PARADIGM pathway analysis of mRNASeq expression data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1833QH4
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 43 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
TCGA08_retinoblastoma 49
IL23-mediated signaling events 37
Syndecan-1-mediated signaling events 36
IL4-mediated signaling events 35
Signaling events regulated by Ret tyrosine kinase 34
TCR signaling in naïve CD8+ T cells 33
FOXA2 and FOXA3 transcription factor networks 32
Glypican 2 network 30
Wnt signaling 29
IL12-mediated signaling events 26
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 261 . 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 ( 261 ).

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
TCGA08_retinoblastoma 0.1877 49 393 8 -0.12 0.065 1000 -1000 -0.015 -1000
IL23-mediated signaling events 0.1418 37 2261 60 -0.48 0.012 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.1379 36 1234 34 -0.2 0.012 1000 -1000 -0.052 -1000
IL4-mediated signaling events 0.1341 35 3195 91 -0.72 0.59 1000 -1000 -0.16 -1000
Signaling events regulated by Ret tyrosine kinase 0.1303 34 2808 82 -0.18 0.012 1000 -1000 -0.077 -1000
TCR signaling in naïve CD8+ T cells 0.1264 33 3098 93 -0.2 0.028 1000 -1000 -0.075 -1000
FOXA2 and FOXA3 transcription factor networks 0.1226 32 1475 46 -0.53 0.011 1000 -1000 -0.12 -1000
Glypican 2 network 0.1149 30 120 4 -0.046 -0.043 1000 -1000 -0.02 -1000
Wnt signaling 0.1111 29 209 7 -0.14 0.009 1000 -1000 -0.037 -1000
IL12-mediated signaling events 0.0996 26 2293 87 -0.29 0.055 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.0996 26 1396 52 -0.26 0.096 1000 -1000 -0.045 -1000
TCGA08_p53 0.0920 24 174 7 -0.095 0.058 1000 -1000 -0.011 -1000
Noncanonical Wnt signaling pathway 0.0881 23 610 26 -0.14 0.012 1000 -1000 -0.049 -1000
amb2 Integrin signaling 0.0881 23 1908 82 -0.23 0.015 1000 -1000 -0.071 -1000
Ephrin B reverse signaling 0.0881 23 1104 48 -0.16 0.016 1000 -1000 -0.063 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0843 22 1514 68 -0.28 0.11 1000 -1000 -0.12 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0805 21 715 34 -0.12 0.012 1000 -1000 -0.04 -1000
p75(NTR)-mediated signaling 0.0805 21 2663 125 -0.23 0.034 1000 -1000 -0.095 -1000
Reelin signaling pathway 0.0805 21 1210 56 -0.22 0.029 1000 -1000 -0.075 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0805 21 1113 52 -0.25 0.039 1000 -1000 -0.044 -1000
Endothelins 0.0805 21 2090 96 -0.16 0.012 1000 -1000 -0.085 -1000
Visual signal transduction: Rods 0.0805 21 1099 52 -0.16 0.012 1000 -1000 -0.074 -1000
Caspase cascade in apoptosis 0.0766 20 1503 74 -0.17 0.061 1000 -1000 -0.042 -1000
Glypican 1 network 0.0766 20 967 48 -0.19 0.022 1000 -1000 -0.049 -1000
BMP receptor signaling 0.0728 19 1540 81 -0.22 0.036 1000 -1000 -0.091 -1000
Signaling mediated by p38-alpha and p38-beta 0.0728 19 850 44 -0.11 0.012 1000 -1000 -0.044 -1000
Syndecan-4-mediated signaling events 0.0728 19 1320 67 -0.15 0.016 1000 -1000 -0.086 -1000
LPA4-mediated signaling events 0.0690 18 216 12 -0.13 0.016 1000 -1000 -0.027 -1000
Visual signal transduction: Cones 0.0690 18 717 38 -0.11 0.012 1000 -1000 -0.057 -1000
Effects of Botulinum toxin 0.0690 18 482 26 -0.17 0.014 1000 -1000 -0.06 -1000
BCR signaling pathway 0.0690 18 1870 99 -0.2 0.017 1000 -1000 -0.094 -1000
Class IB PI3K non-lipid kinase events 0.0690 18 54 3 -0.021 -1000 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 0.0651 17 1887 105 -0.12 0.029 1000 -1000 -0.057 -1000
Glucocorticoid receptor regulatory network 0.0651 17 1982 114 -0.43 0.24 1000 -1000 -0.072 -1000
EGFR-dependent Endothelin signaling events 0.0651 17 365 21 -0.082 0.017 1000 -1000 -0.061 -1000
HIF-1-alpha transcription factor network 0.0613 16 1235 76 -0.26 0.037 1000 -1000 -0.17 -1000
ErbB2/ErbB3 signaling events 0.0575 15 1037 65 -0.16 0.017 1000 -1000 -0.064 -1000
Calcium signaling in the CD4+ TCR pathway 0.0575 15 479 31 -0.13 0.012 1000 -1000 -0.073 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0575 15 1861 120 -0.23 0.074 1000 -1000 -0.07 -1000
Ephrin A reverse signaling 0.0536 14 103 7 -0.02 0 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 0.0536 14 242 17 -0.068 0.012 1000 -1000 -0.037 -1000
Fc-epsilon receptor I signaling in mast cells 0.0536 14 1439 97 -0.13 0.027 1000 -1000 -0.078 -1000
Nongenotropic Androgen signaling 0.0536 14 750 52 -0.098 0.014 1000 -1000 -0.059 -1000
Retinoic acid receptors-mediated signaling 0.0498 13 774 58 -0.22 0.024 1000 -1000 -0.069 -1000
EPHB forward signaling 0.0498 13 1120 85 -0.072 0.064 1000 -1000 -0.078 -1000
IL27-mediated signaling events 0.0498 13 669 51 -0.12 0.046 1000 -1000 -0.076 -1000
ErbB4 signaling events 0.0460 12 881 69 -0.2 0.13 1000 -1000 -0.088 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0460 12 694 54 -0.18 0.023 1000 -1000 -0.089 -1000
PDGFR-alpha signaling pathway 0.0460 12 568 44 -0.081 0.02 1000 -1000 -0.064 -1000
LPA receptor mediated events 0.0460 12 1233 102 -0.1 0.03 1000 -1000 -0.077 -1000
Coregulation of Androgen receptor activity 0.0421 11 878 76 -0.19 0.024 1000 -1000 -0.032 -1000
Osteopontin-mediated events 0.0421 11 435 38 -0.091 0.014 1000 -1000 -0.091 -1000
Arf6 signaling events 0.0421 11 690 62 -0.094 0.027 1000 -1000 -0.051 -1000
Signaling events mediated by PTP1B 0.0421 11 889 76 -0.1 0.034 1000 -1000 -0.075 -1000
Syndecan-3-mediated signaling events 0.0421 11 416 35 -0.15 0.034 1000 -1000 -0.046 -1000
IL2 signaling events mediated by STAT5 0.0421 11 242 22 -0.061 0.012 1000 -1000 -0.055 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0421 11 891 78 -0.068 0.051 1000 -1000 -0.085 -1000
Regulation of nuclear SMAD2/3 signaling 0.0383 10 1365 136 -0.3 0.12 1000 -1000 -0.072 -1000
BARD1 signaling events 0.0383 10 575 57 -0.053 0.043 1000 -1000 -0.055 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0383 10 855 85 -0.075 0.019 1000 -1000 -0.072 -1000
FAS signaling pathway (CD95) 0.0383 10 507 47 -0.13 0.013 1000 -1000 -0.046 -1000
Integrins in angiogenesis 0.0383 10 912 84 -0.094 0.02 1000 -1000 -0.082 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0383 10 920 88 -0.12 0.023 1000 -1000 -0.085 -1000
Ras signaling in the CD4+ TCR pathway 0.0383 10 172 17 -0.041 0.014 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class III 0.0345 9 389 40 -0.16 0.069 1000 -1000 -0.033 -1000
IL1-mediated signaling events 0.0345 9 601 62 -0.082 0.05 1000 -1000 -0.088 -1000
Plasma membrane estrogen receptor signaling 0.0345 9 822 86 -0.098 0.021 1000 -1000 -0.083 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0345 9 321 33 -0.13 0.033 1000 -1000 -0.038 -1000
Regulation of Androgen receptor activity 0.0345 9 695 70 -0.25 0.024 1000 -1000 -0.057 -1000
Syndecan-2-mediated signaling events 0.0307 8 553 69 -0.087 0.03 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 0.0307 8 317 39 -0.084 0.013 1000 -1000 -0.024 -1000
Nectin adhesion pathway 0.0307 8 562 63 -0.054 0.019 1000 -1000 -0.067 -1000
TRAIL signaling pathway 0.0307 8 411 48 -0.038 0.024 1000 -1000 -0.066 -1000
S1P5 pathway 0.0307 8 144 17 -0.098 0.021 1000 -1000 -0.037 -1000
S1P1 pathway 0.0307 8 289 36 -0.098 0.012 1000 -1000 -0.054 -1000
IL2 signaling events mediated by PI3K 0.0307 8 499 58 -0.062 0.028 1000 -1000 -0.08 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0307 8 380 45 -0.096 0.026 1000 -1000 -0.084 -1000
Canonical Wnt signaling pathway 0.0307 8 451 51 -0.14 0.05 1000 -1000 -0.057 -1000
IL6-mediated signaling events 0.0307 8 664 75 -0.12 0.042 1000 -1000 -0.081 -1000
FOXM1 transcription factor network 0.0307 8 438 51 -0.13 0.11 1000 -1000 -0.18 -1000
Presenilin action in Notch and Wnt signaling 0.0268 7 472 61 -0.13 0.034 1000 -1000 -0.072 -1000
IGF1 pathway 0.0268 7 414 57 -0.026 0.024 1000 -1000 -0.089 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0230 6 192 28 -0.098 0.019 1000 -1000 -0.033 -1000
a4b1 and a4b7 Integrin signaling 0.0230 6 30 5 -0.005 0.006 1000 -1000 -0.017 -1000
Aurora C signaling 0.0230 6 45 7 -0.041 0.004 1000 -1000 -0.029 -1000
Ceramide signaling pathway 0.0230 6 457 76 -0.077 0.032 1000 -1000 -0.049 -1000
TCGA08_rtk_signaling 0.0230 6 176 26 -0.045 0.031 1000 -1000 -0.019 -1000
Class I PI3K signaling events 0.0230 6 476 73 -0.076 0.027 1000 -1000 -0.061 -1000
S1P3 pathway 0.0230 6 255 42 -0.098 0.017 1000 -1000 -0.047 -1000
S1P4 pathway 0.0230 6 173 25 -0.098 0.019 1000 -1000 -0.035 -1000
Hedgehog signaling events mediated by Gli proteins 0.0192 5 351 65 -0.24 0.039 1000 -1000 -0.066 -1000
Aurora A signaling 0.0192 5 338 60 -0.11 0.028 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0192 5 341 68 -0.094 0.039 1000 -1000 -0.091 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0192 5 216 37 -0.048 0.021 1000 -1000 -0.048 -1000
Regulation of p38-alpha and p38-beta 0.0192 5 318 54 -0.11 0.03 1000 -1000 -0.063 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0192 5 436 74 -0.076 0.06 1000 -1000 -0.085 -1000
Regulation of Telomerase 0.0192 5 569 102 -0.15 0.033 1000 -1000 -0.1 -1000
Signaling events mediated by PRL 0.0192 5 194 34 -0.099 0.021 1000 -1000 -0.033 -1000
EPO signaling pathway 0.0153 4 228 55 -0.019 0.047 1000 -1000 -0.09 -1000
ceramide signaling pathway 0.0153 4 218 49 -0.077 0.021 1000 -1000 -0.057 -1000
Rapid glucocorticoid signaling 0.0153 4 86 20 -0.027 0.013 1000 -1000 -0.019 -1000
Aurora B signaling 0.0153 4 286 67 -0.089 0.02 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class II 0.0115 3 227 75 -0.046 0.034 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0115 3 170 43 -0.071 0.072 1000 -1000 -0.072 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0115 3 312 83 -0.17 0.044 1000 -1000 -0.076 -1000
Signaling mediated by p38-gamma and p38-delta 0.0115 3 54 15 -0.03 0.024 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 0.0115 3 136 36 -0.048 0.026 1000 -1000 -0.071 -1000
E-cadherin signaling in the nascent adherens junction 0.0115 3 277 76 -0.045 0.038 1000 -1000 -0.074 -1000
Insulin Pathway 0.0115 3 239 74 -0.12 0.03 1000 -1000 -0.086 -1000
PDGFR-beta signaling pathway 0.0115 3 313 97 -0.046 0.042 1000 -1000 -0.076 -1000
E-cadherin signaling events 0.0115 3 15 5 -0.001 0.015 1000 -1000 -0.023 -1000
p38 MAPK signaling pathway 0.0115 3 137 44 -0.094 0.024 1000 -1000 -0.063 -1000
Canonical NF-kappaB pathway 0.0077 2 109 39 -0.077 0.06 1000 -1000 -0.075 -1000
PLK2 and PLK4 events 0.0077 2 8 3 0.002 0.012 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0077 2 49 22 -0.026 0.031 1000 -1000 -0.037 -1000
Arf6 downstream pathway 0.0077 2 94 43 -0.02 0.021 1000 -1000 -0.031 -1000
PLK1 signaling events 0.0077 2 188 85 -0.014 0.028 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0077 2 299 104 -0.077 0.045 1000 -1000 -0.066 -1000
FoxO family signaling 0.0077 2 186 64 -0.11 0.086 1000 -1000 -0.064 -1000
Atypical NF-kappaB pathway 0.0077 2 88 31 -0.03 0.028 1000 -1000 -0.035 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0077 2 258 125 -0.054 0.067 1000 -1000 -0.09 -1000
Arf6 trafficking events 0.0077 2 183 71 -0.058 0.037 1000 -1000 -0.063 -1000
E-cadherin signaling in keratinocytes 0.0077 2 121 43 -0.04 0.033 1000 -1000 -0.062 -1000
Insulin-mediated glucose transport 0.0038 1 58 32 -0.04 0.024 1000 -1000 -0.057 -1000
mTOR signaling pathway 0.0038 1 73 53 -0.004 0.028 1000 -1000 -0.055 -1000
Class I PI3K signaling events mediated by Akt 0.0038 1 88 68 -0.04 0.042 1000 -1000 -0.045 -1000
VEGFR1 specific signals 0.0038 1 111 56 -0.01 0.044 1000 -1000 -0.056 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.006 0.036 1000 -1000 -0.055 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 0 0.028 1000 -1000 -0.047 -1000
Arf1 pathway 0.0000 0 12 54 0 0.026 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0.0000 0 7 13 0 0.033 1000 -1000 -0.039 -1000
Total NA 1504 86898 7203 -16 -1000 131000 -131000 -8.2 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.021 0.14 -10000 0 -0.58 14 14
CDKN2C -0.02 0.14 -10000 0 -0.47 22 22
CDKN2A -0.12 0.26 -10000 0 -0.62 55 55
CCND2 0.049 0.12 0.25 52 -10000 0 52
RB1 -0.05 0.13 -10000 0 -0.26 61 61
CDK4 0.065 0.13 0.28 60 -10000 0 60
CDK6 0.056 0.14 0.27 60 -0.16 8 68
G1/S progression 0.05 0.13 0.26 61 -10000 0 61
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.38 0.51 -10000 0 -1.2 55 55
IL23A -0.4 0.53 -10000 0 -1.2 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.41 0.48 -10000 0 -1.2 60 60
positive regulation of T cell mediated cytotoxicity -0.43 0.6 -10000 0 -1.4 58 58
ITGA3 -0.37 0.5 -10000 0 -1.1 60 60
IL17F -0.24 0.32 -10000 0 -0.72 54 54
IL12B -0.009 0.058 -10000 0 -0.41 4 4
STAT1 (dimer) -0.41 0.56 -10000 0 -1.3 58 58
CD4 -0.36 0.49 -10000 0 -1.1 58 58
IL23 -0.39 0.5 -10000 0 -1.2 61 61
IL23R -0.057 0.099 -10000 0 -0.47 2 2
IL1B -0.41 0.55 -10000 0 -1.2 61 61
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.37 0.48 -10000 0 -1.1 57 57
TYK2 0 0.02 -10000 0 -10000 0 0
STAT4 -0.049 0.18 -10000 0 -0.59 26 26
STAT3 0.012 0 -10000 0 -10000 0 0
IL18RAP -0.062 0.19 -10000 0 -0.55 34 34
IL12RB1 -0.065 0.2 -10000 0 -0.61 28 28
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.048 0.15 -10000 0 -0.46 28 28
IL23R/JAK2 -0.066 0.12 -10000 0 -0.5 3 3
positive regulation of chronic inflammatory response -0.43 0.6 -10000 0 -1.4 58 58
natural killer cell activation 0.006 0.009 0.039 7 -10000 0 7
JAK2 0 0.05 -10000 0 -0.69 1 1
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
NFKB1 0.007 0.042 -10000 0 -0.66 1 1
RELA 0.009 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.37 0.47 -10000 0 -1.1 61 61
ALOX12B -0.43 0.54 -10000 0 -1.2 73 73
CXCL1 -0.46 0.57 -10000 0 -1.3 72 72
T cell proliferation -0.43 0.6 -10000 0 -1.4 58 58
NFKBIA 0.007 0.042 -10000 0 -0.66 1 1
IL17A -0.18 0.26 -10000 0 -0.57 45 45
PI3K -0.42 0.5 -10000 0 -1.2 59 59
IFNG -0.022 0.045 0.088 2 -0.12 26 28
STAT3 (dimer) -0.39 0.46 -10000 0 -1.1 58 58
IL18R1 -0.017 0.13 -10000 0 -0.59 12 12
IL23/IL23R/JAK2/TYK2/SOCS3 -0.22 0.32 -10000 0 -0.81 33 33
IL18/IL18R -0.056 0.19 -10000 0 -0.48 34 34
macrophage activation -0.021 0.018 -10000 0 -0.044 60 60
TNF -0.43 0.57 -10000 0 -1.3 60 60
STAT3/STAT4 -0.44 0.51 -10000 0 -1.2 63 63
STAT4 (dimer) -0.43 0.57 -10000 0 -1.3 63 63
IL18 -0.017 0.13 -10000 0 -0.58 12 12
IL19 -0.37 0.49 -10000 0 -1.2 52 52
STAT5A (dimer) -0.41 0.57 -10000 0 -1.3 59 59
STAT1 0.01 0.025 -10000 0 -0.39 1 1
SOCS3 -0.008 0.11 -10000 0 -0.57 9 9
CXCL9 -0.45 0.58 -10000 0 -1.3 67 67
MPO -0.41 0.53 -10000 0 -1.2 66 66
positive regulation of humoral immune response -0.43 0.6 -10000 0 -1.4 58 58
IL23/IL23R/JAK2/TYK2 -0.48 0.73 -10000 0 -1.6 58 58
IL6 -0.43 0.54 -10000 0 -1.2 69 69
STAT5A 0.006 0.058 -10000 0 -0.65 2 2
IL2 0.002 0.037 -10000 0 -0.4 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.009 0.039 7 -10000 0 7
CD3E -0.4 0.55 -10000 0 -1.2 60 60
keratinocyte proliferation -0.43 0.6 -10000 0 -1.4 58 58
NOS2 -0.4 0.52 -10000 0 -1.2 64 64
Syndecan-1-mediated signaling events

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
TGFB1 0.004 0.071 -9999 0 -0.65 3 3
CCL5 -0.071 0.21 -9999 0 -0.59 36 36
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.24 -9999 0 -0.46 74 74
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.16 0.24 -9999 0 -0.58 42 42
Syndecan-1/Syntenin -0.16 0.23 -9999 0 -0.6 39 39
MAPK3 -0.14 0.21 -9999 0 -0.62 29 29
HGF/MET -0.055 0.18 -9999 0 -0.54 30 30
TGFB1/TGF beta receptor Type II 0.004 0.071 -9999 0 -0.65 3 3
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.16 0.23 -9999 0 -0.57 42 42
Syndecan-1/RANTES -0.2 0.28 -9999 0 -0.61 59 59
Syndecan-1/CD147 -0.15 0.22 -9999 0 -0.57 39 39
Syndecan-1/Syntenin/PIP2 -0.16 0.22 -9999 0 -0.58 39 39
LAMA5 0.007 0.048 -9999 0 -0.52 2 2
positive regulation of cell-cell adhesion -0.15 0.22 -9999 0 -0.56 39 39
MMP7 -0.16 0.27 -9999 0 -0.55 78 78
HGF -0.031 0.16 -9999 0 -0.57 19 19
Syndecan-1/CASK -0.17 0.23 -9999 0 -0.44 74 74
Syndecan-1/HGF/MET -0.2 0.28 -9999 0 -0.61 60 60
regulation of cell adhesion -0.13 0.2 -9999 0 -0.61 27 27
HPSE -0.034 0.16 -9999 0 -0.61 19 19
positive regulation of cell migration -0.18 0.24 -9999 0 -0.46 74 74
SDC1 -0.18 0.25 -9999 0 -0.46 74 74
Syndecan-1/Collagen -0.18 0.24 -9999 0 -0.46 74 74
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.045 0.18 -9999 0 -0.61 24 24
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.099 0.23 -9999 0 -0.54 53 53
MAPK1 -0.14 0.21 -9999 0 -0.61 30 30
homophilic cell adhesion -0.17 0.24 -9999 0 -0.45 74 74
MMP1 -0.14 0.25 -9999 0 -0.51 78 78
IL4-mediated signaling events

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
BCL2L1 -0.51 0.52 -10000 0 -1.3 60 60
STAT6 (cleaved dimer) -0.57 0.54 -10000 0 -1.2 85 85
IGHG1 -0.17 0.17 -10000 0 -0.42 25 25
IGHG3 -0.5 0.49 -10000 0 -1.2 74 74
AKT1 -0.28 0.34 -10000 0 -0.99 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.38 -10000 0 -1.2 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.38 -10000 0 -1.1 31 31
THY1 -0.53 0.55 -10000 0 -1.4 62 62
MYB -0.012 0.12 -10000 0 -0.6 10 10
HMGA1 0.001 0.081 -10000 0 -0.65 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.38 0.43 -10000 0 -1 58 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.31 0.4 -10000 0 -1.2 30 30
SP1 0.018 0.003 -10000 0 -10000 0 0
INPP5D -0.015 0.13 -10000 0 -0.63 11 11
SOCS5 0.026 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.53 0.55 -10000 0 -1.3 74 74
SOCS1 -0.33 0.32 -10000 0 -0.79 56 56
SOCS3 -0.31 0.36 -10000 0 -1 36 36
FCER2 -0.43 0.43 -10000 0 -1.1 51 51
PARP14 0.002 0.082 -10000 0 -0.65 4 4
CCL17 -0.59 0.59 -10000 0 -1.4 73 73
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.24 0.3 -10000 0 -1 24 24
T cell proliferation -0.52 0.55 -10000 0 -1.3 68 68
IL4R/JAK1 -0.52 0.53 -10000 0 -1.3 66 66
EGR2 -0.53 0.54 -10000 0 -1.3 60 60
JAK2 -0.018 0.05 -10000 0 -0.69 1 1
JAK3 0.004 0.081 -10000 0 -0.64 4 4
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
JAK1 0.004 0.009 -10000 0 -10000 0 0
COL1A2 -0.18 0.28 -10000 0 -1.6 8 8
CCL26 -0.54 0.55 -10000 0 -1.4 61 61
IL4R -0.56 0.57 -10000 0 -1.4 62 62
PTPN6 0.024 0.01 -10000 0 -10000 0 0
IL13RA2 -0.59 0.58 -10000 0 -1.3 81 81
IL13RA1 -0.015 0.028 -10000 0 -10000 0 0
IRF4 -0.32 0.52 -10000 0 -1.2 51 51
ARG1 -0.14 0.2 -10000 0 -0.83 12 12
CBL -0.35 0.4 -10000 0 -0.95 54 54
GTF3A 0.017 0.007 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.021 0.05 -10000 0 -0.52 1 1
IRF4/BCL6 -0.3 0.48 -10000 0 -1.2 48 48
CD40LG -0.062 0.2 -10000 0 -0.6 31 31
MAPK14 -0.35 0.41 -10000 0 -1 47 47
mitosis -0.26 0.31 -10000 0 -0.9 33 33
STAT6 -0.61 0.68 -10000 0 -1.5 71 71
SPI1 -0.008 0.12 -10000 0 -0.62 9 9
RPS6KB1 -0.25 0.3 -10000 0 -0.89 30 30
STAT6 (dimer) -0.62 0.68 -10000 0 -1.5 71 71
STAT6 (dimer)/PARP14 -0.56 0.58 -10000 0 -1.4 69 69
mast cell activation 0.013 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.4 -10000 0 -1.2 34 34
FRAP1 -0.28 0.34 -10000 0 -0.99 33 33
LTA -0.54 0.57 -10000 0 -1.4 57 57
FES 0.012 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.59 0.61 1.4 71 -10000 0 71
CCL11 -0.64 0.62 -10000 0 -1.4 83 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.3 0.4 -10000 0 -1.2 32 32
IL2RG -0.048 0.19 -10000 0 -0.61 26 26
IL10 -0.54 0.56 -10000 0 -1.4 62 62
IRS1 0.002 0.075 -10000 0 -0.59 4 4
IRS2 0 0.085 -10000 0 -0.6 5 5
IL4 -0.12 0.11 -10000 0 -10000 0 0
IL5 -0.52 0.52 -10000 0 -1.3 57 57
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.37 -10000 0 -0.93 60 60
COL1A1 -0.23 0.36 -10000 0 -1.5 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.53 0.55 -10000 0 -1.4 56 56
IL2R gamma/JAK3 -0.036 0.16 -10000 0 -0.47 29 29
TFF3 -0.66 0.62 -10000 0 -1.4 92 92
ALOX15 -0.58 0.57 -10000 0 -1.4 72 72
MYBL1 0.006 0.054 -10000 0 -0.48 3 3
T-helper 2 cell differentiation -0.45 0.46 -10000 0 -1.1 68 68
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.011 0.042 -10000 0 -0.65 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.29 0.37 -10000 0 -1.1 29 29
mol:PI-3-4-5-P3 -0.28 0.34 -10000 0 -0.99 33 33
PI3K -0.3 0.38 -10000 0 -1.1 33 33
DOK2 -0.005 0.1 -10000 0 -0.62 7 7
ETS1 0.025 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.22 0.29 -10000 0 -0.93 25 25
ITGB3 -0.55 0.55 -10000 0 -1.3 65 65
PIGR -0.72 0.64 -10000 0 -1.4 102 102
IGHE 0.038 0.048 0.29 1 -0.25 1 2
MAPKKK cascade -0.22 0.28 -10000 0 -0.9 25 25
BCL6 0.006 0.058 -10000 0 -0.65 2 2
OPRM1 -0.52 0.52 -10000 0 -1.3 60 60
RETNLB -0.52 0.52 -10000 0 -1.3 60 60
SELP -0.54 0.55 -10000 0 -1.4 62 62
AICDA -0.5 0.5 -10000 0 -1.3 59 59
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.041 0.051 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.43 20 20
JUN -0.075 0.15 -9999 0 -0.45 18 18
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.14 0.21 -9999 0 -0.44 74 74
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.01 0.025 -9999 0 -0.39 1 1
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.14 0.21 -9999 0 -0.44 74 74
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.008 0.035 -9999 0 -0.39 2 2
RET9/GFRalpha1/GDNF/Enigma -0.11 0.18 -9999 0 -0.41 58 58
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.14 0.18 -9999 0 -0.39 74 74
GRB7 0.002 0.075 -9999 0 -0.59 4 4
RET51/GFRalpha1/GDNF -0.14 0.21 -9999 0 -0.44 74 74
MAPKKK cascade -0.12 0.16 -9999 0 -0.53 18 18
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.19 -9999 0 -0.42 60 60
lamellipodium assembly -0.095 0.13 -9999 0 -0.31 56 56
RET51/GFRalpha1/GDNF/SHC -0.14 0.21 -9999 0 -0.44 74 74
PIK3CA 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.11 0.18 -9999 0 -0.41 58 58
RET9/GFRalpha1/GDNF/Shank3 -0.11 0.18 -9999 0 -0.41 58 58
MAPK3 -0.11 0.18 -9999 0 -0.37 74 74
DOK1 0.012 0 -9999 0 -10000 0 0
DOK6 -0.013 0.12 -9999 0 -0.52 12 12
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.1 0.18 -9999 0 -0.49 23 23
DOK5 -0.057 0.2 -9999 0 -0.62 28 28
GFRA1 -0.17 0.27 -9999 0 -0.53 87 87
MAPK8 -0.082 0.15 -9999 0 -0.41 22 22
HRAS/GTP -0.14 0.19 -9999 0 -0.41 74 74
tube development -0.098 0.17 -9999 0 -0.38 58 58
MAPK1 -0.12 0.18 -9999 0 -0.37 75 75
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.069 0.14 -9999 0 -0.31 54 54
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.21 -9999 0 -0.42 79 79
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.14 0.21 -9999 0 -0.44 74 74
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.24 -9999 0 -0.47 91 91
PRKCA -0.003 0.092 -9999 0 -0.54 7 7
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.085 0.16 -9999 0 -0.36 55 55
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.069 0.14 -9999 0 -0.31 54 54
RET51/GFRalpha1/GDNF/Grb7 -0.15 0.22 -9999 0 -0.45 76 76
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.063 0.19 -9999 0 -0.53 36 36
DOK4 0.012 0 -9999 0 -10000 0 0
JNK cascade -0.073 0.15 -9999 0 -0.44 18 18
RET9/GFRalpha1/GDNF/FRS2 -0.11 0.18 -9999 0 -0.41 59 59
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.069 0.14 -9999 0 -0.3 58 58
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.094 0.16 -9999 0 -0.33 69 69
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.094 0.16 -9999 0 -0.33 69 69
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.098 0.18 -9999 0 -0.35 69 69
PI3K -0.12 0.22 -9999 0 -0.48 57 57
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.098 0.17 -9999 0 -0.38 58 58
GRB10 0.012 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.088 0.15 -9999 0 -0.34 57 57
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.21 -9999 0 -0.44 75 75
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 0.002 0.075 -9999 0 -0.59 4 4
IRS2 0 0.085 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.098 0.18 -9999 0 -0.35 69 69
RET51/GFRalpha1/GDNF/PKC alpha -0.15 0.22 -9999 0 -0.44 78 78
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.041 0.16 -9999 0 -0.51 25 25
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.15 0.22 -9999 0 -0.45 76 76
Rac1/GTP -0.11 0.16 -9999 0 -0.37 56 56
RET9/GFRalpha1/GDNF -0.13 0.2 -9999 0 -0.35 101 101
GFRalpha1/GDNF -0.15 0.23 -9999 0 -0.41 101 101
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.14 0.24 -10000 0 -0.58 54 54
FYN -0.14 0.36 -10000 0 -0.77 55 55
LAT/GRAP2/SLP76 -0.16 0.29 -10000 0 -0.66 57 57
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 -0.08 0.22 -10000 0 -0.48 57 57
B2M -0.005 0.1 -10000 0 -0.66 6 6
IKBKG -0.034 0.055 -10000 0 -0.14 30 30
MAP3K8 0.01 0.025 -10000 0 -0.39 1 1
mol:Ca2+ -0.015 0.028 -10000 0 -0.094 20 20
integrin-mediated signaling pathway -0.001 0.074 -10000 0 -0.31 13 13
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.14 0.34 -10000 0 -0.73 59 59
TRPV6 -0.045 0.17 -10000 0 -0.62 20 20
CD28 -0.006 0.1 -10000 0 -0.62 7 7
SHC1 -0.14 0.35 -10000 0 -0.74 59 59
receptor internalization -0.16 0.38 -10000 0 -0.81 59 59
PRF1 -0.18 0.43 -10000 0 -1.1 42 42
KRAS -0.001 0.07 -10000 0 -0.39 8 8
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 -0.054 0.18 -10000 0 -0.38 52 52
LAT -0.14 0.35 -10000 0 -0.75 59 59
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.11 0.25 -10000 0 -0.6 54 54
CD3E -0.077 0.22 -10000 0 -0.61 37 37
CD3G -0.076 0.22 -10000 0 -0.59 38 38
RASGRP2 -0.007 0.039 -10000 0 -0.17 9 9
RASGRP1 -0.077 0.22 -10000 0 -0.47 57 57
HLA-A 0.009 0.025 -10000 0 -0.39 1 1
RASSF5 -0.015 0.12 -10000 0 -0.51 13 13
RAP1A/GTP/RAPL -0.001 0.074 -10000 0 -0.31 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.065 -10000 0 -0.12 47 47
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.061 0.097 -10000 0 -0.24 48 48
PRKCA -0.072 0.12 -10000 0 -0.3 49 49
GRAP2 -0.068 0.2 -10000 0 -0.58 35 35
mol:IP3 -0.1 0.21 0.24 15 -0.47 55 70
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.41 -10000 0 -0.87 56 56
ORAI1 0.028 0.085 0.32 20 -10000 0 20
CSK -0.15 0.36 -10000 0 -0.76 59 59
B7 family/CD28 -0.19 0.36 -10000 0 -0.79 57 57
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.18 0.43 -10000 0 -0.9 59 59
PTPN6 -0.15 0.36 -10000 0 -0.8 55 55
VAV1 -0.15 0.36 -10000 0 -0.77 59 59
Monovalent TCR/CD3 -0.16 0.36 -10000 0 -0.69 64 64
CBL 0.012 0 -10000 0 -10000 0 0
LCK -0.16 0.38 -10000 0 -0.83 55 55
PAG1 -0.15 0.36 -10000 0 -0.77 58 58
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.18 0.43 -10000 0 -0.92 56 56
CD80 -0.033 0.16 -10000 0 -0.6 19 19
CD86 -0.025 0.15 -10000 0 -0.66 14 14
PDK1/CARD11/BCL10/MALT1 -0.075 0.12 -10000 0 -0.29 52 52
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.11 0.29 -10000 0 -0.62 57 57
CD8A -0.06 0.2 -10000 0 -0.59 31 31
CD8B -0.088 0.22 -10000 0 -0.55 46 46
PTPRC -0.031 0.16 -10000 0 -0.63 17 17
PDK1/PKC theta -0.1 0.28 -10000 0 -0.6 56 56
CSK/PAG1 -0.14 0.35 -10000 0 -0.76 55 55
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.002 0.079 -10000 0 -0.47 7 7
GRAP2/SLP76 -0.19 0.34 -10000 0 -0.78 58 58
STIM1 0.015 0.043 -10000 0 -10000 0 0
RAS family/GTP -0.008 0.089 -10000 0 -0.18 38 38
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.18 0.43 -10000 0 -0.9 58 58
mol:DAG -0.1 0.18 -10000 0 -0.41 57 57
RAP1A/GDP 0 0.028 -10000 0 -0.063 10 10
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 -0.045 0.18 -10000 0 -0.58 25 25
cytotoxic T cell degranulation -0.16 0.4 -10000 0 -0.97 43 43
RAP1A/GTP -0.005 0.012 -10000 0 -0.067 8 8
mol:PI-3-4-5-P3 -0.1 0.27 -10000 0 -0.57 59 59
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.28 0.26 15 -0.63 55 70
NRAS 0.01 0.025 -10000 0 -0.39 1 1
ZAP70 -0.042 0.17 -10000 0 -0.57 24 24
GRB2/SOS1 0.017 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.15 0.27 -10000 0 -0.62 57 57
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.1 0.24 -10000 0 -0.52 59 59
CARD11 -0.038 0.16 -10000 0 -0.55 23 23
PRKCB -0.082 0.14 -10000 0 -0.32 53 53
PRKCE -0.068 0.12 -10000 0 -0.3 48 48
PRKCQ -0.13 0.32 -10000 0 -0.69 58 58
LCP2 -0.019 0.14 -10000 0 -0.65 12 12
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.063 0.19 -10000 0 -0.4 57 57
IKK complex 0.001 0.064 -10000 0 -0.12 35 35
RAS family/GDP -0.008 0.014 -10000 0 -0.067 3 3
MAP3K14 -0.033 0.14 -10000 0 -0.29 46 46
PDPK1 -0.072 0.21 -10000 0 -0.45 55 55
TCR/CD3/MHC I/CD8/Fyn -0.2 0.46 -10000 0 -0.96 60 60
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.32 0.36 -10000 0 -0.91 47 47
PCK1 -0.48 0.53 -10000 0 -1.3 68 68
HNF4A -0.4 0.44 -10000 0 -1.1 52 52
KCNJ11 -0.32 0.37 -10000 0 -0.95 42 42
AKT1 -0.11 0.14 -10000 0 -0.45 4 4
response to starvation -0.012 0.03 -10000 0 -10000 0 0
DLK1 -0.53 0.53 -10000 0 -1.1 93 93
NKX2-1 -0.085 0.19 0.52 1 -0.68 2 3
ACADM -0.32 0.36 -10000 0 -0.91 47 47
TAT -0.26 0.23 -10000 0 -0.75 23 23
CEBPB 0.009 0.041 -10000 0 -0.65 1 1
CEBPA -0.007 0.1 -10000 0 -0.54 9 9
TTR -0.31 0.26 -10000 0 -0.88 27 27
PKLR -0.32 0.36 -10000 0 -0.97 38 38
APOA1 -0.48 0.56 -10000 0 -1.3 61 61
CPT1C -0.36 0.41 -10000 0 -1 51 51
ALAS1 -0.15 0.17 -10000 0 -0.64 4 4
TFRC -0.31 0.28 -10000 0 -0.79 39 39
FOXF1 0.005 0.055 -10000 0 -0.38 5 5
NF1 -0.005 0.12 -10000 0 -0.65 9 9
HNF1A (dimer) -0.015 0.11 -10000 0 -0.46 15 15
CPT1A -0.32 0.36 -10000 0 -0.95 42 42
HMGCS1 -0.32 0.36 -10000 0 -0.92 44 44
NR3C1 -0.011 0.095 -10000 0 -0.64 4 4
CPT1B -0.33 0.37 -10000 0 -0.93 49 49
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.011 0.011 -10000 0 -10000 0 0
GCK -0.41 0.47 -10000 0 -1.1 65 65
CREB1 -0.02 0.06 -10000 0 -10000 0 0
IGFBP1 -0.26 0.39 -10000 0 -1.2 28 28
PDX1 -0.16 0.2 -10000 0 -0.73 10 10
UCP2 -0.33 0.38 -10000 0 -1 33 33
ALDOB -0.32 0.37 -10000 0 -1 36 36
AFP -0.21 0.21 -10000 0 -0.55 48 48
BDH1 -0.32 0.37 -10000 0 -0.95 43 43
HADH -0.32 0.37 -10000 0 -0.99 34 34
F2 -0.38 0.42 -10000 0 -1.2 33 33
HNF1A -0.015 0.11 -10000 0 -0.46 15 15
G6PC -0.11 0.15 -10000 0 -0.63 4 4
SLC2A2 -0.19 0.22 -10000 0 -0.7 11 11
INS 0.011 0.053 0.22 1 -10000 0 1
FOXA1 -0.2 0.26 -10000 0 -0.51 98 98
FOXA3 -0.22 0.27 -10000 0 -0.55 94 94
FOXA2 -0.37 0.42 -10000 0 -1 50 50
ABCC8 -0.33 0.37 -10000 0 -1 36 36
ALB -0.27 0.34 -10000 0 -0.77 59 59
Glypican 2 network

