PARADIGM pathway analysis of mRNASeq expression and copy number data
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1F47NHQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1F47NHQ
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 35 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 164
Reelin signaling pathway 157
Ephrin A reverse signaling 97
Lissencephaly gene (LIS1) in neuronal migration and development 91
Glypican 1 network 83
IL4-mediated signaling events 76
BCR signaling pathway 72
Signaling events mediated by Stem cell factor receptor (c-Kit) 68
Fc-epsilon receptor I signaling in mast cells 65
FOXA2 and FOXA3 transcription factor networks 61
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 623 . 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 ( 623 ).

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 0.2632 164 1318 8 -0.091 0.083 1000 -1000 -0.007 -1000
Reelin signaling pathway 0.2520 157 8814 56 -0.35 0.075 1000 -1000 -0.056 -1000
Ephrin A reverse signaling 0.1557 97 681 7 -0.056 0 1000 -1000 -0.017 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1461 91 4933 54 -0.3 0.037 1000 -1000 -0.053 -1000
Glypican 1 network 0.1332 83 4016 48 -0.19 0.053 1000 -1000 -0.033 -1000
IL4-mediated signaling events 0.1220 76 6979 91 -0.79 0.56 1000 -1000 -0.18 -1000
BCR signaling pathway 0.1156 72 7194 99 -0.19 0.03 1000 -1000 -0.061 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1091 68 5349 78 -0.19 0.073 1000 -1000 -0.053 -1000
Fc-epsilon receptor I signaling in mast cells 0.1043 65 6334 97 -0.14 0.05 1000 -1000 -0.067 -1000
FOXA2 and FOXA3 transcription factor networks 0.0979 61 2830 46 -0.59 0.031 1000 -1000 -0.15 -1000
Signaling events regulated by Ret tyrosine kinase 0.0915 57 4681 82 -0.12 0.035 1000 -1000 -0.063 -1000
Syndecan-1-mediated signaling events 0.0835 52 1786 34 -0.42 0.029 1000 -1000 -0.046 -1000
p75(NTR)-mediated signaling 0.0835 52 6524 125 -0.46 0.071 1000 -1000 -0.084 -1000
Signaling events mediated by the Hedgehog family 0.0819 51 2660 52 -0.059 0.059 1000 -1000 -0.036 -1000
HIF-1-alpha transcription factor network 0.0819 51 3895 76 -0.56 0.036 1000 -1000 -0.17 -1000
BMP receptor signaling 0.0803 50 4101 81 -0.18 0.052 1000 -1000 -0.048 -1000
Visual signal transduction: Rods 0.0787 49 2597 52 -0.19 0.035 1000 -1000 -0.041 -1000
Endothelins 0.0770 48 4659 96 -0.22 0.061 1000 -1000 -0.059 -1000
Syndecan-2-mediated signaling events 0.0754 47 3271 69 -0.23 0.046 1000 -1000 -0.036 -1000
JNK signaling in the CD4+ TCR pathway 0.0690 43 735 17 -0.13 0.041 1000 -1000 -0.033 -1000
Visual signal transduction: Cones 0.0658 41 1572 38 -0.11 0.038 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.0642 40 3460 86 -0.23 0.079 1000 -1000 -0.058 -1000
LPA receptor mediated events 0.0610 38 3936 102 -0.17 0.036 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 0.0610 38 657 17 -0.062 0.049 1000 -1000 -0.03 -1000
TCR signaling in naïve CD8+ T cells 0.0594 37 3487 93 -0.037 0.04 1000 -1000 -0.049 -1000
IGF1 pathway 0.0594 37 2123 57 -0.065 0.054 1000 -1000 -0.049 -1000
Wnt signaling 0.0578 36 255 7 -0.069 0.024 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 0.0562 35 935 26 -0.07 0.049 1000 -1000 -0.016 -1000
IL23-mediated signaling events 0.0562 35 2101 60 -0.27 0.033 1000 -1000 -0.13 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0562 35 3104 88 -0.14 0.061 1000 -1000 -0.074 -1000
LPA4-mediated signaling events 0.0546 34 408 12 -0.097 0.007 1000 -1000 -0.028 -1000
Osteopontin-mediated events 0.0546 34 1308 38 -0.17 0.04 1000 -1000 -0.05 -1000
amb2 Integrin signaling 0.0514 32 2626 82 -0.095 0.037 1000 -1000 -0.05 -1000
Canonical Wnt signaling pathway 0.0514 32 1661 51 -0.28 0.14 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 0.0514 32 1712 52 -0.12 0.063 1000 -1000 -0.04 -1000
Presenilin action in Notch and Wnt signaling 0.0498 31 1915 61 -0.28 0.14 1000 -1000 -0.043 -1000
IL1-mediated signaling events 0.0498 31 1978 62 -0.12 0.063 1000 -1000 -0.044 -1000
Ephrin B reverse signaling 0.0498 31 1504 48 -0.07 0.031 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 0.0498 31 1087 34 -0.062 0.086 1000 -1000 -0.049 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0465 29 1525 52 -0.18 0.061 1000 -1000 -0.053 -1000
TCGA08_p53 0.0465 29 208 7 -0.054 0.028 1000 -1000 -0.007 -1000
Calcium signaling in the CD4+ TCR pathway 0.0465 29 900 31 -0.27 0.028 1000 -1000 -0.053 -1000
Thromboxane A2 receptor signaling 0.0449 28 2968 105 -0.18 0.067 1000 -1000 -0.043 -1000
EPHB forward signaling 0.0449 28 2437 85 -0.071 0.087 1000 -1000 -0.071 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0449 28 3366 120 -0.097 0.088 1000 -1000 -0.053 -1000
Signaling mediated by p38-alpha and p38-beta 0.0433 27 1224 44 -0.035 0.029 1000 -1000 -0.041 -1000
Arf6 signaling events 0.0417 26 1615 62 -0.12 0.062 1000 -1000 -0.04 -1000
Glucocorticoid receptor regulatory network 0.0417 26 3013 114 -0.32 0.19 1000 -1000 -0.062 -1000
S1P5 pathway 0.0417 26 454 17 -0.12 0.052 1000 -1000 -0.023 -1000
Syndecan-3-mediated signaling events 0.0417 26 910 35 -0.23 0.071 1000 -1000 -0.032 -1000
EGFR-dependent Endothelin signaling events 0.0417 26 549 21 -0.06 0.04 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0417 26 2601 97 -0.14 0.09 1000 -1000 -0.058 -1000
Syndecan-4-mediated signaling events 0.0401 25 1740 67 -0.23 0.04 1000 -1000 -0.051 -1000
S1P4 pathway 0.0401 25 644 25 -0.12 0.043 1000 -1000 -0.035 -1000
IL12-mediated signaling events 0.0385 24 2121 87 -0.1 0.051 1000 -1000 -0.1 -1000
Nectin adhesion pathway 0.0369 23 1452 63 -0.4 0.076 1000 -1000 -0.06 -1000
HIF-2-alpha transcription factor network 0.0369 23 1015 43 -0.33 0.16 1000 -1000 -0.085 -1000
Integrins in angiogenesis 0.0353 22 1880 84 -0.18 0.065 1000 -1000 -0.054 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0353 22 1528 68 -0.28 0.038 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.0337 21 1565 74 -0.085 0.064 1000 -1000 -0.041 -1000
Noncanonical Wnt signaling pathway 0.0337 21 546 26 -0.069 0.027 1000 -1000 -0.047 -1000
a4b1 and a4b7 Integrin signaling 0.0337 21 107 5 0.013 0.03 1000 -1000 0.001 -1000
Regulation of Androgen receptor activity 0.0321 20 1429 70 -0.21 0.06 1000 -1000 -0.064 -1000
Signaling events mediated by PTP1B 0.0305 19 1461 76 -0.19 0.047 1000 -1000 -0.046 -1000
Ceramide signaling pathway 0.0305 19 1510 76 -0.062 0.07 1000 -1000 -0.04 -1000
S1P3 pathway 0.0305 19 827 42 -0.11 0.046 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class III 0.0289 18 757 40 -0.13 0.052 1000 -1000 -0.02 -1000
S1P1 pathway 0.0289 18 664 36 -0.12 0.044 1000 -1000 -0.052 -1000
FAS signaling pathway (CD95) 0.0289 18 851 47 -0.03 0.044 1000 -1000 -0.043 -1000
Regulation of p38-alpha and p38-beta 0.0289 18 997 54 -0.09 0.054 1000 -1000 -0.051 -1000
Glypican 2 network 0.0289 18 75 4 0.013 0.025 1000 -1000 -0.001 -1000
Aurora B signaling 0.0289 18 1208 67 -0.41 0.095 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 0.0273 17 1362 76 -0.19 0.064 1000 -1000 -0.022 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0257 16 544 34 -0.027 0.064 1000 -1000 -0.031 -1000
Class I PI3K signaling events 0.0257 16 1179 73 -0.09 0.044 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 0.0241 15 980 65 -0.046 0.04 1000 -1000 -0.054 -1000
Regulation of nuclear SMAD2/3 signaling 0.0241 15 2089 136 -0.44 0.068 1000 -1000 -0.047 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0241 15 447 28 -0.12 0.044 1000 -1000 -0.03 -1000
Cellular roles of Anthrax toxin 0.0241 15 613 39 -0.048 0.031 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0241 15 578 37 -0.15 0.06 1000 -1000 -0.04 -1000
VEGFR1 specific signals 0.0241 15 880 56 -0.013 0.093 1000 -1000 -0.052 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0241 15 525 33 -0.061 0.066 1000 -1000 -0.033 -1000
ErbB4 signaling events 0.0225 14 976 69 -0.16 0.08 1000 -1000 -0.051 -1000
PLK1 signaling events 0.0225 14 1247 85 -0.01 0.06 1000 -1000 -0.038 -1000
Retinoic acid receptors-mediated signaling 0.0225 14 813 58 -0.15 0.051 1000 -1000 -0.038 -1000
IL6-mediated signaling events 0.0225 14 1123 75 -0.059 0.059 1000 -1000 -0.082 -1000
Class I PI3K signaling events mediated by Akt 0.0209 13 938 68 -0.053 0.064 1000 -1000 -0.037 -1000
Signaling mediated by p38-gamma and p38-delta 0.0209 13 200 15 -0.058 0.027 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0193 12 1069 83 -0.13 0.07 1000 -1000 -0.043 -1000
FoxO family signaling 0.0193 12 787 64 -0.056 0.065 1000 -1000 -0.072 -1000
Arf6 downstream pathway 0.0177 11 506 43 -0.029 0.043 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0177 11 353 32 -0.14 0.045 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 0.0177 11 516 44 -0.013 0.064 1000 -1000 -0.042 -1000
Arf6 trafficking events 0.0177 11 795 71 -0.048 0.049 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0161 10 502 49 0 0.045 1000 -1000 -0.046 -1000
FOXM1 transcription factor network 0.0161 10 534 51 -0.096 0.089 1000 -1000 -0.14 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0144 9 805 85 -0.035 0.065 1000 -1000 -0.05 -1000
Hedgehog signaling events mediated by Gli proteins 0.0144 9 589 65 -0.12 0.05 1000 -1000 -0.042 -1000
EPO signaling pathway 0.0144 9 511 55 -0.004 0.065 1000 -1000 -0.049 -1000
IFN-gamma pathway 0.0144 9 659 68 -0.031 0.04 1000 -1000 -0.06 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0144 9 410 45 -0.009 0.073 1000 -1000 -0.053 -1000
IL27-mediated signaling events 0.0144 9 501 51 -0.064 0.042 1000 -1000 -0.052 -1000
TCGA08_rtk_signaling 0.0144 9 238 26 -0.031 0.062 1000 -1000 -0.021 -1000
Regulation of Telomerase 0.0144 9 1017 102 -0.2 0.065 1000 -1000 -0.08 -1000
mTOR signaling pathway 0.0128 8 458 53 -0.067 0.038 1000 -1000 -0.04 -1000
Rapid glucocorticoid signaling 0.0128 8 164 20 -0.016 0.026 1000 -1000 -0.007 -1000
IL2 signaling events mediated by PI3K 0.0112 7 455 58 -0.014 0.046 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class II 0.0096 6 514 75 -0.026 0.07 1000 -1000 -0.036 -1000
Aurora A signaling 0.0096 6 406 60 -0.086 0.076 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0096 6 448 74 -0.062 0.065 1000 -1000 -0.068 -1000
E-cadherin signaling in the nascent adherens junction 0.0096 6 520 76 -0.011 0.093 1000 -1000 -0.071 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 5 648 125 -0.01 0.098 1000 -1000 -0.06 -1000
Class IB PI3K non-lipid kinase events 0.0080 5 15 3 -0.024 0.024 1000 -1000 -0.001 -1000
Arf1 pathway 0.0080 5 272 54 -0.001 0.046 1000 -1000 -0.024 -1000
TRAIL signaling pathway 0.0064 4 212 48 -0.011 0.059 1000 -1000 -0.041 -1000
Paxillin-dependent events mediated by a4b1 0.0064 4 173 36 -0.049 0.051 1000 -1000 -0.042 -1000
Insulin Pathway 0.0064 4 301 74 -0.026 0.085 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 0.0064 4 200 44 -0.013 0.058 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 0.0048 3 10 3 0.01 0.027 1000 -1000 -0.019 -1000
IL2 signaling events mediated by STAT5 0.0048 3 81 22 0.006 0.042 1000 -1000 -0.044 -1000
Canonical NF-kappaB pathway 0.0032 2 96 39 0 0.06 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class I 0.0032 2 231 104 -0.054 0.066 1000 -1000 -0.036 -1000
Circadian rhythm pathway 0.0016 1 26 22 -0.01 0.065 1000 -1000 -0.037 -1000
Aurora C signaling 0.0016 1 9 7 0 0.041 1000 -1000 -0.016 -1000
Atypical NF-kappaB pathway 0.0016 1 35 31 0 0.057 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 0.0016 1 54 43 -0.047 0.086 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 17 23 0.013 0.04 1000 -1000 -0.025 -1000
BARD1 signaling events 0.0000 0 47 57 -0.056 0.078 1000 -1000 -0.053 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 17 27 0 0.052 1000 -1000 -0.039 -1000
E-cadherin signaling events 0.0000 0 2 5 0.027 0.054 1000 -1000 0.002 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.076 1000 -1000 -0.002 -1000
Total NA 3348 193030 7203 -16 8 131000 -131000 -6.2 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.091 0.17 -10000 0 -0.33 206 206
CDKN2C 0.033 0.026 -10000 0 -10000 0 0
CDKN2A -0.065 0.19 0.34 2 -0.46 115 117
CCND2 0.07 0.092 0.19 207 -10000 0 207
RB1 -0.056 0.1 0.28 9 -0.2 173 182
CDK4 0.076 0.097 0.2 202 -0.14 1 203
CDK6 0.083 0.1 0.21 218 -10000 0 218
G1/S progression 0.062 0.1 0.2 175 -0.28 10 185
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.018 -10000 0 -0.32 1 1
VLDLR -0.003 0.1 -10000 0 -0.36 47 47
CRKL 0.027 0.006 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.027 0.016 -10000 0 -0.36 1 1
RELN/VLDLR/Fyn -0.084 0.15 -10000 0 -0.24 278 278
MAPK8IP1/MKK7/MAP3K11/JNK1 0.075 0.035 -10000 0 -0.51 1 1
AKT1 -0.099 0.13 -10000 0 -0.33 78 78
MAP2K7 0.027 0.016 -10000 0 -0.36 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
DAB1 -0.036 0.15 -10000 0 -0.45 71 71
RELN/LRP8/DAB1 -0.26 0.17 -10000 0 -0.33 505 505
LRPAP1/LRP8 -0.21 0.17 0.26 1 -0.32 423 424
RELN/LRP8/DAB1/Fyn -0.25 0.16 -10000 0 -0.33 440 440
DAB1/alpha3/beta1 Integrin -0.24 0.17 -10000 0 -0.4 248 248
long-term memory -0.35 0.21 -10000 0 -0.48 381 381
DAB1/LIS1 -0.24 0.17 -10000 0 -0.41 255 255
DAB1/CRLK/C3G -0.24 0.17 -10000 0 -0.4 252 252
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DAB1/NCK2 -0.25 0.18 -10000 0 -0.41 255 255
ARHGEF2 0.027 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.085 0.16 -10000 0 -0.36 157 157
CDK5R1 0.026 0.019 -10000 0 -0.44 1 1
RELN -0.16 0.19 -10000 0 -0.36 283 283
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.26 0.17 0.25 1 -0.34 482 483
GRIN2A/RELN/LRP8/DAB1/Fyn -0.29 0.19 -10000 0 -0.38 457 457
MAPK8 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.15 -10000 0 -0.24 314 314
ITGB1 0.028 0.002 -10000 0 -10000 0 0
MAP1B -0.26 0.17 -10000 0 -0.42 266 266
RELN/LRP8 -0.26 0.17 0.25 1 -0.34 485 486
GRIN2B/RELN/LRP8/DAB1/Fyn -0.32 0.2 -10000 0 -0.4 475 475
PI3K 0.039 0.015 -10000 0 -0.25 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.014 -10000 0 -0.25 1 1
RAP1A -0.24 0.15 0.32 2 -0.39 247 249
PAFAH1B1 0.023 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.025 -10000 0 -0.4 2 2
CRLK/C3G 0.038 0.015 -10000 0 -0.25 1 1
GRIN2B -0.13 0.22 0.36 1 -0.44 201 202
NCK2 0.028 0.001 -10000 0 -10000 0 0
neuron differentiation -0.13 0.12 0.23 1 -0.26 222 223
neuron adhesion -0.23 0.15 0.3 3 -0.38 233 236
LRP8 -0.3 0.22 0.36 1 -0.44 424 425
GSK3B -0.097 0.12 -10000 0 -0.32 75 75
RELN/VLDLR/DAB1/Fyn -0.092 0.15 -10000 0 -0.32 98 98
MAP3K11 0.026 0.016 -10000 0 -0.36 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.14 -10000 0 -0.29 131 131
CDK5 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.054 0.17 0.83 8 -0.32 124 132
neuron migration -0.23 0.16 0.27 4 -0.4 233 237
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.12 -10000 0 -0.26 219 219
RELN/VLDLR -0.24 0.18 0.25 1 -0.34 418 419
Ephrin A reverse signaling

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
MAPKKK cascade -0.03 0.11 -10000 0 -0.22 149 149
EFNA5 -0.056 0.16 -10000 0 -0.36 130 130
FYN -0.045 0.091 0.18 1 -0.22 74 75
neuron projection morphogenesis -0.03 0.11 -10000 0 -0.22 149 149
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.03 0.11 -10000 0 -0.22 149 149
EPHA5 -0.012 0.081 -10000 0 -0.36 29 29
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR -0.003 0.1 -10000 0 -0.36 47 47
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.26 0.17 0.25 1 -0.34 485 486
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.24 0.16 0.18 9 -0.33 405 414
IQGAP1/CaM 0.037 0.013 -10000 0 -10000 0 0
DAB1 -0.036 0.15 -10000 0 -0.45 71 71
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
PLA2G7 0.024 0.038 -10000 0 -0.36 6 6
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.21 0.17 0.26 1 -0.32 423 424
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.016 -10000 0 -0.36 1 1
CDK5R1 0.026 0.019 -10000 0 -0.44 1 1
LIS1/Poliovirus Protein 3A 0.007 0.005 -10000 0 -10000 0 0
CDK5R2 -0.02 0.12 -10000 0 -0.37 63 63
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.12 0.16 -10000 0 -0.26 314 314
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.2 0.15 0.32 6 -0.35 226 232
MAP1B 0.001 0.032 -10000 0 -0.24 11 11
RAC1 0.01 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.21 0.14 0.18 2 -0.37 197 199
RELN -0.16 0.19 -10000 0 -0.36 283 283
PAFAH/LIS1 0.02 0.026 -10000 0 -0.2 6 6
LIS1/CLIP170 0.022 0.017 -10000 0 -0.21 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.17 0.12 -10000 0 -0.3 178 178
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.097 0.15 -10000 0 -0.37 89 89
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.22 0.15 0.28 7 -0.36 251 258
LIS1/IQGAP1 0.022 0.014 -10000 0 -10000 0 0
RHOA 0.01 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.062 -10000 0 -0.44 11 11
PAFAH1B2 0.027 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.013 0.039 -10000 0 -0.23 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.15 0.32 5 -0.35 224 229
LRP8 -0.3 0.22 0.36 1 -0.44 424 425
NDEL1/Katanin 60 -0.21 0.15 0.32 5 -0.36 227 232
P39/CDK5 -0.23 0.15 0.18 2 -0.39 235 237
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.014 -10000 0 -10000 0 0
CDK5 -0.23 0.14 0.17 3 -0.39 203 206
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.014 -10000 0 -0.18 1 1
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.085 0.14 -10000 0 -0.32 85 85
RELN/VLDLR -0.24 0.18 0.25 1 -0.34 418 419
CDC42 0.01 0.016 -10000 0 -0.35 1 1
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.069 -10000 0 -0.21 38 38
fibroblast growth factor receptor signaling pathway 0.029 0.069 -10000 0 -0.21 38 38
LAMA1 -0.054 0.15 -10000 0 -0.36 121 121
PRNP 0.021 0.024 -10000 0 -0.36 2 2
GPC1/SLIT2 -0.044 0.13 -10000 0 -0.25 176 176
SMAD2 0.011 0.022 0.18 4 -0.24 1 5
GPC1/PrPc/Cu2+ 0.029 0.025 -10000 0 -0.22 4 4
GPC1/Laminin alpha1 -0.026 0.12 -10000 0 -0.25 123 123
TDGF1 -0.19 0.24 0.36 1 -0.44 290 291
CRIPTO/GPC1 -0.13 0.18 0.26 1 -0.32 291 292
APP/GPC1 0.037 0.024 -10000 0 -0.27 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.12 0.14 0.2 1 -0.26 289 290
FLT1 0.021 0.012 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.023 -10000 0 -0.23 3 3
SERPINC1 0.003 0.061 -10000 0 -0.44 10 10
FYN -0.12 0.14 0.2 1 -0.27 288 289
FGR -0.12 0.14 0.2 1 -0.27 291 292
positive regulation of MAPKKK cascade -0.044 0.12 0.21 33 -0.31 45 78
SLIT2 -0.084 0.17 -10000 0 -0.36 174 174
GPC1/NRG 0.004 0.085 -10000 0 -0.25 58 58
NRG1 -0.015 0.11 -10000 0 -0.36 56 56
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.041 0.031 0.25 1 -0.24 2 3
LYN -0.11 0.14 0.2 1 -0.27 260 261
mol:Spermine 0.006 0.017 -10000 0 -0.28 2 2
cell growth 0.029 0.069 -10000 0 -0.21 38 38
BMP signaling pathway -0.026 0.025 0.4 2 -10000 0 2
SRC -0.063 0.11 0.2 1 -0.27 125 126
TGFBR1 0.027 0.016 -10000 0 -0.36 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.071 0.17 -10000 0 -0.36 151 151
GPC1 0.026 0.025 -10000 0 -0.4 2 2
TGFBR1 (dimer) 0.027 0.016 -10000 0 -0.36 1 1
VEGFA 0.028 0.019 0.36 2 -10000 0 2
BLK -0.18 0.16 0.2 1 -0.29 378 379
HCK -0.066 0.11 0.2 1 -0.27 130 131
FGF2 0 0.099 -10000 0 -0.36 43 43
FGFR1 0.021 0.032 -10000 0 -0.36 4 4
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
cell death 0.037 0.024 -10000 0 -0.27 3 3
ATIII/GPC1 0.03 0.049 -10000 0 -0.31 12 12
PLA2G2A/GPC1 -0.036 0.13 -10000 0 -0.26 153 153
LCK -0.12 0.14 0.2 1 -0.27 297 298
neuron differentiation 0.004 0.085 -10000 0 -0.25 58 58
PrPc/Cu2+ 0.016 0.017 -10000 0 -0.25 2 2
APP 0.026 0.017 -10000 0 -0.36 1 1
TGFBR2 (dimer) 0.027 0.003 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.45 0.49 -10000 0 -1.2 109 109
STAT6 (cleaved dimer) -0.55 0.51 -10000 0 -1.2 178 178
IGHG1 -0.16 0.16 -10000 0 -10000 0 0
IGHG3 -0.49 0.46 -10000 0 -1.1 155 155
AKT1 -0.27 0.29 -10000 0 -0.78 76 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.24 -10000 0 -0.86 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.28 -10000 0 -1 33 33
THY1 -0.52 0.48 -10000 0 -1.2 129 129
MYB 0.026 0.016 -10000 0 -0.36 1 1
HMGA1 0.027 0.023 0.36 1 -0.44 1 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.35 -10000 0 -0.84 148 148
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.28 -10000 0 -1 31 31
SP1 0.027 0.02 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
SOCS5 0.045 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.51 -10000 0 -1.2 170 170
SOCS1 -0.37 0.31 -10000 0 -0.77 127 127
SOCS3 -0.31 0.29 -10000 0 -0.77 94 94
FCER2 -0.79 0.65 -10000 0 -1.4 308 308
PARP14 0.009 0.03 -10000 0 -10000 0 0
CCL17 -0.52 0.48 -10000 0 -1.2 127 127
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.73 26 26
T cell proliferation -0.51 0.5 -10000 0 -1.3 133 133
IL4R/JAK1 -0.52 0.49 -10000 0 -1.2 134 134
EGR2 -0.59 0.52 -10000 0 -1.3 143 143
JAK2 -0.032 0.049 -10000 0 -0.39 3 3
JAK3 0.015 0.032 -10000 0 -0.44 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 -0.006 0.025 -10000 0 -10000 0 0
COL1A2 -0.15 0.16 -10000 0 -0.55 16 16
CCL26 -0.53 0.48 -10000 0 -1.2 132 132
IL4R -0.54 0.51 -10000 0 -1.3 130 130
PTPN6 0.038 0.014 -10000 0 -10000 0 0
IL13RA2 -0.53 0.48 -10000 0 -1.2 129 129
IL13RA1 -0.032 0.042 -10000 0 -10000 0 0
IRF4 -0.44 0.62 -10000 0 -1.4 171 171
ARG1 -0.089 0.14 -10000 0 -0.61 6 6
CBL -0.35 0.33 -10000 0 -0.8 148 148
GTF3A 0.023 0.073 0.34 23 -0.44 1 24
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
IL13RA1/JAK2 -0.037 0.061 -10000 0 -0.28 3 3
IRF4/BCL6 -0.38 0.58 -10000 0 -1.3 171 171
CD40LG -0.038 0.1 -10000 0 -0.38 42 42
MAPK14 -0.34 0.32 -10000 0 -0.82 134 134
mitosis -0.26 0.27 -10000 0 -0.73 73 73
STAT6 -0.58 0.58 -10000 0 -1.4 155 155
SPI1 0.024 0.047 -10000 0 -0.36 9 9
RPS6KB1 -0.25 0.26 -10000 0 -0.72 67 67
STAT6 (dimer) -0.58 0.57 -10000 0 -1.4 155 155
STAT6 (dimer)/PARP14 -0.59 0.55 -10000 0 -1.3 163 163
mast cell activation 0.014 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.29 0.29 -10000 0 -0.75 100 100
FRAP1 -0.27 0.29 -10000 0 -0.78 75 75
LTA -0.52 0.49 -10000 0 -1.3 126 126
FES 0.025 0.023 -10000 0 -0.36 2 2
T-helper 1 cell differentiation 0.56 0.55 1.3 155 -10000 0 155
CCL11 -0.55 0.54 -10000 0 -1.3 157 157
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.27 -10000 0 -0.76 61 61
IL2RG 0.014 0.037 -10000 0 -0.35 3 3
IL10 -0.54 0.52 -10000 0 -1.3 141 141
IRS1 0.028 0.002 -10000 0 -10000 0 0
IRS2 0.022 0.012 -10000 0 -10000 0 0
IL4 -0.14 0.2 -10000 0 -1.1 17 17
IL5 -0.52 0.48 -10000 0 -1.2 146 146
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.41 0.38 -10000 0 -0.95 111 111
COL1A1 -0.19 0.21 -10000 0 -1 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.5 -10000 0 -1.3 125 125
IL2R gamma/JAK3 0.018 0.045 -10000 0 -0.27 4 4
TFF3 -0.53 0.5 -10000 0 -1.3 135 135
ALOX15 -0.53 0.5 -10000 0 -1.2 154 154
MYBL1 0.023 0.028 -10000 0 -0.44 2 2
T-helper 2 cell differentiation -0.43 0.4 -10000 0 -0.99 137 137
SHC1 0.027 0.004 -10000 0 -10000 0 0
CEBPB 0.016 0.047 0.36 3 -0.44 4 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.27 -10000 0 -0.95 34 34
mol:PI-3-4-5-P3 -0.27 0.29 -10000 0 -0.78 75 75
PI3K -0.28 0.31 -10000 0 -0.84 75 75
DOK2 0.016 0.045 -10000 0 -0.36 8 8
ETS1 0.036 0.026 -10000 0 -0.32 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.65 29 29
ITGB3 -0.51 0.49 -10000 0 -1.2 142 142
PIGR -0.69 0.65 -10000 0 -1.5 229 229
IGHE 0.082 0.073 0.18 126 -10000 0 126
MAPKKK cascade -0.19 0.19 -10000 0 -0.64 29 29
BCL6 0.034 0.011 -10000 0 -10000 0 0
OPRM1 -0.52 0.48 -10000 0 -1.2 126 126
RETNLB -0.74 0.66 -10000 0 -1.4 263 263
SELP -0.57 0.56 -10000 0 -1.4 157 157
AICDA -0.49 0.46 -10000 0 -1.2 136 136
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.11 0.2 0.34 2 -0.46 120 122
IKBKB -0.037 0.11 0.28 3 -0.29 51 54
AKT1 -0.077 0.11 0.27 7 -0.26 112 119
IKBKG -0.037 0.1 0.41 1 -0.28 54 55
CALM1 -0.097 0.21 0.29 1 -0.53 95 96
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
MAP3K1 -0.14 0.27 0.47 2 -0.62 115 117
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.23 0.31 1 -0.56 99 100
DOK1 0.028 0.001 -10000 0 -10000 0 0
AP-1 -0.067 0.11 0.24 2 -0.27 104 106
LYN 0.024 0.009 -10000 0 -10000 0 0
BLNK 0.022 0.041 -10000 0 -0.36 7 7
SHC1 0.027 0.004 -10000 0 -10000 0 0
BCR complex -0.091 0.18 -10000 0 -0.32 220 220
CD22 -0.18 0.3 -10000 0 -0.62 154 154
CAMK2G -0.092 0.19 0.28 1 -0.49 95 96
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
SHC/GRB2/SOS1 -0.047 0.12 -10000 0 -0.32 63 63
GO:0007205 -0.11 0.23 0.31 1 -0.57 99 100
SYK 0.027 0.004 -10000 0 -10000 0 0
ELK1 -0.1 0.22 0.29 1 -0.54 95 96
NFATC1 -0.16 0.24 0.31 2 -0.52 150 152
B-cell antigen/BCR complex -0.091 0.18 -10000 0 -0.32 220 220
PAG1/CSK 0.03 0.039 -10000 0 -0.25 10 10
NFKBIB -0.001 0.048 0.14 4 -0.13 32 36
HRAS -0.082 0.18 0.25 3 -0.46 94 97
NFKBIA 0 0.047 0.14 4 -0.12 32 36
NF-kappa-B/RelA/I kappa B beta 0.005 0.04 0.16 3 -10000 0 3
RasGAP/Csk -0.054 0.18 -10000 0 -0.41 91 91
mol:GDP -0.098 0.22 0.3 1 -0.55 96 97
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B -0.024 0.13 -10000 0 -0.36 80 80
NF-kappa-B/RelA/I kappa B alpha 0.006 0.04 0.16 3 -10000 0 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.17 0.26 0.33 2 -0.54 169 171
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 0.31 1 -0.58 99 100
CSK 0.027 0.006 -10000 0 -10000 0 0
FOS -0.096 0.2 0.28 1 -0.5 98 99
CHUK -0.046 0.12 0.41 1 -0.29 71 72
IBTK 0.027 0.016 -10000 0 -0.36 1 1
CARD11/BCL10/MALT1/TAK1 -0.071 0.2 0.24 1 -0.47 91 92
PTPN6 -0.17 0.28 0.26 1 -0.59 150 151
RELA 0.027 0.004 -10000 0 -10000 0 0
BCL2A1 0.005 0.029 0.18 1 -0.13 1 2
VAV2 -0.18 0.3 -10000 0 -0.62 153 153
ubiquitin-dependent protein catabolic process 0.001 0.047 0.14 4 -0.12 31 35
BTK -0.11 0.36 -10000 0 -1.1 74 74
CD19 -0.17 0.29 -10000 0 -0.59 163 163
MAP4K1 -0.006 0.11 -10000 0 -0.36 53 53
CD72 0.026 0.016 -10000 0 -0.36 1 1
PAG1 0.018 0.05 -10000 0 -0.36 10 10
MAPK14 -0.12 0.22 0.45 3 -0.52 113 116
SH3BP5 0.024 0.035 -10000 0 -0.36 5 5
PIK3AP1 -0.097 0.23 0.27 2 -0.56 98 100
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.13 0.28 -10000 0 -0.61 115 115
RAF1 -0.078 0.17 0.24 3 -0.43 93 96
RasGAP/p62DOK/SHIP -0.05 0.18 -10000 0 -0.4 91 91
CD79A -0.11 0.19 -10000 0 -0.36 219 219
re-entry into mitotic cell cycle -0.067 0.11 0.24 2 -0.27 104 106
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.067 0.14 0.23 4 -0.38 81 85
MAPK1 -0.067 0.14 0.22 3 -0.38 81 84
CD72/SHP1 -0.15 0.27 0.23 1 -0.56 147 148
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.12 0.22 0.45 2 -0.52 113 115
actin cytoskeleton organization -0.14 0.24 0.31 2 -0.53 144 146
NF-kappa-B/RelA 0.014 0.079 0.33 2 -0.2 9 11
Calcineurin -0.067 0.18 0.27 1 -0.47 82 83
PI3K -0.15 0.22 -10000 0 -0.47 167 167
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.1 0.24 0.29 2 -0.58 103 105
SOS1 0.028 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.17 0.35 -10000 0 -0.82 118 118
DAPP1 -0.19 0.38 -10000 0 -0.91 117 117
cytokine secretion -0.14 0.22 0.3 2 -0.48 150 152
mol:DAG -0.11 0.24 0.31 1 -0.58 99 100
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
MAP2K1 -0.074 0.16 0.24 3 -0.42 82 85
B-cell antigen/BCR complex/FcgammaRIIB -0.084 0.2 -10000 0 -0.32 226 226
mol:PI-3-4-5-P3 -0.11 0.14 0.16 1 -0.35 121 122
ETS1 -0.085 0.18 0.26 1 -0.46 91 92
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.15 -10000 0 -0.35 65 65
B-cell antigen/BCR complex/LYN -0.14 0.27 -10000 0 -0.64 114 114
MALT1 0.02 0.02 -10000 0 -0.36 1 1
TRAF6 0.028 0.003 -10000 0 -10000 0 0
RAC1 -0.15 0.27 0.31 2 -0.57 143 145
B-cell antigen/BCR complex/LYN/SYK -0.14 0.28 0.27 1 -0.58 140 141
CARD11 -0.097 0.23 0.26 5 -0.54 103 108
FCGR2B -0.019 0.12 -10000 0 -0.36 72 72
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.026 0.016 -10000 0 -0.36 1 1
IKK complex -0.011 0.048 0.14 9 -0.12 13 22
PTPRC -0.003 0.1 -10000 0 -0.36 48 48
PDPK1 -0.078 0.1 0.18 7 -0.25 106 113
PPP3CB 0.027 0.004 -10000 0 -10000 0 0
PPP3CC 0.021 0.012 -10000 0 -10000 0 0
POU2F2 0.004 0.033 0.21 2 -10000 0 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.065 0.17 -10000 0 -0.42 101 101
CRKL -0.055 0.16 0.2 1 -0.41 100 101
HRAS -0.041 0.16 -10000 0 -0.37 104 104
mol:PIP3 -0.044 0.16 0.26 2 -0.38 96 98
SPRED1 0.026 0.007 -10000 0 -10000 0 0
SPRED2 0.028 0.001 -10000 0 -10000 0 0
GAB1 -0.056 0.17 -10000 0 -0.43 101 101
FOXO3 -0.051 0.18 0.29 2 -0.41 107 109
AKT1 -0.054 0.2 0.27 1 -0.44 108 109
BAD -0.051 0.18 0.26 1 -0.41 108 109
megakaryocyte differentiation -0.073 0.18 -10000 0 -0.44 103 103
GSK3B -0.05 0.18 0.32 2 -0.41 106 108
RAF1 -0.036 0.13 0.24 1 -0.31 100 101
SHC1 0.027 0.004 -10000 0 -10000 0 0
STAT3 -0.057 0.17 -10000 0 -0.43 100 100
STAT1 -0.14 0.39 -10000 0 -0.95 111 111
HRAS/SPRED1 -0.024 0.14 -10000 0 -0.31 96 96
cell proliferation -0.055 0.17 -10000 0 -0.42 101 101
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
TEC 0.026 0.02 -10000 0 -0.44 1 1
RPS6KB1 -0.051 0.18 -10000 0 -0.43 105 105
HRAS/SPRED2 -0.023 0.14 -10000 0 -0.31 99 99
LYN/TEC/p62DOK -0.019 0.17 -10000 0 -0.41 85 85
MAPK3 -0.023 0.099 0.19 2 -0.26 39 41
STAP1 -0.092 0.19 -10000 0 -0.47 107 107
GRAP2 0.014 0.069 -10000 0 -0.36 20 20
JAK2 -0.12 0.34 -10000 0 -0.81 110 110
STAT1 (dimer) -0.14 0.38 -10000 0 -0.93 111 111
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.032 0.2 -10000 0 -0.44 101 101
actin filament polymerization -0.057 0.17 0.2 1 -0.41 100 101
LYN 0.024 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.25 -10000 0 -0.63 105 105
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.028 0.16 -10000 0 -0.38 98 98
PI3K -0.027 0.19 -10000 0 -0.42 98 98
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.15 0.46 -10000 0 -1.2 98 98
MAPK8 -0.057 0.17 -10000 0 -0.43 101 101
STAT3 (dimer) -0.055 0.17 -10000 0 -0.42 100 100
positive regulation of transcription -0.017 0.083 0.17 3 -0.21 37 40
mol:GDP -0.039 0.17 -10000 0 -0.39 103 103
PIK3C2B -0.056 0.17 -10000 0 -0.43 100 100
CBL/CRKL -0.039 0.16 -10000 0 -0.39 100 100
FER -0.058 0.17 -10000 0 -0.43 101 101
SH2B3 -0.056 0.17 -10000 0 -0.43 100 100
PDPK1 -0.04 0.15 0.25 5 -0.36 93 98
SNAI2 -0.055 0.16 -10000 0 -0.41 100 100
positive regulation of cell proliferation -0.097 0.29 -10000 0 -0.7 110 110
KITLG 0.011 0.066 -10000 0 -0.39 14 14
cell motility -0.097 0.29 -10000 0 -0.7 110 110
PTPN6 0.029 0.011 -10000 0 -10000 0 0
EPOR -0.012 0.14 -10000 0 -1 2 2
STAT5A (dimer) -0.076 0.24 -10000 0 -0.59 101 101
SOCS1 0.011 0.086 -10000 0 -0.44 21 21
cell migration 0.073 0.18 0.45 102 -10000 0 102
SOS1 0.028 0.002 -10000 0 -10000 0 0
EPO 0.012 0.051 0.35 2 -0.45 5 7
VAV1 0.011 0.077 -10000 0 -0.36 25 25
GRB10 -0.055 0.16 -10000 0 -0.41 97 97
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.056 0.18 -10000 0 -0.44 103 103
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.029 0.11 0.22 1 -0.28 46 47
CBL 0.027 0.004 -10000 0 -10000 0 0
KIT -0.17 0.47 -10000 0 -1.2 99 99
MAP2K2 -0.028 0.11 0.22 1 -0.28 44 45
SHC/Grb2/SOS1 -0.018 0.18 -10000 0 -0.41 97 97
STAT5A -0.08 0.25 -10000 0 -0.61 101 101
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.054 0.16 -10000 0 -0.4 100 100
SHC/GRAP2 0.029 0.053 -10000 0 -0.25 20 20
PTPRO -0.075 0.18 -10000 0 -0.45 103 103
SH2B2 -0.058 0.17 0.2 1 -0.42 100 101
DOK1 0.028 0.001 -10000 0 -10000 0 0
MATK -0.074 0.18 -10000 0 -0.46 101 101
CREBBP 0.017 0.057 -10000 0 -10000 0 0
BCL2 -0.19 0.42 -10000 0 -1.2 67 67
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.031 -10000 0 -0.36 4 4
LAT2 -0.085 0.15 -10000 0 -0.36 97 97
AP1 -0.11 0.23 -10000 0 -0.51 122 122
mol:PIP3 -0.11 0.19 0.32 7 -0.44 105 112
IKBKB -0.067 0.13 0.21 26 -0.27 114 140
AKT1 -0.079 0.11 0.34 9 -0.38 7 16
IKBKG -0.078 0.12 0.26 7 -0.27 123 130
MS4A2 -0.087 0.18 -10000 0 -0.36 177 177
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.016 -10000 0 -0.36 1 1
MAP3K1 -0.1 0.17 0.28 4 -0.4 110 114
mol:Ca2+ -0.085 0.15 0.28 8 -0.33 105 113
LYN 0.023 0.011 -10000 0 -10000 0 0
CBLB -0.086 0.15 -10000 0 -0.33 118 118
SHC1 0.027 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.02 -10000 0 -0.19 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
PLD2 -0.083 0.13 0.31 12 -0.32 84 96
PTPN13 -0.096 0.18 -10000 0 -0.49 47 47
PTPN11 0.015 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.072 0.12 0.34 6 -0.29 62 68
SYK 0.026 0.009 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.1 0.2 0.18 1 -0.45 108 109
LAT -0.087 0.15 -10000 0 -0.33 121 121
PAK2 -0.11 0.19 0.29 4 -0.44 115 119
NFATC2 -0.033 0.098 -10000 0 -0.52 19 19
HRAS -0.12 0.2 0.26 5 -0.47 117 122
GAB2 0.027 0.004 -10000 0 -10000 0 0
PLA2G1B 0.019 0.12 -10000 0 -0.86 10 10
Fc epsilon R1 -0.084 0.17 -10000 0 -0.28 232 232
Antigen/IgE/Fc epsilon R1 -0.074 0.15 -10000 0 -0.28 177 177
mol:GDP -0.13 0.23 -10000 0 -0.51 125 125
JUN 0.027 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
FOS 0.022 0.039 -10000 0 -0.36 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.088 0.16 -10000 0 -0.31 158 158
CHUK -0.079 0.12 0.27 5 -0.27 123 128
KLRG1 -0.075 0.13 0.14 1 -0.33 91 92
VAV1 -0.094 0.16 -10000 0 -0.36 116 116
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.086 0.15 -10000 0 -0.35 99 99
negative regulation of mast cell degranulation -0.064 0.13 -10000 0 -0.32 84 84
BTK -0.14 0.26 -10000 0 -0.58 125 125
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.21 -10000 0 -0.49 120 120
GAB2/PI3K/SHP2 -0.093 0.1 -10000 0 -0.31 78 78
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.082 0.15 -10000 0 -0.38 91 91
RAF1 0.022 0.13 -10000 0 -0.93 10 10
Fc epsilon R1/FcgammaRIIB/SHIP -0.073 0.19 -10000 0 -0.39 115 115
FCER1G 0.028 0.041 -10000 0 -0.37 6 6
FCER1A -0.086 0.18 -10000 0 -0.37 168 168
Antigen/IgE/Fc epsilon R1/Fyn -0.061 0.15 -10000 0 -0.3 122 122
MAPK3 0.02 0.12 -10000 0 -0.85 10 10
MAPK1 0.015 0.12 -10000 0 -0.89 10 10
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.1 0.26 -10000 0 -0.66 88 88
DUSP1 0.025 0.027 -10000 0 -0.36 3 3
NF-kappa-B/RelA -0.04 0.08 0.11 1 -0.19 59 60
actin cytoskeleton reorganization -0.089 0.18 -10000 0 -0.43 79 79
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.091 0.18 -10000 0 -0.42 103 103
FER -0.084 0.15 -10000 0 -0.34 111 111
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.035 0.095 -10000 0 -0.38 36 36
SOS1 0.028 0.002 -10000 0 -10000 0 0
PLCG1 -0.079 0.23 0.23 28 -0.49 105 133
cytokine secretion -0.032 0.055 -10000 0 -0.16 5 5
SPHK1 -0.1 0.15 -10000 0 -0.32 155 155
PTK2 -0.093 0.18 -10000 0 -0.45 77 77
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.099 0.21 0.21 6 -0.47 109 115
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.11 0.19 0.31 7 -0.44 109 116
MAP2K2 0.015 0.12 -10000 0 -0.86 10 10
MAP2K1 0.013 0.12 -10000 0 -0.87 10 10
MAP2K7 0.027 0.016 -10000 0 -0.36 1 1
KLRG1/SHP2 -0.059 0.12 0.18 3 -0.3 84 87
MAP2K4 -0.14 0.37 -10000 0 -0.9 116 116
Fc epsilon R1/FcgammaRIIB -0.086 0.19 -10000 0 -0.37 140 140
mol:Choline -0.082 0.13 0.3 13 -0.31 84 97
SHC/Grb2/SOS1 -0.058 0.16 -10000 0 -0.36 85 85
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.028 0.001 -10000 0 -10000 0 0
PXN -0.088 0.17 0.41 2 -0.47 41 43
HCLS1 -0.088 0.15 -10000 0 -0.35 108 108
PRKCB -0.11 0.17 0.31 5 -0.37 144 149
FCGR2B -0.019 0.12 -10000 0 -0.36 72 72
IGHE -0.003 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.065 0.14 -10000 0 -0.32 84 84
LCP2 0.023 0.039 -10000 0 -0.36 6 6
PLA2G4A -0.1 0.17 -10000 0 -0.37 135 135
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.082 0.13 0.3 13 -0.31 84 97
IKK complex -0.049 0.1 0.2 21 -0.23 58 79
WIPF1 0.026 0.027 -10000 0 -0.36 3 3
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.28 0.28 -10000 0 -0.83 64 64
PCK1 -0.59 0.59 -10000 0 -1.2 268 268
HNF4A -0.26 0.29 -10000 0 -0.91 43 43
KCNJ11 -0.29 0.29 -10000 0 -0.84 70 70
AKT1 -0.2 0.18 -10000 0 -0.58 45 45
response to starvation -0.018 0.029 -10000 0 -10000 0 0
DLK1 -0.29 0.29 -10000 0 -0.86 68 68
NKX2-1 -0.12 0.14 0.34 5 -0.37 41 46
ACADM -0.29 0.28 -10000 0 -0.81 81 81
TAT -0.59 0.57 -10000 0 -1.2 246 246
CEBPB 0.004 0.052 0.36 3 -0.44 4 7
CEBPA 0.006 0.047 -10000 0 -0.36 3 3
TTR -0.34 0.47 0.52 2 -1.1 140 142
PKLR -0.34 0.34 -10000 0 -0.91 119 119
APOA1 -0.3 0.32 -10000 0 -0.96 53 53
CPT1C -0.29 0.27 -10000 0 -0.81 74 74
ALAS1 -0.14 0.14 -10000 0 -0.6 2 2
TFRC -0.27 0.23 -10000 0 -0.66 64 64
FOXF1 0.021 0.049 -10000 0 -0.36 10 10
NF1 0.031 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.073 0.051 -10000 0 -0.28 6 6
CPT1A -0.29 0.27 -10000 0 -0.82 69 69
HMGCS1 -0.29 0.28 -10000 0 -0.79 81 81
NR3C1 -0.076 0.13 -10000 0 -0.31 89 89
CPT1B -0.29 0.28 -10000 0 -0.82 72 72
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.066 0.039 -10000 0 -10000 0 0
GCK -0.29 0.29 -10000 0 -0.87 67 67
CREB1 -0.063 0.11 -10000 0 -0.23 86 86
IGFBP1 -0.22 0.2 -10000 0 -0.59 77 77
PDX1 -0.31 0.18 -10000 0 -0.63 26 26
UCP2 -0.29 0.27 -10000 0 -0.8 75 75
ALDOB -0.32 0.32 -10000 0 -0.92 80 80
AFP -0.11 0.13 -10000 0 -0.43 46 46
BDH1 -0.29 0.28 -10000 0 -0.81 75 75
HADH -0.28 0.28 -10000 0 -0.84 64 64
F2 -0.32 0.32 -10000 0 -1 51 51
HNF1A -0.073 0.051 -10000 0 -0.28 6 6
G6PC -0.16 0.32 -10000 0 -1.2 45 45
SLC2A2 -0.22 0.18 -10000 0 -0.78 8 8
INS -0.006 0.04 -10000 0 -10000 0 0
FOXA1 -0.035 0.12 -10000 0 -0.36 56 56
FOXA3 -0.15 0.14 -10000 0 -0.34 121 121
FOXA2 -0.33 0.32 -10000 0 -0.88 91 91
ABCC8 -0.34 0.34 -10000 0 -0.97 95 95
ALB -0.11 0.14 -10000 0 -0.46 39 39
Signaling events regulated by Ret tyrosine kinase

