PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1B856H1
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1B856H1
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 37 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 240
Signaling events mediated by Stem cell factor receptor (c-Kit) 164
Signaling events regulated by Ret tyrosine kinase 142
Reelin signaling pathway 123
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 104
Wnt signaling 99
PDGFR-alpha signaling pathway 95
FOXA2 and FOXA3 transcription factor networks 86
Noncanonical Wnt signaling pathway 85
Signaling events mediated by the Hedgehog family 83
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 482 . 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 ( 482 ).

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 0.4979 240 1680 7 -0.42 0 1000 -1000 -0.006 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3402 164 12794 78 -0.74 0.23 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 0.2946 142 11685 82 -0.37 0.027 1000 -1000 -0.063 -1000
Reelin signaling pathway 0.2552 123 6925 56 -0.46 0.062 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2158 104 7075 68 -0.73 0.35 1000 -1000 -0.084 -1000
Wnt signaling 0.2054 99 696 7 -0.33 0.014 1000 -1000 -0.018 -1000
PDGFR-alpha signaling pathway 0.1971 95 4197 44 -0.41 0.043 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.1784 86 3960 46 -0.86 0.031 1000 -1000 -0.06 -1000
Noncanonical Wnt signaling pathway 0.1763 85 2233 26 -0.33 0.027 1000 -1000 -0.045 -1000
Signaling events mediated by the Hedgehog family 0.1722 83 4345 52 -0.29 0.14 1000 -1000 -0.031 -1000
Nongenotropic Androgen signaling 0.1722 83 4316 52 -0.26 0.19 1000 -1000 -0.039 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1598 77 4163 54 -0.46 0.039 1000 -1000 -0.046 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1328 64 2189 34 -0.1 0.027 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 0.1307 63 1957 31 -0.35 0.027 1000 -1000 -0.042 -1000
IGF1 pathway 0.1307 63 3606 57 -0.14 0.064 1000 -1000 -0.043 -1000
HIF-1-alpha transcription factor network 0.1286 62 4777 76 -0.48 0.041 1000 -1000 -0.063 -1000
Glypican 1 network 0.1245 60 2909 48 -0.3 0.052 1000 -1000 -0.027 -1000
Endothelins 0.1245 60 5792 96 -0.32 0.031 1000 -1000 -0.052 -1000
Ephrin B reverse signaling 0.1079 52 2538 48 -0.24 0.12 1000 -1000 -0.039 -1000
IL23-mediated signaling events 0.1037 50 3002 60 -0.3 0.027 1000 -1000 -0.053 -1000
IL4-mediated signaling events 0.1017 49 4479 91 -1.2 0.56 1000 -1000 -0.088 -1000
EPHB forward signaling 0.1017 49 4201 85 -0.24 0.11 1000 -1000 -0.067 -1000
BMP receptor signaling 0.0996 48 3890 81 -0.44 0.052 1000 -1000 -0.05 -1000
TCR signaling in naïve CD8+ T cells 0.0996 48 4476 93 -0.16 0.046 1000 -1000 -0.052 -1000
Coregulation of Androgen receptor activity 0.0975 47 3572 76 -0.66 0.075 1000 -1000 -0.025 -1000
Glucocorticoid receptor regulatory network 0.0954 46 5326 114 -0.45 0.26 1000 -1000 -0.061 -1000
Arf6 signaling events 0.0892 43 2723 62 -0.26 0.061 1000 -1000 -0.03 -1000
Signaling mediated by p38-alpha and p38-beta 0.0830 40 1801 44 -0.22 0.027 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0726 35 2318 65 -0.59 0.064 1000 -1000 -0.036 -1000
Thromboxane A2 receptor signaling 0.0705 34 3663 105 -0.16 0.051 1000 -1000 -0.048 -1000
Ras signaling in the CD4+ TCR pathway 0.0705 34 586 17 -0.11 0.034 1000 -1000 -0.019 -1000
IL6-mediated signaling events 0.0685 33 2485 75 -0.16 0.053 1000 -1000 -0.044 -1000
IL12-mediated signaling events 0.0643 31 2733 87 -0.37 0.029 1000 -1000 -0.071 -1000
EGFR-dependent Endothelin signaling events 0.0602 29 624 21 -0.074 0.038 1000 -1000 -0.041 -1000
ErbB2/ErbB3 signaling events 0.0519 25 1686 65 -0.17 0.037 1000 -1000 -0.043 -1000
Regulation of p38-alpha and p38-beta 0.0519 25 1379 54 -0.36 0.065 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 0.0519 25 1784 70 -0.44 0.035 1000 -1000 -0.04 -1000
Osteopontin-mediated events 0.0498 24 929 38 -0.16 0.043 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 0.0498 24 2096 86 -0.13 0.049 1000 -1000 -0.063 -1000
FAS signaling pathway (CD95) 0.0477 23 1086 47 -0.23 0.042 1000 -1000 -0.033 -1000
Syndecan-1-mediated signaling events 0.0456 22 760 34 -0.078 0.027 1000 -1000 -0.042 -1000
BCR signaling pathway 0.0456 22 2233 99 -0.1 0.049 1000 -1000 -0.057 -1000
Fc-epsilon receptor I signaling in mast cells 0.0436 21 2051 97 -0.16 0.043 1000 -1000 -0.062 -1000
LPA receptor mediated events 0.0436 21 2167 102 -0.16 0.034 1000 -1000 -0.057 -1000
Syndecan-4-mediated signaling events 0.0436 21 1429 67 -0.14 0.039 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0415 20 1779 85 -0.22 0.13 1000 -1000 -0.043 -1000
IFN-gamma pathway 0.0415 20 1387 68 -0.16 0.035 1000 -1000 -0.05 -1000
Ceramide signaling pathway 0.0415 20 1551 76 -0.15 0.075 1000 -1000 -0.036 -1000
VEGFR1 specific signals 0.0373 18 1019 56 -0.044 0.058 1000 -1000 -0.048 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0373 18 1634 88 -0.25 0.039 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0353 17 833 49 -0.059 0.039 1000 -1000 -0.038 -1000
Integrins in angiogenesis 0.0353 17 1429 84 -0.14 0.055 1000 -1000 -0.046 -1000
Signaling events mediated by PTP1B 0.0332 16 1235 76 -0.19 0.041 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0332 16 1317 82 -0.21 0.035 1000 -1000 -0.036 -1000
IL27-mediated signaling events 0.0332 16 823 51 -0.11 0.044 1000 -1000 -0.055 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0311 15 815 52 -0.18 0.056 1000 -1000 -0.039 -1000
Insulin Pathway 0.0311 15 1143 74 -0.054 0.066 1000 -1000 -0.045 -1000
ErbB4 signaling events 0.0290 14 971 69 -0.053 0.036 1000 -1000 -0.031 -1000
Visual signal transduction: Cones 0.0290 14 557 38 -0.044 0.043 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 0.0290 14 254 17 -0.082 0.029 1000 -1000 -0.027 -1000
p75(NTR)-mediated signaling 0.0290 14 1765 125 -0.28 0.069 1000 -1000 -0.063 -1000
mTOR signaling pathway 0.0290 14 742 53 -0.042 0.03 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0290 14 877 62 -0.083 0.061 1000 -1000 -0.05 -1000
LPA4-mediated signaling events 0.0270 13 167 12 -0.055 0.004 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 0.0270 13 1873 136 -0.26 0.052 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 0.0270 13 544 40 -0.28 0.046 1000 -1000 -0.016 -1000
FOXM1 transcription factor network 0.0270 13 705 51 -0.22 0.052 1000 -1000 -0.075 -1000
Caspase cascade in apoptosis 0.0249 12 910 74 -0.06 0.044 1000 -1000 -0.031 -1000
Presenilin action in Notch and Wnt signaling 0.0249 12 745 61 -0.16 0.069 1000 -1000 -0.054 -1000
Nectin adhesion pathway 0.0249 12 762 63 -0.11 0.073 1000 -1000 -0.046 -1000
Syndecan-3-mediated signaling events 0.0249 12 444 35 -0.12 0.069 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0249 12 568 45 -0.06 0.075 1000 -1000 -0.053 -1000
Rapid glucocorticoid signaling 0.0249 12 248 20 -0.06 0.034 1000 -1000 -0.009 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0249 12 1517 120 -0.24 0.074 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 0.0228 11 464 39 -0.06 0.027 1000 -1000 -0.02 -1000
Visual signal transduction: Rods 0.0228 11 592 52 -0.07 0.048 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0207 10 633 58 -0.056 0.048 1000 -1000 -0.042 -1000
Signaling events mediated by PRL 0.0207 10 342 34 -0.084 0.039 1000 -1000 -0.045 -1000
Syndecan-2-mediated signaling events 0.0187 9 680 69 -0.14 0.05 1000 -1000 -0.036 -1000
S1P1 pathway 0.0187 9 332 36 -0.062 0.027 1000 -1000 -0.045 -1000
Retinoic acid receptors-mediated signaling 0.0187 9 555 58 -0.035 0.053 1000 -1000 -0.04 -1000
TCGA08_rtk_signaling 0.0187 9 259 26 -0.19 0.045 1000 -1000 -0.009 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0187 9 734 74 -0.13 0.069 1000 -1000 -0.066 -1000
BARD1 signaling events 0.0166 8 505 57 -0.042 0.051 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0166 8 611 73 -0.19 0.05 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0166 8 823 102 -0.19 0.071 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0145 7 660 83 -0.17 0.049 1000 -1000 -0.044 -1000
TCGA08_p53 0.0145 7 55 7 -0.025 0.025 1000 -1000 -0.011 -1000
S1P3 pathway 0.0145 7 324 42 -0.13 0.047 1000 -1000 -0.032 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0145 7 253 33 -0.12 0.055 1000 -1000 -0.034 -1000
Class IB PI3K non-lipid kinase events 0.0145 7 21 3 -0.015 0.015 1000 -1000 -0.001 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0124 6 178 28 -0.13 0.056 1000 -1000 -0.026 -1000
PLK1 signaling events 0.0124 6 543 85 -0.006 0.048 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 0.0124 6 133 22 -0.031 0.033 1000 -1000 -0.036 -1000
a4b1 and a4b7 Integrin signaling 0.0104 5 25 5 0.007 0.035 1000 -1000 -0.003 -1000
Signaling events mediated by HDAC Class I 0.0104 5 588 104 -0.06 0.062 1000 -1000 -0.032 -1000
PDGFR-beta signaling pathway 0.0104 5 511 97 -0.14 0.079 1000 -1000 -0.049 -1000
Aurora B signaling 0.0104 5 384 67 -0.33 0.1 1000 -1000 -0.038 -1000
Canonical NF-kappaB pathway 0.0083 4 162 39 -0.06 0.061 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 0.0083 4 149 32 -0.083 0.05 1000 -1000 -0.025 -1000
Class I PI3K signaling events mediated by Akt 0.0083 4 286 68 -0.083 0.05 1000 -1000 -0.037 -1000
S1P5 pathway 0.0083 4 80 17 -0.006 0.032 1000 -1000 -0.017 -1000
Signaling mediated by p38-gamma and p38-delta 0.0083 4 62 15 -0.001 0.027 1000 -1000 -0.032 -1000
Canonical Wnt signaling pathway 0.0083 4 224 51 -0.04 0.064 1000 -1000 -0.047 -1000
Effects of Botulinum toxin 0.0083 4 123 26 -0.066 0.048 1000 -1000 -0.009 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0083 4 550 125 -0.008 0.071 1000 -1000 -0.052 -1000
TCGA08_retinoblastoma 0.0083 4 39 8 -0.033 0.031 1000 -1000 -0.004 -1000
Circadian rhythm pathway 0.0062 3 75 22 -0.013 0.041 1000 -1000 -0.026 -1000
EPO signaling pathway 0.0062 3 170 55 -0.012 0.06 1000 -1000 -0.04 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0062 3 114 37 0 0.064 1000 -1000 -0.036 -1000
HIF-2-alpha transcription factor network 0.0062 3 129 43 -0.16 0.16 1000 -1000 -0.043 -1000
FoxO family signaling 0.0062 3 252 64 -0.083 0.1 1000 -1000 -0.058 -1000
Atypical NF-kappaB pathway 0.0062 3 118 31 -0.015 0.04 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.0062 3 134 43 -0.03 0.05 1000 -1000 -0.038 -1000
S1P4 pathway 0.0062 3 76 25 -0.003 0.047 1000 -1000 -0.032 -1000
p38 MAPK signaling pathway 0.0062 3 159 44 -0.029 0.049 1000 -1000 -0.027 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 61 23 -0.015 0.049 1000 -1000 -0.028 -1000
Paxillin-dependent events mediated by a4b1 0.0041 2 80 36 -0.053 0.055 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0021 1 92 75 -0.036 0.074 1000 -1000 -0.031 -1000
Aurora A signaling 0.0021 1 117 60 -0.021 0.055 1000 -1000 -0.029 -1000
TRAIL signaling pathway 0.0021 1 87 48 -0.014 0.074 1000 -1000 -0.044 -1000
E-cadherin signaling in the nascent adherens junction 0.0021 1 134 76 -0.058 0.066 1000 -1000 -0.063 -1000
Arf6 trafficking events 0.0021 1 96 71 -0.048 0.05 1000 -1000 -0.025 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.015 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.059 0.045 1000 -1000 -0.023 -1000
Aurora C signaling 0.0000 0 4 7 -0.005 0.045 1000 -1000 -0.013 -1000
Glypican 2 network 0.0000 0 0 4 -0.018 0.016 1000 -1000 0.002 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.066 1000 -1000 -0.039 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 1000 -1000 -0.003 -1000
Arf1 pathway 0.0000 0 21 54 -0.001 0.051 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 0 -1000
Total NA 3358 193754 7203 -22 8 131000 -131000 -5 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.32 0.26 -9999 0 -0.48 328 328
EFNA5 -0.073 0.24 -9999 0 -0.68 68 68
FYN -0.3 0.24 -9999 0 -0.44 327 327
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 328 328
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 328 328
EPHA5 -0.42 0.33 -9999 0 -0.67 301 301
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 -0.21 0.21 0.38 1 -0.39 267 268
CRKL -0.22 0.22 -10000 0 -0.41 272 272
HRAS -0.19 0.19 -10000 0 -0.36 226 226
mol:PIP3 -0.2 0.21 -10000 0 -0.39 247 247
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.032 -10000 0 -0.68 1 1
GAB1 -0.24 0.24 -10000 0 -0.44 272 272
FOXO3 -0.19 0.21 0.37 2 -0.37 260 262
AKT1 -0.2 0.22 0.29 2 -0.39 270 272
BAD -0.19 0.21 0.29 3 -0.37 260 263
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 281 281
GSK3B -0.19 0.21 0.31 3 -0.37 262 265
RAF1 -0.16 0.16 0.35 1 -0.34 86 87
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.23 0.23 -10000 0 -0.43 268 268
STAT1 -0.59 0.56 -10000 0 -1.1 274 274
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.34 81 81
cell proliferation -0.24 0.24 -10000 0 -0.43 275 275
PIK3CA 0.022 0.056 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 272 272
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.34 82 82
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 272 272
MAPK3 -0.11 0.13 0.3 6 -0.29 19 25
STAP1 -0.24 0.24 -10000 0 -0.44 272 272
GRAP2 -0.018 0.15 -10000 0 -0.55 31 31
JAK2 -0.49 0.48 -10000 0 -0.89 274 274
STAT1 (dimer) -0.57 0.55 -10000 0 -1 274 274
mol:Gleevec 0.007 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.2 0.24 -10000 0 -0.42 257 257
actin filament polymerization -0.23 0.23 -10000 0 -0.43 270 270
LYN 0.027 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 273 274
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 264 264
PI3K -0.2 0.24 -10000 0 -0.4 270 270
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.69 0.66 -10000 0 -1.3 273 273
MAPK8 -0.24 0.24 -10000 0 -0.44 275 275
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 268 268
positive regulation of transcription -0.083 0.12 0.33 8 -0.24 18 26
mol:GDP -0.2 0.2 -10000 0 -0.38 230 230
PIK3C2B -0.23 0.23 -10000 0 -0.43 264 264
CBL/CRKL -0.2 0.22 -10000 0 -0.39 271 271
FER -0.24 0.24 -10000 0 -0.44 271 271
SH2B3 -0.24 0.23 -10000 0 -0.44 273 273
PDPK1 -0.18 0.2 0.3 3 -0.36 244 247
SNAI2 -0.24 0.24 -10000 0 -0.44 273 273
positive regulation of cell proliferation -0.41 0.4 -10000 0 -0.75 274 274
KITLG -0.016 0.09 -10000 0 -0.71 7 7
cell motility -0.41 0.4 -10000 0 -0.75 274 274
PTPN6 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.2 -10000 0 -0.98 7 7
STAT5A (dimer) -0.33 0.33 -10000 0 -0.61 274 274
SOCS1 0.023 0.035 -10000 0 -0.68 1 1
cell migration 0.23 0.23 0.42 273 -10000 0 273
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.007 0.03 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.57 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 271 271
PTPN11 0.033 0.033 -10000 0 -0.66 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 273 273
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.13 0.27 3 -0.3 27 30
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.74 0.69 -10000 0 -1.3 273 273
MAP2K2 -0.12 0.13 0.37 3 -0.3 25 28
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.41 239 239
STAT5A -0.34 0.34 -10000 0 -0.63 274 274
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 273 273
SHC/GRAP2 0.001 0.11 -10000 0 -0.38 31 31
PTPRO -0.25 0.23 -10000 0 -0.44 281 281
SH2B2 -0.24 0.23 -10000 0 -0.44 270 270
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.43 273 273
CREBBP -0.042 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 38 38
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 -0.063 0.098 -10000 0 -0.67 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 247 247
JUN -0.26 0.26 -10000 0 -0.58 151 151
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.27 0.29 -10000 0 -0.49 282 282
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.27 0.29 -10000 0 -0.49 285 285
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.2 0.22 -10000 0 -0.4 264 264
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 279 279
GRB7 0.001 0.055 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.29 -10000 0 -0.49 278 278
MAPKKK cascade -0.24 0.24 -10000 0 -0.42 276 276
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 279 279
lamellipodium assembly -0.2 0.18 -10000 0 -0.35 253 253
RET51/GFRalpha1/GDNF/SHC -0.26 0.29 -10000 0 -0.49 272 272
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 266 266
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.4 268 268
MAPK3 -0.24 0.23 -10000 0 -0.42 276 276
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.082 0.25 -10000 0 -0.68 74 74
PXN 0.026 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.45 275 275
DOK5 -0.069 0.24 -10000 0 -0.68 65 65
GFRA1 -0.37 0.35 -10000 0 -0.67 274 274
MAPK8 -0.2 0.2 -10000 0 -0.35 237 237
HRAS/GTP -0.26 0.28 -10000 0 -0.47 281 281
tube development -0.19 0.2 -10000 0 -0.38 253 253
MAPK1 -0.24 0.23 0.32 3 -0.42 278 281
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 253 253
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.025 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.33 -10000 0 -0.53 295 295
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.29 -10000 0 -0.49 284 284
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.55 298 298
PRKCA -0.005 0.14 -10000 0 -0.68 21 21
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.2 0.21 -10000 0 -0.38 250 250
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 237 237
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 283 283
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.11 0.26 -10000 0 -0.66 84 84
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 151 151
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.22 -10000 0 -0.4 265 265
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 237 237
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.35 281 281
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.35 286 286
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 272 272
PI3K -0.31 0.29 -10000 0 -0.55 254 254
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 253 253
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.32 262 262
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.29 -10000 0 -0.49 285 285
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.054 0.22 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 270 270
RET51/GFRalpha1/GDNF/PKC alpha -0.28 0.31 -10000 0 -0.5 289 289
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.023 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.54 296 296
Rac1/GTP -0.23 0.22 -10000 0 -0.42 252 252
RET9/GFRalpha1/GDNF -0.24 0.23 -10000 0 -0.44 273 273
GFRalpha1/GDNF -0.27 0.27 -10000 0 -0.5 273 273
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.013 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.64 21 21
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.3 0.23 -10000 0 -0.45 338 338
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.062 -10000 0 -0.38 7 7
AKT1 -0.2 0.15 -10000 0 -0.3 322 322
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.28 0.22 -10000 0 -0.42 328 328
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 19 19
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 328 328
DAB1/alpha3/beta1 Integrin -0.25 0.22 -10000 0 -0.39 316 316
long-term memory -0.26 0.23 -10000 0 -0.41 327 327
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 320 320
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.38 322 322
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DAB1/NCK2 -0.26 0.23 -10000 0 -0.4 328 328
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0 0.13 -10000 0 -0.68 16 16
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.68 331 331
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 335 335
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 327 327
MAPK8 0.016 0.086 -10000 0 -0.64 8 8
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 329 329
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 327 327
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 334 334
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.41 327 327
PI3K 0.036 0.044 -10000 0 -0.51 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.49 3 -0.41 131 134
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.42 36 36
neuron adhesion -0.22 0.21 0.46 10 -0.64 25 35
LRP8 -0.001 0.14 -10000 0 -0.68 19 19
GSK3B -0.19 0.14 -10000 0 -0.44 31 31
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.4 329 329
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 327 327
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.05 0.16 0.82 18 -0.61 3 21
neuron migration -0.26 0.2 -10000 0 -0.39 310 310
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.43 36 36
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 331 331
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.008 0.1 -10000 0 -0.45 14 14
NFATC2 -0.22 0.33 -10000 0 -0.72 120 120
NFATC3 -0.082 0.14 -10000 0 -0.31 56 56
CD40LG -0.62 0.55 -10000 0 -1.1 245 245
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.44 0.51 -10000 0 -1.2 122 122
JUNB 0.02 0.058 -10000 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.018 -10000 0 -0.32 1 1
T cell anergy 0.008 0.077 0.4 6 -0.43 2 8
TLE4 -0.21 0.36 -10000 0 -0.78 111 111
Jun/NFAT1-c-4/p21SNFT -0.55 0.59 -10000 0 -1.1 224 224
AP-1/NFAT1-c-4 -0.71 0.74 -10000 0 -1.4 235 235
IKZF1 -0.16 0.27 -10000 0 -0.59 106 106
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.87 85 85
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.75 193 193
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.78 -10000 0 -1.5 223 223
EGR3 -0.54 0.7 -10000 0 -1.5 130 130
NFAT1/FOXP3 -0.16 0.28 -10000 0 -0.58 121 121
EGR1 -0.12 0.28 -10000 0 -0.68 95 95
JUN -0.13 0.28 -10000 0 -0.67 104 104
EGR4 -0.015 0.14 -10000 0 -0.66 22 22
mol:Ca2+ 0.012 0.009 -10000 0 -0.19 1 1
GBP3 -0.16 0.26 -10000 0 -0.65 73 73
FOSL1 0.007 0.06 -10000 0 -0.52 2 2
NFAT1-c-4/MAF/IRF4 -0.48 0.56 -10000 0 -1 226 226
DGKA -0.15 0.24 -10000 0 -0.61 73 73
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.49 0.55 -10000 0 -1 227 227
CTLA4 -0.18 0.29 -10000 0 -0.69 92 92
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.2 220 220
NFAT1-c-4 (dimer)/EGR4 -0.51 0.56 -10000 0 -1 227 227
FOS -0.16 0.3 -10000 0 -0.68 125 125
IFNG -0.37 0.5 -10000 0 -1.1 121 121
T cell activation -0.39 0.39 -10000 0 -0.89 151 151
MAF 0.026 0.006 -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 0.35 0.41 0.75 219 -10000 0 219
TNF -0.54 0.55 -10000 0 -1 245 245
FASLG -0.7 0.76 -10000 0 -1.4 235 235
TBX21 -0.018 0.15 -10000 0 -0.69 21 21
BATF3 0.018 0.043 -10000 0 -0.68 1 1
PRKCQ 0.018 0.068 -10000 0 -0.61 5 5
PTPN1 -0.15 0.25 -10000 0 -0.57 92 92
NFAT1-c-4/ICER1 -0.49 0.55 -10000 0 -1 225 225
GATA3 -0.006 0.15 -10000 0 -0.64 24 24
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 121 121
IL2RA -0.41 0.46 -10000 0 -1 126 126
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.61 74 74
E2F1 -0.013 0.068 -10000 0 -10000 0 0
PPARG 0.015 0.085 -10000 0 -0.68 7 7
SLC3A2 -0.15 0.25 -10000 0 -0.62 72 72
IRF4 -0.047 0.18 -10000 0 -0.66 33 33
PTGS2 -0.6 0.55 0.5 1 -1.1 229 230
CSF2 -0.61 0.53 -10000 0 -1.1 243 243
JunB/Fra1/NFAT1-c-4 -0.46 0.54 -10000 0 -0.98 221 221
IL4 -0.29 0.35 -10000 0 -0.94 82 82
IL5 -0.59 0.52 -10000 0 -1.1 231 231
IL2 -0.4 0.4 -10000 0 -0.91 150 150
IL3 -0.069 0.086 -10000 0 -1.1 1 1
RNF128 0.035 0.038 -10000 0 -0.75 1 1
NFATC1 -0.35 0.42 -10000 0 -0.75 218 218
CDK4 0.23 0.25 0.55 132 -10000 0 132
PTPRK -0.15 0.25 -10000 0 -0.62 73 73
IL8 -0.6 0.53 0.5 1 -1.1 235 236
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.4 293 293
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.024 -9999 0 -10000 0 0
WNT4 -0.2 0.32 -9999 0 -0.67 151 151
FZD3 0.027 0.004 -9999 0 -10000 0 0
WNT5A 0.014 0.095 -9999 0 -0.68 9 9
WNT11 -0.33 0.35 -9999 0 -0.67 243 243
PDGFR-alpha signaling pathway

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
PDGFRA -0.21 0.32 -10000 0 -0.69 149 149
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 149 149
positive regulation of JUN kinase activity -0.077 0.2 -10000 0 -0.39 136 136
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.52 147 147
AP1 -0.41 0.55 -10000 0 -1.2 135 135
mol:IP3 -0.16 0.24 -10000 0 -0.53 147 147
PLCG1 -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 150 150
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.52 147 147
CAV3 -0.011 0.018 -10000 0 -10000 0 0
CAV1 0.013 0.095 -10000 0 -0.68 9 9
SHC/Grb2/SOS1 -0.077 0.2 -10000 0 -0.39 136 136
PDGF/PDGFRA/Shf -0.14 0.25 -10000 0 -0.51 149 149
FOS -0.4 0.52 -10000 0 -1.2 135 135
JUN -0.15 0.22 -10000 0 -0.58 102 102
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 150 150
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA -0.21 0.32 -10000 0 -0.69 149 149
actin cytoskeleton reorganization -0.14 0.24 -10000 0 -0.5 149 149
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.22 -10000 0 -0.43 149 149
PDGF/PDGFRA/Crk/C3G -0.1 0.22 -10000 0 -0.42 145 145
JAK1 -0.15 0.24 -10000 0 -0.51 149 149
ELK1/SRF -0.12 0.19 0.32 1 -0.41 140 141
SHB 0.025 0.008 -10000 0 -10000 0 0
SHF 0.026 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.54 148 148
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.077 0.2 -10000 0 -0.39 136 136
PDGF/PDGFRA/SHB -0.14 0.24 -10000 0 -0.5 149 149
PDGF/PDGFRA/Caveolin-1 -0.15 0.26 -10000 0 -0.52 151 151
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 145 145
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PDGF/PDGFRA/Crk -0.14 0.24 -10000 0 -0.49 148 148
JAK-STAT cascade -0.15 0.24 -10000 0 -0.5 149 149
cell proliferation -0.14 0.25 -10000 0 -0.5 149 149
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 -0.47 0.49 -10000 0 -1 175 175
PCK1 -0.31 0.45 -10000 0 -1.4 59 59
HNF4A -0.62 0.6 -10000 0 -1.2 230 230
KCNJ11 -0.45 0.48 -10000 0 -1 170 170
AKT1 -0.065 0.14 -10000 0 -0.47 11 11
response to starvation -0.018 0.039 -10000 0 -0.38 2 2
DLK1 -0.45 0.47 -10000 0 -0.99 174 174
NKX2-1 -0.17 0.19 -10000 0 -10000 0 0
ACADM -0.47 0.49 -10000 0 -0.98 191 191
TAT -0.18 0.2 -10000 0 -0.54 20 20
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.072 -10000 0 -0.68 5 5
TTR -0.14 0.23 0.65 7 -0.69 32 39
PKLR -0.46 0.48 -10000 0 -0.97 194 194
APOA1 -0.86 0.83 -10000 0 -1.7 231 231
CPT1C -0.47 0.49 -10000 0 -1 187 187
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.73 31 31
FOXF1 0.013 0.072 -10000 0 -0.68 5 5
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.007 -10000 0 -10000 0 0
CPT1A -0.48 0.49 -10000 0 -0.99 191 191
HMGCS1 -0.47 0.48 -10000 0 -0.99 189 189
NR3C1 0.032 0.011 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -1 173 173
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.6 0.62 -10000 0 -1.2 229 229
CREB1 0.008 0.067 -10000 0 -0.26 9 9
IGFBP1 -0.17 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.64 1 1
UCP2 -0.48 0.48 -10000 0 -0.99 189 189
ALDOB -0.44 0.48 -10000 0 -1 169 169
AFP -0.02 0.086 -10000 0 -0.37 6 6
BDH1 -0.47 0.49 -10000 0 -1 182 182
HADH -0.44 0.48 -10000 0 -0.99 170 170
F2 -0.58 0.58 -10000 0 -1.2 204 204
HNF1A 0.028 0.007 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -0.54 2 2
INS -0.022 0.014 -10000 0 -10000 0 0
FOXA1 -0.016 0.095 -10000 0 -0.31 30 30
FOXA3 -0.029 0.12 -10000 0 -0.35 26 26
FOXA2 -0.5 0.54 -10000 0 -1.1 190 190
ABCC8 -0.7 0.66 -10000 0 -1.3 245 245
ALB -0.063 0.28 -10000 0 -1.1 30 30
Noncanonical Wnt 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
NFATC2 -0.09 0.26 -10000 0 -0.67 80 80
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 111 111
mol:DAG -0.19 0.2 -10000 0 -0.49 108 108
PLCG1 -0.19 0.21 -10000 0 -0.51 108 108
YES1 -0.22 0.22 -10000 0 -0.53 118 118
FZD3 0.027 0.004 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.19 0.22 -10000 0 -0.51 108 108
MAP3K7 -0.16 0.17 0.31 1 -0.42 105 106
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 108 108
mol:IP3 -0.19 0.2 -10000 0 -0.49 108 108
NLK -0.001 0.055 -10000 0 -0.81 2 2
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.17 0.19 0.32 1 -0.45 106 107
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.4 293 293
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.53 116 116
GO:0007205 -0.18 0.2 -10000 0 -0.48 108 108
WNT6 0.021 0.024 -10000 0 -10000 0 0
WNT4 -0.2 0.32 -10000 0 -0.67 151 151
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.55 136 136
GNG2 0.025 0.032 -10000 0 -0.68 1 1
WNT5A 0.014 0.095 -10000 0 -0.68 9 9
WNT11 -0.33 0.35 -10000 0 -0.67 243 243
CDC42 -0.2 0.21 -10000 0 -0.51 112 112
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.09 0.21 -10000 0 -0.62 30 30
IHH -0.16 0.32 -10000 0 -0.7 119 119
SHH Np/Cholesterol/GAS1 -0.055 0.16 -10000 0 -0.4 82 82
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.16 0.39 82 -10000 0 82
SMO/beta Arrestin2 -0.077 0.21 -10000 0 -0.42 110 110
SMO -0.098 0.21 -10000 0 -0.43 122 122
AKT1 -0.017 0.11 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.015 0.09 -10000 0 -0.68 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.096 0.21 -10000 0 -0.43 122 122
STIL -0.067 0.16 0.27 1 -0.49 14 15
DHH N/PTCH2 -0.051 0.2 -10000 0 -0.51 78 78
DHH N/PTCH1 -0.079 0.19 -10000 0 -0.36 142 142
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DHH 0.02 0.064 -10000 0 -0.68 4 4
PTHLH -0.14 0.31 -10000 0 -1 32 32
determination of left/right symmetry -0.096 0.21 -10000 0 -0.43 122 122
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.31 -10000 0 -1 32 32
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 251 251
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 183 183
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.096 0.21 -10000 0 -0.43 122 122
pancreas development -0.25 0.33 -10000 0 -0.67 182 182
HHAT 0.024 0.033 -10000 0 -0.68 1 1
PI3K 0.036 0.044 -10000 0 -0.51 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.26 -10000 0 -0.63 94 94
somite specification -0.096 0.21 -10000 0 -0.43 122 122
SHH Np/Cholesterol/PTCH1 -0.072 0.16 -10000 0 -0.34 109 109
SHH Np/Cholesterol/PTCH2 -0.044 0.15 -10000 0 -0.38 77 77
SHH Np/Cholesterol/Megalin -0.079 0.18 -10000 0 -0.38 119 119
SHH -0.005 0.029 -10000 0 -0.51 1 1
catabolic process -0.096 0.2 -10000 0 -0.4 139 139
SMO/Vitamin D3 -0.078 0.18 -10000 0 -0.38 107 107
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.41 165 165
LRP2 -0.15 0.3 -10000 0 -0.66 124 124
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.56 48 48
SHH Np/Cholesterol/BOC 0.013 0.057 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.093 0.18 -10000 0 -0.38 134 134
mesenchymal cell differentiation 0.14 0.2 0.41 165 -10000 0 165
mol:Vitamin D3 -0.067 0.17 -10000 0 -0.34 109 109
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.53 176 176
CDON -0.18 0.32 -10000 0 -0.67 138 138
IHH N/PTCH1 -0.094 0.21 -10000 0 -0.41 139 139
Megalin/LRPAP1 -0.099 0.24 -10000 0 -0.5 124 124
PTCH2 -0.086 0.26 -10000 0 -0.67 77 77
SHH Np/Cholesterol 0.009 0.023 -10000 0 -0.4 1 1
PTCH1 -0.096 0.2 -10000 0 -0.41 139 139
HHIP -0.25 0.33 -10000 0 -0.67 182 182
Nongenotropic Androgen signaling

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
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.13 0.22 -10000 0 -0.4 182 182
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 191 191
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.059 -10000 0 -0.44 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.2 0.47 4 -0.37 187 191
T-DHT/AR -0.2 0.26 -10000 0 -0.5 197 197
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.005 128 128
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.033 -10000 0 -0.68 1 1
mol:GDP -0.21 0.26 -10000 0 -0.52 194 194
cell proliferation -0.2 0.27 0.48 11 -0.53 138 149
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
FOS -0.26 0.38 0.53 8 -0.85 128 136
mol:Ca2+ -0.026 0.029 -10000 0 -0.067 105 105
MAPK3 -0.16 0.24 0.53 12 -0.5 96 108
MAPK1 -0.17 0.22 0.34 5 -0.42 167 172
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 115 115
cAMP biosynthetic process 0.017 0.07 0.26 10 -0.42 8 18
GNG2 0.025 0.032 -10000 0 -0.68 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 115 115
HRAS/GTP -0.14 0.2 -10000 0 -0.38 187 187
actin cytoskeleton reorganization 0.037 0.034 -10000 0 -0.36 3 3
SRC 0.025 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 115 115
PI3K 0.033 0.038 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.52 147 -0.47 7 154
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 194 194
HRAS/GDP -0.2 0.26 -10000 0 -0.5 194 194
CREB1 -0.21 0.28 0.47 7 -0.57 146 153
RAC1-CDC42/GTP 0.047 0.036 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 197 197
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.54 6 -0.38 187 193
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.48 193 193
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 187 187
MAP2K2 -0.14 0.2 0.51 3 -0.37 183 186
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 191 191
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.014 0.09 -10000 0 -0.68 8 8
Gi family/GNB1/GNG2/GDP -0.033 0.1 -10000 0 -0.5 11 11
mol:T-DHT 0 0.003 -10000 0 -0.005 67 67
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.034 -10000 0 -0.51 2 2
Gi family/GTP -0.087 0.11 -10000 0 -0.3 46 46
CDC42 0.027 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.64 21 21
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 334 334
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.21 -10000 0 -0.42 324 324
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.066 0.24 -10000 0 -0.68 64 64
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 19 19
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.003 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.23 -10000 0 -0.46 329 329
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.18 0.36 5 -0.34 313 318
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.38 314 314
RELN -0.46 0.32 -10000 0 -0.68 331 331
PAFAH/LIS1 -0.031 0.16 -10000 0 -0.44 61 61
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.46 18 18
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.17 -10000 0 -0.46 51 51
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.36 313 314
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.015 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.086 -10000 0 -0.64 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.012 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.3 2 -0.48 26 28
LRP8 -0.001 0.14 -10000 0 -0.68 19 19
NDEL1/Katanin 60 -0.22 0.18 0.29 4 -0.34 310 314
P39/CDK5 -0.25 0.19 -10000 0 -0.38 323 323
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.19 -10000 0 -0.39 324 324
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.4 318 318
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 331 331
CDC42 0.017 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.098 0.24 0.53 109 -10000 0 109
KIRREL -0.041 0.19 -10000 0 -0.69 36 36
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.098 0.24 -10000 0 -0.53 109 109