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
MDK -0.013 0.12 -9999 0 -0.63 10 10
GPC2 -0.046 0.16 -9999 0 -0.49 30 30
GPC2/Midkine -0.043 0.15 -9999 0 -0.37 40 40
neuron projection morphogenesis -0.043 0.15 -9999 0 -0.37 40 40
Wnt signaling

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
Noncanonical Wnts/FZD -0.13 0.24 -9999 0 -0.63 34 34
FZD6 0.009 0.041 -9999 0 -0.65 1 1
WNT6 -0.14 0.26 -9999 0 -0.57 69 69
WNT4 -0.05 0.18 -9999 0 -0.55 29 29
FZD3 0.009 0.041 -9999 0 -0.65 1 1
WNT5A -0.021 0.14 -9999 0 -0.65 13 13
WNT11 -0.11 0.23 -9999 0 -0.51 62 62
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.055 0.19 -10000 0 -0.48 32 32
TBX21 -0.23 0.57 -10000 0 -1.3 49 49
B2M -0.005 0.1 -10000 0 -0.66 6 6
TYK2 0.01 0.022 -10000 0 -10000 0 0
IL12RB1 -0.055 0.2 -10000 0 -0.62 28 28
GADD45B -0.14 0.41 -10000 0 -0.98 37 37
IL12RB2 -0.023 0.13 -10000 0 -0.46 20 20
GADD45G -0.13 0.4 -10000 0 -1 34 34
natural killer cell activation -0.001 0.022 -10000 0 -10000 0 0
RELB 0.009 0.041 -10000 0 -0.65 1 1
RELA 0.012 0 -10000 0 -10000 0 0
IL18 -0.014 0.13 -10000 0 -0.59 12 12
IL2RA -0.042 0.18 -10000 0 -0.63 22 22
IFNG -0.057 0.18 -10000 0 -0.5 34 34
STAT3 (dimer) -0.13 0.39 -10000 0 -0.88 46 46
HLA-DRB5 -0.095 0.22 -10000 0 -0.5 54 54
FASLG -0.23 0.56 -10000 0 -1.3 47 47
NF kappa B2 p52/RelB -0.27 0.46 -10000 0 -1.1 48 48
CD4 0.001 0.082 -10000 0 -0.65 4 4
SOCS1 -0.002 0.088 -10000 0 -0.57 6 6
EntrezGene:6955 -0.002 0.01 -10000 0 -10000 0 0
CD3D -0.12 0.25 -10000 0 -0.6 54 54
CD3E -0.077 0.22 -10000 0 -0.61 37 37
CD3G -0.077 0.22 -10000 0 -0.59 38 38
IL12Rbeta2/JAK2 -0.009 0.11 -10000 0 -0.36 18 18
CCL3 -0.21 0.54 -10000 0 -1.3 43 43
CCL4 -0.21 0.54 -10000 0 -1.3 41 41
HLA-A 0.009 0.026 -10000 0 -0.39 1 1
IL18/IL18R -0.037 0.2 -10000 0 -0.51 32 32
NOS2 -0.21 0.52 -10000 0 -1.1 53 53
IL12/IL12R/TYK2/JAK2/SPHK2 -0.049 0.18 -10000 0 -0.46 29 29
IL1R1 -0.2 0.51 -10000 0 -1.2 45 45
IL4 0.003 0.023 -10000 0 -10000 0 0
JAK2 0.008 0.048 -10000 0 -0.69 1 1
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.26 0.6 -10000 0 -1.2 61 61
RAB7A -0.089 0.33 -10000 0 -0.82 29 29
lysosomal transport -0.082 0.32 -10000 0 -0.76 30 30
FOS -0.19 0.45 -10000 0 -1.2 38 38
STAT4 (dimer) -0.16 0.45 -10000 0 -1 43 43
STAT5A (dimer) -0.29 0.48 -10000 0 -1.1 57 57
GZMA -0.24 0.59 -10000 0 -1.4 46 46
GZMB -0.25 0.59 -10000 0 -1.4 50 50
HLX 0.012 0 -10000 0 -10000 0 0
LCK -0.24 0.6 -10000 0 -1.3 53 53
TCR/CD3/MHC II/CD4 -0.19 0.39 -10000 0 -0.78 61 61
IL2/IL2R -0.084 0.26 -10000 0 -0.63 41 41
MAPK14 -0.13 0.42 -10000 0 -0.96 40 40
CCR5 -0.18 0.49 -10000 0 -1.2 42 42
IL1B -0.038 0.17 -10000 0 -0.6 21 21
STAT6 -0.024 0.12 -10000 0 -0.26 27 27
STAT4 -0.049 0.18 -10000 0 -0.59 26 26
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.025 -10000 0 -0.39 1 1
NFKB1 0.009 0.041 -10000 0 -0.65 1 1
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.003 0.056 -10000 0 -0.41 4 4
CD8A -0.061 0.2 -10000 0 -0.59 31 31
CD8B -0.088 0.22 -10000 0 -0.55 46 46
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.055 0.19 0.47 32 -10000 0 32
IL2RB -0.061 0.2 -10000 0 -0.6 31 31
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.4 -10000 0 -0.91 43 43
IL2RG -0.051 0.19 -10000 0 -0.61 26 26
IL12 -0.044 0.16 -10000 0 -0.42 34 34
STAT5A 0.006 0.058 -10000 0 -0.65 2 2
CD247 -0.045 0.18 -10000 0 -0.57 25 25
IL2 0 0.035 -10000 0 -0.39 2 2
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.067 0.2 -10000 0 -0.55 36 36
IL12/IL12R/TYK2/JAK2 -0.28 0.72 -10000 0 -1.5 53 53
MAP2K3 -0.14 0.42 -10000 0 -0.96 42 42
RIPK2 0.008 0.035 -10000 0 -0.39 2 2
MAP2K6 -0.14 0.42 -10000 0 -0.96 42 42
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.048 0.19 -10000 0 -0.63 24 24
IL18RAP -0.06 0.2 -10000 0 -0.55 34 34
IL12Rbeta1/TYK2 -0.033 0.16 -10000 0 -0.47 28 28
EOMES -0.15 0.42 -10000 0 -1.4 26 26
STAT1 (dimer) -0.16 0.4 -10000 0 -0.88 49 49
T cell proliferation -0.098 0.32 -10000 0 -0.69 45 45
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.014 0.13 -10000 0 -0.59 12 12
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.19 0.3 -10000 0 -0.75 47 47
ATF2 -0.11 0.38 -10000 0 -0.88 38 38
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.057 0.24 -10000 0 -0.77 21 21
IHH -0.058 0.15 -10000 0 -0.4 41 41
SHH Np/Cholesterol/GAS1 -0.063 0.16 -10000 0 -0.44 33 33
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.062 0.16 0.44 33 -10000 0 33
SMO/beta Arrestin2 -0.019 0.12 -10000 0 -0.46 8 8
SMO -0.027 0.13 -10000 0 -0.48 9 9
AKT1 0.004 0.064 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.007 0.096 -10000 0 -0.47 10 10
ADRBK1 0.012 0 -10000 0 -10000 0 0
heart looping -0.026 0.12 -10000 0 -0.47 9 9
STIL -0.062 0.16 -10000 0 -0.47 17 17
DHH N/PTCH2 -0.042 0.15 -10000 0 -0.38 39 39
DHH N/PTCH1 -0.035 0.14 -10000 0 -0.48 13 13
PIK3CA 0.012 0 -10000 0 -10000 0 0
DHH -0.015 0.12 -10000 0 -0.54 12 12
PTHLH -0.052 0.25 -10000 0 -0.83 18 18
determination of left/right symmetry -0.026 0.12 -10000 0 -0.47 9 9
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
skeletal system development -0.051 0.24 -10000 0 -0.82 18 18
IHH N/Hhip -0.099 0.18 -10000 0 -0.42 53 53
DHH N/Hhip -0.072 0.18 -10000 0 -0.39 57 57
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.026 0.12 -10000 0 -0.47 9 9
pancreas development -0.086 0.21 -10000 0 -0.51 48 48
HHAT -0.016 0.13 -10000 0 -0.65 11 11
PI3K 0.015 0.025 -10000 0 -0.27 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.026 0.15 -10000 0 -0.63 15 15
somite specification -0.026 0.12 -10000 0 -0.47 9 9
SHH Np/Cholesterol/PTCH1 -0.067 0.16 -10000 0 -0.42 29 29
SHH Np/Cholesterol/PTCH2 -0.073 0.16 -10000 0 -0.39 41 41
SHH Np/Cholesterol/Megalin -0.19 0.2 -10000 0 -0.42 97 97
SHH -0.062 0.16 -10000 0 -0.36 54 54
catabolic process -0.029 0.14 -10000 0 -0.4 22 22
SMO/Vitamin D3 -0.058 0.16 -10000 0 -0.49 15 15
SHH Np/Cholesterol/Hhip -0.097 0.18 -10000 0 -0.43 46 46
LRP2 -0.26 0.28 -10000 0 -0.53 130 130
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.49 35 35
SHH Np/Cholesterol/BOC -0.052 0.14 -10000 0 -0.41 23 23
SHH Np/Cholesterol/CDO -0.046 0.14 -10000 0 -0.44 21 21
mesenchymal cell differentiation 0.096 0.18 0.42 46 -10000 0 46
mol:Vitamin D3 -0.065 0.16 -10000 0 -0.42 29 29
IHH N/PTCH2 -0.065 0.16 -10000 0 -0.41 35 35
CDON 0.003 0.068 -10000 0 -0.52 4 4
IHH N/PTCH1 -0.029 0.14 -10000 0 -0.4 22 22
Megalin/LRPAP1 -0.18 0.21 -10000 0 -0.38 130 130
PTCH2 -0.045 0.16 -10000 0 -0.48 30 30
SHH Np/Cholesterol -0.049 0.13 -10000 0 -0.4 21 21
PTCH1 -0.029 0.14 -10000 0 -0.4 22 22
HHIP -0.086 0.21 -10000 0 -0.51 48 48
TCGA08_p53

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
CDKN2A -0.095 0.2 -10000 0 -0.49 55 55
TP53 -0.063 0.11 -10000 0 -0.37 22 22
Senescence -0.063 0.11 -10000 0 -0.37 22 22
Apoptosis -0.063 0.11 -10000 0 -0.37 22 22
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.058 0.11 0.28 53 -10000 0 53
MDM4 0.012 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.001 0.081 -9999 0 -0.65 4 4
GNB1/GNG2 -0.11 0.22 -9999 0 -0.58 33 33
mol:DAG -0.095 0.2 -9999 0 -0.55 29 29
PLCG1 -0.099 0.21 -9999 0 -0.57 29 29
YES1 -0.12 0.23 -9999 0 -0.59 34 34
FZD3 0.009 0.041 -9999 0 -0.65 1 1
FZD6 0.009 0.041 -9999 0 -0.65 1 1
G protein -0.099 0.21 -9999 0 -0.58 29 29
MAP3K7 -0.08 0.17 -9999 0 -0.46 29 29
mol:Ca2+ -0.092 0.19 -9999 0 -0.53 29 29
mol:IP3 -0.095 0.2 -9999 0 -0.55 29 29
NLK -0.006 0.012 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.092 0.18 -9999 0 -0.51 29 29
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.24 -9999 0 -0.63 34 34
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.12 0.23 -9999 0 -0.59 34 34
GO:0007205 -0.093 0.19 -9999 0 -0.54 29 29
WNT6 -0.14 0.26 -9999 0 -0.57 69 69
WNT4 -0.05 0.18 -9999 0 -0.55 29 29
NFAT1/CK1 alpha -0.096 0.22 -9999 0 -0.6 28 28
GNG2 0.007 0.043 -9999 0 -0.39 3 3
WNT5A -0.021 0.14 -9999 0 -0.65 13 13
WNT11 -0.11 0.23 -9999 0 -0.51 62 62
CDC42 -0.11 0.22 -9999 0 -0.56 33 33
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.063 0.22 -9999 0 -0.67 27 27
alphaM/beta2 Integrin/GPIbA -0.062 0.21 -9999 0 -0.62 28 28
alphaM/beta2 Integrin/proMMP-9 -0.12 0.27 -9999 0 -0.66 41 41
PLAUR 0.004 0.071 -9999 0 -0.65 3 3
HMGB1 0.001 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.05 0.2 -9999 0 -0.68 22 22
AGER -0.017 0.1 -9999 0 -0.58 8 8
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG -0.01 0.12 -9999 0 -0.62 9 9
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.083 0.22 -9999 0 -0.61 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.099 0.23 -9999 0 -0.54 53 53
CYR61 -0.004 0.078 -9999 0 -0.39 10 10
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.14 0.22 -9999 0 -0.59 34 34
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.029 0.15 -9999 0 -0.54 19 19
MYH2 -0.15 0.22 -9999 0 -0.55 43 43
MST1R -0.037 0.17 -9999 0 -0.59 21 21
leukocyte activation during inflammatory response -0.12 0.21 -9999 0 -0.54 41 41
APOB -0.032 0.13 -9999 0 -0.44 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.011 0.12 -9999 0 -0.57 10 10
JAM3 0.004 0.056 -9999 0 -0.39 5 5
GP1BA -0.007 0.1 -9999 0 -0.56 8 8
alphaM/beta2 Integrin/CTGF -0.062 0.21 -9999 0 -0.66 25 25
alphaM/beta2 Integrin -0.16 0.28 -9999 0 -0.59 49 49
JAM3 homodimer 0.004 0.056 -9999 0 -0.39 5 5
ICAM2 0.007 0.043 -9999 0 -0.39 3 3
ICAM1 -0.035 0.16 -9999 0 -0.57 21 21
phagocytosis triggered by activation of immune response cell surface activating receptor -0.16 0.27 -9999 0 -0.57 49 49
cell adhesion -0.077 0.2 -9999 0 -0.62 28 28
NFKB1 -0.12 0.27 -9999 0 -0.73 28 28
THY1 -0.014 0.12 -9999 0 -0.6 11 11
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.063 0.15 -9999 0 -0.39 31 31
alphaM/beta2 Integrin/LRP/tPA -0.078 0.23 -9999 0 -0.58 38 38
IL6 -0.16 0.32 -9999 0 -0.79 42 42
ITGB2 -0.043 0.17 -9999 0 -0.67 17 17
elevation of cytosolic calcium ion concentration -0.063 0.24 -9999 0 -0.74 25 25
alphaM/beta2 Integrin/JAM2/JAM3 -0.058 0.21 -9999 0 -0.66 24 24
JAM2 -0.017 0.12 -9999 0 -0.46 16 16
alphaM/beta2 Integrin/ICAM1 -0.088 0.27 -9999 0 -0.64 40 40
alphaM/beta2 Integrin/uPA/Plg -0.069 0.24 -9999 0 -0.72 25 25
RhoA/GTP -0.16 0.25 -9999 0 -0.52 57 57
positive regulation of phagocytosis -0.13 0.24 -9999 0 -0.73 30 30
Ron/MSP -0.032 0.14 -9999 0 -0.41 30 30
alphaM/beta2 Integrin/uPAR/uPA -0.063 0.24 -9999 0 -0.76 25 25
alphaM/beta2 Integrin/uPAR -0.054 0.21 -9999 0 -0.7 23 23
PLAU -0.027 0.15 -9999 0 -0.55 18 18
PLAT -0.051 0.18 -9999 0 -0.55 29 29
actin filament polymerization -0.14 0.21 -9999 0 -0.52 43 43
MST1 -0.007 0.096 -9999 0 -0.47 10 10
alphaM/beta2 Integrin/lipoprotein(a) -0.1 0.22 -9999 0 -0.55 41 41
TNF -0.15 0.34 -9999 0 -0.85 42 42
RAP1B 0.01 0.025 -9999 0 -0.39 1 1
alphaM/beta2 Integrin/uPA -0.072 0.25 -9999 0 -0.77 25 25
fibrinolysis -0.08 0.23 -9999 0 -0.71 25 25
HCK -0.014 0.13 -9999 0 -0.65 10 10
dendritic cell antigen processing and presentation -0.16 0.27 -9999 0 -0.57 49 49
VTN -0.051 0.17 -9999 0 -0.5 32 32
alphaM/beta2 Integrin/CYR61 -0.059 0.2 -9999 0 -0.62 26 26
LPA -0.074 0.19 -9999 0 -0.51 41 41
LRP1 0.004 0.071 -9999 0 -0.65 3 3
cell migration -0.11 0.26 -9999 0 -0.61 45 45
FN1 -0.051 0.17 -9999 0 -0.5 32 32
alphaM/beta2 Integrin/Thy1 -0.065 0.22 -9999 0 -0.67 28 28
MPO -0.051 0.18 -9999 0 -0.53 30 30
KNG1 -0.002 0.043 -9999 0 -0.39 3 3
RAP1/GDP 0.015 0.015 -9999 0 -0.22 1 1
ROCK1 -0.14 0.22 -9999 0 -0.55 43 43
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.006 0.054 -9999 0 -0.39 5 5
CTGF -0.009 0.096 -9999 0 -0.44 12 12
alphaM/beta2 Integrin/Hck -0.063 0.25 -9999 0 -0.84 22 22
ITGAM -0.049 0.18 -9999 0 -0.65 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.24 -9999 0 -0.65 33 33
HP -0.23 0.28 -9999 0 -0.52 119 119
leukocyte adhesion -0.12 0.22 -9999 0 -0.74 23 23
SELP -0.029 0.15 -9999 0 -0.54 19 19
Ephrin B reverse signaling

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
EFNB2 -0.004 0.097 -10000 0 -0.58 7 7
EPHB2 0.009 0.042 -10000 0 -0.66 1 1
EFNB1 0.016 0.036 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.11 -10000 0 -0.44 4 4
Ephrin B2/EPHB1-2 -0.026 0.12 -10000 0 -0.38 23 23
neuron projection morphogenesis -0.035 0.095 -10000 0 -0.36 8 8
Ephrin B1/EPHB1-2/Tiam1 -0.011 0.12 -10000 0 -0.36 21 21
DNM1 0.007 0.048 -10000 0 -0.53 2 2
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.093 0.25 -10000 0 -0.66 40 40
YES1 -0.14 0.32 -10000 0 -0.89 40 40
Ephrin B1/EPHB1-2/NCK2 -0.005 0.11 -10000 0 -0.37 17 17
PI3K -0.093 0.25 -10000 0 -0.66 40 40
mol:GDP -0.011 0.12 -10000 0 -0.36 21 21
ITGA2B -0.026 0.15 -10000 0 -0.63 15 15
endothelial cell proliferation -0.008 0.095 -10000 0 -0.39 15 15
FYN -0.14 0.32 -10000 0 -0.9 40 40
MAP3K7 -0.1 0.26 -10000 0 -0.7 40 40
FGR -0.14 0.32 -10000 0 -0.89 40 40
TIAM1 0.001 0.081 -10000 0 -0.65 4 4
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.25 -10000 0 -0.62 46 46
LYN -0.14 0.32 -10000 0 -0.89 40 40
Ephrin B1/EPHB1-2/Src Family Kinases -0.13 0.3 -10000 0 -0.84 40 40
Ephrin B1/EPHB1-2 -0.12 0.27 -10000 0 -0.76 40 40
SRC -0.14 0.32 -10000 0 -0.88 40 40
ITGB3 -0.054 0.18 -10000 0 -0.49 34 34
EPHB1 -0.056 0.18 -10000 0 -0.52 33 33
EPHB4 -0.009 0.11 -10000 0 -0.65 8 8
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.007 0.096 -10000 0 -0.39 15 15
alphaIIb/beta3 Integrin -0.058 0.17 -10000 0 -0.4 47 47
BLK -0.16 0.32 -10000 0 -0.91 40 40
HCK -0.15 0.32 -10000 0 -0.89 40 40
regulation of stress fiber formation 0.005 0.11 0.36 17 -10000 0 17
MAPK8 -0.083 0.24 -10000 0 -0.63 40 40
Ephrin B1/EPHB1-2/RGS3 -0.005 0.11 -10000 0 -0.37 17 17
endothelial cell migration -0.11 0.24 -10000 0 -0.58 49 49
NCK2 0.012 0 -10000 0 -10000 0 0
PTPN13 -0.13 0.28 -10000 0 -0.66 54 54
regulation of focal adhesion formation 0.005 0.11 0.36 17 -10000 0 17
chemotaxis 0.005 0.11 0.36 17 -10000 0 17
PIK3CA 0.012 0 -10000 0 -10000 0 0
Rac1/GTP -0.036 0.097 -10000 0 -0.37 8 8
angiogenesis -0.12 0.27 -10000 0 -0.75 40 40
LCK -0.15 0.33 -10000 0 -0.91 40 40
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.034 0.15 -10000 0 -0.7 10 10
NFATC2 -0.058 0.24 -10000 0 -0.69 24 24
NFATC3 -0.017 0.066 -10000 0 -0.26 1 1
CD40LG -0.21 0.45 -10000 0 -1 47 47
ITCH 0.008 0.086 -10000 0 -10000 0 0
CBLB 0.008 0.086 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.5 -10000 0 -1.2 52 52
JUNB -0.005 0.095 -10000 0 -0.52 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.034 0.09 -10000 0 -0.31 20 20
T cell anergy -0.03 0.14 -10000 0 -0.44 20 20
TLE4 -0.045 0.23 -10000 0 -0.73 21 21
Jun/NFAT1-c-4/p21SNFT -0.15 0.42 -10000 0 -1.2 28 28
AP-1/NFAT1-c-4 -0.22 0.52 -10000 0 -1.3 37 37
IKZF1 -0.048 0.25 -10000 0 -0.78 21 21
T-helper 2 cell differentiation -0.12 0.3 -10000 0 -0.87 29 29
AP-1/NFAT1 -0.064 0.22 -10000 0 -0.61 23 23
CALM1 0.002 0.057 -10000 0 -10000 0 0
EGR2 -0.12 0.43 -10000 0 -1.4 21 21
EGR3 -0.12 0.41 -10000 0 -1.2 24 24
NFAT1/FOXP3 -0.075 0.27 -10000 0 -0.7 30 30
EGR1 -0.034 0.15 -10000 0 -0.51 22 22
JUN -0.002 0.057 -10000 0 -0.48 3 3
EGR4 -0.065 0.19 -10000 0 -0.54 35 35
mol:Ca2+ -0.01 0.06 -10000 0 -10000 0 0
GBP3 -0.077 0.3 -10000 0 -0.88 28 28
FOSL1 -0.012 0.12 -10000 0 -0.56 11 11
NFAT1-c-4/MAF/IRF4 -0.18 0.44 -10000 0 -1.2 33 33
DGKA -0.025 0.18 -10000 0 -0.57 16 16
CREM 0.009 0.041 -10000 0 -0.65 1 1
NFAT1-c-4/PPARG -0.15 0.42 -10000 0 -1.2 28 28
CTLA4 -0.12 0.35 -10000 0 -0.84 43 43
NFAT1-c-4 (dimer)/EGR1 -0.16 0.44 -10000 0 -1.2 34 34
NFAT1-c-4 (dimer)/EGR4 -0.18 0.43 -10000 0 -1.2 31 31
FOS -0.046 0.16 -10000 0 -0.49 26 26
IFNG -0.2 0.39 -10000 0 -0.94 45 45
T cell activation -0.067 0.23 -10000 0 -0.76 13 13
MAF 0.005 0.063 -10000 0 -0.57 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.11 0.37 1.2 23 -10000 0 23
TNF -0.21 0.44 -10000 0 -1.1 45 45
FASLG -0.21 0.57 -10000 0 -1.6 35 35
TBX21 -0.075 0.21 -10000 0 -0.59 35 35
BATF3 -0.005 0.1 -10000 0 -0.62 7 7
PRKCQ -0.015 0.12 -10000 0 -0.66 9 9
PTPN1 -0.025 0.18 -10000 0 -0.62 12 12
NFAT1-c-4/ICER1 -0.14 0.4 -10000 0 -1.2 27 27
GATA3 -0.061 0.2 -10000 0 -0.59 32 32
T-helper 1 cell differentiation -0.17 0.39 -10000 0 -0.9 46 46
IL2RA -0.22 0.41 -10000 0 -1.1 41 41
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.025 0.18 -10000 0 -0.62 12 12
E2F1 0.007 0.082 -10000 0 -0.65 4 4
PPARG -0.017 0.12 -10000 0 -0.52 14 14
SLC3A2 -0.025 0.18 -10000 0 -0.57 16 16
IRF4 -0.12 0.23 -10000 0 -0.51 63 63
PTGS2 -0.2 0.44 -10000 0 -1.1 39 39
CSF2 -0.19 0.42 -10000 0 -1 38 38
JunB/Fra1/NFAT1-c-4 -0.14 0.42 -10000 0 -1.2 28 28
IL4 -0.12 0.32 -10000 0 -0.95 27 27
IL5 -0.18 0.41 -10000 0 -1.1 35 35
IL2 -0.068 0.23 -10000 0 -0.79 12 12
IL3 -0.041 0.053 -10000 0 -10000 0 0
RNF128 -0.041 0.22 -10000 0 -0.56 35 35
NFATC1 -0.11 0.37 -10000 0 -1.2 23 23
CDK4 0.056 0.2 0.66 13 -10000 0 13
PTPRK -0.03 0.19 -10000 0 -0.66 14 14
IL8 -0.22 0.45 -10000 0 -1.1 41 41
POU2F1 0.012 0.001 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.079 0.17 0.46 33 -10000 0 33
KIRREL -0.003 0.043 -10000 0 -0.44 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.08 0.17 -10000 0 -0.46 33 33
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.052 0.13 -10000 0 -0.36 32 32
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.029 0.11 -10000 0 -0.3 25 25
FYN -0.055 0.13 -10000 0 -0.35 34 34
mol:Ca2+ -0.065 0.13 -10000 0 -0.36 32 32
mol:DAG -0.052 0.13 -10000 0 -0.36 32 32
NPHS2 -0.018 0.07 -10000 0 -0.42 7 7
mol:IP3 -0.052 0.13 -10000 0 -0.36 32 32
regulation of endocytosis -0.045 0.12 -10000 0 -0.32 34 34
Nephrin/NEPH1/podocin/Cholesterol -0.06 0.13 -10000 0 -0.37 33 33
establishment of cell polarity -0.079 0.17 -10000 0 -0.46 33 33
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.12 -10000 0 -0.33 32 32
Nephrin/NEPH1/beta Arrestin2 -0.044 0.12 -10000 0 -0.32 34 34
NPHS1 -0.12 0.23 -10000 0 -0.5 64 64
Nephrin/NEPH1/podocin -0.055 0.13 -10000 0 -0.35 34 34
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.052 0.13 -10000 0 -0.36 32 32
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.052 0.13 -10000 0 -0.36 32 32
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.056 0.13 -10000 0 -0.33 37 37
cytoskeleton organization -0.037 0.13 -10000 0 -0.38 27 27
Nephrin/NEPH1 -0.054 0.12 -10000 0 -0.33 33 33
Nephrin/NEPH1/ZO-1 -0.054 0.14 -10000 0 -0.39 28 28
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.017 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.022 0.13 -10000 0 -0.4 25 25
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.046 0.16 -10000 0 -0.39 36 36
NGF (dimer)/p75(NTR)/BEX1 -0.21 0.26 -10000 0 -0.51 93 93
NT-4/5 (dimer)/p75(NTR) -0.097 0.2 -10000 0 -0.5 41 41
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 -0.048 0.15 -10000 0 -0.38 36 36
IKBKG 0.012 0 -10000 0 -10000 0 0
BDNF -0.036 0.16 -10000 0 -0.56 22 22
MGDIs/NGR/p75(NTR)/LINGO1 -0.064 0.18 -10000 0 -0.46 35 35
FURIN 0.012 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.061 0.16 -10000 0 -0.42 31 31
LINGO1 -0.031 0.16 -10000 0 -0.61 18 18
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.036 0.16 -10000 0 -0.56 22 22
NTRK1 -0.036 0.14 -10000 0 -0.47 25 25
RTN4R 0.001 0.079 -10000 0 -0.55 5 5
neuron apoptosis -0.066 0.18 -10000 0 -0.56 14 14
IRAK1 0.012 0 -10000 0 -10000 0 0
SHC1 -0.067 0.17 -10000 0 -0.45 36 36
ARHGDIA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
Gamma Secretase 0.034 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.058 0.17 -10000 0 -0.43 37 37
MAGEH1 0.004 0.071 -10000 0 -0.65 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.19 -10000 0 -0.44 46 46
Mammalian IAPs/DIABLO 0 0.1 -10000 0 -0.37 16 16
proNGF (dimer) -0.049 0.17 -10000 0 -0.5 31 31
MAGED1 0.007 0.048 -10000 0 -0.52 2 2
APP 0.006 0.058 -10000 0 -0.65 2 2
NT-4/5 (dimer) -0.057 0.2 -10000 0 -0.62 28 28
ZNF274 0.012 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.051 0.15 -10000 0 -0.38 36 36
NGF -0.049 0.17 -10000 0 -0.5 31 31
cell cycle arrest -0.025 0.17 -10000 0 -0.37 36 36
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.027 0.12 -10000 0 -0.46 5 5
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.075 0.17 -10000 0 -0.43 41 41
NCSTN 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.067 0.17 -10000 0 -0.45 36 36
PSENEN 0.012 0 -10000 0 -10000 0 0
mol:ceramide -0.054 0.16 -10000 0 -0.4 36 36
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.014 0.098 -10000 0 -0.38 5 5
p75(NTR)/beta APP -0.051 0.15 -10000 0 -0.48 19 19
BEX1 -0.23 0.29 -10000 0 -0.55 112 112
mol:GDP -0.075 0.17 -10000 0 -0.46 36 36
NGF (dimer) -0.11 0.19 -10000 0 -0.41 60 60
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.051 0.16 -10000 0 -0.42 35 35
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
RAC1/GTP -0.058 0.15 -10000 0 -0.39 36 36
MYD88 0.012 0 -10000 0 -10000 0 0
CHUK 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.067 0.17 -10000 0 -0.45 36 36
RHOB 0.012 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.01 0.061 -10000 0 -0.48 4 4
NT3 (dimer) -0.17 0.27 -10000 0 -0.53 88 88
TP53 -0.062 0.17 -10000 0 -0.59 9 9
PRDM4 -0.055 0.16 -10000 0 -0.41 36 36
BDNF (dimer) -0.13 0.19 -10000 0 -0.42 64 64
PIK3CA 0.012 0 -10000 0 -10000 0 0
SORT1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.071 0.14 -10000 0 -0.38 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.054 0.16 -10000 0 -0.41 36 36
RHOC 0.012 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
MAPK10 -0.069 0.18 -10000 0 -0.53 19 19
DIABLO 0.012 0 -10000 0 -10000 0 0
SMPD2 -0.055 0.16 -10000 0 -0.41 36 36
APH1B 0.012 0 -10000 0 -10000 0 0
APH1A 0.012 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.067 0.17 -10000 0 -0.45 36 36
PSEN1 0.012 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.017 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.18 0.24 -10000 0 -0.4 121 121
MAPK8 -0.034 0.15 -10000 0 -0.49 8 8
MAPK9 -0.035 0.15 -10000 0 -0.49 8 8
APAF1 0.012 0 -10000 0 -10000 0 0
NTF3 -0.17 0.27 -10000 0 -0.53 88 88
NTF4 -0.057 0.2 -10000 0 -0.62 28 28
NDN -0.033 0.15 -10000 0 -0.51 22 22
RAC1/GDP 0.009 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.064 0.13 -10000 0 -0.35 36 36
p75 CTF/Sortilin/TRAF6/NRIF 0.03 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.067 0.17 -10000 0 -0.45 36 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.039 0.14 -10000 0 -0.35 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.048 0.14 -10000 0 -0.38 31 31
PRKACB 0.012 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.018 0.12 -10000 0 -0.4 22 22
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.16 -10000 0 -0.57 22 22
BIRC2 0.01 0.025 -10000 0 -0.39 1 1
neuron projection morphogenesis -0.02 0.19 0.21 46 -0.46 21 67
BAD -0.043 0.16 -10000 0 -0.46 14 14
RIPK2 0.008 0.035 -10000 0 -0.39 2 2
NGFR -0.077 0.2 -10000 0 -0.49 46 46
CYCS -0.048 0.15 -10000 0 -0.38 37 37
ADAM17 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.055 0.16 -10000 0 -0.41 36 36
BCL2L11 -0.043 0.16 -10000 0 -0.46 14 14
BDNF (dimer)/p75(NTR) -0.082 0.18 -10000 0 -0.37 66 66
PI3K -0.055 0.16 -10000 0 -0.41 36 36
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.054 0.16 -10000 0 -0.41 36 36
NDNL2 0.012 0 -10000 0 -10000 0 0
YWHAE 0.009 0.041 -10000 0 -0.65 1 1
PRKCI 0.007 0.048 -10000 0 -0.52 2 2
NGF (dimer)/p75(NTR) -0.088 0.2 -10000 0 -0.53 36 36
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.056 0.16 -10000 0 -0.41 37 37
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
PLG -0.006 0.054 -10000 0 -0.39 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.07 0.17 -10000 0 -0.39 48 48
SQSTM1 0.012 0 -10000 0 -10000 0 0
NGFRAP1 0.012 0 -10000 0 -10000 0 0
CASP3 -0.038 0.15 -10000 0 -0.43 14 14
E2F1 0.001 0.081 -10000 0 -0.65 4 4
CASP9 0.012 0 -10000 0 -10000 0 0
IKK complex -0.061 0.12 -10000 0 -0.57 5 5
NGF (dimer)/TRKA -0.06 0.17 -10000 0 -0.51 23 23
MMP7 -0.16 0.27 -10000 0 -0.55 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.045 0.15 -10000 0 -0.38 36 36
MMP3 -0.035 0.12 -10000 0 -0.39 26 26
APAF-1/Caspase 9 -0.069 0.12 -10000 0 -0.48 10 10
Reelin signaling pathway