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.016 0.073 -10000 0 -0.4 14 14
Crk/p130 Cas/Paxillin -0.089 0.12 -10000 0 -0.31 57 57
JUN -0.084 0.12 -10000 0 -0.34 64 64
HRAS 0.027 0.016 -10000 0 -0.36 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.06 0.15 -10000 0 -0.37 52 52
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.063 0.16 -10000 0 -0.37 59 59
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.042 0.12 -10000 0 -0.19 225 225
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.055 0.14 -10000 0 -0.33 57 57
GRB7 0.035 0.049 0.36 14 -10000 0 14
RET51/GFRalpha1/GDNF -0.063 0.16 -10000 0 -0.36 63 63
MAPKKK cascade -0.078 0.14 -10000 0 -0.37 55 55
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.042 0.12 -10000 0 -0.19 228 228
lamellipodium assembly -0.077 0.12 -10000 0 -0.28 64 64
RET51/GFRalpha1/GDNF/SHC -0.062 0.16 -10000 0 -0.36 63 63
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
RET9/GFRalpha1/GDNF/SHC -0.04 0.12 -10000 0 -0.19 223 223
RET9/GFRalpha1/GDNF/Shank3 -0.042 0.12 -10000 0 -0.19 216 216
MAPK3 -0.091 0.11 -10000 0 -0.32 57 57
DOK1 0.028 0.001 -10000 0 -10000 0 0
DOK6 0.014 0.048 -10000 0 -0.36 9 9
PXN 0.028 0.002 -10000 0 -10000 0 0
neurite development -0.067 0.099 -10000 0 -0.32 37 37
DOK5 0.012 0.047 0.36 1 -0.36 8 9
GFRA1 -0.12 0.19 -10000 0 -0.36 235 235
MAPK8 -0.087 0.13 -10000 0 -0.35 71 71
HRAS/GTP -0.076 0.17 -10000 0 -0.41 59 59
tube development -0.039 0.11 0.21 1 -0.35 1 2
MAPK1 -0.089 0.11 0.34 1 -0.32 56 57
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.056 0.1 -10000 0 -0.19 223 223
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
PDLIM7 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.045 0.12 -10000 0 -0.35 41 41
SHC1 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.16 -10000 0 -0.37 57 57
RET51/GFRalpha1/GDNF/Dok5 -0.049 0.13 0.26 1 -0.37 38 39
PRKCA 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
CREB1 -0.086 0.14 -10000 0 -0.26 225 225
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.057 0.11 -10000 0 -0.2 220 220
RET51/GFRalpha1/GDNF/Grb7 -0.058 0.15 0.25 5 -0.35 59 64
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.032 0.14 -10000 0 -0.36 93 93
DOK4 0.027 0.016 -10000 0 -0.36 1 1
JNK cascade -0.082 0.12 -10000 0 -0.34 64 64
RET9/GFRalpha1/GDNF/FRS2 -0.041 0.12 -10000 0 -0.19 226 226
SHANK3 0.026 0.017 -10000 0 -0.36 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.055 0.1 -10000 0 -0.19 220 220
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -10000 0 -0.36 67 67
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.086 0.14 -10000 0 -0.37 71 71
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.09 0.16 -10000 0 -0.44 65 65
PI3K -0.11 0.17 -10000 0 -0.34 186 186
SOS1 0.028 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.031 0.12 -10000 0 -0.35 1 1
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.071 0.12 -10000 0 -0.31 59 59
RET51/GFRalpha1/GDNF/FRS2 -0.063 0.16 -10000 0 -0.37 58 58
GAB1 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
IRS2 0.022 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.09 0.16 -10000 0 -0.43 68 68
RET51/GFRalpha1/GDNF/PKC alpha -0.062 0.15 -10000 0 -0.37 54 54
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.016 0.025 -10000 0 -0.36 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.063 0.16 -10000 0 -0.37 59 59
Rac1/GTP -0.088 0.14 -10000 0 -0.34 64 64
RET9/GFRalpha1/GDNF -0.058 0.12 -10000 0 -0.21 230 230
GFRalpha1/GDNF -0.072 0.14 -10000 0 -0.25 230 230
Syndecan-1-mediated signaling events

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
TGFB1 0.027 0.019 -10000 0 -0.44 1 1
CCL5 0.012 0.075 -10000 0 -0.36 24 24
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
FGFR/FGF2/Syndecan-1 -0.12 0.1 0.29 3 -0.32 45 48
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.092 0.1 0.23 3 -0.3 41 44
Syndecan-1/Syntenin -0.11 0.1 0.28 2 -0.31 41 43
MAPK3 -0.11 0.094 0.26 2 -0.36 18 20
HGF/MET 0.029 0.058 -10000 0 -0.28 19 19
TGFB1/TGF beta receptor Type II 0.026 0.019 -10000 0 -0.44 1 1
BSG 0.027 0.016 -10000 0 -0.36 1 1
keratinocyte migration -0.091 0.1 0.23 3 -0.3 41 44
Syndecan-1/RANTES -0.12 0.11 0.26 3 -0.32 53 56
Syndecan-1/CD147 -0.11 0.1 0.35 1 -0.36 22 23
Syndecan-1/Syntenin/PIP2 -0.1 0.097 0.26 2 -0.3 41 43
LAMA5 0.017 0.036 0.36 3 -0.4 2 5
positive regulation of cell-cell adhesion -0.1 0.095 0.26 2 -0.3 41 43
MMP7 -0.42 0.11 0.36 3 -0.45 583 586
HGF 0.017 0.061 -10000 0 -0.37 15 15
Syndecan-1/CASK -0.12 0.096 0.28 2 -0.31 46 48
Syndecan-1/HGF/MET -0.11 0.11 0.35 1 -0.36 30 31
regulation of cell adhesion -0.11 0.091 0.25 2 -0.36 16 18
HPSE 0.023 0.038 -10000 0 -0.36 6 6
positive regulation of cell migration -0.12 0.1 0.29 3 -0.32 45 48
SDC1 -0.12 0.1 0.29 3 -0.32 45 48
Syndecan-1/Collagen -0.12 0.1 0.29 3 -0.32 45 48
PPIB 0.026 0.006 -10000 0 -10000 0 0
MET 0.023 0.045 0.36 1 -0.44 5 6
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
MAPK1 -0.11 0.093 0.26 2 -0.35 19 21
homophilic cell adhesion -0.12 0.1 0.29 3 -0.32 46 49
MMP1 -0.28 0.23 0.36 2 -0.44 397 399
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.04 0.008 -10000 0 -10000 0 0
Necdin/E2F1 0.018 0.058 0.26 7 -0.27 17 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0 0.12 -10000 0 -0.34 10 10
NGF (dimer)/p75(NTR)/BEX1 -0.083 0.16 -10000 0 -0.26 255 255
NT-4/5 (dimer)/p75(NTR) -0.047 0.14 -10000 0 -0.27 164 164
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.037 0.09 -10000 0 -0.34 8 8
IKBKG 0.027 0.016 -10000 0 -0.36 1 1
BDNF 0.019 0.06 -10000 0 -0.44 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.035 0.14 -10000 0 -0.24 173 173
FURIN 0.026 0.017 -10000 0 -0.36 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.016 0.12 -10000 0 -0.22 152 152
LINGO1 0.008 0.091 -10000 0 -0.44 24 24
Sortilin/TRAF6/NRIF 0.031 0.027 -10000 0 -0.32 1 1
proBDNF (dimer) 0.019 0.06 -10000 0 -0.44 10 10
NTRK1 0.016 0.057 -10000 0 -0.43 9 9
RTN4R 0.011 0.084 -10000 0 -0.44 21 21
neuron apoptosis -0.049 0.14 0.32 2 -0.43 27 29
IRAK1 0.027 0.019 -10000 0 -0.44 1 1
SHC1 -0.045 0.1 -10000 0 -0.22 147 147
ARHGDIA 0.027 0.016 -10000 0 -0.36 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.071 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.005 0.12 -10000 0 -0.36 11 11
MAGEH1 0.024 0.038 -10000 0 -0.36 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.13 -10000 0 -0.36 25 25
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -0.25 1 1
proNGF (dimer) 0.011 0.071 -10000 0 -0.37 20 20
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.026 0.017 -10000 0 -0.36 1 1
NT-4/5 (dimer) -0.017 0.088 -10000 0 -0.45 23 23
ZNF274 0.023 0.038 -10000 0 -0.36 6 6
RhoA/GDP/RHOGDI -0.021 0.1 -10000 0 -0.32 10 10
NGF 0.011 0.071 -10000 0 -0.37 20 20
cell cycle arrest -0.031 0.09 0.2 6 -0.31 9 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.027 0.097 -10000 0 -0.31 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.025 0.13 -10000 0 -0.23 164 164
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.047 0.14 -10000 0 -0.24 198 198
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
mol:ceramide -0.038 0.096 0.18 6 -0.34 10 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.024 0.089 -10000 0 -0.3 22 22
p75(NTR)/beta APP -0.032 0.12 -10000 0 -0.25 150 150
BEX1 -0.084 0.17 -10000 0 -0.36 164 164
mol:GDP -0.062 0.095 -10000 0 -0.22 154 154
NGF (dimer) -0.28 0.12 -10000 0 -0.3 578 578
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.019 0.13 -10000 0 -0.29 41 41
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RAC1/GTP -0.015 0.1 -10000 0 -0.19 143 143
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.047 0.14 -10000 0 -0.24 198 198
RHOB 0.028 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.024 0.043 0.26 8 -0.32 4 12
NT3 (dimer) 0.021 0.043 -10000 0 -0.37 7 7
TP53 -0.044 0.079 0.35 3 -0.34 4 7
PRDM4 -0.041 0.098 -10000 0 -0.34 10 10
BDNF (dimer) -0.46 0.15 0.4 1 -0.48 600 601
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.11 -10000 0 -0.34 10 10
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.12 -10000 0 -0.34 10 10
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
MAPK10 -0.068 0.15 0.31 5 -0.41 49 54
DIABLO 0.028 0.003 -10000 0 -10000 0 0
SMPD2 -0.039 0.097 -10000 0 -0.34 10 10
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.019 0.12 -10000 0 -0.22 152 152
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.033 0.13 -10000 0 -0.26 149 149
MAPK8 -0.048 0.12 0.33 4 -0.33 22 26
MAPK9 -0.047 0.12 0.33 4 -0.34 18 22
APAF1 0.028 0.003 -10000 0 -10000 0 0
NTF3 0.021 0.043 -10000 0 -0.37 7 7
NTF4 -0.017 0.089 -10000 0 -0.45 23 23
NDN 0.011 0.075 -10000 0 -0.36 24 24
RAC1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.02 0.13 -10000 0 -0.34 30 30
p75 CTF/Sortilin/TRAF6/NRIF 0.065 0.031 -10000 0 -0.19 6 6
RhoA-B-C/GTP -0.047 0.14 -10000 0 -0.24 198 198
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.12 -10000 0 -0.27 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.001 0.12 -10000 0 -0.26 10 10
PRKACB -0.019 0.12 -10000 0 -0.36 72 72
proBDNF (dimer)/p75 ECD 0.035 0.046 -10000 0 -0.32 10 10
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.05 -10000 0 -0.37 10 10
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
neuron projection morphogenesis -0.053 0.12 -10000 0 -0.31 44 44
BAD -0.062 0.14 0.28 6 -0.35 47 53
RIPK2 0.024 0.01 -10000 0 -10000 0 0
NGFR -0.067 0.17 -10000 0 -0.36 149 149
CYCS -0.038 0.089 -10000 0 -0.34 8 8
ADAM17 0.028 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.004 0.11 -10000 0 -0.34 8 8
BCL2L11 -0.062 0.14 0.3 5 -0.35 46 51
BDNF (dimer)/p75(NTR) -0.037 0.13 -10000 0 -0.26 158 158
PI3K -0.005 0.12 -10000 0 -0.34 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.005 0.12 -10000 0 -0.34 10 10
NDNL2 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
NGF (dimer)/p75(NTR) -0.04 0.14 -10000 0 -0.26 160 160
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.002 0.12 -10000 0 -0.34 10 10
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.095 0.18 0.36 1 -0.45 127 128
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.046 0.11 -10000 0 -0.39 9 9
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.022 -10000 0 -0.36 2 2
CASP3 -0.061 0.13 0.31 4 -0.33 49 53
E2F1 0.019 0.057 0.36 9 -0.44 4 13
CASP9 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0 0.11 -10000 0 -0.36 11 11
NGF (dimer)/TRKA 0.023 0.069 -10000 0 -0.28 28 28
MMP7 -0.42 0.11 0.36 3 -0.45 583 586
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.005 0.12 -10000 0 -0.35 11 11
MMP3 -0.36 0.18 0.36 1 -0.45 509 510
APAF-1/Caspase 9 -0.054 0.068 -10000 0 -0.3 11 11
Signaling events mediated by the Hedgehog family

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
TGFB2 0.014 0.099 -10000 0 -0.41 27 27
IHH 0.021 0.077 -10000 0 -0.42 16 16
SHH Np/Cholesterol/GAS1 -0.055 0.13 0.18 4 -0.24 183 187
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.13 0.24 183 -0.18 4 187
SMO/beta Arrestin2 0.018 0.088 -10000 0 -0.44 9 9
SMO 0.004 0.083 -10000 0 -0.46 9 9
AKT1 0 0.11 -10000 0 -0.4 19 19
ARRB2 0.023 0.01 -10000 0 -10000 0 0
BOC 0.011 0.078 -10000 0 -0.36 26 26
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
heart looping 0.006 0.083 -10000 0 -0.45 9 9
STIL -0.022 0.11 0.34 1 -0.35 13 14
DHH N/PTCH2 0.027 0.061 -10000 0 -0.26 26 26
DHH N/PTCH1 0.024 0.085 -10000 0 -0.37 13 13
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DHH 0.011 0.072 -10000 0 -0.36 22 22
PTHLH 0.007 0.13 -10000 0 -0.73 14 14
determination of left/right symmetry 0.006 0.083 -10000 0 -0.45 9 9
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
skeletal system development 0.007 0.13 -10000 0 -0.72 14 14
IHH N/Hhip -0.022 0.13 -10000 0 -0.29 117 117
DHH N/Hhip -0.022 0.13 -10000 0 -0.27 120 120
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.006 0.083 -10000 0 -0.45 9 9
pancreas development -0.043 0.15 -10000 0 -0.36 109 109
HHAT 0.024 0.035 -10000 0 -0.36 5 5
PI3K 0.039 0.015 -10000 0 -0.25 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.035 0.14 -10000 0 -0.36 97 97
somite specification 0.006 0.083 -10000 0 -0.45 9 9
SHH Np/Cholesterol/PTCH1 -0.023 0.11 0.19 5 -0.33 18 23
SHH Np/Cholesterol/PTCH2 -0.026 0.11 0.18 5 -0.24 123 128
SHH Np/Cholesterol/Megalin -0.048 0.13 0.18 5 -0.26 158 163
SHH -0.047 0.13 0.32 6 -0.32 118 124
catabolic process 0.019 0.077 -10000 0 -0.38 13 13
SMO/Vitamin D3 -0.019 0.11 -10000 0 -0.4 13 13
SHH Np/Cholesterol/Hhip -0.059 0.13 0.18 5 -0.23 204 209
LRP2 -0.036 0.13 -10000 0 -0.44 56 56
receptor-mediated endocytosis -0.033 0.12 0.23 3 -0.37 26 29
SHH Np/Cholesterol/BOC -0.032 0.11 0.18 4 -0.24 138 142
SHH Np/Cholesterol/CDO -0.025 0.11 0.18 4 -0.24 119 123
mesenchymal cell differentiation 0.059 0.13 0.23 204 -0.18 5 209
mol:Vitamin D3 -0.017 0.12 0.22 11 -0.36 14 25
IHH N/PTCH2 0.031 0.059 -10000 0 -0.27 20 20
CDON 0.027 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.027 0.08 -10000 0 -0.38 13 13
Megalin/LRPAP1 0.004 0.1 -10000 0 -0.32 56 56
PTCH2 0.024 0.038 -10000 0 -0.44 4 4
SHH Np/Cholesterol -0.034 0.1 -10000 0 -0.24 119 119
PTCH1 0.019 0.077 -10000 0 -0.38 13 13
HHIP -0.043 0.15 -10000 0 -0.36 109 109
HIF-1-alpha transcription factor network

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
PKM2 -0.41 0.27 -10000 0 -0.86 89 89
HDAC7 0.027 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.24 -10000 0 -0.88 34 34
SMAD4 0.02 0.013 -10000 0 -10000 0 0
ID2 -0.41 0.28 -10000 0 -0.89 71 71
AP1 0.036 0.031 -10000 0 -0.25 6 6
ABCG2 -0.55 0.3 -10000 0 -0.92 150 150
HIF1A -0.079 0.051 -10000 0 -10000 0 0
TFF3 -0.41 0.28 -10000 0 -0.9 76 76
GATA2 0.022 0.052 -10000 0 -0.36 11 11
AKT1 -0.078 0.055 -10000 0 -10000 0 0
response to hypoxia -0.081 0.046 -10000 0 -0.21 15 15
MCL1 -0.41 0.28 -10000 0 -0.89 71 71
NDRG1 -0.39 0.28 -10000 0 -0.89 66 66
SERPINE1 -0.45 0.3 -10000 0 -0.9 111 111
FECH -0.4 0.28 -10000 0 -0.89 67 67
FURIN -0.41 0.28 -10000 0 -0.89 69 69
NCOA2 0.023 0.029 -10000 0 -0.36 3 3
EP300 -0.074 0.075 -10000 0 -0.32 24 24
HMOX1 -0.41 0.28 -10000 0 -0.9 71 71
BHLHE40 -0.41 0.28 -10000 0 -0.89 74 74
BHLHE41 -0.41 0.28 -10000 0 -0.9 80 80
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.074 0.083 -10000 0 -10000 0 0
ENG -0.077 0.068 0.28 2 -10000 0 2
JUN 0.028 0.005 -10000 0 -10000 0 0
RORA -0.41 0.28 -10000 0 -0.88 78 78
ABCB1 -0.27 0.4 -10000 0 -1.1 118 118
TFRC -0.41 0.28 -10000 0 -0.89 69 69
CXCR4 -0.41 0.28 -10000 0 -0.89 73 73
TF -0.43 0.29 -10000 0 -0.91 91 91
CITED2 -0.41 0.28 -10000 0 -0.89 71 71
HIF1A/ARNT -0.44 0.32 -10000 0 -0.99 70 70
LDHA -0.039 0.055 -10000 0 -0.8 1 1
ETS1 -0.41 0.28 -10000 0 -0.89 71 71
PGK1 -0.41 0.28 -10000 0 -0.88 74 74
NOS2 -0.42 0.28 -10000 0 -0.9 83 83
ITGB2 -0.41 0.28 -10000 0 -0.9 71 71
ALDOA -0.41 0.28 -10000 0 -0.89 71 71
Cbp/p300/CITED2 -0.4 0.29 -10000 0 -0.97 58 58
FOS 0.023 0.039 -10000 0 -0.36 6 6
HK2 -0.41 0.28 -10000 0 -0.89 71 71
SP1 0.008 0.053 -10000 0 -10000 0 0
GCK -0.098 0.2 -10000 0 -1.3 12 12
HK1 -0.41 0.28 -10000 0 -0.88 76 76
NPM1 -0.41 0.28 -10000 0 -0.89 71 71
EGLN1 -0.41 0.28 -10000 0 -0.89 71 71
CREB1 0.033 0 -10000 0 -10000 0 0
PGM1 -0.41 0.28 -10000 0 -0.89 74 74
SMAD3 0.027 0.007 -10000 0 -10000 0 0
EDN1 -0.075 0.11 -10000 0 -0.77 4 4
IGFBP1 -0.43 0.3 -10000 0 -0.92 96 96
VEGFA -0.3 0.21 -10000 0 -0.79 29 29
HIF1A/JAB1 -0.04 0.044 -10000 0 -10000 0 0
CP -0.49 0.31 -10000 0 -0.91 126 126
CXCL12 -0.44 0.3 -10000 0 -0.91 99 99
COPS5 0.024 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.03 0.019 -10000 0 -10000 0 0
BNIP3 -0.41 0.28 -10000 0 -0.89 72 72
EGLN3 -0.41 0.28 -10000 0 -0.9 66 66
CA9 -0.56 0.3 -10000 0 -0.92 165 165
TERT -0.42 0.29 -10000 0 -0.92 83 83
ENO1 -0.41 0.28 -10000 0 -0.88 78 78
PFKL -0.41 0.28 -10000 0 -0.89 71 71
NCOA1 0.028 0.002 -10000 0 -10000 0 0
ADM -0.41 0.28 -10000 0 -0.89 70 70
ARNT -0.082 0.05 -10000 0 -0.42 1 1
HNF4A 0.014 0.025 -10000 0 -0.36 1 1
ADFP -0.41 0.27 -10000 0 -0.86 89 89
SLC2A1 -0.31 0.22 -10000 0 -0.82 37 37
LEP -0.42 0.29 -10000 0 -0.89 95 95
HIF1A/ARNT/Cbp/p300 -0.34 0.24 -10000 0 -0.89 37 37
EPO -0.23 0.18 -10000 0 -0.79 13 13
CREBBP -0.073 0.072 -10000 0 -0.34 16 16
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.25 -10000 0 -0.93 31 31
PFKFB3 -0.41 0.28 -10000 0 -0.89 71 71
NT5E -0.41 0.28 -10000 0 -0.89 75 75
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.009 0.17 0.25 84 -0.26 136 220
SMAD6-7/SMURF1 0.039 0.032 -10000 0 -0.23 3 3
NOG 0.014 0.033 -10000 0 -0.44 2 2
SMAD9 -0.048 0.18 -10000 0 -0.54 64 64
SMAD4 0.02 0.013 -10000 0 -10000 0 0
SMAD5 -0.033 0.12 -10000 0 -0.4 37 37
BMP7/USAG1 -0.05 0.2 0.26 75 -0.33 171 246
SMAD5/SKI -0.035 0.13 0.21 2 -0.39 43 45
SMAD1 0.011 0.05 -10000 0 -0.39 4 4
BMP2 0.008 0.075 -10000 0 -0.36 24 24
SMAD1/SMAD1/SMAD4 0.02 0.06 -10000 0 -0.35 7 7
BMPR1A 0.026 0.006 -10000 0 -10000 0 0
BMPR1B -0.013 0.12 -10000 0 -0.42 47 47
BMPR1A-1B/BAMBI 0.011 0.11 0.25 1 -0.26 78 79
AHSG -0.041 0.15 0.36 2 -0.44 73 75
CER1 -0.012 0.072 0.36 2 -0.44 14 16
BMP2-4/CER1 0.003 0.1 0.25 1 -0.26 70 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.04 0.13 -10000 0 -0.35 47 47
BMP2-4 (homodimer) -0.001 0.1 -10000 0 -0.3 61 61
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.032 0.093 -10000 0 -0.25 36 36
RGMA -0.052 0.16 -10000 0 -0.36 124 124
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.12 -10000 0 -0.34 49 49
BMP2-4/USAG1 -0.027 0.13 -10000 0 -0.25 131 131
SMAD6/SMURF1/SMAD5 -0.037 0.13 -10000 0 -0.42 34 34
SOSTDC1 -0.041 0.14 -10000 0 -0.36 103 103
BMP7/BMPR2/BMPR1A-1B -0.007 0.17 0.25 89 -0.26 146 235
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.013 0.074 -10000 0 -0.36 23 23
HFE2 -0.008 0.031 -10000 0 -0.44 2 2
ZFYVE16 0.026 0.023 -10000 0 -0.36 2 2
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.094 -10000 0 -0.26 60 60
SMAD5/SMAD5/SMAD4 -0.033 0.13 0.21 2 -0.38 43 45
MAPK1 0.026 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.028 0.11 -10000 0 -0.32 38 38
BMP7 (homodimer) -0.026 0.25 0.36 101 -0.44 133 234
NUP214 0.027 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.014 0.13 0.26 1 -0.31 91 92
SMAD1/SKI 0.016 0.07 -10000 0 -0.41 8 8
SMAD6 0.025 0.027 -10000 0 -0.44 2 2
CTDSP2 0.028 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.02 0.13 0.25 1 -0.28 114 115
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.006 0.09 -10000 0 -0.39 30 30
BMPR2 (homodimer) 0.027 0.016 -10000 0 -0.36 1 1
GADD34/PP1CA 0.052 0.02 -10000 0 -0.21 2 2
BMPR1A-1B (homodimer) 0.012 0.09 -10000 0 -0.3 47 47
CHRDL1 -0.18 0.19 -10000 0 -0.36 330 330
ENDOFIN/SMAD1 0.016 0.072 -10000 0 -0.43 7 7
SMAD6-7/SMURF1/SMAD1 0.031 0.072 -10000 0 -0.39 7 7
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.001 0.11 0.36 1 -0.44 35 36
SMURF2 0.025 0.025 -10000 0 -0.4 2 2
BMP2-4/CHRDL1 -0.1 0.15 -10000 0 -0.24 289 289
BMP2-4/GREM1 -0.001 0.11 -10000 0 -0.26 83 83
SMAD7 0.02 0.02 -10000 0 -0.36 1 1
SMAD8A/SMAD8A/SMAD4 -0.045 0.18 -10000 0 -0.49 78 78
SMAD1/SMAD6 0.014 0.072 -10000 0 -0.42 8 8
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 -0.026 0.25 0.36 101 -0.44 133 234
BMP6 0.013 0.074 -10000 0 -0.36 23 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.048 0.13 -10000 0 -0.36 65 65
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.015 0.073 -10000 0 -0.41 9 9
SMAD7/SMURF1 0.029 0.022 -10000 0 -0.25 1 1
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
CTDSP1 0.028 0.001 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.053 0.14 -10000 0 -0.38 72 72
CHRD 0.027 0.016 -10000 0 -0.36 1 1
BMPR2 0.027 0.016 -10000 0 -0.36 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.047 0.12 -10000 0 -0.35 59 59
BMP4 -0.005 0.12 -10000 0 -0.44 41 41
FST 0.012 0.075 -10000 0 -0.37 23 23
BMP2-4/NOG 0.011 0.095 -10000 0 -0.26 61 61
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.005 0.16 0.25 77 -0.25 132 209
Visual signal transduction: Rods

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
mol:K + 0.026 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.014 -10000 0 -0.31 1 1
Metarhodopsin II/Arrestin 0.024 0.021 -10000 0 -0.27 3 3
PDE6G/GNAT1/GTP 0.017 0.057 -10000 0 -0.21 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.009 0.025 -10000 0 -0.44 1 1
GRK1 -0.01 0.032 0.36 1 -0.44 2 3
CNG Channel -0.13 0.15 -10000 0 -0.36 112 112
mol:Na + -0.034 0.13 -10000 0 -0.39 32 32
mol:ADP -0.01 0.032 0.36 1 -0.44 2 3
RGS9-1/Gbeta5/R9AP 0.009 0.096 0.25 1 -0.21 94 95
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.028 0.13 -10000 0 -0.4 32 32
CNGB1 -0.047 0.13 -10000 0 -0.36 83 83
RDH5 0 0.1 -10000 0 -0.36 44 44
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.12 0.34 13 -0.38 31 44
Na + (4 Units) -0.035 0.12 -10000 0 -0.37 32 32
RGS9 -0.033 0.14 -10000 0 -0.36 93 93
GNB1/GNGT1 -0.055 0.16 0.26 14 -0.32 167 181
GNAT1/GDP 0.016 0.088 0.24 1 -0.2 18 19
GUCY2D -0.006 0.094 -10000 0 -0.46 24 24
GNGT1 -0.1 0.22 0.36 15 -0.44 167 182
GUCY2F -0.016 0.02 -10000 0 -0.44 1 1
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.11 0.12 -10000 0 -0.35 40 40
mol:11-cis-retinal 0 0.1 -10000 0 -0.36 44 44
mol:cGMP 0.01 0.093 -10000 0 -0.27 55 55
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin 0.011 0.078 -10000 0 -0.26 47 47
SLC24A1 0.027 0.006 -10000 0 -10000 0 0
CNGA1 -0.007 0.11 -10000 0 -0.36 54 54
Metarhodopsin II 0.017 0.03 0.21 1 -0.3 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.019 0.098 -10000 0 -0.28 56 56
RGS9BP 0.02 0.038 0.36 1 -0.44 3 4
Metarhodopsin II/Transducin -0.023 0.068 0.15 12 -0.23 13 25
GCAP Family/Ca ++ 0.026 0.07 -10000 0 -0.25 37 37
PDE6A/B -0.14 0.15 -10000 0 -0.26 355 355
mol:Pi 0.009 0.096 0.25 1 -0.21 94 95
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.033 0.13 0.23 14 -0.25 167 181
PDE6B 0.008 0.082 -10000 0 -0.36 28 28
PDE6A -0.19 0.19 -10000 0 -0.36 346 346
PDE6G 0.005 0.089 -10000 0 -0.36 34 34
RHO -0.017 0.032 -10000 0 -0.44 3 3
PDE6 -0.11 0.15 -10000 0 -0.36 90 90
GUCA1A -0.011 0.11 0.36 1 -0.44 36 37
GC2/GCAP Family 0.035 0.076 -10000 0 -0.26 37 37
GUCA1C -0.018 0.002 -10000 0 -10000 0 0
GUCA1B 0.028 0.03 0.36 3 -0.44 1 4
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.031 0.16 0.23 1 -0.4 58 59
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
mol:Ca2+ -0.01 0.23 -10000 0 -0.82 36 36
EDN1 0.019 0.12 -10000 0 -0.27 26 26
EDN3 -0.1 0.17 -10000 0 -0.36 186 186
EDN2 -0.085 0.17 -10000 0 -0.36 175 175
HRAS/GDP -0.002 0.15 0.34 7 -0.42 24 31
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.01 0.11 0.2 2 -0.38 18 20
ADCY4 -0.041 0.13 -10000 0 -0.37 50 50
ADCY5 -0.11 0.16 -10000 0 -0.38 115 115
ADCY6 -0.042 0.13 -10000 0 -0.37 50 50
ADCY7 -0.042 0.13 0.2 1 -0.37 50 51
ADCY1 -0.044 0.13 0.38 1 -0.38 48 49
ADCY2 -0.066 0.16 -10000 0 -0.39 77 77
ADCY3 -0.042 0.13 -10000 0 -0.37 51 51
ADCY8 -0.044 0.12 0.22 1 -0.37 43 44
ADCY9 -0.043 0.13 -10000 0 -0.37 50 50
arachidonic acid secretion -0.025 0.16 0.3 9 -0.45 36 45
ETB receptor/Endothelin-1/Gq/GTP 0.007 0.072 -10000 0 -0.34 12 12
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
HRAS 0.027 0.016 -10000 0 -0.36 1 1
ETA receptor/Endothelin-1/G12/GTP 0.061 0.2 0.3 5 -0.38 45 50
ETA receptor/Endothelin-1/Gs/GTP 0.033 0.19 0.29 3 -0.36 61 64
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.034 0.18 -10000 0 -0.45 57 57
EDNRB 0.009 0.063 -10000 0 -0.36 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.041 0.19 0.26 1 -0.54 54 55
CYSLTR1 -0.069 0.23 0.23 1 -0.51 114 115
SLC9A1 -0.008 0.1 -10000 0 -0.25 56 56
mol:GDP -0.013 0.15 0.27 16 -0.42 31 47
SLC9A3 -0.19 0.31 -10000 0 -0.59 152 152
RAF1 -0.015 0.13 0.3 8 -0.45 17 25
JUN 0.01 0.16 -10000 0 -0.61 13 13
JAK2 -0.031 0.16 0.22 2 -0.39 61 63
mol:IP3 0.02 0.11 0.21 9 -0.46 10 19
ETA receptor/Endothelin-1 0.042 0.25 0.34 5 -0.43 71 76
PLCB1 0.024 0.026 0.36 3 -10000 0 3
PLCB2 0.026 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.08 0.16 -10000 0 -0.28 199 199
FOS -0.015 0.16 0.36 3 -0.83 13 16
Gai/GDP -0.22 0.35 -10000 0 -0.66 226 226
CRK 0.024 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.009 0.15 0.23 9 -0.41 41 50
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
PRKCB1 0.017 0.1 0.22 10 -0.44 10 20
GNAQ 0.026 0.025 -10000 0 -0.36 2 2
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
GNAL 0.008 0.073 -10000 0 -0.36 23 23
Gs family/GDP -0.015 0.14 0.3 5 -0.4 31 36
ETA receptor/Endothelin-1/Gq/GTP 0.006 0.12 0.25 1 -0.41 14 15
MAPK14 0.008 0.074 0.21 1 -0.43 7 8
TRPC6 -0.013 0.24 -10000 0 -0.89 36 36
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.011 0.078 -10000 0 -0.4 9 9
ETB receptor/Endothelin-2 -0.037 0.12 -10000 0 -0.26 138 138
ETB receptor/Endothelin-3 -0.065 0.13 -10000 0 -0.26 174 174
ETB receptor/Endothelin-1 0.021 0.099 -10000 0 -0.32 15 15
MAPK3 -0.013 0.14 0.34 5 -0.66 14 19
MAPK1 -0.018 0.16 0.36 4 -0.69 17 21
Rac1/GDP -0.006 0.14 0.31 7 -0.4 29 36
cAMP biosynthetic process -0.088 0.15 0.24 1 -0.38 79 80
MAPK8 0.006 0.18 0.34 1 -0.6 34 35
SRC 0.017 0.014 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.046 0.13 -10000 0 -0.33 61 61
p130Cas/CRK/Src/PYK2 -0.013 0.18 0.32 22 -0.54 34 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.006 0.14 0.34 5 -0.41 26 31
COL1A2 -0.002 0.17 0.24 1 -0.39 56 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.074 0.18 -10000 0 -0.3 199 199
mol:DAG 0.02 0.11 0.21 9 -0.46 10 19
MAP2K2 -0.016 0.13 0.34 6 -0.52 16 22
MAP2K1 -0.015 0.13 0.31 6 -0.52 16 22
EDNRA -0.013 0.17 -10000 0 -0.38 73 73
positive regulation of muscle contraction -0.012 0.15 0.25 28 -0.37 41 69
Gq family/GDP -0.004 0.13 -10000 0 -0.46 15 15
HRAS/GTP -0.016 0.13 0.31 7 -0.4 25 32
PRKCH 0.016 0.1 0.2 9 -0.48 8 17
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.017 0.11 0.22 14 -0.48 8 22
PRKCB -0.017 0.14 0.21 10 -0.36 51 61
PRKCE 0.017 0.1 0.21 10 -0.48 8 18
PRKCD 0.015 0.1 0.2 9 -0.46 9 18
PRKCG -0.053 0.15 0.24 12 -0.39 38 50
regulation of vascular smooth muscle contraction -0.02 0.18 0.45 2 -0.97 13 15
PRKCQ 0.015 0.11 0.22 11 -0.43 13 24
PLA2G4A -0.029 0.17 0.32 7 -0.49 36 43
GNA14 0.024 0.037 -10000 0 -0.36 5 5
GNA15 0.022 0.047 -10000 0 -0.44 6 6
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA11 0.024 0.033 -10000 0 -0.36 4 4
Rac1/GTP 0.061 0.2 0.3 5 -0.36 53 58
MMP1 -0.2 0.18 0.27 2 -0.35 312 314
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.01 0.066 -10000 0 -0.26 34 34
EPHB2 0.024 0.033 -10000 0 -0.44 3 3
Syndecan-2/TACI -0.053 0.1 -10000 0 -0.21 192 192
LAMA1 -0.054 0.15 -10000 0 -0.36 121 121
Syndecan-2/alpha2 ITGB1 0.041 0.034 -10000 0 -0.23 1 1
HRAS 0.027 0.016 -10000 0 -0.36 1 1
Syndecan-2/CASK 0.007 0.012 -10000 0 -0.2 2 2
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
BAX 0.004 0.011 -10000 0 -10000 0 0
EPB41 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.017 -10000 0 -0.18 3 3
LAMA3 0.02 0.034 -10000 0 -0.38 4 4
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.04 -10000 0 -0.41 5 5
Syndecan-2/MMP2 0.022 0.035 -10000 0 -0.26 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.04 0.006 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.026 -10000 0 -0.24 5 5
Syndecan-2/GM-CSF -0.076 0.14 -10000 0 -0.26 223 223
determination of left/right symmetry 0.01 0.015 -10000 0 -0.24 2 2
Syndecan-2/PKC delta 0.025 0.017 -10000 0 -0.2 2 2
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.067 0.14 0.19 45 -0.24 221 266
MAPK1 -0.067 0.14 0.19 46 -0.24 222 268
Syndecan-2/RACK1 0.036 0.022 -10000 0 -0.17 3 3
NF1 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.015 -10000 0 -0.24 2 2
ITGA2 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.013 -10000 0 -0.2 2 2
Syndecan-2/alpha2/beta1 Integrin 0.002 0.086 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.019 0.089 -10000 0 -0.2 114 114
ITGB1 0.028 0.002 -10000 0 -10000 0 0
SRC 0.015 0.037 0.18 25 -10000 0 25
Syndecan-2/CASK/Protein 4.1 0.021 0.016 -10000 0 -0.18 2 2
extracellular matrix organization 0.024 0.02 -10000 0 -0.22 3 3
actin cytoskeleton reorganization 0.01 0.066 -10000 0 -0.26 34 34
Syndecan-2/Caveolin-2/Ras 0.036 0.03 -10000 0 -0.21 6 6
Syndecan-2/Laminin alpha3 0.019 0.023 -10000 0 -0.21 4 4
Syndecan-2/RasGAP 0.046 0.026 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.027 -10000 0 -0.24 5 5
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.02 0.024 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
TNFRSF13B -0.12 0.18 -10000 0 -0.36 214 214
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.04 0.006 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.025 0.017 -10000 0 -0.2 2 2
TGFB1 0.027 0.019 -10000 0 -0.44 1 1
CASP3 0.033 0.058 0.19 68 -0.18 2 70
FN1 0.001 0.11 -10000 0 -0.43 36 36
Syndecan-2/IL8 -0.11 0.15 -10000 0 -0.26 297 297
SDC2 0.01 0.015 -10000 0 -0.24 2 2
KNG1 -0.062 0.15 -10000 0 -0.36 128 128
Syndecan-2/Neurofibromin 0.024 0.017 -10000 0 -0.2 2 2
TRAPPC4 0.027 0.004 -10000 0 -10000 0 0
CSF2 -0.17 0.23 -10000 0 -0.45 250 250
Syndecan-2/TGFB1 0.024 0.021 -10000 0 -0.22 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.017 -10000 0 -0.18 3 3
Syndecan-2/Ezrin 0.038 0.022 -10000 0 -0.19 2 2
PRKACA 0.036 0.061 0.19 77 -0.18 2 79
angiogenesis -0.11 0.15 -10000 0 -0.26 297 297
MMP2 0.022 0.05 -10000 0 -0.41 8 8
IL8 -0.23 0.24 0.36 2 -0.44 338 340
calcineurin-NFAT signaling pathway -0.053 0.1 -10000 0 -0.21 192 192
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.034 0.096 -10000 0 -0.24 57 57
MAP4K1 -0.006 0.11 -10000 0 -0.36 53 53
MAP3K8 0.028 0.002 -10000 0 -10000 0 0
PRKCB -0.062 0.16 -10000 0 -0.36 141 141
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 -0.006 0.089 -10000 0 -0.32 30 30
JUN -0.13 0.27 -10000 0 -0.58 156 156
MAP3K7 -0.006 0.089 -10000 0 -0.32 31 31
GRAP2 0.014 0.069 -10000 0 -0.36 20 20
CRK 0.023 0.01 -10000 0 -10000 0 0
MAP2K4 -0.014 0.1 0.25 3 -0.36 35 38
LAT 0.025 0.035 -10000 0 -0.4 4 4
LCP2 0.023 0.038 -10000 0 -0.36 6 6
MAPK8 -0.13 0.29 -10000 0 -0.61 156 156
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.001 0.096 -10000 0 -0.33 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 0.041 0.091 -10000 0 -0.35 11 11
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.035 0.052 -10000 0 -0.21 24 24
RGS9BP 0.02 0.038 0.36 1 -0.44 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.01 0.032 0.36 1 -0.44 2 3
mol:Na + -0.052 0.12 0.23 6 -0.23 192 198
mol:ADP -0.013 0.035 0.27 1 -0.38 4 5
GNAT2 0.013 0.068 -10000 0 -0.44 13 13
RGS9-1/Gbeta5/R9AP 0.009 0.096 0.25 1 -0.21 94 95
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.022 0.044 -10000 0 -0.27 13 13
GRK7 0.009 0.043 -10000 0 -0.44 4 4
CNGB3 -0.017 0.099 0.36 8 -0.44 25 33
Cone Metarhodopsin II/X-Arrestin 0.013 0.023 -10000 0 -0.31 3 3
mol:Ca2+ -0.069 0.14 0.18 50 -0.3 64 114
Cone PDE6 0.023 0.094 0.25 1 -0.24 4 5
Cone Metarhodopsin II 0.02 0.031 0.22 1 -0.3 4 5
Na + (4 Units) -0.057 0.14 0.23 6 -0.23 216 222
GNAT2/GDP 0.015 0.095 0.24 1 -0.25 15 16
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.039 0.18 5 -0.25 13 18
Cone Transducin 0.038 0.055 -10000 0 -0.22 24 24
SLC24A2 -0.027 0.13 0.36 5 -0.44 52 57
GNB3/GNGT2 0.033 0.044 -10000 0 -0.27 12 12
GNB3 0.024 0.037 -10000 0 -0.42 4 4
GNAT2/GTP 0.012 0.048 -10000 0 -0.31 13 13
CNGA3 -0.11 0.18 -10000 0 -0.36 199 199
ARR3 -0.008 0.037 -10000 0 -0.44 3 3
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.052 0.12 0.23 6 -0.23 192 198
mol:Pi 0.009 0.096 0.25 1 -0.21 94 95
Cone CNG Channel -0.037 0.12 -10000 0 -0.28 33 33
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.027 0.13 0.36 5 -0.44 52 57
RGS9 -0.033 0.14 -10000 0 -0.36 93 93
PDE6C -0.005 0.02 -10000 0 -10000 0 0
GNGT2 0.022 0.044 -10000 0 -0.36 8 8
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.015 0.021 -10000 0 -0.44 1 1
Plasma membrane estrogen 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
GNB1/GNG2 0.028 0.085 -10000 0 -0.26 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.26 -10000 0 -0.57 112 112
AKT1 -0.063 0.28 -10000 0 -0.81 70 70
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.062 0.28 -10000 0 -0.83 70 70
mol:Ca2+ 0.02 0.071 -10000 0 -0.38 7 7
IGF1R 0.027 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.071 -10000 0 -0.21 55 55
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis 0.059 0.26 0.77 70 -10000 0 70
RhoA/GTP 0.007 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.043 0.22 0.21 1 -0.52 71 72
regulation of stress fiber formation 0.017 0.054 0.27 2 -0.3 1 3
E2/ERA-ERB (dimer) 0.011 0.073 -10000 0 -0.21 59 59
KRAS 0.026 0.016 -10000 0 -0.36 1 1
G13/GTP 0.014 0.063 -10000 0 -0.19 54 54
pseudopodium formation -0.017 0.054 0.3 1 -0.27 2 3
E2/ER alpha (dimer)/PELP1 0.011 0.067 -10000 0 -0.2 55 55
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
HRAS 0.027 0.016 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.084 0.23 0.21 3 -0.59 81 84
E2/ER beta (dimer) 0.017 0.025 -10000 0 -0.25 5 5
mol:GDP -0.016 0.099 -10000 0 -0.31 57 57
mol:NADP -0.084 0.23 0.21 3 -0.59 81 84
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.002 0.051 -10000 0 -0.4 7 7
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
PLCB1 0.006 0.055 0.17 3 -0.41 7 10
PLCB2 0.006 0.056 -10000 0 -0.41 8 8
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
mol:L-citrulline -0.084 0.23 0.21 3 -0.59 81 84
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP -0.23 0.35 -10000 0 -0.66 234 234
JNK cascade 0.017 0.025 -10000 0 -0.25 5 5
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
ESR2 0.022 0.036 -10000 0 -0.36 5 5
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
ESR1 -0.009 0.11 -10000 0 -0.36 55 55
Gq family/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.65 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.13 -10000 0 -0.6 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.042 0.21 -10000 0 -0.52 70 70
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
E2/ER alpha (dimer) -0.004 0.077 -10000 0 -0.25 55 55
STRN 0.028 0.003 -10000 0 -10000 0 0
GNAL 0.008 0.073 -10000 0 -0.36 23 23
PELP1 0.023 0.01 -10000 0 -10000 0 0
MAPK11 0.01 0.026 -10000 0 -0.23 7 7
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
HBEGF -0.021 0.26 0.31 133 -0.53 74 207
cAMP biosynthetic process 0 0.07 -10000 0 -0.19 59 59
SRC -0.066 0.25 0.21 109 -0.59 78 187
PI3K 0.039 0.015 -10000 0 -0.25 1 1
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.008 0.11 -10000 0 -0.29 52 52
SOS1 0.028 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.095 0.17 -10000 0 -0.41 106 106
Gs family/GTP 0.005 0.074 -10000 0 -0.19 59 59
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.024 -10000 0 -0.19 4 4
vasodilation -0.079 0.21 0.21 3 -0.56 81 84
mol:DAG 0.002 0.051 -10000 0 -0.4 7 7
Gs family/GDP/Gbeta gamma -0.016 0.1 -10000 0 -0.3 53 53
MSN -0.019 0.057 0.31 1 -0.28 2 3
Gq family/GTP 0.013 0.062 -10000 0 -0.43 8 8
mol:PI-3-4-5-P3 -0.058 0.27 -10000 0 -0.79 70 70
NRAS 0.026 0.023 -10000 0 -0.36 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.079 0.21 0.56 81 -0.21 3 84
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.1 -10000 0 -0.3 53 53
NOS3 -0.09 0.24 0.22 2 -0.63 81 83
GNA11 0.025 0.031 -10000 0 -0.36 4 4
MAPKKK cascade -0.04 0.22 0.3 2 -0.61 69 71
E2/ER alpha (dimer)/PELP1/Src -0.043 0.23 0.24 12 -0.53 75 87
ruffle organization -0.017 0.054 0.3 1 -0.27 2 3
ROCK2 -0.018 0.061 0.32 1 -0.31 2 3
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.025 0.26 0.37 111 -0.53 74 185
MMP2 -0.064 0.24 0.27 9 -0.56 76 85
LPA receptor mediated events

