PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1RR1WZ5
Maintained by Dan DiCara (Broad Institute)
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/C1RR1WZ5
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 52 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 253
Signaling events mediated by Stem cell factor receptor (c-Kit) 166
Signaling events regulated by Ret tyrosine kinase 153
TCGA08_retinoblastoma 138
Reelin signaling pathway 135
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 122
Wnt signaling 107
FOXA2 and FOXA3 transcription factor networks 100
PDGFR-alpha signaling pathway 98
Noncanonical Wnt signaling pathway 93
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 494 . 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 ( 494 ).

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 0.5121 253 1775 7 -0.52 0 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3360 166 12967 78 -0.8 0.24 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 0.3097 153 12554 82 -0.46 0.013 1000 -1000 -0.078 -1000
TCGA08_retinoblastoma 0.2794 138 1104 8 -0.12 0.071 1000 -1000 -0.018 -1000
Reelin signaling pathway 0.2733 135 7575 56 -0.59 0.033 1000 -1000 -0.075 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2470 122 8320 68 -0.9 0.37 1000 -1000 -0.12 -1000
Wnt signaling 0.2166 107 750 7 -0.41 0.013 1000 -1000 -0.029 -1000
FOXA2 and FOXA3 transcription factor networks 0.2024 100 4602 46 -0.91 0.021 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 0.1984 98 4337 44 -0.49 0.033 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 0.1883 93 2434 26 -0.41 0.013 1000 -1000 -0.081 -1000
IL4-mediated signaling events 0.1883 93 8549 91 -1.3 0.67 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.1761 87 4542 52 -0.38 0.2 1000 -1000 -0.069 -1000
Nongenotropic Androgen signaling 0.1700 84 4374 52 -0.34 0.16 1000 -1000 -0.059 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1599 79 4290 54 -0.59 0.028 1000 -1000 -0.089 -1000
Calcium signaling in the CD4+ TCR pathway 0.1599 79 2456 31 -0.52 0.013 1000 -1000 -0.076 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1518 75 2561 34 -0.17 0.013 1000 -1000 -0.052 -1000
Glypican 1 network 0.1316 65 3124 48 -0.38 0.028 1000 -1000 -0.042 -1000
HIF-1-alpha transcription factor network 0.1296 64 4930 76 -0.57 0.041 1000 -1000 -0.081 -1000
Endothelins 0.1255 62 6001 96 -0.39 0.013 1000 -1000 -0.084 -1000
IGF1 pathway 0.1255 62 3580 57 -0.19 0.058 1000 -1000 -0.089 -1000
Glucocorticoid receptor regulatory network 0.1194 59 6818 114 -0.55 0.36 1000 -1000 -0.063 -1000
Ephrin B reverse signaling 0.1134 56 2728 48 -0.3 0.18 1000 -1000 -0.067 -1000
TCR signaling in naïve CD8+ T cells 0.1134 56 5266 93 -0.2 0.087 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.1134 56 3408 60 -0.31 0.019 1000 -1000 -0.14 -1000
Glypican 2 network 0.1073 53 212 4 -0.087 -0.009 1000 -1000 -0.03 -1000
BMP receptor signaling 0.1012 50 4123 81 -0.57 0.026 1000 -1000 -0.094 -1000
Coregulation of Androgen receptor activity 0.0992 49 3750 76 -0.77 0.062 1000 -1000 -0.051 -1000
Arf6 signaling events 0.0972 48 2986 62 -0.32 0.02 1000 -1000 -0.063 -1000
Syndecan-1-mediated signaling events 0.0951 47 1625 34 -0.2 0.013 1000 -1000 -0.059 -1000
IL12-mediated signaling events 0.0830 41 3594 87 -0.4 0.025 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0830 41 3524 85 -0.3 0.15 1000 -1000 -0.087 -1000
Syndecan-4-mediated signaling events 0.0810 40 2743 67 -0.25 0.022 1000 -1000 -0.086 -1000
Hedgehog signaling events mediated by Gli proteins 0.0789 39 2551 65 -0.66 0.061 1000 -1000 -0.055 -1000
amb2 Integrin signaling 0.0789 39 3201 82 -0.24 0.013 1000 -1000 -0.071 -1000
Signaling mediated by p38-alpha and p38-beta 0.0789 39 1732 44 -0.23 0.013 1000 -1000 -0.049 -1000
IL6-mediated signaling events 0.0769 38 2924 75 -0.2 0.059 1000 -1000 -0.082 -1000
EGFR-dependent Endothelin signaling events 0.0688 34 727 21 -0.11 0.013 1000 -1000 -0.072 -1000
Thromboxane A2 receptor signaling 0.0648 32 3434 105 -0.22 0.034 1000 -1000 -0.07 -1000
FAS signaling pathway (CD95) 0.0607 30 1448 47 -0.23 0.03 1000 -1000 -0.042 -1000
TCGA08_p53 0.0587 29 204 7 -0.08 0.051 1000 -1000 -0.009 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0567 28 2447 85 -0.27 0.013 1000 -1000 -0.074 -1000
Regulation of Androgen receptor activity 0.0567 28 2002 70 -0.48 0.034 1000 -1000 -0.071 -1000
Syndecan-2-mediated signaling events 0.0547 27 1907 69 -0.22 0.038 1000 -1000 -0.055 -1000
Regulation of p38-alpha and p38-beta 0.0547 27 1477 54 -0.47 0.013 1000 -1000 -0.059 -1000
IL27-mediated signaling events 0.0547 27 1396 51 -0.15 0.067 1000 -1000 -0.082 -1000
Visual signal transduction: Rods 0.0547 27 1406 52 -0.2 0.015 1000 -1000 -0.078 -1000
Plasma membrane estrogen receptor signaling 0.0526 26 2305 86 -0.18 0.021 1000 -1000 -0.077 -1000
Ras signaling in the CD4+ TCR pathway 0.0526 26 450 17 -0.089 0.013 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 0.0506 25 1672 65 -0.12 0.027 1000 -1000 -0.062 -1000
Osteopontin-mediated events 0.0506 25 971 38 -0.26 0.013 1000 -1000 -0.11 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0506 25 1346 52 -0.28 0.053 1000 -1000 -0.06 -1000
BCR signaling pathway 0.0506 25 2508 99 -0.19 0.023 1000 -1000 -0.089 -1000
LPA receptor mediated events 0.0486 24 2547 102 -0.25 0.031 1000 -1000 -0.086 -1000
VEGFR1 specific signals 0.0486 24 1398 56 -0.07 0.041 1000 -1000 -0.07 -1000
JNK signaling in the CD4+ TCR pathway 0.0466 23 392 17 -0.1 0.018 1000 -1000 -0.061 -1000
Signaling events mediated by PTP1B 0.0466 23 1766 76 -0.24 0.021 1000 -1000 -0.074 -1000
Integrins in angiogenesis 0.0466 23 1995 84 -0.23 0.033 1000 -1000 -0.089 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0466 23 2062 88 -0.32 0.03 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 0.0425 21 2729 125 -0.35 0.066 1000 -1000 -0.093 -1000
Regulation of nuclear SMAD2/3 signaling 0.0405 20 2769 136 -0.34 0.064 1000 -1000 -0.067 -1000
Aurora C signaling 0.0405 20 144 7 -0.061 0 1000 -1000 -0.039 -1000
Fc-epsilon receptor I signaling in mast cells 0.0405 20 2010 97 -0.2 0.03 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 0.0385 19 981 51 -0.18 0.053 1000 -1000 -0.14 -1000
Visual signal transduction: Cones 0.0364 18 715 38 -0.088 0.013 1000 -1000 -0.069 -1000
ErbB4 signaling events 0.0344 17 1226 69 -0.14 0.057 1000 -1000 -0.085 -1000
IL1-mediated signaling events 0.0344 17 1106 62 -0.12 0.066 1000 -1000 -0.084 -1000
TCGA08_rtk_signaling 0.0344 17 458 26 -0.24 0.025 1000 -1000 -0.018 -1000
Aurora B signaling 0.0344 17 1165 67 -0.38 0.014 1000 -1000 -0.066 -1000
Insulin-mediated glucose transport 0.0324 16 513 32 -0.21 0.042 1000 -1000 -0.059 -1000
Syndecan-3-mediated signaling events 0.0324 16 568 35 -0.16 0.013 1000 -1000 -0.073 -1000
Effects of Botulinum toxin 0.0324 16 426 26 -0.16 0.019 1000 -1000 -0.061 -1000
Rapid glucocorticoid signaling 0.0324 16 338 20 -0.094 0.015 1000 -1000 -0.037 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0324 16 1992 120 -0.31 0.042 1000 -1000 -0.074 -1000
LPA4-mediated signaling events 0.0304 15 187 12 -0.12 0.015 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 0.0304 15 939 61 -0.2 0.042 1000 -1000 -0.076 -1000
Ceramide signaling pathway 0.0304 15 1161 76 -0.18 0.024 1000 -1000 -0.059 -1000
IL2 signaling events mediated by STAT5 0.0304 15 347 22 -0.068 0.039 1000 -1000 -0.05 -1000
Insulin Pathway 0.0304 15 1137 74 -0.085 0.035 1000 -1000 -0.088 -1000
Signaling events mediated by PRL 0.0304 15 522 34 -0.11 0.013 1000 -1000 -0.039 -1000
IFN-gamma pathway 0.0283 14 989 68 -0.1 0.042 1000 -1000 -0.082 -1000
Nectin adhesion pathway 0.0283 14 922 63 -0.26 0.029 1000 -1000 -0.073 -1000
IL2 signaling events mediated by PI3K 0.0283 14 820 58 -0.066 0.031 1000 -1000 -0.079 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0283 14 467 33 -0.16 0.035 1000 -1000 -0.061 -1000
Class IB PI3K non-lipid kinase events 0.0283 14 42 3 -0.003 -1000 1000 -1000 -0.013 -1000
a4b1 and a4b7 Integrin signaling 0.0263 13 68 5 -0.033 0.002 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class III 0.0263 13 556 40 -0.35 0.024 1000 -1000 -0.04 -1000
mTOR signaling pathway 0.0243 12 652 53 -0.046 0.02 1000 -1000 -0.059 -1000
BARD1 signaling events 0.0223 11 631 57 -0.036 0.051 1000 -1000 -0.066 -1000
Cellular roles of Anthrax toxin 0.0223 11 455 39 -0.087 0.019 1000 -1000 -0.031 -1000
S1P1 pathway 0.0223 11 416 36 -0.03 0.032 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0223 11 520 45 -0.087 0.039 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0223 11 818 74 -0.18 0.085 1000 -1000 -0.086 -1000
Regulation of Telomerase 0.0223 11 1129 102 -0.28 0.052 1000 -1000 -0.1 -1000
S1P3 pathway 0.0223 11 486 42 -0.18 0.049 1000 -1000 -0.045 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0202 10 898 83 -0.21 0.052 1000 -1000 -0.065 -1000
Caspase cascade in apoptosis 0.0182 9 712 74 -0.087 0.028 1000 -1000 -0.05 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0182 9 256 28 -0.18 0.03 1000 -1000 -0.062 -1000
Retinoic acid receptors-mediated signaling 0.0182 9 544 58 -0.11 0.034 1000 -1000 -0.07 -1000
Class I PI3K signaling events mediated by Akt 0.0162 8 564 68 -0.21 0.052 1000 -1000 -0.056 -1000
TRAIL signaling pathway 0.0162 8 395 48 -0.074 0.047 1000 -1000 -0.065 -1000
ceramide signaling pathway 0.0162 8 422 49 -0.087 0.031 1000 -1000 -0.048 -1000
Canonical NF-kappaB pathway 0.0142 7 296 39 -0.087 0.073 1000 -1000 -0.075 -1000
Canonical Wnt signaling pathway 0.0142 7 374 51 -0.048 0.067 1000 -1000 -0.055 -1000
Class I PI3K signaling events 0.0142 7 553 73 -0.24 0.032 1000 -1000 -0.067 -1000
Circadian rhythm pathway 0.0121 6 143 22 -0.055 0.013 1000 -1000 -0.076 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0121 6 229 37 -0.035 0.039 1000 -1000 -0.057 -1000
FoxO family signaling 0.0121 6 424 64 -0.21 0.16 1000 -1000 -0.055 -1000
S1P4 pathway 0.0121 6 158 25 -0.017 0.032 1000 -1000 -0.044 -1000
S1P5 pathway 0.0101 5 101 17 -0.017 0.022 1000 -1000 -0.044 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0101 5 717 125 -0.036 0.085 1000 -1000 -0.087 -1000
EPO signaling pathway 0.0081 4 243 55 -0.026 0.061 1000 -1000 -0.086 -1000
Signaling events mediated by HDAC Class I 0.0081 4 495 104 -0.087 0.059 1000 -1000 -0.065 -1000
Paxillin-dependent events mediated by a4b1 0.0081 4 145 36 -0.033 0.024 1000 -1000 -0.068 -1000
Atypical NF-kappaB pathway 0.0081 4 147 31 -0.042 0.047 1000 -1000 -0.042 -1000
PLK1 signaling events 0.0061 3 286 85 -0.035 0.033 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0061 3 137 43 -0.2 0.2 1000 -1000 -0.072 -1000
Signaling mediated by p38-gamma and p38-delta 0.0061 3 53 15 0 0.031 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 0.0061 3 367 97 -0.18 0.064 1000 -1000 -0.08 -1000
E-cadherin signaling in keratinocytes 0.0061 3 139 43 -0.005 0.052 1000 -1000 -0.058 -1000
p38 MAPK signaling pathway 0.0061 3 151 44 -0.04 0.026 1000 -1000 -0.06 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 67 23 -0.04 0.049 1000 -1000 -0.076 -1000
Signaling events mediated by HDAC Class II 0.0040 2 177 75 -0.046 0.036 1000 -1000 -0.064 -1000
PLK2 and PLK4 events 0.0040 2 6 3 0.009 0.022 1000 -1000 -0.019 -1000
Aurora A signaling 0.0040 2 168 60 -0.05 0.038 1000 -1000 -0.058 -1000
Arf6 downstream pathway 0.0040 2 122 43 -0.17 0.091 1000 -1000 -0.038 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 118 76 -0.17 0.073 1000 -1000 -0.084 -1000
Arf6 trafficking events 0.0020 1 82 71 -0.023 0.046 1000 -1000 -0.067 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.057 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.036 -1000
Arf1 pathway 0.0000 0 39 54 -0.006 0.035 1000 -1000 -0.045 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.062 -1000
Total NA 4150 228004 7203 -29 -990 131000 -131000 -8.6 -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 -0.42 0.31 -9999 0 -0.61 346 346
EFNA5 -0.11 0.3 -9999 0 -0.81 76 76
FYN -0.38 0.3 -9999 0 -0.55 346 346
neuron projection morphogenesis -0.42 0.31 -9999 0 -0.61 346 346
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.31 -9999 0 -0.61 346 346
EPHA5 -0.52 0.4 -9999 0 -0.81 315 315
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.22 0.22 -10000 0 -0.4 289 289
CRKL -0.22 0.24 -10000 0 -0.42 282 282
HRAS -0.19 0.21 -10000 0 -0.5 48 48
mol:PIP3 -0.22 0.22 -10000 0 -0.41 282 282
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.037 -10000 0 -0.81 1 1
GAB1 -0.24 0.25 -10000 0 -0.45 282 282
FOXO3 -0.2 0.22 -10000 0 -0.38 282 282
AKT1 -0.22 0.23 -10000 0 -0.42 282 282
BAD -0.2 0.22 -10000 0 -0.38 282 282
megakaryocyte differentiation -0.25 0.24 -10000 0 -0.45 290 290
GSK3B -0.2 0.22 -10000 0 -0.38 282 282
RAF1 -0.15 0.18 -10000 0 -0.44 28 28
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 282 282
STAT1 -0.6 0.58 -10000 0 -1.1 284 284
HRAS/SPRED1 -0.18 0.14 -10000 0 -0.44 30 30
cell proliferation -0.24 0.26 -10000 0 -0.45 285 285
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 282 282
HRAS/SPRED2 -0.18 0.14 -10000 0 -0.4 43 43
LYN/TEC/p62DOK -0.24 0.21 -10000 0 -0.41 282 282
MAPK3 -0.097 0.13 -10000 0 -0.31 22 22
STAP1 -0.26 0.25 -10000 0 -0.47 282 282
GRAP2 -0.045 0.21 -10000 0 -0.75 38 38
JAK2 -0.52 0.45 -10000 0 -0.9 284 284
STAT1 (dimer) -0.58 0.57 -10000 0 -1.1 284 284
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.21 -10000 0 -0.42 285 285
actin filament polymerization -0.24 0.24 -10000 0 -0.44 282 282
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.35 0.34 -10000 0 -0.64 282 282
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 282 282
PI3K -0.22 0.24 -10000 0 -0.42 283 283
PTEN 0.012 0.037 -10000 0 -0.81 1 1
SCF/KIT/EPO/EPOR -0.74 0.71 -10000 0 -1.4 282 282
MAPK8 -0.25 0.26 -10000 0 -0.46 285 285
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 282 282
positive regulation of transcription -0.077 0.11 -10000 0 -0.25 22 22
mol:GDP -0.23 0.19 -10000 0 -0.47 79 79
PIK3C2B -0.24 0.25 -10000 0 -0.45 282 282
CBL/CRKL -0.2 0.22 -10000 0 -0.39 282 282
FER -0.24 0.25 -10000 0 -0.45 283 283
SH2B3 -0.24 0.25 -10000 0 -0.45 282 282
PDPK1 -0.2 0.21 -10000 0 -0.37 283 283
SNAI2 -0.25 0.26 -10000 0 -0.46 284 284
positive regulation of cell proliferation -0.42 0.42 -10000 0 -0.77 284 284
KITLG -0.005 0.11 -10000 0 -0.85 8 8
cell motility -0.42 0.42 -10000 0 -0.77 284 284
PTPN6 0.021 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.56 8 8
STAT5A (dimer) -0.34 0.34 -10000 0 -0.63 284 284
SOCS1 0.008 0.049 -10000 0 -0.39 6 6
cell migration 0.24 0.25 0.45 285 -10000 0 285
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.041 -10000 0 -0.32 7 7
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
GRB10 -0.24 0.25 -10000 0 -0.45 282 282
PTPN11 0.02 0.038 -10000 0 -0.8 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 282 282
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.14 -10000 0 -0.34 25 25
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.8 0.74 -10000 0 -1.4 282 282
MAP2K2 -0.11 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.24 0.21 -10000 0 -0.41 282 282
STAT5A -0.35 0.36 -10000 0 -0.65 284 284
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 284 284
SHC/GRAP2 -0.044 0.16 -10000 0 -0.62 33 33
PTPRO -0.26 0.25 -10000 0 -0.46 290 290
SH2B2 -0.24 0.25 -10000 0 -0.45 282 282
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.25 0.25 -10000 0 -0.46 285 285
CREBBP 0.017 0.02 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 36 36
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.088 0.068 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.25 0.2 -9999 0 -0.5 122 122
JUN -0.32 0.31 -9999 0 -0.66 180 180
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.38 0.32 -9999 0 -0.6 304 304
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.38 0.32 -9999 0 -0.6 304 304
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.29 0.25 -9999 0 -0.51 280 280
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.34 0.29 -9999 0 -0.54 304 304
GRB7 -0.04 0.12 -9999 0 -0.31 82 82
RET51/GFRalpha1/GDNF -0.38 0.32 -9999 0 -0.6 304 304
MAPKKK cascade -0.3 0.26 -9999 0 -0.48 304 304
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.34 0.31 -9999 0 -0.58 293 293
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 281 281
RET51/GFRalpha1/GDNF/SHC -0.38 0.32 -9999 0 -0.6 304 304
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.5 280 280
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.5 280 280
MAPK3 -0.31 0.29 -9999 0 -0.51 304 304
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.81 79 79
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.3 0.29 -9999 0 -0.66 131 131
DOK5 -0.099 0.28 -9999 0 -0.81 67 67
GFRA1 -0.46 0.41 -9999 0 -0.81 281 281
MAPK8 -0.23 0.24 -9999 0 -0.39 307 307
HRAS/GTP -0.35 0.3 -9999 0 -0.56 304 304
tube development -0.27 0.23 -9999 0 -0.47 280 280
MAPK1 -0.31 0.29 -9999 0 -0.51 304 304
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 280 280
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -10000 0 0
PDLIM7 0.011 0.029 -9999 0 -0.31 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.43 0.38 -9999 0 -0.66 315 315
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.38 0.32 -9999 0 -0.6 304 304
RET51/GFRalpha1/GDNF/Dok5 -0.44 0.38 -9999 0 -0.68 316 316
PRKCA -0.018 0.16 -9999 0 -0.81 19 19
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
CREB1 -0.24 0.24 -9999 0 -0.43 280 280
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 280 280
RET51/GFRalpha1/GDNF/Grb7 -0.4 0.32 -9999 0 -0.63 304 304
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.16 0.31 -9999 0 -0.63 135 135
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.64 180 180
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.5 280 280
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.18 -9999 0 -0.34 280 280
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.24 0.24 -9999 0 -0.41 304 304
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.24 0.23 -9999 0 -0.41 304 304
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.28 0.31 -9999 0 -0.47 304 304
PI3K -0.36 0.34 -9999 0 -0.62 281 281
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.27 0.23 -9999 0 -0.47 280 280
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.38 280 280
RET51/GFRalpha1/GDNF/FRS2 -0.38 0.32 -9999 0 -0.6 304 304
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.28 0.31 -9999 0 -0.47 304 304
RET51/GFRalpha1/GDNF/PKC alpha -0.4 0.34 -9999 0 -0.63 305 305
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.042 -9999 0 -0.31 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.44 0.36 -9999 0 -0.67 316 316
Rac1/GTP -0.29 0.23 -9999 0 -0.46 281 281
RET9/GFRalpha1/GDNF -0.32 0.27 -9999 0 -0.56 280 280
GFRalpha1/GDNF -0.36 0.31 -9999 0 -0.63 280 280
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.16 -10000 0 -0.31 204 204
CDKN2C 0.026 0.036 -10000 0 -0.32 3 3
CDKN2A -0.12 0.16 -10000 0 -0.31 204 204
CCND2 0.068 0.071 0.17 138 -10000 0 138
RB1 -0.067 0.071 -10000 0 -0.17 138 138
CDK4 0.068 0.07 0.17 139 -10000 0 139
CDK6 0.071 0.076 0.18 138 -0.18 2 140
G1/S progression 0.059 0.078 0.17 138 -10000 0 138
Reelin signaling pathway

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
CDK5R1/CDK5 -0.001 0.015 -9999 0 -10000 0 0
VLDLR -0.02 0.16 -9999 0 -0.81 20 20
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.01 0.032 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.41 0.26 -9999 0 -0.56 366 366
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.067 -9999 0 -0.46 11 11
AKT1 -0.23 0.17 -9999 0 -0.33 367 367
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
RELN/LRP8/DAB1 -0.38 0.24 -9999 0 -0.52 364 364
LRPAP1/LRP8 -0.025 0.12 -9999 0 -0.62 20 20
RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 364 364
DAB1/alpha3/beta1 Integrin -0.34 0.23 -9999 0 -0.45 370 370
long-term memory -0.36 0.24 -9999 0 -0.48 366 366
DAB1/LIS1 -0.35 0.23 -9999 0 -0.47 370 370
DAB1/CRLK/C3G -0.34 0.22 -9999 0 -0.45 370 370
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
DAB1/NCK2 -0.35 0.24 -9999 0 -0.47 370 370
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.022 0.16 -9999 0 -0.63 27 27
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
RELN -0.59 0.37 -9999 0 -0.81 360 360
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.41 0.26 -9999 0 -0.56 364 364
GRIN2A/RELN/LRP8/DAB1/Fyn -0.37 0.25 -9999 0 -0.5 366 366
MAPK8 -0.005 0.12 -9999 0 -0.81 11 11
RELN/VLDLR/DAB1 -0.38 0.24 -9999 0 -0.52 366 366
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.36 0.26 -9999 0 -0.49 370 370
RELN/LRP8 -0.41 0.26 -9999 0 -0.56 364 364
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 364 364
PI3K -0.004 0.048 -9999 0 -0.62 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.02 -9999 0 -10000 0 0
RAP1A -0.3 0.23 -9999 0 -0.82 27 27
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.015 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.52 23 23
neuron adhesion -0.28 0.22 -9999 0 -0.73 31 31
LRP8 -0.02 0.16 -9999 0 -0.81 20 20
GSK3B -0.21 0.16 -9999 0 -0.61 16 16
RELN/VLDLR/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 366 366
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.35 367 367
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.087 -9999 0 -0.56 5 5
neuron migration -0.29 0.22 -9999 0 -0.41 361 361
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.52 23 23
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 370 370
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.04 0.16 -10000 0 -0.52 35 35
NFATC2 -0.24 0.38 -10000 0 -0.81 130 130
NFATC3 -0.084 0.13 -10000 0 -10000 0 0
CD40LG -0.74 0.57 -10000 0 -1.2 296 296
ITCH 0.051 0.015 -10000 0 -10000 0 0
CBLB 0.051 0.015 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.54 0.53 -10000 0 -1.2 147 147
JUNB 0.003 0.091 -10000 0 -0.81 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.015 -10000 0 -0.34 1 1
T cell anergy 0.025 0.065 -10000 0 -0.49 1 1
TLE4 -0.24 0.44 -10000 0 -0.86 141 141
Jun/NFAT1-c-4/p21SNFT -0.66 0.6 -10000 0 -1.2 258 258
AP-1/NFAT1-c-4 -0.9 0.78 -10000 0 -1.4 286 286
IKZF1 -0.18 0.34 -10000 0 -0.72 110 110
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.87 110 110
AP-1/NFAT1 -0.42 0.48 -10000 0 -0.9 217 217
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.85 -10000 0 -1.6 236 236
EGR3 -0.56 0.73 -10000 0 -1.2 219 219
NFAT1/FOXP3 -0.22 0.34 -10000 0 -0.69 132 132
EGR1 -0.17 0.34 -10000 0 -0.82 107 107
JUN -0.19 0.34 -10000 0 -0.82 112 112
EGR4 -0.036 0.18 -10000 0 -0.72 31 31
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.17 0.32 -10000 0 -0.69 107 107
FOSL1 -0.032 0.12 -10000 0 -0.32 68 68
NFAT1-c-4/MAF/IRF4 -0.57 0.56 -10000 0 -1 254 254
DGKA -0.16 0.3 -10000 0 -0.67 101 101
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1 254 254
CTLA4 -0.24 0.39 -10000 0 -0.84 116 116
NFAT1-c-4 (dimer)/EGR1 -0.65 0.66 -10000 0 -1.2 255 255
NFAT1-c-4 (dimer)/EGR4 -0.58 0.56 -10000 0 -1 257 257
FOS -0.21 0.36 -10000 0 -0.82 127 127
IFNG -0.43 0.54 -10000 0 -1.2 142 142
T cell activation -0.44 0.42 -10000 0 -0.94 172 172
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.37 0.42 0.75 234 -10000 0 234
TNF -0.6 0.57 -10000 0 -1.1 270 270
FASLG -0.75 0.78 -10000 0 -1.4 251 251
TBX21 -0.039 0.18 -10000 0 -0.68 33 33
BATF3 -0.005 0.081 -10000 0 -0.33 27 27
PRKCQ 0.003 0.092 -10000 0 -0.81 6 6
PTPN1 -0.16 0.3 -10000 0 -0.66 101 101
NFAT1-c-4/ICER1 -0.55 0.55 -10000 0 -1 252 252
GATA3 -0.029 0.18 -10000 0 -0.78 27 27
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1.1 144 144
IL2RA -0.49 0.46 -10000 0 -1 158 158
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.3 -10000 0 -0.66 104 104
E2F1 -0.078 0.15 -10000 0 -10000 0 0
PPARG -0.002 0.1 -10000 0 -0.6 12 12
SLC3A2 -0.16 0.3 -10000 0 -0.67 98 98
IRF4 -0.1 0.24 -10000 0 -0.47 116 116
PTGS2 -0.71 0.56 -10000 0 -1.1 282 282
CSF2 -0.78 0.53 -10000 0 -1.2 299 299
JunB/Fra1/NFAT1-c-4 -0.54 0.53 -10000 0 -1 250 250
IL4 -0.33 0.37 -10000 0 -0.94 105 105
IL5 -0.7 0.54 -10000 0 -1.1 283 283
IL2 -0.45 0.44 -10000 0 -0.97 171 171
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.041 -10000 0 -0.87 1 1
NFATC1 -0.37 0.42 -10000 0 -0.75 234 234
CDK4 0.22 0.24 0.59 69 -10000 0 69
PTPRK -0.16 0.3 -10000 0 -0.74 74 74
IL8 -0.72 0.54 -10000 0 -1.1 290 290
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.27 0.28 -9999 0 -0.46 307 307
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.003 0.055 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.8 164 164
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 253 253
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.54 -9999 0 -1.1 210 210
PCK1 -0.34 0.49 -9999 0 -1.3 77 77
HNF4A -0.66 0.65 -9999 0 -1.3 246 246
KCNJ11 -0.48 0.54 -9999 0 -1 201 201
AKT1 -0.042 0.12 -9999 0 -0.37 18 18
response to starvation -0.017 0.033 -9999 0 -10000 0 0
DLK1 -0.49 0.53 -9999 0 -1.1 187 187
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.51 0.54 -9999 0 -1 220 220
TAT -0.2 0.22 -9999 0 -0.62 22 22
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.083 -9999 0 -0.81 5 5
TTR -0.19 0.22 -9999 0 -0.74 33 33
PKLR -0.52 0.54 -9999 0 -1 220 220
APOA1 -0.91 0.89 -9999 0 -1.7 254 254
CPT1C -0.53 0.54 -9999 0 -1 227 227
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.7 64 64
FOXF1 -0.007 0.075 -9999 0 -0.72 5 5
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.51 0.54 -9999 0 -1 220 220
HMGCS1 -0.51 0.54 -9999 0 -1 220 220
NR3C1 0.019 0.017 -9999 0 -10000 0 0
CPT1B -0.51 0.54 -9999 0 -1 213 213
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.66 0.7 -9999 0 -1.3 240 240
CREB1 0 0.053 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.56 12 12
PDX1 -0.18 0.21 -9999 0 -0.6 1 1
UCP2 -0.51 0.54 -9999 0 -1 221 221
ALDOB -0.48 0.54 -9999 0 -1 202 202
AFP -0.045 0.11 -9999 0 -0.48 10 10
BDH1 -0.51 0.54 -9999 0 -1 214 214
HADH -0.48 0.53 -9999 0 -1 202 202
F2 -0.62 0.63 -9999 0 -1.3 212 212
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.09 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.7 2 2
INS -0.013 0.066 -9999 0 -0.82 3 3
FOXA1 -0.053 0.14 -9999 0 -0.34 79 79
FOXA3 -0.072 0.17 -9999 0 -0.5 35 35
FOXA2 -0.55 0.6 -9999 0 -1.1 224 224
ABCC8 -0.78 0.74 -9999 0 -1.4 274 274
ALB -0.094 0.31 -9999 0 -1.3 29 29
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.25 0.38 -9999 0 -0.83 151 151
PDGF/PDGFRA/CRKL -0.19 0.29 -9999 0 -0.62 151 151
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 151 151
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.29 -9999 0 -0.63 151 151
AP1 -0.49 0.62 -9999 0 -1.4 134 134
mol:IP3 -0.19 0.3 -9999 0 -0.64 151 151
PLCG1 -0.19 0.3 -9999 0 -0.65 151 151
PDGF/PDGFRA/alphaV Integrin -0.19 0.29 -9999 0 -0.62 152 152
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.3 -9999 0 -0.64 151 151
CAV3 -0.001 0.028 -9999 0 -0.31 4 4
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/Shf -0.19 0.29 -9999 0 -0.62 151 151
FOS -0.44 0.6 -9999 0 -1.4 134 134
JUN -0.17 0.28 -9999 0 -0.7 112 112
oligodendrocyte development -0.19 0.29 -9999 0 -0.62 152 152
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.3 -9999 0 -0.64 151 151
PDGF/PDGFRA -0.25 0.38 -9999 0 -0.83 151 151
actin cytoskeleton reorganization -0.19 0.29 -9999 0 -0.62 151 151
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.53 154 154
PDGF/PDGFRA/Crk/C3G -0.16 0.24 -9999 0 -0.53 151 151
JAK1 -0.18 0.3 -9999 0 -0.62 151 151
ELK1/SRF -0.12 0.24 -9999 0 -0.48 151 151
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.027 0.027 -9999 0 -10000 0 0
GO:0007205 -0.2 0.31 -9999 0 -0.66 151 151
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/SHB -0.19 0.29 -9999 0 -0.62 151 151
PDGF/PDGFRA/Caveolin-1 -0.2 0.31 -9999 0 -0.66 154 154
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
ELK1 -0.18 0.28 -9999 0 -0.59 151 151
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PDGF/PDGFRA/Crk -0.19 0.29 -9999 0 -0.62 151 151
JAK-STAT cascade -0.18 0.29 -9999 0 -0.62 151 151
cell proliferation -0.19 0.29 -9999 0 -0.62 151 151
Noncanonical Wnt signaling pathway

