PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C18K77ZH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C18K77ZH
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 48 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 383
HIF-1-alpha transcription factor network 212
Nephrin/Neph1 signaling in the kidney podocyte 188
TCGA08_p53 146
TCR signaling in naïve CD8+ T cells 141
FOXA2 and FOXA3 transcription factor networks 120
Syndecan-4-mediated signaling events 119
Aurora B signaling 119
FOXM1 transcription factor network 110
IL12-mediated signaling events 107
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 531 . 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 ( 531 ).

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 0.7213 383 3069 8 -0.84 0.22 1000 -1000 -0.031 -1000
HIF-1-alpha transcription factor network 0.3992 212 16112 76 -1.3 0.026 1000 -1000 -0.16 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.3540 188 6408 34 -0.61 0.016 1000 -1000 -0.098 -1000
TCGA08_p53 0.2750 146 1023 7 -0.65 0.31 1000 -1000 -0.022 -1000
TCR signaling in naïve CD8+ T cells 0.2655 141 13123 93 -0.66 0.33 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.2260 120 5537 46 -1.2 0.025 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.2241 119 7998 67 -0.64 0.11 1000 -1000 -0.14 -1000
Aurora B signaling 0.2241 119 7979 67 -0.4 0.016 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 0.2072 110 5633 51 -0.82 0.04 1000 -1000 -0.19 -1000
IL12-mediated signaling events 0.2015 107 9370 87 -0.69 0.16 1000 -1000 -0.16 -1000
Glypican 1 network 0.1996 106 5100 48 -0.56 0.045 1000 -1000 -0.069 -1000
PDGFR-alpha signaling pathway 0.1959 104 4618 44 -0.28 0.034 1000 -1000 -0.09 -1000
JNK signaling in the CD4+ TCR pathway 0.1582 84 1429 17 -0.41 0.016 1000 -1000 -0.092 -1000
amb2 Integrin signaling 0.1582 84 6941 82 -0.55 0.016 1000 -1000 -0.12 -1000
IL4-mediated signaling events 0.1412 75 6852 91 -0.84 0.54 1000 -1000 -0.18 -1000
EGFR-dependent Endothelin signaling events 0.1394 74 1561 21 -0.67 0.016 1000 -1000 -0.12 -1000
HIF-2-alpha transcription factor network 0.1356 72 3104 43 -0.76 0.34 1000 -1000 -0.11 -1000
Aurora C signaling 0.1337 71 497 7 -0.39 0.012 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 0.1318 70 5239 74 -0.32 0.16 1000 -1000 -0.076 -1000
Glypican 2 network 0.1299 69 278 4 -0.12 -1000 1000 -1000 -0.054 -1000
Syndecan-1-mediated signaling events 0.1262 67 2282 34 -0.41 0.016 1000 -1000 -0.1 -1000
BMP receptor signaling 0.1205 64 5240 81 -0.69 0.016 1000 -1000 -0.13 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1130 60 2004 33 -0.83 0.016 1000 -1000 -0.094 -1000
IL23-mediated signaling events 0.1111 59 3582 60 -0.39 0.021 1000 -1000 -0.18 -1000
Signaling events mediated by the Hedgehog family 0.0923 49 2577 52 -0.44 0.12 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 0.0866 46 4510 97 -0.32 0.04 1000 -1000 -0.12 -1000
S1P1 pathway 0.0810 43 1562 36 -0.38 0.018 1000 -1000 -0.088 -1000
IL27-mediated signaling events 0.0791 42 2159 51 -0.62 0.074 1000 -1000 -0.13 -1000
Ephrin A reverse signaling 0.0772 41 292 7 -0.059 0 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 0.0772 41 1083 26 -0.36 0.016 1000 -1000 -0.099 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0772 41 2829 68 -0.54 0.063 1000 -1000 -0.18 -1000
Arf6 signaling events 0.0734 39 2448 62 -0.67 0.016 1000 -1000 -0.089 -1000
VEGFR1 specific signals 0.0716 38 2131 56 -0.47 0.045 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 0.0697 37 1175 31 -0.46 0.016 1000 -1000 -0.17 -1000
p75(NTR)-mediated signaling 0.0678 36 4539 125 -0.42 0.016 1000 -1000 -0.15 -1000
LPA4-mediated signaling events 0.0640 34 417 12 -0.17 0.026 1000 -1000 -0.033 -1000
IL2 signaling events mediated by STAT5 0.0640 34 759 22 -0.44 0.038 1000 -1000 -0.07 -1000
IL2 signaling events mediated by PI3K 0.0621 33 1953 58 -0.43 0.032 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0584 31 2651 85 -0.38 0.016 1000 -1000 -0.075 -1000
IL6-mediated signaling events 0.0584 31 2367 75 -0.29 0.076 1000 -1000 -0.12 -1000
BCR signaling pathway 0.0584 31 3150 99 -0.34 0.035 1000 -1000 -0.14 -1000
Coregulation of Androgen receptor activity 0.0565 30 2349 76 -0.92 0.033 1000 -1000 -0.07 -1000
Regulation of Telomerase 0.0546 29 3020 102 -0.67 0.051 1000 -1000 -0.15 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0546 29 2335 78 -0.32 0.045 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0527 28 1550 54 -0.65 0.031 1000 -1000 -0.14 -1000
Reelin signaling pathway 0.0527 28 1570 56 -0.24 0.016 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0508 27 3146 114 -0.41 0.16 1000 -1000 -0.11 -1000
Integrins in angiogenesis 0.0508 27 2331 84 -0.38 0.04 1000 -1000 -0.13 -1000
Aurora A signaling 0.0452 24 1484 60 -0.24 0.053 1000 -1000 -0.091 -1000
EPO signaling pathway 0.0452 24 1372 55 -0.29 0.018 1000 -1000 -0.14 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0452 24 2125 88 -0.31 0.075 1000 -1000 -0.15 -1000
Visual signal transduction: Rods 0.0452 24 1285 52 -0.29 0.016 1000 -1000 -0.11 -1000
Signaling events mediated by PTP1B 0.0433 23 1755 76 -0.67 0.049 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 0.0377 20 1439 69 -0.55 0.053 1000 -1000 -0.092 -1000
Endothelins 0.0377 20 1958 96 -0.35 0.086 1000 -1000 -0.11 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0377 20 900 45 -0.57 0.062 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 0.0358 19 2673 136 -0.45 0.1 1000 -1000 -0.11 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0358 19 2347 120 -0.16 0.14 1000 -1000 -0.13 -1000
Wnt signaling 0.0339 18 127 7 -0.068 0.016 1000 -1000 -0.077 -1000
S1P3 pathway 0.0320 17 719 42 -0.38 0.062 1000 -1000 -0.084 -1000
Thromboxane A2 receptor signaling 0.0301 16 1732 105 -0.67 0.067 1000 -1000 -0.11 -1000
Presenilin action in Notch and Wnt signaling 0.0301 16 1035 61 -0.19 0.093 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0301 16 609 37 -0.29 0.026 1000 -1000 -0.12 -1000
Ceramide signaling pathway 0.0282 15 1159 76 -0.67 0.23 1000 -1000 -0.085 -1000
FoxO family signaling 0.0282 15 1003 64 -0.57 0.12 1000 -1000 -0.1 -1000
LPA receptor mediated events 0.0282 15 1612 102 -0.4 0.061 1000 -1000 -0.12 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0264 14 416 28 -0.14 0.024 1000 -1000 -0.076 -1000
PLK2 and PLK4 events 0.0264 14 44 3 -0.016 0.011 1000 -1000 -0.046 -1000
E-cadherin signaling events 0.0264 14 71 5 -0.023 0.016 1000 -1000 -0.066 -1000
FAS signaling pathway (CD95) 0.0245 13 638 47 -0.42 0.027 1000 -1000 -0.066 -1000
Canonical Wnt signaling pathway 0.0245 13 708 51 -0.19 0.096 1000 -1000 -0.085 -1000
Class I PI3K signaling events 0.0245 13 1003 73 -0.47 0.036 1000 -1000 -0.11 -1000
Regulation of Androgen receptor activity 0.0245 13 932 70 -0.96 0.04 1000 -1000 -0.096 -1000
ErbB4 signaling events 0.0226 12 839 69 -0.18 0.1 1000 -1000 -0.13 -1000
IFN-gamma pathway 0.0226 12 879 68 -0.37 0.018 1000 -1000 -0.14 -1000
Nongenotropic Androgen signaling 0.0226 12 638 52 -0.18 0.07 1000 -1000 -0.088 -1000
S1P5 pathway 0.0207 11 193 17 -0.14 0.045 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0207 11 1495 125 -0.39 0.043 1000 -1000 -0.16 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0207 11 863 74 -0.67 0.098 1000 -1000 -0.13 -1000
S1P4 pathway 0.0207 11 277 25 -0.14 0.034 1000 -1000 -0.078 -1000
Noncanonical Wnt signaling pathway 0.0188 10 270 26 -0.12 0.016 1000 -1000 -0.13 -1000
Visual signal transduction: Cones 0.0169 9 370 38 -0.041 0.016 1000 -1000 -0.088 -1000
a4b1 and a4b7 Integrin signaling 0.0169 9 48 5 -0.02 0.016 1000 -1000 -0.048 -1000
TCGA08_rtk_signaling 0.0169 9 239 26 -0.28 0.041 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0151 8 731 82 -0.064 0.025 1000 -1000 -0.12 -1000
Class IB PI3K non-lipid kinase events 0.0151 8 24 3 -0.003 0.003 1000 -1000 -0.016 -1000
Signaling events mediated by PRL 0.0132 7 245 34 -0.055 0.045 1000 -1000 -0.089 -1000
Canonical NF-kappaB pathway 0.0113 6 270 39 -0.19 0.075 1000 -1000 -0.11 -1000
Insulin-mediated glucose transport 0.0113 6 194 32 -0.083 0.068 1000 -1000 -0.091 -1000
Signaling events mediated by HDAC Class III 0.0113 6 240 40 -0.057 0.032 1000 -1000 -0.074 -1000
IL1-mediated signaling events 0.0113 6 401 62 -0.091 0.059 1000 -1000 -0.14 -1000
Ephrin B reverse signaling 0.0113 6 319 48 -0.03 0.031 1000 -1000 -0.12 -1000
p38 MAPK signaling pathway 0.0113 6 276 44 -0.099 0.049 1000 -1000 -0.088 -1000
ErbB2/ErbB3 signaling events 0.0094 5 388 65 -0.13 0.059 1000 -1000 -0.11 -1000
Arf6 downstream pathway 0.0094 5 225 43 -0.033 0.033 1000 -1000 -0.063 -1000
Signaling mediated by p38-gamma and p38-delta 0.0094 5 85 15 0 0.036 1000 -1000 -0.05 -1000
Paxillin-dependent events mediated by a4b1 0.0094 5 211 36 -0.027 0.031 1000 -1000 -0.098 -1000
Syndecan-3-mediated signaling events 0.0094 5 209 35 -0.039 0.016 1000 -1000 -0.099 -1000
E-cadherin signaling in the nascent adherens junction 0.0094 5 430 76 -0.026 0.067 1000 -1000 -0.12 -1000
Arf6 trafficking events 0.0094 5 411 71 -0.12 0.058 1000 -1000 -0.1 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0075 4 369 85 -0.037 0.079 1000 -1000 -0.1 -1000
EPHB forward signaling 0.0075 4 369 85 -0.075 0.069 1000 -1000 -0.14 -1000
Plasma membrane estrogen receptor signaling 0.0075 4 372 86 -0.16 0.07 1000 -1000 -0.12 -1000
Ras signaling in the CD4+ TCR pathway 0.0075 4 84 17 -0.038 0.055 1000 -1000 -0.069 -1000
BARD1 signaling events 0.0056 3 222 57 -0.17 0.044 1000 -1000 -0.096 -1000
Osteopontin-mediated events 0.0056 3 122 38 -0.03 0.097 1000 -1000 -0.16 -1000
Cellular roles of Anthrax toxin 0.0056 3 119 39 -0.022 0.027 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 0.0056 3 380 97 -0.056 0.087 1000 -1000 -0.12 -1000
E-cadherin signaling in keratinocytes 0.0056 3 164 43 -0.29 0.054 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0038 2 135 65 -0.06 0.093 1000 -1000 -0.09 -1000
ceramide signaling pathway 0.0038 2 131 49 -0.12 0.054 1000 -1000 -0.068 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0038 2 130 52 -0.031 0.092 1000 -1000 -0.088 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0038 2 181 83 -0.083 0.081 1000 -1000 -0.11 -1000
Retinoic acid receptors-mediated signaling 0.0038 2 126 58 -0.025 0.062 1000 -1000 -0.11 -1000
Signaling mediated by p38-alpha and p38-beta 0.0038 2 115 44 -0.046 0.049 1000 -1000 -0.072 -1000
Regulation of p38-alpha and p38-beta 0.0038 2 153 54 -0.04 0.073 1000 -1000 -0.086 -1000
Insulin Pathway 0.0038 2 214 74 -0.032 0.055 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class II 0.0019 1 124 75 -0.026 0.051 1000 -1000 -0.099 -1000
Circadian rhythm pathway 0.0019 1 33 22 -0.019 0.064 1000 -1000 -0.089 -1000
mTOR signaling pathway 0.0019 1 103 53 -0.01 0.044 1000 -1000 -0.089 -1000
Class I PI3K signaling events mediated by Akt 0.0019 1 104 68 -0.083 0.059 1000 -1000 -0.1 -1000
Nectin adhesion pathway 0.0019 1 98 63 -0.016 0.078 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class I 0.0019 1 194 104 -0.028 0.063 1000 -1000 -0.1 -1000
Atypical NF-kappaB pathway 0.0019 1 55 31 -0.02 0.037 1000 -1000 -0.099 -1000
IGF1 pathway 0.0019 1 98 57 -0.065 0.071 1000 -1000 -0.14 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.062 1000 -1000 -0.1 -1000
TRAIL signaling pathway 0.0000 0 27 48 -0.002 0.07 1000 -1000 -0.092 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.087 -1000
Rapid glucocorticoid signaling 0.0000 0 16 20 -0.006 0.016 1000 -1000 -0.068 -1000
Arf1 pathway 0.0000 0 31 54 -0.01 0.043 1000 -1000 -0.077 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 -0.005 0.016 1000 -1000 -0.097 -1000
Total NA 4254 222079 7203 -40 -990 131000 -131000 -13 -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 -0.011 0.099 -10000 0 -0.87 7 7
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.84 0.17 -10000 0 -0.87 511 511
CCND2 0.18 0.049 0.19 510 -10000 0 510
RB1 -0.2 0.051 -10000 0 -0.21 510 510
CDK4 0.22 0.052 0.23 510 -10000 0 510
CDK6 0.2 0.055 0.21 510 -0.18 1 511
G1/S progression 0.2 0.055 0.21 510 -10000 0 510
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.98 0.53 -9999 0 -1.3 324 324
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.91 317 317
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.98 0.53 -9999 0 -1.3 336 336
AP1 -0.014 0.087 -9999 0 -0.56 13 13
ABCG2 -0.98 0.53 -9999 0 -1.3 325 325
HIF1A -0.1 0.068 -9999 0 -0.89 2 2
TFF3 -0.99 0.53 -9999 0 -1.3 326 326
GATA2 -0.001 0.12 -9999 0 -0.74 13 13
AKT1 -0.093 0.053 -9999 0 -10000 0 0
response to hypoxia -0.13 0.058 -9999 0 -10000 0 0
MCL1 -0.98 0.53 -9999 0 -1.3 324 324
NDRG1 -0.98 0.53 -9999 0 -1.4 308 308
SERPINE1 -1 0.56 -9999 0 -1.4 335 335
FECH -0.98 0.53 -9999 0 -1.3 326 326
FURIN -0.98 0.53 -9999 0 -1.3 326 326
NCOA2 -0.005 0.11 -9999 0 -0.74 11 11
EP300 -0.1 0.076 -9999 0 -0.36 6 6
HMOX1 -1 0.54 -9999 0 -1.4 328 328
BHLHE40 -0.98 0.53 -9999 0 -1.3 334 334
BHLHE41 -1.1 0.58 -9999 0 -1.4 342 342
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.08 0.056 -9999 0 -0.6 2 2
ENG -0.059 0.064 -9999 0 -0.55 1 1
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.98 0.53 -9999 0 -1.4 308 308
ABCB1 -0.3 0.42 -9999 0 -1.3 70 70
TFRC -0.98 0.53 -9999 0 -1.3 326 326
CXCR4 -1.1 0.59 -9999 0 -1.5 341 341
TF -1 0.58 -9999 0 -1.4 334 334
CITED2 -0.98 0.53 -9999 0 -1.4 308 308
HIF1A/ARNT -1.3 0.85 -9999 0 -1.8 346 346
LDHA -0.086 0.062 -9999 0 -0.86 2 2
ETS1 -0.98 0.53 -9999 0 -1.3 326 326
PGK1 -0.98 0.53 -9999 0 -1.3 326 326
NOS2 -0.99 0.53 -9999 0 -1.3 326 326
ITGB2 -1 0.57 -9999 0 -1.4 331 331
ALDOA -0.98 0.53 -9999 0 -1.3 323 323
Cbp/p300/CITED2 -0.98 0.53 -9999 0 -1.4 302 302
FOS -0.002 0.12 -9999 0 -0.75 13 13
HK2 -1.2 0.58 -9999 0 -1.5 396 396
SP1 0.021 0.029 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.1 10 10
HK1 -0.98 0.53 -9999 0 -1.4 301 301
NPM1 -0.98 0.53 -9999 0 -1.3 324 324
EGLN1 -0.98 0.53 -9999 0 -1.3 325 325
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.98 0.53 -9999 0 -1.3 326 326
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.092 0.17 -9999 0 -0.8 19 19
IGFBP1 -1 0.57 -9999 0 -1.4 315 315
VEGFA -0.78 0.41 -9999 0 -1.2 243 243
HIF1A/JAB1 -0.055 0.047 -9999 0 -0.69 2 2
CP -1.2 0.59 -9999 0 -1.5 393 393
CXCL12 -0.99 0.53 -9999 0 -1.3 330 330
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.98 0.53 -9999 0 -1.3 324 324
EGLN3 -1.3 0.51 -9999 0 -1.5 419 419
CA9 -1.3 0.48 -9999 0 -1.5 429 429
TERT -1 0.55 -9999 0 -1.4 335 335
ENO1 -0.98 0.53 -9999 0 -1.3 324 324
PFKL -0.98 0.53 -9999 0 -1.3 336 336
NCOA1 0.015 0.003 -9999 0 -10000 0 0
ADM -1.1 0.57 -9999 0 -1.4 341 341
ARNT -0.1 0.047 -9999 0 -10000 0 0
HNF4A -0.043 0.21 -9999 0 -0.74 44 44
ADFP -0.99 0.53 -9999 0 -1.3 340 340
SLC2A1 -0.63 0.34 -9999 0 -0.97 177 177
LEP -1 0.54 -9999 0 -1.4 316 316
HIF1A/ARNT/Cbp/p300 -0.71 0.34 -9999 0 -0.93 319 319
EPO -0.61 0.4 -9999 0 -1.1 186 186
CREBBP -0.099 0.074 -9999 0 -0.35 5 5
HIF1A/ARNT/Cbp/p300/HDAC7 -0.75 0.39 -9999 0 -1 322 322
PFKFB3 -0.98 0.53 -9999 0 -1.4 306 306
NT5E -0.98 0.53 -9999 0 -1.3 324 324
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.48 0.26 0.62 414 -10000 0 414
KIRREL -0.056 0.11 -10000 0 -0.81 10 10
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.49 0.26 -10000 0 -0.62 414 414
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.53 0.31 -10000 0 -0.84 230 230
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.41 0.26 -10000 0 -0.66 230 230
FYN -0.5 0.3 -10000 0 -0.79 230 230
mol:Ca2+ -0.52 0.3 -10000 0 -0.82 230 230
mol:DAG -0.52 0.3 -10000 0 -0.83 230 230
NPHS2 -0.41 0.38 -10000 0 -0.8 254 254
mol:IP3 -0.52 0.3 -10000 0 -0.83 230 230
regulation of endocytosis -0.47 0.28 -10000 0 -0.74 230 230
Nephrin/NEPH1/podocin/Cholesterol -0.54 0.31 -10000 0 -0.65 441 441
establishment of cell polarity -0.48 0.26 -10000 0 -0.62 414 414
Nephrin/NEPH1/podocin/NCK1-2 -0.49 0.29 -10000 0 -0.78 230 230
Nephrin/NEPH1/beta Arrestin2 -0.48 0.28 -10000 0 -0.76 230 230
NPHS1 -0.61 0.32 -10000 0 -0.78 411 411
Nephrin/NEPH1/podocin -0.5 0.3 -10000 0 -0.8 230 230
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.033 -10000 0 -0.74 1 1
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.53 0.31 -10000 0 -0.84 230 230
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.53 0.31 -10000 0 -0.84 230 230
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.49 0.3 -10000 0 -0.78 230 230
cytoskeleton organization -0.53 0.32 -10000 0 -0.84 230 230
Nephrin/NEPH1 -0.36 0.2 -10000 0 -0.46 414 414
Nephrin/NEPH1/ZO-1 -0.39 0.21 -10000 0 -0.5 414 414
TCGA08_p53

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
CDKN2A -0.65 0.13 -10000 0 -0.68 511 511
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.037 -10000 0 -10000 0 0
Apoptosis -0.17 0.037 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.062 0.32 511 -10000 0 511
MDM4 0.014 0.038 -10000 0 -0.86 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.69 229 229
FYN -0.41 0.49 -10000 0 -0.93 235 235
LAT/GRAP2/SLP76 -0.36 0.38 -10000 0 -0.76 236 236
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.25 0.28 -10000 0 -0.54 241 241
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.079 0.072 -10000 0 -0.19 84 84
MAP3K8 0.012 0.054 -10000 0 -0.86 2 2
mol:Ca2+ -0.11 0.045 -10000 0 -0.14 281 281
integrin-mediated signaling pathway -0.02 0.1 -10000 0 -0.58 18 18
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.41 0.45 -10000 0 -0.85 249 249
TRPV6 -0.66 0.26 -10000 0 -0.76 459 459
CD28 -0.058 0.23 -10000 0 -0.87 40 40
SHC1 -0.44 0.49 -10000 0 -0.94 244 244
receptor internalization -0.51 0.56 -10000 0 -1.1 251 251
PRF1 -0.48 0.59 -10000 0 -1.1 244 244
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.18 0.22 -10000 0 -0.41 225 225
LAT -0.5 0.53 -10000 0 -1 260 260
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 239 239
CD3E -0.34 0.44 -10000 0 -0.87 213 213
CD3G -0.32 0.43 -10000 0 -0.87 203 203
RASGRP2 -0.023 0.029 -10000 0 -0.14 2 2
RASGRP1 -0.23 0.27 -10000 0 -0.5 238 238
HLA-A 0.005 0.055 -10000 0 -0.87 2 2
RASSF5 -0.014 0.16 -10000 0 -0.86 18 18
RAP1A/GTP/RAPL -0.02 0.11 -10000 0 -0.59 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.081 -10000 0 -0.14 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 103 103
PRKCA -0.14 0.17 -10000 0 -0.31 199 199
GRAP2 -0.042 0.22 -10000 0 -0.86 35 35
mol:IP3 -0.16 0.34 0.28 113 -0.5 220 333
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.52 0.63 -10000 0 -1.1 251 251
ORAI1 0.33 0.13 -10000 0 -10000 0 0
CSK -0.45 0.51 -10000 0 -0.97 243 243
B7 family/CD28 -0.51 0.51 -10000 0 -1 246 246
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.56 0.62 -10000 0 -1.2 251 251
PTPN6 -0.43 0.52 -10000 0 -1 232 232
VAV1 -0.48 0.53 -10000 0 -1 256 256
Monovalent TCR/CD3 -0.45 0.53 -10000 0 -0.99 239 239
CBL 0.014 0.033 -10000 0 -0.74 1 1
LCK -0.44 0.53 -10000 0 -0.98 239 239
PAG1 -0.45 0.51 -10000 0 -0.97 244 244
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.63 -10000 0 -1.2 241 241
CD80 -0.18 0.36 -10000 0 -0.87 115 115
CD86 -0.13 0.32 -10000 0 -0.87 82 82
PDK1/CARD11/BCL10/MALT1 -0.18 0.17 -10000 0 -0.36 192 192
HRAS 0.014 0.038 -10000 0 -0.86 1 1
GO:0035030 -0.35 0.41 -10000 0 -0.77 245 245
CD8A -0.38 0.44 -10000 0 -0.87 236 236
CD8B -0.3 0.42 -10000 0 -0.87 186 186
PTPRC -0.084 0.27 -10000 0 -0.87 56 56
PDK1/PKC theta -0.32 0.36 -10000 0 -0.69 242 242
CSK/PAG1 -0.43 0.49 -10000 0 -0.95 240 240
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.042 -10000 0 -0.68 2 2
GRAP2/SLP76 -0.43 0.44 -10000 0 -0.88 243 243
STIM1 0.17 0.064 -10000 0 -10000 0 0
RAS family/GTP -0.063 0.11 -10000 0 -0.25 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.59 0.65 -10000 0 -1.2 251 251
mol:DAG -0.2 0.26 -10000 0 -0.46 236 236
RAP1A/GDP -0.014 0.035 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.27 0.41 -10000 0 -0.87 172 172
cytotoxic T cell degranulation -0.44 0.55 -10000 0 -0.99 244 244
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.31 0.35 -10000 0 -0.66 248 248
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.26 0.44 0.3 107 -0.7 233 340
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.47 0.44 -10000 0 -0.86 294 294
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.38 0.35 -10000 0 -0.73 244 244
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.49 0.56 -10000 0 -1.1 242 242
CARD11 -0.17 0.36 -10000 0 -0.86 110 110
PRKCB -0.14 0.17 -10000 0 -0.32 200 200
PRKCE -0.14 0.17 -10000 0 -0.31 208 208
PRKCQ -0.39 0.42 -10000 0 -0.8 252 252
LCP2 -0.04 0.22 -10000 0 -0.86 34 34
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.2 0.24 -10000 0 -0.45 239 239
IKK complex -0.028 0.084 -10000 0 -10000 0 0
RAS family/GDP -0.011 0.012 -10000 0 -0.11 1 1
MAP3K14 -0.13 0.18 -10000 0 -0.32 141 141
PDPK1 -0.23 0.27 -10000 0 -0.51 237 237
TCR/CD3/MHC I/CD8/Fyn -0.55 0.65 -10000 0 -1.2 242 242
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.47 -10000 0 -1.2 112 112
PCK1 -0.93 0.71 -10000 0 -1.5 285 285
HNF4A -0.58 0.58 -10000 0 -1.4 140 140
KCNJ11 -0.44 0.51 -10000 0 -1.3 105 105
AKT1 -0.17 0.18 -10000 0 -10000 0 0
response to starvation -0.02 0.038 -10000 0 -10000 0 0
DLK1 -0.55 0.57 -10000 0 -1.2 174 174
NKX2-1 -0.057 0.21 0.58 1 -0.84 4 5
ACADM -0.45 0.47 -10000 0 -1.1 121 121
TAT -0.51 0.35 -10000 0 -0.94 161 161
CEBPB -0.024 0.14 -10000 0 -0.92 12 12
CEBPA -0.019 0.12 -10000 0 -0.9 10 10
TTR -0.88 0.48 -10000 0 -1.2 330 330
PKLR -0.5 0.56 -10000 0 -1.3 128 128
APOA1 -0.55 0.56 -10000 0 -1.3 141 141
CPT1C -0.45 0.48 -10000 0 -1.1 122 122
ALAS1 -0.17 0.19 -10000 0 -10000 0 0
TFRC -0.62 0.42 -10000 0 -1 228 228
FOXF1 -0.001 0.12 -10000 0 -0.84 10 10
NF1 0.025 0.001 -10000 0 -10000 0 0
HNF1A (dimer) -0.003 0.086 -10000 0 -0.79 5 5
CPT1A -0.45 0.47 -10000 0 -1.1 129 129
HMGCS1 -0.45 0.47 -10000 0 -1.1 118 118
NR3C1 0.003 0.065 -10000 0 -0.96 1 1
CPT1B -0.46 0.5 -10000 0 -1.2 121 121
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.017 0.005 -10000 0 -10000 0 0
GCK -0.45 0.48 -10000 0 -1.1 133 133
CREB1 -0.028 0.066 -10000 0 -10000 0 0
IGFBP1 -0.32 0.42 -10000 0 -1 120 120
PDX1 -0.19 0.22 -10000 0 -1 6 6
UCP2 -0.45 0.47 -10000 0 -1.1 118 118
ALDOB -0.94 0.62 -10000 0 -1.2 408 408
AFP -0.7 0.49 -10000 0 -0.96 329 329
BDH1 -0.59 0.57 -10000 0 -1.2 191 191
HADH -0.44 0.49 -10000 0 -1.2 104 104
F2 -0.65 0.62 -10000 0 -1.3 192 192
HNF1A -0.003 0.086 -10000 0 -0.79 5 5
G6PC -0.81 0.66 -10000 0 -1.5 254 254
SLC2A2 -0.32 0.48 -10000 0 -1.7 48 48
INS 0.009 0.055 -10000 0 -10000 0 0
FOXA1 -0.36 0.38 -10000 0 -1 127 127
FOXA3 -0.61 0.37 -10000 0 -0.84 334 334
FOXA2 -0.51 0.57 -10000 0 -1.3 139 139
ABCC8 -0.44 0.49 -10000 0 -1.2 111 111
ALB -1.2 0.48 -10000 0 -1.4 460 460
Syndecan-4-mediated signaling events

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
PTK2 -0.053 0.14 -9999 0 -0.54 38 38
Syndecan-4/Syndesmos -0.46 0.39 -9999 0 -0.84 234 234
positive regulation of JNK cascade -0.53 0.37 -9999 0 -0.84 285 285
Syndecan-4/ADAM12 -0.56 0.49 -9999 0 -1 258 258
CCL5 -0.35 0.43 -9999 0 -0.86 223 223
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.047 0.23 -9999 0 -0.86 38 38
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.36 0.37 -9999 0 -0.72 273 273
ADAM12 -0.22 0.39 -9999 0 -0.86 141 141
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.47 0.4 -9999 0 -0.86 236 236
Syndecan-4/CXCL12/CXCR4 -0.59 0.43 -9999 0 -0.94 285 285
Syndecan-4/Laminin alpha3 -0.46 0.39 -9999 0 -0.85 239 239
MDK -0.049 0.23 -9999 0 -0.86 39 39
Syndecan-4/FZD7 -0.46 0.39 -9999 0 -0.84 235 235
Syndecan-4/Midkine -0.49 0.41 -9999 0 -0.88 247 247
FZD7 0.014 0.033 -9999 0 -0.74 1 1
Syndecan-4/FGFR1/FGF -0.43 0.33 -9999 0 -0.77 236 236
THBS1 0.011 0.057 -9999 0 -0.74 3 3
integrin-mediated signaling pathway -0.44 0.36 -9999 0 -0.79 240 240
positive regulation of MAPKKK cascade -0.53 0.37 -9999 0 -0.84 285 285
Syndecan-4/TACI -0.5 0.42 -9999 0 -0.9 247 247
CXCR4 -0.29 0.42 -9999 0 -0.86 184 184
cell adhesion -0.007 0.12 -9999 0 -0.51 14 14
Syndecan-4/Dynamin -0.46 0.39 -9999 0 -0.84 234 234
Syndecan-4/TSP1 -0.46 0.39 -9999 0 -0.84 236 236
Syndecan-4/GIPC -0.46 0.39 -9999 0 -0.84 235 235
Syndecan-4/RANTES -0.64 0.46 -9999 0 -1 292 292
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.006 0.13 -9999 0 -0.75 15 15
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.066 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.46 0.39 -9999 0 -0.85 235 235
TFPI 0.002 0.11 -9999 0 -0.81 9 9
F2 -0.32 0.42 -9999 0 -0.87 199 199
alpha5/beta1 Integrin -0.048 0.17 -9999 0 -0.66 38 38
positive regulation of cell adhesion -0.45 0.38 -9999 0 -0.82 241 241
ACTN1 0.013 0.05 -9999 0 -0.8 2 2
TNC -0.004 0.12 -9999 0 -0.74 14 14
Syndecan-4/CXCL12 -0.47 0.39 -9999 0 -0.85 240 240
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.001 0.11 -9999 0 -0.74 12 12
TNFRSF13B -0.069 0.26 -9999 0 -0.86 50 50
FGF2 0.008 0.076 -9999 0 -0.77 5 5
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.47 0.39 -9999 0 -0.85 234 234
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.038 0.22 -9999 0 -0.83 38 38
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.045 -9999 0 -0.85 1 1
vasculogenesis -0.44 0.36 -9999 0 -0.79 236 236
SDC4 -0.5 0.43 -9999 0 -0.93 234 234
Syndecan-4/Tenascin C -0.47 0.39 -9999 0 -0.84 240 240
Syndecan-4/PI-4-5-P2/PKC alpha -0.079 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.46 0.39 -9999 0 -0.84 234 234
MMP9 -0.4 0.44 -9999 0 -0.86 249 249
Rac1/GTP -0.007 0.12 -9999 0 -0.53 14 14
cytoskeleton organization -0.43 0.36 -9999 0 -0.79 234 234
GIPC1 0.014 0.033 -9999 0 -0.74 1 1
Syndecan-4/TFPI -0.46 0.39 -9999 0 -0.85 238 238
Aurora B signaling

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
Condensin I complex -0.24 0.32 -9999 0 -0.68 162 162
STMN1 -0.29 0.34 -9999 0 -0.66 247 247
Aurora B/RasGAP/Survivin -0.4 0.48 -9999 0 -0.87 252 252
Chromosomal passenger complex/Cul3 protein complex -0.16 0.23 -9999 0 -0.49 151 151
BIRC5 -0.25 0.41 -9999 0 -0.89 154 154
DES -0.38 0.34 -9999 0 -0.6 315 315
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 248 248
Aurora B/TACC1 -0.26 0.3 -9999 0 -0.58 247 247
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 247 247
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.072 0.09 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.4 0.5 -9999 0 -0.89 252 252
Cul3 protein complex -0.015 0.083 -9999 0 -0.47 17 17
KIF2C -0.15 0.18 -9999 0 -0.35 192 192
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.38 0.44 -9999 0 -0.86 237 237
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 248 248
SEPT1 -0.095 0.29 -9999 0 -0.86 67 67
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.18 0.24 -9999 0 -0.46 181 181
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.004 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 247 247
AURKB -0.4 0.44 -9999 0 -0.87 247 247
AURKC 0.012 0.054 -9999 0 -0.86 2 2
CDCA8 -0.026 0.17 -9999 0 -0.89 20 20
cytokinesis -0.34 0.37 -9999 0 -0.76 211 211
Aurora B/Septin1 -0.36 0.42 -9999 0 -0.84 207 207
AURKA 0.002 0.094 -9999 0 -0.87 6 6
INCENP 0.008 0.009 -9999 0 -10000 0 0
KLHL13 -0.009 0.13 -9999 0 -0.74 17 17
BUB1 -0.37 0.44 -9999 0 -0.86 232 232
hSgo1/Aurora B/Survivin -0.4 0.48 -9999 0 -0.85 253 253
EVI5 0.01 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.34 -9999 0 -0.72 193 193
SGOL1 -0.014 0.16 -9999 0 -0.86 18 18
CENPA -0.29 0.35 -9999 0 -0.63 254 254
NCAPG -0.27 0.41 -9999 0 -0.86 175 175
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 247 247
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 247 247
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.13 0.33 -9999 0 -0.86 90 90
NPM1 -0.21 0.24 -9999 0 -0.47 247 247
RASA1 0.014 0.033 -9999 0 -0.74 1 1
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 247 247
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.34 0.38 -9999 0 -0.78 200 200
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.21 0.24 -9999 0 -0.47 247 247
MYLK -0.17 0.21 -9999 0 -0.39 247 247
KIF23 -0.006 0.11 -9999 0 -0.88 8 8
VIM -0.34 0.4 -9999 0 -0.73 262 262
RACGAP1 0.004 0.055 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.21 0.24 -9999 0 -0.47 247 247
Chromosomal passenger complex -0.34 0.41 -9999 0 -0.76 239 239
Chromosomal passenger complex/EVI5 -0.36 0.48 -9999 0 -1 149 149
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.18 0.68 -10000 0 -1.2 124 124
PLK1 -0.098 0.41 -10000 0 -0.8 129 129
BIRC5 -0.13 0.43 -10000 0 -0.79 154 154
HSPA1B -0.18 0.68 -10000 0 -1.2 125 125
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.19 0.68 -10000 0 -1.2 130 130
FOXM1 -0.37 1 -10000 0 -1.9 135 135
XRCC1 -0.18 0.68 -10000 0 -1.2 125 125
FOXM1B/p19 -0.49 0.49 0.5 1 -1.2 137 138
Cyclin D1/CDK4 -0.18 0.61 -10000 0 -1.1 119 119
CDC2 -0.21 0.72 -10000 0 -1.3 135 135
TGFA -0.16 0.6 -10000 0 -1 125 125
SKP2 -0.18 0.68 -10000 0 -1.2 124 124
CCNE1 0.002 0.11 -10000 0 -0.88 8 8
CKS1B -0.18 0.68 -10000 0 -1.2 124 124
RB1 -0.19 0.26 -10000 0 -0.69 95 95
FOXM1C/SP1 -0.28 0.78 -10000 0 -1.4 137 137
AURKB -0.25 0.46 -10000 0 -0.74 243 243
CENPF -0.21 0.72 -10000 0 -1.3 127 127
CDK4 0.021 0.022 -10000 0 -10000 0 0
MYC -0.15 0.6 -10000 0 -1 123 123
CHEK2 0.037 0.075 -10000 0 -0.91 2 2
ONECUT1 -0.19 0.65 -10000 0 -1.2 125 125
CDKN2A -0.82 0.17 -10000 0 -0.86 511 511
LAMA4 -0.28 0.69 -10000 0 -1.3 137 137
FOXM1B/HNF6 -0.27 0.79 -10000 0 -1.5 127 127
FOS -0.2 0.69 -10000 0 -1.2 128 128
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.18 0.68 -10000 0 -1.2 125 125
response to radiation 0.014 0.05 -10000 0 -10000 0 0
CENPB -0.18 0.68 -10000 0 -1.2 124 124
CENPA -0.28 0.78 -10000 0 -1.3 162 162
NEK2 -0.24 0.75 -10000 0 -1.3 141 141
HIST1H2BA -0.19 0.68 -10000 0 -1.2 124 124
CCNA2 -0.15 0.35 -10000 0 -0.88 102 102
EP300 0.014 0.033 -10000 0 -0.74 1 1
CCNB1/CDK1 -0.27 0.81 -10000 0 -1.5 134 134
CCNB2 -0.24 0.75 -10000 0 -1.4 135 135
CCNB1 -0.21 0.72 -10000 0 -1.3 134 134
ETV5 -0.18 0.68 -10000 0 -1.2 125 125
ESR1 -0.19 0.68 -10000 0 -1.2 126 126
CCND1 -0.18 0.63 -10000 0 -1.1 121 121
GSK3A 0.036 0.041 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.08 0.28 -10000 0 -0.64 103 103
CDK2 0.015 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.58 -10000 0 -1.3 139 139
GAS1 -0.23 0.7 -10000 0 -1.2 138 138
MMP2 -0.19 0.68 -10000 0 -1.2 125 125
RB1/FOXM1C -0.21 0.67 -10000 0 -1.2 124 124
CREBBP 0.016 0 -10000 0 -10000 0 0
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 -0.16 0.26 -10000 0 -0.64 72 72
TBX21 -0.54 0.67 -10000 0 -1.3 212 212
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.021 -10000 0 -10000 0 0
IL12RB1 -0.26 0.42 -10000 0 -0.9 160 160
GADD45B -0.29 0.42 -10000 0 -0.83 139 139
IL12RB2 -0.11 0.31 -10000 0 -0.87 75 75
GADD45G -0.3 0.43 -10000 0 -0.82 161 161
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.002 0.1 -10000 0 -0.87 7 7
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IFNG -0.38 0.44 -10000 0 -0.86 238 238
STAT3 (dimer) -0.37 0.46 -10000 0 -0.88 200 200
HLA-DRB5 -0.036 0.21 -10000 0 -0.86 32 32
FASLG -0.6 0.7 -10000 0 -1.3 233 233
NF kappa B2 p52/RelB -0.51 0.53 -10000 0 -1.1 216 216
CD4 0.001 0.11 -10000 0 -0.86 9 9
SOCS1 0.006 0.093 -10000 0 -0.86 6 6
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 239 239
CD3E -0.34 0.43 -10000 0 -0.87 213 213
CD3G -0.32 0.43 -10000 0 -0.87 203 203
IL12Rbeta2/JAK2 -0.083 0.25 -10000 0 -0.68 75 75
CCL3 -0.48 0.63 -10000 0 -1.2 197 197
CCL4 -0.5 0.66 -10000 0 -1.3 193 193
HLA-A 0.007 0.054 -10000 0 -0.86 2 2
IL18/IL18R -0.12 0.3 -10000 0 -0.6 147 147
NOS2 -0.36 0.49 -10000 0 -0.95 172 172
IL12/IL12R/TYK2/JAK2/SPHK2 -0.16 0.26 -10000 0 -0.51 136 136
IL1R1 -0.44 0.59 -10000 0 -1.2 177 177
IL4 0.013 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.021 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.69 0.81 -10000 0 -1.4 260 260
RAB7A -0.23 0.37 -10000 0 -0.79 51 51
lysosomal transport -0.22 0.36 -10000 0 -0.74 52 52
FOS -0.37 0.5 -10000 0 -0.95 201 201
STAT4 (dimer) -0.4 0.53 -10000 0 -0.98 202 202
STAT5A (dimer) -0.65 0.61 -10000 0 -1.3 240 240
GZMA -0.56 0.7 -10000 0 -1.3 218 218
GZMB -0.53 0.67 -10000 0 -1.3 206 206
HLX -0.092 0.29 -10000 0 -0.86 65 65
LCK -0.51 0.69 -10000 0 -1.2 213 213
TCR/CD3/MHC II/CD4 -0.37 0.47 -10000 0 -0.86 230 230
IL2/IL2R -0.41 0.42 -10000 0 -0.71 306 306
MAPK14 -0.3 0.44 -10000 0 -0.82 161 161
CCR5 -0.45 0.59 -10000 0 -1.1 200 200
IL1B 0.002 0.095 -10000 0 -0.86 6 6
STAT6 -0.083 0.15 -10000 0 -10000 0 0
STAT4 -0.034 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.038 -10000 0 -0.86 1 1
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.091 0.29 -10000 0 -0.89 61 61
CD8A -0.38 0.44 -10000 0 -0.87 236 236
CD8B -0.3 0.42 -10000 0 -0.87 186 186
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.16 0.26 0.64 72 -10000 0 72
IL2RB -0.44 0.44 -10000 0 -0.86 273 273
proteasomal ubiquitin-dependent protein catabolic process -0.36 0.47 -10000 0 -0.87 201 201
IL2RG -0.04 0.21 -10000 0 -0.86 34 34
IL12 -0.069 0.24 -10000 0 -0.71 62 62
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.27 0.41 -10000 0 -0.87 172 172
IL2 -0.007 0.12 -10000 0 -0.86 10 10
SPHK2 0.013 0.046 -10000 0 -0.74 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.046 -10000 0 -0.91 1 1
IL12/IL12R/TYK2/JAK2 -0.57 0.77 -10000 0 -1.4 220 220
MAP2K3 -0.3 0.44 -10000 0 -0.83 162 162
RIPK2 0.014 0.038 -10000 0 -0.86 1 1
MAP2K6 -0.3 0.44 -10000 0 -0.83 165 165
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.076 -10000 0 -0.86 4 4
IL18RAP -0.21 0.39 -10000 0 -0.87 135 135
IL12Rbeta1/TYK2 -0.2 0.34 -10000 0 -0.72 160 160
EOMES -0.29 0.37 -10000 0 -0.74 215 215
STAT1 (dimer) -0.44 0.51 -10000 0 -0.96 232 232
T cell proliferation -0.26 0.37 -10000 0 -0.68 171 171
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.002 0.1 -10000 0 -0.8 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.36 0.33 -10000 0 -0.75 190 190
ATF2 -0.27 0.41 -10000 0 -0.78 136 136
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.052 -10000 0 -0.49 6 6
fibroblast growth factor receptor signaling pathway -0.006 0.052 -10000 0 -0.49 6 6
LAMA1 -0.006 0.13 -10000 0 -0.75 15 15
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.56 118 118
SMAD2 0.045 0.02 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.021 -10000 0 -0.48 1 1
GPC1/Laminin alpha1 -0.017 0.096 -10000 0 -0.56 16 16
TDGF1 -0.56 0.32 -10000 0 -0.74 399 399
CRIPTO/GPC1 -0.42 0.24 -10000 0 -0.56 399 399
APP/GPC1 -0.002 0.034 -10000 0 -0.56 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.35 0.22 -10000 0 -0.47 399 399
FLT1 0.007 0.085 -10000 0 -0.86 5 5
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.02 -10000 0 -0.47 1 1
SERPINC1 -0.052 0.22 -10000 0 -0.76 45 45
FYN -0.35 0.22 -10000 0 -0.47 399 399
FGR -0.35 0.22 -10000 0 -0.48 399 399
positive regulation of MAPKKK cascade -0.36 0.24 -10000 0 -0.67 65 65
SLIT2 -0.15 0.32 -10000 0 -0.75 117 117
GPC1/NRG -0.019 0.1 -10000 0 -0.56 18 18
NRG1 -0.009 0.13 -10000 0 -0.74 17 17
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.27 0.3 -10000 0 -0.58 241 241
LYN -0.35 0.22 -10000 0 -0.47 399 399
mol:Spermine 0.014 0.025 -10000 0 -0.57 1 1