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
GNB1/GNG2 0.01 0.098 -10000 0 -0.32 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.004 0.09 0.31 2 -0.36 3 5
AP1 -0.031 0.085 -10000 0 -0.3 15 15
mol:PIP3 -0.026 0.073 -10000 0 -0.3 11 11
AKT1 0.005 0.076 0.24 5 -0.4 3 8
PTK2B -0.051 0.11 0.2 2 -0.31 49 51
RHOA 0.008 0.064 0.23 6 -0.33 12 18
PIK3CB 0.028 0.014 0.36 1 -10000 0 1
mol:Ca2+ -0.001 0.055 0.2 5 -0.33 2 7
MAGI3 0.026 0.016 -10000 0 -0.36 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.028 0.097 -10000 0 -0.22 110 110
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
positive regulation of microtubule depolymerization -0.081 0.12 0.23 5 -0.32 75 80
NF kappa B1 p50/RelA -0.032 0.082 -10000 0 -0.35 9 9
endothelial cell migration -0.014 0.088 -10000 0 -0.44 8 8
ADCY4 -0.084 0.17 0.24 1 -0.42 100 101
ADCY5 -0.17 0.23 0.24 1 -0.45 201 202
ADCY6 -0.08 0.16 0.24 1 -0.44 87 88
ADCY7 -0.079 0.16 0.24 1 -0.44 85 86
ADCY1 -0.08 0.16 -10000 0 -0.43 86 86
ADCY2 -0.11 0.21 0.24 1 -0.46 132 133
ADCY3 -0.08 0.16 0.24 1 -0.44 87 88
ADCY8 -0.076 0.16 0.24 1 -0.43 82 83
ADCY9 -0.08 0.16 0.24 1 -0.43 88 89
GSK3B -0.049 0.11 0.2 2 -0.36 29 31
arachidonic acid secretion -0.099 0.18 -10000 0 -0.44 96 96
GNG2 0.011 0.074 -10000 0 -0.36 23 23
TRIP6 0.012 0.019 -10000 0 -0.3 1 1
GNAO1 -0.089 0.14 -10000 0 -0.25 241 241
HRAS 0.027 0.016 -10000 0 -0.36 1 1
NFKBIA -0.021 0.089 0.3 3 -0.34 8 11
GAB1 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.089 0.32 -10000 0 -0.84 94 94
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.021 -10000 0 -0.24 2 2
TIAM1 -0.12 0.37 -10000 0 -0.99 94 94
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.01 0.052 0.21 5 -0.34 2 7
PLCB3 0.016 0.025 0.18 8 -0.21 2 10
FOS 0.022 0.039 -10000 0 -0.36 6 6
positive regulation of mitosis -0.099 0.18 -10000 0 -0.44 96 96
LPA/LPA1-2-3 0.001 0.1 -10000 0 -0.31 17 17
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
stress fiber formation -0.028 0.093 0.22 3 -0.29 27 30
GNAZ -0.013 0.08 -10000 0 -0.21 79 79
EGFR/PI3K-beta/Gab1 -0.012 0.082 -10000 0 -0.31 11 11
positive regulation of dendritic cell cytokine production 0 0.1 -10000 0 -0.31 17 17
LPA/LPA2/MAGI-3 0.036 0.021 -10000 0 -0.23 2 2
ARHGEF1 0.008 0.089 0.33 5 -0.33 2 7
GNAI2 -0.01 0.076 -10000 0 -0.21 63 63
GNAI3 -0.012 0.078 -10000 0 -0.21 80 80
GNAI1 -0.018 0.091 -10000 0 -0.23 85 85
LPA/LPA3 -0.001 0.072 -10000 0 -0.26 44 44
LPA/LPA2 0.02 0.018 -10000 0 -0.31 1 1
LPA/LPA1 -0.012 0.095 -10000 0 -0.24 86 86
HB-EGF/EGFR 0.004 0.072 0.2 14 -0.26 34 48
HBEGF -0.004 0.086 0.27 15 -0.31 34 49
mol:DAG -0.01 0.052 0.21 5 -0.34 2 7
cAMP biosynthetic process -0.11 0.18 0.27 5 -0.47 86 91
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.003 0.091 0.28 7 -0.35 6 13
GNAQ -0.001 0.058 -10000 0 -0.2 47 47
LPAR2 0.026 0.019 -10000 0 -0.44 1 1
LPAR3 -0.009 0.1 -10000 0 -0.37 44 44
LPAR1 -0.022 0.13 -10000 0 -0.36 80 80
IL8 -0.085 0.14 0.32 2 -0.39 15 17
PTK2 -0.021 0.079 -10000 0 -0.34 8 8
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
CASP3 -0.028 0.098 -10000 0 -0.22 110 110
EGFR 0.023 0.023 -10000 0 -0.36 2 2
PLCG1 -0.008 0.053 -10000 0 -0.2 37 37
PLD2 -0.022 0.081 -10000 0 -0.33 10 10
G12/G13 0.02 0.082 -10000 0 -0.35 2 2
PI3K-beta -0.004 0.073 -10000 0 -0.38 6 6
cell migration -0.017 0.11 -10000 0 -0.25 87 87
SLC9A3R2 0.026 0.016 -10000 0 -0.36 1 1
PXN -0.028 0.095 0.22 3 -0.29 27 30
HRAS/GTP -0.1 0.18 -10000 0 -0.45 97 97
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
PRKCE 0.027 0.003 -10000 0 -10000 0 0
PRKCD -0.003 0.058 0.24 7 -0.4 1 8
Gi(beta/gamma) -0.085 0.17 -10000 0 -0.41 100 100
mol:LPA 0.001 0.014 -10000 0 -0.13 6 6
TRIP6/p130 Cas/FAK1/Paxillin 0.01 0.1 0.23 1 -0.36 10 11
MAPKKK cascade -0.099 0.18 -10000 0 -0.44 96 96
contractile ring contraction involved in cytokinesis 0.01 0.065 0.23 6 -0.33 12 18
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.002 0.06 -10000 0 -0.2 50 50
GNA15 -0.002 0.059 -10000 0 -0.19 51 51
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.083 0.12 0.24 4 -0.33 75 79
GNA11 -0.001 0.058 -10000 0 -0.2 49 49
Rac1/GTP -0.095 0.34 -10000 0 -0.89 94 94
MMP2 -0.014 0.089 -10000 0 -0.44 8 8
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.008 0.14 -9999 0 -0.53 25 25
MAP3K8 0.028 0.003 -9999 0 -10000 0 0
FOS -0.022 0.14 -9999 0 -0.53 25 25
PRKCA 0.027 0.007 -9999 0 -10000 0 0
PTPN7 0.017 0.066 -9999 0 -0.41 14 14
HRAS 0.027 0.016 -9999 0 -0.36 1 1
PRKCB -0.062 0.16 -9999 0 -0.36 141 141
NRAS 0.026 0.023 -9999 0 -0.36 2 2
RAS family/GTP 0.049 0.024 -9999 0 -0.19 4 4
MAPK3 -0.002 0.097 -9999 0 -0.6 9 9
MAP2K1 -0.057 0.16 -9999 0 -0.34 134 134
ELK1 0.027 0.007 -9999 0 -10000 0 0
BRAF -0.052 0.14 -9999 0 -0.33 124 124
mol:GTP 0 0 -9999 0 -0.004 10 10
MAPK1 -0.022 0.15 -9999 0 -0.58 32 32
RAF1 -0.056 0.15 -9999 0 -0.33 135 135
KRAS 0.026 0.016 -9999 0 -0.36 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0 0.15 0.27 9 -0.48 39 48
FYN -0.027 0.18 0.21 8 -0.54 53 61
LAT/GRAP2/SLP76 -0.006 0.16 0.19 2 -0.49 45 47
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.022 0.13 0.19 6 -0.39 55 61
B2M 0.025 0.018 -10000 0 -0.36 1 1
IKBKG -0.002 0.045 0.088 27 -0.14 19 46
MAP3K8 0.028 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.032 0.088 5 -0.11 53 58
integrin-mediated signaling pathway 0.033 0.025 -10000 0 -0.2 6 6
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.19 0.22 4 -0.55 56 60
TRPV6 -0.002 0.26 1.2 22 -0.44 52 74
CD28 0.012 0.078 -10000 0 -0.36 25 25
SHC1 -0.027 0.18 0.27 10 -0.51 54 64
receptor internalization -0.034 0.2 -10000 0 -0.56 58 58
PRF1 -0.032 0.22 -10000 0 -0.84 31 31
KRAS 0.026 0.016 -10000 0 -0.36 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.005 0.11 0.19 6 -0.32 49 55
LAT -0.03 0.18 0.19 4 -0.51 55 59
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.017 0.063 -10000 0 -0.37 16 16
CD3E 0.014 0.072 -10000 0 -0.37 21 21
CD3G -0.003 0.1 -10000 0 -0.36 47 47
RASGRP2 -0.01 0.055 -10000 0 -0.17 61 61
RASGRP1 -0.001 0.14 0.23 6 -0.4 48 54
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.023 0.038 -10000 0 -0.36 6 6
RAP1A/GTP/RAPL 0.033 0.025 -10000 0 -0.2 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.058 0.15 17 -0.12 37 54
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.018 0.063 -10000 0 -0.21 40 40
PRKCA 0.023 0.094 0.16 35 -0.26 32 67
GRAP2 0.014 0.069 -10000 0 -0.36 20 20
mol:IP3 -0.008 0.12 0.2 50 -0.39 37 87
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.16 -10000 0 -0.52 49 49
ORAI1 -0.013 0.2 -10000 0 -0.97 22 22
CSK -0.026 0.17 0.22 3 -0.52 53 56
B7 family/CD28 -0.002 0.19 -10000 0 -0.59 46 46
CHUK 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.034 0.2 0.19 1 -0.57 58 59
PTPN6 -0.03 0.18 0.21 6 -0.51 55 61
VAV1 -0.035 0.18 0.23 4 -0.53 57 61
Monovalent TCR/CD3 -0.014 0.13 -10000 0 -0.36 58 58
CBL 0.027 0.004 -10000 0 -10000 0 0
LCK -0.03 0.18 0.19 10 -0.52 57 67
PAG1 -0.018 0.18 0.19 49 -0.52 52 101
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.033 0.2 0.19 1 -0.57 57 58
CD80 0.024 0.035 -10000 0 -0.4 4 4
CD86 0.019 0.057 -10000 0 -0.36 13 13
PDK1/CARD11/BCL10/MALT1 -0.013 0.08 -10000 0 -0.25 41 41
HRAS 0.027 0.016 -10000 0 -0.36 1 1
GO:0035030 -0.027 0.15 0.16 1 -0.47 50 51
CD8A -0.001 0.1 -10000 0 -0.37 45 45
CD8B 0.018 0.062 -10000 0 -0.37 15 15
PTPRC -0.004 0.1 -10000 0 -0.36 48 48
PDK1/PKC theta -0.018 0.16 0.23 8 -0.48 48 56
CSK/PAG1 -0.015 0.17 0.2 51 -0.53 45 96
SOS1 0.028 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.015 -10000 0 -0.25 1 1
GRAP2/SLP76 -0.007 0.18 0.2 3 -0.55 49 52
STIM1 0.008 0.11 1.2 4 -0.93 1 5
RAS family/GTP 0.022 0.068 0.15 15 -0.18 26 41
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.037 0.21 -10000 0 -0.6 58 58
mol:DAG -0.021 0.098 0.12 1 -0.33 42 43
RAP1A/GDP 0.011 0.028 0.077 14 -0.063 13 27
PLCG1 0.016 0.014 -10000 0 -10000 0 0
CD247 0.018 0.059 -10000 0 -0.37 14 14
cytotoxic T cell degranulation -0.029 0.21 -10000 0 -0.8 31 31
RAP1A/GTP -0.004 0.021 -10000 0 -0.063 61 61
mol:PI-3-4-5-P3 -0.025 0.16 0.2 5 -0.46 54 59
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.15 0.22 44 -0.5 37 81
NRAS 0.026 0.023 -10000 0 -0.36 2 2
ZAP70 0.019 0.06 -10000 0 -0.37 14 14
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.015 0.16 0.21 1 -0.48 47 48
MALT1 0.02 0.02 -10000 0 -0.36 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.014 0.096 -10000 0 -0.29 52 52
CARD11 0.004 0.099 0.36 2 -0.41 31 33
PRKCB 0.001 0.12 0.15 29 -0.28 59 88
PRKCE 0.024 0.096 0.15 37 -0.26 33 70
PRKCQ -0.021 0.18 0.24 4 -0.53 51 55
LCP2 0.023 0.038 -10000 0 -0.36 6 6
BCL10 0.026 0.016 -10000 0 -0.36 1 1
regulation of survival gene product expression -0.017 0.12 0.19 6 -0.34 53 59
IKK complex 0.021 0.064 0.11 147 -0.11 28 175
RAS family/GDP -0.002 0.011 -10000 0 -0.06 2 2
MAP3K14 -0.007 0.086 0.16 6 -0.25 45 51
PDPK1 -0.018 0.12 0.19 9 -0.38 48 57
TCR/CD3/MHC I/CD8/Fyn -0.037 0.2 -10000 0 -0.58 58 58
IGF1 pathway

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.028 0.001 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.028 0.083 -10000 0 -0.19 129 129
GRB2/SOS1/SHC 0.054 0.012 -10000 0 -10000 0 0
HRAS 0.027 0.016 -10000 0 -0.36 1 1
IRS1/Crk -0.023 0.087 -10000 0 -0.19 106 106
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.085 -10000 0 -0.2 88 88
AKT1 -0.043 0.068 0.2 3 -0.29 1 4
BAD -0.043 0.065 0.19 3 -0.28 1 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.076 -10000 0 -0.19 103 103
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.018 0.093 -10000 0 -0.19 141 141
RAF1 -0.028 0.088 0.27 1 -0.46 9 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.007 0.1 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.019 0.1 -10000 0 -0.2 141 141
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
RPS6KB1 -0.043 0.068 0.2 3 -0.32 1 4
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.011 0.082 0.25 4 -0.39 4 8
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.012 0.084 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.023 0.1 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.008 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.005 0.1 -10000 0 -0.19 141 141
Crk/p130 Cas/Paxillin 0.009 0.098 -10000 0 -10000 0 0
IGF1R 0.008 0.038 -10000 0 -10000 0 0
IGF1 -0.065 0.17 -10000 0 -0.38 141 141
IRS2/Crk -0.015 0.073 -10000 0 -10000 0 0
PI3K 0.006 0.1 -10000 0 -0.34 1 1
apoptosis 0.035 0.057 -10000 0 -0.24 1 1
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
PRKCD -0.055 0.13 -10000 0 -0.29 134 134
RAF1/14-3-3 E -0.011 0.082 0.26 2 -0.38 10 12
BAD/14-3-3 -0.037 0.06 0.25 1 -10000 0 1
PRKCZ -0.043 0.068 0.2 3 -0.32 1 4
Crk/p130 Cas/Paxillin/FAK1 -0.007 0.074 -10000 0 -10000 0 0
PTPN1 0.016 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.052 0.14 -10000 0 -0.3 143 143
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.011 0.097 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.018 0.094 -10000 0 -0.19 141 141
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.031 0.086 -10000 0 -0.19 141 141
IRS1 -0.034 0.093 -10000 0 -0.2 141 141
IRS2 -0.022 0.075 -10000 0 -0.19 103 103
IGF-1R heterotetramer/IGF1 -0.032 0.13 -10000 0 -0.27 141 141
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 -0.028 0.079 0.28 1 -0.33 1 2
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKD1 -0.056 0.13 0.2 1 -0.3 133 134
SHC1 0.027 0.004 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.032 0.1 0.17 1 -0.3 44 45
FZD6 0.024 0.01 -10000 0 -10000 0 0
WNT6 -0.011 0.11 -10000 0 -0.38 52 52
WNT4 0.013 0.072 -10000 0 -0.38 20 20
FZD3 0.021 0.035 0.36 2 -0.44 2 4
WNT5A 0.022 0.05 -10000 0 -0.44 7 7
WNT11 -0.069 0.19 -10000 0 -0.44 127 127
Effects of Botulinum toxin

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
STX1A -0.008 0.073 0.26 3 -0.31 31 34
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.026 -10000 0 -0.32 3 3
STXBP1 0.022 0.05 -10000 0 -0.44 7 7
ACh/CHRNA1 -0.039 0.085 -10000 0 -0.21 77 77
RAB3GAP2/RIMS1/UNC13B 0.049 0.029 -10000 0 -0.26 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.009 0.042 -10000 0 -0.44 4 4
mol:ACh -0.037 0.064 0.08 44 -0.11 212 256
RAB3GAP2 0.027 0.016 -10000 0 -0.36 1 1
STX1A/SNAP25/VAMP2 -0.038 0.1 -10000 0 -0.28 10 10
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.039 0.085 -10000 0 -0.21 77 77
UNC13B 0.027 0.004 -10000 0 -10000 0 0
CHRNA1 -0.008 0.11 -10000 0 -0.36 55 55
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.045 0.095 -10000 0 -0.23 95 95
SNAP25 -0.07 0.11 0.18 1 -0.24 188 189
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.02 0.13 -10000 0 -0.36 75 75
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.008 0.071 0.2 3 -0.27 35 38
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.1 -10000 0 -0.28 10 10
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.23 0.35 -10000 0 -1.1 48 48
IL23A -0.27 0.35 -10000 0 -1.1 50 50
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.35 -10000 0 -1 56 56
positive regulation of T cell mediated cytotoxicity -0.24 0.36 -10000 0 -1.1 55 55
ITGA3 -0.23 0.33 -10000 0 -1 42 42
IL17F -0.21 0.26 -10000 0 -0.67 75 75
IL12B -0.014 0.054 -10000 0 -0.47 4 4
STAT1 (dimer) -0.23 0.35 -10000 0 -1 55 55
CD4 -0.23 0.36 -10000 0 -1.1 55 55
IL23 -0.26 0.34 -10000 0 -1 51 51
IL23R -0.071 0.25 -10000 0 -1.1 32 32
IL1B -0.26 0.36 -10000 0 -1.1 50 50
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.34 -10000 0 -0.99 60 60
TYK2 -0.004 0.033 -10000 0 -10000 0 0
STAT4 0.011 0.08 -10000 0 -0.36 27 27
STAT3 0.026 0.006 -10000 0 -10000 0 0
IL18RAP 0.006 0.083 -10000 0 -0.36 29 29
IL12RB1 -0.016 0.076 -10000 0 -0.39 20 20
PIK3CA 0.026 0.017 -10000 0 -0.36 1 1
IL12Rbeta1/TYK2 -0.01 0.066 -10000 0 -0.28 20 20
IL23R/JAK2 -0.072 0.24 -10000 0 -1 29 29
positive regulation of chronic inflammatory response -0.24 0.36 -10000 0 -1.1 55 55
natural killer cell activation 0.005 0.013 0.079 15 -10000 0 15
JAK2 -0.008 0.047 -10000 0 -0.38 3 3
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.33 -10000 0 -0.98 51 51
ALOX12B -0.22 0.33 -10000 0 -1 40 40
CXCL1 -0.27 0.35 -10000 0 -0.98 65 65
T cell proliferation -0.24 0.36 -10000 0 -1.1 55 55
NFKBIA 0.024 0.007 -10000 0 -10000 0 0
IL17A -0.2 0.23 -10000 0 -0.56 86 86
PI3K -0.23 0.35 -10000 0 -1 58 58
IFNG -0.01 0.036 0.14 13 -0.11 8 21
STAT3 (dimer) -0.24 0.35 -10000 0 -0.97 59 59
IL18R1 0.019 0.05 -10000 0 -0.36 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.23 -10000 0 -0.73 43 43
IL18/IL18R 0.033 0.073 -10000 0 -0.22 31 31
macrophage activation -0.017 0.017 -10000 0 -0.044 34 34
TNF -0.25 0.35 -10000 0 -1.1 44 44
STAT3/STAT4 -0.23 0.35 -10000 0 -1 56 56
STAT4 (dimer) -0.24 0.36 -10000 0 -1.1 57 57
IL18 0.023 0.03 -10000 0 -0.36 3 3
IL19 -0.22 0.32 -10000 0 -1 45 45
STAT5A (dimer) -0.23 0.35 -10000 0 -1 53 53
STAT1 0.027 0.019 -10000 0 -0.44 1 1
SOCS3 0.026 0.027 -10000 0 -0.44 2 2
CXCL9 -0.24 0.34 -10000 0 -1 53 53
MPO -0.22 0.32 -10000 0 -1 45 45
positive regulation of humoral immune response -0.24 0.36 -10000 0 -1.1 55 55
IL23/IL23R/JAK2/TYK2 -0.25 0.38 -10000 0 -1.1 55 55
IL6 -0.24 0.36 -10000 0 -1.1 53 53
STAT5A 0.027 0.004 -10000 0 -10000 0 0
IL2 0.013 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.013 0.079 15 -10000 0 15
CD3E -0.24 0.37 -10000 0 -1.1 66 66
keratinocyte proliferation -0.24 0.36 -10000 0 -1.1 55 55
NOS2 -0.25 0.37 -10000 0 -1.1 58 58
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.036 0.24 0.39 3 -0.78 42 45
NCK1/PAK1/Dok-R -0.029 0.099 -10000 0 -0.39 40 40
NCK1/Dok-R 0.007 0.26 -10000 0 -0.91 41 41
PIK3CA 0.026 0.016 -10000 0 -0.36 1 1
mol:beta2-estradiol 0.004 0.053 0.25 27 -10000 0 27
RELA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.028 0.005 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
F2 -0.14 0.23 0.27 27 -0.46 197 224
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.042 0.25 -10000 0 -0.85 42 42
FN1 0.001 0.11 -10000 0 -0.43 36 36
PLD2 -0.028 0.26 -10000 0 -0.93 42 42
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB14 -0.005 0.1 -10000 0 -0.39 42 42
ELK1 0.009 0.25 0.37 1 -0.85 43 44
GRB7 0.035 0.049 0.36 14 -10000 0 14
PAK1 0.027 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.031 0.27 -10000 0 -0.9 42 42
CDKN1A 0.038 0.19 0.41 5 -0.6 29 34
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.007 0.26 -10000 0 -0.91 41 41
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:NO 0.05 0.2 0.39 19 -0.59 43 62
PLG -0.059 0.27 -10000 0 -0.96 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.026 0.23 -10000 0 -0.75 42 42
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
ANGPT2 -0.025 0.2 0.43 2 -0.74 15 17
BMX -0.063 0.28 -10000 0 -1 42 42
ANGPT1 0.007 0.25 0.34 1 -1.1 28 29
tube development 0.027 0.21 0.4 10 -0.64 33 43
ANGPT4 0.012 0.039 -10000 0 -0.44 4 4
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.007 0.29 -10000 0 -0.96 43 43
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
FGF2 -0.001 0.099 -10000 0 -0.36 43 43
STAT5A (dimer) 0.035 0.23 0.43 1 -0.74 32 33
mol:L-citrulline 0.05 0.2 0.39 19 -0.59 43 62
AGTR1 -0.11 0.18 -10000 0 -0.36 214 214
MAPK14 -0.001 0.28 -10000 0 -0.97 43 43
Tie2/SHP2 0.019 0.2 -10000 0 -0.98 22 22
TEK -0.007 0.22 -10000 0 -1.1 22 22
RPS6KB1 0.034 0.24 0.44 3 -0.75 43 46
Angiotensin II/AT1 -0.073 0.13 -10000 0 -0.25 214 214
Tie2/Ang1/GRB2 0.018 0.28 -10000 0 -0.96 42 42
MAPK3 -0.017 0.24 -10000 0 -0.86 42 42
MAPK1 -0.018 0.24 -10000 0 -0.86 42 42
Tie2/Ang1/GRB7 0.022 0.28 -10000 0 -0.95 42 42
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.024 0.26 -10000 0 -0.94 42 42
PI3K 0.022 0.27 -10000 0 -0.89 43 43
FES -0.01 0.29 -10000 0 -0.98 43 43
Crk/Dok-R 0.003 0.26 -10000 0 -0.91 41 41
Tie2/Ang1/ABIN2 0.018 0.28 -10000 0 -0.95 43 43
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.044 0.22 0.37 5 -0.69 43 48
STAT5A 0.028 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.055 0.25 0.42 20 -0.74 41 61
Tie2/Ang2 -0.009 0.25 0.45 1 -0.88 32 33
Tie2/Ang1 -0.022 0.28 -10000 0 -1 42 42
FOXO1 0.061 0.24 0.41 19 -0.72 36 55
ELF1 0.021 0.029 -10000 0 -10000 0 0
ELF2 -0.021 0.26 -10000 0 -0.94 42 42
mol:Choline -0.026 0.25 -10000 0 -0.89 42 42
cell migration -0.014 0.06 -10000 0 -0.22 42 42
FYN 0.021 0.23 0.44 5 -0.74 32 37
DOK2 0.016 0.045 -10000 0 -0.36 8 8
negative regulation of cell cycle 0.041 0.18 0.37 14 -0.55 29 43
ETS1 0.02 0.064 -10000 0 -0.27 27 27
PXN 0.06 0.22 0.39 33 -0.62 41 74
ITGB1 0.028 0.002 -10000 0 -10000 0 0
NOS3 0.046 0.22 0.4 15 -0.67 42 57
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF 0.019 0.07 -10000 0 -0.28 29 29
MAPKKK cascade -0.026 0.25 -10000 0 -0.89 42 42
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.02 0.28 -10000 0 -0.96 42 42
NCK1 0.028 0.002 -10000 0 -10000 0 0
vasculogenesis 0.053 0.19 0.36 27 -0.53 43 70
mol:Phosphatidic acid -0.026 0.25 -10000 0 -0.89 42 42
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.05 0.2 0.39 19 -0.59 43 62
Rac1/GTP 0.03 0.22 -10000 0 -0.71 41 41
MMP2 -0.026 0.26 -10000 0 -0.94 42 42
LPA4-mediated signaling events

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
ADCY4 -0.006 0.002 -10000 0 -10000 0 0
ADCY5 -0.097 0.1 -10000 0 -0.21 272 272
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.001 -10000 0 -10000 0 0
ADCY1 -0.011 0.039 0.21 2 -0.26 14 16
ADCY2 -0.035 0.071 -10000 0 -0.21 85 85
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.012 0.031 0.21 1 -0.27 8 9
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.012 -10000 0 -0.21 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.017 0.075 0.19 19 -0.2 5 24
Osteopontin-mediated 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
IKK alpha homodimer -0.078 0.13 -10000 0 -0.28 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.063 0.13 0.31 6 -0.33 3 9
alphaV/beta3 Integrin/Osteopontin/Src -0.11 0.18 -10000 0 -0.31 263 263
AP1 -0.06 0.14 -10000 0 -0.46 7 7
ILK -0.088 0.13 -10000 0 -0.28 34 34
bone resorption -0.073 0.12 0.33 1 -0.35 4 5
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
PYK2/p130Cas -0.06 0.14 -10000 0 -0.32 10 10
ITGAV 0.03 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.017 -10000 0 -0.25 2 2
alphaV/beta3 Integrin/Osteopontin -0.082 0.16 -10000 0 -0.26 259 259
MAP3K1 -0.091 0.13 -10000 0 -0.29 36 36
JUN 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.093 0.12 0.19 1 -0.32 37 38
MAPK1 -0.092 0.12 0.19 1 -0.31 36 37
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.09 0.12 0.19 7 -0.28 35 42
ITGB3 0.025 0.041 -10000 0 -0.36 7 7
NFKBIA -0.083 0.11 -10000 0 -0.31 37 37
FOS 0.022 0.039 -10000 0 -0.36 6 6
CD44 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
PLAU -0.08 0.14 -10000 0 -0.47 7 7
NF kappa B1 p50/RelA -0.061 0.14 -10000 0 -0.34 6 6
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.04 0.033 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.09 0.13 -10000 0 -0.28 36 36
VAV3 -0.1 0.13 0.19 7 -0.33 65 72
MAP3K14 -0.092 0.13 -10000 0 -0.3 36 36
ROCK2 0.026 0.022 -10000 0 -0.36 2 2
SPP1 -0.17 0.23 -10000 0 -0.44 263 263
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.085 0.13 -10000 0 -0.34 41 41
MMP2 -0.072 0.11 -10000 0 -0.53 7 7
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.019 0.091 -10000 0 -0.28 37 37
alphaM/beta2 Integrin/GPIbA 0.012 0.085 -10000 0 -0.35 14 14
alphaM/beta2 Integrin/proMMP-9 0.003 0.1 0.25 15 -0.3 36 51
PLAUR 0.027 0.004 -10000 0 -10000 0 0
HMGB1 0.015 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.022 0.083 -10000 0 -0.37 12 12
AGER 0.018 0.033 -10000 0 -0.49 1 1
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.026 0.022 -10000 0 -0.36 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.021 0.094 -10000 0 -0.39 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0 0.12 0.36 15 -0.44 32 47
CYR61 0.022 0.046 -10000 0 -0.44 6 6
TLN1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.022 0.1 -10000 0 -0.32 23 23
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.019 0.12 -10000 0 -0.36 72 72
MYH2 -0.038 0.095 -10000 0 -0.32 19 19
MST1R 0.027 0.016 -10000 0 -0.36 1 1
leukocyte activation during inflammatory response -0.02 0.12 -10000 0 -0.27 66 66
APOB -0.046 0.14 -10000 0 -0.38 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.05 -10000 0 -0.41 8 8
JAM3 0.027 0.004 -10000 0 -10000 0 0
GP1BA 0.014 0.043 -10000 0 -0.36 7 7
alphaM/beta2 Integrin/CTGF 0.02 0.086 -10000 0 -0.35 15 15
alphaM/beta2 Integrin -0.037 0.1 -10000 0 -0.3 41 41
JAM3 homodimer 0.027 0.004 -10000 0 -10000 0 0
ICAM2 0.027 0.005 -10000 0 -10000 0 0
ICAM1 0.027 0.019 -10000 0 -0.44 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.037 0.1 -10000 0 -0.3 41 41
cell adhesion 0.012 0.085 -10000 0 -0.35 14 14
NFKB1 0.02 0.13 0.48 4 -0.44 12 16
THY1 0.01 0.087 -10000 0 -0.44 22 22
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.021 0.11 -10000 0 -0.24 118 118
alphaM/beta2 Integrin/LRP/tPA 0.037 0.078 -10000 0 -0.31 11 11
IL6 -0.01 0.16 -10000 0 -0.59 12 12
ITGB2 0.012 0.055 -10000 0 -0.36 10 10
elevation of cytosolic calcium ion concentration 0.02 0.11 -10000 0 -0.28 52 52
alphaM/beta2 Integrin/JAM2/JAM3 -0.008 0.14 -10000 0 -0.38 36 36
JAM2 -0.058 0.16 -10000 0 -0.36 133 133
alphaM/beta2 Integrin/ICAM1 0.006 0.13 -10000 0 -0.33 28 28
alphaM/beta2 Integrin/uPA/Plg -0.047 0.15 -10000 0 -0.27 164 164
RhoA/GTP -0.041 0.1 -10000 0 -0.31 38 38
positive regulation of phagocytosis -0.026 0.094 0.18 2 -0.41 15 17
Ron/MSP -0.017 0.13 -10000 0 -0.32 99 99
alphaM/beta2 Integrin/uPAR/uPA 0.021 0.11 -10000 0 -0.28 52 52
alphaM/beta2 Integrin/uPAR 0.022 0.083 -10000 0 -0.37 12 12
PLAU -0.005 0.12 -10000 0 -0.44 42 42
PLAT 0.022 0.03 -10000 0 -0.39 3 3
actin filament polymerization -0.038 0.096 0.22 3 -0.32 18 21
MST1 -0.048 0.17 -10000 0 -0.44 98 98
alphaM/beta2 Integrin/lipoprotein(a) -0.017 0.12 -10000 0 -0.27 66 66
TNF 0.012 0.13 0.37 2 -0.66 7 9
RAP1B 0.028 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.11 -10000 0 -0.3 54 54
fibrinolysis -0.048 0.15 -10000 0 -0.27 164 164
HCK 0.011 0.047 -10000 0 -0.36 9 9
dendritic cell antigen processing and presentation -0.037 0.1 -10000 0 -0.3 41 41
VTN 0.006 0.082 -10000 0 -0.44 19 19
alphaM/beta2 Integrin/CYR61 0.02 0.088 -10000 0 -0.27 36 36
LPA -0.015 0.099 -10000 0 -0.45 29 29
LRP1 0.026 0.022 -10000 0 -0.36 2 2
cell migration -0.002 0.097 0.21 12 -0.3 39 51
FN1 0.001 0.11 -10000 0 -0.43 36 36
alphaM/beta2 Integrin/Thy1 0.011 0.1 -10000 0 -0.31 34 34
MPO 0.008 0.084 -10000 0 -0.44 20 20
KNG1 -0.062 0.15 -10000 0 -0.36 128 128
RAP1/GDP 0.036 0.008 -10000 0 -10000 0 0
ROCK1 -0.035 0.097 0.25 2 -0.34 14 16
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.095 0.18 0.36 1 -0.45 127 128
CTGF 0.025 0.033 -10000 0 -0.44 3 3
alphaM/beta2 Integrin/Hck 0.011 0.076 -10000 0 -0.29 22 22
ITGAM -0.002 0.092 -10000 0 -0.36 34 34
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.016 0.12 -10000 0 -0.38 24 24
HP -0.007 0.11 -10000 0 -0.44 34 34
leukocyte adhesion -0.027 0.13 -10000 0 -0.4 31 31
SELP -0.019 0.12 -10000 0 -0.36 72 72
Canonical Wnt signaling 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
HDAC1 0.027 0.011 -10000 0 -10000 0 0
AES 0.027 0.009 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.02 -10000 0 -0.25 2 2
SMAD4 0.02 0.013 -10000 0 -10000 0 0
DKK2 -0.042 0.16 -10000 0 -0.44 89 89
TLE1 0.027 0.017 -10000 0 -0.35 1 1
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.044 0.078 0.28 11 -0.31 2 13
WIF1 -0.08 0.18 0.35 1 -0.44 125 126
beta catenin/RanBP3 0.03 0.082 0.29 12 -10000 0 12
KREMEN2 -0.028 0.15 0.36 2 -0.44 73 75
DKK1 -0.075 0.19 0.36 1 -0.44 128 129
beta catenin/beta TrCP1 0.056 0.076 0.3 9 -0.32 1 10
FZD1 0.026 0.023 -10000 0 -0.36 2 2
AXIN2 -0.009 0.12 0.55 10 -10000 0 10
AXIN1 0.027 0.016 -10000 0 -0.36 1 1
RAN 0.028 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.032 0.062 -10000 0 -0.51 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.15 0.3 3 -0.5 26 29
Axin1/APC/GSK3 0.055 0.065 0.22 10 -0.28 6 16
Axin1/APC/GSK3/beta catenin/Macf1 0.025 0.07 0.28 2 -0.35 2 4
HNF1A 0.026 0.024 -10000 0 -0.36 2 2
CTBP1 0.027 0.009 -10000 0 -10000 0 0
MYC 0.097 0.21 0.58 91 -10000 0 91
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.03 0.14 0.23 2 -0.27 154 156
NKD1 -0.28 0.23 0.36 8 -0.44 401 409
TCF4 0.019 0.026 -10000 0 -0.36 2 2
TCF3 0.027 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.062 0.035 -10000 0 -0.22 6 6
Ran/GTP 0.02 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.013 0.09 0.31 1 -0.42 7 8
LEF1 -0.031 0.16 -10000 0 -0.45 75 75
DVL1 0.027 0.057 0.18 1 -0.37 5 6
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.021 0.1 0.34 2 -0.58 8 10
DKK1/LRP6/Kremen 2 -0.049 0.16 0.25 1 -0.29 183 184
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.01 -10000 0 -10000 0 0
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 0.003 0.049 0.55 1 -10000 0 1
WNT1 0.018 0.036 -10000 0 -0.44 3 3
GSK3A 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.028 0.002 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.14 0.1 0.24 138 -0.26 1 139
APC 0.009 0.067 0.22 35 -0.23 3 38
WNT1/LRP6/FZD1 0.041 0.053 0.22 6 -0.2 1 7
CREBBP 0.027 0.009 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.02 0.079 -10000 0 -0.2 66 66
regulation of S phase of mitotic cell cycle 0.003 0.047 -10000 0 -0.2 30 30
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
HRAS 0.027 0.016 -10000 0 -0.36 1 1
SHBG/T-DHT 0.011 0.037 -10000 0 -0.32 7 7
PELP1 0.023 0.01 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 0.049 0.097 0.17 212 -10000 0 212
T-DHT/AR -0.002 0.072 -10000 0 -0.25 47 47
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.009 10 10
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
mol:GDP -0.019 0.078 -10000 0 -0.28 45 45
cell proliferation 0.041 0.11 0.25 10 -0.35 8 18
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
FOS 0.034 0.12 0.26 1 -0.73 10 11
mol:Ca2+ -0.017 0.03 -10000 0 -0.078 68 68
MAPK3 0.046 0.1 0.27 11 -0.28 2 13
MAPK1 0.021 0.1 0.21 1 -0.4 22 23
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 10 10
cAMP biosynthetic process 0.002 0.039 -10000 0 -0.3 7 7
GNG2 0.011 0.074 -10000 0 -0.36 23 23
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 10 10
HRAS/GTP 0.018 0.051 -10000 0 -0.22 1 1
actin cytoskeleton reorganization 0.035 0.021 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 10 10
PI3K 0.035 0.013 -10000 0 -0.21 1 1
apoptosis -0.042 0.096 0.35 12 -0.22 5 17
T-DHT/AR/PELP1 0.012 0.064 -10000 0 -0.2 47 47
HRAS/GDP -0.008 0.078 -10000 0 -0.29 39 39
CREB1 0.042 0.1 0.24 3 -0.37 12 15
RAC1-CDC42/GTP 0.044 0.025 -10000 0 -10000 0 0
AR -0.009 0.1 -10000 0 -0.36 47 47
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 0.063 0.097 0.18 193 -10000 0 193
RAC1-CDC42/GDP 0.033 0.093 -10000 0 -0.31 29 29
T-DHT/AR/PELP1/Src 0.017 0.054 -10000 0 -0.19 30 30
MAP2K2 0.048 0.098 0.17 214 -0.31 1 215
T-DHT/AR/PELP1/Src/PI3K 0.003 0.048 -10000 0 -0.2 30 30
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
SHBG 0.01 0.061 -10000 0 -0.52 7 7
Gi family/GNB1/GNG2/GDP -0.1 0.19 -10000 0 -0.43 101 101
mol:T-DHT 0 0.001 -10000 0 -0.004 10 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.011 -10000 0 -0.25 1 1
Gi family/GTP -0.062 0.11 -10000 0 -0.3 67 67
CDC42 0.025 0.017 -10000 0 -0.36 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.024 0.098 -10000 0 -0.35 37 37
HDAC1 0.024 0.006 -10000 0 -10000 0 0
AES 0.027 0.004 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
DTX1 0.024 0.035 -10000 0 -0.36 5 5
LRP6/FZD1 0.037 0.02 -10000 0 -0.25 2 2
TLE1 0.026 0.016 -10000 0 -0.36 1 1
AP1 -0.083 0.098 0.21 7 -0.29 57 64
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.026 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.081 -10000 0 -0.57 9 9
NICD/RBPSUH 0.023 0.096 -10000 0 -0.35 34 34
WIF1 -0.08 0.18 0.36 1 -0.44 125 126
NOTCH1 0.005 0.096 -10000 0 -0.37 37 37
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
KREMEN2 -0.028 0.15 0.36 2 -0.44 73 75
DKK1 -0.075 0.19 0.36 1 -0.44 128 129
beta catenin/beta TrCP1 0.093 0.075 0.28 10 -0.29 1 11
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
AXIN1 -0.027 0.065 -10000 0 -0.41 8 8
CtBP/CBP/TCF1/TLE1/AES 0.019 0.025 -10000 0 -0.28 1 1
PSEN1 0.026 0.007 -10000 0 -10000 0 0
FOS 0.022 0.039 -10000 0 -0.36 6 6
JUN 0.027 0.004 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.082 0.078 0.27 14 -0.3 1 15
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
DKK2/LRP6/Kremen 2 -0.03 0.14 0.23 2 -0.27 154 156
HNF1A 0.026 0.022 -10000 0 -0.36 2 2
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.023 0.042 -10000 0 -10000 0 0
NKD1 -0.28 0.23 0.36 8 -0.44 401 409
FZD1 0.025 0.023 -10000 0 -0.36 2 2
NOTCH1 precursor/Deltex homolog 1 0.022 0.098 -10000 0 -0.35 37 37
apoptosis -0.082 0.098 0.21 7 -0.29 57 64
Delta 1/NOTCHprecursor 0.022 0.098 -10000 0 -0.35 37 37
DLL1 0.025 0.031 -10000 0 -0.36 4 4
PPARD 0.028 0.075 -10000 0 -0.86 4 4
Gamma Secretase 0.071 0.031 -10000 0 -10000 0 0
APC -0.05 0.12 -10000 0 -0.42 45 45
DVL1 0.001 0.081 -10000 0 -0.35 24 24
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.049 0.16 0.25 1 -0.29 183 184
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.018 0.11 -10000 0 -0.8 10 10
WNT1 0.011 0.038 -10000 0 -0.44 3 3
Axin1/APC/beta catenin 0.022 0.12 0.49 2 -0.44 16 18
DKK2 -0.042 0.16 -10000 0 -0.44 89 89
NOTCH1 precursor/DVL1 -0.001 0.14 -10000 0 -0.49 30 30
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.098 -10000 0 -0.35 37 37
PPP2R5D 0.14 0.1 0.25 72 -0.27 4 76
MAPK1 0.026 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0 0.12 -10000 0 -0.25 122 122
RBPJ 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.029 0.005 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.043 -10000 0 -10000 0 0
IRAK/TOLLIP 0.03 0.013 -10000 0 -0.24 1 1
IKBKB 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.027 0.016 -10000 0 -0.36 1 1
IL1 alpha/IL1R2 -0.12 0.18 -10000 0 -0.3 297 297
IL1A -0.1 0.21 -10000 0 -0.44 166 166
IL1B -0.019 0.097 -10000 0 -0.31 61 61
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.028 -10000 0 -10000 0 0
IL1R2 -0.068 0.17 -10000 0 -0.36 151 151
IL1R1 0.023 0.041 -10000 0 -0.36 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.044 -10000 0 -10000 0 0
TOLLIP 0.027 0.003 -10000 0 -10000 0 0
TICAM2 0.014 0.055 -10000 0 -0.36 12 12
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.022 0.056 -10000 0 -0.35 1 1
JUN -0.011 0.022 0.2 4 -10000 0 4
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.038 0.091 -10000 0 -0.31 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.018 0.14 -10000 0 -0.25 165 165
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.14 -10000 0 -0.24 162 162
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.089 -10000 0 -0.24 67 67
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.009 0.023 0.21 4 -10000 0 4
IRAK1 0.014 0.012 -10000 0 -0.27 1 1
IL1RN/IL1R1 0.002 0.11 -10000 0 -0.31 69 69
IRAK4 0.028 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.015 -10000 0 -0.25 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.048 -10000 0 -0.3 1 1
CHUK 0.027 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.089 -10000 0 -0.24 67 67
IL1 beta/IL1R2 -0.054 0.13 -10000 0 -0.24 201 201
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.014 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA 0.026 0.083 -10000 0 -0.28 1 1
IRAK3 0.02 0.054 -10000 0 -0.36 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.095 -10000 0 -0.34 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.064 -10000 0 -0.31 3 3
IL1 alpha/IL1R1/IL1RAP -0.034 0.15 -10000 0 -0.27 170 170
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
MYD88 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.017 -10000 0 -0.23 1 1
IL1RAP 0.028 0.002 -10000 0 -10000 0 0
UBE2N 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.078 -10000 0 -0.32 2 2
CASP1 0.025 0.027 -10000 0 -0.36 3 3
IL1RN/IL1R2 -0.067 0.15 -10000 0 -0.27 212 212
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.029 0.09 -10000 0 -0.23 55 55
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.06 -10000 0 -0.31 8 8
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
IL1RN -0.02 0.14 -10000 0 -0.44 62 62
TRAF6/TAK1/TAB1/TAB2 0.039 0.008 -10000 0 -10000 0 0
MAP2K6 0.013 0.023 0.22 4 -10000 0 4
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.011 -10000 0 -10000 0 0
EPHB2 0.024 0.034 -10000 0 -0.44 3 3
EFNB1 0.007 0.035 0.27 2 -0.31 5 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.015 0.13 -10000 0 -0.36 16 16
Ephrin B2/EPHB1-2 -0.006 0.1 0.26 1 -0.24 89 90
neuron projection morphogenesis -0.026 0.11 -10000 0 -0.34 18 18
Ephrin B1/EPHB1-2/Tiam1 -0.027 0.13 -10000 0 -0.26 106 106
DNM1 0.025 0.046 0.35 2 -0.44 5 7
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.007 0.066 0.24 1 -0.41 14 15
YES1 -0.008 0.11 -10000 0 -0.65 15 15
Ephrin B1/EPHB1-2/NCK2 -0.004 0.12 0.28 1 -0.23 113 114
PI3K 0.031 0.082 -10000 0 -0.39 18 18
mol:GDP -0.028 0.13 -10000 0 -0.25 107 107
ITGA2B 0.006 0.089 -10000 0 -0.44 23 23
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.006 0.11 -10000 0 -0.64 16 16
MAP3K7 -0.011 0.071 -10000 0 -0.44 15 15
FGR -0.009 0.11 -10000 0 -0.63 18 18
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RGS3 0.027 0.004 -10000 0 -10000 0 0
cell adhesion 0.01 0.09 -10000 0 -0.4 16 16
LYN -0.006 0.11 -10000 0 -0.63 17 17
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.092 -10000 0 -0.54 17 17
Ephrin B1/EPHB1-2 -0.009 0.074 -10000 0 -0.49 13 13
SRC -0.007 0.1 -10000 0 -0.61 16 16
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
EPHB1 -0.07 0.19 0.35 1 -0.44 129 130
EPHB4 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.074 -10000 0 -0.3 30 30
BLK -0.043 0.12 -10000 0 -0.66 15 15
HCK -0.01 0.1 -10000 0 -0.63 15 15
regulation of stress fiber formation 0.005 0.12 0.23 113 -0.27 1 114
MAPK8 -0.006 0.067 0.22 1 -0.39 14 15
Ephrin B1/EPHB1-2/RGS3 -0.005 0.12 0.28 1 -0.24 95 96
endothelial cell migration 0.018 0.091 0.23 60 -0.36 9 69
NCK2 0.028 0.001 -10000 0 -10000 0 0
PTPN13 0.005 0.088 -10000 0 -0.4 27 27
regulation of focal adhesion formation 0.005 0.12 0.23 113 -0.27 1 114
chemotaxis 0.006 0.12 0.24 95 -0.27 1 96
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GTP -0.02 0.12 -10000 0 -0.35 17 17
angiogenesis -0.01 0.075 -10000 0 -0.49 14 14
LCK -0.009 0.11 -10000 0 -0.62 18 18
Signaling events mediated by PRL

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
CCNE1 0.027 0.036 0.36 3 -0.44 2 5
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.027 0.003 -10000 0 -10000 0 0
CDKN1A 0.007 0.048 -10000 0 -0.31 13 13
PRL-3/alpha Tubulin 0.021 0.12 0.26 42 -0.32 53 95
mol:Ca2+ -0.062 0.13 0.18 35 -0.3 118 153
AGT -0.035 0.16 0.36 2 -0.44 82 84
CCNA2 -0.003 0.01 -10000 0 -10000 0 0
TUBA1B 0.028 0.002 -10000 0 -10000 0 0
EGR1 0.014 0.015 -10000 0 -0.24 2 2
CDK2/Cyclin E1 0.074 0.077 0.33 2 -0.34 1 3
MAPK3 0.001 0.12 0.28 42 -0.32 54 96
PRL-2 /Rab GGTase beta 0.039 0.009 -10000 0 -10000 0 0
MAPK1 0.001 0.12 0.28 41 -0.32 53 94
PTP4A1 0.002 0.011 -10000 0 -10000 0 0
PTP4A3 0.007 0.16 0.36 42 -0.44 53 95
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.002 0.12 0.28 42 -0.32 53 95
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1 0.024 0.069 0.3 25 -0.3 4 29
Rab GGTase beta/Rab GGTase alpha 0.037 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.085 0.083 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.019 0.081 0.16 53 -0.25 42 95
RHOC 0.023 0.082 0.3 28 -0.32 11 39
RHOA 0.024 0.076 0.3 27 -0.3 8 35
cell motility 0.048 0.11 0.32 25 -0.36 6 31
PRL-1/alpha Tubulin 0.086 0.083 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.02 0.12 0.26 40 -0.32 53 93
ROCK1 0.05 0.1 0.32 25 -0.37 5 30
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.028 0.002 -10000 0 -10000 0 0
mitosis 0.002 0.011 -10000 0 -10000 0 0
ATF5 0.027 0.004 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.069 0.6 4 -10000 0 4
VDR 0.028 0.002 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.051 0.11 -10000 0 -0.35 6 6
RXRs/LXRs/DNA/Oxysterols -0.037 0.11 -10000 0 -0.4 10 10
MED1 0.028 0.019 0.36 2 -10000 0 2
mol:9cRA 0.003 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.033 0.1 0.17 1 -0.32 7 8
RXRs/NUR77 -0.041 0.13 -10000 0 -0.32 12 12
RXRs/PPAR -0.061 0.11 -10000 0 -0.28 29 29
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.061 0.028 0.24 1 -0.18 5 6
RARA 0.027 0.021 0.36 1 -0.36 1 2
NCOA1 0.028 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.028 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.046 0.026 0.22 1 -0.18 5 6
RARG 0.028 0.002 -10000 0 -10000 0 0
RPS6KB1 0.032 0.077 0.59 10 -0.34 1 11
RARs/THRs/DNA/SMRT -0.033 0.1 0.17 1 -0.34 7 8
THRA 0.027 0.014 0.36 1 -10000 0 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.042 0.12 -10000 0 -0.29 2 2
NR1H4 -0.18 0.19 -10000 0 -0.36 308 308
RXRs/LXRs/DNA -0.02 0.13 -10000 0 -0.34 3 3
NR1H2 0.029 0.019 -10000 0 -0.36 1 1
NR1H3 0.03 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.12 -10000 0 -0.24 2 2
NR4A1 0.02 0.059 -10000 0 -0.43 10 10
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.15 0.14 -10000 0 -0.3 215 215
RXRG -0.13 0.19 -10000 0 -0.36 253 253
RXR alpha/CCPG 0.041 0.017 -10000 0 -0.25 1 1
RXRA 0.029 0.019 -10000 0 -0.36 1 1
RXRB 0.03 0.012 -10000 0 -10000 0 0
THRB -0.086 0.18 -10000 0 -0.36 178 178
PPARG 0.026 0.022 -10000 0 -0.36 2 2
PPARD 0.027 0.016 -10000 0 -0.36 1 1
TNF -0.041 0.12 -10000 0 -0.85 6 6
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport -0.037 0.1 -10000 0 -0.4 10 10
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.025 0.031 -10000 0 -0.36 4 4
RXRs/NUR77/BCL2 -0.085 0.12 -10000 0 -0.22 257 257
SREBF1 -0.029 0.09 -10000 0 -0.49 2 2
RXRs/RXRs/DNA/9cRA -0.042 0.12 -10000 0 -0.29 2 2
ABCA1 -0.042 0.13 -10000 0 -0.89 7 7
RARs/THRs 0.003 0.12 0.26 1 -0.35 2 3
RXRs/FXR -0.15 0.16 -10000 0 -0.36 141 141
BCL2 0.014 0.05 -10000 0 -0.36 10 10
TCGA08_p53