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
NFATC2 -0.13 0.31 -9999 0 -0.81 86 86
GNB1/GNG2 -0.26 0.24 -9999 0 -0.61 119 119
mol:DAG -0.21 0.24 -9999 0 -0.55 117 117
PLCG1 -0.22 0.24 -9999 0 -0.57 117 117
YES1 -0.25 0.26 -9999 0 -0.62 126 126
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.22 0.24 -9999 0 -0.57 117 117
MAP3K7 -0.17 0.2 -9999 0 -0.45 117 117
mol:Ca2+ -0.2 0.23 -9999 0 -0.53 117 117
mol:IP3 -0.21 0.24 -9999 0 -0.55 117 117
NLK -0.01 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.19 0.22 -9999 0 -0.48 131 131
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.27 0.28 -9999 0 -0.46 307 307
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.26 -9999 0 -0.62 126 126
GO:0007205 -0.2 0.23 -9999 0 -0.54 117 117
WNT6 0.003 0.055 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.8 164 164
NFAT1/CK1 alpha -0.3 0.25 -9999 0 -0.62 150 150
GNG2 0.012 0.037 -9999 0 -0.81 1 1
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 253 253
CDC42 -0.23 0.25 -9999 0 -0.58 126 126
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 -0.6 0.44 -10000 0 -1.1 166 166
STAT6 (cleaved dimer) -0.65 0.44 -10000 0 -1 258 258
IGHG1 -0.21 0.14 -10000 0 -0.36 44 44
IGHG3 -0.59 0.42 -10000 0 -0.97 223 223
AKT1 -0.32 0.26 -10000 0 -0.71 79 79
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.25 -10000 0 -0.74 58 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.36 0.28 -10000 0 -0.75 104 104
THY1 -0.6 0.44 -10000 0 -1.1 138 138
MYB -0.009 0.13 -10000 0 -0.64 17 17
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.42 0.31 -10000 0 -0.73 169 169
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.77 58 58
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.63 0.44 -10000 0 -1 229 229
SOCS1 -0.41 0.29 -10000 0 -0.72 138 138
SOCS3 -0.37 0.34 -10000 0 -0.97 73 73
FCER2 -0.63 0.47 -10000 0 -1 213 213
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.47 -10000 0 -1.1 196 196
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.68 46 46
T cell proliferation -0.61 0.46 -10000 0 -1.1 182 182
IL4R/JAK1 -0.6 0.44 -10000 0 -1.1 164 164
EGR2 -0.96 0.72 -10000 0 -1.6 248 248
JAK2 -0.02 0.058 -10000 0 -0.85 2 2
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.2 0.17 -10000 0 -0.61 19 19
CCL26 -0.62 0.45 -10000 0 -1.1 169 169
IL4R -0.64 0.46 -10000 0 -1.2 164 164
PTPN6 0.029 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.56 -10000 0 -1.3 194 194
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.36 0.5 -10000 0 -1.2 106 106
ARG1 -0.15 0.11 -10000 0 -10000 0 0
CBL -0.39 0.29 -10000 0 -0.73 139 139
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
IL13RA1/JAK2 -0.026 0.052 -10000 0 -0.66 2 2
IRF4/BCL6 -0.32 0.46 -10000 0 -1.1 101 101
CD40LG -0.13 0.31 -10000 0 -0.8 87 87
MAPK14 -0.39 0.31 -10000 0 -0.77 130 130
mitosis -0.31 0.24 -10000 0 -0.66 81 81
STAT6 -0.68 0.51 -10000 0 -1.2 204 204
SPI1 0 0.074 -10000 0 -0.31 27 27
RPS6KB1 -0.29 0.23 -10000 0 -0.67 66 66
STAT6 (dimer) -0.68 0.51 -10000 0 -1.2 204 204
STAT6 (dimer)/PARP14 -0.64 0.47 -10000 0 -1.1 198 198
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.27 -10000 0 -0.75 79 79
FRAP1 -0.32 0.26 -10000 0 -0.71 80 80
LTA -0.62 0.45 -10000 0 -1.1 175 175
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.67 0.49 1.1 207 -10000 0 207
CCL11 -0.59 0.43 -10000 0 -1.1 154 154
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.73 81 81
IL2RG -0.045 0.19 -10000 0 -0.52 57 57
IL10 -0.62 0.47 -10000 0 -1.1 174 174
IRS1 -0.085 0.27 -10000 0 -0.81 59 59
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.094 -10000 0 -10000 0 0
IL5 -0.61 0.44 -10000 0 -1.1 173 173
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.49 0.33 -10000 0 -0.84 170 170
COL1A1 -0.26 0.23 -10000 0 -0.67 48 48
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.45 -10000 0 -1.2 125 125
IL2R gamma/JAK3 -0.081 0.18 -10000 0 -0.5 57 57
TFF3 -1.3 0.61 -10000 0 -1.6 402 402
ALOX15 -0.6 0.44 -10000 0 -1.1 165 165
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.52 0.36 -10000 0 -0.87 194 194
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.018 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.31 0.25 -10000 0 -0.72 64 64
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.71 80 80
PI3K -0.34 0.28 -10000 0 -0.77 76 76
DOK2 -0.001 0.078 -10000 0 -0.36 19 19
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.25 0.21 -10000 0 -0.67 45 45
ITGB3 -0.62 0.47 -10000 0 -1.2 157 157
PIGR -0.65 0.5 -10000 0 -1.2 151 151
IGHE 0.052 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.66 45 45
BCL6 0.012 0.037 -10000 0 -0.81 1 1
OPRM1 -0.61 0.44 -10000 0 -1.1 166 166
RETNLB -0.61 0.44 -10000 0 -1.1 167 167
SELP -0.61 0.45 -10000 0 -1.1 165 165
AICDA -0.59 0.42 -10000 0 -1.1 163 163
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.68 35 35
IHH -0.2 0.37 -10000 0 -0.83 123 123
SHH Np/Cholesterol/GAS1 -0.1 0.2 -10000 0 -0.51 96 96
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.1 0.2 0.51 96 -10000 0 96
SMO/beta Arrestin2 -0.095 0.24 -10000 0 -0.48 126 126
SMO -0.11 0.25 -10000 0 -0.51 127 127
AKT1 -0.027 0.12 -10000 0 -0.54 3 3
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0 0.1 -10000 0 -0.81 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.1 0.25 -10000 0 -0.5 127 127
STIL -0.077 0.2 -10000 0 -0.59 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 82 82
DHH N/PTCH1 -0.099 0.22 -10000 0 -0.45 130 130
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
DHH 0.007 0.074 -10000 0 -0.81 4 4
PTHLH -0.16 0.36 -10000 0 -1.2 35 35
determination of left/right symmetry -0.1 0.25 -10000 0 -0.5 127 127
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.15 0.36 -10000 0 -1.1 35 35
IHH N/Hhip -0.38 0.4 -10000 0 -0.73 263 263
DHH N/Hhip -0.25 0.31 -10000 0 -0.63 195 195
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.1 0.25 -10000 0 -0.5 127 127
pancreas development -0.31 0.4 -10000 0 -0.81 195 195
HHAT 0.012 0.037 -10000 0 -0.81 1 1
PI3K -0.004 0.048 -10000 0 -0.62 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.33 -10000 0 -0.81 95 95
somite specification -0.1 0.25 -10000 0 -0.5 127 127
SHH Np/Cholesterol/PTCH1 -0.087 0.2 -10000 0 -0.42 86 86
SHH Np/Cholesterol/PTCH2 -0.087 0.19 -10000 0 -0.51 81 81
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.51 134 134
SHH 0.007 0.049 -10000 0 -0.62 1 1
catabolic process -0.11 0.25 -10000 0 -0.5 128 128
SMO/Vitamin D3 -0.091 0.22 -10000 0 -0.44 127 127
SHH Np/Cholesterol/Hhip -0.2 0.24 -10000 0 -0.5 195 195
LRP2 -0.21 0.37 -10000 0 -0.81 133 133
receptor-mediated endocytosis -0.2 0.23 -10000 0 -0.71 49 49
SHH Np/Cholesterol/BOC -0.014 0.073 -10000 0 -0.52 9 9
SHH Np/Cholesterol/CDO -0.15 0.23 -10000 0 -0.51 146 146
mesenchymal cell differentiation 0.2 0.24 0.5 195 -10000 0 195
mol:Vitamin D3 -0.086 0.2 -10000 0 -0.42 86 86
IHH N/PTCH2 -0.23 0.34 -10000 0 -0.66 181 181
CDON -0.23 0.38 -10000 0 -0.81 145 145
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.51 128 128
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.62 133 133
PTCH2 -0.12 0.3 -10000 0 -0.81 80 80
SHH Np/Cholesterol -0.006 0.035 -10000 0 -0.5 1 1
PTCH1 -0.11 0.25 -10000 0 -0.5 128 128
HHIP -0.31 0.4 -10000 0 -0.81 195 195
Nongenotropic Androgen 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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.5 210 210
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 211 211
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
HRAS 0.012 0.021 -10000 0 -0.31 2 2
SHBG/T-DHT -0.008 0.07 -10000 0 -0.56 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.16 0.23 -10000 0 -0.43 209 209
T-DHT/AR -0.27 0.31 -10000 0 -0.64 209 209
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 127 127
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.82 1 1
mol:GDP -0.26 0.3 -10000 0 -0.61 210 210
cell proliferation -0.2 0.28 -10000 0 -0.68 78 78
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
FOS -0.24 0.39 -10000 0 -0.89 127 127
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 92 92
MAPK3 -0.18 0.26 -10000 0 -0.6 84 84
MAPK1 -0.082 0.13 -10000 0 -0.31 75 75
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 127 127
cAMP biosynthetic process 0.016 0.074 -10000 0 -0.52 8 8
GNG2 0.012 0.037 -10000 0 -0.81 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 127 127
HRAS/GTP -0.2 0.23 -10000 0 -0.46 209 209
actin cytoskeleton reorganization -0.003 0.034 -10000 0 -0.44 3 3
SRC 0.012 0.015 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 127 127
PI3K -0.003 0.042 -10000 0 -0.55 3 3
apoptosis 0.16 0.25 0.52 127 -10000 0 127
T-DHT/AR/PELP1 -0.23 0.27 -10000 0 -0.55 209 209
HRAS/GDP -0.25 0.29 -10000 0 -0.58 210 210
CREB1 -0.17 0.27 -10000 0 -0.57 127 127
RAC1-CDC42/GTP -0.003 0.035 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.82 209 209
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.17 0.24 -10000 0 -0.45 209 209
RAC1-CDC42/GDP -0.23 0.27 -10000 0 -0.55 209 209
T-DHT/AR/PELP1/Src -0.21 0.25 -10000 0 -0.5 209 209
MAP2K2 -0.16 0.23 -10000 0 -0.43 209 209
T-DHT/AR/PELP1/Src/PI3K -0.13 0.18 -10000 0 -0.34 211 211
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG 0 0.1 -10000 0 -0.81 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.53 17 17
mol:T-DHT 0 0.001 0.001 75 -0.003 50 125
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.042 -10000 0 -0.63 2 2
Gi family/GTP -0.095 0.12 -10000 0 -0.46 18 18
CDC42 0.013 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.02 0.16 -9999 0 -0.81 20 20
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.41 0.26 -9999 0 -0.56 364 364
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.36 0.25 -9999 0 -0.51 364 364
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.092 0.28 -9999 0 -0.81 63 63
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.025 0.12 -9999 0 -0.62 20 20
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.021 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.42 0.26 -9999 0 -0.56 366 366
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.27 0.2 -9999 0 -0.68 18 18
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.31 0.22 -9999 0 -0.44 364 364
RELN -0.59 0.37 -9999 0 -0.81 360 360
PAFAH/LIS1 -0.044 0.19 -9999 0 -0.54 63 63
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.54 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.24 0.18 -9999 0 -0.34 371 371
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.29 0.22 -9999 0 -0.42 364 364
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.029 -9999 0 -0.31 4 4
PAFAH1B2 -0.002 0.11 -9999 0 -0.81 9 9
MAP1B/LIS1/Dynein heavy chain 0.027 0.003 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.27 0.17 -9999 0 -0.69 16 16
LRP8 -0.02 0.16 -9999 0 -0.81 20 20
NDEL1/Katanin 60 -0.27 0.2 -9999 0 -0.68 18 18
P39/CDK5 -0.32 0.23 -9999 0 -0.44 364 364
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.47 364 364
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.22 -9999 0 -0.48 366 366
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 370 370
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.079 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.57 86 86
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.88 204 204
PTGS2 -0.41 0.4 -9999 0 -0.84 188 188
JUNB 0.003 0.091 -9999 0 -0.81 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.82 112 112
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.032 0.12 -9999 0 -0.32 68 68
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.58 178 178
FOS -0.21 0.36 -9999 0 -0.82 127 127
IFNG -0.44 0.41 -9999 0 -0.86 201 201
AP-1/NFAT1-c-4 -0.52 0.52 -9999 0 -0.97 229 229
FASLG -0.42 0.39 -9999 0 -0.84 194 194
NFAT1-c-4/ICER1 -0.12 0.2 -9999 0 -0.5 94 94
IL2RA -0.41 0.39 -9999 0 -0.83 185 185
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.47 0.36 -9999 0 -0.76 268 268
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.5 96 96
IL4 -0.39 0.36 -9999 0 -0.8 183 183
IL2 -0.012 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.005 0.081 -9999 0 -0.33 27 27
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.015 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.17 0.3 0.68 121 -10000 0 121
KIRREL -0.073 0.24 -10000 0 -0.84 44 44
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 121 121
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 -0.13 0.24 -10000 0 -0.54 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.077 0.2 -10000 0 -0.41 121 121
FYN -0.11 0.24 -10000 0 -0.51 121 121
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 121 121
mol:DAG -0.13 0.24 -10000 0 -0.53 121 121
NPHS2 -0.017 0.052 -10000 0 -0.89 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.53 121 121
regulation of endocytosis -0.12 0.21 -10000 0 -0.47 121 121
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.54 121 121
establishment of cell polarity -0.17 0.3 -10000 0 -0.68 121 121
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 121 121
Nephrin/NEPH1/beta Arrestin2 -0.1 0.23 -10000 0 -0.48 121 121
NPHS1 -0.15 0.32 -10000 0 -0.82 92 92
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 121 121
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 121 121
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 121 121
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.25 -10000 0 -0.51 125 125
cytoskeleton organization -0.1 0.26 -10000 0 -0.53 121 121
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.52 121 121
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 121 121
Glypican 1 network

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.001 0.025 -10000 0 -0.54 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.025 -10000 0 -0.54 1 1
LAMA1 -0.048 0.22 -10000 0 -0.8 37 37
PRNP 0.012 0.037 -10000 0 -0.81 1 1
GPC1/SLIT2 -0.095 0.22 -10000 0 -0.62 74 74
SMAD2 0.028 0.048 -10000 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -10000 0 -0.55 1 1
GPC1/Laminin alpha1 -0.046 0.16 -10000 0 -0.62 36 36
TDGF1 -0.34 0.41 -10000 0 -0.81 209 209
CRIPTO/GPC1 -0.26 0.31 -10000 0 -0.62 209 209
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.28 -10000 0 -0.54 209 209
FLT1 0.012 0.037 -10000 0 -0.81 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.048 -10000 0 -0.54 3 3
SERPINC1 0.006 0.046 -10000 0 -0.31 10 10
FYN -0.21 0.28 -10000 0 -0.54 209 209
FGR -0.21 0.28 -10000 0 -0.54 209 209
positive regulation of MAPKKK cascade -0.28 0.31 -10000 0 -0.61 211 211
SLIT2 -0.11 0.3 -10000 0 -0.79 77 77
GPC1/NRG -0.058 0.18 -10000 0 -0.62 45 45
NRG1 -0.063 0.24 -10000 0 -0.79 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.058 -10000 0 -0.7 3 3
LYN -0.21 0.28 -10000 0 -0.54 209 209
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.001 0.025 -10000 0 -0.54 1 1
BMP signaling pathway -0.013 0.015 0.31 1 -10000 0 1
SRC -0.21 0.28 -10000 0 -0.54 209 209
TGFBR1 0.006 0.05 -10000 0 -0.31 12 12
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.24 0.36 -10000 0 -0.68 185 185
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.006 0.05 -10000 0 -0.31 12 12
VEGFA 0.008 0.064 -10000 0 -0.81 3 3
BLK -0.38 0.37 -10000 0 -0.66 284 284
HCK -0.22 0.28 -10000 0 -0.55 209 209
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.037 -10000 0 -0.81 1 1
VEGFR1 homodimer 0.012 0.037 -10000 0 -0.81 1 1
TGFBR2 0.008 0.064 -10000 0 -0.81 3 3
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.004 0.029 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.19 0.27 -10000 0 -0.62 134 134
LCK -0.22 0.28 -10000 0 -0.54 214 214
neuron differentiation -0.058 0.18 -10000 0 -0.62 45 45
PrPc/Cu2+ -0.001 0.028 -10000 0 -0.63 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.064 -10000 0 -0.81 3 3
HIF-1-alpha transcription factor network

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
PKM2 -0.19 0.42 -9999 0 -0.9 70 70
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.81 112 112
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.19 0.42 -9999 0 -0.9 70 70
AP1 -0.28 0.45 -9999 0 -0.92 151 151
ABCG2 -0.19 0.43 -9999 0 -0.92 71 71
HIF1A -0.009 0.068 -9999 0 -10000 0 0
TFF3 -0.57 0.51 -9999 0 -1 207 207
GATA2 0.014 0.015 -9999 0 -0.31 1 1
AKT1 -0.038 0.1 -9999 0 -10000 0 0
response to hypoxia -0.059 0.11 -9999 0 -0.23 63 63
MCL1 -0.19 0.42 -9999 0 -0.9 70 70
NDRG1 -0.19 0.42 -9999 0 -0.9 70 70
SERPINE1 -0.2 0.43 -9999 0 -0.9 76 76
FECH -0.19 0.42 -9999 0 -0.9 70 70
FURIN -0.19 0.42 -9999 0 -0.9 70 70
NCOA2 -0.066 0.24 -9999 0 -0.81 48 48
EP300 -0.062 0.18 -9999 0 -0.32 133 133
HMOX1 -0.19 0.42 -9999 0 -0.9 72 72
BHLHE40 -0.2 0.42 -9999 0 -0.91 72 72
BHLHE41 -0.19 0.42 -9999 0 -0.91 71 71
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.037 -9999 0 -10000 0 0
ENG 0.041 0.092 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.81 112 112
RORA -0.19 0.42 -9999 0 -0.91 70 70
ABCB1 -0.076 0.19 -9999 0 -1.4 8 8
TFRC -0.19 0.42 -9999 0 -0.91 71 71
CXCR4 -0.19 0.42 -9999 0 -0.9 70 70
TF -0.24 0.49 -9999 0 -1 92 92
CITED2 -0.22 0.47 -9999 0 -1 83 83
HIF1A/ARNT -0.29 0.38 -9999 0 -1 72 72
LDHA -0.039 0.05 -9999 0 -10000 0 0
ETS1 -0.19 0.42 -9999 0 -0.9 70 70
PGK1 -0.19 0.42 -9999 0 -0.9 70 70
NOS2 -0.2 0.43 -9999 0 -0.9 80 80
ITGB2 -0.2 0.42 -9999 0 -0.92 71 71
ALDOA -0.19 0.42 -9999 0 -0.9 70 70
Cbp/p300/CITED2 -0.32 0.51 -9999 0 -1 130 130
FOS -0.2 0.36 -9999 0 -0.81 127 127
HK2 -0.19 0.42 -9999 0 -0.9 72 72
SP1 0.022 0.007 -9999 0 -10000 0 0
GCK -0.38 0.71 -9999 0 -1.5 136 136
HK1 -0.19 0.42 -9999 0 -0.9 70 70
NPM1 -0.19 0.42 -9999 0 -0.9 70 70
EGLN1 -0.19 0.42 -9999 0 -0.9 71 71
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.19 0.42 -9999 0 -0.9 70 70
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.31 -9999 0 -0.73 64 64
IGFBP1 -0.2 0.42 -9999 0 -0.9 76 76
VEGFA -0.16 0.38 -9999 0 -0.75 77 77
HIF1A/JAB1 -0.011 0.021 -9999 0 -10000 0 0
CP -0.35 0.55 -9999 0 -1 152 152
CXCL12 -0.23 0.48 -9999 0 -1 90 90
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.19 0.42 -9999 0 -0.9 70 70
EGLN3 -0.2 0.44 -9999 0 -0.93 76 76
CA9 -0.2 0.42 -9999 0 -0.91 74 74
TERT -0.2 0.42 -9999 0 -0.91 71 71
ENO1 -0.19 0.42 -9999 0 -0.9 70 70
PFKL -0.19 0.42 -9999 0 -0.9 70 70
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -0.88 97 97
ARNT -0.01 0.067 -9999 0 -10000 0 0
HNF4A -0.025 0.064 -9999 0 -0.35 10 10
ADFP -0.2 0.41 -9999 0 -0.91 70 70
SLC2A1 -0.15 0.38 -9999 0 -0.74 78 78
LEP -0.2 0.42 -9999 0 -0.92 70 70
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.83 118 118
EPO -0.14 0.33 -9999 0 -0.9 32 32
CREBBP -0.062 0.18 -9999 0 -0.32 133 133
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.81 109 109
PFKFB3 -0.19 0.42 -9999 0 -0.9 71 71
NT5E -0.2 0.43 -9999 0 -0.92 70 70
Endothelins

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
AKT1 -0.052 0.14 -9999 0 -0.56 11 11
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.7 63 63
EDN1 -0.044 0.12 -9999 0 -0.71 8 8
EDN3 -0.39 0.41 -9999 0 -0.81 244 244
EDN2 -0.014 0.11 -9999 0 -0.4 32 32
HRAS/GDP -0.1 0.24 -9999 0 -0.54 80 80
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.18 -9999 0 -0.4 86 86
ADCY4 -0.097 0.19 -9999 0 -0.5 72 72
ADCY5 -0.16 0.25 -9999 0 -0.55 118 118
ADCY6 -0.097 0.19 -9999 0 -0.5 72 72
ADCY7 -0.097 0.19 -9999 0 -0.5 72 72
ADCY1 -0.1 0.21 -9999 0 -0.53 74 74
ADCY2 -0.14 0.24 -9999 0 -0.55 105 105
ADCY3 -0.097 0.19 -9999 0 -0.5 72 72
ADCY8 -0.2 0.21 -9999 0 -0.55 97 97
ADCY9 -0.097 0.19 -9999 0 -0.5 72 72
arachidonic acid secretion -0.17 0.32 -9999 0 -0.65 133 133
ETB receptor/Endothelin-1/Gq/GTP -0.097 0.22 -9999 0 -0.44 111 111
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.018 0.16 -9999 0 -0.56 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.086 0.22 -9999 0 -0.53 72 72
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.069 0.17 -9999 0 -0.51 36 36
EDNRB 0.003 0.094 -9999 0 -0.75 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.15 0.24 -9999 0 -0.64 52 52
CYSLTR1 -0.063 0.18 -9999 0 -0.77 17 17
SLC9A1 -0.022 0.075 -9999 0 -0.32 6 6
mol:GDP -0.12 0.26 -9999 0 -0.56 92 92
SLC9A3 -0.049 0.19 -9999 0 -0.8 21 21
RAF1 -0.15 0.3 -9999 0 -0.57 137 137
JUN -0.28 0.52 -9999 0 -1.2 121 121
JAK2 -0.054 0.15 -9999 0 -0.57 13 13
mol:IP3 -0.11 0.23 -9999 0 -0.49 107 107
ETA receptor/Endothelin-1 -0.039 0.2 -9999 0 -0.55 19 19
PLCB1 0.009 0.038 -9999 0 -0.82 1 1
PLCB2 0.004 0.047 -9999 0 -0.32 10 10
ETA receptor/Endothelin-3 -0.32 0.33 -9999 0 -0.66 243 243
FOS -0.25 0.47 -9999 0 -1 127 127
Gai/GDP -0.002 0.13 -9999 0 -0.64 17 17
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.24 -9999 0 -0.6 56 56
BCAR1 0.013 0.001 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 107 107
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.094 0.28 -9999 0 -0.81 64 64
Gs family/GDP -0.19 0.25 -9999 0 -0.57 120 120
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.46 98 98
MAPK14 -0.065 0.18 -9999 0 -0.44 45 45
TRPC6 -0.14 0.3 -9999 0 -0.74 62 62
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.077 0.19 -9999 0 -0.4 85 85
ETB receptor/Endothelin-2 -0.026 0.1 -9999 0 -0.63 12 12
ETB receptor/Endothelin-3 -0.31 0.32 -9999 0 -0.63 245 245
ETB receptor/Endothelin-1 -0.021 0.12 -9999 0 -0.62 13 13
MAPK3 -0.23 0.43 -9999 0 -0.9 133 133
MAPK1 -0.23 0.43 -9999 0 -0.9 132 132
Rac1/GDP -0.1 0.24 -9999 0 -0.53 80 80
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.55 77 77
MAPK8 -0.18 0.35 -9999 0 -0.66 124 124
SRC 0.013 0.015 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.008 0.078 -9999 0 -0.29 25 25
p130Cas/CRK/Src/PYK2 -0.13 0.3 -9999 0 -0.59 107 107
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.54 78 78
COL1A2 -0.039 0.17 -9999 0 -0.64 13 13
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.54 11 11
mol:DAG -0.11 0.23 -9999 0 -0.49 107 107
MAP2K2 -0.18 0.35 -9999 0 -0.7 136 136
MAP2K1 -0.18 0.35 -9999 0 -0.7 137 137
EDNRA -0.038 0.098 -9999 0 -0.52 5 5
positive regulation of muscle contraction -0.036 0.12 -9999 0 -0.52 9 9
Gq family/GDP -0.19 0.29 -9999 0 -0.66 118 118
HRAS/GTP -0.13 0.26 -9999 0 -0.57 96 96
PRKCH -0.1 0.22 -9999 0 -0.51 86 86
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.25 -9999 0 -0.55 96 96
PRKCB -0.12 0.23 -9999 0 -0.52 91 91
PRKCE -0.11 0.24 -9999 0 -0.53 86 86
PRKCD -0.1 0.22 -9999 0 -0.51 85 85
PRKCG -0.11 0.23 -9999 0 -0.52 86 86
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 127 127
PRKCQ -0.11 0.23 -9999 0 -0.52 89 89
PLA2G4A -0.19 0.36 -9999 0 -0.72 133 133
GNA14 -0.19 0.36 -9999 0 -0.82 118 118
GNA15 -0.014 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.006 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.018 0.16 -9999 0 -0.54 10 10
MMP1 -0.09 0.15 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.13 0.23 -10000 0 -0.45 159 159
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.021 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.52 113 113
AKT1 -0.09 0.21 -10000 0 -0.41 114 114
BAD -0.076 0.2 -10000 0 -0.7 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.23 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.45 159 159
RAF1 -0.067 0.19 -10000 0 -0.65 16 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.42 159 159
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.25 -10000 0 -0.49 159 159
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
RPS6KB1 -0.09 0.21 -10000 0 -0.77 16 16
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.16 -10000 0 -0.53 16 16
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.72 14 14
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.099 0.17 -10000 0 -0.42 113 113
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.45 159 159
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.43 113 113
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.35 -10000 0 -0.81 119 119
IRS2/Crk -0.11 0.22 -10000 0 -0.42 159 159
PI3K -0.14 0.22 -10000 0 -0.43 159 159
apoptosis 0.058 0.18 0.57 16 -10000 0 16
HRAS/GDP -0.001 0.013 -10000 0 -10000 0 0
PRKCD -0.1 0.24 -10000 0 -0.53 113 113
RAF1/14-3-3 E -0.049 0.17 -10000 0 -0.53 16 16
BAD/14-3-3 -0.063 0.19 -10000 0 -0.62 16 16
PRKCZ -0.09 0.21 -10000 0 -0.41 114 114
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.63 16 16
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.25 -10000 0 -0.56 113 113
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.23 -10000 0 -0.45 159 159
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.45 159 159
IRS1 -0.14 0.25 -10000 0 -0.49 159 159
IRS2 -0.13 0.23 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1 -0.16 0.27 -10000 0 -0.65 113 113
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.44 114 114
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.24 -10000 0 -0.53 114 114
SHC1 0.013 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.045 0.093 -10000 0 -10000 0 0
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.014 0.014 -10000 0 -10000 0 0
TBX21 -0.15 0.28 -10000 0 -0.76 58 58
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.3 12 12
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.091 -10000 0 -0.81 6 6
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.33 53 -0.49 6 59
PRL -0.086 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.24 0.31 0.58 157 -0.49 23 180
RELA -0.029 0.087 -10000 0 -10000 0 0
FGG 0.24 0.19 0.51 112 -10000 0 112
GR beta/TIF2 0.078 0.24 0.35 71 -0.56 48 119
IFNG -0.49 0.51 -10000 0 -1.1 154 154
apoptosis 0.034 0.24 0.49 69 -0.51 5 74
CREB1 0.012 0.023 -10000 0 -10000 0 0
histone acetylation -0.068 0.17 -10000 0 -0.38 76 76
BGLAP -0.096 0.15 -10000 0 -0.53 12 12
GR/PKAc 0.13 0.1 0.34 31 -0.4 1 32
NF kappa B1 p50/RelA -0.061 0.16 -10000 0 -0.45 27 27
SMARCD1 0.014 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.095 0.27 104 -10000 0 104
GATA3 -0.026 0.18 -10000 0 -0.78 27 27
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.49 74 74
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.24 0.5 51 -0.73 5 56
CSN2 0.2 0.14 0.41 104 -10000 0 104
BRG1/BAF155/BAF170/BAF60A 0.022 0.048 -10000 0 -0.34 2 2
NFATC1 0.001 0.11 -10000 0 -0.81 9 9
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.025 0.052 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.044 0.16 0.32 21 -0.46 17 38
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.078 0.45 0.48 53 -0.88 107 160
JUN -0.33 0.3 -10000 0 -0.68 181 181
IL4 -0.12 0.18 -10000 0 -0.68 21 21
CDK5R1 0.011 0.027 -10000 0 -0.32 3 3
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.36 0.41 -10000 0 -0.81 187 187
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 29 -0.47 5 34
cortisol/GR alpha (monomer) 0.36 0.3 0.68 187 -10000 0 187
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.24 0.35 -10000 0 -0.84 127 127
AP-1/NFAT1-c-4 -0.55 0.48 -10000 0 -0.95 241 241
AFP -0.22 0.22 -10000 0 -0.63 67 67
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.47 59 -10000 0 59
TP53 0.033 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.47 0.37 -10000 0 -0.8 200 200
KRT14 -0.23 0.17 -10000 0 -0.6 22 22
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.065 -10000 0 -0.28 1 1
HDAC1 0.011 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.013 -10000 0 -10000 0 0
AP-1 -0.55 0.48 -10000 0 -0.96 241 241
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.04 -10000 0 -0.82 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.53 0.52 -10000 0 -1 196 196
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.3 12 12
CGA -0.12 0.16 -10000 0 -0.56 18 18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.36 223 -10000 0 223
MAPK3 0.015 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.24 0.26 -10000 0 -0.68 88 88
NFKB1 -0.031 0.096 -10000 0 -0.94 1 1
MAPK8 -0.19 0.21 -10000 0 -0.48 118 118
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.029 0.25 0.5 68 -0.53 5 73
BAX 0.029 0.034 -10000 0 -10000 0 0
POMC -0.54 0.69 -10000 0 -1.5 138 138
EP300 0.065 0.065 -10000 0 -0.28 1 1
cortisol/GR alpha (dimer)/p53 0.32 0.24 0.59 177 -10000 0 177
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.072 0.24 31 -10000 0 31
SGK1 0.1 0.22 -10000 0 -1.4 10 10
IL13 -0.29 0.25 -10000 0 -0.7 89 89
IL6 -0.37 0.52 -10000 0 -1.2 124 124
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.66 60 60
IL2 -0.36 0.27 -10000 0 -0.69 142 142
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.037 -10000 0 -0.81 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.26 0.32 -10000 0 -0.76 94 94
CDK5R1/CDK5 0.007 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.023 0.12 -10000 0 -0.63 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.56 167 -10000 0 167
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.4 119 -0.39 1 120
NF kappa B1 p50/RelA/Cbp 0.028 0.16 -10000 0 -0.45 10 10
JUN (dimer) -0.33 0.3 -10000 0 -0.67 181 181
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.41 -10000 0 -1 94 94
NR3C1 0.21 0.19 0.48 125 -10000 0 125
NR4A1 -0.31 0.41 -10000 0 -0.75 212 212
TIF2/SUV420H1 -0.061 0.18 -10000 0 -0.62 48 48
MAPKKK cascade 0.034 0.24 0.49 69 -0.51 5 74
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.58 178 -10000 0 178
PBX1 0.014 0.004 -10000 0 -10000 0 0
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.33 0.5 -10000 0 -1.2 104 104
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.4 116 -0.4 1 117
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.56 167 -10000 0 167
mol:cortisol 0.2 0.19 0.4 195 -10000 0 195
MMP1 -0.21 0.15 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.82 3 3
EFNB1 0.001 0.12 -10000 0 -0.63 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.24 0.24 -10000 0 -0.52 201 201
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
neuron projection morphogenesis -0.23 0.23 -10000 0 -0.49 201 201
Ephrin B1/EPHB1-2/Tiam1 -0.26 0.26 -10000 0 -0.56 201 201
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.005 0.088 -10000 0 -0.78 6 6
YES1 -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.18 0.24 -10000 0 -0.46 201 201
PI3K 0.003 0.12 -10000 0 -1 6 6
mol:GDP -0.25 0.26 -10000 0 -0.55 201 201
ITGA2B -0.075 0.26 -10000 0 -0.81 53 53
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.01 0.11 -10000 0 -1 6 6
MAP3K7 -0.012 0.091 -10000 0 -0.83 6 6
FGR -0.012 0.11 -10000 0 -1 6 6
TIAM1 -0.17 0.16 -10000 0 -0.81 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.044 0.2 -10000 0 -0.53 66 66
LYN -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.014 0.1 -10000 0 -0.96 6 6
Ephrin B1/EPHB1-2 -0.019 0.098 -10000 0 -0.89 6 6
SRC -0.012 0.11 -10000 0 -1 6 6
ITGB3 -0.012 0.14 -10000 0 -0.81 15 15
EPHB1 -0.3 0.4 -10000 0 -0.82 186 186
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.084 0.23 -10000 0 -0.67 62 62
BLK -0.066 0.14 -10000 0 -1.1 6 6
HCK -0.013 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.18 0.24 0.46 201 -10000 0 201
MAPK8 0.003 0.13 -10000 0 -0.77 12 12
Ephrin B1/EPHB1-2/RGS3 -0.18 0.24 -10000 0 -0.46 201 201
endothelial cell migration -0.006 0.08 -10000 0 -0.72 6 6
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.005 0.1 -10000 0 -0.93 6 6
regulation of focal adhesion formation 0.18 0.24 0.46 201 -10000 0 201
chemotaxis 0.18 0.24 0.46 201 -10000 0 201
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
Rac1/GTP -0.24 0.24 -10000 0 -0.51 201 201
angiogenesis -0.019 0.097 -10000 0 -0.88 6 6
LCK -0.015 0.12 -10000 0 -1 6 6
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 78 78
FYN -0.11 0.35 -10000 0 -0.79 86 86
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.66 89 89
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.056 0.22 -10000 0 -0.47 90 90
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.051 -10000 0 -0.15 46 46
MAP3K8 0.002 0.098 -10000 0 -0.81 7 7
mol:Ca2+ -0.031 0.05 -10000 0 -0.12 108 108
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.33 -10000 0 -0.73 92 92
TRPV6 -0.17 0.34 -10000 0 -0.79 110 110
CD28 -0.045 0.19 -10000 0 -0.59 48 48
SHC1 -0.12 0.34 -10000 0 -0.8 85 85
receptor internalization -0.14 0.38 -10000 0 -0.83 95 95
PRF1 -0.12 0.35 -10000 0 -0.9 70 70
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.038 0.18 -10000 0 -0.38 89 89
LAT -0.12 0.35 -10000 0 -0.82 85 85
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.093 0.27 -10000 0 -0.69 75 75
CD3E -0.068 0.24 -10000 0 -0.74 54 54
CD3G -0.14 0.32 -10000 0 -0.78 99 99
RASGRP2 0 0.031 -10000 0 -0.14 10 10
RASGRP1 -0.053 0.22 -10000 0 -0.46 97 97
HLA-A 0.011 0.021 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.068 -10000 0 -0.12 71 71
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.091 -10000 0 -0.26 65 65
PRKCA -0.06 0.13 -10000 0 -0.29 101 101
GRAP2 -0.045 0.21 -10000 0 -0.75 38 38
mol:IP3 -0.053 0.23 0.27 85 -0.46 89 174
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.97 82 82
ORAI1 0.087 0.16 0.39 103 -10000 0 103
CSK -0.12 0.35 -10000 0 -0.83 85 85
B7 family/CD28 -0.2 0.35 -10000 0 -0.75 115 115
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.42 -10000 0 -0.94 93 93
PTPN6 -0.12 0.36 -10000 0 -0.83 85 85
VAV1 -0.13 0.35 -10000 0 -0.79 90 90
Monovalent TCR/CD3 -0.16 0.4 -10000 0 -0.72 124 124
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.82 89 89
PAG1 -0.12 0.35 -10000 0 -0.83 85 85
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.42 -10000 0 -0.94 92 92
CD80 -0.071 0.25 -10000 0 -0.8 51 51
CD86 -0.009 0.1 -10000 0 -0.41 26 26
PDK1/CARD11/BCL10/MALT1 -0.07 0.11 -10000 0 -0.3 70 70
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.29 -10000 0 -0.59 115 115
CD8A -0.052 0.22 -10000 0 -0.81 39 39
CD8B -0.091 0.27 -10000 0 -0.72 71 71
PTPRC -0.035 0.18 -10000 0 -0.59 39 39
PDK1/PKC theta -0.071 0.27 -10000 0 -0.59 89 89
CSK/PAG1 -0.11 0.34 -10000 0 -0.8 84 84
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.78 91 91
STIM1 0.047 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.007 0.091 -10000 0 -0.18 57 57
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.94 93 93
mol:DAG -0.072 0.18 -10000 0 -0.41 90 90
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.024 0.16 -10000 0 -0.62 30 30
cytotoxic T cell degranulation -0.11 0.33 -10000 0 -0.85 70 70
RAP1A/GTP -0.003 0.009 -10000 0 -0.068 6 6
mol:PI-3-4-5-P3 -0.076 0.26 -10000 0 -0.57 92 92
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.083 0.29 0.3 75 -0.62 89 164
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.026 0.17 -10000 0 -0.62 31 31
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.62 90 90
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.053 -10000 0 -0.81 2 2
CD8 heterodimer -0.11 0.29 -10000 0 -0.75 77 77
CARD11 -0.07 0.17 -10000 0 -0.36 109 109
PRKCB -0.059 0.13 -10000 0 -0.3 89 89
PRKCE -0.053 0.12 -10000 0 -0.29 88 88
PRKCQ -0.094 0.31 -10000 0 -0.69 89 89
LCP2 0.008 0.043 -10000 0 -0.31 9 9
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.042 0.18 -10000 0 -0.4 90 90
IKK complex 0.013 0.068 -10000 0 -0.11 60 60
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.018 0.14 -10000 0 -0.3 72 72
PDPK1 -0.049 0.21 -10000 0 -0.45 88 88
TCR/CD3/MHC I/CD8/Fyn -0.17 0.45 -10000 0 -1.1 86 86
IL23-mediated signaling events