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.054 0.2 -10000 0 -0.43 100 100
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.056 0.16 -10000 0 -0.35 98 98
FYN -0.062 0.19 0.27 23 -0.41 100 123
mol:Ca2+ -0.054 0.2 -10000 0 -0.43 99 99
mol:DAG -0.053 0.2 -10000 0 -0.43 99 99
NPHS2 -0.005 0.054 -10000 0 -0.74 1 1
mol:IP3 -0.053 0.2 -10000 0 -0.43 99 99
regulation of endocytosis -0.048 0.18 -10000 0 -0.38 98 98
Nephrin/NEPH1/podocin/Cholesterol -0.066 0.2 -10000 0 -0.43 102 102
establishment of cell polarity -0.098 0.24 -10000 0 -0.53 109 109
Nephrin/NEPH1/podocin/NCK1-2 -0.038 0.2 -10000 0 -0.4 99 99
Nephrin/NEPH1/beta Arrestin2 -0.047 0.18 -10000 0 -0.39 98 98
NPHS1 -0.1 0.26 -10000 0 -0.68 82 82
Nephrin/NEPH1/podocin -0.059 0.19 -10000 0 -0.41 102 102
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.053 0.2 -10000 0 -0.43 99 99
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.053 0.2 -10000 0 -0.43 97 97
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.075 0.19 0.28 20 -0.41 101 121
cytoskeleton organization -0.08 0.2 -10000 0 -0.45 97 97
Nephrin/NEPH1 -0.07 0.18 -10000 0 -0.39 109 109
Nephrin/NEPH1/ZO-1 -0.067 0.21 -10000 0 -0.45 103 103
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.068 -9999 0 -0.45 9 9
NFATC2 -0.077 0.17 -9999 0 -0.45 80 80
NFATC3 -0.001 0.031 -9999 0 -10000 0 0
CD40LG -0.33 0.36 -9999 0 -0.76 170 170
PTGS2 -0.31 0.35 -9999 0 -0.74 156 156
JUNB 0.02 0.058 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.02 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.67 104 104
mol:Ca2+ -0.008 0.02 -9999 0 -0.18 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.007 0.06 -9999 0 -0.52 2 2
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -9999 0 -0.46 160 160
FOS -0.17 0.3 -9999 0 -0.68 125 125
IFNG -0.33 0.36 -9999 0 -0.74 175 175
AP-1/NFAT1-c-4 -0.35 0.44 -9999 0 -0.87 160 160
FASLG -0.31 0.34 -9999 0 -0.72 158 158
NFAT1-c-4/ICER1 -0.077 0.17 -9999 0 -0.4 86 86
IL2RA -0.31 0.34 -9999 0 -0.72 159 159
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.31 -9999 0 -0.7 163 163
JunB/Fra1/NFAT1-c-4 -0.068 0.17 -9999 0 -0.4 83 83
IL4 -0.3 0.32 -9999 0 -0.69 154 154
IL2 0.001 0.08 -9999 0 -0.95 3 3
IL3 -0.009 0.053 -9999 0 -0.88 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.043 -9999 0 -0.68 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.025 0.01 -9999 0 -10000 0 0
IGF1 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
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.36 148 148
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.092 0.19 -10000 0 -0.36 144 144
IGF-1R heterotetramer/IGF1/PTP1B -0.066 0.2 -10000 0 -0.43 105 105
AKT1 -0.09 0.17 -10000 0 -0.36 104 104
BAD -0.088 0.16 -10000 0 -0.34 99 99
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.098 0.18 -10000 0 -0.36 144 144
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.089 0.19 -10000 0 -0.37 148 148
RAF1 -0.069 0.15 0.39 1 -0.54 16 17
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.063 0.19 -10000 0 -0.35 142 142
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.097 0.2 -10000 0 -0.39 150 150
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
RPS6KB1 -0.089 0.17 -10000 0 -0.36 102 102
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 6 -0.45 15 21
PXN 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.071 0.16 -10000 0 -0.35 98 98
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.03 0.17 -10000 0 -0.34 98 98
IGF-1R heterotetramer -0.009 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.078 0.2 -10000 0 -0.36 148 148
Crk/p130 Cas/Paxillin -0.058 0.19 -10000 0 -0.33 143 143
IGF1R -0.009 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.3 -10000 0 -0.69 106 106
IRS2/Crk -0.086 0.18 -10000 0 -0.34 144 144
PI3K -0.066 0.2 -10000 0 -0.35 148 148
apoptosis 0.064 0.15 0.5 14 -0.32 2 16
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.091 0.2 -10000 0 -0.45 105 105
RAF1/14-3-3 E -0.044 0.14 0.33 3 -0.46 16 19
BAD/14-3-3 -0.068 0.16 0.4 2 -0.54 14 16
PRKCZ -0.088 0.17 0.25 1 -0.36 104 105
Crk/p130 Cas/Paxillin/FAK1 -0.059 0.16 -10000 0 -0.54 14 14
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.094 0.21 -10000 0 -0.47 106 106
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.044 0.18 -10000 0 -0.38 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.088 0.19 -10000 0 -0.36 148 148
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.099 0.19 -10000 0 -0.36 148 148
IRS1 -0.11 0.2 -10000 0 -0.39 150 150
IRS2 -0.1 0.18 -10000 0 -0.36 149 149
IGF-1R heterotetramer/IGF1 -0.1 0.24 -10000 0 -0.54 106 106
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.09 0.18 -10000 0 -0.38 105 105
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.091 0.2 -10000 0 -0.45 105 105
SHC1 0.025 0.007 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.35 0.61 4 -0.77 66 70
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -10000 0 -0.78 120 120
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.19 0.35 0.62 3 -0.8 56 59
AP1 -0.19 0.37 -10000 0 -0.72 148 148
ABCG2 -0.19 0.35 0.61 1 -0.8 61 62
HIF1A -0.018 0.072 -10000 0 -0.2 1 1
TFF3 -0.48 0.43 0.62 3 -0.86 198 201
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.053 0.11 -10000 0 -0.29 6 6
response to hypoxia -0.068 0.11 -10000 0 -0.23 94 94
MCL1 -0.18 0.34 0.61 3 -0.79 58 61
NDRG1 -0.19 0.34 0.6 2 -0.77 65 67
SERPINE1 -0.19 0.34 0.61 1 -0.76 71 72
FECH -0.18 0.35 0.61 4 -0.79 59 63
FURIN -0.18 0.35 0.61 4 -0.79 61 65
NCOA2 -0.034 0.2 -10000 0 -0.68 42 42
EP300 -0.1 0.18 -10000 0 -0.35 151 151
HMOX1 -0.2 0.33 0.62 2 -0.79 61 63
BHLHE40 -0.19 0.35 0.62 2 -0.78 66 68
BHLHE41 -0.19 0.35 0.61 1 -0.77 68 69
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.1 -10000 0 -10000 0 0
ENG 0.013 0.094 0.47 4 -10000 0 4
JUN -0.12 0.29 -10000 0 -0.67 103 103
RORA -0.19 0.35 0.61 4 -0.78 68 72
ABCB1 -0.051 0.16 -10000 0 -1.2 8 8
TFRC -0.19 0.35 0.62 2 -0.81 59 61
CXCR4 -0.19 0.35 0.62 3 -0.82 52 55
TF -0.22 0.4 0.62 2 -0.88 86 88
CITED2 -0.21 0.39 0.61 3 -0.83 88 91
HIF1A/ARNT -0.21 0.38 -10000 0 -0.88 59 59
LDHA -0.032 0.11 -10000 0 -0.65 10 10
ETS1 -0.18 0.35 0.62 3 -0.76 69 72
PGK1 -0.19 0.34 0.61 1 -0.8 56 57
NOS2 -0.19 0.35 0.62 2 -0.8 57 59
ITGB2 -0.19 0.35 0.62 3 -0.83 52 55
ALDOA -0.19 0.34 0.61 1 -0.81 54 55
Cbp/p300/CITED2 -0.29 0.46 -10000 0 -0.95 118 118
FOS -0.16 0.31 -10000 0 -0.67 125 125
HK2 -0.19 0.35 0.62 3 -0.78 64 67
SP1 0.031 0.018 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 133 133
HK1 -0.19 0.35 0.62 3 -0.78 63 66
NPM1 -0.19 0.34 0.61 1 -0.79 59 60
EGLN1 -0.18 0.34 0.61 3 -0.78 60 63
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.35 0.61 3 -0.76 71 74
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.5 1 -0.71 69 70
IGFBP1 -0.19 0.34 0.61 1 -0.75 73 74
VEGFA -0.2 0.35 -10000 0 -0.7 105 105
HIF1A/JAB1 0.005 0.058 -10000 0 -10000 0 0
CP -0.31 0.46 0.62 2 -0.87 153 155
CXCL12 -0.22 0.4 0.62 3 -0.91 77 80
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.008 -10000 0 -10000 0 0
BNIP3 -0.19 0.35 0.62 3 -0.82 53 56
EGLN3 -0.2 0.35 -10000 0 -0.8 68 68
CA9 -0.19 0.35 0.6 2 -0.8 61 63
TERT -0.19 0.34 0.6 1 -0.78 64 65
ENO1 -0.18 0.35 0.61 3 -0.8 58 61
PFKL -0.18 0.35 0.62 3 -0.78 61 64
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.2 0.36 0.62 3 -0.77 75 78
ARNT -0.014 0.071 -10000 0 -0.31 2 2
HNF4A -0.016 0.058 -10000 0 -0.22 4 4
ADFP -0.2 0.33 -10000 0 -0.71 95 95
SLC2A1 -0.19 0.35 -10000 0 -0.7 98 98
LEP -0.19 0.34 0.61 1 -0.74 80 81
HIF1A/ARNT/Cbp/p300 -0.25 0.41 -10000 0 -0.79 132 132
EPO -0.13 0.28 -10000 0 -0.83 25 25
CREBBP -0.08 0.17 -10000 0 -0.33 131 131
HIF1A/ARNT/Cbp/p300/HDAC7 -0.22 0.4 -10000 0 -0.78 118 118
PFKFB3 -0.19 0.35 0.62 3 -0.83 50 53
NT5E -0.19 0.36 0.61 3 -0.81 59 62
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 0.052 0.026 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.025 -9999 0 -0.44 1 1
LAMA1 -0.021 0.18 -9999 0 -0.67 33 33
PRNP 0.025 0.032 -9999 0 -0.68 1 1
GPC1/SLIT2 -0.042 0.19 -9999 0 -0.5 71 71
SMAD2 0.016 0.039 -9999 0 -0.4 3 3
GPC1/PrPc/Cu2+ 0.034 0.024 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.001 0.14 -9999 0 -0.5 33 33
TDGF1 -0.27 0.34 -9999 0 -0.67 202 202
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.51 202 202
APP/GPC1 0.038 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.22 -9999 0 -0.44 201 201
FLT1 0.024 0.033 -9999 0 -0.68 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.042 -9999 0 -0.43 3 3
SERPINC1 0.02 0.022 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.44 201 201
FGR -0.17 0.22 -9999 0 -0.43 201 201
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.51 201 201
SLIT2 -0.077 0.25 -9999 0 -0.67 71 71
GPC1/NRG -0.011 0.16 -9999 0 -0.5 44 44
NRG1 -0.037 0.2 -9999 0 -0.67 44 44
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.053 -9999 0 -0.57 3 3
LYN -0.17 0.22 -9999 0 -0.44 201 201
mol:Spermine 0.009 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.44 1 1
BMP signaling pathway -0.026 0.008 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.44 200 200
TGFBR1 0.021 0.024 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.68 128 128
GPC1 0.026 0.008 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.021 0.024 -9999 0 -10000 0 0
VEGFA 0.023 0.055 -9999 0 -0.68 3 3
BLK -0.3 0.3 -9999 0 -0.54 271 271
HCK -0.18 0.22 -9999 0 -0.44 200 200
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.032 -9999 0 -0.68 1 1
VEGFR1 homodimer 0.024 0.033 -9999 0 -0.67 1 1
TGFBR2 0.023 0.055 -9999 0 -0.68 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.019 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.51 128 128
LCK -0.18 0.23 -9999 0 -0.44 206 206
neuron differentiation -0.011 0.16 -9999 0 -0.5 44 44
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.51 1 1
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.055 -9999 0 -0.67 3 3
Endothelins

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
AKT1 -0.029 0.091 -10000 0 -0.43 9 9
PTK2B 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.67 72 73
EDN1 -0.002 0.097 -10000 0 -0.59 7 7
EDN3 -0.31 0.35 -10000 0 -0.68 228 228
EDN2 0.01 0.084 -10000 0 -0.68 6 6
HRAS/GDP -0.11 0.23 0.44 3 -0.5 85 88
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.15 -10000 0 -0.35 76 76
ADCY4 -0.069 0.14 0.35 1 -0.4 63 64
ADCY5 -0.12 0.2 0.35 1 -0.45 108 109
ADCY6 -0.067 0.14 0.35 1 -0.4 62 63
ADCY7 -0.067 0.14 0.35 1 -0.4 63 64
ADCY1 -0.07 0.15 0.35 1 -0.41 64 65
ADCY2 -0.1 0.18 -10000 0 -0.44 90 90
ADCY3 -0.069 0.15 0.35 1 -0.4 66 67
ADCY8 -0.097 0.15 0.35 1 -0.43 65 66
ADCY9 -0.067 0.14 0.35 1 -0.4 63 64
arachidonic acid secretion -0.19 0.32 0.36 11 -0.64 130 141
ETB receptor/Endothelin-1/Gq/GTP -0.081 0.18 -10000 0 -0.36 115 115
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.031 0.1 -10000 0 -0.38 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.026 0.18 -10000 0 -0.42 67 67
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.033 0.099 -10000 0 -0.47 8 8
EDNRB 0.016 0.073 -10000 0 -0.68 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.068 0.15 -10000 0 -0.61 23 23
CYSLTR1 -0.034 0.12 -10000 0 -0.64 13 13
SLC9A1 0 0.056 -10000 0 -0.27 10 10
mol:GDP -0.12 0.24 0.36 8 -0.51 92 100
SLC9A3 -0.051 0.2 0.37 1 -0.68 34 35
RAF1 -0.16 0.28 0.44 3 -0.56 129 132
JUN -0.28 0.49 0.45 1 -1.1 122 123
JAK2 -0.029 0.094 -10000 0 -0.45 10 10
mol:IP3 -0.1 0.2 -10000 0 -0.43 102 102
ETA receptor/Endothelin-1 0.014 0.13 -10000 0 -0.46 16 16
PLCB1 0.023 0.033 -10000 0 -0.68 1 1
PLCB2 0.02 0.022 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 229 229
FOS -0.28 0.45 0.61 2 -0.99 129 131
Gai/GDP -0.013 0.15 -10000 0 -0.66 22 22
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.48 53 53
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.44 95 95
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.06 0.23 -10000 0 -0.66 61 61
Gs family/GDP -0.15 0.25 0.28 1 -0.53 111 112
ETA receptor/Endothelin-1/Gq/GTP -0.088 0.17 -10000 0 -0.38 104 104
MAPK14 -0.069 0.15 -10000 0 -0.37 58 58
TRPC6 -0.16 0.3 0.47 1 -0.71 71 72
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.033 -10000 0 -0.68 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.07 0.16 -10000 0 -0.35 84 84
ETB receptor/Endothelin-2 0.021 0.085 -10000 0 -0.51 11 11
ETB receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.51 231 231
ETB receptor/Endothelin-1 0.016 0.094 -10000 0 -0.52 10 10
MAPK3 -0.24 0.41 0.37 9 -0.88 128 137
MAPK1 -0.29 0.45 0.63 2 -0.98 130 132
Rac1/GDP -0.11 0.22 0.37 1 -0.48 86 87
cAMP biosynthetic process -0.076 0.18 0.45 10 -0.44 62 72
MAPK8 -0.18 0.35 0.48 1 -0.68 119 120
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.002 0.075 -10000 0 -0.38 8 8
p130Cas/CRK/Src/PYK2 -0.15 0.29 0.39 12 -0.55 128 140
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.48 86 87
COL1A2 -0.004 0.095 -10000 0 -0.47 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.014 0.085 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.43 102 102
MAP2K2 -0.19 0.34 0.41 10 -0.68 133 143
MAP2K1 -0.21 0.34 0.5 2 -0.7 135 137
EDNRA 0.002 0.072 -10000 0 -0.36 5 5
positive regulation of muscle contraction -0.023 0.076 -10000 0 -0.38 6 6
Gq family/GDP -0.14 0.28 0.38 3 -0.56 120 123
HRAS/GTP -0.14 0.24 0.32 6 -0.51 102 108
PRKCH -0.1 0.2 0.3 1 -0.45 88 89
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 0.3 1 -0.48 100 101
PRKCB -0.11 0.2 0.3 1 -0.45 91 92
PRKCE -0.11 0.2 -10000 0 -0.46 88 88
PRKCD -0.11 0.2 -10000 0 -0.45 88 88
PRKCG -0.1 0.19 -10000 0 -0.45 87 87
regulation of vascular smooth muscle contraction -0.32 0.53 0.65 2 -1.2 129 131
PRKCQ -0.11 0.2 -10000 0 -0.45 90 90
PLA2G4A -0.21 0.35 0.38 9 -0.71 130 139
GNA14 -0.14 0.29 -10000 0 -0.65 112 112
GNA15 0.006 0.051 -10000 0 -0.68 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.009 0.081 -10000 0 -0.63 7 7
Rac1/GTP 0.031 0.1 -10000 0 -0.38 8 8
MMP1 -0.035 0.079 0.62 2 -10000 0 2
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.056 -10000 0 -0.68 3 3
EFNB1 -0.003 0.087 -10000 0 -0.48 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.22 -10000 0 -0.39 184 184
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 186 186
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 184 184
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.24 -10000 0 -0.42 185 185
DNM1 0.004 0.12 -10000 0 -0.64 15 15
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.001 0.091 0.41 1 -0.65 7 8
YES1 0.005 0.1 -10000 0 -0.9 6 6
Ephrin B1/EPHB1-2/NCK2 -0.12 0.22 -10000 0 -0.39 185 185
PI3K 0.025 0.1 -10000 0 -0.86 6 6
mol:GDP -0.13 0.23 -10000 0 -0.42 185 185
ITGA2B -0.041 0.2 -10000 0 -0.67 46 46
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.005 0.11 -10000 0 -0.86 7 7
MAP3K7 -0.01 0.085 -10000 0 -0.68 7 7
FGR 0.003 0.11 -10000 0 -0.85 7 7
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.025 0.16 -10000 0 -0.43 52 52
LYN 0.005 0.11 -10000 0 -0.86 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.1 -10000 0 -0.81 7 7
Ephrin B1/EPHB1-2 -0.009 0.088 -10000 0 -0.78 6 6
SRC 0.003 0.11 -10000 0 -0.85 7 7
ITGB3 0.012 0.097 -10000 0 -0.64 10 10
EPHB1 -0.24 0.34 -10000 0 -0.67 186 186
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.024 0.18 -10000 0 -0.52 53 53
BLK -0.048 0.14 -10000 0 -0.93 7 7
HCK 0.004 0.11 -10000 0 -0.85 7 7
regulation of stress fiber formation 0.12 0.21 0.38 185 -10000 0 185
MAPK8 -0.003 0.12 0.36 5 -0.67 10 15
Ephrin B1/EPHB1-2/RGS3 -0.12 0.22 -10000 0 -0.39 184 184
endothelial cell migration -0.006 0.078 0.41 1 -0.62 6 7
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.025 0.085 -10000 0 -0.8 5 5
regulation of focal adhesion formation 0.12 0.21 0.38 185 -10000 0 185
chemotaxis 0.12 0.21 0.38 184 -10000 0 184
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.39 184 184
angiogenesis -0.01 0.09 -10000 0 -0.73 7 7
LCK 0.001 0.11 -10000 0 -0.9 7 7
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.2 0.54 -10000 0 -1.3 78 78
IL23A -0.21 0.56 -10000 0 -1.3 90 90
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.55 -10000 0 -1.3 80 80
positive regulation of T cell mediated cytotoxicity -0.24 0.62 -10000 0 -1.4 82 82
ITGA3 -0.18 0.51 -10000 0 -1.2 78 78
IL17F -0.1 0.34 0.64 3 -0.74 77 80
IL12B 0.004 0.088 -10000 0 -0.7 5 5
STAT1 (dimer) -0.22 0.59 -10000 0 -1.4 81 81
CD4 -0.18 0.5 -10000 0 -1.2 76 76
IL23 -0.2 0.54 -10000 0 -1.2 88 88
IL23R 0.003 0.11 -10000 0 -0.79 3 3
IL1B -0.23 0.58 -10000 0 -1.4 80 80
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.51 -10000 0 -1.2 75 75
TYK2 0.015 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.009 0.14 -10000 0 -0.68 20 20
IL12RB1 -0.001 0.077 -10000 0 -0.63 4 4
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
IL12Rbeta1/TYK2 0.014 0.069 -10000 0 -0.49 4 4
IL23R/JAK2 0.009 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.24 0.62 -10000 0 -1.4 82 82
natural killer cell activation 0.001 0.008 -10000 0 -0.055 1 1
JAK2 0.015 0.049 -10000 0 -0.4 1 1
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.5 -10000 0 -1.1 89 89
ALOX12B -0.18 0.5 -10000 0 -1.2 78 78
CXCL1 -0.2 0.53 -10000 0 -1.3 79 79
T cell proliferation -0.24 0.62 -10000 0 -1.4 82 82
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.058 0.27 -10000 0 -0.58 64 64
PI3K -0.2 0.56 -10000 0 -1.3 79 79
IFNG -0.015 0.054 0.16 2 -0.13 64 66
STAT3 (dimer) -0.18 0.52 -10000 0 -1.2 78 78
IL18R1 -0.003 0.098 -10000 0 -0.59 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.098 0.34 -10000 0 -0.79 65 65
IL18/IL18R -0.002 0.15 -10000 0 -0.47 35 35
macrophage activation -0.009 0.021 -10000 0 -0.044 98 98
TNF -0.26 0.61 -10000 0 -1.4 97 97
STAT3/STAT4 -0.2 0.56 -10000 0 -1.3 80 80
STAT4 (dimer) -0.22 0.6 -10000 0 -1.4 81 81
IL18 -0.009 0.11 -10000 0 -0.65 11 11
IL19 -0.18 0.51 -10000 0 -1.2 75 75
STAT5A (dimer) -0.22 0.59 -10000 0 -1.4 80 80
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.008 0.15 -10000 0 -0.68 23 23
CXCL9 -0.27 0.62 -10000 0 -1.4 103 103
MPO -0.18 0.51 -10000 0 -1.2 78 78
positive regulation of humoral immune response -0.24 0.62 -10000 0 -1.4 82 82
IL23/IL23R/JAK2/TYK2 -0.28 0.76 -10000 0 -1.7 80 80
IL6 -0.3 0.64 -10000 0 -1.3 121 121
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.008 -10000 0 -0.055 1 1
CD3E -0.21 0.56 -10000 0 -1.3 85 85
keratinocyte proliferation -0.24 0.62 -10000 0 -1.4 82 82
NOS2 -0.18 0.5 -10000 0 -1.2 76 76
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.51 0.4 -10000 0 -1.2 70 70
STAT6 (cleaved dimer) -0.52 0.41 -10000 0 -1 120 120
IGHG1 -0.18 0.13 -10000 0 -0.63 1 1
IGHG3 -0.49 0.38 -10000 0 -0.99 114 114
AKT1 -0.27 0.28 0.62 2 -0.87 50 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.97 50 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.31 0.3 -10000 0 -0.88 58 58
THY1 -0.51 0.4 -10000 0 -1.2 65 65
MYB 0.011 0.098 -10000 0 -0.64 10 10
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.31 -10000 0 -0.88 73 73
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.93 44 44
SP1 0.031 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.41 -10000 0 -1.1 96 96
SOCS1 -0.35 0.26 -10000 0 -0.74 61 61
SOCS3 -0.32 0.35 0.6 2 -1.1 59 61
FCER2 -0.51 0.42 -10000 0 -1.1 99 99
PARP14 0.027 0.005 -10000 0 -10000 0 0
CCL17 -0.54 0.42 -10000 0 -1.2 80 80
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.2 -10000 0 -0.69 37 37
T cell proliferation -0.5 0.41 -10000 0 -1.2 80 80
IL4R/JAK1 -0.5 0.4 -10000 0 -1.1 77 77
EGR2 -0.84 0.68 -10000 0 -1.5 217 217
JAK2 -0.031 0.038 -10000 0 -0.4 1 1
JAK3 -0.011 0.064 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.004 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.13 -10000 0 -0.97 2 2
CCL26 -0.51 0.4 -10000 0 -1.2 73 73
IL4R -0.53 0.42 -10000 0 -1.2 75 75
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.6 0.54 -10000 0 -1.5 99 99
IL13RA1 -0.03 0.033 -10000 0 -10000 0 0
IRF4 -0.29 0.48 -10000 0 -1.1 95 95
ARG1 -0.13 0.14 -10000 0 -1 3 3
CBL -0.32 0.29 -10000 0 -0.86 66 66
GTF3A 0.025 0.016 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
IL13RA1/JAK2 -0.036 0.046 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.44 -10000 0 -1.1 88 88
CD40LG -0.069 0.23 -10000 0 -0.64 66 66
MAPK14 -0.34 0.33 -10000 0 -0.96 68 68
mitosis -0.26 0.26 0.62 2 -0.8 51 53
STAT6 -0.57 0.48 -10000 0 -1.3 97 97
SPI1 0.022 0.032 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.78 2 -0.77 45 47
STAT6 (dimer) -0.57 0.48 -10000 0 -1.3 97 97
STAT6 (dimer)/PARP14 -0.53 0.44 -10000 0 -1.2 86 86
mast cell activation 0.014 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.31 -10000 0 -1 49 49
FRAP1 -0.27 0.28 0.62 2 -0.86 51 53
LTA -0.52 0.4 -10000 0 -1.2 75 75
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.56 0.45 1.2 101 -10000 0 101
CCL11 -0.49 0.38 -10000 0 -1.1 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -1 49 49
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
IL10 -0.51 0.42 -10000 0 -1.3 71 71
IRS1 -0.054 0.22 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.09 -10000 0 -10000 0 0
IL5 -0.51 0.4 -10000 0 -1.2 68 68
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.36 -10000 0 -0.99 82 82
COL1A1 -0.21 0.23 -10000 0 -1 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.41 -10000 0 -1.3 61 61
IL2R gamma/JAK3 -0.02 0.12 -10000 0 -0.48 20 20
TFF3 -1.2 0.58 -10000 0 -1.4 387 387
ALOX15 -0.5 0.4 -10000 0 -1.2 71 71
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.43 0.35 -10000 0 -0.97 82 82
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.27 -10000 0 -0.94 42 42
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.87 50 52
PI3K -0.29 0.3 0.67 1 -0.95 50 51
DOK2 0.02 0.051 -10000 0 -0.68 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.69 31 31
ITGB3 -0.52 0.43 -10000 0 -1.2 72 72
PIGR -0.53 0.45 -10000 0 -1.3 81 81
IGHE 0.046 0.045 0.24 9 -10000 0 9
MAPKKK cascade -0.19 0.19 0.58 1 -0.68 31 32
BCL6 0.025 0.032 -10000 0 -0.67 1 1
OPRM1 -0.52 0.4 -10000 0 -1.2 76 76
RETNLB -0.51 0.4 -10000 0 -1.2 69 69
SELP -0.5 0.41 -10000 0 -1.2 65 65
AICDA -0.49 0.38 -10000 0 -1.1 74 74
EPHB forward 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
Ephrin A5/EPHB2 -0.035 0.17 -10000 0 -0.44 70 70
cell-cell adhesion 0.11 0.16 0.32 171 -10000 0 171
Ephrin B/EPHB2/RasGAP 0.064 0.061 -10000 0 -0.38 7 7
ITSN1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.025 0.046 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.43 184 184
HRAS/GDP -0.083 0.16 -10000 0 -0.35 17 17
Ephrin B/EPHB1/GRB7 -0.1 0.23 -10000 0 -0.4 176 176
Endophilin/SYNJ1 0.023 0.073 0.46 5 -0.35 7 12
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.22 -10000 0 -0.38 177 177
endothelial cell migration 0.051 0.038 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.055 -10000 0 -10000 0 0
PAK1 0.024 0.075 0.46 5 -0.36 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.067 0.44 4 -0.36 6 10
DNM1 0.004 0.12 -10000 0 -0.62 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.19 -10000 0 -0.37 177 177
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 171 171
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.088 0.16 -10000 0 -0.3 161 161
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.056 -10000 0 -0.68 3 3
EPHB3 -0.065 0.073 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.67 186 186
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.074 0.14 0.25 1 -0.38 12 13
Ephrin B/EPHB2 0.05 0.057 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.058 0.055 -10000 0 -0.43 4 4
JNK cascade -0.13 0.19 -10000 0 -0.38 175 175
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 179 179
RAP1/GDP -0.049 0.14 -10000 0 -0.34 9 9
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.069 -10000 0 -0.68 4 4
EFNB1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 186 186
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.089 0.19 -10000 0 -0.38 19 19
Rap1/GTP -0.1 0.17 -10000 0 -0.33 162 162
axon guidance -0.035 0.17 -10000 0 -0.44 70 70
MAPK3 -0.084 0.14 -10000 0 -0.44 10 10
MAPK1 -0.081 0.14 -10000 0 -0.43 10 10
Rac1/GDP -0.06 0.14 -10000 0 -0.35 11 11
actin cytoskeleton reorganization -0.081 0.12 -10000 0 -0.32 5 5
CDC42/GDP -0.058 0.14 0.37 1 -0.35 12 13
PI3K 0.057 0.039 -10000 0 -0.38 3 3
EFNA5 -0.073 0.24 -10000 0 -0.68 68 68
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.045 -10000 0 -0.32 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.32 157 157
PTK2 0.041 0.087 0.64 8 -10000 0 8
MAP4K4 -0.13 0.2 -10000 0 -0.38 175 175
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.003 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.078 0.14 0.4 2 -10000 0 2
MAP2K1 -0.084 0.15 -10000 0 -0.4 15 15
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.23 -10000 0 -0.41 175 175
cell migration -0.086 0.18 0.52 5 -0.44 16 21
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.46 5 -0.36 7 12
PXN 0.026 0.005 -10000 0 -10000 0 0
TF -0.022 0.13 0.47 3 -0.38 49 52
HRAS/GTP -0.095 0.19 -10000 0 -0.34 171 171
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.4 186 186
cell adhesion mediated by integrin -0.008 0.074 0.39 4 -0.3 13 17
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.36 175 175
RAC1-CDC42/GTP -0.14 0.17 -10000 0 -0.37 131 131
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.051 0.14 -10000 0 -0.37 4 4
ruffle organization -0.1 0.18 0.58 4 -0.39 5 9
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization 0.002 0.086 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.064 0.061 -10000 0 -0.38 7 7
ROCK1 -0.023 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.075 0.1 -10000 0 -0.34 3 3
Rac1/GTP -0.12 0.17 -10000 0 -0.34 171 171
Ephrin B/EPHB1/Src/Paxillin -0.095 0.16 -10000 0 -0.3 179 179
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.17 0.3 -10000 0 -0.49 205 205
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.02 0.17 -10000 0 -0.68 29 29
SMAD9 -0.19 0.27 -10000 0 -0.54 172 172
SMAD4 0.027 0.004 -10000 0 -10000 0 0
SMAD5 -0.084 0.17 -10000 0 -0.45 30 30
BMP7/USAG1 -0.24 0.27 -10000 0 -0.51 244 244
SMAD5/SKI -0.07 0.17 0.31 3 -0.44 31 34
SMAD1 -0.036 0.095 -10000 0 -0.52 2 2
BMP2 -0.001 0.14 -10000 0 -0.68 19 19
SMAD1/SMAD1/SMAD4 -0.021 0.085 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.21 0.33 -10000 0 -0.68 158 158
BMPR1A-1B/BAMBI -0.11 0.24 -10000 0 -0.45 158 158
AHSG -0.004 0.04 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.012 0.12 -10000 0 -0.44 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.068 0.17 -10000 0 -0.55 28 28
BMP2-4 (homodimer) 0.003 0.13 -10000 0 -0.51 30 30
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.089 0.22 -10000 0 -0.4 158 158
RGMA 0.001 0.13 -10000 0 -0.66 18 18
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.081 0.16 -10000 0 -0.47 34 34
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.46 257 257
SMAD6/SMURF1/SMAD5 -0.069 0.17 0.32 1 -0.43 29 30
SOSTDC1 -0.33 0.35 -10000 0 -0.67 244 244
BMP7/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 155 155
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.007 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.012 0.14 -10000 0 -0.45 39 39
SMAD5/SMAD5/SMAD4 -0.068 0.17 0.33 2 -0.43 31 33
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.055 0.15 -10000 0 -0.43 29 29
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.028 0.031 -10000 0 -10000 0 0
SMAD1/SKI -0.026 0.1 0.33 1 -0.62 1 2
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.019 0.12 -10000 0 -0.45 30 30
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 114 114
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.053 -10000 0 -0.44 5 5
BMPR1A-1B (homodimer) -0.14 0.26 -10000 0 -0.51 158 158
CHRDL1 -0.44 0.32 -10000 0 -0.66 329 329
ENDOFIN/SMAD1 -0.029 0.099 -10000 0 -0.5 2 2
SMAD6-7/SMURF1/SMAD1 -0.012 0.1 -10000 0 -0.47 2 2
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.053 -10000 0 -0.68 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.25 -10000 0 -0.47 318 318
BMP2-4/GREM1 -0.085 0.24 -10000 0 -0.48 121 121
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.26 -10000 0 -0.51 170 170
SMAD1/SMAD6 -0.027 0.097 -10000 0 -0.5 2 2
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.059 0.14 -10000 0 -0.41 30 30
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.026 0.098 0.31 1 -0.5 2 3
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.018 0.071 -10000 0 -0.68 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 86 86
CHRD 0.012 0.1 -10000 0 -0.68 10 10
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.082 0.16 -10000 0 -0.5 31 31
BMP4 0.008 0.11 -10000 0 -0.65 12 12
FST -0.14 0.29 -10000 0 -0.68 111 111
BMP2-4/NOG -0.009 0.16 -10000 0 -0.44 58 58
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.073 0.21 -10000 0 -0.38 152 152
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.056 0.25 0.29 19 -0.6 68 87
FYN -0.1 0.32 0.9 1 -0.79 73 74
LAT/GRAP2/SLP76 -0.083 0.26 -10000 0 -0.61 78 78
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.062 0.21 0.54 8 -0.47 77 85
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.055 0.12 2 -0.15 30 32
MAP3K8 0.016 0.086 -10000 0 -0.64 8 8
mol:Ca2+ -0.03 0.043 0.092 5 -0.1 99 104
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.31 0.63 5 -0.72 81 86
TRPV6 -0.1 0.36 1 19 -0.68 99 118
CD28 -0.013 0.15 -10000 0 -0.65 23 23
SHC1 -0.1 0.32 0.31 20 -0.79 73 93
receptor internalization -0.13 0.35 -10000 0 -0.8 85 85
PRF1 -0.11 0.34 -10000 0 -0.82 72 72
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.18 0.52 6 -0.37 79 85
LAT -0.11 0.32 0.3 3 -0.78 76 79
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.051 0.21 -10000 0 -0.64 53 53
CD3E -0.033 0.19 -10000 0 -0.63 42 42
CD3G -0.099 0.26 -10000 0 -0.65 87 87
RASGRP2 -0.004 0.034 0.095 3 -0.18 12 15
RASGRP1 -0.048 0.22 0.57 11 -0.47 76 87
HLA-A 0.026 0.012 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.14 0.34 30 -0.13 43 73
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.047 0.085 -10000 0 -0.24 61 61
PRKCA -0.036 0.13 -10000 0 -0.29 75 75
GRAP2 -0.018 0.15 -10000 0 -0.55 31 31
mol:IP3 -0.032 0.21 0.26 70 -0.44 72 142
EntrezGene:6957 0 0.005 0.059 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.13 0.36 -10000 0 -0.87 75 75
ORAI1 0.046 0.21 0.7 2 -0.8 15 17
CSK -0.11 0.32 -10000 0 -0.8 77 77
B7 family/CD28 -0.11 0.35 -10000 0 -0.8 80 80
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.39 -10000 0 -0.94 77 77
PTPN6 -0.12 0.33 0.25 1 -0.8 76 77
VAV1 -0.11 0.32 -10000 0 -0.77 76 76
Monovalent TCR/CD3 -0.12 0.32 -10000 0 -0.62 104 104
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.34 0.88 1 -0.83 73 74
PAG1 -0.11 0.32 -10000 0 -0.8 77 77
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.39 -10000 0 -0.94 77 77
CD80 -0.042 0.21 -10000 0 -0.68 46 46
CD86 0.013 0.077 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.04 0.11 -10000 0 -0.29 62 62
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.63 80 80
CD8A -0.024 0.18 -10000 0 -0.65 36 36
CD8B -0.053 0.22 -10000 0 -0.65 54 54
PTPRC -0.008 0.14 -10000 0 -0.68 19 19
PDK1/PKC theta -0.074 0.27 0.64 11 -0.58 77 88
CSK/PAG1 -0.11 0.31 -10000 0 -0.78 74 74
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.31 -10000 0 -0.74 79 79
STIM1 0.018 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.012 0.11 0.26 26 -0.19 42 68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.89 85 85
mol:DAG -0.06 0.16 0.14 5 -0.39 75 80
RAP1A/GDP 0.011 0.083 0.25 17 -10000 0 17
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.002 0.13 -10000 0 -0.68 17 17
cytotoxic T cell degranulation -0.1 0.32 0.45 1 -0.78 73 74
RAP1A/GTP -0.001 0.013 -10000 0 -0.068 10 10
mol:PI-3-4-5-P3 -0.083 0.25 0.58 6 -0.56 81 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.26 0.28 64 -0.59 72 136
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0 0.12 -10000 0 -0.66 16 16
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.081 0.24 -10000 0 -0.58 77 77
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
CD8 heterodimer -0.057 0.24 -10000 0 -0.6 71 71
CARD11 -0.018 0.1 -10000 0 -0.68 8 8
PRKCB -0.03 0.12 -10000 0 -0.3 67 67
PRKCE -0.029 0.12 -10000 0 -0.28 67 67
PRKCQ -0.093 0.29 0.64 8 -0.68 78 86
LCP2 0.024 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.046 0.19 0.54 9 -0.39 77 86
IKK complex 0.019 0.14 0.4 24 -0.12 23 47
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.034 0.12 0.26 3 -0.29 61 64
PDPK1 -0.057 0.21 0.56 10 -0.44 77 87
TCR/CD3/MHC I/CD8/Fyn -0.16 0.42 -10000 0 -0.99 83 83
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.052 -10000 0 -10000 0 0
SVIL -0.002 0.048 -10000 0 -10000 0 0
ZNF318 0.075 0.088 0.24 9 -0.68 1 10
JMJD2C -0.065 0.067 -10000 0 -0.12 270 270
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.49 197 197
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.028 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.002 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.02 -10000 0 -10000 0 0
PTK2B 0.008 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.068 0.11 0.2 134 -0.65 6 140
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.064 -10000 0 -0.68 2 2
GSN 0 0.044 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.68 42 42
NCOA6 -0.003 0.055 -10000 0 -0.68 1 1
DNA-PK 0.074 0.078 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation 0.002 0.14 -10000 0 -0.89 7 7
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -0.18 1 1
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.52 203 203
FHL2 -0.14 0.34 -10000 0 -1.2 42 42
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 34 34
CDK6 0.023 0.056 -10000 0 -0.67 3 3
TGFB1I1 -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.5 202 202
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 223 223
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 0.2 1 -10000 0 1
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.003 0.083 -10000 0 -10000 0 0
SRF 0.034 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.6 15 15
KLK3 -0.39 0.65 -10000 0 -1.4 136 136
TMF1 0.017 0.047 -10000 0 -0.68 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 136 136
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.21 0.24 -10000 0 -0.49 194 194
AR -0.31 0.34 -10000 0 -0.71 197 197
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.033 0.031 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.017 -10000 0 -10000 0 0
PA2G4 0.048 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.45 197 197
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.5 198 198
LATS2 0.04 0.043 -10000 0 -0.68 1 1
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.44 194 194
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.085 -10000 0 -0.68 6 6
KLK2 -0.66 0.56 -10000 0 -1.1 273 273
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 201 201
TMPRSS2 -0.16 0.28 -10000 0 -1 37 37
CCND1 0.014 0.03 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.04 -10000 0 -0.077 179 179
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.03 0.09 -10000 0 -0.22 1 1
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.49 199 199