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
CDKN2A -0.054 0.13 0.26 2 -0.32 115 117
TP53 -0.017 0.062 -10000 0 -0.28 27 27
Senescence -0.017 0.062 -10000 0 -0.27 27 27
Apoptosis -0.017 0.062 -10000 0 -0.27 27 27
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.022 0.068 0.31 7 -0.18 2 9
MDM4 0.028 0.014 0.36 1 -10000 0 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.013 0.036 -10000 0 -0.22 3 3
NFATC2 -0.015 0.044 -10000 0 -0.23 16 16
NFATC3 -0.014 0.037 -10000 0 -10000 0 0
CD40LG -0.058 0.2 0.37 2 -0.56 29 31
PTGS2 -0.057 0.2 0.36 1 -0.57 34 35
JUNB 0.026 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.029 -10000 0 -10000 0 0
CaM/Ca2+ -0.005 0.029 -10000 0 -10000 0 0
CALM1 0.009 0.026 -10000 0 -10000 0 0
JUN 0.009 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 -0.27 0.23 0.36 1 -0.44 385 386
CREM 0.028 0.002 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.013 0.13 -10000 0 -0.41 9 9
FOS 0.005 0.045 -10000 0 -0.36 6 6
IFNG -0.066 0.21 0.36 1 -0.55 46 47
AP-1/NFAT1-c-4 -0.055 0.21 -10000 0 -0.48 55 55
FASLG -0.055 0.2 0.36 1 -0.55 22 23
NFAT1-c-4/ICER1 -0.018 0.077 -10000 0 -0.34 2 2
IL2RA -0.051 0.19 0.37 2 -0.58 16 18
FKBP12/FK506 0.017 0.008 -10000 0 -10000 0 0
CSF2 -0.12 0.25 0.37 2 -0.54 75 77
JunB/Fra1/NFAT1-c-4 -0.097 0.16 -10000 0 -0.32 138 138
IL4 -0.053 0.18 0.36 2 -0.56 13 15
IL2 -0.016 0.14 -10000 0 -0.84 18 18
IL3 0 0.086 -10000 0 -0.6 11 11
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
BATF3 0.022 0.049 -10000 0 -0.43 7 7
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.02 -10000 0 -0.44 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.013 0.039 -10000 0 -0.44 4 4
GNB1/GNG2 -0.052 0.049 -10000 0 -0.18 28 28
AKT1 -0.041 0.093 0.29 4 -0.28 39 43
EGF -0.06 0.16 -10000 0 -0.37 127 127
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.069 0.077 0.39 1 -0.28 2 3
mol:Ca2+ -0.053 0.097 0.29 4 -0.28 43 47
LYN -0.06 0.075 0.39 1 -10000 0 1
RhoA/GTP -0.024 0.043 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.059 0.1 0.3 5 -0.32 23 28
GNG2 0.011 0.074 -10000 0 -0.36 23 23
ARRB2 0.023 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.11 -10000 0 -0.59 15 15
G beta5/gamma2 -0.06 0.066 -10000 0 -0.23 28 28
PRKCH -0.056 0.1 0.28 4 -0.32 28 32
DNM1 0.025 0.046 0.36 2 -0.44 5 7
TXA2/TP beta/beta Arrestin3 -0.01 0.049 -10000 0 -0.62 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.18 0.19 -10000 0 -0.36 317 317
G12 family/GTP -0.055 0.087 -10000 0 -0.29 24 24
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
ADRBK2 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.03 0.018 -10000 0 -0.21 1 1
mol:GDP 0.067 0.098 0.31 39 -0.29 2 41
mol:NADP 0.02 0.058 0.36 1 -0.44 9 10
RAB11A 0.027 0.006 -10000 0 -10000 0 0
PRKG1 0.013 0.071 -10000 0 -0.36 21 21
mol:IP3 -0.066 0.12 0.31 4 -0.35 43 47
cell morphogenesis 0.029 0.017 -10000 0 -0.21 1 1
PLCB2 -0.089 0.15 0.46 1 -0.47 43 44
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.099 0.11 -10000 0 -0.28 101 101
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.041 0.069 -10000 0 -0.28 5 5
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.026 0.027 -10000 0 -0.44 2 2
PRKCB1 -0.06 0.11 0.29 4 -0.33 35 39
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
mol:L-citrulline 0.02 0.058 0.36 1 -0.44 9 10
TXA2/TXA2-R family -0.085 0.14 0.38 2 -0.48 25 27
LCK -0.072 0.079 0.39 1 -0.3 6 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.078 0.097 -10000 0 -0.23 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.029 0.11 -10000 0 -0.48 31 31
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.071 0.096 -10000 0 -0.23 2 2
MAPK14 -0.041 0.075 0.3 5 -0.23 16 21
TGM2/GTP -0.076 0.12 0.3 3 -0.4 32 35
MAPK11 -0.041 0.073 0.24 5 -0.23 18 23
ARHGEF1 -0.034 0.057 0.25 1 -0.18 16 17
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.066 0.11 0.31 4 -0.36 25 29
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.044 0.084 0.26 4 -0.28 17 21
cAMP biosynthetic process -0.069 0.11 0.31 4 -0.34 42 46
Gq family/GTP/EBP50 0.016 0.045 0.24 5 -0.29 7 12
actin cytoskeleton reorganization 0.029 0.017 -10000 0 -0.21 1 1
SRC -0.039 0.066 -10000 0 -10000 0 0
GNB5 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.061 0.099 0.21 7 -0.27 36 43
VCAM1 -0.049 0.092 0.27 4 -0.35 17 21
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.11 -10000 0 -0.59 15 15
platelet activation -0.054 0.098 0.35 5 -0.3 22 27
PGI2/IP 0.019 0.019 -10000 0 -0.31 2 2
PRKACA -0.09 0.1 -10000 0 -0.19 309 309
Gq family/GDP/G beta5/gamma2 -0.033 0.1 -10000 0 -0.5 16 16
TXA2/TP beta/beta Arrestin2 -0.026 0.061 -10000 0 -0.37 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.091 0.094 -10000 0 -0.18 303 303
mol:DAG -0.067 0.12 0.31 4 -0.37 36 40
EGFR 0.024 0.023 -10000 0 -0.36 2 2
TXA2/TP alpha -0.089 0.15 0.35 4 -0.45 42 46
Gq family/GTP 0.01 0.055 0.31 5 -0.24 16 21
YES1 -0.06 0.076 0.39 1 -10000 0 1
GNAI2/GTP -0.071 0.089 -10000 0 -0.23 2 2
PGD2/DP -0.12 0.13 -10000 0 -0.25 317 317
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
FYN -0.07 0.076 0.39 1 -10000 0 1
mol:NO 0.02 0.058 0.36 1 -0.44 9 10
GNA15 0.023 0.046 -10000 0 -0.44 6 6
PGK/cGMP 0.022 0.058 0.23 1 -0.23 28 29
RhoA/GDP 0.028 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.037 0.096 -10000 0 -0.31 12 12
NOS3 0.02 0.058 0.36 1 -0.44 9 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.056 0.1 0.31 4 -0.32 28 32
PRKCB -0.077 0.12 0.34 3 -0.38 33 36
PRKCE -0.054 0.1 0.32 2 -0.32 24 26
PRKCD -0.058 0.11 0.28 4 -0.35 22 26
PRKCG -0.086 0.13 0.32 4 -0.36 42 46
muscle contraction -0.083 0.14 0.35 4 -0.44 31 35
PRKCZ -0.06 0.1 0.29 4 -0.33 21 25
ARR3 -0.008 0.037 -10000 0 -0.44 3 3
TXA2/TP beta -0.072 0.1 -10000 0 -0.23 3 3
PRKCQ -0.055 0.1 0.32 4 -0.32 25 29
MAPKKK cascade -0.078 0.13 0.32 4 -0.41 40 44
SELE -0.058 0.099 0.27 4 -0.26 36 40
TP beta/GNAI2/GDP/G beta/gamma -0.072 0.11 -10000 0 -0.3 17 17
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
GNA14 0.024 0.035 -10000 0 -0.36 5 5
chemotaxis -0.087 0.15 0.47 1 -0.57 18 19
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.031 -10000 0 -0.36 4 4
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
EPHB forward signaling

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.02 0.1 -10000 0 -0.21 133 133
cell-cell adhesion 0.04 0.068 0.36 3 -10000 0 3
Ephrin B/EPHB2/RasGAP 0.049 0.05 -10000 0 -0.23 4 4
ITSN1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.018 0.073 -10000 0 -0.27 38 38
Ephrin B1/EPHB1 -0.027 0.12 0.23 1 -0.27 129 130
HRAS/GDP -0.023 0.1 -10000 0 -0.31 19 19
Ephrin B/EPHB1/GRB7 0.012 0.11 0.26 6 -0.24 65 71
Endophilin/SYNJ1 0.029 0.079 0.18 122 -10000 0 122
KRAS 0.026 0.016 -10000 0 -0.36 1 1
Ephrin B/EPHB1/Src 0.01 0.085 -10000 0 -0.24 43 43
endothelial cell migration 0.043 0.028 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.035 0.049 0.36 14 -10000 0 14
PAK1 0.03 0.085 0.26 9 -10000 0 9
HRAS 0.027 0.016 -10000 0 -0.36 1 1
RRAS 0.031 0.081 0.18 124 -10000 0 124
DNM1 0.025 0.046 0.36 2 -0.44 5 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.019 0.1 0.18 73 -0.42 1 74
lamellipodium assembly -0.04 0.068 -10000 0 -0.36 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.06 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.024 0.033 -10000 0 -0.44 3 3
EPHB3 -0.002 0.11 -10000 0 -0.44 38 38
EPHB1 -0.071 0.19 0.36 1 -0.44 129 130
EPHB4 0.027 0.006 -10000 0 -10000 0 0
mol:GDP -0.012 0.09 0.27 3 -0.3 18 21
Ephrin B/EPHB2 0.039 0.043 -10000 0 -0.23 5 5
Ephrin B/EPHB3 0.026 0.073 -10000 0 -0.23 36 36
JNK cascade -0.038 0.1 0.35 4 -0.4 3 7
Ephrin B/EPHB1 -0.001 0.1 -10000 0 -0.23 88 88
RAP1/GDP 0.003 0.11 0.31 16 -0.28 16 32
EFNB2 0.022 0.011 -10000 0 -10000 0 0
EFNB3 0.018 0.045 -10000 0 -0.38 7 7
EFNB1 0.028 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.007 0.1 0.24 1 -0.24 89 90
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.096 -10000 0 -0.36 3 3
Rap1/GTP -0.016 0.082 -10000 0 -0.37 3 3
axon guidance -0.02 0.1 -10000 0 -0.21 133 133
MAPK3 0.007 0.054 0.21 2 -10000 0 2
MAPK1 0.008 0.051 0.17 1 -10000 0 1
Rac1/GDP -0.013 0.097 0.24 4 -0.29 15 19
actin cytoskeleton reorganization -0.034 0.076 -10000 0 -0.31 4 4
CDC42/GDP -0.003 0.11 0.31 17 -0.28 17 34
PI3K 0.048 0.031 -10000 0 -10000 0 0
EFNA5 -0.056 0.16 -10000 0 -0.36 130 130
Ephrin B2/EPHB4 0.029 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.017 0.026 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RAS family/GTP -0.02 0.082 -10000 0 -0.35 5 5
PTK2 0.087 0.21 0.58 89 -10000 0 89
MAP4K4 -0.038 0.11 0.35 4 -0.4 3 7
SRC 0.017 0.014 -10000 0 -10000 0 0
KALRN 0.027 0.016 -10000 0 -0.36 1 1
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.007 0.092 0.3 15 -0.31 1 16
MAP2K1 0.01 0.055 -10000 0 -10000 0 0
WASL 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.001 0.13 -10000 0 -0.25 129 129
cell migration 0.033 0.088 0.22 50 -10000 0 50
NRAS 0.026 0.023 -10000 0 -0.36 2 2
SYNJ1 0.029 0.08 0.18 122 -10000 0 122
PXN 0.028 0.002 -10000 0 -10000 0 0
TF 0.004 0.098 0.19 27 -0.41 1 28
HRAS/GTP -0.004 0.094 -10000 0 -0.38 3 3
Ephrin B1/EPHB1-2 -0.013 0.12 0.24 1 -0.25 130 131
cell adhesion mediated by integrin -0.034 0.091 0.24 3 -0.2 123 126
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.003 0.097 -10000 0 -0.4 3 3
RAC1-CDC42/GTP -0.034 0.095 -10000 0 -0.39 14 14
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.005 0.099 0.26 3 -0.28 14 17
ruffle organization -0.003 0.13 0.39 29 -0.37 3 32
NCK1 0.028 0.002 -10000 0 -10000 0 0
receptor internalization 0.026 0.079 0.2 28 -10000 0 28
Ephrin B/EPHB2/KALRN 0.049 0.051 -10000 0 -0.23 4 4
ROCK1 -0.003 0.061 0.18 1 -0.23 38 39
RAS family/GDP -0.043 0.062 -10000 0 -0.31 3 3
Rac1/GTP -0.021 0.081 -10000 0 -0.38 3 3
Ephrin B/EPHB1/Src/Paxillin 0.001 0.048 -10000 0 -0.21 1 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.029 0.093 -10000 0 -0.29 34 34
NT3 (dimer)/TRKC -0.023 0.12 -10000 0 -0.26 124 124
NT3 (dimer)/TRKB -0.079 0.17 -10000 0 -0.27 248 248
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.016 -10000 0 -0.27 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
BDNF 0.019 0.06 -10000 0 -0.44 10 10
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.016 0.057 -10000 0 -0.43 9 9
NTRK2 -0.087 0.18 -10000 0 -0.37 177 177
NTRK3 -0.058 0.15 -10000 0 -0.36 123 123
NT-4/5 (dimer)/TRKB -0.092 0.17 -10000 0 -0.27 267 267
neuron apoptosis 0.088 0.16 0.38 88 -10000 0 88
SHC 2-3/Grb2 -0.095 0.17 -10000 0 -0.41 88 88
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 -0.093 0.16 -10000 0 -0.42 93 93
SHC3 -0.097 0.16 -10000 0 -0.42 89 89
STAT3 (dimer) 0.031 0.024 -10000 0 -0.35 1 1
NT3 (dimer)/TRKA -0.016 0.12 -10000 0 -0.22 151 151
RIN/GDP -0.005 0.08 0.26 8 -0.24 9 17
GIPC1 0.027 0.016 -10000 0 -0.36 1 1
KRAS 0.026 0.016 -10000 0 -0.36 1 1
DNAJA3 -0.061 0.12 -10000 0 -0.27 135 135
RIN/GTP 0.009 0.014 -10000 0 -0.31 1 1
CCND1 0.017 0.03 -10000 0 -0.35 4 4
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.017 0.088 -10000 0 -0.45 23 23
SHC/GRB2/SOS1 0.054 0.012 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.009 0.1 -10000 0 -0.23 91 91
TRKA/NEDD4-2 0.024 0.045 -10000 0 -0.3 10 10
ELMO1 0.023 0.028 -10000 0 -0.36 3 3
RhoG/GTP/ELMO1/DOCK1 0.032 0.023 -10000 0 -0.21 4 4
NGF 0.011 0.071 -10000 0 -0.37 20 20
HRAS 0.027 0.016 -10000 0 -0.36 1 1
DOCK1 0.026 0.016 -10000 0 -0.36 1 1
GAB2 0.027 0.004 -10000 0 -10000 0 0
RIT2 -0.012 0.021 -10000 0 -0.44 1 1
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
DNM1 0.025 0.046 0.36 2 -0.44 5 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.046 0.12 -10000 0 -0.26 130 130
mol:GDP -0.012 0.11 0.29 12 -0.34 13 25
NGF (dimer) 0.011 0.071 -10000 0 -0.37 20 20
RhoG/GDP 0.017 0.02 -10000 0 -0.25 3 3
RIT1/GDP -0.002 0.083 0.19 10 -0.24 9 19
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.03 0.13 -10000 0 -0.22 170 170
KIDINS220/CRKL/C3G 0.038 0.015 -10000 0 -0.25 1 1
SHC/RasGAP 0.039 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.055 0.012 0.24 1 -10000 0 1
SHC/GRB2/SOS1/GAB1 0.067 0.018 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.021 0.043 -10000 0 -0.37 7 7
RAP1/GDP -0.005 0.069 0.13 3 -0.2 9 12
KIDINS220/CRKL 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.019 0.06 -10000 0 -0.44 10 10
ubiquitin-dependent protein catabolic process 0.026 0.064 -10000 0 -0.23 29 29
Schwann cell development -0.026 0.027 -10000 0 -10000 0 0
EHD4 0.026 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.068 0.018 0.25 1 -10000 0 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.042 0.25 1 -0.24 2 3
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.051 0.12 -10000 0 -0.33 35 35
ABL1 0.027 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.013 0.095 -10000 0 -0.42 17 17
STAT3 0.031 0.024 -10000 0 -0.35 1 1
axon guidance -0.054 0.11 -10000 0 -0.32 35 35
MAPK3 -0.02 0.083 0.18 8 -0.31 10 18
MAPK1 -0.019 0.082 0.18 6 -0.31 10 16
CDC42/GDP 0.001 0.088 0.22 16 -0.24 10 26
NTF3 0.021 0.043 -10000 0 -0.37 7 7
NTF4 -0.017 0.089 -10000 0 -0.45 23 23
NGF (dimer)/TRKA/FAIM 0.039 0.064 0.25 1 -0.24 28 29
PI3K 0.039 0.015 -10000 0 -0.25 1 1
FRS3 0.028 0.014 0.36 1 -10000 0 1
FAIM 0.028 0.014 0.36 1 -10000 0 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
RASGRF1 -0.077 0.13 -10000 0 -0.28 146 146
SOS1 0.028 0.002 -10000 0 -10000 0 0
MCF2L -0.031 0.085 -10000 0 -0.22 101 101
RGS19 0.017 0.014 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RAS family/GTP 0.007 0.078 0.47 1 -0.39 6 7
Rac1/GDP -0.004 0.082 0.22 11 -0.24 10 21
NGF (dimer)/TRKA/GRIT 0.022 0.058 -10000 0 -0.24 28 28
neuron projection morphogenesis -0.046 0.14 -10000 0 -0.89 3 3
NGF (dimer)/TRKA/NEDD4-2 0.026 0.064 -10000 0 -0.23 29 29
MAP2K1 0.017 0.029 -10000 0 -10000 0 0
NGFR -0.067 0.17 -10000 0 -0.36 149 149
NGF (dimer)/TRKA/GIPC/GAIP 0.011 0.038 0.17 1 -10000 0 1
RAS family/GTP/PI3K 0.022 0.026 -10000 0 -0.26 4 4
FRS2 family/SHP2/GRB2/SOS1 0.079 0.02 0.25 1 -10000 0 1
NRAS 0.026 0.023 -10000 0 -0.36 2 2
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.14 -10000 0 -0.57 37 37
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.043 -10000 0 -0.31 9 9
SQSTM1 0.027 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.013 0.12 -10000 0 -0.27 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.059 0.067 -10000 0 -0.28 8 8
MATK -0.02 0.13 -10000 0 -0.36 74 74
NEDD4L 0.02 0.02 -10000 0 -0.36 1 1
RAS family/GDP -0.027 0.044 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.058 0.13 -10000 0 -0.28 139 139
Rac1/GTP -0.064 0.1 -10000 0 -0.27 58 58
FRS2 family/SHP2/CRK family 0.067 0.034 0.25 1 -10000 0 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.015 0.16 -10000 0 -0.79 18 18
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.01 0.089 -10000 0 -0.3 33 33
ATF2/c-Jun 0.004 0.069 -10000 0 -0.36 4 4
MAPK11 0.01 0.089 -10000 0 -0.31 34 34
MITF -0.005 0.11 -10000 0 -0.37 39 39
MAPKAPK5 0.002 0.096 -10000 0 -0.34 37 37
KRT8 0.002 0.096 -10000 0 -0.34 37 37
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.011 0.13 -10000 0 -0.44 35 35
CEBPB -0.002 0.082 0.26 3 -0.35 23 26
SLC9A1 -0.001 0.1 -10000 0 -0.36 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.003 0.097 -10000 0 -0.34 35 35
p38alpha-beta/MNK1 0.028 0.11 -10000 0 -0.36 34 34
JUN 0.002 0.067 -10000 0 -0.35 4 4
PPARGC1A -0.035 0.14 -10000 0 -0.4 44 44
USF1 0.004 0.092 -10000 0 -0.34 34 34
RAB5/GDP/GDI1 0.008 0.077 -10000 0 -0.25 32 32
NOS2 -0.028 0.21 -10000 0 -0.91 28 28
DDIT3 0.002 0.097 -10000 0 -0.35 37 37
RAB5A 0.026 0.022 -10000 0 -0.36 2 2
HSPB1 0.004 0.091 0.28 18 -0.29 30 48
p38alpha-beta/HBP1 0.028 0.11 -10000 0 -0.36 31 31
CREB1 0.002 0.1 -10000 0 -0.38 36 36
RAB5/GDP 0.019 0.016 -10000 0 -0.25 2 2
EIF4E -0.004 0.089 -10000 0 -0.32 34 34
RPS6KA4 0.002 0.095 -10000 0 -0.34 36 36
PLA2G4A -0.027 0.11 -10000 0 -0.35 33 33
GDI1 0.003 0.093 -10000 0 -0.34 35 35
TP53 -0.013 0.11 -10000 0 -0.43 32 32
RPS6KA5 -0.001 0.1 -10000 0 -0.37 36 36
ESR1 -0.021 0.13 -10000 0 -0.42 38 38
HBP1 0.027 0.005 -10000 0 -10000 0 0
MEF2C -0.005 0.11 -10000 0 -0.37 37 37
MEF2A 0.001 0.1 -10000 0 -0.36 37 37
EIF4EBP1 -0.001 0.1 -10000 0 -0.39 34 34
KRT19 0.003 0.093 -10000 0 -0.34 34 34
ELK4 0.003 0.093 -10000 0 -0.34 35 35
ATF6 0.004 0.092 -10000 0 -0.34 34 34
ATF1 0.002 0.1 -10000 0 -0.38 36 36
p38alpha-beta/MAPKAPK2 0.029 0.11 -10000 0 -0.35 32 32
p38alpha-beta/MAPKAPK3 0.028 0.11 -10000 0 -0.36 34 34
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.024 -10000 0 -0.39 1 1
ARNO/beta Arrestin1-2 0.006 0.092 -10000 0 -0.83 3 3
EGFR 0.024 0.023 -10000 0 -0.36 2 2
EPHA2 0.025 0.027 -10000 0 -0.44 2 2
USP6 0.022 0.026 -10000 0 -0.4 2 2
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.021 0.12 -10000 0 -0.26 115 115
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.004 0.04 0.13 9 -0.17 6 15
ARRB1 0.027 0.016 -10000 0 -0.36 1 1
FBXO8 0.026 0.017 -10000 0 -0.36 1 1
TSHR 0.013 0.033 -10000 0 -0.44 2 2
EGF -0.059 0.16 -10000 0 -0.37 127 127
somatostatin receptor activity 0 0 0.001 33 -0.001 34 67
ARAP2 0.026 0.023 -10000 0 -0.36 2 2
mol:GDP -0.034 0.11 0.19 13 -0.27 51 64
mol:PI-3-4-5-P3 0 0 0.001 13 -0.001 7 20
ITGA2B 0.006 0.089 -10000 0 -0.44 23 23
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.03 -10000 0 -0.25 2 2
ADAP1 0.025 0.017 -10000 0 -0.36 1 1
KIF13B 0.021 0.019 -10000 0 -0.36 1 1
HGF/MET 0.029 0.058 -10000 0 -0.28 19 19
PXN 0.028 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.11 0.22 30 -0.26 36 66
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.003 0.11 -10000 0 -0.22 115 115
ADRB2 -0.032 0.14 -10000 0 -0.36 93 93
receptor agonist activity 0 0 0 15 0 32 47
actin filament binding 0 0 0 33 -0.001 36 69
SRC 0.017 0.014 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
EFA6/PI-4-5-P2 0 0.001 0.001 37 -0.001 18 55
ARF6/GDP -0.047 0.16 0.2 5 -0.42 76 81
ARF6/GDP/GULP/ACAP1 -0.022 0.12 0.22 4 -0.37 21 25
alphaIIb/beta3 Integrin/paxillin/GIT1 0.054 0.066 -10000 0 -0.24 29 29
ACAP1 0.013 0.06 -10000 0 -0.36 15 15
ACAP2 0.027 0.016 -10000 0 -0.36 1 1
LHCGR/beta Arrestin2 0.007 0.026 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.017 0.061 -10000 0 -0.37 15 15
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 0.015 0.071 -10000 0 -1 3 3
NCK1 0.028 0.002 -10000 0 -10000 0 0
fibronectin binding 0 0 0 44 0 18 62
endosomal lumen acidification 0 0 0 47 0 18 65
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.007 0.088 -10000 0 -0.36 33 33
GNAQ/ARNO 0.03 0.068 -10000 0 -0.92 3 3
mol:Phosphatidic acid 0 0 0 7 -10000 0 7
PIP3-E 0 0 0 16 0 7 23
MET 0.023 0.045 0.36 1 -0.44 5 6
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GIT1 0.026 0.016 -10000 0 -0.36 1 1
mol:PI-4-5-P2 0 0 0.001 32 -0.001 27 59
GNA11 0.025 0.031 -10000 0 -0.36 4 4
LHCGR -0.012 0.015 -10000 0 -10000 0 0
AGTR1 -0.12 0.18 -10000 0 -0.36 214 214
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.026 -10000 0 -10000 0 0
IPCEF1/ARNO 0.001 0.098 -10000 0 -0.89 3 3
alphaIIb/beta3 Integrin 0.023 0.074 -10000 0 -0.3 30 30
Glucocorticoid receptor regulatory network

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
PCK2 0.055 0.063 -10000 0 -10000 0 0
SMARCC2 0.025 0.017 -10000 0 -10000 0 0
SMARCC1 0.025 0.018 -10000 0 -10000 0 0
TBX21 -0.096 0.18 0.29 2 -0.64 43 45
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.019 -10000 0 -0.43 1 1
FKBP4 0.027 0.014 0.36 1 -10000 0 1
FKBP5 0.027 0.016 -10000 0 -0.36 1 1
GR alpha/HSP90/FKBP51/HSP90 0.087 0.1 0.29 21 -0.29 8 29
PRL -0.041 0.087 -10000 0 -0.5 3 3
cortisol/GR alpha (dimer)/TIF2 0.16 0.19 0.49 69 -0.37 8 77
RELA -0.039 0.073 -10000 0 -0.24 1 1
FGG 0.075 0.18 0.42 33 -0.42 26 59
GR beta/TIF2 0.074 0.11 0.29 25 -0.29 25 50
IFNG -0.19 0.16 -10000 0 -0.6 40 40
apoptosis -0.001 0.14 0.46 16 -0.51 8 24
CREB1 0.028 0.018 -10000 0 -10000 0 0
histone acetylation -0.043 0.098 0.32 5 -0.33 23 28
BGLAP -0.044 0.088 -10000 0 -0.44 2 2
GR/PKAc 0.066 0.13 0.29 15 -0.34 18 33
NF kappa B1 p50/RelA -0.065 0.12 -10000 0 -0.31 37 37
SMARCD1 0.025 0.018 -10000 0 -10000 0 0
MDM2 0.057 0.059 0.21 34 -0.24 1 35
GATA3 0.023 0.044 -10000 0 -0.38 5 5
AKT1 0.022 0.006 -10000 0 -10000 0 0
CSF2 -0.12 0.12 -10000 0 -0.42 15 15
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR1I3 0.003 0.15 0.47 14 -0.68 6 20
CSN2 0.072 0.12 0.35 28 -0.36 5 33
BRG1/BAF155/BAF170/BAF60A 0.064 0.052 -10000 0 -0.26 4 4
NFATC1 0.019 0.03 -10000 0 -0.36 3 3
POU2F1 0.026 0.025 -10000 0 -0.44 1 1
CDKN1A -0.009 0.085 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.093 0.1 0.3 16 -0.28 5 21
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.13 0.44 13 -0.63 4 17
JUN -0.18 0.12 -10000 0 -0.42 52 52
IL4 -0.05 0.083 -10000 0 -0.44 7 7
CDK5R1 0.027 0.02 -10000 0 -0.44 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.16 -10000 0 -0.41 166 166
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.1 0.3 17 -0.29 5 22
cortisol/GR alpha (monomer) 0.19 0.22 0.55 79 -0.45 5 84
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.074 0.054 -10000 0 -0.38 7 7
AP-1/NFAT1-c-4 -0.28 0.17 -10000 0 -0.53 121 121
AFP -0.13 0.11 -10000 0 -0.52 3 3
SUV420H1 0.027 0.004 -10000 0 -10000 0 0
IRF1 0.092 0.1 0.4 11 -10000 0 11
TP53 0.034 0.026 -10000 0 -0.48 1 1
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.32 0.18 -10000 0 -0.53 146 146
KRT14 -0.076 0.18 0.4 5 -0.92 16 21
TBP 0.033 0.011 -10000 0 -10000 0 0
CREBBP 0.034 0.069 0.32 9 -0.25 21 30
HDAC1 0.026 0.008 -10000 0 -10000 0 0
HDAC2 0.036 0.014 -10000 0 -10000 0 0
AP-1 -0.28 0.17 -10000 0 -0.54 122 122
MAPK14 0.028 0.007 -10000 0 -10000 0 0
MAPK10 -0.019 0.12 -10000 0 -0.36 73 73
MAPK11 0.025 0.029 -10000 0 -0.45 2 2
KRT5 -0.2 0.18 -10000 0 -0.56 77 77
interleukin-1 receptor activity 0.009 0.012 -10000 0 -10000 0 0
NCOA1 0.03 0.001 -10000 0 -10000 0 0
STAT1 0.033 0.019 -10000 0 -0.44 1 1
CGA -0.055 0.094 -10000 0 -0.42 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.084 0.14 0.34 43 -0.39 15 58
MAPK3 0.027 0.017 -10000 0 -0.36 1 1
MAPK1 0.027 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.14 -10000 0 -0.43 32 32
NFKB1 -0.039 0.073 -10000 0 -0.23 5 5
MAPK8 -0.13 0.11 -10000 0 -0.37 43 43
MAPK9 0.028 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.002 0.15 0.47 16 -0.53 8 24
BAX -0.006 0.073 -10000 0 -10000 0 0
POMC -0.099 0.25 -10000 0 -1.3 22 22
EP300 0.034 0.07 0.32 10 -0.25 21 31
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.5 65 -0.41 3 68
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.059 0.26 20 -0.21 1 21
SGK1 0.001 0.26 0.37 4 -1.2 25 29
IL13 -0.14 0.13 -10000 0 -0.54 17 17
IL6 -0.13 0.19 -10000 0 -0.53 78 78
PRKACG -0.006 0.032 -10000 0 -0.44 2 2
IL5 -0.12 0.11 -10000 0 -0.52 8 8
IL2 -0.18 0.14 -10000 0 -0.52 40 40
CDK5 0.027 0.006 -10000 0 -10000 0 0
PRKACB -0.019 0.12 -10000 0 -0.36 72 72
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.21 0.21 -10000 0 -0.48 132 132
CDK5R1/CDK5 0.039 0.019 -10000 0 -0.31 1 1
NF kappa B1 p50/RelA/PKAc -0.056 0.12 -10000 0 -0.32 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.48 68 -0.37 4 72
SMARCA4 0.025 0.017 -10000 0 -10000 0 0
chromatin remodeling 0.081 0.15 0.34 35 -0.48 21 56
NF kappa B1 p50/RelA/Cbp -0.011 0.13 0.35 6 -0.35 10 16
JUN (dimer) -0.18 0.12 -10000 0 -0.42 52 52
YWHAH 0.027 0.006 -10000 0 -10000 0 0
VIPR1 -0.091 0.17 -10000 0 -0.69 34 34
NR3C1 0.093 0.15 0.38 45 -0.37 32 77
NR4A1 0.006 0.12 -10000 0 -0.5 30 30
TIF2/SUV420H1 0.034 0.025 -10000 0 -0.25 3 3
MAPKKK cascade -0.001 0.14 0.46 16 -0.51 8 24
cortisol/GR alpha (dimer)/Src-1 0.18 0.19 0.49 78 -0.4 4 82
PBX1 0.019 0.058 -10000 0 -0.36 13 13
POU1F1 0.002 0.033 -10000 0 -0.53 1 1
SELE -0.13 0.18 -10000 0 -0.48 87 87
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.081 0.15 0.34 35 -0.49 21 56
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.48 68 -0.37 4 72
mol:cortisol 0.093 0.11 0.3 79 -10000 0 79
MMP1 -0.24 0.17 -10000 0 -0.78 13 13
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.052 0.12 0.29 45 -10000 0 45
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.027 0.046 -10000 0 -0.27 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
RhoA/GTP -0.052 0.12 -10000 0 -0.3 45 45
negative regulation of cAMP metabolic process -0.063 0.12 -10000 0 -0.33 43 43
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
S1PR5 0.016 0.073 -10000 0 -0.44 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.063 0.12 -10000 0 -0.33 43 43
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.001 0.098 -10000 0 -0.38 20 20
Syndecan-3/Neurocan 0.007 0.088 -10000 0 -0.37 30 30
POMC 0.011 0.075 -10000 0 -0.36 23 23
EGFR 0.024 0.023 -10000 0 -0.36 2 2
Syndecan-3/EGFR 0.008 0.087 -10000 0 -0.37 29 29
AGRP -0.006 0.049 -10000 0 -0.44 6 6
NCSTN 0.027 0.004 -10000 0 -10000 0 0
PSENEN 0.026 0.016 -10000 0 -0.36 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
NCAN 0.002 0.034 -10000 0 -0.44 2 2
long-term memory 0.027 0.088 -10000 0 -0.35 30 30
Syndecan-3/IL8 -0.12 0.14 0.23 2 -0.44 33 35
PSEN1 0.026 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.024 0.02 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
limb bud formation -0.005 0.084 -10000 0 -0.38 30 30
MC4R -0.008 0.039 -10000 0 -0.44 4 4
SRC 0.017 0.014 -10000 0 -10000 0 0
PTN -0.034 0.14 -10000 0 -0.36 95 95
FGFR/FGF/Syndecan-3 -0.006 0.085 -10000 0 -0.38 30 30
neuron projection morphogenesis 0.031 0.12 -10000 0 -0.37 20 20
Syndecan-3/AgRP 0.005 0.09 -10000 0 -0.37 30 30
Syndecan-3/AgRP/MC4R 0.008 0.089 -10000 0 -0.34 31 31
Fyn/Cortactin 0.039 0.009 -10000 0 -10000 0 0
SDC3 -0.006 0.086 -10000 0 -0.38 30 30
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.14 0.23 2 -0.43 33 35
IL8 -0.23 0.24 0.36 2 -0.44 338 340
Syndecan-3/Fyn/Cortactin 0.027 0.09 -10000 0 -0.36 30 30
Syndecan-3/CASK -0.007 0.083 -10000 0 -0.36 30 30
alpha-MSH/MC4R 0.013 0.06 -10000 0 -0.26 27 27
Gamma Secretase 0.071 0.031 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.027 0.016 -9999 0 -0.36 1 1
EGFR 0.024 0.023 -9999 0 -0.36 2 2
EGF/EGFR -0.011 0.11 -9999 0 -0.26 51 51
EGF/EGFR dimer/SHC/GRB2/SOS1 0.02 0.1 -9999 0 -0.23 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.003 0.12 -9999 0 -0.45 39 39
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.06 0.16 -9999 0 -0.37 127 127
EGF/EGFR dimer/SHC -0.003 0.11 -9999 0 -0.22 113 113
mol:GDP 0.015 0.1 -9999 0 -0.23 20 20
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.027 0.016 -9999 0 -0.36 1 1
GRB2/SOS1 0.04 0.007 -9999 0 -10000 0 0
HRAS/GTP 0.002 0.088 -9999 0 -10000 0 0
SHC1 0.027 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.015 0.098 -9999 0 -10000 0 0
FRAP1 -0.042 0.067 -9999 0 -0.22 20 20
EGF/EGFR dimer -0.021 0.12 -9999 0 -0.26 115 115
SOS1 0.028 0.002 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.016 0.089 -9999 0 -0.32 40 40
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.045 0.11 0.22 44 -0.3 7 51
PDGFB-D/PDGFRB/SLAP 0.03 0.045 -10000 0 -0.3 10 10
PDGFB-D/PDGFRB/APS/CBL 0.045 0.054 0.26 1 -0.26 16 17
AKT1 0.055 0.095 0.25 22 -10000 0 22
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.067 0.13 0.24 76 -0.33 8 84
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
FGR 0.011 0.12 -10000 0 -0.46 26 26
mol:Ca2+ 0.061 0.12 0.24 74 -0.42 5 79
MYC 0.09 0.16 0.39 78 -0.4 1 79
SHC1 0.027 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.063 0.076 -10000 0 -0.22 2 2
LRP1/PDGFRB/PDGFB 0.05 0.04 -10000 0 -0.25 9 9
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0.061 0.12 0.24 73 -0.42 5 78
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.035 0.049 0.36 14 -10000 0 14
PDGFB-D/PDGFRB/SHP2 0.038 0.038 -10000 0 -0.31 7 7
PDGFB-D/PDGFRB/GRB10 0.034 0.037 -10000 0 -0.31 6 6
cell cycle arrest 0.03 0.045 -10000 0 -0.29 10 10
HRAS 0.027 0.016 -10000 0 -0.36 1 1
HIF1A 0.048 0.088 0.24 22 -10000 0 22
GAB1 0.044 0.12 0.24 15 -0.34 9 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.058 0.12 0.23 88 -0.33 4 92
PDGFB-D/PDGFRB 0.026 0.042 -10000 0 -0.27 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.038 -10000 0 -0.31 7 7
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.004 0.062 -10000 0 -0.28 3 3
positive regulation of MAPKKK cascade 0.037 0.038 -10000 0 -0.31 7 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.061 0.12 0.24 73 -0.42 5 78
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.051 0.26 14 -0.31 7 21
SHB 0.026 0.03 0.36 1 -0.44 2 3
BLK -0.14 0.23 -10000 0 -0.46 200 200
PTPN2 0.024 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.039 -10000 0 -0.31 7 7
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
VAV2 0.054 0.13 0.25 87 -0.38 7 94
CBL 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.038 -10000 0 -0.31 7 7
LCK 0.019 0.11 -10000 0 -0.44 18 18
PDGFRB 0.024 0.05 -10000 0 -0.44 7 7
ACP1 0.028 0.002 -10000 0 -10000 0 0
HCK 0.005 0.076 -10000 0 -0.48 10 10
ABL1 0.038 0.13 0.23 76 -0.34 15 91
PDGFB-D/PDGFRB/CBL 0.031 0.12 0.29 2 -0.42 9 11
PTPN1 0.016 0.014 -10000 0 -10000 0 0
SNX15 0.027 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.44 1 1
cell proliferation 0.089 0.15 0.38 81 -0.36 1 82
SLA 0.022 0.029 -10000 0 -0.36 3 3
actin cytoskeleton reorganization 0.086 0.088 0.34 7 -10000 0 7
SRC 0.009 0.04 -10000 0 -10000 0 0
PI3K -0.003 0.026 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.046 0.25 12 -0.26 7 19
SH2B2 0.02 0.058 0.36 1 -0.44 9 10
PLCgamma1/SPHK1 0.068 0.13 0.25 73 -0.34 8 81
LYN 0.023 0.077 -10000 0 -0.47 5 5
LRP1 0.026 0.022 -10000 0 -0.36 2 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
STAT5A 0.027 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.04 0.051 -10000 0 -10000 0 0
SPHK1 0 0.12 -10000 0 -0.44 40 40
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.061 0.12 0.24 73 -0.42 5 78
PLCG1 0.061 0.12 0.24 73 -0.44 5 78
NHERF/PDGFRB 0.05 0.038 -10000 0 -0.26 8 8
YES1 -0.002 0.15 -10000 0 -0.51 39 39
cell migration 0.05 0.038 -10000 0 -0.26 8 8
SHC/Grb2/SOS1 0.038 0.05 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.016 -10000 0 -0.36 1 1
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.041 -10000 0 -0.23 8 8
FYN 0.019 0.093 -10000 0 -0.47 11 11
DOK1 0.057 0.083 0.18 183 -0.24 6 189
HRAS/GTP 0.02 0.011 -10000 0 -0.25 1 1
PDGFB 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.067 0.15 0.34 56 -0.45 3 59
PRKCD 0.057 0.085 0.18 178 -0.24 6 184
FER 0.056 0.086 0.18 175 -0.24 6 181
MAPKKK cascade 0.063 0.099 0.32 11 -10000 0 11
RASA1 0.058 0.086 0.18 176 -0.24 6 182
NCK1 0.028 0.002 -10000 0 -10000 0 0
NCK2 0.028 0.001 -10000 0 -10000 0 0
p62DOK/Csk 0.065 0.075 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.036 0.044 0.26 1 -0.31 9 10
chemotaxis 0.038 0.12 0.23 76 -0.33 15 91
STAT1-3-5/STAT1-3-5 0.032 0.044 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.018 0.036 -10000 0 -0.31 7 7
PTPRJ 0.028 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.017 0.072 -10000 0 -0.37 7 7
Syndecan-4/Syndesmos 0.026 0.13 0.32 8 -0.5 3 11
positive regulation of JNK cascade 0.001 0.14 0.3 8 -0.51 5 13
Syndecan-4/ADAM12 -0.07 0.18 0.35 3 -0.43 35 38
CCL5 0.012 0.075 -10000 0 -0.36 24 24
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.027 -10000 0 -0.44 2 2
SDCBP 0.024 0.018 -10000 0 -0.36 1 1
PLG -0.1 0.19 0.35 1 -0.46 127 128
ADAM12 -0.23 0.24 -10000 0 -0.45 330 330
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.043 0.05 -10000 0 -0.16 4 4
Syndecan-4/Laminin alpha1 -0.011 0.13 0.31 7 -0.45 5 12
Syndecan-4/CXCL12/CXCR4 0.002 0.15 0.32 8 -0.54 5 13
Syndecan-4/Laminin alpha3 0.016 0.12 0.31 9 -0.5 3 12
MDK 0.023 0.046 -10000 0 -0.44 6 6
Syndecan-4/FZD7 0.028 0.13 0.32 10 -0.47 4 14
Syndecan-4/Midkine 0.026 0.14 0.32 10 -0.49 3 13
FZD7 0.028 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.008 0.13 0.35 1 -0.48 3 4
THBS1 0.025 0.025 -10000 0 -0.4 2 2
integrin-mediated signaling pathway 0.023 0.13 0.31 9 -0.46 5 14
positive regulation of MAPKKK cascade 0.001 0.14 0.3 8 -0.51 5 13
Syndecan-4/TACI -0.029 0.14 0.32 6 -0.41 17 23
CXCR4 0.028 0.002 -10000 0 -10000 0 0
cell adhesion 0.009 0.049 0.2 14 -0.22 8 22
Syndecan-4/Dynamin 0.028 0.13 0.32 10 -0.5 3 13
Syndecan-4/TSP1 0.027 0.13 0.32 10 -0.45 5 15
Syndecan-4/GIPC 0.028 0.13 0.32 10 -0.5 3 13
Syndecan-4/RANTES 0.021 0.14 0.32 9 -0.5 4 13
ITGB1 0.028 0.002 -10000 0 -10000 0 0
LAMA1 -0.054 0.15 -10000 0 -0.36 121 121
LAMA3 0.02 0.034 -10000 0 -0.38 4 4
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.02 0.12 0.79 15 -10000 0 15
Syndecan-4/alpha-Actinin 0.024 0.13 0.31 9 -0.47 4 13
TFPI 0.025 0.035 -10000 0 -0.36 5 5
F2 -0.12 0.22 -10000 0 -0.43 210 210
alpha5/beta1 Integrin 0.04 0.021 -10000 0 -0.32 2 2
positive regulation of cell adhesion -0.018 0.13 0.3 7 -0.45 5 12
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.018 0.064 -10000 0 -0.4 14 14
Syndecan-4/CXCL12 0.004 0.14 0.32 8 -0.56 5 13
FGF6 -0.017 0.024 0.36 1 -0.44 1 2
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.046 0.15 -10000 0 -0.36 116 116
TNFRSF13B -0.12 0.18 -10000 0 -0.36 214 214
FGF2 0 0.099 -10000 0 -0.36 43 43
FGFR1 0.021 0.032 -10000 0 -0.36 4 4
Syndecan-4/PI-4-5-P2 -0.015 0.099 0.29 7 -0.46 4 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.11 -10000 0 -0.43 36 36
cell migration -0.022 0.02 -10000 0 -10000 0 0
PRKCD 0.015 0.024 -10000 0 -10000 0 0
vasculogenesis 0.027 0.13 0.32 10 -0.44 5 15
SDC4 -0.013 0.1 0.32 7 -0.49 4 11
Syndecan-4/Tenascin C 0.023 0.14 0.31 9 -0.48 5 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.035 0.038 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.02 0.12 0.32 7 -0.5 3 10
MMP9 -0.001 0.12 0.37 15 -0.44 32 47
Rac1/GTP 0.009 0.05 0.2 14 -0.22 8 22
cytoskeleton organization 0.026 0.13 0.31 8 -0.45 4 12
GIPC1 0.027 0.016 -10000 0 -0.36 1 1
Syndecan-4/TFPI 0.027 0.13 0.32 10 -0.5 3 13
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
CDC42/GTP -0.054 0.12 -10000 0 -0.32 45 45
PLCG1 -0.042 0.1 -10000 0 -0.34 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
cell migration -0.054 0.12 -10000 0 -0.32 45 45
S1PR5 0.016 0.073 -10000 0 -0.44 15 15
S1PR4 0.021 0.049 -10000 0 -0.36 10 10
MAPK3 -0.068 0.12 -10000 0 -0.33 49 49
MAPK1 -0.059 0.11 -10000 0 -0.35 33 33
S1P/S1P5/Gi -0.063 0.12 -10000 0 -0.33 43 43
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
CDC42/GDP 0.019 0.012 -10000 0 -0.25 1 1
S1P/S1P5/G12 0.027 0.046 -10000 0 -0.27 14 14
RHOA 0.027 0.058 0.19 60 -10000 0 60
S1P/S1P4/Gi -0.063 0.13 -10000 0 -0.36 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.035 -10000 0 -0.36 5 5
S1P/S1P4/G12/G13 0.043 0.032 -10000 0 -0.19 7 7
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.002 0.1 0.22 2 -0.33 27 29
TBX21 -0.086 0.38 -10000 0 -1.2 51 51
B2M 0.023 0.022 -10000 0 -0.36 1 1
TYK2 0.02 0.031 -10000 0 -10000 0 0
IL12RB1 0.008 0.079 -10000 0 -0.39 20 20
GADD45B -0.028 0.26 -10000 0 -0.85 35 35
IL12RB2 0.012 0.066 -10000 0 -0.4 12 12
GADD45G -0.029 0.26 -10000 0 -0.9 28 28
natural killer cell activation 0 0.018 0.046 8 -0.043 33 41
RELB 0.027 0.003 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.026 0.03 -10000 0 -0.36 3 3
IL2RA 0.019 0.056 -10000 0 -0.36 13 13
IFNG -0.026 0.14 -10000 0 -0.44 60 60
STAT3 (dimer) -0.032 0.26 0.34 2 -0.73 48 50
HLA-DRB5 0 0.002 -10000 0 -0.021 4 4
FASLG -0.083 0.37 0.58 1 -1.1 52 53
NF kappa B2 p52/RelB -0.05 0.3 -10000 0 -0.87 49 49
CD4 0.016 0.064 -10000 0 -0.36 17 17
SOCS1 0.011 0.086 -10000 0 -0.44 21 21
EntrezGene:6955 0 0.009 -10000 0 -0.036 30 30
CD3D 0.015 0.064 -10000 0 -0.36 16 16
CD3E 0.012 0.072 -10000 0 -0.36 21 21
CD3G -0.004 0.1 -10000 0 -0.37 47 47
IL12Rbeta2/JAK2 0.024 0.066 -10000 0 -0.29 15 15
CCL3 -0.062 0.31 -10000 0 -0.94 44 44
CCL4 -0.057 0.3 -10000 0 -0.94 41 41
HLA-A -0.001 0.008 -10000 0 -0.038 26 26
IL18/IL18R 0.051 0.084 -10000 0 -0.24 25 25
NOS2 -0.072 0.36 -10000 0 -1.2 46 46
IL12/IL12R/TYK2/JAK2/SPHK2 0.007 0.097 0.22 2 -0.33 24 26
IL1R1 -0.064 0.32 -10000 0 -0.98 45 45
IL4 -0.003 0.034 -10000 0 -10000 0 0
JAK2 0.017 0.042 -10000 0 -0.38 3 3
EntrezGene:6957 0 0.009 -10000 0 -0.038 28 28
TCR/CD3/MHC I/CD8 -0.054 0.25 -10000 0 -0.8 52 52
RAB7A -0.019 0.23 0.52 1 -0.77 25 26
lysosomal transport -0.016 0.22 0.51 1 -0.73 25 26
FOS -0.061 0.29 -10000 0 -0.83 56 56
STAT4 (dimer) -0.03 0.28 0.44 2 -0.82 46 48
STAT5A (dimer) -0.067 0.31 -10000 0 -0.83 57 57
GZMA -0.1 0.4 -10000 0 -1.2 61 61
GZMB -0.086 0.31 -10000 0 -0.93 44 44
HLX 0.027 0.016 -10000 0 -0.36 1 1
LCK -0.069 0.32 0.38 1 -0.92 53 54
TCR/CD3/MHC II/CD4 -0.017 0.14 -10000 0 -0.44 43 43
IL2/IL2R 0.05 0.065 -10000 0 -0.26 22 22
MAPK14 -0.031 0.28 -10000 0 -0.88 35 35
CCR5 -0.038 0.29 -10000 0 -1.1 26 26
IL1B -0.023 0.14 -10000 0 -0.44 58 58
STAT6 0.007 0.091 -10000 0 -10000 0 0
STAT4 0.011 0.08 -10000 0 -0.36 27 27
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.44 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.006 -10000 0 -10000 0 0
IL12B 0.012 0.05 -10000 0 -0.44 4 4
CD8A -0.003 0.1 -10000 0 -0.37 45 45
CD8B 0.016 0.063 -10000 0 -0.37 15 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.002 0.1 0.33 27 -0.22 2 29
IL2RB 0.018 0.058 -10000 0 -0.36 14 14
proteasomal ubiquitin-dependent protein catabolic process -0.023 0.26 0.43 2 -0.75 45 47
IL2RG 0.026 0.027 -10000 0 -0.36 3 3
IL12 0.022 0.065 -10000 0 -0.29 12 12
STAT5A 0.027 0.004 -10000 0 -10000 0 0
CD247 0.017 0.06 -10000 0 -0.36 14 14
IL2 -0.006 0.02 -10000 0 -10000 0 0
SPHK2 0.027 0.016 -10000 0 -0.36 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.056 -10000 0 -0.38 8 8
IL12/IL12R/TYK2/JAK2 -0.069 0.34 0.41 2 -0.98 53 55
MAP2K3 -0.051 0.3 -10000 0 -0.88 46 46
RIPK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K6 -0.025 0.27 -10000 0 -0.86 34 34
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.002 -10000 0 -0.023 5 5
IL18RAP 0.009 0.086 -10000 0 -0.37 29 29
IL12Rbeta1/TYK2 0.022 0.07 -10000 0 -0.29 20 20
EOMES -0.043 0.25 -10000 0 -1.1 32 32
STAT1 (dimer) -0.029 0.25 0.35 2 -0.71 46 48
T cell proliferation -0.012 0.22 0.38 2 -0.63 39 41
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.022 0.052 -10000 0 -0.37 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.019 0.24 -10000 0 -0.68 40 40
ATF2 -0.029 0.26 -10000 0 -0.83 32 32
Nectin adhesion pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
alphaV beta3 Integrin 0.037 0.032 -10000 0 -0.25 7 7
PTK2 0.016 0.067 -10000 0 -0.34 13 13
positive regulation of JNK cascade 0.028 0.068 -10000 0 -0.28 11 11
CDC42/GDP 0.059 0.097 0.3 3 -0.36 11 14
Rac1/GDP 0.053 0.095 0.32 2 -0.36 11 13
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.047 0.084 -10000 0 -0.34 10 10
nectin-3/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
RAPGEF1 0.034 0.091 0.3 4 -0.39 10 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.089 -10000 0 -0.44 10 10
PDGFB-D/PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
TLN1 -0.001 0.025 -10000 0 -0.3 2 2
Rap1/GTP 0.022 0.065 -10000 0 -0.3 9 9
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
PVR 0.027 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.003 -10000 0 -10000 0 0
mol:GDP 0.052 0.11 0.34 2 -0.43 11 13
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PI3K 0.066 0.057 -10000 0 -0.23 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.029 0.077 -10000 0 -0.29 10 10
PVRL1 0.027 0.004 -10000 0 -10000 0 0
PVRL3 0.017 0.062 -10000 0 -0.36 16 16
PVRL2 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
CLDN1 -0.4 0.14 0.36 3 -0.44 557 560
JAM-A/CLDN1 -0.22 0.096 -10000 0 -0.25 543 543
SRC 0.007 0.094 -10000 0 -0.45 16 16
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
FARP2 0.053 0.11 0.38 1 -0.44 11 12
RAC1 0.025 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.047 0.044 -10000 0 -0.21 16 16
nectin-1/I-afadin 0.039 0.008 -10000 0 -10000 0 0
nectin-2/I-afadin 0.04 0.008 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.046 0.044 -10000 0 -0.21 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.034 0.015 -10000 0 -0.21 1 1
F11R 0.027 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.028 0.068 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Talin 0.008 0.069 -10000 0 -0.28 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
PIP5K1C 0.002 0.028 -10000 0 -0.27 3 3
VAV2 0.047 0.12 0.36 1 -0.47 5 6
RAP1/GDP 0.061 0.09 0.25 4 -0.34 10 14
ITGAV 0.028 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.047 0.044 -10000 0 -0.21 16 16
nectin-3(dimer)/I-afadin/I-afadin 0.032 0.047 -10000 0 -0.25 16 16
Rac1/GTP 0.037 0.093 -10000 0 -0.35 10 10
PTPRM 0.007 0.034 -10000 0 -0.34 3 3
E-cadherin/beta catenin/alpha catenin 0.076 0.023 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.029 0.16 -10000 0 -0.61 37 37
oxygen homeostasis -0.01 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.44 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.041 0.074 -10000 0 -10000 0 0
EPO -0.14 0.16 -10000 0 -0.56 15 15
FIH (dimer) 0.008 0.023 -10000 0 -10000 0 0
APEX1 -0.014 0.024 -10000 0 -10000 0 0
SERPINE1 -0.19 0.23 -10000 0 -0.58 115 115
FLT1 -0.002 0.089 -10000 0 -0.62 10 10
ADORA2A -0.15 0.17 0.36 1 -0.53 49 50
germ cell development -0.15 0.17 -10000 0 -0.53 50 50
SLC11A2 -0.15 0.17 -10000 0 -0.55 48 48
BHLHE40 -0.15 0.18 -10000 0 -0.55 48 48
HIF1AN 0.008 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.084 0.11 -10000 0 -0.4 3 3
ETS1 0.036 0.018 -10000 0 -0.36 1 1
CITED2 -0.007 0.11 -10000 0 -0.71 12 12
KDR -0.01 0.13 -10000 0 -0.64 20 20
PGK1 -0.15 0.17 -10000 0 -0.55 48 48
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.17 0.21 -10000 0 -0.62 50 50
EPAS1 -0.047 0.066 -10000 0 -0.3 4 4
SP1 0.031 0.01 -10000 0 -10000 0 0
ABCG2 -0.33 0.24 -10000 0 -0.62 146 146
EFNA1 -0.15 0.17 -10000 0 -0.55 49 49
FXN -0.15 0.17 0.36 1 -0.53 48 49
POU5F1 -0.16 0.18 -10000 0 -0.55 50 50
neuron apoptosis 0.16 0.2 0.61 50 -10000 0 50
EP300 0.026 0.006 -10000 0 -10000 0 0
EGLN3 0.005 0.035 -10000 0 -0.36 3 3
EGLN2 0.008 0.028 -10000 0 -0.37 1 1
EGLN1 0.009 0.024 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.047 0.024 -10000 0 -0.27 1 1
VHL 0.027 0.004 -10000 0 -10000 0 0
ARNT -0.013 0.029 -10000 0 -0.38 1 1
SLC2A1 -0.16 0.18 0.36 1 -0.56 54 55
TWIST1 -0.16 0.19 0.36 1 -0.64 47 48
ELK1 0.032 0.006 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.084 0.11 -10000 0 -0.39 3 3
VEGFA -0.15 0.17 -10000 0 -0.55 46 46
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.04 0.019 0.26 2 -0.25 1 3
alphaV beta3 Integrin 0.032 0.076 -10000 0 -0.22 47 47
PTK2 0.031 0.11 0.26 36 -0.38 6 42
IGF1R 0.027 0.006 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.027 0.006 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
CDKN1B 0.01 0.044 -10000 0 -0.38 2 2
VEGFA 0.028 0.019 0.36 2 -10000 0 2
ILK 0.011 0.039 -10000 0 -10000 0 0
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
AKT1 0.004 0.033 -10000 0 -10000 0 0
PTK2B 0.011 0.034 -10000 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A 0.029 0.081 -10000 0 -0.24 20 20
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.045 0.037 -10000 0 -0.23 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.008 0.11 -10000 0 -0.19 131 131
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.016 0.038 -10000 0 -0.32 4 4
alphaV/beta3 Integrin/Syndecan-1 0.052 0.03 -10000 0 -0.21 7 7
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.021 0.14 -10000 0 -0.35 41 41
PI4 Kinase 0.039 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
alphaV/beta3 Integrin/Osteopontin -0.088 0.16 -10000 0 -0.27 269 269
RPS6KB1 -0.069 0.1 -10000 0 -0.34 41 41
TLN1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.043 0.15 -10000 0 -0.48 54 54
GPR124 0.023 0.018 -10000 0 -0.36 1 1
MAPK1 -0.042 0.15 -10000 0 -0.48 54 54
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.081 -10000 0 -0.22 57 57
cell adhesion 0.04 0.036 -10000 0 -0.22 7 7
ANGPTL3 -0.003 0.038 -10000 0 -0.44 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.029 0.25 1 -10000 0 1
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.044 0.035 -10000 0 -0.2 8 8
apoptosis 0.028 0.002 -10000 0 -10000 0 0
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.051 0.03 -10000 0 -0.21 7 7
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.006 0.11 -10000 0 -0.22 104 104
CSF1 0.025 0.027 -10000 0 -0.36 3 3
PIK3C2A 0.01 0.045 -10000 0 -0.38 2 2
PI4 Kinase/Pyk2 0.01 0.067 -10000 0 -0.31 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.064 0.035 0.26 2 -10000 0 2
FAK1/Vinculin 0.045 0.1 0.23 49 -0.33 4 53
alphaV beta3/Integrin/ppsTEM5 0.044 0.035 -10000 0 -0.2 8 8
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN 0.006 0.082 -10000 0 -0.44 19 19
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
FGF2 0 0.099 -10000 0 -0.36 43 43
F11R -0.005 0.067 -10000 0 -0.25 42 42
alphaV/beta3 Integrin/Lactadherin 0.05 0.031 -10000 0 -0.21 7 7
alphaV/beta3 Integrin/TGFBR2 0.051 0.03 -10000 0 -0.21 7 7
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.027 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.048 0.028 -10000 0 -0.19 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.001 0.11 -10000 0 -0.43 36 36
alphaV/beta3 Integrin/Pyk2 0.037 0.039 -10000 0 -10000 0 0
SDC1 0.028 0 -10000 0 -10000 0 0
VAV3 -0.004 0.056 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.044 0.1 0.23 38 -0.34 3 41
cell migration 0.039 0.095 0.21 53 -0.31 3 56
ITGAV 0.028 0.002 -10000 0 -10000 0 0
PI3K 0.041 0.083 -10000 0 -0.33 2 2
SPP1 -0.18 0.23 -10000 0 -0.44 263 263
KDR 0.026 0.016 -10000 0 -0.36 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.002 -10000 0 -10000 0 0
COL4A3 -0.013 0.11 -10000 0 -0.38 51 51
angiogenesis -0.038 0.15 0.24 1 -0.48 55 56
Rac1/GTP 0.009 0.055 -10000 0 -10000 0 0
EDIL3 -0.04 0.15 -10000 0 -0.36 106 106
cell proliferation 0.051 0.03 -10000 0 -0.21 7 7
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.006 0.11 -10000 0 -0.46 29 29
NFATC2 -0.004 0.12 -10000 0 -0.56 10 10
NFATC3 -0.018 0.066 -10000 0 -0.29 5 5
CD40LG -0.18 0.27 -10000 0 -0.83 36 36
ITCH 0.018 0.018 -10000 0 -10000 0 0
CBLB 0.029 0.026 -10000 0 -0.36 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.11 0.2 -10000 0 -0.81 24 24
JUNB 0.026 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.023 -10000 0 -0.26 3 3
T cell anergy 0.037 0.055 0.24 1 -0.31 1 2
TLE4 -0.003 0.084 -10000 0 -0.48 6 6
Jun/NFAT1-c-4/p21SNFT -0.078 0.18 -10000 0 -0.78 10 10
AP-1/NFAT1-c-4 -0.2 0.27 -10000 0 -0.9 29 29
IKZF1 -0.014 0.13 -10000 0 -0.62 21 21
T-helper 2 cell differentiation -0.052 0.16 0.4 1 -0.67 20 21
AP-1/NFAT1 -0.033 0.1 -10000 0 -0.42 6 6
CALM1 0.034 0.017 -10000 0 -10000 0 0
EGR2 -0.039 0.16 -10000 0 -1.1 7 7
EGR3 -0.041 0.17 -10000 0 -0.99 11 11
NFAT1/FOXP3 -0.002 0.12 -10000 0 -0.49 14 14
EGR1 0.027 0.023 -10000 0 -0.36 2 2
JUN -0.032 0.047 -10000 0 -10000 0 0
EGR4 -0.052 0.17 -10000 0 -0.44 102 102
mol:Ca2+ 0.009 0.011 -10000 0 -0.18 1 1
GBP3 -0.024 0.15 -10000 0 -0.58 34 34
FOSL1 -0.27 0.23 0.36 1 -0.44 385 386
NFAT1-c-4/MAF/IRF4 -0.069 0.18 -10000 0 -0.79 17 17
DGKA -0.003 0.082 -10000 0 -0.44 6 6
CREM 0.027 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.042 0.15 -10000 0 -0.81 7 7
CTLA4 -0.017 0.11 -10000 0 -0.49 21 21
NFAT1-c-4 (dimer)/EGR1 -0.04 0.15 -10000 0 -0.81 7 7
NFAT1-c-4 (dimer)/EGR4 -0.072 0.17 -10000 0 -0.85 8 8
FOS -0.033 0.057 -10000 0 -0.37 6 6
IFNG -0.062 0.18 -10000 0 -0.73 18 18
T cell activation -0.021 0.14 -10000 0 -0.57 2 2
MAF 0.019 0.058 -10000 0 -0.36 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.038 0.13 0.88 8 -10000 0 8
TNF -0.067 0.15 -10000 0 -0.81 9 9
FASLG -0.085 0.34 -10000 0 -1.2 44 44
TBX21 -0.002 0.094 -10000 0 -0.36 35 35
BATF3 0.022 0.049 -10000 0 -0.43 7 7
PRKCQ 0.019 0.052 -10000 0 -0.36 8 8
PTPN1 -0.003 0.082 -10000 0 -0.44 6 6
NFAT1-c-4/ICER1 -0.041 0.15 -10000 0 -0.81 7 7
GATA3 0.024 0.037 -10000 0 -0.38 5 5
T-helper 1 cell differentiation -0.06 0.18 -10000 0 -0.72 18 18
IL2RA -0.1 0.2 -10000 0 -0.76 28 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.08 -10000 0 -0.44 6 6
E2F1 0.021 0.057 0.36 9 -0.44 4 13
PPARG 0.026 0.022 -10000 0 -0.36 2 2
SLC3A2 -0.003 0.08 -10000 0 -0.44 6 6
IRF4 -0.072 0.17 -10000 0 -0.36 156 156
PTGS2 -0.18 0.27 -10000 0 -0.81 41 41
CSF2 -0.25 0.32 -10000 0 -0.76 80 80
JunB/Fra1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.78 16 16
IL4 -0.054 0.17 0.4 1 -0.7 19 20
IL5 -0.17 0.26 -10000 0 -0.79 33 33
IL2 -0.022 0.14 -10000 0 -0.58 2 2
IL3 -0.033 0.089 -10000 0 -0.67 8 8
RNF128 0.029 0.026 -10000 0 -0.36 2 2
NFATC1 -0.038 0.14 -10000 0 -0.88 8 8
CDK4 0.023 0.096 0.64 4 -10000 0 4
PTPRK -0.004 0.081 -10000 0 -0.45 5 5
IL8 -0.28 0.32 -10000 0 -0.77 81 81
POU2F1 0.026 0.02 -10000 0 -0.44 1 1
Caspase cascade in apoptosis