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
CCL2 -0.21 0.55 -10000 0 -1.3 81 81
IL23A -0.22 0.56 -10000 0 -1.3 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.29 0.46 -10000 0 -1.2 91 91
positive regulation of T cell mediated cytotoxicity -0.24 0.61 -10000 0 -1.3 96 96
ITGA3 -0.19 0.51 -10000 0 -1.1 87 87
IL17F -0.1 0.34 -10000 0 -0.74 73 73
IL12B -0.003 0.11 -10000 0 -0.58 12 12
STAT1 (dimer) -0.23 0.58 -10000 0 -1.3 90 90
CD4 -0.19 0.5 -10000 0 -1.1 85 85
IL23 -0.22 0.53 -10000 0 -1.2 83 83
IL23R -0.003 0.099 -10000 0 -10000 0 0
IL1B -0.23 0.58 -10000 0 -1.3 90 90
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.19 0.5 -10000 0 -1.1 85 85
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.025 0.14 -10000 0 -0.81 11 11
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.028 0.18 -10000 0 -0.78 25 25
IL12RB1 -0.024 0.13 -10000 0 -0.39 48 48
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
IL12Rbeta1/TYK2 -0.011 0.1 -10000 0 -0.67 6 6
IL23R/JAK2 0 0.13 -10000 0 -0.63 2 2
positive regulation of chronic inflammatory response -0.24 0.61 -10000 0 -1.3 96 96
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.019 0.061 -10000 0 -0.84 2 2
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.5 -10000 0 -1.1 84 84
ALOX12B -0.21 0.51 -10000 0 -1.1 87 87
CXCL1 -0.22 0.53 -10000 0 -1.2 85 85
T cell proliferation -0.24 0.61 -10000 0 -1.3 96 96
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.058 0.28 -10000 0 -0.58 61 61
PI3K -0.3 0.48 -10000 0 -1.2 90 90
IFNG -0.02 0.055 -10000 0 -0.13 73 73
STAT3 (dimer) -0.28 0.44 -10000 0 -1.1 87 87
IL18R1 -0.03 0.14 -10000 0 -0.42 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.095 0.33 -10000 0 -0.73 62 62
IL18/IL18R -0.067 0.18 -10000 0 -0.56 49 49
macrophage activation -0.014 0.018 -10000 0 -0.044 88 88
TNF -0.26 0.62 -10000 0 -1.3 103 103
STAT3/STAT4 -0.31 0.49 -10000 0 -1.2 91 91
STAT4 (dimer) -0.24 0.58 -10000 0 -1.3 91 91
IL18 -0.039 0.15 -10000 0 -0.41 60 60
IL19 -0.19 0.5 -10000 0 -1.1 86 86
STAT5A (dimer) -0.23 0.57 -10000 0 -1.3 93 93
STAT1 0.006 0.05 -10000 0 -0.31 12 12
SOCS3 -0.026 0.18 -10000 0 -0.79 24 24
CXCL9 -0.3 0.64 -10000 0 -1.4 112 112
MPO -0.2 0.51 -10000 0 -1.1 87 87
positive regulation of humoral immune response -0.24 0.61 -10000 0 -1.3 96 96
IL23/IL23R/JAK2/TYK2 -0.28 0.74 -10000 0 -1.5 96 96
IL6 -0.31 0.64 -10000 0 -1.4 118 118
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.23 0.57 -10000 0 -1.3 90 90
keratinocyte proliferation -0.24 0.61 -10000 0 -1.3 96 96
NOS2 -0.2 0.5 -10000 0 -1.1 89 89
Glypican 2 network

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
MDK -0.087 0.15 -9999 0 -0.31 152 152
GPC2 -0.009 0.082 -9999 0 -0.31 34 34
GPC2/Midkine -0.076 0.11 -9999 0 -0.41 13 13
neuron projection morphogenesis -0.076 0.11 -9999 0 -0.41 13 13
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.26 0.32 -9999 0 -0.59 217 217
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.047 0.21 -9999 0 -0.69 42 42
SMAD9 -0.22 0.28 -9999 0 -0.59 162 162
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.092 0.2 -9999 0 -0.55 29 29
BMP7/USAG1 -0.32 0.31 -9999 0 -0.62 254 254
SMAD5/SKI -0.081 0.19 -9999 0 -0.52 28 28
SMAD1 0.019 0.044 -9999 0 -10000 0 0
BMP2 -0.017 0.16 -9999 0 -0.81 18 18
SMAD1/SMAD1/SMAD4 -0.001 0.001 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.39 -9999 0 -0.81 161 161
BMPR1A-1B/BAMBI -0.18 0.26 -9999 0 -0.55 161 161
AHSG -0.018 0.086 -9999 0 -0.31 39 39
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.037 0.13 -9999 0 -0.55 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.073 0.19 -9999 0 -0.62 31 31
BMP2-4 (homodimer) -0.042 0.15 -9999 0 -0.62 31 31
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 161 161
RGMA -0.017 0.16 -9999 0 -0.81 18 18
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.085 0.18 -9999 0 -0.56 29 29
BMP2-4/USAG1 -0.31 0.3 -9999 0 -0.57 270 270
SMAD6/SMURF1/SMAD5 -0.081 0.19 -9999 0 -0.52 28 28
SOSTDC1 -0.41 0.41 -9999 0 -0.81 254 254
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 161 161
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.011 0.029 -9999 0 -0.31 4 4
HFE2 0.001 0.032 -9999 0 -0.31 5 5
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.047 0.15 -9999 0 -0.55 40 40
SMAD5/SMAD5/SMAD4 -0.081 0.19 -9999 0 -0.52 28 28
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.091 0.14 -9999 0 -0.48 29 29
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.017 0.058 -9999 0 -0.39 1 1
SMAD1/SKI 0.026 0.042 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.048 0.14 -9999 0 -0.56 31 31
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.35 -9999 0 -0.72 140 140
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.007 0.059 -9999 0 -0.54 6 6
BMPR1A-1B (homodimer) -0.2 0.29 -9999 0 -0.62 161 161
CHRDL1 -0.57 0.38 -9999 0 -0.81 350 350
ENDOFIN/SMAD1 0.026 0.042 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.08 -9999 0 -0.36 20 20
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.57 356 356
BMP2-4/GREM1 -0.17 0.27 -9999 0 -0.59 132 132
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.27 -9999 0 -0.55 162 162
SMAD1/SMAD6 0.026 0.042 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.011 0.029 -9999 0 -0.31 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.064 0.16 -9999 0 -0.49 29 29
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 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 0.003 0.091 -9999 0 -0.81 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.31 -9999 0 -0.78 85 85
CHRD -0.003 0.12 -9999 0 -0.81 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.09 0.19 -9999 0 -0.6 29 29
BMP4 -0.013 0.14 -9999 0 -0.64 20 20
FST -0.19 0.35 -9999 0 -0.78 127 127
BMP2-4/NOG -0.074 0.18 -9999 0 -0.55 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.21 -9999 0 -0.46 161 161
Coregulation of Androgen receptor activity

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
NRIP1 -0.015 0.064 -10000 0 -0.35 14 14
SVIL -0.007 0.031 -10000 0 -10000 0 0
ZNF318 0.062 0.092 -10000 0 -0.81 1 1
JMJD2C -0.064 0.069 -10000 0 -0.12 282 282
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.61 209 209
CARM1 0.012 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.024 -10000 0 -10000 0 0
AKT1 0.026 0.02 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.052 0.13 -10000 0 -0.79 7 7
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.06 -10000 0 -0.81 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.069 0.24 -10000 0 -0.82 48 48
NCOA6 -0.007 0.047 -10000 0 -0.81 1 1
DNA-PK 0.059 0.084 0.26 1 -10000 0 1
NCOA4 0.012 0.003 -10000 0 -10000 0 0
PIAS3 -0.002 0.024 -10000 0 -10000 0 0
cell proliferation -0.011 0.15 -10000 0 -1 7 7
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.047 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.33 -10000 0 -0.66 217 217
FHL2 -0.15 0.36 -10000 0 -1.3 38 38
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.002 0.037 -10000 0 -0.12 36 36
CDK6 0.01 0.064 -10000 0 -0.81 3 3
TGFB1I1 -0.007 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.29 0.3 -10000 0 -0.62 212 212
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.31 -10000 0 -0.63 235 235
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.046 0.051 -10000 0 -10000 0 0
BRCA1 -0.007 0.031 -10000 0 -10000 0 0
TCF4 0.036 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.16 -10000 0 -0.31 136 136
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1 6 6
KLK3 -0.44 0.71 -10000 0 -1.6 142 142
TMF1 0.006 0.053 -10000 0 -0.81 2 2
HNRNPA1 0.032 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 142 142
APPL1 0.052 0.043 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.27 0.29 -10000 0 -0.6 209 209
AR -0.38 0.42 -10000 0 -0.86 209 209
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.032 0.028 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.025 0.018 -10000 0 -10000 0 0
PA2G4 0.037 0.036 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.56 209 209
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.29 -10000 0 -0.61 211 211
LATS2 0.03 0.047 -10000 0 -0.81 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 209 209
Cyclin D3/CDK11 p58 0.001 0.004 -10000 0 -10000 0 0
VAV3 -0.012 0.093 -10000 0 -0.82 6 6
KLK2 -0.77 0.62 -10000 0 -1.3 281 281
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.66 216 216
TMPRSS2 -0.18 0.31 -10000 0 -1.3 34 34
CCND1 0.001 0.05 -10000 0 -0.31 12 12
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.041 -10000 0 -0.082 165 165
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.61 213 213
CMTM2 0.014 0.026 -10000 0 -0.31 3 3
SNURF -0.038 0.2 -10000 0 -0.81 30 30
ZMIZ1 -0.013 0.051 -10000 0 -0.8 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.032 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
Arf6 signaling events

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.47 12 12
EGFR 0.005 0.083 -9999 0 -0.81 5 5
EPHA2 0.011 0.025 -9999 0 -0.31 3 3
USP6 0.011 0.025 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.1 0.23 -9999 0 -0.62 77 77
ARRB2 -0.044 0.15 -9999 0 -0.44 61 61
mol:GTP 0.02 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.037 -9999 0 -0.81 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.01 0.053 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 78 78
somatostatin receptor activity 0 0 -9999 0 -0.001 135 135
ARAP2 0.01 0.053 -9999 0 -0.81 2 2
mol:GDP -0.12 0.14 -9999 0 -0.31 135 135
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 70 70
ITGA2B -0.075 0.26 -9999 0 -0.81 53 53
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.16 0.24 -9999 0 -0.68 74 74
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.32 137 137
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.086 0.2 -9999 0 -0.54 77 77
ADRB2 -0.007 0.13 -9999 0 -0.81 12 12
receptor agonist activity 0 0 -9999 0 0 144 144
actin filament binding 0 0 -9999 0 -0.001 134 134
SRC 0.013 0.015 -9999 0 -10000 0 0
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 118 118
ARF6/GDP 0 0.068 -9999 0 -0.33 2 2
ARF6/GDP/GULP/ACAP1 -0.18 0.2 -9999 0 -0.49 116 116
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.067 0.18 -9999 0 -0.54 62 62
ACAP1 -0.001 0.078 -9999 0 -0.36 19 19
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.079 0.22 -9999 0 -0.67 61 61
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.81 74 74
CYTH3 0.009 0.041 -9999 0 -0.64 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 112 112
endosomal lumen acidification 0 0 -9999 0 -0.001 142 142
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.32 -9999 0 -0.81 89 89
GNAQ/ARNO 0.009 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 21 21
MET -0.1 0.16 -9999 0 -0.31 179 179
GNA14 -0.18 0.35 -9999 0 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 127 127
GNA11 -0.004 0.12 -9999 0 -0.81 10 10
LHCGR -0.098 0.27 -9999 0 -0.76 68 68
AGTR1 -0.32 0.4 -9999 0 -0.81 200 200
desensitization of G-protein coupled receptor protein signaling pathway -0.078 0.22 -9999 0 -0.67 61 61
IPCEF1/ARNO -0.057 0.16 -9999 0 -0.43 77 77
alphaIIb/beta3 Integrin -0.084 0.23 -9999 0 -0.67 62 62
Syndecan-1-mediated signaling events

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
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CCL5 -0.047 0.21 -9999 0 -0.69 42 42
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.48 51 51
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 -0.09 0.16 -9999 0 -0.56 29 29
Syndecan-1/Syntenin -0.09 0.16 -9999 0 -0.61 24 24
MAPK3 -0.067 0.14 -9999 0 -0.6 19 19
HGF/MET -0.16 0.24 -9999 0 -0.68 74 74
TGFB1/TGF beta receptor Type II 0.008 0.041 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.088 0.15 -9999 0 -0.55 29 29
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.64 57 57
Syndecan-1/CD147 -0.079 0.15 -9999 0 -0.59 23 23
Syndecan-1/Syntenin/PIP2 -0.097 0.14 -9999 0 -0.59 24 24
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.096 0.14 -9999 0 -0.57 24 24
MMP7 -0.17 0.22 -9999 0 -0.37 243 243
HGF -0.11 0.3 -9999 0 -0.81 74 74
Syndecan-1/CASK -0.098 0.15 -9999 0 -0.46 51 51
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.63 89 89
regulation of cell adhesion -0.057 0.14 -9999 0 -0.57 19 19
HPSE -0.016 0.13 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.48 51 51
SDC1 -0.1 0.16 -9999 0 -0.48 51 51
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.48 51 51
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 179 179
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
MAPK1 -0.067 0.14 -9999 0 -0.6 19 19
homophilic cell adhesion -0.1 0.16 -9999 0 -0.47 51 51
MMP1 -0.14 0.16 -9999 0 -0.31 226 226
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.026 0.16 -10000 0 -0.44 31 31
TBX21 -0.12 0.44 -10000 0 -1.1 67 67
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.022 0.13 -10000 0 -0.39 48 48
GADD45B -0.092 0.38 -10000 0 -0.94 60 60
IL12RB2 -0.015 0.16 -10000 0 -0.72 21 21
GADD45G -0.075 0.34 -10000 0 -0.88 50 50
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.035 0.15 -10000 0 -0.4 60 60
IL2RA -0.047 0.2 -10000 0 -0.81 28 28
IFNG -0.11 0.28 -10000 0 -0.72 79 79
STAT3 (dimer) -0.073 0.32 -10000 0 -0.73 70 70
HLA-DRB5 -0.04 0.13 -10000 0 -0.34 71 71
FASLG -0.14 0.48 -10000 0 -1.1 78 78
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.82 76 76
CD4 -0.002 0.063 -10000 0 -0.31 19 19
SOCS1 0.008 0.049 -10000 0 -0.39 6 6
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.097 0.27 -10000 0 -0.7 75 75
CD3E -0.072 0.24 -10000 0 -0.74 54 54
CD3G -0.15 0.32 -10000 0 -0.78 99 99
IL12Rbeta2/JAK2 -0.002 0.13 -10000 0 -0.63 19 19
CCL3 -0.11 0.43 -10000 0 -1.1 60 60
CCL4 -0.15 0.51 -10000 0 -1.3 65 65
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.032 0.2 -10000 0 -0.56 49 49
NOS2 -0.089 0.34 -10000 0 -0.81 63 63
IL12/IL12R/TYK2/JAK2/SPHK2 -0.024 0.15 -10000 0 -0.41 32 32
IL1R1 -0.088 0.37 -10000 0 -0.95 54 54
IL4 0.002 0.023 -10000 0 -10000 0 0
JAK2 0.012 0.057 -10000 0 -0.82 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.25 0.56 -10000 0 -1.2 106 106
RAB7A -0.042 0.29 -10000 0 -0.68 52 52
lysosomal transport -0.037 0.28 -10000 0 -0.64 53 53
FOS -0.4 0.65 -10000 0 -1.3 159 159
STAT4 (dimer) -0.08 0.35 -10000 0 -0.81 65 65
STAT5A (dimer) -0.22 0.36 -10000 0 -0.86 98 98
GZMA -0.11 0.41 -10000 0 -1 58 58
GZMB -0.1 0.39 -10000 0 -1 54 54
HLX 0.004 0.054 -10000 0 -0.31 14 14
LCK -0.11 0.43 -10000 0 -0.94 76 76
TCR/CD3/MHC II/CD4 -0.19 0.35 -10000 0 -0.62 136 136
IL2/IL2R -0.081 0.22 -10000 0 -0.67 48 48
MAPK14 -0.07 0.35 -10000 0 -0.78 68 68
CCR5 -0.1 0.41 -10000 0 -1.1 53 53
IL1B -0.044 0.22 -10000 0 -0.76 39 39
STAT6 -0.005 0.11 0.24 2 -0.24 27 29
STAT4 -0.025 0.14 -10000 0 -0.81 11 11
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 12 12
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.003 0.1 -10000 0 -0.58 12 12
CD8A -0.052 0.22 -10000 0 -0.81 39 39
CD8B -0.092 0.27 -10000 0 -0.71 71 71
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.025 0.16 0.43 31 -10000 0 31
IL2RB -0.014 0.13 -10000 0 -0.5 27 27
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.32 -10000 0 -0.74 64 64
IL2RG -0.048 0.19 -10000 0 -0.52 57 57
IL12 -0.057 0.21 -10000 0 -0.63 57 57
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.028 0.16 -10000 0 -0.62 30 30
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.073 0.26 -10000 0 -0.79 54 54
IL12/IL12R/TYK2/JAK2 -0.13 0.48 -10000 0 -1 77 77
MAP2K3 -0.072 0.34 -10000 0 -0.77 68 68
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.079 0.36 -10000 0 -0.78 72 72
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.029 0.13 -10000 0 -0.4 48 48
IL18RAP -0.025 0.18 -10000 0 -0.78 25 25
IL12Rbeta1/TYK2 -0.006 0.1 -10000 0 -0.65 6 6
EOMES -0.15 0.43 -10000 0 -1.5 45 45
STAT1 (dimer) -0.13 0.37 -10000 0 -0.77 96 96
T cell proliferation -0.05 0.27 -10000 0 -0.58 66 66
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.026 0.14 -10000 0 -0.42 47 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.24 -10000 0 -0.67 66 66
ATF2 -0.075 0.33 -10000 0 -0.73 66 66
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.087 0.2 -10000 0 -0.55 77 77
cell-cell adhesion 0.15 0.18 0.54 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.013 0.067 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.08 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.26 -10000 0 -0.55 186 186
HRAS/GDP -0.13 0.17 -10000 0 -0.49 13 13
Ephrin B/EPHB1/GRB7 -0.2 0.24 -10000 0 -0.5 191 191
Endophilin/SYNJ1 0.025 0.07 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.18 0.23 -10000 0 -0.47 191 191
endothelial cell migration -0.003 0.036 -10000 0 -0.46 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.04 0.12 -10000 0 -0.31 82 82
PAK1 0.033 0.072 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.072 -10000 0 -0.44 10 10
DNM1 -0.014 0.15 -10000 0 -0.78 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.24 -10000 0 -0.44 191 191
lamellipodium assembly -0.15 0.18 -10000 0 -0.54 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.43 11 11
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.81 3 3
EPHB3 -0.18 0.16 -10000 0 -10000 0 0
EPHB1 -0.3 0.4 -10000 0 -0.81 186 186
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.066 0.17 -10000 0 -0.46 11 11
Ephrin B/EPHB2 -0.014 0.069 -10000 0 -0.46 10 10
Ephrin B/EPHB3 -0.085 0.085 -10000 0 -0.56 7 7
JNK cascade -0.14 0.24 -10000 0 -0.45 188 188
Ephrin B/EPHB1 -0.19 0.23 -10000 0 -0.48 191 191
RAP1/GDP -0.05 0.15 -10000 0 -0.52 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.11 -10000 0 -0.45 25 25
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.19 -10000 0 -0.51 18 18
Rap1/GTP -0.15 0.18 -10000 0 -0.55 11 11
axon guidance -0.086 0.2 -10000 0 -0.55 77 77
MAPK3 -0.075 0.16 -10000 0 -0.53 2 2
MAPK1 -0.075 0.16 -10000 0 -0.53 2 2
Rac1/GDP -0.041 0.17 -10000 0 -0.46 7 7
actin cytoskeleton reorganization -0.1 0.13 -10000 0 -0.45 6 6
CDC42/GDP -0.041 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.036 -10000 0 -0.46 3 3
EFNA5 -0.11 0.3 -10000 0 -0.81 76 76
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.054 -10000 0 -0.33 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.14 0.18 -10000 0 -0.52 12 12
PTK2 0.04 0.051 -10000 0 -10000 0 0
MAP4K4 -0.15 0.24 -10000 0 -0.46 188 188
SRC 0.013 0.015 -10000 0 -10000 0 0
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.065 0.18 -10000 0 -0.54 3 3
MAP2K1 -0.087 0.17 -10000 0 -0.4 11 11
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.24 -10000 0 -0.49 188 188
cell migration -0.083 0.19 -10000 0 -0.43 11 11
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.072 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.022 0.17 -10000 0 -0.44 62 62
HRAS/GTP -0.16 0.2 -10000 0 -0.4 193 193
Ephrin B1/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
cell adhesion mediated by integrin 0.014 0.074 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.17 0.21 -10000 0 -0.43 193 193
RAC1-CDC42/GTP -0.2 0.21 -10000 0 -0.49 144 144
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.05 0.15 -10000 0 -0.48 4 4
ruffle organization -0.11 0.22 -10000 0 -0.55 11 11
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.018 0.11 -10000 0 -0.45 24 24
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -0.46 10 10
ROCK1 -0.073 0.08 -10000 0 -10000 0 0
RAS family/GDP -0.081 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.58 11 11
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.33 191 191
Syndecan-4-mediated signaling events

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.082 0.062 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.14 0.18 -9999 0 -0.65 43 43
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.6 72 72
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.64 45 45
CCL5 -0.047 0.21 -9999 0 -0.69 42 42
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.002 0.038 -9999 0 -0.29 8 8
ADAM12 -0.067 0.14 -9999 0 -0.31 123 123
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 -0.063 0.043 -9999 0 -0.23 5 5
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.68 52 52
Syndecan-4/CXCL12/CXCR4 -0.17 0.23 -9999 0 -0.65 72 72
Syndecan-4/Laminin alpha3 -0.16 0.2 -9999 0 -0.66 48 48
MDK -0.087 0.15 -9999 0 -0.31 152 152
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 45 45
Syndecan-4/Midkine -0.18 0.2 -9999 0 -0.66 45 45
FZD7 0.007 0.074 -9999 0 -0.81 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 44 44
THBS1 -0.017 0.095 -9999 0 -0.31 47 47
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 44 44
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.6 72 72
Syndecan-4/TACI -0.25 0.26 -9999 0 -0.63 134 134
CXCR4 0.011 0.025 -9999 0 -0.31 3 3
cell adhesion -0.063 0.09 -9999 0 -0.44 19 19
Syndecan-4/Dynamin -0.14 0.18 -9999 0 -0.65 43 43
Syndecan-4/TSP1 -0.15 0.18 -9999 0 -0.65 44 44
Syndecan-4/GIPC -0.14 0.18 -9999 0 -0.65 43 43
Syndecan-4/RANTES -0.17 0.22 -9999 0 -0.74 52 52
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.048 0.22 -9999 0 -0.8 37 37
LAMA3 -0.025 0.16 -9999 0 -0.58 32 32
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.022 0.15 -9999 0 -0.73 19 19
Syndecan-4/alpha-Actinin -0.14 0.18 -9999 0 -0.65 43 43
TFPI -0.034 0.19 -9999 0 -0.81 28 28
F2 -0.007 0.052 -9999 0 -0.31 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.66 57 57
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.11 0.17 -9999 0 -0.32 181 181
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 72 72
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.074 0.25 -9999 0 -0.81 52 52
TNFRSF13B -0.2 0.36 -9999 0 -0.79 131 131
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.037 -9999 0 -0.81 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 354 354
cell migration -0.021 0.016 -9999 0 -10000 0 0
PRKCD 0.008 0.014 -9999 0 -10000 0 0
vasculogenesis -0.14 0.18 -9999 0 -0.62 44 44
SDC4 -0.15 0.19 -9999 0 -0.7 43 43
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.69 44 44
Syndecan-4/PI-4-5-P2/PKC alpha -0.05 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.18 -9999 0 -0.65 43 43
MMP9 -0.085 0.24 -9999 0 -0.58 80 80
Rac1/GTP -0.07 0.087 -9999 0 -0.46 19 19
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 43 43
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.64 61 61
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.046 -9999 0 -1 1 1
forebrain development -0.31 0.28 -9999 0 -0.55 256 256
GNAO1 -0.02 0.15 -9999 0 -0.7 21 21
SMO/beta Arrestin2 0.011 0.031 -9999 0 -0.62 1 1
SMO 0.006 0.038 -9999 0 -0.81 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.056 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.029 -9999 0 -0.49 1 1
GNAI1 0.008 0.038 -9999 0 -0.82 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 135 135
SAP30 0.013 0.037 -9999 0 -0.81 1 1
mol:GDP 0.006 0.038 -9999 0 -0.81 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.3 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.033 0.061 -9999 0 -10000 0 0
GLI3 0.039 0.058 -9999 0 -0.3 14 14
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 0.012 0.037 -9999 0 -0.81 1 1
Gi family/GTP 0.008 0.07 -9999 0 -0.33 18 18
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.058 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 239 239
neural tube patterning -0.31 0.28 -9999 0 -0.55 256 256
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.022 -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 0.043 -9999 0 -0.3 1 1
embryonic limb morphogenesis -0.31 0.28 -9999 0 -0.55 256 256
SUFU 0.016 0.021 -9999 0 -0.28 1 1
LGALS3 -0.09 0.15 -9999 0 -0.31 157 157
catabolic process 0.061 0.068 -9999 0 -0.39 2 2
GLI3A/CBP -0.19 0.2 -9999 0 -0.38 255 255
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.32 0.29 -9999 0 -0.57 256 256
RAB23 0.007 0.074 -9999 0 -0.81 4 4
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 -0.029 0.079 -9999 0 -0.44 2 2
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.81 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.057 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.062 -9999 0 -0.27 18 18
PTCH1 -0.28 0.27 -9999 0 -0.62 136 136
MIM/GLI1 -0.45 0.39 -9999 0 -0.75 257 257
CREBBP -0.19 0.2 -9999 0 -0.38 255 255
Su(fu)/SIN3/HDAC complex 0.055 0.026 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.042 0.12 -9999 0 -0.45 29 29
alphaM/beta2 Integrin/GPIbA -0.053 0.14 -9999 0 -0.49 38 38
alphaM/beta2 Integrin/proMMP-9 -0.092 0.2 -9999 0 -0.55 65 65
PLAUR -0.089 0.15 -9999 0 -0.31 156 156
HMGB1 0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.033 0.098 -9999 0 -0.42 21 21
AGER -0.057 0.22 -9999 0 -0.78 38 38
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.01 0.083 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.19 -9999 0 -0.53 63 63
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
CYR61 -0.24 0.38 -9999 0 -0.81 150 150
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.068 0.088 -9999 0 -0.41 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.002 0.1 -9999 0 -0.58 13 13
MYH2 -0.099 0.11 -9999 0 -0.39 36 36
MST1R 0.001 0.095 -9999 0 -0.61 10 10
leukocyte activation during inflammatory response -0.039 0.092 -9999 0 -0.41 14 14
APOB -0.011 0.079 -9999 0 -0.31 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.61 25 25
alphaM/beta2 Integrin/CTGF -0.12 0.22 -9999 0 -0.56 93 93
alphaM/beta2 Integrin -0.091 0.11 -9999 0 -0.34 48 48
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.064 0.14 -9999 0 -0.31 119 119
phagocytosis triggered by activation of immune response cell surface activating receptor -0.09 0.11 -9999 0 -0.33 48 48
cell adhesion -0.053 0.14 -9999 0 -0.48 38 38
NFKB1 -0.12 0.29 -9999 0 -0.71 64 64
THY1 0.011 0.029 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.049 -9999 0 -0.33 2 2
alphaM/beta2 Integrin/LRP/tPA -0.033 0.1 -9999 0 -0.48 15 15
IL6 -0.21 0.44 -9999 0 -1.1 94 94
ITGB2 -0.018 0.086 -9999 0 -0.33 30 30
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.5 39 39
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.099 -9999 0 -0.48 15 15
JAM2 0.006 0.076 -9999 0 -0.71 5 5
alphaM/beta2 Integrin/ICAM1 -0.059 0.12 -9999 0 -0.49 22 22
alphaM/beta2 Integrin/uPA/Plg -0.097 0.12 -9999 0 -0.5 21 21
RhoA/GTP -0.1 0.12 -9999 0 -0.4 41 41
positive regulation of phagocytosis -0.067 0.12 -9999 0 -0.46 20 20
Ron/MSP -0.011 0.076 -9999 0 -0.62 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.51 39 39
alphaM/beta2 Integrin/uPAR -0.083 0.13 -9999 0 -0.45 35 35
PLAU -0.14 0.16 -9999 0 -0.31 230 230
PLAT 0.003 0.076 -9999 0 -0.45 11 11
actin filament polymerization -0.095 0.11 -9999 0 -0.37 37 37
MST1 0.011 0.04 -9999 0 -0.56 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.039 0.093 -9999 0 -0.42 14 14
TNF -0.17 0.39 -9999 0 -0.97 79 79
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.43 39 39
fibrinolysis -0.097 0.12 -9999 0 -0.5 21 21
HCK -0.01 0.084 -9999 0 -0.31 36 36
dendritic cell antigen processing and presentation -0.09 0.11 -9999 0 -0.33 48 48
VTN -0.067 0.24 -9999 0 -0.75 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.27 -9999 0 -0.57 164 164
LPA -0.002 0.042 -9999 0 -0.31 9 9
LRP1 0.012 0.037 -9999 0 -0.81 1 1
cell migration -0.089 0.2 -9999 0 -0.57 60 60
FN1 -0.22 0.14 -9999 0 -0.31 359 359
alphaM/beta2 Integrin/Thy1 -0.034 0.099 -9999 0 -0.41 22 22
MPO 0 0.094 -9999 0 -0.65 9 9
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.09 0.11 -9999 0 -0.38 38 38
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.039 -9999 0 -0.31 8 8
CTGF -0.11 0.3 -9999 0 -0.81 76 76
alphaM/beta2 Integrin/Hck -0.045 0.12 -9999 0 -0.45 35 35
ITGAM -0.022 0.11 -9999 0 -0.38 32 32
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.046 0.13 -9999 0 -0.52 26 26
HP -0.082 0.16 -9999 0 -0.33 135 135
leukocyte adhesion -0.087 0.16 -9999 0 -0.59 27 27
SELP -0.002 0.1 -9999 0 -0.58 13 13
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.38 -9999 0 -1.3 40 40
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.033 0.11 -9999 0 -0.39 20 20
ATF2/c-Jun -0.22 0.42 -9999 0 -0.97 113 113
MAPK11 -0.033 0.11 -9999 0 -0.39 20 20
MITF -0.026 0.13 -9999 0 -0.41 40 40
MAPKAPK5 -0.026 0.13 -9999 0 -0.41 40 40
KRT8 -0.026 0.13 -9999 0 -0.41 40 40
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.044 0.16 -9999 0 -0.52 40 40
CEBPB -0.026 0.13 -9999 0 -0.41 40 40
SLC9A1 -0.026 0.13 -9999 0 -0.41 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.19 -9999 0 -0.56 40 40
p38alpha-beta/MNK1 -0.022 0.13 -9999 0 -0.49 20 20
JUN -0.22 0.42 -9999 0 -0.96 113 113
PPARGC1A -0.23 0.25 -9999 0 -0.45 258 258
USF1 -0.026 0.13 -9999 0 -0.41 40 40
RAB5/GDP/GDI1 -0.036 0.082 -9999 0 -0.35 20 20
NOS2 -0.045 0.16 -9999 0 -0.54 20 20
DDIT3 -0.028 0.13 -9999 0 -0.41 40 40
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.01 0.11 -9999 0 -0.39 20 20
p38alpha-beta/HBP1 -0.022 0.13 -9999 0 -0.49 20 20
CREB1 -0.046 0.15 -9999 0 -0.46 40 40
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.012 0.12 -9999 0 -0.43 20 20
RPS6KA4 -0.026 0.13 -9999 0 -0.41 40 40
PLA2G4A -0.045 0.19 -9999 0 -0.58 45 45
GDI1 -0.026 0.13 -9999 0 -0.41 40 40
TP53 -0.034 0.16 -9999 0 -0.51 40 40
RPS6KA5 -0.075 0.2 -9999 0 -0.46 87 87
ESR1 -0.06 0.2 -9999 0 -0.54 55 55
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.027 0.13 -9999 0 -0.41 41 41
MEF2A -0.027 0.13 -9999 0 -0.41 41 41
EIF4EBP1 -0.046 0.15 -9999 0 -0.46 41 41
KRT19 -0.1 0.2 -9999 0 -0.53 57 57
ELK4 -0.026 0.13 -9999 0 -0.41 40 40
ATF6 -0.026 0.13 -9999 0 -0.41 40 40
ATF1 -0.047 0.16 -9999 0 -0.47 41 41
p38alpha-beta/MAPKAPK2 -0.022 0.13 -9999 0 -0.49 20 20
p38alpha-beta/MAPKAPK3 -0.022 0.13 -9999 0 -0.49 20 20
IL6-mediated signaling events