CMTM2 0.028 0.012 -10000 0 -10000 0 0
SNURF -0.01 0.15 -10000 0 -0.64 25 25
ZMIZ1 -0.024 0.057 -10000 0 -0.34 3 3
CCND3 0.028 0.003 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.045 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.085 0.086 0.36 1 -10000 0 1
SMARCC2 0.025 0.019 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 0.32 1 -0.68 51 52
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.023 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.018 0.078 -10000 0 -0.68 6 6
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.33 52 -0.39 5 57
PRL -0.063 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.54 136 -0.46 19 155
RELA -0.03 0.1 -10000 0 -0.28 23 23
FGG 0.17 0.2 0.46 107 -10000 0 107
GR beta/TIF2 0.076 0.2 0.33 68 -0.45 42 110
IFNG -0.36 0.48 -10000 0 -1.1 108 108
apoptosis -0.011 0.23 0.47 45 -0.53 19 64
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.077 0.16 -10000 0 -0.43 57 57
BGLAP -0.077 0.13 -10000 0 -0.51 11 11
GR/PKAc 0.11 0.1 0.34 35 -0.34 1 36
NF kappa B1 p50/RelA -0.053 0.18 -10000 0 -0.46 40 40
SMARCD1 0.025 0.019 -10000 0 -10000 0 0
MDM2 0.085 0.097 0.24 92 -10000 0 92
GATA3 -0.004 0.15 -10000 0 -0.64 24 24
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.51 27 27
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.008 0.23 0.5 34 -0.53 17 51
CSN2 0.14 0.16 0.4 78 -10000 0 78
BRG1/BAF155/BAF170/BAF60A 0.062 0.055 -10000 0 -0.31 7 7
NFATC1 0.015 0.096 -10000 0 -0.68 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.026 0.034 -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 -0.083 0.12 -10000 0 -0.68 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.34 45 -0.38 11 56
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.39 0.47 31 -0.83 98 129
JUN -0.24 0.27 -10000 0 -0.58 156 156
IL4 -0.1 0.16 -10000 0 -0.66 18 18
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.31 -10000 0 -0.66 147 147
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.35 34 -0.39 4 38
cortisol/GR alpha (monomer) 0.26 0.3 0.63 147 -10000 0 147
NCOA2 -0.035 0.2 -10000 0 -0.68 42 42
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.19 0.3 -10000 0 -0.69 126 126
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.82 182 182
AFP -0.17 0.2 -10000 0 -0.61 38 38
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.44 48 -10000 0 48
TP53 0.04 0.015 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
KRT17 -0.3 0.34 -10000 0 -0.8 103 103
KRT14 -0.084 0.12 -10000 0 -0.46 11 11
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.034 0.048 -10000 0 -0.26 11 11
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.39 0.41 -10000 0 -0.83 182 182
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.036 -10000 0 -0.68 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.39 0.5 -10000 0 -1.1 125 125
interleukin-1 receptor activity 0.003 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.023 -10000 0 -10000 0 0
CGA -0.095 0.14 -10000 0 -0.48 21 21
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.12 0.32 53 -10000 0 53
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.17 0.24 -10000 0 -0.66 68 68
NFKB1 -0.029 0.099 -10000 0 -0.26 32 32
MAPK8 -0.14 0.18 -10000 0 -0.46 78 78
MAPK9 0.027 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.016 0.23 0.47 43 -0.56 19 62
BAX 0.038 0.086 0.84 4 -10000 0 4
POMC -0.45 0.64 -10000 0 -1.3 141 141
EP300 0.025 0.045 -10000 0 -0.26 9 9
cortisol/GR alpha (dimer)/p53 0.23 0.24 0.55 148 -10000 0 148
proteasomal ubiquitin-dependent protein catabolic process 0.081 0.13 0.33 83 -10000 0 83
SGK1 0.009 0.22 0.45 3 -1.3 11 14
IL13 -0.21 0.25 -10000 0 -0.81 39 39
IL6 -0.31 0.5 -10000 0 -1.2 110 110
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.71 31 31
IL2 -0.26 0.28 -10000 0 -0.74 74 74
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.025 0.032 -10000 0 -0.68 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.73 69 69
CDK5R1/CDK5 0.038 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.005 0.14 -10000 0 -0.37 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.51 151 -10000 0 151
SMARCA4 0.024 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.38 90 -0.4 3 93
NF kappa B1 p50/RelA/Cbp -0.014 0.16 -10000 0 -0.41 29 29
JUN (dimer) -0.24 0.27 -10000 0 -0.57 156 156
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.89 92 92
NR3C1 0.16 0.19 0.44 111 -10000 0 111
NR4A1 -0.26 0.36 -10000 0 -0.66 202 202
TIF2/SUV420H1 -0.009 0.16 -10000 0 -0.51 42 42
MAPKKK cascade -0.011 0.23 0.47 45 -0.53 19 64
cortisol/GR alpha (dimer)/Src-1 0.23 0.24 0.55 142 -10000 0 142
PBX1 0.024 0.033 -10000 0 -0.68 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.26 0.46 -10000 0 -1.1 90 90
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.38 90 -0.4 3 93
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.51 151 -10000 0 151
mol:cortisol 0.14 0.19 0.37 144 -10000 0 144
MMP1 -0.1 0.15 -10000 0 -0.9 10 10
Arf6 signaling events

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
CENTA1/KIF3B 0.035 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.02 0.15 -10000 0 -0.72 13 13
EGFR 0.02 0.064 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.014 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.042 0.19 -10000 0 -0.5 71 71
ARRB2 -0.037 0.13 -10000 0 -0.39 59 59
mol:GTP 0.024 0.037 0.17 19 -10000 0 19
ARRB1 0.025 0.032 -10000 0 -0.68 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.023 0.045 -10000 0 -0.68 2 2
EGF -0.074 0.24 -10000 0 -0.67 68 68
somatostatin receptor activity 0 0.001 0.002 15 -0.001 140 155
ARAP2 0.024 0.045 -10000 0 -0.68 2 2
mol:GDP -0.11 0.15 0.27 5 -0.3 118 123
mol:PI-3-4-5-P3 0 0.001 0.002 11 -0.001 73 84
ITGA2B -0.041 0.2 -10000 0 -0.67 46 46
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.004 -10000 0 -10000 0 0
HGF/MET -0.079 0.19 -10000 0 -0.52 68 68
PXN 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.51 9 -0.29 145 154
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.02 0.17 -10000 0 -0.44 71 71
ADRB2 0.009 0.11 -10000 0 -0.68 12 12
receptor agonist activity 0 0 0.001 17 0 145 162
actin filament binding 0 0 0.002 16 -0.001 141 157
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.012 0.097 -10000 0 -0.64 10 10
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 16 -0.001 71 87
ARF6/GDP -0.007 0.093 0.24 2 -0.46 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 110 110
alphaIIb/beta3 Integrin/paxillin/GIT1 0.012 0.15 -10000 0 -0.42 53 53
ACAP1 0.019 0.044 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.051 0.19 -10000 0 -0.56 59 59
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.074 0.24 -10000 0 -0.68 68 68
CYTH3 0.006 0.034 -10000 0 -0.51 2 2
CYTH2 -0.011 0.16 -10000 0 -0.93 14 14
NCK1 0.027 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 21 0 96 117
endosomal lumen acidification 0 0 0.002 7 -0.001 138 145
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 -0.094 0.26 -10000 0 -0.66 85 85
GNAQ/ARNO 0.002 0.15 -10000 0 -0.85 14 14
mol:Phosphatidic acid 0 0 0.001 13 -10000 0 13
PIP3-E 0 0 0.001 10 0 16 26
MET -0.029 0.072 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 115 130
GNA11 0.015 0.08 -10000 0 -0.63 7 7
LHCGR -0.076 0.23 -10000 0 -0.68 59 59
AGTR1 -0.26 0.34 -10000 0 -0.67 193 193
desensitization of G-protein coupled receptor protein signaling pathway -0.051 0.19 -10000 0 -0.56 59 59
IPCEF1/ARNO -0.036 0.18 -10000 0 -0.76 14 14
alphaIIb/beta3 Integrin -0.024 0.18 -10000 0 -0.52 53 53
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.095 0.33 -10000 0 -1.1 43 43
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.019 0.11 -10000 0 -0.34 36 36
ATF2/c-Jun -0.2 0.35 -10000 0 -0.79 118 118
MAPK11 -0.013 0.097 -10000 0 -0.35 29 29
MITF -0.025 0.12 -10000 0 -0.41 39 39
MAPKAPK5 -0.021 0.12 -10000 0 -0.4 35 35
KRT8 -0.021 0.12 -10000 0 -0.4 35 35
MAPKAPK3 0.027 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.15 -10000 0 -0.48 39 39
CEBPB -0.023 0.12 -10000 0 -0.4 37 37
SLC9A1 -0.026 0.12 -10000 0 -0.4 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.075 0.18 -10000 0 -0.42 80 80
p38alpha-beta/MNK1 -0.012 0.13 -10000 0 -0.4 34 34
JUN -0.2 0.35 -10000 0 -0.78 118 118
PPARGC1A -0.22 0.25 -10000 0 -0.45 244 244
USF1 -0.026 0.12 -10000 0 -0.4 40 40
RAB5/GDP/GDI1 -0.036 0.1 -10000 0 -0.31 37 37
NOS2 -0.031 0.12 -10000 0 -0.49 11 11
DDIT3 -0.022 0.12 -10000 0 -0.4 35 35
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.095 0.37 2 -0.38 14 16
p38alpha-beta/HBP1 -0.008 0.12 -10000 0 -0.41 28 28
CREB1 -0.056 0.16 -10000 0 -0.47 42 42
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.027 0.1 -10000 0 -0.37 30 30
RPS6KA4 -0.023 0.12 -10000 0 -0.41 37 37
PLA2G4A -0.053 0.16 -10000 0 -0.49 49 49
GDI1 -0.021 0.12 -10000 0 -0.42 34 34
TP53 -0.033 0.14 -10000 0 -0.48 34 34
RPS6KA5 -0.063 0.18 -10000 0 -0.45 76 76
ESR1 -0.053 0.19 -10000 0 -0.54 52 52
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.021 0.12 -10000 0 -0.4 36 36
MEF2A -0.027 0.13 -10000 0 -0.42 41 41
EIF4EBP1 -0.056 0.16 -10000 0 -0.46 43 43
KRT19 -0.054 0.17 -10000 0 -0.5 45 45
ELK4 -0.026 0.12 -10000 0 -0.4 40 40
ATF6 -0.026 0.12 -10000 0 -0.4 40 40
ATF1 -0.054 0.16 -10000 0 -0.47 40 40
p38alpha-beta/MAPKAPK2 -0.013 0.13 -10000 0 -0.4 34 34
p38alpha-beta/MAPKAPK3 -0.012 0.13 -10000 0 -0.41 34 34
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.045 0.043 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.41 2 -0.54 241 243
GNAO1 0.001 0.12 -10000 0 -0.68 15 15
SMO/beta Arrestin2 0.015 0.036 -10000 0 -0.51 1 1
SMO 0.015 0.035 -10000 0 -0.68 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.037 0.073 -10000 0 -0.34 5 5
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.033 -10000 0 -0.4 1 1
GNAI1 0.023 0.033 -10000 0 -0.68 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.22 -10000 0 -0.49 133 133
SAP30 0.026 0.032 -10000 0 -0.68 1 1
mol:GDP 0.015 0.035 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.066 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.024 0.007 -10000 0 -10000 0 0
GLI2 0 0.08 0.28 2 -0.38 7 9
GLI3 0.027 0.077 0.26 4 -0.35 5 9
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.68 1 1
Gi family/GTP -0.016 0.07 -10000 0 -0.3 17 17
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.065 -10000 0 -0.45 2 2
GLI2/Su(fu) 0.009 0.077 -10000 0 -0.49 3 3
FOXA2 -0.59 0.62 -10000 0 -1.2 235 235
neural tube patterning -0.3 0.28 0.41 2 -0.54 241 243
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.029 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.066 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.41 2 -0.54 241 243
SUFU 0.018 0.016 -10000 0 -0.24 1 1
LGALS3 -0.026 0.071 -10000 0 -10000 0 0
catabolic process 0.032 0.1 0.29 1 -0.44 8 9
GLI3A/CBP -0.18 0.2 -10000 0 -0.38 240 240
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.41 2 -0.55 241 243
RAB23 0.021 0.064 -10000 0 -0.68 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.049 -10000 0 -0.26 1 1
GNAZ 0.019 0.012 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.011 0.082 -10000 0 -0.36 8 8
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.056 -10000 0 -0.36 3 3
PTCH1 -0.27 0.26 0.52 2 -0.59 133 135
MIM/GLI1 -0.43 0.38 -10000 0 -0.7 263 263
CREBBP -0.18 0.2 -10000 0 -0.38 240 240
Su(fu)/SIN3/HDAC complex 0.036 0.065 -10000 0 -0.53 4 4
Thromboxane A2 receptor signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.052 -10000 0 -10000 0 0
GNB1/GNG2 -0.033 0.067 -10000 0 -0.19 66 66
AKT1 0.01 0.13 0.4 21 -0.26 1 22
EGF -0.074 0.24 -10000 0 -0.67 68 68
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.019 0.09 0.36 14 -0.5 3 17
mol:Ca2+ -0.019 0.15 0.39 14 -0.3 67 81
LYN 0.018 0.089 0.37 13 -0.5 3 16
RhoA/GTP -0.01 0.054 -10000 0 -0.15 3 3
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.02 0.17 0.4 18 -0.34 67 85
GNG2 0.025 0.032 -10000 0 -0.68 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.61 12 13
G beta5/gamma2 -0.044 0.091 -10000 0 -0.26 65 65
PRKCH -0.026 0.17 0.44 13 -0.36 67 80
DNM1 0.004 0.12 -10000 0 -0.62 16 16
TXA2/TP beta/beta Arrestin3 -0.011 0.12 -10000 0 -0.5 23 23
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.004 0.14 -10000 0 -0.68 21 21
G12 family/GTP -0.035 0.12 -10000 0 -0.31 66 66
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.051 0.14 0.41 35 -0.35 6 41
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.67 130 130
mol:IP3 -0.03 0.18 0.44 12 -0.38 67 79
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.053 0.22 0.43 10 -0.52 67 77
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.077 0.18 0.36 10 -0.33 133 143
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.013 0.083 0.34 10 -0.5 3 13
RHOA 0.027 0.003 -10000 0 -10000 0 0
PTGIR 0.018 0.072 -10000 0 -0.68 5 5
PRKCB1 -0.03 0.17 0.42 12 -0.38 69 81
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.048 0.23 0.48 12 -0.53 69 81
LCK 0.014 0.1 0.36 14 -0.53 6 20
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.024 0.088 -10000 0 -0.34 18 18
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.029 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.088 -10000 0 -0.34 19 19
MAPK14 -0.007 0.12 0.32 21 -0.24 33 54
TGM2/GTP -0.046 0.18 0.34 5 -0.43 64 69
MAPK11 -0.011 0.12 0.34 20 -0.23 57 77
ARHGEF1 -0.016 0.074 0.17 1 -0.19 32 33
GNAI2 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.027 0.18 0.41 17 -0.39 69 86
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.018 0.14 0.36 17 -0.29 69 86
cAMP biosynthetic process -0.031 0.17 0.42 14 -0.36 64 78
Gq family/GTP/EBP50 -0.044 0.11 0.24 2 -0.33 25 27
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.015 0.082 0.34 10 -0.5 3 13
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.02 0.13 0.44 15 -0.3 16 31
VCAM1 -0.014 0.14 0.35 17 -0.3 68 85
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.61 12 13
platelet activation -0.007 0.16 0.43 22 -0.3 64 86
PGI2/IP 0.013 0.054 -10000 0 -0.51 5 5
PRKACA 0.002 0.088 -10000 0 -0.37 22 22
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.55 13 14
TXA2/TP beta/beta Arrestin2 0.005 0.11 -10000 0 -0.54 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.088 -10000 0 -0.37 20 20
mol:DAG -0.036 0.19 0.45 11 -0.43 69 80
EGFR 0.02 0.064 -10000 0 -0.68 4 4
TXA2/TP alpha -0.048 0.22 0.5 11 -0.49 64 75
Gq family/GTP -0.064 0.13 0.22 2 -0.28 115 117
YES1 0.02 0.091 0.37 14 -0.5 3 17
GNAI2/GTP 0.007 0.076 -10000 0 -0.6 3 3
PGD2/DP -0.004 0.11 -10000 0 -0.51 21 21
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.021 0.092 0.36 16 -0.5 3 19
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.05 -10000 0 -0.68 1 1
PGK/cGMP -0.091 0.21 -10000 0 -0.44 127 127
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.038 0.099 -10000 0 -0.51 7 7
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.032 0.18 0.43 14 -0.38 71 85
PRKCB -0.029 0.17 0.43 14 -0.37 68 82
PRKCE -0.033 0.16 0.36 10 -0.37 69 79
PRKCD -0.031 0.17 0.42 11 -0.38 68 79
PRKCG -0.031 0.17 0.42 13 -0.39 67 80
muscle contraction -0.041 0.22 0.48 13 -0.49 69 82
PRKCZ -0.02 0.16 0.42 16 -0.35 64 80
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.014 0.088 -10000 0 -0.42 9 9
PRKCQ -0.03 0.16 0.4 12 -0.36 70 82
MAPKKK cascade -0.04 0.2 0.44 14 -0.46 69 83
SELE -0.032 0.18 0.36 17 -0.42 69 86
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.097 -10000 0 -0.76 3 3
ROCK1 0.027 0.004 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
chemotaxis -0.056 0.26 0.55 9 -0.61 69 78
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.016 0.08 -10000 0 -0.63 7 7
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.22 -10000 0 -0.43 130 130
MAP3K8 0.013 0.086 -10000 0 -0.64 8 8
FOS -0.079 0.18 0.29 3 -0.45 59 62
PRKCA -0.015 0.14 -10000 0 -0.68 21 21
PTPN7 -0.021 0.13 -10000 0 -0.67 16 16
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.006 0.083 -10000 0 -0.68 5 5
NRAS 0.025 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.031 -10000 0 -10000 0 0
MAPK3 -0.016 0.12 -10000 0 -0.48 22 22
MAP2K1 -0.022 0.14 -10000 0 -0.51 29 29
ELK1 0.012 0.025 -10000 0 -10000 0 0
BRAF -0.017 0.13 -10000 0 -0.53 25 25
mol:GTP -0.002 0.004 -10000 0 -0.006 128 128
MAPK1 -0.1 0.2 -10000 0 -0.41 115 115
RAF1 -0.016 0.12 -10000 0 -0.52 25 25
KRAS 0.026 0.005 -10000 0 -10000 0 0
IL6-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
BCL2L1 -0.003 0.2 0.6 5 -0.6 18 23
CRP 0 0.21 0.59 9 -0.62 20 29
cell cycle arrest -0.019 0.21 0.55 3 -0.66 27 30
TIMP1 -0.042 0.22 0.6 3 -0.65 30 33
IL6ST -0.063 0.24 -10000 0 -0.67 62 62
Rac1/GDP -0.05 0.2 0.29 1 -0.53 49 50
AP1 -0.12 0.27 0.34 1 -0.6 93 94
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.015 0.2 0.62 4 -0.64 15 19
HSP90B1 0.04 0.069 -10000 0 -0.78 2 2
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.25 -10000 0 -0.69 53 53
AKT1 0.039 0.063 -10000 0 -0.98 1 1
FOXO1 0.038 0.06 -10000 0 -0.91 1 1
MAP2K6 -0.086 0.23 0.25 1 -0.58 60 61
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.035 0.2 0.33 7 -0.52 43 50
MITF -0.073 0.21 -10000 0 -0.56 51 51
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.072 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.005 0.1 -10000 0 -0.52 8 8
STAT3 -0.028 0.22 0.76 1 -0.71 27 28
STAT1 0.009 0.1 -10000 0 -0.94 5 5
CEBPD -0.007 0.2 0.64 2 -0.6 20 22
PIK3CA 0.024 0.056 -10000 0 -0.68 3 3
PI3K 0.038 0.044 -10000 0 -0.51 3 3
JUN -0.12 0.29 -10000 0 -0.67 103 103
PIAS3/MITF -0.057 0.21 0.27 1 -0.55 46 47
MAPK11 -0.095 0.24 -10000 0 -0.7 49 49
STAT3 (dimer)/FOXO1 0.012 0.17 -10000 0 -0.53 19 19
GRB2/SOS1/GAB family -0.033 0.2 -10000 0 -0.53 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.076 0.21 -10000 0 -0.38 133 133
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.019 -10000 0 -0.36 1 1
LBP 0.003 0.19 0.6 8 -0.6 8 16
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.026 0.015 -10000 0 -10000 0 0
MYC -0.02 0.25 0.63 3 -0.97 18 21
FGG -0.013 0.2 0.68 3 -0.62 19 22
macrophage differentiation -0.019 0.21 0.55 3 -0.66 27 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.074 0.25 -10000 0 -0.45 133 133
JUNB -0.007 0.21 0.6 3 -0.68 22 25
FOS -0.16 0.31 -10000 0 -0.67 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.23 -10000 0 -0.41 116 116
STAT1/PIAS1 -0.042 0.21 -10000 0 -0.53 44 44
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.065 -10000 0 -0.44 5 5
STAT3 (dimer) -0.023 0.22 0.6 2 -0.69 27 29
PRKCD -0.023 0.19 0.4 7 -0.56 30 37
IL6R 0.003 0.12 -10000 0 -0.67 15 15
SOCS3 -0.11 0.33 0.43 2 -0.95 49 51
gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.17 -10000 0 -0.44 60 60
Rac1/GTP -0.047 0.2 -10000 0 -0.54 46 46
HCK 0.018 0.035 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.11 0.34 1 -0.59 8 9
bone resorption -0.013 0.19 0.62 4 -0.61 15 19
IRF1 -0.003 0.2 0.64 6 -0.6 18 24
mol:GDP -0.07 0.21 0.25 1 -0.52 56 57
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.071 0.21 0.25 1 -0.54 55 56
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.089 0.25 -10000 0 -0.7 51 51
PTPN11 0.013 0.076 -10000 0 -0.87 3 3
IL6/IL6RA -0.081 0.23 -10000 0 -0.53 99 99
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.16 -10000 0 -0.41 62 62
gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.16 -10000 0 -0.43 62 62
IL6 -0.11 0.27 -10000 0 -0.68 90 90
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.021 0.075 -10000 0 -0.68 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.078 0.21 -10000 0 -0.38 131 131
LMO4 0.027 0.018 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.025 0.21 -10000 0 -0.7 26 26
MCL1 0.053 0.073 -10000 0 -0.82 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.027 0.14 -10000 0 -0.41 29 29
TBX21 -0.12 0.42 -10000 0 -1.1 55 55
B2M 0.023 0.017 -10000 0 -10000 0 0
TYK2 0.02 0.03 -10000 0 -10000 0 0
IL12RB1 0.003 0.075 -10000 0 -0.61 4 4
GADD45B -0.097 0.39 -10000 0 -1 59 59
IL12RB2 -0.004 0.13 -10000 0 -0.68 17 17
GADD45G -0.092 0.36 -10000 0 -1 44 44
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.025 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.003 0.11 -10000 0 -0.66 11 11
IL2RA -0.016 0.15 -10000 0 -0.64 26 26
IFNG -0.072 0.23 -10000 0 -0.68 59 59
STAT3 (dimer) -0.078 0.31 -10000 0 -0.8 57 57
HLA-DRB5 -0.009 0.082 -10000 0 -0.68 4 4
FASLG -0.13 0.45 -10000 0 -1.2 56 56
NF kappa B2 p52/RelB -0.1 0.38 -10000 0 -0.98 56 56
CD4 0.011 0.033 -10000 0 -10000 0 0
SOCS1 0.023 0.035 -10000 0 -0.68 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.065 0.21 -10000 0 -0.64 53 53
CD3E -0.046 0.19 -10000 0 -0.63 42 42
CD3G -0.11 0.26 -10000 0 -0.66 87 87
IL12Rbeta2/JAK2 0.011 0.11 -10000 0 -0.5 18 18
CCL3 -0.11 0.42 -10000 0 -1.2 46 46
CCL4 -0.15 0.49 -10000 0 -1.4 57 57
HLA-A 0.023 0.019 -10000 0 -10000 0 0
IL18/IL18R 0.029 0.16 -10000 0 -0.49 34 34
NOS2 -0.085 0.35 -10000 0 -0.99 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.027 0.14 -10000 0 -0.41 29 29
IL1R1 -0.1 0.37 -10000 0 -1.1 45 45
IL4 0 0.033 -10000 0 -10000 0 0
JAK2 0.019 0.035 -10000 0 -0.4 1 1
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 96 96
RAB7A -0.056 0.3 -10000 0 -0.75 52 52
lysosomal transport -0.051 0.28 -10000 0 -0.7 53 53
FOS -0.37 0.61 -10000 0 -1.2 157 157
STAT4 (dimer) -0.082 0.36 -10000 0 -0.86 61 61
STAT5A (dimer) -0.14 0.4 -10000 0 -0.99 66 66
GZMA -0.11 0.4 -10000 0 -1.1 48 48
GZMB -0.11 0.39 -10000 0 -1.1 46 46
HLX 0.021 0.025 -10000 0 -10000 0 0
LCK -0.12 0.42 -10000 0 -1.1 57 57
TCR/CD3/MHC II/CD4 -0.15 0.29 -10000 0 -0.68 80 80
IL2/IL2R -0.008 0.17 -10000 0 -0.54 36 36
MAPK14 -0.083 0.37 0.46 1 -0.89 63 64
CCR5 -0.092 0.4 -10000 0 -1.1 46 46
IL1B -0.035 0.2 -10000 0 -0.7 38 38
STAT6 -0.007 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.007 0.08 -10000 0 -0.69 5 5
CD8A -0.027 0.18 -10000 0 -0.65 36 36
CD8B -0.056 0.22 -10000 0 -0.65 54 54
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.026 0.14 0.4 29 -10000 0 29
IL2RB 0.003 0.092 -10000 0 -0.58 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.32 -10000 0 -0.77 61 61
IL2RG -0.012 0.14 -10000 0 -0.63 21 21
IL12 -0.033 0.18 -10000 0 -0.52 54 54
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.014 0.13 -10000 0 -0.68 17 17
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.053 0.22 -10000 0 -0.68 50 50
IL12/IL12R/TYK2/JAK2 -0.14 0.5 -10000 0 -1.2 62 62
MAP2K3 -0.085 0.37 -10000 0 -0.9 60 60
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.092 0.38 -10000 0 -0.92 63 63
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.093 -10000 0 -0.68 7 7
IL18RAP -0.003 0.14 -10000 0 -0.68 20 20
IL12Rbeta1/TYK2 0.024 0.065 -10000 0 -0.46 4 4
EOMES -0.12 0.4 -10000 0 -1.3 47 47
STAT1 (dimer) -0.12 0.36 -10000 0 -0.8 80 80
T cell proliferation -0.05 0.26 -10000 0 -0.62 61 61
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.097 -10000 0 -0.58 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.28 -10000 0 -0.67 65 65
ATF2 -0.085 0.34 -10000 0 -0.79 67 67
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.02 0.064 -9999 0 -0.68 4 4
EGF/EGFR -0.015 0.15 -9999 0 -0.37 73 73
EGF/EGFR dimer/SHC/GRB2/SOS1 0.005 0.16 -9999 0 -0.38 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.034 -9999 0 -0.68 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.074 0.24 -9999 0 -0.67 68 68
EGF/EGFR dimer/SHC -0.022 0.17 -9999 0 -0.43 71 71
mol:GDP 0 0.15 -9999 0 -0.38 65 65
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.019 0.072 -9999 0 -0.68 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.012 0.14 -9999 0 -0.35 65 65
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP 0.001 0.15 -9999 0 -0.36 65 65
FRAP1 -0.05 0.13 -9999 0 -0.36 65 65
EGF/EGFR dimer -0.042 0.19 -9999 0 -0.5 71 71
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.062 -9999 0 -0.51 6 6
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.005 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.12 -10000 0 -0.36 22 22
NFATC4 -0.02 0.088 0.3 3 -0.28 38 41
ERBB2IP 0.027 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.016 0.11 -10000 0 -0.35 40 40
JUN -0.005 0.097 0.37 10 -0.2 7 17
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.026 0.1 -10000 0 -0.34 42 42
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.002 0.13 -10000 0 -0.4 42 42
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.005 -10000 0 -10000 0 0
MAPK10 -0.01 0.066 0.28 3 -0.39 1 4
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.017 0.12 -10000 0 -0.38 40 40
RAF1 -0.011 0.13 0.36 10 -0.38 21 31
ErbB2/ErbB3/neuregulin 2 -0.027 0.15 -10000 0 -0.42 59 59
STAT3 0.026 0.082 -10000 0 -0.86 4 4
cell migration 0.008 0.12 0.42 20 -0.28 4 24
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.16 0.32 0.42 2 -0.68 114 116
FOS -0.13 0.27 0.37 7 -0.5 150 157
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.11 -10000 0 -0.35 40 40
MAPK3 -0.081 0.24 0.41 4 -0.51 89 93
MAPK1 -0.17 0.31 0.44 2 -0.63 117 119
JAK2 -0.025 0.1 -10000 0 -0.34 39 39
NF2 -0.011 0.12 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.013 0.11 -10000 0 -0.34 43 43
NRG1 -0.038 0.2 -10000 0 -0.67 44 44
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.019 0.11 -10000 0 -0.33 45 45
MAPK9 -0.01 0.062 0.26 2 -10000 0 2
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.015 0.08 -10000 0 -0.63 7 7
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.08 -10000 0 -0.84 4 4
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.077 -10000 0 -0.25 38 38
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.077 0.19 0.4 2 -0.4 95 97
myelination -0.009 0.14 0.57 16 -0.27 37 53
PPP3CB -0.023 0.097 -10000 0 -0.32 40 40
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.11 -10000 0 -0.3 38 38
NRG2 -0.053 0.22 -10000 0 -0.68 53 53
mol:GDP -0.012 0.11 -10000 0 -0.34 43 43
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.13 0.36 7 -0.38 21 28
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.024 0.1 0.25 1 -0.34 41 42
MAP2K1 -0.076 0.23 0.36 1 -0.6 33 34
heart morphogenesis -0.016 0.11 -10000 0 -0.35 40 40
RAS family/GDP 0.015 0.12 -10000 0 -0.36 19 19
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.012 0.13 -10000 0 -0.65 18 18
CHRNE 0.007 0.038 0.19 11 -0.23 1 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.016 0.11 -10000 0 -0.35 40 40
CDC42 0.027 0.005 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.1 -10000 0 -0.68 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 245 245
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.026 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.044 0.071 -10000 0 -0.3 10 10
PRKG1 -0.16 0.31 -10000 0 -0.67 130 130
DUSP8 0.019 0.066 -10000 0 -0.68 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 126 126
apoptosis -0.042 0.068 -10000 0 -0.29 10 10
RAL/GTP 0.035 0.008 -10000 0 -10000 0 0
LYN 0.027 0.004 -10000 0 -10000 0 0
DUSP1 -0.083 0.26 -10000 0 -0.68 75 75
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.44 17 -0.33 33 50
BLK -0.19 0.31 -10000 0 -0.67 142 142
HCK 0.018 0.035 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.034 -10000 0 -0.68 1 1
TRAF6/MEKK3 0.031 0.03 -10000 0 -0.4 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.12 0.36 18 -0.33 10 28
positive regulation of innate immune response -0.043 0.17 0.47 18 -0.41 14 32
LCK 0.012 0.083 -10000 0 -0.68 6 6
p38alpha-beta/MKP7 -0.046 0.14 0.34 7 -0.48 7 14
p38alpha-beta/MKP5 -0.035 0.16 0.47 14 -0.46 9 23
PGK/cGMP -0.12 0.23 -10000 0 -0.5 130 130
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.098 0.18 0.28 3 -0.41 70 73
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.34 -10000 0 -0.66 266 266
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.01 0.17 -10000 0 -0.66 29 29
HDAC7 -0.068 0.11 -10000 0 -0.48 18 18
JUN -0.12 0.29 -10000 0 -0.67 103 103
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.077 -10000 0 -0.52 10 10
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.067 0.13 -10000 0 -0.5 19 19
MAP2K6 0.004 0.1 -10000 0 -0.68 10 10
BRM/BAF57 0.018 0.032 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.012 0.075 -10000 0 -0.58 2 2
NCOA2 -0.041 0.2 -10000 0 -0.68 42 42
CEBPA 0.019 0.072 -10000 0 -0.68 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.082 0.2 0.57 19 -0.47 19 38
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.12 0.28 -10000 0 -0.68 95 95
RXRs/9cRA 0.019 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.14 0.33 2 -0.54 17 19
AR/GR -0.12 0.18 0.28 2 -0.32 188 190
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.006 -10000 0 -0.011 184 184
MAPK8 -0.012 0.064 -10000 0 -0.52 7 7
T-DHT/AR/TIF2/CARM1 -0.13 0.18 0.34 3 -0.56 45 48
SRC -0.042 0.082 0.23 1 -0.45 14 15
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.36 0.55 0.38 2 -1.2 137 139
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.014 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.068 0.12 0.32 7 -0.54 15 22
TMPRSS2 -0.048 0.28 -10000 0 -1.1 33 33
RXRG -0.1 0.075 -10000 0 -0.68 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.011 9 9
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.014 0.09 -10000 0 -0.68 8 8
KLK2 -0.44 0.38 0.34 2 -0.76 273 275
AR -0.14 0.18 -10000 0 -0.35 192 192
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.035 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.032 136 -10000 0 136
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.012 0.034 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.097 0.13 0.33 4 -0.56 14 18
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.091 0.14 0.28 2 -0.43 48 50
T-DHT/AR/Hsp90 -0.069 0.12 0.33 7 -0.53 15 22
GSK3B 0.025 0.006 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.036 0.086 0.26 1 -0.46 15 16
SIRT1 0.025 0.032 -10000 0 -0.68 1 1
ZMIZ2 0.035 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.073 0.12 0.32 6 -0.55 15 21
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.012 0.022 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.001 0.1 -10000 0 -0.38 29 29
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.11 0.35 3 -0.46 3 6
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.12 -10000 0 -0.5 24 24
AP1 -0.14 0.3 -10000 0 -0.67 95 95
ILK -0.005 0.11 -10000 0 -0.4 28 28
bone resorption -0.006 0.12 -10000 0 -0.52 8 8
PTK2B 0.027 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.043 0.11 -10000 0 -0.37 29 29
ITGAV 0.026 0.045 -10000 0 -0.67 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.017 0.11 -10000 0 -0.5 20 20
alphaV/beta3 Integrin/Osteopontin 0.028 0.12 -10000 0 -0.44 30 30
MAP3K1 -0.007 0.11 -10000 0 -0.4 29 29
JUN -0.12 0.29 -10000 0 -0.67 103 103
MAPK3 -0.021 0.098 -10000 0 -0.38 29 29
MAPK1 -0.022 0.096 -10000 0 -0.37 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.017 0.12 -10000 0 -0.41 33 33
ITGB3 0.014 0.096 -10000 0 -0.64 10 10
NFKBIA -0.017 0.094 -10000 0 -0.37 29 29
FOS -0.16 0.31 -10000 0 -0.67 125 125
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.038 0.11 0.52 3 -0.61 1 4
NF kappa B1 p50/RelA 0.022 0.1 -10000 0 -0.51 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.029 0.087 -10000 0 -0.54 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.006 0.11 -10000 0 -0.4 29 29
VAV3 -0.014 0.12 0.4 1 -0.39 33 34
MAP3K14 -0.012 0.11 -10000 0 -0.4 29 29
ROCK2 -0.002 0.14 -10000 0 -0.66 20 20
SPP1 -0.029 0.15 -10000 0 -0.67 22 22
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.36 33 33
MMP2 -0.13 0.24 -10000 0 -0.56 88 88
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.039 0.1 -10000 0 -0.41 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.64 14 14
AKT1 -0.014 0.2 -10000 0 -0.78 29 29
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.01 0.2 -10000 0 -0.8 28 28
mol:Ca2+ -0.096 0.19 -10000 0 -0.42 114 114
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.15 -10000 0 -0.45 49 49
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.012 0.19 0.74 29 -10000 0 29
RhoA/GTP 0.005 0.073 -10000 0 -0.34 18 18
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.005 0.13 -10000 0 -0.56 18 18
regulation of stress fiber formation 0.008 0.086 0.37 4 -0.28 1 5
E2/ERA-ERB (dimer) 0.005 0.11 -10000 0 -0.44 25 25
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.009 0.087 -10000 0 -0.37 22 22
pseudopodium formation -0.008 0.086 0.28 1 -0.37 4 5
E2/ER alpha (dimer)/PELP1 0.008 0.095 -10000 0 -0.4 22 22
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.68 1 1
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.009 0.16 0.48 8 -0.58 23 31
E2/ER beta (dimer) 0.015 0.048 -10000 0 -0.51 4 4
mol:GDP 0.001 0.11 -10000 0 -0.47 24 24
mol:NADP 0.009 0.16 0.48 8 -0.58 23 31
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 114 114
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.099 0.2 -10000 0 -0.45 115 115
PLCB2 -0.1 0.21 -10000 0 -0.45 115 115
IGF1 -0.13 0.29 -10000 0 -0.67 106 106
mol:L-citrulline 0.009 0.16 0.48 8 -0.58 23 31
RHOA 0.027 0.003 -10000 0 -10000 0 0
Gai/GDP 0.002 0.15 -10000 0 -0.67 21 21
JNK cascade 0.015 0.048 -10000 0 -0.51 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.021 0.064 -10000 0 -0.68 4 4
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.65 23 23
Gq family/GDP/Gbeta gamma -0.058 0.19 -10000 0 -0.67 26 26
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.1 -10000 0 -0.63 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.55 19 19
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.011 0.11 -10000 0 -0.49 23 23
STRN -0.015 0.16 -10000 0 -0.66 29 29
GNAL -0.06 0.23 -10000 0 -0.66 61 61
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.041 -10000 0 -0.43 4 4
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.033 -10000 0 -0.68 1 1
HBEGF -0.017 0.14 0.49 2 -0.55 19 21
cAMP biosynthetic process -0.041 0.16 -10000 0 -0.38 77 77
SRC -0.004 0.13 -10000 0 -0.63 12 12
PI3K 0.036 0.044 -10000 0 -0.51 3 3
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.03 0.11 -10000 0 -0.45 21 21
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.071 0.16 -10000 0 -0.5 29 29
Gs family/GTP -0.031 0.16 -10000 0 -0.39 77 77
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.01 0.15 0.48 8 -0.55 23 31
mol:DAG -0.1 0.2 -10000 0 -0.44 114 114
Gs family/GDP/Gbeta gamma -0.027 0.14 -10000 0 -0.44 25 25
MSN -0.009 0.092 0.29 1 -0.4 4 5
Gq family/GTP -0.1 0.22 -10000 0 -0.47 116 116
mol:PI-3-4-5-P3 -0.009 0.2 -10000 0 -0.76 28 28
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.01 0.15 0.55 23 -0.48 8 31
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.11 -10000 0 -0.44 24 24
NOS3 0.002 0.16 0.49 2 -0.62 23 25
GNA11 0.016 0.08 -10000 0 -0.63 7 7
MAPKKK cascade -0.015 0.18 0.37 1 -0.6 28 29
E2/ER alpha (dimer)/PELP1/Src 0 0.14 -10000 0 -0.57 20 20
ruffle organization -0.008 0.086 0.28 1 -0.37 4 5
ROCK2 -0.002 0.11 0.36 5 -0.34 32 37
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.032 0.16 -10000 0 -0.61 20 20
MMP2 -0.004 0.13 0.34 1 -0.6 13 14
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.061 0.24 30 -10000 0 30
RFC1 0.014 0.063 0.24 32 -10000 0 32
PRKDC 0.015 0.066 0.25 33 -10000 0 33
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.004 0.098 -10000 0 -0.76 6 6