cell growth -0.006 0.052 -10000 0 -0.49 6 6
BMP signaling pathway -0.014 0.033 0.74 1 -10000 0 1
SRC -0.35 0.22 -10000 0 -0.47 399 399
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.06 0.24 -10000 0 -0.86 43 43
GPC1 0.014 0.033 -10000 0 -0.74 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.38 0.44 -10000 0 -0.86 240 240
BLK -0.38 0.26 -10000 0 -0.51 404 404
HCK -0.38 0.24 -10000 0 -0.5 410 410
FGF2 0.008 0.076 -10000 0 -0.77 5 5
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.085 -10000 0 -0.86 5 5
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.034 -10000 0 -0.56 2 2
ATIII/GPC1 -0.05 0.16 -10000 0 -0.57 46 46
PLA2G2A/GPC1 -0.055 0.18 -10000 0 -0.66 44 44
LCK -0.37 0.24 -10000 0 -0.49 407 407
neuron differentiation -0.019 0.1 -10000 0 -0.56 18 18
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.033 -10000 0 -0.74 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.28 0.37 -9999 0 -0.74 205 205
PDGF/PDGFRA/CRKL -0.21 0.26 -9999 0 -0.54 205 205
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.52 1 1
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.55 208 208
AP1 -0.16 0.24 -9999 0 -1.2 13 13
mol:IP3 -0.19 0.29 -9999 0 -0.55 205 205
PLCG1 -0.19 0.29 -9999 0 -0.56 205 205
PDGF/PDGFRA/alphaV Integrin -0.21 0.26 -9999 0 -0.54 205 205
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.55 205 205
CAV3 0 0.065 -9999 0 -0.86 3 3
CAV1 -0.046 0.22 -9999 0 -0.86 37 37
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/Shf -0.21 0.26 -9999 0 -0.54 206 206
FOS -0.12 0.27 -9999 0 -1.2 13 13
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.26 -9999 0 -0.54 205 205
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:DAG -0.19 0.29 -9999 0 -0.55 205 205
PDGF/PDGFRA -0.28 0.37 -9999 0 -0.74 205 205
actin cytoskeleton reorganization -0.21 0.26 -9999 0 -0.54 205 205
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
PI3K -0.18 0.22 -9999 0 -0.46 206 206
PDGF/PDGFRA/Crk/C3G -0.18 0.22 -9999 0 -0.45 205 205
JAK1 -0.19 0.28 -9999 0 -0.54 205 205
ELK1/SRF -0.15 0.19 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.033 -9999 0 -0.74 1 1
CSNK2A1 0.017 0.022 -9999 0 -10000 0 0
GO:0007205 -0.2 0.29 -9999 0 -0.56 205 205
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/SHB -0.21 0.26 -9999 0 -0.54 205 205
PDGF/PDGFRA/Caveolin-1 -0.25 0.3 -9999 0 -0.58 234 234
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.26 -9999 0 -0.49 205 205
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PDGF/PDGFRA/Crk -0.21 0.26 -9999 0 -0.54 205 205
JAK-STAT cascade -0.19 0.28 -9999 0 -0.54 205 205
cell proliferation -0.21 0.26 -9999 0 -0.54 206 206
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.41 0.54 -9999 0 -0.9 243 243
MAP4K1 -0.34 0.43 -9999 0 -0.86 216 216
MAP3K8 0.012 0.054 -9999 0 -0.86 2 2
PRKCB 0.008 0.08 -9999 0 -0.82 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.15 0.29 -9999 0 -0.62 123 123
JUN 0 0.087 -9999 0 -0.6 6 6
MAP3K7 -0.15 0.29 -9999 0 -0.62 123 123
GRAP2 -0.042 0.22 -9999 0 -0.86 35 35
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.13 0.28 -9999 0 -0.59 123 123
LAT -0.23 0.39 -9999 0 -0.86 147 147
LCP2 -0.041 0.22 -9999 0 -0.86 34 34
MAPK8 -0.012 0.092 -9999 0 -0.64 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.2 0.29 -9999 0 -0.67 123 123
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.39 0.51 -9999 0 -0.85 243 243
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 -0.14 0.28 -9999 0 -0.67 108 108
alphaM/beta2 Integrin/GPIbA -0.13 0.28 -9999 0 -0.67 104 104
alphaM/beta2 Integrin/proMMP-9 -0.39 0.43 -9999 0 -0.74 280 280
PLAUR -0.029 0.19 -9999 0 -0.86 27 27
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.28 -9999 0 -0.67 103 103
AGER -0.14 0.34 -9999 0 -0.86 95 95
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.042 0.22 -9999 0 -0.86 35 35
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.23 0.33 -9999 0 -0.65 175 175
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 249 249
CYR61 0.007 0.08 -9999 0 -0.74 6 6
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.56 115 115
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.02 0.16 -9999 0 -0.74 25 25
MYH2 -0.34 0.26 -9999 0 -0.65 184 184
MST1R 0.005 0.091 -9999 0 -0.78 7 7
leukocyte activation during inflammatory response -0.27 0.35 -9999 0 -0.63 223 223
APOB -0.26 0.41 -9999 0 -0.86 169 169
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.006 0.091 -9999 0 -0.84 6 6
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.033 -9999 0 -0.74 1 1
alphaM/beta2 Integrin/CTGF -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.53 229 229
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.002 0.12 -9999 0 -0.86 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.24 -9999 0 -0.52 229 229
cell adhesion -0.13 0.28 -9999 0 -0.67 104 104
NFKB1 -0.18 0.36 -9999 0 -0.94 63 63
THY1 0.014 0.033 -9999 0 -0.74 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.19 0.28 -9999 0 -0.59 170 170
alphaM/beta2 Integrin/LRP/tPA -0.13 0.27 -9999 0 -0.63 103 103
IL6 -0.2 0.41 -9999 0 -0.91 101 101
ITGB2 -0.15 0.34 -9999 0 -0.86 100 100
elevation of cytosolic calcium ion concentration -0.15 0.29 -9999 0 -0.64 121 121
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.26 -9999 0 -0.62 103 103
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.13 0.28 -9999 0 -0.91 35 35
alphaM/beta2 Integrin/uPA/Plg -0.35 0.34 -9999 0 -0.86 109 109
RhoA/GTP -0.37 0.27 -9999 0 -0.68 189 189
positive regulation of phagocytosis -0.25 0.27 -9999 0 -0.81 72 72
Ron/MSP -0.018 0.1 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.15 0.3 -9999 0 -0.64 121 121
alphaM/beta2 Integrin/uPAR -0.16 0.32 -9999 0 -0.7 120 120
PLAU 0.003 0.098 -9999 0 -0.74 9 9
PLAT -0.004 0.12 -9999 0 -0.74 14 14
actin filament polymerization -0.33 0.24 -9999 0 -0.61 184 184
MST1 0.003 0.1 -9999 0 -0.85 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.28 0.36 -9999 0 -0.64 223 223
TNF -0.15 0.34 -9999 0 -0.84 67 67
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.14 0.28 -9999 0 -0.66 112 112
fibrinolysis -0.34 0.33 -9999 0 -0.84 109 109
HCK -0.032 0.2 -9999 0 -0.86 29 29
dendritic cell antigen processing and presentation -0.3 0.24 -9999 0 -0.52 229 229
VTN -0.1 0.28 -9999 0 -0.75 82 82
alphaM/beta2 Integrin/CYR61 -0.14 0.28 -9999 0 -0.66 109 109
LPA 0.003 0.066 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.4 -9999 0 -0.69 282 282
FN1 -0.047 0.23 -9999 0 -0.86 38 38
alphaM/beta2 Integrin/Thy1 -0.13 0.28 -9999 0 -0.67 104 104
MPO -0.013 0.16 -9999 0 -0.86 17 17
KNG1 -0.55 0.32 -9999 0 -0.74 395 395
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.33 0.26 -9999 0 -0.64 176 176
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.38 0.38 -9999 0 -0.74 273 273
CTGF 0.006 0.086 -9999 0 -0.74 7 7
alphaM/beta2 Integrin/Hck -0.16 0.35 -9999 0 -0.79 107 107
ITGAM -0.022 0.18 -9999 0 -0.86 22 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.34 -9999 0 -0.74 111 111
HP -0.2 0.38 -9999 0 -0.86 132 132
leukocyte adhesion -0.18 0.27 -9999 0 -0.77 61 61
SELP -0.02 0.16 -9999 0 -0.74 25 25
IL4-mediated signaling events

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
BCL2L1 -0.48 0.48 -10000 0 -1.2 108 108
STAT6 (cleaved dimer) -0.58 0.49 -10000 0 -1.2 167 167
IGHG1 -0.17 0.18 -10000 0 -0.69 11 11
IGHG3 -0.48 0.46 -10000 0 -1.1 127 127
AKT1 -0.28 0.33 -10000 0 -0.84 83 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.24 0.31 -10000 0 -0.82 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.8 64 64
THY1 -0.48 0.48 -10000 0 -1.2 106 106
MYB -0.21 0.39 -10000 0 -0.86 139 139
HMGA1 0.014 0.038 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.42 -10000 0 -1 118 118
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.82 62 62
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.86 4 4
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.48 -10000 0 -1.2 150 150
SOCS1 -0.33 0.34 -10000 0 -0.83 67 67
SOCS3 -0.3 0.34 -10000 0 -0.91 74 74
FCER2 -0.41 0.44 -10000 0 -1.1 78 78
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.5 0.5 -10000 0 -1.2 114 114
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.28 -10000 0 -0.78 55 55
T cell proliferation -0.5 0.51 -10000 0 -1.2 126 126
IL4R/JAK1 -0.48 0.47 -10000 0 -1.2 113 113
EGR2 -0.49 0.5 -10000 0 -1.2 109 109
JAK2 0.006 0.023 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 106 106
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
JAK1 0.007 0.015 -10000 0 -10000 0 0
COL1A2 -0.21 0.3 -10000 0 -0.89 66 66
CCL26 -0.49 0.49 -10000 0 -1.2 109 109
IL4R -0.51 0.51 -10000 0 -1.2 114 114
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.56 0.56 -10000 0 -1.3 132 132
IL13RA1 0.006 0.023 -10000 0 -10000 0 0
IRF4 -0.27 0.42 -10000 0 -1 115 115
ARG1 -0.18 0.26 -10000 0 -0.77 50 50
CBL -0.36 0.4 -10000 0 -0.96 109 109
GTF3A 0.01 0.03 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
IL13RA1/JAK2 -0.007 0.043 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.37 -10000 0 -0.93 114 114
CD40LG -0.075 0.29 -10000 0 -0.92 55 55
MAPK14 -0.35 0.39 -10000 0 -0.96 108 108
mitosis -0.26 0.31 -10000 0 -0.79 83 83
STAT6 -0.55 0.56 -10000 0 -1.3 121 121
SPI1 -0.1 0.3 -10000 0 -0.86 73 73
RPS6KB1 -0.24 0.3 -10000 0 -0.78 69 69
STAT6 (dimer) -0.56 0.56 -10000 0 -1.3 121 121
STAT6 (dimer)/PARP14 -0.51 0.51 -10000 0 -1.3 121 121
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.36 -10000 0 -0.91 96 96
FRAP1 -0.28 0.33 -10000 0 -0.84 83 83
LTA -0.6 0.56 -10000 0 -1.3 143 143
FES 0.013 0.046 -10000 0 -0.74 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 121 -10000 0 121
CCL11 -0.69 0.6 -10000 0 -1.3 225 225
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.29 0.34 -10000 0 -0.88 89 89
IL2RG -0.035 0.21 -10000 0 -0.85 34 34
IL10 -0.5 0.5 -10000 0 -1.2 115 115
IRS1 0.01 0.066 -10000 0 -0.74 4 4
IRS2 0.002 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 108 108
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.37 -10000 0 -0.9 97 97
COL1A1 -0.41 0.43 -10000 0 -0.92 204 204
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.48 -10000 0 -1.3 94 94
IL2R gamma/JAK3 -0.16 0.36 -10000 0 -0.83 110 110
TFF3 -0.5 0.51 -10000 0 -1.2 119 119
ALOX15 -0.49 0.48 -10000 0 -1.2 108 108
MYBL1 -0.044 0.22 -10000 0 -0.86 36 36
T-helper 2 cell differentiation -0.43 0.41 -10000 0 -0.98 123 123
SHC1 0.014 0.038 -10000 0 -0.86 1 1
CEBPB 0 0.13 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.29 -10000 0 -0.78 68 68
mol:PI-3-4-5-P3 -0.28 0.33 -10000 0 -0.84 83 83
PI3K -0.29 0.36 -10000 0 -0.92 83 83
DOK2 -0.035 0.2 -10000 0 -0.86 31 31
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.27 -10000 0 -0.77 55 55
ITGB3 -0.49 0.49 -10000 0 -1.2 103 103
PIGR -0.84 0.7 -10000 0 -1.4 274 274
IGHE 0.028 0.089 0.29 14 -0.37 4 18
MAPKKK cascade -0.2 0.26 -10000 0 -0.75 55 55
BCL6 0.014 0.004 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 111 111
RETNLB -0.49 0.48 -10000 0 -1.2 112 112
SELP -0.51 0.52 -10000 0 -1.3 119 119
AICDA -0.62 0.54 -10000 0 -1.2 180 180
EGFR-dependent Endothelin signaling events

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
HRAS 0.014 0.038 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EGF/EGFR -0.37 0.16 -9999 0 -0.86 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.36 0.14 -9999 0 -0.89 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.054 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.74 478 478
EGF/EGFR dimer/SHC -0.44 0.16 -9999 0 -0.48 479 479
mol:GDP -0.36 0.13 -9999 0 -0.88 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.014 0.16 -9999 0 -0.86 18 18
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.33 0.12 -9999 0 -0.82 10 10
SHC1 0.014 0.038 -9999 0 -0.86 1 1
HRAS/GDP -0.33 0.13 -9999 0 -0.82 10 10
FRAP1 -0.34 0.14 -9999 0 -0.85 9 9
EGF/EGFR dimer -0.51 0.18 -9999 0 -0.57 479 479
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.025 0.13 -9999 0 -0.66 20 20
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.03 0.089 -10000 0 -0.71 8 8
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.011 0.063 -10000 0 -0.82 3 3
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.56 7 7
EPO -0.4 0.41 -10000 0 -0.83 202 202
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.013 -10000 0 -10000 0 0
SERPINE1 -0.35 0.41 -10000 0 -0.92 121 121
FLT1 -0.019 0.077 -10000 0 -0.76 5 5
ADORA2A -0.3 0.34 -10000 0 -0.82 84 84
germ cell development -0.41 0.44 -10000 0 -0.89 211 211
SLC11A2 -0.29 0.34 -10000 0 -0.81 84 84
BHLHE40 -0.29 0.34 -10000 0 -0.81 84 84
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.52 220 220
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.023 0.056 -10000 0 -1.2 1 1
KDR -0.015 0.065 -10000 0 -1.4 1 1
PGK1 -0.29 0.34 -10000 0 -0.81 84 84
SIRT1 0.014 0.005 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.36 0.42 -10000 0 -0.86 160 160
EPAS1 -0.27 0.19 -10000 0 -0.44 223 223
SP1 0.026 0.006 -10000 0 -10000 0 0
ABCG2 -0.3 0.35 -10000 0 -0.81 85 85
EFNA1 -0.3 0.34 -10000 0 -0.81 85 85
FXN -0.3 0.34 -10000 0 -0.82 84 84
POU5F1 -0.43 0.47 -10000 0 -0.95 211 211
neuron apoptosis 0.34 0.4 0.82 160 -10000 0 160
EP300 0.014 0.033 -10000 0 -0.74 1 1
EGLN3 -0.76 0.29 -10000 0 -0.87 468 468
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.004 0.046 -10000 0 -0.52 4 4
VHL 0.014 0.033 -10000 0 -0.74 1 1
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.32 0.37 -10000 0 -0.89 88 88
TWIST1 -0.31 0.34 -10000 0 -0.83 87 87
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.55 85 85
VEGFA -0.47 0.49 -10000 0 -0.94 247 247
CREBBP 0.016 0 -10000 0 -10000 0 0
Aurora C 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
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.25 0.27 -9999 0 -0.53 248 248
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.063 0.068 -9999 0 -10000 0 0
AURKB -0.39 0.44 -9999 0 -0.86 247 247
AURKC 0.012 0.054 -9999 0 -0.86 2 2
Caspase cascade in apoptosis

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
TOP1 -0.13 0.26 -10000 0 -0.57 109 109
ACTA1 -0.19 0.36 -10000 0 -0.67 172 172
NUMA1 -0.13 0.26 -10000 0 -0.57 109 109
SPTAN1 -0.19 0.35 -10000 0 -0.66 171 171
LIMK1 -0.19 0.35 -10000 0 -0.66 172 172
BIRC3 -0.12 0.31 -10000 0 -0.86 80 80
BIRC2 0.012 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.46 -10000 0 -0.86 189 189
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.016 0 -10000 0 -10000 0 0
PTK2 -0.13 0.26 -10000 0 -0.49 171 171
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.34 -10000 0 -0.65 171 171
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.19 0.35 -10000 0 -0.66 171 171
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.3 0.28 -10000 0 -0.54 293 293
BID -0.09 0.17 -10000 0 -0.37 105 105
MAP3K1 -0.044 0.11 -10000 0 -0.22 78 78
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.19 0.35 -10000 0 -0.66 171 171
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.013 0.094 -10000 0 -0.21 35 35
neuron apoptosis 0.011 0.044 -10000 0 -0.61 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.34 -10000 0 -0.77 105 105
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.05 0.15 -10000 0 -0.49 4 4
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.34 -10000 0 -0.77 105 105
CASP7 0.05 0.12 0.34 80 -10000 0 80
KRT18 -0.002 0.046 -10000 0 -0.3 2 2
apoptosis -0.17 0.32 -10000 0 -0.7 113 113
DFFA -0.19 0.35 -10000 0 -0.66 171 171
DFFB -0.19 0.35 -10000 0 -0.66 171 171
PARP1 -0.014 0.094 0.21 35 -10000 0 35
actin filament polymerization 0.16 0.32 0.72 106 -10000 0 106
TNF 0.003 0.1 -10000 0 -0.8 8 8
CYCS -0.069 0.13 -10000 0 -0.28 105 105
SATB1 -0.037 0.15 -10000 0 -0.48 3 3
SLK -0.19 0.35 -10000 0 -0.67 171 171
p15 BID/BAX -0.073 0.15 -10000 0 -10000 0 0
CASP2 0.031 0.088 -10000 0 -0.42 1 1
JNK cascade 0.044 0.11 0.22 78 -10000 0 78
CASP3 -0.21 0.37 -10000 0 -0.71 171 171
LMNB2 0.011 0.085 -10000 0 -0.39 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.079 0.19 -10000 0 -0.52 80 80
negative regulation of DNA binding -0.3 0.28 -10000 0 -0.54 293 293
stress fiber formation -0.18 0.35 -10000 0 -0.65 171 171
GZMB -0.32 0.5 -10000 0 -0.97 189 189
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.009 0.089 -10000 0 -0.37 7 7
APP 0.011 0.045 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.66 114 114
LMNA 0.011 0.085 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.09 -10000 0 -0.41 7 7
LRDD 0.003 0.1 -10000 0 -0.85 8 8
SREBF1 -0.19 0.35 -10000 0 -0.66 172 172
APAF-1/Caspase 9 -0.01 0.062 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.13 0.26 -10000 0 -0.5 148 148
CFL2 -0.17 0.34 -10000 0 -0.75 106 106
GAS2 -0.2 0.36 -10000 0 -0.67 173 173
positive regulation of apoptosis 0.015 0.085 -10000 0 -0.4 3 3
PRF1 -0.2 0.38 -10000 0 -0.86 132 132
Glypican 2 network

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
MDK -0.049 0.23 -9999 0 -0.86 39 39
GPC2 -0.085 0.28 -9999 0 -0.86 61 61
GPC2/Midkine -0.12 0.28 -9999 0 -0.73 89 89
neuron projection morphogenesis -0.12 0.28 -9999 0 -0.73 89 89
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.007 0.085 -9999 0 -0.86 5 5
CCL5 -0.35 0.43 -9999 0 -0.86 223 223
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.59 92 92
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 -0.2 0.22 -9999 0 -0.56 93 93
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.56 92 92
MAPK3 -0.16 0.2 -9999 0 -0.7 15 15
HGF/MET -0.032 0.15 -9999 0 -0.66 26 26
TGFB1/TGF beta receptor Type II 0.007 0.085 -9999 0 -0.86 5 5
BSG 0.014 0.038 -9999 0 -0.86 1 1
keratinocyte migration -0.2 0.21 -9999 0 -0.55 93 93
Syndecan-1/RANTES -0.41 0.33 -9999 0 -0.68 278 278
Syndecan-1/CD147 -0.2 0.18 -9999 0 -0.53 93 93
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 92 92
LAMA5 0.013 0.05 -9999 0 -0.8 2 2
positive regulation of cell-cell adhesion -0.2 0.18 -9999 0 -0.52 92 92
MMP7 -0.13 0.3 -9999 0 -0.75 98 98
HGF -0.02 0.17 -9999 0 -0.8 23 23
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.56 92 92
Syndecan-1/HGF/MET -0.22 0.22 -9999 0 -0.58 108 108
regulation of cell adhesion -0.15 0.2 -9999 0 -0.67 15 15
HPSE 0.013 0.046 -9999 0 -0.74 2 2
positive regulation of cell migration -0.22 0.23 -9999 0 -0.59 92 92
SDC1 -0.22 0.23 -9999 0 -0.6 92 92
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.59 92 92
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 249 249
MAPK1 -0.16 0.2 -9999 0 -0.7 15 15
homophilic cell adhesion -0.21 0.22 -9999 0 -0.58 92 92
MMP1 -0.15 0.34 -9999 0 -0.83 105 105
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.59 0.31 -9999 0 -0.84 289 289
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.32 -9999 0 -0.84 85 85
SMAD9 -0.065 0.086 -9999 0 -0.57 11 11
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.51 19 19
BMP7/USAG1 -0.69 0.34 -9999 0 -0.8 461 461
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 15 15
SMAD1 0.002 0.041 -9999 0 -10000 0 0
BMP2 0.01 0.068 -9999 0 -0.77 4 4
SMAD1/SMAD1/SMAD4 0 0.001 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.35 -9999 0 -0.74 365 365
BMPR1A-1B/BAMBI -0.33 0.22 -9999 0 -0.48 369 369
AHSG -0.014 0.14 -9999 0 -0.86 13 13
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.007 0.057 -9999 0 -0.5 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.49 19 19
BMP2-4 (homodimer) -0.008 0.065 -9999 0 -0.57 7 7
RGMB 0.012 0.054 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.78 5 5
RGMA 0.009 0.073 -9999 0 -0.74 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.15 0.15 -9999 0 -0.56 19 19
BMP2-4/USAG1 -0.31 0.24 -9999 0 -0.48 342 342
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 15 15
SOSTDC1 -0.47 0.36 -9999 0 -0.74 341 341
BMP7/BMPR2/BMPR1A-1B -0.58 0.3 -9999 0 -0.85 263 263
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.092 -9999 0 -0.74 8 8
HFE2 -0.019 0.16 -9999 0 -0.86 19 19
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.017 0.098 -9999 0 -0.55 16 16
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.5 15 15
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.5 15 15
BMP7 (homodimer) -0.5 0.35 -9999 0 -0.74 357 357
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.025 0.12 -9999 0 -0.62 21 21
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.021 0.1 -9999 0 -0.55 20 20
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.18 0.33 -9999 0 -0.75 134 134
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.26 -9999 0 -0.56 365 365
CHRDL1 -0.38 0.38 -9999 0 -0.74 277 277
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.004 0.092 -9999 0 -0.74 8 8
SMURF2 0.014 0.033 -9999 0 -0.74 1 1
BMP2-4/CHRDL1 -0.25 0.24 -9999 0 -0.48 279 279
BMP2-4/GREM1 -0.13 0.22 -9999 0 -0.49 139 139
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.038 0.09 -9999 0 -0.53 11 11
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.5 0.35 -9999 0 -0.74 357 357
BMP6 0.004 0.092 -9999 0 -0.74 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.12 -9999 0 -0.46 19 19
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.19 -9999 0 -0.6 65 65
CHRD -0.001 0.11 -9999 0 -0.78 11 11
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 19 19
BMP4 0.011 0.057 -9999 0 -0.74 3 3
FST -0.077 0.25 -9999 0 -0.76 63 63
BMP2-4/NOG -0.096 0.21 -9999 0 -0.56 91 91
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.55 0.29 -9999 0 -0.8 263 263
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.007 0.13 -9999 0 -0.78 15 15
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.063 -9999 0 -0.82 3 3
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.047 -9999 0 -0.39 1 1
HIF1A -0.099 0.039 -9999 0 -0.42 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.038 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 511 511
ARNT/IPAS -0.017 0.097 -9999 0 -0.58 15 15
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.047 -9999 0 -0.39 1 1
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.048 -9999 0 -0.55 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.047 -9999 0 -0.39 1 1
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 466 466
HIF1A/RACK1/Elongin B/Elongin C -0.067 0.049 -9999 0 -0.59 3 3
VHL 0.014 0.033 -9999 0 -0.74 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.047 -9999 0 -0.39 1 1
EGLN3 -0.76 0.28 -9999 0 -0.86 468 468
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.003 0.038 -9999 0 -0.61 1 1
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.55 0.11 -9999 0 -0.57 511 511
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.25 0.47 -10000 0 -1.1 67 67
IL23A -0.24 0.47 -10000 0 -1.1 62 62
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.39 -10000 0 -1 80 80
positive regulation of T cell mediated cytotoxicity -0.28 0.52 -10000 0 -1.1 86 86
ITGA3 -0.24 0.46 -10000 0 -1 65 65
IL17F -0.15 0.34 -10000 0 -0.74 36 36
IL12B -0.084 0.29 -10000 0 -0.88 61 61
STAT1 (dimer) -0.27 0.5 -10000 0 -1.1 75 75
CD4 -0.24 0.47 -10000 0 -1.1 62 62
IL23 -0.27 0.48 -10000 0 -1.1 78 78
IL23R -0.012 0.15 -10000 0 -0.8 10 10
IL1B -0.25 0.48 -10000 0 -1.1 67 67
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.47 -10000 0 -1.1 65 65
TYK2 0.016 0.025 -10000 0 -10000 0 0
STAT4 -0.034 0.2 -10000 0 -0.86 30 30
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.22 0.39 -10000 0 -0.88 135 135
IL12RB1 -0.26 0.42 -10000 0 -0.89 160 160
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
IL12Rbeta1/TYK2 -0.2 0.33 -10000 0 -0.7 160 160
IL23R/JAK2 -0.011 0.16 -10000 0 -0.78 9 9
positive regulation of chronic inflammatory response -0.28 0.52 -10000 0 -1.1 86 86
natural killer cell activation 0.002 0.012 0.063 10 -10000 0 10
JAK2 0.021 0.034 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
NFKB1 0.01 0.033 -10000 0 -0.74 1 1
RELA 0.012 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.46 -10000 0 -1 79 79
ALOX12B -0.31 0.5 -10000 0 -1.1 77 77
CXCL1 -0.28 0.52 -10000 0 -1.2 73 73
T cell proliferation -0.28 0.52 -10000 0 -1.1 86 86
NFKBIA 0.012 0.009 -10000 0 -10000 0 0
IL17A -0.099 0.29 -10000 0 -0.59 13 13
PI3K -0.33 0.4 -10000 0 -1 88 88
IFNG -0.051 0.069 0.13 4 -0.12 214 218
STAT3 (dimer) -0.31 0.38 -10000 0 -1 76 76
IL18R1 -0.003 0.1 -10000 0 -0.8 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.38 -10000 0 -0.8 80 80
IL18/IL18R -0.17 0.28 -10000 0 -0.61 147 147
macrophage activation -0.017 0.018 -10000 0 -0.045 13 13
TNF -0.25 0.49 -10000 0 -1.1 68 68
STAT3/STAT4 -0.35 0.43 -10000 0 -1.1 89 89
STAT4 (dimer) -0.3 0.53 -10000 0 -1.2 88 88
IL18 -0.002 0.1 -10000 0 -0.86 7 7
IL19 -0.25 0.46 -10000 0 -1.1 64 64
STAT5A (dimer) -0.27 0.5 -10000 0 -1.2 70 70
STAT1 0.014 0.038 -10000 0 -0.86 1 1
SOCS3 0.011 0.066 -10000 0 -0.86 3 3
CXCL9 -0.39 0.59 -10000 0 -1.1 163 163
MPO -0.25 0.48 -10000 0 -1.1 67 67
positive regulation of humoral immune response -0.28 0.52 -10000 0 -1.1 86 86
IL23/IL23R/JAK2/TYK2 -0.3 0.54 -10000 0 -1.2 82 82
IL6 -0.3 0.53 -10000 0 -1.2 93 93
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.016 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 10 -10000 0 10
CD3E -0.38 0.6 -10000 0 -1.1 163 163
keratinocyte proliferation -0.28 0.52 -10000 0 -1.1 86 86
NOS2 -0.25 0.47 -10000 0 -1.1 67 67
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.24 0.26 -10000 0 -0.74 32 32
IHH -0.096 0.23 -10000 0 -0.82 47 47
SHH Np/Cholesterol/GAS1 -0.036 0.12 -10000 0 -0.45 43 43
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.12 0.45 43 -10000 0 43
SMO/beta Arrestin2 -0.14 0.15 -10000 0 -0.6 33 33
SMO -0.13 0.19 -10000 0 -0.64 33 33
AKT1 -0.04 0.092 -10000 0 -0.46 1 1
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.13 0.19 -10000 0 -0.62 33 33
STIL -0.093 0.16 -10000 0 -0.81 5 5
DHH N/PTCH2 -0.044 0.16 -10000 0 -0.63 37 37
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.62 37 37
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
DHH -0.002 0.11 -10000 0 -0.74 12 12
PTHLH -0.44 0.41 -10000 0 -0.74 327 327
determination of left/right symmetry -0.13 0.19 -10000 0 -0.62 33 33
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
skeletal system development -0.43 0.4 -10000 0 -0.73 327 327
IHH N/Hhip -0.2 0.31 -10000 0 -0.65 164 164
DHH N/Hhip -0.15 0.26 -10000 0 -0.57 142 142
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.19 -10000 0 -0.62 33 33
pancreas development -0.18 0.33 -10000 0 -0.75 133 133
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.032 0.18 -10000 0 -0.75 33 33
somite specification -0.13 0.19 -10000 0 -0.62 33 33
SHH Np/Cholesterol/PTCH1 -0.13 0.14 -10000 0 -0.67 10 10
SHH Np/Cholesterol/PTCH2 -0.034 0.13 -10000 0 -0.5 36 36
SHH Np/Cholesterol/Megalin -0.047 0.15 -10000 0 -0.48 52 52
SHH 0.018 0.085 -10000 0 -0.57 11 11
catabolic process -0.15 0.19 -10000 0 -0.65 32 32
SMO/Vitamin D3 -0.11 0.18 -10000 0 -0.72 7 7
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.46 139 139
LRP2 -0.05 0.21 -10000 0 -0.74 46 46
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.76 19 19
SHH Np/Cholesterol/BOC -0.009 0.063 -10000 0 -0.44 11 11
SHH Np/Cholesterol/CDO -0.069 0.18 -10000 0 -0.53 70 70
mesenchymal cell differentiation 0.12 0.2 0.46 139 -10000 0 139
mol:Vitamin D3 -0.11 0.17 -10000 0 -0.67 10 10
IHH N/PTCH2 -0.081 0.21 -10000 0 -0.62 70 70
CDON -0.084 0.28 -10000 0 -0.86 60 60
IHH N/PTCH1 -0.16 0.19 -10000 0 -0.66 32 32
Megalin/LRPAP1 -0.048 0.16 -10000 0 -0.56 46 46
PTCH2 -0.026 0.19 -10000 0 -0.86 25 25
SHH Np/Cholesterol -0.009 0.065 -10000 0 -0.45 11 11
PTCH1 -0.15 0.19 -10000 0 -0.65 32 32
HHIP -0.18 0.33 -10000 0 -0.75 133 133
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.16 0.23 -9999 0 -0.7 62 62
AP1 -0.16 0.21 -9999 0 -0.57 81 81
mol:PIP3 -0.23 0.34 -9999 0 -0.7 144 144
IKBKB -0.086 0.17 -9999 0 -0.34 73 73
AKT1 -0.16 0.21 -9999 0 -0.73 22 22
IKBKG -0.086 0.17 -9999 0 -0.34 81 81
MS4A2 -0.18 0.36 -9999 0 -0.86 116 116
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.034 -9999 0 -0.75 1 1
MAP3K1 -0.12 0.26 -9999 0 -0.6 78 78
mol:Ca2+ -0.16 0.24 -9999 0 -0.49 134 134
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.11 0.15 -9999 0 -0.54 21 21
SHC1 0.014 0.038 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.002 0.03 -9999 0 -0.48 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
PLD2 -0.17 0.28 -9999 0 -0.62 62 62
PTPN13 -0.067 0.16 -9999 0 -0.5 17 17
PTPN11 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.042 0.17 -9999 0 -0.4 14 14
SYK 0.008 0.048 -9999 0 -0.75 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.29 0.32 -9999 0 -0.76 140 140
LAT -0.25 0.29 -9999 0 -0.65 157 157
PAK2 -0.15 0.29 -9999 0 -0.64 113 113
NFATC2 -0.069 0.097 -9999 0 -0.7 4 4
HRAS -0.17 0.32 -9999 0 -0.71 117 117
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.039 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.25 0.32 -9999 0 -0.62 215 215
Antigen/IgE/Fc epsilon R1 -0.23 0.3 -9999 0 -0.58 215 215
mol:GDP -0.2 0.35 -9999 0 -0.77 128 128
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.033 -9999 0 -0.74 1 1
FOS -0.003 0.12 -9999 0 -0.75 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.12 0.16 -9999 0 -0.58 21 21
CHUK -0.086 0.17 -9999 0 -0.34 74 74
KLRG1 -0.12 0.15 -9999 0 -0.55 21 21
VAV1 -0.2 0.32 -9999 0 -0.69 135 135
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.15 -9999 0 -0.55 22 22
negative regulation of mast cell degranulation -0.11 0.15 -9999 0 -0.56 23 23
BTK -0.18 0.24 -9999 0 -0.63 91 91
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.22 -9999 0 -0.58 85 85
GAB2/PI3K/SHP2 -0.18 0.24 -9999 0 -0.82 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.15 -9999 0 -0.55 21 21
RAF1 0.026 0.027 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.3 0.39 -9999 0 -0.81 144 144
FCER1G -0.15 0.34 -9999 0 -0.87 97 97
FCER1A -0.021 0.16 -9999 0 -0.77 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.28 -9999 0 -0.54 202 202
MAPK3 0.04 0.025 -9999 0 -10000 0 0
MAPK1 0.04 0.025 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 -0.012 0.079 -9999 0 -0.58 2 2
DUSP1 0.014 0.038 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.069 0.074 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.072 0.16 -9999 0 -0.48 20 20
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.22 0.29 -9999 0 -0.72 115 115
FER -0.12 0.15 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.14 0.19 -9999 0 -0.42 163 163
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.2 0.36 -9999 0 -0.76 128 128
cytokine secretion -0.05 0.053 -9999 0 -10000 0 0
SPHK1 -0.15 0.22 -9999 0 -0.64 59 59
PTK2 -0.075 0.16 -9999 0 -0.5 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.24 0.31 -9999 0 -0.77 109 109
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.18 0.31 -9999 0 -0.68 109 109
MAP2K2 0.034 0.031 -9999 0 -0.42 1 1
MAP2K1 0.035 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.53 21 21
MAP2K4 0.017 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.32 0.4 -9999 0 -0.73 227 227
mol:Choline -0.17 0.28 -9999 0 -0.56 86 86
SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.52 13 13
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.06 0.15 -9999 0 -0.48 10 10
HCLS1 -0.13 0.18 -9999 0 -0.68 30 30
PRKCB -0.14 0.23 -9999 0 -0.49 107 107
FCGR2B -0.14 0.34 -9999 0 -0.86 96 96
IGHE -0.005 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.15 -9999 0 -0.57 23 23
LCP2 -0.041 0.22 -9999 0 -0.87 34 34
PLA2G4A -0.12 0.16 -9999 0 -0.56 25 25
RASA1 0.014 0.033 -9999 0 -0.74 1 1
mol:Phosphatidic acid -0.17 0.28 -9999 0 -0.56 86 86
IKK complex -0.046 0.13 -9999 0 -0.28 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 240 240
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.031 0.1 -9999 0 -0.36 44 44
mol:S1P -0.024 0.095 -9999 0 -0.37 16 16
S1P1/S1P/Gi -0.048 0.14 -9999 0 -0.51 15 15
GNAO1 0.01 0.083 -9999 0 -0.84 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.055 0.089 -9999 0 -0.63 2 2
PLCG1 -0.029 0.13 -9999 0 -0.5 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.25 0.3 -9999 0 -0.58 240 240
S1P1/S1P -0.21 0.21 -9999 0 -0.42 241 241
negative regulation of cAMP metabolic process -0.046 0.14 -9999 0 -0.49 15 15
MAPK3 -0.039 0.17 -9999 0 -0.57 26 26
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.014 0.033 -9999 0 -0.74 1 1
PLCB2 -0.2 0.26 -9999 0 -0.6 78 78
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.18 0.17 -9999 0 -0.51 24 24
receptor internalization -0.2 0.2 -9999 0 -0.39 241 241
PTGS2 -0.049 0.24 -9999 0 -0.99 27 27
Rac1/GTP -0.18 0.17 -9999 0 -0.5 25 25
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 240 240
negative regulation of T cell proliferation -0.046 0.14 -9999 0 -0.49 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.75 3 3
MAPK1 -0.039 0.17 -9999 0 -0.57 26 26
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.63 25 25
ABCC1 0.016 0.002 -9999 0 -10000 0 0
IL27-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
TGFB1 0.009 0.085 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.074 0.2 0.63 28 -0.44 3 31
IL27/IL27R/JAK1 -0.08 0.35 0.58 1 -1 30 31
TBX21 -0.2 0.41 0.5 1 -0.76 157 158
IL12B -0.092 0.28 -10000 0 -0.87 61 61
IL12A 0.008 0.031 -10000 0 -0.68 1 1
IL6ST -0.016 0.14 -10000 0 -0.75 19 19
IL27RA/JAK1 0.011 0.062 -10000 0 -0.7 1 1
IL27 -0.044 0.21 -10000 0 -0.88 32 32
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.074 0.2 0.63 28 -0.44 3 31
T cell proliferation during immune response 0.074 0.2 0.63 28 -0.44 3 31
MAPKKK cascade -0.074 0.2 0.44 3 -0.63 28 31
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.86 1 1
IL12RB1 -0.25 0.4 -10000 0 -0.87 160 160
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.72 95 96
IL27/IL27R/JAK2/TYK2 -0.078 0.2 0.44 3 -0.64 28 31
positive regulation of T cell mediated cytotoxicity -0.074 0.2 0.44 3 -0.63 28 31
STAT1 (dimer) -0.063 0.51 0.54 125 -1 65 190
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.08 0.18 0.39 3 -0.63 23 26
T cell proliferation -0.12 0.25 0.4 1 -0.72 49 50
IL12/IL12R/TYK2/JAK2 -0.17 0.27 -10000 0 -0.74 47 47
IL17A -0.025 0.13 -10000 0 -0.74 2 2
mast cell activation 0.074 0.2 0.63 28 -0.44 3 31
IFNG -0.04 0.066 0.13 3 -0.11 236 239
T cell differentiation -0.011 0.011 0.03 3 -0.026 140 143
STAT3 (dimer) -0.08 0.18 0.39 3 -0.63 23 26
STAT5A (dimer) -0.08 0.18 0.39 3 -0.63 23 26
STAT4 (dimer) -0.11 0.24 0.39 2 -0.76 43 45
STAT4 -0.034 0.2 -10000 0 -0.86 30 30
T cell activation -0.012 0.007 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.043 0.1 -10000 0 -0.71 1 1
GATA3 -0.62 0.68 -10000 0 -1.3 262 262
IL18 0.005 0.079 -10000 0 -0.68 7 7
positive regulation of mast cell cytokine production -0.08 0.18 0.38 3 -0.62 23 26
IL27/EBI3 -0.12 0.33 -10000 0 -0.83 86 86
IL27RA -0.003 0.063 -10000 0 -0.76 1 1
IL6 -0.088 0.28 -10000 0 -0.81 67 67
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.001 0.086 -10000 0 -0.59 10 10
IL1B 0.006 0.071 -10000 0 -0.66 6 6
EBI3 -0.12 0.31 -10000 0 -0.88 76 76
TNF 0.004 0.078 -10000 0 -0.62 8 8
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.057 0.17 -9999 0 -0.52 58 58
EFNA5 -0.059 0.23 -9999 0 -0.75 52 52
FYN -0.028 0.16 -9999 0 -0.47 58 58
neuron projection morphogenesis -0.057 0.17 -9999 0 -0.52 58 58
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.057 0.17 -9999 0 -0.53 58 58
EPHA5 -0.008 0.11 -9999 0 -0.86 8 8
