PARADIGM pathway analysis of mRNASeq expression data
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1RJ4HDH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1RJ4HDH
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 49 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 113
Glypican 2 network 106
FOXM1 transcription factor network 90
Angiopoietin receptor Tie2-mediated signaling 87
Aurora B signaling 82
Signaling mediated by p38-alpha and p38-beta 70
Endothelins 64
IL23-mediated signaling events 61
Syndecan-1-mediated signaling events 58
Glucocorticoid receptor regulatory network 56
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 486 . 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 ( 486 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 0.2325 113 791 7 -0.11 0 1000 -1000 -0.022 -1000
Glypican 2 network 0.2181 106 425 4 -0.14 -0.11 1000 -1000 -0.016 -1000
FOXM1 transcription factor network 0.1852 90 4637 51 -0.42 0.013 1000 -1000 -0.17 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1790 87 7703 88 -0.32 0.06 1000 -1000 -0.077 -1000
Aurora B signaling 0.1687 82 5533 67 -0.26 0.013 1000 -1000 -0.052 -1000
Signaling mediated by p38-alpha and p38-beta 0.1440 70 3114 44 -0.18 0.013 1000 -1000 -0.04 -1000
Endothelins 0.1317 64 6178 96 -0.17 0.013 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.1255 61 3671 60 -0.42 0.013 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.1193 58 1997 34 -0.31 0.013 1000 -1000 -0.046 -1000
Glucocorticoid receptor regulatory network 0.1152 56 6469 114 -0.52 0.28 1000 -1000 -0.064 -1000
IL4-mediated signaling events 0.1091 53 4843 91 -0.6 0.5 1000 -1000 -0.16 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0967 47 3743 78 -0.18 0.17 1000 -1000 -0.056 -1000
Aurora C signaling 0.0947 46 325 7 -0.18 0.009 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.0947 46 3866 84 -0.22 0.027 1000 -1000 -0.084 -1000
Signaling events mediated by the Hedgehog family 0.0905 44 2319 52 -0.091 0.087 1000 -1000 -0.04 -1000
Glypican 1 network 0.0905 44 2150 48 -0.2 0.022 1000 -1000 -0.031 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0905 44 3043 68 -0.26 0.081 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 0.0905 44 749 17 -0.099 0.018 1000 -1000 -0.029 -1000
Thromboxane A2 receptor signaling 0.0885 43 4590 105 -0.13 0.035 1000 -1000 -0.061 -1000
IL6-mediated signaling events 0.0844 41 3078 75 -0.2 0.049 1000 -1000 -0.069 -1000
LPA receptor mediated events 0.0802 39 4045 102 -0.31 0.027 1000 -1000 -0.079 -1000
PLK1 signaling events 0.0782 38 3310 85 -0.21 0.03 1000 -1000 -0.038 -1000
amb2 Integrin signaling 0.0782 38 3154 82 -0.31 0.018 1000 -1000 -0.068 -1000
Reelin signaling pathway 0.0761 37 2110 56 -0.17 0.033 1000 -1000 -0.075 -1000
FOXA2 and FOXA3 transcription factor networks 0.0720 35 1630 46 -0.22 0.02 1000 -1000 -0.098 -1000
S1P1 pathway 0.0720 35 1290 36 -0.19 0.013 1000 -1000 -0.05 -1000
Nongenotropic Androgen signaling 0.0720 35 1825 52 -0.1 0.039 1000 -1000 -0.045 -1000
Signaling events mediated by PRL 0.0679 33 1130 34 -0.11 0.051 1000 -1000 -0.033 -1000
Aurora A signaling 0.0658 32 1941 60 -0.2 0.026 1000 -1000 -0.025 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0658 32 3897 120 -0.25 0.076 1000 -1000 -0.063 -1000
JNK signaling in the CD4+ TCR pathway 0.0638 31 537 17 -0.12 0.019 1000 -1000 -0.037 -1000
HIF-1-alpha transcription factor network 0.0638 31 2424 76 -0.22 0.048 1000 -1000 -0.16 -1000
S1P5 pathway 0.0638 31 532 17 -0.081 0.067 1000 -1000 -0.026 -1000
TCGA08_p53 0.0638 31 222 7 -0.081 0.045 1000 -1000 -0.013 -1000
BMP receptor signaling 0.0617 30 2478 81 -0.16 0.047 1000 -1000 -0.076 -1000
Signaling events regulated by Ret tyrosine kinase 0.0617 30 2494 82 -0.1 0.013 1000 -1000 -0.075 -1000
Calcium signaling in the CD4+ TCR pathway 0.0617 30 946 31 -0.16 0.013 1000 -1000 -0.058 -1000
IL12-mediated signaling events 0.0597 29 2589 87 -0.2 0.015 1000 -1000 -0.13 -1000
Osteopontin-mediated events 0.0597 29 1126 38 -0.08 0.014 1000 -1000 -0.088 -1000
Wnt signaling 0.0597 29 204 7 -0.085 0.013 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 0.0556 27 3487 125 -0.15 0.039 1000 -1000 -0.094 -1000
EPHB forward signaling 0.0556 27 2341 85 -0.14 0.089 1000 -1000 -0.077 -1000
Syndecan-4-mediated signaling events 0.0556 27 1843 67 -0.31 0.02 1000 -1000 -0.064 -1000
S1P4 pathway 0.0556 27 676 25 -0.081 0.02 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.0535 26 695 26 -0.097 0.014 1000 -1000 -0.048 -1000
IL27-mediated signaling events 0.0535 26 1356 51 -0.34 0.027 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.0535 26 551 21 -0.09 0.02 1000 -1000 -0.064 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0514 25 879 34 -0.087 0.013 1000 -1000 -0.038 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0514 25 1357 54 -0.17 0.025 1000 -1000 -0.093 -1000
Noncanonical Wnt signaling pathway 0.0494 24 635 26 -0.085 0.013 1000 -1000 -0.048 -1000
PDGFR-alpha signaling pathway 0.0494 24 1083 44 -0.16 0.023 1000 -1000 -0.042 -1000
BCR signaling pathway 0.0494 24 2469 99 -0.15 0.041 1000 -1000 -0.08 -1000
ErbB4 signaling events 0.0473 23 1591 69 -0.16 0.041 1000 -1000 -0.078 -1000
Visual signal transduction: Cones 0.0473 23 894 38 -0.092 0.013 1000 -1000 -0.055 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0473 23 2003 85 -0.12 0.017 1000 -1000 -0.064 -1000
Signaling events mediated by PTP1B 0.0473 23 1772 76 -0.27 0.048 1000 -1000 -0.075 -1000
TCR signaling in naïve CD8+ T cells 0.0473 23 2142 93 -0.066 0.026 1000 -1000 -0.07 -1000
a4b1 and a4b7 Integrin signaling 0.0432 21 107 5 -0.014 0 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0432 21 1294 61 -0.22 0.04 1000 -1000 -0.062 -1000
Canonical Wnt signaling pathway 0.0432 21 1110 51 -0.22 0.11 1000 -1000 -0.057 -1000
Plasma membrane estrogen receptor signaling 0.0432 21 1883 86 -0.19 0.021 1000 -1000 -0.072 -1000
Visual signal transduction: Rods 0.0432 21 1136 52 -0.11 0.013 1000 -1000 -0.067 -1000
Regulation of nuclear SMAD2/3 signaling 0.0412 20 2831 136 -0.52 0.06 1000 -1000 -0.063 -1000
FAS signaling pathway (CD95) 0.0412 20 961 47 -0.27 0.02 1000 -1000 -0.04 -1000
TCGA08_retinoblastoma 0.0412 20 165 8 -0.11 0.029 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 0.0412 20 412 20 -0.11 0.018 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 0.0391 19 1329 69 -0.067 0.031 1000 -1000 -0.023 -1000
Arf6 signaling events 0.0391 19 1225 62 -0.12 0.017 1000 -1000 -0.041 -1000
S1P3 pathway 0.0391 19 839 42 -0.078 0.02 1000 -1000 -0.034 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0370 18 684 37 -0.095 0.03 1000 -1000 -0.047 -1000
EPO signaling pathway 0.0350 17 957 55 -0.066 0.019 1000 -1000 -0.083 -1000
Fc-epsilon receptor I signaling in mast cells 0.0350 17 1741 97 -0.1 0.027 1000 -1000 -0.084 -1000
Regulation of p38-alpha and p38-beta 0.0350 17 919 54 -0.17 0.034 1000 -1000 -0.052 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0350 17 2175 125 -0.083 0.036 1000 -1000 -0.09 -1000
IL2 signaling events mediated by STAT5 0.0350 17 376 22 -0.078 0.034 1000 -1000 -0.043 -1000
Cellular roles of Anthrax toxin 0.0329 16 629 39 -0.038 0.014 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 0.0329 16 666 40 -0.14 0.025 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 0.0329 16 788 48 -0.14 0.049 1000 -1000 -0.051 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0329 16 531 33 -0.13 0.033 1000 -1000 -0.032 -1000
BARD1 signaling events 0.0309 15 865 57 -0.039 0.033 1000 -1000 -0.047 -1000
Insulin Pathway 0.0309 15 1155 74 -0.22 0.027 1000 -1000 -0.083 -1000
ErbB2/ErbB3 signaling events 0.0288 14 918 65 -0.16 0.02 1000 -1000 -0.059 -1000
Coregulation of Androgen receptor activity 0.0288 14 1126 76 -0.15 0.025 1000 -1000 -0.028 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0288 14 409 28 -0.079 0.034 1000 -1000 -0.029 -1000
IL1-mediated signaling events 0.0288 14 885 62 -0.088 0.058 1000 -1000 -0.081 -1000
LPA4-mediated signaling events 0.0267 13 160 12 -0.03 0.018 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0267 13 721 52 -0.11 0.027 1000 -1000 -0.05 -1000
HIF-2-alpha transcription factor network 0.0267 13 575 43 -0.087 0.021 1000 -1000 -0.069 -1000
Signaling mediated by p38-gamma and p38-delta 0.0267 13 201 15 -0.01 0.016 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0267 13 784 58 -0.18 0.028 1000 -1000 -0.074 -1000
Nectin adhesion pathway 0.0247 12 810 63 -0.083 0.027 1000 -1000 -0.058 -1000
Retinoic acid receptors-mediated signaling 0.0247 12 722 58 -0.075 0.028 1000 -1000 -0.064 -1000
Syndecan-3-mediated signaling events 0.0247 12 445 35 -0.073 0.039 1000 -1000 -0.041 -1000
VEGFR1 specific signals 0.0247 12 704 56 -0.058 0.027 1000 -1000 -0.05 -1000
Caspase cascade in apoptosis 0.0226 11 841 74 -0.061 0.03 1000 -1000 -0.038 -1000
Class I PI3K signaling events 0.0226 11 825 73 -0.1 0.035 1000 -1000 -0.049 -1000
IGF1 pathway 0.0226 11 654 57 -0.048 0.027 1000 -1000 -0.09 -1000
Hedgehog signaling events mediated by Gli proteins 0.0206 10 687 65 -0.29 0.054 1000 -1000 -0.054 -1000
Regulation of Telomerase 0.0206 10 1043 102 -0.22 0.038 1000 -1000 -0.1 -1000
TRAIL signaling pathway 0.0185 9 473 48 -0.037 0.04 1000 -1000 -0.058 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0185 9 762 83 -0.097 0.055 1000 -1000 -0.07 -1000
TCGA08_rtk_signaling 0.0185 9 256 26 -0.033 0.043 1000 -1000 -0.02 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0165 8 630 74 -0.18 0.054 1000 -1000 -0.069 -1000
p38 MAPK signaling pathway 0.0165 8 370 44 -0.057 0.026 1000 -1000 -0.056 -1000
IFN-gamma pathway 0.0144 7 485 68 -0.085 0.051 1000 -1000 -0.083 -1000
Atypical NF-kappaB pathway 0.0144 7 222 31 -0.034 0.043 1000 -1000 -0.038 -1000
Class IB PI3K non-lipid kinase events 0.0144 7 21 3 -0.005 0.005 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 0.0144 7 556 70 -0.11 0.063 1000 -1000 -0.049 -1000
PLK2 and PLK4 events 0.0123 6 20 3 0.007 0.013 1000 -1000 -0.015 -1000
Ceramide signaling pathway 0.0123 6 529 76 -0.056 0.039 1000 -1000 -0.041 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0123 6 286 45 -0.029 0.06 1000 -1000 -0.084 -1000
Canonical NF-kappaB pathway 0.0103 5 203 39 -0.029 0.063 1000 -1000 -0.074 -1000
Signaling events mediated by HDAC Class II 0.0103 5 426 75 -0.044 0.036 1000 -1000 -0.038 -1000
mTOR signaling pathway 0.0103 5 299 53 -0.016 0.027 1000 -1000 -0.058 -1000
FoxO family signaling 0.0103 5 350 64 -0.08 0.081 1000 -1000 -0.06 -1000
Paxillin-dependent events mediated by a4b1 0.0103 5 185 36 -0.024 0.025 1000 -1000 -0.065 -1000
ceramide signaling pathway 0.0082 4 227 49 -0.029 0.039 1000 -1000 -0.044 -1000
Arf6 trafficking events 0.0082 4 287 71 -0.091 0.04 1000 -1000 -0.062 -1000
Circadian rhythm pathway 0.0062 3 68 22 -0.023 0.04 1000 -1000 -0.046 -1000
Arf6 downstream pathway 0.0062 3 132 43 -0.022 0.024 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0062 3 120 32 -0.036 0.029 1000 -1000 -0.045 -1000
PDGFR-beta signaling pathway 0.0062 3 355 97 -0.085 0.044 1000 -1000 -0.076 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 60 23 -0.013 0.042 1000 -1000 -0.04 -1000
E-cadherin signaling in keratinocytes 0.0041 2 119 43 -0.038 0.042 1000 -1000 -0.039 -1000
Class I PI3K signaling events mediated by Akt 0.0021 1 80 68 -0.036 0.046 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class I 0.0021 1 118 104 -0.029 0.051 1000 -1000 -0.065 -1000
E-cadherin signaling in the nascent adherens junction 0.0021 1 125 76 -0.007 0.056 1000 -1000 -0.072 -1000
E-cadherin signaling events 0.0021 1 6 5 0.011 0.026 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 -0.001 0.034 1000 -1000 -0.048 -1000
Arf1 pathway 0.0000 0 28 54 -0.001 0.031 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0000 0 9 13 0 0.037 1000 -1000 -0.028 -1000
Total NA 3120 177986 7203 -17 5 131000 -131000 -7.5 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.087 0.16 -9999 0 -0.31 154 154
EFNA5 -0.041 0.15 -9999 0 -0.47 54 54
FYN -0.072 0.15 -9999 0 -0.28 154 154
neuron projection morphogenesis -0.087 0.16 -9999 0 -0.31 154 154
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.087 0.16 -9999 0 -0.31 154 154
EPHA5 -0.11 0.21 -9999 0 -0.47 121 121
Glypican 2 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
MDK -0.012 0.12 -9999 0 -0.57 21 21
GPC2 -0.14 0.26 -9999 0 -0.57 128 128
GPC2/Midkine -0.11 0.21 -9999 0 -0.44 138 138
neuron projection morphogenesis -0.11 0.21 -9999 0 -0.44 138 138
FOXM1 transcription factor network

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
NFATC3 -0.28 0.56 -9999 0 -1.1 114 114
PLK1 -0.12 0.23 -9999 0 -0.46 31 31
BIRC5 -0.14 0.24 -9999 0 -0.46 171 171
HSPA1B -0.28 0.57 -9999 0 -1.1 109 109
MAP2K1 0.011 0.04 -9999 0 -10000 0 0
BRCA2 -0.3 0.59 -9999 0 -1.1 128 128
FOXM1 -0.41 0.82 -9999 0 -1.5 128 128
XRCC1 -0.28 0.56 -9999 0 -1.1 117 117
FOXM1B/p19 -0.4 0.5 -9999 0 -1.1 128 128
Cyclin D1/CDK4 -0.25 0.52 -9999 0 -1 100 100
CDC2 -0.3 0.6 -9999 0 -1.1 124 124
TGFA -0.25 0.52 -9999 0 -1 105 105
SKP2 -0.28 0.57 -9999 0 -1.1 113 113
CCNE1 0.006 0.061 -9999 0 -0.59 5 5
CKS1B -0.28 0.56 -9999 0 -1.1 114 114
RB1 -0.16 0.18 -9999 0 -0.49 51 51
FOXM1C/SP1 -0.34 0.66 -9999 0 -1.3 124 124
AURKB -0.12 0.23 -9999 0 -0.45 152 152
CENPF -0.33 0.62 -9999 0 -1.2 141 141
CDK4 0.012 0.015 -9999 0 -10000 0 0
MYC -0.25 0.51 -9999 0 -0.98 116 116
CHEK2 0.01 0.049 -9999 0 -0.63 1 1
ONECUT1 -0.27 0.55 -9999 0 -1.1 113 113
CDKN2A -0.11 0.24 -9999 0 -0.57 102 102
LAMA4 -0.28 0.57 -9999 0 -1.1 114 114
FOXM1B/HNF6 -0.34 0.66 -9999 0 -1.3 118 118
FOS -0.36 0.64 -9999 0 -1.2 148 148
SP1 0.013 0.005 -9999 0 -10000 0 0
CDC25B -0.28 0.57 -9999 0 -1.1 108 108
response to radiation -0.003 0.036 -9999 0 -10000 0 0
CENPB -0.28 0.56 -9999 0 -1.1 112 112
CENPA -0.36 0.63 -9999 0 -1.2 149 149
NEK2 -0.36 0.62 -9999 0 -1.2 148 148
HIST1H2BA -0.28 0.56 -9999 0 -1.1 112 112
CCNA2 -0.079 0.22 -9999 0 -0.59 75 75
EP300 0.01 0.038 -9999 0 -0.47 3 3
CCNB1/CDK1 -0.34 0.67 -9999 0 -1.3 120 120
CCNB2 -0.3 0.59 -9999 0 -1.2 116 116
CCNB1 -0.3 0.6 -9999 0 -1.2 118 118
ETV5 -0.3 0.6 -9999 0 -1.2 117 117
ESR1 -0.29 0.58 -9999 0 -1.1 118 118
CCND1 -0.26 0.53 -9999 0 -1 107 107
GSK3A 0.012 0.041 -9999 0 -0.51 1 1
Cyclin A-E1/CDK1-2 -0.035 0.16 -9999 0 -0.4 76 76
CDK2 0.012 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.043 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.52 -9999 0 -1.1 135 135
GAS1 -0.32 0.61 -9999 0 -1.2 126 126
MMP2 -0.29 0.58 -9999 0 -1.1 118 118
RB1/FOXM1C -0.27 0.56 -9999 0 -1.1 111 111
CREBBP 0.013 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.18 0.41 -10000 0 -0.79 146 146
NCK1/PAK1/Dok-R -0.12 0.18 -10000 0 -0.39 146 146
NCK1/Dok-R -0.24 0.48 -10000 0 -0.95 146 146
PIK3CA 0.011 0.038 -10000 0 -0.47 3 3
mol:beta2-estradiol 0.06 0.11 0.23 144 -10000 0 144
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.002 -10000 0 -10000 0 0
Rac/GDP 0.01 0 -10000 0 -10000 0 0
F2 0.036 0.17 0.24 122 -0.5 26 148
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.22 0.45 -10000 0 -0.89 146 146
FN1 -0.002 0.086 -10000 0 -0.5 14 14
PLD2 -0.25 0.5 -10000 0 -0.99 146 146
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
GRB14 -0.098 0.23 -10000 0 -0.57 92 92
ELK1 -0.22 0.45 -10000 0 -0.89 146 146
GRB7 0.013 0 -10000 0 -10000 0 0
PAK1 0.007 0.053 -10000 0 -0.47 6 6
Tie2/Ang1/alpha5/beta1 Integrin -0.24 0.48 -10000 0 -0.96 146 146
CDKN1A -0.11 0.28 -10000 0 -0.58 74 74
ITGA5 -0.002 0.085 -10000 0 -0.48 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.48 -10000 0 -0.95 146 146
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO -0.13 0.32 -10000 0 -0.6 146 146
PLG -0.27 0.5 -10000 0 -1 146 146
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.18 0.4 -10000 0 -0.77 146 146
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.049 -10000 0 -0.48 5 5
ANGPT2 -0.11 0.24 -10000 0 -0.57 54 54
BMX -0.28 0.51 -10000 0 -1 146 146
ANGPT1 -0.32 0.55 -10000 0 -1.2 145 145
tube development -0.12 0.3 -10000 0 -0.57 138 138
ANGPT4 0.01 0.027 -10000 0 -0.57 1 1
response to hypoxia -0.017 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.32 0.52 -10000 0 -1.1 146 146
alpha5/beta1 Integrin 0.009 0.061 -10000 0 -0.33 15 15
FGF2 -0.024 0.13 -10000 0 -0.47 37 37
STAT5A (dimer) -0.14 0.34 -10000 0 -0.66 133 133
mol:L-citrulline -0.13 0.32 -10000 0 -0.6 146 146
AGTR1 -0.12 0.24 -10000 0 -0.55 111 111
MAPK14 -0.24 0.48 -10000 0 -0.95 146 146
Tie2/SHP2 -0.072 0.26 -10000 0 -1.2 19 19
TEK -0.085 0.29 -10000 0 -1.4 19 19
RPS6KB1 -0.18 0.39 -10000 0 -0.76 146 146
Angiotensin II/AT1 -0.082 0.18 -10000 0 -0.4 111 111
Tie2/Ang1/GRB2 -0.26 0.51 -10000 0 -1 146 146
MAPK3 -0.23 0.46 -10000 0 -0.91 146 146
MAPK1 -0.23 0.46 -10000 0 -0.91 146 146
Tie2/Ang1/GRB7 -0.26 0.51 -10000 0 -1 146 146
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.26 0.5 -10000 0 -1 146 146
PI3K -0.22 0.46 -10000 0 -0.9 146 146
FES -0.24 0.48 -10000 0 -0.95 146 146
Crk/Dok-R -0.24 0.48 -10000 0 -0.95 146 146
Tie2/Ang1/ABIN2 -0.26 0.51 -10000 0 -1 146 146
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.16 0.37 -10000 0 -0.71 146 146
STAT5A 0.011 0.031 -10000 0 -0.47 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.39 -10000 0 -0.76 146 146
Tie2/Ang2 -0.18 0.39 -10000 0 -0.76 134 134
Tie2/Ang1 -0.28 0.54 -10000 0 -1.1 146 146
FOXO1 -0.16 0.37 -10000 0 -0.72 146 146
ELF1 0.008 0.068 -10000 0 -0.5 8 8
ELF2 -0.25 0.49 -10000 0 -0.98 146 146
mol:Choline -0.24 0.47 -10000 0 -0.95 146 146
cell migration -0.069 0.1 -10000 0 -0.22 146 146
FYN -0.14 0.34 -10000 0 -0.65 134 134
DOK2 0.01 0.046 -10000 0 -0.58 3 3
negative regulation of cell cycle -0.094 0.26 -10000 0 -0.51 88 88
ETS1 -0.05 0.12 -10000 0 -0.36 12 12
PXN -0.14 0.33 -10000 0 -0.64 146 146
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 -0.15 0.35 -10000 0 -0.68 146 146
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.088 0.17 -10000 0 -0.5 47 47
MAPKKK cascade -0.24 0.47 -10000 0 -0.95 146 146
RASA1 0.01 0.038 -10000 0 -0.47 3 3
Tie2/Ang1/Shc -0.26 0.51 -10000 0 -1 146 146
NCK1 0.012 0.027 -10000 0 -0.58 1 1
vasculogenesis -0.11 0.29 -10000 0 -0.54 146 146
mol:Phosphatidic acid -0.24 0.47 -10000 0 -0.95 146 146
mol:Angiotensin II 0.001 0.003 -10000 0 -10000 0 0
mol:NADP -0.13 0.32 -10000 0 -0.6 146 146
Rac1/GTP -0.22 0.33 -10000 0 -0.72 146 146
MMP2 -0.26 0.51 -10000 0 -1 146 146
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.11 0.19 -9999 0 -0.39 147 147
STMN1 -0.12 0.21 -9999 0 -0.42 159 159
Aurora B/RasGAP/Survivin -0.21 0.31 -9999 0 -0.57 197 197
Chromosomal passenger complex/Cul3 protein complex -0.089 0.17 -9999 0 -0.32 148 148
BIRC5 -0.21 0.29 -9999 0 -0.59 179 179
DES -0.17 0.29 -9999 0 -0.75 88 88
Aurora C/Aurora B/INCENP -0.087 0.16 -9999 0 -0.32 162 162
Aurora B/TACC1 -0.11 0.18 -9999 0 -0.36 161 161
Aurora B/PP2A -0.12 0.2 -9999 0 -0.41 159 159
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.021 0.053 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.004 -9999 0 -10000 0 0
NDC80 -0.12 0.2 -9999 0 -0.41 162 162
Cul3 protein complex 0.01 0.069 -9999 0 -0.27 28 28
KIF2C -0.074 0.12 -9999 0 -0.23 164 164
PEBP1 0.008 0.006 -9999 0 -10000 0 0
KIF20A -0.21 0.29 -9999 0 -0.58 185 185
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.12 0.21 -9999 0 -0.42 159 159
SEPT1 0.001 0.084 -9999 0 -0.58 10 10
SMC2 0.012 0.027 -9999 0 -0.58 1 1
SMC4 0.012 0.027 -9999 0 -0.58 1 1
NSUN2/NPM1/Nucleolin -0.048 0.1 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -9999 0 -10000 0 0
H3F3B -0.062 0.11 -9999 0 -0.23 159 159
AURKB -0.18 0.28 -9999 0 -0.58 159 159
AURKC 0.009 0.049 -9999 0 -0.52 4 4
CDCA8 -0.057 0.19 -9999 0 -0.6 53 53
cytokinesis -0.14 0.24 -9999 0 -0.47 147 147
Aurora B/Septin1 -0.16 0.22 -9999 0 -0.47 146 146
AURKA -0.029 0.15 -9999 0 -0.58 35 35
INCENP 0.007 0.008 -9999 0 -10000 0 0
KLHL13 -0.014 0.11 -9999 0 -0.47 27 27
BUB1 -0.12 0.25 -9999 0 -0.58 110 110
hSgo1/Aurora B/Survivin -0.26 0.37 -9999 0 -0.66 204 204
EVI5 0.012 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.15 0.22 -9999 0 -0.45 143 143
SGOL1 -0.11 0.24 -9999 0 -0.58 102 102
CENPA -0.14 0.19 -9999 0 -0.36 182 182
NCAPG -0.18 0.28 -9999 0 -0.58 161 161
Aurora B/HC8 Proteasome -0.12 0.2 -9999 0 -0.41 159 159
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.12 0.2 -9999 0 -0.41 159 159
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.14 0.26 -9999 0 -0.58 130 130
NPM1 -0.062 0.11 -9999 0 -0.23 84 84
RASA1 0.01 0.038 -9999 0 -0.47 3 3
KLHL9 0.012 0.022 -9999 0 -0.47 1 1
mitotic prometaphase -0.006 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.2 -9999 0 -0.41 159 159
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.15 0.26 -9999 0 -0.49 145 145
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
NSUN2 -0.062 0.11 -9999 0 -0.24 53 53
MYLK -0.15 0.21 -9999 0 -0.35 219 219
KIF23 -0.028 0.15 -9999 0 -0.59 32 32
VIM -0.12 0.2 -9999 0 -0.41 159 159
RACGAP1 0.004 0.061 -9999 0 -0.59 5 5
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.062 0.11 -9999 0 -0.23 141 141
Chromosomal passenger complex -0.15 0.22 -9999 0 -0.42 180 180
Chromosomal passenger complex/EVI5 -0.22 0.32 -9999 0 -0.65 151 151
TACC1 0.002 0.072 -9999 0 -0.47 11 11
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.18 0.41 -9999 0 -1 91 91
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.053 0.14 -9999 0 -0.41 15 15
ATF2/c-Jun -0.052 0.17 -9999 0 -0.55 31 31
MAPK11 -0.063 0.16 -9999 0 -0.32 114 114
MITF -0.063 0.18 -9999 0 -0.36 110 110
MAPKAPK5 -0.06 0.17 -9999 0 -0.35 109 109
KRT8 -0.06 0.17 -9999 0 -0.35 110 110
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.085 0.22 -9999 0 -0.44 114 114
CEBPB -0.06 0.17 -9999 0 -0.35 109 109
SLC9A1 -0.06 0.17 -9999 0 -0.35 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.076 0.21 -9999 0 -0.39 113 113
p38alpha-beta/MNK1 -0.056 0.18 -9999 0 -0.51 25 25
JUN -0.051 0.17 -9999 0 -0.55 31 31
PPARGC1A -0.17 0.29 -9999 0 -0.58 123 123
USF1 -0.06 0.17 -9999 0 -0.35 109 109
RAB5/GDP/GDI1 -0.04 0.12 -9999 0 -0.36 25 25
NOS2 -0.11 0.3 -9999 0 -0.71 66 66
DDIT3 -0.06 0.17 -9999 0 -0.35 109 109
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.058 0.16 -9999 0 -0.45 31 31
p38alpha-beta/HBP1 -0.056 0.18 -9999 0 -0.49 28 28
CREB1 -0.066 0.19 -9999 0 -0.38 110 110
RAB5/GDP 0.01 0 -9999 0 -10000 0 0
EIF4E -0.047 0.15 -9999 0 -0.52 18 18
RPS6KA4 -0.061 0.17 -9999 0 -0.36 110 110
PLA2G4A -0.061 0.18 -9999 0 -0.54 36 36
GDI1 -0.06 0.17 -9999 0 -0.35 109 109
TP53 -0.081 0.21 -9999 0 -0.44 110 110
RPS6KA5 -0.07 0.19 -9999 0 -0.38 112 112
ESR1 -0.072 0.2 -9999 0 -0.39 110 110
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.063 0.18 -9999 0 -0.36 111 111
MEF2A -0.062 0.18 -9999 0 -0.36 110 110
EIF4EBP1 -0.072 0.19 -9999 0 -0.4 111 111
KRT19 -0.092 0.22 -9999 0 -0.44 112 112
ELK4 -0.061 0.17 -9999 0 -0.35 110 110
ATF6 -0.06 0.17 -9999 0 -0.35 109 109
ATF1 -0.066 0.19 -9999 0 -0.38 111 111
p38alpha-beta/MAPKAPK2 -0.056 0.18 -9999 0 -0.49 28 28
p38alpha-beta/MAPKAPK3 -0.056 0.18 -9999 0 -0.51 25 25
Endothelins

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
AKT1 -0.04 0.21 0.27 18 -0.57 42 60
PTK2B 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.41 -10000 0 -0.95 93 93
EDN1 -0.025 0.17 -10000 0 -0.49 40 40
EDN3 -0.17 0.24 -10000 0 -0.47 184 184
EDN2 -0.022 0.13 -10000 0 -0.5 33 33
HRAS/GDP -0.06 0.23 -10000 0 -0.52 75 75
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.025 0.17 -10000 0 -0.42 54 54
ADCY4 -0.091 0.24 -10000 0 -0.54 86 86
ADCY5 -0.12 0.3 -10000 0 -0.62 106 106
ADCY6 -0.09 0.24 -10000 0 -0.53 86 86
ADCY7 -0.09 0.24 -10000 0 -0.53 87 87
ADCY1 -0.12 0.25 -10000 0 -0.55 91 91
ADCY2 -0.1 0.25 -10000 0 -0.56 89 89
ADCY3 -0.09 0.24 -10000 0 -0.53 86 86
ADCY8 -0.099 0.24 -10000 0 -0.54 87 87
ADCY9 -0.09 0.24 -10000 0 -0.54 86 86
arachidonic acid secretion -0.098 0.31 -10000 0 -0.56 117 117
ETB receptor/Endothelin-1/Gq/GTP -0.039 0.16 -10000 0 -0.38 66 66
GNAO1 -0.079 0.19 -10000 0 -0.47 93 93
HRAS 0.006 0.059 -10000 0 -0.58 5 5
ETA receptor/Endothelin-1/G12/GTP -0.024 0.22 0.3 56 -0.55 40 96
ETA receptor/Endothelin-1/Gs/GTP -0.1 0.26 0.28 51 -0.57 86 137
mol:GTP -0.001 0.007 -10000 0 -10000 0 0
COL3A1 -0.046 0.22 -10000 0 -0.58 48 48
EDNRB -0.051 0.17 -10000 0 -0.47 67 67
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.083 0.28 -10000 0 -0.63 84 84
CYSLTR1 -0.06 0.26 -10000 0 -0.71 50 50
SLC9A1 -0.034 0.11 0.19 23 -0.3 40 63
mol:GDP -0.069 0.25 -10000 0 -0.55 75 75
SLC9A3 -0.16 0.37 -10000 0 -0.84 90 90
RAF1 -0.076 0.25 -10000 0 -0.56 75 75
JUN -0.069 0.29 -10000 0 -0.68 65 65
JAK2 -0.041 0.21 -10000 0 -0.58 42 42
mol:IP3 -0.03 0.17 -10000 0 -0.42 48 48
ETA receptor/Endothelin-1 -0.066 0.26 0.35 59 -0.61 51 110
PLCB1 0.008 0.044 -10000 0 -0.47 4 4
PLCB2 0.009 0.038 -10000 0 -0.57 2 2
ETA receptor/Endothelin-3 -0.15 0.23 -10000 0 -0.4 190 190
FOS -0.13 0.38 -10000 0 -0.9 87 87
Gai/GDP -0.14 0.36 -10000 0 -0.85 93 93
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.065 0.26 -10000 0 -0.64 59 59
BCAR1 0.013 0.001 -10000 0 -10000 0 0
PRKCB1 -0.033 0.16 -10000 0 -0.41 50 50
GNAQ 0.012 0.007 -10000 0 -10000 0 0
GNAZ -0.033 0.14 -10000 0 -0.47 46 46
GNAL -0.11 0.21 -10000 0 -0.47 124 124
Gs family/GDP -0.15 0.24 -10000 0 -0.56 110 110
ETA receptor/Endothelin-1/Gq/GTP -0.038 0.2 -10000 0 -0.46 63 63
MAPK14 -0.021 0.14 -10000 0 -0.4 35 35
TRPC6 -0.15 0.44 -10000 0 -1 92 92
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.005 0.065 -10000 0 -0.53 7 7
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.03 0.15 -10000 0 -0.38 50 50
ETB receptor/Endothelin-2 -0.051 0.15 -10000 0 -0.34 97 97
ETB receptor/Endothelin-3 -0.15 0.22 -10000 0 -0.4 201 201
ETB receptor/Endothelin-1 -0.05 0.18 -10000 0 -0.39 91 91
MAPK3 -0.12 0.35 -10000 0 -0.8 92 92
MAPK1 -0.12 0.35 -10000 0 -0.79 94 94
Rac1/GDP -0.057 0.23 -10000 0 -0.52 71 71
cAMP biosynthetic process -0.098 0.26 -10000 0 -0.56 91 91
MAPK8 -0.096 0.34 -10000 0 -0.68 101 101
SRC 0.013 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.075 0.21 -10000 0 -0.49 80 80
p130Cas/CRK/Src/PYK2 -0.083 0.29 -10000 0 -0.61 94 94
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.057 0.23 -10000 0 -0.52 69 69
COL1A2 -0.065 0.25 -10000 0 -0.64 56 56
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.047 0.17 -10000 0 -0.38 79 79
mol:DAG -0.031 0.17 -10000 0 -0.42 48 48
MAP2K2 -0.094 0.29 -10000 0 -0.62 93 93
MAP2K1 -0.094 0.29 -10000 0 -0.62 92 92
EDNRA -0.042 0.19 -10000 0 -0.5 60 60
positive regulation of muscle contraction -0.029 0.19 -10000 0 -0.52 40 40
Gq family/GDP -0.11 0.2 -10000 0 -0.53 71 71
HRAS/GTP -0.064 0.22 -10000 0 -0.49 73 73
PRKCH -0.026 0.16 -10000 0 -0.42 43 43
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.036 0.18 -10000 0 -0.46 52 52
PRKCB -0.081 0.23 -10000 0 -0.5 84 84
PRKCE -0.025 0.16 -10000 0 -0.42 43 43
PRKCD -0.027 0.17 -10000 0 -0.43 43 43
PRKCG -0.039 0.18 -10000 0 -0.43 54 54
regulation of vascular smooth muscle contraction -0.16 0.44 -10000 0 -1.1 87 87
PRKCQ -0.048 0.19 -10000 0 -0.47 56 56
PLA2G4A -0.11 0.35 -10000 0 -0.63 117 117
GNA14 0.011 0.023 -10000 0 -0.48 1 1
GNA15 -0.012 0.11 -10000 0 -0.48 24 24
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 -0.004 0.087 -10000 0 -0.47 16 16
Rac1/GTP -0.024 0.22 0.3 57 -0.55 40 97
MMP1 -0.068 0.26 -10000 0 -0.6 82 82
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.3 0.53 -10000 0 -1.2 89 89
IL23A -0.31 0.54 -10000 0 -1.2 92 92
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.47 -10000 0 -1.1 102 102
positive regulation of T cell mediated cytotoxicity -0.34 0.6 -10000 0 -1.3 102 102
ITGA3 -0.29 0.52 -10000 0 -1.2 87 87
IL17F -0.18 0.34 -10000 0 -0.74 80 80
IL12B -0.029 0.15 -10000 0 -0.61 29 29
STAT1 (dimer) -0.32 0.57 -10000 0 -1.2 102 102
CD4 -0.28 0.5 -10000 0 -1.1 89 89
IL23 -0.31 0.53 -10000 0 -1.2 95 95
IL23R -0.031 0.1 -10000 0 -0.54 4 4
IL1B -0.34 0.58 -10000 0 -1.3 99 99
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.28 0.5 -10000 0 -1.1 95 95
TYK2 0.006 0.023 -10000 0 -10000 0 0
STAT4 -0.008 0.11 -10000 0 -0.55 18 18
STAT3 0.013 0.001 -10000 0 -10000 0 0
IL18RAP -0.023 0.14 -10000 0 -0.52 33 33
IL12RB1 -0.02 0.13 -10000 0 -0.59 22 22
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
IL12Rbeta1/TYK2 -0.011 0.098 -10000 0 -0.44 22 22
IL23R/JAK2 -0.034 0.13 -10000 0 -0.53 4 4
positive regulation of chronic inflammatory response -0.34 0.6 -10000 0 -1.3 102 102
natural killer cell activation 0.003 0.009 0.046 5 -10000 0 5
JAK2 0.009 0.038 -10000 0 -0.47 1 1
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
NFKB1 0.012 0.004 -10000 0 -10000 0 0
RELA 0.012 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.29 0.5 -10000 0 -1.1 95 95
ALOX12B -0.3 0.51 -10000 0 -1.1 110 110
CXCL1 -0.4 0.62 -10000 0 -1.3 140 140
T cell proliferation -0.34 0.6 -10000 0 -1.3 102 102
NFKBIA 0.012 0.004 -10000 0 -10000 0 0
IL17A -0.14 0.28 -10000 0 -0.6 66 66
PI3K -0.37 0.48 -10000 0 -1.2 104 104
IFNG -0.008 0.031 0.1 1 -0.1 7 8
STAT3 (dimer) -0.35 0.45 -10000 0 -1.1 104 104
IL18R1 0.006 0.061 -10000 0 -0.47 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.34 -10000 0 -0.77 78 78
IL18/IL18R -0.004 0.11 -10000 0 -0.4 19 19
macrophage activation -0.018 0.018 -10000 0 -0.045 79 79
TNF -0.32 0.56 -10000 0 -1.3 97 97
STAT3/STAT4 -0.37 0.49 -10000 0 -1.2 104 104
STAT4 (dimer) -0.33 0.57 -10000 0 -1.2 104 104
IL18 0.002 0.075 -10000 0 -0.47 12 12
IL19 -0.28 0.49 -10000 0 -1.1 101 101
STAT5A (dimer) -0.32 0.56 -10000 0 -1.2 102 102
STAT1 0.001 0.084 -10000 0 -0.58 10 10
SOCS3 -0.053 0.17 -10000 0 -0.48 65 65
CXCL9 -0.32 0.52 -10000 0 -1.2 84 84
MPO -0.32 0.55 -10000 0 -1.1 123 123
positive regulation of humoral immune response -0.34 0.6 -10000 0 -1.3 102 102
IL23/IL23R/JAK2/TYK2 -0.37 0.68 -10000 0 -1.4 102 102
IL6 -0.42 0.62 -10000 0 -1.2 149 149
STAT5A 0.011 0.031 -10000 0 -0.47 2 2
IL2 0.006 0.039 -10000 0 -0.59 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.046 5 -10000 0 5
CD3E -0.28 0.51 -10000 0 -1.1 98 98
keratinocyte proliferation -0.34 0.6 -10000 0 -1.3 102 102
NOS2 -0.32 0.54 -10000 0 -1.1 114 114
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 0.013 0 -9999 0 -10000 0 0
CCL5 -0.007 0.1 -9999 0 -0.5 19 19
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.16 0.15 -9999 0 -0.36 118 118
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.14 0.14 -9999 0 -0.42 55 55
Syndecan-1/Syntenin -0.14 0.14 -9999 0 -0.42 55 55
MAPK3 -0.12 0.14 -9999 0 -0.4 49 49
HGF/MET -0.039 0.15 -9999 0 -0.41 67 67
TGFB1/TGF beta receptor Type II 0.013 0 -9999 0 -10000 0 0
BSG 0.012 0.027 -9999 0 -0.58 1 1
keratinocyte migration -0.14 0.14 -9999 0 -0.42 55 55
Syndecan-1/RANTES -0.15 0.16 -9999 0 -0.44 64 64
Syndecan-1/CD147 -0.13 0.14 -9999 0 -0.41 59 59
Syndecan-1/Syntenin/PIP2 -0.14 0.14 -9999 0 -0.41 55 55
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.13 0.14 -9999 0 -0.4 55 55
MMP7 -0.091 0.22 -9999 0 -0.53 93 93
HGF -0.026 0.14 -9999 0 -0.5 37 37
Syndecan-1/CASK -0.15 0.14 -9999 0 -0.34 118 118
Syndecan-1/HGF/MET -0.17 0.18 -9999 0 -0.46 98 98
regulation of cell adhesion -0.11 0.13 -9999 0 -0.41 39 39
HPSE -0.015 0.12 -9999 0 -0.5 26 26
positive regulation of cell migration -0.16 0.15 -9999 0 -0.36 118 118
SDC1 -0.16 0.15 -9999 0 -0.36 118 118
Syndecan-1/Collagen -0.16 0.15 -9999 0 -0.36 118 118
PPIB 0.007 0.059 -9999 0 -0.58 5 5
MET -0.033 0.14 -9999 0 -0.47 46 46
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 270 270
MAPK1 -0.12 0.14 -9999 0 -0.4 49 49
homophilic cell adhesion -0.15 0.15 -9999 0 -0.36 118 118
MMP1 -0.092 0.22 -9999 0 -0.54 92 92
Glucocorticoid receptor regulatory network