FASLG/FAS/FADD/FAF1 -0.015 0.093 0.24 4 -0.34 29 33
MAP2K4 -0.031 0.17 0.32 2 -0.51 26 28
mol:ceramide -0.021 0.13 -10000 0 -0.44 31 31
GSN 0.013 0.061 0.24 30 -10000 0 30
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.12 -10000 0 -0.43 30 30
FAS 0.019 0.019 -10000 0 -10000 0 0
BID -0.018 0.035 0.28 3 -10000 0 3
MAP3K1 -0.011 0.12 0.26 4 -0.4 20 24
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.013 0.065 0.25 30 -10000 0 30
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.019 0.19 -10000 0 -0.47 70 70
ARHGDIB 0.015 0.068 0.25 35 -10000 0 35
FADD 0.019 0.019 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.061 -10000 0 -0.24 30 30
NFKB1 -0.02 0.1 -10000 0 -0.5 4 4
MAPK8 -0.07 0.23 0.4 2 -0.48 99 101
DFFA 0.014 0.063 0.24 32 -10000 0 32
DNA fragmentation during apoptosis 0.014 0.063 0.24 32 -10000 0 32
FAS/FADD/MET 0.042 0.042 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.017 0.061 -10000 0 -0.67 3 3
FAF1 0.018 0.021 -10000 0 -10000 0 0
PARP1 0.018 0.079 0.29 33 -10000 0 33
DFFB 0.014 0.063 0.24 32 -10000 0 32
CHUK -0.018 0.092 -10000 0 -0.52 3 3
FASLG -0.031 0.17 -10000 0 -0.68 29 29
FAS/FADD 0.028 0.028 -10000 0 -10000 0 0
HGF -0.074 0.24 -10000 0 -0.68 68 68
LMNA 0.013 0.068 0.25 30 -10000 0 30
CASP6 0.014 0.063 0.24 32 -10000 0 32
CASP10 0.019 0.019 -10000 0 -10000 0 0
CASP3 0.018 0.078 0.3 34 -10000 0 34
PTPN13 0.02 0.071 -10000 0 -0.68 5 5
CASP8 -0.012 0.034 0.4 3 -10000 0 3
IL6 -0.23 0.53 -10000 0 -1.3 98 98
MET -0.029 0.072 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.13 -10000 0 -0.44 31 31
activation of caspase activity by cytochrome c -0.018 0.035 0.28 3 -10000 0 3
PAK2 0.014 0.063 0.24 33 -10000 0 33
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.015 -10000 0 -10000 0 0
CCL5 -0.018 0.16 -10000 0 -0.68 28 28
SDCBP 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.038 0.14 -10000 0 -0.43 39 39
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.032 0.14 -10000 0 -0.54 22 22
Syndecan-1/Syntenin -0.031 0.14 -10000 0 -0.55 22 22
MAPK3 -0.03 0.12 -10000 0 -0.51 20 20
HGF/MET -0.078 0.19 -10000 0 -0.52 68 68
TGFB1/TGF beta receptor Type II 0.024 0.015 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.032 0.14 -10000 0 -0.53 22 22
Syndecan-1/RANTES -0.05 0.19 -10000 0 -0.6 41 41
Syndecan-1/CD147 -0.015 0.14 -10000 0 -0.54 21 21
Syndecan-1/Syntenin/PIP2 -0.031 0.14 -10000 0 -0.53 22 22
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.03 0.13 -10000 0 -0.52 22 22
MMP7 -0.078 0.16 -10000 0 -0.66 25 25
HGF -0.074 0.24 -10000 0 -0.68 68 68
Syndecan-1/CASK -0.045 0.13 -10000 0 -0.45 34 34
Syndecan-1/HGF/MET -0.075 0.21 -10000 0 -0.51 70 70
regulation of cell adhesion -0.032 0.12 -10000 0 -0.51 18 18
HPSE 0.008 0.1 -10000 0 -0.64 10 10
positive regulation of cell migration -0.038 0.14 -10000 0 -0.43 39 39
SDC1 -0.038 0.14 -10000 0 -0.44 39 39
Syndecan-1/Collagen -0.038 0.14 -10000 0 -0.43 39 39
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
MAPK1 -0.031 0.12 -10000 0 -0.53 19 19
homophilic cell adhesion -0.035 0.14 0.43 2 -0.46 32 34
MMP1 -0.045 0.073 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.065 0.17 0.43 10 -0.42 38 48
IKBKB 0.01 0.12 0.48 15 -0.31 7 22
AKT1 0 0.16 0.5 27 -0.24 14 41
IKBKG -0.003 0.12 0.44 15 -0.34 15 30
CALM1 -0.021 0.094 0.41 3 -0.4 8 11
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
MAP3K1 -0.012 0.17 0.48 11 -0.53 20 31
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.093 0.33 1 -0.4 9 10
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.16 0.56 11 -0.26 93 104
LYN 0.027 0.004 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.066 0.18 -10000 0 -0.5 61 61
CD22 -0.067 0.17 -10000 0 -0.42 79 79
CAMK2G -0.018 0.091 0.36 4 -0.43 5 9
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.036 0.12 -10000 0 -0.34 54 54
GO:0007205 -0.024 0.095 0.34 1 -0.42 9 10
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.018 0.093 0.36 3 -0.42 7 10
NFATC1 -0.038 0.14 0.39 7 -0.43 22 29
B-cell antigen/BCR complex -0.066 0.18 -10000 0 -0.5 61 61
PAG1/CSK 0.038 0.026 -10000 0 -0.51 1 1
NFKBIB 0.019 0.046 0.22 12 -0.13 8 20
HRAS -0.017 0.096 0.31 4 -0.36 8 12
NFKBIA 0.019 0.047 0.22 12 -0.13 8 20
NF-kappa-B/RelA/I kappa B beta 0.024 0.043 0.22 12 -10000 0 12
RasGAP/Csk -0.001 0.18 -10000 0 -0.41 68 68
mol:GDP -0.023 0.093 0.29 1 -0.4 10 11
PTEN 0.026 0.018 -10000 0 -0.36 1 1
CD79B 0.008 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.043 0.22 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.034 0.16 0.45 5 -0.48 19 24
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.022 0.091 0.34 1 -0.4 8 9
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.1 0.18 0.46 7 -0.36 126 133
CHUK 0.007 0.11 0.4 16 -0.33 8 24
IBTK 0.027 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.1 -10000 0 -0.45 8 8
PTPN6 -0.062 0.16 -10000 0 -0.4 76 76
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.036 0.17 7 -0.12 10 17
VAV2 -0.053 0.15 -10000 0 -0.63 14 14
ubiquitin-dependent protein catabolic process 0.023 0.046 0.22 12 -0.12 7 19
BTK -0.04 0.24 -10000 0 -0.98 30 30
CD19 -0.058 0.15 -10000 0 -0.4 63 63
MAP4K1 0.009 0.079 -10000 0 -0.68 5 5
CD72 0.025 0.012 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.68 1 1
MAPK14 -0.005 0.15 0.45 13 -0.45 19 32
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.015 0.094 -10000 0 -0.43 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.047 0.18 -10000 0 -0.42 73 73
RAF1 -0.014 0.095 0.33 7 -0.4 4 11
RasGAP/p62DOK/SHIP -0.004 0.17 -10000 0 -0.39 68 68
CD79A -0.097 0.23 -10000 0 -0.66 62 62
re-entry into mitotic cell cycle -0.057 0.15 0.55 11 -0.26 94 105
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.1 0.39 14 -0.42 2 16
MAPK1 -0.01 0.087 0.36 8 -0.4 2 10
CD72/SHP1 -0.044 0.17 0.28 4 -0.46 39 43
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.01 0.16 0.49 12 -0.49 18 30
actin cytoskeleton organization -0.042 0.14 0.34 2 -0.53 13 15
NF-kappa-B/RelA 0.049 0.076 0.38 12 -0.2 2 14
Calcineurin 0.009 0.09 -10000 0 -0.41 4 4
PI3K -0.06 0.14 -10000 0 -0.45 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.097 -10000 0 -0.44 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.021 0.22 -10000 0 -0.92 20 20
DAPP1 -0.042 0.25 -10000 0 -1.1 19 19
cytokine secretion -0.035 0.13 0.38 7 -0.4 22 29
mol:DAG -0.022 0.091 0.34 1 -0.4 8 9
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.091 0.33 7 -0.46 2 9
B-cell antigen/BCR complex/FcgammaRIIB -0.052 0.19 -10000 0 -0.44 76 76
mol:PI-3-4-5-P3 -0.053 0.096 -10000 0 -0.36 15 15
ETS1 -0.014 0.089 0.42 4 -0.41 4 8
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.013 0.15 -10000 0 -0.38 58 58
B-cell antigen/BCR complex/LYN -0.046 0.16 -10000 0 -0.42 64 64
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 -0.046 0.14 0.36 1 -0.59 12 13
B-cell antigen/BCR complex/LYN/SYK -0.036 0.19 -10000 0 -0.45 64 64
CARD11 -0.035 0.11 0.37 5 -0.42 16 21
FCGR2B -0.009 0.15 -10000 0 -0.68 23 23
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.019 0.096 0.43 18 -0.13 6 24
PTPRC -0.007 0.14 -10000 0 -0.68 19 19
PDPK1 -0.027 0.087 0.24 10 -0.26 16 26
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.004 -10000 0 -10000 0 0
POU2F2 0.02 0.034 0.16 16 -10000 0 16
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.003 0.067 -10000 0 -0.26 6 6
AP1 -0.12 0.26 -10000 0 -0.54 104 104
mol:PIP3 0.026 0.18 0.62 20 -0.37 28 48
IKBKB 0.037 0.17 0.66 23 -0.24 12 35
AKT1 -0.007 0.13 0.32 24 -0.36 27 51
IKBKG 0.04 0.18 0.67 25 -0.26 8 33
MS4A2 -0.014 0.062 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.056 -10000 0 -0.68 3 3
MAP3K1 0.024 0.12 0.45 14 -0.4 7 21
mol:Ca2+ 0.032 0.17 0.55 26 -0.28 28 54
LYN 0.027 0.01 -10000 0 -10000 0 0
CBLB -0.001 0.065 -10000 0 -0.24 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.16 -10000 0 -0.4 75 75
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 33 -0.37 30 63
PTPN13 0.01 0.14 0.48 2 -0.63 14 16
PTPN11 0.022 0.036 -10000 0 -0.7 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.03 0.16 0.63 20 -0.36 7 27
SYK 0.025 0.013 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 -10000 0 -0.38 28 28
LAT -0.004 0.07 -10000 0 -0.27 11 11
PAK2 0.016 0.1 0.32 8 -0.39 11 19
NFATC2 -0.1 0.23 -10000 0 -0.61 80 80
HRAS 0.011 0.1 0.25 1 -0.43 10 11
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.006 0.094 -10000 0 -0.7 6 6
Fc epsilon R1 0.005 0.13 -10000 0 -0.44 33 33
Antigen/IgE/Fc epsilon R1 0.008 0.12 -10000 0 -0.41 32 32
mol:GDP 0.001 0.11 -10000 0 -0.46 14 14
JUN -0.12 0.29 -10000 0 -0.67 103 103
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.07 -10000 0 -0.23 29 29
CHUK 0.035 0.16 0.63 23 -0.25 11 34
KLRG1 -0.009 0.078 -10000 0 -0.26 37 37
VAV1 -0.004 0.074 0.21 1 -0.34 7 8
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.064 -10000 0 -0.24 8 8
negative regulation of mast cell degranulation 0.005 0.081 -10000 0 -0.28 15 15
BTK -0.007 0.13 -10000 0 -0.51 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.019 0.15 -10000 0 -0.46 40 40
GAB2/PI3K/SHP2 -0.029 0.1 -10000 0 -0.38 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.073 -10000 0 -0.26 30 30
RAF1 0.013 0.086 -10000 0 -0.86 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.021 0.17 -10000 0 -0.49 42 42
FCER1G 0.018 0.035 -10000 0 -0.14 4 4
FCER1A -0.034 0.18 -10000 0 -0.68 33 33
Antigen/IgE/Fc epsilon R1/Fyn 0.023 0.12 -10000 0 -0.38 32 32
MAPK3 0.021 0.085 -10000 0 -0.78 4 4
MAPK1 -0.013 0.11 -10000 0 -0.73 6 6
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0 0.18 -10000 0 -0.64 28 28
DUSP1 -0.083 0.26 -10000 0 -0.68 75 75
NF-kappa-B/RelA 0.015 0.048 -10000 0 -0.17 3 3
actin cytoskeleton reorganization 0.012 0.13 0.4 2 -0.69 11 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.098 -10000 0 -0.45 8 8
FER -0.004 0.072 -10000 0 -0.31 8 8
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.044 0.15 -10000 0 -0.47 54 54
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.009 0.12 0.4 8 -0.52 10 18
cytokine secretion 0.004 0.03 -10000 0 -10000 0 0
SPHK1 -0.001 0.067 0.23 2 -0.27 3 5
PTK2 0.012 0.14 0.41 2 -0.74 11 13
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.006 0.11 -10000 0 -0.39 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.033 0.18 0.7 18 -0.38 20 38
MAP2K2 0.019 0.091 -10000 0 -0.8 4 4
MAP2K1 0.011 0.08 -10000 0 -0.8 4 4
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.083 -10000 0 -0.31 16 16
MAP2K4 -0.009 0.2 -10000 0 -0.84 24 24
Fc epsilon R1/FcgammaRIIB 0.005 0.18 -10000 0 -0.52 42 42
mol:Choline -0.009 0.13 0.32 33 -0.37 30 63
SHC/Grb2/SOS1 0.036 0.077 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.017 0.13 0.49 4 -0.67 10 14
HCLS1 -0.002 0.065 -10000 0 -0.24 8 8
PRKCB 0.034 0.18 0.67 23 -0.32 17 40
FCGR2B -0.009 0.15 -10000 0 -0.68 23 23
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.005 0.083 -10000 0 -0.29 15 15
LCP2 0.024 0.019 -10000 0 -10000 0 0
PLA2G4A -0.025 0.12 -10000 0 -0.4 36 36
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 33 -0.37 30 63
IKK complex 0.043 0.18 0.69 25 -0.21 3 28
WIPF1 0.027 0.004 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.017 0.13 -10000 0 -0.42 34 34
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.087 0.42 1 -0.46 1 2
AP1 -0.16 0.3 -10000 0 -0.55 156 156
mol:PIP3 -0.012 0.093 -10000 0 -0.35 30 30
AKT1 0.03 0.099 0.32 5 -0.57 2 7
PTK2B -0.01 0.089 0.24 2 -0.36 12 14
RHOA 0.014 0.042 -10000 0 -10000 0 0
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.073 0.28 9 -10000 0 9
MAGI3 0.025 0.032 -10000 0 -0.67 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.01 0.1 -10000 0 -0.35 37 37
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.002 0.1 0.38 9 -0.37 9 18
NF kappa B1 p50/RelA -0.019 0.1 -10000 0 -0.44 10 10
endothelial cell migration -0.017 0.15 -10000 0 -0.52 34 34
ADCY4 -0.032 0.15 -10000 0 -0.52 36 36
ADCY5 -0.058 0.17 -10000 0 -0.54 42 42
ADCY6 -0.032 0.15 -10000 0 -0.52 36 36
ADCY7 -0.032 0.15 -10000 0 -0.52 36 36
ADCY1 -0.033 0.15 -10000 0 -0.51 38 38
ADCY2 -0.053 0.17 -10000 0 -0.54 40 40
ADCY3 -0.031 0.15 -10000 0 -0.53 35 35
ADCY8 -0.04 0.15 -10000 0 -0.52 37 37
ADCY9 -0.032 0.15 -10000 0 -0.52 36 36
GSK3B -0.009 0.087 0.37 2 -0.4 7 9
arachidonic acid secretion -0.032 0.15 -10000 0 -0.49 37 37
GNG2 0.025 0.032 -10000 0 -0.67 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.027 0.15 -10000 0 -0.47 47 47
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.005 0.097 0.45 6 -0.52 1 7
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.014 0.18 -10000 0 -0.78 22 22
JUN -0.12 0.29 -10000 0 -0.67 103 103
LPA/LPA2/NHERF2 0.034 0.017 -10000 0 -10000 0 0
TIAM1 0 0.21 -10000 0 -0.92 23 23
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
mol:IP3 -0.01 0.066 0.36 2 -10000 0 2
PLCB3 0.027 0.034 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 125 125
positive regulation of mitosis -0.032 0.15 -10000 0 -0.49 37 37
LPA/LPA1-2-3 0.017 0.12 -10000 0 -0.41 30 30
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.001 0.1 0.38 3 -0.39 12 15
GNAZ -0.016 0.12 -10000 0 -0.43 36 36
EGFR/PI3K-beta/Gab1 -0.002 0.1 -10000 0 -0.36 30 30
positive regulation of dendritic cell cytokine production 0.016 0.12 -10000 0 -0.4 30 30
LPA/LPA2/MAGI-3 0.034 0.028 -10000 0 -0.45 1 1
ARHGEF1 0.004 0.1 0.36 3 -0.39 24 27
GNAI2 -0.014 0.13 -10000 0 -0.44 35 35
GNAI3 -0.013 0.12 -10000 0 -0.43 37 37
GNAI1 -0.014 0.12 -10000 0 -0.43 36 36
LPA/LPA3 0.015 0.024 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.017 0.14 -10000 0 -0.47 41 41
HB-EGF/EGFR -0.019 0.13 -10000 0 -0.44 39 39
HBEGF -0.035 0.14 -10000 0 -0.49 38 38
mol:DAG -0.01 0.066 0.36 2 -10000 0 2
cAMP biosynthetic process -0.037 0.17 0.41 11 -0.46 50 61
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.007 0.093 0.37 7 -0.52 1 8
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.033 -10000 0 -10000 0 0
LPAR1 -0.025 0.18 -10000 0 -0.6 41 41
IL8 -0.083 0.17 0.32 2 -0.46 39 41
PTK2 -0.003 0.11 -10000 0 -0.4 26 26
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.01 0.1 -10000 0 -0.36 37 37
EGFR 0.02 0.064 -10000 0 -0.68 4 4
PLCG1 -0.012 0.062 -10000 0 -0.3 2 2
PLD2 -0.003 0.1 -10000 0 -0.39 25 25
G12/G13 0.019 0.12 -10000 0 -0.4 33 33
PI3K-beta 0.004 0.09 -10000 0 -0.68 2 2
cell migration 0.018 0.074 -10000 0 -0.25 16 16
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN -0.001 0.1 0.26 2 -0.4 12 14
HRAS/GTP -0.029 0.15 -10000 0 -0.5 37 37
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
PRKCE 0.021 0.064 -10000 0 -0.68 4 4
PRKCD -0.006 0.086 0.35 10 -10000 0 10
Gi(beta/gamma) -0.026 0.14 -10000 0 -0.51 34 34
mol:LPA 0.002 0.017 -10000 0 -0.2 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.017 0.12 -10000 0 -0.42 14 14
MAPKKK cascade -0.032 0.15 -10000 0 -0.49 37 37
contractile ring contraction involved in cytokinesis 0.016 0.046 0.28 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.065 0.15 -10000 0 -0.35 101 101
GNA15 0.013 0.027 -10000 0 -0.36 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.004 0.096 0.35 7 -0.39 9 16
GNA11 0.012 0.044 -10000 0 -0.32 7 7
Rac1/GTP 0.014 0.19 -10000 0 -0.83 22 22
MMP2 -0.018 0.15 -10000 0 -0.52 34 34
Syndecan-4-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
PTK2 -0.008 0.11 -10000 0 -0.75 7 7
Syndecan-4/Syndesmos -0.036 0.16 -10000 0 -0.55 38 38
positive regulation of JNK cascade -0.05 0.19 -10000 0 -0.57 40 40
Syndecan-4/ADAM12 -0.044 0.16 -10000 0 -0.56 38 38
CCL5 -0.018 0.16 -10000 0 -0.68 28 28
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
PLG 0.009 0.03 -10000 0 -10000 0 0
ADAM12 -0.01 0.064 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.057 0.03 -10000 0 -0.18 4 4
Syndecan-4/Laminin alpha1 -0.058 0.18 -10000 0 -0.6 37 37
Syndecan-4/CXCL12/CXCR4 -0.053 0.2 -10000 0 -0.61 40 40
Syndecan-4/Laminin alpha3 -0.047 0.17 -10000 0 -0.58 36 36
MDK -0.018 0.068 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.036 0.16 -10000 0 -0.56 38 38
Syndecan-4/Midkine -0.046 0.16 -10000 0 -0.56 37 37
FZD7 0.022 0.052 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.011 0.16 -10000 0 -0.52 37 37
THBS1 0.016 0.04 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.051 0.16 -10000 0 -0.56 38 38
positive regulation of MAPKKK cascade -0.05 0.19 -10000 0 -0.57 40 40
Syndecan-4/TACI -0.12 0.21 -10000 0 -0.62 38 38
CXCR4 0.026 0.011 -10000 0 -10000 0 0
cell adhesion -0.005 0.072 0.19 11 -0.31 21 32
Syndecan-4/Dynamin -0.036 0.16 -10000 0 -0.55 38 38
Syndecan-4/TSP1 -0.037 0.16 -10000 0 -0.56 38 38
Syndecan-4/GIPC -0.036 0.16 -10000 0 -0.55 38 38
Syndecan-4/RANTES -0.057 0.2 -10000 0 -0.66 39 39
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.021 0.18 -10000 0 -0.67 33 33
LAMA3 -0.001 0.13 -10000 0 -0.68 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.01 0.2 0.76 19 -0.62 21 40
Syndecan-4/alpha-Actinin -0.034 0.16 -10000 0 -0.56 37 37
TFPI -0.014 0.16 -10000 0 -0.66 28 28
F2 0.011 0.028 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.072 0.18 -10000 0 -0.6 37 37
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.032 0.091 -10000 0 -0.68 4 4
Syndecan-4/CXCL12 -0.071 0.2 -10000 0 -0.63 40 40
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CXCL12 -0.048 0.22 -10000 0 -0.68 51 51
TNFRSF13B -0.14 0.29 -10000 0 -0.67 108 108
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.032 -10000 0 -0.68 1 1
Syndecan-4/PI-4-5-P2 -0.047 0.16 -10000 0 -0.56 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.076 0.074 -10000 0 -0.16 12 12
cell migration -0.026 0.012 -10000 0 -10000 0 0
PRKCD 0.025 0.023 -10000 0 -10000 0 0
vasculogenesis -0.036 0.15 -10000 0 -0.54 38 38
SDC4 -0.047 0.16 -10000 0 -0.59 38 38
Syndecan-4/Tenascin C -0.053 0.17 -10000 0 -0.59 38 38
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.035 0.16 -10000 0 -0.56 38 38
MMP9 -0.039 0.19 -10000 0 -0.66 38 38
Rac1/GTP -0.005 0.074 0.19 11 -0.32 21 32
cytoskeleton organization -0.034 0.15 -10000 0 -0.53 38 38
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.054 0.18 -10000 0 -0.58 39 39
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.056 -10000 0 -10000 0 0
CRKL -0.015 0.091 0.36 1 -0.42 1 2
mol:PIP3 -0.002 0.017 0.33 1 -10000 0 1
AKT1 0.003 0.056 0.37 2 -0.45 3 5
PTK2B 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.002 0.11 0.44 9 -0.4 1 10
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
HGF/MET/SHIP2 -0.015 0.18 -10000 0 -0.45 68 68
MAP3K5 0.013 0.13 0.5 14 -0.41 5 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.002 0.17 -10000 0 -0.42 64 64
AP1 -0.18 0.33 -10000 0 -0.65 147 147
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 -10000 0 -0.81 149 149
STAT3 (dimer) -0.019 0.11 -10000 0 -0.3 26 26
GAB1/CRKL/SHP2/PI3K 0.024 0.11 -10000 0 -0.5 3 3
INPP5D 0.019 0.033 -10000 0 -10000 0 0
CBL/CRK 0.015 0.12 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
ELK1 0.035 0.14 0.44 28 -0.23 4 32
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.069 -10000 0 -0.24 5 5
PAK1 0.007 0.062 0.37 6 -0.4 2 8
HGF/MET/RANBP10 -0.016 0.18 -10000 0 -0.45 68 68
HRAS -0.02 0.13 -10000 0 -0.55 3 3
DOCK1 0 0.12 0.48 9 -0.4 4 13
GAB1 -0.012 0.097 0.26 1 -0.35 4 5
CRK -0.007 0.098 0.37 2 -0.43 1 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.19 -10000 0 -0.51 68 68
JUN -0.12 0.29 -10000 0 -0.67 103 103
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.031 0.086 -10000 0 -0.24 66 66
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.009 0.12 0.5 4 -0.51 3 7
GRB2/SHC 0.004 0.086 -10000 0 -0.28 1 1
FOS -0.16 0.31 -10000 0 -0.67 125 125
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.034 0.14 0.44 28 -0.23 4 32
HGF/MET/MUC20 -0.066 0.16 -10000 0 -0.45 68 68
cell migration 0.003 0.084 -10000 0 -0.27 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.005 0.056 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.11 -10000 0 -0.3 63 63
MET/MUC20 -0.017 0.047 -10000 0 -10000 0 0
RAP1B 0.011 0.13 0.57 13 -0.37 1 14
RAP1A 0.008 0.11 0.42 12 -0.37 1 13
HGF/MET/RANBP9 -0.014 0.18 -10000 0 -0.45 68 68
RAF1 -0.017 0.12 -10000 0 -0.49 2 2
STAT3 -0.02 0.11 -10000 0 -0.52 1 1
cell proliferation -0.025 0.15 -10000 0 -0.39 59 59
RPS6KB1 0 0.034 -10000 0 -0.22 2 2
MAPK3 -0.02 0.11 0.49 17 -10000 0 17
MAPK1 0.13 0.29 0.61 126 -10000 0 126
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.63 16 -0.65 7 23
SRC -0.021 0.1 -10000 0 -0.3 26 26
PI3K 0.003 0.094 -10000 0 -0.39 4 4
MET/Glomulin -0.007 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.011 0.12 0.34 1 -0.46 2 3
MET -0.029 0.072 -10000 0 -10000 0 0
MAP4K1 0.007 0.12 0.52 8 -0.43 6 14
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.008 0.12 0.34 1 -0.44 1 2
BAD 0.007 0.062 0.37 6 -0.4 2 8
MAP2K4 0.021 0.15 0.54 19 -0.4 4 23
SHP2/GRB2/SOS1/GAB1 0.017 0.099 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.026 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.008 -10000 0 -10000 0 0
HGS -0.029 0.078 -10000 0 -0.24 28 28
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.074 0.24 -10000 0 -0.68 68 68
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.099 -10000 0 -0.26 28 28
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.019 0.18 -10000 0 -0.46 68 68
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.14 -10000 0 -0.36 59 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -10000 0 -0.44 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.052 -10000 0 -0.29 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.008 0.071 -10000 0 -0.24 4 4
CaM/Ca2+ 0.014 0.13 -10000 0 -0.33 59 59
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.012 0.13 -10000 0 -0.34 59 59
AKT1 -0.016 0.12 0.38 5 -0.38 6 11
MAP2K1 -0.024 0.12 0.29 2 -0.32 56 58
MAP3K11 -0.022 0.12 0.3 5 -0.34 59 64
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.073 -10000 0 -0.53 1 1
Rap1/GTP -0.02 0.094 -10000 0 -0.31 4 4
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.017 0.15 -10000 0 -0.37 58 58
CEBPB -0.059 0.19 0.52 6 -0.58 26 32
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.017 0.16 -10000 0 -0.74 5 5
STAT1 -0.021 0.13 0.32 6 -0.34 59 65
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.066 0.23 -10000 0 -0.68 59 59
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
STAT1 (dimer)/PIAS1 -0.006 0.12 0.3 4 -0.37 5 9
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.4 13 13
mol:Ca2+ 0.007 0.14 -10000 0 -0.35 59 59
MAPK3 -0.01 0.13 -10000 0 -0.59 8 8
STAT1 (dimer) 0.018 0.097 -10000 0 -0.34 3 3
MAPK1 -0.16 0.3 0.44 1 -0.67 115 116
JAK2 0.018 0.032 -10000 0 -0.4 1 1
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.041 0.18 0.5 9 -0.59 28 37
SMAD7 0.019 0.065 0.42 6 -10000 0 6
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.32 41 43
PI3K 0.012 0.13 -10000 0 -0.34 59 59
IFNG -0.066 0.23 -10000 0 -0.68 59 59
apoptosis -0.035 0.16 0.56 6 -0.46 35 41
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.012 0.034 -10000 0 -10000 0 0
CAMK2B 0.02 0.064 -10000 0 -0.68 4 4
FRAP1 -0.023 0.11 0.37 5 -0.36 6 11
PRKCD -0.011 0.13 0.43 10 -0.38 7 17
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.071 -10000 0 -0.24 4 4
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
IRF1 -0.014 0.086 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.011 0.12 0.3 1 -0.33 50 51
SOCS1 0.017 0.12 -10000 0 -1 6 6
mol:GDP -0.01 0.11 0.28 2 -0.31 41 43
CASP1 0.016 0.064 0.45 4 -0.32 2 6
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.058 0.35 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 0.12 -10000 0 -0.33 59 59
RAP1/GDP -0.005 0.1 -10000 0 -0.36 1 1
CBL -0.022 0.12 0.29 6 -0.34 59 65
MAP3K1 -0.022 0.12 0.3 2 -0.34 57 59
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.008 0.071 -10000 0 -0.24 4 4
PTPN11 -0.025 0.13 -10000 0 -0.36 59 59
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
Ceramide signaling 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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.017 0.12 -10000 0 -0.49 16 16
BAG4 0.025 0.032 -10000 0 -0.68 1 1
PKC zeta/ceramide -0.02 0.097 -10000 0 -0.29 34 34
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX -0.014 0.078 -10000 0 -0.35 21 21
RIPK1 0.027 0.002 -10000 0 -10000 0 0
AKT1 0.027 0.14 0.79 15 -10000 0 15
BAD -0.033 0.088 0.18 1 -0.28 34 35
SMPD1 -0.013 0.093 0.29 7 -0.23 62 69
RB1 -0.033 0.09 0.19 1 -0.31 29 30
FADD/Caspase 8 -0.006 0.12 -10000 0 -0.5 15 15
MAP2K4 -0.019 0.072 0.22 2 -0.39 7 9
NSMAF 0.027 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.083 -10000 0 -0.42 11 11
EGF -0.074 0.24 -10000 0 -0.67 68 68
mol:ceramide -0.037 0.098 -10000 0 -0.3 37 37
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.016 0.024 -10000 0 -0.51 1 1
ASAH1 0.025 0.032 -10000 0 -0.68 1 1
negative regulation of cell cycle -0.032 0.089 0.19 1 -0.3 29 30
cell proliferation -0.06 0.15 -10000 0 -0.32 103 103
BID -0.15 0.28 -10000 0 -0.61 121 121
MAP3K1 -0.028 0.078 0.19 1 -0.29 24 25
EIF2A -0.029 0.078 -10000 0 -0.45 10 10
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.07 -10000 0 -0.36 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.042 0.085 -10000 0 -0.38 12 12
Cathepsin D/ceramide -0.019 0.093 -10000 0 -0.28 34 34
FADD -0.017 0.12 -10000 0 -0.49 16 16
KSR1 -0.026 0.088 0.18 9 -0.29 28 37
MAPK8 -0.017 0.089 -10000 0 -0.38 16 16
PRKRA -0.034 0.091 -10000 0 -0.29 34 34
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 106 106
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.037 0.097 -10000 0 -0.29 37 37
CTSD 0.026 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.064 0.16 -10000 0 -0.35 103 103
PRKCD 0.027 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.016 0.024 -10000 0 -0.51 1 1
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.5 17 17
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.44 58 58
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.023 0.078 -10000 0 -0.39 11 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.071 0.17 24 -0.24 19 43
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
EIF2AK2 -0.031 0.084 -10000 0 -0.36 17 17
TNF-alpha/TNFR1A/FAN -0.005 0.16 -10000 0 -0.44 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.089 -10000 0 -0.51 6 6
MAP2K2 -0.015 0.066 -10000 0 -0.38 7 7
SMPD3 -0.019 0.11 -10000 0 -0.34 27 27
TNF -0.06 0.23 -10000 0 -0.68 57 57
PKC zeta/PAR4 0.038 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.015 0.11 0.25 67 -0.26 16 83
NF kappa B1/RelA/I kappa B alpha 0.075 0.023 -10000 0 -10000 0 0
AIFM1 -0.011 0.086 0.17 24 -0.27 26 50
BCL2 -0.024 0.18 -10000 0 -0.67 35 35
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.041 -10000 0 -0.82 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.82 1 1
mol:DAG -0.021 0.13 -10000 0 -0.4 48 48
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.06 -10000 0 -0.64 3 3
CaM/Ca2+ -0.006 0.13 -10000 0 -0.38 48 48
HIF1A 0.032 0.02 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.02 0.13 -10000 0 -0.4 46 46
PLCG1 -0.022 0.13 -10000 0 -0.4 48 48
NOS3 -0.014 0.12 -10000 0 -0.53 3 3
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.008 0.12 0.47 3 -0.5 3 6
FLT1 0.02 0.043 -10000 0 -0.91 1 1
PGF -0.043 0.21 -10000 0 -0.67 48 48
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.063 -10000 0 -0.64 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
eNOS/Hsp90 0.004 0.12 -10000 0 -0.74 1 1
endothelial cell proliferation -0.04 0.15 0.36 2 -0.44 48 50
mol:Ca2+ -0.021 0.13 -10000 0 -0.4 48 48
MAPK3 -0.041 0.14 0.36 2 -0.37 66 68
MAPK1 -0.044 0.13 0.36 1 -0.37 59 60
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.043 0.21 -10000 0 -0.67 48 48
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.013 0.095 -10000 0 -0.68 9 9
VEGFA homodimer 0.023 0.055 -10000 0 -0.67 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.064 -10000 0 -0.68 3 3
platelet activating factor biosynthetic process -0.044 0.13 -10000 0 -0.4 17 17
PI3K 0.015 0.14 -10000 0 -0.39 49 49
PRKCA -0.042 0.14 -10000 0 -0.39 66 66
PRKCB -0.035 0.13 -10000 0 -0.39 52 52
VEGFR1 homodimer/PLGF homodimer -0.013 0.14 -10000 0 -0.44 48 48
VEGFA 0.023 0.055 -10000 0 -0.68 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.021 0.13 -10000 0 -0.4 48 48
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.043 -10000 0 -0.91 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.001 0.14 0.55 4 -0.62 4 8
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
mol:PI-3-4-5-P3 0.014 0.14 -10000 0 -0.38 49 49
mol:L-citrulline -0.008 0.12 0.47 3 -0.5 3 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.062 -10000 0 -0.61 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.062 -10000 0 -0.64 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.026 0.14 -10000 0 -0.37 49 49
PDPK1 -0.017 0.13 0.34 3 -0.38 49 52
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.075 -10000 0 -0.75 3 3
mol:NADP -0.008 0.12 0.47 3 -0.5 3 6
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.061 -10000 0 -0.6 3 3
VEGFR1 homodimer/NRP2 0.026 0.047 -10000 0 -0.82 1 1
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.015 0.2 -10000 0 -0.93 20 20
NCK1/PAK1/Dok-R -0.029 0.089 -10000 0 -0.42 20 20
NCK1/Dok-R -0.005 0.25 -10000 0 -1.1 21 21
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
mol:beta2-estradiol 0 0.046 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 -0.011 0.055 0.27 13 -10000 0 13
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.009 0.23 -10000 0 -1 20 20
FN1 -0.081 0.067 -10000 0 -10000 0 0
PLD2 -0.026 0.24 -10000 0 -1.1 20 20
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GRB14 0.008 0.11 -10000 0 -0.65 13 13
ELK1 -0.027 0.22 -10000 0 -1 20 20
GRB7 0.001 0.055 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.005 0.25 -10000 0 -1.1 20 20
CDKN1A -0.024 0.16 0.49 4 -0.63 20 24
ITGA5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.006 0.24 -10000 0 -1.1 21 21
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.009 0.17 0.53 10 -0.67 20 30
PLG -0.033 0.25 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.014 0.19 -10000 0 -0.88 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 -10000 0 -0.81 16 16
BMX -0.036 0.25 -10000 0 -1.2 20 20
ANGPT1 -0.047 0.27 -10000 0 -1.3 18 18
tube development -0.039 0.17 0.49 2 -0.72 20 22
ANGPT4 -0.032 0.19 -10000 0 -0.68 39 39
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.027 0.27 -10000 0 -1.2 20 20
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.039 0.19 -10000 0 -0.82 20 20
mol:L-citrulline 0.009 0.17 0.53 10 -0.67 20 30
AGTR1 -0.25 0.34 -10000 0 -0.67 193 193
MAPK14 -0.027 0.25 -10000 0 -1.1 20 20
Tie2/SHP2 -0.003 0.18 -10000 0 -1.2 7 7
TEK 0.005 0.18 -10000 0 -1.4 7 7
RPS6KB1 -0.01 0.2 0.5 2 -0.88 20 22
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.51 193 193
Tie2/Ang1/GRB2 -0.018 0.26 -10000 0 -1.2 20 20
MAPK3 -0.022 0.22 -10000 0 -1 20 20
MAPK1 -0.031 0.22 -10000 0 -1 20 20
Tie2/Ang1/GRB7 -0.019 0.26 -10000 0 -1.2 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.032 0.25 -10000 0 -1.1 21 21
PI3K -0.023 0.23 -10000 0 -1.1 20 20
FES -0.031 0.25 -10000 0 -1.2 20 20
Crk/Dok-R -0.005 0.24 -10000 0 -1.1 21 21
Tie2/Ang1/ABIN2 -0.017 0.26 -10000 0 -1.2 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.006 0.19 0.5 4 -0.82 20 24
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.2 0.48 1 -0.89 20 21
Tie2/Ang2 -0.058 0.22 -10000 0 -1 20 20
Tie2/Ang1 -0.029 0.27 -10000 0 -1.2 20 20
FOXO1 -0.002 0.19 0.56 4 -0.83 20 24
ELF1 0.028 0.053 -10000 0 -0.59 3 3
ELF2 -0.025 0.24 -10000 0 -1.1 20 20
mol:Choline -0.023 0.23 -10000 0 -1.1 20 20
cell migration -0.014 0.056 -10000 0 -0.24 20 20
FYN -0.048 0.19 0.53 1 -0.83 20 21
DOK2 0.02 0.051 -10000 0 -0.68 2 2
negative regulation of cell cycle -0.021 0.15 0.45 6 -0.57 20 26
ETS1 0.026 0.047 -10000 0 -0.24 13 13
PXN 0 0.18 0.57 6 -0.72 20 26
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.003 0.19 0.58 7 -0.77 20 27
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.061 0.24 -10000 0 -0.6 72 72
MAPKKK cascade -0.023 0.23 -10000 0 -1.1 20 20
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.019 0.26 -10000 0 -1.2 20 20
NCK1 0.027 0.003 -10000 0 -10000 0 0
vasculogenesis 0.012 0.16 0.5 12 -0.6 20 32
mol:Phosphatidic acid -0.023 0.23 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.009 0.17 0.53 10 -0.67 20 30
Rac1/GTP -0.008 0.18 -10000 0 -0.82 20 20
MMP2 -0.031 0.25 -10000 0 -1.2 20 20
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.018 0.12 -10000 0 -0.44 21 21
BAG4 0.025 0.032 -10000 0 -0.68 1 1
BAD 0.007 0.068 0.36 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX 0.012 0.073 0.26 22 -10000 0 22
EnzymeConsortium:3.1.4.12 0.002 0.042 0.16 11 -0.1 19 30
IKBKB -0.017 0.12 0.29 1 -0.45 16 17
MAP2K2 0.016 0.096 0.36 20 -0.3 2 22
MAP2K1 0.01 0.086 0.32 20 -0.3 2 22
SMPD1 0.005 0.048 0.26 7 -0.16 2 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.012 0.13 -10000 0 -0.47 18 18
MAP2K4 0.017 0.1 0.35 26 -10000 0 26
protein ubiquitination -0.013 0.13 0.45 4 -0.46 15 19
EnzymeConsortium:2.7.1.37 0.017 0.11 0.38 25 -0.31 2 27
response to UV 0 0.002 0.006 27 -0.002 4 31
RAF1 0.011 0.088 0.32 21 -0.32 2 23
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.004 0.062 0.25 11 -0.16 15 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.08 0.33 17 -10000 0 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.091 0.34 19 -0.28 3 22
MAPK1 -0.005 0.093 0.34 16 -0.27 5 21
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.017 0.12 -10000 0 -0.44 20 20
KSR1 0.01 0.083 0.27 24 -0.28 3 27
MAPK8 0.012 0.11 0.39 22 -0.36 7 29
TRAF2 0.024 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.016 0.12 0.33 1 -0.44 16 17
TNF R/SODD 0.038 0.026 -10000 0 -0.51 1 1
TNF -0.059 0.23 -10000 0 -0.68 57 57
CYCS 0.019 0.083 0.25 28 -0.18 1 29
IKBKG -0.014 0.12 0.38 1 -0.45 14 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.018 0.13 -10000 0 -0.46 21 21
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
AIFM1 0.017 0.082 0.26 24 -0.18 2 26
TNF/TNF R/SODD -0.006 0.16 -10000 0 -0.44 58 58
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.008 0.13 -10000 0 -0.75 13 13
NSMAF -0.018 0.12 -10000 0 -0.44 20 20
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 4 31
BCL2 -0.024 0.18 -10000 0 -0.67 35 35
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.066 -10000 0 -0.59 5 5
alphaV beta3 Integrin 0.04 0.08 -10000 0 -0.48 10 10
PTK2 0.012 0.14 0.41 11 -0.5 11 22
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.01 0.048 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.029 0.17 -10000 0 -0.54 45 45
VEGFA 0.023 0.055 -10000 0 -0.68 3 3
ILK -0.029 0.17 -10000 0 -0.53 46 46
ROCK1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.03 0.16 -10000 0 -0.5 45 45
PTK2B 0.013 0.088 0.36 1 -0.43 14 15
alphaV/beta3 Integrin/JAM-A 0.006 0.14 -10000 0 -0.4 50 50
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.037 0.078 -10000 0 -0.46 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.089 0.24 -10000 0 -0.43 148 148