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 0.008 0.072 -9999 0 -0.66 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.02 0.11 -9999 0 -0.66 16 16
STXBP1 0.014 0.033 -9999 0 -0.74 1 1
ACh/CHRNA1 -0.27 0.31 -9999 0 -0.63 227 227
RAB3GAP2/RIMS1/UNC13B -0.017 0.098 -9999 0 -0.57 16 16
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 -0.014 0.15 -9999 0 -0.86 16 16
mol:ACh -0.01 0.053 -9999 0 -0.13 83 83
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.099 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.27 0.31 -9999 0 -0.62 227 227
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.36 0.43 -9999 0 -0.86 227 227
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.082 0.2 -9999 0 -0.53 85 85
SNAP25 -0.04 0.12 -9999 0 -0.33 79 79
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.74 85 85
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.007 0.064 -9999 0 -0.56 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.099 -9999 0 -0.62 4 4
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.35 -10000 0 -1.1 69 69
NFATC2 -0.08 0.24 -10000 0 -0.69 30 30
NFATC3 -0.021 0.063 -10000 0 -10000 0 0
CD40LG -0.23 0.44 -10000 0 -1.2 58 58
ITCH 0.054 0.057 -10000 0 -10000 0 0
CBLB 0.054 0.057 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.54 0.56 -10000 0 -1.2 192 192
JUNB 0.013 0.046 -10000 0 -0.74 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.057 -10000 0 -10000 0 0
T cell anergy 0.023 0.093 -10000 0 -0.6 1 1
TLE4 -0.031 0.17 -10000 0 -0.7 8 8
Jun/NFAT1-c-4/p21SNFT -0.24 0.28 -10000 0 -1 25 25
AP-1/NFAT1-c-4 -0.29 0.37 -10000 0 -1.2 34 34
IKZF1 -0.12 0.36 -10000 0 -0.88 93 93
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.74 104 104
AP-1/NFAT1 -0.093 0.16 -10000 0 -0.69 12 12
CALM1 0.029 0.036 -10000 0 -10000 0 0
EGR2 -0.11 0.29 -10000 0 -1.3 10 10
EGR3 -0.11 0.29 -10000 0 -1.4 9 9
NFAT1/FOXP3 -0.28 0.4 -10000 0 -0.96 111 111
EGR1 0 0.11 -10000 0 -0.74 12 12
JUN 0.006 0.022 -10000 0 -10000 0 0
EGR4 0.004 0.085 -10000 0 -0.86 5 5
mol:Ca2+ 0.01 0.04 -10000 0 -10000 0 0
GBP3 -0.034 0.18 -10000 0 -0.78 10 10
FOSL1 -0.027 0.19 -10000 0 -0.86 26 26
NFAT1-c-4/MAF/IRF4 -0.26 0.36 -10000 0 -0.94 86 86
DGKA -0.034 0.19 -10000 0 -0.96 8 8
CREM 0.015 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.22 -10000 0 -1.1 8 8
CTLA4 -0.43 0.58 -10000 0 -1 241 241
NFAT1-c-4 (dimer)/EGR1 -0.17 0.24 -10000 0 -1.2 12 12
NFAT1-c-4 (dimer)/EGR4 -0.17 0.23 -10000 0 -1.1 10 10
FOS -0.013 0.12 -10000 0 -0.75 13 13
IFNG -0.49 0.52 -10000 0 -1 225 225
T cell activation -0.049 0.22 -10000 0 -0.83 16 16
MAF 0.016 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.063 0.2 0.91 3 -10000 0 3
TNF -0.096 0.28 -10000 0 -1.1 14 14
FASLG -0.33 0.48 -10000 0 -1.1 36 36
TBX21 -0.3 0.44 -10000 0 -0.93 172 172
BATF3 -0.059 0.24 -10000 0 -0.86 45 45
PRKCQ -0.034 0.13 -10000 0 -0.74 16 16
PTPN1 -0.031 0.17 -10000 0 -0.7 8 8
NFAT1-c-4/ICER1 -0.17 0.22 -10000 0 -1.1 7 7
GATA3 -0.36 0.38 -10000 0 -0.74 262 262
T-helper 1 cell differentiation -0.48 0.5 -10000 0 -1 227 227
IL2RA -0.38 0.46 -10000 0 -1.1 127 127
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.031 0.17 -10000 0 -0.7 8 8
E2F1 -0.081 0.29 -10000 0 -0.85 64 64
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.031 0.17 -10000 0 -0.7 8 8
IRF4 -0.18 0.36 -10000 0 -0.86 118 118
PTGS2 -0.21 0.4 -10000 0 -1.1 34 34
CSF2 -0.21 0.4 -10000 0 -1.1 32 32
JunB/Fra1/NFAT1-c-4 -0.18 0.22 -10000 0 -0.99 11 11
IL4 -0.36 0.29 -10000 0 -0.78 95 95
IL5 -0.2 0.38 -10000 0 -1.1 25 25
IL2 -0.05 0.22 -10000 0 -0.85 16 16
IL3 -0.049 0.049 -10000 0 -10000 0 0
RNF128 0.034 0.16 -10000 0 -0.78 19 19
NFATC1 -0.064 0.2 -10000 0 -0.91 3 3
CDK4 0.034 0.18 -10000 0 -10000 0 0
PTPRK -0.032 0.18 -10000 0 -0.73 9 9
IL8 -0.22 0.42 -10000 0 -1.1 40 40
POU2F1 0.016 0.003 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.042 -9999 0 -0.48 4 4
ARNO/beta Arrestin1-2 -0.019 0.064 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.74 1 1
USP6 0.014 0.038 -9999 0 -0.86 1 1
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.51 0.18 -9999 0 -0.57 479 479
ARRB2 -0.017 0.11 -9999 0 -0.39 42 42
mol:GTP -0.011 0.048 -9999 0 -0.23 2 2
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.086 0.28 -9999 0 -0.86 61 61
EGF -0.67 0.23 -9999 0 -0.74 478 478
somatostatin receptor activity 0 0 -9999 0 -0.001 11 11
ARAP2 0.013 0.046 -9999 0 -0.74 2 2
mol:GDP -0.058 0.094 -9999 0 -0.34 24 24
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 8 8
ITGA2B -0.016 0.16 -9999 0 -0.86 19 19
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.52 1 1
ADAP1 0.01 0.066 -9999 0 -0.74 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.032 0.15 -9999 0 -0.66 26 26
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.088 0.091 -9999 0 -0.34 19 19
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.44 0.16 -9999 0 -0.48 479 479
ADRB2 0.013 0.046 -9999 0 -0.74 2 2
receptor agonist activity 0 0 -9999 0 0 12 12
actin filament binding 0 0 -9999 0 -0.001 17 17
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
GNAQ 0.015 0.001 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 10 10
ARF6/GDP -0.069 0.14 -9999 0 -0.4 6 6
ARF6/GDP/GULP/ACAP1 -0.23 0.26 -9999 0 -0.53 205 205
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.023 0.11 -9999 0 -0.55 18 18
ACAP1 -0.32 0.43 -9999 0 -0.86 202 202
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.047 0.16 -9999 0 -0.59 42 42
EFNA1 0.014 0.038 -9999 0 -0.86 1 1
HGF -0.02 0.17 -9999 0 -0.8 23 23
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
fibronectin binding 0 0 -9999 0 -0.001 10 10
endosomal lumen acidification 0 0 -9999 0 -0.001 18 18
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.012 0.14 -9999 0 -0.75 19 19
GNAQ/ARNO 0.009 0.01 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
GNA14 0.006 0.087 -9999 0 -0.74 7 7
GNA15 -0.011 0.15 -9999 0 -0.86 16 16
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 11 11
GNA11 0.011 0.057 -9999 0 -0.74 3 3
LHCGR -0.062 0.23 -9999 0 -0.86 41 41
AGTR1 -0.026 0.17 -9999 0 -0.74 29 29
desensitization of G-protein coupled receptor protein signaling pathway -0.047 0.16 -9999 0 -0.59 42 42
IPCEF1/ARNO -0.34 0.12 -9999 0 -0.81 8 8
alphaIIb/beta3 Integrin -0.03 0.14 -9999 0 -0.66 24 24
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.071 -9999 0 -0.68 5 5
VEGFR1 homodimer/NRP1 -0.008 0.072 -9999 0 -0.62 7 7
mol:DAG -0.26 0.29 -9999 0 -0.97 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 241 241
CaM/Ca2+ -0.27 0.25 -9999 0 -0.92 7 7
HIF1A 0.02 0.057 -9999 0 -0.72 2 2
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.22 0.21 -9999 0 -0.94 6 6
PLCG1 -0.26 0.29 -9999 0 -0.98 7 7
NOS3 -0.18 0.24 -9999 0 -0.85 6 6
CBL 0.014 0.033 -9999 0 -0.74 1 1
mol:NO -0.17 0.24 -9999 0 -0.8 6 6
FLT1 0.031 0.086 -9999 0 -0.71 7 7
PGF -0.47 0.44 -9999 0 -0.86 291 291
VEGFR1 homodimer/NRP2/VEGFR121 -0.25 0.27 -9999 0 -1 7 7
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.76 6 6
endothelial cell proliferation -0.2 0.26 -9999 0 -0.86 8 8
mol:Ca2+ -0.26 0.29 -9999 0 -0.95 7 7
MAPK3 -0.21 0.26 -9999 0 -0.88 6 6
MAPK1 -0.21 0.26 -9999 0 -0.88 6 6
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
PLGF homodimer -0.46 0.44 -9999 0 -0.86 291 291
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.046 0.22 -9999 0 -0.86 37 37
VEGFA homodimer -0.38 0.44 -9999 0 -0.86 240 240
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 241 241
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.85 6 6
PI3K -0.27 0.25 -9999 0 -0.99 7 7
PRKCA -0.23 0.27 -9999 0 -0.89 7 7
PRKCB -0.24 0.28 -9999 0 -0.91 9 9
VEGFR1 homodimer/PLGF homodimer -0.32 0.3 -9999 0 -0.58 292 292
VEGFA -0.38 0.44 -9999 0 -0.86 240 240
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.97 7 7
RASA1 0.045 0.078 -9999 0 -0.65 6 6
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.031 0.086 -9999 0 -0.7 7 7
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.8 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.25 -9999 0 -0.96 7 7
mol:L-citrulline -0.17 0.24 -9999 0 -0.8 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.94 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -0.99 6 6
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.99 6 6
PDPK1 -0.22 0.27 -9999 0 -0.94 7 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -1 5 5
mol:NADP -0.17 0.24 -9999 0 -0.8 6 6
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.25 -9999 0 -0.92 6 6
VEGFR1 homodimer/NRP2 -0.016 0.095 -9999 0 -0.61 12 12
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.013 0.047 -9999 0 -10000 0 0
NFATC2 -0.017 0.068 -9999 0 -0.58 4 4
NFATC3 -0.013 0.047 -9999 0 -10000 0 0
CD40LG -0.3 0.42 -9999 0 -0.94 101 101
PTGS2 -0.29 0.39 -9999 0 -0.86 95 95
JUNB 0.013 0.046 -9999 0 -0.74 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.02 0.018 -9999 0 -10000 0 0
CALM1 0.006 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.027 0.19 -9999 0 -0.86 26 26
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.73 36 36
FOS -0.013 0.12 -9999 0 -0.76 13 13
IFNG -0.43 0.52 -9999 0 -0.99 225 225
AP-1/NFAT1-c-4 -0.41 0.41 -9999 0 -1.1 92 92
FASLG -0.46 0.52 -9999 0 -0.98 228 228
NFAT1-c-4/ICER1 -0.08 0.083 -9999 0 -0.57 3 3
IL2RA -0.34 0.44 -9999 0 -1 106 106
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.28 0.38 -9999 0 -0.87 92 92
JunB/Fra1/NFAT1-c-4 -0.094 0.12 -9999 0 -0.63 8 8
IL4 -0.28 0.37 -9999 0 -0.84 89 89
IL2 -0.012 0.11 -9999 0 -0.77 10 10
IL3 -0.028 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.059 0.24 -9999 0 -0.86 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.024 -9999 0 -0.56 1 1
Necdin/E2F1 -0.083 0.22 -9999 0 -0.68 65 65
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.079 0.2 -9999 0 -0.98 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.3 -9999 0 -0.56 252 252
NT-4/5 (dimer)/p75(NTR) -0.053 0.18 -9999 0 -0.67 42 42
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.033 0.22 -9999 0 -0.54 77 77
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.1 0.3 -9999 0 -0.86 71 71
MGDIs/NGR/p75(NTR)/LINGO1 -0.071 0.2 -9999 0 -0.61 62 62
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.25 -9999 0 -0.61 100 100
LINGO1 -0.022 0.18 -9999 0 -0.86 23 23
Sortilin/TRAF6/NRIF -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.3 -9999 0 -0.86 71 71
NTRK1 -0.045 0.2 -9999 0 -0.75 41 41
RTN4R 0.004 0.098 -9999 0 -0.85 7 7
neuron apoptosis -0.066 0.23 -9999 0 -0.68 32 32
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.061 0.24 -9999 0 -0.62 79 79
ARHGDIA 0.014 0.033 -9999 0 -0.74 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.085 0.21 -9999 0 -0.57 77 77
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.087 0.22 -9999 0 -0.58 78 78
Mammalian IAPs/DIABLO -0.079 0.19 -9999 0 -0.52 80 80
proNGF (dimer) -0.067 0.26 -9999 0 -0.86 50 50
MAGED1 0.014 0.038 -9999 0 -0.86 1 1
APP 0.014 0.033 -9999 0 -0.74 1 1
NT-4/5 (dimer) -0.004 0.092 -9999 0 -0.86 6 6
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.08 0.2 -9999 0 -0.54 77 77
NGF -0.067 0.26 -9999 0 -0.86 50 50
cell cycle arrest -0.014 0.25 -9999 0 -0.59 59 59
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.045 0.11 -9999 0 -0.57 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.046 0.16 -9999 0 -0.58 42 42
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.092 0.23 -9999 0 -0.62 78 78
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.045 0.22 -9999 0 -0.56 77 77
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.035 0.086 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.046 0.17 -9999 0 -0.66 37 37
BEX1 -0.26 0.37 -9999 0 -0.75 194 194
mol:GDP -0.072 0.24 -9999 0 -0.64 78 78
NGF (dimer) -0.35 0.3 -9999 0 -0.84 91 91
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.065 0.18 -9999 0 -0.56 62 62
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RAC1/GTP -0.081 0.2 -9999 0 -0.55 78 78
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.092 0.23 -9999 0 -0.63 78 78
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.08 0.22 -9999 0 -0.66 64 64
NT3 (dimer) 0.005 0.09 -9999 0 -0.78 7 7
TP53 -0.041 0.22 -9999 0 -0.91 8 8
PRDM4 -0.046 0.23 -9999 0 -0.57 77 77
BDNF (dimer) -0.42 0.36 -9999 0 -0.87 143 143
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
SORT1 0.014 0.033 -9999 0 -0.74 1 1
activation of caspase activity -0.078 0.2 -9999 0 -0.96 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.085 0.21 -9999 0 -0.57 77 77
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.024 0.21 -9999 0 -0.64 23 23
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.046 0.23 -9999 0 -0.57 77 77
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.093 0.23 -9999 0 -0.62 79 79
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.053 0.18 -9999 0 -0.67 42 42
MAPK8 -0.023 0.21 -9999 0 -0.63 22 22
MAPK9 -0.021 0.2 -9999 0 -0.63 22 22
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.091 -9999 0 -0.78 7 7
NTF4 -0.004 0.092 -9999 0 -0.86 6 6
NDN 0.011 0.057 -9999 0 -0.74 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.072 0.18 -9999 0 -0.91 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.018 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.091 0.23 -9999 0 -0.62 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.098 0.21 -9999 0 -0.97 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.23 -9999 0 -0.56 98 98
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.089 0.22 -9999 0 -0.66 71 71
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.31 -9999 0 -0.86 80 80
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.006 0.24 -9999 0 -0.53 58 58
BAD -0.011 0.2 -9999 0 -0.6 22 22
RIPK2 0.014 0.038 -9999 0 -0.86 1 1
NGFR -0.044 0.22 -9999 0 -0.86 36 36
CYCS -0.035 0.22 -9999 0 -0.97 9 9
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.085 0.21 -9999 0 -0.57 78 78
BCL2L11 -0.01 0.2 -9999 0 -0.6 22 22
BDNF (dimer)/p75(NTR) -0.13 0.28 -9999 0 -0.7 100 100
PI3K -0.085 0.21 -9999 0 -0.58 77 77
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.085 0.21 -9999 0 -0.57 77 77
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.26 -9999 0 -0.72 78 78
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.086 0.21 -9999 0 -0.57 78 78
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.057 -9999 0 -0.74 3 3
PLG -0.38 0.38 -9999 0 -0.74 273 273
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.12 0.23 -9999 0 -0.88 22 22
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.005 0.18 -9999 0 -0.53 22 22
E2F1 -0.09 0.29 -9999 0 -0.86 64 64
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.07 0.15 -9999 0 -0.59 13 13
NGF (dimer)/TRKA -0.11 0.24 -9999 0 -0.63 89 89
MMP7 -0.13 0.3 -9999 0 -0.75 98 98
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.079 0.2 -9999 0 -0.98 8 8
MMP3 -0.069 0.25 -9999 0 -0.86 47 47
APAF-1/Caspase 9 -0.11 0.17 -9999 0 -0.69 11 11
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.026 0.022 -9999 0 -0.48 1 1
ADCY5 0.006 0.1 -9999 0 -0.49 22 22
ADCY6 0.025 0.041 -9999 0 -0.92 1 1
ADCY7 0.009 0.1 -9999 0 -0.58 16 16
ADCY1 0.013 0.085 -9999 0 -0.5 14 14
ADCY2 -0.13 0.27 -9999 0 -0.58 141 141
ADCY3 0.026 0.022 -9999 0 -0.48 1 1
ADCY8 -0.17 0.28 -9999 0 -0.59 165 165
PRKCE 0.014 0.025 -9999 0 -0.57 1 1
ADCY9 0.026 0.022 -9999 0 -0.48 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.093 0.17 -9999 0 -0.5 54 54
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.044 0.14 -9999 0 -0.72 1 1
CCNA2 -0.15 0.35 -9999 0 -0.86 102 102
PIK3CA 0.015 0.033 -9999 0 -0.74 1 1
JAK3 -0.16 0.35 -9999 0 -0.86 106 106
PIK3R1 0.015 0.033 -9999 0 -0.74 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.1 0.25 -9999 0 -0.66 59 59
SHC1 0.015 0.038 -9999 0 -0.86 1 1
SP1 0.025 0.022 -9999 0 -10000 0 0
IL2RA -0.12 0.32 -9999 0 -0.77 105 105
IL2RB -0.44 0.44 -9999 0 -0.86 273 273
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.039 0.21 -9999 0 -0.86 34 34
G1/S transition of mitotic cell cycle -0.045 0.2 -9999 0 -0.55 13 13
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.05 -9999 0 -0.78 2 2
LCK -0.019 0.17 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.006 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.033 -9999 0 -0.74 1 1
CCND3 -0.074 0.21 -9999 0 -0.66 28 28
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.12 0.24 -10000 0 -0.77 35 35
UGCG -0.024 0.055 -10000 0 -0.77 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.077 0.19 -10000 0 -0.52 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.064 -10000 0 -0.76 2 2
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.16 -10000 0 -0.56 36 36
FRAP1 -0.081 0.23 -10000 0 -0.61 50 50
FOXO3 -0.072 0.22 -10000 0 -0.64 36 36
AKT1 -0.089 0.24 -10000 0 -0.64 52 52
GAB2 0.016 0.003 -10000 0 -10000 0 0
SMPD1 -0.021 0.03 -10000 0 -10000 0 0
SGMS1 -0.021 0.03 -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 0.027 0.032 -10000 0 -0.48 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.021 0.1 -10000 0 -0.49 2 2
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.55 2 2
RPS6KB1 -0.026 0.087 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 106 106
PIK3R1 0.017 0.033 -10000 0 -0.74 1 1
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MYC -0.073 0.23 -10000 0 -0.66 36 36
MYB -0.18 0.34 -10000 0 -0.74 139 139
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.12 0.26 -10000 0 -0.68 63 63
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.035 0.067 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 -0.11 0.25 -10000 0 -0.65 63 63
Rac1/GDP 0.021 0.033 -10000 0 -0.43 2 2
T cell proliferation -0.093 0.24 -10000 0 -0.64 51 51
SHC1 0.014 0.038 -10000 0 -0.86 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.05 139 139
PRKCZ -0.098 0.25 -10000 0 -0.67 52 52
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.58 31 31
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.14 0.26 -10000 0 -0.58 102 102
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 104 104
IL2RB -0.43 0.44 -10000 0 -0.86 273 273
TERT -0.11 0.3 -10000 0 -0.86 74 74
E2F1 -0.1 0.2 -10000 0 -0.38 166 166
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.012 0.054 -10000 0 -0.86 2 2
mol:cAMP 0.003 0.013 0.025 139 -10000 0 139
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.038 0.22 -10000 0 -0.86 34 34
actin cytoskeleton organization -0.093 0.24 -10000 0 -0.64 51 51
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 -0.004 0.12 -10000 0 -0.86 10 10
PIK3CA 0.017 0.033 -10000 0 -0.74 1 1
Rac1/GTP 0.032 0.034 -10000 0 -0.41 2 2
LCK -0.017 0.17 -10000 0 -0.85 22 22
BCL2 -0.049 0.18 -10000 0 -0.53 24 24
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.057 0.29 18 -10000 0 18
BUB1B -0.022 0.12 -10000 0 -0.51 26 26
PLK1 -0.011 0.059 -10000 0 -0.2 10 10
PLK1S1 0.001 0.031 -10000 0 -10000 0 0
KIF2A -0.003 0.072 -10000 0 -0.56 4 4
regulation of mitotic centrosome separation -0.012 0.058 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.33 -10000 0 -0.72 129 129
WEE1 -0.001 0.055 -10000 0 -0.3 5 5
cytokinesis -0.2 0.27 -10000 0 -0.5 237 237
PP2A-alpha B56 -0.14 0.16 -10000 0 -10000 0 0
AURKA -0.002 0.044 -10000 0 -0.3 6 6
PICH/PLK1 -0.045 0.16 -10000 0 -0.82 19 19
CENPE -0.063 0.21 -10000 0 -0.62 62 62
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.071 -10000 0 -0.55 4 4
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.033 -10000 0 -0.74 1 1
TPX2 -0.049 0.12 -10000 0 -0.25 127 127
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.077 0.27 -10000 0 -0.86 56 56
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.025 0.096 -10000 0 -0.28 60 60
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.009 -10000 0 -0.02 129 129
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.012 0.058 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.16 0.19 -10000 0 -0.46 9 9
TPT1 0.001 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 242 242
CDC25B 0.007 0.086 -10000 0 -0.88 5 5
SGOL1 0.001 0.057 -10000 0 -0.29 18 18
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.023 0.1 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.055 0.24 -10000 0 -0.86 43 43
PLK1/PBIP1 -0.041 0.12 -10000 0 -0.59 19 19
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.003 0.044 -10000 0 -0.19 5 5
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.17 0.36 -10000 0 -0.86 111 111
metaphase plate congression -0.004 0.041 -10000 0 -10000 0 0
ERCC6L -0.037 0.16 -10000 0 -0.81 19 19
NLP/gamma Tubulin -0.003 0.034 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0.001 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.25 0.29 -10000 0 -0.56 237 237
GRASP65/GM130/RAB1/GTP/PLK1 -0.013 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.038 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 121 121
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.043 -10000 0 -10000 0 0
microtubule-based process -0.24 0.3 -10000 0 -0.58 237 237
Golgi organization -0.012 0.058 -10000 0 -0.2 10 10
Cohesin/SA2 -0.024 0.044 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.38 0.44 -10000 0 -0.86 237 237
APC/C/CDC20 -0.045 0.18 -10000 0 -0.64 43 43
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.04 0.11 -10000 0 -0.58 19 19
PRC1 0.006 0.093 -10000 0 -0.86 6 6
ECT2 0.001 0.053 -10000 0 -10000 0 0
C13orf34 0.004 0.042 -10000 0 -10000 0 0
NUDC -0.004 0.041 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.022 0.12 -10000 0 -0.5 26 26
spindle assembly -0.006 0.047 -10000 0 -0.16 8 8
spindle stabilization 0.001 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.021 -10000 0 -0.49 1 1
MKLP2/PLK1 -0.25 0.31 -10000 0 -0.59 237 237
CCNB1 0.002 0.11 -10000 0 -0.87 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.004 0.058 -10000 0 -0.48 4 4
TUBG1 0.001 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.025 0.097 -10000 0 -0.71 9 9
MLF1IP -0.013 0.13 -10000 0 -0.69 19 19
INCENP 0.009 0.008 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.14 0.3 -9999 0 -0.75 42 42
CRP -0.2 0.39 -9999 0 -0.9 95 95
cell cycle arrest -0.18 0.35 -9999 0 -0.78 84 84
TIMP1 -0.15 0.33 -9999 0 -0.77 70 70
IL6ST -0.015 0.14 -9999 0 -0.74 19 19
Rac1/GDP -0.14 0.26 -9999 0 -0.59 95 95
AP1 0.021 0.1 -9999 0 -0.58 2 2
GAB2 0.011 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.37 -9999 0 -0.86 77 77
HSP90B1 0.004 0.087 -9999 0 -10000 0 0
GAB1 0.013 0.006 -9999 0 -10000 0 0
MAPK14 0.015 0.14 -9999 0 -0.72 5 5
AKT1 0.06 0.035 -9999 0 -10000 0 0
FOXO1 0.076 0.023 -9999 0 -10000 0 0
MAP2K6 -0.019 0.14 -9999 0 -0.66 7 7
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.27 -9999 0 -0.61 96 96
MITF -0.026 0.14 -9999 0 -0.64 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.003 0.13 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0 0.069 -9999 0 -10000 0 0
STAT3 -0.18 0.36 -9999 0 -0.83 84 84
STAT1 -0.005 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.3 -9999 0 -0.76 39 39
PIK3CA 0.017 0.033 -9999 0 -0.74 1 1
PI3K -0.002 0.034 -9999 0 -0.56 2 2
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.02 0.13 -9999 0 -0.71 4 4
MAPK11 0.013 0.14 -9999 0 -0.78 6 6
STAT3 (dimer)/FOXO1 -0.073 0.27 -9999 0 -0.64 22 22
GRB2/SOS1/GAB family -0.048 0.11 -9999 0 -0.66 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.04 0.16 -9999 0 -0.65 13 13
GRB2 0.013 0.006 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.29 0.45 -9999 0 -0.88 165 165
PIK3R1 0.016 0.033 -9999 0 -0.74 1 1
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.32 -9999 0 -0.78 53 53
FGG -0.27 0.43 -9999 0 -0.85 144 144
macrophage differentiation -0.18 0.35 -9999 0 -0.78 84 84
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.07 0.17 -9999 0 -0.55 39 39
JUNB -0.14 0.3 -9999 0 -0.74 43 43
FOS -0.009 0.12 -9999 0 -0.75 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.037 0.15 -9999 0 -0.45 29 29
STAT1/PIAS1 -0.049 0.16 -9999 0 -0.49 25 25
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.038 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.82 84 84
PRKCD -0.14 0.3 -9999 0 -0.69 68 68
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.029 0.14 -9999 0 -0.69 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.093 -9999 0 -0.47 19 19
Rac1/GTP -0.18 0.23 -9999 0 -0.59 105 105
HCK -0.033 0.2 -9999 0 -0.86 29 29
MAPKKK cascade 0.025 0.061 -9999 0 -10000 0 0
bone resorption -0.18 0.35 -9999 0 -0.8 78 78
IRF1 -0.14 0.3 -9999 0 -0.76 41 41
mol:GDP -0.15 0.27 -9999 0 -0.55 135 135
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.56 135 135
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.01 0.13 -9999 0 -0.67 5 5
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.079 0.21 -9999 0 -0.63 67 67
gp130 (dimer)/TYK2/TYK2/LMO4 -0.014 0.088 -9999 0 -0.47 19 19
gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.088 -9999 0 -0.47 19 19
IL6 -0.092 0.28 -9999 0 -0.82 67 67
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.017 0.017 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.037 0.14 -9999 0 -0.4 26 26
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.29 -9999 0 -0.76 81 81
MCL1 0.075 0.023 -9999 0 -10000 0 0
BCR signaling 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
JUN -0.053 0.16 -10000 0 -0.41 42 42
IKBKB -0.022 0.1 -10000 0 -0.28 2 2
AKT1 -0.022 0.12 -10000 0 -0.32 4 4
IKBKG -0.022 0.11 -10000 0 -0.3 3 3
CALM1 -0.041 0.1 -10000 0 -0.5 3 3
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
MAP3K1 -0.11 0.25 -10000 0 -0.63 71 71
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.054 0.11 0.27 1 -0.5 4 5
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.011 0.089 -10000 0 -10000 0 0
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.033 -10000 0 -0.74 1 1
SHC1 0.014 0.038 -10000 0 -0.86 1 1
BCR complex -0.16 0.29 -10000 0 -0.68 129 129
CD22 -0.14 0.23 -10000 0 -0.67 51 51
CAMK2G -0.029 0.097 -10000 0 -0.49 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.1 0.18 -10000 0 -0.85 4 4
GO:0007205 -0.054 0.11 0.27 1 -0.51 4 5
SYK 0.013 0.046 -10000 0 -0.74 2 2
ELK1 -0.042 0.1 -10000 0 -0.51 3 3
NFATC1 -0.069 0.2 -10000 0 -0.5 66 66
B-cell antigen/BCR complex -0.16 0.29 -10000 0 -0.68 129 129
PAG1/CSK -0.003 0.041 -10000 0 -0.66 2 2
NFKBIB 0.005 0.039 -10000 0 -0.13 1 1
HRAS -0.037 0.12 -10000 0 -0.49 4 4
NFKBIA 0.006 0.038 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.013 0.032 -10000 0 -0.18 1 1
RasGAP/Csk -0.21 0.32 -10000 0 -0.99 47 47
mol:GDP -0.05 0.1 0.29 1 -0.47 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.011 0.066 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.014 0.032 -10000 0 -0.19 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.076 0.22 -10000 0 -0.57 63 63
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 -0.065 0.1 0.27 1 -0.51 4 5
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.039 0.11 -10000 0 -0.48 6 6
CHUK -0.022 0.11 -10000 0 -0.3 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.12 0.2 -10000 0 -0.54 84 84
PTPN6 -0.13 0.21 -10000 0 -0.68 39 39
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.011 0.068 -10000 0 -0.14 108 108
VAV2 -0.16 0.28 -10000 0 -0.79 74 74
ubiquitin-dependent protein catabolic process 0.011 0.037 -10000 0 -0.12 1 1
BTK -0.085 0.17 0.46 1 -0.42 106 107
CD19 -0.19 0.32 -10000 0 -0.88 79 79
MAP4K1 -0.34 0.43 -10000 0 -0.86 216 216
CD72 -0.19 0.37 -10000 0 -0.86 123 123
PAG1 0.012 0.054 -10000 0 -0.86 2 2
MAPK14 -0.082 0.21 -10000 0 -0.52 67 67
SH3BP5 0.014 0.033 -10000 0 -0.74 1 1
PIK3AP1 -0.036 0.11 -10000 0 -0.54 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.23 -10000 0 -0.58 77 77
RAF1 -0.024 0.11 -10000 0 -0.53 2 2
RasGAP/p62DOK/SHIP -0.2 0.31 -10000 0 -0.97 48 48
CD79A -0.2 0.38 -10000 0 -0.86 129 129
re-entry into mitotic cell cycle -0.011 0.089 -10000 0 -0.26 1 1
RASA1 0.014 0.033 -10000 0 -0.74 1 1
MAPK3 -0.001 0.099 -10000 0 -10000 0 0
MAPK1 -0.001 0.099 -10000 0 -10000 0 0
CD72/SHP1 -0.22 0.33 -10000 0 -0.82 100 100
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MAPK8 -0.084 0.21 -10000 0 -0.53 65 65
actin cytoskeleton organization -0.094 0.26 -10000 0 -0.66 67 67
NF-kappa-B/RelA 0.035 0.059 -10000 0 -10000 0 0
Calcineurin -0.042 0.069 -10000 0 -0.44 2 2
PI3K -0.14 0.22 -10000 0 -0.6 69 69
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.061 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.27 0.32 -10000 0 -0.74 135 135
DAPP1 -0.11 0.18 -10000 0 -0.61 36 36
cytokine secretion -0.063 0.19 -10000 0 -0.46 66 66
mol:DAG -0.065 0.1 0.27 1 -0.51 4 5
PLCG2 0.003 0.1 -10000 0 -0.82 8 8
MAP2K1 -0.012 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.24 0.37 -10000 0 -0.72 178 178
mol:PI-3-4-5-P3 -0.096 0.15 -10000 0 -0.4 65 65
ETS1 -0.016 0.091 -10000 0 -0.44 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.22 -10000 0 -0.98 3 3
B-cell antigen/BCR complex/LYN -0.14 0.21 -10000 0 -0.57 71 71
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.1 0.28 -10000 0 -0.73 67 67
B-cell antigen/BCR complex/LYN/SYK -0.16 0.25 -10000 0 -0.76 37 37
CARD11 -0.14 0.26 -10000 0 -0.62 110 110
FCGR2B -0.14 0.34 -10000 0 -0.86 96 96
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.006 0.047 -10000 0 -10000 0 0
PTPRC -0.077 0.27 -10000 0 -0.86 56 56
PDPK1 -0.06 0.1 -10000 0 -0.34 4 4
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0.001 0.057 -10000 0 -0.14 66 66
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.013 0.035 -9999 0 -0.78 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.023 -9999 0 -10000 0 0
JMJD2C -0.001 0.022 -9999 0 -0.11 19 19
T-DHT/AR/Ubc9 -0.078 0.11 -9999 0 -0.54 26 26
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.013 0.009 -9999 0 -10000 0 0
MAK 0.014 0.044 -9999 0 -0.86 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.009 0.068 -9999 0 -0.77 4 4
GSN 0.015 0.008 -9999 0 -10000 0 0
NCOA2 0 0.11 -9999 0 -0.74 11 11
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.026 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.028 0.036 -9999 0 -0.61 1 1
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.15 -9999 0 -0.59 39 39
FHL2 -0.04 0.11 -9999 0 -1.1 5 5
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.056 -9999 0 -0.14 458 458
CDK6 0.014 0.033 -9999 0 -0.74 1 1
TGFB1I1 0.013 0.039 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.15 -9999 0 -0.59 46 46
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.58 26 26
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.017 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 511 511
SRF 0.026 0.012 -9999 0 -10000 0 0
NKX3-1 -0.19 0.07 -9999 0 -10000 0 0
KLK3 0.024 0.15 -9999 0 -0.7 21 21
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.013 -9999 0 -10000 0 0
AOF2 -0.001 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.077 0.11 -9999 0 -0.54 26 26
AR -0.07 0.16 -9999 0 -0.78 26 26
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.013 -9999 0 -10000 0 0
PAWR 0.014 0.033 -9999 0 -0.74 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.1 -9999 0 -0.5 26 26
RPS6KA3 0.013 0.035 -9999 0 -0.78 1 1
T-DHT/AR/ARA70 -0.079 0.11 -9999 0 -0.54 26 26
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.069 0.1 -9999 0 -0.5 26 26
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.005 0.12 -9999 0 -0.74 14 14
KLK2 -0.085 0.14 -9999 0 -0.8 19 19
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.069 0.13 -9999 0 -0.6 26 26
TMPRSS2 -0.92 0.36 -9999 0 -1.1 458 458
CCND1 -0.018 0.17 -9999 0 -0.86 20 20
PIAS1 0.014 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.027 -9999 0 -0.072 454 454
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.079 0.11 -9999 0 -0.56 26 26
CMTM2 -0.004 0.13 -9999 0 -0.86 12 12
SNURF -0.009 0.13 -9999 0 -0.74 17 17
ZMIZ1 -0.031 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.013 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.23 0.28 -9999 0 -0.85 76 76
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.014 0.088 -9999 0 -0.57 13 13
IFNAR2 0.015 0.007 -9999 0 -10000 0 0
AKT1 0.013 0.069 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.006 0.057 -9999 0 -0.59 5 5
NFX1/SIN3/HDAC complex 0.044 0.055 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.74 478 478
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.79 74 74
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.38 -9999 0 -0.74 246 246
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.23 -9999 0 -0.72 63 63
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.24 0.29 -9999 0 -0.88 76 76
CCND1 -0.22 0.27 -9999 0 -0.8 78 78
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.033 -9999 0 -0.74 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0.004 0.029 -9999 0 -10000 0 0
CDKN1B -0.22 0.3 -9999 0 -0.55 238 238
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.018 0.16 -9999 0 -0.86 19 19
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.005 0.12 -9999 0 -0.75 13 13
IFN-gamma/IRF1 -0.29 0.32 -9999 0 -0.65 238 238
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.004 0.13 -9999 0 -0.86 12 12
Telomerase -0.02 0.16 -9999 0 -0.48 8 8
IRF1 0.016 0.039 -9999 0 -0.86 1 1
ESR1 0.006 0.076 -9999 0 -0.77 5 5
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.021 -9999 0 -0.49 1 1
ubiquitin-dependent protein catabolic process 0.051 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.007 0.034 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM -0.001 0.023 -9999 0 -0.52 1 1
SMAD3 0.025 0.067 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.25 -9999 0 -0.76 64 64
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.009 0.094 -9999 0 -0.67 10 10
MAPK1 0.009 0.094 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.008 0.084 -9999 0 -0.86 5 5
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.023 -9999 0 -0.52 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.51 0.18 -9999 0 -0.57 479 479
MYC -0.019 0.17 -9999 0 -0.86 20 20
IL2 -0.008 0.12 -9999 0 -0.86 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.008 0.085 -9999 0 -0.86 5 5
TRF2/BLM -0.014 0.093 -9999 0 -0.62 12 12
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.21 0.26 -9999 0 -0.79 73 73
SP1/HDAC2 0.007 0.014 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.18 0.23 -9999 0 -0.72 63 63
Smad3/Myc -0.02 0.13 -9999 0 -0.6 24 24
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.37 0.43 -9999 0 -0.85 238 238
Telomerase/PinX1 -0.18 0.23 -9999 0 -0.74 52 52
Telomerase/AKT1/mTOR/p70S6K -0.012 0.079 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.18 0.23 -9999 0 -0.72 63 63
response to DNA damage stimulus 0.004 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.23 -9999 0 -0.72 62 62
E2F1 -0.091 0.29 -9999 0 -0.87 64 64
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.14 0.33 -9999 0 -0.86 92 92
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.17 0.27 -10000 0 -0.54 95 95
CRKL 0.015 0.12 -10000 0 -0.55 9 9
HRAS -0.043 0.18 -10000 0 -0.51 41 41
mol:PIP3 -0.005 0.11 -10000 0 -0.44 24 24
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.014 0.033 -10000 0 -0.74 1 1
GAB1 0.004 0.12 -10000 0 -0.49 24 24
FOXO3 0.022 0.11 -10000 0 -0.49 9 9
AKT1 0.012 0.12 -10000 0 -0.45 24 24
BAD 0.02 0.11 -10000 0 -0.59 6 6
megakaryocyte differentiation -0.074 0.22 -10000 0 -0.45 117 117