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
TOP1 -0.037 0.1 -10000 0 -0.33 37 37
ACTA1 -0.054 0.1 -10000 0 -0.34 34 34
NUMA1 -0.037 0.11 -10000 0 -0.36 38 38
SPTAN1 -0.054 0.1 0.21 1 -0.34 33 34
LIMK1 -0.048 0.11 0.29 5 -0.35 28 33
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
BAX 0.027 0.004 -10000 0 -10000 0 0
CASP10 -0.078 0.12 -10000 0 -0.28 153 153
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.002 -10000 0 -10000 0 0
PTK2 -0.035 0.11 -10000 0 -0.33 40 40
DIABLO 0.028 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.053 0.1 0.21 1 -0.33 33 34
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
GSN -0.057 0.11 0.21 1 -0.34 37 38
MADD 0.028 0.003 -10000 0 -10000 0 0
TFAP2A -0.001 0.095 0.35 1 -0.57 13 14
BID -0.028 0.064 -10000 0 -0.22 25 25
MAP3K1 -0.02 0.08 -10000 0 -0.43 16 16
TRADD 0.028 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.053 0.1 0.28 2 -0.34 33 35
CASP9 0.026 0.007 -10000 0 -10000 0 0
DNA repair 0.009 0.04 0.18 4 -0.14 3 7
neuron apoptosis -0.021 0.17 -10000 0 -0.66 37 37
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.048 0.11 -10000 0 -0.34 44 44
APAF1 0.028 0.003 -10000 0 -10000 0 0
CASP6 -0.025 0.16 0.34 1 -0.87 19 20
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
ICAD/CAD -0.054 0.097 -10000 0 -0.34 29 29
CASP7 0.002 0.056 0.23 6 -0.25 12 18
KRT18 0.011 0.038 -10000 0 -0.51 1 1
apoptosis -0.051 0.12 0.31 1 -0.37 41 42
DFFA -0.055 0.1 -10000 0 -0.34 33 33
DFFB -0.055 0.1 0.19 1 -0.34 33 34
PARP1 -0.009 0.04 0.14 3 -0.18 4 7
actin filament polymerization 0.048 0.1 0.33 29 -0.27 3 32
TNF 0.024 0.035 -10000 0 -0.36 5 5
CYCS -0.014 0.056 0.19 1 -0.17 16 17
SATB1 -0.027 0.15 0.32 1 -0.81 19 20
SLK -0.055 0.1 -10000 0 -0.34 35 35
p15 BID/BAX -0.018 0.07 -10000 0 -0.22 20 20
CASP2 0.021 0.045 0.21 16 -0.22 1 17
JNK cascade 0.019 0.079 0.43 16 -10000 0 16
CASP3 -0.056 0.11 -10000 0 -0.35 34 34
LMNB2 0.011 0.11 0.41 3 -0.62 10 13
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP4 0.027 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -0.24 1 1
negative regulation of DNA binding -0.001 0.094 0.34 1 -0.56 13 14
stress fiber formation -0.055 0.1 -10000 0 -0.33 35 35
GZMB -0.074 0.15 -10000 0 -0.34 153 153
CASP1 0.013 0.019 -10000 0 -0.26 3 3
LMNB1 0.007 0.11 0.41 3 -0.55 14 17
APP -0.022 0.17 -10000 0 -0.68 37 37
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM -0.048 0.12 0.32 1 -0.38 39 40
LMNA 0.018 0.069 0.4 3 -0.31 4 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.022 0.034 -10000 0 -0.23 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.098 -10000 0 -0.34 30 30
APAF-1/Caspase 9 -0.02 0.14 -10000 0 -0.61 33 33
nuclear fragmentation during apoptosis -0.037 0.11 -10000 0 -0.35 38 38
CFL2 -0.049 0.1 0.3 2 -0.34 29 31
GAS2 -0.085 0.13 -10000 0 -0.38 67 67
positive regulation of apoptosis 0.016 0.099 0.36 4 -0.45 17 21
PRF1 0.019 0.058 -10000 0 -0.39 12 12
Noncanonical Wnt signaling pathway

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
NFATC2 0.005 0.063 -10000 0 -0.36 17 17
GNB1/GNG2 -0.028 0.12 -10000 0 -0.33 25 25
mol:DAG -0.026 0.082 0.19 1 -0.34 15 16
PLCG1 -0.027 0.084 0.19 1 -0.34 15 16
YES1 -0.035 0.091 -10000 0 -0.3 30 30
FZD3 0.021 0.035 0.36 2 -0.44 2 4
FZD6 0.024 0.01 -10000 0 -10000 0 0
G protein 0.021 0.13 0.28 13 -0.38 12 25
MAP3K7 -0.033 0.076 0.16 1 -0.32 17 18
mol:Ca2+ -0.026 0.08 0.19 1 -0.33 15 16
mol:IP3 -0.026 0.082 0.19 1 -0.34 15 16
NLK -0.003 0.094 -10000 0 -0.77 9 9
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.032 0.082 0.18 1 -0.34 17 18
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.032 0.1 0.17 1 -0.3 44 45
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.021 0.086 0.33 1 -0.32 22 23
GO:0007205 -0.029 0.08 -10000 0 -0.35 12 12
WNT6 -0.011 0.11 -10000 0 -0.38 52 52
WNT4 0.013 0.072 -10000 0 -0.38 20 20
NFAT1/CK1 alpha -0.019 0.092 -10000 0 -0.39 12 12
GNG2 0.011 0.074 -10000 0 -0.36 23 23
WNT5A 0.022 0.05 -10000 0 -0.44 7 7
WNT11 -0.069 0.19 -10000 0 -0.44 127 127
CDC42 -0.034 0.087 0.19 1 -0.33 14 15
a4b1 and a4b7 Integrin 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
ITGB1 0.028 0.002 -9999 0 -10000 0 0
ITGB7 0.013 0.074 -9999 0 -0.36 23 23
ITGA4 0.014 0.072 -9999 0 -0.36 22 22
alpha4/beta7 Integrin 0.02 0.081 -9999 0 -0.28 40 40
alpha4/beta1 Integrin 0.03 0.055 -9999 0 -0.25 22 22
Regulation of Androgen receptor activity

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
HDAC1 0.008 0.012 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.03 0.008 -10000 0 -10000 0 0
HDAC7 -0.023 0.082 -10000 0 -0.38 3 3
JUN 0.026 0.006 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
KAT2B 0.01 0.078 -10000 0 -0.36 26 26
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.001 0.03 -10000 0 -0.27 4 4
FOXO1 0.02 0.019 -10000 0 -0.36 1 1
T-DHT/AR -0.004 0.097 -10000 0 -0.4 3 3
MAP2K6 0.016 0.037 -10000 0 -0.37 4 4
BRM/BAF57 0.028 0.031 -10000 0 -0.28 1 1
MAP2K4 0.016 0.02 -10000 0 -10000 0 0
SMARCA2 0.019 0.025 -10000 0 -0.38 1 1
PDE9A -0.15 0.38 -10000 0 -0.94 108 108
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
CEBPA 0.026 0.027 -10000 0 -0.36 3 3
EHMT2 0.026 0.015 0.36 1 -10000 0 1
cell proliferation 0.034 0.13 0.28 38 -0.4 3 41
NR0B1 -0.005 0.045 -10000 0 -0.44 5 5
EGR1 0.019 0.028 -10000 0 -0.36 2 2
RXRs/9cRA -0.059 0.12 -10000 0 -0.19 252 252
AR/RACK1/Src 0.051 0.099 0.27 10 -0.33 1 11
AR/GR -0.019 0.089 -10000 0 -0.28 25 25
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -10000 0 -0.011 2 2
MAPK8 0.003 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.004 0.061 -10000 0 -0.34 1 1
SRC 0.024 0.083 0.19 118 -10000 0 118
NR3C1 -0.001 0.1 -10000 0 -0.36 44 44
KLK3 -0.21 0.42 -10000 0 -1.1 102 102
APPBP2 0.018 0.025 -10000 0 -0.36 1 1
TRIM24 0.02 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.005 0.057 0.2 3 -0.3 3 6
TMPRSS2 -0.023 0.15 -10000 0 -0.76 13 13
RXRG -0.15 0.18 -10000 0 -0.36 253 253
mol:9cRA -0.001 0.002 -10000 0 -0.01 3 3
RXRA 0.026 0.016 -10000 0 -0.36 1 1
RXRB 0.027 0.004 -10000 0 -10000 0 0
CARM1 0.028 0.003 -10000 0 -10000 0 0
NR2C2 0.026 0.016 -10000 0 -0.36 1 1
KLK2 0.021 0.091 0.28 2 -0.36 3 5
AR -0.011 0.063 0.16 2 -0.24 37 39
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.02 -10000 0 -0.36 1 1
SRY 0.004 0.011 0.028 105 -10000 0 105
GATA2 0.021 0.052 -10000 0 -0.36 11 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.008 0.099 -10000 0 -0.36 42 42
T-DHT/AR/RACK1/Src 0.06 0.1 0.28 13 -0.34 1 14
positive regulation of transcription 0.021 0.051 -10000 0 -0.36 11 11
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.014 -10000 0 -0.28 1 1
NCOA1 0.025 0.02 -10000 0 -10000 0 0
SPDEF -0.065 0.16 -10000 0 -0.36 138 138
T-DHT/AR/TIF2 -0.003 0.068 0.26 3 -0.3 3 6
T-DHT/AR/Hsp90 -0.006 0.054 0.2 2 -0.3 3 5
GSK3B 0.027 0.004 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.033 0.22 2 -0.25 3 5
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.029 0.015 -10000 0 -10000 0 0
POU2F1 0.015 0.055 -10000 0 -0.26 3 3
T-DHT/AR/DAX-1 -0.014 0.058 -10000 0 -0.3 4 4
CREBBP 0.027 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.019 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
Jak2/Leptin Receptor 0.022 0.087 -10000 0 -0.37 11 11
PTP1B/AKT1 0.017 0.078 0.18 3 -0.33 6 9
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.012 0.084 0.2 14 -0.34 7 21
EGFR 0.017 0.029 -10000 0 -0.37 2 2
EGF/EGFR -0.013 0.11 -10000 0 -0.27 43 43
CSF1 0.025 0.027 -10000 0 -0.36 3 3
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.028 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.007 0.08 0.2 6 -0.32 10 16
Insulin Receptor/Insulin 0.025 0.074 -10000 0 -0.38 3 3
HCK 0.011 0.047 -10000 0 -0.36 9 9
CRK 0.023 0.01 -10000 0 -10000 0 0
TYK2 0.01 0.082 0.24 11 -0.33 6 17
EGF -0.057 0.16 -10000 0 -0.38 127 127
YES1 0.022 0.019 -10000 0 -0.36 1 1
CAV1 0.02 0.11 0.22 49 -0.32 7 56
TXN 0.027 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.027 0.087 -10000 0 -0.36 4 4
cell migration -0.012 0.084 0.34 7 -0.2 14 21
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR 0.017 0.062 -10000 0 -0.36 16 16
ITGA2B 0.006 0.089 -10000 0 -0.44 23 23
CSF1R 0.006 0.088 -10000 0 -0.36 33 33
Prolactin Receptor/Prolactin 0.02 0.069 -10000 0 -0.29 27 27
FGR 0.023 0.034 -10000 0 -0.38 4 4
PTP1B/p130 Cas 0.018 0.084 0.2 8 -0.34 6 14
Crk/p130 Cas 0.018 0.081 -10000 0 -0.33 5 5
DOK1 0.014 0.077 0.21 3 -0.37 4 7
JAK2 0.014 0.088 0.23 2 -0.35 14 16
Jak2/Leptin Receptor/Leptin 0.01 0.097 -10000 0 -0.33 5 5
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0.012 0.084 0.2 14 -0.34 7 21
LYN 0.024 0.009 -10000 0 -10000 0 0
CDH2 0.005 0.077 -10000 0 -0.37 24 24
SRC 0.026 0.088 -10000 0 -0.41 15 15
ITGB3 0.022 0.042 -10000 0 -0.36 7 7
CAT1/PTP1B 0.005 0.16 0.24 80 -0.4 24 104
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.07 -10000 0 -0.41 2 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.014 0.089 -10000 0 -0.32 3 3
negative regulation of transcription 0.014 0.087 0.23 2 -0.35 14 16
FCGR2A 0.023 0.041 -10000 0 -0.43 5 5
FER 0.024 0.025 -10000 0 -0.4 2 2
alphaIIb/beta3 Integrin 0.022 0.074 -10000 0 -0.3 30 30
BLK -0.09 0.17 -10000 0 -0.36 172 172
Insulin Receptor/Insulin/Shc 0.046 0.013 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.022 0.044 -10000 0 -0.36 8 8
BCAR1 0.027 0.016 -10000 0 -0.36 1 1
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.065 0.17 0.24 18 -0.39 77 95
PRL -0.005 0.066 -10000 0 -0.44 12 12
SOCS3 0.009 0.12 -10000 0 -1.1 8 8
SPRY2 0.023 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.018 0.097 0.22 4 -0.33 11 15
Ras protein signal transduction -0.006 0.051 0.43 6 -10000 0 6
IRS1 0.028 0.002 -10000 0 -10000 0 0
INS 0.003 0.018 -10000 0 -10000 0 0
LEP -0.021 0.11 -10000 0 -0.37 54 54
STAT5B 0.018 0.082 0.2 10 -0.33 9 19
STAT5A 0.018 0.082 0.19 12 -0.33 9 21
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.089 0.19 12 -0.31 12 24
CSN2 -0.007 0.051 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
LAT 0.029 0.058 -10000 0 -0.45 5 5
YBX1 0.036 0.008 -10000 0 -10000 0 0
LCK 0.019 0.058 -10000 0 -0.43 10 10
SHC1 0.027 0.004 -10000 0 -10000 0 0
NOX4 -0.19 0.24 0.35 1 -0.44 280 281
Ceramide signaling pathway

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
SPHK2 0.012 0.011 -10000 0 -0.25 1 1
MAP4K4 0.017 0.037 -10000 0 -0.26 1 1
BAG4 0.024 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.014 0.073 -10000 0 -0.21 59 59
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.021 0.05 -10000 0 -0.37 10 10
BAX -0.003 0.041 -10000 0 -0.3 6 6
RIPK1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.002 0.012 -10000 0 -10000 0 0
BAD -0.03 0.067 -10000 0 -0.21 60 60
SMPD1 0.02 0.047 0.22 7 -0.22 5 12
RB1 0.01 0.087 0.19 80 -0.2 29 109
FADD/Caspase 8 0.024 0.04 0.2 2 -10000 0 2
MAP2K4 -0.028 0.063 -10000 0 -0.21 46 46
NSMAF 0.024 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.025 0.069 0.18 13 -0.21 42 55
EGF -0.06 0.16 -10000 0 -0.37 127 127
mol:ceramide -0.029 0.071 -10000 0 -0.22 60 60
MADD 0.028 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.006 -10000 0 -10000 0 0
ASAH1 0.021 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle 0.01 0.087 0.19 80 -0.2 29 109
cell proliferation -0.036 0.096 -10000 0 -0.31 17 17
BID 0 0.13 -10000 0 -0.58 27 27
MAP3K1 -0.03 0.067 -10000 0 -0.21 61 61
EIF2A -0.031 0.062 0.18 1 -0.26 16 17
TRADD 0.028 0.003 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.021 0.066 0.18 5 -0.26 13 18
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.067 0.18 3 -0.26 14 17
Cathepsin D/ceramide -0.015 0.074 -10000 0 -0.21 60 60
FADD 0.018 0.036 0.21 2 -10000 0 2
KSR1 -0.024 0.072 0.19 11 -0.21 56 67
MAPK8 -0.024 0.071 -10000 0 -0.24 24 24
PRKRA -0.03 0.067 -10000 0 -0.21 60 60
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.029 0.071 -10000 0 -0.22 60 60
CTSD 0.027 0.016 -10000 0 -0.36 1 1
regulation of nitric oxide biosynthetic process 0.039 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.037 0.1 -10000 0 -0.33 17 17
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.039 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.031 -10000 0 -0.26 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.031 -10000 0 -0.21 5 5
mol:Sphingosine-1-phosphate 0.012 0.011 -10000 0 -0.25 1 1
MAP2K1 -0.025 0.066 0.19 4 -0.26 14 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0.02 0.051 0.15 8 -0.18 3 11
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.031 0.064 -10000 0 -0.21 50 50
TNF-alpha/TNFR1A/FAN 0.046 0.03 -10000 0 -0.21 5 5
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.052 -10000 0 -0.32 3 3
MAP2K2 -0.025 0.066 0.18 4 -0.26 14 18
SMPD3 0.017 0.056 0.17 2 -0.28 15 17
TNF 0.024 0.035 -10000 0 -0.36 5 5
PKC zeta/PAR4 0.039 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.029 0.08 0.18 96 -0.16 4 100
NF kappa B1/RelA/I kappa B alpha 0.07 0.03 -10000 0 -10000 0 0
AIFM1 0.013 0.06 0.14 8 -0.17 10 18
BCL2 0.014 0.05 -10000 0 -0.36 10 10
S1P3 pathway

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
PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.055 0.11 -10000 0 -0.31 46 46
GNAO1 -0.11 0.19 -10000 0 -0.36 225 225
S1P/S1P3/G12/G13 0.046 0.024 -10000 0 -0.24 1 1
AKT1 -0.034 0.14 -10000 0 -0.47 48 48
AKT3 -0.012 0.15 -10000 0 -1.1 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.05 -10000 0 -0.44 7 7
GNAI2 0.027 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GNAI1 0.015 0.068 -10000 0 -0.36 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.027 0.021 -10000 0 -0.44 1 1
S1PR2 0.027 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.13 -10000 0 -0.34 47 47
MAPK3 -0.059 0.12 -10000 0 -0.33 52 52
MAPK1 -0.051 0.12 -10000 0 -0.34 36 36
JAK2 -0.012 0.14 0.23 6 -0.38 27 33
CXCR4 -0.058 0.12 -10000 0 -0.33 51 51
FLT1 0.021 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC -0.039 0.1 -10000 0 -0.33 33 33
S1P/S1P3/Gi -0.056 0.13 -10000 0 -0.35 47 47
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.046 0.13 -10000 0 -0.35 34 34
VEGFA 0.029 0.021 0.36 2 -10000 0 2
S1P/S1P2/Gi -0.058 0.12 -10000 0 -0.33 48 48
VEGFR1 homodimer/VEGFA homodimer 0.033 0.025 0.26 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.04 -10000 0 -0.26 9 9
GNAQ 0.026 0.022 -10000 0 -0.36 2 2
GNAZ 0.023 0.036 -10000 0 -0.36 5 5
G12/G13 0.036 0.013 -10000 0 -10000 0 0
GNA14 0.024 0.035 -10000 0 -0.36 5 5
GNA15 0.023 0.046 -10000 0 -0.44 6 6
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.025 0.031 -10000 0 -0.36 4 4
Rac1/GTP -0.045 0.12 -10000 0 -0.32 48 48
Signaling events mediated by HDAC Class III

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
EP300 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.028 0.002 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.007 0.039 0.31 8 -0.27 1 9
CDKN1A -0.008 0.024 -10000 0 -0.59 1 1
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
BAX 0.027 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.021 0.019 -10000 0 -0.36 1 1
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
TAT -0.13 0.18 -10000 0 -0.36 224 224
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.025 0.049 -10000 0 -0.26 26 26
PPARGC1A -0.026 0.13 -10000 0 -0.36 84 84
FHL2 0.028 0.001 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.011 -10000 0 -10000 0 0
HIST2H4A 0.007 0.039 0.27 1 -0.31 8 9
SIRT1/FOXO3a 0.019 0.02 -10000 0 -10000 0 0
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.052 0.013 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.047 -10000 0 -0.22 4 4
apoptosis -0.05 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A 0.001 0.084 -10000 0 -0.21 83 83
p53/SIRT1 0.027 0.019 0.37 1 -10000 0 1
SIRT1/FOXO4 0.023 0.031 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.039 0.025 -10000 0 -0.19 1 1
HIST1H1E 0.006 0.039 0.2 2 -0.25 4 6
SIRT1/p300 0.037 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.052 0.22 25 -0.22 3 28
TP53 0.02 0.012 0.19 1 -10000 0 1
KU70/SIRT1/BAX 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.07 0.14 -10000 0 -0.25 222 222
ACSS2 0.007 0.013 -10000 0 -0.25 1 1
SIRT1/PCAF/MYOD 0.02 0.052 0.22 3 -0.22 25 28
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.041 0.02 0.26 2 -0.25 1 3
PDGFRB 0.023 0.05 -10000 0 -0.44 7 7
SPHK1 -0.005 0.068 -10000 0 -0.64 6 6
mol:S1P -0.007 0.061 -10000 0 -0.54 6 6
S1P1/S1P/Gi -0.059 0.16 -10000 0 -0.43 47 47
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.17 0.29 15 -0.43 30 45
PLCG1 -0.056 0.13 0.28 5 -0.45 31 36
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.05 -10000 0 -0.44 7 7
GNAI2 0.028 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.008 -10000 0 -10000 0 0
GNAI1 0.014 0.068 -10000 0 -0.36 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.016 0.19 2 -0.2 1 3
S1P1/S1P 0.021 0.065 0.22 4 -0.38 4 8
negative regulation of cAMP metabolic process -0.058 0.16 -10000 0 -0.42 48 48
MAPK3 -0.064 0.17 0.26 2 -0.55 33 35
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.027 0.017 -10000 0 -0.36 1 1
PLCB2 0.022 0.069 0.25 12 -0.34 4 16
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.053 -10000 0 -0.32 4 4
receptor internalization 0.019 0.061 0.2 4 -0.33 5 9
PTGS2 -0.059 0.2 0.38 2 -0.8 23 25
Rac1/GTP 0.015 0.051 -10000 0 -0.34 3 3
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.029 0.019 0.36 2 -10000 0 2
negative regulation of T cell proliferation -0.058 0.16 -10000 0 -0.42 48 48
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.036 -10000 0 -0.37 5 5
MAPK1 -0.06 0.16 -10000 0 -0.51 37 37
S1P1/S1P/PDGFB-D/PDGFRB 0.044 0.09 0.28 15 -0.32 4 19
ABCC1 0.028 0.004 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.035 0.2 17 -10000 0 17
RFC1 0 0.029 0.18 15 -10000 0 15
PRKDC 0.015 0.065 0.22 51 -10000 0 51
RIPK1 0.028 0.004 -10000 0 -10000 0 0
CASP7 0.006 0.098 -10000 0 -0.54 16 16
FASLG/FAS/FADD/FAF1 0.008 0.063 0.2 16 -0.22 27 43
MAP2K4 -0.015 0.098 0.25 1 -0.36 19 20
mol:ceramide 0.005 0.079 -10000 0 -0.28 31 31
GSN 0 0.039 0.2 17 -0.19 5 22
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.072 0.26 1 -0.28 24 25
FAS 0.02 0.045 -10000 0 -0.36 8 8
BID -0.01 0.05 0.25 21 -0.28 1 22
MAP3K1 0.007 0.081 0.21 6 -0.35 15 21
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
RB1 0.023 0.075 0.22 73 -10000 0 73
CFLAR 0.028 0.002 -10000 0 -10000 0 0
HGF/MET 0.03 0.083 -10000 0 -0.27 40 40
ARHGDIB 0.001 0.036 0.21 15 -10000 0 15
FADD 0.026 0.008 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.047 0.19 5 -0.2 17 22
NFKB1 -0.007 0.12 -10000 0 -0.68 18 18
MAPK8 -0.022 0.11 0.24 1 -0.41 20 21
DFFA 0 0.029 0.18 15 -10000 0 15
DNA fragmentation during apoptosis -0.003 0.039 0.18 16 -10000 0 16
FAS/FADD/MET 0.044 0.045 0.25 1 -0.24 12 13
CFLAR/RIP1 0.041 0.007 -10000 0 -10000 0 0
FAIM3 0.01 0.081 -10000 0 -0.36 28 28
FAF1 0.022 0.017 -10000 0 -10000 0 0
PARP1 0 0.029 0.18 15 -10000 0 15
DFFB 0.001 0.03 0.18 16 -10000 0 16
CHUK -0.011 0.12 -10000 0 -0.62 19 19
FASLG 0.001 0.087 -10000 0 -0.36 32 32
FAS/FADD 0.033 0.036 -10000 0 -0.25 8 8
HGF 0.017 0.061 -10000 0 -0.37 15 15
LMNA -0.003 0.039 0.24 5 -10000 0 5
CASP6 0 0.029 0.18 15 -10000 0 15
CASP10 0.027 0.007 -10000 0 -10000 0 0
CASP3 0.003 0.035 0.22 15 -10000 0 15
PTPN13 0.007 0.094 -10000 0 -0.43 27 27
CASP8 -0.006 0.068 0.31 27 -10000 0 27
IL6 -0.03 0.19 -10000 0 -0.93 17 17
MET 0.023 0.045 0.36 1 -0.44 5 6
ICAD/CAD -0.001 0.027 0.24 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 0.005 0.08 -10000 0 -0.28 31 31
activation of caspase activity by cytochrome c -0.01 0.05 0.25 21 -0.28 1 22
PAK2 0.001 0.032 0.18 17 -10000 0 17
BCL2 0.014 0.05 -10000 0 -0.36 10 10
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.031 -10000 0 -0.36 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.023 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.011 -10000 0 -0.17 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.028 0.002 -10000 0 -10000 0 0
FGR 0.023 0.034 -10000 0 -0.38 4 4
p38 alpha/TAB1 -0.06 0.11 -10000 0 -0.31 74 74
PRKG1 0.013 0.071 -10000 0 -0.36 21 21
DUSP8 0.026 0.022 -10000 0 -0.36 2 2
PGK/cGMP/p38 alpha -0.026 0.14 0.16 14 -0.34 59 73
apoptosis -0.058 0.1 -10000 0 -0.3 74 74
RAL/GTP 0.034 0.011 -10000 0 -10000 0 0
LYN 0.024 0.009 -10000 0 -10000 0 0
DUSP1 0.025 0.027 -10000 0 -0.36 3 3
PAK1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.054 0.032 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.025 0.017 -10000 0 -0.36 1 1
RAC1-CDC42/GTP 0.032 0.017 -10000 0 -0.21 1 1
MAPK11 -0.009 0.14 0.22 45 -0.35 31 76
BLK -0.09 0.17 -10000 0 -0.36 172 172
HCK 0.011 0.047 -10000 0 -0.36 9 9
MAP2K3 0.024 0.01 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.025 0.036 0.36 1 -0.44 3 4
TRAF6/MEKK3 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.15 0.21 40 -0.34 70 110
positive regulation of innate immune response -0.02 0.17 0.25 41 -0.41 47 88
LCK 0.019 0.058 -10000 0 -0.43 10 10
p38alpha-beta/MKP7 -0.013 0.16 0.25 38 -0.4 43 81
p38alpha-beta/MKP5 -0.012 0.16 0.25 40 -0.4 44 84
PGK/cGMP 0.01 0.049 -10000 0 -0.25 21 21
PAK2 0.028 0.002 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.013 0.16 0.25 40 -0.41 42 82
CDC42 0.025 0.017 -10000 0 -0.36 1 1
RALB 0.028 0.001 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
PAK3 0.01 0.022 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.023 0.046 -10000 0 -0.44 6 6
GPC2 0.013 0.081 0.36 1 -0.44 18 19
GPC2/Midkine 0.025 0.07 0.26 1 -0.32 24 25
neuron projection morphogenesis 0.025 0.07 0.26 1 -0.32 24 25
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.01 0.046 -10000 0 -0.35 1 1
STMN1 0.013 0.013 -10000 0 -0.25 1 1
Aurora B/RasGAP/Survivin 0.052 0.03 0.25 1 -0.26 1 2
Chromosomal passenger complex/Cul3 protein complex -0.012 0.082 0.15 1 -0.27 25 26
BIRC5 0.03 0.023 0.35 1 -0.44 1 2
DES -0.41 0.3 -10000 0 -0.58 437 437
Aurora C/Aurora B/INCENP 0.048 0.032 -10000 0 -0.19 4 4
Aurora B/TACC1 0.031 0.018 -10000 0 -10000 0 0
Aurora B/PP2A 0.037 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.013 0.008 -10000 0 -10000 0 0
Cul3 protein complex 0.018 0.092 -10000 0 -0.21 83 83
KIF2C 0.015 0.049 -10000 0 -0.35 8 8
PEBP1 0.029 0.003 -10000 0 -10000 0 0
KIF20A 0.029 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.038 0.018 -10000 0 -10000 0 0
SEPT1 0.023 0.041 -10000 0 -0.36 7 7
SMC2 0.027 0.016 -10000 0 -0.36 1 1
SMC4 0.026 0.022 -10000 0 -0.36 2 2
NSUN2/NPM1/Nucleolin -0.072 0.2 -10000 0 -0.5 106 106
PSMA3 0.026 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.015 0.007 -10000 0 -10000 0 0
AURKB 0.028 0.014 -10000 0 -10000 0 0
AURKC 0.023 0.033 -10000 0 -0.36 4 4
CDCA8 0.03 0.005 -10000 0 -10000 0 0
cytokinesis 0.005 0.039 -10000 0 -0.37 3 3
Aurora B/Septin1 0.005 0.11 -10000 0 -0.3 15 15
AURKA 0.017 0.014 -10000 0 -10000 0 0
INCENP 0.03 0.005 -10000 0 -10000 0 0
KLHL13 -0.026 0.13 -10000 0 -0.36 84 84
BUB1 0.03 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.05 0.033 0.24 1 -0.24 3 4
EVI5 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.049 0.065 -10000 0 -0.29 1 1
SGOL1 0.026 0.027 -10000 0 -0.44 2 2
CENPA 0.033 0.059 0.14 1 -0.19 11 12
NCAPG 0.027 0.005 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.038 0.018 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.038 0.018 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.028 0 -10000 0 -10000 0 0
NPM1 -0.042 0.15 -10000 0 -0.33 101 101
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.027 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.018 -10000 0 -10000 0 0
PPP1CC 0.028 0.002 -10000 0 -10000 0 0
Centraspindlin 0.044 0.065 -10000 0 -0.26 3 3
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 -0.032 0.11 -10000 0 -0.28 98 98
MYLK -0.023 0.092 -10000 0 -0.26 83 83
KIF23 0.027 0.02 -10000 0 -0.44 1 1
VIM 0.014 0.008 -10000 0 -10000 0 0
RACGAP1 0.028 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.032 0.11 -10000 0 -0.28 99 99
Chromosomal passenger complex 0.02 0.052 0.17 1 -0.18 15 16
Chromosomal passenger complex/EVI5 0.095 0.057 0.3 1 -0.22 1 2
TACC1 0.024 0.01 -10000 0 -10000 0 0
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.028 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Coregulation 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
NRIP1 0.007 0.047 -10000 0 -0.36 2 2
SVIL 0.011 0.04 -10000 0 -0.36 1 1
ZNF318 0.05 0.057 0.19 41 -10000 0 41
JMJD2C 0.004 0.021 0.048 2 -0.073 29 31
T-DHT/AR/Ubc9 0.019 0.069 -10000 0 -0.21 47 47
CARM1 0.02 0.019 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.026 0.015 -10000 0 -10000 0 0
CTNNB1 0.013 0.034 -10000 0 -10000 0 0
AKT1 0.032 0.019 -10000 0 -10000 0 0
PTK2B 0.011 0.034 -10000 0 -0.36 2 2
MED1 0.036 0.029 0.38 2 -10000 0 2
MAK 0.033 0.1 0.19 57 -0.43 21 78
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 0.011 0.039 -10000 0 -0.36 1 1
GSN 0.001 0.07 -10000 0 -0.38 13 13
NCOA2 0.017 0.032 -10000 0 -0.36 3 3
NCOA6 0.009 0.028 -10000 0 -10000 0 0
DNA-PK 0.064 0.055 0.22 6 -10000 0 6
NCOA4 0.024 0.019 -10000 0 -0.36 1 1
PIAS3 0.012 0.034 -10000 0 -10000 0 0
cell proliferation 0.028 0.071 0.25 3 -0.38 5 8
XRCC5 0.033 0.013 -10000 0 -10000 0 0
UBE3A 0.007 0.05 -10000 0 -0.36 1 1
T-DHT/AR/SNURF -0.007 0.1 -10000 0 -0.23 98 98
FHL2 0.042 0.053 -10000 0 -10000 0 0
RANBP9 0.009 0.044 -10000 0 -0.36 1 1
JMJD1A 0.002 0.012 -10000 0 -0.12 4 4
CDK6 0.027 0.007 -10000 0 -10000 0 0
TGFB1I1 0.012 0.037 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.005 0.077 0.18 1 -0.22 51 52
XRCC6 0.032 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.027 0.076 -10000 0 -0.2 43 43
CTDSP1 0.018 0.024 -10000 0 -10000 0 0
CTDSP2 0.043 0.038 -10000 0 -10000 0 0
BRCA1 0.012 0.036 -10000 0 -10000 0 0
TCF4 0.026 0.035 -10000 0 -0.36 2 2
CDKN2A -0.053 0.19 0.38 2 -0.44 115 117
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.004 0.033 -10000 0 -0.17 6 6
KLK3 -0.19 0.48 -10000 0 -1.3 99 99
TMF1 0.019 0.024 -10000 0 -0.36 1 1
HNRNPA1 0.037 0.022 -10000 0 -10000 0 0
AOF2 -0.012 0.029 -10000 0 -0.078 99 99
APPL1 0.025 0.041 0.15 2 -0.25 3 5
T-DHT/AR/Caspase 8 0.029 0.074 -10000 0 -0.2 47 47
AR -0.004 0.1 -10000 0 -0.36 47 47
UBA3 0.017 0.023 -10000 0 -10000 0 0
PATZ1 0.035 0.022 -10000 0 -10000 0 0
PAWR 0.02 0.019 -10000 0 -10000 0 0
PRKDC 0.029 0.02 0.36 1 -10000 0 1
PA2G4 0.038 0.025 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.026 0.065 -10000 0 -0.18 46 46
RPS6KA3 0.009 0.043 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.014 0.07 -10000 0 -0.21 48 48
LATS2 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.032 0.072 0.16 12 -0.18 42 54
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.017 0.11 -10000 0 -0.37 49 49
KLK2 -0.002 0.072 -10000 0 -0.3 28 28
CASP8 0.031 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.018 0.072 -10000 0 -0.2 43 43
TMPRSS2 0.004 0.071 -10000 0 -0.69 5 5
CCND1 0.014 0.047 0.35 1 -0.44 4 5
PIAS1 0.007 0.049 -10000 0 -10000 0 0
mol:T-DHT 0.001 0.01 -10000 0 -0.056 6 6
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.002 0.07 -10000 0 -0.16 89 89
T-DHT/AR/CDK6 0.022 0.07 -10000 0 -0.2 45 45
CMTM2 0.011 0.09 -10000 0 -0.44 23 23
SNURF -0.024 0.12 -10000 0 -0.37 61 61
ZMIZ1 0.027 0.018 -10000 0 -10000 0 0
CCND3 0.028 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.023 -10000 0 -10000 0 0
FKBP4 0.01 0.044 0.36 1 -10000 0 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.027 0.067 0.3 23 -0.24 2 25
KIRREL 0.021 0.048 -10000 0 -0.38 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.027 0.067 0.24 2 -0.3 23 25
PLCG1 0.016 0.014 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
WASL 0.027 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.043 0.079 0.23 2 -0.23 42 44
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.02 0.037 0.2 2 -0.22 7 9
FYN 0.01 0.062 0.28 12 -0.21 25 37
mol:Ca2+ 0.027 0.061 0.22 1 -0.24 21 22
mol:DAG 0.027 0.062 0.22 1 -0.24 21 22
NPHS2 0.013 0.049 -10000 0 -0.45 6 6
mol:IP3 0.027 0.062 0.22 1 -0.24 21 22
regulation of endocytosis 0.036 0.054 0.21 2 -0.2 18 20
Nephrin/NEPH1/podocin/Cholesterol 0.035 0.059 0.21 2 -0.23 25 27
establishment of cell polarity 0.027 0.067 0.24 2 -0.3 23 25
Nephrin/NEPH1/podocin/NCK1-2 0.064 0.063 -10000 0 -0.24 11 11
Nephrin/NEPH1/beta Arrestin2 0.037 0.056 0.22 2 -0.2 18 20
NPHS1 0.013 0.076 0.32 2 -0.44 15 17
Nephrin/NEPH1/podocin 0.037 0.054 0.21 2 -0.21 25 27
TJP1 0.026 0.007 -10000 0 -10000 0 0
NCK1 0.028 0.002 -10000 0 -10000 0 0
NCK2 0.028 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.062 0.23 1 -0.24 21 22
CD2AP 0.016 0.066 -10000 0 -0.36 18 18
Nephrin/NEPH1/podocin/GRB2 0.05 0.064 0.23 2 -0.24 25 27
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.076 0.3 12 -0.21 43 55
cytoskeleton organization 0.009 0.046 0.2 7 -0.35 2 9
Nephrin/NEPH1 0.025 0.047 0.19 2 -0.21 22 24
Nephrin/NEPH1/ZO-1 0.04 0.058 0.22 2 -0.24 20 22
Class I PI3K signaling events