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.093 -10000 0 -0.41 5 5
alphaV/beta3 Integrin/Syndecan-1 0.04 0.08 -10000 0 -0.48 10 10
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.093 0.23 -10000 0 -0.43 148 148
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
alphaV/beta3 Integrin/Osteopontin 0.021 0.13 -10000 0 -0.43 33 33
RPS6KB1 -0.14 0.19 0.42 2 -0.4 148 150
TLN1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.051 0.13 -10000 0 -0.63 12 12
GPR124 0.027 0.004 -10000 0 -10000 0 0
MAPK1 -0.06 0.14 -10000 0 -0.58 19 19
PXN 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.027 0.12 -10000 0 -0.51 20 20
cell adhesion 0.031 0.076 -10000 0 -0.46 9 9
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.061 -10000 0 -0.52 5 5
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.055 -10000 0 -0.68 3 3
ITGB3 0.012 0.097 -10000 0 -0.64 10 10
IGF1 -0.13 0.29 -10000 0 -0.67 106 106
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.079 -10000 0 -0.48 10 10
apoptosis 0.024 0.045 -10000 0 -0.67 2 2
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.04 0.08 -10000 0 -0.48 10 10
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.1 -10000 0 -0.49 16 16
CSF1 0.015 0.09 -10000 0 -0.68 8 8
PIK3C2A -0.03 0.17 -10000 0 -0.53 48 48
PI4 Kinase/Pyk2 -0.014 0.12 -10000 0 -0.65 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.094 -10000 0 -0.46 14 14
FAK1/Vinculin 0.023 0.12 0.38 9 -0.45 6 15
alphaV beta3/Integrin/ppsTEM5 0.04 0.079 -10000 0 -0.48 10 10
RHOA 0.027 0.003 -10000 0 -10000 0 0
VTN -0.041 0.2 -10000 0 -0.68 44 44
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.042 0.08 -10000 0 -0.48 10 10
alphaV/beta3 Integrin/TGFBR2 0.038 0.085 -10000 0 -0.44 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.073 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.074 -10000 0 -0.44 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.035 0.086 -10000 0 -0.43 14 14
SDC1 0.025 0.014 -10000 0 -10000 0 0
VAV3 0.009 0.083 0.36 1 -0.43 14 15
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IRS1 -0.054 0.22 -10000 0 -0.68 55 55
FAK1/Paxillin 0.022 0.12 0.35 8 -0.4 10 18
cell migration 0.017 0.11 0.34 6 -0.41 6 12
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
PI3K 0.015 0.14 -10000 0 -0.38 51 51
SPP1 -0.032 0.15 -10000 0 -0.68 22 22
KDR 0.023 0.055 -10000 0 -0.68 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.045 -10000 0 -0.67 2 2
COL4A3 0.007 0.12 -10000 0 -0.65 14 14
angiogenesis -0.054 0.15 -10000 0 -0.51 32 32
Rac1/GTP 0.021 0.076 -10000 0 -0.4 14 14
EDIL3 0.007 0.09 -10000 0 -0.68 7 7
cell proliferation 0.037 0.084 -10000 0 -0.44 13 13
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
Jak2/Leptin Receptor -0.006 0.12 0.32 1 -0.37 30 31
PTP1B/AKT1 0.006 0.072 0.41 1 -0.32 4 5
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.001 0.087 0.34 11 -0.3 9 20
EGFR 0.015 0.066 -10000 0 -0.68 4 4
EGF/EGFR -0.034 0.16 -10000 0 -0.39 70 70
CSF1 0.015 0.09 -10000 0 -0.68 8 8
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.11 0.32 7 -0.36 19 26
Insulin Receptor/Insulin 0.016 0.067 -10000 0 -0.32 2 2
HCK 0.018 0.035 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.009 0.095 0.32 21 -0.3 4 25
EGF -0.073 0.24 -10000 0 -0.68 68 68
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.002 0.12 0.44 12 -0.32 9 21
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.028 0.14 0.27 1 -0.38 54 55
cell migration -0.001 0.087 0.3 9 -0.34 11 20
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.015 0.16 -10000 0 -0.68 25 25
ITGA2B -0.041 0.2 -10000 0 -0.67 46 46
CSF1R 0.023 0.036 -10000 0 -0.68 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
FGR 0.025 0.014 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.005 0.074 0.27 3 -0.3 6 9
Crk/p130 Cas 0.013 0.073 -10000 0 -0.31 4 4
DOK1 0.014 0.094 0.41 12 -0.36 4 16
JAK2 -0.011 0.13 0.33 7 -0.38 34 41
Jak2/Leptin Receptor/Leptin -0.013 0.14 -10000 0 -0.49 25 25
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.001 0.088 0.34 11 -0.3 9 20
LYN 0.027 0.004 -10000 0 -10000 0 0
CDH2 -0.072 0.13 -10000 0 -0.63 15 15
SRC 0.022 0.062 0.32 1 -0.44 5 6
ITGB3 0.011 0.097 -10000 0 -0.65 10 10
CAT1/PTP1B -0.059 0.16 0.43 14 -0.36 43 57
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.022 0.078 -10000 0 -0.46 4 4
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.013 0.14 -10000 0 -0.53 24 24
negative regulation of transcription -0.01 0.13 0.33 7 -0.37 34 41
FCGR2A 0.017 0.044 -10000 0 -0.68 1 1
FER 0.021 0.056 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.025 0.18 -10000 0 -0.53 53 53
BLK -0.19 0.31 -10000 0 -0.67 142 142
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.02 0.066 -10000 0 -0.6 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.09 0.18 0.37 5 -0.47 41 46
PRL -0.006 0.02 -10000 0 -10000 0 0
SOCS3 -0.052 0.32 -10000 0 -1.3 30 30
SPRY2 0.022 0.047 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.013 0.16 -10000 0 -0.44 55 55
CSF1/CSF1R 0.008 0.098 0.28 1 -0.45 11 12
Ras protein signal transduction 0.025 0.1 0.45 23 -10000 0 23
IRS1 -0.054 0.22 -10000 0 -0.68 55 55
INS 0.011 0.014 -10000 0 -10000 0 0
LEP 0.009 0.031 -10000 0 -10000 0 0
STAT5B 0.002 0.096 0.32 11 -0.3 15 26
STAT5A 0.002 0.096 0.32 11 -0.3 15 26
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.075 0.28 1 -0.34 7 8
CSN2 0 0.063 0.81 1 -10000 0 1
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
LAT 0.019 0.081 0.29 3 -0.46 10 13
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.083 -10000 0 -0.68 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.039 0.074 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.006 0.1 -10000 0 -0.52 11 11
alphaM/beta2 Integrin/GPIbA -0.002 0.12 -10000 0 -0.5 18 18
alphaM/beta2 Integrin/proMMP-9 -0.023 0.16 -10000 0 -0.49 41 41
PLAUR -0.021 0.068 -10000 0 -10000 0 0
HMGB1 0.007 0.037 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.011 0.087 -10000 0 -0.57 5 5
AGER -0.041 0.18 -10000 0 -0.7 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.017 0.036 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.041 0.2 -10000 0 -0.48 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
CYR61 -0.18 0.32 -10000 0 -0.67 139 139
TLN1 0.025 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.089 -10000 0 -0.37 9 9
RHOA 0.027 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.015 0.08 -10000 0 -0.67 6 6
MYH2 -0.032 0.098 -10000 0 -0.4 10 10
MST1R 0.02 0.065 -10000 0 -0.68 4 4
leukocyte activation during inflammatory response 0.011 0.082 -10000 0 -0.49 5 5
APOB 0.007 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.016 0.08 -10000 0 -0.63 7 7
JAM3 0.026 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.051 0.19 -10000 0 -0.47 71 71
alphaM/beta2 Integrin -0.025 0.09 -10000 0 -0.37 13 13
JAM3 homodimer 0.026 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.018 0.067 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.025 0.091 -10000 0 -0.37 14 14
cell adhesion -0.002 0.12 -10000 0 -0.49 18 18
NFKB1 -0.12 0.26 0.38 1 -0.49 137 138
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
Lipoprotein(a) 0.021 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.02 0.099 -10000 0 -0.47 10 10
IL6 -0.21 0.39 -10000 0 -0.95 97 97
ITGB2 -0.004 0.058 -10000 0 -0.71 1 1
elevation of cytosolic calcium ion concentration -0.022 0.1 -10000 0 -0.58 4 4
alphaM/beta2 Integrin/JAM2/JAM3 0.022 0.096 -10000 0 -0.48 9 9
JAM2 0.02 0.064 -10000 0 -0.68 4 4
alphaM/beta2 Integrin/ICAM1 0.029 0.11 -10000 0 -0.52 8 8
alphaM/beta2 Integrin/uPA/Plg 0.01 0.099 -10000 0 -0.59 4 4
RhoA/GTP -0.027 0.1 -10000 0 -0.34 27 27
positive regulation of phagocytosis -0.009 0.098 -10000 0 -0.63 4 4
Ron/MSP 0.034 0.057 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.11 -10000 0 -0.58 4 4
alphaM/beta2 Integrin/uPAR 0.003 0.095 -10000 0 -0.63 4 4
PLAU -0.042 0.074 -10000 0 -10000 0 0
PLAT 0.018 0.067 -10000 0 -0.68 4 4
actin filament polymerization -0.03 0.095 -10000 0 -0.39 10 10
MST1 0.026 0.032 -10000 0 -0.68 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.015 0.084 -10000 0 -0.5 5 5
TNF -0.17 0.35 0.38 1 -0.92 74 75
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.1 -10000 0 -0.57 5 5
fibrinolysis 0.009 0.097 -10000 0 -0.58 4 4
HCK 0.018 0.035 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.025 0.091 -10000 0 -0.37 14 14
VTN -0.041 0.2 -10000 0 -0.68 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -10000 0 -0.47 141 141
LPA -0.005 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.032 -10000 0 -0.68 1 1
cell migration -0.031 0.16 -10000 0 -0.49 40 40
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.012 0.088 -10000 0 -0.56 5 5
MPO 0.013 0.072 -10000 0 -0.68 5 5
KNG1 -0.004 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.025 0.098 -10000 0 -0.4 9 9
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.013 0.018 -10000 0 -10000 0 0
CTGF -0.073 0.24 -10000 0 -0.66 70 70
alphaM/beta2 Integrin/Hck 0.008 0.092 -10000 0 -0.57 5 5
ITGAM -0.008 0.081 -10000 0 -0.73 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.015 0.1 -10000 0 -0.53 10 10
HP -0.021 0.097 -10000 0 -0.68 6 6
leukocyte adhesion -0.032 0.17 -10000 0 -0.52 25 25
SELP 0.015 0.08 -10000 0 -0.68 6 6
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.044 0.13 0.49 13 -10000 0 13
IL27/IL27R/JAK1 -0.012 0.17 -10000 0 -0.5 8 8
TBX21 -0.062 0.18 0.39 5 -0.59 26 31
IL12B 0.006 0.074 -10000 0 -0.68 5 5
IL12A -0.048 0.16 -10000 0 -0.51 50 50
IL6ST -0.07 0.24 -10000 0 -0.68 62 62
IL27RA/JAK1 0.019 0.053 0.55 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.047 0.14 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.044 0.13 0.49 13 -10000 0 13
T cell proliferation during immune response 0.044 0.13 0.49 13 -10000 0 13
MAPKKK cascade -0.044 0.13 -10000 0 -0.49 13 13
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.07 -10000 0 -0.6 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.057 0.19 0.5 10 -0.57 23 33
IL27/IL27R/JAK2/TYK2 -0.045 0.13 -10000 0 -0.5 13 13
positive regulation of T cell mediated cytotoxicity -0.044 0.13 -10000 0 -0.49 13 13
STAT1 (dimer) -0.025 0.21 0.53 10 -0.64 12 22
JAK2 0.019 0.026 -10000 0 -0.37 1 1
JAK1 0.027 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.49 12 12
T cell proliferation -0.11 0.2 -10000 0 -0.52 54 54
IL12/IL12R/TYK2/JAK2 -0.069 0.23 -10000 0 -0.81 27 27
IL17A -0.048 0.14 -10000 0 -10000 0 0
mast cell activation 0.044 0.13 0.49 13 -10000 0 13
IFNG -0.016 0.051 0.099 2 -0.13 66 68
T cell differentiation -0.004 0.008 -10000 0 -0.023 56 56
STAT3 (dimer) -0.032 0.13 -10000 0 -0.47 12 12
STAT5A (dimer) -0.032 0.13 -10000 0 -0.47 12 12
STAT4 (dimer) -0.039 0.15 0.33 1 -0.47 19 20
STAT4 0.004 0.1 -10000 0 -0.59 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.023 0.15 -10000 0 -0.48 7 7
GATA3 -0.058 0.3 -10000 0 -1.3 24 24
IL18 -0.012 0.078 -10000 0 -0.49 11 11
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.46 12 12
IL27/EBI3 -0.027 0.059 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.11 0.27 -10000 0 -0.67 90 90
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.018 -10000 0 -10000 0 0
IL1B -0.034 0.14 -10000 0 -0.51 38 38
EBI3 -0.048 0.073 -10000 0 -0.37 1 1
TNF -0.056 0.17 -10000 0 -0.51 57 57
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.12 0.88 6 -10000 0 6
VDR 0.026 0.008 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.007 0.11 -10000 0 -0.41 8 8
RXRs/LXRs/DNA/Oxysterols -0.013 0.15 -10000 0 -0.42 52 52
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.002 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.069 -10000 0 -0.3 20 20
RXRs/NUR77 -0.09 0.23 -10000 0 -0.45 130 130
RXRs/PPAR -0.019 0.081 -10000 0 -0.38 11 11
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.073 -10000 0 -0.39 12 12
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.07 -10000 0 -0.37 13 13
RARG 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.051 0.12 0.56 26 -10000 0 26
RARs/THRs/DNA/SMRT 0.021 0.069 -10000 0 -0.3 20 20
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.036 0.099 -10000 0 -0.44 5 5
NR1H4 -0.004 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.055 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.022 0.027 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.047 0.081 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.68 140 140
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.056 -10000 0 -0.28 4 4
RXRG -0.1 0.077 -10000 0 -0.6 5 5
RXR alpha/CCPG 0.031 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.026 -10000 0 -10000 0 0
RXRB 0.023 0.027 -10000 0 -10000 0 0
THRB 0.013 0.097 -10000 0 -0.64 10 10
PPARG 0.015 0.085 -10000 0 -0.68 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.1 0.38 -10000 0 -1.1 58 58
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.012 0.15 -10000 0 -0.42 52 52
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.008 0.11 -10000 0 -0.68 13 13
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 144 144
SREBF1 -0.013 0.14 -10000 0 -0.54 6 6
RXRs/RXRs/DNA/9cRA 0.036 0.099 -10000 0 -0.44 5 5
ABCA1 -0.012 0.14 -10000 0 -0.59 4 4
RARs/THRs 0.056 0.097 -10000 0 -0.4 19 19
RXRs/FXR 0.047 0.086 -10000 0 -0.48 3 3
BCL2 -0.024 0.18 -10000 0 -0.67 35 35
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0 0.14 -10000 0 -0.37 55 55
TC10/GTP 0.042 0.034 -10000 0 -0.35 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.003 0.16 -10000 0 -0.42 54 54
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.026 0.009 -10000 0 -10000 0 0
GRB14 0.008 0.11 -10000 0 -0.65 13 13
FOXO3 0 0.12 -10000 0 -0.65 15 15
AKT1 -0.025 0.14 0.35 6 -0.34 63 69
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 0.022 0.055 -10000 0 -0.68 3 3
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.017 0.027 -10000 0 -10000 0 0
CAV1 -0.033 0.14 -10000 0 -0.38 62 62
CBL/APS/CAP/Crk-II/C3G 0.066 0.043 -10000 0 -0.38 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.005 0.15 -10000 0 -0.42 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.14 -10000 0 -0.38 56 56
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.005 0.098 -10000 0 -0.4 7 7
RPS6KB1 -0.029 0.12 0.3 3 -0.32 59 62
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.025 -10000 0 -0.5 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.13 -10000 0 -0.34 50 50
HRAS/GTP -0.022 0.1 -10000 0 -0.34 43 43
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.017 0.14 -10000 0 -0.39 43 43
PRKCI 0.014 0.072 -10000 0 -0.5 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.14 -10000 0 -0.36 64 64
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.046 0.041 -10000 0 -0.4 1 1
PI3K 0.007 0.14 -10000 0 -0.38 56 56
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.027 0.14 0.38 7 -0.34 62 69
PRKCZ 0.014 0.071 -10000 0 -0.52 4 4
SH2B2 0.026 0.009 -10000 0 -10000 0 0
SHC/SHIP -0.011 0.12 0.3 1 -0.37 45 46
F2RL2 -0.018 0.084 -10000 0 -0.68 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.064 0.031 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.061 0.039 -10000 0 -0.4 2 2
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.025 -10000 0 -10000 0 0
INPP5D -0.029 0.13 0.31 1 -0.39 54 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.016 0.16 -10000 0 -0.84 16 16
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IRS1 -0.054 0.22 -10000 0 -0.68 55 55
p62DOK/RasGAP 0.046 0.042 -10000 0 -0.4 1 1
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.029 0.13 0.31 1 -0.39 54 55
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.03 0.12 0.36 3 -0.38 12 15
PTPRA 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.006 0.096 -10000 0 -0.29 43 43
Insulin Receptor/Insulin/IRS1 -0.009 0.15 -10000 0 -0.41 55 55
Insulin Receptor/Insulin/IRS3 0.032 0.012 -10000 0 -10000 0 0
Par3/Par6 0.058 0.039 -10000 0 -0.38 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.001 0.086 -10000 0 -0.38 3 3
epithelial cell differentiation -0.005 0.1 -10000 0 -0.42 8 8
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.008 0.068 -10000 0 -0.38 1 1
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.02 0.064 -10000 0 -0.68 4 4
PRL -0.012 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.02 0.11 0.34 3 -0.46 7 10
PTPRZ1 0.002 0.1 -10000 0 -0.68 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.001 0.13 -10000 0 -0.37 37 37
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.14 -10000 0 -0.42 45 45
ADAM17 0.033 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.013 0.087 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.03 0.14 -10000 0 -0.45 35 35
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.026 0.14 -10000 0 -0.4 46 46
GRIN2B -0.036 0.13 0.25 1 -0.38 45 46
ErbB4/ErbB2/betacellulin 0.003 0.1 -10000 0 -0.47 14 14
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.034 -10000 0 -10000 0 0
PRLR -0.016 0.16 -10000 0 -0.68 25 25
E4ICDs/ETO2 -0.002 0.087 -10000 0 -0.42 4 4
axon guidance -0.007 0.079 -10000 0 -0.4 6 6
NEDD4 0.033 0.049 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.001 0.12 -10000 0 -0.51 25 25
CBFA2T3 0.024 0.033 -10000 0 -0.68 1 1
ErbB4/ErbB2/HBEGF 0.011 0.073 -10000 0 -0.39 4 4
MAPK3 -0.014 0.12 -10000 0 -0.36 36 36
STAT1 (dimer) 0 0.086 -10000 0 -0.37 3 3
MAPK1 -0.019 0.11 -10000 0 -0.37 25 25
JAK2 0.024 0.019 -10000 0 -0.36 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.032 0.13 -10000 0 -0.4 42 42
NRG1 -0.028 0.16 -10000 0 -0.52 44 44
NRG3 -0.023 0.18 -10000 0 -0.65 35 35
NRG2 -0.053 0.22 -10000 0 -0.68 53 53
NRG4 0.021 0.021 -10000 0 -10000 0 0
heart development -0.007 0.079 -10000 0 -0.4 6 6
neural crest cell migration -0.031 0.13 -10000 0 -0.39 42 42
ERBB2 0.019 0.036 -10000 0 -0.5 2 2
WWOX/E4ICDs -0.002 0.089 -10000 0 -0.5 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.01 0.096 -10000 0 -0.5 5 5
apoptosis 0.023 0.13 0.4 38 -10000 0 38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.16 -10000 0 -0.43 57 57
ErbB4/ErbB2/epiregulin 0.012 0.085 -10000 0 -0.4 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.12 -10000 0 -0.5 15 15
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.37 27 27
MDM2 -0.012 0.077 0.26 2 -0.34 2 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.13 -10000 0 -0.4 43 43
STAT5A -0.002 0.078 -10000 0 -0.5 3 3
ErbB4/EGFR/neuregulin 1 beta -0.028 0.14 -10000 0 -0.41 47 47
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.001 0.076 -10000 0 -0.34 3 3
STAT5A (dimer) 0.003 0.11 -10000 0 -0.46 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.004 0.08 -10000 0 -0.5 3 3
LRIG1 0.015 0.09 -10000 0 -0.68 8 8
EREG -0.049 0.07 -10000 0 -10000 0 0
BTC 0.009 0.11 -10000 0 -0.68 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.007 0.079 -10000 0 -0.4 6 6
ERBB4 -0.013 0.087 -10000 0 -0.38 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.004 0.069 -10000 0 -0.46 9 9
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.011 0.072 -10000 0 -0.37 4 4
glial cell differentiation 0.001 0.076 0.34 3 -10000 0 3
WWOX 0.024 0.033 -10000 0 -0.68 1 1
cell proliferation -0.025 0.14 0.3 1 -0.4 46 47
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.029 0.075 -9999 0 -0.38 15 15
RGS9BP -0.015 0.16 -9999 0 -0.66 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.04 0.2 -9999 0 -0.65 46 46
mol:Na + 0.018 0.032 -9999 0 -10000 0 0
mol:ADP -0.044 0.15 -9999 0 -0.5 45 45
GNAT2 0.016 0.021 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.025 0.18 -9999 0 -0.45 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.005 0.022 -9999 0 -10000 0 0
CNGB3 -0.007 0.018 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.026 -9999 0 -10000 0 0
Cone PDE6 -0.007 0.17 -9999 0 -0.4 70 70
Cone Metarhodopsin II -0.011 0.13 -9999 0 -0.39 46 46
Na + (4 Units) 0.023 0.037 -9999 0 -10000 0 0
GNAT2/GDP -0.011 0.16 -9999 0 -0.38 71 71
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.023 -9999 0 -10000 0 0
Cone Transducin 0.032 0.08 -9999 0 -0.4 15 15
SLC24A2 -0.006 0.029 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.096 -9999 0 -0.51 15 15
GNB3 0.006 0.12 -9999 0 -0.68 14 14
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.008 0.049 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.032 -9999 0 -10000 0 0
mol:Pi -0.026 0.18 -9999 0 -0.44 72 72
Cone CNG Channel 0.043 0.033 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.006 0.029 -9999 0 -10000 0 0
RGS9 -0.044 0.21 -9999 0 -0.68 47 47
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.035 -9999 0 -0.68 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.02 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.019 0.12 -10000 0 -0.44 24 24
MAP4K1 0.009 0.079 -10000 0 -0.68 5 5
MAP3K8 0.016 0.086 -10000 0 -0.64 8 8
PRKCB 0.005 0.082 -10000 0 -0.68 5 5
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.003 0.079 -10000 0 -0.32 23 23
JUN -0.082 0.21 0.42 2 -0.49 57 59
MAP3K7 0.003 0.079 -10000 0 -0.41 8 8
GRAP2 -0.018 0.15 -10000 0 -0.55 31 31
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.004 0.097 0.38 2 -0.38 16 18
LAT 0.021 0.059 -10000 0 -0.6 4 4
LCP2 0.024 0.019 -10000 0 -10000 0 0
MAPK8 -0.005 0.14 -10000 0 -0.61 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.085 -10000 0 -0.33 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55 0.029 0.12 -10000 0 -0.43 22 22
p75(NTR)-mediated 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
Sortilin/TRAF6 0.036 0.037 -10000 0 -0.51 2 2
Necdin/E2F1 -0.001 0.078 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.056 0.093 -10000 0 -0.4 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.45 218 218
NT-4/5 (dimer)/p75(NTR) -0.012 0.13 -10000 0 -0.52 28 28
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.098 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.093 -10000 0 -0.45 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.026 0.11 -10000 0 -0.44 24 24
LINGO1 0.02 0.032 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.35 2 2
proBDNF (dimer) 0.009 0.1 -10000 0 -0.67 10 10
NTRK1 0.011 0.03 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.13 0.47 10 -0.61 5 15
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.007 0.091 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.046 0.094 -10000 0 -0.43 16 16
MAGEH1 0.025 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.1 -10000 0 -0.42 20 20
Mammalian IAPs/DIABLO 0.044 0.095 -10000 0 -0.4 19 19
proNGF (dimer) 0.021 0.057 -10000 0 -0.67 3 3
MAGED1 0.025 0.008 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.65 13 13
ZNF274 0.025 0.008 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.011 0.086 -10000 0 -0.4 16 16
NGF 0.021 0.057 -10000 0 -0.68 3 3
cell cycle arrest 0.055 0.14 0.43 16 -0.38 16 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.071 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.019 0.12 -10000 0 -0.46 30 30
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.033 0.099 -10000 0 -0.45 18 18
PSENEN 0.025 0.007 -10000 0 -10000 0 0
mol:ceramide 0.002 0.093 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.004 0.1 -10000 0 -0.51 16 16
BEX1 -0.28 0.35 -10000 0 -0.67 208 208
mol:GDP -0.019 0.089 -10000 0 -0.44 18 18
NGF (dimer) 0.037 0.11 -10000 0 -0.41 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.091 -10000 0 -0.41 16 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.084 -10000 0 -0.39 17 17
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.099 -10000 0 -0.45 18 18
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.004 0.054 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.16 -10000 0 -0.67 26 26
TP53 -0.002 0.1 0.35 1 -0.36 25 26
PRDM4 0 0.091 -10000 0 -0.42 16 16
BDNF (dimer) 0.007 0.14 -10000 0 -0.44 32 32
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.05 0.09 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.046 0.098 -10000 0 -0.43 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
MAPK10 0.016 0.12 0.38 15 -0.4 15 30
DIABLO 0.026 0.005 -10000 0 -10000 0 0
SMPD2 0.002 0.093 -10000 0 -0.42 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.097 -10000 0 -0.45 17 17
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.51 1 1
NT3 (dimer)/p75(NTR) -0.029 0.16 -10000 0 -0.51 41 41
MAPK8 0.012 0.12 0.38 14 -0.41 15 29
MAPK9 0.01 0.1 0.35 9 -0.39 14 23
APAF1 0.025 0.032 -10000 0 -0.68 1 1
NTF3 -0.019 0.16 -10000 0 -0.68 26 26
NTF4 0.004 0.11 -10000 0 -0.65 13 13
NDN 0.019 0.071 -10000 0 -0.68 5 5
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.087 -10000 0 -0.38 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.053 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.098 -10000 0 -0.45 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.38 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.11 -10000 0 -0.4 26 26
PRKACB 0.025 0.032 -10000 0 -0.68 1 1
proBDNF (dimer)/p75 ECD 0.023 0.087 -10000 0 -0.51 12 12
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.069 0.14 0.49 11 -0.39 16 27
BAD 0.029 0.15 0.47 25 -0.4 16 41
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.017 0.13 -10000 0 -0.68 16 16
CYCS 0.008 0.1 0.36 12 -0.4 16 28
ADAM17 0.024 0.045 -10000 0 -0.68 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.099 -10000 0 -0.43 18 18
BCL2L11 0.029 0.15 0.46 25 -0.4 16 41
BDNF (dimer)/p75(NTR) -0.009 0.13 -10000 0 -0.51 26 26
PI3K 0.045 0.1 -10000 0 -0.43 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.094 -10000 0 -0.43 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.001 0.11 -10000 0 -0.51 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.046 0.094 -10000 0 -0.43 16 16
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
PLG -0.013 0.018 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.006 0.099 -10000 0 -0.4 25 25
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.025 0.007 -10000 0 -10000 0 0
CASP3 0.032 0.14 0.46 25 -0.36 16 41
E2F1 -0.018 0.068 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.075 -10000 0 -0.47 3 3
NGF (dimer)/TRKA 0.028 0.049 -10000 0 -0.51 3 3
MMP7 -0.078 0.16 -10000 0 -0.66 25 25
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.054 0.097 -10000 0 -0.4 18 18
MMP3 -0.016 0.046 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.015 0.097 -10000 0 -0.54 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.03 0.11 -10000 0 -0.33 55 55
FRAP1 0.01 0.051 0.33 4 -0.41 2 6
AKT1 -0.025 0.095 -10000 0 -0.29 52 52
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.004 0.088 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP 0 0.074 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.023 0.13 -10000 0 -0.38 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.24 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.018 0.097 0.37 19 -0.37 3 22
MAP3K5 0.006 0.028 0.18 1 -0.41 1 2
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.03 0.18 1 -0.41 1 2
mol:LY294002 0 0.001 0.001 1 -0.002 68 69
EIF4B 0.024 0.11 0.45 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.07 0.34 6 -0.31 3 9
eIF4E/eIF4G1/eIF4A1 0.015 0.027 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.13 -10000 0 -0.36 56 56
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.047 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.012 0.08 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 68 69
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.031 0.11 -10000 0 -0.32 54 54
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.075 -10000 0 -0.5 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.006 0.096 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 68 -0.001 1 69
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.042 0.13 -10000 0 -0.38 61 61
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.025 0.019 -10000 0 -0.36 1 1
PDK2 -0.029 0.1 0.22 3 -0.31 52 55
EIF4EBP1 0.016 0.098 -10000 0 -0.93 5 5
PIK3CA 0.023 0.056 -10000 0 -0.68 3 3
PPP2R5D 0.019 0.075 0.37 13 -0.37 2 15
peptide biosynthetic process 0.013 0.016 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.008 20 -0.003 3 23
EEF2 0.014 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.03 0.089 -10000 0 -0.83 5 5
IL1-mediated signaling events

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
UBC13/UEV1A 0.033 0.008 -9999 0 -10000 0 0
PRKCZ 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.065 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.029 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.004 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.055 0.21 -9999 0 -0.53 71 71
IL1A -0.032 0.19 -9999 0 -0.67 38 38
IL1B -0.028 0.15 -9999 0 -0.51 39 39
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.038 -9999 0 -0.36 2 2
IL1R2 -0.041 0.19 -9999 0 -0.66 39 39
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.052 -9999 0 -10000 0 0
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.018 0.072 -9999 0 -0.68 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.034 0.058 -9999 0 -10000 0 0
JUN -0.083 0.16 -9999 0 -0.37 107 107
MAP3K7 0.027 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.035 0.13 -9999 0 -0.38 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88 0.034 0.13 -9999 0 -0.41 37 37
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.045 0.13 -9999 0 -0.39 37 37
IL1 beta fragment/IL1R1/IL1RAP 0.011 0.13 -9999 0 -0.42 38 38
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.012 0.083 -9999 0 -0.43 15 15
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.01 0.088 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.003 -9999 0 -10000 0 0
TRAF6 0.024 0.045 -9999 0 -0.68 2 2
PI3K 0.036 0.044 -9999 0 -0.51 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.071 -9999 0 -0.38 3 3
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.011 0.13 -9999 0 -0.42 38 38
IL1 beta/IL1R2 -0.046 0.19 -9999 0 -0.49 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.029 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.024 0.12 -9999 0 -0.36 37 37
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.13 -9999 0 -0.39 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.086 -9999 0 -0.29 37 37
IL1 alpha/IL1R1/IL1RAP 0.017 0.14 -9999 0 -0.45 37 37
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.003 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.033 -9999 0 -0.39 2 2
IL1RAP -0.012 0.066 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.011 0.11 -9999 0 -0.38 13 13
CASP1 0.023 0.047 -9999 0 -0.68 2 2
IL1RN/IL1R2 -0.04 0.17 -9999 0 -0.52 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.13 -9999 0 -0.4 38 38
TMEM189-UBE2V1 -0.004 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.069 -9999 0 -0.36 1 1
PIK3CA 0.023 0.055 -9999 0 -0.68 3 3
IL1RN -0.012 0.11 -9999 0 -0.65 11 11
TRAF6/TAK1/TAB1/TAB2 0.045 0.03 -9999 0 -0.37 2 2
MAP2K6 0.007 0.063 -9999 0 -0.36 12 12
LPA4-mediated signaling events

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
ADCY4 0.003 0.041 -10000 0 -0.44 4 4
ADCY5 -0.055 0.15 -10000 0 -0.44 65 65
ADCY6 0.003 0.041 -10000 0 -0.44 4 4
ADCY7 0.002 0.041 -10000 0 -0.44 4 4
ADCY1 -0.001 0.055 -10000 0 -0.45 7 7
ADCY2 -0.038 0.13 -10000 0 -0.44 45 45
ADCY3 0.003 0.041 -10000 0 -0.44 4 4
ADCY8 -0.047 0.05 -10000 0 -0.49 4 4
PRKCE 0.004 0.047 -10000 0 -0.51 4 4
ADCY9 0.002 0.041 -10000 0 -0.44 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.094 0.37 6 -0.34 16 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.058 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.005 0.13 -10000 0 -0.48 21 21
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.18 0.51 -10000 0 -1.4 70 70
NKX2-5 0.018 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.008 0.083 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.036 0.095 -10000 0 -10000 0 0
SMAD4 -0.008 0.071 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.041 0.069 -10000 0 -0.44 3 3
SMAD3/SMAD4/VDR 0.049 0.073 -10000 0 -10000 0 0
MYC 0.011 0.11 -10000 0 -0.65 12 12
CDKN2B -0.021 0.11 -10000 0 -0.51 1 1
AP1 -0.19 0.41 -10000 0 -0.75 149 149
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.066 -10000 0 -0.55 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.034 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.004 0.053 -10000 0 -0.22 1 1
SMAD3/SMAD4/GR 0.02 0.078 -10000 0 -10000 0 0
GATA3 -0.009 0.15 -10000 0 -0.63 24 24
SKI/SIN3/HDAC complex/NCoR1 0.026 0.055 -10000 0 -0.71 2 2
MEF2C/TIF2 -0.032 0.14 0.32 2 -0.4 39 41
endothelial cell migration -0.023 0.08 0.76 3 -10000 0 3
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.008 -10000 0 -10000 0 0
RBBP4 0.023 0.045 -10000 0 -0.68 2 2
RUNX2 -0.015 0.078 -10000 0 -0.68 2 2
RUNX3 0.013 0.091 -10000 0 -0.68 8 8
RUNX1 -0.038 0.073 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
CDKN1A 0.02 0.043 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.011 0.12 -10000 0 -0.29 45 45
DCP1A 0.027 0.003 -10000 0 -10000 0 0
SKI 0.026 0.005 -10000 0 -10000 0 0
SERPINE1 0.023 0.081 -10000 0 -0.76 3 3
SMAD3/SMAD4/ATF2 0.005 0.12 -10000 0 -0.48 16 16
SMAD3/SMAD4/ATF3 -0.077 0.24 -10000 0 -0.51 103 103
SAP30 0.025 0.032 -10000 0 -0.68 1 1
Cbp/p300/PIAS3 0.049 0.045 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.75 148 149
SMAD3/SMAD4/IRF7 0.023 0.079 -10000 0 -10000 0 0
TFE3 0.03 0.01 -10000 0 -10000 0 0
COL1A2 0.028 0.04 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.014 0.096 0.46 2 -10000 0 2
DLX1 -0.01 0.16 -10000 0 -0.65 26 26
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.17 0.33 -10000 0 -0.73 125 125
SMAD3/SMAD4/Max 0.019 0.079 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.042 0.036 -10000 0 -0.42 1 1
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.011 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.079 -10000 0 -10000 0 0
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.017 0.15 -10000 0 -0.65 23 23
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.014 0.1 0.39 3 -0.89 1 4
SMAD2-3/SMAD4 0.01 0.095 -10000 0 -0.3 1 1
Cbp/p300/Src-1 0.047 0.035 -10000 0 -10000 0 0
IGHV3OR16-13 0.002 0.029 -10000 0 -0.32 2 2
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.032 -10000 0 -0.68 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.032 -10000 0 -0.68 1 1
GCN5L2 0.005 0.013 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.028 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.063 0.07 -10000 0 -0.46 8 8
SMAD2 0.011 0.048 -10000 0 -10000 0 0
SMAD3 0.005 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.066 -10000 0 -0.41 5 5
SMAD2/SMAD2/SMAD4 0.003 0.036 0.23 3 -10000 0 3
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.035 0.2 -10000 0 -0.68 42 42
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.094 -10000 0 -10000 0 0
IFNB1 -0.001 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.002 0.11 -10000 0 -0.62 2 2
CITED1 -0.096 0.075 -10000 0 -0.6 4 4
SMAD2-3/SMAD4/ARC105 0.011 0.086 -10000 0 -10000 0 0
RBL1 0.013 0.095 -10000 0 -0.68 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.035 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.046 0.069 -10000 0 -0.43 8 8
SMAD7 -0.09 0.25 -10000 0 -0.54 91 91