GSK3B 0.022 0.11 -10000 0 -0.59 5 5
RAF1 -0.011 0.15 -10000 0 -0.54 3 3
SHC1 0.014 0.038 -10000 0 -0.86 1 1
STAT3 0.005 0.12 -10000 0 -0.49 24 24
STAT1 -0.02 0.25 -10000 0 -1 24 24
HRAS/SPRED1 -0.068 0.12 -10000 0 -0.42 20 20
cell proliferation 0.004 0.13 -10000 0 -0.51 24 24
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.006 0.12 -10000 0 -0.44 33 33
HRAS/SPRED2 -0.068 0.12 -10000 0 -0.43 21 21
LYN/TEC/p62DOK -0.02 0.1 -10000 0 -0.66 5 5
MAPK3 0.011 0.12 -10000 0 -0.37 2 2
STAP1 -0.32 0.22 -10000 0 -0.42 406 406
GRAP2 -0.042 0.22 -10000 0 -0.86 35 35
JAK2 -0.071 0.2 -10000 0 -0.9 24 24
STAT1 (dimer) -0.019 0.24 -10000 0 -1 24 24
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.13 0.22 -10000 0 -0.47 131 131
actin filament polymerization -0.002 0.14 -10000 0 -0.49 30 30
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.3 0.23 -10000 0 -0.88 33 33
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
CBL/CRKL/GRB2 -0.016 0.096 -10000 0 -0.59 5 5
PI3K -0.022 0.11 -10000 0 -0.45 25 25
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.35 -10000 0 -1.3 26 26
MAPK8 0.003 0.13 -10000 0 -0.52 24 24
STAT3 (dimer) 0.005 0.12 -10000 0 -0.48 24 24
positive regulation of transcription 0.015 0.099 -10000 0 -0.31 1 1
mol:GDP -0.11 0.19 -10000 0 -0.62 44 44
PIK3C2B 0.005 0.12 -10000 0 -0.49 24 24
CBL/CRKL 0.024 0.11 -10000 0 -0.62 5 5
FER 0.003 0.13 -10000 0 -0.5 26 26
SH2B3 0.005 0.12 -10000 0 -0.49 24 24
PDPK1 0.005 0.1 -10000 0 -0.48 10 10
SNAI2 0.004 0.13 -10000 0 -0.5 24 24
positive regulation of cell proliferation -0.004 0.19 -10000 0 -0.78 24 24
KITLG 0 0.11 -10000 0 -0.76 10 10
cell motility -0.004 0.19 -10000 0 -0.78 24 24
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.039 0.073 -10000 0 -10000 0 0
STAT5A (dimer) 0.001 0.17 -10000 0 -0.65 25 25
SOCS1 0.006 0.093 -10000 0 -0.86 6 6
cell migration 0.045 0.2 0.5 72 -10000 0 72
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.29 0.42 -10000 0 -0.86 186 186
VAV1 -0.19 0.37 -10000 0 -0.86 124 124
GRB10 0.004 0.12 -10000 0 -0.49 24 24
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.037 0.12 -10000 0 -0.46 36 36
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.005 0.13 -10000 0 -0.42 2 2
CBL 0.014 0.033 -10000 0 -0.74 1 1
KIT -0.016 0.29 -10000 0 -1.2 31 31
MAP2K2 0.004 0.13 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.021 0.1 -10000 0 -0.66 5 5
STAT5A 0 0.17 -10000 0 -0.67 25 25
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.004 0.13 -10000 0 -0.49 24 24
SHC/GRAP2 -0.045 0.17 -10000 0 -0.66 36 36
PTPRO -0.076 0.22 -10000 0 -0.46 117 117
SH2B2 -0.002 0.14 -10000 0 -0.5 30 30
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.047 0.2 -10000 0 -0.52 72 72
CREBBP 0.044 0.012 -10000 0 -10000 0 0
BCL2 0.041 0.071 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.22 -9999 0 -0.48 179 179
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.11 0.22 -9999 0 -0.52 6 6
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.011 0.14 -9999 0 -0.86 13 13
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.65 0.38 -9999 0 -0.86 403 403
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.86 67 67
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.18 0.24 -9999 0 -0.49 190 190
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.16 -9999 0 -0.59 16 16
MAP1B -0.001 0.02 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.17 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 178 178
PAFAH/LIS1 -0.44 0.25 -9999 0 -0.57 403 403
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.098 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.7 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.13 0.19 -9999 0 -0.64 16 16
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.033 -9999 0 -0.74 1 1
PAFAH1B2 0.014 0.033 -9999 0 -0.74 1 1
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 -9999 0 -0.56 16 16
LRP8 0.014 0.038 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.13 0.16 -9999 0 -0.59 16 16
P39/CDK5 -0.18 0.22 -9999 0 -0.86 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.094 0.21 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.2 -9999 0 -0.51 18 18
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
CDC42 0 0 -9999 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.012 0.054 -9999 0 -0.86 2 2
RELN/VLDLR/Fyn -0.16 0.22 -9999 0 -0.48 178 178
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.045 -9999 0 -0.8 1 1
AKT1 -0.068 0.16 -9999 0 -0.57 2 2
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.011 0.14 -9999 0 -0.86 13 13
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.45 191 191
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 19 19
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.82 1 1
long-term memory -0.2 0.24 -9999 0 -0.88 24 24
DAB1/LIS1 -0.14 0.18 -9999 0 -0.85 1 1
DAB1/CRLK/C3G -0.13 0.18 -9999 0 -0.82 1 1
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
DAB1/NCK2 -0.14 0.18 -9999 0 -0.86 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.3 -9999 0 -0.83 76 76
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.75 178 178
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RELN/LRP8/Fyn -0.16 0.22 -9999 0 -0.48 179 179
GRIN2A/RELN/LRP8/DAB1/Fyn -0.21 0.25 -9999 0 -0.62 77 77
MAPK8 0.013 0.046 -9999 0 -0.74 2 2
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.45 190 190
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.51 19 19
RELN/LRP8 -0.16 0.22 -9999 0 -0.48 179 179
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.61 7 7
PI3K -0.002 0.034 -9999 0 -0.56 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.041 -9999 0 -0.66 2 2
RAP1A -0.11 0.17 -9999 0 -0.75 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.046 -9999 0 -0.74 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.054 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.03 0.12 -9999 0 -0.53 3 3
neuron adhesion -0.051 0.19 -9999 0 -0.7 1 1
LRP8 0.014 0.038 -9999 0 -0.86 1 1
GSK3B -0.054 0.15 -9999 0 -0.53 2 2
RELN/VLDLR/DAB1/Fyn -0.15 0.2 -9999 0 -0.42 190 190
MAP3K11 0.014 0.033 -9999 0 -0.74 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.61 2 2
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.016 0.082 -9999 0 -0.69 6 6
neuron migration -0.061 0.21 -9999 0 -0.54 2 2
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.031 0.12 -9999 0 -0.54 3 3
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.25 0.41 -10000 0 -0.82 175 175
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.053 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.004 0.098 -10000 0 -0.85 7 7
GR alpha/HSP90/FKBP51/HSP90 0.055 0.13 0.39 5 -0.57 8 13
PRL -0.015 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.57 82 -0.58 3 85
RELA 0.005 0.076 -10000 0 -10000 0 0
FGG -0.14 0.43 0.53 20 -0.7 172 192
GR beta/TIF2 0.051 0.14 0.42 6 -0.53 10 16
IFNG -0.41 0.44 -10000 0 -0.9 184 184
apoptosis -0.094 0.21 -10000 0 -0.64 11 11
CREB1 -0.015 0.1 -10000 0 -0.4 5 5
histone acetylation 0.02 0.13 0.39 10 -0.55 3 13
BGLAP -0.008 0.13 -10000 0 -0.74 3 3
GR/PKAc 0.065 0.1 0.37 4 -0.6 1 5
NF kappa B1 p50/RelA 0.011 0.14 -10000 0 -0.56 8 8
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.047 0.093 0.35 6 -10000 0 6
GATA3 -0.35 0.38 -10000 0 -0.74 262 262
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.027 0.15 -10000 0 -0.69 16 16
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.057 0.22 -10000 0 -0.82 13 13
CSN2 0.045 0.19 0.48 5 -0.66 1 6
BRG1/BAF155/BAF170/BAF60A 0.004 0.014 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.019 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.052 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.004 0.21 0.37 3 -0.55 37 40
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.22 -10000 0 -0.85 13 13
JUN -0.22 0.25 -10000 0 -0.67 63 63
IL4 -0.023 0.12 -10000 0 -0.63 1 1
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 0.31 2 -0.7 79 81
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.061 0.12 0.38 4 -0.6 4 8
cortisol/GR alpha (monomer) 0.15 0.34 0.66 96 -0.8 1 97
NCOA2 0 0.11 -10000 0 -0.74 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.054 0.14 -10000 0 -0.82 13 13
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.88 79 79
AFP -0.35 0.56 -10000 0 -1.4 112 112
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.085 0.15 0.55 5 -0.62 1 6
TP53 0.044 0.021 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.25 0.41 -10000 0 -1.2 67 67
KRT14 -0.15 0.3 -10000 0 -0.83 81 81
TBP 0.028 0.01 -10000 0 -10000 0 0
CREBBP 0.049 0.082 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.33 0.34 -10000 0 -0.88 81 81
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 0.005 0.074 -10000 0 -0.75 5 5
MAPK11 0.008 0.055 -10000 0 -0.88 2 2
KRT5 -0.27 0.39 -10000 0 -0.95 104 104
interleukin-1 receptor activity 0 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.053 -10000 0 -1.2 1 1
CGA -0.13 0.37 -10000 0 -1.2 52 52
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.091 0.15 0.45 35 -10000 0 35
MAPK3 0.012 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.049 0.23 -10000 0 -0.81 24 24
NFKB1 0.003 0.085 -10000 0 -0.9 1 1
MAPK8 -0.14 0.2 -10000 0 -0.57 34 34
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.099 0.22 -10000 0 -0.68 11 11
BAX 0.052 0.028 -10000 0 -10000 0 0
POMC -0.037 0.17 -10000 0 -0.86 6 6
EP300 0.047 0.086 -10000 0 -0.6 1 1
cortisol/GR alpha (dimer)/p53 0.16 0.29 0.6 77 -0.7 1 78
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.071 0.29 1 -10000 0 1
SGK1 0.1 0.098 -10000 0 -10000 0 0
IL13 -0.36 0.28 -10000 0 -0.81 92 92
IL6 -0.12 0.38 -10000 0 -0.98 75 75
PRKACG 0.004 0.007 -10000 0 -10000 0 0
IL5 -0.29 0.21 -10000 0 -0.71 41 41
IL2 -0.17 0.25 -10000 0 -0.86 26 26
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.077 0.3 -10000 0 -0.9 46 46
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.1 -10000 0 -0.62 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.55 77 -0.65 1 78
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.15 0.42 27 -10000 0 27
NF kappa B1 p50/RelA/Cbp 0.065 0.14 -10000 0 -0.94 1 1
JUN (dimer) -0.21 0.25 -10000 0 -0.67 64 64
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.057 0.22 -10000 0 -1 16 16
NR3C1 0.081 0.19 0.48 37 -0.95 1 38
NR4A1 0.002 0.13 -10000 0 -0.73 16 16
TIF2/SUV420H1 -0.012 0.079 -10000 0 -0.56 11 11
MAPKKK cascade -0.094 0.21 -10000 0 -0.64 11 11
cortisol/GR alpha (dimer)/Src-1 0.15 0.28 0.58 82 -0.8 1 83
PBX1 -0.003 0.13 -10000 0 -0.74 16 16
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.095 0.36 -10000 0 -1.3 39 39
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.42 27 -10000 0 27
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.55 77 -0.65 1 78
mol:cortisol 0.064 0.2 0.42 61 -10000 0 61
MMP1 -0.23 0.4 -10000 0 -0.98 105 105
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 240 240
alphaV beta3 Integrin -0.01 0.074 -9999 0 -0.53 10 10
PTK2 -0.15 0.23 -9999 0 -0.67 6 6
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.038 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.084 0.19 -9999 0 -0.52 82 82
VEGFA -0.38 0.44 -9999 0 -0.86 240 240
ILK -0.084 0.19 -9999 0 -0.52 82 82
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.077 0.18 -9999 0 -0.49 74 74
PTK2B -0.19 0.27 -9999 0 -0.88 1 1
alphaV/beta3 Integrin/JAM-A -0.07 0.16 -9999 0 -0.52 10 10
CBL 0.014 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.47 252 252
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.066 -9999 0 -0.52 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.14 -9999 0 -0.47 46 46
alphaV/beta3 Integrin/Syndecan-1 -0.011 0.07 -9999 0 -0.47 12 12
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.14 -9999 0 -0.8 4 4
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Osteopontin -0.009 0.064 -9999 0 -0.47 10 10
RPS6KB1 -0.043 0.13 -9999 0 -0.73 4 4
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.044 0.1 -9999 0 -0.7 5 5
GPR124 0.011 0.066 -9999 0 -0.86 3 3
MAPK1 -0.044 0.1 -9999 0 -0.82 3 3
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Tumstatin -0.058 0.16 -9999 0 -0.49 63 63
cell adhesion -0.17 0.18 -9999 0 -0.83 1 1
ANGPTL3 -0.34 0.38 -9999 0 -0.74 246 246
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 240 240
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
IGF1 0.006 0.093 -9999 0 -0.86 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.009 0.065 -9999 0 -0.5 9 9
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.005 0.05 -9999 0 -0.47 6 6
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.019 0.099 -9999 0 -0.52 19 19
CSF1 0.014 0.033 -9999 0 -0.74 1 1
PIK3C2A -0.086 0.2 -9999 0 -0.53 83 83
PI4 Kinase/Pyk2 -0.24 0.24 -9999 0 -0.75 48 48
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 240 240
FAK1/Vinculin -0.11 0.19 -9999 0 -0.56 3 3
alphaV beta3/Integrin/ppsTEM5 -0.009 0.066 -9999 0 -0.51 9 9
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.1 0.28 -9999 0 -0.75 82 82
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
FGF2 0.008 0.076 -9999 0 -0.77 5 5
F11R 0.025 0.059 -9999 0 -0.58 5 5
alphaV/beta3 Integrin/Lactadherin -0.006 0.056 -9999 0 -0.49 7 7
alphaV/beta3 Integrin/TGFBR2 -0.005 0.05 -9999 0 -0.47 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.041 -9999 0 -0.85 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.005 0.046 -9999 0 -0.44 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.047 0.23 -9999 0 -0.86 38 38
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.88 1 1
SDC1 0.007 0.08 -9999 0 -0.74 6 6
VAV3 0.04 0.082 -9999 0 -0.8 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.066 -9999 0 -0.74 4 4
FAK1/Paxillin -0.11 0.19 -9999 0 -0.56 3 3
cell migration -0.092 0.17 -9999 0 -0.52 2 2
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.063 0.14 -9999 0 -1.1 1 1
SPP1 0.01 0.066 -9999 0 -0.74 4 4
KDR 0.014 0.033 -9999 0 -0.74 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.069 0.24 -9999 0 -0.74 59 59
angiogenesis 0.002 0.15 -9999 0 -0.8 3 3
Rac1/GTP -0.011 0.066 -9999 0 -0.72 1 1
EDIL3 -0.005 0.13 -9999 0 -0.78 14 14
cell proliferation -0.005 0.05 -9999 0 -0.47 6 6
Aurora A signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.019 0.045 -9999 0 -10000 0 0
BIRC5 -0.24 0.4 -9999 0 -0.86 154 154
NFKBIA 0.047 0.039 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.76 109 109
AKT1 0.047 0.039 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.017 0.04 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.075 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.013 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.019 0.045 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.011 0.057 -9999 0 -0.74 3 3
TPX2 -0.14 0.3 -9999 0 -0.67 127 127
TP53 0.024 0.036 -9999 0 -10000 0 0
DLG7 0.019 0.043 -9999 0 -0.29 6 6
AURKAIP1 0.011 0.06 -9999 0 -0.78 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.078 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.017 0.04 -9999 0 -10000 0 0
AURKA 0.026 0.054 -9999 0 -0.34 6 6
AURKB -0.14 0.15 -9999 0 -0.29 247 247
CDC25B 0.017 0.061 -9999 0 -0.58 2 2
G2/M transition checkpoint 0.014 0.052 -9999 0 -0.44 3 3
mRNA polyadenylation -0.076 0.19 -9999 0 -0.44 109 109
Aurora A/CPEB -0.076 0.19 -9999 0 -0.44 109 109
Aurora A/TACC1/TRAP/chTOG 0.023 0.044 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.019 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.006 0.064 -9999 0 -0.73 4 4
spindle assembly -0.002 0.022 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.21 -9999 0 -0.47 151 151
CENPA -0.12 0.14 -9999 0 -0.3 170 170
Aurora A/PP2A 0.019 0.045 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.053 0.035 -9999 0 -10000 0 0
negative regulation of DNA binding 0.024 0.036 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
Ajuba/Aurora A 0.015 0.053 -9999 0 -0.44 3 3
mitotic prometaphase 0.037 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -9999 0 -0.34 6 6
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.009 0.076 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.017 0.06 -9999 0 -0.49 3 3
Aurora A/RasGAP 0.018 0.05 -9999 0 -0.47 1 1
OAZ1 0.014 0.038 -9999 0 -0.86 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.66 127 127
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.086 0.24 -9999 0 -0.52 127 127
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.18 -9999 0 -10000 0 0
CRKL -0.094 0.22 -9999 0 -10000 0 0
mol:DAG -0.12 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -0.7 1 1
MAPK8 -0.14 0.26 -9999 0 -0.7 2 2
RAP1A -0.094 0.22 -9999 0 -10000 0 0
GAB1 -0.094 0.22 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.48 186 186
EPO -0.29 0.42 -9999 0 -0.85 186 186
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.19 0.26 -9999 0 -0.55 187 187
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.31 -9999 0 -0.65 186 186
IRS2 -0.1 0.23 -9999 0 -0.88 2 2
STAT1 -0.065 0.21 -9999 0 -10000 0 0
STAT5B -0.069 0.21 -9999 0 -10000 0 0
cell proliferation -0.12 0.24 -9999 0 -0.86 1 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.11 0.15 -9999 0 -0.71 1 1
TEC -0.094 0.22 -9999 0 -10000 0 0
SOCS3 0.011 0.066 -9999 0 -0.86 3 3
STAT1 (dimer) -0.063 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -10000 0 0
EPO/EPOR -0.23 0.31 -9999 0 -0.65 186 186
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.081 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 186 186
mol:IP3 -0.12 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.13 0.26 -9999 0 -0.48 186 186
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 2 2
PTPN6 -0.11 0.23 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.12 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.12 0.17 -9999 0 -0.73 1 1
VAV2 -0.094 0.22 -9999 0 -10000 0 0
CBL -0.094 0.22 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.12 0.17 -9999 0 -10000 0 0
STAT5A -0.069 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.045 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.009 0.076 -9999 0 -0.62 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.29 -9999 0 -0.88 30 30
BCL2 -0.02 0.18 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.084 0.31 -10000 0 -0.9 30 30
NCK1/PAK1/Dok-R -0.083 0.11 -10000 0 -0.41 34 34
NCK1/Dok-R -0.083 0.26 -10000 0 -1 32 32
PIK3CA 0.005 0.033 -10000 0 -0.74 1 1
mol:beta2-estradiol -0.006 0.038 0.3 7 -10000 0 7
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.007 0.039 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.31 0.42 -10000 0 -0.85 199 199
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.058 0.23 -10000 0 -0.96 31 31
FN1 -0.047 0.23 -10000 0 -0.86 38 38
PLD2 0.032 0.3 -10000 0 -1.1 31 31
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.024 0.17 -10000 0 -0.74 28 28
ELK1 0.061 0.27 -10000 0 -0.96 31 31
GRB7 0.006 0.086 -10000 0 -0.74 7 7
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.29 -10000 0 -1 43 43
CDKN1A -0.11 0.31 -10000 0 -0.68 20 20
ITGA5 -0.047 0.23 -10000 0 -0.86 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.083 0.26 -10000 0 -1 32 32
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.049 0.26 -10000 0 -0.65 30 30
PLG -0.19 0.34 -10000 0 -1.2 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.21 -10000 0 -0.84 30 30
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.034 -10000 0 -0.74 1 1
ANGPT2 -0.2 0.38 -10000 0 -0.65 172 172
BMX -0.036 0.34 -10000 0 -1.1 31 31
ANGPT1 0.075 0.19 -10000 0 -1.2 8 8
tube development -0.13 0.34 -10000 0 -0.7 33 33
ANGPT4 -0.018 0.15 -10000 0 -0.87 16 16
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.024 0.32 -10000 0 -1.2 31 31
alpha5/beta1 Integrin -0.048 0.17 -10000 0 -0.66 38 38
FGF2 0.01 0.077 -10000 0 -0.76 5 5
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 26 26
mol:L-citrulline -0.049 0.26 -10000 0 -0.65 30 30
AGTR1 -0.036 0.17 -10000 0 -0.75 29 29
MAPK14 -0.003 0.31 -10000 0 -1.1 30 30
Tie2/SHP2 -0.061 0.25 -10000 0 -1.1 29 29
TEK -0.046 0.29 -10000 0 -1.2 29 29
RPS6KB1 -0.047 0.28 -10000 0 -0.86 30 30
Angiotensin II/AT1 -0.043 0.13 -10000 0 -0.58 29 29
Tie2/Ang1/GRB2 -0.004 0.3 -10000 0 -1.1 31 31
MAPK3 0.045 0.27 -10000 0 -0.99 31 31
MAPK1 0.045 0.27 -10000 0 -0.99 31 31
Tie2/Ang1/GRB7 -0.009 0.31 -10000 0 -1.2 31 31
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MAPK8 0.031 0.3 -10000 0 -1.1 31 31
PI3K -0.07 0.32 -10000 0 -1 30 30
FES -0.008 0.31 -10000 0 -1.1 31 31
Crk/Dok-R -0.083 0.26 -10000 0 -1 31 31
Tie2/Ang1/ABIN2 -0.004 0.3 -10000 0 -1.1 31 31
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.073 0.29 -10000 0 -0.8 30 30
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.047 0.28 -10000 0 -0.86 30 30
Tie2/Ang2 -0.19 0.41 -10000 0 -0.98 33 33
Tie2/Ang1 0.024 0.33 -10000 0 -1.2 31 31
FOXO1 -0.11 0.31 -10000 0 -0.8 30 30
ELF1 0.023 0.035 -10000 0 -0.73 1 1
ELF2 0.028 0.3 -10000 0 -1.1 31 31
mol:Choline 0.035 0.28 -10000 0 -1 31 31
cell migration -0.055 0.071 -10000 0 -10000 0 0
FYN -0.15 0.36 -10000 0 -0.8 33 33
DOK2 -0.035 0.2 -10000 0 -0.86 31 31
negative regulation of cell cycle -0.095 0.3 -10000 0 -0.61 20 20
ETS1 0.028 0.037 -10000 0 -10000 0 0
PXN -0.025 0.25 -10000 0 -0.7 30 30
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.06 0.28 -10000 0 -0.74 30 30
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.009 0.11 -10000 0 -0.79 8 8
MAPKKK cascade 0.035 0.28 -10000 0 -1 31 31
RASA1 0.014 0.033 -10000 0 -0.74 1 1
Tie2/Ang1/Shc -0.003 0.3 -10000 0 -1.1 31 31
NCK1 0.014 0.033 -10000 0 -0.74 1 1
vasculogenesis -0.04 0.24 -10000 0 -0.58 30 30
mol:Phosphatidic acid 0.035 0.28 -10000 0 -1 31 31
mol:Angiotensin II -0.016 0.022 -10000 0 -10000 0 0
mol:NADP -0.049 0.26 -10000 0 -0.65 30 30
Rac1/GTP -0.13 0.19 -10000 0 -0.8 30 30
MMP2 0.027 0.3 -10000 0 -1.1 31 31
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.01 0.082 -9999 0 -0.68 8 8
Metarhodopsin II/Arrestin -0.019 0.1 -9999 0 -0.59 17 17
PDE6G/GNAT1/GTP -0.014 0.086 -9999 0 -0.56 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.007 0.11 -9999 0 -0.86 8 8
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.94 12 12
mol:Na + -0.11 0.21 -9999 0 -0.81 22 22
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.036 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.85 22 22
CNGB1 -0.009 0.12 -9999 0 -0.86 11 11
RDH5 -0.003 0.13 -9999 0 -0.83 12 12
SAG 0.001 0.038 -9999 0 -0.86 1 1
mol:Ca2+ -0.069 0.22 -9999 0 -0.78 22 22
Na + (4 Units) -0.1 0.2 -9999 0 -0.74 22 22
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
GNB1/GNGT1 -0.23 0.32 -9999 0 -0.66 182 182
GNAT1/GDP -0.038 0.13 -9999 0 -0.53 16 16
GUCY2D -0.031 0.19 -9999 0 -0.86 26 26
GNGT1 -0.29 0.42 -9999 0 -0.86 182 182
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.15 -9999 0 -0.59 29 29
mol:11-cis-retinal -0.003 0.13 -9999 0 -0.83 12 12
mol:cGMP -0.041 0.14 -9999 0 -0.53 39 39
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.034 0.15 -9999 0 -0.65 28 28
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.13 0.3 -9999 0 -0.74 99 99
Metarhodopsin II -0.017 0.094 -9999 0 -0.55 16 16
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.15 -9999 0 -0.55 41 41
RGS9BP -0.018 0.15 -9999 0 -0.74 23 23
Metarhodopsin II/Transducin -0.12 0.16 -9999 0 -0.62 11 11
GCAP Family/Ca ++ -0.017 0.098 -9999 0 -0.56 16 16
PDE6A/B -0.035 0.15 -9999 0 -0.66 28 28
mol:Pi -0.035 0.13 -9999 0 -0.5 38 38
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.27 -9999 0 -0.55 185 185
PDE6B 0.007 0.08 -9999 0 -0.74 6 6
PDE6A -0.024 0.18 -9999 0 -0.86 23 23
PDE6G 0.008 0.076 -9999 0 -0.77 5 5
RHO -0.016 0.15 -9999 0 -0.86 16 16
PDE6 -0.056 0.16 -9999 0 -0.82 8 8
GUCA1A -0.01 0.12 -9999 0 -0.86 10 10
GC2/GCAP Family -0.017 0.098 -9999 0 -0.56 16 16
GUCA1C 0.001 0.046 -9999 0 -0.74 2 2
GUCA1B 0.007 0.085 -9999 0 -0.86 5 5
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.048 0.1 -10000 0 -0.55 5 5
PTP1B/AKT1 -0.032 0.047 -10000 0 -0.39 3 3
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.049 0.053 -10000 0 -0.41 4 4
EGFR -0.013 0.11 -10000 0 -0.87 9 9
EGF/EGFR -0.37 0.14 -10000 0 -0.41 476 476
CSF1 0.014 0.033 -10000 0 -0.74 1 1
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.05 0.091 -10000 0 -0.45 20 20
Insulin Receptor/Insulin -0.008 0.035 -10000 0 -10000 0 0
HCK -0.032 0.2 -10000 0 -0.86 29 29
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.035 0.05 -10000 0 -0.44 2 2
EGF -0.67 0.23 -10000 0 -0.75 478 478
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 40 40
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.033 0.055 -10000 0 -0.45 6 6
cell migration 0.049 0.053 0.41 4 -10000 0 4
STAT3 0.015 0.002 -10000 0 -10000 0 0
PRLR -0.087 0.26 -10000 0 -0.74 70 70
ITGA2B -0.02 0.16 -10000 0 -0.86 19 19
CSF1R 0.004 0.1 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.074 0.19 -10000 0 -0.56 70 70
FGR 0.011 0.066 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.052 -10000 0 -0.42 3 3
Crk/p130 Cas -0.031 0.042 -10000 0 -0.42 2 2
DOK1 -0.019 0.046 -10000 0 -0.36 3 3
JAK2 -0.054 0.11 -10000 0 -0.49 10 10
Jak2/Leptin Receptor/Leptin -0.053 0.13 -10000 0 -0.69 4 4
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
PTPN1 -0.049 0.053 -10000 0 -0.41 4 4
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.01 0.14 -10000 0 -0.74 18 18
SRC 0 0.021 -10000 0 -10000 0 0
ITGB3 0.003 0.08 -10000 0 -0.74 6 6
CAT1/PTP1B -0.23 0.13 -10000 0 -0.58 35 35
CAPN1 0.002 0.006 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.008 0.043 -10000 0 -0.63 1 1
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.035 0.12 -10000 0 -0.67 4 4
negative regulation of transcription -0.053 0.11 -10000 0 -0.48 10 10
FCGR2A -0.024 0.18 -10000 0 -0.86 24 24
FER -0.001 0.047 -10000 0 -0.75 2 2
alphaIIb/beta3 Integrin -0.03 0.14 -10000 0 -0.66 24 24
BLK -0.04 0.21 -10000 0 -0.86 33 33
Insulin Receptor/Insulin/Shc -0.001 0.026 -10000 0 -0.59 1 1
RHOA 0.002 0.006 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.22 0.15 -10000 0 -0.55 61 61
PRL 0.004 0.007 -10000 0 -10000 0 0
SOCS3 0.027 0.058 -10000 0 -0.73 3 3
SPRY2 0.002 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.042 -10000 0 -0.49 4 4
CSF1/CSF1R -0.037 0.075 -10000 0 -0.53 10 10
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.01 0.066 -10000 0 -0.74 4 4
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.071 0.26 -10000 0 -0.86 50 50
STAT5B -0.045 0.068 -10000 0 -0.46 5 5
STAT5A -0.045 0.068 -10000 0 -0.46 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.036 0.05 -10000 0 -0.42 3 3
CSN2 -0.008 0.069 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
LAT -0.1 0.17 -10000 0 -0.35 149 149
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.02 0.17 -10000 0 -0.85 22 22
SHC1 0.014 0.038 -10000 0 -0.86 1 1
NOX4 -0.006 0.073 -10000 0 -0.75 5 5
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.041 0.15 -9999 0 -0.58 38 38
EPHB2 0 0.11 -9999 0 -0.76 11 11
Syndecan-2/TACI -0.054 0.17 -9999 0 -0.58 50 50
LAMA1 -0.006 0.13 -9999 0 -0.75 15 15
Syndecan-2/alpha2 ITGB1 -0.01 0.067 -9999 0 -0.49 7 7
HRAS 0.014 0.038 -9999 0 -0.86 1 1
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.047 0.23 -9999 0 -0.86 38 38
BAX 0.053 0.028 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.001 0.11 -9999 0 -0.85 9 9
Syndecan-2/MMP2 -0.006 0.059 -9999 0 -0.56 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.005 0.054 -9999 0 -0.56 5 5
dendrite morphogenesis -0.01 0.07 -9999 0 -0.49 11 11
Syndecan-2/GM-CSF -0.016 0.096 -9999 0 -0.58 15 15
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.025 -9999 0 -0.58 1 1
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
MAPK3 0.022 0.093 -9999 0 -0.52 15 15
MAPK1 0.022 0.093 -9999 0 -0.52 15 15
Syndecan-2/RACK1 -0.002 0.031 -9999 0 -0.5 2 2
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.009 0.073 -9999 0 -0.74 5 5
MAPK8 0.045 0.031 -9999 0 -0.46 2 2
Syndecan-2/alpha2/beta1 Integrin -0.015 0.08 -9999 0 -0.65 2 2
Syndecan-2/Kininogen -0.35 0.21 -9999 0 -0.48 395 395
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.048 0.032 -9999 0 -0.46 2 2
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.005 0.055 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.041 0.15 -9999 0 -0.57 38 38
Syndecan-2/Caveolin-2/Ras -0.01 0.07 -9999 0 -0.51 10 10
Syndecan-2/Laminin alpha3 -0.008 0.066 -9999 0 -0.58 7 7
Syndecan-2/RasGAP -0.003 0.043 -9999 0 -0.67 2 2
alpha5/beta1 Integrin -0.048 0.17 -9999 0 -0.66 38 38
PRKCD 0.014 0.038 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.071 -9999 0 -0.49 11 11
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.041 -9999 0 -0.83 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.069 0.26 -9999 0 -0.86 50 50
RASA1 0.014 0.033 -9999 0 -0.74 1 1
alpha2/beta1 Integrin -0.005 0.054 -9999 0 -0.56 5 5
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.085 -9999 0 -0.86 5 5
CASP3 0.043 0.025 -9999 0 -0.52 1 1
FN1 -0.047 0.23 -9999 0 -0.86 38 38
Syndecan-2/IL8 -0.036 0.14 -9999 0 -0.56 34 34
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.55 0.32 -9999 0 -0.74 395 395
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.018 0.14 -9999 0 -0.86 15 15
Syndecan-2/TGFB1 -0.005 0.056 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.044 0 -9999 0 -10000 0 0
angiogenesis -0.035 0.14 -9999 0 -0.55 34 34
MMP2 0.006 0.091 -9999 0 -0.84 6 6
IL8 -0.039 0.21 -9999 0 -0.84 34 34
calcineurin-NFAT signaling pathway -0.054 0.17 -9999 0 -0.57 50 50
Endothelins

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
AKT1 0.008 0.21 -10000 0 -0.88 3 3
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.083 0.13 -10000 0 -0.83 3 3
EDN1 -0.015 0.19 -10000 0 -0.74 20 20
EDN3 -0.019 0.15 -10000 0 -0.86 17 17
EDN2 -0.09 0.28 -10000 0 -0.82 67 67
HRAS/GDP 0.052 0.17 -10000 0 -0.7 9 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.021 0.15 -10000 0 -0.51 15 15
ADCY4 0.01 0.17 -10000 0 -0.74 3 3
ADCY5 -0.007 0.2 -10000 0 -0.71 13 13
ADCY6 0.009 0.17 -10000 0 -0.74 3 3
ADCY7 -0.004 0.19 -10000 0 -0.72 7 7
ADCY1 -0.001 0.18 -10000 0 -0.74 4 4
ADCY2 -0.13 0.27 -10000 0 -0.7 31 31
ADCY3 0.01 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.28 -10000 0 -0.74 35 35
ADCY9 0.01 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.076 0.15 -10000 0 -0.53 10 10
ETB receptor/Endothelin-1/Gq/GTP 0.035 0.11 -10000 0 -0.46 11 11
GNAO1 0.008 0.083 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
ETA receptor/Endothelin-1/G12/GTP -0.013 0.22 0.38 73 -0.82 3 76
ETA receptor/Endothelin-1/Gs/GTP -0.013 0.21 0.36 73 -0.79 3 76
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.041 0.34 -10000 0 -0.95 52 52
EDNRB 0.007 0.068 -10000 0 -0.78 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.043 0.3 -10000 0 -0.75 51 51
CYSLTR1 0.008 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.013 0.11 -10000 0 -0.39 2 2
mol:GDP 0.045 0.18 -10000 0 -0.64 14 14
SLC9A3 -0.35 0.3 -10000 0 -0.53 333 333
RAF1 0.048 0.17 -10000 0 -0.68 10 10
JUN 0.086 0.12 -10000 0 -0.57 1 1
JAK2 0.008 0.21 -10000 0 -0.88 3 3
mol:IP3 0.018 0.17 -10000 0 -0.57 17 17
ETA receptor/Endothelin-1 -0.026 0.27 0.45 73 -0.57 53 126
PLCB1 0.001 0.11 -10000 0 -0.74 11 11
PLCB2 -0.079 0.27 -10000 0 -0.86 58 58
ETA receptor/Endothelin-3 -0.022 0.15 -10000 0 -0.68 19 19
FOS 0.06 0.2 -10000 0 -0.86 15 15
Gai/GDP 0.039 0.069 -10000 0 -0.62 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.003 0.24 -10000 0 -0.77 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
PRKCB1 0.019 0.16 -10000 0 -0.54 17 17
GNAQ 0.02 0.004 -10000 0 -10000 0 0
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.044 0.11 -10000 0 -0.61 11 11
ETA receptor/Endothelin-1/Gq/GTP 0.045 0.14 -10000 0 -0.48 10 10
MAPK14 0.024 0.13 -10000 0 -0.56 10 10
TRPC6 0.083 0.14 -10000 0 -1 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.014 0.14 -10000 0 -0.54 14 14
ETB receptor/Endothelin-2 -0.085 0.21 -10000 0 -0.62 70 70
ETB receptor/Endothelin-3 -0.028 0.12 -10000 0 -0.66 20 20
ETB receptor/Endothelin-1 -0.032 0.16 -10000 0 -0.62 20 20
MAPK3 0.06 0.19 -10000 0 -0.72 17 17
MAPK1 0.06 0.19 -10000 0 -0.72 17 17
Rac1/GDP 0.052 0.17 -10000 0 -0.63 11 11
cAMP biosynthetic process -0.061 0.19 -10000 0 -0.61 13 13
MAPK8 0.078 0.13 -10000 0 -0.58 3 3
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.03 0.09 -10000 0 -0.51 4 4
p130Cas/CRK/Src/PYK2 0.072 0.17 -10000 0 -0.67 10 10
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.052 0.17 -10000 0 -0.71 8 8
COL1A2 -0.099 0.33 -10000 0 -0.88 68 68
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.079 0.23 -10000 0 -0.63 69 69
mol:DAG 0.018 0.17 -10000 0 -0.57 17 17
MAP2K2 0.057 0.18 -10000 0 -0.68 11 11
MAP2K1 0.058 0.17 -10000 0 -0.68 10 10
EDNRA -0.007 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.019 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.035 0.14 -10000 0 -0.7 15 15
HRAS/GTP 0.036 0.17 -10000 0 -0.63 14 14
PRKCH 0.029 0.16 -10000 0 -0.6 12 12
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.029 0.16 -10000 0 -0.6 12 12
PRKCB 0.025 0.18 -10000 0 -0.67 15 15
PRKCE 0.028 0.16 -10000 0 -0.62 11 11
PRKCD 0.028 0.16 -10000 0 -0.6 12 12
PRKCG 0.003 0.2 -10000 0 -0.7 22 22
regulation of vascular smooth muscle contraction 0.059 0.23 -10000 0 -0.99 15 15
PRKCQ 0.016 0.18 -10000 0 -0.64 18 18
PLA2G4A 0.076 0.16 -10000 0 -0.57 10 10
GNA14 0.01 0.087 -10000 0 -0.74 7 7
GNA15 -0.008 0.15 -10000 0 -0.86 16 16
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.057 -10000 0 -0.74 3 3
Rac1/GTP -0.013 0.22 0.38 73 -0.83 3 76
MMP1 -0.14 0.37 -10000 0 -0.85 105 105
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.033 -9999 0 -0.74 1 1
Caspase 8 (4 units) -0.096 0.092 -9999 0 -10000 0 0
NEF -0.057 0.084 -9999 0 -10000 0 0
NFKBIA 0.002 0.044 -9999 0 -10000 0 0
BIRC3 -0.068 0.31 -9999 0 -0.79 80 80
CYCS -0.077 0.14 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.36 0.48 -9999 0 -1 172 172
MAP2K7 -0.04 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.061 0.07 -9999 0 -0.42 3 3
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.091 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.05 0.12 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.05 0.12 -9999 0 -10000 0 0
MAPK8 -0.029 0.1 -9999 0 -0.51 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.038 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.13 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.048 0.066 -9999 0 -10000 0 0
CHUK 0.062 0.074 -9999 0 -0.47 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.4 0.44 -9999 0 -1 172 172
TNF 0.003 0.1 -9999 0 -0.8 8 8
FASLG -0.57 0.61 -9999 0 -1.1 282 282
NFKB1 0 0.055 -9999 0 -0.73 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.067 -9999 0 -0.52 9 9
CASP6 -0.048 0.052 -9999 0 -10000 0 0
CASP7 -0.059 0.21 -9999 0 -0.55 54 54
RELA 0.002 0.044 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.059 0.21 -9999 0 -0.55 54 54
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.024 -9999 0 -0.56 1 1
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.079 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.56 54 54
BCL2 -0.017 0.099 -9999 0 -0.46 1 1
