2RB 0.035 0.012 -10000 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.25 0.58 51 -0.53 12 63
IL2RG 0.037 0.009 -10000 0 0 26 26
IL12 0.072 0.083 0.23 46 -10000 0 46
STAT5A 0.038 0.005 -10000 0 0 10 10
CD247 0.027 0.034 -10000 0 -0.05 76 76
IL2 0.038 0.005 -10000 0 0 9 9
SPHK2 0.036 0.01 -10000 0 0 39 39
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.045 0.055 0.15 43 -0.067 13 56
IL12/IL12R/TYK2/JAK2 0.1 0.27 0.6 66 -0.54 16 82
MAP2K3 0.12 0.28 0.6 53 -0.68 20 73
RIPK2 0.038 0.007 -10000 0 0 16 16
MAP2K6 0.13 0.27 0.6 55 -0.63 20 75
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.013 0.025 30 -0.026 55 85
IL18RAP 0.041 0.032 0.1 13 -0.045 45 58
IL12Rbeta1/TYK2 0.058 0.076 0.2 38 -0.15 12 50
EOMES -0.032 0.062 0.12 1 -0.15 76 77
STAT1 (dimer) 0.11 0.23 0.54 51 -0.53 8 59
T cell proliferation 0.11 0.23 0.53 53 -0.47 13 66
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.042 0.032 0.1 14 -0.045 45 59
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.062 0.2 0.44 23 -0.5 20 43
ATF2 0.11 0.27 0.58 46 -0.66 21 67
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.032 0.17 -10000 0 -0.47 63 63
HDAC1 0.026 0.041 0.1 14 -0.057 83 97
AES 0.027 0.027 0.077 7 -0.036 64 71
FBXW11 0.037 0.009 -10000 0 0 27 27
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.029 -10000 0 -10000 0 0
TLE1 0.027 0.028 0.077 5 -0.037 70 75
AP1 -0.012 0.071 -10000 0 -0.2 52 52
NCSTN 0.037 0.009 -10000 0 0 31 31
ADAM10 0.034 0.013 -10000 0 0 59 59
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.13 -10000 0 -0.48 14 14
NICD/RBPSUH -0.011 0.18 -10000 0 -0.48 62 62
WIF1 0.03 0.016 -10000 0 0 112 112
NOTCH1 -0.03 0.18 -10000 0 -0.5 62 62
PSENEN 0.035 0.011 -10000 0 0 48 48
KREMEN2 0.039 0.004 -10000 0 0 6 6
DKK1 0.018 0.019 -10000 0 0 272 272
beta catenin/beta TrCP1 0.062 0.1 0.27 22 -0.31 7 29
APH1B 0.038 0.007 -10000 0 0 18 18
APH1A 0.038 0.007 -10000 0 0 19 19
AXIN1 0.016 0.074 0.29 2 -0.42 2 4
CtBP/CBP/TCF1/TLE1/AES 0.006 0.083 0.24 13 -0.22 14 27
PSEN1 0.035 0.012 -10000 0 0 53 53
FOS 0.026 0.018 -10000 0 0 168 168
JUN 0.036 0.011 -10000 0 0 43 43
MAP3K7 0.024 0.032 -10000 0 -0.043 81 81
CTNNB1 0.049 0.1 0.25 32 -0.32 5 37
MAPK3 0.039 0.004 -10000 0 0 5 5
DKK2/LRP6/Kremen 2 0.067 0.029 -10000 0 -0.12 1 1
HNF1A 0.029 0.028 0.077 7 -0.037 72 79
CTBP1 0.028 0.028 0.077 7 -0.037 69 76
MYC -0.067 0.36 -10000 0 -1.1 52 52
NKD1 0 0.003 -10000 0 -10000 0 0
FZD1 0.022 0.019 -10000 0 0 220 220
NOTCH1 precursor/Deltex homolog 1 -0.034 0.17 -10000 0 -0.47 63 63
apoptosis -0.013 0.071 -10000 0 -0.2 54 54
Delta 1/NOTCHprecursor -0.034 0.17 -10000 0 -0.47 63 63
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.024 0.069 -10000 0 -0.7 3 3
Gamma Secretase 0.078 0.076 -10000 0 -0.15 28 28
APC -0.019 0.17 0.29 2 -0.62 31 33
DVL1 0.014 0.092 -10000 0 -0.38 18 18
CSNK2A1 0.03 0.019 -10000 0 -0.007 100 100
MAP3K7IP1 0 0.009 0.027 8 -0.027 4 12
DKK1/LRP6/Kremen 2 0.033 0.039 -10000 0 -10000 0 0
LRP6 0.035 0.011 -10000 0 0 48 48
CSNK1A1 0.034 0.018 -10000 0 -0.022 43 43
NLK 0.003 0.042 0.13 2 -0.2 14 16
CCND1 -0.029 0.35 -10000 0 -1.1 43 43
WNT1 0.037 0.008 -10000 0 0 22 22
Axin1/APC/beta catenin 0.016 0.14 0.31 8 -0.44 26 34
DKK2 0.037 0.009 -10000 0 0 32 32
NOTCH1 precursor/DVL1 -0.013 0.19 0.3 1 -0.49 57 58
GSK3B 0.036 0.011 -10000 0 -0.002 42 42
FRAT1 0.025 0.022 -10000 0 -0.004 173 173
NOTCH/Deltex homolog 1 -0.032 0.17 -10000 0 -0.47 63 63
PPP2R5D 0.021 0.047 -10000 0 -0.28 7 7
MAPK1 0.035 0.011 -10000 0 0 47 47
WNT1/LRP6/FZD1 0.054 0.051 -10000 0 -10000 0 0
RBPJ 0.037 0.008 -10000 0 0 21 21
CREBBP 0.034 0.026 0.085 14 -0.03 62 76
PLK2 and PLK4 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
PLK2 0.032 0.015 -10000 0 0 87 87
PLK4 0.038 0.007 -10000 0 0 18 18
regulation of centriole replication -0.019 0.043 0.12 43 -9999 0 43
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.069 0.063 -10000 0 -0.11 31 31
MAP4K1 0.036 0.01 -10000 0 0 36 36
MAP3K8 0.024 0.019 -10000 0 0 190 190
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.037 0.009 -10000 0 0 32 32
MAP3K1 -0.016 0.058 0.17 2 -0.25 9 11
JUN -0.14 0.24 0.24 1 -0.52 138 139
MAP3K7 -0.014 0.054 0.16 1 -0.24 9 10
GRAP2 0.036 0.01 -10000 0 0 39 39
CRK 0.037 0.008 -10000 0 0 25 25
MAP2K4 -0.021 0.074 0.2 2 -0.27 20 22
LAT 0.038 0.006 -10000 0 0 11 11
LCP2 0.033 0.014 -10000 0 0 80 80
MAPK8 -0.14 0.26 -10000 0 -0.55 138 138
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.008 0.057 -10000 0 -0.17 31 31
LAT/GRAP2/SLP76/HPK1/HIP-55 0.064 0.059 -10000 0 -0.11 31 31
FoxO family signaling

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
G6PC -0.021 0.076 -10000 0 -0.38 1 1
PLK1 -0.067 0.23 0.52 7 -0.72 20 27
CDKN1B -0.12 0.22 0.48 7 -0.39 112 119
FOXO3 -0.078 0.23 0.45 7 -0.52 78 85
KAT2B 0.001 0.024 0.065 24 -0.042 62 86
FOXO1/SIRT1 0 0.08 -10000 0 -0.28 22 22
CAT -0.083 0.27 0.49 1 -1 22 23
CTNNB1 0.038 0.007 -10000 0 0 18 18
AKT1 0.02 0.05 0.13 8 -0.074 54 62
FOXO1 -0.017 0.084 0.25 1 -0.3 20 21
MAPK10 0.049 0.1 0.19 165 -0.16 4 169
mol:GTP 0 0.006 0.03 2 -10000 0 2
FOXO4 -0.023 0.21 0.32 20 -0.51 50 70
response to oxidative stress 0.002 0.027 0.072 22 -0.05 28 50
FOXO3A/SIRT1 -0.068 0.23 0.4 6 -0.51 78 84
XPO1 0.036 0.014 -10000 0 -0.029 21 21
EP300 0.035 0.013 0.088 1 -0.037 1 2
BCL2L11 0.025 0.039 -10000 0 -10000 0 0
FOXO1/SKP2 0 0.086 0.22 1 -0.28 21 22
mol:GDP 0.002 0.027 0.072 22 -0.05 28 50
RAN 0.029 0.026 -10000 0 -0.037 65 65
GADD45A -0.15 0.33 0.55 4 -0.85 70 74
YWHAQ 0.038 0.005 -10000 0 0 9 9
FOXO1/14-3-3 family -0.002 0.15 0.22 1 -0.48 26 27
MST1 0.022 0.05 0.12 11 -0.07 79 90
CSNK1D 0.037 0.008 -10000 0 0 25 25
CSNK1E 0.034 0.013 -10000 0 0 68 68
FOXO4/14-3-3 family -0.008 0.15 -10000 0 -0.5 25 25
YWHAB 0.033 0.014 -10000 0 0 72 72
MAPK8 0.024 0.091 0.19 101 -0.14 5 106
MAPK9 0.058 0.11 0.19 192 -0.16 4 196
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.037 0.009 -10000 0 0 29 29
YWHAZ 0.037 0.008 -10000 0 0 23 23
SIRT1 0.018 0.028 -10000 0 -0.053 12 12
SOD2 -0.14 0.36 0.45 15 -0.77 101 116
RBL2 -0.072 0.29 0.5 1 -0.92 37 38
RAL/GDP 0.018 0.05 0.15 3 -0.12 17 20
CHUK 0.012 0.044 0.12 7 -0.07 63 70
Ran/GTP 0.018 0.029 0.088 2 -0.082 9 11
CSNK1G2 0.036 0.01 -10000 0 0 37 37
RAL/GTP 0.018 0.053 0.18 7 -0.11 17 24
CSNK1G1 0.038 0.006 -10000 0 0 13 13
FASLG 0.022 0.046 -10000 0 -0.6 1 1
SKP2 0.037 0.008 -10000 0 0 21 21
USP7 0.031 0.024 -10000 0 -0.037 51 51
IKBKB 0.024 0.051 0.12 12 -0.069 83 95
CCNB1 -0.17 0.42 0.55 8 -1 87 95
FOXO1-3a-4/beta catenin -0.038 0.23 0.44 20 -0.4 73 93
proteasomal ubiquitin-dependent protein catabolic process 0 0.086 0.22 1 -0.27 22 23
CSNK1A1 0.038 0.007 -10000 0 0 16 16
SGK1 0.001 0.024 0.065 24 -0.042 62 86
CSNK1G3 0.038 0.006 -10000 0 0 14 14
Ran/GTP/Exportin 1 0.039 0.043 0.14 2 -0.12 8 10
ZFAND5 -0.014 0.19 0.37 11 -0.55 29 40
SFN 0.033 0.014 -10000 0 0 79 79
CDK2 0.035 0.018 0.092 1 -0.037 17 18
FOXO3A/14-3-3 -0.018 0.16 0.22 2 -0.46 31 33
CREBBP 0.038 0.017 0.092 1 -0.038 22 23
FBXO32 -0.065 0.22 0.41 8 -0.47 78 86
BCL6 -0.092 0.33 0.48 2 -0.99 46 48
RALB 0.028 0.027 -10000 0 -0.039 67 67
RALA 0.018 0.024 -10000 0 -0.038 30 30
YWHAH 0.033 0.014 -10000 0 0 76 76
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.035 0.012 -10000 0 0 53 53
VLDLR 0.029 0.017 -10000 0 0 135 135
LRPAP1 0.038 0.007 -10000 0 0 18 18
NUDC 0.037 0.009 -10000 0 0 30 30
RELN/LRP8 0.036 0.045 -10000 0 -0.12 10 10
CaM/Ca2+ 0.022 0.023 -10000 0 -0.11 13 13
KATNA1 0.035 0.011 -10000 0 0 48 48
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.047 0.11 0.18 178 -10000 0 178
IQGAP1/CaM 0.035 0.055 -10000 0 -0.13 43 43
DAB1 0.038 0.007 -10000 0 0 18 18
IQGAP1 0.035 0.012 -10000 0 0 49 49
PLA2G7 0.035 0.012 -10000 0 0 58 58
CALM1 0.034 0.013 -10000 0 0 62 62
DYNLT1 0.035 0.011 -10000 0 0 47 47
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.048 0.035 -10000 0 -0.14 14 14
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.037 0.009 -10000 0 0 29 29
CDK5R1 0.037 0.009 -10000 0 0 26 26
LIS1/Poliovirus Protein 3A -0.029 0.025 -10000 0 -0.12 24 24
CDK5R2 0.038 0.007 -10000 0 0 17 17
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.029 0.046 -10000 0 -0.12 14 14
YWHAE 0.037 0.009 -10000 0 0 29 29
NDEL1/14-3-3 E 0.08 0.19 0.32 171 -0.28 9 180
MAP1B -0.013 0.063 -10000 0 -0.2 49 49
RAC1 -0.001 0.051 -10000 0 -0.36 6 6
p35/CDK5 -0.027 0.062 0.18 11 -0.24 2 13
RELN 0.021 0.019 -10000 0 0 233 233
PAFAH/LIS1 -0.036 0.029 -10000 0 -0.14 21 21
LIS1/CLIP170 -0.038 0.03 0.11 1 -0.14 24 25
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.004 0.13 0.22 102 -0.3 14 116
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.016 0.082 0.18 1 -0.22 58 59
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.068 0.17 0.31 151 -0.25 13 164
LIS1/IQGAP1 -0.038 0.035 0.11 1 -0.16 24 25
RHOA 0.003 0.07 -10000 0 -0.26 18 18
PAFAH1B1 -0.028 0.015 0.12 1 -10000 0 1
PAFAH1B3 0.033 0.014 -10000 0 0 83 83
PAFAH1B2 0.038 0.005 -10000 0 0 9 9
MAP1B/LIS1/Dynein heavy chain 0.003 0.075 0.18 1 -0.19 55 56
NDEL1/Katanin 60/Dynein heavy chain 0.066 0.18 0.32 148 -0.29 8 156
LRP8 0.036 0.011 -10000 0 0 40 40
NDEL1/Katanin 60 0.071 0.18 0.32 158 -0.28 9 167
P39/CDK5 -0.027 0.063 0.18 12 -0.24 2 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.041 0.036 0.11 1 -0.17 24 25
CDK5 -0.022 0.051 0.17 12 -0.18 5 17
PPP2R5D 0.038 0.005 -10000 0 0 10 10
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.032 0.025 0.098 1 -0.12 25 26
CSNK2A1 0.033 0.014 -10000 0 0 81 81
RELN/VLDLR/DAB1/LIS1 0.028 0.059 -10000 0 -0.13 26 26
RELN/VLDLR 0.041 0.06 -10000 0 -0.12 19 19
CDC42 0.005 0.054 -10000 0 -0.2 14 14
IL2 signaling events mediated by STAT5

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
GAB2 0.034 0.015 -10000 0 -0.005 60 60
ELF1 0.044 0.02 -10000 0 -10000 0 0
CCNA2 0.03 0.017 -10000 0 0 119 119
PIK3CA 0.032 0.017 -10000 0 -0.004 88 88
JAK3 0.035 0.015 -10000 0 -0.038 11 11
PIK3R1 0.033 0.015 -10000 0 -0.039 5 5
JAK1 0.035 0.013 -10000 0 -0.004 48 48
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.17 0.27 3 -0.5 42 45
SHC1 0.033 0.016 -10000 0 -0.039 11 11
SP1 -0.008 0.12 -10000 0 -0.27 88 88
IL2RA -0.018 0.018 0.12 2 -10000 0 2
IL2RB 0.034 0.016 -10000 0 -0.04 9 9
SOS1 0 0.002 -10000 0 -10000 0 0
IL2RG 0.036 0.014 -10000 0 -0.011 37 37
G1/S transition of mitotic cell cycle -0.053 0.27 0.3 30 -0.57 92 122
PTPN11 0.036 0.014 -10000 0 -0.038 12 12
CCND2 -0.1 0.17 -10000 0 -0.47 87 87
LCK 0.036 0.013 -10000 0 -0.039 10 10
GRB2 0.036 0.013 -10000 0 -0.01 35 35
IL2 0.037 0.013 -10000 0 -0.038 12 12
CDK6 0.022 0.019 -10000 0 0 222 222
CCND3 -0.033 0.2 0.41 4 -0.71 28 32
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.019 0.044 -10000 0 -0.066 95 95
HSPA8 0.028 0.027 -10000 0 -0.036 70 70
SMAD3/SMAD4/ER alpha 0.035 0.094 0.26 4 -0.16 25 29
AKT1 0.029 0.025 -10000 0 -0.041 41 41
GSC 0 0.035 0.12 16 -10000 0 16
NKX2-5 -0.002 0.005 -10000 0 -0.036 11 11
muscle cell differentiation -0.014 0.13 0.31 47 -10000 0 47
SMAD2-3/SMAD4/SP1 0.053 0.16 0.36 19 -0.26 43 62
SMAD4 0.011 0.065 0.18 4 -0.14 28 32
CBFB 0.038 0.006 -10000 0 0 13 13
SAP18 0.035 0.012 -10000 0 0 50 50
Cbp/p300/MSG1 0.014 0.091 -10000 0 -0.11 149 149
SMAD3/SMAD4/VDR 0.041 0.13 0.28 4 -0.21 28 32
MYC 0.03 0.015 -10000 0 -10000 0 0
CDKN2B -0.22 0.2 -10000 0 -0.54 48 48
AP1 -0.014 0.096 0.24 5 -0.22 45 50
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.023 0.13 -10000 0 -0.34 46 46
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.053 0.14 0.22 2 -0.39 55 57
SP3 0.037 0.019 0.1 14 -0.059 10 24
CREB1 0.038 0.005 -10000 0 0 8 8
FOXH1 0.036 0.017 0.094 10 -0.063 9 19
SMAD3/SMAD4/GR 0.032 0.1 0.26 2 -0.17 29 31
GATA3 0.028 0.02 0.11 3 -0.043 2 5
SKI/SIN3/HDAC complex/NCoR1 -0.016 0.099 0.16 1 -0.29 38 39
MEF2C/TIF2 -0.035 0.073 0.26 11 -0.23 8 19
endothelial cell migration 0.17 0.5 1.1 107 -10000 0 107
MAX 0.023 0.053 0.089 80 -0.081 88 168
RBBP7 0.038 0.006 -10000 0 0 10 10
RBBP4 0.034 0.013 -10000 0 0 62 62
RUNX2 0.038 0.005 -10000 0 0 7 7
RUNX3 0.036 0.01 -10000 0 0 36 36
RUNX1 0.038 0.007 -10000 0 0 17 17
CTBP1 0.037 0.009 -10000 0 0 30 30
NR3C1 0.024 0.053 0.089 81 -0.081 89 170
VDR 0.037 0.009 -10000 0 0 26 26
CDKN1A -0.093 0.35 0.4 11 -1 58 69
KAT2B -0.002 0.008 -10000 0 -0.026 8 8
SMAD2/SMAD2/SMAD4/FOXH1 0.048 0.081 0.22 7 -0.16 31 38
DCP1A 0.037 0.009 -10000 0 0 27 27
SKI 0.037 0.009 -10000 0 0 26 26
SERPINE1 -0.18 0.5 -10000 0 -1.1 107 107
SMAD3/SMAD4/ATF2 0.037 0.095 0.24 4 -0.16 34 38
SMAD3/SMAD4/ATF3 0.017 0.1 0.24 4 -0.18 56 60
SAP30 0.038 0.008 -10000 0 0 20 20
Cbp/p300/PIAS3 0.044 0.084 -10000 0 -0.11 92 92
JUN -0.025 0.099 0.23 13 -0.25 32 45
SMAD3/SMAD4/IRF7 0.04 0.098 0.25 4 -0.16 40 44
TFE3 0.018 0.066 0.14 14 -0.1 103 117
COL1A2 -0.023 0.19 0.26 44 -0.62 42 86
mesenchymal cell differentiation -0.036 0.094 0.16 41 -0.24 5 46
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.036 0.01 -10000 0 0 35 35
FOS 0.015 0.036 0.15 1 -0.065 13 14
SMAD3/SMAD4/Max 0.032 0.098 0.26 2 -0.17 21 23
Cbp/p300/SNIP1 0.043 0.065 -10000 0 -0.077 89 89
ZBTB17 0.037 0.007 -10000 0 -10000 0 0
LAMC1 -0.047 0.099 0.19 5 -0.29 37 42
TGIF2/HDAC complex/SMAD3/SMAD4 0.032 0.09 0.24 4 -0.16 34 38
IRF7 0.035 0.013 -10000 0 -0.036 5 5
ESR1 0.034 0.047 0.13 65 -0.039 80 145
HNF4A 0.034 0.013 -10000 0 0 66 66
MEF2C -0.033 0.069 0.24 14 -0.23 9 23
SMAD2-3/SMAD4 0.039 0.1 0.27 6 -0.19 29 35
Cbp/p300/Src-1 0.033 0.08 -10000 0 -0.099 113 113
IGHV3OR16-13 0.001 0.054 -10000 0 -0.46 6 6
TGIF2/HDAC complex 0.033 0.014 -10000 0 0 72 72
CREBBP 0.022 0.04 -10000 0 -0.056 105 105
SKIL 0.038 0.007 -10000 0 0 17 17
HDAC1 0.037 0.008 -10000 0 0 24 24
HDAC2 0.034 0.013 -10000 0 0 62 62
SNIP1 0.036 0.017 -10000 0 -0.022 35 35
GCN5L2 -0.002 0.014 0.025 3 -0.027 92 95
SMAD3/SMAD4/TFE3 0.029 0.13 0.28 13 -0.22 54 67
MSG1/HSC70 0.013 0.075 -10000 0 -0.13 101 101
SMAD2 0.036 0.022 0.12 4 -0.049 19 23
SMAD3 0.008 0.068 0.16 5 -0.14 34 39
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.006 0.076 0.16 3 -0.2 31 34
SMAD2/SMAD2/SMAD4 -0.013 0.07 0.18 8 -0.2 41 49
NCOR1 0.037 0.009 -10000 0 0 28 28
NCOA2 0.038 0.006 -10000 0 0 14 14
NCOA1 0.035 0.012 -10000 0 0 52 52
MYOD/E2A 0.052 0.017 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.062 0.16 0.36 17 -0.26 36 53
IFNB1 -0.016 0.067 0.19 8 -0.19 1 9
SMAD3/SMAD4/MEF2C 0.017 0.096 0.32 4 -0.23 11 15
CITED1 0.027 0.018 -10000 0 0 153 153
SMAD2-3/SMAD4/ARC105 0.053 0.11 0.29 4 -0.19 18 22
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.029 0.14 -10000 0 -0.45 35 35
RUNX1-3/PEBPB2 0.07 0.026 -10000 0 -10000 0 0
SMAD7 -0.051 0.18 0.32 5 -0.43 59 64
MYC/MIZ-1 0.031 0.056 -10000 0 -0.13 49 49
SMAD3/SMAD4 -0.082 0.24 0.23 23 -0.47 117 140
IL10 -0.027 0.07 0.2 8 -10000 0 8
PIASy/HDAC complex 0.027 0.037 0.08 5 -0.047 89 94
PIAS3 0.023 0.034 -10000 0 -0.046 96 96
CDK2 0.021 0.037 -10000 0 -0.053 92 92
IL5 -0.027 0.071 0.21 8 -10000 0 8
CDK4 0.021 0.035 -10000 0 -0.056 68 68
PIAS4 0.027 0.037 0.08 5 -0.047 89 94
ATF3 0.029 0.017 -10000 0 0 129 129
SMAD3/SMAD4/SP1 0.029 0.14 0.3 23 -0.25 54 77
FOXG1 0.027 0.023 0.072 1 -0.052 17 18
FOXO3 -0.028 0.017 0.12 2 -10000 0 2
FOXO1 -0.021 0.032 0.12 19 -10000 0 19
FOXO4 -0.03 0.014 0.12 1 -10000 0 1
heart looping -0.032 0.069 0.24 14 -0.22 9 23
CEBPB 0.031 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.019 0.078 0.2 5 -0.14 46 51
MYOD1 0.038 0.006 -10000 0 0 14 14
SMAD3/SMAD4/HNF4 0.032 0.092 0.24 5 -0.16 33 38
SMAD3/SMAD4/GATA3 0.028 0.094 0.26 4 -0.18 17 21
SnoN/SIN3/HDAC complex/NCoR1 0.038 0.007 -10000 0 0 17 17
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.063 0.1 0.27 2 -0.18 7 9
SMAD3/SMAD4/SP1-3 0.047 0.15 0.32 17 -0.25 48 65
MED15 0.036 0.01 -10000 0 0 34 34
SP1 0.02 0.082 0.14 46 -0.12 103 149
SIN3B 0.036 0.011 -10000 0 0 46 46
SIN3A 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.046 0.076 0.19 1 -0.16 25 26
ITGB5 -0.04 0.11 0.26 14 -0.27 31 45
TGIF/SIN3/HDAC complex/CtBP -0.02 0.11 -10000 0 -0.32 41 41
SMAD3/SMAD4/AR 0.036 0.094 0.24 4 -0.16 33 37
AR 0.037 0.008 -10000 0 0 23 23
negative regulation of cell growth -0.021 0.12 0.2 4 -0.3 54 58
SMAD3/SMAD4/MYOD 0.037 0.094 0.24 4 -0.16 34 38
E2F5 0.038 0.006 -10000 0 0 11 11
E2F4 0.038 0.005 -10000 0 0 8 8
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.056 0.11 0.29 2 -0.18 23 25
SMAD2-3/SMAD4/FOXO1-3a-4 -0.033 0.13 0.23 3 -0.4 38 41
TFDP1 0.035 0.012 -10000 0 0 58 58
SMAD3/SMAD4/AP1 0.021 0.12 0.27 8 -0.23 42 50
SMAD3/SMAD4/RUNX2 0.037 0.095 0.24 5 -0.16 41 46
TGIF2 0.033 0.014 -10000 0 0 72 72
TGIF1 0.034 0.013 -10000 0 0 69 69
ATF2 0.038 0.006 -10000 0 0 12 12
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.045 0.017 0.12 18 -0.067 1 19
NFATC2 0.029 0.17 0.3 17 -0.37 35 52
NFATC3 0.02 0.15 0.27 53 -0.25 72 125
CD40LG -0.007 0.37 0.59 59 -0.72 63 122
ITCH 0.006 0.071 0.18 71 -10000 0 71
CBLB 0.008 0.079 0.18 83 -10000 0 83
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.058 0.28 0.43 30 -0.64 53 83
JUNB 0.032 0.015 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.027 -10000 0 -0.12 6 6
T cell anergy 0.02 0.089 0.26 50 -0.23 1 51
TLE4 0.015 0.12 0.38 3 -0.32 18 21
Jun/NFAT1-c-4/p21SNFT -0.02 0.33 0.5 11 -0.72 71 82
AP-1/NFAT1-c-4 -0.047 0.35 0.58 3 -0.8 62 65
IKZF1 0.031 0.11 0.4 16 -0.33 8 24
T-helper 2 cell differentiation -0.079 0.24 -10000 0 -0.65 37 37
AP-1/NFAT1 0.02 0.15 0.33 24 -0.29 34 58
CALM1 0.049 0.032 0.16 4 -10000 0 4
EGR2 -0.058 0.43 0.61 29 -0.97 73 102
EGR3 -0.034 0.44 0.59 46 -0.97 70 116
NFAT1/FOXP3 0.048 0.14 0.29 10 -0.3 23 33
EGR1 0.031 0.016 0.097 1 -10000 0 1
JUN 0.037 0.054 0.15 48 -0.066 7 55
EGR4 0.039 0.005 0.086 2 -10000 0 2
mol:Ca2+ 0.003 0.004 -10000 0 -10000 0 0
GBP3 0.014 0.11 0.21 14 -0.25 31 45
FOSL1 0.035 0.012 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.021 0.35 0.48 21 -0.73 72 93
DGKA 0.015 0.11 0.28 4 -0.31 18 22
CREM 0.028 0.017 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.005 0.34 0.49 17 -0.73 72 89
CTLA4 0 0.1 0.21 8 -0.27 19 27
NFAT1-c-4 (dimer)/EGR1 -0.017 0.35 0.48 13 -0.77 72 85
NFAT1-c-4 (dimer)/EGR4 0.014 0.35 0.49 21 -0.74 72 93
FOS 0.027 0.047 0.14 34 -0.062 8 42
IFNG -0.008 0.14 0.34 4 -0.42 17 21
T cell activation -0.003 0.24 0.51 14 -0.54 31 45
MAF 0.036 0.01 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.007 0.31 0.61 70 -0.51 51 121
TNF -0.035 0.32 0.45 29 -0.71 72 101
FASLG -0.083 0.48 0.67 15 -1.1 73 88
TBX21 0.042 0.01 0.15 3 -10000 0 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.028 0.019 -10000 0 -10000 0 0
PTPN1 0.016 0.12 0.4 6 -0.35 21 27
NFAT1-c-4/ICER1 -0.021 0.34 0.49 17 -0.74 72 89
GATA3 0.029 0.018 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.009 0.16 0.36 12 -0.41 17 29
IL2RA -0.077 0.25 0.41 6 -0.62 56 62
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.012 0.12 0.22 7 -0.34 21 28
E2F1 0.036 0.054 0.12 38 -0.26 12 50
PPARG 0.037 0.009 -10000 0 -10000 0 0
SLC3A2 0.012 0.13 0.32 2 -0.38 22 24
IRF4 0.038 0.005 -10000 0 -10000 0 0
PTGS2 -0.081 0.29 0.53 4 -0.71 62 66
CSF2 -0.006 0.37 0.59 57 -0.72 63 120
JunB/Fra1/NFAT1-c-4 -0.01 0.32 0.47 5 -0.71 71 76
IL4 -0.083 0.25 -10000 0 -0.68 37 37
IL5 -0.007 0.37 0.59 57 -0.72 63 120
IL2 -0.004 0.24 0.51 14 -0.55 31 45
IL3 0.003 0.09 -10000 0 -0.53 9 9
RNF128 -0.02 0.032 0.19 7 -10000 0 7
NFATC1 0.007 0.31 0.51 51 -0.61 70 121
CDK4 -0.007 0.31 0.6 43 -0.75 31 74
PTPRK 0.003 0.14 0.22 9 -0.4 35 44
IL8 -0.11 0.29 0.56 8 -0.74 64 72
POU2F1 0.04 0.009 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.03 -10000 0 -0.069 40 40
CDKN2C -0.012 0.029 -10000 0 -0.057 67 67
CDKN2A 0.005 0.015 -10000 0 -10000 0 0
CCND2 -0.002 0.018 0.1 3 -10000 0 3
RB1 -0.04 0.087 0.18 3 -0.19 118 121
CDK4 -0.003 0.022 0.12 3 -0.22 1 4
CDK6 -0.002 0.019 0.12 3 -10000 0 3
G1/S progression 0.048 0.096 0.2 134 -0.18 3 137
BCR signaling pathway

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.014 0.13 0.27 5 -0.32 31 36
IKBKB 0.017 0.087 0.26 11 -0.3 7 18
AKT1 0.012 0.1 0.24 47 -0.2 7 54
IKBKG 0.009 0.079 0.28 4 -0.27 7 11
CALM1 -0.024 0.12 0.2 5 -0.37 38 43
PIK3CA 0.033 0.014 -10000 0 0 79 79
MAP3K1 0.032 0.14 0.29 19 -0.34 33 52
MAP3K7 0.035 0.011 -10000 0 0 47 47
mol:Ca2+ -0.021 0.13 0.23 6 -0.38 39 45
DOK1 0.039 0.003 -10000 0 0 3 3
AP-1 -0.022 0.1 0.23 13 -0.22 36 49
LYN 0.033 0.014 -10000 0 0 76 76
BLNK 0.02 0.019 -10000 0 0 241 241
SHC1 0.035 0.012 -10000 0 0 56 56
BCR complex 0.052 0.018 -10000 0 -10000 0 0
CD22 -0.023 0.088 -10000 0 -0.28 34 34
CAMK2G -0.019 0.12 0.23 6 -0.36 36 42
CSNK2A1 0.033 0.014 -10000 0 0 81 81
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.049 0.056 0.049 57 -0.21 15 72
GO:0007205 -0.022 0.13 0.23 6 -0.38 40 46
SYK 0.033 0.014 -10000 0 0 78 78
ELK1 -0.031 0.13 0.22 4 -0.37 39 43
NFATC1 -0.027 0.1 0.28 7 -0.27 32 39
B-cell antigen/BCR complex 0.052 0.018 -10000 0 -10000 0 0
PAG1/CSK 0.025 0.02 -10000 0 -0.11 10 10
NFKBIB 0.021 0.046 0.14 7 -0.13 19 26
HRAS -0.025 0.12 0.21 17 -0.33 39 56
NFKBIA 0.022 0.042 0.14 6 -0.12 15 21
NF-kappa-B/RelA/I kappa B beta 0.026 0.042 0.13 12 -0.1 20 32
RasGAP/Csk 0.05 0.099 -10000 0 -0.12 106 106
mol:GDP -0.02 0.13 0.23 5 -0.37 39 44
PTEN 0.024 0.019 -10000 0 0 196 196
CD79B 0.038 0.005 -10000 0 0 10 10
NF-kappa-B/RelA/I kappa B alpha 0.026 0.039 0.13 11 -0.1 11 22
GRB2 0.037 0.009 -10000 0 0 26 26
PI3K/BCAP/CD19 -0.032 0.16 0.31 9 -0.43 41 50
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:IP3 -0.019 0.13 0.23 5 -0.38 36 41
CSK 0.037 0.008 -10000 0 0 22 22
FOS -0.026 0.13 0.26 8 -0.38 36 44
CHUK -0.058 0.14 0.28 4 -0.27 95 99
IBTK 0.036 0.01 -10000 0 0 34 34
CARD11/BCL10/MALT1/TAK1 0.002 0.13 0.23 1 -0.35 34 35
PTPN6 -0.024 0.093 0.17 11 -0.29 33 44
RELA 0.038 0.006 -10000 0 0 12 12
BCL2A1 0.018 0.037 0.1 21 -0.093 20 41
VAV2 -0.023 0.1 -10000 0 -0.3 44 44
ubiquitin-dependent protein catabolic process 0.022 0.045 0.14 7 -0.13 20 27
BTK 0.018 0.013 -10000 0 -10000 0 0
CD19 -0.021 0.091 -10000 0 -0.28 35 35
MAP4K1 0.036 0.01 -10000 0 0 36 36
CD72 0.034 0.013 -10000 0 0 66 66
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.12 0.28 16 -0.31 29 45
SH3BP5 0.035 0.012 -10000 0 0 54 54
PIK3AP1 -0.02 0.13 0.22 4 -0.41 34 38
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.034 0.18 -10000 0 -0.5 51 51
RAF1 -0.032 0.11 0.2 12 -0.33 36 48
RasGAP/p62DOK/SHIP 0.041 0.087 -10000 0 -0.11 108 108
CD79A 0.036 0.011 -10000 0 0 45 45
re-entry into mitotic cell cycle -0.023 0.1 0.23 13 -0.22 35 48
RASA1 0.036 0.01 -10000 0 0 37 37
MAPK3 -0.045 0.098 0.21 5 -0.32 31 36
MAPK1 -0.041 0.099 0.22 5 -0.31 33 38
CD72/SHP1 -0.011 0.11 0.26 24 -0.29 31 55
NFKB1 0.038 0.007 -10000 0 0 18 18
MAPK8 0.024 0.12 0.28 15 -0.31 27 42
actin cytoskeleton organization 0.041 0.12 0.26 28 -0.29 17 45
NF-kappa-B/RelA 0.044 0.092 0.26 7 -0.25 23 30
Calcineurin -0.007 0.13 0.31 1 -0.35 35 36
PI3K -0.053 0.082 0.13 1 -0.27 31 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.13 0.22 6 -0.43 32 38
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.019 0.15 -10000 0 -0.63 10 10
DAPP1 0 0.15 -10000 0 -0.69 10 10
cytokine secretion -0.025 0.095 0.28 7 -0.25 32 39
mol:DAG -0.019 0.13 0.23 5 -0.38 36 41
PLCG2 0.034 0.013 -10000 0 0 64 64
MAP2K1 -0.039 0.11 0.2 9 -0.33 33 42
B-cell antigen/BCR complex/FcgammaRIIB 0.019 0.073 -10000 0 -0.12 94 94
mol:PI-3-4-5-P3 -0.015 0.085 0.26 21 -0.24 6 27
ETS1 -0.031 0.11 0.27 2 -0.38 28 30
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.037 0.094 -10000 0 -0.14 57 57
B-cell antigen/BCR complex/LYN -0.004 0.089 -10000 0 -0.28 32 32
MALT1 0.036 0.01 -10000 0 0 36 36
TRAF6 0.038 0.007 -10000 0 0 17 17
RAC1 0.037 0.12 0.26 25 -0.29 22 47
B-cell antigen/BCR complex/LYN/SYK 0.023 0.11 0.26 3 -0.26 29 32
CARD11 -0.021 0.13 0.22 5 -0.36 40 45
FCGR2B 0.022 0.019 -10000 0 0 221 221
PPP3CA 0.036 0.01 -10000 0 0 37 37
BCL10 0.037 0.008 -10000 0 0 21 21
IKK complex 0.004 0.049 0.15 13 -0.13 8 21
PTPRC 0.03 0.016 -10000 0 0 114 114
PDPK1 -0.014 0.069 0.21 22 -0.18 4 26
PPP3CB 0.027 0.018 -10000 0 0 154 154
PPP3CC 0.038 0.007 -10000 0 0 16 16
POU2F2 0.016 0.034 0.11 16 -0.086 20 36
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.036 0.01 -10000 0 0 39 39
SPHK1 0.035 0.012 -10000 0 0 50 50
GNAI2 0.035 0.011 -10000 0 0 46 46
mol:S1P 0.015 0.02 -10000 0 -10000 0 0
GNAO1 0.032 0.015 -10000 0 0 88 88
mol:Sphinganine-1-P -0.021 0.041 0.12 38 -10000 0 38
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.026 0.044 -10000 0 -0.17 2 2
GNAI3 0.038 0.007 -10000 0 0 16 16
G12/G13 0.025 0.044 -10000 0 -0.13 24 24
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.021 -10000 0 -0.1 19 19
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.016 0.019 -10000 0 0 297 297
S1P/S1P5/G12 0.015 0.035 -10000 0 -0.17 2 2
S1P/S1P3/Gq 0.023 0.044 0.16 9 -0.25 8 17
S1P/S1P4/Gi 0.002 0.1 0.14 15 -0.21 69 84
GNAQ 0.036 0.01 -10000 0 0 37 37
GNAZ 0.033 0.014 -10000 0 0 83 83
GNA14 0.036 0.01 -10000 0 0 36 36
GNA15 0.034 0.013 -10000 0 0 62 62
GNA12 0.022 0.019 -10000 0 0 227 227
GNA13 0.037 0.008 -10000 0 0 22 22
GNA11 0.034 0.013 -10000 0 0 63 63
ABCC1 0.038 0.007 -10000 0 0 19 19
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.036 0.01 -10000 0 0 39 39
mol:PIP3 -0.019 0.052 0.11 14 -0.22 17 31
FRAP1 0.035 0.1 0.25 3 -0.47 13 16
AKT1 0.019 0.11 0.17 105 -0.25 24 129
INSR 0.036 0.01 -10000 0 0 34 34
Insulin Receptor/Insulin 0.047 0.016 -10000 0 -10000 0 0
mol:GTP 0.028 0.12 0.19 99 -0.27 20 119
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.018 0.05 -10000 0 -0.2 16 16
TSC2 0.037 0.009 -10000 0 0 26 26
RHEB/GDP -0.018 0.068 0.13 9 -0.23 19 28
TSC1 0.036 0.011 -10000 0 0 43 43
Insulin Receptor/IRS1 0.023 0.061 -10000 0 -0.25 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.075 0.17 5 -0.24 10 15
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.018 -10000 0 0 170 170
RPS6KB1 0.045 0.092 0.24 18 -0.29 5 23
MAP3K5 -0.027 0.084 0.18 2 -0.22 75 77
PIK3R1 0.034 0.014 -10000 0 0 69 69
apoptosis -0.027 0.084 0.18 2 -0.22 75 77
mol:LY294002 0 0 0.001 3 -0.001 20 23
EIF4B 0.038 0.092 0.25 23 -0.3 5 28
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.072 0.24 4 -0.28 4 8
eIF4E/eIF4G1/eIF4A1 -0.004 0.075 -10000 0 -0.33 13 13
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.029 0.08 -10000 0 -0.22 32 32
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.057 0.18 21 -0.17 8 29
FKBP1A 0.032 0.015 -10000 0 0 91 91
RHEB/GTP -0.007 0.084 0.19 24 -0.25 15 39
mol:Amino Acids 0 0 0.001 3 -0.001 20 23
FKBP12/Rapamycin 0.022 0.022 -10000 0 -0.12 10 10
PDPK1 -0.02 0.058 0.16 16 -0.24 12 28
EIF4E 0.036 0.01 -10000 0 0 37 37
ASK1/PP5C -0.035 0.24 -10000 0 -0.56 83 83
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.007 0.081 -10000 0 -0.29 30 30
TSC1/TSC2 0.031 0.13 0.21 101 -0.28 20 121
tumor necrosis factor receptor activity 0 0 0.001 20 -0.001 3 23
RPS6 0.033 0.014 -10000 0 0 83 83
PPP5C 0.036 0.011 -10000 0 0 44 44
EIF4G1 0.035 0.012 -10000 0 0 54 54
IRS1 0.002 0.058 -10000 0 -0.25 24 24
INS 0.037 0.008 -10000 0 0 21 21
PTEN 0.024 0.019 -10000 0 0 197 197
PDK2 -0.021 0.058 0.16 15 -0.24 12 27
EIF4EBP1 -0.022 0.25 -10000 0 -1.1 26 26
PIK3CA 0.034 0.014 -10000 0 0 79 79
PPP2R5D 0.026 0.095 0.25 5 -0.43 13 18
peptide biosynthetic process -0.031 0.025 0.18 6 -10000 0 6
RHEB 0.022 0.019 -10000 0 0 216 216
EIF4A1 0.037 0.008 -10000 0 0 20 20
mol:Rapamycin 0 0.001 0.004 23 -0.003 11 34
EEF2 -0.031 0.025 0.18 6 -10000 0 6
eIF4E/4E-BP1 -0.005 0.25 -10000 0 -1.1 26 26
Paxillin-dependent events mediated by a4b1

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
CRKL 0.037 0.009 -10000 0 0 32 32
Rac1/GDP 0.023 0.026 -10000 0 -10000 0 0
DOCK1 0.026 0.019 -10000 0 0 175 175
ITGA4 0.038 0.006 -10000 0 0 13 13
RAC1 0.023 0.019 -10000 0 0 209 209
alpha4/beta7 Integrin 0.055 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.037 0.008 -10000 0 0 25 25
alpha4/beta1 Integrin 0.056 0.036 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.031 0.17 29 -10000 0 29
lamellipodium assembly -0.047 0.14 -10000 0 -0.38 64 64
PIK3CA 0.033 0.014 -10000 0 0 79 79
PI3K 0.023 0.07 -10000 0 -0.14 72 72
ARF6 0.036 0.01 -10000 0 0 33 33
TLN1 0.03 0.016 -10000 0 0 113 113
PXN -0.032 0.015 0.12 3 -10000 0 3
PIK3R1 0.034 0.013 -10000 0 0 69 69
ARF6/GTP 0.047 0.057 -10000 0 -0.12 1 1
cell adhesion 0.042 0.055 0.18 9 -0.12 10 19
CRKL/CBL 0.053 0.016 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.043 0.033 0.17 13 -10000 0 13
ITGB1 0.029 0.017 -10000 0 0 131 131
ITGB7 0.038 0.007 -10000 0 0 18 18
ARF6/GDP 0.036 0.024 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.011 0.083 -10000 0 -0.12 112 112
p130Cas/Crk/Dock1 0.03 0.035 -10000 0 -0.11 16 16
VCAM1 0.024 0.019 -10000 0 0 196 196
alpha4/beta1 Integrin/Paxillin/Talin 0.044 0.057 0.19 9 -0.12 10 19
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.055 0.19 13 -10000 0 13
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.049 0.054 -10000 0 -0.18 13 13
CBL 0.038 0.006 -10000 0 0 11 11
PRKACA 0.036 0.01 -10000 0 0 36 36
GIT1 0.038 0.005 -10000 0 0 9 9
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.044 0.057 0.19 9 -0.12 10 19
Rac1/GTP -0.053 0.16 -10000 0 -0.42 64 64
BMP receptor signaling