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
ARF5/GTP -0.007 0.048 0.29 1 -10000 0 1
DAPP1 -0.012 0.14 0.18 75 -0.38 34 109
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.18 0.24 13 -0.5 52 65
mol:DAG 0 0.093 0.18 71 -0.23 17 88
HRAS 0.027 0.017 -10000 0 -0.36 1 1
RAP1A 0.027 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.027 0.12 0.2 4 -0.39 22 26
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
PLCG1 0.016 0.014 -10000 0 -10000 0 0
ARF5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.014 0.031 0.3 1 -10000 0 1
ARF1/GTP 0.002 0.04 0.25 3 -10000 0 3
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
RAP1A/GTP -0.014 0.03 0.16 14 -10000 0 14
ADAP1 -0.015 0.03 0.28 1 -0.33 1 2
ARAP3 -0.013 0.031 0.3 1 -10000 0 1
INPPL1 0.027 0.004 -10000 0 -10000 0 0
PREX1 0.015 0.025 -10000 0 -0.36 2 2
ARHGEF6 0.019 0.056 -10000 0 -0.36 13 13
ARHGEF7 0.022 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.026 0.023 -10000 0 -0.36 2 2
FYN 0.027 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
FGR 0.023 0.034 -10000 0 -0.38 4 4
mol:Ca2+ 0.004 0.057 0.16 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
ZAP70 0.018 0.06 -10000 0 -0.37 14 14
mol:IP3 -0.002 0.07 0.14 71 -0.18 8 79
LYN 0.024 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.12 0.2 6 -0.4 23 29
RhoA/GDP 0.04 0.069 0.25 5 -0.29 3 8
PDK1/Src/Hsp90 0.032 0.028 -10000 0 -10000 0 0
BLNK 0.022 0.041 -10000 0 -0.36 7 7
actin cytoskeleton reorganization 0.035 0.092 0.23 35 -0.34 8 43
SRC 0.017 0.014 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.01 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.035 0.29 1 -10000 0 1
RhoA/GTP -0.014 0.033 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.032 0.099 -10000 0 -0.35 29 29
BLK -0.09 0.17 -10000 0 -0.36 172 172
PDPK1 0.027 0.004 -10000 0 -10000 0 0
CYTH1 -0.015 0.029 0.28 1 -10000 0 1
HCK 0.011 0.047 -10000 0 -0.36 9 9
CYTH3 -0.015 0.028 0.28 1 -10000 0 1
CYTH2 -0.015 0.029 0.28 1 -10000 0 1
KRAS 0.027 0.017 -10000 0 -0.36 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.013 0.079 -10000 0 -0.36 22 22
SGK1 -0.003 0.082 -10000 0 -0.37 26 26
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
mol:GDP 0.017 0.12 0.18 9 -0.32 40 49
SOS1 0.028 0.002 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.066 0.24 9 -0.29 3 12
mol:PI-3-4-5-P3 -0.014 0.03 0.28 1 -10000 0 1
ARAP3/RAP1A/GTP -0.014 0.03 0.16 14 -10000 0 14
VAV1 0.011 0.077 -10000 0 -0.36 25 25
mol:PI-3-4-P2 0.013 0.011 -10000 0 -0.25 1 1
RAS family/GTP/PI3K Class I 0.044 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.008 -10000 0 -0.21 1 1
Rac1/GDP 0.022 0.11 0.2 4 -0.4 21 25
LAT 0.025 0.035 -10000 0 -0.4 4 4
Rac1/GTP -0.016 0.1 -10000 0 -0.34 42 42
ITK -0.022 0.041 0.28 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.009 0.11 0.2 65 -0.31 23 88
LCK 0.019 0.058 -10000 0 -0.43 10 10
BTK -0.032 0.056 0.28 1 -10000 0 1
ErbB2/ErbB3 signaling events

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
USP8 -0.007 0.013 -10000 0 -0.2 2 2
RAS family/GTP 0.011 0.088 0.23 1 -0.26 9 10
NFATC4 -0.022 0.055 0.25 2 -10000 0 2
ERBB2IP 0.023 0.041 -10000 0 -0.36 7 7
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis 0.003 0.068 0.19 1 -10000 0 1
JUN 0.005 0.067 0.21 3 -0.23 3 6
HRAS 0.027 0.016 -10000 0 -0.36 1 1
DOCK7 -0.026 0.061 0.16 1 -10000 0 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.074 0.22 4 -0.2 9 13
AKT1 0.004 0.006 -10000 0 -10000 0 0
BAD -0.006 0.009 -10000 0 -0.21 1 1
MAPK10 -0.02 0.064 0.21 4 -0.22 12 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.006 0.074 0.21 1 -10000 0 1
RAF1 -0.005 0.087 0.28 5 -0.29 8 13
ErbB2/ErbB3/neuregulin 2 -0.002 0.084 0.2 12 -0.2 76 88
STAT3 0.017 0.06 -10000 0 -0.79 3 3
cell migration -0.013 0.066 0.21 10 -0.2 11 21
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.042 0.22 0.37 2 -0.58 71 73
FOS -0.017 0.14 0.33 2 -0.35 74 76
NRAS 0.026 0.023 -10000 0 -0.36 2 2
mol:Ca2+ 0.003 0.068 0.19 1 -10000 0 1
MAPK3 -0.024 0.17 0.31 4 -0.48 57 61
MAPK1 -0.039 0.19 0.36 2 -0.52 66 68
JAK2 -0.027 0.062 0.16 1 -10000 0 1
NF2 0.004 0.06 -10000 0 -0.59 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.003 0.067 0.18 2 -0.21 52 54
NRG1 -0.015 0.11 -10000 0 -0.36 56 56
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
MAPK8 -0.018 0.089 0.17 1 -0.24 45 46
MAPK9 -0.008 0.052 0.2 5 -10000 0 5
ERBB2 -0.012 0.05 0.27 18 -10000 0 18
ERBB3 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.005 0.011 0.2 1 -10000 0 1
STAT3 (dimer) 0.017 0.059 -10000 0 -0.78 3 3
RNF41 -0.009 0.012 -10000 0 -10000 0 0
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.01 0.047 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.012 0.039 0.21 18 -10000 0 18
CHRNA1 -0.032 0.2 0.29 4 -0.59 58 62
myelination -0.018 0.062 0.27 5 -10000 0 5
PPP3CB -0.025 0.058 0.16 1 -10000 0 1
KRAS 0.026 0.016 -10000 0 -0.36 1 1
RAC1-CDC42/GDP 0.009 0.077 -10000 0 -10000 0 0
NRG2 -0.04 0.13 -10000 0 -0.36 88 88
mol:GDP -0.003 0.067 0.18 2 -0.21 52 54
SOS1 0.028 0.002 -10000 0 -10000 0 0
MAP2K2 -0.013 0.09 0.28 4 -0.32 11 15
SRC 0.017 0.014 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.062 0.16 1 -10000 0 1
MAP2K1 -0.046 0.2 0.36 1 -0.56 54 55
heart morphogenesis 0.003 0.068 0.19 1 -10000 0 1
RAS family/GDP 0.015 0.089 0.25 1 -0.28 1 2
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.007 0.063 -10000 0 -0.62 6 6
CHRNE 0.005 0.025 0.077 1 -0.14 11 12
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.006 -10000 0 -10000 0 0
nervous system development 0.003 0.068 0.19 1 -10000 0 1
CDC42 0.025 0.017 -10000 0 -0.36 1 1
Regulation of nuclear SMAD2/3 signaling

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.023 -10000 0 -10000 0 0
HSPA8 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0 0.1 -10000 0 -0.29 35 35
AKT1 -0.008 0.054 -10000 0 -10000 0 0
GSC -0.038 0.13 -10000 0 -0.55 6 6
NKX2-5 -0.001 0.011 -10000 0 -10000 0 0
muscle cell differentiation 0.041 0.12 0.37 18 -10000 0 18
SMAD2-3/SMAD4/SP1 -0.01 0.11 -10000 0 -0.29 3 3
SMAD4 0.001 0.047 -10000 0 -10000 0 0
CBFB 0.028 0.003 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.018 0.14 -10000 0 -0.27 137 137
SMAD3/SMAD4/VDR 0.057 0.06 -10000 0 -10000 0 0
MYC 0.048 0.06 0.36 9 -0.38 2 11
CDKN2B -0.44 0.62 -10000 0 -1.3 217 217
AP1 0.013 0.053 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.019 0.12 -10000 0 -0.35 43 43
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.15 0.22 -10000 0 -0.42 206 206
SP3 0.029 0.001 -10000 0 -10000 0 0
CREB1 0.028 0 -10000 0 -10000 0 0
FOXH1 0.009 0.07 0.36 3 -0.38 15 18
SMAD3/SMAD4/GR 0.01 0.1 -10000 0 -0.28 37 37
GATA3 0.017 0.051 -10000 0 -0.39 5 5
SKI/SIN3/HDAC complex/NCoR1 0.022 0.062 -10000 0 -0.44 4 4
MEF2C/TIF2 0 0.087 -10000 0 -0.36 15 15
endothelial cell migration 0.025 0.12 0.54 1 -10000 0 1
MAX 0.03 0.012 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
RUNX2 0.027 0.004 -10000 0 -10000 0 0
RUNX3 0.025 0.017 -10000 0 -0.36 1 1
RUNX1 0.026 0.007 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.003 0.1 -10000 0 -0.36 44 44
VDR 0.028 0.002 -10000 0 -10000 0 0
CDKN1A -0.009 0.081 -10000 0 -0.88 2 2
KAT2B 0.012 0.077 -10000 0 -0.35 26 26
SMAD2/SMAD2/SMAD4/FOXH1 -0.001 0.078 0.27 2 -0.27 11 13
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 -0.025 0.12 -10000 0 -0.54 1 1
SMAD3/SMAD4/ATF2 0.018 0.064 -10000 0 -0.27 1 1
SMAD3/SMAD4/ATF3 0.018 0.065 -10000 0 -0.3 2 2
SAP30 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.054 0.048 -10000 0 -10000 0 0
JUN 0.003 0.045 -10000 0 -0.3 1 1
SMAD3/SMAD4/IRF7 0.018 0.064 -10000 0 -10000 0 0
TFE3 0.018 0.025 -10000 0 -10000 0 0
COL1A2 0.002 0.083 -10000 0 -0.3 40 40
mesenchymal cell differentiation -0.018 0.063 -10000 0 -10000 0 0
DLX1 0.002 0.081 -10000 0 -0.43 19 19
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS 0.02 0.042 -10000 0 -0.37 6 6
SMAD3/SMAD4/Max 0.026 0.069 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.055 0.019 -10000 0 -10000 0 0
ZBTB17 0.044 0.036 -10000 0 -0.36 1 1
LAMC1 -0.003 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.015 0.052 0.28 2 -10000 0 2
IRF7 0.027 0.016 -10000 0 -0.36 1 1
ESR1 -0.01 0.11 -10000 0 -0.36 55 55
HNF4A 0.015 0.02 -10000 0 -0.36 1 1
MEF2C -0.003 0.093 -10000 0 -0.39 14 14
SMAD2-3/SMAD4 -0.003 0.089 -10000 0 -0.28 3 3
Cbp/p300/Src-1 0.058 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.01 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.02 0.036 0.36 6 -10000 0 6
CREBBP 0.027 0.017 -10000 0 -10000 0 0
SKIL 0.027 0.016 -10000 0 -0.36 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
SNIP1 0.026 0.006 -10000 0 -10000 0 0
GCN5L2 0.004 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.061 -10000 0 -10000 0 0
MSG1/HSC70 -0.043 0.15 -10000 0 -0.32 138 138
SMAD2 -0.009 0.049 -10000 0 -0.21 1 1
SMAD3 0.002 0.05 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.048 0.21 6 -0.24 4 10
SMAD2/SMAD2/SMAD4 -0.059 0.12 -10000 0 -0.4 44 44
NCOR1 0.023 0.011 -10000 0 -10000 0 0
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
NCOA1 0.028 0 -10000 0 -10000 0 0
MYOD/E2A 0.033 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.001 0.12 -10000 0 -0.32 1 1
IFNB1 -0.007 0.043 0.2 1 -10000 0 1
SMAD3/SMAD4/MEF2C 0.003 0.11 -10000 0 -0.4 13 13
CITED1 -0.08 0.2 -10000 0 -0.44 138 138
SMAD2-3/SMAD4/ARC105 0.008 0.089 -10000 0 -10000 0 0
RBL1 0.017 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.15 0.27 -10000 0 -0.52 189 189
RUNX1-3/PEBPB2 0.049 0.021 -10000 0 -0.21 1 1
SMAD7 -0.005 0.087 -10000 0 -0.47 3 3
MYC/MIZ-1 0.068 0.075 0.23 16 -0.29 2 18
SMAD3/SMAD4 -0.001 0.11 0.25 12 -0.34 9 21
IL10 -0.019 0.11 -10000 0 -0.41 38 38
PIASy/HDAC complex 0.013 0.025 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.029 0.012 -10000 0 -10000 0 0
IL5 -0.013 0.074 -10000 0 -0.38 7 7
CDK4 0.026 0.027 -10000 0 -0.43 1 1
PIAS4 0.013 0.025 -10000 0 -10000 0 0
ATF3 0.026 0.027 -10000 0 -0.44 2 2
SMAD3/SMAD4/SP1 0.003 0.082 -10000 0 -10000 0 0
FOXG1 -0.069 0.16 -10000 0 -0.46 82 82
FOXO3 -0.023 0.059 -10000 0 -10000 0 0
FOXO1 -0.016 0.05 -10000 0 -0.32 1 1
FOXO4 -0.022 0.057 -10000 0 -10000 0 0
heart looping -0.003 0.092 -10000 0 -0.38 14 14
CEBPB 0 0.052 0.33 3 -0.45 4 7
SMAD3/SMAD4/DLX1 0.008 0.08 -10000 0 -0.27 18 18
MYOD1 -0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.012 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.012 0.089 -10000 0 -0.32 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.016 -10000 0 -0.36 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.035 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.015 0.083 -10000 0 -10000 0 0
MED15 0.026 0.017 -10000 0 -0.36 1 1
SP1 0.003 0.04 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.001 0.076 0.26 2 -0.26 13 15
ITGB5 -0.01 0.053 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.025 0.053 -10000 0 -0.44 2 2
SMAD3/SMAD4/AR 0 0.094 -10000 0 -0.28 28 28
AR -0.009 0.1 -10000 0 -0.36 47 47
negative regulation of cell growth -0.01 0.075 0.22 1 -0.3 17 18
SMAD3/SMAD4/MYOD 0.013 0.063 -10000 0 -10000 0 0
E2F5 0.027 0.051 0.36 9 -0.42 3 12
E2F4 0.028 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.022 0.073 0.27 2 -0.3 1 3
SMAD2-3/SMAD4/FOXO1-3a-4 -0.12 0.23 -10000 0 -0.43 200 200
TFDP1 0.022 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.026 0.064 -10000 0 -0.3 1 1
SMAD3/SMAD4/RUNX2 0.018 0.063 -10000 0 -10000 0 0
TGIF2 0.02 0.036 0.36 6 -10000 0 6
TGIF1 0.022 0.011 -10000 0 -10000 0 0
ATF2 0.027 0.016 -10000 0 -0.36 1 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.016 -9999 0 -0.36 1 1
SPHK1 -0.004 0.12 -9999 0 -0.44 40 40
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.006 0.034 -9999 0 -0.23 1 1
GNAO1 -0.12 0.19 -9999 0 -0.36 225 225
mol:Sphinganine-1-P -0.009 0.082 -9999 0 -0.32 41 41
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.045 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.036 0.013 -9999 0 -10000 0 0
S1PR3 0.026 0.019 -9999 0 -0.44 1 1
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.001 0.031 -9999 0 -0.2 1 1
S1PR5 0.016 0.073 -9999 0 -0.44 15 15
S1PR4 0.021 0.049 -9999 0 -0.36 10 10
GNAI1 0.015 0.067 -9999 0 -0.36 19 19
S1P/S1P5/G12 0.027 0.061 -9999 0 -0.27 14 14
S1P/S1P3/Gq 0.023 0.056 -9999 0 -0.34 10 10
S1P/S1P4/Gi -0.063 0.13 -9999 0 -0.36 47 47
GNAQ 0.026 0.022 -9999 0 -0.36 2 2
GNAZ 0.023 0.035 -9999 0 -0.36 5 5
GNA14 0.024 0.035 -9999 0 -0.36 5 5
GNA15 0.023 0.046 -9999 0 -0.44 6 6
GNA12 0.025 0.008 -9999 0 -10000 0 0
GNA13 0.027 0.005 -9999 0 -10000 0 0
GNA11 0.025 0.031 -9999 0 -0.36 4 4
ABCC1 0.027 0.003 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.056 -10000 0 -0.43 9 9
ANTXR2 0.026 0.023 -10000 0 -0.36 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.052 11 11
monocyte activation -0.002 0.09 -10000 0 -0.34 41 41
MAP2K2 0.006 0.078 -10000 0 -0.57 11 11
MAP2K1 -0.004 0.006 -10000 0 -10000 0 0
MAP2K7 -0.004 0.009 -10000 0 -0.18 1 1
MAP2K6 -0.005 0.015 -10000 0 -0.18 4 4
CYAA -0.009 0.028 -10000 0 -0.21 11 11
MAP2K4 -0.003 0.007 -10000 0 -10000 0 0
IL1B -0.023 0.064 -10000 0 -0.22 57 57
Channel 0.03 0.035 -10000 0 -0.23 11 11
NLRP1 -0.005 0.016 -10000 0 -0.21 3 3
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.1 -10000 0 -0.38 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.052 11 -10000 0 11
MAPK3 -0.004 0.011 0.14 1 -0.18 1 2
MAPK1 -0.004 0.006 -10000 0 -10000 0 0
PGR -0.048 0.075 -10000 0 -0.18 156 156
PA/Cellular Receptors 0.031 0.039 -10000 0 -0.25 11 11
apoptosis -0.002 0.007 -10000 0 -0.052 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.032 -10000 0 -0.2 11 11
macrophage activation -0.003 0.024 0.17 10 -0.17 1 11
TNF 0.024 0.035 -10000 0 -0.36 5 5
VCAM1 -0.001 0.09 -10000 0 -0.34 40 40
platelet activation -0.016 0.1 -10000 0 -0.38 44 44
MAPKKK cascade 0.002 0.014 0.13 1 -0.075 9 10
IL18 -0.003 0.016 -10000 0 -0.17 3 3
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.052 11 11
LEF -0.002 0.007 -10000 0 -0.052 11 11
CASP1 -0.001 0.011 -10000 0 -0.095 5 5
mol:cAMP -0.017 0.1 -10000 0 -0.38 44 44
necrosis -0.002 0.007 -10000 0 -0.052 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.033 -10000 0 -0.21 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.007 0.064 -10000 0 -0.26 30 30
CRKL 0.027 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DOCK1 0.026 0.016 -10000 0 -0.36 1 1
ITGA4 0.014 0.072 -10000 0 -0.36 22 22
alpha4/beta7 Integrin/MAdCAM1 -0.063 0.15 -10000 0 -0.39 29 29
EPO 0.005 0.05 0.36 2 -0.44 5 7
alpha4/beta7 Integrin 0.02 0.081 -10000 0 -0.28 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.055 -10000 0 -0.25 22 22
EPO/EPOR (dimer) 0.033 0.038 0.26 2 -0.32 6 8
lamellipodium assembly 0.006 0.081 -10000 0 -0.38 12 12
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PI3K 0.039 0.015 -10000 0 -0.25 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.015 0.051 0.17 1 -0.41 3 4
PXN 0.028 0.002 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
MADCAM1 -0.15 0.19 -10000 0 -0.36 274 274
cell adhesion -0.063 0.14 -10000 0 -0.39 29 29
CRKL/CBL 0.039 0.01 -10000 0 -10000 0 0
ITGB1 0.028 0.002 -10000 0 -10000 0 0
SRC 0.002 0.046 0.18 1 -0.36 7 8
ITGB7 0.013 0.074 -10000 0 -0.36 23 23
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.07 -10000 0 -0.28 26 26
p130Cas/Crk/Dock1 0.056 0.076 -10000 0 -0.31 7 7
VCAM1 0.019 0.056 -10000 0 -0.36 13 13
RHOA 0.027 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.06 0.049 -10000 0 -10000 0 0
BCAR1 -0.013 0.042 0.18 1 -0.34 7 8
EPOR 0.027 0.019 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
Rac1/GTP 0.006 0.083 -10000 0 -0.4 11 11
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.01 0.007 -10000 0 -10000 0 0
mol:DAG 0.015 0.061 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.017 0.22 1 -10000 0 1
CaM/Ca2+ 0.024 0.06 -10000 0 -10000 0 0
HIF1A 0.032 0.009 -10000 0 -10000 0 0
GAB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.037 0.076 0.33 2 -10000 0 2
PLCG1 0.015 0.061 -10000 0 -10000 0 0
NOS3 0.081 0.11 0.29 85 -10000 0 85
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:NO 0.083 0.11 0.3 91 -0.4 1 92
FLT1 0.014 0.009 -10000 0 -10000 0 0
PGF 0.011 0.083 -10000 0 -0.44 20 20
VEGFR1 homodimer/NRP2/VEGFR121 0.036 0.032 0.3 2 -10000 0 2
CALM1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
eNOS/Hsp90 0.093 0.11 0.3 91 -0.37 1 92
endothelial cell proliferation 0.048 0.12 0.33 57 -10000 0 57
mol:Ca2+ 0.015 0.061 -10000 0 -10000 0 0
MAPK3 0.002 0.056 -10000 0 -10000 0 0
MAPK1 0.001 0.054 0.17 38 -10000 0 38
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PLGF homodimer 0.011 0.083 -10000 0 -0.44 20 20
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.019 0.054 -10000 0 -0.36 12 12
VEGFA homodimer 0.028 0.019 0.36 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer 0.026 0.024 0.32 2 -10000 0 2
platelet activating factor biosynthetic process 0.074 0.13 0.34 77 -10000 0 77
PI3K 0.038 0.054 -10000 0 -10000 0 0
PRKCA 0.004 0.059 0.18 42 -10000 0 42
PRKCB -0.013 0.074 0.18 33 -10000 0 33
VEGFR1 homodimer/PLGF homodimer 0.018 0.049 -10000 0 -0.26 16 16
VEGFA 0.028 0.019 0.36 2 -10000 0 2
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.015 0.061 -10000 0 -10000 0 0
RASA1 0.051 0.074 -10000 0 -10000 0 0
NRP2 0.026 0.027 -10000 0 -0.36 3 3
VEGFR1 homodimer 0.014 0.009 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.028 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.083 0.1 0.29 72 -0.39 1 73
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.052 -10000 0 -10000 0 0
mol:L-citrulline 0.083 0.11 0.3 91 -0.4 1 92
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.045 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.028 0.3 2 -10000 0 2
CD2AP 0.016 0.066 -10000 0 -0.36 18 18
PI3K/GAB1 0.08 0.071 -10000 0 -10000 0 0
PDPK1 0.039 0.081 0.34 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.037 0.028 0.3 2 -10000 0 2
mol:NADP 0.083 0.11 0.3 91 -0.4 1 92
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.044 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.024 0.023 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.046 0.15 -10000 0 -0.36 116 116
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.44 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.013 0.058 0.26 1 -0.25 25 26
HIF1A 0.003 0.046 -10000 0 -0.26 17 17
COPS5 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.066 0.035 -10000 0 -0.23 1 1
FIH (dimer) 0.027 0.006 -10000 0 -10000 0 0
CDKN2A -0.061 0.19 0.36 2 -0.45 115 117
ARNT/IPAS -0.014 0.11 -10000 0 -0.25 113 113
HIF1AN 0.027 0.006 -10000 0 -10000 0 0
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.011 0.062 -10000 0 -0.26 25 25
CUL2 0.028 0.002 -10000 0 -10000 0 0
OS9 0.028 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.047 0.024 -10000 0 -0.27 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.016 0.06 0.26 1 -0.26 24 25
PHD1-3/OS9 0.062 0.031 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.066 -10000 0 -0.29 7 7
VHL 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.061 0.26 1 -0.26 23 24
EGLN3 0.024 0.028 -10000 0 -0.36 3 3
EGLN2 0.027 0.016 -10000 0 -0.36 1 1
EGLN1 0.027 0.005 -10000 0 -10000 0 0
TP53 0.023 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.078 -10000 0 -0.51 11 11
ARNT 0.027 0.016 -10000 0 -0.36 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.017 -10000 0 -0.36 1 1
HIF1A/p19ARF -0.029 0.11 0.24 2 -0.29 32 34
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.056 0.05 -10000 0 -0.58 1 1
epithelial cell differentiation 0.049 0.073 -10000 0 -0.62 1 1
ITCH 0.018 0.016 -10000 0 -10000 0 0
WWP1 0.014 0.06 -10000 0 -1.1 1 1
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.024 0.023 -10000 0 -0.36 2 2
PRL -0.007 0.066 -10000 0 -0.44 12 12
neuron projection morphogenesis 0.025 0.074 0.28 8 -0.43 1 9
PTPRZ1 -0.12 0.18 -10000 0 -0.36 222 222
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.037 0.074 -10000 0 -0.46 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.012 0.06 -10000 0 -0.51 1 1
ADAM17 0.021 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 0.015 0.036 -10000 0 -0.63 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.053 0.049 -10000 0 -0.58 1 1
NCOR1 0.023 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.023 0.067 -10000 0 -0.48 1 1
GRIN2B -0.052 0.12 0.3 3 -0.36 13 16
ErbB4/ErbB2/betacellulin 0.053 0.049 0.28 1 -0.48 1 2
STAT1 0.027 0.019 -10000 0 -0.44 1 1
HBEGF 0.026 0.027 -10000 0 -0.44 2 2
PRLR 0.017 0.062 -10000 0 -0.36 16 16
E4ICDs/ETO2 0.037 0.077 -10000 0 -0.58 1 1
axon guidance 0.046 0.084 0.3 9 -0.72 1 10
NEDD4 0.019 0.015 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.021 0.068 -10000 0 -0.29 27 27
CBFA2T3 -0.022 0.13 -10000 0 -0.36 77 77
ErbB4/ErbB2/HBEGF 0.055 0.047 0.28 1 -0.48 1 2
MAPK3 0.023 0.071 0.26 6 -0.44 1 7
STAT1 (dimer) 0.057 0.049 -10000 0 -0.57 1 1
MAPK1 0.023 0.07 0.26 7 -0.44 1 8
JAK2 0.025 0.028 -10000 0 -0.36 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.063 0.27 1 -0.48 1 2
NRG1 -0.019 0.076 -10000 0 -0.26 56 56
NRG3 0.005 0.032 -10000 0 -0.4 2 2
NRG2 -0.04 0.13 -10000 0 -0.36 88 88
NRG4 -0.014 0.1 -10000 0 -0.36 50 50
heart development 0.046 0.084 0.3 9 -0.72 1 10
neural crest cell migration 0.012 0.063 0.23 6 -0.48 1 7
ERBB2 0.012 0.038 0.27 11 -10000 0 11
WWOX/E4ICDs 0.053 0.049 -10000 0 -0.58 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.042 0.072 -10000 0 -0.55 1 1
apoptosis -0.039 0.074 0.39 9 -10000 0 9
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.079 -10000 0 -0.58 1 1
ErbB4/ErbB2/epiregulin -0.036 0.12 0.3 4 -0.34 5 9
ErbB4/ErbB4/betacellulin/betacellulin 0.054 0.052 -10000 0 -0.58 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.07 0.075 -10000 0 -0.44 2 2
MDM2 0.011 0.032 0.25 1 -0.58 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.005 0.053 -10000 0 -0.4 1 1
STAT5A 0.05 0.08 0.34 2 -0.69 1 3
ErbB4/EGFR/neuregulin 1 beta 0.02 0.066 -10000 0 -0.48 1 1
DLG4 0.022 0.022 -10000 0 -0.44 1 1
GRB2/SHC 0.039 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.042 0.043 -10000 0 -0.54 1 1
STAT5A (dimer) 0.075 0.09 0.3 2 -0.68 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.08 0.083 0.33 2 -0.69 1 3
LRIG1 0.027 0.016 -10000 0 -0.36 1 1
EREG -0.16 0.23 0.36 3 -0.44 249 252
BTC 0.021 0.047 -10000 0 -0.36 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.029 0.071 0.36 1 -0.72 1 2
ERBB4 0.011 0.029 -10000 0 -0.64 1 1
STAT5B 0.027 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.06 -10000 0 -0.42 10 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.039 0.067 0.28 1 -0.49 1 2
glial cell differentiation -0.042 0.043 0.54 1 -10000 0 1
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation 0.023 0.087 0.29 6 -0.52 1 7
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.01 0.021 0.12 7 -0.11 2 9
BUB1B 0.017 0.04 0.12 4 -0.14 5 9
PLK1 0.023 0.028 0.073 55 -0.099 3 58
PLK1S1 0.021 0.049 0.13 4 -0.17 22 26
KIF2A 0.018 0.027 0.18 2 -10000 0 2
regulation of mitotic centrosome separation 0.023 0.028 0.073 55 -0.098 3 58
GOLGA2 0.027 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.038 0.043 -10000 0 -0.21 10 10
WEE1 0.029 0.038 -10000 0 -0.31 2 2
cytokinesis 0.025 0.036 -10000 0 -10000 0 0
PP2A-alpha B56 0.055 0.083 -10000 0 -0.5 12 12
AURKA 0.025 0.023 0.11 1 -10000 0 1
PICH/PLK1 0.016 0.056 0.18 19 -0.2 5 24
CENPE 0.017 0.027 0.11 1 -0.23 1 2
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.027 0.18 2 -10000 0 2
PPP2CA 0.027 0.005 -10000 0 -10000 0 0
FZR1 0.027 0.016 -10000 0 -0.36 1 1
TPX2 0.04 0.04 0.11 60 -10000 0 60
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.02 0.061 0.36 1 -0.44 10 11
FBXW11 0.027 0.004 -10000 0 -10000 0 0
CLSPN 0.015 0.042 -10000 0 -0.22 17 17
GORASP1 0.027 0.003 -10000 0 -10000 0 0
metaphase 0 0.002 0.017 8 -0.011 1 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 0.04 55 -0.052 3 58
G2 phase of mitotic cell cycle 0.001 0.003 0.015 8 -10000 0 8
STAG2 0.027 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.015 0.051 -10000 0 -0.48 6 6
spindle elongation 0.023 0.028 0.073 55 -0.098 3 58
ODF2 0.03 0.005 -10000 0 -10000 0 0
BUB1 0.019 0.08 -10000 0 -0.54 12 12
TPT1 0.026 0.037 0.1 22 -0.17 8 30
CDC25C 0.018 0.04 -10000 0 -0.24 12 12
CDC25B 0.012 0.11 0.35 17 -0.44 27 44
SGOL1 0.01 0.021 0.11 2 -0.12 7 9
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.035 0.056 0.24 17 -10000 0 17
CDC14B 0.007 0.011 -10000 0 -0.25 1 1
CDC20 0.026 0.019 -10000 0 -0.44 1 1
PLK1/PBIP1 0.018 0.021 0.099 2 -10000 0 2
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.016 0.031 0.15 5 -10000 0 5
CDC2 0.002 0.003 0.015 17 -0.01 1 18
NDC80 0.022 0.011 -10000 0 -10000 0 0
metaphase plate congression 0.007 0.064 -10000 0 -0.22 43 43
ERCC6L 0.017 0.054 0.19 17 -0.21 4 21
NLP/gamma Tubulin 0.012 0.016 0.07 8 -0.086 1 9
microtubule cytoskeleton organization 0.027 0.037 0.1 22 -0.17 8 30
G2/M transition DNA damage checkpoint 0 0.002 0.013 10 -10000 0 10
PPP1R12A 0.027 0.023 -10000 0 -0.36 2 2
interphase 0 0.002 0.013 10 -10000 0 10
PLK1/PRC1-2 0.05 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.06 0.025 -10000 0 -10000 0 0
RAB1A 0.028 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.031 0.064 219 -10000 0 219
mitotic prometaphase 0.001 0.005 0.018 43 -10000 0 43
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.026 -10000 0 -10000 0 0
microtubule-based process 0.035 0.027 0.12 1 -10000 0 1
Golgi organization 0.023 0.028 0.073 55 -0.098 3 58
Cohesin/SA2 0.034 0.023 0.12 1 -10000 0 1
PPP1CB/MYPT1 0.041 0.024 -10000 0 -0.36 2 2
KIF20A 0.027 0.004 -10000 0 -10000 0 0
APC/C/CDC20 0.036 0.029 0.12 1 -0.23 1 2
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.017 0.021 0.098 2 -10000 0 2
PRC1 0.027 0.006 -10000 0 -10000 0 0
ECT2 0.017 0.034 0.19 4 -0.2 4 8
C13orf34 0.022 0.026 0.066 71 -10000 0 71
NUDC 0.007 0.065 -10000 0 -0.22 43 43
regulation of attachment of spindle microtubules to kinetochore 0.017 0.04 0.12 4 -0.14 5 9
spindle assembly 0.018 0.024 0.091 12 -0.085 3 15
spindle stabilization 0.021 0.049 0.13 4 -0.17 22 26
APC/C/HCDH1 0.025 0.014 -10000 0 -0.21 2 2
MKLP2/PLK1 0.036 0.027 0.12 1 -10000 0 1
CCNB1 0.027 0.009 -10000 0 -10000 0 0
PPP1CB 0.028 0.016 -10000 0 -0.37 1 1
BTRC 0.027 0.006 -10000 0 -10000 0 0
ROCK2 0.025 0.036 -10000 0 -0.31 3 3
TUBG1 0.018 0.02 0.097 1 -0.16 3 4
G2/M transition of mitotic cell cycle 0.01 0.047 0.18 17 -10000 0 17
MLF1IP 0.007 0.003 -10000 0 -10000 0 0
INCENP 0.028 0.004 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.004 -10000 0 -10000 0 0
VDR 0.028 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.041 0.054 -10000 0 -0.21 24 24
EP300 0.026 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.041 -10000 0 -0.29 3 3
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.05 0.18 2 -0.23 3 5
RAR alpha/9cRA/Cyclin H 0.009 0.072 0.22 1 -0.25 2 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.006 0.054 0.2 3 -0.22 13 16
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.004 0.059 -10000 0 -0.22 7 7
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.031 0.087 0.4 3 -0.41 8 11
NCOA2 0.022 0.028 -10000 0 -0.36 3 3
NCOA3 0.016 0.014 -10000 0 -10000 0 0
NCOA1 0.028 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.028 0.002 -10000 0 -10000 0 0
RARG 0.028 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.037 0.005 -10000 0 -10000 0 0
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.034 0.085 0.26 1 -0.36 10 11
RARA -0.016 0.061 0.18 4 -0.23 12 16
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.053 0.2 3 -0.23 14 17
PRKCA 0.028 0.008 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.037 0.091 0.35 3 -0.39 11 14
RXRG -0.15 0.16 0.3 4 -0.31 253 257
RXRA -0.013 0.058 0.26 2 -0.21 2 4
RXRB -0.033 0.089 0.29 5 -0.35 7 12
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RBP1 -0.003 0.12 0.36 1 -0.44 40 41
CRBP1/9-cic-RA -0.001 0.083 0.24 1 -0.31 40 41
RARB 0.026 0.032 -10000 0 -0.36 4 4
PRKCG -0.13 0.23 0.36 5 -0.44 209 214
MNAT1 0.026 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs -0.031 0.081 -10000 0 -0.39 11 11
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.023 0.079 0.4 3 -0.36 5 8
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.077 0.27 7 -0.28 5 12
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.091 0.35 3 -0.39 11 14
positive regulation of DNA binding 0.001 0.063 -10000 0 -0.23 3 3
NRIP1 -0.036 0.1 0.36 1 -0.86 3 4
RXRs/RARs -0.037 0.091 0.32 3 -0.35 14 17
RXRs/RXRs/DNA/9cRA -0.043 0.077 -10000 0 -0.37 10 10
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.005 -10000 0 -10000 0 0
TFIIH 0.051 0.017 -10000 0 -10000 0 0
RAR alpha/9cRA 0.017 0.068 0.23 1 -0.25 2 3
CCNH 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.018 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.063 0.16 0.43 1 -0.84 1 2
CRP -0.002 0.14 0.43 1 -0.68 4 5
cell cycle arrest -0.003 0.14 -10000 0 -0.73 4 4
TIMP1 0.007 0.14 -10000 0 -0.6 4 4
IL6ST 0.019 0.061 -10000 0 -0.36 15 15
Rac1/GDP -0.03 0.12 0.3 1 -0.37 32 33
AP1 0.048 0.09 -10000 0 -0.45 6 6
GAB2 0.028 0.004 -10000 0 -10000 0 0
TNFSF11 0.028 0.17 -10000 0 -0.86 5 5
HSP90B1 0.035 0.049 -10000 0 -10000 0 0
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.029 0.11 -10000 0 -0.38 19 19
AKT1 0.032 0.037 -10000 0 -0.35 2 2
FOXO1 0.059 0.078 0.23 15 -0.36 1 16
MAP2K6 -0.037 0.11 -10000 0 -0.38 24 24
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.028 0.12 0.29 2 -0.42 16 18
MITF -0.036 0.12 -10000 0 -0.39 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.004 -10000 0 -10000 0 0
A2M 0.008 0.15 -10000 0 -1.1 10 10
CEBPB 0.017 0.047 0.35 3 -0.44 4 7
GRB2/SOS1/GAB family/SHP2 0.025 0.079 0.24 1 -0.38 10 11
STAT3 -0.008 0.14 -10000 0 -0.78 4 4
STAT1 0.021 0.017 -10000 0 -10000 0 0
CEBPD 0.015 0.14 -10000 0 -0.96 2 2
PIK3CA 0.028 0.016 -10000 0 -0.36 1 1
PI3K 0.04 0.015 -10000 0 -0.25 1 1
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.025 0.12 0.22 1 -0.37 29 30
MAPK11 -0.028 0.11 -10000 0 -0.39 16 16
STAT3 (dimer)/FOXO1 0.04 0.14 0.36 15 -0.62 2 17
GRB2/SOS1/GAB family 0.026 0.13 0.24 3 -0.37 16 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.025 0.1 0.24 3 -0.37 28 31
GRB2 0.027 0.004 -10000 0 -10000 0 0
JAK2 0.025 0.028 -10000 0 -0.36 3 3
LBP 0.054 0.17 0.4 10 -0.6 1 11
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.009 -10000 0 -10000 0 0
MYC 0.027 0.15 0.41 1 -0.75 2 3
FGG -0.016 0.15 -10000 0 -0.65 5 5
macrophage differentiation -0.003 0.14 -10000 0 -0.73 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.14 0.26 4 -0.32 39 43
JUNB -0.002 0.13 -10000 0 -0.93 3 3
FOS 0.022 0.039 -10000 0 -0.36 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.033 0.12 0.2 3 -0.37 33 36
STAT1/PIAS1 -0.005 0.11 -10000 0 -0.4 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.039 -10000 0 -0.33 3 3
STAT3 (dimer) -0.004 0.14 -10000 0 -0.76 4 4
PRKCD -0.012 0.14 0.32 23 -0.48 9 32
IL6R -0.052 0.16 -10000 0 -0.36 128 128
SOCS3 -0.025 0.11 0.4 1 -0.52 3 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.052 0.047 -10000 0 -0.21 4 4
Rac1/GTP -0.029 0.12 -10000 0 -0.42 19 19
HCK 0.011 0.047 -10000 0 -0.36 9 9
MAPKKK cascade 0.038 0.081 -10000 0 -0.48 7 7
bone resorption 0.03 0.17 0.42 1 -0.8 5 6
IRF1 -0.001 0.13 -10000 0 -0.74 2 2
mol:GDP -0.035 0.12 -10000 0 -0.36 38 38
SOS1 0.028 0.002 -10000 0 -10000 0 0
VAV1 -0.039 0.12 0.19 1 -0.37 38 39
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.059 0.16 0.33 1 -0.5 31 32
PTPN11 0.019 0.048 -10000 0 -0.77 2 2
IL6/IL6RA -0.054 0.15 0.26 4 -0.29 175 179
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.044 -10000 0 -0.21 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.048 -10000 0 -0.21 17 17
IL6 -0.027 0.16 0.36 7 -0.43 77 84
PIAS3 0.027 0.005 -10000 0 -10000 0 0
PTPRE 0.022 0.011 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.037 0.11 0.18 3 -0.34 35 38
LMO4 0.029 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.001 0.14 -10000 0 -0.73 4 4
MCL1 0.032 0.045 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.008 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.025 -10000 0 -10000 0 0
CDKN1B 0.026 0.067 0.24 4 -0.33 12 16
CDKN1A 0.024 0.069 0.22 2 -0.32 14 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.016 0.36 1 -10000 0 1
FOXO3 0.026 0.059 0.24 1 -0.31 10 11
AKT1 0.003 0.061 0.26 1 -0.32 18 19
BAD 0.027 0.016 -10000 0 -0.36 1 1
AKT3 0.01 0.033 -10000 0 -0.26 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.025 0.067 0.24 1 -0.33 12 13
AKT1/ASK1 0.042 0.091 0.23 3 -0.34 12 15
BAD/YWHAZ 0.046 0.024 -10000 0 -0.21 1 1
RICTOR 0.024 0.035 -10000 0 -0.36 5 5
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.039 0.087 0.33 12 -0.22 2 14
TSC1 0.023 0.069 0.24 1 -0.32 14 15
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.046 0.094 0.24 5 -0.34 14 19
EP300 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.071 0.26 1 -0.31 18 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.025 0.067 0.26 2 -0.33 12 14
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
TBC1D4 0.053 0.093 0.24 122 -0.2 1 123
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAPKAP1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.053 0.093 0.3 10 -0.21 59 69
YWHAH 0.027 0.006 -10000 0 -10000 0 0
AKT1S1 0.026 0.071 0.26 5 -0.33 13 18
CASP9 0.025 0.062 0.24 1 -0.34 10 11
YWHAB 0.016 0.014 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.094 0.3 8 -0.53 3 11
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0.028 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.075 0.21 2 -0.4 6 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.031 -10000 0 -0.27 2 2
CHUK 0.027 0.052 0.24 1 -0.28 8 9
BAD/BCL-XL 0.017 0.065 -10000 0 -0.57 2 2
mTORC2 0.032 0.021 -10000 0 -0.19 5 5
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.064 0.12 0.24 92 -0.41 11 103
PDPK1 0.027 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.069 0.24 3 -0.33 13 16
MAPKKK cascade -0.046 0.093 0.33 14 -0.24 5 19
MDM2/Cbp/p300 0.052 0.091 0.26 2 -0.51 3 5
TSC1/TSC2 0.023 0.067 0.27 4 -0.32 12 16
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.087 0.25 2 -0.48 3 5
glucose import 0.013 0.093 0.21 83 -10000 0 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.048 0.18 6 -0.33 2 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.013 0.093 0.21 83 -10000 0 83
GSK3A 0.027 0.07 0.24 7 -0.33 13 20
FOXO1 0.053 0.098 0.24 91 -0.31 10 101
GSK3B 0.025 0.07 0.24 3 -0.32 14 17
SFN 0.025 0.023 -10000 0 -0.36 2 2
G1/S transition of mitotic cell cycle 0.036 0.081 0.27 10 -0.54 3 13
p27Kip1/14-3-3 family 0.048 0.054 0.28 1 -10000 0 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.028 0.002 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
RHEB 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.004 -10000 0 -10000 0 0
SNTA1 0.016 0.02 -10000 0 -0.36 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.008 0.009 -10000 0 -0.21 1 1
MAPK12 -0.007 0.035 -10000 0 -0.26 11 11
CCND1 0.006 0.039 0.19 1 -0.32 6 7
p38 gamma/SNTA1 0.008 0.041 0.19 5 -0.26 9 14
MAP2K3 0.024 0.01 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.042 0.2 8 -0.25 11 19
MAP2K6 0.001 0.016 -10000 0 -0.2 4 4
MAPT -0.058 0.12 0.22 4 -0.27 139 143
MAPK13 0.011 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0.014 -10000 0 -10000 0 0
NFATC1 -0.021 0.13 0.31 3 -0.38 42 45
NFATC2 0.034 0.053 0.16 6 -0.22 4 10
NFATC3 0.02 0.008 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.054 0.1 0.19 2 -0.27 76 78
Exportin 1/Ran/NUP214 0.055 0.009 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.037 0.12 -10000 0 -0.32 40 40
BCL2/BAX 0.025 0.04 -10000 0 -0.25 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
BAD 0.027 0.016 -10000 0 -0.36 1 1
CABIN1/MEF2D -0.043 0.1 0.18 1 -0.31 36 37
Calcineurin A alpha-beta B1/BCL2 0.014 0.05 -10000 0 -0.36 10 10
FKBP8 0.027 0.016 -10000 0 -0.36 1 1
activation-induced cell death of T cells 0.043 0.1 0.31 36 -0.18 1 37
KPNB1 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.028 0.014 0.36 1 -10000 0 1
XPO1 0.028 0 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
MAP3K8 0.028 0.003 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.028 0.023 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.07 0.067 -10000 0 -0.29 3 3
CABIN1 -0.055 0.1 0.19 1 -0.27 76 77
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
CAMK4 0.006 0.085 -10000 0 -0.36 31 31
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
YWHAH 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.057 -10000 0 -0.25 24 24
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.027 0.004 -10000 0 -10000 0 0
MAPK9 0.027 0.004 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.008 0.13 0.33 2 -0.38 28 30
PRKCH 0.025 0.017 -10000 0 -0.36 1 1
CABIN1/Cbp/p300 0.038 0.013 -10000 0 -10000 0 0
CASP3 0.026 0.007 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.007 -10000 0 -10000 0 0
apoptosis 0.01 0.014 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.045 -10000 0 -0.35 1 1
PRKCB -0.062 0.16 -10000 0 -0.36 141 141
PRKCE 0.028 0.002 -10000 0 -10000 0 0
JNK2/NFAT4 0.025 0.039 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0.023 -10000 0 -0.25 1 1
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
PRKCG -0.13 0.23 0.36 5 -0.44 209 214
PRKCQ 0.022 0.044 -10000 0 -0.36 8 8
FKBP38/BCL2 0.025 0.042 -10000 0 -0.25 11 11
EP300 0.026 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.011 -10000 0 -10000 0 0
NFATc/JNK1 -0.007 0.13 0.31 3 -0.36 40 43
CaM/Ca2+/FKBP38 0.035 0.015 -10000 0 -0.22 1 1
FKBP12/FK506 0.017 0.008 -10000 0 -10000 0 0
CSNK1A1 0.014 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.022 0.053 -10000 0 -0.2 31 31
NFATc/ERK1 -0.008 0.13 0.34 2 -0.36 41 43
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.039 0.12 -10000 0 -0.33 41 41
NR4A1 0.038 0.073 0.25 5 -0.38 10 15
GSK3B 0.028 0.002 -10000 0 -10000 0 0
positive T cell selection 0.02 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.039 0.16 1 -10000 0 1
RCH1/ KPNB1 0.04 0.007 -10000 0 -10000 0 0
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -10000 0 -10000 0 0
AKAP5 0.011 0.075 -10000 0 -0.36 24 24
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha -0.009 0.13 0.34 2 -0.36 42 44
CREBBP 0.027 0.007 -10000 0 -10000 0 0
BCL2 0.014 0.05 -10000 0 -0.36 10 10
FoxO family signaling