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.014 0.034 -10000 0 -0.73 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.02 0.089 -10000 0 -0.51 5 5
AKT1 0.02 0.007 -10000 0 -10000 0 0
GSC -0.027 0.22 -10000 0 -0.76 44 44
NKX2-5 -0.046 0.21 -10000 0 -0.86 34 34
muscle cell differentiation 0.034 0.11 0.57 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.043 0.08 -10000 0 -10000 0 0
SMAD4 0.032 0.029 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.003 0.046 -10000 0 -0.57 2 2
SMAD3/SMAD4/VDR 0.011 0.05 -10000 0 -10000 0 0
MYC -0.032 0.16 -10000 0 -0.86 20 20
CDKN2B 0.055 0.092 -10000 0 -0.68 6 6
AP1 0.064 0.073 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.012 0.049 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.051 0.069 -10000 0 -0.45 4 4
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.061 0.25 -10000 0 -0.88 46 46
SMAD3/SMAD4/GR 0.01 0.044 -10000 0 -0.6 1 1
GATA3 -0.36 0.38 -10000 0 -0.74 262 262
SKI/SIN3/HDAC complex/NCoR1 0.054 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 -0.077 0.2 -10000 0 -0.79 23 23
endothelial cell migration 0.095 0.26 0.73 75 -10000 0 75
MAX 0.019 0.016 -10000 0 -10000 0 0
RBBP7 0.015 0.004 -10000 0 -10000 0 0
RBBP4 0.013 0.033 -10000 0 -0.74 1 1
RUNX2 -0.007 0.14 -10000 0 -0.86 14 14
RUNX3 -0.36 0.44 -10000 0 -0.86 227 227
RUNX1 -0.047 0.23 -10000 0 -0.86 38 38
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.017 0.042 -10000 0 -0.87 1 1
VDR 0.011 0.057 -10000 0 -0.74 3 3
CDKN1A 0.083 0.074 -10000 0 -0.64 2 2
KAT2B 0.013 0.033 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.055 0.18 -10000 0 -0.61 46 46
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.004 -10000 0 -10000 0 0
SERPINE1 -0.097 0.26 -10000 0 -0.74 75 75
SMAD3/SMAD4/ATF2 0.008 0.037 -10000 0 -0.48 1 1
SMAD3/SMAD4/ATF3 0.004 0.057 -10000 0 -0.49 5 5
SAP30 -0.016 0.16 -10000 0 -0.86 19 19
Cbp/p300/PIAS3 0.007 0.035 -10000 0 -10000 0 0
JUN 0.075 0.071 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.012 0.11 -10000 0 -0.56 19 19
TFE3 0.022 0.012 -10000 0 -10000 0 0
COL1A2 -0.091 0.25 -10000 0 -0.75 66 66
mesenchymal cell differentiation 0.007 0.1 0.59 14 -10000 0 14
DLX1 -0.45 0.44 -10000 0 -0.86 282 282
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.006 0.12 -10000 0 -0.74 13 13
SMAD3/SMAD4/Max 0.011 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.02 -10000 0 -10000 0 0
ZBTB17 -0.001 0.044 -10000 0 -0.71 2 2
LAMC1 0.071 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.03 -10000 0 -10000 0 0
IRF7 -0.013 0.16 -10000 0 -0.85 19 19
ESR1 0.001 0.077 -10000 0 -0.76 5 5
HNF4A -0.047 0.21 -10000 0 -0.74 44 44
MEF2C -0.008 0.22 -10000 0 -0.8 21 21
SMAD2-3/SMAD4 0.005 0.031 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.028 -10000 0 -10000 0 0
IGHV3OR16-13 -0.05 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.004 -10000 0 -10000 0 0
HDAC2 0.015 0.004 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.01 0.036 -10000 0 -10000 0 0
MSG1/HSC70 0.002 0.043 -10000 0 -0.67 2 2
SMAD2 0.022 0.019 -10000 0 -10000 0 0
SMAD3 0.032 0.026 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.062 0.033 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.032 -10000 0 -0.52 1 1
NCOR1 0.015 0.004 -10000 0 -10000 0 0
NCOA2 0 0.11 -10000 0 -0.74 11 11
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.036 0.15 -10000 0 -0.66 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.084 -10000 0 -10000 0 0
IFNB1 0.045 0.11 -10000 0 -0.54 1 1
SMAD3/SMAD4/MEF2C -0.009 0.21 -10000 0 -0.75 21 21
CITED1 0.011 0.054 -10000 0 -0.86 2 2
SMAD2-3/SMAD4/ARC105 0.007 0.03 -10000 0 -10000 0 0
RBL1 0.016 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.076 0.067 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.28 0.32 -10000 0 -0.61 249 249
SMAD7 0.1 0.079 -10000 0 -10000 0 0
MYC/MIZ-1 -0.026 0.13 -10000 0 -0.64 22 22
SMAD3/SMAD4 -0.02 0.12 -10000 0 -10000 0 0
IL10 -0.2 0.31 -10000 0 -0.99 31 31
PIASy/HDAC complex 0.018 0.009 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.25 -10000 0 -0.75 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.009 -10000 0 -10000 0 0
ATF3 0.009 0.073 -10000 0 -0.74 5 5
SMAD3/SMAD4/SP1 -0.011 0.053 -10000 0 -10000 0 0
FOXG1 -0.025 0.17 -10000 0 -0.86 20 20
FOXO3 0.036 0.01 -10000 0 -10000 0 0
FOXO1 0.036 0.009 -10000 0 -10000 0 0
FOXO4 0.036 0.009 -10000 0 -10000 0 0
heart looping -0.007 0.22 -10000 0 -0.78 21 21
CEBPB -0.002 0.13 -10000 0 -0.86 12 12
SMAD3/SMAD4/DLX1 -0.31 0.29 -10000 0 -0.58 282 282
MYOD1 -0.042 0.2 -10000 0 -0.86 29 29
SMAD3/SMAD4/HNF4 -0.033 0.14 -10000 0 -0.49 44 44
SMAD3/SMAD4/GATA3 -0.23 0.25 -10000 0 -0.5 152 152
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.23 0.28 -10000 0 -0.59 90 90
SMAD3/SMAD4/SP1-3 -0.005 0.043 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.013 0.049 -10000 0 -10000 0 0
SIN3B 0.015 0.004 -10000 0 -10000 0 0
SIN3A 0.015 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.078 0.22 -10000 0 -0.61 69 69
ITGB5 0.085 0.064 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.015 0.11 -10000 0 -0.49 26 26
AR -0.021 0.16 -10000 0 -0.74 26 26
negative regulation of cell growth 0.065 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.024 0.14 -10000 0 -0.6 29 29
E2F5 0.014 0.033 -10000 0 -0.74 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.043 0.15 -10000 0 -0.64 16 16
SMAD2-3/SMAD4/FOXO1-3a-4 0.076 0.045 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.008 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 14 14
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.014 0.033 -10000 0 -0.74 1 1
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.058 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.04 0.15 -10000 0 -0.61 35 35
NT3 (dimer)/TRKB -0.13 0.24 -10000 0 -0.54 132 132
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.021 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.1 0.3 -10000 0 -0.86 71 71
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.045 0.2 -10000 0 -0.75 41 41
NTRK2 -0.13 0.3 -10000 0 -0.74 100 100
NTRK3 -0.029 0.18 -10000 0 -0.75 31 31
NT-4/5 (dimer)/TRKB -0.14 0.25 -10000 0 -0.55 130 130
neuron apoptosis 0.14 0.18 0.57 48 -10000 0 48
SHC 2-3/Grb2 -0.15 0.2 -10000 0 -0.64 48 48
SHC1 0.014 0.038 -10000 0 -0.86 1 1
SHC2 -0.098 0.14 -10000 0 -0.48 41 41
SHC3 -0.16 0.24 -10000 0 -0.63 87 87
STAT3 (dimer) 0.013 0.067 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.082 0.2 -10000 0 -0.55 79 79
RIN/GDP 0.049 0.064 -10000 0 -0.32 1 1
GIPC1 0.014 0.033 -10000 0 -0.74 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.069 0.14 -10000 0 -0.63 13 13
RIN/GTP -0.001 0.029 -10000 0 -0.68 1 1
CCND1 0.01 0.16 -10000 0 -0.78 20 20
MAGED1 0.014 0.038 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.092 -10000 0 -0.86 6 6
SHC/GRB2/SOS1 -0.001 0.025 -10000 0 -0.57 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.27 -10000 0 -0.59 132 132
TRKA/NEDD4-2 -0.044 0.16 -10000 0 -0.57 41 41
ELMO1 0.012 0.054 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.042 -10000 0 -0.55 3 3
NGF -0.067 0.26 -10000 0 -0.86 50 50
HRAS 0.014 0.038 -10000 0 -0.86 1 1
DOCK1 0.014 0.033 -10000 0 -0.74 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.038 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.069 0.14 -10000 0 -0.59 15 15
mol:GDP 0.062 0.086 -10000 0 -0.48 2 2
NGF (dimer) -0.067 0.26 -10000 0 -0.86 50 50
RhoG/GDP -0.003 0.041 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.062 -10000 0 -10000 0 0
TIAM1 0.014 0.033 -10000 0 -0.74 1 1
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
BDNF (dimer)/TRKB -0.16 0.26 -10000 0 -0.55 159 159
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.038 -10000 0 -0.61 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.023 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.09 -10000 0 -0.78 7 7
RAP1/GDP -0.008 0.031 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.1 0.3 -10000 0 -0.86 71 71
ubiquitin-dependent protein catabolic process -0.091 0.21 -10000 0 -0.6 53 53
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.24 -10000 0 -0.81 31 31
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.078 -10000 0 -10000 0 0
STAT3 0.013 0.067 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.76 31 31
MAPK3 -0.1 0.26 -10000 0 -0.58 97 97
MAPK1 -0.1 0.26 -10000 0 -0.58 97 97
CDC42/GDP 0.055 0.062 -10000 0 -10000 0 0
NTF3 0.005 0.091 -10000 0 -0.78 7 7
NTF4 -0.004 0.092 -10000 0 -0.86 6 6
NGF (dimer)/TRKA/FAIM -0.091 0.2 -10000 0 -0.54 89 89
PI3K -0.002 0.034 -10000 0 -0.56 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.08 0.16 -10000 0 -0.61 24 24
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0.001 0.14 -10000 0 -0.74 6 6
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.062 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.093 0.21 -10000 0 -0.55 89 89
neuron projection morphogenesis -0.022 0.14 -10000 0 -0.54 13 13
NGF (dimer)/TRKA/NEDD4-2 -0.092 0.21 -10000 0 -0.6 53 53
MAP2K1 0.053 0.023 -10000 0 -0.48 1 1
NGFR -0.044 0.22 -10000 0 -0.86 36 36
NGF (dimer)/TRKA/GIPC/GAIP -0.056 0.12 -10000 0 -0.62 4 4
RAS family/GTP/PI3K -0.002 0.029 -10000 0 -0.6 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
MAPKKK cascade -0.095 0.18 -10000 0 -0.61 45 45
RASA1 0.014 0.033 -10000 0 -0.74 1 1
TRKA/c-Abl -0.044 0.15 -10000 0 -0.56 41 41
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.15 0.24 -10000 0 -0.59 70 70
NGF (dimer)/TRKA/p62/Atypical PKCs -0.079 0.18 -10000 0 -0.86 3 3
MATK -0.072 0.26 -10000 0 -0.86 53 53
NEDD4L 0.014 0.033 -10000 0 -0.74 1 1
RAS family/GDP -0.008 0.031 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.075 0.15 -10000 0 -0.47 38 38
Rac1/GTP -0.045 0.085 -10000 0 -0.41 7 7
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.018 0.17 -9999 0 -0.86 20 20
WNT4 -0.068 0.24 -9999 0 -0.75 58 58
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.057 -9999 0 -0.74 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 38 38
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.044 -9999 0 -10000 0 0
GNAO1 0.01 0.083 -9999 0 -0.84 5 5
S1P/S1P3/G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
AKT1 -0.002 0.012 -9999 0 -10000 0 0
AKT3 -0.025 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.057 -9999 0 -0.74 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.053 0.048 -9999 0 -0.53 1 1
MAPK3 0.062 0.046 -9999 0 -0.5 1 1
MAPK1 0.062 0.046 -9999 0 -0.5 1 1
JAK2 -0.024 0.13 -9999 0 -0.48 2 2
CXCR4 -0.12 0.26 -9999 0 -0.47 185 185
FLT1 0.011 0.085 -9999 0 -0.86 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.046 -9999 0 -0.5 1 1
S1P/S1P3/Gi 0.054 0.049 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.036 -9999 0 -0.49 1 1
VEGFA -0.38 0.44 -9999 0 -0.86 240 240
S1P/S1P2/Gi 0.049 0.043 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 241 241
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.072 -9999 0 -10000 0 0
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.057 -9999 0 -0.74 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.006 0.086 -9999 0 -0.74 7 7
GNA15 -0.011 0.15 -9999 0 -0.86 16 16
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.057 -9999 0 -0.74 3 3
Rac1/GTP -0.005 0.036 -9999 0 -0.49 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.004 0.12 -10000 0 -0.86 11 11
GNB1/GNG2 -0.034 0.063 -10000 0 -0.22 14 14
AKT1 0.055 0.1 -10000 0 -0.25 1 1
EGF -0.67 0.23 -10000 0 -0.74 478 478
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.032 0.08 -10000 0 -0.61 2 2
mol:Ca2+ 0.041 0.14 -10000 0 -0.33 28 28
LYN -0.03 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.037 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.05 0.15 -10000 0 -0.38 19 19
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.43 5 5
G beta5/gamma2 -0.044 0.083 -10000 0 -0.3 15 15
PRKCH 0.043 0.15 -10000 0 -0.39 21 21
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
TXA2/TP beta/beta Arrestin3 -0.014 0.045 -10000 0 -0.28 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.11 0.31 -10000 0 -0.86 77 77
G12 family/GTP -0.042 0.091 -10000 0 -0.32 25 25
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.11 0.33 8 -10000 0 8
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.006 0.13 -10000 0 -0.74 15 15
mol:IP3 0.038 0.17 -10000 0 -0.42 28 28
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.028 0.22 -10000 0 -0.58 28 28
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.054 0.13 -10000 0 -0.6 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.051 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.013 0.05 -10000 0 -0.8 2 2
PRKCB1 0.037 0.16 -10000 0 -0.39 41 41
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.036 0.21 -10000 0 -0.53 44 44
LCK -0.046 0.12 -10000 0 -0.6 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.04 0.096 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.04 0.095 -10000 0 -10000 0 0
MAPK14 0.054 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.036 0.19 -10000 0 -0.48 30 30
MAPK11 0.053 0.11 -10000 0 -0.35 3 3
ARHGEF1 0.042 0.088 -10000 0 -0.33 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.045 0.17 -10000 0 -0.39 43 43
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.045 0.13 -10000 0 -0.35 18 18
cAMP biosynthetic process 0.035 0.16 -10000 0 -0.39 28 28
Gq family/GTP/EBP50 0.025 0.06 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.03 0.071 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.085 0.1 -10000 0 -0.42 13 13
VCAM1 0.043 0.14 -10000 0 -0.34 27 27
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.079 -10000 0 -0.43 5 5
platelet activation 0.067 0.15 -10000 0 -0.34 15 15
PGI2/IP -0.002 0.038 -10000 0 -0.62 2 2
PRKACA -0.051 0.12 -10000 0 -0.34 79 79
Gq family/GDP/G beta5/gamma2 0.024 0.079 -10000 0 -0.43 5 5
TXA2/TP beta/beta Arrestin2 -0.015 0.065 -10000 0 -0.41 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.12 -10000 0 -10000 0 0
mol:DAG 0.037 0.18 -10000 0 -0.44 42 42
EGFR 0.001 0.11 -10000 0 -0.85 9 9
TXA2/TP alpha 0.034 0.21 -10000 0 -0.54 32 32
Gq family/GTP -0.006 0.053 -10000 0 -0.26 7 7
YES1 -0.03 0.071 -10000 0 -10000 0 0
GNAI2/GTP -0.034 0.082 -10000 0 -10000 0 0
PGD2/DP -0.098 0.24 -10000 0 -0.68 77 77
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.03 0.071 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.011 0.15 -10000 0 -0.86 16 16
PGK/cGMP -0.014 0.08 -10000 0 -0.49 15 15
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.046 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.043 0.15 -10000 0 -0.4 19 19
PRKCB 0.041 0.16 -10000 0 -0.43 22 22
PRKCE 0.044 0.16 -10000 0 -0.41 19 19
PRKCD 0.042 0.16 -10000 0 -0.41 22 22
PRKCG 0.03 0.18 -10000 0 -0.49 32 32
muscle contraction 0.043 0.2 -10000 0 -0.49 44 44
PRKCZ 0.05 0.15 -10000 0 -0.37 27 27
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.039 0.093 -10000 0 -10000 0 0
PRKCQ 0.035 0.16 -10000 0 -0.43 23 23
MAPKKK cascade 0.036 0.19 -10000 0 -0.49 29 29
SELE 0.037 0.16 -10000 0 -0.42 38 38
TP beta/GNAI2/GDP/G beta/gamma -0.038 0.09 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.006 0.086 -10000 0 -0.74 7 7
chemotaxis 0.036 0.23 -10000 0 -0.61 43 43
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.011 0.057 -10000 0 -0.74 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.028 -10000 0 -0.66 1 1
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.005 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.053 0.22 -10000 0 -0.74 48 48
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.097 0.16 -10000 0 -0.34 151 151
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.014 0.033 -10000 0 -0.74 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH -0.001 0.028 -10000 0 -0.64 1 1
WIF1 0.001 0.075 -10000 0 -0.77 5 5
NOTCH1 -0.001 0.029 -10000 0 -0.68 1 1
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.089 0.28 -10000 0 -0.86 63 63
DKK1 -0.019 0.17 -10000 0 -0.82 22 22
beta catenin/beta TrCP1 0.084 0.084 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.008 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.003 0.12 -10000 0 -0.75 13 13
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.008 -10000 0 -10000 0 0
CTNNB1 0.08 0.091 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.21 -10000 0 -0.57 88 88
HNF1A -0.002 0.073 -10000 0 -0.74 5 5
CTBP1 0.005 0.008 -10000 0 -10000 0 0
MYC 0.003 0.15 -10000 0 -0.73 20 20
NKD1 -0.19 0.34 -10000 0 -0.74 142 142
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.036 0.11 -10000 0 -0.64 1 1
apoptosis -0.096 0.16 -10000 0 -0.34 151 151
Delta 1/NOTCHprecursor -0.001 0.028 -10000 0 -0.64 1 1
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.029 0.023 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.005 0.032 -10000 0 -0.47 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.09 0.22 -10000 0 -0.61 78 78
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.015 0.013 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -0.73 20 20
WNT1 -0.027 0.19 -10000 0 -0.86 25 25
Axin1/APC/beta catenin 0.081 0.052 -10000 0 -10000 0 0
DKK2 -0.026 0.18 -10000 0 -0.83 26 26
NOTCH1 precursor/DVL1 -0.003 0.033 -10000 0 -0.58 1 1
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.012 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.036 0.11 -10000 0 -0.66 1 1
PPP2R5D 0.093 0.16 0.36 141 -10000 0 141
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.029 0.12 -10000 0 -0.52 26 26
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.019 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.025 0.096 -9999 0 -0.52 16 16
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.033 -9999 0 -0.74 1 1
ITGA4 -0.011 0.15 -9999 0 -0.86 16 16
alpha4/beta7 Integrin/MAdCAM1 -0.028 0.12 -9999 0 -0.52 28 28
EPO -0.29 0.42 -9999 0 -0.86 186 186
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 16 16
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.66 186 186
lamellipodium assembly 0 0.035 -9999 0 -0.53 2 2
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PI3K -0.002 0.034 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.12 0.17 -9999 0 -0.66 7 7
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
MADCAM1 -0.007 0.13 -9999 0 -0.86 12 12
cell adhesion -0.027 0.12 -9999 0 -0.52 28 28
CRKL/CBL -0.001 0.024 -9999 0 -0.56 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.014 0.13 -9999 0 -0.52 25 25
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.032 0.13 -9999 0 -0.56 30 30
p130Cas/Crk/Dock1 -0.024 0.1 -9999 0 -0.8 1 1
VCAM1 -0.006 0.13 -9999 0 -0.82 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.016 0.089 -9999 0 -0.52 16 16
BCAR1 0.026 0.12 -9999 0 -0.89 1 1
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.037 -9999 0 -0.55 2 2
Ceramide signaling 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
SPHK2 0.027 0.044 -10000 0 -0.56 3 3
MAP4K4 0.026 0.093 -10000 0 -0.48 1 1
BAG4 0.014 0.033 -10000 0 -0.74 1 1
PKC zeta/ceramide -0.098 0.046 -10000 0 -0.48 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.31 -10000 0 -0.86 80 80
BAX -0.042 0.018 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.046 0.008 -10000 0 -10000 0 0
BAD -0.098 0.043 -10000 0 -0.45 2 2
SMPD1 0.027 0.042 -10000 0 -0.28 1 1
RB1 -0.096 0.037 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.087 -10000 0 -10000 0 0
MAP2K4 -0.081 0.035 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.084 0.056 -10000 0 -0.59 4 4
EGF -0.67 0.23 -10000 0 -0.74 478 478
mol:ceramide -0.11 0.04 0.2 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.025 -10000 0 -0.56 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.095 0.037 -10000 0 -10000 0 0
cell proliferation -0.052 0.059 -10000 0 -0.46 10 10
BID -0.011 0.065 -10000 0 -10000 0 0
MAP3K1 -0.096 0.037 -10000 0 -10000 0 0
EIF2A -0.067 0.034 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.065 0.052 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.065 0.052 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.097 0.035 -10000 0 -0.26 1 1
FADD 0.026 0.093 -10000 0 -0.48 1 1
KSR1 -0.1 0.059 -10000 0 -0.63 4 4
MAPK8 -0.076 0.041 -10000 0 -0.35 4 4
PRKRA -0.096 0.037 -10000 0 -10000 0 0
PDGFA 0.014 0.033 -10000 0 -0.74 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.006 0.093 -10000 0 -0.86 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.039 0.2 2 -10000 0 2
CTSD 0.014 0.033 -10000 0 -0.74 1 1
regulation of nitric oxide biosynthetic process -0.001 0.024 -10000 0 -0.56 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.055 0.065 -10000 0 -0.5 10 10
PRKCD 0.014 0.038 -10000 0 -0.86 1 1
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.025 -10000 0 -0.56 1 1
RelA/NF kappa B1 -0.001 0.024 -10000 0 -0.56 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.033 -10000 0 -0.74 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.033 0.077 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.067 -10000 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0.027 0.044 -10000 0 -0.56 3 3
MAP2K1 -0.07 0.054 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.063 0.023 -10000 0 -0.23 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
TNFR1A/BAG4 -0.001 0.024 -10000 0 -0.56 1 1
EIF2AK2 -0.081 0.035 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.008 0.064 -10000 0 -0.52 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.037 -10000 0 -10000 0 0
MAP2K2 -0.071 0.053 -10000 0 -0.55 4 4
SMPD3 0.026 0.051 -10000 0 -0.33 2 2
TNF 0.003 0.1 -10000 0 -0.8 8 8
PKC zeta/PAR4 -0.004 0.048 -10000 0 -0.56 4 4
mol:PHOSPHOCHOLINE 0.23 0.083 0.26 480 -10000 0 480
NF kappa B1/RelA/I kappa B alpha -0.004 0.038 -10000 0 -10000 0 0
AIFM1 -0.063 0.025 -10000 0 -0.23 1 1
BCL2 0.016 0 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.57 0.68 -9999 0 -1.3 249 249
PLK1 -0.12 0.37 -9999 0 -0.8 93 93
CDKN1B 0.062 0.16 -9999 0 -10000 0 0
FOXO3 -0.036 0.23 -9999 0 -0.66 14 14
KAT2B 0.012 0.04 -9999 0 -0.78 1 1
FOXO1/SIRT1 -0.14 0.21 -9999 0 -10000 0 0
CAT -0.025 0.22 -9999 0 -0.89 7 7
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.007 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 249 249
MAPK10 0.033 0.049 -9999 0 -0.43 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.048 -9999 0 -10000 0 0
response to oxidative stress -0.029 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.029 0.2 -9999 0 -0.58 13 13
XPO1 0.017 0 -9999 0 -10000 0 0
EP300 -0.006 0.042 -9999 0 -0.74 1 1
BCL2L11 0.013 0.043 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -0.4 3 3
mol:GDP -0.029 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.098 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.085 -9999 0 -10000 0 0
MST1 0.001 0.11 -9999 0 -0.86 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.095 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.036 0.035 -9999 0 -0.43 2 2
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.035 0.028 -9999 0 -10000 0 0
SOD2 0.015 0.2 -9999 0 -0.68 7 7
RBL2 0.024 0.17 -9999 0 -1.3 1 1
RAL/GDP 0.009 0.024 -9999 0 -10000 0 0
CHUK 0.014 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.003 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.74 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.34 0.39 -9999 0 -0.73 265 265
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.001 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
CCNB1 -0.028 0.23 -9999 0 -0.92 10 10
FOXO1-3a-4/beta catenin -0.069 0.1 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -0.4 3 3
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.014 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.044 -9999 0 -10000 0 0
SFN -0.083 0.27 -9999 0 -0.83 62 62
CDK2 -0.019 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.013 0.099 -9999 0 -10000 0 0
CREBBP -0.019 0.041 -9999 0 -10000 0 0
FBXO32 -0.025 0.22 -9999 0 -0.79 8 8
BCL6 0.026 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.021 0.088 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
AP1 -0.03 0.1 -9999 0 -0.6 1 1
mol:PIP3 -0.026 0.091 -9999 0 -0.54 1 1
AKT1 -0.014 0.057 -9999 0 -10000 0 0
PTK2B 0.033 0.059 -9999 0 -0.28 1 1
RHOA 0.036 0.035 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.05 0.051 -9999 0 -0.45 2 2
MAGI3 0.013 0.046 -9999 0 -0.74 2 2
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.022 0.085 -9999 0 -0.37 27 27
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
positive regulation of microtubule depolymerization 0.046 0.068 -9999 0 -0.38 3 3
NF kappa B1 p50/RelA -0.018 0.073 -9999 0 -10000 0 0
endothelial cell migration 0.007 0.13 -9999 0 -0.53 29 29
ADCY4 0.032 0.12 -9999 0 -0.47 25 25
ADCY5 0.023 0.13 -9999 0 -0.49 28 28
ADCY6 0.031 0.12 -9999 0 -0.47 25 25
ADCY7 0.026 0.12 -9999 0 -0.48 25 25
ADCY1 0.026 0.13 -9999 0 -0.48 26 26
ADCY2 -0.019 0.14 -9999 0 -0.51 26 26
ADCY3 0.032 0.12 -9999 0 -0.47 25 25
ADCY8 -0.027 0.14 -9999 0 -0.48 25 25
ADCY9 0.032 0.12 -9999 0 -0.47 25 25
GSK3B 0.042 0.056 -9999 0 -10000 0 0
arachidonic acid secretion 0.038 0.11 -9999 0 -0.44 23 23
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0.001 0.008 -9999 0 -10000 0 0
GNAO1 0.007 0.12 -9999 0 -0.48 28 28
HRAS 0.014 0.038 -9999 0 -0.86 1 1
NFKBIA 0.061 0.061 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.053 -9999 0 -0.86 2 2
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.48 1 1
TIAM1 -0.003 0.062 -9999 0 -1 2 2
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.051 0.052 -9999 0 -0.46 2 2
PLCB3 0.037 0.023 -9999 0 -0.43 1 1
FOS -0.003 0.12 -9999 0 -0.75 13 13
positive regulation of mitosis 0.038 0.11 -9999 0 -0.44 23 23
LPA/LPA1-2-3 -0.025 0.1 -9999 0 -0.52 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
stress fiber formation 0.039 0.076 -9999 0 -10000 0 0
GNAZ 0.01 0.12 -9999 0 -0.48 26 26
EGFR/PI3K-beta/Gab1 -0.027 0.094 -9999 0 -0.57 1 1
positive regulation of dendritic cell cytokine production -0.025 0.099 -9999 0 -0.52 4 4
LPA/LPA2/MAGI-3 -0.003 0.031 -9999 0 -0.48 2 2
ARHGEF1 0.03 0.095 -9999 0 -0.49 1 1
GNAI2 0.013 0.11 -9999 0 -0.46 23 23
GNAI3 0.013 0.11 -9999 0 -0.46 23 23
GNAI1 0.01 0.12 -9999 0 -0.48 26 26
LPA/LPA3 -0.007 0.06 -9999 0 -0.67 4 4
LPA/LPA2 -0.001 0.013 -9999 0 -10000 0 0
LPA/LPA1 -0.028 0.12 -9999 0 -0.51 29 29
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 255 255
HBEGF -0.3 0.35 -9999 0 -0.66 249 249
mol:DAG 0.051 0.052 -9999 0 -0.46 2 2
cAMP biosynthetic process 0.019 0.12 -9999 0 -0.46 27 27
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.061 0.061 -9999 0 -10000 0 0
GNAQ -0.004 0.035 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.003 0.076 -9999 0 -0.86 4 4
LPAR1 -0.013 0.15 -9999 0 -0.73 23 23
IL8 -0.077 0.2 -9999 0 -0.49 44 44
PTK2 0.024 0.1 -9999 0 -0.48 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.085 -9999 0 -0.37 27 27
EGFR 0 0.11 -9999 0 -0.85 9 9
PLCG1 0.019 0.054 -9999 0 -0.41 4 4
PLD2 0.024 0.1 -9999 0 -0.48 4 4
G12/G13 -0.021 0.088 -9999 0 -0.42 23 23
PI3K-beta -0.016 0.067 -9999 0 -0.52 1 1
cell migration -0.009 0.034 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.74 1 1
PXN 0.039 0.077 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.098 -9999 0 -0.45 23 23
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 249 249
PRKCE 0.013 0.033 -9999 0 -0.74 1 1
PRKCD 0.058 0.054 -9999 0 -10000 0 0
Gi(beta/gamma) -0.025 0.097 -9999 0 -0.44 25 25
mol:LPA 0.004 0.023 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.017 0.08 -9999 0 -10000 0 0
MAPKKK cascade 0.038 0.11 -9999 0 -0.44 23 23
contractile ring contraction involved in cytokinesis 0.036 0.035 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.009 0.058 -9999 0 -0.4 11 11
GNA15 -0.016 0.08 -9999 0 -0.42 19 19
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.046 0.07 -9999 0 -0.39 3 3
GNA11 -0.006 0.045 -9999 0 -0.39 7 7
Rac1/GTP -0.002 0.056 -9999 0 -0.91 2 2
MMP2 0.007 0.13 -9999 0 -0.53 29 29
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0.046 -9999 0 -0.74 2 2
SPHK1 -0.057 0.24 -9999 0 -0.86 44 44
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.095 -9999 0 -0.31 46 46
GNAO1 0.008 0.083 -9999 0 -0.84 5 5
mol:Sphinganine-1-P -0.029 0.2 -9999 0 -0.66 46 46
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.055 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.023 0.074 -9999 0 -0.29 2 2
S1PR5 -0.14 0.33 -9999 0 -0.86 91 91
S1PR4 -0.031 0.2 -9999 0 -0.86 28 28
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
S1P/S1P5/G12 -0.11 0.21 -9999 0 -0.54 91 91
S1P/S1P3/Gq 0.023 0.097 -9999 0 -0.42 16 16
S1P/S1P4/Gi 0.024 0.096 -9999 0 -0.38 12 12
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
GNA14 0.006 0.086 -9999 0 -0.74 7 7
GNA15 -0.011 0.15 -9999 0 -0.86 16 16
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.057 -9999 0 -0.74 3 3
ABCC1 0.016 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.016 0.16 -9999 0 -0.86 19 19
PLK4 0.011 0.066 -9999 0 -0.86 3 3
regulation of centriole replication 0.002 0.14 -9999 0 -0.66 22 22
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.022 0.1 -9999 0 -0.49 24 24
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.56 22 22
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.057 -9999 0 -0.74 3 3
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.042 -10000 0 -10000 0 0
RFC1 0.011 0.042 -10000 0 -10000 0 0
PRKDC 0.011 0.042 -10000 0 -10000 0 0
RIPK1 0.015 0.004 -10000 0 -10000 0 0
CASP7 -0.024 0.065 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.14 0.16 -10000 0 -0.35 22 22
MAP2K4 -0.084 0.16 -10000 0 -0.43 23 23
mol:ceramide -0.15 0.2 -10000 0 -0.48 32 32
GSN 0.011 0.042 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.17 0.18 -10000 0 -0.44 22 22
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.018 0.066 -10000 0 -10000 0 0
MAP3K1 -0.035 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.011 0.042 -10000 0 -10000 0 0
CFLAR 0.015 0.004 -10000 0 -10000 0 0
HGF/MET -0.036 0.15 -10000 0 -0.57 33 33
ARHGDIB 0.011 0.042 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.042 -10000 0 -10000 0 0
NFKB1 -0.065 0.077 -10000 0 -0.71 1 1
MAPK8 -0.085 0.18 -10000 0 -0.53 25 25
DFFA 0.011 0.042 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.011 0.042 -10000 0 -10000 0 0
FAS/FADD/MET -0.005 0.055 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.044 0.22 -10000 0 -0.86 36 36
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.011 0.042 -10000 0 -10000 0 0
DFFB 0.011 0.042 -10000 0 -10000 0 0
CHUK -0.053 0.067 -10000 0 -0.65 1 1
FASLG -0.42 0.44 -10000 0 -0.86 265 265
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.02 0.17 -10000 0 -0.8 23 23
LMNA 0.01 0.046 -10000 0 -0.52 1 1
CASP6 0.011 0.042 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.013 0.049 -10000 0 -10000 0 0
PTPN13 0.003 0.098 -10000 0 -0.74 9 9
CASP8 0.027 0.1 0.4 36 -10000 0 36
IL6 -0.13 0.34 -10000 0 -0.96 67 67
MET 0.007 0.085 -10000 0 -0.86 5 5
ICAD/CAD 0.011 0.042 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.15 0.2 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c 0.018 0.065 -10000 0 -10000 0 0
PAK2 0.011 0.042 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.005 0.019 -10000 0 -10000 0 0
AES 0.005 0.016 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.026 0.18 -10000 0 -0.83 26 26
TLE1 0.005 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.049 0.1 -10000 0 -0.45 1 1
WIF1 -0.001 0.075 -10000 0 -0.77 5 5
beta catenin/RanBP3 0.004 0.1 0.36 20 -10000 0 20
KREMEN2 -0.089 0.28 -10000 0 -0.86 63 63
DKK1 -0.019 0.17 -10000 0 -0.82 22 22
beta catenin/beta TrCP1 0.056 0.094 -10000 0 -10000 0 0
FZD1 0.016 0.002 -10000 0 -10000 0 0
AXIN2 0.009 0.099 -10000 0 -1.4 2 2
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.017 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.072 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.04 0.083 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.002 0.074 -10000 0 -0.74 5 5
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.009 0.15 -10000 0 -0.75 20 20
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.21 -10000 0 -0.57 88 88
NKD1 -0.19 0.34 -10000 0 -0.74 142 142
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.024 0.11 -10000 0 -0.52 25 25
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.11 0.48 4 -10000 0 4
LEF1 -0.021 0.15 -10000 0 -0.86 16 16
DVL1 0.003 0.034 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.082 0.07 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.09 0.22 -10000 0 -0.61 78 78
LRP6 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.005 0.019 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.009 0.15 -10000 0 -0.75 20 20
WNT1 -0.026 0.19 -10000 0 -0.86 25 25
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.002 -10000 0 -10000 0 0
FRAT1 0.015 0.004 -10000 0 -10000 0 0
PPP2R5D 0.096 0.15 0.35 141 -10000 0 141
APC -0.005 0.11 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.012 0.063 0.27 5 -10000 0 5
CREBBP 0.005 0.017 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.017 -9999 0 -10000 0 0
DAPP1 0.03 0.11 -9999 0 -0.45 17 17
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.26 -9999 0 -0.73 54 54
mol:DAG -0.071 0.15 -9999 0 -0.33 39 39
HRAS 0.015 0.038 -9999 0 -0.86 1 1
RAP1A 0.017 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.019 0.073 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.019 -9999 0 -10000 0 0
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.018 -9999 0 -10000 0 0
ADAP1 -0.004 0.036 -9999 0 -10000 0 0
ARAP3 -0.001 0.018 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.011 0.066 -9999 0 -0.86 3 3
mol:Ca2+ -0.023 0.077 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.033 -9999 0 -0.74 1 1
ZAP70 -0.47 0.44 -9999 0 -0.86 294 294
mol:IP3 -0.037 0.1 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.019 0.073 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.017 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.02 -9999 0 -0.47 1 1
BLNK 0.014 0.033 -9999 0 -0.74 1 1
actin cytoskeleton reorganization 0.045 0.081 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.053 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.017 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.017 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.2 0.24 -9999 0 -0.56 131 131
BLK -0.04 0.21 -9999 0 -0.86 33 33
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
CYTH1 -0.001 0.017 -9999 0 -10000 0 0
HCK -0.032 0.2 -9999 0 -0.86 29 29
CYTH3 -0.001 0.017 -9999 0 -10000 0 0
CYTH2 -0.001 0.017 -9999 0 -10000 0 0
KRAS 0.017 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.024 -9999 0 -0.54 1 1
SGK1 -0.001 0.026 -9999 0 -0.6 1 1
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
mol:GDP 0.01 0.077 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.046 -9999 0 -0.74 2 2
ARF6/GDP -0.004 0.016 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.019 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.019 -9999 0 -10000 0 0
VAV1 -0.19 0.37 -9999 0 -0.86 124 124
mol:PI-3-4-P2 0.025 0.06 -9999 0 -0.66 4 4
RAS family/GTP/PI3K Class I -0.001 0.019 -9999 0 -10000 0 0
PLEKHA1 0.036 0.053 -9999 0 -0.57 4 4
Rac1/GDP 0.019 0.073 -9999 0 -10000 0 0
LAT -0.23 0.39 -9999 0 -0.86 147 147
Rac1/GTP 0 0.1 -9999 0 -10000 0 0