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.061 0.073 -10000 0 -0.12 11 11
SMAD6-7/SMURF1 0.04 0.041 -10000 0 -0.12 2 2
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.024 0.16 -10000 0 -0.47 51 51
SMAD4 0.034 0.013 -10000 0 0 62 62
SMAD5 -0.032 0.099 -10000 0 -0.34 38 38
BMP7/USAG1 0.029 0.029 -10000 0 -10000 0 0
SMAD5/SKI -0.029 0.11 -10000 0 -0.32 48 48
SMAD1 -0.035 0.14 -10000 0 -0.42 45 45
BMP2 0.027 0.018 -10000 0 0 154 154
SMAD1/SMAD1/SMAD4 -0.015 0.12 -10000 0 -0.39 36 36
BMPR1A 0.026 0.018 -10000 0 0 168 168
BMPR1B 0.038 0.006 -10000 0 0 12 12
BMPR1A-1B/BAMBI 0.023 0.063 -10000 0 -0.12 56 56
AHSG 0.037 0.009 -10000 0 0 26 26
CER1 0.034 0.014 -10000 0 0 71 71
BMP2-4/CER1 0.039 0.055 -10000 0 -0.12 34 34
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.014 0.079 -10000 0 -0.22 43 43
BMP2-4 (homodimer) 0.028 0.049 -10000 0 -0.13 34 34
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.053 0.067 -10000 0 -0.12 12 12
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.023 0.019 -10000 0 0 214 214
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.018 0.07 -10000 0 -0.17 62 62
BMP2-4/USAG1 0.028 0.045 -10000 0 -0.12 13 13
SMAD6/SMURF1/SMAD5 -0.018 0.095 -10000 0 -0.31 36 36
SOSTDC1 0.022 0.019 -10000 0 0 227 227
BMP7/BMPR2/BMPR1A-1B 0.053 0.064 -10000 0 -0.12 13 13
SKI 0.037 0.009 -10000 0 0 26 26
BMP6 (homodimer) 0.037 0.009 -10000 0 0 29 29
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.036 0.011 -10000 0 0 40 40
MAP3K7 0.035 0.011 -10000 0 0 47 47
BMP2-4/CHRD 0.04 0.055 -10000 0 -0.12 32 32
SMAD5/SMAD5/SMAD4 -0.03 0.11 -10000 0 -0.32 51 51
MAPK1 0.035 0.011 -10000 0 0 47 47
TAK1/TAB family 0.005 0.062 -10000 0 -0.19 23 23
BMP7 (homodimer) 0.033 0.014 -10000 0 0 73 73
NUP214 0.037 0.008 -10000 0 0 23 23
BMP6/FETUA 0.052 0.017 -10000 0 -10000 0 0
SMAD1/SKI -0.018 0.15 0.23 1 -0.4 45 46
SMAD6 0.038 0.006 -10000 0 0 14 14
CTDSP2 0.032 0.015 -10000 0 0 87 87
BMP2-4/FETUA 0.041 0.055 -10000 0 -0.12 33 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.034 0.013 -10000 0 0 70 70
BMPR2 (homodimer) 0.038 0.006 -10000 0 0 13 13
GADD34/PP1CA 0.054 0.053 -10000 0 -0.12 30 30
BMPR1A-1B (homodimer) 0.037 0.033 -10000 0 -0.13 6 6
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.02 0.15 0.23 1 -0.4 48 49
SMAD6-7/SMURF1/SMAD1 -0.005 0.13 -10000 0 -0.39 37 37
SMAD6/SMURF1 0.023 0.019 -10000 0 0 214 214
BAMBI 0.02 0.019 -10000 0 0 250 250
SMURF2 0.037 0.008 -10000 0 0 20 20
BMP2-4/CHRDL1 0.026 0.042 -10000 0 -0.1 34 34
BMP2-4/GREM1 0.035 0.055 -10000 0 -0.12 33 33
SMAD7 0.035 0.011 -10000 0 0 48 48
SMAD8A/SMAD8A/SMAD4 -0.017 0.17 -10000 0 -0.44 63 63
SMAD1/SMAD6 -0.02 0.13 0.23 1 -0.4 37 38
TAK1/SMAD6 0.03 0.034 -10000 0 -0.13 7 7
BMP7 0.033 0.014 -10000 0 0 73 73
BMP6 0.037 0.009 -10000 0 0 29 29
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.007 0.061 -10000 0 -0.22 19 19
PPM1A 0.036 0.01 -10000 0 0 37 37
SMAD1/SMURF2 -0.019 0.15 0.23 1 -0.41 46 47
SMAD7/SMURF1 0.029 0.031 -10000 0 -0.13 2 2
CTDSPL 0.038 0.007 -10000 0 0 15 15
PPP1CA 0.037 0.008 -10000 0 0 22 22
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.038 0.007 -10000 0 0 16 16
PPP1R15A 0.034 0.013 -10000 0 0 61 61
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.014 0.071 -10000 0 -0.21 33 33
CHRD 0.037 0.009 -10000 0 0 27 27
BMPR2 0.038 0.006 -10000 0 0 13 13
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.069 -10000 0 -0.18 57 57
BMP4 0.035 0.012 -10000 0 0 56 56
FST 0.035 0.012 -10000 0 0 51 51
BMP2-4/NOG 0.026 0.042 -10000 0 -0.1 34 34
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.048 0.065 -10000 0 -0.12 7 7
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.028 0.036 0.13 8 -10000 0 8
CRKL 0.037 0.009 -10000 0 0 32 32
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
DOCK1 0.026 0.019 -10000 0 0 175 175
ITGA4 0.038 0.006 -10000 0 0 13 13
alpha4/beta7 Integrin/MAdCAM1 0.084 0.041 -10000 0 -0.12 4 4
EPO 0.023 0.019 -10000 0 0 214 214
alpha4/beta7 Integrin 0.055 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.037 0.008 -10000 0 0 25 25
alpha4/beta1 Integrin 0.042 0.026 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.032 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.019 0.11 -10000 0 -0.34 33 33
PIK3CA 0.033 0.014 -10000 0 0 79 79
PI3K 0.023 0.07 -10000 0 -0.14 72 72
ARF6 0.036 0.01 -10000 0 0 33 33
JAK2 0.009 0.025 -10000 0 -10000 0 0
PXN 0.038 0.006 -10000 0 0 11 11
PIK3R1 0.034 0.013 -10000 0 0 69 69
MADCAM1 0.036 0.011 -10000 0 0 41 41
cell adhesion 0.081 0.04 -10000 0 -0.12 4 4
CRKL/CBL 0.053 0.016 -10000 0 -10000 0 0
ITGB1 0.029 0.017 -10000 0 0 131 131
SRC -0.038 0.062 0.21 5 -10000 0 5
ITGB7 0.038 0.007 -10000 0 0 18 18
RAC1 0.023 0.019 -10000 0 0 209 209
alpha4/beta1 Integrin/VCAM1 0.007 0.077 -10000 0 -0.11 123 123
p130Cas/Crk/Dock1 -0.037 0.071 0.22 5 -0.23 1 6
VCAM1 0.024 0.019 -10000 0 0 196 196
RHOA 0.037 0.008 -10000 0 0 24 24
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.06 -10000 0 -10000 0 0
BCAR1 -0.036 0.055 0.2 5 -10000 0 5
EPOR 0.036 0.01 -10000 0 0 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.038 0.006 -10000 0 0 11 11
GIT1 0.038 0.005 -10000 0 0 9 9
Rac1/GTP -0.02 0.11 -10000 0 -0.35 33 33
Ephrin B reverse signaling

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
EFNB2 0.03 0.016 -10000 0 0 118 118
EPHB2 0.036 0.011 0.062 1 0 43 44
EFNB1 -0.03 0.022 0.12 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.044 0.054 -10000 0 -0.15 6 6
Ephrin B2/EPHB1-2 0.034 0.056 -10000 0 -0.098 50 50
neuron projection morphogenesis -0.004 0.051 -10000 0 -0.16 1 1
Ephrin B1/EPHB1-2/Tiam1 0.058 0.052 -10000 0 -0.12 10 10
DNM1 0.037 0.01 -10000 0 0 30 30
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.055 0.15 0.22 1 -0.49 51 52
YES1 -0.046 0.22 -10000 0 -0.72 49 49
Ephrin B1/EPHB1-2/NCK2 0.062 0.048 -10000 0 -0.12 4 4
PI3K -0.011 0.18 -10000 0 -0.53 50 50
mol:GDP 0.056 0.051 -10000 0 -0.12 10 10
ITGA2B 0.039 0.004 -10000 0 0 5 5
endothelial cell proliferation 0.015 0.042 -10000 0 -0.1 38 38
FYN -0.056 0.23 -10000 0 -0.74 48 48
MAP3K7 -0.047 0.15 -10000 0 -0.52 47 47
FGR -0.047 0.22 -10000 0 -0.7 51 51
TIAM1 0.035 0.012 -10000 0 0 50 50
PIK3R1 0.034 0.013 -10000 0 0 69 69
RGS3 0.037 0.008 -10000 0 0 25 25
cell adhesion -0.056 0.16 -10000 0 -0.51 50 50
LYN -0.053 0.22 -10000 0 -0.71 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.053 0.2 -10000 0 -0.65 51 51
Ephrin B1/EPHB1-2 -0.041 0.16 -10000 0 -0.56 45 45
SRC -0.045 0.21 -10000 0 -0.69 49 49
ITGB3 0.038 0.005 -10000 0 0 7 7
EPHB1 0.032 0.016 -10000 0 0 98 98
EPHB4 0.023 0.019 -10000 0 0 214 214
RAC1 0.023 0.019 -10000 0 0 209 209
Ephrin B2/EPHB4 0.015 0.042 -10000 0 -0.1 38 38
alphaIIb/beta3 Integrin 0.057 0.007 -10000 0 -10000 0 0
BLK -0.049 0.22 -10000 0 -0.7 51 51
HCK -0.057 0.22 -10000 0 -0.71 49 49
regulation of stress fiber formation -0.06 0.046 0.12 4 -10000 0 4
MAPK8 -0.06 0.14 -10000 0 -0.48 51 51
Ephrin B1/EPHB1-2/RGS3 0.067 0.039 -10000 0 -0.12 5 5
endothelial cell migration 0.026 0.16 0.23 46 -0.44 37 83
NCK2 0.037 0.008 -10000 0 0 20 20
PTPN13 0.036 0.015 -10000 0 0 61 61
regulation of focal adhesion formation -0.06 0.046 0.12 4 -10000 0 4
chemotaxis -0.065 0.038 0.12 5 -10000 0 5
PIK3CA 0.033 0.014 -10000 0 0 79 79
Rac1/GTP 0.038 0.047 -10000 0 -0.14 7 7
angiogenesis -0.042 0.16 -10000 0 -0.55 47 47
LCK -0.045 0.22 -10000 0 -0.69 51 51
FAS signaling pathway (CD95)

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
SPTAN1 -0.021 0.06 0.22 8 -0.22 24 32
RFC1 -0.025 0.053 0.21 3 -0.22 27 30
PRKDC -0.019 0.06 0.21 7 -0.22 25 32
RIPK1 0.021 0.034 -10000 0 -0.048 96 96
CASP7 -0.16 0.29 -10000 0 -0.58 157 157
FASLG/FAS/FADD/FAF1 -0.006 0.084 0.21 8 -0.17 32 40
MAP2K4 -0.044 0.16 0.25 7 -0.34 47 54
mol:ceramide 0.003 0.1 0.21 20 -0.25 19 39
GSN -0.011 0.067 0.21 12 -0.23 22 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.012 0.1 0.21 12 -0.27 23 35
FAS 0.023 0.022 -10000 0 -10000 0 0
BID -0.035 0.037 0.098 27 -10000 0 27
MAP3K1 -0.098 0.2 0.24 2 -0.39 149 151
MAP3K7 0.037 0.012 -10000 0 -10000 0 0
RB1 -0.021 0.048 0.23 1 -0.22 25 26
CFLAR 0.022 0.034 -10000 0 -0.044 103 103
HGF/MET 0.031 0.049 -10000 0 -0.12 20 20
ARHGDIB -0.016 0.061 0.22 10 -0.23 21 31
FADD 0.042 0.01 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.069 0.22 22 -0.22 14 36
NFKB1 0.04 0.12 -10000 0 -0.62 11 11
MAPK8 -0.037 0.16 0.29 6 -0.39 21 27
DFFA -0.022 0.052 0.22 3 -0.22 26 29
DNA fragmentation during apoptosis -0.02 0.049 0.22 2 -0.22 24 26
FAS/FADD/MET 0.023 0.05 -10000 0 -0.12 24 24
CFLAR/RIP1 0.032 0.048 -10000 0 -0.065 93 93
FAIM3 0.036 0.01 -10000 0 -0.006 24 24
FAF1 0.041 0.015 -10000 0 -10000 0 0
PARP1 -0.024 0.052 0.22 2 -0.22 28 30
DFFB -0.021 0.049 0.22 2 -0.22 24 26
CHUK 0.021 0.11 0.28 1 -0.59 11 12
FASLG 0.043 0.012 -10000 0 -10000 0 0
FAS/FADD 0.026 0.053 -10000 0 -0.13 35 35
HGF 0.022 0.019 -10000 0 0 216 216
LMNA -0.027 0.055 0.19 10 -0.21 24 34
CASP6 -0.022 0.051 0.2 3 -0.22 26 29
CASP10 0.043 0.007 -10000 0 -10000 0 0
CASP3 -0.012 0.055 -10000 0 -0.23 28 28
PTPN13 0.034 0.013 -10000 0 0 60 60
CASP8 -0.034 0.025 0.11 13 -10000 0 13
IL6 0.038 0.16 -10000 0 -0.67 4 4
MET 0.021 0.019 -10000 0 0 239 239
ICAD/CAD -0.029 0.052 0.25 4 -0.22 24 28
FASLG/FAS/FADD/FAF1/Caspase 10 0.002 0.1 0.21 20 -0.25 19 39
activation of caspase activity by cytochrome c -0.035 0.036 0.098 27 -10000 0 27
PAK2 -0.013 0.061 0.22 11 -0.22 24 35
BCL2 0.037 0.008 -10000 0 0 21 21
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.047 0.016 -10000 0 -10000 0 0
cell-cell adhesion 0.033 0.045 0.19 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.064 0.092 -10000 0 -0.13 70 70
ITSN1 0.038 0.007 -10000 0 0 19 19
PIK3CA 0.033 0.014 -10000 0 0 79 79
SHC1 0.035 0.012 -10000 0 0 56 56
Ephrin B1/EPHB3 0.047 0.017 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.041 0.026 -10000 0 -0.1 6 6
HRAS/GDP 0.002 0.081 0.2 4 -0.22 33 37
Ephrin B/EPHB1/GRB7 0.073 0.078 -10000 0 -0.12 45 45
Endophilin/SYNJ1 -0.037 0.063 0.18 17 -10000 0 17
KRAS 0.036 0.011 -10000 0 0 40 40
Ephrin B/EPHB1/Src 0.061 0.08 -10000 0 -0.12 49 49
endothelial cell migration 0.019 0.066 -10000 0 -0.13 52 52
GRB2 0.037 0.009 -10000 0 0 26 26
GRB7 0.038 0.007 -10000 0 0 17 17
PAK1 -0.042 0.073 0.28 8 -10000 0 8
HRAS 0.036 0.01 -10000 0 0 39 39
RRAS -0.035 0.064 0.21 12 -10000 0 12
DNM1 0.037 0.009 -10000 0 0 30 30
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.027 0.074 0.19 21 -10000 0 21
lamellipodium assembly -0.033 0.045 -10000 0 -0.19 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.013 0.074 -10000 0 -0.28 14 14
PIK3R1 0.034 0.013 -10000 0 0 69 69
EPHB2 0.036 0.011 -10000 0 0 43 43
EPHB3 0.035 0.012 -10000 0 0 55 55
EPHB1 0.031 0.015 -10000 0 0 98 98
EPHB4 0.023 0.019 -10000 0 0 214 214
mol:GDP 0.028 0.12 0.19 129 -0.25 27 156
Ephrin B/EPHB2 0.055 0.07 -10000 0 -0.11 62 62
Ephrin B/EPHB3 0.055 0.069 -10000 0 -0.11 60 60
JNK cascade -0.014 0.086 0.25 28 -10000 0 28
Ephrin B/EPHB1 0.056 0.067 -10000 0 -0.11 52 52
RAP1/GDP 0.04 0.13 0.2 144 -0.28 12 156
EFNB2 0.03 0.016 -10000 0 0 118 118
EFNB3 0.037 0.008 -10000 0 0 25 25
EFNB1 0.039 0.002 -10000 0 0 2 2
Ephrin B2/EPHB1-2 0.034 0.058 -10000 0 -0.11 50 50
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.038 0.006 -10000 0 0 13 13
CDC42/GTP 0.052 0.083 -10000 0 -0.2 26 26
Rap1/GTP -0.06 0.056 0.059 6 -0.2 21 27
axon guidance 0.047 0.016 -10000 0 -10000 0 0
MAPK3 -0.01 0.073 0.19 5 -0.29 11 16
MAPK1 -0.009 0.077 0.21 6 -0.29 15 21
Rac1/GDP -0.008 0.097 0.24 25 -0.3 12 37
actin cytoskeleton reorganization -0.044 0.063 -10000 0 -0.23 19 19
CDC42/GDP 0.044 0.14 0.22 142 -0.3 11 153
PI3K 0.022 0.07 -10000 0 -0.13 52 52
EFNA5 0.038 0.006 -10000 0 0 12 12
Ephrin B2/EPHB4 0.015 0.042 -10000 0 -0.1 38 38
Ephrin B/EPHB2/Intersectin/N-WASP -0.001 0.056 -10000 0 -0.27 7 7
CDC42 0.037 0.009 -10000 0 0 27 27
RAS family/GTP -0.067 0.064 -10000 0 -0.23 23 23
PTK2 -0.014 0.087 0.54 12 -10000 0 12
MAP4K4 -0.014 0.087 0.25 28 -10000 0 28
SRC 0.034 0.013 -10000 0 0 65 65
KALRN 0.037 0.009 -10000 0 0 28 28
Intersectin/N-WASP 0.03 0.033 -10000 0 -0.13 6 6
neuron projection morphogenesis 0.074 0.18 0.34 139 -0.28 2 141
MAP2K1 -0.007 0.072 0.16 2 -0.28 14 16
WASL 0.023 0.019 -10000 0 0 214 214
Ephrin B1/EPHB1-2/NCK1 0.086 0.043 -10000 0 -0.12 10 10
cell migration -0.012 0.09 0.23 3 -0.31 14 17
NRAS 0.034 0.013 -10000 0 0 66 66
SYNJ1 -0.037 0.064 0.19 17 -10000 0 17
PXN 0.038 0.006 -10000 0 0 11 11
TF -0.05 0.062 0.17 7 -10000 0 7
HRAS/GTP 0.035 0.082 -10000 0 -0.19 20 20
Ephrin B1/EPHB1-2 0.055 0.037 -10000 0 -0.1 6 6
cell adhesion mediated by integrin 0.026 0.05 0.16 2 -0.21 8 10
RAC1 0.023 0.019 -10000 0 0 209 209
mol:GTP 0.044 0.08 -10000 0 -0.14 58 58
RAC1-CDC42/GTP -0.035 0.053 -10000 0 -0.2 11 11
RASA1 0.036 0.01 -10000 0 0 37 37
RAC1-CDC42/GDP -0.011 0.096 0.23 24 -0.31 11 35
ruffle organization 0.088 0.18 0.3 181 -0.24 5 186
NCK1 0.037 0.009 -10000 0 0 31 31
receptor internalization -0.045 0.059 0.17 16 -0.18 2 18
Ephrin B/EPHB2/KALRN 0.069 0.083 -10000 0 -0.12 59 59
ROCK1 -0.017 0.056 0.18 25 -10000 0 25
RAS family/GDP -0.047 0.065 -10000 0 -0.22 35 35
Rac1/GTP -0.031 0.05 -10000 0 -0.2 11 11
Ephrin B/EPHB1/Src/Paxillin 0.004 0.063 -10000 0 -0.23 4 4
IL6-mediated signaling events

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
BCL2L1 0.097 0.3 0.63 37 -0.73 23 60
CRP 0.076 0.28 0.6 26 -0.73 22 48
cell cycle arrest 0.07 0.32 0.6 35 -0.8 28 63
TIMP1 0.027 0.38 0.62 31 -0.76 73 104
IL6ST 0.027 0.042 0.12 7 -0.063 28 35
Rac1/GDP 0.04 0.12 0.34 29 -0.32 9 38
AP1 0.023 0.19 0.36 10 -0.54 34 44
GAB2 0.034 0.018 0.079 1 -0.039 15 16
TNFSF11 0.074 0.28 0.61 22 -0.74 22 44
HSP90B1 0.009 0.28 -10000 0 -0.93 37 37
GAB1 0.033 0.018 -10000 0 -0.037 15 15
MAPK14 0.042 0.084 0.34 1 -0.31 2 3
AKT1 -0.015 0.17 0.26 7 -0.51 34 41
FOXO1 -0.021 0.17 0.3 4 -0.52 34 38
MAP2K6 0.027 0.078 0.25 8 -0.29 5 13
mol:GTP 0 0.005 0.025 1 -10000 0 1
MAP2K4 0.066 0.19 0.44 65 -0.39 13 78
MITF 0.036 0.1 0.29 30 -0.29 9 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.013 -10000 0 0 62 62
A2M -0.076 0.34 -10000 0 -1.1 46 46
CEBPB 0.031 0.026 0.17 1 -0.12 7 8
GRB2/SOS1/GAB family/SHP2 0.025 0.13 0.27 7 -0.44 24 31
STAT3 0.055 0.32 0.59 35 -0.87 28 63
STAT1 0.022 0.068 -10000 0 -0.71 3 3
CEBPD 0.043 0.35 0.61 23 -0.86 43 66
PIK3CA 0.033 0.015 0.075 2 -0.043 2 4
PI3K 0.024 0.071 -10000 0 -0.14 73 73
JUN 0.036 0.011 -10000 0 0 43 43
PIAS3/MITF 0.085 0.12 0.31 38 -0.3 9 47
MAPK11 0.035 0.08 0.34 1 -0.31 2 3
STAT3 (dimer)/FOXO1 -0.008 0.28 0.52 30 -0.62 47 77
GRB2/SOS1/GAB family 0.047 0.12 0.26 7 -0.32 23 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.017 0.11 0.22 25 -0.29 30 55
GRB2 0.036 0.016 -10000 0 -0.037 16 16
JAK2 0.032 0.015 -10000 0 0 89 89
LBP 0.092 0.29 0.59 38 -0.68 25 63
PIK3R1 0.034 0.015 -10000 0 -0.041 3 3
JAK1 0.028 0.034 -10000 0 -0.057 31 31
MYC 0.033 0.38 0.62 30 -0.85 60 90
FGG 0.075 0.28 0.59 27 -0.72 23 50
macrophage differentiation 0.07 0.32 0.6 35 -0.8 28 63
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.049 0.08 -10000 0 -0.19 5 5
JUNB 0.075 0.32 0.61 38 -0.82 29 67
FOS 0.026 0.018 -10000 0 0 168 168
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.039 0.1 0.3 22 -0.29 9 31
STAT1/PIAS1 0.091 0.14 0.36 37 -0.35 7 44
GRB2/SOS1/GAB family/SHP2/PI3K 0 0.16 0.23 2 -0.5 33 35
STAT3 (dimer) 0.058 0.32 0.59 35 -0.85 28 63
PRKCD 0.13 0.25 0.48 96 -0.49 16 112
IL6R 0.027 0.036 -10000 0 -0.053 53 53
SOCS3 0.055 0.093 0.48 4 -10000 0 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.048 0.092 0.22 7 -0.17 34 41
Rac1/GTP 0.037 0.13 0.34 31 -0.36 9 40
HCK 0.026 0.019 -10000 0 0 172 172
MAPKKK cascade 0.022 0.18 0.32 6 -0.56 33 39
bone resorption 0.076 0.28 0.6 24 -0.69 22 46
IRF1 0.071 0.32 0.62 35 -0.82 28 63
mol:GDP 0.036 0.11 0.31 30 -0.3 8 38
SOS1 0.001 0.005 0.027 5 -10000 0 5
VAV1 0.034 0.11 0.31 27 -0.3 8 35
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.013 0.071 -10000 0 -0.34 9 9
PTPN11 0.015 0.095 -10000 0 -0.67 8 8
IL6/IL6RA 0.02 0.041 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.048 0.077 0.18 2 -0.15 35 37
gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.069 0.18 1 -0.13 23 24
IL6 0.011 0.031 0.1 3 -0.057 8 11
PIAS3 0.037 0.008 -10000 0 0 24 24
PTPRE -0.005 0.039 -10000 0 -0.1 17 17
PIAS1 0.037 0.009 -10000 0 0 27 27
RAC1 0.023 0.021 -10000 0 -0.001 215 215
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.022 0.063 0.2 13 -0.25 4 17
LMO4 0.028 0.043 0.11 10 -0.062 30 40
STAT3 (dimer)/PIAS3 0.053 0.3 0.56 21 -0.79 28 49
MCL1 -0.014 0.16 0.42 2 -0.68 17 19
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.025 0.051 0.17 10 -0.19 8 18
DAPP1 -0.018 0.13 0.2 9 -0.29 62 71
Src family/SYK family/BLNK-LAT/BTK-ITK -0.039 0.19 0.27 13 -0.47 56 69
mol:DAG -0.004 0.1 0.2 43 -0.21 38 81
HRAS 0.038 0.022 0.086 2 -0.042 21 23
RAP1A 0.037 0.023 -10000 0 -0.043 33 33
ARF5/GDP -0.002 0.09 0.18 2 -0.31 27 29
PLCG2 0.034 0.013 -10000 0 0 64 64
PLCG1 0.034 0.013 -10000 0 0 70 70
ARF5 0.022 0.019 -10000 0 0 222 222
mol:GTP -0.027 0.056 0.3 5 -0.17 9 14
ARF1/GTP -0.021 0.047 0.42 1 -0.18 12 13
RHOA 0.037 0.008 -10000 0 0 24 24
YES1 0.035 0.011 -10000 0 0 47 47
RAP1A/GTP -0.028 0.049 0.15 14 -0.17 9 23
ADAP1 -0.026 0.053 0.16 16 -0.17 9 25
ARAP3 -0.026 0.055 0.29 5 -0.17 9 14
INPPL1 0.038 0.007 -10000 0 0 15 15
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.035 0.012 -10000 0 0 52 52
ARHGEF7 0.034 0.013 -10000 0 0 65 65
ARF1 0.037 0.008 -10000 0 0 25 25
NRAS 0.037 0.02 -10000 0 -0.043 11 11
FYN 0.032 0.015 -10000 0 0 95 95
ARF6 0.036 0.01 -10000 0 0 33 33
FGR 0.034 0.012 -10000 0 0 59 59
mol:Ca2+ 0.009 0.069 0.16 52 -0.12 10 62
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 0 50 50
ZAP70 0.039 0.003 -10000 0 0 3 3
mol:IP3 -0.004 0.074 0.19 26 -0.17 14 40
LYN 0.033 0.014 -10000 0 0 76 76
ARF1/GDP 0.011 0.11 0.2 3 -0.33 34 37
RhoA/GDP 0.004 0.099 0.22 15 -0.24 16 31
PDK1/Src/Hsp90 0.063 0.033 -10000 0 -0.12 2 2
BLNK 0.021 0.019 -10000 0 0 241 241
actin cytoskeleton reorganization 0.013 0.11 0.22 31 -0.29 22 53
SRC 0.034 0.013 -10000 0 0 65 65
PLEKHA2 -0.019 0.031 0.11 28 -10000 0 28
RAC1 0.023 0.019 -10000 0 0 209 209
PTEN 0.022 0.026 -10000 0 -0.063 4 4
HSP90AA1 0.036 0.01 -10000 0 0 39 39
ARF6/GTP -0.03 0.06 0.19 15 -0.18 9 24
RhoA/GTP -0.031 0.061 0.3 5 -0.21 2 7
Src family/SYK family/BLNK-LAT -0.047 0.15 0.2 1 -0.35 75 76
BLK 0.038 0.007 -10000 0 0 19 19
PDPK1 0.038 0.005 -10000 0 0 7 7
CYTH1 -0.026 0.053 0.16 16 -0.17 9 25
HCK 0.026 0.018 -10000 0 0 170 170
CYTH3 -0.026 0.053 0.16 16 -0.17 9 25
CYTH2 -0.026 0.053 0.16 16 -0.17 9 25
KRAS 0.036 0.024 0.088 1 -0.042 29 30
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.011 0.042 0.22 3 -0.26 6 9
SGK1 -0.002 0.045 0.25 3 -0.21 12 15
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.11 0.2 4 -0.32 35 39
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.033 0.014 -10000 0 0 78 78
ARF6/GDP -0.031 0.068 0.25 7 -0.23 16 23
mol:PI-3-4-5-P3 -0.027 0.054 0.17 15 -0.17 9 24
ARAP3/RAP1A/GTP -0.028 0.05 0.15 14 -0.17 9 23
VAV1 0.036 0.011 -10000 0 0 44 44
mol:PI-3-4-P2 -0.017 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.074 0.097 0.21 135 -0.13 35 170
PLEKHA1 -0.013 0.029 0.11 22 -10000 0 22
Rac1/GDP 0.001 0.091 0.21 2 -0.3 28 30
LAT 0.038 0.006 -10000 0 0 11 11
Rac1/GTP -0.001 0.14 0.17 4 -0.43 36 40
ITK -0.031 0.054 0.32 3 -0.18 9 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.021 0.12 0.26 20 -0.29 41 61
LCK 0.037 0.008 -10000 0 0 20 20
BTK -0.031 0.057 0.28 5 -0.18 9 14
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.031 0.12 0.27 50 -0.29 20 70
PDGFB-D/PDGFRB/SLAP 0.022 0.068 -10000 0 -0.14 71 71
PDGFB-D/PDGFRB/APS/CBL 0.048 0.023 -10000 0 -0.1 7 7
AKT1 -0.032 0.1 0.28 16 -0.24 11 27
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.12 0.28 44 -0.32 20 64
PIK3CA 0.033 0.014 -10000 0 0 79 79
FGR 0.012 0.1 0.28 8 -0.44 13 21
mol:Ca2+ 0.027 0.12 0.26 44 -0.36 19 63
MYC 0.037 0.27 0.41 57 -0.64 52 109
SHC1 0.035 0.012 -10000 0 0 56 56
HRAS/GDP -0.021 0.085 0.17 65 -0.19 8 73
LRP1/PDGFRB/PDGFB 0.052 0.054 -10000 0 -0.12 29 29
GRB10 0.02 0.02 -10000 0 0 254 254
PTPN11 0.038 0.007 -10000 0 0 17 17
GO:0007205 0.027 0.12 0.26 44 -0.36 19 63
PTEN 0.024 0.019 -10000 0 0 196 196
GRB2 0.037 0.009 -10000 0 0 26 26
GRB7 0.038 0.007 -10000 0 0 17 17
PDGFB-D/PDGFRB/SHP2 0.05 0.034 -10000 0 -0.11 16 16
PDGFB-D/PDGFRB/GRB10 0.02 0.048 -10000 0 -0.13 31 31
cell cycle arrest 0.022 0.068 -10000 0 -0.14 71 71
HRAS 0.036 0.01 -10000 0 0 39 39
HIF1A -0.039 0.093 0.24 16 -0.24 12 28
GAB1 0.025 0.14 0.32 30 -0.36 29 59
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.15 0.35 37 -0.33 29 66
PDGFB-D/PDGFRB 0.054 0.059 0.18 5 -0.099 24 29
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.04 -10000 0 -0.12 23 23
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.11 0.23 12 -0.29 37 49
positive regulation of MAPKKK cascade 0.05 0.033 -10000 0 -0.11 16 16
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:IP3 0.027 0.12 0.26 44 -0.36 19 63
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.027 0.027 -10000 0 -0.029 87 87
PDGFB-D/PDGFRB/GRB7 0.053 0.024 -10000 0 -0.13 4 4
SHB 0.035 0.012 -10000 0 0 58 58
BLK 0.02 0.082 0.26 10 -0.38 6 16
PTPN2 0.031 0.027 0.084 1 -0.039 56 57
PDGFB-D/PDGFRB/SNX15 0.052 0.027 -10000 0 -0.094 11 11
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.013 0.18 0.34 32 -0.42 42 74
CBL 0.038 0.006 -10000 0 0 11 11
PDGFB-D/PDGFRB/DEP1 0.052 0.028 -10000 0 -0.096 11 11
LCK 0.022 0.076 0.27 9 -0.34 4 13
PDGFRB 0.032 0.027 0.079 3 -0.04 52 55
ACP1 0.037 0.009 -10000 0 0 28 28
HCK -0.039 0.16 0.24 1 -0.48 54 55
ABL1 0.02 0.13 0.27 43 -0.32 30 73
PDGFB-D/PDGFRB/CBL 0.023 0.15 0.32 21 -0.4 28 49
PTPN1 0.028 0.026 -10000 0 -0.04 48 48
SNX15 0.038 0.005 -10000 0 0 9 9
STAT3 0.036 0.011 -10000 0 0 42 42
STAT1 0.036 0.011 -10000 0 0 41 41
cell proliferation 0.045 0.26 0.39 67 -0.58 52 119
SLA 0.029 0.017 -10000 0 0 136 136
actin cytoskeleton reorganization -0.023 0.089 0.2 57 -0.2 1 58
SRC 0.011 0.058 0.32 2 -0.63 1 3
PI3K -0.059 0.05 -10000 0 -0.19 26 26
PDGFB-D/PDGFRB/GRB7/SHC 0.064 0.039 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.12 0.28 44 -0.33 20 64
LYN -0.027 0.16 0.26 3 -0.46 50 53
LRP1 0.033 0.014 -10000 0 0 79 79
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.038 0.005 -10000 0 0 10 10
STAT5A 0.038 0.005 -10000 0 0 10 10
NCK1-2/p130 Cas 0.06 0.074 0.2 1 -0.14 20 21
SPHK1 0.033 0.021 0.074 1 -0.036 26 27
EDG1 0.001 0.005 0.029 3 -10000 0 3
mol:DAG 0.027 0.12 0.26 44 -0.36 19 63
PLCG1 0.027 0.12 0.28 32 -0.37 19 51
NHERF/PDGFRB 0.066 0.037 -10000 0 -0.12 11 11
YES1 -0.006 0.15 0.3 2 -0.55 27 29
cell migration 0.066 0.037 -10000 0 -0.12 11 11
SHC/Grb2/SOS1 0.061 0.07 -10000 0 -0.14 17 17
SLC9A3R2 0.038 0.005 -10000 0 0 7 7
SLC9A3R1 0.036 0.01 -10000 0 0 37 37
NHERF1-2/PDGFRB/PTEN 0.046 0.067 -10000 0 -0.11 11 11
FYN -0.047 0.19 0.28 3 -0.45 75 78
DOK1 -0.014 0.082 0.18 67 -10000 0 67
HRAS/GTP 0.023 0.025 -10000 0 -0.11 16 16
PDGFB 0.036 0.01 -10000 0 0 39 39
RAC1 0.059 0.21 0.38 68 -0.41 45 113
PRKCD -0.012 0.083 0.19 64 -10000 0 64
FER -0.015 0.081 0.18 61 -10000 0 61
MAPKKK cascade -0.006 0.09 0.17 79 -0.18 1 80
RASA1 -0.013 0.078 0.18 63 -0.2 1 64
NCK1 0.037 0.009 -10000 0 0 31 31
NCK2 0.037 0.008 -10000 0 0 20 20
p62DOK/Csk -0.022 0.082 0.18 61 -0.18 3 64
PDGFB-D/PDGFRB/SHB 0.048 0.028 -10000 0 -0.13 4 4
chemotaxis 0.02 0.13 0.26 43 -0.32 30 73
STAT1-3-5/STAT1-3-5 0.057 0.081 -10000 0 -0.15 27 27
Bovine Papilomavirus E5/PDGFRB 0.022 0.024 0.077 1 -0.049 26 27
PTPRJ 0.038 0.007 -10000 0 0 16 16
Osteopontin-mediated events