MYC/MIZ-1 0.027 0.084 -10000 0 -0.49 12 12
SMAD3/SMAD4 0.025 0.11 0.28 39 -0.52 1 40
IL10 -0.029 0.15 -10000 0 -0.53 32 32
PIASy/HDAC complex 0.017 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.008 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.11 -10000 0 -0.41 21 21
CDK4 0.031 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.67 104 104
SMAD3/SMAD4/SP1 0.032 0.081 -10000 0 -10000 0 0
FOXG1 0.008 0.042 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.008 -10000 0 -10000 0 0
FOXO4 0.014 0.008 -10000 0 -10000 0 0
heart looping -0.014 0.1 0.39 3 -0.87 1 4
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.005 0.14 -10000 0 -0.49 24 24
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.015 0.08 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 -0.001 0.14 -10000 0 -0.42 30 30
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.032 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.11 -10000 0 -0.5 7 7
SMAD3/SMAD4/SP1-3 0.052 0.08 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.027 0.12 -10000 0 -0.41 3 3
ITGB5 0.015 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.029 0.046 -10000 0 -0.57 2 2
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.48 191 191
AR -0.26 0.34 -10000 0 -0.66 197 197
negative regulation of cell growth -0.023 0.12 -10000 0 -0.46 6 6
SMAD3/SMAD4/MYOD 0.015 0.08 -10000 0 -10000 0 0
E2F5 0.025 0.032 -10000 0 -0.68 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.026 0.098 -10000 0 -0.31 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.037 -10000 0 -10000 0 0
TFDP1 0.025 0.019 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.18 0.43 -10000 0 -0.77 148 148
SMAD3/SMAD4/RUNX2 0.014 0.097 -10000 0 -0.47 2 2
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.004 -10000 0 -10000 0 0
ATF2 0.003 0.13 -10000 0 -0.66 17 17
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.024 0.51 1 -10000 0 1
CDKN1A -0.007 0.013 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.025 0.008 -10000 0 -10000 0 0
FOXO3 -0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.024 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.009 -10000 0 -10000 0 0
PPARGC1A -0.28 0.35 -10000 0 -0.67 209 209
FHL2 -0.03 0.19 -10000 0 -0.68 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.03 -10000 0 -0.51 1 1
HIST2H4A 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/FOXO3a 0.038 0.052 -10000 0 -0.43 1 1
SIRT1 0.022 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.071 -10000 0 -0.3 11 11
apoptosis -0.036 0.032 0.44 1 -10000 0 1
SIRT1/PGC1A -0.17 0.24 -10000 0 -0.44 209 209
p53/SIRT1 0.028 0.028 -10000 0 -0.51 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.23 14 14
FOXO1/FHL2/SIRT1 0.008 0.12 -10000 0 -0.4 40 40
HIST1H1E 0.008 0.047 -10000 0 -0.34 8 8
SIRT1/p300 0.026 0.03 -10000 0 -0.51 1 1
muscle cell differentiation -0.03 0.029 0.45 1 -10000 0 1
TP53 0.022 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.029 -10000 0 -0.51 1 1
ACSS2 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.03 0.03 -10000 0 -0.45 1 1
FOXM1 transcription factor network

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
NFATC3 -0.011 0.32 0.8 2 -0.93 11 13
PLK1 0.029 0.096 -10000 0 -0.81 5 5
BIRC5 0.025 0.1 -10000 0 -1.1 3 3
HSPA1B -0.018 0.31 -10000 0 -0.92 12 12
MAP2K1 0.025 0.045 -10000 0 -10000 0 0
BRCA2 -0.021 0.33 0.8 1 -0.99 14 15
FOXM1 -0.043 0.34 -10000 0 -0.97 21 21
XRCC1 -0.009 0.31 -10000 0 -0.92 11 11
FOXM1B/p19 -0.042 0.34 -10000 0 -0.9 24 24
Cyclin D1/CDK4 0.004 0.29 -10000 0 -0.83 11 11
CDC2 -0.02 0.32 0.62 1 -0.86 21 22
TGFA -0.009 0.29 -10000 0 -0.81 12 12
SKP2 -0.014 0.33 0.8 2 -0.99 14 16
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B -0.007 0.31 0.79 1 -0.92 11 12
RB1 0.028 0.19 -10000 0 -0.69 9 9
FOXM1C/SP1 -0.025 0.33 -10000 0 -0.95 20 20
AURKB 0.01 0.13 -10000 0 -0.79 10 10
CENPF -0.007 0.31 0.79 1 -0.92 11 12
CDK4 0.027 0.019 -10000 0 -10000 0 0
MYC -0.024 0.31 -10000 0 -0.94 16 16
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.008 0.3 -10000 0 -0.86 13 13
CDKN2A -0.034 0.071 -10000 0 -10000 0 0
LAMA4 -0.018 0.31 -10000 0 -0.93 11 11
FOXM1B/HNF6 -0.015 0.33 -10000 0 -0.98 13 13
FOS -0.22 0.6 0.8 2 -1.2 128 130
SP1 0.026 0.009 -10000 0 -10000 0 0
CDC25B -0.013 0.31 0.8 1 -0.93 11 12
response to radiation 0.007 0.026 -10000 0 -10000 0 0
CENPB -0.013 0.31 0.8 1 -0.93 11 12
CENPA -0.025 0.32 -10000 0 -0.96 14 14
NEK2 -0.008 0.31 0.79 1 -0.92 11 12
HIST1H2BA -0.024 0.31 -10000 0 -0.91 13 13
CCNA2 0.026 0.021 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.028 0.33 -10000 0 -1 14 14
CCNB2 -0.019 0.31 -10000 0 -0.93 11 11
CCNB1 -0.019 0.32 0.68 2 -0.93 14 16
ETV5 -0.017 0.31 -10000 0 -0.92 12 12
ESR1 -0.055 0.39 -10000 0 -1.1 28 28
CCND1 -0.002 0.3 -10000 0 -0.85 11 11
GSK3A 0.022 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.052 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.033 0.31 -10000 0 -0.94 14 14
GAS1 -0.17 0.55 0.8 1 -1.2 98 99
MMP2 -0.02 0.34 0.8 2 -1.2 12 14
RB1/FOXM1C -0.002 0.3 -10000 0 -0.88 12 12
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.022 0.086 0.32 5 -0.42 10 15
ACTA1 0.01 0.1 0.34 6 -0.51 10 16
NUMA1 0.016 0.1 0.28 6 -0.52 12 18
SPTAN1 0.008 0.1 0.35 6 -0.5 10 16
LIMK1 0.014 0.11 0.44 8 -0.52 9 17
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.025 0.008 -10000 0 -10000 0 0
CASP10 -0.009 0.088 -10000 0 -0.54 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
PTK2 0.015 0.098 0.39 2 -0.43 15 17
DIABLO 0.026 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.008 0.099 0.35 6 -0.49 10 16
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.007 0.1 0.36 5 -0.5 10 15
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.6 61 61
BID -0.012 0.061 -10000 0 -0.33 11 11
MAP3K1 0.018 0.041 0.27 3 -0.22 2 5
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.51 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.011 0.11 0.44 8 -0.52 9 17
CASP9 0.026 0.005 -10000 0 -10000 0 0
DNA repair -0.018 0.056 0.42 2 -0.21 19 21
neuron apoptosis 0.006 0.11 -10000 0 -0.56 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.11 0.35 4 -0.53 12 16
APAF1 0.025 0.032 -10000 0 -0.68 1 1
CASP6 0.02 0.091 0.37 2 -0.59 5 7
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.11 0.4 13 -0.51 9 22
CASP7 0.008 0.096 0.31 22 -0.48 6 28
KRT18 0.021 0.041 -10000 0 -0.44 2 2
apoptosis 0.017 0.098 0.48 4 -0.46 9 13
DFFA 0.01 0.1 0.36 6 -0.5 10 16
DFFB 0.01 0.1 0.36 6 -0.52 9 15
PARP1 0.018 0.057 0.21 19 -0.43 2 21
actin filament polymerization -0.019 0.12 0.48 9 -0.52 12 21
TNF -0.06 0.23 -10000 0 -0.68 57 57
CYCS 0 0.049 0.23 4 -0.22 10 14
SATB1 0.021 0.09 0.46 3 -0.6 4 7
SLK 0.006 0.1 0.46 3 -0.5 11 14
p15 BID/BAX -0.01 0.069 -10000 0 -0.3 11 11
CASP2 -0.016 0.11 -10000 0 -0.37 19 19
JNK cascade -0.019 0.041 0.21 2 -0.27 3 5
CASP3 0.007 0.1 0.34 6 -0.51 11 17
LMNB2 0.005 0.12 0.37 10 -0.41 12 22
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.044 0.095 -10000 0 -0.4 19 19
negative regulation of DNA binding -0.041 0.22 -10000 0 -0.6 61 61
stress fiber formation 0.006 0.1 0.41 4 -0.49 11 15
GZMB -0.005 0.1 -10000 0 -0.62 11 11
CASP1 0.015 0.027 -10000 0 -0.39 2 2
LMNB1 0.019 0.094 0.35 11 -0.36 4 15
APP 0.006 0.12 -10000 0 -0.56 17 17
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.019 0.091 0.45 3 -0.46 8 11
LMNA 0.015 0.1 0.36 12 -0.42 5 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.015 0.11 -10000 0 -0.4 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.016 0.11 0.45 8 -0.55 8 16
APAF-1/Caspase 9 0.014 0.057 -10000 0 -0.53 3 3
nuclear fragmentation during apoptosis 0.017 0.1 0.28 6 -0.51 12 18
CFL2 0.019 0.12 0.53 12 -0.5 9 21
GAS2 0.005 0.1 0.36 4 -0.49 12 16
positive regulation of apoptosis 0.016 0.1 0.37 10 -0.39 7 17
PRF1 0.016 0.085 -10000 0 -0.68 7 7
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.004 0.14 -10000 0 -0.69 10 10
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.045 -10000 0 -0.68 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.056 -10000 0 -0.68 3 3
AP1 -0.13 0.24 -10000 0 -0.48 140 140
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.012 0.1 -10000 0 -0.68 10 10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.076 -10000 0 -0.55 4 4
NICD/RBPSUH 0.005 0.14 -10000 0 -0.64 10 10
WIF1 -0.014 0.045 -10000 0 -10000 0 0
NOTCH1 -0.005 0.13 -10000 0 -0.69 9 9
PSENEN 0.025 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0 0.063 -10000 0 -0.68 1 1
beta catenin/beta TrCP1 0.046 0.047 0.29 2 -10000 0 2
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.007 0.083 0.38 1 -0.4 11 12
CtBP/CBP/TCF1/TLE1/AES 0.019 0.032 -10000 0 -0.3 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 125 125
JUN -0.12 0.29 -10000 0 -0.67 103 103
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.063 0.32 11 -10000 0 11
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.094 -10000 0 -0.43 18 18
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.019 0.25 -10000 0 -1.2 19 19
NKD1 0.006 0.11 -10000 0 -0.68 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.004 0.14 -10000 0 -0.64 12 12
apoptosis -0.13 0.24 -10000 0 -0.48 140 140
Delta 1/NOTCHprecursor 0.005 0.14 -10000 0 -0.67 10 10
DLL1 0.025 0.033 -10000 0 -0.68 1 1
PPARD 0.025 0.055 -10000 0 -0.77 2 2
Gamma Secretase 0.069 0.03 -10000 0 -10000 0 0
APC 0 0.074 0.33 2 -0.55 3 5
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.049 0.039 -10000 0 -0.49 1 1
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.009 0.13 -10000 0 -0.85 10 10
WNT1 0.018 0.019 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.046 0.098 0.42 13 -0.61 1 14
DKK2 -0.004 0.14 -10000 0 -0.68 19 19
NOTCH1 precursor/DVL1 0.011 0.12 -10000 0 -0.59 10 10
GSK3B 0.027 0.003 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.004 0.14 -10000 0 -0.65 12 12
PPP2R5D 0.029 0.057 0.33 13 -0.44 1 14
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.064 0.017 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
alphaV beta3 Integrin 0.025 0.087 -10000 0 -0.52 11 11
PTK2 0.011 0.14 -10000 0 -0.55 24 24
positive regulation of JNK cascade 0.015 0.095 -10000 0 -0.33 27 27
CDC42/GDP 0.032 0.14 0.44 1 -0.45 29 30
Rac1/GDP 0.031 0.13 -10000 0 -0.46 25 25
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.12 -10000 0 -0.4 27 27
nectin-3/I-afadin 0.009 0.12 -10000 0 -0.5 27 27
RAPGEF1 0.014 0.13 0.32 2 -0.5 26 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0.15 -10000 0 -0.57 27 27
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.003 0.06 -10000 0 -0.79 1 1
Rap1/GTP 0.013 0.093 -10000 0 -0.36 25 25
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.12 -10000 0 -0.5 27 27
PVR 0.025 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.018 0.16 0.47 1 -0.55 32 33
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PI3K 0.051 0.12 -10000 0 -0.42 25 25
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.01 0.11 -10000 0 -0.36 26 26
PVRL1 0.022 0.025 -10000 0 -10000 0 0
PVRL3 -0.012 0.16 -10000 0 -0.68 27 27
PVRL2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.095 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.041 0.13 -10000 0 -0.41 32 32
SRC 0.007 0.16 -10000 0 -0.64 27 27
ITGB3 0.012 0.097 -10000 0 -0.64 10 10
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
FARP2 0.022 0.16 -10000 0 -0.54 30 30
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.11 -10000 0 -0.43 27 27
nectin-1/I-afadin 0.036 0.02 -10000 0 -10000 0 0
nectin-2/I-afadin 0.037 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.027 0.11 -10000 0 -0.44 26 26
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.015 0.095 -10000 0 -0.33 27 27
alphaV/beta3 Integrin/Talin 0.024 0.11 -10000 0 -0.56 10 10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.037 0.011 -10000 0 -10000 0 0
PIP5K1C -0.001 0.065 -10000 0 -0.83 1 1
VAV2 0 0.18 0.37 1 -0.6 30 31
RAP1/GDP 0.035 0.12 0.28 1 -0.42 27 28
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.024 0.11 -10000 0 -0.43 27 27
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.12 -10000 0 -0.5 27 27
Rac1/GTP 0.016 0.13 -10000 0 -0.45 26 26
PTPRM 0.002 0.071 -10000 0 -0.27 26 26
E-cadherin/beta catenin/alpha catenin 0.073 0.027 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.026 0.12 -9999 0 -0.34 35 35
Syndecan-3/Neurocan 0.003 0.097 -9999 0 -0.36 29 29
POMC -0.12 0.28 -9999 0 -0.66 98 98
EGFR 0.02 0.064 -9999 0 -0.68 4 4
Syndecan-3/EGFR 0.028 0.041 -9999 0 -0.33 5 5
AGRP 0.004 0.032 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.025 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.027 0.18 -9999 0 -0.67 34 34
long-term memory 0.05 0.029 -9999 0 -0.27 1 1
Syndecan-3/IL8 0.03 0.066 -9999 0 -0.36 11 11
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.011 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0 0.026 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.039 0.2 -9999 0 -0.68 44 44
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.024 0.13 -9999 0 -0.34 60 60
Syndecan-3/AgRP 0.03 0.023 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.029 -9999 0 -0.29 1 1
Fyn/Cortactin 0.039 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.03 0.065 -9999 0 -0.35 11 11
IL8 -0.023 0.11 -9999 0 -0.68 10 10
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -0.28 1 1
Syndecan-3/CASK 0.012 0.022 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.077 0.22 -9999 0 -0.5 98 98
Gamma Secretase 0.069 0.03 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.032 -10000 0 -0.68 1 1
Caspase 8 (4 units) 0.025 0.088 -10000 0 -0.44 5 5
NEF -0.011 0.059 -10000 0 -0.23 25 25
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.005 0.15 -10000 0 -0.66 23 23
CYCS -0.007 0.089 0.22 1 -0.38 9 10
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CD247 -0.014 0.15 -10000 0 -0.75 17 17
MAP2K7 -0.001 0.16 0.36 1 -0.64 22 23
protein ubiquitination 0.008 0.1 0.36 6 -0.4 3 9
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.008 0.095 0.22 1 -0.33 22 23
NF-kappa-B/RelA/I kappa B alpha 0.042 0.081 -10000 0 -0.33 19 19
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.025 0.032 -10000 0 -0.68 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.042 0.081 -10000 0 -0.33 20 20
MAPK8 -0.004 0.16 0.35 2 -0.58 24 26
APAF1 0.025 0.032 -10000 0 -0.68 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.096 -10000 0 -0.33 29 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.11 -10000 0 -0.37 20 20
CHUK 0.003 0.099 0.28 3 -0.4 5 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.03 -10000 0 -0.38 1 1
TCRz/NEF -0.02 0.15 -10000 0 -0.47 39 39
TNF -0.06 0.23 -10000 0 -0.68 57 57
FASLG -0.044 0.22 -10000 0 -0.74 39 39
NFKB1 0.021 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.44 58 58
CASP6 0.04 0.094 -10000 0 -0.72 4 4
CASP7 0.011 0.16 0.39 2 -0.58 26 28
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.011 0.15 0.32 2 -0.57 26 28
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0.001 0.1 -10000 0 -0.41 7 7
APAF-1/Caspase 9 -0.001 0.12 -10000 0 -0.48 22 22
BCL2 -0.024 0.16 0.42 2 -0.57 22 24
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.007 0.14 -10000 0 -0.38 55 55
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.021 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.023 -10000 0 -0.44 1 1
GNB1 0.026 0.005 -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 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.035 0.14 -10000 0 -0.39 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.012 0.032 0.096 61 -10000 0 61
GNAL -0.06 0.23 -10000 0 -0.66 61 61
GNG2 0.025 0.032 -10000 0 -0.68 1 1
CRH 0 0.038 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.05 -10000 0 -0.38 8 8
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.066 -10000 0 -0.38 2 2
NT3 (dimer)/TRKC -0.022 0.14 -10000 0 -0.51 36 36
NT3 (dimer)/TRKB 0.002 0.15 -10000 0 -0.44 45 45
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.29 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.011 0.03 -10000 0 -10000 0 0
NTRK2 0.018 0.066 -10000 0 -0.61 5 5
NTRK3 -0.011 0.11 -10000 0 -0.62 12 12
NT-4/5 (dimer)/TRKB 0.013 0.13 -10000 0 -0.45 32 32
neuron apoptosis -0.009 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.01 0.12 -10000 0 -0.42 18 18
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.001 0.1 -10000 0 -0.55 10 10
SHC3 -0.007 0.12 -10000 0 -0.42 29 29
STAT3 (dimer) 0.03 0.014 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.001 0.14 -10000 0 -0.46 36 36
RIN/GDP -0.005 0.079 0.29 8 -0.26 4 12
GIPC1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.006 0.072 -10000 0 -0.38 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.017 -10000 0 -10000 0 0
MAGED1 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.65 13 13
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.038 0.064 -10000 0 -0.44 7 7
TRKA/NEDD4-2 0.031 0.022 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.68 183 183
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.45 183 183
NGF 0.021 0.057 -10000 0 -0.68 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.68 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.004 0.12 -10000 0 -0.62 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.19 -10000 0 -0.36 170 170
mol:GDP -0.012 0.11 0.39 10 -0.38 5 15
NGF (dimer) 0.021 0.057 -10000 0 -0.67 3 3
RhoG/GDP -0.18 0.26 -10000 0 -0.51 183 183
RIT1/GDP -0.002 0.083 0.35 8 -0.26 4 12
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.089 -10000 0 -0.48 13 13
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.025 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.06 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.019 0.16 -10000 0 -0.67 26 26
RAP1/GDP -0.006 0.058 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.1 -10000 0 -0.67 10 10
ubiquitin-dependent protein catabolic process 0.045 0.043 -10000 0 -0.44 3 3
Schwann cell development -0.03 0.029 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.039 -10000 0 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.12 -10000 0 -0.37 43 43
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.5 6 6
STAT3 0.03 0.014 -10000 0 -10000 0 0
axon guidance -0.016 0.12 -10000 0 -0.36 43 43
MAPK3 0.018 0.069 -10000 0 -0.4 7 7
MAPK1 0.01 0.063 -10000 0 -0.4 7 7
CDC42/GDP -0.001 0.085 0.35 8 -0.26 3 11
NTF3 -0.019 0.16 -10000 0 -0.68 26 26
NTF4 0.004 0.11 -10000 0 -0.65 13 13
NGF (dimer)/TRKA/FAIM 0.046 0.043 -10000 0 -0.44 3 3
PI3K 0.036 0.044 -10000 0 -0.51 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.042 0.084 -10000 0 -0.4 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.028 0.12 -10000 0 -0.44 35 35
RGS19 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.069 -10000 0 -0.59 1 1
Rac1/GDP -0.005 0.068 0.22 1 -0.25 3 4
NGF (dimer)/TRKA/GRIT 0.026 0.043 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.023 0.089 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.045 0.043 -10000 0 -0.44 3 3
MAP2K1 0.038 0.056 0.36 3 -10000 0 3
NGFR -0.017 0.13 -10000 0 -0.68 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.073 -10000 0 -0.36 15 15
RAS family/GTP/PI3K 0.026 0.027 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.074 0.031 -10000 0 -0.38 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
MAPKKK cascade 0.021 0.075 -10000 0 -0.54 6 6
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.023 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.047 0.085 -10000 0 -0.44 12 12
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.045 -10000 0 -0.38 3 3
MATK 0.017 0.068 -10000 0 -0.61 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.003 0.078 -10000 0 -0.39 16 16
Rac1/GTP -0.11 0.12 -10000 0 -0.29 71 71
FRS2 family/SHP2/CRK family 0.057 0.042 -10000 0 -0.38 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.093 -10000 0 -0.61 10 10
ANTXR2 0.023 0.055 -10000 0 -0.68 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.014 -10000 0 -0.082 13 13
monocyte activation -0.038 0.16 -10000 0 -0.44 63 63
MAP2K2 -0.01 0.12 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.009 0.057 0.11 1 -0.39 10 11
CYAA -0.008 0.058 -10000 0 -0.35 13 13
MAP2K4 -0.001 0.013 -10000 0 -10000 0 0
IL1B -0.027 0.1 0.18 1 -0.35 40 41
Channel 0.023 0.067 -10000 0 -0.37 13 13
NLRP1 -0.002 0.028 -10000 0 -0.38 2 2
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.029 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.014 0.082 13 -10000 0 13
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.012 0.056 -10000 0 -0.32 13 13
PA/Cellular Receptors 0.024 0.073 -10000 0 -0.4 13 13
apoptosis -0.002 0.014 -10000 0 -0.082 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.063 -10000 0 -0.35 13 13
macrophage activation -0.001 0.011 -10000 0 -10000 0 0
TNF -0.06 0.23 -10000 0 -0.68 57 57
VCAM1 -0.039 0.16 -10000 0 -0.44 63 63
platelet activation 0.011 0.029 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.11 9 -0.13 8 17
IL18 -0.009 0.061 -10000 0 -0.33 13 13
negative regulation of macrophage activation -0.002 0.014 -10000 0 -0.082 13 13
LEF -0.002 0.014 -10000 0 -0.082 13 13
CASP1 0.001 0.018 -10000 0 -0.17 3 3
mol:cAMP 0.011 0.029 -10000 0 -0.52 1 1
necrosis -0.002 0.014 -10000 0 -0.082 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.064 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.008 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.019 0.049 -10000 0 -0.44 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.023 -10000 0 -10000 0 0
GRK1 -0.04 0.2 -10000 0 -0.65 46 46
CNG Channel 0.037 0.059 -10000 0 -0.38 7 7
mol:Na + 0.029 0.07 -10000 0 -0.39 9 9
mol:ADP -0.04 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.025 0.18 -10000 0 -0.45 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.073 -10000 0 -0.4 9 9
CNGB1 0.017 0.029 -10000 0 -10000 0 0
RDH5 -0.07 0.071 -10000 0 -10000 0 0
SAG -0.008 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.1 0.49 11 -0.4 6 17
Na + (4 Units) 0.022 0.065 -10000 0 -0.37 9 9
RGS9 -0.044 0.21 -10000 0 -0.68 47 47
GNB1/GNGT1 0.029 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.014 0.16 -10000 0 -0.39 70 70
GUCY2D 0.012 0.078 -10000 0 -0.62 6 6
GNGT1 -0.015 0.013 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.044 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.07 0.07 -10000 0 -10000 0 0
mol:cGMP 0.032 0.058 -10000 0 -0.4 6 6
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin -0.041 0.055 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.018 0.073 -10000 0 -0.68 5 5
Metarhodopsin II -0.011 0.13 -10000 0 -0.4 45 45
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.063 -10000 0 -0.41 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 28 28
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.038 -10000 0 -0.41 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.026 0.18 -10000 0 -0.44 72 72
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.015 -10000 0 -10000 0 0
PDE6B 0.027 0.005 -10000 0 -10000 0 0
PDE6A 0.012 0.036 -10000 0 -10000 0 0
PDE6G 0.01 0.073 -10000 0 -0.68 4 4
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 0.001 0.17 -10000 0 -0.39 71 71
GUCA1A 0.006 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.037 -10000 0 -0.42 2 2
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.022 0.056 -10000 0 -0.68 3 3
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.68 6 6
UGCG -0.054 0.21 -10000 0 -0.63 53 53
AKT1/mTOR/p70S6K/Hsp90/TERT 0.013 0.14 0.46 4 -0.42 18 22
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.056 0.21 -10000 0 -0.61 57 57
mol:DAG -0.008 0.12 -10000 0 -0.77 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.17 -10000 0 -0.52 24 24
FRAP1 -0.015 0.19 0.44 2 -0.6 27 29
FOXO3 -0.002 0.16 0.44 2 -0.64 18 20
AKT1 -0.007 0.18 -10000 0 -0.68 20 20
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.009 0.087 -10000 0 -0.77 5 5
SGMS1 0.003 0.1 -10000 0 -0.61 11 11
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 0.007 0.037 -10000 0 -0.45 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.027 0.18 0.33 5 -0.56 31 36
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.045 -10000 0 -0.52 3 3
RPS6KB1 0.016 0.067 -10000 0 -0.82 2 2
mol:sphingomyelin -0.008 0.12 -10000 0 -0.77 11 11
natural killer cell activation 0 0.004 -10000 0 -0.023 4 4
JAK3 -0.01 0.063 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.007 0.21 0.47 4 -0.93 17 21
MYB 0.003 0.19 -10000 0 -1.3 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.005 0.15 -10000 0 -0.56 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.068 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.54 22 22
Rac1/GDP 0.023 0.037 -10000 0 -0.41 3 3
T cell proliferation -0.004 0.13 -10000 0 -0.52 19 19
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.062 10 10
PRKCZ -0.005 0.14 -10000 0 -0.55 19 19
NF kappa B1 p50/RelA 0.012 0.17 -10000 0 -0.56 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.56 12 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.016 0.15 -10000 0 -0.64 26 26
IL2RB 0.004 0.092 -10000 0 -0.58 10 10
TERT -0.005 0.022 -10000 0 -10000 0 0
E2F1 0.022 0.077 -10000 0 -0.47 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.031 10 -10000 0 10
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
actin cytoskeleton organization -0.004 0.13 -10000 0 -0.52 19 19
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.014 -10000 0 -10000 0 0
PIK3CA 0.024 0.056 -10000 0 -0.68 3 3
Rac1/GTP 0.048 0.042 -10000 0 -0.39 3 3
LCK 0.013 0.083 -10000 0 -0.68 6 6
BCL2 -0.039 0.27 0.47 4 -0.82 44 48
Signaling events mediated by PRL

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
CCNE1 0.025 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.017 0.078 -10000 0 -0.68 6 6
CDKN1A -0.005 0.065 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.029 0.032 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.073 0.24 4 -0.5 9 13
AGT 0.005 0.099 -10000 0 -0.68 9 9
CCNA2 -0.065 0.15 -10000 0 -0.41 3 3
TUBA1B 0.026 0.005 -10000 0 -10000 0 0
EGR1 -0.084 0.21 -10000 0 -0.5 95 95
CDK2/Cyclin E1 0.019 0.076 -10000 0 -0.54 1 1
MAPK3 0.009 0.025 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.039 0.007 -10000 0 -10000 0 0
MAPK1 0.008 0.022 -10000 0 -10000 0 0
PTP4A1 -0.067 0.16 -10000 0 -0.39 94 94
PTP4A3 0.015 0.04 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.009 0.025 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.01 0.078 -10000 0 -0.62 1 1
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.049 0.16 -10000 0 -0.41 3 3
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.012 0.013 -10000 0 -10000 0 0
RHOC -0.01 0.077 -10000 0 -0.62 1 1
RHOA -0.009 0.076 -10000 0 -0.34 6 6
cell motility -0.004 0.096 0.31 4 -0.72 2 6
PRL-1/alpha Tubulin -0.048 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.022 0.069 -10000 0 -0.52 6 6
ROCK1 -0.005 0.094 0.33 2 -0.73 2 4
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.067 0.16 -10000 0 -0.39 94 94
ATF5 0.02 0.028 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.037 0.059 -10000 0 -0.37 7 7
EPHB2 0.022 0.056 -10000 0 -0.68 3 3
Syndecan-2/TACI -0.082 0.2 -10000 0 -0.44 111 111
LAMA1 -0.021 0.18 -10000 0 -0.67 33 33
Syndecan-2/alpha2 ITGB1 0.042 0.093 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.006 0.044 -10000 0 -0.33 7 7
ITGA5 0.026 0.005 -10000 0 -10000 0 0
BAX 0.004 0.06 -10000 0 -10000 0 0
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.041 -10000 0 -0.39 4 4
LAMA3 -0.001 0.13 -10000 0 -0.68 16 16
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.046 -10000 0 -0.68 2 2
Syndecan-2/MMP2 0.02 0.072 -10000 0 -0.48 9 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.008 0.057 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.058 -10000 0 -0.38 9 9
Syndecan-2/GM-CSF -0.034 0.055 -10000 0 -0.36 6 6
determination of left/right symmetry 0.01 0.051 -10000 0 -0.39 7 7
Syndecan-2/PKC delta 0.026 0.046 -10000 0 -0.33 7 7
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.031 0.047 -10000 0 -0.41 4 4
MAPK1 -0.025 0.046 -10000 0 -0.41 4 4
Syndecan-2/RACK1 0.038 0.042 -10000 0 -0.38 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.051 -10000 0 -0.39 7 7
ITGA2 -0.033 0.073 -10000 0 -10000 0 0
MAPK8 0.006 0.069 -10000 0 -0.42 12 12
Syndecan-2/alpha2/beta1 Integrin 0.032 0.12 -10000 0 -0.42 31 31
Syndecan-2/Kininogen 0.016 0.05 -10000 0 -0.34 7 7
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.021 0.044 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.042 -10000 0 -0.3 7 7
extracellular matrix organization 0.024 0.044 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.037 0.059 -10000 0 -0.37 7 7
Syndecan-2/Caveolin-2/Ras 0.039 0.05 -10000 0 -0.4 6 6
Syndecan-2/Laminin alpha3 0.008 0.095 -10000 0 -0.44 20 20
Syndecan-2/RasGAP 0.05 0.043 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.059 -10000 0 -0.38 9 9
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.042 -10000 0 -0.35 4 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
TNFRSF13B -0.14 0.29 -10000 0 -0.67 108 108
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.057 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.045 -10000 0 -0.43 4 4
TGFB1 0.024 0.015 -10000 0 -10000 0 0
CASP3 0.018 0.044 -10000 0 -0.4 4 4
FN1 -0.081 0.067 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.004 0.085 -10000 0 -0.39 17 17
SDC2 0.01 0.051 -10000 0 -0.39 7 7
KNG1 -0.004 0.037 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.044 -10000 0 -0.43 4 4
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.078 0.064 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.045 -10000 0 -0.43 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.042 -10000 0 -0.4 4 4
Syndecan-2/Ezrin 0.042 0.044 -10000 0 -0.4 4 4
PRKACA 0.016 0.04 -10000 0 -0.4 4 4
angiogenesis -0.004 0.085 -10000 0 -0.39 17 17
MMP2 0.016 0.08 -10000 0 -0.63 7 7
IL8 -0.023 0.11 -10000 0 -0.68 10 10
calcineurin-NFAT signaling pathway -0.081 0.2 -10000 0 -0.44 111 111
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.031 0.067 -10000 0 -0.59 5 5
PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
SPHK1 0.009 0.061 -10000 0 -0.86 2 2
mol:S1P 0.007 0.059 -10000 0 -0.79 2 2
S1P1/S1P/Gi -0.01 0.13 -10000 0 -0.43 35 35
GNAO1 0.001 0.12 -10000 0 -0.68 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.008 0.12 -10000 0 -0.48 17 17
PLCG1 -0.011 0.12 -10000 0 -0.52 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
GNAI2 0.025 0.013 -10000 0 -10000 0 0
GNAI3 0.024 0.013 -10000 0 -10000 0 0
GNAI1 0.023 0.034 -10000 0 -0.68 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.056 -10000 0 -0.51 5 5
S1P1/S1P 0.003 0.07 -10000 0 -0.48 6 6
negative regulation of cAMP metabolic process -0.01 0.13 -10000 0 -0.42 35 35
MAPK3 -0.023 0.17 -10000 0 -0.6 35 35
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
KDR 0.022 0.056 -10000 0 -0.68 3 3
PLCB2 0.013 0.077 0.4 5 -0.49 4 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.009 0.061 -10000 0 -0.4 6 6
receptor internalization 0.003 0.065 -10000 0 -0.44 6 6
PTGS2 -0.062 0.31 0.64 3 -1 43 46
Rac1/GTP 0.01 0.06 -10000 0 -0.46 4 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFA 0.022 0.056 -10000 0 -0.67 3 3
negative regulation of T cell proliferation -0.01 0.13 -10000 0 -0.42 35 35
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.025 0.18 -10000 0 -0.61 37 37
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.08 -10000 0 -0.46 7 7
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.025 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.068 -10000 0 -0.31 8 8
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.012 0.08 0.25 11 -0.35 13 24
RAR alpha/9cRA/Cyclin H 0.031 0.1 -10000 0 -0.37 23 23
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.065 0.24 1 -0.37 6 7
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.094 -10000 0 -0.58 8 8
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.007 0.14 -10000 0 -0.53 25 25
NCOA2 -0.035 0.2 -10000 0 -0.68 42 42
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.017 0.086 -10000 0 -0.64 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.005 0.13 -10000 0 -0.52 23 23
RARA 0.004 0.078 -10000 0 -0.3 26 26
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.12 -10000 0 -0.38 37 37
PRKCA -0.003 0.14 -10000 0 -0.67 21 21
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.15 0.39 4 -0.53 26 30
RXRG -0.03 0.086 -10000 0 -0.39 25 25
RXRA 0.004 0.08 -10000 0 -0.31 26 26
RXRB 0.005 0.082 -10000 0 -0.38 21 21
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RBP1 0.016 0.085 -10000 0 -0.68 7 7
CRBP1/9-cic-RA 0.012 0.064 -10000 0 -0.51 7 7
RARB 0.01 0.11 -10000 0 -0.68 13 13
PRKCG 0.021 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.011 0.14 -10000 0 -0.56 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.004 0.12 -10000 0 -0.48 25 25
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.09 0.41 2 -0.42 10 12
RXRs/RARs/NRIP1/9cRA/HDAC3 0.007 0.15 0.42 5 -0.53 26 31
positive regulation of DNA binding 0.02 0.093 -10000 0 -0.35 23 23
NRIP1 0.008 0.13 0.5 1 -0.72 5 6
RXRs/RARs 0.001 0.14 -10000 0 -0.53 26 26
RXRs/RXRs/DNA/9cRA -0.015 0.12 -10000 0 -0.54 23 23
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.07 -10000 0 -0.42 3 3
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.018 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.19 0.32 -10000 0 -0.67 150 150
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.02 0.064 -10000 0 -0.68 4 4
AKT 0.015 0.085 0.35 9 -10000 0 9
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.007 -10000 0 -10000 0 0
FOXO4 0.025 0.008 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.008 0.11 -10000 0 -0.68 11 11
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.033 0.088 -10000 0 -0.19 44 44
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.036 0.068 0.36 8 -10000 0 8
PI3K -0.017 0.1 0.41 8 -0.24 13 21
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.06 0.32 8 -10000 0 8
AKT2 0.025 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.023 0.079 0.46 11 -10000 0 11
EGFR 0.02 0.064 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.033 0.07 0.43 12 -10000 0 12
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.002 0.11 -10000 0 -0.54 18 18
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.052 0.4 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.01 0.057 0.39 6 -10000 0 6
EGF -0.074 0.24 -10000 0 -0.67 68 68
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.043 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.014 0.053 0.39 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.06 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.014 0.028 -10000 0 -10000 0 0
PVRL2 0.025 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.009 0.14 -10000 0 -0.36 69 69
RhoA/GDP 0.056 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.022 0.056 0.4 9 -10000 0 9
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 106 106
DIAPH1 0.051 0.045 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.022 0.056 0.4 9 -10000 0 9