ITK -0.14 0.21 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.11 0.2 -9999 0 -0.46 77 77
LCK -0.02 0.17 -9999 0 -0.85 22 22
BTK -0.094 0.18 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.03 0.002 -9999 0 -10000 0 0
SMARCC1 0.026 0.01 -9999 0 -10000 0 0
REL 0.008 0.066 -9999 0 -0.74 4 4
HDAC7 -0.098 0.088 -9999 0 -0.66 3 3
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.014 0.033 -9999 0 -0.74 1 1
KAT2B 0.014 0.033 -9999 0 -0.74 1 1
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0.001 0.046 -9999 0 -0.59 3 3
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.091 -9999 0 -0.68 4 4
MAP2K6 -0.002 0.058 -9999 0 -0.76 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -0.82 11 11
NCOA2 0 0.11 -9999 0 -0.74 11 11
CEBPA -0.001 0.12 -9999 0 -0.86 10 10
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.093 0.098 -9999 0 -0.54 3 3
NR0B1 -0.051 0.21 -9999 0 -0.86 34 34
EGR1 -0.002 0.11 -9999 0 -0.74 12 12
RXRs/9cRA -0.004 0.047 -9999 0 -0.54 4 4
AR/RACK1/Src -0.016 0.064 -9999 0 -0.58 2 2
AR/GR 0 0.088 -9999 0 -0.69 4 4
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.002 0.037 -9999 0 -0.57 2 2
T-DHT/AR/TIF2/CARM1 -0.022 0.098 -9999 0 -0.77 5 5
SRC 0.003 0.049 -9999 0 -10000 0 0
NR3C1 0.014 0.038 -9999 0 -0.86 1 1
KLK3 -0.052 0.19 -9999 0 -0.74 24 24
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.027 0.057 -9999 0 -0.57 4 4
TMPRSS2 -0.96 0.38 -9999 0 -1.1 458 458
RXRG 0.006 0.076 -9999 0 -0.86 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.014 0.033 -9999 0 -0.74 1 1
KLK2 -0.025 0.14 -9999 0 -0.63 22 22
AR -0.011 0.089 -9999 0 -0.43 14 14
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.16 0.35 -9999 0 -0.86 104 104
T-DHT/AR/RACK1/Src -0.016 0.063 -9999 0 -0.59 2 2
positive regulation of transcription -0.003 0.12 -9999 0 -0.74 13 13
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.17 0.36 -9999 0 -0.86 114 114
T-DHT/AR/TIF2 0.018 0.076 -9999 0 -0.66 4 4
T-DHT/AR/Hsp90 -0.028 0.056 -9999 0 -0.57 4 4
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.011 0.053 -9999 0 -0.49 4 4
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.014 0.008 -9999 0 -10000 0 0
POU2F1 0.005 0.015 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.067 0.14 -9999 0 -0.6 28 28
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.07 -10000 0 -0.4 1 1
epithelial cell differentiation -0.051 0.11 -10000 0 -0.57 1 1
ITCH 0.055 0.017 -10000 0 -10000 0 0
WWP1 -0.097 0.067 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.019 0.081 -10000 0 -0.57 1 1
PTPRZ1 -0.083 0.25 -10000 0 -0.75 65 65
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.054 0.074 -10000 0 -0.6 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.084 0.094 -10000 0 -0.55 12 12
ADAM17 0.055 0.017 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.085 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.61 13 13
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.076 0.078 -10000 0 -0.53 10 10
GRIN2B -0.058 0.092 -10000 0 -0.61 3 3
ErbB4/ErbB2/betacellulin -0.13 0.16 -10000 0 -0.51 74 74
STAT1 0.014 0.038 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.084 0.26 -10000 0 -0.74 70 70
E4ICDs/ETO2 -0.11 0.079 -10000 0 -0.7 2 2
axon guidance -0.017 0.072 -10000 0 -10000 0 0
NEDD4 0.052 0.051 -10000 0 -0.73 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.074 0.19 -10000 0 -0.56 70 70
CBFA2T3 0.012 0.054 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.064 0.038 -10000 0 -0.51 1 1
MAPK3 -0.03 0.082 -10000 0 -0.6 1 1
STAT1 (dimer) -0.11 0.072 -10000 0 -0.54 1 1
MAPK1 -0.03 0.082 -10000 0 -0.6 1 1
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.078 0.082 -10000 0 -0.53 11 11
NRG1 0.035 0.11 -10000 0 -0.56 17 17
NRG3 -0.004 0.13 -10000 0 -0.86 12 12
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
NRG4 -0.055 0.22 -10000 0 -0.77 47 47
heart development -0.017 0.072 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.081 -10000 0 -0.52 11 11
ERBB2 0.052 0.039 -10000 0 -0.56 2 2
WWOX/E4ICDs -0.11 0.075 -10000 0 -0.55 2 2
SHC1 0.014 0.038 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.14 0.15 -10000 0 -0.56 51 51
apoptosis 0.1 0.064 0.39 8 -10000 0 8
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.088 -10000 0 -0.52 11 11
ErbB4/ErbB2/epiregulin -0.097 0.13 -10000 0 -0.57 34 34
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.19 -10000 0 -0.58 82 82
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.14 -10000 0 -0.73 1 1
MDM2 -0.1 0.073 -10000 0 -0.4 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.078 -10000 0 -0.51 10 10
STAT5A -0.005 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.085 0.1 -10000 0 -0.56 18 18
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.029 -10000 0 -0.66 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.048 -10000 0 -10000 0 0
STAT5A (dimer) -0.054 0.12 -10000 0 -0.62 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.064 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.04 0.21 -10000 0 -0.86 33 33
BTC -0.1 0.27 -10000 0 -0.74 81 81
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.017 0.072 -10000 0 -10000 0 0
ERBB4 -0.14 0.085 -10000 0 -0.46 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.1 0.13 -10000 0 -0.52 37 37
glial cell differentiation 0.1 0.048 -10000 0 -10000 0 0
WWOX 0.014 0.038 -10000 0 -0.86 1 1
cell proliferation -0.076 0.16 -10000 0 -0.63 12 12
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.19 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.15 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.029 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.1 0.09 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.12 0.22 -9999 0 -10000 0 0
MAP3K11 -0.14 0.23 -9999 0 -0.8 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.27 0.29 -9999 0 -0.73 115 115
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.067 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.19 0.21 -9999 0 -1 2 2
STAT1 -0.14 0.23 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.37 0.43 -9999 0 -0.85 238 238
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.075 0.084 -9999 0 -0.47 1 1
mol:Ca2+ -0.19 0.21 -9999 0 -10000 0 0
MAPK3 -0.087 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.087 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.024 0.15 -9999 0 -0.63 3 3
SMAD7 -0.02 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.17 0.19 -9999 0 -10000 0 0
IFNG -0.37 0.43 -9999 0 -0.85 238 238
apoptosis -0.036 0.12 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.36 -9999 0 -0.74 178 178
CAMK2B -0.099 0.27 -9999 0 -0.76 79 79
FRAP1 -0.1 0.2 -9999 0 -10000 0 0
PRKCD -0.12 0.21 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.1 0.09 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.033 -9999 0 -0.74 1 1
IRF1 -0.057 0.19 -9999 0 -0.93 1 1
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.011 0.082 -9999 0 -0.73 6 6
mol:GDP -0.15 0.17 -9999 0 -10000 0 0
CASP1 -0.02 0.082 -9999 0 -10000 0 0
PTGES2 0.013 0.046 -9999 0 -0.74 2 2
IRF9 0.018 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.14 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.1 0.09 -9999 0 -0.37 1 1
PTPN11 -0.16 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.021 0.094 -10000 0 -0.43 26 26
regulation of S phase of mitotic cell cycle -0.015 0.069 -10000 0 -0.62 1 1
GNAO1 0.008 0.083 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
SHBG/T-DHT -0.05 0.15 -10000 0 -0.5 54 54
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.046 0.092 -10000 0 -10000 0 0
T-DHT/AR -0.028 0.12 -10000 0 -0.57 26 26
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 13 13
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
mol:GDP -0.027 0.12 -10000 0 -0.55 26 26
cell proliferation 0.07 0.11 -10000 0 -0.64 4 4
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
FOS 0.056 0.15 -10000 0 -0.81 13 13
mol:Ca2+ -0.003 0.014 -10000 0 -0.11 4 4
MAPK3 0.062 0.1 -10000 0 -0.57 4 4
MAPK1 0.044 0.054 -10000 0 -0.3 1 1
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process -0.045 0.15 -10000 0 -0.48 54 54
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.02 0.086 -10000 0 -0.48 1 1
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K -0.002 0.03 -10000 0 -0.48 2 2
apoptosis -0.06 0.094 0.59 4 -10000 0 4
T-DHT/AR/PELP1 -0.024 0.1 -10000 0 -0.48 26 26
HRAS/GDP -0.027 0.12 -10000 0 -0.52 27 27
CREB1 0.061 0.1 -10000 0 -0.64 4 4
RAC1-CDC42/GTP -0.001 0.024 -10000 0 -10000 0 0
AR -0.021 0.16 -10000 0 -0.74 26 26
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.035 0.094 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -10000 0 -0.49 26 26
T-DHT/AR/PELP1/Src -0.021 0.094 -10000 0 -0.44 26 26
MAP2K2 0.045 0.094 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.015 0.07 -10000 0 -0.62 1 1
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
SHBG -0.062 0.23 -10000 0 -0.74 54 54
Gi family/GNB1/GNG2/GDP -0.008 0.044 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.18 0.31 -10000 0 -0.68 147 147
Gi family/GTP -0.014 0.058 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.045 0.092 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 91 91
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.083 -9999 0 -0.84 5 5
RhoA/GTP -0.046 0.094 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.014 0.12 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 91 91
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.006 0.059 -9999 0 -0.56 6 6
AKT1 -0.056 0.2 -9999 0 -0.71 3 3
PTK2B -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.002 0.041 -9999 0 -0.83 1 1
CAV1 -0.046 0.22 -9999 0 -0.86 37 37
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.23 0.25 -9999 0 -1.2 1 1
endothelial cell proliferation -0.042 0.19 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.038 -9999 0 -0.86 1 1
VEGFA homodimer -0.24 0.26 -9999 0 -0.52 240 240
SHC1 0.014 0.038 -9999 0 -0.86 1 1
SHC2 0.006 0.089 -9999 0 -0.82 6 6
HRAS/GDP -0.17 0.19 -9999 0 -0.83 2 2
SH2D2A -0.27 0.41 -9999 0 -0.86 171 171
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.39 0.33 -9999 0 -1 67 67
VEGFR1 homodimer 0.007 0.085 -9999 0 -0.86 5 5
SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.014 0.038 -9999 0 -0.86 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.086 0.094 -9999 0 -0.58 1 1
HIF1A 0.013 0.046 -9999 0 -0.74 2 2
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.001 0.024 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.23 0.25 -9999 0 -1.2 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.064 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.053 0.18 -9999 0 -0.57 1 1
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 -0.16 0.27 -9999 0 -1.1 1 1
HIF1A/ARNT -0.002 0.034 -9999 0 -0.56 2 2
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 240 240
VEGFC 0.014 0.038 -9999 0 -0.86 1 1
FAK1/Vinculin -0.11 0.22 -9999 0 -0.99 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.22 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.036 -9999 0 -0.72 1 1
mol:L-citrulline -0.064 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2/3 heterodimer -0.002 0.041 -9999 0 -0.83 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -0.83 2 2
VEGFR2 homodimer 0.043 0.049 -9999 0 -0.73 2 2
FLT1 0.007 0.085 -9999 0 -0.86 5 5
NEDD4 0.015 0.046 -9999 0 -0.74 2 2
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.31 0.33 -9999 0 -0.66 245 245
VEGFR1/2 heterodimer -0.008 0.068 -9999 0 -0.61 6 6
KDR 0.043 0.049 -9999 0 -0.73 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -0.77 2 2
PI3K -0.16 0.18 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.2 1 1
FES -0.17 0.27 -9999 0 -1 2 2
GAB1 -0.17 0.19 -9999 0 -0.8 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.23 0.25 -9999 0 -1.2 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.083 0.2 -9999 0 -0.61 13 13
VEGFR2 homodimer/VEGFA homodimer/Yes -0.23 0.25 -9999 0 -1.2 1 1
PI3K/GAB1 -0.056 0.19 -9999 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.1 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.043 -9999 0 -0.77 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.17 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.39 0.33 -9999 0 -1 67 67
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.27 -9999 0 -1.1 1 1
CaM/Ca2+ -0.19 0.2 -9999 0 -1 1 1
MAP2K3 -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.17 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.23 0.25 -9999 0 -1.2 1 1
cell migration -0.055 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.7 6 6
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.064 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.19 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.014 0.033 -9999 0 -0.74 1 1
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
NOS3 -0.075 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -1 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.15 0.25 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.22 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 5 5
VEGFA165/NRP2 -0.31 0.33 -9999 0 -0.66 245 245
MAPKKK cascade -0.17 0.18 -9999 0 -0.8 2 2
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.038 -9999 0 -0.86 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.11 0.22 -9999 0 -0.99 1 1
MAP3K13 -0.17 0.27 -9999 0 -1.2 1 1
PDPK1 -0.074 0.2 -9999 0 -0.65 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.059 -9999 0 -10000 0 0
epithelial cell differentiation -0.016 0.079 -9999 0 -10000 0 0
CYFIP2 0.004 0.092 -9999 0 -0.74 8 8
ENAH 0.078 0.065 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.74 1 1
MYO6 0.032 0.096 -9999 0 -0.78 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.058 -9999 0 -0.47 8 8
AQP5 -0.17 0.24 -9999 0 -0.52 161 161
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.083 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.12 -9999 0 -0.49 15 15
EGF -0.67 0.23 -9999 0 -0.74 478 478
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.051 0.16 -9999 0 -0.58 39 39
cortical microtubule organization -0.016 0.079 -9999 0 -10000 0 0
GO:0000145 0.034 0.08 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.08 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.014 0.063 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.05 0.084 -9999 0 -0.58 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.034 0.084 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.031 -9999 0 -0.48 1 1
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
EGFR/EGFR/EGF/EGF -0.34 0.14 -9999 0 -0.77 28 28
RhoA/GDP -0.015 0.073 -9999 0 -10000 0 0
actin cytoskeleton organization 0.041 0.092 -9999 0 -0.71 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.006 0.093 -9999 0 -0.86 6 6
DIAPH1 -0.01 0.085 -9999 0 -0.69 8 8
Wnt receptor signaling pathway 0.016 0.079 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.063 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.042 0.094 -9999 0 -0.74 2 2
EFNA1 0.014 0.038 -9999 0 -0.86 1 1
LPP 0.043 0.089 -9999 0 -0.8 1 1
Ephrin A1/EPHA2 -0.016 0.074 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.063 -9999 0 -10000 0 0
MGAT3 0.018 0.12 -9999 0 -0.5 15 15
HGF/MET -0.036 0.13 -9999 0 -0.95 4 4
HGF -0.02 0.17 -9999 0 -0.8 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.098 0.07 -9999 0 -10000 0 0
KIAA1543 0.036 0.12 -9999 0 -0.85 6 6
KIFC3 0.034 0.086 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.033 0.093 -9999 0 -0.86 1 1
NCK1/GIT1 -0.001 0.024 -9999 0 -0.56 1 1
mol:GDP -0.016 0.079 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.034 0.084 -9999 0 -10000 0 0
PIP5K1C 0.034 0.084 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.055 -9999 0 -10000 0 0
adherens junction assembly 0.058 0.12 -9999 0 -0.79 7 7
IGF-1R heterotetramer/IGF1 -0.02 0.084 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PLEKHA7 0.03 0.1 -9999 0 -0.78 3 3
mol:GTP -0.003 0.034 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.07 0.076 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.059 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.041 0.092 -9999 0 -0.71 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.083 -9999 0 -0.84 5 5
CDC42/GTP -0.017 0.061 -9999 0 -10000 0 0
PLCG1 0.034 0.078 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.017 0.06 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 91 91
S1PR4 -0.031 0.2 -9999 0 -0.86 28 28
MAPK3 0.034 0.078 -9999 0 -10000 0 0
MAPK1 0.034 0.078 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 91 91
RHOA 0.015 0.12 -9999 0 -0.49 28 28
S1P/S1P4/Gi -0.02 0.07 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
S1P/S1P4/G12/G13 -0.028 0.12 -9999 0 -0.53 28 28
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.01 0.068 -9999 0 -0.77 4 4
GNB1/GNG2 -0.054 0.11 -9999 0 -0.53 8 8
mol:DAG 0.009 0.13 -9999 0 -10000 0 0
PLCG1 0.009 0.13 -9999 0 -10000 0 0
YES1 -0.012 0.14 -9999 0 -0.56 8 8
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.05 0.1 -9999 0 -0.5 7 7
MAP3K7 -0.095 0.22 -9999 0 -0.54 50 50
mol:Ca2+ 0.009 0.12 -9999 0 -10000 0 0
mol:IP3 0.009 0.13 -9999 0 -10000 0 0
NLK -0.007 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.24 -9999 0 -0.61 50 50
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.012 0.14 -9999 0 -0.56 8 8
GO:0007205 0.01 0.13 -9999 0 -10000 0 0
WNT6 -0.018 0.17 -9999 0 -0.86 20 20
WNT4 -0.068 0.24 -9999 0 -0.75 58 58
NFAT1/CK1 alpha -0.05 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.057 -9999 0 -0.74 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 38 38
CDC42 0 0.14 -9999 0 -0.52 8 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.032 0.12 -9999 0 -0.51 33 33
RGS9BP -0.018 0.15 -9999 0 -0.74 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.012 0.084 -9999 0 -0.59 11 11
mol:ADP 0.012 0.043 -9999 0 -0.68 2 2
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.036 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.025 -9999 0 -0.59 1 1
GRK7 0.008 0.054 -9999 0 -0.86 2 2
CNGB3 -0.007 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.11 -9999 0 -0.64 15 15
Cone PDE6 -0.033 0.12 -9999 0 -0.53 12 12
Cone Metarhodopsin II -0.002 0.034 -9999 0 -0.55 2 2
Na + (4 Units) -0.018 0.11 -9999 0 -0.64 15 15
GNAT2/GDP -0.03 0.11 -9999 0 -0.5 9 9
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.043 -9999 0 -0.54 3 3
Cone Transducin -0.033 0.13 -9999 0 -0.54 33 33
SLC24A2 -0.008 0.099 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.041 0.16 -9999 0 -0.66 33 33
GNB3 -0.038 0.21 -9999 0 -0.86 32 32
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.065 -9999 0 -0.86 3 3
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.012 0.085 -9999 0 -0.6 11 11
mol:Pi -0.035 0.13 -9999 0 -0.5 38 38
Cone CNG Channel -0.013 0.084 -9999 0 -0.52 13 13
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.008 0.099 -9999 0 -0.86 7 7
RGS9 -0.008 0.14 -9999 0 -0.82 15 15
PDE6C 0.004 0.054 -9999 0 -0.86 2 2
GNGT2 0.014 0.038 -9999 0 -0.86 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.038 -9999 0 -0.86 1 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.011 0.15 -9999 0 -0.86 16 16
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 16 16
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 16 16
TCGA08_rtk_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
PDGFRA -0.28 0.37 -9999 0 -0.74 205 205
HRAS 0.014 0.038 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
AKT 0.035 0.029 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.011 0.066 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.041 0.097 -9999 0 -0.38 5 5
ERBB2 0.013 0.046 -9999 0 -0.74 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.022 0.092 -9999 0 -0.28 7 7
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.036 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.036 0.097 -9999 0 -0.48 7 7
JUN 0.025 0.12 -9999 0 -0.56 8 8
HRAS 0.014 0.038 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.052 0.16 -9999 0 -0.7 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.052 0.16 -9999 0 -0.5 47 47
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.041 0.13 -9999 0 -0.46 47 47
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.046 0.14 -9999 0 -0.67 9 9
GRB7 0.006 0.086 -9999 0 -0.74 7 7
RET51/GFRalpha1/GDNF -0.052 0.16 -9999 0 -0.7 11 11
MAPKKK cascade -0.041 0.12 -9999 0 -0.7 6 6
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.04 0.13 -9999 0 -0.46 46 46
lamellipodium assembly -0.034 0.091 -9999 0 -0.44 7 7
RET51/GFRalpha1/GDNF/SHC -0.053 0.16 -9999 0 -0.69 12 12
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC -0.038 0.13 -9999 0 -0.46 44 44
RET9/GFRalpha1/GDNF/Shank3 -0.037 0.12 -9999 0 -0.46 43 43
MAPK3 0.006 0.15 -9999 0 -0.77 5 5
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.001 0.11 -9999 0 -0.74 12 12
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.042 0.13 -9999 0 -0.73 5 5
DOK5 -0.006 0.13 -9999 0 -0.76 15 15
GFRA1 -0.042 0.2 -9999 0 -0.75 40 40
MAPK8 0.014 0.12 -9999 0 -0.6 8 8
HRAS/GTP -0.048 0.14 -9999 0 -0.84 6 6
tube development -0.034 0.12 -9999 0 -0.5 6 6
MAPK1 0.006 0.15 -9999 0 -0.77 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.082 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.076 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.058 0.17 -9999 0 -0.87 12 12
SHC1 0.014 0.038 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.052 0.16 -9999 0 -0.7 11 11
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.19 -9999 0 -0.8 19 19
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
CREB1 -0.032 0.098 -9999 0 -0.53 5 5
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.083 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.058 0.18 -9999 0 -0.79 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.012 0.14 -9999 0 -0.76 19 19
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.025 0.11 -9999 0 -0.54 8 8
RET9/GFRalpha1/GDNF/FRS2 -0.037 0.12 -9999 0 -0.46 43 43
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.025 0.083 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.1 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.036 0.11 -9999 0 -0.6 6 6
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.11 -9999 0 -0.77 5 5
PI3K -0.051 0.14 -9999 0 -0.73 7 7
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.034 0.12 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.031 0.092 -9999 0 -0.52 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.052 0.16 -9999 0 -0.7 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.066 -9999 0 -0.74 4 4
IRS2 0.002 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.11 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF/PKC alpha -0.052 0.16 -9999 0 -0.7 11 11
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.066 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.055 0.16 -9999 0 -0.72 12 12
Rac1/GTP -0.04 0.11 -9999 0 -0.54 7 7
RET9/GFRalpha1/GDNF -0.041 0.14 -9999 0 -0.51 43 43
GFRalpha1/GDNF -0.047 0.16 -9999 0 -0.58 43 43
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.003 0.1 0.8 8 -10000 0 8
PI3K Class IB/PDE3B 0.003 0.1 -10000 0 -0.8 8 8
PDE3B 0.003 0.1 -10000 0 -0.8 8 8
Signaling events mediated by PRL

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
CCNE1 0.002 0.11 -10000 0 -0.86 8 8
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0 -10000 0 -10000 0 0
CDKN1A 0.04 0.035 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.024 0.12 -10000 0 -0.66 19 19
mol:Ca2+ -0.016 0.16 0.4 19 -0.65 25 44
AGT -0.024 0.18 -10000 0 -0.82 25 25
CCNA2 -0.055 0.23 -10000 0 -0.88 7 7
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 0.019 0.086 -10000 0 -0.55 12 12
CDK2/Cyclin E1 -0.01 0.063 -10000 0 -0.49 8 8
MAPK3 0.006 0.13 -10000 0 -0.66 19 19
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.13 -10000 0 -0.66 19 19
PTP4A1 0.041 0.069 -10000 0 -10000 0 0
PTP4A3 -0.016 0.16 -10000 0 -0.86 19 19
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.006 0.13 -10000 0 -0.66 19 19
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.03 0.062 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.002 0.034 -10000 0 -0.56 2 2
PRL-1/ATF-5 0.042 0.075 -10000 0 -10000 0 0
RABGGTA 0.013 0.046 -10000 0 -0.74 2 2
BCAR1 0.013 0.079 0.4 19 -0.58 1 20
RHOC 0.03 0.062 -10000 0 -10000 0 0
RHOA 0.03 0.062 -10000 0 -10000 0 0
cell motility 0.035 0.064 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.045 0.064 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.024 0.12 -10000 0 -0.66 19 19
ROCK1 0.036 0.065 -10000 0 -10000 0 0
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.041 0.068 -10000 0 -10000 0 0
ATF5 0.011 0.066 -10000 0 -0.86 3 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.074 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.16 0.28 -9999 0 -0.67 124 124
NFKBIA 0.063 0.02 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.038 -9999 0 -0.86 1 1
IKBKG -0.046 0.084 -9999 0 -10000 0 0
IKK complex/A20 -0.041 0.079 -9999 0 -0.59 2 2
NEMO/A20/RIP2 0.014 0.038 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.042 0.077 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.034 0.062 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.19 0.37 -9999 0 -0.86 124 124
NFKB1 0.019 0.033 -9999 0 -0.73 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.033 -9999 0 -0.74 1 1
TNF/TNFR1A -0.009 0.075 -9999 0 -0.61 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
NF kappa B1 p50/RelA -0.001 0.02 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.038 0.07 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.035 0.064 -9999 0 -10000 0 0
Insulin-mediated glucose transport

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.006 0.034 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.066 0.09 0.32 36 -0.36 2 38
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.031 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.072 0.26 -10000 0 -0.86 51 51
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.043 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.033 0.083 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.068 0.094 0.33 36 -0.4 2 38
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.034 0 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
LNPEP 0.013 0.046 -10000 0 -0.74 2 2
YWHAE 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.014 0.033 -10000 0 -0.74 1 1
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.043 0.67 2 -10000 0 2
CDKN1A -0.002 0.04 -10000 0 -0.65 2 2
KAT2B 0.014 0.033 -10000 0 -0.74 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0.001 0.023 0.53 1 -10000 0 1
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.03 0.016 -10000 0 -0.33 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.006 0.12 -10000 0 -0.86 11 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.16 -10000 0 -0.66 30 30
PPARGC1A -0.057 0.22 -10000 0 -0.74 51 51
FHL2 0.008 0.076 -10000 0 -0.77 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.008 -10000 0 -10000 0 0
HIST2H4A 0.025 0.043 -10000 0 -0.67 2 2
SIRT1/FOXO3a 0.001 0.016 0.32 1 -10000 0 1
SIRT1 0.001 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b 0 0.019 -10000 0 -10000 0 0
apoptosis 0 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.046 0.14 -10000 0 -0.48 51 51
p53/SIRT1 0.001 0.023 0.38 2 -10000 0 2
SIRT1/FOXO4 0 0.015 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.004 0.045 -10000 0 -0.46 5 5
HIST1H1E 0.029 0.022 -10000 0 -0.32 2 2
SIRT1/p300 -0.001 0.026 -10000 0 -0.56 1 1
muscle cell differentiation 0.032 0.13 0.57 30 -10000 0 30
TP53 0.001 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.013 0.095 -10000 0 -0.67 11 11
ACSS2 0.027 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.032 0.13 -10000 0 -0.57 30 30
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.057 -9999 0 -0.74 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.029 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.087 0.22 -9999 0 -0.62 74 74
IL1A -0.009 0.14 -9999 0 -0.86 14 14
IL1B 0.023 0.072 -9999 0 -0.65 6 6
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.026 -9999 0 -10000 0 0
IL1R2 -0.078 0.26 -9999 0 -0.79 62 62
IL1R1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.025 -9999 0 -10000 0 0
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.016 0.001 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.04 0.046 -9999 0 -10000 0 0
JUN 0.059 0.037 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.069 -9999 0 -0.77 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.018 0.094 -9999 0 -0.52 17 17
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.016 0.087 -9999 0 -0.5 1 1
IL1 beta fragment/IL1R1/IL1RAP -0.009 0.068 -9999 0 -0.52 8 8
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 0.05 0.039 -9999 0 -10000 0 0
IRAK1 0.03 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.021 0.12 -9999 0 -0.66 17 17
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.034 -9999 0 -0.56 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.031 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.009 0.068 -9999 0 -0.52 8 8
IL1 beta/IL1R2 -0.066 0.17 -9999 0 -0.52 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.069 -9999 0 -1 1 1
IRAK3 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.06 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.05 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.019 0.1 -9999 0 -0.57 18 18
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.009 0.073 -9999 0 -0.83 4 4
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.007 0.048 -9999 0 -10000 0 0
CASP1 0.016 0 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.091 0.22 -9999 0 -0.62 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.009 0.064 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.007 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.034 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
IL1RN -0.012 0.16 -9999 0 -0.86 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.042 0.032 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0 -10000 0 -10000 0 0
EPHB2 0 0.11 -10000 0 -0.77 11 11
EFNB1 0.014 0.11 -10000 0 -0.66 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.022 0.11 -10000 0 -0.79 5 5
Ephrin B2/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
neuron projection morphogenesis -0.021 0.1 -10000 0 -0.75 5 5
Ephrin B1/EPHB1-2/Tiam1 -0.024 0.12 -10000 0 -0.86 5 5
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.023 0.092 -10000 0 -0.67 9 9
YES1 -0.015 0.12 -10000 0 -0.89 9 9
Ephrin B1/EPHB1-2/NCK2 -0.024 0.11 -10000 0 -0.87 4 4
PI3K -0.011 0.096 -10000 0 -0.69 10 10
mol:GDP -0.024 0.12 -10000 0 -0.84 5 5
ITGA2B -0.016 0.16 -10000 0 -0.86 19 19
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.015 0.12 -10000 0 -0.89 9 9
MAP3K7 -0.012 0.093 -10000 0 -0.71 9 9
FGR -0.015 0.12 -10000 0 -0.89 9 9
TIAM1 0.014 0.033 -10000 0 -0.74 1 1
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion 0.016 0.15 -10000 0 -0.66 14 14
LYN -0.015 0.12 -10000 0 -0.89 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.11 -10000 0 -0.84 9 9
Ephrin B1/EPHB1-2 -0.015 0.1 -10000 0 -0.78 9 9
SRC -0.015 0.12 -10000 0 -0.89 9 9
ITGB3 0.007 0.08 -10000 0 -0.74 6 6
EPHB1 0.009 0.071 -10000 0 -0.8 4 4
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.03 0.14 -10000 0 -0.66 24 24
BLK -0.022 0.12 -10000 0 -0.88 9 9
HCK -0.021 0.12 -10000 0 -0.93 9 9
regulation of stress fiber formation 0.023 0.11 0.85 4 -10000 0 4
MAPK8 0.031 0.091 -10000 0 -0.63 9 9
Ephrin B1/EPHB1-2/RGS3 -0.024 0.11 -10000 0 -0.87 4 4
endothelial cell migration -0.009 0.08 -10000 0 -0.61 9 9
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.01 0.11 -10000 0 -0.85 9 9
regulation of focal adhesion formation 0.023 0.11 0.85 4 -10000 0 4
chemotaxis 0.023 0.11 0.85 4 -10000 0 4
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
Rac1/GTP -0.022 0.11 -10000 0 -0.78 5 5
angiogenesis -0.015 0.1 -10000 0 -0.77 9 9
LCK -0.02 0.12 -10000 0 -0.9 9 9
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.014 0.033 -10000 0 -0.74 1 1
MAP2K3 0.038 0.044 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.049 0.045 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.002 0.12 -10000 0 -0.85 11 11
TXN 0.011 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
GADD45A 0.016 0 -10000 0 -10000 0 0
GADD45B 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
MAP3K6 0.014 0.033 -10000 0 -0.74 1 1
MAP3K7 0.016 0 -10000 0 -10000 0 0
MAP3K4 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.001 0.024 -10000 0 -0.56 1 1
TAK1/TAB family 0.001 0.012 0.2 2 -10000 0 2
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.014 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.099 0.27 -10000 0 -0.76 79 79
CCM2 0.016 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.074 0.18 -10000 0 -0.49 79 79
MAPK11 0.012 0.054 -10000 0 -0.86 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.066 0.16 -10000 0 -0.44 79 79
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 0.016 0.053 -10000 0 -0.41 8 8
TAOK2 0.022 0.019 -10000 0 -0.41 1 1
TAOK3 0.022 0.019 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.016 0 -10000 0 -10000 0 0
MAP3K10 0.014 0.033 -10000 0 -0.74 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TRX/ASK1 0 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.01 0.07 -10000 0 -0.5 10 10
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.073 -10000 0 -0.72 3 3
NFATC4 0.047 0.077 -10000 0 -0.54 2 2
ERBB2IP 0.008 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.018 0.077 -10000 0 -0.64 1 1
JUN 0.037 0.079 -10000 0 -0.41 2 2
HRAS 0.013 0.038 -10000 0 -0.86 1 1
DOCK7 0.02 0.091 -10000 0 -0.62 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.022 0.1 -10000 0 -0.87 2 2
AKT1 0.016 0.002 -10000 0 -10000 0 0
BAD 0.026 0.035 -10000 0 -0.54 2 2
MAPK10 -0.011 0.044 -10000 0 -0.39 1 1
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.083 -10000 0 -0.72 1 1
RAF1 0.04 0.095 -10000 0 -0.68 3 3
ErbB2/ErbB3/neuregulin 2 -0.019 0.095 -10000 0 -0.48 21 21
STAT3 0 0.002 -10000 0 -10000 0 0
cell migration 0.059 0.057 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.085 0.26 -10000 0 -0.6 9 9
FOS -0.035 0.19 -10000 0 -0.51 12 12
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.077 -10000 0 -0.64 1 1
MAPK3 -0.055 0.21 -10000 0 -0.56 8 8
MAPK1 -0.055 0.21 -10000 0 -0.74 2 2
JAK2 0.021 0.088 -10000 0 -0.6 1 1
NF2 -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.09 -10000 0 -0.45 8 8
NRG1 -0.015 0.13 -10000 0 -0.74 17 17
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.024 0.086 -10000 0 -0.47 3 3
MAPK9 -0.008 0.036 -10000 0 -10000 0 0
ERBB2 -0.002 0.035 -10000 0 -0.58 2 2
ERBB3 -0.004 0.098 -10000 0 -0.74 9 9
SHC1 0.008 0.039 -10000 0 -0.86 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.002 0.022 0.35 2 -10000 0 2
STAT3 (dimer) 0 0.002 -10000 0 -10000 0 0
RNF41 0.038 0.005 -10000 0 -10000 0 0
FRAP1 0.014 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.012 0.052 -10000 0 -0.41 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.03 -10000 0 -0.49 2 2