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.028 0.082 0.19 8 -0.24 11 19
NF kappa B1 p50/RelA/I kappa B alpha -0.053 0.13 0.27 4 -0.35 36 40
alphaV/beta3 Integrin/Osteopontin/Src 0.033 0.077 -10000 0 -0.14 76 76
AP1 -0.051 0.14 0.29 20 -0.34 36 56
ILK -0.038 0.074 0.16 8 -0.23 26 34
bone resorption -0.051 0.084 0.22 4 -0.26 16 20
PTK2B 0.038 0.007 -10000 0 0 18 18
PYK2/p130Cas 0.05 0.092 0.23 5 -0.18 38 43
ITGAV 0.033 0.03 -10000 0 -0.061 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.065 -10000 0 -0.13 71 71
alphaV/beta3 Integrin/Osteopontin 0.057 0.093 -10000 0 -0.15 67 67
MAP3K1 -0.036 0.068 0.18 4 -0.21 16 20
JUN 0.034 0.018 -10000 0 -0.011 63 63
MAPK3 -0.039 0.097 0.2 13 -0.26 29 42
MAPK1 -0.037 0.098 0.2 18 -0.27 28 46
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
NFKB1 0.038 0.007 -10000 0 0 18 18
MAPK8 -0.034 0.066 0.18 4 -0.21 16 20
ITGB3 0.034 0.03 -10000 0 -0.061 42 42
NFKBIA -0.045 0.12 0.22 9 -0.35 37 46
FOS 0.024 0.022 -10000 0 -0.035 17 17
CD44 0.03 0.016 -10000 0 0 115 115
CHUK 0.027 0.018 -10000 0 0 155 155
PLAU -0.077 0.26 0.36 8 -0.96 32 40
NF kappa B1 p50/RelA -0.055 0.14 0.28 13 -0.37 32 45
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.038 0.006 -10000 0 0 12 12
alphaV beta3 Integrin 0.045 0.058 -10000 0 -0.12 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.039 0.065 0.18 4 -0.22 21 25
VAV3 -0.034 0.075 0.16 9 -0.23 20 29
MAP3K14 -0.033 0.083 0.19 6 -0.23 16 22
ROCK2 0.037 0.008 -10000 0 0 20 20
SPP1 0.032 0.029 -10000 0 -0.062 31 31
RAC1 0.023 0.019 -10000 0 0 209 209
Rac1/GTP -0.023 0.071 0.17 8 -0.25 10 18
MMP2 -0.07 0.12 0.23 4 -0.32 56 60
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.056 0.055 -10000 0 -0.12 34 34
fibroblast growth factor receptor signaling pathway 0.055 0.054 -10000 0 -0.12 34 34
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.031 0.016 -10000 0 0 102 102
GPC1/SLIT2 0.035 0.044 -10000 0 -0.13 24 24
SMAD2 -0.033 0.058 0.2 15 -10000 0 15
GPC1/PrPc/Cu2+ 0.026 0.052 -10000 0 -0.12 47 47
GPC1/Laminin alpha1 0.018 0.035 -10000 0 -0.11 34 34
TDGF1 0.037 0.008 -10000 0 0 21 21
CRIPTO/GPC1 0.042 0.045 -10000 0 -0.13 28 28
APP/GPC1 0.039 0.052 -10000 0 -0.14 35 35
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.031 0.043 0.12 27 -10000 0 27
FLT1 0.036 0.011 -10000 0 0 40 40
GPC1/TGFB/TGFBR1/TGFBR2 0.055 0.053 -10000 0 -0.12 33 33
SERPINC1 0.038 0.006 -10000 0 0 14 14
FYN -0.026 0.04 0.12 28 -10000 0 28
FGR -0.029 0.045 0.13 29 -10000 0 29
positive regulation of MAPKKK cascade -0.024 0.13 0.25 14 -0.28 53 67
SLIT2 0.031 0.016 -10000 0 0 101 101
GPC1/NRG 0.041 0.047 -10000 0 -0.13 33 33
NRG1 0.038 0.006 -10000 0 0 12 12
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.011 0.084 -10000 0 -0.13 120 120
LYN -0.029 0.043 0.12 27 -10000 0 27
mol:Spermine -0.016 0.006 -10000 0 -10000 0 0
cell growth 0.055 0.054 -10000 0 -0.12 34 34
BMP signaling pathway -0.034 0.013 0 65 -10000 0 65
SRC -0.03 0.044 0.12 27 -10000 0 27
TGFBR1 0.038 0.007 -10000 0 0 19 19
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.019 0.019 -10000 0 0 266 266
GPC1 0.034 0.013 -10000 0 0 65 65
TGFBR1 (dimer) 0.037 0.007 -10000 0 0 19 19
VEGFA 0.025 0.019 -10000 0 0 181 181
BLK -0.033 0.045 0.12 30 -10000 0 30
HCK -0.022 0.042 0.13 23 -10000 0 23
FGF2 0.037 0.008 -10000 0 0 25 25
FGFR1 0.038 0.006 -10000 0 0 12 12
VEGFR1 homodimer 0.036 0.01 -10000 0 0 40 40
TGFBR2 0.037 0.009 -10000 0 0 31 31
cell death 0.039 0.052 -10000 0 -0.14 35 35
ATIII/GPC1 0.041 0.046 -10000 0 -0.13 31 31
PLA2G2A/GPC1 0 0.069 -10000 0 -0.14 91 91
LCK -0.033 0.045 0.12 30 -10000 0 30
neuron differentiation 0.041 0.047 -10000 0 -0.13 33 33
PrPc/Cu2+ 0.017 0.033 -10000 0 -0.11 29 29
APP 0.037 0.009 -10000 0 0 26 26
TGFBR2 (dimer) 0.037 0.009 -10000 0 0 31 31
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.037 0.098 0.35 15 -10000 0 15
CRKL 0.046 0.12 0.27 55 -10000 0 55
mol:DAG 0.022 0.075 0.23 11 -0.21 23 34
HRAS 0.043 0.13 0.25 87 -0.23 2 89
MAPK8 0.013 0.089 0.16 111 -10000 0 111
RAP1A 0.049 0.12 0.26 64 -10000 0 64
GAB1 0.041 0.11 0.28 46 -10000 0 46
MAPK14 0.043 0.12 0.18 198 -10000 0 198
EPO 0.02 0.027 0.098 1 -0.043 30 31
PLCG1 0.022 0.076 0.23 11 -0.22 23 34
EPOR/TRPC2/IP3 Receptors 0.039 0.027 0.1 6 -0.043 31 37
RAPGEF1 0.037 0.008 -10000 0 0 23 23
EPO/EPOR (dimer)/SOCS3 0.046 0.043 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.027 0.11 0.24 46 -10000 0 46
EPO/EPOR (dimer) 0.031 0.038 0.16 1 -10000 0 1
IRS2 0.037 0.11 0.28 46 -10000 0 46
STAT1 0.027 0.081 0.27 10 -0.24 12 22
STAT5B 0.026 0.081 0.25 12 -0.23 15 27
cell proliferation 0.008 0.088 0.15 111 -10000 0 111
GAB1/SHIP/PIK3R1/SHP2/SHC 0.004 0.094 0.18 29 -0.22 3 32
TEC 0.049 0.12 0.27 57 -10000 0 57
SOCS3 0.038 0.005 -10000 0 0 9 9
STAT1 (dimer) 0.027 0.08 0.27 10 -0.23 12 22
JAK2 0.035 0.027 0.1 3 -0.044 23 26
PIK3R1 0.034 0.013 -10000 0 0 69 69
EPO/EPOR (dimer)/JAK2 0.045 0.074 0.26 14 -10000 0 14
EPO/EPOR 0.031 0.038 0.16 1 -10000 0 1
LYN 0.034 0.015 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.11 0.24 49 -10000 0 49
elevation of cytosolic calcium ion concentration 0.039 0.027 0.1 6 -0.043 31 37
SHC1 0.035 0.012 -10000 0 0 56 56
EPO/EPOR (dimer)/LYN 0.036 0.059 0.2 4 -0.13 25 29
mol:IP3 0.022 0.075 0.23 11 -0.21 23 34
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.024 0.12 0.27 37 -0.23 4 41
SH2B3 0.04 0.022 0.1 1 -0.042 8 9
NFKB1 0.043 0.12 0.18 198 -10000 0 198
EPO/EPOR (dimer)/JAK2/SOCS3 0.016 0.031 0.16 17 -10000 0 17
PTPN6 0.047 0.11 0.28 43 -10000 0 43
TEC/VAV2/GRB2 0.037 0.12 0.25 62 -10000 0 62
EPOR 0.039 0.027 0.1 6 -0.043 31 37
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.11 0.24 46 -10000 0 46
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.034 0.013 -10000 0 0 64 64
CRKL/CBL/C3G 0.036 0.12 0.24 59 -10000 0 59
VAV2 0.046 0.12 0.27 54 -10000 0 54
CBL 0.049 0.12 0.27 59 -10000 0 59
SHC/Grb2/SOS1 0.02 0.051 -10000 0 -0.17 7 7
STAT5A 0.026 0.08 0.25 11 -0.21 24 35
GRB2 0.037 0.009 -10000 0 0 26 26
STAT5 (dimer) 0.039 0.087 0.31 13 -0.23 7 20
LYN/PLCgamma2 0.031 0.065 -10000 0 -0.15 52 52
PTPN11 0.038 0.007 -10000 0 0 17 17
BTK 0.047 0.12 0.27 56 -10000 0 56
BCL2 0.041 0.097 0.42 3 -10000 0 3
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.026 0.027 0.12 13 -10000 0 13
BAD/BCL-XL/YWHAZ 0.062 0.05 0.17 58 -0.12 10 68
CDKN1B -0.026 0.13 0.26 3 -0.34 62 65
CDKN1A -0.028 0.13 0.25 1 -0.34 62 63
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.035 0.011 -10000 0 0 46 46
FOXO3 -0.024 0.12 -10000 0 -0.35 54 54
AKT1 -0.02 0.12 -10000 0 -0.34 60 60
BAD 0.038 0.007 -10000 0 0 16 16
AKT3 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.031 0.12 -10000 0 -0.33 66 66
AKT1/ASK1 -0.009 0.13 0.23 1 -0.33 68 69
BAD/YWHAZ 0.065 0.038 -10000 0 -0.12 11 11
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.037 0.009 -10000 0 0 31 31
JNK cascade 0.009 0.13 0.32 68 -0.22 1 69
TSC1 -0.027 0.13 0.24 8 -0.34 62 70
YWHAZ 0.037 0.008 -10000 0 0 23 23
AKT1/RAF1 -0.003 0.14 0.24 2 -0.34 68 70
EP300 0.035 0.012 -10000 0 0 52 52
mol:GDP -0.021 0.12 -10000 0 -0.34 63 63
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.031 0.13 0.26 2 -0.34 66 68
YWHAQ 0.038 0.005 -10000 0 0 9 9
TBC1D4 -0.008 0.029 0.15 15 -10000 0 15
MAP3K5 0.032 0.015 -10000 0 0 94 94
MAPKAP1 0.036 0.01 -10000 0 0 33 33
negative regulation of cell cycle 0.007 0.11 0.33 31 -0.17 4 35
YWHAH 0.033 0.014 -10000 0 0 76 76
AKT1S1 -0.022 0.12 -10000 0 -0.32 66 66
CASP9 -0.026 0.12 -10000 0 -0.33 62 62
YWHAB 0.033 0.014 -10000 0 0 72 72
p27Kip1/KPNA1 -0.009 0.14 0.28 5 -0.33 66 71
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.063 0.033 -10000 0 -0.12 2 2
YWHAE 0.037 0.009 -10000 0 0 29 29
SRC 0.034 0.013 -10000 0 0 65 65
AKT2/p21CIP1 -0.029 0.12 0.23 1 -0.31 60 61
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL -0.002 0.036 -10000 0 -0.2 1 1
CHUK -0.024 0.1 -10000 0 -0.34 44 44
BAD/BCL-XL -0.01 0.13 -10000 0 -0.34 61 61
mTORC2 0.023 0.012 -10000 0 -0.081 5 5
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.019 0.14 0.21 2 -0.4 39 41
PDPK1 0.038 0.005 -10000 0 0 7 7
MDM2 -0.012 0.13 0.25 4 -0.33 58 62
MAPKKK cascade 0.002 0.14 0.33 68 -0.24 2 70
MDM2/Cbp/p300 0.019 0.14 0.28 5 -0.33 58 63
TSC1/TSC2 -0.037 0.13 0.24 13 -0.36 61 74
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.14 0.27 5 -0.32 58 63
glucose import -0.018 0.03 0.19 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.006 0.077 0.15 1 -0.19 55 56
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.018 0.03 0.19 4 -10000 0 4
GSK3A -0.02 0.13 0.26 12 -0.33 60 72
FOXO1 -0.024 0.12 -10000 0 -0.35 54 54
GSK3B -0.029 0.13 -10000 0 -0.35 62 62
SFN 0.033 0.014 -10000 0 0 79 79
G1/S transition of mitotic cell cycle -0.031 0.14 0.24 15 -0.35 63 78
p27Kip1/14-3-3 family 0.007 0.11 -10000 0 -0.5 14 14
PRKACA 0.036 0.01 -10000 0 0 36 36
KPNA1 0.037 0.009 -10000 0 0 27 27
HSP90AA1 0.036 0.01 -10000 0 0 39 39
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.022 0.019 -10000 0 0 216 216
CREBBP 0.038 0.005 -10000 0 0 7 7
Reelin signaling pathway

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
CDK5R1/CDK5 0.026 0.04 -10000 0 -0.13 17 17
VLDLR 0.029 0.017 -10000 0 0 135 135
CRKL 0.037 0.009 -10000 0 0 32 32
LRPAP1 0.038 0.007 -10000 0 0 18 18
FYN 0.032 0.015 -10000 0 0 95 95
ITGA3 0.034 0.013 -10000 0 0 60 60
RELN/VLDLR/Fyn 0.019 0.056 -10000 0 -0.12 41 41
MAPK8IP1/MKK7/MAP3K11/JNK1 0.067 0.071 -10000 0 -0.12 4 4
AKT1 -0.002 0.072 0.12 1 -0.2 38 39
MAP2K7 0.036 0.01 -10000 0 0 35 35
RAPGEF1 0.037 0.008 -10000 0 0 23 23
DAB1 0.038 0.007 -10000 0 0 18 18
RELN/LRP8/DAB1 0.037 0.039 -10000 0 -0.1 2 2
LRPAP1/LRP8 0.048 0.035 -10000 0 -0.14 14 14
RELN/LRP8/DAB1/Fyn 0.036 0.06 -10000 0 -0.11 29 29
DAB1/alpha3/beta1 Integrin 0.03 0.06 -10000 0 -10000 0 0
long-term memory 0.034 0.065 -10000 0 -0.13 29 29
DAB1/LIS1 0.043 0.072 -10000 0 -0.18 3 3
DAB1/CRLK/C3G 0.035 0.06 -10000 0 -0.13 18 18
PIK3CA 0.033 0.014 -10000 0 0 79 79
DAB1/NCK2 0.045 0.072 -10000 0 -0.18 3 3
ARHGEF2 0.037 0.008 -10000 0 0 25 25
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.038 0.007 -10000 0 0 16 16
CDK5R1 0.037 0.009 -10000 0 0 26 26
RELN 0.021 0.019 -10000 0 0 233 233
PIK3R1 0.034 0.013 -10000 0 0 69 69
RELN/LRP8/Fyn 0.027 0.053 -10000 0 -0.12 29 29
GRIN2A/RELN/LRP8/DAB1/Fyn 0.045 0.072 -10000 0 -0.12 29 29
MAPK8 0.028 0.017 -10000 0 0 138 138
RELN/VLDLR/DAB1 0.027 0.044 -10000 0 -0.1 14 14
ITGB1 0.029 0.017 -10000 0 0 131 131
MAP1B 0.039 0.098 0.17 135 -0.19 2 137
RELN/LRP8 0.036 0.045 -10000 0 -0.12 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn 0.044 0.072 -10000 0 -0.12 29 29
PI3K 0.023 0.07 -10000 0 -0.14 72 72
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.029 -10000 0 -0.13 1 1
RAP1A 0.036 0.12 0.28 42 -10000 0 42
PAFAH1B1 0.037 0.009 -10000 0 0 28 28
MAPK8IP1 0.037 0.009 -10000 0 0 30 30
CRLK/C3G 0.052 0.018 -10000 0 -10000 0 0
GRIN2B 0.037 0.009 -10000 0 0 32 32
NCK2 0.037 0.008 -10000 0 0 20 20
neuron differentiation 0.007 0.069 -10000 0 -0.24 16 16
neuron adhesion 0.033 0.13 0.32 30 -10000 0 30
LRP8 0.036 0.011 -10000 0 0 40 40
GSK3B -0.006 0.074 0.12 9 -0.22 30 39
RELN/VLDLR/DAB1/Fyn 0.029 0.062 -10000 0 -0.11 41 41
MAP3K11 0.038 0.006 -10000 0 0 13 13
RELN/VLDLR/DAB1/P13K -0.007 0.067 -10000 0 -0.19 44 44
CDK5 0.021 0.019 -10000 0 0 232 232
MAPT -0.01 0.086 0.51 5 -10000 0 5
neuron migration 0.005 0.12 0.27 21 -0.28 21 42
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.007 0.069 0.15 2 -0.24 16 18
RELN/VLDLR 0.041 0.06 -10000 0 -0.12 19 19
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.05 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.037 0.008 -10000 0 0 22 22
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.038 0.005 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.037 0.008 -10000 0 0 22 22
RAC1-CDC42/GTP/PAK family -0.002 0.043 -10000 0 -0.14 35 35
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.035 0.011 -10000 0 0 47 47
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.038 0.005 -10000 0 0 7 7
FYN 0.032 0.015 -10000 0 0 95 95
MAP3K12 0.038 0.007 -10000 0 0 15 15
FGR 0.034 0.012 -10000 0 0 59 59
p38 alpha/TAB1 -0.034 0.077 -10000 0 -0.25 44 44
PRKG1 0.028 0.018 -10000 0 0 149 149
DUSP8 0.036 0.011 -10000 0 0 44 44
PGK/cGMP/p38 alpha 0.003 0.1 0.2 2 -0.27 37 39
apoptosis -0.033 0.074 -10000 0 -0.24 44 44
RAL/GTP 0.025 0.035 -10000 0 -0.1 17 17
LYN 0.033 0.014 -10000 0 0 76 76
DUSP1 0.033 0.014 -10000 0 0 80 80
PAK1 0.037 0.008 -10000 0 0 20 20
SRC 0.034 0.013 -10000 0 0 65 65
RAC1/OSM/MEKK3/MKK3 0.041 0.04 -10000 0 -0.1 5 5
TRAF6 0.038 0.007 -10000 0 0 17 17
RAC1 0.023 0.019 -10000 0 0 209 209
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.029 -10000 0 -0.1 5 5
MAPK11 0.007 0.13 0.22 21 -0.31 40 61
BLK 0.038 0.007 -10000 0 0 19 19
HCK 0.026 0.018 -10000 0 0 170 170
MAP2K3 0.038 0.006 -10000 0 0 14 14
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.035 0.012 -10000 0 0 49 49
TRAF6/MEKK3 0.048 0.012 -10000 0 -0.093 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0.12 0.19 25 -0.29 38 63
positive regulation of innate immune response 0.009 0.15 0.24 19 -0.35 43 62
LCK 0.037 0.008 -10000 0 0 20 20
p38alpha-beta/MKP7 0.006 0.14 0.22 19 -0.34 43 62
p38alpha-beta/MKP5 0.02 0.15 0.25 19 -0.34 40 59
PGK/cGMP 0.02 0.013 -10000 0 -10000 0 0
PAK2 0.036 0.011 -10000 0 0 41 41
p38alpha-beta/MKP1 0.012 0.15 0.25 18 -0.34 44 62
CDC42 0.037 0.009 -10000 0 0 27 27
RALB 0.038 0.007 -10000 0 0 17 17
RALA 0.022 0.019 -10000 0 0 222 222
PAK3 0.028 0.018 -10000 0 0 146 146
ErbB2/ErbB3 signaling events