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.012 0.054 0.35 3 -0.36 6 9
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.01 0.058 0.4 6 -10000 0 6
HGF/MET -0.006 0.15 -10000 0 -0.38 62 62
HGF -0.074 0.24 -10000 0 -0.68 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.069 0.14 0.51 29 -0.33 1 30
KIAA1543 0.014 0.053 0.37 8 -0.35 1 9
KIFC3 0.022 0.024 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.025 0.038 0.36 4 -10000 0 4
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.022 0.024 -10000 0 -10000 0 0
PIP5K1C 0.026 0.053 0.4 8 -10000 0 8
LIMA1 0.026 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.045 0.1 0.43 22 -10000 0 22
adherens junction assembly 0.028 0.093 0.48 13 -0.56 1 14
IGF-1R heterotetramer/IGF1 -0.038 0.17 -10000 0 -0.36 100 100
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.011 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PLEKHA7 0.026 0.053 0.38 8 -0.37 1 9
mol:GTP 0.059 0.023 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.033 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.022 0.056 0.4 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.014 0.11 -10000 0 -0.47 24 24
ATM 0.025 0.032 -10000 0 -0.68 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
ATR 0.026 0.032 -10000 0 -0.68 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.027 -10000 0 -0.38 2 2
protein ubiquitination 0.045 0.091 -10000 0 -0.38 18 18
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.05 0.035 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.68 2 2
DNA-PK 0.04 0.025 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.019 0.092 -10000 0 -0.58 10 10
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.008 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.014 0.11 -10000 0 -0.45 24 24
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.019 0.03 -10000 0 -10000 0 0
DNA repair 0.019 0.086 0.41 2 -0.48 4 6
BRCA1/BARD1/ubiquitin 0.014 0.11 -10000 0 -0.45 24 24
BARD1/DNA-PK 0.03 0.098 -10000 0 -0.4 21 21
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.014 0.11 0.47 24 -10000 0 24
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.073 -10000 0 -0.29 21 21
BRCA1/BACH1/BARD1/TopBP1 0.03 0.099 -10000 0 -0.41 21 21
BRCA1/BARD1/P53 0.044 0.096 -10000 0 -0.4 19 19
BARD1/CSTF1/BRCA1 0.03 0.098 -10000 0 -0.42 20 20
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.007 0.15 -10000 0 -0.62 25 25
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.099 -10000 0 -0.39 24 24
BRCA1/BARD1/UbcH7 0.019 0.097 -10000 0 -0.41 21 21
BRCA1/BARD1/RAD51/PCNA 0.045 0.095 -10000 0 -0.4 18 18
BARD1/DNA-PK/P53 0.039 0.095 -10000 0 -0.38 19 19
BRCA1/BARD1/Ubiquitin 0.014 0.11 -10000 0 -0.45 24 24
BRCA1/BARD1/CTIP 0.025 0.092 -10000 0 -0.4 19 19
FA complex 0.028 0.035 -10000 0 -0.24 3 3
BARD1/EWS 0.004 0.11 -10000 0 -0.46 25 25
RBBP8 0.016 0.024 -10000 0 -0.51 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.042 0.095 0.4 19 -10000 0 19
BRCA1/BARD1 0.051 0.094 -10000 0 -0.38 18 18
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.006 0.11 -10000 0 -0.47 25 25
CDK2 0.026 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.011 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.014 0.11 -10000 0 -0.45 24 24
EWSR1 0.02 0.012 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.026 0.047 0.29 10 -0.36 1 11
DAPP1 -0.037 0.13 0.34 4 -0.5 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.053 0.17 0.29 5 -0.53 21 26
mol:DAG -0.017 0.093 0.33 10 -0.26 14 24
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.033 0.068 0.28 2 -0.33 6 8
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.049 0.3 10 -10000 0 10
ARF1/GTP 0.004 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
ADAP1 0 0.046 0.29 10 -10000 0 10
ARAP3 0 0.048 0.3 10 -10000 0 10
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.019 -10000 0 -0.36 1 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.007 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.065 0.26 14 -10000 0 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
ZAP70 0 0.12 -10000 0 -0.66 16 16
mol:IP3 -0.012 0.069 0.23 12 -0.2 7 19
LYN 0.027 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.078 0.32 8 -0.33 8 16
RhoA/GDP 0.038 0.043 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.078 0.36 15 -10000 0 15
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.021 -10000 0 -0.34 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.026 0.04 0.29 9 -10000 0 9
RhoA/GTP 0.025 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.045 0.14 -10000 0 -0.45 24 24
BLK -0.19 0.31 -10000 0 -0.67 142 142
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
CYTH1 0.002 0.055 0.31 12 -10000 0 12
HCK 0.018 0.035 -10000 0 -10000 0 0
CYTH3 -0.001 0.05 0.29 10 -0.36 1 11
CYTH2 0.004 0.058 0.31 14 -10000 0 14
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.097 -10000 0 -0.57 11 11
SGK1 0.016 0.11 -10000 0 -0.59 12 12
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.025 0.085 0.3 13 -0.33 10 23
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.051 0.28 9 -10000 0 9
mol:PI-3-4-5-P3 -0.007 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.57 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.03 0.33 1 -10000 0 1
PLEKHA1 0.005 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.068 0.35 1 -0.31 8 9
LAT 0.021 0.059 -10000 0 -0.6 4 4
Rac1/GTP 0.017 0.063 0.28 2 -0.48 3 5
ITK -0.04 0.12 0.28 10 -0.37 49 59
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.029 0.12 0.37 9 -0.36 16 25
LCK 0.012 0.083 -10000 0 -0.68 6 6
BTK -0.005 0.067 0.29 13 -0.36 6 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.1 0.54 5 -0.48 1 6
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.37 -10000 0 -0.72 148 148
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.054 -10000 0 -10000 0 0
ER alpha/Oestrogen -0.01 0.11 -10000 0 -0.49 23 23
NFX1/SIN3/HDAC complex 0.03 0.047 -10000 0 -0.56 2 2
EGF -0.073 0.24 -10000 0 -0.67 68 68
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.004 0.088 0.55 2 -0.44 1 3
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.05 0.035 -10000 0 -0.44 2 2
WT1 0.008 0.046 -10000 0 -10000 0 0
WRN 0.025 0.032 -10000 0 -0.68 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.01 0.084 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.002 0.11 0.54 5 -0.49 1 6
CCND1 0.001 0.11 0.6 5 -10000 0 5
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.008 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.68 2 2
TERF2 0.023 0.009 -10000 0 -10000 0 0
PTGES3 0.026 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.024 0.061 -10000 0 -10000 0 0
CDKN1B -0.029 0.14 -10000 0 -0.42 54 54
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.68 1 1
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.67 103 103
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 125 125
IFN-gamma/IRF1 -0.018 0.18 -10000 0 -0.48 59 59
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.026 0.008 -10000 0 -10000 0 0
Telomerase 0.013 0.11 0.27 1 -0.55 10 11
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.65 23 23
KU/TER 0.029 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.025 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.037 0.043 -10000 0 -0.37 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.043 -10000 0 -0.38 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.01 0.024 -10000 0 -0.48 1 1
SMAD3 0.015 0.01 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.045 -10000 0 -0.68 2 2
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.015 0.084 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.015 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.024 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.064 -10000 0 -0.68 4 4
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.041 0.19 -10000 0 -0.5 71 71
MYC 0.01 0.11 -10000 0 -0.65 12 12
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.018 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.015 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.013 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.001 0.088 0.51 2 -10000 0 2
SP1/HDAC2 0.042 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.004 -10000 0 -10000 0 0
Telomerase/EST1A 0.01 0.082 -10000 0 -10000 0 0
Smad3/Myc 0.018 0.07 -10000 0 -0.44 10 10
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.061 0.23 -10000 0 -0.67 59 59
Telomerase/PinX1 0.009 0.084 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.012 0.066 0.37 1 -0.42 3 4
SIN3B 0.025 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.008 0.08 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.026 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.009 0.084 -10000 0 -10000 0 0
E2F1 -0.017 0.068 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.018 0.073 -10000 0 -0.68 5 5
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.036 0.098 0.45 10 -0.52 2 12
NFATC2 -0.021 0.096 0.28 9 -0.27 26 35
NFATC3 0.018 0.01 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.009 0.088 0.28 1 -0.3 26 27
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.003 0.1 -10000 0 -0.45 11 11
BCL2/BAX -0.001 0.14 -10000 0 -0.49 35 35
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.025 0.008 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.005 0.094 0.33 4 -0.38 10 14
Calcineurin A alpha-beta B1/BCL2 -0.024 0.18 -10000 0 -0.66 35 35
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.005 0.093 0.38 10 -0.33 4 14
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
MAP3K8 0.014 0.086 -10000 0 -0.64 8 8
NFAT4/CK1 alpha 0.02 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.072 0.17 -10000 0 -0.34 105 105
CABIN1 -0.009 0.086 0.28 1 -0.29 25 26
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.086 -10000 0 -0.68 7 7
mol:Ca2+ -0.004 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.035 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.086 -10000 0 -0.64 8 8
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.087 0.37 2 -0.46 3 5
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.01 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.053 -10000 0 -0.32 5 5
PRKCB 0.005 0.082 -10000 0 -0.68 5 5
PRKCE 0.021 0.064 -10000 0 -0.68 4 4
JNK2/NFAT4 0.031 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.007 -10000 0 -10000 0 0
PRKCA -0.005 0.14 -10000 0 -0.68 21 21
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.02 0.066 -10000 0 -0.61 5 5
FKBP38/BCL2 -0.001 0.14 -10000 0 -0.49 35 35
EP300 0.01 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.039 0.1 0.41 8 -0.51 3 11
CaM/Ca2+/FKBP38 0.019 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.063 -10000 0 -0.45 7 7
NFATc/ERK1 0.042 0.082 0.44 3 -0.48 2 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.007 0.1 -10000 0 -0.44 12 12
NR4A1 -0.17 0.29 -10000 0 -0.61 142 142
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.022 0.07 -10000 0 -0.36 5 5
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.049 0.097 0.42 11 -0.49 2 13
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.024 0.18 -10000 0 -0.67 35 35
TCGA08_p53

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
CDKN2A -0.025 0.042 -10000 0 -10000 0 0
TP53 -0.008 0.035 -10000 0 -0.18 18 18
Senescence -0.008 0.035 -10000 0 -0.18 18 18
Apoptosis -0.008 0.035 -10000 0 -0.18 18 18
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.35 1 -10000 0 1
MDM4 0.025 0.007 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.025 0.032 -9999 0 -0.68 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.054 -9999 0 -0.26 16 16
GNAO1 0.005 0.12 -9999 0 -0.67 15 15
S1P/S1P3/G12/G13 0.047 0.019 -9999 0 -10000 0 0
AKT1 0.023 0.041 -9999 0 -0.35 3 3
AKT3 0.02 0.067 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
GNAI2 0.028 0.003 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.033 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.41 3 3
MAPK3 0.003 0.066 -9999 0 -0.4 3 3
MAPK1 0.013 0.059 -9999 0 -0.38 3 3
JAK2 0.007 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.065 -9999 0 -0.4 3 3
FLT1 0.027 0.033 -9999 0 -0.68 1 1
RhoA/GDP 0.02 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC 0.004 0.063 -9999 0 -0.34 3 3
S1P/S1P3/Gi 0.006 0.071 -9999 0 -0.42 3 3
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.074 -9999 0 -0.38 3 3
VEGFA 0.025 0.056 -9999 0 -0.67 3 3
S1P/S1P2/Gi 0.004 0.075 -9999 0 -0.33 15 15
VEGFR1 homodimer/VEGFA homodimer 0.04 0.057 -9999 0 -0.64 3 3
RHOA 0.027 0.003 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.055 0.15 -9999 0 -0.31 115 115
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.64 112 112
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.016 0.08 -9999 0 -0.63 7 7
Rac1/GTP 0.01 0.073 -9999 0 -0.38 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.12 0.28 -10000 0 -0.67 97 97
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.039 0.35 1 -10000 0 1
HIF1A 0.009 0.024 -10000 0 -0.25 2 2
COPS5 0.027 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.052 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.032 0.071 -10000 0 -10000 0 0
ARNT/IPAS -0.07 0.21 -10000 0 -0.48 97 97
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.05 0.3 8 -10000 0 8
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.026 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.038 0.28 1 -10000 0 1
PHD1-3/OS9 0.049 0.074 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.04 -10000 0 -10000 0 0
VHL 0.023 0.055 -10000 0 -0.68 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.047 0.34 4 -0.24 2 6
EGLN3 0.007 0.1 -10000 0 -0.68 10 10
EGLN2 0.025 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.033 -10000 0 -0.68 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.076 -10000 0 -0.57 6 6
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.038 0.053 0.31 7 -10000 0 7
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.015 0.081 0.63 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.082 -10000 0 -0.63 7 7
PDE3B 0.015 0.082 -10000 0 -0.63 7 7
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.008 -9999 0 -10000 0 0
SPHK1 0.023 0.022 -9999 0 -10000 0 0
GNAI2 0.027 0.003 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.003 0.12 -9999 0 -0.68 15 15
mol:Sphinganine-1-P 0.014 0.014 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.028 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.018 -9999 0 -10000 0 0
S1PR5 0.023 0.034 -9999 0 -0.68 1 1
S1PR4 0.024 0.017 -9999 0 -10000 0 0
GNAI1 0.025 0.033 -9999 0 -0.68 1 1
S1P/S1P5/G12 0.043 0.032 -9999 0 -0.39 1 1
S1P/S1P3/Gq -0.054 0.16 -9999 0 -0.39 36 36
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.5 4 4
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.64 112 112
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.016 0.08 -9999 0 -0.63 7 7
ABCC1 0.026 0.006 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.006 0.017 0.12 1 -0.13 4 5
BUB1B 0.014 0.031 0.18 9 -0.17 1 10
PLK1 0.012 0.032 0.16 13 -0.12 1 14
PLK1S1 0.015 0.027 0.18 10 -10000 0 10
KIF2A 0.018 0.069 0.32 20 -0.39 1 21
regulation of mitotic centrosome separation 0.012 0.032 0.16 13 -0.12 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.037 0.17 1 -10000 0 1
WEE1 0.022 0.048 0.3 5 -0.31 3 8
cytokinesis 0.012 0.06 0.28 7 -0.27 2 9
PP2A-alpha B56 0.048 0.095 -10000 0 -0.55 9 9
AURKA 0.014 0.027 0.17 7 -0.26 1 8
PICH/PLK1 0.019 0.016 -10000 0 -10000 0 0
CENPE 0.01 0.052 0.26 10 -0.39 3 13
RhoA/GTP 0.02 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.069 0.32 20 -0.39 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.03 0.18 11 -0.25 1 12
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.036 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.03 0.15 3 -0.28 3 6
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 26 -10000 0 26
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.019 0.096 14 -0.049 1 15
G2 phase of mitotic cell cycle 0 0.004 0.02 11 -10000 0 11
STAG2 0.025 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.03 -10000 0 -0.41 2 2
spindle elongation 0.012 0.032 0.16 13 -0.12 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.024 0.095 -10000 0 -0.56 12 12
TPT1 0.005 0.045 0.15 6 -0.18 23 29
CDC25C 0.019 0.026 0.19 6 -10000 0 6
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.017 0.13 4 -0.12 1 5
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.015 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.41 5 5
CDC20 0.025 0.017 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.022 0.15 4 -10000 0 4
mitosis -0.001 0.003 0.02 6 -10000 0 6
FBXO5 0.013 0.038 0.19 11 -0.23 2 13
CDC2 0.002 0.001 0.01 1 -10000 0 1
NDC80 0.006 0.052 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.027 0.17 2 -0.24 3 5
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.028 0.14 15 -10000 0 15
microtubule cytoskeleton organization 0.005 0.045 0.15 6 -0.18 23 29
G2/M transition DNA damage checkpoint 0 0.004 0.02 13 -10000 0 13
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.02 13 -10000 0 13
PLK1/PRC1-2 0.038 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.022 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.028 0.14 14 -0.11 1 15
mitotic prometaphase 0 0.003 0.026 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.026 -10000 0 -10000 0 0
microtubule-based process 0.015 0.031 -10000 0 -10000 0 0
Golgi organization 0.012 0.032 0.16 13 -0.12 1 14
Cohesin/SA2 0.02 0.017 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.039 0.009 -10000 0 -10000 0 0
KIF20A 0.002 0.055 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.026 0.2 3 -10000 0 3
PPP2R1A 0.025 0.008 -10000 0 -10000 0 0
chromosome segregation 0.011 0.022 0.15 4 -10000 0 4
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.042 0.21 9 -0.4 2 11
C13orf34 0.01 0.027 0.14 13 -0.11 1 14
NUDC 0.014 0.027 0.17 2 -0.24 3 5
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.18 9 -0.17 1 10
spindle assembly 0.014 0.038 0.17 19 -0.086 1 20
spindle stabilization 0.015 0.027 0.18 10 -10000 0 10
APC/C/HCDH1 0.019 0.041 -10000 0 -0.35 5 5
MKLP2/PLK1 0.015 0.031 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.002 0.1 0.26 2 -0.42 25 27
TUBG1 0.015 0.029 0.18 9 -0.16 2 11
G2/M transition of mitotic cell cycle 0.013 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.012 -10000 0 -10000 0 0
INCENP 0.024 0.046 -10000 0 -0.68 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.004 0.1 -10000 0 -0.39 27 27
CCNA2 0.024 0.02 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
JAK3 -0.011 0.063 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.002 0.13 -10000 0 -0.55 18 18
SHC1 0.026 0.007 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.031 0.2 -10000 0 -0.87 26 26
IL2RB 0.004 0.092 -10000 0 -0.58 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.012 0.14 -10000 0 -0.63 21 21
G1/S transition of mitotic cell cycle 0.03 0.068 0.43 6 -0.5 3 9
PTPN11 0.026 0.032 -10000 0 -0.68 1 1
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.012 0.083 -10000 0 -0.68 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.022 0.056 -10000 0 -0.68 3 3
CCND3 0.007 0.12 -10000 0 -0.6 9 9
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.007 0.1 -9999 0 -0.64 10 10
ITGA4 0.021 0.05 -9999 0 -0.68 2 2
alpha4/beta7 Integrin 0.019 0.087 -9999 0 -0.51 11 11
alpha4/beta1 Integrin 0.035 0.039 -9999 0 -0.51 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.003 0.16 -10000 0 -0.44 57 57
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.021 0.14 -10000 0 -0.38 56 56
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.025 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.034 0.085 -10000 0 -10000 0 0
YY1/LSF 0.006 0.066 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.009 0.11 -10000 0 -0.31 55 55
I kappa B alpha/HDAC1 0.009 0.082 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA -0.018 0.11 -10000 0 -0.32 57 57
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.011 0.082 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.038 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.025 0.12 0.32 1 -0.42 16 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.012 0.02 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.068 -10000 0 -0.49 5 5
RBBP7 0.025 0.008 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.68 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.004 0.085 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.032 -10000 0 -0.4 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.032 -10000 0 -0.68 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.081 -10000 0 -10000 0 0
YY1/HDAC2 0.009 0.055 -10000 0 -0.28 1 1
YY1/HDAC1 0.01 0.053 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.031 0.031 -10000 0 -0.4 1 1
PPARG -0.024 0.14 -10000 0 -0.39 61 61
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.011 0.082 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.034 0.062 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.004 0.085 -10000 0 -0.24 56 56
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.019 0.012 -10000 0 -10000 0 0
HDAC8 0.025 0.008 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.026 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.066 -10000 0 -0.4 4 4
YY1/SAP30/HDAC1 0.021 0.057 -10000 0 -0.31 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.084 -10000 0 -10000 0 0
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.076 -10000 0 -0.27 10 10
nuclear export -0.045 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.011 0.082 -10000 0 -10000 0 0
GATA1/HDAC1 0.034 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.007 0.081 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.028 0.18 -10000 0 -0.51 57 57
SIN3/HDAC complex/Mad/Max 0.031 0.046 -10000 0 -0.57 2 2
NuRD Complex 0.041 0.052 -10000 0 -0.42 3 3
positive regulation of chromatin silencing 0.032 0.083 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.057 -10000 0 -0.26 2 2
HDAC complex 0.062 0.036 -10000 0 -0.4 2 2
GATA1/Fog1 0.034 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.052 0.014 -10000 0 -10000 0 0
TNF -0.06 0.23 -10000 0 -0.68 57 57
negative regulation of cell growth 0.034 0.047 -10000 0 -0.57 2 2
NuRD/MBD2/PRMT5 Complex 0.031 0.031 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.033 0.14 -10000 0 -0.4 57 57
SIN3/HDAC complex/NCoR1 0.03 0.054 -10000 0 -0.5 3 3
TFCP2 0.021 0.064 -10000 0 -0.68 4 4
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.024 0.058 0.35 2 -0.55 2 4
PDGFB-D/PDGFRB/SLAP 0.037 0.028 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.051 0.026 -10000 0 -0.42 1 1
AKT1 0.03 0.088 0.5 11 -0.33 2 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.028 0.06 0.35 2 -0.62 2 4
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
FGR 0.017 0.048 0.33 2 -0.59 2 4
mol:Ca2+ 0.033 0.086 0.4 13 -0.68 2 15
MYC 0.028 0.18 0.57 18 -0.77 14 32
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.024 -10000 0 -0.38 1 1
LRP1/PDGFRB/PDGFB 0.038 0.04 -10000 0 -0.44 2 2
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GO:0007205 0.033 0.087 0.4 13 -0.69 2 15
PTEN 0.026 0.018 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.055 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.037 -10000 0 -0.52 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.027 -10000 0 -0.51 1 1
cell cycle arrest 0.037 0.028 -10000 0 -0.51 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.024 0.085 0.48 11 -10000 0 11
GAB1 0.028 0.094 0.42 12 -0.64 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.033 0.11 0.47 17 -0.56 2 19
PDGFB-D/PDGFRB 0.053 0.029 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.027 -10000 0 -0.51 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.033 0.055 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.037 -10000 0 -0.51 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.033 0.087 0.4 13 -0.7 2 15
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.051 -10000 0 -0.57 1 1
SHB 0.025 0.008 -10000 0 -10000 0 0
BLK -0.14 0.26 -10000 0 -0.56 138 138
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.49 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.033 0.11 0.48 14 -0.6 3 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.027 -10000 0 -0.51 1 1
LCK 0.01 0.083 -10000 0 -0.67 6 6
PDGFRB 0.026 0.033 -10000 0 -0.69 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.022 0.046 0.29 1 -0.59 2 3
ABL1 0.026 0.098 0.41 14 -0.68 2 16
PDGFB-D/PDGFRB/CBL 0.022 0.086 0.41 5 -0.72 2 7
PTPN1 0.027 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.03 0.17 0.55 19 -0.68 14 33
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.026 -10000 0 -0.37 1 1
SRC 0.017 0.049 0.29 1 -0.51 3 4
PI3K 0.012 0.034 -10000 0 -0.35 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.3 1 1
SH2B2 0.026 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.062 0.36 2 -0.64 2 4
LYN 0.018 0.035 -10000 0 -0.44 2 2
LRP1 0.025 0.032 -10000 0 -0.68 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.032 -10000 0 -0.38 1 1
SPHK1 0.023 0.022 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.033 0.087 0.4 13 -0.7 2 15
PLCG1 0.033 0.089 0.4 13 -0.72 2 15
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.06 0.32 2 -0.5 5 7
cell migration 0.049 0.028 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.4 1 1
FYN 0.016 0.053 0.29 1 -0.44 5 6
DOK1 0.023 0.029 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.038 0.14 0.54 19 -0.47 11 30
PRKCD 0.024 0.03 -10000 0 -0.42 1 1
FER 0.02 0.043 -10000 0 -0.42 4 4
MAPKKK cascade 0.016 0.055 0.37 1 -10000 0 1
RASA1 0.023 0.027 -10000 0 -0.42 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.029 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.026 0.097 0.41 14 -0.65 2 16
STAT1-3-5/STAT1-3-5 0.063 0.029 -10000 0 -0.37 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.52 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.017 0.043 -10000 0 -0.28 3 3
STMN1 0.002 0.041 0.19 2 -10000 0 2
Aurora B/RasGAP/Survivin 0.049 0.055 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.013 0.053 -10000 0 -0.27 6 6
BIRC5 0.014 0.051 -10000 0 -0.68 1 1
DES -0.33 0.3 -10000 0 -0.56 290 290
Aurora C/Aurora B/INCENP 0.053 0.045 -10000 0 -0.45 2 2
Aurora B/TACC1 0.031 0.042 -10000 0 -0.5 1 1
Aurora B/PP2A 0.021 0.048 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.01 0.059 0.18 1 -10000 0 1
Cul3 protein complex 0.038 0.071 -10000 0 -0.44 9 9
KIF2C 0.015 0.03 -10000 0 -0.52 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.002 0.055 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.021 0.048 -10000 0 -10000 0 0
SEPT1 0.024 0.02 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.003 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.016 0.08 0.28 2 -0.54 8 10
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.016 -10000 0 -10000 0 0
AURKB 0.003 0.063 -10000 0 -10000 0 0
AURKC 0.02 0.029 -10000 0 -10000 0 0
CDCA8 0.028 0.014 -10000 0 -10000 0 0
cytokinesis -0.019 0.057 -10000 0 -0.39 4 4
Aurora B/Septin1 0.044 0.067 -10000 0 -0.37 3 3
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.025 0.047 -10000 0 -0.69 2 2
KLHL13 0.007 0.1 -10000 0 -0.62 11 11
BUB1 -0.026 0.077 -10000 0 -0.68 1 1
hSgo1/Aurora B/Survivin 0.047 0.056 -10000 0 -0.4 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.049 0.048 -10000 0 -10000 0 0
SGOL1 0.021 0.029 -10000 0 -10000 0 0
CENPA 0.019 0.037 0.19 1 -0.22 5 6
NCAPG 0.013 0.044 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.021 0.048 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.021 0.048 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
NCAPH 0.006 0.052 -10000 0 -10000 0 0
NPM1 0.012 0.041 -10000 0 -0.3 7 7
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.048 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.042 0.048 -10000 0 -0.3 1 1
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
NSUN2 0.011 0.044 -10000 0 -0.3 6 6
MYLK 0.012 0.016 -10000 0 -10000 0 0
KIF23 0.021 0.033 -10000 0 -10000 0 0
VIM 0.001 0.038 -10000 0 -10000 0 0
RACGAP1 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.005 0.081 -10000 0 -0.51 8 8
Chromosomal passenger complex 0.016 0.037 -10000 0 -0.28 3 3
Chromosomal passenger complex/EVI5 0.1 0.066 -10000 0 -0.42 3 3
TACC1 0.025 0.032 -10000 0 -0.68 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.07 0.38 1 -0.36 1 2
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.052 -10000 0 -0.51 2 2
NFKBIA 0.022 0.011 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.004 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.033 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.012 0.15 0.32 1 -0.52 7 8
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.032 0.076 -10000 0 -0.44 2 2
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.072 -10000 0 -0.51 1 1
BCL10/MALT1/TRAF6 0.05 0.035 -10000 0 -0.44 2 2
NOD2 0.005 0.066 -10000 0 -0.68 2 2
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.032 -10000 0 -0.68 1 1
TNF/TNFR1A -0.028 0.18 -10000 0 -0.51 57 57
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
PRKCA -0.005 0.14 -10000 0 -0.68 21 21
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.06 0.23 -10000 0 -0.68 57 57
NF kappa B1 p50/RelA 0.061 0.015 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.046 0.077 -10000 0 -0.55 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.038 0.11 -10000 0 -0.51 4 4
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.029 0.1 -10000 0 -0.45 8 8
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.033 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.025 0.11 0.37 7 -0.47 8 15
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.053 0.18 -10000 0 -0.49 65 65
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.028 -10000 0 -0.44 1 1
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.048 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.032 0.093 -10000 0 -0.34 16 16
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.023 0.11 0.41 5 -0.54 8 13
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.008 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
LNPEP 0.003 0.13 -10000 0 -0.68 16 16
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.016 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.02 0.025 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
FOXO3 0.022 0.024 -10000 0 -10000 0 0
AKT1 0.022 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.027 -10000 0 -0.39 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.027 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.037 -10000 0 -0.33 1 1
BAD/YWHAZ 0.05 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.033 -10000 0 -0.68 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.035 0.32 1 -10000 0 1
TSC1 0.021 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.036 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.024 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.021 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.046 0.15 -10000 0 -0.43 61 61
MAP3K5 0.025 0.032 -10000 0 -0.68 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.082 0.38 6 -0.36 8 14
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.027 0.038 -10000 0 -10000 0 0
CASP9 0.023 0.029 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.047 0.4 4 -10000 0 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.021 0.029 -10000 0 -0.36 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 -10000 0 -10000 0 0
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.027 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.021 0.088 0.4 9 -0.37 4 13
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
MDM2 0.022 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.024 0.04 0.3 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.032 -10000 0 -10000 0 0
glucose import -0.056 0.16 0.21 4 -0.41 74 78
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.058 0.16 -10000 0 -0.42 74 74
GSK3A 0.026 0.037 -10000 0 -10000 0 0
FOXO1 0.021 0.024 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
G1/S transition of mitotic cell cycle 0.028 0.045 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.015 0.063 0.26 1 -0.41 6 7
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.006 0.075 0.3 15 -10000 0 15
GNAI2 0.027 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
RhoA/GTP 0.007 0.077 -10000 0 -0.3 15 15
negative regulation of cAMP metabolic process -0.001 0.075 -10000 0 -0.32 16 16
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.076 -10000 0 -0.33 16 16
RhoA/GDP 0.02 0.002 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.033 -10000 0 -0.68 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.009 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.009 0.004 -10000 0 -10000 0 0
MAPK12 -0.001 0.053 -10000 0 -0.38 9 9
CCND1 0.007 0.046 -10000 0 -0.4 4 4
p38 gamma/SNTA1 0.02 0.066 -10000 0 -0.36 11 11
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.062 0.21 7 -0.38 10 17
MAP2K6 0.001 0.064 -10000 0 -0.42 11 11
MAPT 0.009 0.051 0.32 6 -0.36 3 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.019 -10000 0 -0.39 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.024 0.24 3 -10000 0 3
AES 0.025 0.02 0.2 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.004 -10000 0 -10000 0 0
DKK2 -0.004 0.14 -10000 0 -0.67 19 19
TLE1 0.021 0.058 0.22 2 -0.66 3 5
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.05 0.093 0.49 15 -10000 0 15
WIF1 -0.014 0.045 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.084 0.39 22 -10000 0 22
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0.001 0.063 -10000 0 -0.68 1 1
beta catenin/beta TrCP1 0.048 0.046 0.49 1 -10000 0 1
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.6 15 -1.4 18 33
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.068 -10000 0 -0.53 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.038 0.098 0.3 1 -0.59 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.036 0.042 0.51 2 -10000 0 2
HNF1A 0.027 0.021 0.23 1 -10000 0 1
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.04 0.25 0.6 2 -1.4 14 16
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.094 -10000 0 -0.43 18 18
NKD1 0.006 0.11 -10000 0 -0.68 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.026 0.023 0.25 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.064 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.024 0.13 0.53 22 -10000 0 22
LEF1 0.023 0.05 0.22 1 -0.63 2 3
DVL1 0.028 0.016 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.12 -10000 0 -0.54 9 9
DKK1/LRP6/Kremen 2 0.049 0.039 -10000 0 -0.49 1 1
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.019 -10000 0 -10000 0 0
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.087 0.58 2 -0.68 3 5
WNT1 0.023 0.013 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.055 0.33 13 -0.33 1 14
APC 0.022 0.039 0.36 3 -0.39 1 4
WNT1/LRP6/FZD1 0.031 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.009 0.039 -10000 0 -0.17 3 3