CHRNA1 -0.13 0.28 -10000 0 -0.45 227 227
myelination 0.05 0.074 -10000 0 -0.48 2 2
PPP3CB 0.02 0.082 -10000 0 -0.55 1 1
KRAS 0.015 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.014 0.069 -10000 0 -0.72 2 2
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
mol:GDP 0.007 0.089 -10000 0 -0.45 8 8
SOS1 0.009 0.008 -10000 0 -10000 0 0
MAP2K2 0.046 0.097 -10000 0 -0.7 2 2
SRC 0.016 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.02 0.087 -10000 0 -0.6 1 1
MAP2K1 -0.039 0.18 -10000 0 -0.57 8 8
heart morphogenesis -0.018 0.077 -10000 0 -0.64 1 1
RAS family/GDP -0.015 0.073 -10000 0 -0.72 3 3
GRB2 0.009 0.008 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.021 0.026 -10000 0 -0.24 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.016 0.002 -10000 0 -10000 0 0
nervous system development -0.018 0.077 -10000 0 -0.64 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
Arf6 downstream pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.02 0.17 -10000 0 -0.72 27 27
regulation of axonogenesis -0.033 0.034 -10000 0 -10000 0 0
myoblast fusion 0.016 0.07 0.32 27 -10000 0 27
mol:GTP -0.01 0.043 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.01 0.047 0.49 2 -10000 0 2
ARF1/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.035 -10000 0 -10000 0 0
mol:Choline 0.033 0.031 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.073 -10000 0 -0.33 27 27
MAPK3 0.024 0.069 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.01 0.047 -10000 0 -0.5 2 2
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.07 -10000 0 -0.32 27 27
ARF1/GDP 0.02 0.07 -10000 0 -10000 0 0
ARF6 0.009 0.024 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.016 0.033 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.069 -10000 0 -10000 0 0
actin filament bundle formation 0.014 0.062 -10000 0 -10000 0 0
KALRN -0.012 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.024 -10000 0 -0.56 1 1
RhoA/GDP -0.014 0.062 -10000 0 -10000 0 0
NME1 0.016 0.038 -10000 0 -0.86 1 1
Rac1/GDP -0.014 0.062 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.01 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.016 0.074 -10000 0 -0.33 27 27
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.01 0.043 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.043 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GDP -0.016 0.071 -10000 0 -0.32 27 27
ARF6/GTP/RAB11FIP3/RAB11A -0.006 0.029 -10000 0 -0.45 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.021 0.035 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.033 -10000 0 -0.74 1 1
tube morphogenesis -0.016 0.073 -10000 0 -0.33 27 27
ruffle organization 0.033 0.034 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.043 -10000 0 -10000 0 0
PLD2 0.021 0.035 -10000 0 -10000 0 0
PIP5K1A 0.033 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.033 0.031 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.074 -10000 0 -0.33 27 27
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.035 0.056 -9999 0 -0.49 6 6
SNTA1 0.013 0.05 -9999 0 -0.8 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.036 0.05 -9999 0 -0.47 5 5
MAPK12 0.028 0.084 -9999 0 -0.49 13 13
CCND1 0.014 0.07 -9999 0 -0.3 20 20
p38 gamma/SNTA1 0.033 0.088 -9999 0 -0.51 11 11
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.028 0.083 -9999 0 -0.49 13 13
MAP2K6 0.03 0.041 -9999 0 -0.47 3 3
MAPT 0.032 0.069 -9999 0 -0.49 6 6
MAPK13 0.025 0.057 -9999 0 -0.56 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.018 -9999 0 -0.39 1 1
Paxillin-dependent events mediated by a4b1

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.013 -10000 0 -10000 0 0
DOCK1 0.014 0.033 -10000 0 -0.74 1 1
ITGA4 -0.011 0.15 -10000 0 -0.86 16 16
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.02 0.11 -10000 0 -0.66 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.017 0.098 -10000 0 -0.57 16 16
alpha4/beta7 Integrin/Paxillin -0.016 0.089 -10000 0 -0.52 16 16
lamellipodium assembly -0.001 0.043 -10000 0 -0.77 1 1
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
PI3K -0.002 0.034 -10000 0 -0.56 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.016 0 -10000 0 -10000 0 0
PXN 0.031 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
ARF6/GTP -0.013 0.075 -10000 0 -10000 0 0
cell adhesion -0.014 0.082 -10000 0 -0.48 16 16
CRKL/CBL -0.001 0.024 -10000 0 -0.56 1 1
alpha4/beta1 Integrin/Paxillin -0.016 0.089 -10000 0 -0.52 16 16
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.002 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.027 0.11 -10000 0 -0.49 25 25
p130Cas/Crk/Dock1 -0.002 0.029 -10000 0 -0.47 2 2
VCAM1 -0.006 0.13 -10000 0 -0.82 14 14
alpha4/beta1 Integrin/Paxillin/Talin -0.015 0.083 -10000 0 -0.49 16 16
alpha4/beta1 Integrin/Paxillin/GIT1 -0.015 0.083 -10000 0 -0.49 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
mol:GDP 0.014 0.082 0.48 16 -10000 0 16
CBL 0.014 0.033 -10000 0 -0.74 1 1
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.015 0.083 -10000 0 -0.49 16 16
Rac1/GTP -0.001 0.05 -10000 0 -0.93 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 0.069 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.013 0.078 -9999 0 -0.48 14 14
POMC 0.012 0.05 -9999 0 -0.8 2 2
EGFR 0.001 0.11 -9999 0 -0.85 9 9
Syndecan-3/EGFR -0.009 0.064 -9999 0 -0.47 10 10
AGRP 0.007 0.047 -9999 0 -0.74 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.01 0.14 -9999 0 -0.86 13 13
long-term memory -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.031 0.12 -9999 0 -0.47 35 35
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.018 -9999 0 -0.43 1 1
MC4R -0.01 0.11 -9999 0 -0.86 9 9
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.012 0.14 -9999 0 -0.75 19 19
FGFR/FGF/Syndecan-3 -0.001 0.019 -9999 0 -0.43 1 1
neuron projection morphogenesis -0.023 0.091 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.002 0.03 -9999 0 -0.4 3 3
Syndecan-3/AgRP/MC4R -0.01 0.066 -9999 0 -0.47 9 9
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.019 -9999 0 -0.43 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.03 0.12 -9999 0 -0.46 35 35
IL8 -0.039 0.21 -9999 0 -0.84 34 34
Syndecan-3/Fyn/Cortactin -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.018 -9999 0 -0.41 1 1
alpha-MSH/MC4R -0.014 0.094 -9999 0 -0.66 11 11
Gamma Secretase 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.021 0.1 -9999 0 -0.51 22 22
KLHL20 -0.013 0.046 -9999 0 -0.35 2 2
CYFIP2 0.004 0.092 -9999 0 -0.74 8 8
Rac1/GDP 0.067 0.076 -9999 0 -10000 0 0
ENAH -0.021 0.1 -9999 0 -0.51 22 22
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.047 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -9999 0 -0.22 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.084 -9999 0 -10000 0 0
RAPGEF1 0.053 0.099 -9999 0 -10000 0 0
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.11 -9999 0 -0.53 22 22
CRK 0.042 0.11 -9999 0 -0.47 22 22
E-cadherin/gamma catenin/alpha catenin -0.022 0.1 -9999 0 -0.49 24 24
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.021 0.1 -9999 0 -0.51 22 22
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.035 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.03 -9999 0 -0.48 2 2
PI3K -0.01 0.044 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.026 0.12 -9999 0 -0.58 24 24
TIAM1 0.014 0.033 -9999 0 -0.74 1 1
E-cadherin(dimer)/Ca2+ -0.017 0.08 -9999 0 -10000 0 0
AKT1 -0.005 0.025 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
RhoA/GDP 0.067 0.076 -9999 0 -10000 0 0
actin cytoskeleton organization -0.01 0.034 -9999 0 -0.24 2 2
CDC42/GDP 0.067 0.076 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.068 -9999 0 -0.32 24 24
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.018 0.084 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.017 0.082 -9999 0 -0.41 22 22
mol:GDP 0.063 0.087 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.057 -9999 0 -0.74 3 3
p120 catenin/RhoA/GDP -0.012 0.06 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.035 0.063 -9999 0 -0.26 20 20
NME1 0.014 0.038 -9999 0 -0.86 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.021 0.1 -9999 0 -0.51 22 22
regulation of cell-cell adhesion -0.009 0.041 -9999 0 -10000 0 0
WASF2 -0.005 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.054 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.087 -9999 0 -0.8 1 1
CCND1 -0.016 0.065 -9999 0 -0.33 20 20
VAV2 0.049 0.1 -9999 0 -0.5 1 1
RAP1/GDP -0.011 0.056 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.11 -9999 0 -0.49 22 22
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.081 -9999 0 -0.77 1 1
E-cadherin/beta catenin -0.019 0.09 -9999 0 -0.45 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.021 0.1 -9999 0 -0.51 22 22
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
Rac1/GTP -0.021 0.072 -9999 0 -0.6 1 1
E-cadherin/beta catenin/alpha catenin -0.02 0.094 -9999 0 -0.47 22 22
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.11 -9999 0 -0.55 22 22
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.003 0.12 -10000 0 -0.81 12 12
CLTC 0.043 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.036 0.001 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.023 -10000 0 -0.53 1 1
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.039 0.009 -10000 0 -10000 0 0
CPE 0 0.12 -10000 0 -0.58 22 22
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.042 0.023 -10000 0 -0.49 1 1
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.006 -10000 0 -10000 0 0
TSHR -0.045 0.2 -10000 0 -0.59 61 61
INS 0.016 0.002 -10000 0 -10000 0 0
BIN1 0.016 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.026 -10000 0 -0.58 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.023 -10000 0 -0.53 1 1
JUP 0.037 0.023 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.019 -10000 0 -0.44 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.027 0.056 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 -0.049 0.23 -10000 0 -0.86 39 39
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.058 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.007 0.035 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.025 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.043 0.15 -10000 0 -0.59 39 39
ACAP1 -0.019 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.032 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.042 0.017 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.042 0.023 -10000 0 -0.49 1 1
NME1 0.024 0.027 -10000 0 -0.59 1 1
clathrin coat assembly 0.042 0.014 -10000 0 -10000 0 0
IL2RA -0.015 0.11 -10000 0 -10000 0 0
VAMP3 0.025 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.06 -10000 0 -0.43 7 7
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.044 0.006 -10000 0 -10000 0 0
SDC1 0.036 0.031 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.025 -10000 0 -0.58 1 1
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.007 0.036 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.019 0.43 1 -10000 0 1
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.049 0.029 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0.014 0.033 -10000 0 -0.74 1 1
Dynamin 2/GDP -0.001 0.023 -10000 0 -0.53 1 1
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 -0.12 0.21 -10000 0 -0.37 220 220
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.03 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.006 0.064 -9999 0 -0.66 5 5
CRKL 0.04 0.064 -9999 0 -0.46 2 2
mol:PIP3 -0.03 0.003 -9999 0 -10000 0 0
AKT1 0 0.019 -9999 0 -0.45 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.049 0.061 -9999 0 -0.43 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
HGF/MET/SHIP2 -0.028 0.13 -9999 0 -0.57 26 26
MAP3K5 -0.024 0.12 -9999 0 -0.41 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.026 0.12 -9999 0 -0.61 15 15
AP1 -0.014 0.081 -9999 0 -0.51 13 13
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
apoptosis 0.004 0.11 -9999 0 -0.7 12 12
STAT3 (dimer) 0.041 0.077 -9999 0 -0.53 3 3
GAB1/CRKL/SHP2/PI3K -0.011 0.054 -9999 0 -0.58 2 2
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
CBL/CRK 0.047 0.067 -9999 0 -0.51 3 3
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 0.001 0.029 -9999 0 -0.29 5 5
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.008 0.038 -9999 0 -0.34 2 2
PAK1 0.01 0.019 -9999 0 -0.41 1 1
HGF/MET/RANBP10 -0.028 0.13 -9999 0 -0.57 26 26
HRAS 0.032 0.097 -9999 0 -0.71 3 3
DOCK1 0.048 0.068 -9999 0 -0.51 3 3
GAB1 0.031 0.067 -9999 0 -0.44 3 3
CRK 0.04 0.064 -9999 0 -0.46 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.1 -9999 0 -0.54 14 14
JUN 0.016 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.013 0.059 -9999 0 -0.4 5 5
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
cell morphogenesis 0.079 0.083 -9999 0 -0.65 2 2
GRB2/SHC -0.011 0.056 -9999 0 -0.54 3 3
FOS -0.003 0.12 -9999 0 -0.75 13 13
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0.001 0.029 -9999 0 -0.29 5 5
HGF/MET/MUC20 -0.028 0.13 -9999 0 -0.58 26 26
cell migration -0.011 0.055 -9999 0 -0.52 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
MET/RANBP10 -0.006 0.064 -9999 0 -0.66 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.071 -9999 0 -0.58 3 3
MET/MUC20 -0.006 0.065 -9999 0 -0.68 5 5
RAP1B 0.058 0.059 -9999 0 -10000 0 0
RAP1A 0.058 0.059 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.028 0.13 -9999 0 -0.57 26 26
RAF1 0.041 0.092 -9999 0 -0.66 3 3
STAT3 -0.014 0.066 -9999 0 -0.54 3 3
cell proliferation 0.055 0.1 -9999 0 -0.62 4 4
RPS6KB1 -0.004 0.019 -9999 0 -10000 0 0
MAPK3 -0.006 0.026 -9999 0 -0.27 5 5
MAPK1 -0.006 0.026 -9999 0 -0.27 5 5
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.011 0.1 -9999 0 -0.56 2 2
SRC 0.042 0.078 -9999 0 -0.54 3 3
PI3K -0.012 0.06 -9999 0 -0.53 4 4
MET/Glomulin 0.009 0.06 -9999 0 -0.61 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.05 0.086 -9999 0 -0.6 3 3
MET 0.007 0.085 -9999 0 -0.86 5 5
MAP4K1 -0.037 0.12 -9999 0 -0.4 12 12
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.05 0.088 -9999 0 -0.6 3 3
BAD 0.008 0.044 -9999 0 -0.66 2 2
MAP2K4 -0.012 0.11 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.055 -9999 0 -0.57 2 2
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.011 0.053 -9999 0 -0.49 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.02 0.17 -9999 0 -0.8 23 23
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.012 0.059 -9999 0 -0.53 3 3
PDPK1 -0.014 0.021 -9999 0 -0.49 1 1
HGF/MET/SHIP -0.032 0.14 -9999 0 -0.59 29 29
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.058 0.16 -10000 0 -0.49 63 63
cell-cell adhesion 0.014 0.074 0.63 3 -10000 0 3
Ephrin B/EPHB2/RasGAP -0.015 0.081 -10000 0 -0.8 1 1
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
SHC1 0.014 0.038 -10000 0 -0.86 1 1
Ephrin B1/EPHB3 -0.013 0.079 -10000 0 -0.49 14 14
Ephrin B1/EPHB1 -0.004 0.046 -10000 0 -0.54 4 4
HRAS/GDP -0.009 0.055 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.014 0.075 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.035 0.086 -10000 0 -0.74 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.009 0.061 -10000 0 -10000 0 0
endothelial cell migration -0.001 0.024 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 0.006 0.086 -10000 0 -0.74 7 7
PAK1 0.047 0.084 -10000 0 -0.76 1 1
HRAS 0.014 0.038 -10000 0 -0.86 1 1
RRAS 0.035 0.087 -10000 0 -0.76 1 1
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.042 0.065 -10000 0 -10000 0 0
lamellipodium assembly -0.014 0.074 -10000 0 -0.63 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.006 0.038 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
EPHB2 0 0.11 -10000 0 -0.76 11 11
EPHB3 -0.005 0.12 -10000 0 -0.75 14 14
EPHB1 0.01 0.071 -10000 0 -0.8 4 4
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.061 -10000 0 -10000 0 0
Ephrin B/EPHB2 -0.015 0.081 -10000 0 -0.6 3 3
Ephrin B/EPHB3 -0.017 0.089 -10000 0 -0.71 3 3
JNK cascade 0.04 0.086 -10000 0 -0.78 2 2
Ephrin B/EPHB1 -0.009 0.062 -10000 0 -0.5 2 2
RAP1/GDP -0.003 0.053 -10000 0 -10000 0 0
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 0.004 0.092 -10000 0 -0.74 8 8
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.016 0.082 -10000 0 -0.7 3 3
Rap1/GTP -0.014 0.074 -10000 0 -0.64 3 3
axon guidance -0.058 0.16 -10000 0 -0.49 63 63
MAPK3 0.064 0.042 -10000 0 -10000 0 0
MAPK1 0.064 0.042 -10000 0 -10000 0 0
Rac1/GDP -0.004 0.056 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.011 0.059 -10000 0 -0.49 2 2
CDC42/GDP -0.004 0.056 -10000 0 -10000 0 0
PI3K -0.002 0.025 -10000 0 -10000 0 0
EFNA5 -0.059 0.23 -10000 0 -0.75 52 52
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.057 -10000 0 -0.6 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.077 -10000 0 -0.64 4 4
PTK2 0.003 0.018 -10000 0 -10000 0 0
MAP4K4 0.04 0.087 -10000 0 -0.8 2 2
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.012 0.059 -10000 0 -0.5 1 1
MAP2K1 0.056 0.044 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.014 0.085 -10000 0 -0.63 6 6
cell migration 0.066 0.05 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.035 0.088 -10000 0 -0.76 1 1
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.075 0.23 -10000 0 -0.79 3 3
HRAS/GTP -0.016 0.086 -10000 0 -0.71 4 4
Ephrin B1/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
cell adhesion mediated by integrin 0.01 0.064 0.63 2 -10000 0 2
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.017 0.087 -10000 0 -0.74 3 3
RAC1-CDC42/GTP -0.022 0.099 -10000 0 -0.77 5 5
RASA1 0.014 0.033 -10000 0 -0.74 1 1
RAC1-CDC42/GDP -0.003 0.053 -10000 0 -10000 0 0
ruffle organization 0.069 0.09 -10000 0 -0.64 3 3
NCK1 0.014 0.033 -10000 0 -0.74 1 1
receptor internalization 0.033 0.12 -10000 0 -0.77 2 2
Ephrin B/EPHB2/KALRN -0.014 0.079 -10000 0 -0.8 1 1
ROCK1 0.022 0.076 -10000 0 -0.44 14 14
RAS family/GDP -0.011 0.059 -10000 0 -0.53 1 1
Rac1/GTP -0.015 0.079 -10000 0 -0.68 3 3
Ephrin B/EPHB1/Src/Paxillin -0.006 0.042 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.01 0.067 -10000 0 -0.5 6 6
ER alpha/Gai/GDP/Gbeta gamma 0.053 0.057 -10000 0 -10000 0 0
AKT1 0.045 0.08 -10000 0 -0.8 4 4
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.04 0.08 -10000 0 -0.73 5 5
mol:Ca2+ -0.015 0.18 -10000 0 -0.68 12 12
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.008 0.07 -10000 0 -0.55 8 8
SHC1 0.014 0.038 -10000 0 -0.86 1 1
apoptosis -0.045 0.076 0.76 4 -10000 0 4
RhoA/GTP -0.004 0.04 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.008 0.048 -10000 0 -10000 0 0
regulation of stress fiber formation -0.066 0.053 0.54 2 -10000 0 2
E2/ERA-ERB (dimer) -0.012 0.08 -10000 0 -0.54 12 12
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.004 0.045 -10000 0 -0.46 5 5
pseudopodium formation 0.066 0.053 -10000 0 -0.54 2 2
E2/ER alpha (dimer)/PELP1 -0.005 0.049 -10000 0 -0.5 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
GNAO1 0.008 0.083 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.062 0.064 -10000 0 -0.46 5 5
E2/ER beta (dimer) -0.009 0.074 -10000 0 -0.65 7 7
mol:GDP -0.01 0.063 -10000 0 -0.47 5 5
mol:NADP 0.062 0.064 -10000 0 -0.46 5 5
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 -0.018 0.19 -10000 0 -0.72 12 12
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 -0.025 0.099 -10000 0 -0.58 9 9
PLCB2 -0.067 0.16 -10000 0 -0.48 64 64
IGF1 0.006 0.093 -10000 0 -0.86 6 6
mol:L-citrulline 0.062 0.064 -10000 0 -0.46 5 5
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.047 -10000 0 -0.63 1 1
JNK cascade -0.008 0.074 -10000 0 -0.64 7 7
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
ESR2 0.004 0.096 -10000 0 -0.83 7 7
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 0.008 0.076 -10000 0 -0.77 5 5
Gq family/GDP/Gbeta gamma -0.016 0.074 -10000 0 -0.49 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.051 0.035 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.049 -10000 0 -10000 0 0
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
E2/ER alpha (dimer) -0.006 0.057 -10000 0 -0.59 5 5
STRN 0.01 0.066 -10000 0 -0.74 4 4
GNAL 0.016 0 -10000 0 -10000 0 0
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.015 0.076 -10000 0 -0.56 9 9
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
HBEGF -0.041 0.14 -10000 0 -0.5 7 7
cAMP biosynthetic process -0.01 0.065 -10000 0 -0.43 12 12
SRC 0.062 0.055 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.008 0.054 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.01 0.051 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.066 -10000 0 -0.44 12 12
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.023 -10000 0 -0.53 1 1
vasodilation 0.062 0.062 -10000 0 -0.44 5 5
mol:DAG -0.018 0.19 -10000 0 -0.72 12 12
Gs family/GDP/Gbeta gamma -0.008 0.049 -10000 0 -10000 0 0
MSN 0.068 0.057 -10000 0 -0.59 2 2
Gq family/GTP -0.019 0.077 -10000 0 -0.46 10 10
mol:PI-3-4-5-P3 0.04 0.077 -10000 0 -0.7 5 5
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.062 0.062 0.44 5 -10000 0 5
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.058 -10000 0 -0.45 4 4
NOS3 0.063 0.067 -10000 0 -0.48 5 5
GNA11 0.011 0.057 -10000 0 -0.74 3 3
MAPKKK cascade 0.07 0.075 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src -0.008 0.049 -10000 0 -0.47 4 4
ruffle organization 0.066 0.053 -10000 0 -0.54 2 2
ROCK2 -0.006 0.055 -10000 0 -0.68 2 2
GNA14 0.006 0.086 -10000 0 -0.74 7 7
GNA15 -0.011 0.15 -10000 0 -0.86 16 16
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.16 0.25 -10000 0 -0.66 8 8
MMP2 0.065 0.081 -10000 0 -0.66 3 3
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.049 0.12 -9999 0 -0.68 5 5
MAP3K8 0.013 0.054 -9999 0 -0.86 2 2
FOS 0.041 0.11 -9999 0 -0.57 5 5
PRKCA 0.017 0.003 -9999 0 -10000 0 0
PTPN7 -0.038 0.22 -9999 0 -0.86 34 34
HRAS 0.014 0.038 -9999 0 -0.86 1 1
PRKCB 0.009 0.082 -9999 0 -0.82 5 5
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.023 -9999 0 -0.53 1 1
MAPK3 0.029 0.085 -9999 0 -0.52 3 3
MAP2K1 0.055 0.055 -9999 0 -0.48 5 5
ELK1 0.017 0.003 -9999 0 -10000 0 0
BRAF -0.004 0.043 -9999 0 -0.46 4 4
mol:GTP 0 0.001 -9999 0 -0.006 12 12
MAPK1 0.029 0.085 -9999 0 -0.52 3 3
RAF1 -0.004 0.043 -9999 0 -0.46 4 4
KRAS 0.016 0.001 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.004 0.048 -10000 0 -0.56 4 4
ATM 0.014 0.033 -10000 0 -0.74 1 1
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.034 0.019 -10000 0 -0.4 1 1
protein ubiquitination -0.011 0.074 -10000 0 -0.87 1 1
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.034 0.068 -10000 0 -0.52 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.016 0 -10000 0 -10000 0 0
CCNE1 0.002 0.11 -10000 0 -0.86 8 8
CDK2/Cyclin E1 -0.01 0.081 -10000 0 -0.66 8 8
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.048 -10000 0 -0.56 4 4
FANCE 0.014 0.038 -10000 0 -0.86 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.17 0.36 -10000 0 -0.86 111 111
DNA repair 0.044 0.13 -10000 0 -0.67 5 5
BRCA1/BARD1/ubiquitin -0.004 0.048 -10000 0 -0.56 4 4
BARD1/DNA-PK -0.003 0.037 -10000 0 -10000 0 0
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.004 0.048 0.56 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex -0.004 0.041 -10000 0 -0.78 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BARD1/P53 -0.003 0.037 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BACH1 0.016 0 -10000 0 -10000 0 0
BARD1 0.01 0.066 -10000 0 -0.74 4 4
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BARD1/UbcH7 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BARD1/RAD51/PCNA -0.017 0.091 -10000 0 -0.52 14 14
BARD1/DNA-PK/P53 -0.003 0.034 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.048 -10000 0 -0.56 4 4
BRCA1/BARD1/CTIP -0.005 0.052 -10000 0 -0.86 1 1
FA complex -0.057 0.11 -10000 0 -0.57 1 1
BARD1/EWS -0.004 0.048 -10000 0 -0.56 4 4
RBBP8 0.029 0.045 -10000 0 -1 1 1
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.036 -10000 0 -10000 0 0
BRCA1/BARD1 -0.011 0.075 -10000 0 -0.89 1 1
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.004 0.049 -10000 0 -0.57 4 4
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.007 0.14 -10000 0 -0.86 14 14
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.048 -10000 0 -0.56 4 4
EWSR1 0.016 0 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.011 0.063 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.059 -9999 0 -0.67 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.047 -9999 0 -0.54 4 4
AP1 -0.019 0.092 -9999 0 -0.69 6 6
ILK 0.06 0.065 -9999 0 -10000 0 0
bone resorption -0.026 0.1 -9999 0 -0.72 4 4
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.008 0.054 -9999 0 -10000 0 0
ITGAV 0.022 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.14 -9999 0 -0.65 25 25
alphaV/beta3 Integrin/Osteopontin -0.009 0.062 -9999 0 -0.48 2 2
MAP3K1 0.06 0.066 -9999 0 -10000 0 0
JUN 0.016 0.002 -9999 0 -10000 0 0
MAPK3 0.072 0.081 -9999 0 -10000 0 0
MAPK1 0.072 0.081 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 0.072 0.078 -9999 0 -0.77 2 2
ITGB3 0.014 0.08 -9999 0 -0.73 6 6
NFKBIA 0.085 0.081 -9999 0 -10000 0 0
FOS -0.002 0.12 -9999 0 -0.75 13 13
CD44 -0.019 0.17 -9999 0 -0.86 21 21
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU 0.084 0.17 -9999 0 -1.1 9 9
NF kappa B1 p50/RelA -0.012 0.06 -9999 0 -0.64 1 1
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.006 0.057 -9999 0 -0.54 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.057 0.071 -9999 0 -10000 0 0
VAV3 0.055 0.1 -9999 0 -0.78 1 1
MAP3K14 0.059 0.082 -9999 0 -0.5 4 4
ROCK2 0.01 0.066 -9999 0 -0.74 4 4
SPP1 0.017 0.065 -9999 0 -0.73 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.075 -9999 0 -0.71 1 1
MMP2 0.097 0.12 -9999 0 -0.76 6 6
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.014 0.033 -10000 0 -0.74 1 1
ANTXR2 0.014 0.033 -10000 0 -0.74 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.006 -10000 0 -0.093 2 2
monocyte activation 0.006 0.083 -10000 0 -0.37 21 21
MAP2K2 -0.002 0.035 -10000 0 -0.8 1 1
MAP2K1 0 0.005 -10000 0 -10000 0 0
MAP2K7 0 0.005 -10000 0 -10000 0 0
MAP2K6 -0.003 0.032 -10000 0 -0.43 3 3
CYAA 0.02 0.027 -10000 0 -0.42 2 2
MAP2K4 0 0.005 -10000 0 -10000 0 0
IL1B 0.017 0.059 -10000 0 -0.49 6 6
Channel -0.002 0.027 -10000 0 -0.44 2 2
NLRP1 -0.005 0.051 -10000 0 -0.52 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.006 0.093 2 -10000 0 2
MAPK3 0 0.005 -10000 0 -10000 0 0
MAPK1 0 0.005 -10000 0 -10000 0 0
PGR -0.015 0.08 -10000 0 -0.44 18 18
PA/Cellular Receptors -0.002 0.03 -10000 0 -0.48 2 2
apoptosis 0 0.006 -10000 0 -0.093 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.025 -10000 0 -0.42 2 2
macrophage activation 0.027 0.005 -10000 0 -10000 0 0
TNF 0.003 0.1 -10000 0 -0.8 8 8
VCAM1 -0.015 0.08 -10000 0 -0.37 21 21
platelet activation 0 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.01 -10000 0 -10000 0 0
IL18 0.016 0.066 -10000 0 -0.52 7 7
negative regulation of macrophage activation 0 0.006 -10000 0 -0.093 2 2
LEF 0 0.006 -10000 0 -0.094 2 2
CASP1 -0.002 0.023 -10000 0 -0.23 5 5
mol:cAMP 0 0.007 -10000 0 -10000 0 0
necrosis 0 0.006 -10000 0 -0.093 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.026 -10000 0 -0.42 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.036 0.12 -9999 0 -0.42 44 44
PDGFB-D/PDGFRB/SLAP -0.033 0.14 -9999 0 -0.67 26 26
PDGFB-D/PDGFRB/APS/CBL -0.008 0.069 -9999 0 -0.56 8 8
AKT1 -0.002 0.022 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0.14 -9999 0 -0.44 44 44
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
FGR -0.004 0.029 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.041 -9999 0 -10000 0 0
MYC 0.042 0.14 -9999 0 -0.57 20 20
SHC1 0.014 0.038 -9999 0 -0.86 1 1
HRAS/GDP -0.002 0.038 -9999 0 -0.88 1 1
LRP1/PDGFRB/PDGFB 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.038 0.041 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.006 0.086 -9999 0 -0.74 7 7
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.033 0.14 -9999 0 -0.67 26 26
HRAS 0.014 0.038 -9999 0 -0.86 1 1
HIF1A 0.087 0.04 -9999 0 -0.6 1 1
GAB1 0.032 0.075 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.036 0.082 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.038 0.12 -9999 0 -0.47 18 18
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.038 0.041 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.007 0.064 -9999 0 -0.56 7 7
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.023 0.085 -9999 0 -0.43 6 6
PTPN2 0.016 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
VAV2 0.035 0.088 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.017 0.081 -9999 0 -0.54 4 4
PDGFRB 0.016 0.006 -9999 0 -10000 0 0
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.02 0.082 -9999 0 -10000 0 0
ABL1 0.033 0.059 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.033 0.07 -9999 0 -10000 0 0
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.014 0.038 -9999 0 -0.86 1 1
cell proliferation 0.043 0.12 -9999 0 -0.52 20 20
SLA -0.027 0.19 -9999 0 -0.86 26 26
actin cytoskeleton reorganization 0.001 0.025 -9999 0 -10000 0 0
SRC -0.001 0.013 -9999 0 -10000 0 0
PI3K -0.002 0.024 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.007 0.06 -9999 0 -0.49 8 8
SH2B2 0.004 0.1 -9999 0 -0.86 7 7
PLCgamma1/SPHK1 0.012 0.14 -9999 0 -0.45 44 44
LYN -0.001 0.014 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.023 -9999 0 -10000 0 0
SPHK1 -0.056 0.24 -9999 0 -0.86 44 44
EDG1 0.001 0.003 -9999 0 -10000 0 0
mol:DAG 0.038 0.041 -9999 0 -10000 0 0
PLCG1 0.038 0.041 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.021 -9999 0 -0.47 1 1
YES1 -0.001 0.014 -9999 0 -10000 0 0
cell migration -0.001 0.02 -9999 0 -0.47 1 1
SHC/Grb2/SOS1 -0.001 0.02 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.74 1 1
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.018 -9999 0 -10000 0 0
FYN -0.001 0.013 -9999 0 -10000 0 0
DOK1 0.044 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.029 -9999 0 -0.68 1 1
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 0.045 0.1 -9999 0 -0.48 3 3
PRKCD 0.042 0.028 -9999 0 -0.53 1 1
FER 0.041 0.033 -9999 0 -0.44 2 2
MAPKKK cascade 0 0.021 -9999 0 -10000 0 0
RASA1 0.042 0.025 -9999 0 -0.44 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.018 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.033 0.059 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.001 0.02 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.057 0.052 -10000 0 -0.46 1 1
adherens junction organization 0.039 0.08 -10000 0 -0.53 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.06 -10000 0 -10000 0 0
FMN1 0.021 0.12 -10000 0 -0.66 2 2
mol:IP3 -0.008 0.04 -10000 0 -0.48 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.065 -10000 0 -0.71 1 1
CTNNB1 0.001 0.006 -10000 0 -10000 0 0
AKT1 0.054 0.057 -10000 0 -0.5 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.11 -10000 0 -0.53 22 22
CTNND1 0.016 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.074 -10000 0 -0.56 2 2
VASP 0.044 0.072 -10000 0 -0.66 1 1
ZYX 0.044 0.072 -10000 0 -0.66 1 1
JUB 0.042 0.08 -10000 0 -0.58 2 2
EGFR(dimer) -0.02 0.082 -10000 0 -0.48 9 9
E-cadherin/beta catenin-gamma catenin -0.021 0.1 -10000 0 -0.47 24 24
mol:PI-3-4-5-P3 -0.01 0.048 -10000 0 -0.54 1 1
PIK3CA 0.015 0.033 -10000 0 -0.74 1 1
PI3K -0.01 0.048 -10000 0 -0.56 1 1
FYN -0.23 0.13 -10000 0 -0.45 18 18
mol:Ca2+ -0.008 0.039 -10000 0 -0.46 1 1
JUP -0.003 0.056 -10000 0 -0.74 3 3
PIK3R1 0.015 0.033 -10000 0 -0.74 1 1
mol:DAG -0.008 0.04 -10000 0 -0.48 1 1
CDH1 -0.031 0.15 -10000 0 -0.74 22 22
RhoA/GDP -0.013 0.06 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.044 0.071 -10000 0 -0.64 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
CASR -0.29 0.15 -10000 0 -0.53 19 19
RhoA/GTP -0.007 0.035 -10000 0 -10000 0 0
AKT2 0.054 0.057 -10000 0 -0.5 1 1
actin cable formation 0.031 0.12 -10000 0 -0.63 2 2
apoptosis 0.009 0.043 0.49 1 -10000 0 1
CTNNA1 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.015 0.066 -10000 0 -0.48 1 1
PIP5K1A 0.044 0.076 -10000 0 -0.58 2 2
PLCG1 -0.008 0.041 -10000 0 -0.49 1 1
Rac1/GTP -0.018 0.074 -10000 0 -0.43 9 9
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.02 -9999 0 -0.47 1 1
forebrain development 0.055 0.094 -9999 0 -0.5 2 2
GNAO1 0.008 0.083 -9999 0 -0.84 5 5
SMO/beta Arrestin2 -0.002 0.038 -9999 0 -0.61 2 2
SMO 0.016 0.033 -9999 0 -0.74 1 1
ARRB2 0.014 0.038 -9999 0 -0.86 1 1
GLI3/SPOP 0.061 0.024 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex -0.019 0.097 -9999 0 -0.52 19 19
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
XPO1 0.019 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.013 0.061 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 19 19
mol:GDP 0.016 0.033 -9999 0 -0.74 1 1
MIM/GLI2A 0.023 0.008 -9999 0 -10000 0 0
IFT88 0.014 0.033 -9999 0 -0.74 1 1
GNAI3 0.016 0.004 -9999 0 -10000 0 0
GLI2 0.058 0.031 -9999 0 -10000 0 0
GLI3 0.055 0.026 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.015 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0.033 -9999 0 -0.74 1 1
GNG2 0.016 0 -9999 0 -10000 0 0
Gi family/GTP 0.044 0.051 -9999 0 -0.55 1 1
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.015 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.073 0.034 -9999 0 -10000 0 0
GLI2/Su(fu) 0.075 0.037 -9999 0 -10000 0 0
FOXA2 -0.06 0.22 -9999 0 -0.83 38 38
neural tube patterning 0.055 0.094 -9999 0 -0.5 2 2
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.013 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.74 1 1
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.023 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.055 0.094 -9999 0 -0.5 2 2
SUFU 0.038 0.021 -9999 0 -10000 0 0
LGALS3 -0.006 0.14 -9999 0 -0.86 13 13
catabolic process 0.093 0.03 -9999 0 -10000 0 0
GLI3A/CBP 0.017 0.056 -9999 0 -10000 0 0
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 0.055 0.095 -9999 0 -0.51 2 2
RAB23 0.016 0 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.014 0.084 -9999 0 -0.54 13 13
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
RBBP4 0.014 0.033 -9999 0 -0.74 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.061 0.028 -9999 0 -10000 0 0
STK36 0.019 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.052 0.047 -9999 0 -0.48 1 1
PTCH1 0.062 0.1 -9999 0 -1.1 1 1
MIM/GLI1 0.052 0.15 -9999 0 -0.71 1 1
CREBBP 0.017 0.056 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.056 0.048 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.028 0.1 -9999 0 -10000 0 0
BAG4 0.014 0.033 -9999 0 -0.74 1 1
BAD 0.03 0.045 -9999 0 -0.42 2 2
NFKBIA 0.016 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.31 -9999 0 -0.86 80 80
BAX 0.032 0.036 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.027 -9999 0 -0.099 1 1
IKBKB 0.038 0.096 -9999 0 -10000 0 0
MAP2K2 0.046 0.052 -9999 0 -0.38 4 4
MAP2K1 0.047 0.05 -9999 0 -0.38 4 4
SMPD1 0.019 0.027 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.038 0.097 -9999 0 -10000 0 0
MAP2K4 0.041 0.035 -9999 0 -10000 0 0
protein ubiquitination 0.04 0.097 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.054 0.051 -9999 0 -0.38 4 4