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
USP8 -0.023 0.015 0.11 2 -10000 0 2
RAS family/GTP 0.016 0.11 0.24 2 -0.18 62 64
NFATC4 -0.036 0.076 0.19 17 -0.2 4 21
ERBB2IP 0.034 0.018 -10000 0 -0.035 20 20
HSP90 (dimer) 0.036 0.01 -10000 0 0 39 39
mammary gland morphogenesis -0.035 0.083 0.2 8 -0.23 3 11
JUN -0.001 0.093 0.23 15 -0.34 7 22
HRAS 0.035 0.014 -10000 0 -0.006 47 47
DOCK7 -0.042 0.072 0.18 7 -0.21 4 11
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.082 0.21 13 -0.13 74 87
AKT1 -0.015 0.01 0.015 24 -10000 0 24
BAD -0.024 0.015 0.11 3 -10000 0 3
MAPK10 0.011 0.085 0.19 45 -0.16 6 51
mol:GTP 0 0.002 0.004 5 -0.006 24 29
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.089 0.22 8 -0.25 3 11
RAF1 -0.016 0.12 0.31 14 -0.24 26 40
ErbB2/ErbB3/neuregulin 2 -0.029 0.066 0.2 16 -10000 0 16
STAT3 -0.029 0.25 -10000 0 -0.89 38 38
cell migration -0.006 0.079 0.21 27 -0.17 12 39
mol:PI-3-4-5-P3 -0.001 0.002 0.004 18 -0.005 3 21
cell proliferation -0.033 0.25 0.47 10 -0.58 57 67
FOS -0.023 0.22 0.37 34 -0.41 89 123
NRAS 0.033 0.016 -10000 0 -0.004 73 73
mol:Ca2+ -0.035 0.083 0.2 8 -0.23 3 11
MAPK3 -0.013 0.19 0.42 10 -0.49 33 43
MAPK1 -0.037 0.23 0.42 10 -0.59 47 57
JAK2 -0.034 0.082 0.18 17 -0.23 3 20
NF2 0.008 0.017 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.079 0.16 14 -0.16 81 95
NRG1 0.035 0.015 -10000 0 -0.021 30 30
GRB2/SOS1 0.026 0.019 -10000 0 -0.1 9 9
MAPK8 -0.017 0.088 0.19 5 -0.23 40 45
MAPK9 0.018 0.089 0.2 53 -0.16 1 54
ERBB2 -0.022 0.069 0.25 31 -10000 0 31
ERBB3 0.018 0.02 -10000 0 -0.001 266 266
SHC1 0.035 0.013 -10000 0 -0.001 57 57
RAC1 0.023 0.019 -10000 0 0 209 209
apoptosis 0.017 0.032 0.18 11 -0.16 3 14
STAT3 (dimer) -0.026 0.24 -10000 0 -0.87 38 38
RNF41 -0.031 0.023 0.091 6 -0.11 8 14
FRAP1 -0.013 0.006 0.001 66 -10000 0 66
RAC1-CDC42/GTP -0.025 0.049 0.085 1 -0.16 7 8
ErbB2/ErbB2/HSP90 (dimer) -0.029 0.057 0.19 29 -0.13 1 30
CHRNA1 -0.002 0.16 0.42 10 -0.37 38 48
myelination -0.037 0.088 0.25 19 -0.22 2 21
PPP3CB -0.03 0.072 0.18 12 -0.22 4 16
KRAS 0.035 0.014 -10000 0 -0.006 48 48
RAC1-CDC42/GDP 0.022 0.073 0.24 1 -0.17 41 42
NRG2 0.038 0.006 -10000 0 0 12 12
mol:GDP -0.006 0.078 0.16 14 -0.16 81 95
SOS1 0 0.001 0.004 3 -0.004 7 10
MAP2K2 -0.027 0.11 0.3 13 -0.26 27 40
SRC 0.034 0.013 -10000 0 0 65 65
mol:cAMP -0.001 0.001 0.003 1 -10000 0 1
PTPN11 -0.039 0.087 0.18 17 -0.25 3 20
MAP2K1 -0.03 0.21 0.45 5 -0.58 32 37
heart morphogenesis -0.035 0.083 0.2 8 -0.23 3 11
RAS family/GDP 0.02 0.11 0.25 1 -0.19 66 67
GRB2 0.037 0.009 -10000 0 -0.001 27 27
PRKACA 0.018 0.01 -10000 0 -10000 0 0
CHRNE 0.001 0.027 0.089 7 -0.11 7 14
HSP90AA1 0.036 0.01 -10000 0 0 39 39
activation of caspase activity 0.015 0.01 -10000 0 -0.015 24 24
nervous system development -0.035 0.083 0.2 8 -0.23 3 11
CDC42 0.037 0.009 -10000 0 0 27 27
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.003 0.099 -10000 0 -0.25 26 26
mol:DAG -0.028 0.085 0.2 12 -0.25 24 36
PLCG1 -0.029 0.086 0.19 11 -0.25 25 36
YES1 -0.025 0.083 0.18 5 -0.26 22 27
FZD3 0.03 0.016 -10000 0 0 111 111
FZD6 0.029 0.017 -10000 0 0 133 133
G protein 0.007 0.11 0.2 40 -0.26 27 67
MAP3K7 -0.041 0.076 0.19 8 -0.23 28 36
mol:Ca2+ -0.027 0.085 0.2 13 -0.24 24 37
mol:IP3 -0.028 0.085 0.2 12 -0.25 24 36
NLK -0.013 0.16 -10000 0 -0.81 20 20
GNB1 0.035 0.011 -10000 0 0 46 46
CAMK2A -0.035 0.08 0.19 11 -0.24 25 36
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.008 0.089 -10000 0 -0.17 89 89
CSNK1A1 0.038 0.007 -10000 0 0 16 16
GNAS -0.014 0.091 0.18 30 -0.26 20 50
GO:0007205 -0.025 0.084 0.2 12 -0.25 25 37
WNT6 0.039 0.002 -10000 0 0 2 2
WNT4 0.037 0.008 -10000 0 0 21 21
NFAT1/CK1 alpha -0.035 0.093 0.2 7 -0.27 25 32
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.031 0.016 -10000 0 0 102 102
WNT11 0.037 0.008 -10000 0 0 20 20
CDC42 -0.031 0.081 0.17 8 -0.26 23 31
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.028 0.035 -10000 0 -0.13 8 8
CRKL 0.059 0.11 0.29 11 -0.39 15 26
mol:PIP3 0.004 0.06 -10000 0 -0.57 2 2
AKT1 -0.014 0.061 -10000 0 -0.72 1 1
PTK2B 0.038 0.007 -10000 0 0 18 18
RAPGEF1 0.053 0.12 0.32 16 -0.37 15 31
RANBP10 0.038 0.005 -10000 0 0 10 10
PIK3CA 0.033 0.014 -10000 0 0 79 79
HGF/MET/SHIP2 0.038 0.041 -10000 0 -0.12 2 2
MAP3K5 0.055 0.11 0.28 12 -0.38 13 25
HGF/MET/CIN85/CBL/ENDOPHILINS 0.036 0.038 -10000 0 -10000 0 0
AP1 0.02 0.091 0.15 136 -0.18 11 147
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.035 0.012 -10000 0 0 56 56
apoptosis -0.12 0.37 -10000 0 -0.77 116 116
STAT3 (dimer) 0.043 0.088 0.16 115 -0.28 10 125
GAB1/CRKL/SHP2/PI3K 0.073 0.13 0.33 4 -0.42 14 18
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.074 0.12 0.28 8 -0.39 15 23
PTPN11 0.038 0.007 -10000 0 0 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.034 0.013 -10000 0 0 70 70
PTEN 0.024 0.019 -10000 0 0 196 196
ELK1 0.14 0.19 0.35 217 -10000 0 217
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.034 0.16 1 -0.18 7 8
PAK1 -0.02 0.062 -10000 0 -0.7 1 1
HGF/MET/RANBP10 0.039 0.04 -10000 0 -10000 0 0
HRAS 0.049 0.1 -10000 0 -0.48 9 9
DOCK1 0.045 0.11 0.3 8 -0.39 14 22
GAB1 0.05 0.11 0.3 3 -0.41 15 18
CRK 0.058 0.11 0.28 8 -0.4 15 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.06 -10000 0 -0.43 7 7
JUN 0.036 0.011 -10000 0 0 43 43
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.005 0.017 0.087 8 -0.13 1 9
PIK3R1 0.034 0.013 -10000 0 0 69 69
cell morphogenesis 0.036 0.12 0.33 25 -0.31 13 38
GRB2/SHC 0.078 0.073 0.18 110 -0.15 2 112
FOS 0.026 0.018 -10000 0 0 168 168
GLMN 0.004 0.004 0.062 2 -10000 0 2
cell motility 0.14 0.19 0.34 217 -10000 0 217
HGF/MET/MUC20 0.026 0.026 -10000 0 -10000 0 0
cell migration 0.077 0.072 0.18 110 -0.15 2 112
GRB2 0.037 0.009 -10000 0 0 26 26
CBL 0.038 0.006 -10000 0 0 11 11
MET/RANBP10 0.03 0.029 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.008 0.045 -10000 0 -0.29 5 5
MET/MUC20 0.015 0.014 -10000 0 -10000 0 0
RAP1B 0.052 0.11 0.31 16 -0.35 15 31
RAP1A 0.045 0.11 0.32 15 -0.36 15 30
HGF/MET/RANBP9 0.037 0.043 -10000 0 -0.11 7 7
RAF1 0.041 0.1 0.29 3 -0.47 9 12
STAT3 0.043 0.089 0.16 115 -0.28 10 125
cell proliferation 0.036 0.092 0.28 20 -0.3 7 27
RPS6KB1 0.011 0.021 -10000 0 -10000 0 0
MAPK3 0.11 0.17 0.52 10 -10000 0 10
MAPK1 0.14 0.21 0.59 47 -10000 0 47
RANBP9 0.038 0.007 -10000 0 0 19 19
MAPK8 -0.039 0.16 0.29 3 -0.39 34 37
SRC -0.001 0.054 0.18 15 -0.3 4 19
PI3K 0.067 0.08 0.18 98 -0.16 7 105
MET/Glomulin 0.012 0.03 -10000 0 -0.091 24 24
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.033 0.1 0.28 3 -0.44 11 14
MET 0.021 0.019 -10000 0 0 239 239
MAP4K1 0.065 0.12 0.3 8 -0.38 15 23
PTK2 0.036 0.01 -10000 0 0 37 37
MAP2K2 0.044 0.12 0.31 23 -0.44 10 33
BAD -0.023 0.061 -10000 0 -0.52 2 2
MAP2K4 0.045 0.11 0.3 8 -0.37 12 20
SHP2/GRB2/SOS1/GAB1 0.014 0.077 -10000 0 -0.35 15 15
INPPL1 0.038 0.007 -10000 0 0 15 15
PXN 0.038 0.006 -10000 0 0 11 11
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.004 0.02 0.1 3 -0.13 1 4
PLCgamma1/PKC 0.024 0.014 -10000 0 -0.11 3 3
HGF 0.022 0.019 -10000 0 0 216 216
RASA1 0.036 0.01 -10000 0 0 37 37
NCK1 0.037 0.009 -10000 0 0 31 31
PTPRJ 0.038 0.007 -10000 0 0 16 16
NCK/PLCgamma1 0.078 0.068 0.18 120 -0.12 10 130
PDPK1 -0.003 0.058 -10000 0 -0.75 1 1
HGF/MET/SHIP 0.026 0.026 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.037 0.009 -10000 0 0 29 29
Jak2/Leptin Receptor -0.006 0.14 -10000 0 -0.36 47 47
PTP1B/AKT1 0.003 0.12 0.22 4 -0.28 41 45
FYN 0.032 0.015 -10000 0 0 95 95
p210 bcr-abl/PTP1B -0.008 0.12 0.22 7 -0.29 38 45
EGFR 0.008 0.018 -10000 0 -0.04 11 11
EGF/EGFR -0.032 0.089 -10000 0 -0.28 40 40
CSF1 0.038 0.005 -10000 0 0 9 9
AKT1 0.034 0.015 -10000 0 -0.037 6 6
INSR 0.032 0.02 -10000 0 -0.036 30 30
PTP1B/N-cadherin -0.003 0.12 0.21 4 -0.28 47 51
Insulin Receptor/Insulin 0.013 0.12 -10000 0 -0.28 31 31
HCK 0.026 0.018 -10000 0 0 170 170
CRK 0.037 0.008 -10000 0 0 25 25
TYK2 -0.005 0.14 0.3 31 -0.32 32 63
EGF 0.027 0.03 -10000 0 -0.04 79 79
YES1 0.035 0.011 -10000 0 0 47 47
CAV1 0.021 0.15 0.25 53 -0.3 47 100
TXN 0.033 0.02 -10000 0 -0.035 26 26
PTP1B/IRS1/GRB2 0.008 0.13 0.25 2 -0.3 37 39
cell migration 0.008 0.12 0.29 38 -0.22 7 45
STAT3 0.036 0.011 -10000 0 0 42 42
PRLR 0.04 0.006 -10000 0 -10000 0 0
ITGA2B 0.039 0.004 -10000 0 0 5 5
CSF1R 0.029 0.017 -10000 0 0 134 134
Prolactin Receptor/Prolactin 0.058 0.015 -10000 0 -10000 0 0
FGR 0.034 0.012 -10000 0 0 59 59
PTP1B/p130 Cas -0.01 0.11 0.19 6 -0.26 45 51
Crk/p130 Cas 0 0.12 0.21 5 -0.26 45 50
DOK1 -0.009 0.11 0.24 5 -0.31 30 35
JAK2 -0.017 0.14 0.26 2 -0.36 49 51
Jak2/Leptin Receptor/Leptin -0.023 0.12 -10000 0 -0.33 31 31
PIK3R1 0.034 0.013 -10000 0 0 69 69
PTPN1 -0.008 0.12 0.22 7 -0.29 38 45
LYN 0.033 0.014 -10000 0 0 76 76
CDH2 0.034 0.013 -10000 0 0 61 61
SRC 0.015 0.11 -10000 0 -0.5 17 17
ITGB3 0.038 0.005 -10000 0 -10000 0 0
CAT1/PTP1B 0.008 0.18 0.29 48 -0.38 56 104
CAPN1 0.037 0.011 -10000 0 -0.035 9 9
CSK 0.037 0.008 -10000 0 0 22 22
PI3K 0.006 0.13 -10000 0 -0.29 43 43
mol:H2O2 0.004 0.005 0.032 3 -10000 0 3
STAT3 (dimer) -0.021 0.11 -10000 0 -0.3 31 31
negative regulation of transcription -0.017 0.14 0.26 2 -0.36 49 51
FCGR2A 0.03 0.016 -10000 0 0 117 117
FER 0.035 0.019 -10000 0 -0.035 28 28
alphaIIb/beta3 Integrin 0.056 0.007 -10000 0 -10000 0 0
BLK 0.038 0.007 -10000 0 0 19 19
Insulin Receptor/Insulin/Shc 0.06 0.039 -10000 0 -0.12 8 8
RHOA 0.036 0.012 -10000 0 -0.035 7 7
LEPR 0.037 0.008 -10000 0 0 22 22
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.037 0.009 -10000 0 0 26 26
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 0.01 0.16 0.22 36 -0.34 57 93
PRL 0.039 0.008 -10000 0 -10000 0 0
SOCS3 0.023 0.018 -10000 0 -10000 0 0
SPRY2 0.03 0.02 -10000 0 -0.037 1 1
Insulin Receptor/Insulin/IRS1 0.057 0.048 -10000 0 -0.12 23 23
CSF1/CSF1R -0.002 0.13 0.24 3 -0.29 44 47
Ras protein signal transduction -0.005 0.11 0.54 18 -10000 0 18
IRS1 0.035 0.012 -10000 0 0 53 53
INS 0.035 0.018 -10000 0 -0.035 24 24
LEP 0.022 0.019 -10000 0 0 217 217
STAT5B -0.006 0.11 0.24 4 -0.32 28 32
STAT5A -0.005 0.11 0.24 4 -0.31 31 35
GRB2 0.037 0.009 -10000 0 0 26 26
PDGFB-D/PDGFRB 0.003 0.12 0.22 5 -0.27 45 50
CSN2 0.007 0.043 -10000 0 -10000 0 0
PIK3CA 0.033 0.014 -10000 0 0 79 79
LAT -0.026 0.18 -10000 0 -0.46 65 65
YBX1 0.043 0.036 -10000 0 -0.28 6 6
LCK 0.037 0.008 -10000 0 0 20 20
SHC1 0.035 0.012 -10000 0 0 56 56
NOX4 0.036 0.017 -10000 0 -0.037 1 1
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.002 0.012 -10000 0 -0.035 30 30
BUB1B -0.01 0.085 0.13 33 -0.2 59 92
PLK1 0.009 0.033 0.095 29 -0.088 1 30
PLK1S1 0.004 0.019 0.055 31 -0.048 1 32
KIF2A -0.006 0.049 0.21 13 -0.12 7 20
regulation of mitotic centrosome separation 0.009 0.033 0.095 29 -0.088 1 30
GOLGA2 0.037 0.009 -10000 0 0 28 28
Hec1/SPC24 0.014 0.042 0.11 4 -0.096 30 34
WEE1 -0.015 0.13 0.17 1 -0.42 40 41
cytokinesis -0.016 0.12 0.18 22 -0.29 59 81
PP2A-alpha B56 0.059 0.095 -10000 0 -0.52 10 10
AURKA 0.008 0.039 0.11 2 -0.2 13 15
PICH/PLK1 -0.022 0.083 0.15 50 -0.19 37 87
CENPE 0.007 0.058 0.16 45 -0.12 2 47
RhoA/GTP 0.026 0.017 -10000 0 -0.11 7 7
positive regulation of microtubule depolymerization -0.006 0.05 0.2 13 -0.12 7 20
PPP2CA 0.037 0.008 -10000 0 0 24 24
FZR1 0.036 0.01 -10000 0 0 35 35
TPX2 -0.019 0.093 0.11 14 -0.22 84 98
PAK1 0.038 0.008 -10000 0 0 20 20
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.037 0.009 -10000 0 0 27 27
CLSPN 0.012 0.033 0.12 2 -0.22 7 9
GORASP1 0.036 0.01 -10000 0 0 35 35
metaphase 0.001 0.003 0.016 9 -0.011 5 14
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.019 0.055 31 -0.048 1 32
G2 phase of mitotic cell cycle 0 0.003 0.016 4 -10000 0 4
STAG2 0.037 0.008 -10000 0 0 24 24
GRASP65/GM130/RAB1/GTP -0.013 0.14 -10000 0 -0.59 26 26
spindle elongation 0.009 0.033 0.095 29 -0.088 1 30
ODF2 0.037 0.014 -10000 0 -0.035 10 10
BUB1 0.023 0.085 -10000 0 -0.55 10 10
TPT1 -0.003 0.055 -10000 0 -0.18 40 40
CDC25C 0.014 0.033 -10000 0 -0.21 7 7
CDC25B 0.022 0.029 -10000 0 -0.04 70 70
SGOL1 0.002 0.012 0.035 30 -10000 0 30
RHOA 0.037 0.008 -10000 0 0 24 24
CCNB1/CDK1 0 0.099 -10000 0 -0.2 90 90
CDC14B -0.017 0.005 0.001 37 -10000 0 37
CDC20 0.029 0.017 -10000 0 0 128 128
PLK1/PBIP1 -0.012 0.037 0.069 19 -0.083 66 85
mitosis -0.003 0.006 0.029 15 -10000 0 15
FBXO5 -0.009 0.062 0.13 21 -0.16 41 62
CDC2 0 0.005 -10000 0 -0.013 65 65
NDC80 0.031 0.016 -10000 0 0 100 100
metaphase plate congression 0.004 0.061 -10000 0 -0.25 24 24
ERCC6L -0.04 0.082 0.13 3 -0.2 88 91
NLP/gamma Tubulin 0.003 0.029 0.083 13 -0.098 20 33
microtubule cytoskeleton organization -0.003 0.055 -10000 0 -0.18 40 40
G2/M transition DNA damage checkpoint 0 0.002 0.013 3 -10000 0 3
PPP1R12A 0.037 0.012 -10000 0 -0.005 35 35
interphase 0 0.002 0.013 3 -10000 0 3
PLK1/PRC1-2 0.014 0.075 0.15 1 -0.15 56 57
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.058 -10000 0 -0.15 11 11
RAB1A 0.038 0.007 -10000 0 0 18 18
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.032 0.076 60 -0.067 3 63
mitotic prometaphase 0 0.005 0.02 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process -0.047 0.11 0.18 1 -0.24 73 74
microtubule-based process 0.024 0.031 0.12 5 -10000 0 5
Golgi organization 0.009 0.033 0.095 29 -0.088 1 30
Cohesin/SA2 0.022 0.038 0.1 11 -0.09 14 25
PPP1CB/MYPT1 0.05 0.035 -10000 0 -0.14 15 15
KIF20A 0.03 0.016 -10000 0 0 112 112
APC/C/CDC20 0.024 0.03 0.12 6 -10000 0 6
PPP2R1A 0.034 0.013 -10000 0 0 68 68
chromosome segregation -0.012 0.036 0.068 19 -0.082 66 85
PRC1 0.029 0.017 -10000 0 0 129 129
ECT2 0.006 0.068 0.17 49 -0.12 7 56
C13orf34 0.007 0.029 0.082 30 -0.066 1 31
NUDC 0.004 0.061 -10000 0 -0.26 24 24
regulation of attachment of spindle microtubules to kinetochore -0.01 0.084 0.13 33 -0.2 59 92
spindle assembly 0.004 0.032 0.09 26 -0.082 9 35
spindle stabilization 0.004 0.019 0.055 31 -0.048 1 32
APC/C/HCDH1 0.022 0.027 0.11 1 -0.1 16 17
MKLP2/PLK1 0.024 0.031 0.12 5 -10000 0 5
CCNB1 0.029 0.021 -10000 0 -0.04 15 15
PPP1CB 0.037 0.011 -10000 0 -0.011 22 22
BTRC 0.028 0.018 -10000 0 0 147 147
ROCK2 0.019 0.034 0.15 1 -0.21 3 4
TUBG1 0.004 0.051 0.11 2 -0.21 23 25
G2/M transition of mitotic cell cycle -0.032 0.084 0.12 11 -0.2 88 99
MLF1IP -0.013 0.008 0 147 -10000 0 147
INCENP 0.038 0.007 -10000 0 -0.033 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.026 0.017 -10000 0 -0.11 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.034 0.013 -10000 0 0 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.009 0.11 -10000 0 -0.28 56 56
IRAK/TOLLIP -0.034 0.031 0.16 8 -0.17 2 10
IKBKB 0.038 0.005 -10000 0 0 7 7
IKBKG 0.039 0.004 -10000 0 0 5 5
IL1 alpha/IL1R2 0.046 0.023 -10000 0 -10000 0 0
IL1A 0.037 0.008 -10000 0 0 22 22
IL1B 0 0.058 0.12 95 -10000 0 95
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.053 0.19 6 -0.13 28 34
IL1R2 0.032 0.015 -10000 0 0 88 88
IL1R1 0.038 0.006 -10000 0 0 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.017 0.1 0.16 1 -0.3 37 38
TOLLIP 0.036 0.01 -10000 0 0 35 35
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.038 0.005 -10000 0 0 7 7
TAK1/TAB1/TAB2 0.022 0.019 -10000 0 -0.091 13 13
IKK complex/ELKS -0.054 0.12 -10000 0 -0.32 32 32
JUN -0.042 0.038 0.13 4 -0.17 5 9
MAP3K7 0.035 0.011 -10000 0 0 47 47
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.036 0.11 0.22 7 -0.15 105 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.071 0.07 -10000 0 -0.12 50 50
PIK3R1 0.034 0.013 -10000 0 0 69 69
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.079 0.079 -10000 0 -0.13 46 46
IL1 beta fragment/IL1R1/IL1RAP 0.03 0.083 0.2 8 -0.13 83 91
NFKB1 0.038 0.007 -10000 0 0 18 18
MAPK8 -0.035 0.034 0.15 5 -0.16 3 8
IRAK1 -0.027 0.01 -10000 0 -0.1 5 5
IL1RN/IL1R1 0.056 0.01 -10000 0 -10000 0 0
IRAK4 0.037 0.008 -10000 0 0 25 25
PRKCI 0.037 0.009 -10000 0 0 28 28
TRAF6 0.038 0.007 -10000 0 0 17 17
PI3K 0.023 0.07 -10000 0 -0.14 72 72
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.11 0.2 2 -0.28 55 57
CHUK 0.027 0.018 -10000 0 0 155 155
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.03 0.083 0.2 8 -0.13 83 91
IL1 beta/IL1R2 0.021 0.073 -10000 0 -0.13 69 69
IRAK/TRAF6/TAK1/TAB1/TAB2 0.034 0.045 0.17 5 -0.11 31 36
NF kappa B1 p50/RelA -0.047 0.091 0.12 65 -0.2 34 99
IRAK3 0.036 0.01 -10000 0 0 35 35
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.085 0.2 8 -0.13 79 87
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.075 -10000 0 -0.28 15 15
IL1 alpha/IL1R1/IL1RAP 0.053 0.054 -10000 0 -0.12 34 34
RELA 0.038 0.006 -10000 0 0 12 12
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.036 0.011 -10000 0 0 40 40
MYD88 0.036 0.01 -10000 0 0 38 38
IRAK/TRAF6/MEKK3 0.05 0.041 0.2 5 -0.11 22 27
IL1RAP 0.032 0.015 -10000 0 0 91 91
UBE2N 0.038 0.007 -10000 0 0 17 17
IRAK/TRAF6 -0.05 0.069 0.071 71 -0.19 24 95
CASP1 0.031 0.016 -10000 0 0 110 110
IL1RN/IL1R2 0.048 0.022 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.043 0.098 0.21 8 -0.14 91 99
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.1 0.19 4 -0.32 34 38
PIK3CA 0.033 0.014 -10000 0 0 79 79
IL1RN 0.039 0.004 -10000 0 0 5 5
TRAF6/TAK1/TAB1/TAB2 0.045 0.036 -10000 0 -0.1 18 18
MAP2K6 -0.036 0.036 0.17 10 -0.16 3 13
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.003 0.073 -10000 0 -0.13 104 104
alphaV beta3 Integrin 0.064 0.047 -10000 0 -0.12 25 25
PTK2 -0.033 0.14 0.31 8 -0.38 25 33
IGF1R 0.035 0.012 -10000 0 0 54 54
PI4KB 0.038 0.007 -10000 0 0 17 17
MFGE8 0.038 0.007 -10000 0 0 18 18
SRC 0.034 0.013 -10000 0 0 65 65
CDKN1B -0.003 0.092 -10000 0 -0.31 39 39
VEGFA 0.025 0.019 -10000 0 0 181 181
ILK 0.008 0.071 -10000 0 -0.3 23 23
ROCK1 0.037 0.008 -10000 0 0 22 22
AKT1 -0.021 0.068 0.2 3 -0.31 22 25
PTK2B -0.021 0.097 0.19 45 -0.24 1 46
alphaV/beta3 Integrin/JAM-A 0.073 0.047 0.21 1 -0.12 14 15
CBL 0.038 0.006 -10000 0 0 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.066 0.044 -10000 0 -0.12 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.074 0.068 -10000 0 -0.13 43 43
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.016 0.1 -10000 0 -0.31 30 30
alphaV/beta3 Integrin/Syndecan-1 0.059 0.043 -10000 0 -0.12 15 15
PI4KA 0.034 0.013 -10000 0 0 70 70
IGF-1R heterotetramer/IGF1/IRS1 0.053 0.085 -10000 0 -0.15 63 63
PI4 Kinase 0.04 0.048 -10000 0 -0.13 33 33
PIK3CA 0.033 0.014 -10000 0 0 79 79
alphaV/beta3 Integrin/Osteopontin 0.053 0.067 -10000 0 -0.13 53 53
RPS6KB1 -0.06 0.078 0.29 7 -0.26 4 11
TLN1 0.03 0.016 -10000 0 0 113 113
MAPK3 -0.014 0.083 -10000 0 -0.34 20 20
GPR124 0.037 0.008 -10000 0 0 25 25
MAPK1 -0.014 0.082 -10000 0 -0.35 20 20
PXN 0.038 0.006 -10000 0 0 11 11
PIK3R1 0.034 0.013 -10000 0 0 69 69
alphaV/beta3 Integrin/Tumstatin 0.067 0.043 -10000 0 -0.12 23 23
cell adhesion 0.051 0.055 -10000 0 -0.16 24 24
ANGPTL3 0.038 0.006 -10000 0 0 12 12
VEGFR2 homodimer/VEGFA homodimer/Src 0.013 0.074 -10000 0 -0.12 96 96
IGF-1R heterotetramer 0.035 0.012 -10000 0 0 54 54
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
TGFBR2 0.037 0.009 -10000 0 0 31 31
ITGB3 0.038 0.005 -10000 0 0 7 7
IGF1 0.037 0.009 -10000 0 0 28 28
RAC1 0.023 0.019 -10000 0 0 209 209
regulation of cell-matrix adhesion 0.063 0.045 -10000 0 -0.12 23 23
apoptosis 0.036 0.01 -10000 0 0 34 34
CD47 0.037 0.009 -10000 0 0 27 27
alphaV/beta3 Integrin/CD47 0.064 0.047 -10000 0 -0.12 24 24
VCL 0.027 0.018 -10000 0 0 151 151
alphaV/beta3 Integrin/Del1 0.067 0.043 -10000 0 -0.12 22 22
CSF1 0.038 0.005 -10000 0 0 9 9
PIK3C2A 0.006 0.02 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.053 0.093 0.1 94 -0.21 25 119
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.094 -10000 0 -0.13 111 111
FAK1/Vinculin -0.035 0.12 0.29 5 -0.32 24 29
alphaV beta3/Integrin/ppsTEM5 0.064 0.045 -10000 0 -0.12 23 23
RHOA 0.037 0.008 -10000 0 0 24 24
VTN 0.038 0.005 -10000 0 0 9 9
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.037 0.008 -10000 0 0 25 25
F11R -0.021 0.043 0.12 43 -10000 0 43
alphaV/beta3 Integrin/Lactadherin 0.065 0.045 -10000 0 -0.12 23 23
alphaV/beta3 Integrin/TGFBR2 0.063 0.046 -10000 0 -0.12 25 25
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.063 0.041 -10000 0 -0.1 23 23
HSP90AA1 0.036 0.01 -10000 0 0 39 39
alphaV/beta3 Integrin/Talin 0.047 0.051 -10000 0 -0.11 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.037 0.009 -10000 0 0 31 31
alphaV/beta3 Integrin/Pyk2 -0.015 0.11 0.16 118 -0.18 15 133
SDC1 0.033 0.014 -10000 0 0 82 82
VAV3 -0.037 0.031 0.17 2 -0.17 5 7
PTPN11 0.038 0.007 -10000 0 0 17 17
IRS1 0.035 0.012 -10000 0 0 53 53
FAK1/Paxillin -0.022 0.13 0.3 9 -0.33 22 31
cell migration -0.04 0.1 0.26 6 -0.31 22 28
ITGAV 0.036 0.01 -10000 0 0 34 34
PI3K 0.058 0.084 -10000 0 -0.18 11 11
SPP1 0.035 0.012 -10000 0 0 54 54
KDR 0.032 0.015 -10000 0 0 91 91
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.036 0.01 -10000 0 0 34 34
COL4A3 0.039 0.002 -10000 0 0 1 1
angiogenesis -0.013 0.093 -10000 0 -0.37 22 22
Rac1/GTP -0.031 0.037 0.18 1 -10000 0 1
EDIL3 0.038 0.005 -10000 0 0 10 10
cell proliferation 0.062 0.046 -10000 0 -0.12 25 25
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.038 0.006 -10000 0 0 13 13
Caspase 8 (4 units) -0.014 0.099 -10000 0 -0.2 36 36
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.042 0.026 0.1 62 -0.08 1 63
BIRC3 -0.038 0.037 0.17 5 -0.21 3 8
CYCS 0.002 0.085 0.16 75 -0.24 9 84
RIPK1 0.037 0.008 -10000 0 0 22 22
CD247 0.039 0.008 -10000 0 -10000 0 0
MAP2K7 -0.015 0.11 -10000 0 -0.42 8 8
protein ubiquitination 0.006 0.074 0.21 4 -0.27 10 14
CRADD 0.038 0.007 -10000 0 0 18 18
DAXX 0.038 0.005 -10000 0 0 9 9
FAS 0.021 0.019 -10000 0 0 235 235
BID -0.028 0.065 0.18 5 -0.27 8 13
NF-kappa-B/RelA/I kappa B alpha 0.081 0.065 0.21 60 -0.13 17 77
TRADD 0.038 0.005 -10000 0 0 9 9
MAP3K5 0.032 0.015 -10000 0 0 94 94
CFLAR 0.038 0.005 -10000 0 0 9 9
FADD 0.038 0.006 -10000 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.082 0.065 0.21 60 -0.13 17 77
MAPK8 -0.014 0.1 -10000 0 -0.4 8 8
APAF1 0.038 0.006 -10000 0 0 11 11
TRAF1 0.037 0.009 -10000 0 0 30 30
TRAF2 0.037 0.008 -10000 0 0 20 20
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.002 0.059 0.17 3 -0.17 44 47
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.026 0.085 0.22 1 -0.3 12 13
CHUK 0.006 0.076 0.22 4 -0.28 10 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.041 0.09 -10000 0 -0.12 56 56
TCRz/NEF 0.034 0.007 -10000 0 -10000 0 0
TNF 0.038 0.005 -10000 0 0 8 8
FASLG -0.024 0.017 0.12 7 -10000 0 7
NFKB1 0.046 0.024 0.1 71 -0.08 1 72
TNFR1A/BAG4/TNF-alpha 0.057 0.056 -10000 0 -0.12 40 40
CASP6 0.003 0.11 -10000 0 -0.56 6 6
CASP7 -0.041 0.16 0.28 36 -0.29 67 103
RELA 0.047 0.024 0.1 73 -0.08 1 74
CASP2 0.023 0.019 -10000 0 0 213 213
CASP3 -0.008 0.13 0.28 35 -0.34 19 54
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
TNFR1A/BAG4 0.039 0.052 -10000 0 -0.13 41 41
CASP8 0.038 0.007 -10000 0 0 15 15
CASP9 0.037 0.009 -10000 0 0 31 31
MAP3K14 0.02 0.086 0.22 8 -0.29 12 20
APAF-1/Caspase 9 -0.013 0.093 0.21 5 -0.25 12 17
BCL2 -0.027 0.097 -10000 0 -0.38 8 8
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.004 0.079 -10000 0 -0.21 52 52
epithelial cell differentiation 0.066 0.052 -10000 0 -0.13 22 22
CYFIP2 0.033 0.014 -10000 0 0 78 78
ENAH -0.058 0.082 0.31 11 -0.26 6 17
EGFR 0.009 0.017 -10000 0 0 385 385
EPHA2 0.035 0.012 -10000 0 0 57 57
MYO6 -0.042 0.051 0.22 4 -0.24 4 8
CTNNB1 0.038 0.007 -10000 0 0 18 18
ABI1/Sra1/Nap1 0.034 0.064 -10000 0 -0.12 55 55
AQP5 -0.028 0.079 0.25 2 -0.37 17 19
CTNND1 0.036 0.01 -10000 0 0 37 37
mol:PI-4-5-P2 -0.042 0.046 0.17 2 -0.23 4 6
regulation of calcium-dependent cell-cell adhesion -0.04 0.051 0.18 12 -0.23 1 13
EGF 0.037 0.008 -10000 0 0 25 25
NCKAP1 0.039 0.003 -10000 0 0 3 3
AQP3 -0.048 0.1 0.27 2 -0.34 47 49
cortical microtubule organization 0.066 0.052 -10000 0 -0.13 22 22
GO:0000145 -0.041 0.041 0.16 2 -0.22 4 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.074 0.055 -10000 0 -0.13 22 22
MLLT4 0.036 0.011 -10000 0 0 45 45
ARF6/GDP -0.073 0.045 -10000 0 -0.22 12 12
ARF6 0.036 0.01 -10000 0 0 33 33
Ephrin A1/EPHA2/NCK1/GIT1 0.077 0.058 -10000 0 -0.12 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.029 0.07 -10000 0 -0.3 24 24
PVRL2 0.036 0.011 -10000 0 0 44 44
ZYX -0.026 0.044 0.17 2 -0.23 4 6
ARF6/GTP 0.08 0.066 -10000 0 -0.13 24 24
CDH1 0.036 0.01 -10000 0 0 38 38
EGFR/EGFR/EGF/EGF 0.001 0.058 -10000 0 -0.13 58 58
RhoA/GDP 0.066 0.058 -10000 0 -0.14 26 26
actin cytoskeleton organization -0.036 0.048 0.17 7 -0.21 11 18
IGF-1R heterotetramer 0.035 0.012 -10000 0 0 54 54
GIT1 0.038 0.005 -10000 0 0 9 9
IGF1R 0.035 0.012 -10000 0 0 54 54
IGF1 0.037 0.009 -10000 0 0 28 28
DIAPH1 -0.13 0.28 -10000 0 -0.52 143 143
Wnt receptor signaling pathway -0.066 0.052 0.13 22 -10000 0 22
RHOA 0.037 0.008 -10000 0 0 24 24
RhoA/GTP -0.073 0.046 -10000 0 -0.22 13 13
CTNNA1 0.037 0.008 -10000 0 0 20 20
VCL -0.036 0.049 0.17 7 -0.22 11 18
EFNA1 0.035 0.012 -10000 0 0 56 56
LPP -0.049 0.051 0.16 6 -0.26 6 12
Ephrin A1/EPHA2 0.047 0.065 -10000 0 -0.14 38 38
SEC6/SEC8 -0.061 0.031 -10000 0 -0.18 10 10
MGAT3 -0.041 0.052 0.18 12 -0.23 1 13
HGF/MET 0.032 0.05 -10000 0 -0.14 12 12
HGF 0.022 0.019 -10000 0 0 216 216
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.004 0.079 -10000 0 -0.21 52 52
actin cable formation -0.049 0.11 0.36 10 -0.31 29 39
KIAA1543 -0.036 0.039 0.16 10 -0.21 1 11
KIFC3 -0.044 0.049 0.23 4 -0.23 1 5
NCK1 0.037 0.009 -10000 0 0 31 31
EXOC3 0.037 0.008 -10000 0 0 22 22
ACTN1 -0.037 0.054 0.19 9 -0.24 6 15
NCK1/GIT1 0.052 0.024 -10000 0 -0.13 6 6
mol:GDP 0.066 0.052 -10000 0 -0.13 22 22
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.045 0.052 0.23 4 -0.24 4 8
PIP5K1C -0.043 0.047 0.17 2 -0.23 4 6
LIMA1 0.033 0.014 -10000 0 0 78 78
ABI1 0.027 0.018 -10000 0 0 150 150
ROCK1 -0.051 0.1 0.35 16 -0.28 4 20
adherens junction assembly -0.033 0.065 0.26 3 -0.29 12 15
IGF-1R heterotetramer/IGF1 0.051 0.064 -10000 0 -0.14 35 35
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.048 0.025 -10000 0 -0.13 3 3
MET 0.021 0.019 -10000 0 0 239 239
PLEKHA7 -0.041 0.029 0.063 18 -0.13 22 40
mol:GTP 0.075 0.056 -10000 0 -0.12 25 25
establishment of epithelial cell apical/basal polarity -0.054 0.069 0.22 3 -0.24 4 7
cortical actin cytoskeleton stabilization -0.004 0.079 -10000 0 -0.21 52 52
regulation of cell-cell adhesion -0.036 0.048 0.17 7 -0.21 11 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.004 0.079 -10000 0 -0.21 52 52
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.021 0.12 0.31 24 -0.38 19 43
CRKL 0.022 0.11 0.28 18 -0.39 20 38
HRAS 0.034 0.11 0.28 19 -0.32 19 38
mol:PIP3 0.081 0.14 0.34 48 -0.36 14 62
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.038 0.005 -10000 0 0 7 7
GAB1 0.033 0.12 0.26 31 -0.39 21 52
FOXO3 0.062 0.18 0.37 35 -0.38 32 67
AKT1 0.072 0.18 0.37 36 -0.38 32 68
BAD 0.061 0.17 0.35 37 -0.37 32 69
megakaryocyte differentiation 0.032 0.11 0.27 22 -0.38 19 41
GSK3B 0.061 0.18 0.36 38 -0.38 33 71
RAF1 0.02 0.1 0.25 22 -0.28 19 41
SHC1 0.035 0.012 -10000 0 0 56 56
STAT3 0.025 0.11 0.26 24 -0.39 21 45
STAT1 0.018 0.2 -10000 0 -0.84 20 20
HRAS/SPRED1 0.025 0.096 0.23 19 -0.27 19 38
cell proliferation 0.012 0.1 0.26 9 -0.38 20 29
PIK3CA 0.033 0.014 -10000 0 0 79 79
TEC 0.037 0.008 -10000 0 0 21 21
RPS6KB1 0.068 0.13 0.32 28 -0.35 20 48
HRAS/SPRED2 0.046 0.11 0.28 19 -0.28 19 38
LYN/TEC/p62DOK 0.068 0.13 0.31 4 -0.4 20 24
MAPK3 0.019 0.094 0.26 24 -0.22 14 38
STAP1 0.028 0.11 0.26 22 -0.39 20 42
GRAP2 0.036 0.01 -10000 0 0 39 39
JAK2 0.02 0.17 0.45 2 -0.71 20 22
STAT1 (dimer) 0.029 0.2 0.48 3 -0.82 20 23
mol:Gleevec -0.003 0.007 -10000 0 -0.026 7 7
GRB2/SOCS1/VAV1 0.077 0.12 0.33 5 -0.38 19 24
actin filament polymerization 0.034 0.11 0.25 23 -0.37 21 44
LYN 0.033 0.014 -10000 0 0 76 76
STAP1/STAT5A (dimer) 0.025 0.14 0.35 9 -0.52 20 29
PIK3R1 0.034 0.014 -10000 0 0 69 69
CBL/CRKL/GRB2 0.055 0.12 0.32 15 -0.38 20 35
PI3K 0.075 0.14 0.35 28 -0.37 18 46
PTEN 0.024 0.019 -10000 0 0 196 196
SCF/KIT/EPO/EPOR 0.02 0.22 -10000 0 -0.96 20 20
MAPK8 0.012 0.1 0.26 11 -0.39 20 31
STAT3 (dimer) 0.025 0.11 0.27 20 -0.39 20 40
positive regulation of transcription 0.02 0.084 0.24 25 -0.2 6 31
mol:GDP 0.045 0.11 0.28 12 -0.33 19 31
PIK3C2B 0.026 0.12 0.29 24 -0.39 21 45
CBL/CRKL 0.044 0.12 0.3 18 -0.38 20 38
FER 0.03 0.11 0.26 21 -0.39 20 41
SH2B3 0.026 0.11 0.25 23 -0.4 19 42
PDPK1 0.071 0.14 0.34 40 -0.34 14 54
SNAI2 0.035 0.12 0.26 27 -0.39 20 47
positive regulation of cell proliferation 0.034 0.17 0.4 8 -0.64 20 28
KITLG 0.039 0.028 0.1 3 -0.061 20 23
cell motility 0.034 0.17 0.4 8 -0.64 20 28
PTPN6 0.018 0.033 -10000 0 -0.044 97 97
EPOR 0.052 0.095 -10000 0 -0.52 1 1
STAT5A (dimer) 0.039 0.15 0.36 10 -0.52 20 30
SOCS1 0.038 0.005 -10000 0 0 10 10
cell migration -0.031 0.11 0.37 19 -0.27 24 43
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.023 0.025 -10000 0 -0.046 12 12
VAV1 0.036 0.011 -10000 0 0 44 44
GRB10 0.021 0.11 0.35 20 -0.41 11 31
PTPN11 0.017 0.035 -10000 0 -0.042 128 128
SCF/KIT 0.039 0.12 0.27 28 -0.4 21 49
GO:0007205 -0.002 0.008 -10000 0 -0.026 16 16
MAP2K1 0.009 0.088 0.23 16 -0.24 16 32
CBL 0.038 0.006 -10000 0 0 11 11
KIT 0.024 0.24 -10000 0 -1.1 20 20
MAP2K2 0.017 0.1 0.3 26 -0.24 14 40
SHC/Grb2/SOS1 0.057 0.11 0.28 6 -0.36 20 26
STAT5A 0.037 0.15 0.36 9 -0.54 20 29
GRB2 0.037 0.009 -10000 0 0 26 26
response to radiation 0.037 0.12 0.27 26 -0.38 20 46
SHC/GRAP2 0.045 0.031 -10000 0 -0.13 8 8
PTPRO 0.031 0.11 0.27 25 -0.39 19 44
SH2B2 0.034 0.11 0.25 27 -0.38 21 48
DOK1 0.039 0.003 -10000 0 0 3 3
MATK 0.026 0.11 0.26 20 -0.38 19 39
CREBBP 0.058 0.056 0.17 52 -0.13 20 72
BCL2 0.044 0.14 -10000 0 -0.92 4 4
p38 MAPK 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
TRAF6/ASK1 0.016 0.034 -10000 0 -0.09 40 40
TRAF2/ASK1 0.035 0.041 -10000 0 -0.1 33 33
ATM 0.036 0.011 -10000 0 0 41 41
MAP2K3 0.019 0.085 0.22 5 -0.3 14 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.087 0.22 7 -0.28 16 23
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.034 0.013 -10000 0 0 70 70
TXN 0.006 0.002 -10000 0 0 43 43
CALM1 0.034 0.013 -10000 0 0 62 62
GADD45A 0.033 0.014 -10000 0 0 78 78
GADD45B 0.032 0.015 -10000 0 0 95 95
MAP3K1 0.037 0.008 -10000 0 0 25 25
MAP3K6 0.037 0.008 -10000 0 0 24 24
MAP3K7 0.035 0.011 -10000 0 0 47 47
MAP3K4 0.034 0.013 -10000 0 0 70 70
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.05 -10000 0 -0.13 36 36
TAK1/TAB family 0.005 0.03 -10000 0 -0.13 13 13
RAC1/OSM/MEKK3 0.028 0.027 -10000 0 -0.093 5 5
TRAF2 0.037 0.008 -10000 0 0 20 20
RAC1/OSM/MEKK3/MKK3 0.006 0.066 -10000 0 -0.25 14 14
TRAF6 0.006 0.001 -10000 0 0 17 17
RAC1 0.023 0.019 -10000 0 0 209 209
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.016 0.019 -10000 0 0 294 294
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.01 0.049 -10000 0 -0.12 48 48
MAPK11 0.035 0.012 -10000 0 0 54 54
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.011 0.062 -10000 0 -0.12 60 60
OSM/MEKK3 0.028 0.003 -10000 0 -10000 0 0
TAOK1 0.006 0.002 -10000 0 0 41 41
TAOK2 0.009 0.022 -10000 0 -0.19 6 6
TAOK3 0.004 0.039 -10000 0 -0.19 19 19
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.038 0.005 -10000 0 0 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.032 0.015 -10000 0 0 94 94
MAP3K10 0.036 0.01 -10000 0 0 33 33
MAP3K3 0.038 0.005 -10000 0 0 7 7
TRX/ASK1 0.025 0.036 -10000 0 -0.16 13 13
GADD45/MTK1/MTK1 0.046 0.075 -10000 0 -0.12 59 59
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.051 0.082 0.23 5 -0.13 37 42
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.037 0.009 -10000 0 0 32 32
STAT1 (dimer)/Cbp/p300 -0.04 0.099 0.27 25 -0.28 4 29
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.046 0.064 0.18 2 -0.13 38 40
antigen processing and presentation of peptide antigen via MHC class I -0.042 0.077 0.15 7 -0.19 53 60
CaM/Ca2+ 0.046 0.087 0.23 4 -0.14 34 38
RAP1A 0.038 0.006 -10000 0 0 13 13
STAT1 (dimer)/SHP2 -0.033 0.073 0.21 12 -0.2 3 15
AKT1 -0.039 0.098 0.32 11 -0.26 14 25
MAP2K1 -0.039 0.072 0.22 16 -0.22 5 21
MAP3K11 -0.029 0.081 0.25 20 -0.2 1 21
IFNGR1 0.026 0.03 0.12 1 -0.04 67 68
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.12 -10000 0 -0.3 61 61
Rap1/GTP -0.056 0.045 -10000 0 -0.17 6 6
CRKL/C3G 0.052 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.064 0.085 -10000 0 -0.13 34 34
CEBPB -0.008 0.14 0.38 16 -0.44 21 37
STAT3 0.036 0.011 -10000 0 0 42 42
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.058 0.1 -10000 0 -0.76 4 4
STAT1 -0.033 0.08 0.27 15 -0.2 3 18
CALM1 0.034 0.013 -10000 0 0 62 62
IFN-gamma (dimer) 0.023 0.032 -10000 0 -0.042 89 89
PIK3CA 0.033 0.014 -10000 0 0 79 79
STAT1 (dimer)/PIAS1 -0.037 0.088 0.28 15 -0.24 4 19
CEBPB/PTGES2/Cbp/p300 0 0.11 0.25 5 -0.32 25 30
mol:Ca2+ 0.047 0.079 0.22 5 -0.12 38 43
MAPK3 -0.001 0.1 0.42 6 -0.65 4 10
STAT1 (dimer) -0.048 0.11 0.23 9 -0.27 44 53
MAPK1 -0.046 0.21 0.42 6 -0.76 34 40
JAK2 0.024 0.03 -10000 0 -0.043 61 61
PIK3R1 0.034 0.013 -10000 0 0 69 69
JAK1 0.027 0.03 -10000 0 -0.042 42 42
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0 0.12 0.36 16 -0.41 10 26
SMAD7 -0.014 0.073 0.2 31 -0.15 13 44
CBL/CRKL/C3G -0.037 0.09 0.26 19 -10000 0 19
PI3K 0.029 0.1 0.22 5 -0.19 30 35
IFNG 0.024 0.032 -10000 0 -0.042 89 89
apoptosis 0.018 0.11 0.38 12 -0.46 8 20
CAMK2G 0.025 0.019 -10000 0 0 180 180
STAT3 (dimer) 0.036 0.011 -10000 0 0 42 42
CAMK2A 0.038 0.006 -10000 0 0 12 12
CAMK2B 0.016 0.019 -10000 0 0 294 294
FRAP1 -0.041 0.088 0.29 11 -0.24 14 25
PRKCD -0.039 0.098 0.32 13 -0.26 5 18
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.042 0.077 0.15 7 -0.19 53 60
PTPN2 0.037 0.008 -10000 0 0 25 25
EP300 0.035 0.015 -10000 0 -0.035 8 8
IRF1 -0.052 0.068 0.24 8 -0.27 12 20
STAT1 (dimer)/PIASy -0.035 0.082 0.26 14 -0.22 1 15
SOCS1 0.017 0.095 -10000 0 -1 4 4
mol:GDP -0.037 0.085 0.24 19 -0.2 1 20
CASP1 -0.022 0.08 0.23 21 -0.16 51 72
PTGES2 0.037 0.008 -10000 0 0 24 24
IRF9 -0.009 0.066 0.19 17 -0.17 22 39
mol:PI-3-4-5-P3 0.008 0.087 0.18 3 -0.17 42 45
RAP1/GDP -0.049 0.065 0.15 14 -0.19 2 16
CBL -0.03 0.08 0.25 19 -0.2 1 20
MAP3K1 -0.032 0.072 0.24 13 -0.2 1 14
PIAS1 0.037 0.009 -10000 0 0 27 27
PIAS4 0.036 0.01 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.042 0.077 0.15 7 -0.19 53 60
PTPN11 -0.024 0.075 0.23 17 -0.18 3 20
CREBBP 0.038 0.011 -10000 0 -0.035 9 9
RAPGEF1 0.037 0.008 -10000 0 0 23 23
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 0.037 0.009 -10000 0 0 32 32
RAS family/GTP/Tiam1 -0.01 0.083 -10000 0 -0.2 61 61
NT3 (dimer)/TRKC 0.049 0.028 -10000 0 -0.13 7 7
NT3 (dimer)/TRKB 0.029 0.069 -10000 0 -0.12 73 73
SHC/Grb2/SOS1/GAB1/PI3K -0.007 0.089 -10000 0 -0.21 67 67
RAPGEF1 0.037 0.008 -10000 0 0 23 23
BDNF 0.033 0.014 -10000 0 0 72 72
PIK3CA 0.033 0.014 -10000 0 0 79 79
DYNLT1 0.035 0.011 -10000 0 0 47 47
NTRK1 0.038 0.007 -10000 0 0 16 16
NTRK2 0.028 0.017 -10000 0 0 141 141
NTRK3 0.036 0.01 -10000 0 0 38 38
NT-4/5 (dimer)/TRKB 0.016 0.056 -10000 0 -0.1 78 78
neuron apoptosis -0.009 0.12 0.31 39 -0.26 3 42
SHC 2-3/Grb2 0.009 0.13 0.27 3 -0.33 39 42
SHC1 0.035 0.012 -10000 0 0 56 56
SHC2 -0.009 0.12 -10000 0 -0.43 25 25
SHC3 -0.01 0.12 -10000 0 -0.4 30 30
STAT3 (dimer) 0.033 0.072 -10000 0 -0.26 25 25
NT3 (dimer)/TRKA 0.062 0.033 -10000 0 -10000 0 0
RIN/GDP -0.001 0.076 0.22 10 -0.23 22 32
GIPC1 0.036 0.01 -10000 0 0 36 36
KRAS 0.036 0.011 -10000 0 0 40 40
DNAJA3 -0.008 0.043 0.12 7 -0.17 3 10
RIN/GTP 0.013 0.032 -10000 0 -0.11 26 26
CCND1 -0.046 0.098 -10000 0 -0.47 25 25
MAGED1 0.037 0.009 -10000 0 0 27 27
PTPN11 0.038 0.007 -10000 0 0 17 17
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.041 0.031 -10000 0 -0.11 14 14
GRB2 0.037 0.009 -10000 0 0 26 26
NGF (dimer)/TRKA/MATK 0.047 0.016 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.05 0.021 -10000 0 -0.13 1 1
ELMO1 0.017 0.019 -10000 0 0 290 290
RhoG/GTP/ELMO1/DOCK1 0.01 0.041 -10000 0 -0.1 39 39
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.036 0.01 -10000 0 0 39 39
DOCK1 0.026 0.019 -10000 0 0 175 175
GAB2 0.035 0.012 -10000 0 0 52 52
RIT2 0.026 0.018 -10000 0 0 171 171
RIT1 0.034 0.013 -10000 0 0 62 62
FRS2 0.037 0.009 -10000 0 0 31 31
DNM1 0.037 0.009 -10000 0 0 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.037 0.008 -10000 0 0 25 25
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.009 0.044 -10000 0 -0.15 10 10
mol:GDP -0.005 0.11 0.28 14 -0.31 26 40
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.004 0.036 -10000 0 -0.11 38 38
RIT1/GDP 0.005 0.086 0.24 13 -0.23 21 34
TIAM1 0.035 0.012 -10000 0 0 50 50
PIK3R1 0.034 0.013 -10000 0 0 69 69
BDNF (dimer)/TRKB 0.029 0.07 -10000 0 -0.12 75 75
KIDINS220/CRKL/C3G 0.052 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.04 0.048 -10000 0 -0.14 30 30
FRS2 family/SHP2 0.071 0.029 -10000 0 -0.12 6 6
SHC/GRB2/SOS1/GAB1 0.051 0.047 -10000 0 -0.11 25 25
RIT1/GTP 0.017 0.036 -10000 0 -0.11 36 36
NT3 (dimer) 0.037 0.009 -10000 0 0 30 30
RAP1/GDP -0.006 0.061 0.11 1 -0.18 28 29
KIDINS220/CRKL 0.036 0.009 -10000 0 0 32 32
BDNF (dimer) 0.033 0.014 -10000 0 0 72 72
ubiquitin-dependent protein catabolic process 0.045 0.018 -10000 0 -0.1 1 1
Schwann cell development -0.012 0.017 -10000 0 -0.056 27 27
EHD4 0.036 0.011 -10000 0 0 43 43
FRS2 family/GRB2/SOS1 0.065 0.031 -10000 0 -0.1 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.002 0.071 -10000 0 -0.25 23 23
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.038 0.006 -10000 0 0 13 13
CDC42/GTP -0.05 0.07 0.15 14 -0.19 24 38
ABL1 0.033 0.014 -10000 0 0 72 72
SH2B family/GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
Rap1/GTP -0.003 0.076 -10000 0 -0.23 30 30
STAT3 0.033 0.072 -10000 0 -0.26 25 25
axon guidance -0.052 0.061 0.11 10 -0.19 26 36
MAPK3 -0.016 0.066 0.18 48 -10000 0 48
MAPK1 -0.016 0.061 0.19 39 -10000 0 39
CDC42/GDP 0.005 0.083 0.22 12 -0.22 22 34
NTF3 0.037 0.009 -10000 0 0 30 30
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.046 0.025 -10000 0 -0.1 9 9
PI3K 0.023 0.07 -10000 0 -0.14 72 72
FRS3 0.039 0.003 -10000 0 0 4 4
FAIM 0.036 0.01 -10000 0 0 34 34
GAB1 0.035 0.012 -10000 0 0 56 56
RASGRF1 -0.009 0.043 0.12 6 -0.16 2 8
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.023 0.044 0.15 24 -10000 0 24
RGS19 0.033 0.014 -10000 0 0 81 81
CDC42 0.037 0.009 -10000 0 0 27 27
RAS family/GTP 0.006 0.1 0.24 3 -0.4 19 22
Rac1/GDP 0.004 0.068 0.24 7 -0.23 13 20
NGF (dimer)/TRKA/GRIT 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.037 0.24 -10000 0 -0.82 39 39
NGF (dimer)/TRKA/NEDD4-2 0.046 0.019 -10000 0 -0.1 1 1
MAP2K1 -0.015 0.075 0.18 34 -0.17 6 40
NGFR 0.033 0.014 -10000 0 0 74 74
NGF (dimer)/TRKA/GIPC/GAIP 0.008 0.043 -10000 0 -0.21 11 11
RAS family/GTP/PI3K -0.027 0.1 -10000 0 -0.21 100 100
FRS2 family/SHP2/GRB2/SOS1 0.079 0.042 -10000 0 -0.13 10 10
NRAS 0.034 0.013 -10000 0 0 66 66
GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
PRKCI 0.037 0.009 -10000 0 0 28 28
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.085 -10000 0 -0.45 13 13
RASA1 0.036 0.01 -10000 0 0 37 37
TRKA/c-Abl 0.036 0.055 -10000 0 -0.13 48 48
SQSTM1 0.036 0.011 -10000 0 0 40 40
BDNF (dimer)/TRKB/GIPC 0.05 0.078 -10000 0 -0.12 64 64
NGF (dimer)/TRKA/p62/Atypical PKCs 0.056 0.035 -10000 0 -0.097 14 14
MATK 0.036 0.01 -10000 0 0 37 37
NEDD4L 0.035 0.012 -10000 0 0 50 50
RAS family/GDP -0.03 0.053 -10000 0 -0.16 46 46
NGF (dimer)/TRKA 0.012 0.042 0.14 4 -0.15 2 6
Rac1/GTP -0.026 0.049 -10000 0 -0.2 20 20
FRS2 family/SHP2/CRK family 0.09 0.062 -10000 0 -0.12 17 17
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.03 0.097 0.19 2 -0.34 29 31
adherens junction organization -0.003 0.076 0.19 1 -0.34 15 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.1 0.25 18 -0.34 11 29
FMN1 0.007 0.061 0.16 2 -0.3 9 11
mol:IP3 -0.027 0.073 0.14 12 -0.3 18 30
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.012 0.064 -10000 0 -0.31 9 9
CTNNB1 0.036 0.012 -10000 0 -0.012 27 27
AKT1 -0.024 0.082 0.15 7 -0.32 20 27
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.026 0.076 -10000 0 -0.35 8 8
CTNND1 0.036 0.013 -10000 0 -0.004 41 41
mol:PI-4-5-P2 -0.005 0.069 0.17 7 -0.3 13 20
VASP -0.008 0.064 0.16 3 -0.3 12 15
ZYX 0.001 0.046 0.16 5 -0.3 5 10
JUB 0.007 0.061 0.16 2 -0.3 9 11
EGFR(dimer) 0.001 0.059 0.21 1 -0.3 11 12
E-cadherin/beta catenin-gamma catenin 0.067 0.031 -10000 0 -0.11 3 3
mol:PI-3-4-5-P3 0.028 0.096 0.21 5 -0.3 19 24
PIK3CA 0.03 0.022 -10000 0 -0.038 29 29
PI3K 0.029 0.098 0.22 5 -0.3 19 24
FYN -0.043 0.12 0.21 2 -0.31 68 70
mol:Ca2+ -0.027 0.072 0.14 12 -0.3 18 30
JUP 0.035 0.014 -10000 0 -0.002 58 58
PIK3R1 0.03 0.023 -10000 0 -0.038 31 31
mol:DAG -0.027 0.073 0.14 12 -0.3 18 30
CDH1 0.036 0.011 -10000 0 -0.002 40 40
RhoA/GDP 0.041 0.12 0.25 28 -0.34 12 40
establishment of polarity of embryonic epithelium -0.005 0.067 0.18 9 -0.3 12 21
SRC 0.034 0.013 -10000 0 0 65 65
RAC1 0.023 0.019 -10000 0 0 209 209
RHOA 0.037 0.008 -10000 0 0 24 24
EGFR 0.009 0.017 -10000 0 0 385 385
CASR -0.032 0.072 0.16 6 -0.29 18 24
RhoA/GTP -0.03 0.075 0.18 4 -0.29 18 22
AKT2 -0.026 0.077 0.16 7 -0.3 19 26
actin cable formation -0.007 0.067 0.17 9 -0.29 13 22
apoptosis 0.018 0.093 0.32 26 -0.19 5 31
CTNNA1 0.037 0.013 -10000 0 -0.011 29 29
mol:GDP -0.021 0.066 0.2 3 -0.3 16 19
PIP5K1A -0.007 0.067 0.16 3 -0.29 14 17
PLCG1 -0.028 0.074 0.15 12 -0.31 18 30
Rac1/GTP -0.003 0.063 -10000 0 -0.28 12 12
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.05 0.042 -10000 0 -0.094 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.047 0.17 -10000 0 -0.5 44 44
AKT1 -0.056 0.23 -10000 0 -0.63 60 60
PIK3CA 0.033 0.014 -10000 0 0 79 79
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.046 0.24 -10000 0 -0.64 60 60
mol:Ca2+ -0.001 0.063 -10000 0 -0.23 4 4
IGF1R 0.035 0.012 -10000 0 0 54 54
E2/ER alpha (dimer)/Striatin 0.049 0.014 -10000 0 -10000 0 0
SHC1 0.035 0.012 -10000 0 0 56 56
apoptosis 0.053 0.22 0.6 61 -10000 0 61
RhoA/GTP -0.056 0.039 -10000 0 -0.18 14 14
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.004 0.16 0.23 20 -0.4 44 64
regulation of stress fiber formation 0.055 0.064 0.22 5 -0.24 4 9
E2/ERA-ERB (dimer) 0.046 0.017 -10000 0 -10000 0 0
KRAS 0.036 0.011 -10000 0 0 40 40
G13/GTP 0.045 0.015 -10000 0 -10000 0 0
pseudopodium formation -0.055 0.064 0.24 4 -0.22 5 9
E2/ER alpha (dimer)/PELP1 0.046 0.023 -10000 0 -0.1 7 7
GRB2 0.037 0.009 -10000 0 0 26 26
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.032 0.015 -10000 0 0 88 88
HRAS 0.036 0.01 -10000 0 0 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.011 0.17 0.27 1 -0.43 47 48
E2/ER beta (dimer) 0.027 0.008 -10000 0 -10000 0 0
mol:GDP -0.034 0.054 0.13 4 -0.21 26 30
mol:NADP -0.011 0.17 0.27 1 -0.43 47 48
PIK3R1 0.034 0.013 -10000 0 0 69 69
mol:IP3 -0.003 0.061 0.16 33 -0.24 3 36
IGF-1R heterotetramer 0.035 0.012 -10000 0 0 54 54
PLCB1 0.003 0.038 -10000 0 -0.22 1 1
PLCB2 0.002 0.037 -10000 0 -0.22 1 1
IGF1 0.037 0.009 -10000 0 0 28 28
mol:L-citrulline -0.011 0.17 0.27 1 -0.43 47 48
RHOA 0.037 0.008 -10000 0 0 24 24
Gai/GDP -0.07 0.23 -10000 0 -0.63 68 68
JNK cascade 0.027 0.008 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.036 0.01 -10000 0 0 38 38
GNAQ 0.036 0.01 -10000 0 0 37 37
ESR1 0.036 0.01 -10000 0 0 36 36
Gq family/GDP/Gbeta gamma -0.01 0.15 -10000 0 -0.49 33 33
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.14 -10000 0 -0.7 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.009 0.17 0.25 24 -0.42 40 64
GNAZ 0.033 0.014 -10000 0 0 83 83
E2/ER alpha (dimer) 0.027 0.007 -10000 0 -10000 0 0
STRN 0.039 0.003 -10000 0 0 4 4
GNAL 0.037 0.008 -10000 0 0 21 21
PELP1 0.037 0.008 -10000 0 0 20 20
MAPK11 -0.024 0.01 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 0 46 46
GNAI3 0.038 0.007 -10000 0 0 16 16
GNAI1 0.016 0.019 -10000 0 0 297 297
HBEGF 0.001 0.2 0.34 46 -0.47 42 88
cAMP biosynthetic process 0.037 0.022 -10000 0 -10000 0 0
SRC -0.045 0.16 0.2 6 -0.47 45 51
PI3K 0.023 0.07 -10000 0 -0.14 72 72
GNB1 0.035 0.011 -10000 0 0 46 46
G13/GDP/Gbeta gamma 0.019 0.074 -10000 0 -0.19 31 31
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.029 0.12 -10000 0 -0.32 48 48
Gs family/GTP 0.047 0.026 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.064 -10000 0 -0.12 53 53
vasodilation -0.009 0.16 0.27 1 -0.41 47 48
mol:DAG -0.003 0.061 0.16 33 -0.24 3 36
Gs family/GDP/Gbeta gamma -0.048 0.05 0.086 4 -0.2 28 32
MSN -0.059 0.066 0.25 3 -0.24 5 8
Gq family/GTP 0.018 0.041 -10000 0 -0.22 1 1
mol:PI-3-4-5-P3 -0.044 0.23 -10000 0 -0.61 61 61
NRAS 0.034 0.013 -10000 0 0 66 66
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.009 0.16 0.41 47 -0.27 1 48
GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
RhoA/GDP 0.014 0.074 -10000 0 -0.21 27 27
NOS3 -0.013 0.18 0.27 1 -0.46 47 48
GNA11 0.034 0.013 -10000 0 0 63 63
MAPKKK cascade 0.004 0.16 -10000 0 -0.48 36 36
E2/ER alpha (dimer)/PELP1/Src 0.007 0.17 0.26 25 -0.42 43 68
ruffle organization -0.055 0.064 0.24 4 -0.22 5 9
ROCK2 -0.047 0.072 0.28 4 -0.25 2 6
GNA14 0.036 0.01 -10000 0 0 36 36
GNA15 0.034 0.013 -10000 0 0 62 62
GNA13 0.037 0.008 -10000 0 0 22 22
MMP9 -0.026 0.17 0.33 8 -0.44 47 55
MMP2 -0.024 0.18 0.26 25 -0.47 45 70
IGF1 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
NCK2 0.037 0.008 -10000 0 0 20 20
PTK2 0.036 0.01 -10000 0 0 37 37
CRKL -0.023 0.05 0.12 27 -0.14 22 49
GRB2/SOS1/SHC 0.041 0.031 -10000 0 -0.11 14 14
HRAS 0.036 0.01 -10000 0 0 39 39
IRS1/Crk -0.031 0.041 0.069 41 -0.15 23 64
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.056 -10000 0 -0.14 27 27
AKT1 -0.045 0.076 0.16 26 -0.21 24 50
BAD -0.052 0.072 0.17 16 -0.22 23 39
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.023 0.05 0.12 27 -0.15 20 47
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.025 0.048 0.22 2 -0.14 27 29
RAF1 -0.044 0.14 0.31 4 -0.55 28 32
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.049 0.053 -10000 0 -0.13 26 26
YWHAZ 0.037 0.008 -10000 0 0 23 23
IGF-1R heterotetramer/IGF1/IRS1 0.035 0.048 -10000 0 -0.15 22 22
PIK3CA 0.033 0.014 -10000 0 0 79 79
RPS6KB1 -0.044 0.077 0.17 31 -0.2 15 46
GNB2L1 0.038 0.006 -10000 0 0 13 13
positive regulation of MAPKKK cascade -0.041 0.12 0.29 4 -0.42 29 33
PXN 0.038 0.006 -10000 0 0 11 11
PIK3R1 0.034 0.013 -10000 0 0 69 69
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
HRAS/GTP -0.044 0.04 0.071 12 -0.16 22 34
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.07 0.058 -10000 0 -0.12 31 31
IGF-1R heterotetramer 0.039 0.016 -10000 0 -0.047 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.052 0.059 -10000 0 -0.14 32 32
Crk/p130 Cas/Paxillin 0.038 0.054 0.2 2 -0.13 34 36
IGF1R 0.039 0.016 -10000 0 -0.047 2 2
IGF1 0.036 0.027 -10000 0 -0.066 27 27
IRS2/Crk -0.037 0.056 0.12 18 -0.19 20 38
PI3K 0.044 0.085 -10000 0 -0.13 72 72
apoptosis 0.05 0.083 0.24 13 -0.24 10 23
HRAS/GDP 0.023 0.025 -10000 0 -0.11 16 16
PRKCD -0.001 0.066 0.18 18 -0.21 22 40
RAF1/14-3-3 E -0.037 0.13 0.31 4 -0.48 28 32
BAD/14-3-3 -0.052 0.086 0.25 10 -0.26 13 23
PRKCZ -0.035 0.076 0.18 32 -0.19 15 47
Crk/p130 Cas/Paxillin/FAK1 -0.064 0.076 0.13 22 -0.23 22 44
PTPN1 0.034 0.013 -10000 0 0 70 70
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.003 0.058 -10000 0 -0.22 24 24
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.036 0.069 -10000 0 -0.14 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.027 0.05 0.14 8 -0.14 32 40
GRB10 0.02 0.02 -10000 0 0 254 254
PTPN11 -0.025 0.049 0.12 26 -0.15 21 47
IRS1 -0.019 0.037 0.095 33 -0.13 15 48
IRS2 -0.021 0.045 0.15 9 -0.16 12 21
IGF-1R heterotetramer/IGF1 0.044 0.048 -10000 0 -0.16 22 22
GRB2 0.037 0.009 -10000 0 0 26 26
PDPK1 -0.034 0.084 0.2 32 -0.2 14 46
YWHAE 0.037 0.009 -10000 0 0 29 29
PRKD1 -0.006 0.058 0.16 4 -0.23 20 24
SHC1 0.035 0.012 -10000 0 0 56 56
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.002 0.097 -10000 0 -0.39 28 28
Crk/p130 Cas/Paxillin -0.076 0.085 -10000 0 -0.21 110 110
JUN -0.027 0.049 -10000 0 -0.25 11 11
HRAS 0.036 0.01 -10000 0 0 39 39
RET51/GFRalpha1/GDNF/GRB10 0.034 0.063 -10000 0 -0.12 28 28
RAP1A 0.038 0.006 -10000 0 0 13 13
FRS2 0.037 0.009 -10000 0 0 31 31
RAP1A/GDP 0.028 0.008 -10000 0 -0.11 1 1
RET51/GFRalpha1/GDNF/DOK1 0.06 0.058 -10000 0 -10000 0 0
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.038 0.007 -10000 0 0 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.037 0.008 -10000 0 0 25 25
RET9/GFRalpha1/GDNF/Enigma 0.043 0.046 -10000 0 -10000 0 0
RHOA 0.037 0.008 -10000 0 0 24 24
RAP1A/GTP 0.053 0.06 -10000 0 -0.11 1 1
GRB7 0.038 0.007 -10000 0 0 17 17
RET51/GFRalpha1/GDNF 0.06 0.057 -10000 0 -10000 0 0
MAPKKK cascade -0.067 0.052 -10000 0 -0.21 9 9
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.035 0.054 -10000 0 -0.099 24 24
lamellipodium assembly -0.024 0.078 -10000 0 -0.21 44 44
RET51/GFRalpha1/GDNF/SHC 0.056 0.062 -10000 0 -0.12 8 8
PIK3CA 0.033 0.014 -10000 0 0 79 79
RET9/GFRalpha1/GDNF/SHC 0.036 0.049 -10000 0 -0.1 8 8
RET9/GFRalpha1/GDNF/Shank3 0.034 0.023 -10000 0 -10000 0 0
MAPK3 -0.045 0.047 0.27 4 -10000 0 4
DOK1 0.039 0.003 -10000 0 0 3 3
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.038 0.006 -10000 0 0 11 11
neurite development -0.034 0.054 0.25 7 -0.22 8 15
DOK5 0.029 0.017 -10000 0 0 133 133
GFRA1 0.027 0.018 -10000 0 0 158 158
MAPK8 -0.017 0.044 -10000 0 -0.25 6 6
HRAS/GTP 0.019 0.1 -10000 0 -0.15 115 115
tube development 0.021 0.04 0.2 10 -0.094 8 18
MAPK1 -0.041 0.049 0.27 4 -10000 0 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.064 -10000 0 -0.21 13 13
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
SRC 0.034 0.013 -10000 0 0 65 65
PDLIM7 0.038 0.006 -10000 0 0 13 13
RET51/GFRalpha1/GDNF/Dok6 0.056 0.052 -10000 0 -10000 0 0
SHC1 0.035 0.012 -10000 0 0 56 56
RET51/GFRalpha1/GDNF/Dok4 0.06 0.058 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.038 0.076 -10000 0 -0.11 63 63
PRKCA 0.038 0.005 -10000 0 0 10 10
HRAS/GDP 0.023 0.025 -10000 0 -0.11 16 16
CREB1 -0.034 0.1 -10000 0 -0.2 117 117
PIK3R1 0.034 0.013 -10000 0 0 69 69
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.067 -10000 0 -0.18 27 27
RET51/GFRalpha1/GDNF/Grb7 0.06 0.058 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.028 0.017 -10000 0 0 137 137
DOK4 0.038 0.006 -10000 0 0 11 11
JNK cascade -0.026 0.049 -10000 0 -0.25 11 11
RET9/GFRalpha1/GDNF/FRS2 0.042 0.046 -10000 0 -10000 0 0
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.036 0.01 -10000 0 0 37 37
NCK1 0.037 0.009 -10000 0 0 31 31
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.017 0.061 -10000 0 -0.18 17 17
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.099 -10000 0 -0.21 110 110
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.042 0.1 -10000 0 -0.2 133 133
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.047 -10000 0 -0.19 17 17
PI3K -0.07 0.13 0.19 1 -0.28 95 96
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.037 0.045 -10000 0 -0.094 8 8
GRB10 0.02 0.02 -10000 0 0 254 254
activation of MAPKK activity -0.023 0.077 -10000 0 -0.28 10 10
RET51/GFRalpha1/GDNF/FRS2 0.057 0.058 -10000 0 -10000 0 0
GAB1 0.035 0.012 -10000 0 0 56 56
IRS1 0.035 0.012 -10000 0 0 53 53
IRS2 0.032 0.015 -10000 0 0 96 96
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.008 0.053 -10000 0 -0.26 6 6
RET51/GFRalpha1/GDNF/PKC alpha 0.059 0.058 -10000 0 -10000 0 0
GRB2 0.037 0.009 -10000 0 0 26 26
PRKACA 0.036 0.01 -10000 0 0 36 36
GDNF 0.038 0.006 -10000 0 0 11 11
RAC1 0.023 0.019 -10000 0 0 209 209
RET51/GFRalpha1/GDNF/IRS1 0.054 0.066 -10000 0 -0.11 23 23
Rac1/GTP -0.027 0.092 -10000 0 -0.25 43 43
RET9/GFRalpha1/GDNF 0.036 0.025 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.039 0.027 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.035 0.11 36 -10000 0 36
SNTA1 0.031 0.016 -10000 0 0 105 105
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.024 0.044 0.1 51 -10000 0 51
MAPK12 -0.02 0.032 0.15 7 -0.16 10 17
CCND1 -0.024 0.1 -10000 0 -0.37 41 41
p38 gamma/SNTA1 -0.022 0.041 0.19 5 -0.16 11 16
MAP2K3 0.038 0.006 -10000 0 0 14 14
PKN1 0.034 0.013 -10000 0 0 60 60
G2/M transition checkpoint -0.02 0.033 0.19 5 -0.16 10 15
MAP2K6 -0.016 0.024 0.12 1 -0.17 11 12
MAPT -0.032 0.075 0.18 4 -0.21 57 61
MAPK13 -0.024 0.039 0.12 36 -10000 0 36
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.002 -10000 0 0 60 60
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.03 0.083 0.24 32 -0.28 6 38
FYN -0.009 0.1 0.26 19 -0.29 27 46
LAT/GRAP2/SLP76 0.013 0.077 0.3 7 -0.3 7 14
IKBKB 0.038 0.005 -10000 0 0 7 7
AKT1 0.002 0.094 0.27 20 -0.26 15 35
B2M 0.04 0.011 0.075 1 -10000 0 1
IKBKG -0.008 0.043 0.12 20 -0.12 4 24
MAP3K8 0.024 0.019 -10000 0 0 190 190
mol:Ca2+ -0.011 0.013 -10000 0 -0.047 2 2
integrin-mediated signaling pathway 0.025 0.006 -10000 0 -0.091 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.008 0.11 0.31 19 -0.33 12 31
TRPV6 0.49 0.61 1.2 211 -10000 0 211
CD28 0.04 0.003 -10000 0 0 2 2
SHC1 0.019 0.091 0.26 35 -0.35 5 40
receptor internalization 0.02 0.07 0.22 12 -0.41 6 18
PRF1 -0.12 0.32 0.48 3 -0.61 140 143
KRAS 0.036 0.011 -10000 0 0 40 40
GRB2 0.037 0.009 -10000 0 0 26 26
COT/AKT1 0.002 0.068 0.24 6 -0.23 14 20
LAT 0.011 0.081 0.27 15 -0.35 6 21
EntrezGene:6955 0.002 0.006 0.026 8 -10000 0 8
CD3D 0.037 0.013 -10000 0 -10000 0 0
CD3E 0.04 0.01 0.076 2 -0.034 1 3
CD3G 0.039 0.01 -10000 0 -10000 0 0
RASGRP2 0.005 0.02 0.082 2 -0.15 5 7
RASGRP1 -0.017 0.13 0.26 32 -0.25 77 109
HLA-A 0.002 0.007 0.029 14 -10000 0 14
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.025 0.007 -10000 0 -0.091 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.063 0.16 45 -0.1 9 54
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.025 0.033 -10000 0 -0.13 18 18
PRKCA 0.006 0.083 0.21 46 -0.18 5 51
GRAP2 0.036 0.01 -10000 0 0 39 39
mol:IP3 -0.026 0.052 -10000 0 -0.25 6 6
EntrezGene:6957 0.002 0.007 0.028 11 -10000 0 11
TCR/CD3/MHC I/CD8 0.021 0.059 0.17 41 -0.29 5 46
ORAI1 -0.43 0.51 -10000 0 -1 211 211
CSK 0.012 0.079 0.25 19 -0.34 6 25
B7 family/CD28 0.068 0.11 0.32 44 -0.3 8 52
CHUK 0.027 0.018 -10000 0 0 155 155
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.017 0.077 0.24 16 -0.38 6 22
PTPN6 0.013 0.089 0.26 22 -0.33 7 29
VAV1 0.023 0.089 0.27 24 -0.36 5 29
Monovalent TCR/CD3 0.025 0.027 0.15 9 -10000 0 9
CBL 0.038 0.006 -10000 0 0 11 11
LCK 0.007 0.094 0.27 22 -0.33 8 30
PAG1 0.018 0.076 0.23 22 -0.34 6 28
RAP1A 0.038 0.006 -10000 0 0 13 13
TCR/CD3/MHC I/CD8/LCK 0.017 0.079 0.24 19 -0.37 6 25
CD80 0.038 0.008 -10000 0 0 18 18
CD86 0.034 0.013 -10000 0 0 67 67
PDK1/CARD11/BCL10/MALT1 -0.017 0.046 -10000 0 -0.17 12 12
HRAS 0.036 0.01 -10000 0 0 39 39
GO:0035030 0.003 0.088 0.21 47 -0.26 8 55
CD8A 0.002 0.007 0.028 13 -10000 0 13
CD8B 0.04 0.01 0.075 1 -0.035 3 4
PTPRC 0.03 0.016 -10000 0 0 114 114
PDK1/PKC theta 0.005 0.1 0.29 22 -0.31 8 30
CSK/PAG1 0.009 0.075 0.23 18 -0.32 6 24
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.019 0.087 5 -0.12 4 9
GRAP2/SLP76 0.032 0.082 0.3 7 -0.34 7 14
STIM1 -0.087 0.14 1 4 -10000 0 4
RAS family/GTP 0.007 0.079 0.19 28 -0.18 27 55
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.02 0.072 0.23 12 -0.42 6 18
mol:DAG -0.028 0.038 -10000 0 -0.23 6 6
RAP1A/GDP 0.011 0.032 0.084 36 -0.055 7 43
PLCG1 0.034 0.013 -10000 0 0 70 70
CD247 0.04 0.01 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.12 0.31 0.48 3 -0.6 140 143
RAP1A/GTP 0.005 0.008 -10000 0 -0.055 5 5
mol:PI-3-4-5-P3 0.01 0.1 0.3 20 -0.29 12 32
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.025 0.067 0.21 5 -0.3 6 11
NRAS 0.034 0.013 -10000 0 0 66 66
ZAP70 0.039 0.003 -10000 0 0 3 3
GRB2/SOS1 0.026 0.018 -10000 0 -0.11 8 8
LAT/GRAP2/SLP76/VAV1 -0.01 0.072 0.23 6 -0.32 5 11
MALT1 0.036 0.01 -10000 0 0 36 36
TRAF6 0.038 0.007 -10000 0 0 17 17
CD8 heterodimer 0.032 0.013 0.079 12 -0.025 2 14
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.022 0.028 -10000 0 -0.17 6 6
PRKCE 0.006 0.083 0.21 45 -0.19 4 49
PRKCQ 0.01 0.1 0.31 22 -0.32 10 32
LCP2 0.033 0.014 -10000 0 0 80 80
BCL10 0.037 0.008 -10000 0 0 21 21
regulation of survival gene product expression 0.003 0.087 0.26 20 -0.23 15 35
IKK complex 0.001 0.048 0.17 19 -10000 0 19
RAS family/GDP -0.007 0.014 -10000 0 -0.042 26 26
MAP3K14 0 0.076 0.21 31 -0.18 14 45
PDPK1 0.002 0.088 0.26 21 -0.25 11 32
TCR/CD3/MHC I/CD8/Fyn 0.01 0.066 -10000 0 -0.36 8 8
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0.073 -10000 0 -0.3 21 21
KLHL20 0.051 0.12 0.25 90 -0.2 17 107
CYFIP2 0.033 0.014 -10000 0 0 78 78
Rac1/GDP -0.008 0.065 0.21 6 -0.27 8 14
ENAH 0.003 0.07 -10000 0 -0.32 17 17
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0.001 65 0 8 73
RAP1A 0.038 0.006 -10000 0 0 13 13
CTNNB1 0.038 0.007 -10000 0 0 18 18
CDC42/GTP -0.035 0.064 0.12 41 -0.23 13 54
ABI1/Sra1/Nap1 -0.02 0.034 -10000 0 -0.13 31 31
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.086 0.044 -10000 0 -0.12 8 8
RAPGEF1 -0.006 0.089 0.25 5 -0.3 15 20
CTNND1 0.036 0.01 -10000 0 0 37 37
regulation of calcium-dependent cell-cell adhesion 0.017 0.077 -10000 0 -0.3 22 22
CRK 0 0.089 0.21 8 -0.31 17 25
E-cadherin/gamma catenin/alpha catenin 0.065 0.036 -10000 0 -0.12 8 8
alphaE/beta7 Integrin 0.052 0.024 -10000 0 -0.13 6 6
IQGAP1 0.035 0.012 -10000 0 0 49 49
NCKAP1 0.039 0.003 -10000 0 0 3 3
Rap1/GTP/I-afadin 0.045 0.017 -10000 0 -0.09 1 1
DLG1 -0.001 0.075 -10000 0 -0.31 21 21
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.046 0.044 -10000 0 -0.18 27 27
MLLT4 0.036 0.011 -10000 0 0 45 45
ARF6/GTP/NME1/Tiam1 0.039 0.032 -10000 0 -0.091 22 22
PI3K -0.054 0.059 0.078 1 -0.23 27 28
ARF6 0.037 0.01 -10000 0 0 33 33
mol:Ca2+ 0 0.001 0.001 70 0 15 85
E-cadherin/gamma catenin 0.051 0.019 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 0 50 50
E-cadherin(dimer)/Ca2+ 0.075 0.055 -10000 0 -0.13 22 22
AKT1 -0.024 0.066 0.16 21 -0.18 18 39
PIK3R1 0.034 0.013 -10000 0 0 69 69
CDH1 0.036 0.01 -10000 0 0 38 38
RhoA/GDP -0.007 0.088 0.22 12 -0.28 9 21
actin cytoskeleton organization 0.044 0.099 0.21 90 -0.15 17 107
CDC42/GDP -0.008 0.086 0.22 10 -0.28 8 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.051 -10000 0 -0.19 25 25
ITGB7 0.038 0.007 -10000 0 0 18 18
RAC1 0.023 0.019 -10000 0 0 209 209
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.081 0.059 -10000 0 -0.14 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.058 0.034 -10000 0 -0.1 10 10
mol:GDP -0.006 0.089 0.26 7 -0.31 9 16
CDC42/GTP/IQGAP1 0.039 0.04 -10000 0 -0.1 32 32
JUP 0.035 0.012 -10000 0 0 55 55
p120 catenin/RhoA/GDP -0.004 0.096 0.23 14 -0.27 10 24
RAC1/GTP/IQGAP1 0.023 0.039 -10000 0 -0.1 26 26
PIP5K1C/AP1M1 0.021 0.027 -10000 0 -0.11 19 19
RHOA 0.037 0.008 -10000 0 0 24 24
CDC42 0.037 0.009 -10000 0 0 27 27
CTNNA1 0.038 0.008 -10000 0 0 20 20
positive regulation of S phase of mitotic cell cycle 0.011 0.05 0.12 33 -0.11 26 59
NME1 0 0 -10000 0 0 26 26
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.002 0.073 -10000 0 -0.31 19 19
regulation of cell-cell adhesion -0.041 0.041 0.076 3 -0.18 20 23
WASF2 -0.011 0.019 -10000 0 -0.073 31 31
Rap1/GTP -0.028 0.076 0.15 50 -0.25 14 64
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.094 0.056 -10000 0 -0.13 12 12
CCND1 0.012 0.059 0.13 33 -0.13 29 62
VAV2 0.017 0.14 -10000 0 -0.55 18 18
RAP1/GDP -0.015 0.079 0.2 14 -0.25 13 27
adherens junction assembly 0.002 0.074 0.19 1 -0.3 21 22
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.018 -10000 0 0 150 150
PIP5K1C 0.034 0.013 -10000 0 0 60 60
regulation of heterotypic cell-cell adhesion 0.067 0.053 0.21 1 -0.14 14 15
E-cadherin/beta catenin 0.001 0.027 -10000 0 -0.13 10 10
mol:GTP 0 0 0.001 66 0 26 92
SRC 0.002 0.073 0.21 7 -0.3 18 25
PIK3CA 0.033 0.014 -10000 0 0 79 79
Rac1/GTP -0.01 0.076 0.2 8 -0.28 24 32
E-cadherin/beta catenin/alpha catenin 0.067 0.037 -10000 0 -0.12 10 10
ITGAE 0.037 0.008 -10000 0 0 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.078 -10000 0 -0.31 22 22
S1P3 pathway