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
G6PC -0.056 0.32 0.47 1 -1.2 44 45
PLK1 0.02 0.12 0.4 1 -0.57 7 8
CDKN1B 0.057 0.12 0.37 8 -0.35 11 19
FOXO3 0.026 0.13 -10000 0 -0.54 11 11
KAT2B 0.015 0.08 -10000 0 -0.36 26 26
FOXO1/SIRT1 0.019 0.12 0.27 3 -0.36 41 44
CAT 0.02 0.12 -10000 0 -0.58 5 5
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.029 -10000 0 -10000 0 0
FOXO1 0.009 0.13 0.38 5 -0.38 44 49
MAPK10 0.012 0.08 0.19 47 -0.19 15 62
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.037 0.076 0.31 7 -10000 0 7
response to oxidative stress 0.004 0.017 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.038 0.12 -10000 0 -0.5 9 9
XPO1 0.028 0 -10000 0 -10000 0 0
EP300 0.02 0.026 -10000 0 -10000 0 0
BCL2L11 0.031 0.024 -10000 0 -10000 0 0
FOXO1/SKP2 0.018 0.12 0.27 4 -0.36 44 48
mol:GDP 0.004 0.017 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
GADD45A 0.043 0.13 -10000 0 -0.55 20 20
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.12 0.28 4 -0.4 21 25
MST1 -0.043 0.17 -10000 0 -0.44 98 98
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.006 0.11 -10000 0 -0.38 32 32
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.036 0.05 0.19 55 -10000 0 55
MAPK9 0.036 0.05 0.19 55 -10000 0 55
YWHAG 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
SIRT1 0.028 0.014 -10000 0 -10000 0 0
SOD2 0.053 0.11 0.44 4 -0.54 1 5
RBL2 0.044 0.11 -10000 0 -0.72 2 2
RAL/GDP 0.037 0.023 -10000 0 -10000 0 0
CHUK 0.031 0.017 -10000 0 -10000 0 0
Ran/GTP 0.023 0.002 -10000 0 -10000 0 0
CSNK1G2 0.027 0.016 -10000 0 -0.36 1 1
RAL/GTP 0.04 0.022 -10000 0 -10000 0 0
CSNK1G1 0.026 0.017 -10000 0 -0.36 1 1
FASLG -0.035 0.29 -10000 0 -1.2 33 33
SKP2 0.027 0.004 -10000 0 -10000 0 0
USP7 0.028 0.004 -10000 0 -10000 0 0
IKBKB 0.029 0.018 -10000 0 -10000 0 0
CCNB1 0.022 0.12 -10000 0 -0.58 5 5
FOXO1-3a-4/beta catenin 0.065 0.12 0.33 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.12 0.27 4 -0.35 44 48
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.017 0.077 -10000 0 -0.36 24 24
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.004 -10000 0 -10000 0 0
ZFAND5 0.036 0.072 0.35 4 -10000 0 4
SFN 0.025 0.023 -10000 0 -0.36 2 2
CDK2 0.019 0.034 -10000 0 -10000 0 0
FOXO3A/14-3-3 0 0.097 -10000 0 -0.4 19 19
CREBBP 0.018 0.034 -10000 0 -10000 0 0
FBXO32 0.048 0.16 -10000 0 -0.98 2 2
BCL6 0.044 0.11 -10000 0 -0.82 1 1
RALB 0.029 0.001 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.015 0.028 -10000 0 -10000 0 0
regulation of axonogenesis -0.009 0.027 0.23 7 -10000 0 7
myoblast fusion -0.029 0.019 -10000 0 -10000 0 0
mol:GTP 0.016 0.032 -10000 0 -0.15 22 22
regulation of calcium-dependent cell-cell adhesion -0.02 0.085 0.21 59 -10000 0 59
ARF1/GTP 0.029 0.036 -10000 0 -10000 0 0
mol:GM1 0.004 0.027 -10000 0 -10000 0 0
mol:Choline 0.008 0.015 -10000 0 -0.19 1 1
lamellipodium assembly 0.004 0.082 -10000 0 -0.34 32 32
MAPK3 0.018 0.026 -10000 0 -0.22 1 1
ARF6/GTP/NME1/Tiam1 0.021 0.086 -10000 0 -0.21 59 59
ARF1 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.019 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.058 -10000 0 -0.24 8 8
ARF6 0.032 0.009 -10000 0 -10000 0 0
RAB11A 0.027 0.006 -10000 0 -10000 0 0
TIAM1 -0.01 0.11 -10000 0 -0.36 59 59
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.026 0.058 0.24 8 -10000 0 8
KALRN 0.02 0.017 -10000 0 -0.18 1 1
RAB11FIP3/RAB11A 0.039 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.058 -10000 0 -0.24 8 8
NME1 0.023 0.057 0.36 2 -0.44 8 10
Rac1/GDP 0.025 0.056 -10000 0 -0.24 7 7
substrate adhesion-dependent cell spreading 0.016 0.032 -10000 0 -0.15 22 22
cortical actin cytoskeleton organization 0.005 0.081 -10000 0 -0.34 30 30
RAC1 0.025 0.008 -10000 0 -10000 0 0
liver development 0.016 0.032 -10000 0 -0.15 22 22
ARF6/GTP 0.016 0.032 -10000 0 -0.15 22 22
RhoA/GTP 0.029 0.036 -10000 0 -10000 0 0
mol:GDP 0.012 0.05 -10000 0 -0.2 27 27
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.037 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.013 0.034 -10000 0 -0.22 2 2
RAB11FIP3 0.027 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.082 -10000 0 -0.34 32 32
ruffle organization 0.009 0.027 -10000 0 -0.23 7 7
regulation of epithelial cell migration 0.016 0.032 -10000 0 -0.15 22 22
PLD2 0.016 0.017 -10000 0 -10000 0 0
PIP5K1A 0.009 0.027 -10000 0 -0.23 7 7
mol:Phosphatidic acid 0.008 0.015 -10000 0 -0.19 1 1
Rac1/GTP 0.005 0.081 -10000 0 -0.34 30 30
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.17 -10000 0 -0.39 103 103
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.004 -10000 0 -10000 0 0
STXBP4 0.026 0.016 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.17 -10000 0 -0.41 115 115
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
YWHAQ 0.028 0.002 -10000 0 -10000 0 0
TBC1D4 0.01 0.012 -10000 0 -0.25 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
SNARE/Synip 0.045 0.025 -10000 0 -0.21 1 1
YWHAG 0.027 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.045 0.36 5 -0.44 2 7
PRKCI 0.026 0.022 -10000 0 -0.36 2 2
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
GYS1 0.011 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.013 0.042 -10000 0 -0.24 5 5
VAMP2 0.023 0.011 -10000 0 -10000 0 0
SLC2A4 -0.14 0.19 -10000 0 -0.46 116 116
STX4 0.027 0.003 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
SFN 0.025 0.023 -10000 0 -0.36 2 2
LNPEP 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.024 0.058 -10000 0 -0.36 13 13
PDGF/PDGFRA/CRKL 0.036 0.043 -10000 0 -0.24 13 13
positive regulation of JUN kinase activity 0.062 0.041 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.029 0.049 -10000 0 -0.26 16 16
AP1 0.023 0.098 0.3 5 -0.6 6 11
mol:IP3 0.004 0.036 -10000 0 -0.25 11 11
PLCG1 0.004 0.036 -10000 0 -0.25 11 11
PDGF/PDGFRA/alphaV Integrin 0.038 0.043 -10000 0 -0.24 13 13
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.036 -10000 0 -0.25 11 11
CAV3 -0.013 0.035 -10000 0 -0.44 3 3
CAV1 0.019 0.054 -10000 0 -0.36 12 12
SHC/Grb2/SOS1 0.064 0.042 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.027 0.07 -10000 0 -0.28 28 28
FOS -0.004 0.08 0.31 14 -0.63 5 19
JUN -0.006 0.021 -10000 0 -10000 0 0
oligodendrocyte development 0.037 0.043 -10000 0 -0.24 13 13
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:DAG 0.004 0.036 -10000 0 -0.25 11 11
PDGF/PDGFRA 0.024 0.058 -10000 0 -0.36 13 13
actin cytoskeleton reorganization 0.037 0.047 0.26 1 -0.25 14 15
SRF 0.004 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.051 0.04 -10000 0 -0.2 10 10
PDGF/PDGFRA/Crk/C3G 0.044 0.042 -10000 0 -0.2 11 11
JAK1 0.012 0.037 -10000 0 -0.24 12 12
ELK1/SRF 0.026 0.077 0.16 140 -10000 0 140
SHB 0.026 0.03 0.36 1 -0.44 2 3
SHF 0.015 0.072 -10000 0 -0.44 15 15
CSNK2A1 0.012 0.021 -10000 0 -10000 0 0
GO:0007205 -0.001 0.038 -10000 0 -0.28 11 11
SOS1 0.028 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.062 0.041 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.037 0.047 0.26 1 -0.25 14 15
PDGF/PDGFRA/Caveolin-1 0.032 0.057 -10000 0 -0.26 20 20
ITGAV 0.028 0.002 -10000 0 -10000 0 0
ELK1 -0.006 0.034 0.25 1 -0.24 10 11
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PDGF/PDGFRA/Crk 0.031 0.043 -10000 0 -0.23 13 13
JAK-STAT cascade 0.012 0.037 -10000 0 -0.24 12 12
cell proliferation 0.027 0.069 -10000 0 -0.28 28 28
Arf6 trafficking 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
SLC2A4 -0.018 0.12 -10000 0 -0.36 64 64
CLTC -0.002 0.1 0.19 1 -0.4 37 38
calcium ion-dependent exocytosis 0.012 0.043 -10000 0 -10000 0 0
Dynamin 2/GTP 0.023 0.031 0.18 1 -0.23 8 9
EXOC4 0.027 0.006 -10000 0 -10000 0 0
CD59 0.002 0.075 -10000 0 -0.32 29 29
CPE -0.002 0.057 -10000 0 -0.21 42 42
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.018 0.027 -10000 0 -10000 0 0
CTNND1 0.009 0.032 0.18 7 -0.22 8 15
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.064 -10000 0 -0.24 30 30
TSHR 0.006 0.019 -10000 0 -0.27 2 2
INS 0.006 0.045 -10000 0 -0.49 4 4
BIN1 0.027 0.016 -10000 0 -0.36 1 1
mol:Choline 0.018 0.027 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.032 0.23 1 -0.26 8 9
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.031 0.18 1 -0.23 8 9
JUP 0.002 0.074 0.21 1 -0.31 29 30
ASAP2/amphiphysin II 0.049 0.017 -10000 0 -0.19 1 1
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.002 0.074 -10000 0 -0.31 29 29
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.025 -10000 0 -0.4 2 2
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.027 0.016 -10000 0 -0.36 1 1
substrate adhesion-dependent cell spreading 0.024 0.041 -10000 0 -0.37 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.02 0.093 0.32 35 -10000 0 35
positive regulation of phagocytosis 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.019 -10000 0 -0.24 2 2
ACAP1 0.018 0.03 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.036 0.11 -10000 0 -0.39 32 32
clathrin heavy chain/ACAP1 0.001 0.09 0.19 4 -0.33 35 39
JIP4/KLC1 0.048 0.016 -10000 0 -10000 0 0
EXOC1 0.026 0.016 -10000 0 -0.36 1 1
exocyst 0.024 0.041 -10000 0 -0.37 4 4
RALA/GTP 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.009 0.032 0.18 7 -0.22 8 15
NME1 0.01 0.032 0.23 1 -0.26 8 9
clathrin coat assembly -0.002 0.1 0.19 1 -0.39 37 38
IL2RA -0.001 0.076 -10000 0 -0.31 30 30
VAMP3 0.013 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.006 0.098 0.2 1 -0.3 38 39
EXOC6 0.027 0.006 -10000 0 -10000 0 0
PLD1 0.013 0.011 -10000 0 -0.23 1 1
PLD2 0.012 0.007 -10000 0 -10000 0 0
EXOC5 0.024 0.028 -10000 0 -0.36 3 3
PIP5K1C 0.007 0.055 0.14 1 -0.22 25 26
SDC1 0.002 0.074 -10000 0 -0.31 29 29
ARF6/GDP 0.021 0.033 0.2 1 -0.26 8 9
EXOC7 0.027 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.023 0.096 -10000 0 -0.33 35 35
mol:Phosphatidic acid 0.018 0.027 -10000 0 -10000 0 0
endocytosis -0.048 0.016 0.19 1 -10000 0 1
SCAMP2 0.027 0.006 -10000 0 -10000 0 0
ADRB2 -0.028 0.12 0.39 1 -0.41 40 41
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ASAP2 0.028 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.032 0.21 1 -0.23 8 9
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 -0.014 0.11 0.26 7 -0.39 38 45
RALA 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.018 0.09 -10000 0 -0.32 32 32
ceramide signaling 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
MAP4K4 0.021 0.054 -10000 0 -0.33 1 1
BAG4 0.024 0.01 -10000 0 -10000 0 0
BAD 0.013 0.028 0.15 4 -0.33 1 5
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.05 -10000 0 -0.37 10 10
BAX 0.014 0.037 0.2 11 -0.18 1 12
EnzymeConsortium:3.1.4.12 0.008 0.017 0.092 5 -0.076 1 6
IKBKB 0.033 0.067 0.21 30 -0.31 1 31
MAP2K2 0.013 0.041 0.18 20 -0.28 1 21
MAP2K1 0.012 0.039 0.18 19 -10000 0 19
SMPD1 0.009 0.026 0.14 4 -0.16 7 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.058 0.21 2 -0.33 2 4
MAP2K4 0.009 0.026 0.17 3 -0.21 1 4
protein ubiquitination 0.027 0.06 0.32 3 -0.3 2 5
EnzymeConsortium:2.7.1.37 0.014 0.042 0.18 20 -0.22 1 21
response to UV 0 0 0.002 21 -10000 0 21
RAF1 0.015 0.04 0.18 19 -10000 0 19
CRADD 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide 0.015 0.029 0.12 10 -0.18 1 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.011 -10000 0 -10000 0 0
MADD 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.012 0.029 0.14 6 -0.2 2 8
TRADD 0.028 0.003 -10000 0 -10000 0 0
RELA/p50 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.041 0.18 19 -0.23 1 20
MAPK1 0.013 0.043 0.18 18 -0.23 1 19
p50/RELA/I-kappa-B-alpha 0.038 0.012 -10000 0 -10000 0 0
FADD 0.023 0.052 0.21 2 -0.29 2 4
KSR1 0.016 0.039 0.18 19 -0.18 1 20
MAPK8 0.009 0.029 0.21 3 -10000 0 3
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
response to radiation 0 0 0.002 6 -10000 0 6
CHUK 0.019 0.051 0.24 1 -0.29 1 2
TNF R/SODD 0.035 0.015 -10000 0 -10000 0 0
TNF 0.024 0.035 -10000 0 -0.36 5 5
CYCS 0.037 0.05 0.14 47 -0.26 1 48
IKBKG 0.021 0.056 0.22 3 -0.35 2 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.026 0.055 -10000 0 -0.3 3 3
RELA 0.027 0.004 -10000 0 -10000 0 0
RIPK1 0.027 0.004 -10000 0 -10000 0 0
AIFM1 0.032 0.046 0.14 40 -0.26 1 41
TNF/TNF R/SODD 0.045 0.031 -10000 0 -0.21 5 5
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 6 -10000 0 6
CASP8 0.023 0.098 -10000 0 -0.56 16 16
NSMAF 0.038 0.072 0.21 57 -0.32 1 58
response to hydrogen peroxide 0 0 0.002 21 -10000 0 21
BCL2 0.014 0.05 -10000 0 -0.36 10 10
FOXM1 transcription factor network

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
NFATC3 0.05 0.24 -10000 0 -0.91 3 3
PLK1 0.039 0.081 -10000 0 -0.84 4 4
BIRC5 0.034 0.1 -10000 0 -0.81 8 8
HSPA1B 0.04 0.25 -10000 0 -0.87 5 5
MAP2K1 0.031 0.038 -10000 0 -10000 0 0
BRCA2 0.089 0.25 0.61 1 -0.91 3 4
FOXM1 0.05 0.26 -10000 0 -1 6 6
XRCC1 0.052 0.24 0.61 1 -0.91 3 4
FOXM1B/p19 0.015 0.27 -10000 0 -0.94 9 9
Cyclin D1/CDK4 0.058 0.23 -10000 0 -0.92 3 3
CDC2 0.051 0.25 -10000 0 -0.89 6 6
TGFA 0.047 0.22 -10000 0 -0.96 3 3
SKP2 0.052 0.24 -10000 0 -0.99 2 2
CCNE1 0.028 0.037 0.35 3 -0.44 2 5
CKS1B 0.051 0.24 -10000 0 -0.85 6 6
RB1 0.05 0.13 -10000 0 -0.67 3 3
FOXM1C/SP1 0.055 0.26 -10000 0 -0.93 6 6
AURKB -0.096 0.33 -10000 0 -0.8 105 105
CENPF 0.053 0.24 -10000 0 -0.95 3 3
CDK4 0.029 0.026 -10000 0 -0.42 1 1
MYC 0.039 0.21 -10000 0 -0.82 2 2
CHEK2 0.032 0.038 -10000 0 -10000 0 0
ONECUT1 0.048 0.23 -10000 0 -0.96 3 3
CDKN2A -0.064 0.19 0.35 2 -0.45 115 117
LAMA4 0.05 0.24 -10000 0 -0.91 3 3
FOXM1B/HNF6 0.046 0.25 -10000 0 -1.1 3 3
FOS 0.04 0.27 -10000 0 -1 13 13
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B 0.067 0.25 0.61 1 -0.95 4 5
response to radiation 0.011 0.021 -10000 0 -10000 0 0
CENPB 0.073 0.24 0.61 1 -0.91 3 4
CENPA 0.049 0.24 -10000 0 -0.95 3 3
NEK2 0.053 0.24 -10000 0 -0.95 3 3
HIST1H2BA 0.046 0.24 -10000 0 -0.91 3 3
CCNA2 0.028 0.012 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.046 0.26 -10000 0 -0.99 5 5
CCNB2 0.05 0.24 -10000 0 -0.95 3 3
CCNB1 0.05 0.25 -10000 0 -0.92 5 5
ETV5 0.049 0.24 -10000 0 -0.95 3 3
ESR1 -0.012 0.39 -10000 0 -1.1 58 58
CCND1 0.047 0.23 -10000 0 -0.93 3 3
GSK3A 0.03 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.061 0.044 0.24 3 -0.26 2 5
CDK2 0.029 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.012 0.025 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.06 0.25 -10000 0 -0.88 6 6
GAS1 -0.057 0.45 -10000 0 -1 93 93
MMP2 0.047 0.25 -10000 0 -1.1 5 5
RB1/FOXM1C 0.041 0.22 -10000 0 -0.92 3 3
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.036 0.26 1 -0.31 6 7
CRKL 0.027 0.096 0.27 11 -0.42 16 27
mol:PIP3 -0.002 0.011 -10000 0 -10000 0 0
AKT1 -0.007 0.02 -10000 0 -10000 0 0
PTK2B 0.02 0.025 -10000 0 -0.36 2 2
RAPGEF1 0.03 0.095 0.27 15 -0.42 14 29
RANBP10 0.028 0.002 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
HGF/MET/SHIP2 0.044 0.053 -10000 0 -0.24 18 18
MAP3K5 0.017 0.12 0.29 9 -0.44 20 29
HGF/MET/CIN85/CBL/ENDOPHILINS 0.057 0.053 -10000 0 -0.27 6 6
AP1 0.029 0.035 -10000 0 -0.22 4 4
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.035 0.23 -10000 0 -0.72 58 58
STAT3 (dimer) 0.003 0.051 -10000 0 -0.33 6 6
GAB1/CRKL/SHP2/PI3K 0.065 0.093 0.3 4 -0.41 12 16
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
CBL/CRK 0.048 0.093 0.26 11 -0.41 14 25
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.014 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 0.005 0.094 0.36 29 -10000 0 29
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.04 -10000 0 -0.22 7 7
PAK1 -0.008 0.022 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.045 0.053 -10000 0 -0.24 19 19
HRAS 0.02 0.061 0.32 1 -0.47 3 4
DOCK1 0.028 0.091 0.26 11 -0.42 14 25
GAB1 0.018 0.087 -10000 0 -0.45 15 15
CRK 0.024 0.09 0.27 9 -0.43 13 22
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.079 -10000 0 -0.43 15 15
JUN 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.012 0.039 -10000 0 -0.18 17 17
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell morphogenesis 0.049 0.1 0.26 43 -0.42 4 47
GRB2/SHC 0.009 0.054 -10000 0 -0.21 5 5
FOS 0.022 0.039 -10000 0 -0.36 6 6
GLMN 0.001 0.012 -10000 0 -0.21 2 2
cell motility 0.004 0.094 0.35 29 -10000 0 29
HGF/MET/MUC20 0.027 0.049 -10000 0 -0.24 19 19
cell migration 0.008 0.053 -10000 0 -0.2 5 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.037 0.034 0.26 1 -0.32 5 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.047 -10000 0 -0.3 8 8
MET/MUC20 0.017 0.032 0.24 1 -0.31 5 6
RAP1B 0.028 0.092 0.27 16 -0.4 14 30
RAP1A 0.027 0.09 0.27 11 -0.4 14 25
HGF/MET/RANBP9 0.044 0.054 -10000 0 -0.24 20 20
RAF1 0.023 0.065 0.31 1 -0.48 2 3
STAT3 0.004 0.051 -10000 0 -0.35 5 5
cell proliferation 0.03 0.074 0.33 2 -0.39 5 7
RPS6KB1 0.003 0.036 -10000 0 -0.29 7 7
MAPK3 -0.013 0.083 0.53 8 -10000 0 8
MAPK1 0.016 0.16 0.65 32 -10000 0 32
RANBP9 0.027 0.016 -10000 0 -0.36 1 1
MAPK8 0.028 0.11 0.33 6 -0.44 12 18
SRC 0.005 0.039 -10000 0 -0.3 6 6
PI3K 0.009 0.054 -10000 0 -0.22 1 1
MET/Glomulin -0.014 0.052 0.2 1 -0.2 17 18
SOS1 0.028 0.002 -10000 0 -10000 0 0
MAP2K1 0.021 0.061 0.31 2 -0.45 2 4
MET 0.023 0.045 0.36 1 -0.44 5 6
MAP4K1 0.018 0.12 0.27 9 -0.46 21 30
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.022 0.064 0.31 2 -0.45 2 4
BAD -0.008 0.021 -10000 0 -10000 0 0
MAP2K4 0.013 0.11 0.31 7 -0.43 14 21
SHP2/GRB2/SOS1/GAB1 0.049 0.083 0.25 1 -0.38 14 15
INPPL1 0.027 0.004 -10000 0 -10000 0 0
PXN 0.028 0.002 -10000 0 -10000 0 0
SH3KBP1 0.027 0.004 -10000 0 -10000 0 0
HGS -0.014 0.035 -10000 0 -0.2 7 7
PLCgamma1/PKC 0.012 0.01 -10000 0 -10000 0 0
HGF 0.017 0.061 -10000 0 -0.37 15 15
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.002 -10000 0 -10000 0 0
PTPRJ 0.028 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.039 -10000 0 -0.26 1 1
PDPK1 -0.005 0.023 -10000 0 -10000 0 0
HGF/MET/SHIP 0.044 0.054 -10000 0 -0.3 6 6
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.04 0.05 -10000 0 -0.21 20 20
forebrain development 0.001 0.085 0.38 1 -0.5 6 7
GNAO1 -0.12 0.19 -10000 0 -0.36 225 225
SMO/beta Arrestin2 0.034 0.018 -10000 0 -10000 0 0
SMO 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.024 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.038 0.094 -10000 0 -0.36 7 7
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.028 0.002 -10000 0 -10000 0 0
GNAI2 0.028 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.05 0.032 -10000 0 -10000 0 0
GNAI1 0.015 0.067 -10000 0 -0.36 19 19
XPO1 0.029 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0 0.088 -10000 0 -0.57 3 3
SAP30 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.007 -10000 0 -10000 0 0
MIM/GLI2A 0.022 0.039 -10000 0 -0.36 5 5
IFT88 0.021 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.012 0.058 0.18 2 -0.26 16 18
GLI3 0.026 0.095 0.25 4 -0.35 9 13
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.021 0.012 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.012 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
Gi family/GTP -0.059 0.12 -10000 0 -0.32 45 45
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.033 0.084 0.27 3 -0.34 8 11
GLI2/Su(fu) 0.021 0.063 -10000 0 -0.35 8 8
FOXA2 0 0.14 -10000 0 -0.61 21 21
neural tube patterning 0.001 0.085 0.38 1 -0.5 6 7
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.039 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.027 0.016 -10000 0 -0.36 1 1
CSNK1G3 0.027 0.005 -10000 0 -10000 0 0
MTSS1 0.022 0.039 -10000 0 -0.36 5 5
embryonic limb morphogenesis 0.001 0.085 0.38 1 -0.5 6 7
SUFU 0.021 0.011 -10000 0 -10000 0 0
LGALS3 0.025 0.017 -10000 0 -0.36 1 1
catabolic process 0.042 0.1 -10000 0 -0.4 10 10
GLI3A/CBP 0.032 0.025 -10000 0 -0.31 3 3
KIF3A 0.027 0.005 -10000 0 -10000 0 0
GLI1 0.001 0.087 0.38 1 -0.51 6 7
RAB23 0.026 0.022 -10000 0 -0.36 2 2
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.028 0 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.029 0.039 -10000 0 -10000 0 0
GNAZ 0.024 0.035 -10000 0 -0.36 5 5
RBBP4 0.027 0.005 -10000 0 -10000 0 0
CSNK1G1 0.026 0.017 -10000 0 -0.36 1 1
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.026 0.058 -10000 0 -0.28 8 8
STK36 0.029 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.061 0.13 -10000 0 -0.33 74 74
PTCH1 0.001 0.098 0.36 1 -0.98 3 4
MIM/GLI1 0.008 0.098 0.37 1 -0.54 6 7
CREBBP 0.032 0.024 -10000 0 -0.31 3 3
Su(fu)/SIN3/HDAC complex 0.027 0.082 -10000 0 -0.34 19 19
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.059 -10000 0 -10000 0 0
CRKL 0.022 0.052 0.3 4 -0.29 2 6
mol:DAG 0.018 0.031 -10000 0 -10000 0 0
HRAS 0.008 0.06 0.3 6 -0.3 1 7
MAPK8 0.035 0.063 0.19 59 -10000 0 59
RAP1A 0.021 0.052 0.33 3 -0.29 2 5
GAB1 0.021 0.052 0.31 3 -0.29 2 5
MAPK14 0.035 0.062 0.19 57 -10000 0 57
EPO 0.02 0.048 0.33 2 -0.45 5 7
PLCG1 0.018 0.032 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.027 0.022 -10000 0 -0.41 1 1
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
EPO/EPOR (dimer)/SOCS3 0.047 0.042 0.23 2 -0.26 8 10
GAB1/SHC/GRB2/SOS1 0.051 0.05 0.26 1 -0.31 1 2
EPO/EPOR (dimer) 0.034 0.041 0.24 2 -0.31 6 8
IRS2 0.014 0.039 0.23 1 -0.34 1 2
STAT1 0.03 0.049 -10000 0 -10000 0 0
STAT5B 0.028 0.045 -10000 0 -10000 0 0
cell proliferation 0.015 0.074 0.19 83 -10000 0 83
GAB1/SHIP/PIK3R1/SHP2/SHC 0.041 0.044 -10000 0 -0.3 1 1
TEC 0.02 0.052 0.31 3 -0.29 2 5
SOCS3 0.026 0.027 -10000 0 -0.44 2 2
STAT1 (dimer) 0.031 0.05 -10000 0 -10000 0 0
JAK2 0.026 0.03 -10000 0 -0.37 3 3
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.065 0.053 0.24 1 -0.3 2 3
EPO/EPOR 0.034 0.041 0.24 2 -0.31 6 8
LYN 0.024 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.052 -10000 0 -0.26 1 1
elevation of cytosolic calcium ion concentration 0.027 0.022 -10000 0 -0.41 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.046 0.041 0.24 2 -0.25 5 7
mol:IP3 0.018 0.031 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.035 0.046 0.24 1 -0.32 1 2
SH2B3 0.028 0.011 -10000 0 -10000 0 0
NFKB1 0.034 0.062 0.19 59 -0.23 4 63
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.028 -10000 0 -0.24 3 3
PTPN6 0.021 0.05 0.3 2 -0.3 2 4
TEC/VAV2/GRB2 0.043 0.056 0.26 1 -10000 0 1
EPOR 0.027 0.022 -10000 0 -0.41 1 1
INPP5D 0.027 0.016 -10000 0 -0.36 1 1
mol:GDP 0.05 0.05 0.26 1 -0.32 1 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
PLCG2 -0.004 0.1 -10000 0 -0.36 49 49
CRKL/CBL/C3G 0.047 0.049 0.26 2 -10000 0 2
VAV2 0.018 0.056 0.3 4 -0.25 2 6
CBL 0.02 0.052 0.3 4 -0.34 1 5
SHC/Grb2/SOS1 0.038 0.042 -10000 0 -0.32 1 1
STAT5A 0.028 0.045 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.041 0.068 -10000 0 -0.32 1 1
LYN/PLCgamma2 0.016 0.075 -10000 0 -0.25 43 43
PTPN11 0.028 0.002 -10000 0 -10000 0 0
BTK 0.001 0.079 0.3 4 -0.31 6 10
BCL2 0.007 0.17 0.34 1 -0.68 32 33
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.082 -10000 0 -0.2 54 54
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.074 0.3 1 -0.36 1 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.041 -10000 0 -0.22 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.005 0.054 -10000 0 -0.26 1 1
CaM/Ca2+ 0.034 0.08 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.012 0.073 -10000 0 -0.39 1 1
AKT1 -0.007 0.064 0.32 3 -10000 0 3
MAP2K1 -0.022 0.064 0.35 2 -0.24 1 3
MAP3K11 -0.004 0.07 0.35 2 -10000 0 2
IFNGR1 0.022 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.13 -10000 0 -0.36 56 56
Rap1/GTP 0.001 0.056 -10000 0 -10000 0 0
CRKL/C3G 0.038 0.015 -10000 0 -0.25 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.033 0.091 -10000 0 -0.22 52 52
CEBPB 0.021 0.14 0.33 6 -0.53 13 19
STAT3 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.036 0.12 -10000 0 -0.68 5 5
STAT1 -0.003 0.07 0.35 2 -0.39 1 3
CALM1 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.02 0.14 -10000 0 -0.44 60 60
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
STAT1 (dimer)/PIAS1 0.011 0.072 0.35 2 -0.38 1 3
CEBPB/PTGES2/Cbp/p300 0.028 0.092 -10000 0 -0.38 7 7
mol:Ca2+ 0.032 0.08 -10000 0 -0.2 54 54
MAPK3 -0.003 0.09 0.39 1 -0.69 4 5
STAT1 (dimer) 0.001 0.075 -10000 0 -0.36 1 1
MAPK1 -0.031 0.17 0.41 1 -0.72 28 29
JAK2 0.02 0.033 -10000 0 -0.37 3 3
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.022 0.02 -10000 0 -10000 0 0
CAMK2D 0.026 0.023 -10000 0 -0.36 2 2
DAPK1 0.014 0.14 0.33 8 -0.54 28 36
SMAD7 0.002 0.034 0.18 3 -0.22 1 4
CBL/CRKL/C3G 0.021 0.074 0.35 2 -10000 0 2
PI3K 0.034 0.079 -10000 0 -10000 0 0
IFNG -0.02 0.14 -10000 0 -0.44 60 60
apoptosis 0.009 0.12 0.32 6 -0.42 35 41
CAMK2G 0.027 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.007 0.1 -10000 0 -0.36 49 49
CAMK2B -0.013 0.11 0.36 1 -0.37 50 51
FRAP1 -0.019 0.058 0.3 3 -10000 0 3
PRKCD -0.017 0.065 0.32 3 -10000 0 3
RAP1B 0.028 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.005 0.054 -10000 0 -0.26 1 1
PTPN2 0.022 0.011 -10000 0 -10000 0 0
EP300 0.027 0.006 -10000 0 -10000 0 0
IRF1 -0.007 0.063 0.33 4 -10000 0 4
STAT1 (dimer)/PIASy 0.01 0.072 0.4 1 -0.38 1 2
SOCS1 0.012 0.11 -10000 0 -1 5 5
mol:GDP 0.017 0.069 0.27 1 -10000 0 1
CASP1 0.001 0.038 0.18 3 -0.22 3 6
PTGES2 0.027 0.004 -10000 0 -10000 0 0
IRF9 0.024 0.052 0.19 12 -0.19 1 13
mol:PI-3-4-5-P3 0.021 0.071 -10000 0 -10000 0 0
RAP1/GDP 0.019 0.065 -10000 0 -10000 0 0
CBL -0.006 0.069 0.35 2 -10000 0 2
MAP3K1 -0.003 0.07 0.36 2 -0.22 1 3
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PIAS4 0.027 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.005 0.054 -10000 0 -0.26 1 1
PTPN11 -0.003 0.069 -10000 0 -0.21 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.024 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.03 0.069 -10000 0 -0.32 7 7
NEF -0.004 0.033 -10000 0 -0.23 2 2
NFKBIA 0.026 0.016 -10000 0 -10000 0 0
BIRC3 0.013 0.056 -10000 0 -0.4 10 10
CYCS 0.012 0.078 0.18 50 -0.35 6 56
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CD247 0.013 0.077 -10000 0 -0.26 37 37
MAP2K7 0.018 0.11 0.28 1 -0.62 12 13
protein ubiquitination 0.027 0.052 0.25 9 -0.29 1 10
CRADD 0.027 0.003 -10000 0 -10000 0 0
DAXX 0.027 0.004 -10000 0 -10000 0 0
FAS 0.022 0.044 -10000 0 -0.36 8 8
BID 0.004 0.069 0.19 9 -0.25 31 40
NF-kappa-B/RelA/I kappa B alpha 0.052 0.041 -10000 0 -0.23 9 9
TRADD 0.028 0.003 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
CFLAR 0.028 0 -10000 0 -10000 0 0
FADD 0.027 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.052 0.041 -10000 0 -0.23 9 9
MAPK8 0.017 0.1 0.36 2 -0.57 12 14
APAF1 0.028 0.003 -10000 0 -10000 0 0
TRAF1 0.027 0.004 -10000 0 -10000 0 0
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.01 0.073 0.2 9 -0.26 32 41
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.048 -10000 0 -0.36 2 2
CHUK 0.027 0.054 0.35 4 -0.3 2 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.037 -10000 0 -10000 0 0
TCRz/NEF 0.007 0.079 -10000 0 -0.29 38 38
TNF 0.024 0.035 -10000 0 -0.36 5 5
FASLG -0.009 0.12 -10000 0 -0.47 34 34
NFKB1 0.027 0.016 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.045 0.031 -10000 0 -0.21 5 5
CASP6 0.033 0.1 -10000 0 -0.48 10 10
CASP7 0.015 0.09 0.35 2 -0.39 15 17
RELA 0.027 0.016 -10000 0 -10000 0 0
CASP2 0.027 0.005 -10000 0 -10000 0 0
CASP3 0.012 0.091 0.35 2 -0.42 14 16
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.015 -10000 0 -10000 0 0
CASP8 0.028 0.001 -10000 0 -10000 0 0
CASP9 0.026 0.007 -10000 0 -10000 0 0
MAP3K14 0.03 0.051 0.23 1 -0.33 2 3
APAF-1/Caspase 9 0.024 0.072 -10000 0 -0.3 4 4
BCL2 0.009 0.093 0.35 2 -0.52 11 13
IL27-mediated signaling events

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
TGFB1 -0.011 0.071 -10000 0 -0.44 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.004 0.088 0.41 4 -10000 0 4
IL27/IL27R/JAK1 0.036 0.11 -10000 0 -0.54 1 1
TBX21 -0.02 0.12 -10000 0 -0.47 18 18
IL12B 0.015 0.041 -10000 0 -0.45 4 4
IL12A 0.002 0.03 -10000 0 -0.26 8 8
IL6ST 0.016 0.062 -10000 0 -0.37 15 15
IL27RA/JAK1 0.023 0.027 -10000 0 -10000 0 0
IL27 0.003 0.089 -10000 0 -0.44 23 23
TYK2 0.024 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.055 0.16 0.77 3 -10000 0 3
T-helper 2 cell differentiation 0.004 0.088 0.41 4 -10000 0 4
T cell proliferation during immune response 0.004 0.088 0.41 4 -10000 0 4
MAPKKK cascade -0.004 0.088 -10000 0 -0.41 4 4
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT2 0.028 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.019 -10000 0 -0.45 1 1
IL12RB1 0.014 0.07 -10000 0 -0.36 20 20
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.014 0.11 0.37 1 -0.51 10 11
IL27/IL27R/JAK2/TYK2 -0.004 0.089 -10000 0 -0.41 4 4
positive regulation of T cell mediated cytotoxicity -0.004 0.088 -10000 0 -0.41 4 4
STAT1 (dimer) 0.042 0.15 -10000 0 -0.54 7 7
JAK2 0.022 0.031 -10000 0 -0.36 3 3
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) 0.007 0.093 -10000 0 -0.4 4 4
T cell proliferation -0.043 0.11 0.45 1 -0.4 14 15
IL12/IL12R/TYK2/JAK2 0.002 0.15 -10000 0 -0.76 19 19
IL17A -0.055 0.16 0.77 3 -10000 0 3
mast cell activation 0.004 0.088 0.41 4 -10000 0 4
IFNG 0.002 0.027 0.077 1 -0.11 2 3
T cell differentiation -0.001 0.004 -10000 0 -0.017 3 3
STAT3 (dimer) 0.008 0.093 -10000 0 -0.4 4 4
STAT5A (dimer) 0.008 0.093 -10000 0 -0.4 4 4
STAT4 (dimer) 0.001 0.11 -10000 0 -0.37 16 16
STAT4 0.011 0.08 -10000 0 -0.36 27 27
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.059 -10000 0 -10000 0 0
GATA3 -0.011 0.1 0.52 2 -1.2 4 6
IL18 0.004 0.018 -10000 0 -0.25 3 3
positive regulation of mast cell cytokine production 0.008 0.092 -10000 0 -0.39 4 4
IL27/EBI3 0.004 0.097 -10000 0 -0.28 61 61
IL27RA 0.008 0.022 -10000 0 -10000 0 0
IL6 -0.064 0.17 0.34 7 -0.46 77 84
STAT5A 0.027 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.016 0.013 -10000 0 -10000 0 0
IL1B -0.024 0.093 -10000 0 -0.31 58 58
EBI3 0.002 0.095 -10000 0 -0.36 39 39
TNF 0.004 0.023 -10000 0 -0.25 5 5
TCGA08_rtk_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
PDGFRA 0.019 0.056 -10000 0 -0.36 13 13
HRAS 0.027 0.016 -10000 0 -0.36 1 1
EGFR 0.024 0.023 -10000 0 -0.36 2 2
AKT 0.039 0.073 0.27 14 -0.28 6 20
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.021 0.019 -10000 0 -0.36 1 1
AKT3 0.021 0.047 -10000 0 -0.36 9 9
FOXO4 0.028 0.002 -10000 0 -10000 0 0
MET 0.023 0.045 0.36 1 -0.44 5 6
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PIK3CB 0.028 0.014 0.36 1 -10000 0 1
NRAS 0.026 0.023 -10000 0 -0.36 2 2
PIK3CG -0.031 0.14 -10000 0 -0.36 91 91
PIK3R3 0.027 0.004 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.027 0.005 -10000 0 -10000 0 0
RAS 0.023 0.038 0.18 4 -0.28 1 5
ERBB2 0.033 0.044 0.36 11 -10000 0 11
proliferation/survival/translation -0.025 0.071 0.26 17 -0.23 3 20
PI3K 0.025 0.065 0.23 24 -0.21 6 30
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
KRAS 0.026 0.016 -10000 0 -0.36 1 1
FOXO 0.062 0.055 0.22 24 -10000 0 24
AKT2 0.027 0.004 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.001 0.13 -10000 0 -0.89 3 3
RAD9A 0.027 0.004 -10000 0 -10000 0 0
AP1 0.035 0.031 -10000 0 -0.25 6 6
IFNAR2 0.025 0.013 -10000 0 -10000 0 0
AKT1 -0.002 0.063 -10000 0 -0.29 15 15
ER alpha/Oestrogen -0.005 0.077 -10000 0 -0.25 55 55
NFX1/SIN3/HDAC complex 0.039 0.047 -10000 0 -0.29 2 2
EGF -0.057 0.16 -10000 0 -0.37 127 127
SMG5 0.027 0.004 -10000 0 -10000 0 0
SMG6 0.023 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.02 -10000 0 -10000 0 0
TERT/c-Abl 0.008 0.13 -10000 0 -0.74 4 4
SAP18 0.022 0.012 -10000 0 -10000 0 0
MRN complex 0.046 0.024 -10000 0 -10000 0 0
WT1 -0.2 0.24 0.35 3 -0.44 299 302
WRN 0.021 0.019 -10000 0 -0.36 1 1
SP1 0.025 0.016 -10000 0 -10000 0 0
SP3 0.028 0.004 -10000 0 -10000 0 0
TERF2IP 0.027 0.003 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.027 0.12 -10000 0 -0.9 2 2
Mad/Max 0.037 0.021 -10000 0 -0.25 2 2
TERT -0.002 0.13 -10000 0 -0.93 3 3
CCND1 -0.001 0.12 -10000 0 -0.92 2 2
MAX 0.026 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
TERF2 0.025 0.009 -10000 0 -10000 0 0
PTGES3 0.028 0.002 -10000 0 -10000 0 0
SIN3A 0.027 0.006 -10000 0 -10000 0 0
Telomerase/911 0.041 0.045 0.22 1 -0.3 3 4
CDKN1B -0.007 0.084 -10000 0 -0.26 60 60
RAD1 0.028 0.014 0.36 1 -10000 0 1
XRCC5 0.028 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.012 -10000 0 -10000 0 0
UBE3A 0.025 0.017 -10000 0 -0.36 1 1
JUN 0.027 0.005 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.015 -10000 0 -0.25 1 1
FOS 0.022 0.039 -10000 0 -0.36 6 6
IFN-gamma/IRF1 0.01 0.11 -10000 0 -0.31 60 60
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.027 0.014 0.36 1 -10000 0 1
Telomerase -0.001 0.11 -10000 0 -0.56 14 14
IRF1 0.03 0.006 -10000 0 -10000 0 0
ESR1 -0.008 0.11 -10000 0 -0.36 55 55
KU/TER 0.039 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.04 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.06 -10000 0 -0.29 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.033 0.061 -10000 0 -0.3 6 6
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.024 0.016 -10000 0 -10000 0 0
ATM 0.011 0.003 -10000 0 -10000 0 0
SMAD3 0.012 0.014 -10000 0 -0.32 1 1
ABL1 0.027 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.022 -10000 0 -0.36 2 2
MRE11A 0.027 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.026 0.016 -10000 0 -0.36 1 1
TERT/NF kappa B1/14-3-3 0.012 0.14 -10000 0 -0.68 6 6
NR2F2 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.017 -10000 0 -0.27 1 1
MAPK1 -0.007 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.019 -10000 0 -0.44 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.003 -10000 0 -10000 0 0
NBN 0.023 0.018 -10000 0 -0.36 1 1
EGFR 0.024 0.024 -10000 0 -0.36 2 2
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.021 0.12 -10000 0 -0.26 115 115
MYC 0.027 0.049 0.36 9 -0.44 2 11
IL2 0.017 0.017 -10000 0 -10000 0 0
KU 0.039 0.009 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
TGFB1 0.026 0.019 -10000 0 -0.44 1 1
TRF2/BLM 0.039 0.014 0.24 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.021 0.13 -10000 0 -1 2 2
SP1/HDAC2 0.037 0.023 -10000 0 -10000 0 0
PINX1 0.021 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.023 0.12 -10000 0 -0.9 2 2
Smad3/Myc 0.025 0.036 0.25 9 -0.27 3 12
911 complex 0.05 0.02 0.25 1 -10000 0 1
IFNG -0.017 0.14 -10000 0 -0.44 60 60
Telomerase/PinX1 0.016 0.12 -10000 0 -0.9 2 2
Telomerase/AKT1/mTOR/p70S6K 0.001 0.1 0.27 1 -0.42 20 21
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.026 0.12 -10000 0 -0.9 2 2
response to DNA damage stimulus 0.002 0.017 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.065 0.032 -10000 0 -10000 0 0
TRF2/WRN 0.031 0.021 -10000 0 -0.24 1 1
Telomerase/hnRNP C1/C2 0.028 0.12 -10000 0 -0.9 2 2
E2F1 0.017 0.058 0.36 9 -0.45 4 13
ZNFX1 0.016 0.014 -10000 0 -10000 0 0
PIF1 0.013 0.077 -10000 0 -0.44 17 17
NCL 0.028 0.002 -10000 0 -10000 0 0
DKC1 0.027 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.016 -10000 0 -0.2 1 1
FRAP1 -0.011 0.11 -10000 0 -0.44 38 38
AKT1 0.002 0.036 0.17 4 -0.31 1 5
INSR 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0.03 0.042 0.23 1 -0.24 1 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.04 -10000 0 -0.22 7 7
TSC2 0.027 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.03 -10000 0 -0.22 1 1
TSC1 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.015 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.017 0.05 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.007 0.076 0.22 3 -0.36 10 13
MAP3K5 0.005 0.029 0.2 4 -0.18 10 14
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.2 4 -0.18 10 14
mol:LY294002 0 0 0.001 1 -0.001 2 3
EIF4B 0.006 0.071 0.27 4 -0.34 8 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.069 0.22 1 -0.34 6 7
eIF4E/eIF4G1/eIF4A1 0.003 0.069 -10000 0 -0.26 35 35
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.038 0.023 -10000 0 -0.19 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.032 0.2 6 -10000 0 6
FKBP1A 0.023 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.035 0.038 0.2 1 -10000 0 1
mol:Amino Acids 0 0 0.001 1 -0.001 2 3
FKBP12/Rapamycin 0.017 0.008 -10000 0 -10000 0 0
PDPK1 -0.006 0.018 0.17 1 -10000 0 1
EIF4E 0.026 0.023 -10000 0 -0.36 2 2
ASK1/PP5C 0.006 0.13 -10000 0 -0.44 43 43
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.047 -10000 0 -0.24 20 20
TSC1/TSC2 0.034 0.045 0.24 1 -0.26 1 2
tumor necrosis factor receptor activity 0 0 0.001 2 -0.001 1 3
RPS6 0.026 0.02 -10000 0 -0.44 1 1
PPP5C 0.027 0.004 -10000 0 -10000 0 0
EIF4G1 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.007 0.013 -10000 0 -0.21 2 2
INS -0.017 0.003 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 -0.006 0.02 0.17 1 -10000 0 1
EIF4EBP1 -0.067 0.3 -10000 0 -1 53 53
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
PPP2R5D -0.008 0.11 0.25 3 -0.4 38 41
peptide biosynthetic process -0.007 0.035 0.18 19 -0.25 1 20
RHEB 0.027 0.005 -10000 0 -10000 0 0
EIF4A1 0.023 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 21 -0.003 1 22
EEF2 -0.007 0.035 0.18 19 -0.25 1 20
eIF4E/4E-BP1 -0.05 0.28 -10000 0 -0.97 53 53
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.022 0.061 -10000 0 -0.18 43 43
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.018 -10000 0 -0.31 2 2
GNB1/GNG2 0.024 0.047 -10000 0 -0.21 23 23
GNB1 0.026 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.007 0.039 -10000 0 -0.19 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0.01 0.053 23 -10000 0 23
GNAL 0.008 0.073 -10000 0 -0.36 23 23
GNG2 0.011 0.074 -10000 0 -0.36 23 23
CRH -0.016 0.026 -10000 0 -0.44 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.007 0.01 -10000 0 -0.16 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 0.081 0.1 -10000 0 -0.52 1 1
UGCG 0.019 0.061 -10000 0 -0.62 5 5
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.13 0.22 1 -0.45 26 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.019 0.06 -10000 0 -0.61 5 5
mol:DAG -0.002 0.11 -10000 0 -0.82 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.13 0.23 1 -0.4 36 37
FRAP1 0.011 0.14 0.24 1 -0.45 39 40
FOXO3 0.017 0.11 0.3 3 -0.41 14 17
AKT1 0.018 0.11 0.25 1 -0.41 18 19
GAB2 0.028 0.004 -10000 0 -10000 0 0
SMPD1 0.014 0.084 -10000 0 -0.65 9 9
SGMS1 0.013 0.087 -10000 0 -0.61 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.011 -10000 0 -0.21 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.034 0.083 -10000 0 -0.41 10 10
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.042 0.016 -10000 0 -0.25 1 1
RPS6KB1 0.014 0.1 -10000 0 -0.8 9 9
mol:sphingomyelin -0.002 0.11 -10000 0 -0.82 11 11
natural killer cell activation 0 0.002 -10000 0 -0.011 3 3
JAK3 0.028 0.019 -10000 0 -0.44 1 1
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.046 0.12 0.3 1 -0.43 5 6
MYB 0.03 0.073 -10000 0 -1.1 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.025 0.09 -10000 0 -0.4 11 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.1 -10000 0 -0.74 9 9
mol:PI-3-4-5-P3 0.024 0.089 -10000 0 -0.39 11 11
Rac1/GDP 0.02 0.016 -10000 0 -0.19 1 1
T cell proliferation 0.024 0.076 0.24 1 -0.4 6 7
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.004 -10000 0 -0.066 2 2
PRKCZ 0.024 0.078 0.24 1 -0.42 6 7
NF kappa B1 p50/RelA 0.035 0.13 -10000 0 -0.42 32 32
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.053 -10000 0 -0.38 5 5
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL2RA 0.02 0.056 -10000 0 -0.36 13 13
IL2RB 0.019 0.058 -10000 0 -0.36 14 14
TERT -0.014 0.14 0.36 2 -0.44 55 57
E2F1 0.032 0.044 -10000 0 -0.43 2 2
SOS1 0.028 0.002 -10000 0 -10000 0 0
RPS6 0.026 0.02 -10000 0 -0.44 1 1
mol:cAMP -0.002 0.002 0.031 2 -10000 0 2
PTPN11 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.028 0.027 -10000 0 -0.36 3 3
actin cytoskeleton organization 0.024 0.076 0.24 1 -0.4 6 7
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.019 0.012 -10000 0 -10000 0 0
PIK3CA 0.029 0.016 -10000 0 -0.36 1 1
Rac1/GTP 0.046 0.027 -10000 0 -0.18 1 1
LCK 0.021 0.058 -10000 0 -0.42 10 10
BCL2 -0.004 0.2 -10000 0 -0.78 33 33
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.052 0.054 -10000 0 -0.19 20 20
HDAC3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.038 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.037 0.014 -10000 0 -0.26 1 1
GATA2/HDAC5 0.034 0.041 -10000 0 -0.25 12 12
HDAC5/BCL6/BCoR 0.054 0.016 -10000 0 -0.21 1 1
HDAC9 -0.026 0.13 -10000 0 -0.36 80 80
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.069 -10000 0 -0.21 36 36
HDAC4/ANKRA2 0.04 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.023 0.023 -10000 0 -0.25 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.012 -10000 0 -0.17 2 2
GATA2 0.021 0.052 -10000 0 -0.36 11 11
HDAC4/RFXANK 0.04 0.015 -10000 0 -0.32 1 1
BCOR 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.026 0.017 -10000 0 -0.36 1 1
HDAC5 0.027 0.016 -10000 0 -0.36 1 1
GNB1/GNG2 0.026 0.056 -10000 0 -0.25 23 23
Histones 0.003 0.081 -10000 0 -0.3 13 13
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
HDAC4 0.028 0.002 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.015 -10000 0 -0.25 1 1
HDAC4/Ubc9 0.04 0.007 -10000 0 -10000 0 0
HDAC7 0.028 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.034 0.019 -10000 0 -0.25 1 1
TUBA1B 0.028 0.002 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.02 -10000 0 -0.28 2 2
CAMK4 0.006 0.085 -10000 0 -0.36 31 31
Tubulin/HDAC6 0.051 0.036 -10000 0 -0.27 7 7
SUMO1 0.027 0.022 -10000 0 -0.36 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
GATA1 0.011 0.022 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NR3C1 -0.001 0.1 -10000 0 -0.36 44 44
SUMO1/HDAC4 0.038 0.034 -10000 0 -0.26 2 2
SRF 0.027 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.024 0.02 -10000 0 -10000 0 0
Tubulin 0.036 0.038 -10000 0 -0.32 7 7
HDAC4/14-3-3 E 0.034 0.016 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
RANGAP1 0.026 0.02 -10000 0 -0.44 1 1
BCL6/BCoR 0.04 0.006 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.054 0.015 -10000 0 -0.21 1 1
HDAC4/SRF 0.038 0.06 -10000 0 -0.21 31 31
HDAC4/ER alpha 0.014 0.083 -10000 0 -0.25 55 55
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.003 0.081 -10000 0 -0.3 13 13
cell motility 0.05 0.036 -10000 0 -0.27 7 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.007 -10000 0 -10000 0 0
BCL6 0.028 0.002 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.002 -10000 0 -10000 0 0
Hsp90/HDAC6 0.038 0.011 -10000 0 -10000 0 0
ESR1 -0.009 0.11 -10000 0 -0.36 55 55
HDAC6/HDAC11 0.04 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.031 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
MEF2C 0.016 0.066 -10000 0 -0.36 18 18
RAN 0.028 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.07 0.048 -10000 0 -10000 0 0
GNG2 0.011 0.074 -10000 0 -0.36 23 23
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
TUBB2A 0.022 0.05 -10000 0 -0.44 7 7
HDAC11 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RANBP2 0.028 0 -10000 0 -10000 0 0
ANKRA2 0.027 0.005 -10000 0 -10000 0 0
RFXANK 0.027 0.019 -10000 0 -0.44 1 1
nuclear import -0.018 0.021 0.23 1 -10000 0 1
Aurora A signaling