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
BCL2L1 -0.049 0.21 -10000 0 -0.64 25 25
CRP -0.054 0.21 -10000 0 -0.71 16 16
cell cycle arrest -0.07 0.23 -10000 0 -0.72 30 30
TIMP1 -0.15 0.21 -10000 0 -0.6 37 37
IL6ST -0.11 0.29 -10000 0 -0.81 72 72
Rac1/GDP -0.078 0.24 -10000 0 -0.58 62 62
AP1 -0.19 0.32 -10000 0 -0.66 137 137
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.09 0.22 -10000 0 -0.68 21 21
HSP90B1 0.024 0.042 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.085 0.29 -10000 0 -0.77 56 56
AKT1 0.053 0.056 -10000 0 -1.1 1 1
FOXO1 0.059 0.053 -10000 0 -0.98 1 1
MAP2K6 -0.091 0.28 -10000 0 -0.65 71 71
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.067 0.23 -10000 0 -0.63 44 44
MITF -0.079 0.25 -10000 0 -0.55 75 75
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.024 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.019 0.085 -10000 0 -0.49 1 1
STAT3 -0.082 0.24 -10000 0 -0.78 30 30
STAT1 -0.01 0.022 -10000 0 -10000 0 0
CEBPD -0.049 0.21 -10000 0 -0.69 16 16
PIK3CA 0.01 0.064 -10000 0 -0.81 3 3
PI3K 0.019 0.05 -10000 0 -0.62 3 3
JUN -0.18 0.35 -10000 0 -0.81 112 112
PIAS3/MITF -0.067 0.24 -10000 0 -0.61 52 52
MAPK11 -0.085 0.29 -10000 0 -0.77 56 56
STAT3 (dimer)/FOXO1 -0.001 0.2 -10000 0 -0.58 19 19
GRB2/SOS1/GAB family -0.11 0.19 -10000 0 -0.68 31 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.11 0.25 -10000 0 -0.44 147 147
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.01 0.053 -10000 0 -0.81 2 2
LBP -0.055 0.19 -10000 0 -0.61 14 14
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.063 0.26 -10000 0 -0.87 27 27
FGG -0.058 0.21 -10000 0 -0.69 19 19
macrophage differentiation -0.07 0.23 -10000 0 -0.72 30 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.17 0.28 -10000 0 -0.56 147 147
JUNB -0.055 0.23 -10000 0 -0.73 27 27
FOS -0.2 0.36 -10000 0 -0.81 127 127
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.089 0.27 -10000 0 -0.46 137 137
STAT1/PIAS1 -0.072 0.23 -10000 0 -0.55 60 60
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.06 -10000 0 -0.59 3 3
STAT3 (dimer) -0.079 0.24 -10000 0 -0.76 30 30
PRKCD -0.055 0.22 -10000 0 -0.62 38 38
IL6R -0.014 0.15 -10000 0 -0.81 17 17
SOCS3 -0.097 0.35 -10000 0 -1 49 49
gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.2 -10000 0 -0.54 72 72
Rac1/GTP -0.088 0.24 -10000 0 -0.59 61 61
HCK -0.011 0.084 -10000 0 -0.31 36 36
MAPKKK cascade 0.012 0.076 -10000 0 -0.98 1 1
bone resorption -0.085 0.21 -10000 0 -0.63 24 24
IRF1 -0.049 0.21 -10000 0 -0.64 24 24
mol:GDP -0.09 0.25 -10000 0 -0.59 68 68
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.092 0.26 -10000 0 -0.61 68 68
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.097 0.29 -10000 0 -0.79 54 54
PTPN11 -0.01 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.13 0.27 -10000 0 -0.65 99 99
gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.2 -10000 0 -0.54 72 72
gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.2 -10000 0 -0.55 72 72
IL6 -0.15 0.32 -10000 0 -0.69 116 116
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.087 0.15 -10000 0 -0.31 148 148
PIAS1 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.093 0.26 -10000 0 -0.46 131 131
LMO4 0.013 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.097 0.23 0.38 1 -0.77 30 31
MCL1 0.059 0.048 -10000 0 -0.88 1 1
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.021 -9999 0 -0.31 2 2
EGFR 0.005 0.083 -9999 0 -0.81 5 5
EGF/EGFR -0.078 0.17 -9999 0 -0.45 83 83
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.073 0.17 -9999 0 -0.46 77 77
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.047 -9999 0 -0.41 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
EGF/EGFR dimer/SHC -0.086 0.2 -9999 0 -0.54 77 77
mol:GDP -0.072 0.16 -9999 0 -0.45 77 77
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.003 0.086 -9999 0 -0.62 8 8
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.15 -9999 0 -0.42 77 77
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.067 0.15 -9999 0 -0.42 77 77
FRAP1 -0.036 0.17 -9999 0 -0.44 77 77
EGF/EGFR dimer -0.1 0.23 -9999 0 -0.62 77 77
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.073 -9999 0 -0.59 7 7
Thromboxane A2 receptor signaling

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.033 0.11 -10000 0 -0.31 69 69
GNB1/GNG2 -0.042 0.067 -10000 0 -0.2 44 44
AKT1 -0.007 0.1 -10000 0 -0.2 70 70
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.033 0.07 -10000 0 -0.71 1 1
mol:Ca2+ -0.035 0.14 -10000 0 -0.31 73 73
LYN 0.034 0.07 -10000 0 -0.71 1 1
RhoA/GTP -0.029 0.045 -10000 0 -0.14 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.034 0.16 -10000 0 -0.34 72 72
GNG2 0.012 0.037 -10000 0 -0.82 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.55 12 12
G beta5/gamma2 -0.056 0.091 -10000 0 -0.27 45 45
PRKCH -0.042 0.16 -10000 0 -0.36 72 72
DNM1 -0.014 0.15 -10000 0 -0.78 17 17
TXA2/TP beta/beta Arrestin3 -0.012 0.054 -10000 0 -0.3 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.02 0.16 -10000 0 -0.81 20 20
G12 family/GTP -0.072 0.11 -10000 0 -0.31 70 70
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.1 0.34 14 -10000 0 14
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.37 -10000 0 -0.81 137 137
mol:IP3 -0.05 0.18 -10000 0 -0.38 73 73
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.075 0.23 -10000 0 -0.53 72 72
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.094 0.2 -10000 0 -0.38 145 145
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.025 0.076 -10000 0 -0.71 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.005 0.083 -10000 0 -0.81 5 5
PRKCB1 -0.05 0.17 -10000 0 -0.38 73 73
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.072 0.23 -10000 0 -0.54 73 73
LCK 0.024 0.091 -10000 0 -0.54 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.081 -10000 0 -1.1 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.029 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.08 -10000 0 -1.1 1 1
MAPK14 -0.012 0.11 -10000 0 -0.23 70 70
TGM2/GTP -0.062 0.2 -10000 0 -0.43 74 74
MAPK11 -0.012 0.11 -10000 0 -0.23 70 70
ARHGEF1 -0.01 0.088 -10000 0 -0.18 29 29
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.046 0.18 -10000 0 -0.39 73 73
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.04 0.15 -10000 0 -0.3 79 79
cAMP biosynthetic process -0.05 0.16 -10000 0 -0.36 74 74
Gq family/GTP/EBP50 -0.045 0.12 -10000 0 -0.35 23 23
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.034 0.07 -10000 0 -0.71 1 1
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.018 0.1 -10000 0 -0.3 15 15
VCAM1 -0.029 0.14 -10000 0 -0.3 74 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.55 12 12
platelet activation -0.017 0.15 -10000 0 -0.3 70 70
PGI2/IP -0.006 0.063 -10000 0 -0.63 5 5
PRKACA 0.002 0.095 -10000 0 -0.4 24 24
Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.5 12 12
TXA2/TP beta/beta Arrestin2 -0.023 0.12 -10000 0 -0.66 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.1 -10000 0 -0.39 24 24
mol:DAG -0.057 0.19 -10000 0 -0.43 73 73
EGFR 0.005 0.083 -10000 0 -0.81 5 5
TXA2/TP alpha -0.071 0.22 -10000 0 -0.49 73 73
Gq family/GTP -0.077 0.13 -10000 0 -0.3 125 125
YES1 0.034 0.07 -10000 0 -0.71 1 1
GNAI2/GTP -0.015 0.07 -10000 0 -0.9 1 1
PGD2/DP -0.026 0.12 -10000 0 -0.63 20 20
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.034 0.07 -10000 0 -0.71 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.011 0.09 -10000 0 -0.32 36 36
PGK/cGMP -0.15 0.24 -10000 0 -0.55 137 137
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.029 0.092 -10000 0 -0.6 5 5
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.052 0.18 -10000 0 -0.38 80 80
PRKCB -0.051 0.17 -10000 0 -0.38 75 75
PRKCE -0.045 0.17 -10000 0 -0.37 74 74
PRKCD -0.045 0.17 -10000 0 -0.38 72 72
PRKCG -0.049 0.17 -10000 0 -0.39 74 74
muscle contraction -0.062 0.22 -10000 0 -0.49 73 73
PRKCZ -0.034 0.16 -10000 0 -0.34 72 72
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.081 -10000 0 -1.1 1 1
PRKCQ -0.044 0.17 -10000 0 -0.36 78 78
MAPKKK cascade -0.063 0.2 -10000 0 -0.47 73 73
SELE -0.049 0.18 -10000 0 -0.43 72 72
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.086 -10000 0 -1.3 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.81 118 118
chemotaxis -0.083 0.26 -10000 0 -0.62 73 73
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.12 -10000 0 -0.81 10 10
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.025 0.077 0.29 36 -10000 0 36
RFC1 0.025 0.077 0.29 36 -10000 0 36
PRKDC 0.025 0.077 0.29 36 -10000 0 36
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.012 0.045 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.029 0.1 0.26 5 -0.37 37 42
MAP2K4 -0.02 0.16 -10000 0 -0.4 39 39
mol:ceramide -0.022 0.15 -10000 0 -0.47 38 38
GSN 0.025 0.077 0.29 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.14 -10000 0 -0.46 37 37
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.028 0.077 0.32 3 -10000 0 3
MAP3K1 0.006 0.097 -10000 0 -0.28 16 16
MAP3K7 0.011 0.005 -10000 0 -10000 0 0
RB1 0.024 0.078 0.29 35 -0.31 1 36
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.14 0.22 -10000 0 -0.61 77 77
ARHGDIB 0.022 0.08 0.29 36 -10000 0 36
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.077 -10000 0 -0.29 36 36
NFKB1 -0.049 0.09 -10000 0 -0.32 17 17
MAPK8 -0.052 0.21 -10000 0 -0.44 95 95
DFFA 0.025 0.077 0.29 36 -10000 0 36
DNA fragmentation during apoptosis 0.025 0.077 0.29 36 -10000 0 36
FAS/FADD/MET -0.057 0.075 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.003 0.089 -10000 0 -0.38 22 22
FAF1 0.011 0.006 -10000 0 -10000 0 0
PARP1 0.025 0.077 0.29 36 -10000 0 36
DFFB 0.025 0.077 0.29 36 -10000 0 36
CHUK -0.042 0.08 -10000 0 -0.73 1 1
FASLG -0.064 0.23 -10000 0 -0.66 55 55
FAS/FADD -0.001 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.81 74 74
LMNA 0.023 0.07 0.26 36 -10000 0 36
CASP6 0.025 0.077 0.29 36 -10000 0 36
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.03 0.094 0.34 39 -10000 0 39
PTPN13 0.003 0.091 -10000 0 -0.81 6 6
CASP8 0.008 0.045 0.45 3 -10000 0 3
IL6 -0.23 0.54 -10000 0 -1.4 88 88
MET -0.1 0.16 -10000 0 -0.31 179 179
ICAD/CAD 0.023 0.072 0.27 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.15 -10000 0 -0.48 38 38
activation of caspase activity by cytochrome c -0.028 0.077 0.32 3 -10000 0 3
PAK2 0.025 0.077 0.29 36 -10000 0 36
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
TCGA08_p53