response to UV 0.001 0 -9999 0 -10000 0 0
RAF1 0.039 0.052 -9999 0 -0.41 4 4
CRADD 0.016 0.001 -9999 0 -10000 0 0
mol:ceramide 0.022 0.037 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.016 0.001 -9999 0 -10000 0 0
MAP3K1 0.032 0.036 -9999 0 -10000 0 0
TRADD 0.016 0.001 -9999 0 -10000 0 0
RELA/p50 0.016 0 -9999 0 -10000 0 0
MAPK3 0.05 0.05 -9999 0 -0.37 4 4
MAPK1 0.05 0.05 -9999 0 -0.37 4 4
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.028 0.1 -9999 0 -10000 0 0
KSR1 0.03 0.055 -9999 0 -0.45 4 4
MAPK8 0.048 0.04 -9999 0 -10000 0 0
TRAF2 0.016 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.038 0.096 -9999 0 -10000 0 0
TNF R/SODD -0.001 0.024 -9999 0 -0.56 1 1
TNF 0.004 0.1 -9999 0 -0.8 8 8
CYCS 0.033 0.038 -9999 0 -10000 0 0
IKBKG 0.038 0.096 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.018 0.1 -9999 0 -0.44 1 1
RELA 0.016 0 -9999 0 -10000 0 0
RIPK1 0.016 0.001 -9999 0 -10000 0 0
AIFM1 0.033 0.037 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.009 0.067 -9999 0 -0.52 9 9
TNFRSF1A 0.016 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.029 0.029 -9999 0 -10000 0 0
NSMAF 0.029 0.098 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -10000 0 0
BCL2 0.016 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.005 0.072 -9999 0 -0.73 5 5
VDR 0.011 0.057 -9999 0 -0.74 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.077 0.05 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.087 0.062 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.009 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.02 0.073 -9999 0 -10000 0 0
RXRs/NUR77 -0.007 0.087 -9999 0 -0.5 6 6
RXRs/PPAR 0.058 0.029 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.043 -9999 0 -0.57 3 3
RARs/VDR/DNA/Vit D3 -0.004 0.039 -9999 0 -10000 0 0
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.057 -9999 0 -0.74 3 3
RARs/RARs/DNA/9cRA -0.001 0.025 -9999 0 -0.41 2 2
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.034 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.02 0.073 -9999 0 -10000 0 0
THRA 0.014 0.033 -9999 0 -0.74 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.003 0.043 -9999 0 -0.57 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.005 0.056 -9999 0 -0.5 4 4
NR1H4 -0.009 0.14 -9999 0 -0.75 17 17
RXRs/LXRs/DNA 0.008 0.056 -9999 0 -10000 0 0
NR1H2 0.023 0.033 -9999 0 -0.73 1 1
NR1H3 0.025 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.005 0.052 -9999 0 -0.48 4 4
NR4A1 -0.006 0.13 -9999 0 -0.75 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.041 0.067 -9999 0 -0.41 2 2
RXRG 0.015 0.076 -9999 0 -0.85 4 4
RXR alpha/CCPG 0 0.004 -9999 0 -10000 0 0
RXRA 0.024 0.005 -9999 0 -10000 0 0
RXRB 0.025 0.006 -9999 0 -10000 0 0
THRB -0.031 0.18 -9999 0 -0.74 33 33
PPARG 0.016 0 -9999 0 -10000 0 0
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.084 0.13 -9999 0 -0.87 8 8
mol:Oxysterols 0.009 0.007 -9999 0 -10000 0 0
cholesterol transport 0.086 0.061 -9999 0 -10000 0 0
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0.046 -9999 0 -0.74 2 2
RXRs/NUR77/BCL2 -0.01 0.055 -9999 0 -10000 0 0
SREBF1 0.092 0.064 -9999 0 -0.66 1 1
RXRs/RXRs/DNA/9cRA 0.005 0.056 -9999 0 -0.5 4 4
ABCA1 0.092 0.071 -9999 0 -0.66 2 2
RARs/THRs -0.027 0.098 -9999 0 -10000 0 0
RXRs/FXR -0.008 0.091 -9999 0 -0.5 7 7
BCL2 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.075 0.027 -10000 0 -10000 0 0
NFATC2 0.053 0.036 -10000 0 -0.32 2 2
NFATC3 0.029 0.039 -10000 0 -0.49 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.032 0.072 -10000 0 -0.46 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.013 0.053 -10000 0 -0.52 2 2
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.001 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0.003 -10000 0 -10000 0 0
BAD 0.013 0.05 -10000 0 -0.8 2 2
CABIN1/MEF2D 0.038 0.067 -10000 0 -0.43 4 4
Calcineurin A alpha-beta B1/BCL2 0.016 0 -10000 0 -10000 0 0
FKBP8 0.014 0.033 -10000 0 -0.74 1 1
activation-induced cell death of T cells -0.037 0.067 0.43 4 -10000 0 4
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
MAP3K8 0.013 0.054 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.002 0.023 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.011 0.056 -10000 0 -10000 0 0
CABIN1 0.032 0.072 -10000 0 -0.47 4 4
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0.013 0.046 -10000 0 -0.74 2 2
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.034 -10000 0 -0.56 2 2
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.013 0.047 -10000 0 -0.74 2 2
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.028 -10000 0 -10000 0 0
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.024 -10000 0 -0.55 1 1
CASP3 0.016 0.003 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.019 -10000 0 -0.39 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.076 -10000 0 -0.47 2 2
PRKCB 0.008 0.08 -10000 0 -0.82 5 5
PRKCE 0.014 0.033 -10000 0 -0.74 1 1
JNK2/NFAT4 -0.002 0.033 -10000 0 -0.44 3 3
BAD/BCL-XL -0.002 0.038 -10000 0 -0.61 2 2
PRKCD 0.014 0.038 -10000 0 -0.86 1 1
NUP214 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.057 -10000 0 -0.75 3 3
PRKCA 0.016 0 -10000 0 -10000 0 0
PRKCG -0.03 0.18 -10000 0 -0.86 23 23
PRKCQ -0.007 0.13 -10000 0 -0.74 16 16
FKBP38/BCL2 -0.001 0.024 -10000 0 -0.56 1 1
EP300 0.015 0.033 -10000 0 -0.74 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.079 0.038 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.022 -10000 0 -0.5 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.03 -10000 0 -0.48 2 2
NFATc/ERK1 0.081 0.025 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.013 0.054 -10000 0 -0.52 2 2
NR4A1 0.073 0.13 -10000 0 -0.67 15 15
GSK3B 0.016 0.003 -10000 0 -10000 0 0
positive T cell selection 0.029 0.039 -10000 0 -0.48 3 3
NFAT1/CK1 alpha -0.003 0.02 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0.003 -10000 0 -10000 0 0
AKAP5 0.013 0.046 -10000 0 -0.74 2 2
MEF2D 0.016 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.08 0.028 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.011 0.057 -10000 0 -0.74 3 3
Cbp/p300/PCAF -0.002 0.04 -10000 0 -0.91 1 1
EP300 0.014 0.033 -10000 0 -0.74 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.056 0.034 -10000 0 -0.43 1 1
KAT2B 0.014 0.033 -10000 0 -0.74 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.03 0.038 0.24 1 -0.3 2 3
RAR alpha/9cRA/Cyclin H -0.009 0.038 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.052 0.037 -10000 0 -0.48 1 1
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.002 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.011 0.053 -10000 0 -0.58 2 2
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.043 -10000 0 -0.57 3 3
RXRs/RARs/NRIP1/9cRA 0.062 0.082 -10000 0 -0.52 1 1
NCOA2 0 0.11 -10000 0 -0.74 11 11
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.057 -10000 0 -0.74 3 3
RARG 0.017 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.001 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.015 0.046 -10000 0 -0.74 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.018 0.073 -10000 0 -10000 0 0
RARA 0.024 0.06 -10000 0 -0.28 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.046 0.065 -10000 0 -0.89 1 1
PRKCA 0.02 0.001 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.054 0.083 -10000 0 -0.57 1 1
RXRG 0.013 0.091 -10000 0 -0.38 27 27
RXRA 0.035 0.056 -10000 0 -10000 0 0
RXRB 0.017 0.084 -10000 0 -0.37 23 23
VDR/Vit D3/DNA -0.003 0.043 -10000 0 -0.57 3 3
RBP1 0.009 0.073 -10000 0 -0.83 4 4
CRBP1/9-cic-RA -0.005 0.056 -10000 0 -0.65 4 4
RARB 0.016 0.047 -10000 0 -0.74 2 2
PRKCG -0.025 0.18 -10000 0 -0.86 23 23
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.053 0.084 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.06 0.074 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.047 -10000 0 -0.33 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 0.054 0.083 -10000 0 -0.57 1 1
positive regulation of DNA binding -0.008 0.037 -10000 0 -10000 0 0
NRIP1 0.052 0.091 -10000 0 -1.2 1 1
RXRs/RARs 0.046 0.081 -10000 0 -0.41 1 1
RXRs/RXRs/DNA/9cRA -0.017 0.073 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.006 0.026 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 0.006 0.26 -9999 0 -1.1 27 27
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.022 0.075 -9999 0 -0.44 1 1
ATF2/c-Jun 0.043 0.066 -9999 0 -0.61 1 1
MAPK11 0.019 0.091 -9999 0 -0.69 3 3
MITF 0.042 0.094 -9999 0 -0.55 1 1
MAPKAPK5 0.042 0.094 -9999 0 -0.46 2 2
KRT8 0.041 0.095 -9999 0 -0.55 1 1
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.03 0.12 -9999 0 -0.65 3 3
CEBPB 0.033 0.11 -9999 0 -0.55 1 1
SLC9A1 0.042 0.094 -9999 0 -0.55 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.049 0.098 -9999 0 -0.68 2 2
p38alpha-beta/MNK1 -0.021 0.079 -9999 0 -0.53 3 3
JUN 0.044 0.065 -9999 0 -0.6 1 1
PPARGC1A 0.001 0.16 -9999 0 -0.68 3 3
USF1 0.042 0.094 -9999 0 -0.46 2 2
RAB5/GDP/GDI1 -0.014 0.053 -9999 0 -0.41 1 1
NOS2 0.036 0.14 -9999 0 -0.87 8 8
DDIT3 0.04 0.099 -9999 0 -0.46 2 2
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 0.045 0.095 -9999 0 -0.65 4 4
p38alpha-beta/HBP1 -0.021 0.079 -9999 0 -0.53 3 3
CREB1 0.048 0.097 -9999 0 -0.55 1 1
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.046 0.083 -9999 0 -0.54 1 1
RPS6KA4 0.042 0.094 -9999 0 -0.46 2 2
PLA2G4A 0.04 0.11 -9999 0 -0.74 4 4
GDI1 0.042 0.094 -9999 0 -0.46 2 2
TP53 0.044 0.12 -9999 0 -0.56 3 3
RPS6KA5 0.042 0.094 -9999 0 -0.46 2 2
ESR1 0.038 0.1 -9999 0 -0.66 2 2
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C 0.042 0.094 -9999 0 -0.55 1 1
MEF2A 0.042 0.094 -9999 0 -0.46 2 2
EIF4EBP1 0.041 0.1 -9999 0 -0.47 4 4
KRT19 -0.046 0.21 -9999 0 -0.82 11 11
ELK4 0.042 0.094 -9999 0 -0.55 1 1
ATF6 0.042 0.094 -9999 0 -0.46 2 2
ATF1 0.048 0.097 -9999 0 -0.55 1 1
p38alpha-beta/MAPKAPK2 -0.021 0.079 -9999 0 -0.53 3 3
p38alpha-beta/MAPKAPK3 -0.021 0.079 -9999 0 -0.53 3 3
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.011 0.057 -9999 0 -0.74 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.006 0.037 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
MAP3K12 0.014 0.033 -9999 0 -0.74 1 1
FGR 0.011 0.066 -9999 0 -0.86 3 3
p38 alpha/TAB1 -0.012 0.038 -9999 0 -0.31 2 2
PRKG1 -0.006 0.13 -9999 0 -0.74 15 15
DUSP8 0.014 0.033 -9999 0 -0.74 1 1
PGK/cGMP/p38 alpha -0.02 0.064 -9999 0 -0.43 3 3
apoptosis -0.012 0.036 -9999 0 -0.3 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 0.014 0.038 -9999 0 -0.86 1 1
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.056 0.084 -9999 0 -0.42 2 2
BLK -0.04 0.21 -9999 0 -0.86 33 33
HCK -0.032 0.2 -9999 0 -0.86 29 29
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.011 0.066 -9999 0 -0.86 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.057 0.065 -9999 0 -0.34 2 2
positive regulation of innate immune response 0.068 0.09 -9999 0 -0.44 2 2
LCK -0.02 0.17 -9999 0 -0.85 22 22
p38alpha-beta/MKP7 0.073 0.087 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.071 0.092 -9999 0 -10000 0 0
PGK/cGMP -0.016 0.094 -9999 0 -0.57 15 15
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.072 0.089 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.007 0.14 -9999 0 -0.83 14 14
Insulin Pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.01 0.064 -9999 0 -10000 0 0
TC10/GTP -0.007 0.054 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.038 -9999 0 -0.44 4 4
HRAS 0.014 0.038 -9999 0 -0.86 1 1
APS homodimer 0.004 0.1 -9999 0 -0.86 7 7
GRB14 -0.024 0.17 -9999 0 -0.74 28 28
FOXO3 -0.003 0.012 -9999 0 -10000 0 0
AKT1 -0.021 0.084 -9999 0 -0.66 2 2
INSR 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
SORBS1 0.014 0.033 -9999 0 -0.74 1 1
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.049 0.001 -9999 0 -10000 0 0
CAV1 -0.005 0.14 -9999 0 -0.51 37 37
CBL/APS/CAP/Crk-II/C3G -0.008 0.06 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.038 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.04 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.002 0.023 -9999 0 -10000 0 0
RPS6KB1 0.055 0.094 -9999 0 -0.58 2 2
PARD6A 0.011 0.057 -9999 0 -0.74 3 3
CBL 0.014 0.033 -9999 0 -0.74 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.073 -9999 0 -0.59 2 2
HRAS/GTP -0.007 0.055 -9999 0 -0.73 1 1
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.004 0.041 -9999 0 -0.5 1 1
PRKCI -0.005 0.019 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.092 -9999 0 -0.72 2 2
SHC1 0.014 0.038 -9999 0 -0.86 1 1
negative regulation of MAPKKK cascade -0.001 0.035 -9999 0 -0.82 1 1
PI3K -0.004 0.041 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
AKT2 -0.021 0.084 -9999 0 -0.66 2 2
PRKCZ -0.008 0.055 -9999 0 -0.69 3 3
SH2B2 0.004 0.1 -9999 0 -0.86 7 7
SHC/SHIP -0.007 0.062 -9999 0 -0.55 5 5
F2RL2 -0.032 0.2 -9999 0 -0.86 29 29
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.024 -9999 0 -0.55 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.022 -9999 0 -0.5 1 1
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
CBL/APS/CAP/Crk-II -0.008 0.065 -9999 0 -0.52 7 7
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.023 -9999 0 -0.54 1 1
INPP5D 0.029 0.067 -9999 0 -0.53 7 7
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.001 0.006 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.066 -9999 0 -0.74 4 4
p62DOK/RasGAP -0.001 0.036 -9999 0 -0.83 1 1
INS 0.005 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.029 0.066 -9999 0 -0.52 7 7
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.031 0.15 -9999 0 -0.73 6 6
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.003 0.028 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.039 -9999 0 -0.45 4 4
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.029 0.12 -9999 0 -0.5 29 29
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.001 0.018 -9999 0 -10000 0 0
HDAC3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.025 0.13 -9999 0 -0.66 20 20
GATA1/HDAC5 -0.026 0.13 -9999 0 -0.66 21 21
GATA2/HDAC5 -0.015 0.089 -9999 0 -0.56 14 14
HDAC5/BCL6/BCoR -0.001 0.02 -9999 0 -0.47 1 1
HDAC9 0.016 0 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.025 -9999 0 -0.57 1 1
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB -0.001 0.024 -9999 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
HDAC4/RFXANK -0.001 0.029 -9999 0 -0.66 1 1
BCOR 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0.033 -9999 0 -0.74 1 1
HDAC5 0.014 0.033 -9999 0 -0.74 1 1
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones -0.003 0.039 -9999 0 -0.83 1 1
ADRBK1 0.016 0 -9999 0 -10000 0 0
HDAC4 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.024 -9999 0 -0.56 1 1
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.016 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.024 -9999 0 -0.56 1 1
TUBA1B 0.016 0 -9999 0 -10000 0 0
HDAC6 0.016 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.002 0.038 -9999 0 -0.61 2 2
CAMK4 0.013 0.046 -9999 0 -0.74 2 2
Tubulin/HDAC6 -0.001 0.02 -9999 0 -0.47 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
GATA1 -0.02 0.17 -9999 0 -0.86 20 20
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
NR3C1 0.014 0.038 -9999 0 -0.86 1 1
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0.016 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.024 -9999 0 -0.56 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.002 0.029 -9999 0 -0.47 2 2
HDAC4/ER alpha -0.005 0.056 -9999 0 -0.58 5 5
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.051 0.042 -9999 0 -0.82 1 1
cell motility -0.001 0.02 -9999 0 -0.47 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.016 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 0.008 0.076 -9999 0 -0.77 5 5
HDAC6/HDAC11 -0.002 0.034 -9999 0 -0.56 2 2
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
TUBB2A 0.014 0.033 -9999 0 -0.74 1 1
HDAC11 0.013 0.046 -9999 0 -0.74 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
ANKRA2 0.016 0 -9999 0 -10000 0 0
RFXANK 0.014 0.038 -9999 0 -0.86 1 1
nuclear import 0.001 0.017 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.001 0.016 -10000 0 -10000 0 0
CLOCK 0.019 0.033 -10000 0 -0.74 1 1
TIMELESS/CRY2 0.056 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.029 -10000 0 -0.66 1 1
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.053 0.069 -10000 0 -1 2 2
ARNTL 0.02 0.003 -10000 0 -10000 0 0
TIMELESS 0.055 0.028 -10000 0 -10000 0 0
NPAS2 0.006 0.1 -10000 0 -0.74 10 10
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.019 0.009 0.12 2 -10000 0 2
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.019 0.009 -10000 0 -0.12 2 2
PER1 0.016 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.074 -10000 0 -0.46 11 11
BMAL1/CLOCK 0.064 0.055 -10000 0 -0.82 1 1
S phase of mitotic cell cycle -0.001 0.016 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.016 -10000 0 -10000 0 0
mol:NADPH 0.019 0.009 -10000 0 -0.12 2 2
PER1/TIMELESS 0.056 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.038 -10000 0 -0.86 1 1
mTOR signaling pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.036 -10000 0 -0.4 2 2
FRAP1 0.02 0.012 -10000 0 -10000 0 0
AKT1 -0.004 0.036 -10000 0 -0.47 2 2
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.028 -10000 0 -0.46 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.009 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.025 -10000 0 -0.42 1 1
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.035 -10000 0 -0.39 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.036 0.024 -10000 0 -0.34 1 1
MAP3K5 0.014 0.001 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
apoptosis 0.014 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 0.001 1 -0.002 4 5
EIF4B 0.044 0.022 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.031 -10000 0 -0.45 2 2
eIF4E/eIF4G1/eIF4A1 0 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.039 -10000 0 -0.36 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.042 0.018 -10000 0 -10000 0 0
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.024 -10000 0 -0.41 1 1
mol:Amino Acids 0 0 0.001 1 -0.002 4 5
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.043 -10000 0 -0.75 1 1
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.008 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.023 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.03 -10000 0 -0.5 1 1
tumor necrosis factor receptor activity 0 0 0.002 4 -0.001 1 5
RPS6 0.012 0.054 -10000 0 -0.86 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.008 0.038 -10000 0 -0.42 4 4
INS 0 0.001 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.004 0.033 -10000 0 -0.38 1 1
EIF4EBP1 -0.01 0.1 -10000 0 -0.46 28 28
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
PPP2R5D 0.029 0.012 -10000 0 -10000 0 0
peptide biosynthetic process 0.023 0.001 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.004 1 1
EEF2 0.023 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.001 0.094 -10000 0 -0.4 28 28
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.002 0.029 -9999 0 -0.52 1 1
CDKN1B 0.05 0.007 -9999 0 -10000 0 0
CDKN1A 0.048 0.032 -9999 0 -0.47 2 2
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.05 0.007 -9999 0 -10000 0 0
AKT1 0 0.006 -9999 0 -10000 0 0
BAD 0.013 0.05 -9999 0 -0.8 2 2
AKT3 0.022 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.05 0.007 -9999 0 -10000 0 0
AKT1/ASK1 0 0.005 -9999 0 -10000 0 0
BAD/YWHAZ -0.002 0.032 -9999 0 -0.52 2 2
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.016 0 -9999 0 -10000 0 0
JNK cascade 0 0.005 -9999 0 -10000 0 0
TSC1 0.05 0.007 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0.048 0.007 -9999 0 -10000 0 0
EP300 0.014 0.033 -9999 0 -0.74 1 1
mol:GDP 0 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.05 0.007 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.033 0.016 -9999 0 -0.34 1 1
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.041 0.052 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.05 0.007 -9999 0 -10000 0 0
CASP9 0.05 0.007 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.057 0.007 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.02 -9999 0 -0.47 1 1
YWHAE 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.002 0.03 -9999 0 -0.45 2 2
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.002 -9999 0 -10000 0 0
CHUK 0.05 0.007 -9999 0 -10000 0 0
BAD/BCL-XL -0.002 0.028 -9999 0 -0.56 1 1
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.022 0.019 -9999 0 -0.41 1 1
FOXO1-3a-4/14-3-3 family 0.059 0.059 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
MDM2 0.05 0.007 -9999 0 -10000 0 0
MAPKKK cascade -0.048 0.007 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.001 0.021 -9999 0 -0.48 1 1
TSC1/TSC2 0.059 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.02 -9999 0 -0.46 1 1
glucose import 0.03 0.079 -9999 0 -0.48 12 12
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.043 0.005 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.03 0.08 -9999 0 -0.48 12 12
GSK3A 0.05 0.007 -9999 0 -10000 0 0
FOXO1 0.05 0.007 -9999 0 -10000 0 0
GSK3B 0.05 0.007 -9999 0 -10000 0 0
SFN -0.083 0.27 -9999 0 -0.83 62 62
G1/S transition of mitotic cell cycle 0.059 0.007 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.036 0.078 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.006 0.059 -9999 0 -0.56 6 6
PTK2 -0.005 0.045 -9999 0 -0.77 1 1
positive regulation of JNK cascade -0.003 0.027 -9999 0 -0.37 1 1
CDC42/GDP 0.076 0.041 -9999 0 -0.51 1 1
Rac1/GDP 0.078 0.04 -9999 0 -0.5 1 1
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.003 0.033 -9999 0 -0.46 1 1
nectin-3/I-afadin -0.003 0.042 -9999 0 -0.56 3 3
RAPGEF1 0.073 0.044 -9999 0 -0.49 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.066 0.049 -9999 0 -0.57 3 3
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 0.045 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.002 0.025 -9999 0 -0.39 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.003 0.042 -9999 0 -0.56 3 3
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.077 0.049 -9999 0 -0.53 3 3
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PI3K -0.004 0.038 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.002 0.025 -9999 0 -0.33 3 3
PVRL1 0.016 0 -9999 0 -10000 0 0
PVRL3 0.011 0.057 -9999 0 -0.74 3 3
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
CLDN1 0.008 0.078 -9999 0 -0.79 5 5
JAM-A/CLDN1 -0.007 0.055 -9999 0 -0.52 2 2
SRC -0.004 0.049 -9999 0 -0.64 3 3
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.068 0.053 -9999 0 -0.53 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.003 0.035 -9999 0 -0.47 3 3
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.003 0.035 -9999 0 -0.47 3 3
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.003 0.027 -9999 0 -0.37 1 1
alphaV/beta3 Integrin/Talin -0.005 0.043 -9999 0 -0.57 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.001 0.017 -9999 0 -10000 0 0
VAV2 0.068 0.047 -9999 0 -0.54 3 3
RAP1/GDP -0.003 0.03 -9999 0 -0.46 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.003 0.035 -9999 0 -0.47 3 3
nectin-3(dimer)/I-afadin/I-afadin -0.003 0.042 -9999 0 -0.56 3 3
Rac1/GTP -0.003 0.031 -9999 0 -0.41 3 3
PTPRM -0.001 0.02 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.015 0.073 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.008 0.058 -9999 0 -0.55 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.047 -9999 0 -0.54 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.057 -9999 0 -0.74 3 3
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.031 -9999 0 -0.72 1 1
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.039 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.003 0.027 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.046 0.042 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.003 0.027 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.062 0.025 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA 0.048 0.047 -9999 0 -0.64 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
GATA1 -0.02 0.17 -9999 0 -0.86 20 20
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.045 -9999 0 -0.53 2 2
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.014 0.033 -9999 0 -0.74 1 1
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.031 -9999 0 -10000 0 0
KAT2B 0.014 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.008 0.038 -9999 0 -10000 0 0
SIN3 complex -0.019 0.097 -9999 0 -0.52 19 19
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 19 19
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.004 0.036 -9999 0 -0.64 1 1
YY1/HDAC2 -0.001 0.031 -9999 0 -0.72 1 1
YY1/HDAC1 -0.001 0.031 -9999 0 -0.72 1 1
NuRD/MBD2 Complex (MeCP1) 0.063 0.01 -9999 0 -10000 0 0
PPARG -0.006 0.046 -9999 0 -10000 0 0
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.003 0.027 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.024 -9999 0 -0.52 1 1
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.031 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.039 0.037 -9999 0 -0.81 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.034 0.019 -9999 0 -0.4 1 1
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.029 -9999 0 -0.67 1 1
YY1/SAP30/HDAC1 -0.019 0.098 -9999 0 -0.52 20 20
EP300 0.014 0.033 -9999 0 -0.74 1 1
STAT3 (dimer non-phopshorylated) 0.033 0.019 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.031 -9999 0 -10000 0 0
histone deacetylation 0.063 0.01 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.026 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.014 0.07 -9999 0 -10000 0 0
GATA1/HDAC1 -0.025 0.13 -9999 0 -0.66 20 20
GATA1/HDAC3 -0.023 0.1 -9999 0 -0.52 20 20
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.009 0.075 -9999 0 -0.61 8 8
SIN3/HDAC complex/Mad/Max 0.056 0.041 -9999 0 -10000 0 0
NuRD Complex -0.001 0.019 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.021 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.018 -9999 0 -10000 0 0
GATA1/Fog1 -0.028 0.13 -9999 0 -0.65 23 23
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
negative regulation of cell growth 0.056 0.041 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.063 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.045 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.053 0.041 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.013 0.05 -9999 0 -0.8 2 2
MBD2 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.003 0.041 -9999 0 -0.66 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.004 0.046 -9999 0 -0.48 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
NFKBIA 0.028 0.055 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.02 -9999 0 -0.47 1 1
ARRB2 0.022 0.018 -9999 0 -0.39 1 1
REL 0.01 0.066 -9999 0 -0.74 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.003 0.041 -9999 0 -0.54 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.02 -9999 0 -0.47 1 1
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
NF kappa B1 p50 dimer 0.025 0.025 -9999 0 -0.56 1 1
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
NFKB1 0.03 0.026 -9999 0 -0.56 1 1
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.054 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.008 0.037 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.034 -9999 0 -0.56 2 2
NF kappa B1 p50/RelA 0.037 0.055 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.046 -9999 0 -0.74 2 2
I kappa B alpha/PIK3R1 0.034 0.055 -9999 0 -0.39 1 1
cell death -0.008 0.035 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.004 0.046 -9999 0 -0.48 5 5
LCK -0.02 0.17 -9999 0 -0.85 22 22
BCL3 0.012 0.054 -9999 0 -0.86 2 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL 0.029 0.055 -10000 0 -10000 0 0
GRB2/SOS1/SHC -0.001 0.025 -10000 0 -0.57 1 1
HRAS 0.014 0.038 -10000 0 -0.86 1 1
IRS1/Crk -0.007 0.051 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.055 -10000 0 -0.52 6 6
AKT1 0.054 0.061 -10000 0 -0.71 1 1
BAD 0.062 0.071 -10000 0 -1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.055 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.051 -10000 0 -0.41 6 6
RAF1 0.067 0.057 -10000 0 -0.7 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.047 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.008 0.056 -10000 0 -0.45 6 6
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
RPS6KB1 0.054 0.061 -10000 0 -0.71 1 1
GNB2L1 0.014 0.038 -10000 0 -0.86 1 1
positive regulation of MAPKKK cascade 0.059 0.049 -10000 0 -0.57 1 1
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.048 -10000 0 -0.5 1 1
IGF-1R heterotetramer 0.015 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.051 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.007 0.047 -10000 0 -10000 0 0
IGF1R 0.015 0.012 -10000 0 -10000 0 0
IGF1 0.006 0.092 -10000 0 -0.85 6 6
IRS2/Crk 0.029 0.083 -10000 0 -0.49 8 8
PI3K -0.008 0.052 -10000 0 -10000 0 0
apoptosis -0.065 0.059 0.79 1 -10000 0 1
HRAS/GDP -0.001 0.029 -10000 0 -0.68 1 1
PRKCD 0.05 0.057 -10000 0 -0.82 1 1
RAF1/14-3-3 E 0.071 0.05 -10000 0 -0.57 1 1
BAD/14-3-3 0.068 0.064 -10000 0 -0.89 1 1
PRKCZ 0.052 0.068 -10000 0 -0.71 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.006 0.043 -10000 0 -0.56 1 1
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.042 0.047 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.006 0.053 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.007 0.05 -10000 0 -10000 0 0
GRB10 0.016 0 -10000 0 -10000 0 0
PTPN11 0.029 0.055 -10000 0 -0.41 6 6
IRS1 0.018 0.059 -10000 0 -0.45 6 6
IRS2 0.02 0.087 -10000 0 -0.47 14 14
IGF-1R heterotetramer/IGF1 -0.008 0.07 -10000 0 -0.66 6 6
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 0.044 0.064 -10000 0 -0.76 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 0.05 0.049 -10000 0 -10000 0 0
SHC1 0.014 0.038 -10000 0 -0.86 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.019 0 -9999 0 -10000 0 0
SMAD3 0.056 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.062 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.027 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.024 -9999 0 -0.56 1 1
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.014 0.033 -9999 0 -0.74 1 1
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
TRAIL signaling pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.014 0.033 -9999 0 -0.74 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.024 -9999 0 -0.56 1 1
MAP2K4 0.063 0.017 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
TNFRSF10B 0.014 0.038 -9999 0 -0.86 1 1
TNFRSF10A 0.014 0.033 -9999 0 -0.74 1 1
SMPD1 -0.001 0.016 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.002 0.038 -9999 0 -0.61 2 2
TRAIL/TRAILR3 -0.002 0.038 -9999 0 -0.61 2 2
TRAIL/TRAILR1 -0.002 0.034 -9999 0 -0.56 2 2
TRAIL/TRAILR4 -0.001 0.024 -9999 0 -0.56 1 1
TRAIL/TRAILR1/DAP3/GTP -0.002 0.027 -9999 0 -0.44 2 2
IKK complex -0.001 0.009 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.03 0.025 -9999 0 -0.56 1 1
MAP3K1 -0.001 0.014 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.018 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
MAPK1 0.03 0.025 -9999 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.024 -9999 0 -10000 0 0
mol:ceramide -0.001 0.016 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
MAPK8 0.07 0.031 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.038 -9999 0 -0.86 1 1
CHUK 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.029 -9999 0 -0.47 2 2
DAP3 0.016 0 -9999 0 -10000 0 0
CASP10 -0.002 0.025 -9999 0 -0.45 1 1
JNK cascade -0.001 0.024 -9999 0 -0.56 1 1
TRAIL (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TNFRSF10C 0.014 0.038 -9999 0 -0.86 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.025 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD -0.002 0.032 -9999 0 -0.52 2 2
cell death -0.001 0.016 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.017 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.014 0.038 -9999 0 -0.86 1 1
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.027 -9999 0 -0.49 1 1
Sumoylation by RanBP2 regulates transcriptional repression

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.023 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.039 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0 0 -9999 0 -10000 0 0
MAPK9 0.011 0 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.072 -9999 0 -0.68 6 6
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.011 0 -9999 0 -10000 0 0
Gs family/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.016 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
CRH -0.006 0.092 -9999 0 -0.86 6 6
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.027 -9999 0 -0.42 2 2
MAPK11 0.01 0.025 -9999 0 -0.4 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.022 -9999 0 -0.52 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.009 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.002 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 0.001 0.11 -9999 0 -0.86 9 9
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.014 0.025 -9999 0 -0.57 1 1
mol:PI-4-5-P2 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.02 -9999 0 -0.46 1 1
mol:Choline -0.001 0.016 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GDP -0.001 0.021 -9999 0 -0.46 1 1
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.018 -9999 0 -0.42 1 1
ARFIP2 0 0.003 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.034 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.006 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.01 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.005 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.043 0.034 -9999 0 -10000 0 0
PLD2 -0.001 0.016 -9999 0 -0.38 1 1
ARF-GAP1/v-SNARE 0.014 0.025 -9999 0 -0.57 1 1
PIP5K1A -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.009 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.016 -9999 0 -0.38 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.025 -9999 0 -0.57 1 1
GOSR2 0 0.007 -9999 0 -10000 0 0
USO1 0 0.007 -9999 0 -10000 0 0
GBF1 0 0.007 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.01 0.074 -9999 0 -0.57 9 9
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.005 0.058 -9999 0 -0.66 4 4
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.042 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAP3K14 0.009 0.076 -9999 0 -0.86 4 4
NF kappa B1 p50/RelB -0.001 0.024 -9999 0 -0.56 1 1
RELB 0.016 0 -9999 0 -10000 0 0
NFKB2 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 531 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T7.A92I TCGA.MW.A4EC TCGA.MM.A84U TCGA.MM.A564
109_MAP3K5 0.074 0.074 -0.13 0.074
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 1.4e-15 -0.74 -0.74
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR -0.42 -0.42 0 -0.42
30_TGFB1/TGF beta receptor Type II 0.015 0.015 0.015 0.021
84_STAT5B -0.03 -0.031 -0.14 -0.14
84_STAT5A -0.03 -0.031 -0.14 -0.14
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/11493509/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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