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
PDGFRB 0.037 0.009 -10000 0 0 29 29
mol:S1P 0.001 0.003 0.031 4 -10000 0 4
S1P1/S1P/Gi -0.012 0.082 -10000 0 -0.2 63 63
GNAO1 0.033 0.015 0.077 2 -10000 0 2
S1P/S1P3/G12/G13 0.023 0.036 -10000 0 -0.092 24 24
AKT1 -0.016 0.16 -10000 0 -0.45 56 56
AKT3 -0.025 0.12 -10000 0 -0.47 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.009 -10000 0 0 29 29
GNAI2 0.036 0.012 0.077 2 -10000 0 2
GNAI3 0.039 0.008 -10000 0 -10000 0 0
GNAI1 0.016 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.003 0.033 4 -10000 0 4
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.094 0.26 2 -0.27 32 34
MAPK3 -0.007 0.096 0.18 6 -0.27 35 41
MAPK1 0 0.089 0.18 8 -0.26 27 35
JAK2 -0.003 0.1 0.2 15 -0.32 28 43
CXCR4 -0.001 0.097 0.18 13 -0.28 33 46
FLT1 0.037 0.012 0.087 4 -10000 0 4
RhoA/GDP 0.026 0.017 -10000 0 -0.11 7 7
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
SRC -0.009 0.091 0.17 5 -0.28 29 34
S1P/S1P3/Gi 0.004 0.094 0.26 2 -0.27 32 34
RAC1 0.023 0.019 -10000 0 0 209 209
RhoA/GTP 0.017 0.11 0.24 2 -0.26 37 39
VEGFA 0.026 0.02 0.087 4 -10000 0 4
S1P/S1P2/Gi 0.003 0.093 0.2 2 -0.24 42 44
VEGFR1 homodimer/VEGFA homodimer 0.01 0.076 0.17 4 -0.13 107 111
RHOA 0.037 0.008 -10000 0 0 24 24
S1P/S1P3/Gq 0.012 0.039 -10000 0 -0.14 25 25
GNAQ 0.036 0.01 -10000 0 0 37 37
GNAZ 0.033 0.015 -10000 0 -10000 0 0
G12/G13 0.025 0.044 -10000 0 -0.13 24 24
GNA14 0.036 0.01 -10000 0 0 36 36
GNA15 0.034 0.013 -10000 0 0 62 62
GNA12 0.022 0.019 -10000 0 0 227 227
GNA13 0.037 0.008 -10000 0 0 22 22
GNA11 0.034 0.013 -10000 0 0 63 63
Rac1/GTP 0.003 0.085 0.24 1 -0.29 19 20
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.029 -9999 0 -0.13 2 2
FBXW11 0.037 0.009 -9999 0 0 27 27
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.037 0.009 -9999 0 0 27 27
CHUK 0.027 0.018 -9999 0 0 155 155
NF kappa B2 p100/RelB 0.064 0.073 -9999 0 -0.11 13 13
NFKB1 0.038 0.007 -9999 0 0 18 18
MAP3K14 0.038 0.006 -9999 0 0 14 14
NF kappa B1 p50/RelB 0.05 0.024 -9999 0 -0.13 4 4
RELB 0.036 0.011 -9999 0 0 42 42
NFKB2 0.028 0.018 -9999 0 0 149 149
NF kappa B2 p52/RelB 0.036 0.025 -9999 0 -10000 0 0
regulation of B cell activation 0.035 0.024 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.053 0.024 -10000 0 -0.13 6 6
Necdin/E2F1 -0.009 0.075 -10000 0 -0.13 131 131
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.078 0.05 -10000 0 -0.12 23 23
NGF (dimer)/p75(NTR)/BEX1 0.014 0.06 -10000 0 -0.1 95 95
NT-4/5 (dimer)/p75(NTR) 0.025 0.01 -10000 0 -10000 0 0
IKBKB 0.038 0.005 -10000 0 0 7 7
AKT1 -0.021 0.083 0.21 27 -0.18 22 49
IKBKG 0.039 0.004 -10000 0 0 5 5
BDNF 0.033 0.014 -10000 0 0 72 72
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.009 -10000 0 -10000 0 0
FURIN 0.038 0.007 -10000 0 0 17 17
proBDNF (dimer)/p75(NTR)/Sortilin 0.057 0.038 -10000 0 -0.12 3 3
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.075 0.044 0.058 7 -0.24 13 20
proBDNF (dimer) 0.033 0.014 -10000 0 0 72 72
NTRK1 0.038 0.007 -10000 0 0 16 16
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.004 0.14 0.28 4 -0.39 32 36
IRAK1 0.037 0.008 -10000 0 0 23 23
SHC1 -0.008 0.046 0.12 60 -10000 0 60
ARHGDIA 0.037 0.008 -10000 0 0 24 24
RhoA/GTP 0.026 0.017 -10000 0 -0.11 7 7
Gamma Secretase 0.078 0.076 -10000 0 -0.15 28 28
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.043 0.058 -10000 0 -0.1 52 52
MAGEH1 0.034 0.013 -10000 0 0 70 70
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0 0.073 -10000 0 -0.1 142 142
Mammalian IAPs/DIABLO 0.059 0.037 -10000 0 -0.13 7 7
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.037 0.009 -10000 0 0 27 27
APP 0.037 0.009 -10000 0 0 26 26
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.032 0.015 -10000 0 0 85 85
RhoA/GDP/RHOGDI 0.052 0.035 0.18 1 -0.097 6 7
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.004 0.062 0.23 9 -10000 0 9
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.012 0.057 -10000 0 -0.18 33 33
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.043 0.021 -10000 0 -0.1 1 1
NCSTN 0.037 0.009 -10000 0 0 31 31
mol:GTP 0.034 0.039 -10000 0 -0.1 28 28
PSENEN 0.035 0.011 -10000 0 0 48 48
mol:ceramide -0.015 0.054 0.12 65 -10000 0 65
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.056 -10000 0 -0.26 11 11
p75(NTR)/beta APP 0.045 0.031 -10000 0 -0.13 8 8
BEX1 0.03 0.016 -10000 0 0 117 117
mol:GDP -0.012 0.005 -10000 0 -10000 0 0
NGF (dimer) 0.045 0.04 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.042 0.019 -10000 0 -10000 0 0
PIK3R1 0.034 0.013 -10000 0 0 69 69
RAC1/GTP 0.022 0.025 -10000 0 -0.086 5 5
MYD88 0.036 0.01 -10000 0 0 38 38
CHUK 0.027 0.018 -10000 0 0 155 155
NGF (dimer)/p75(NTR)/PKA 0.035 0.039 -10000 0 -0.1 28 28
RHOB 0.033 0.014 -10000 0 0 75 75
RHOA 0.037 0.008 -10000 0 0 24 24
MAGE-G1/E2F1 0.025 0.01 -10000 0 -10000 0 0
NT3 (dimer) 0.037 0.009 -10000 0 0 30 30
TP53 -0.013 0.093 0.23 32 -0.24 1 33
PRDM4 -0.014 0.056 0.2 9 -10000 0 9
BDNF (dimer) 0.082 0.044 -10000 0 -10000 0 0
PIK3CA 0.033 0.014 -10000 0 0 79 79
SORT1 0.038 0.007 -10000 0 0 15 15
activation of caspase activity 0.07 0.047 -10000 0 -0.12 23 23
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.059 0.035 -10000 0 -0.1 5 5
RHOC 0.037 0.008 -10000 0 0 21 21
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.022 0.12 0.25 59 -0.3 12 71
DIABLO 0.038 0.006 -10000 0 0 12 12
SMPD2 -0.015 0.054 0.12 65 -10000 0 65
APH1B 0.038 0.007 -10000 0 0 18 18
APH1A 0.038 0.007 -10000 0 0 19 19
proNGF (dimer)/p75(NTR)/Sortilin 0.043 0.023 -10000 0 -0.1 4 4
PSEN1 0.035 0.012 -10000 0 0 53 53
APAF-1/Pro-Caspase 9 0.053 0.019 -10000 0 -0.13 2 2
NT3 (dimer)/p75(NTR) 0.047 0.023 -10000 0 -10000 0 0
MAPK8 0.001 0.083 0.22 26 -0.24 6 32
MAPK9 0.034 0.11 0.25 66 -0.24 7 73
APAF1 0.038 0.006 -10000 0 0 11 11
NTF3 0.037 0.009 -10000 0 0 30 30
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.019 0.019 -10000 0 0 265 265
RAC1/GDP 0.016 0.019 -10000 0 -0.11 5 5
RhoA-B-C/GDP 0.053 0.072 -10000 0 -0.14 51 51
p75 CTF/Sortilin/TRAF6/NRIF 0.072 0.062 -10000 0 -0.12 30 30
RhoA-B-C/GTP 0.034 0.039 -10000 0 -0.1 28 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.082 0.067 -10000 0 -0.12 24 24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.089 0.036 -10000 0 -0.12 3 3
PRKACB 0.035 0.012 -10000 0 0 52 52
proBDNF (dimer)/p75 ECD 0.049 0.021 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.032 0.015 -10000 0 0 85 85
BIRC2 0.038 0.007 -10000 0 0 15 15
neuron projection morphogenesis -0.016 0.072 0.19 14 -0.17 13 27
BAD 0.016 0.11 0.24 47 -0.27 11 58
RIPK2 0.038 0.007 -10000 0 0 16 16
NGFR 0.033 0.014 -10000 0 0 74 74
CYCS -0.015 0.048 0.2 6 -0.17 3 9
ADAM17 0.038 0.006 -10000 0 0 14 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.059 0.033 -10000 0 -0.1 3 3
BCL2L11 0.016 0.11 0.24 47 -0.27 11 58
BDNF (dimer)/p75(NTR) 0.043 0.025 -10000 0 -10000 0 0
PI3K 0.032 0.066 -10000 0 -0.11 69 69
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.041 0.022 -10000 0 -0.093 4 4
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.037 0.009 -10000 0 0 29 29
PRKCI 0.037 0.009 -10000 0 0 28 28
NGF (dimer)/p75(NTR) 0.025 0.01 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.053 0.047 -10000 0 -0.11 26 26
TRAF6 0.038 0.007 -10000 0 0 17 17
RAC1 0.023 0.019 -10000 0 0 209 209
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.036 0.011 -10000 0 0 43 43
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.001 0.06 0.16 21 -0.15 3 24
SQSTM1 0.036 0.011 -10000 0 0 40 40
NGFRAP1 0.038 0.006 -10000 0 0 14 14
CASP3 0.016 0.1 0.24 46 -0.26 13 59
E2F1 0.034 0.013 -10000 0 0 67 67
CASP9 0.037 0.009 -10000 0 0 31 31
IKK complex 0.032 0.075 -10000 0 -0.25 10 10
NGF (dimer)/TRKA 0.028 0.005 -10000 0 -10000 0 0
MMP7 0.028 0.017 -10000 0 0 140 140
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.066 0.057 -10000 0 -0.11 29 29
MMP3 0.037 0.008 -10000 0 0 24 24
APAF-1/Caspase 9 -0.03 0.049 -10000 0 -0.2 5 5
IL4-mediated 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
BCL2L1 -0.017 0.41 0.84 8 -1.1 19 27
STAT6 (cleaved dimer) -0.054 0.36 0.61 3 -0.94 28 31
IGHG1 0.007 0.28 0.53 28 -0.82 20 48
IGHG3 -0.045 0.38 0.68 5 -0.96 25 30
AKT1 -0.013 0.29 0.56 11 -0.74 25 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.025 0.2 0.5 13 -0.56 7 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 0.008 0.28 0.56 15 -0.74 18 33
THY1 -0.11 0.52 0.86 11 -1.2 59 70
MYB 0.034 0.013 -10000 0 0 61 61
HMGA1 0.038 0.006 -10000 0 0 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.019 0.28 0.63 19 -0.63 10 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.009 0.27 0.55 14 -0.77 15 29
SP1 0.034 0.091 0.16 94 -0.16 72 166
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.001 0.054 -10000 0 -0.1 2 2
STAT6 (dimer)/ETS1 -0.034 0.39 0.65 6 -0.98 24 30
SOCS1 -0.031 0.31 0.54 16 -0.68 25 41
SOCS3 0.006 0.24 0.55 3 -0.69 2 5
FCER2 -0.01 0.35 0.71 6 -0.82 12 18
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.044 0.41 0.79 4 -1.1 17 21
GRB2 0.037 0.009 -10000 0 0 26 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.018 0.23 0.52 17 -0.6 14 31
T cell proliferation -0.052 0.39 0.76 5 -1 24 29
IL4R/JAK1 -0.052 0.4 0.72 5 -1 23 28
EGR2 -0.089 0.51 0.8 7 -1.3 49 56
JAK2 0.022 0.078 0.18 32 -10000 0 32
JAK3 0.029 0.028 -10000 0 -0.063 5 5
PIK3R1 0.034 0.013 -10000 0 0 69 69
JAK1 0.023 0.05 0.13 12 -10000 0 12
COL1A2 -0.077 0.48 0.57 26 -1.1 76 102
CCL26 -0.039 0.41 0.73 14 -1 25 39
IL4R -0.032 0.44 0.93 14 -1.1 19 33
PTPN6 0 0.046 -10000 0 -0.096 1 1
IL13RA2 -0.28 0.67 0.87 14 -1.1 156 170
IL13RA1 0.029 0.08 0.18 32 -10000 0 32
IRF4 0.052 0.14 -10000 0 -0.52 2 2
ARG1 0.02 0.24 0.58 15 -0.76 10 25
CBL 0.005 0.26 0.54 19 -0.61 10 29
GTF3A 0.055 0.048 0.17 70 -0.16 3 73
PIK3CA 0.033 0.014 -10000 0 0 79 79
IL13RA1/JAK2 0.031 0.12 0.26 36 -0.17 2 38
IRF4/BCL6 0.047 0.13 -10000 0 -0.44 1 1
CD40LG 0.042 0.008 0.2 1 -10000 0 1
MAPK14 0.007 0.26 0.54 19 -0.61 8 27
mitosis -0.008 0.28 0.54 14 -0.69 25 39
STAT6 -0.037 0.46 0.94 19 -1.1 24 43
SPI1 0.039 0.016 0.14 6 -10000 0 6
RPS6KB1 -0.015 0.27 0.53 11 -0.68 25 36
STAT6 (dimer) -0.033 0.46 0.95 20 -1.1 24 44
STAT6 (dimer)/PARP14 -0.069 0.39 0.7 1 -1.1 25 26
mast cell activation -0.004 0.019 -10000 0 -0.05 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.02 0.23 0.53 13 -0.61 3 16
FRAP1 -0.012 0.28 0.56 11 -0.74 25 36
LTA -0.044 0.4 0.78 5 -1.1 19 24
FES 0.037 0.008 -10000 0 0 22 22
T-helper 1 cell differentiation 0.028 0.46 1.1 24 -0.95 20 44
CCL11 -0.047 0.38 0.74 1 -1.1 17 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.024 0.23 0.55 13 -0.6 3 16
IL2RG 0.028 0.03 -10000 0 -0.062 2 2
IL10 -0.038 0.41 0.83 7 -1.1 17 24
IRS1 0.035 0.012 -10000 0 0 53 53
IRS2 0.032 0.015 -10000 0 0 96 96
IL4 0.043 0.2 0.58 13 -0.84 6 19
IL5 -0.042 0.41 0.79 5 -1.1 17 22
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.033 0.42 0.83 20 -0.97 29 49
COL1A1 0.041 0.3 0.69 34 -0.95 9 43
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.06 0.4 0.75 1 -1.1 19 20
IL2R gamma/JAK3 0.052 0.028 -10000 0 -10000 0 0
TFF3 -0.035 0.41 0.83 6 -1.1 17 23
ALOX15 -0.045 0.41 0.79 4 -1.1 17 21
MYBL1 0.031 0.015 -10000 0 0 99 99
T-helper 2 cell differentiation -0.025 0.37 0.7 14 -0.85 25 39
SHC1 0.035 0.012 -10000 0 0 56 56
CEBPB 0.033 0.019 0.14 4 -10000 0 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.001 0.27 0.56 14 -0.77 18 32
mol:PI-3-4-5-P3 -0.011 0.29 0.57 11 -0.74 25 36
PI3K -0.015 0.3 0.59 9 -0.79 25 34
DOK2 0 0 -10000 0 -10000 0 0
ETS1 -0.005 0.056 -10000 0 -0.11 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.019 0.23 0.48 24 -0.59 16 40
ITGB3 -0.044 0.41 0.79 4 -1.1 17 21
PIGR -0.038 0.41 0.85 5 -1.1 16 21
IGHE -0.008 0.091 0.17 47 -0.18 25 72
MAPKKK cascade 0.02 0.23 0.48 24 -0.58 16 40
BCL6 0.033 0.014 -10000 0 -10000 0 0
OPRM1 -0.043 0.41 0.79 4 -1.1 17 21
RETNLB -0.039 0.41 0.73 14 -1 25 39
SELP -0.039 0.41 0.88 5 -1.1 17 22
AICDA -0.044 0.38 0.74 2 -1 19 21
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.005 0.074 -10000 0 -0.13 103 103
PDGFRB 0.037 0.015 -10000 0 -0.036 11 11
SPHK1 0.018 0.02 -10000 0 -10000 0 0
mol:S1P 0.024 0.036 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.005 0.12 0.28 26 -0.4 18 44
GNAO1 0.036 0.018 0.083 2 -10000 0 2
PDGFB-D/PDGFRB/PLCgamma1 0.042 0.14 0.28 65 -0.35 18 83
PLCG1 0.005 0.12 0.26 42 -0.39 16 58
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.015 -10000 0 -0.036 11 11
GNAI2 0.039 0.014 -10000 0 -10000 0 0
GNAI3 0.041 0.01 -10000 0 -0.034 1 1
GNAI1 0.017 0.021 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.052 0.066 60 -0.1 103 163
S1P1/S1P 0.003 0.059 0.26 4 -10000 0 4
negative regulation of cAMP metabolic process 0.005 0.12 0.28 26 -0.39 18 44
MAPK3 0.01 0.14 0.32 41 -0.41 16 57
calcium-dependent phospholipase C activity 0.001 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.019 -10000 0 -0.11 5 5
RhoA/GDP 0.026 0.017 -10000 0 -0.11 7 7
KDR 0.033 0.016 -10000 0 -10000 0 0
PLCB2 0.034 0.093 0.26 28 -10000 0 28
RAC1 0.023 0.019 -10000 0 0 209 209
RhoA/GTP -0.001 0.053 0.21 1 -10000 0 1
receptor internalization 0.002 0.056 0.24 4 -10000 0 4
PTGS2 0.042 0.16 0.39 37 -0.47 8 45
Rac1/GTP -0.004 0.042 -10000 0 -10000 0 0
RHOA 0.037 0.008 -10000 0 0 24 24
VEGFA 0.026 0.02 -10000 0 0 181 181
negative regulation of T cell proliferation 0.005 0.12 0.28 26 -0.39 18 44
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.035 0.016 -10000 0 -10000 0 0
MAPK1 0.013 0.14 0.33 39 -0.44 12 51
S1P1/S1P/PDGFB-D/PDGFRB 0.041 0.1 0.26 38 -0.22 1 39
ABCC1 0.039 0.011 -10000 0 -0.037 4 4
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.014 0.097 -10000 0 -0.25 55 55
STMN1 -0.026 0.032 0.12 22 -10000 0 22
Aurora B/RasGAP/Survivin 0.037 0.074 -10000 0 -0.13 73 73
Chromosomal passenger complex/Cul3 protein complex -0.037 0.076 -10000 0 -0.19 66 66
BIRC5 0.031 0.017 -10000 0 -0.035 2 2
DES 0.026 0.089 -10000 0 -0.61 9 9
Aurora C/Aurora B/INCENP 0.059 0.032 -10000 0 -10000 0 0
Aurora B/TACC1 0.044 0.026 -10000 0 -0.1 9 9
Aurora B/PP2A 0.052 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.005 0.049 0.07 1 -0.19 30 31
mitotic metaphase/anaphase transition -0.001 0.003 -10000 0 -10000 0 0
NDC80 -0.022 0.036 0.12 26 -10000 0 26
Cul3 protein complex 0.028 0.032 -10000 0 -0.12 7 7
KIF2C -0.021 0.12 -10000 0 -0.45 34 34
PEBP1 0.035 0.016 -10000 0 -0.016 38 38
KIF20A 0.03 0.017 -10000 0 -0.001 116 116
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.043 0.043 -10000 0 -0.13 25 25
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.034 0.013 -10000 0 0 67 67
SMC4 0.034 0.013 -10000 0 0 70 70
NSUN2/NPM1/Nucleolin -0.007 0.086 -10000 0 -0.5 10 10
PSMA3 0.036 0.011 -10000 0 0 42 42
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.006 0.03 -10000 0 -0.19 11 11
AURKB 0.027 0.027 -10000 0 -0.039 59 59
AURKC 0.034 0.012 -10000 0 0 59 59
CDCA8 0.03 0.023 -10000 0 -0.038 38 38
cytokinesis -0.031 0.14 0.22 6 -0.42 49 55
Aurora B/Septin1 -0.018 0.14 0.24 4 -0.4 48 52
AURKA 0.03 0.018 -10000 0 -0.005 104 104
INCENP 0.032 0.024 0.069 2 -0.039 49 51
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.037 0.013 -10000 0 -0.016 24 24
hSgo1/Aurora B/Survivin 0.024 0.048 -10000 0 -0.1 57 57
EVI5 0.036 0.014 -10000 0 -0.014 34 34
RhoA/GTP 0.009 0.13 -10000 0 -0.31 55 55
SGOL1 0 0 -10000 0 -10000 0 0
CENPA -0.001 0.1 0.17 5 -0.34 33 38
NCAPG 0.032 0.015 -10000 0 0 88 88
Aurora B/HC8 Proteasome 0.047 0.031 -10000 0 -0.13 9 9
NCAPD2 0.033 0.014 -10000 0 0 83 83
Aurora B/PP1-gamma 0.049 0.027 -10000 0 -0.13 6 6
RHOA 0.037 0.008 -10000 0 0 24 24
NCAPH 0.037 0.009 -10000 0 0 29 29
NPM1 0.002 0.083 -10000 0 -0.37 17 17
RASA1 0.036 0.01 -10000 0 0 37 37
KLHL9 0.022 0.019 -10000 0 0 216 216
mitotic prometaphase -0.001 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.031 -10000 0 -0.13 9 9
PPP1CC 0.038 0.007 -10000 0 0 16 16
Centraspindlin 0 0.13 -10000 0 -0.33 53 53
RhoA/GDP 0.026 0.017 -10000 0 -0.11 7 7
NSUN2 0.001 0.04 -10000 0 -0.29 8 8
MYLK -0.015 0.065 -10000 0 -0.19 60 60
KIF23 0.028 0.023 -10000 0 -0.038 37 37
VIM -0.021 0.024 0.11 8 -10000 0 8
RACGAP1 0.031 0.02 -10000 0 -0.038 18 18
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.001 0.062 -10000 0 -0.28 21 21
Chromosomal passenger complex -0.018 0.1 0.15 8 -0.27 55 63
Chromosomal passenger complex/EVI5 0.065 0.088 -10000 0 -0.15 56 56
TACC1 0.037 0.008 -10000 0 0 25 25
PPP2R5D 0.038 0.005 -10000 0 0 10 10
CUL3 0.039 0.003 -10000 0 0 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.13 -10000 0 -0.62 18 18
epithelial cell differentiation -0.026 0.15 -10000 0 -0.66 18 18
ITCH 0.025 0.038 0.13 1 -0.12 17 18
WWP1 -0.026 0.21 -10000 0 -1.1 18 18
FYN 0.032 0.015 -10000 0 0 95 95
EGFR 0.009 0.017 -10000 0 0 385 385
PRL 0.038 0.007 -10000 0 0 18 18
neuron projection morphogenesis -0.039 0.12 0.3 9 -0.5 18 27
PTPRZ1 0.021 0.019 -10000 0 0 241 241
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.054 0.12 -10000 0 -0.52 18 18
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.001 0.11 -10000 0 -0.56 18 18
ADAM17 0.021 0.043 -10000 0 -0.12 19 19
ErbB4/ErbB4 -0.007 0.13 0.29 9 -0.67 18 27
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.014 0.12 -10000 0 -0.61 18 18
NCOR1 0.037 0.009 -10000 0 0 28 28
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.015 0.12 0.25 1 -0.57 18 19
GRIN2B -0.035 0.11 0.24 3 -0.54 18 21
ErbB4/ErbB2/betacellulin 0.025 0.12 0.26 3 -0.54 18 21
STAT1 0.036 0.011 -10000 0 0 41 41
HBEGF 0.037 0.008 -10000 0 0 25 25
PRLR 0.038 0.006 -10000 0 0 13 13
E4ICDs/ETO2 0.023 0.13 -10000 0 -0.62 18 18
axon guidance -0.044 0.16 -10000 0 -0.79 18 18
NEDD4 0.02 0.041 0.13 1 -0.13 18 19
Prolactin receptor/Prolactin receptor/Prolactin 0.054 0.014 -10000 0 -10000 0 0
CBFA2T3 0.037 0.009 -10000 0 0 28 28
ErbB4/ErbB2/HBEGF 0.023 0.12 0.26 2 -0.54 18 20
MAPK3 -0.029 0.12 0.3 9 -0.5 18 27
STAT1 (dimer) 0.022 0.13 -10000 0 -0.62 18 18
MAPK1 -0.03 0.12 0.32 8 -0.5 18 26
JAK2 0.032 0.015 -10000 0 0 89 89
ErbB4/ErbB2/neuregulin 1 beta -0.024 0.11 0.28 1 -0.54 18 19
NRG1 -0.034 0.024 0.1 6 -0.096 18 24
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.038 0.006 -10000 0 0 12 12
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.044 0.16 -10000 0 -0.79 18 18
neural crest cell migration -0.024 0.11 0.28 1 -0.54 18 19
ERBB2 -0.034 0.026 0.13 7 -0.096 18 25
WWOX/E4ICDs 0.024 0.13 -10000 0 -0.62 18 18
SHC1 0.035 0.012 -10000 0 0 56 56
ErbB4/EGFR/neuregulin 4 -0.011 0.093 -10000 0 -0.44 18 18
apoptosis -0.005 0.12 0.57 18 -0.24 1 19
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.025 0.13 -10000 0 -0.62 18 18
ErbB4/ErbB2/epiregulin 0.023 0.12 0.25 2 -0.54 18 20
ErbB4/ErbB4/betacellulin/betacellulin 0.025 0.13 -10000 0 -0.62 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.062 0.13 -10000 0 -0.57 18 18
MDM2 0.008 0.14 0.26 43 -0.6 17 60
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.014 0.1 -10000 0 -0.5 18 18
STAT5A -0.05 0.16 0.34 1 -0.77 18 19
ErbB4/EGFR/neuregulin 1 beta -0.004 0.086 -10000 0 -0.41 18 18
DLG4 0.038 0.006 -10000 0 0 14 14
GRB2/SHC 0.045 0.036 -10000 0 -0.14 14 14
E4ICDs/TAB2/NCoR1 0.018 0.12 -10000 0 -0.59 18 18
STAT5A (dimer) -0.021 0.16 -10000 0 -0.73 18 18
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.029 0.17 0.34 2 -0.77 18 20
LRIG1 0.032 0.015 -10000 0 0 89 89
EREG 0.037 0.008 -10000 0 0 22 22
BTC 0.038 0.005 -10000 0 0 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.046 0.16 -10000 0 -0.81 18 18
ERBB4 -0.007 0.14 0.29 9 -0.67 18 27
STAT5B 0.038 0.005 -10000 0 0 10 10
YAP1 -0.066 0.2 -10000 0 -0.48 92 92
GRB2 0.037 0.009 -10000 0 0 26 26
ErbB4/ErbB2/neuregulin 4 -0.001 0.11 -10000 0 -0.53 18 18
glial cell differentiation -0.017 0.12 0.59 18 -10000 0 18
WWOX 0.037 0.008 -10000 0 0 21 21
cell proliferation -0.023 0.12 -10000 0 -0.57 18 18
a4b1 and a4b7 Integrin 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
ITGB1 0.029 0.017 -9999 0 0 131 131
ITGB7 0.038 0.007 -9999 0 0 18 18
ITGA4 0.038 0.006 -9999 0 0 13 13
alpha4/beta7 Integrin 0.055 0.013 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.042 0.026 -9999 0 -9999 0 0
Signaling events mediated by PRL

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
CCNE1 0.033 0.014 -10000 0 0 77 77
mol:Halofuginone -0.002 0.03 -10000 0 -0.17 16 16
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.023 0.15 -10000 0 -0.41 56 56
PRL-3/alpha Tubulin 0.042 0.041 -10000 0 -0.13 22 22
mol:Ca2+ -0.019 0.05 0.17 27 -10000 0 27
AGT 0.031 0.016 -10000 0 0 109 109
CCNA2 -0.023 0.12 -10000 0 -0.57 15 15
TUBA1B 0.037 0.008 -10000 0 0 20 20
EGR1 -0.02 0.057 0.16 4 -0.33 15 19
CDK2/Cyclin E1 -0.001 0.15 -10000 0 -0.39 48 48
MAPK3 -0.021 0.041 0.12 38 -10000 0 38
PRL-2 /Rab GGTase beta 0.051 0.033 -10000 0 -0.14 12 12
MAPK1 -0.017 0.042 0.12 42 -10000 0 42
PTP4A1 -0.027 0.098 0.22 3 -0.61 12 15
PTP4A3 0.033 0.014 -10000 0 0 78 78
PTP4A2 0.038 0.007 -10000 0 0 19 19
ITGB1 -0.016 0.036 0.12 28 -10000 0 28
SRC 0.034 0.013 -10000 0 0 65 65
RAC1 -0.002 0.09 -10000 0 -0.41 18 18
Rab GGTase beta/Rab GGTase alpha 0.048 0.032 -10000 0 -0.13 11 11
PRL-1/ATF-5 -0.026 0.12 0.34 2 -0.53 15 17
RABGGTA 0.036 0.011 -10000 0 0 44 44
BCAR1 -0.02 0.009 -10000 0 -10000 0 0
RHOC -0.002 0.12 -10000 0 -0.4 33 33
RHOA -0.003 0.13 -10000 0 -0.41 38 38
cell motility 0.001 0.13 0.3 1 -0.42 28 29
PRL-1/alpha Tubulin -0.025 0.13 0.34 2 -0.56 15 17
PRL-3/alpha1 Integrin 0.02 0.029 -10000 0 -0.11 21 21
ROCK1 0.003 0.13 0.26 2 -0.42 28 30
RABGGTB 0.037 0.008 -10000 0 0 25 25
CDK2 0.035 0.011 -10000 0 0 46 46
mitosis -0.026 0.098 0.22 3 -0.61 12 15
ATF5 0.036 0.011 -10000 0 0 42 42
Caspase cascade in apoptosis

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
TOP1 -0.015 0.11 -10000 0 -0.37 18 18
ACTA1 -0.045 0.098 0.21 2 -0.31 35 37
NUMA1 -0.007 0.094 -10000 0 -0.34 22 22
SPTAN1 -0.054 0.098 0.23 4 -0.31 37 41
LIMK1 0.011 0.11 0.22 18 -0.35 15 33
BIRC3 0.033 0.015 -10000 0 0 85 85
BIRC2 0.038 0.007 -10000 0 0 15 15
BAX 0.035 0.012 -10000 0 0 49 49
CASP10 -0.015 0.042 0.1 46 -10000 0 46
CRMA 0 0 -10000 0 -0.001 3 3
XIAP 0 0 0.001 2 -0.001 13 15
PTK2 -0.015 0.099 -10000 0 -0.32 30 30
DIABLO 0.038 0.006 -10000 0 0 12 12
apoptotic nuclear changes -0.054 0.097 0.23 4 -0.3 37 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.038 0.007 -10000 0 0 18 18
GSN -0.046 0.1 0.22 6 -0.32 35 41
MADD 0.037 0.008 -10000 0 0 20 20
TFAP2A 0.042 0.095 -10000 0 -0.63 8 8
BID -0.005 0.041 -10000 0 -0.18 19 19
MAP3K1 -0.006 0.057 -10000 0 -0.4 6 6
TRADD 0.038 0.005 -10000 0 0 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.053 0.019 -10000 0 -0.13 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.1 0.2 12 -0.31 39 51
CASP9 0.036 0.009 -10000 0 0 31 31
DNA repair 0.036 0.071 0.2 38 -10000 0 38
neuron apoptosis 0.017 0.12 -10000 0 -0.61 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.035 0.097 -10000 0 -0.34 29 29
APAF1 0.038 0.006 -10000 0 0 11 11
CASP6 0.027 0.12 -10000 0 -0.87 7 7
TRAF2 0.037 0.008 -10000 0 0 20 20
ICAD/CAD -0.061 0.091 0.26 2 -0.32 33 35
CASP7 -0.078 0.11 -10000 0 -0.23 127 127
KRT18 0.028 0.056 -10000 0 -0.44 5 5
apoptosis -0.045 0.1 0.27 1 -0.43 13 14
DFFA -0.054 0.092 0.16 2 -0.31 35 37
DFFB -0.053 0.091 -10000 0 -0.32 33 33
PARP1 -0.036 0.071 -10000 0 -0.2 38 38
actin filament polymerization -0.021 0.11 0.33 15 -0.2 18 33
TNF 0.038 0.005 -10000 0 0 8 8
CYCS 0.015 0.045 0.17 7 -0.22 4 11
SATB1 0.018 0.11 -10000 0 -0.74 7 7
SLK -0.039 0.092 0.19 2 -0.3 36 38
p15 BID/BAX -0.006 0.078 0.15 7 -0.19 54 61
CASP2 0.066 0.11 0.21 169 -0.26 7 176
JNK cascade 0.006 0.056 0.4 6 -10000 0 6
CASP3 -0.048 0.096 0.17 1 -0.31 37 38
LMNB2 0.069 0.096 0.24 22 -0.3 3 25
RIPK1 0.037 0.008 -10000 0 0 22 22
CASP4 0.032 0.015 -10000 0 0 95 95
Mammalian IAPs/DIABLO 0.059 0.037 -10000 0 -0.13 7 7
negative regulation of DNA binding 0.042 0.093 -10000 0 -0.63 8 8
stress fiber formation -0.049 0.091 0.18 2 -0.3 36 38
GZMB -0.01 0.043 0.12 46 -10000 0 46
CASP1 -0.012 0.064 -10000 0 -0.19 56 56
LMNB1 0.049 0.13 0.27 10 -0.36 16 26
APP 0.016 0.12 -10000 0 -0.62 16 16
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
response to stress 0 0 0.001 8 -0.001 25 33
CASP8 -0.017 0.003 0 15 -10000 0 15
VIM -0.042 0.1 0.28 1 -0.37 22 23
LMNA 0.072 0.095 0.26 15 -0.28 3 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.007 0.061 0.15 1 -0.24 14 15
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.053 0.093 0.18 2 -0.32 34 36
APAF-1/Caspase 9 0.023 0.09 -10000 0 -0.61 9 9
nuclear fragmentation during apoptosis -0.007 0.092 -10000 0 -0.33 22 22
CFL2 0.021 0.11 0.2 18 -0.33 15 33
GAS2 -0.042 0.098 0.19 5 -0.3 35 40
positive regulation of apoptosis 0.069 0.11 0.24 30 -0.34 6 36
PRF1 0.024 0.019 -10000 0 0 189 189
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.034 0.013 -10000 0 0 62 62
SMAD2 -0.026 0.069 -10000 0 -0.26 23 23
SMAD3 0.002 0.067 0.26 1 -0.27 12 13
SMAD3/SMAD4 -0.013 0.16 -10000 0 -0.48 46 46
SMAD4/Ubc9/PIASy 0.057 0.052 -10000 0 -0.12 32 32
SMAD2/SMAD2/SMAD4 0.011 0.11 -10000 0 -0.27 24 24
PPM1A 0.036 0.01 -10000 0 0 37 37
CALM1 0.034 0.013 -10000 0 0 62 62
SMAD2/SMAD4 -0.007 0.073 -10000 0 -0.22 32 32
MAP3K1 0.037 0.008 -10000 0 0 25 25
TRAP-1/SMAD4 0.041 0.05 -10000 0 -0.13 38 38
MAPK3 0.039 0.004 -10000 0 0 5 5
MAPK1 0.035 0.011 -10000 0 0 47 47
NUP214 0.037 0.008 -10000 0 0 23 23
CTDSP1 0.038 0.007 -10000 0 0 16 16
CTDSP2 0.032 0.015 -10000 0 0 87 87
CTDSPL 0.038 0.007 -10000 0 0 15 15
KPNB1 0.037 0.008 -10000 0 0 24 24
TGFBRAP1 0.038 0.005 -10000 0 0 10 10
UBE2I 0.039 0.004 -10000 0 0 5 5
NUP153 0.036 0.01 -10000 0 0 33 33
KPNA2 0.036 0.011 -10000 0 0 41 41
PIAS4 0.036 0.01 -10000 0 0 35 35
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.004 0.11 -10000 0 -0.24 53 53
CaM/Ca2+ 0.022 0.023 -10000 0 -0.11 13 13
AKT1 0.034 0.013 -10000 0 0 61 61
AKT2 0.036 0.01 -10000 0 0 34 34
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.018 0.1 0.18 1 -0.26 55 56
YWHAZ 0.037 0.008 -10000 0 0 23 23
CALM1 0.034 0.013 -10000 0 0 62 62
YWHAQ 0.038 0.005 -10000 0 0 9 9
TBC1D4 -0.025 0.027 0.12 13 -10000 0 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 0 76 76
YWHAB 0.033 0.014 -10000 0 0 72 72
SNARE/Synip 0.042 0.034 -10000 0 -0.11 19 19
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.034 0.013 -10000 0 0 66 66
PRKCI 0.037 0.009 -10000 0 0 28 28
AS160/CaM/Ca2+ 0.022 0.023 -10000 0 -0.11 13 13
RHOQ 0.038 0.007 -10000 0 0 15 15
GYS1 -0.018 0.04 0.13 8 -0.21 6 14
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.036 0.011 -10000 0 0 43 43
TC10/GTP/CIP4/Exocyst 0.044 0.029 -10000 0 -0.1 14 14
AS160/14-3-3 -0.013 0.095 0.16 3 -0.37 22 25
VAMP2 0.035 0.012 -10000 0 0 50 50
SLC2A4 -0.021 0.11 -10000 0 -0.28 56 56
STX4 0.038 0.007 -10000 0 0 16 16
GSK3B 0.011 0.036 -10000 0 -0.2 14 14
SFN 0.033 0.014 -10000 0 0 79 79
LNPEP 0.038 0.006 -10000 0 0 14 14
YWHAE 0.037 0.009 -10000 0 0 29 29
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 0.033 0.014 -10000 0 0 80 80
NFATC1 -0.002 0.1 0.24 1 -0.42 19 20
NFATC2 -0.04 0.086 0.15 2 -0.18 98 100
NFATC3 0.008 0.019 -10000 0 -0.096 13 13
YWHAE 0.037 0.009 -10000 0 0 29 29
Calcineurin A alpha-beta B1/CABIN1 -0.02 0.075 -10000 0 -0.22 36 36
Exportin 1/Ran/NUP214 0.071 0.031 -10000 0 -0.14 6 6
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.013 0.095 0.22 1 -0.24 23 24
BCL2/BAX 0.05 0.023 -10000 0 -0.13 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.023 -10000 0 -0.11 13 13
CaM/Ca2+ 0.022 0.023 -10000 0 -0.11 13 13
BAX 0.035 0.012 -10000 0 0 49 49
MAPK14 0.038 0.005 -10000 0 0 8 8
BAD 0.038 0.007 -10000 0 0 16 16
CABIN1/MEF2D -0.005 0.083 -10000 0 -0.22 34 34
Calcineurin A alpha-beta B1/BCL2 0.037 0.008 -10000 0 0 21 21
FKBP8 0.036 0.011 -10000 0 0 44 44
activation-induced cell death of T cells 0.005 0.083 0.22 34 -10000 0 34
KPNB1 0.037 0.008 -10000 0 0 24 24
KPNA2 0.036 0.011 -10000 0 0 41 41
XPO1 0.039 0.003 -10000 0 0 4 4
SFN 0.033 0.014 -10000 0 0 79 79
MAP3K8 0.024 0.019 -10000 0 0 190 190
NFAT4/CK1 alpha -0.038 0.03 0.085 1 -0.17 13 14
MEF2D/NFAT1/Cbp/p300 0.004 0.12 0.3 1 -0.23 39 40
CABIN1 -0.019 0.074 -10000 0 -0.22 35 35
CALM1 0.034 0.013 -10000 0 0 62 62
RAN 0.038 0.007 -10000 0 0 16 16
MAP3K1 0.037 0.008 -10000 0 0 25 25
CAMK4 0.038 0.006 -10000 0 0 11 11
mol:Ca2+ 0 0.001 0.026 1 -10000 0 1
MAPK3 0.039 0.004 -10000 0 0 5 5
YWHAH 0.033 0.014 -10000 0 0 76 76
Calcineurin A alpha-beta B1/AKAP79/PKA 0.05 0.02 -10000 0 -10000 0 0
YWHAB 0.033 0.014 -10000 0 0 72 72
MAPK8 0.028 0.017 -10000 0 0 138 138
MAPK9 0.038 0.007 -10000 0 0 17 17
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.032 0.015 -10000 0 0 91 91
NFAT1-c-4/YWHAQ -0.006 0.11 -10000 0 -0.36 23 23
PRKCH 0.035 0.012 -10000 0 0 51 51
CABIN1/Cbp/p300 0.05 0.028 -10000 0 -0.13 7 7
CASP3 0.037 0.009 -10000 0 0 32 32
PIM1 0.038 0.006 -10000 0 0 11 11
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.018 -10000 0 -0.09 10 10
apoptosis 0.017 0.036 -10000 0 -0.16 12 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.095 0.14 1 -0.3 28 29
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.038 0.005 -10000 0 0 7 7
JNK2/NFAT4 0.024 0.039 -10000 0 -0.12 20 20
BAD/BCL-XL 0.046 0.028 -10000 0 -0.13 5 5
PRKCD 0.036 0.011 -10000 0 0 43 43
NUP214 0.037 0.008 -10000 0 0 23 23
PRKCZ 0 0.001 -10000 0 -10000 0 0
PRKCA 0.038 0.005 -10000 0 0 10 10
PRKCG 0.036 0.011 -10000 0 0 42 42
PRKCQ 0.027 0.018 -10000 0 0 155 155
FKBP38/BCL2 0.051 0.019 -10000 0 -10000 0 0
EP300 0.035 0.012 -10000 0 0 52 52
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.014 -10000 0 0 81 81
NFATc/JNK1 0.004 0.1 -10000 0 -0.41 19 19
CaM/Ca2+/FKBP38 0.04 0.03 -10000 0 -0.1 13 13
FKBP12/FK506 0.021 0.022 -10000 0 -0.11 10 10
CSNK1A1 -0.024 0.025 0.11 12 -0.1 9 21
CaM/Ca2+/CAMK IV 0.043 0.029 -10000 0 -0.1 13 13
NFATc/ERK1 0.016 0.11 -10000 0 -0.41 19 19
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.013 0.096 -10000 0 -0.24 24 24
NR4A1 -0.054 0.077 0.18 4 -0.22 33 37
GSK3B 0.036 0.011 -10000 0 0 40 40
positive T cell selection 0.008 0.019 -10000 0 -0.095 13 13
NFAT1/CK1 alpha -0.035 0.067 0.096 6 -0.19 46 52
RCH1/ KPNB1 0.04 0.055 -10000 0 -0.13 44 44
YWHAQ 0.038 0.005 -10000 0 0 9 9
PRKACA 0.036 0.01 -10000 0 0 36 36
AKAP5 0.036 0.01 -10000 0 0 37 37
MEF2D 0.038 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.037 0.008 -10000 0 0 23 23
NFATc/p38 alpha 0.016 0.11 0.25 1 -0.41 19 20
CREBBP 0.039 0.005 -10000 0 0 7 7
BCL2 0.037 0.008 -10000 0 0 21 21
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.043 0.038 -10000 0 -0.13 18 18
ATM 0.036 0.011 -10000 0 0 41 41
UBE2D3 0.038 0.006 -10000 0 0 12 12
PRKDC 0.035 0.011 -10000 0 0 46 46
ATR 0.037 0.009 -10000 0 0 32 32
UBE2L3 0.036 0.01 -10000 0 0 36 36
FANCD2 0.006 0.034 -10000 0 -0.19 14 14
protein ubiquitination 0.076 0.061 -10000 0 -0.13 21 21
XRCC5 0.038 0.005 -10000 0 0 9 9
XRCC6 0.036 0.011 -10000 0 0 44 44
M/R/N Complex 0.072 0.026 -10000 0 -0.12 4 4
MRE11A 0.038 0.006 -10000 0 0 11 11
DNA-PK 0.061 0.048 -10000 0 -0.14 20 20
FA complex/FANCD2/Ubiquitin -0.007 0.089 -10000 0 -0.3 25 25
FANCF 0.037 0.009 -10000 0 0 31 31
BRCA1 0.038 0.007 -10000 0 0 16 16
CCNE1 0.033 0.014 -10000 0 0 77 77
CDK2/Cyclin E1 0.045 0.026 -10000 0 -0.13 2 2
FANCG 0.032 0.015 -10000 0 0 96 96
BRCA1/BACH1/BARD1 0.049 0.037 -10000 0 -0.13 19 19
FANCE 0.038 0.005 -10000 0 0 8 8
FANCC 0.037 0.008 -10000 0 0 20 20
NBN 0.038 0.007 -10000 0 0 16 16
FANCA 0.038 0.007 -10000 0 0 19 19
DNA repair -0.02 0.095 0.23 15 -0.32 12 27
BRCA1/BARD1/ubiquitin 0.049 0.037 -10000 0 -0.13 19 19
BARD1/DNA-PK 0.072 0.067 -10000 0 -0.13 33 33
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.043 0.038 0.13 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.003 0.067 -10000 0 -0.26 18 18
BRCA1/BACH1/BARD1/TopBP1 0.055 0.061 -10000 0 -0.12 46 46
BRCA1/BARD1/P53 0.07 0.069 -10000 0 -0.12 44 44
BARD1/CSTF1/BRCA1 0.06 0.044 -10000 0 -0.12 18 18
BRCA1/BACH1 0.038 0.007 -10000 0 0 16 16
BARD1 0.037 0.008 -10000 0 0 23 23
PCNA 0.032 0.015 -10000 0 0 91 91
BRCA1/BARD1/UbcH5C 0.067 0.043 -10000 0 -0.12 20 20
BRCA1/BARD1/UbcH7 0.063 0.047 -10000 0 -0.12 23 23
BRCA1/BARD1/RAD51/PCNA 0.066 0.066 -10000 0 -0.13 33 33
BARD1/DNA-PK/P53 0.071 0.086 -10000 0 -0.13 53 53
BRCA1/BARD1/Ubiquitin 0.049 0.037 -10000 0 -0.13 19 19
BRCA1/BARD1/CTIP 0.042 0.061 0.17 9 -0.13 44 53
FA complex 0.006 0.059 -10000 0 -0.2 26 26
BARD1/EWS 0.046 0.038 -10000 0 -0.13 19 19
RBBP8 -0.022 0.038 0.12 32 -10000 0 32
TP53 0.033 0.014 -10000 0 0 73 73
TOPBP1 0.035 0.012 -10000 0 0 53 53
G1/S transition of mitotic cell cycle -0.068 0.068 0.12 44 -10000 0 44
BRCA1/BARD1 0.084 0.065 -10000 0 -0.13 21 21
CSTF1 0.034 0.013 -10000 0 0 65 65
BARD1/EWS-Fli1 0.023 0.027 -10000 0 -0.11 19 19
CDK2 0.035 0.011 -10000 0 0 46 46
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.037 0.008 -10000 0 0 22 22
RAD50 0.038 0.006 -10000 0 0 14 14
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.049 0.037 -10000 0 -0.13 19 19
EWSR1 0.036 0.01 -10000 0 0 36 36
Glucocorticoid receptor regulatory network

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
PCK2 -0.025 0.1 0.27 2 -0.45 17 19
SMARCC2 0.035 0.012 -10000 0 0 54 54
SMARCC1 0.036 0.01 -10000 0 0 37 37
TBX21 0.029 0.062 0.35 1 -10000 0 1
SUMO2 0.031 0.027 -10000 0 -0.038 63 63
STAT1 (dimer) 0.039 0.043 0.14 24 -0.18 13 37
FKBP4 0.036 0.011 -10000 0 0 40 40
FKBP5 0.03 0.017 -10000 0 0 121 121
GR alpha/HSP90/FKBP51/HSP90 -0.034 0.081 -10000 0 -0.23 5 5
PRL 0.038 0.075 0.46 7 -10000 0 7
cortisol/GR alpha (dimer)/TIF2 -0.05 0.13 -10000 0 -10000 0 0
RELA 0.025 0.12 0.2 71 -0.17 119 190
FGG -0.058 0.11 -10000 0 -0.33 2 2
GR beta/TIF2 -0.032 0.084 -10000 0 -0.24 1 1
IFNG 0.033 0.092 0.41 3 -10000 0 3
apoptosis -0.024 0.2 0.46 17 -0.52 24 41
CREB1 0.045 0.013 -10000 0 -10000 0 0
histone acetylation 0.021 0.058 0.23 1 -10000 0 1
BGLAP 0.041 0.078 0.33 14 -10000 0 14
GR/PKAc 0.014 0.1 -10000 0 -0.2 8 8
NF kappa B1 p50/RelA 0.043 0.2 0.33 67 -0.27 115 182
SMARCD1 0.037 0.008 -10000 0 0 25 25
MDM2 -0.012 0.039 0.14 1 -10000 0 1
GATA3 0.032 0.021 0.17 1 -10000 0 1
AKT1 0.029 0.037 0.16 8 -0.14 17 25
CSF2 -0.003 0.037 -10000 0 -10000 0 0
GSK3B 0.029 0.028 -10000 0 -0.038 60 60
NR1I3 -0.019 0.18 0.47 10 -0.5 14 24
CSN2 -0.055 0.098 -10000 0 -0.3 2 2
BRG1/BAF155/BAF170/BAF60A 0.063 0.075 -10000 0 -0.16 39 39
NFATC1 0.042 0.009 -10000 0 -10000 0 0
POU2F1 0.041 0.015 0.14 8 -10000 0 8
CDKN1A -0.12 0.4 0.4 5 -1.2 60 65
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.008 0.029 23 -10000 0 23
SFN 0.033 0.014 -10000 0 0 79 79
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.022 0.092 -10000 0 -0.23 2 2
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.07 0.27 0.47 6 -0.65 68 74
JUN 0.016 0.069 0.38 6 -10000 0 6
IL4 0.033 0.058 -10000 0 -10000 0 0
CDK5R1 0.033 0.022 -10000 0 -0.037 37 37
PRKACA 0.036 0.01 -10000 0 0 36 36
cortisol/GR alpha (monomer)/AP-1 -0.06 0.062 -10000 0 -0.24 9 9
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.014 0.097 -10000 0 -0.2 9 9
cortisol/GR alpha (monomer) -0.062 0.14 -10000 0 -0.38 1 1
NCOA2 0.038 0.006 -10000 0 0 14 14
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.04 0.038 0.22 9 -10000 0 9
AP-1/NFAT1-c-4 0.042 0.09 0.47 6 -10000 0 6
AFP 0.017 0.082 0.5 2 -10000 0 2
SUV420H1 0.035 0.012 -10000 0 0 58 58
IRF1 -0.033 0.13 0.35 1 -0.62 14 15
TP53 -0.013 0.17 0.29 2 -0.49 57 59
PPP5C 0.036 0.011 -10000 0 0 44 44
KRT17 0.041 0.095 0.44 7 -10000 0 7
KRT14 0.034 0.077 0.37 2 -10000 0 2
TBP 0.044 0.023 0.15 16 -10000 0 16
CREBBP 0.031 0.024 -10000 0 -0.13 10 10
HDAC1 0.035 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.013 -10000 0 -10000 0 0
AP-1 0.042 0.091 0.47 6 -10000 0 6
MAPK14 0.031 0.028 -10000 0 -0.038 67 67
MAPK10 0.027 0.028 -10000 0 -0.038 53 53
MAPK11 0.028 0.028 -10000 0 -0.038 59 59
KRT5 0.038 0.091 0.42 5 -10000 0 5
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.035 0.02 0.094 8 -0.072 8 16
STAT1 0.039 0.043 0.14 24 -0.18 13 37
CGA 0.035 0.061 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.036 0.077 -10000 0 -0.36 8 8
MAPK3 0.031 0.029 -10000 0 -0.038 69 69
MAPK1 0.028 0.028 -10000 0 -0.038 63 63
ICAM1 0.037 0.16 0.43 23 -10000 0 23
NFKB1 0.026 0.12 0.2 70 -0.17 116 186
MAPK8 0.033 0.071 0.3 7 -10000 0 7
MAPK9 0.03 0.028 -10000 0 -0.038 64 64
cortisol/GR alpha (dimer) -0.027 0.2 0.46 18 -0.55 24 42
BAX -0.031 0.18 0.44 1 -0.87 9 10
POMC 0.031 0.089 0.55 3 -10000 0 3
EP300 0.028 0.025 -10000 0 -0.13 10 10
cortisol/GR alpha (dimer)/p53 -0.077 0.15 -10000 0 -0.44 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.076 0.23 39 -10000 0 39
SGK1 -0.019 0.063 0.2 1 -0.24 14 15
IL13 0.023 0.078 -10000 0 -10000 0 0
IL6 0.041 0.15 0.42 37 -10000 0 37
PRKACG 0.037 0.008 -10000 0 0 21 21
IL5 0.009 0.093 0.48 1 -10000 0 1
IL2 0.04 0.086 0.4 3 -10000 0 3
CDK5 0.019 0.023 -10000 0 -0.036 18 18
PRKACB 0.035 0.012 -10000 0 0 52 52
HSP90AA1 0.036 0.01 -10000 0 0 39 39
IL8 -0.094 0.41 0.41 46 -0.77 126 172
CDK5R1/CDK5 0.024 0.043 -10000 0 -0.12 17 17
NF kappa B1 p50/RelA/PKAc 0.063 0.18 0.33 60 -0.22 101 161
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.053 0.12 -10000 0 -0.43 1 1
SMARCA4 0.033 0.014 -10000 0 0 83 83
chromatin remodeling -0.043 0.11 -10000 0 -0.37 24 24
NF kappa B1 p50/RelA/Cbp 0.055 0.18 0.36 26 -0.23 64 90
JUN (dimer) 0.016 0.069 0.38 6 -10000 0 6
YWHAH 0.033 0.014 -10000 0 0 76 76
VIPR1 0.035 0.078 0.36 11 -10000 0 11
NR3C1 -0.047 0.096 -10000 0 -0.33 1 1
NR4A1 0.041 0.011 -10000 0 -10000 0 0
TIF2/SUV420H1 0.039 0.052 -10000 0 -0.13 42 42
MAPKKK cascade -0.024 0.2 0.46 17 -0.52 24 41
cortisol/GR alpha (dimer)/Src-1 -0.055 0.14 -10000 0 -0.38 2 2
PBX1 0.042 0.013 0.14 7 -10000 0 7
POU1F1 0.043 0.015 0.13 10 -10000 0 10
SELE 0.032 0.15 0.33 19 -10000 0 19
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.044 0.11 -10000 0 -0.37 25 25
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.053 0.12 -10000 0 -0.43 1 1
mol:cortisol -0.035 0.067 -10000 0 -10000 0 0
MMP1 0.039 0.099 0.33 29 -0.49 5 34
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.012 -10000 0 0 52 52
HDAC4 0.037 0.009 -10000 0 0 32 32
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.003 0.037 -10000 0 -0.12 37 37
CDKN1A -0.019 0.11 0.26 1 -0.46 26 27
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 0 49 49
FOXO3 0.004 0.022 0.24 2 -10000 0 2
FOXO1 0.031 0.015 -10000 0 0 98 98
FOXO4 0.007 0.022 -10000 0 -0.17 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.036 0.011 -10000 0 0 44 44
TAT 0.038 0.006 -10000 0 0 13 13
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.003 -10000 0 -10000 0 0
PPARGC1A 0.033 0.014 -10000 0 0 79 79
FHL2 0.029 0.017 -10000 0 0 126 126
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.046 0.16 28 -0.13 5 33
HIST2H4A -0.003 0.037 0.12 37 -10000 0 37
SIRT1/FOXO3a 0.023 0.043 0.17 6 -0.14 2 8
SIRT1 0.033 0.046 0.18 37 -0.039 2 39
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.045 0.057 0.18 23 -0.12 15 38
SIRT1/Histone H1b 0.027 0.044 0.22 1 -0.16 5 6
apoptosis -0.047 0.052 0.12 8 -0.17 21 29
SIRT1/PGC1A 0.03 0.043 0.14 30 -0.1 13 43
p53/SIRT1 0.04 0.079 0.33 26 -0.14 17 43
SIRT1/FOXO4 0.026 0.043 0.18 3 -0.14 10 13
FOXO1/FHL2/SIRT1 0.021 0.057 0.17 12 -0.1 31 43
HIST1H1E 0.009 0.024 -10000 0 -0.17 6 6
SIRT1/p300 0.038 0.049 0.16 29 -0.13 10 39
muscle cell differentiation 0.01 0.038 -10000 0 -0.12 31 31
TP53 0.042 0.046 0.18 43 -0.039 2 45
KU70/SIRT1/BAX 0.048 0.053 0.18 21 -0.12 8 29
CREBBP 0.038 0.005 -10000 0 0 7 7
MEF2D 0.038 0.007 -10000 0 0 17 17
HIV-1 Tat/SIRT1 0.04 0.045 0.16 29 -0.13 4 33
ACSS2 -0.003 0.037 0.12 37 -10000 0 37
SIRT1/PCAF/MYOD -0.01 0.038 0.12 31 -10000 0 31
Regulation of Telomerase

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
Telomerase catalytic core complex 0.025 0.16 0.41 2 -0.55 11 13
RAD9A 0.038 0.006 -10000 0 0 12 12
AP1 0.014 0.076 -10000 0 -0.15 74 74
IFNAR2 0.035 0.024 -10000 0 -0.046 34 34
AKT1 0.008 0.057 -10000 0 -0.25 20 20
ER alpha/Oestrogen 0.025 0.017 -10000 0 -0.029 18 18
NFX1/SIN3/HDAC complex -0.014 0.085 -10000 0 -0.26 36 36
EGF 0.033 0.021 -10000 0 -0.041 33 33
SMG5 0.038 0.007 -10000 0 0 17 17
SMG6 0.037 0.008 -10000 0 0 21 21
SP3/HDAC2 0.041 0.053 -10000 0 -0.097 50 50
TERT/c-Abl 0.034 0.17 -10000 0 -0.52 18 18
SAP18 0.035 0.012 -10000 0 -0.001 51 51
MRN complex 0.072 0.026 -10000 0 -0.12 4 4
WT1 0.034 0.024 -10000 0 -0.045 37 37
WRN 0.037 0.009 -10000 0 0 31 31
SP1 0.036 0.027 -10000 0 -0.052 37 37
SP3 0.034 0.021 -10000 0 -0.04 34 34
TERF2IP 0.036 0.011 -10000 0 0 40 40
Telomerase/Nucleolin 0.044 0.17 -10000 0 -0.51 17 17
Mad/Max 0.049 0.033 -10000 0 -10000 0 0
TERT 0.018 0.16 0.42 1 -0.56 11 12
CCND1 -0.013 0.29 0.47 3 -0.93 39 42
MAX 0.032 0.023 -10000 0 -0.04 35 35
RBBP7 0.038 0.009 -10000 0 -0.01 14 14
RBBP4 0.034 0.013 -10000 0 -0.001 63 63
TERF2 -0.035 0.02 0.086 7 -10000 0 7
PTGES3 0.037 0.009 -10000 0 0 29 29
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.046 0.11 0.25 1 -0.47 13 14
CDKN1B -0.035 0.085 0.19 13 -0.32 26 39
RAD1 0.037 0.008 -10000 0 0 24 24
XRCC5 0.038 0.005 -10000 0 0 9 9
XRCC6 0.036 0.011 -10000 0 0 44 44
SAP30 0.037 0.01 -10000 0 -0.006 24 24
TRF2/PARP2 0.033 0.052 -10000 0 -0.12 44 44
UBE3A 0.033 0.021 -10000 0 -0.038 36 36
JUN 0.033 0.021 -10000 0 -0.039 27 27
E6 0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.026 0.022 -10000 0 -0.039 40 40
FOS 0.023 0.024 -10000 0 -0.039 24 24
IFN-gamma/IRF1 0.033 0.071 0.18 1 -0.18 38 39
PARP2 0.035 0.012 -10000 0 0 56 56
BLM 0.03 0.016 -10000 0 0 113 113
Telomerase 0.005 0.092 0.22 1 -0.28 32 33
IRF1 0.024 0.042 0.12 2 -0.081 55 57
ESR1 0.033 0.02 -10000 0 -0.036 30 30
KU/TER 0.05 0.028 -10000 0 -0.13 8 8
ATM/TRF2 0.046 0.029 -10000 0 -0.097 10 10
ubiquitin-dependent protein catabolic process -0.009 0.083 0.15 1 -0.26 30 31
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.009 0.085 0.15 1 -0.26 30 31
HDAC1 0.037 0.009 -10000 0 -0.001 25 25
HDAC2 0.032 0.027 -10000 0 -0.052 33 33
ATM 0.023 0.034 0.12 37 -0.17 4 41
SMAD3 -0.025 0.035 0.12 26 -10000 0 26
ABL1 0.033 0.014 -10000 0 0 72 72
MXD1 0.035 0.021 -10000 0 -0.039 38 38
MRE11A 0.038 0.006 -10000 0 0 11 11
HUS1 0.023 0.019 -10000 0 0 205 205
RPS6KB1 0.038 0.005 -10000 0 0 10 10
TERT/NF kappa B1/14-3-3 0.041 0.18 -10000 0 -0.55 16 16
NR2F2 0.021 0.029 -10000 0 -0.045 57 57
MAPK3 -0.03 0.018 0.12 2 -10000 0 2
MAPK1 -0.026 0.026 0.12 9 -10000 0 9
TGFB1/TGF beta receptor Type II 0.027 0.024 -10000 0 -0.037 45 45
NFKB1 0.038 0.007 -10000 0 0 18 18
HNRNPC 0.036 0.01 -10000 0 0 37 37
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.023 0.034 0.12 37 -0.17 4 41
NBN 0.038 0.007 -10000 0 0 16 16
EGFR 0.009 0.018 -10000 0 -0.038 7 7
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.002 0.051 -10000 0 -0.12 58 58
MYC 0.029 0.022 -10000 0 -0.039 22 22
IL2 0.036 0.027 0.083 1 -0.052 37 38
KU 0.05 0.028 -10000 0 -0.13 8 8
RAD50 0.038 0.006 -10000 0 0 14 14
HSP90AA1 0.036 0.01 -10000 0 0 39 39
TGFB1 0.027 0.024 -10000 0 -0.037 44 44
TRF2/BLM 0.016 0.071 -10000 0 -0.13 90 90
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.049 0.17 -10000 0 -0.51 15 15
SP1/HDAC2 0.045 0.049 -10000 0 -0.091 38 38
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.043 0.17 -10000 0 -0.48 19 19
Smad3/Myc -0.023 0.039 0.11 24 -0.13 5 29
911 complex 0.044 0.042 -10000 0 -0.12 4 4
IFNG 0.025 0.043 0.12 2 -0.081 60 62
Telomerase/PinX1 0.034 0.16 -10000 0 -0.48 18 18
Telomerase/AKT1/mTOR/p70S6K 0.009 0.13 0.25 2 -0.39 26 28
SIN3B 0.036 0.012 -10000 0 -0.001 48 48
YWHAE 0.037 0.009 -10000 0 0 29 29
Telomerase/EST1B 0.044 0.17 -10000 0 -0.49 18 18
response to DNA damage stimulus 0.009 0.02 -10000 0 -0.087 13 13
MRN complex/TRF2/Rap1 0.079 0.073 -10000 0 -0.13 39 39
TRF2/WRN 0.038 0.042 -10000 0 -0.1 36 36
Telomerase/hnRNP C1/C2 0.042 0.17 -10000 0 -0.49 19 19
E2F1 0.031 0.024 -10000 0 -0.044 30 30
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.038 0.007 -10000 0 0 19 19
DKC1 0.037 0.008 -10000 0 0 22 22
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.032 0.055 -10000 0 -0.11 22 22
TC10/GTP 0.024 0.055 -10000 0 -0.12 21 21
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.066 -10000 0 -0.12 29 29
HRAS 0.036 0.01 -10000 0 0 39 39
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.034 0.013 -10000 0 0 70 70
FOXO3 -0.051 0.2 -10000 0 -0.65 50 50
AKT1 -0.034 0.094 0.24 16 -0.24 6 22
INSR 0.035 0.026 -10000 0 -0.048 31 31
Insulin Receptor/Insulin 0.051 0.063 0.23 4 -0.14 31 35
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.02 0.02 -10000 0 0 254 254
SORBS1 0.027 0.018 -10000 0 0 154 154
CRK 0.037 0.008 -10000 0 0 25 25
PTPN1 -0.031 0.049 0.14 23 -0.23 7 30
CAV1 -0.013 0.041 0.18 8 -0.18 5 13
CBL/APS/CAP/Crk-II/C3G 0.047 0.062 -10000 0 -0.1 14 14
Insulin Receptor/Insulin/IRS1/NCK2 0.076 0.069 -10000 0 -0.13 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.081 -10000 0 -0.13 74 74
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.073 -10000 0 -0.36 8 8
RPS6KB1 -0.044 0.087 0.21 17 -0.24 6 23
PARD6A 0.038 0.007 -10000 0 0 18 18
CBL 0.038 0.006 -10000 0 0 11 11
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.02 0.021 -10000 0 -10000 0 0
PIK3R1 0.034 0.013 -10000 0 0 69 69
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.045 0.093 0.17 19 -0.25 7 26
HRAS/GTP -0.043 0.04 0.037 41 -0.15 14 55
Insulin Receptor 0.035 0.026 -10000 0 -0.048 31 31
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.083 0.076 -10000 0 -0.13 32 32
PRKCI 0.025 0.086 -10000 0 -0.41 17 17
Insulin Receptor/Insulin/GRB14/PDK1 -0.046 0.062 0.075 25 -0.19 13 38
SHC1 0.035 0.012 -10000 0 0 56 56
negative regulation of MAPKKK cascade 0.024 0.06 -10000 0 -10000 0 0
PI3K 0.049 0.089 -10000 0 -0.13 74 74
NCK2 0.037 0.008 -10000 0 0 20 20
RHOQ 0.038 0.007 -10000 0 0 15 15
mol:H2O2 -0.005 0.006 0.03 2 -0.032 6 8
HRAS/GDP 0.023 0.025 -10000 0 -0.11 16 16
AKT2 -0.038 0.089 0.24 15 -10000 0 15
PRKCZ 0.003 0.072 -10000 0 -0.4 14 14
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.017 0.063 0.16 35 -0.18 1 36
F2RL2 0.038 0.006 -10000 0 0 12 12
TRIP10 0.036 0.011 -10000 0 0 43 43
Insulin Receptor/Insulin/Shc 0.059 0.044 -10000 0 -0.11 9 9
TC10/GTP/CIP4/Exocyst 0.044 0.029 -10000 0 -0.1 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.054 -10000 0 -0.12 14 14
RAPGEF1 0.037 0.008 -10000 0 0 23 23
RASA1 0.036 0.01 -10000 0 0 37 37
NCK1 0.037 0.009 -10000 0 0 31 31
CBL/APS/CAP/Crk-II 0.041 0.05 -10000 0 -0.1 14 14
TC10/GDP 0.025 0.022 -10000 0 -0.11 12 12
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.067 -10000 0 -0.13 29 29
INPP5D -0.025 0.034 0.085 23 -0.1 22 45
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.007 0.005 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.038 0.007 -10000 0 0 17 17
IRS1 0.035 0.012 -10000 0 0 53 53
p62DOK/RasGAP 0.024 0.061 -10000 0 -10000 0 0
INS 0.039 0.028 0.1 19 -0.048 30 49
mol:PI-3-4-P2 -0.025 0.034 0.084 23 -0.1 22 45
GRB2 0.037 0.009 -10000 0 0 26 26
EIF4EBP1 -0.046 0.085 0.21 16 -0.24 8 24
PTPRA 0.032 0.019 -10000 0 -0.059 6 6
PIK3CA 0.033 0.014 -10000 0 0 79 79
TC10/GTP/CIP4 0.044 0.029 -10000 0 -0.1 14 14
PDPK1 0.038 0.005 -10000 0 0 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.01 0.053 -10000 0 -0.16 32 32
Insulin Receptor/Insulin/IRS1 0.057 0.051 -10000 0 -0.11 23 23
Insulin Receptor/Insulin/IRS3 0.051 0.038 -10000 0 -0.077 6 6
Par3/Par6 0.077 0.045 -10000 0 -0.11 16 16
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.043 0.012 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.057 -10000 0 -0.1 87 87
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.038 0.005 -10000 0 0 9 9
RGS9-1/Gbeta5/R9AP 0.048 0.015 -10000 0 -0.1 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.049 0.014 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.038 0.006 -10000 0 0 11 11
Cone Metarhodopsin II/X-Arrestin 0.029 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.062 0.18 6 -10000 0 6
Cone PDE6 0.052 0.058 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.015 0.065 -10000 0 -0.1 86 86
GNAT2/GDP 0.062 0.024 -10000 0 -0.097 1 1
GNB5 0.037 0.008 -10000 0 0 20 20
mol:GMP (4 units) -0.019 0.043 0.19 16 -10000 0 16
Cone Transducin 0.047 0.012 -10000 0 -10000 0 0
SLC24A2 0.03 0.016 -10000 0 0 116 116
GNB3/GNGT2 0.027 0.006 -10000 0 -10000 0 0
GNB3 0.037 0.008 -10000 0 0 25 25
GNAT2/GTP 0.028 0.004 -10000 0 -10000 0 0
CNGA3 0.024 0.019 -10000 0 0 200 200
ARR3 0.039 0.002 -10000 0 0 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.013 0.058 -10000 0 -0.1 87 87
mol:Pi 0.048 0.015 -10000 0 -0.1 1 1
Cone CNG Channel 0.028 0.081 -10000 0 -0.11 80 80
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.03 0.016 -10000 0 0 116 116
RGS9 0.037 0.008 -10000 0 0 20 20
PDE6C 0.027 0.018 -10000 0 0 151 151
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.037 0.009 -10000 0 0 30 30
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.036 0.011 -10000 0 -0.006 29 29
HDAC2 0.033 0.015 -10000 0 -0.003 68 68
GNB1/GNG2 0.025 0.034 -10000 0 -0.1 13 13
forebrain development 0.059 0.096 0.44 15 -0.4 1 16
GNAO1 0.033 0.015 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.031 0.034 -10000 0 -0.13 4 4
SMO 0.023 0.02 0.083 1 -10000 0 1
ARRB2 0.038 0.009 -10000 0 -10000 0 0
GLI3/SPOP -0.007 0.11 -10000 0 -0.32 31 31
mol:GTP 0.001 0.003 0.026 2 -10000 0 2
GSK3B 0.036 0.011 -10000 0 0 40 40
GNAI2 0.036 0.012 0.08 1 -10000 0 1
SIN3/HDAC complex 0.053 0.047 -10000 0 -0.11 20 20
GNAI1 0.017 0.02 -10000 0 -10000 0 0
XPO1 0.042 0.012 0.1 12 -10000 0 12
GLI1/Su(fu) 0.017 0.06 0.36 7 -0.33 1 8
SAP30 0.036 0.011 -10000 0 -0.009 26 26
mol:GDP 0.023 0.02 0.083 1 -10000 0 1
MIM/GLI2A 0.043 0.02 0.17 11 -10000 0 11
IFT88 0.036 0.01 -10000 0 0 38 38
GNAI3 0.039 0.007 -10000 0 -10000 0 0
GLI2 -0.004 0.089 0.23 3 -0.32 22 25
GLI3 -0.02 0.099 -10000 0 -0.31 31 31
CSNK1D 0.037 0.008 -10000 0 0 25 25
CSNK1E 0.034 0.013 -10000 0 0 68 68
SAP18 0.034 0.014 -10000 0 -0.004 56 56
embryonic digit morphogenesis 0.036 0.01 -10000 0 0 38 38
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.007 0.081 0.16 5 -0.25 32 37
SIN3B 0.035 0.013 -10000 0 -0.004 51 51
SIN3A 0 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) -0.017 0.071 0.15 3 -0.27 23 26
GLI2/Su(fu) -0.009 0.069 -10000 0 -0.3 17 17
FOXA2 0.043 0.066 -10000 0 -0.49 5 5
neural tube patterning 0.059 0.096 0.44 15 -0.4 1 16
SPOP 0.037 0.009 -10000 0 0 27 27
Su(fu)/PIAS1 0.054 0.043 0.1 196 -0.081 11 207
GNB1 0.035 0.011 -10000 0 0 46 46
CSNK1G2 0.036 0.01 -10000 0 0 37 37
CSNK1G3 0.038 0.006 -10000 0 0 14 14
MTSS1 0.043 0.02 0.17 11 -10000 0 11
embryonic limb morphogenesis 0.059 0.096 0.44 15 -0.4 1 16
SUFU -0.003 0.011 0.042 9 -0.099 4 13
LGALS3 0.03 0.017 -10000 0 0 121 121
catabolic process 0.006 0.14 0.27 4 -0.41 34 38
GLI3A/CBP 0.046 0.011 -10000 0 -10000 0 0
KIF3A 0.035 0.012 -10000 0 0 55 55
GLI1 0.056 0.095 0.43 16 -0.4 1 17
RAB23 0.036 0.01 -10000 0 0 33 33
CSNK1A1 0.038 0.007 -10000 0 0 16 16
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.037 0.01 -10000 0 -0.015 17 17
Su(fu)/Galectin3 0.044 0.043 0.1 158 -0.1 5 163
GNAZ 0.033 0.015 -10000 0 -10000 0 0
RBBP4 0.033 0.014 -10000 0 -0.003 67 67
CSNK1G1 0.038 0.006 -10000 0 0 13 13
PIAS1 0.037 0.009 -10000 0 0 27 27
PRKACA 0.036 0.01 -10000 0 0 36 36
GLI2/SPOP 0.014 0.097 0.23 3 -0.33 23 26
STK36 0.003 0.011 0.048 25 -10000 0 25
Gi family/GNB1/GNG2/GDP -0.011 0.092 0.17 1 -0.34 25 26
PTCH1 0.057 0.11 0.53 15 -10000 0 15
MIM/GLI1 0.08 0.098 0.43 14 -0.4 1 15
CREBBP 0.046 0.011 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.007 0.095 0.16 2 -0.29 35 37
Aurora A signaling

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.026 0.066 0.17 1 -0.2 29 30
BIRC5 0.031 0.016 -10000 0 0 110 110
NFKBIA -0.016 0.048 0.23 5 -0.18 16 21
CPEB1 0.035 0.012 -10000 0 0 56 56
AKT1 -0.014 0.038 0.2 4 -0.18 7 11
NDEL1 0.037 0.008 -10000 0 0 21 21
Aurora A/BRCA1 0.03 0.052 -10000 0 -0.17 20 20
NDEL1/TACC3 0.038 0.068 -10000 0 -0.18 27 27
GADD45A 0.033 0.014 -10000 0 0 78 78
GSK3B 0.037 0.016 0.09 26 0 40 66
PAK1/Aurora A 0.033 0.058 0.17 1 -0.18 25 26
MDM2 0.035 0.012 -10000 0 0 57 57
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.018 0.032 0.12 20 -10000 0 20
TP53 0 0.065 0.16 1 -0.24 25 26
DLG7 -0.007 0.038 0.096 17 -0.17 19 36
AURKAIP1 0.037 0.009 -10000 0 0 28 28
ARHGEF7 0.034 0.013 -10000 0 0 65 65
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.04 0.072 -10000 0 -0.2 27 27
G2/M transition of mitotic cell cycle 0.03 0.052 -10000 0 -0.17 20 20
AURKA 0.007 0.049 0.14 18 -0.2 19 37
AURKB 0.007 0.032 -10000 0 -0.14 20 20
CDC25B -0.002 0.071 0.16 1 -0.28 25 26
G2/M transition checkpoint -0.001 0.038 -10000 0 -0.16 21 21
mRNA polyadenylation 0.023 0.055 -10000 0 -0.17 20 20
Aurora A/CPEB 0.024 0.055 -10000 0 -0.17 20 20
Aurora A/TACC1/TRAP/chTOG 0.058 0.088 -10000 0 -0.22 22 22
BRCA1 0.038 0.007 -10000 0 0 16 16
centrosome duplication 0.033 0.058 0.17 1 -0.17 25 26
regulation of centrosome cycle 0.037 0.067 -10000 0 -0.18 27 27
spindle assembly 0.056 0.086 -10000 0 -0.22 22 22
TDRD7 0.035 0.011 -10000 0 0 48 48
Aurora A/RasGAP/Survivin 0.048 0.085 -10000 0 -0.2 25 25
CENPA -0.003 0.078 -10000 0 -0.32 26 26
Aurora A/PP2A 0.034 0.058 0.17 1 -0.18 24 25
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.001 0.059 -10000 0 -0.22 19 19
negative regulation of DNA binding 0.007 0.068 -10000 0 -0.24 25 25
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.044 -10000 0 -0.13 27 27
RASA1 0.036 0.01 -10000 0 0 37 37
Ajuba/Aurora A -0.001 0.039 -10000 0 -0.16 21 21
mitotic prometaphase -0.004 0.012 0.07 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.049 0.14 18 -0.2 19 37
TACC1 0.037 0.008 -10000 0 0 25 25
TACC3 0.034 0.013 -10000 0 0 64 64
Aurora A/Antizyme1 0.047 0.063 -10000 0 -0.18 21 21
Aurora A/RasGAP 0.031 0.067 0.17 1 -0.21 26 27
OAZ1 0.036 0.011 -10000 0 0 40 40
RAN 0.038 0.007 -10000 0 0 16 16
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.037 0.016 0.09 26 0 36 62
GIT1 0.038 0.005 -10000 0 0 9 9
GIT1/beta-PIX/PAK1 0.06 0.048 -10000 0 -0.12 26 26
Importin alpha/Importin beta/TPX2 -0.018 0.032 0.12 20 -10000 0 20
PPP2R5D 0.038 0.005 -10000 0 0 10 10
Aurora A/TPX2 -0.034 0.06 0.13 1 -0.21 29 30
PAK1 0.037 0.008 -10000 0 0 20 20
CKAP5 0.036 0.011 -10000 0 0 42 42
Nectin adhesion pathway

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
PDGFRB 0.037 0.009 -10000 0 0 29 29
alphaV beta3 Integrin 0.047 0.04 -10000 0 -0.13 23 23
PTK2 0.006 0.11 0.23 1 -0.3 43 44
positive regulation of JNK cascade 0.019 0.098 -10000 0 -0.28 25 25
CDC42/GDP 0.029 0.13 0.31 1 -0.36 34 35
Rac1/GDP 0.015 0.11 0.31 1 -0.34 18 19
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.038 0.006 -10000 0 0 13 13
CTNNB1 0.038 0.007 -10000 0 0 18 18
CDC42/GTP 0.025 0.12 -10000 0 -0.35 20 20
nectin-3/I-afadin 0.045 0.028 -10000 0 -0.12 5 5
RAPGEF1 -0.002 0.12 0.34 1 -0.36 35 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.001 0.13 -10000 0 -0.4 36 36
PDGFB-D/PDGFRB 0.037 0.009 -10000 0 0 29 29
TLN1 -0.008 0.07 0.17 35 -0.23 15 50
Rap1/GTP -0.009 0.089 -10000 0 -0.26 46 46
IQGAP1 0.035 0.012 -10000 0 0 49 49
Rap1/GTP/I-afadin 0.044 0.017 -10000 0 -0.093 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.045 0.028 -10000 0 -0.12 5 5
PVR 0.036 0.011 -10000 0 0 41 41
Necl-5(dimer) 0.036 0.011 -10000 0 0 41 41
mol:GDP 0.013 0.15 0.31 1 -0.42 37 38
MLLT4 0.036 0.011 -10000 0 0 45 45
PIK3CA 0.033 0.014 -10000 0 0 79 79
PI3K 0.059 0.092 -10000 0 -0.13 68 68
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.051 0.018 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.009 0.085 -10000 0 -0.29 18 18
PVRL1 0.038 0.006 -10000 0 0 11 11
PVRL3 0.034 0.013 -10000 0 0 64 64
PVRL2 0.036 0.011 -10000 0 0 44 44
PIK3R1 0.034 0.013 -10000 0 0 69 69
CDH1 0.036 0.01 -10000 0 0 38 38
CLDN1 0.036 0.01 -10000 0 0 34 34
JAM-A/CLDN1 0.076 0.051 -10000 0 -0.12 7 7
SRC 0.003 0.14 -10000 0 -0.42 36 36
ITGB3 0.038 0.005 -10000 0 0 7 7
nectin-1(dimer)/I-afadin/I-afadin 0.051 0.018 -10000 0 -10000 0 0
FARP2 0.022 0.15 -10000 0 -0.46 19 19
RAC1 0.023 0.019 -10000 0 0 209 209
CTNNA1 0.037 0.008 -10000 0 0 20 20
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.059 0.038 -10000 0 -0.12 5 5
nectin-1/I-afadin 0.051 0.018 -10000 0 -10000 0 0
nectin-2/I-afadin 0.048 0.025 -10000 0 -0.13 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.023 0.039 -10000 0 -0.11 26 26
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.061 0.036 -10000 0 -0.12 5 5
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.04 -10000 0 -0.1 32 32
F11R 0.035 0.012 -10000 0 0 51 51
positive regulation of filopodium formation 0.019 0.098 -10000 0 -0.28 25 25
alphaV/beta3 Integrin/Talin -0.013 0.1 0.22 48 -0.24 16 64
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.048 0.025 -10000 0 -0.13 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.048 0.025 -10000 0 -0.13 3 3
PIP5K1C -0.019 0.046 0.11 4 -0.22 18 22
VAV2 0.016 0.16 -10000 0 -0.51 20 20
RAP1/GDP 0.019 0.12 0.27 1 -0.33 37 38
ITGAV 0.036 0.01 -10000 0 0 34 34
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.057 0.04 -10000 0 -0.13 7 7
nectin-3(dimer)/I-afadin/I-afadin 0.045 0.028 -10000 0 -0.12 5 5
Rac1/GTP 0.013 0.1 -10000 0 -0.35 17 17
PTPRM 0.003 0.042 -10000 0 -0.21 14 14
E-cadherin/beta catenin/alpha catenin 0.082 0.068 -10000 0 -0.18 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.037 0.009 -10000 0 0 27 27
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 0.031 0.016 -10000 0 0 107 107
positive regulation of NF-kappaB transcription factor activity 0.039 0.043 -10000 0 -0.13 24 24
MAP2K4 0.008 0.058 0.2 2 -0.26 6 8
IKBKB 0.038 0.005 -10000 0 0 7 7
TNFRSF10B 0.037 0.009 -10000 0 0 26 26
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.012 0.031 -10000 0 -0.1 20 20
IKBKG 0.039 0.004 -10000 0 0 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.038 0.006 -10000 0 0 13 13
TRAIL/TRAILR2 0.038 0.043 -10000 0 -0.13 23 23
TRAIL/TRAILR3 0.039 0.043 -10000 0 -0.13 24 24
TRAIL/TRAILR1 0.017 0.031 -10000 0 -0.11 25 25
TRAIL/TRAILR4 0.039 0.043 -10000 0 -0.13 24 24
TRAIL/TRAILR1/DAP3/GTP 0.032 0.038 -10000 0 -0.095 32 32
IKK complex -0.038 0.12 -10000 0 -0.24 124 124
RIPK1 0.037 0.008 -10000 0 0 22 22
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.025 0.022 -10000 0 -0.11 12 12
MAPK3 -0.012 0.051 0.12 67 -10000 0 67
MAP3K1 0.021 0.055 -10000 0 -0.26 5 5
TRAILR4 (trimer) 0.038 0.006 -10000 0 0 13 13
TRADD 0.038 0.005 -10000 0 0 9 9
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.015 0.049 -10000 0 -0.16 24 24
CFLAR 0.038 0.005 -10000 0 0 9 9
MAPK1 -0.01 0.051 0.12 67 -10000 0 67
TRAIL/TRAILR1/FADD/TRADD/RIP 0.074 0.051 -10000 0 -0.11 25 25
mol:ceramide 0.012 0.031 -10000 0 -0.1 20 20
FADD 0.038 0.006 -10000 0 0 13 13
MAPK8 -0.002 0.047 0.18 1 -0.26 5 6
TRAF2 0.037 0.008 -10000 0 0 20 20
TRAILR3 (trimer) 0.038 0.007 -10000 0 0 15 15
CHUK 0.027 0.018 -10000 0 0 155 155
TRAIL/TRAILR1/FADD 0.036 0.037 -10000 0 -0.1 25 25
DAP3 0.037 0.009 -10000 0 0 27 27
CASP10 -0.008 0.057 0.15 18 -0.16 21 39
JNK cascade 0.039 0.043 -10000 0 -0.13 24 24
TRAIL (trimer) 0.031 0.016 -10000 0 0 107 107
TNFRSF10C 0.038 0.007 -10000 0 0 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.045 0.047 -10000 0 -0.1 31 31
TRAIL/TRAILR2/FADD 0.054 0.049 -10000 0 -0.12 23 23
cell death 0.012 0.031 -10000 0 -0.1 20 20
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.02 0.053 -10000 0 -0.24 4 4
TRAILR2 (trimer) 0.037 0.009 -10000 0 0 26 26
CASP8 0.015 0.034 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.091 0.062 -10000 0 -0.12 19 19
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.033 0.024 0.14 4 -10000 0 4
VEGFR1 homodimer/NRP1 -0.022 0.014 -10000 0 -10000 0 0
mol:DAG -0.027 0.042 0.19 5 -10000 0 5
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.056 -10000 0 -0.17 7 7
CaM/Ca2+ -0.032 0.051 0.2 5 -10000 0 5
HIF1A 0.042 0.014 -10000 0 -10000 0 0
GAB1 0.035 0.012 -10000 0 0 56 56
AKT1 -0.045 0.086 0.25 4 -0.3 20 24
PLCG1 -0.027 0.042 0.2 5 -10000 0 5
NOS3 0.007 0.079 0.27 2 -0.3 6 8
CBL 0.038 0.006 -10000 0 0 11 11
mol:NO 0.011 0.082 0.27 2 -0.3 6 8
FLT1 -0.025 0.014 0.12 2 -10000 0 2
PGF 0.033 0.014 -10000 0 0 77 77
VEGFR1 homodimer/NRP2/VEGFR121 0.007 0.072 -10000 0 -0.18 7 7
CALM1 0.034 0.013 -10000 0 0 62 62
PIK3CA 0.033 0.014 -10000 0 0 79 79
eNOS/Hsp90 0.022 0.1 0.29 2 -0.31 6 8
endothelial cell proliferation -0.006 0.063 0.22 4 -0.24 3 7
mol:Ca2+ -0.027 0.042 0.19 5 -10000 0 5
MAPK3 -0.041 0.041 0.24 1 -10000 0 1
MAPK1 -0.039 0.043 0.24 1 -10000 0 1
PIK3R1 0.034 0.013 -10000 0 0 69 69
PLGF homodimer 0.033 0.014 -10000 0 0 77 77
PRKACA 0.036 0.01 -10000 0 0 36 36
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.015 0.019 -10000 0 0 315 315
VEGFA homodimer 0.025 0.019 -10000 0 0 181 181
VEGFR1 homodimer/VEGFA homodimer -0.023 0.031 0.14 3 -0.19 7 10
platelet activating factor biosynthetic process -0.033 0.068 0.22 5 -10000 0 5
PI3K 0.036 0.078 -10000 0 -0.19 14 14
PRKCA -0.033 0.042 0.17 5 -10000 0 5
PRKCB -0.025 0.038 0.18 5 -10000 0 5
VEGFR1 homodimer/PLGF homodimer -0.031 0.025 0.14 4 -10000 0 4
VEGFA 0.025 0.019 -10000 0 0 181 181
VEGFB 0.038 0.005 -10000 0 0 9 9
mol:IP3 -0.027 0.042 0.19 5 -10000 0 5
RASA1 -0.038 0.03 0.18 6 -10000 0 6
NRP2 0.038 0.005 -10000 0 0 9 9
VEGFR1 homodimer -0.025 0.014 0.12 2 -10000 0 2
VEGFB homodimer 0.038 0.005 -10000 0 0 9 9
NCK1 0.037 0.009 -10000 0 0 31 31
eNOS/Caveolin-1 -0.01 0.068 0.32 1 -0.31 4 5
PTPN11 0.038 0.007 -10000 0 0 17 17
mol:PI-3-4-5-P3 0.035 0.077 -10000 0 -0.18 14 14
mol:L-citrulline 0.011 0.082 0.27 2 -0.3 6 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.024 0.087 -10000 0 -0.19 9 9
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.007 0.073 -10000 0 -0.19 9 9
CD2AP 0.035 0.011 -10000 0 0 47 47
PI3K/GAB1 0.043 0.09 -10000 0 -0.18 21 21
PDPK1 -0.044 0.072 0.31 4 -0.24 2 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.006 0.074 -10000 0 -0.19 10 10
mol:NADP 0.011 0.082 0.27 2 -0.3 6 8
HSP90AA1 0.036 0.01 -10000 0 0 39 39
ubiquitin-dependent protein catabolic process 0.022 0.085 -10000 0 -0.19 9 9
VEGFR1 homodimer/NRP2 -0.033 0.024 0.14 4 -10000 0 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.037 0.008 -10000 0 0 24 24
HDAC3 0.038 0.005 -10000 0 0 10 10
VDR 0.037 0.009 -10000 0 0 26 26
Cbp/p300/PCAF 0.045 0.024 -10000 0 -0.1 7 7
EP300 0.035 0.012 -10000 0 0 52 52
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.008 0.057 -10000 0 -0.25 12 12
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.038 0.005 -10000 0 0 8 8
AKT1 0 0.08 0.2 4 -0.23 13 17
RAR alpha/9cRA/Cyclin H -0.011 0.12 -10000 0 -0.28 35 35
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.016 0.063 0.14 1 -0.21 24 25
CDC2 -0.001 0.004 -10000 0 -10000 0 0
response to UV -0.001 0.007 0.032 1 -0.026 31 32
RAR alpha/Jnk1 0.017 0.041 -10000 0 -0.36 2 2
NCOR2 0.038 0.006 -10000 0 0 11 11
VDR/VDR/Vit D3 0.027 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.034 0.15 0.33 1 -0.52 35 36
NCOA2 0.038 0.006 -10000 0 0 14 14
NCOA3 0.034 0.013 -10000 0 0 69 69
NCOA1 0.035 0.012 -10000 0 0 52 52
VDR/VDR/DNA 0.037 0.009 -10000 0 0 26 26
RARG 0.033 0.021 -10000 0 -0.042 33 33
RAR gamma1/9cRA 0.047 0.016 -10000 0 -0.036 2 2
MAPK3 0.034 0.021 -10000 0 -0.046 32 32
MAPK1 0.035 0.011 -10000 0 0 47 47
MAPK8 0.025 0.024 -10000 0 -0.055 21 21
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.008 0.11 -10000 0 -0.32 47 47
RARA 0.002 0.036 -10000 0 -0.2 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.008 0.053 0.14 1 -0.2 15 16
PRKCA 0.032 0.031 0.1 4 -0.083 32 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.032 0.16 0.34 1 -0.55 38 39
RXRG 0.013 0.029 0.13 1 -10000 0 1
RXRA -0.025 0.065 -10000 0 -0.21 29 29
RXRB 0.013 0.027 0.12 1 -0.11 1 2
VDR/Vit D3/DNA 0.027 0.006 -10000 0 -10000 0 0
RBP1 0.028 0.018 -10000 0 0 145 145
CRBP1/9-cic-RA 0 0.053 -10000 0 -0.11 91 91
RARB 0.033 0.024 0.088 3 -0.056 32 35
PRKCG 0.03 0.031 0.1 4 -0.082 32 36
MNAT1 0.035 0.011 -10000 0 0 47 47
RAR alpha/RXRs -0.018 0.12 -10000 0 -0.4 29 29
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.094 0.23 1 -0.3 27 28
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.067 0.2 2 -0.23 17 19
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.032 0.16 0.34 1 -0.56 37 38
positive regulation of DNA binding -0.016 0.11 -10000 0 -0.26 41 41
NRIP1 -0.055 0.27 0.45 1 -1 33 34
RXRs/RARs -0.015 0.12 -10000 0 -0.39 39 39
RXRs/RXRs/DNA/9cRA -0.024 0.1 -10000 0 -0.31 48 48
PRKACA 0.036 0.01 -10000 0 0 36 36
CDK7 0.037 0.009 -10000 0 0 27 27
TFIIH 0.062 0.05 -10000 0 -0.15 19 19
RAR alpha/9cRA 0.018 0.097 -10000 0 -0.21 19 19
CCNH 0.037 0.008 -10000 0 0 23 23
CREBBP 0.038 0.005 -10000 0 0 7 7
RAR gamma2/9cRA 0.056 0.055 -10000 0 -0.15 17 17
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.006 0.049 0.13 29 -0.11 5 34
NFATC2 -0.002 0.036 0.12 19 -0.098 6 25
NFATC3 -0.007 0.05 0.13 29 -0.11 6 35
CD40LG 0.008 0.15 0.36 42 -10000 0 42
PTGS2 -0.038 0.083 0.31 3 -10000 0 3
JUNB 0.032 0.015 -10000 0 0 91 91
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.024 0.097 13 -0.12 6 19
CaM/Ca2+ 0.03 0.024 0.097 13 -0.12 6 19
CALM1 0.037 0.016 0.087 4 -10000 0 4
JUN 0.039 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.02 -10000 0 -0.091 10 10
FOSL1 0.035 0.012 -10000 0 0 58 58
CREM 0.028 0.017 -10000 0 0 136 136
Jun/NFAT1-c-4/p21SNFT -0.001 0.11 0.27 34 -10000 0 34
FOS 0.029 0.021 -10000 0 -10000 0 0
IFNG 0.004 0.14 0.38 33 -10000 0 33
AP-1/NFAT1-c-4 0.069 0.12 0.36 3 -0.25 2 5
FASLG 0.005 0.15 0.37 36 -10000 0 36
NFAT1-c-4/ICER1 -0.006 0.087 0.26 16 -10000 0 16
IL2RA -0.003 0.11 0.37 4 -10000 0 4
FKBP12/FK506 0.021 0.022 -10000 0 -0.11 10 10
CSF2 0.008 0.15 0.37 40 -10000 0 40
JunB/Fra1/NFAT1-c-4 -0.016 0.081 0.25 11 -10000 0 11
IL4 0.008 0.15 0.37 37 -10000 0 37
IL2 0.015 0.084 -10000 0 -0.8 5 5
IL3 0.027 0.089 -10000 0 -0.61 9 9
FKBP1A 0.032 0.015 -10000 0 0 91 91
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.04 0.009 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.031 0.15 0.39 1 -0.96 10 11
CLOCK 0.036 0.021 0.097 1 -0.075 10 11
TIMELESS/CRY2 0.026 0.16 0.41 1 -0.99 10 11
DEC1/BMAL1 0.037 0.054 -10000 0 -0.12 47 47
ATR 0.037 0.009 -10000 0 0 32 32
NR1D1 0.013 0.079 0.48 1 -10000 0 1
ARNTL 0.034 0.022 0.097 1 -0.078 8 9
TIMELESS -0.001 0.16 -10000 0 -1.1 10 10
NPAS2 0.039 0.019 0.097 1 -0.075 10 11
CRY2 0.037 0.009 -10000 0 0 27 27
mol:CO -0.012 0.035 0.12 10 -0.1 47 57
CHEK1 0.035 0.012 -10000 0 0 54 54
mol:HEME 0.012 0.035 0.1 47 -0.12 10 57
PER1 0.035 0.012 -10000 0 0 54 54
BMAL/CLOCK/NPAS2 0.06 0.079 0.23 4 -0.14 47 51
BMAL1/CLOCK 0.007 0.12 0.4 1 -0.51 17 18
S phase of mitotic cell cycle 0.031 0.15 0.39 1 -0.96 10 11
TIMELESS/CHEK1/ATR 0.032 0.16 -10000 0 -0.99 10 10
mol:NADPH 0.012 0.035 0.1 47 -0.12 10 57
PER1/TIMELESS 0.024 0.16 0.41 1 -1 10 11
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.037 0.008 -10000 0 0 20 20
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.009 0.16 0.72 3 -0.98 8 11
VDR 0.037 0.009 -10000 0 0 26 26
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.006 0.1 0.28 6 -0.29 40 46
RXRs/LXRs/DNA/Oxysterols 0.001 0.15 0.33 8 -0.41 45 53
MED1 0.036 0.011 -10000 0 0 42 42
mol:9cRA 0 0.018 0.046 23 -0.047 43 66
RARs/THRs/DNA/Src-1 0.009 0.055 -10000 0 -0.21 8 8
RXRs/NUR77 0.078 0.075 0.27 2 -0.13 32 34
RXRs/PPAR 0.013 0.058 -10000 0 -0.21 9 9
NCOR2 0.038 0.006 -10000 0 0 11 11
VDR/VDR/Vit D3 0.027 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.084 0.03 -10000 0 -10000 0 0
RARA 0.038 0.005 -10000 0 0 7 7
NCOA1 0.035 0.012 -10000 0 0 52 52
VDR/VDR/DNA 0.037 0.009 -10000 0 0 26 26
RARs/RARs/DNA/9cRA 0.056 0.039 -10000 0 -10000 0 0
RARG 0.038 0.007 -10000 0 0 15 15
RPS6KB1 -0.012 0.091 0.53 7 -0.4 8 15
RARs/THRs/DNA/SMRT 0.022 0.032 -10000 0 -0.19 7 7
THRA 0.038 0.007 -10000 0 0 15 15
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.027 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.058 0.083 0.3 6 -0.17 38 44
NR1H4 0.038 0.006 -10000 0 0 11 11
RXRs/LXRs/DNA 0.083 0.12 0.36 5 -0.24 39 44
NR1H2 0.03 0.036 0.12 2 -0.07 47 49
NR1H3 0.031 0.036 0.13 2 -0.077 43 45
RXRs/VDR/DNA/Vit D3 0.071 0.07 0.23 5 -0.12 32 37
NR4A1 0.037 0.008 -10000 0 0 21 21
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.065 0.16 4 -0.22 17 21
RXRG 0.032 0.034 0.12 2 -0.068 46 48
RXR alpha/CCPG 0.023 0.024 0.087 2 -0.047 39 41
RXRA 0.031 0.034 0.12 2 -0.07 44 46
RXRB 0.032 0.037 0.12 2 -0.075 48 50
THRB 0.038 0.006 -10000 0 0 11 11
PPARG 0.037 0.009 -10000 0 0 29 29
PPARD 0.039 0.003 -10000 0 0 4 4
TNF -0.009 0.14 0.39 2 -0.4 38 40
mol:Oxysterols 0 0.016 0.043 27 -0.043 42 69
cholesterol transport 0.001 0.15 0.33 8 -0.4 45 53
PPARA 0.035 0.012 -10000 0 0 51 51
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.038 0.006 -10000 0 0 14 14
RXRs/NUR77/BCL2 0.013 0.035 -10000 0 -0.16 3 3
SREBF1 -0.016 0.17 0.44 3 -0.72 16 19
RXRs/RXRs/DNA/9cRA 0.058 0.083 0.3 6 -0.17 38 44
ABCA1 -0.049 0.26 0.49 2 -0.83 45 47
RARs/THRs 0.11 0.035 -10000 0 -0.12 1 1
RXRs/FXR 0.079 0.075 0.27 2 -0.13 32 34
BCL2 0.037 0.008 -10000 0 0 21 21
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 0.044 0.1 -10000 0 -0.21 46 46
Ran/GTP/Exportin 1/HDAC1 -0.041 0.019 -10000 0 -0.11 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.11 -10000 0 -0.27 50 50
SUMO1 0.039 0.004 -10000 0 0 5 5
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.004 0.042 -10000 0 -0.15 22 22
FKBP3 0.036 0.011 -10000 0 0 41 41
Histones 0.033 0.076 -10000 0 -0.24 22 22
YY1/LSF 0.011 0.067 -10000 0 -0.22 21 21
SMG5 0.038 0.007 -10000 0 0 17 17
RAN 0.038 0.007 -10000 0 0 16 16
I kappa B alpha/HDAC3 -0.005 0.075 -10000 0 -0.2 55 55
I kappa B alpha/HDAC1 0.006 0.097 -10000 0 -0.23 62 62
SAP18 0.035 0.012 -10000 0 0 50 50
RELA -0.009 0.081 0.2 1 -0.33 14 15
HDAC1/Smad7 0.038 0.042 -10000 0 -0.12 5 5
RANGAP1 0.035 0.011 -10000 0 0 47 47
HDAC3/TR2 0.023 0.072 -10000 0 -0.25 22 22
NuRD/MBD3 Complex -0.017 0.11 -10000 0 -0.31 43 43
NF kappa B1 p50/RelA 0.006 0.093 -10000 0 -0.31 20 20
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.037 0.008 -10000 0 0 20 20
GATA1 0.039 0.002 -10000 0 0 2 2
Mad/Max 0.053 0.016 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.017 0.11 -10000 0 -0.32 39 39
RBBP7 0.038 0.005 -10000 0 0 10 10
NPC 0.019 0.018 -10000 0 -0.075 18 18
RBBP4 0.034 0.013 -10000 0 0 62 62
MAX 0.036 0.011 -10000 0 0 40 40
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.037 0.009 -10000 0 0 27 27
NFKBIA -0.001 0.07 -10000 0 -0.3 22 22
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.013 0.088 -10000 0 -0.29 31 31
SIN3 complex 0.054 0.046 -10000 0 -0.12 18 18
SMURF1 0.023 0.019 -10000 0 0 214 214
CHD3 0.038 0.006 -10000 0 0 13 13
SAP30 0.037 0.008 -10000 0 0 20 20
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.037 0.009 -10000 0 0 28 28
YY1/HDAC3 -0.007 0.079 -10000 0 -0.25 32 32
YY1/HDAC2 0.011 0.064 -10000 0 -0.22 20 20
YY1/HDAC1 0.013 0.066 -10000 0 -0.22 21 21
NuRD/MBD2 Complex (MeCP1) -0.012 0.096 -10000 0 -0.27 41 41
PPARG -0.007 0.08 -10000 0 -0.26 26 26
HDAC8/hEST1B 0.047 0.016 -10000 0 -10000 0 0
UBE2I 0.039 0.004 -10000 0 0 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.037 0.009 -10000 0 0 27 27
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
HDAC3/SMRT (N-CoR2) 0.023 0.072 -10000 0 -0.25 22 22
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.042 -10000 0 -0.12 5 5
CREBBP 0.038 0.005 -10000 0 0 7 7
NuRD/MBD3/MBD3L2 Complex -0.013 0.1 0.15 2 -0.31 38 40
HDAC1 0.037 0.008 -10000 0 0 24 24
HDAC3 0.002 0.061 -10000 0 -0.29 16 16
HDAC2 0.034 0.013 -10000 0 0 62 62
YY1 0.006 0.027 -10000 0 -0.2 7 7
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.035 0.011 -10000 0 0 48 48
NCOR2 0.038 0.006 -10000 0 0 11 11
MXD1 0.039 0.002 -10000 0 0 2 2
STAT3 0.004 0.052 -10000 0 -0.2 31 31
NFKB1 0.038 0.007 -10000 0 0 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.037 0.008 -10000 0 0 25 25
YY1/LSF/HDAC1 0.027 0.075 -10000 0 -0.22 20 20
YY1/SAP30/HDAC1 0.028 0.074 -10000 0 -0.22 21 21
EP300 0.035 0.012 -10000 0 0 52 52
STAT3 (dimer non-phopshorylated) 0.004 0.052 -10000 0 -0.2 31 31
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.072 -10000 0 -0.3 22 22
histone deacetylation -0.012 0.096 -10000 0 -0.28 38 38
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.092 -10000 0 -0.3 29 29
nuclear export -0.047 0.016 -10000 0 -10000 0 0
PRKACA 0.036 0.01 -10000 0 0 36 36
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.034 0.013 -10000 0 0 69 69
GATA2/HDAC3 0.023 0.072 -10000 0 -0.26 21 21
GATA1/HDAC1 0.053 0.023 -10000 0 -0.13 6 6
GATA1/HDAC3 0.024 0.073 -10000 0 -0.25 22 22
CHD4 0.036 0.011 -10000 0 0 44 44
TNF-alpha/TNFR1A 0.038 0.053 -10000 0 -0.13 43 43
SIN3/HDAC complex/Mad/Max -0.014 0.088 -10000 0 -0.26 40 40
NuRD Complex -0.013 0.11 -10000 0 -0.33 35 35
positive regulation of chromatin silencing 0.031 0.074 -10000 0 -0.23 22 22
SIN3B 0.035 0.011 -10000 0 0 46 46
MTA2 0.038 0.005 -10000 0 0 10 10
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.039 0.003 -10000 0 0 4 4
SUMO1/HDAC1 0.035 0.057 -10000 0 -0.14 21 21
HDAC complex 0.069 0.073 -10000 0 -0.14 41 41
GATA1/Fog1 0.029 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.057 0.049 -10000 0 -0.13 21 21
TNF 0.038 0.005 -10000 0 0 8 8
negative regulation of cell growth -0.014 0.088 -10000 0 -0.26 40 40
NuRD/MBD2/PRMT5 Complex -0.012 0.096 -10000 0 -0.27 41 41
Ran/GTP/Exportin 1 0.034 0.062 -10000 0 -0.16 22 22
NF kappa B/RelA/I kappa B alpha -0.013 0.095 -10000 0 -0.26 52 52
SIN3/HDAC complex/NCoR1 -0.008 0.091 -10000 0 -0.3 29 29
TFCP2 0.037 0.009 -10000 0 0 28 28
NR2C1 0.038 0.005 -10000 0 0 10 10
MBD3 0.035 0.012 -10000 0 0 52 52
MBD2 0.037 0.008 -10000 0 0 20 20
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.004 0.001 25 -10000 0 25
SMARCC1 -0.008 0.12 -10000 0 -1 5 5
REL 0.038 0.004 -10000 0 -0.043 1 1
HDAC7 -0.05 0.059 0.21 2 -0.26 6 8
JUN 0.036 0.011 -10000 0 0 43 43
EP300 0.035 0.012 -10000 0 0 52 52
KAT2B 0 0 0.003 1 -10000 0 1
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.031 0.021 0.13 3 -10000 0 3
FOXO1 0.032 0.015 -10000 0 0 98 98
T-DHT/AR -0.043 0.079 0.26 1 -0.28 5 6
MAP2K6 0.036 0.016 -10000 0 -0.042 18 18
BRM/BAF57 0.049 0.025 -10000 0 -0.13 3 3
MAP2K4 0.035 0.018 -10000 0 -0.042 19 19
SMARCA2 0.034 0.014 -10000 0 0 72 72
PDE9A -0.019 0.19 -10000 0 -0.78 28 28
NCOA2 0.038 0.006 -10000 0 0 14 14
CEBPA 0.029 0.017 -10000 0 0 134 134
EHMT2 0.039 0.004 -10000 0 0 5 5
cell proliferation -0.026 0.099 0.31 6 -0.35 10 16
NR0B1 0.032 0.015 -10000 0 0 90 90
EGR1 0.031 0.016 -10000 0 0 107 107
RXRs/9cRA 0.069 0.025 -10000 0 -0.1 1 1
AR/RACK1/Src -0.025 0.077 0.25 2 -0.23 1 3
AR/GR -0.029 0.059 -10000 0 -0.24 16 16
GNB2L1 0.038 0.006 -10000 0 0 13 13
PKN1 0.034 0.013 -10000 0 0 60 60
RCHY1 0.038 0.007 -10000 0 0 16 16
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.022 0.025 0.12 6 -10000 0 6
T-DHT/AR/TIF2/CARM1 -0.04 0.058 0.21 2 -0.23 1 3
SRC -0.031 0.051 0.16 22 -10000 0 22
NR3C1 0.037 0.008 -10000 0 0 25 25
KLK3 -0.04 0.087 0.48 1 -0.39 6 7
APPBP2 0.035 0.017 -10000 0 -0.043 17 17
TRIM24 0.022 0.02 -10000 0 0 227 227
T-DHT/AR/TIP60 -0.039 0.031 0.093 4 -0.16 9 13
TMPRSS2 0.007 0.092 -10000 0 -0.59 9 9
RXRG 0.038 0.007 -10000 0 0 15 15
mol:9cRA 0 0 0.004 1 -10000 0 1
RXRA 0.037 0.009 -10000 0 0 27 27
RXRB 0.039 0.003 -10000 0 0 4 4
CARM1 0.036 0.011 -10000 0 0 44 44
NR2C2 0.038 0.005 -10000 0 0 10 10
KLK2 -0.021 0.055 0.22 1 -0.26 1 2
AR -0.022 0.047 0.15 2 -0.2 19 21
SENP1 0 0 0.004 1 -10000 0 1
HSP90AA1 0.036 0.01 -10000 0 0 39 39
MDM2 0.034 0.013 -10000 0 -0.057 1 1
SRY -0.001 0.001 -10000 0 -0.027 1 1
GATA2 0.037 0.008 -10000 0 0 20 20
MYST2 0 0 -10000 0 -0.004 1 1
HOXB13 0.039 0.005 0.085 1 -10000 0 1
T-DHT/AR/RACK1/Src -0.026 0.079 0.24 3 -0.24 1 4
positive regulation of transcription 0.037 0.008 -10000 0 0 20 20
DNAJA1 0.032 0.02 -10000 0 -0.043 17 17
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.037 -10000 0 -0.23 11 11
NCOA1 0.042 0.028 0.18 3 -0.19 2 5
SPDEF 0.039 0.005 0.077 1 0 6 7
T-DHT/AR/TIF2 -0.044 0.086 0.19 1 -0.27 37 38
T-DHT/AR/Hsp90 -0.041 0.048 0.19 1 -0.26 1 2
GSK3B 0.036 0.011 -10000 0 0 40 40
NR2C1 0.038 0.006 -10000 0 -0.041 1 1
mol:T-DHT -0.031 0.038 0.19 5 -10000 0 5
SIRT1 0.026 0.018 -10000 0 0 170 170
ZMIZ2 0.023 0.019 -10000 0 -10000 0 0
POU2F1 0.038 0.04 0.16 13 -0.12 20 33
T-DHT/AR/DAX-1 -0.038 0.044 0.19 1 -0.2 1 2
CREBBP 0.039 0.005 -10000 0 0 7 7
SMARCE1 0.039 0.005 -10000 0 0 10 10
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.042 -10000 0 -0.11 20 20
HDAC3 0.038 0.005 -10000 0 0 10 10
Ran/GTP/Exportin 1/HDAC4 -0.042 0.019 -10000 0 -0.1 35 35
GATA1/HDAC4 0.05 0.033 -10000 0 -0.13 15 15
GATA1/HDAC5 0.055 0.014 -10000 0 -0.13 1 1
GATA2/HDAC5 0.053 0.017 -10000 0 -0.13 1 1
HDAC5/BCL6/BCoR 0.055 0.051 -10000 0 -0.12 27 27
HDAC9 0.02 0.02 -10000 0 0 252 252
Glucocorticoid receptor/Hsp90/HDAC6 0.066 0.04 -10000 0 -0.12 16 16
HDAC4/ANKRA2 0.048 0.038 -10000 0 -0.13 19 19
HDAC5/YWHAB 0.046 0.031 -10000 0 -0.14 7 7
NPC/RanGAP1/SUMO1/Ubc9 -0.004 0.042 -10000 0 -0.15 22 22
GATA2 0.037 0.008 -10000 0 0 20 20
HDAC4/RFXANK 0.041 0.047 -10000 0 -0.13 30 30
BCOR 0.036 0.01 -10000 0 0 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.038 0.007 -10000 0 0 19 19
GNB1/GNG2 0.022 0.028 -10000 0 -0.11 20 20
Histones 0.028 0.066 -10000 0 -0.16 34 34
ADRBK1 0.038 0.006 -10000 0 0 13 13
HDAC4 0.037 0.009 -10000 0 0 32 32
XPO1 0.039 0.003 -10000 0 0 4 4
HDAC5/ANKRA2 0.052 0.025 -10000 0 -0.13 7 7
HDAC4/Ubc9 0.05 0.033 -10000 0 -0.13 15 15
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.05 0.03 -10000 0 -0.13 11 11
TUBA1B 0.037 0.008 -10000 0 0 20 20
HDAC6 0.039 0.002 -10000 0 0 2 2
HDAC5/RFXANK 0.045 0.038 -10000 0 -0.13 18 18
CAMK4 0.038 0.006 -10000 0 0 11 11
Tubulin/HDAC6 0.061 0.053 -10000 0 -0.12 36 36
SUMO1 0.039 0.004 -10000 0 0 5 5
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.033 0.014 -10000 0 0 72 72
GATA1 0.039 0.002 -10000 0 0 2 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.037 0.009 -10000 0 0 29 29
NR3C1 0.037 0.008 -10000 0 0 25 25
SUMO1/HDAC4 0.034 0.058 -10000 0 -0.14 20 20
SRF 0.039 0.004 -10000 0 0 6 6
HDAC4/YWHAB 0.041 0.042 -10000 0 -0.14 20 20
Tubulin 0.042 0.049 -10000 0 -0.13 36 36
HDAC4/14-3-3 E 0.045 0.042 -10000 0 -0.13 24 24
GNB1 0.035 0.011 -10000 0 0 46 46
RANGAP1 0.035 0.011 -10000 0 0 47 47
BCL6/BCoR 0.039 0.045 -10000 0 -0.13 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.068 0.038 -10000 0 -0.12 15 15
HDAC4/SRF 0.069 0.036 -10000 0 -0.12 13 13
HDAC4/ER alpha 0.047 0.035 -10000 0 -0.13 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.028 0.065 -10000 0 -0.16 34 34
cell motility 0.06 0.053 -10000 0 -0.12 36 36
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.039 0.004 -10000 0 0 5 5
HDAC7/HDAC3 0.028 0.007 -10000 0 -0.11 1 1
BCL6 0.033 0.014 -10000 0 0 76 76
HDAC4/CaMK II delta B 0.036 0.009 -10000 0 0 32 32
Hsp90/HDAC6 0.053 0.019 -10000 0 -0.13 2 2
ESR1 0.036 0.01 -10000 0 0 36 36
HDAC6/HDAC11 0.056 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.062 -10000 0 -0.16 22 22
NPC 0.019 0.018 -10000 0 -0.075 18 18
MEF2C 0.036 0.01 -10000 0 0 34 34
RAN 0.038 0.007 -10000 0 0 16 16
HDAC4/MEF2C 0.095 0.06 -10000 0 -0.12 25 25
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.038 0.006 -10000 0 0 11 11
TUBB2A 0.035 0.011 -10000 0 0 47 47
HDAC11 0.038 0.006 -10000 0 0 11 11
HSP90AA1 0.036 0.01 -10000 0 0 39 39
RANBP2 0.037 0.008 -10000 0 0 25 25
ANKRA2 0.038 0.007 -10000 0 0 18 18
RFXANK 0.035 0.012 -10000 0 0 55 55
nuclear import -0.023 0.058 0.2 26 -10000 0 26
Signaling events mediated by the Hedgehog family