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
CDKN2A -0.08 0.11 -9999 0 -0.21 204 204
TP53 -0.027 0.032 -9999 0 -10000 0 0
Senescence -0.027 0.032 -9999 0 -10000 0 0
Apoptosis -0.027 0.032 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.051 0.061 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.072 0.096 -10000 0 -10000 0 0
CRKL -0.03 0.11 -10000 0 -0.33 25 25
mol:PIP3 -0.019 0.032 0.68 1 -10000 0 1
AKT1 0.001 0.039 0.45 1 -0.53 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.021 0.11 -10000 0 -0.3 25 25
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
HGF/MET/SHIP2 -0.14 0.2 -10000 0 -0.59 74 74
MAP3K5 -0.018 0.11 -10000 0 -0.47 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.54 74 74
AP1 -0.27 0.42 -10000 0 -0.87 151 151
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 151 151
STAT3 (dimer) -0.038 0.13 -10000 0 -0.33 74 74
GAB1/CRKL/SHP2/PI3K -0.042 0.093 -10000 0 -0.69 2 2
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
CBL/CRK -0.021 0.11 -10000 0 -10000 0 0
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.81 1 1
ELK1 -0.047 0.061 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.039 0.071 -10000 0 -0.24 26 26
PAK1 0.009 0.037 0.42 1 -0.49 2 3
HGF/MET/RANBP10 -0.14 0.2 -10000 0 -0.59 74 74
HRAS -0.057 0.16 -10000 0 -0.42 74 74
DOCK1 -0.025 0.12 -10000 0 -0.55 4 4
GAB1 -0.04 0.12 -10000 0 -0.3 74 74
CRK -0.03 0.11 -10000 0 -0.33 25 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 74 74
JUN -0.17 0.35 -10000 0 -0.81 112 112
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.07 0.1 -10000 0 -0.29 74 74
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.011 0.14 -10000 0 -0.64 2 2
GRB2/SHC -0.037 0.096 -10000 0 -0.3 25 25
FOS -0.2 0.36 -10000 0 -0.81 127 127
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.047 0.061 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.6 74 74
cell migration -0.037 0.094 -10000 0 -0.29 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.072 0.096 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.05 0.14 -10000 0 -0.36 74 74
MET/MUC20 -0.076 0.1 -10000 0 -0.21 179 179
RAP1B -0.012 0.1 -10000 0 -10000 0 0
RAP1A -0.012 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.2 -10000 0 -0.59 74 74
RAF1 -0.047 0.15 -10000 0 -0.45 26 26
STAT3 -0.039 0.13 -10000 0 -0.39 25 25
cell proliferation -0.046 0.17 -10000 0 -0.45 74 74
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.049 0.056 -10000 0 -10000 0 0
MAPK1 -0.049 0.056 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.008 0.14 -10000 0 -0.57 15 15
SRC -0.039 0.13 -10000 0 -0.38 25 25
PI3K -0.04 0.1 -10000 0 -0.32 28 28
MET/Glomulin -0.056 0.092 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.036 0.14 -10000 0 -0.41 26 26
MET -0.1 0.16 -10000 0 -0.31 179 179
MAP4K1 -0.027 0.12 -10000 0 -0.33 29 29
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.036 0.14 -10000 0 -0.41 26 26
BAD 0.009 0.037 0.42 1 -0.49 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.42 5 5
SHP2/GRB2/SOS1/GAB1 -0.056 0.09 -10000 0 -0.38 1 1
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 -0.048 0.1 -10000 0 -0.32 25 25
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.81 74 74
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.04 0.11 -10000 0 -0.27 74 74
PDPK1 -0.009 0.043 0.51 1 -0.57 2 3
HGF/MET/SHIP -0.14 0.2 -10000 0 -0.59 74 74
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.036 0.21 -9999 0 -0.81 33 33
HDAC7 -0.034 0.15 -9999 0 -0.64 17 17
JUN -0.18 0.34 -9999 0 -0.81 112 112
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.013 0.001 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.002 0.097 -9999 0 -0.64 11 11
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.047 0.16 -9999 0 -0.66 19 19
MAP2K6 -0.01 0.12 -9999 0 -0.78 12 12
BRM/BAF57 -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.058 -9999 0 -10000 0 0
NCOA2 -0.074 0.24 -9999 0 -0.82 48 48
CEBPA 0.006 0.083 -9999 0 -0.81 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.07 0.15 -9999 0 -0.55 17 17
NR0B1 -0.002 0.04 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.82 107 107
RXRs/9cRA -0.13 0.058 -9999 0 -0.5 4 4
AR/RACK1/Src -0.12 0.16 -9999 0 -0.67 19 19
AR/GR -0.13 0.2 -9999 0 -0.36 163 163
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 -0.002 0.097 -9999 0 -0.63 11 11
T-DHT/AR/TIF2/CARM1 -0.13 0.24 -9999 0 -0.69 56 56
SRC -0.005 0.12 -9999 0 -0.55 19 19
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 142 142
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.056 0.15 -9999 0 -0.67 19 19
TMPRSS2 -0.059 0.31 -9999 0 -1.2 32 32
RXRG -0.28 0.11 -9999 0 -0.32 437 437
mol:9cRA -0.002 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.006 0.12 -9999 0 -0.81 11 11
KLK2 -0.48 0.42 -9999 0 -0.82 291 291
AR -0.15 0.22 -9999 0 -0.38 214 214
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.023 0.015 -9999 0 -10000 0 0
SRY 0.01 0.015 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.013 0.05 -9999 0 -0.32 11 11
T-DHT/AR/RACK1/Src -0.079 0.15 -9999 0 -0.66 19 19
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.027 0.1 -9999 0 -0.32 54 54
T-DHT/AR/TIF2 -0.057 0.16 -9999 0 -0.46 50 50
T-DHT/AR/Hsp90 -0.058 0.15 -9999 0 -0.67 19 19
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.008 0.12 -9999 0 -0.59 19 19
SIRT1 0.011 0.037 -9999 0 -0.81 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.019 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.076 0.14 -9999 0 -0.68 19 19
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin -0.11 0.1 -9999 0 -0.64 7 7
EPHB2 0.008 0.064 -9999 0 -0.81 3 3
Syndecan-2/TACI -0.13 0.25 -9999 0 -0.56 128 128
LAMA1 -0.048 0.22 -9999 0 -0.8 37 37
Syndecan-2/alpha2 ITGB1 -0.071 0.11 -9999 0 -0.46 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.064 -9999 0 -0.54 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.023 0.1 -9999 0 -0.5 18 18
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.058 -9999 0 -0.49 7 7
LAMA3 -0.025 0.16 -9999 0 -0.58 32 32
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.064 -9999 0 -0.81 3 3
Syndecan-2/MMP2 0.008 0.1 -9999 0 -0.57 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.078 0.097 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.079 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.097 -9999 0 -0.56 7 7
determination of left/right symmetry 0.012 0.076 -9999 0 -0.62 7 7
Syndecan-2/PKC delta 0.018 0.066 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.086 0.09 -9999 0 -0.51 7 7
MAPK1 -0.086 0.09 -9999 0 -0.51 7 7
Syndecan-2/RACK1 -0.007 0.055 -9999 0 -0.46 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.076 -9999 0 -0.62 7 7
ITGA2 -0.11 0.16 -9999 0 -0.31 193 193
MAPK8 0.015 0.11 -9999 0 -0.55 18 18
Syndecan-2/alpha2/beta1 Integrin -0.084 0.14 -9999 0 -0.51 40 40
Syndecan-2/Kininogen -0.007 0.077 -9999 0 -0.54 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.057 -9999 0 -0.43 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.058 -9999 0 -0.5 7 7
extracellular matrix organization 0.015 0.07 -9999 0 -0.53 7 7
actin cytoskeleton reorganization -0.11 0.1 -9999 0 -0.64 7 7
Syndecan-2/Caveolin-2/Ras -0.01 0.075 -9999 0 -0.54 9 9
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.54 24 24
Syndecan-2/RasGAP -0.007 0.052 -9999 0 -0.44 7 7
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.014 0.079 -9999 0 -0.54 10 10
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.056 -9999 0 -0.42 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.2 0.36 -9999 0 -0.79 131 131
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.078 0.097 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.066 -9999 0 -0.54 7 7
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CASP3 0.027 0.061 -9999 0 -0.48 7 7
FN1 -0.22 0.14 -9999 0 -0.31 359 359
Syndecan-2/IL8 -0.038 0.12 -9999 0 -0.54 18 18
SDC2 0.012 0.076 -9999 0 -0.62 7 7
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
Syndecan-2/Neurofibromin 0.018 0.066 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 335 335
Syndecan-2/TGFB1 0.015 0.07 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.058 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.058 -9999 0 -0.49 7 7
PRKACA 0.027 0.061 -9999 0 -0.48 7 7
angiogenesis -0.038 0.12 -9999 0 -0.54 18 18
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
IL8 -0.082 0.18 -9999 0 -0.35 128 128
calcineurin-NFAT signaling pathway -0.13 0.25 -9999 0 -0.55 128 128
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 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 -0.006 0.12 -9999 0 -0.77 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 286 286
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 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.029 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.048 0.068 -9999 0 -0.31 5 5
PRKG1 -0.22 0.37 -9999 0 -0.81 137 137
DUSP8 0.003 0.082 -9999 0 -0.51 10 10
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.46 140 140
apoptosis -0.046 0.066 -9999 0 -0.3 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.3 -9999 0 -0.81 80 80
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
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 0.012 0.021 -9999 0 -0.31 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.061 0.13 -9999 0 -0.36 17 17
BLK -0.24 0.37 -9999 0 -0.74 168 168
HCK -0.01 0.084 -9999 0 -0.31 36 36
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.042 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.032 -9999 0 -0.5 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.092 -9999 0 -0.32 6 6
positive regulation of innate immune response -0.059 0.14 -9999 0 -0.4 14 14
LCK -0.01 0.11 -9999 0 -0.42 27 27
p38alpha-beta/MKP7 -0.05 0.13 -9999 0 -0.44 6 6
p38alpha-beta/MKP5 -0.051 0.13 -9999 0 -0.48 7 7
PGK/cGMP -0.18 0.28 -9999 0 -0.63 137 137
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.47 85 85
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 -0.47 0.41 -9999 0 -0.81 286 286
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.041 -10000 0 -0.31 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.067 0.15 0.44 27 -10000 0 27
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.57 52 52
TBX21 -0.093 0.22 -10000 0 -0.62 38 38
IL12B -0.006 0.098 -10000 0 -0.54 13 13
IL12A -0.058 0.2 -10000 0 -0.61 54 54
IL6ST -0.11 0.29 -10000 0 -0.82 72 72
IL27RA/JAK1 0.012 0.026 -10000 0 -10000 0 0
IL27 0.001 0.039 -10000 0 -0.32 7 7
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.15 -10000 0 -0.51 1 1
T-helper 2 cell differentiation 0.067 0.15 0.44 27 -10000 0 27
T cell proliferation during immune response 0.067 0.15 0.44 27 -10000 0 27
MAPKKK cascade -0.067 0.15 -10000 0 -0.44 27 27
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 12 12
IL12RB1 -0.026 0.13 -10000 0 -0.37 48 48
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.091 0.21 -10000 0 -0.64 28 28
IL27/IL27R/JAK2/TYK2 -0.068 0.15 -10000 0 -0.44 27 27
positive regulation of T cell mediated cytotoxicity -0.067 0.15 -10000 0 -0.44 27 27
STAT1 (dimer) -0.12 0.24 0.52 16 -0.74 19 35
JAK2 0.011 0.054 -10000 0 -0.82 2 2
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
T cell proliferation -0.15 0.23 -10000 0 -0.53 99 99
IL12/IL12R/TYK2/JAK2 -0.058 0.17 -10000 0 -0.72 15 15
IL17A -0.054 0.15 -10000 0 -0.51 1 1
mast cell activation 0.067 0.15 0.44 27 -10000 0 27
IFNG -0.021 0.048 -10000 0 -0.13 68 68
T cell differentiation -0.005 0.008 -10000 0 -0.022 63 63
STAT3 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT5A (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT4 (dimer) -0.076 0.16 -10000 0 -0.52 25 25
STAT4 -0.025 0.14 -10000 0 -0.81 11 11
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.19 -10000 0 -0.62 14 14
GATA3 -0.042 0.33 -10000 0 -1.5 25 25
IL18 -0.025 0.11 -10000 0 -0.57 13 13
positive regulation of mast cell cytokine production -0.055 0.14 -10000 0 -0.51 11 11
IL27/EBI3 -0.099 0.12 -10000 0 -0.43 7 7
IL27RA 0.003 0.027 -10000 0 -10000 0 0
IL6 -0.15 0.32 -10000 0 -0.72 107 107
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.014 -10000 0 -10000 0 0
IL1B -0.034 0.16 -10000 0 -0.57 39 39
EBI3 -0.15 0.16 -10000 0 -0.31 242 242
TNF -0.067 0.21 -10000 0 -0.59 64 64
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.016 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.018 0.07 -9999 0 -0.55 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.025 -9999 0 -0.31 3 3
GRK1 -0.066 0.24 -9999 0 -0.81 47 47
CNG Channel -0.029 0.083 -9999 0 -0.51 9 9
mol:Na + -0.023 0.081 -9999 0 -0.45 13 13
mol:ADP -0.066 0.24 -9999 0 -0.81 47 47
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.024 0.083 -9999 0 -0.46 13 13
CNGB1 -0.002 0.067 -9999 0 -0.31 22 22
RDH5 -0.2 0.16 -9999 0 -0.31 319 319
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.015 0.088 -9999 0 -0.48 5 5
Na + (4 Units) -0.021 0.074 -9999 0 -0.44 8 8
RGS9 -0.072 0.25 -9999 0 -0.79 53 53
GNB1/GNGT1 -0.003 0.024 -9999 0 -10000 0 0
GNAT1/GDP -0.077 0.18 -9999 0 -0.48 78 78
GUCY2D -0.01 0.11 -9999 0 -0.43 26 26
GNGT1 -0.004 0.037 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.072 -9999 0 -0.47 5 5
mol:11-cis-retinal -0.2 0.15 -9999 0 -0.31 319 319
mol:cGMP -0.016 0.07 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.097 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.09 -9999 0 -0.54 11 11
Metarhodopsin II -0.049 0.15 -9999 0 -0.51 47 47
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.074 -9999 0 -0.5 9 9
RGS9BP -0.037 0.2 -9999 0 -0.81 30 30
Metarhodopsin II/Transducin 0.011 0.015 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.51 3 3
PDE6A/B -0.012 0.047 -9999 0 -10000 0 0
mol:Pi -0.087 0.2 -9999 0 -0.55 78 78
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.022 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.076 -9999 0 -0.31 29 29
PDE6G -0.017 0.11 -9999 0 -0.38 38 38
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.089 0.18 -9999 0 -0.48 81 81
GUCA1A 0.004 0.032 -9999 0 -0.31 5 5
GC2/GCAP Family -0.005 0.043 -9999 0 -0.51 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.066 -9999 0 -0.69 4 4
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.033 0.12 -10000 0 -0.5 25 25
ER alpha/Gai/GDP/Gbeta gamma 0.007 0.15 -10000 0 -0.47 35 35
AKT1 -0.014 0.2 -10000 0 -0.86 25 25
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.013 0.2 -10000 0 -0.87 25 25
mol:Ca2+ -0.1 0.23 -10000 0 -0.49 120 120
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.071 0.18 -10000 0 -0.58 53 53
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.81 25 -10000 0 25
RhoA/GTP -0.025 0.087 -10000 0 -0.4 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.036 0.13 -10000 0 -0.58 23 23
regulation of stress fiber formation -0.011 0.12 0.46 5 -10000 0 5
E2/ERA-ERB (dimer) -0.039 0.13 -10000 0 -0.57 25 25
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.033 0.11 -10000 0 -0.5 23 23
pseudopodium formation 0.011 0.12 -10000 0 -0.46 5 5
E2/ER alpha (dimer)/PELP1 -0.036 0.12 -10000 0 -0.55 23 23
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.037 -10000 0 -0.81 1 1
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
HRAS 0.012 0.021 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.013 0.15 -10000 0 -0.59 24 24
E2/ER beta (dimer) -0.004 0.049 -10000 0 -0.63 3 3
mol:GDP -0.034 0.12 -10000 0 -0.56 25 25
mol:NADP 0.013 0.15 -10000 0 -0.59 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 -10000 0 -0.52 120 120
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.25 -10000 0 -0.53 120 120
PLCB2 -0.12 0.25 -10000 0 -0.54 119 119
IGF1 -0.18 0.35 -10000 0 -0.79 119 119
mol:L-citrulline 0.013 0.15 -10000 0 -0.59 24 24
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.026 0.14 -10000 0 -0.78 16 16
JNK cascade -0.004 0.049 -10000 0 -0.63 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.008 0.064 -10000 0 -0.81 3 3
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.046 0.19 -10000 0 -0.52 55 55
Gq family/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.68 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.08 -10000 0 -0.36 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.13 -10000 0 -0.58 23 23
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.043 0.14 -10000 0 -0.63 23 23
STRN -0.04 0.2 -10000 0 -0.81 32 32
GNAL -0.094 0.28 -10000 0 -0.81 64 64
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.016 0.044 -10000 0 -0.55 3 3
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.81 1 1
HBEGF -0.004 0.16 -10000 0 -0.52 29 29
cAMP biosynthetic process -0.089 0.18 -10000 0 -0.48 85 85
SRC 0.015 0.14 -10000 0 -0.5 24 24
PI3K -0.004 0.048 -10000 0 -0.62 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.029 0.11 -10000 0 -0.51 23 23
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.52 38 38
Gs family/GTP -0.091 0.19 -10000 0 -0.48 85 85
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.014 0.14 -10000 0 -0.55 25 25
mol:DAG -0.11 0.24 -10000 0 -0.52 120 120
Gs family/GDP/Gbeta gamma -0.072 0.16 -10000 0 -0.51 27 27
MSN 0.01 0.12 -10000 0 -0.5 5 5
Gq family/GTP -0.15 0.24 -10000 0 -0.57 119 119
mol:PI-3-4-5-P3 -0.011 0.19 -10000 0 -0.83 25 25
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.014 0.14 0.55 25 -10000 0 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.12 -10000 0 -0.52 25 25
NOS3 0.012 0.16 -10000 0 -0.63 24 24
GNA11 -0.003 0.12 -10000 0 -0.81 10 10
MAPKKK cascade -0.008 0.19 -10000 0 -0.54 53 53
E2/ER alpha (dimer)/PELP1/Src -0.038 0.14 -10000 0 -0.62 23 23
ruffle organization 0.011 0.12 -10000 0 -0.46 5 5
ROCK2 0.001 0.14 -10000 0 -0.43 25 25
GNA14 -0.18 0.35 -10000 0 -0.81 118 118
GNA15 -0.011 0.09 -10000 0 -0.32 36 36
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.19 -10000 0 -0.48 63 63
MMP2 0.015 0.15 -10000 0 -0.67 11 11
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.089 0.22 -9999 0 -0.53 45 45
MAP3K8 -0.001 0.098 -9999 0 -0.82 7 7
FOS -0.055 0.17 -9999 0 -0.5 35 35
PRKCA -0.021 0.16 -9999 0 -0.82 19 19
PTPN7 -0.047 0.18 -9999 0 -0.46 61 61
HRAS 0.011 0.021 -9999 0 -0.31 2 2
PRKCB -0.024 0.12 -9999 0 -0.37 46 46
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.029 0.12 -9999 0 -0.51 19 19
MAP2K1 -0.017 0.14 -9999 0 -0.57 25 25
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.039 0.12 -9999 0 -0.57 23 23
mol:GTP -0.001 0.003 -9999 0 -0.006 126 126
MAPK1 -0.029 0.12 -9999 0 -0.51 19 19
RAF1 -0.039 0.12 -9999 0 -0.57 23 23
KRAS 0.013 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.01 0.12 -9999 0 -0.63 2 2
NFATC4 0.001 0.11 -9999 0 -0.5 3 3
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.044 0.13 -9999 0 -0.4 54 54
JUN 0.004 0.097 -9999 0 -0.27 12 12
HRAS 0.012 0.021 -9999 0 -0.31 2 2
DOCK7 -0.013 0.14 -9999 0 -0.38 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.054 0.15 -9999 0 -0.48 54 54
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.022 0.062 -9999 0 -0.32 3 3
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.15 -9999 0 -0.44 54 54
RAF1 -0.001 0.12 -9999 0 -0.4 18 18
ErbB2/ErbB3/neuregulin 2 -0.067 0.17 -9999 0 -0.51 64 64
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.082 -9999 0 -0.29 6 6
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.12 0.33 -9999 0 -0.68 116 116
FOS -0.1 0.28 -9999 0 -0.51 151 151
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.13 -9999 0 -0.4 54 54
MAPK3 -0.08 0.26 -9999 0 -0.5 113 113
MAPK1 -0.08 0.26 -9999 0 -0.5 113 113
JAK2 -0.012 0.13 -9999 0 -0.38 56 56
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.014 0.13 -9999 0 -0.37 54 54
NRG1 -0.065 0.24 -9999 0 -0.79 47 47
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.13 -9999 0 -0.35 64 64
MAPK9 -0.022 0.06 -9999 0 -0.26 2 2
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.007 0.12 -9999 0 -0.73 12 12
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0.002 0.006 -9999 0 -10000 0 0
RNF41 0.027 0.007 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.086 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.053 0.2 -9999 0 -0.38 115 115
myelination 0.01 0.11 -9999 0 -0.46 3 3
PPP3CB -0.009 0.12 -9999 0 -0.36 28 28
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -9999 0 -0.64 2 2
NRG2 -0.079 0.26 -9999 0 -0.79 57 57
mol:GDP -0.014 0.13 -9999 0 -0.37 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.004 0.13 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.012 0.13 -9999 0 -0.38 55 55
MAP2K1 -0.072 0.23 -9999 0 -0.45 96 96
heart morphogenesis -0.044 0.13 -9999 0 -0.4 54 54
RAS family/GDP -0.005 0.11 -9999 0 -0.63 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.008 -9999 0 -10000 0 0
CHRNE 0.01 0.035 -9999 0 -0.13 18 18
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.044 0.13 -9999 0 -0.4 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.031 0.14 -9999 0 -0.58 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.054 0.11 -9999 0 -0.61 3 3
alphaV/beta3 Integrin/Osteopontin/Src -0.064 0.15 -9999 0 -0.61 25 25
AP1 -0.26 0.35 -9999 0 -0.85 110 110
ILK -0.031 0.15 -9999 0 -0.61 6 6
bone resorption -0.04 0.16 -9999 0 -0.64 11 11
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.051 0.12 -9999 0 -0.56 6 6
ITGAV 0.01 0.052 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.032 0.14 -9999 0 -0.62 25 25
alphaV/beta3 Integrin/Osteopontin -0.068 0.15 -9999 0 -0.54 39 39
MAP3K1 -0.031 0.15 -9999 0 -0.49 39 39
JUN -0.17 0.35 -9999 0 -0.81 112 112
MAPK3 -0.031 0.14 -9999 0 -0.59 6 6
MAPK1 -0.031 0.14 -9999 0 -0.59 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 -0.031 0.17 -9999 0 -0.49 46 46
ITGB3 -0.011 0.14 -9999 0 -0.81 15 15
NFKBIA -0.025 0.14 -9999 0 -0.61 5 5
FOS -0.2 0.36 -9999 0 -0.81 127 127
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.17 -9999 0 -0.69 4 4
NF kappa B1 p50/RelA -0.059 0.11 -9999 0 -0.66 2 2
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.65 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.031 0.15 -9999 0 -0.49 39 39
VAV3 -0.026 0.15 -9999 0 -0.46 44 44
MAP3K14 -0.039 0.15 -9999 0 -0.49 39 39
ROCK2 -0.028 0.18 -9999 0 -0.81 25 25
SPP1 -0.078 0.2 -9999 0 -0.42 104 104
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.045 0.13 -9999 0 -0.57 7 7
MMP2 -0.17 0.29 -9999 0 -0.66 101 101
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.038 0.037 -9999 0 -10000 0 0
VDR 0.013 0.015 -9999 0 -0.31 1 1
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.057 0.11 -9999 0 -0.35 47 47
RXRs/LXRs/DNA/Oxysterols -0.047 0.15 -9999 0 -0.46 57 57
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.083 -9999 0 -0.34 24 24
RXRs/NUR77 -0.26 0.25 -9999 0 -0.62 149 149
RXRs/PPAR -0.054 0.064 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.009 -9999 0 -0.21 1 1
RARs/VDR/DNA/Vit D3 -0.013 0.079 -9999 0 -0.47 14 14
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.013 0.078 -9999 0 -0.47 14 14
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.053 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.021 0.083 -9999 0 -0.34 24 24
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.009 -9999 0 -0.21 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.082 -9999 0 -0.58 4 4
NR1H4 0.001 0.032 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.096 0.091 -9999 0 -0.57 4 4
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.1 0.067 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.81 147 147
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.047 0.048 -9999 0 -0.32 4 4
RXRG -0.28 0.12 -9999 0 -0.31 437 437
RXR alpha/CCPG 0.021 0.009 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.005 0.12 -9999 0 -0.81 11 11
PPARG -0.002 0.1 -9999 0 -0.6 12 12
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 57 57
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.046 0.15 -9999 0 -0.45 57 57
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.14 -9999 0 -0.81 14 14
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.44 172 172
SREBF1 -0.036 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.082 -9999 0 -0.58 4 4
ABCA1 -0.036 0.14 -9999 0 -0.62 3 3
RARs/THRs -0.023 0.1 -9999 0 -0.48 24 24
RXRs/FXR -0.12 0.071 -9999 0 -0.55 4 4
BCL2 -0.047 0.22 -9999 0 -0.81 36 36
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 -0.11 0.18 -9999 0 -0.46 65 65
IKBKB -0.018 0.073 -9999 0 -0.29 7 7
AKT1 -0.042 0.1 -9999 0 -0.26 25 25
IKBKG -0.017 0.077 -9999 0 -0.3 8 8
CALM1 -0.036 0.087 -9999 0 -0.35 3 3
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
MAP3K1 -0.076 0.18 -9999 0 -0.65 18 18
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.046 0.091 -9999 0 -0.37 3 3
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.081 0.13 -9999 0 -0.28 111 111
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.17 0.24 -9999 0 -0.52 145 145
CD22 -0.15 0.23 -9999 0 -0.51 109 109
CAMK2G -0.026 0.082 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
SHC/GRB2/SOS1 -0.098 0.15 -9999 0 -10000 0 0
GO:0007205 -0.046 0.092 -9999 0 -0.38 3 3
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.037 0.088 -9999 0 -0.35 3 3
NFATC1 -0.071 0.16 -9999 0 -0.55 22 22
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.52 145 145
PAG1/CSK -0.002 0.029 -9999 0 -0.62 1 1
NFKBIB 0.003 0.028 -9999 0 -0.11 3 3
HRAS -0.039 0.1 -9999 0 -0.34 4 4
NFKBIA 0.003 0.028 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.009 0.025 -9999 0 -0.19 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 100 100
mol:GDP -0.042 0.084 -9999 0 -0.35 3 3
PTEN 0.012 0.037 -9999 0 -0.81 1 1
CD79B -0.03 0.11 -9999 0 -0.31 67 67
NF-kappa-B/RelA/I kappa B alpha 0.009 0.025 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.089 0.18 -9999 0 -0.43 77 77
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.052 0.089 -9999 0 -0.38 3 3
CSK 0.013 0.015 -9999 0 -0.31 1 1
FOS -0.14 0.21 -9999 0 -0.47 127 127
CHUK -0.017 0.077 -9999 0 -0.31 7 7
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.068 0.1 -9999 0 -0.5 12 12
PTPN6 -0.14 0.21 -9999 0 -0.61 53 53
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.035 -9999 0 -0.13 19 19
VAV2 -0.14 0.19 -9999 0 -0.85 13 13
ubiquitin-dependent protein catabolic process 0.008 0.027 -9999 0 -0.11 3 3
BTK -0.018 0.16 -9999 0 -1.2 8 8
CD19 -0.15 0.2 -9999 0 -0.46 102 102
MAP4K1 -0.021 0.13 -9999 0 -0.81 7 7
CD72 0.011 0.029 -9999 0 -0.31 4 4
PAG1 0.012 0.037 -9999 0 -0.81 1 1
MAPK14 -0.057 0.16 -9999 0 -0.53 18 18
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.036 0.09 -9999 0 -0.32 1 1
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.064 0.17 -9999 0 -0.43 76 76
RAF1 -0.029 0.096 -9999 0 -10000 0 0
RasGAP/p62DOK/SHIP -0.14 0.2 -9999 0 -0.47 97 97
CD79A -0.19 0.3 -9999 0 -0.52 190 190
re-entry into mitotic cell cycle -0.08 0.13 -9999 0 -0.28 111 111
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.01 0.085 -9999 0 -10000 0 0
MAPK1 -0.01 0.085 -9999 0 -10000 0 0
CD72/SHP1 -0.1 0.21 -9999 0 -0.58 49 49
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 -0.065 0.17 -9999 0 -0.54 26 26
actin cytoskeleton organization -0.089 0.18 -9999 0 -0.68 13 13
NF-kappa-B/RelA 0.023 0.045 -9999 0 -0.2 1 1
Calcineurin -0.036 0.06 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.54 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.056 0.087 -9999 0 -0.34 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -0.98 23 23
DAPP1 -0.14 0.26 -9999 0 -1.2 20 20
cytokine secretion -0.066 0.15 -9999 0 -0.5 22 22
mol:DAG -0.052 0.089 -9999 0 -0.38 3 3
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.019 0.091 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.24 -9999 0 -0.57 99 99
mol:PI-3-4-5-P3 -0.097 0.12 -9999 0 -0.36 32 32
ETS1 -0.017 0.077 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.46 79 79
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.49 85 85
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
RAC1 -0.095 0.19 -9999 0 -0.75 13 13
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.55 85 85
CARD11 -0.075 0.14 -9999 0 -0.55 16 16
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0 0.036 -9999 0 -0.14 2 2
PTPRC -0.034 0.18 -9999 0 -0.58 39 39
PDPK1 -0.044 0.1 -9999 0 -0.27 25 25
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.025 -9999 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.044 0.15 -9999 0 -0.54 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.59 1 1
AP1 -0.25 0.36 -9999 0 -0.68 176 176
mol:PIP3 -0.041 0.12 -9999 0 -0.42 43 43
AKT1 -0.002 0.11 -9999 0 -0.58 5 5
PTK2B 0 0.085 -9999 0 -0.27 40 40
RHOA 0.031 0.046 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.074 -9999 0 -10000 0 0
MAGI3 0.012 0.037 -9999 0 -0.81 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.014 0.13 -9999 0 -0.44 39 39
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.087 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.54 13 13
endothelial cell migration -0.027 0.2 -9999 0 -0.64 41 41
ADCY4 -0.014 0.19 -9999 0 -0.61 40 40
ADCY5 -0.044 0.21 -9999 0 -0.64 43 43
ADCY6 -0.014 0.19 -9999 0 -0.61 40 40
ADCY7 -0.014 0.19 -9999 0 -0.61 40 40
ADCY1 -0.017 0.19 -9999 0 -0.62 40 40
ADCY2 -0.036 0.21 -9999 0 -0.66 40 40
ADCY3 -0.014 0.19 -9999 0 -0.61 40 40
ADCY8 -0.055 0.19 -9999 0 -0.63 43 43
ADCY9 -0.014 0.19 -9999 0 -0.61 40 40
GSK3B 0.009 0.081 -9999 0 -0.3 13 13
arachidonic acid secretion -0.007 0.18 -9999 0 -0.5 53 53
GNG2 0.012 0.037 -9999 0 -0.81 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.039 0.2 -9999 0 -0.59 54 54
HRAS 0.012 0.021 -9999 0 -0.31 2 2
NFKBIA 0.01 0.079 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.035 0.11 -9999 0 -0.97 6 6
JUN -0.17 0.35 -9999 0 -0.81 112 112
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.045 0.13 -9999 0 -1.2 6 6
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.003 0.075 -9999 0 -10000 0 0
PLCB3 0.03 0.009 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
positive regulation of mitosis -0.007 0.18 -9999 0 -0.5 53 53
LPA/LPA1-2-3 -0.049 0.15 -9999 0 -0.54 39 39
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 0.004 0.11 -9999 0 -0.35 39 39
GNAZ -0.02 0.17 -9999 0 -0.56 41 41
EGFR/PI3K-beta/Gab1 -0.043 0.13 -9999 0 -0.46 34 34
positive regulation of dendritic cell cytokine production -0.049 0.15 -9999 0 -0.53 39 39
LPA/LPA2/MAGI-3 -0.002 0.027 -9999 0 -0.59 1 1
ARHGEF1 0 0.15 -9999 0 -0.49 39 39
GNAI2 -0.02 0.17 -9999 0 -0.56 41 41
GNAI3 -0.02 0.17 -9999 0 -0.56 41 41
GNAI1 -0.021 0.17 -9999 0 -0.56 42 42
LPA/LPA3 -0.01 0.044 -9999 0 -0.27 2 2
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.055 0.18 -9999 0 -0.65 41 41
HB-EGF/EGFR -0.054 0.17 -9999 0 -0.53 50 50
HBEGF -0.061 0.19 -9999 0 -0.61 45 45
mol:DAG 0.003 0.075 -9999 0 -10000 0 0
cAMP biosynthetic process -0.026 0.2 -9999 0 -0.56 53 53
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
SRC 0.013 0.015 -9999 0 -10000 0 0
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.01 0.079 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -0.31 21 21
LPAR1 -0.05 0.23 -9999 0 -0.83 39 39
IL8 -0.13 0.2 -9999 0 -0.48 58 58
PTK2 -0.009 0.15 -9999 0 -0.5 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.014 0.13 -9999 0 -0.44 39 39
EGFR 0.005 0.083 -9999 0 -0.81 5 5
PLCG1 -0.016 0.085 -9999 0 -0.3 13 13
PLD2 -0.009 0.15 -9999 0 -0.5 39 39
G12/G13 -0.043 0.15 -9999 0 -0.53 39 39
PI3K-beta -0.031 0.11 -9999 0 -0.7 5 5
cell migration -0.016 0.059 -9999 0 -0.25 11 11
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.11 -9999 0 -0.36 39 39
HRAS/GTP -0.009 0.19 -9999 0 -0.52 53 53
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
PRKCE 0.005 0.083 -9999 0 -0.82 5 5
PRKCD 0.011 0.072 -9999 0 -10000 0 0
Gi(beta/gamma) -0.008 0.18 -9999 0 -0.58 40 40
mol:LPA 0.003 0.019 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.029 0.13 -9999 0 -0.45 39 39
MAPKKK cascade -0.007 0.18 -9999 0 -0.5 53 53
contractile ring contraction involved in cytokinesis 0.031 0.045 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.088 0.2 -9999 0 -0.43 118 118
GNA15 0.009 0.054 -9999 0 -0.35 2 2
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.009 0.089 -9999 0 -0.43 5 5
GNA11 0.01 0.069 -9999 0 -0.42 10 10
Rac1/GTP -0.036 0.11 -9999 0 -1 6 6
MMP2 -0.028 0.2 -9999 0 -0.64 41 41
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.043 -9999 0 -0.92 1 1
VEGFR1 homodimer/NRP1 -0.002 0.042 -9999 0 -0.93 1 1
mol:DAG -0.012 0.16 -9999 0 -0.48 51 51
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.067 -9999 0 -0.76 3 3
CaM/Ca2+ -0.004 0.15 -9999 0 -0.45 51 51
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.16 -9999 0 -0.44 53 53
PLCG1 -0.012 0.16 -9999 0 -0.49 51 51
NOS3 0.017 0.15 -9999 0 -0.42 51 51
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.018 0.15 -9999 0 -0.41 51 51
FLT1 0.031 0.048 -9999 0 -1 1 1
PGF -0.07 0.25 -9999 0 -0.81 50 50
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.073 -9999 0 -0.76 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
eNOS/Hsp90 0.024 0.14 -9999 0 -0.39 51 51
endothelial cell proliferation -0.024 0.19 -9999 0 -0.51 52 52
mol:Ca2+ -0.012 0.16 -9999 0 -0.48 51 51
MAPK3 -0.012 0.17 -9999 0 -0.43 68 68
MAPK1 -0.012 0.17 -9999 0 -0.43 68 68
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.07 0.25 -9999 0 -0.81 50 50
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
VEGFA homodimer 0.008 0.064 -9999 0 -0.81 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.073 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.004 0.17 -9999 0 -0.46 19 19
PI3K -0.05 0.15 -9999 0 -0.46 53 53
PRKCA -0.021 0.18 -9999 0 -0.46 68 68
PRKCB -0.02 0.16 -9999 0 -0.46 55 55
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.54 51 51
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.012 0.16 -9999 0 -0.48 51 51
RASA1 0.041 0.04 -9999 0 -0.85 1 1
NRP2 -0.013 0.088 -9999 0 -0.31 40 40
VEGFR1 homodimer 0.03 0.047 -9999 0 -1 1 1
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.42 51 51
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
mol:PI-3-4-5-P3 -0.049 0.15 -9999 0 -0.46 53 53
mol:L-citrulline 0.018 0.15 -9999 0 -0.41 51 51
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.004 0.063 -9999 0 -0.72 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.066 -9999 0 -0.76 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.14 -9999 0 -0.44 53 53
PDPK1 0 0.16 -9999 0 -0.44 53 53
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.005 0.083 -9999 0 -0.89 3 3
mol:NADP 0.018 0.15 -9999 0 -0.41 51 51
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.061 -9999 0 -0.7 3 3
VEGFR1 homodimer/NRP2 0.018 0.065 -9999 0 -0.92 1 1
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.057 0.16 -9999 0 -0.55 43 43
MAP4K1 -0.021 0.13 -9999 0 -0.81 7 7
MAP3K8 0.002 0.098 -9999 0 -0.81 7 7
PRKCB -0.022 0.12 -9999 0 -0.36 46 46
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.012 0.11 -9999 0 -0.55 6 6
JUN -0.1 0.25 -9999 0 -0.51 123 123
MAP3K7 0.012 0.11 -9999 0 -0.55 6 6
GRAP2 -0.045 0.21 -9999 0 -0.75 38 38
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.11 -9999 0 -0.52 7 7
LAT 0.005 0.077 -9999 0 -0.65 6 6
LCP2 0.007 0.043 -9999 0 -0.31 9 9
MAPK8 -0.003 0.14 -9999 0 -0.75 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.003 0.12 -9999 0 -0.36 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.053 0.15 -9999 0 -0.52 43 43
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 0.012 0.037 -10000 0 -0.81 1 1
Jak2/Leptin Receptor -0.025 0.097 0.2 18 -0.39 18 36
PTP1B/AKT1 -0.004 0.064 -10000 0 -0.3 4 4
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.013 0.07 -10000 0 -0.31 5 5
EGFR 0.003 0.084 -10000 0 -0.82 5 5
EGF/EGFR -0.085 0.18 -10000 0 -0.5 77 77
CSF1 0 0.1 -10000 0 -0.81 8 8
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.33 52 52
Insulin Receptor/Insulin -0.016 0.054 -10000 0 -0.44 4 4
HCK -0.01 0.084 -10000 0 -0.31 36 36
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.004 0.067 -10000 0 -0.31 4 4
EGF -0.11 0.29 -10000 0 -0.78 78 78
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.019 0.1 -10000 0 -0.36 8 8
TXN 0.011 0.015 -10000 0 -0.31 1 1
PTP1B/IRS1/GRB2 -0.055 0.17 -10000 0 -0.49 60 60
cell migration 0.013 0.07 0.31 5 -10000 0 5
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.044 0.19 -10000 0 -0.64 40 40
ITGA2B -0.076 0.26 -10000 0 -0.82 53 53
CSF1R 0.008 0.049 -10000 0 -0.39 6 6
Prolactin Receptor/Prolactin -0.039 0.15 -10000 0 -0.63 26 26
FGR 0.011 0.029 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.005 0.066 -10000 0 -0.31 4 4
Crk/p130 Cas 0 0.061 -10000 0 -0.34 2 2
DOK1 0.005 0.064 -10000 0 -0.3 3 3
JAK2 -0.013 0.092 -10000 0 -0.4 14 14
Jak2/Leptin Receptor/Leptin -0.051 0.13 -10000 0 -0.56 25 25
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.013 0.071 -10000 0 -0.32 5 5
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.18 0.19 -10000 0 -0.34 279 279
SRC 0.011 0.03 -10000 0 -10000 0 0
ITGB3 -0.013 0.14 -10000 0 -0.82 15 15
CAT1/PTP1B -0.09 0.15 -10000 0 -0.38 63 63
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0.015 -10000 0 -0.31 1 1
PI3K -0.018 0.061 -10000 0 -0.5 6 6
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.049 0.13 -10000 0 -0.6 24 24
negative regulation of transcription -0.013 0.091 -10000 0 -0.39 14 14
FCGR2A -0.007 0.084 -10000 0 -0.33 30 30
FER 0.007 0.065 -10000 0 -0.82 3 3
alphaIIb/beta3 Integrin -0.083 0.23 -10000 0 -0.68 62 62
BLK -0.24 0.37 -10000 0 -0.74 168 168
Insulin Receptor/Insulin/Shc -0.003 0.042 -10000 0 -0.54 3 3
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.004 0.085 -10000 0 -0.67 7 7
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 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.44 67 67
PRL 0.001 0.015 -10000 0 -0.3 1 1
SOCS3 -0.056 0.32 -10000 0 -1.5 23 23
SPRY2 0.009 0.055 -10000 0 -0.65 3 3
Insulin Receptor/Insulin/IRS1 -0.069 0.18 -10000 0 -0.55 62 62
CSF1/CSF1R -0.009 0.094 -10000 0 -0.48 11 11
Ras protein signal transduction 0.021 0.023 -10000 0 -10000 0 0
IRS1 -0.085 0.27 -10000 0 -0.81 59 59
INS -0.004 0.063 -10000 0 -0.82 3 3
LEP -0.008 0.067 -10000 0 -0.31 23 23
STAT5B -0.009 0.071 -10000 0 -0.27 10 10
STAT5A -0.009 0.071 -10000 0 -0.27 10 10
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.069 -10000 0 -0.36 4 4
CSN2 -0.007 0.054 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
LAT 0.001 0.066 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.01 0.11 -10000 0 -0.42 27 27
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 214 214
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.08 -9999 0 -0.71 6 6
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.57 16 16
PTK2 0.015 0.15 -9999 0 -0.53 17 17
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.025 0.1 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -10000 0 0
CDKN1B -0.063 0.18 -9999 0 -0.61 45 45
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
ILK -0.063 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.024 0.18 -9999 0 -0.56 45 45
PTK2B 0.018 0.11 -9999 0 -0.49 22 22
alphaV/beta3 Integrin/JAM-A -0.059 0.16 -9999 0 -0.47 60 60
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.1 -9999 0 -0.57 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.26 -9999 0 -0.53 159 159
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.003 0.11 -9999 0 -0.54 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.1 -9999 0 -0.57 16 16
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.25 -9999 0 -0.55 169 169
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
alphaV/beta3 Integrin/Osteopontin -0.069 0.16 -9999 0 -0.56 39 39
RPS6KB1 -0.2 0.24 -9999 0 -0.56 119 119
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.094 0.15 -9999 0 -0.74 16 16
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.094 0.15 -9999 0 -0.74 16 16
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.034 0.15 -9999 0 -0.61 28 28
cell adhesion -0.029 0.099 -9999 0 -0.53 16 16
ANGPTL3 0.005 0.026 -9999 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.071 -9999 0 -0.62 6 6
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.064 -9999 0 -0.81 3 3
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
IGF1 -0.18 0.35 -9999 0 -0.79 119 119
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.1 -9999 0 -0.57 16 16
apoptosis 0.01 0.052 -9999 0 -0.81 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.1 -9999 0 -0.57 16 16
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.039 0.14 -9999 0 -0.6 24 24
CSF1 0 0.1 -9999 0 -0.81 8 8
PIK3C2A -0.064 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.054 0.14 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.11 -9999 0 -0.53 22 22
FAK1/Vinculin 0.023 0.12 -9999 0 -0.48 8 8
alphaV beta3/Integrin/ppsTEM5 -0.018 0.1 -9999 0 -0.57 16 16
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.067 0.24 -9999 0 -0.75 52 52
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.037 0.11 -9999 0 -0.57 16 16
alphaV/beta3 Integrin/TGFBR2 -0.022 0.12 -9999 0 -0.59 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.075 -9999 0 -0.54 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.095 -9999 0 -0.53 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.14 -9999 0 -0.31 359 359
alphaV/beta3 Integrin/Pyk2 -0.022 0.11 -9999 0 -0.5 22 22
SDC1 0.01 0.032 -9999 0 -0.31 5 5
VAV3 0.026 0.097 -9999 0 -0.52 14 14
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
FAK1/Paxillin 0.023 0.12 -9999 0 -0.48 8 8
cell migration 0.033 0.12 -9999 0 -0.42 8 8
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
PI3K -0.055 0.15 -9999 0 -0.84 4 4
SPP1 -0.078 0.2 -9999 0 -0.42 104 104
KDR 0.007 0.074 -9999 0 -0.81 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.052 -9999 0 -0.81 2 2
COL4A3 -0.012 0.14 -9999 0 -0.81 15 15
angiogenesis -0.083 0.18 -9999 0 -0.59 37 37
Rac1/GTP -0.013 0.082 -9999 0 -0.47 14 14
EDIL3 -0.024 0.14 -9999 0 -0.43 42 42
cell proliferation -0.021 0.11 -9999 0 -0.59 18 18
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.011 0.22 -10000 0 -0.97 21 21
NCK1/PAK1/Dok-R -0.028 0.09 -10000 0 -0.43 21 21
NCK1/Dok-R -0.068 0.25 -10000 0 -1.2 21 21
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
mol:beta2-estradiol -0.003 0.047 0.25 15 -10000 0 15
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.01 0.069 0.26 4 -0.33 12 16
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.06 0.23 -10000 0 -1.1 21 21
FN1 -0.22 0.14 -10000 0 -0.31 359 359
PLD2 0 0.28 -10000 0 -1.3 21 21
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
GRB14 -0.01 0.14 -10000 0 -0.81 14 14
ELK1 0.016 0.24 -10000 0 -1.1 21 21
GRB7 -0.04 0.12 -10000 0 -0.31 82 82
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.1 0.25 -10000 0 -1.2 21 21
CDKN1A -0.009 0.17 -10000 0 -0.64 21 21
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.068 0.25 -10000 0 -1.2 21 21
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.027 0.17 -10000 0 -0.69 21 21
PLG -0.009 0.28 -10000 0 -1.3 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.01 0.21 -10000 0 -0.93 21 21
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
ANGPT2 -0.11 0.22 -10000 0 -0.78 19 19
BMX -0.014 0.29 -10000 0 -1.3 21 21
ANGPT1 -0.037 0.29 -10000 0 -1.5 18 18
tube development -0.016 0.18 -10000 0 -0.73 21 21
ANGPT4 -0.061 0.23 -10000 0 -0.74 49 49
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 0.3 -10000 0 -1.3 21 21
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.019 0.21 -10000 0 -0.84 21 21
mol:L-citrulline 0.027 0.17 -10000 0 -0.69 21 21
AGTR1 -0.32 0.4 -10000 0 -0.81 200 200
MAPK14 -0.011 0.27 -10000 0 -1.2 21 21
Tie2/SHP2 -0.027 0.16 -10000 0 -1.4 6 6
TEK 0.014 0.19 -10000 0 -1.5 6 6
RPS6KB1 0.011 0.21 -10000 0 -0.93 21 21
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.63 199 199
Tie2/Ang1/GRB2 -0.005 0.29 -10000 0 -1.3 21 21
MAPK3 0.011 0.25 -10000 0 -1.1 21 21
MAPK1 0.011 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.028 0.29 -10000 0 -1.3 21 21
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
MAPK8 -0.008 0.29 -10000 0 -1.3 21 21
PI3K -0.004 0.26 -10000 0 -1.1 21 21
FES -0.011 0.27 -10000 0 -1.2 21 21
Crk/Dok-R -0.068 0.25 -10000 0 -1.2 21 21
Tie2/Ang1/ABIN2 -0.005 0.29 -10000 0 -1.3 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.016 0.2 -10000 0 -0.85 21 21
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.011 0.21 -10000 0 -0.93 21 21
Tie2/Ang2 -0.039 0.24 -10000 0 -1 21 21
Tie2/Ang1 -0.012 0.31 -10000 0 -1.4 21 21
FOXO1 0.022 0.2 -10000 0 -0.86 21 21
ELF1 0.015 0.078 -10000 0 -0.84 4 4
ELF2 -0.003 0.27 -10000 0 -1.2 21 21
mol:Choline 0.003 0.26 -10000 0 -1.2 21 21
cell migration -0.023 0.055 -10000 0 -0.24 21 21
FYN -0.022 0.21 -10000 0 -0.85 21 21
DOK2 -0.001 0.078 -10000 0 -0.36 19 19
negative regulation of cell cycle -0.006 0.16 -10000 0 -0.58 21 21
ETS1 0.016 0.045 -10000 0 -10000 0 0
PXN 0.024 0.18 -10000 0 -0.75 21 21
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.024 0.19 -10000 0 -0.8 21 21
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.085 0.27 -10000 0 -0.77 64 64
MAPKKK cascade 0.003 0.26 -10000 0 -1.2 21 21
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.008 0.29 -10000 0 -1.3 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.15 -10000 0 -0.61 21 21
mol:Phosphatidic acid 0.003 0.26 -10000 0 -1.2 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.027 0.17 -10000 0 -0.69 21 21
Rac1/GTP -0.049 0.18 -10000 0 -0.86 21 21
MMP2 -0.007 0.29 -10000 0 -1.3 21 21
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.003 0.04 -10000 0 -0.62 2 2
Necdin/E2F1 -0.067 0.11 -10000 0 -0.75 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.035 0.1 -10000 0 -0.48 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.28 -10000 0 -0.56 234 234
NT-4/5 (dimer)/p75(NTR) -0.074 0.18 -10000 0 -0.66 37 37
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.003 0.12 -10000 0 -0.48 23 23
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.61 22 22
MGDIs/NGR/p75(NTR)/LINGO1 -0.048 0.12 -10000 0 -0.56 18 18
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.057 0.14 -10000 0 -0.54 32 32
LINGO1 -0.003 0.071 -10000 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.025 -10000 0 -10000 0 0
proBDNF (dimer) -0.014 0.14 -10000 0 -0.61 22 22
NTRK1 -0.002 0.062 -10000 0 -0.31 19 19
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.01 0.13 -10000 0 -0.48 26 26
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.02 0.13 -10000 0 -0.56 20 20
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.039 0.11 -10000 0 -0.51 20 20
MAGEH1 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.044 0.12 -10000 0 -0.51 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.49 25 25
proNGF (dimer) 0.006 0.069 -10000 0 -0.56 6 6
MAGED1 0.013 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.66 26 26
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.036 0.1 -10000 0 -0.48 20 20
NGF 0.006 0.069 -10000 0 -0.56 6 6
cell cycle arrest 0.043 0.16 -10000 0 -0.46 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.085 -10000 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.064 0.16 -10000 0 -0.57 39 39
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.045 0.12 -10000 0 -0.56 21 21
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.009 0.12 -10000 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.07 -10000 0 -0.43 2 2
p75(NTR)/beta APP -0.049 0.13 -10000 0 -0.62 18 18
BEX1 -0.35 0.41 -10000 0 -0.81 219 219
mol:GDP -0.03 0.13 -10000 0 -0.57 20 20
NGF (dimer) -0.093 0.12 -10000 0 -0.5 30 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.042 0.11 -10000 0 -0.51 18 18
PIK3R1 0.013 0 -10000 0 -10000 0 0
RAC1/GTP -0.038 0.1 -10000 0 -0.49 20 20
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.045 0.12 -10000 0 -0.56 21 21
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.061 0.092 -10000 0 -10000 0 0
NT3 (dimer) -0.048 0.2 -10000 0 -0.6 49 49
TP53 -0.005 0.13 -10000 0 -0.44 32 32
PRDM4 -0.009 0.12 -10000 0 -0.51 20 20
BDNF (dimer) -0.13 0.16 -10000 0 -0.53 41 41
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.035 0.1 -10000 0 -0.47 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.11 -10000 0 -0.52 22 22
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 0.023 0.12 -10000 0 -0.44 20 20
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.009 0.12 -10000 0 -0.51 20 20
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.044 0.12 -10000 0 -0.56 20 20
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -10000 0 -0.62 1 1
NT3 (dimer)/p75(NTR) -0.092 0.2 -10000 0 -0.66 45 45
MAPK8 0.017 0.13 -10000 0 -0.45 20 20
MAPK9 0.024 0.12 -10000 0 -0.43 19 19
APAF1 0.012 0.037 -10000 0 -0.81 1 1
NTF3 -0.048 0.2 -10000 0 -0.6 49 49
NTF4 -0.022 0.16 -10000 0 -0.66 26 26
NDN 0.005 0.083 -10000 0 -0.81 5 5
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.094 -10000 0 -0.44 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.053 -10000 0 -0.65 3 3
RhoA-B-C/GTP -0.045 0.12 -10000 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.12 -10000 0 -0.48 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.052 0.13 -10000 0 -0.51 32 32
PRKACB 0.012 0.037 -10000 0 -0.81 1 1
proBDNF (dimer)/p75 ECD -0.023 0.11 -10000 0 -0.62 15 15
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.066 0.17 0.24 188 -0.46 20 208
BAD 0.028 0.12 -10000 0 -0.43 20 20
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.06 0.18 -10000 0 -0.42 84 84
CYCS 0 0.11 -10000 0 -0.48 20 20
ADAM17 0.01 0.053 -10000 0 -0.81 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.041 0.11 -10000 0 -0.52 22 22
BCL2L11 0.028 0.12 -10000 0 -0.43 20 20
BDNF (dimer)/p75(NTR) -0.069 0.16 -10000 0 -0.62 32 32
PI3K -0.042 0.12 -10000 0 -0.52 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.039 0.11 -10000 0 -0.51 20 20
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.054 0.14 -10000 0 -0.65 20 20
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.039 0.11 -10000 0 -0.51 20 20
TRAF6 0.01 0.053 -10000 0 -0.81 2 2
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG -0.004 0.039 -10000 0 -0.31 8 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.017 0.14 -10000 0 -0.48 32 32
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 0.03 0.11 -10000 0 -0.4 20 20
E2F1 -0.085 0.15 -10000 0 -0.31 151 151
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.013 0.058 -10000 0 -0.53 3 3
NGF (dimer)/TRKA -0.013 0.063 -10000 0 -0.63 3 3
MMP7 -0.17 0.22 -10000 0 -0.37 243 243
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.037 0.11 -10000 0 -0.48 22 22
MMP3 -0.039 0.11 -10000 0 -0.31 69 69
APAF-1/Caspase 9 -0.04 0.11 -10000 0 -0.6 7 7
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.005 0.074 -10000 0 -0.81 4 4
SMAD3/SMAD4/ER alpha -0.051 0.14 -10000 0 -0.58 24 24
AKT1 0.008 0.011 -10000 0 -10000 0 0
GSC -0.2 0.54 -10000 0 -1.5 68 68
NKX2-5 0.002 0.028 -10000 0 -10000 0 0
muscle cell differentiation 0.025 0.05 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.08 -10000 0 -10000 0 0
SMAD4 -0.011 0.06 -10000 0 -0.26 1 1
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.076 -10000 0 -0.54 5 5
SMAD3/SMAD4/VDR 0.009 0.044 -10000 0 -10000 0 0
MYC 0.003 0.13 -10000 0 -0.82 12 12
CDKN2B -0.075 0.14 -10000 0 -10000 0 0
AP1 -0.25 0.5 -10000 0 -0.95 151 151
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.055 -10000 0 -0.7 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.061 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.011 0.075 -10000 0 -0.31 23 23
SMAD3/SMAD4/GR -0.017 0.046 -10000 0 -10000 0 0
GATA3 -0.031 0.18 -10000 0 -0.79 26 26
SKI/SIN3/HDAC complex/NCoR1 0.041 0.029 -10000 0 -10000 0 0
MEF2C/TIF2 -0.039 0.17 -10000 0 -0.6 20 20
endothelial cell migration -0.007 0.1 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.012 0.004 -10000 0 -10000 0 0
RBBP4 0.007 0.064 -10000 0 -0.81 3 3
RUNX2 -0.072 0.15 -10000 0 -0.32 128 128
RUNX3 -0.012 0.13 -10000 0 -0.61 20 20
RUNX1 -0.13 0.16 -10000 0 -0.31 215 215
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
CDKN1A 0.025 0.069 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.035 0.094 -10000 0 -0.44 3 3
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.007 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.043 0.13 -10000 0 -0.59 22 22
SMAD3/SMAD4/ATF3 -0.16 0.26 -10000 0 -0.62 118 118
SAP30 0.01 0.037 -10000 0 -0.82 1 1
Cbp/p300/PIAS3 0.032 0.044 -10000 0 -10000 0 0
JUN -0.24 0.5 -10000 0 -0.94 150 150
SMAD3/SMAD4/IRF7 -0.017 0.046 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.004 0.1 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.064 0.094 0.46 4 -10000 0 4
DLX1 -0.03 0.18 -10000 0 -0.81 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.39 -10000 0 -0.88 127 127
SMAD3/SMAD4/Max -0.017 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.04 -10000 0 -0.54 2 2
ZBTB17 0.021 0.011 -10000 0 -10000 0 0
LAMC1 0.025 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.018 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.015 -10000 0 -0.31 1 1
ESR1 -0.047 0.19 -10000 0 -0.52 55 55
HNF4A -0.003 0.044 -10000 0 -0.31 10 10
MEF2C 0.005 0.097 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.032 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.024 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.016 0.025 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.037 -10000 0 -0.81 1 1
HDAC1 0.012 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.053 -10000 0 -0.81 2 2
GCN5L2 0.005 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.01 0.048 -10000 0 -10000 0 0
MSG1/HSC70 -0.17 0.1 -10000 0 -0.68 9 9
SMAD2 -0.002 0.039 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.074 -10000 0 -0.36 13 13
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.014 0.076 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.098 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 407 407
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.007 0.13 -10000 0 -0.81 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.08 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.083 0.11 -10000 0 -0.56 12 12
SMAD7 -0.1 0.28 -10000 0 -0.6 96 96
MYC/MIZ-1 0.014 0.11 -10000 0 -0.62 12 12
SMAD3/SMAD4 0.061 0.1 0.31 43 -0.35 1 44
IL10 -0.028 0.19 -10000 0 -0.62 39 39
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.016 0.14 -10000 0 -0.5 25 25
CDK4 0.018 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.35 -10000 0 -0.79 125 125
SMAD3/SMAD4/SP1 -0.016 0.055 -10000 0 -10000 0 0
FOXG1 -0.001 0.06 -10000 0 -0.35 12 12
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.005 0.096 -10000 0 -0.99 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.048 0.14 -10000 0 -0.59 26 26
MYOD1 -0.001 0.028 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.053 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.052 0.14 -10000 0 -0.53 31 31
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.037 -10000 0 -0.81 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.076 0.11 -10000 0 -0.53 15 15
SMAD3/SMAD4/SP1-3 0.008 0.059 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.021 -10000 0 -10000 0 0
SIN3B 0.012 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.013 0.095 -10000 0 -0.52 2 2
ITGB5 0.036 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.59 209 209
AR -0.34 0.41 -10000 0 -0.81 209 209
negative regulation of cell growth -0.04 0.13 -10000 0 -0.44 8 8
SMAD3/SMAD4/MYOD -0.023 0.05 -10000 0 -10000 0 0
E2F5 0.012 0.037 -10000 0 -0.81 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.01 0.067 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.066 -10000 0 -10000 0 0
TFDP1 0.012 0.037 -10000 0 -0.81 1 1
SMAD3/SMAD4/AP1 -0.26 0.51 -10000 0 -0.97 150 150
SMAD3/SMAD4/RUNX2 -0.064 0.094 -10000 0 -0.46 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.023 0.17 -10000 0 -0.81 22 22
Aurora C 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
INCENP 0.01 0.053 -9999 0 -0.81 2 2
Aurora C/Aurora B/INCENP -0.04 0.076 -9999 0 -0.38 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.02 -9999 0 -10000 0 0
AURKB -0.061 0.14 -9999 0 -0.31 113 113
AURKC 0 0.065 -9999 0 -0.31 21 21
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.018 0.1 -9999 0 -0.33 10 10
AP1 -0.2 0.28 -9999 0 -0.61 137 137
mol:PIP3 -0.016 0.15 -9999 0 -0.42 39 39
IKBKB 0.004 0.092 -9999 0 -0.28 15 15
AKT1 -0.015 0.14 -9999 0 -0.58 6 6
IKBKG 0.004 0.092 -9999 0 -0.26 20 20
MS4A2 -0.065 0.14 -9999 0 -0.31 114 114
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
MAP3K1 0.01 0.1 -9999 0 -0.46 7 7
mol:Ca2+ -0.008 0.12 -9999 0 -0.31 39 39
LYN 0.012 0.005 -9999 0 -10000 0 0
CBLB -0.009 0.087 -9999 0 -0.35 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.081 0.18 -9999 0 -0.5 80 80
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
PLD2 -0.046 0.14 -9999 0 -0.44 39 39
PTPN13 -0.001 0.099 -9999 0 -0.55 6 6
PTPN11 0.011 0.039 -9999 0 -0.85 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.019 0.1 -9999 0 -0.34 6 6
SYK 0.012 0.005 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.43 39 39
LAT -0.014 0.098 -9999 0 -0.42 8 8
PAK2 0.002 0.11 -9999 0 -0.5 8 8
NFATC2 -0.15 0.28 -9999 0 -0.75 86 86
HRAS -0.007 0.12 -9999 0 -0.5 11 11
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.096 0.16 -9999 0 -0.46 66 66
Antigen/IgE/Fc epsilon R1 -0.087 0.15 -9999 0 -0.42 66 66
mol:GDP -0.016 0.13 -9999 0 -0.5 15 15
JUN -0.17 0.35 -9999 0 -0.81 112 112
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.077 -9999 0 -0.32 8 8
CHUK 0.004 0.092 -9999 0 -0.28 14 14
KLRG1 -0.021 0.1 -9999 0 -0.41 14 14
VAV1 -0.022 0.11 -9999 0 -0.48 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.009 0.087 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.019 0.1 -9999 0 -0.38 13 13
BTK -0.021 0.12 -9999 0 -0.58 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.19 -9999 0 -0.52 46 46
GAB2/PI3K/SHP2 -0.063 0.12 -9999 0 -0.59 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.017 0.092 -9999 0 -0.29 34 34
RAF1 0.018 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.2 -9999 0 -0.58 56 56
FCER1G -0.008 0.081 -9999 0 -0.32 32 32
FCER1A -0.073 0.22 -9999 0 -0.54 75 75
Antigen/IgE/Fc epsilon R1/Fyn -0.078 0.14 -9999 0 -0.47 40 40
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 0.005 0.11 -9999 0 -0.66 11 11
DUSP1 -0.12 0.3 -9999 0 -0.81 80 80
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.004 0.082 -9999 0 -0.33 3 3
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.042 0.1 -9999 0 -0.55 10 10
FER -0.012 0.096 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.073 0.17 -9999 0 -0.52 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.012 0.13 -9999 0 -0.53 12 12
cytokine secretion -0.014 0.032 -9999 0 -0.22 1 1
SPHK1 -0.013 0.091 -9999 0 -0.37 5 5
PTK2 -0.004 0.084 -9999 0 -0.36 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.13 -9999 0 -0.42 47 47
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.01 0.14 -9999 0 -0.4 39 39
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.046 0.092 -9999 0 -0.42 14 14
MAP2K4 0.021 0.007 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.2 -9999 0 -0.62 52 52
mol:Choline -0.045 0.14 -9999 0 -0.44 39 39
SHC/Grb2/SOS1 -0.03 0.064 -9999 0 -0.39 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.08 -9999 0 -0.36 1 1
HCLS1 -0.012 0.092 -9999 0 -0.38 5 5
PRKCB -0.009 0.12 -9999 0 -0.34 32 32
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.1 -9999 0 -0.39 13 13
LCP2 0.007 0.043 -9999 0 -0.31 9 9
PLA2G4A -0.039 0.15 -9999 0 -0.51 35 35
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.045 0.14 -9999 0 -0.44 39 39
IKK complex 0.019 0.075 -9999 0 -0.22 5 5
WIPF1 0.013 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.053 0.35 -9999 0 -0.91 13 13
PLK1 0.044 0.069 -9999 0 -10000 0 0
BIRC5 0.029 0.12 -9999 0 -1.5 1 1
HSPA1B 0.053 0.35 -9999 0 -0.9 14 14
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.048 0.36 -9999 0 -0.97 17 17
FOXM1 0.043 0.39 -9999 0 -0.99 21 21
XRCC1 0.053 0.35 -9999 0 -0.9 14 14
FOXM1B/p19 -0.092 0.3 -9999 0 -0.86 30 30
Cyclin D1/CDK4 0.04 0.33 -9999 0 -0.85 14 14
CDC2 0.047 0.36 -9999 0 -0.88 21 21
TGFA 0.025 0.34 -9999 0 -0.84 16 16
SKP2 0.046 0.36 -9999 0 -0.97 17 17
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.053 0.35 -9999 0 -0.91 13 13
RB1 -0.052 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.039 0.36 -9999 0 -0.96 21 21
AURKB -0.005 0.12 -9999 0 -10000 0 0
CENPF 0.048 0.36 -9999 0 -0.94 14 14
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.047 0.35 -9999 0 -0.92 21 21
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.037 0.34 -9999 0 -0.89 15 15
CDKN2A -0.12 0.16 -9999 0 -0.31 204 204
LAMA4 0.053 0.35 -9999 0 -0.9 14 14
FOXM1B/HNF6 0.031 0.37 -9999 0 -0.99 17 17
FOS -0.18 0.65 -9999 0 -1.2 128 128
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.053 0.35 -9999 0 -0.91 14 14
response to radiation 0.016 0.034 -9999 0 -10000 0 0
CENPB 0.053 0.35 -9999 0 -0.9 14 14
CENPA 0.039 0.37 -9999 0 -0.96 20 20
NEK2 0.044 0.36 -9999 0 -0.92 17 17
HIST1H2BA 0.045 0.35 -9999 0 -0.91 14 14
CCNA2 0.01 0.049 -9999 0 -0.32 10 10
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.042 0.37 -9999 0 -1 15 15
CCNB2 0.05 0.35 -9999 0 -0.93 15 15
CCNB1 0.049 0.36 -9999 0 -0.94 15 15
ETV5 0.053 0.35 -9999 0 -0.91 14 14
ESR1 0.006 0.43 -9999 0 -1.1 35 35
CCND1 0.043 0.34 -9999 0 -0.87 14 14
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.051 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.22 -9999 0 -0.87 22 22
GAS1 -0.12 0.6 -9999 0 -1.2 104 104
MMP2 0.044 0.38 -9999 0 -1.1 17 17
RB1/FOXM1C 0.051 0.34 -9999 0 -0.9 15 15
CREBBP 0.013 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.085 -9999 0 -0.47 16 16
RGS9BP -0.037 0.2 -9999 0 -0.81 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.066 0.24 -9999 0 -0.81 47 47
mol:Na + -0.021 0.056 -9999 0 -10000 0 0
mol:ADP -0.044 0.19 -9999 0 -0.63 47 47
GNAT2 0.009 0.021 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.062 -9999 0 -0.29 2 2
Cone PDE6 -0.076 0.18 -9999 0 -0.48 78 78
Cone Metarhodopsin II -0.049 0.15 -9999 0 -0.51 47 47
Na + (4 Units) -0.025 0.057 -9999 0 -10000 0 0
GNAT2/GDP -0.076 0.18 -9999 0 -0.48 78 78
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.089 -9999 0 -0.5 16 16
SLC24A2 -0.009 0.064 -9999 0 -0.31 21 21
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.62 16 16
GNB3 -0.012 0.14 -9999 0 -0.78 16 16
GNAT2/GTP -0.001 0.013 -9999 0 -0.21 2 2
CNGA3 -0.027 0.11 -9999 0 -0.31 61 61
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.056 -9999 0 -10000 0 0
mol:Pi -0.087 0.2 -9999 0 -0.55 78 78
Cone CNG Channel -0.016 0.042 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.064 -9999 0 -0.31 21 21
RGS9 -0.072 0.25 -9999 0 -0.79 53 53
PDE6C 0.003 0.015 -9999 0 -0.31 1 1
GNGT2 0.009 0.047 -9999 0 -0.41 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.094 -10000 0 -0.45 1 1
epithelial cell differentiation -0.047 0.1 -10000 0 -0.47 12 12
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 -0.001 0.08 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.083 -10000 0 -0.81 5 5
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.004 0.14 -10000 0 -0.51 10 10
PTPRZ1 -0.017 0.14 -10000 0 -0.56 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.13 -10000 0 -0.56 11 11
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.043 0.17 -10000 0 -0.52 47 47
ADAM17 0.021 0.057 -10000 0 -0.81 2 2
ErbB4/ErbB4 -0.012 0.1 -10000 0 -0.51 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.045 0.17 -10000 0 -0.55 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.14 -10000 0 -0.49 46 46
GRIN2B -0.028 0.15 -10000 0 -0.46 46 46
ErbB4/ErbB2/betacellulin -0.04 0.12 -10000 0 -0.6 17 17
STAT1 0.006 0.05 -10000 0 -0.31 12 12
HBEGF -0.004 0.072 -10000 0 -0.31 26 26
PRLR -0.044 0.19 -10000 0 -0.59 47 47
E4ICDs/ETO2 -0.007 0.091 -10000 0 -0.56 2 2
axon guidance -0.001 0.086 -10000 0 -0.43 3 3
NEDD4 0.021 0.056 -10000 0 -0.8 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.043 0.15 -10000 0 -0.63 26 26
CBFA2T3 0.01 0.042 -10000 0 -0.48 3 3
ErbB4/ErbB2/HBEGF -0.03 0.061 -10000 0 -0.57 2 2
MAPK3 -0.005 0.14 -10000 0 -0.53 10 10
STAT1 (dimer) -0.009 0.091 -10000 0 -0.45 1 1
MAPK1 -0.005 0.14 -10000 0 -0.53 10 10
JAK2 0.01 0.053 -10000 0 -0.81 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.16 -10000 0 -0.49 46 46
NRG1 -0.032 0.2 -10000 0 -0.64 46 46
NRG3 -0.047 0.22 -10000 0 -0.81 36 36
NRG2 -0.079 0.26 -10000 0 -0.79 57 57
NRG4 0.008 0.035 -10000 0 -0.31 6 6
heart development -0.001 0.086 -10000 0 -0.43 3 3
neural crest cell migration -0.032 0.16 -10000 0 -0.48 46 46
ERBB2 0.028 0.042 -10000 0 -0.61 2 2
WWOX/E4ICDs -0.006 0.093 -10000 0 -0.94 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.038 0.086 -10000 0 -0.61 5 5
apoptosis 0.057 0.14 0.46 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.066 0.19 -10000 0 -0.55 55 55
ErbB4/ErbB2/epiregulin -0.079 0.087 -10000 0 -0.54 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.023 0.14 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.12 -10000 0 -0.48 28 28
MDM2 -0.001 0.088 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.14 -10000 0 -0.5 46 46
STAT5A 0.007 0.081 -10000 0 -0.44 2 2
ErbB4/EGFR/neuregulin 1 beta -0.071 0.16 -10000 0 -0.51 50 50
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.064 -10000 0 -0.42 1 1
STAT5A (dimer) -0.05 0.11 -10000 0 -0.51 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.08 -10000 0 -0.51 1 1
LRIG1 0 0.1 -10000 0 -0.81 8 8
EREG -0.14 0.16 -10000 0 -0.31 230 230
BTC -0.015 0.15 -10000 0 -0.81 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.087 -10000 0 -0.44 3 3
ERBB4 -0.012 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.057 -10000 0 -0.5 2 2
glial cell differentiation 0.033 0.063 0.42 1 -10000 0 1
WWOX 0.012 0.037 -10000 0 -0.81 1 1
cell proliferation -0.025 0.17 -10000 0 -0.45 56 56
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -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 -0.027 0.064 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.24 -9999 0 -0.66 75 75
IL1A -0.053 0.22 -9999 0 -0.78 41 41
IL1B -0.026 0.17 -9999 0 -0.63 36 36
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.42 2 2
IL1R2 -0.082 0.24 -9999 0 -0.58 79 79
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.067 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.005 0.083 -9999 0 -0.81 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.027 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.43 124 124
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.061 0.13 -9999 0 -0.47 37 37
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.072 0.14 -9999 0 -0.5 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.065 0.13 -9999 0 -0.47 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.071 0.14 -9999 0 -0.52 35 35
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 0.019 0.11 -9999 0 -0.52 19 19
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.043 0.11 -9999 0 -0.62 11 11
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
PI3K -0.004 0.048 -9999 0 -0.62 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.082 -9999 0 -0.34 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.071 0.14 -9999 0 -0.52 35 35
IL1 beta/IL1R2 -0.098 0.22 -9999 0 -0.59 72 72
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.053 0.11 -9999 0 -0.55 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.063 0.13 -9999 0 -0.48 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.1 -9999 0 -0.43 4 4
IL1 alpha/IL1R1/IL1RAP -0.082 0.15 -9999 0 -0.55 38 38
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 0.022 0.035 -9999 0 -0.46 2 2
IL1RAP -0.069 0.14 -9999 0 -0.31 126 126
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.049 0.11 -9999 0 -0.49 11 11
CASP1 0.007 0.062 -9999 0 -0.45 7 7
IL1RN/IL1R2 -0.11 0.21 -9999 0 -0.61 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.064 0.13 -9999 0 -0.49 35 35
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.08 -9999 0 -0.33 4 4
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
IL1RN -0.052 0.16 -9999 0 -0.38 83 83
TRAF6/TAK1/TAB1/TAB2 -0.002 0.029 -9999 0 -0.46 2 2
MAP2K6 0.021 0.075 -9999 0 -0.43 13 13
TCGA08_rtk_signaling