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
CDK5R1/CDK5 0.017 0 -9999 0 -10000 0 0
VLDLR -0.005 0.1 -9999 0 -0.62 7 7
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN -0.002 0.077 -9999 0 -0.43 8 8
ITGA3 0 0.076 -9999 0 -0.48 6 6
RELN/VLDLR/Fyn -0.11 0.18 -9999 0 -0.44 44 44
MAPK8IP1/MKK7/MAP3K11/JNK1 0.029 0.036 -9999 0 -0.34 1 1
AKT1 -0.075 0.14 -9999 0 -0.46 11 11
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.063 0.17 -9999 0 -0.45 41 41
RELN/LRP8/DAB1 -0.13 0.17 -9999 0 -0.4 55 55
LRPAP1/LRP8 0.014 0.035 -9999 0 -0.48 1 1
RELN/LRP8/DAB1/Fyn -0.12 0.17 -9999 0 -0.38 58 58
DAB1/alpha3/beta1 Integrin -0.12 0.15 -9999 0 -0.54 12 12
long-term memory -0.22 0.22 -9999 0 -0.46 95 95
DAB1/LIS1 -0.12 0.15 -9999 0 -0.57 9 9
DAB1/CRLK/C3G -0.12 0.14 -9999 0 -0.55 9 9
PIK3CA 0.012 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.12 0.15 -9999 0 -0.57 9 9
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.19 0.27 -9999 0 -0.52 100 100
CDK5R1 0.012 0 -9999 0 -10000 0 0
RELN -0.18 0.26 -9999 0 -0.49 100 100
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
RELN/LRP8/Fyn -0.11 0.17 -9999 0 -0.42 40 40
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.22 -9999 0 -0.44 110 110
MAPK8 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.14 0.18 -9999 0 -0.42 58 58
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.12 0.18 -9999 0 -0.39 62 62
RELN/LRP8 -0.098 0.16 -9999 0 -0.41 38 38
GRIN2B/RELN/LRP8/DAB1/Fyn -0.13 0.18 -9999 0 -0.39 63 63
PI3K 0.015 0.025 -9999 0 -0.27 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.009 0.055 -9999 0 -0.34 6 6
RAP1A -0.087 0.15 -9999 0 -0.52 9 9
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 0.001 0.069 -9999 0 -0.44 6 6
CRLK/C3G 0.017 0 -9999 0 -10000 0 0
GRIN2B -0.019 0.099 -9999 0 -0.39 17 17
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.044 0.099 -9999 0 -0.33 8 8
neuron adhesion -0.078 0.15 -9999 0 -0.47 12 12
LRP8 0.007 0.048 -9999 0 -0.52 2 2
GSK3B -0.065 0.13 -9999 0 -0.44 11 11
RELN/VLDLR/DAB1/Fyn -0.13 0.18 -9999 0 -0.4 61 61
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.085 0.14 -9999 0 -0.32 48 48
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.027 0.15 -9999 0 -0.44 27 27
neuron migration -0.073 0.16 -9999 0 -0.48 11 11
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.044 0.1 -9999 0 -0.33 8 8
RELN/VLDLR -0.091 0.16 -9999 0 -0.39 43 43
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.012 0.14 -10000 0 -1.3 3 3
VDR -0.004 0.099 -10000 0 -0.65 6 6
FAM120B 0.012 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.096 0.16 -10000 0 -0.42 20 20
RXRs/LXRs/DNA/Oxysterols -0.09 0.18 -10000 0 -0.45 34 34
MED1 0.012 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.016 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.004 0.085 -10000 0 -10000 0 0
RXRs/NUR77 -0.14 0.19 -10000 0 -0.39 77 77
RXRs/PPAR -0.096 0.15 -10000 0 -0.37 21 21
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.075 -10000 0 -0.49 6 6
RARs/VDR/DNA/Vit D3 0.009 0.079 -10000 0 -0.35 11 11
RARA 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.004 0.099 -10000 0 -0.65 6 6
RARs/RARs/DNA/9cRA 0.01 0.057 -10000 0 -0.35 5 5
RARG 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.039 0.065 -10000 0 -0.42 3 3
RARs/THRs/DNA/SMRT 0.004 0.085 -10000 0 -10000 0 0
THRA 0.01 0.025 -10000 0 -0.39 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.003 0.075 -10000 0 -0.49 6 6
RXRs/PPAR/9cRA/PGJ2/DNA -0.13 0.18 0.29 1 -0.38 82 83
NR1H4 -0.042 0.14 -10000 0 -0.45 27 27
RXRs/LXRs/DNA -0.12 0.18 -10000 0 -0.35 82 82
NR1H2 0.012 0.013 -10000 0 -10000 0 0
NR1H3 0.011 0.014 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.13 0.18 -10000 0 -0.36 86 86
NR4A1 -0.016 0.1 -10000 0 -0.41 17 17
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.094 0.12 -10000 0 -0.25 82 82
RXRG -0.25 0.29 -10000 0 -0.55 121 121
RXR alpha/CCPG 0.012 0.055 -10000 0 -0.49 3 3
RXRA 0.004 0.073 -10000 0 -0.66 3 3
RXRB 0.011 0.014 -10000 0 -10000 0 0
THRB -0.031 0.16 -10000 0 -0.64 17 17
PPARG -0.017 0.12 -10000 0 -0.52 14 14
PPARD 0.012 0 -10000 0 -10000 0 0
TNF -0.16 0.36 -10000 0 -1 34 34
mol:Oxysterols 0 0.015 -10000 0 -10000 0 0
cholesterol transport -0.089 0.18 -10000 0 -0.44 34 34
PPARA 0.009 0.041 -10000 0 -0.65 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.007 0.1 -10000 0 -0.54 9 9
RXRs/NUR77/BCL2 -0.1 0.15 -10000 0 -0.3 78 78
SREBF1 -0.075 0.16 -10000 0 -0.58 6 6
RXRs/RXRs/DNA/9cRA -0.13 0.18 0.28 1 -0.38 82 83
ABCA1 -0.075 0.16 -10000 0 -0.51 12 12
RARs/THRs 0 0.1 -10000 0 -0.34 21 21
RXRs/FXR -0.16 0.18 -10000 0 -0.38 93 93
BCL2 -0.003 0.083 -10000 0 -0.46 8 8
Endothelins

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
AKT1 -0.025 0.24 -10000 0 -0.57 29 29
PTK2B 0.007 0.058 -10000 0 -0.65 2 2
mol:Ca2+ 0.004 0.18 -10000 0 -0.71 9 9
EDN1 -0.006 0.16 0.23 22 -0.42 22 44
EDN3 -0.16 0.27 -10000 0 -0.57 75 75
EDN2 -0.08 0.21 -10000 0 -0.54 43 43
HRAS/GDP -0.031 0.18 -10000 0 -0.5 19 19
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.009 0.15 -10000 0 -0.44 16 16
ADCY4 -0.058 0.22 -10000 0 -0.54 31 31
ADCY5 -0.071 0.23 -10000 0 -0.54 32 32
ADCY6 -0.04 0.2 -10000 0 -0.54 24 24
ADCY7 -0.042 0.2 -10000 0 -0.52 26 26
ADCY1 -0.066 0.22 -10000 0 -0.52 36 36
ADCY2 -0.11 0.24 -10000 0 -0.49 53 53
ADCY3 -0.04 0.2 -10000 0 -0.59 20 20
ADCY8 -0.16 0.25 -10000 0 -0.46 77 77
ADCY9 -0.044 0.21 -10000 0 -0.58 22 22
arachidonic acid secretion -0.027 0.18 -10000 0 -0.5 19 19
ETB receptor/Endothelin-1/Gq/GTP -0.003 0.12 -10000 0 -0.38 13 13
GNAO1 -0.098 0.22 -10000 0 -0.51 55 55
HRAS 0.011 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.013 0.24 0.37 27 -0.54 27 54
ETA receptor/Endothelin-1/Gs/GTP -0.034 0.24 0.34 26 -0.53 30 56
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.052 0.3 -10000 0 -0.81 25 25
EDNRB -0.022 0.13 -10000 0 -0.46 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.05 0.29 -10000 0 -0.76 27 27
CYSLTR1 -0.046 0.28 -10000 0 -0.65 33 33
SLC9A1 -0.015 0.12 0.19 26 -0.33 16 42
mol:GDP -0.039 0.19 -10000 0 -0.52 21 21
SLC9A3 -0.037 0.21 -10000 0 -0.59 25 25
RAF1 -0.039 0.18 -10000 0 -0.51 20 20
JUN 0.011 0.16 -10000 0 -0.77 4 4
JAK2 -0.025 0.24 -10000 0 -0.57 28 28
mol:IP3 -0.013 0.15 -10000 0 -0.49 11 11
ETA receptor/Endothelin-1 -0.025 0.3 0.44 27 -0.66 28 55
PLCB1 -0.021 0.14 -10000 0 -0.63 13 13
PLCB2 -0.002 0.089 -10000 0 -0.57 6 6
ETA receptor/Endothelin-3 -0.14 0.25 -10000 0 -0.52 67 67
FOS -0.043 0.23 -10000 0 -0.87 12 12
Gai/GDP -0.057 0.21 -10000 0 -0.69 24 24
CRK 0.009 0.035 -10000 0 -0.39 2 2
mol:Ca ++ -0.038 0.24 -10000 0 -0.65 23 23
BCAR1 0.012 0 -10000 0 -10000 0 0
PRKCB1 -0.013 0.14 -10000 0 -0.46 12 12
GNAQ 0.01 0.041 -10000 0 -0.65 1 1
GNAZ 0.006 0.058 -10000 0 -0.65 2 2
GNAL -0.027 0.13 -10000 0 -0.47 21 21
Gs family/GDP -0.088 0.16 -10000 0 -0.5 22 22
ETA receptor/Endothelin-1/Gq/GTP -0.002 0.16 -10000 0 -0.47 15 15
MAPK14 -0.003 0.11 -10000 0 -0.44 7 7
TRPC6 0.002 0.19 -10000 0 -0.83 7 7
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.091 -10000 0 -0.65 5 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.009 0.12 -10000 0 -0.42 10 10
ETB receptor/Endothelin-2 -0.073 0.18 -10000 0 -0.42 48 48
ETB receptor/Endothelin-3 -0.13 0.22 -10000 0 -0.42 84 84
ETB receptor/Endothelin-1 -0.015 0.15 -10000 0 -0.41 20 20
MAPK3 -0.042 0.22 -10000 0 -0.72 16 16
MAPK1 -0.042 0.22 -10000 0 -0.73 15 15
Rac1/GDP -0.031 0.18 -10000 0 -0.5 18 18
cAMP biosynthetic process -0.12 0.22 -10000 0 -0.53 36 36
MAPK8 0.004 0.17 -10000 0 -0.61 9 9
SRC 0.012 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.025 0.12 -10000 0 -0.37 13 13
p130Cas/CRK/Src/PYK2 -0.037 0.19 -10000 0 -0.52 20 20
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.031 0.18 -10000 0 -0.5 19 19
COL1A2 -0.037 0.28 -10000 0 -0.87 18 18
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.089 0.21 -10000 0 -0.48 48 48
mol:DAG -0.013 0.15 -10000 0 -0.49 11 11
MAP2K2 -0.037 0.19 -10000 0 -0.59 17 17
MAP2K1 -0.037 0.19 -10000 0 -0.59 17 17
EDNRA -0.025 0.21 -10000 0 -0.62 22 22
positive regulation of muscle contraction -0.015 0.21 -10000 0 -0.59 19 19
Gq family/GDP -0.078 0.16 -10000 0 -0.55 21 21
HRAS/GTP -0.041 0.17 -10000 0 -0.48 21 21
PRKCH -0.007 0.14 -10000 0 -0.48 10 10
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.015 0.16 -10000 0 -0.51 13 13
PRKCB -0.034 0.18 -10000 0 -0.55 19 19
PRKCE -0.007 0.14 -10000 0 -0.48 10 10
PRKCD -0.009 0.14 -10000 0 -0.49 11 11
PRKCG -0.096 0.2 -10000 0 -0.5 32 32
regulation of vascular smooth muscle contraction -0.051 0.26 -10000 0 -1.1 10 10
PRKCQ -0.019 0.16 -10000 0 -0.49 15 15
PLA2G4A -0.032 0.2 -10000 0 -0.55 19 19
GNA14 -0.009 0.11 -10000 0 -0.51 11 11
GNA15 -0.01 0.12 -10000 0 -0.62 9 9
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.012 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.24 0.37 27 -0.55 26 53
MMP1 -0.16 0.36 0.31 3 -0.69 69 72
Visual signal transduction: Rods

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
mol:K + 0.009 0.041 -9999 0 -0.65 1 1
GNAT1/GTP -0.003 0.055 -9999 0 -0.3 8 8
Metarhodopsin II/Arrestin -0.001 0.049 -9999 0 -0.25 9 9
PDE6G/GNAT1/GTP -0.058 0.14 -9999 0 -0.28 63 63
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.005 0.077 -9999 0 -0.43 8 8
GRK1 -0.013 0.09 -9999 0 -0.42 12 12
CNG Channel -0.16 0.2 -9999 0 -0.41 82 82
mol:Na + -0.13 0.17 -9999 0 -0.46 30 30
mol:ADP -0.013 0.09 -9999 0 -0.42 12 12
RGS9-1/Gbeta5/R9AP -0.057 0.16 -9999 0 -0.42 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.17 -9999 0 -0.5 25 25
CNGB1 -0.074 0.21 -9999 0 -0.55 40 40
RDH5 -0.043 0.17 -9999 0 -0.52 27 27
SAG 0.001 0.025 -9999 0 -0.39 1 1
mol:Ca2+ -0.11 0.18 -9999 0 -0.55 18 18
Na + (4 Units) -0.12 0.16 -9999 0 -0.53 18 18
RGS9 -0.073 0.21 -9999 0 -0.54 40 40
GNB1/GNGT1 -0.038 0.16 -9999 0 -0.47 29 29
GNAT1/GDP -0.05 0.14 -9999 0 -0.36 36 36
GUCY2D -0.033 0.15 -9999 0 -0.5 22 22
GNGT1 -0.062 0.21 -9999 0 -0.64 29 29
GUCY2F 0.002 0.004 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.074 0.17 -9999 0 -0.42 35 35
mol:11-cis-retinal -0.043 0.17 -9999 0 -0.52 27 27
mol:cGMP -0.044 0.13 -9999 0 -0.36 28 28
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.034 0.13 -9999 0 -0.36 34 34
SLC24A1 0.009 0.041 -9999 0 -0.65 1 1
CNGA1 -0.082 0.2 -9999 0 -0.49 49 49
Metarhodopsin II -0.007 0.068 -9999 0 -0.36 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.048 0.14 -9999 0 -0.38 28 28
RGS9BP -0.033 0.15 -9999 0 -0.51 22 22
Metarhodopsin II/Transducin -0.025 0.1 -9999 0 -0.3 29 29
GCAP Family/Ca ++ -0.031 0.11 -9999 0 -0.38 18 18
PDE6A/B -0.036 0.15 -9999 0 -0.41 32 32
mol:Pi -0.057 0.16 -9999 0 -0.42 34 34
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.031 0.13 -9999 0 -0.38 29 29
PDE6B -0.004 0.099 -9999 0 -0.65 6 6
PDE6A -0.045 0.17 -9999 0 -0.54 27 27
PDE6G -0.093 0.2 -9999 0 -0.47 57 57
RHO -0.005 0.074 -9999 0 -0.39 9 9
PDE6 -0.14 0.2 -9999 0 -0.59 25 25
GUCA1A -0.025 0.12 -9999 0 -0.42 21 21
GC2/GCAP Family -0.029 0.11 -9999 0 -0.38 18 18
GUCA1C -0.005 0.049 -9999 0 -0.39 4 4
GUCA1B -0.029 0.15 -9999 0 -0.61 17 17
Caspase cascade in apoptosis

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
TOP1 -0.054 0.18 0.2 1 -0.45 39 40
ACTA1 -0.085 0.23 0.24 2 -0.58 39 41
NUMA1 -0.054 0.18 0.2 2 -0.45 39 41
SPTAN1 -0.073 0.23 0.24 2 -0.57 38 40
LIMK1 -0.073 0.23 0.24 2 -0.57 38 40
BIRC3 -0.037 0.16 -10000 0 -0.57 22 22
BIRC2 0.01 0.025 -10000 0 -0.39 1 1
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.094 0.25 -10000 0 -0.6 43 43
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
PTK2 -0.054 0.18 -10000 0 -0.47 35 35
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.071 0.22 0.24 2 -0.56 38 40
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.078 0.23 0.24 2 -0.57 40 42
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.17 0.33 -10000 0 -0.7 63 63
BID -0.035 0.11 -10000 0 -0.28 42 42
MAP3K1 -0.019 0.08 -10000 0 -0.24 18 18
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.018 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.08 0.25 0.25 1 -0.61 38 39
CASP9 0.012 0 -10000 0 -10000 0 0
DNA repair 0.003 0.054 0.18 1 -0.21 3 4
neuron apoptosis 0.004 0.064 -10000 0 -0.65 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.066 0.22 0.23 2 -0.54 39 41
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 -0.026 0.12 -10000 0 -0.45 12 12
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD -0.068 0.22 0.24 1 -0.56 37 38
CASP7 0.022 0.086 0.34 15 -10000 0 15
KRT18 -0.003 0.064 -10000 0 -0.63 2 2
apoptosis -0.052 0.2 0.26 2 -0.52 31 33
DFFA -0.075 0.23 0.24 2 -0.56 39 41
DFFB -0.075 0.23 0.24 2 -0.56 39 41
PARP1 -0.004 0.054 0.21 3 -0.18 1 4
actin filament polymerization 0.061 0.21 0.52 38 -0.24 1 39
TNF -0.077 0.21 -10000 0 -0.57 40 40
CYCS -0.024 0.086 -10000 0 -0.26 20 20
SATB1 -0.031 0.14 -10000 0 -0.46 14 14
SLK -0.074 0.23 0.24 2 -0.58 38 40
p15 BID/BAX -0.025 0.1 -10000 0 -0.32 17 17
CASP2 -0.002 0.11 -10000 0 -0.4 10 10
JNK cascade 0.019 0.08 0.24 18 -10000 0 18
CASP3 -0.084 0.24 0.24 3 -0.6 39 42
LMNB2 -0.005 0.098 -10000 0 -0.37 10 10
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.009 0.041 -10000 0 -0.65 1 1
Mammalian IAPs/DIABLO 0 0.1 -10000 0 -0.37 16 16
negative regulation of DNA binding -0.16 0.33 -10000 0 -0.69 63 63
stress fiber formation -0.073 0.23 0.24 2 -0.56 38 40
GZMB -0.1 0.25 -10000 0 -0.53 57 57
CASP1 -0.012 0.11 -10000 0 -0.42 16 16
LMNB1 -0.006 0.1 -10000 0 -0.37 11 11
APP 0.004 0.065 -10000 0 -0.66 2 2
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0 -10000 0 -10000 0 0
VIM -0.053 0.18 0.26 2 -0.47 35 37
LMNA -0.004 0.097 -10000 0 -0.37 10 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.008 0.11 -10000 0 -0.43 10 10
LRDD 0.012 0 -10000 0 -10000 0 0
SREBF1 -0.073 0.23 0.24 2 -0.57 38 40
APAF-1/Caspase 9 -0.002 0.041 0.29 1 -10000 0 1
nuclear fragmentation during apoptosis -0.053 0.18 0.19 2 -0.44 39 41
CFL2 -0.063 0.22 0.24 1 -0.54 38 39
GAS2 -0.11 0.25 0.24 1 -0.56 50 51
positive regulation of apoptosis -0.002 0.098 -10000 0 -0.35 11 11
PRF1 -0.049 0.18 -10000 0 -0.57 27 27
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.012 0.11 -10000 0 -0.44 12 12
fibroblast growth factor receptor signaling pathway -0.013 0.11 -10000 0 -0.44 12 12
LAMA1 -0.085 0.21 -10000 0 -0.49 50 50
PRNP 0.012 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.011 0.12 -10000 0 -0.44 16 16
SMAD2 0.022 0.048 -10000 0 -0.37 4 4
GPC1/PrPc/Cu2+ 0.011 0.046 -10000 0 -0.42 3 3
GPC1/Laminin alpha1 -0.058 0.16 -10000 0 -0.36 52 52
TDGF1 -0.08 0.2 -10000 0 -0.51 45 45
CRIPTO/GPC1 -0.055 0.16 -10000 0 -0.48 24 24
APP/GPC1 0.008 0.068 -10000 0 -0.48 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.04 0.14 -10000 0 -0.41 24 24
FLT1 0.009 0.041 -10000 0 -0.65 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.019 0.046 -10000 0 -0.41 3 3
SERPINC1 0 0.055 -10000 0 -0.39 5 5
FYN -0.046 0.14 -10000 0 -0.42 27 27
FGR -0.05 0.15 -10000 0 -0.42 29 29
positive regulation of MAPKKK cascade -0.071 0.18 -10000 0 -0.47 31 31
SLIT2 -0.019 0.13 -10000 0 -0.56 14 14
GPC1/NRG -0.11 0.19 -10000 0 -0.48 43 43
NRG1 -0.16 0.26 -10000 0 -0.52 84 84
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.014 0.061 -10000 0 -0.41 5 5
LYN -0.043 0.14 -10000 0 -0.42 27 27
mol:Spermine 0.004 0.053 -10000 0 -0.49 3 3
cell growth -0.013 0.11 -10000 0 -0.44 12 12
BMP signaling pathway -0.004 0.071 0.65 3 -10000 0 3
SRC -0.039 0.14 -10000 0 -0.41 24 24
TGFBR1 0.012 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.19 0.26 -10000 0 -0.5 104 104
GPC1 0.004 0.071 -10000 0 -0.65 3 3
TGFBR1 (dimer) 0.012 0 -10000 0 -10000 0 0
VEGFA 0.007 0.048 -10000 0 -0.52 2 2
BLK -0.092 0.17 -10000 0 -0.44 36 36
HCK -0.055 0.16 -10000 0 -0.42 34 34
FGF2 -0.019 0.12 -10000 0 -0.46 17 17
FGFR1 -0.009 0.11 -10000 0 -0.52 10 10
VEGFR1 homodimer 0.009 0.041 -10000 0 -0.65 1 1
TGFBR2 0.012 0 -10000 0 -10000 0 0
cell death 0.008 0.068 -10000 0 -0.48 5 5
ATIII/GPC1 0.003 0.066 -10000 0 -0.35 8 8
PLA2G2A/GPC1 -0.14 0.2 -10000 0 -0.36 106 106
LCK -0.065 0.16 -10000 0 -0.42 38 38
neuron differentiation -0.11 0.19 -10000 0 -0.48 43 43
PrPc/Cu2+ 0.009 0 -10000 0 -10000 0 0
APP 0.006 0.058 -10000 0 -0.65 2 2
TGFBR2 (dimer) 0.012 0 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.14 0.22 -9999 0 -0.4 88 88
SMAD6-7/SMURF1 0.02 0.038 -9999 0 -0.41 2 2
NOG -0.085 0.22 -9999 0 -0.56 44 44
SMAD9 -0.02 0.11 -9999 0 -0.48 12 12
SMAD4 0.012 0 -9999 0 -10000 0 0
SMAD5 -0.008 0.11 -9999 0 -0.44 8 8
BMP7/USAG1 -0.22 0.28 -9999 0 -0.47 129 129
SMAD5/SKI -0.001 0.11 -9999 0 -0.43 7 7
SMAD1 0.031 0.035 -9999 0 -0.39 1 1
BMP2 -0.033 0.15 -9999 0 -0.5 23 23
SMAD1/SMAD1/SMAD4 -0.004 0.028 -9999 0 -10000 0 0
BMPR1A 0.004 0.071 -9999 0 -0.65 3 3
BMPR1B -0.034 0.17 -9999 0 -0.65 18 18
BMPR1A-1B/BAMBI -0.054 0.16 -9999 0 -0.44 33 33
AHSG -0.016 0.097 -9999 0 -0.39 16 16
CER1 -0.005 0.06 -9999 0 -0.39 6 6
BMP2-4/CER1 -0.037 0.13 -9999 0 -0.42 17 17
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.01 0.1 -9999 0 -0.37 9 9
BMP2-4 (homodimer) -0.042 0.14 -9999 0 -0.36 41 41
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.005 0.12 -9999 0 -0.4 20 20
RGMA -0.004 0.097 -9999 0 -0.58 7 7
SMURF1 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.11 -9999 0 -0.43 9 9
BMP2-4/USAG1 -0.15 0.21 -9999 0 -0.45 70 70
SMAD6/SMURF1/SMAD5 -0.001 0.11 -9999 0 -0.43 7 7
SOSTDC1 -0.18 0.27 -9999 0 -0.53 92 92
BMP7/BMPR2/BMPR1A-1B -0.085 0.2 -9999 0 -0.42 61 61
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.005 0.05 -9999 0 -0.39 4 4
HFE2 -0.011 0.084 -9999 0 -0.39 12 12
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.056 0.17 -9999 0 -0.47 31 31
SMAD5/SMAD5/SMAD4 -0.001 0.11 -9999 0 -0.43 7 7
MAPK1 0.007 0.048 -9999 0 -0.52 2 2
TAK1/TAB family -0.036 0.083 -9999 0 -0.42 6 6
BMP7 (homodimer) -0.13 0.26 -9999 0 -0.6 61 61
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.007 0.075 -9999 0 -0.27 20 20
SMAD1/SKI 0.036 0.033 -9999 0 -0.36 1 1
SMAD6 0.009 0.041 -9999 0 -0.65 1 1
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.043 0.14 -9999 0 -0.44 18 18
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.21 0.28 -9999 0 -0.53 109 109
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.022 0.021 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.023 0.14 -9999 0 -0.5 20 20
CHRDL1 -0.09 0.22 -9999 0 -0.56 46 46
ENDOFIN/SMAD1 0.036 0.033 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.005 0.032 -9999 0 -10000 0 0
SMAD6/SMURF1 0.012 0 -9999 0 -10000 0 0
BAMBI -0.058 0.18 -9999 0 -0.49 36 36
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.089 0.19 -9999 0 -0.46 47 47
BMP2-4/GREM1 -0.17 0.22 -9999 0 -0.47 69 69
SMAD7 0.009 0.041 -9999 0 -0.65 1 1
SMAD8A/SMAD8A/SMAD4 -0.013 0.11 -9999 0 -0.45 12 12
SMAD1/SMAD6 0.036 0.033 -9999 0 -0.36 1 1
TAK1/SMAD6 0.017 0 -9999 0 -10000 0 0
BMP7 -0.13 0.26 -9999 0 -0.6 61 61
BMP6 0.005 0.05 -9999 0 -0.39 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.012 0.1 -9999 0 -0.4 9 9
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.036 0.033 -9999 0 -0.36 1 1
SMAD7/SMURF1 0.015 0.031 -9999 0 -0.48 1 1
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.008 0.035 -9999 0 -0.39 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.06 0.14 -9999 0 -0.4 18 18
CHRD -0.036 0.16 -9999 0 -0.58 21 21
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.024 0.12 -9999 0 -0.45 9 9
BMP4 -0.026 0.13 -9999 0 -0.46 21 21
FST -0.11 0.23 -9999 0 -0.52 59 59
BMP2-4/NOG -0.087 0.18 -9999 0 -0.44 46 46
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.074 0.19 -9999 0 -0.39 61 61
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.054 0.25 -9999 0 -1.1 12 12
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.017 0.099 -9999 0 -0.29 24 24
ATF2/c-Jun -0.003 0.11 -9999 0 -0.6 3 3
MAPK11 -0.023 0.12 -9999 0 -0.6 3 3
MITF -0.018 0.13 -9999 0 -0.35 28 28
MAPKAPK5 -0.014 0.12 -9999 0 -0.35 26 26
KRT8 -0.017 0.13 -9999 0 -0.36 28 28
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.029 0.15 -9999 0 -0.44 26 26
CEBPB -0.016 0.12 -9999 0 -0.35 27 27
SLC9A1 -0.014 0.12 -9999 0 -0.35 26 26
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.01 0.12 -9999 0 -0.34 26 26
p38alpha-beta/MNK1 -0.012 0.12 -9999 0 -0.35 26 26
JUN -0.003 0.1 -9999 0 -0.6 3 3
PPARGC1A -0.11 0.21 -9999 0 -0.42 66 66
USF1 -0.014 0.12 -9999 0 -0.35 26 26
RAB5/GDP/GDI1 -0.032 0.076 -9999 0 -0.32 3 3
NOS2 -0.067 0.28 -9999 0 -1.1 15 15
DDIT3 -0.015 0.12 -9999 0 -0.35 26 26
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.006 0.1 -9999 0 -0.39 3 3
p38alpha-beta/HBP1 -0.012 0.12 -9999 0 -0.35 26 26
CREB1 -0.012 0.13 -9999 0 -0.37 26 26
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.006 0.11 -9999 0 -0.44 2 2
RPS6KA4 -0.014 0.12 -9999 0 -0.35 26 26
PLA2G4A -0.029 0.14 -9999 0 -0.41 15 15
GDI1 -0.014 0.12 -9999 0 -0.35 26 26
TP53 -0.046 0.17 -9999 0 -0.46 30 30
RPS6KA5 -0.014 0.12 -9999 0 -0.35 26 26
ESR1 -0.036 0.16 -9999 0 -0.38 39 39
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.015 0.12 -9999 0 -0.35 26 26
MEF2A -0.014 0.12 -9999 0 -0.35 26 26
EIF4EBP1 -0.012 0.13 -9999 0 -0.37 26 26
KRT19 -0.021 0.14 -9999 0 -0.38 29 29
ELK4 -0.014 0.12 -9999 0 -0.35 26 26
ATF6 -0.014 0.12 -9999 0 -0.35 26 26
ATF1 -0.012 0.13 -9999 0 -0.37 26 26
p38alpha-beta/MAPKAPK2 -0.012 0.12 -9999 0 -0.35 26 26
p38alpha-beta/MAPKAPK3 -0.012 0.12 -9999 0 -0.35 26 26
Syndecan-4-mediated 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
PTK2 -0.029 0.14 -9999 0 -0.6 13 13
Syndecan-4/Syndesmos -0.068 0.2 -9999 0 -0.58 29 29
positive regulation of JNK cascade -0.084 0.22 -9999 0 -0.57 35 35
Syndecan-4/ADAM12 -0.1 0.23 -9999 0 -0.61 36 36
CCL5 -0.071 0.21 -9999 0 -0.59 36 36
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.01 0.025 -9999 0 -0.39 1 1
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.005 0.054 -9999 0 -0.39 5 5
ADAM12 -0.065 0.19 -9999 0 -0.52 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.02 0.032 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.11 0.22 -9999 0 -0.59 35 35
Syndecan-4/CXCL12/CXCR4 -0.09 0.23 -9999 0 -0.61 35 35
Syndecan-4/Laminin alpha3 -0.12 0.23 -9999 0 -0.62 33 33
MDK -0.013 0.12 -9999 0 -0.63 10 10
Syndecan-4/FZD7 -0.078 0.21 -9999 0 -0.58 33 33
Syndecan-4/Midkine -0.081 0.21 -9999 0 -0.57 31 31
FZD7 -0.01 0.11 -9999 0 -0.55 10 10
Syndecan-4/FGFR1/FGF -0.11 0.19 -9999 0 -0.54 34 34
THBS1 -0.001 0.082 -9999 0 -0.52 6 6
integrin-mediated signaling pathway -0.1 0.22 -9999 0 -0.58 38 38
positive regulation of MAPKKK cascade -0.084 0.22 -9999 0 -0.57 35 35
Syndecan-4/TACI -0.083 0.2 -9999 0 -0.58 30 30
CXCR4 0.006 0.058 -9999 0 -0.65 2 2
cell adhesion -0.01 0.094 -9999 0 -0.33 17 17
Syndecan-4/Dynamin -0.068 0.2 -9999 0 -0.58 29 29
Syndecan-4/TSP1 -0.074 0.21 -9999 0 -0.59 31 31
Syndecan-4/GIPC -0.069 0.2 -9999 0 -0.57 30 30
Syndecan-4/RANTES -0.11 0.25 -9999 0 -0.67 34 34
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.085 0.21 -9999 0 -0.49 50 50
LAMA3 -0.087 0.21 -9999 0 -0.52 48 48
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.009 0.094 -9999 0 -0.49 7 7
Syndecan-4/alpha-Actinin -0.068 0.2 -9999 0 -0.58 29 29
TFPI 0 0.073 -9999 0 -0.43 7 7
F2 -0.003 0.05 -9999 0 -0.4 4 4
alpha5/beta1 Integrin 0.016 0.018 -9999 0 -0.27 1 1
positive regulation of cell adhesion -0.15 0.24 -9999 0 -0.6 45 45
ACTN1 0.012 0 -9999 0 -10000 0 0
TNC -0.063 0.2 -9999 0 -0.58 33 33
Syndecan-4/CXCL12 -0.096 0.24 -9999 0 -0.62 37 37
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.047 0.18 -9999 0 -0.56 27 27
TNFRSF13B -0.021 0.1 -9999 0 -0.39 19 19
FGF2 -0.019 0.12 -9999 0 -0.46 17 17
FGFR1 -0.009 0.11 -9999 0 -0.52 10 10
Syndecan-4/PI-4-5-P2 -0.075 0.2 -9999 0 -0.58 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.049 0.17 -9999 0 -0.49 32 32
cell migration -0.004 0.013 -9999 0 -10000 0 0
PRKCD 0.011 0.041 -9999 0 -0.64 1 1
vasculogenesis -0.071 0.2 -9999 0 -0.56 31 31
SDC4 -0.079 0.21 -9999 0 -0.62 29 29
Syndecan-4/Tenascin C -0.1 0.24 -9999 0 -0.61 38 38
Syndecan-4/PI-4-5-P2/PKC alpha -0.016 0.026 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.068 0.2 -9999 0 -0.58 29 29
MMP9 -0.098 0.23 -9999 0 -0.53 53 53
Rac1/GTP -0.011 0.096 -9999 0 -0.33 17 17
cytoskeleton organization -0.065 0.19 -9999 0 -0.56 29 29
GIPC1 0.008 0.035 -9999 0 -0.39 2 2
Syndecan-4/TFPI -0.074 0.2 -9999 0 -0.57 30 30
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.006 0.084 -9999 0 -0.42 7 7
ADCY5 -0.022 0.11 -9999 0 -0.42 13 13
ADCY6 0.016 0 -9999 0 -10000 0 0
ADCY7 0.015 0.027 -9999 0 -0.42 1 1
ADCY1 -0.016 0.095 -9999 0 -0.27 30 30
ADCY2 -0.075 0.15 -9999 0 -0.28 78 78
ADCY3 0.016 0 -9999 0 -10000 0 0
ADCY8 -0.13 0.17 -9999 0 -0.42 51 51
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.011 0.046 -9999 0 -0.42 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.093 0.11 -9999 0 -0.3 33 33
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.029 0.12 -9999 0 -0.37 20 20
RGS9BP -0.033 0.15 -9999 0 -0.51 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.013 0.09 -9999 0 -0.42 12 12
mol:Na + -0.07 0.15 -9999 0 -0.34 60 60
mol:ADP -0.004 0.07 -9999 0 -0.28 15 15
GNAT2 -0.007 0.098 -9999 0 -0.51 9 9
RGS9-1/Gbeta5/R9AP -0.057 0.16 -9999 0 -0.42 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.002 0.063 -9999 0 -0.3 10 10
GRK7 0.004 0.043 -9999 0 -0.39 3 3
CNGB3 -0.11 0.24 -9999 0 -0.56 53 53
Cone Metarhodopsin II/X-Arrestin 0.003 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.071 0.15 -9999 0 -0.39 40 40
Cone PDE6 -0.045 0.14 -9999 0 -0.36 34 34
Cone Metarhodopsin II -0.003 0.053 -9999 0 -0.21 15 15
Na + (4 Units) -0.071 0.15 -9999 0 -0.39 40 40
GNAT2/GDP -0.052 0.14 -9999 0 -0.36 38 38
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0 0.059 -9999 0 -0.38 4 4
Cone Transducin -0.031 0.12 -9999 0 -0.39 20 20
SLC24A2 -0.015 0.1 -9999 0 -0.48 12 12
GNB3/GNGT2 -0.037 0.14 -9999 0 -0.37 36 36
GNB3 -0.047 0.16 -9999 0 -0.48 31 31
GNAT2/GTP -0.005 0.072 -9999 0 -0.37 9 9
CNGA3 -0.006 0.069 -9999 0 -0.39 8 8
ARR3 0.005 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.07 0.15 -9999 0 -0.34 60 60
mol:Pi -0.057 0.16 -9999 0 -0.42 34 34
Cone CNG Channel -0.072 0.14 -9999 0 -0.37 37 37
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.015 0.1 -9999 0 -0.48 12 12
RGS9 -0.073 0.21 -9999 0 -0.54 40 40
PDE6C 0.004 0.025 -9999 0 -0.39 1 1
GNGT2 -0.005 0.1 -9999 0 -0.62 7 7
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.025 -9999 0 -0.39 1 1
Effects of Botulinum toxin

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
STX1A 0.007 0.025 -9999 0 -0.28 2 2
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.027 0.12 -9999 0 -0.35 30 30
STXBP1 0.012 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.12 0.19 -9999 0 -0.37 87 87
RAB3GAP2/RIMS1/UNC13B -0.014 0.1 -9999 0 -0.41 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.047 0.16 -9999 0 -0.49 29 29
mol:ACh -0.01 0.043 -9999 0 -0.13 24 24
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.042 0.081 -9999 0 -0.36 2 2
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.12 0.19 -9999 0 -0.37 87 87
UNC13B 0.009 0.041 -9999 0 -0.65 1 1
CHRNA1 -0.17 0.27 -9999 0 -0.55 87 87
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.047 0.12 -9999 0 -0.32 39 39
SNAP25 -0.033 0.099 -9999 0 -0.25 41 41
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.062 0.18 -9999 0 -0.48 39 39
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.014 0.021 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.042 0.081 -9999 0 -0.36 2 2
BCR signaling 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
JUN -0.077 0.15 -10000 0 -0.45 22 22
IKBKB -0.033 0.074 -10000 0 -0.24 3 3
AKT1 -0.077 0.1 0.22 1 -0.26 30 31
IKBKG -0.033 0.077 -10000 0 -0.26 3 3
CALM1 -0.064 0.14 -10000 0 -0.49 17 17
PIK3CA 0.012 0 -10000 0 -10000 0 0
MAP3K1 -0.13 0.22 -10000 0 -0.59 34 34
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.074 0.15 -10000 0 -0.47 22 22
DOK1 0.012 0 -10000 0 -10000 0 0
AP-1 -0.04 0.091 -10000 0 -0.26 19 19
LYN 0.004 0.071 -10000 0 -0.65 3 3
BLNK 0 0.085 -10000 0 -0.6 5 5
SHC1 0.012 0 -10000 0 -10000 0 0
BCR complex -0.15 0.23 -10000 0 -0.54 53 53
CD22 -0.2 0.26 -10000 0 -0.67 45 45
CAMK2G -0.054 0.13 -10000 0 -0.48 14 14
CSNK2A1 0.012 0 -10000 0 -10000 0 0
INPP5D -0.015 0.13 -10000 0 -0.63 11 11
SHC/GRB2/SOS1 -0.1 0.15 -10000 0 -0.59 10 10
GO:0007205 -0.075 0.15 -10000 0 -0.48 22 22
SYK 0.012 0 -10000 0 -10000 0 0
ELK1 -0.066 0.14 -10000 0 -0.46 20 20
NFATC1 -0.13 0.22 -10000 0 -0.53 45 45
B-cell antigen/BCR complex -0.15 0.23 -10000 0 -0.54 53 53
PAG1/CSK 0.017 0 -10000 0 -10000 0 0
NFKBIB -0.005 0.027 -10000 0 -0.13 1 1
HRAS -0.064 0.14 -10000 0 -0.46 17 17
NFKBIA -0.004 0.027 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.002 0.024 -10000 0 -0.18 1 1
RasGAP/Csk -0.13 0.22 -10000 0 -0.44 69 69
mol:GDP -0.069 0.14 -10000 0 -0.45 22 22
PTEN 0.001 0.081 -10000 0 -0.65 4 4
CD79B -0.04 0.16 -10000 0 -0.53 25 25
NF-kappa-B/RelA/I kappa B alpha 0.002 0.023 -10000 0 -0.18 1 1
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.14 0.21 -10000 0 -0.57 36 36
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
mol:IP3 -0.076 0.15 -10000 0 -0.49 22 22
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.078 0.16 -10000 0 -0.48 25 25
CHUK -0.033 0.077 -10000 0 -0.29 1 1
IBTK 0.012 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.079 0.13 -10000 0 -0.44 22 22
PTPN6 -0.18 0.25 -10000 0 -0.66 40 40
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 -0.002 0.032 -10000 0 -0.11 12 12
VAV2 -0.18 0.27 -10000 0 -0.68 44 44
ubiquitin-dependent protein catabolic process -0.001 0.026 -10000 0 -0.13 1 1
BTK -0.077 0.28 0.38 3 -1 20 23
CD19 -0.2 0.27 -10000 0 -0.68 46 46
MAP4K1 -0.002 0.086 -10000 0 -0.5 7 7
CD72 0.009 0.041 -10000 0 -0.65 1 1
PAG1 0.012 0 -10000 0 -10000 0 0
MAPK14 -0.1 0.18 -10000 0 -0.49 33 33
SH3BP5 0.012 0 -10000 0 -10000 0 0
PIK3AP1 -0.076 0.17 -10000 0 -0.55 20 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.092 0.2 -10000 0 -0.47 44 44
RAF1 -0.054 0.13 -10000 0 -0.46 14 14
RasGAP/p62DOK/SHIP -0.15 0.22 -10000 0 -0.61 34 34
CD79A -0.18 0.26 -10000 0 -0.5 96 96
re-entry into mitotic cell cycle -0.04 0.091 -10000 0 -0.26 19 19
RASA1 0.012 0 -10000 0 -10000 0 0
MAPK3 -0.035 0.11 -10000 0 -0.38 12 12
MAPK1 -0.037 0.11 -10000 0 -0.38 12 12
CD72/SHP1 -0.16 0.24 -10000 0 -0.63 38 38
NFKB1 0.009 0.041 -10000 0 -0.65 1 1
MAPK8 -0.1 0.18 -10000 0 -0.5 31 31
actin cytoskeleton organization -0.14 0.23 -10000 0 -0.6 37 37
NF-kappa-B/RelA 0.005 0.044 -10000 0 -0.2 1 1
Calcineurin -0.061 0.11 -10000 0 -0.44 15 15
PI3K -0.18 0.19 -10000 0 -0.52 42 42
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.08 0.16 -10000 0 -0.51 24 24
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.15 0.29 -10000 0 -0.84 33 33
DAPP1 -0.18 0.33 -10000 0 -1 32 32
cytokine secretion -0.12 0.2 -10000 0 -0.49 45 45
mol:DAG -0.076 0.15 -10000 0 -0.49 22 22
PLCG2 0.009 0.041 -10000 0 -0.65 1 1
MAP2K1 -0.045 0.12 -10000 0 -0.42 14 14
B-cell antigen/BCR complex/FcgammaRIIB -0.16 0.25 -10000 0 -0.52 69 69
mol:PI-3-4-5-P3 -0.13 0.13 0.3 1 -0.37 36 37
ETS1 -0.044 0.12 -10000 0 -0.43 14 14
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.1 0.19 -10000 0 -0.4 58 58
B-cell antigen/BCR complex/LYN -0.15 0.25 -10000 0 -0.76 29 29
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.15 0.24 -10000 0 -0.65 37 37
B-cell antigen/BCR complex/LYN/SYK -0.19 0.24 -10000 0 -0.64 41 41
CARD11 -0.09 0.16 -10000 0 -0.45 35 35
FCGR2B -0.058 0.2 -10000 0 -0.62 29 29
PPP3CA 0.006 0.058 -10000 0 -0.65 2 2
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex -0.01 0.034 -10000 0 -10000 0 0
PTPRC -0.03 0.16 -10000 0 -0.62 17 17
PDPK1 -0.077 0.099 0.2 1 -0.26 24 25
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0.012 0 -10000 0 -10000 0 0
POU2F2 0.005 0.02 -10000 0 -0.12 2 2
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.021 0.12 0.46 18 -10000 0 18
PI3K Class IB/PDE3B -0.021 0.12 -10000 0 -0.46 18 18
PDE3B -0.021 0.12 -10000 0 -0.47 18 18
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.019 0.12 -10000 0 -0.46 17 17
GNB1/GNG2 -0.053 0.075 -10000 0 -0.2 45 45
AKT1 -0.024 0.1 -10000 0 -0.21 35 35
EGF -0.07 0.2 -10000 0 -0.51 41 41
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.006 0.095 -10000 0 -0.4 8 8
mol:Ca2+ -0.051 0.14 -10000 0 -0.31 47 47
LYN 0.011 0.087 -10000 0 -0.44 4 4
RhoA/GTP -0.033 0.049 -10000 0 -0.14 12 12
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.057 0.16 -10000 0 -0.36 46 46
GNG2 0.007 0.043 -10000 0 -0.39 3 3
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.008 0.089 -10000 0 -0.44 8 8
G beta5/gamma2 -0.067 0.099 -10000 0 -0.26 46 46
PRKCH -0.058 0.16 -10000 0 -0.36 46 46
DNM1 0.007 0.048 -10000 0 -0.52 2 2
TXA2/TP beta/beta Arrestin3 -0.005 0.024 -10000 0 -0.3 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.034 0.16 -10000 0 -0.64 18 18
G12 family/GTP -0.081 0.12 -10000 0 -0.31 47 47
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.025 -10000 0 -0.39 1 1
RhoA/GTP/ROCK1 0.012 0.007 -10000 0 -10000 0 0
mol:GDP 0.029 0.1 0.33 12 -10000 0 12
mol:NADP 0.006 0.058 -10000 0 -0.65 2 2
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.018 0.13 -10000 0 -0.54 14 14
mol:IP3 -0.068 0.18 -10000 0 -0.4 47 47
cell morphogenesis 0.012 0.007 -10000 0 -10000 0 0
PLCB2 -0.098 0.23 -10000 0 -0.54 47 47
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.027 0.11 -10000 0 -0.36 10 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.003 0.1 -10000 0 -0.39 10 10
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR -0.004 0.099 -10000 0 -0.65 6 6
PRKCB1 -0.066 0.17 -10000 0 -0.38 48 48
GNAQ 0.009 0.041 -10000 0 -0.65 1 1
mol:L-citrulline 0.006 0.058 -10000 0 -0.65 2 2
TXA2/TXA2-R family -0.1 0.24 -10000 0 -0.56 46 46
LCK -0.005 0.11 -10000 0 -0.36 11 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.024 0.085 -10000 0 -0.65 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.031 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.023 0.084 -10000 0 -0.65 2 2
MAPK14 -0.03 0.11 -10000 0 -0.23 46 46
TGM2/GTP -0.083 0.2 -10000 0 -0.46 47 47
MAPK11 -0.032 0.11 -10000 0 -0.23 46 46
ARHGEF1 -0.024 0.087 -10000 0 -0.19 30 30
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.07 0.18 -10000 0 -0.4 46 46
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.053 0.15 -10000 0 -0.32 47 47
cAMP biosynthetic process -0.069 0.17 -10000 0 -0.38 47 47
Gq family/GTP/EBP50 0.008 0.061 -10000 0 -0.24 12 12
actin cytoskeleton reorganization 0.012 0.007 -10000 0 -10000 0 0
SRC 0.014 0.077 -10000 0 -0.48 2 2
GNB5 0.011 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.1 -10000 0 -0.35 12 12
VCAM1 -0.059 0.16 -10000 0 -0.35 48 48
TP beta/Gq family/GDP/G beta5/gamma2 0.008 0.089 -10000 0 -0.44 8 8
platelet activation -0.042 0.15 -10000 0 -0.31 46 46
PGI2/IP -0.003 0.075 -10000 0 -0.49 6 6
PRKACA -0.013 0.11 -10000 0 -0.36 21 21
Gq family/GDP/G beta5/gamma2 0.006 0.089 -10000 0 -0.42 8 8
TXA2/TP beta/beta Arrestin2 -0.005 0.04 -10000 0 -0.62 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.1 -10000 0 -0.33 21 21
mol:DAG -0.075 0.19 -10000 0 -0.44 47 47
EGFR -0.011 0.12 -10000 0 -0.57 10 10
TXA2/TP alpha -0.096 0.23 -10000 0 -0.52 47 47
Gq family/GTP -0.013 0.055 -10000 0 -0.23 14 14
YES1 0.013 0.079 -10000 0 -0.44 3 3
GNAI2/GTP -0.022 0.077 -10000 0 -0.57 2 2
PGD2/DP -0.025 0.12 -10000 0 -0.48 18 18
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.009 0.087 -10000 0 -0.45 4 4
mol:NO 0.006 0.058 -10000 0 -0.65 2 2
GNA15 -0.01 0.12 -10000 0 -0.62 9 9
PGK/cGMP -0.007 0.089 -10000 0 -0.42 10 10
RhoA/GDP 0.012 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.004 0.11 -10000 0 -0.62 3 3
NOS3 0.006 0.058 -10000 0 -0.65 2 2
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.062 0.16 -10000 0 -0.37 46 46
PRKCB -0.072 0.18 -10000 0 -0.39 49 49
PRKCE -0.056 0.16 -10000 0 -0.36 46 46
PRKCD -0.063 0.17 -10000 0 -0.38 46 46
PRKCG -0.1 0.21 -10000 0 -0.45 52 52
muscle contraction -0.092 0.22 -10000 0 -0.52 46 46
PRKCZ -0.057 0.16 -10000 0 -0.36 46 46
ARR3 0.005 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.002 0.094 -10000 0 -0.66 2 2
PRKCQ -0.064 0.17 -10000 0 -0.38 48 48
MAPKKK cascade -0.086 0.21 -10000 0 -0.48 46 46
SELE -0.062 0.16 -10000 0 -0.36 48 48
TP beta/GNAI2/GDP/G beta/gamma 0.01 0.094 -10000 0 -0.64 2 2
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.01 0.11 -10000 0 -0.51 11 11
chemotaxis -0.12 0.26 -10000 0 -0.63 46 46
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.009 0.041 -10000 0 -0.65 1 1
GNA11 0.012 0 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.004 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.025 0.07 0.37 1 -10000 0 1
SMARCC2 0.013 0.007 -10000 0 -10000 0 0
SMARCC1 0.012 0.008 -10000 0 -10000 0 0
TBX21 -0.14 0.3 -10000 0 -0.81 37 37
SUMO2 0.011 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.01 0.052 -10000 0 -0.33 5 5
FKBP4 0.012 0 -10000 0 -10000 0 0
FKBP5 -0.014 0.12 -10000 0 -0.6 11 11
GR alpha/HSP90/FKBP51/HSP90 0.075 0.13 0.31 12 -0.39 9 21
PRL -0.062 0.11 -10000 0 -0.52 1 1
cortisol/GR alpha (dimer)/TIF2 0.21 0.21 0.54 49 -0.4 1 50
RELA -0.038 0.083 -10000 0 -0.31 3 3
FGG 0.16 0.17 0.46 28 -0.39 1 29
GR beta/TIF2 0.095 0.11 0.33 13 -0.5 2 15
IFNG -0.27 0.35 -10000 0 -0.89 44 44
apoptosis -0.005 0.16 0.61 5 -0.58 5 10
CREB1 0.01 0.019 -10000 0 -10000 0 0
histone acetylation 0.024 0.15 0.36 15 -0.38 7 22
BGLAP -0.058 0.13 -10000 0 -0.86 2 2
GR/PKAc 0.09 0.086 0.31 9 -10000 0 9
NF kappa B1 p50/RelA -0.067 0.16 -10000 0 -0.5 13 13
SMARCD1 0.012 0.008 -10000 0 -10000 0 0
MDM2 0.081 0.076 0.25 20 -10000 0 20
GATA3 -0.059 0.2 -10000 0 -0.58 32 32
AKT1 -0.001 0.035 -10000 0 -0.4 2 2
CSF2 -0.023 0.12 0.36 1 -0.44 2 3
GSK3B 0.011 0.01 -10000 0 -10000 0 0
NR1I3 0.02 0.17 0.62 4 -0.84 3 7
CSN2 0.14 0.14 0.4 20 -10000 0 20
BRG1/BAF155/BAF170/BAF60A 0.032 0.038 -10000 0 -0.36 1 1
NFATC1 -0.022 0.15 -10000 0 -0.63 14 14
POU2F1 0.01 0.019 -10000 0 -10000 0 0
CDKN1A -0.025 0.2 -10000 0 -1.6 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.012 -10000 0 -10000 0 0
SFN -0.04 0.18 -10000 0 -0.63 21 21
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.16 0.32 7 -0.42 15 22
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.004 0.21 0.59 4 -0.75 12 16
JUN -0.15 0.17 -10000 0 -0.48 26 26
IL4 -0.09 0.15 -10000 0 -0.65 8 8
CDK5R1 0.012 0.006 -10000 0 -10000 0 0
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.11 0.21 0.22 17 -0.53 31 48
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.08 0.12 0.3 11 -0.37 7 18
cortisol/GR alpha (monomer) 0.24 0.25 0.64 51 -10000 0 51
NCOA2 0.009 0.041 -10000 0 -0.65 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.088 0.17 -10000 0 -0.55 26 26
AP-1/NFAT1-c-4 -0.28 0.31 -10000 0 -0.73 58 58
AFP -0.12 0.15 -10000 0 -0.57 7 7
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.11 0.19 0.48 6 -0.82 6 12
TP53 -0.032 0.19 -10000 0 -0.63 24 24
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.3 0.4 -10000 0 -1.1 43 43
KRT14 -0.43 0.56 -10000 0 -1.4 64 64
TBP 0.017 0.025 -10000 0 -0.36 1 1
CREBBP 0.098 0.12 0.3 55 -10000 0 55
HDAC1 0.01 0.003 -10000 0 -10000 0 0
HDAC2 0.006 0.058 -10000 0 -0.65 2 2
AP-1 -0.28 0.32 -10000 0 -0.74 59 59
MAPK14 0.011 0.009 -10000 0 -10000 0 0
MAPK10 -0.094 0.22 -10000 0 -0.53 51 51
MAPK11 0.006 0.059 -10000 0 -0.65 2 2
KRT5 -0.4 0.5 -10000 0 -1.1 67 67
interleukin-1 receptor activity 0 0.006 -10000 0 -10000 0 0
NCOA1 0.014 0.001 -10000 0 -10000 0 0
STAT1 0.01 0.052 -10000 0 -0.33 5 5
CGA -0.074 0.12 -10000 0 -0.51 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.13 0.14 0.35 46 -0.35 1 47
MAPK3 0.012 0.012 -10000 0 -10000 0 0
MAPK1 0.007 0.049 -10000 0 -0.52 2 2
ICAM1 -0.18 0.32 -10000 0 -0.79 39 39
NFKB1 -0.041 0.095 -10000 0 -0.34 8 8
MAPK8 -0.13 0.15 -10000 0 -0.42 27 27
MAPK9 0.009 0.042 -10000 0 -0.65 1 1
cortisol/GR alpha (dimer) -0.012 0.17 0.62 5 -0.61 5 10
BAX -0.01 0.12 -10000 0 -0.71 1 1
POMC -0.15 0.25 -10000 0 -1 12 12
EP300 0.096 0.13 0.31 44 -0.65 1 45
cortisol/GR alpha (dimer)/p53 0.18 0.24 0.55 45 -0.45 3 48
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.06 0.23 5 -10000 0 5
SGK1 0.14 0.19 -10000 0 -1.3 2 2
IL13 -0.21 0.26 -10000 0 -0.86 24 24
IL6 -0.23 0.36 -10000 0 -0.92 41 41
PRKACG 0.001 0.004 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.79 16 16
IL2 -0.22 0.23 -10000 0 -0.68 29 29
CDK5 0.012 0.006 -10000 0 -10000 0 0
PRKACB 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.2 0.34 -10000 0 -0.95 32 32
CDK5R1/CDK5 0.017 0.014 0.2 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc -0.03 0.12 -10000 0 -0.43 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.19 0.51 50 -10000 0 50
SMARCA4 0.008 0.048 -10000 0 -0.52 2 2
chromatin remodeling 0.14 0.12 0.37 31 -10000 0 31
NF kappa B1 p50/RelA/Cbp 0.038 0.18 0.34 29 -0.57 4 33
JUN (dimer) -0.15 0.17 -10000 0 -0.48 26 26
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.081 0.2 -10000 0 -0.64 19 19
NR3C1 0.14 0.15 0.42 35 -0.43 2 37
NR4A1 -0.029 0.13 -10000 0 -0.43 22 22
TIF2/SUV420H1 0.015 0.031 -10000 0 -0.48 1 1
MAPKKK cascade -0.005 0.16 0.61 5 -0.58 5 10
cortisol/GR alpha (dimer)/Src-1 0.22 0.21 0.55 50 -10000 0 50
PBX1 0.01 0.019 -10000 0 -10000 0 0
POU1F1 -0.003 0.047 -10000 0 -0.39 3 3
SELE -0.22 0.37 -10000 0 -0.97 40 40
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.12 0.37 30 -10000 0 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.19 0.51 50 -10000 0 50
mol:cortisol 0.13 0.15 0.36 55 -10000 0 55
MMP1 -0.28 0.45 -10000 0 -1 57 57
EGFR-dependent Endothelin 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
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.011 0.12 -9999 0 -0.57 10 10
EGF/EGFR -0.082 0.14 -9999 0 -0.37 44 44
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.022 0.12 -9999 0 -0.34 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.032 0.16 -9999 0 -0.58 19 19
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.07 0.2 -9999 0 -0.51 41 41
EGF/EGFR dimer/SHC -0.042 0.14 -9999 0 -0.41 26 26
mol:GDP -0.049 0.11 -9999 0 -0.34 26 26
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.016 0.11 -9999 0 -0.46 15 15
GRB2/SOS1 0.017 0 -9999 0 -10000 0 0
HRAS/GTP -0.045 0.098 -9999 0 -0.31 26 26
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.046 0.1 -9999 0 -0.32 26 26
FRAP1 -0.023 0.11 -9999 0 -0.32 26 26
EGF/EGFR dimer -0.059 0.16 -9999 0 -0.38 50 50
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.033 0.15 -9999 0 -0.42 30 30
HIF-1-alpha transcription factor network

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
PKM2 -0.16 0.45 -9999 0 -1.3 20 20
HDAC7 0.013 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 -9999 0 -0.87 23 23
SMAD4 0.013 0 -9999 0 -10000 0 0
ID2 -0.16 0.46 -9999 0 -1.3 20 20
AP1 -0.021 0.13 -9999 0 -0.51 12 12
ABCG2 -0.18 0.46 -9999 0 -1.3 22 22
HIF1A -0.007 0.07 -9999 0 -10000 0 0
TFF3 -0.25 0.5 -9999 0 -1.2 34 34
GATA2 -0.046 0.15 -9999 0 -0.41 36 36
AKT1 -0.028 0.097 -9999 0 -0.45 2 2
response to hypoxia -0.04 0.093 -9999 0 -0.24 1 1
MCL1 -0.16 0.45 -9999 0 -1.3 19 19
NDRG1 -0.17 0.47 -9999 0 -1.3 20 20
SERPINE1 -0.19 0.47 -9999 0 -1.2 25 25
FECH -0.16 0.45 -9999 0 -1.3 20 20
FURIN -0.16 0.45 -9999 0 -1.3 20 20
NCOA2 0.01 0.041 -9999 0 -0.65 1 1
EP300 -0.038 0.15 -9999 0 -0.34 15 15
HMOX1 -0.17 0.46 -9999 0 -1.3 21 21
BHLHE40 -0.16 0.46 -9999 0 -1.3 20 20
BHLHE41 -0.19 0.5 -9999 0 -1.4 24 24
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.016 0.047 -9999 0 -10000 0 0
ENG 0.037 0.087 -9999 0 -10000 0 0
JUN 0.006 0.054 -9999 0 -0.48 3 3
RORA -0.16 0.45 -9999 0 -1.3 19 19
ABCB1 -0.067 0.16 -9999 0 -1.2 4 4
TFRC -0.16 0.45 -9999 0 -1.3 20 20
CXCR4 -0.16 0.46 -9999 0 -1.3 21 21
TF -0.21 0.48 -9999 0 -1.2 30 30
CITED2 -0.16 0.46 -9999 0 -1.3 19 19
HIF1A/ARNT -0.26 0.53 -9999 0 -1.6 20 20
LDHA -0.036 0.051 -9999 0 -10000 0 0
ETS1 -0.16 0.45 -9999 0 -1.3 20 20
PGK1 -0.16 0.45 -9999 0 -1.3 19 19
NOS2 -0.19 0.48 -9999 0 -1.2 29 29
ITGB2 -0.18 0.48 -9999 0 -1.2 26 26
ALDOA -0.16 0.45 -9999 0 -1.3 20 20
Cbp/p300/CITED2 -0.21 0.47 -9999 0 -1.2 23 23
FOS -0.038 0.15 -9999 0 -0.48 26 26
HK2 -0.16 0.45 -9999 0 -1.3 20 20
SP1 0.019 0.007 -9999 0 -10000 0 0
GCK -0.2 0.48 -9999 0 -1.2 37 37
HK1 -0.16 0.45 -9999 0 -1.3 20 20
NPM1 -0.16 0.45 -9999 0 -1.3 20 20
EGLN1 -0.16 0.45 -9999 0 -1.3 20 20
CREB1 0.018 0.001 -9999 0 -10000 0 0
PGM1 -0.16 0.45 -9999 0 -1.3 19 19
SMAD3 0.013 0 -9999 0 -10000 0 0
EDN1 -0.09 0.25 -9999 0 -0.92 10 10
IGFBP1 -0.21 0.48 -9999 0 -1.2 25 25
VEGFA -0.11 0.34 -9999 0 -0.85 13 13
HIF1A/JAB1 -0.013 0.03 -9999 0 -10000 0 0
CP -0.2 0.51 -9999 0 -1.3 30 30
CXCL12 -0.19 0.48 -9999 0 -1.2 25 25
COPS5 0.011 0.025 -9999 0 -0.39 1 1
SMAD3/SMAD4 0.019 0 -9999 0 -10000 0 0
BNIP3 -0.17 0.46 -9999 0 -1.3 20 20
EGLN3 -0.18 0.48 -9999 0 -1.3 23 23
CA9 -0.23 0.51 -9999 0 -1.3 31 31
TERT -0.19 0.48 -9999 0 -1.3 21 21
ENO1 -0.16 0.45 -9999 0 -1.3 19 19
PFKL -0.16 0.45 -9999 0 -1.3 20 20
NCOA1 0.012 0 -9999 0 -10000 0 0
ADM -0.17 0.46 -9999 0 -1.3 20 20
ARNT -0.007 0.07 -9999 0 -10000 0 0
HNF4A -0.042 0.11 -9999 0 -0.4 21 21
ADFP -0.18 0.44 -9999 0 -1.3 20 20
SLC2A1 -0.11 0.35 -9999 0 -0.84 14 14
LEP -0.18 0.47 -9999 0 -1.3 22 22
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -9999 0 -0.88 26 26
EPO -0.063 0.27 -9999 0 -0.94 3 3
CREBBP -0.037 0.15 -9999 0 -0.33 15 15
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 -9999 0 -0.9 22 22
PFKFB3 -0.16 0.46 -9999 0 -1.3 19 19
NT5E -0.19 0.49 -9999 0 -1.3 25 25
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.011 0.022 -10000 0 -0.23 2 2
RAS family/GTP -0.059 0.13 -10000 0 -0.44 7 7
NFATC4 -0.046 0.12 -10000 0 -0.36 8 8
ERBB2IP 0.013 0.003 -10000 0 -10000 0 0
HSP90 (dimer) 0.012 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.071 0.14 -10000 0 -0.33 51 51
JUN -0.013 0.081 -10000 0 -0.32 6 6
HRAS 0.011 0.001 -10000 0 -10000 0 0
DOCK7 -0.064 0.14 -10000 0 -0.44 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.092 0.16 -10000 0 -0.38 51 51
AKT1 0.006 0.025 -10000 0 -0.28 2 2
BAD 0.013 0.021 -10000 0 -0.22 2 2
MAPK10 -0.056 0.11 -10000 0 -0.28 31 31
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.075 0.15 -10000 0 -0.35 51 51
RAF1 -0.057 0.13 -10000 0 -0.48 4 4
ErbB2/ErbB3/neuregulin 2 -0.05 0.13 -10000 0 -0.4 26 26
STAT3 0.003 0.004 -10000 0 -10000 0 0
cell migration -0.035 0.096 -10000 0 -0.27 10 10
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.16 0.28 -10000 0 -0.63 55 55
FOS -0.093 0.19 -10000 0 -0.42 35 35
NRAS 0.009 0.025 -10000 0 -0.39 1 1
mol:Ca2+ -0.071 0.14 -10000 0 -0.33 51 51
MAPK3 -0.12 0.23 -10000 0 -0.5 53 53
MAPK1 -0.13 0.23 -10000 0 -0.51 54 54
JAK2 -0.065 0.14 -10000 0 -0.44 7 7
NF2 -0.005 0.026 -10000 0 -0.36 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.067 0.14 -10000 0 -0.32 51 51
NRG1 -0.16 0.26 -10000 0 -0.52 84 84
GRB2/SOS1 0.017 0.001 -10000 0 -10000 0 0
MAPK8 -0.052 0.13 -10000 0 -0.31 25 25
MAPK9 -0.021 0.078 -10000 0 -0.23 3 3
ERBB2 -0.004 0.031 -10000 0 -0.29 3 3
ERBB3 -0.021 0.14 -10000 0 -0.65 12 12
SHC1 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.003 0.021 0.21 2 -10000 0 2
STAT3 (dimer) 0.014 0.006 -10000 0 -10000 0 0
RNF41 0.015 0.021 -10000 0 -10000 0 0
FRAP1 0.005 0.021 -10000 0 -0.23 2 2
RAC1-CDC42/GTP -0.058 0.089 -10000 0 -0.31 7 7
ErbB2/ErbB2/HSP90 (dimer) -0.003 0.025 -10000 0 -0.23 3 3
CHRNA1 -0.16 0.28 -10000 0 -0.65 56 56
myelination -0.042 0.12 -10000 0 -0.36 8 8
PPP3CB -0.06 0.13 -10000 0 -0.4 7 7
KRAS -0.001 0.07 -10000 0 -0.4 8 8
RAC1-CDC42/GDP -0.046 0.12 -10000 0 -0.42 6 6
NRG2 -0.057 0.18 -10000 0 -0.5 35 35
mol:GDP -0.067 0.14 -10000 0 -0.32 51 51
SOS1 0.011 0.001 -10000 0 -10000 0 0
MAP2K2 -0.059 0.14 -10000 0 -0.39 16 16
SRC 0.012 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.064 0.14 -10000 0 -0.44 7 7
MAP2K1 -0.12 0.21 -10000 0 -0.61 18 18
heart morphogenesis -0.071 0.14 -10000 0 -0.33 51 51
RAS family/GDP -0.054 0.13 -10000 0 -0.44 7 7
GRB2 0.011 0.001 -10000 0 -10000 0 0
PRKACA -0.006 0.009 -10000 0 -10000 0 0
CHRNE 0.002 0.033 -10000 0 -0.17 7 7
HSP90AA1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.025 0.28 2 -10000 0 2
nervous system development -0.071 0.14 -10000 0 -0.33 51 51
CDC42 0.012 0 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.018 0.1 -9999 0 -0.44 14 14
NFATC2 -0.001 0.06 -9999 0 -0.42 4 4
NFATC3 0.005 0.03 -9999 0 -10000 0 0
CD40LG -0.13 0.3 -9999 0 -0.65 51 51
PTGS2 -0.11 0.28 -9999 0 -0.62 42 42
JUNB -0.005 0.095 -9999 0 -0.52 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.013 -9999 0 -10000 0 0
CaM/Ca2+ -0.007 0.012 -9999 0 -10000 0 0
CALM1 0.008 0.009 -9999 0 -10000 0 0
JUN 0.002 0.055 -9999 0 -0.48 3 3
mol:Ca2+ -0.007 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.012 0.12 -9999 0 -0.56 11 11
CREM 0.009 0.041 -9999 0 -0.65 1 1
Jun/NFAT1-c-4/p21SNFT -0.083 0.15 -9999 0 -0.49 20 20
FOS -0.042 0.16 -9999 0 -0.49 26 26
IFNG -0.12 0.29 -9999 0 -0.6 54 54
AP-1/NFAT1-c-4 -0.12 0.31 -9999 0 -0.72 37 37
FASLG -0.13 0.31 -9999 0 -0.67 49 49
NFAT1-c-4/ICER1 -0.03 0.12 -9999 0 -0.43 15 15
IL2RA -0.12 0.3 -9999 0 -0.68 42 42
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.1 0.26 -9999 0 -0.59 39 39
JunB/Fra1/NFAT1-c-4 -0.063 0.14 -9999 0 -0.46 21 21
IL4 -0.099 0.25 -9999 0 -0.59 35 35
IL2 -0.008 0.033 -9999 0 -10000 0 0
IL3 -0.015 0.02 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 -0.005 0.1 -9999 0 -0.62 7 7
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.001 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk 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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.079 0.11 -10000 0 -0.3 28 28
NT3 (dimer)/TRKC -0.23 0.26 -10000 0 -0.44 143 143
NT3 (dimer)/TRKB -0.17 0.23 -10000 0 -0.47 75 75
SHC/Grb2/SOS1/GAB1/PI3K 0.031 0.011 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.036 0.16 -10000 0 -0.56 22 22
PIK3CA 0.012 0 -10000 0 -10000 0 0
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.036 0.14 -10000 0 -0.47 25 25
NTRK2 -0.033 0.14 -10000 0 -0.46 25 25
NTRK3 -0.16 0.25 -10000 0 -0.5 87 87
NT-4/5 (dimer)/TRKB -0.1 0.19 -10000 0 -0.44 52 52
neuron apoptosis 0.074 0.15 0.42 25 -10000 0 25
SHC 2-3/Grb2 -0.081 0.17 -10000 0 -0.46 25 25
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.092 0.16 -10000 0 -0.55 18 18
SHC3 -0.086 0.15 0.22 1 -0.51 19 20
STAT3 (dimer) -0.022 0.12 -10000 0 -0.36 26 26
NT3 (dimer)/TRKA -0.17 0.22 -10000 0 -0.49 70 70
RIN/GDP -0.049 0.088 -10000 0 -0.24 9 9
GIPC1 0.008 0.035 -10000 0 -0.39 2 2
KRAS -0.001 0.07 -10000 0 -0.39 8 8
DNAJA3 -0.07 0.13 0.25 1 -0.42 23 24
RIN/GTP 0 0.017 -10000 0 -0.28 1 1
CCND1 -0.068 0.27 -10000 0 -0.88 26 26
MAGED1 0.007 0.048 -10000 0 -0.52 2 2
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.057 0.2 -10000 0 -0.62 28 28
SHC/GRB2/SOS1 0.024 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.088 0.2 -10000 0 -0.48 41 41
TRKA/NEDD4-2 -0.017 0.1 -10000 0 -0.48 7 7
ELMO1 0.012 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.014 0.027 -10000 0 -0.42 1 1
NGF -0.049 0.17 -10000 0 -0.5 31 31
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.009 0.041 -10000 0 -0.65 1 1
GAB2 -0.007 0.1 -10000 0 -0.54 9 9
RIT2 0 0.025 -10000 0 -0.39 1 1
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.01 0.025 -10000 0 -0.39 1 1
DNM1 0.007 0.048 -10000 0 -0.52 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.035 -10000 0 -0.39 2 2
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.068 0.13 0.24 1 -0.4 23 24
mol:GDP -0.071 0.13 -10000 0 -0.34 17 17
NGF (dimer) -0.049 0.17 -10000 0 -0.5 31 31
RhoG/GDP 0.009 0 -10000 0 -10000 0 0
RIT1/GDP -0.044 0.088 -10000 0 -0.25 7 7
TIAM1 0.001 0.081 -10000 0 -0.65 4 4
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
BDNF (dimer)/TRKB -0.034 0.14 -10000 0 -0.44 20 20
KIDINS220/CRKL/C3G 0.017 0 -10000 0 -10000 0 0
SHC/RasGAP 0.017 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0.023 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.03 0 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.17 0.27 -10000 0 -0.53 88 88
RAP1/GDP -0.051 0.061 -10000 0 -0.23 4 4
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.036 0.16 -10000 0 -0.56 22 22
ubiquitin-dependent protein catabolic process -0.043 0.14 -10000 0 -0.44 23 23
Schwann cell development -0.04 0.034 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.029 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.043 -10000 0 -0.36 1 1
RAP1B 0.01 0.025 -10000 0 -0.39 1 1
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.22 -10000 0 -0.59 46 46
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.017 0 -10000 0 -10000 0 0
Rap1/GTP 0.016 0.064 -10000 0 -10000 0 0
STAT3 -0.022 0.12 -10000 0 -0.36 26 26
axon guidance -0.2 0.21 -10000 0 -0.56 46 46
MAPK3 -0.074 0.18 -10000 0 -0.44 41 41
MAPK1 -0.076 0.18 -10000 0 -0.43 43 43
CDC42/GDP -0.044 0.088 -10000 0 -0.25 7 7
NTF3 -0.17 0.27 -10000 0 -0.53 88 88
NTF4 -0.057 0.2 -10000 0 -0.62 28 28
NGF (dimer)/TRKA/FAIM -0.043 0.14 -10000 0 -0.44 23 23
PI3K 0.015 0.025 -10000 0 -0.27 2 2
FRS3 0.012 0 -10000 0 -10000 0 0
FAIM 0.012 0 -10000 0 -10000 0 0
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.11 0.17 0.25 1 -0.43 39 40
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.22 0.25 -10000 0 -0.51 90 90
RGS19 0.012 0 -10000 0 -10000 0 0
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.067 -10000 0 -10000 0 0
Rac1/GDP -0.044 0.088 -10000 0 -0.25 6 6
NGF (dimer)/TRKA/GRIT -0.05 0.14 -10000 0 -0.44 23 23
neuron projection morphogenesis -0.063 0.15 -10000 0 -0.53 11 11
NGF (dimer)/TRKA/NEDD4-2 -0.043 0.14 -10000 0 -0.44 23 23
MAP2K1 0.033 0 -10000 0 -10000 0 0
NGFR -0.077 0.2 -10000 0 -0.49 46 46
NGF (dimer)/TRKA/GIPC/GAIP -0.013 0.1 -10000 0 -0.32 19 19
RAS family/GTP/PI3K 0.021 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.034 0.013 -10000 0 -10000 0 0
NRAS 0.01 0.025 -10000 0 -0.39 1 1
GRB2/SOS1 0.017 0 -10000 0 -10000 0 0
PRKCI 0.007 0.048 -10000 0 -0.52 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.072 0.16 -10000 0 -0.6 19 19
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.017 0.1 -10000 0 -0.48 7 7
SQSTM1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.024 0.13 -10000 0 -0.4 21 21
NGF (dimer)/TRKA/p62/Atypical PKCs -0.025 0.13 -10000 0 -0.37 24 24
MATK -0.063 0.19 -10000 0 -0.54 35 35
NEDD4L 0.012 0 -10000 0 -10000 0 0
RAS family/GDP -0.051 0.06 -10000 0 -0.23 1 1
NGF (dimer)/TRKA -0.075 0.14 0.28 1 -0.38 37 38
Rac1/GTP -0.1 0.1 -10000 0 -0.33 24 24
FRS2 family/SHP2/CRK family 0.032 0.022 -10000 0 -10000 0 0
Ephrin A reverse signaling

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.012 0.086 -9999 0 -0.27 24 24
EFNA5 -0.003 0.094 -9999 0 -0.61 6 6
FYN -0.011 0.087 -9999 0 -0.37 7 7
neuron projection morphogenesis -0.012 0.086 -9999 0 -0.27 24 24
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.012 0.086 -9999 0 -0.27 24 24
EPHA5 -0.02 0.11 -9999 0 -0.41 18 18
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.045 0.18 -9999 0 -0.46 34 34
MAP4K1 -0.002 0.086 -9999 0 -0.5 7 7
MAP3K8 0.01 0.025 -9999 0 -0.39 1 1
PRKCB -0.041 0.17 -9999 0 -0.56 24 24
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 -0.02 0.15 -9999 0 -0.6 10 10
JUN -0.025 0.17 -9999 0 -0.67 16 16
MAP3K7 -0.018 0.15 -9999 0 -0.63 9 9
GRAP2 -0.068 0.2 -9999 0 -0.58 35 35
CRK 0.008 0.035 -9999 0 -0.39 2 2
MAP2K4 -0.013 0.15 -9999 0 -0.63 9 9
LAT 0.005 0.063 -9999 0 -0.57 3 3
LCP2 -0.019 0.14 -9999 0 -0.65 12 12
MAPK8 -0.029 0.18 -9999 0 -0.73 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.026 0.16 -9999 0 -0.39 31 31
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.037 0.17 -9999 0 -0.43 34 34
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.012 0 -9999 0 -10000 0 0
LAT2 -0.047 0.18 -9999 0 -0.71 13 13
AP1 -0.091 0.19 -9999 0 -0.63 23 23
mol:PIP3 -0.062 0.21 -9999 0 -0.59 23 23
IKBKB -0.025 0.11 -9999 0 -0.3 23 23
AKT1 -0.045 0.15 -9999 0 -0.5 11 11
IKBKG -0.025 0.11 -9999 0 -0.31 22 22
MS4A2 -0.032 0.14 -9999 0 -0.53 19 19
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.001 -9999 0 -10000 0 0
MAP3K1 -0.03 0.15 -9999 0 -0.51 16 16
mol:Ca2+ -0.041 0.15 -9999 0 -0.41 23 23
LYN 0.003 0.073 -9999 0 -0.67 3 3
CBLB -0.031 0.13 -9999 0 -0.38 20 20
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.009 0.058 -9999 0 -0.37 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.015 0.13 -9999 0 -0.63 11 11
PLD2 -0.064 0.16 -9999 0 -0.38 43 43
PTPN13 -0.084 0.18 -9999 0 -0.51 18 18
PTPN11 0.009 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.015 0.12 -9999 0 -0.38 8 8
SYK 0.011 0.004 -9999 0 -10000 0 0
GRB2 0.011 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.1 0.19 -9999 0 -0.53 31 31
LAT -0.035 0.13 -9999 0 -0.38 23 23
PAK2 -0.039 0.17 -9999 0 -0.57 17 17
NFATC2 -0.038 0.084 -9999 0 -0.36 9 9
HRAS -0.05 0.19 -9999 0 -0.61 18 18
GAB2 -0.007 0.1 -9999 0 -0.54 9 9
PLA2G1B 0.027 0.021 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.18 -9999 0 -0.46 43 43
Antigen/IgE/Fc epsilon R1 -0.093 0.16 -9999 0 -0.42 43 43
mol:GDP -0.064 0.21 -9999 0 -0.6 25 25
JUN 0.006 0.054 -9999 0 -0.48 3 3
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
FOS -0.038 0.15 -9999 0 -0.48 26 26
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.04 0.14 -9999 0 -0.41 20 20
CHUK -0.025 0.11 -9999 0 -0.32 20 20
KLRG1 -0.035 0.12 -9999 0 -0.41 14 14
VAV1 -0.049 0.15 -9999 0 -0.4 29 29
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.031 0.13 -9999 0 -0.38 20 20
negative regulation of mast cell degranulation -0.039 0.15 -9999 0 -0.52 15 15
BTK -0.072 0.24 -9999 0 -0.74 23 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.085 0.23 -9999 0 -0.5 43 43
GAB2/PI3K/SHP2 -0.083 0.14 -9999 0 -0.55 11 11
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.042 0.14 -9999 0 -0.5 13 13
RAF1 0.019 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.24 -9999 0 -0.52 57 57
FCER1G -0.016 0.13 -9999 0 -0.63 11 11
FCER1A -0.1 0.22 -9999 0 -0.5 58 58
Antigen/IgE/Fc epsilon R1/Fyn -0.091 0.16 -9999 0 -0.41 43 43
MAPK3 0.027 0.02 -9999 0 -10000 0 0
MAPK1 0.027 0.021 -9999 0 -10000 0 0
NFKB1 0.009 0.041 -9999 0 -0.65 1 1
MAPK8 0.003 0.057 -9999 0 -0.38 1 1
DUSP1 -0.014 0.1 -9999 0 -0.43 15 15
NF-kappa-B/RelA -0.032 0.058 -9999 0 -0.23 8 8
actin cytoskeleton reorganization -0.031 0.13 -9999 0 -0.53 8 8
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.071 0.15 -9999 0 -0.6 13 13
FER -0.035 0.13 -9999 0 -0.38 23 23
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.066 0.15 -9999 0 -0.48 28 28
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.062 0.21 -9999 0 -0.63 23 23
cytokine secretion -0.023 0.041 -9999 0 -0.24 1 1
SPHK1 -0.049 0.16 -9999 0 -0.42 28 28
PTK2 -0.032 0.14 -9999 0 -0.56 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.2 -9999 0 -0.57 30 30
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.056 0.2 -9999 0 -0.56 23 23
MAP2K2 0.024 0.02 -9999 0 -10000 0 0
MAP2K1 0.024 0.02 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.047 0.11 -9999 0 -0.43 10 10
MAP2K4 0.012 0.057 -9999 0 -0.89 1 1
Fc epsilon R1/FcgammaRIIB -0.13 0.22 -9999 0 -0.51 54 54
mol:Choline -0.063 0.16 -9999 0 -0.38 43 43
SHC/Grb2/SOS1 -0.047 0.11 -9999 0 -0.5 8 8
FYN -0.002 0.077 -9999 0 -0.43 8 8
DOK1 0.012 0 -9999 0 -10000 0 0
PXN -0.024 0.13 -9999 0 -0.53 7 7
HCLS1 -0.041 0.16 -9999 0 -0.47 22 22
PRKCB -0.046 0.16 -9999 0 -0.44 24 24
FCGR2B -0.058 0.2 -9999 0 -0.62 29 29
IGHE -0.001 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.04 0.15 -9999 0 -0.53 15 15
LCP2 -0.019 0.14 -9999 0 -0.65 12 12
PLA2G4A -0.052 0.15 -9999 0 -0.38 31 31
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.063 0.16 -9999 0 -0.38 43 43
IKK complex -0.006 0.088 -9999 0 -0.24 16 16
WIPF1 0.006 0.058 -9999 0 -0.65 2 2
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.027 0.13 -10000 0 -0.38 30 30
regulation of S phase of mitotic cell cycle -0.011 0.098 -10000 0 -0.28 30 30
GNAO1 -0.098 0.22 -10000 0 -0.51 55 55
HRAS 0.011 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.026 0.11 -10000 0 -0.34 25 25
PELP1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.007 0.025 -10000 0 -0.28 2 2
MAP2K1 -0.007 0.11 -10000 0 -0.38 2 2
T-DHT/AR -0.051 0.16 -10000 0 -0.48 32 32
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.005 25 25
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.091 -10000 0 -0.65 5 5
mol:GDP -0.058 0.16 -10000 0 -0.49 30 30
cell proliferation -0.011 0.13 -10000 0 -0.48 4 4
PIK3CA 0.012 0 -10000 0 -10000 0 0
FOS -0.022 0.18 -10000 0 -0.79 10 10
mol:Ca2+ -0.016 0.027 -10000 0 -0.075 31 31
MAPK3 -0.008 0.12 -10000 0 -0.44 3 3
MAPK1 -0.002 0.071 -10000 0 -0.36 2 2
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
mol:IP3 0 0.001 -10000 0 -0.003 26 26
cAMP biosynthetic process -0.017 0.1 -10000 0 -0.31 25 25
GNG2 0.007 0.043 -10000 0 -0.39 3 3
potassium channel inhibitor activity 0 0.001 -10000 0 -0.003 26 26
HRAS/GTP -0.041 0.11 -10000 0 -0.33 30 30
actin cytoskeleton reorganization -0.001 0.014 -10000 0 -10000 0 0
SRC 0.011 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.003 26 26
PI3K 0.014 0.021 -10000 0 -10000 0 0
apoptosis 0.007 0.11 0.41 10 -10000 0 10
T-DHT/AR/PELP1 -0.036 0.14 -10000 0 -0.42 30 30
HRAS/GDP -0.054 0.15 -10000 0 -0.46 30 30
CREB1 -0.008 0.12 -10000 0 -0.44 10 10
RAC1-CDC42/GTP -0.001 0.014 -10000 0 -10000 0 0
AR -0.068 0.21 -10000 0 -0.64 32 32
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 -0.012 0.11 -10000 0 -0.31 30 30
RAC1-CDC42/GDP -0.05 0.14 -10000 0 -0.44 30 30
T-DHT/AR/PELP1/Src -0.025 0.13 -10000 0 -0.37 30 30
MAP2K2 -0.007 0.11 -10000 0 -0.38 2 2
T-DHT/AR/PELP1/Src/PI3K -0.011 0.099 -10000 0 -0.28 30 30
GNAZ 0.006 0.058 -10000 0 -0.65 2 2
SHBG -0.042 0.17 -10000 0 -0.54 25 25
Gi family/GNB1/GNG2/GDP -0.032 0.14 -10000 0 -0.41 25 25
mol:T-DHT 0 0.001 -10000 0 -0.003 7 7
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 -0.019 0.11 -10000 0 -0.43 17 17
Gi family/GTP -0.042 0.12 -10000 0 -0.38 16 16
CDC42 0.012 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR -0.004 0.099 -10000 0 -0.65 6 6
Cbp/p300/PCAF 0.022 0.027 -10000 0 -0.41 1 1
EP300 0.009 0.041 -10000 0 -0.65 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.005 0.057 -10000 0 -0.28 2 2
KAT2B 0.012 0 -10000 0 -10000 0 0
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 -0.012 0.083 0.22 9 -0.31 6 15
RAR alpha/9cRA/Cyclin H -0.053 0.091 -10000 0 -0.36 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.06 -10000 0 -0.28 3 3
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.038 0.089 -10000 0 -0.3 3 3
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.075 -10000 0 -0.49 6 6
RXRs/RARs/NRIP1/9cRA -0.11 0.21 -10000 0 -0.52 43 43
NCOA2 0.009 0.041 -10000 0 -0.65 1 1
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.004 0.099 -10000 0 -0.65 6 6
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.016 0.001 -10000 0 -10000 0 0
MAPK3 0.012 0.001 -10000 0 -10000 0 0
MAPK1 0.007 0.048 -10000 0 -0.52 2 2
MAPK8 0.012 0.001 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.14 0.22 -10000 0 -0.56 46 46
RARA -0.048 0.11 -10000 0 -0.27 44 44
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.001 0.063 -10000 0 -0.29 4 4
PRKCA -0.001 0.092 -10000 0 -0.54 7 7
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.12 0.21 -10000 0 -0.53 43 43
RXRG -0.22 0.23 -10000 0 -0.44 119 119
RXRA -0.04 0.11 -10000 0 -0.32 8 8
RXRB -0.077 0.15 -10000 0 -0.38 44 44
VDR/Vit D3/DNA -0.003 0.075 -10000 0 -0.49 6 6
RBP1 -0.015 0.13 -10000 0 -0.63 11 11
CRBP1/9-cic-RA -0.012 0.097 -10000 0 -0.47 11 11
RARB -0.006 0.1 -10000 0 -0.54 9 9
PRKCG -0.17 0.26 -10000 0 -0.5 91 91
MNAT1 0.012 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.12 0.22 -10000 0 -0.56 43 43
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.089 0.18 -10000 0 -0.44 44 44
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.088 -10000 0 -0.33 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.12 0.21 -10000 0 -0.53 43 43
positive regulation of DNA binding -0.051 0.086 -10000 0 -0.34 5 5
NRIP1 -0.11 0.2 -10000 0 -0.69 12 12
RXRs/RARs -0.12 0.2 -10000 0 -0.53 43 43
RXRs/RXRs/DNA/9cRA -0.14 0.22 -10000 0 -0.58 44 44
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.012 0 -10000 0 -10000 0 0
TFIIH 0.024 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.035 0.06 -10000 0 -10000 0 0
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.005 0.066 -10000 0 -0.39 7 7
cell-cell adhesion 0.064 0.13 0.55 7 -10000 0 7
Ephrin B/EPHB2/RasGAP -0.007 0.12 -10000 0 -0.37 24 24
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.012 0.1 -10000 0 -0.4 17 17
Ephrin B1/EPHB1 -0.026 0.12 -10000 0 -0.32 33 33
HRAS/GDP -0.066 0.13 -10000 0 -0.38 24 24
Ephrin B/EPHB1/GRB7 -0.047 0.16 -10000 0 -0.37 44 44
Endophilin/SYNJ1 -0.008 0.12 -10000 0 -0.35 24 24
KRAS -0.001 0.07 -10000 0 -0.39 8 8
Ephrin B/EPHB1/Src -0.042 0.15 -10000 0 -0.37 41 41
endothelial cell migration -0.02 0.077 -10000 0 -0.34 13 13
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 0.002 0.075 -10000 0 -0.59 4 4
PAK1 -0.01 0.13 -10000 0 -0.36 26 26
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS -0.014 0.12 -10000 0 -0.36 28 28
DNM1 0.007 0.048 -10000 0 -0.52 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.042 0.15 -10000 0 -0.35 41 41
lamellipodium assembly -0.064 0.13 -10000 0 -0.55 7 7
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.021 0.12 -10000 0 -0.3 22 22
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
EPHB2 0.009 0.041 -10000 0 -0.65 1 1
EPHB3 -0.031 0.16 -10000 0 -0.64 17 17
EPHB1 -0.056 0.18 -10000 0 -0.52 33 33
EPHB4 -0.009 0.11 -10000 0 -0.65 8 8
mol:GDP -0.032 0.16 -10000 0 -0.4 27 27
Ephrin B/EPHB2 -0.014 0.12 -10000 0 -0.38 24 24
Ephrin B/EPHB3 -0.036 0.15 -10000 0 -0.4 36 36
JNK cascade -0.004 0.1 -10000 0 -0.34 17 17
Ephrin B/EPHB1 -0.049 0.15 -10000 0 -0.37 41 41
RAP1/GDP -0.018 0.14 -10000 0 -0.44 10 10
EFNB2 -0.004 0.097 -10000 0 -0.58 7 7
EFNB3 -0.045 0.18 -10000 0 -0.61 24 24
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.027 0.12 -10000 0 -0.38 23 23
RAP1B 0.01 0.025 -10000 0 -0.39 1 1
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.06 0.13 -10000 0 -0.63 4 4
Rap1/GTP -0.056 0.12 -10000 0 -0.56 4 4
axon guidance 0.005 0.066 -10000 0 -0.39 7 7
MAPK3 -0.007 0.1 -10000 0 -0.52 2 2
MAPK1 -0.009 0.11 -10000 0 -0.52 3 3
Rac1/GDP -0.023 0.14 -10000 0 -0.46 10 10
actin cytoskeleton reorganization -0.053 0.1 -10000 0 -0.42 8 8
CDC42/GDP -0.023 0.14 -10000 0 -0.37 24 24
PI3K 0.006 0.084 -10000 0 -0.34 13 13
EFNA5 -0.003 0.094 -10000 0 -0.61 6 6
Ephrin B2/EPHB4 -0.008 0.096 -10000 0 -0.39 15 15
Ephrin B/EPHB2/Intersectin/N-WASP -0.002 0.1 -10000 0 -0.3 24 24
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.058 0.12 -10000 0 -0.55 5 5
PTK2 0.009 0.024 -10000 0 -10000 0 0
MAP4K4 -0.005 0.1 -10000 0 -0.34 17 17
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.002 0.075 -10000 0 -0.59 4 4
Intersectin/N-WASP 0.017 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.01 0.13 -10000 0 -0.45 8 8
MAP2K1 -0.014 0.11 -10000 0 -0.48 3 3
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.01 0.11 -10000 0 -0.37 17 17
cell migration -0.014 0.13 -10000 0 -0.52 4 4
NRAS 0.01 0.025 -10000 0 -0.39 1 1
SYNJ1 -0.008 0.12 -10000 0 -0.35 24 24
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.047 0.16 -10000 0 -0.37 43 43
HRAS/GTP -0.06 0.12 -10000 0 -0.6 4 4
Ephrin B1/EPHB1-2 -0.017 0.11 -10000 0 -0.37 17 17
cell adhesion mediated by integrin 0.041 0.12 0.38 25 -10000 0 25
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.035 0.15 -10000 0 -0.34 41 41
RAC1-CDC42/GTP -0.072 0.14 -10000 0 -0.59 8 8
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.14 -10000 0 -0.44 10 10
ruffle organization -0.026 0.15 -10000 0 -0.56 7 7
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.003 0.12 -10000 0 -0.34 24 24
Ephrin B/EPHB2/KALRN -0.012 0.13 -10000 0 -0.38 26 26
ROCK1 -0.004 0.095 -10000 0 -0.37 16 16
RAS family/GDP -0.052 0.1 -10000 0 -0.45 7 7
Rac1/GTP -0.067 0.14 -10000 0 -0.59 7 7
Ephrin B/EPHB1/Src/Paxillin -0.028 0.12 -10000 0 -0.3 39 39
IL27-mediated signaling events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.071 -10000 0 -0.65 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.046 0.2 0.83 11 -10000 0 11
IL27/IL27R/JAK1 -0.062 0.25 -10000 0 -1.1 11 11
TBX21 -0.075 0.24 -10000 0 -0.62 33 33
IL12B 0.002 0.05 -10000 0 -0.4 4 4
IL12A -0.048 0.15 -10000 0 -0.4 36 36
IL6ST 0.006 0.048 -10000 0 -0.52 2 2
IL27RA/JAK1 -0.035 0.23 -10000 0 -1.3 8 8
IL27 -0.013 0.1 -10000 0 -0.49 11 11
TYK2 0.011 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.042 0.11 -10000 0 -0.76 1 1
T-helper 2 cell differentiation 0.046 0.2 0.83 11 -10000 0 11
T cell proliferation during immune response 0.046 0.2 0.83 11 -10000 0 11
MAPKKK cascade -0.046 0.2 -10000 0 -0.83 11 11
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.025 -10000 0 -0.39 1 1
IL12RB1 -0.054 0.19 -10000 0 -0.59 28 28
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.21 -10000 0 -0.59 23 23
IL27/IL27R/JAK2/TYK2 -0.047 0.2 -10000 0 -0.85 11 11
positive regulation of T cell mediated cytotoxicity -0.046 0.2 -10000 0 -0.83 11 11
STAT1 (dimer) -0.1 0.26 0.5 5 -0.91 16 21
JAK2 0.009 0.041 -10000 0 -0.65 1 1
JAK1 0.011 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.038 0.19 -10000 0 -0.79 11 11
T cell proliferation -0.09 0.23 -10000 0 -0.73 18 18
IL12/IL12R/TYK2/JAK2 -0.05 0.15 -10000 0 -0.6 8 8
IL17A -0.042 0.11 -10000 0 -0.76 1 1
mast cell activation 0.046 0.2 0.83 11 -10000 0 11
IFNG -0.012 0.041 -10000 0 -0.12 23 23
T cell differentiation -0.005 0.007 0.013 1 -0.022 27 28
STAT3 (dimer) -0.038 0.19 -10000 0 -0.79 11 11
STAT5A (dimer) -0.041 0.19 -10000 0 -0.76 12 12
STAT4 (dimer) -0.069 0.23 -10000 0 -0.74 18 18
STAT4 -0.049 0.18 -10000 0 -0.59 26 26
T cell activation -0.001 0.025 0.088 17 -10000 0 17
IL27R/JAK2/TYK2 -0.032 0.22 -10000 0 -1.2 8 8
GATA3 -0.12 0.39 -10000 0 -1.3 24 24
IL18 -0.011 0.095 -10000 0 -0.44 12 12
positive regulation of mast cell cytokine production -0.037 0.18 -10000 0 -0.76 11 11
IL27/EBI3 -0.039 0.15 -10000 0 -0.49 24 24
IL27RA -0.044 0.24 -10000 0 -1.4 8 8
IL6 -0.094 0.21 -10000 0 -0.49 55 55
STAT5A 0.006 0.058 -10000 0 -0.65 2 2
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.022 0.095 0.49 8 -10000 0 8
IL1B -0.026 0.12 -10000 0 -0.43 21 21
EBI3 -0.042 0.17 -10000 0 -0.58 23 23
TNF -0.057 0.16 -10000 0 -0.42 40 40
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.003 0.078 -10000 0 -0.42 3 3
epithelial cell differentiation -0.063 0.1 -10000 0 -0.39 2 2
ITCH 0.017 0.015 -10000 0 -10000 0 0
WWP1 0.01 0.056 -10000 0 -10000 0 0
FYN -0.002 0.077 -10000 0 -0.43 8 8
EGFR -0.011 0.12 -10000 0 -0.57 10 10
PRL -0.012 0.08 -10000 0 -0.39 11 11
neuron projection morphogenesis -0.043 0.14 -10000 0 -0.5 2 2
PTPRZ1 -0.042 0.15 -10000 0 -0.45 29 29
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.15 -10000 0 -0.46 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.082 0.16 -10000 0 -0.38 40 40
ADAM17 0.017 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 0.005 0.072 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.18 -10000 0 -0.4 65 65
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.077 0.16 -10000 0 -0.5 9 9
GRIN2B -0.081 0.16 -10000 0 -0.49 12 12
ErbB4/ErbB2/betacellulin -0.007 0.1 -10000 0 -0.46 2 2
STAT1 0.01 0.025 -10000 0 -0.39 1 1
HBEGF 0.002 0.072 -10000 0 -0.5 5 5
PRLR -0.074 0.2 -10000 0 -0.49 44 44
E4ICDs/ETO2 -0.011 0.096 -10000 0 -0.37 8 8
axon guidance -0.011 0.075 -10000 0 -0.35 1 1
NEDD4 0.01 0.064 -10000 0 -0.55 3 3
Prolactin receptor/Prolactin receptor/Prolactin -0.061 0.16 -10000 0 -0.36 51 51
CBFA2T3 -0.022 0.13 -10000 0 -0.48 18 18
ErbB4/ErbB2/HBEGF 0.013 0.064 -10000 0 -0.4 2 2
MAPK3 -0.048 0.14 -10000 0 -0.52 2 2
STAT1 (dimer) 0.008 0.062 -10000 0 -10000 0 0
MAPK1 -0.05 0.14 -10000 0 -0.52 2 2
JAK2 0.009 0.041 -10000 0 -0.65 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.073 0.15 -10000 0 -0.48 8 8
NRG1 -0.1 0.19 -10000 0 -0.37 84 84
NRG3 -0.2 0.28 -10000 0 -0.57 93 93
NRG2 -0.057 0.18 -10000 0 -0.5 35 35
NRG4 -0.13 0.27 -10000 0 -0.61 61 61
heart development -0.011 0.075 -10000 0 -0.35 1 1
neural crest cell migration -0.072 0.15 -10000 0 -0.48 8 8
ERBB2 0.02 0.033 -10000 0 -0.27 3 3
WWOX/E4ICDs 0.007 0.065 -10000 0 -0.38 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.08 0.18 -10000 0 -0.51 16 16
apoptosis 0.13 0.19 0.42 62 -10000 0 62
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.031 0.12 -10000 0 -0.38 22 22
ErbB4/ErbB2/epiregulin -0.034 0.12 -10000 0 -0.49 2 2
ErbB4/ErbB4/betacellulin/betacellulin -0.02 0.11 -10000 0 -0.4 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.051 0.12 -10000 0 -0.46 6 6
MDM2 0.01 0.065 -10000 0 -0.36 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.092 0.14 -10000 0 -0.45 6 6
STAT5A -0.007 0.078 -10000 0 -0.4 1 1
ErbB4/EGFR/neuregulin 1 beta -0.083 0.16 -10000 0 -0.49 9 9
DLG4 0.004 0.071 -10000 0 -0.65 3 3
GRB2/SHC 0.017 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.018 0.046 -10000 0 -10000 0 0
STAT5A (dimer) -0.066 0.11 -10000 0 -0.43 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.005 0.07 -10000 0 -10000 0 0
LRIG1 0.001 0.079 -10000 0 -0.55 5 5
EREG -0.084 0.21 -10000 0 -0.54 45 45
BTC -0.035 0.16 -10000 0 -0.57 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.011 0.076 -10000 0 -10000 0 0
ERBB4 0.005 0.072 -10000 0 -10000 0 0
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.006 0.02 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.062 0.16 -10000 0 -0.46 14 14
glial cell differentiation 0.018 0.046 -10000 0 -10000 0 0
WWOX 0.009 0.041 -10000 0 -0.65 1 1
cell proliferation -0.093 0.17 -10000 0 -0.47 20 20
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.005 0.1 -9999 0 -0.62 7 7
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.098 0.16 -9999 0 -0.41 38 38
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.082 0.15 -9999 0 -0.37 38 38
IQGAP1/CaM 0.017 0 -9999 0 -10000 0 0
DAB1 -0.063 0.17 -9999 0 -0.45 41 41
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 -0.022 0.14 -9999 0 -0.57 15 15
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.035 -9999 0 -0.48 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 0.012 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.097 0.23 -9999 0 -0.55 50 50
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.15 0.2 -9999 0 -0.46 58 58
YWHAE 0.009 0.041 -9999 0 -0.65 1 1
NDEL1/14-3-3 E -0.082 0.15 -9999 0 -0.43 18 18
MAP1B -0.006 0.042 -9999 0 -0.33 4 4
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.06 0.13 -9999 0 -0.32 38 38
RELN -0.18 0.26 -9999 0 -0.49 100 100
PAFAH/LIS1 0.002 0.088 -9999 0 -0.41 10 10
LIS1/CLIP170 0.023 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.079 0.1 -9999 0 -0.41 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.073 0.14 -9999 0 -0.5 9 9
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.091 0.16 -9999 0 -0.46 18 18
LIS1/IQGAP1 0.023 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.019 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0 -9999 0 -10000 0 0
PAFAH1B2 0.012 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.029 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.073 0.15 -9999 0 -0.41 18 18
LRP8 0.007 0.048 -9999 0 -0.52 2 2
NDEL1/Katanin 60 -0.08 0.15 -9999 0 -0.43 18 18
P39/CDK5 -0.12 0.18 -9999 0 -0.38 65 65
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0 -9999 0 -10000 0 0
CDK5 -0.07 0.14 -9999 0 -0.34 38 38
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.12 0.17 -9999 0 -0.38 58 58
RELN/VLDLR -0.091 0.16 -9999 0 -0.39 43 43
CDC42 0 0 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.039 0.17 -9999 0 -0.6 21 21
PDGF/PDGFRA/CRKL -0.019 0.12 -9999 0 -0.43 21 21
positive regulation of JUN kinase activity 0.001 0.095 -9999 0 -0.35 17 17
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.031 0.14 -9999 0 -0.41 28 28
AP1 -0.081 0.22 -9999 0 -0.95 11 11
mol:IP3 -0.019 0.13 -9999 0 -0.44 21 21
PLCG1 -0.02 0.13 -9999 0 -0.44 21 21
PDGF/PDGFRA/alphaV Integrin -0.019 0.12 -9999 0 -0.47 17 17
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.008 0.035 -9999 0 -0.39 2 2
mol:Ca2+ -0.019 0.13 -9999 0 -0.44 21 21
CAV3 -0.006 0.074 -9999 0 -0.39 9 9
CAV1 0 0.073 -9999 0 -0.43 7 7
SHC/Grb2/SOS1 0.002 0.096 -9999 0 -0.35 17 17
PDGF/PDGFRA/Shf -0.022 0.13 -9999 0 -0.44 22 22
FOS -0.049 0.22 -9999 0 -0.93 11 11
JUN -0.011 0.046 -9999 0 -0.4 3 3
oligodendrocyte development -0.019 0.12 -9999 0 -0.47 17 17
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
mol:DAG -0.019 0.13 -9999 0 -0.44 21 21
PDGF/PDGFRA -0.039 0.17 -9999 0 -0.6 21 21
actin cytoskeleton reorganization -0.019 0.12 -9999 0 -0.43 21 21
SRF 0.02 0.007 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.009 0.11 -9999 0 -0.39 17 17
PDGF/PDGFRA/Crk/C3G -0.009 0.11 -9999 0 -0.4 17 17
JAK1 -0.017 0.12 -9999 0 -0.43 21 21
ELK1/SRF 0.002 0.097 -9999 0 -0.35 17 17
SHB 0.012 0 -9999 0 -10000 0 0
SHF 0.007 0.048 -9999 0 -0.52 2 2
CSNK2A1 0.007 0.016 -9999 0 -10000 0 0
GO:0007205 -0.02 0.13 -9999 0 -0.5 17 17
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.001 0.095 -9999 0 -0.35 17 17
PDGF/PDGFRA/SHB -0.019 0.12 -9999 0 -0.43 21 21
PDGF/PDGFRA/Caveolin-1 -0.027 0.14 -9999 0 -0.44 25 25
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 -0.013 0.12 -9999 0 -0.42 18 18
PIK3CA 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.021 0.13 -9999 0 -0.43 22 22
JAK-STAT cascade -0.017 0.12 -9999 0 -0.42 21 21
cell proliferation -0.022 0.13 -9999 0 -0.44 22 22
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.089 -9999 0 -0.46 6 6
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.11 -9999 0 -0.38 7 7
AP1 -0.069 0.15 -9999 0 -0.38 37 37
mol:PIP3 -0.05 0.12 -9999 0 -0.51 5 5
AKT1 0.03 0.07 -9999 0 -0.43 3 3
PTK2B 0.005 0.067 -9999 0 -0.32 5 5
RHOA 0.019 0.035 -9999 0 -10000 0 0
PIK3CB 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ -0.003 0.098 -9999 0 -0.3 23 23
MAGI3 0.009 0.041 -9999 0 -0.65 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.026 0.13 -9999 0 -0.36 29 29
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.095 -9999 0 -0.31 13 13
NF kappa B1 p50/RelA -0.047 0.11 -9999 0 -0.43 9 9
endothelial cell migration -0.011 0.15 -9999 0 -0.61 14 14
ADCY4 -0.034 0.14 -9999 0 -0.51 14 14
ADCY5 -0.041 0.15 -9999 0 -0.48 18 18
ADCY6 -0.024 0.14 -9999 0 -0.52 12 12
ADCY7 -0.025 0.14 -9999 0 -0.52 12 12
ADCY1 -0.038 0.16 -9999 0 -0.58 14 14
ADCY2 -0.064 0.17 -9999 0 -0.53 21 21
ADCY3 -0.024 0.14 -9999 0 -0.52 12 12
ADCY8 -0.088 0.16 -9999 0 -0.51 22 22
ADCY9 -0.027 0.14 -9999 0 -0.51 13 13
GSK3B 0.011 0.064 -9999 0 -0.31 4 4
arachidonic acid secretion -0.024 0.14 -9999 0 -0.51 12 12
GNG2 0.007 0.043 -9999 0 -0.4 3 3
TRIP6 0.02 0.01 -9999 0 -10000 0 0
GNAO1 -0.065 0.17 -9999 0 -0.44 33 33
HRAS 0.012 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.12 -9999 0 -0.36 23 23
GAB1 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.008 0.12 -9999 0 -0.91 4 4
JUN 0.006 0.054 -9999 0 -0.48 3 3
LPA/LPA2/NHERF2 0.014 0.017 -9999 0 -10000 0 0
TIAM1 -0.015 0.13 -9999 0 -1.1 4 4
PIK3R1 0.008 0.035 -9999 0 -0.4 2 2
mol:IP3 -0.004 0.1 -9999 0 -0.3 23 23
PLCB3 0.021 0.015 -9999 0 -10000 0 0
FOS -0.038 0.15 -9999 0 -0.48 26 26
positive regulation of mitosis -0.024 0.14 -9999 0 -0.51 12 12
LPA/LPA1-2-3 -0.032 0.14 -9999 0 -0.4 29 29
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
stress fiber formation 0.001 0.089 -9999 0 -0.35 6 6
GNAZ -0.001 0.1 -9999 0 -0.44 12 12
EGFR/PI3K-beta/Gab1 -0.052 0.12 -9999 0 -0.54 5 5
positive regulation of dendritic cell cytokine production -0.032 0.14 -9999 0 -0.39 29 29
LPA/LPA2/MAGI-3 0.013 0.031 -9999 0 -0.41 1 1
ARHGEF1 0.013 0.085 -9999 0 -0.42 7 7
GNAI2 0.003 0.094 -9999 0 -0.4 11 11
GNAI3 0.003 0.094 -9999 0 -0.4 11 11
GNAI1 -0.005 0.11 -9999 0 -0.43 15 15
LPA/LPA3 -0.041 0.14 -9999 0 -0.46 27 27
LPA/LPA2 0.006 0.021 -9999 0 -10000 0 0
LPA/LPA1 -0.009 0.11 -9999 0 -0.46 12 12
HB-EGF/EGFR -0.069 0.16 -9999 0 -0.42 39 39
HBEGF -0.07 0.17 -9999 0 -0.38 58 58
mol:DAG -0.004 0.1 -9999 0 -0.3 23 23
cAMP biosynthetic process -0.056 0.16 -9999 0 -0.43 30 30
NFKB1 0.009 0.041 -9999 0 -0.65 1 1
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
LYN -0.007 0.13 -9999 0 -0.37 25 25
GNAQ -0.017 0.11 -9999 0 -0.34 24 24
LPAR2 0.011 0 -9999 0 -10000 0 0
LPAR3 -0.053 0.19 -9999 0 -0.61 27 27
LPAR1 -0.008 0.12 -9999 0 -0.66 7 7
IL8 -0.083 0.19 -9999 0 -0.47 33 33
PTK2 -0.021 0.13 -9999 0 -0.37 29 29
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.026 0.13 -9999 0 -0.36 29 29
EGFR -0.011 0.12 -9999 0 -0.57 10 10
PLCG1 -0.019 0.12 -9999 0 -0.36 23 23
PLD2 -0.021 0.13 -9999 0 -0.37 29 29
G12/G13 0.008 0.09 -9999 0 -0.36 12 12
PI3K-beta -0.016 0.062 -9999 0 -0.52 2 2
cell migration -0.017 0.054 -9999 0 -0.27 4 4
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
PXN 0 0.091 -9999 0 -0.36 6 6
HRAS/GTP -0.026 0.14 -9999 0 -0.52 12 12
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.1 0.23 -9999 0 -0.54 53 53
PRKCE 0.012 0 -9999 0 -10000 0 0
PRKCD 0.001 0.1 -9999 0 -0.39 5 5
Gi(beta/gamma) -0.022 0.14 -9999 0 -0.5 12 12
mol:LPA -0.002 0.032 -9999 0 -0.2 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.04 0.11 -9999 0 -0.46 5 5
MAPKKK cascade -0.024 0.14 -9999 0 -0.51 12 12
contractile ring contraction involved in cytokinesis 0.019 0.034 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.027 0.12 -9999 0 -0.36 28 28
GNA15 -0.028 0.12 -9999 0 -0.34 31 31
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.041 -9999 0 -0.65 1 1
MAPT -0.008 0.098 -9999 0 -0.32 13 13
GNA11 -0.016 0.1 -9999 0 -0.34 23 23
Rac1/GTP 0.008 0.12 -9999 0 -0.97 4 4
MMP2 -0.011 0.15 -9999 0 -0.61 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.007 0.048 -9999 0 -0.52 2 2
SVIL 0.007 0.048 -9999 0 -0.52 2 2
ZNF318 0.012 0.011 -9999 0 -10000 0 0
JMJD2C 0.001 0.018 -9999 0 -0.074 13 13
T-DHT/AR/Ubc9 -0.053 0.15 -9999 0 -0.43 31 31
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.012 0.001 -9999 0 -10000 0 0
PELP1 0.012 0.002 -9999 0 -10000 0 0
CTNNB1 0.012 0.002 -9999 0 -10000 0 0
AKT1 0.009 0.035 -9999 0 -0.39 2 2
PTK2B 0.006 0.058 -9999 0 -0.65 2 2
MED1 0.012 0.003 -9999 0 -10000 0 0
MAK -0.015 0.11 -9999 0 -0.46 15 15
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.012 0.003 -9999 0 -10000 0 0
GSN 0.004 0.071 -9999 0 -0.65 3 3
NCOA2 0.009 0.041 -9999 0 -0.65 1 1
NCOA6 0.012 0.002 -9999 0 -10000 0 0
DNA-PK 0.024 0.011 -9999 0 -10000 0 0
NCOA4 0.012 0 -9999 0 -10000 0 0
PIAS3 0.01 0.025 -9999 0 -0.39 1 1
cell proliferation -0.036 0.11 -9999 0 -0.68 5 5
XRCC5 0.012 0.002 -9999 0 -10000 0 0
UBE3A 0.011 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.2 -9999 0 -0.46 59 59
FHL2 -0.026 0.17 -9999 0 -1 6 6
RANBP9 0.012 0.002 -9999 0 -10000 0 0
JMJD1A -0.026 0.063 -9999 0 -0.12 76 76
CDK6 -0.024 0.14 -9999 0 -0.6 15 15
TGFB1I1 0.006 0.054 -9999 0 -0.48 3 3
T-DHT/AR/CyclinD1 -0.097 0.21 -9999 0 -0.49 50 50
XRCC6 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.066 0.17 -9999 0 -0.43 36 36
CTDSP1 0.011 0.002 -9999 0 -10000 0 0
CTDSP2 0.012 0.007 -9999 0 -10000 0 0
BRCA1 -0.052 0.2 -9999 0 -0.65 25 25
TCF4 0.008 0.048 -9999 0 -0.52 2 2
CDKN2A -0.13 0.27 -9999 0 -0.65 55 55
SRF 0.016 0.019 -9999 0 -10000 0 0
NKX3-1 -0.095 0.25 -9999 0 -0.98 15 15
KLK3 -0.005 0.071 -9999 0 -10000 0 0
TMF1 0.011 0.002 -9999 0 -10000 0 0
HNRNPA1 0.012 0.004 -9999 0 -10000 0 0
AOF2 0 0.005 -9999 0 -10000 0 0
APPL1 0.017 0.026 -9999 0 -0.27 2 2
T-DHT/AR/Caspase 8 -0.053 0.15 -9999 0 -0.43 31 31
AR -0.082 0.22 -9999 0 -0.65 32 32
UBA3 0.011 0.002 -9999 0 -10000 0 0
PATZ1 0.01 0.025 -9999 0 -0.4 1 1
PAWR 0.011 0.002 -9999 0 -10000 0 0
PRKDC 0.012 0.002 -9999 0 -10000 0 0
PA2G4 0.012 0.004 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.047 0.14 -9999 0 -0.4 31 31
RPS6KA3 0.011 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.053 0.15 -9999 0 -0.43 31 31
LATS2 0.012 0.004 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.047 0.14 -9999 0 -0.4 31 31
Cyclin D3/CDK11 p58 0.009 0.001 -9999 0 -10000 0 0
VAV3 -0.13 0.25 -9999 0 -0.55 67 67
KLK2 -0.049 0.095 -9999 0 -0.47 5 5
CASP8 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.042 0.14 -9999 0 -0.4 31 31
TMPRSS2 -0.19 0.37 -9999 0 -1 39 39
CCND1 -0.059 0.2 -9999 0 -0.62 29 29
PIAS1 0.011 0.006 -9999 0 -10000 0 0
mol:T-DHT -0.015 0.032 -9999 0 -0.074 45 45
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.011 0.01 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.074 0.18 -9999 0 -0.47 40 40
CMTM2 -0.012 0.11 -9999 0 -0.54 11 11
SNURF -0.073 0.22 -9999 0 -0.65 33 33
ZMIZ1 -0.001 0.029 -9999 0 -10000 0 0
CCND3 0.012 0 -9999 0 -10000 0 0
TGIF1 0.012 0.004 -9999 0 -10000 0 0
FKBP4 0.012 0.002 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.014 0.14 -9999 0 -0.51 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0 0.16 -9999 0 -0.62 10 10
alphaV/beta3 Integrin/Osteopontin/Src -0.006 0.12 -9999 0 -0.49 13 13
AP1 -0.023 0.19 -9999 0 -0.73 10 10
ILK -0.021 0.15 -9999 0 -0.51 11 11
bone resorption -0.002 0.14 -9999 0 -0.7 4 4
PTK2B 0.006 0.058 -9999 0 -0.65 2 2
PYK2/p130Cas -0.01 0.14 -9999 0 -0.46 11 11
ITGAV 0.014 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.01 0.061 -9999 0 -0.48 4 4
alphaV/beta3 Integrin/Osteopontin -0.032 0.16 -9999 0 -0.48 23 23
MAP3K1 -0.023 0.15 -9999 0 -0.44 24 24
JUN 0.006 0.054 -9999 0 -0.48 3 3
MAPK3 -0.015 0.15 -9999 0 -0.55 12 12
MAPK1 -0.017 0.16 -9999 0 -0.53 13 13
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.009 0.041 -9999 0 -0.65 1 1
MAPK8 -0.015 0.14 -9999 0 -0.49 13 13
ITGB3 -0.051 0.18 -9999 0 -0.49 34 34
NFKBIA -0.011 0.16 -9999 0 -0.63 11 11
FOS -0.038 0.15 -9999 0 -0.48 26 26
CD44 0.001 0.081 -9999 0 -0.65 4 4
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.038 0.28 -9999 0 -1.2 13 13
NF kappa B1 p50/RelA -0.053 0.14 -9999 0 -0.6 11 11
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.44 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.022 0.15 -9999 0 -0.43 23 23
VAV3 -0.091 0.21 -9999 0 -0.43 58 58
MAP3K14 -0.022 0.15 -9999 0 -0.44 24 24
ROCK2 0.012 0 -9999 0 -10000 0 0
SPP1 -0.024 0.15 -9999 0 -0.61 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.078 0.2 -9999 0 -0.56 20 20
MMP2 -0.02 0.18 -9999 0 -0.64 13 13
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.002 0.076 -9999 0 -0.39 9 9
ARNO/beta Arrestin1-2 -0.013 0.056 -9999 0 -0.4 2 2
EGFR -0.011 0.12 -9999 0 -0.57 10 10
EPHA2 0.009 0.041 -9999 0 -0.65 1 1
USP6 0.001 0.066 -9999 0 -0.39 7 7
IQSEC1 0.011 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.059 0.16 -9999 0 -0.38 50 50
ARRB2 -0.001 0.05 -9999 0 -0.38 1 1
mol:GTP 0.005 0.045 -9999 0 -0.2 8 8
ARRB1 0.012 0 -9999 0 -10000 0 0
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR -0.094 0.21 -9999 0 -0.48 56 56
EGF -0.07 0.2 -9999 0 -0.51 41 41
somatostatin receptor activity 0 0 -9999 0 -0.001 12 12
ARAP2 -0.004 0.099 -9999 0 -0.65 6 6
mol:GDP -0.032 0.084 -9999 0 -0.27 14 14
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 4 4
ITGA2B -0.026 0.15 -9999 0 -0.63 15 15
ARF6 0.011 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.035 -9999 0 -0.37 2 2
ADAP1 -0.01 0.12 -9999 0 -0.62 9 9
KIF13B 0.012 0 -9999 0 -10000 0 0
HGF/MET -0.055 0.18 -9999 0 -0.54 30 30
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.031 0.089 -9999 0 -0.27 12 12
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.042 0.14 -9999 0 -0.41 26 26
ADRB2 -0.009 0.11 -9999 0 -0.52 10 10
receptor agonist activity 0 0 -9999 0 0 14 14
actin filament binding 0 0 -9999 0 0 15 15
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.18 -9999 0 -0.49 34 34
GNAQ 0.009 0.041 -9999 0 -0.65 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 9 9
ARF6/GDP 0.007 0.093 -9999 0 -0.43 8 8
ARF6/GDP/GULP/ACAP1 -0.049 0.15 -9999 0 -0.43 26 26
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.029 0.13 -9999 0 -0.38 27 27
ACAP1 -0.01 0.12 -9999 0 -0.62 9 9
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.009 0.068 -9999 0 -0.54 1 1
EFNA1 0.009 0.041 -9999 0 -0.65 1 1
HGF -0.031 0.16 -9999 0 -0.57 19 19
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 13 13
endosomal lumen acidification 0 0 0 1 0 13 14
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.043 0.18 -9999 0 -0.61 23 23
GNAQ/ARNO 0.012 0.023 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 3 3
MET -0.046 0.18 -9999 0 -0.61 24 24
GNA14 -0.011 0.11 -9999 0 -0.51 11 11
GNA15 -0.01 0.12 -9999 0 -0.62 9 9
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 10 10
GNA11 0.011 0 -9999 0 -10000 0 0
LHCGR -0.022 0.11 -9999 0 -0.41 19 19
AGTR1 -0.04 0.16 -9999 0 -0.48 27 27
desensitization of G-protein coupled receptor protein signaling pathway -0.009 0.068 -9999 0 -0.54 1 1
IPCEF1/ARNO -0.031 0.11 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.058 0.17 -9999 0 -0.4 47 47
Signaling events mediated by PTP1B

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
PDGFRB 0.004 0.059 -10000 0 -0.46 4 4
Jak2/Leptin Receptor -0.051 0.11 -10000 0 -0.43 13 13
PTP1B/AKT1 -0.026 0.095 -10000 0 -0.39 8 8
FYN -0.002 0.077 -10000 0 -0.43 8 8
p210 bcr-abl/PTP1B -0.034 0.1 -10000 0 -0.37 11 11
EGFR -0.013 0.12 -10000 0 -0.58 10 10
EGF/EGFR -0.081 0.14 -10000 0 -0.39 33 33
CSF1 -0.021 0.14 -10000 0 -0.63 13 13
AKT1 0.008 0.035 -10000 0 -0.4 2 2
INSR 0.01 0.025 -10000 0 -0.39 1 1
PTP1B/N-cadherin -0.081 0.16 -10000 0 -0.4 42 42
Insulin Receptor/Insulin -0.03 0.066 -10000 0 -0.39 3 3
HCK -0.014 0.13 -10000 0 -0.65 10 10
CRK 0.008 0.035 -10000 0 -0.39 2 2
TYK2 -0.027 0.098 -10000 0 -0.4 8 8
EGF -0.071 0.2 -10000 0 -0.51 41 41
YES1 0.01 0.025 -10000 0 -0.39 1 1
CAV1 -0.032 0.1 -10000 0 -0.33 13 13
TXN 0.009 0.025 -10000 0 -0.39 1 1
PTP1B/IRS1/GRB2 -0.025 0.11 -10000 0 -0.48 9 9
cell migration 0.034 0.1 0.37 11 -10000 0 11
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.075 0.2 -10000 0 -0.5 44 44
ITGA2B -0.026 0.15 -10000 0 -0.64 15 15
CSF1R -0.021 0.14 -10000 0 -0.6 14 14
Prolactin Receptor/Prolactin -0.067 0.16 -10000 0 -0.48 23 23
FGR -0.007 0.1 -10000 0 -0.54 9 9
PTP1B/p130 Cas -0.027 0.098 -10000 0 -0.4 8 8
Crk/p130 Cas -0.022 0.094 -10000 0 -0.42 6 6
DOK1 -0.019 0.09 -10000 0 -0.37 7 7
JAK2 -0.041 0.11 -10000 0 -0.43 14 14
Jak2/Leptin Receptor/Leptin -0.067 0.13 -10000 0 -0.48 13 13
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
PTPN1 -0.035 0.1 -10000 0 -0.38 11 11
LYN 0.004 0.071 -10000 0 -0.65 3 3
CDH2 -0.091 0.23 -10000 0 -0.61 43 43
SRC 0.001 0.039 -10000 0 -10000 0 0
ITGB3 -0.055 0.18 -10000 0 -0.49 34 34
CAT1/PTP1B -0.062 0.16 -10000 0 -0.5 19 19
CAPN1 0.012 0.002 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.025 0.06 -10000 0 -0.39 2 2
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.061 0.13 -10000 0 -0.5 12 12
negative regulation of transcription -0.04 0.11 -10000 0 -0.42 14 14
FCGR2A -0.013 0.12 -10000 0 -0.63 10 10
FER 0.004 0.063 -10000 0 -0.57 3 3
alphaIIb/beta3 Integrin -0.061 0.17 -10000 0 -0.4 47 47
BLK -0.076 0.19 -10000 0 -0.46 47 47
Insulin Receptor/Insulin/Shc 0.015 0.015 -10000 0 -10000 0 0
RHOA 0.012 0.002 -10000 0 -10000 0 0
LEPR -0.001 0.08 -10000 0 -0.47 7 7
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.051 0.17 -10000 0 -0.57 15 15
PRL -0.014 0.082 -10000 0 -0.4 11 11
SOCS3 -0.021 0.21 -10000 0 -1.4 6 6
SPRY2 -0.035 0.16 -10000 0 -0.55 22 22
Insulin Receptor/Insulin/IRS1 0.009 0.051 -10000 0 -0.42 3 3
CSF1/CSF1R -0.053 0.16 -10000 0 -0.46 24 24
Ras protein signal transduction 0.022 0.029 -10000 0 -10000 0 0
IRS1 0.002 0.075 -10000 0 -0.59 4 4
INS 0 0.002 -10000 0 -10000 0 0
LEP -0.036 0.15 -10000 0 -0.49 24 24
STAT5B -0.034 0.098 -10000 0 -0.34 15 15
STAT5A -0.035 0.1 -10000 0 -0.34 16 16
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.03 0.1 -10000 0 -0.38 10 10
CSN2 -0.019 0.077 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
LAT -0.023 0.12 -10000 0 -0.57 11 11
YBX1 0.016 0.025 -10000 0 -0.38 1 1
LCK -0.03 0.16 -10000 0 -0.59 18 18
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.1 0.22 -10000 0 -0.49 58 58
Syndecan-3-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
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.023 0.12 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.007 0.044 -9999 0 -10000 0 0
POMC -0.031 0.14 -9999 0 -0.45 24 24
EGFR -0.011 0.12 -9999 0 -0.57 10 10
Syndecan-3/EGFR 0.01 0.062 -9999 0 -0.34 7 7
AGRP 0.007 0.035 -9999 0 -0.39 2 2
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.013 0.091 -9999 0 -0.39 14 14
long-term memory 0.021 0.037 -9999 0 -0.32 1 1
Syndecan-3/IL8 -0.02 0.1 -9999 0 -0.34 15 15
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.017 0 -9999 0 -10000 0 0
FYN -0.002 0.077 -9999 0 -0.43 8 8
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.15 0.25 -9999 0 -0.5 80 80
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.1 0.23 -9999 0 -0.54 54 54
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.033 0.12 -9999 0 -0.46 2 2
Syndecan-3/AgRP 0.017 0.019 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.057 0.13 -9999 0 -0.32 34 34
Fyn/Cortactin 0.008 0.055 -9999 0 -0.29 8 8
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.02 0.099 -9999 0 -0.34 15 15
IL8 -0.072 0.19 -9999 0 -0.48 44 44
Syndecan-3/Fyn/Cortactin 0.022 0.037 -9999 0 -0.32 1 1
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.13 0.2 -9999 0 -0.37 97 97
Gamma Secretase 0.034 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.007 0.1 -9999 0 -0.54 9 9
ELF1 -0.012 0.1 -9999 0 -0.36 20 20
CCNA2 0.002 0.075 -9999 0 -0.59 4 4
PIK3CA 0.012 0 -9999 0 -10000 0 0
JAK3 0.002 0.082 -9999 0 -0.65 4 4
PIK3R1 0.009 0.035 -9999 0 -0.39 2 2
JAK1 0.012 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.019 0.2 -9999 0 -0.55 25 25
SHC1 0.012 0 -9999 0 -10000 0 0
SP1 -0.009 0.07 -9999 0 -10000 0 0
IL2RA -0.045 0.24 -9999 0 -0.83 22 22
IL2RB -0.061 0.2 -9999 0 -0.6 31 31
SOS1 0.012 0 -9999 0 -10000 0 0
IL2RG -0.05 0.19 -9999 0 -0.61 26 26
G1/S transition of mitotic cell cycle -0.027 0.13 -9999 0 -0.45 15 15
PTPN11 0.012 0 -9999 0 -10000 0 0
CCND2 -0.024 0.13 -9999 0 -0.34 35 35
LCK -0.03 0.16 -9999 0 -0.59 18 18
GRB2 0.012 0 -9999 0 -10000 0 0
IL2 0.001 0.035 -9999 0 -0.39 2 2
CDK6 -0.024 0.14 -9999 0 -0.6 15 15
CCND3 -0.006 0.17 -9999 0 -0.56 14 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.008 0.12 -10000 0 -0.4 15 15
CRKL -0.008 0.11 -10000 0 -0.41 12 12
HRAS -0.031 0.16 -10000 0 -0.52 12 12
mol:PIP3 -0.018 0.11 -10000 0 -0.38 13 13
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.015 0.12 -10000 0 -0.42 13 13
FOXO3 -0.003 0.1 -10000 0 -0.37 12 12
AKT1 -0.009 0.11 -10000 0 -0.39 13 13
BAD -0.002 0.1 -10000 0 -0.37 12 12
megakaryocyte differentiation -0.025 0.13 -10000 0 -0.41 20 20
GSK3B -0.002 0.1 -10000 0 -0.37 12 12
RAF1 -0.016 0.13 -10000 0 -0.42 11 11
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.015 0.12 -10000 0 -0.41 14 14
STAT1 -0.042 0.26 -10000 0 -0.97 15 15
HRAS/SPRED1 -0.018 0.13 -10000 0 -0.42 11 11
cell proliferation -0.014 0.12 -10000 0 -0.42 13 13
PIK3CA 0.012 0 -10000 0 -10000 0 0
TEC 0.002 0.075 -10000 0 -0.59 4 4
RPS6KB1 -0.013 0.12 -10000 0 -0.42 13 13
HRAS/SPRED2 -0.018 0.13 -10000 0 -0.42 11 11
LYN/TEC/p62DOK -0.011 0.13 -10000 0 -0.43 17 17
MAPK3 -0.001 0.097 -10000 0 -0.32 7 7
STAP1 -0.048 0.15 -10000 0 -0.4 30 30
GRAP2 -0.068 0.2 -10000 0 -0.58 35 35
JAK2 -0.035 0.22 -10000 0 -0.82 15 15
STAT1 (dimer) -0.04 0.25 -10000 0 -0.95 15 15
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.026 0.15 -10000 0 -0.46 17 17
actin filament polymerization -0.016 0.12 -10000 0 -0.44 14 14
LYN 0.004 0.071 -10000 0 -0.65 3 3
STAP1/STAT5A (dimer) -0.049 0.18 -10000 0 -0.6 17 17
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
CBL/CRKL/GRB2 0.005 0.1 -10000 0 -0.36 12 12
PI3K -0.004 0.11 -10000 0 -0.4 12 12
PTEN 0.001 0.081 -10000 0 -0.65 4 4
SCF/KIT/EPO/EPOR -0.052 0.31 -10000 0 -1.3 14 14
MAPK8 -0.015 0.12 -10000 0 -0.42 13 13
STAT3 (dimer) -0.014 0.12 -10000 0 -0.4 14 14
positive regulation of transcription 0.003 0.082 -10000 0 -0.25 7 7
mol:GDP -0.04 0.17 -10000 0 -0.46 24 24
PIK3C2B -0.017 0.12 -10000 0 -0.41 15 15
CBL/CRKL -0.001 0.11 -10000 0 -0.38 12 12
FER -0.018 0.12 -10000 0 -0.44 14 14
SH2B3 -0.015 0.12 -10000 0 -0.42 13 13
PDPK1 -0.011 0.1 -10000 0 -0.36 12 12
SNAI2 -0.025 0.13 -10000 0 -0.44 18 18
positive regulation of cell proliferation -0.027 0.19 -10000 0 -0.71 15 15
KITLG 0.006 0.052 -10000 0 -0.4 4 4
cell motility -0.027 0.19 -10000 0 -0.71 15 15
PTPN6 0.012 0.007 -10000 0 -10000 0 0
EPOR -0.002 0.14 -10000 0 -0.92 3 3
STAT5A (dimer) -0.022 0.16 -10000 0 -0.59 15 15
SOCS1 -0.002 0.088 -10000 0 -0.57 6 6
cell migration 0.051 0.17 0.45 30 -10000 0 30
SOS1 0.012 0 -10000 0 -10000 0 0
EPO 0.004 0.037 -10000 0 -0.41 2 2
VAV1 -0.022 0.14 -10000 0 -0.62 14 14
GRB10 -0.015 0.12 -10000 0 -0.42 13 13
PTPN11 0.012 0.005 -10000 0 -10000 0 0
SCF/KIT -0.022 0.12 -10000 0 -0.41 17 17
GO:0007205 0 0.007 -10000 0 -10000 0 0
MAP2K1 -0.005 0.1 -10000 0 -0.34 8 8
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.061 0.3 -10000 0 -1.3 12 12
MAP2K2 -0.005 0.1 -10000 0 -0.34 8 8
SHC/Grb2/SOS1 -0.003 0.11 -10000 0 -0.4 12 12
STAT5A -0.023 0.17 -10000 0 -0.61 15 15
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.024 0.13 -10000 0 -0.43 18 18
SHC/GRAP2 -0.042 0.15 -10000 0 -0.42 35 35
PTPRO -0.026 0.13 -10000 0 -0.41 20 20
SH2B2 -0.017 0.12 -10000 0 -0.45 14 14
DOK1 0.012 0 -10000 0 -10000 0 0
MATK -0.052 0.17 -10000 0 -0.46 30 30
CREBBP 0.022 0.03 -10000 0 -10000 0 0
BCL2 -0.003 0.16 -10000 0 -1.2 3 3
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.045 -10000 0 -0.66 1 1
HSPA8 0.01 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.018 0.11 0.22 2 -0.44 14 16
AKT1 0.007 0.043 -10000 0 -0.44 2 2
GSC -0.3 0.53 -10000 0 -1.3 51 51
NKX2-5 -0.15 0.25 -10000 0 -0.5 80 80
muscle cell differentiation 0.12 0.16 0.49 29 -10000 0 29
SMAD2-3/SMAD4/SP1 0.018 0.086 -10000 0 -0.43 1 1
SMAD4 -0.003 0.052 -10000 0 -10000 0 0
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.011 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.01 0.12 -10000 0 -0.41 13 13
SMAD3/SMAD4/VDR 0.02 0.083 -10000 0 -0.43 3 3
MYC -0.011 0.12 -10000 0 -0.59 10 10
CDKN2B -0.047 0.3 -10000 0 -1.4 12 12
AP1 0.013 0.12 -10000 0 -0.57 6 6
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.03 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0 0.095 -10000 0 -0.37 7 7
SP3 0.014 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.085 0.19 -10000 0 -0.51 39 39
SMAD3/SMAD4/GR -0.001 0.082 -10000 0 -0.52 4 4
GATA3 -0.066 0.21 -10000 0 -0.6 32 32
SKI/SIN3/HDAC complex/NCoR1 0.028 0.033 -10000 0 -10000 0 0
MEF2C/TIF2 -0.12 0.18 -10000 0 -0.5 24 24
endothelial cell migration 0.035 0.23 1.2 7 -10000 0 7
MAX 0.014 0.011 -10000 0 -10000 0 0
RBBP7 0.011 0.002 -10000 0 -10000 0 0
RBBP4 0.009 0.025 -10000 0 -0.4 1 1
RUNX2 -0.013 0.12 -10000 0 -0.63 10 10
RUNX3 -0.086 0.22 -10000 0 -0.54 46 46
RUNX1 -0.008 0.11 -10000 0 -0.62 8 8
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.003 0.083 -10000 0 -0.65 4 4
VDR -0.004 0.099 -10000 0 -0.65 6 6
CDKN1A 0.031 0.16 -10000 0 -1.4 3 3
KAT2B 0.014 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.08 0.16 -10000 0 -0.46 26 26
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.011 0.002 -10000 0 -10000 0 0
SERPINE1 -0.035 0.24 -10000 0 -1.2 7 7
SMAD3/SMAD4/ATF2 0.007 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.014 0.094 -10000 0 -0.39 7 7
SAP30 0.006 0.058 -10000 0 -0.65 2 2
Cbp/p300/PIAS3 0.043 0.052 -10000 0 -0.43 1 1
JUN 0.013 0.12 -10000 0 -0.6 5 5
SMAD3/SMAD4/IRF7 -0.013 0.1 -10000 0 -0.42 9 9
TFE3 0.012 0.027 -10000 0 -0.38 1 1
COL1A2 -0.021 0.18 -10000 0 -1 8 8
mesenchymal cell differentiation 0.011 0.1 0.48 9 -10000 0 9
DLX1 -0.024 0.11 -10000 0 -0.41 21 21
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.034 0.16 -10000 0 -0.49 26 26
SMAD3/SMAD4/Max 0.005 0.052 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.026 0.038 -10000 0 -0.42 1 1
ZBTB17 0.012 0.011 -10000 0 -10000 0 0
LAMC1 0.029 0.049 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.007 0.05 -10000 0 -10000 0 0
IRF7 -0.014 0.12 -10000 0 -0.58 10 10
ESR1 -0.024 0.15 -10000 0 -0.65 14 14
HNF4A -0.027 0.11 -10000 0 -0.39 21 21
MEF2C -0.13 0.19 -10000 0 -0.48 37 37
SMAD2-3/SMAD4 -0.005 0.073 -10000 0 -0.5 1 1
Cbp/p300/Src-1 0.034 0.038 -10000 0 -0.42 1 1
IGHV3OR16-13 -0.014 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0 -10000 0 -10000 0 0
CREBBP 0.017 0.011 -10000 0 -10000 0 0
SKIL 0.009 0.041 -10000 0 -0.65 1 1
HDAC1 0.011 0.002 -10000 0 -10000 0 0
HDAC2 0.006 0.058 -10000 0 -0.65 2 2
SNIP1 0.006 0.036 -10000 0 -0.4 2 2
GCN5L2 0.006 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.031 0.059 -10000 0 -10000 0 0
MSG1/HSC70 -0.04 0.13 -10000 0 -0.33 39 39
SMAD2 -0.013 0.058 -10000 0 -0.69 1 1
SMAD3 0.017 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.034 0.034 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.025 -10000 0 -10000 0 0
NCOR1 0.011 0.002 -10000 0 -10000 0 0
NCOA2 0.009 0.041 -10000 0 -0.65 1 1
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A -0.079 0.17 -10000 0 -0.35 67 67
SMAD2-3/SMAD4/SP1/MIZ-1 0.025 0.083 -10000 0 -0.4 1 1
IFNB1 0.002 0.13 -10000 0 -0.45 9 9
SMAD3/SMAD4/MEF2C -0.12 0.18 -10000 0 -0.49 27 27
CITED1 -0.062 0.18 -10000 0 -0.47 39 39
SMAD2-3/SMAD4/ARC105 0.008 0.068 -10000 0 -0.44 1 1
RBL1 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.13 -10000 0 -0.53 12 12
RUNX1-3/PEBPB2 -0.049 0.17 -10000 0 -0.47 29 29
SMAD7 0.027 0.11 -10000 0 -0.64 3 3
MYC/MIZ-1 0.001 0.089 -10000 0 -0.43 9 9
SMAD3/SMAD4 0.057 0.14 0.28 32 -0.43 6 38
IL10 -0.044 0.22 -10000 0 -0.66 22 22
PIASy/HDAC complex 0.007 0.012 -10000 0 -10000 0 0
PIAS3 0.012 0.025 -10000 0 -0.39 1 1
CDK2 0.017 0.011 -10000 0 -10000 0 0
IL5 -0.024 0.16 -10000 0 -0.63 5 5
CDK4 0.018 0.013 -10000 0 -10000 0 0
PIAS4 0.007 0.012 -10000 0 -10000 0 0
ATF3 -0.022 0.12 -10000 0 -0.45 19 19
SMAD3/SMAD4/SP1 0.029 0.075 -10000 0 -0.36 1 1
FOXG1 -0.065 0.16 -10000 0 -0.41 45 45
FOXO3 0.014 0.048 -10000 0 -0.43 2 2
FOXO1 0.011 0.059 -10000 0 -0.37 5 5
FOXO4 0.016 0.037 -10000 0 -0.32 2 2
heart looping -0.13 0.18 -10000 0 -0.47 37 37
CEBPB 0.008 0.042 -10000 0 -0.65 1 1
SMAD3/SMAD4/DLX1 -0.015 0.083 -10000 0 -0.41 1 1
MYOD1 -0.12 0.23 -10000 0 -0.49 67 67
SMAD3/SMAD4/HNF4 -0.014 0.082 -10000 0 -0.32 2 2
SMAD3/SMAD4/GATA3 -0.055 0.17 -10000 0 -0.46 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.009 0.041 -10000 0 -0.65 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.029 0.17 -10000 0 -0.47 26 26
SMAD3/SMAD4/SP1-3 0.041 0.067 -10000 0 -10000 0 0
MED15 0.012 0 -10000 0 -10000 0 0
SP1 0.013 0.029 -10000 0 -10000 0 0
SIN3B 0.009 0.025 -10000 0 -0.4 1 1
SIN3A 0.011 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.15 0.2 -10000 0 -0.46 57 57
ITGB5 0.042 0.058 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.034 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.046 0.15 -10000 0 -0.42 31 31
AR -0.068 0.21 -10000 0 -0.64 32 32
negative regulation of cell growth 0.031 0.058 -10000 0 -0.39 1 1
SMAD3/SMAD4/MYOD -0.076 0.15 -10000 0 -0.44 27 27
E2F5 0.01 0.025 -10000 0 -0.39 1 1
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.046 0.13 -10000 0 -0.4 20 20
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.098 -10000 0 -0.36 12 12
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.015 0.12 -10000 0 -0.61 5 5
SMAD3/SMAD4/RUNX2 -0.009 0.1 -10000 0 -0.48 9 9
TGIF2 0.012 0 -10000 0 -10000 0 0
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.015 0.031 -10000 0 -0.48 1 1
ATM 0.012 0 -10000 0 -10000 0 0
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.012 0 -10000 0 -10000 0 0
ATR 0.012 0 -10000 0 -10000 0 0
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.02 0.024 -10000 0 -0.37 1 1
protein ubiquitination -0.053 0.12 -10000 0 -0.34 37 37
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex 0.024 0 -10000 0 -10000 0 0
MRE11A 0.012 0 -10000 0 -10000 0 0
DNA-PK 0.024 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.033 0.041 -10000 0 -0.46 1 1
FANCF 0.012 0 -10000 0 -10000 0 0
BRCA1 -0.052 0.2 -10000 0 -0.65 25 25
CCNE1 -0.029 0.15 -10000 0 -0.54 19 19
CDK2/Cyclin E1 -0.013 0.11 -10000 0 -0.39 19 19
FANCG 0.012 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.032 0.15 -10000 0 -0.48 26 26
FANCE 0.012 0 -10000 0 -10000 0 0
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.012 0 -10000 0 -10000 0 0
FANCA 0.006 0.058 -10000 0 -0.65 2 2
DNA repair 0.019 0.11 -10000 0 -0.62 2 2
BRCA1/BARD1/ubiquitin -0.032 0.15 -10000 0 -0.48 26 26
BARD1/DNA-PK 0.028 0.025 -10000 0 -0.37 1 1
FANCL 0.012 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.015 0.031 0.48 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.057 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.019 0.13 -10000 0 -0.41 26 26
BRCA1/BARD1/P53 -0.043 0.17 -10000 0 -0.4 44 44
BARD1/CSTF1/BRCA1 -0.019 0.13 -10000 0 -0.41 26 26
BRCA1/BACH1 -0.052 0.2 -10000 0 -0.65 25 25
BARD1 0.009 0.041 -10000 0 -0.65 1 1
PCNA 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.019 0.13 -10000 0 -0.41 26 26
BRCA1/BARD1/UbcH7 -0.019 0.13 -10000 0 -0.41 26 26
BRCA1/BARD1/RAD51/PCNA -0.014 0.12 -10000 0 -0.37 28 28
BARD1/DNA-PK/P53 0.001 0.11 -10000 0 -0.34 23 23
BRCA1/BARD1/Ubiquitin -0.032 0.15 -10000 0 -0.48 26 26
BRCA1/BARD1/CTIP -0.012 0.12 -10000 0 -0.37 26 26
FA complex 0.032 0.027 -10000 0 -0.27 2 2
BARD1/EWS 0.015 0.031 -10000 0 -0.48 1 1
RBBP8 0.018 0.018 -10000 0 -0.27 1 1
TP53 -0.044 0.18 -10000 0 -0.65 22 22
TOPBP1 0.012 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.043 0.16 0.4 44 -10000 0 44
BRCA1/BARD1 -0.025 0.13 -10000 0 -0.34 37 37
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.007 0.031 -10000 0 -0.49 1 1
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.005 0.063 -10000 0 -0.57 3 3
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.032 0.15 -10000 0 -0.48 26 26
EWSR1 0.012 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.025 0.14 -10000 0 -0.45 24 24
CRKL -0.007 0.11 -10000 0 -0.44 5 5
mol:PIP3 -0.007 0.071 0.56 4 -10000 0 4
AKT1 0.006 0.051 0.38 4 -10000 0 4
PTK2B 0.006 0.058 -10000 0 -0.65 2 2
RAPGEF1 -0.001 0.1 -10000 0 -0.42 5 5
RANBP10 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.04 0.16 -10000 0 -0.46 30 30
MAP3K5 0.003 0.11 -10000 0 -0.42 7 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.028 0.15 -10000 0 -0.42 30 30
AP1 -0.03 0.12 -10000 0 -0.47 11 11
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis -0.024 0.14 -10000 0 -0.71 9 9
STAT3 (dimer) -0.008 0.11 -10000 0 -0.47 5 5
GAB1/CRKL/SHP2/PI3K -0.031 0.084 -10000 0 -0.45 3 3
INPP5D -0.015 0.13 -10000 0 -0.63 11 11
CBL/CRK -0.001 0.11 -10000 0 -0.45 5 5
PTPN11 0.012 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
PTEN 0.001 0.081 -10000 0 -0.65 4 4
ELK1 -0.019 0.066 0.23 1 -0.23 21 22
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.024 0.065 -10000 0 -0.32 5 5
PAK1 0.008 0.053 0.36 4 -10000 0 4
HGF/MET/RANBP10 -0.039 0.16 -10000 0 -0.46 30 30
HRAS -0.041 0.21 -10000 0 -0.69 21 21
DOCK1 -0.002 0.11 -10000 0 -0.48 5 5
GAB1 -0.014 0.11 -10000 0 -0.34 21 21
CRK -0.008 0.11 -10000 0 -0.48 5 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.075 0.2 -10000 0 -0.62 30 30
JUN 0.006 0.054 -10000 0 -0.48 3 3
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.027 0.11 -10000 0 -0.31 30 30
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
cell morphogenesis 0.012 0.12 -10000 0 -0.52 3 3
GRB2/SHC -0.01 0.096 -10000 0 -0.3 21 21
FOS -0.038 0.15 -10000 0 -0.48 26 26
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.019 0.066 0.23 1 -0.23 21 22
HGF/MET/MUC20 -0.047 0.16 -10000 0 -0.47 30 30
cell migration -0.01 0.095 -10000 0 -0.29 21 21
GRB2 0.012 0 -10000 0 -10000 0 0
CBL 0.012 0 -10000 0 -10000 0 0
MET/RANBP10 -0.025 0.14 -10000 0 -0.45 24 24
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.12 -10000 0 -0.5 5 5
MET/MUC20 -0.034 0.14 -10000 0 -0.45 24 24
RAP1B 0.005 0.098 -10000 0 -0.42 4 4
RAP1A 0.006 0.097 -10000 0 -0.42 4 4
HGF/MET/RANBP9 -0.039 0.16 -10000 0 -0.46 30 30
RAF1 -0.032 0.19 -10000 0 -0.64 21 21
STAT3 -0.009 0.12 -10000 0 -0.48 5 5
cell proliferation -0.014 0.16 -10000 0 -0.43 30 30
RPS6KB1 -0.003 0.04 -10000 0 -10000 0 0
MAPK3 -0.023 0.058 -10000 0 -0.22 4 4
MAPK1 -0.02 0.072 0.67 1 -10000 0 1
RANBP9 0.012 0 -10000 0 -10000 0 0
MAPK8 0.019 0.091 -10000 0 -0.37 4 4
SRC -0.007 0.11 -10000 0 -0.46 5 5
PI3K -0.012 0.097 -10000 0 -0.4 5 5
MET/Glomulin -0.027 0.12 -10000 0 -0.4 24 24
SOS1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.023 0.18 -10000 0 -0.58 21 21
MET -0.045 0.18 -10000 0 -0.61 24 24
MAP4K1 -0.003 0.11 -10000 0 -0.46 6 6
PTK2 0.012 0 -10000 0 -10000 0 0
MAP2K2 -0.023 0.18 -10000 0 -0.58 21 21
BAD 0.011 0.047 0.36 4 -10000 0 4
MAP2K4 0.008 0.1 -10000 0 -0.42 5 5
SHP2/GRB2/SOS1/GAB1 -0.043 0.12 -10000 0 -0.43 21 21
INPPL1 0.01 0.025 -10000 0 -0.39 1 1
PXN 0.012 0 -10000 0 -10000 0 0
SH3KBP1 0.012 0 -10000 0 -10000 0 0
HGS -0.018 0.1 -10000 0 -0.31 21 21
PLCgamma1/PKC 0.009 0 -10000 0 -10000 0 0
HGF -0.031 0.16 -10000 0 -0.57 19 19
RASA1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
PTPRJ 0.012 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.01 0.099 -10000 0 -0.3 21 21
PDPK1 0 0.055 0.44 4 -10000 0 4
HGF/MET/SHIP -0.056 0.18 -10000 0 -0.48 37 37
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.048 0.34 2 -10000 0 2
RFC1 0.011 0.048 0.34 2 -10000 0 2
PRKDC 0.011 0.048 0.34 2 -10000 0 2
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.011 0.045 0.23 2 -10000 0 2
FASLG/FAS/FADD/FAF1 0.004 0.12 0.23 25 -0.31 14 39
MAP2K4 -0.03 0.14 -10000 0 -0.43 12 12
mol:ceramide -0.041 0.16 -10000 0 -0.46 25 25
GSN 0.006 0.059 0.44 1 -0.4 2 3
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.12 -10000 0 -0.38 13 13
FAS -0.003 0.091 -10000 0 -0.65 5 5
BID 0.007 0.06 0.3 8 -0.42 1 9
MAP3K1 -0.006 0.08 0.21 1 -0.27 3 4
MAP3K7 0.01 0.003 -10000 0 -10000 0 0
RB1 0.003 0.073 0.34 2 -0.4 5 7
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.12 0.23 -10000 0 -0.49 62 62
ARHGDIB 0.003 0.063 0.34 2 -0.36 3 5
FADD 0.01 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.006 0.059 0.39 2 -0.44 1 3
NFKB1 -0.042 0.086 -10000 0 -0.39 6 6
MAPK8 -0.042 0.16 -10000 0 -0.46 24 24
DFFA 0.01 0.054 0.34 2 -0.4 1 3
DNA fragmentation during apoptosis 0.01 0.054 0.34 2 -0.39 1 3
FAS/FADD/MET -0.025 0.13 -10000 0 -0.43 24 24
CFLAR/RIP1 0.013 0.007 -10000 0 -10000 0 0
FAIM3 -0.008 0.11 -10000 0 -0.65 8 8
FAF1 0.009 0.007 -10000 0 -10000 0 0
PARP1 0.011 0.048 0.34 2 -10000 0 2
DFFB 0.01 0.054 0.34 2 -0.4 1 3
CHUK -0.036 0.078 -10000 0 -0.57 2 2
FASLG -0.07 0.2 -10000 0 -0.56 36 36
FAS/FADD 0.005 0.069 -10000 0 -0.49 5 5
HGF -0.031 0.16 -10000 0 -0.57 19 19
LMNA 0.01 0.043 0.3 2 -10000 0 2
CASP6 0.011 0.048 0.34 2 -10000 0 2
CASP10 -0.013 0.12 -10000 0 -0.65 9 9
CASP3 0.013 0.058 0.27 9 -10000 0 9
PTPN13 -0.11 0.25 -10000 0 -0.58 54 54
CASP8 0.013 0.071 0.41 8 -10000 0 8
IL6 -0.13 0.36 -10000 0 -1.3 21 21
MET -0.045 0.18 -10000 0 -0.61 24 24
ICAD/CAD 0.008 0.055 0.31 2 -0.36 2 4
FASLG/FAS/FADD/FAF1/Caspase 10 -0.041 0.16 -10000 0 -0.46 25 25
activation of caspase activity by cytochrome c 0.007 0.06 0.3 8 -0.42 1 9
PAK2 0.011 0.048 0.34 2 -10000 0 2
BCL2 -0.003 0.083 -10000 0 -0.46 8 8
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.013 0.039 -9999 0 -0.34 3 3
alphaV beta3 Integrin -0.035 0.14 -9999 0 -0.44 18 18
PTK2 -0.034 0.15 -9999 0 -0.51 10 10
IGF1R -0.014 0.13 -9999 0 -0.65 10 10
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 -0.001 0.08 -9999 0 -0.47 7 7
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.043 0.15 -9999 0 -0.56 16 16
VEGFA 0.007 0.048 -9999 0 -0.52 2 2
ILK -0.039 0.14 -9999 0 -0.56 14 14
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.031 0.14 -9999 0 -0.53 14 14
PTK2B -0.008 0.1 -9999 0 -0.34 17 17
alphaV/beta3 Integrin/JAM-A -0.05 0.16 -9999 0 -0.41 34 34
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.023 0.12 -9999 0 -0.42 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.13 -9999 0 -0.43 18 18
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.007 0.093 -9999 0 -0.39 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.039 0.14 -9999 0 -0.41 24 24
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.094 0.19 -9999 0 -0.61 18 18
PI4 Kinase 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.041 0.15 -9999 0 -0.46 23 23
RPS6KB1 -0.055 0.19 -9999 0 -0.66 13 13
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.052 0.19 -9999 0 -0.66 17 17
GPR124 0.003 0.064 -9999 0 -0.44 5 5
MAPK1 -0.054 0.19 -9999 0 -0.66 17 17
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
alphaV/beta3 Integrin/Tumstatin -0.074 0.16 -9999 0 -0.43 35 35
cell adhesion -0.032 0.12 -9999 0 -0.45 13 13
ANGPTL3 0.003 0.043 -9999 0 -0.39 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.034 -9999 0 -0.41 1 1
IGF-1R heterotetramer -0.014 0.13 -9999 0 -0.65 10 10
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.054 0.18 -9999 0 -0.49 34 34
IGF1 -0.017 0.13 -9999 0 -0.55 13 13
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.022 0.12 -9999 0 -0.44 13 13
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.01 0.025 -9999 0 -0.39 1 1
alphaV/beta3 Integrin/CD47 -0.018 0.11 -9999 0 -0.41 13 13
VCL 0.009 0.041 -9999 0 -0.65 1 1
alphaV/beta3 Integrin/Del1 -0.05 0.16 -9999 0 -0.46 24 24
CSF1 -0.021 0.14 -9999 0 -0.63 13 13
PIK3C2A -0.039 0.14 -9999 0 -0.56 14 14
PI4 Kinase/Pyk2 -0.065 0.12 -9999 0 -0.52 8 8
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.01 0.11 -9999 0 -0.37 15 15
FAK1/Vinculin -0.022 0.12 -9999 0 -0.44 8 8
alphaV beta3/Integrin/ppsTEM5 -0.022 0.12 -9999 0 -0.44 13 13
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.051 0.17 -9999 0 -0.5 32 32
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 -0.019 0.12 -9999 0 -0.46 17 17
F11R -0.004 0.095 -9999 0 -0.34 17 17
alphaV/beta3 Integrin/Lactadherin -0.025 0.13 -9999 0 -0.47 13 13
alphaV/beta3 Integrin/TGFBR2 -0.017 0.11 -9999 0 -0.41 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.011 0.084 -9999 0 -0.37 12 12
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.015 0.1 -9999 0 -0.37 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.051 0.17 -9999 0 -0.5 32 32
alphaV/beta3 Integrin/Pyk2 -0.007 0.1 -9999 0 -0.34 17 17
SDC1 -0.023 0.14 -9999 0 -0.58 15 15
VAV3 -0.063 0.16 -9999 0 -0.36 50 50
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.002 0.075 -9999 0 -0.59 4 4
FAK1/Paxillin -0.021 0.12 -9999 0 -0.44 7 7
cell migration -0.013 0.12 -9999 0 -0.4 8 8
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.068 0.13 -9999 0 -0.55 8 8
SPP1 -0.026 0.15 -9999 0 -0.6 16 16
KDR 0.01 0.025 -9999 0 -0.39 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.08 0.2 -9999 0 -0.51 45 45
angiogenesis -0.054 0.19 -9999 0 -0.64 19 19
Rac1/GTP -0.052 0.15 -9999 0 -0.58 3 3
EDIL3 -0.042 0.16 -9999 0 -0.52 26 26
cell proliferation -0.017 0.11 -9999 0 -0.41 13 13
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.009 0.21 -10000 0 -0.83 13 13
NCK1/PAK1/Dok-R -0.033 0.096 -10000 0 -0.4 15 15
NCK1/Dok-R -0.022 0.25 -10000 0 -0.99 14 14
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.005 0.054 0.23 12 -10000 0 12
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.012 0.001 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 0.002 0.075 0.25 10 -0.41 4 14
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.063 0.21 -10000 0 -0.95 13 13
FN1 -0.051 0.17 -10000 0 -0.5 32 32
PLD2 -0.02 0.25 -10000 0 -1 13 13
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.12 0.25 -10000 0 -0.58 56 56
ELK1 -0.008 0.22 -10000 0 -0.94 13 13
GRB7 0.002 0.075 -10000 0 -0.59 4 4
PAK1 0.005 0.05 -10000 0 -0.39 4 4
Tie2/Ang1/alpha5/beta1 Integrin -0.087 0.25 -10000 0 -1.1 13 13
CDKN1A 0.018 0.17 -10000 0 -0.58 15 15
ITGA5 0.01 0.025 -10000 0 -0.39 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.022 0.25 -10000 0 -0.99 14 14
CRK 0.008 0.035 -10000 0 -0.39 2 2
mol:NO 0.02 0.17 -10000 0 -0.61 14 14
PLG -0.028 0.25 -10000 0 -1 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.008 0.2 -10000 0 -0.81 13 13
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.035 -10000 0 -0.39 2 2
ANGPT2 -0.001 0.12 -10000 0 -0.43 11 11
BMX -0.041 0.26 -10000 0 -1 14 14
ANGPT1 -0.063 0.29 -10000 0 -1.2 14 14
tube development 0.015 0.16 -10000 0 -0.59 13 13
ANGPT4 -0.012 0.091 -10000 0 -0.39 14 14
response to hypoxia -0.002 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.088 0.28 -10000 0 -1.2 13 13
alpha5/beta1 Integrin 0.016 0.018 -10000 0 -0.27 1 1
FGF2 -0.02 0.12 -10000 0 -0.46 17 17
STAT5A (dimer) 0.018 0.18 -10000 0 -0.62 16 16
mol:L-citrulline 0.02 0.17 -10000 0 -0.61 14 14
AGTR1 -0.038 0.16 -10000 0 -0.48 27 27
MAPK14 -0.012 0.23 -10000 0 -0.98 13 13
Tie2/SHP2 -0.016 0.056 -10000 0 -0.43 1 1
TEK 0.016 0.078 -10000 0 -0.48 1 1
RPS6KB1 0.012 0.2 -10000 0 -0.79 13 13
Angiotensin II/AT1 -0.025 0.11 -10000 0 -0.34 27 27
Tie2/Ang1/GRB2 -0.022 0.25 -10000 0 -1.1 13 13
MAPK3 -0.011 0.23 -10000 0 -0.96 13 13
MAPK1 -0.013 0.23 -10000 0 -0.96 13 13
Tie2/Ang1/GRB7 -0.027 0.26 -10000 0 -1.1 14 14
NFKB1 0.009 0.041 -10000 0 -0.65 1 1
MAPK8 -0.02 0.25 -10000 0 -1 13 13
PI3K 0.001 0.23 -10000 0 -0.93 13 13
FES -0.012 0.23 -10000 0 -0.97 13 13
Crk/Dok-R -0.023 0.25 -10000 0 -0.99 14 14
Tie2/Ang1/ABIN2 -0.022 0.25 -10000 0 -1.1 13 13
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.013 0.19 -10000 0 -0.74 13 13
STAT5A 0.007 0.058 -10000 0 -0.65 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.012 0.2 -10000 0 -0.79 13 13
Tie2/Ang2 0.009 0.19 -10000 0 -0.73 13 13
Tie2/Ang1 -0.028 0.26 -10000 0 -1.1 13 13
FOXO1 0.015 0.19 -10000 0 -0.75 13 13
ELF1 0.017 0.008 -10000 0 -10000 0 0
ELF2 -0.022 0.24 -10000 0 -1 13 13
mol:Choline -0.017 0.24 -10000 0 -1 13 13
cell migration -0.024 0.057 -10000 0 -0.24 12 12
FYN 0.012 0.18 -10000 0 -0.66 13 13
DOK2 -0.005 0.1 -10000 0 -0.62 7 7
negative regulation of cell cycle 0.021 0.16 -10000 0 -0.52 16 16
ETS1 0.006 0.051 -10000 0 -10000 0 0
PXN 0.022 0.17 -10000 0 -0.66 13 13
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 0.017 0.18 -10000 0 -0.69 14 14
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.083 0.22 -10000 0 -0.58 40 40
MAPKKK cascade -0.017 0.24 -10000 0 -1 13 13
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.022 0.25 -10000 0 -1.1 13 13
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis 0.023 0.15 -10000 0 -0.55 14 14
mol:Phosphatidic acid -0.017 0.24 -10000 0 -1 13 13
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.02 0.17 -10000 0 -0.61 14 14
Rac1/GTP -0.05 0.16 -10000 0 -0.74 13 13
MMP2 -0.031 0.26 -10000 0 -1.1 13 13
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.015 0.17 -9999 0 -0.57 14 14
MAP3K8 0.01 0.025 -9999 0 -0.39 1 1
FOS -0.012 0.14 -9999 0 -0.62 9 9
PRKCA -0.004 0.092 -9999 0 -0.54 7 7
PTPN7 -0.01 0.12 -9999 0 -0.58 10 10
HRAS 0.011 0.001 -9999 0 -10000 0 0
PRKCB -0.041 0.17 -9999 0 -0.56 24 24
NRAS 0.01 0.025 -9999 0 -0.39 1 1
RAS family/GTP 0.014 0.041 -9999 0 -10000 0 0
MAPK3 -0.007 0.12 -9999 0 -0.58 8 8
MAP2K1 -0.012 0.13 -9999 0 -0.45 19 19
ELK1 0.01 0.027 -9999 0 -0.43 1 1
BRAF -0.018 0.13 -9999 0 -0.45 19 19
mol:GTP 0 0.001 -9999 0 -0.004 24 24
MAPK1 -0.009 0.12 -9999 0 -0.6 8 8
RAF1 -0.018 0.13 -9999 0 -0.45 19 19
KRAS -0.001 0.07 -9999 0 -0.4 8 8
Signaling events mediated by HDAC Class III

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 0.009 0.041 -10000 0 -0.65 1 1
HDAC4 0.012 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.006 0.066 0.31 10 -10000 0 10
CDKN1A -0.002 0.099 -10000 0 -0.83 3 3
KAT2B 0.012 0 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
FOXO3 0.001 0.035 0.48 1 -0.28 1 2
FOXO1 0.005 0.063 -10000 0 -0.57 3 3
FOXO4 0.018 0.021 -10000 0 -0.32 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT 0.003 0.059 -10000 0 -0.46 4 4
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.078 0.17 -10000 0 -0.35 67 67
PPARGC1A -0.16 0.26 -10000 0 -0.53 83 83
FHL2 -0.003 0.094 -10000 0 -0.61 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.003 0.015 -10000 0 -10000 0 0
HIST2H4A 0.006 0.066 -10000 0 -0.31 10 10
SIRT1/FOXO3a 0.002 0.026 0.3 1 -0.21 1 2
SIRT1 0.01 0.018 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.004 0.015 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.002 0.033 -10000 0 -0.27 2 2
apoptosis -0.004 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.1 0.16 -10000 0 -0.33 82 82
p53/SIRT1 -0.035 0.14 0.41 2 -0.48 22 24
SIRT1/FOXO4 0.003 0.023 -10000 0 -0.27 1 1
FOXO1/FHL2/SIRT1 0.009 0.076 -10000 0 -0.43 7 7
HIST1H1E 0.012 0.038 -10000 0 -0.32 2 2
SIRT1/p300 0.001 0.034 -10000 0 -0.48 1 1
muscle cell differentiation 0.069 0.14 0.41 26 -10000 0 26
TP53 -0.046 0.18 -10000 0 -0.65 22 22
KU70/SIRT1/BAX 0.004 0.015 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.044 -10000 0 -0.32 4 4
ACSS2 0.018 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.069 0.14 -10000 0 -0.41 26 26
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.009 0.061 -9999 0 -0.48 4 4
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.009 0.041 -9999 0 -0.65 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.032 0.1 -9999 0 -0.43 10 10
IRAK/TOLLIP 0.022 0.048 -9999 0 -0.36 4 4
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.076 0.19 -9999 0 -0.4 58 58
IL1A -0.039 0.16 -9999 0 -0.48 27 27
IL1B -0.045 0.19 -9999 0 -0.52 31 31
IRAK/TRAF6/p62/Atypical PKCs -0.006 0.043 -9999 0 -10000 0 0
IL1R2 -0.068 0.2 -9999 0 -0.54 38 38
IL1R1 -0.003 0.094 -9999 0 -0.61 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.11 -9999 0 -0.37 13 13
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.004 0.071 -9999 0 -0.65 3 3
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.008 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.05 0.045 -9999 0 -10000 0 0
JUN 0.03 0.051 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.024 0.17 -9999 0 -0.46 29 29
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.12 -9999 0 -0.41 16 16
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.12 -9999 0 -0.38 16 16
IL1 beta fragment/IL1R1/IL1RAP -0.038 0.18 -9999 0 -0.5 29 29
NFKB1 0.009 0.041 -9999 0 -0.65 1 1
MAPK8 0.028 0.047 -9999 0 -0.3 1 1
IRAK1 0.017 0.053 -9999 0 -0.41 4 4
IL1RN/IL1R1 -0.009 0.12 -9999 0 -0.48 14 14
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.007 0.048 -9999 0 -0.52 2 2
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.015 0.025 -9999 0 -0.27 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.12 -9999 0 -0.42 14 14
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.038 0.18 -9999 0 -0.5 29 29
IL1 beta/IL1R2 -0.082 0.21 -9999 0 -0.51 42 42
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.005 0.039 -9999 0 -0.32 4 4
NF kappa B1 p50/RelA -0.052 0.15 -9999 0 -0.64 11 11
IRAK3 -0.001 0.07 -9999 0 -0.39 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.027 0.18 -9999 0 -0.72 10 10
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.001 0.096 -9999 0 -0.32 16 16
IL1 alpha/IL1R1/IL1RAP -0.026 0.13 -9999 0 -0.46 16 16
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0 -9999 0 -10000 0 0
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.028 0.046 -9999 0 -0.34 4 4
IL1RAP -0.003 0.092 -9999 0 -0.54 7 7
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.052 0.14 -9999 0 -0.62 10 10
CASP1 -0.029 0.16 -9999 0 -0.65 16 16
IL1RN/IL1R2 -0.057 0.17 -9999 0 -0.41 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.029 0.17 -9999 0 -0.47 29 29
TMEM189-UBE2V1 0.001 0.081 -9999 0 -0.65 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.09 -9999 0 -0.41 7 7
PIK3CA 0.012 0 -9999 0 -10000 0 0
IL1RN -0.01 0.12 -9999 0 -0.62 9 9
TRAF6/TAK1/TAB1/TAB2 -0.005 0.041 -9999 0 -0.33 4 4
MAP2K6 0.022 0.05 -9999 0 -0.31 5 5
Plasma membrane estrogen receptor signaling

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.006 0.11 -10000 0 -0.4 17 17
ER alpha/Gai/GDP/Gbeta gamma -0.034 0.15 -10000 0 -0.44 17 17
AKT1 -0.019 0.18 -10000 0 -0.79 14 14
PIK3CA 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.023 0.19 -10000 0 -0.8 14 14
mol:Ca2+ -0.017 0.13 -10000 0 -0.49 8 8
IGF1R -0.014 0.13 -10000 0 -0.65 10 10
E2/ER alpha (dimer)/Striatin -0.007 0.097 -10000 0 -0.42 14 14
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.017 0.18 0.75 14 -10000 0 14
RhoA/GTP -0.022 0.077 -10000 0 -0.39 2 2
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.052 0.12 -10000 0 -0.46 17 17
regulation of stress fiber formation -0.021 0.071 0.36 1 -10000 0 1
E2/ERA-ERB (dimer) -0.02 0.12 -10000 0 -0.39 23 23
KRAS -0.001 0.07 -10000 0 -0.39 8 8
G13/GTP -0.008 0.092 -10000 0 -0.38 15 15
pseudopodium formation 0.021 0.071 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1 -0.007 0.097 -10000 0 -0.42 14 14
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.007 0.043 -10000 0 -0.39 3 3
GNAO1 -0.098 0.22 -10000 0 -0.51 55 55
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.018 0.14 -10000 0 -0.53 14 14
E2/ER beta (dimer) -0.007 0.076 -10000 0 -0.35 11 11
mol:GDP -0.037 0.12 -10000 0 -0.46 18 18
mol:NADP -0.018 0.14 -10000 0 -0.53 14 14
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
mol:IP3 -0.018 0.13 -10000 0 -0.51 8 8
IGF-1R heterotetramer -0.014 0.13 -10000 0 -0.65 10 10
PLCB1 -0.018 0.13 -10000 0 -0.39 20 20
PLCB2 -0.008 0.12 -10000 0 -0.48 10 10
IGF1 -0.017 0.13 -10000 0 -0.55 13 13
mol:L-citrulline -0.018 0.14 -10000 0 -0.53 14 14
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.056 0.21 -10000 0 -0.69 24 24
JNK cascade -0.007 0.075 -10000 0 -0.35 11 11
BCAR1 0.012 0 -10000 0 -10000 0 0
ESR2 -0.009 0.1 -10000 0 -0.49 11 11
GNAQ 0.009 0.041 -10000 0 -0.65 1 1
ESR1 -0.024 0.15 -10000 0 -0.65 14 14
Gq family/GDP/Gbeta gamma 0.008 0.099 -10000 0 -0.46 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.009 0.073 -10000 0 -0.32 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.052 0.12 -10000 0 -0.46 17 17
GNAZ 0.006 0.058 -10000 0 -0.65 2 2
E2/ER alpha (dimer) -0.018 0.11 -10000 0 -0.49 14 14
STRN 0.012 0 -10000 0 -10000 0 0
GNAL -0.027 0.13 -10000 0 -0.47 21 21
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0 0.074 -10000 0 -0.41 6 6
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.091 -10000 0 -0.65 5 5
HBEGF -0.052 0.15 -10000 0 -0.42 20 20
cAMP biosynthetic process -0.045 0.11 -10000 0 -0.37 23 23
SRC -0.027 0.14 -10000 0 -0.42 17 17
PI3K 0.015 0.025 -10000 0 -0.27 2 2
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.034 0.11 -10000 0 -0.44 15 15
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.06 0.12 -10000 0 -0.43 17 17
Gs family/GTP -0.046 0.12 -10000 0 -0.38 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.039 -10000 0 -10000 0 0
vasodilation -0.017 0.13 -10000 0 -0.5 14 14
mol:DAG -0.018 0.13 -10000 0 -0.51 8 8
Gs family/GDP/Gbeta gamma -0.044 0.11 -10000 0 -0.44 15 15
MSN 0.021 0.076 -10000 0 -0.39 1 1
Gq family/GTP -0.008 0.11 -10000 0 -0.53 7 7
mol:PI-3-4-5-P3 -0.021 0.18 -10000 0 -0.77 14 14
NRAS 0.01 0.025 -10000 0 -0.39 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.13 0.5 14 -10000 0 14
GRB2/SOS1 0.017 0 -10000 0 -10000 0 0
RhoA/GDP -0.034 0.11 -10000 0 -0.44 17 17
NOS3 -0.02 0.15 -10000 0 -0.56 14 14
GNA11 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.006 0.15 -10000 0 -0.6 14 14
E2/ER alpha (dimer)/PELP1/Src -0.055 0.13 -10000 0 -0.48 17 17
ruffle organization 0.021 0.071 -10000 0 -0.36 1 1
ROCK2 0.016 0.081 -10000 0 -0.44 1 1
GNA14 -0.01 0.11 -10000 0 -0.51 11 11
GNA15 -0.01 0.12 -10000 0 -0.62 9 9
GNA13 0.009 0.041 -10000 0 -0.65 1 1
MMP9 -0.073 0.17 -10000 0 -0.47 19 19
MMP2 -0.03 0.15 -10000 0 -0.48 11 11
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.13 0.26 -9999 0 -0.57 64 64
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0 -9999 0 -10000 0 0
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 -0.01 0.099 -9999 0 -0.32 22 22
HIF1A 0.013 0.028 -9999 0 -10000 0 0
COPS5 0.01 0.025 -9999 0 -0.39 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.033 0.023 -9999 0 -0.34 1 1
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.27 -9999 0 -0.65 55 55
ARNT/IPAS -0.088 0.19 -9999 0 -0.41 64 64
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.019 0.027 -9999 0 -10000 0 0
CUL2 0.009 0.041 -9999 0 -0.65 1 1
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.024 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.019 0.027 -9999 0 -10000 0 0
PHD1-3/OS9 0.001 0.098 -9999 0 -0.37 15 15
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.025 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.019 0.029 -9999 0 -10000 0 0
EGLN3 -0.037 0.16 -9999 0 -0.57 22 22
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 -0.044 0.18 -9999 0 -0.65 22 22
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.018 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.053 0.14 -9999 0 -0.32 54 54
Regulation of Androgen receptor activity

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
HDAC1 0.019 0.001 -9999 0 -10000 0 0
SMARCC1 0.007 0.009 -9999 0 -10000 0 0
REL 0.012 0.002 -9999 0 -10000 0 0
HDAC7 -0.009 0.11 -9999 0 -0.49 2 2
JUN 0.006 0.054 -9999 0 -0.48 3 3
EP300 0.009 0.041 -9999 0 -0.65 1 1
KAT2B 0.012 0 -9999 0 -10000 0 0
KAT5 0.012 0 -9999 0 -10000 0 0
MAPK14 0.01 0.045 -9999 0 -0.36 3 3
FOXO1 0.005 0.063 -9999 0 -0.57 3 3
T-DHT/AR -0.013 0.12 -9999 0 -0.52 2 2
MAP2K6 0.003 0.056 -9999 0 -0.5 3 3
BRM/BAF57 0.01 0.061 -9999 0 -0.48 4 4
MAP2K4 0.006 0.041 -9999 0 -0.65 1 1
SMARCA2 0.001 0.081 -9999 0 -0.65 4 4
PDE9A -0.12 0.3 -9999 0 -1.2 18 18
NCOA2 0.009 0.041 -9999 0 -0.65 1 1
CEBPA -0.007 0.1 -9999 0 -0.54 9 9
EHMT2 0.011 0.002 -9999 0 -10000 0 0
cell proliferation -0.006 0.12 -9999 0 -0.45 2 2
NR0B1 -0.12 0.23 -9999 0 -0.5 66 66
EGR1 -0.032 0.15 -9999 0 -0.5 22 22
RXRs/9cRA -0.13 0.18 -9999 0 -0.38 76 76
AR/RACK1/Src 0.009 0.067 -9999 0 -0.44 1 1
AR/GR -0.017 0.1 -9999 0 -0.33 11 11
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.008 0.035 -9999 0 -0.39 2 2
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.012 0.034 -9999 0 -0.48 1 1
T-DHT/AR/TIF2/CARM1 0.01 0.07 -9999 0 -0.45 1 1
SRC 0.017 0.051 -9999 0 -0.38 2 2
NR3C1 0.001 0.081 -9999 0 -0.65 4 4
KLK3 -0.088 0.14 -9999 0 -0.47 13 13
APPBP2 0.006 0.042 -9999 0 -0.66 1 1
TRIM24 0.011 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.003 0.067 -9999 0 -0.41 2 2
TMPRSS2 -0.22 0.4 -9999 0 -1 44 44
RXRG -0.25 0.29 -9999 0 -0.55 121 121
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.004 0.071 -9999 0 -0.65 3 3
RXRB 0.012 0 -9999 0 -10000 0 0
CARM1 0.012 0.001 -9999 0 -10000 0 0
NR2C2 0.012 0 -9999 0 -10000 0 0
KLK2 0.01 0.092 -9999 0 -0.41 2 2
AR -0.017 0.11 -9999 0 -0.29 31 31
SENP1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 0.01 0.025 -9999 0 -0.4 1 1
SRY 0 0.003 -9999 0 -10000 0 0
GATA2 -0.046 0.15 -9999 0 -0.41 36 36
MYST2 0.012 0 -9999 0 -10000 0 0
HOXB13 -0.11 0.21 -9999 0 -0.46 64 64
T-DHT/AR/RACK1/Src 0.01 0.066 -9999 0 -0.45 1 1
positive regulation of transcription -0.046 0.15 -9999 0 -0.41 36 36
DNAJA1 0.009 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.008 -9999 0 -10000 0 0
NCOA1 0.016 0.003 -9999 0 -10000 0 0
SPDEF -0.12 0.25 -9999 0 -0.57 61 61
T-DHT/AR/TIF2 0.021 0.05 -9999 0 -0.29 1 1
T-DHT/AR/Hsp90 0.003 0.067 -9999 0 -0.41 2 2
GSK3B 0.011 0.003 -9999 0 -10000 0 0
NR2C1 0.012 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.011 0.054 -9999 0 -0.41 2 2
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0.003 -9999 0 -10000 0 0
POU2F1 0.003 0.04 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.065 0.14 -9999 0 -0.36 32 32
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 0.012 0.001 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.025 0.13 -9999 0 -0.49 14 14
EPHB2 0.009 0.041 -9999 0 -0.65 1 1
Syndecan-2/TACI -0.007 0.08 -9999 0 -0.41 3 3
LAMA1 -0.085 0.21 -9999 0 -0.49 50 50
Syndecan-2/alpha2 ITGB1 -0.038 0.14 -9999 0 -0.38 31 31
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.004 0.053 -9999 0 -0.3 7 7
ITGA5 0.01 0.025 -9999 0 -0.39 1 1
BAX 0.025 0.049 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.011 0.049 -9999 0 -0.37 3 3
LAMA3 -0.087 0.21 -9999 0 -0.52 48 48
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.006 0.054 -9999 0 -0.48 3 3
Syndecan-2/MMP2 -0.001 0.1 -9999 0 -0.5 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.003 0.082 -9999 0 -0.46 8 8
dendrite morphogenesis 0.011 0.068 -9999 0 -0.35 7 7
Syndecan-2/GM-CSF 0.002 0.065 -9999 0 -0.32 6 6
determination of left/right symmetry 0.007 0.063 -9999 0 -0.36 7 7
Syndecan-2/PKC delta 0.011 0.06 -9999 0 -0.41 4 4
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 0.01 0.059 -9999 0 -0.37 3 3
MAPK1 0.008 0.065 -9999 0 -0.37 4 4
Syndecan-2/RACK1 0.019 0.046 -9999 0 -0.34 3 3
NF1 -0.011 0.12 -9999 0 -0.65 9 9
FGFR/FGF/Syndecan-2 0.007 0.063 -9999 0 -0.36 7 7
ITGA2 -0.008 0.11 -9999 0 -0.62 8 8
MAPK8 0.02 0.054 -9999 0 -0.4 3 3
Syndecan-2/alpha2/beta1 Integrin -0.036 0.14 -9999 0 -0.38 27 27
Syndecan-2/Kininogen 0.003 0.059 -9999 0 -0.41 3 3
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.024 0.044 -9999 0 -0.32 3 3
Syndecan-2/CASK/Protein 4.1 0.012 0.049 -9999 0 -0.37 3 3
extracellular matrix organization 0.008 0.077 -9999 0 -0.48 5 5
actin cytoskeleton reorganization -0.025 0.13 -9999 0 -0.49 14 14
Syndecan-2/Caveolin-2/Ras 0.016 0.06 -9999 0 -0.37 5 5
Syndecan-2/Laminin alpha3 -0.049 0.15 -9999 0 -0.42 26 26
Syndecan-2/RasGAP 0.024 0.044 -9999 0 -0.33 3 3
alpha5/beta1 Integrin 0.016 0.018 -9999 0 -0.27 1 1
PRKCD 0.009 0.041 -9999 0 -0.65 1 1
Syndecan-2 dimer 0.011 0.068 -9999 0 -0.35 7 7
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.03 0.043 -9999 0 -0.31 3 3
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.021 0.1 -9999 0 -0.39 19 19
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.003 0.082 -9999 0 -0.46 8 8
Syndecan-2/Synbindin 0.013 0.054 -9999 0 -0.41 3 3
TGFB1 0.004 0.071 -9999 0 -0.65 3 3
CASP3 0.018 0.054 -9999 0 -0.36 4 4
FN1 -0.051 0.17 -9999 0 -0.5 32 32
Syndecan-2/IL8 -0.038 0.14 -9999 0 -0.44 18 18
SDC2 0.007 0.063 -9999 0 -0.36 7 7
KNG1 -0.002 0.043 -9999 0 -0.39 3 3
Syndecan-2/Neurofibromin -0.002 0.094 -9999 0 -0.41 12 12
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.005 0.065 -9999 0 -0.39 7 7
Syndecan-2/TGFB1 0.008 0.077 -9999 0 -0.48 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.012 0.049 -9999 0 -0.37 3 3
Syndecan-2/Ezrin 0.019 0.049 -9999 0 -0.37 3 3
PRKACA 0.006 0.086 -9999 0 -0.37 12 12
angiogenesis -0.038 0.14 -9999 0 -0.44 18 18
MMP2 -0.011 0.12 -9999 0 -0.57 10 10
IL8 -0.072 0.19 -9999 0 -0.48 44 44
calcineurin-NFAT signaling pathway -0.007 0.079 -9999 0 -0.4 3 3
Cellular roles of Anthrax toxin

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.009 0.041 -10000 0 -0.65 1 1
ANTXR2 0.005 0.063 -10000 0 -0.57 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.009 -10000 0 -0.084 3 3
monocyte activation -0.075 0.21 -10000 0 -0.52 40 40
MAP2K2 0 0.004 -10000 0 -10000 0 0
MAP2K1 -0.001 0.008 -10000 0 -10000 0 0
MAP2K7 -0.001 0.008 -10000 0 -10000 0 0
MAP2K6 -0.004 0.029 -10000 0 -0.25 3 3
CYAA 0.007 0.041 -10000 0 -0.36 3 3
MAP2K4 -0.002 0.024 -10000 0 -0.36 1 1
IL1B -0.024 0.11 -10000 0 -0.31 27 27
Channel 0.01 0.044 -10000 0 -0.38 3 3
NLRP1 -0.013 0.061 -10000 0 -0.29 11 11
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.009 0.084 3 -10000 0 3
MAPK3 -0.001 0.008 -10000 0 -10000 0 0
MAPK1 -0.003 0.026 -10000 0 -0.28 2 2
PGR -0.084 0.13 -10000 0 -0.26 85 85
PA/Cellular Receptors 0.01 0.048 -10000 0 -0.42 3 3
apoptosis -0.001 0.009 -10000 0 -0.084 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.01 0.041 -10000 0 -0.36 3 3
macrophage activation 0.013 0.026 -10000 0 -0.34 1 1
TNF -0.077 0.21 -10000 0 -0.57 40 40
VCAM1 -0.075 0.21 -10000 0 -0.52 40 40
platelet activation -0.001 0.011 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.013 -10000 0 -10000 0 0
IL18 -0.013 0.088 -10000 0 -0.3 19 19
negative regulation of macrophage activation -0.001 0.009 -10000 0 -0.084 3 3
LEF -0.001 0.009 -10000 0 -0.084 3 3
CASP1 -0.013 0.05 -10000 0 -0.21 11 11
mol:cAMP -0.001 0.011 -10000 0 -10000 0 0
necrosis -0.001 0.009 -10000 0 -0.084 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.01 0.042 -10000 0 -0.36 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.059 -9999 0 -0.46 4 4
alphaV beta3 Integrin -0.031 0.13 -9999 0 -0.35 34 34
PTK2 -0.044 0.13 -9999 0 -0.5 16 16
positive regulation of JNK cascade -0.019 0.073 -9999 0 -0.32 14 14
CDC42/GDP 0.014 0.11 -9999 0 -0.44 14 14
Rac1/GDP 0.015 0.11 -9999 0 -0.43 14 14
RAP1B 0.01 0.025 -9999 0 -0.39 1 1
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.024 0.09 -9999 0 -0.4 14 14
nectin-3/I-afadin -0.013 0.12 -9999 0 -0.44 17 17
RAPGEF1 0.008 0.12 -9999 0 -0.49 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.001 0.14 -9999 0 -0.57 14 14
PDGFB-D/PDGFRB 0.004 0.059 -9999 0 -0.46 4 4
TLN1 0.007 0.088 -9999 0 -0.56 4 4
Rap1/GTP -0.022 0.078 -9999 0 -0.34 14 14
IQGAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.019 0.037 -9999 0 -0.37 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.013 0.12 -9999 0 -0.44 17 17
PVR 0.012 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.007 0.14 -9999 0 -0.54 14 14
MLLT4 0.006 0.058 -9999 0 -0.65 2 2
PIK3CA 0.012 0 -9999 0 -10000 0 0
PI3K 0.007 0.092 -9999 0 -0.34 15 15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.008 0.076 -9999 0 -0.58 4 4
positive regulation of lamellipodium assembly -0.024 0.083 -9999 0 -0.32 18 18
PVRL1 0.004 0.071 -9999 0 -0.65 3 3
PVRL3 -0.024 0.14 -9999 0 -0.6 15 15
PVRL2 0.009 0.041 -9999 0 -0.65 1 1
PIK3R1 0.008 0.035 -9999 0 -0.39 2 2
CDH1 -0.001 0.091 -9999 0 -0.65 5 5
CLDN1 -0.041 0.17 -9999 0 -0.56 24 24
JAM-A/CLDN1 -0.025 0.14 -9999 0 -0.41 27 27
SRC -0.008 0.16 -9999 0 -0.64 14 14
ITGB3 -0.054 0.18 -9999 0 -0.49 34 34
nectin-1(dimer)/I-afadin/I-afadin 0.008 0.076 -9999 0 -0.58 4 4
FARP2 0.006 0.13 -9999 0 -0.53 14 14
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.009 0.041 -9999 0 -0.65 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.002 0.1 -9999 0 -0.41 14 14
nectin-1/I-afadin 0.008 0.076 -9999 0 -0.58 4 4
nectin-2/I-afadin 0.011 0.053 -9999 0 -0.48 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.016 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.007 0.11 -9999 0 -0.43 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.016 0 -9999 0 -10000 0 0
F11R 0.009 0.041 -9999 0 -0.65 1 1
positive regulation of filopodium formation -0.019 0.073 -9999 0 -0.32 14 14
alphaV/beta3 Integrin/Talin -0.013 0.13 -9999 0 -0.58 6 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.011 0.053 -9999 0 -0.48 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.011 0.053 -9999 0 -0.48 3 3
PIP5K1C 0 0.094 -9999 0 -0.6 4 4
VAV2 -0.003 0.15 -9999 0 -0.53 18 18
RAP1/GDP -0.025 0.092 -9999 0 -0.4 14 14
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.004 0.1 -9999 0 -0.41 15 15
nectin-3(dimer)/I-afadin/I-afadin -0.013 0.12 -9999 0 -0.44 17 17
Rac1/GTP -0.029 0.1 -9999 0 -0.39 18 18
PTPRM -0.007 0.1 -9999 0 -0.34 16 16
E-cadherin/beta catenin/alpha catenin -0.015 0.079 -9999 0 -0.66 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.027 0.15 -10000 0 -0.55 18 18
positive regulation of NF-kappaB transcription factor activity -0.022 0.14 -10000 0 -0.43 23 23
MAP2K4 0.019 0.073 -10000 0 -0.37 3 3
IKBKB 0.012 0 -10000 0 -10000 0 0
TNFRSF10B 0.012 0 -10000 0 -10000 0 0
TNFRSF10A -0.004 0.099 -10000 0 -0.65 6 6
SMPD1 0.002 0.055 -10000 0 -0.24 11 11
IKBKG 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.004 0.097 -10000 0 -0.58 7 7
TRAIL/TRAILR2 -0.011 0.11 -10000 0 -0.48 11 11
TRAIL/TRAILR3 -0.038 0.14 -10000 0 -0.35 39 39
TRAIL/TRAILR1 -0.022 0.14 -10000 0 -0.53 15 15
TRAIL/TRAILR4 -0.023 0.14 -10000 0 -0.43 23 23
TRAIL/TRAILR1/DAP3/GTP -0.009 0.11 -10000 0 -0.42 15 15
IKK complex -0.01 0.036 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.009 0 -10000 0 -10000 0 0
MAPK3 -0.01 0.11 -10000 0 -0.4 18 18
MAP3K1 0.015 0.073 -10000 0 -0.43 2 2
TRAILR4 (trimer) -0.004 0.097 -10000 0 -0.58 7 7
TRADD 0.012 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.004 0.099 -10000 0 -0.65 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.086 -10000 0 -0.56 2 2
CFLAR 0.012 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.11 -10000 0 -0.48 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP 0.005 0.11 -10000 0 -0.39 15 15
mol:ceramide 0.003 0.055 -10000 0 -0.24 11 11
FADD 0.012 0 -10000 0 -10000 0 0
MAPK8 0.024 0.07 -10000 0 -0.38 2 2
TRAF2 0.012 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.027 0.13 -10000 0 -0.44 22 22
CHUK 0.012 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.011 0.12 -10000 0 -0.46 15 15
DAP3 0.012 0 -10000 0 -10000 0 0
CASP10 -0.034 0.13 0.28 2 -0.48 15 17
JNK cascade -0.022 0.14 -10000 0 -0.43 23 23
TRAIL (trimer) -0.027 0.15 -10000 0 -0.55 18 18
TNFRSF10C -0.027 0.13 -10000 0 -0.44 22 22
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.11 -10000 0 -0.39 15 15
TRAIL/TRAILR2/FADD -0.001 0.094 -10000 0 -0.41 11 11
cell death 0.003 0.055 -10000 0 -0.24 11 11
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.065 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.012 0 -10000 0 -10000 0 0
CASP8 0.008 0.033 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.013 0.081 -10000 0 -0.34 11 11
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.021 0.11 0.6 3 -10000 0 3
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.003 0.063 -10000 0 -0.27 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.098 0.22 -10000 0 -0.51 55 55
RhoA/GTP -0.021 0.11 -10000 0 -0.62 3 3
negative regulation of cAMP metabolic process -0.029 0.12 -10000 0 -0.32 26 26
GNAZ 0.006 0.058 -10000 0 -0.65 2 2
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 -0.01 0.1 -10000 0 -0.46 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.029 0.12 -10000 0 -0.32 26 26
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.091 -10000 0 -0.65 5 5
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.013 0.04 -9999 0 -0.34 3 3
PDGFRB 0.004 0.059 -9999 0 -0.46 4 4
SPHK1 -0.045 0.17 -9999 0 -0.82 12 12
mol:S1P -0.042 0.15 -9999 0 -0.72 12 12
S1P1/S1P/Gi -0.033 0.15 -9999 0 -0.45 14 14
GNAO1 -0.098 0.22 -9999 0 -0.51 55 55
PDGFB-D/PDGFRB/PLCgamma1 -0.022 0.13 -9999 0 -0.45 10 10
PLCG1 -0.026 0.14 -9999 0 -0.49 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.059 -9999 0 -0.46 4 4
GNAI2 0.011 0.004 -9999 0 -10000 0 0
GNAI3 0.011 0.004 -9999 0 -10000 0 0
GNAI1 -0.002 0.092 -9999 0 -0.66 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.012 0.034 -9999 0 -0.32 2 2
S1P1/S1P -0.031 0.12 -9999 0 -0.52 13 13
negative regulation of cAMP metabolic process -0.032 0.14 -9999 0 -0.44 14 14
MAPK3 -0.033 0.17 -9999 0 -0.57 14 14
calcium-dependent phospholipase C activity -0.001 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR 0.01 0.025 -9999 0 -0.39 1 1
PLCB2 -0.005 0.12 -9999 0 -0.42 17 17
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.027 0.098 -9999 0 -0.43 13 13
receptor internalization -0.029 0.11 -9999 0 -0.48 13 13
PTGS2 -0.05 0.24 -9999 0 -0.9 14 14
Rac1/GTP -0.027 0.098 -9999 0 -0.43 13 13
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.007 0.048 -9999 0 -0.53 2 2
negative regulation of T cell proliferation -0.032 0.14 -9999 0 -0.44 14 14
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.006 0.058 -9999 0 -0.65 2 2
MAPK1 -0.035 0.17 -9999 0 -0.57 14 14
S1P1/S1P/PDGFB-D/PDGFRB -0.001 0.12 -9999 0 -0.47 14 14
ABCC1 0.01 0.025 -9999 0 -0.39 1 1
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.016 0.16 -10000 0 -0.72 5 5
UGCG 0.008 0.036 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.01 0.14 -10000 0 -0.43 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.036 -10000 0 -10000 0 0
mol:DAG -0.002 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.062 0.15 -10000 0 -0.5 19 19
FRAP1 -0.016 0.2 -10000 0 -0.6 19 19
FOXO3 -0.012 0.19 -10000 0 -0.58 18 18
AKT1 -0.02 0.21 -10000 0 -0.6 22 22
GAB2 -0.007 0.1 -10000 0 -0.54 9 9
SMPD1 0.008 0.036 -10000 0 -10000 0 0
SGMS1 0.008 0.036 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.021 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.007 0.084 -10000 0 -0.28 3 3
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K 0.019 0.025 -10000 0 -10000 0 0
RPS6KB1 0.01 0.042 -10000 0 -10000 0 0
mol:sphingomyelin -0.002 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 0.003 0.082 -10000 0 -0.65 4 4
PIK3R1 0.01 0.035 -10000 0 -0.39 2 2
JAK1 0.014 0.002 -10000 0 -10000 0 0
NFKB1 0.009 0.041 -10000 0 -0.65 1 1
MYC -0.024 0.24 -10000 0 -0.86 15 15
MYB -0.02 0.23 -10000 0 -1.1 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.21 -10000 0 -0.54 28 28
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.039 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.2 -10000 0 -0.52 28 28
Rac1/GDP 0.022 0.019 -10000 0 -10000 0 0
T cell proliferation -0.014 0.18 -10000 0 -0.49 27 27
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.012 -10000 0 -0.056 10 10
PRKCZ -0.017 0.2 -10000 0 -0.51 27 27
NF kappa B1 p50/RelA -0.061 0.15 -10000 0 -0.51 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.025 0.18 -10000 0 -0.53 22 22
HSP90AA1 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.042 0.18 -10000 0 -0.63 22 22
IL2RB -0.059 0.2 -10000 0 -0.6 31 31
TERT -0.055 0.17 -10000 0 -0.47 36 36
E2F1 0 0.11 -10000 0 -0.5 11 11
SOS1 0.012 0.002 -10000 0 -10000 0 0
RPS6 0.012 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.028 10 -10000 0 10
PTPN11 0.012 0.002 -10000 0 -10000 0 0
IL2RG -0.048 0.19 -10000 0 -0.61 26 26
actin cytoskeleton organization -0.014 0.18 -10000 0 -0.49 27 27
GRB2 0.012 0.002 -10000 0 -10000 0 0
IL2 0.002 0.035 -10000 0 -0.39 2 2
PIK3CA 0.014 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.02 -10000 0 -10000 0 0
LCK -0.028 0.16 -10000 0 -0.59 18 18
BCL2 -0.004 0.17 -10000 0 -0.62 10 10
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.003 0.094 -9999 0 -0.38 5 5
NEF -0.017 0.057 -9999 0 -0.2 18 18
NFKBIA 0.003 0.056 -9999 0 -0.77 1 1
BIRC3 -0.017 0.19 -9999 0 -0.6 22 22
CYCS -0.004 0.11 -9999 0 -0.39 5 5
RIPK1 0.012 0 -9999 0 -10000 0 0
CD247 -0.064 0.2 -9999 0 -0.64 25 25
MAP2K7 0.002 0.094 -9999 0 -0.35 5 5
protein ubiquitination 0.024 0.081 -9999 0 -10000 0 0
CRADD 0.012 0 -9999 0 -10000 0 0
DAXX 0.012 0 -9999 0 -10000 0 0
FAS -0.001 0.091 -9999 0 -0.65 5 5
BID -0.011 0.11 -9999 0 -0.4 6 6
NF-kappa-B/RelA/I kappa B alpha 0.004 0.1 -9999 0 -0.36 15 15
TRADD 0.012 0 -9999 0 -10000 0 0
MAP3K5 0.01 0.025 -9999 0 -0.39 1 1
CFLAR 0.012 0 -9999 0 -10000 0 0
FADD 0.012 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.004 0.1 -9999 0 -0.36 15 15
MAPK8 0.008 0.09 -9999 0 -0.39 2 2
APAF1 0.012 0 -9999 0 -10000 0 0
TRAF1 0.012 0 -9999 0 -10000 0 0
TRAF2 0.012 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.016 0.12 -9999 0 -0.31 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.098 -9999 0 -0.36 8 8
CHUK 0.023 0.086 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.026 0.053 -9999 0 -0.34 5 5
TCRz/NEF -0.066 0.19 -9999 0 -0.46 43 43
TNF -0.077 0.21 -9999 0 -0.57 40 40
FASLG -0.096 0.27 -9999 0 -0.62 48 48
NFKB1 0.003 0.056 -9999 0 -0.77 1 1
TNFR1A/BAG4/TNF-alpha -0.033 0.14 -9999 0 -0.41 27 27
CASP6 -0.021 0.058 -9999 0 -0.39 1 1
CASP7 0.004 0.17 -9999 0 -0.63 15 15
RELA 0.006 0.029 -9999 0 -10000 0 0
CASP2 0.012 0 -9999 0 -10000 0 0
CASP3 0.004 0.17 -9999 0 -0.63 15 15
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.017 0 -9999 0 -10000 0 0
CASP8 0.012 0 -9999 0 -10000 0 0
CASP9 0.012 0 -9999 0 -10000 0 0
MAP3K14 0.018 0.093 -9999 0 -0.33 6 6
APAF-1/Caspase 9 -0.052 0.13 -9999 0 -0.53 15 15
BCL2 0.007 0.1 -9999 0 -0.46 4 4
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.018 0.03 -10000 0 -10000 0 0
AES 0.017 0.026 0.23 1 -10000 0 1
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.013 0.036 -10000 0 -0.38 2 2
SMAD4 0.012 0 -10000 0 -10000 0 0
DKK2 -0.028 0.15 -10000 0 -0.57 18 18
TLE1 0.017 0.023 -10000 0 -10000 0 0
MACF1 0.01 0.025 -10000 0 -0.39 1 1
CTNNB1 0.019 0.073 -10000 0 -0.37 1 1
WIF1 -0.06 0.16 -10000 0 -0.45 38 38
beta catenin/RanBP3 0.033 0.14 0.36 32 -10000 0 32
KREMEN2 -0.097 0.23 -10000 0 -0.55 50 50
DKK1 -0.1 0.22 -10000 0 -0.48 60 60
beta catenin/beta TrCP1 0.026 0.07 -10000 0 -0.33 1 1
FZD1 0.009 0.041 -10000 0 -0.65 1 1
AXIN2 -0.023 0.15 -10000 0 -1.5 2 2
AXIN1 0.012 0.001 -10000 0 -10000 0 0
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.016 0.027 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.043 0.067 -10000 0 -0.34 1 1
Axin1/APC/GSK3 0.018 0.036 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.037 0.044 -10000 0 -0.36 1 1
HNF1A -0.009 0.11 -10000 0 -0.42 15 15
CTBP1 0.017 0.025 -10000 0 -10000 0 0
MYC -0.056 0.27 -10000 0 -1.4 10 10
RANBP3 0.012 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.071 0.17 -10000 0 -0.43 43 43
NKD1 -0.008 0.1 -10000 0 -0.54 9 9
TCF4 0.014 0.045 -10000 0 -0.41 2 2
TCF3 0.017 0.025 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.019 0.046 -10000 0 -0.37 1 1
Ran/GTP 0.009 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.05 0.16 0.43 33 -10000 0 33
LEF1 -0.012 0.12 -10000 0 -0.52 14 14
DVL1 0.037 0.027 -10000 0 -10000 0 0
CSNK2A1 0.012 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.019 0.11 -10000 0 -0.53 3 3
DKK1/LRP6/Kremen 2 -0.12 0.2 -10000 0 -0.46 54 54
LRP6 0.01 0.025 -10000 0 -0.39 1 1
CSNK1A1 0.018 0.03 0.24 1 -10000 0 1
NLK 0.008 0.036 -10000 0 -0.4 2 2
CCND1 -0.14 0.44 -10000 0 -1.4 27 27
WNT1 -0.003 0.07 -10000 0 -0.39 8 8
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.011 0.001 -10000 0 -10000 0 0
PPP2R5D 0.028 0.05 0.27 9 -10000 0 9
APC 0.024 0.043 -10000 0 -0.34 1 1
WNT1/LRP6/FZD1 0.034 0.061 0.24 8 -0.29 1 9
CREBBP 0.017 0.025 -10000 0 -10000 0 0
IL6-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
BCL2L1 -0.038 0.22 -9999 0 -0.76 10 10
CRP -0.043 0.22 -9999 0 -0.77 10 10
cell cycle arrest -0.058 0.25 -9999 0 -0.83 14 14
TIMP1 -0.025 0.2 -9999 0 -0.72 8 8
IL6ST 0.009 0.048 -9999 0 -0.52 2 2
Rac1/GDP -0.033 0.16 -9999 0 -0.51 18 18
AP1 -0.003 0.14 -9999 0 -0.62 8 8
GAB2 -0.007 0.1 -9999 0 -0.54 9 9
TNFSF11 -0.12 0.36 -9999 0 -1 32 32
HSP90B1 0.016 0.079 -9999 0 -1.1 1 1
GAB1 0.012 0.001 -9999 0 -10000 0 0
MAPK14 -0.019 0.16 -9999 0 -0.79 6 6
AKT1 0.037 0.046 -9999 0 -10000 0 0
FOXO1 0.039 0.055 -9999 0 -10000 0 0
MAP2K6 -0.025 0.14 -9999 0 -0.57 9 9
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.03 0.19 -9999 0 -0.63 14 14
MITF -0.027 0.15 -9999 0 -0.49 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0 -9999 0 -10000 0 0
A2M 0.017 0.022 -9999 0 -10000 0 0
CEBPB 0.015 0.041 -9999 0 -0.65 1 1
GRB2/SOS1/GAB family/SHP2 -0.002 0.1 -9999 0 -0.55 5 5
STAT3 -0.064 0.26 -9999 0 -0.89 14 14
STAT1 -0.005 0.014 -9999 0 -10000 0 0
CEBPD -0.045 0.24 -9999 0 -0.87 12 12
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K 0.017 0.025 -9999 0 -0.26 2 2
JUN 0.006 0.054 -9999 0 -0.48 3 3
PIAS3/MITF -0.02 0.14 -9999 0 -0.47 13 13
MAPK11 -0.022 0.17 -9999 0 -0.83 7 7
STAT3 (dimer)/FOXO1 -0.002 0.2 -9999 0 -0.62 10 10
GRB2/SOS1/GAB family -0.051 0.12 -9999 0 -0.49 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.031 0.14 -9999 0 -0.42 17 17
GRB2 0.012 0.001 -9999 0 -10000 0 0
JAK2 0.009 0.041 -9999 0 -0.65 1 1
LBP -0.058 0.24 -9999 0 -0.86 11 11
PIK3R1 0.009 0.035 -9999 0 -0.39 2 2
JAK1 0.012 0.006 -9999 0 -10000 0 0
MYC -0.057 0.28 -9999 0 -1.1 13 13
FGG -0.048 0.23 -9999 0 -0.76 12 12
macrophage differentiation -0.058 0.25 -9999 0 -0.83 14 14
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.058 0.13 -9999 0 -0.48 12 12
JUNB -0.046 0.24 -9999 0 -0.82 13 13
FOS -0.038 0.15 -9999 0 -0.48 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.14 -9999 0 -0.49 13 13
STAT1/PIAS1 -0.024 0.13 -9999 0 -0.45 11 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.045 -9999 0 -10000 0 0
STAT3 (dimer) -0.063 0.26 -9999 0 -0.88 14 14
PRKCD -0.029 0.21 -9999 0 -0.72 13 13
IL6R -0.007 0.11 -9999 0 -0.63 8 8
SOCS3 -0.026 0.21 -9999 0 -1.3 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 0.024 0.037 -9999 0 -0.4 1 1
Rac1/GTP -0.035 0.17 -9999 0 -0.56 17 17
HCK -0.014 0.13 -9999 0 -0.65 10 10
MAPKKK cascade 0.009 0.11 -9999 0 -0.66 5 5
bone resorption -0.11 0.34 -9999 0 -0.92 32 32
IRF1 -0.05 0.26 -9999 0 -0.93 12 12
mol:GDP -0.04 0.17 -9999 0 -0.52 19 19
SOS1 0.012 0.001 -9999 0 -10000 0 0
VAV1 -0.041 0.17 -9999 0 -0.52 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.025 0.16 -9999 0 -0.55 13 13
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.072 0.18 -9999 0 -0.45 35 35
gp130 (dimer)/TYK2/TYK2/LMO4 0.02 0.034 -9999 0 -0.4 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.019 0.044 -9999 0 -0.41 2 2
IL6 -0.093 0.21 -9999 0 -0.49 55 55
PIAS3 0.01 0.025 -9999 0 -0.39 1 1
PTPRE 0.007 0.042 -9999 0 -0.63 1 1
PIAS1 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.029 0.11 -9999 0 -0.38 11 11
LMO4 0.013 0.01 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.077 0.23 -9999 0 -0.83 13 13
MCL1 0.042 0.042 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.11 0.32 -9999 0 -1.1 7 7
PLK1 0.045 0.14 -9999 0 -1.5 2 2
BIRC5 0.038 0.17 -9999 0 -1.5 3 3
HSPA1B 0.11 0.32 -9999 0 -1.1 7 7
MAP2K1 0.037 0.029 -9999 0 -10000 0 0
BRCA2 0.11 0.34 -9999 0 -1.2 9 9
FOXM1 0.086 0.48 -9999 0 -2 7 7
XRCC1 0.11 0.32 -9999 0 -1.2 6 6
FOXM1B/p19 -0.12 0.27 -9999 0 -1.1 13 13
Cyclin D1/CDK4 0.028 0.41 -9999 0 -1.1 16 16
CDC2 0.11 0.33 -9999 0 -1.2 7 7
TGFA 0.027 0.41 -9999 0 -1.1 15 15
SKP2 0.11 0.32 -9999 0 -1.1 7 7
CCNE1 -0.024 0.15 -9999 0 -0.54 19 19
CKS1B 0.11 0.32 -9999 0 -1.2 6 6
RB1 -0.085 0.19 -9999 0 -0.88 8 8
FOXM1C/SP1 0.094 0.36 -9999 0 -1.3 8 8
AURKB 0.04 0.17 -9999 0 -1.5 3 3
CENPF 0.11 0.33 -9999 0 -1.2 7 7
CDK4 0.019 0.013 -9999 0 -10000 0 0
MYC 0.097 0.33 -9999 0 -1 12 12
CHEK2 0.037 0.029 -9999 0 -10000 0 0
ONECUT1 0.057 0.37 -9999 0 -1.1 11 11
CDKN2A -0.13 0.27 -9999 0 -0.65 55 55
LAMA4 0.11 0.33 -9999 0 -1.2 7 7
FOXM1B/HNF6 0.044 0.42 -9999 0 -1.3 11 11
FOS 0.078 0.39 -9999 0 -1.3 13 13
SP1 0.012 0.005 -9999 0 -10000 0 0
CDC25B 0.11 0.33 -9999 0 -1.2 8 8
response to radiation 0.021 0.027 -9999 0 -10000 0 0
CENPB 0.11 0.32 -9999 0 -1.1 7 7
CENPA 0.11 0.33 -9999 0 -1.2 6 6
NEK2 0.11 0.33 -9999 0 -1.2 7 7
HIST1H2BA 0.11 0.32 -9999 0 -1.2 6 6
CCNA2 0.007 0.077 -9999 0 -0.6 4 4
EP300 0.009 0.041 -9999 0 -0.65 1 1
CCNB1/CDK1 0.1 0.36 -9999 0 -1.4 7 7
CCNB2 0.11 0.33 -9999 0 -1.2 7 7
CCNB1 0.11 0.34 -9999 0 -1.2 7 7
ETV5 0.086 0.38 -9999 0 -1.2 14 14
ESR1 0.07 0.42 -9999 0 -1.2 19 19
CCND1 0.028 0.43 -9999 0 -1.1 19 19
GSK3A 0.033 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.014 0.13 -9999 0 -0.47 13 13
CDK2 0.016 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.031 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.085 0.25 -9999 0 -1.2 9 9
GAS1 0.07 0.41 -9999 0 -1.2 20 20
MMP2 0.092 0.37 -9999 0 -1.2 12 12
RB1/FOXM1C 0.038 0.4 -9999 0 -1 13 13
CREBBP 0.012 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.024 0.084 -10000 0 -0.63 3 3
HDAC1 0.013 0.013 -10000 0 -10000 0 0
AES 0.012 0.004 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 -0.002 0.086 -10000 0 -0.5 7 7
LRP6/FZD1 0.014 0.035 -10000 0 -0.37 2 2
TLE1 0.012 0.003 -10000 0 -10000 0 0
AP1 -0.01 0.097 -10000 0 -0.36 13 13
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.012 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.005 0.1 -10000 0 -0.35 4 4
NICD/RBPSUH 0.021 0.071 -10000 0 -0.63 3 3
WIF1 -0.06 0.16 -10000 0 -0.45 38 38
NOTCH1 -0.008 0.072 -10000 0 -0.67 3 3
PSENEN 0.012 0 -10000 0 -10000 0 0
KREMEN2 -0.097 0.23 -10000 0 -0.55 50 50
DKK1 -0.1 0.22 -10000 0 -0.48 60 60
beta catenin/beta TrCP1 0.017 0.04 0.24 1 -10000 0 1
APH1B 0.012 0 -10000 0 -10000 0 0
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 0.001 0.027 -10000 0 -0.26 1 1
CtBP/CBP/TCF1/TLE1/AES 0.028 0.062 -10000 0 -0.29 3 3
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.038 0.15 -10000 0 -0.48 26 26
JUN 0.006 0.054 -10000 0 -0.48 3 3
MAP3K7 0.012 0.006 -10000 0 -10000 0 0
CTNNB1 0.01 0.042 0.23 3 -10000 0 3
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.071 0.17 -10000 0 -0.43 43 43
HNF1A -0.014 0.11 -10000 0 -0.44 15 15
CTBP1 0.012 0.004 -10000 0 -10000 0 0
MYC -0.039 0.26 -10000 0 -1.4 9 9
NKD1 -0.007 0.1 -10000 0 -0.54 9 9
FZD1 0.009 0.041 -10000 0 -0.65 1 1
NOTCH1 precursor/Deltex homolog 1 0.014 0.083 -10000 0 -0.63 3 3
apoptosis -0.01 0.096 -10000 0 -0.36 13 13
Delta 1/NOTCHprecursor 0.003 0.092 -10000 0 -0.63 3 3
DLL1 -0.027 0.12 -10000 0 -0.4 24 24
PPARD 0.009 0.032 -10000 0 -10000 0 0
Gamma Secretase 0.034 0.003 -10000 0 -10000 0 0
APC 0.001 0.027 -10000 0 -0.26 1 1
DVL1 0.006 0.023 -10000 0 -10000 0 0
CSNK2A1 0.011 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.2 -10000 0 -0.46 54 54
LRP6 0.01 0.025 -10000 0 -0.39 1 1
CSNK1A1 0.011 0.002 -10000 0 -10000 0 0
NLK 0.015 0.02 -10000 0 -10000 0 0
CCND1 -0.13 0.43 -10000 0 -1.4 26 26
WNT1 -0.003 0.07 -10000 0 -0.39 8 8
Axin1/APC/beta catenin 0.024 0.034 -10000 0 -10000 0 0
DKK2 -0.028 0.15 -10000 0 -0.57 18 18
NOTCH1 precursor/DVL1 -0.003 0.062 -10000 0 -0.56 3 3
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.014 0.078 -10000 0 -0.63 3 3
PPP2R5D 0.006 0.049 0.31 5 -10000 0 5
MAPK1 0.007 0.048 -10000 0 -0.52 2 2
WNT1/LRP6/FZD1 -0.023 0.1 -10000 0 -0.37 11 11
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.013 0.005 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.012 0 -10000 0 -10000 0 0
PTK2 0.012 0 -10000 0 -10000 0 0
CRKL -0.009 0.11 -10000 0 -0.38 18 18
GRB2/SOS1/SHC 0.024 0 -10000 0 -10000 0 0
HRAS 0.012 0 -10000 0 -10000 0 0
IRS1/Crk -0.01 0.11 -10000 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.11 -10000 0 -0.42 17 17
AKT1 0.007 0.099 -10000 0 -0.68 2 2
BAD 0.013 0.093 -10000 0 -0.62 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.01 0.11 -10000 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.11 -10000 0 -0.38 18 18
RAF1 0.018 0.088 -10000 0 -0.58 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0 0.11 -10000 0 -0.37 17 17
YWHAZ 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.016 0.12 -10000 0 -0.42 18 18
PIK3CA 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.098 -10000 0 -0.68 2 2
GNB2L1 0.012 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.016 0.078 -10000 0 -0.48 2 2
PXN 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.017 0 -10000 0 -10000 0 0
HRAS/GTP -0.024 0.089 -10000 0 -0.7 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.007 0.095 -10000 0 -0.33 17 17
IGF-1R heterotetramer -0.018 0.13 -10000 0 -0.68 10 10
IGF-1R heterotetramer/IGF1/IRS/Nck -0.008 0.11 -10000 0 -0.38 18 18
Crk/p130 Cas/Paxillin 0.003 0.1 -10000 0 -0.74 2 2
IGF1R -0.018 0.13 -10000 0 -0.68 10 10
IGF1 -0.02 0.13 -10000 0 -0.57 13 13
IRS2/Crk -0.009 0.13 -10000 0 -0.4 19 19
PI3K -0.002 0.11 -10000 0 -0.36 17 17
apoptosis -0.019 0.082 0.52 2 -10000 0 2
HRAS/GDP 0.009 0 -10000 0 -10000 0 0
PRKCD 0.003 0.11 -10000 0 -0.38 18 18
RAF1/14-3-3 E 0.023 0.08 -10000 0 -0.48 2 2
BAD/14-3-3 0.02 0.087 -10000 0 -0.56 2 2
PRKCZ 0.009 0.098 -10000 0 -0.68 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.021 0.074 -10000 0 -0.57 2 2
PTPN1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.002 0.12 -10000 0 -0.41 17 17
BCAR1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.001 0.1 -10000 0 -0.36 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.008 0.11 -10000 0 -0.38 18 18
GRB10 0.012 0 -10000 0 -10000 0 0
PTPN11 -0.009 0.11 -10000 0 -0.38 18 18
IRS1 -0.017 0.12 -10000 0 -0.42 18 18
IRS2 -0.015 0.14 -10000 0 -0.43 19 19
IGF-1R heterotetramer/IGF1 -0.026 0.14 -10000 0 -0.53 17 17
GRB2 0.012 0 -10000 0 -10000 0 0
PDPK1 0.003 0.1 -10000 0 -0.73 2 2
YWHAE 0.009 0.041 -10000 0 -0.65 1 1
PRKD1 -0.008 0.14 -10000 0 -0.48 15 15
SHC1 0.012 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0 -9999 0 -10000 0 0
SPHK1 -0.022 0.14 -9999 0 -0.62 14 14
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.072 -9999 0 -0.32 12 12
GNAO1 -0.098 0.22 -9999 0 -0.51 55 55
mol:Sphinganine-1-P -0.006 0.11 -9999 0 -0.45 14 14
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.019 0.059 -9999 0 -0.34 1 1
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.015 0.031 -9999 0 -0.48 1 1
S1PR3 -0.008 0.1 -9999 0 -0.5 10 10
S1PR2 0.01 0.025 -9999 0 -0.39 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.058 -9999 0 -0.27 12 12
S1PR5 -0.01 0.1 -9999 0 -0.46 12 12
S1PR4 0 0.085 -9999 0 -0.6 5 5
GNAI1 -0.001 0.091 -9999 0 -0.65 5 5
S1P/S1P5/G12 0.003 0.079 -9999 0 -0.34 4 4
S1P/S1P3/Gq -0.001 0.1 -9999 0 -0.33 17 17
S1P/S1P4/Gi -0.024 0.11 -9999 0 -0.48 4 4
GNAQ 0.009 0.041 -9999 0 -0.65 1 1
GNAZ 0.006 0.058 -9999 0 -0.65 2 2
GNA14 -0.01 0.11 -9999 0 -0.51 11 11
GNA15 -0.01 0.12 -9999 0 -0.62 9 9
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.009 0.041 -9999 0 -0.65 1 1
GNA11 0.012 0 -9999 0 -10000 0 0
ABCC1 0.01 0.025 -9999 0 -0.39 1 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0 -9999 0 -10000 0 0
ITGB7 -0.003 0.094 -9999 0 -0.61 6 6
ITGA4 -0.004 0.099 -9999 0 -0.65 6 6
alpha4/beta7 Integrin -0.005 0.1 -9999 0 -0.46 12 12
alpha4/beta1 Integrin 0.006 0.075 -9999 0 -0.48 6 6
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.013 0.1 -9999 0 -0.37 17 17
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.029 -9999 0 -10000 0 0
AURKB 0.004 0.071 -9999 0 -0.65 3 3
AURKC -0.041 0.17 -9999 0 -0.54 25 25
Ceramide signaling pathway

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
SPHK2 0.003 0.082 -10000 0 -0.4 10 10
MAP4K4 -0.011 0.13 -10000 0 -0.57 10 10
BAG4 0.012 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.005 0.037 0.16 5 -10000 0 5
NFKBIA 0.009 0.041 -10000 0 -0.65 1 1
BIRC3 -0.037 0.16 -10000 0 -0.57 22 22
BAX 0.001 0.02 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.013 0.034 -10000 0 -0.36 2 2
BAD -0.005 0.038 0.17 5 -10000 0 5
SMPD1 -0.008 0.081 -10000 0 -0.23 27 27
RB1 -0.012 0.066 0.17 5 -0.39 5 10
FADD/Caspase 8 -0.001 0.13 -10000 0 -0.56 10 10
MAP2K4 -0.002 0.047 0.17 5 -0.35 2 7
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.001 0.036 -10000 0 -10000 0 0
EGF -0.07 0.2 -10000 0 -0.51 41 41
mol:ceramide -0.013 0.041 0.18 5 -10000 0 5
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.003 0.082 -10000 0 -0.4 10 10
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.065 0.17 5 -0.39 5 10
cell proliferation 0.002 0.065 -10000 0 -0.29 9 9
BID -0.006 0.099 -10000 0 -0.41 9 9
MAP3K1 -0.007 0.044 0.17 5 -0.37 1 6
EIF2A 0.007 0.035 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 0.01 0.034 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.035 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.005 0.037 0.16 5 -10000 0 5
FADD -0.011 0.13 -10000 0 -0.57 10 10
KSR1 -0.005 0.038 0.17 5 -10000 0 5
MAPK8 0.003 0.04 0.17 5 -0.2 2 7
PRKRA -0.005 0.038 0.17 5 -10000 0 5
PDGFA -0.01 0.11 -10000 0 -0.55 10 10
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.017 0.13 -10000 0 -0.55 13 13
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.013 0.041 0.18 5 -10000 0 5
CTSD 0.012 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.015 0.031 -10000 0 -0.48 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.004 0.069 -10000 0 -0.32 9 9
PRKCD 0.009 0.041 -10000 0 -0.65 1 1
PRKCZ 0.012 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.003 0.082 -10000 0 -0.4 10 10
RelA/NF kappa B1 0.015 0.031 -10000 0 -0.48 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.018 0.14 -10000 0 -0.61 10 10
TNFR1A/BAG4/TNF-alpha -0.033 0.14 -10000 0 -0.41 27 27
mol:Sphingosine-1-phosphate 0.003 0.082 -10000 0 -0.4 10 10
MAP2K1 0.007 0.035 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS 0.001 0.033 0.17 3 -10000 0 3
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.009 0.041 -10000 0 -0.65 1 1
TNFR1A/BAG4 0.017 0 -10000 0 -10000 0 0
EIF2AK2 0.001 0.036 0.17 1 -10000 0 1
TNF-alpha/TNFR1A/FAN -0.033 0.14 -10000 0 -0.41 27 27
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.088 -10000 0 -0.34 10 10
MAP2K2 0.007 0.035 -10000 0 -10000 0 0
SMPD3 -0.014 0.095 -10000 0 -0.34 12 12
TNF -0.077 0.21 -10000 0 -0.57 40 40
PKC zeta/PAR4 0.017 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.018 0.079 0.24 21 -10000 0 21
NF kappa B1/RelA/I kappa B alpha 0.032 0.033 -10000 0 -0.34 2 2
AIFM1 0.001 0.036 0.17 3 -0.23 1 4
BCL2 -0.003 0.083 -10000 0 -0.46 8 8
TCGA08_rtk_signaling

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
PDGFRA -0.038 0.17 -10000 0 -0.6 21 21
HRAS 0.012 0 -10000 0 -10000 0 0
EGFR -0.011 0.12 -10000 0 -0.57 10 10
AKT 0.007 0.09 -10000 0 -0.33 11 11
FOXO3 0.009 0.041 -10000 0 -0.65 1 1
AKT1 0.008 0.035 -10000 0 -0.39 2 2
FOXO1 0.005 0.063 -10000 0 -0.57 3 3
AKT3 -0.026 0.13 -10000 0 -0.46 21 21
FOXO4 0.012 0 -10000 0 -10000 0 0
MET -0.045 0.18 -10000 0 -0.61 24 24
PIK3CA 0.012 0 -10000 0 -10000 0 0
PIK3CB 0.012 0 -10000 0 -10000 0 0
NRAS 0.01 0.025 -10000 0 -0.39 1 1
PIK3CG -0.018 0.14 -10000 0 -0.63 12 12
PIK3R3 0.001 0.081 -10000 0 -0.65 4 4
PIK3R2 0.012 0 -10000 0 -10000 0 0
NF1 -0.011 0.12 -10000 0 -0.65 9 9
RAS -0.007 0.095 0.23 9 -0.35 7 16
ERBB2 0.007 0.043 -10000 0 -0.39 3 3
proliferation/survival/translation -0.01 0.05 0.2 3 -10000 0 3
PI3K -0.005 0.089 0.19 3 -0.29 12 15
PIK3R1 0.008 0.035 -10000 0 -0.39 2 2
KRAS -0.001 0.07 -10000 0 -0.39 8 8
FOXO 0.031 0.038 0.17 3 -0.21 1 4
AKT2 0.008 0.035 -10000 0 -0.39 2 2
PTEN 0.001 0.081 -10000 0 -0.65 4 4
Class I PI3K signaling events

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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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 -0.006 0.055 0.26 4 -10000 0 4
DAPP1 -0.039 0.18 -10000 0 -0.57 16 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.047 0.2 -10000 0 -0.58 24 24
mol:DAG -0.007 0.098 -10000 0 -0.27 18 18
HRAS 0.012 0.004 -10000 0 -10000 0 0
RAP1A 0.012 0.004 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.062 -10000 0 -0.34 3 3
PLCG2 0.009 0.041 -10000 0 -0.65 1 1
PLCG1 0.012 0 -10000 0 -10000 0 0
ARF5 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.057 0.24 4 -0.3 5 9
ARF1/GTP -0.006 0.055 0.25 4 -10000 0 4
RHOA 0.012 0 -10000 0 -10000 0 0
YES1 0.01 0.025 -10000 0 -0.39 1 1
RAP1A/GTP -0.007 0.056 0.23 4 -0.29 5 9
ADAP1 -0.017 0.079 0.23 4 -0.34 8 12
ARAP3 -0.007 0.057 0.24 4 -0.3 5 9
INPPL1 0.01 0.025 -10000 0 -0.39 1 1
PREX1 0.009 0.041 -10000 0 -0.65 1 1
ARHGEF6 0.007 0.048 -10000 0 -0.52 2 2
ARHGEF7 0.012 0 -10000 0 -10000 0 0
ARF1 0.012 0 -10000 0 -10000 0 0