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
TGFB2 0.002 0.071 0.26 33 -10000 0 33
IHH 0.057 0.031 0.2 8 -10000 0 8
SHH Np/Cholesterol/GAS1 -0.021 0.023 -10000 0 -10000 0 0
LRPAP1 0.038 0.007 -10000 0 0 18 18
dorsoventral neural tube patterning 0.021 0.023 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.1 0.083 0.32 24 -10000 0 24
SMO 0.023 0.05 0.28 5 -10000 0 5
AKT1 -0.01 0.13 -10000 0 -0.43 31 31
ARRB2 0.037 0.009 -10000 0 0 28 28
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.038 0.006 -10000 0 0 13 13
heart looping 0.023 0.051 0.28 6 -10000 0 6
STIL 0.057 0.12 0.3 39 -10000 0 39
DHH N/PTCH2 0.028 0.004 -10000 0 -10000 0 0
DHH N/PTCH1 0.026 0.031 0.18 20 -10000 0 20
PIK3CA 0.033 0.014 -10000 0 0 79 79
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.042 0.081 0.31 23 -10000 0 23
determination of left/right symmetry 0.023 0.051 0.28 6 -10000 0 6
PIK3R1 0.034 0.013 -10000 0 0 69 69
skeletal system development 0.041 0.081 0.31 23 -10000 0 23
IHH N/Hhip 0.037 0.019 0.12 8 -10000 0 8
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.023 0.051 0.28 6 -10000 0 6
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.037 0.008 -10000 0 0 21 21
PI3K 0.023 0.07 -10000 0 -0.14 72 72
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.032 0.015 -10000 0 0 90 90
somite specification 0.023 0.051 0.28 6 -10000 0 6
SHH Np/Cholesterol/PTCH1 -0.009 0.04 0.16 22 -10000 0 22
SHH Np/Cholesterol/PTCH2 -0.021 0.019 0.1 1 -10000 0 1
SHH Np/Cholesterol/Megalin -0.02 0.019 0.1 1 -10000 0 1
SHH -0.02 0.019 0.12 1 -10000 0 1
catabolic process 0.039 0.05 0.21 38 -10000 0 38
SMO/Vitamin D3 0.004 0.065 0.29 16 -10000 0 16
SHH Np/Cholesterol/Hhip -0.014 0.012 -10000 0 -10000 0 0
LRP2 0.038 0.006 -10000 0 0 13 13
receptor-mediated endocytosis 0.006 0.052 0.24 6 -10000 0 6
SHH Np/Cholesterol/BOC -0.014 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO -0.021 0.019 0.1 1 -10000 0 1
mesenchymal cell differentiation 0.014 0.012 -10000 0 -10000 0 0
mol:Vitamin D3 0.069 0.12 0.21 201 -10000 0 201
IHH N/PTCH2 0.066 0.021 0.17 5 -10000 0 5
CDON 0.038 0.005 -10000 0 0 9 9
IHH N/PTCH1 0.054 0.044 0.25 21 -10000 0 21
Megalin/LRPAP1 0.052 0.028 -10000 0 -0.13 10 10
PTCH2 0.038 0.006 -10000 0 0 11 11
SHH Np/Cholesterol 0.06 0.1 0.19 196 -10000 0 196
PTCH1 0.039 0.05 0.21 38 -10000 0 38
HHIP 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.052 0.092 0.32 3 -10000 0 3
MKNK1 0.036 0.01 -10000 0 0 39 39
MAPK14 0.053 0.046 0.18 4 -0.09 20 24
ATF2/c-Jun 0.002 0.083 -10000 0 -0.31 23 23
MAPK11 0.049 0.047 0.18 3 -0.09 20 23
MITF 0.033 0.061 0.21 9 -0.21 8 17
MAPKAPK5 0.034 0.052 0.18 5 -0.21 2 7
KRT8 0.036 0.053 0.2 12 -0.21 1 13
MAPKAPK3 0.037 0.008 -10000 0 0 23 23
MAPKAPK2 0.037 0.008 -10000 0 0 20 20
p38alpha-beta/CK2 0.07 0.069 0.26 3 -10000 0 3
CEBPB 0.026 0.076 0.22 17 -0.2 23 40
SLC9A1 0.032 0.054 0.19 3 -0.23 4 7
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.032 0.062 0.26 4 -0.26 2 6
p38alpha-beta/MNK1 0.072 0.077 -10000 0 -0.14 17 17
JUN -0.002 0.082 -10000 0 -0.31 23 23
PPARGC1A 0.035 0.066 0.2 6 -0.21 13 19
USF1 0.03 0.048 0.19 3 -10000 0 3
RAB5/GDP/GDI1 0.015 0.077 -10000 0 -0.23 17 17
NOS2 0.03 0.048 0.19 3 -10000 0 3
DDIT3 0.025 0.064 0.2 8 -0.19 17 25
RAB5A 0.036 0.01 -10000 0 0 34 34
HSPB1 0.092 0.14 0.28 167 -10000 0 167
p38alpha-beta/HBP1 0.053 0.068 0.25 2 -10000 0 2
CREB1 0.025 0.078 0.22 1 -0.2 30 31
RAB5/GDP 0.022 0.03 -10000 0 -0.11 24 24
EIF4E -0.023 0.067 0.21 11 -0.23 1 12
RPS6KA4 0.034 0.052 0.18 5 -0.21 2 7
PLA2G4A -0.02 0.06 0.24 5 -0.23 1 6
GDI1 0.024 0.064 0.2 3 -0.22 17 20
TP53 0.007 0.065 0.19 12 -10000 0 12
RPS6KA5 0.035 0.056 0.2 6 -0.2 5 11
ESR1 0.031 0.052 0.19 3 -0.2 4 7
HBP1 0.023 0.019 -10000 0 0 213 213
MEF2C 0.031 0.06 0.19 7 -0.21 9 16
MEF2A 0.032 0.056 0.18 5 -0.21 6 11
EIF4EBP1 0.021 0.081 0.22 1 -0.2 27 28
KRT19 0.037 0.053 0.2 12 -0.21 1 13
ELK4 0.032 0.051 0.19 4 -0.21 2 6
ATF6 0.033 0.052 0.18 5 -0.21 2 7
ATF1 0.021 0.078 0.22 1 -0.2 26 27
p38alpha-beta/MAPKAPK2 0.08 0.067 0.26 2 -10000 0 2
p38alpha-beta/MAPKAPK3 0.08 0.068 0.26 2 -10000 0 2
Arf6 trafficking events

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
SLC2A4 0.038 0.006 -10000 0 0 14 14
CLTC 0.01 0.098 -10000 0 -0.33 32 32
calcium ion-dependent exocytosis 0.02 0.066 0.16 6 -0.21 17 23
Dynamin 2/GTP 0.024 0.012 0.099 1 -0.092 1 2
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0 0.084 -10000 0 -0.29 31 31
CPE -0.022 0.012 -10000 0 -0.1 1 1
CTNNB1 0.038 0.007 -10000 0 0 18 18
membrane fusion 0.024 0.06 -10000 0 -0.2 11 11
CTNND1 -0.016 0.051 0.16 39 -10000 0 39
DNM2 0.036 0.011 -10000 0 0 41 41
mol:PI-4-5-P2 0.016 0.077 0.19 25 -0.23 18 43
TSHR -0.025 0.011 0.12 1 -0.1 1 2
INS 0.008 0.096 -10000 0 -0.46 19 19
BIN1 0.033 0.014 -10000 0 0 76 76
mol:Choline 0.024 0.06 -10000 0 -0.2 11 11
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.013 0.005 -10000 0 -0.09 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.036 0.01 -10000 0 0 33 33
mol:Ca2+ 0.024 0.011 0.098 1 -0.092 1 2
JUP 0.01 0.076 -10000 0 -0.27 26 26
ASAP2/amphiphysin II 0.031 0.043 -10000 0 -0.093 48 48
ARF6/GTP 0.027 0.009 -10000 0 -0.11 1 1
CDH1 0.006 0.078 -10000 0 -0.27 29 29
clathrin-independent pinocytosis 0.027 0.009 -10000 0 -0.11 1 1
MAPK8IP3 0.039 0.004 -10000 0 0 6 6
positive regulation of endocytosis 0.027 0.009 -10000 0 -0.11 1 1
EXOC2 0.037 0.008 -10000 0 0 24 24
substrate adhesion-dependent cell spreading -0.001 0.058 -10000 0 -0.27 9 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.036 0.01 -10000 0 0 37 37
regulation of calcium-dependent cell-cell adhesion -0.035 0.085 0.28 28 -10000 0 28
positive regulation of phagocytosis -0.023 0.011 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.048 0.015 -10000 0 -0.1 1 1
ACAP1 0.024 0.06 -10000 0 -0.2 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.001 0.064 -10000 0 -0.28 19 19
clathrin heavy chain/ACAP1 0.018 0.092 0.19 17 -0.24 34 51
JIP4/KLC1 0.051 0.058 -10000 0 -0.14 36 36
EXOC1 0.035 0.011 -10000 0 0 48 48
exocyst -0.001 0.059 -10000 0 -0.28 9 9
RALA/GTP 0.013 0.025 -10000 0 -0.11 14 14
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.037 -10000 0 -0.11 25 25
receptor recycling 0.027 0.009 -10000 0 -0.11 1 1
CTNNA1 -0.017 0.052 0.16 39 -10000 0 39
NME1 -0.013 0.005 -10000 0 -0.091 1 1
clathrin coat assembly 0.01 0.099 0.19 1 -0.33 33 34
IL2RA 0.003 0.072 -10000 0 -0.33 16 16
VAMP3 -0.023 0.011 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.032 0.091 -10000 0 -0.24 35 35
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.027 0.055 -10000 0 -0.19 10 10
PLD2 0.029 0.055 -10000 0 -0.19 10 10
EXOC5 0.032 0.015 -10000 0 0 93 93
PIP5K1C 0.008 0.066 0.16 4 -0.24 17 21
SDC1 0.013 0.081 -10000 0 -0.28 28 28
ARF6/GDP 0.027 0.007 -10000 0 0 33 33
EXOC7 0.038 0.006 -10000 0 0 12 12
E-cadherin/beta catenin 0.037 0.088 -10000 0 -0.28 28 28
mol:Phosphatidic acid 0.024 0.06 -10000 0 -0.2 11 11
endocytosis -0.03 0.042 0.093 48 -10000 0 48
SCAMP2 0.037 0.009 -10000 0 0 31 31
ADRB2 0.007 0.1 0.24 3 -0.33 32 35
EXOC3 0.037 0.008 -10000 0 0 22 22
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.021 0.011 0.11 1 -0.092 1 2
KLC1 0.034 0.013 -10000 0 0 67 67
AVPR2 0 0.095 0.21 3 -0.32 32 35
RALA 0.022 0.019 -10000 0 0 222 222
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.013 0.09 -10000 0 -0.29 29 29
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.066 0.031 -9999 0 -0.12 3 3
E-cadherin/beta catenin 0.051 0.022 -9999 0 -0.13 3 3
CTNNB1 0.038 0.007 -9999 0 0 18 18
JUP 0.035 0.012 -9999 0 0 55 55
CDH1 0.036 0.01 -9999 0 0 38 38
Arf1 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
coatomer protein complex 0.007 0.048 0.14 52 -0.16 6 58
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.008 0.049 0.14 6 -0.18 11 17
AP2 0.023 0.024 -10000 0 -0.11 14 14
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.025 0.036 -10000 0 -0.11 14 14
CLTB 0.038 0.006 -10000 0 0 13 13
coatomer protein complex/ARF1/GTP/ER cargo protein 0.004 0.04 -10000 0 -0.18 12 12
CD4 0.033 0.014 -10000 0 0 79 79
CLTA 0.035 0.012 -10000 0 0 53 53
mol:GTP -0.004 0.002 -10000 0 -0.018 6 6
ARFGAP1 -0.015 0.006 0 72 -10000 0 72
mol:PI-4-5-P2 -0.001 0.019 0.09 16 -10000 0 16
ARF1/GTP 0.02 0.019 -10000 0 -0.11 6 6
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.002 0.059 0.16 49 -0.18 9 58
mol:Choline -0.001 0.019 0.093 16 -10000 0 16
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.038 0.009 -10000 0 0 25 25
DDEF1 0.001 0.019 0.1 12 -10000 0 12
ARF1/GDP 0.003 0.017 -10000 0 -0.092 11 11
AP2M1 0.036 0.011 -10000 0 0 44 44
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.016 0.018 0.082 1 -0.1 7 8
Rac/GTP 0.016 0.02 -10000 0 -0.093 7 7
ARF1/GTP/GGA3/ARF-GAP1 0.039 0.027 -10000 0 -0.1 8 8
ARFIP2 0.031 0.022 -10000 0 -0.052 12 12
COPA 0.038 0.007 -10000 0 0 16 16
RAC1 0.023 0.019 -10000 0 0 209 209
ARF1/GTP/coatomer protein complex 0 0.046 0.13 1 -0.18 14 15
ARF1/GTP/ARHGAP10 0.023 0.014 -10000 0 -0.098 6 6
GGA3 0.038 0.006 -10000 0 0 14 14
ARF1/GTP/Membrin 0.027 0.027 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.035 -10000 0 -0.19 10 10
ARF1/GDP/Membrin 0.031 0.03 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.025 0.035 -10000 0 -0.11 14 14
CYTH2 -0.004 0.002 -10000 0 -0.018 6 6
ARF1/GTP/GGA3 0.046 0.022 -10000 0 -0.11 6 6
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 0.019 -10000 0 -0.11 5 5
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 0.057 -10000 0 -0.19 30 30
PLD2 -0.001 0.019 0.093 16 -10000 0 16
ARF-GAP1/v-SNARE -0.015 0.006 0 72 -10000 0 72
PIP5K1A -0.001 0.019 0.091 16 -10000 0 16
ARF1/GTP/Membrin/GBF1/p115 0 0.04 -10000 0 -0.1 15 15
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.019 0.093 16 -10000 0 16
KDEL Receptor/Ligand/ARF-GAP1 -0.015 0.006 0 72 -10000 0 72
GOSR2 0.013 0.03 -10000 0 -0.36 3 3
USO1 0.01 0.038 -10000 0 -0.3 7 7
GBF1 -0.07 0.15 -10000 0 -0.32 129 129
ARF1/GTP/Arfaptin 2 0.044 0.032 -10000 0 -0.11 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.033 0.043 -10000 0 -0.11 33 33
Atypical NF-kappaB pathway

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
BCL3/RelA 0.051 0.021 -10000 0 -0.13 2 2
FBXW11 0.037 0.009 -10000 0 0 27 27
NF kappa B1 p50/c-Rel -0.04 0.017 0.11 4 -0.12 5 9
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.078 0.19 6 -0.26 16 22
NFKBIA 0.005 0.062 -10000 0 -0.3 8 8
MAPK14 0.038 0.005 -10000 0 0 8 8
NF kappa B1 p105/p50 -0.039 0.019 0.11 3 -0.13 5 8
ARRB2 0.009 0.024 -10000 0 -0.19 7 7
REL 0.039 0.002 -10000 0 0 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.037 0.02 0.11 4 -0.12 4 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.039 0.018 0.11 4 -0.12 5 9
PIK3CA 0.033 0.014 -10000 0 0 79 79
NF kappa B1 p50 dimer -0.032 0.028 0.19 6 -10000 0 6
PIK3R1 0.034 0.013 -10000 0 0 69 69
NFKB1 -0.033 0.015 0.12 4 -10000 0 4
RELA 0.038 0.006 -10000 0 0 12 12
positive regulation of anti-apoptosis 0.011 0.047 0.14 4 -0.21 5 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.082 0.21 2 -0.26 17 19
SRC 0.034 0.013 -10000 0 0 65 65
PI3K 0.023 0.07 -10000 0 -0.14 72 72
NF kappa B1 p50/RelA 0.011 0.048 0.14 4 -0.22 5 9
IKBKB 0.038 0.005 -10000 0 0 7 7
beta TrCP1/SCF ubiquitin ligase complex 0.037 0.009 -10000 0 0 27 27
SYK 0.033 0.014 -10000 0 0 78 78
I kappa B alpha/PIK3R1 0.019 0.076 0.19 7 -0.24 23 30
cell death 0.022 0.079 0.2 3 -0.25 17 20
NF kappa B1 p105/c-Rel -0.04 0.017 0.11 4 -0.12 5 9
LCK 0.037 0.008 -10000 0 0 20 20
BCL3 0.036 0.011 -10000 0 0 40 40
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.021 0.1 8 -0.076 11 19
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.088 0.24 4 -0.27 21 25
ERC1 0.034 0.013 -10000 0 0 62 62
RIP2/NOD2 0.053 0.018 -10000 0 -0.13 2 2
NFKBIA -0.046 0.045 0.19 4 -0.25 13 17
BIRC2 0.038 0.007 -10000 0 0 15 15
IKBKB 0.038 0.005 -10000 0 0 7 7
RIPK2 0.038 0.007 -10000 0 0 16 16
IKBKG 0.013 0.064 -10000 0 -0.35 11 11
IKK complex/A20 0.055 0.086 -10000 0 -0.36 10 10
NEMO/A20/RIP2 0.038 0.007 -10000 0 0 16 16
XPO1 0.039 0.003 -10000 0 0 4 4
NEMO/ATM 0.032 0.071 -10000 0 -0.36 11 11
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.038 0.007 -10000 0 0 16 16
Exportin 1/RanGTP 0.049 0.021 -10000 0 -0.13 6 6
IKK complex/ELKS 0.029 0.077 -10000 0 -0.33 11 11
BCL10/MALT1/TRAF6 0.066 0.036 -10000 0 -0.12 10 10
NOD2 0.037 0.008 -10000 0 0 22 22
NFKB1 0.036 0.021 0.1 9 -0.075 12 21
RELA 0.036 0.021 0.1 9 -0.068 14 23
MALT1 0.036 0.01 -10000 0 0 36 36
cIAP1/UbcH5C 0.053 0.026 -10000 0 -0.16 6 6
ATM 0.036 0.011 -10000 0 0 41 41
TNF/TNFR1A 0.038 0.053 -10000 0 -0.13 43 43
TRAF6 0.038 0.007 -10000 0 0 17 17
PRKCA 0.038 0.005 -10000 0 0 10 10
CHUK 0.027 0.018 -10000 0 0 155 155
UBE2D3 0.038 0.006 -10000 0 0 12 12
TNF 0.038 0.005 -10000 0 0 8 8
NF kappa B1 p50/RelA 0.067 0.06 0.21 7 -0.16 26 33
BCL10 0.037 0.008 -10000 0 0 21 21
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.059 0.25 11 -0.27 10 21
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.021 0.1 8 -0.076 11 19
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
IKK complex 0.037 0.075 -10000 0 -0.35 10 10
CYLD 0.038 0.006 -10000 0 0 14 14
IKK complex/PKC alpha 0.047 0.082 -10000 0 -0.35 10 10
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.056 0.022 -10000 0 -10000 0 0
KIRREL 0.041 0.013 0.093 1 -0.04 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.057 0.022 -10000 0 -10000 0 0
PLCG1 0.034 0.013 -10000 0 0 70 70
ARRB2 0.037 0.009 -10000 0 0 28 28
WASL 0.023 0.019 -10000 0 0 214 214
Nephrin/NEPH1/podocin/CD2AP 0.085 0.056 0.21 1 -0.12 13 14
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.043 0.051 0.16 1 -0.24 3 4
FYN -0.013 0.057 0.16 40 -10000 0 40
mol:Ca2+ 0.081 0.048 -10000 0 -0.12 3 3
mol:DAG 0.082 0.049 -10000 0 -0.12 3 3
NPHS2 0.042 0.012 0.093 1 -0.04 5 6
mol:IP3 0.082 0.049 -10000 0 -0.12 3 3
regulation of endocytosis 0.051 0.053 -10000 0 -0.12 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.072 0.034 0.18 1 -10000 0 1
establishment of cell polarity 0.056 0.022 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.098 0.064 -10000 0 -0.14 14 14
Nephrin/NEPH1/beta Arrestin2 0.053 0.054 -10000 0 -0.12 4 4
NPHS1 0.04 0.014 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.054 0.046 0.22 1 -0.11 1 2
TJP1 0.036 0.01 -10000 0 0 38 38
NCK1 0.037 0.009 -10000 0 0 31 31
NCK2 0.037 0.008 -10000 0 0 20 20
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.084 0.05 -10000 0 -0.12 3 3
CD2AP 0.035 0.011 -10000 0 0 47 47
Nephrin/NEPH1/podocin/GRB2 0.088 0.049 -10000 0 -0.13 5 5
GRB2 0.037 0.009 -10000 0 0 26 26
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.021 0.065 0.17 46 -10000 0 46
cytoskeleton organization -0.005 0.059 0.24 15 -0.22 1 16
Nephrin/NEPH1 0.047 0.019 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.067 0.039 -10000 0 -0.13 7 7
Coregulation of Androgen receptor activity

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
NRIP1 0.035 0.012 -10000 0 -10000 0 0
SVIL 0.025 0.019 -10000 0 -10000 0 0
ZNF318 0.037 0.007 -10000 0 -0.064 1 1
JMJD2C 0.004 0.001 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0.054 0.046 -10000 0 -0.088 19 19
CARM1 0.036 0.011 -10000 0 0 44 44
PRDX1 0.037 0.008 -10000 0 0 24 24
PELP1 0.037 0.008 -10000 0 -0.002 21 21
CTNNB1 0.038 0.007 -10000 0 -10000 0 0
AKT1 0.034 0.013 -10000 0 -0.05 1 1
PTK2B 0.038 0.007 -10000 0 -10000 0 0
MED1 0.035 0.011 -10000 0 -0.04 1 1
MAK 0.035 0.01 -10000 0 -0.064 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.02 0.02 -10000 0 -10000 0 0
GSN 0.034 0.014 -10000 0 -10000 0 0
NCOA2 0.038 0.006 -10000 0 0 14 14
NCOA6 0.032 0.015 -10000 0 -10000 0 0
DNA-PK 0.059 0.048 -10000 0 -0.13 21 21
NCOA4 0.028 0.018 -10000 0 0 146 146
PIAS3 0.038 0.008 -10000 0 -10000 0 0
cell proliferation 0.012 0.051 -10000 0 -0.44 5 5
XRCC5 0.038 0.006 -10000 0 -0.042 1 1
UBE3A 0.038 0.008 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.032 0.037 0.11 5 -0.068 33 38
FHL2 0.003 0.2 0.29 62 -0.64 33 95
RANBP9 0.038 0.008 -10000 0 -10000 0 0
JMJD1A 0.005 0.009 0.1 4 -10000 0 4
CDK6 0.022 0.019 -10000 0 0 222 222
TGFB1I1 0.035 0.013 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.037 0.057 -10000 0 -0.095 53 53
XRCC6 0.035 0.011 -10000 0 -0.042 1 1
T-DHT/AR 0.044 0.08 0.2 66 -0.12 50 116
CTDSP1 0.038 0.007 -10000 0 0 16 16
CTDSP2 0.031 0.015 -10000 0 -0.057 1 1
BRCA1 0.038 0.007 -10000 0 -10000 0 0
TCF4 0.033 0.013 -10000 0 -0.048 1 1
CDKN2A 0.004 0.012 -10000 0 -0.041 1 1
SRF 0.048 0.067 0.14 92 -0.15 33 125
NKX3-1 -0.002 0.027 0.053 62 -10000 0 62
KLK3 0.018 0.053 0.41 1 -10000 0 1
TMF1 0.038 0.008 -10000 0 0 21 21
HNRNPA1 0.037 0.009 -10000 0 -0.041 1 1
AOF2 0.001 0.001 -10000 0 -10000 0 0
APPL1 -0.028 0.023 0.12 8 -10000 0 8
T-DHT/AR/Caspase 8 0.052 0.045 -10000 0 -0.082 33 33
AR 0.038 0.034 0.11 1 -0.073 33 34
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.035 0.011 -10000 0 -0.041 1 1
PAWR 0.038 0.008 -10000 0 0 20 20
PRKDC 0.035 0.012 -10000 0 -0.042 1 1
PA2G4 0.036 0.01 -10000 0 -0.051 1 1
UBE2I 0.039 0.004 -10000 0 0 5 5
T-DHT/AR/Cyclin D3/CDK11 p58 0.047 0.047 0.15 1 -0.078 42 43
RPS6KA3 0.038 0.008 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.041 0.051 -10000 0 -0.092 21 21
LATS2 0 0.001 -10000 0 -0.016 1 1
T-DHT/AR/PRX1 0.048 0.046 0.15 1 -0.089 23 24
Cyclin D3/CDK11 p58 0.024 0.025 -10000 0 -0.11 16 16
VAV3 0.031 0.016 -10000 0 -10000 0 0
KLK2 0.006 0.041 -10000 0 -0.33 3 3
CASP8 0.038 0.007 -10000 0 -0.038 1 1
T-DHT/AR/TIF2/CARM1 0.068 0.053 -10000 0 -0.1 2 2
TMPRSS2 0.005 0.036 -10000 0 -0.33 1 1
CCND1 0.031 0.016 -10000 0 -10000 0 0
PIAS1 0.038 0.009 -10000 0 -10000 0 0
mol:T-DHT 0.004 0.018 0.037 70 -0.043 33 103
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.037 0.01 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.034 0.045 -10000 0 -0.084 14 14
CMTM2 0 0 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.027 0.032 -10000 0 -0.077 14 14
CCND3 0.037 0.009 -10000 0 0 28 28
TGIF1 0.033 0.014 -10000 0 -0.041 1 1
FKBP4 0.037 0.011 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 -0.006 0.092 0.22 2 -0.36 16 18
BAG4 0.038 0.006 -10000 0 0 13 13
BAD -0.011 0.036 0.12 4 -0.15 9 13
NFKBIA 0.034 0.013 -10000 0 0 61 61
BIRC3 0.032 0.015 -10000 0 0 85 85
BAX -0.004 0.052 0.19 19 -0.16 9 28
EnzymeConsortium:3.1.4.12 0.001 0.023 0.08 3 -0.087 12 15
IKBKB -0.019 0.09 0.22 3 -0.36 14 17
MAP2K2 -0.018 0.06 0.16 35 -0.19 4 39
MAP2K1 -0.026 0.043 0.16 4 -0.19 4 8
SMPD1 -0.002 0.032 0.12 4 -0.12 15 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.088 0.24 1 -0.36 13 14
MAP2K4 -0.017 0.042 0.19 6 -0.18 5 11
protein ubiquitination -0.019 0.09 0.23 1 -0.35 16 17
EnzymeConsortium:2.7.1.37 -0.026 0.053 0.2 3 -0.2 3 6
response to UV 0 0.001 0.002 5 -10000 0 5
RAF1 -0.02 0.041 0.16 6 -0.17 7 13
CRADD 0.037 0.007 -10000 0 0 18 18
mol:ceramide -0.003 0.036 0.12 4 -0.14 12 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.031 -10000 0 -0.1 16 16
MADD 0.037 0.008 -10000 0 0 20 20
MAP3K1 -0.009 0.041 0.21 5 -0.16 7 12
TRADD 0.038 0.005 -10000 0 0 9 9
RELA/p50 0.038 0.006 -10000 0 0 12 12
MAPK3 -0.017 0.052 0.21 3 -0.2 3 6
MAPK1 -0.023 0.06 0.21 3 -0.21 14 17
p50/RELA/I-kappa-B-alpha 0.046 0.036 -10000 0 -0.13 16 16
FADD -0.003 0.085 0.24 1 -0.34 13 14
KSR1 -0.011 0.035 0.12 2 -0.16 8 10
MAPK8 -0.02 0.038 0.17 6 -0.18 4 10
TRAF2 0.037 0.008 -10000 0 0 20 20
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.019 0.084 0.21 1 -0.36 13 14
TNF R/SODD 0.039 0.052 -10000 0 -0.13 41 41
TNF 0.038 0.005 -10000 0 0 8 8
CYCS 0.016 0.058 0.18 18 -0.17 5 23
IKBKG -0.019 0.089 0.22 1 -0.36 14 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.093 -10000 0 -0.38 14 14
RELA 0.038 0.006 -10000 0 0 12 12
RIPK1 0.037 0.008 -10000 0 0 22 22
AIFM1 -0.011 0.046 0.15 8 -0.16 8 16
TNF/TNF R/SODD 0.056 0.055 -10000 0 -0.12 40 40
TNFRSF1A 0.034 0.013 -10000 0 0 69 69
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.035 0.089 -10000 0 -0.64 8 8
NSMAF -0.003 0.093 0.24 4 -0.34 17 21
response to hydrogen peroxide 0 0.001 0.002 5 -10000 0 5
BCL2 0.037 0.008 -10000 0 0 21 21
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.037 0.008 -9999 0 0 24 24
Ran/GTP/Exportin 1/HDAC4 -0.047 0.028 -9999 0 -0.15 20 20
MDM2/SUMO1 0.032 0.056 -9999 0 -0.14 21 21
HDAC4 0.037 0.009 -9999 0 0 32 32
Ran/GTP/Exportin 1/HDAC1 -0.046 0.027 -9999 0 -0.15 19 19
SUMO1 0.039 0.004 -9999 0 0 5 5
NPC/RanGAP1/SUMO1 0.002 0.034 -9999 0 -0.15 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.019 0.035 -9999 0 -0.14 19 19
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.038 0.007 -9999 0 0 16 16
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.037 0.008 -9999 0 0 25 25
SUMO1/HDAC4 0.034 0.058 -9999 0 -0.14 20 20
SUMO1/HDAC1 0.035 0.057 -9999 0 -0.14 21 21
RANGAP1 0.035 0.011 -9999 0 0 47 47
MDM2/SUMO1/SUMO1 0.076 0.053 -9999 0 -0.12 15 15
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.004 0.042 -9999 0 -0.15 22 22
Ran/GTP 0.016 0.051 -9999 0 -0.15 22 22
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.035 0.012 -9999 0 0 57 57
UBE2I 0.039 0.004 -9999 0 0 5 5
Ran/GTP/Exportin 1 0.006 0.052 -9999 0 -0.16 22 22
NPC 0.019 0.018 -9999 0 -0.075 18 18
PIAS2 0.037 0.008 -9999 0 0 25 25
PIAS1 0.037 0.009 -9999 0 0 27 27
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.037 0.029 -9999 0 -0.086 20 20
MAPK9 0.006 0.001 -9999 0 0 17 17
adrenocorticotropin secretion -0.017 0.003 0 19 -10000 0 19
GNB1/GNG2 0.02 0.023 -9999 0 -0.091 20 20
GNB1 0.035 0.011 -9999 0 0 46 46
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.006 0.001 -9999 0 0 8 8
Gs family/GTP 0.024 0.005 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.004 0.001 -9999 0 -10000 0 0
GNAL 0.037 0.008 -9999 0 0 21 21
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.038 0.007 -9999 0 0 19 19
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.005 0.003 -9999 0 0 138 138
MAPK11 0.006 0.002 -9999 0 0 54 54
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.038 0.006 -9999 0 0 11 11
Aurora C/Aurora B/INCENP 0.06 0.032 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.003 0.06 -9999 0 -0.4 11 11
AURKB 0.036 0.011 -9999 0 0 43 43
AURKC 0.034 0.012 -9999 0 0 59 59
Cellular roles of Anthrax toxin

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
ANTXR1 0.038 0.007 -10000 0 0 18 18
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0 -10000 0 -10000 0 0
monocyte activation -0.069 0.16 -10000 0 -0.34 138 138
MAP2K2 0.018 0.038 -10000 0 -0.58 2 2
MAP2K1 -0.013 0.004 -10000 0 -10000 0 0
MAP2K7 -0.013 0.004 -10000 0 -10000 0 0
MAP2K6 -0.013 0.003 -10000 0 -10000 0 0
CYAA -0.011 0.002 -10000 0 -10000 0 0
MAP2K4 -0.013 0.004 -10000 0 -10000 0 0
IL1B -0.007 0.049 0.098 70 -10000 0 70
Channel 0.024 0.005 -10000 0 -10000 0 0
NLRP1 -0.013 0.003 -10000 0 -10000 0 0
CALM1 0.034 0.013 -10000 0 0 62 62
negative regulation of phagocytosis -0.022 0.12 -10000 0 -0.41 45 45
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.003 -10000 0 -10000 0 0
MAPK1 -0.012 0.005 -10000 0 -10000 0 0
PGR -0.013 0.003 -10000 0 -10000 0 0
PA/Cellular Receptors 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.003 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.004 -10000 0 -10000 0 0
macrophage activation -0.018 0.024 0.17 5 -10000 0 5
TNF 0.038 0.005 -10000 0 0 8 8
VCAM1 -0.074 0.16 -10000 0 -0.34 137 137
platelet activation -0.022 0.12 -10000 0 -0.41 45 45
MAPKKK cascade 0.007 0.024 0.071 1 -0.068 26 27
IL18 -0.013 0.041 0.1 39 -10000 0 39
negative regulation of macrophage activation -0.003 0 -10000 0 -10000 0 0
LEF -0.003 0 -10000 0 -10000 0 0
CASP1 -0.003 0.005 -10000 0 -10000 0 0
mol:cAMP -0.022 0.12 -10000 0 -0.41 45 45
necrosis -0.003 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.005 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.038 0.007 0 15 -9999 0 15
PI3K Class IB/PDE3B 0.038 0.007 -9999 0 0 15 15
PDE3B 0.038 0.007 -9999 0 0 15 15
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.044 0.2 0.54 5 -0.66 17 22
PCK1 0.042 0.14 0.65 5 -0.57 4 9
HNF4A 0.079 0.21 0.64 16 -0.67 8 24
KCNJ11 0.074 0.2 0.53 5 -0.6 15 20
AKT1 0.062 0.15 0.4 4 -0.44 13 17
response to starvation 0.003 0.002 -10000 0 -10000 0 0
DLK1 0.087 0.22 0.55 13 -0.69 9 22
NKX2-1 0.035 0.12 0.34 5 -0.35 11 16
ACADM 0.052 0.19 0.51 8 -0.72 10 18
TAT 0.05 0.14 0.6 3 -0.63 5 8
CEBPB 0.033 0.019 0.18 1 -10000 0 1
CEBPA 0.031 0.02 0.11 4 -10000 0 4
TTR 0.05 0.2 0.6 9 -0.7 9 18
PKLR 0.059 0.18 0.52 8 -0.67 8 16
APOA1 0.093 0.24 0.75 8 -0.83 8 16
CPT1C 0.06 0.18 0.54 5 -0.59 12 17
ALAS1 0.035 0.25 0.55 1 -1.2 15 16
TFRC 0.028 0.29 0.59 9 -0.93 33 42
FOXF1 0.033 0.014 -10000 0 -10000 0 0
NF1 0.035 0.037 0.14 1 -0.18 14 15
HNF1A (dimer) 0.047 0.009 0.21 1 -10000 0 1
CPT1A 0.053 0.18 0.55 4 -0.66 8 12
HMGCS1 0.062 0.19 0.56 9 -0.67 8 17
NR3C1 0.049 0.027 0.16 6 -10000 0 6
CPT1B 0.043 0.17 0.54 5 -0.67 8 13
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.007 -10000 0 -10000 0 0
GCK 0.12 0.22 0.54 47 -0.63 7 54
CREB1 0.046 0.019 0.15 15 -10000 0 15
IGFBP1 0.071 0.14 0.52 4 -0.58 6 10
PDX1 0.059 0.12 -10000 0 -10000 0 0
UCP2 0.036 0.24 0.59 6 -0.68 32 38
ALDOB 0.074 0.2 0.56 8 -0.7 9 17
AFP 0.012 0.039 0.33 3 -10000 0 3
BDH1 0.05 0.2 0.53 10 -0.66 17 27
HADH 0.067 0.21 0.53 6 -0.72 13 19
F2 0.09 0.24 0.74 7 -0.85 8 15
HNF1A 0.047 0.009 0.21 1 -10000 0 1
G6PC 0.012 0.087 0.47 2 -10000 0 2
SLC2A2 0.075 0.14 0.49 1 -10000 0 1
INS -0.033 0.048 0.18 15 -0.15 6 21
FOXA1 0.013 0.019 0.21 2 -10000 0 2
FOXA3 0.019 0.063 0.26 6 -0.19 23 29
FOXA2 0.11 0.24 0.7 5 -0.69 15 20
ABCC8 0.069 0.2 0.56 5 -0.7 9 14
ALB 0.013 0.038 0.32 2 -10000 0 2
IL27-mediated signaling events

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
TGFB1 0.036 0.015 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.007 0.07 0.42 5 -10000 0 5
IL27/IL27R/JAK1 0.038 0.065 -10000 0 -10000 0 0
TBX21 -0.024 0.11 0.33 25 -10000 0 25
IL12B 0.039 0.006 -10000 0 0 11 11
IL12A -0.017 0.004 0.002 19 -10000 0 19
IL6ST 0.036 0.012 -10000 0 -0.049 1 1
IL27RA/JAK1 0.029 0.057 -10000 0 -10000 0 0
IL27 -0.001 0.005 -10000 0 -10000 0 0
TYK2 0.034 0.014 -10000 0 -0.049 1 1
T-helper cell lineage commitment 0.081 0.092 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.007 0.07 0.42 5 -10000 0 5
T cell proliferation during immune response 0.007 0.07 0.42 5 -10000 0 5
MAPKKK cascade -0.007 0.07 -10000 0 -0.42 5 5
STAT3 0.036 0.011 -10000 0 0 42 42
STAT2 0.037 0.008 -10000 0 0 24 24
STAT1 0.035 0.011 -10000 0 0 41 41
IL12RB1 0.036 0.011 -10000 0 0 40 40
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.026 0.11 0.33 22 -10000 0 22
IL27/IL27R/JAK2/TYK2 -0.007 0.071 -10000 0 -0.42 5 5
positive regulation of T cell mediated cytotoxicity -0.007 0.07 -10000 0 -0.42 5 5
STAT1 (dimer) 0.044 0.085 -10000 0 -10000 0 0
JAK2 0.031 0.017 -10000 0 -0.039 6 6
JAK1 0.035 0.011 -10000 0 0 43 43
STAT2 (dimer) 0.014 0.11 -10000 0 -0.36 10 10
T cell proliferation 0.003 0.063 -10000 0 -0.48 1 1
IL12/IL12R/TYK2/JAK2 0.001 0.18 -10000 0 -0.76 27 27
IL17A 0.081 0.092 -10000 0 -10000 0 0
mast cell activation 0.007 0.07 0.42 5 -10000 0 5
IFNG 0.003 0.03 0.088 1 -0.09 20 21
T cell differentiation -0.002 0.003 -10000 0 -0.017 10 10
STAT3 (dimer) 0.012 0.11 -10000 0 -0.4 10 10
STAT5A (dimer) 0.016 0.11 -10000 0 -0.36 10 10
STAT4 (dimer) 0.015 0.11 -10000 0 -0.37 8 8
STAT4 0.037 0.009 -10000 0 0 31 31
T cell activation -0.004 0.006 -10000 0 -0.12 1 1
IL27R/JAK2/TYK2 0.035 0.066 -10000 0 -10000 0 0
GATA3 0.005 0.095 0.68 9 -10000 0 9
IL18 -0.015 0.006 0 75 -10000 0 75
positive regulation of mast cell cytokine production 0.012 0.11 -10000 0 -0.38 11 11
IL27/EBI3 0.025 0.013 -10000 0 -10000 0 0
IL27RA 0 0.04 -10000 0 -10000 0 0
IL6 0.019 0.021 -10000 0 -10000 0 0
STAT5A 0.038 0.005 -10000 0 0 10 10
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.009 0.029 -10000 0 -10000 0 0
IL1B -0.014 0.007 0 100 -10000 0 100
EBI3 0.035 0.015 -10000 0 -0.039 7 7
TNF -0.018 0.002 0 8 -10000 0 8
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.014 0.002 0 7 -9999 0 7
ADCY5 -0.014 0.002 0 7 -9999 0 7
ADCY6 -0.026 0.009 0.11 1 -9999 0 1
ADCY7 -0.022 0.024 0.11 15 -9999 0 15
ADCY1 -0.017 0.014 -10000 0 -9999 0 0
ADCY2 -0.026 0.01 0.11 2 -9999 0 2
ADCY3 -0.014 0.002 0 7 -9999 0 7
ADCY8 -0.012 0.042 0.11 53 -9999 0 53
PRKCE -0.018 0.002 0 7 -9999 0 7
ADCY9 -0.026 0.014 0.11 5 -9999 0 5
mol:DAG 0 0 -10000 0 -9999 0 0
cAMP biosynthetic process 0.013 0.051 0.17 17 -9999 0 17
Visual signal transduction: Rods

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
mol:K + 0.038 0.006 -10000 0 0 12 12
GNAT1/GTP 0.028 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.05 0.012 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.05 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.038 0.007 -10000 0 0 16 16
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.07 0.031 -10000 0 -10000 0 0
mol:Na + -0.049 0.009 -10000 0 -10000 0 0
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.048 0.015 -10000 0 -0.1 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.053 0.023 -10000 0 -10000 0 0
CNGB1 0.038 0.006 -10000 0 0 13 13
RDH5 0.037 0.009 -10000 0 0 27 27
SAG 0.038 0.006 -10000 0 0 11 11
mol:Ca2+ -0.053 0.031 -10000 0 -10000 0 0
Na + (4 Units) -0.056 0.012 0.048 3 -10000 0 3
RGS9 0.037 0.008 -10000 0 0 20 20
GNB1/GNGT1 0.028 0.037 -10000 0 -0.13 12 12
GNAT1/GDP 0.061 0.025 -10000 0 -0.097 1 1
GUCY2D 0.038 0.006 -10000 0 0 13 13
GNGT1 0.022 0.019 -10000 0 0 217 217
GUCY2F 0.039 0.003 -10000 0 0 3 3
GNB5 0.037 0.008 -10000 0 0 20 20
mol:GMP (4 units) -0.038 0.033 0.15 13 -10000 0 13
mol:11-cis-retinal 0.037 0.009 -10000 0 0 27 27
mol:cGMP -0.034 0.004 -10000 0 -10000 0 0
GNB1 0.035 0.011 -10000 0 0 46 46
Rhodopsin 0.053 0.016 -10000 0 -10000 0 0
SLC24A1 0.038 0.006 -10000 0 0 12 12
CNGA1 0.038 0.005 -10000 0 0 9 9
Metarhodopsin II 0.024 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.009 -10000 0 -10000 0 0
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.003 0.032 -10000 0 -0.16 13 13
GCAP Family/Ca ++ 0.025 0.003 -10000 0 -10000 0 0
PDE6A/B 0.055 0.012 -10000 0 -10000 0 0
mol:Pi 0.048 0.015 -10000 0 -0.1 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.043 -10000 0 -0.1 11 11
PDE6B 0.038 0.006 -10000 0 0 12 12
PDE6A 0.038 0.006 -10000 0 0 11 11
PDE6G 0.038 0.005 -10000 0 0 7 7
RHO 0.038 0.007 -10000 0 0 17 17
PDE6 0.088 0.033 -10000 0 -0.11 1 1
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.049 0.007 -10000 0 -10000 0 0
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.039 0.004 -10000 0 0 6 6
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.05 0.011 -10000 0 -9999 0 0
EFNA5 0.038 0.006 -10000 0 0 12 12
FYN -0.028 0.022 0.18 3 -9999 0 3
neuron projection morphogenesis 0.05 0.011 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.05 0.011 -10000 0 -9999 0 0
EPHA5 0.038 0.006 -10000 0 0 13 13
Inferred Pathway Levels Matrix

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

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.4 0.049 -0.28 0.031
47_PPARGC1A 0.039 0.039 0.039 0
105_BMP4 0.039 0.039 0 0.039
105_BMP6 0.039 0.039 0 0.039
105_BMP7 0.039 0.039 0 0.039
105_BMP2 0.039 0.039 0 0.039
131_RELN/VLDLR 0 0 0.1 0.1
30_TGFB1/TGF beta receptor Type II 0 0.039 0 0
84_STAT5B 0.2 0.11 -0.26 0.055
84_STAT5A 0.2 0.11 -0.26 0.055
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBMLGG-TP/14517638/GDAC_MergeDataFiles_12184409/GBMLGG-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/GBMLGG-TP/15078930/GDAC_Gistic2Report_15096437/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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