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
PDGFRA -0.24 0.38 -10000 0 -0.81 151 151
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.005 0.083 -10000 0 -0.81 5 5
AKT 0.019 0.025 0.2 1 -10000 0 1
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.1 0.16 -10000 0 -0.31 179 179
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.014 0.14 -10000 0 -0.73 18 18
PIK3R3 0.012 0.037 -10000 0 -0.81 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.058 0.098 -10000 0 -0.26 42 42
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.18 2 -0.17 1 3
PI3K -0.039 0.095 0.22 1 -0.22 50 51
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.025 0.027 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.81 1 1
Aurora B signaling

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
Condensin I complex -0.001 0.079 -9999 0 -10000 0 0
STMN1 -0.022 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.024 0.11 -9999 0 -0.32 34 34
Chromosomal passenger complex/Cul3 protein complex 0.007 0.069 -9999 0 -0.28 14 14
BIRC5 -0.011 0.091 -9999 0 -0.33 35 35
DES -0.38 0.3 -9999 0 -0.61 300 300
Aurora C/Aurora B/INCENP -0.016 0.087 -9999 0 -0.39 7 7
Aurora B/TACC1 -0.022 0.08 -9999 0 -0.7 1 1
Aurora B/PP2A -0.027 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.046 0.14 -9999 0 -0.39 56 56
Cul3 protein complex -0.018 0.086 -9999 0 -0.54 12 12
KIF2C 0 0.042 -9999 0 -0.18 2 2
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.035 0.12 -9999 0 -0.31 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.091 -9999 0 -10000 0 0
SEPT1 0.007 0.043 -9999 0 -0.31 9 9
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.007 0.044 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.008 0.055 -9999 0 -10000 0 0
AURKB -0.052 0.14 -9999 0 -0.31 113 113
AURKC 0 0.065 -9999 0 -0.31 21 21
CDCA8 0.01 0.03 -9999 0 -0.32 4 4
cytokinesis -0.064 0.081 -9999 0 -0.39 11 11
Aurora B/Septin1 -0.025 0.1 -9999 0 -0.42 10 10
AURKA 0.013 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.054 -9999 0 -0.83 2 2
KLHL13 -0.017 0.14 -9999 0 -0.53 27 27
BUB1 -0.1 0.16 -9999 0 -0.31 171 171
hSgo1/Aurora B/Survivin -0.024 0.11 -9999 0 -0.44 17 17
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.029 0.071 -9999 0 -0.36 4 4
SGOL1 0.001 0.062 -9999 0 -0.31 19 19
CENPA -0.008 0.07 -9999 0 -0.22 20 20
NCAPG -0.019 0.097 -9999 0 -0.31 49 49
Aurora B/HC8 Proteasome -0.027 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.036 0.12 -9999 0 -0.31 75 75
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.09 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.034 0.079 -9999 0 -0.35 18 18
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.008 0.06 -9999 0 -0.55 1 1
KIF23 -0.003 0.072 -9999 0 -0.32 25 25
VIM -0.022 0.092 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.012 0.081 -9999 0 -0.25 25 25
Chromosomal passenger complex/EVI5 0.011 0.12 -9999 0 -0.47 7 7
TACC1 0.012 0.037 -9999 0 -0.81 1 1
PPP2R5D 0.013 0 -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
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.003 0.077 -10000 0 -0.36 8 8
CaM/Ca2+ 0 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 0.012 0.037 -10000 0 -0.81 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.077 0.23 16 -0.27 12 28
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 -0.066 0.22 -10000 0 -0.62 69 69
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 -0.001 0.024 -10000 0 -0.54 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 64 64
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 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 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.038 0.1 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.042 0.082 0.26 2 -0.3 12 14
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
LNPEP -0.013 0.15 -10000 0 -0.81 16 16
YWHAE 0.013 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.04 0.12 -9999 0 -0.42 46 46
Syndecan-3/Neurocan -0.033 0.12 -9999 0 -0.46 34 34
POMC -0.16 0.34 -9999 0 -0.8 106 106
EGFR 0.005 0.083 -9999 0 -0.81 5 5
Syndecan-3/EGFR -0.005 0.046 -9999 0 -0.46 5 5
AGRP -0.006 0.064 -9999 0 -0.31 21 21
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 -0.048 0.21 -9999 0 -0.75 39 39
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.081 -9999 0 -0.46 11 11
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.009 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R -0.001 0.045 -9999 0 -0.31 10 10
SRC 0.013 0.015 -9999 0 -10000 0 0
PTN -0.064 0.24 -9999 0 -0.81 46 46
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.066 0.15 -9999 0 -0.6 3 3
Syndecan-3/AgRP -0.006 0.025 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.008 0.029 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.039 0.08 -9999 0 -0.45 11 11
IL8 -0.082 0.18 -9999 0 -0.35 128 128
Syndecan-3/Fyn/Cortactin 0 0.005 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.26 -9999 0 -0.63 103 103
Gamma Secretase 0 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.013 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.013 0.065 -9999 0 -0.2 39 39
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
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 0.01 0.021 -9999 0 -0.31 2 2
mol:ACh -0.007 0.04 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.013 0.065 -9999 0 -0.2 39 39
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.015 0.093 -9999 0 -0.32 39 39
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.16 -9999 0 -0.6 30 30
SNAP25 -0.031 0.095 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.22 -9999 0 -0.38 219 219
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.062 0.16 -10000 0 -0.47 65 65
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.055 -10000 0 -0.21 34 34
GNB1/GNG2 -0.001 0.025 -10000 0 -0.55 1 1
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 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.067 0.17 -10000 0 -0.51 64 64
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 0.015 0.039 0.12 64 -10000 0 64
GNAL -0.094 0.28 -10000 0 -0.81 64 64
GNG2 0.012 0.037 -10000 0 -0.81 1 1
CRH -0.014 0.081 -10000 0 -0.31 34 34
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.069 -10000 0 -0.46 11 11
MAPK11 0.009 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.063 0.08 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.087 0.19 -10000 0 -0.67 39 39
NT3 (dimer)/TRKB -0.083 0.18 -10000 0 -0.57 50 50
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.028 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.61 22 22
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.002 0.062 -10000 0 -0.31 19 19
NTRK2 0.005 0.083 -10000 0 -0.81 5 5
NTRK3 -0.054 0.16 -10000 0 -0.38 84 84
NT-4/5 (dimer)/TRKB -0.068 0.16 -10000 0 -0.57 42 42
neuron apoptosis 0.04 0.091 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.042 0.099 -10000 0 -0.46 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.029 0.092 -10000 0 -0.63 6 6
SHC3 -0.047 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.025 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.17 -10000 0 -0.56 47 47
RIN/GDP -0.008 0.061 -10000 0 -0.28 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.091 -10000 0 -0.41 23 23
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.045 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.66 26 26
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.079 -10000 0 -0.5 10 10
TRKA/NEDD4-2 -0.008 0.038 -10000 0 -10000 0 0
ELMO1 -0.31 0.4 -10000 0 -0.81 192 192
RhoG/GTP/ELMO1/DOCK1 -0.22 0.27 -10000 0 -0.55 193 193
NGF 0.006 0.069 -10000 0 -0.56 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.007 0.074 -10000 0 -0.81 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.014 0.15 -10000 0 -0.78 17 17
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 -0.2 0.23 -10000 0 -0.46 209 209
mol:GDP -0.014 0.088 -10000 0 -0.39 4 4
NGF (dimer) 0.006 0.069 -10000 0 -0.56 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.63 192 192
RIT1/GDP -0.003 0.062 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.81 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.57 17 17
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.024 -10000 0 -0.54 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.048 0.2 -10000 0 -0.6 49 49
RAP1/GDP -0.017 0.041 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.14 -10000 0 -0.61 22 22
ubiquitin-dependent protein catabolic process -0.01 0.052 -10000 0 -0.54 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.016 -10000 0 -0.32 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.065 0.14 -10000 0 -0.5 25 25
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.036 -10000 0 -10000 0 0
STAT3 0.018 0.025 -10000 0 -10000 0 0
axon guidance -0.063 0.14 -10000 0 -0.43 54 54
MAPK3 0.014 0.078 -10000 0 -0.49 8 8
MAPK1 0.014 0.078 -10000 0 -0.49 8 8
CDC42/GDP -0.003 0.062 -10000 0 -0.28 2 2
NTF3 -0.048 0.2 -10000 0 -0.6 49 49
NTF4 -0.022 0.16 -10000 0 -0.66 26 26
NGF (dimer)/TRKA/FAIM -0.01 0.052 -10000 0 -0.54 3 3
PI3K -0.004 0.048 -10000 0 -0.62 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.46 28 28
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.05 0.17 -10000 0 -0.58 39 39
RGS19 0.013 0.015 -10000 0 -0.31 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.046 -10000 0 -0.42 1 1
Rac1/GDP -0.003 0.062 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.011 0.054 -10000 0 -0.55 3 3
neuron projection morphogenesis 0 0.093 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.052 -10000 0 -0.54 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.06 0.18 -10000 0 -0.42 84 84
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.076 -10000 0 -0.35 18 18
RAS family/GTP/PI3K 0.03 0.031 -10000 0 -0.36 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.021 -10000 0 -0.46 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
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 -0.01 0.056 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.038 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.098 -10000 0 -0.52 17 17
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.042 -10000 0 -0.46 3 3
MATK -0.003 0.096 -10000 0 -0.46 17 17
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.014 0.041 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.035 0.097 -10000 0 -0.44 23 23
Rac1/GTP -0.19 0.14 -10000 0 -0.35 196 196
FRS2 family/SHP2/CRK family -0.001 0.021 -10000 0 -0.46 1 1
LPA4-mediated signaling events

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.015 0.057 -9999 0 -0.55 5 5
ADCY5 -0.057 0.19 -9999 0 -0.55 66 66
ADCY6 0.015 0.057 -9999 0 -0.55 5 5
ADCY7 0.015 0.057 -9999 0 -0.55 5 5
ADCY1 0.008 0.09 -9999 0 -0.62 9 9
ADCY2 -0.039 0.17 -9999 0 -0.56 46 46
ADCY3 0.015 0.057 -9999 0 -0.55 5 5
ADCY8 -0.12 0.1 -9999 0 -0.7 5 5
PRKCE 0.006 0.065 -9999 0 -0.63 5 5
ADCY9 0.015 0.057 -9999 0 -0.55 5 5
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.055 0.1 -9999 0 -0.37 31 31
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.019 0.12 -10000 0 -0.78 12 12
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.002 0.098 -10000 0 -0.81 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.064 -10000 0 -0.81 3 3
AP1 -0.14 0.26 -10000 0 -0.52 139 139
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.007 0.13 -10000 0 -0.81 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.052 -10000 0 -0.34 1 1
NICD/RBPSUH -0.018 0.11 -10000 0 -0.73 12 12
WIF1 -0.033 0.1 -10000 0 -0.31 60 60
NOTCH1 -0.019 0.12 -10000 0 -0.76 12 12
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.041 0.13 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.036 0.037 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.037 -10000 0 -0.22 1 1
CtBP/CBP/TCF1/TLE1/AES 0.024 0.036 -10000 0 -0.34 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.2 0.36 -10000 0 -0.81 127 127
JUN -0.17 0.35 -10000 0 -0.81 112 112
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.029 0.04 0.24 13 -10000 0 13
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.034 0.11 -10000 0 -0.55 19 19
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.011 0.24 -10000 0 -1.5 12 12
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.62 19 19
apoptosis -0.14 0.26 -10000 0 -0.52 139 139
Delta 1/NOTCHprecursor -0.019 0.12 -10000 0 -0.75 12 12
DLL1 0.011 0.04 -10000 0 -0.56 2 2
PPARD 0.024 0.016 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.06 -10000 0 -1.1 1 1
DVL1 0.003 0.01 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 0.018 0.044 -10000 0 -10000 0 0
WNT1 0.008 0.033 -10000 0 -0.31 5 5
Axin1/APC/beta catenin 0.042 0.052 -10000 0 -0.67 1 1
DKK2 -0.024 0.16 -10000 0 -0.65 28 28
NOTCH1 precursor/DVL1 -0.012 0.1 -10000 0 -0.64 12 12
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.024 0.12 -10000 0 -0.64 19 19
PPP2R5D 0.011 0.063 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.017 0.044 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.002 0.14 -10000 0 -0.7 11 11
BAG4 0.012 0.037 -10000 0 -0.81 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BAX -0.006 0.02 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.008 -10000 0 -10000 0 0
BAD -0.018 0.041 -10000 0 -10000 0 0
SMPD1 -0.005 0.094 -10000 0 -0.26 57 57
RB1 -0.019 0.046 -10000 0 -0.49 1 1
FADD/Caspase 8 0.01 0.13 -10000 0 -0.66 11 11
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.05 -10000 0 -0.51 2 2
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:ceramide -0.029 0.043 -10000 0 -0.13 68 68
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.029 -10000 0 -0.62 1 1
ASAH1 0.012 0.037 -10000 0 -0.81 1 1
negative regulation of cell cycle -0.019 0.045 -10000 0 -0.49 1 1
cell proliferation -0.097 0.16 -10000 0 -0.39 114 114
BID -0.015 0.091 -10000 0 -0.4 11 11
MAP3K1 -0.018 0.041 -10000 0 -10000 0 0
EIF2A -0.001 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.047 -10000 0 -0.47 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.47 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -10000 0 0
FADD -0.002 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.052 -10000 0 -0.54 2 2
MAPK8 -0.01 0.06 -10000 0 -0.32 11 11
PRKRA -0.018 0.041 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.79 119 119
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -0.13 68 68
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.028 -10000 0 -0.62 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.084 0.19 -10000 0 -0.42 114 114
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 0.023 0.029 -10000 0 -0.62 1 1
RelA/NF kappa B1 -0.001 0.028 -10000 0 -0.62 1 1
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 -0.011 0.15 -10000 0 -0.74 11 11
TNFR1A/BAG4/TNF-alpha -0.065 0.17 -10000 0 -0.54 58 58
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.003 0.048 -10000 0 -0.48 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.003 0.052 0.18 27 -10000 0 27
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
TNFR1A/BAG4 -0.001 0.028 -10000 0 -0.62 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.064 0.17 -10000 0 -0.54 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.079 -10000 0 -0.33 11 11
MAP2K2 -0.003 0.048 -10000 0 -0.48 2 2
SMPD3 -0.011 0.12 -10000 0 -0.3 62 62
TNF -0.087 0.26 -10000 0 -0.76 64 64
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.024 0.11 0.28 72 -0.13 2 74
NF kappa B1/RelA/I kappa B alpha -0.001 0.021 -10000 0 -0.46 1 1
AIFM1 0.003 0.052 0.18 27 -10000 0 27
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.014 0.12 -9999 0 -0.44 32 32
CCNA2 0.007 0.046 -9999 0 -0.31 10 10
PIK3CA 0.009 0.064 -9999 0 -0.81 3 3
JAK3 -0.068 0.14 -9999 0 -0.31 125 125
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.15 -9999 0 -0.57 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.044 0.25 -9999 0 -0.97 32 32
IL2RB -0.014 0.13 -9999 0 -0.5 27 27
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.048 0.19 -9999 0 -0.52 57 57
G1/S transition of mitotic cell cycle 0.039 0.054 -9999 0 -0.59 3 3
PTPN11 0.013 0.037 -9999 0 -0.81 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.01 0.11 -9999 0 -0.42 27 27
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.064 -9999 0 -0.81 3 3
CCND3 0.027 0.13 -9999 0 -0.62 8 8
Insulin Pathway