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
Aurora A/GADD45A 0.048 0.036 -10000 0 -10000 0 0
BIRC5 0.027 0.024 0.36 1 -0.44 1 2
NFKBIA 0.005 0.011 0.25 1 -10000 0 1
CPEB1 -0.086 0.17 -10000 0 -0.36 165 165
AKT1 0.004 0.004 -10000 0 -10000 0 0
NDEL1 0.023 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.017 0.016 -10000 0 -10000 0 0
NDEL1/TACC3 0.054 0.038 -10000 0 -0.22 1 1
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.002 -10000 0 -10000 0 0
PAK1/Aurora A 0.049 0.036 -10000 0 -10000 0 0
MDM2 0.027 0.016 -10000 0 -0.36 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.011 0.027 0.27 6 -10000 0 6
TP53 0.013 0.012 -10000 0 -10000 0 0
DLG7 0.006 0.005 -10000 0 -10000 0 0
AURKAIP1 0.026 0.02 -10000 0 -0.44 1 1
ARHGEF7 0.022 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.057 0.04 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle 0.017 0.016 -10000 0 -10000 0 0
AURKA 0.01 0.009 -10000 0 -10000 0 0
AURKB 0.009 0.009 -10000 0 -10000 0 0
CDC25B 0.013 0.049 0.29 15 -10000 0 15
G2/M transition checkpoint 0.006 0.007 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.074 -10000 0 -0.18 96 96
Aurora A/CPEB -0.027 0.075 -10000 0 -0.18 96 96
Aurora A/TACC1/TRAP/chTOG 0.071 0.041 -10000 0 -10000 0 0
BRCA1 0.027 0.004 -10000 0 -10000 0 0
centrosome duplication 0.049 0.036 -10000 0 -10000 0 0
regulation of centrosome cycle 0.052 0.037 -10000 0 -0.22 1 1
spindle assembly 0.069 0.04 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.076 0.035 -10000 0 -0.22 1 1
CENPA 0.011 0.011 -10000 0 -10000 0 0
Aurora A/PP2A 0.048 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.036 0.041 0.2 2 -10000 0 2
negative regulation of DNA binding 0.012 0.016 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.021 -10000 0 -0.25 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0.01 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.009 -10000 0 -10000 0 0
TACC1 0.024 0.01 -10000 0 -10000 0 0
TACC3 0.026 0.02 -10000 0 -0.44 1 1
Aurora A/Antizyme1 0.067 0.036 -10000 0 -0.24 1 1
Aurora A/RasGAP 0.049 0.036 -10000 0 -10000 0 0
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.028 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.003 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
GIT1/beta-PIX/PAK1 0.042 0.027 -10000 0 -0.21 1 1
Importin alpha/Importin beta/TPX2 0.011 0.027 0.27 6 -10000 0 6
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.027 0.25 6 -10000 0 6
PAK1 0.027 0.004 -10000 0 -10000 0 0
CKAP5 0.027 0.003 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.022 0.028 -10000 0 -0.2 9 9
epithelial cell differentiation 0.057 0.014 -10000 0 -10000 0 0
CYFIP2 0.027 0.016 -10000 0 -0.36 1 1
ENAH -0.012 0.027 0.27 1 -10000 0 1
EGFR 0.024 0.023 -10000 0 -0.36 2 2
EPHA2 0.025 0.027 -10000 0 -0.44 2 2
MYO6 -0.009 0.015 0.18 3 -10000 0 3
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.054 0.015 -10000 0 -0.21 1 1
AQP5 -0.006 0.047 -10000 0 -0.51 1 1
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.019 0.18 5 -10000 0 5
regulation of calcium-dependent cell-cell adhesion -0.015 0.037 0.18 5 -10000 0 5
EGF -0.06 0.16 -10000 0 -0.37 127 127
NCKAP1 0.028 0 -10000 0 -10000 0 0
AQP3 0.009 0.036 -10000 0 -0.41 2 2
cortical microtubule organization 0.057 0.014 -10000 0 -10000 0 0
GO:0000145 -0.009 0.018 0.16 5 -10000 0 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.016 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.014 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.03 -10000 0 -0.25 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.006 0.009 -10000 0 -10000 0 0
PVRL2 0.027 0.003 -10000 0 -10000 0 0
ZYX -0.01 0.011 0.18 1 -10000 0 1
ARF6/GTP 0.065 0.035 -10000 0 -0.23 2 2
CDH1 0.028 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.003 0.09 -10000 0 -10000 0 0
RhoA/GDP 0.058 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization -0.009 0.011 0.16 2 -10000 0 2
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.016 -10000 0 -0.36 1 1
IGF1R 0.027 0.006 -10000 0 -10000 0 0
IGF1 -0.062 0.16 -10000 0 -0.36 141 141
DIAPH1 0.044 0.096 -10000 0 -0.52 12 12
Wnt receptor signaling pathway -0.057 0.014 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.014 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
VCL -0.009 0.011 0.17 2 -10000 0 2
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.01 0.019 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.047 0.023 -10000 0 -10000 0 0
SEC6/SEC8 -0.015 0.006 -10000 0 -10000 0 0
MGAT3 -0.015 0.038 0.18 5 -10000 0 5
HGF/MET 0.042 0.046 -10000 0 -0.37 1 1
HGF 0.017 0.061 -10000 0 -0.37 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.022 0.028 -10000 0 -0.2 9 9
actin cable formation 0.009 0.057 0.23 19 -0.29 1 20
KIAA1543 -0.009 0.018 0.16 5 -10000 0 5
KIFC3 -0.016 0.037 0.18 1 -10000 0 1
NCK1 0.028 0.002 -10000 0 -10000 0 0
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ACTN1 -0.008 0.018 0.18 5 -10000 0 5
NCK1/GIT1 0.039 0.014 -10000 0 -0.25 1 1
mol:GDP 0.057 0.014 -10000 0 -10000 0 0
EXOC4 0.027 0.006 -10000 0 -10000 0 0
STX4 -0.009 0.013 0.18 2 -10000 0 2
PIP5K1C -0.009 0.02 0.18 5 -10000 0 5
LIMA1 0.022 0.047 -10000 0 -0.36 9 9
ABI1 0.028 0.002 -10000 0 -10000 0 0
ROCK1 -0.008 0.039 0.29 3 -10000 0 3
adherens junction assembly 0.003 0.041 0.27 4 -10000 0 4
IGF-1R heterotetramer/IGF1 0 0.093 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.008 -10000 0 -10000 0 0
MET 0.023 0.045 0.36 1 -0.44 5 6
PLEKHA7 -0.009 0.02 0.18 5 -10000 0 5
mol:GTP 0.06 0.03 -10000 0 -0.24 2 2
establishment of epithelial cell apical/basal polarity -0.005 0.046 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.022 0.028 -10000 0 -0.2 9 9
regulation of cell-cell adhesion -0.009 0.011 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.022 0.028 -10000 0 -0.2 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.022 0.034 -10000 0 -0.31 3 3
KLHL20 0.041 0.07 0.2 29 -0.24 8 37
CYFIP2 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GDP 0.071 0.08 0.24 15 -10000 0 15
ENAH 0.021 0.035 -10000 0 -0.31 3 3
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.028 0.003 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.017 0.022 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.025 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.052 0.05 -10000 0 -0.19 10 10
RAPGEF1 0.06 0.082 0.29 10 -10000 0 10
CTNND1 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.036 -10000 0 -0.32 3 3
CRK 0.06 0.077 -10000 0 -0.3 1 1
E-cadherin/gamma catenin/alpha catenin 0.053 0.017 -10000 0 -0.21 1 1
alphaE/beta7 Integrin 0.024 0.054 -10000 0 -0.24 23 23
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
NCKAP1 0.028 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.013 -10000 0 -10000 0 0
DLG1 0.022 0.035 -10000 0 -0.31 3 3
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.004 0.01 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.022 0.077 -10000 0 -0.2 60 60
PI3K 0.008 0.015 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.039 0.014 -10000 0 -0.25 1 1
TIAM1 -0.011 0.11 -10000 0 -0.36 59 59
E-cadherin(dimer)/Ca2+ 0.063 0.016 -10000 0 -10000 0 0
AKT1 0.025 0.045 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.084 0.083 0.26 19 -10000 0 19
actin cytoskeleton organization 0.039 0.059 0.17 35 -0.18 6 41
CDC42/GDP 0.079 0.083 0.28 16 -10000 0 16
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.02 0.01 -10000 0 -0.19 1 1
ITGB7 0.013 0.074 -10000 0 -0.36 23 23
RAC1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.068 0.017 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.048 0.01 -10000 0 -10000 0 0
mol:GDP 0.075 0.09 0.31 13 -10000 0 13
CDC42/GTP/IQGAP1 0.034 0.015 -10000 0 -0.21 1 1
JUP 0.027 0.016 -10000 0 -0.36 1 1
p120 catenin/RhoA/GDP 0.093 0.082 0.27 19 -10000 0 19
RAC1/GTP/IQGAP1 0.033 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.013 -10000 0 -0.25 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.017 -10000 0 -0.36 1 1
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.033 0.047 0.14 40 -0.16 5 45
NME1 0.022 0.057 0.36 2 -0.44 8 10
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.021 0.034 -10000 0 -0.31 3 3
regulation of cell-cell adhesion 0.011 0.016 -10000 0 -10000 0 0
WASF2 0.015 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.08 0.072 0.31 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.053 -10000 0 -10000 0 0
CCND1 0.037 0.054 0.16 39 -0.2 5 44
VAV2 0.076 0.13 0.41 1 -0.62 10 11
RAP1/GDP 0.09 0.079 0.31 10 -10000 0 10
adherens junction assembly 0.02 0.033 -10000 0 -0.3 3 3
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.028 0.002 -10000 0 -10000 0 0
PIP5K1C 0.027 0.016 -10000 0 -0.36 1 1
regulation of heterotypic cell-cell adhesion 0.046 0.047 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.014 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.014 0.027 -10000 0 -0.31 2 2
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
Rac1/GTP -0.002 0.061 -10000 0 -0.39 8 8
E-cadherin/beta catenin/alpha catenin 0.054 0.011 -10000 0 -10000 0 0
ITGAE 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.036 -10000 0 -0.32 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.032 -10000 0 -0.25 7 7
AKT1 0.089 0.096 0.38 15 -0.38 2 17
PTK2B 0.014 0.039 -10000 0 -0.38 2 2
VEGFR2 homodimer/Frs2 0.035 0.026 -10000 0 -0.55 1 1
CAV1 0.019 0.054 -10000 0 -0.36 12 12
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.051 0.03 0.25 2 -0.51 1 3
endothelial cell proliferation 0.098 0.13 0.28 159 -0.36 1 160
mol:Ca2+ 0.013 0.018 -10000 0 -0.3 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.058 0.037 -10000 0 -0.48 1 1
RP11-342D11.1 0.011 0.025 -10000 0 -0.47 1 1
CDH5 0.028 0.002 -10000 0 -10000 0 0
VEGFA homodimer 0.064 0.024 0.26 1 -10000 0 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 0.019 0.059 -10000 0 -0.41 11 11
HRAS/GDP 0.046 0.03 -10000 0 -0.42 1 1
SH2D2A 0.026 0.019 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.097 0.084 0.28 11 -0.37 3 14
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.05 0.032 0.25 2 -0.51 1 3
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.074 0.039 -10000 0 -0.45 1 1
GRB10 0.02 0.026 -10000 0 -0.47 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.074 0.036 -10000 0 -0.47 1 1
HRAS 0.027 0.016 -10000 0 -0.36 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.079 -10000 0 -0.39 5 5
HIF1A 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.056 0.036 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.031 -10000 0 -0.36 4 4
Nck/Pak 0.04 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.051 0.03 0.25 2 -0.51 1 3
mol:GDP 0.059 0.033 -10000 0 -0.44 1 1
mol:NADP 0.087 0.091 0.3 23 -0.36 3 26
eNOS/Hsp90 0.091 0.087 0.3 22 -0.36 1 23
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.013 0.019 -10000 0 -0.3 1 1
HIF1A/ARNT 0.037 0.017 -10000 0 -0.25 1 1
SHB 0.026 0.03 0.36 1 -0.44 2 3
VEGFA 0.03 0.019 0.36 2 -10000 0 2
VEGFC 0.02 0.049 -10000 0 -0.36 10 10
FAK1/Vinculin 0.055 0.075 0.28 5 -0.54 1 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.062 0.041 -10000 0 -0.4 2 2
PTPN6 0.027 0.004 -10000 0 -10000 0 0
EPAS1 0.034 0.021 -10000 0 -0.33 2 2
mol:L-citrulline 0.087 0.091 0.3 23 -0.36 3 26
ITGAV 0.028 0.002 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.064 0.032 0.25 2 -0.48 1 3
VEGFR2 homodimer/VEGFA homodimer 0.053 0.032 -10000 0 -0.51 1 1
VEGFR2/3 heterodimer 0.033 0.033 -10000 0 -0.55 1 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
MAPK11 0.006 0.036 0.25 1 -0.43 2 3
VEGFR2 homodimer 0.021 0.026 -10000 0 -0.62 1 1
FLT1 0.021 0.012 -10000 0 -10000 0 0
NEDD4 0.028 0.007 -10000 0 -10000 0 0
MAPK3 0.033 0.081 0.3 7 -10000 0 7
MAPK1 0.033 0.08 0.3 7 -0.3 1 8
VEGFA145/NRP2 0.041 0.025 0.26 2 -0.25 3 5
VEGFR1/2 heterodimer 0.026 0.03 -10000 0 -0.55 1 1
KDR 0.021 0.026 -10000 0 -0.62 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.034 0.24 2 -0.47 1 3
SRC 0.017 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.047 0.087 0.3 13 -0.31 1 14
PI3K 0.055 0.058 0.3 1 -0.39 1 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.03 0.25 2 -0.51 1 3
FES 0.021 0.027 -10000 0 -0.48 1 1
GAB1 0.028 0.036 -10000 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.032 0.032 0.25 1 -0.33 1 2
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.028 0.002 -10000 0 -10000 0 0
ARNT 0.027 0.016 -10000 0 -0.36 1 1
eNOS/Caveolin-1 0.086 0.083 0.29 10 -0.35 2 12
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.038 0.25 1 -0.67 1 2
PI3K/GAB1 0.053 0.055 0.27 1 -0.42 1 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.076 0.034 -10000 0 -0.47 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.046 -10000 0 -0.43 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.021 0.026 -10000 0 -0.48 1 1
actin cytoskeleton reorganization 0.049 0.032 0.24 2 -0.5 1 3
PTK2 0.028 0.054 0.26 4 -0.57 1 5
EDG1 0.011 0.025 -10000 0 -0.47 1 1
mol:DAG 0.013 0.019 -10000 0 -0.3 1 1
CaM/Ca2+ 0.022 0.026 -10000 0 -10000 0 0
MAP2K3 0.012 0.034 -10000 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.064 0.056 -10000 0 -0.48 1 1
PLCG1 0.013 0.019 -10000 0 -0.31 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.039 0.041 -10000 0 -0.31 1 1
IQGAP1 0.027 0.006 -10000 0 -10000 0 0
YES1 0.022 0.019 -10000 0 -0.36 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.03 0.25 2 -0.51 1 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.05 0.029 0.25 1 -0.51 1 2
cell migration 0.06 0.078 0.29 10 -0.48 1 11
mol:PI-3-4-5-P3 0.054 0.056 0.29 1 -0.36 1 2
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.026 -10000 0 -0.45 1 1
mol:NO 0.087 0.091 0.3 23 -0.36 3 26
PXN 0.028 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.027 0.024 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.04 0.031 -10000 0 -0.48 1 1
VHL 0.027 0.004 -10000 0 -10000 0 0
ITGB3 0.023 0.041 -10000 0 -0.36 7 7
NOS3 0.09 0.094 0.32 21 -0.4 3 24
VEGFR2 homodimer/VEGFA homodimer/Sck 0.046 0.046 0.25 1 -0.51 1 2
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.007 0.02 -10000 0 -10000 0 0
PRKCB -0.01 0.052 -10000 0 -10000 0 0
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.03 0.028 0.23 2 -0.47 1 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.035 0.25 1 -0.51 1 2
VEGFA165/NRP2 0.041 0.025 0.26 2 -0.25 3 5
MAPKKK cascade 0.033 0.037 -10000 0 -0.42 1 1
NRP2 0.026 0.027 -10000 0 -0.36 3 3
VEGFC homodimer 0.02 0.049 -10000 0 -0.36 10 10
NCK1 0.028 0.002 -10000 0 -10000 0 0
ROCK1 0.022 0.019 -10000 0 -0.36 1 1
FAK1/Paxillin 0.055 0.075 0.28 5 -0.54 1 6
MAP3K13 0.022 0.028 -10000 0 -0.48 1 1
PDPK1 0.078 0.087 0.25 85 -0.34 1 86
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.024 0.035 0.36 5 -10000 0 5
PI3K Class IB/PDE3B 0.024 0.035 -10000 0 -0.36 5 5
PDE3B 0.024 0.035 -10000 0 -0.36 5 5
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.058 0.07 0.15 177 -0.29 1 178
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.011 0.035 0.15 11 -0.17 2 13
AP2 0.04 0.013 -10000 0 -0.25 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.006 -10000 0 -10000 0 0
CD4 0.016 0.064 -10000 0 -0.36 17 17
CLTA 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.005 0.018 0.26 2 -0.25 1 3
mol:PI-4-5-P2 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.036 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.015 0.18 2 -0.23 1 3
mol:Choline 0.006 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.005 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.016 0.18 2 -0.21 1 3
AP2M1 0.028 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.024 0.19 2 -0.18 1 3
ARFIP2 0.017 0.021 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.018 0.14 1 -10000 0 1
ARF1/GTP/ARHGAP10 0.02 0.006 -10000 0 -10000 0 0
GGA3 0.027 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.027 -10000 0 -0.24 5 5
AP2A1 0.027 0.016 -10000 0 -0.36 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.019 0.13 2 -0.21 1 3
ARF1/GDP/Membrin 0.018 0.034 -10000 0 -0.27 6 6
Arfaptin 2/Rac/GDP 0.032 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.038 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.034 -10000 0 -10000 0 0
PLD2 0.006 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.018 0.26 2 -0.25 1 3
PIP5K1A 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.027 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.018 0.26 2 -0.25 1 3
GOSR2 0.012 0.007 -10000 0 -10000 0 0
USO1 0.01 0.023 -10000 0 -0.31 3 3
GBF1 0.007 0.037 -10000 0 -0.31 8 8
ARF1/GTP/Arfaptin 2 0.037 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.046 0.047 -10000 0 -0.21 18 18
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.035 -9999 0 -0.36 5 5
positive regulation of NF-kappaB transcription factor activity 0.028 0.031 -9999 0 -0.25 5 5
MAP2K4 0.017 0.026 -9999 0 -10000 0 0
IKBKB 0.024 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.021 0.012 -9999 0 -10000 0 0
TNFRSF10A 0.021 0.012 -9999 0 -10000 0 0
SMPD1 0.007 0.037 -9999 0 -0.36 5 5
IKBKG 0.027 0.016 -9999 0 -0.36 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR3 0.005 0.091 -9999 0 -0.31 46 46
TRAIL/TRAILR1 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR4 0.029 0.031 -9999 0 -0.25 5 5
TRAIL/TRAILR1/DAP3/GTP 0.037 0.031 -9999 0 -0.19 5 5
IKK complex 0.019 0.042 -9999 0 -0.33 2 2
RIPK1 0.027 0.004 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.02 0.003 -9999 0 -10000 0 0
MAPK3 0.011 0.024 -9999 0 -0.25 5 5
MAP3K1 0.02 0.029 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRADD 0.028 0.003 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.024 -9999 0 -10000 0 0
CFLAR 0.028 0 -9999 0 -10000 0 0
MAPK1 0.011 0.022 -9999 0 -0.25 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.042 -9999 0 -10000 0 0
mol:ceramide 0.007 0.037 -9999 0 -0.36 5 5
FADD 0.027 0.004 -9999 0 -10000 0 0
MAPK8 0.014 0.03 -9999 0 -10000 0 0
TRAF2 0.027 0.016 -9999 0 -0.36 1 1
TRAILR3 (trimer) -0.01 0.12 -9999 0 -0.44 41 41
CHUK 0.027 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.04 0.034 -9999 0 -0.21 5 5
DAP3 0.027 0.004 -9999 0 -10000 0 0
CASP10 0.005 0.025 -9999 0 -0.24 5 5
JNK cascade 0.028 0.031 -9999 0 -0.25 5 5
TRAIL (trimer) 0.024 0.035 -9999 0 -0.36 5 5
TNFRSF10C -0.011 0.12 -9999 0 -0.44 41 41
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.036 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.04 0.034 -9999 0 -0.21 5 5
cell death 0.007 0.037 -9999 0 -0.36 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.024 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.012 -9999 0 -10000 0 0
CASP8 0.015 0.023 -9999 0 -0.47 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.059 0.042 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.026 0.011 -9999 0 -10000 0 0
DOCK1 0.026 0.016 -9999 0 -0.36 1 1
ITGA4 0.014 0.072 -9999 0 -0.36 22 22
RAC1 0.025 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.02 0.081 -9999 0 -0.28 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.023 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.046 0.05 -9999 0 -0.21 22 22
alpha4/beta7 Integrin/Paxillin 0.029 0.066 -9999 0 -0.36 5 5
lamellipodium assembly 0.008 0.081 -9999 0 -0.4 16 16
PIK3CA 0.027 0.016 -9999 0 -0.36 1 1
PI3K 0.039 0.015 -9999 0 -0.25 1 1
ARF6 0.026 0.007 -9999 0 -10000 0 0
TLN1 0.027 0.004 -9999 0 -10000 0 0
PXN 0.013 0.002 -9999 0 -10000 0 0
PIK3R1 0.027 0.006 -9999 0 -10000 0 0
ARF6/GTP 0.047 0.044 -9999 0 -10000 0 0
cell adhesion 0.049 0.046 -9999 0 -10000 0 0
CRKL/CBL 0.039 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.045 -9999 0 -10000 0 0
ITGB1 0.028 0.002 -9999 0 -10000 0 0
ITGB7 0.013 0.074 -9999 0 -0.36 23 23
ARF6/GDP 0.026 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.046 0.064 -9999 0 -0.35 9 9
p130Cas/Crk/Dock1 0.045 0.027 -9999 0 -0.21 2 2
VCAM1 0.019 0.056 -9999 0 -0.36 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.047 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.045 -9999 0 -10000 0 0
BCAR1 0.027 0.016 -9999 0 -0.36 1 1
mol:GDP -0.049 0.045 -9999 0 -10000 0 0
CBL 0.027 0.004 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GIT1 0.026 0.016 -9999 0 -0.36 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.047 -9999 0 -10000 0 0
Rac1/GTP 0.006 0.088 -9999 0 -0.45 16 16
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 0.048 0.052 -10000 0 -0.22 4 4
TC10/GTP 0.033 0.049 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.077 0.026 -10000 0 -10000 0 0
HRAS 0.027 0.016 -10000 0 -0.36 1 1
APS homodimer 0.02 0.058 0.36 1 -0.44 9 10
GRB14 -0.005 0.1 -10000 0 -0.39 42 42
FOXO3 -0.01 0.15 -10000 0 -0.57 38 38
AKT1 -0.002 0.06 0.21 3 -10000 0 3
INSR 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.078 0.072 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 0.017 0.06 -10000 0 -0.36 15 15
CRK 0.023 0.01 -10000 0 -10000 0 0
PTPN1 0.006 0.022 -10000 0 -10000 0 0
CAV1 0.012 0.046 0.18 10 -10000 0 10
CBL/APS/CAP/Crk-II/C3G 0.054 0.061 0.26 1 -0.23 6 7
Insulin Receptor/Insulin/IRS1/NCK2 0.077 0.026 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.059 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.063 0.068 -10000 0 -0.3 5 5
RPS6KB1 -0.007 0.054 0.19 3 -10000 0 3
PARD6A 0.026 0.027 -10000 0 -0.44 2 2
CBL 0.027 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.031 0.057 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.013 -10000 0 -10000 0 0
Insulin Receptor 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.085 0.032 -10000 0 -10000 0 0
PRKCI 0.027 0.055 -10000 0 -0.4 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.022 0.055 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.043 0.028 -10000 0 -0.35 1 1
PI3K 0.071 0.029 -10000 0 -10000 0 0
NCK2 0.028 0.001 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 -10000 0 -0.25 1 1
AKT2 -0.003 0.059 0.21 1 -10000 0 1
PRKCZ 0.017 0.077 -10000 0 -0.4 4 4
SH2B2 0.02 0.058 0.36 1 -0.44 9 10
SHC/SHIP 0.044 0.03 0.19 4 -10000 0 4
F2RL2 0.002 0.1 -10000 0 -0.43 33 33
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.059 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.084 0.032 -10000 0 -10000 0 0
RAPGEF1 0.027 0.016 -10000 0 -0.36 1 1
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.028 0.002 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.046 0.058 0.26 1 -0.24 9 10
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.068 0.034 -10000 0 -10000 0 0
INPP5D 0.016 0.041 0.18 10 -10000 0 10
SOS1 0.028 0.002 -10000 0 -10000 0 0
SGK1 -0.026 0.18 -10000 0 -0.74 35 35
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.028 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.044 0.029 -10000 0 -0.35 1 1
INS 0.028 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.016 0.041 0.18 10 -10000 0 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.007 0.054 0.23 4 -10000 0 4
PTPRA 0.029 0.016 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
TC10/GTP/CIP4 0.037 0.006 -10000 0 -10000 0 0
PDPK1 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.019 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.06 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.051 0.025 -10000 0 -10000 0 0
Par3/Par6 0.046 0.068 -10000 0 -0.23 31 31
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.009 -10000 0 -10000 0 0
TRAF2/ASK1 0.036 0.013 -10000 0 -0.21 1 1
ATM 0.027 0.005 -10000 0 -10000 0 0
MAP2K3 0.008 0.074 0.3 2 -0.32 11 13
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.063 0.26 4 -0.34 6 10
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.023 0.047 0.36 1 -0.43 6 7
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
MAP3K6 0.025 0.017 -10000 0 -0.36 1 1
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.037 0.017 -10000 0 -0.25 1 1
TAK1/TAB family 0 0.014 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.047 0.02 -10000 0 -0.19 1 1
TRAF2 0.027 0.016 -10000 0 -0.36 1 1
RAC1/OSM/MEKK3/MKK3 0.019 0.064 -10000 0 -0.3 5 5
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.013 0.11 0.36 1 -0.37 50 51
CCM2 0.025 0.017 -10000 0 -0.36 1 1
CaM/Ca2+/CAMKIIB 0.011 0.069 0.23 1 -0.22 50 51
MAPK11 0.025 0.027 -10000 0 -0.44 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.025 0.069 0.24 1 -0.2 45 46
OSM/MEKK3 0.036 0.018 -10000 0 -0.25 1 1
TAOK1 0.014 0.004 -10000 0 -10000 0 0
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAP3K10 0.028 0.014 0.36 1 -10000 0 1
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.009 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.058 0.034 0.24 1 -0.23 5 6
PLK2 and PLK4 events

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
PLK2 0.023 0.042 -9999 0 -0.44 5 5
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.01 0.03 -9999 0 -0.32 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.004 -10000 0 -10000 0 0
ELF1 0.021 0.042 -10000 0 -0.31 9 9
CCNA2 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
JAK3 0.027 0.019 -10000 0 -0.44 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.086 -10000 0 -0.46 7 7
SHC1 0.028 0.004 -10000 0 -10000 0 0
SP1 0.03 0.036 -10000 0 -0.3 7 7
IL2RA 0.006 0.078 -10000 0 -0.63 9 9
IL2RB 0.018 0.058 -10000 0 -0.36 14 14
SOS1 0.028 0.002 -10000 0 -10000 0 0
IL2RG 0.026 0.027 -10000 0 -0.36 3 3
G1/S transition of mitotic cell cycle 0.024 0.084 0.4 2 -0.59 6 8
PTPN11 0.028 0.002 -10000 0 -10000 0 0
CCND2 0.013 0.058 -10000 0 -0.63 5 5
LCK 0.02 0.058 -10000 0 -0.43 10 10
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.019 0.01 -10000 0 -10000 0 0
CDK6 0.026 0.006 -10000 0 -10000 0 0
CCND3 0.041 0.085 0.34 4 -0.5 3 7
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.077 0.23 27 -0.27 1 28
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.058 -10000 0 -0.31 16 16
NFKBIA 0.012 0.01 -10000 0 -10000 0 0
BIRC2 0.026 0.016 -10000 0 -0.36 1 1
IKBKB 0.024 0.009 -10000 0 -10000 0 0
RIPK2 0.024 0.01 -10000 0 -10000 0 0
IKBKG 0.025 0.044 -10000 0 -0.33 4 4
IKK complex/A20 0.053 0.061 -10000 0 -0.33 1 1
NEMO/A20/RIP2 0.024 0.01 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
NEMO/ATM 0.045 0.055 0.27 2 -0.32 5 7
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.028 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.051 -10000 0 -0.31 2 2
BCL10/MALT1/TRAF6 0.04 0.029 -10000 0 -0.21 2 2
NOD2 0.014 0.077 -10000 0 -0.44 17 17
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.02 0.02 -10000 0 -0.36 1 1
cIAP1/UbcH5C 0.039 0.015 -10000 0 -0.25 1 1
ATM 0.027 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.037 0.027 -10000 0 -0.25 5 5
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
TNF 0.024 0.035 -10000 0 -0.36 5 5
NF kappa B1 p50/RelA 0.06 0.016 -10000 0 -10000 0 0
BCL10 0.026 0.016 -10000 0 -0.36 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.047 0.054 -10000 0 -0.33 2 2
CYLD 0.027 0.016 -10000 0 -0.36 1 1
IKK complex/PKC alpha 0.053 0.057 -10000 0 -0.32 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.058 0.049 -10000 0 -0.39 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.057 -10000 0 -0.34 3 3
SUMO1 0.027 0.022 -10000 0 -0.36 2 2
ZFPM1 0.018 0.065 -10000 0 -0.44 12 12
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.012 -10000 0 -0.17 2 2
FKBP3 0.025 0.017 -10000 0 -0.36 1 1
Histones 0.061 0.038 -10000 0 -10000 0 0
YY1/LSF 0.01 0.068 -10000 0 -0.31 6 6
SMG5 0.027 0.004 -10000 0 -10000 0 0
RAN 0.028 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.024 0.022 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.047 -10000 0 -10000 0 0
SAP18 0.022 0.012 -10000 0 -10000 0 0
RELA 0.023 0.033 -10000 0 -0.51 1 1
HDAC1/Smad7 0.039 0.028 -10000 0 -0.21 1 1
RANGAP1 0.026 0.02 -10000 0 -0.44 1 1
HDAC3/TR2 0.035 0.033 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.019 0.043 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.028 0.061 0.23 3 -0.31 7 10
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.021 0.052 -10000 0 -0.36 11 11
GATA1 0.011 0.022 -10000 0 -10000 0 0
Mad/Max 0.037 0.02 -10000 0 -0.25 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.013 0.066 -10000 0 -0.31 5 5
RBBP7 0.027 0.004 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
MAX 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NFKBIA 0.021 0.017 -10000 0 -10000 0 0
KAT2B 0.011 0.078 -10000 0 -0.36 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.014 -10000 0 -10000 0 0
SIN3 complex 0.051 0.033 -10000 0 -10000 0 0
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.023 0.011 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.023 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.012 0.058 -10000 0 -0.29 5 5
YY1/HDAC2 0.011 0.067 -10000 0 -0.31 6 6
YY1/HDAC1 0.011 0.066 -10000 0 -0.31 6 6
NuRD/MBD2 Complex (MeCP1) 0.016 0.039 -10000 0 -0.33 1 1
PPARG 0.021 0.036 -10000 0 -0.23 7 7
HDAC8/hEST1B 0.054 0.011 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.035 0.034 -10000 0 -10000 0 0
MBD3L2 -0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.027 -10000 0 -0.21 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.013 0.069 -10000 0 -0.31 9 9
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.022 0.016 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
YY1 0.01 0.044 -10000 0 -0.22 21 21
HDAC8 0.028 0.002 -10000 0 -10000 0 0
SMAD7 0.02 0.02 -10000 0 -0.36 1 1
NCOR2 0.027 0.016 -10000 0 -0.36 1 1
MXD1 0.026 0.022 -10000 0 -0.36 2 2
STAT3 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.068 -10000 0 -0.29 6 6
YY1/SAP30/HDAC1 0.025 0.066 -10000 0 -0.29 6 6
EP300 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.021 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.017 -10000 0 -10000 0 0
histone deacetylation 0.014 0.046 -10000 0 -0.4 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.03 0.022 -10000 0 -10000 0 0
nuclear export -0.054 0.011 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.027 0.004 -10000 0 -10000 0 0
GATAD2A 0.027 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.031 0.044 -10000 0 -0.3 1 1
GATA1/HDAC1 0.037 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.033 0.032 -10000 0 -10000 0 0
CHD4 0.027 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.037 0.027 -10000 0 -0.25 5 5
SIN3/HDAC complex/Mad/Max 0.033 0.046 -10000 0 -0.33 2 2
NuRD Complex -0.007 0.091 -10000 0 -0.3 24 24
positive regulation of chromatin silencing 0.058 0.037 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.006 -10000 0 -10000 0 0
XPO1 0.028 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.038 0.031 -10000 0 -0.26 2 2
HDAC complex 0.066 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.031 0.05 -10000 0 -0.32 12 12
FKBP25/HDAC1/HDAC2 0.049 0.021 -10000 0 -0.21 1 1
TNF 0.024 0.035 -10000 0 -0.36 5 5
negative regulation of cell growth 0.033 0.046 -10000 0 -0.32 2 2
NuRD/MBD2/PRMT5 Complex 0.016 0.039 -10000 0 -0.33 1 1
Ran/GTP/Exportin 1 0.039 0.031 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.047 -10000 0 -0.36 3 3
SIN3/HDAC complex/NCoR1 0.01 0.052 -10000 0 -0.31 10 10
TFCP2 0.027 0.016 -10000 0 -0.36 1 1
NR2C1 0.028 0.002 -10000 0 -10000 0 0
MBD3 0.026 0.025 -10000 0 -0.4 2 2
MBD2 0.02 0.012 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.053 0.015 -10000 0 -10000 0 0
CLOCK 0.029 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.039 0.013 -10000 0 -10000 0 0
DEC1/BMAL1 0.03 0.05 -10000 0 -0.33 11 11
ATR 0.028 0.002 -10000 0 -10000 0 0
NR1D1 0.023 0.01 -10000 0 -10000 0 0
ARNTL 0.03 0.004 -10000 0 -10000 0 0
TIMELESS 0.023 0.009 -10000 0 -10000 0 0
NPAS2 0.03 0.003 -10000 0 -10000 0 0
CRY2 0.027 0.003 -10000 0 -10000 0 0
mol:CO -0.009 0.003 0.069 1 -10000 0 1
CHEK1 0.027 0.004 -10000 0 -10000 0 0
mol:HEME 0.009 0.003 -10000 0 -0.069 1 1
PER1 0.022 0.019 -10000 0 -0.36 1 1
BMAL/CLOCK/NPAS2 0.065 0.014 -10000 0 -10000 0 0
BMAL1/CLOCK 0.024 0.045 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.053 0.015 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.054 0.015 -10000 0 -10000 0 0
mol:NADPH 0.009 0.003 -10000 0 -0.069 1 1
PER1/TIMELESS 0.033 0.019 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.01 0.065 -10000 0 -0.46 11 11
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.041 0.028 -9999 0 -0.19 4 4
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.015 -9999 0 -0.3 1 1
AURKB 0.023 0.011 -9999 0 -10000 0 0
AURKC 0.023 0.033 -9999 0 -0.36 4 4
Atypical NF-kappaB 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
BCL3/RelA 0.04 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.054 0.055 0.21 6 -10000 0 6
NFKBIA 0.047 0.055 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0.011 -10000 0 -10000 0 0
ARRB2 0.012 0.006 -10000 0 -10000 0 0
REL 0.028 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.016 -10000 0 -0.36 1 1
NF kappa B1 p50 dimer 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.012 0.005 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.038 0.045 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.046 0.054 0.2 5 -10000 0 5
SRC 0.017 0.014 -10000 0 -10000 0 0
PI3K 0.039 0.015 -10000 0 -0.25 1 1
NF kappa B1 p50/RelA 0.038 0.045 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.057 0.059 0.22 7 -10000 0 7
cell death 0.044 0.053 0.19 5 -10000 0 5
NF kappa B1 p105/c-Rel 0.026 0.011 -10000 0 -10000 0 0
LCK 0.019 0.058 -10000 0 -0.43 10 10
BCL3 0.027 0.003 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.01 0.023 -10000 0 -0.25 1 1
adherens junction organization 0.036 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.027 -10000 0 -10000 0 0
FMN1 0.038 0.037 -10000 0 -10000 0 0
mol:IP3 0.011 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.043 0.036 -10000 0 -0.21 1 1
CTNNB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.051 0.049 0.18 8 -10000 0 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.065 0.063 0.22 2 -0.48 1 3
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.039 0.037 -10000 0 -10000 0 0
VASP 0.039 0.037 -10000 0 -10000 0 0
ZYX 0.037 0.036 -10000 0 -10000 0 0
JUB 0.039 0.035 0.15 2 -0.2 1 3
EGFR(dimer) 0.05 0.043 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.051 0.015 -10000 0 -0.2 1 1
mol:PI-3-4-5-P3 0.084 0.061 0.21 9 -10000 0 9
PIK3CA 0.03 0.017 -10000 0 -0.36 1 1
PI3K 0.086 0.063 0.22 9 -10000 0 9
FYN -0.003 0.044 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.019 -10000 0 -10000 0 0
JUP 0.027 0.016 -10000 0 -0.36 1 1
PIK3R1 0.03 0.008 -10000 0 -10000 0 0
mol:DAG 0.011 0.02 -10000 0 -10000 0 0
CDH1 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.033 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0.036 -10000 0 -10000 0 0
SRC 0.017 0.014 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.023 -10000 0 -0.36 2 2
CASR -0.006 0.044 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.025 -10000 0 -10000 0 0
AKT2 0.054 0.049 0.18 6 -10000 0 6
actin cable formation 0.033 0.036 0.18 1 -10000 0 1
apoptosis -0.047 0.05 0.24 1 -0.19 7 8
CTNNA1 0.03 0.006 -10000 0 -10000 0 0
mol:GDP 0.008 0.02 -10000 0 -10000 0 0
PIP5K1A 0.039 0.037 -10000 0 -10000 0 0
PLCG1 0.011 0.02 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.043 -10000 0 -10000 0 0
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.013 -10000 0 -10000 0 0
SMAD2 0.013 0.032 0.17 1 -0.2 1 2
SMAD3 0.019 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.061 -10000 0 -0.42 10 10
SMAD4/Ubc9/PIASy 0.04 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.039 0.045 -10000 0 -10000 0 0
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.023 -10000 0 -10000 0 0
MAP3K1 0.026 0.016 -10000 0 -0.36 1 1
TRAP-1/SMAD4 0.029 0.022 -10000 0 -0.25 1 1
MAPK3 0.027 0.016 -10000 0 -0.36 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.004 -10000 0 -10000 0 0
CTDSP1 0.028 0.001 -10000 0 -10000 0 0
CTDSP2 0.028 0.002 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
KPNB1 0.027 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.027 0.016 -10000 0 -0.36 1 1
UBE2I 0.027 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.028 0.014 0.36 1 -10000 0 1
PIAS4 0.027 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.024 0.02 -10000 0 -10000 0 0
ATM 0.027 0.005 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.016 0.36 1 -10000 0 1
ATR 0.028 0.002 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.021 0.012 -10000 0 -0.26 1 1
protein ubiquitination 0.071 0.027 0.24 3 -0.23 1 4
XRCC5 0.028 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.024 -10000 0 -10000 0 0
MRE11A 0.027 0.004 -10000 0 -10000 0 0
DNA-PK 0.048 0.022 0.25 1 -10000 0 1
FA complex/FANCD2/Ubiquitin 0.03 0.043 -10000 0 -0.39 4 4
FANCF 0.027 0.003 -10000 0 -10000 0 0
BRCA1 0.027 0.004 -10000 0 -10000 0 0
CCNE1 0.027 0.036 0.36 3 -0.44 2 5
CDK2/Cyclin E1 0.04 0.026 0.26 3 -0.32 2 5
FANCG 0.028 0.014 0.36 1 -10000 0 1
BRCA1/BACH1/BARD1 0.041 0.005 -10000 0 -10000 0 0
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.027 0.004 -10000 0 -10000 0 0
NBN 0.023 0.018 -10000 0 -0.36 1 1
FANCA 0.027 0.004 -10000 0 -10000 0 0
DNA repair 0.042 0.063 0.24 10 -10000 0 10
BRCA1/BARD1/ubiquitin 0.041 0.005 -10000 0 -10000 0 0
BARD1/DNA-PK 0.061 0.027 0.26 1 -10000 0 1
FANCL 0.028 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.024 0.02 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.044 -10000 0 -0.26 6 6
BRCA1/BACH1/BARD1/TopBP1 0.055 0.009 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.058 0.028 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.033 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.027 0.004 -10000 0 -10000 0 0
BARD1 0.028 0.001 -10000 0 -10000 0 0
PCNA 0.023 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.053 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.054 0.031 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.061 0.038 0.26 1 -10000 0 1
BRCA1/BARD1/Ubiquitin 0.041 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.036 0.022 -10000 0 -10000 0 0
FA complex 0.03 0.017 0.17 1 -10000 0 1
BARD1/EWS 0.039 0.009 -10000 0 -10000 0 0
RBBP8 0.01 0.012 -10000 0 -0.25 1 1
TP53 0.023 0.011 -10000 0 -10000 0 0
TOPBP1 0.028 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.056 0.027 -10000 0 -10000 0 0
BRCA1/BARD1 0.078 0.029 0.25 3 -0.23 1 4
CSTF1 0.016 0.014 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.021 0.001 -10000 0 -10000 0 0
CDK2 0.028 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.007 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.041 0.005 -10000 0 -10000 0 0
EWSR1 0.027 0.006 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.01 -9999 0 -10000 0 0
MDM2/SUMO1 0.038 0.036 -9999 0 -0.33 2 2
HDAC4 0.028 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.009 -9999 0 -10000 0 0
SUMO1 0.027 0.022 -9999 0 -0.36 2 2
NPC/RanGAP1/SUMO1 0.012 0.012 -9999 0 -0.17 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.01 0.011 -9999 0 -0.16 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.028 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.028 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.034 -9999 0 -0.26 2 2
SUMO1/HDAC1 0.038 0.031 -9999 0 -0.26 2 2
RANGAP1 0.026 0.02 -9999 0 -0.44 1 1
MDM2/SUMO1/SUMO1 0.052 0.037 -9999 0 -0.37 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.012 -9999 0 -0.17 2 2
Ran/GTP 0.025 0.027 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.016 -9999 0 -0.36 1 1
UBE2I 0.027 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0.026 -9999 0 -10000 0 0
NPC 0.016 0 -9999 0 -10000 0 0
PIAS2 0.021 0.012 -9999 0 -10000 0 0
PIAS1 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.054 0.016 -9999 0 -0.21 1 1
E-cadherin/beta catenin 0.04 0.006 -9999 0 -10000 0 0
CTNNB1 0.027 0.003 -9999 0 -10000 0 0
JUP 0.027 0.016 -9999 0 -0.36 1 1
CDH1 0.028 0.003 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.01 -9999 0 -9999 0 0
FBXW11 0.027 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -9999 0 -9999 0 0
CHUK 0.027 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.076 0.023 -9999 0 -9999 0 0
NFKB1 0.027 0.005 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.04 0.008 -9999 0 -9999 0 0
RELB 0.027 0.003 -9999 0 -9999 0 0
NFKB2 0.027 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.036 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.035 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 613 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WS.AB45 TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL
109_MAP3K5 0.031 0.031 -0.19 -0.17
47_PPARGC1A 0.028 0.028 0.028 0.028
105_BMP4 0.028 0 0 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 -0.36 0.028 0.028 0.36
105_BMP2 0.028 0.028 0 -0.36
131_RELN/VLDLR -0.24 -0.41 -0.058 -0.23
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.03 0.032
84_STAT5B 0.0059 0.028 0 0.04
84_STAT5A 0.0059 0.028 0 0.04
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/COADREAD-TP/22314768/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COADREAD-TP/22506542/Gistic2_Analysis_22507117/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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