RAB3GAP2/RIMS1/UNC13B 0.048 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.017 -10000 0 -10000 0 0
mol:ACh 0.002 0.044 0.14 19 -0.14 24 43
RAB3GAP2 0.025 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.039 -10000 0 -0.17 3 3
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.009 0.043 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.04 0.11 -10000 0 -0.48 24 24
SNAP25 -0.016 0.076 -10000 0 -0.34 25 25
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.066 0.15 -10000 0 -0.68 23 23
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.087 -10000 0 -0.52 11 11
AKT1 0.04 0.087 0.37 3 -0.58 6 9
PTK2B 0.019 0.1 0.35 1 -0.82 4 5
VEGFR2 homodimer/Frs2 0.034 0.076 -10000 0 -0.9 3 3
CAV1 0.013 0.095 -10000 0 -0.68 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.089 -10000 0 -0.73 5 5
endothelial cell proliferation 0.053 0.15 0.6 18 -0.55 5 23
mol:Ca2+ 0.024 0.085 -10000 0 -0.64 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.062 0.086 -10000 0 -0.78 4 4
RP11-342D11.1 0.013 0.084 -10000 0 -0.64 6 6
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.059 -10000 0 -0.44 5 5
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.02 0.056 -10000 0 -0.68 3 3
HRAS/GDP 0.041 0.074 -10000 0 -0.74 3 3
SH2D2A -0.008 0.14 -10000 0 -0.68 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.094 -10000 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.026 0.13 -10000 0 -0.46 26 26
VEGFR1 homodimer 0.024 0.033 -10000 0 -0.67 1 1
SHC/GRB2/SOS1 0.067 0.09 -10000 0 -0.86 3 3
GRB10 0.025 0.084 -10000 0 -0.92 3 3
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.087 -10000 0 -0.68 5 5
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.028 0.063 -10000 0 -0.43 5 5
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.059 0.084 -10000 0 -0.76 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.071 -10000 0 -0.68 5 5
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.048 0.089 -10000 0 -0.73 5 5
mol:GDP 0.053 0.081 -10000 0 -0.8 3 3
mol:NADP 0.04 0.1 0.46 8 -0.53 4 12
eNOS/Hsp90 0.044 0.08 -10000 0 -0.49 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.024 0.088 -10000 0 -0.66 6 6
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.008 -10000 0 -10000 0 0
VEGFA 0.025 0.055 -10000 0 -0.67 3 3
VEGFC 0.025 0.032 -10000 0 -0.68 1 1
FAK1/Vinculin 0.04 0.099 -10000 0 -0.75 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.11 -10000 0 -0.52 14 14
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.031 0.054 -10000 0 -0.58 3 3
mol:L-citrulline 0.04 0.1 0.46 8 -0.53 4 12
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.06 0.087 -10000 0 -0.78 4 4
VEGFR2 homodimer/VEGFA homodimer 0.051 0.1 -10000 0 -0.72 6 6
VEGFR2/3 heterodimer 0.029 0.1 -10000 0 -0.78 6 6
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.008 0.094 0.38 1 -0.69 6 7
VEGFR2 homodimer 0.021 0.082 -10000 0 -1 3 3
FLT1 0.024 0.033 -10000 0 -0.68 1 1
NEDD4 0.026 0.045 -10000 0 -0.67 2 2
MAPK3 0.001 0.088 0.38 1 -0.76 4 5
MAPK1 -0.003 0.088 0.38 1 -0.76 4 5
VEGFA145/NRP2 0.028 0.053 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.031 0.087 -10000 0 -1 3 3
KDR 0.021 0.082 -10000 0 -1 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.055 0.095 -10000 0 -0.67 6 6
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.012 0.12 0.42 12 -0.93 3 15
PI3K 0.043 0.093 -10000 0 -0.8 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.049 0.089 -10000 0 -0.73 5 5
FES 0.025 0.092 -10000 0 -0.67 6 6
GAB1 0.031 0.088 -10000 0 -0.79 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.089 -10000 0 -0.73 5 5
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.091 0.4 1 -0.54 5 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.089 -10000 0 -0.73 5 5
PI3K/GAB1 0.052 0.08 -10000 0 -0.62 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.071 0.087 -10000 0 -0.89 3 3
PRKACA 0.025 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.1 -10000 0 -0.69 7 7
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.092 -10000 0 -0.67 6 6
actin cytoskeleton reorganization 0.025 0.12 -10000 0 -0.45 26 26
PTK2 0.027 0.1 -10000 0 -0.75 5 5
EDG1 0.013 0.084 -10000 0 -0.64 6 6
mol:DAG 0.024 0.088 -10000 0 -0.66 6 6
CaM/Ca2+ 0.037 0.081 -10000 0 -0.86 3 3
MAP2K3 0.012 0.099 0.37 1 -0.97 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.053 0.098 -10000 0 -1 3 3
PLCG1 0.024 0.092 -10000 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.088 -10000 0 -0.7 5 5
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.099 -10000 0 -0.79 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.089 -10000 0 -0.73 5 5
cell migration 0.047 0.081 0.34 1 -0.68 3 4
mol:PI-3-4-5-P3 0.043 0.081 -10000 0 -0.69 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.029 0.081 -10000 0 -0.6 6 6
mol:NO 0.04 0.1 0.46 8 -0.53 4 12
PXN 0.026 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.071 -10000 0 -0.74 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.045 0.095 -10000 0 -1 3 3
VHL 0.023 0.055 -10000 0 -0.68 3 3
ITGB3 0.012 0.097 -10000 0 -0.64 10 10
NOS3 0.04 0.11 0.5 7 -0.61 4 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.094 -10000 0 -0.64 7 7
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0 0.12 0.36 1 -1.1 3 4
PRKCB 0.007 0.09 0.36 1 -0.86 3 4
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.091 -10000 0 -0.66 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.099 -10000 0 -0.79 5 5
VEGFA165/NRP2 0.028 0.053 -10000 0 -0.51 3 3
MAPKKK cascade 0.054 0.086 0.35 1 -0.74 3 4
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.032 -10000 0 -0.67 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
ROCK1 0.027 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.098 -10000 0 -0.75 4 4
MAP3K13 0.019 0.11 -10000 0 -0.54 12 12
PDPK1 0.029 0.077 -10000 0 -0.62 5 5
TCGA08_retinoblastoma

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
CDKN2B -0.033 0.074 -10000 0 -10000 0 0
CDKN2C 0.031 0.019 -10000 0 -10000 0 0
CDKN2A -0.033 0.075 -10000 0 -10000 0 0
CCND2 0.01 0.023 -10000 0 -10000 0 0
RB1 -0.014 0.046 0.32 2 -0.24 10 12
CDK4 0.009 0.022 -10000 0 -10000 0 0
CDK6 0.016 0.043 0.26 10 -0.16 1 11
G1/S progression 0.016 0.05 0.24 14 -0.32 2 16
Circadian rhythm 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
chromatin modification 0.04 0.042 -9999 0 -0.45 1 1
CLOCK -0.013 0.16 -9999 0 -0.68 28 28
TIMELESS/CRY2 0.027 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0.019 0.035 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.68 1 1
NR1D1 0 0.04 -9999 0 -10000 0 0
ARNTL 0.013 0.044 -9999 0 -10000 0 0
TIMELESS 0.011 0.03 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.36 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.004 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.004 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.026 0.12 -9999 0 -0.44 28 28
BMAL1/CLOCK -0.003 0.1 -9999 0 -0.43 14 14
S phase of mitotic cell cycle 0.04 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.041 0.042 -9999 0 -0.46 1 1
mol:NADPH 0.004 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.032 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
EPO signaling 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
BCL2L1 0.032 0.097 -10000 0 -10000 0 0
CRKL 0.014 0.047 0.46 3 -10000 0 3
mol:DAG 0.028 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.062 0.36 5 -10000 0 5
MAPK8 0.014 0.064 -10000 0 -0.44 7 7
RAP1A 0.024 0.064 0.48 6 -10000 0 6
GAB1 0.022 0.055 0.45 4 -10000 0 4
MAPK14 0.021 0.032 -10000 0 -10000 0 0
EPO 0.019 0.023 -10000 0 -10000 0 0
PLCG1 0.029 0.047 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.022 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.023 0.1 -10000 0 -0.41 23 23
GAB1/SHC/GRB2/SOS1 0.047 0.043 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.027 -10000 0 -10000 0 0
IRS2 0.022 0.06 0.47 5 -10000 0 5
STAT1 0.03 0.071 -10000 0 -10000 0 0
STAT5B 0.028 0.06 -10000 0 -10000 0 0
cell proliferation 0.013 0.073 0.35 7 -0.41 7 14
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.04 -10000 0 -0.41 1 1
TEC 0.022 0.055 0.45 4 -10000 0 4
SOCS3 -0.008 0.15 -10000 0 -0.68 23 23
STAT1 (dimer) 0.029 0.07 -10000 0 -10000 0 0
JAK2 0.027 0.02 -10000 0 -0.33 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.052 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.027 -10000 0 -10000 0 0
LYN 0.025 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.04 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.023 0.022 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.044 0.045 -10000 0 -10000 0 0
SH2B3 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.032 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0 0.061 -10000 0 -0.26 20 20
PTPN6 0.022 0.046 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.043 -10000 0 -10000 0 0
EPOR 0.024 0.022 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.047 0.043 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.03 0.041 -10000 0 -10000 0 0
VAV2 0.024 0.061 0.46 6 -10000 0 6
CBL 0.022 0.055 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.028 0.06 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.097 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.01 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
BTK 0.01 0.059 0.26 1 -0.36 6 7
BCL2 -0.012 0.25 -10000 0 -0.91 34 34
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.062 -9999 0 -0.38 11 11
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.055 -9999 0 -0.68 3 3
ITGA4 0.021 0.05 -9999 0 -0.68 2 2
alpha4/beta7 Integrin/MAdCAM1 0.048 0.081 -9999 0 -0.4 13 13
EPO 0.004 0.026 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.087 -9999 0 -0.51 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.039 -9999 0 -0.51 2 2
EPO/EPOR (dimer) 0.03 0.021 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.037 -9999 0 -0.4 3 3
PIK3CA 0.023 0.055 -9999 0 -0.68 3 3
PI3K 0.036 0.044 -9999 0 -0.51 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.023 0.032 -9999 0 -0.42 2 2
PXN 0.026 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.006 0.056 -9999 0 -0.68 2 2
cell adhesion 0.046 0.08 -9999 0 -0.4 13 13
CRKL/CBL 0.03 0.018 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.017 0.064 -9999 0 -0.46 6 6
ITGB7 0.007 0.1 -9999 0 -0.64 10 10
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.066 -9999 0 -0.5 6 6
p130Cas/Crk/Dock1 0.035 0.064 -9999 0 -0.37 9 9
VCAM1 0.018 0.073 -9999 0 -0.68 5 5
RHOA 0.027 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.064 0.032 -9999 0 -0.4 1 1
BCAR1 0.008 0.059 -9999 0 -0.44 6 6
EPOR 0.024 0.017 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.038 -9999 0 -0.41 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.014 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.087 -10000 0 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.91 1 1
FIH (dimer) 0.037 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.11 -10000 0 -0.75 2 2
FLT1 -0.003 0.12 -10000 0 -0.7 9 9
ADORA2A 0.1 0.11 0.42 2 -0.95 1 3
germ cell development 0.13 0.11 -10000 0 -0.94 1 1
SLC11A2 0.12 0.11 -10000 0 -1 1 1
BHLHE40 0.13 0.11 -10000 0 -1 1 1
HIF1AN 0.037 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.096 0.36 1 -0.66 2 3
ETS1 0.038 0.014 -10000 0 -10000 0 0
CITED2 -0.034 0.31 -10000 0 -1 41 41
KDR 0.005 0.12 -10000 0 -0.98 5 5
PGK1 0.12 0.11 -10000 0 -1 1 1
SIRT1 0.025 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.13 -10000 0 -1.3 1 1
EPAS1 0.061 0.069 -10000 0 -0.46 2 2
SP1 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.12 -10000 0 -0.76 3 3
EFNA1 0.13 0.11 -10000 0 -1 1 1
FXN 0.12 0.12 0.51 3 -0.95 1 4
POU5F1 0.13 0.11 -10000 0 -1 1 1
neuron apoptosis -0.16 0.13 1.2 1 -10000 0 1
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.016 0.1 -10000 0 -0.66 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.034 0.035 -10000 0 -0.68 1 1
VHL/Elongin B/Elongin C 0.049 0.042 -10000 0 -0.46 3 3
VHL 0.023 0.055 -10000 0 -0.68 3 3
ARNT 0.035 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.45 11 -0.95 1 12
TWIST1 0.12 0.14 0.42 3 -0.58 7 10
ELK1 0.022 0.036 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.091 0.097 -10000 0 -0.49 2 2
VEGFA 0.12 0.12 -10000 0 -0.77 3 3
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.025 0.11 0.66 10 -10000 0 10
PLK1 0.072 0.11 0.58 3 -0.61 3 6
CDKN1B 0.074 0.095 0.53 4 -0.4 1 5
FOXO3 0.068 0.11 -10000 0 -0.63 4 4
KAT2B 0.033 0.018 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.055 0.42 2 -0.4 1 3
CAT 0.065 0.13 0.53 1 -1.4 2 3
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.034 0.018 -10000 0 -10000 0 0
FOXO1 0.018 0.082 0.44 12 -10000 0 12
MAPK10 0.033 0.033 0.2 6 -0.41 1 7
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.071 0.09 0.52 10 -0.51 3 13
response to oxidative stress 0.011 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.084 0.088 -10000 0 -0.79 2 2
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.027 0.1 -10000 0 -0.67 8 8
FOXO1/SKP2 0.015 0.055 -10000 0 -0.43 3 3
mol:GDP 0.011 0.011 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.099 0.095 0.48 6 -0.59 3 9
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.11 -10000 0 -0.5 7 7
MST1 0.031 0.036 -10000 0 -0.66 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.007 0.12 -10000 0 -0.55 11 11
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.058 0.21 5 -0.39 7 12
MAPK9 0.031 0.017 0.2 3 -10000 0 3
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.025 0.037 -10000 0 -0.67 1 1
SOD2 0.1 0.11 0.61 9 -0.62 2 11
RBL2 0.077 0.16 0.51 2 -0.87 8 10
RAL/GDP 0.046 0.014 -10000 0 -10000 0 0
CHUK 0.032 0.018 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.05 0.015 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.056 0.36 -10000 0 -1.4 33 33
SKP2 0.022 0.056 -10000 0 -0.68 3 3
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.018 -10000 0 -10000 0 0
CCNB1 0.073 0.11 0.58 3 -0.71 1 4
FOXO1-3a-4/beta catenin 0.1 0.097 0.45 6 -0.42 4 10
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.054 -10000 0 -0.43 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.017 0.11 -10000 0 -0.67 11 11
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.078 0.11 0.61 13 -0.44 2 15
SFN -0.083 0.12 -10000 0 -0.68 13 13
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.01 0.11 -10000 0 -0.53 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.069 0.11 0.56 2 -0.71 1 3
BCL6 0.086 0.12 0.53 2 -0.83 4 6
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.004 0.11 -10000 0 -0.44 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.04 -10000 0 -10000 0 0
NFKBIA 0.014 0.029 -10000 0 -0.24 5 5
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.007 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.015 0.16 -10000 0 -0.66 29 29
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
NF kappa B1 p50 dimer 0.025 0.021 0.25 4 -10000 0 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.041 -10000 0 -0.31 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.041 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.044 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.02 0.041 -10000 0 -0.31 6 6
IKBKB 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.039 -10000 0 -10000 0 0
cell death 0.038 0.039 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.004 0.11 -10000 0 -0.44 28 28
LCK 0.012 0.083 -10000 0 -0.68 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.028 0.042 0.29 3 -0.38 3 6
adherens junction organization 0.021 0.04 0.25 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.05 -10000 0 -0.36 6 6
FMN1 0.009 0.079 -10000 0 -0.35 21 21
mol:IP3 0.027 0.033 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.022 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.036 0.25 1 -0.33 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.034 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.033 -10000 0 -0.39 2 2
VASP 0.025 0.018 -10000 0 -10000 0 0
ZYX 0.025 0.021 -10000 0 -10000 0 0
JUB 0.025 0.02 -10000 0 -10000 0 0
EGFR(dimer) 0.039 0.046 -10000 0 -0.37 4 4
E-cadherin/beta catenin-gamma catenin 0.05 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.039 0.25 1 -0.34 3 4
PIK3CA 0.024 0.056 -10000 0 -0.68 3 3
PI3K 0.049 0.04 0.26 1 -0.35 3 4
FYN 0.026 0.037 0.29 3 -0.29 3 6
mol:Ca2+ 0.027 0.032 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.033 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.051 -10000 0 -0.36 6 6
establishment of polarity of embryonic epithelium 0.025 0.018 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
EGFR 0.02 0.064 -10000 0 -0.68 4 4
CASR 0.018 0.032 -10000 0 -0.32 3 3
RhoA/GTP 0.039 0.033 -10000 0 -0.3 3 3
AKT2 0.031 0.034 -10000 0 -0.32 3 3
actin cable formation 0.007 0.074 -10000 0 -0.34 20 20
apoptosis -0.03 0.044 0.36 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.051 -10000 0 -0.39 6 6
PIP5K1A 0.023 0.034 -10000 0 -0.39 2 2
PLCG1 0.027 0.034 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.045 -10000 0 -0.34 4 4
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
CDC42/GTP 0.007 0.075 -10000 0 -0.48 3 3
PLCG1 -0.002 0.067 -10000 0 -0.5 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.011 -10000 0 -10000 0 0
cell migration 0.006 0.074 -10000 0 -0.47 3 3
S1PR5 0.023 0.034 -10000 0 -0.68 1 1
S1PR4 0.024 0.017 -10000 0 -10000 0 0
MAPK3 -0.003 0.069 -10000 0 -0.5 3 3
MAPK1 0.009 0.061 -10000 0 -0.48 3 3
S1P/S1P5/Gi -0.001 0.076 -10000 0 -0.33 16 16
GNAI1 0.025 0.033 -10000 0 -0.68 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
RHOA 0.034 0.069 0.41 11 -10000 0 11
S1P/S1P4/Gi 0 0.074 -10000 0 -0.33 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.025 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.68 1 1
MAP2K3 0.036 0.095 0.42 15 -0.38 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.41 6 20
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.085 -10000 0 -0.68 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.005 0.12 -10000 0 -0.63 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.51 1 1
TAK1/TAB family 0.011 0.032 -10000 0 -0.19 3 3
RAC1/OSM/MEKK3 0.049 0.014 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.037 0.055 -10000 0 -0.33 2 2
TRAF6 0.007 0.026 -10000 0 -0.4 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.02 0.064 -10000 0 -0.68 4 4
CCM2 0.026 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.044 -10000 0 -0.44 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.045 0.053 -10000 0 -0.5 4 4
OSM/MEKK3 0.037 0.012 -10000 0 -10000 0 0
TAOK1 -0.029 0.13 -10000 0 -0.4 52 52
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 0.019 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.025 0.032 -10000 0 -0.68 1 1
MAP3K10 0.025 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.037 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.036 0.093 -10000 0 -0.4 18 18
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.027 0.004 -9999 0 -10000 0 0
SMAD2 -0.015 0.043 -9999 0 -10000 0 0
SMAD3 0.021 0.015 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.048 -9999 0 -0.43 4 4
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.063 -9999 0 -0.42 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.054 -9999 0 -0.43 1 1
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.009 0.12 -9999 0 -0.49 27 27
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.026 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.003 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.012 0.16 -9999 0 -0.66 27 27
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.032 -9999 0 -0.68 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.68 3 3
ITGA4 0.021 0.05 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.087 -10000 0 -0.51 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.036 -10000 0 -0.44 2 2
alpha4/beta7 Integrin/Paxillin 0.034 0.07 -10000 0 -0.4 11 11
lamellipodium assembly 0.025 0.064 -10000 0 -0.53 5 5
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PI3K 0.036 0.044 -10000 0 -0.51 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.008 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.053 0.03 -10000 0 -0.35 1 1
cell adhesion 0.051 0.036 -10000 0 -0.37 2 2
CRKL/CBL 0.03 0.018 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.042 0.033 -10000 0 -0.4 2 2
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.007 0.1 -10000 0 -0.64 10 10
ARF6/GDP 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.061 -10000 0 -0.44 6 6
p130Cas/Crk/Dock1 0.047 0.042 -10000 0 -0.44 3 3
VCAM1 0.018 0.073 -10000 0 -0.68 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.037 -10000 0 -0.37 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.032 -10000 0 -0.38 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.053 0.031 0.38 1 -10000 0 1
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.037 -10000 0 -0.37 2 2
Rac1/GTP 0.025 0.072 -10000 0 -0.61 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.39 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.044 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.017 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.036 0.014 -9999 0 -10000 0 0
BCOR 0.025 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -9999 0 -0.51 1 1
Histones 0.008 0.049 -9999 0 -0.24 1 1
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.026 0.005 -9999 0 -10000 0 0
HDAC6 0.025 0.008 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.086 -9999 0 -0.68 7 7
Tubulin/HDAC6 0.046 0.049 -9999 0 -0.4 5 5
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.02 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.059 -9999 0 -0.3 2 2
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.033 0.056 -9999 0 -0.51 5 5
HDAC4/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.005 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.036 0.027 -9999 0 -0.51 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.045 0.061 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.007 0.12 -9999 0 -0.49 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.048 -9999 0 -0.24 1 1
cell motility 0.046 0.049 -9999 0 -0.4 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.032 -9999 0 -0.68 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.015 0.15 -9999 0 -0.65 23 23
HDAC6/HDAC11 0.037 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.032 -9999 0 -0.68 1 1
RAN 0.026 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.031 -9999 0 -0.38 1 1
GNG2 0.025 0.032 -9999 0 -0.68 1 1
NCOR2 0.026 0.005 -9999 0 -10000 0 0
TUBB2A 0.02 0.071 -9999 0 -0.68 5 5
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.011 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.029 0.024 -10000 0 -10000 0 0
BIRC5 0.013 0.05 -10000 0 -0.68 1 1
NFKBIA 0.014 0.021 0.25 3 -10000 0 3
CPEB1 -0.021 0.18 -10000 0 -0.65 34 34
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.026 0.02 -10000 0 -10000 0 0
NDEL1/TACC3 0.043 0.023 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.029 0.024 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.009 0.027 -10000 0 -10000 0 0
TP53 0.025 0.011 -10000 0 -10000 0 0
DLG7 0.012 0.009 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.026 0.02 -10000 0 -10000 0 0
AURKA 0.02 0.013 -10000 0 -10000 0 0
AURKB 0.013 0.021 -10000 0 -0.15 7 7
CDC25B 0.02 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.001 0.11 -10000 0 -0.4 30 30
Aurora A/CPEB -0.001 0.11 -10000 0 -0.41 30 30
Aurora A/TACC1/TRAP/chTOG 0.054 0.038 -10000 0 -0.38 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.029 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.052 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.034 -10000 0 -0.36 1 1
CENPA 0.017 0.026 -10000 0 -0.25 4 4
Aurora A/PP2A 0.03 0.023 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.017 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.011 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.018 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.013 -10000 0 -10000 0 0
TACC1 0.025 0.032 -10000 0 -0.68 1 1
TACC3 0.026 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.02 -10000 0 -10000 0 0
Aurora A/RasGAP 0.029 0.024 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.009 0.027 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.017 0.029 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.046 -10000 0 -0.68 2 2
positive regulation of NF-kappaB transcription factor activity 0.037 0.036 -10000 0 -0.51 2 2
MAP2K4 0.026 0.047 -10000 0 -0.34 3 3
IKBKB 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.055 -10000 0 -0.68 3 3
SMPD1 0.015 0.028 -10000 0 -0.39 2 2
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.036 -10000 0 -0.51 2 2
TRAIL/TRAILR3 0.005 0.062 -10000 0 -0.51 2 2
TRAIL/TRAILR1 0.034 0.056 -10000 0 -0.51 5 5
TRAIL/TRAILR4 0.037 0.036 -10000 0 -0.51 2 2
TRAIL/TRAILR1/DAP3/GTP 0.043 0.049 -10000 0 -0.4 5 5
IKK complex 0.024 0.054 -10000 0 -0.4 2 2
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.034 -10000 0 -0.51 2 2
MAP3K1 0.027 0.049 -10000 0 -0.38 4 4
TRAILR4 (trimer) 0.027 0.004 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.022 0.055 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.041 -10000 0 -0.34 5 5
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.011 0.034 -10000 0 -0.5 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.051 -10000 0 -0.38 5 5
mol:ceramide 0.015 0.028 -10000 0 -0.39 2 2
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.069 0.28 1 -0.37 8 9
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.066 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.051 -10000 0 -0.44 5 5
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.011 0.036 -10000 0 -0.43 2 2
JNK cascade 0.037 0.036 -10000 0 -0.51 2 2
TRAIL (trimer) 0.024 0.046 -10000 0 -0.67 2 2
TNFRSF10C -0.014 0.067 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.054 0.049 -10000 0 -0.38 5 5
TRAIL/TRAILR2/FADD 0.051 0.033 -10000 0 -0.43 2 2
cell death 0.015 0.028 -10000 0 -0.39 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.033 -10000 0 -0.42 2 2
TRAILR2 (trimer) 0.027 0.004 -10000 0 -10000 0 0
CASP8 0.012 0.03 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.074 0.036 -10000 0 -0.37 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.032 -10000 0 -10000 0 0
KLHL20 0.012 0.051 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.043 0.26 3 -10000 0 3
ENAH 0.027 0.03 -10000 0 -10000 0 0
AP1M1 0.025 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.067 -10000 0 -0.4 9 9
RAPGEF1 0.026 0.036 0.27 1 -10000 0 1
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.036 -10000 0 -10000 0 0
CRK 0.026 0.029 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.023 0.078 -10000 0 -0.51 9 9
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.014 -10000 0 -10000 0 0
DLG1 0.029 0.036 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.054 0.031 -10000 0 -0.4 1 1
PI3K 0.016 0.022 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.037 0.011 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.018 -10000 0 -10000 0 0
AKT1 0.018 0.021 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.047 0.074 0.41 11 -10000 0 11
actin cytoskeleton organization 0.012 0.042 0.19 3 -10000 0 3
CDC42/GDP 0.047 0.081 0.48 11 -10000 0 11
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.008 -10000 0 -10000 0 0
ITGB7 0.007 0.1 -10000 0 -0.64 10 10
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.038 0.087 0.48 12 -10000 0 12
CDC42/GTP/IQGAP1 0.035 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.045 0.27 2 -10000 0 2
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.037 0.21 4 -10000 0 4
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.036 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.012 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.027 0.25 1 -10000 0 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.065 0.067 -10000 0 -0.38 9 9
CCND1 0.012 0.04 0.2 3 -10000 0 3
VAV2 0.005 0.14 -10000 0 -0.53 27 27
RAP1/GDP 0.048 0.039 0.3 5 -10000 0 5
adherens junction assembly 0.028 0.035 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.063 -10000 0 -0.37 9 9
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.032 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
Rac1/GTP -0.007 0.078 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.052 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.037 -10000 0 -10000 0 0
Arf6 trafficking 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
SLC2A4 -0.001 0.13 -10000 0 -0.66 18 18
CLTC 0.028 0.021 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.022 0.011 -10000 0 -10000 0 0
CPE 0.01 0.055 -10000 0 -0.44 7 7
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.018 0.006 -10000 0 -10000 0 0
CTNND1 0.022 0.036 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.031 0.24 1 -10000 0 1
TSHR 0.015 0.03 -10000 0 -0.44 2 2
INS 0.009 0.06 -10000 0 -0.43 8 8
BIN1 0.027 0.004 -10000 0 -10000 0 0
mol:Choline 0.018 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.009 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.024 -10000 0 -0.4 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.013 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.046 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.01 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.029 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.013 -10000 0 -10000 0 0
RALA/GTP 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.02 0.028 0.36 1 -10000 0 1
NME1 0.016 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.008 0.055 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.025 0.068 -10000 0 -0.32 17 17
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.018 0.006 -10000 0 -10000 0 0
endocytosis -0.048 0.023 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.028 0.085 0.43 8 -0.34 10 18
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.032 -10000 0 -0.68 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.029 0.079 0.48 6 -0.34 9 15
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.025 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.016 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.01 -9999 0 -9999 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 -0.002 0.04 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.021 0.27 2 -10000 0 2
myoblast fusion -0.011 0.028 -10000 0 -10000 0 0
mol:GTP 0.009 0.018 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.025 0.062 0.42 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.009 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.027 -10000 0 -10000 0 0
MAPK3 0.009 0.026 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.026 0.063 -10000 0 -0.42 1 1
ARF1 0.025 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.028 -10000 0 -10000 0 0
ARF1/GDP 0.021 0.029 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.059 0.079 -10000 0 -0.68 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.023 0.029 -10000 0 -10000 0 0
KALRN 0.009 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.03 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.026 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.027 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.009 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.018 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.009 0.02 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.027 -10000 0 -10000 0 0
ruffle organization 0.012 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.009 0.018 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.012 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.009 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.027 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.045 -9999 0 -0.68 2 2
Aurora C/Aurora B/INCENP 0.045 0.042 -9999 0 -0.45 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.013 -9999 0 -10000 0 0
AURKB -0.005 0.06 -9999 0 -10000 0 0
AURKC 0.02 0.029 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.018 0.068 -9999 0 -9999 0 0
GPC2 0.016 0.037 -9999 0 -9999 0 0
GPC2/Midkine -0.003 0.058 -9999 0 -9999 0 0
neuron projection morphogenesis -0.003 0.058 -9999 0 -9999 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 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.001 0.013 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.055 -9999 0 -0.31 1 1
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.038 -9999 0 -0.24 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.059 -9999 0 -0.3 2 2
SUMO1/HDAC1 0.014 0.057 -9999 0 -0.26 2 2
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.045 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 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 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.003 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -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 0.011 0.017 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.035 0.2 1 -0.22 1 2
AP2 0.037 0.012 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.022 0.026 -10000 0 -10000 0 0
CLTA 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.025 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.024 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.028 -10000 0 -0.37 2 2
ARF1/GDP 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.034 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.017 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.023 -10000 0 -0.28 1 1
AP2A1 0.025 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.025 -10000 0 -0.31 1 1
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.027 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.026 -10000 0 -10000 0 0
PLD2 0.006 0.025 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.025 -10000 0 -0.37 2 2
ARF1/GTP/Membrin/GBF1/p115 0.022 0.02 -10000 0 -0.19 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.024 -10000 0 -0.37 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.013 0.024 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.051 0.017 -10000 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 0.038 0.01 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.025 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 480 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.2 0.026 0.026 0.026
47_PPARGC1A -0.68 -0.68 -0.68 0.027
105_BMP4 0.027 -0.12 0.027 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 0.027 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 0.027
131_RELN/VLDLR -0.4 -0.4 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.04 -0.05 0.032 -0.049
84_STAT5A 0.04 -0.05 0.032 -0.049
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/4403501/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/4469040/GDAC_Gistic2Report_4469777/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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