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
CBL/APS/CAP -0.057 0.15 -9999 0 -0.44 64 64
TC10/GTP -0.004 0.037 -9999 0 -0.42 4 4
Insulin Receptor/Insulin/IRS1/Shp2 -0.064 0.17 -9999 0 -0.51 62 62
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.01 0.14 -9999 0 -0.81 14 14
FOXO3 -0.023 0.1 -9999 0 -0.69 10 10
AKT1 -0.015 0.16 -9999 0 -0.88 2 2
INSR 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.035 0.036 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.007 0.074 -9999 0 -0.81 4 4
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.035 0.035 -9999 0 -0.41 3 3
CAV1 -0.047 0.18 -9999 0 -0.47 75 75
CBL/APS/CAP/Crk-II/C3G -0.004 0.041 -9999 0 -0.46 4 4
Insulin Receptor/Insulin/IRS1/NCK2 -0.063 0.17 -9999 0 -0.5 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.058 0.15 -9999 0 -0.45 64 64
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.11 -9999 0 -0.38 3 3
RPS6KB1 -0.004 0.15 -9999 0 -0.76 2 2
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.057 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.052 0.13 -9999 0 -0.49 4 4
Insulin Receptor 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.059 0.16 -9999 0 -0.47 62 62
PRKCI -0.015 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.066 0.16 -9999 0 -0.42 75 75
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.004 -9999 0 -10000 0 0
PI3K -0.059 0.15 -9999 0 -0.45 64 64
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
AKT2 -0.015 0.16 -9999 0 -0.88 2 2
PRKCZ -0.015 0.034 -9999 0 -10000 0 0
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
SHC/SHIP -0.031 0.16 -9999 0 -0.45 62 62
F2RL2 -0.079 0.16 -9999 0 -0.32 137 137
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.003 0.036 -9999 0 -0.47 3 3
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.003 0.033 -9999 0 -0.42 3 3
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.004 0.044 -9999 0 -0.49 4 4
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.003 0.036 -9999 0 -0.46 3 3
INPP5D -0.042 0.17 -9999 0 -0.48 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.025 0.14 -9999 0 -1 10 10
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
p62DOK/RasGAP 0 0.004 -9999 0 -10000 0 0
INS -0.001 0.063 -9999 0 -0.81 3 3
mol:PI-3-4-P2 -0.041 0.17 -9999 0 -0.47 62 62
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.005 0.15 -9999 0 -0.63 4 4
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.053 -9999 0 -0.81 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.01 0.12 -9999 0 -0.33 62 62
Insulin Receptor/Insulin/IRS1 -0.064 0.17 -9999 0 -0.51 62 62
Insulin Receptor/Insulin/IRS3 -0.004 0.048 -9999 0 -0.62 3 3
Par3/Par6 -0.035 0.063 -9999 0 -0.46 3 3
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.002 0.098 -9999 0 -0.81 7 7
CDKN1A -0.013 0.088 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.018 0.057 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.11 -9999 0 -0.64 10 10
AGT -0.02 0.14 -9999 0 -0.45 36 36
CCNA2 -0.063 0.2 -9999 0 -0.58 5 5
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.26 -9999 0 -0.62 107 107
CDK2/Cyclin E1 0.004 0.077 -9999 0 -10000 0 0
MAPK3 0.004 0.064 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.004 0.064 -9999 0 -10000 0 0
PTP4A1 -0.072 0.21 -9999 0 -0.48 107 107
PTP4A3 -0.015 0.092 -9999 0 -0.31 44 44
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.004 0.064 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -10000 0 0
RAC1 -0.017 0.093 -9999 0 -0.25 17 17
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.068 0.2 -9999 0 -0.58 4 4
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.013 0.042 -9999 0 -10000 0 0
RHOC -0.017 0.093 -9999 0 -0.25 17 17
RHOA -0.017 0.093 -9999 0 -10000 0 0
cell motility -0.016 0.099 -9999 0 -0.26 17 17
PRL-1/alpha Tubulin -0.062 0.2 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.026 0.095 -9999 0 -0.67 7 7
ROCK1 -0.016 0.1 -9999 0 -0.26 17 17
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.072 0.21 -9999 0 -0.47 107 107
ATF5 0 0.064 -9999 0 -0.31 20 20
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.027 0.16 -9999 0 -0.43 66 66
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 -0.048 0.12 -9999 0 -0.74 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.011 0.043 -9999 0 -0.59 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.056 0.14 -9999 0 -0.4 66 66
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.16 -9999 0 -0.4 66 66
AKT1 -0.003 0.15 -9999 0 -0.61 3 3
MAP2K1 -0.006 0.15 -9999 0 -0.5 6 6
MAP3K11 -0.017 0.16 -9999 0 -0.4 66 66
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.066 -9999 0 -0.63 1 1
Rap1/GTP -0.041 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.063 0.15 -9999 0 -0.45 65 65
CEBPB 0.018 0.17 -9999 0 -0.8 6 6
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.15 -9999 0 -1.1 2 2
STAT1 -0.019 0.16 -9999 0 -0.4 66 66
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.28 -9999 0 -0.71 79 79
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
STAT1 (dimer)/PIAS1 -0.01 0.15 -9999 0 -0.46 6 6
CEBPB/PTGES2/Cbp/p300 -0.035 0.082 -9999 0 -0.44 6 6
mol:Ca2+ -0.06 0.15 -9999 0 -0.43 66 66
MAPK3 0.01 0.14 -9999 0 -0.52 6 6
STAT1 (dimer) -0.031 0.08 -9999 0 -0.42 2 2
MAPK1 0.01 0.14 -9999 0 -0.52 6 6
JAK2 0.006 0.056 -9999 0 -0.84 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.017 0.18 -9999 0 -0.66 23 23
SMAD7 0.04 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.75 1 1
PI3K -0.056 0.14 -9999 0 -0.5 9 9
IFNG -0.1 0.28 -9999 0 -0.72 79 79
apoptosis 0.014 0.13 -9999 0 -0.45 23 23
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.068 -9999 0 -0.31 23 23
CAMK2B 0.005 0.083 -9999 0 -0.81 5 5
FRAP1 -0.001 0.14 -9999 0 -0.51 4 4
PRKCD -0.002 0.15 -9999 0 -0.62 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -0.3 2 2
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.028 0.12 -9999 0 -0.53 1 1
STAT1 (dimer)/PIASy -0.054 0.13 -9999 0 -0.45 7 7
SOCS1 0.001 0.074 -9999 0 -1.5 1 1
mol:GDP -0.048 0.12 -9999 0 -0.7 1 1
CASP1 0.038 0.063 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.042 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.054 0.13 -9999 0 -0.48 9 9
RAP1/GDP -0.041 0.1 -9999 0 -0.6 1 1
CBL -0.017 0.16 -9999 0 -0.4 66 66
MAP3K1 -0.016 0.16 -9999 0 -0.4 66 66
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -0.3 2 2
PTPN11 -0.027 0.16 -9999 0 -0.43 66 66
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
PTK2 -0.043 0.16 -9999 0 -0.6 32 32
positive regulation of JNK cascade -0.023 0.085 -9999 0 -0.34 32 32
CDC42/GDP 0.027 0.13 -9999 0 -0.47 32 32
Rac1/GDP 0.029 0.13 -9999 0 -0.46 32 32
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 -0.028 0.1 -9999 0 -0.42 32 32
nectin-3/I-afadin -0.04 0.15 -9999 0 -0.62 32 32
RAPGEF1 0.02 0.15 -9999 0 -0.53 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.17 -9999 0 -0.62 32 32
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
TLN1 0.017 0.077 -9999 0 -0.93 1 1
Rap1/GTP -0.024 0.09 -9999 0 -0.36 32 32
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.04 0.15 -9999 0 -0.62 32 32
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.02 0.16 -9999 0 -0.59 32 32
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PI3K -0.033 0.13 -9999 0 -0.5 33 33
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.024 0.089 -9999 0 -0.36 32 32
PVRL1 0.005 0.052 -9999 0 -0.31 13 13
PVRL3 -0.04 0.2 -9999 0 -0.81 32 32
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.15 -9999 0 -0.81 10 10
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.56 42 42
SRC -0.047 0.18 -9999 0 -0.71 32 32
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
FARP2 0.015 0.16 -9999 0 -0.57 32 32
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) -0.035 0.13 -9999 0 -0.54 32 32
nectin-1/I-afadin -0.005 0.032 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.039 0.14 -9999 0 -0.54 32 32
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.023 0.085 -9999 0 -0.34 32 32
alphaV/beta3 Integrin/Talin 0.016 0.13 -9999 0 -0.59 16 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.009 0.082 -9999 0 -0.99 1 1
VAV2 0.013 0.16 -9999 0 -0.59 32 32
RAP1/GDP -0.028 0.11 -9999 0 -0.43 32 32
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.035 0.13 -9999 0 -0.54 32 32
nectin-3(dimer)/I-afadin/I-afadin -0.04 0.15 -9999 0 -0.62 32 32
Rac1/GTP -0.029 0.11 -9999 0 -0.44 32 32
PTPRM -0.02 0.084 -9999 0 -0.31 32 32
E-cadherin/beta catenin/alpha catenin -0.003 0.016 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.12 -10000 0 -0.57 9 9
UGCG -0.03 0.18 -10000 0 -0.8 25 25
AKT1/mTOR/p70S6K/Hsp90/TERT 0.019 0.13 -10000 0 -0.4 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.024 0.18 -10000 0 -0.78 25 25
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.059 0.14 -10000 0 -0.45 37 37
FRAP1 0.002 0.2 -10000 0 -0.48 52 52
FOXO3 0.019 0.16 -10000 0 -0.59 19 19
AKT1 0.01 0.18 -10000 0 -0.56 28 28
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 0.009 0.031 -10000 0 -10000 0 0
SGMS1 0.009 0.031 -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 0.019 0.045 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.003 0.16 -10000 0 -0.53 26 26
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.051 -10000 0 -0.63 3 3
RPS6KB1 0.016 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
MYC 0.009 0.21 -10000 0 -0.91 18 18
MYB -0.018 0.2 -10000 0 -1.3 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.007 0.16 -10000 0 -0.55 25 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.16 -10000 0 -0.53 25 25
Rac1/GDP 0.024 0.042 -10000 0 -0.5 3 3
T cell proliferation 0.017 0.15 -10000 0 -0.51 22 22
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.052 17 17
PRKCZ 0.016 0.15 -10000 0 -0.53 22 22
NF kappa B1 p50/RelA -0.057 0.14 -10000 0 -0.45 37 37
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.13 -10000 0 -0.59 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.047 0.2 -10000 0 -0.81 28 28
IL2RB -0.013 0.13 -10000 0 -0.5 27 27
TERT -0.002 0.042 -10000 0 -0.31 9 9
E2F1 -0.005 0.078 -10000 0 -0.45 11 11
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.025 17 -10000 0 17
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
IL2RG -0.046 0.19 -10000 0 -0.52 57 57
actin cytoskeleton organization 0.017 0.15 -10000 0 -0.51 22 22
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.065 -10000 0 -0.82 3 3
Rac1/GTP 0.031 0.042 -10000 0 -0.48 3 3
LCK -0.008 0.11 -10000 0 -0.42 27 27
BCL2 -0.026 0.28 -10000 0 -0.82 48 48
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.34 -9999 0 -0.81 103 103
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.025 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.04 -9999 0 -0.5 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -0.31 204 204
ARNT/IPAS -0.13 0.25 -9999 0 -0.62 103 103
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -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 -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.087 -9999 0 -0.53 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.017 -9999 0 -10000 0 0
VHL 0.008 0.064 -9999 0 -0.81 3 3
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.017 0.14 -9999 0 -0.5 30 30
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.053 -9999 0 -0.81 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.05 -9999 0 -0.6 3 3
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 -0.029 0.072 -9999 0 -0.29 1 1
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.003 0.1 0.56 14 -10000 0 14
PI3K Class IB/PDE3B -0.003 0.1 -10000 0 -0.56 14 14
PDE3B -0.003 0.1 -10000 0 -0.56 14 14
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
ITGA4 0.002 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.62 3 3
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
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 -0.021 0.029 0.62 1 -10000 0 1
CDKN1A -0.006 0.035 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.006 0.033 -10000 0 -0.31 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.019 -10000 0 -10000 0 0
PPARGC1A -0.35 0.41 -10000 0 -0.81 219 219
FHL2 -0.05 0.22 -10000 0 -0.81 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.03 -10000 0 -0.62 1 1
HIST2H4A 0.021 0.029 -10000 0 -0.62 1 1
SIRT1/FOXO3a 0 0.026 -10000 0 -0.55 1 1
SIRT1 0 0.039 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.027 -10000 0 -0.54 1 1
SIRT1/Histone H1b -0.006 0.049 -10000 0 -0.33 10 10
apoptosis 0 0.028 0.54 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.55 219 219
p53/SIRT1 0.004 0.042 -10000 0 -0.62 1 1
SIRT1/FOXO4 0.001 0.027 -10000 0 -0.52 1 1
FOXO1/FHL2/SIRT1 -0.038 0.14 -10000 0 -0.5 39 39
HIST1H1E 0.015 0.053 -10000 0 -0.36 9 9
SIRT1/p300 0.001 0.03 -10000 0 -0.62 1 1
muscle cell differentiation 0.001 0.03 0.55 1 -10000 0 1
TP53 0.002 0.012 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.028 -10000 0 -0.54 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.036 -10000 0 -0.62 1 1
ACSS2 0.021 0.029 -10000 0 -0.62 1 1
SIRT1/PCAF/MYOD -0.001 0.03 -10000 0 -0.55 1 1
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.043 0.12 0.33 1 -0.36 61 62
FRAP1 0.008 0.027 -10000 0 -10000 0 0
AKT1 -0.009 0.11 0.24 1 -0.3 61 62
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.042 -10000 0 -0.55 3 3
mol:GTP -0.028 0.077 -10000 0 -0.5 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.022 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.066 -10000 0 -0.45 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.035 0.14 -10000 0 -0.42 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.06 -10000 0 -0.35 3 3
MAP3K5 0.011 0.021 -10000 0 -0.45 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.021 -10000 0 -0.45 1 1
mol:LY294002 0 0.001 0.001 2 -0.002 58 60
EIF4B 0.017 0.055 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.014 0.039 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.14 -10000 0 -0.39 61 61
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.04 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.023 0.065 -10000 0 -0.44 3 3
mol:Amino Acids 0 0.001 0.001 2 -0.002 58 60
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.041 0.12 0.26 1 -0.33 61 62
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.034 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.029 0.083 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 58 -0.001 2 60
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.046 0.15 -10000 0 -0.46 59 59
INS -0.005 0.063 -10000 0 -0.81 3 3
PTEN 0.011 0.037 -10000 0 -0.81 1 1
PDK2 -0.039 0.11 0.26 1 -0.32 61 62
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.015 0.04 -10000 0 -0.49 3 3
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 3 4
EEF2 0.015 0.04 -10000 0 -0.5 3 3
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.035 0.14 -10000 0 -0.62 28 28
ATM 0.012 0.037 -10000 0 -0.81 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.037 -10000 0 -0.81 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.029 -10000 0 -0.44 2 2
protein ubiquitination -0.027 0.11 -10000 0 -0.45 29 29
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.042 -10000 0 -0.54 3 3
MRE11A 0.008 0.064 -10000 0 -0.81 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.035 0.14 -10000 0 -0.62 28 28
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA 0 0.065 -10000 0 -0.31 21 21
DNA repair 0.051 0.1 -10000 0 -0.46 2 2
BRCA1/BARD1/ubiquitin -0.035 0.14 -10000 0 -0.62 28 28
BARD1/DNA-PK -0.028 0.11 -10000 0 -0.49 28 28
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.035 0.14 0.62 28 -10000 0 28
BRCA1/BARD1/CTIP/M/R/N Complex 0.019 0.092 -10000 0 -0.57 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/P53 -0.029 0.12 -10000 0 -0.49 29 29
BARD1/CSTF1/BRCA1 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.034 0.19 -10000 0 -0.81 28 28
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/UbcH7 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/RAD51/PCNA -0.029 0.12 -10000 0 -0.49 28 28
BARD1/DNA-PK/P53 -0.026 0.11 -10000 0 -0.46 28 28
BRCA1/BARD1/Ubiquitin -0.035 0.14 -10000 0 -0.62 28 28
BRCA1/BARD1/CTIP -0.029 0.12 -10000 0 -0.49 29 29
FA complex 0.038 0.024 -10000 0 -10000 0 0
BARD1/EWS -0.035 0.14 -10000 0 -0.62 28 28
RBBP8 0.023 0.029 -10000 0 -0.62 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.029 0.11 0.49 29 -10000 0 29
BRCA1/BARD1 -0.027 0.11 -10000 0 -0.46 29 29
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.036 0.15 -10000 0 -0.63 28 28
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0.025 -10000 0 -0.31 3 3
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.035 0.14 -10000 0 -0.62 28 28
EWSR1 0.013 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.12 -10000 0 -0.81 10 10
ANTXR2 0.008 0.064 -10000 0 -0.81 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 13 13
monocyte activation -0.046 0.17 -10000 0 -0.48 60 60
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.013 0.074 -10000 0 -0.49 11 11
CYAA 0.003 0.079 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.019 0.12 -10000 0 -0.46 35 35
Channel -0.013 0.081 -10000 0 -0.5 13 13
NLRP1 -0.004 0.034 -10000 0 -0.49 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 13 -10000 0 13
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.022 0.083 -10000 0 -0.25 40 40
PA/Cellular Receptors -0.014 0.088 -10000 0 -0.55 13 13
apoptosis -0.003 0.016 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.078 -10000 0 -0.47 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.087 0.26 -10000 0 -0.76 64 64
VCAM1 -0.046 0.17 -10000 0 -0.48 60 60
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.024 0.1 11 -10000 0 11
IL18 -0.01 0.085 -10000 0 -0.41 14 14
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 13 13
LEF -0.003 0.016 -10000 0 -0.1 13 13
CASP1 -0.003 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.077 -10000 0 -0.48 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.081 -9999 0 -0.71 6 6
PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.009 0.025 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.015 0.14 -9999 0 -0.38 51 51
GNAO1 -0.017 0.15 -9999 0 -0.7 21 21
PDGFB-D/PDGFRB/PLCgamma1 0.025 0.13 -9999 0 -0.54 10 10
PLCG1 0.022 0.14 -9999 0 -0.35 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
GNAI2 0.014 0.004 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.073 -9999 0 -0.62 6 6
S1P1/S1P -0.016 0.066 -9999 0 -0.5 6 6
negative regulation of cAMP metabolic process 0.016 0.14 -9999 0 -0.37 51 51
MAPK3 0.009 0.19 -9999 0 -0.57 41 41
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.006 0.074 -9999 0 -0.82 4 4
PLCB2 0.03 0.072 -9999 0 -0.43 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.054 -9999 0 -0.41 6 6
receptor internalization -0.015 0.061 -9999 0 -0.46 6 6
PTGS2 -0.03 0.33 -9999 0 -1.1 41 41
Rac1/GTP -0.013 0.054 -9999 0 -0.41 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
negative regulation of T cell proliferation 0.016 0.14 -9999 0 -0.37 51 51
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.009 0.19 -9999 0 -0.57 41 41
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.086 -9999 0 -0.49 7 7
ABCC1 0.014 0.002 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.037 -9999 0 -0.81 1 1
Caspase 8 (4 units) -0.022 0.063 -9999 0 -10000 0 0
NEF -0.013 0.056 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.8 26 26
CYCS -0.004 0.1 -9999 0 -0.39 7 7
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.039 0.19 -9999 0 -0.78 25 25
MAP2K7 0.023 0.081 -9999 0 -0.31 2 2
protein ubiquitination 0.039 0.086 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.013 0.11 -9999 0 -0.42 7 7
NF-kappa-B/RelA/I kappa B alpha -0.022 0.08 -9999 0 -0.34 26 26
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.037 -9999 0 -0.81 1 1
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 -0.022 0.08 -9999 0 -0.35 26 26
MAPK8 0.02 0.1 -9999 0 -0.41 11 11
APAF1 0.012 0.037 -9999 0 -0.81 1 1
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.098 -9999 0 -0.31 30 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.1 -9999 0 -0.39 3 3
CHUK 0.039 0.091 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.021 -9999 0 -0.46 1 1
TCRz/NEF -0.062 0.18 -9999 0 -0.52 54 54
TNF -0.087 0.26 -9999 0 -0.76 64 64
FASLG -0.074 0.29 -9999 0 -0.85 54 54
NFKB1 0.007 0.047 -9999 0 -0.81 1 1
TNFR1A/BAG4/TNF-alpha -0.065 0.17 -9999 0 -0.54 58 58
CASP6 -0.006 0.045 -9999 0 -10000 0 0
CASP7 0.028 0.16 -9999 0 -0.62 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.028 0.16 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.028 -9999 0 -0.62 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.098 -9999 0 -0.37 2 2
APAF-1/Caspase 9 -0.047 0.12 -9999 0 -0.52 25 25
BCL2 -0.004 0.15 -9999 0 -0.4 44 44
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.07 0.009 -9999 0 -10000 0 0
EGFR 0.005 0.083 -9999 0 -0.81 5 5
EPHA2 0.011 0.025 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.039 0.13 -9999 0 -0.59 26 26
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.037 0.073 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.072 0.19 -9999 0 -0.59 60 60
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.048 0.034 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.067 0.15 -9999 0 -0.42 77 77
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.35 -9999 0 -0.79 119 119
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.04 0.06 -9999 0 -0.42 8 8
Ephrin A1/EPHA2 -0.001 0.007 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.037 0.074 -9999 0 -10000 0 0
HGF/MET -0.099 0.16 -9999 0 -0.46 74 74
HGF -0.11 0.3 -9999 0 -0.81 74 74
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.085 0.021 -9999 0 -10000 0 0
KIAA1543 0.047 0.021 -9999 0 -0.41 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -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 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.097 0.18 -9999 0 -0.42 113 113
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 179 179
PLEKHA7 0.04 0.022 -9999 0 -0.44 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.066 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.024 0.095 -9999 0 -10000 0 0
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.28 0.45 -9999 0 -0.92 151 151
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.069 -9999 0 -0.29 23 23
ER alpha/Oestrogen -0.041 0.14 -9999 0 -0.58 26 26
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.007 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.035 0.072 -9999 0 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.042 -9999 0 -0.54 3 3
WT1 -0.025 0.1 -9999 0 -0.31 54 54
WRN 0.012 0.037 -9999 0 -0.81 1 1
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.014 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.03 0.056 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.024 0.096 -9999 0 -10000 0 0
CCND1 -0.016 0.095 -9999 0 -10000 0 0
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.81 3 3
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.019 -9999 0 -10000 0 0
CDKN1B -0.039 0.19 -9999 0 -0.52 64 64
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 0.037 -9999 0 -0.81 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.81 112 112
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.006 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
IFN-gamma/IRF1 -0.085 0.2 -9999 0 -0.6 65 65
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -0.31 1 1
Telomerase 0.013 0.074 -9999 0 -0.48 6 6
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.046 0.19 -9999 0 -0.52 55 55
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.55 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.052 0.027 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.014 0.003 -9999 0 -10000 0 0
ATM -0.001 0.025 -9999 0 -0.56 1 1
SMAD3 0.02 0.028 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.014 0.002 -9999 0 -10000 0 0
MRE11A 0.008 0.064 -9999 0 -0.81 3 3
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 -0.032 0.067 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.041 -9999 0 -0.31 8 8
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
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 0.025 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.005 0.083 -9999 0 -0.82 5 5
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.1 0.23 -9999 0 -0.62 77 77
MYC -0.006 0.13 -9999 0 -0.81 12 12
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 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 0.008 0.041 -9999 0 -0.31 8 8
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.015 0.084 -9999 0 -10000 0 0
SP1/HDAC2 0.023 0.005 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.03 0.056 -9999 0 -10000 0 0
Smad3/Myc 0.011 0.091 -9999 0 -0.55 12 12
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.099 0.28 -9999 0 -0.8 64 64
Telomerase/PinX1 -0.03 0.056 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.03 0.056 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.035 -9999 0 -0.45 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.03 0.056 -9999 0 -10000 0 0
E2F1 -0.085 0.15 -9999 0 -0.31 151 151
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.001 0.095 -9999 0 -0.61 10 10
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
S1P3 pathway

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
PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.057 -9999 0 -0.27 17 17
GNAO1 -0.015 0.15 -9999 0 -0.69 21 21
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.028 -9999 0 -0.47 1 1
AKT3 0.049 0.049 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.037 -9999 0 -0.81 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.032 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.066 -9999 0 -0.31 17 17
MAPK3 0.042 0.063 -9999 0 -0.29 16 16
MAPK1 0.042 0.063 -9999 0 -0.29 16 16
JAK2 0.045 0.065 -9999 0 -0.29 16 16
CXCR4 0.041 0.064 -9999 0 -0.29 16 16
FLT1 0.015 0.037 -9999 0 -0.81 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.063 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.067 -9999 0 -0.31 17 17
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.051 -9999 0 -0.28 16 16
VEGFA 0.012 0.064 -9999 0 -0.81 3 3
S1P/S1P2/Gi 0.03 0.067 -9999 0 -0.32 17 17
VEGFR1 homodimer/VEGFA homodimer 0.024 0.066 -9999 0 -0.79 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.068 0.17 -9999 0 -0.35 125 125
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.81 10 10
Rac1/GTP -0.01 0.051 -9999 0 -0.28 16 16
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.059 -10000 0 -0.38 9 9
NFATC2 -0.02 0.097 -10000 0 -0.3 29 29
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.014 0.088 -10000 0 -0.32 22 22
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.024 0.089 -10000 0 -0.53 9 9
BCL2/BAX -0.046 0.16 -10000 0 -0.62 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.01 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.084 -10000 0 -0.56 4 4
Calcineurin A alpha-beta B1/BCL2 -0.047 0.22 -10000 0 -0.81 36 36
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.082 0.55 4 -10000 0 4
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
MAP3K8 -0.002 0.098 -10000 0 -0.82 7 7
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.49 24 24
CABIN1 0.014 0.089 -10000 0 -0.32 22 22
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.11 -10000 0 -0.53 16 16
mol:Ca2+ -0.005 0.009 -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 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.12 -10000 0 -0.82 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 -0.007 0.05 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.014 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.049 -10000 0 -10000 0 0
PRKCB -0.022 0.12 -10000 0 -0.36 46 46
PRKCE 0.005 0.083 -10000 0 -0.81 5 5
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.81 19 19
PRKCG 0.005 0.025 -10000 0 -0.31 3 3
PRKCQ 0.003 0.091 -10000 0 -0.81 6 6
FKBP38/BCL2 -0.045 0.16 -10000 0 -0.62 36 36
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.089 -10000 0 -0.38 19 19
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.07 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.056 -10000 0 -0.35 8 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.023 0.088 -10000 0 -0.52 9 9
NR4A1 -0.19 0.36 -10000 0 -0.73 148 148
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.036 0.064 -10000 0 -0.39 5 5
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -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 0.041 0.061 -10000 0 -0.36 8 8
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
Caspase cascade in apoptosis

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
TOP1 0.017 0.093 -10000 0 -0.46 13 13
ACTA1 0.008 0.12 -10000 0 -0.62 11 11
NUMA1 0.017 0.093 -10000 0 -0.46 13 13
SPTAN1 0.013 0.12 -10000 0 -0.62 11 11
LIMK1 0.013 0.12 -10000 0 -0.62 11 11
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
CASP10 -0.003 0.12 -10000 0 -0.65 13 13
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.017 0.093 -10000 0 -0.46 13 13
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.013 0.12 -10000 0 -0.6 11 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.013 0.12 -10000 0 -0.62 11 11
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.055 0.22 -10000 0 -0.65 59 59
BID -0.01 0.069 -10000 0 -0.31 13 13
MAP3K1 0.013 0.043 -10000 0 -0.23 3 3
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.029 -10000 0 -0.62 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.01 0.12 -10000 0 -0.6 12 12
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.015 0.052 0.17 1 -0.23 22 23
neuron apoptosis 0.023 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.019 0.11 -10000 0 -0.59 11 11
APAF1 0.012 0.037 -10000 0 -0.81 1 1
CASP6 0.021 0.064 -10000 0 -0.49 2 2
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.02 0.11 -10000 0 -0.59 11 11
CASP7 0.01 0.08 0.34 25 -10000 0 25
KRT18 0.016 0.018 -10000 0 -10000 0 0
apoptosis 0.024 0.11 -10000 0 -0.55 13 13
DFFA 0.013 0.12 -10000 0 -0.62 11 11
DFFB 0.013 0.12 -10000 0 -0.62 11 11
PARP1 0.015 0.052 0.23 22 -0.18 1 23
actin filament polymerization -0.02 0.11 0.56 11 -10000 0 11
TNF -0.087 0.26 -10000 0 -0.76 64 64
CYCS 0.004 0.047 -10000 0 -0.22 13 13
SATB1 0.028 0.061 -10000 0 -0.46 2 2
SLK 0.01 0.13 -10000 0 -0.65 13 13
p15 BID/BAX -0.002 0.062 -10000 0 -0.34 5 5
CASP2 0.007 0.11 -10000 0 -0.46 11 11
JNK cascade -0.013 0.042 0.23 3 -10000 0 3
CASP3 0.005 0.12 -10000 0 -0.61 13 13
LMNB2 0.021 0.075 -10000 0 -0.33 3 3
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.49 25 25
negative regulation of DNA binding -0.054 0.22 -10000 0 -0.64 59 59
stress fiber formation 0.01 0.13 -10000 0 -0.63 13 13
GZMB -0.017 0.14 -10000 0 -0.68 16 16
CASP1 0.015 0.032 -10000 0 -0.45 2 2
LMNB1 0.02 0.075 -10000 0 -0.36 2 2
APP 0.023 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.02 0.1 -10000 0 -0.5 11 11
LMNA 0.021 0.075 -10000 0 -0.33 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.002 0.12 -10000 0 -0.49 11 11
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.012 0.12 -10000 0 -0.62 11 11
APAF-1/Caspase 9 0.004 0.041 -10000 0 -0.39 1 1
nuclear fragmentation during apoptosis 0.017 0.092 -10000 0 -0.45 13 13
CFL2 0.02 0.11 -10000 0 -0.58 11 11
GAS2 0.007 0.13 -10000 0 -0.58 17 17
positive regulation of apoptosis 0.023 0.078 -10000 0 -0.36 2 2
PRF1 -0.004 0.11 -10000 0 -0.69 12 12
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.017 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
mol:Sphinganine-1-P 0.019 0.034 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.01 0.032 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.011 -9999 0 -10000 0 0
S1PR5 0.007 0.053 -9999 0 -0.37 8 8
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
S1P/S1P5/G12 -0.004 0.028 -9999 0 -0.48 1 1
S1P/S1P3/Gq -0.051 0.16 -9999 0 -0.41 25 25
S1P/S1P4/Gi 0.03 0.067 -9999 0 -0.32 17 17
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.81 10 10
ABCC1 0.013 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.061 -10000 0 -0.34 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.012 0.086 0.24 6 -0.41 15 21
RAR alpha/9cRA/Cyclin H -0.021 0.087 -10000 0 -0.41 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.068 -10000 0 -0.37 8 8
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.015 0.12 -10000 0 -0.42 28 28
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.009 -10000 0 -0.21 1 1
RXRs/RARs/NRIP1/9cRA -0.016 0.15 -10000 0 -0.62 24 24
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -0.31 1 1
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 -10000 0 -0.81 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.033 0.13 -10000 0 -0.66 19 19
RARA 0.008 0.088 -10000 0 -0.33 28 28
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.14 -10000 0 -0.57 17 17
PRKCA -0.015 0.16 -10000 0 -0.81 19 19
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.027 0.15 -10000 0 -0.64 24 24
RXRG -0.11 0.1 -10000 0 -0.52 23 23
RXRA 0.014 0.088 -10000 0 -0.33 28 28
RXRB 0.008 0.091 -10000 0 -0.44 19 19
VDR/Vit D3/DNA 0 0.009 -10000 0 -0.21 1 1
RBP1 -0.003 0.11 -10000 0 -0.65 12 12
CRBP1/9-cic-RA -0.012 0.082 -10000 0 -0.63 8 8
RARB -0.008 0.14 -10000 0 -0.81 14 14
PRKCG 0.008 0.026 -10000 0 -0.31 3 3
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.16 -10000 0 -0.66 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.13 -10000 0 -0.54 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.087 -10000 0 -0.48 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.027 0.15 -10000 0 -0.64 24 24
positive regulation of DNA binding -0.02 0.082 -10000 0 -0.39 19 19
NRIP1 -0.023 0.14 -10000 0 -0.64 16 16
RXRs/RARs -0.034 0.15 -10000 0 -0.63 24 24
RXRs/RXRs/DNA/9cRA -0.044 0.13 -10000 0 -0.68 19 19
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.012 0.052 -10000 0 -0.52 2 2
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.016 -10000 0 -10000 0 0
CDKN1A 0.034 0.029 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.029 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.023 -10000 0 -0.42 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.037 -10000 0 -0.81 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.022 0.41 1 -10000 0 1
TSC1 0.039 0.016 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.016 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.054 0.2 -10000 0 -0.54 69 69
MAP3K5 0.012 0.037 -10000 0 -0.81 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.036 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.016 -10000 0 -10000 0 0
CASP9 0.039 0.016 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.015 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.035 -10000 0 -0.54 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.004 0.028 -10000 0 -0.36 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.015 -10000 0 -10000 0 0
mTORC2 -0.001 0.023 -10000 0 -0.5 1 1
AKT2 0.016 0.029 -10000 0 -0.44 2 2
FOXO1-3a-4/14-3-3 family 0.025 0.042 -10000 0 -10000 0 0
PDPK1 0.01 0.053 -10000 0 -0.81 2 2
MDM2 0.039 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.015 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.045 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.062 0.21 -10000 0 -0.52 84 84
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.063 0.22 -10000 0 -0.52 84 84
GSK3A 0.039 0.016 -10000 0 -10000 0 0
FOXO1 0.039 0.016 -10000 0 -10000 0 0
GSK3B 0.039 0.016 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
G1/S transition of mitotic cell cycle 0.046 0.015 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.053 -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
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 0.076 -9999 0 -0.71 5 5
positive regulation of NF-kappaB transcription factor activity -0.005 0.056 -9999 0 -0.62 4 4
MAP2K4 0.047 0.034 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.064 -9999 0 -0.81 3 3
SMPD1 -0.002 0.026 -9999 0 -0.29 4 4
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.005 0.057 -9999 0 -0.62 4 4
TRAIL/TRAILR3 -0.059 0.1 -9999 0 -0.66 4 4
TRAIL/TRAILR1 -0.009 0.074 -9999 0 -0.62 7 7
TRAIL/TRAILR4 -0.005 0.057 -9999 0 -0.62 4 4
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -9999 0 -0.5 7 7
IKK complex -0.002 0.019 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.019 0.059 -9999 0 -0.62 4 4
MAP3K1 -0.004 0.031 -9999 0 -0.32 4 4
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.064 -9999 0 -0.81 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.034 0.043 -9999 0 -0.33 7 7
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.019 0.059 -9999 0 -0.62 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP -0.007 0.054 -9999 0 -0.46 7 7
mol:ceramide 0.018 0.028 -9999 0 -0.29 4 4
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.042 0.082 -9999 0 -0.46 11 11
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.074 0.14 -9999 0 -0.31 133 133
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.008 0.064 -9999 0 -0.54 7 7
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.006 0.051 -9999 0 -0.51 4 4
JNK cascade -0.005 0.056 -9999 0 -0.62 4 4
TRAIL (trimer) 0.006 0.075 -9999 0 -0.71 5 5
TNFRSF10C -0.074 0.14 -9999 0 -0.31 133 133
TRAIL/TRAILR1/DAP3/GTP/FADD -0.007 0.055 -9999 0 -0.46 7 7
TRAIL/TRAILR2/FADD -0.005 0.049 -9999 0 -0.54 4 4
cell death 0.018 0.028 -9999 0 -0.29 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.036 0.033 -9999 0 -0.33 4 4
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.015 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.004 0.041 -9999 0 -0.46 4 4
ceramide signaling pathway

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
MAP4K4 0.006 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.037 -10000 0 -0.81 1 1
BAD 0.018 0.045 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BAX 0.017 0.047 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.033 -10000 0 -0.12 11 11
IKBKB 0.014 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.056 -10000 0 -0.36 2 2
MAP2K1 0.027 0.056 -10000 0 -0.36 2 2
SMPD1 0.01 0.033 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.014 0.12 -10000 0 -0.53 11 11
MAP2K4 0.024 0.046 -10000 0 -10000 0 0
protein ubiquitination 0.015 0.12 -10000 0 -0.52 11 11
EnzymeConsortium:2.7.1.37 0.031 0.061 -10000 0 -0.37 2 2
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.022 0.056 -10000 0 -0.39 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.047 -10000 0 -0.17 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.018 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.055 -10000 0 -0.35 2 2
MAPK1 0.03 0.055 -10000 0 -0.35 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.006 0.13 -10000 0 -0.56 11 11
KSR1 0.016 0.056 -10000 0 -0.42 2 2
MAPK8 0.021 0.08 -10000 0 -0.42 11 11
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.014 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.028 -10000 0 -0.62 1 1
TNF -0.087 0.27 -10000 0 -0.76 64 64
CYCS 0.027 0.056 0.16 30 -10000 0 30
IKBKG 0.014 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.13 -10000 0 -0.44 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.056 0.16 30 -10000 0 30
TNF/TNF R/SODD -0.065 0.17 -10000 0 -0.54 58 58
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.006 0.13 -10000 0 -0.55 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.073 0.051 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.029 0.078 -9999 0 -0.62 2 2
NFKBIA 0.048 0.023 -9999 0 -0.47 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.048 0.13 -9999 0 -0.39 57 57
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.038 -9999 0 -0.42 1 1
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 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.014 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.034 -9999 0 -0.54 2 2
NOD2 -0.033 0.12 -9999 0 -0.32 68 68
NFKB1 0.015 0.037 -9999 0 -0.81 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.037 -9999 0 -0.81 1 1
TNF/TNFR1A -0.075 0.2 -9999 0 -0.62 57 57
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
PRKCA -0.018 0.16 -9999 0 -0.81 19 19
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.087 0.26 -9999 0 -0.76 64 64
NF kappa B1 p50/RelA -0.001 0.023 -9999 0 -0.52 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -9999 0 -0.46 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.003 0.016 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.016 0.076 -9999 0 -0.39 19 19
Canonical Wnt signaling pathway