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.02 0.081 0.32 11 -10000 0 11
SMARCC2 0.001 0.033 -10000 0 -10000 0 0
SMARCC1 0.001 0.033 -10000 0 -10000 0 0
TBX21 -0.098 0.21 -10000 0 -0.48 86 86
SUMO2 0.016 0.015 -10000 0 -10000 0 0
STAT1 (dimer) 0.005 0.094 -10000 0 -0.62 10 10
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.011 0.031 -10000 0 -0.47 2 2
GR alpha/HSP90/FKBP51/HSP90 0.11 0.12 0.3 72 -0.29 1 73
PRL -0.077 0.13 -10000 0 -0.65 3 3
cortisol/GR alpha (dimer)/TIF2 0.2 0.29 0.57 132 -0.46 8 140
RELA -0.053 0.1 -10000 0 -0.29 9 9
FGG 0.19 0.24 0.51 107 -0.54 11 118
GR beta/TIF2 0.071 0.18 0.32 80 -0.36 38 118
IFNG -0.29 0.33 -10000 0 -0.73 139 139
apoptosis 0.067 0.23 0.51 67 -0.52 9 76
CREB1 -0.042 0.11 -10000 0 -0.33 28 28
histone acetylation -0.06 0.18 0.36 10 -0.39 75 85
BGLAP -0.086 0.18 -10000 0 -0.46 48 48
GR/PKAc 0.11 0.11 0.29 69 -10000 0 69
NF kappa B1 p50/RelA -0.093 0.19 -10000 0 -0.45 63 63
SMARCD1 0.001 0.033 -10000 0 -10000 0 0
MDM2 0.1 0.1 0.26 101 -10000 0 101
GATA3 -0.13 0.22 -10000 0 -0.47 142 142
AKT1 0.004 0.003 -10000 0 -10000 0 0
CSF2 -0.081 0.14 0.34 1 -0.46 17 18
GSK3B 0.016 0.015 -10000 0 -10000 0 0
NR1I3 0.086 0.22 0.5 61 -0.63 7 68
CSN2 0.17 0.18 0.43 99 -0.55 2 101
BRG1/BAF155/BAF170/BAF60A -0.007 0.11 -10000 0 -0.32 41 41
NFATC1 0.014 0.003 -10000 0 -10000 0 0
POU2F1 0.012 0.028 -10000 0 -0.57 1 1
CDKN1A 0.005 0.13 -10000 0 -1.3 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.014 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.47 49 49
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.082 0.12 0.3 53 -10000 0 53
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.035 0.29 0.48 59 -0.72 40 99
JUN -0.17 0.21 -10000 0 -0.49 103 103
IL4 -0.09 0.16 -10000 0 -0.51 11 11
CDK5R1 -0.014 0.13 -10000 0 -0.57 24 24
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.22 0.22 2 -0.52 69 71
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.11 0.3 66 -10000 0 66
cortisol/GR alpha (monomer) 0.28 0.32 0.68 146 -10000 0 146
NCOA2 -0.047 0.16 -10000 0 -0.47 60 60
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.12 0.2 -10000 0 -0.53 88 88
AP-1/NFAT1-c-4 -0.31 0.35 -10000 0 -0.77 145 145
AFP -0.14 0.19 -10000 0 -0.63 29 29
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.15 0.18 0.44 74 -0.53 4 78
TP53 0.021 0.071 -10000 0 -0.44 10 10
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.4 0.52 -10000 0 -1.2 134 134
KRT14 -0.39 0.58 0.41 2 -1.2 149 151
TBP 0.016 0.034 -10000 0 -0.24 1 1
CREBBP 0.045 0.13 0.28 60 -0.26 2 62
HDAC1 0.013 0.009 -10000 0 -10000 0 0
HDAC2 0.012 0.023 -10000 0 -0.47 1 1
AP-1 -0.31 0.36 -10000 0 -0.78 145 145
MAPK14 0.016 0.012 -10000 0 -10000 0 0
MAPK10 0.01 0.056 -10000 0 -0.48 6 6
MAPK11 0.007 0.077 -10000 0 -0.58 8 8
KRT5 -0.52 0.59 -10000 0 -1.2 188 188
interleukin-1 receptor activity 0 0.005 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0.005 0.094 -10000 0 -0.62 10 10
CGA -0.24 0.38 -10000 0 -0.87 106 106
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.1 0.18 0.38 106 -0.49 4 110
MAPK3 0.016 0.014 -10000 0 -10000 0 0
MAPK1 0.016 0.012 -10000 0 -10000 0 0
ICAM1 -0.2 0.28 -10000 0 -0.66 92 92
NFKB1 -0.053 0.1 -10000 0 -0.29 5 5
MAPK8 -0.15 0.19 -10000 0 -0.44 108 108
MAPK9 0.016 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.06 0.23 0.51 68 -0.54 9 77
BAX 0.014 0.062 -10000 0 -0.4 4 4
POMC -0.27 0.47 -10000 0 -1.3 67 67
EP300 0.042 0.14 0.28 60 -0.37 7 67
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.58 133 -10000 0 133
proteasomal ubiquitin-dependent protein catabolic process 0.073 0.081 0.22 54 -10000 0 54
SGK1 -0.066 0.48 0.39 12 -1.1 77 89
IL13 -0.36 0.41 -10000 0 -0.87 161 161
IL6 -0.35 0.48 -10000 0 -0.96 161 161
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.3 0.33 -10000 0 -0.79 125 125
IL2 -0.28 0.32 -10000 0 -0.72 127 127
CDK5 0.015 0.006 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.25 0.38 -10000 0 -0.82 114 114
CDK5R1/CDK5 0.001 0.095 -10000 0 -0.41 24 24
NF kappa B1 p50/RelA/PKAc -0.048 0.14 -10000 0 -0.38 19 19
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.55 137 -10000 0 137
SMARCA4 0.001 0.033 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.21 0.39 90 -0.38 25 115
NF kappa B1 p50/RelA/Cbp -0.043 0.21 0.34 21 -0.52 31 52
JUN (dimer) -0.17 0.21 -10000 0 -0.49 103 103
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.077 0.16 -10000 0 -0.45 53 53
NR3C1 0.17 0.2 0.48 103 -0.43 3 106
NR4A1 -0.053 0.18 -10000 0 -0.46 72 72
TIF2/SUV420H1 -0.023 0.11 -10000 0 -0.33 60 60
MAPKKK cascade 0.067 0.23 0.51 67 -0.52 9 76
cortisol/GR alpha (dimer)/Src-1 0.25 0.26 0.57 144 -10000 0 144
PBX1 0.011 0.032 -10000 0 -0.47 2 2
POU1F1 0.001 0.043 -10000 0 -0.64 2 2
SELE -0.34 0.48 -10000 0 -1 141 141
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.21 0.39 90 -0.38 25 115
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.55 137 -10000 0 137
mol:cortisol 0.16 0.2 0.4 156 -0.21 7 163
MMP1 -0.18 0.31 -10000 0 -0.92 56 56
IL4-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
BCL2L1 -0.45 0.45 -10000 0 -1.2 95 95
STAT6 (cleaved dimer) -0.48 0.46 -10000 0 -1.1 145 145
IGHG1 -0.16 0.14 -10000 0 -0.42 7 7
IGHG3 -0.44 0.43 -10000 0 -1.1 118 118
AKT1 -0.22 0.26 -10000 0 -0.71 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.23 -10000 0 -0.73 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.26 -10000 0 -0.76 38 38
THY1 -0.45 0.45 -10000 0 -1.2 87 87
MYB -0.015 0.12 -10000 0 -0.58 23 23
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.33 -10000 0 -0.83 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.27 -10000 0 -0.76 50 50
SP1 0.021 0.002 -10000 0 -10000 0 0
INPP5D -0.013 0.11 -10000 0 -0.47 26 26
SOCS5 0.028 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.48 -10000 0 -1.2 104 104
SOCS1 -0.29 0.3 -10000 0 -0.77 79 79
SOCS3 -0.33 0.42 -10000 0 -1.1 85 85
FCER2 -0.4 0.4 -10000 0 -1.1 92 92
PARP14 0.013 0.005 -10000 0 -10000 0 0
CCL17 -0.48 0.47 -10000 0 -1.2 102 102
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.22 -10000 0 -0.7 39 39
T cell proliferation -0.44 0.47 -10000 0 -1.2 99 99
IL4R/JAK1 -0.45 0.45 -10000 0 -1.2 97 97
EGR2 -0.49 0.48 -10000 0 -1.2 103 103
JAK2 -0.015 0.033 -10000 0 -0.51 1 1
JAK3 0 0.091 -10000 0 -0.55 13 13
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
JAK1 0.004 0.009 -10000 0 -10000 0 0
COL1A2 -0.14 0.15 -10000 0 -0.9 4 4
CCL26 -0.45 0.45 -10000 0 -1.2 88 88
IL4R -0.48 0.48 -10000 0 -1.2 95 95
PTPN6 0.025 0.009 -10000 0 -10000 0 0
IL13RA2 -0.53 0.55 -10000 0 -1.4 119 119
IL13RA1 -0.014 0.024 -10000 0 -10000 0 0
IRF4 -0.18 0.34 -10000 0 -1 52 52
ARG1 -0.14 0.16 -10000 0 -0.64 11 11
CBL -0.28 0.3 -10000 0 -0.79 82 82
GTF3A 0.018 0.012 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
IL13RA1/JAK2 -0.019 0.037 -10000 0 -0.37 1 1
IRF4/BCL6 -0.16 0.32 -10000 0 -0.95 52 52
CD40LG -0.038 0.17 -10000 0 -0.54 49 49
MAPK14 -0.3 0.34 -10000 0 -0.91 82 82
mitosis -0.21 0.24 -10000 0 -0.67 54 54
STAT6 -0.52 0.54 -10000 0 -1.3 102 102
SPI1 0.007 0.057 -10000 0 -0.57 4 4
RPS6KB1 -0.2 0.23 -10000 0 -0.65 49 49
STAT6 (dimer) -0.52 0.54 -10000 0 -1.3 102 102
STAT6 (dimer)/PARP14 -0.48 0.49 -10000 0 -1.2 103 103
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.26 -10000 0 -0.71 53 53
FRAP1 -0.22 0.26 -10000 0 -0.71 56 56
LTA -0.46 0.46 -10000 0 -1.2 96 96
FES 0.008 0.049 -10000 0 -0.47 5 5
T-helper 1 cell differentiation 0.5 0.51 1.3 102 -10000 0 102
CCL11 -0.47 0.46 -10000 0 -1.1 118 118
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.26 -10000 0 -0.7 55 55
IL2RG -0.01 0.12 -10000 0 -0.54 22 22
IL10 -0.48 0.48 -10000 0 -1.2 99 99
IRS1 -0.003 0.086 -10000 0 -0.47 16 16
IRS2 0.007 0.059 -10000 0 -0.58 5 5
IL4 -0.11 0.1 -10000 0 -10000 0 0
IL5 -0.46 0.45 -10000 0 -1.2 97 97
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.88 93 93
COL1A1 -0.17 0.18 -10000 0 -0.6 32 32
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.46 -10000 0 -1.2 88 88
IL2R gamma/JAK3 -0.008 0.13 -10000 0 -0.56 24 24
TFF3 -0.53 0.48 -10000 0 -1.2 126 126
ALOX15 -0.58 0.48 -10000 0 -1.3 127 127
MYBL1 0.012 0.022 -10000 0 -0.47 1 1
T-helper 2 cell differentiation -0.38 0.37 -10000 0 -0.95 100 100
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.012 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.24 -10000 0 -0.73 35 35
mol:PI-3-4-5-P3 -0.22 0.26 -10000 0 -0.71 56 56
PI3K -0.23 0.28 -10000 0 -0.76 56 56
DOK2 0.01 0.046 -10000 0 -0.58 3 3
ETS1 0.022 0.045 -10000 0 -0.46 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.21 -10000 0 -0.65 37 37
ITGB3 -0.57 0.6 -10000 0 -1.4 136 136
PIGR -0.6 0.6 -10000 0 -1.4 153 153
IGHE 0.038 0.035 0.26 1 -10000 0 1
MAPKKK cascade -0.17 0.2 -10000 0 -0.64 37 37
BCL6 0.014 0.004 -10000 0 -10000 0 0
OPRM1 -0.46 0.45 -10000 0 -1.2 93 93
RETNLB -0.46 0.45 -10000 0 -1.2 95 95
SELP -0.46 0.46 -10000 0 -1.2 94 94
AICDA -0.44 0.43 -10000 0 -1.1 95 95
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.042 0.17 -10000 0 -0.42 65 65
CRKL -0.033 0.17 -10000 0 -0.45 60 60
HRAS -0.019 0.18 -10000 0 -0.5 38 38
mol:PIP3 -0.039 0.15 -10000 0 -0.42 58 58
SPRED1 0.007 0.053 -10000 0 -0.47 6 6
SPRED2 0.008 0.049 -10000 0 -0.47 5 5
GAB1 -0.041 0.17 -10000 0 -0.48 60 60
FOXO3 -0.023 0.15 -10000 0 -0.4 60 60
AKT1 -0.032 0.16 -10000 0 -0.43 60 60
BAD -0.023 0.15 -10000 0 -0.4 61 61
megakaryocyte differentiation -0.051 0.18 -10000 0 -0.48 68 68
GSK3B -0.023 0.15 -10000 0 -0.4 60 60
RAF1 -0.005 0.14 -10000 0 -0.44 28 28
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.041 0.17 -10000 0 -0.47 60 60
STAT1 -0.12 0.38 -10000 0 -1 68 68
HRAS/SPRED1 -0.008 0.15 -10000 0 -0.43 34 34
cell proliferation -0.045 0.18 -10000 0 -0.48 62 62
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.04 0.18 -10000 0 -0.47 61 61
HRAS/SPRED2 -0.008 0.14 -10000 0 -0.44 30 30
LYN/TEC/p62DOK -0.025 0.16 -10000 0 -0.44 60 60
MAPK3 0.01 0.1 -10000 0 -0.3 26 26
STAP1 -0.11 0.22 -10000 0 -0.42 133 133
GRAP2 -0.008 0.1 -10000 0 -0.48 21 21
JAK2 -0.094 0.32 -10000 0 -0.85 68 68
STAT1 (dimer) -0.11 0.37 -10000 0 -0.98 68 68
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.037 0.18 -10000 0 -0.47 63 63
actin filament polymerization -0.052 0.18 -10000 0 -0.48 63 63
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.13 0.28 -10000 0 -0.67 83 83
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
CBL/CRKL/GRB2 -0.016 0.15 -10000 0 -0.4 59 59
PI3K -0.029 0.18 -10000 0 -0.46 62 62
PTEN 0 0.078 -10000 0 -0.47 13 13
SCF/KIT/EPO/EPOR -0.15 0.44 -10000 0 -1.2 62 62
MAPK8 -0.046 0.18 -10000 0 -0.49 62 62
STAT3 (dimer) -0.04 0.17 -10000 0 -0.46 60 60
positive regulation of transcription 0.013 0.088 -10000 0 -0.27 17 17
mol:GDP -0.024 0.18 -10000 0 -0.45 62 62
PIK3C2B -0.041 0.17 -10000 0 -0.47 60 60
CBL/CRKL -0.024 0.16 -10000 0 -0.42 60 60
FER -0.051 0.19 -10000 0 -0.49 68 68
SH2B3 -0.041 0.17 -10000 0 -0.47 60 60
PDPK1 -0.03 0.14 -10000 0 -0.39 55 55
SNAI2 -0.097 0.23 -10000 0 -0.59 73 73
positive regulation of cell proliferation -0.078 0.29 -10000 0 -0.76 68 68
KITLG -0.012 0.11 -10000 0 -0.5 24 24
cell motility -0.078 0.29 -10000 0 -0.76 68 68
PTPN6 0.014 0.009 -10000 0 -10000 0 0
EPOR -0.01 0.13 -10000 0 -0.46 1 1
STAT5A (dimer) -0.065 0.24 -10000 0 -0.62 72 72
SOCS1 0.009 0.051 -10000 0 -0.55 4 4
cell migration 0.17 0.24 0.37 242 -10000 0 242
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.067 0.19 -10000 0 -0.52 74 74
VAV1 -0.01 0.1 -10000 0 -0.48 23 23
GRB10 -0.041 0.17 -10000 0 -0.47 60 60
PTPN11 0.013 0.022 -10000 0 -0.46 1 1
SCF/KIT -0.05 0.18 -10000 0 -0.49 63 63
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.006 0.11 -10000 0 -0.34 26 26
CBL 0.012 0.022 -10000 0 -0.47 1 1
KIT -0.12 0.42 -10000 0 -1.3 58 58
MAP2K2 0.006 0.12 -10000 0 -0.34 26 26
SHC/Grb2/SOS1 -0.025 0.16 -10000 0 -0.44 60 60
STAT5A -0.068 0.25 -10000 0 -0.64 72 72
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.095 0.23 -10000 0 -0.57 73 73
SHC/GRAP2 0.004 0.073 -10000 0 -0.34 21 21
PTPRO -0.052 0.19 -10000 0 -0.48 68 68
SH2B2 -0.053 0.19 -10000 0 -0.49 63 63
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.18 0.24 -10000 0 -0.38 242 242
CREBBP 0.027 0.027 -10000 0 -10000 0 0
BCL2 -0.05 0.3 -10000 0 -1.3 23 23
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.089 0.16 -9999 0 -0.32 162 162
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.03 0.042 -9999 0 -10000 0 0
AURKB -0.18 0.28 -9999 0 -0.58 159 159
AURKC 0.009 0.049 -9999 0 -0.52 4 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.018 0.12 -9999 0 -0.36 48 48
alphaV beta3 Integrin -0.053 0.17 -9999 0 -0.36 101 101
PTK2 -0.1 0.24 -9999 0 -0.53 92 92
IGF1R 0.011 0.035 -9999 0 -0.52 2 2
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.01 0.038 -9999 0 -0.47 3 3
SRC 0.013 0 -9999 0 -10000 0 0
CDKN1B -0.083 0.19 -9999 0 -0.48 69 69
VEGFA -0.019 0.12 -9999 0 -0.49 31 31
ILK -0.083 0.19 -9999 0 -0.48 69 69
ROCK1 0.012 0.022 -9999 0 -0.47 1 1
AKT1 -0.07 0.18 -9999 0 -0.44 69 69
PTK2B -0.042 0.14 -9999 0 -0.48 26 26
alphaV/beta3 Integrin/JAM-A -0.091 0.2 -9999 0 -0.44 87 87
CBL 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.18 0.22 -9999 0 -0.38 244 244
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.01 0.12 -9999 0 -0.4 28 28
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.064 0.15 -9999 0 -0.4 57 57
alphaV/beta3 Integrin/Syndecan-1 -0.045 0.14 -9999 0 -0.29 110 110
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.095 0.2 -9999 0 -0.61 51 51
PI4 Kinase 0.02 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
alphaV/beta3 Integrin/Osteopontin -0.089 0.17 -9999 0 -0.32 160 160
RPS6KB1 -0.051 0.2 -9999 0 -0.56 51 51
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.11 0.28 -9999 0 -0.6 100 100
GPR124 -0.009 0.1 -9999 0 -0.47 22 22
MAPK1 -0.11 0.28 -9999 0 -0.6 100 100
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
alphaV/beta3 Integrin/Tumstatin -0.05 0.16 -9999 0 -0.33 106 106
cell adhesion -0.14 0.19 -9999 0 -0.56 47 47
ANGPTL3 -0.22 0.29 -9999 0 -0.58 191 191
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.1 -9999 0 -0.3 48 48
IGF-1R heterotetramer 0.011 0.034 -9999 0 -0.52 2 2
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
TGFBR2 -0.001 0.081 -9999 0 -0.47 14 14
ITGB3 -0.083 0.19 -9999 0 -0.47 97 97
IGF1 -0.046 0.17 -9999 0 -0.51 55 55
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.045 0.15 -9999 0 -0.33 97 97
apoptosis 0.011 0.031 -9999 0 -0.47 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.033 0.12 -9999 0 -0.53 2 2
VCL -0.016 0.12 -9999 0 -0.47 29 29
alphaV/beta3 Integrin/Del1 -0.089 0.2 -9999 0 -0.4 133 133
CSF1 0.003 0.069 -9999 0 -0.47 10 10
PIK3C2A -0.083 0.19 -9999 0 -0.48 69 69
PI4 Kinase/Pyk2 -0.12 0.18 -9999 0 -0.5 66 66
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.16 -9999 0 -0.48 30 30
FAK1/Vinculin -0.078 0.2 -9999 0 -0.49 70 70
alphaV beta3/Integrin/ppsTEM5 -0.045 0.15 -9999 0 -0.33 97 97
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.1 0.22 -9999 0 -0.52 104 104
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 -0.024 0.13 -9999 0 -0.47 37 37
F11R -0.006 0.093 -9999 0 -0.33 37 37
alphaV/beta3 Integrin/Lactadherin -0.035 0.13 -9999 0 -0.28 97 97
alphaV/beta3 Integrin/TGFBR2 -0.041 0.14 -9999 0 -0.31 97 97
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.027 0.046 -9999 0 -0.48 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.029 0.11 -9999 0 -0.25 97 97
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.002 0.086 -9999 0 -0.5 14 14
alphaV/beta3 Integrin/Pyk2 -0.04 0.15 -9999 0 -0.48 26 26
SDC1 -0.007 0.096 -9999 0 -0.47 20 20
VAV3 0.001 0.098 -9999 0 -0.48 7 7
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.086 -9999 0 -0.47 16 16
FAK1/Paxillin -0.071 0.19 -9999 0 -0.45 64 64
cell migration -0.063 0.19 -9999 0 -0.44 69 69
ITGAV 0.011 0.031 -9999 0 -0.47 2 2
PI3K -0.11 0.17 -9999 0 -0.52 52 52
SPP1 -0.076 0.21 -9999 0 -0.57 74 74
KDR -0.008 0.098 -9999 0 -0.47 21 21
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0.031 -9999 0 -0.47 2 2
COL4A3 -0.017 0.12 -9999 0 -0.48 30 30
angiogenesis -0.12 0.28 -9999 0 -0.6 101 101
Rac1/GTP 0.008 0.09 -9999 0 -0.44 7 7
EDIL3 -0.085 0.2 -9999 0 -0.47 98 98
cell proliferation -0.041 0.14 -9999 0 -0.31 97 97
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.003 0.16 -10000 0 -0.65 22 22
IHH -0.038 0.17 -10000 0 -0.53 52 52
SHH Np/Cholesterol/GAS1 -0.088 0.16 -10000 0 -0.3 167 167
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.087 0.16 0.3 167 -10000 0 167
SMO/beta Arrestin2 0.002 0.11 -10000 0 -0.45 15 15
SMO -0.005 0.12 -10000 0 -0.46 18 18
AKT1 0.014 0.08 -10000 0 -0.51 5 5
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0.001 0.075 -10000 0 -0.47 12 12
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.005 0.12 -10000 0 -0.46 18 18
STIL -0.064 0.17 -10000 0 -0.46 37 37
DHH N/PTCH2 0.008 0.067 -10000 0 -0.36 15 15
DHH N/PTCH1 0.004 0.11 -10000 0 -0.44 13 13
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
DHH 0.003 0.073 -10000 0 -0.5 10 10
PTHLH -0.003 0.2 -10000 0 -0.82 22 22
determination of left/right symmetry -0.005 0.12 -10000 0 -0.46 18 18
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
skeletal system development -0.002 0.2 -10000 0 -0.8 22 22
IHH N/Hhip -0.05 0.16 -10000 0 -0.38 91 91
DHH N/Hhip -0.024 0.12 -10000 0 -0.34 60 60
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.005 0.12 -10000 0 -0.46 18 18
pancreas development -0.037 0.15 -10000 0 -0.48 50 50
HHAT 0.005 0.062 -10000 0 -0.47 8 8
PI3K 0.014 0.048 -10000 0 -0.37 7 7
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.039 0.15 -10000 0 -0.47 52 52
somite specification -0.005 0.12 -10000 0 -0.46 18 18
SHH Np/Cholesterol/PTCH1 -0.059 0.16 -10000 0 -0.47 27 27
SHH Np/Cholesterol/PTCH2 -0.063 0.14 -10000 0 -0.28 138 138
SHH Np/Cholesterol/Megalin -0.091 0.16 -10000 0 -0.3 171 171
SHH -0.087 0.18 -10000 0 -0.37 135 135
catabolic process 0.004 0.12 -10000 0 -0.48 11 11
SMO/Vitamin D3 -0.05 0.16 -10000 0 -0.47 26 26
SHH Np/Cholesterol/Hhip -0.087 0.17 -10000 0 -0.32 157 157
LRP2 -0.043 0.16 -10000 0 -0.49 54 54
receptor-mediated endocytosis -0.065 0.17 -10000 0 -0.48 38 38
SHH Np/Cholesterol/BOC -0.066 0.14 -10000 0 -0.33 62 62
SHH Np/Cholesterol/CDO -0.064 0.14 -10000 0 -0.33 62 62
mesenchymal cell differentiation 0.086 0.17 0.32 157 -10000 0 157
mol:Vitamin D3 -0.057 0.16 -10000 0 -0.46 28 28
IHH N/PTCH2 -0.016 0.11 -10000 0 -0.32 56 56
CDON 0.006 0.063 -10000 0 -0.56 6 6
IHH N/PTCH1 0.005 0.12 -10000 0 -0.48 11 11
Megalin/LRPAP1 -0.021 0.12 -10000 0 -0.34 54 54
PTCH2 0.008 0.055 -10000 0 -0.53 5 5
SHH Np/Cholesterol -0.068 0.14 -10000 0 -0.28 135 135
PTCH1 0.004 0.12 -10000 0 -0.48 11 11
HHIP -0.037 0.15 -10000 0 -0.48 50 50
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.002 0.089 -10000 0 -0.3 37 37
fibroblast growth factor receptor signaling pathway 0.002 0.089 -10000 0 -0.3 37 37
LAMA1 -0.041 0.16 -10000 0 -0.53 48 48
PRNP 0.012 0.022 -10000 0 -0.47 1 1
GPC1/SLIT2 -0.024 0.12 -10000 0 -0.33 60 60
SMAD2 0.022 0.049 -10000 0 -0.48 1 1
GPC1/PrPc/Cu2+ 0.017 0.019 -10000 0 -0.28 2 2
GPC1/Laminin alpha1 -0.02 0.12 -10000 0 -0.38 48 48
TDGF1 -0.052 0.17 -10000 0 -0.48 63 63
CRIPTO/GPC1 -0.028 0.12 -10000 0 -0.34 64 64
APP/GPC1 0.017 0.036 -10000 0 -0.42 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.015 0.1 -10000 0 -0.28 64 64
FLT1 0.006 0.061 -10000 0 -0.5 7 7
GPC1/TGFB/TGFBR1/TGFBR2 0.018 0.054 -10000 0 -0.29 14 14
SERPINC1 -0.022 0.13 -10000 0 -0.58 27 27
FYN -0.015 0.1 -10000 0 -0.28 64 64
FGR -0.017 0.1 -10000 0 -0.28 67 67
positive regulation of MAPKKK cascade -0.036 0.14 -10000 0 -0.34 62 62
SLIT2 -0.047 0.16 -10000 0 -0.47 60 60
GPC1/NRG -0.08 0.16 -10000 0 -0.33 139 139
NRG1 -0.12 0.22 -10000 0 -0.47 138 138
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.002 0.09 -10000 0 -0.31 36 36
LYN -0.015 0.1 -10000 0 -0.28 64 64
mol:Spermine 0.01 0.016 -10000 0 -0.34 1 1
cell growth 0.002 0.089 -10000 0 -0.3 37 37
BMP signaling pathway -0.012 0.022 0.47 1 -10000 0 1
SRC -0.015 0.1 -10000 0 -0.28 64 64
TGFBR1 0.013 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.28 -10000 0 -0.56 183 183
GPC1 0.012 0.022 -10000 0 -0.47 1 1
TGFBR1 (dimer) 0.013 0 -10000 0 -10000 0 0
VEGFA -0.019 0.12 -10000 0 -0.49 31 31
BLK -0.086 0.17 -10000 0 -0.32 155 155
HCK -0.017 0.1 -10000 0 -0.28 68 68
FGF2 -0.024 0.13 -10000 0 -0.47 37 37
FGFR1 0.01 0.038 -10000 0 -0.47 3 3
VEGFR1 homodimer 0.006 0.061 -10000 0 -0.5 7 7
TGFBR2 -0.001 0.081 -10000 0 -0.47 14 14
cell death 0.017 0.036 -10000 0 -0.42 3 3
ATIII/GPC1 -0.007 0.1 -10000 0 -0.41 28 28
PLA2G2A/GPC1 -0.14 0.21 -10000 0 -0.4 184 184
LCK -0.021 0.11 -10000 0 -0.29 70 70
neuron differentiation -0.08 0.16 -10000 0 -0.33 139 139
PrPc/Cu2+ 0.009 0.016 -10000 0 -0.34 1 1
APP 0.01 0.038 -10000 0 -0.47 3 3
TGFBR2 (dimer) -0.001 0.081 -10000 0 -0.47 14 14
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.029 0.14 -10000 0 -0.68 19 19
NFATC2 -0.097 0.25 -10000 0 -0.66 44 44
NFATC3 -0.009 0.086 -10000 0 -10000 0 0
CD40LG -0.22 0.4 -10000 0 -0.99 70 70
ITCH -0.012 0.1 -10000 0 -10000 0 0
CBLB -0.012 0.1 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.4 -10000 0 -0.89 107 107
JUNB -0.016 0.12 -10000 0 -0.52 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.12 -10000 0 -10000 0 0
T cell anergy -0.076 0.18 -10000 0 -0.42 88 88
TLE4 -0.049 0.18 -10000 0 -0.66 17 17
Jun/NFAT1-c-4/p21SNFT -0.14 0.33 -10000 0 -0.88 49 49
AP-1/NFAT1-c-4 -0.23 0.45 -10000 0 -1.1 67 67
IKZF1 -0.063 0.21 -10000 0 -0.64 31 31
T-helper 2 cell differentiation -0.21 0.31 -10000 0 -0.79 69 69
AP-1/NFAT1 -0.11 0.23 -10000 0 -0.57 66 66
CALM1 -0.011 0.07 -10000 0 -10000 0 0
EGR2 -0.13 0.36 -10000 0 -0.94 52 52
EGR3 -0.15 0.4 -10000 0 -1.1 54 54
NFAT1/FOXP3 -0.094 0.24 -10000 0 -0.65 48 48
EGR1 -0.059 0.18 -10000 0 -0.51 66 66
JUN 0 0.065 -10000 0 -0.51 7 7
EGR4 -0.15 0.26 -10000 0 -0.58 130 130
mol:Ca2+ -0.026 0.073 -10000 0 -10000 0 0
GBP3 -0.1 0.27 -10000 0 -0.73 61 61
FOSL1 -0.11 0.22 -10000 0 -0.5 113 113
NFAT1-c-4/MAF/IRF4 -0.13 0.33 -10000 0 -0.89 51 51
DGKA -0.048 0.18 -10000 0 -0.63 18 18
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.32 -10000 0 -0.86 48 48
CTLA4 -0.11 0.28 -10000 0 -0.68 78 78
NFAT1-c-4 (dimer)/EGR1 -0.16 0.37 -10000 0 -0.93 66 66
NFAT1-c-4 (dimer)/EGR4 -0.21 0.36 -10000 0 -0.86 81 81
FOS -0.084 0.2 -10000 0 -0.5 88 88
IFNG -0.13 0.27 -10000 0 -0.73 50 50
T cell activation -0.086 0.22 -10000 0 -0.7 25 25
MAF 0.006 0.058 -10000 0 -0.47 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.081 0.23 0.68 25 -10000 0 25
TNF -0.22 0.38 -10000 0 -0.91 84 84
FASLG -0.19 0.45 -10000 0 -1.3 50 50
TBX21 -0.016 0.13 -10000 0 -0.56 26 26
BATF3 -0.017 0.13 -10000 0 -0.57 25 25
PRKCQ -0.03 0.15 -10000 0 -0.5 42 42
PTPN1 -0.048 0.18 -10000 0 -0.61 18 18
NFAT1-c-4/ICER1 -0.12 0.31 -10000 0 -0.85 46 46
GATA3 -0.13 0.22 -10000 0 -0.47 142 142
T-helper 1 cell differentiation -0.12 0.27 -10000 0 -0.71 51 51
IL2RA -0.26 0.33 -10000 0 -0.8 103 103
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.048 0.18 -10000 0 -0.61 18 18
E2F1 -0.008 0.12 -10000 0 -0.57 22 22
PPARG -0.017 0.12 -10000 0 -0.48 30 30
SLC3A2 -0.048 0.18 -10000 0 -0.64 15 15
IRF4 -0.036 0.16 -10000 0 -0.53 44 44
PTGS2 -0.24 0.42 -10000 0 -1 80 80
CSF2 -0.21 0.38 -10000 0 -0.96 64 64
JunB/Fra1/NFAT1-c-4 -0.18 0.36 -10000 0 -0.95 58 58
IL4 -0.22 0.32 -10000 0 -0.83 69 69
IL5 -0.21 0.38 -10000 0 -0.95 66 66
IL2 -0.087 0.22 -10000 0 -0.71 25 25
IL3 -0.046 0.053 -10000 0 -10000 0 0
RNF128 -0.091 0.25 -10000 0 -0.54 111 111
NFATC1 -0.081 0.23 -10000 0 -0.69 25 25
CDK4 0.074 0.18 0.59 8 -10000 0 8
PTPRK -0.048 0.18 -10000 0 -0.61 18 18
IL8 -0.23 0.41 -10000 0 -0.98 81 81
POU2F1 0.012 0.027 -10000 0 -0.58 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.069 0.19 -9999 0 -0.5 55 55
MAP3K8 -0.001 0.08 -9999 0 -0.48 13 13
FOS -0.056 0.16 -9999 0 -0.4 57 57
PRKCA -0.008 0.096 -9999 0 -0.47 20 20
PTPN7 -0.014 0.12 -9999 0 -0.58 22 22
HRAS 0.007 0.059 -9999 0 -0.58 5 5
PRKCB -0.099 0.2 -9999 0 -0.47 111 111
NRAS 0.012 0.022 -9999 0 -0.48 1 1
RAS family/GTP 0.018 0.038 -9999 0 -0.31 6 6
MAPK3 -0.027 0.091 -9999 0 -0.27 12 12
MAP2K1 -0.091 0.24 -9999 0 -0.48 113 113
ELK1 0.011 0.008 -9999 0 -10000 0 0
BRAF -0.087 0.22 -9999 0 -0.46 113 113
mol:GTP -0.001 0.002 -9999 0 -0.005 86 86
MAPK1 -0.027 0.091 -9999 0 -0.25 22 22
RAF1 -0.086 0.22 -9999 0 -0.45 113 113
KRAS 0.013 0.001 -9999 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.002 0.076 -10000 0 -0.55 9 9
GNB1/GNG2 -0.058 0.078 -10000 0 -0.19 84 84
AKT1 -0.023 0.11 -10000 0 -0.21 32 32
EGF -0.056 0.18 -10000 0 -0.54 61 61
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.006 0.076 -10000 0 -0.32 7 7
mol:Ca2+ -0.054 0.15 -10000 0 -0.29 117 117
LYN 0.008 0.073 -10000 0 -0.31 5 5
RhoA/GTP -0.036 0.052 -10000 0 -0.14 4 4
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.061 0.18 -10000 0 -0.34 117 117
GNG2 0.008 0.049 -10000 0 -0.47 5 5
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.003 0.11 -10000 0 -0.35 40 40
G beta5/gamma2 -0.075 0.1 -10000 0 -0.26 85 85
PRKCH -0.062 0.17 -10000 0 -0.33 117 117
DNM1 0.011 0.035 -10000 0 -0.52 2 2
TXA2/TP beta/beta Arrestin3 -0.007 0.018 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.023 0.13 -10000 0 -0.47 36 36
G12 family/GTP -0.089 0.12 -10000 0 -0.3 116 116
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.022 -10000 0 -0.47 1 1
RhoA/GTP/ROCK1 0.017 0.013 -10000 0 -0.28 1 1
mol:GDP 0.035 0.11 0.29 33 -10000 0 33
mol:NADP 0.005 0.07 -10000 0 -0.57 7 7
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.13 0.22 -10000 0 -0.47 139 139
mol:IP3 -0.072 0.18 -10000 0 -0.37 117 117
cell morphogenesis 0.017 0.013 -10000 0 -0.28 1 1
PLCB2 -0.1 0.24 -10000 0 -0.49 117 117
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.045 0.12 -10000 0 -0.34 36 36
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.006 0.078 -10000 0 -0.35 7 7
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR -0.044 0.17 -10000 0 -0.57 48 48
PRKCB1 -0.071 0.18 -10000 0 -0.36 117 117
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.005 0.07 -10000 0 -0.57 7 7
TXA2/TXA2-R family -0.11 0.25 -10000 0 -0.52 118 118
LCK 0.003 0.084 -10000 0 -0.34 11 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.025 0.079 -10000 0 -0.38 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.017 0.034 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.004 0.083 -10000 0 -0.38 5 5
MAPK14 -0.032 0.12 -10000 0 -0.24 39 39
TGM2/GTP -0.086 0.21 -10000 0 -0.42 117 117
MAPK11 -0.035 0.12 -10000 0 -0.23 81 81
ARHGEF1 -0.024 0.094 -10000 0 -0.19 19 19
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.073 0.19 -10000 0 -0.38 118 118
RAB11/GDP 0.013 0.002 -10000 0 -10000 0 0
ICAM1 -0.048 0.14 -10000 0 -0.28 119 119
cAMP biosynthetic process -0.072 0.18 -10000 0 -0.35 117 117
Gq family/GTP/EBP50 0.007 0.066 -10000 0 -0.21 40 40
actin cytoskeleton reorganization 0.017 0.013 -10000 0 -0.28 1 1
SRC 0.008 0.073 -10000 0 -0.31 5 5
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.01 0.089 -10000 0 -0.26 15 15
VCAM1 -0.052 0.15 -10000 0 -0.29 116 116
TP beta/Gq family/GDP/G beta5/gamma2 -0.003 0.11 -10000 0 -0.35 40 40
platelet activation -0.044 0.16 -10000 0 -0.3 116 116
PGI2/IP -0.032 0.13 -10000 0 -0.42 48 48
PRKACA -0.02 0.09 -10000 0 -0.22 83 83
Gq family/GDP/G beta5/gamma2 -0.003 0.1 -10000 0 -0.33 40 40
TXA2/TP beta/beta Arrestin2 -0.005 0.023 -10000 0 -0.45 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.017 0.094 -10000 0 -0.41 6 6
mol:DAG -0.08 0.2 -10000 0 -0.41 117 117
EGFR -0.026 0.13 -10000 0 -0.47 39 39
TXA2/TP alpha -0.1 0.23 -10000 0 -0.48 117 117
Gq family/GTP -0.01 0.052 -10000 0 -0.18 27 27
YES1 0.008 0.073 -10000 0 -0.31 5 5
GNAI2/GTP -0.03 0.066 -10000 0 -0.35 5 5
PGD2/DP -0.016 0.092 -10000 0 -0.34 36 36
SLC9A3R1 0.013 0 -10000 0 -10000 0 0
FYN 0.008 0.073 -10000 0 -0.31 5 5
mol:NO 0.005 0.07 -10000 0 -0.57 7 7
GNA15 -0.011 0.1 -10000 0 -0.47 24 24
PGK/cGMP -0.072 0.14 -10000 0 -0.28 146 146
RhoA/GDP 0.013 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.003 0.095 -10000 0 -0.41 6 6
NOS3 0.005 0.07 -10000 0 -0.58 7 7
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.067 0.18 -10000 0 -0.35 117 117
PRKCB -0.093 0.2 -10000 0 -0.4 121 121
PRKCE -0.06 0.17 -10000 0 -0.34 109 109
PRKCD -0.07 0.18 -10000 0 -0.37 117 117
PRKCG -0.075 0.19 -10000 0 -0.38 117 117
muscle contraction -0.098 0.24 -10000 0 -0.48 118 118
PRKCZ -0.059 0.17 -10000 0 -0.34 116 116
ARR3 0.002 0.038 -10000 0 -0.58 2 2
TXA2/TP beta -0.009 0.086 -10000 0 -0.4 5 5
PRKCQ -0.073 0.18 -10000 0 -0.36 120 120
MAPKKK cascade -0.095 0.22 -10000 0 -0.45 118 118
SELE -0.078 0.19 -10000 0 -0.39 119 119
TP beta/GNAI2/GDP/G beta/gamma 0.003 0.09 -10000 0 -0.41 6 6
ROCK1 0.012 0.022 -10000 0 -0.47 1 1
GNA14 0.012 0.022 -10000 0 -0.47 1 1
chemotaxis -0.12 0.28 -10000 0 -0.6 118 118
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.086 -10000 0 -0.47 16 16
Rac1/GTP 0.008 0.004 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.058 0.22 -9999 0 -0.68 19 19
CRP -0.077 0.24 -9999 0 -0.71 28 28
cell cycle arrest -0.075 0.25 -9999 0 -0.67 39 39
TIMP1 -0.052 0.22 -9999 0 -0.74 17 17
IL6ST -0.085 0.2 -9999 0 -0.47 100 100
Rac1/GDP -0.11 0.23 -9999 0 -0.48 100 100
AP1 -0.017 0.14 -9999 0 -0.5 10 10
GAB2 0.014 0.002 -9999 0 -10000 0 0
TNFSF11 -0.068 0.24 -9999 0 -0.78 22 22
HSP90B1 0.018 0.044 -9999 0 -10000 0 0
GAB1 0.013 0.022 -9999 0 -0.47 1 1
MAPK14 -0.15 0.3 -9999 0 -0.64 107 107
AKT1 0.044 0.057 -9999 0 -1 1 1
FOXO1 0.049 0.053 -9999 0 -0.94 1 1
MAP2K6 -0.14 0.27 -9999 0 -0.56 112 112
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.087 0.23 -9999 0 -0.52 75 75
MITF -0.11 0.23 -9999 0 -0.47 111 111
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.016 0.05 -9999 0 -10000 0 0
CEBPB 0.02 0.002 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.016 0.086 -9999 0 -0.41 2 2
STAT3 -0.076 0.26 -9999 0 -0.71 39 39
STAT1 -0.009 0.026 -9999 0 -10000 0 0
CEBPD -0.063 0.23 -9999 0 -0.73 23 23
PIK3CA 0.012 0.038 -9999 0 -0.47 3 3
PI3K 0.017 0.048 -9999 0 -0.37 7 7
JUN 0.006 0.062 -9999 0 -0.5 7 7
PIAS3/MITF -0.1 0.22 -9999 0 -0.46 104 104
MAPK11 -0.16 0.31 -9999 0 -0.65 110 110
STAT3 (dimer)/FOXO1 -0.014 0.2 -9999 0 -0.57 15 15
GRB2/SOS1/GAB family -0.11 0.17 -9999 0 -0.47 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.22 -9999 0 -0.45 112 112
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 0.012 0.022 -9999 0 -0.47 1 1
LBP -0.053 0.2 -9999 0 -0.64 15 15
PIK3R1 0.009 0.049 -9999 0 -0.47 5 5
JAK1 0.013 0.006 -9999 0 -10000 0 0
MYC -0.073 0.24 -9999 0 -0.73 21 21
FGG -0.072 0.23 -9999 0 -0.69 26 26
macrophage differentiation -0.075 0.25 -9999 0 -0.67 39 39
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.21 -9999 0 -0.46 92 92
JUNB -0.074 0.26 -9999 0 -0.82 30 30
FOS -0.076 0.19 -9999 0 -0.48 88 88
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.13 0.24 -9999 0 -0.49 116 116
STAT1/PIAS1 -0.093 0.2 -9999 0 -0.46 78 78
GRB2/SOS1/GAB family/SHP2/PI3K 0.034 0.06 -9999 0 -1.1 1 1
STAT3 (dimer) -0.073 0.26 -9999 0 -0.7 39 39
PRKCD -0.071 0.24 -9999 0 -0.57 52 52
IL6R -0.022 0.13 -9999 0 -0.47 36 36
SOCS3 -0.2 0.42 -9999 0 -1 82 82
gp130 (dimer)/JAK1/JAK1/LMO4 -0.032 0.13 -9999 0 -0.29 61 61
Rac1/GTP -0.1 0.23 -9999 0 -0.52 84 84
HCK 0.009 0.046 -9999 0 -0.5 4 4
MAPKKK cascade 0.009 0.074 -9999 0 -0.85 1 1
bone resorption -0.064 0.23 -9999 0 -0.72 23 23
IRF1 -0.063 0.23 -9999 0 -0.74 20 20
mol:GDP -0.12 0.24 -9999 0 -0.49 114 114
SOS1 0.014 0.002 -9999 0 -10000 0 0
VAV1 -0.12 0.24 -9999 0 -0.5 114 114
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.31 -9999 0 -0.67 110 110
PTPN11 -0.008 0.047 -9999 0 -1 1 1
IL6/IL6RA -0.12 0.2 -9999 0 -0.38 180 180
gp130 (dimer)/TYK2/TYK2/LMO4 -0.034 0.12 -9999 0 -0.28 63 63
gp130 (dimer)/JAK2/JAK2/LMO4 -0.034 0.12 -9999 0 -0.29 44 44
IL6 -0.15 0.25 -9999 0 -0.51 155 155
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE 0.007 0.042 -9999 0 -0.5 3 3
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
RAC1 0.014 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.21 -9999 0 -0.43 118 118
LMO4 0.014 0.026 -9999 0 -0.51 1 1
STAT3 (dimer)/PIAS3 -0.078 0.25 -9999 0 -0.68 37 37
MCL1 0.049 0.049 -9999 0 -0.85 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.003 0.11 -9999 0 -0.48 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.12 -9999 0 -0.39 11 11
AP1 -0.099 0.16 -9999 0 -0.5 50 50
mol:PIP3 -0.069 0.14 -9999 0 -0.43 42 42
AKT1 0.027 0.084 -9999 0 -0.34 12 12
PTK2B -0.006 0.09 -9999 0 -0.3 29 29
RHOA 0.018 0.034 -9999 0 -0.29 1 1
PIK3CB 0.012 0.027 -9999 0 -0.57 1 1
mol:Ca2+ -0.011 0.11 -9999 0 -0.34 21 21
MAGI3 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.047 0.15 -9999 0 -0.3 108 108
HRAS/GDP 0.005 0.044 -9999 0 -0.42 5 5
positive regulation of microtubule depolymerization 0.006 0.082 -9999 0 -0.3 17 17
NF kappa B1 p50/RelA -0.059 0.12 -9999 0 -0.46 22 22
endothelial cell migration -0.018 0.14 -9999 0 -0.67 16 16
ADCY4 -0.056 0.22 -9999 0 -0.56 67 67
ADCY5 -0.096 0.3 -9999 0 -0.69 83 83
ADCY6 -0.055 0.22 -9999 0 -0.55 67 67
ADCY7 -0.055 0.22 -9999 0 -0.55 67 67
ADCY1 -0.066 0.22 -9999 0 -0.55 70 70
ADCY2 -0.066 0.24 -9999 0 -0.57 74 74
ADCY3 -0.055 0.22 -9999 0 -0.55 67 67
ADCY8 -0.059 0.22 -9999 0 -0.55 67 67
ADCY9 -0.056 0.22 -9999 0 -0.55 67 67
GSK3B 0.001 0.086 -9999 0 -0.31 22 22
arachidonic acid secretion -0.055 0.22 -9999 0 -0.54 68 68
GNG2 0.008 0.049 -9999 0 -0.47 5 5
TRIP6 0.017 0.047 -9999 0 -0.36 7 7
GNAO1 -0.062 0.19 -9999 0 -0.4 99 99
HRAS 0.007 0.059 -9999 0 -0.58 5 5
NFKBIA -0.016 0.13 -9999 0 -0.38 25 25
GAB1 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.071 -9999 0 -0.88 3 3
JUN 0.006 0.062 -9999 0 -0.5 7 7
LPA/LPA2/NHERF2 0.014 0.042 -9999 0 -0.34 6 6
TIAM1 -0.005 0.081 -9999 0 -1 3 3
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
mol:IP3 -0.012 0.11 -9999 0 -0.35 21 21
PLCB3 0.02 0.038 -9999 0 -0.31 6 6
FOS -0.076 0.19 -9999 0 -0.48 88 88
positive regulation of mitosis -0.055 0.22 -9999 0 -0.54 68 68
LPA/LPA1-2-3 -0.044 0.15 -9999 0 -0.47 28 28
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation -0.012 0.11 -9999 0 -0.38 23 23
GNAZ -0.035 0.16 -9999 0 -0.38 70 70
EGFR/PI3K-beta/Gab1 -0.072 0.14 -9999 0 -0.45 42 42
positive regulation of dendritic cell cytokine production -0.045 0.15 -9999 0 -0.47 28 28
LPA/LPA2/MAGI-3 0.018 0.019 -9999 0 -0.31 1 1
ARHGEF1 0.006 0.091 -9999 0 -0.43 9 9
GNAI2 -0.009 0.11 -9999 0 -0.31 49 49
GNAI3 -0.009 0.11 -9999 0 -0.3 51 51
GNAI1 -0.014 0.12 -9999 0 -0.32 55 55
LPA/LPA3 -0.046 0.13 -9999 0 -0.34 78 78
LPA/LPA2 0.01 0.023 -9999 0 -0.38 1 1
LPA/LPA1 -0.022 0.12 -9999 0 -0.36 52 52
HB-EGF/EGFR -0.21 0.2 -9999 0 -0.37 286 286
HBEGF -0.23 0.22 -9999 0 -0.42 274 274
mol:DAG -0.012 0.11 -9999 0 -0.35 21 21
cAMP biosynthetic process -0.069 0.24 -9999 0 -0.6 71 71
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
LYN -0.016 0.13 -9999 0 -0.38 25 25
GNAQ -0.022 0.099 -9999 0 -0.24 79 79
LPAR2 0.012 0.022 -9999 0 -0.47 1 1
LPAR3 -0.066 0.18 -9999 0 -0.48 78 78
LPAR1 -0.032 0.15 -9999 0 -0.5 45 45
IL8 -0.15 0.19 -9999 0 -0.46 105 105
PTK2 -0.035 0.14 -9999 0 -0.44 28 28
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
CASP3 -0.047 0.15 -9999 0 -0.3 108 108
EGFR -0.026 0.13 -9999 0 -0.47 39 39
PLCG1 -0.027 0.12 -9999 0 -0.29 73 73
PLD2 -0.035 0.14 -9999 0 -0.44 28 28
G12/G13 0.001 0.098 -9999 0 -0.46 9 9
PI3K-beta -0.025 0.078 -9999 0 -0.38 15 15
cell migration 0.011 0.067 -9999 0 -0.24 8 8
SLC9A3R2 0.007 0.059 -9999 0 -0.58 5 5
PXN -0.013 0.11 -9999 0 -0.38 23 23
HRAS/GTP -0.058 0.23 -9999 0 -0.56 68 68
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 270 270
PRKCE 0.013 0 -9999 0 -10000 0 0
PRKCD -0.005 0.1 -9999 0 -0.34 19 19
Gi(beta/gamma) -0.05 0.21 -9999 0 -0.53 67 67
mol:LPA 0 0.024 -9999 0 -0.17 7 7
TRIP6/p130 Cas/FAK1/Paxillin -0.056 0.12 -9999 0 -0.46 25 25
MAPKKK cascade -0.055 0.22 -9999 0 -0.54 68 68
contractile ring contraction involved in cytokinesis 0.018 0.034 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.022 0.1 -9999 0 -0.25 79 79
GNA15 -0.035 0.12 -9999 0 -0.27 95 95
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.006 0.084 -9999 0 -0.3 17 17
GNA11 -0.031 0.12 -9999 0 -0.27 87 87
Rac1/GTP 0.02 0.075 -9999 0 -0.93 3 3
MMP2 -0.018 0.14 -9999 0 -0.67 16 16
PLK1 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
regulation of centriole-centriole cohesion 0.03 0.073 0.17 102 -10000 0 102
BUB1B -0.056 0.12 -10000 0 -0.25 130 130
PLK1 -0.011 0.048 -10000 0 -0.14 35 35
PLK1S1 0 0.025 -10000 0 -0.13 2 2
KIF2A -0.003 0.045 -10000 0 -0.25 3 3
regulation of mitotic centrosome separation -0.011 0.048 -10000 0 -0.14 35 35
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.084 0.17 -10000 0 -0.34 141 141
WEE1 -0.003 0.05 -10000 0 -0.28 4 4
cytokinesis -0.1 0.15 -10000 0 -0.27 190 190
PP2A-alpha B56 0.001 0.069 -10000 0 -0.6 1 1
AURKA -0.006 0.043 -10000 0 -0.15 35 35
PICH/PLK1 -0.024 0.14 -10000 0 -0.44 43 43
CENPE -0.044 0.14 -10000 0 -0.4 62 62
RhoA/GTP 0.01 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.045 -10000 0 -0.25 3 3
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.013 0 -10000 0 -10000 0 0
TPX2 -0.032 0.067 -10000 0 -0.13 136 136
PAK1 0.007 0.055 -10000 0 -0.48 6 6
SPC24 -0.15 0.26 -10000 0 -0.58 138 138
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN -0.018 0.065 -10000 0 -0.17 67 67
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase -0.002 0.005 -10000 0 -0.011 103 103
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.005 0.025 -10000 0 -0.068 35 35
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.009 19 19
STAG2 0.013 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.009 -10000 0 -10000 0 0
spindle elongation -0.011 0.048 -10000 0 -0.14 35 35
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.03 0.067 -10000 0 -0.66 1 1
TPT1 0 0.025 -10000 0 -0.13 2 2
CDC25C -0.062 0.085 -10000 0 -0.16 157 157
CDC25B 0.011 0.035 -10000 0 -0.53 2 2
SGOL1 -0.03 0.073 -10000 0 -0.17 102 102
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.022 0.071 -10000 0 -0.32 23 23
CDC14B 0.007 0.036 -10000 0 -0.34 5 5
CDC20 -0.19 0.28 -10000 0 -0.58 164 164
PLK1/PBIP1 -0.037 0.12 -10000 0 -0.39 48 48
mitosis 0.001 0.006 0.021 32 -0.021 3 35
FBXO5 0 0.037 -10000 0 -0.19 3 3
CDC2 0 0.004 -10000 0 -0.014 24 24
NDC80 0.01 0.038 -10000 0 -0.47 3 3
metaphase plate congression -0.004 0.031 -10000 0 -0.14 2 2
ERCC6L -0.019 0.13 -10000 0 -0.41 43 43
NLP/gamma Tubulin -0.003 0.027 -10000 0 -0.13 3 3
microtubule cytoskeleton organization 0 0.025 -10000 0 -0.13 2 2
G2/M transition DNA damage checkpoint 0 0.001 0.009 4 -10000 0 4
PPP1R12A 0.013 0.001 -10000 0 -10000 0 0
interphase 0 0.001 0.009 4 -10000 0 4
PLK1/PRC1-2 -0.13 0.22 -10000 0 -0.38 185 185
GRASP65/GM130/RAB1/GTP/PLK1 0.011 0.038 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.04 -10000 0 -0.22 3 3
mitotic prometaphase -0.002 0.003 -10000 0 -0.009 19 19
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.062 -10000 0 -0.3 4 4
microtubule-based process -0.13 0.19 -10000 0 -0.36 185 185
Golgi organization -0.011 0.048 -10000 0 -0.14 35 35
Cohesin/SA2 -0.006 0.043 -10000 0 -0.23 2 2
PPP1CB/MYPT1 0.019 0.002 -10000 0 -10000 0 0
KIF20A -0.21 0.29 -10000 0 -0.58 185 185
APC/C/CDC20 -0.11 0.19 -10000 0 -0.37 164 164
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation -0.036 0.12 -10000 0 -0.38 48 48
PRC1 -0.02 0.14 -10000 0 -0.58 27 27
ECT2 -0.013 0.082 -10000 0 -0.39 17 17
C13orf34 -0.002 0.04 -10000 0 -0.22 3 3
NUDC -0.004 0.031 -10000 0 -0.14 2 2
regulation of attachment of spindle microtubules to kinetochore -0.055 0.12 -10000 0 -0.24 130 130
spindle assembly -0.006 0.038 -10000 0 -0.12 19 19
spindle stabilization 0 0.025 -10000 0 -0.13 2 2
APC/C/HCDH1 0.014 0.03 -10000 0 -0.28 5 5
MKLP2/PLK1 -0.13 0.19 -10000 0 -0.37 185 185
CCNB1 -0.013 0.12 -10000 0 -0.58 22 22
PPP1CB 0.013 0.001 -10000 0 -10000 0 0
BTRC 0.013 0 -10000 0 -10000 0 0
ROCK2 -0.032 0.12 -10000 0 -0.4 43 43
TUBG1 0 0.025 -10000 0 -0.13 2 2
G2/M transition of mitotic cell cycle -0.023 0.069 -10000 0 -0.32 23 23
MLF1IP -0.036 0.13 -10000 0 -0.44 48 48
INCENP 0.013 0.002 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.01 0.097 -9999 0 -0.38 23 23
alphaM/beta2 Integrin/GPIbA -0.008 0.095 -9999 0 -0.39 20 20
alphaM/beta2 Integrin/proMMP-9 -0.2 0.2 -9999 0 -0.37 271 271
PLAUR 0.003 0.075 -9999 0 -0.58 8 8
HMGB1 0 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0 0.073 -9999 0 -0.42 10 10
AGER -0.027 0.12 -9999 0 -0.59 22 22
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.006 0.065 -9999 0 -0.58 6 6
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.05 0.14 -9999 0 -0.53 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 270 270
CYR61 -0.006 0.1 -9999 0 -0.51 18 18
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.065 0.098 -9999 0 -0.33 32 32
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer 0.004 0.065 -9999 0 -0.47 9 9
MYH2 -0.13 0.17 -9999 0 -0.42 85 85
MST1R -0.006 0.096 -9999 0 -0.49 18 18
leukocyte activation during inflammatory response -0.1 0.15 -9999 0 -0.35 83 83
APOB -0.1 0.21 -9999 0 -0.47 117 117
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.003 0.088 -9999 0 -0.48 16 16
JAM3 -0.006 0.094 -9999 0 -0.47 19 19
GP1BA 0 0.079 -9999 0 -0.5 12 12
alphaM/beta2 Integrin/CTGF -0.013 0.096 -9999 0 -0.38 21 21
alphaM/beta2 Integrin -0.068 0.13 -9999 0 -0.36 45 45
JAM3 homodimer -0.006 0.094 -9999 0 -0.47 19 19
ICAM2 0.01 0.041 -9999 0 -0.51 3 3
ICAM1 0 0.088 -9999 0 -0.58 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.068 0.13 -9999 0 -0.35 45 45
cell adhesion -0.008 0.094 -9999 0 -0.39 20 20
NFKB1 -0.09 0.21 -9999 0 -0.61 32 32
THY1 0.003 0.075 -9999 0 -0.58 8 8
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.093 0.17 -9999 0 -0.32 161 161
alphaM/beta2 Integrin/LRP/tPA -0.01 0.1 -9999 0 -0.36 35 35
IL6 -0.18 0.33 -9999 0 -0.7 119 119
ITGB2 -0.009 0.075 -9999 0 -0.6 7 7
elevation of cytosolic calcium ion concentration -0.004 0.1 -9999 0 -0.39 21 21
alphaM/beta2 Integrin/JAM2/JAM3 -0.005 0.098 -9999 0 -0.39 21 21
JAM2 0.006 0.058 -9999 0 -0.47 7 7
alphaM/beta2 Integrin/ICAM1 -0.041 0.15 -9999 0 -0.39 38 38
alphaM/beta2 Integrin/uPA/Plg -0.02 0.11 -9999 0 -0.35 38 38
RhoA/GTP -0.08 0.15 -9999 0 -0.4 49 49
positive regulation of phagocytosis -0.056 0.096 -9999 0 -0.42 15 15
Ron/MSP -0.049 0.16 -9999 0 -0.41 77 77
alphaM/beta2 Integrin/uPAR/uPA -0.004 0.1 -9999 0 -0.39 21 21
alphaM/beta2 Integrin/uPAR -0.006 0.093 -9999 0 -0.43 17 17
PLAU 0 0.08 -9999 0 -0.48 13 13
PLAT -0.018 0.13 -9999 0 -0.55 27 27
actin filament polymerization -0.13 0.17 -9999 0 -0.4 85 85
MST1 -0.062 0.2 -9999 0 -0.58 62 62
alphaM/beta2 Integrin/lipoprotein(a) -0.087 0.16 -9999 0 -0.34 92 92
TNF -0.1 0.25 -9999 0 -0.72 47 47
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.008 0.093 -9999 0 -0.37 22 22
fibrinolysis -0.02 0.11 -9999 0 -0.35 38 38
HCK 0.009 0.046 -9999 0 -0.5 4 4
dendritic cell antigen processing and presentation -0.068 0.13 -9999 0 -0.35 45 45
VTN -0.1 0.22 -9999 0 -0.52 104 104
alphaM/beta2 Integrin/CYR61 -0.012 0.1 -9999 0 -0.39 25 25
LPA -0.055 0.17 -9999 0 -0.48 66 66
LRP1 0.01 0.041 -9999 0 -0.51 3 3
cell migration -0.19 0.18 -9999 0 -0.34 272 272
FN1 -0.002 0.086 -9999 0 -0.5 14 14
alphaM/beta2 Integrin/Thy1 -0.006 0.09 -9999 0 -0.43 15 15
MPO -0.027 0.13 -9999 0 -0.47 40 40
KNG1 -0.067 0.19 -9999 0 -0.58 60 60
RAP1/GDP 0.018 0 -9999 0 -10000 0 0
ROCK1 -0.07 0.14 -9999 0 -0.4 40 40
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.023 0.13 -9999 0 -0.58 24 24
CTGF -0.007 0.097 -9999 0 -0.48 20 20
alphaM/beta2 Integrin/Hck -0.003 0.083 -9999 0 -0.41 13 13
ITGAM -0.006 0.059 -9999 0 -0.53 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0 0.098 -9999 0 -0.44 15 15
HP -0.076 0.2 -9999 0 -0.54 78 78
leukocyte adhesion -0.072 0.12 -9999 0 -0.43 30 30
SELP 0.004 0.065 -9999 0 -0.47 9 9
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.002 0.094 -9999 0 -0.42 24 24
VLDLR 0.012 0.022 -9999 0 -0.47 1 1
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0.001 -9999 0 -10000 0 0
ITGA3 0.003 0.069 -9999 0 -0.47 10 10
RELN/VLDLR/Fyn -0.034 0.14 -9999 0 -0.35 74 74
MAPK8IP1/MKK7/MAP3K11/JNK1 0.033 0.04 -9999 0 -10000 0 0
AKT1 -0.086 0.14 -9999 0 -0.38 47 47
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.17 0.24 -9999 0 -0.47 187 187
RELN/LRP8/DAB1 -0.14 0.19 -9999 0 -0.32 226 226
LRPAP1/LRP8 0.013 0.052 -9999 0 -0.42 7 7
RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.43 79 79
DAB1/alpha3/beta1 Integrin -0.12 0.16 -9999 0 -0.52 47 47
long-term memory -0.16 0.22 -9999 0 -0.54 85 85
DAB1/LIS1 -0.13 0.16 -9999 0 -0.51 46 46
DAB1/CRLK/C3G -0.12 0.15 -9999 0 -0.49 46 46
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
DAB1/NCK2 -0.13 0.16 -9999 0 -0.51 46 46
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.093 0.2 -9999 0 -0.47 106 106
CDK5R1 -0.016 0.13 -9999 0 -0.58 24 24
RELN -0.081 0.22 -9999 0 -0.57 79 79
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
RELN/LRP8/Fyn -0.038 0.15 -9999 0 -0.36 83 83
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.23 -9999 0 -0.56 84 84
MAPK8 0.002 0.072 -9999 0 -0.47 11 11
RELN/VLDLR/DAB1 -0.13 0.19 -9999 0 -0.45 78 78
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.14 0.2 -9999 0 -0.55 63 63
RELN/LRP8 -0.038 0.15 -9999 0 -0.36 83 83
GRIN2B/RELN/LRP8/DAB1/Fyn -0.12 0.19 -9999 0 -0.54 46 46
PI3K 0.014 0.048 -9999 0 -0.37 7 7
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.012 0.049 -9999 0 -0.33 10 10
RAP1A -0.085 0.16 -9999 0 -0.46 46 46
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.027 -9999 0 -0.58 1 1
CRLK/C3G 0.02 0 -9999 0 -10000 0 0
GRIN2B 0.002 0.027 -9999 0 -0.58 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.065 0.12 -9999 0 -0.3 49 49
neuron adhesion -0.074 0.17 -9999 0 -0.46 45 45
LRP8 0.005 0.07 -9999 0 -0.58 7 7
GSK3B -0.076 0.14 -9999 0 -0.35 47 47
RELN/VLDLR/DAB1/Fyn -0.12 0.18 -9999 0 -0.42 76 76
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.099 0.15 -9999 0 -0.4 47 47
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.02 0.043 -9999 0 -0.41 3 3
neuron migration -0.088 0.17 -9999 0 -0.41 54 54
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.065 0.12 -9999 0 -0.3 49 49
RELN/VLDLR -0.026 0.14 -9999 0 -0.32 78 78
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.15 0.33 -10000 0 -0.9 44 44
PCK1 -0.14 0.25 -10000 0 -0.72 39 39
HNF4A -0.19 0.4 -10000 0 -1.2 42 42
KCNJ11 -0.15 0.35 -10000 0 -0.94 42 42
AKT1 -0.031 0.13 -10000 0 -0.44 7 7
response to starvation -0.006 0.02 -10000 0 -10000 0 0
DLK1 -0.2 0.39 -10000 0 -0.93 73 73
NKX2-1 -0.15 0.26 0.48 1 -0.66 41 42
ACADM -0.15 0.33 -10000 0 -0.92 44 44
TAT -0.14 0.26 -10000 0 -0.82 36 36
CEBPB 0.007 0.015 -10000 0 -10000 0 0
CEBPA 0.01 0.013 -10000 0 -10000 0 0
TTR -0.21 0.35 -10000 0 -0.89 68 68
PKLR -0.18 0.36 -10000 0 -0.94 54 54
APOA1 -0.22 0.44 -10000 0 -1.2 54 54
CPT1C -0.16 0.34 -10000 0 -0.94 49 49
ALAS1 -0.043 0.16 -10000 0 -10000 0 0
TFRC -0.15 0.29 -10000 0 -0.8 45 45
FOXF1 0.002 0.14 -10000 0 -0.45 41 41
NF1 0.02 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.059 0.19 -10000 0 -0.58 57 57
CPT1A -0.15 0.33 -10000 0 -0.92 41 41
HMGCS1 -0.15 0.33 -10000 0 -0.94 38 38
NR3C1 -0.001 0.082 -10000 0 -0.47 13 13
CPT1B -0.19 0.36 -10000 0 -0.94 56 56
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.012 0.018 -10000 0 -10000 0 0
GCK -0.17 0.37 -10000 0 -0.95 57 57
CREB1 0.008 0.03 -10000 0 -10000 0 0
IGFBP1 -0.078 0.2 -10000 0 -0.69 25 25
PDX1 -0.092 0.22 -10000 0 -0.77 15 15
UCP2 -0.15 0.33 -10000 0 -0.92 43 43
ALDOB -0.16 0.37 -10000 0 -1 44 44
AFP -0.087 0.2 -10000 0 -0.55 50 50
BDH1 -0.15 0.33 -10000 0 -0.92 41 41
HADH -0.15 0.34 -10000 0 -0.95 39 39
F2 -0.2 0.4 -10000 0 -1.2 38 38
HNF1A -0.06 0.19 -10000 0 -0.58 57 57
G6PC -0.071 0.16 -10000 0 -0.59 19 19
SLC2A2 -0.11 0.23 -10000 0 -0.85 14 14
INS -0.021 0.098 -10000 0 -0.58 14 14
FOXA1 -0.012 0.12 -10000 0 -0.34 13 13
FOXA3 -0.11 0.21 -10000 0 -0.54 71 71
FOXA2 -0.18 0.39 -10000 0 -1 46 46
ABCC8 -0.21 0.42 -10000 0 -0.97 84 84
ALB -0.14 0.25 -10000 0 -0.58 75 75
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.02 0.12 -9999 0 -0.36 48 48
PDGFRB 0.009 0.038 -9999 0 -0.58 2 2
SPHK1 -0.02 0.034 -9999 0 -10000 0 0
mol:S1P -0.024 0.039 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.1 0.25 -9999 0 -0.49 120 120
GNAO1 -0.081 0.19 -9999 0 -0.48 93 93
PDGFB-D/PDGFRB/PLCgamma1 -0.081 0.22 -9999 0 -0.52 72 72
PLCG1 -0.091 0.23 -9999 0 -0.45 120 120
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.038 -9999 0 -0.58 2 2
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.011 0.006 -9999 0 -10000 0 0
GNAI1 0.003 0.065 -9999 0 -0.53 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.018 0.099 -9999 0 -0.31 48 48
S1P1/S1P -0.024 0.1 -9999 0 -0.39 17 17
negative regulation of cAMP metabolic process -0.1 0.24 -9999 0 -0.47 120 120
MAPK3 -0.12 0.3 -9999 0 -0.6 120 120
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
KDR -0.009 0.099 -9999 0 -0.47 21 21
PLCB2 -0.016 0.098 -9999 0 -0.34 17 17
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.041 0.077 -9999 0 -0.33 17 17
receptor internalization -0.046 0.085 -9999 0 -0.36 17 17
PTGS2 -0.19 0.42 -9999 0 -0.99 96 96
Rac1/GTP -0.041 0.077 -9999 0 -0.33 17 17
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA -0.02 0.12 -9999 0 -0.49 31 31
negative regulation of T cell proliferation -0.1 0.24 -9999 0 -0.47 120 120
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.035 0.14 -9999 0 -0.48 46 46
MAPK1 -0.12 0.3 -9999 0 -0.6 120 120
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.12 -9999 0 -0.41 19 19
ABCC1 0.012 0.003 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.002 0.081 -10000 0 -0.24 49 49
regulation of S phase of mitotic cell cycle 0.002 0.087 -10000 0 -0.24 46 46
GNAO1 -0.08 0.19 -10000 0 -0.47 93 93
HRAS 0.007 0.059 -10000 0 -0.58 5 5
SHBG/T-DHT -0.001 0.055 -10000 0 -0.32 14 14
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.001 0.09 -10000 0 -0.38 11 11
T-DHT/AR -0.022 0.1 -10000 0 -0.34 44 44
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 88 88
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.005 0.065 -10000 0 -0.53 7 7
mol:GDP -0.036 0.12 -10000 0 -0.4 44 44
cell proliferation -0.037 0.17 -10000 0 -0.38 87 87
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
FOS -0.1 0.31 -10000 0 -0.75 88 88
mol:Ca2+ -0.019 0.033 -10000 0 -0.087 78 78
MAPK3 -0.02 0.13 -10000 0 -0.46 11 11
MAPK1 -0.013 0.088 -10000 0 -0.19 84 84
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 88 88
cAMP biosynthetic process 0.006 0.057 -10000 0 -0.28 14 14
GNG2 0.008 0.049 -10000 0 -0.47 5 5
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 88 88
HRAS/GTP -0.027 0.077 -10000 0 -0.38 11 11
actin cytoskeleton reorganization -0.003 0.03 -10000 0 -0.43 1 1
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 88 88
PI3K 0.013 0.041 -10000 0 -0.31 7 7
apoptosis 0.039 0.17 0.38 87 -10000 0 87
T-DHT/AR/PELP1 -0.01 0.085 -10000 0 -0.28 44 44
HRAS/GDP -0.036 0.12 -10000 0 -0.4 44 44
CREB1 -0.043 0.18 -10000 0 -0.41 87 87
RAC1-CDC42/GTP 0 0.032 -10000 0 -0.44 1 1
AR -0.031 0.14 -10000 0 -0.47 44 44
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.002 0.087 -10000 0 -0.38 11 11
RAC1-CDC42/GDP -0.028 0.11 -10000 0 -0.36 43 43
T-DHT/AR/PELP1/Src -0.002 0.078 -10000 0 -0.25 44 44
MAP2K2 -0.001 0.093 -10000 0 -0.4 11 11
T-DHT/AR/PELP1/Src/PI3K 0.001 0.088 -10000 0 -0.25 46 46
GNAZ -0.033 0.14 -10000 0 -0.47 46 46
SHBG -0.002 0.089 -10000 0 -0.52 14 14
Gi family/GNB1/GNG2/GDP -0.051 0.18 -10000 0 -0.4 93 93
mol:T-DHT 0 0.001 0.002 1 -0.003 81 82
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.001 0.062 -10000 0 -0.42 10 10
Gi family/GTP -0.046 0.14 -10000 0 -0.36 59 59
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.007 0.059 -10000 0 -0.58 5 5
mol:Halofuginone 0.005 0.001 -10000 0 -10000 0 0
ITGA1 -0.023 0.13 -10000 0 -0.47 36 36
CDKN1A 0.008 0.069 -10000 0 -0.53 4 4
PRL-3/alpha Tubulin -0.07 0.18 -10000 0 -0.42 100 100
mol:Ca2+ -0.014 0.18 0.25 86 -0.39 72 158
AGT -0.07 0.2 -10000 0 -0.55 72 72
CCNA2 -0.048 0.15 -10000 0 -0.52 13 13
TUBA1B 0.013 0 -10000 0 -10000 0 0
EGR1 -0.029 0.13 -10000 0 -0.36 66 66
CDK2/Cyclin E1 0.019 0.07 -10000 0 -0.44 6 6
MAPK3 -0.069 0.18 -10000 0 -0.42 100 100
PRL-2 /Rab GGTase beta 0.02 0 -10000 0 -10000 0 0
MAPK1 -0.069 0.18 -10000 0 -0.42 100 100
PTP4A1 -0.006 0.1 -10000 0 -10000 0 0
PTP4A3 -0.11 0.24 -10000 0 -0.58 100 100
PTP4A2 0.013 0 -10000 0 -10000 0 0
ITGB1 -0.069 0.18 -10000 0 -0.42 100 100
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 -0.015 0.071 -10000 0 -0.23 13 13
Rab GGTase beta/Rab GGTase alpha 0.02 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.004 0.1 -10000 0 -0.51 1 1
RABGGTA 0.013 0 -10000 0 -10000 0 0
BCAR1 0.051 0.1 0.25 100 -10000 0 100
RHOC -0.015 0.071 -10000 0 -10000 0 0
RHOA -0.015 0.071 -10000 0 -0.23 13 13
cell motility -0.012 0.074 -10000 0 -0.26 5 5
PRL-1/alpha Tubulin 0.001 0.094 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.094 0.2 -10000 0 -0.42 125 125
ROCK1 -0.012 0.075 -10000 0 -0.26 5 5
RABGGTB 0.013 0 -10000 0 -10000 0 0
CDK2 0.013 0 -10000 0 -10000 0 0
mitosis -0.006 0.1 -10000 0 -10000 0 0
ATF5 0.003 0.075 -10000 0 -0.58 8 8
Aurora A signaling

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.016 0.055 -9999 0 -0.26 2 2
BIRC5 -0.2 0.28 -9999 0 -0.57 179 179
NFKBIA 0.019 0.052 -9999 0 -10000 0 0
CPEB1 -0.12 0.22 -9999 0 -0.47 134 134
AKT1 0.019 0.052 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.014 0.055 -9999 0 -0.47 2 2
NDEL1/TACC3 -0.002 0.12 -9999 0 -0.37 40 40
GADD45A 0.011 0.031 -9999 0 -0.47 2 2
GSK3B 0.018 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.014 0.064 -9999 0 -0.32 6 6
MDM2 0.013 0 -9999 0 -10000 0 0
JUB -0.015 0.11 -9999 0 -0.47 28 28
TPX2 -0.12 0.2 -9999 0 -0.42 153 153
TP53 0.019 0.047 -9999 0 -0.27 6 6
DLG7 0.01 0.052 -9999 0 -0.18 35 35
AURKAIP1 0.003 0.075 -9999 0 -0.58 8 8
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.003 0.12 -9999 0 -0.39 40 40
G2/M transition of mitotic cell cycle 0.014 0.055 -9999 0 -0.47 2 2
AURKA 0.014 0.065 -9999 0 -0.21 35 35
AURKB -0.048 0.078 -9999 0 -0.16 143 143
CDC25B 0.013 0.055 -9999 0 -0.29 3 3
G2/M transition checkpoint 0 0.076 -9999 0 -0.24 28 28
mRNA polyadenylation -0.058 0.13 -9999 0 -0.26 134 134
Aurora A/CPEB -0.058 0.13 -9999 0 -0.26 134 134
Aurora A/TACC1/TRAP/chTOG 0.026 0.061 -9999 0 -0.37 3 3
BRCA1 0.011 0.038 -9999 0 -0.58 2 2
centrosome duplication 0.014 0.064 -9999 0 -0.32 6 6
regulation of centrosome cycle -0.003 0.12 -9999 0 -0.37 40 40
spindle assembly 0.025 0.06 -9999 0 -0.36 3 3
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.087 0.17 -9999 0 -0.3 178 178
CENPA -0.045 0.076 -9999 0 -0.15 143 143
Aurora A/PP2A 0.017 0.052 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.024 0.044 -9999 0 -10000 0 0
negative regulation of DNA binding 0.019 0.047 -9999 0 -0.27 6 6
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.02 0 -9999 0 -10000 0 0
RASA1 0.01 0.038 -9999 0 -0.47 3 3
Ajuba/Aurora A 0 0.076 -9999 0 -0.24 28 28
mitotic prometaphase 0.013 0.02 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.064 -9999 0 -0.21 35 35
TACC1 0.002 0.072 -9999 0 -0.47 11 11
TACC3 -0.035 0.16 -9999 0 -0.58 40 40
Aurora A/Antizyme1 0.019 0.064 -9999 0 -0.31 8 8
Aurora A/RasGAP 0.016 0.057 -9999 0 -0.27 3 3
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.007 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.023 0.033 -9999 0 -0.27 6 6
Importin alpha/Importin beta/TPX2 -0.12 0.2 -9999 0 -0.42 153 153
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
Aurora A/TPX2 -0.083 0.18 -9999 0 -0.34 153 153
PAK1 0.007 0.053 -9999 0 -0.47 6 6
CKAP5 0.013 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.018 0.096 -10000 0 -0.26 42 42
NT3 (dimer)/TRKC -0.085 0.2 -10000 0 -0.43 112 112
NT3 (dimer)/TRKB -0.072 0.19 -10000 0 -0.37 121 121
SHC/Grb2/SOS1/GAB1/PI3K 0.031 0.036 -10000 0 -0.43 1 1
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.088 0.2 -10000 0 -0.47 102 102
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
DYNLT1 0.013 0.001 -10000 0 -10000 0 0
NTRK1 -0.029 0.14 -10000 0 -0.49 40 40
NTRK2 -0.056 0.17 -10000 0 -0.47 69 69
NTRK3 -0.081 0.19 -10000 0 -0.47 95 95
NT-4/5 (dimer)/TRKB -0.1 0.21 -10000 0 -0.38 158 158
neuron apoptosis 0.076 0.19 0.5 60 -10000 0 60
SHC 2-3/Grb2 -0.084 0.21 -10000 0 -0.55 60 60
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.088 0.16 -10000 0 -0.49 52 52
SHC3 -0.12 0.21 -10000 0 -0.56 73 73
STAT3 (dimer) 0.02 0.012 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.057 0.17 -10000 0 -0.34 110 110
RIN/GDP -0.011 0.097 -10000 0 -0.25 23 23
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.029 0.12 -10000 0 -0.34 43 43
RIN/GTP -0.024 0.11 -10000 0 -0.42 34 34
CCND1 0.028 0.022 -10000 0 -0.47 1 1
MAGED1 0.012 0.027 -10000 0 -0.58 1 1
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.099 0.2 -10000 0 -0.47 113 113
SHC/GRB2/SOS1 0.027 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.18 0.21 -10000 0 -0.37 251 251
TRKA/NEDD4-2 -0.024 0.13 -10000 0 -0.4 51 51
ELMO1 0.01 0.038 -10000 0 -0.47 3 3
RhoG/GTP/ELMO1/DOCK1 0.014 0.033 -10000 0 -0.28 6 6
NGF -0.009 0.1 -10000 0 -0.48 22 22
HRAS 0.007 0.059 -10000 0 -0.58 5 5
DOCK1 0.01 0.038 -10000 0 -0.47 3 3
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 -0.033 0.15 -10000 0 -0.58 34 34
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 0.011 0.035 -10000 0 -0.52 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.029 0.12 -10000 0 -0.34 43 43
mol:GDP -0.003 0.12 -10000 0 -0.35 21 21
NGF (dimer) -0.009 0.1 -10000 0 -0.48 22 22
RhoG/GDP 0.008 0.027 -10000 0 -0.34 3 3
RIT1/GDP 0.006 0.085 -10000 0 -0.24 15 15
TIAM1 0.01 0.038 -10000 0 -0.47 3 3
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
BDNF (dimer)/TRKB -0.074 0.18 -10000 0 -0.36 126 126
KIDINS220/CRKL/C3G 0.02 0 -10000 0 -10000 0 0
SHC/RasGAP 0.017 0.027 -10000 0 -0.33 3 3
FRS2 family/SHP2 0.026 0.013 -10000 0 -0.27 1 1
SHC/GRB2/SOS1/GAB1 0.034 0.012 -10000 0 -10000 0 0
RIT1/GTP 0.01 0 -10000 0 -10000 0 0
NT3 (dimer) -0.045 0.16 -10000 0 -0.47 58 58
RAP1/GDP -0.027 0.053 -10000 0 -0.22 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.088 0.2 -10000 0 -0.47 102 102
ubiquitin-dependent protein catabolic process -0.025 0.13 -10000 0 -0.32 71 71
Schwann cell development -0.026 0.034 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.034 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.037 0.011 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.21 -10000 0 -0.54 85 85
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.079 -10000 0 -10000 0 0
STAT3 0.02 0.012 -10000 0 -10000 0 0
axon guidance -0.12 0.2 -10000 0 -0.51 85 85
MAPK3 -0.16 0.19 -10000 0 -0.34 228 228
MAPK1 -0.16 0.19 -10000 0 -0.34 228 228
CDC42/GDP 0.006 0.085 -10000 0 -0.24 12 12
NTF3 -0.045 0.16 -10000 0 -0.47 58 58
NTF4 -0.1 0.2 -10000 0 -0.47 113 113
NGF (dimer)/TRKA/FAIM -0.013 0.11 -10000 0 -0.29 61 61
PI3K 0.014 0.048 -10000 0 -0.37 7 7
FRS3 0.013 0.001 -10000 0 -10000 0 0
FAIM 0.012 0.027 -10000 0 -0.58 1 1
GAB1 0.012 0.022 -10000 0 -0.47 1 1
RASGRF1 -0.073 0.17 -10000 0 -0.43 61 61
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.064 0.17 -10000 0 -0.36 112 112
RGS19 0.012 0.027 -10000 0 -0.58 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.085 -10000 0 -0.23 17 17
NGF (dimer)/TRKA/GRIT -0.021 0.11 -10000 0 -0.3 60 60
neuron projection morphogenesis -0.016 0.12 -10000 0 -0.47 15 15
NGF (dimer)/TRKA/NEDD4-2 -0.025 0.13 -10000 0 -0.32 71 71
MAP2K1 0.035 0.011 -10000 0 -10000 0 0
NGFR -0.028 0.14 -10000 0 -0.47 41 41
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.082 -10000 0 -0.43 2 2
RAS family/GTP/PI3K 0.023 0.045 -10000 0 -0.43 3 3
FRS2 family/SHP2/GRB2/SOS1 0.039 0.012 -10000 0 -10000 0 0
NRAS 0.012 0.022 -10000 0 -0.47 1 1
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
PRKCI 0.012 0.027 -10000 0 -0.58 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.079 0.19 -10000 0 -0.62 49 49
RASA1 0.01 0.038 -10000 0 -0.47 3 3
TRKA/c-Abl -0.011 0.1 -10000 0 -0.35 40 40
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.059 0.17 -10000 0 -0.48 46 46
NGF (dimer)/TRKA/p62/Atypical PKCs 0.005 0.093 -10000 0 -0.45 2 2
MATK -0.25 0.29 -10000 0 -0.57 219 219
NEDD4L -0.006 0.1 -10000 0 -0.58 16 16
RAS family/GDP -0.026 0.052 -10000 0 -0.23 3 3
NGF (dimer)/TRKA -0.053 0.12 -10000 0 -0.36 44 44
Rac1/GTP -0.066 0.1 -10000 0 -0.33 46 46
FRS2 family/SHP2/CRK family 0.039 0.012 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.012 0.14 -9999 0 -0.45 33 33
MAP4K1 -0.024 0.14 -9999 0 -0.56 32 32
MAP3K8 0 0.08 -9999 0 -0.48 13 13
PRKCB -0.097 0.2 -9999 0 -0.47 111 111
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.015 0.085 -9999 0 -0.5 6 6
JUN -0.11 0.25 -9999 0 -0.53 121 121
MAP3K7 0.016 0.085 -9999 0 -0.5 6 6
GRAP2 -0.008 0.1 -9999 0 -0.48 21 21
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.019 0.091 -9999 0 -0.44 9 9
LAT -0.003 0.095 -9999 0 -0.55 14 14
LCP2 0.006 0.061 -9999 0 -0.54 6 6
MAPK8 -0.12 0.26 -9999 0 -0.56 120 120
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.009 0.089 -9999 0 -0.4 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.004 0.14 -9999 0 -0.42 33 33
HIF-1-alpha transcription factor 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
PKM2 -0.1 0.43 -9999 0 -1.1 37 37
HDAC7 0.013 0.008 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.1 0.34 -9999 0 -0.9 39 39
SMAD4 0.014 0 -9999 0 -10000 0 0
ID2 -0.11 0.44 -9999 0 -1.2 34 34
AP1 -0.049 0.15 -9999 0 -0.36 88 88
ABCG2 -0.13 0.46 -9999 0 -1.2 44 44
HIF1A 0 0.077 -9999 0 -0.55 1 1
TFF3 -0.22 0.48 -9999 0 -1.1 70 70
GATA2 0.012 0.027 -9999 0 -0.57 1 1
AKT1 -0.002 0.086 -9999 0 -10000 0 0
response to hypoxia -0.02 0.089 -9999 0 -0.24 12 12
MCL1 -0.1 0.43 -9999 0 -1.1 38 38
NDRG1 -0.1 0.43 -9999 0 -1.1 37 37
SERPINE1 -0.14 0.45 -9999 0 -1.1 46 46
FECH -0.11 0.43 -9999 0 -1.1 39 39
FURIN -0.1 0.43 -9999 0 -1.1 37 37
NCOA2 -0.048 0.16 -9999 0 -0.47 60 60
EP300 0.01 0.13 -9999 0 -0.35 22 22
HMOX1 -0.11 0.43 -9999 0 -1.1 41 41
BHLHE40 -0.11 0.44 -9999 0 -1.1 43 43
BHLHE41 -0.11 0.43 -9999 0 -1.1 38 38
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.013 0.076 -9999 0 -10000 0 0
ENG 0.048 0.091 -9999 0 -10000 0 0
JUN 0.006 0.062 -9999 0 -0.5 7 7
RORA -0.1 0.43 -9999 0 -1.1 37 37
ABCB1 -0.06 0.19 -9999 0 -1.3 9 9
TFRC -0.1 0.43 -9999 0 -1.1 40 40
CXCR4 -0.11 0.44 -9999 0 -1.1 42 42
TF -0.16 0.48 -9999 0 -1.1 58 58
CITED2 -0.11 0.43 -9999 0 -1.1 36 36
HIF1A/ARNT -0.14 0.47 -9999 0 -1.2 47 47
LDHA -0.023 0.06 -9999 0 -0.53 3 3
ETS1 -0.11 0.43 -9999 0 -1.1 37 37
PGK1 -0.1 0.43 -9999 0 -1.1 36 36
NOS2 -0.14 0.46 -9999 0 -1.1 51 51
ITGB2 -0.11 0.43 -9999 0 -1.1 36 36
ALDOA -0.1 0.43 -9999 0 -1.1 37 37
Cbp/p300/CITED2 -0.11 0.45 -9999 0 -1.2 37 37
FOS -0.076 0.19 -9999 0 -0.48 88 88
HK2 -0.11 0.44 -9999 0 -1.1 39 39
SP1 0.021 0.003 -9999 0 -10000 0 0
GCK -0.035 0.34 -9999 0 -1.3 25 25
HK1 -0.1 0.43 -9999 0 -1.1 37 37
NPM1 -0.1 0.43 -9999 0 -1.1 36 36
EGLN1 -0.1 0.43 -9999 0 -1.1 37 37
CREB1 0.02 0.002 -9999 0 -10000 0 0
PGM1 -0.1 0.43 -9999 0 -1.1 37 37
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.051 0.32 -9999 0 -1.1 33 33
IGFBP1 -0.13 0.44 -9999 0 -1.1 42 42
VEGFA -0.053 0.34 -9999 0 -0.84 33 33
HIF1A/JAB1 -0.001 0.043 -9999 0 -0.39 1 1
CP -0.16 0.47 -9999 0 -1.1 53 53
CXCL12 -0.11 0.44 -9999 0 -1.2 39 39
COPS5 0.011 0.009 -9999 0 -10000 0 0
SMAD3/SMAD4 0.022 0 -9999 0 -10000 0 0
BNIP3 -0.1 0.43 -9999 0 -1.1 38 38
EGLN3 -0.11 0.44 -9999 0 -1.1 41 41
CA9 -0.12 0.43 -9999 0 -1.1 40 40
TERT -0.2 0.48 -9999 0 -1.1 69 69
ENO1 -0.1 0.43 -9999 0 -1.1 36 36
PFKL -0.1 0.43 -9999 0 -1.1 37 37
NCOA1 0.012 0.005 -9999 0 -10000 0 0
ADM -0.12 0.44 -9999 0 -1.1 44 44
ARNT 0.002 0.072 -9999 0 -10000 0 0
HNF4A -0.029 0.14 -9999 0 -0.58 28 28
ADFP -0.12 0.42 -9999 0 -1.1 46 46
SLC2A1 -0.041 0.33 -9999 0 -0.8 29 29
LEP -0.12 0.43 -9999 0 -1.1 38 38
HIF1A/ARNT/Cbp/p300 -0.069 0.38 -9999 0 -0.94 36 36
EPO -0.13 0.41 -9999 0 -0.95 63 63
CREBBP 0.012 0.13 -9999 0 -0.36 19 19
HIF1A/ARNT/Cbp/p300/HDAC7 -0.1 0.34 -9999 0 -0.91 37 37
PFKFB3 -0.11 0.43 -9999 0 -1.1 37 37
NT5E -0.13 0.46 -9999 0 -1.2 46 46
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.067 0.18 0.5 56 -10000 0 56
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.031 0.11 -10000 0 -0.28 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.079 0.19 -10000 0 -0.47 93 93
RhoA/GTP -0.068 0.19 -10000 0 -0.51 56 56
negative regulation of cAMP metabolic process -0.08 0.2 -10000 0 -0.55 57 57
GNAZ -0.033 0.14 -10000 0 -0.47 46 46
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.067 0.18 -10000 0 -0.47 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.081 0.2 -10000 0 -0.56 57 57
RhoA/GDP 0.01 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.005 0.065 -10000 0 -0.53 7 7
TCGA08_p53

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
CDKN2A -0.081 0.18 -10000 0 -0.42 102 102
TP53 -0.027 0.056 -10000 0 -0.32 6 6
Senescence -0.027 0.056 -10000 0 -0.32 6 6
Apoptosis -0.027 0.056 -10000 0 -0.32 6 6
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.045 0.087 0.21 102 -10000 0 102
MDM4 0.013 0 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.037 0.14 -9999 0 -0.46 27 27
SMAD6-7/SMURF1 0.022 0.038 -9999 0 -0.27 8 8
NOG -0.046 0.16 -9999 0 -0.47 59 59
SMAD9 -0.04 0.16 -9999 0 -0.47 52 52
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.004 0.096 -9999 0 -0.38 15 15
BMP7/USAG1 -0.16 0.23 -9999 0 -0.41 201 201
SMAD5/SKI 0.004 0.092 -9999 0 -0.37 13 13
SMAD1 0.034 0.023 -9999 0 -10000 0 0
BMP2 -0.019 0.12 -9999 0 -0.47 32 32
SMAD1/SMAD1/SMAD4 -0.002 0.019 -9999 0 -10000 0 0
BMPR1A 0.012 0.022 -9999 0 -0.47 1 1
BMPR1B 0.006 0.063 -9999 0 -0.52 7 7
BMPR1A-1B/BAMBI 0.006 0.084 -9999 0 -0.33 28 28
AHSG -0.035 0.14 -9999 0 -0.58 32 32
CER1 -0.008 0.082 -9999 0 -0.58 10 10
BMP2-4/CER1 -0.021 0.12 -9999 0 -0.36 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.007 0.13 -9999 0 -0.43 28 28
BMP2-4 (homodimer) -0.02 0.13 -9999 0 -0.41 44 44
RGMB 0.005 0.062 -9999 0 -0.47 8 8
BMP6/BMPR2/BMPR1A-1B -0.015 0.12 -9999 0 -0.31 66 66
RGMA -0.009 0.1 -9999 0 -0.47 22 22
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.014 0.13 -9999 0 -0.44 28 28
BMP2-4/USAG1 -0.11 0.2 -9999 0 -0.34 174 174
SMAD6/SMURF1/SMAD5 0.004 0.092 -9999 0 -0.37 13 13
SOSTDC1 -0.15 0.23 -9999 0 -0.47 167 167
BMP7/BMPR2/BMPR1A-1B -0.023 0.11 -9999 0 -0.34 5 5
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.063 0.2 -9999 0 -0.57 63 63
HFE2 -0.052 0.18 -9999 0 -0.58 49 49
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0.001 -9999 0 -10000 0 0
BMP2-4/CHRD -0.041 0.16 -9999 0 -0.37 84 84
SMAD5/SMAD5/SMAD4 0.004 0.092 -9999 0 -0.37 13 13
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.036 0.094 -9999 0 -0.38 27 27
BMP7 (homodimer) -0.081 0.19 -9999 0 -0.47 94 94
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.071 0.18 -9999 0 -0.43 91 91
SMAD1/SKI 0.04 0.022 -9999 0 -10000 0 0
SMAD6 0.005 0.062 -9999 0 -0.47 8 8
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.037 0.14 -9999 0 -0.36 74 74
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.068 0.19 -9999 0 -0.52 74 74
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.024 0.034 -9999 0 -0.35 4 4
BMPR1A-1B (homodimer) 0.013 0.049 -9999 0 -0.36 8 8
CHRDL1 -0.11 0.21 -9999 0 -0.47 126 126
ENDOFIN/SMAD1 0.04 0.022 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.047 0.033 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.011 0.12 -9999 0 -0.58 20 20
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.081 0.19 -9999 0 -0.6 36 36
BMP2-4/GREM1 -0.056 0.17 -9999 0 -0.35 107 107
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.031 0.15 -9999 0 -0.44 52 52
SMAD1/SMAD6 0.04 0.022 -9999 0 -10000 0 0
TAK1/SMAD6 0.02 0 -9999 0 -10000 0 0
BMP7 -0.081 0.19 -9999 0 -0.47 94 94
BMP6 -0.063 0.2 -9999 0 -0.58 63 63
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.007 0.12 -9999 0 -0.41 28 28
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.04 0.022 -9999 0 -10000 0 0
SMAD7/SMURF1 0.02 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.008 0.053 -9999 0 -0.58 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.036 0.19 -9999 0 -0.6 38 38
CHRD -0.042 0.17 -9999 0 -0.57 46 46
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.14 -9999 0 -0.49 28 28
BMP4 -0.012 0.11 -9999 0 -0.47 25 25
FST -0.031 0.14 -9999 0 -0.48 44 44
BMP2-4/NOG -0.041 0.17 -9999 0 -0.37 84 84
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.015 0.11 -9999 0 -0.45 1 1
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.022 0.042 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.062 0.11 -9999 0 -0.37 32 32
JUN -0.033 0.13 -9999 0 -0.41 31 31
HRAS 0.007 0.059 -9999 0 -0.58 5 5
RET51/GFRalpha1/GDNF/GRB10 -0.072 0.17 -9999 0 -0.36 99 99
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.072 0.17 -9999 0 -0.36 99 99
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.022 0.12 -9999 0 -0.3 70 70
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.086 0.15 -9999 0 -0.45 34 34
GRB7 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.072 0.17 -9999 0 -0.36 99 99
MAPKKK cascade -0.073 0.12 -9999 0 -0.45 26 26
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.023 0.12 -9999 0 -0.29 74 74
lamellipodium assembly -0.058 0.1 -9999 0 -0.34 33 33
RET51/GFRalpha1/GDNF/SHC -0.072 0.17 -9999 0 -0.36 99 99
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
RET9/GFRalpha1/GDNF/SHC -0.015 0.1 -9999 0 -0.27 65 65
RET9/GFRalpha1/GDNF/Shank3 -0.015 0.1 -9999 0 -0.27 65 65
MAPK3 -0.054 0.15 -9999 0 -0.49 24 24
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.024 0.14 -9999 0 -0.52 34 34
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.046 0.15 -9999 0 -0.47 27 27
DOK5 -0.02 0.13 -9999 0 -0.5 31 31
GFRA1 -0.03 0.14 -9999 0 -0.47 43 43
MAPK8 -0.037 0.13 -9999 0 -0.42 29 29
HRAS/GTP -0.085 0.14 -9999 0 -0.52 26 26
tube development -0.008 0.097 -9999 0 -0.42 8 8
MAPK1 -0.054 0.15 -9999 0 -0.49 24 24
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.093 -9999 0 -0.44 6 6
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PDLIM7 -0.001 0.084 -9999 0 -0.49 14 14
RET51/GFRalpha1/GDNF/Dok6 -0.08 0.18 -9999 0 -0.36 114 114
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.075 0.18 -9999 0 -0.37 100 100
RET51/GFRalpha1/GDNF/Dok5 -0.089 0.19 -9999 0 -0.39 109 109
PRKCA -0.007 0.096 -9999 0 -0.47 20 20
HRAS/GDP 0.005 0.044 -9999 0 -0.42 5 5
CREB1 -0.024 0.12 -9999 0 -0.41 22 22
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.095 -9999 0 -0.31 18 18
RET51/GFRalpha1/GDNF/Grb7 -0.072 0.17 -9999 0 -0.36 99 99
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.1 0.23 -9999 0 -0.56 96 96
DOK4 0.007 0.053 -9999 0 -0.47 6 6
JNK cascade -0.032 0.13 -9999 0 -0.4 31 31
RET9/GFRalpha1/GDNF/FRS2 -0.015 0.1 -9999 0 -0.27 65 65
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.01 0.038 -9999 0 -0.47 3 3
NCK1 0.012 0.027 -9999 0 -0.58 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.007 0.093 -9999 0 -0.44 6 6
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.04 0.13 -9999 0 -0.44 23 23
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.041 0.13 -9999 0 -0.44 24 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.041 0.13 -9999 0 -0.47 23 23
PI3K -0.045 0.17 -9999 0 -0.53 33 33
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.007 0.098 -9999 0 -0.42 8 8
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.036 0.13 -9999 0 -0.36 40 40
RET51/GFRalpha1/GDNF/FRS2 -0.072 0.17 -9999 0 -0.36 99 99
GAB1 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.086 -9999 0 -0.47 16 16
IRS2 0.007 0.059 -9999 0 -0.58 5 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.041 0.14 -9999 0 -0.49 23 23
RET51/GFRalpha1/GDNF/PKC alpha -0.082 0.19 -9999 0 -0.39 103 103
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.017 0.11 -9999 0 -0.48 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.08 0.18 -9999 0 -0.37 104 104
Rac1/GTP -0.068 0.12 -9999 0 -0.41 33 33
RET9/GFRalpha1/GDNF -0.026 0.11 -9999 0 -0.3 65 65
GFRalpha1/GDNF -0.032 0.13 -9999 0 -0.36 65 65
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.009 0.027 -9999 0 -10000 0 0
NFATC2 -0.046 0.12 -9999 0 -0.29 88 88
NFATC3 0.009 0.027 -9999 0 -10000 0 0
CD40LG -0.14 0.29 -9999 0 -0.7 70 70
PTGS2 -0.16 0.31 -9999 0 -0.69 90 90
JUNB -0.016 0.12 -9999 0 -0.52 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.015 -9999 0 -10000 0 0
CaM/Ca2+ 0 0.015 -9999 0 -10000 0 0
CALM1 0.011 0.008 -9999 0 -10000 0 0
JUN 0.003 0.063 -9999 0 -0.51 7 7
mol:Ca2+ -0.006 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.005 -9999 0 -10000 0 0
FOSL1 -0.11 0.22 -9999 0 -0.5 113 113
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.059 0.16 -9999 0 -0.46 24 24
FOS -0.079 0.19 -9999 0 -0.49 88 88
IFNG -0.13 0.28 -9999 0 -0.7 58 58
AP-1/NFAT1-c-4 -0.14 0.32 -9999 0 -0.76 62 62
FASLG -0.13 0.28 -9999 0 -0.72 56 56
NFAT1-c-4/ICER1 -0.044 0.11 -9999 0 -0.37 7 7
IL2RA -0.16 0.31 -9999 0 -0.71 76 76
FKBP12/FK506 0.01 0 -9999 0 -10000 0 0
CSF2 -0.12 0.26 -9999 0 -0.67 52 52
JunB/Fra1/NFAT1-c-4 -0.097 0.17 -9999 0 -0.45 49 49
IL4 -0.12 0.26 -9999 0 -0.66 52 52
IL2 -0.004 0.03 -9999 0 -0.42 2 2
IL3 -0.017 0.022 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.017 0.13 -9999 0 -0.57 25 25
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.027 -9999 0 -0.58 1 1
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.002 0.13 -10000 0 -0.42 23 23
TBX21 -0.088 0.37 -10000 0 -0.92 56 56
B2M 0.012 0.009 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.011 0.12 -10000 0 -0.58 22 22
GADD45B -0.06 0.31 -10000 0 -0.77 47 47
IL12RB2 -0.007 0.11 -10000 0 -0.5 21 21
GADD45G -0.079 0.32 -10000 0 -0.76 54 54
natural killer cell activation 0.002 0.021 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 0.002 0.077 -10000 0 -0.48 12 12
IL2RA -0.078 0.21 -10000 0 -0.57 76 76
IFNG -0.026 0.14 -10000 0 -0.58 30 30
STAT3 (dimer) -0.065 0.3 -10000 0 -0.7 59 59
HLA-DRB5 -0.01 0.11 -10000 0 -0.55 19 19
FASLG -0.091 0.38 -10000 0 -1.1 41 41
NF kappa B2 p52/RelB -0.15 0.28 -10000 0 -0.75 67 67
CD4 0.005 0.063 -10000 0 -0.56 6 6
SOCS1 0.009 0.051 -10000 0 -0.55 4 4
EntrezGene:6955 -0.005 0.014 -10000 0 -10000 0 0
CD3D -0.03 0.14 -10000 0 -0.55 35 35
CD3E -0.011 0.1 -10000 0 -0.52 19 19
CD3G -0.046 0.16 -10000 0 -0.51 52 52
IL12Rbeta2/JAK2 0.007 0.087 -10000 0 -0.36 22 22
CCL3 -0.1 0.38 -10000 0 -0.9 63 63
CCL4 -0.083 0.35 -10000 0 -0.86 57 57
HLA-A 0 0.079 -10000 0 -0.51 11 11
IL18/IL18R 0.012 0.12 -10000 0 -0.37 29 29
NOS2 -0.12 0.41 -10000 0 -0.98 68 68
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.12 -10000 0 -0.4 21 21
IL1R1 -0.075 0.34 -10000 0 -0.84 52 52
IL4 0 0.021 -10000 0 -10000 0 0
JAK2 0.014 0.031 -10000 0 -0.49 1 1
EntrezGene:6957 -0.004 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.07 0.29 -10000 0 -0.79 47 47
RAB7A -0.04 0.27 -10000 0 -0.72 27 27
lysosomal transport -0.036 0.26 -10000 0 -0.68 28 28
FOS -0.2 0.5 -10000 0 -1.1 99 99
STAT4 (dimer) -0.061 0.32 -10000 0 -0.79 52 52
STAT5A (dimer) -0.17 0.3 -10000 0 -0.8 69 69
GZMA -0.086 0.36 -10000 0 -0.91 54 54
GZMB -0.1 0.39 -10000 0 -0.94 64 64
HLX -0.006 0.1 -10000 0 -0.58 16 16
LCK -0.087 0.37 -10000 0 -0.85 64 64
TCR/CD3/MHC II/CD4 -0.055 0.18 -10000 0 -0.44 59 59
IL2/IL2R -0.055 0.18 -10000 0 -0.4 85 85
MAPK14 -0.064 0.32 -10000 0 -0.76 54 54
CCR5 -0.061 0.32 -10000 0 -0.92 32 32
IL1B -0.062 0.19 -10000 0 -0.52 72 72
STAT6 -0.005 0.11 -10000 0 -0.49 2 2
STAT4 -0.008 0.11 -10000 0 -0.55 18 18
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.001 0.084 -10000 0 -0.58 10 10
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.01 0.046 -10000 0 -0.58 3 3
IL12B -0.022 0.14 -10000 0 -0.59 29 29
CD8A -0.007 0.099 -10000 0 -0.51 18 18
CD8B -0.01 0.11 -10000 0 -0.52 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.002 0.13 0.41 23 -10000 0 23
IL2RB -0.017 0.12 -10000 0 -0.49 29 29
proteasomal ubiquitin-dependent protein catabolic process -0.051 0.3 -10000 0 -0.72 51 51
IL2RG -0.012 0.12 -10000 0 -0.55 22 22
IL12 -0.016 0.14 -10000 0 -0.45 41 41
STAT5A 0.011 0.031 -10000 0 -0.47 2 2
CD247 -0.014 0.12 -10000 0 -0.56 21 21
IL2 0.004 0.038 -10000 0 -0.58 2 2
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.004 0.099 -10000 0 -0.53 16 16
IL12/IL12R/TYK2/JAK2 -0.095 0.38 -10000 0 -0.88 66 66
MAP2K3 -0.067 0.32 -10000 0 -0.74 57 57
RIPK2 0.002 0.079 -10000 0 -0.58 9 9
MAP2K6 -0.07 0.32 -10000 0 -0.75 58 58
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.006 0.056 -10000 0 -0.54 5 5
IL18RAP -0.022 0.14 -10000 0 -0.53 33 33
IL12Rbeta1/TYK2 0.002 0.099 -10000 0 -0.43 22 22
EOMES -0.058 0.24 -10000 0 -1.2 17 17
STAT1 (dimer) -0.068 0.3 -10000 0 -0.71 58 58
T cell proliferation -0.044 0.26 -10000 0 -0.59 56 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.007 0.063 -10000 0 -0.48 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.13 0.22 -10000 0 -0.64 54 54
ATF2 -0.065 0.31 -10000 0 -0.74 50 50
Osteopontin-mediated events

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
IKK alpha homodimer -0.048 0.15 -9999 0 -0.44 18 18
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.14 -9999 0 -0.42 18 18
alphaV/beta3 Integrin/Osteopontin/Src -0.04 0.16 -9999 0 -0.4 76 76
AP1 -0.07 0.21 -9999 0 -0.56 41 41
ILK -0.059 0.16 -9999 0 -0.5 14 14
bone resorption -0.053 0.18 -9999 0 -0.45 53 53
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.044 0.15 -9999 0 -0.47 17 17
ITGAV 0.014 0.031 -9999 0 -0.47 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.019 0.11 -9999 0 -0.34 51 51
alphaV/beta3 Integrin/Osteopontin -0.075 0.17 -9999 0 -0.37 78 78
MAP3K1 -0.061 0.16 -9999 0 -0.47 19 19
JUN 0.006 0.062 -9999 0 -0.5 7 7
MAPK3 -0.047 0.15 -9999 0 -0.46 18 18
MAPK1 -0.047 0.15 -9999 0 -0.46 18 18
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.054 0.16 -9999 0 -0.46 25 25
ITGB3 -0.08 0.19 -9999 0 -0.47 97 97
NFKBIA -0.037 0.15 -9999 0 -0.46 18 18
FOS -0.075 0.19 -9999 0 -0.48 88 88
CD44 0.002 0.072 -9999 0 -0.47 11 11
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.047 0.22 -9999 0 -0.91 17 17
NF kappa B1 p50/RelA -0.068 0.11 -9999 0 -0.43 16 16
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.044 0.14 -9999 0 -0.33 97 97
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.065 0.16 -9999 0 -0.34 83 83
VAV3 -0.08 0.18 -9999 0 -0.51 41 41
MAP3K14 -0.06 0.16 -9999 0 -0.48 18 18
ROCK2 -0.03 0.14 -9999 0 -0.47 43 43
SPP1 -0.072 0.21 -9999 0 -0.56 74 74
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.068 0.17 -9999 0 -0.47 41 41
MMP2 -0.058 0.19 -9999 0 -0.61 27 27
Wnt 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
Noncanonical Wnts/FZD -0.048 0.15 -9999 0 -0.46 28 28
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 -0.085 0.2 -9999 0 -0.48 97 97
WNT4 0.007 0.053 -9999 0 -0.47 6 6
FZD3 0.011 0.031 -9999 0 -0.47 2 2
WNT5A -0.027 0.14 -9999 0 -0.51 38 38
WNT11 -0.025 0.14 -9999 0 -0.55 33 33
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.02 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.003 0.1 -9999 0 -0.44 24 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.006 0.088 -9999 0 -0.34 3 3
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.18 -9999 0 -0.32 182 182
NT-4/5 (dimer)/p75(NTR) -0.086 0.2 -9999 0 -0.41 121 121
IKBKB 0.012 0.027 -9999 0 -0.58 1 1
AKT1 -0.001 0.092 -9999 0 -0.45 3 3
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.088 0.2 -9999 0 -0.47 102 102
MGDIs/NGR/p75(NTR)/LINGO1 -0.039 0.14 -9999 0 -0.33 90 90
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.059 0.16 -9999 0 -0.31 122 122
LINGO1 -0.052 0.18 -9999 0 -0.58 54 54
Sortilin/TRAF6/NRIF 0 0 -9999 0 -10000 0 0
proBDNF (dimer) -0.088 0.2 -9999 0 -0.47 102 102
NTRK1 -0.029 0.14 -9999 0 -0.49 40 40
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.036 0.16 -9999 0 -0.45 36 36
IRAK1 0.012 0.027 -9999 0 -0.58 1 1
SHC1 -0.013 0.1 -9999 0 -0.28 62 62
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0.01 0 -9999 0 -10000 0 0
Gamma Secretase 0.039 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.007 0.1 -9999 0 -0.38 11 11
MAGEH1 0.003 0.076 -9999 0 -0.55 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.004 0.1 -9999 0 -0.43 7 7
Mammalian IAPs/DIABLO 0.03 0.034 -9999 0 -0.31 3 3
proNGF (dimer) -0.009 0.1 -9999 0 -0.48 22 22
MAGED1 0.012 0.027 -9999 0 -0.58 1 1
APP 0.01 0.038 -9999 0 -0.47 3 3
NT-4/5 (dimer) -0.099 0.2 -9999 0 -0.47 113 113
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.002 0.086 -9999 0 -0.34 3 3
NGF -0.009 0.1 -9999 0 -0.48 22 22
cell cycle arrest 0.011 0.1 -9999 0 -0.38 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0 0.089 -9999 0 -0.39 5 5
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.17 -9999 0 -0.34 121 121
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.012 0.1 -9999 0 -0.28 62 62
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.005 0.095 -9999 0 -0.39 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.077 -9999 0 -0.33 5 5
p75(NTR)/beta APP -0.012 0.1 -9999 0 -0.34 42 42
BEX1 -0.14 0.23 -9999 0 -0.47 155 155
mol:GDP -0.022 0.1 -9999 0 -0.28 62 62
NGF (dimer) -0.059 0.15 -9999 0 -0.33 80 80
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.027 0.13 -9999 0 -0.29 90 90
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
RAC1/GTP -0.009 0.086 -9999 0 -0.23 62 62
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.012 0.1 -9999 0 -0.28 62 62
RHOB 0.005 0.062 -9999 0 -0.47 8 8
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0.091 -9999 0 -0.42 22 22
NT3 (dimer) -0.045 0.16 -9999 0 -0.47 58 58
TP53 -0.032 0.13 -9999 0 -0.44 24 24
PRDM4 -0.004 0.092 -9999 0 -0.37 3 3
BDNF (dimer) -0.15 0.2 -9999 0 -0.42 129 129
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity 0.003 0.086 -9999 0 -0.34 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.001 0.093 -9999 0 -0.37 3 3
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 -0.018 0.14 -9999 0 -0.43 32 32
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.006 0.095 -9999 0 -0.39 5 5
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.012 0.1 -9999 0 -0.28 62 62
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.049 0.16 -9999 0 -0.38 84 84
MAPK8 -0.021 0.14 -9999 0 -0.41 31 31
MAPK9 -0.016 0.14 -9999 0 -0.41 30 30
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.045 0.16 -9999 0 -0.47 58 58
NTF4 -0.1 0.2 -9999 0 -0.47 113 113
NDN 0.008 0.049 -9999 0 -0.47 5 5
RAC1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.029 0.075 -9999 0 -0.42 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.031 0.027 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.012 0.1 -9999 0 -0.27 62 62
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.035 0.14 -9999 0 -0.45 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.044 0.14 -9999 0 -0.48 21 21
PRKACB 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.057 0.15 -9999 0 -0.33 105 105
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.007 0.06 -9999 0 -0.52 6 6
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.013 0.12 -9999 0 -0.34 8 8
BAD -0.014 0.14 -9999 0 -0.4 33 33
RIPK2 0.002 0.079 -9999 0 -0.58 9 9
NGFR -0.028 0.14 -9999 0 -0.47 41 41
CYCS 0.002 0.089 -9999 0 -0.48 2 2
ADAM17 0.008 0.049 -9999 0 -0.47 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.007 0.11 -9999 0 -0.38 12 12
BCL2L11 -0.013 0.14 -9999 0 -0.4 34 34
BDNF (dimer)/p75(NTR) -0.08 0.18 -9999 0 -0.38 122 122
PI3K -0.006 0.1 -9999 0 -0.41 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.001 0.093 -9999 0 -0.37 3 3
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.012 0.027 -9999 0 -0.58 1 1
NGF (dimer)/p75(NTR) -0.026 0.12 -9999 0 -0.34 62 62
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.002 0.096 -9999 0 -0.41 4 4
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.023 0.13 -9999 0 -0.58 24 24
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.052 0.15 -9999 0 -0.49 29 29
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 -0.01 0.13 -9999 0 -0.37 34 34
E2F1 -0.013 0.12 -9999 0 -0.58 22 22
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.039 0.088 -9999 0 -0.36 14 14
NGF (dimer)/TRKA -0.027 0.12 -9999 0 -0.35 60 60
MMP7 -0.091 0.22 -9999 0 -0.53 93 93
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.006 0.088 -9999 0 -0.45 1 1
MMP3 -0.076 0.2 -9999 0 -0.51 81 81
APAF-1/Caspase 9 -0.021 0.056 -9999 0 -0.38 1 1
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.019 0.1 -10000 0 -0.3 57 57
cell-cell adhesion 0.089 0.13 0.43 41 -10000 0 41
Ephrin B/EPHB2/RasGAP -0.012 0.13 -10000 0 -0.6 9 9
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.013 0.038 -10000 0 -0.3 7 7
Ephrin B1/EPHB1 -0.079 0.14 -10000 0 -0.28 155 155
HRAS/GDP -0.091 0.14 -10000 0 -0.43 42 42
Ephrin B/EPHB1/GRB7 -0.086 0.18 -10000 0 -0.51 40 40
Endophilin/SYNJ1 -0.012 0.12 -10000 0 -0.6 7 7
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.086 0.18 -10000 0 -0.51 40 40
endothelial cell migration 0.014 0.068 -10000 0 -0.31 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 0.013 0 -10000 0 -10000 0 0
PAK1 -0.011 0.13 -10000 0 -0.62 9 9
HRAS 0.007 0.059 -10000 0 -0.58 5 5
RRAS -0.015 0.12 -10000 0 -0.6 9 9
DNM1 0.011 0.035 -10000 0 -0.52 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.084 0.17 -10000 0 -0.48 40 40
lamellipodium assembly -0.089 0.13 -10000 0 -0.43 41 41
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.075 0.16 -10000 0 -0.45 40 40
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
EPHB2 0.006 0.063 -10000 0 -0.52 7 7
EPHB3 0.011 0.038 -10000 0 -0.58 2 2
EPHB1 -0.14 0.23 -10000 0 -0.47 155 155
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.061 0.15 -10000 0 -0.44 40 40
Ephrin B/EPHB2 -0.018 0.12 -10000 0 -0.41 22 22
Ephrin B/EPHB3 -0.016 0.12 -10000 0 -0.38 20 20
JNK cascade -0.05 0.13 -10000 0 -0.5 10 10
Ephrin B/EPHB1 -0.094 0.18 -10000 0 -0.48 48 48
RAP1/GDP -0.042 0.13 -10000 0 -0.38 39 39
EFNB2 -0.006 0.1 -10000 0 -0.58 16 16
EFNB3 -0.05 0.16 -10000 0 -0.47 63 63
EFNB1 0.008 0.049 -10000 0 -0.47 5 5
Ephrin B2/EPHB1-2 -0.075 0.15 -10000 0 -0.27 165 165
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.096 0.15 -10000 0 -0.48 41 41
Rap1/GTP -0.089 0.14 -10000 0 -0.43 41 41
axon guidance -0.019 0.1 -10000 0 -0.3 57 57
MAPK3 -0.055 0.14 -10000 0 -0.39 40 40
MAPK1 -0.055 0.14 -10000 0 -0.39 40 40
Rac1/GDP -0.05 0.14 -10000 0 -0.4 40 40
actin cytoskeleton reorganization -0.07 0.11 -10000 0 -0.34 44 44
CDC42/GDP -0.05 0.14 -10000 0 -0.4 40 40
PI3K 0.017 0.069 -10000 0 -0.31 17 17
EFNA5 -0.041 0.15 -10000 0 -0.47 54 54
Ephrin B2/EPHB4 0.006 0.067 -10000 0 -0.36 16 16
Ephrin B/EPHB2/Intersectin/N-WASP -0.009 0.12 -10000 0 -0.64 7 7
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.089 0.13 -10000 0 -0.42 44 44
PTK2 0.023 0.034 -10000 0 -10000 0 0
MAP4K4 -0.051 0.13 -10000 0 -0.5 10 10
SRC 0.013 0 -10000 0 -10000 0 0
KALRN 0.01 0.046 -10000 0 -0.58 3 3
Intersectin/N-WASP 0.02 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.035 0.14 -10000 0 -0.37 37 37
MAP2K1 -0.064 0.15 -10000 0 -0.42 40 40
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.059 0.14 -10000 0 -0.54 10 10
cell migration -0.072 0.17 -10000 0 -0.47 40 40
NRAS 0.012 0.022 -10000 0 -0.47 1 1
SYNJ1 -0.012 0.12 -10000 0 -0.62 7 7
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.061 0.17 -10000 0 -0.46 44 44
HRAS/GTP -0.099 0.15 -10000 0 -0.46 44 44
Ephrin B1/EPHB1-2 -0.067 0.14 -10000 0 -0.26 157 157
cell adhesion mediated by integrin 0.026 0.11 0.36 20 -10000 0 20
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.08 0.17 -10000 0 -0.5 41 41
RAC1-CDC42/GTP -0.089 0.14 -10000 0 -0.43 43 43
RASA1 0.01 0.038 -10000 0 -0.47 3 3
RAC1-CDC42/GDP -0.042 0.13 -10000 0 -0.38 39 39
ruffle organization -0.056 0.16 -10000 0 -0.43 41 41
NCK1 0.012 0.027 -10000 0 -0.58 1 1
receptor internalization -0.007 0.11 -10000 0 -0.56 8 8
Ephrin B/EPHB2/KALRN -0.012 0.13 -10000 0 -0.63 8 8
ROCK1 0.019 0.036 -10000 0 -0.26 8 8
RAS family/GDP -0.065 0.1 -10000 0 -0.44 13 13
Rac1/GTP -0.094 0.14 -10000 0 -0.46 41 41
Ephrin B/EPHB1/Src/Paxillin -0.082 0.17 -10000 0 -0.48 40 40
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.074 -9999 0 -0.4 14 14
Syndecan-4/Syndesmos -0.1 0.14 -9999 0 -0.46 28 28
positive regulation of JNK cascade -0.1 0.15 -9999 0 -0.46 34 34
Syndecan-4/ADAM12 -0.12 0.16 -9999 0 -0.48 45 45
CCL5 -0.007 0.1 -9999 0 -0.5 19 19
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 -0.002 0.085 -9999 0 -0.48 15 15
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.018 0.13 -9999 0 -0.57 24 24
ADAM12 -0.017 0.13 -9999 0 -0.56 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.062 0.054 -9999 0 -0.17 11 11
Syndecan-4/Laminin alpha1 -0.13 0.16 -9999 0 -0.48 51 51
Syndecan-4/CXCL12/CXCR4 -0.11 0.16 -9999 0 -0.49 34 34
Syndecan-4/Laminin alpha3 -0.12 0.16 -9999 0 -0.45 50 50
MDK -0.012 0.12 -9999 0 -0.57 21 21
Syndecan-4/FZD7 -0.11 0.15 -9999 0 -0.47 34 34
Syndecan-4/Midkine -0.12 0.16 -9999 0 -0.48 41 41
FZD7 -0.004 0.089 -9999 0 -0.47 17 17
Syndecan-4/FGFR1/FGF -0.12 0.13 -9999 0 -0.47 31 31
THBS1 -0.011 0.11 -9999 0 -0.49 23 23
integrin-mediated signaling pathway -0.11 0.15 -9999 0 -0.44 42 42
positive regulation of MAPKKK cascade -0.1 0.15 -9999 0 -0.46 34 34
Syndecan-4/TACI -0.14 0.17 -9999 0 -0.47 70 70
CXCR4 0.004 0.07 -9999 0 -0.54 8 8
cell adhesion 0.01 0.077 -9999 0 -0.35 13 13
Syndecan-4/Dynamin -0.1 0.14 -9999 0 -0.46 28 28
Syndecan-4/TSP1 -0.12 0.15 -9999 0 -0.47 38 38
Syndecan-4/GIPC -0.1 0.14 -9999 0 -0.46 28 28
Syndecan-4/RANTES -0.11 0.15 -9999 0 -0.47 37 37
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.041 0.16 -9999 0 -0.53 48 48
LAMA3 -0.03 0.14 -9999 0 -0.48 43 43
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.019 0.097 -9999 0 -0.42 20 20
Syndecan-4/alpha-Actinin -0.11 0.15 -9999 0 -0.46 31 31
TFPI -0.019 0.13 -9999 0 -0.52 29 29
F2 -0.03 0.13 -9999 0 -0.58 26 26
alpha5/beta1 Integrin 0.009 0.061 -9999 0 -0.33 15 15
positive regulation of cell adhesion -0.14 0.17 -9999 0 -0.46 72 72
ACTN1 0.007 0.053 -9999 0 -0.47 6 6
TNC -0.016 0.12 -9999 0 -0.47 29 29
Syndecan-4/CXCL12 -0.11 0.15 -9999 0 -0.48 35 35
FGF6 -0.001 0.037 -9999 0 -0.58 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.008 0.1 -9999 0 -0.48 21 21
TNFRSF13B -0.052 0.18 -9999 0 -0.56 53 53
FGF2 -0.024 0.13 -9999 0 -0.47 37 37
FGFR1 0.01 0.038 -9999 0 -0.47 3 3
Syndecan-4/PI-4-5-P2 -0.11 0.14 -9999 0 -0.43 41 41
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.005 0.085 -9999 0 -0.48 14 14
cell migration -0.024 0.021 -9999 0 -10000 0 0
PRKCD 0.02 0.009 -9999 0 -10000 0 0
vasculogenesis -0.11 0.15 -9999 0 -0.45 38 38
SDC4 -0.12 0.15 -9999 0 -0.45 41 41
Syndecan-4/Tenascin C -0.12 0.16 -9999 0 -0.46 42 42
Syndecan-4/PI-4-5-P2/PKC alpha -0.049 0.043 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.1 0.14 -9999 0 -0.46 28 28
MMP9 -0.31 0.29 -9999 0 -0.57 270 270
Rac1/GTP 0.009 0.078 -9999 0 -0.36 13 13
cytoskeleton organization -0.1 0.14 -9999 0 -0.45 28 28
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.12 0.16 -9999 0 -0.5 42 42
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.079 0.19 -9999 0 -0.47 93 93
CDC42/GTP -0.033 0.14 -9999 0 -0.39 42 42
PLCG1 -0.034 0.14 -9999 0 -0.4 42 42
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
cell migration -0.033 0.13 -9999 0 -0.38 42 42
S1PR5 -0.067 0.18 -9999 0 -0.47 80 80
S1PR4 -0.012 0.12 -9999 0 -0.57 21 21
MAPK3 -0.034 0.14 -9999 0 -0.4 42 42
MAPK1 -0.034 0.14 -9999 0 -0.4 42 42
S1P/S1P5/Gi -0.081 0.2 -9999 0 -0.56 57 57
GNAI1 0.005 0.065 -9999 0 -0.53 7 7
CDC42/GDP 0.01 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.031 0.11 -9999 0 -0.28 80 80
RHOA 0.015 0.064 -9999 0 -0.29 20 20
S1P/S1P4/Gi -0.044 0.15 -9999 0 -0.43 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.47 46 46
S1P/S1P4/G12/G13 0.011 0.069 -9999 0 -0.32 20 20
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.009 0.028 -9999 0 -0.42 2 2
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.003 0.08 -9999 0 -0.38 20 20
STXBP1 0.01 0.041 -9999 0 -0.51 3 3
ACh/CHRNA1 -0.072 0.15 -9999 0 -0.38 90 90
RAB3GAP2/RIMS1/UNC13B 0.013 0.069 -9999 0 -0.32 20 20
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.003 0.093 -9999 0 -0.52 15 15
mol:ACh -0.01 0.044 -9999 0 -0.11 75 75
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.029 0.071 -9999 0 -0.35 11 11
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.072 0.15 -9999 0 -0.38 90 90
UNC13B 0.007 0.059 -9999 0 -0.58 5 5
CHRNA1 -0.097 0.23 -9999 0 -0.58 90 90
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.058 0.14 -9999 0 -0.33 92 92
SNAP25 -0.035 0.099 -9999 0 -0.27 74 74
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.081 0.2 -9999 0 -0.48 92 92
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.014 0.035 -9999 0 -0.32 5 5
STX1A/SNAP25 fragment 1/VAMP2 -0.029 0.071 -9999 0 -0.35 11 11
IL27-mediated signaling events

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
TGFB1 0.007 0.038 -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 0.027 0.17 0.61 22 -10000 0 22
IL27/IL27R/JAK1 0.002 0.25 0.4 1 -0.82 21 22
TBX21 0.009 0.22 0.35 1 -0.61 32 33
IL12B -0.024 0.14 -10000 0 -0.58 29 29
IL12A -0.003 0.069 -10000 0 -0.38 16 16
IL6ST -0.084 0.2 -10000 0 -0.48 100 100
IL27RA/JAK1 0.002 0.17 -10000 0 -1 12 12
IL27 -0.01 0.11 -10000 0 -0.57 18 18
TYK2 0.015 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.087 0.15 -10000 0 -0.61 7 7
T-helper 2 cell differentiation 0.027 0.17 0.61 22 -10000 0 22
T cell proliferation during immune response 0.027 0.17 0.61 22 -10000 0 22
MAPKKK cascade -0.027 0.17 -10000 0 -0.61 22 22
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.003 0.084 -10000 0 -0.58 10 10
IL12RB1 -0.012 0.12 -10000 0 -0.55 22 22
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.011 0.21 0.35 1 -0.6 25 26
IL27/IL27R/JAK2/TYK2 -0.027 0.18 -10000 0 -0.62 22 22
positive regulation of T cell mediated cytotoxicity -0.027 0.17 -10000 0 -0.61 22 22
STAT1 (dimer) 0.02 0.31 0.49 102 -0.86 19 121
JAK2 0.012 0.023 -10000 0 -0.47 1 1
JAK1 0.016 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.02 0.16 -10000 0 -0.58 22 22
T cell proliferation -0.11 0.21 -10000 0 -0.5 66 66
IL12/IL12R/TYK2/JAK2 0.009 0.085 -10000 0 -0.43 6 6
IL17A -0.09 0.14 -10000 0 -0.61 7 7
mast cell activation 0.027 0.17 0.61 22 -10000 0 22
IFNG -0.001 0.032 -10000 0 -0.087 24 24
T cell differentiation -0.003 0.006 0.015 1 -0.02 31 32
STAT3 (dimer) -0.02 0.16 -10000 0 -0.58 22 22
STAT5A (dimer) -0.021 0.17 -10000 0 -0.6 22 22
STAT4 (dimer) -0.03 0.18 -10000 0 -0.57 33 33
STAT4 -0.008 0.11 -10000 0 -0.55 18 18
T cell activation -0.007 0.02 0.12 12 -10000 0 12
IL27R/JAK2/TYK2 -0.051 0.19 -10000 0 -1.1 12 12
GATA3 -0.34 0.56 -10000 0 -1.2 142 142
IL18 0.002 0.054 -10000 0 -0.34 12 12
positive regulation of mast cell cytokine production -0.019 0.16 -10000 0 -0.56 22 22
IL27/EBI3 -0.004 0.1 -10000 0 -0.41 30 30
IL27RA -0.017 0.18 -10000 0 -1.1 12 12
IL6 -0.16 0.25 -10000 0 -0.51 155 155
STAT5A 0.011 0.031 -10000 0 -0.47 2 2
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.012 0.075 0.48 11 -10000 0 11
IL1B -0.045 0.13 -10000 0 -0.36 72 72
EBI3 0.002 0.089 -10000 0 -0.55 12 12
TNF -0.02 0.1 -10000 0 -0.36 39 39
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.007 0.059 -9999 0 -0.58 5 5
EGFR -0.026 0.13 -9999 0 -0.47 39 39
EGF/EGFR -0.09 0.16 -9999 0 -0.4 69 69
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.12 -9999 0 -0.45 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.039 0.15 -9999 0 -0.47 52 52
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.056 0.18 -9999 0 -0.54 61 61
EGF/EGFR dimer/SHC -0.04 0.14 -9999 0 -0.31 97 97
mol:GDP -0.021 0.12 -9999 0 -0.45 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.024 0.13 -9999 0 -0.5 35 35
GRB2/SOS1 0.02 0 -9999 0 -10000 0 0
HRAS/GTP -0.048 0.098 -9999 0 -0.44 6 6
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.049 0.1 -9999 0 -0.46 6 6
FRAP1 -0.022 0.11 -9999 0 -0.43 3 3
EGF/EGFR dimer -0.059 0.16 -9999 0 -0.37 97 97
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.043 0.15 -9999 0 -0.39 75 75
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.067 0.15 0.35 109 -10000 0 109
KIRREL -0.087 0.2 -10000 0 -0.48 99 99
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.068 0.15 -10000 0 -0.35 109 109
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.039 0.12 -10000 0 -0.54 2 2
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.029 0.1 -10000 0 -0.42 3 3
FYN -0.041 0.11 -10000 0 -0.29 13 13
mol:Ca2+ -0.04 0.11 -10000 0 -0.32 14 14
mol:DAG -0.04 0.12 -10000 0 -0.32 14 14
NPHS2 -0.011 0.05 -10000 0 -0.59 3 3
mol:IP3 -0.04 0.12 -10000 0 -0.32 14 14
regulation of endocytosis -0.031 0.1 -10000 0 -0.47 2 2
Nephrin/NEPH1/podocin/Cholesterol -0.048 0.12 -10000 0 -0.26 109 109
establishment of cell polarity -0.067 0.15 -10000 0 -0.35 109 109
Nephrin/NEPH1/podocin/NCK1-2 -0.028 0.11 -10000 0 -0.5 3 3
Nephrin/NEPH1/beta Arrestin2 -0.03 0.1 -10000 0 -0.48 2 2
NPHS1 -0.016 0.087 -10000 0 -0.57 11 11
Nephrin/NEPH1/podocin -0.041 0.11 -10000 0 -0.29 14 14
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.012 0.027 -10000 0 -0.58 1 1
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.039 0.12 -10000 0 -0.33 14 14
CD2AP 0.013 0.001 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.039 0.12 -10000 0 -0.33 14 14
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.079 0.16 -10000 0 -0.34 96 96
cytoskeleton organization -0.029 0.12 -10000 0 -0.46 3 3
Nephrin/NEPH1 -0.045 0.11 -10000 0 -0.24 109 109
Nephrin/NEPH1/ZO-1 -0.043 0.12 -10000 0 -0.34 12 12
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR 0.012 0.022 -9999 0 -0.47 1 1
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.038 0.15 -9999 0 -0.36 83 83
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
KATNA1 0.013 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.028 0.13 -9999 0 -0.32 78 78
IQGAP1/CaM 0.02 0 -9999 0 -10000 0 0
DAB1 -0.17 0.24 -9999 0 -0.47 187 187
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.14 0.26 -9999 0 -0.57 124 124
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.013 0.052 -9999 0 -0.42 7 7
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 -0.016 0.13 -9999 0 -0.58 24 24
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.053 0.18 -9999 0 -0.58 54 54
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.14 0.2 -9999 0 -0.34 224 224
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.022 0.13 -9999 0 -0.41 20 20
MAP1B -0.022 0.074 -9999 0 -0.27 40 40
RAC1 0.02 0 -9999 0 -10000 0 0
p35/CDK5 -0.026 0.14 -9999 0 -0.61 9 9
RELN -0.081 0.22 -9999 0 -0.57 79 79
PAFAH/LIS1 -0.069 0.16 -9999 0 -0.35 124 124
LIS1/CLIP170 0.025 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.045 0.084 -9999 0 -0.44 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.16 -9999 0 -0.44 58 58
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.031 0.14 -9999 0 -0.44 21 21
LIS1/IQGAP1 0.025 0 -9999 0 -10000 0 0
RHOA 0.02 0 -9999 0 -10000 0 0
PAFAH1B1 0.021 0 -9999 0 -10000 0 0
PAFAH1B3 -0.01 0.11 -9999 0 -0.57 19 19
PAFAH1B2 -0.002 0.084 -9999 0 -0.47 15 15
MAP1B/LIS1/Dynein heavy chain 0.009 0.051 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.015 0.13 -9999 0 -0.39 20 20
LRP8 0.005 0.07 -9999 0 -0.58 7 7
NDEL1/Katanin 60 -0.022 0.13 -9999 0 -0.41 21 21
P39/CDK5 -0.046 0.16 -9999 0 -0.55 15 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0 -9999 0 -10000 0 0
CDK5 -0.02 0.12 -9999 0 -0.58 3 3
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.11 0.18 -9999 0 -0.52 43 43
RELN/VLDLR -0.026 0.14 -9999 0 -0.32 78 78
CDC42 0.02 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.075 0.19 -9999 0 -0.47 88 88
GNB1/GNG2 -0.031 0.14 -9999 0 -0.44 27 27
mol:DAG -0.023 0.13 -9999 0 -0.44 19 19
PLCG1 -0.024 0.13 -9999 0 -0.46 19 19
YES1 -0.038 0.14 -9999 0 -0.45 25 25
FZD3 0.011 0.031 -9999 0 -0.47 2 2
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.024 0.13 -9999 0 -0.46 19 19
MAP3K7 -0.05 0.15 -9999 0 -0.4 38 38
mol:Ca2+ -0.022 0.12 -9999 0 -0.42 19 19
mol:IP3 -0.023 0.13 -9999 0 -0.44 19 19
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.06 0.16 -9999 0 -0.41 52 52
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.048 0.15 -9999 0 -0.46 28 28
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.038 0.14 -9999 0 -0.45 25 25
GO:0007205 -0.023 0.13 -9999 0 -0.43 19 19
WNT6 -0.085 0.2 -9999 0 -0.48 97 97
WNT4 0.007 0.053 -9999 0 -0.47 6 6
NFAT1/CK1 alpha -0.056 0.16 -9999 0 -0.44 32 32
GNG2 0.008 0.049 -9999 0 -0.47 5 5
WNT5A -0.027 0.14 -9999 0 -0.51 38 38
WNT11 -0.025 0.14 -9999 0 -0.55 33 33
CDC42 -0.03 0.13 -9999 0 -0.42 25 25
PDGFR-alpha signaling pathway

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
PDGFRA -0.017 0.11 -9999 0 -0.5 25 25
PDGF/PDGFRA/CRKL -0.001 0.08 -9999 0 -0.34 25 25
positive regulation of JUN kinase activity 0.017 0.061 -9999 0 -0.32 1 1
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.088 0.17 -9999 0 -0.36 134 134
AP1 -0.16 0.34 -9999 0 -0.87 88 88
mol:IP3 -0.005 0.088 -9999 0 -0.37 25 25
PLCG1 -0.005 0.089 -9999 0 -0.37 25 25
PDGF/PDGFRA/alphaV Integrin -0.003 0.087 -9999 0 -0.36 25 25
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.088 -9999 0 -0.37 25 25
CAV3 -0.1 0.21 -9999 0 -0.49 114 114
CAV1 -0.049 0.16 -9999 0 -0.47 62 62
SHC/Grb2/SOS1 0.018 0.061 -9999 0 -0.32 1 1
PDGF/PDGFRA/Shf -0.003 0.086 -9999 0 -0.36 26 26
FOS -0.13 0.35 -9999 0 -0.86 88 88
JUN -0.017 0.054 -9999 0 -0.42 7 7
oligodendrocyte development -0.003 0.087 -9999 0 -0.36 25 25
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
mol:DAG -0.005 0.088 -9999 0 -0.37 25 25
PDGF/PDGFRA -0.017 0.11 -9999 0 -0.5 25 25
actin cytoskeleton reorganization -0.004 0.09 -9999 0 -0.36 27 27
SRF 0.023 0.01 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K 0.005 0.084 -9999 0 -0.34 21 21
PDGF/PDGFRA/Crk/C3G 0.009 0.068 -9999 0 -0.28 25 25
JAK1 0 0.08 -9999 0 -0.34 25 25
ELK1/SRF 0.017 0.067 -9999 0 -0.3 1 1
SHB 0.009 0.044 -9999 0 -0.47 4 4
SHF 0.011 0.035 -9999 0 -0.52 2 2
CSNK2A1 0.011 0.022 -9999 0 -10000 0 0
GO:0007205 -0.007 0.095 -9999 0 -0.4 25 25
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.017 0.061 -9999 0 -0.32 1 1
PDGF/PDGFRA/SHB -0.004 0.09 -9999 0 -0.36 27 27
PDGF/PDGFRA/Caveolin-1 -0.044 0.16 -9999 0 -0.42 68 68
ITGAV 0.011 0.031 -9999 0 -0.47 2 2
ELK1 -0.004 0.091 -9999 0 -0.36 25 25
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
PDGF/PDGFRA/Crk -0.001 0.08 -9999 0 -0.34 25 25
JAK-STAT cascade 0 0.08 -9999 0 -0.34 25 25
cell proliferation -0.003 0.086 -9999 0 -0.36 26 26
BCR signaling pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.029 0.12 -10000 0 -0.34 38 38
IKBKB 0.01 0.058 -10000 0 -0.22 6 6
AKT1 -0.015 0.097 0.2 8 -0.24 30 38
IKBKG 0.013 0.059 -10000 0 -0.24 6 6
CALM1 -0.006 0.08 0.23 11 -0.33 8 19
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
MAP3K1 -0.059 0.17 -10000 0 -0.41 68 68
MAP3K7 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.084 0.23 11 -0.28 22 33
DOK1 0.013 0 -10000 0 -10000 0 0
AP-1 -0.015 0.08 -10000 0 -0.23 22 22
LYN 0.013 0 -10000 0 -10000 0 0
BLNK 0.012 0.022 -10000 0 -0.47 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.064 0.19 -10000 0 -0.45 86 86
CD22 -0.076 0.17 -10000 0 -0.52 47 47
CAMK2G 0 0.076 0.22 11 -0.37 4 15
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D -0.013 0.11 -10000 0 -0.47 26 26
SHC/GRB2/SOS1 -0.051 0.12 -10000 0 -0.5 18 18
GO:0007205 -0.014 0.085 0.23 11 -0.29 22 33
SYK 0.006 0.06 -10000 0 -0.49 7 7
ELK1 -0.007 0.081 0.23 11 -0.3 13 24
NFATC1 -0.032 0.14 -10000 0 -0.34 60 60
B-cell antigen/BCR complex -0.064 0.19 -10000 0 -0.45 86 86
PAG1/CSK 0.018 0.028 -10000 0 -0.42 2 2
NFKBIB 0.014 0.023 0.082 4 -10000 0 4
HRAS -0.008 0.089 0.21 10 -0.32 17 27
NFKBIA 0.014 0.023 0.082 4 -10000 0 4
NF-kappa-B/RelA/I kappa B beta 0.018 0.02 -10000 0 -10000 0 0
RasGAP/Csk -0.038 0.17 -10000 0 -0.61 25 25
mol:GDP -0.012 0.08 0.24 11 -0.27 21 32
PTEN 0 0.078 -10000 0 -0.47 13 13
CD79B -0.016 0.12 -10000 0 -0.53 26 26
NF-kappa-B/RelA/I kappa B alpha 0.018 0.019 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.057 0.17 -10000 0 -0.43 50 50
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
mol:IP3 -0.014 0.086 0.23 11 -0.29 22 33
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.04 0.12 0.23 5 -0.37 25 30
CHUK 0.013 0.059 -10000 0 -0.24 6 6
IBTK 0.012 0.022 -10000 0 -0.47 1 1
CARD11/BCL10/MALT1/TAK1 -0.028 0.077 -10000 0 -0.43 11 11
PTPN6 -0.042 0.17 -10000 0 -0.52 42 42
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 0.016 0.022 -10000 0 -0.11 8 8
VAV2 -0.079 0.19 -10000 0 -0.49 69 69
ubiquitin-dependent protein catabolic process 0.018 0.022 0.085 4 -10000 0 4
BTK 0.01 0.08 0.31 1 -0.79 1 2
CD19 -0.12 0.2 -10000 0 -0.53 72 72
MAP4K1 -0.024 0.14 -10000 0 -0.56 32 32
CD72 -0.013 0.12 -10000 0 -0.56 22 22
PAG1 0.011 0.038 -10000 0 -0.58 2 2
MAPK14 -0.044 0.15 -10000 0 -0.39 44 44
SH3BP5 0.013 0 -10000 0 -10000 0 0
PIK3AP1 -0.014 0.092 -10000 0 -0.32 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.015 0.12 -10000 0 -0.35 45 45
RAF1 -0.001 0.085 0.21 3 -0.34 9 12
RasGAP/p62DOK/SHIP -0.076 0.16 -10000 0 -0.54 36 36
CD79A -0.076 0.2 -10000 0 -0.55 77 77
re-entry into mitotic cell cycle -0.015 0.079 -10000 0 -0.23 22 22
RASA1 0.01 0.038 -10000 0 -0.47 3 3
MAPK3 0.012 0.075 -10000 0 -0.32 5 5
MAPK1 0.012 0.075 -10000 0 -0.32 5 5
CD72/SHP1 -0.044 0.19 -10000 0 -0.56 46 46
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.048 0.16 -10000 0 -0.38 60 60
actin cytoskeleton organization -0.062 0.17 -10000 0 -0.42 69 69
NF-kappa-B/RelA 0.041 0.036 0.16 4 -10000 0 4
Calcineurin 0.003 0.066 -10000 0 -0.33 4 4
PI3K -0.094 0.16 -10000 0 -0.43 73 73
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.017 0.089 -10000 0 -0.31 27 27
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.3 -10000 0 -0.69 94 94
DAPP1 -0.15 0.31 -10000 0 -0.86 71 71
cytokine secretion -0.029 0.13 0.19 2 -0.32 60 62
mol:DAG -0.014 0.086 0.23 11 -0.29 22 33
PLCG2 0.004 0.069 -10000 0 -0.49 9 9
MAP2K1 0.006 0.08 -10000 0 -0.36 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.059 0.19 -10000 0 -0.48 61 61
mol:PI-3-4-5-P3 -0.064 0.12 0.25 8 -0.3 68 76
ETS1 0.005 0.077 0.22 11 -0.38 5 16
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.029 0.15 -10000 0 -0.38 59 59
B-cell antigen/BCR complex/LYN -0.062 0.14 -10000 0 -0.43 40 40
MALT1 0.009 0.051 -10000 0 -0.55 4 4
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 -0.067 0.18 -10000 0 -0.45 69 69
B-cell antigen/BCR complex/LYN/SYK -0.078 0.17 -10000 0 -0.55 42 42
CARD11 -0.015 0.1 0.23 8 -0.4 17 25
FCGR2B -0.01 0.11 -10000 0 -0.53 21 21
PPP3CA 0.01 0.046 -10000 0 -0.58 3 3
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex 0.013 0.031 0.089 4 -10000 0 4
PTPRC -0.013 0.11 -10000 0 -0.5 25 25
PDPK1 -0.019 0.094 0.18 8 -0.24 29 37
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.013 0 -10000 0 -10000 0 0
POU2F2 0.016 0.021 -10000 0 -0.1 2 2
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.011 0.075 -10000 0 -0.35 12 12
epithelial cell differentiation -0.032 0.077 -10000 0 -0.4 5 5
ITCH 0.018 0.013 -10000 0 -10000 0 0
WWP1 0.018 0.054 -10000 0 -0.56 1 1
FYN 0.013 0.001 -10000 0 -10000 0 0
EGFR -0.026 0.13 -10000 0 -0.47 39 39
PRL -0.003 0.052 -10000 0 -0.58 4 4
neuron projection morphogenesis -0.018 0.12 -10000 0 -0.41 11 11
PTPRZ1 -0.16 0.24 -10000 0 -0.48 174 174
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.033 0.13 -10000 0 -0.46 11 11
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.055 0.14 -10000 0 -0.35 36 36
ADAM17 0.012 0.049 -10000 0 -0.46 5 5
ErbB4/ErbB4 0.015 0.068 -10000 0 -0.43 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.026 0.11 -10000 0 -0.36 25 25
NCOR1 0.012 0.022 -10000 0 -0.47 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.044 0.13 -10000 0 -0.33 33 33
GRIN2B -0.041 0.12 -10000 0 -0.57 2 2
ErbB4/ErbB2/betacellulin 0.009 0.1 -10000 0 -0.4 18 18
STAT1 0.001 0.084 -10000 0 -0.58 10 10
HBEGF 0.002 0.078 -10000 0 -0.53 10 10
PRLR -0.042 0.16 -10000 0 -0.52 50 50
E4ICDs/ETO2 0.015 0.065 -10000 0 -0.38 5 5
axon guidance 0.033 0.077 -10000 0 -0.3 2 2
NEDD4 0.007 0.068 -10000 0 -0.46 10 10
Prolactin receptor/Prolactin receptor/Prolactin -0.033 0.12 -10000 0 -0.38 54 54
CBFA2T3 0.008 0.049 -10000 0 -0.47 5 5
ErbB4/ErbB2/HBEGF 0.018 0.073 -10000 0 -0.37 6 6
MAPK3 -0.025 0.13 -10000 0 -0.43 11 11
STAT1 (dimer) 0.01 0.079 -10000 0 -0.36 14 14
MAPK1 -0.025 0.13 -10000 0 -0.43 11 11
JAK2 0.012 0.022 -10000 0 -0.47 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.047 0.13 -10000 0 -0.34 34 34
NRG1 -0.081 0.16 -10000 0 -0.33 142 142
NRG3 -0.048 0.16 -10000 0 -0.51 53 53
NRG2 -0.16 0.23 -10000 0 -0.47 172 172
NRG4 -0.15 0.23 -10000 0 -0.48 163 163
heart development 0.033 0.077 -10000 0 -0.3 2 2
neural crest cell migration -0.046 0.13 -10000 0 -0.34 34 34
ERBB2 0.017 0.047 -10000 0 -0.32 9 9
WWOX/E4ICDs 0.017 0.06 -10000 0 -0.38 4 4
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.083 0.17 -10000 0 -0.47 40 40
apoptosis 0.029 0.11 0.34 38 -10000 0 38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.08 0.16 -10000 0 -0.4 41 41
ErbB4/ErbB2/epiregulin -0.01 0.098 -10000 0 -0.4 6 6
ErbB4/ErbB4/betacellulin/betacellulin 0 0.1 -10000 0 -0.43 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.006 0.12 -10000 0 -0.44 12 12
MDM2 0.02 0.059 -10000 0 -0.38 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.048 0.13 -10000 0 -0.31 33 33
STAT5A 0.041 0.072 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.064 0.16 -10000 0 -0.39 50 50
DLG4 0.001 0.075 -10000 0 -0.47 12 12
GRB2/SHC 0.02 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.058 -10000 0 -0.41 4 4
STAT5A (dimer) -0.033 0.082 -10000 0 -0.43 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.04 0.068 -10000 0 -10000 0 0
LRIG1 0.012 0.027 -10000 0 -0.58 1 1
EREG -0.041 0.16 -10000 0 -0.52 47 47
BTC -0.018 0.12 -10000 0 -0.47 31 31
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.031 0.076 -10000 0 -0.3 2 2
ERBB4 0.015 0.068 -10000 0 -0.43 4 4
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 0.011 0.067 -10000 0 -0.72 4 4
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.061 0.14 -10000 0 -0.37 27 27
glial cell differentiation -0.015 0.057 0.41 4 -10000 0 4
WWOX 0.012 0.022 -10000 0 -0.47 1 1
cell proliferation -0.06 0.16 -10000 0 -0.5 25 25
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.002 0.078 -9999 0 -0.24 45 45
RGS9BP 0.009 0.049 -9999 0 -0.52 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.001 0.053 -9999 0 -0.58 4 4
mol:Na + -0.015 0.089 -9999 0 -0.37 28 28
mol:ADP 0.004 0.044 -9999 0 -0.42 5 5
GNAT2 0.005 0.059 -9999 0 -0.58 5 5
RGS9-1/Gbeta5/R9AP -0.04 0.12 -9999 0 -0.27 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.003 0.054 -9999 0 -0.4 8 8
GRK7 0.006 0.027 -9999 0 -0.58 1 1
CNGB3 -0.014 0.1 -9999 0 -0.58 15 15
Cone Metarhodopsin II/X-Arrestin 0.001 0.028 -9999 0 -0.42 2 2
mol:Ca2+ -0.04 0.13 -9999 0 -0.34 72 72
Cone PDE6 -0.033 0.11 -9999 0 -0.52 2 2
Cone Metarhodopsin II 0.004 0.034 -9999 0 -0.33 5 5
Na + (4 Units) -0.04 0.13 -9999 0 -0.34 72 72
GNAT2/GDP -0.03 0.11 -9999 0 -0.36 10 10
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.004 0.049 -9999 0 -0.36 8 8
Cone Transducin -0.002 0.083 -9999 0 -0.26 45 45
SLC24A2 -0.047 0.17 -9999 0 -0.58 46 46
GNB3/GNGT2 -0.01 0.099 -9999 0 -0.34 40 40
GNB3 -0.022 0.12 -9999 0 -0.47 35 35
GNAT2/GTP 0.004 0.044 -9999 0 -0.42 5 5
CNGA3 -0.011 0.098 -9999 0 -0.58 14 14
ARR3 0.002 0.038 -9999 0 -0.58 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.015 0.089 -9999 0 -0.37 28 28
mol:Pi -0.04 0.12 -9999 0 -0.27 109 109
Cone CNG Channel -0.022 0.081 -9999 0 -0.33 14 14
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.047 0.17 -9999 0 -0.57 46 46
RGS9 -0.092 0.2 -9999 0 -0.47 105 105
PDE6C 0.003 0.005 -9999 0 -10000 0 0
GNGT2 0.007 0.056 -9999 0 -0.49 6 6
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.053 -9999 0 -0.58 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.013 0.1 -10000 0 -0.33 46 46
CRKL -0.003 0.11 -10000 0 -0.44 17 17
mol:PIP3 -0.005 0.073 0.44 13 -10000 0 13
AKT1 0.01 0.051 0.32 13 -10000 0 13
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 0.004 0.11 -10000 0 -0.42 17 17
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
HGF/MET/SHIP2 -0.024 0.13 -10000 0 -0.34 67 67
MAP3K5 0.004 0.11 -10000 0 -0.41 19 19
HGF/MET/CIN85/CBL/ENDOPHILINS -0.013 0.12 -10000 0 -0.42 27 27
AP1 -0.05 0.14 -10000 0 -0.33 88 88
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.12 0.29 -10000 0 -0.73 83 83
STAT3 (dimer) -0.001 0.11 -10000 0 -0.44 18 18
GAB1/CRKL/SHP2/PI3K 0.012 0.12 -10000 0 -0.42 21 21
INPP5D -0.013 0.11 -10000 0 -0.47 26 26
CBL/CRK 0.005 0.11 -10000 0 -0.43 17 17
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0 0.078 -10000 0 -0.47 13 13
ELK1 -0.016 0.051 -10000 0 -0.17 46 46
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.023 0.065 -10000 0 -0.3 17 17
PAK1 0.012 0.054 0.3 13 -10000 0 13
HGF/MET/RANBP10 -0.024 0.13 -10000 0 -0.34 67 67
HRAS -0.038 0.2 -10000 0 -0.63 46 46
DOCK1 0.003 0.11 -10000 0 -0.43 17 17
GAB1 -0.01 0.12 -10000 0 -0.32 47 47
CRK -0.003 0.11 -10000 0 -0.44 17 17
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.2 -10000 0 -0.58 57 57
JUN 0.006 0.061 -10000 0 -0.5 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.022 0.099 -10000 0 -0.27 57 57
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
cell morphogenesis 0.017 0.13 -10000 0 -0.47 21 21
GRB2/SHC -0.004 0.09 -10000 0 -0.36 16 16
FOS -0.076 0.19 -10000 0 -0.48 88 88
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.016 0.051 -10000 0 -0.17 46 46
HGF/MET/MUC20 -0.033 0.13 -10000 0 -0.35 67 67
cell migration -0.004 0.088 -10000 0 -0.35 16 16
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.012 0.022 -10000 0 -0.47 1 1
MET/RANBP10 -0.013 0.1 -10000 0 -0.33 46 46
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.006 0.11 -10000 0 -0.44 18 18
MET/MUC20 -0.023 0.1 -10000 0 -0.34 46 46
RAP1B 0.011 0.1 -10000 0 -0.38 17 17
RAP1A 0.011 0.1 -10000 0 -0.38 17 17
HGF/MET/RANBP9 -0.024 0.13 -10000 0 -0.34 67 67
RAF1 -0.029 0.19 -10000 0 -0.59 46 46
STAT3 -0.001 0.11 -10000 0 -0.44 18 18
cell proliferation -0.005 0.15 -10000 0 -0.42 47 47
RPS6KB1 -0.001 0.038 -10000 0 -10000 0 0
MAPK3 -0.02 0.046 -10000 0 -10000 0 0
MAPK1 -0.02 0.046 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 0.012 0.12 -10000 0 -0.39 29 29
SRC 0.001 0.1 -10000 0 -0.41 18 18
PI3K -0.008 0.1 -10000 0 -0.39 21 21
MET/Glomulin -0.016 0.089 -10000 0 -0.29 46 46
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.019 0.18 -10000 0 -0.54 46 46
MET -0.033 0.14 -10000 0 -0.47 46 46
MAP4K1 -0.002 0.12 -10000 0 -0.44 19 19
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.02 0.18 -10000 0 -0.54 47 47
BAD 0.014 0.049 0.3 13 -0.3 1 14
MAP2K4 0.011 0.1 -10000 0 -0.37 19 19
SHP2/GRB2/SOS1/GAB1 -0.04 0.11 -10000 0 -0.37 46 46
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.014 0.092 -10000 0 -0.27 46 46
PLCgamma1/PKC 0.01 0 -10000 0 -10000 0 0
HGF -0.026 0.14 -10000 0 -0.5 37 37
RASA1 0.01 0.038 -10000 0 -0.47 3 3
NCK1 0.012 0.027 -10000 0 -0.58 1 1
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.004 0.094 -10000 0 -0.37 17 17
PDPK1 0.002 0.058 0.35 13 -10000 0 13
HGF/MET/SHIP -0.038 0.17 -10000 0 -0.41 73 73
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.038 -10000 0 -0.58 2 2
Jak2/Leptin Receptor -0.03 0.12 0.19 15 -0.41 19 34
PTP1B/AKT1 -0.037 0.081 -10000 0 -0.32 11 11
FYN 0.013 0.001 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.048 0.089 -10000 0 -0.3 23 23
EGFR -0.028 0.13 -10000 0 -0.48 39 39
EGF/EGFR -0.079 0.14 -10000 0 -0.36 69 69
CSF1 0.003 0.069 -10000 0 -0.47 10 10
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.11 0.15 -10000 0 -0.34 100 100
Insulin Receptor/Insulin -0.042 0.067 -10000 0 -0.31 12 12
HCK 0.009 0.046 -10000 0 -0.5 4 4
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.039 0.085 -10000 0 -0.32 13 13
EGF -0.058 0.18 -10000 0 -0.54 61 61
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.062 0.12 -10000 0 -0.39 36 36
TXN 0.011 0.027 -10000 0 -0.58 1 1
PTP1B/IRS1/GRB2 -0.038 0.1 -10000 0 -0.38 17 17
cell migration 0.048 0.089 0.3 23 -10000 0 23
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.041 0.16 -10000 0 -0.52 50 50
ITGA2B -0.004 0.091 -10000 0 -0.51 15 15
CSF1R 0.011 0.035 -10000 0 -0.52 2 2
Prolactin Receptor/Prolactin -0.033 0.13 -10000 0 -0.38 54 54
FGR 0.01 0.041 -10000 0 -0.51 3 3
PTP1B/p130 Cas -0.039 0.085 -10000 0 -0.33 12 12
Crk/p130 Cas -0.031 0.083 -10000 0 -0.32 11 11
DOK1 -0.029 0.079 -10000 0 -0.33 7 7
JAK2 -0.033 0.1 -10000 0 -0.41 16 16
Jak2/Leptin Receptor/Leptin -0.085 0.14 -10000 0 -0.43 54 54
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
PTPN1 -0.049 0.09 -10000 0 -0.3 23 23
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.12 0.22 -10000 0 -0.48 136 136
SRC -0.004 0.036 -10000 0 -10000 0 0
ITGB3 -0.084 0.19 -10000 0 -0.47 97 97
CAT1/PTP1B -0.039 0.1 -10000 0 -0.41 9 9
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.035 0.074 -10000 0 -0.48 4 4
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.084 0.15 -10000 0 -0.42 70 70
negative regulation of transcription -0.03 0.1 -10000 0 -0.4 16 16
FCGR2A 0.01 0.044 -10000 0 -0.54 3 3
FER -0.009 0.1 -10000 0 -0.48 21 21
alphaIIb/beta3 Integrin -0.062 0.16 -10000 0 -0.34 108 108
BLK -0.1 0.22 -10000 0 -0.5 109 109
Insulin Receptor/Insulin/Shc 0.008 0.06 -10000 0 -0.34 14 14
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR -0.007 0.098 -10000 0 -0.47 21 21
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.013 0.097 -10000 0 -0.41 4 4
PRL -0.002 0.053 -10000 0 -0.57 4 4
SOCS3 -0.14 0.41 -10000 0 -1.2 60 60
SPRY2 0.011 0.045 -10000 0 -0.48 4 4
Insulin Receptor/Insulin/IRS1 -0.002 0.081 -10000 0 -0.32 29 29
CSF1/CSF1R -0.037 0.1 -10000 0 -0.45 14 14
Ras protein signal transduction 0.028 0.027 -10000 0 -10000 0 0
IRS1 -0.003 0.086 -10000 0 -0.47 16 16
INS -0.016 0.096 -10000 0 -0.57 14 14
LEP -0.006 0.083 -10000 0 -0.58 10 10
STAT5B -0.037 0.087 -10000 0 -0.3 18 18
STAT5A -0.037 0.087 -10000 0 -0.3 18 18
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.04 0.087 -10000 0 -0.33 14 14
CSN2 -0.002 0.054 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
LAT -0.012 0.063 -10000 0 -0.51 4 4
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK 0.003 0.075 -10000 0 -0.58 8 8
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.27 0.29 -10000 0 -0.57 237 237
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.049 0.14 -10000 0 -0.52 31 31
FYN -0.011 0.2 -10000 0 -0.67 33 33
LAT/GRAP2/SLP76 -0.06 0.16 -10000 0 -0.54 40 40
IKBKB 0.012 0.027 -10000 0 -0.58 1 1
AKT1 0.001 0.14 -10000 0 -0.44 35 35
B2M 0.014 0.003 -10000 0 -10000 0 0
IKBKG -0.012 0.036 -10000 0 -0.15 20 20
MAP3K8 0 0.08 -10000 0 -0.48 13 13
mol:Ca2+ -0.003 0.013 -10000 0 -0.13 2 2
integrin-mediated signaling pathway 0.004 0.061 -10000 0 -0.28 22 22
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.016 0.21 -10000 0 -0.65 37 37
TRPV6 -0.002 0.049 -10000 0 -0.53 4 4
CD28 -0.039 0.17 -10000 0 -0.56 45 45
SHC1 -0.016 0.2 -10000 0 -0.64 34 34
receptor internalization -0.028 0.21 -10000 0 -0.6 43 43
PRF1 -0.016 0.23 -10000 0 -1.1 18 18
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 0.006 0.12 -10000 0 -0.38 30 30
LAT -0.022 0.21 -10000 0 -0.64 40 40
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.55 35 35
CD3E -0.007 0.1 -10000 0 -0.52 19 19
CD3G -0.042 0.16 -10000 0 -0.51 52 52
RASGRP2 0.001 0.04 -10000 0 -0.17 22 22
RASGRP1 0.004 0.14 -10000 0 -0.44 35 35
HLA-A 0.002 0.079 -10000 0 -0.51 11 11
RASSF5 -0.009 0.1 -10000 0 -0.47 22 22
RAP1A/GTP/RAPL 0.005 0.061 -10000 0 -0.28 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.048 -10000 0 -0.13 24 24
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.025 0.064 -10000 0 -0.26 27 27
PRKCA -0.034 0.081 -10000 0 -0.29 34 34
GRAP2 -0.008 0.1 -10000 0 -0.48 21 21
mol:IP3 -0.047 0.12 0.2 3 -0.45 32 35
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.022 0.21 -10000 0 -0.65 34 34
ORAI1 0.005 0.027 0.29 4 -10000 0 4
CSK -0.018 0.2 -10000 0 -0.66 34 34
B7 family/CD28 -0.036 0.23 -10000 0 -0.73 36 36
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.03 0.23 -10000 0 -0.75 35 35
PTPN6 -0.015 0.2 -10000 0 -0.68 32 32
VAV1 -0.025 0.22 -10000 0 -0.68 37 37
Monovalent TCR/CD3 -0.029 0.16 -10000 0 -0.39 61 61
CBL 0.012 0.022 -10000 0 -0.47 1 1
LCK -0.014 0.21 -10000 0 -0.69 34 34
PAG1 -0.018 0.2 -10000 0 -0.67 34 34
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.025 0.23 -10000 0 -0.72 36 36
CD80 -0.027 0.15 -10000 0 -0.58 33 33
CD86 0.004 0.074 -10000 0 -0.57 8 8
PDK1/CARD11/BCL10/MALT1 -0.03 0.078 -10000 0 -0.31 28 28
HRAS 0.007 0.059 -10000 0 -0.58 5 5
GO:0035030 -0.024 0.19 -10000 0 -0.58 36 36
CD8A -0.005 0.099 -10000 0 -0.51 18 18
CD8B -0.008 0.11 -10000 0 -0.52 20 20
PTPRC -0.013 0.12 -10000 0 -0.5 25 25
PDK1/PKC theta -0.004 0.18 -10000 0 -0.56 35 35
CSK/PAG1 -0.013 0.2 -10000 0 -0.67 31 31
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.058 -10000 0 -0.37 11 11
GRAP2/SLP76 -0.066 0.19 -10000 0 -0.65 36 36
STIM1 0.003 0.014 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.063 -10000 0 -0.17 26 26
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.032 0.23 -10000 0 -0.64 43 43
mol:DAG -0.043 0.11 -10000 0 -0.39 35 35
RAP1A/GDP 0.01 0.021 -10000 0 -0.063 5 5
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.01 0.12 -10000 0 -0.56 21 21
cytotoxic T cell degranulation -0.013 0.22 -10000 0 -0.93 20 20
RAP1A/GTP -0.004 0.013 -10000 0 -0.066 12 12
mol:PI-3-4-5-P3 -0.007 0.17 -10000 0 -0.52 37 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.06 0.16 0.22 2 -0.58 34 36
NRAS 0.012 0.022 -10000 0 -0.47 1 1
ZAP70 -0.054 0.19 -10000 0 -0.57 56 56
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.062 0.16 -10000 0 -0.54 40 40
MALT1 0.009 0.051 -10000 0 -0.55 4 4
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.007 0.12 -10000 0 -0.45 30 30
CARD11 -0.004 0.095 -10000 0 -0.52 16 16
PRKCB -0.058 0.1 -10000 0 -0.29 58 58
PRKCE -0.029 0.074 -10000 0 -0.28 29 29
PRKCQ -0.016 0.2 -10000 0 -0.65 36 36
LCP2 0.006 0.061 -10000 0 -0.54 6 6
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.006 0.12 -10000 0 -0.37 35 35
IKK complex 0.014 0.054 -10000 0 -0.12 28 28
RAS family/GDP -0.003 0.01 -10000 0 -0.074 4 4
MAP3K14 0.014 0.095 -10000 0 -0.29 28 28
PDPK1 0.005 0.14 -10000 0 -0.44 31 31
TCR/CD3/MHC I/CD8/Fyn -0.021 0.23 -10000 0 -0.74 34 34
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.1 -9999 0 -0.49 20 20
ITGA4 -0.013 0.12 -9999 0 -0.52 24 24
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.39 39 39
alpha4/beta1 Integrin 0 0.085 -9999 0 -0.37 24 24
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.027 0.12 -10000 0 -0.54 22 22
HDAC1 0.011 0.006 -10000 0 -10000 0 0
AES 0.013 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.011 0.12 -10000 0 -0.56 20 20
LRP6/FZD1 0.019 0.016 -10000 0 -0.33 1 1
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.051 0.16 -10000 0 -0.32 101 101
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.007 0.096 -10000 0 -0.47 20 20
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.061 -10000 0 -10000 0 0
NICD/RBPSUH 0.008 0.12 -10000 0 -0.52 22 22
WIF1 -0.22 0.24 -10000 0 -0.47 236 236
NOTCH1 -0.025 0.12 -10000 0 -0.55 22 22
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.025 0.14 -10000 0 -0.54 34 34
DKK1 -0.089 0.2 -10000 0 -0.48 100 100
beta catenin/beta TrCP1 0.026 0.048 0.21 1 -10000 0 1
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 -0.008 0.045 -10000 0 -0.23 7 7
CtBP/CBP/TCF1/TLE1/AES 0.004 0.062 -10000 0 -10000 0 0
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.076 0.19 -10000 0 -0.48 88 88
JUN 0.006 0.061 -10000 0 -0.5 7 7
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.02 0.05 0.22 1 -10000 0 1
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.12 -10000 0 -0.33 64 64
HNF1A -0.057 0.19 -10000 0 -0.58 57 57
CTBP1 0.013 0.002 -10000 0 -10000 0 0
MYC -0.009 0.11 -10000 0 -10000 0 0
NKD1 -0.035 0.15 -10000 0 -0.48 47 47
FZD1 0.012 0.022 -10000 0 -0.47 1 1
NOTCH1 precursor/Deltex homolog 1 -0.005 0.13 -10000 0 -0.52 22 22
apoptosis -0.05 0.16 -10000 0 -0.32 101 101
Delta 1/NOTCHprecursor 0.004 0.12 -10000 0 -0.53 22 22
DLL1 0.006 0.058 -10000 0 -0.47 7 7
PPARD 0.021 0.014 -10000 0 -10000 0 0
Gamma Secretase 0.04 0.001 -10000 0 -10000 0 0
APC -0.01 0.055 -10000 0 -0.29 10 10
DVL1 -0.002 0.034 -10000 0 -10000 0 0
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.059 0.15 -10000 0 -0.31 126 126
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.02 0.024 -10000 0 -10000 0 0
WNT1 -0.002 0.087 -10000 0 -0.58 11 11
Axin1/APC/beta catenin 0.018 0.049 -10000 0 -10000 0 0
DKK2 -0.023 0.13 -10000 0 -0.51 34 34
NOTCH1 precursor/DVL1 -0.024 0.1 -10000 0 -0.5 22 22
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.035 0.12 -10000 0 -0.53 22 22
PPP2R5D 0.015 0.075 0.24 47 -10000 0 47
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.11 0.14 -10000 0 -0.37 19 19
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.015 0.005 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0.013 -10000 0 -10000 0 0
AES 0.012 0.011 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.02 0.016 -10000 0 -0.33 1 1
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.023 0.13 -10000 0 -0.51 34 34
TLE1 0.012 0.011 -10000 0 -10000 0 0
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.087 0.081 0.26 15 -10000 0 15
WIF1 -0.22 0.24 -10000 0 -0.47 236 236
beta catenin/RanBP3 0.019 0.087 0.34 21 -10000 0 21
KREMEN2 -0.025 0.14 -10000 0 -0.54 34 34
DKK1 -0.089 0.2 -10000 0 -0.48 100 100
beta catenin/beta TrCP1 0.09 0.077 0.25 15 -10000 0 15
FZD1 0.013 0.022 -10000 0 -0.47 1 1
AXIN2 0.003 0.14 -10000 0 -1.3 5 5
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.039 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.076 -10000 0 -0.44 1 1
Axin1/APC/GSK3 0.02 0.054 0.21 17 -10000 0 17
Axin1/APC/GSK3/beta catenin/Macf1 0.064 0.055 -10000 0 -10000 0 0
HNF1A -0.057 0.19 -10000 0 -0.57 57 57
CTBP1 0.012 0.011 -10000 0 -10000 0 0
MYC -0.012 0.12 -10000 0 -0.54 2 2
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.12 -10000 0 -0.32 64 64
NKD1 -0.035 0.15 -10000 0 -0.48 47 47
TCF4 0.008 0.043 -10000 0 -0.45 4 4
TCF3 0.012 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.026 0.052 -10000 0 -0.31 11 11
Ran/GTP 0.01 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0 0.089 0.46 4 -0.43 1 5
LEF1 -0.02 0.13 -10000 0 -0.55 27 27
DVL1 0.066 0.043 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.082 -10000 0 -0.4 2 2
DKK1/LRP6/Kremen 2 -0.059 0.15 -10000 0 -0.31 123 123
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.012 0.013 -10000 0 -10000 0 0
NLK 0.014 0.002 -10000 0 -10000 0 0
CCND1 0.014 0.041 -10000 0 -10000 0 0
WNT1 -0.002 0.087 -10000 0 -0.57 11 11
GSK3A 0.013 0.022 -10000 0 -0.47 1 1
GSK3B 0.013 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.059 0.078 0.29 47 -10000 0 47
APC 0.028 0.052 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.11 0.1 0.21 229 -10000 0 229
CREBBP 0.012 0.011 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.083 -10000 0 -0.3 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.046 0.19 -10000 0 -0.48 55 55
AKT1 -0.007 0.16 -10000 0 -0.77 18 18
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.007 0.16 -10000 0 -0.77 18 18
mol:Ca2+ 0.013 0.076 -10000 0 -0.5 3 3
IGF1R 0.011 0.035 -10000 0 -0.52 2 2
E2/ER alpha (dimer)/Striatin -0.013 0.097 -10000 0 -0.3 48 48
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.006 0.15 0.73 18 -10000 0 18
RhoA/GTP -0.009 0.046 -10000 0 -0.46 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.13 -10000 0 -0.38 55 55
regulation of stress fiber formation -0.017 0.086 0.38 12 -10000 0 12
E2/ERA-ERB (dimer) -0.008 0.091 -10000 0 -0.32 37 37
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP 0.008 0.048 -10000 0 -0.25 16 16
pseudopodium formation 0.017 0.086 -10000 0 -0.38 12 12
E2/ER alpha (dimer)/PELP1 0.008 0.054 -10000 0 -0.28 16 16
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.008 0.049 -10000 0 -0.47 5 5
GNAO1 -0.079 0.19 -10000 0 -0.47 93 93
HRAS 0.007 0.059 -10000 0 -0.58 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.017 0.14 -10000 0 -0.51 20 20
E2/ER beta (dimer) -0.009 0.088 -10000 0 -0.42 21 21
mol:GDP -0.021 0.074 -10000 0 -0.35 15 15
mol:NADP -0.017 0.14 -10000 0 -0.51 20 20
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
mol:IP3 0.013 0.079 -10000 0 -0.52 3 3
IGF-1R heterotetramer 0.011 0.034 -10000 0 -0.52 2 2
PLCB1 0.008 0.079 -10000 0 -0.44 5 5
PLCB2 0.009 0.075 -10000 0 -0.43 3 3
IGF1 -0.046 0.17 -10000 0 -0.51 55 55
mol:L-citrulline -0.017 0.14 -10000 0 -0.51 20 20
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.11 0.29 -10000 0 -0.7 93 93
JNK cascade -0.009 0.088 -10000 0 -0.42 21 21
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 -0.012 0.12 -10000 0 -0.58 21 21
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.003 0.088 -10000 0 -0.48 16 16
Gq family/GDP/Gbeta gamma 0.003 0.12 -10000 0 -0.38 40 40
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.06 0.13 -10000 0 -0.38 55 55
GNAZ -0.033 0.14 -10000 0 -0.47 46 46
E2/ER alpha (dimer) -0.002 0.063 -10000 0 -0.34 16 16
STRN -0.023 0.13 -10000 0 -0.47 36 36
GNAL -0.11 0.21 -10000 0 -0.47 124 124
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 -0.005 0.088 -10000 0 -0.35 29 29
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.005 0.065 -10000 0 -0.53 7 7
HBEGF -0.12 0.18 -10000 0 -0.46 77 77
cAMP biosynthetic process -0.075 0.12 -10000 0 -0.24 146 146
SRC -0.038 0.18 -10000 0 -0.45 55 55
PI3K 0.014 0.048 -10000 0 -0.37 7 7
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.068 -10000 0 -0.5 2 2
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.068 0.14 -10000 0 -0.42 46 46
Gs family/GTP -0.076 0.12 -10000 0 -0.34 32 32
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.037 -10000 0 -0.3 6 6
vasodilation -0.015 0.13 -10000 0 -0.48 20 20
mol:DAG 0.013 0.079 -10000 0 -0.52 3 3
Gs family/GDP/Gbeta gamma -0.061 0.1 -10000 0 -0.42 18 18
MSN 0.016 0.093 -10000 0 -0.42 12 12
Gq family/GTP 0.003 0.077 -10000 0 -0.46 3 3
mol:PI-3-4-5-P3 -0.006 0.15 -10000 0 -0.74 18 18
NRAS 0.012 0.022 -10000 0 -0.47 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.015 0.13 0.48 20 -10000 0 20
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
RhoA/GDP -0.02 0.069 -10000 0 -0.33 15 15
NOS3 -0.019 0.14 -10000 0 -0.54 20 20
GNA11 -0.003 0.086 -10000 0 -0.47 16 16
MAPKKK cascade -0.019 0.16 -10000 0 -0.58 22 22
E2/ER alpha (dimer)/PELP1/Src -0.063 0.14 -10000 0 -0.4 55 55
ruffle organization 0.017 0.086 -10000 0 -0.38 12 12
ROCK2 0.013 0.09 -10000 0 -0.44 9 9
GNA14 0.012 0.022 -10000 0 -0.47 1 1
GNA15 -0.011 0.1 -10000 0 -0.47 24 24
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.19 0.2 -10000 0 -0.51 82 82
MMP2 -0.035 0.19 -10000 0 -0.5 48 48
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP 0.001 0.028 -9999 0 -0.42 2 2
Metarhodopsin II/Arrestin 0.002 0.029 -9999 0 -0.36 3 3
PDE6G/GNAT1/GTP -0.026 0.11 -9999 0 -0.36 48 48
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.038 -9999 0 -0.58 2 2
GRK1 -0.001 0.053 -9999 0 -0.58 4 4
CNG Channel -0.072 0.13 -9999 0 -0.48 20 20
mol:Na + -0.055 0.11 -9999 0 -0.53 7 7
mol:ADP -0.001 0.053 -9999 0 -0.57 4 4
RGS9-1/Gbeta5/R9AP -0.04 0.12 -9999 0 -0.27 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.056 0.12 -9999 0 -0.55 7 7
CNGB1 -0.003 0.079 -9999 0 -0.58 9 9
RDH5 -0.009 0.1 -9999 0 -0.48 22 22
SAG 0.001 0.027 -9999 0 -0.58 1 1
mol:Ca2+ -0.025 0.12 -9999 0 -0.51 7 7
Na + (4 Units) -0.051 0.11 -9999 0 -0.5 7 7
RGS9 -0.092 0.2 -9999 0 -0.47 105 105
GNB1/GNGT1 0.009 0.027 -9999 0 -0.42 2 2
GNAT1/GDP -0.033 0.11 -9999 0 -0.29 7 7
GUCY2D -0.065 0.2 -9999 0 -0.55 67 67
GNGT1 -0.002 0.037 -9999 0 -0.58 2 2
GUCY2F -0.001 0.026 -9999 0 -0.58 1 1
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.051 0.14 -9999 0 -0.34 61 61
mol:11-cis-retinal -0.009 0.1 -9999 0 -0.48 22 22
mol:cGMP -0.035 0.13 -9999 0 -0.32 68 68
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.005 0.08 -9999 0 -0.35 24 24
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.003 0.073 -9999 0 -0.53 9 9
Metarhodopsin II 0.001 0.037 -9999 0 -0.33 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.037 0.13 -9999 0 -0.34 72 72
RGS9BP 0.009 0.049 -9999 0 -0.52 4 4
Metarhodopsin II/Transducin 0.007 0.02 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0 0.067 -9999 0 -0.32 20 20
PDE6A/B -0.041 0.15 -9999 0 -0.37 75 75
mol:Pi -0.04 0.12 -9999 0 -0.27 109 109
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.008 0.03 -9999 0 -0.32 4 4
PDE6B -0.047 0.16 -9999 0 -0.47 60 60
PDE6A -0.013 0.11 -9999 0 -0.49 25 25
PDE6G -0.043 0.17 -9999 0 -0.58 46 46
RHO 0.002 0.038 -9999 0 -0.58 2 2
PDE6 -0.11 0.16 -9999 0 -0.46 53 53
GUCA1A 0.005 0.038 -9999 0 -0.58 2 2
GC2/GCAP Family -0.001 0.068 -9999 0 -0.32 20 20
GUCA1C -0.001 0.026 -9999 0 -0.58 1 1
GUCA1B -0.007 0.11 -9999 0 -0.57 17 17
Regulation of nuclear SMAD2/3 signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0.039 -10000 0 -0.46 3 3
HSPA8 0.013 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.006 0.064 -10000 0 -0.34 8 8
AKT1 0.016 0.004 -10000 0 -10000 0 0
GSC -0.12 0.22 -10000 0 -0.51 48 48
NKX2-5 -0.045 0.16 -10000 0 -0.57 42 42
muscle cell differentiation 0.045 0.086 0.41 4 -10000 0 4
SMAD2-3/SMAD4/SP1 0.048 0.054 -10000 0 -0.42 1 1
SMAD4 0.01 0.035 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.039 0.13 -10000 0 -0.28 86 86
SMAD3/SMAD4/VDR 0.016 0.056 -10000 0 -0.34 1 1
MYC -0.037 0.16 -10000 0 -0.58 39 39
CDKN2B 0.035 0.097 -10000 0 -1.3 2 2
AP1 0.004 0.13 -10000 0 -0.73 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.047 0.037 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.035 0.048 -10000 0 -0.61 1 1
SP3 0.016 0 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.12 0.24 -10000 0 -0.6 96 96
SMAD3/SMAD4/GR 0.023 0.068 -10000 0 -0.35 7 7
GATA3 -0.13 0.22 -10000 0 -0.47 142 142
SKI/SIN3/HDAC complex/NCoR1 0.042 0.019 -10000 0 -10000 0 0
MEF2C/TIF2 -0.092 0.2 -10000 0 -0.56 46 46
endothelial cell migration 0.059 0.24 0.66 43 -10000 0 43
MAX 0.016 0.012 -10000 0 -10000 0 0
RBBP7 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.011 0.031 -10000 0 -0.47 2 2
RUNX2 0.01 0.041 -10000 0 -0.51 3 3
RUNX3 0 0.084 -10000 0 -0.55 11 11
RUNX1 0.009 0.046 -10000 0 -0.5 4 4
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.003 0.08 -10000 0 -0.47 13 13
VDR 0.005 0.065 -10000 0 -0.5 8 8
CDKN1A 0.047 0.12 -10000 0 -1.2 4 4
KAT2B 0.014 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.072 0.18 -10000 0 -0.4 97 97
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.013 0.001 -10000 0 -10000 0 0
SERPINE1 -0.06 0.24 -10000 0 -0.68 41 41
SMAD3/SMAD4/ATF2 0.011 0.083 -10000 0 -0.37 2 2
SMAD3/SMAD4/ATF3 -0.025 0.14 -10000 0 -0.35 63 63
SAP30 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.032 0.036 -10000 0 -0.27 1 1
JUN 0.003 0.13 -10000 0 -0.72 7 7
SMAD3/SMAD4/IRF7 0.009 0.099 -10000 0 -0.37 26 26
TFE3 0.015 0.013 -10000 0 -10000 0 0
COL1A2 0.002 0.061 -10000 0 -0.56 4 4
mesenchymal cell differentiation -0.027 0.048 0.34 3 -10000 0 3
DLX1 -0.52 0.18 -10000 0 -0.58 438 438
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.071 0.19 -10000 0 -0.48 88 88
SMAD3/SMAD4/Max 0.031 0.039 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.026 0.026 -10000 0 -0.26 3 3
ZBTB17 0.011 0.004 -10000 0 -10000 0 0
LAMC1 0.038 0.036 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.039 -10000 0 -10000 0 0
IRF7 -0.018 0.13 -10000 0 -0.57 26 26
ESR1 -0.005 0.088 -10000 0 -0.48 16 16
HNF4A -0.029 0.14 -10000 0 -0.58 28 28
MEF2C -0.074 0.18 -10000 0 -0.56 20 20
SMAD2-3/SMAD4 0.023 0.047 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.028 0.029 -10000 0 -0.26 3 3
IGHV3OR16-13 -0.002 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.014 0.008 -10000 0 -10000 0 0
SKIL 0.001 0.078 -10000 0 -0.51 11 11
HDAC1 0.013 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.022 -10000 0 -0.47 1 1
SNIP1 0.013 0.002 -10000 0 -10000 0 0
GCN5L2 0.001 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.063 0.15 -10000 0 -0.34 108 108
SMAD2 0.006 0.023 -10000 0 -10000 0 0
SMAD3 0.02 0.03 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.068 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.015 0.022 -10000 0 -10000 0 0
NCOR1 0.012 0.022 -10000 0 -0.47 1 1
NCOA2 -0.047 0.16 -10000 0 -0.47 60 60
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.073 -10000 0 -0.39 16 16
SMAD2-3/SMAD4/SP1/MIZ-1 0.06 0.051 -10000 0 -0.38 1 1
IFNB1 0.012 0.086 -10000 0 -0.39 5 5
SMAD3/SMAD4/MEF2C -0.063 0.18 -10000 0 -0.57 17 17
CITED1 -0.097 0.21 -10000 0 -0.48 108 108
SMAD2-3/SMAD4/ARC105 0.031 0.044 -10000 0 -10000 0 0
RBL1 -0.015 0.11 -10000 0 -0.47 28 28
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.052 0.044 -10000 0 -0.53 2 2
RUNX1-3/PEBPB2 0.016 0.06 -10000 0 -0.35 9 9
SMAD7 0.028 0.12 -10000 0 -0.57 4 4
MYC/MIZ-1 -0.02 0.12 -10000 0 -0.42 39 39
SMAD3/SMAD4 0.018 0.12 0.35 1 -0.38 10 11
IL10 -0.061 0.18 -10000 0 -0.57 28 28
PIASy/HDAC complex 0.012 0.009 -10000 0 -10000 0 0
PIAS3 0.014 0.004 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.057 0.15 -10000 0 -0.48 18 18
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.012 0.009 -10000 0 -10000 0 0
ATF3 -0.074 0.19 -10000 0 -0.5 82 82
SMAD3/SMAD4/SP1 0.043 0.051 -10000 0 -0.4 1 1
FOXG1 -0.034 0.14 -10000 0 -0.58 30 30
FOXO3 0.025 0.006 -10000 0 -10000 0 0
FOXO1 0.025 0.006 -10000 0 -10000 0 0
FOXO4 0.024 0.02 -10000 0 -0.41 1 1
heart looping -0.073 0.18 -10000 0 -0.56 20 20
CEBPB 0.015 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.32 0.12 -10000 0 -0.36 438 438
MYOD1 -0.017 0.099 -10000 0 -0.55 16 16
SMAD3/SMAD4/HNF4 0.003 0.1 -10000 0 -0.37 28 28
SMAD3/SMAD4/GATA3 -0.067 0.16 -10000 0 -0.51 14 14
SnoN/SIN3/HDAC complex/NCoR1 0.001 0.078 -10000 0 -0.51 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.031 0.065 -10000 0 -0.35 2 2
SMAD3/SMAD4/SP1-3 0.054 0.048 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.021 0.015 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.084 0.19 -10000 0 -0.46 62 62
ITGB5 0.057 0.037 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.043 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.001 0.098 -10000 0 -0.34 9 9
AR -0.031 0.14 -10000 0 -0.47 44 44
negative regulation of cell growth 0.008 0.087 -10000 0 -0.36 3 3
SMAD3/SMAD4/MYOD 0.011 0.076 -10000 0 -0.37 12 12
E2F5 -0.009 0.11 -10000 0 -0.58 18 18
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.045 0.15 -10000 0 -0.4 45 45
SMAD2-3/SMAD4/FOXO1-3a-4 0.046 0.04 -10000 0 -0.4 2 2
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.004 0.13 -10000 0 -0.74 7 7
SMAD3/SMAD4/RUNX2 0.028 0.049 -10000 0 -0.34 3 3
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.016 0.12 -10000 0 -0.47 29 29
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.012 0.047 0.21 23 -10000 0 23
RFC1 0.012 0.047 0.21 23 -10000 0 23
PRKDC 0.011 0.049 0.21 23 -0.34 1 24
RIPK1 0.015 0.004 -10000 0 -10000 0 0
CASP7 -0.017 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.024 0.064 0.2 1 -0.26 24 25
MAP2K4 -0.038 0.14 -10000 0 -0.4 18 18
mol:ceramide -0.025 0.11 -10000 0 -0.37 18 18
GSN 0.01 0.046 0.21 20 -0.26 1 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.014 0.081 -10000 0 -0.32 15 15
FAS 0 0.069 -10000 0 -0.48 10 10
BID 0.003 0.02 -10000 0 -10000 0 0
MAP3K1 -0.011 0.081 -10000 0 -0.24 4 4
MAP3K7 0.01 0.005 -10000 0 -10000 0 0
RB1 0.011 0.049 0.21 23 -0.26 1 24
CFLAR 0.015 0.004 -10000 0 -10000 0 0
HGF/MET -0.025 0.14 -10000 0 -0.35 67 67
ARHGDIB 0.008 0.055 0.21 22 -0.31 4 26
FADD 0.01 0.007 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.046 0.26 1 -0.21 20 21
NFKB1 -0.058 0.084 -10000 0 -10000 0 0
MAPK8 -0.078 0.2 -10000 0 -0.42 108 108
DFFA 0.012 0.047 0.21 23 -10000 0 23
DNA fragmentation during apoptosis 0.012 0.047 0.21 23 -10000 0 23
FAS/FADD/MET -0.014 0.099 -10000 0 -0.29 53 53
CFLAR/RIP1 0.013 0.009 -10000 0 -10000 0 0
FAIM3 0.002 0.084 -10000 0 -0.57 10 10
FAF1 0.01 0.007 -10000 0 -10000 0 0
PARP1 0.012 0.047 0.21 23 -10000 0 23
DFFB 0.012 0.047 0.21 23 -10000 0 23
CHUK -0.05 0.074 -10000 0 -10000 0 0
FASLG -0.022 0.13 -10000 0 -0.54 28 28
FAS/FADD 0.006 0.051 -10000 0 -0.34 10 10
HGF -0.026 0.14 -10000 0 -0.5 37 37
LMNA 0.02 0.044 0.2 23 -0.31 1 24
CASP6 0.012 0.047 0.21 23 -10000 0 23
CASP10 0.002 0.06 -10000 0 -0.49 7 7
CASP3 0.014 0.055 0.25 23 -10000 0 23
PTPN13 0.011 0.031 -10000 0 -0.47 2 2
CASP8 0.005 0.035 0.25 10 -10000 0 10
IL6 -0.27 0.49 -10000 0 -1.2 105 105
MET -0.033 0.14 -10000 0 -0.47 46 46
ICAD/CAD 0.011 0.044 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.025 0.11 -10000 0 -0.38 18 18
activation of caspase activity by cytochrome c 0.003 0.02 -10000 0 -10000 0 0
PAK2 0.012 0.047 0.21 23 -10000 0 23
BCL2 -0.009 0.1 -10000 0 -0.47 23 23
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.011 0.034 -10000 0 -0.49 2 2
CDKN2C 0.019 0.056 -10000 0 -0.55 4 4
CDKN2A -0.11 0.24 -10000 0 -0.59 102 102
CCND2 0.018 0.059 0.25 2 -0.13 21 23
RB1 -0.012 0.066 0.14 5 -0.23 4 9
CDK4 0.029 0.064 0.26 4 -10000 0 4
CDK6 0.02 0.067 0.24 4 -0.2 8 12
G1/S progression 0.012 0.066 0.23 4 -0.14 5 9
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.043 0.12 -10000 0 -0.46 5 5
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.033 -10000 0 -0.42 3 3
GNB1/GNG2 0.015 0.03 -10000 0 -0.28 5 5
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.059 0.12 -10000 0 -0.26 124 124
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.018 0.03 0.07 124 -10000 0 124
GNAL -0.11 0.21 -10000 0 -0.47 124 124
GNG2 0.008 0.049 -10000 0 -0.47 5 5
CRH -0.003 0.045 -10000 0 -0.58 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.047 -10000 0 -0.31 11 11
MAPK11 0.004 0.031 -10000 0 -0.24 8 8
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.011 0.066 -9999 0 -0.32 18 18
EPHB2 0.006 0.063 -9999 0 -0.52 7 7
Syndecan-2/TACI -0.021 0.12 -9999 0 -0.33 59 59
LAMA1 -0.041 0.16 -9999 0 -0.53 48 48
Syndecan-2/alpha2 ITGB1 -0.02 0.13 -9999 0 -0.45 24 24
HRAS 0.007 0.059 -9999 0 -0.58 5 5
Syndecan-2/CASK 0.01 0.032 -9999 0 -0.28 6 6
ITGA5 -0.002 0.085 -9999 0 -0.48 15 15
BAX 0.025 0.06 -9999 0 -0.54 2 2
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.029 -9999 0 -0.24 6 6
LAMA3 -0.03 0.14 -9999 0 -0.48 43 43
EZR 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.038 0.15 -9999 0 -0.47 51 51
Syndecan-2/MMP2 0.01 0.066 -9999 0 -0.3 20 20
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.024 0.12 -9999 0 -0.33 61 61
dendrite morphogenesis 0.015 0.056 -9999 0 -0.34 11 11
Syndecan-2/GM-CSF 0.009 0.052 -9999 0 -0.31 12 12
determination of left/right symmetry 0.014 0.039 -9999 0 -0.33 6 6
Syndecan-2/PKC delta 0.02 0.033 -9999 0 -0.27 6 6
GNB2L1 0.01 0.046 -9999 0 -0.58 3 3
MAPK3 0.017 0.047 -9999 0 -0.28 11 11
MAPK1 0.017 0.047 -9999 0 -0.28 12 12
Syndecan-2/RACK1 0.02 0.052 -9999 0 -0.28 13 13
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.039 -9999 0 -0.33 6 6
ITGA2 -0.048 0.16 -9999 0 -0.47 61 61
MAPK8 0.02 0.059 -9999 0 -0.28 17 17
Syndecan-2/alpha2/beta1 Integrin -0.026 0.14 -9999 0 -0.36 40 40
Syndecan-2/Kininogen -0.032 0.12 -9999 0 -0.34 66 66
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.025 0.05 -9999 0 -0.3 8 8
Syndecan-2/CASK/Protein 4.1 0.018 0.03 -9999 0 -0.24 6 6
extracellular matrix organization 0.02 0.033 -9999 0 -0.27 6 6
actin cytoskeleton reorganization 0.011 0.066 -9999 0 -0.32 18 18
Syndecan-2/Caveolin-2/Ras -0.004 0.1 -9999 0 -0.28 55 55
Syndecan-2/Laminin alpha3 -0.007 0.093 -9999 0 -0.29 47 47
Syndecan-2/RasGAP 0.025 0.056 -9999 0 -0.32 9 9
alpha5/beta1 Integrin 0.009 0.061 -9999 0 -0.33 15 15
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.015 0.056 -9999 0 -0.34 11 11
GO:0007205 0.003 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.031 0.055 -9999 0 -0.31 9 9
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.052 0.18 -9999 0 -0.56 53 53
RASA1 0.01 0.038 -9999 0 -0.47 3 3
alpha2/beta1 Integrin -0.024 0.12 -9999 0 -0.33 61 61
Syndecan-2/Synbindin 0.02 0.033 -9999 0 -0.27 6 6
TGFB1 0.013 0 -9999 0 -10000 0 0
CASP3 0.026 0.03 -9999 0 -0.23 6 6
FN1 -0.002 0.086 -9999 0 -0.5 14 14
Syndecan-2/IL8 -0.022 0.11 -9999 0 -0.3 67 67
SDC2 0.014 0.039 -9999 0 -0.33 6 6
KNG1 -0.067 0.19 -9999 0 -0.58 60 60
Syndecan-2/Neurofibromin 0.02 0.033 -9999 0 -0.27 6 6
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.003 0.064 -9999 0 -0.58 6 6
Syndecan-2/TGFB1 0.02 0.033 -9999 0 -0.27 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.03 -9999 0 -0.24 6 6
Syndecan-2/Ezrin 0.027 0.03 -9999 0 -0.24 6 6
PRKACA 0.026 0.03 -9999 0 -0.23 6 6
angiogenesis -0.022 0.11 -9999 0 -0.3 67 67
MMP2 -0.003 0.088 -9999 0 -0.48 16 16
IL8 -0.054 0.18 -9999 0 -0.51 62 62
calcineurin-NFAT signaling pathway -0.021 0.12 -9999 0 -0.33 59 59
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.032 -9999 0 -0.34 4 4
ARNO/beta Arrestin1-2 0.013 0.036 -9999 0 -10000 0 0
EGFR -0.026 0.13 -9999 0 -0.47 39 39
EPHA2 -0.036 0.15 -9999 0 -0.48 49 49
USP6 0.011 0.038 -9999 0 -0.58 2 2
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.059 0.16 -9999 0 -0.37 97 97
ARRB2 0.008 0.022 -9999 0 -0.23 4 4
mol:GTP 0.012 0.019 -9999 0 -0.13 3 3
ARRB1 0.012 0.022 -9999 0 -0.47 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.009 0.1 -9999 0 -0.5 20 20
EGF -0.056 0.18 -9999 0 -0.54 61 61
somatostatin receptor activity 0 0 -9999 0 -0.001 24 24
ARAP2 0.012 0.022 -9999 0 -0.47 1 1
mol:GDP -0.025 0.084 -9999 0 -0.26 32 32
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 14 14
ITGA2B -0.003 0.091 -9999 0 -0.51 15 15
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.006 0.084 -9999 0 -0.31 4 4
ADAP1 0.009 0.051 -9999 0 -0.55 4 4
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.04 0.15 -9999 0 -0.41 67 67
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.018 0.088 -9999 0 -0.26 24 24
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.04 0.14 -9999 0 -0.31 97 97
ADRB2 0.006 0.065 -9999 0 -0.58 6 6
receptor agonist activity 0 0 -9999 0 0 18 18
actin filament binding 0 0 -9999 0 0 24 24
SRC 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.083 0.19 -9999 0 -0.47 97 97
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 19 19
ARF6/GDP 0.014 0.066 -9999 0 -0.34 4 4
ARF6/GDP/GULP/ACAP1 -0.019 0.1 -9999 0 -0.35 20 20
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.029 0.12 -9999 0 -0.47 6 6
ACAP1 -0.015 0.12 -9999 0 -0.56 24 24
ACAP2 0.012 0.022 -9999 0 -0.47 1 1
LHCGR/beta Arrestin2 0.001 0.031 -9999 0 -0.33 4 4
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.026 0.14 -9999 0 -0.5 37 37
CYTH3 0.006 0.044 -9999 0 -0.42 5 5
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.012 0.027 -9999 0 -0.58 1 1
fibronectin binding 0 0 -9999 0 0 23 23
endosomal lumen acidification 0 0 -9999 0 0 25 25
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.009 0.049 -9999 0 -0.52 4 4
GNAQ/ARNO 0.017 0.004 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 9 9
MET -0.033 0.14 -9999 0 -0.47 46 46
GNA14 0.012 0.022 -9999 0 -0.47 1 1
GNA15 -0.011 0.1 -9999 0 -0.47 24 24
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 19 19
GNA11 -0.003 0.086 -9999 0 -0.47 16 16
LHCGR -0.002 0.053 -9999 0 -0.58 4 4
AGTR1 -0.12 0.24 -9999 0 -0.55 111 111
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.031 -9999 0 -0.33 4 4
IPCEF1/ARNO -0.028 0.1 -9999 0 -0.42 3 3
alphaIIb/beta3 Integrin -0.061 0.15 -9999 0 -0.34 108 108
S1P3 pathway

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
PDGFRB 0.011 0.038 -9999 0 -0.58 2 2
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.034 0.14 -9999 0 -0.4 47 47
GNAO1 -0.078 0.19 -9999 0 -0.47 93 93
S1P/S1P3/G12/G13 0.018 0.052 -9999 0 -0.25 15 15
AKT1 0.003 0.062 -9999 0 -10000 0 0
AKT3 -0.014 0.13 -9999 0 -0.85 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.038 -9999 0 -0.57 2 2
GNAI2 0.015 0.001 -9999 0 -10000 0 0
GNAI3 0.014 0.001 -9999 0 -10000 0 0
GNAI1 0.007 0.065 -9999 0 -0.53 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.093 -9999 0 -0.48 18 18
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.037 0.17 -9999 0 -0.48 48 48
MAPK3 -0.029 0.16 -9999 0 -0.45 48 48
MAPK1 -0.029 0.16 -9999 0 -0.45 48 48
JAK2 -0.03 0.17 -9999 0 -0.46 50 50
CXCR4 -0.033 0.17 -9999 0 -0.44 54 54
FLT1 0.008 0.062 -9999 0 -0.5 7 7
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC -0.029 0.16 -9999 0 -0.45 48 48
S1P/S1P3/Gi -0.037 0.17 -9999 0 -0.48 48 48
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.16 -9999 0 -0.44 48 48
VEGFA -0.016 0.12 -9999 0 -0.49 31 31
S1P/S1P2/Gi -0.029 0.14 -9999 0 -0.42 41 41
VEGFR1 homodimer/VEGFA homodimer -0.001 0.1 -9999 0 -0.37 35 35
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.001 0.1 -9999 0 -0.55 10 10
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.031 0.14 -9999 0 -0.47 46 46
G12/G13 0.02 0 -9999 0 -10000 0 0
GNA14 0.012 0.022 -9999 0 -0.47 1 1
GNA15 -0.011 0.1 -9999 0 -0.47 24 24
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.086 -9999 0 -0.47 16 16
Rac1/GTP -0.028 0.16 -9999 0 -0.44 48 48
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.002 0.094 -9999 0 -0.35 24 24
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DOCK1 0.01 0.038 -9999 0 -0.47 3 3
ITGA4 -0.013 0.12 -9999 0 -0.52 24 24
alpha4/beta7 Integrin/MAdCAM1 -0.055 0.16 -9999 0 -0.34 100 100
EPO -0.067 0.19 -9999 0 -0.51 74 74
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.39 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0.085 -9999 0 -0.37 24 24
EPO/EPOR (dimer) -0.047 0.15 -9999 0 -0.38 82 82
lamellipodium assembly 0.03 0.042 -9999 0 -0.44 2 2
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
PI3K 0.014 0.048 -9999 0 -0.37 7 7
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.021 0.11 -9999 0 -0.46 7 7
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
MADCAM1 -0.095 0.23 -9999 0 -0.57 89 89
cell adhesion -0.056 0.16 -9999 0 -0.34 100 100
CRKL/CBL 0.019 0.016 -9999 0 -0.33 1 1
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.008 0.091 -9999 0 -0.4 16 16
ITGB7 -0.007 0.1 -9999 0 -0.49 20 20
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.002 0.1 -9999 0 -0.44 16 16
p130Cas/Crk/Dock1 0.027 0.084 -9999 0 -0.47 7 7
VCAM1 -0.001 0.086 -9999 0 -0.54 12 12
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.019 0.066 -9999 0 -0.31 11 11
BCAR1 0.015 0.086 -9999 0 -0.55 5 5
EPOR 0.001 0.084 -9999 0 -0.58 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.012 0.022 -9999 0 -0.47 1 1
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.041 -9999 0 -0.46 2 2
EPO 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
BCL2L1 0.013 0.13 -9999 0 -0.5 6 6
CRKL -0.001 0.099 -9999 0 -0.43 3 3
mol:DAG 0 0.11 -9999 0 -0.37 8 8
HRAS 0.019 0.09 -9999 0 -0.39 2 2
MAPK8 -0.02 0.12 -9999 0 -0.31 39 39
RAP1A -0.001 0.099 -9999 0 -0.43 3 3
GAB1 -0.002 0.1 -9999 0 -0.4 4 4
MAPK14 -0.014 0.11 -9999 0 -0.3 37 37
EPO -0.065 0.19 -9999 0 -0.51 74 74
PLCG1 0 0.11 -9999 0 -0.38 8 8
EPOR/TRPC2/IP3 Receptors -0.001 0.084 -9999 0 -0.57 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.066 0.16 -9999 0 -0.31 136 136
GAB1/SHC/GRB2/SOS1 -0.031 0.069 -9999 0 -0.42 2 2
EPO/EPOR (dimer) -0.043 0.15 -9999 0 -0.37 82 82
IRS2 -0.004 0.1 -9999 0 -0.43 5 5
STAT1 -0.001 0.12 -9999 0 -0.45 10 10
STAT5B 0.002 0.11 -9999 0 -0.41 8 8
cell proliferation -0.012 0.11 -9999 0 -0.47 5 5
GAB1/SHIP/PIK3R1/SHP2/SHC -0.041 0.087 -9999 0 -0.41 10 10
TEC -0.001 0.099 -9999 0 -0.43 3 3
SOCS3 -0.053 0.17 -9999 0 -0.48 65 65
STAT1 (dimer) 0 0.12 -9999 0 -0.44 10 10
JAK2 0.009 0.024 -9999 0 -0.47 1 1
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
EPO/EPOR (dimer)/JAK2 0.004 0.11 -9999 0 -0.35 8 8
EPO/EPOR -0.043 0.15 -9999 0 -0.37 82 82
LYN 0.014 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.007 0.098 -9999 0 -0.42 3 3
elevation of cytosolic calcium ion concentration -0.001 0.084 -9999 0 -0.57 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.019 0.13 -9999 0 -0.29 82 82
mol:IP3 0 0.11 -9999 0 -0.37 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.005 0.12 -9999 0 -0.41 13 13
SH2B3 0.01 0.011 -9999 0 -10000 0 0
NFKB1 -0.014 0.11 -9999 0 -0.3 37 37
EPO/EPOR (dimer)/JAK2/SOCS3 -0.061 0.1 -9999 0 -0.27 56 56
PTPN6 -0.009 0.1 -9999 0 -0.35 8 8
TEC/VAV2/GRB2 0.013 0.095 -9999 0 -0.45 2 2
EPOR -0.001 0.084 -9999 0 -0.58 10 10
INPP5D -0.013 0.11 -9999 0 -0.47 26 26
mol:GDP -0.032 0.07 -9999 0 -0.43 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.004 0.069 -9999 0 -0.49 9 9
CRKL/CBL/C3G 0.013 0.096 -9999 0 -0.42 3 3
VAV2 -0.001 0.099 -9999 0 -0.43 3 3
CBL -0.002 0.1 -9999 0 -0.43 4 4
SHC/Grb2/SOS1 -0.033 0.073 -9999 0 -0.45 2 2
STAT5A 0.001 0.12 -9999 0 -0.41 8 8
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.016 0.12 -9999 0 -0.44 8 8
LYN/PLCgamma2 0.013 0.05 -9999 0 -0.35 9 9
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
BTK -0.007 0.11 -9999 0 -0.44 4 4
BCL2 -0.01 0.21 -9999 0 -0.83 23 23
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.006 0.061 -10000 0 -0.54 6 6
LAT2 -0.007 0.12 -10000 0 -0.4 26 26
AP1 -0.069 0.14 -10000 0 -0.43 44 44
mol:PIP3 -0.005 0.15 -10000 0 -0.48 30 30
IKBKB -0.007 0.1 0.15 2 -0.28 34 36
AKT1 0.012 0.11 -10000 0 -0.4 7 7
IKBKG -0.007 0.1 0.15 2 -0.27 36 38
MS4A2 -0.016 0.12 -10000 0 -0.49 27 27
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
MAP3K1 0.013 0.12 -10000 0 -0.41 22 22
mol:Ca2+ 0.002 0.12 -10000 0 -0.35 30 30
LYN 0.014 0.003 -10000 0 -10000 0 0
CBLB -0.001 0.11 -10000 0 -0.42 18 18
SHC1 0.013 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.013 0.056 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.013 0.11 -10000 0 -0.47 26 26
PLD2 -0.009 0.11 -10000 0 -0.42 14 14
PTPN13 0.004 0.11 -10000 0 -0.44 17 17
PTPN11 0.012 0.023 -10000 0 -0.48 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.027 0.097 -10000 0 -0.3 17 17
SYK 0.006 0.062 -10000 0 -0.5 7 7
GRB2 0.013 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.13 -10000 0 -0.49 29 29
LAT -0.01 0.12 -10000 0 -0.4 27 27
PAK2 0.006 0.13 -10000 0 -0.42 28 28
NFATC2 -0.1 0.21 -10000 0 -0.52 88 88
HRAS -0.001 0.14 -10000 0 -0.46 28 28
GAB2 0.013 0 -10000 0 -10000 0 0
PLA2G1B 0.023 0.018 -10000 0 -10000 0 0
Fc epsilon R1 -0.052 0.13 -10000 0 -0.34 66 66
Antigen/IgE/Fc epsilon R1 -0.026 0.12 -10000 0 -0.31 66 66
mol:GDP -0.006 0.14 -10000 0 -0.49 27 27
JUN 0.006 0.061 -10000 0 -0.5 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
FOS -0.076 0.19 -10000 0 -0.48 88 88
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.11 -10000 0 -0.41 22 22
CHUK -0.007 0.1 0.15 2 -0.28 33 35
KLRG1 -0.004 0.1 -10000 0 -0.41 18 18
VAV1 -0.013 0.14 -10000 0 -0.49 26 26
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.002 0.11 -10000 0 -0.42 19 19
negative regulation of mast cell degranulation -0.009 0.13 -10000 0 -0.46 28 28
BTK -0.005 0.12 -10000 0 -0.45 22 22
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.029 0.17 -10000 0 -0.54 35 35
GAB2/PI3K/SHP2 -0.038 0.095 -10000 0 -0.39 19 19
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.013 0.13 -10000 0 -0.56 18 18
RAF1 0.015 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.035 0.17 -10000 0 -0.54 35 35
FCER1G 0.008 0.054 -10000 0 -0.59 4 4
FCER1A -0.046 0.16 -10000 0 -0.48 59 59
Antigen/IgE/Fc epsilon R1/Fyn -0.017 0.12 -10000 0 -0.4 21 21
MAPK3 0.024 0.017 -10000 0 -10000 0 0
MAPK1 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.009 0.11 -10000 0 -0.65 11 11
DUSP1 -0.006 0.094 -10000 0 -0.47 19 19
NF-kappa-B/RelA -0.026 0.049 -10000 0 -0.22 1 1
actin cytoskeleton reorganization -0.001 0.11 -10000 0 -0.46 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.046 0.12 -10000 0 -0.45 31 31
FER -0.012 0.13 -10000 0 -0.46 23 23
RELA 0.013 0 -10000 0 -10000 0 0
ITK -0.028 0.076 -10000 0 -0.37 15 15
SOS1 0.013 0 -10000 0 -10000 0 0
PLCG1 -0.003 0.14 -10000 0 -0.48 28 28
cytokine secretion -0.019 0.035 -10000 0 -10000 0 0
SPHK1 -0.012 0.12 -10000 0 -0.37 33 33
PTK2 -0.002 0.11 -10000 0 -0.48 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.055 0.13 -10000 0 -0.51 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.15 -10000 0 -0.46 30 30
MAP2K2 0.02 0.021 -10000 0 -10000 0 0
MAP2K1 0.021 0.017 -10000 0 -10000 0 0
MAP2K7 0.013 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.003 0.099 -10000 0 -0.37 19 19
MAP2K4 0.021 0.008 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.031 0.15 -10000 0 -0.45 35 35
mol:Choline -0.008 0.11 -10000 0 -0.42 14 14
SHC/Grb2/SOS1 0.011 0.1 -10000 0 -0.4 17 17
FYN 0.013 0.001 -10000 0 -10000 0 0
DOK1 0.013 0 -10000 0 -10000 0 0
PXN 0.005 0.11 -10000 0 -0.44 16 16
HCLS1 -0.004 0.11 -10000 0 -0.44 20 20
PRKCB -0.023 0.14 -10000 0 -0.35 53 53
FCGR2B -0.01 0.11 -10000 0 -0.53 21 21
IGHE 0 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.009 0.14 -10000 0 -0.47 28 28
LCP2 0.006 0.062 -10000 0 -0.54 6 6
PLA2G4A -0.014 0.14 -10000 0 -0.48 28 28
RASA1 0.01 0.038 -10000 0 -0.47 3 3
mol:Phosphatidic acid -0.008 0.11 -10000 0 -0.42 14 14
IKK complex 0.008 0.083 0.15 2 -0.22 20 22
WIPF1 0.008 0.049 -10000 0 -0.47 5 5
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.018 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.003 0.095 -9999 0 -0.55 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.057 0.1 -9999 0 -0.19 187 187
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0.001 -9999 0 -10000 0 0
MAP3K12 0.007 0.053 -9999 0 -0.47 6 6
FGR 0.01 0.041 -9999 0 -0.51 3 3
p38 alpha/TAB1 -0.021 0.044 -9999 0 -0.27 4 4
PRKG1 -0.12 0.22 -9999 0 -0.47 139 139
DUSP8 0.007 0.059 -9999 0 -0.58 5 5
PGK/cGMP/p38 alpha -0.074 0.1 -9999 0 -0.3 52 52
apoptosis -0.02 0.042 -9999 0 -0.28 3 3
RAL/GTP 0.018 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.006 0.094 -9999 0 -0.47 19 19
PAK1 0.007 0.053 -9999 0 -0.47 6 6
SRC 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.034 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.018 0 -9999 0 -10000 0 0
MAPK11 -0.005 0.089 -9999 0 -0.36 7 7
BLK -0.1 0.22 -9999 0 -0.5 109 109
HCK 0.009 0.046 -9999 0 -0.5 4 4
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.012 0.022 -9999 0 -0.47 1 1
DUSP10 0.013 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.065 -9999 0 -0.29 4 4
positive regulation of innate immune response 0 0.094 -9999 0 -0.38 7 7
LCK 0.003 0.075 -9999 0 -0.58 8 8
p38alpha-beta/MKP7 0.007 0.092 -9999 0 -0.36 7 7
p38alpha-beta/MKP5 0.007 0.092 -9999 0 -0.37 6 6
PGK/cGMP -0.089 0.16 -9999 0 -0.34 139 139
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.001 0.1 -9999 0 -0.41 7 7
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.17 0.23 -9999 0 -0.47 182 182
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.051 0.14 -9999 0 -0.33 97 97
AKT1 0.027 0.16 -9999 0 -0.61 21 21
PTK2B -0.036 0.18 -9999 0 -0.67 27 27
VEGFR2 homodimer/Frs2 0.006 0.13 -9999 0 -0.62 21 21
CAV1 -0.049 0.16 -9999 0 -0.47 62 62
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.001 0.15 -9999 0 -0.61 21 21
endothelial cell proliferation 0.003 0.17 -9999 0 -0.59 24 24
mol:Ca2+ 0.006 0.15 -9999 0 -0.62 21 21
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.008 0.14 -9999 0 -0.57 21 21
RP11-342D11.1 -0.002 0.15 -9999 0 -0.62 21 21
CDH5 0.012 0.022 -9999 0 -0.47 1 1
VEGFA homodimer 0.016 0.071 -9999 0 -0.31 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0 0.086 -9999 0 -0.57 11 11
HRAS/GDP -0.036 0.12 -9999 0 -0.55 21 21
SH2D2A -0.016 0.13 -9999 0 -0.56 25 25
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.035 0.11 -9999 0 -0.52 21 21
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.018 0.16 -9999 0 -0.62 22 22
VEGFR1 homodimer 0.006 0.061 -9999 0 -0.5 7 7
SHC/GRB2/SOS1 -0.037 0.13 -9999 0 -0.58 21 21
GRB10 0.007 0.15 -9999 0 -0.62 21 21
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.007 0.053 -9999 0 -0.47 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.013 0.14 -9999 0 -0.56 21 21
HRAS 0.007 0.059 -9999 0 -0.58 5 5
VEGF/Rho/ROCK1/Integrin Complex -0.023 0.15 -9999 0 -0.52 27 27
HIF1A 0.012 0.022 -9999 0 -0.47 1 1
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.007 0.14 -9999 0 -0.56 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.01 0.041 -9999 0 -0.51 3 3
Nck/Pak 0.014 0.043 -9999 0 -0.34 7 7
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.15 -9999 0 -0.61 21 21
mol:GDP -0.036 0.12 -9999 0 -0.56 21 21
mol:NADP 0.031 0.12 -9999 0 -0.44 21 21
eNOS/Hsp90 0.036 0.11 -9999 0 -0.44 15 15
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
mol:IP3 0.006 0.15 -9999 0 -0.63 21 21
HIF1A/ARNT 0.019 0.016 -9999 0 -0.33 1 1
SHB 0.009 0.044 -9999 0 -0.47 4 4
VEGFA -0.017 0.12 -9999 0 -0.48 31 31
VEGFC 0.011 0.035 -9999 0 -0.52 2 2
FAK1/Vinculin -0.031 0.22 -9999 0 -0.82 25 25
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.042 0.2 -9999 0 -0.71 27 27
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.005 0.085 -9999 0 -0.36 22 22
mol:L-citrulline 0.031 0.12 -9999 0 -0.44 21 21
ITGAV 0.011 0.031 -9999 0 -0.47 2 2
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.008 0.14 -9999 0 -0.57 21 21
VEGFR2 homodimer/VEGFA homodimer 0 0.16 -9999 0 -0.68 21 21
VEGFR2/3 heterodimer 0.004 0.14 -9999 0 -0.63 21 21
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.003 0.16 -9999 0 -0.66 21 21
VEGFR2 homodimer 0.001 0.15 -9999 0 -0.69 22 22
FLT1 0.006 0.061 -9999 0 -0.5 7 7
NEDD4 0.005 0.069 -9999 0 -0.47 10 10
MAPK3 -0.016 0.16 -9999 0 -0.63 22 22
MAPK1 -0.016 0.16 -9999 0 -0.63 22 22
VEGFA145/NRP2 -0.024 0.12 -9999 0 -0.35 60 60
VEGFR1/2 heterodimer 0.002 0.15 -9999 0 -0.67 21 21
KDR 0.001 0.15 -9999 0 -0.69 22 22
VEGFA165/NRP1/VEGFR2 homodimer -0.008 0.18 -9999 0 -0.7 24 24
SRC 0.013 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.015 0.16 -9999 0 -0.65 22 22
PI3K 0.015 0.18 -9999 0 -0.74 21 21
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.001 0.15 -9999 0 -0.61 21 21
FES 0.003 0.16 -9999 0 -0.66 21 21
GAB1 -0.046 0.15 -9999 0 -0.68 22 22
VEGFR2 homodimer/VEGFA homodimer/Src -0.001 0.15 -9999 0 -0.61 21 21
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.012 0.14 -9999 0 -0.53 20 20
VEGFR2 homodimer/VEGFA homodimer/Yes -0.001 0.15 -9999 0 -0.61 21 21
PI3K/GAB1 0.028 0.17 -9999 0 -0.62 22 22
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.01 0.14 -9999 0 -0.56 21 21
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.011 0.13 -9999 0 -0.58 21 21
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.006 0.15 -9999 0 -0.64 21 21
actin cytoskeleton reorganization -0.018 0.16 -9999 0 -0.61 22 22
PTK2 -0.029 0.21 -9999 0 -0.8 24 24
EDG1 -0.002 0.15 -9999 0 -0.62 21 21
mol:DAG 0.006 0.15 -9999 0 -0.63 21 21
CaM/Ca2+ 0.012 0.14 -9999 0 -0.57 21 21
MAP2K3 0.007 0.15 -9999 0 -0.6 23 23
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.008 0.16 -9999 0 -0.64 21 21
PLCG1 0.006 0.15 -9999 0 -0.64 21 21
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.006 0.14 -9999 0 -0.57 21 21
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.001 0.15 -9999 0 -0.62 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.001 0.15 -9999 0 -0.61 21 21
cell migration -0.004 0.19 -9999 0 -0.68 25 25
mol:PI-3-4-5-P3 0.017 0.17 -9999 0 -0.66 21 21
FYN 0.013 0.001 -9999 0 -10000 0 0
VEGFB/NRP1 0.006 0.14 -9999 0 -0.59 21 21
mol:NO 0.031 0.12 -9999 0 -0.44 21 21
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.036 0.12 -9999 0 -0.55 21 21
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.007 0.16 -9999 0 -0.64 21 21
VHL 0.012 0.022 -9999 0 -0.47 1 1
ITGB3 -0.083 0.19 -9999 0 -0.47 97 97
NOS3 0.03 0.13 -9999 0 -0.5 21 21
VEGFR2 homodimer/VEGFA homodimer/Sck -0.007 0.17 -9999 0 -0.69 21 21
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.003 0.16 -9999 0 -0.61 22 22
PRKCB -0.042 0.19 -9999 0 -0.66 27 27
VCL -0.016 0.12 -9999 0 -0.47 29 29
VEGFA165/NRP1 -0.001 0.15 -9999 0 -0.63 21 21
VEGFR1/2 heterodimer/VEGFA homodimer -0.004 0.16 -9999 0 -0.66 22 22
VEGFA165/NRP2 -0.024 0.12 -9999 0 -0.35 60 60
MAPKKK cascade 0.028 0.14 -9999 0 -0.66 11 11
NRP2 -0.019 0.12 -9999 0 -0.47 32 32
VEGFC homodimer 0.011 0.034 -9999 0 -0.52 2 2
NCK1 0.012 0.027 -9999 0 -0.58 1 1
ROCK1 0.012 0.022 -9999 0 -0.47 1 1
FAK1/Paxillin -0.019 0.19 -9999 0 -0.74 23 23
MAP3K13 0 0.16 -9999 0 -0.64 23 23
PDPK1 0.025 0.15 -9999 0 -0.57 21 21
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.028 0.11 -9999 0 -0.41 12 12
CCNA2 -0.078 0.21 -9999 0 -0.58 75 75
PIK3CA 0.011 0.038 -9999 0 -0.47 3 3
JAK3 -0.001 0.091 -9999 0 -0.55 13 13
PIK3R1 0.009 0.049 -9999 0 -0.47 5 5
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.11 -9999 0 -0.48 11 11
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0 0.081 -9999 0 -0.32 29 29
IL2RA -0.055 0.19 -9999 0 -0.48 76 76
IL2RB -0.016 0.12 -9999 0 -0.49 29 29
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.011 0.12 -9999 0 -0.55 22 22
G1/S transition of mitotic cell cycle -0.047 0.22 -9999 0 -0.76 35 35
PTPN11 0.013 0.022 -9999 0 -0.47 1 1
CCND2 -0.016 0.17 -9999 0 -0.69 30 30
LCK 0.004 0.075 -9999 0 -0.57 8 8
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.004 0.038 -9999 0 -0.57 2 2
CDK6 -0.004 0.091 -9999 0 -0.48 17 17
CCND3 0.034 0.099 -9999 0 -0.44 8 8
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.088 -10000 0 -0.48 16 16
ANTXR2 0.001 0.075 -10000 0 -0.47 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.015 -10000 0 -0.065 26 26
monocyte activation -0.016 0.1 -10000 0 -0.38 33 33
MAP2K2 -0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.003 0.012 -10000 0 -10000 0 0
MAP2K7 -0.003 0.012 -10000 0 -10000 0 0
MAP2K6 -0.011 0.052 -10000 0 -0.3 14 14
CYAA -0.001 0.062 -10000 0 -0.25 26 26
MAP2K4 -0.003 0.012 -10000 0 -10000 0 0
IL1B -0.033 0.11 -10000 0 -0.28 76 76
Channel 0.002 0.067 -10000 0 -0.27 26 26
NLRP1 -0.009 0.043 -10000 0 -0.27 12 12
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.015 0.065 26 -10000 0 26
MAPK3 -0.003 0.012 -10000 0 -10000 0 0
MAPK1 -0.003 0.012 -10000 0 -10000 0 0
PGR -0.038 0.09 -10000 0 -0.26 70 70
PA/Cellular Receptors 0.001 0.073 -10000 0 -0.3 26 26
apoptosis -0.003 0.015 -10000 0 -0.065 26 26
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.063 -10000 0 -0.26 26 26
macrophage activation 0.014 0.014 -10000 0 -10000 0 0
TNF -0.029 0.14 -10000 0 -0.5 39 39
VCAM1 -0.017 0.1 -10000 0 -0.38 33 33
platelet activation -0.004 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.021 0.1 4 -10000 0 4
IL18 0 0.067 -10000 0 -0.32 16 16
negative regulation of macrophage activation -0.003 0.015 -10000 0 -0.065 26 26
LEF -0.004 0.015 -10000 0 -0.065 26 26
CASP1 -0.01 0.044 -10000 0 -0.21 18 18
mol:cAMP -0.004 0.016 -10000 0 -10000 0 0
necrosis -0.003 0.015 -10000 0 -0.065 26 26
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.063 -10000 0 -0.26 26 26
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.01 0.038 -10000 0 -0.47 3 3
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.06 0.42 9 -10000 0 9
CDKN1A -0.007 0.069 -10000 0 -0.51 8 8
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.011 0.038 -10000 0 -0.58 2 2
FOXO3 0.002 0.03 0.38 3 -10000 0 3
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.019 0.025 -10000 0 -0.26 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT -0.02 0.13 -10000 0 -0.58 24 24
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.002 0.073 -10000 0 -0.4 16 16
PPARGC1A -0.14 0.22 -10000 0 -0.47 150 150
FHL2 -0.01 0.1 -10000 0 -0.47 23 23
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.018 0.013 -10000 0 -10000 0 0
HIST2H4A 0.012 0.06 -10000 0 -0.42 9 9
SIRT1/FOXO3a 0.003 0.024 0.26 3 -10000 0 3
SIRT1 0.011 0.018 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.025 0.012 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.029 0.079 -10000 0 -0.21 6 6
apoptosis -0.023 0.027 0.35 2 -10000 0 2
SIRT1/PGC1A -0.075 0.14 -10000 0 -0.28 146 146
p53/SIRT1 0.001 0.056 0.32 8 -0.33 6 14
SIRT1/FOXO4 0.021 0.025 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.011 0.057 -10000 0 -0.24 22 22
HIST1H1E -0.042 0.094 -10000 0 -0.18 151 151
SIRT1/p300 0.016 0.03 -10000 0 -0.33 3 3
muscle cell differentiation -0.006 0.063 0.33 16 -10000 0 16
TP53 0.005 0.056 -10000 0 -0.47 6 6
KU70/SIRT1/BAX 0.024 0.027 -10000 0 -0.35 2 2
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.009 0.093 -10000 0 -0.41 24 24
ACSS2 0.02 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.006 0.063 -10000 0 -0.33 16 16
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.006 0.1 -10000 0 -0.58 16 16
EPHB2 0.005 0.064 -10000 0 -0.52 7 7
EFNB1 0.015 0.044 -10000 0 -0.35 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.042 0.13 -10000 0 -0.57 9 9
Ephrin B2/EPHB1-2 -0.074 0.15 -10000 0 -0.27 165 165
neuron projection morphogenesis -0.067 0.11 -10000 0 -0.54 9 9
Ephrin B1/EPHB1-2/Tiam1 -0.051 0.14 -10000 0 -0.53 12 12
DNM1 0.011 0.035 -10000 0 -0.52 2 2
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.039 -10000 0 -0.57 2 2
YES1 -0.002 0.05 -10000 0 -0.78 2 2
Ephrin B1/EPHB1-2/NCK2 -0.049 0.14 -10000 0 -0.48 12 12
PI3K 0.015 0.061 -10000 0 -0.61 3 3
mol:GDP -0.051 0.14 -10000 0 -0.52 12 12
ITGA2B -0.003 0.091 -10000 0 -0.51 15 15
endothelial cell proliferation 0.005 0.066 -10000 0 -0.36 16 16
FYN -0.002 0.05 -10000 0 -0.78 2 2
MAP3K7 0.009 0.041 -10000 0 -0.61 2 2
FGR -0.002 0.052 -10000 0 -0.79 2 2
TIAM1 0.01 0.038 -10000 0 -0.47 3 3
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.028 0.13 -10000 0 -0.54 11 11
LYN -0.002 0.05 -10000 0 -0.78 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.004 0.048 -10000 0 -0.75 2 2
Ephrin B1/EPHB1-2 -0.005 0.042 -10000 0 -0.66 2 2
SRC -0.001 0.051 -10000 0 -0.79 2 2
ITGB3 -0.083 0.19 -10000 0 -0.47 97 97
EPHB1 -0.14 0.23 -10000 0 -0.47 155 155
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.006 0.067 -10000 0 -0.36 16 16
alphaIIb/beta3 Integrin -0.061 0.15 -10000 0 -0.34 108 108
BLK -0.03 0.076 -10000 0 -0.79 2 2
HCK -0.002 0.053 -10000 0 -0.79 2 2
regulation of stress fiber formation 0.049 0.13 0.47 12 -10000 0 12
MAPK8 0.016 0.055 -10000 0 -0.64 2 2
Ephrin B1/EPHB1-2/RGS3 -0.049 0.14 -10000 0 -0.48 12 12
endothelial cell migration 0.004 0.065 -10000 0 -0.32 18 18
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.012 0.039 -10000 0 -0.59 2 2
regulation of focal adhesion formation 0.049 0.13 0.47 12 -10000 0 12
chemotaxis 0.049 0.13 0.47 12 -10000 0 12
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
Rac1/GTP -0.067 0.12 -10000 0 -0.56 9 9
angiogenesis -0.005 0.042 -10000 0 -0.66 2 2
LCK -0.002 0.051 -10000 0 -0.79 2 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.22 -9999 0 -0.47 142 142
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.005 0.07 -9999 0 -0.58 7 7
TCEB1 0.012 0.027 -9999 0 -0.58 1 1
HIF1A/p53 0.025 0.031 -9999 0 -0.28 1 1
HIF1A 0.021 0.016 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.033 0.046 -9999 0 -0.52 1 1
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.24 -9999 0 -0.58 102 102
ARNT/IPAS -0.082 0.16 -9999 0 -0.33 142 142
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.01 0.046 -9999 0 -0.58 3 3
HIF1A/ARNT 0.028 0.015 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.019 0.063 -9999 0 -0.42 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.028 0.015 -9999 0 -10000 0 0
PHD1-3/OS9 0.029 0.038 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.052 -9999 0 -0.48 3 3
VHL 0.012 0.022 -9999 0 -0.47 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.028 0.015 -9999 0 -10000 0 0
EGLN3 0.003 0.069 -9999 0 -0.47 10 10
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.007 0.053 -9999 0 -0.47 6 6
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.037 -9999 0 -0.65 1 1
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.034 0.12 -9999 0 -0.27 102 102
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.018 0.11 -10000 0 -0.33 52 52
ATM 0.012 0.022 -10000 0 -0.47 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.012 0.027 -10000 0 -0.58 1 1
ATR 0.012 0.027 -10000 0 -0.58 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.022 0.031 -10000 0 -0.34 3 3
protein ubiquitination 0.004 0.09 -10000 0 -0.53 3 3
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0.027 0 -10000 0 -10000 0 0
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0.026 0.017 -10000 0 -0.35 1 1
FA complex/FANCD2/Ubiquitin 0.033 0.043 -10000 0 -0.34 1 1
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.011 0.038 -10000 0 -0.58 2 2
CCNE1 0.007 0.059 -10000 0 -0.58 5 5
CDK2/Cyclin E1 0.015 0.044 -10000 0 -0.42 5 5
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.02 0.11 -10000 0 -0.33 54 54
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.012 0.027 -10000 0 -0.58 1 1
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.031 0.16 -10000 0 -0.57 37 37
DNA repair 0.011 0.12 -10000 0 -0.49 10 10
BRCA1/BARD1/ubiquitin -0.02 0.11 -10000 0 -0.33 54 54
BARD1/DNA-PK 0.004 0.085 -10000 0 -0.31 1 1
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.018 0.11 0.33 52 -10000 0 52
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.077 -10000 0 -0.34 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.006 0.094 -10000 0 -0.27 54 54
BRCA1/BARD1/P53 0 0.093 -10000 0 -0.39 3 3
BARD1/CSTF1/BRCA1 -0.006 0.094 -10000 0 -0.27 54 54
BRCA1/BACH1 0.011 0.038 -10000 0 -0.57 2 2
BARD1 -0.039 0.15 -10000 0 -0.47 52 52
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.006 0.094 -10000 0 -0.27 54 54
BRCA1/BARD1/UbcH7 -0.006 0.094 -10000 0 -0.27 54 54
BRCA1/BARD1/RAD51/PCNA -0.023 0.13 -10000 0 -0.36 38 38
BARD1/DNA-PK/P53 0.008 0.083 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.02 0.11 -10000 0 -0.33 54 54
BRCA1/BARD1/CTIP 0.001 0.088 -10000 0 -0.37 3 3
FA complex 0.023 0.052 -10000 0 -0.29 1 1
BARD1/EWS -0.018 0.11 -10000 0 -0.33 52 52
RBBP8 0.02 0.022 -10000 0 -0.33 2 2
TP53 0.007 0.053 -10000 0 -0.47 6 6
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.001 0.092 0.39 3 -10000 0 3
BRCA1/BARD1 0.007 0.092 -10000 0 -0.54 3 3
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.027 0.11 -10000 0 -0.34 52 52
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.033 0.16 -10000 0 -0.58 38 38
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.02 0.11 -10000 0 -0.33 54 54
EWSR1 0.013 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP -0.061 0.12 -9999 0 -0.47 20 20
TC10/GTP -0.045 0.093 -9999 0 -0.46 6 6
Insulin Receptor/Insulin/IRS1/Shp2 0.01 0.075 -9999 0 -0.32 15 15
HRAS 0.007 0.059 -9999 0 -0.58 5 5
APS homodimer -0.011 0.12 -9999 0 -0.57 20 20
GRB14 -0.098 0.23 -9999 0 -0.57 92 92
FOXO3 -0.08 0.22 -9999 0 -0.57 76 76
AKT1 -0.024 0.13 -9999 0 -0.43 14 14
INSR 0.014 0.005 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.047 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 -0.073 0.19 -9999 0 -0.47 87 87
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.023 0.045 -9999 0 -10000 0 0
CAV1 -0.024 0.11 -9999 0 -0.36 23 23
CBL/APS/CAP/Crk-II/C3G -0.02 0.12 -9999 0 -0.51 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.011 0.073 -9999 0 -0.3 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.071 -9999 0 -0.48 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.049 -9999 0 -0.36 1 1
RPS6KB1 -0.016 0.12 -9999 0 -0.4 13 13
PARD6A 0.007 0.059 -9999 0 -0.58 5 5
CBL 0.012 0.022 -9999 0 -0.47 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.006 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.052 0.1 -9999 0 -0.41 13 13
HRAS/GTP -0.024 0.074 -9999 0 -0.42 8 8
Insulin Receptor 0.014 0.005 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.018 0.068 -9999 0 -0.5 1 1
PRKCI -0.015 0.029 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.064 0.12 -9999 0 -0.47 14 14
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.024 0.025 -9999 0 -10000 0 0
PI3K -0.016 0.073 -9999 0 -0.49 5 5
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 -0.001 0.005 -9999 0 -10000 0 0
HRAS/GDP 0.005 0.044 -9999 0 -0.42 5 5
AKT2 -0.024 0.13 -9999 0 -0.43 14 14
PRKCZ -0.014 0.027 -9999 0 -10000 0 0
SH2B2 -0.011 0.12 -9999 0 -0.57 20 20
SHC/SHIP 0.004 0.091 -9999 0 -0.45 8 8
F2RL2 -0.22 0.29 -9999 0 -0.58 191 191
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.011 0.052 -9999 0 -0.29 14 14
TC10/GTP/CIP4/Exocyst 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.026 0.049 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.01 0.038 -9999 0 -0.47 3 3
NCK1 0.012 0.027 -9999 0 -0.58 1 1
CBL/APS/CAP/Crk-II -0.029 0.13 -9999 0 -0.38 20 20
TC10/GDP 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.02 0.052 -9999 0 -0.28 14 14
INPP5D -0.005 0.095 -9999 0 -0.35 20 20
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.13 0.3 -9999 0 -0.82 76 76
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.086 -9999 0 -0.47 16 16
p62DOK/RasGAP 0.024 0.025 -9999 0 -10000 0 0
INS -0.013 0.096 -9999 0 -0.57 14 14
mol:PI-3-4-P2 -0.005 0.094 -9999 0 -0.34 20 20
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.041 0.15 -9999 0 -0.46 29 29
PTPRA 0.014 0.005 -9999 0 -10000 0 0
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
TC10/GTP/CIP4 0.018 0 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.019 0.053 -9999 0 -0.41 1 1
Insulin Receptor/Insulin/IRS1 0.002 0.072 -9999 0 -0.28 29 29
Insulin Receptor/Insulin/IRS3 0.001 0.071 -9999 0 -0.41 14 14
Par3/Par6 -0.099 0.16 -9999 0 -0.3 193 193
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.015 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.11 -10000 0 -0.36 5 5
NFATC4 -0.021 0.097 -10000 0 -0.32 7 7
ERBB2IP 0.013 0.022 -10000 0 -0.47 1 1
HSP90 (dimer) 0.013 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.04 0.11 -10000 0 -0.4 4 4
JUN 0.003 0.073 -10000 0 -0.33 1 1
HRAS 0.007 0.059 -10000 0 -0.58 5 5
DOCK7 -0.034 0.11 -10000 0 -0.37 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.05 0.12 -10000 0 -0.47 4 4
AKT1 0.009 0.003 -10000 0 -10000 0 0
BAD 0.016 0.017 -10000 0 -0.36 1 1
MAPK10 -0.006 0.07 -10000 0 -0.28 4 4
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.042 0.12 -10000 0 -0.43 4 4
RAF1 -0.024 0.11 -10000 0 -0.37 4 4
ErbB2/ErbB3/neuregulin 2 -0.082 0.13 -10000 0 -0.26 173 173
STAT3 0.004 0.006 -10000 0 -10000 0 0
cell migration -0.001 0.073 -10000 0 -0.23 4 4
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.073 0.21 -10000 0 -0.56 25 25
FOS -0.075 0.22 -10000 0 -0.49 85 85
NRAS 0.012 0.022 -10000 0 -0.47 1 1
mol:Ca2+ -0.04 0.11 -10000 0 -0.4 4 4
MAPK3 -0.053 0.17 -10000 0 -0.51 16 16
MAPK1 -0.053 0.17 -10000 0 -0.51 16 16
JAK2 -0.035 0.11 -10000 0 -0.38 5 5
NF2 -0.002 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.047 0.12 -10000 0 -0.26 33 33
NRG1 -0.12 0.22 -10000 0 -0.47 138 138
GRB2/SOS1 0.019 0.001 -10000 0 -10000 0 0
MAPK8 -0.044 0.12 -10000 0 -0.36 6 6
MAPK9 -0.004 0.065 -10000 0 -10000 0 0
ERBB2 -0.002 0.035 0.35 1 -0.35 4 5
ERBB3 0.011 0.022 -10000 0 -0.48 1 1
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.005 0.013 0.22 1 -10000 0 1
STAT3 (dimer) 0.018 0.006 -10000 0 -10000 0 0
RNF41 0.02 0.007 -10000 0 -10000 0 0
FRAP1 0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.042 0.067 -10000 0 -0.27 4 4
ErbB2/ErbB2/HSP90 (dimer) 0.006 0.029 0.24 1 -0.28 4 5
CHRNA1 -0.055 0.17 -10000 0 -0.42 37 37
myelination -0.019 0.095 -10000 0 -0.3 7 7
PPP3CB -0.032 0.1 -10000 0 -0.35 4 4
KRAS 0.013 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.027 0.11 -10000 0 -0.34 4 4
NRG2 -0.16 0.23 -10000 0 -0.47 172 172
mol:GDP -0.047 0.12 -10000 0 -0.26 33 33
SOS1 0.013 0.001 -10000 0 -10000 0 0
MAP2K2 -0.022 0.12 -10000 0 -0.35 9 9
SRC 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.031 0.11 -10000 0 -0.38 5 5
MAP2K1 -0.068 0.18 -10000 0 -0.42 67 67
heart morphogenesis -0.04 0.11 -10000 0 -0.4 4 4
RAS family/GDP -0.029 0.11 -10000 0 -0.36 5 5
GRB2 0.013 0.001 -10000 0 -10000 0 0
PRKACA -0.004 0.007 -10000 0 -10000 0 0
CHRNE 0.009 0.02 -10000 0 -0.2 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.009 0.003 -10000 0 -10000 0 0
nervous system development -0.04 0.11 -10000 0 -0.4 4 4
CDC42 0.013 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.033 -9999 0 -0.69 1 1
SVIL -0.007 0.099 -9999 0 -0.47 21 21
ZNF318 0.012 0.018 -9999 0 -10000 0 0
JMJD2C 0.006 0.012 -9999 0 -0.097 6 6
T-DHT/AR/Ubc9 0.001 0.09 -9999 0 -0.27 44 44
CARM1 0.013 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.001 -9999 0 -10000 0 0
PELP1 0.013 0.003 -9999 0 -10000 0 0
CTNNB1 0.014 0.006 -9999 0 -10000 0 0
AKT1 0.013 0.005 -9999 0 -10000 0 0
PTK2B 0.013 0.005 -9999 0 -10000 0 0
MED1 0.013 0.006 -9999 0 -10000 0 0
MAK -0.15 0.27 -9999 0 -0.58 137 137
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.001 0.079 -9999 0 -0.47 13 13
GSN 0.01 0.045 -9999 0 -0.47 4 4
NCOA2 -0.047 0.16 -9999 0 -0.47 60 60
NCOA6 0.014 0.007 -9999 0 -10000 0 0
DNA-PK 0.025 0.02 -9999 0 -10000 0 0
NCOA4 0.013 0.001 -9999 0 -10000 0 0
PIAS3 0.014 0.006 -9999 0 -10000 0 0
cell proliferation -0.074 0.11 -9999 0 -0.29 21 21
XRCC5 0.013 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.01 0.11 -9999 0 -0.3 57 57
FHL2 -0.012 0.2 -9999 0 -0.86 23 23
RANBP9 0.014 0.007 -9999 0 -10000 0 0
JMJD1A 0.013 0.016 -9999 0 -0.13 6 6
CDK6 -0.004 0.091 -9999 0 -0.48 17 17
TGFB1I1 -0.027 0.14 -9999 0 -0.47 41 41
T-DHT/AR/CyclinD1 0.001 0.092 -9999 0 -0.28 45 45
XRCC6 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR 0.016 0.11 -9999 0 -0.28 44 44
CTDSP1 0.013 0.002 -9999 0 -10000 0 0
CTDSP2 0.013 0.013 -9999 0 -10000 0 0
BRCA1 0.011 0.041 -9999 0 -0.61 2 2
TCF4 0.009 0.045 -9999 0 -0.47 4 4
CDKN2A -0.11 0.24 -9999 0 -0.57 102 102
SRF 0.014 0.031 -9999 0 -10000 0 0
NKX3-1 0.022 0.051 -9999 0 -10000 0 0
KLK3 0.023 0.15 -9999 0 -1.2 7 7
TMF1 0.013 0.001 -9999 0 -10000 0 0
HNRNPA1 0.013 0.007 -9999 0 -10000 0 0
AOF2 0.001 0.008 -9999 0 -0.069 6 6
APPL1 0.02 0.012 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.001 0.09 -9999 0 -0.27 44 44
AR -0.027 0.14 -9999 0 -0.47 44 44
UBA3 0.013 0.002 -9999 0 -10000 0 0
PATZ1 0.013 0.007 -9999 0 -10000 0 0
PAWR 0.013 0.001 -9999 0 -10000 0 0
PRKDC 0.012 0.025 -9999 0 -0.52 1 1
PA2G4 0.013 0.008 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.002 0.082 -9999 0 -0.25 44 44
RPS6KA3 0.013 0.024 -9999 0 -0.47 1 1
T-DHT/AR/ARA70 0.001 0.09 -9999 0 -0.27 44 44
LATS2 0.013 0.006 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.002 0.082 -9999 0 -0.25 44 44
Cyclin D3/CDK11 p58 0.01 0.001 -9999 0 -10000 0 0
VAV3 -0.04 0.15 -9999 0 -0.47 54 54
KLK2 0.01 0.098 -9999 0 -0.74 6 6
CASP8 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.02 0.15 -9999 0 -0.4 63 63
TMPRSS2 0.013 0.11 -9999 0 -0.88 6 6
CCND1 0.012 0.027 -9999 0 -0.57 1 1
PIAS1 0.013 0.025 -9999 0 -0.47 1 1
mol:T-DHT 0.004 0.017 -9999 0 -0.062 29 29
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.014 0.017 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.01 0.11 -9999 0 -0.29 59 59
CMTM2 0.007 0.049 -9999 0 -0.52 4 4
SNURF -0.006 0.094 -9999 0 -0.47 19 19
ZMIZ1 0.016 0.028 -9999 0 -0.5 1 1
CCND3 0.013 0.001 -9999 0 -10000 0 0
TGIF1 0.013 0.007 -9999 0 -10000 0 0
FKBP4 0.014 0.007 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 -0.006 0.1 -9999 0 -0.58 16 16
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.015 0.035 -9999 0 -0.18 16 16
GNAO1 -0.079 0.19 -9999 0 -0.47 93 93
mol:Sphinganine-1-P 0.007 0.078 -9999 0 -0.42 16 16
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.026 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
S1PR3 -0.005 0.093 -9999 0 -0.48 18 18
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.009 0.029 -9999 0 -10000 0 0
S1PR5 -0.067 0.18 -9999 0 -0.47 80 80
S1PR4 -0.012 0.12 -9999 0 -0.57 21 21
GNAI1 0.005 0.065 -9999 0 -0.53 7 7
S1P/S1P5/G12 -0.017 0.099 -9999 0 -0.37 1 1
S1P/S1P3/Gq 0.004 0.1 -9999 0 -0.52 11 11
S1P/S1P4/Gi -0.038 0.15 -9999 0 -0.42 43 43
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.47 46 46
GNA14 0.012 0.022 -9999 0 -0.47 1 1
GNA15 -0.011 0.1 -9999 0 -0.47 24 24
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.086 -9999 0 -0.47 16 16
ABCC1 0.013 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.013 0.005 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.071 -9999 0 -0.28 9 9
IRAK/TOLLIP 0.026 0.016 -9999 0 -0.31 1 1
IKBKB 0.012 0.027 -9999 0 -0.58 1 1
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.059 0.14 -9999 0 -0.34 103 103
IL1A 0.001 0.059 -9999 0 -0.52 6 6
IL1B -0.044 0.15 -9999 0 -0.38 79 79
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.019 -9999 0 -10000 0 0
IL1R2 -0.083 0.19 -9999 0 -0.47 97 97
IL1R1 0.011 0.031 -9999 0 -0.47 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.063 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.006 0.058 -9999 0 -0.47 7 7
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.009 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.058 0.013 -9999 0 -10000 0 0
JUN 0.023 0.063 -9999 0 -0.39 2 2
MAP3K7 0.013 0.001 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.009 0.12 -9999 0 -0.47 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88 0.024 0.048 -9999 0 -0.31 7 7
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.029 0.045 -9999 0 -0.33 4 4
IL1 beta fragment/IL1R1/IL1RAP -0.022 0.12 -9999 0 -0.36 31 31
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.021 0.056 -9999 0 -10000 0 0
IRAK1 0.02 0.017 -9999 0 -0.35 1 1
IL1RN/IL1R1 -0.005 0.093 -9999 0 -0.35 33 33
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.012 0.027 -9999 0 -0.58 1 1
TRAF6 0.013 0 -9999 0 -10000 0 0
PI3K 0.014 0.048 -9999 0 -0.37 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.08 -9999 0 -0.31 9 9
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.022 0.12 -9999 0 -0.36 31 31
IL1 beta/IL1R2 -0.088 0.18 -9999 0 -0.33 155 155
IRAK/TRAF6/TAK1/TAB1/TAB2 0.028 0.014 -9999 0 -0.26 1 1
NF kappa B1 p50/RelA -0.04 0.092 -9999 0 -0.42 11 11
IRAK3 -0.011 0.1 -9999 0 -0.47 24 24
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.009 0.11 -9999 0 -0.43 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.027 0.038 -9999 0 -0.43 1 1
IL1 alpha/IL1R1/IL1RAP 0.016 0.052 -9999 0 -0.32 11 11
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.015 -9999 0 -0.28 1 1
IL1RAP 0.009 0.044 -9999 0 -0.47 4 4
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.036 0.08 -9999 0 -0.36 10 10
CASP1 -0.002 0.084 -9999 0 -0.47 15 15
IL1RN/IL1R2 -0.072 0.17 -9999 0 -0.36 118 118
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.012 0.12 -9999 0 -0.33 31 31
TMEM189-UBE2V1 0.005 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.033 0.037 -9999 0 -0.38 2 2
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
IL1RN -0.019 0.12 -9999 0 -0.5 31 31
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.021 0.048 -9999 0 -0.27 11 11
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0.023 -9999 0 -0.28 3 3
ADCY5 -0.03 0.11 -9999 0 -0.28 78 78
ADCY6 0.018 0 -9999 0 -10000 0 0
ADCY7 0.017 0.017 -9999 0 -0.36 1 1
ADCY1 -0.017 0.11 -9999 0 -0.35 46 46
ADCY2 0.004 0.064 -9999 0 -0.29 22 22
ADCY3 0.018 0 -9999 0 -10000 0 0
ADCY8 0.008 0.037 -9999 0 -0.36 5 5
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.016 0.019 -9999 0 -0.28 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.006 0.051 -9999 0 -0.24 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.023 -9999 0 -10000 0 0
VDR 0.005 0.065 -9999 0 -0.5 8 8
FAM120B 0.013 0.001 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.022 0.12 -9999 0 -0.42 9 9
RXRs/LXRs/DNA/Oxysterols -0.016 0.14 -9999 0 -0.51 13 13
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0.002 0.014 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.025 0.048 -9999 0 -0.44 1 1
RXRs/NUR77 -0.041 0.14 -9999 0 -0.38 31 31
RXRs/PPAR -0.035 0.12 -9999 0 -0.37 20 20
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.047 -9999 0 -0.36 8 8
RARs/VDR/DNA/Vit D3 0.02 0.061 -9999 0 -0.4 6 6
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.005 0.065 -9999 0 -0.5 8 8
RARs/RARs/DNA/9cRA 0.018 0.042 -9999 0 -0.23 13 13
RARG 0.005 0.062 -9999 0 -0.47 8 8
RPS6KB1 0.023 0.035 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.025 0.048 -9999 0 -0.44 1 1
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.004 0.047 -9999 0 -0.36 8 8
RXRs/PPAR/9cRA/PGJ2/DNA -0.035 0.12 -9999 0 -0.32 13 13
NR1H4 -0.1 0.21 -9999 0 -0.49 108 108
RXRs/LXRs/DNA -0.013 0.12 -9999 0 -0.37 6 6
NR1H2 0.016 0.011 -9999 0 -10000 0 0
NR1H3 0.016 0.012 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.031 0.12 -9999 0 -0.3 17 17
NR4A1 -0.012 0.11 -9999 0 -0.52 23 23
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.073 0.13 -9999 0 -0.35 45 45
RXRG -0.11 0.21 -9999 0 -0.47 120 120
RXR alpha/CCPG 0.022 0.007 -9999 0 -10000 0 0
RXRA 0.016 0.011 -9999 0 -10000 0 0
RXRB 0.016 0.012 -9999 0 -10000 0 0
THRB 0.003 0.075 -9999 0 -0.58 8 8
PPARG -0.017 0.12 -9999 0 -0.48 30 30
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.046 0.26 -9999 0 -0.97 29 29
mol:Oxysterols 0.003 0.012 -9999 0 -10000 0 0
cholesterol transport -0.016 0.14 -9999 0 -0.42 29 29
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.008 0.049 -9999 0 -0.47 5 5
RXRs/NUR77/BCL2 -0.052 0.14 -9999 0 -0.37 43 43
SREBF1 -0.008 0.13 -9999 0 -0.56 8 8
RXRs/RXRs/DNA/9cRA -0.034 0.12 -9999 0 -0.32 13 13
ABCA1 -0.008 0.14 -9999 0 -0.6 9 9
RARs/THRs 0.027 0.06 -9999 0 -0.52 1 1
RXRs/FXR -0.092 0.17 -9999 0 -0.4 57 57
BCL2 -0.01 0.1 -9999 0 -0.47 23 23
HIF-2-alpha transcription factor network

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
MMP14 -0.022 0.16 -10000 0 -1.2 9 9
oxygen homeostasis -0.001 0.016 -10000 0 -10000 0 0
TCEB2 0.005 0.07 -10000 0 -0.58 7 7
TCEB1 0.012 0.027 -10000 0 -0.58 1 1
VHL/Elongin B/Elongin C/HIF2A -0.019 0.076 -10000 0 -0.43 8 8
EPO -0.053 0.29 -10000 0 -0.69 41 41
FIH (dimer) 0.013 0.015 -10000 0 -10000 0 0
APEX1 0.012 0.017 -10000 0 -10000 0 0
SERPINE1 -0.049 0.28 -10000 0 -0.71 30 30
FLT1 -0.022 0.16 -10000 0 -1.2 8 8
ADORA2A -0.018 0.24 -10000 0 -0.67 22 22
germ cell development -0.037 0.27 -10000 0 -0.66 41 41
SLC11A2 -0.013 0.24 -10000 0 -0.67 22 22
BHLHE40 -0.019 0.26 -10000 0 -0.68 28 28
HIF1AN 0.013 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.007 0.16 -10000 0 -0.44 6 6
ETS1 0.021 0.05 -10000 0 -0.5 4 4
CITED2 -0.003 0.034 -10000 0 -0.41 2 2
KDR -0.05 0.26 -10000 0 -1.3 21 21
PGK1 -0.014 0.24 -10000 0 -0.67 22 22
SIRT1 0.012 0.003 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.022 0.28 -10000 0 -0.77 25 25
EPAS1 0.014 0.11 -10000 0 -0.36 6 6
SP1 0.02 0.003 -10000 0 -10000 0 0
ABCG2 -0.04 0.29 -10000 0 -0.76 38 38
EFNA1 -0.013 0.24 -10000 0 -0.67 22 22
FXN -0.018 0.24 -10000 0 -0.66 22 22
POU5F1 -0.04 0.28 -10000 0 -0.68 41 41
neuron apoptosis 0.021 0.27 0.74 25 -10000 0 25
EP300 0.01 0.038 -10000 0 -0.47 3 3
EGLN3 0.004 0.071 -10000 0 -0.47 10 10
EGLN2 0.014 0.015 -10000 0 -10000 0 0
EGLN1 0.013 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.02 0.053 -10000 0 -0.38 8 8
VHL 0.012 0.022 -10000 0 -0.47 1 1
ARNT 0.012 0.018 -10000 0 -10000 0 0
SLC2A1 -0.018 0.24 -10000 0 -0.66 22 22
TWIST1 -0.087 0.31 -10000 0 -0.74 44 44
ELK1 0.02 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.019 0.15 -10000 0 -0.49 4 4
VEGFA -0.03 0.27 -10000 0 -0.69 32 32
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.021 0.04 -9999 0 -0.27 9 9
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.016 0.063 -9999 0 -0.34 13 13
MAPK12 -0.01 0.12 -9999 0 -0.39 33 33
CCND1 0.005 0.047 -9999 0 -0.23 4 4
p38 gamma/SNTA1 -0.002 0.11 -9999 0 -0.37 33 33
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.003 0.075 -9999 0 -0.58 8 8
G2/M transition checkpoint -0.01 0.12 -9999 0 -0.39 33 33
MAP2K6 -0.002 0.089 -9999 0 -0.32 30 30
MAPT 0.011 0.057 -9999 0 -0.34 5 5
MAPK13 0.015 0.047 -9999 0 -0.33 9 9
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0 0.072 -9999 0 -0.3 24 24
IL2 signaling events mediated by PI3K

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
BCL2L1 0.028 0.099 -10000 0 -0.49 8 8
UGCG -0.039 0.19 -10000 0 -0.64 41 41
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.12 -10000 0 -0.37 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.038 0.18 -10000 0 -0.63 41 41
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.042 0.11 -10000 0 -0.44 21 21
FRAP1 0.013 0.16 -10000 0 -0.46 33 33
FOXO3 0.023 0.13 -10000 0 -0.48 13 13
AKT1 0.017 0.14 -10000 0 -0.51 14 14
GAB2 0.013 0.002 -10000 0 -10000 0 0
SMPD1 0.015 0.027 -10000 0 -10000 0 0
SGMS1 0.015 0.027 -10000 0 -10000 0 0
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 0.014 0.041 -10000 0 -0.31 7 7
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.011 0.13 -10000 0 -0.35 44 44
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.017 0.049 -10000 0 -0.37 7 7
RPS6KB1 0.015 0.032 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0 0.092 -10000 0 -0.55 13 13
PIK3R1 0.01 0.049 -10000 0 -0.47 5 5
JAK1 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.012 0.15 -10000 0 -0.61 7 7
MYB 0.008 0.089 -10000 0 -0.39 6 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.12 -10000 0 -0.46 17 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.038 -10000 0 -0.41 1 1
mol:PI-3-4-5-P3 0.017 0.12 -10000 0 -0.45 17 17
Rac1/GDP 0.02 0.038 -10000 0 -0.29 5 5
T cell proliferation 0.023 0.11 -10000 0 -0.43 16 16
SHC1 0.013 0.002 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.039 23 23
PRKCZ 0.023 0.12 -10000 0 -0.44 16 16
NF kappa B1 p50/RelA -0.039 0.11 -10000 0 -0.48 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.019 0.11 -10000 0 -0.46 17 17
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.078 0.21 -10000 0 -0.57 76 76
IL2RB -0.015 0.12 -10000 0 -0.49 29 29
TERT -0.18 0.28 -10000 0 -0.58 159 159
E2F1 0.01 0.058 -10000 0 -0.24 6 6
SOS1 0.013 0.003 -10000 0 -10000 0 0
RPS6 0.011 0.038 -10000 0 -0.58 2 2
mol:cAMP -0.002 0.005 0.019 23 -10000 0 23
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
IL2RG -0.01 0.12 -10000 0 -0.55 22 22
actin cytoskeleton organization 0.023 0.11 -10000 0 -0.43 16 16
GRB2 0.013 0.003 -10000 0 -10000 0 0
IL2 0.006 0.038 -10000 0 -0.57 2 2
PIK3CA 0.012 0.038 -10000 0 -0.47 3 3
Rac1/GTP 0.027 0.038 -10000 0 -0.29 4 4
LCK 0.006 0.075 -10000 0 -0.57 8 8
BCL2 0.001 0.21 -10000 0 -0.83 24 24
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.038 -9999 0 -0.58 2 2
alphaV beta3 Integrin -0.051 0.14 -9999 0 -0.33 97 97
PTK2 -0.042 0.092 -9999 0 -0.48 13 13
positive regulation of JNK cascade -0.014 0.052 -9999 0 -0.31 13 13
CDC42/GDP 0.025 0.083 -9999 0 -0.42 13 13
Rac1/GDP 0.027 0.083 -9999 0 -0.41 13 13
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.016 0.063 -9999 0 -0.38 13 13
nectin-3/I-afadin -0.014 0.11 -9999 0 -0.39 40 40
RAPGEF1 0.017 0.091 -9999 0 -0.46 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.1 -9999 0 -0.53 13 13
PDGFB-D/PDGFRB 0.011 0.038 -9999 0 -0.57 2 2
TLN1 0.014 0.05 -9999 0 -10000 0 0
Rap1/GTP -0.014 0.055 -9999 0 -0.33 13 13
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.014 0.11 -9999 0 -0.39 40 40
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.021 0.099 -9999 0 -0.52 13 13
MLLT4 0.013 0.001 -9999 0 -10000 0 0
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
PI3K 0.009 0.096 -9999 0 -0.53 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.014 0.054 -9999 0 -0.33 13 13
PVRL1 0.013 0 -9999 0 -10000 0 0
PVRL3 -0.032 0.15 -9999 0 -0.54 40 40
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
CDH1 0.011 0.031 -9999 0 -0.47 2 2
CLDN1 -0.043 0.16 -9999 0 -0.47 56 56
JAM-A/CLDN1 -0.023 0.12 -9999 0 -0.34 30 30
SRC 0.003 0.11 -9999 0 -0.6 13 13
ITGB3 -0.083 0.19 -9999 0 -0.47 97 97
nectin-1(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
FARP2 0.016 0.097 -9999 0 -0.51 13 13
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.002 0.097 -9999 0 -0.32 40 40
nectin-1/I-afadin 0.02 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.02 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.002 0.097 -9999 0 -0.32 40 40
CDC42/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.014 0.052 -9999 0 -0.31 13 13
alphaV/beta3 Integrin/Talin -0.02 0.11 -9999 0 -0.35 16 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
PIP5K1C 0.007 0.053 -9999 0 -10000 0 0
VAV2 0.015 0.098 -9999 0 -0.52 13 13
RAP1/GDP -0.015 0.064 -9999 0 -0.38 13 13
ITGAV 0.011 0.031 -9999 0 -0.47 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.002 0.097 -9999 0 -0.32 40 40
nectin-3(dimer)/I-afadin/I-afadin -0.014 0.11 -9999 0 -0.39 40 40
Rac1/GTP -0.017 0.066 -9999 0 -0.4 13 13
PTPRM -0.001 0.059 -9999 0 -0.23 7 7
E-cadherin/beta catenin/alpha catenin -0.001 0.013 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.005 0.065 -10000 0 -0.5 8 8
Cbp/p300/PCAF 0.025 0.023 -10000 0 -0.27 3 3
EP300 0.01 0.038 -10000 0 -0.47 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.028 0.054 -10000 0 -0.3 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.025 0.066 0.2 33 -0.24 10 43
RAR alpha/9cRA/Cyclin H -0.018 0.064 -10000 0 -0.4 4 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.026 0.053 -10000 0 -0.28 7 7
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.001 0.082 -10000 0 -0.45 11 11
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.047 -10000 0 -0.36 8 8
RXRs/RARs/NRIP1/9cRA 0.006 0.12 -10000 0 -0.54 13 13
NCOA2 -0.047 0.16 -10000 0 -0.47 60 60
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.005 0.065 -10000 0 -0.5 8 8
RARG 0.006 0.062 -10000 0 -0.47 8 8
RAR gamma1/9cRA 0.014 0.038 -10000 0 -0.28 8 8
MAPK3 0.014 0 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.072 -10000 0 -0.47 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.01 0.12 -10000 0 -0.47 21 21
RARA 0.005 0.073 -10000 0 -0.25 29 29
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.1 -10000 0 -0.34 22 22
PRKCA -0.004 0.097 -10000 0 -0.47 20 20
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.12 -10000 0 -0.49 20 20
RXRG -0.075 0.17 -10000 0 -0.33 127 127
RXRA 0.013 0.067 -10000 0 -0.39 4 4
RXRB 0.004 0.075 -10000 0 -0.29 20 20
VDR/Vit D3/DNA 0.004 0.047 -10000 0 -0.36 8 8
RBP1 -0.036 0.15 -10000 0 -0.48 49 49
CRBP1/9-cic-RA -0.026 0.11 -10000 0 -0.34 49 49
RARB 0.01 0.049 -10000 0 -0.47 5 5
PRKCG -0.008 0.1 -10000 0 -0.57 15 15
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.12 -10000 0 -0.51 16 16
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.1 -10000 0 -0.43 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.065 -10000 0 -0.32 9 9
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.12 -10000 0 -0.49 20 20
positive regulation of DNA binding -0.018 0.061 -10000 0 -0.38 4 4
NRIP1 -0.003 0.11 -10000 0 -0.52 11 11
RXRs/RARs -0.012 0.12 -10000 0 -0.49 21 21
RXRs/RXRs/DNA/9cRA -0.023 0.11 -10000 0 -0.47 22 22
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0.025 0.029 -10000 0 -0.35 3 3
RAR alpha/9cRA -0.012 0.044 -10000 0 -0.29 6 6
CCNH 0.01 0.046 -10000 0 -0.58 3 3
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.005 0.032 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.004 0.092 -9999 0 -0.49 1 1
Syndecan-3/Neurocan -0.003 0.079 -9999 0 -0.29 32 32
POMC -0.047 0.16 -9999 0 -0.48 59 59
EGFR -0.026 0.13 -9999 0 -0.47 39 39
Syndecan-3/EGFR 0.004 0.07 -9999 0 -0.53 1 1
AGRP 0.002 0.046 -9999 0 -0.58 3 3
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.028 0.14 -9999 0 -0.58 31 31
long-term memory 0.03 0.024 -9999 0 -0.49 1 1
Syndecan-3/IL8 -0.011 0.094 -9999 0 -0.3 26 26
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.02 0 -9999 0 -10000 0 0
FYN 0.013 0.001 -9999 0 -10000 0 0
limb bud formation -0.001 0.025 -9999 0 -0.55 1 1
MC4R 0 0.046 -9999 0 -0.58 3 3
SRC 0.013 0 -9999 0 -10000 0 0
PTN -0.073 0.19 -9999 0 -0.48 86 86
FGFR/FGF/Syndecan-3 -0.001 0.025 -9999 0 -0.56 1 1
neuron projection morphogenesis -0.028 0.11 -9999 0 -0.46 6 6
Syndecan-3/AgRP 0.007 0.036 -9999 0 -0.54 1 1
Syndecan-3/AgRP/MC4R -0.001 0.04 -9999 0 -0.52 1 1
Fyn/Cortactin 0.02 0 -9999 0 -10000 0 0
SDC3 -0.001 0.025 -9999 0 -0.56 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.093 -9999 0 -0.29 26 26
IL8 -0.054 0.18 -9999 0 -0.51 62 62
Syndecan-3/Fyn/Cortactin 0.031 0.024 -9999 0 -0.51 1 1
Syndecan-3/CASK -0.001 0.024 -9999 0 -0.54 1 1
alpha-MSH/MC4R -0.033 0.12 -9999 0 -0.34 62 62
Gamma Secretase 0.039 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.022 0.071 -9999 0 -0.55 7 7
VEGFR1 homodimer/NRP1 0.012 0.071 -9999 0 -0.56 7 7
mol:DAG -0.008 0.11 -9999 0 -0.49 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.003 0.1 -9999 0 -0.51 11 11
CaM/Ca2+ 0 0.1 -9999 0 -0.52 5 5
HIF1A 0.015 0.044 -9999 0 -0.34 6 6
GAB1 0.012 0.022 -9999 0 -0.47 1 1
AKT1 0.007 0.11 -9999 0 -0.49 8 8
PLCG1 -0.008 0.11 -9999 0 -0.5 7 7
NOS3 0.012 0.11 -9999 0 -0.5 5 5
CBL 0.012 0.022 -9999 0 -0.47 1 1
mol:NO 0.012 0.1 -9999 0 -0.48 5 5
FLT1 0.019 0.081 -9999 0 -0.63 7 7
PGF -0.052 0.17 -9999 0 -0.47 65 65
VEGFR1 homodimer/NRP2/VEGFR121 -0.006 0.12 -9999 0 -0.59 11 11
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
eNOS/Hsp90 0.019 0.1 -9999 0 -0.46 5 5
endothelial cell proliferation -0.058 0.19 -9999 0 -0.52 55 55
mol:Ca2+ -0.007 0.11 -9999 0 -0.49 7 7
MAPK3 -0.003 0.12 -9999 0 -0.49 13 13
MAPK1 -0.003 0.12 -9999 0 -0.49 13 13
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
PLGF homodimer -0.052 0.17 -9999 0 -0.47 65 65
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.049 0.16 -9999 0 -0.47 62 62
VEGFA homodimer -0.019 0.12 -9999 0 -0.49 31 31
VEGFR1 homodimer/VEGFA homodimer 0.003 0.11 -9999 0 -0.55 11 11
platelet activating factor biosynthetic process 0.003 0.11 -9999 0 -0.47 13 13
PI3K -0.002 0.11 -9999 0 -0.52 8 8
PRKCA -0.01 0.12 -9999 0 -0.52 13 13
PRKCB -0.056 0.17 -9999 0 -0.46 47 47
VEGFR1 homodimer/PLGF homodimer -0.017 0.12 -9999 0 -0.5 9 9
VEGFA -0.019 0.12 -9999 0 -0.49 31 31
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.008 0.11 -9999 0 -0.49 7 7
RASA1 0.027 0.07 -9999 0 -0.49 8 8
NRP2 -0.019 0.12 -9999 0 -0.47 32 32
VEGFR1 homodimer 0.019 0.081 -9999 0 -0.63 7 7
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.012 0.027 -9999 0 -0.58 1 1
eNOS/Caveolin-1 -0.009 0.14 -9999 0 -0.43 33 33
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
mol:PI-3-4-5-P3 -0.003 0.11 -9999 0 -0.52 8 8
mol:L-citrulline 0.012 0.1 -9999 0 -0.48 5 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.019 0.099 -9999 0 -0.59 7 7
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.011 0.1 -9999 0 -0.61 7 7
CD2AP 0.013 0.001 -9999 0 -10000 0 0
PI3K/GAB1 0.004 0.11 -9999 0 -0.49 8 8
PDPK1 0.002 0.11 -9999 0 -0.48 8 8
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.011 0.1 -9999 0 -0.59 8 8
mol:NADP 0.012 0.1 -9999 0 -0.48 5 5
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.097 -9999 0 -0.58 7 7
VEGFR1 homodimer/NRP2 0.003 0.1 -9999 0 -0.57 8 8
Caspase cascade in apoptosis

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
TOP1 0.001 0.095 -10000 0 -0.35 23 23
ACTA1 -0.061 0.13 -10000 0 -0.45 35 35
NUMA1 0.001 0.095 -10000 0 -0.42 14 14
SPTAN1 -0.009 0.12 0.22 1 -0.43 23 24
LIMK1 -0.009 0.12 0.22 1 -0.43 23 24
BIRC3 0.007 0.06 -10000 0 -0.52 6 6
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.011 0.038 -10000 0 -0.58 2 2
CASP10 -0.014 0.13 -10000 0 -0.38 49 49
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.001 0.095 -10000 0 -0.42 14 14
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.008 0.11 0.21 1 -0.42 23 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN -0.011 0.12 0.22 1 -0.44 25 26
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.014 0.14 -10000 0 -0.57 28 28
BID 0.003 0.063 -10000 0 -0.22 23 23
MAP3K1 0.003 0.046 -10000 0 -0.22 8 8
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.12 0.22 1 -0.44 26 27
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.001 0.032 0.14 1 -0.16 4 5
neuron apoptosis 0.016 0.056 -10000 0 -0.66 3 3
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.001 0.11 -10000 0 -0.54 12 12
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 0.014 0.065 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD -0.002 0.11 -10000 0 -0.54 12 12
CASP7 -0.005 0.033 0.25 6 -0.2 1 7
KRT18 0.012 0.025 -10000 0 -10000 0 0
apoptosis 0.005 0.1 0.23 1 -0.46 12 13
DFFA -0.009 0.12 -10000 0 -0.43 23 23
DFFB -0.009 0.12 0.22 1 -0.43 23 24
PARP1 0.001 0.032 0.16 4 -0.14 1 5
actin filament polymerization 0.002 0.11 0.53 12 -10000 0 12
TNF -0.029 0.14 -10000 0 -0.5 39 39
CYCS 0.005 0.049 -10000 0 -0.2 12 12
SATB1 0.015 0.072 -10000 0 -0.41 2 2
SLK -0.009 0.12 0.22 1 -0.43 23 24
p15 BID/BAX 0.008 0.06 -10000 0 -0.27 11 11
CASP2 0.025 0.063 -10000 0 -0.34 3 3
JNK cascade -0.003 0.046 0.22 8 -10000 0 8
CASP3 -0.016 0.12 0.22 1 -0.36 45 46
LMNB2 0.027 0.053 -10000 0 -0.25 1 1
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.012 0.022 -10000 0 -0.47 1 1
Mammalian IAPs/DIABLO 0.03 0.034 -10000 0 -0.31 3 3
negative regulation of DNA binding -0.014 0.14 -10000 0 -0.56 28 28
stress fiber formation -0.008 0.11 0.21 1 -0.42 23 24
GZMB -0.021 0.14 -10000 0 -0.44 45 45
CASP1 0.006 0.062 -10000 0 -0.33 15 15
LMNB1 0.023 0.057 -10000 0 -0.26 3 3
APP 0.016 0.056 -10000 0 -0.67 3 3
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM 0 0.098 0.22 1 -0.45 12 13
LMNA 0.027 0.053 -10000 0 -0.25 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.022 0.059 -10000 0 -0.34 1 1
LRDD 0.001 0.084 -10000 0 -0.58 10 10
SREBF1 -0.01 0.12 -10000 0 -0.42 24 24
APAF-1/Caspase 9 -0.004 0.019 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.094 -10000 0 -0.41 14 14
CFL2 -0.003 0.11 -10000 0 -0.54 12 12
GAS2 -0.024 0.14 -10000 0 -0.4 41 41
positive regulation of apoptosis 0.028 0.055 -10000 0 -0.26 1 1
PRF1 -0.001 0.084 -10000 0 -0.5 13 13
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0.051 0.23 12 -10000 0 12
DAPP1 -0.027 0.13 -10000 0 -0.38 38 38
Src family/SYK family/BLNK-LAT/BTK-ITK -0.008 0.14 -10000 0 -0.5 15 15
mol:DAG 0.019 0.08 0.18 10 -0.27 10 20
HRAS 0.008 0.059 -10000 0 -0.57 5 5
RAP1A 0.014 0.003 -10000 0 -10000 0 0
ARF5/GDP 0.033 0.045 -10000 0 -0.31 2 2
PLCG2 0.004 0.069 -10000 0 -0.49 9 9
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.044 0.22 12 -10000 0 12
ARF1/GTP 0.035 0.045 0.22 12 -10000 0 12
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0.026 0.043 -10000 0 -10000 0 0
ADAP1 0 0.05 0.21 12 -0.39 1 13
ARAP3 0.002 0.044 0.22 12 -10000 0 12
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.012 0.022 -10000 0 -0.47 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0.022 -10000 0 -0.47 1 1
FYN 0.013 0.001 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.01 0.041 -10000 0 -0.51 3 3
mol:Ca2+ 0.016 0.042 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.01 0.038 -10000 0 -0.47 3 3
ZAP70 -0.054 0.19 -10000 0 -0.57 56 56
mol:IP3 0.018 0.056 -10000 0 -0.21 2 2
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.033 0.045 -10000 0 -0.31 2 2
RhoA/GDP 0 0.043 0.22 9 -10000 0 9
PDK1/Src/Hsp90 0.027 0 -10000 0 -10000 0 0
BLNK 0.012 0.022 -10000 0 -0.47 1 1
actin cytoskeleton reorganization 0.05 0.053 0.22 9 -10000 0 9
SRC 0.013 0 -10000 0 -10000 0 0
PLEKHA2 -0.001 0.11 -10000 0 -0.38 33 33
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.074 -10000 0 -0.45 13 13
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.044 0.23 12 -10000 0 12
RhoA/GTP 0.031 0.041 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.013 0.12 -10000 0 -0.44 17 17
BLK -0.1 0.22 -10000 0 -0.5 109 109
PDPK1 0.013 0 -10000 0 -10000 0 0
CYTH1 0.002 0.043 0.21 12 -10000 0 12
HCK 0.009 0.046 -10000 0 -0.5 4 4
CYTH3 -0.001 0.05 0.21 12 -10000 0 12
CYTH2 0.002 0.043 0.21 12 -10000 0 12
KRAS 0.014 0.003 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.03 0.16 -10000 0 -0.4 76 76
SGK1 -0.068 0.16 0.18 6 -0.43 76 82
INPP5D -0.013 0.11 -10000 0 -0.47 26 26
mol:GDP 0.026 0.047 -10000 0 -0.3 3 3
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.006 0.06 -10000 0 -0.49 7 7
ARF6/GDP 0 0.043 0.23 9 -10000 0 9
mol:PI-3-4-5-P3 0.003 0.05 0.26 12 -10000 0 12
ARAP3/RAP1A/GTP 0.026 0.043 -10000 0 -10000 0 0
VAV1 -0.01 0.1 -10000 0 -0.48 23 23
mol:PI-3-4-P2 0.002 0.079 -10000 0 -0.33 26 26
RAS family/GTP/PI3K Class I 0.025 0.033 -10000 0 -10000 0 0
PLEKHA1 0.011 0.066 -10000 0 -0.27 26 26
Rac1/GDP 0.033 0.045 -10000 0 -0.31 2 2
LAT -0.003 0.095 -10000 0 -0.55 14 14
Rac1/GTP 0.028 0.051 -10000 0 -0.36 2 2
ITK -0.02 0.084 0.21 12 -0.39 1 13
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.017 0.1 0.21 10 -0.36 13 23
LCK 0.003 0.075 -10000 0 -0.58 8 8
BTK -0.004 0.057 0.21 12 -10000 0 12
IGF1 pathway

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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.01 0.096 -10000 0 -0.42 12 12
GRB2/SOS1/SHC 0.027 0 -10000 0 -10000 0 0
HRAS 0.007 0.059 -10000 0 -0.58 5 5
IRS1/Crk -0.009 0.097 -10000 0 -0.42 12 12
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.1 -10000 0 -0.29 55 55
AKT1 0.007 0.094 -10000 0 -0.4 11 11
BAD 0.012 0.09 -10000 0 -0.39 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.01 0.096 -10000 0 -0.42 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.01 0.1 -10000 0 -0.44 12 12
RAF1 0.018 0.086 -10000 0 -0.57 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0 0.093 -10000 0 -0.39 12 12
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.018 0.1 -10000 0 -0.29 55 55
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
RPS6KB1 0.007 0.094 -10000 0 -0.38 14 14
GNB2L1 0.01 0.046 -10000 0 -0.58 3 3
positive regulation of MAPKKK cascade 0.015 0.075 -10000 0 -0.47 2 2
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
HRAS/GTP -0.028 0.078 -10000 0 -0.37 12 12
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.01 0.083 -10000 0 -0.45 2 2
IGF-1R heterotetramer 0.003 0.045 -10000 0 -0.59 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.008 0.098 -10000 0 -0.42 12 12
Crk/p130 Cas/Paxillin 0.006 0.089 -10000 0 -0.37 12 12
IGF1R 0.003 0.045 -10000 0 -0.59 2 2
IGF1 -0.048 0.17 -10000 0 -0.52 55 55
IRS2/Crk -0.005 0.098 -10000 0 -0.37 17 17
PI3K -0.003 0.1 -10000 0 -0.44 14 14
apoptosis -0.019 0.08 0.5 2 -10000 0 2
HRAS/GDP 0.005 0.044 -10000 0 -0.42 5 5
PRKCD 0.001 0.11 -10000 0 -0.35 36 36
RAF1/14-3-3 E 0.025 0.077 -10000 0 -0.48 2 2
BAD/14-3-3 0.02 0.085 -10000 0 -0.54 2 2
PRKCZ 0.007 0.094 -10000 0 -0.4 11 11
Crk/p130 Cas/Paxillin/FAK1 -0.023 0.067 -10000 0 -0.54 2 2
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.006 0.11 -10000 0 -0.37 36 36
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.001 0.09 -10000 0 -0.38 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.009 0.096 -10000 0 -0.42 12 12
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.01 0.099 -10000 0 -0.44 12 12
IRS1 -0.019 0.1 -10000 0 -0.29 55 55
IRS2 -0.013 0.1 -10000 0 -0.4 17 17
IGF-1R heterotetramer/IGF1 -0.029 0.13 -10000 0 -0.39 55 55
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 0.001 0.099 -10000 0 -0.41 14 14
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 0 0.11 -10000 0 -0.35 36 36
SHC1 0.013 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.022 -9999 0 -0.47 1 1
GNB1/GNG2 0.017 0.032 -9999 0 -0.27 5 5
forebrain development -0.038 0.13 -9999 0 -0.38 20 20
GNAO1 -0.081 0.19 -9999 0 -0.47 93 93
SMO/beta Arrestin2 0.016 0.011 -9999 0 -10000 0 0
SMO 0.01 0.007 -9999 0 -10000 0 0
ARRB2 0.01 0.006 -9999 0 -10000 0 0
GLI3/SPOP 0.034 0.06 -9999 0 -0.53 1 1
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.012 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.036 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.065 -9999 0 -0.53 7 7
XPO1 0.011 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.029 0.12 -9999 0 -0.42 2 2
SAP30 0.014 0.001 -9999 0 -10000 0 0
mol:GDP 0.01 0.007 -9999 0 -10000 0 0
MIM/GLI2A -0.007 0.06 -9999 0 -0.55 3 3
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.012 0.003 -9999 0 -10000 0 0
GLI2 0.035 0.036 -9999 0 -10000 0 0
GLI3 0.028 0.063 -9999 0 -0.56 1 1
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.008 0.049 -9999 0 -0.47 5 5
Gi family/GTP -0.044 0.15 -9999 0 -0.36 67 67
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.045 0.048 -9999 0 -0.38 1 1
GLI2/Su(fu) 0.036 0.039 -9999 0 -10000 0 0
FOXA2 -0.29 0.45 -9999 0 -1 137 137
neural tube patterning -0.038 0.13 -9999 0 -0.38 20 20
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.015 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.007 0.06 -9999 0 -0.56 3 3
embryonic limb morphogenesis -0.038 0.13 -9999 0 -0.38 20 20
SUFU 0.021 0.014 -9999 0 -10000 0 0
LGALS3 -0.025 0.13 -9999 0 -0.47 38 38
catabolic process 0.054 0.068 -9999 0 -0.55 1 1
GLI3A/CBP 0.014 0.039 -9999 0 -0.32 4 4
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.039 0.13 -9999 0 -0.39 20 20
RAB23 0.012 0.022 -9999 0 -0.47 1 1
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.008 0.072 -9999 0 -10000 0 0
GNAZ -0.034 0.14 -9999 0 -0.47 46 46
RBBP4 0.012 0.031 -9999 0 -0.47 2 2
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.04 0.034 -9999 0 -10000 0 0
STK36 0.011 0.007 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.032 0.14 -9999 0 -0.4 43 43
PTCH1 -0.027 0.12 -9999 0 -0.53 2 2
MIM/GLI1 -0.099 0.24 -9999 0 -0.45 139 139
CREBBP 0.014 0.039 -9999 0 -0.32 4 4
Su(fu)/SIN3/HDAC complex 0.048 0.018 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.21 -9999 0 -0.53 29 29
RAD9A 0.01 0.046 -9999 0 -0.58 3 3
AP1 -0.053 0.15 -9999 0 -0.36 88 88
IFNAR2 0.01 0.007 -9999 0 -10000 0 0
AKT1 0.004 0.042 -9999 0 -0.21 8 8
ER alpha/Oestrogen -0.004 0.063 -9999 0 -0.34 16 16
NFX1/SIN3/HDAC complex 0.03 0.026 -9999 0 -10000 0 0
EGF -0.057 0.18 -9999 0 -0.54 61 61
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.019 -9999 0 -0.33 1 1
TERT/c-Abl -0.11 0.2 -9999 0 -0.52 21 21
SAP18 0.012 0.002 -9999 0 -10000 0 0
MRN complex 0.027 0 -9999 0 -10000 0 0
WT1 -0.22 0.28 -9999 0 -0.56 191 191
WRN 0.012 0.022 -9999 0 -0.47 1 1
SP1 0.011 0.008 -9999 0 -10000 0 0
SP3 0.011 0.004 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.16 -9999 0 -0.5 11 11
Mad/Max 0.015 0.01 -9999 0 -10000 0 0
TERT -0.13 0.22 -9999 0 -0.56 24 24
CCND1 -0.11 0.2 -9999 0 -0.62 2 2
MAX 0.011 0.004 -9999 0 -10000 0 0
RBBP7 0.012 0.002 -9999 0 -10000 0 0
RBBP4 0.01 0.031 -9999 0 -0.47 2 2
TERF2 0.012 0.003 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.012 0.002 -9999 0 -10000 0 0
Telomerase/911 0.017 0.036 -9999 0 -10000 0 0
CDKN1B -0.002 0.11 -9999 0 -0.42 17 17
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.002 -9999 0 -10000 0 0
TRF2/PARP2 0.02 0.003 -9999 0 -10000 0 0
UBE3A 0.012 0.004 -9999 0 -10000 0 0
JUN 0.004 0.061 -9999 0 -0.5 7 7
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.006 -9999 0 -10000 0 0
FOS -0.077 0.19 -9999 0 -0.48 88 88
IFN-gamma/IRF1 -0.018 0.13 -9999 0 -0.44 40 40
PARP2 0.013 0 -9999 0 -10000 0 0
BLM -0.016 0.13 -9999 0 -0.58 24 24
Telomerase -0.006 0.046 -9999 0 -0.32 1 1
IRF1 -0.001 0.098 -9999 0 -0.57 14 14
ESR1 -0.004 0.088 -9999 0 -0.48 16 16
KU/TER 0.02 0 -9999 0 -10000 0 0
ATM/TRF2 0.02 0.014 -9999 0 -0.3 1 1
ubiquitin-dependent protein catabolic process 0.034 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.034 0.028 -9999 0 -10000 0 0
HDAC1 0.012 0.002 -9999 0 -10000 0 0
HDAC2 0.009 0.023 -9999 0 -0.47 1 1
ATM -0.001 0.017 -9999 0 -0.38 1 1
SMAD3 0.023 0.005 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.011 0.004 -9999 0 -10000 0 0
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.095 0.2 -9999 0 -0.54 11 11
NR2F2 0.017 0.008 -9999 0 -10000 0 0
MAPK3 0.01 0.029 -9999 0 -0.41 2 2
MAPK1 0.01 0.029 -9999 0 -0.41 2 2
TGFB1/TGF beta receptor Type II 0.014 0.002 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.017 -9999 0 -0.38 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR -0.027 0.13 -9999 0 -0.48 39 39
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.063 0.16 -9999 0 -0.38 97 97
MYC -0.037 0.16 -9999 0 -0.58 39 39
IL2 0 0.039 -9999 0 -0.57 2 2
KU 0.02 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.014 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.001 0.088 -9999 0 -0.38 24 24
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.2 -9999 0 -0.52 18 18
SP1/HDAC2 0.015 0.021 -9999 0 -0.33 1 1
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.16 -9999 0 -0.51 9 9
Smad3/Myc -0.003 0.1 -9999 0 -0.35 39 39
911 complex 0.025 0.029 -9999 0 -0.35 3 3
IFNG -0.023 0.14 -9999 0 -0.57 30 30
Telomerase/PinX1 -0.12 0.16 -9999 0 -0.51 9 9
Telomerase/AKT1/mTOR/p70S6K -0.005 0.061 -9999 0 -10000 0 0
SIN3B 0.012 0.002 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.12 0.16 -9999 0 -0.51 9 9
response to DNA damage stimulus 0.003 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.038 0.002 -9999 0 -10000 0 0
TRF2/WRN 0.019 0.015 -9999 0 -0.3 1 1
Telomerase/hnRNP C1/C2 -0.12 0.16 -9999 0 -0.51 9 9
E2F1 -0.017 0.12 -9999 0 -0.58 22 22
ZNFX1 0.012 0.002 -9999 0 -10000 0 0
PIF1 0.004 0.073 -9999 0 -0.56 8 8
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.006 0.061 -10000 0 -0.54 6 6
positive regulation of NF-kappaB transcription factor activity -0.011 0.11 -10000 0 -0.36 39 39
MAP2K4 0.04 0.025 -10000 0 -10000 0 0
IKBKB 0.012 0.027 -10000 0 -0.58 1 1
TNFRSF10B 0.013 0 -10000 0 -10000 0 0
TNFRSF10A 0.008 0.049 -10000 0 -0.47 5 5
SMPD1 0.016 0.021 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.024 0.13 -10000 0 -0.47 37 37
TRAIL/TRAILR2 0.015 0.045 -10000 0 -0.39 6 6
TRAIL/TRAILR3 -0.021 0.12 -10000 0 -0.35 54 54
TRAIL/TRAILR1 0.011 0.057 -10000 0 -0.36 11 11
TRAIL/TRAILR4 -0.011 0.11 -10000 0 -0.37 39 39
TRAIL/TRAILR1/DAP3/GTP 0.019 0.044 -10000 0 -0.32 4 4
IKK complex -0.002 0.015 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.01 0 -10000 0 -10000 0 0
MAPK3 0.016 0.045 -10000 0 -0.39 6 6
MAP3K1 0.035 0.026 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.024 0.13 -10000 0 -0.47 37 37
TRADD 0.013 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.049 -10000 0 -0.47 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.03 0.033 -10000 0 -10000 0 0
CFLAR 0.013 0 -10000 0 -10000 0 0
MAPK1 0.016 0.045 -10000 0 -0.39 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.033 0.042 -10000 0 -0.28 4 4
mol:ceramide 0.016 0.021 -10000 0 -10000 0 0
FADD 0.013 0 -10000 0 -10000 0 0
MAPK8 0.039 0.045 -10000 0 -0.3 3 3
TRAF2 0.013 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.037 0.15 -10000 0 -0.47 50 50
CHUK 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.02 0.049 -10000 0 -0.3 11 11
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 0.009 0.072 0.24 32 -0.26 8 40
JNK cascade -0.011 0.11 -10000 0 -0.36 39 39
TRAIL (trimer) 0.006 0.061 -10000 0 -0.54 6 6
TNFRSF10C -0.037 0.15 -10000 0 -0.47 50 50
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.042 -10000 0 -0.29 4 4
TRAIL/TRAILR2/FADD 0.023 0.039 -10000 0 -0.32 6 6
cell death 0.016 0.021 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.033 0.023 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.013 0 -10000 0 -10000 0 0
CASP8 0.001 0.012 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.033 -10000 0 -0.28 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.049 0.022 -10000 0 -10000 0 0
NFATC2 0.005 0.067 -10000 0 -0.25 14 14
NFATC3 0.022 0.005 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.036 0.13 -10000 0 -0.4 41 41
Exportin 1/Ran/NUP214 0.026 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.064 0.13 -10000 0 -0.43 38 38
BCL2/BAX 0.001 0.079 -10000 0 -0.34 25 25
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.004 -10000 0 -10000 0 0
BAX 0.011 0.038 -10000 0 -0.58 2 2
MAPK14 0.013 0.002 -10000 0 -10000 0 0
BAD 0.012 0.027 -10000 0 -0.58 1 1
CABIN1/MEF2D -0.028 0.13 -10000 0 -0.37 41 41
Calcineurin A alpha-beta B1/BCL2 -0.01 0.1 -10000 0 -0.47 23 23
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.027 0.12 0.37 41 -10000 0 41
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.007 0.059 -10000 0 -0.58 5 5
XPO1 0.013 0 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.47 49 49
MAP3K8 0 0.08 -10000 0 -0.48 13 13
NFAT4/CK1 alpha 0.031 0.013 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.023 0.089 -10000 0 -0.4 6 6
CABIN1 -0.037 0.13 -10000 0 -0.4 41 41
CALM1 0.013 0.002 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0.022 -10000 0 -0.47 1 1
CAMK4 -0.024 0.13 -10000 0 -0.47 37 37
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.012 0.058 -10000 0 -0.41 9 9
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.002 0.072 -10000 0 -0.47 11 11
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.054 0.034 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.028 -10000 0 -0.33 3 3
CASP3 0.013 0.002 -10000 0 -10000 0 0
PIM1 0.006 0.065 -10000 0 -0.58 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.002 -10000 0 -10000 0 0
apoptosis -0.006 0.025 -10000 0 -0.22 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.056 -10000 0 -10000 0 0
PRKCB -0.097 0.2 -10000 0 -0.47 111 111
PRKCE 0.013 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.027 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0.019 0.02 -10000 0 -0.42 1 1
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.003 -10000 0 -10000 0 0
PRKCA -0.007 0.096 -10000 0 -0.47 20 20
PRKCG -0.011 0.1 -10000 0 -0.58 15 15
PRKCQ -0.031 0.14 -10000 0 -0.5 42 42
FKBP38/BCL2 0.003 0.074 -10000 0 -0.33 23 23
EP300 0.01 0.038 -10000 0 -0.47 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.049 0.041 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.018 0.004 -10000 0 -10000 0 0
FKBP12/FK506 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.004 0.079 -10000 0 -0.28 37 37
NFATc/ERK1 0.055 0.021 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.064 0.13 -10000 0 -0.43 38 38
NR4A1 0.015 0.12 -10000 0 -0.45 26 26
GSK3B 0.013 0.003 -10000 0 -10000 0 0
positive T cell selection 0.022 0.005 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.018 0.04 -10000 0 -0.27 1 1
RCH1/ KPNB1 0.015 0.044 -10000 0 -0.42 5 5
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0.002 -10000 0 -10000 0 0
AKAP5 0.002 0.078 -10000 0 -0.56 9 9
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.053 0.024 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 -0.01 0.1 -10000 0 -0.47 23 23
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.11 -10000 0 -0.48 25 25
HRAS 0.007 0.059 -10000 0 -0.58 5 5
EGFR -0.026 0.13 -10000 0 -0.47 39 39
AKT 0.035 0.029 -10000 0 -0.41 1 1
FOXO3 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.012 0.022 -10000 0 -0.47 1 1
FOXO4 0.012 0.022 -10000 0 -0.47 1 1
MET -0.033 0.14 -10000 0 -0.47 46 46
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
PIK3CB 0.012 0.027 -10000 0 -0.58 1 1
NRAS 0.012 0.022 -10000 0 -0.47 1 1
PIK3CG -0.03 0.14 -10000 0 -0.48 42 42
PIK3R3 0.013 0 -10000 0 -10000 0 0
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.012 0.094 -10000 0 -0.34 24 24
ERBB2 0.009 0.044 -10000 0 -0.47 4 4
proliferation/survival/translation -0.024 0.039 0.21 3 -10000 0 3
PI3K -0.006 0.11 0.17 5 -0.32 37 42
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.043 0.024 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0 0.078 -10000 0 -0.47 13 13
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.028 0.015 -9999 0 -0.21 2 2
epithelial cell differentiation 0.027 0.016 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.038 0.056 -9999 0 -10000 0 0
EGFR -0.026 0.13 -9999 0 -0.47 39 39
EPHA2 -0.036 0.15 -9999 0 -0.48 49 49
MYO6 0 0.098 -9999 0 -0.28 52 52
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0.027 0 -9999 0 -10000 0 0
AQP5 -0.18 0.2 -9999 0 -0.4 213 213
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.015 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.023 0.05 -9999 0 -0.27 3 3
EGF -0.056 0.18 -9999 0 -0.54 61 61
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.011 0.065 -9999 0 -0.4 13 13
cortical microtubule organization 0.027 0.016 -9999 0 -10000 0 0
GO:0000145 0.031 0.014 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0.001 -9999 0 -10000 0 0
ARF6/GDP -0.018 0.051 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.006 0.084 -9999 0 -0.31 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.03 0.046 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.033 0.015 -9999 0 -10000 0 0
ARF6/GTP 0.011 0.078 -9999 0 -0.28 4 4
CDH1 0.011 0.031 -9999 0 -0.47 2 2
EGFR/EGFR/EGF/EGF -0.046 0.093 -9999 0 -0.42 3 3
RhoA/GDP -0.001 0.013 -9999 0 -10000 0 0
actin cytoskeleton organization -0.006 0.1 -9999 0 -0.46 3 3
IGF-1R heterotetramer 0.011 0.034 -9999 0 -0.52 2 2
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.011 0.035 -9999 0 -0.52 2 2
IGF1 -0.046 0.17 -9999 0 -0.51 55 55
DIAPH1 0.002 0.005 -9999 0 -10000 0 0
Wnt receptor signaling pathway -0.027 0.016 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.017 0.051 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL -0.006 0.1 -9999 0 -0.47 3 3
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.019 0.065 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.021 0.061 -9999 0 -10000 0 0
SEC6/SEC8 -0.001 0.011 -9999 0 -10000 0 0
MGAT3 0.023 0.051 -9999 0 -0.28 3 3
HGF/MET -0.036 0.096 -9999 0 -0.42 17 17
HGF -0.026 0.14 -9999 0 -0.5 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.028 0.015 -9999 0 -0.21 2 2
actin cable formation 0.05 0.053 -9999 0 -10000 0 0
KIAA1543 0.038 0.018 -9999 0 -10000 0 0
KIFC3 0.032 0.024 -9999 0 -10000 0 0
NCK1 0.012 0.027 -9999 0 -0.58 1 1
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.03 0.031 -9999 0 -10000 0 0
NCK1/GIT1 0.019 0.02 -9999 0 -0.42 1 1
mol:GDP 0.027 0.016 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.033 0.015 -9999 0 -10000 0 0
PIP5K1C 0.033 0.015 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.034 0.062 -9999 0 -10000 0 0
adherens junction assembly 0.049 0.032 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.075 -9999 0 -0.48 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
MET -0.033 0.14 -9999 0 -0.47 46 46
PLEKHA7 0.033 0.019 -9999 0 -10000 0 0
mol:GTP 0.005 0.083 -9999 0 -0.31 4 4
establishment of epithelial cell apical/basal polarity 0.054 0.014 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.028 0.015 -9999 0 -0.21 2 2
regulation of cell-cell adhesion -0.006 0.1 -9999 0 -0.46 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.028 0.015 -9999 0 -0.21 2 2
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.012 0.018 -10000 0 -0.27 2 2
TRAF2/ASK1 0.017 0.022 -10000 0 -0.32 2 2
ATM 0.012 0.022 -10000 0 -0.47 1 1
MAP2K3 0.017 0.046 -10000 0 -0.32 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.06 -10000 0 -0.32 5 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.057 0.19 -10000 0 -0.57 58 58
TXN 0.008 0.011 -10000 0 -0.24 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
GADD45A 0.011 0.031 -10000 0 -0.47 2 2
GADD45B -0.011 0.12 -10000 0 -0.57 20 20
MAP3K1 0.012 0.022 -10000 0 -0.47 1 1
MAP3K6 0.013 0 -10000 0 -10000 0 0
MAP3K7 0.013 0.001 -10000 0 -10000 0 0
MAP3K4 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.018 0.025 -10000 0 -0.37 2 2
TAK1/TAB family 0.002 0.018 0.14 8 -10000 0 8
RAC1/OSM/MEKK3 0.026 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.023 -10000 0 -0.29 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.026 0.15 -10000 0 -0.57 33 33
CCM2 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.007 0.093 -10000 0 -0.35 33 33
MAPK11 0.003 0.075 -10000 0 -0.58 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.001 0.089 -10000 0 -0.32 34 34
OSM/MEKK3 0.02 0 -10000 0 -10000 0 0
TAOK1 -0.04 0.12 -10000 0 -0.3 87 87
TAOK2 0.015 0.014 -10000 0 -0.3 1 1
TAOK3 0.015 0.018 -10000 0 -0.26 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.011 0.035 -10000 0 -0.52 2 2
MAP3K10 0.013 0 -10000 0 -10000 0 0
MAP3K3 0.013 0 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.023 -10000 0 -0.27 3 3
GADD45/MTK1/MTK1 -0.021 0.14 -10000 0 -0.37 61 61
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.017 0.073 -9999 0 -0.32 5 5
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.032 0.11 -9999 0 -0.51 10 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.023 -9999 0 -0.33 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.027 0.057 -9999 0 -0.26 14 14
CaM/Ca2+ 0.018 0.068 -9999 0 -0.33 3 3
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.015 0.095 -9999 0 -0.47 10 10
AKT1 0.027 0.073 -9999 0 -0.72 1 1
MAP2K1 0.027 0.069 -9999 0 -0.58 1 1
MAP3K11 0.02 0.069 -9999 0 -0.33 3 3
IFNGR1 0.013 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.064 0.14 -9999 0 -0.34 82 82
Rap1/GTP -0.011 0.046 -9999 0 -0.46 1 1
CRKL/C3G 0.02 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.02 0.076 -9999 0 -0.29 5 5
CEBPB 0.051 0.08 -9999 0 -0.44 3 3
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.094 -9999 0 -0.68 4 4
STAT1 0.014 0.094 -9999 0 -0.47 10 10
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.024 0.14 -9999 0 -0.57 30 30
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
STAT1 (dimer)/PIAS1 0.021 0.091 -9999 0 -0.44 10 10
CEBPB/PTGES2/Cbp/p300 -0.012 0.036 -9999 0 -0.34 1 1
mol:Ca2+ 0.015 0.072 -9999 0 -0.32 5 5
MAPK3 0.038 0.066 -9999 0 -0.58 1 1
STAT1 (dimer) -0.035 0.077 -9999 0 -0.35 14 14
MAPK1 0.038 0.066 -9999 0 -0.58 1 1
JAK2 0.012 0.024 -9999 0 -0.5 1 1
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
JAK1 0.013 0.008 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.046 0.085 -9999 0 -0.5 3 3
SMAD7 0.025 0.051 -9999 0 -10000 0 0
CBL/CRKL/C3G 0.032 0.067 -9999 0 -0.56 1 1
PI3K -0.018 0.067 -9999 0 -0.8 1 1
IFNG -0.024 0.14 -9999 0 -0.57 30 30
apoptosis 0.032 0.067 -9999 0 -0.4 3 3
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.085 0.2 -9999 0 -0.49 95 95
CAMK2B -0.026 0.15 -9999 0 -0.57 33 33
FRAP1 0.026 0.068 -9999 0 -0.65 1 1
PRKCD 0.029 0.074 -9999 0 -0.73 1 1
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.027 0.057 -9999 0 -0.26 14 14
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.011 0.038 -9999 0 -0.47 3 3
IRF1 0.033 0.12 -9999 0 -0.48 18 18
STAT1 (dimer)/PIASy 0.018 0.09 -9999 0 -0.44 10 10
SOCS1 -0.002 0.066 -9999 0 -0.61 4 4
mol:GDP 0.028 0.064 -9999 0 -0.53 1 1
CASP1 0.02 0.069 -9999 0 -0.27 15 15
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.045 0.032 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.065 -9999 0 -0.76 1 1
RAP1/GDP -0.011 0.046 -9999 0 -0.46 1 1
CBL 0.02 0.072 -9999 0 -0.4 3 3
MAP3K1 0.02 0.072 -9999 0 -0.4 3 3
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.027 0.057 -9999 0 -0.26 14 14
PTPN11 0.014 0.071 -9999 0 -0.32 5 5
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.008 0.07 -9999 0 -0.42 13 13
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.004 0.088 -9999 0 -0.27 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.032 -9999 0 -10000 0 0
NFKBIA 0.022 0.032 -9999 0 -0.27 1 1
MAPK14 0.013 0.001 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.017 -9999 0 -0.35 1 1
ARRB2 0.016 0 -9999 0 -10000 0 0
REL -0.034 0.14 -9999 0 -0.47 47 47
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.015 0.062 -9999 0 -0.35 14 14
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.017 -9999 0 -0.35 1 1
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
NF kappa B1 p50 dimer 0.018 0.02 -9999 0 -0.42 1 1
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
NFKB1 0.02 0.02 -9999 0 -0.42 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.028 0.031 -9999 0 -0.25 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.043 0.031 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PI3K 0.014 0.048 -9999 0 -0.37 7 7
NF kappa B1 p50/RelA 0.028 0.032 -9999 0 -0.25 1 1
IKBKB 0.012 0.027 -9999 0 -0.58 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.006 0.06 -9999 0 -0.49 7 7
I kappa B alpha/PIK3R1 0.025 0.039 -9999 0 -0.25 1 1
cell death 0.041 0.03 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.004 0.088 -9999 0 -0.27 48 48
LCK 0.003 0.075 -9999 0 -0.58 8 8
BCL3 -0.003 0.095 -9999 0 -0.58 13 13
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.005 0.07 0.57 7 -10000 0 7
PI3K Class IB/PDE3B 0.005 0.07 -10000 0 -0.57 7 7
PDE3B 0.005 0.07 -10000 0 -0.58 7 7
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.001 -9999 0 -10000 0 0
SMARCC1 0.003 0.007 -9999 0 -10000 0 0
REL -0.034 0.14 -9999 0 -0.47 47 47
HDAC7 0.047 0.075 -9999 0 -10000 0 0
JUN 0.006 0.062 -9999 0 -0.5 7 7
EP300 0.01 0.038 -9999 0 -0.47 3 3
KAT2B 0.013 0 -9999 0 -10000 0 0
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.013 0.07 -9999 0 -0.39 14 14
FOXO1 0.013 0 -9999 0 -10000 0 0
T-DHT/AR 0.049 0.081 -9999 0 -10000 0 0
MAP2K6 -0.001 0.095 -9999 0 -0.55 14 14
BRM/BAF57 0.019 0.023 -9999 0 -0.33 2 2
MAP2K4 0.015 0.002 -9999 0 -10000 0 0
SMARCA2 0.012 0.031 -9999 0 -0.47 2 2
PDE9A -0.003 0.055 -9999 0 -0.97 1 1
NCOA2 -0.046 0.16 -9999 0 -0.47 60 60
CEBPA 0.013 0 -9999 0 -10000 0 0
EHMT2 0.014 0.002 -9999 0 -10000 0 0
cell proliferation 0.063 0.093 -9999 0 -0.4 6 6
NR0B1 -0.002 0.064 -9999 0 -0.58 6 6
EGR1 -0.058 0.18 -9999 0 -0.51 66 66
RXRs/9cRA -0.041 0.12 -9999 0 -0.31 7 7
AR/RACK1/Src 0.037 0.083 -9999 0 -0.45 5 5
AR/GR 0.004 0.1 -9999 0 -0.44 14 14
GNB2L1 0.01 0.046 -9999 0 -0.57 3 3
PKN1 0.004 0.075 -9999 0 -0.58 8 8
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.017 0.053 -9999 0 -0.33 11 11
T-DHT/AR/TIF2/CARM1 0.011 0.13 -9999 0 -0.49 14 14
SRC 0.03 0.064 -9999 0 -0.33 1 1
NR3C1 0 0.078 -9999 0 -0.47 13 13
KLK3 0.015 0.13 -9999 0 -1.1 6 6
APPBP2 0.015 0.002 -9999 0 -10000 0 0
TRIM24 0.014 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.027 0.076 -9999 0 -0.33 12 12
TMPRSS2 -0.011 0.11 -9999 0 -0.98 6 6
RXRG -0.11 0.21 -9999 0 -0.48 120 120
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.013 0 -9999 0 -10000 0 0
RXRB 0.013 0 -9999 0 -10000 0 0
CARM1 0.014 0.001 -9999 0 -10000 0 0
NR2C2 -0.002 0.084 -9999 0 -0.47 15 15
KLK2 0.022 0.13 -9999 0 -0.51 16 16
AR 0.007 0.1 -9999 0 -0.41 15 15
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.012 0.004 -9999 0 -10000 0 0
SRY 0.003 0.027 -9999 0 -0.58 1 1
GATA2 0.012 0.027 -9999 0 -0.58 1 1
MYST2 0.013 0 -9999 0 -10000 0 0
HOXB13 0.014 0.003 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.034 0.083 -9999 0 -0.44 5 5
positive regulation of transcription 0.012 0.027 -9999 0 -0.57 1 1
DNAJA1 0.015 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.001 -9999 0 -10000 0 0
NCOA1 0.017 0.003 -9999 0 -10000 0 0
SPDEF 0.014 0.027 -9999 0 -0.57 1 1
T-DHT/AR/TIF2 0.014 0.12 -9999 0 -0.45 17 17
T-DHT/AR/Hsp90 0.028 0.077 -9999 0 -0.33 12 12
GSK3B 0.014 0.001 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.025 0.069 -9999 0 -0.3 11 11
SIRT1 0.013 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0.004 -9999 0 -10000 0 0
POU2F1 0.025 0.029 -9999 0 -0.56 1 1
T-DHT/AR/DAX-1 0.018 0.085 -9999 0 -0.36 12 12
CREBBP 0.013 0 -9999 0 -10000 0 0
SMARCE1 0.014 0.002 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.007 0.053 -9999 0 -0.47 6 6
PLK4 0.008 0.053 -9999 0 -0.58 4 4
regulation of centriole replication 0.013 0.055 -9999 0 -0.36 10 10
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0 -10000 0 -10000 0 0
MAP4K4 0.028 0.056 -10000 0 -0.43 1 1
BAG4 -0.017 0.12 -10000 0 -0.47 30 30
PKC zeta/ceramide -0.007 0.025 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.007 0.06 -10000 0 -0.52 6 6
BAX -0.001 0.014 -10000 0 -0.13 2 2
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.017 0.006 -10000 0 -10000 0 0
BAD -0.01 0.028 -10000 0 -0.31 1 1
SMPD1 0.014 0.047 -10000 0 -0.22 1 1
RB1 -0.01 0.027 -10000 0 -0.24 1 1
FADD/Caspase 8 0.037 0.054 -10000 0 -0.42 1 1
MAP2K4 -0.003 0.025 -10000 0 -0.23 1 1
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.012 0.053 -10000 0 -0.25 19 19
EGF -0.056 0.18 -10000 0 -0.54 61 61
mol:ceramide -0.018 0.026 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0 -10000 0 -10000 0 0
ASAH1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.027 -10000 0 -0.24 1 1
cell proliferation -0.014 0.093 -10000 0 -0.29 31 31
BID 0.021 0.04 -10000 0 -0.28 1 1
MAP3K1 -0.01 0.027 -10000 0 -0.24 1 1
EIF2A 0.004 0.022 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 -0.001 0.05 -10000 0 -0.27 6 6
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.05 -10000 0 -0.26 7 7
Cathepsin D/ceramide -0.007 0.025 -10000 0 -10000 0 0
FADD 0.028 0.056 -10000 0 -0.43 1 1
KSR1 -0.019 0.056 -10000 0 -0.27 19 19
MAPK8 -0.003 0.043 -10000 0 -0.23 11 11
PRKRA -0.009 0.025 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.046 0.17 -10000 0 -0.51 55 55
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.018 0.026 -10000 0 -10000 0 0
CTSD 0.013 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.02 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.099 -10000 0 -0.32 31 31
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0.02 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.059 -10000 0 -0.36 2 2
TNFR1A/BAG4/TNF-alpha -0.017 0.11 -10000 0 -0.38 16 16
mol:Sphingosine-1-phosphate 0.021 0 -10000 0 -10000 0 0
MAP2K1 -0.005 0.051 -10000 0 -0.28 6 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.002 0.035 0.15 19 -10000 0 19
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.084 -10000 0 -0.33 30 30
EIF2AK2 -0.003 0.023 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.001 0.088 -10000 0 -0.35 12 12
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.032 0.035 -10000 0 -10000 0 0
MAP2K2 -0.005 0.052 -10000 0 -0.27 8 8
SMPD3 0.01 0.062 -10000 0 -0.29 7 7
TNF -0.029 0.14 -10000 0 -0.5 39 39
PKC zeta/PAR4 0.02 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.065 0.18 60 -10000 0 60
NF kappa B1/RelA/I kappa B alpha 0.039 0 -10000 0 -10000 0 0
AIFM1 0.002 0.035 0.15 19 -10000 0 19
BCL2 -0.01 0.1 -10000 0 -0.47 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.017 0.12 -9999 0 -0.47 30 30
Caspase 8 (4 units) 0.023 0.061 -9999 0 -0.39 1 1
NEF -0.004 0.036 -9999 0 -10000 0 0
NFKBIA 0.015 0.011 -9999 0 -10000 0 0
BIRC3 0.034 0.06 -9999 0 -0.51 6 6
CYCS 0.027 0.066 -9999 0 -0.34 2 2
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.016 0.13 -9999 0 -0.61 21 21
MAP2K7 0.031 0.06 -9999 0 -0.47 1 1
protein ubiquitination 0.049 0.05 -9999 0 -0.32 1 1
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.003 0.069 -9999 0 -0.47 10 10
BID 0.021 0.069 -9999 0 -0.36 2 2
NF-kappa-B/RelA/I kappa B alpha 0.034 0.032 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.011 0.035 -9999 0 -0.52 2 2
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.034 0.032 -9999 0 -10000 0 0
MAPK8 0.031 0.066 -9999 0 -0.44 1 1
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 0.012 0.027 -9999 0 -0.58 1 1
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.015 0.072 -9999 0 -0.27 13 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.041 0.06 -9999 0 -0.38 2 2
CHUK 0.05 0.053 -9999 0 -0.35 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.033 0.04 -9999 0 -0.28 1 1
TCRz/NEF -0.015 0.12 -9999 0 -0.39 41 41
TNF -0.029 0.14 -9999 0 -0.5 39 39
FASLG -0.02 0.16 -9999 0 -0.55 38 38
NFKB1 0.015 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.017 0.11 -9999 0 -0.38 16 16
CASP6 0.04 0.046 -9999 0 -10000 0 0
CASP7 0.059 0.071 -9999 0 -0.45 4 4
RELA 0.015 0.011 -9999 0 -10000 0 0
CASP2 0.007 0.053 -9999 0 -0.47 6 6
CASP3 0.06 0.071 -9999 0 -0.45 4 4
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.084 -9999 0 -0.33 30 30
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.046 0.057 -9999 0 -0.39 1 1
APAF-1/Caspase 9 -0.013 0.048 -9999 0 -0.41 3 3
BCL2 0.026 0.084 -9999 0 -0.36 9 9
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.063 0.049 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.008 0.11 -9999 0 -0.4 32 32
NFKBIA 0.041 0 -9999 0 -10000 0 0
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.012 0.027 -9999 0 -0.58 1 1
RIPK2 0.002 0.079 -9999 0 -0.58 9 9
IKBKG 0.028 0.057 -9999 0 -0.28 6 6
IKK complex/A20 0.023 0.089 -9999 0 -0.36 7 7
NEMO/A20/RIP2 0.002 0.079 -9999 0 -0.57 9 9
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.033 0.055 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.018 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.01 0.038 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.024 0.032 -9999 0 -0.33 4 4
NOD2 -0.015 0.12 -9999 0 -0.48 28 28
NFKB1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
MALT1 0.009 0.051 -9999 0 -0.55 4 4
cIAP1/UbcH5C 0.02 0 -9999 0 -10000 0 0
ATM 0.012 0.022 -9999 0 -0.47 1 1
TNF/TNFR1A -0.011 0.1 -9999 0 -0.36 39 39
TRAF6 0.013 0 -9999 0 -10000 0 0
PRKCA -0.007 0.096 -9999 0 -0.47 20 20
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.029 0.14 -9999 0 -0.5 39 39
NF kappa B1 p50/RelA 0.038 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex 0.04 0.055 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.034 0.073 -9999 0 -0.37 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.031 0.027 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.012 -9999 0 -0.26 1 1
GATA1/HDAC4 0.016 0.025 -9999 0 -0.37 2 2
GATA1/HDAC5 0.016 0.025 -9999 0 -0.37 2 2
GATA2/HDAC5 0.019 0.02 -9999 0 -0.42 1 1
HDAC5/BCL6/BCoR 0.027 0 -9999 0 -10000 0 0
HDAC9 -0.043 0.16 -9999 0 -0.5 53 53
Glucocorticoid receptor/Hsp90/HDAC6 0.019 0.048 -9999 0 -0.27 13 13
HDAC4/ANKRA2 0.02 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.02 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.013 -9999 0 -10000 0 0
GATA2 0.012 0.027 -9999 0 -0.58 1 1
HDAC4/RFXANK 0.014 0.048 -9999 0 -0.42 6 6
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.008 0.053 -9999 0 -0.58 4 4
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 0.016 0.035 -9999 0 -0.33 5 5
Histones 0.016 0.063 -9999 0 -0.36 1 1
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.02 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0.02 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.02 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.014 0.048 -9999 0 -0.42 6 6
CAMK4 -0.024 0.13 -9999 0 -0.47 37 37
Tubulin/HDAC6 -0.009 0.11 -9999 0 -0.35 47 47
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.035 -9999 0 -0.52 2 2
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0 0.078 -9999 0 -0.47 13 13
SUMO1/HDAC4 0.028 0.012 -9999 0 -10000 0 0
SRF 0.013 0.001 -9999 0 -10000 0 0
HDAC4/YWHAB 0.02 0 -9999 0 -10000 0 0
Tubulin -0.022 0.13 -9999 0 -0.42 47 47
HDAC4/14-3-3 E 0.02 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.01 0.046 -9999 0 -0.58 3 3
BCL6/BCoR 0.02 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.027 0 -9999 0 -10000 0 0
HDAC4/SRF 0.004 0.079 -9999 0 -0.27 37 37
HDAC4/ER alpha 0.008 0.063 -9999 0 -0.33 16 16
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.063 -9999 0 -0.35 1 1
cell motility -0.01 0.11 -9999 0 -0.35 47 47
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.02 0 -9999 0 -10000 0 0
BCL6 0.013 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.02 0 -9999 0 -10000 0 0
ESR1 -0.003 0.088 -9999 0 -0.48 16 16
HDAC6/HDAC11 0.02 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.012 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
MEF2C 0.008 0.055 -9999 0 -0.53 5 5
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.036 0.03 -9999 0 -10000 0 0
GNG2 0.008 0.049 -9999 0 -0.47 5 5
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A -0.044 0.17 -9999 0 -0.58 47 47
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.012 0.027 -9999 0 -0.58 1 1
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.006 0.065 -9999 0 -0.58 6 6
nuclear import -0.028 0 -9999 0 -10000 0 0
mTOR signaling pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.074 0.25 12 -0.32 16 28
FRAP1 0.013 0.023 -10000 0 -10000 0 0
AKT1 0.018 0.067 0.21 12 -0.43 4 16
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.001 0.061 -10000 0 -0.36 14 14
mol:GTP 0.023 0.049 -10000 0 -0.38 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.003 0.014 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.037 -10000 0 -0.34 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.059 -10000 0 -0.32 16 16
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.023 0.041 -10000 0 -0.26 3 3
MAP3K5 0.009 0.02 -10000 0 -0.29 2 2
PIK3R1 0.008 0.049 -10000 0 -0.47 5 5
apoptosis 0.009 0.02 -10000 0 -0.29 2 2
mol:LY294002 0 0 -10000 0 -0.001 15 15
EIF4B 0.027 0.038 -10000 0 -0.28 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.035 -10000 0 -0.3 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.011 0.073 -10000 0 -0.35 16 16
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.031 0.15 12 -0.23 1 13
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.007 0.036 -10000 0 -0.34 3 3
mol:Amino Acids 0 0 -10000 0 -0.001 15 15
FKBP12/Rapamycin 0.01 0.002 -10000 0 -10000 0 0
PDPK1 -0.005 0.067 0.22 12 -0.45 4 16
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.02 0.031 -10000 0 -0.58 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.003 -10000 0 -10000 0 0
TSC1/TSC2 0.026 0.053 -10000 0 -0.42 3 3
tumor necrosis factor receptor activity 0 0 0.001 15 -10000 0 15
RPS6 0.011 0.038 -10000 0 -0.58 2 2
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.003 0.063 -10000 0 -0.34 16 16
INS -0.016 0.096 -10000 0 -0.58 14 14
PTEN 0 0.078 -10000 0 -0.47 13 13
PDK2 -0.007 0.069 0.22 12 -0.45 4 16
EIF4EBP1 -0.004 0.066 -10000 0 -1.1 1 1
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
PPP2R5D 0.019 0.021 -10000 0 -10000 0 0
peptide biosynthetic process 0.007 0.055 -10000 0 -0.31 14 14
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 12 -0.003 1 13
EEF2 0.007 0.056 -10000 0 -0.32 14 14
eIF4E/4E-BP1 0.004 0.06 -10000 0 -0.97 1 1
FoxO family signaling

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
G6PC 0.009 0.095 -9999 0 -10000 0 0
PLK1 -0.08 0.25 -9999 0 -0.77 19 19
CDKN1B 0.045 0.1 -9999 0 -0.34 1 1
FOXO3 -0.029 0.2 -9999 0 -0.67 18 18
KAT2B 0.016 0.015 -9999 0 -10000 0 0
FOXO1/SIRT1 0.012 0.051 -9999 0 -10000 0 0
CAT -0.019 0.18 -9999 0 -0.68 12 12
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.016 0.018 -9999 0 -10000 0 0
FOXO1 0.021 0.055 -9999 0 -10000 0 0
MAPK10 0.03 0.032 -9999 0 -0.3 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.079 0.054 -9999 0 -0.37 1 1
response to oxidative stress 0.002 0.019 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.072 0.14 -9999 0 -0.6 16 16
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.01 0.039 -9999 0 -0.47 3 3
BCL2L11 0.014 0.068 -9999 0 -1.3 1 1
FOXO1/SKP2 0.021 0.063 -9999 0 -0.43 2 2
mol:GDP 0.002 0.019 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.045 0.11 -9999 0 -0.93 2 2
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.051 0.05 -9999 0 -10000 0 0
MST1 -0.06 0.2 -9999 0 -0.58 62 62
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.027 0.085 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.028 0.041 -9999 0 -0.26 4 4
MAPK9 0.033 0.009 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.013 0.01 -9999 0 -10000 0 0
SOD2 0.044 0.13 -9999 0 -0.44 1 1
RBL2 0.009 0.17 -9999 0 -0.87 7 7
RAL/GDP 0.022 0.015 -9999 0 -10000 0 0
CHUK 0.016 0.014 -9999 0 -10000 0 0
Ran/GTP 0.013 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.03 0.014 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.027 0.22 -9999 0 -1.3 12 12
SKP2 0.005 0.063 -9999 0 -0.48 8 8
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.014 0.031 -9999 0 -0.6 1 1
CCNB1 -0.027 0.2 -9999 0 -0.79 15 15
FOXO1-3a-4/beta catenin 0.065 0.12 -9999 0 -0.4 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.063 -9999 0 -0.42 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.068 0.19 -9999 0 -0.48 82 82
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.004 -9999 0 -10000 0 0
ZFAND5 0.081 0.048 -9999 0 -10000 0 0
SFN -0.036 0.15 -9999 0 -0.47 49 49
CDK2 0.012 0.012 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.018 0.089 -9999 0 -0.31 10 10
CREBBP 0.012 0.012 -9999 0 -10000 0 0
FBXO32 -0.023 0.2 -9999 0 -0.8 13 13
BCL6 0.016 0.13 -9999 0 -0.54 3 3
RALB 0.014 0.001 -9999 0 -10000 0 0
RALA 0.014 0.001 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.002 0.011 -9999 0 -10000 0 0
DOCK1 0.01 0.038 -9999 0 -0.47 3 3
ITGA4 -0.013 0.12 -9999 0 -0.52 24 24
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.39 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.01 0.072 -9999 0 -0.3 24 24
alpha4/beta7 Integrin/Paxillin 0.006 0.094 -9999 0 -0.41 13 13
lamellipodium assembly -0.005 0.058 -9999 0 -0.44 7 7
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
PI3K 0.014 0.048 -9999 0 -0.37 7 7
ARF6 0.013 0 -9999 0 -10000 0 0
TLN1 0.013 0 -9999 0 -10000 0 0
PXN 0.021 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
ARF6/GTP -0.011 0.048 -9999 0 -10000 0 0
cell adhesion 0.024 0.062 -9999 0 -10000 0 0
CRKL/CBL 0.019 0.016 -9999 0 -0.33 1 1
alpha4/beta1 Integrin/Paxillin 0.017 0.066 -9999 0 -0.31 11 11
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.1 -9999 0 -0.49 20 20
ARF6/GDP 0.002 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.018 0.087 -9999 0 -0.56 5 5
p130Cas/Crk/Dock1 0.025 0.023 -9999 0 -0.27 3 3
VCAM1 -0.001 0.086 -9999 0 -0.54 12 12
alpha4/beta1 Integrin/Paxillin/Talin 0.025 0.063 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.025 0.063 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
mol:GDP -0.024 0.062 -9999 0 -10000 0 0
CBL 0.012 0.022 -9999 0 -0.47 1 1
PRKACA 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.025 0.063 -9999 0 -10000 0 0
Rac1/GTP -0.005 0.067 -9999 0 -0.5 7 7
ceramide signaling 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
MAP4K4 0.033 0.055 -10000 0 -0.44 1 1
BAG4 -0.017 0.12 -10000 0 -0.47 30 30
BAD 0.023 0.027 -10000 0 -0.26 1 1
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.006 0.06 -10000 0 -0.52 6 6
BAX 0.022 0.03 -10000 0 -0.26 2 2
EnzymeConsortium:3.1.4.12 0.01 0.017 -10000 0 -0.11 1 1
IKBKB 0.037 0.054 -10000 0 -0.41 1 1
MAP2K2 0.025 0.05 -10000 0 -0.27 3 3
MAP2K1 0.026 0.049 -10000 0 -0.28 2 2
SMPD1 0.015 0.017 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.039 0.054 -10000 0 -0.42 1 1
MAP2K4 0.028 0.026 -10000 0 -10000 0 0
protein ubiquitination 0.039 0.053 -10000 0 -0.42 1 1
EnzymeConsortium:2.7.1.37 0.029 0.051 -10000 0 -0.3 2 2
response to UV 0 0.001 -10000 0 -0.002 2 2
RAF1 0.021 0.05 -10000 0 -0.3 2 2
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.018 0.024 -10000 0 -0.16 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.026 -10000 0 -0.19 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.028 0.048 -10000 0 -0.28 2 2
MAPK1 0.028 0.048 -10000 0 -0.28 2 2
p50/RELA/I-kappa-B-alpha 0.02 0 -10000 0 -10000 0 0
FADD 0.033 0.055 -10000 0 -0.44 1 1
KSR1 0.016 0.051 -10000 0 -0.21 19 19
MAPK8 0.028 0.043 -10000 0 -0.31 2 2
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.038 0.052 -10000 0 -0.41 1 1
TNF R/SODD -0.002 0.084 -10000 0 -0.33 30 30
TNF -0.029 0.14 -10000 0 -0.5 39 39
CYCS 0.028 0.031 0.13 15 -10000 0 15
IKBKG 0.038 0.052 -10000 0 -0.41 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.057 -10000 0 -0.46 1 1
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.028 0.031 0.13 15 -10000 0 15
TNF/TNF R/SODD -0.017 0.11 -10000 0 -0.38 16 16
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.012 -10000 0 -10000 0 0
NSMAF 0.032 0.055 -10000 0 -0.44 1 1
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 2 2
BCL2 -0.01 0.1 -10000 0 -0.47 23 23
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.091 0.2 -10000 0 -0.47 104 104
CLTC 0.024 0.031 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.018 0.031 -10000 0 -10000 0 0
Dynamin 2/GTP 0.016 0.051 -10000 0 -0.32 11 11
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.021 0.024 -10000 0 -10000 0 0
CPE 0.015 0.029 -10000 0 -0.3 4 4
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.017 0.032 -10000 0 -10000 0 0
CTNND1 0.022 0.047 -10000 0 -0.29 11 11
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.022 -10000 0 -10000 0 0
TSHR 0.004 0.064 -10000 0 -0.3 20 20
INS 0.006 0.021 -10000 0 -10000 0 0
BIN1 0.011 0.038 -10000 0 -0.58 2 2
mol:Choline 0.017 0.032 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.055 -10000 0 -0.35 11 11
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.05 -10000 0 -0.31 11 11
JUP 0.021 0.024 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.024 0.022 -10000 0 -0.32 2 2
ARF6/GTP 0.01 0 -10000 0 -10000 0 0
CDH1 0.02 0.027 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.01 0 -10000 0 -10000 0 0
MAPK8IP3 0.008 0.053 -10000 0 -0.58 4 4
positive regulation of endocytosis 0.01 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.04 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.036 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.017 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0.034 -10000 0 -0.36 4 4
ACAP1 0.016 0.031 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.029 0.086 -10000 0 -0.3 4 4
clathrin heavy chain/ACAP1 0.026 0.034 -10000 0 -10000 0 0
JIP4/KLC1 0.026 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.04 0 -10000 0 -10000 0 0
RALA/GTP 0.01 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.018 0 -10000 0 -10000 0 0
receptor recycling 0.01 0 -10000 0 -10000 0 0
CTNNA1 0.022 0.047 -10000 0 -0.29 11 11
NME1 0.009 0.056 -10000 0 -0.36 11 11
clathrin coat assembly 0.024 0.031 -10000 0 -10000 0 0
IL2RA -0.005 0.064 -10000 0 -0.36 1 1
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.046 0.084 -10000 0 -0.28 15 15
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0.009 0.055 -10000 0 -0.25 21 21
PLD2 0.021 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.024 0.022 -10000 0 -10000 0 0
SDC1 0.013 0.051 -10000 0 -0.28 6 6
ARF6/GDP 0.009 0.055 -10000 0 -0.35 11 11
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.037 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.017 0.032 -10000 0 -10000 0 0
endocytosis -0.023 0.022 0.32 2 -10000 0 2
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.025 0.044 -10000 0 -0.27 6 6
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.013 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.017 0.05 -10000 0 -0.32 11 11
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.023 0.048 -10000 0 -0.27 3 3
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.033 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.029 -10000 0 -10000 0 0
CLOCK -0.023 0.13 -10000 0 -0.47 39 39
TIMELESS/CRY2 0.035 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.012 0.022 -10000 0 -0.33 2 2
ATR 0.012 0.027 -10000 0 -0.58 1 1
NR1D1 0.032 0.025 -10000 0 -10000 0 0
ARNTL 0.014 0.031 -10000 0 -0.47 2 2
TIMELESS 0.032 0.03 -10000 0 -10000 0 0
NPAS2 0.014 0.035 -10000 0 -0.52 2 2
CRY2 0.013 0 -10000 0 -10000 0 0
mol:CO -0.013 0.004 0.077 1 -10000 0 1
CHEK1 0.013 0 -10000 0 -10000 0 0
mol:HEME 0.013 0.004 -10000 0 -0.077 1 1
PER1 -0.003 0.086 -10000 0 -0.47 16 16
BMAL/CLOCK/NPAS2 0.016 0.089 -10000 0 -0.59 1 1
BMAL1/CLOCK 0.015 0.1 -10000 0 -0.58 2 2
S phase of mitotic cell cycle 0.039 0.029 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.04 0.029 -10000 0 -10000 0 0
mol:NADPH 0.013 0.004 -10000 0 -0.077 1 1
PER1/TIMELESS 0.026 0.054 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.002 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.032 0.056 -10000 0 -0.4 8 8
regulation of axonogenesis -0.017 0.04 -10000 0 -10000 0 0
myoblast fusion -0.015 0.03 0.2 8 -10000 0 8
mol:GTP 0.008 0.019 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.06 0.31 14 -10000 0 14
ARF1/GTP 0.017 0.014 -10000 0 -10000 0 0
mol:GM1 0.009 0.014 -10000 0 -10000 0 0
mol:Choline 0.013 0.058 -10000 0 -0.26 21 21
lamellipodium assembly -0.001 0.032 -10000 0 -10000 0 0
MAPK3 0.024 0.027 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.06 -10000 0 -0.31 14 14
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP 0.015 0.03 -10000 0 -0.2 8 8
ARF1/GDP 0.024 0.028 -10000 0 -10000 0 0
ARF6 0.012 0.011 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 0.012 0.038 -10000 0 -0.47 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.027 -10000 0 -10000 0 0
actin filament bundle formation -0.021 0.027 -10000 0 -10000 0 0
KALRN -0.002 0.032 -10000 0 -0.28 3 3
RAB11FIP3/RAB11A 0.02 0 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.027 -10000 0 -10000 0 0
NME1 0.001 0.087 -10000 0 -0.57 11 11
Rac1/GDP 0.022 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.008 0.019 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.032 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development 0.008 0.019 -10000 0 -10000 0 0
ARF6/GTP 0.008 0.019 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.014 -10000 0 -10000 0 0
mol:GDP -0.001 0.03 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.024 0.013 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.005 0.066 -10000 0 -0.3 21 21
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.032 -10000 0 -10000 0 0
ruffle organization 0.017 0.04 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.008 0.019 -10000 0 -10000 0 0
PLD2 0.019 0.014 -10000 0 -10000 0 0
PIP5K1A 0.017 0.04 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.013 0.058 -10000 0 -0.26 21 21
Rac1/GTP -0.001 0.032 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.015 0.095 -10000 0 -0.32 4 4
CaM/Ca2+ 0.01 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.011 0.031 -10000 0 -0.47 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.007 0.097 0.24 8 -10000 0 8
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.018 0.034 -10000 0 -0.42 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip 0.026 0.019 -10000 0 -0.27 2 2
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.001 0.073 -10000 0 -0.53 9 9
PRKCI 0.012 0.027 -10000 0 -0.58 1 1
AS160/CaM/Ca2+ 0.01 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.029 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.018 0 -10000 0 -10000 0 0
AS160/14-3-3 0.022 0.063 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 -0.009 0.1 0.24 8 -10000 0 8
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.024 0 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.47 49 49
LNPEP -0.021 0.12 -10000 0 -0.47 34 34
YWHAE 0.013 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.021 0.055 -9999 0 -0.34 2 2
PDGFB-D/PDGFRB/SLAP 0.002 0.09 -9999 0 -0.46 17 17
PDGFB-D/PDGFRB/APS/CBL 0.01 0.079 -9999 0 -0.34 23 23
AKT1 0.04 0.058 -9999 0 -0.37 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.021 0.057 -9999 0 -0.35 2 2
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
FGR -0.003 0.037 -9999 0 -0.42 3 3
mol:Ca2+ 0.022 0.03 -9999 0 -10000 0 0
MYC 0.015 0.11 -9999 0 -0.38 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.027 0.045 -9999 0 -0.31 7 7
LRP1/PDGFRB/PDGFB 0.023 0.035 -9999 0 -0.32 5 5
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
GO:0007205 0.022 0.03 -9999 0 -10000 0 0
PTEN 0 0.078 -9999 0 -0.47 13 13
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.016 0.032 -9999 0 -0.38 3 3
PDGFB-D/PDGFRB/GRB10 0.017 0.028 -9999 0 -0.41 2 2
cell cycle arrest 0.002 0.09 -9999 0 -0.46 17 17
HRAS 0.007 0.059 -9999 0 -0.58 5 5
HIF1A 0.044 0.057 -9999 0 -0.44 2 2
GAB1 0.018 0.048 -9999 0 -0.28 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.022 0.048 -9999 0 -0.29 1 1
PDGFB-D/PDGFRB 0.025 0.026 -9999 0 -0.35 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.028 -9999 0 -0.41 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.01 0.05 -9999 0 -0.36 2 2
positive regulation of MAPKKK cascade 0.016 0.032 -9999 0 -0.38 3 3
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
mol:IP3 0.023 0.03 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.028 -9999 0 -0.41 2 2
SHB 0.009 0.044 -9999 0 -0.47 4 4
BLK -0.085 0.17 -9999 0 -0.48 74 74
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.028 -9999 0 -0.41 2 2
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.02 0.057 -9999 0 -10000 0 0
CBL 0.012 0.022 -9999 0 -0.47 1 1
PDGFB-D/PDGFRB/DEP1 0.017 0.028 -9999 0 -0.41 2 2
LCK -0.002 0.026 -9999 0 -0.28 1 1
PDGFRB 0.011 0.038 -9999 0 -0.57 2 2
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0 0.046 -9999 0 -0.52 3 3
ABL1 0.016 0.044 -9999 0 -0.28 1 1
PDGFB-D/PDGFRB/CBL 0.017 0.048 -9999 0 -10000 0 0
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.001 0.084 -9999 0 -0.58 10 10
cell proliferation 0.016 0.1 -9999 0 -0.34 10 10
SLA -0.007 0.11 -9999 0 -0.58 17 17
actin cytoskeleton reorganization 0.04 0.034 -9999 0 -10000 0 0
SRC 0.001 0.019 -9999 0 -10000 0 0
PI3K -0.011 0.053 -9999 0 -0.41 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.025 0.024 -9999 0 -0.34 2 2
SH2B2 -0.011 0.12 -9999 0 -0.57 20 20
PLCgamma1/SPHK1 0.021 0.058 -9999 0 -0.36 2 2
LYN 0.001 0.019 -9999 0 -10000 0 0
LRP1 0.01 0.041 -9999 0 -0.51 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.011 0.031 -9999 0 -0.47 2 2
NCK1-2/p130 Cas 0.036 0.027 -9999 0 -10000 0 0
SPHK1 -0.006 0.1 -9999 0 -0.57 16 16
EDG1 0.001 0.002 -9999 0 -10000 0 0
mol:DAG 0.023 0.03 -9999 0 -10000 0 0
PLCG1 0.023 0.03 -9999 0 -10000 0 0
NHERF/PDGFRB 0.022 0.045 -9999 0 -0.35 7 7
YES1 0 0.019 -9999 0 -0.28 1 1
cell migration 0.021 0.044 -9999 0 -0.35 7 7
SHC/Grb2/SOS1 0.037 0.023 -9999 0 -10000 0 0
SLC9A3R2 0.007 0.059 -9999 0 -0.58 5 5
SLC9A3R1 0.013 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.022 0.059 -9999 0 -0.31 7 7
FYN 0.001 0.019 -9999 0 -10000 0 0
DOK1 0.029 0.022 -9999 0 -0.3 2 2
HRAS/GTP 0.005 0.044 -9999 0 -0.42 5 5
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.023 0.076 -9999 0 -10000 0 0
PRKCD 0.028 0.023 -9999 0 -0.3 2 2
FER 0.016 0.059 -9999 0 -0.3 2 2
MAPKKK cascade 0.001 0.022 -9999 0 -10000 0 0
RASA1 0.026 0.031 -9999 0 -0.3 2 2
NCK1 0.012 0.027 -9999 0 -0.58 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.035 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.014 0.042 -9999 0 -0.36 6 6
chemotaxis 0.016 0.043 -9999 0 -0.27 1 1
STAT1-3-5/STAT1-3-5 -0.007 0.041 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.008 0.028 -9999 0 -0.42 2 2
PTPRJ 0.013 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.013 0.005 -9999 0 -10000 0 0
SMAD3 0.038 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.042 0.021 -9999 0 -0.33 1 1
SMAD4/Ubc9/PIASy 0.027 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.035 0.031 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.02 0.004 -9999 0 -10000 0 0
MAP3K1 0.012 0.022 -9999 0 -0.47 1 1
TRAP-1/SMAD4 0.001 0.078 -9999 0 -0.33 26 26
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.013 0.11 -9999 0 -0.47 26 26
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.022 -9999 0 -0.47 1 1
KPNA2 0.007 0.059 -9999 0 -0.58 5 5
PIAS4 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.041 0.039 -10000 0 -0.44 1 1
adherens junction organization 0.022 0.047 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.073 -10000 0 -0.41 5 5
FMN1 0.006 0.088 -10000 0 -0.27 18 18
mol:IP3 0.034 0.034 -10000 0 -0.4 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.033 0.02 -10000 0 -0.22 2 2
CTNNB1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.04 0.034 -10000 0 -0.39 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.039 0.025 -10000 0 -0.35 2 2
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.019 -10000 0 -10000 0 0
VASP 0.038 0.019 -10000 0 -10000 0 0
ZYX 0.038 0.019 -10000 0 -10000 0 0
JUB 0.024 0.059 -10000 0 -0.31 2 2
EGFR(dimer) 0.02 0.07 -10000 0 -0.29 5 5
E-cadherin/beta catenin-gamma catenin 0.024 0.018 -10000 0 -0.25 2 2
mol:PI-3-4-5-P3 0.035 0.035 -10000 0 -0.42 1 1
PIK3CA 0.011 0.038 -10000 0 -0.48 3 3
PI3K 0.036 0.036 -10000 0 -0.43 1 1
FYN 0.042 0.039 -10000 0 -0.35 1 1
mol:Ca2+ 0.034 0.033 -10000 0 -0.39 1 1
JUP 0.013 0.001 -10000 0 -10000 0 0
PIK3R1 0.009 0.049 -10000 0 -0.47 5 5
mol:DAG 0.034 0.034 -10000 0 -0.4 1 1
CDH1 0.011 0.031 -10000 0 -0.47 2 2
RhoA/GDP 0.03 0.073 -10000 0 -0.41 5 5
establishment of polarity of embryonic epithelium 0.038 0.019 -10000 0 -10000 0 0
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR -0.026 0.13 -10000 0 -0.47 39 39
CASR 0.035 0.043 -10000 0 -0.37 1 1
RhoA/GTP 0.038 0.031 -10000 0 -0.36 1 1
AKT2 0.04 0.034 -10000 0 -0.39 1 1
actin cable formation 0.012 0.086 -10000 0 -0.28 4 4
apoptosis -0.038 0.036 0.41 1 -10000 0 1
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.023 0.077 -10000 0 -0.45 5 5
PIP5K1A 0.038 0.019 -10000 0 -10000 0 0
PLCG1 0.035 0.034 -10000 0 -0.41 1 1
Rac1/GTP 0.023 0.065 -10000 0 -0.26 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.021 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.016 -10000 0 -0.31 1 1
CDKN1B 0.034 0.008 -10000 0 -10000 0 0
CDKN1A 0.029 0.035 -10000 0 -0.27 4 4
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.012 0.027 -10000 0 -0.58 1 1
FOXO3 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
BAD 0.012 0.027 -10000 0 -0.58 1 1
AKT3 0.015 0.014 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.033 0.013 -10000 0 -10000 0 0
AKT1/ASK1 0.032 0.018 -10000 0 -0.26 1 1
BAD/YWHAZ 0.026 0.017 -10000 0 -0.35 1 1
RICTOR 0.013 0 -10000 0 -10000 0 0
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.031 0.018 0.26 1 -10000 0 1
TSC1 0.034 0.008 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.008 -10000 0 -10000 0 0
EP300 0.01 0.038 -10000 0 -0.47 3 3
mol:GDP 0.028 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.034 0.008 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.02 0.029 -10000 0 -0.34 3 3
MAP3K5 0.011 0.035 -10000 0 -0.52 2 2
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.027 0.041 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.034 0.008 -10000 0 -10000 0 0
CASP9 0.034 0.008 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.04 0.007 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.027 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.033 0.034 -10000 0 -0.26 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.003 -10000 0 -10000 0 0
CHUK 0.034 0.008 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.015 -10000 0 -10000 0 0
mTORC2 0.017 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.039 0.048 -10000 0 -10000 0 0
PDPK1 0.013 0 -10000 0 -10000 0 0
MDM2 0.034 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.034 0.007 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.045 0.019 -10000 0 -10000 0 0
TSC1/TSC2 0.039 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.018 -10000 0 -10000 0 0
glucose import -0.031 0.11 -10000 0 -0.3 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.029 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.031 0.11 -10000 0 -0.31 4 4
GSK3A 0.033 0.013 -10000 0 -10000 0 0
FOXO1 0.034 0.008 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.47 49 49
G1/S transition of mitotic cell cycle 0.039 0.013 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.026 0.058 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.021 0.07 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.012 -9999 0 -0.26 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.075 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.013 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones 0.031 0.044 -9999 0 -10000 0 0
YY1/LSF 0.028 0.022 -9999 0 -0.25 1 1
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.013 0.065 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.017 0.047 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA 0.016 0.063 -9999 0 -10000 0 0
HDAC1/Smad7 0.027 0 -9999 0 -10000 0 0
RANGAP1 0.01 0.046 -9999 0 -0.58 3 3
HDAC3/TR2 0.017 0.047 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.043 0.016 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.021 0.058 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.012 0.027 -9999 0 -0.58 1 1
GATA1 0.009 0.035 -9999 0 -0.52 2 2
Mad/Max 0.02 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.051 0.02 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
RBBP4 0.011 0.031 -9999 0 -0.47 2 2
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.011 0.053 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.039 0.016 -9999 0 -10000 0 0
SIN3 complex 0.034 0 -9999 0 -10000 0 0
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0.022 -9999 0 -0.47 1 1
YY1/HDAC3 0.027 0.046 -9999 0 -10000 0 0
YY1/HDAC2 0.028 0.022 -9999 0 -0.25 1 1
YY1/HDAC1 0.028 0.018 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.043 0.015 -9999 0 -10000 0 0
PPARG -0.004 0.1 -9999 0 -0.6 2 2
HDAC8/hEST1B 0.027 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.017 0.047 -9999 0 -10000 0 0
MBD3L2 0 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.046 0.018 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.011 0.053 -9999 0 -10000 0 0
HDAC2 0.012 0.022 -9999 0 -0.47 1 1
YY1 0.027 0.022 -9999 0 -0.25 3 3
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.022 0.025 -9999 0 -0.29 3 3
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0.027 -9999 0 -0.58 1 1
YY1/LSF/HDAC1 0.034 0.021 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.035 0.017 -9999 0 -10000 0 0
EP300 0.01 0.038 -9999 0 -0.47 3 3
STAT3 (dimer non-phopshorylated) 0.022 0.025 -9999 0 -0.29 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.052 -9999 0 -10000 0 0
histone deacetylation 0.043 0.015 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.047 -9999 0 -10000 0 0
nuclear export -0.027 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.017 0.049 -9999 0 -0.31 1 1
GATA1/HDAC1 0.016 0.025 -9999 0 -0.37 2 2
GATA1/HDAC3 0.015 0.051 -9999 0 -0.31 1 1
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.1 -9999 0 -0.36 39 39
SIN3/HDAC complex/Mad/Max 0.043 0.014 -9999 0 -10000 0 0
NuRD Complex 0.05 0.019 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.043 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.028 0.012 -9999 0 -10000 0 0
HDAC complex 0.032 0.021 -9999 0 -10000 0 0
GATA1/Fog1 0.016 0.025 -9999 0 -0.37 2 2
FKBP25/HDAC1/HDAC2 0.026 0.013 -9999 0 -0.27 1 1
TNF -0.029 0.14 -9999 0 -0.5 39 39
negative regulation of cell growth 0.043 0.014 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.043 0.015 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.012 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.016 0.078 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.041 0.018 -9999 0 -10000 0 0
TFCP2 0.012 0.022 -9999 0 -0.47 1 1
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.011 0.038 -9999 0 -0.58 2 2
MBD2 0.012 0.027 -9999 0 -0.58 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.037 0.028 -9999 0 -0.4 2 2
KLHL20 -0.003 0.02 -9999 0 -0.22 1 1
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.056 0.018 -9999 0 -10000 0 0
ENAH 0.037 0.028 -9999 0 -0.4 2 2
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.009 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.011 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.022 0.061 -9999 0 -0.35 4 4
RAPGEF1 0.047 0.025 -9999 0 -0.34 2 2
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.031 0.029 -9999 0 -0.42 2 2
CRK 0.043 0.027 -9999 0 -0.37 2 2
E-cadherin/gamma catenin/alpha catenin 0.026 0.019 -9999 0 -0.27 2 2
alphaE/beta7 Integrin 0.005 0.072 -9999 0 -0.34 20 20
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0 -9999 0 -10000 0 0
DLG1 0.037 0.028 -9999 0 -0.4 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.015 -9999 0 -10000 0 0
MLLT4 0.013 0.001 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.016 0.055 -9999 0 -0.3 14 14
PI3K -0.002 0.019 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.018 0.022 -9999 0 -0.33 2 2
TIAM1 0.01 0.038 -9999 0 -0.47 3 3
E-cadherin(dimer)/Ca2+ 0.031 0.016 -9999 0 -10000 0 0
AKT1 -0.001 0.011 -9999 0 -10000 0 0
PIK3R1 0.008 0.049 -9999 0 -0.47 5 5
CDH1 0.011 0.031 -9999 0 -0.47 2 2
RhoA/GDP 0.055 0.018 -9999 0 -10000 0 0
actin cytoskeleton organization 0.038 0.022 -9999 0 -0.16 1 1
CDC42/GDP 0.055 0.018 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.022 0.016 -9999 0 -0.22 2 2
ITGB7 -0.007 0.1 -9999 0 -0.49 20 20
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.033 0.017 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0.016 -9999 0 -0.23 2 2
mol:GDP 0.052 0.021 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0.053 0.02 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.02 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.031 0.017 -9999 0 -0.2 1 1
NME1 0 0.088 -9999 0 -0.58 11 11
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.037 0.028 -9999 0 -0.4 2 2
regulation of cell-cell adhesion -0.001 0.008 -9999 0 -10000 0 0
WASF2 -0.001 0.006 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.011 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.057 -9999 0 -0.33 4 4
CCND1 0.036 0.021 -9999 0 -0.25 1 1
VAV2 0.047 0.026 -9999 0 -0.36 2 2
RAP1/GDP 0.05 0.018 -9999 0 -10000 0 0
adherens junction assembly 0.037 0.027 -9999 0 -0.39 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.033 0.055 -9999 0 -0.43 1 1
E-cadherin/beta catenin -0.001 0.021 -9999 0 -0.33 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.028 -9999 0 -0.4 2 2
PIK3CA 0.01 0.038 -9999 0 -0.47 3 3
Rac1/GTP -0.005 0.027 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.026 0.019 -9999 0 -0.27 2 2
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.029 -9999 0 -0.42 2 2
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.026 0.019 -9999 0 -0.27 2 2
E-cadherin/beta catenin 0.018 0.022 -9999 0 -0.33 2 2
CTNNB1 0.013 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
CDH1 0.011 0.031 -9999 0 -0.47 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.011 -9999 0 -10000 0 0
MDM2/SUMO1 0.028 0.012 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.015 0.016 -9999 0 -0.17 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.025 0.013 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0.027 -9999 0 -0.58 1 1
SUMO1/HDAC4 0.028 0.012 -9999 0 -10000 0 0
SUMO1/HDAC1 0.028 0.012 -9999 0 -10000 0 0
RANGAP1 0.01 0.046 -9999 0 -0.58 3 3
MDM2/SUMO1/SUMO1 0.034 0.012 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.019 0.013 -9999 0 -10000 0 0
Ran/GTP 0.025 0.012 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.012 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
PIAS2 0.013 0 -9999 0 -10000 0 0
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.018 -9999 0 -0.23 3 3
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.019 0 -9999 0 -10000 0 0
AP2 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0 -9999 0 -10000 0 0
CLTB 0.012 0.027 -9999 0 -0.58 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0.008 -9999 0 -10000 0 0
CD4 0.006 0.063 -9999 0 -0.56 6 6
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0.028 -9999 0 -0.42 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.024 0.019 -9999 0 -0.27 2 2
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0.007 0.019 -9999 0 -0.29 2 2
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.016 0 -9999 0 -10000 0 0
Rac/GTP 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.023 0.021 -9999 0 -0.3 2 2
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.024 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.01 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.018 0 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.024 0.013 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.017 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.019 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.01 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.031 0.019 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0.028 -9999 0 -0.42 2 2
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.02 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.028 -9999 0 -0.42 2 2
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.019 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.022 0.04 -9999 0 -0.34 6 6
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.02 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.037 0.025 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.02 0 -9999 0 -10000 0 0
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.01 0.046 -9999 0 -0.58 3 3
NF kappa B2 p52/RelB 0.016 0.029 -9999 0 -0.36 3 3
regulation of B cell activation 0.015 0.029 -9999 0 -0.35 3 3
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 486 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZG.A9NI TCGA.ZG.A9ND TCGA.ZG.A9MC TCGA.ZG.A9M4
109_MAP3K5 0.05 -0.19 -0.051 -0.051
47_PPARGC1A 0.013 -0.47 0.013 -0.47
105_BMP4 0.013 0.013 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 -0.47 0.013 -0.47
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR 0.034 -0.31 0.034 0.034
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B -0.025 -0.023 -0.042 -0.023
84_STAT5A -0.025 -0.023 -0.042 -0.023
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/PRAD-TP/11493681/PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

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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