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.023 0.22 1 -10000 0 1
AES 0.005 0.02 -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 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.024 0.16 -10000 0 -0.65 28 28
TLE1 0 0.065 -10000 0 -0.8 3 3
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.039 -10000 0 -10000 0 0
WIF1 -0.034 0.1 -10000 0 -0.31 60 60
beta catenin/RanBP3 0.021 0.09 0.36 27 -10000 0 27
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.041 0.13 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.052 0.037 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.048 0.31 -10000 0 -1.6 19 19
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.044 0.29 1 -0.4 1 2
Axin1/APC/GSK3 0.007 0.031 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.021 -10000 0 -10000 0 0
HNF1A 0.006 0.021 -10000 0 -10000 0 0
CTBP1 0.006 0.021 -10000 0 -10000 0 0
MYC -0.028 0.25 -10000 0 -1.6 12 12
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.034 0.11 -10000 0 -0.55 19 19
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.013 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.12 0.48 27 -10000 0 27
LEF1 -0.003 0.066 -10000 0 -0.4 10 10
DVL1 0.019 0.027 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.074 -10000 0 -0.49 3 3
DKK1/LRP6/Kremen 2 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.014 0 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 -10000 0 -10000 0 0
NLK 0.014 0.004 -10000 0 -10000 0 0
CCND1 0 0.075 -10000 0 -0.8 1 1
WNT1 0.008 0.032 -10000 0 -0.31 5 5
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.03 0.059 0.36 14 -10000 0 14
APC 0.038 0.028 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 0.034 0.037 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.033 0.3 1 -0.46 2 3
DAPP1 -0.054 0.14 -10000 0 -0.49 12 12
Src family/SYK family/BLNK-LAT/BTK-ITK -0.059 0.18 -10000 0 -0.49 32 32
mol:DAG -0.006 0.097 -10000 0 -0.27 16 16
HRAS 0.013 0.02 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.035 -10000 0 -0.46 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.014 0.27 1 -10000 0 1
ARF1/GTP -0.001 0.022 0.28 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
ADAP1 0 0.013 0.26 1 -10000 0 1
ARAP3 0 0.013 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.012 0.037 -10000 0 -0.81 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.011 0.029 -10000 0 -0.31 4 4
mol:Ca2+ 0.006 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.81 1 1
ZAP70 -0.026 0.16 -10000 0 -0.62 31 31
mol:IP3 0.004 0.072 -10000 0 -0.21 1 1
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.035 -10000 0 -0.46 1 1
RhoA/GDP -0.001 0.019 0.28 1 -10000 0 1
PDK1/Src/Hsp90 -0.002 0.035 -10000 0 -0.54 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.037 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -10000 0 0
PLEKHA2 0.022 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.79 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.014 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 0.26 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.051 0.16 -10000 0 -0.59 14 14
BLK -0.24 0.37 -10000 0 -0.74 168 168
PDPK1 0.01 0.053 -10000 0 -0.81 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.01 0.084 -10000 0 -0.31 36 36
CYTH3 -0.002 0.033 0.26 1 -0.49 2 3
CYTH2 0 0.013 0.26 1 -10000 0 1
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.012 0.086 0.22 1 -0.59 10 11
SGK1 -0.013 0.096 0.24 1 -0.66 10 11
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
mol:GDP 0.015 0.037 -10000 0 -0.49 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.019 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.017 0.36 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.032 0.009 -10000 0 -10000 0 0
PLEKHA1 0.022 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.005 0.077 -10000 0 -0.65 6 6
Rac1/GTP -0.006 0.054 -10000 0 -0.47 2 2
ITK -0.056 0.14 -10000 0 -0.43 61 61
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.015 0.13 -10000 0 -0.4 16 16
LCK -0.01 0.11 -10000 0 -0.42 27 27
BTK -0.013 0.06 0.26 1 -0.43 8 9
Circadian rhythm 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
chromatin modification -0.025 0.047 -9999 0 -0.62 1 1
CLOCK -0.044 0.21 -9999 0 -0.82 33 33
TIMELESS/CRY2 -0.004 0.065 -9999 0 -10000 0 0
DEC1/BMAL1 -0.024 0.067 -9999 0 -10000 0 0
ATR 0.012 0.037 -9999 0 -0.81 1 1
NR1D1 -0.054 0.13 -9999 0 -10000 0 0
ARNTL -0.025 0.1 -9999 0 -0.31 55 55
TIMELESS -0.012 0.073 -9999 0 -10000 0 0
NPAS2 0.009 0.04 -9999 0 -0.81 1 1
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.006 0.03 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.006 0.03 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.035 0.16 -9999 0 -0.56 34 34
BMAL1/CLOCK -0.055 0.16 -9999 0 -0.62 15 15
S phase of mitotic cell cycle -0.025 0.047 -9999 0 -0.62 1 1
TIMELESS/CHEK1/ATR -0.025 0.048 -9999 0 -0.64 1 1
mol:NADPH -0.006 0.03 -9999 0 -10000 0 0
PER1/TIMELESS -0.004 0.065 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.014 -9999 0 -0.31 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.094 -9999 0 -0.45 17 17
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0.074 -9999 0 -0.81 4 4
ITGA4 0.002 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin/MAdCAM1 -0.035 0.11 -9999 0 -0.5 20 20
EPO 0.002 0.038 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.62 3 3
EPO/EPOR (dimer) -0.007 0.036 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.037 -9999 0 -0.46 3 3
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PI3K -0.004 0.048 -9999 0 -0.62 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.022 0.067 -9999 0 -0.62 4 4
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.012 0.096 -9999 0 -0.36 30 30
cell adhesion -0.035 0.1 -9999 0 -0.49 20 20
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.022 0.078 -9999 0 -0.55 7 7
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.08 -9999 0 -0.55 9 9
p130Cas/Crk/Dock1 0.039 0.079 -9999 0 -0.81 1 1
VCAM1 0.002 0.089 -9999 0 -0.56 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.042 -9999 0 -0.49 3 3
BCAR1 0.031 0.074 -9999 0 -0.51 7 7
EPOR 0.007 0.046 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.038 -9999 0 -0.48 3 3
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.038 0.025 -9999 0 -10000 0 0
PLK1 0.1 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.047 -9999 0 -0.39 1 1
FOXO3 0.1 0.11 -9999 0 -0.58 4 4
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.01 0.038 -9999 0 -0.59 1 1
CAT 0.1 0.15 -9999 0 -1.4 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.011 -9999 0 -10000 0 0
FOXO1 0.042 0.016 -9999 0 -10000 0 0
MAPK10 0.043 0.025 -9999 0 -0.5 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.065 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.013 0.087 -9999 0 -0.72 3 3
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.002 -9999 0 -10000 0 0
BCL2L11 0.04 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.05 -9999 0 -0.49 4 4
mol:GDP 0.015 0.013 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.061 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.042 -9999 0 -10000 0 0
MST1 0.023 0.042 -9999 0 -0.57 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.066 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.033 0.077 -9999 0 -0.48 11 11
MAPK9 0.044 0.007 -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 0.006 0.042 -9999 0 -0.81 1 1
SOD2 0.16 0.073 -9999 0 -0.53 3 3
RBL2 0.11 0.15 -9999 0 -1.4 4 4
RAL/GDP 0.033 0.013 -9999 0 -10000 0 0
CHUK 0.025 0.01 -9999 0 -10000 0 0
Ran/GTP 0.015 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.042 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.082 0.42 -9999 0 -1.5 38 38
SKP2 0.007 0.074 -9999 0 -0.81 4 4
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.01 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.73 1 1
FOXO1-3a-4/beta catenin -0.003 0.049 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.05 -9999 0 -0.49 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.008 0.12 -9999 0 -0.81 10 10
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.055 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.33 312 312
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.016 0.065 -9999 0 -10000 0 0
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.1 0.11 -9999 0 -0.73 1 1
BCL6 0.11 0.11 -9999 0 -0.69 4 4
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
CDC42/GTP -0.011 0.054 -9999 0 -0.29 17 17
PLCG1 0.03 0.064 -9999 0 -0.3 17 17
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 0 -9999 0 -10000 0 0
cell migration -0.011 0.053 -9999 0 -0.29 17 17
S1PR5 0.007 0.053 -9999 0 -0.37 8 8
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
MAPK3 0.03 0.064 -9999 0 -0.3 17 17
MAPK1 0.03 0.064 -9999 0 -0.3 17 17
S1P/S1P5/Gi 0.022 0.07 -9999 0 -0.33 18 18
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -9999 0 -0.55 1 1
RHOA 0.032 0.018 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.022 0.068 -9999 0 -0.33 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.002 0.016 -9999 0 -10000 0 0
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
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.011 0.054 0.29 17 -10000 0 17
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
RhoA/GTP -0.012 0.055 -10000 0 -0.3 17 17
negative regulation of cAMP metabolic process 0.022 0.07 -10000 0 -0.33 18 18
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.053 -10000 0 -0.37 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.07 -10000 0 -0.33 18 18
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.81 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
AKT1 0.083 0.089 -9999 0 -0.6 7 7
PTK2B 0.036 0.13 -9999 0 -0.53 22 22
VEGFR2 homodimer/Frs2 0.03 0.096 -9999 0 -1 4 4
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.01 0.1 -9999 0 -0.86 6 6
endothelial cell proliferation 0.079 0.099 -9999 0 -0.55 7 7
mol:Ca2+ 0.05 0.1 -9999 0 -0.72 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.01 0.098 -9999 0 -0.81 6 6
RP11-342D11.1 0.041 0.1 -9999 0 -0.73 7 7
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.061 -9999 0 -0.58 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.064 -9999 0 -0.81 3 3
HRAS/GDP -0.009 0.082 -9999 0 -0.74 5 5
SH2D2A -0.036 0.18 -9999 0 -0.61 39 39
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.069 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.036 0.15 -9999 0 -0.56 29 29
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.81 1 1
SHC/GRB2/SOS1 -0.01 0.094 -9999 0 -0.93 4 4
GRB10 0.05 0.1 -9999 0 -0.72 7 7
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.094 -9999 0 -0.78 6 6
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.077 -9999 0 -0.48 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.01 0.095 -9999 0 -0.79 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.091 -9999 0 -0.81 6 6
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.01 0.1 -9999 0 -0.86 6 6
mol:GDP -0.009 0.087 -9999 0 -0.87 4 4
mol:NADP 0.076 0.066 -9999 0 -0.56 4 4
eNOS/Hsp90 0.079 0.062 -9999 0 -0.52 4 4
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.11 -9999 0 -0.75 7 7
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.064 -9999 0 -0.81 3 3
VEGFC 0.012 0.037 -9999 0 -0.81 1 1
FAK1/Vinculin 0.058 0.11 -9999 0 -0.71 7 7
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 -0.025 0.13 -9999 0 -0.57 22 22
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.019 0.063 -9999 0 -0.58 4 4
mol:L-citrulline 0.076 0.066 -9999 0 -0.56 4 4
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.01 0.098 -9999 0 -0.81 6 6
VEGFR2 homodimer/VEGFA homodimer -0.012 0.12 -9999 0 -0.84 7 7
VEGFR2/3 heterodimer 0.024 0.13 -9999 0 -1 7 7
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.051 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer 0.029 0.1 -9999 0 -1.1 4 4
FLT1 0.012 0.037 -9999 0 -0.81 1 1
NEDD4 0.013 0.053 -9999 0 -0.81 2 2
MAPK3 0.045 0.1 -9999 0 -0.64 8 8
MAPK1 0.045 0.1 -9999 0 -0.64 8 8
VEGFA145/NRP2 -0.02 0.071 -9999 0 -0.62 3 3
VEGFR1/2 heterodimer 0.029 0.11 -9999 0 -1.1 4 4
KDR 0.029 0.11 -9999 0 -1.1 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.018 0.11 -9999 0 -0.78 7 7
SRC 0.013 0.015 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.047 0.11 -9999 0 -0.66 8 8
PI3K -0.011 0.094 -9999 0 -0.75 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.01 0.1 -9999 0 -0.86 6 6
FES 0.05 0.11 -9999 0 -0.77 7 7
GAB1 -0.01 0.093 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.1 -9999 0 -0.86 6 6
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 0.068 0.092 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.01 0.1 -9999 0 -0.86 6 6
PI3K/GAB1 0.085 0.084 -9999 0 -0.61 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.094 -9999 0 -0.78 6 6
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.014 0.12 -9999 0 -0.88 8 8
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.05 0.11 -9999 0 -0.77 7 7
actin cytoskeleton reorganization -0.036 0.14 -9999 0 -0.55 29 29
PTK2 0.052 0.12 -9999 0 -0.79 7 7
EDG1 0.041 0.1 -9999 0 -0.73 7 7
mol:DAG 0.05 0.11 -9999 0 -0.75 7 7
CaM/Ca2+ -0.009 0.088 -9999 0 -0.67 7 7
MAP2K3 0.048 0.12 -9999 0 -0.98 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.11 -9999 0 -0.8 7 7
PLCG1 0.05 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.01 0.099 -9999 0 -0.81 6 6
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.011 0.12 -9999 0 -0.91 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.01 0.1 -9999 0 -0.86 6 6
cell migration 0.082 0.096 -9999 0 -0.64 5 5
mol:PI-3-4-5-P3 -0.01 0.081 -9999 0 -0.66 6 6
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.047 0.095 -9999 0 -0.68 7 7
mol:NO 0.076 0.066 -9999 0 -0.56 4 4
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.081 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.12 -9999 0 -0.8 7 7
VHL 0.008 0.064 -9999 0 -0.81 3 3
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
NOS3 0.078 0.076 -9999 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.013 0.11 -9999 0 -0.73 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.039 0.14 -9999 0 -0.52 24 24
PRKCB 0.04 0.11 -9999 0 -0.57 12 12
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.04 0.11 -9999 0 -0.77 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.011 0.12 -9999 0 -0.91 6 6
VEGFA165/NRP2 -0.02 0.071 -9999 0 -0.62 3 3
MAPKKK cascade -0.009 0.08 -9999 0 -0.73 5 5
NRP2 -0.013 0.088 -9999 0 -0.31 40 40
VEGFC homodimer 0.012 0.037 -9999 0 -0.81 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.058 0.11 -9999 0 -0.71 7 7
MAP3K13 0.04 0.14 -9999 0 -0.6 16 16
PDPK1 0.076 0.09 -9999 0 -0.71 5 5
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.051 0.1 -9999 0 -10000 0 0
CRKL 0.037 0.049 -9999 0 -0.46 2 2
mol:DAG 0.041 0.051 -9999 0 -0.37 1 1
HRAS 0.061 0.044 -9999 0 -0.42 1 1
MAPK8 0.018 0.091 -9999 0 -0.55 11 11
RAP1A 0.037 0.049 -9999 0 -0.46 2 2
GAB1 0.037 0.049 -9999 0 -0.46 2 2
MAPK14 0.03 0.03 -9999 0 -10000 0 0
EPO 0.005 0.038 -9999 0 -0.3 7 7
PLCG1 0.041 0.052 -9999 0 -0.38 1 1
EPOR/TRPC2/IP3 Receptors 0.009 0.046 -9999 0 -0.31 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.021 0.12 -9999 0 -0.57 23 23
GAB1/SHC/GRB2/SOS1 -0.006 0.029 -9999 0 -0.45 1 1
EPO/EPOR (dimer) 0.013 0.041 -9999 0 -0.28 1 1
IRS2 0.037 0.049 -9999 0 -0.46 2 2
STAT1 0.041 0.078 -9999 0 -10000 0 0
STAT5B 0.042 0.066 -9999 0 -0.38 1 1
cell proliferation 0.026 0.086 -9999 0 -0.51 11 11
GAB1/SHIP/PIK3R1/SHP2/SHC -0.009 0.036 -9999 0 -0.44 2 2
TEC 0.037 0.049 -9999 0 -0.46 2 2
SOCS3 -0.026 0.18 -9999 0 -0.79 24 24
STAT1 (dimer) 0.041 0.077 -9999 0 -0.36 1 1
JAK2 0.011 0.053 -9999 0 -0.82 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.042 0.055 -9999 0 -0.49 2 2
EPO/EPOR 0.013 0.041 -9999 0 -0.28 1 1
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.045 0.048 -9999 0 -0.44 2 2
elevation of cytosolic calcium ion concentration 0.009 0.046 -9999 0 -0.31 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.028 0.035 -9999 0 -10000 0 0
mol:IP3 0.041 0.051 -9999 0 -0.37 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.011 0.036 -9999 0 -0.47 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.038 -9999 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.017 0.066 -9999 0 -0.29 25 25
PTPN6 0.03 0.051 -9999 0 -0.49 2 2
TEC/VAV2/GRB2 0.05 0.046 -9999 0 -0.48 1 1
EPOR 0.009 0.046 -9999 0 -0.31 10 10
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
mol:GDP -0.006 0.029 -9999 0 -0.46 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.05 0.046 -9999 0 -0.48 1 1
VAV2 0.037 0.049 -9999 0 -0.46 2 2
CBL 0.037 0.049 -9999 0 -0.46 2 2
SHC/Grb2/SOS1 -0.007 0.031 -9999 0 -0.48 1 1
STAT5A 0.042 0.066 -9999 0 -0.38 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.052 0.098 -9999 0 -0.41 1 1
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
BTK 0.021 0.087 -9999 0 -0.48 9 9
BCL2 0.002 0.28 -9999 0 -0.98 36 36
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.059 0.16 -9999 0 -0.5 58 58
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.15 -9999 0 -0.41 58 58
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.024 0.065 -9999 0 -10000 0 0
YY1/LSF 0.028 0.049 -9999 0 -0.52 4 4
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.012 0.13 -9999 0 -0.36 57 57
I kappa B alpha/HDAC1 0.001 0.089 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.002 0.11 -9999 0 -0.32 57 57
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0.001 0.089 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -0.47 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.008 0.016 -9999 0 -0.31 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.022 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.064 -9999 0 -0.81 3 3
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 -0.007 0.099 -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 0.044 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.49 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.037 -9999 0 -0.81 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.016 0.083 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.049 0.02 -9999 0 -10000 0 0
PPARG -0.059 0.15 -9999 0 -0.45 62 62
HDAC8/hEST1B 0 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) 0.001 0.089 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.021 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.099 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
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 0.027 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.043 -9999 0 -0.48 4 4
YY1/SAP30/HDAC1 -0.001 0.021 -9999 0 -0.48 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.099 -9999 0 -10000 0 0
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.083 -9999 0 -10000 0 0
nuclear export 0 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 0.001 0.089 -9999 0 -10000 0 0
GATA1/HDAC1 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC3 -0.009 0.088 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.075 0.2 -9999 0 -0.62 57 57
SIN3/HDAC complex/Mad/Max 0.049 0.023 -9999 0 -10000 0 0
NuRD Complex 0.058 0.021 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.064 -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 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.038 -9999 0 -0.49 3 3
GATA1/Fog1 0 0.009 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.087 0.26 -9999 0 -0.76 64 64
negative regulation of cell growth 0.049 0.023 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.051 0.14 -9999 0 -0.43 57 57
SIN3/HDAC complex/NCoR1 0.046 0.026 -9999 0 -10000 0 0
TFCP2 0.007 0.074 -9999 0 -0.81 4 4
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.007 0.074 -10000 0 -0.81 4 4
ITGA4 0.002 0.077 -10000 0 -0.44 12 12
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.033 0.12 -10000 0 -0.62 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.046 -10000 0 -0.54 3 3
alpha4/beta7 Integrin/Paxillin -0.025 0.095 -10000 0 -0.5 17 17
lamellipodium assembly -0.004 0.057 -10000 0 -0.54 5 5
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
PI3K -0.004 0.048 -10000 0 -0.62 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.034 -10000 0 -0.42 3 3
cell adhesion -0.005 0.038 -10000 0 -0.45 3 3
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.042 -10000 0 -0.49 3 3
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.024 0.15 -10000 0 -0.51 35 35
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.011 0.068 -10000 0 -0.52 7 7
p130Cas/Crk/Dock1 -0.004 0.048 -10000 0 -0.54 4 4
VCAM1 0.002 0.089 -10000 0 -0.56 10 10
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.038 -10000 0 -0.46 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.038 -10000 0 -0.46 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.038 0.45 3 -10000 0 3
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.038 -10000 0 -0.46 3 3
Rac1/GTP -0.005 0.067 -10000 0 -0.76 3 3
Atypical NF-kappaB 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
BCL3/RelA 0 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.011 0.15 -9999 0 -0.55 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.039 -9999 0 -0.41 1 1
NFKBIA 0.024 0.037 -9999 0 -0.27 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.025 -9999 0 -0.54 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.042 0.21 -9999 0 -0.81 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.027 -9999 0 -0.54 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.025 -9999 0 -0.54 1 1
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
NF kappa B1 p50 dimer 0.02 0.029 -9999 0 -0.62 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.029 -9999 0 -0.62 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.038 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.038 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -10000 0 0
PI3K -0.004 0.048 -9999 0 -0.62 3 3
NF kappa B1 p50/RelA 0.031 0.038 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.035 -9999 0 -10000 0 0
cell death 0.045 0.036 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.011 0.15 -9999 0 -0.55 33 33
LCK -0.01 0.11 -9999 0 -0.42 27 27
BCL3 0.013 0.015 -9999 0 -0.31 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.009 0.018 -9999 0 -10000 0 0
BUB1B 0.017 0.027 -9999 0 -10000 0 0
PLK1 0.017 0.012 -9999 0 -10000 0 0
PLK1S1 0.015 0.007 -9999 0 -10000 0 0
KIF2A 0.023 0.029 -9999 0 -0.58 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -10000 0 0
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 0.001 0.073 -9999 0 -0.28 16 16
WEE1 0.022 0.011 -9999 0 -10000 0 0
cytokinesis 0.002 0.072 -9999 0 -0.31 5 5
PP2A-alpha B56 0.006 0.068 -9999 0 -0.72 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.018 -9999 0 -10000 0 0
CENPE 0.019 0.048 -9999 0 -0.52 3 3
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.029 -9999 0 -0.58 1 1
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.009 0.022 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.008 0.08 -9999 0 -0.31 32 32
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.034 -9999 0 -0.35 2 2
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.007 -9999 0 -0.065 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.012 -9999 0 -10000 0 0
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.027 0.067 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.012 0.022 -9999 0 -10000 0 0
CDC25B 0.012 0.025 -9999 0 -0.31 3 3
SGOL1 0.009 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.005 0.013 -9999 0 -10000 0 0
CDC14B 0.004 0.072 -9999 0 -0.64 6 6
CDC20 0.008 0.041 -9999 0 -0.31 8 8
PLK1/PBIP1 0.002 0.022 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.021 -9999 0 -0.39 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.027 0.11 -9999 0 -0.31 61 61
metaphase plate congression 0.015 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.016 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.009 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 3 3
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 3 3
PLK1/PRC1-2 0.008 0.057 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.004 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.038 -9999 0 -0.47 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.035 -9999 0 -0.3 3 3
microtubule-based process -0.001 0.06 -9999 0 -10000 0 0
Golgi organization 0.017 0.012 -9999 0 -10000 0 0
Cohesin/SA2 -0.001 0.005 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.035 0.12 -9999 0 -0.31 74 74
APC/C/CDC20 0.02 0.025 -9999 0 -0.18 1 1
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.022 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.038 -9999 0 -0.55 2 2
C13orf34 0.018 0.039 -9999 0 -0.47 3 3
NUDC 0.015 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.027 -9999 0 -10000 0 0
spindle assembly 0.017 0.011 -9999 0 -10000 0 0
spindle stabilization 0.015 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.012 0.062 -9999 0 -0.55 6 6
MKLP2/PLK1 -0.001 0.061 -9999 0 -10000 0 0
CCNB1 0.014 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 -0.003 0.12 -9999 0 -0.52 25 25
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.009 -9999 0 -10000 0 0
MLF1IP 0.008 0.032 -9999 0 -0.22 10 10
INCENP 0.009 0.053 -9999 0 -0.82 2 2
HIF-2-alpha transcription factor network

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
MMP14 -0.001 0.025 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.025 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.072 -10000 0 -0.69 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.028 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.17 0.17 -10000 0 -0.8 3 3
FLT1 -0.002 0.072 -10000 0 -1.6 1 1
ADORA2A 0.18 0.14 -10000 0 -0.85 2 2
germ cell development 0.19 0.14 -10000 0 -0.84 2 2
SLC11A2 0.19 0.15 -10000 0 -0.89 2 2
BHLHE40 0.18 0.16 -10000 0 -0.89 2 2
HIF1AN 0.028 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.003 0.076 -10000 0 -0.96 2 2
ETS1 0.03 0.003 -10000 0 -10000 0 0
CITED2 -0.093 0.32 -10000 0 -1.2 39 39
KDR -0.009 0.13 -10000 0 -1.4 4 4
PGK1 0.19 0.15 -10000 0 -0.89 2 2
SIRT1 0.012 0.037 -10000 0 -0.81 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.17 -10000 0 -0.96 3 3
EPAS1 0.1 0.1 -10000 0 -0.55 4 4
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.18 0.17 -10000 0 -0.88 5 5
EFNA1 0.19 0.15 -10000 0 -0.89 2 2
FXN 0.18 0.14 -10000 0 -0.85 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 0.91 3 -10000 0 3
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.002 0.14 -10000 0 -0.57 21 21
EGLN2 0.028 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.055 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.047 -10000 0 -0.59 3 3
VHL 0.008 0.064 -10000 0 -0.81 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.18 0.14 -10000 0 -0.85 2 2
TWIST1 0.17 0.18 -10000 0 -0.65 10 10
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.002 0.067 -10000 0 -0.76 2 2
VEGFA 0.19 0.16 -10000 0 -0.84 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.031 0.008 -9999 0 -10000 0 0
MAPK12 0.019 0.079 -9999 0 -0.47 12 12
CCND1 0.017 0.034 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.075 -9999 0 -0.44 12 12
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.079 -9999 0 -0.47 12 12
MAP2K6 0.012 0.085 -9999 0 -0.52 12 12
MAPT 0.024 0.045 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.021 -9999 0 -0.45 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.73 1 1
PDGFB-D/PDGFRB/SLAP 0.004 0.031 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/APS/CBL -0.001 0.025 -9999 0 -0.54 1 1
AKT1 0.059 0.043 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.05 -9999 0 -0.78 1 1
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
FGR 0.002 0.028 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.048 -9999 0 -0.82 1 1
MYC 0.02 0.15 -9999 0 -0.84 13 13
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.028 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.002 0.034 -9999 0 -0.54 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
GO:0007205 0.02 0.049 -9999 0 -0.84 1 1
PTEN 0.012 0.037 -9999 0 -0.81 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.04 0.12 -9999 0 -0.31 82 82
PDGFB-D/PDGFRB/SHP2 0.003 0.041 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/GRB10 0.005 0.03 -9999 0 -0.63 1 1
cell cycle arrest -0.001 0.03 -9999 0 -0.62 1 1
HRAS 0.012 0.021 -9999 0 -0.31 2 2
HIF1A 0.064 0.039 -9999 0 -10000 0 0
GAB1 0.013 0.063 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.059 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.031 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.005 0.03 -9999 0 -0.63 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.047 -9999 0 -0.74 1 1
positive regulation of MAPKKK cascade -0.002 0.04 -9999 0 -0.63 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.049 -9999 0 -0.85 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.015 -9999 0 -0.31 1 1
PDGFB-D/PDGFRB/GRB7 -0.029 0.084 -9999 0 -0.78 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 145 145
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.005 0.03 -9999 0 -0.63 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.017 0.07 -9999 0 -0.86 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.005 0.03 -9999 0 -0.63 1 1
LCK -0.008 0.087 -9999 0 -0.73 6 6
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.54 1 1
ABL1 0.009 0.061 -9999 0 -0.83 1 1
PDGFB-D/PDGFRB/CBL 0.01 0.067 -9999 0 -0.94 1 1
PTPN1 0.014 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 0.006 0.05 -9999 0 -0.31 12 12
cell proliferation 0.022 0.13 -9999 0 -0.73 13 13
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.024 -9999 0 -0.42 1 1
SRC 0.006 0.028 -9999 0 -0.55 1 1
PI3K -0.004 0.04 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.027 0.065 -9999 0 -0.69 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.052 -9999 0 -0.82 1 1
LYN 0.006 0.029 -9999 0 -0.55 1 1
LRP1 0.012 0.037 -9999 0 -0.81 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.021 -9999 0 -0.44 1 1
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.049 -9999 0 -0.85 1 1
PLCG1 0.02 0.051 -9999 0 -0.89 1 1
NHERF/PDGFRB -0.002 0.026 -9999 0 -0.54 1 1
YES1 0.004 0.027 -9999 0 -0.55 1 1
cell migration -0.002 0.026 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.44 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.021 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.003 0.032 -9999 0 -0.49 2 2
FYN 0.006 0.028 -9999 0 -0.55 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.013 -9999 0 -10000 0 0
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.028 0.087 -9999 0 -0.44 13 13
PRKCD 0.034 0.025 -9999 0 -0.5 1 1
FER 0.031 0.049 -9999 0 -0.5 4 4
MAPKKK cascade -0.001 0.02 -9999 0 -0.43 1 1
RASA1 0.034 0.025 -9999 0 -0.5 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.45 1 1
PDGFB-D/PDGFRB/SHB 0.005 0.03 -9999 0 -0.63 1 1
chemotaxis 0.01 0.059 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -0.42 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.029 -9999 0 -0.64 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.05 0.038 -10000 0 -0.43 3 3
adherens junction organization 0.04 0.038 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.059 -10000 0 -0.42 7 7
FMN1 0.019 0.11 -10000 0 -0.43 28 28
mol:IP3 -0.002 0.031 -10000 0 -0.4 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.035 -10000 0 -0.39 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.035 -10000 0 -0.48 2 2
VASP 0.046 0.011 -10000 0 -10000 0 0
ZYX 0.046 0.011 -10000 0 -10000 0 0
JUB 0.045 0.024 -10000 0 -0.43 1 1
EGFR(dimer) 0.041 0.051 -10000 0 -0.45 5 5
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.42 3 3
PIK3CA 0.009 0.064 -10000 0 -0.81 3 3
PI3K -0.003 0.033 -10000 0 -0.43 3 3
FYN 0.051 0.034 -10000 0 -0.35 3 3
mol:Ca2+ 0.042 0.034 -10000 0 -0.39 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.002 0.031 -10000 0 -0.4 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.052 0.059 -10000 0 -0.42 7 7
establishment of polarity of embryonic epithelium 0.046 0.011 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.083 -10000 0 -0.81 5 5
CASR 0.042 0.037 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.028 -10000 0 -0.36 3 3
AKT2 0.049 0.035 -10000 0 -0.39 3 3
actin cable formation 0.027 0.11 -10000 0 -0.41 28 28
apoptosis 0.002 0.032 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.046 0.063 -10000 0 -0.46 7 7
PIP5K1A 0.044 0.036 -10000 0 -0.5 2 2
PLCG1 -0.003 0.032 -10000 0 -0.41 3 3
Rac1/GTP -0.005 0.042 -10000 0 -0.41 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 -0.002 0.03 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.025 -9999 0 -0.55 1 1
ATM 0.012 0.037 -9999 0 -0.81 1 1
MAP2K3 0.026 0.057 -9999 0 -0.52 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.023 0.079 -9999 0 -0.42 7 7
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.1 -9999 0 -0.66 10 10
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.013 0.15 -9999 0 -0.81 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.028 -9999 0 -0.62 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.21 2 2
RAC1/OSM/MEKK3 -0.001 0.009 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.009 0.033 -9999 0 -0.38 2 2
TRAF6 0.007 0.03 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.005 0.083 -9999 0 -0.81 5 5
CCM2 0.012 0.021 -9999 0 -0.31 2 2
CaM/Ca2+/CAMKIIB -0.006 0.055 -9999 0 -0.55 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.062 -9999 0 -0.59 5 5
OSM/MEKK3 -0.001 0.013 -9999 0 -10000 0 0
TAOK1 -0.04 0.16 -9999 0 -0.46 61 61
TAOK2 0.017 0.021 -9999 0 -0.44 1 1
TAOK3 0.017 0.021 -9999 0 -0.44 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.037 -9999 0 -0.81 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.025 -9999 0 -0.54 1 1
GADD45/MTK1/MTK1 -0.022 0.1 -9999 0 -0.48 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.02 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.019 -9999 0 -0.42 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.04 0.15 -9999 0 -0.62 32 32
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 -0.04 0.2 -9999 0 -0.81 32 32
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.037 -9999 0 -0.81 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.49 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC5 0 0.009 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.024 -9999 0 -0.54 1 1
HDAC9 -0.015 0.092 -9999 0 -0.31 44 44
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.028 -9999 0 -0.62 1 1
Histones 0.036 0.023 -9999 0 -10000 0 0
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 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 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 -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.004 0.11 -9999 0 -0.53 16 16
Tubulin/HDAC6 -0.005 0.054 -9999 0 -0.54 5 5
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 0.008 0.016 -9999 0 -0.31 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.062 -9999 0 -0.62 5 5
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.028 -9999 0 -0.62 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.067 -9999 0 -0.54 7 7
HDAC4/ER alpha -0.042 0.14 -9999 0 -0.62 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.022 -9999 0 -10000 0 0
cell motility -0.005 0.054 -9999 0 -0.54 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.037 -9999 0 -0.81 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.046 0.19 -9999 0 -0.52 55 55
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.037 -9999 0 -0.81 1 1
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.021 -9999 0 -0.46 1 1
GNG2 0.012 0.037 -9999 0 -0.81 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.005 0.083 -9999 0 -0.81 5 5
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.021 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.035 -9999 0 -0.31 6 6
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.024 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.008 -9999 0 -10000 0 0
BIRC5 -0.011 0.089 -9999 0 -0.32 35 35
NFKBIA 0.032 0.009 -9999 0 -10000 0 0
CPEB1 -0.05 0.22 -9999 0 -0.81 38 38
AKT1 0.032 0.009 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.012 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.015 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.013 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.028 0.008 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.037 -9999 0 -0.81 1 1
TPX2 0.001 0.068 -9999 0 -10000 0 0
TP53 0.031 0.007 -9999 0 -10000 0 0
DLG7 0.021 0.009 -9999 0 -10000 0 0
AURKAIP1 0.012 0.021 -9999 0 -0.31 2 2
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 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.012 -9999 0 -10000 0 0
AURKB -0.014 0.028 -9999 0 -0.14 4 4
CDC25B 0.007 0.019 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.025 -9999 0 -0.49 1 1
mRNA polyadenylation -0.036 0.13 -9999 0 -0.49 38 38
Aurora A/CPEB -0.036 0.13 -9999 0 -0.5 38 38
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.46 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.008 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.012 -9999 0 -10000 0 0
spindle assembly 0.002 0.023 -9999 0 -0.45 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.007 0.033 -9999 0 -0.44 1 1
CENPA -0.01 0.028 -9999 0 -0.26 4 4
Aurora A/PP2A 0.028 0.008 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.007 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.025 -9999 0 -0.5 1 1
mitotic prometaphase 0.006 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.012 -9999 0 -10000 0 0
TACC1 0.012 0.037 -9999 0 -0.81 1 1
TACC3 0.012 0.021 -9999 0 -0.31 2 2
Aurora A/Antizyme1 0.003 0.016 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.008 -9999 0 -10000 0 0
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 0.013 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.001 0.068 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR -0.06 0.12 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.037 0.32 2 -10000 0 2
myoblast fusion 0.023 0.052 -10000 0 -10000 0 0
mol:GTP -0.027 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.091 0.11 0.51 1 -10000 0 1
ARF1/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.034 -10000 0 -10000 0 0
mol:Choline 0.012 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.064 -10000 0 -10000 0 0
MAPK3 -0.017 0.065 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.091 0.11 -10000 0 -0.52 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.023 0.053 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.059 -10000 0 -10000 0 0
ARF6 -0.002 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.33 114 114
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.065 -10000 0 -10000 0 0
actin filament bundle formation 0.025 0.038 -10000 0 -10000 0 0
KALRN -0.006 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.038 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.026 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.026 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GDP -0.011 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.026 0.039 -10000 0 -10000 0 0
PLD2 0 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.32 2 2
mol:Phosphatidic acid 0.012 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.064 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.045 0.002 -9999 0 -10000 0 0
KLHL20 -0.009 0.021 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.073 0.009 -9999 0 -10000 0 0
ENAH 0.045 0.002 -9999 0 -10000 0 0
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 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.084 -9999 0 -0.49 14 14
RAPGEF1 0.057 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.006 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.026 0.11 -9999 0 -0.62 14 14
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.045 0.002 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.078 0.071 -9999 0 -0.5 1 1
PI3K -0.002 0.021 -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 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.81 1 1
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.011 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.073 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.073 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 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 0.013 0.032 -9999 0 -0.15 11 11
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.045 0.002 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.078 -9999 0 -0.46 14 14
CCND1 0.015 0.039 -9999 0 -0.18 11 11
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
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 -0.016 0.074 -9999 0 -0.43 14 14
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
Rac1/GTP -0.017 0.033 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.023 0.16 -10000 0 -0.73 24 24
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.012 0.067 -10000 0 -0.55 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.028 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.018 0.036 -10000 0 -0.55 2 2
INS 0.009 0.045 -10000 0 -0.56 3 3
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0.028 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.022 -10000 0 -0.5 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.015 -10000 0 -0.31 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 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 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.007 -10000 0 -10000 0 0
ACAP1 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.01 0.071 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.08 -10000 0 -0.4 20 20
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.028 0 -10000 0 -10000 0 0
endocytosis 0.001 0.022 0.49 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.029 0.073 -10000 0 -0.43 12 12
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.037 -10000 0 -0.81 1 1
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.067 -10000 0 -0.43 10 10
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.03 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -9999 0 -9999 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 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.015 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.001 0.062 -9999 0 -0.31 19 19
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.027 -9999 0 -0.42 2 2
ARF1/GTP -0.001 0.016 -9999 0 -0.25 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.027 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.005 -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 0.027 0.008 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.009 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.009 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 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 0.035 0.016 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.42 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.015 -9999 0 -0.23 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.027 -9999 0 -0.42 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 -0.001 0.011 -9999 0 -10000 0 0
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -0.17 2 2
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.006 0.03 -9999 0 -10000 0 0
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 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 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.028 -9999 0 -0.62 1 1
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 494 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.28 -0.017 -0.017 -0.017
47_PPARGC1A -0.81 -0.81 -0.81 0.013
105_BMP4 0.013 -0.31 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.49 -0.49 -0.49 -0.49
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.016
84_STAT5B 0.047 -0.096 0 -0.097
84_STAT5A 0.047 -0.096 0 -0.097
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/THCA-TP/8100651/THCA-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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle