PARADIGM pathway analysis of mRNASeq expression and copy number data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C16H4GXH
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/C16H4GXH
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 53 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
Aurora B signaling 172
Aurora C signaling 122
Endothelins 118
Signaling events regulated by Ret tyrosine kinase 109
Angiopoietin receptor Tie2-mediated signaling 105
p75(NTR)-mediated signaling 98
PDGFR-alpha signaling pathway 87
FOXM1 transcription factor network 87
HIF-1-alpha transcription factor network 85
Integrins in angiogenesis 81
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 545 . 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 ( 545 ).

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
Aurora B signaling 0.3156 172 11556 67 -0.29 0.37 1000 -1000 -0.02 -1000
Aurora C signaling 0.2239 122 855 7 0 0.23 1000 -1000 -0.008 -1000
Endothelins 0.2165 118 11403 96 -0.4 0.16 1000 -1000 -0.028 -1000
Signaling events regulated by Ret tyrosine kinase 0.2000 109 8975 82 -0.14 0.038 1000 -1000 -0.039 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1927 105 9324 88 -0.3 0.11 1000 -1000 -0.054 -1000
p75(NTR)-mediated signaling 0.1798 98 12261 125 -0.17 0.075 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.1596 87 3867 44 -0.28 0.037 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.1596 87 4483 51 -0.28 0.27 1000 -1000 -0.077 -1000
HIF-1-alpha transcription factor network 0.1560 85 6475 76 -0.25 0.044 1000 -1000 -0.025 -1000
Integrins in angiogenesis 0.1486 81 6854 84 -0.26 0.096 1000 -1000 -0.023 -1000
PLK1 signaling events 0.1468 80 6844 85 -0.056 0.25 1000 -1000 -0.022 -1000
Signaling events mediated by the Hedgehog family 0.1450 79 4144 52 -0.2 0.11 1000 -1000 -0.024 -1000
Reelin signaling pathway 0.1358 74 4174 56 -0.12 0.045 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.1229 67 2628 39 -0.093 0.053 1000 -1000 -0.02 -1000
S1P3 pathway 0.1174 64 2723 42 -0.39 0.031 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 0.1156 63 6118 97 -0.096 0.024 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 0.1156 63 3285 52 -0.24 0.14 1000 -1000 -0.017 -1000
Aurora A signaling 0.1083 59 3567 60 -0.14 0.22 1000 -1000 -0.014 -1000
Effects of Botulinum toxin 0.1064 58 1512 26 -0.1 0.11 1000 -1000 -0.008 -1000
Wnt signaling 0.1028 56 395 7 -0.065 0.037 1000 -1000 0 -1000
Signaling mediated by p38-alpha and p38-beta 0.0972 53 2342 44 -0.079 0.023 1000 -1000 -0.012 -1000
IGF1 pathway 0.0954 52 2979 57 -0.076 0.035 1000 -1000 -0.025 -1000
LPA4-mediated signaling events 0.0936 51 622 12 -0.11 0 1000 -1000 -0.015 -1000
TCGA08_p53 0.0936 51 357 7 -0.033 0.019 1000 -1000 -0.009 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0936 51 6180 120 -0.15 0.11 1000 -1000 -0.036 -1000
Ephrin B reverse signaling 0.0899 49 2389 48 -0.095 0.028 1000 -1000 -0.028 -1000
Glypican 1 network 0.0881 48 2322 48 -0.17 0.1 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 0.0862 47 2190 46 -0.2 0.19 1000 -1000 -0.059 -1000
TCGA08_retinoblastoma 0.0844 46 369 8 -0.04 0.13 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0844 46 3659 78 -0.13 0.055 1000 -1000 -0.038 -1000
Noncanonical Wnt signaling pathway 0.0826 45 1171 26 -0.12 0.037 1000 -1000 -0.03 -1000
Thromboxane A2 receptor signaling 0.0826 45 4816 105 -0.14 0.048 1000 -1000 -0.028 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0771 42 1436 34 -0.017 0.029 1000 -1000 -0.026 -1000
Osteopontin-mediated events 0.0771 42 1632 38 -0.089 0.097 1000 -1000 -0.017 -1000
BMP receptor signaling 0.0752 41 3344 81 -0.23 0.043 1000 -1000 -0.023 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0752 41 2844 68 -0.15 0.074 1000 -1000 -0.062 -1000
S1P4 pathway 0.0752 41 1048 25 -0.065 0.038 1000 -1000 -0.008 -1000
Plasma membrane estrogen receptor signaling 0.0734 40 3491 86 -0.19 0.08 1000 -1000 -0.028 -1000
S1P1 pathway 0.0716 39 1423 36 -0.15 0.022 1000 -1000 -0.015 -1000
Ras signaling in the CD4+ TCR pathway 0.0716 39 669 17 -0.091 0.022 1000 -1000 -0.007 -1000
Syndecan-1-mediated signaling events 0.0697 38 1325 34 -0.05 0.16 1000 -1000 -0.018 -1000
amb2 Integrin signaling 0.0697 38 3131 82 -0.1 0.13 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 0.0679 37 262 7 -0.027 0.012 1000 -1000 -0.009 -1000
EPHB forward signaling 0.0661 36 3091 85 -0.055 0.048 1000 -1000 -0.042 -1000
LPA receptor mediated events 0.0642 35 3627 102 -0.13 0.13 1000 -1000 -0.048 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0606 33 2830 85 -0.21 0.031 1000 -1000 -0.032 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0550 30 1621 54 -0.1 0.048 1000 -1000 -0.023 -1000
IL4-mediated signaling events 0.0550 30 2733 91 -0.3 0.094 1000 -1000 -0.089 -1000
Visual signal transduction: Rods 0.0550 30 1606 52 -0.057 0.11 1000 -1000 -0.017 -1000
Arf6 signaling events 0.0532 29 1849 62 -0.063 0.043 1000 -1000 -0.034 -1000
EGFR-dependent Endothelin signaling events 0.0532 29 618 21 -0.082 0.048 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 0.0514 28 1245 43 -0.16 0.075 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 0.0514 28 1359 47 -0.05 0.038 1000 -1000 -0.024 -1000
S1P5 pathway 0.0495 27 470 17 -0.065 0.036 1000 -1000 -0.004 -1000
Glypican 2 network 0.0495 27 108 4 0.023 0.043 1000 -1000 0.019 -1000
Coregulation of Androgen receptor activity 0.0477 26 2040 76 -0.09 0.12 1000 -1000 -0.022 -1000
Glucocorticoid receptor regulatory network 0.0477 26 3076 114 -0.15 0.21 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0477 26 1369 52 -0.055 0.047 1000 -1000 -0.027 -1000
Calcium signaling in the CD4+ TCR pathway 0.0477 26 806 31 -0.09 0.042 1000 -1000 -0.024 -1000
Syndecan-4-mediated signaling events 0.0477 26 1767 67 -0.2 0.13 1000 -1000 -0.026 -1000
IL12-mediated signaling events 0.0459 25 2233 87 -0.3 0.061 1000 -1000 -0.054 -1000
Visual signal transduction: Cones 0.0459 25 973 38 -0.057 0.033 1000 -1000 -0.015 -1000
Syndecan-2-mediated signaling events 0.0459 25 1739 69 -0.01 0.1 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 0.0459 25 1942 76 -0.086 0.037 1000 -1000 -0.032 -1000
Presenilin action in Notch and Wnt signaling 0.0459 25 1533 61 -0.089 0.083 1000 -1000 -0.03 -1000
TCR signaling in naïve CD8+ T cells 0.0459 25 2397 93 -0.015 0.053 1000 -1000 -0.033 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0459 25 3125 125 -0.055 0.044 1000 -1000 -0.024 -1000
TCGA08_rtk_signaling 0.0459 25 672 26 -0.096 0.032 1000 -1000 -0.006 -1000
Insulin Pathway 0.0459 25 1920 74 -0.096 0.11 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 0.0440 24 1722 70 -0.038 0.19 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0422 23 774 33 -0.12 0.13 1000 -1000 -0.032 -1000
Canonical Wnt signaling pathway 0.0404 22 1138 51 -0.046 0.083 1000 -1000 -0.028 -1000
IL2 signaling events mediated by STAT5 0.0404 22 504 22 -0.095 0.077 1000 -1000 -0.026 -1000
BARD1 signaling events 0.0385 21 1198 57 -0.045 0.13 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0385 21 1384 65 -0.096 0.052 1000 -1000 -0.03 -1000
IL6-mediated signaling events 0.0385 21 1587 75 -0.088 0.089 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0367 20 1376 68 -0.082 0.21 1000 -1000 -0.016 -1000
Retinoic acid receptors-mediated signaling 0.0367 20 1176 58 -0.018 0.05 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 0.0367 20 1116 54 -0.14 0.054 1000 -1000 -0.039 -1000
BCR signaling pathway 0.0367 20 2021 99 -0.035 0.058 1000 -1000 -0.054 -1000
Regulation of nuclear SMAD2/3 signaling 0.0330 18 2470 136 -0.088 0.14 1000 -1000 -0.023 -1000
EPO signaling pathway 0.0330 18 995 55 -0.04 0.038 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0330 18 1271 68 -0.18 0.074 1000 -1000 -0.037 -1000
Nectin adhesion pathway 0.0330 18 1136 63 -0.04 0.054 1000 -1000 -0.032 -1000
Rapid glucocorticoid signaling 0.0330 18 365 20 -0.031 0.026 1000 -1000 -0.008 -1000
mTOR signaling pathway 0.0312 17 902 53 -0.029 0.025 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 0.0312 17 609 35 -0.06 0.095 1000 -1000 -0.014 -1000
PDGFR-beta signaling pathway 0.0312 17 1691 97 -0.021 0.05 1000 -1000 -0.034 -1000
Insulin-mediated glucose transport 0.0294 16 534 32 -0.085 0.21 1000 -1000 -0.016 -1000
IL2 signaling events mediated by PI3K 0.0294 16 935 58 -0.03 0.12 1000 -1000 -0.034 -1000
Regulation of Telomerase 0.0294 16 1680 102 -0.24 0.087 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 0.0275 15 992 65 -0.076 0.048 1000 -1000 -0.041 -1000
Ceramide signaling pathway 0.0275 15 1151 76 -0.046 0.061 1000 -1000 -0.019 -1000
JNK signaling in the CD4+ TCR pathway 0.0257 14 252 17 -0.044 0.056 1000 -1000 -0.014 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0257 14 1199 83 -0.023 0.21 1000 -1000 -0.018 -1000
FoxO family signaling 0.0257 14 957 64 -0.016 0.21 1000 -1000 -0.041 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0257 14 662 45 -0.006 0.058 1000 -1000 -0.027 -1000
IL23-mediated signaling events 0.0257 14 887 60 -0.007 0.23 1000 -1000 -0.073 -1000
Signaling events mediated by PRL 0.0257 14 498 34 -0.036 0.091 1000 -1000 -0.028 -1000
Caspase cascade in apoptosis 0.0239 13 1009 74 -0.027 0.15 1000 -1000 -0.028 -1000
ErbB4 signaling events 0.0239 13 951 69 -0.05 0.054 1000 -1000 -0.022 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0239 13 365 28 -0.065 0.041 1000 -1000 -0.012 -1000
IL1-mediated signaling events 0.0239 13 862 62 -0.014 0.067 1000 -1000 -0.021 -1000
ceramide signaling pathway 0.0220 12 626 49 -0.008 0.054 1000 -1000 -0.019 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0202 11 411 37 -0.021 0.063 1000 -1000 -0.016 -1000
IL27-mediated signaling events 0.0202 11 577 51 -0.033 0.038 1000 -1000 -0.045 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0202 11 873 74 -0.05 0.077 1000 -1000 -0.042 -1000
E-cadherin signaling in keratinocytes 0.0202 11 488 43 -0.009 0.038 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class III 0.0183 10 402 40 -0.054 0.04 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 0.0183 10 815 76 -0.028 0.056 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 0.0183 10 30 3 -0.022 0.022 1000 -1000 -0.018 -1000
Canonical NF-kappaB pathway 0.0165 9 388 39 -0.008 0.053 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 0.0147 8 353 44 -0.002 0.063 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class II 0.0128 7 576 75 -0.031 0.045 1000 -1000 -0.02 -1000
Arf6 trafficking events 0.0128 7 536 71 -0.16 0.04 1000 -1000 -0.027 -1000
Class I PI3K signaling events 0.0110 6 459 73 -0.023 0.042 1000 -1000 -0.029 -1000
TRAIL signaling pathway 0.0092 5 243 48 -0.01 0.05 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 0.0092 5 592 104 -0.035 0.057 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 0.0092 5 79 15 -0.011 0.022 1000 -1000 -0.017 -1000
PLK2 and PLK4 events 0.0073 4 12 3 -0.011 0.025 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 0.0073 4 177 36 -0.041 0.043 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0055 3 80 23 0.002 0.046 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0055 3 160 43 -0.037 0.041 1000 -1000 -0.024 -1000
VEGFR1 specific signals 0.0055 3 200 56 -0.04 0.047 1000 -1000 -0.027 -1000
Arf1 pathway 0.0055 3 190 54 -0.005 0.041 1000 -1000 -0.011 -1000
a4b1 and a4b7 Integrin signaling 0.0037 2 10 5 0.022 0.034 1000 -1000 0.014 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0037 2 62 27 -0.014 0.054 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 0.0018 1 51 31 -0.011 0.027 1000 -1000 -0.016 -1000
E-cadherin signaling events 0.0018 1 7 5 0.019 0.038 1000 -1000 0.019 -1000
Circadian rhythm pathway 0.0000 0 16 22 -0.006 0.048 1000 -1000 -0.03 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.059 1000 -1000 0 -1000
Total NA 4219 252977 7203 -12 10 131000 -131000 -3.3 -131000
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.13 0.093 0.19 285 -0.3 6 291
STMN1 0.088 0.045 0.11 338 -10000 0 338
Aurora B/RasGAP/Survivin 0.26 0.15 0.34 408 -0.18 5 413
Chromosomal passenger complex/Cul3 protein complex 0.077 0.099 0.17 196 -0.19 18 214
BIRC5 0.23 0.11 0.29 410 -10000 0 410
DES -0.29 0.25 -10000 0 -0.52 144 144
Aurora C/Aurora B/INCENP 0.16 0.084 0.2 365 -10000 0 365
Aurora B/TACC1 0.083 0.14 0.19 323 -0.2 83 406
Aurora B/PP2A 0.17 0.079 0.21 419 -10000 0 419
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.041 0.025 0.12 21 -10000 0 21
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.097 0.075 0.28 34 -10000 0 34
Cul3 protein complex -0.004 0.1 -10000 0 -0.21 101 101
KIF2C 0.16 0.076 0.21 311 -10000 0 311
PEBP1 0.024 0.003 -10000 0 -10000 0 0
KIF20A 0.25 0.083 0.28 475 -10000 0 475
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.16 0.088 0.21 413 -0.23 5 418
SEPT1 0.021 0.017 -10000 0 -0.35 1 1
SMC2 0.022 0.012 0.28 1 -10000 0 1
SMC4 0.022 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.17 0.29 23 -0.42 42 65
PSMA3 0.023 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.09 0.048 0.22 16 -10000 0 16
AURKB 0.23 0.11 0.29 431 -10000 0 431
AURKC 0.024 0.02 0.28 3 -10000 0 3
CDCA8 0.18 0.13 0.29 312 -10000 0 312
cytokinesis 0.14 0.092 0.22 247 -0.3 1 248
Aurora B/Septin1 0.2 0.14 0.29 351 -0.27 7 358
AURKA 0.094 0.12 0.28 161 -10000 0 161
INCENP 0.03 0.006 -10000 0 -10000 0 0
KLHL13 -0.049 0.15 -10000 0 -0.35 104 104
BUB1 0.21 0.12 0.28 415 -10000 0 415
hSgo1/Aurora B/Survivin 0.36 0.19 0.44 449 -0.16 2 451
EVI5 0.03 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.088 0.24 196 -0.25 2 198
SGOL1 0.22 0.11 0.28 406 -10000 0 406
CENPA 0.18 0.11 0.24 375 -0.26 5 380
NCAPG 0.19 0.12 0.28 349 -10000 0 349
Aurora B/HC8 Proteasome 0.17 0.078 0.21 424 -10000 0 424
NCAPD2 0.022 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.17 0.077 0.21 427 -10000 0 427
RHOA 0.022 0.005 -10000 0 -10000 0 0
NCAPH 0.22 0.11 0.28 413 -10000 0 413
NPM1 0.087 0.12 0.24 4 -0.33 33 37
RASA1 0.019 0.036 -10000 0 -0.35 5 5
KLHL9 0.022 0.017 -10000 0 -0.35 1 1
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.17 0.077 0.21 424 -10000 0 424
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.18 0.096 0.25 228 -0.27 2 230
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
NSUN2 0.098 0.1 0.26 19 -0.28 27 46
MYLK -0.079 0.16 0.22 7 -0.22 295 302
KIF23 0.041 0.054 0.29 23 -10000 0 23
VIM 0.092 0.073 0.34 18 -0.23 6 24
RACGAP1 0.031 0.017 0.3 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.09 0.12 0.23 1 -0.34 30 31
Chromosomal passenger complex 0.19 0.093 0.23 399 -0.28 3 402
Chromosomal passenger complex/EVI5 0.37 0.19 0.45 423 -10000 0 423
TACC1 -0.037 0.13 -10000 0 -0.35 83 83
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
CUL3 0.023 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.023 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.15 0.083 0.19 415 -10000 0 415
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.012 0.039 -10000 0 -0.34 6 6
AURKB 0.23 0.11 0.28 431 -10000 0 431
AURKC 0.024 0.02 0.28 3 -10000 0 3
Endothelins

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
AKT1 -0.14 0.15 -10000 0 -0.3 198 198
PTK2B 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -10000 0 -0.75 110 110
EDN1 -0.053 0.079 -10000 0 -0.24 41 41
EDN3 0.03 0.16 0.28 98 -0.35 55 153
EDN2 0.063 0.094 0.28 83 -10000 0 83
HRAS/GDP -0.19 0.22 -10000 0 -0.49 146 146
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.19 -10000 0 -0.4 125 125
ADCY4 -0.14 0.16 0.3 1 -0.32 177 178
ADCY5 -0.16 0.16 0.24 2 -0.33 214 216
ADCY6 -0.13 0.15 0.3 1 -0.32 167 168
ADCY7 -0.13 0.15 0.24 2 -0.31 178 180
ADCY1 -0.14 0.16 0.24 2 -0.32 178 180
ADCY2 -0.21 0.18 -10000 0 -0.36 276 276
ADCY3 -0.13 0.15 0.3 1 -0.32 169 170
ADCY8 -0.13 0.14 -10000 0 -0.31 156 156
ADCY9 -0.15 0.17 0.3 1 -0.34 198 199
arachidonic acid secretion -0.24 0.27 -10000 0 -0.5 226 226
ETB receptor/Endothelin-1/Gq/GTP -0.085 0.14 -10000 0 -0.31 120 120
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
HRAS 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.12 0.14 -10000 0 -0.3 153 153
ETA receptor/Endothelin-1/Gs/GTP -0.14 0.16 -10000 0 -0.32 187 187
mol:GTP -0.003 0.005 -10000 0 -10000 0 0
COL3A1 -0.14 0.17 -10000 0 -0.38 139 139
EDNRB -0.056 0.15 -10000 0 -0.35 111 111
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.16 0.19 -10000 0 -0.44 149 149
CYSLTR1 -0.14 0.16 -10000 0 -0.37 136 136
SLC9A1 -0.085 0.097 -10000 0 -0.22 134 134
mol:GDP -0.2 0.24 -10000 0 -0.52 147 147
SLC9A3 -0.19 0.32 -10000 0 -0.7 131 131
RAF1 -0.22 0.25 -10000 0 -0.49 207 207
JUN -0.18 0.28 -10000 0 -0.7 103 103
JAK2 -0.14 0.15 -10000 0 -0.31 192 192
mol:IP3 -0.14 0.2 -10000 0 -0.47 100 100
ETA receptor/Endothelin-1 -0.16 0.18 -10000 0 -0.35 202 202
PLCB1 0.013 0.031 -10000 0 -0.35 3 3
PLCB2 0.011 0.019 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.093 0.18 0.21 34 -0.3 187 221
FOS -0.33 0.39 -10000 0 -0.82 195 195
Gai/GDP -0.26 0.39 -10000 0 -0.78 182 182
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.19 0.22 -10000 0 -0.46 160 160
BCAR1 0.021 0.008 -10000 0 -10000 0 0
PRKCB1 -0.14 0.19 -10000 0 -0.46 103 103
GNAQ 0.008 0.026 -10000 0 -0.35 1 1
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
GNAL -0.031 0.13 -10000 0 -0.35 77 77
Gs family/GDP -0.2 0.22 -10000 0 -0.47 168 168
ETA receptor/Endothelin-1/Gq/GTP -0.14 0.19 -10000 0 -0.38 165 165
MAPK14 -0.085 0.14 0.2 2 -0.36 81 83
TRPC6 -0.21 0.34 -10000 0 -0.82 108 108
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.15 -10000 0 -0.37 84 84
ETB receptor/Endothelin-2 -0.005 0.13 0.21 56 -0.24 107 163
ETB receptor/Endothelin-3 -0.02 0.17 0.21 87 -0.28 136 223
ETB receptor/Endothelin-1 -0.077 0.12 -10000 0 -0.28 121 121
MAPK3 -0.32 0.37 -10000 0 -0.77 199 199
MAPK1 -0.32 0.37 -10000 0 -0.77 199 199
Rac1/GDP -0.19 0.22 -10000 0 -0.49 142 142
cAMP biosynthetic process -0.21 0.2 0.3 4 -0.41 216 220
MAPK8 -0.22 0.35 -10000 0 -0.8 113 113
SRC 0.022 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.1 0.15 -10000 0 -0.33 124 124
p130Cas/CRK/Src/PYK2 -0.2 0.26 -10000 0 -0.58 132 132
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.19 0.22 -10000 0 -0.49 143 143
COL1A2 -0.17 0.19 -10000 0 -0.42 161 161
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.16 0.22 21 -0.3 152 173
mol:DAG -0.14 0.2 -10000 0 -0.48 100 100
MAP2K2 -0.26 0.29 -10000 0 -0.59 209 209
MAP2K1 -0.26 0.29 -10000 0 -0.6 208 208
EDNRA -0.15 0.18 -10000 0 -0.39 178 178
positive regulation of muscle contraction -0.12 0.13 0.2 2 -0.3 133 135
Gq family/GDP -0.16 0.22 -10000 0 -0.49 127 127
HRAS/GTP -0.19 0.24 -10000 0 -0.5 146 146
PRKCH -0.14 0.19 0.21 2 -0.47 100 102
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.14 0.19 0.21 1 -0.48 95 96
PRKCB -0.14 0.19 -10000 0 -0.46 108 108
PRKCE -0.14 0.19 -10000 0 -0.46 98 98
PRKCD -0.13 0.19 0.21 1 -0.46 100 101
PRKCG -0.14 0.19 -10000 0 -0.46 102 102
regulation of vascular smooth muscle contraction -0.4 0.46 -10000 0 -0.97 196 196
PRKCQ -0.15 0.2 -10000 0 -0.45 120 120
PLA2G4A -0.26 0.3 -10000 0 -0.56 226 226
GNA14 -0.022 0.1 -10000 0 -0.35 45 45
GNA15 0.018 0.033 0.27 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.007 0.052 -10000 0 -0.35 10 10
Rac1/GTP -0.12 0.14 -10000 0 -0.3 150 150
MMP1 0.16 0.13 0.35 111 -10000 0 111
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.019 0.06 -10000 0 -0.39 9 9
Crk/p130 Cas/Paxillin -0.12 0.13 -10000 0 -0.27 196 196
JUN -0.086 0.12 -10000 0 -0.38 32 32
HRAS 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.062 0.14 0.23 13 -0.2 240 253
RAP1A 0.023 0.002 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.017 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.061 0.14 0.23 14 -0.2 239 253
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.06 0.11 0.27 2 -0.19 231 233
RHOA 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.057 0.12 0.43 1 -0.18 240 241
GRB7 0.038 0.074 0.32 31 -0.35 2 33
RET51/GFRalpha1/GDNF -0.06 0.14 0.23 13 -0.2 234 247
MAPKKK cascade -0.079 0.12 0.32 1 -0.22 213 214
BCAR1 0.021 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.077 0.13 0.27 2 -0.21 250 252
lamellipodium assembly -0.11 0.13 -10000 0 -0.25 201 201
RET51/GFRalpha1/GDNF/SHC -0.048 0.13 0.25 6 -0.21 192 198
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RET9/GFRalpha1/GDNF/SHC -0.046 0.1 0.31 1 -0.19 183 184
RET9/GFRalpha1/GDNF/Shank3 -0.062 0.11 0.27 2 -0.19 233 235
MAPK3 -0.076 0.11 0.32 12 -0.31 20 32
DOK1 0.023 0.003 -10000 0 -10000 0 0
DOK6 -0.046 0.14 -10000 0 -0.35 98 98
PXN 0.023 0.003 -10000 0 -10000 0 0
neurite development -0.088 0.12 0.3 11 -0.26 80 91
DOK5 -0.01 0.1 0.28 1 -0.35 46 47
GFRA1 -0.14 0.19 0.28 2 -0.35 241 243
MAPK8 -0.087 0.12 0.17 1 -0.39 29 30
HRAS/GTP -0.076 0.15 0.44 1 -0.23 227 228
tube development -0.057 0.11 0.21 9 -0.18 228 237
MAPK1 -0.076 0.11 0.32 12 -0.31 20 32
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.076 0.1 0.15 1 -0.19 229 230
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
PDLIM7 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.081 0.16 0.5 1 -0.23 263 264
SHC1 0.019 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.14 0.23 11 -0.2 240 251
RET51/GFRalpha1/GDNF/Dok5 -0.075 0.15 0.25 8 -0.23 246 254
PRKCA 0 0.087 -10000 0 -0.35 31 31
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
CREB1 -0.075 0.13 0.26 1 -0.24 183 184
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.1 0.22 1 -0.2 183 184
RET51/GFRalpha1/GDNF/Grb7 -0.054 0.14 0.25 24 -0.21 234 258
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.014 0.097 0.28 21 -0.35 27 48
DOK4 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.085 0.12 -10000 0 -0.37 32 32
RET9/GFRalpha1/GDNF/FRS2 -0.061 0.11 0.27 2 -0.19 233 235
SHANK3 0.021 0.007 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.06 0.098 0.19 2 -0.19 181 183
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.12 0.22 1 -0.21 228 229
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.13 0.22 1 -0.22 228 229
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.067 0.12 0.18 8 -0.22 187 195
PI3K -0.14 0.19 0.3 1 -0.36 201 202
SOS1 0.023 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.053 0.11 0.26 2 -0.18 228 230
GRB10 0.022 0.017 -10000 0 -0.35 1 1
activation of MAPKK activity -0.072 0.11 0.18 1 -0.2 147 148
RET51/GFRalpha1/GDNF/FRS2 -0.061 0.14 0.24 9 -0.2 239 248
GAB1 0.02 0.032 -10000 0 -0.35 4 4
IRS1 -0.013 0.11 -10000 0 -0.35 51 51
IRS2 -0.024 0.12 -10000 0 -0.35 66 66
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.069 0.13 0.29 1 -0.22 186 187
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.15 0.25 8 -0.22 248 256
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.02 0.28 3 -10000 0 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.077 0.15 0.23 13 -0.22 255 268
Rac1/GTP -0.12 0.16 0.25 1 -0.29 199 200
RET9/GFRalpha1/GDNF -0.074 0.12 0.27 2 -0.2 234 236
GFRalpha1/GDNF -0.091 0.14 0.3 2 -0.25 234 236
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.22 0.41 0.45 2 -0.82 166 168
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.4 164 164
NCK1/Dok-R -0.26 0.48 -10000 0 -0.95 162 162
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
mol:beta2-estradiol 0.046 0.092 0.23 109 -10000 0 109
RELA 0.022 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.009 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -10000 0 -10000 0 0
F2 0.078 0.13 0.28 144 -10000 0 144
TNIP2 0.022 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.23 0.46 -10000 0 -0.89 163 163
FN1 0.019 0.036 -10000 0 -0.35 5 5
PLD2 -0.28 0.49 -10000 0 -1 161 161
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 190 -0.35 3 193
ELK1 -0.26 0.44 -10000 0 -0.9 163 163
GRB7 0.038 0.074 0.32 31 -0.35 2 33
PAK1 0.022 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.25 0.48 -10000 0 -0.94 162 162
CDKN1A -0.14 0.29 0.47 1 -0.59 132 133
ITGA5 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -0.95 163 163
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:NO -0.16 0.31 0.4 3 -0.61 166 169
PLG -0.29 0.49 -10000 0 -1 161 161
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.38 -10000 0 -0.78 166 166
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
ANGPT2 -0.11 0.23 -10000 0 -0.61 50 50
BMX -0.3 0.5 -10000 0 -1 163 163
ANGPT1 -0.22 0.45 -10000 0 -1.1 109 109
tube development -0.16 0.32 0.58 1 -0.62 162 163
ANGPT4 0.006 0.042 0.28 2 -0.35 5 7
response to hypoxia -0.019 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.54 -10000 0 -1 162 162
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 -0.17 0.18 -10000 0 -0.35 276 276
STAT5A (dimer) -0.18 0.36 -10000 0 -0.74 136 136
mol:L-citrulline -0.16 0.31 0.4 3 -0.61 166 169
AGTR1 -0.057 0.15 0.29 2 -0.35 113 115
MAPK14 -0.29 0.51 -10000 0 -1 166 166
Tie2/SHP2 -0.19 0.4 -10000 0 -1 98 98
TEK -0.21 0.44 -10000 0 -1.1 96 96
RPS6KB1 -0.21 0.4 -10000 0 -0.79 165 165
Angiotensin II/AT1 -0.037 0.11 0.21 2 -0.24 113 115
Tie2/Ang1/GRB2 -0.28 0.51 -10000 0 -1 163 163
MAPK3 -0.26 0.45 -10000 0 -0.92 161 161
MAPK1 -0.26 0.45 -10000 0 -0.92 161 161
Tie2/Ang1/GRB7 -0.28 0.52 -10000 0 -1 164 164
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.28 0.49 -10000 0 -0.99 163 163
PI3K -0.26 0.47 -10000 0 -0.94 166 166
FES -0.29 0.51 -10000 0 -1 166 166
Crk/Dok-R -0.26 0.48 -10000 0 -0.95 163 163
Tie2/Ang1/ABIN2 -0.28 0.52 -10000 0 -1 164 164
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.37 0.45 2 -0.73 166 168
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.4 0.52 2 -0.78 162 164
Tie2/Ang2 -0.23 0.43 -10000 0 -0.85 151 151
Tie2/Ang1 -0.3 0.54 -10000 0 -1.1 163 163
FOXO1 -0.19 0.38 0.46 2 -0.74 165 167
ELF1 -0.006 0.061 -10000 0 -0.13 79 79
ELF2 -0.28 0.49 -10000 0 -0.99 161 161
mol:Choline -0.27 0.47 -10000 0 -0.95 161 161
cell migration -0.069 0.1 -10000 0 -0.22 165 165
FYN -0.19 0.36 0.59 1 -0.7 161 162
DOK2 0.021 0.021 0.28 3 -10000 0 3
negative regulation of cell cycle -0.13 0.26 0.46 1 -0.53 133 134
ETS1 -0.032 0.11 -10000 0 -0.24 104 104
PXN -0.16 0.34 0.45 4 -0.66 160 164
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.18 0.35 0.43 2 -0.69 166 168
RAC1 0.022 0.005 -10000 0 -10000 0 0
TNF -0.005 0.14 0.28 56 -0.24 108 164
MAPKKK cascade -0.27 0.47 -10000 0 -0.95 161 161
RASA1 0.019 0.036 -10000 0 -0.35 5 5
Tie2/Ang1/Shc -0.28 0.51 -10000 0 -1 164 164
NCK1 0.021 0.023 -10000 0 -0.35 2 2
vasculogenesis -0.14 0.28 0.4 3 -0.55 166 169
mol:Phosphatidic acid -0.27 0.47 -10000 0 -0.95 161 161
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.16 0.31 0.4 3 -0.61 166 169
Rac1/GTP -0.19 0.37 -10000 0 -0.73 166 166
MMP2 -0.29 0.5 -10000 0 -1 161 161
p75(NTR)-mediated signaling

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.033 0.008 -10000 0 -10000 0 0
Necdin/E2F1 -0.076 0.15 0.21 37 -0.24 234 271
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.057 0.15 -10000 0 -0.22 222 222
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.19 0.2 3 -0.29 267 270
NT-4/5 (dimer)/p75(NTR) -0.052 0.14 0.22 19 -0.25 173 192
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 -0.085 0.12 0.17 31 -0.22 197 228
IKBKG 0.023 0.004 -10000 0 -10000 0 0
BDNF 0.062 0.094 0.28 84 -10000 0 84
MGDIs/NGR/p75(NTR)/LINGO1 -0.037 0.12 0.2 6 -0.21 173 179
FURIN 0.022 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.018 0.14 0.2 70 -0.21 173 243
LINGO1 0.024 0.03 0.28 5 -0.35 1 6
Sortilin/TRAF6/NRIF 0.019 0.026 -10000 0 -10000 0 0
proBDNF (dimer) 0.062 0.093 0.28 84 -10000 0 84
NTRK1 0.019 0.044 0.28 7 -0.35 4 11
RTN4R 0.021 0.017 -10000 0 -0.35 1 1
neuron apoptosis -0.078 0.15 -10000 0 -0.4 40 40
IRAK1 0.023 0.003 -10000 0 -10000 0 0
SHC1 -0.096 0.13 -10000 0 -0.25 191 191
ARHGDIA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.18 -10000 0 -0.27 277 277
MAGEH1 -0.067 0.16 -10000 0 -0.35 129 129
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.16 0.18 -10000 0 -0.28 341 341
Mammalian IAPs/DIABLO 0.054 0.033 0.21 2 -0.19 7 9
proNGF (dimer) -0.055 0.15 -10000 0 -0.35 113 113
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
APP 0.023 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.032 0.055 0.28 23 -0.35 1 24
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.073 0.13 -10000 0 -0.22 217 217
NGF -0.056 0.15 -10000 0 -0.35 113 113
cell cycle arrest -0.079 0.11 0.24 4 -0.31 59 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.084 0.14 -10000 0 -0.25 204 204
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.034 0.12 0.21 17 -0.21 172 189
NCSTN 0.019 0.009 -10000 0 -10000 0 0
mol:GTP -0.082 0.16 0.2 1 -0.25 227 228
PSENEN 0.022 0.005 -10000 0 -10000 0 0
mol:ceramide -0.1 0.12 0.18 3 -0.23 217 220
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.072 0.12 -10000 0 -0.33 65 65
p75(NTR)/beta APP -0.058 0.13 0.21 1 -0.24 173 174
BEX1 -0.05 0.15 0.28 2 -0.35 107 109
mol:GDP -0.11 0.13 -10000 0 -0.25 224 224
NGF (dimer) -0.016 0.14 0.21 42 -0.21 165 207
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.025 0.12 -10000 0 -0.19 172 172
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RAC1/GTP -0.066 0.13 0.18 1 -0.21 220 221
MYD88 0.022 0.004 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.083 0.16 0.2 1 -0.26 227 228
RHOB 0.022 0.017 -10000 0 -0.35 1 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.062 0.068 0.21 91 -10000 0 91
NT3 (dimer) 0.002 0.092 0.28 5 -0.35 32 37
TP53 -0.054 0.087 0.18 7 -10000 0 7
PRDM4 -0.1 0.12 0.18 3 -0.23 220 223
BDNF (dimer) 0.075 0.15 0.25 132 -0.19 76 208
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SORT1 0.023 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.06 0.14 -10000 0 -0.22 222 222
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.065 0.15 -10000 0 -0.24 219 219
RHOC 0.023 0.001 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
MAPK10 -0.14 0.17 0.22 4 -0.34 174 178
DIABLO 0.023 0.003 -10000 0 -10000 0 0
SMPD2 -0.1 0.12 0.18 3 -0.23 217 220
APH1B 0.018 0.039 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.079 0.16 0.2 1 -0.26 220 221
PSEN1 0.022 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.069 0.14 0.21 5 -0.26 186 191
MAPK8 -0.1 0.14 0.23 5 -0.28 155 160
MAPK9 -0.1 0.14 0.23 5 -0.28 154 159
APAF1 0.023 0.002 -10000 0 -10000 0 0
NTF3 0.002 0.092 0.28 5 -0.35 32 37
NTF4 0.032 0.055 0.28 23 -0.35 1 24
NDN -0.15 0.18 -10000 0 -0.35 246 246
RAC1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.056 0.14 -10000 0 -0.21 221 221
p75 CTF/Sortilin/TRAF6/NRIF 0.053 0.019 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.082 0.16 0.2 1 -0.25 227 228
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.001 0.13 -10000 0 -0.18 168 168
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.14 -10000 0 -0.19 172 172
PRKACB 0.019 0.039 -10000 0 -0.35 6 6
proBDNF (dimer)/p75 ECD 0.059 0.065 0.21 83 -10000 0 83
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.018 0.045 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.17 0.16 -10000 0 -0.32 241 241
BAD -0.12 0.15 0.22 4 -0.31 171 175
RIPK2 0.021 0.007 -10000 0 -10000 0 0
NGFR -0.099 0.17 0.28 1 -0.35 174 175
CYCS -0.094 0.11 0.2 7 -0.33 58 65
ADAM17 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.062 0.15 -10000 0 -0.23 209 209
BCL2L11 -0.12 0.15 0.23 2 -0.31 173 175
BDNF (dimer)/p75(NTR) -0.036 0.16 0.21 70 -0.24 174 244
PI3K -0.065 0.14 -10000 0 -0.23 215 215
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.064 0.15 -10000 0 -0.23 219 219
NDNL2 0.022 0.005 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.17 0.21 1 -0.3 224 225
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.064 0.15 -10000 0 -0.23 218 218
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
PLG -0.006 0.11 0.28 9 -0.35 45 54
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.089 0.14 0.16 4 -0.26 208 212
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
NGFRAP1 0.019 0.039 -10000 0 -0.35 6 6
CASP3 -0.12 0.15 0.22 3 -0.3 170 173
E2F1 0.071 0.1 0.28 100 -10000 0 100
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex -0.057 0.14 -10000 0 -0.32 89 89
NGF (dimer)/TRKA -0.023 0.11 0.21 5 -0.25 101 106
MMP7 0.027 0.13 0.28 62 -0.35 36 98
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.055 0.15 -10000 0 -0.22 214 214
MMP3 0.066 0.097 0.28 92 -10000 0 92
APAF-1/Caspase 9 -0.094 0.09 -10000 0 -0.29 54 54
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.094 0.16 -10000 0 -0.36 141 141
PDGF/PDGFRA/CRKL -0.053 0.12 -10000 0 -0.25 139 139
positive regulation of JUN kinase activity -0.002 0.088 -10000 0 -0.19 92 92
CRKL 0.022 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.056 0.12 0.19 1 -0.25 139 140
AP1 -0.28 0.36 -10000 0 -0.81 165 165
mol:IP3 -0.084 0.11 -10000 0 -0.27 129 129
PLCG1 -0.084 0.11 -10000 0 -0.27 129 129
PDGF/PDGFRA/alphaV Integrin -0.054 0.12 -10000 0 -0.25 140 140
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.084 0.11 -10000 0 -0.27 129 129
CAV3 0.018 0.012 0.28 1 -10000 0 1
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
SHC/Grb2/SOS1 -0.001 0.089 -10000 0 -0.19 92 92
PDGF/PDGFRA/Shf -0.057 0.12 -10000 0 -0.25 143 143
FOS -0.28 0.36 0.31 2 -0.8 164 166
JUN -0.043 0.042 -10000 0 -0.3 7 7
oligodendrocyte development -0.054 0.12 -10000 0 -0.25 140 140
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:DAG -0.084 0.11 -10000 0 -0.27 129 129
PDGF/PDGFRA -0.094 0.16 -10000 0 -0.36 141 141
actin cytoskeleton reorganization -0.053 0.12 -10000 0 -0.25 139 139
SRF 0.005 0.02 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
PI3K -0.028 0.1 -10000 0 -0.21 114 114
PDGF/PDGFRA/Crk/C3G -0.035 0.1 -10000 0 -0.2 139 139
JAK1 -0.077 0.1 -10000 0 -0.25 138 138
ELK1/SRF -0.067 0.09 0.16 11 -0.22 120 131
SHB 0.022 0.004 -10000 0 -10000 0 0
SHF 0.018 0.039 -10000 0 -0.35 6 6
CSNK2A1 0.037 0.022 -10000 0 -10000 0 0
GO:0007205 -0.089 0.12 -10000 0 -0.3 130 130
SOS1 0.023 0.003 -10000 0 -10000 0 0
Ras protein signal transduction -0.002 0.088 -10000 0 -0.19 92 92
PDGF/PDGFRA/SHB -0.053 0.12 -10000 0 -0.25 139 139
PDGF/PDGFRA/Caveolin-1 -0.09 0.16 -10000 0 -0.31 174 174
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.088 0.11 0.26 1 -0.27 126 127
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PDGF/PDGFRA/Crk -0.053 0.12 -10000 0 -0.24 139 139
JAK-STAT cascade -0.077 0.1 -10000 0 -0.25 138 138
cell proliferation -0.057 0.12 -10000 0 -0.25 143 143
FOXM1 transcription factor network

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.2 0.4 0.79 74 -0.88 8 82
PLK1 0.18 0.18 0.48 24 -0.66 10 34
BIRC5 0.21 0.16 0.5 17 -0.92 3 20
HSPA1B 0.2 0.4 0.78 83 -0.9 8 91
MAP2K1 0.062 0.084 0.23 56 -10000 0 56
BRCA2 0.2 0.4 0.79 72 -1 8 80
FOXM1 0.22 0.45 0.88 81 -1 9 90
XRCC1 0.2 0.4 0.79 75 -0.92 7 82
FOXM1B/p19 0.001 0.34 0.72 33 -0.99 12 45
Cyclin D1/CDK4 0.2 0.37 0.71 89 -0.82 9 98
CDC2 0.21 0.42 0.82 82 -0.91 10 92
TGFA 0.19 0.37 0.7 93 -0.79 10 103
SKP2 0.21 0.4 0.79 80 -0.89 8 88
CCNE1 0.14 0.14 0.3 217 -10000 0 217
CKS1B 0.2 0.4 0.77 84 -0.86 10 94
RB1 0.16 0.25 0.51 117 -0.66 5 122
FOXM1C/SP1 0.18 0.39 0.75 69 -0.98 9 78
AURKB 0.18 0.24 0.48 18 -0.75 22 40
CENPF 0.26 0.42 0.83 107 -0.89 8 115
CDK4 0.038 0.038 0.16 2 -10000 0 2
MYC 0.14 0.35 0.7 67 -0.86 9 76
CHEK2 0.063 0.086 0.23 68 -10000 0 68
ONECUT1 0.19 0.38 0.73 87 -0.85 9 96
CDKN2A 0.059 0.14 0.24 188 -0.15 22 210
LAMA4 0.14 0.48 0.78 79 -0.94 41 120
FOXM1B/HNF6 0.19 0.4 0.76 79 -0.96 9 88
FOS -0.023 0.61 0.79 74 -1 83 157
SP1 0.022 0.012 -10000 0 -0.15 1 1
CDC25B 0.2 0.4 0.79 77 -0.9 7 84
response to radiation 0.037 0.058 0.16 58 -10000 0 58
CENPB 0.2 0.4 0.79 78 -0.9 7 85
CENPA 0.25 0.42 0.8 105 -0.89 7 112
NEK2 0.27 0.42 0.83 110 -0.89 7 117
HIST1H2BA 0.2 0.4 0.79 74 -0.9 8 82
CCNA2 0.083 0.11 0.3 114 -10000 0 114
EP300 0.021 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.2 0.42 0.83 72 -1 9 81
CCNB2 0.25 0.41 0.8 102 -0.9 7 109
CCNB1 0.21 0.42 0.83 81 -0.92 9 90
ETV5 0.22 0.41 0.8 86 -0.93 8 94
ESR1 0.13 0.5 0.8 78 -0.98 33 111
CCND1 0.19 0.38 0.73 90 -0.83 9 99
GSK3A 0.051 0.068 0.2 32 -10000 0 32
Cyclin A-E1/CDK1-2 0.16 0.15 0.32 204 -10000 0 204
CDK2 0.029 0.026 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.051 0.076 0.19 79 -10000 0 79
FOXM1B/Cbp/p300 0.14 0.36 0.68 48 -0.92 10 58
GAS1 -0.28 0.63 0.8 71 -0.94 157 228
MMP2 0.17 0.45 0.79 75 -1.1 24 99
RB1/FOXM1C 0.18 0.37 0.7 94 -0.88 8 102
CREBBP 0.022 0.005 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.16 0.3 0.38 8 -0.61 108 116
HDAC7 0.023 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.15 0.34 0.57 5 -0.7 96 101
SMAD4 0.023 0.005 -10000 0 -10000 0 0
ID2 -0.15 0.31 0.42 3 -0.63 100 103
AP1 -0.053 0.13 -10000 0 -0.25 162 162
ABCG2 -0.23 0.36 0.43 2 -0.64 181 183
HIF1A -0.032 0.078 0.18 1 -0.19 22 23
TFF3 -0.12 0.36 0.44 39 -0.66 97 136
GATA2 -0.012 0.11 -10000 0 -0.35 50 50
AKT1 -0.047 0.098 -10000 0 -0.22 67 67
response to hypoxia -0.054 0.093 0.16 2 -0.21 89 91
MCL1 -0.15 0.29 0.41 3 -0.63 93 96
NDRG1 -0.14 0.3 0.41 4 -0.62 96 100
SERPINE1 -0.15 0.31 0.42 3 -0.64 95 98
FECH -0.15 0.31 0.42 3 -0.63 100 103
FURIN -0.15 0.31 0.42 3 -0.63 99 102
NCOA2 0.008 0.066 -10000 0 -0.35 17 17
EP300 -0.062 0.14 0.22 2 -0.32 94 96
HMOX1 -0.15 0.31 0.45 4 -0.63 99 103
BHLHE40 -0.15 0.31 0.42 3 -0.63 98 101
BHLHE41 -0.16 0.33 0.42 3 -0.65 116 119
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.009 0.11 0.3 2 -0.28 2 4
ENG -0.002 0.11 0.3 6 -0.26 2 8
JUN 0.018 0.043 -10000 0 -0.35 7 7
RORA -0.16 0.32 0.42 3 -0.65 105 108
ABCB1 -0.25 0.44 -10000 0 -0.97 139 139
TFRC -0.14 0.31 0.47 5 -0.63 94 99
CXCR4 -0.15 0.31 0.42 3 -0.63 102 105
TF -0.15 0.32 0.45 6 -0.65 99 105
CITED2 -0.15 0.32 0.42 3 -0.64 103 106
HIF1A/ARNT -0.14 0.39 0.66 19 -0.73 85 104
LDHA -0.03 0.13 -10000 0 -0.62 15 15
ETS1 -0.15 0.31 0.42 3 -0.63 101 104
PGK1 -0.15 0.31 0.42 3 -0.63 101 104
NOS2 -0.15 0.32 0.42 3 -0.64 99 102
ITGB2 -0.14 0.31 0.46 5 -0.64 97 102
ALDOA -0.15 0.31 0.42 3 -0.64 96 99
Cbp/p300/CITED2 -0.19 0.38 0.47 4 -0.75 116 120
FOS -0.089 0.17 -10000 0 -0.35 160 160
HK2 -0.14 0.31 0.47 4 -0.64 96 100
SP1 -0.007 0.058 -10000 0 -0.13 20 20
GCK -0.18 0.43 -10000 0 -1.2 76 76
HK1 -0.15 0.31 0.42 3 -0.63 99 102
NPM1 -0.15 0.31 0.42 3 -0.64 98 101
EGLN1 -0.15 0.3 0.42 2 -0.63 94 96
CREB1 0.026 0.003 -10000 0 -10000 0 0
PGM1 -0.15 0.31 0.42 3 -0.63 101 104
SMAD3 0.02 0.032 -10000 0 -0.35 4 4
EDN1 -0.14 0.24 -10000 0 -0.6 73 73
IGFBP1 -0.17 0.34 0.46 6 -0.67 109 115
VEGFA -0.13 0.29 0.44 2 -0.6 97 99
HIF1A/JAB1 -0.011 0.061 -10000 0 -0.16 4 4
CP -0.13 0.33 0.46 15 -0.64 96 111
CXCL12 -0.24 0.36 0.42 3 -0.64 180 183
COPS5 0.02 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.031 0.026 -10000 0 -0.24 4 4
BNIP3 -0.15 0.31 0.42 3 -0.64 97 100
EGLN3 -0.15 0.31 0.5 2 -0.63 99 101
CA9 -0.1 0.34 0.45 43 -0.62 98 141
TERT -0.12 0.33 0.45 30 -0.63 92 122
ENO1 -0.15 0.31 0.42 3 -0.64 96 99
PFKL -0.15 0.31 0.42 3 -0.64 97 100
NCOA1 0.021 0.018 -10000 0 -0.35 1 1
ADM -0.14 0.32 0.44 8 -0.63 98 106
ARNT -0.02 0.064 -10000 0 -10000 0 0
HNF4A 0.044 0.1 0.28 73 -0.14 1 74
ADFP -0.16 0.3 0.38 8 -0.61 108 116
SLC2A1 -0.13 0.29 0.44 3 -0.6 95 98
LEP -0.15 0.31 0.44 4 -0.63 99 103
HIF1A/ARNT/Cbp/p300 -0.16 0.34 0.58 5 -0.7 100 105
EPO -0.11 0.27 0.44 1 -0.75 39 40
CREBBP -0.062 0.14 0.2 1 -0.32 94 95
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.34 0.57 5 -0.69 95 100
PFKFB3 -0.15 0.31 0.42 3 -0.64 96 99
NT5E -0.17 0.34 0.42 3 -0.65 122 125
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.065 -10000 0 -0.25 31 31
alphaV beta3 Integrin -0.12 0.15 0.2 1 -0.24 298 299
PTK2 -0.11 0.18 0.27 14 -0.38 118 132
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
PI4KB 0.018 0.01 -10000 0 -10000 0 0
MFGE8 0.021 0.023 -10000 0 -0.35 2 2
SRC 0.022 0.005 -10000 0 -10000 0 0
CDKN1B -0.12 0.19 -10000 0 -0.52 91 91
VEGFA 0.023 0.003 -10000 0 -10000 0 0
ILK -0.1 0.17 -10000 0 -0.49 75 75
ROCK1 0.023 0.004 -10000 0 -10000 0 0
AKT1 -0.099 0.16 -10000 0 -0.46 73 73
PTK2B -0.042 0.085 0.2 14 -0.2 89 103
alphaV/beta3 Integrin/JAM-A -0.099 0.14 0.2 3 -0.22 276 279
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.095 0.2 3 -0.21 89 92
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.016 0.13 -10000 0 -0.24 130 130
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.048 0.11 -10000 0 -0.33 37 37
alphaV/beta3 Integrin/Syndecan-1 0.043 0.13 0.21 133 -0.2 85 218
PI4KA 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.18 -10000 0 -0.26 328 328
PI4 Kinase 0.025 0.015 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
alphaV/beta3 Integrin/Osteopontin 0.04 0.13 0.2 129 -0.2 88 217
RPS6KB1 -0.16 0.14 0.32 1 -0.36 138 139
TLN1 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.26 0.25 -10000 0 -0.48 277 277
GPR124 -0.057 0.15 -10000 0 -0.35 112 112
MAPK1 -0.26 0.25 -10000 0 -0.48 279 279
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Tumstatin -0.012 0.12 0.2 18 -0.23 120 138
cell adhesion -0.006 0.097 0.23 2 -0.22 85 87
ANGPTL3 0.021 0.02 0.28 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.058 -10000 0 -0.21 29 29
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
TGFBR2 0.015 0.051 -10000 0 -0.35 10 10
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
IGF1 -0.046 0.14 -10000 0 -0.35 100 100
RAC1 0.022 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.045 0.13 0.2 1 -0.24 161 162
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.002 0.093 0.2 1 -0.21 86 87
VCL 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.04 0.14 0.2 2 -0.25 153 155
CSF1 0.016 0.05 -10000 0 -0.35 10 10
PIK3C2A -0.1 0.17 -10000 0 -0.49 74 74
PI4 Kinase/Pyk2 -0.096 0.13 -10000 0 -0.23 204 204
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.11 0.21 1 -0.21 101 102
FAK1/Vinculin -0.083 0.15 0.24 13 -0.31 108 121
alphaV beta3/Integrin/ppsTEM5 -0.045 0.14 0.2 1 -0.24 161 162
RHOA 0.022 0.005 -10000 0 -10000 0 0
VTN -0.022 0.12 0.3 3 -0.35 65 68
BCAR1 0.021 0.007 -10000 0 -10000 0 0
FGF2 -0.17 0.19 -10000 0 -0.35 276 276
F11R -0.1 0.12 -10000 0 -0.25 219 219
alphaV/beta3 Integrin/Lactadherin 0.001 0.096 0.2 2 -0.21 88 90
alphaV/beta3 Integrin/TGFBR2 -0.001 0.1 0.2 2 -0.22 90 92
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.039 -10000 0 -0.19 10 10
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.003 0.085 0.19 2 -0.19 88 90
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Pyk2 -0.01 0.095 0.19 1 -0.2 97 98
SDC1 0.095 0.12 0.28 150 -10000 0 150
VAV3 0.026 0.085 0.24 20 -0.18 8 28
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.013 0.11 -10000 0 -0.35 51 51
FAK1/Paxillin -0.084 0.15 0.26 13 -0.31 114 127
cell migration -0.079 0.13 0.23 14 -0.29 104 118
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.082 0.13 -10000 0 -0.22 207 207
SPP1 0.096 0.12 0.28 153 -10000 0 153
KDR 0.001 0.088 -10000 0 -0.35 32 32
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 -0.001 0.12 0.28 19 -0.35 46 65
angiogenesis -0.26 0.26 -10000 0 -0.49 272 272
Rac1/GTP 0.022 0.079 0.23 16 -10000 0 16
EDIL3 -0.048 0.14 -10000 0 -0.35 101 101
cell proliferation -0.001 0.1 0.2 2 -0.22 90 92
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.056 0.046 0.14 15 -0.1 55 70
BUB1B 0.062 0.064 0.12 151 -0.17 14 165
PLK1 0.035 0.033 0.1 45 -0.1 7 52
PLK1S1 0.021 0.026 0.11 9 -0.18 4 13
KIF2A 0.028 0.033 0.15 12 -0.11 1 13
regulation of mitotic centrosome separation 0.035 0.033 0.1 43 -0.1 7 50
GOLGA2 0.022 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.16 0.11 0.24 318 -10000 0 318
WEE1 0.024 0.072 0.17 1 -0.29 21 22
cytokinesis 0.094 0.069 0.18 63 -0.23 8 71
PP2A-alpha B56 0.14 0.11 -10000 0 -0.54 9 9
AURKA 0.046 0.05 0.12 137 -0.2 4 141
PICH/PLK1 0.077 0.078 0.17 198 -10000 0 198
CENPE 0.033 0.035 0.15 10 -0.14 3 13
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.029 0.033 0.15 12 -0.11 1 13
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.021 0.006 -10000 0 -10000 0 0
TPX2 0.089 0.047 0.12 342 -0.24 1 343
PAK1 0.021 0.004 -10000 0 -10000 0 0
SPC24 0.18 0.13 0.28 322 -10000 0 322
FBXW11 0.023 0.004 -10000 0 -10000 0 0
CLSPN 0.075 0.064 0.12 260 -0.23 8 268
GORASP1 0.022 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.012 8 -0.011 11 19
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.016 0.016 0.051 42 -0.051 7 49
G2 phase of mitotic cell cycle 0 0.004 0.014 29 -10000 0 29
STAG2 0.023 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.005 0.087 -10000 0 -0.52 14 14
spindle elongation 0.035 0.033 0.1 43 -0.1 7 50
ODF2 0.022 0.006 -10000 0 -10000 0 0
BUB1 0.14 0.12 -10000 0 -0.58 9 9
TPT1 0.011 0.051 0.11 3 -0.19 29 32
CDC25C 0.12 0.067 0.14 327 -0.28 10 337
CDC25B 0.023 0.009 -10000 0 -10000 0 0
SGOL1 0.056 0.047 0.1 55 -0.14 15 70
RHOA 0.022 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.055 0.064 0.19 78 -0.17 2 80
CDC14B -0.005 0.005 -10000 0 -10000 0 0
CDC20 0.25 0.083 0.28 474 -10000 0 474
PLK1/PBIP1 0.007 0.027 0.098 33 -0.093 5 38
mitosis -0.005 0.007 0.021 4 -0.017 109 113
FBXO5 0.022 0.03 0.13 13 -0.13 3 16
CDC2 0.002 0.003 0.009 81 -0.01 6 87
NDC80 0.042 0.071 0.29 40 -10000 0 40
metaphase plate congression 0.022 0.05 0.14 2 -0.22 18 20
ERCC6L 0.068 0.075 0.18 121 -0.17 1 122
NLP/gamma Tubulin 0.015 0.026 0.067 17 -0.091 16 33
microtubule cytoskeleton organization 0.011 0.05 0.11 3 -0.18 29 32
G2/M transition DNA damage checkpoint -0.001 0.002 0.013 6 -10000 0 6
PPP1R12A 0.023 0.016 -10000 0 -0.35 1 1
interphase -0.001 0.002 0.013 6 -10000 0 6
PLK1/PRC1-2 0.19 0.081 0.22 457 -0.16 1 458
GRASP65/GM130/RAB1/GTP/PLK1 0.056 0.03 -10000 0 -10000 0 0
RAB1A 0.023 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.027 0.029 0.091 48 -0.089 3 51
mitotic prometaphase 0.001 0.004 0.02 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.069 0.18 2 -0.36 9 11
microtubule-based process 0.19 0.068 0.22 472 -0.17 1 473
Golgi organization 0.035 0.033 0.1 43 -0.1 7 50
Cohesin/SA2 0.041 0.027 0.11 9 -0.11 2 11
PPP1CB/MYPT1 0.033 0.015 -10000 0 -0.25 1 1
KIF20A 0.25 0.083 0.28 475 -10000 0 475
APC/C/CDC20 0.19 0.07 0.22 471 -0.14 2 473
PPP2R1A 0.023 0.004 -10000 0 -10000 0 0
chromosome segregation 0.007 0.026 0.097 33 -0.092 5 38
PRC1 0.034 0.053 0.28 23 -10000 0 23
ECT2 0.052 0.079 0.25 65 -10000 0 65
C13orf34 0.027 0.028 0.087 45 -0.089 4 49
NUDC 0.022 0.05 0.14 2 -0.22 18 20
regulation of attachment of spindle microtubules to kinetochore 0.061 0.063 0.12 151 -0.17 14 165
spindle assembly 0.024 0.027 0.084 32 -0.09 7 39
spindle stabilization 0.021 0.026 0.11 9 -0.18 4 13
APC/C/HCDH1 0.018 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.19 0.068 0.22 472 -0.17 1 473
CCNB1 0.068 0.098 0.28 93 -10000 0 93
PPP1CB 0.023 0.005 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.023 0.069 0.2 2 -0.31 16 18
TUBG1 0.011 0.048 0.12 1 -0.17 30 31
G2/M transition of mitotic cell cycle 0.022 0.038 0.2 5 -0.18 1 6
MLF1IP 0.003 0.027 0.11 33 -10000 0 33
INCENP 0.023 0.004 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.042 0.15 -10000 0 -0.54 31 31
IHH -0.041 0.21 0.31 58 -0.39 123 181
SHH Np/Cholesterol/GAS1 -0.083 0.1 0.23 1 -0.19 261 262
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.083 0.1 0.18 261 -0.23 1 262
SMO/beta Arrestin2 -0.038 0.16 -10000 0 -0.32 95 95
SMO -0.056 0.15 -10000 0 -0.32 110 110
AKT1 -0.018 0.12 -10000 0 -0.48 21 21
ARRB2 0.021 0.006 -10000 0 -10000 0 0
BOC 0.011 0.065 -10000 0 -0.35 17 17
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
heart looping -0.054 0.15 -10000 0 -0.32 110 110
STIL -0.01 0.12 0.22 13 -0.28 28 41
DHH N/PTCH2 -0.004 0.099 -10000 0 -0.26 69 69
DHH N/PTCH1 -0.042 0.13 -10000 0 -0.24 130 130
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DHH -0.008 0.1 -10000 0 -0.35 44 44
PTHLH -0.061 0.19 -10000 0 -0.59 31 31
determination of left/right symmetry -0.054 0.15 -10000 0 -0.32 110 110
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
skeletal system development -0.06 0.19 -10000 0 -0.59 31 31
IHH N/Hhip -0.004 0.14 0.22 73 -0.23 122 195
DHH N/Hhip 0.016 0.091 0.21 26 -0.24 49 75
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.054 0.15 -10000 0 -0.32 110 110
pancreas development 0.032 0.068 0.28 28 -0.35 5 33
HHAT 0.017 0.033 -10000 0 -0.35 4 4
PI3K 0.027 0.029 -10000 0 -0.25 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.2 0.18 -10000 0 -0.35 321 321
somite specification -0.054 0.15 -10000 0 -0.32 110 110
SHH Np/Cholesterol/PTCH1 -0.022 0.11 0.24 5 -0.28 30 35
SHH Np/Cholesterol/PTCH2 0.015 0.059 0.22 6 -0.2 28 34
SHH Np/Cholesterol/Megalin 0.079 0.094 0.2 173 -0.18 6 179
SHH 0.004 0.058 0.13 64 -0.25 6 70
catabolic process -0.036 0.12 -10000 0 -0.25 128 128
SMO/Vitamin D3 -0.014 0.15 0.3 8 -0.26 104 112
SHH Np/Cholesterol/Hhip 0.03 0.059 0.21 33 -0.18 11 44
LRP2 0.11 0.12 0.28 184 -10000 0 184
receptor-mediated endocytosis -0.008 0.14 0.23 11 -0.33 29 40
SHH Np/Cholesterol/BOC 0.017 0.054 0.22 6 -0.19 22 28
SHH Np/Cholesterol/CDO 0.006 0.069 0.22 6 -0.19 47 53
mesenchymal cell differentiation -0.03 0.059 0.18 11 -0.2 33 44
mol:Vitamin D3 0 0.13 0.29 16 -0.29 29 45
IHH N/PTCH2 -0.021 0.15 0.2 57 -0.25 134 191
CDON -0.014 0.11 -10000 0 -0.35 52 52
IHH N/PTCH1 -0.025 0.15 -10000 0 -0.25 128 128
Megalin/LRPAP1 0.09 0.084 0.21 177 -10000 0 177
PTCH2 0.002 0.084 -10000 0 -0.35 29 29
SHH Np/Cholesterol 0.008 0.022 -10000 0 -0.18 6 6
PTCH1 -0.037 0.13 -10000 0 -0.25 128 128
HHIP 0.032 0.068 0.28 28 -0.35 5 33
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.031 0.013 0.21 1 -10000 0 1
VLDLR 0.021 0.023 -10000 0 -0.35 2 2
CRKL 0.022 0.005 -10000 0 -10000 0 0
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
ITGA3 0.021 0.017 -10000 0 -0.35 1 1
RELN/VLDLR/Fyn -0.039 0.12 0.2 6 -0.21 174 180
MAPK8IP1/MKK7/MAP3K11/JNK1 0.045 0.04 -10000 0 -0.18 5 5
AKT1 -0.055 0.093 0.15 3 -0.19 168 171
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
RELN/LRP8/DAB1 -0.03 0.12 0.21 20 -0.19 180 200
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
RELN/LRP8/DAB1/Fyn -0.02 0.12 0.21 20 -0.18 175 195
DAB1/alpha3/beta1 Integrin -0.025 0.1 -10000 0 -0.18 159 159
long-term memory -0.09 0.15 0.29 4 -0.22 280 284
DAB1/LIS1 -0.02 0.11 -10000 0 -0.18 170 170
DAB1/CRLK/C3G -0.028 0.1 -10000 0 -0.18 161 161
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DAB1/NCK2 -0.017 0.12 -10000 0 -0.18 173 173
ARHGEF2 0.018 0.01 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.12 0.18 0.28 1 -0.35 198 199
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
RELN -0.1 0.18 0.28 7 -0.35 182 189
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RELN/LRP8/Fyn -0.036 0.12 0.22 9 -0.21 175 184
GRIN2A/RELN/LRP8/DAB1/Fyn -0.092 0.15 -10000 0 -0.22 285 285
MAPK8 0.019 0.036 -10000 0 -0.35 5 5
RELN/VLDLR/DAB1 -0.033 0.11 0.2 16 -0.19 178 194
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.072 0.099 0.17 11 -0.2 189 200
RELN/LRP8 -0.039 0.12 0.23 8 -0.21 179 187
GRIN2B/RELN/LRP8/DAB1/Fyn -0.01 0.13 0.36 6 -0.18 174 180
PI3K 0.027 0.029 -10000 0 -0.25 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.015 -10000 0 -0.25 1 1
RAP1A -0.058 0.092 0.3 4 -0.31 1 5
PAFAH1B1 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.02 0.28 1 -0.35 1 2
CRLK/C3G 0.031 0.01 -10000 0 -10000 0 0
GRIN2B 0.03 0.052 0.29 21 -10000 0 21
NCK2 0.023 0.002 -10000 0 -10000 0 0
neuron differentiation -0.027 0.092 -10000 0 -0.31 12 12
neuron adhesion -0.054 0.099 0.31 10 -0.3 2 12
LRP8 0.025 0.026 0.29 5 -10000 0 5
GSK3B -0.057 0.087 0.14 2 -0.24 8 10
RELN/VLDLR/DAB1/Fyn -0.023 0.11 0.2 16 -0.18 172 188
MAP3K11 0.022 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.053 0.1 0.16 4 -0.2 174 178
CDK5 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.08 0.66 4 -0.31 16 20
neuron migration -0.073 0.13 0.26 11 -0.26 159 170
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.028 0.092 -10000 0 -0.31 12 12
RELN/VLDLR -0.027 0.12 0.21 7 -0.19 176 183
Cellular roles of Anthrax toxin

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
ANTXR1 0.01 0.069 -10000 0 -0.35 19 19
ANTXR2 -0.093 0.17 -10000 0 -0.35 166 166
negative regulation of myeloid dendritic cell antigen processing and presentation -0.017 0.024 -10000 0 -0.051 166 166
monocyte activation -0.006 0.12 -10000 0 -0.37 43 43
MAP2K2 -0.045 0.17 -10000 0 -0.6 45 45
MAP2K1 -0.018 0.022 0.12 1 -0.077 13 14
MAP2K7 -0.017 0.022 0.12 1 -0.077 12 13
MAP2K6 -0.015 0.028 0.19 3 -0.079 11 14
CYAA -0.062 0.085 -10000 0 -0.18 166 166
MAP2K4 -0.017 0.023 -10000 0 -0.083 15 15
IL1B -0.017 0.045 0.17 11 -0.14 25 36
Channel -0.042 0.11 -10000 0 -0.2 166 166
NLRP1 -0.024 0.042 -10000 0 -0.16 34 34
CALM1 0.022 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.065 -10000 0 -0.46 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.017 0.024 0.051 166 -10000 0 166
MAPK3 -0.018 0.021 -10000 0 -0.075 14 14
MAPK1 -0.018 0.021 -10000 0 -0.077 11 11
PGR -0.062 0.081 -10000 0 -0.19 149 149
PA/Cellular Receptors -0.047 0.12 -10000 0 -0.22 166 166
apoptosis -0.017 0.024 -10000 0 -0.051 166 166
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.04 0.1 -10000 0 -0.19 166 166
macrophage activation -0.018 0.026 0.13 6 -10000 0 6
TNF 0.053 0.088 0.28 66 -0.35 2 68
VCAM1 -0.006 0.12 -10000 0 -0.38 42 42
platelet activation -0.016 0.065 -10000 0 -0.46 9 9
MAPKKK cascade 0.015 0.029 0.09 20 -0.078 10 30
IL18 -0.018 0.029 -10000 0 -0.13 16 16
negative regulation of macrophage activation -0.017 0.024 -10000 0 -0.051 166 166
LEF -0.017 0.024 -10000 0 -0.052 166 166
CASP1 -0.018 0.033 -10000 0 -0.11 40 40
mol:cAMP -0.016 0.065 -10000 0 -0.46 9 9
necrosis -0.017 0.024 -10000 0 -0.051 166 166
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.038 0.1 -10000 0 -0.18 166 166
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.071 -10000 0 -0.35 20 20
mol:S1P -0.009 0.013 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.083 0.12 -10000 0 -0.24 164 164
GNAO1 -0.08 0.16 -10000 0 -0.36 124 124
S1P/S1P3/G12/G13 0.007 0.053 -10000 0 -0.2 16 16
AKT1 -0.065 0.17 -10000 0 -0.68 31 31
AKT3 -0.39 0.5 -10000 0 -1 204 204
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.071 -10000 0 -0.35 20 20
GNAI2 0 0.031 -10000 0 -10000 0 0
GNAI3 0.002 0.029 -10000 0 -10000 0 0
GNAI1 -0.003 0.052 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.011 0.071 -10000 0 -0.36 17 17
S1PR2 0.022 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.19 -10000 0 -0.33 228 228
MAPK3 -0.13 0.18 -10000 0 -0.34 188 188
MAPK1 -0.13 0.18 -10000 0 -0.34 188 188
JAK2 -0.14 0.19 -10000 0 -0.36 196 196
CXCR4 -0.14 0.18 -10000 0 -0.34 196 196
FLT1 -0.003 0.036 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC -0.13 0.18 -10000 0 -0.34 188 188
S1P/S1P3/Gi -0.14 0.19 -10000 0 -0.33 235 235
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.13 0.18 -10000 0 -0.33 206 206
VEGFA -0.003 0.035 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.084 0.13 -10000 0 -0.26 151 151
VEGFR1 homodimer/VEGFA homodimer -0.002 0.053 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.024 0.094 -10000 0 -0.26 61 61
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ -0.009 0.068 -10000 0 -0.35 17 17
G12/G13 0.031 0.01 -10000 0 -10000 0 0
GNA14 -0.01 0.1 -10000 0 -0.35 45 45
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
Rac1/GTP -0.13 0.18 -10000 0 -0.33 202 202
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.023 -10000 0 -0.35 2 2
LAT2 -0.063 0.12 -10000 0 -0.25 121 121
AP1 -0.086 0.17 -10000 0 -0.38 81 81
mol:PIP3 -0.049 0.17 0.33 14 -0.29 117 131
IKBKB -0.019 0.12 0.24 32 -0.22 51 83
AKT1 -0.003 0.16 0.31 71 -0.28 26 97
IKBKG -0.029 0.11 0.26 18 -0.22 53 71
MS4A2 -0.096 0.16 -10000 0 -0.34 165 165
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
MAP3K1 -0.027 0.14 0.25 31 -0.3 43 74
mol:Ca2+ -0.034 0.14 0.22 53 -0.23 114 167
LYN 0.022 0.01 -10000 0 -10000 0 0
CBLB -0.063 0.12 -10000 0 -0.25 124 124
SHC1 0.019 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.011 0.099 -10000 0 -0.19 121 121
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
PLD2 -0.015 0.16 0.28 92 -0.24 61 153
PTPN13 -0.078 0.16 0.32 1 -0.43 40 41
PTPN11 0.018 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.02 0.14 0.34 17 -0.27 31 48
SYK 0.024 0.014 0.28 1 -10000 0 1
GRB2 0.022 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.07 0.14 -10000 0 -0.29 122 122
LAT -0.062 0.12 -10000 0 -0.25 119 119
PAK2 -0.03 0.15 0.25 34 -0.32 46 80
NFATC2 -0.057 0.14 -10000 0 -0.49 46 46
HRAS -0.042 0.15 0.23 12 -0.27 115 127
GAB2 0.02 0.032 -10000 0 -0.35 4 4
PLA2G1B -0.011 0.14 -10000 0 -0.88 13 13
Fc epsilon R1 -0.052 0.13 0.2 1 -0.23 176 177
Antigen/IgE/Fc epsilon R1 -0.044 0.12 0.19 1 -0.2 175 176
mol:GDP -0.062 0.13 -10000 0 -0.36 44 44
JUN 0.018 0.042 -10000 0 -0.35 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
FOS -0.089 0.17 -10000 0 -0.35 160 160
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.062 0.12 -10000 0 -0.26 127 127
CHUK -0.029 0.12 0.31 14 -0.22 53 67
KLRG1 -0.052 0.1 0.15 1 -0.21 122 123
VAV1 -0.059 0.12 -10000 0 -0.25 113 113
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.061 0.12 -10000 0 -0.25 119 119
negative regulation of mast cell degranulation -0.034 0.11 0.23 1 -0.29 40 41
BTK -0.063 0.13 -10000 0 -0.37 43 43
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.067 0.13 -10000 0 -0.24 161 161
GAB2/PI3K/SHP2 -0.062 0.079 -10000 0 -0.23 62 62
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.054 0.11 -10000 0 -0.21 144 144
RAF1 -0.008 0.16 -10000 0 -0.96 13 13
Fc epsilon R1/FcgammaRIIB/SHIP -0.031 0.12 -10000 0 -0.2 172 172
FCER1G 0.022 0.025 0.29 2 -10000 0 2
FCER1A -0.037 0.13 -10000 0 -0.36 74 74
Antigen/IgE/Fc epsilon R1/Fyn -0.034 0.11 0.2 1 -0.19 173 174
MAPK3 -0.011 0.14 -10000 0 -0.89 13 13
MAPK1 -0.014 0.15 -10000 0 -0.91 13 13
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.054 0.21 -10000 0 -0.59 56 56
DUSP1 -0.062 0.16 -10000 0 -0.35 122 122
NF-kappa-B/RelA -0.016 0.068 0.14 2 -0.14 42 44
actin cytoskeleton reorganization -0.06 0.16 -10000 0 -0.44 30 30
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.043 0.14 -10000 0 -0.33 43 43
FER -0.062 0.12 -10000 0 -0.25 121 121
RELA 0.022 0.004 -10000 0 -10000 0 0
ITK -0.02 0.059 -10000 0 -0.32 14 14
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG1 -0.051 0.15 0.26 7 -0.28 112 119
cytokine secretion -0.019 0.042 -10000 0 -10000 0 0
SPHK1 -0.061 0.12 -10000 0 -0.25 119 119
PTK2 -0.062 0.16 -10000 0 -0.47 29 29
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.07 0.14 0.23 1 -0.29 123 124
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.05 0.17 0.32 14 -0.35 57 71
MAP2K2 -0.013 0.14 -10000 0 -0.89 13 13
MAP2K1 -0.013 0.14 -10000 0 -0.89 13 13
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.039 0.095 0.2 3 -0.26 43 46
MAP2K4 -0.087 0.32 -10000 0 -0.91 67 67
Fc epsilon R1/FcgammaRIIB -0.039 0.13 0.21 1 -0.21 175 176
mol:Choline -0.015 0.16 0.28 92 -0.24 61 153
SHC/Grb2/SOS1 -0.042 0.13 -10000 0 -0.25 109 109
FYN 0.023 0.004 -10000 0 -10000 0 0
DOK1 0.023 0.003 -10000 0 -10000 0 0
PXN -0.059 0.15 0.3 1 -0.43 30 31
HCLS1 -0.062 0.12 -10000 0 -0.25 121 121
PRKCB -0.044 0.14 0.3 13 -0.29 59 72
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.033 0.12 0.24 1 -0.29 40 41
LCP2 0.023 0.012 0.28 1 -10000 0 1
PLA2G4A -0.069 0.12 -10000 0 -0.26 131 131
RASA1 0.019 0.036 -10000 0 -0.35 5 5
mol:Phosphatidic acid -0.015 0.16 0.28 92 -0.24 61 153
IKK complex -0.009 0.11 0.25 32 -0.18 33 65
WIPF1 0.021 0.023 -10000 0 -0.35 2 2
Nongenotropic Androgen signaling

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
PTK2 -0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0 0.089 -10000 0 -0.19 96 96
regulation of S phase of mitotic cell cycle -0.014 0.072 -10000 0 -0.2 65 65
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
HRAS 0.021 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.019 -10000 0 -0.2 4 4
PELP1 0.02 0.008 -10000 0 -10000 0 0
AKT1 -0.005 0.002 -10000 0 -10000 0 0
MAP2K1 -0.061 0.086 0.19 14 -0.26 28 42
T-DHT/AR -0.032 0.095 -10000 0 -0.24 90 90
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 162 162
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
mol:GDP -0.054 0.11 -10000 0 -0.3 87 87
cell proliferation -0.15 0.2 0.28 2 -0.41 170 172
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FOS -0.24 0.34 -10000 0 -0.74 166 166
mol:Ca2+ -0.02 0.029 -10000 0 -0.062 148 148
MAPK3 -0.11 0.15 0.26 3 -0.3 157 160
MAPK1 -0.083 0.14 0.2 1 -0.36 57 58
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 162 162
cAMP biosynthetic process 0.005 0.025 -10000 0 -0.16 4 4
GNG2 0.017 0.049 0.28 1 -0.35 9 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 162 162
HRAS/GTP -0.018 0.082 -10000 0 -0.18 77 77
actin cytoskeleton reorganization 0.027 0.023 -10000 0 -0.16 5 5
SRC 0.021 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 162 162
PI3K 0.024 0.025 -10000 0 -0.2 5 5
apoptosis 0.14 0.2 0.42 166 -0.26 1 167
T-DHT/AR/PELP1 -0.019 0.085 -10000 0 -0.21 88 88
HRAS/GDP -0.043 0.11 -10000 0 -0.28 87 87
CREB1 -0.15 0.22 0.27 1 -0.45 166 167
RAC1-CDC42/GTP 0.034 0.026 -10000 0 -0.16 5 5
AR -0.042 0.14 -10000 0 -0.35 90 90
GNB1 0.022 0.004 -10000 0 -10000 0 0
RAF1 -0.05 0.08 0.2 17 -0.24 26 43
RAC1-CDC42/GDP -0.022 0.12 -10000 0 -0.28 81 81
T-DHT/AR/PELP1/Src -0.011 0.081 -10000 0 -0.19 77 77
MAP2K2 -0.061 0.083 0.18 11 -0.27 27 38
T-DHT/AR/PELP1/Src/PI3K -0.014 0.073 -10000 0 -0.21 65 65
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
SHBG 0.019 0.033 -10000 0 -0.35 4 4
Gi family/GNB1/GNG2/GDP -0.098 0.17 -10000 0 -0.34 141 141
mol:T-DHT -0.001 0.001 0.002 1 -0.002 98 99
RAC1 0.022 0.005 -10000 0 -10000 0 0
GNRH1 -0.007 0.02 -10000 0 -0.24 4 4
Gi family/GTP -0.06 0.1 -10000 0 -0.21 137 137
CDC42 0.022 0.005 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.002 0.053 0.21 1 -10000 0 1
BIRC5 0.22 0.11 0.28 410 -10000 0 410
NFKBIA -0.006 0.055 0.21 15 -10000 0 15
CPEB1 -0.14 0.18 -10000 0 -0.35 227 227
AKT1 -0.007 0.051 0.3 4 -10000 0 4
NDEL1 0.021 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0 0.045 -10000 0 -0.16 1 1
NDEL1/TACC3 0.037 0.091 0.22 73 -10000 0 73
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GSK3B -0.022 0.024 -10000 0 -10000 0 0
PAK1/Aurora A 0.002 0.052 0.21 1 -10000 0 1
MDM2 0.023 0.002 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.097 0.075 0.12 428 -10000 0 428
TP53 0 0.051 -10000 0 -0.23 9 9
DLG7 -0.004 0.045 0.13 29 -10000 0 29
AURKAIP1 0.022 0.004 -10000 0 -10000 0 0
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.097 0.24 73 -10000 0 73
G2/M transition of mitotic cell cycle 0 0.044 -10000 0 -0.16 1 1
AURKA 0.001 0.062 0.18 29 -10000 0 29
AURKB 0.12 0.074 0.16 374 -0.29 3 377
CDC25B 0.004 0.044 0.21 1 -0.17 2 3
G2/M transition checkpoint -0.008 0.032 0.12 2 -0.13 3 5
mRNA polyadenylation -0.077 0.1 -10000 0 -0.19 208 208
Aurora A/CPEB -0.078 0.1 -10000 0 -0.2 208 208
Aurora A/TACC1/TRAP/chTOG -0.018 0.085 -10000 0 -0.2 51 51
BRCA1 0.022 0.006 -10000 0 -10000 0 0
centrosome duplication 0.002 0.052 0.21 1 -10000 0 1
regulation of centrosome cycle 0.036 0.089 0.22 73 -10000 0 73
spindle assembly -0.018 0.083 -10000 0 -0.2 51 51
TDRD7 0.022 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.13 0.095 0.23 146 -0.18 4 150
CENPA 0.13 0.072 0.17 373 -0.28 3 376
Aurora A/PP2A 0.002 0.053 0.21 1 -0.18 1 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.003 0.051 0.25 9 -10000 0 9
negative regulation of DNA binding 0 0.052 -10000 0 -0.23 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.01 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
Ajuba/Aurora A -0.008 0.032 0.12 2 -0.13 3 5
mitotic prometaphase -0.023 0.031 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.062 0.18 29 -10000 0 29
TACC1 -0.037 0.13 -10000 0 -0.35 83 83
TACC3 0.084 0.11 0.29 126 -10000 0 126
Aurora A/Antizyme1 0.005 0.053 -10000 0 -10000 0 0
Aurora A/RasGAP 0.001 0.056 0.21 1 -0.23 5 6
OAZ1 0.021 0.006 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.021 0.024 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.042 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.097 0.075 0.12 428 -10000 0 428
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.077 0.074 0.24 60 -10000 0 60
PAK1 0.022 0.004 -10000 0 -10000 0 0
CKAP5 0.022 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.005 0.013 0.29 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.019 0.21 5 -10000 0 5
STXBP1 -0.004 0.095 -10000 0 -0.35 38 38
ACh/CHRNA1 0.044 0.11 0.18 188 -0.13 12 200
RAB3GAP2/RIMS1/UNC13B 0.037 0.024 0.21 4 -10000 0 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 0.023 0.026 0.29 5 -10000 0 5
mol:ACh -0.046 0.058 0.087 21 -0.1 241 262
RAB3GAP2 0.02 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.044 0.095 -10000 0 -0.24 40 40
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.043 0.11 0.18 188 -0.13 12 200
UNC13B 0.022 0.005 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.28 191 -10000 0 191
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.073 0.11 -10000 0 -0.25 127 127
SNAP25 -0.1 0.12 -10000 0 -0.23 243 243
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 -0.058 0.15 -10000 0 -0.35 117 117
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.003 0.058 0.22 1 -0.2 38 39
STX1A/SNAP25 fragment 1/VAMP2 -0.044 0.095 -10000 0 -0.24 40 40
Wnt signaling

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
Noncanonical Wnts/FZD -0.046 0.14 -10000 0 -0.25 131 131
FZD6 0.02 0.018 -10000 0 -0.35 1 1
WNT6 0.01 0.11 0.28 23 -0.35 34 57
WNT4 -0.065 0.16 -10000 0 -0.35 126 126
FZD3 0.02 0.008 -10000 0 -10000 0 0
WNT5A 0.011 0.065 -10000 0 -0.35 17 17
WNT11 0.037 0.098 0.28 49 -0.35 14 63
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.079 0.28 0.35 4 -0.81 66 70
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 -0.005 0.1 -10000 0 -0.28 63 63
ATF2/c-Jun -0.025 0.1 -10000 0 -0.37 21 21
MAPK11 -0.005 0.1 -10000 0 -0.29 57 57
MITF -0.04 0.15 -10000 0 -0.34 91 91
MAPKAPK5 -0.019 0.12 -10000 0 -0.33 63 63
KRT8 -0.009 0.12 0.24 2 -0.33 62 64
MAPKAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.01 0.15 -10000 0 -0.39 64 64
CEBPB -0.015 0.11 0.25 1 -0.33 57 58
SLC9A1 -0.018 0.11 -10000 0 -0.33 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.02 0.12 -10000 0 -0.33 65 65
p38alpha-beta/MNK1 0.008 0.12 -10000 0 -0.32 60 60
JUN -0.026 0.1 -10000 0 -0.37 21 21
PPARGC1A -0.073 0.17 -10000 0 -0.32 144 144
USF1 -0.017 0.11 0.27 5 -0.33 58 63
RAB5/GDP/GDI1 -0.013 0.091 -10000 0 -0.24 60 60
NOS2 -0.02 0.15 -10000 0 -0.63 15 15
DDIT3 -0.019 0.12 -10000 0 -0.33 64 64
RAB5A 0.022 0.004 -10000 0 -10000 0 0
HSPB1 -0.019 0.097 0.28 6 -0.27 60 66
p38alpha-beta/HBP1 0.006 0.12 -10000 0 -0.31 63 63
CREB1 -0.021 0.13 -10000 0 -0.36 62 62
RAB5/GDP 0.017 0.003 -10000 0 -10000 0 0
EIF4E -0.018 0.1 0.19 2 -0.31 50 52
RPS6KA4 -0.019 0.12 -10000 0 -0.33 63 63
PLA2G4A -0.025 0.11 0.22 4 -0.31 62 66
GDI1 -0.018 0.12 -10000 0 -0.33 62 62
TP53 -0.029 0.13 -10000 0 -0.41 54 54
RPS6KA5 -0.02 0.12 -10000 0 -0.33 64 64
ESR1 -0.042 0.15 -10000 0 -0.35 90 90
HBP1 0.022 0.004 -10000 0 -10000 0 0
MEF2C -0.04 0.15 -10000 0 -0.35 89 89
MEF2A -0.022 0.12 -10000 0 -0.34 68 68
EIF4EBP1 -0.022 0.13 -10000 0 -0.37 61 61
KRT19 -0.017 0.12 0.21 1 -0.33 61 62
ELK4 -0.017 0.11 0.27 6 -0.32 60 66
ATF6 -0.017 0.11 0.27 5 -0.33 58 63
ATF1 -0.021 0.12 -10000 0 -0.36 62 62
p38alpha-beta/MAPKAPK2 0 0.12 -10000 0 -0.31 63 63
p38alpha-beta/MAPKAPK3 0.007 0.12 -10000 0 -0.31 62 62
IGF1 pathway

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
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTK2 0.021 0.007 -10000 0 -10000 0 0
CRKL -0.055 0.095 0.16 1 -0.24 101 102
GRB2/SOS1/SHC 0.035 0.021 -10000 0 -10000 0 0
HRAS 0.022 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.036 0.11 -10000 0 -0.24 103 103
IGF-1R heterotetramer/IGF1/PTP1B -0.008 0.11 -10000 0 -0.23 97 97
AKT1 -0.039 0.099 0.16 33 -0.31 32 65
BAD -0.04 0.093 0.15 32 -0.29 32 64
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.054 0.095 0.16 1 -0.24 96 97
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.032 0.11 0.2 2 -0.24 108 110
RAF1 -0.027 0.1 0.28 2 -0.4 14 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.01 0.12 -10000 0 -0.23 102 102
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.033 0.12 -10000 0 -0.23 130 130
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RPS6KB1 -0.04 0.097 0.16 31 -0.31 32 63
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.018 0.095 0.28 5 -0.34 8 13
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
HRAS/GTP -0.02 0.088 -10000 0 -0.21 76 76
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.014 0.09 -10000 0 -0.19 76 76
IGF-1R heterotetramer -0.01 0.084 -10000 0 -0.4 19 19
IGF-1R heterotetramer/IGF1/IRS/Nck -0.021 0.12 -10000 0 -0.24 108 108
Crk/p130 Cas/Paxillin -0.013 0.11 0.2 1 -0.22 98 99
IGF1R -0.01 0.084 -10000 0 -0.4 19 19
IGF1 -0.055 0.16 -10000 0 -0.38 99 99
IRS2/Crk -0.055 0.12 0.15 1 -0.23 147 148
PI3K -0.01 0.11 -10000 0 -0.23 93 93
apoptosis 0.034 0.083 0.26 30 -0.22 2 32
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
PRKCD -0.056 0.13 -10000 0 -0.32 102 102
RAF1/14-3-3 E -0.011 0.1 0.28 2 -0.36 13 15
BAD/14-3-3 -0.036 0.087 0.22 2 -0.28 30 32
PRKCZ -0.037 0.099 0.16 36 -0.31 32 68
Crk/p130 Cas/Paxillin/FAK1 -0.013 0.09 -10000 0 -0.29 30 30
PTPN1 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.058 0.14 -10000 0 -0.33 106 106
BCAR1 0.021 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.006 0.093 -10000 0 -0.2 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.032 0.11 -10000 0 -0.23 108 108
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 -0.058 0.096 0.16 1 -0.23 108 109
IRS1 -0.04 0.11 0.12 7 -0.25 105 112
IRS2 -0.076 0.12 0.16 1 -0.24 149 150
IGF-1R heterotetramer/IGF1 -0.037 0.14 -10000 0 -0.3 107 107
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDPK1 -0.04 0.1 0.17 33 -0.23 79 112
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKD1 -0.068 0.15 -10000 0 -0.33 110 110
SHC1 0.019 0.009 -10000 0 -10000 0 0
LPA4-mediated signaling 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
ADCY4 -0.016 0.037 -10000 0 -0.2 20 20
ADCY5 -0.045 0.076 -10000 0 -0.2 101 101
ADCY6 -0.009 0.002 -10000 0 -10000 0 0
ADCY7 -0.008 0.003 -10000 0 -10000 0 0
ADCY1 -0.014 0.038 0.24 1 -0.2 18 19
ADCY2 -0.11 0.098 -10000 0 -0.2 280 280
ADCY3 -0.01 0.012 -10000 0 -0.2 2 2
ADCY8 -0.009 0.016 0.24 2 -10000 0 2
PRKCE -0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.035 0.067 -10000 0 -0.2 73 73
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.052 0.094 0.21 20 -0.17 105 125
TCGA08_p53

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
CDKN2A 0.042 0.062 0.11 216 -10000 0 216
TP53 0.003 0.047 -10000 0 -0.15 43 43
Senescence 0.003 0.047 -10000 0 -0.15 43 43
Apoptosis 0.003 0.047 -10000 0 -0.15 43 43
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.033 0.047 0.27 5 -0.2 7 12
MDM4 0.019 0.009 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.057 0.081 -10000 0 -0.23 39 39
NT3 (dimer)/TRKC -0.11 0.15 0.21 3 -0.26 254 257
NT3 (dimer)/TRKB -0.068 0.15 0.2 7 -0.24 212 219
SHC/Grb2/SOS1/GAB1/PI3K 0.011 0.03 -10000 0 -0.19 4 4
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
BDNF 0.062 0.094 0.28 84 -10000 0 84
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DYNLT1 0.023 0.004 -10000 0 -10000 0 0
NTRK1 0.019 0.044 0.28 7 -0.35 4 11
NTRK2 -0.01 0.12 0.28 8 -0.35 52 60
NTRK3 -0.15 0.18 -10000 0 -0.35 251 251
NT-4/5 (dimer)/TRKB -0.055 0.14 0.2 20 -0.23 202 222
neuron apoptosis 0.11 0.19 0.39 127 -10000 0 127
SHC 2-3/Grb2 -0.12 0.21 -10000 0 -0.42 128 128
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.15 0.24 -10000 0 -0.5 140 140
SHC3 -0.092 0.18 0.22 1 -0.41 92 93
STAT3 (dimer) 0.026 0.014 0.22 2 -10000 0 2
NT3 (dimer)/TRKA -0.041 0.12 0.2 6 -0.22 156 162
RIN/GDP -0.043 0.1 0.24 3 -0.24 38 41
GIPC1 0.022 0.006 -10000 0 -10000 0 0
KRAS 0.023 0.014 0.33 1 -10000 0 1
DNAJA3 -0.099 0.15 0.22 2 -0.28 182 184
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.013 0.027 0.36 3 -10000 0 3
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.032 0.055 0.28 23 -0.35 1 24
SHC/GRB2/SOS1 0.035 0.021 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.014 0.1 0.2 5 -0.21 108 113
TRKA/NEDD4-2 0.026 0.035 0.21 6 -0.25 5 11
ELMO1 0.02 0.032 -10000 0 -0.35 4 4
RhoG/GTP/ELMO1/DOCK1 0.024 0.036 -10000 0 -0.22 10 10
NGF -0.056 0.15 -10000 0 -0.35 113 113
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK1 0.017 0.042 -10000 0 -0.35 7 7
GAB2 0.02 0.032 -10000 0 -0.35 4 4
RIT2 0.017 0.005 -10000 0 -10000 0 0
RIT1 0.018 0.01 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
DNM1 0.018 0.039 -10000 0 -0.35 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.086 0.16 0.18 1 -0.28 180 181
mol:GDP -0.067 0.14 0.26 5 -0.33 48 53
NGF (dimer) -0.055 0.15 -10000 0 -0.35 113 113
RhoG/GDP 0.015 0.022 -10000 0 -0.24 4 4
RIT1/GDP -0.048 0.085 0.22 2 -0.24 32 34
TIAM1 0.014 0.057 -10000 0 -0.35 13 13
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
BDNF (dimer)/TRKB 0.042 0.1 0.2 83 -0.21 51 134
KIDINS220/CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.024 0.03 -10000 0 -0.25 5 5
FRS2 family/SHP2 0.045 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.042 0.032 -10000 0 -0.18 3 3
RIT1/GTP 0.013 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.002 0.092 0.28 5 -0.35 32 37
RAP1/GDP -0.041 0.083 -10000 0 -0.2 39 39
KIDINS220/CRKL 0.022 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.062 0.093 0.28 84 -10000 0 84
ubiquitin-dependent protein catabolic process -0.009 0.099 0.2 5 -0.21 100 105
Schwann cell development -0.035 0.029 -10000 0 -10000 0 0
EHD4 0.022 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.053 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.006 0.059 -10000 0 -0.24 21 21
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.072 0.14 0.18 2 -0.2 254 256
ABL1 0.02 0.023 -10000 0 -0.35 2 2
SH2B family/GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.079 -10000 0 -0.28 16 16
STAT3 0.026 0.014 0.22 2 -10000 0 2
axon guidance -0.076 0.13 -10000 0 -0.19 257 257
MAPK3 -0.021 0.1 0.18 72 -0.19 101 173
MAPK1 -0.021 0.11 0.18 72 -0.19 102 174
CDC42/GDP -0.042 0.099 0.21 6 -0.24 34 40
NTF3 0.002 0.092 0.28 5 -0.35 32 37
NTF4 0.032 0.055 0.28 23 -0.35 1 24
NGF (dimer)/TRKA/FAIM -0.008 0.098 0.2 5 -0.21 98 103
PI3K 0.027 0.029 -10000 0 -0.25 5 5
FRS3 0.023 0.003 -10000 0 -10000 0 0
FAIM 0.022 0.017 -10000 0 -0.35 1 1
GAB1 0.02 0.032 -10000 0 -0.35 4 4
RASGRF1 -0.11 0.16 0.22 2 -0.3 187 189
SOS1 0.023 0.003 -10000 0 -10000 0 0
MCF2L -0.11 0.11 -10000 0 -0.23 243 243
RGS19 0.022 0.006 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.096 -10000 0 -0.38 11 11
Rac1/GDP -0.043 0.099 0.21 5 -0.24 36 41
NGF (dimer)/TRKA/GRIT -0.017 0.092 0.19 5 -0.2 101 106
neuron projection morphogenesis -0.12 0.24 -10000 0 -0.6 73 73
NGF (dimer)/TRKA/NEDD4-2 -0.009 0.099 0.2 5 -0.21 100 105
MAP2K1 0.026 0.086 0.18 117 -0.18 2 119
NGFR -0.099 0.17 0.28 1 -0.35 174 175
NGF (dimer)/TRKA/GIPC/GAIP -0.021 0.08 -10000 0 -0.2 88 88
RAS family/GTP/PI3K 0.013 0.027 0.17 1 -0.2 7 8
FRS2 family/SHP2/GRB2/SOS1 0.061 0.022 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAPKKK cascade -0.13 0.25 -10000 0 -0.57 120 120
RASA1 0.019 0.036 -10000 0 -0.35 5 5
TRKA/c-Abl 0.025 0.037 0.21 6 -0.24 6 12
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.052 0.096 0.21 82 -0.19 47 129
NGF (dimer)/TRKA/p62/Atypical PKCs 0.008 0.09 -10000 0 -0.18 88 88
MATK 0.013 0.056 0.28 1 -0.35 12 13
NEDD4L 0.021 0.017 -10000 0 -0.35 1 1
RAS family/GDP -0.052 0.06 -10000 0 -0.18 43 43
NGF (dimer)/TRKA -0.1 0.15 0.19 1 -0.29 185 186
Rac1/GTP -0.1 0.11 -10000 0 -0.24 175 175
FRS2 family/SHP2/CRK family 0.06 0.024 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.028 -10000 0 -0.35 3 3
EPHB2 0.025 0.02 0.28 3 -10000 0 3
EFNB1 -0.007 0.033 -10000 0 -0.28 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.077 -10000 0 -0.18 61 61
Ephrin B2/EPHB1-2 0.02 0.069 0.19 3 -0.18 53 56
neuron projection morphogenesis 0.012 0.068 -10000 0 -0.17 61 61
Ephrin B1/EPHB1-2/Tiam1 0.019 0.079 0.2 3 -0.18 64 67
DNM1 0.019 0.039 -10000 0 -0.35 6 6
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.071 0.18 0.22 4 -0.48 82 86
YES1 -0.095 0.26 -10000 0 -0.7 82 82
Ephrin B1/EPHB1-2/NCK2 0.025 0.072 0.2 2 -0.18 54 56
PI3K -0.046 0.19 -10000 0 -0.49 79 79
mol:GDP 0.018 0.078 0.2 2 -0.18 64 66
ITGA2B 0.018 0.041 0.28 1 -0.35 6 7
endothelial cell proliferation 0.027 0.019 -10000 0 -0.2 3 3
FYN -0.094 0.26 -10000 0 -0.7 82 82
MAP3K7 -0.075 0.19 0.23 1 -0.51 81 82
FGR -0.094 0.26 -10000 0 -0.7 81 81
TIAM1 0.014 0.057 -10000 0 -0.35 13 13
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RGS3 0.022 0.006 -10000 0 -10000 0 0
cell adhesion -0.078 0.19 0.25 1 -0.51 80 81
LYN -0.094 0.26 -10000 0 -0.69 82 82
Ephrin B1/EPHB1-2/Src Family Kinases -0.093 0.24 -10000 0 -0.64 84 84
Ephrin B1/EPHB1-2 -0.075 0.2 -10000 0 -0.56 77 77
SRC -0.093 0.26 -10000 0 -0.69 82 82
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
EPHB1 -0.011 0.11 0.28 1 -0.35 50 51
EPHB4 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.02 -10000 0 -0.2 3 3
alphaIIb/beta3 Integrin -0.016 0.11 0.21 3 -0.24 96 99
BLK -0.088 0.26 -10000 0 -0.69 81 81
HCK -0.09 0.25 -10000 0 -0.7 79 79
regulation of stress fiber formation -0.023 0.071 0.18 54 -0.2 1 55
MAPK8 -0.068 0.17 0.22 2 -0.47 80 82
Ephrin B1/EPHB1-2/RGS3 0.024 0.072 0.2 4 -0.18 54 58
endothelial cell migration -0.058 0.16 0.26 3 -0.44 74 77
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTPN13 -0.039 0.16 -10000 0 -0.46 67 67
regulation of focal adhesion formation -0.023 0.071 0.18 54 -0.2 1 55
chemotaxis -0.022 0.071 0.18 54 -0.2 2 56
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP 0.019 0.073 -10000 0 -0.17 61 61
angiogenesis -0.076 0.2 -10000 0 -0.55 79 79
LCK -0.093 0.26 -10000 0 -0.69 82 82
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.081 0.12 -10000 0 -0.21 258 258
fibroblast growth factor receptor signaling pathway -0.081 0.12 -10000 0 -0.21 258 258
LAMA1 0.1 0.13 0.28 174 -0.35 4 178
PRNP -0.03 0.13 -10000 0 -0.35 76 76
GPC1/SLIT2 -0.002 0.091 -10000 0 -0.24 65 65
SMAD2 -0.016 0.032 0.18 6 -0.19 10 16
GPC1/PrPc/Cu2+ -0.004 0.082 -10000 0 -0.2 76 76
GPC1/Laminin alpha1 0.086 0.088 0.21 170 -0.25 4 174
TDGF1 0.014 0.091 0.28 17 -0.35 24 41
CRIPTO/GPC1 0.026 0.067 0.21 17 -0.24 24 41
APP/GPC1 0.033 0.007 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.042 -10000 0 -0.21 23 23
FLT1 0.022 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.038 0.036 -10000 0 -0.21 10 10
SERPINC1 0.022 0.034 0.29 8 -10000 0 8
FYN -0.018 0.041 -10000 0 -0.21 22 22
FGR -0.022 0.05 -10000 0 -0.21 32 32
positive regulation of MAPKKK cascade 0.01 0.089 0.24 32 -0.28 20 52
SLIT2 -0.023 0.12 -10000 0 -0.35 65 65
GPC1/NRG 0.025 0.038 0.21 1 -0.24 9 10
NRG1 0.014 0.049 0.28 1 -0.35 9 10
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.043 0.013 -10000 0 -10000 0 0
LYN -0.017 0.04 -10000 0 -0.21 20 20
mol:Spermine -0.006 0.001 -10000 0 -10000 0 0
cell growth -0.081 0.12 -10000 0 -0.21 258 258
BMP signaling pathway -0.023 0.003 -10000 0 -10000 0 0
SRC -0.018 0.042 -10000 0 -0.21 23 23
TGFBR1 0.022 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.004 0.11 0.28 10 -0.35 43 53
GPC1 0.023 0.003 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.006 -10000 0 -10000 0 0
VEGFA 0.023 0.003 -10000 0 -10000 0 0
BLK -0.005 0.059 0.15 37 -0.21 19 56
HCK -0.016 0.045 0.13 6 -0.21 22 28
FGF2 -0.17 0.19 -10000 0 -0.35 276 276
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 0.015 0.051 -10000 0 -0.35 10 10
cell death 0.033 0.007 -10000 0 -10000 0 0
ATIII/GPC1 0.03 0.026 0.22 8 -10000 0 8
PLA2G2A/GPC1 0.013 0.08 0.21 10 -0.24 43 53
LCK -0.017 0.043 0.14 3 -0.21 22 25
neuron differentiation 0.025 0.038 0.21 1 -0.24 9 10
PrPc/Cu2+ -0.02 0.09 -10000 0 -0.24 76 76
APP 0.023 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.015 0.05 -10000 0 -0.35 10 10
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.09 0.26 0.48 6 -0.62 53 59
PCK1 -0.069 0.33 0.53 5 -1.1 37 42
HNF4A -0.1 0.34 0.67 12 -0.78 67 79
KCNJ11 -0.081 0.27 0.6 5 -0.64 44 49
AKT1 -0.031 0.17 0.38 11 -0.36 23 34
response to starvation -0.004 0.034 -10000 0 -0.16 5 5
DLK1 -0.13 0.34 0.61 8 -0.78 80 88
NKX2-1 -0.079 0.16 0.36 8 -0.36 58 66
ACADM -0.094 0.27 0.5 5 -0.64 48 53
TAT -0.078 0.23 0.54 3 -0.63 31 34
CEBPB 0.023 0.008 -10000 0 -10000 0 0
CEBPA 0.023 0.033 0.28 2 -0.35 3 5
TTR 0.071 0.18 0.55 12 -0.68 7 19
PKLR -0.052 0.27 0.54 17 -0.63 34 51
APOA1 -0.16 0.44 0.68 10 -1.1 73 83
CPT1C -0.094 0.27 0.5 5 -0.69 40 45
ALAS1 -0.044 0.17 0.46 3 -0.67 3 6
TFRC -0.011 0.21 0.58 8 -0.58 10 18
FOXF1 0.017 0.036 -10000 0 -0.35 5 5
NF1 0.024 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.04 0.043 0.31 8 -10000 0 8
CPT1A -0.089 0.26 0.48 7 -0.63 45 52
HMGCS1 -0.086 0.26 0.52 6 -0.64 41 47
NR3C1 -0.051 0.14 -10000 0 -0.29 127 127
CPT1B -0.088 0.26 0.54 6 -0.64 44 50
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.024 -10000 0 -10000 0 0
GCK -0.15 0.35 0.58 5 -0.75 97 102
CREB1 0.017 0.056 -10000 0 -0.19 28 28
IGFBP1 -0.2 0.43 0.51 4 -1.1 87 91
PDX1 -0.008 0.18 0.49 11 -0.53 4 15
UCP2 -0.088 0.27 0.53 7 -0.65 41 48
ALDOB -0.079 0.27 0.57 7 -0.66 37 44
AFP 0.068 0.073 0.35 5 -0.37 1 6
BDH1 -0.076 0.27 0.54 9 -0.64 40 49
HADH -0.08 0.26 0.54 5 -0.67 33 38
F2 -0.099 0.34 0.67 13 -0.82 37 50
HNF1A 0.04 0.043 0.31 8 -10000 0 8
G6PC 0.028 0.072 0.4 1 -10000 0 1
SLC2A2 -0.027 0.19 0.6 5 -0.48 2 7
INS 0.006 0.069 0.2 37 -10000 0 37
FOXA1 0.19 0.14 0.29 342 -0.26 7 349
FOXA3 0.075 0.13 0.31 102 -0.27 10 112
FOXA2 -0.08 0.33 0.72 11 -0.72 46 57
ABCC8 -0.16 0.37 0.6 5 -0.8 106 111
ALB 0.061 0.12 0.38 3 -0.74 9 12
TCGA08_retinoblastoma

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
CDKN2B 0.018 0.045 0.29 9 -10000 0 9
CDKN2C 0.021 0.049 -10000 0 -0.34 9 9
CDKN2A 0.13 0.13 0.28 216 -10000 0 216
CCND2 -0.037 0.06 0.14 1 -0.16 55 56
RB1 0.035 0.067 0.31 14 -0.14 2 16
CDK4 -0.035 0.068 0.13 3 -0.32 14 17
CDK6 -0.04 0.073 0.16 1 -0.27 25 26
G1/S progression -0.035 0.072 0.16 5 -0.32 15 20
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.047 0.13 0.2 1 -0.39 52 53
CRKL -0.052 0.14 0.21 1 -0.37 70 71
HRAS -0.035 0.12 -10000 0 -0.36 44 44
mol:PIP3 -0.02 0.15 0.26 5 -0.37 49 54
SPRED1 0.022 0.005 -10000 0 -10000 0 0
SPRED2 0.022 0.016 -10000 0 -0.35 1 1
GAB1 -0.054 0.15 -10000 0 -0.37 77 77
FOXO3 -0.035 0.14 0.3 3 -0.4 48 51
AKT1 -0.036 0.15 0.25 1 -0.43 49 50
BAD -0.033 0.14 0.24 1 -0.4 46 47
megakaryocyte differentiation -0.054 0.14 -10000 0 -0.36 77 77
GSK3B -0.033 0.14 0.26 3 -0.4 47 50
RAF1 -0.017 0.12 0.24 6 -0.3 42 48
SHC1 0.019 0.009 -10000 0 -10000 0 0
STAT3 -0.052 0.14 -10000 0 -0.37 75 75
STAT1 -0.12 0.33 -10000 0 -0.82 82 82
HRAS/SPRED1 -0.01 0.12 0.23 1 -0.3 42 43
cell proliferation -0.054 0.15 -10000 0 -0.36 77 77
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TEC 0.023 0.012 0.28 1 -10000 0 1
RPS6KB1 -0.048 0.16 -10000 0 -0.44 61 61
HRAS/SPRED2 -0.01 0.12 0.23 1 -0.3 42 43
LYN/TEC/p62DOK -0.019 0.15 -10000 0 -0.4 49 49
MAPK3 -0.012 0.096 0.21 8 -0.23 47 55
STAP1 -0.053 0.14 -10000 0 -0.36 80 80
GRAP2 0.011 0.061 -10000 0 -0.35 15 15
JAK2 -0.1 0.29 -10000 0 -0.71 83 83
STAT1 (dimer) -0.12 0.32 -10000 0 -0.8 82 82
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.02 0.15 -10000 0 -0.4 50 50
actin filament polymerization -0.051 0.14 0.3 1 -0.35 76 77
LYN 0.021 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.083 0.22 -10000 0 -0.53 84 84
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CBL/CRKL/GRB2 -0.03 0.14 -10000 0 -0.38 49 49
PI3K -0.024 0.16 -10000 0 -0.43 51 51
PTEN 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.36 -10000 0 -1.1 52 52
MAPK8 -0.055 0.15 -10000 0 -0.37 77 77
STAT3 (dimer) -0.051 0.14 0.26 1 -0.36 75 76
positive regulation of transcription -0.008 0.082 0.19 9 -0.19 45 54
mol:GDP -0.033 0.12 -10000 0 -0.37 44 44
PIK3C2B -0.051 0.14 -10000 0 -0.36 72 72
CBL/CRKL -0.041 0.14 -10000 0 -0.39 54 54
FER -0.054 0.14 -10000 0 -0.36 77 77
SH2B3 -0.054 0.15 -10000 0 -0.37 76 76
PDPK1 -0.018 0.14 0.26 7 -0.36 45 52
SNAI2 -0.065 0.16 -10000 0 -0.39 81 81
positive regulation of cell proliferation -0.095 0.26 -10000 0 -0.63 86 86
KITLG -0.018 0.11 -10000 0 -0.37 48 48
cell motility -0.095 0.26 -10000 0 -0.63 86 86
PTPN6 0.024 0.017 0.33 1 -10000 0 1
EPOR -0.042 0.19 -10000 0 -0.83 15 15
STAT5A (dimer) -0.082 0.22 0.28 1 -0.54 83 84
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
cell migration 0.055 0.14 0.36 79 -10000 0 79
SOS1 0.023 0.003 -10000 0 -10000 0 0
EPO 0.002 0.067 0.28 1 -0.36 16 17
VAV1 0.023 0.03 0.28 5 -0.35 1 6
GRB10 -0.055 0.14 -10000 0 -0.37 74 74
PTPN11 0.024 0.009 -10000 0 -10000 0 0
SCF/KIT -0.052 0.15 -10000 0 -0.37 81 81
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.013 0.096 0.22 7 -0.24 40 47
CBL 0.022 0.005 -10000 0 -10000 0 0
KIT -0.1 0.34 -10000 0 -1 55 55
MAP2K2 -0.011 0.093 0.22 7 -0.24 37 44
SHC/Grb2/SOS1 -0.022 0.14 -10000 0 -0.4 46 46
STAT5A -0.083 0.23 -10000 0 -0.56 84 84
GRB2 0.022 0.006 -10000 0 -10000 0 0
response to radiation -0.063 0.16 0.29 2 -0.38 81 83
SHC/GRAP2 0.021 0.04 -10000 0 -0.25 10 10
PTPRO -0.055 0.15 -10000 0 -0.36 78 78
SH2B2 -0.053 0.14 -10000 0 -0.36 76 76
DOK1 0.023 0.003 -10000 0 -10000 0 0
MATK -0.056 0.15 -10000 0 -0.36 79 79
CREBBP 0.012 0.052 -10000 0 -0.18 9 9
BCL2 -0.13 0.39 -10000 0 -1.1 69 69
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.011 0.1 -10000 0 -0.35 47 47
GNB1/GNG2 -0.034 0.14 -10000 0 -0.38 39 39
mol:DAG -0.044 0.12 0.2 8 -0.36 37 45
PLCG1 -0.045 0.13 0.21 8 -0.37 37 45
YES1 -0.051 0.12 0.2 2 -0.4 33 35
FZD3 0.02 0.008 -10000 0 -10000 0 0
FZD6 0.02 0.018 -10000 0 -0.35 1 1
G protein -0.031 0.14 0.25 3 -0.37 37 40
MAP3K7 -0.12 0.13 0.2 4 -0.31 115 119
mol:Ca2+ -0.043 0.12 0.2 8 -0.35 37 45
mol:IP3 -0.044 0.12 0.2 8 -0.36 37 45
NLK -0.028 0.16 -10000 0 -0.82 20 20
GNB1 0.022 0.004 -10000 0 -10000 0 0
CAMK2A -0.12 0.14 0.23 4 -0.32 115 119
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.046 0.14 -10000 0 -0.25 131 131
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
GNAS -0.05 0.12 0.21 3 -0.38 36 39
GO:0007205 -0.047 0.12 0.21 9 -0.35 38 47
WNT6 0.01 0.11 0.28 23 -0.35 34 57
WNT4 -0.065 0.16 -10000 0 -0.35 126 126
NFAT1/CK1 alpha -0.047 0.14 0.26 2 -0.36 45 47
GNG2 0.017 0.049 0.28 1 -0.35 9 10
WNT5A 0.011 0.065 -10000 0 -0.35 17 17
WNT11 0.037 0.098 0.28 49 -0.35 14 63
CDC42 -0.05 0.12 0.2 3 -0.39 31 34
Thromboxane A2 receptor signaling

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
TGM2 -0.013 0.11 -10000 0 -0.35 50 50
GNB1/GNG2 -0.044 0.073 -10000 0 -0.19 98 98
AKT1 -0.037 0.098 0.21 3 -0.24 42 45
EGF 0.031 0.055 0.28 21 -0.35 2 23
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.012 0.062 0.26 5 -0.26 2 7
mol:Ca2+ -0.066 0.14 0.25 2 -0.31 109 111
LYN -0.01 0.054 0.27 4 -10000 0 4
RhoA/GTP -0.027 0.057 -10000 0 -0.13 87 87
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.15 -10000 0 -0.35 98 98
GNG2 0.017 0.049 0.28 1 -0.35 9 10
ARRB2 0.021 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.051 0.18 -10000 0 -0.56 51 51
G beta5/gamma2 -0.054 0.098 -10000 0 -0.25 96 96
PRKCH -0.076 0.16 -10000 0 -0.37 96 96
DNM1 0.018 0.039 -10000 0 -0.35 6 6
TXA2/TP beta/beta Arrestin3 0.012 0.026 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.01 0.1 -10000 0 -0.35 45 45
G12 family/GTP -0.068 0.13 -10000 0 -0.3 103 103
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.021 0.017 -10000 0 -0.35 1 1
RhoA/GTP/ROCK1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.048 0.13 0.41 37 -10000 0 37
mol:NADP 0.022 0.02 0.28 1 -0.35 1 2
RAB11A 0.022 0.005 -10000 0 -10000 0 0
PRKG1 -0.14 0.18 -10000 0 -0.35 226 226
mol:IP3 -0.085 0.18 -10000 0 -0.39 111 111
cell morphogenesis 0.029 0.008 -10000 0 -10000 0 0
PLCB2 -0.12 0.24 -10000 0 -0.54 110 110
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.002 0.07 0.3 9 -0.21 1 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.009 0.056 0.24 4 -0.22 1 5
RHOA 0.022 0.005 -10000 0 -10000 0 0
PTGIR 0.022 0.017 -10000 0 -0.35 1 1
PRKCB1 -0.081 0.17 -10000 0 -0.39 101 101
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
mol:L-citrulline 0.022 0.02 0.28 1 -0.35 1 2
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.54 98 98
LCK -0.008 0.062 0.26 6 -0.22 1 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.011 0.055 -10000 0 -0.17 34 34
TXA2-R family/G12 family/GDP/G beta/gamma -0.002 0.093 -10000 0 -0.42 22 22
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.053 -10000 0 -0.17 30 30
MAPK14 -0.047 0.1 0.21 1 -0.23 93 94
TGM2/GTP -0.1 0.2 0.32 2 -0.44 121 123
MAPK11 -0.048 0.1 -10000 0 -0.23 97 97
ARHGEF1 -0.04 0.077 -10000 0 -0.18 93 93
GNAI2 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.08 0.17 -10000 0 -0.39 98 98
RAB11/GDP 0.022 0.005 -10000 0 -10000 0 0
ICAM1 -0.055 0.12 -10000 0 -0.28 96 96
cAMP biosynthetic process -0.084 0.16 0.26 2 -0.36 122 124
Gq family/GTP/EBP50 -0.014 0.081 -10000 0 -0.26 35 35
actin cytoskeleton reorganization 0.029 0.008 -10000 0 -10000 0 0
SRC -0.01 0.058 0.25 5 -0.22 1 6
GNB5 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
EGF/EGFR 0.014 0.074 0.25 21 -0.23 4 25
VCAM1 -0.062 0.14 -10000 0 -0.32 98 98
TP beta/Gq family/GDP/G beta5/gamma2 -0.051 0.18 -10000 0 -0.56 51 51
platelet activation -0.064 0.14 -10000 0 -0.31 98 98
PGI2/IP 0.016 0.011 -10000 0 -0.24 1 1
PRKACA -0.003 0.055 -10000 0 -0.19 40 40
Gq family/GDP/G beta5/gamma2 -0.041 0.16 -10000 0 -0.48 48 48
TXA2/TP beta/beta Arrestin2 -0.003 0.071 -10000 0 -0.37 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.046 -10000 0 -0.18 35 35
mol:DAG -0.093 0.19 -10000 0 -0.45 101 101
EGFR 0.014 0.059 0.33 1 -0.35 13 14
TXA2/TP alpha -0.12 0.22 -10000 0 -0.49 122 122
Gq family/GTP -0.027 0.092 -10000 0 -0.24 70 70
YES1 -0.008 0.059 0.26 6 -10000 0 6
GNAI2/GTP 0 0.049 -10000 0 -0.16 35 35
PGD2/DP -0.005 0.071 -10000 0 -0.24 45 45
SLC9A3R1 0.024 0.023 0.28 4 -10000 0 4
FYN -0.011 0.058 0.26 5 -0.22 1 6
mol:NO 0.022 0.02 0.28 1 -0.35 1 2
GNA15 0.025 0.03 0.28 7 -10000 0 7
PGK/cGMP -0.07 0.12 -10000 0 -0.2 225 225
RhoA/GDP 0.022 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.006 0.086 -10000 0 -0.21 42 42
NOS3 0.022 0.02 0.28 1 -0.35 1 2
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.079 0.16 -10000 0 -0.37 100 100
PRKCB -0.081 0.16 -10000 0 -0.38 101 101
PRKCE -0.074 0.16 0.28 1 -0.37 95 96
PRKCD -0.079 0.17 -10000 0 -0.39 98 98
PRKCG -0.082 0.17 0.28 1 -0.4 100 101
muscle contraction -0.11 0.21 -10000 0 -0.5 102 102
PRKCZ -0.073 0.15 0.25 1 -0.35 98 99
ARR3 0.019 0.012 0.28 1 -10000 0 1
TXA2/TP beta 0.011 0.057 -10000 0 -0.17 34 34
PRKCQ -0.081 0.17 0.31 3 -0.38 104 107
MAPKKK cascade -0.1 0.21 -10000 0 -0.48 106 106
SELE -0.066 0.15 -10000 0 -0.35 96 96
TP beta/GNAI2/GDP/G beta/gamma 0.022 0.064 -10000 0 -0.18 35 35
ROCK1 0.023 0.004 -10000 0 -10000 0 0
GNA14 -0.01 0.1 -10000 0 -0.35 45 45
chemotaxis -0.12 0.24 -10000 0 -0.6 98 98
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
Rac1/GTP 0.016 0.004 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.09 0.26 52 -0.21 12 64
KIRREL -0.017 0.11 -10000 0 -0.36 54 54
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.003 0.091 0.22 12 -0.26 52 64
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARRB2 0.021 0.006 -10000 0 -10000 0 0
WASL 0.022 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.023 0.079 0.31 2 -0.19 50 52
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.006 0.07 0.2 3 -0.21 50 53
FYN 0.017 0.12 0.23 101 -0.18 51 152
mol:Ca2+ 0.019 0.075 0.34 1 -0.19 51 52
mol:DAG 0.02 0.076 0.34 1 -0.19 51 52
NPHS2 -0.008 0.033 0.3 3 -10000 0 3
mol:IP3 0.02 0.076 0.34 1 -0.19 51 52
regulation of endocytosis 0.015 0.068 0.19 7 -0.17 51 58
Nephrin/NEPH1/podocin/Cholesterol 0.013 0.073 0.2 13 -0.19 52 65
establishment of cell polarity 0.003 0.09 0.21 12 -0.26 52 64
Nephrin/NEPH1/podocin/NCK1-2 0.029 0.08 0.31 2 -0.18 51 53
Nephrin/NEPH1/beta Arrestin2 0.016 0.069 0.2 7 -0.18 51 58
NPHS1 0.02 0.054 0.29 14 -10000 0 14
Nephrin/NEPH1/podocin 0.014 0.072 0.2 12 -0.18 51 63
TJP1 0.022 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.021 0.077 0.35 1 -0.19 51 52
CD2AP 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.02 0.077 0.35 1 -0.19 51 52
GRB2 0.022 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.006 0.13 0.23 94 -0.2 67 161
cytoskeleton organization -0.017 0.079 0.22 19 -0.22 49 68
Nephrin/NEPH1 0.007 0.064 0.18 12 -0.17 52 64
Nephrin/NEPH1/ZO-1 0.014 0.078 0.2 12 -0.2 52 64
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.003 0.081 0.2 1 -0.18 67 68
NF kappa B1 p50/RelA/I kappa B alpha 0 0.093 0.37 4 -0.26 4 8
alphaV/beta3 Integrin/Osteopontin/Src 0.084 0.08 0.21 148 -10000 0 148
AP1 -0.046 0.14 -10000 0 -0.33 56 56
ILK -0.006 0.082 0.29 4 -0.21 2 6
bone resorption -0.019 0.082 0.32 2 -0.31 6 8
PTK2B 0.02 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.042 0.11 0.24 4 -0.17 58 62
ITGAV 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.047 -10000 0 -0.25 15 15
alphaV/beta3 Integrin/Osteopontin 0.045 0.13 0.21 125 -0.2 88 213
MAP3K1 -0.008 0.083 0.21 9 -0.18 85 94
JUN 0.018 0.043 -10000 0 -0.35 7 7
MAPK3 -0.022 0.071 0.22 9 -0.19 2 11
MAPK1 -0.023 0.072 0.21 9 -0.19 2 11
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.026 0.074 0.21 9 -0.18 71 80
ITGB3 -0.038 0.14 0.28 2 -0.35 90 92
NFKBIA -0.016 0.072 0.32 3 -0.22 2 5
FOS -0.089 0.17 -10000 0 -0.35 160 160
CD44 0.019 0.042 0.33 1 -0.35 6 7
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU -0.026 0.1 0.47 2 -0.49 4 6
NF kappa B1 p50/RelA 0.018 0.083 0.31 3 -10000 0 3
BCAR1 0.021 0.007 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.01 0.1 0.21 2 -0.24 89 91
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.007 0.084 0.23 11 -0.18 84 95
VAV3 -0.012 0.083 0.25 11 -0.18 60 71
MAP3K14 -0.007 0.083 0.21 9 -0.18 75 84
ROCK2 0.015 0.051 -10000 0 -0.35 10 10
SPP1 0.097 0.12 0.28 153 -10000 0 153
RAC1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.079 0.23 11 -10000 0 11
MMP2 -0.071 0.12 0.29 1 -0.33 55 56
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.018 0.11 0.32 3 -0.19 95 98
SMAD6-7/SMURF1 0.041 0.023 -10000 0 -0.21 3 3
NOG 0.041 0.075 0.28 44 -0.35 2 46
SMAD9 -0.071 0.19 -10000 0 -0.49 86 86
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.026 0.096 -10000 0 -0.33 26 26
BMP7/USAG1 0.021 0.11 0.22 54 -0.25 57 111
SMAD5/SKI -0.021 0.11 -10000 0 -0.35 28 28
SMAD1 0.004 0.063 0.24 2 -0.46 5 7
BMP2 -0.009 0.1 -10000 0 -0.35 45 45
SMAD1/SMAD1/SMAD4 0.016 0.06 -10000 0 -0.32 6 6
BMPR1A 0.022 0.006 -10000 0 -10000 0 0
BMPR1B 0.002 0.086 0.28 1 -0.35 30 31
BMPR1A-1B/BAMBI 0.024 0.074 0.21 7 -0.22 40 47
AHSG 0.025 0.039 0.28 12 -10000 0 12
CER1 0.018 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 0.015 0.085 0.2 8 -0.22 56 64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.11 -10000 0 -0.33 41 41
BMP2-4 (homodimer) 0.002 0.098 0.21 8 -0.26 60 68
RGMB 0.022 0.017 -10000 0 -0.35 1 1
BMP6/BMPR2/BMPR1A-1B 0.036 0.066 -10000 0 -0.2 36 36
RGMA -0.059 0.15 -10000 0 -0.35 117 117
SMURF1 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.1 -10000 0 -0.3 44 44
BMP2-4/USAG1 0.012 0.12 0.2 41 -0.23 84 125
SMAD6/SMURF1/SMAD5 -0.023 0.11 -10000 0 -0.35 29 29
SOSTDC1 0.018 0.11 0.28 38 -0.35 32 70
BMP7/BMPR2/BMPR1A-1B 0.035 0.082 0.21 20 -0.2 48 68
SKI 0.022 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.015 0.053 -10000 0 -0.35 11 11
HFE2 0.016 0.018 0.28 2 -10000 0 2
ZFYVE16 0.022 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.016 0.12 0.2 8 -0.23 113 121
SMAD5/SMAD5/SMAD4 -0.021 0.11 -10000 0 -0.35 29 29
MAPK1 0.022 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.025 0.11 -10000 0 -0.28 43 43
BMP7 (homodimer) 0.017 0.11 0.29 30 -0.35 29 59
NUP214 0.022 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.027 0.049 0.21 12 -0.25 11 23
SMAD1/SKI 0.013 0.071 -10000 0 -0.41 6 6
SMAD6 0.021 0.017 -10000 0 -0.35 1 1
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
BMP2-4/FETUA 0.021 0.083 0.2 17 -0.22 48 65
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.068 0.16 -10000 0 -0.35 129 129
BMPR2 (homodimer) 0.023 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.014 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.017 0.063 0.21 1 -0.25 28 29
CHRDL1 -0.23 0.17 -10000 0 -0.35 365 365
ENDOFIN/SMAD1 0.012 0.071 -10000 0 -0.4 6 6
SMAD6-7/SMURF1/SMAD1 0.029 0.075 -10000 0 -0.38 6 6
SMAD6/SMURF1 0.022 0.004 -10000 0 -10000 0 0
BAMBI 0.014 0.073 0.28 8 -0.35 17 25
SMURF2 0.022 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.14 0.2 2 -0.23 372 374
BMP2-4/GREM1 -0.042 0.14 0.2 7 -0.24 165 172
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
SMAD8A/SMAD8A/SMAD4 -0.066 0.19 -10000 0 -0.46 92 92
SMAD1/SMAD6 0.011 0.073 -10000 0 -0.39 7 7
TAK1/SMAD6 0.033 0.007 -10000 0 -10000 0 0
BMP7 0.017 0.11 0.29 30 -0.35 29 59
BMP6 0.015 0.053 -10000 0 -0.35 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.11 -10000 0 -0.3 51 51
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.013 0.069 -10000 0 -0.41 6 6
SMAD7/SMURF1 0.031 0.019 -10000 0 -0.25 2 2
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
PPP1CA 0.022 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
PPP1R15A 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.064 0.14 -10000 0 -0.38 65 65
CHRD -0.036 0.13 -10000 0 -0.35 82 82
BMPR2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.11 -10000 0 -0.33 41 41
BMP4 0.011 0.083 0.28 9 -0.35 23 32
FST -0.016 0.12 0.28 6 -0.35 58 64
BMP2-4/NOG 0.026 0.1 0.21 43 -0.22 62 105
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.041 0.082 0.23 2 -0.19 48 50
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.061 0.094 0.32 62 -10000 0 62
NFATC2 0 0.17 -10000 0 -0.48 35 35
NFATC3 0.001 0.09 -10000 0 -0.27 37 37
CD40LG -0.11 0.3 -10000 0 -0.8 64 64
ITCH 0.021 0.02 -10000 0 -0.2 1 1
CBLB 0.022 0.02 -10000 0 -0.2 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.045 0.25 0.44 13 -0.67 39 52
JUNB 0.018 0.036 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.035 -10000 0 -0.24 1 1
T cell anergy 0.018 0.053 0.27 8 -0.33 1 9
TLE4 -0.03 0.18 -10000 0 -0.57 46 46
Jun/NFAT1-c-4/p21SNFT -0.041 0.31 -10000 0 -0.76 65 65
AP-1/NFAT1-c-4 -0.072 0.38 0.59 3 -0.9 63 66
IKZF1 -0.004 0.12 0.34 1 -0.36 28 29
T-helper 2 cell differentiation -0.065 0.21 -10000 0 -0.79 21 21
AP-1/NFAT1 -0.034 0.18 0.31 3 -0.36 65 68
CALM1 0.031 0.016 -10000 0 -0.15 1 1
EGR2 -0.11 0.37 -10000 0 -1.1 53 53
EGR3 -0.13 0.41 -10000 0 -1.1 73 73
NFAT1/FOXP3 0.045 0.17 0.42 33 -0.34 28 61
EGR1 -0.023 0.12 -10000 0 -0.35 68 68
JUN 0.018 0.047 -10000 0 -0.35 7 7
EGR4 0.03 0.043 0.28 15 -10000 0 15
mol:Ca2+ 0.009 0.014 -10000 0 -0.14 1 1
GBP3 -0.007 0.12 -10000 0 -0.41 25 25
FOSL1 0.042 0.069 0.28 42 -10000 0 42
NFAT1-c-4/MAF/IRF4 -0.063 0.33 0.48 1 -0.8 69 70
DGKA -0.002 0.11 -10000 0 -0.36 17 17
CREM 0.021 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.058 0.32 -10000 0 -0.78 72 72
CTLA4 0.023 0.13 0.3 53 -0.29 27 80
NFAT1-c-4 (dimer)/EGR1 -0.066 0.34 -10000 0 -0.82 72 72
NFAT1-c-4 (dimer)/EGR4 -0.039 0.32 0.5 1 -0.77 71 72
FOS -0.087 0.17 -10000 0 -0.35 160 160
IFNG -0.032 0.2 -10000 0 -0.72 20 20
T cell activation -0.069 0.2 -10000 0 -0.61 39 39
MAF -0.032 0.13 -10000 0 -0.35 76 76
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.066 0.28 0.71 69 -10000 0 69
TNF -0.071 0.3 0.47 1 -0.75 69 70
FASLG -0.15 0.45 -10000 0 -1.1 84 84
TBX21 0.026 0.058 0.35 3 -0.35 9 12
BATF3 0.02 0.014 0.28 1 -10000 0 1
PRKCQ -0.005 0.1 0.32 1 -0.35 43 44
PTPN1 -0.004 0.11 -10000 0 -0.34 30 30
NFAT1-c-4/ICER1 -0.051 0.31 -10000 0 -0.77 71 71
GATA3 0.025 0.057 0.28 13 -0.35 6 19
T-helper 1 cell differentiation -0.031 0.2 -10000 0 -0.71 20 20
IL2RA -0.043 0.26 0.46 13 -0.64 46 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.11 -10000 0 -0.34 29 29
E2F1 0.074 0.1 0.29 100 -10000 0 100
PPARG 0.004 0.084 0.33 1 -0.35 28 29
SLC3A2 -0.003 0.11 -10000 0 -0.34 27 27
IRF4 0.02 0.061 0.28 9 -0.35 10 19
PTGS2 -0.12 0.31 0.41 1 -0.78 70 71
CSF2 -0.11 0.3 -10000 0 -0.78 64 64
JunB/Fra1/NFAT1-c-4 -0.031 0.31 0.48 1 -0.76 64 65
IL4 -0.067 0.22 -10000 0 -0.84 20 20
IL5 -0.11 0.29 -10000 0 -0.78 64 64
IL2 -0.071 0.2 -10000 0 -0.62 38 38
IL3 -0.021 0.11 -10000 0 -0.66 12 12
RNF128 0.031 0.059 0.22 42 -0.47 1 43
NFATC1 -0.067 0.28 -10000 0 -0.71 69 69
CDK4 0.062 0.19 0.58 35 -10000 0 35
PTPRK -0.003 0.12 0.34 1 -0.35 28 29
IL8 -0.073 0.32 0.43 2 -0.79 63 65
POU2F1 0.019 0.009 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
CDC42/GTP -0.042 0.11 -10000 0 -0.2 129 129
PLCG1 -0.043 0.097 -10000 0 -0.21 116 116
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
cell migration -0.042 0.1 -10000 0 -0.2 129 129
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
MAPK3 -0.045 0.099 -10000 0 -0.21 118 118
MAPK1 -0.041 0.098 -10000 0 -0.21 114 114
S1P/S1P5/Gi -0.038 0.1 0.17 2 -0.22 113 115
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
CDC42/GDP 0.017 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.029 0.19 10 -0.2 3 13
RHOA -0.008 0.034 0.18 16 -0.17 2 18
S1P/S1P4/Gi -0.039 0.1 -10000 0 -0.21 124 124
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
S1P/S1P4/G12/G13 0.038 0.022 0.19 1 -0.18 2 3
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.024 0.074 -10000 0 -0.18 62 62
ER alpha/Gai/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.48 92 92
AKT1 -0.081 0.25 -10000 0 -0.72 69 69
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.08 0.26 -10000 0 -0.74 69 69
mol:Ca2+ -0.032 0.11 -10000 0 -0.36 49 49
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
E2/ER alpha (dimer)/Striatin 0.005 0.072 -10000 0 -0.2 56 56
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis 0.077 0.24 0.69 69 -10000 0 69
RhoA/GTP 0.002 0.053 -10000 0 -0.16 48 48
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.075 0.18 -10000 0 -0.42 77 77
regulation of stress fiber formation 0.02 0.067 0.26 2 -0.25 11 13
E2/ERA-ERB (dimer) 0.005 0.072 0.19 1 -0.2 56 57
KRAS 0.023 0.014 0.33 1 -10000 0 1
G13/GTP 0.005 0.064 -10000 0 -0.18 55 55
pseudopodium formation -0.02 0.067 0.25 11 -0.26 2 13
E2/ER alpha (dimer)/PELP1 0.004 0.07 -10000 0 -0.2 54 54
GRB2 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.017 0.049 0.28 1 -0.35 9 10
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
HRAS 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.085 0.2 -10000 0 -0.5 77 77
E2/ER beta (dimer) 0.017 0.008 0.19 1 -10000 0 1
mol:GDP -0.02 0.097 -10000 0 -0.3 54 54
mol:NADP -0.085 0.2 -10000 0 -0.5 77 77
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.035 0.11 -10000 0 -0.37 49 49
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
PLCB1 -0.033 0.12 -10000 0 -0.38 52 52
PLCB2 -0.031 0.12 -10000 0 -0.37 51 51
IGF1 -0.046 0.14 -10000 0 -0.35 100 100
mol:L-citrulline -0.085 0.2 -10000 0 -0.5 77 77
RHOA 0.022 0.005 -10000 0 -10000 0 0
Gai/GDP -0.19 0.31 -10000 0 -0.62 180 180
JNK cascade 0.017 0.008 0.19 1 -10000 0 1
BCAR1 0.021 0.007 -10000 0 -10000 0 0
ESR2 0.023 0.012 0.28 1 -10000 0 1
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
ESR1 -0.017 0.11 -10000 0 -0.35 56 56
Gq family/GDP/Gbeta gamma -0.067 0.23 -10000 0 -0.65 62 62
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.019 0.12 -10000 0 -0.63 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.071 0.17 -10000 0 -0.43 69 69
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
E2/ER alpha (dimer) -0.011 0.079 -10000 0 -0.24 56 56
STRN 0.021 0.023 -10000 0 -0.35 2 2
GNAL -0.031 0.13 -10000 0 -0.35 77 77
PELP1 0.021 0.006 -10000 0 -10000 0 0
MAPK11 0.008 0.013 -10000 0 -0.2 2 2
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
HBEGF -0.091 0.19 0.28 3 -0.49 67 70
cAMP biosynthetic process -0.019 0.087 -10000 0 -0.18 113 113
SRC -0.1 0.2 0.26 1 -0.47 83 84
PI3K 0.027 0.029 -10000 0 -0.25 5 5
GNB1 0.022 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.098 -10000 0 -0.28 48 48
SOS1 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.09 0.16 -10000 0 -0.38 91 91
Gs family/GTP -0.015 0.091 0.15 1 -0.18 113 114
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.014 0.22 1 -10000 0 1
vasodilation -0.08 0.18 -10000 0 -0.47 77 77
mol:DAG -0.035 0.11 -10000 0 -0.37 49 49
Gs family/GDP/Gbeta gamma -0.032 0.11 -10000 0 -0.3 54 54
MSN -0.022 0.07 0.25 11 -0.28 2 13
Gq family/GTP -0.026 0.12 -10000 0 -0.4 48 48
mol:PI-3-4-5-P3 -0.076 0.25 -10000 0 -0.7 70 70
NRAS 0.023 0.001 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.08 0.18 0.47 77 -10000 0 77
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.007 0.098 -10000 0 -0.3 49 49
NOS3 -0.09 0.21 -10000 0 -0.52 77 77
GNA11 0.014 0.051 -10000 0 -0.35 10 10
MAPKKK cascade -0.069 0.2 -10000 0 -0.53 73 73
E2/ER alpha (dimer)/PELP1/Src -0.081 0.18 0.25 1 -0.43 81 82
ruffle organization -0.02 0.067 0.25 11 -0.26 2 13
ROCK2 -0.018 0.076 0.27 11 -0.3 2 13
GNA14 -0.01 0.1 -10000 0 -0.35 45 45
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA13 0.022 0.005 -10000 0 -10000 0 0
MMP9 -0.089 0.19 0.3 6 -0.47 71 77
MMP2 -0.1 0.19 0.25 2 -0.46 84 86
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.067 -10000 0 -0.25 31 31
PDGFRB 0.006 0.072 -10000 0 -0.36 20 20
SPHK1 -0.018 0.12 -10000 0 -0.78 12 12
mol:S1P -0.021 0.11 -10000 0 -0.68 12 12
S1P1/S1P/Gi -0.1 0.19 0.24 1 -0.35 164 165
GNAO1 -0.069 0.16 -10000 0 -0.35 124 124
PDGFB-D/PDGFRB/PLCgamma1 -0.086 0.18 0.28 4 -0.4 98 102
PLCG1 -0.098 0.18 0.27 3 -0.41 97 100
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.072 -10000 0 -0.36 20 20
GNAI2 0.018 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.012 0.048 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.047 -10000 0 -0.2 31 31
S1P1/S1P -0.027 0.095 0.22 2 -0.38 20 22
negative regulation of cAMP metabolic process -0.1 0.19 0.24 1 -0.34 164 165
MAPK3 -0.12 0.22 0.25 4 -0.53 97 101
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
KDR -0.002 0.089 -10000 0 -0.35 32 32
PLCB2 -0.019 0.089 0.21 6 -0.34 18 24
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.081 -10000 0 -0.32 20 20
receptor internalization -0.027 0.087 -10000 0 -0.33 22 22
PTGS2 -0.15 0.32 0.37 1 -0.87 75 76
Rac1/GTP -0.022 0.081 -10000 0 -0.32 20 20
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFA 0.02 0.011 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.1 0.19 0.24 1 -0.34 164 165
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.006 0.067 -10000 0 -0.36 17 17
MAPK1 -0.12 0.23 0.23 1 -0.54 95 96
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.11 0.25 5 -0.33 33 38
ABCC1 0.018 0.014 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.091 0.2 -10000 0 -0.36 146 146
MAP3K8 0.01 0.033 -10000 0 -0.35 3 3
FOS -0.061 0.16 -10000 0 -0.47 47 47
PRKCA -0.012 0.087 -10000 0 -0.35 31 31
PTPN7 0.009 0.036 0.26 6 -10000 0 6
HRAS 0.021 0.005 -10000 0 -10000 0 0
PRKCB -0.012 0.087 -10000 0 -0.35 31 31
NRAS 0.022 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.034 0.22 1 -10000 0 1
MAPK3 -0.029 0.14 -10000 0 -0.66 17 17
MAP2K1 -0.059 0.15 -10000 0 -0.4 72 72
ELK1 0.006 0.027 -10000 0 -10000 0 0
BRAF -0.04 0.13 -10000 0 -0.36 62 62
mol:GTP -0.001 0.002 -10000 0 -0.005 165 165
MAPK1 -0.036 0.14 -10000 0 -0.55 27 27
RAF1 -0.041 0.13 -10000 0 -0.38 60 60
KRAS 0.022 0.014 0.33 1 -10000 0 1
Syndecan-1-mediated signaling events

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CCL5 0.021 0.045 0.28 6 -0.35 5 11
SDCBP 0.021 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.071 0.09 0.25 35 -0.26 3 38
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 0.064 0.089 0.24 22 -0.26 5 27
Syndecan-1/Syntenin 0.065 0.089 0.25 17 -0.28 4 21
MAPK3 0.052 0.081 0.23 15 -0.26 4 19
HGF/MET -0.022 0.12 0.21 4 -0.25 106 110
TGFB1/TGF beta receptor Type II 0.022 0.017 -10000 0 -0.35 1 1
BSG 0.021 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.063 0.089 0.24 22 -0.26 5 27
Syndecan-1/RANTES 0.07 0.092 0.25 25 -0.31 5 30
Syndecan-1/CD147 0.071 0.091 0.26 13 -0.27 4 17
Syndecan-1/Syntenin/PIP2 0.061 0.084 0.25 13 -0.27 4 17
LAMA5 0.022 0.015 0.33 1 -10000 0 1
positive regulation of cell-cell adhesion 0.059 0.082 0.24 12 -0.26 4 16
MMP7 0.027 0.13 0.28 62 -0.35 36 98
HGF -0.05 0.15 -10000 0 -0.35 104 104
Syndecan-1/CASK 0.055 0.087 0.2 34 -0.24 8 42
Syndecan-1/HGF/MET 0.043 0.13 0.27 17 -0.29 27 44
regulation of cell adhesion 0.044 0.075 0.23 11 -0.28 2 13
HPSE 0.016 0.053 0.28 2 -0.35 10 12
positive regulation of cell migration 0.071 0.09 0.25 35 -0.26 3 38
SDC1 0.072 0.088 0.24 34 -0.3 2 36
Syndecan-1/Collagen 0.071 0.09 0.25 35 -0.26 3 38
PPIB 0.023 0.012 0.28 1 -10000 0 1
MET 0.021 0.042 0.28 4 -0.35 5 9
PRKACA 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 220 -10000 0 220
MAPK1 0.053 0.079 0.23 10 -0.25 4 14
homophilic cell adhesion 0.07 0.093 0.25 36 -0.27 3 39
MMP1 0.16 0.13 0.28 281 -10000 0 281
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.033 0.059 0.21 5 -0.21 22 27
alphaM/beta2 Integrin/GPIbA 0.042 0.043 0.26 6 -0.21 4 10
alphaM/beta2 Integrin/proMMP-9 0.11 0.093 0.22 209 -0.21 2 211
PLAUR 0.024 0.021 0.3 3 -10000 0 3
HMGB1 0.022 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.044 0.038 0.24 6 -0.2 3 9
AGER 0.022 0.022 -10000 0 -0.35 1 1
RAP1A 0.023 0.002 -10000 0 -10000 0 0
SELPLG 0.024 0.016 0.28 2 -10000 0 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.061 0.065 0.33 2 -0.19 19 21
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 220 -10000 0 220
CYR61 -0.01 0.1 -10000 0 -0.35 47 47
TLN1 0.022 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.1 0.21 1 -0.31 28 29
RHOA 0.022 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.096 0.17 -10000 0 -0.35 166 166
MYH2 -0.017 0.12 0.25 8 -0.44 21 29
MST1R 0.045 0.077 0.28 50 -0.35 1 51
leukocyte activation during inflammatory response 0.047 0.055 0.27 5 -0.17 10 15
APOB 0.017 0.047 0.3 3 -0.35 7 10
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.007 0.071 -10000 0 -0.35 20 20
JAM3 -0.072 0.16 -10000 0 -0.35 136 136
GP1BA 0.02 0.021 0.28 1 -0.35 1 2
alphaM/beta2 Integrin/CTGF 0.039 0.051 0.24 5 -0.2 15 20
alphaM/beta2 Integrin -0.008 0.099 0.22 8 -0.34 21 29
JAM3 homodimer -0.072 0.16 -10000 0 -0.35 136 136
ICAM2 0.022 0.005 -10000 0 -10000 0 0
ICAM1 0.024 0.025 0.3 4 -10000 0 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.007 0.1 0.22 8 -0.34 23 31
cell adhesion 0.042 0.042 0.26 6 -0.21 4 10
NFKB1 0.024 0.088 0.3 10 -0.32 16 26
THY1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.033 0.048 0.19 31 -0.2 7 38
alphaM/beta2 Integrin/LRP/tPA 0.029 0.077 0.23 1 -0.19 49 50
IL6 -0.005 0.12 0.29 10 -0.58 16 26
ITGB2 0.025 0.029 0.28 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.053 0.042 0.23 12 -0.19 2 14
alphaM/beta2 Integrin/JAM2/JAM3 -0.075 0.16 0.28 2 -0.24 233 235
JAM2 -0.1 0.18 -10000 0 -0.35 184 184
alphaM/beta2 Integrin/ICAM1 0.074 0.064 0.27 11 -0.17 3 14
alphaM/beta2 Integrin/uPA/Plg 0.04 0.076 0.28 5 -0.18 38 43
RhoA/GTP -0.021 0.13 0.24 8 -0.44 27 35
positive regulation of phagocytosis 0.007 0.083 0.3 4 -0.28 11 15
Ron/MSP 0.05 0.055 0.21 55 -0.25 1 56
alphaM/beta2 Integrin/uPAR/uPA 0.055 0.043 0.23 12 -0.19 2 14
alphaM/beta2 Integrin/uPAR 0.046 0.04 0.23 9 -0.2 3 12
PLAU 0.023 0.02 0.28 3 -10000 0 3
PLAT -0.014 0.11 -10000 0 -0.35 49 49
actin filament polymerization -0.017 0.12 0.26 8 -0.41 23 31
MST1 0.025 0.027 0.28 6 -10000 0 6
alphaM/beta2 Integrin/lipoprotein(a) 0.052 0.059 0.29 5 -0.18 10 15
TNF 0.008 0.1 0.33 10 -0.36 12 22
RAP1B 0.023 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.045 0.038 0.23 9 -0.21 2 11
fibrinolysis 0.038 0.074 0.28 5 -0.18 38 43
HCK 0.025 0.03 0.28 7 -10000 0 7
dendritic cell antigen processing and presentation -0.007 0.1 0.22 8 -0.34 23 31
VTN -0.022 0.12 0.3 3 -0.35 65 68
alphaM/beta2 Integrin/CYR61 0.023 0.079 0.21 5 -0.21 48 53
LPA 0.035 0.06 0.28 30 -10000 0 30
LRP1 0.022 0.023 -10000 0 -0.35 2 2
cell migration 0.052 0.065 0.24 10 -0.18 18 28
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaM/beta2 Integrin/Thy1 0.044 0.038 0.24 6 -0.2 3 9
MPO 0.025 0.03 0.28 7 -10000 0 7
KNG1 0.031 0.058 0.29 25 -10000 0 25
RAP1/GDP 0.031 0.004 -10000 0 -10000 0 0
ROCK1 -0.02 0.13 0.27 7 -0.41 28 35
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.006 0.11 0.28 9 -0.35 45 54
CTGF 0.014 0.057 -10000 0 -0.35 13 13
alphaM/beta2 Integrin/Hck 0.045 0.044 0.26 10 -0.21 2 12
ITGAM 0.021 0.035 0.28 2 -0.35 3 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.021 0.11 0.37 3 -0.19 157 160
HP 0.049 0.15 0.28 112 -0.35 36 148
leukocyte adhesion -0.063 0.14 0.35 1 -0.3 86 87
SELP -0.096 0.17 -10000 0 -0.35 166 166
Ephrin A reverse 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
MAPKKK cascade 0.005 0.07 0.18 1 -0.21 51 52
EFNA5 0.012 0.066 0.28 2 -0.35 16 18
FYN -0.027 0.054 0.18 4 -0.19 48 52
neuron projection morphogenesis 0.005 0.07 0.18 1 -0.21 51 52
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.005 0.07 0.19 1 -0.21 51 52
EPHA5 -0.006 0.092 -10000 0 -0.35 36 36
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 0.024 0.043 0.19 4 -0.2 16 20
cell-cell adhesion 0.048 0.061 0.17 95 -10000 0 95
Ephrin B/EPHB2/RasGAP 0.032 0.081 -10000 0 -0.18 60 60
ITSN1 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.03 0.04 0.19 15 -0.23 6 21
Ephrin B1/EPHB1 0.008 0.069 0.19 1 -0.2 51 52
HRAS/GDP -0.028 0.098 -10000 0 -0.23 61 61
Ephrin B/EPHB1/GRB7 0.016 0.11 0.23 17 -0.2 95 112
Endophilin/SYNJ1 -0.026 0.057 0.17 12 -0.32 1 13
KRAS 0.023 0.014 0.33 1 -10000 0 1
Ephrin B/EPHB1/Src 0.01 0.1 -10000 0 -0.19 97 97
endothelial cell migration 0.037 0.033 -10000 0 -0.18 8 8
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.038 0.074 0.32 31 -0.35 2 33
PAK1 -0.025 0.074 0.31 5 -0.33 3 8
HRAS 0.022 0.005 -10000 0 -10000 0 0
RRAS -0.026 0.057 0.17 11 -0.18 52 63
DNM1 0.018 0.039 -10000 0 -0.35 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.038 0.079 0.18 19 -0.18 95 114
lamellipodium assembly -0.048 0.061 -10000 0 -0.17 95 95
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.014 0.081 -10000 0 -0.21 49 49
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
EPHB2 0.024 0.019 0.28 3 -10000 0 3
EPHB3 0.024 0.06 0.28 16 -0.35 6 22
EPHB1 -0.012 0.11 0.28 1 -0.35 50 51
EPHB4 0.022 0.004 -10000 0 -10000 0 0
mol:GDP -0.04 0.084 0.23 3 -0.24 53 56
Ephrin B/EPHB2 0.025 0.073 0.19 3 -0.18 55 58
Ephrin B/EPHB3 0.024 0.075 0.2 7 -0.19 51 58
JNK cascade -0.022 0.081 0.29 20 -0.18 50 70
Ephrin B/EPHB1 0.004 0.094 -10000 0 -0.19 97 97
RAP1/GDP -0.028 0.099 0.24 6 -0.28 23 29
EFNB2 0.02 0.028 -10000 0 -0.35 3 3
EFNB3 -0.015 0.11 -10000 0 -0.35 52 52
EFNB1 0.022 0.016 -10000 0 -0.35 1 1
Ephrin B2/EPHB1-2 0.019 0.07 0.19 3 -0.19 53 56
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.097 -10000 0 -0.23 55 55
Rap1/GTP -0.051 0.063 -10000 0 -0.3 8 8
axon guidance 0.024 0.043 0.18 4 -0.2 16 20
MAPK3 -0.021 0.073 0.18 6 -0.28 11 17
MAPK1 -0.02 0.069 0.17 2 -0.3 8 10
Rac1/GDP -0.038 0.093 0.36 1 -0.26 32 33
actin cytoskeleton reorganization -0.054 0.06 -10000 0 -0.19 53 53
CDC42/GDP -0.035 0.096 0.24 6 -0.26 32 38
PI3K 0.041 0.035 -10000 0 -0.18 8 8
EFNA5 0.012 0.066 0.28 2 -0.35 16 18
Ephrin B2/EPHB4 0.027 0.019 -10000 0 -0.2 3 3
Ephrin B/EPHB2/Intersectin/N-WASP -0.007 0.073 -10000 0 -0.19 70 70
CDC42 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.051 0.062 -10000 0 -0.18 97 97
PTK2 0.044 0.16 0.55 48 -10000 0 48
MAP4K4 -0.022 0.081 0.29 20 -0.18 50 70
SRC 0.022 0.005 -10000 0 -10000 0 0
KALRN 0.019 0.036 -10000 0 -0.35 5 5
Intersectin/N-WASP 0.032 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.035 0.098 0.3 21 -0.29 10 31
MAP2K1 -0.017 0.074 -10000 0 -0.2 47 47
WASL 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.033 0.077 -10000 0 -0.19 52 52
cell migration -0.018 0.11 0.24 13 -0.23 73 86
NRAS 0.023 0.001 -10000 0 -10000 0 0
SYNJ1 -0.026 0.058 0.17 12 -0.32 1 13
PXN 0.023 0.003 -10000 0 -10000 0 0
TF -0.031 0.061 0.17 10 -0.31 2 12
HRAS/GTP -0.003 0.087 -10000 0 -0.18 98 98
Ephrin B1/EPHB1-2 0.021 0.069 0.19 4 -0.19 51 55
cell adhesion mediated by integrin 0.015 0.065 0.18 48 -0.2 9 57
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.091 -10000 0 -0.18 98 98
RAC1-CDC42/GTP -0.048 0.065 -10000 0 -0.18 86 86
RASA1 0.019 0.036 -10000 0 -0.35 5 5
RAC1-CDC42/GDP -0.03 0.095 0.35 1 -0.26 31 32
ruffle organization -0.037 0.091 0.34 11 -0.3 8 19
NCK1 0.021 0.023 -10000 0 -0.35 2 2
receptor internalization -0.03 0.06 0.16 11 -0.27 7 18
Ephrin B/EPHB2/KALRN 0.032 0.082 -10000 0 -0.19 58 58
ROCK1 0.003 0.058 0.18 44 -0.21 6 50
RAS family/GDP -0.055 0.062 -10000 0 -0.2 54 54
Rac1/GTP -0.049 0.065 -10000 0 -0.18 95 95
Ephrin B/EPHB1/Src/Paxillin -0.024 0.092 -10000 0 -0.21 100 100
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.027 0.068 -10000 0 -0.22 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.089 0.34 3 -0.27 7 10
AP1 -0.033 0.12 -10000 0 -0.19 181 181
mol:PIP3 -0.024 0.062 -10000 0 -0.26 15 15
AKT1 -0.01 0.07 0.26 7 -0.29 9 16
PTK2B -0.024 0.096 0.19 1 -0.28 44 45
RHOA 0 0.057 0.22 3 -0.29 12 15
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.062 0.22 8 -0.26 5 13
MAGI3 0.023 0.002 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
apoptosis -0.007 0.071 -10000 0 -0.21 51 51
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.028 0.092 0.21 8 -0.28 37 45
NF kappa B1 p50/RelA 0.009 0.091 0.22 2 -0.24 35 37
endothelial cell migration -0.009 0.093 -10000 0 -0.39 28 28
ADCY4 -0.053 0.12 -10000 0 -0.34 56 56
ADCY5 -0.08 0.14 -10000 0 -0.35 77 77
ADCY6 -0.046 0.11 -10000 0 -0.32 48 48
ADCY7 -0.044 0.11 -10000 0 -0.34 42 42
ADCY1 -0.051 0.12 -10000 0 -0.34 53 53
ADCY2 -0.13 0.16 -10000 0 -0.39 120 120
ADCY3 -0.047 0.11 -10000 0 -0.32 52 52
ADCY8 -0.043 0.11 -10000 0 -0.32 43 43
ADCY9 -0.072 0.14 -10000 0 -0.35 84 84
GSK3B -0.024 0.095 0.23 8 -0.27 42 50
arachidonic acid secretion -0.063 0.13 -10000 0 -0.35 58 58
GNG2 0.017 0.049 0.28 1 -0.35 9 10
TRIP6 0.011 0.035 -10000 0 -0.33 5 5
GNAO1 -0.047 0.11 -10000 0 -0.23 131 131
HRAS 0.022 0.005 -10000 0 -10000 0 0
NFKBIA -0.017 0.087 0.26 6 -0.25 28 34
GAB1 0.02 0.032 -10000 0 -0.35 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.18 -10000 0 -0.82 24 24
JUN 0.018 0.042 -10000 0 -0.35 7 7
LPA/LPA2/NHERF2 0.027 0.023 0.19 2 -10000 0 2
TIAM1 -0.014 0.21 -10000 0 -0.96 24 24
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.009 0.061 0.22 8 -0.19 22 30
PLCB3 0.013 0.036 0.18 18 -10000 0 18
FOS -0.088 0.17 -10000 0 -0.35 160 160
positive regulation of mitosis -0.063 0.13 -10000 0 -0.35 58 58
LPA/LPA1-2-3 0.027 0.084 0.2 19 -0.2 49 68
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.007 -10000 0 -10000 0 0
stress fiber formation -0.01 0.081 0.21 1 -0.3 18 19
GNAZ -0.007 0.067 -10000 0 -0.23 40 40
EGFR/PI3K-beta/Gab1 0 0.072 -10000 0 -0.27 15 15
positive regulation of dendritic cell cytokine production 0.026 0.083 0.19 15 -0.2 49 64
LPA/LPA2/MAGI-3 0.028 0.024 0.19 2 -10000 0 2
ARHGEF1 -0.006 0.056 0.18 20 -0.2 23 43
GNAI2 0 0.055 -10000 0 -0.23 27 27
GNAI3 -0.001 0.056 -10000 0 -0.23 28 28
GNAI1 -0.003 0.06 -10000 0 -0.23 33 33
LPA/LPA3 0.01 0.07 0.19 24 -0.19 39 63
LPA/LPA2 0.015 0.023 0.19 2 -0.095 13 15
LPA/LPA1 0.004 0.067 -10000 0 -0.26 30 30
HB-EGF/EGFR 0.046 0.055 0.22 5 -0.2 12 17
HBEGF 0.042 0.066 0.12 217 -10000 0 217
mol:DAG -0.009 0.061 0.22 8 -0.19 22 30
cAMP biosynthetic process -0.083 0.13 0.23 1 -0.3 100 101
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
SRC 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
LYN -0.008 0.089 0.27 10 -0.24 25 35
GNAQ 0.001 0.051 -10000 0 -0.2 27 27
LPAR2 0.024 0.021 0.3 3 -10000 0 3
LPAR3 0.017 0.099 0.28 25 -0.35 26 51
LPAR1 0.009 0.068 -10000 0 -0.26 26 26
IL8 0.033 0.14 0.34 8 -0.36 20 28
PTK2 -0.015 0.062 0.18 9 -0.19 36 45
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
CASP3 -0.007 0.071 -10000 0 -0.21 51 51
EGFR 0.015 0.059 0.33 1 -0.35 13 14
PLCG1 -0.007 0.062 0.16 7 -0.21 32 39
PLD2 -0.017 0.064 0.18 8 -0.19 49 57
G12/G13 0.029 0.059 -10000 0 -0.21 25 25
PI3K-beta 0.001 0.064 -10000 0 -0.28 14 14
cell migration 0.001 0.064 -10000 0 -0.26 22 22
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
PXN -0.01 0.082 0.21 1 -0.3 18 19
HRAS/GTP -0.064 0.13 -10000 0 -0.36 58 58
RAC1 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 220 -10000 0 220
PRKCE 0.023 0.003 -10000 0 -10000 0 0
PRKCD -0.015 0.068 0.21 12 -0.25 7 19
Gi(beta/gamma) -0.046 0.11 -10000 0 -0.33 47 47
mol:LPA -0.003 0.026 -10000 0 -0.14 16 16
TRIP6/p130 Cas/FAK1/Paxillin 0.006 0.081 -10000 0 -0.34 11 11
MAPKKK cascade -0.063 0.13 -10000 0 -0.35 58 58
contractile ring contraction involved in cytokinesis -0.002 0.061 0.22 3 -0.28 15 18
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.078 -10000 0 -0.22 66 66
GNA15 0.003 0.051 0.12 3 -0.2 26 29
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.028 0.094 0.22 8 -0.28 38 46
GNA11 -0.003 0.057 -10000 0 -0.2 36 36
Rac1/GTP 0.001 0.19 -10000 0 -0.87 24 24
MMP2 -0.009 0.094 -10000 0 -0.39 28 28
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.031 0.031 0.21 3 -0.25 5 8
CRKL -0.032 0.13 0.31 3 -0.54 22 25
mol:PIP3 -0.01 0.12 -10000 0 -0.78 12 12
AKT1 -0.01 0.11 0.35 2 -0.69 12 14
PTK2B 0.02 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.033 0.13 0.29 4 -0.51 22 26
RANBP10 0.021 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
HGF/MET/SHIP2 -0.005 0.1 0.2 4 -0.21 106 110
MAP3K5 -0.025 0.13 0.29 5 -0.49 24 29
HGF/MET/CIN85/CBL/ENDOPHILINS 0.006 0.1 0.21 4 -0.19 105 109
AP1 -0.049 0.12 0.17 2 -0.22 149 151
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis -0.21 0.35 -10000 0 -0.71 172 172
STAT3 (dimer) -0.027 0.092 -10000 0 -0.33 17 17
GAB1/CRKL/SHP2/PI3K -0.008 0.13 -10000 0 -0.47 22 22
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
CBL/CRK -0.022 0.13 0.3 3 -0.52 22 25
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
ELK1 0.011 0.1 0.3 47 -10000 0 47
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.02 0.074 -10000 0 -0.26 26 26
PAK1 -0.009 0.11 0.36 6 -0.66 12 18
HGF/MET/RANBP10 -0.007 0.1 0.2 4 -0.21 106 110
HRAS -0.039 0.14 -10000 0 -0.54 24 24
DOCK1 -0.032 0.14 0.32 8 -0.49 25 33
GAB1 -0.032 0.14 -10000 0 -0.58 22 22
CRK -0.031 0.13 0.33 2 -0.56 21 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.069 0.19 -10000 0 -0.42 110 110
JUN 0.018 0.042 -10000 0 -0.35 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.073 -10000 0 -0.17 104 104
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
cell morphogenesis -0.023 0.13 0.3 15 -0.4 22 37
GRB2/SHC -0.002 0.071 -10000 0 -0.22 18 18
FOS -0.089 0.17 -10000 0 -0.35 160 160
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.011 0.1 0.3 47 -10000 0 47
HGF/MET/MUC20 -0.016 0.098 0.19 4 -0.21 106 110
cell migration -0.002 0.07 -10000 0 -0.21 18 18
GRB2 0.022 0.006 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.028 0.033 0.21 4 -0.25 5 9
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.088 0.17 1 -0.21 89 90
MET/MUC20 0.015 0.029 0.19 4 -0.24 5 9
RAP1B -0.034 0.12 0.27 4 -0.49 21 25
RAP1A -0.035 0.12 0.27 4 -0.48 22 26
HGF/MET/RANBP9 -0.004 0.1 0.2 3 -0.21 102 105
RAF1 -0.036 0.14 -10000 0 -0.5 25 25
STAT3 -0.026 0.092 -10000 0 -0.33 16 16
cell proliferation -0.017 0.14 0.29 14 -0.31 73 87
RPS6KB1 -0.009 0.054 -10000 0 -0.28 13 13
MAPK3 0.006 0.14 0.62 21 -10000 0 21
MAPK1 0.019 0.16 0.62 32 -10000 0 32
RANBP9 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.019 0.13 0.3 3 -0.46 27 30
SRC -0.028 0.08 0.15 1 -0.2 85 86
PI3K -0.004 0.078 -10000 0 -0.24 19 19
MET/Glomulin 0.015 0.032 0.21 4 -0.21 5 9
SOS1 0.023 0.003 -10000 0 -10000 0 0
MAP2K1 -0.034 0.13 -10000 0 -0.47 25 25
MET 0.021 0.042 0.28 4 -0.35 5 9
MAP4K1 -0.026 0.14 0.3 4 -0.52 24 28
PTK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K2 -0.035 0.13 -10000 0 -0.47 24 24
BAD -0.009 0.11 0.4 4 -0.66 12 16
MAP2K4 -0.023 0.12 0.27 5 -0.44 23 28
SHP2/GRB2/SOS1/GAB1 -0.013 0.13 -10000 0 -0.48 22 22
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PXN 0.023 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.003 -10000 0 -10000 0 0
HGS -0.027 0.065 -10000 0 -0.16 98 98
PLCgamma1/PKC 0.016 0.004 -10000 0 -10000 0 0
HGF -0.05 0.15 -10000 0 -0.35 104 104
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.005 0.085 -10000 0 -0.17 101 101
PDPK1 -0.011 0.11 0.24 3 -0.73 12 15
HGF/MET/SHIP -0.005 0.1 0.2 4 -0.21 106 110
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.022 0.004 -10000 0 -10000 0 0
VLDLR 0.021 0.023 -10000 0 -0.35 2 2
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.039 0.12 0.23 8 -0.21 179 187
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.065 0.09 0.18 12 -0.19 170 182
IQGAP1/CaM 0.032 0.008 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
PLA2G7 0.02 0.038 0.28 1 -0.35 5 6
CALM1 0.022 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.003 -10000 0 -10000 0 0
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
LIS1/Poliovirus Protein 3A -0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.048 0.079 0.28 56 -10000 0 56
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.038 0.12 0.21 16 -0.21 178 194
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.041 0.096 0.29 11 -0.22 5 16
MAP1B -0.006 0.047 -10000 0 -0.23 23 23
RAC1 0.008 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.064 0.08 0.18 9 -10000 0 9
RELN -0.1 0.18 0.28 7 -0.35 182 189
PAFAH/LIS1 0.019 0.025 0.2 1 -0.21 5 6
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.036 0.08 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.05 0.11 0.25 2 -0.27 16 18
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.05 0.084 0.22 10 -0.21 5 15
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.008 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.034 0.28 9 -10000 0 9
PAFAH1B2 0.022 0.017 -10000 0 -0.35 1 1
MAP1B/LIS1/Dynein heavy chain 0.009 0.041 -10000 0 -0.17 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.032 0.1 0.3 9 -0.22 8 17
LRP8 0.025 0.026 0.29 5 -10000 0 5
NDEL1/Katanin 60 -0.044 0.095 0.29 10 -0.22 9 19
P39/CDK5 -0.052 0.1 0.18 44 -0.18 56 100
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.008 -10000 0 -10000 0 0
CDK5 -0.064 0.084 0.18 10 -0.18 169 179
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.03 0.11 0.21 12 -0.18 173 185
RELN/VLDLR -0.027 0.12 0.21 7 -0.19 176 183
CDC42 0.008 0.003 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.083 0.46 -10000 0 -1.1 46 46
STAT6 (cleaved dimer) -0.11 0.44 0.59 1 -1.1 55 56
IGHG1 0.005 0.22 0.4 10 -0.7 7 17
IGHG3 -0.097 0.44 0.59 1 -1 55 56
AKT1 -0.023 0.27 0.59 1 -0.85 11 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.009 0.22 0.52 2 -0.91 7 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.026 0.28 0.53 2 -0.76 21 23
THY1 -0.094 0.46 0.67 1 -1.1 49 50
MYB 0.048 0.076 0.28 52 -10000 0 52
HMGA1 0.061 0.092 0.28 78 -10000 0 78
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.018 0.31 0.58 4 -0.69 29 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.009 0.27 0.51 3 -0.87 10 13
SP1 0.025 0.012 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
SOCS5 0.004 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.098 0.45 0.6 1 -1.1 53 54
SOCS1 -0.046 0.32 0.51 2 -0.7 45 47
SOCS3 -0.015 0.27 0.55 1 -0.98 6 7
FCER2 -0.073 0.4 0.72 2 -0.94 44 46
PARP14 0.024 0.006 -10000 0 -10000 0 0
CCL17 -0.09 0.46 0.74 2 -1.1 52 54
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.014 0.22 0.46 5 -0.69 8 13
T cell proliferation -0.11 0.45 0.64 1 -1.1 50 51
IL4R/JAK1 -0.11 0.45 -10000 0 -1.1 51 51
EGR2 -0.12 0.52 0.72 1 -1.3 56 57
JAK2 0.011 0.081 -10000 0 -0.36 9 9
JAK3 0.024 0.027 0.3 4 -10000 0 4
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
JAK1 0.017 0.037 -10000 0 -0.35 1 1
COL1A2 0.001 0.23 -10000 0 -1.1 8 8
CCL26 -0.094 0.46 -10000 0 -1.1 47 47
IL4R -0.096 0.49 0.74 2 -1.2 49 51
PTPN6 0.008 0.035 0.34 1 -10000 0 1
IL13RA2 -0.089 0.46 0.67 1 -1.1 50 51
IL13RA1 0.018 0.066 0.18 1 -10000 0 1
IRF4 0.001 0.24 0.51 2 -1 19 21
ARG1 0.017 0.18 0.44 2 -0.55 7 9
CBL -0.022 0.28 0.51 4 -0.66 27 31
GTF3A 0.025 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL13RA1/JAK2 0.03 0.1 0.22 8 -0.26 7 15
IRF4/BCL6 0 0.22 -10000 0 -0.95 19 19
CD40LG 0.017 0.06 -10000 0 -0.32 15 15
MAPK14 -0.02 0.28 0.52 4 -0.7 23 27
mitosis -0.019 0.26 0.52 2 -0.79 11 13
STAT6 -0.098 0.53 0.8 3 -1.2 54 57
SPI1 0.025 0.02 0.28 3 -10000 0 3
RPS6KB1 -0.016 0.25 0.56 1 -0.76 11 12
STAT6 (dimer) -0.098 0.53 0.8 3 -1.2 54 57
STAT6 (dimer)/PARP14 -0.11 0.47 0.64 1 -1.2 53 54
mast cell activation -0.002 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.27 0.57 3 -0.85 12 15
FRAP1 -0.023 0.27 0.59 1 -0.85 11 12
LTA -0.092 0.46 0.69 2 -1.1 48 50
FES 0.022 0.017 -10000 0 -0.35 1 1
T-helper 1 cell differentiation 0.094 0.52 1.2 54 -0.8 3 57
CCL11 -0.11 0.46 -10000 0 -1.1 56 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.007 0.26 0.53 3 -0.9 9 12
IL2RG 0.023 0.042 0.29 6 -0.35 3 9
IL10 -0.064 0.47 0.76 10 -1.1 44 54
IRS1 -0.013 0.11 -10000 0 -0.35 51 51
IRS2 -0.024 0.12 -10000 0 -0.35 66 66
IL4 0.015 0.21 -10000 0 -0.95 9 9
IL5 -0.099 0.46 0.67 1 -1.1 52 53
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.056 0.41 0.66 4 -0.9 49 53
COL1A1 -0.017 0.29 -10000 0 -1 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.11 0.46 -10000 0 -1.2 45 45
IL2R gamma/JAK3 0.036 0.044 0.31 7 -0.25 3 10
TFF3 -0.095 0.53 0.77 1 -1.2 62 63
ALOX15 -0.077 0.47 0.72 2 -1.1 47 49
MYBL1 0.021 0.007 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.095 0.42 0.64 2 -0.95 57 59
SHC1 0.019 0.009 -10000 0 -10000 0 0
CEBPB 0.023 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.029 0.27 0.51 2 -0.82 14 16
mol:PI-3-4-5-P3 -0.022 0.27 0.59 1 -0.85 11 12
PI3K -0.027 0.28 0.59 1 -0.93 11 12
DOK2 0.021 0.021 0.28 3 -10000 0 3
ETS1 0.001 0.04 -10000 0 -0.33 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.018 0.21 0.44 5 -0.59 10 15
ITGB3 -0.22 0.62 0.67 1 -1.2 119 120
PIGR -0.097 0.57 0.78 9 -1.2 73 82
IGHE 0 0.071 0.18 27 -0.17 6 33
MAPKKK cascade 0.019 0.21 0.44 5 -0.58 10 15
BCL6 0.019 0.019 -10000 0 -0.35 1 1
OPRM1 -0.096 0.46 0.69 1 -1.1 48 49
RETNLB -0.096 0.46 0.7 1 -1.1 48 49
SELP -0.3 0.69 0.78 8 -1.2 185 193
AICDA -0.098 0.44 0.66 1 -1.1 51 52
Visual signal transduction: Rods

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:K + 0.022 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.017 0.19 5 -10000 0 5
Metarhodopsin II/Arrestin 0.026 0.014 0.19 3 -10000 0 3
PDE6G/GNAT1/GTP 0.037 0.043 0.19 38 -0.2 1 39
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.022 0.026 0.28 5 -10000 0 5
GRK1 0.018 0.013 0.28 1 -10000 0 1
CNG Channel 0.039 0.059 0.23 8 -0.17 22 30
mol:Na + 0.041 0.047 0.27 3 -0.18 7 10
mol:ADP 0.018 0.012 0.28 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 111 125
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.051 0.054 0.32 3 -0.18 7 10
CNGB1 0.032 0.055 0.28 25 -10000 0 25
RDH5 0.024 0.019 0.28 3 -10000 0 3
SAG 0.019 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.064 0.31 16 -10000 0 16
Na + (4 Units) 0.031 0.039 0.2 3 -0.17 7 10
RGS9 -0.057 0.15 -10000 0 -0.35 113 113
GNB1/GNGT1 0.091 0.084 0.21 179 -10000 0 179
GNAT1/GDP 0.001 0.097 0.2 15 -0.18 111 126
GUCY2D 0.026 0.039 0.28 12 -10000 0 12
GNGT1 0.11 0.12 0.28 188 -10000 0 188
GUCY2F 0.019 0.003 -10000 0 -10000 0 0
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.016 0.048 0.17 11 -0.18 22 33
mol:11-cis-retinal 0.024 0.019 0.28 3 -10000 0 3
mol:cGMP 0.038 0.04 0.25 1 -0.18 7 8
GNB1 0.022 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.019 0.21 5 -10000 0 5
SLC24A1 0.022 0.005 -10000 0 -10000 0 0
CNGA1 0.03 0.042 0.28 15 -10000 0 15
Metarhodopsin II 0.023 0.015 0.18 4 -10000 0 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.05 0.048 0.35 1 -0.19 7 8
RGS9BP 0.033 0.056 0.29 23 -10000 0 23
Metarhodopsin II/Transducin 0.036 0.043 0.16 27 -10000 0 27
GCAP Family/Ca ++ 0.038 0.037 0.19 15 -0.19 7 22
PDE6A/B 0.023 0.057 0.21 4 -0.24 21 25
mol:Pi -0.008 0.11 0.21 14 -0.21 111 125
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.086 0.075 0.2 166 -10000 0 166
PDE6B 0.008 0.074 0.28 2 -0.35 21 23
PDE6A 0.024 0.022 0.28 4 -10000 0 4
PDE6G 0.043 0.075 0.29 45 -0.35 1 46
RHO 0.02 0.02 0.28 3 -10000 0 3
PDE6 0.009 0.12 0.27 10 -0.19 124 134
GUCA1A 0.028 0.046 0.28 17 -10000 0 17
GC2/GCAP Family 0.05 0.04 -10000 0 -0.2 7 7
GUCA1C 0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.018 0.042 -10000 0 -0.35 7 7
Arf6 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
CENTA1/KIF3B 0.026 0.012 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.012 0.13 -10000 0 -0.78 11 11
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
USP6 0.021 0.006 -10000 0 -10000 0 0
IQSEC1 0.022 0.017 -10000 0 -0.35 1 1
EGFR/EGFR/EGF/EGF 0.031 0.058 0.21 21 -0.25 14 35
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP 0.011 0.05 0.13 26 -0.15 15 41
ARRB1 0.021 0.023 -10000 0 -0.35 2 2
FBXO8 0.022 0.004 -10000 0 -10000 0 0
TSHR 0.026 0.057 0.28 19 -0.35 3 22
EGF 0.03 0.056 0.28 21 -0.35 2 23
somatostatin receptor activity 0 0 0.001 6 -0.001 68 74
ARAP2 0.02 0.028 -10000 0 -0.35 3 3
mol:GDP -0.063 0.12 0.18 5 -0.3 76 81
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 31 34
ITGA2B 0.018 0.041 0.28 1 -0.35 6 7
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 0.21 1 -0.19 2 3
ADAP1 0.022 0.005 -10000 0 -10000 0 0
KIF13B 0.02 0.008 -10000 0 -10000 0 0
HGF/MET -0.022 0.12 0.21 4 -0.25 106 110
PXN 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.059 0.11 0.22 6 -0.27 69 75
EGFR/EGFR/EGF/EGF/ARFGEP100 0.041 0.054 0.2 20 -0.21 15 35
ADRB2 -0.043 0.14 -10000 0 -0.35 93 93
receptor agonist activity 0 0 0 3 0 58 61
actin filament binding 0 0 0 5 -0.001 69 74
SRC 0.022 0.005 -10000 0 -10000 0 0
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
EFA6/PI-4-5-P2 0 0 0.001 10 -0.001 39 49
ARF6/GDP -0.016 0.14 0.25 11 -0.42 44 55
ARF6/GDP/GULP/ACAP1 -0.058 0.14 -10000 0 -0.34 68 68
alphaIIb/beta3 Integrin/paxillin/GIT1 0.013 0.094 0.21 3 -0.19 92 95
ACAP1 0.022 0.026 0.28 3 -0.35 1 4
ACAP2 0.02 0.017 -10000 0 -0.35 1 1
LHCGR/beta Arrestin2 0.011 0.018 -10000 0 -10000 0 0
EFNA1 0.02 0.02 0.3 2 -10000 0 2
HGF -0.05 0.15 -10000 0 -0.35 104 104
CYTH3 -0.006 0.001 -10000 0 -10000 0 0
CYTH2 -0.005 0.14 -10000 0 -0.99 11 11
NCK1 0.021 0.023 -10000 0 -0.35 2 2
fibronectin binding 0 0 0.001 7 0 54 61
endosomal lumen acidification 0 0 0.001 11 0 55 66
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.018 0.12 -10000 0 -0.35 59 59
GNAQ/ARNO 0.007 0.13 -10000 0 -0.92 11 11
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 6 0 8 14
MET 0.021 0.042 0.28 4 -0.35 5 9
GNA14 -0.01 0.1 -10000 0 -0.35 45 45
GNA15 0.025 0.03 0.28 7 -10000 0 7
GIT1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 9 -0.001 49 58
GNA11 0.014 0.051 -10000 0 -0.35 10 10
LHCGR 0.004 0.017 -10000 0 -10000 0 0
AGTR1 -0.061 0.15 0.28 2 -0.35 113 115
desensitization of G-protein coupled receptor protein signaling pathway 0.011 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO 0.019 0.13 -10000 0 -0.83 11 11
alphaIIb/beta3 Integrin -0.017 0.11 0.21 3 -0.24 96 99
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 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EGF/EGFR -0.019 0.1 0.18 1 -0.18 151 152
EGF/EGFR dimer/SHC/GRB2/SOS1 0.048 0.052 0.23 1 -0.18 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.082 0.17 -10000 0 -0.35 150 150
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.031 0.055 0.28 21 -0.35 2 23
EGF/EGFR dimer/SHC 0.037 0.049 0.2 18 -0.21 10 28
mol:GDP 0.043 0.049 0.21 1 -0.18 10 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.042 -10000 0 -0.35 7 7
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.028 0.037 -10000 0 -0.17 10 10
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.046 -10000 0 -0.17 10 10
FRAP1 -0.013 0.029 0.17 5 -0.17 10 15
EGF/EGFR dimer 0.032 0.058 0.21 21 -0.24 14 35
SOS1 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.048 0.13 -10000 0 -0.25 152 152
HIF-2-alpha transcription factor network

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
MMP14 -0.003 0.089 -10000 0 -0.63 8 8
oxygen homeostasis -0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.023 0.012 0.28 1 -10000 0 1
TCEB1 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.002 0.092 0.24 1 -0.26 6 7
EPO -0.084 0.17 -10000 0 -0.5 27 27
FIH (dimer) -0.003 0.028 -10000 0 -10000 0 0
APEX1 -0.008 0.031 -10000 0 -10000 0 0
SERPINE1 -0.081 0.16 -10000 0 -0.41 52 52
FLT1 -0.043 0.19 -10000 0 -0.71 33 33
ADORA2A -0.065 0.17 0.3 28 -0.39 51 79
germ cell development -0.08 0.17 -10000 0 -0.42 54 54
SLC11A2 -0.08 0.16 -10000 0 -0.4 50 50
BHLHE40 -0.079 0.16 -10000 0 -0.4 51 51
HIF1AN -0.003 0.028 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.037 0.11 -10000 0 -0.31 14 14
ETS1 0.021 0.033 -10000 0 -0.36 1 1
CITED2 -0.031 0.19 -10000 0 -0.88 24 24
KDR -0.072 0.28 -10000 0 -0.88 52 52
PGK1 -0.08 0.16 -10000 0 -0.4 51 51
SIRT1 0.02 0.024 -10000 0 -0.35 2 2
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.076 0.19 -10000 0 -0.44 51 51
EPAS1 -0.031 0.07 -10000 0 -0.27 11 11
SP1 0.025 0.007 -10000 0 -10000 0 0
ABCG2 -0.16 0.24 -10000 0 -0.44 207 207
EFNA1 -0.076 0.16 0.35 1 -0.4 51 52
FXN -0.065 0.17 0.3 29 -0.39 49 78
POU5F1 -0.082 0.17 -10000 0 -0.43 54 54
neuron apoptosis 0.075 0.18 0.44 51 -10000 0 51
EP300 0.021 0.006 -10000 0 -10000 0 0
EGLN3 -0.003 0.038 0.28 3 -0.37 1 4
EGLN2 -0.004 0.028 -10000 0 -10000 0 0
EGLN1 -0.002 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.04 0.021 0.2 1 -0.21 1 2
VHL 0.022 0.017 -10000 0 -0.35 1 1
ARNT -0.005 0.027 -10000 0 -10000 0 0
SLC2A1 -0.064 0.18 0.3 30 -0.39 49 79
TWIST1 -0.084 0.21 0.3 29 -0.5 62 91
ELK1 0.022 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.033 0.11 -10000 0 -0.32 8 8
VEGFA -0.079 0.16 -10000 0 -0.4 50 50
CREBBP 0.022 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.044 0.16 36 -0.18 2 38
RFC1 0.006 0.046 0.16 38 -0.18 3 41
PRKDC 0.02 0.071 0.2 67 -0.18 2 69
RIPK1 0.022 0.007 -10000 0 -10000 0 0
CASP7 -0.002 0.096 -10000 0 -0.55 15 15
FASLG/FAS/FADD/FAF1 0.018 0.053 0.17 40 -0.2 3 43
MAP2K4 0.018 0.093 0.28 7 -0.32 18 25
mol:ceramide 0.012 0.049 0.19 1 -0.22 4 5
GSN 0.005 0.046 0.16 36 -0.18 5 41
FASLG/FAS/FADD/FAF1/Caspase 8 0.021 0.055 0.24 4 -10000 0 4
FAS 0.018 0.033 -10000 0 -0.35 4 4
BID -0.015 0.019 0.24 2 -0.16 1 3
MAP3K1 0.015 0.091 0.27 6 -0.38 15 21
MAP3K7 0.022 0.007 -10000 0 -10000 0 0
RB1 0.006 0.044 0.16 36 -0.18 2 38
CFLAR 0.022 0.006 -10000 0 -10000 0 0
HGF/MET -0.034 0.13 0.2 3 -0.23 153 156
ARHGDIB 0.006 0.047 0.17 38 -0.18 3 41
FADD 0.022 0.01 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.053 0.18 16 -0.16 36 52
NFKB1 -0.003 0.11 -10000 0 -0.58 17 17
MAPK8 0.013 0.11 0.32 9 -0.44 20 29
DFFA 0.007 0.05 0.17 40 -0.18 2 42
DNA fragmentation during apoptosis 0.002 0.054 0.17 39 -0.18 15 54
FAS/FADD/MET 0.038 0.04 0.2 4 -0.21 9 13
CFLAR/RIP1 0.032 0.01 -10000 0 -10000 0 0
FAIM3 0.019 0.026 0.28 1 -0.35 2 3
FAF1 0.022 0.01 -10000 0 -10000 0 0
PARP1 0.007 0.048 0.17 40 -0.18 3 43
DFFB 0.007 0.046 0.17 39 -0.18 2 41
CHUK -0.007 0.1 0.31 1 -0.55 16 17
FASLG 0.021 0.042 0.29 8 -0.35 2 10
FAS/FADD 0.029 0.028 -10000 0 -0.24 4 4
HGF -0.05 0.15 -10000 0 -0.35 104 104
LMNA 0.012 0.068 0.23 27 -0.17 7 34
CASP6 0.006 0.049 0.17 38 -0.18 3 41
CASP10 0.021 0.024 -10000 0 -0.35 2 2
CASP3 0.012 0.052 0.2 37 -10000 0 37
PTPN13 -0.025 0.12 -10000 0 -0.35 68 68
CASP8 -0.016 0.022 0.3 2 -0.19 1 3
IL6 -0.012 0.22 -10000 0 -0.86 28 28
MET 0.021 0.042 0.28 4 -0.35 5 9
ICAD/CAD 0.005 0.047 0.16 40 -0.17 1 41
FASLG/FAS/FADD/FAF1/Caspase 10 0.012 0.049 0.19 1 -0.22 4 5
activation of caspase activity by cytochrome c -0.015 0.019 0.24 2 -0.16 1 3
PAK2 0.021 0.076 0.21 69 -0.18 2 71
BCL2 -0.008 0.1 -10000 0 -0.35 44 44
S1P5 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
telencephalon oligodendrocyte cell migration 0.036 0.1 0.29 29 -10000 0 29
GNAI2 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.029 0.19 10 -0.2 3 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
RhoA/GTP -0.036 0.1 -10000 0 -0.29 29 29
negative regulation of cAMP metabolic process -0.039 0.1 0.17 2 -0.22 116 118
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.038 0.1 0.17 2 -0.22 113 115
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
Glypican 2 network

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
MDK 0.023 0.014 0.33 1 -9999 0 1
GPC2 0.041 0.068 0.28 39 -9999 0 39
GPC2/Midkine 0.043 0.045 0.21 34 -9999 0 34
neuron projection morphogenesis 0.043 0.045 0.21 34 -9999 0 34
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.028 -10000 0 -0.35 3 3
SVIL -0.017 0.12 -10000 0 -0.35 57 57
ZNF318 0.02 0.011 -10000 0 -10000 0 0
JMJD2C -0.003 0.031 0.083 9 -0.13 27 36
T-DHT/AR/Ubc9 -0.01 0.095 -10000 0 -0.21 92 92
CARM1 0.022 0.006 -10000 0 -10000 0 0
PRDX1 0.023 0.003 -10000 0 -10000 0 0
PELP1 0.021 0.006 -10000 0 -10000 0 0
CTNNB1 0.023 0.005 -10000 0 -10000 0 0
AKT1 0.021 0.009 -10000 0 -10000 0 0
PTK2B 0.02 0.008 -10000 0 -10000 0 0
MED1 0.02 0.009 -10000 0 -10000 0 0
MAK 0.038 0.067 0.28 38 -10000 0 38
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.02 0.032 -10000 0 -0.35 4 4
GSN 0.019 0.036 -10000 0 -0.35 5 5
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
NCOA6 0.023 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.022 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.019 0.009 -10000 0 -10000 0 0
cell proliferation 0.017 0.066 0.21 33 -0.52 2 35
XRCC5 0.021 0.008 -10000 0 -10000 0 0
UBE3A 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.028 0.11 0.19 1 -0.22 126 127
FHL2 -0.005 0.092 -10000 0 -0.76 6 6
RANBP9 0.023 0.005 -10000 0 -10000 0 0
JMJD1A 0.005 0.022 0.087 22 -0.11 8 30
CDK6 0.014 0.055 -10000 0 -0.35 12 12
TGFB1I1 -0.09 0.17 -10000 0 -0.35 163 163
T-DHT/AR/CyclinD1 -0.008 0.095 0.19 1 -0.21 90 91
XRCC6 0.02 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.007 0.11 -10000 0 -0.21 106 106
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.021 0.009 -10000 0 -10000 0 0
BRCA1 0.023 0.006 -10000 0 -10000 0 0
TCF4 0.007 0.069 -10000 0 -0.35 19 19
CDKN2A 0.12 0.13 0.28 216 -10000 0 216
SRF 0.024 0.017 -10000 0 -0.14 4 4
NKX3-1 -0.015 0.053 0.086 3 -0.12 89 92
KLK3 -0.014 0.059 -10000 0 -10000 0 0
TMF1 0.022 0.005 -10000 0 -10000 0 0
HNRNPA1 0.021 0.009 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 -0.012 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.01 0.094 -10000 0 -0.21 89 89
AR -0.042 0.14 -10000 0 -0.35 91 91
UBA3 0.023 0.005 -10000 0 -10000 0 0
PATZ1 0.02 0.009 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
PRKDC 0.019 0.01 -10000 0 -10000 0 0
PA2G4 0.02 0.009 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.007 0.085 -10000 0 -0.19 89 89
RPS6KA3 0.023 0.017 -10000 0 -0.35 1 1
T-DHT/AR/ARA70 -0.01 0.095 -10000 0 -0.21 90 90
LATS2 0.02 0.018 -10000 0 -0.35 1 1
T-DHT/AR/PRX1 -0.007 0.085 -10000 0 -0.19 90 90
Cyclin D3/CDK11 p58 0.017 0.003 -10000 0 -10000 0 0
VAV3 0.083 0.11 0.28 125 -10000 0 125
KLK2 -0.044 0.18 -10000 0 -0.74 32 32
CASP8 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.001 0.094 -10000 0 -0.2 84 84
TMPRSS2 -0.011 0.12 0.3 1 -0.73 11 12
CCND1 0.024 0.022 0.31 3 -10000 0 3
PIAS1 0.023 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.001 0.015 -10000 0 -0.051 36 36
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.013 0.098 -10000 0 -0.21 97 97
CMTM2 0.021 0.021 0.28 3 -10000 0 3
SNURF -0.006 0.097 0.28 1 -0.35 39 40
ZMIZ1 0.017 0.036 -10000 0 -0.3 4 4
CCND3 0.023 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.01 -10000 0 -10000 0 0
FKBP4 0.023 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 -0.047 0.069 -10000 0 -0.34 8 8
SMARCC2 0.023 0.006 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 0.055 0.12 0.45 4 -0.65 10 14
SUMO2 0.018 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.027 0.016 0.28 2 -10000 0 2
FKBP4 0.022 0.004 -10000 0 -10000 0 0
FKBP5 0.018 0.042 -10000 0 -0.35 7 7
GR alpha/HSP90/FKBP51/HSP90 -0.063 0.1 0.26 2 -0.26 62 64
PRL 0.018 0.24 0.4 24 -1.1 20 44
cortisol/GR alpha (dimer)/TIF2 -0.12 0.16 0.46 4 -0.39 43 47
RELA 0.014 0.078 -10000 0 -0.19 44 44
FGG -0.12 0.15 0.42 4 -0.37 46 50
GR beta/TIF2 -0.081 0.11 0.27 2 -0.31 70 72
IFNG 0.089 0.15 0.41 11 -0.46 4 15
apoptosis -0.12 0.2 0.51 6 -0.52 63 69
CREB1 0.03 0.023 -10000 0 -10000 0 0
histone acetylation 0.035 0.071 0.22 1 -0.25 4 5
BGLAP 0.086 0.096 0.35 6 -10000 0 6
GR/PKAc -0.054 0.097 0.27 1 -0.24 59 60
NF kappa B1 p50/RelA 0.028 0.14 -10000 0 -0.31 66 66
SMARCD1 0.023 0.005 -10000 0 -10000 0 0
MDM2 -0.024 0.047 0.18 4 -10000 0 4
GATA3 0.027 0.057 0.28 13 -0.35 6 19
AKT1 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.023 0.055 -10000 0 -10000 0 0
GSK3B 0.019 0.014 -10000 0 -10000 0 0
NR1I3 -0.078 0.19 0.5 7 -0.53 28 35
CSN2 -0.12 0.13 0.32 4 -0.33 50 54
BRG1/BAF155/BAF170/BAF60A 0.054 0.025 -10000 0 -10000 0 0
NFATC1 0.014 0.057 -10000 0 -0.35 13 13
POU2F1 0.012 0.052 -10000 0 -0.26 17 17
CDKN1A 0.014 0.071 -10000 0 -1 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 0.21 0.12 0.28 385 -10000 0 385
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.062 0.15 0.29 23 -0.24 55 78
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.15 0.27 0.46 7 -0.75 76 83
JUN 0.096 0.11 0.3 45 -0.38 3 48
IL4 0.055 0.079 -10000 0 -10000 0 0
CDK5R1 0.021 0.015 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.11 0.1 -10000 0 -0.26 119 119
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.052 0.1 0.28 1 -0.24 61 62
cortisol/GR alpha (monomer) -0.14 0.18 0.51 6 -0.42 52 58
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.04 0.19 0.21 6 -0.33 158 164
AP-1/NFAT1-c-4 0.1 0.19 0.4 59 -0.5 10 69
AFP 0.072 0.091 -10000 0 -10000 0 0
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 -0.062 0.09 0.34 1 -0.35 1 2
TP53 0.028 0.038 -10000 0 -0.83 1 1
PPP5C 0.023 0.004 -10000 0 -10000 0 0
KRT17 0.094 0.2 0.41 47 -0.85 10 57
KRT14 0.098 0.12 0.44 8 -10000 0 8
TBP 0.026 0.005 -10000 0 -10000 0 0
CREBBP -0.009 0.048 -10000 0 -0.25 1 1
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.007 -10000 0 -10000 0 0
AP-1 0.1 0.19 0.4 59 -0.5 10 69
MAPK14 0.018 0.014 -10000 0 -10000 0 0
MAPK10 -0.058 0.15 -10000 0 -0.35 111 111
MAPK11 0.016 0.026 -10000 0 -0.35 2 2
KRT5 0.1 0.23 0.4 56 -0.93 14 70
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.023 0.016 -10000 0 -0.35 1 1
STAT1 0.027 0.016 0.28 2 -10000 0 2
CGA 0.074 0.088 0.46 3 -10000 0 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.087 0.11 0.29 1 -0.35 33 34
MAPK3 0.018 0.015 -10000 0 -10000 0 0
MAPK1 0.018 0.015 -10000 0 -10000 0 0
ICAM1 0.063 0.13 0.38 5 -0.42 5 10
NFKB1 0.011 0.083 -10000 0 -0.24 22 22
MAPK8 0.1 0.1 0.28 53 -0.3 3 56
MAPK9 0.018 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.12 0.2 0.51 6 -0.54 65 71
BAX 0.011 0.061 -10000 0 -0.46 1 1
POMC 0.058 0.21 0.58 7 -1.2 10 17
EP300 -0.009 0.047 -10000 0 -0.25 1 1
cortisol/GR alpha (dimer)/p53 -0.12 0.16 0.46 6 -0.42 22 28
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.043 0.26 3 -10000 0 3
SGK1 -0.037 0.12 -10000 0 -0.74 6 6
IL13 0.065 0.13 0.42 2 -0.61 1 3
IL6 0.043 0.19 0.35 8 -0.84 17 25
PRKACG 0.017 0.005 -10000 0 -10000 0 0
IL5 0.056 0.11 0.38 1 -0.54 2 3
IL2 0.071 0.15 0.37 5 -0.46 8 13
CDK5 0.021 0.008 -10000 0 -10000 0 0
PRKACB 0.019 0.039 -10000 0 -0.35 6 6
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
IL8 0.094 0.15 0.38 9 -0.43 2 11
CDK5R1/CDK5 0.027 0.02 0.21 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc 0.049 0.12 -10000 0 -0.3 26 26
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.43 7 -0.37 28 35
SMARCA4 0.022 0.008 -10000 0 -10000 0 0
chromatin remodeling -0.068 0.1 0.29 5 -0.34 16 21
NF kappa B1 p50/RelA/Cbp 0.012 0.13 -10000 0 -0.32 32 32
JUN (dimer) 0.095 0.11 0.3 45 -0.38 3 48
YWHAH 0.022 0.006 -10000 0 -10000 0 0
VIPR1 0.065 0.092 0.33 10 -0.57 3 13
NR3C1 -0.12 0.15 0.36 3 -0.4 70 73
NR4A1 -0.007 0.12 -10000 0 -0.4 44 44
TIF2/SUV420H1 0.021 0.05 -10000 0 -0.25 17 17
MAPKKK cascade -0.12 0.2 0.51 6 -0.52 63 69
cortisol/GR alpha (dimer)/Src-1 -0.12 0.16 0.45 6 -0.39 30 36
PBX1 0 0.086 -10000 0 -0.33 32 32
POU1F1 0.01 0.06 0.28 2 -0.29 19 21
SELE -0.012 0.31 0.36 6 -0.82 64 70
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.068 0.11 0.3 4 -0.34 16 20
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.43 7 -0.37 28 35
mol:cortisol -0.066 0.09 0.28 6 -0.21 30 36
MMP1 0.11 0.16 0.39 4 -0.58 6 10
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.007 0.084 0.77 3 -0.62 1 4
VDR 0.029 0.042 0.29 13 -10000 0 13
FAM120B 0.022 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.013 0.076 0.26 2 -0.31 4 6
RXRs/LXRs/DNA/Oxysterols 0.029 0.085 0.29 2 -0.37 5 7
MED1 0.021 0.006 -10000 0 -10000 0 0
mol:9cRA 0.005 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.037 0.1 -10000 0 -0.2 144 144
RXRs/NUR77 0.016 0.1 0.25 5 -0.2 82 87
RXRs/PPAR -0.015 0.087 0.18 5 -0.21 56 61
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.023 0.19 9 -10000 0 9
RARs/VDR/DNA/Vit D3 0.047 0.039 0.2 9 -0.18 8 17
RARA 0.022 0.006 -10000 0 -10000 0 0
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.042 0.29 13 -10000 0 13
RARs/RARs/DNA/9cRA 0.036 0.031 -10000 0 -0.17 9 9
RARG 0.023 0.003 -10000 0 -10000 0 0
RPS6KB1 0.014 0.09 0.57 13 -10000 0 13
RARs/THRs/DNA/SMRT -0.037 0.099 -10000 0 -0.2 142 142
THRA 0.015 0.048 -10000 0 -0.35 9 9
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.023 0.19 9 -10000 0 9
RXRs/PPAR/9cRA/PGJ2/DNA 0.025 0.081 0.28 5 -0.18 40 45
NR1H4 0.027 0.048 0.28 19 -10000 0 19
RXRs/LXRs/DNA 0.041 0.087 0.34 1 -0.26 2 3
NR1H2 0.027 0.009 -10000 0 -10000 0 0
NR1H3 0.028 0.015 0.28 1 -10000 0 1
RXRs/VDR/DNA/Vit D3 0.029 0.079 0.23 8 -0.17 56 64
NR4A1 -0.001 0.092 -10000 0 -0.35 35 35
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0 0.072 0.19 8 -0.17 45 53
RXRG -0.014 0.12 0.31 9 -0.34 60 69
RXR alpha/CCPG 0.034 0.013 -10000 0 -10000 0 0
RXRA 0.026 0.011 -10000 0 -10000 0 0
RXRB 0.028 0.01 -10000 0 -10000 0 0
THRB -0.055 0.15 -10000 0 -0.35 111 111
PPARG 0.004 0.084 0.33 1 -0.35 28 29
PPARD 0.023 0.003 -10000 0 -10000 0 0
TNF 0.029 0.11 0.4 3 -0.77 3 6
mol:Oxysterols 0.005 0.007 -10000 0 -10000 0 0
cholesterol transport 0.029 0.084 0.29 2 -0.37 5 7
PPARA 0.021 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.048 -10000 0 -0.35 9 9
RXRs/NUR77/BCL2 -0.034 0.11 0.17 2 -0.25 98 100
SREBF1 0.023 0.077 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA 0.025 0.081 0.28 5 -0.18 40 45
ABCA1 0.025 0.073 -10000 0 -0.5 1 1
RARs/THRs 0.002 0.11 -10000 0 -0.19 123 123
RXRs/FXR 0.03 0.086 0.25 6 -0.18 54 60
BCL2 -0.008 0.1 -10000 0 -0.35 44 44
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.003 0.036 -10000 0 -0.2 13 13
NFATC2 -0.009 0.061 -10000 0 -0.21 44 44
NFATC3 0.007 0.019 -10000 0 -10000 0 0
CD40LG -0.052 0.14 0.32 1 -0.36 49 50
PTGS2 -0.058 0.16 0.24 1 -0.38 75 76
JUNB 0.018 0.036 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.016 -10000 0 -10000 0 0
CALM1 0.02 0.014 -10000 0 -10000 0 0
JUN 0.016 0.044 -10000 0 -0.35 7 7
mol:Ca2+ 0 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
FOSL1 0.042 0.069 0.28 42 -10000 0 42
CREM 0.021 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.007 0.088 0.24 1 -0.28 16 17
FOS -0.09 0.17 -10000 0 -0.35 160 160
IFNG -0.039 0.14 0.26 9 -0.33 45 54
AP-1/NFAT1-c-4 -0.027 0.17 0.36 9 -0.37 50 59
FASLG -0.043 0.13 0.26 5 -0.33 46 51
NFAT1-c-4/ICER1 -0.001 0.074 -10000 0 -0.22 24 24
IL2RA -0.042 0.13 0.28 6 -0.34 40 46
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSF2 -0.046 0.13 0.27 4 -0.33 50 54
JunB/Fra1/NFAT1-c-4 0.018 0.09 0.22 16 -0.23 17 33
IL4 -0.049 0.13 0.32 1 -0.34 39 40
IL2 -0.009 0.16 -10000 0 -0.86 18 18
IL3 -0.003 0.1 -10000 0 -0.66 12 12
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
BATF3 0.02 0.014 0.28 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.009 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.026 0.074 0.23 1 -0.42 8 9
Syndecan-4/Syndesmos 0.057 0.11 0.33 9 -0.74 2 11
positive regulation of JNK cascade -0.034 0.13 0.36 2 -0.43 9 11
Syndecan-4/ADAM12 0.06 0.11 0.32 11 -0.74 2 13
CCL5 0.021 0.045 0.28 6 -0.35 5 11
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DNM2 0.021 0.006 -10000 0 -10000 0 0
ITGA5 0.023 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
PLG -0.008 0.11 0.27 9 -0.34 45 54
ADAM12 0.027 0.035 0.28 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.04 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.1 0.14 0.36 24 -0.74 2 26
Syndecan-4/CXCL12/CXCR4 -0.035 0.14 0.45 1 -0.46 9 10
Syndecan-4/Laminin alpha3 0.053 0.11 0.33 10 -0.74 2 12
MDK 0.023 0.014 0.33 1 -10000 0 1
Syndecan-4/FZD7 0.041 0.12 0.32 9 -0.74 2 11
Syndecan-4/Midkine 0.058 0.11 0.33 8 -0.74 2 10
FZD7 -0.036 0.14 -10000 0 -0.35 85 85
Syndecan-4/FGFR1/FGF -0.029 0.13 -10000 0 -0.55 4 4
THBS1 -0.023 0.12 -10000 0 -0.35 65 65
integrin-mediated signaling pathway 0.052 0.11 0.31 9 -0.7 2 11
positive regulation of MAPKKK cascade -0.034 0.13 0.36 2 -0.43 9 11
Syndecan-4/TACI 0.058 0.11 0.36 8 -0.74 2 10
CXCR4 0.023 0.002 -10000 0 -10000 0 0
cell adhesion 0.008 0.046 0.18 12 -0.23 5 17
Syndecan-4/Dynamin 0.054 0.1 0.33 9 -0.74 2 11
Syndecan-4/TSP1 0.042 0.12 0.33 7 -0.53 5 12
Syndecan-4/GIPC 0.053 0.1 0.33 8 -0.74 2 10
Syndecan-4/RANTES 0.057 0.11 0.32 10 -0.74 2 12
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.1 0.13 0.28 174 -0.35 4 178
LAMA3 0.013 0.057 -10000 0 -0.35 13 13
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.013 0.14 0.72 14 -0.32 29 43
Syndecan-4/alpha-Actinin 0.057 0.11 0.33 10 -0.74 2 12
TFPI -0.021 0.12 -10000 0 -0.35 63 63
F2 0.05 0.077 0.29 48 -10000 0 48
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.065 0.12 0.33 16 -0.71 2 18
ACTN1 0.022 0.005 -10000 0 -10000 0 0
TNC 0.014 0.056 0.28 1 -0.35 12 13
Syndecan-4/CXCL12 -0.018 0.13 0.38 2 -0.47 9 11
FGF6 0.016 0.003 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CXCL12 -0.2 0.18 -10000 0 -0.35 327 327
TNFRSF13B 0.027 0.045 0.28 16 -10000 0 16
FGF2 -0.17 0.19 -10000 0 -0.35 276 276
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
Syndecan-4/PI-4-5-P2 0.039 0.1 0.29 6 -0.74 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.015 0.04 -10000 0 -0.3 6 6
cell migration -0.022 0.016 -10000 0 -10000 0 0
PRKCD 0.019 0.019 -10000 0 -0.12 1 1
vasculogenesis 0.042 0.11 0.33 7 -0.51 5 12
SDC4 0.048 0.095 0.31 6 -0.88 1 7
Syndecan-4/Tenascin C 0.053 0.11 0.33 4 -0.74 2 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.055 0.1 0.33 9 -0.74 2 11
MMP9 0.13 0.13 0.28 220 -10000 0 220
Rac1/GTP 0.008 0.047 0.19 12 -0.23 5 17
cytoskeleton organization 0.056 0.1 0.33 9 -0.7 2 11
GIPC1 0.022 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.043 0.12 0.32 8 -0.55 4 12
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.017 0.084 0.3 12 -0.3 9 21
TBX21 -0.02 0.25 0.64 7 -1 17 24
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.012 0.031 0.18 1 -10000 0 1
IL12RB1 0.017 0.069 0.35 13 -0.38 4 17
GADD45B -0.009 0.2 0.58 6 -0.72 17 23
IL12RB2 0.028 0.07 0.28 32 -10000 0 32
GADD45G -0.022 0.26 0.56 7 -0.9 28 35
natural killer cell activation 0.001 0.02 0.077 13 -0.047 15 28
RELB 0.022 0.005 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL18 0.027 0.036 0.28 9 -10000 0 9
IL2RA 0.031 0.052 0.28 20 -0.35 1 21
IFNG 0.05 0.081 0.28 60 -10000 0 60
STAT3 (dimer) -0.015 0.2 0.53 7 -0.64 24 31
HLA-DRB5 -0.006 0.01 -10000 0 -0.023 149 149
FASLG 0.011 0.24 0.71 7 -0.86 16 23
NF kappa B2 p52/RelB -0.012 0.2 0.45 1 -0.79 17 18
CD4 0.007 0.027 0.23 1 -10000 0 1
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
EntrezGene:6955 -0.007 0.013 0.017 1 -0.027 158 159
CD3D 0.008 0.065 0.26 14 -0.35 7 21
CD3E 0.003 0.06 0.28 5 -0.36 9 14
CD3G 0.007 0.047 0.28 7 -0.36 2 9
IL12Rbeta2/JAK2 0.027 0.073 0.22 30 -0.25 9 39
CCL3 -0.009 0.22 0.72 6 -0.98 10 16
CCL4 -0.014 0.23 0.68 7 -1 13 20
HLA-A 0 0.005 -10000 0 -0.044 7 7
IL18/IL18R 0.056 0.058 0.28 9 -0.22 8 17
NOS2 -0.015 0.24 0.66 6 -0.95 19 25
IL12/IL12R/TYK2/JAK2/SPHK2 0.018 0.082 0.29 13 -0.27 9 22
IL1R1 -0.024 0.25 0.64 6 -1 18 24
IL4 -0.001 0.033 -10000 0 -0.17 2 2
JAK2 0.006 0.058 0.18 1 -0.36 9 10
EntrezGene:6957 -0.006 0.012 -10000 0 -0.023 154 154
TCR/CD3/MHC I/CD8 -0.017 0.12 0.29 3 -0.55 20 23
RAB7A -0.001 0.2 0.58 4 -0.67 16 20
lysosomal transport 0.001 0.19 0.52 7 -0.63 17 24
FOS -0.3 0.54 0.54 4 -1.1 172 176
STAT4 (dimer) 0.016 0.2 0.55 7 -0.61 22 29
STAT5A (dimer) 0.008 0.23 0.6 10 -0.76 19 29
GZMA -0.024 0.26 0.66 6 -1.1 19 25
GZMB -0.008 0.23 0.64 8 -1.1 11 19
HLX 0.02 0.008 -10000 0 -10000 0 0
LCK -0.014 0.23 0.62 7 -0.85 18 25
TCR/CD3/MHC II/CD4 -0.042 0.12 0.18 5 -0.22 135 140
IL2/IL2R 0.061 0.057 0.27 25 -0.19 3 28
MAPK14 -0.01 0.23 0.56 7 -0.7 29 36
CCR5 -0.002 0.21 0.59 7 -0.83 16 23
IL1B 0.01 0.046 0.18 1 -0.38 4 5
STAT6 0.015 0.084 0.35 9 -0.29 5 14
STAT4 0.022 0.016 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.024 0.016 0.28 2 -10000 0 2
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.011 0.035 0.22 3 -10000 0 3
CD8A 0.019 0.052 0.29 4 -0.35 8 12
CD8B 0.03 0.07 0.28 25 -0.35 7 32
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.017 0.084 0.3 9 -0.3 12 21
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.19 0.53 8 -0.57 22 30
IL2RG 0.024 0.039 0.28 6 -0.35 3 9
IL12 0.022 0.059 0.22 15 -0.26 4 19
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
CD247 0.004 0.035 0.28 1 -0.36 2 3
IL2 0.027 0.046 0.28 17 -10000 0 17
SPHK2 0.023 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.06 0.28 12 -0.37 4 16
IL12/IL12R/TYK2/JAK2 -0.014 0.25 0.64 9 -0.92 18 27
MAP2K3 -0.02 0.23 0.56 7 -0.69 32 39
RIPK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K6 -0.005 0.22 0.56 7 -0.68 30 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.012 -10000 0 -0.026 154 154
IL18RAP 0.021 0.041 0.3 3 -0.35 4 7
IL12Rbeta1/TYK2 0.022 0.062 0.29 12 -0.29 4 16
EOMES -0.017 0.16 -10000 0 -0.79 18 18
STAT1 (dimer) 0.018 0.2 0.59 11 -0.64 18 29
T cell proliferation 0.014 0.17 0.48 7 -0.5 22 29
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.035 -10000 0 -0.35 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.005 0.16 0.5 2 -0.56 20 22
ATF2 -0.01 0.21 0.53 7 -0.67 27 34
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.024 0.055 0.18 2 -0.18 34 36
RGS9BP 0.033 0.056 0.29 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.018 0.013 0.28 1 -10000 0 1
mol:Na + 0.016 0.047 0.18 3 -0.2 21 24
mol:ADP -0.014 0.009 0.11 2 -10000 0 2
GNAT2 0.023 0.019 0.28 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 111 125
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.013 0.18 3 -10000 0 3
GRK7 0.021 0.012 0.28 1 -10000 0 1
CNGB3 0.004 0.072 -10000 0 -0.35 21 21
Cone Metarhodopsin II/X-Arrestin 0.014 0.008 0.19 1 -10000 0 1
mol:Ca2+ -0.008 0.062 0.18 37 -0.19 20 57
Cone PDE6 0.005 0.1 0.22 5 -0.18 109 114
Cone Metarhodopsin II 0.023 0.012 0.18 2 -10000 0 2
Na + (4 Units) 0.025 0.046 0.19 3 -0.19 21 24
GNAT2/GDP 0.003 0.097 0.2 15 -0.18 111 126
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.012 0.026 0.18 9 -10000 0 9
Cone Transducin 0.026 0.059 0.19 2 -0.19 34 36
SLC24A2 0.019 0.014 0.33 1 -10000 0 1
GNB3/GNGT2 0.013 0.07 -10000 0 -0.25 34 34
GNB3 -0.001 0.09 -10000 0 -0.35 33 33
GNAT2/GTP 0.017 0.013 0.19 3 -10000 0 3
CNGA3 0.022 0.023 0.28 4 -10000 0 4
ARR3 0.019 0.012 0.28 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.016 0.047 0.19 3 -0.2 21 24
mol:Pi -0.008 0.11 0.21 14 -0.21 111 125
Cone CNG Channel 0.033 0.048 0.19 1 -0.18 21 22
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.019 0.014 0.33 1 -10000 0 1
RGS9 -0.057 0.15 -10000 0 -0.35 113 113
PDE6C 0.018 0.014 0.33 1 -10000 0 1
GNGT2 0.02 0.028 -10000 0 -0.35 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.015 0.036 -10000 0 -0.2 14 14
EPHB2 0.024 0.019 0.28 3 -10000 0 3
Syndecan-2/TACI 0.019 0.043 0.2 15 -0.19 11 26
LAMA1 0.1 0.13 0.28 174 -0.35 4 178
Syndecan-2/alpha2 ITGB1 0.028 0.056 -10000 0 -0.19 28 28
HRAS 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.029 -10000 0 -0.2 11 11
ITGA5 0.023 0.003 -10000 0 -10000 0 0
BAX -0.01 0.028 -10000 0 -10000 0 0
EPB41 0.022 0.017 -10000 0 -0.35 1 1
positive regulation of cell-cell adhesion 0.014 0.029 -10000 0 -0.18 11 11
LAMA3 0.013 0.057 -10000 0 -0.35 13 13
EZR 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.008 0.1 -10000 0 -0.35 44 44
Syndecan-2/MMP2 0.008 0.05 -10000 0 -0.21 24 24
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.026 0.04 -10000 0 -0.25 11 11
dendrite morphogenesis 0.017 0.038 0.28 3 -0.2 11 14
Syndecan-2/GM-CSF 0.016 0.038 0.2 7 -0.2 11 18
determination of left/right symmetry 0.002 0.035 -10000 0 -0.24 11 11
Syndecan-2/PKC delta 0.015 0.032 -10000 0 -0.2 11 11
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 0.004 0.061 0.19 45 -0.18 10 55
MAPK1 0.003 0.06 0.19 42 -0.18 11 53
Syndecan-2/RACK1 0.025 0.031 -10000 0 -0.17 11 11
NF1 0.021 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.002 0.035 -10000 0 -0.24 11 11
ITGA2 0.014 0.053 -10000 0 -0.35 11 11
MAPK8 -0.002 0.032 -10000 0 -0.2 14 14
Syndecan-2/alpha2/beta1 Integrin 0.078 0.095 0.21 150 -0.17 23 173
Syndecan-2/Kininogen 0.022 0.05 0.21 24 -0.2 8 32
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.002 0.058 0.18 45 -0.17 11 56
Syndecan-2/CASK/Protein 4.1 0.014 0.03 -10000 0 -0.18 12 12
extracellular matrix organization 0.015 0.033 -10000 0 -0.2 12 12
actin cytoskeleton reorganization 0.015 0.036 -10000 0 -0.2 14 14
Syndecan-2/Caveolin-2/Ras 0.014 0.061 -10000 0 -0.19 41 41
Syndecan-2/Laminin alpha3 0.01 0.047 -10000 0 -0.21 22 22
Syndecan-2/RasGAP 0.032 0.039 -10000 0 -0.17 16 16
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.017 0.038 0.28 3 -0.2 11 14
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.019 0.037 -10000 0 -0.17 16 16
RHOA 0.022 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.027 0.045 0.28 16 -10000 0 16
RASA1 0.019 0.036 -10000 0 -0.35 5 5
alpha2/beta1 Integrin 0.026 0.04 -10000 0 -0.25 11 11
Syndecan-2/Synbindin 0.016 0.031 -10000 0 -0.2 10 10
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CASP3 0.004 0.06 0.19 44 -0.18 11 55
FN1 0.019 0.036 -10000 0 -0.35 5 5
Syndecan-2/IL8 0.066 0.092 0.2 150 -0.2 11 161
SDC2 0.002 0.035 -10000 0 -0.24 11 11
KNG1 0.031 0.058 0.29 25 -10000 0 25
Syndecan-2/Neurofibromin 0.015 0.032 -10000 0 -0.2 11 11
TRAPPC4 0.022 0.005 -10000 0 -10000 0 0
CSF2 0.024 0.032 0.28 8 -10000 0 8
Syndecan-2/TGFB1 0.015 0.034 -10000 0 -0.2 12 12
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.029 -10000 0 -0.18 11 11
Syndecan-2/Ezrin 0.027 0.033 -10000 0 -0.18 11 11
PRKACA 0.002 0.055 0.19 36 -0.18 10 46
angiogenesis 0.066 0.092 0.2 150 -0.2 11 161
MMP2 0.007 0.071 -10000 0 -0.35 20 20
IL8 0.095 0.12 0.28 152 -10000 0 152
calcineurin-NFAT signaling pathway 0.019 0.043 0.2 15 -0.19 11 26
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 0.009 0.071 -10000 0 -0.35 20 20
Jak2/Leptin Receptor -0.073 0.17 -10000 0 -0.37 95 95
PTP1B/AKT1 -0.003 0.085 0.26 1 -0.28 27 28
FYN 0.023 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.014 0.088 0.3 1 -0.3 30 31
EGFR 0.013 0.06 0.32 1 -0.36 13 14
EGF/EGFR 0.007 0.092 0.25 3 -0.25 33 36
CSF1 0.016 0.05 -10000 0 -0.35 10 10
AKT1 0.022 0.007 -10000 0 -10000 0 0
INSR 0.021 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.024 0.1 -10000 0 -0.29 45 45
Insulin Receptor/Insulin 0.01 0.082 0.24 1 -0.28 19 20
HCK 0.025 0.03 0.28 7 -10000 0 7
CRK 0.021 0.006 -10000 0 -10000 0 0
TYK2 -0.005 0.092 0.23 20 -0.29 25 45
EGF 0.03 0.057 0.28 21 -0.35 2 23
YES1 0.022 0.005 -10000 0 -10000 0 0
CAV1 -0.028 0.11 0.26 4 -0.32 37 41
TXN 0.022 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.01 0.1 -10000 0 -0.28 45 45
cell migration 0.014 0.088 0.3 30 -0.3 1 31
STAT3 0.022 0.006 -10000 0 -10000 0 0
PRLR -0.05 0.15 -10000 0 -0.35 104 104
ITGA2B 0.017 0.041 0.28 1 -0.35 6 7
CSF1R 0.021 0.03 0.28 1 -0.35 3 4
Prolactin Receptor/Prolactin -0.028 0.12 0.21 4 -0.25 114 118
FGR 0.016 0.051 -10000 0 -0.35 10 10
PTP1B/p130 Cas -0.003 0.085 0.27 1 -0.28 30 31
Crk/p130 Cas 0.005 0.087 0.27 1 -0.29 23 24
DOK1 -0.018 0.098 0.23 3 -0.33 30 33
JAK2 -0.055 0.15 0.26 1 -0.37 66 67
Jak2/Leptin Receptor/Leptin -0.011 0.095 -10000 0 -0.32 24 24
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
PTPN1 -0.014 0.089 0.3 1 -0.3 30 31
LYN 0.021 0.007 -10000 0 -10000 0 0
CDH2 -0.028 0.13 -10000 0 -0.35 73 73
SRC 0 0.11 -10000 0 -0.52 20 20
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
CAT1/PTP1B -0.003 0.12 0.29 13 -0.38 22 35
CAPN1 0.022 0.004 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.013 0.078 -10000 0 -0.29 13 13
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.009 0.087 -10000 0 -0.31 20 20
negative regulation of transcription -0.055 0.15 0.26 1 -0.36 66 67
FCGR2A 0.02 0.014 0.28 1 -10000 0 1
FER 0.023 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.017 0.11 0.21 3 -0.25 96 99
BLK 0.037 0.068 0.28 38 -10000 0 38
Insulin Receptor/Insulin/Shc 0.032 0.019 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
LEPR -0.086 0.17 -10000 0 -0.35 158 158
BCAR1 0.021 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.006 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 0.008 0.11 0.26 12 -0.41 17 29
PRL 0.006 0.071 0.28 5 -0.35 17 22
SOCS3 0.001 0.16 -10000 0 -1.1 11 11
SPRY2 0.019 0.033 -10000 0 -0.36 4 4
Insulin Receptor/Insulin/IRS1 0.015 0.075 -10000 0 -0.21 51 51
CSF1/CSF1R 0.001 0.096 -10000 0 -0.28 33 33
Ras protein signal transduction 0.02 0.12 0.56 24 -10000 0 24
IRS1 -0.013 0.11 -10000 0 -0.35 51 51
INS 0.009 0.015 -10000 0 -10000 0 0
LEP 0.016 0.021 0.28 2 -10000 0 2
STAT5B -0.033 0.12 0.29 1 -0.37 43 44
STAT5A -0.032 0.12 0.29 1 -0.36 44 45
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.096 -10000 0 -0.3 35 35
CSN2 -0.022 0.078 -10000 0 -0.5 2 2
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
LAT 0.008 0.091 -10000 0 -0.54 12 12
YBX1 0.026 0.017 -10000 0 -0.35 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
SHC1 0.019 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.034 0.28 1 -0.35 4 5
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.12 -10000 0 -0.41 39 39
HDAC1 0.021 0.007 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
DTX1 0.019 0.039 -10000 0 -0.35 6 6
LRP6/FZD1 0.032 0.018 -10000 0 -0.25 2 2
TLE1 0.022 0.006 -10000 0 -10000 0 0
AP1 -0.048 0.11 -10000 0 -0.22 136 136
NCSTN 0.019 0.009 -10000 0 -10000 0 0
ADAM10 0.02 0.028 -10000 0 -0.35 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.15 -10000 0 -0.67 24 24
NICD/RBPSUH -0.005 0.12 -10000 0 -0.4 38 38
WIF1 0.059 0.15 0.28 127 -0.35 34 161
NOTCH1 -0.007 0.099 -10000 0 -0.42 29 29
PSENEN 0.022 0.005 -10000 0 -10000 0 0
KREMEN2 0.045 0.073 0.28 47 -10000 0 47
DKK1 0.069 0.12 0.28 109 -0.35 8 117
beta catenin/beta TrCP1 0.029 0.069 0.23 1 -0.41 4 5
APH1B 0.018 0.039 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
AXIN1 -0.012 0.11 -10000 0 -0.45 22 22
CtBP/CBP/TCF1/TLE1/AES 0.01 0.039 -10000 0 -0.2 1 1
PSEN1 0.022 0.004 -10000 0 -10000 0 0
FOS -0.089 0.17 -10000 0 -0.35 160 160
JUN 0.018 0.042 -10000 0 -0.35 7 7
MAP3K7 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.018 0.07 0.23 2 -0.4 5 7
MAPK3 0.022 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.042 0.077 0.21 43 -0.2 30 73
HNF1A 0.026 0.031 0.28 8 -10000 0 8
CTBP1 0.022 0.005 -10000 0 -10000 0 0
MYC -0.005 0.17 -10000 0 -1.2 11 11
NKD1 0.034 0.081 0.28 38 -0.35 8 46
FZD1 0.021 0.023 -10000 0 -0.35 2 2
NOTCH1 precursor/Deltex homolog 1 -0.007 0.12 -10000 0 -0.4 36 36
apoptosis -0.047 0.11 -10000 0 -0.22 136 136
Delta 1/NOTCHprecursor -0.01 0.12 -10000 0 -0.41 39 39
DLL1 0.01 0.067 -10000 0 -0.35 18 18
PPARD 0.017 0.058 -10000 0 -0.88 2 2
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
APC -0.01 0.11 -10000 0 -0.53 17 17
DVL1 0.011 0.034 -10000 0 -0.37 3 3
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.083 0.084 0.21 144 -0.2 8 152
LRP6 0.023 0.003 -10000 0 -10000 0 0
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
NLK 0.009 0.005 -10000 0 -10000 0 0
CCND1 0.009 0.11 -10000 0 -0.85 8 8
WNT1 0.025 0.029 0.28 7 -10000 0 7
Axin1/APC/beta catenin 0.016 0.12 0.25 3 -0.43 22 25
DKK2 0.002 0.087 0.28 2 -0.35 30 32
NOTCH1 precursor/DVL1 -0.013 0.13 -10000 0 -0.51 26 26
GSK3B 0.022 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.12 -10000 0 -0.4 36 36
PPP2R5D 0.014 0.033 0.26 1 -0.29 2 3
MAPK1 0.022 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.076 0.097 0.36 3 -0.19 34 37
RBPJ 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.059 0.13 0.28 85 -0.34 20 105
FYN 0.028 0.12 0.26 27 -0.38 23 50
LAT/GRAP2/SLP76 0.031 0.11 0.3 10 -0.35 25 35
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.019 0.1 0.26 18 -0.31 28 46
B2M 0.023 0.008 -10000 0 -10000 0 0
IKBKG 0.009 0.036 0.13 12 -0.11 12 24
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
mol:Ca2+ -0.013 0.012 0.086 1 -0.078 4 5
integrin-mediated signaling pathway 0.026 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.017 0.14 0.31 14 -0.42 30 44
TRPV6 -0.015 0.18 1.2 9 -10000 0 9
CD28 0.024 0.017 0.28 2 -10000 0 2
SHC1 0.045 0.15 0.29 86 -0.38 24 110
receptor internalization 0.017 0.12 0.28 8 -0.4 30 38
PRF1 0.01 0.17 0.42 4 -0.82 15 19
KRAS 0.023 0.014 0.33 1 -10000 0 1
GRB2 0.022 0.006 -10000 0 -10000 0 0
COT/AKT1 0.027 0.09 0.26 14 -0.26 24 38
LAT 0.021 0.12 0.28 16 -0.38 27 43
EntrezGene:6955 0 0.003 -10000 0 -0.034 1 1
CD3D 0.025 0.061 0.29 14 -0.36 7 21
CD3E 0.02 0.056 0.3 5 -0.36 9 14
CD3G 0.024 0.039 0.29 7 -0.35 2 9
RASGRP2 -0.014 0.058 0.084 2 -0.16 74 76
RASGRP1 0.013 0.12 0.28 19 -0.35 27 46
HLA-A 0.001 0.003 -10000 0 -10000 0 0
RASSF5 0.02 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.027 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.067 0.15 77 -0.12 20 97
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.04 -10000 0 -0.17 22 22
PRKCA 0.004 0.066 0.18 15 -0.2 18 33
GRAP2 0.011 0.061 -10000 0 -0.35 15 15
mol:IP3 0.014 0.086 0.2 38 -0.28 21 59
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.007 0.082 0.27 6 -0.42 13 19
ORAI1 0 0.15 0.4 3 -0.98 9 12
CSK 0.02 0.12 0.26 13 -0.37 29 42
B7 family/CD28 0.053 0.12 0.41 11 -0.39 17 28
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.017 0.13 0.27 11 -0.4 32 43
PTPN6 0.016 0.12 0.25 16 -0.36 29 45
VAV1 0.019 0.12 0.29 10 -0.39 26 36
Monovalent TCR/CD3 0.011 0.053 0.23 8 -0.26 13 21
CBL 0.022 0.005 -10000 0 -10000 0 0
LCK 0.026 0.13 0.26 26 -0.39 24 50
PAG1 0.025 0.12 0.28 14 -0.37 27 41
RAP1A 0.023 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.017 0.13 0.25 15 -0.39 31 46
CD80 0.036 0.059 0.28 29 -10000 0 29
CD86 0.024 0.017 0.29 2 -10000 0 2
PDK1/CARD11/BCL10/MALT1 0.004 0.052 0.16 2 -0.2 23 25
HRAS 0.022 0.005 -10000 0 -10000 0 0
GO:0035030 0.018 0.094 0.27 11 -0.34 17 28
CD8A 0.02 0.052 0.3 4 -0.36 8 12
CD8B 0.031 0.071 0.28 25 -0.36 7 32
PTPRC 0.015 0.047 0.28 1 -0.35 8 9
PDK1/PKC theta 0.015 0.12 0.29 21 -0.37 27 48
CSK/PAG1 0.025 0.12 0.29 16 -0.38 24 40
SOS1 0.023 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.008 -10000 0 -10000 0 0
GRAP2/SLP76 0.034 0.12 0.36 6 -0.4 26 32
STIM1 0.002 0.062 1.2 1 -10000 0 1
RAS family/GTP 0.036 0.072 0.2 29 -0.16 16 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.016 0.12 0.31 6 -0.42 30 36
mol:DAG -0.004 0.062 0.096 6 -0.24 26 32
RAP1A/GDP 0.015 0.032 0.085 33 -0.062 11 44
PLCG1 0.022 0.005 -10000 0 -10000 0 0
CD247 0.019 0.027 0.3 1 -0.35 2 3
cytotoxic T cell degranulation 0.011 0.16 0.41 4 -0.78 15 19
RAP1A/GTP -0.006 0.022 -10000 0 -0.059 76 76
mol:PI-3-4-5-P3 0.019 0.12 0.28 18 -0.36 30 48
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.028 0.11 0.22 36 -0.34 21 57
NRAS 0.023 0.001 -10000 0 -10000 0 0
ZAP70 0.03 0.05 0.28 16 -0.35 2 18
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.022 0.1 0.32 5 -0.34 24 29
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.038 0.069 0.24 26 -0.27 14 40
CARD11 0.027 0.042 0.28 12 -0.35 1 13
PRKCB 0.004 0.072 0.18 17 -0.23 23 40
PRKCE 0.009 0.062 0.18 15 -0.2 17 32
PRKCQ 0.014 0.13 0.3 18 -0.4 30 48
LCP2 0.023 0.012 0.28 1 -10000 0 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression 0.02 0.095 0.24 21 -0.27 27 48
IKK complex 0.015 0.058 0.19 27 -0.11 10 37
RAS family/GDP -0.001 0.009 -10000 0 -0.039 7 7
MAP3K14 0.019 0.07 0.2 16 -0.21 21 37
PDPK1 0.019 0.1 0.27 17 -0.3 27 44
TCR/CD3/MHC I/CD8/Fyn -0.006 0.15 0.39 4 -0.49 33 37
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 89 91
AKT1 -0.015 0.15 0.33 6 -0.48 37 43
PTK2B -0.055 0.13 -10000 0 -0.5 31 31
VEGFR2 homodimer/Frs2 -0.006 0.13 -10000 0 -0.53 31 31
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
CALM1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.009 0.12 -10000 0 -0.49 31 31
endothelial cell proliferation -0.021 0.15 0.34 15 -0.44 44 59
mol:Ca2+ -0.044 0.12 0.18 4 -0.49 32 36
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.019 0.12 -10000 0 -0.46 31 31
RP11-342D11.1 -0.042 0.12 0.17 6 -0.49 32 38
CDH5 0.016 0.04 -10000 0 -0.35 6 6
VEGFA homodimer 0.044 0.029 -10000 0 -0.19 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.025 0.12 -10000 0 -0.35 67 67
HRAS/GDP -0.004 0.11 -10000 0 -0.43 30 30
SH2D2A 0.029 0.053 0.29 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.002 0.14 -10000 0 -0.44 36 36
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.009 0.12 0.22 3 -0.47 31 34
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.009 0.13 -10000 0 -0.47 30 30
GRB10 -0.044 0.12 -10000 0 -0.51 31 31
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
PAK1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.025 0.13 -10000 0 -0.48 30 30
HRAS 0.022 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.03 0.11 -10000 0 -0.35 37 37
HIF1A 0.023 0.004 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.018 0.12 -10000 0 -0.46 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.009 0.069 -10000 0 -0.35 19 19
Nck/Pak 0.031 0.019 -10000 0 -0.25 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.009 0.12 -10000 0 -0.48 31 31
mol:GDP 0.002 0.12 -10000 0 -0.45 30 30
mol:NADP -0.008 0.12 0.33 8 -0.38 37 45
eNOS/Hsp90 0 0.12 0.35 6 -0.37 36 42
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.045 0.12 0.18 4 -0.5 32 36
HIF1A/ARNT 0.026 0.015 -10000 0 -10000 0 0
SHB 0.022 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFC 0.017 0.045 -10000 0 -0.35 8 8
FAK1/Vinculin -0.029 0.16 0.26 3 -0.56 32 35
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.015 0.15 -10000 0 -0.5 33 33
PTPN6 0.023 0.014 0.33 1 -10000 0 1
EPAS1 0.008 0.078 -10000 0 -0.31 31 31
mol:L-citrulline -0.008 0.12 0.33 8 -0.38 37 45
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.02 0.12 -10000 0 -0.44 31 31
VEGFR2 homodimer/VEGFA homodimer -0.004 0.14 -10000 0 -0.53 32 32
VEGFR2/3 heterodimer -0.014 0.14 -10000 0 -0.43 47 47
VEGFB 0.022 0.004 -10000 0 -10000 0 0
MAPK11 -0.041 0.14 0.31 3 -0.51 35 38
VEGFR2 homodimer -0.021 0.14 -10000 0 -0.61 30 30
FLT1 0.022 0.005 -10000 0 -10000 0 0
NEDD4 -0.003 0.094 -10000 0 -0.35 37 37
MAPK3 -0.04 0.13 0.29 11 -0.44 37 48
MAPK1 -0.041 0.13 0.29 10 -0.44 37 47
VEGFA145/NRP2 0.021 0.058 -10000 0 -0.24 24 24
VEGFR1/2 heterodimer -0.006 0.13 -10000 0 -0.53 31 31
KDR -0.021 0.14 -10000 0 -0.61 30 30
VEGFA165/NRP1/VEGFR2 homodimer -0.009 0.14 -10000 0 -0.49 35 35
SRC 0.022 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.041 0.14 0.29 11 -0.44 39 50
PI3K -0.017 0.14 -10000 0 -0.54 31 31
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.008 0.12 -10000 0 -0.48 31 31
FES -0.046 0.13 0.18 6 -0.5 33 39
GAB1 -0.004 0.15 -10000 0 -0.54 32 32
VEGFR2 homodimer/VEGFA homodimer/Src 0.008 0.12 -10000 0 -0.48 31 31
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.14 0.31 4 -0.42 37 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.008 0.12 -10000 0 -0.48 31 31
PI3K/GAB1 -0.002 0.14 -10000 0 -0.5 32 32
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.03 0.12 -10000 0 -0.43 31 31
PRKACA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.14 -10000 0 -0.39 52 52
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
CDC42 -0.045 0.12 0.18 6 -0.5 32 38
actin cytoskeleton reorganization 0.009 0.12 0.22 3 -0.47 31 34
PTK2 -0.043 0.15 0.25 3 -0.6 31 34
EDG1 -0.042 0.12 0.17 6 -0.49 32 38
mol:DAG -0.045 0.12 0.18 4 -0.5 32 36
CaM/Ca2+ -0.013 0.12 -10000 0 -0.46 32 32
MAP2K3 -0.041 0.11 -10000 0 -0.48 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.002 0.14 -10000 0 -0.52 32 32
PLCG1 -0.045 0.12 0.18 4 -0.5 32 36
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.019 0.12 -10000 0 -0.46 31 31
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.009 0.12 -10000 0 -0.49 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.009 0.12 -10000 0 -0.49 31 31
cell migration -0.027 0.14 0.26 2 -0.5 34 36
mol:PI-3-4-5-P3 -0.015 0.13 -10000 0 -0.5 31 31
FYN 0.023 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 -0.02 0.12 -10000 0 -0.46 32 32
mol:NO -0.008 0.12 0.33 8 -0.38 37 45
PXN 0.023 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.014 0.11 -10000 0 -0.43 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.011 0.14 -10000 0 -0.52 32 32
VHL 0.022 0.017 -10000 0 -0.35 1 1
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
NOS3 -0.011 0.14 0.36 6 -0.43 37 43
VEGFR2 homodimer/VEGFA homodimer/Sck -0.02 0.14 -10000 0 -0.49 32 32
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.051 0.12 -10000 0 -0.47 34 34
PRKCB -0.051 0.12 -10000 0 -0.48 34 34
VCL 0.022 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.018 0.13 -10000 0 -0.49 32 32
VEGFR1/2 heterodimer/VEGFA homodimer 0.008 0.12 -10000 0 -0.48 31 31
VEGFA165/NRP2 0.021 0.058 -10000 0 -0.24 24 24
MAPKKK cascade -0.013 0.13 0.33 2 -0.46 27 29
NRP2 0.006 0.077 -10000 0 -0.35 24 24
VEGFC homodimer 0.017 0.045 -10000 0 -0.35 8 8
NCK1 0.021 0.023 -10000 0 -0.35 2 2
ROCK1 0.023 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.03 0.16 0.26 3 -0.55 33 36
MAP3K13 -0.043 0.12 0.18 4 -0.5 30 34
PDPK1 -0.024 0.12 0.25 1 -0.45 31 32
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.075 0.16 -10000 0 -0.35 141 141
HRAS 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
AKT -0.041 0.13 0.29 4 -0.25 125 129
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.023 0.004 -10000 0 -10000 0 0
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
AKT3 -0.096 0.17 -10000 0 -0.35 166 166
FOXO4 0.022 0.023 -10000 0 -0.35 2 2
MET 0.021 0.042 0.28 4 -0.35 5 9
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
PIK3CG 0.013 0.062 0.28 2 -0.35 14 16
PIK3R3 0.023 0.012 0.28 1 -10000 0 1
PIK3R2 0.022 0.005 -10000 0 -10000 0 0
NF1 0.021 0.006 -10000 0 -10000 0 0
RAS -0.011 0.066 0.16 9 -0.13 106 115
ERBB2 0.029 0.049 0.33 14 -10000 0 14
proliferation/survival/translation 0.004 0.088 0.27 15 -0.28 5 20
PI3K 0.003 0.07 0.21 20 -0.22 9 29
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
KRAS 0.023 0.014 0.33 1 -10000 0 1
FOXO 0.032 0.048 0.24 7 -10000 0 7
AKT2 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.041 0.12 -10000 0 -0.2 175 175
TC10/GTP -0.026 0.094 -10000 0 -0.17 155 155
Insulin Receptor/Insulin/IRS1/Shp2 0.028 0.075 -10000 0 -0.19 51 51
HRAS 0.022 0.005 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 190 -0.35 3 193
FOXO3 0.016 0.066 -10000 0 -0.57 6 6
AKT1 -0.006 0.079 0.24 14 -0.3 2 16
INSR 0.024 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.045 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.017 -10000 0 -0.35 1 1
SORBS1 -0.096 0.17 -10000 0 -0.35 170 170
CRK 0.021 0.006 -10000 0 -10000 0 0
PTPN1 -0.004 0.027 0.15 16 -10000 0 16
CAV1 -0.05 0.088 0.16 5 -0.21 107 112
CBL/APS/CAP/Crk-II/C3G -0.017 0.11 -10000 0 -0.18 158 158
Insulin Receptor/Insulin/IRS1/NCK2 0.029 0.075 -10000 0 -0.19 51 51
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.019 0.063 -10000 0 -0.18 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.008 0.089 -10000 0 -0.32 28 28
RPS6KB1 -0.012 0.072 0.23 13 -0.28 2 15
PARD6A 0.021 0.007 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.027 -10000 0 -0.57 1 1
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.007 0.064 -10000 0 -0.29 2 2
HRAS/GTP -0.025 0.038 -10000 0 -0.17 28 28
Insulin Receptor 0.024 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.033 0.064 -10000 0 -0.18 33 33
PRKCI 0.005 0.07 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.021 0.065 -10000 0 -0.17 40 40
SHC1 0.019 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.034 0.041 -10000 0 -0.35 4 4
PI3K 0.026 0.067 -10000 0 -0.18 44 44
NCK2 0.023 0.002 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
AKT2 -0.008 0.077 0.25 12 -0.3 2 14
PRKCZ 0.002 0.077 -10000 0 -0.3 14 14
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.007 0.05 -10000 0 -0.17 33 33
F2RL2 0.003 0.088 0.28 3 -0.35 30 33
TRIP10 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.048 0.032 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
CBL/APS/CAP/Crk-II -0.025 0.11 -10000 0 -0.19 163 163
TC10/GDP 0.017 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.029 -10000 0 -0.2 1 1
INPP5D -0.027 0.053 0.15 4 -0.18 50 54
SOS1 0.023 0.003 -10000 0 -10000 0 0
SGK1 0.005 0.068 -10000 0 -0.7 5 5
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.013 0.11 -10000 0 -0.35 51 51
p62DOK/RasGAP 0.034 0.042 -10000 0 -0.36 4 4
INS 0.018 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.027 0.052 0.15 4 -0.18 50 54
GRB2 0.022 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.011 0.075 0.25 16 -0.28 2 18
PTPRA 0.024 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.056 -10000 0 -0.19 40 40
Insulin Receptor/Insulin/IRS1 0.017 0.069 -10000 0 -0.19 51 51
Insulin Receptor/Insulin/IRS3 0.031 0.013 -10000 0 -10000 0 0
Par3/Par6 0.034 0.055 -10000 0 -0.18 28 28
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.005 -10000 0 -10000 0 0
SMARCC1 0.009 0.014 -10000 0 -10000 0 0
REL 0.021 0.009 -10000 0 -10000 0 0
HDAC7 -0.012 0.062 0.2 8 -0.26 8 16
JUN 0.018 0.042 -10000 0 -0.35 7 7
EP300 0.022 0.006 -10000 0 -10000 0 0
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
KAT5 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.007 0.045 0.12 62 -10000 0 62
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
T-DHT/AR 0.021 0.075 0.27 5 -0.26 8 13
MAP2K6 0.052 0.087 0.28 66 -10000 0 66
BRM/BAF57 0.025 0.043 -10000 0 -0.24 13 13
MAP2K4 0.018 0.02 -10000 0 -0.34 1 1
SMARCA2 0.013 0.06 -10000 0 -0.35 14 14
PDE9A -0.003 0.1 -10000 0 -0.63 9 9
NCOA2 0.008 0.066 -10000 0 -0.35 17 17
CEBPA 0.021 0.032 0.28 2 -0.35 3 5
EHMT2 0.023 0.004 -10000 0 -10000 0 0
cell proliferation 0.003 0.14 0.35 19 -0.37 23 42
NR0B1 0.033 0.06 0.28 30 -10000 0 30
EGR1 -0.024 0.12 -10000 0 -0.35 68 68
RXRs/9cRA 0.012 0.075 0.21 8 -0.19 59 67
AR/RACK1/Src 0.002 0.074 0.22 11 -0.25 8 19
AR/GR -0.038 0.12 0.21 3 -0.22 127 130
GNB2L1 0.021 0.009 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
RCHY1 0.023 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.013 6 6
MAPK8 -0.009 0.024 -10000 0 -0.25 4 4
T-DHT/AR/TIF2/CARM1 0.009 0.074 0.22 2 -0.28 10 12
SRC -0.003 0.05 0.18 29 -0.18 3 32
NR3C1 -0.031 0.13 -10000 0 -0.35 77 77
KLK3 0.023 0.11 0.39 2 -0.46 2 4
APPBP2 0.022 0.009 -10000 0 -10000 0 0
TRIM24 0.023 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.001 0.064 0.21 12 -0.25 4 16
TMPRSS2 -0.006 0.14 0.39 1 -0.8 13 14
RXRG -0.018 0.12 0.31 9 -0.35 60 69
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.022 0.006 -10000 0 -10000 0 0
RXRB 0.023 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.01 -10000 0 -10000 0 0
NR2C2 0.016 0.051 -10000 0 -0.35 10 10
KLK2 -0.015 0.13 -10000 0 -0.49 28 28
AR -0.02 0.086 0.15 18 -0.22 74 92
SENP1 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
MDM2 0.021 0.009 -10000 0 -10000 0 0
SRY -0.001 0.003 -10000 0 -0.016 19 19
GATA2 -0.012 0.11 -10000 0 -0.35 50 50
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.19 0.12 0.28 349 -10000 0 349
T-DHT/AR/RACK1/Src -0.003 0.072 0.22 19 -0.23 6 25
positive regulation of transcription -0.012 0.11 -10000 0 -0.35 50 50
DNAJA1 0.022 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.004 -10000 0 -10000 0 0
NCOA1 0.026 0.022 -10000 0 -0.38 1 1
SPDEF 0.083 0.15 0.28 160 -0.35 24 184
T-DHT/AR/TIF2 -0.002 0.093 0.23 14 -0.32 23 37
T-DHT/AR/Hsp90 0.003 0.065 0.21 13 -0.24 4 17
GSK3B 0.023 0.006 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.035 0.21 8 -0.19 3 11
SIRT1 0.021 0.023 -10000 0 -0.35 2 2
ZMIZ2 0.02 0.01 -10000 0 -10000 0 0
POU2F1 0.024 0.025 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.003 0.075 0.22 21 -0.27 3 24
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.022 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.12 0.18 0.28 2 -0.35 209 211
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.023 0.012 0.28 1 -10000 0 1
TCEB1 0.021 0.007 -10000 0 -10000 0 0
HIF1A/p53 0.024 0.062 0.25 1 -0.26 17 18
HIF1A 0.007 0.056 -10000 0 -0.27 17 17
COPS5 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.03 -10000 0 -0.18 1 1
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.13 0.13 0.28 216 -10000 0 216
ARNT/IPAS -0.058 0.12 0.21 2 -0.25 163 165
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.052 -10000 0 -0.26 14 14
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.001 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.018 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.023 0.062 -10000 0 -0.26 18 18
PHD1-3/OS9 0.047 0.03 0.21 3 -0.19 1 4
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.06 0.23 1 -0.25 15 16
VHL 0.022 0.017 -10000 0 -0.35 1 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.022 0.058 -10000 0 -0.26 14 14
EGLN3 0.023 0.025 0.28 3 -0.35 1 4
EGLN2 0.022 0.005 -10000 0 -10000 0 0
EGLN1 0.02 0.009 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.017 0.1 -10000 0 -0.54 16 16
ARNT 0.018 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.082 0.1 0.25 40 -0.26 17 57
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.024 0.22 4 -10000 0 4
AES 0.024 0.021 0.19 4 -10000 0 4
FBXW11 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.019 -10000 0 -0.25 2 2
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 0.002 0.087 0.28 2 -0.35 30 32
TLE1 0.024 0.021 0.2 4 -10000 0 4
MACF1 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.009 0.082 0.31 7 -0.34 8 15
WIF1 0.059 0.15 0.28 127 -0.35 34 161
beta catenin/RanBP3 0.016 0.12 0.41 31 -0.34 3 34
KREMEN2 0.045 0.074 0.28 47 -10000 0 47
DKK1 0.069 0.12 0.28 109 -0.35 8 117
beta catenin/beta TrCP1 0.017 0.079 0.29 6 -0.31 8 14
FZD1 0.021 0.023 -10000 0 -0.35 2 2
AXIN2 -0.046 0.28 0.65 10 -1.2 27 37
AXIN1 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.11 -10000 0 -0.54 19 19
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.18 0.3 2 -0.57 39 41
Axin1/APC/GSK3 0.006 0.057 0.25 3 -0.32 4 7
Axin1/APC/GSK3/beta catenin/Macf1 0.011 0.065 0.29 4 -0.34 8 12
HNF1A 0.029 0.037 0.26 11 -10000 0 11
CTBP1 0.024 0.02 0.2 3 -10000 0 3
MYC 0.066 0.27 0.59 79 -1.1 10 89
RANBP3 0.022 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.042 0.077 0.21 43 -0.2 30 73
NKD1 0.034 0.082 0.28 38 -0.35 8 46
TCF4 0.012 0.07 0.2 4 -0.35 18 22
TCF3 0.024 0.022 0.2 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.055 0.027 -10000 0 -0.19 2 2
Ran/GTP 0.017 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.004 0.14 0.47 22 -0.43 14 36
LEF1 0.023 0.039 0.22 5 -0.33 4 9
DVL1 0.009 0.06 0.24 2 -0.53 4 6
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.037 0.19 -10000 0 -0.58 43 43
DKK1/LRP6/Kremen 2 0.083 0.084 0.21 144 -0.2 8 152
LRP6 0.023 0.003 -10000 0 -10000 0 0
CSNK1A1 0.025 0.022 0.22 3 -10000 0 3
NLK 0.02 0.011 -10000 0 -10000 0 0
CCND1 0.002 0.1 0.58 9 -0.6 3 12
WNT1 0.024 0.03 0.28 7 -10000 0 7
GSK3A 0.023 0.004 -10000 0 -10000 0 0
GSK3B 0.023 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.006 -10000 0 -10000 0 0
PPP2R5D 0.015 0.046 0.26 6 -0.27 3 9
APC -0.01 0.041 0.18 21 -0.18 1 22
WNT1/LRP6/FZD1 0.003 0.06 0.18 28 -0.2 6 34
CREBBP 0.024 0.021 0.2 3 -10000 0 3
IL2 signaling events mediated by STAT5

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
GAB2 0.02 0.032 -10000 0 -0.35 4 4
ELF1 0.026 0.042 -10000 0 -0.34 5 5
CCNA2 0.077 0.1 0.28 114 -10000 0 114
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
JAK3 0.024 0.023 0.28 4 -10000 0 4
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
JAK1 0.023 0.016 -10000 0 -0.35 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.076 -10000 0 -0.44 4 4
SHC1 0.019 0.009 -10000 0 -10000 0 0
SP1 -0.035 0.13 -10000 0 -0.31 98 98
IL2RA 0.016 0.052 0.21 20 -0.32 5 25
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
SOS1 0.023 0.003 -10000 0 -10000 0 0
IL2RG 0.024 0.039 0.28 6 -0.35 3 9
G1/S transition of mitotic cell cycle -0.088 0.27 0.28 4 -0.61 99 103
PTPN11 0.023 0.003 -10000 0 -10000 0 0
CCND2 -0.095 0.23 -10000 0 -0.61 92 92
LCK 0.024 0.028 0.28 4 -0.35 1 5
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL2 0.027 0.046 0.28 17 -10000 0 17
CDK6 0.014 0.055 -10000 0 -0.35 12 12
CCND3 0.039 0.081 0.35 2 -0.46 2 4
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.026 0.04 -10000 0 -0.25 11 11
ATM 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
ATR 0.022 0.004 -10000 0 -10000 0 0
UBE2L3 0.022 0.005 -10000 0 -10000 0 0
FANCD2 0.015 0.011 0.24 1 -10000 0 1
protein ubiquitination 0.093 0.079 0.21 36 -0.17 10 46
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.04 0.017 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.01 0.095 -10000 0 -0.46 13 13
FANCF 0.021 0.023 -10000 0 -0.35 2 2
BRCA1 0.022 0.006 -10000 0 -10000 0 0
CCNE1 0.13 0.13 0.29 217 -10000 0 217
CDK2/Cyclin E1 0.1 0.089 0.22 207 -10000 0 207
FANCG 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.026 0.04 -10000 0 -0.25 11 11
FANCE 0.023 0.004 -10000 0 -10000 0 0
FANCC 0.022 0.006 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
FANCA 0.079 0.11 0.28 123 -10000 0 123
DNA repair 0.012 0.078 0.27 7 -0.36 8 15
BRCA1/BARD1/ubiquitin 0.026 0.04 -10000 0 -0.25 11 11
BARD1/DNA-PK 0.045 0.041 -10000 0 -0.19 11 11
FANCL 0.023 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.04 0.24 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.049 -10000 0 -0.2 21 21
BRCA1/BACH1/BARD1/TopBP1 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/P53 0.046 0.04 -10000 0 -0.19 11 11
BARD1/CSTF1/BRCA1 0.037 0.038 -10000 0 -0.21 11 11
BRCA1/BACH1 0.022 0.006 -10000 0 -10000 0 0
BARD1 0.015 0.053 -10000 0 -0.35 11 11
PCNA 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/UbcH7 0.037 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/RAD51/PCNA 0.084 0.081 0.21 133 -0.18 11 144
BARD1/DNA-PK/P53 0.051 0.043 -10000 0 -0.18 11 11
BRCA1/BARD1/Ubiquitin 0.026 0.04 -10000 0 -0.25 11 11
BRCA1/BARD1/CTIP 0.028 0.034 -10000 0 -0.19 11 11
FA complex 0.025 0.059 0.24 2 -0.28 3 5
BARD1/EWS 0.026 0.04 -10000 0 -0.25 11 11
RBBP8 -0.011 0.003 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
TOPBP1 0.023 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.045 0.039 0.19 11 -10000 0 11
BRCA1/BARD1 0.1 0.084 0.23 36 -0.18 10 46
CSTF1 0.022 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.012 0.037 -10000 0 -0.24 11 11
CDK2 0.023 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.099 0.12 0.28 160 -10000 0 160
RAD50 0.023 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.026 0.04 -10000 0 -0.25 11 11
EWSR1 0.022 0.006 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.039 0.2 1 -0.21 11 12
forebrain development -0.093 0.21 -10000 0 -0.48 103 103
GNAO1 -0.066 0.16 -10000 0 -0.35 124 124
SMO/beta Arrestin2 0.026 0.03 -10000 0 -0.24 4 4
SMO 0.017 0.034 -10000 0 -0.35 4 4
ARRB2 0.02 0.01 -10000 0 -10000 0 0
GLI3/SPOP -0.036 0.13 -10000 0 -0.42 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.022 0.004 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.052 0.021 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
XPO1 0.021 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.065 0.18 -10000 0 -0.55 44 44
SAP30 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.034 -10000 0 -0.35 4 4
MIM/GLI2A 0.015 0.032 -10000 0 -10000 0 0
IFT88 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.005 -10000 0 -10000 0 0
GLI2 -0.037 0.099 0.18 1 -0.34 22 23
GLI3 -0.044 0.13 -10000 0 -0.45 16 16
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.022 0.006 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.005 -10000 0 -10000 0 0
GNG2 0.017 0.049 0.28 1 -0.35 9 10
Gi family/GTP -0.043 0.11 -10000 0 -0.22 124 124
SIN3B 0.022 0.006 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.026 0.11 -10000 0 -0.4 18 18
GLI2/Su(fu) -0.029 0.1 -10000 0 -0.32 33 33
FOXA2 -0.075 0.29 -10000 0 -0.92 54 54
neural tube patterning -0.093 0.21 -10000 0 -0.48 103 103
SPOP 0.022 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.036 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
CSNK1G3 0.023 0.004 -10000 0 -10000 0 0
MTSS1 0.015 0.032 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.093 0.21 -10000 0 -0.48 103 103
SUFU 0.013 0.016 -10000 0 -10000 0 0
LGALS3 0.021 0.023 -10000 0 -0.35 2 2
catabolic process -0.06 0.15 -10000 0 -0.33 74 74
GLI3A/CBP -0.03 0.12 -10000 0 -0.31 88 88
KIF3A 0.022 0.016 -10000 0 -0.35 1 1
GLI1 -0.096 0.21 -10000 0 -0.49 103 103
RAB23 0.019 0.036 -10000 0 -0.35 5 5
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
IFT172 0.022 0.004 -10000 0 -10000 0 0
RBBP7 0.023 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.042 -10000 0 -0.17 2 2
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GLI2/SPOP -0.027 0.1 -10000 0 -0.33 25 25
STK36 0.021 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.044 0.1 -10000 0 -0.34 28 28
PTCH1 -0.086 0.19 -10000 0 -0.56 46 46
MIM/GLI1 -0.088 0.22 -10000 0 -0.53 85 85
CREBBP -0.03 0.12 -10000 0 -0.31 88 88
Su(fu)/SIN3/HDAC complex 0.007 0.083 0.19 1 -0.42 13 14
IL6-mediated 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
BCL2L1 0.073 0.15 0.48 4 -0.76 3 7
CRP 0.089 0.18 0.51 22 -0.69 4 26
cell cycle arrest 0.066 0.16 0.47 6 -0.72 6 12
TIMP1 0.064 0.15 0.44 5 -0.62 7 12
IL6ST -0.027 0.13 -10000 0 -0.34 79 79
Rac1/GDP 0.021 0.12 0.28 5 -0.34 29 34
AP1 0.014 0.14 -10000 0 -0.53 12 12
GAB2 0.021 0.032 -10000 0 -0.35 4 4
TNFSF11 0.077 0.16 0.47 3 -0.69 4 7
HSP90B1 0.044 0.092 -10000 0 -0.65 6 6
GAB1 0.02 0.032 -10000 0 -0.35 4 4
MAPK14 -0.005 0.12 -10000 0 -0.38 25 25
AKT1 0.026 0.06 -10000 0 -0.44 4 4
FOXO1 0.026 0.06 0.32 1 -0.45 3 4
MAP2K6 -0.007 0.11 0.22 6 -0.37 29 35
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.034 0.12 0.31 9 -0.36 20 29
MITF -0.015 0.13 0.23 6 -0.36 44 50
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.007 -10000 0 -10000 0 0
A2M 0.002 0.15 -10000 0 -1.1 9 9
CEBPB 0.026 0.008 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.022 0.11 -10000 0 -0.52 11 11
STAT3 0.062 0.17 0.47 6 -0.77 6 12
STAT1 0.024 0.059 -10000 0 -0.82 2 2
CEBPD 0.074 0.16 0.46 7 -0.77 4 11
PIK3CA 0.021 0.018 -10000 0 -0.35 1 1
PI3K 0.028 0.029 -10000 0 -0.24 5 5
JUN 0.018 0.042 -10000 0 -0.35 7 7
PIAS3/MITF -0.014 0.13 0.27 1 -0.35 43 44
MAPK11 -0.005 0.11 0.24 1 -0.38 24 25
STAT3 (dimer)/FOXO1 0.065 0.15 0.41 10 -0.52 9 19
GRB2/SOS1/GAB family 0.024 0.12 -10000 0 -0.35 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.11 0.21 5 -0.35 30 35
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.016 0.048 -10000 0 -0.35 9 9
LBP 0.084 0.17 0.48 16 -0.63 6 22
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
JAK1 0.025 0.018 -10000 0 -0.34 1 1
MYC 0.078 0.2 0.5 6 -0.9 10 16
FGG 0.062 0.15 0.5 4 -0.76 3 7
macrophage differentiation 0.066 0.16 0.47 6 -0.72 6 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.12 0.23 5 -0.25 64 69
JUNB 0.062 0.17 0.49 1 -0.83 8 9
FOS -0.088 0.17 -10000 0 -0.35 160 160
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.002 0.12 0.26 4 -0.37 31 35
STAT1/PIAS1 0.033 0.12 0.31 5 -0.34 22 27
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.06 -10000 0 -0.43 5 5
STAT3 (dimer) 0.064 0.17 0.47 6 -0.75 6 12
PRKCD 0.049 0.14 0.37 14 -0.5 7 21
IL6R -0.006 0.096 -10000 0 -0.35 39 39
SOCS3 -0.012 0.13 -10000 0 -0.71 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.093 -10000 0 -0.2 78 78
Rac1/GTP 0.026 0.12 0.28 6 -0.36 24 30
HCK 0.025 0.03 0.28 7 -10000 0 7
MAPKKK cascade 0.037 0.11 -10000 0 -0.55 11 11
bone resorption 0.077 0.16 0.45 6 -0.65 4 10
IRF1 0.061 0.15 0.56 2 -0.76 3 5
mol:GDP 0.004 0.11 0.24 7 -0.36 28 35
SOS1 0.023 0.004 -10000 0 -10000 0 0
VAV1 0 0.11 0.24 7 -0.36 28 35
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.021 0.15 -10000 0 -0.47 40 40
PTPN11 0.022 0.064 -10000 0 -0.66 4 4
IL6/IL6RA 0.008 0.09 0.22 6 -0.26 49 55
gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.089 -10000 0 -0.2 75 75
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.096 -10000 0 -0.2 85 85
IL6 0.023 0.071 0.29 9 -0.35 14 23
PIAS3 0.019 0.009 -10000 0 -10000 0 0
PTPRE 0 0.03 0.26 1 -0.35 1 2
PIAS1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.11 0.2 2 -0.28 64 66
LMO4 0.029 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.036 0.15 0.42 1 -0.66 8 9
MCL1 0.059 0.1 0.39 4 -0.52 1 5
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.01 0.014 0.3 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.03 0.017 0.21 1 -10000 0 1
CDKN1B 0.002 0.047 0.19 1 -0.29 7 8
CDKN1A 0.009 0.046 0.19 8 -0.29 8 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
FOXO3 0.008 0.037 0.19 2 -0.28 6 8
AKT1 0.007 0.036 -10000 0 -0.3 7 7
BAD 0.022 0.004 -10000 0 -10000 0 0
AKT3 -0.068 0.12 -10000 0 -0.26 155 155
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.042 0.19 1 -0.29 8 9
AKT1/ASK1 0.029 0.051 0.23 3 -0.28 8 11
BAD/YWHAZ 0.039 0.018 -10000 0 -10000 0 0
RICTOR 0.021 0.023 -10000 0 -0.35 2 2
RAF1 0.022 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.047 0.27 8 -10000 0 8
TSC1 0.009 0.024 -10000 0 -0.27 2 2
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.051 0.24 2 -0.28 7 9
EP300 0.021 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.04 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.038 0.19 1 -0.29 7 8
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 0.001 0.012 -10000 0 -0.19 2 2
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
MAPKAP1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.046 0.079 0.37 8 -0.24 14 22
YWHAH 0.022 0.006 -10000 0 -10000 0 0
AKT1S1 0.007 0.042 -10000 0 -0.29 8 8
CASP9 0.009 0.035 0.19 3 -0.28 5 8
YWHAB 0.022 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.023 0.067 0.28 7 -0.28 8 15
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.014 0.047 0.2 11 -0.26 7 18
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.047 -10000 0 -0.28 13 13
CHUK 0.009 0.04 -10000 0 -0.28 6 6
BAD/BCL-XL 0.03 0.043 0.26 1 -0.28 5 6
mTORC2 0.026 0.016 -10000 0 -0.18 2 2
AKT2 0.01 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.054 0.09 0.27 15 -0.37 10 25
PDPK1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.008 0.04 0.19 3 -0.29 7 10
MAPKKK cascade -0.032 0.05 0.28 7 -0.24 2 9
MDM2/Cbp/p300 0.039 0.055 0.28 2 -0.27 7 9
TSC1/TSC2 0.007 0.039 0.26 4 -0.26 5 9
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.053 0.27 2 -0.25 8 10
glucose import -0.08 0.091 0.2 5 -0.18 242 247
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.037 0.18 3 -0.18 11 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.082 0.09 0.2 2 -0.18 242 244
GSK3A 0.008 0.043 0.19 5 -0.29 8 13
FOXO1 0.007 0.036 -10000 0 -0.29 6 6
GSK3B 0.008 0.043 0.19 4 -0.29 8 12
SFN 0.21 0.12 0.28 385 -10000 0 385
G1/S transition of mitotic cell cycle 0.015 0.058 0.24 11 -0.28 8 19
p27Kip1/14-3-3 family 0.054 0.083 0.28 4 -0.51 6 10
PRKACA 0.022 0.005 -10000 0 -10000 0 0
KPNA1 0.022 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.023 0.003 -10000 0 -10000 0 0
VDR 0.029 0.042 0.29 13 -10000 0 13
Cbp/p300/PCAF 0.038 0.033 -10000 0 -0.2 8 8
EP300 0.021 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.075 0.16 2 -0.28 25 27
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
MAPK14 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.07 0.18 21 -0.22 19 40
RAR alpha/9cRA/Cyclin H 0.016 0.095 0.22 1 -0.26 39 40
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.087 0.16 1 -0.28 34 35
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.004 0.079 -10000 0 -0.21 50 50
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.023 0.19 9 -10000 0 9
RXRs/RARs/NRIP1/9cRA -0.011 0.15 0.28 3 -0.43 47 50
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
NCOA3 0.022 0.015 0.33 1 -10000 0 1
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.042 0.29 13 -10000 0 13
RARG 0.023 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.029 0.008 -10000 0 -10000 0 0
MAPK3 0.022 0.006 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.036 -10000 0 -0.35 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.007 0.13 0.27 4 -0.37 40 44
RARA 0.006 0.066 0.18 5 -0.22 33 38
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.089 0.16 1 -0.27 38 39
PRKCA 0.001 0.087 -10000 0 -0.35 31 31
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.011 0.16 0.26 1 -0.43 46 47
RXRG -0.016 0.12 0.23 11 -0.27 80 91
RXRA 0.004 0.061 0.18 6 -0.2 34 40
RXRB 0.009 0.081 0.22 5 -0.26 35 40
VDR/Vit D3/DNA 0.019 0.023 0.19 9 -10000 0 9
RBP1 0.008 0.072 -10000 0 -0.35 21 21
CRBP1/9-cic-RA 0.007 0.05 -10000 0 -0.24 21 21
RARB 0.017 0.048 -10000 0 -0.35 9 9
PRKCG 0.05 0.095 0.28 65 -0.35 6 71
MNAT1 0.022 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.14 0.27 3 -0.42 42 45
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.004 0.13 0.25 4 -0.36 49 53
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.11 0.21 8 -0.32 37 45
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.012 0.16 0.26 2 -0.43 46 48
positive regulation of DNA binding 0.007 0.086 -10000 0 -0.25 39 39
NRIP1 -0.013 0.16 -10000 0 -0.66 17 17
RXRs/RARs -0.009 0.16 0.26 1 -0.42 47 48
RXRs/RXRs/DNA/9cRA -0.018 0.12 0.2 3 -0.37 43 46
PRKACA 0.022 0.005 -10000 0 -10000 0 0
CDK7 0.022 0.005 -10000 0 -10000 0 0
TFIIH 0.044 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.029 0.075 -10000 0 -0.25 17 17
CCNH 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.04 0.017 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.054 0.085 0.28 66 -10000 0 66
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.017 -10000 0 -0.35 1 1
RAC1-CDC42/GTP/PAK family -0.014 0.062 -10000 0 -0.17 70 70
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
MAP3K12 0.02 0.032 -10000 0 -0.35 4 4
FGR 0.016 0.051 -10000 0 -0.35 10 10
p38 alpha/TAB1 -0.022 0.073 -10000 0 -0.31 22 22
PRKG1 -0.14 0.18 -10000 0 -0.35 226 226
DUSP8 0.019 0.036 -10000 0 -0.35 5 5
PGK/cGMP/p38 alpha -0.046 0.11 -10000 0 -0.3 41 41
apoptosis -0.021 0.069 -10000 0 -0.29 23 23
RAL/GTP 0.03 0.006 -10000 0 -10000 0 0
LYN 0.021 0.007 -10000 0 -10000 0 0
DUSP1 -0.062 0.16 -10000 0 -0.35 122 122
PAK1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.051 0.021 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -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 0.023 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.021 0.097 0.25 13 -0.38 13 26
BLK 0.037 0.068 0.28 38 -10000 0 38
HCK 0.025 0.03 0.28 7 -10000 0 7
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
DUSP16 0.023 0.003 -10000 0 -10000 0 0
DUSP10 0.02 0.008 -10000 0 -10000 0 0
TRAF6/MEKK3 0.027 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.019 0.1 0.22 16 -0.36 18 34
positive regulation of innate immune response 0.024 0.11 0.28 14 -0.45 14 28
LCK 0.024 0.028 0.28 4 -0.35 1 5
p38alpha-beta/MKP7 0.032 0.11 0.28 12 -0.43 14 26
p38alpha-beta/MKP5 0.023 0.11 0.3 9 -0.43 14 23
PGK/cGMP -0.092 0.13 -10000 0 -0.24 226 226
PAK2 0.021 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.009 0.12 0.29 9 -0.39 24 33
CDC42 0.022 0.005 -10000 0 -10000 0 0
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.004 -10000 0 -10000 0 0
PAK3 -0.034 0.13 -10000 0 -0.35 80 80
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.009 0.12 0.31 11 -0.32 34 45
IKBKB 0.021 0.087 0.27 12 -0.3 9 21
AKT1 0.014 0.098 0.27 32 -0.22 16 48
IKBKG 0.019 0.081 0.25 4 -0.33 6 10
CALM1 0.012 0.097 0.23 7 -0.35 10 17
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
MAP3K1 0.002 0.16 0.33 10 -0.45 41 51
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.099 0.23 5 -0.37 10 15
DOK1 0.023 0.003 -10000 0 -10000 0 0
AP-1 -0.006 0.089 0.26 8 -0.23 17 25
LYN 0.021 0.007 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
BCR complex 0.034 0.085 0.21 51 -0.26 25 76
CD22 -0.024 0.12 0.23 4 -0.45 28 32
CAMK2G 0.017 0.098 0.26 16 -0.37 6 22
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
SHC/GRB2/SOS1 0.018 0.041 -10000 0 -0.18 12 12
GO:0007205 0.014 0.1 0.23 5 -0.36 11 16
SYK 0.022 0.012 0.28 1 -10000 0 1
ELK1 0.012 0.1 0.25 8 -0.35 11 19
NFATC1 0.004 0.13 0.26 15 -0.37 30 45
B-cell antigen/BCR complex 0.034 0.085 0.21 51 -0.26 25 76
PAG1/CSK 0.029 0.02 -10000 0 -0.25 2 2
NFKBIB 0.022 0.046 0.15 9 -0.13 19 28
HRAS 0.016 0.094 0.25 10 -0.32 14 24
NFKBIA 0.022 0.045 0.16 8 -0.12 17 25
NF-kappa-B/RelA/I kappa B beta 0.025 0.04 0.15 9 -0.13 1 10
RasGAP/Csk 0.05 0.077 0.29 2 -0.19 25 27
mol:GDP 0.012 0.1 0.23 3 -0.35 12 15
PTEN 0.021 0.006 -10000 0 -10000 0 0
CD79B 0.005 0.077 -10000 0 -0.35 24 24
NF-kappa-B/RelA/I kappa B alpha 0.025 0.039 0.15 9 -0.13 1 10
GRB2 0.022 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.011 0.16 0.38 6 -0.45 36 42
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 0.018 0.096 0.23 5 -0.39 9 14
CSK 0.022 0.005 -10000 0 -10000 0 0
FOS -0.032 0.12 0.28 6 -0.33 26 32
CHUK 0.013 0.098 0.25 6 -0.36 18 24
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.029 0.093 0.26 2 -0.33 8 10
PTPN6 -0.027 0.11 0.22 4 -0.44 26 30
RELA 0.022 0.004 -10000 0 -10000 0 0
BCL2A1 0.02 0.028 0.12 4 -10000 0 4
VAV2 0.009 0.12 0.46 1 -0.43 24 25
ubiquitin-dependent protein catabolic process 0.023 0.045 0.15 9 -0.12 21 30
BTK 0.007 0.12 -10000 0 -0.94 8 8
CD19 -0.003 0.094 0.2 4 -0.4 23 27
MAP4K1 0.028 0.04 0.29 12 -10000 0 12
CD72 0.024 0.02 0.28 3 -10000 0 3
PAG1 0.02 0.024 -10000 0 -0.35 2 2
MAPK14 0.007 0.14 0.3 12 -0.39 38 50
SH3BP5 -0.03 0.13 -10000 0 -0.35 76 76
PIK3AP1 0.02 0.099 0.26 9 -0.35 10 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.015 0.091 0.24 1 -0.49 9 10
RAF1 0.014 0.092 0.24 12 -0.31 13 25
RasGAP/p62DOK/SHIP 0.048 0.074 0.32 1 -0.19 26 27
CD79A 0.045 0.084 0.28 53 -0.35 4 57
re-entry into mitotic cell cycle -0.006 0.088 0.25 9 -0.23 17 26
RASA1 0.019 0.036 -10000 0 -0.35 5 5
MAPK3 0.013 0.082 0.25 11 -0.28 8 19
MAPK1 0.011 0.079 0.24 8 -0.28 8 16
CD72/SHP1 0.004 0.14 0.3 9 -0.42 26 35
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 0.004 0.15 0.36 11 -0.38 41 52
actin cytoskeleton organization 0.01 0.12 0.32 9 -0.37 27 36
NF-kappa-B/RelA 0.051 0.078 0.27 10 -0.2 6 16
Calcineurin 0.026 0.088 0.24 1 -0.33 7 8
PI3K -0.02 0.095 -10000 0 -0.36 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.024 0.1 0.25 8 -0.34 15 23
SOS1 0.023 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.013 0.22 -10000 0 -0.62 53 53
DAPP1 -0.035 0.24 -10000 0 -0.71 52 52
cytokine secretion 0.005 0.12 0.26 15 -0.35 30 45
mol:DAG 0.018 0.096 0.23 5 -0.39 9 14
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
MAP2K1 0.013 0.084 0.24 9 -0.29 10 19
B-cell antigen/BCR complex/FcgammaRIIB 0.04 0.075 0.21 47 -0.22 20 67
mol:PI-3-4-5-P3 -0.014 0.084 0.21 7 -0.28 18 25
ETS1 0.014 0.094 0.26 16 -0.34 6 22
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.058 0.073 0.29 2 -0.19 19 21
B-cell antigen/BCR complex/LYN 0.001 0.097 0.22 2 -0.4 24 26
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.008 0.12 0.35 4 -0.4 24 28
B-cell antigen/BCR complex/LYN/SYK 0.008 0.13 0.35 4 -0.41 26 30
CARD11 0.014 0.1 0.26 10 -0.35 12 22
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
PPP3CA 0.022 0.004 -10000 0 -10000 0 0
BCL10 0.023 0.002 -10000 0 -10000 0 0
IKK complex 0.021 0.055 0.18 28 -0.13 10 38
PTPRC 0.015 0.047 0.28 1 -0.35 8 9
PDPK1 0.002 0.083 0.24 25 -0.21 14 39
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.017 0.033 -10000 0 -0.35 4 4
POU2F2 0.02 0.031 0.14 9 -10000 0 9
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.019 -10000 0 -10000 0 0
HSPA8 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.002 0.092 -10000 0 -0.23 57 57
AKT1 0.024 0.006 -10000 0 -10000 0 0
GSC 0.055 0.1 0.47 2 -0.45 3 5
NKX2-5 -0.005 0.018 -10000 0 -0.12 1 1
muscle cell differentiation -0.015 0.11 0.43 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.059 0.061 -10000 0 -0.25 4 4
SMAD4 0.013 0.038 -10000 0 -10000 0 0
CBFB 0.02 0.008 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.038 0.04 0.2 13 -0.21 3 16
SMAD3/SMAD4/VDR 0.051 0.052 0.24 2 -0.18 1 3
MYC 0.012 0.046 -10000 0 -0.35 8 8
CDKN2B -0.008 0.1 -10000 0 -0.53 10 10
AP1 -0.027 0.11 -10000 0 -0.3 22 22
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.019 0.072 -10000 0 -0.45 8 8
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.027 0.048 0.18 3 -0.24 4 7
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.088 0.12 0.29 134 -10000 0 134
SMAD3/SMAD4/GR -0.008 0.1 -10000 0 -0.23 77 77
GATA3 0.028 0.057 0.28 13 -0.35 6 19
SKI/SIN3/HDAC complex/NCoR1 0.008 0.075 -10000 0 -0.38 13 13
MEF2C/TIF2 0.008 0.11 0.28 6 -0.34 41 47
endothelial cell migration -0.014 0.12 0.92 7 -10000 0 7
MAX 0.022 0.005 -10000 0 -10000 0 0
RBBP7 0.023 0.003 -10000 0 -10000 0 0
RBBP4 0.021 0.028 -10000 0 -0.35 3 3
RUNX2 0.029 0.045 0.28 15 -0.35 1 16
RUNX3 0.029 0.041 0.28 14 -10000 0 14
RUNX1 0.023 0.003 -10000 0 -10000 0 0
CTBP1 0.022 0.005 -10000 0 -10000 0 0
NR3C1 -0.031 0.13 -10000 0 -0.35 77 77
VDR 0.029 0.042 0.29 13 -10000 0 13
CDKN1A 0.008 0.063 -10000 0 -0.84 2 2
KAT2B 0.016 0.046 -10000 0 -0.35 8 8
SMAD2/SMAD2/SMAD4/FOXH1 0.087 0.1 0.25 82 -10000 0 82
DCP1A 0.022 0.005 -10000 0 -10000 0 0
SKI 0.023 0.004 -10000 0 -10000 0 0
SERPINE1 0.014 0.12 -10000 0 -0.93 7 7
SMAD3/SMAD4/ATF2 0.028 0.058 -10000 0 -0.29 5 5
SMAD3/SMAD4/ATF3 0.007 0.083 -10000 0 -0.24 41 41
SAP30 0.023 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.022 0.03 -10000 0 -10000 0 0
JUN -0.037 0.1 -10000 0 -0.32 18 18
SMAD3/SMAD4/IRF7 0.033 0.062 0.3 6 -0.25 3 9
TFE3 0.024 0.01 -10000 0 -10000 0 0
COL1A2 0.02 0.074 -10000 0 -0.54 7 7
mesenchymal cell differentiation -0.032 0.061 0.24 4 -0.24 12 16
DLX1 0.05 0.082 0.28 60 -10000 0 60
TCF3 0.021 0.006 -10000 0 -10000 0 0
FOS -0.088 0.17 -10000 0 -0.36 160 160
SMAD3/SMAD4/Max 0.028 0.052 -10000 0 -0.25 3 3
Cbp/p300/SNIP1 0.04 0.016 -10000 0 -10000 0 0
ZBTB17 0.02 0.009 -10000 0 -10000 0 0
LAMC1 0.007 0.043 0.2 8 -0.22 3 11
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.052 -10000 0 -0.25 3 3
IRF7 0.028 0.037 0.29 10 -10000 0 10
ESR1 -0.017 0.11 -10000 0 -0.35 55 55
HNF4A 0.058 0.092 0.28 76 -10000 0 76
MEF2C 0.009 0.12 0.22 35 -0.35 41 76
SMAD2-3/SMAD4 0.033 0.062 -10000 0 -0.27 3 3
Cbp/p300/Src-1 0.037 0.02 -10000 0 -0.19 1 1
IGHV3OR16-13 0.005 0.034 -10000 0 -0.34 5 5
TGIF2/HDAC complex 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.014 0.017 -10000 0 -10000 0 0
SKIL 0.021 0.007 -10000 0 -10000 0 0
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
SNIP1 0.023 0.004 -10000 0 -10000 0 0
GCN5L2 -0.002 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.054 -10000 0 -0.25 3 3
MSG1/HSC70 0.038 0.038 0.21 16 -0.25 3 19
SMAD2 0.022 0.027 -10000 0 -10000 0 0
SMAD3 0.009 0.046 -10000 0 -0.37 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.031 -10000 0 -0.21 5 5
SMAD2/SMAD2/SMAD4 0.001 0.057 0.18 4 -0.24 14 18
NCOR1 0.021 0.007 -10000 0 -10000 0 0
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
MYOD/E2A 0.04 0.046 0.21 35 -10000 0 35
SMAD2-3/SMAD4/SP1/MIZ-1 0.067 0.062 -10000 0 -0.27 2 2
IFNB1 0.004 0.048 0.24 10 -0.23 2 12
SMAD3/SMAD4/MEF2C 0.026 0.12 0.24 7 -0.36 39 46
CITED1 0.029 0.053 0.28 17 -0.35 3 20
SMAD2-3/SMAD4/ARC105 0.043 0.062 -10000 0 -0.24 3 3
RBL1 0.022 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.047 0.22 1 -0.34 3 4
RUNX1-3/PEBPB2 0.044 0.028 0.2 11 -10000 0 11
SMAD7 -0.025 0.12 -10000 0 -0.44 14 14
MYC/MIZ-1 0.02 0.037 -10000 0 -0.25 8 8
SMAD3/SMAD4 -0.011 0.068 -10000 0 -0.38 8 8
IL10 0.015 0.069 0.24 24 -0.22 5 29
PIASy/HDAC complex 0.023 0.008 -10000 0 -10000 0 0
PIAS3 0.018 0.009 -10000 0 -10000 0 0
CDK2 0.018 0.012 -10000 0 -10000 0 0
IL5 0.005 0.05 0.2 7 -0.21 8 15
CDK4 0.014 0.017 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
ATF3 -0.008 0.097 -10000 0 -0.35 40 40
SMAD3/SMAD4/SP1 0.035 0.057 -10000 0 -0.24 5 5
FOXG1 0.14 0.13 0.28 254 -10000 0 254
FOXO3 0.009 0.007 -10000 0 -10000 0 0
FOXO1 0.007 0.017 -10000 0 -0.24 2 2
FOXO4 0.007 0.017 -10000 0 -0.24 2 2
heart looping 0.009 0.12 0.22 35 -0.35 41 76
CEBPB 0.023 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.044 0.074 0.23 35 -0.24 3 38
MYOD1 0.041 0.075 0.28 47 -10000 0 47
SMAD3/SMAD4/HNF4 0.049 0.079 0.22 48 -0.24 3 51
SMAD3/SMAD4/GATA3 0.037 0.07 0.25 4 -0.23 9 13
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.052 0.27 2 -0.21 3 5
SMAD3/SMAD4/SP1-3 0.058 0.049 -10000 0 -0.21 5 5
MED15 0.022 0.005 -10000 0 -10000 0 0
SP1 0.025 0.016 -10000 0 -0.14 2 2
SIN3B 0.022 0.006 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.078 0.11 0.24 78 -0.2 36 114
ITGB5 0.007 0.044 0.32 1 -0.22 2 3
TGIF/SIN3/HDAC complex/CtBP 0.016 0.054 -10000 0 -0.36 6 6
SMAD3/SMAD4/AR -0.013 0.11 -10000 0 -0.22 91 91
AR -0.04 0.14 -10000 0 -0.35 90 90
negative regulation of cell growth 0.006 0.069 -10000 0 -0.3 9 9
SMAD3/SMAD4/MYOD 0.038 0.071 0.23 29 -0.25 3 32
E2F5 0.021 0.007 -10000 0 -10000 0 0
E2F4 0.02 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.091 0.093 0.27 42 -10000 0 42
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.039 -10000 0 -0.27 3 3
TFDP1 0.022 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.012 0.12 -10000 0 -0.32 18 18
SMAD3/SMAD4/RUNX2 0.033 0.061 0.24 12 -0.24 4 16
TGIF2 0.022 0.005 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
ATF2 0.021 0.028 -10000 0 -0.35 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0.11 -10000 0 -0.41 8 8
CRKL -0.01 0.068 0.2 14 -0.24 5 19
mol:DAG 0.003 0.066 0.19 1 -0.25 17 18
HRAS 0.013 0.094 0.28 21 -0.23 5 26
MAPK8 0 0.073 0.18 60 -0.19 19 79
RAP1A -0.01 0.07 0.2 14 -0.24 5 19
GAB1 -0.012 0.071 0.2 12 -0.25 7 19
MAPK14 0.002 0.07 0.18 60 -0.18 14 74
EPO 0.008 0.067 0.29 1 -0.35 16 17
PLCG1 0.003 0.067 0.19 1 -0.25 17 18
EPOR/TRPC2/IP3 Receptors 0.021 0.037 0.29 7 -10000 0 7
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.031 0.055 0.21 8 -0.2 18 26
GAB1/SHC/GRB2/SOS1 0.019 0.06 0.26 1 -0.23 5 6
EPO/EPOR (dimer) 0.021 0.057 0.22 7 -0.25 16 23
IRS2 -0.031 0.083 0.19 13 -0.26 15 28
STAT1 -0.001 0.087 -10000 0 -0.28 21 21
STAT5B 0 0.079 -10000 0 -0.26 23 23
cell proliferation 0.003 0.081 0.2 66 -0.2 5 71
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.06 -10000 0 -0.24 9 9
TEC -0.011 0.068 0.22 11 -0.24 5 16
SOCS3 0.021 0.023 -10000 0 -0.35 2 2
STAT1 (dimer) -0.001 0.087 0.28 1 -0.27 21 22
JAK2 0.013 0.051 -10000 0 -0.35 9 9
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
EPO/EPOR (dimer)/JAK2 0.038 0.072 -10000 0 -0.19 23 23
EPO/EPOR 0.021 0.057 0.22 7 -0.25 16 23
LYN 0.017 0.015 -10000 0 -10000 0 0
TEC/VAV2 0.014 0.065 0.27 3 -0.24 5 8
elevation of cytosolic calcium ion concentration 0.021 0.037 0.29 7 -10000 0 7
SHC1 0.019 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.03 0.054 0.21 6 -0.2 15 21
mol:IP3 0.003 0.066 0.19 1 -0.25 17 18
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.001 0.095 0.28 4 -0.27 18 22
SH2B3 0.019 0.024 -10000 0 -0.35 1 1
NFKB1 0.001 0.071 0.19 38 -0.18 16 54
EPO/EPOR (dimer)/JAK2/SOCS3 0.001 0.053 0.2 1 -0.21 27 28
PTPN6 -0.009 0.066 0.16 33 -0.23 7 40
TEC/VAV2/GRB2 0.022 0.064 0.27 2 -0.24 5 7
EPOR 0.021 0.037 0.29 7 -10000 0 7
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
mol:GDP 0.018 0.061 0.26 1 -0.24 5 6
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
CRKL/CBL/C3G 0.023 0.066 0.27 3 -0.23 5 8
VAV2 -0.011 0.067 0.21 13 -0.24 5 18
CBL -0.01 0.069 0.22 10 -0.24 5 15
SHC/Grb2/SOS1 0.013 0.052 -10000 0 -0.24 4 4
STAT5A 0 0.078 -10000 0 -0.26 22 22
GRB2 0.022 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.004 0.1 -10000 0 -0.32 34 34
LYN/PLCgamma2 0.025 0.023 0.21 1 -0.24 1 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
BTK -0.01 0.072 0.32 4 -0.28 5 9
BCL2 -0.04 0.23 -10000 0 -0.74 50 50
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.065 0.059 -10000 0 -0.17 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.037 0.039 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.038 -10000 0 -0.21 10 10
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.055 -10000 0 -0.21 6 6
CaM/Ca2+ 0.063 0.053 -10000 0 -0.17 7 7
RAP1A 0.023 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.026 0.036 0.17 4 -0.17 8 12
AKT1 0.008 0.072 0.27 14 -0.28 1 15
MAP2K1 -0.01 0.039 0.19 9 -10000 0 9
MAP3K11 -0.005 0.043 0.21 7 -0.17 2 9
IFNGR1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.18 0.26 1 -0.31 275 276
Rap1/GTP -0.019 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.074 0.061 -10000 0 -0.18 10 10
CEBPB -0.006 0.13 0.31 7 -0.54 21 28
STAT3 0.022 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.051 0.15 -10000 0 -0.68 19 19
STAT1 -0.006 0.045 0.19 11 -10000 0 11
CALM1 0.022 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.045 0.088 0.29 60 -10000 0 60
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
STAT1 (dimer)/PIAS1 0.018 0.044 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.011 0.08 -10000 0 -0.37 16 16
mol:Ca2+ 0.062 0.056 -10000 0 -0.17 10 10
MAPK3 -0.016 0.14 -10000 0 -0.64 22 22
STAT1 (dimer) -0.037 0.075 -10000 0 -0.28 6 6
MAPK1 -0.029 0.17 -10000 0 -0.68 32 32
JAK2 0.017 0.049 -10000 0 -0.35 9 9
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
JAK1 0.023 0.018 -10000 0 -0.35 1 1
CAMK2D 0.022 0.017 -10000 0 -0.35 1 1
DAPK1 0.001 0.087 0.3 4 -0.38 15 19
SMAD7 -0.011 0.05 0.17 13 -0.2 3 16
CBL/CRKL/C3G 0.032 0.04 0.27 3 -10000 0 3
PI3K 0.052 0.053 -10000 0 -0.2 4 4
IFNG 0.045 0.088 0.29 60 -10000 0 60
apoptosis 0.001 0.075 0.26 2 -0.31 15 17
CAMK2G 0.022 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.006 -10000 0 -10000 0 0
CAMK2A -0.18 0.18 -10000 0 -0.35 292 292
CAMK2B 0.064 0.097 0.28 86 -0.35 1 87
FRAP1 0.006 0.067 0.23 20 -0.26 1 21
PRKCD 0.007 0.074 0.24 20 -0.29 1 21
RAP1B 0.023 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.032 0.055 -10000 0 -0.21 6 6
PTPN2 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.006 -10000 0 -10000 0 0
IRF1 -0.004 0.046 0.28 5 -0.31 1 6
STAT1 (dimer)/PIASy 0.016 0.043 0.27 3 -10000 0 3
SOCS1 -0.014 0.19 -10000 0 -1 19 19
mol:GDP 0.03 0.038 0.25 3 -10000 0 3
CASP1 -0.01 0.05 0.17 13 -0.16 4 17
PTGES2 0.022 0.006 -10000 0 -10000 0 0
IRF9 0.01 0.04 0.17 6 -0.15 11 17
mol:PI-3-4-5-P3 0.038 0.044 -10000 0 -0.18 9 9
RAP1/GDP 0.029 0.031 -10000 0 -10000 0 0
CBL -0.006 0.043 0.2 9 -0.17 7 16
MAP3K1 -0.006 0.042 0.2 9 -0.17 2 11
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PIAS4 0.021 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.055 -10000 0 -0.21 6 6
PTPN11 -0.004 0.045 0.17 19 -0.17 9 28
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.009 0.071 -10000 0 -0.35 20 20
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 89 91
PTK2 -0.018 0.096 -10000 0 -0.37 23 23
positive regulation of JNK cascade 0.002 0.081 -10000 0 -0.29 22 22
CDC42/GDP 0.01 0.11 -10000 0 -0.39 28 28
Rac1/GDP 0.007 0.12 0.3 2 -0.39 29 31
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.1 -10000 0 -0.36 22 22
nectin-3/I-afadin 0.021 0.056 -10000 0 -0.25 22 22
RAPGEF1 -0.002 0.1 0.31 4 -0.4 26 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.11 -10000 0 -0.45 27 27
PDGFB-D/PDGFRB 0.009 0.071 -10000 0 -0.35 20 20
TLN1 -0.02 0.058 -10000 0 -0.27 23 23
Rap1/GTP -0.002 0.078 -10000 0 -0.3 25 25
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.011 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.021 0.056 -10000 0 -0.25 22 22
PVR 0.022 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.005 -10000 0 -10000 0 0
mol:GDP -0.003 0.13 0.33 1 -0.47 30 31
MLLT4 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.042 0.066 -10000 0 -0.2 31 31
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.014 0.21 2 -10000 0 2
positive regulation of lamellipodium assembly -0.004 0.096 -10000 0 -0.32 31 31
PVRL1 0.023 0.016 0.28 2 -10000 0 2
PVRL3 0.007 0.074 -10000 0 -0.35 22 22
PVRL2 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
CLDN1 -0.02 0.12 -10000 0 -0.35 59 59
JAM-A/CLDN1 0.013 0.082 -10000 0 -0.2 61 61
SRC -0.01 0.12 -10000 0 -0.49 29 29
ITGB3 -0.04 0.14 0.28 2 -0.35 90 92
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.014 0.21 2 -10000 0 2
FARP2 0.002 0.13 -10000 0 -0.46 25 25
RAC1 0.022 0.005 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.033 0.051 -10000 0 -0.21 21 21
nectin-1/I-afadin 0.032 0.014 0.21 2 -10000 0 2
nectin-2/I-afadin 0.031 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.051 -10000 0 -0.21 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.008 -10000 0 -10000 0 0
F11R 0.019 0.018 -10000 0 -0.35 1 1
positive regulation of filopodium formation 0.002 0.081 -10000 0 -0.29 22 22
alphaV/beta3 Integrin/Talin -0.021 0.11 0.31 4 -0.3 35 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
PIP5K1C -0.015 0.064 -10000 0 -0.22 43 43
VAV2 -0.013 0.16 0.34 1 -0.51 35 36
RAP1/GDP 0.013 0.11 0.3 1 -0.36 26 27
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.032 0.051 -10000 0 -0.21 21 21
nectin-3(dimer)/I-afadin/I-afadin 0.021 0.056 -10000 0 -0.25 22 22
Rac1/GTP -0.002 0.12 -10000 0 -0.39 29 29
PTPRM -0.013 0.075 -10000 0 -0.24 48 48
E-cadherin/beta catenin/alpha catenin 0.054 0.033 -10000 0 -0.17 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.004 0.08 0.18 1 -0.18 82 83
MAPK9 0.005 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.021 0.12 12 -10000 0 12
GNB1/GNG2 0.026 0.031 0.19 1 -0.2 9 10
GNB1 0.022 0.004 -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 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.013 0.068 -10000 0 -0.18 77 77
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 0.008 0.018 0.051 77 -10000 0 77
GNAL -0.031 0.13 -10000 0 -0.35 77 77
GNG2 0.017 0.049 0.28 1 -0.35 9 10
CRH 0.022 0.04 0.28 12 -10000 0 12
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.025 -10000 0 -0.26 5 5
MAPK11 0.004 0.016 -10000 0 -0.26 2 2
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.023 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.029 0.069 -10000 0 -0.25 46 46
FRAP1 0.008 0.058 0.28 2 -0.38 6 8
AKT1 -0.01 0.077 0.16 38 -0.22 40 78
INSR 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0.011 0.073 0.27 2 -0.26 4 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.036 -10000 0 -0.18 8 8
TSC2 0.022 0.005 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.051 -10000 0 -0.26 3 3
TSC1 0.021 0.017 -10000 0 -0.35 1 1
Insulin Receptor/IRS1 -0.012 0.093 -10000 0 -0.28 58 58
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.006 0.045 -10000 0 -0.2 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.007 0.08 0.26 9 -0.3 11 20
MAP3K5 0.004 0.032 0.2 7 -0.21 6 13
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
apoptosis 0.004 0.032 0.2 7 -0.21 6 13
mol:LY294002 0 0 -10000 0 -0.001 57 57
EIF4B 0.008 0.077 0.24 12 -0.28 9 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.069 0.26 6 -0.26 8 14
eIF4E/eIF4G1/eIF4A1 0.007 0.032 -10000 0 -0.26 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.086 -10000 0 -0.26 49 49
mTOR/RHEB/GTP/Raptor/GBL 0 0.052 0.2 14 -0.15 6 20
FKBP1A 0.023 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.014 0.062 -10000 0 -0.25 3 3
mol:Amino Acids 0 0 -10000 0 -0.001 57 57
FKBP12/Rapamycin 0.017 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.077 0.15 34 -0.24 42 76
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.023 0.085 -10000 0 -0.52 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.003 0.079 -10000 0 -0.29 27 27
TSC1/TSC2 0.013 0.079 0.3 3 -0.27 4 7
tumor necrosis factor receptor activity 0 0 0.001 57 -10000 0 57
RPS6 0.022 0.005 -10000 0 -10000 0 0
PPP5C 0.023 0.004 -10000 0 -10000 0 0
EIF4G1 0.021 0.007 -10000 0 -10000 0 0
IRS1 -0.025 0.093 -10000 0 -0.29 58 58
INS 0.016 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
PDK2 -0.019 0.078 0.15 35 -0.24 40 75
EIF4EBP1 -0.025 0.23 -10000 0 -1 27 27
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PPP2R5D 0.009 0.064 0.27 9 -0.35 6 15
peptide biosynthetic process -0.012 0.017 0.18 4 -10000 0 4
RHEB 0.022 0.005 -10000 0 -10000 0 0
EIF4A1 0.021 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 23 -10000 0 23
EEF2 -0.012 0.017 0.18 4 -10000 0 4
eIF4E/4E-BP1 -0.014 0.22 -10000 0 -0.94 27 27
Syndecan-3-mediated signaling events

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
CTTN 0.023 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.011 0.098 -10000 0 -0.35 9 9
Syndecan-3/Neurocan 0.018 0.06 0.28 3 -0.37 8 11
POMC 0.027 0.075 0.28 24 -0.35 10 34
EGFR 0.014 0.059 0.33 1 -0.35 13 14
Syndecan-3/EGFR 0.011 0.062 0.3 1 -0.35 11 12
AGRP 0.019 0.017 0.28 2 -10000 0 2
NCSTN 0.019 0.009 -10000 0 -10000 0 0
PSENEN 0.022 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.018 0.039 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
NCAN 0.027 0.047 0.29 16 -10000 0 16
long-term memory 0.044 0.064 -10000 0 -0.33 11 11
Syndecan-3/IL8 0.064 0.1 0.26 29 -0.35 11 40
PSEN1 0.022 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.032 0.009 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
limb bud formation 0 0.051 -10000 0 -0.39 9 9
MC4R 0.026 0.042 0.28 14 -10000 0 14
SRC 0.022 0.005 -10000 0 -10000 0 0
PTN -0.06 0.15 -10000 0 -0.35 118 118
FGFR/FGF/Syndecan-3 0 0.051 -10000 0 -0.39 9 9
neuron projection morphogenesis -0.016 0.084 0.32 3 -0.34 8 11
Syndecan-3/AgRP 0.011 0.055 -10000 0 -0.34 11 11
Syndecan-3/AgRP/MC4R 0.041 0.069 0.27 1 -0.34 10 11
Fyn/Cortactin 0.033 0.007 -10000 0 -10000 0 0
SDC3 0 0.052 -10000 0 -0.39 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.064 0.1 0.26 29 -0.34 11 40
IL8 0.095 0.12 0.28 152 -10000 0 152
Syndecan-3/Fyn/Cortactin 0.045 0.065 -10000 0 -0.33 11 11
Syndecan-3/CASK -0.001 0.051 -10000 0 -0.35 11 11
alpha-MSH/MC4R 0.036 0.061 0.22 32 -0.25 10 42
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.014 0.091 0.26 8 -0.33 23 31
PDGFB-D/PDGFRB/SLAP 0.025 0.043 0.21 1 -0.24 12 13
PDGFB-D/PDGFRB/APS/CBL 0.036 0.044 -10000 0 -0.2 16 16
AKT1 0.014 0.098 0.31 34 -0.3 1 35
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.11 0.26 17 -0.36 25 42
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FGR -0.013 0.12 0.33 1 -0.54 19 20
mol:Ca2+ 0.01 0.11 0.26 15 -0.39 28 43
MYC 0.035 0.15 0.37 20 -0.7 11 31
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.048 0.17 2 -0.18 17 19
LRP1/PDGFRB/PDGFB 0.034 0.05 -10000 0 -0.21 20 20
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0.009 0.11 0.26 15 -0.4 28 43
PTEN 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.038 0.074 0.32 31 -0.35 2 33
PDGFB-D/PDGFRB/SHP2 0.024 0.052 -10000 0 -0.24 19 19
PDGFB-D/PDGFRB/GRB10 0.023 0.053 -10000 0 -0.24 20 20
cell cycle arrest 0.024 0.043 0.21 1 -0.24 12 13
HRAS 0.022 0.005 -10000 0 -10000 0 0
HIF1A 0.01 0.092 0.28 37 -0.27 1 38
GAB1 0.016 0.11 0.29 11 -0.37 25 36
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.018 0.11 0.28 25 -0.32 24 49
PDGFB-D/PDGFRB 0.036 0.043 -10000 0 -0.21 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.024 0.05 -10000 0 -0.24 18 18
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.013 0.077 0.21 4 -0.32 16 20
positive regulation of MAPKKK cascade 0.024 0.051 -10000 0 -0.24 19 19
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 0.009 0.12 0.26 15 -0.4 28 43
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.02 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.03 0.069 0.24 22 -0.24 21 43
SHB 0.022 0.004 -10000 0 -10000 0 0
BLK -0.016 0.14 0.38 2 -0.48 35 37
PTPN2 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.024 0.05 -10000 0 -0.24 18 18
BCAR1 0.021 0.007 -10000 0 -10000 0 0
VAV2 0.018 0.12 0.29 14 -0.38 25 39
CBL 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.052 -10000 0 -0.24 20 20
LCK -0.001 0.087 0.33 1 -0.5 9 10
PDGFRB 0.009 0.071 -10000 0 -0.35 20 20
ACP1 0.022 0.005 -10000 0 -10000 0 0
HCK 0.006 0.063 0.32 1 -0.91 1 2
ABL1 0.015 0.1 0.25 18 -0.33 25 43
PDGFB-D/PDGFRB/CBL 0.013 0.12 0.3 8 -0.41 31 39
PTPN1 0.021 0.009 -10000 0 -10000 0 0
SNX15 0.022 0.004 -10000 0 -10000 0 0
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.024 0.016 0.28 2 -10000 0 2
cell proliferation 0.036 0.14 0.36 21 -0.62 11 32
SLA 0.021 0.013 0.28 1 -10000 0 1
actin cytoskeleton reorganization -0.005 0.066 0.31 8 -0.33 1 9
SRC 0.003 0.07 0.33 1 -0.82 2 3
PI3K -0.021 0.025 -10000 0 -0.19 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.06 0.23 21 -0.2 16 37
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.02 0.11 0.27 16 -0.38 25 41
LYN 0.003 0.055 0.33 1 -0.44 2 3
LRP1 0.022 0.023 -10000 0 -0.35 2 2
SOS1 0.023 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.023 -10000 0 -0.35 2 2
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
NCK1-2/p130 Cas 0.05 0.049 -10000 0 -0.18 12 12
SPHK1 0.024 0.022 0.31 3 -10000 0 3
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.009 0.12 0.26 15 -0.4 28 43
PLCG1 0.009 0.12 0.26 15 -0.41 28 43
NHERF/PDGFRB 0.037 0.047 0.2 4 -0.2 17 21
YES1 -0.005 0.087 -10000 0 -0.43 15 15
cell migration 0.036 0.047 0.2 4 -0.2 17 21
SHC/Grb2/SOS1 0.044 0.045 -10000 0 -0.17 9 9
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.024 0.023 0.28 4 -10000 0 4
NHERF1-2/PDGFRB/PTEN 0.045 0.047 -10000 0 -0.18 16 16
FYN 0.003 0.068 0.33 1 -0.61 3 4
DOK1 -0.007 0.05 0.17 26 -0.19 13 39
HRAS/GTP 0.016 0.004 -10000 0 -10000 0 0
PDGFB 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.016 0.13 0.34 10 -0.44 25 35
PRKCD -0.005 0.051 0.18 29 -0.19 11 40
FER -0.006 0.051 0.18 28 -0.19 12 40
MAPKKK cascade 0.028 0.098 0.19 119 -0.18 1 120
RASA1 -0.007 0.056 0.18 29 -0.2 16 45
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.023 0.044 0.16 21 -0.18 12 33
PDGFB-D/PDGFRB/SHB 0.023 0.051 -10000 0 -0.24 19 19
chemotaxis 0.015 0.099 0.25 19 -0.32 25 44
STAT1-3-5/STAT1-3-5 0.043 0.044 -10000 0 -0.19 10 10
Bovine Papilomavirus E5/PDGFRB 0.008 0.049 -10000 0 -0.24 20 20
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.069 0.13 -10000 0 -0.36 39 39
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
AKT1 0.023 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.005 -10000 0 -10000 0 0
STXBP4 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.077 0.14 0.25 2 -0.38 44 46
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 -0.012 0.015 -10000 0 -0.25 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.041 0.016 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.013 0.28 1 -10000 0 1
PRKCI 0.021 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
GYS1 0.006 0.014 0.24 2 -10000 0 2
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
TRIP10 0.021 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.052 0.055 0.24 6 -0.25 6 12
VAMP2 0.021 0.007 -10000 0 -10000 0 0
SLC2A4 -0.085 0.15 0.31 1 -0.42 44 45
STX4 0.022 0.005 -10000 0 -10000 0 0
GSK3B 0.014 0.005 -10000 0 -10000 0 0
SFN 0.21 0.12 0.28 385 -10000 0 385
LNPEP 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.019 0.055 -10000 0 -10000 0 0
UGCG -0.03 0.18 -10000 0 -0.64 42 42
AKT1/mTOR/p70S6K/Hsp90/TERT 0.043 0.14 0.28 8 -0.5 17 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.028 0.18 -10000 0 -0.62 43 43
mol:DAG 0.004 0.094 -10000 0 -0.77 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.15 0.26 2 -0.39 44 46
FRAP1 0.007 0.17 0.28 2 -0.44 48 50
FOXO3 0.02 0.14 0.32 7 -0.5 16 23
AKT1 0.02 0.15 0.29 2 -0.53 17 19
GAB2 0.018 0.033 -10000 0 -0.35 4 4
SMPD1 -0.007 0.14 -10000 0 -0.63 23 23
SGMS1 0.012 0.072 -10000 0 -0.58 7 7
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 -0.008 0.02 -10000 0 -0.21 5 5
CALM1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.01 0.14 0.25 3 -0.45 29 32
EIF3A 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.032 -10000 0 -0.25 5 5
RPS6KB1 0.005 0.14 -10000 0 -0.81 15 15
mol:sphingomyelin 0.004 0.094 -10000 0 -0.77 7 7
natural killer cell activation 0 0.003 -10000 0 -0.016 1 1
JAK3 0.023 0.024 0.28 4 -10000 0 4
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
JAK1 0.022 0.018 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MYC 0.039 0.17 0.38 5 -0.85 11 16
MYB 0.052 0.082 0.48 2 -0.78 1 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.025 0.094 0.24 1 -0.46 8 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.13 -10000 0 -0.72 15 15
mol:PI-3-4-5-P3 0.029 0.095 0.24 1 -0.44 8 9
Rac1/GDP 0.011 0.023 -10000 0 -0.18 5 5
T cell proliferation 0.028 0.094 0.23 9 -0.4 9 18
SHC1 0.018 0.011 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.016 0.055 53 -10000 0 53
PRKCZ 0.027 0.095 0.24 5 -0.42 9 14
NF kappa B1 p50/RelA 0.026 0.15 -10000 0 -0.4 40 40
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.048 -10000 0 -0.41 3 3
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.053 0.28 20 -0.35 1 21
IL2RB 0.021 0.018 -10000 0 -0.35 1 1
TERT 0.12 0.13 0.28 194 -10000 0 194
E2F1 0.055 0.08 0.3 7 -0.9 1 8
SOS1 0.021 0.01 -10000 0 -10000 0 0
RPS6 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.004 0.008 -10000 0 -0.028 52 52
PTPN11 0.02 0.012 -10000 0 -10000 0 0
IL2RG 0.023 0.04 0.28 6 -0.35 3 9
actin cytoskeleton organization 0.028 0.094 0.23 9 -0.4 9 18
GRB2 0.02 0.01 -10000 0 -10000 0 0
IL2 0.024 0.048 0.28 17 -10000 0 17
PIK3CA 0.019 0.019 -10000 0 -0.35 1 1
Rac1/GTP 0.032 0.032 -10000 0 -0.17 5 5
LCK 0.023 0.029 0.28 4 -0.35 1 5
BCL2 -0.03 0.26 -10000 0 -0.76 54 54
Regulation of Telomerase

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
Telomerase catalytic core complex 0.003 0.12 0.41 2 -0.49 2 4
RAD9A 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.047 0.13 -10000 0 -0.25 162 162
IFNAR2 0.028 0.018 -10000 0 -0.34 1 1
AKT1 0.009 0.061 0.18 6 -0.16 38 44
ER alpha/Oestrogen -0.007 0.079 -10000 0 -0.24 56 56
NFX1/SIN3/HDAC complex 0.018 0.059 -10000 0 -0.35 9 9
EGF 0.033 0.055 0.28 21 -0.34 2 23
SMG5 0.019 0.009 -10000 0 -10000 0 0
SMG6 0.021 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.042 0.013 -10000 0 -10000 0 0
TERT/c-Abl 0.001 0.12 0.39 1 -0.57 1 2
SAP18 0.023 0.005 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 -0.24 0.17 -10000 0 -0.35 384 384
WRN 0.02 0.008 -10000 0 -10000 0 0
SP1 0.03 0.01 -10000 0 -10000 0 0
SP3 0.025 0.004 -10000 0 -10000 0 0
TERF2IP 0.02 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0 0.11 -10000 0 -0.51 1 1
Mad/Max 0.039 0.012 -10000 0 -10000 0 0
TERT 0.003 0.13 0.45 1 -0.5 2 3
CCND1 0.005 0.12 0.41 2 -0.5 1 3
MAX 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.024 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.028 -10000 0 -0.35 3 3
TERF2 0.018 0.01 -10000 0 -10000 0 0
PTGES3 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.023 0.005 -10000 0 -10000 0 0
Telomerase/911 0.025 0.042 0.21 2 -0.29 2 4
CDKN1B -0.001 0.1 -10000 0 -0.46 23 23
RAD1 0.022 0.004 -10000 0 -10000 0 0
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.023 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.029 0.013 -10000 0 -10000 0 0
UBE3A 0.024 0.006 -10000 0 -10000 0 0
JUN 0.02 0.042 -10000 0 -0.35 7 7
E6 0.002 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.008 -10000 0 -10000 0 0
FOS -0.086 0.17 -10000 0 -0.35 160 160
IFN-gamma/IRF1 0.05 0.084 0.22 60 -0.25 23 83
PARP2 0.022 0.004 -10000 0 -10000 0 0
BLM 0.051 0.081 0.28 59 -10000 0 59
Telomerase 0.027 0.085 0.22 4 -0.46 6 10
IRF1 0.02 0.036 -10000 0 -0.15 23 23
ESR1 -0.016 0.11 -10000 0 -0.35 56 56
KU/TER 0.032 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.058 -10000 0 -0.3 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.021 0.059 -10000 0 -0.31 11 11
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.029 0.009 -10000 0 -10000 0 0
ATM 0.015 0.019 -10000 0 -10000 0 0
SMAD3 -0.015 0.021 -10000 0 -0.25 4 4
ABL1 0.02 0.023 -10000 0 -0.35 2 2
MXD1 0.025 0.005 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.12 0.38 1 -0.48 2 3
NR2F2 -0.011 0.078 -10000 0 -0.35 25 25
MAPK3 0.002 0.025 0.11 17 -10000 0 17
MAPK1 0.002 0.024 0.11 16 -10000 0 16
TGFB1/TGF beta receptor Type II 0.02 0.017 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
HNRNPC 0.022 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.015 0.019 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.016 0.059 0.33 1 -0.35 13 14
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.036 0.058 0.21 21 -0.24 14 35
MYC 0.016 0.046 -10000 0 -0.35 8 8
IL2 0.034 0.047 0.29 17 -10000 0 17
KU 0.032 0.009 -10000 0 -10000 0 0
RAD50 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
TGFB1 0.02 0.017 -10000 0 -0.35 1 1
TRF2/BLM 0.044 0.051 0.2 48 -10000 0 48
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.009 0.12 0.41 1 -0.53 1 2
SP1/HDAC2 0.048 0.02 -10000 0 -10000 0 0
PINX1 0.02 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.003 0.11 -10000 0 -0.51 1 1
Smad3/Myc 0.003 0.036 -10000 0 -0.23 9 9
911 complex 0.043 0.013 -10000 0 -10000 0 0
IFNG 0.047 0.091 0.28 60 -0.15 23 83
Telomerase/PinX1 -0.005 0.11 -10000 0 -0.51 1 1
Telomerase/AKT1/mTOR/p70S6K 0.018 0.076 0.27 3 -0.36 10 13
SIN3B 0.023 0.006 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.001 0.1 -10000 0 -0.51 1 1
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.052 0.028 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.001 0.11 -10000 0 -0.51 1 1
E2F1 0.077 0.1 0.29 100 -10000 0 100
ZNFX1 0.023 0.005 -10000 0 -10000 0 0
PIF1 0.087 0.11 0.28 135 -10000 0 135
NCL 0.023 0.003 -10000 0 -10000 0 0
DKC1 0.023 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.007 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.075 0.24 2 -0.22 7 9
NFATC4 -0.004 0.077 0.34 15 -0.2 1 16
ERBB2IP 0.021 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.004 0.051 0.19 1 -0.21 10 11
JUN 0.007 0.085 0.25 5 -0.33 4 9
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK7 -0.016 0.054 0.29 3 -0.21 7 10
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.045 0.21 12 -0.2 8 20
AKT1 -0.003 0.008 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.023 0.076 0.21 19 -0.18 9 28
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.007 0.058 0.34 2 -0.22 10 12
RAF1 0.035 0.088 0.27 14 -0.25 6 20
ErbB2/ErbB3/neuregulin 2 -0.003 0.081 0.2 10 -0.2 68 78
STAT3 -0.011 0.17 -10000 0 -0.78 25 25
cell migration -0.011 0.089 0.24 28 -0.2 9 37
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.025 0.23 0.37 4 -0.56 32 36
FOS -0.076 0.26 0.32 6 -0.44 168 174
NRAS 0.023 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.051 0.19 1 -0.21 10 11
MAPK3 0 0.19 0.35 7 -0.57 24 31
MAPK1 -0.005 0.2 0.34 4 -0.6 24 28
JAK2 -0.018 0.053 0.29 3 -0.21 5 8
NF2 0.005 0.028 -10000 0 -0.64 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.009 0.041 0.18 5 -0.22 9 14
NRG1 0.014 0.05 0.28 1 -0.35 9 10
GRB2/SOS1 0.032 0.01 -10000 0 -10000 0 0
MAPK8 -0.002 0.067 0.28 4 -0.24 14 18
MAPK9 0 0.062 0.22 23 -10000 0 23
ERBB2 -0.009 0.056 0.32 14 -10000 0 14
ERBB3 0.02 0.028 -10000 0 -0.35 3 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.17 -10000 0 -0.76 26 26
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.003 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.031 -10000 0 -0.16 9 9
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.035 0.21 12 -10000 0 12
CHRNA1 0.025 0.16 0.34 7 -0.37 20 27
myelination 0.013 0.1 0.32 39 -10000 0 39
PPP3CB -0.016 0.049 0.29 2 -0.2 7 9
KRAS 0.023 0.014 0.33 1 -10000 0 1
RAC1-CDC42/GDP 0.044 0.056 0.22 4 -0.2 8 12
NRG2 -0.03 0.13 -10000 0 -0.35 75 75
mol:GDP 0.009 0.041 0.18 5 -0.22 9 14
SOS1 0.023 0.004 -10000 0 -10000 0 0
MAP2K2 0.028 0.092 0.21 40 -0.28 5 45
SRC 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.016 0.053 0.29 3 -0.2 7 10
MAP2K1 -0.008 0.19 0.39 2 -0.56 26 28
heart morphogenesis 0.004 0.051 0.19 1 -0.21 10 11
RAS family/GDP 0.048 0.069 0.24 4 -0.22 6 10
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.039 -10000 0 -0.61 2 2
CHRNE 0.006 0.025 0.097 1 -0.16 4 5
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.003 0.008 -10000 0 -10000 0 0
nervous system development 0.004 0.051 0.19 1 -0.21 10 11
CDC42 0.022 0.005 -10000 0 -10000 0 0
Ceramide 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
SPHK2 -0.011 0.011 -10000 0 -0.25 1 1
MAP4K4 0.007 0.057 0.21 4 -0.28 7 11
BAG4 0.019 0.024 -10000 0 -0.35 2 2
PKC zeta/ceramide 0.013 0.041 0.2 1 -0.19 18 19
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.045 0.28 2 -0.35 7 9
BAX 0.003 0.049 -10000 0 -0.33 10 10
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0 0.081 0.65 8 -10000 0 8
BAD -0.001 0.044 0.2 10 -0.18 19 29
SMPD1 0.012 0.058 0.16 24 -0.22 14 38
RB1 -0.005 0.036 0.2 1 -0.18 20 21
FADD/Caspase 8 0.011 0.065 0.23 4 -0.31 10 14
MAP2K4 -0.006 0.039 0.18 6 -0.17 20 26
NSMAF 0.021 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.047 0.2 12 -0.17 21 33
EGF 0.031 0.055 0.28 21 -0.35 2 23
mol:ceramide -0.001 0.038 0.12 2 -0.19 19 21
MADD 0.022 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.011 -10000 0 -0.25 1 1
ASAH1 0.02 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.005 0.036 0.2 1 -0.18 20 21
cell proliferation -0.013 0.075 0.18 1 -0.22 16 17
BID -0.013 0.17 -10000 0 -0.62 33 33
MAP3K1 -0.004 0.038 0.18 4 -0.18 19 23
EIF2A 0.002 0.055 0.18 34 -0.17 14 48
TRADD 0.02 0.008 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.004 0.048 0.2 11 -0.18 11 22
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.007 0.051 0.19 12 -0.19 12 24
Cathepsin D/ceramide 0.014 0.039 0.18 1 -0.18 18 19
FADD 0.007 0.06 0.21 6 -0.28 8 14
KSR1 -0.003 0.043 0.2 7 -0.18 21 28
MAPK8 -0.003 0.051 -10000 0 -0.2 12 12
PRKRA -0.002 0.04 0.19 6 -0.18 18 24
PDGFA 0.021 0.017 -10000 0 -0.35 1 1
TRAF2 0.022 0.006 -10000 0 -10000 0 0
IGF1 -0.046 0.14 -10000 0 -0.35 100 100
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.037 0.12 2 -0.19 19 21
CTSD 0.022 0.012 0.28 1 -10000 0 1
regulation of nitric oxide biosynthetic process 0.032 0.015 -10000 0 -0.24 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.079 0.2 1 -0.23 16 17
PRKCD 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.011 -10000 0 -0.25 1 1
RelA/NF kappa B1 0.032 0.015 -10000 0 -0.25 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.011 0.052 0.23 1 -0.38 2 3
TNFR1A/BAG4/TNF-alpha 0.054 0.054 0.2 51 -0.21 2 53
mol:Sphingosine-1-phosphate -0.011 0.011 -10000 0 -0.24 1 1
MAP2K1 -0.006 0.046 0.19 13 -0.17 16 29
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
CYCS 0.016 0.051 0.14 41 -0.17 5 46
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.25 2 2
EIF2AK2 -0.003 0.044 0.2 12 -0.18 17 29
TNF-alpha/TNFR1A/FAN 0.056 0.052 0.2 52 -0.21 1 53
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.058 -10000 0 -0.36 7 7
MAP2K2 -0.006 0.046 0.19 12 -0.17 16 28
SMPD3 0.003 0.088 0.2 8 -0.27 39 47
TNF 0.053 0.088 0.28 66 -0.35 2 68
PKC zeta/PAR4 0.033 0.016 0.21 1 -0.25 1 2
mol:PHOSPHOCHOLINE -0.001 0.036 0.14 4 -0.13 13 17
NF kappa B1/RelA/I kappa B alpha 0.061 0.026 -10000 0 -0.18 2 2
AIFM1 0.014 0.052 0.15 16 -0.16 7 23
BCL2 -0.008 0.1 -10000 0 -0.35 44 44
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.048 0.051 0.23 10 -0.19 14 24
MAP4K1 0.028 0.04 0.29 12 -10000 0 12
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
PRKCB 0.001 0.087 -10000 0 -0.35 31 31
DBNL 0.023 0.004 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.045 -10000 0 -0.24 4 4
JUN -0.044 0.19 -10000 0 -0.56 60 60
MAP3K7 0.006 0.047 -10000 0 -0.26 3 3
GRAP2 0.011 0.061 -10000 0 -0.35 15 15
CRK 0.021 0.006 -10000 0 -10000 0 0
MAP2K4 0.005 0.061 -10000 0 -0.25 14 14
LAT 0.022 0.005 -10000 0 -10000 0 0
LCP2 0.023 0.012 0.28 1 -10000 0 1
MAPK8 -0.04 0.2 -10000 0 -0.58 60 60
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.049 -10000 0 -0.2 11 11
LAT/GRAP2/SLP76/HPK1/HIP-55 0.056 0.049 0.27 3 -0.18 11 14
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.015 0.33 1 -10000 0 1
NFATC1 0.012 0.08 0.27 4 -0.39 5 9
NFATC2 -0.001 0.066 0.14 9 -0.21 22 31
NFATC3 0.012 0.016 -10000 0 -0.3 1 1
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.022 0.12 0.21 4 -0.35 35 39
Exportin 1/Ran/NUP214 0.043 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.001 0.1 -10000 0 -0.32 27 27
BCL2/BAX 0.009 0.077 -10000 0 -0.25 44 44
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.01 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.005 -10000 0 -10000 0 0
BAD 0.022 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.009 0.1 -10000 0 -0.35 26 26
Calcineurin A alpha-beta B1/BCL2 -0.008 0.1 -10000 0 -0.35 44 44
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.009 0.1 0.35 26 -10000 0 26
KPNB1 0.022 0.005 -10000 0 -10000 0 0
KPNA2 0.035 0.059 0.3 25 -10000 0 25
XPO1 0.023 0.003 -10000 0 -10000 0 0
SFN 0.21 0.12 0.28 385 -10000 0 385
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
NFAT4/CK1 alpha 0.017 0.022 -10000 0 -0.16 1 1
MEF2D/NFAT1/Cbp/p300 0.012 0.088 -10000 0 -0.24 34 34
CABIN1 -0.023 0.12 0.21 4 -0.36 34 38
CALM1 0.02 0.01 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
CAMK4 0.023 0.037 0.28 5 -0.35 3 8
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.022 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.019 -10000 0 -0.25 2 2
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.036 -10000 0 -0.35 5 5
MAPK9 0.023 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.013 0.085 0.26 3 -0.37 7 10
PRKCH 0.021 0.023 -10000 0 -0.35 2 2
CABIN1/Cbp/p300 0.028 0.019 -10000 0 -10000 0 0
CASP3 0.022 0.006 -10000 0 -10000 0 0
PIM1 0.023 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
apoptosis 0.008 0.031 0.19 1 -0.25 2 3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.058 0.2 6 -0.29 6 12
PRKCB 0.001 0.087 -10000 0 -0.35 31 31
PRKCE 0.023 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.012 0.053 -10000 0 -0.27 1 1
BAD/BCL-XL 0.032 0.014 0.24 1 -10000 0 1
PRKCD 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.022 0.006 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
PRKCA 0 0.087 -10000 0 -0.35 31 31
PRKCG 0.049 0.095 0.28 65 -0.35 6 71
PRKCQ -0.007 0.1 0.28 1 -0.35 43 44
FKBP38/BCL2 0.009 0.077 -10000 0 -0.25 44 44
EP300 0.019 0.012 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.023 0.079 0.28 3 -0.37 5 8
CaM/Ca2+/FKBP38 0.026 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.027 0.027 0.19 5 -0.2 3 8
NFATc/ERK1 0.023 0.078 0.28 3 -0.37 5 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.002 0.11 -10000 0 -0.32 33 33
NR4A1 0.01 0.13 0.23 16 -0.38 32 48
GSK3B 0.022 0.006 -10000 0 -10000 0 0
positive T cell selection 0.012 0.016 -10000 0 -0.3 1 1
NFAT1/CK1 alpha 0.002 0.048 0.12 1 -0.18 13 14
RCH1/ KPNB1 0.04 0.04 0.22 24 -10000 0 24
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.021 0.006 -10000 0 -10000 0 0
AKAP5 0.021 0.023 -10000 0 -0.35 2 2
MEF2D 0.017 0.013 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.022 0.078 0.28 3 -0.37 5 8
CREBBP 0.019 0.012 -10000 0 -10000 0 0
BCL2 -0.008 0.1 -10000 0 -0.35 44 44
FoxO family signaling

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
G6PC 0.004 0.048 -10000 0 -10000 0 0
PLK1 0.13 0.19 0.47 12 -0.61 5 17
CDKN1B 0.06 0.16 0.38 7 -0.41 28 35
FOXO3 0.1 0.18 0.41 20 -0.55 11 31
KAT2B 0.028 0.056 -10000 0 -0.34 8 8
FOXO1/SIRT1 0.012 0.046 0.25 1 -0.21 1 2
CAT 0.093 0.18 0.52 4 -0.66 5 9
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.033 -10000 0 -10000 0 0
FOXO1 0.007 0.052 0.25 4 -0.22 1 5
MAPK10 -0.016 0.081 0.2 11 -0.17 108 119
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.007 0.079 0.3 3 -0.35 2 5
response to oxidative stress 0.017 0.023 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.083 0.17 0.37 14 -0.45 19 33
XPO1 0.023 0.003 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.037 0.092 -10000 0 -0.74 6 6
FOXO1/SKP2 0.018 0.048 0.28 1 -10000 0 1
mol:GDP 0.017 0.023 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
GADD45A 0.071 0.12 -10000 0 -0.64 2 2
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.14 0.24 3 -0.53 25 28
MST1 0.036 0.043 0.29 6 -10000 0 6
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.022 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.12 0.24 1 -0.45 21 22
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.036 0.21 10 -0.16 5 15
MAPK9 0.021 0.033 0.2 13 -10000 0 13
YWHAG 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
SIRT1 0.013 0.027 -10000 0 -0.35 2 2
SOD2 0.078 0.14 0.44 5 -0.49 4 9
RBL2 0.031 0.26 0.45 1 -0.69 41 42
RAL/GDP 0.04 0.025 -10000 0 -10000 0 0
CHUK 0.033 0.032 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
RAL/GTP 0.041 0.024 -10000 0 -10000 0 0
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
FASLG 0.038 0.11 -10000 0 -1.2 4 4
SKP2 0.022 0.005 -10000 0 -10000 0 0
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.029 0.032 -10000 0 -10000 0 0
CCNB1 0.1 0.18 0.45 11 -0.62 5 16
FOXO1-3a-4/beta catenin 0.07 0.12 0.37 8 -0.37 5 13
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.048 0.28 1 -10000 0 1
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
SGK1 0.033 0.037 -10000 0 -0.37 1 1
CSNK1G3 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0.007 -10000 0 -10000 0 0
ZFAND5 0.007 0.071 0.32 1 -10000 0 1
SFN 0.21 0.12 0.28 385 -10000 0 385
CDK2 0.022 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.068 0.12 0.25 5 -0.44 18 23
CREBBP 0.022 0.006 -10000 0 -10000 0 0
FBXO32 0.023 0.4 0.5 29 -0.96 68 97
BCL6 0.085 0.16 0.45 1 -0.67 5 6
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.004 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.024 -10000 0 -0.35 2 2
Caspase 8 (4 units) 0.029 0.048 -10000 0 -0.24 6 6
NEF 0.001 0.019 -10000 0 -0.2 4 4
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC3 0.011 0.057 0.2 2 -0.41 7 9
CYCS 0.024 0.067 0.17 71 -0.24 6 77
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.02 0.03 0.33 1 -0.25 4 5
MAP2K7 0.004 0.19 -10000 0 -0.67 33 33
protein ubiquitination 0.01 0.076 0.28 7 -0.29 8 15
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.023 0.003 -10000 0 -10000 0 0
FAS 0.019 0.032 -10000 0 -0.35 4 4
BID 0.03 0.069 0.18 72 -0.25 6 78
NF-kappa-B/RelA/I kappa B alpha 0.044 0.037 -10000 0 -0.22 8 8
TRADD 0.02 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
CFLAR 0.023 0.003 -10000 0 -10000 0 0
FADD 0.022 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.037 -10000 0 -0.23 8 8
MAPK8 0.006 0.18 0.4 5 -0.62 33 38
APAF1 0.023 0.002 -10000 0 -10000 0 0
TRAF1 0.022 0.005 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.037 0.071 0.19 72 -0.26 6 78
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.004 0.089 0.21 3 -0.34 15 18
CHUK 0.011 0.078 0.29 7 -0.31 8 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.033 -10000 0 -0.18 5 5
TCRz/NEF 0.018 0.03 0.16 7 -0.24 4 11
TNF 0.053 0.088 0.28 66 -0.35 2 68
FASLG 0.012 0.045 0.25 8 -0.33 4 12
NFKB1 0.021 0.021 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.054 0.054 0.2 51 -0.21 2 53
CASP6 0.041 0.1 -10000 0 -0.46 14 14
CASP7 0.031 0.1 0.35 9 -0.43 9 18
RELA 0.022 0.014 -10000 0 -10000 0 0
CASP2 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.03 0.1 0.36 10 -0.4 12 22
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.25 2 2
CASP8 0.023 0.003 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.009 0.081 0.2 2 -0.33 12 14
APAF-1/Caspase 9 0.029 0.058 -10000 0 -0.29 7 7
BCL2 -0.006 0.17 0.38 4 -0.58 32 36
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.19 0.26 0.66 8 -1.2 7 15
IL23A 0.2 0.24 0.72 9 -1.2 4 13
NF kappa B1 p50/RelA/I kappa B alpha 0.18 0.22 0.58 3 -1.1 5 8
positive regulation of T cell mediated cytotoxicity 0.21 0.26 0.66 20 -1.2 5 25
ITGA3 0.19 0.24 0.65 9 -1.2 4 13
IL17F 0.15 0.19 0.49 31 -0.68 5 36
IL12B 0.063 0.049 0.2 9 -10000 0 9
STAT1 (dimer) 0.19 0.24 0.61 8 -1.2 5 13
CD4 0.2 0.23 0.64 9 -1.1 4 13
IL23 0.19 0.24 0.67 8 -1.2 4 12
IL23R 0.1 0.097 0.44 2 -0.58 2 4
IL1B 0.2 0.25 0.72 8 -1.1 7 15
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.22 0.25 0.67 21 -1.1 4 25
TYK2 0.044 0.034 -10000 0 -10000 0 0
STAT4 0.022 0.016 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
IL18RAP 0.022 0.038 0.29 3 -0.35 4 7
IL12RB1 0.049 0.067 0.35 13 -0.38 4 17
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL12Rbeta1/TYK2 0.058 0.059 0.28 12 -0.27 4 16
IL23R/JAK2 0.13 0.12 0.45 2 -0.48 1 3
positive regulation of chronic inflammatory response 0.21 0.26 0.66 20 -1.2 5 25
natural killer cell activation -0.007 0.008 -10000 0 -0.042 2 2
JAK2 0.057 0.072 0.19 6 -0.35 9 15
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
NFKB1 0.026 0.018 -10000 0 -0.35 1 1
RELA 0.026 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.19 0.23 0.66 8 -1.1 4 12
ALOX12B 0.19 0.23 0.66 8 -1.1 4 12
CXCL1 0.2 0.28 0.68 16 -1.1 12 28
T cell proliferation 0.21 0.26 0.66 20 -1.2 5 25
NFKBIA 0.026 0.008 -10000 0 -10000 0 0
IL17A 0.15 0.17 0.44 42 -0.55 4 46
PI3K 0.16 0.23 0.58 3 -1.1 5 8
IFNG 0.027 0.038 0.11 49 -0.11 2 51
STAT3 (dimer) 0.16 0.22 0.56 3 -1 5 8
IL18R1 0.021 0.032 -10000 0 -0.35 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.17 0.2 0.53 28 -0.75 5 33
IL18/IL18R 0.048 0.049 0.26 10 -0.21 8 18
macrophage activation 0.012 0.017 0.041 65 -0.044 4 69
TNF 0.2 0.25 0.68 13 -1.3 4 17
STAT3/STAT4 0.18 0.23 0.6 5 -1.1 5 10
STAT4 (dimer) 0.19 0.24 0.62 6 -1.2 5 11
IL18 0.027 0.034 0.29 9 -10000 0 9
IL19 0.23 0.25 0.68 18 -1.1 4 22
STAT5A (dimer) 0.18 0.24 0.61 7 -1.2 5 12
STAT1 0.024 0.016 0.28 2 -10000 0 2
SOCS3 0.021 0.023 -10000 0 -0.35 2 2
CXCL9 0.2 0.27 0.68 13 -1.2 8 21
MPO 0.2 0.24 0.68 8 -1.1 4 12
positive regulation of humoral immune response 0.21 0.26 0.66 20 -1.2 5 25
IL23/IL23R/JAK2/TYK2 0.21 0.26 0.68 16 -1.2 5 21
IL6 0.18 0.29 0.65 11 -1.1 17 28
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
IL2 0.009 0.055 0.28 17 -10000 0 17
positive regulation of tyrosine phosphorylation of STAT protein -0.007 0.008 -10000 0 -0.042 2 2
CD3E 0.18 0.27 0.66 9 -1.1 12 21
keratinocyte proliferation 0.21 0.26 0.66 20 -1.2 5 25
NOS2 0.18 0.27 0.66 9 -1 12 21
Signaling events mediated by PRL

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
CCNE1 0.13 0.13 0.29 217 -10000 0 217
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.021 0.023 -10000 0 -0.35 2 2
CDKN1A 0.002 0.042 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.075 0.15 7 -0.25 53 60
AGT -0.022 0.13 0.29 8 -0.35 65 73
CCNA2 -0.021 0.057 0.21 6 -10000 0 6
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 -0.022 0.082 -10000 0 -0.24 68 68
CDK2/Cyclin E1 0.091 0.1 0.29 19 -0.27 9 28
MAPK3 -0.01 0.004 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.006 -10000 0 -10000 0 0
MAPK1 -0.01 0.004 -10000 0 -10000 0 0
PTP4A1 -0.027 0.056 -10000 0 -10000 0 0
PTP4A3 0.021 0.007 -10000 0 -10000 0 0
PTP4A2 0.023 0.004 -10000 0 -10000 0 0
ITGB1 -0.01 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.001 0.046 -10000 0 -0.33 7 7
Rab GGTase beta/Rab GGTase alpha 0.033 0.007 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.001 0.071 0.35 1 -10000 0 1
RABGGTA 0.022 0.004 -10000 0 -10000 0 0
BCAR1 -0.016 0.008 -10000 0 -10000 0 0
RHOC 0.002 0.04 -10000 0 -0.35 4 4
RHOA -0.001 0.052 -10000 0 -0.34 9 9
cell motility 0.012 0.06 0.34 1 -0.35 5 6
PRL-1/alpha Tubulin -0.001 0.071 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.03 0.017 -10000 0 -0.25 1 1
ROCK1 0.012 0.06 0.34 1 -0.35 5 6
RABGGTB 0.023 0.002 -10000 0 -10000 0 0
CDK2 0.023 0.004 -10000 0 -10000 0 0
mitosis -0.027 0.055 -10000 0 -10000 0 0
ATF5 0.024 0.022 0.28 4 -10000 0 4
Caspase cascade in apoptosis

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
TOP1 0.009 0.091 0.22 1 -0.41 16 17
ACTA1 0.012 0.066 0.21 8 -0.26 10 18
NUMA1 0.008 0.094 0.22 1 -0.41 17 18
SPTAN1 0.002 0.062 0.22 3 -0.27 10 13
LIMK1 0.004 0.069 0.24 12 -0.26 12 24
BIRC3 0.018 0.045 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
CASP10 -0.008 0.04 0.26 3 -0.27 6 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
PTK2 0.009 0.09 0.22 1 -0.4 16 17
DIABLO 0.023 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.002 0.062 0.22 3 -0.27 10 13
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN 0 0.062 0.21 3 -0.27 11 14
MADD 0.022 0.005 -10000 0 -10000 0 0
TFAP2A 0.15 0.12 0.33 50 -0.62 6 56
BID 0.004 0.023 0.16 3 -0.17 5 8
MAP3K1 -0.008 0.1 -10000 0 -0.41 28 28
TRADD 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.067 0.23 8 -0.26 12 20
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.044 0.26 4 -0.16 3 7
neuron apoptosis 0.008 0.11 -10000 0 -0.83 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.004 0.087 0.22 2 -0.41 13 15
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.004 0.17 -10000 0 -0.88 17 17
TRAF2 0.022 0.006 -10000 0 -10000 0 0
ICAD/CAD 0 0.064 0.26 6 -0.33 5 11
CASP7 -0.002 0.058 0.25 6 -0.25 5 11
KRT18 0.018 0.057 -10000 0 -0.64 2 2
apoptosis 0.003 0.11 0.4 12 -0.42 18 30
DFFA 0.003 0.065 0.25 6 -0.27 10 16
DFFB 0.001 0.062 0.2 4 -0.27 11 15
PARP1 0.015 0.044 0.16 3 -0.27 4 7
actin filament polymerization -0.002 0.072 0.28 6 -0.28 13 19
TNF 0.053 0.088 0.28 66 -0.35 2 68
CYCS 0.007 0.042 0.16 10 -0.2 8 18
SATB1 -0.027 0.17 0.33 1 -0.83 18 19
SLK 0.004 0.072 0.31 10 -0.27 10 20
p15 BID/BAX 0.015 0.042 -10000 0 -0.17 8 8
CASP2 0.012 0.055 0.21 9 -0.29 6 15
JNK cascade 0.007 0.1 0.41 28 -10000 0 28
CASP3 0.004 0.066 0.21 5 -0.28 12 17
LMNB2 -0.014 0.16 0.28 2 -0.47 45 47
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.022 0.017 -10000 0 -0.35 1 1
Mammalian IAPs/DIABLO 0.054 0.033 0.21 2 -0.19 7 9
negative regulation of DNA binding 0.15 0.11 0.33 51 -0.61 6 57
stress fiber formation 0.004 0.072 0.31 10 -0.28 9 19
GZMB -0.001 0.05 0.12 51 -0.29 5 56
CASP1 0.009 0.02 -10000 0 -0.26 3 3
LMNB1 0.006 0.12 0.27 3 -0.5 20 23
APP 0.008 0.11 -10000 0 -0.85 8 8
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.001 -10000 0 -10000 0 0
VIM 0.002 0.1 0.31 10 -0.43 18 28
LMNA 0.01 0.085 0.27 2 -0.36 17 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.014 0.058 0.22 3 -0.32 6 9
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.004 0.064 0.2 6 -0.34 5 11
APAF-1/Caspase 9 0.007 0.097 -10000 0 -0.64 11 11
nuclear fragmentation during apoptosis 0.009 0.092 0.22 1 -0.4 17 18
CFL2 0.002 0.072 0.28 13 -0.27 7 20
GAS2 -0.01 0.075 0.21 3 -0.28 15 18
positive regulation of apoptosis 0.001 0.13 0.24 5 -0.49 25 30
PRF1 0.022 0.036 0.28 4 -0.35 3 7
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.027 0.054 -10000 0 -10000 0 0
epithelial cell differentiation -0.01 0.09 0.24 1 -0.31 6 7
ITCH 0.016 0.024 -10000 0 -10000 0 0
WWP1 0.019 0.056 0.31 2 -10000 0 2
FYN 0.023 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
PRL 0.012 0.07 0.28 5 -0.35 17 22
neuron projection morphogenesis 0.035 0.094 0.26 34 -10000 0 34
PTPRZ1 0.035 0.062 0.28 32 -10000 0 32
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.028 0.051 -10000 0 -0.24 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.008 0.042 -10000 0 -0.27 2 2
ADAM17 0.016 0.024 -10000 0 -10000 0 0
ErbB4/ErbB4 0.017 0.05 0.23 2 -10000 0 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.031 0.066 0.25 11 -10000 0 11
NCOR1 0.021 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.046 -10000 0 -0.25 2 2
GRIN2B 0.016 0.063 0.24 17 -0.24 2 19
ErbB4/ErbB2/betacellulin 0.022 0.06 0.25 7 -0.22 1 8
STAT1 0.024 0.016 0.28 2 -10000 0 2
HBEGF 0.023 0.004 -10000 0 -10000 0 0
PRLR -0.05 0.15 -10000 0 -0.35 104 104
E4ICDs/ETO2 0.006 0.077 -10000 0 -0.29 6 6
axon guidance 0.012 0.049 0.24 1 -10000 0 1
NEDD4 -0.014 0.094 -10000 0 -0.35 37 37
Prolactin receptor/Prolactin receptor/Prolactin -0.028 0.12 0.21 4 -0.25 114 118
CBFA2T3 -0.025 0.12 -10000 0 -0.35 65 65
ErbB4/ErbB2/HBEGF 0.028 0.05 0.25 7 -10000 0 7
MAPK3 0.03 0.083 0.25 17 -10000 0 17
STAT1 (dimer) 0.026 0.055 0.25 1 -10000 0 1
MAPK1 0.03 0.084 0.25 18 -10000 0 18
JAK2 0.016 0.048 -10000 0 -0.35 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.011 0.051 0.23 11 -0.25 2 13
NRG1 -0.012 0.034 -10000 0 -0.25 9 9
NRG3 0.03 0.052 0.29 21 -10000 0 21
NRG2 -0.03 0.13 -10000 0 -0.35 75 75
NRG4 0.045 0.073 0.28 47 -10000 0 47
heart development 0.012 0.049 0.24 1 -10000 0 1
neural crest cell migration 0.011 0.051 0.23 11 -0.25 2 13
ERBB2 0.001 0.051 0.3 14 -10000 0 14
WWOX/E4ICDs 0.025 0.05 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.043 0.078 0.34 2 -0.28 2 4
apoptosis -0.033 0.061 0.31 2 -0.27 2 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.004 0.083 -10000 0 -0.29 10 10
ErbB4/ErbB2/epiregulin 0.049 0.082 0.31 16 -10000 0 16
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.065 -10000 0 -0.24 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.11 0.28 1 -0.29 23 24
MDM2 0.013 0.048 0.26 3 -10000 0 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.015 0.037 -10000 0 -0.23 2 2
STAT5A 0.01 0.052 0.28 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta 0.014 0.057 0.31 1 -0.29 6 7
DLG4 0.02 0.023 -10000 0 -0.35 2 2
GRB2/SHC 0.026 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.022 0.048 -10000 0 -10000 0 0
STAT5A (dimer) -0.003 0.1 0.29 1 -0.34 5 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.024 0.058 -10000 0 -0.27 2 2
LRIG1 0.02 0.028 -10000 0 -0.35 3 3
EREG 0.054 0.086 0.28 68 -10000 0 68
BTC 0.011 0.065 -10000 0 -0.35 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.009 0.041 0.23 1 -10000 0 1
ERBB4 0.017 0.05 0.23 2 -10000 0 2
STAT5B 0.02 0.023 -10000 0 -0.35 2 2
YAP1 0.013 0.073 -10000 0 -0.47 10 10
GRB2 0.022 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.042 0.073 0.32 14 -10000 0 14
glial cell differentiation -0.022 0.047 -10000 0 -10000 0 0
WWOX 0.02 0.008 -10000 0 -10000 0 0
cell proliferation 0.014 0.088 0.28 11 -0.36 3 14
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.023 0.004 -10000 0 -10000 0 0
SPHK1 0.024 0.022 0.31 3 -10000 0 3
GNAI2 0.022 0.005 -10000 0 -10000 0 0
mol:S1P 0.01 0.01 0.21 1 -10000 0 1
GNAO1 -0.065 0.16 -10000 0 -0.35 124 124
mol:Sphinganine-1-P -0.01 0.02 0.23 3 -10000 0 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.038 -10000 0 -0.19 5 5
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
S1PR3 0.01 0.065 -10000 0 -0.35 17 17
S1PR2 0.022 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.03 0.14 1 -0.22 5 6
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
S1P/S1P5/G12 0.034 0.044 0.2 8 -0.19 8 16
S1P/S1P3/Gq -0.014 0.11 -10000 0 -0.31 53 53
S1P/S1P4/Gi -0.038 0.11 -10000 0 -0.35 29 29
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ 0.01 0.065 -10000 0 -0.35 17 17
GNA14 -0.01 0.1 -10000 0 -0.35 45 45
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
ABCC1 0.022 0.005 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.017 0.002 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.022 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.041 -10000 0 -0.22 12 12
IRAK/TOLLIP 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.023 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.053 0.07 0.23 62 -0.25 4 66
IL1A 0.038 0.063 0.28 34 -10000 0 34
IL1B -0.014 0.028 -10000 0 -0.29 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.046 0.025 -10000 0 -0.17 1 1
IL1R2 0.036 0.071 0.28 34 -0.35 4 38
IL1R1 0.017 0.048 -10000 0 -0.35 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.059 0.22 2 -0.24 14 16
TOLLIP 0.022 0.005 -10000 0 -10000 0 0
TICAM2 0.017 0.045 -10000 0 -0.35 8 8
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.017 0.049 0.23 1 -0.32 1 2
JUN -0.01 0.041 0.17 15 -0.18 9 24
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.053 -10000 0 -0.22 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.055 0.21 31 -0.21 9 40
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.055 -10000 0 -0.2 9 9
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.042 -10000 0 -0.21 14 14
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.002 0.042 0.19 14 -0.16 4 18
IRAK1 0.01 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 0.053 0.073 0.21 74 -0.24 9 83
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.027 0.029 -10000 0 -0.25 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.052 -10000 0 -0.27 9 9
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.042 -10000 0 -0.21 14 14
IL1 beta/IL1R2 0.038 0.059 0.2 45 -0.23 9 54
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.048 -10000 0 -0.36 3 3
IRAK3 0.007 0.076 -10000 0 -0.35 23 23
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.055 -10000 0 -0.2 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.044 -10000 0 -0.23 8 8
IL1 alpha/IL1R1/IL1RAP 0.046 0.055 0.2 31 -0.23 9 40
RELA 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
MYD88 0.022 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.035 0.013 -10000 0 -10000 0 0
IL1RAP 0.019 0.028 -10000 0 -0.35 3 3
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.017 0.043 -10000 0 -0.3 3 3
CASP1 0.021 0.023 -10000 0 -0.35 2 2
IL1RN/IL1R2 0.067 0.083 0.23 99 -0.24 3 102
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.036 0.044 -10000 0 -0.2 14 14
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.057 -10000 0 -0.28 13 13
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL1RN 0.059 0.092 0.28 76 -10000 0 76
TRAF6/TAK1/TAB1/TAB2 0.032 0.008 -10000 0 -10000 0 0
MAP2K6 0.012 0.061 0.16 73 -10000 0 73
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.008 0.084 0.27 2 -0.39 12 14
BAG4 0.019 0.024 -10000 0 -0.35 2 2
BAD 0.005 0.043 0.18 10 -0.16 7 17
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.045 0.28 2 -0.35 7 9
BAX 0.004 0.041 0.17 7 -0.15 9 16
EnzymeConsortium:3.1.4.12 0.003 0.024 0.073 7 -0.085 15 22
IKBKB 0.018 0.097 0.28 19 -0.38 9 28
MAP2K2 0.002 0.042 0.22 7 -0.16 3 10
MAP2K1 0.002 0.042 0.21 8 -0.17 4 12
SMPD1 0.001 0.033 -10000 0 -0.14 16 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.015 0.086 0.27 4 -0.36 14 18
MAP2K4 0.003 0.035 0.23 3 -0.17 3 6
protein ubiquitination 0.012 0.09 0.35 3 -0.39 10 13
EnzymeConsortium:2.7.1.37 0.001 0.047 0.22 9 -0.18 3 12
response to UV 0 0 0.002 9 -0.002 1 10
RAF1 0.003 0.045 0.21 9 -0.16 7 16
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.038 0.11 9 -0.14 15 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.03 0.008 -10000 0 -10000 0 0
MADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.004 0.038 0.19 5 -0.15 8 13
TRADD 0.02 0.008 -10000 0 -10000 0 0
RELA/p50 0.022 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.048 0.21 9 -0.18 5 14
MAPK1 0 0.052 0.2 9 -0.22 7 16
p50/RELA/I-kappa-B-alpha 0.032 0.008 -10000 0 -10000 0 0
FADD 0.009 0.081 0.23 2 -0.38 12 14
KSR1 0.004 0.04 0.18 6 -0.15 10 16
MAPK8 0.001 0.041 0.19 8 -0.16 2 10
TRAF2 0.022 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -10000 0 4
CHUK 0.007 0.084 0.3 3 -0.38 11 14
TNF R/SODD 0.029 0.021 -10000 0 -0.25 2 2
TNF 0.053 0.088 0.28 66 -0.35 2 68
CYCS 0.013 0.049 0.16 18 -0.16 6 24
IKBKG 0.006 0.085 0.3 5 -0.39 10 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.085 -10000 0 -0.42 11 11
RELA 0.022 0.004 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.012 0.046 0.15 14 -0.16 5 19
TNF/TNF R/SODD 0.054 0.054 0.2 51 -0.21 2 53
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.018 0.08 -10000 0 -0.59 8 8
NSMAF 0.018 0.09 0.26 13 -0.41 9 22
response to hydrogen peroxide 0 0 0.002 9 -0.002 1 10
BCL2 -0.008 0.1 -10000 0 -0.35 44 44
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.014 0.015 -10000 0 -0.27 1 1
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DOCK1 0.017 0.042 -10000 0 -0.35 7 7
ITGA4 0.022 0.025 0.28 1 -0.35 2 3
alpha4/beta7 Integrin/MAdCAM1 0.063 0.047 0.21 41 -0.19 1 42
EPO 0.01 0.064 0.28 1 -0.35 16 17
alpha4/beta7 Integrin 0.034 0.017 0.21 2 -0.25 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.25 2 3
EPO/EPOR (dimer) 0.025 0.054 0.23 8 -0.25 16 24
lamellipodium assembly 0.013 0.074 -10000 0 -0.42 8 8
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.027 0.029 -10000 0 -0.25 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
JAK2 0.008 0.052 0.17 4 -0.22 24 28
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
MADCAM1 0.04 0.069 0.28 41 -10000 0 41
cell adhesion 0.061 0.046 0.2 41 -0.19 1 42
CRKL/CBL 0.032 0.01 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.021 0.056 0.18 14 -0.2 33 47
ITGB7 0.023 0.011 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.027 0.068 0.2 1 -0.22 36 37
p130Cas/Crk/Dock1 0.008 0.056 -10000 0 -0.38 2 2
VCAM1 -0.004 0.097 -10000 0 -0.35 39 39
RHOA 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.024 0.21 1 -0.19 2 3
BCAR1 -0.02 0.049 0.18 12 -0.19 26 38
EPOR 0.026 0.034 0.31 7 -10000 0 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.076 -10000 0 -0.46 7 7
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.017 -10000 0 -0.35 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.013 0.11 0.42 11 -0.37 1 12
IL27/IL27R/JAK1 0.025 0.12 0.47 4 -0.95 2 6
TBX21 -0.017 0.11 0.35 4 -0.4 9 13
IL12B 0.023 0.013 0.28 1 -10000 0 1
IL12A -0.003 0.029 0.12 11 -0.24 4 15
IL6ST -0.033 0.13 -10000 0 -0.35 79 79
IL27RA/JAK1 0.018 0.084 -10000 0 -1 2 2
IL27 0.025 0.043 0.29 12 -10000 0 12
TYK2 0.022 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.007 0.065 0.44 2 -10000 0 2
T-helper 2 cell differentiation 0.013 0.11 0.42 11 -0.37 1 12
T cell proliferation during immune response 0.013 0.11 0.42 11 -0.37 1 12
MAPKKK cascade -0.013 0.11 0.37 1 -0.42 11 12
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT2 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.024 0.016 0.28 2 -10000 0 2
IL12RB1 0.026 0.053 0.29 13 -0.35 4 17
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.008 0.11 0.36 8 -0.51 3 11
IL27/IL27R/JAK2/TYK2 -0.012 0.11 0.37 1 -0.44 9 10
positive regulation of T cell mediated cytotoxicity -0.013 0.11 0.37 1 -0.42 11 12
STAT1 (dimer) 0.017 0.14 0.59 5 -0.72 3 8
JAK2 0.017 0.049 -10000 0 -0.35 9 9
JAK1 0.022 0.016 -10000 0 -0.35 1 1
STAT2 (dimer) -0.005 0.12 0.34 1 -0.4 11 12
T cell proliferation -0.019 0.11 0.35 1 -0.39 16 17
IL12/IL12R/TYK2/JAK2 0.006 0.17 -10000 0 -0.71 25 25
IL17A 0.006 0.063 0.44 2 -10000 0 2
mast cell activation 0.013 0.11 0.42 11 -0.37 1 12
IFNG 0.007 0.034 0.11 9 -0.098 7 16
T cell differentiation -0.001 0.005 0.013 3 -0.018 12 15
STAT3 (dimer) -0.005 0.12 0.34 1 -0.39 14 15
STAT5A (dimer) -0.005 0.12 0.34 1 -0.39 14 15
STAT4 (dimer) -0.007 0.12 0.34 1 -0.4 13 14
STAT4 0.022 0.016 -10000 0 -0.35 1 1
T cell activation -0.005 0.01 0.12 2 -0.087 2 4
IL27R/JAK2/TYK2 0.007 0.11 -10000 0 -0.77 3 3
GATA3 0.001 0.16 0.58 14 -1.1 6 20
IL18 -0.002 0.015 0.11 9 -10000 0 9
positive regulation of mast cell cytokine production -0.004 0.12 0.33 1 -0.38 14 15
IL27/EBI3 0.038 0.048 0.25 20 -10000 0 20
IL27RA 0.005 0.084 -10000 0 -1.1 2 2
IL6 0.017 0.069 0.28 9 -0.35 14 23
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.007 0.038 0.43 2 -10000 0 2
IL1B -0.006 0.021 -10000 0 -0.24 4 4
EBI3 0.027 0.043 0.29 13 -10000 0 13
TNF 0.009 0.043 0.11 66 -0.24 2 68
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.025 -10000 0 -0.18 8 8
epithelial cell differentiation 0.042 0.022 -10000 0 -0.17 2 2
CYFIP2 0.021 0.028 -10000 0 -0.35 3 3
ENAH -0.006 0.056 0.27 12 -10000 0 12
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
MYO6 -0.012 0.025 0.17 7 -10000 0 7
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.043 0.017 -10000 0 -0.21 1 1
AQP5 0.077 0.088 0.28 2 -0.41 5 7
CTNND1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.018 0.17 3 -10000 0 3
regulation of calcium-dependent cell-cell adhesion -0.016 0.037 0.17 7 -0.3 1 8
EGF 0.031 0.055 0.28 21 -0.35 2 23
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
AQP3 -0.001 0.057 -10000 0 -0.34 8 8
cortical microtubule organization 0.042 0.022 -10000 0 -0.17 2 2
GO:0000145 -0.013 0.017 0.16 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.024 -10000 0 -0.17 2 2
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.018 -10000 0 -0.17 3 3
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 0.21 1 -0.19 2 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.016 0.16 3 -10000 0 3
PVRL2 0.022 0.005 -10000 0 -10000 0 0
ZYX -0.012 0.024 0.17 6 -10000 0 6
ARF6/GTP 0.047 0.033 -10000 0 -0.18 2 2
CDH1 0.019 0.024 -10000 0 -0.35 2 2
EGFR/EGFR/EGF/EGF 0.033 0.044 -10000 0 -0.18 14 14
RhoA/GDP 0.042 0.023 -10000 0 -0.16 2 2
actin cytoskeleton organization -0.014 0.022 0.16 6 -10000 0 6
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
GIT1 0.022 0.005 -10000 0 -10000 0 0
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
IGF1 -0.046 0.14 -10000 0 -0.35 100 100
DIAPH1 0.018 0.096 -10000 0 -0.5 11 11
Wnt receptor signaling pathway -0.042 0.022 0.17 2 -10000 0 2
RHOA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.018 -10000 0 -0.17 3 3
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
VCL -0.014 0.022 0.16 6 -10000 0 6
EFNA1 0.02 0.02 0.3 2 -10000 0 2
LPP -0.014 0.023 0.17 6 -10000 0 6
Ephrin A1/EPHA2 0.03 0.025 -10000 0 -0.16 2 2
SEC6/SEC8 -0.02 0.012 -10000 0 -10000 0 0
MGAT3 -0.016 0.037 0.17 7 -0.31 1 8
HGF/MET -0.003 0.088 -10000 0 -0.18 96 96
HGF -0.05 0.15 -10000 0 -0.35 104 104
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.025 -10000 0 -0.18 8 8
actin cable formation 0.046 0.1 0.23 95 -0.24 2 97
KIAA1543 -0.013 0.023 0.16 6 -0.17 2 8
KIFC3 -0.013 0.023 0.17 6 -10000 0 6
NCK1 0.021 0.023 -10000 0 -0.35 2 2
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ACTN1 -0.012 0.025 0.17 7 -10000 0 7
NCK1/GIT1 0.03 0.019 -10000 0 -0.25 2 2
mol:GDP 0.042 0.022 -10000 0 -0.17 2 2
EXOC4 0.022 0.005 -10000 0 -10000 0 0
STX4 -0.012 0.025 0.17 7 -10000 0 7
PIP5K1C -0.013 0.019 0.17 3 -10000 0 3
LIMA1 0.023 0.003 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
ROCK1 0.018 0.086 0.32 16 -10000 0 16
adherens junction assembly -0.044 0.14 0.2 1 -0.55 31 32
IGF-1R heterotetramer/IGF1 -0.007 0.092 -10000 0 -0.18 107 107
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
MET 0.021 0.042 0.28 4 -0.35 5 9
PLEKHA7 -0.013 0.025 0.17 6 -0.17 1 7
mol:GTP 0.042 0.03 0.2 1 -0.19 2 3
establishment of epithelial cell apical/basal polarity 0.001 0.077 0.35 13 -10000 0 13
cortical actin cytoskeleton stabilization 0.013 0.025 -10000 0 -0.18 8 8
regulation of cell-cell adhesion -0.014 0.022 0.16 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.025 -10000 0 -0.18 8 8
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.005 0.061 0.2 2 -0.24 14 16
adherens junction organization -0.007 0.089 0.29 1 -0.37 22 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.062 0.21 2 -0.26 3 5
FMN1 -0.002 0.076 -10000 0 -0.32 21 21
mol:IP3 0.001 0.042 -10000 0 -0.21 7 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.086 -10000 0 -0.31 28 28
CTNNB1 0.023 0.006 -10000 0 -10000 0 0
AKT1 0 0.052 -10000 0 -0.24 9 9
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.12 -10000 0 -0.7 10 10
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.072 -10000 0 -0.31 21 21
VASP -0.006 0.079 -10000 0 -0.3 26 26
ZYX -0.006 0.078 -10000 0 -0.3 26 26
JUB -0.004 0.081 -10000 0 -0.29 28 28
EGFR(dimer) 0.002 0.094 0.26 1 -0.3 31 32
E-cadherin/beta catenin-gamma catenin 0.038 0.026 -10000 0 -0.28 2 2
mol:PI-3-4-5-P3 0.015 0.062 -10000 0 -0.24 11 11
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.015 0.063 -10000 0 -0.25 10 10
FYN 0.005 0.053 0.18 4 -0.29 4 8
mol:Ca2+ 0.001 0.042 -10000 0 -0.21 7 7
JUP 0.022 0.017 -10000 0 -0.34 1 1
PIK3R1 0.02 0.036 -10000 0 -0.35 5 5
mol:DAG 0.001 0.042 -10000 0 -0.21 7 7
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0.013 0.063 0.21 1 -0.32 3 4
establishment of polarity of embryonic epithelium -0.007 0.08 -10000 0 -0.3 27 27
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
CASR 0.002 0.054 0.21 6 -0.21 6 12
RhoA/GTP 0.018 0.052 -10000 0 -0.23 3 3
AKT2 0 0.052 -10000 0 -0.25 9 9
actin cable formation -0.002 0.073 0.2 8 -0.32 17 25
apoptosis -0.009 0.072 0.24 18 -0.24 10 28
CTNNA1 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0 0.059 -10000 0 -0.25 8 8
PIP5K1A -0.006 0.072 -10000 0 -0.31 20 20
PLCG1 0.001 0.043 -10000 0 -0.22 7 7
Rac1/GTP 0.01 0.09 0.24 1 -0.3 24 25
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.021 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.008 0.034 0.25 2 -0.23 7 9
CDKN1A -0.008 0.007 -10000 0 -10000 0 0
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
BAX 0.023 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.006 -10000 0 -10000 0 0
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
FOXO4 0.009 0.015 -10000 0 -0.22 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
TAT 0.019 0.013 0.28 1 -10000 0 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.005 0.05 0.12 45 -0.24 8 53
PPARGC1A -0.054 0.15 0.28 2 -0.35 111 113
FHL2 0.02 0.036 -10000 0 -0.35 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.019 -10000 0 -0.25 2 2
HIST2H4A -0.008 0.034 0.23 7 -0.25 2 9
SIRT1/FOXO3a 0.016 0.033 -10000 0 -0.2 7 7
SIRT1 0.019 0.023 -10000 0 -0.35 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.024 -10000 0 -0.21 2 2
SIRT1/Histone H1b 0.016 0.05 -10000 0 -0.22 12 12
apoptosis -0.039 0.021 0.21 2 -10000 0 2
SIRT1/PGC1A -0.021 0.096 0.19 2 -0.21 112 114
p53/SIRT1 0.025 0.019 -10000 0 -0.25 2 2
SIRT1/FOXO4 0.011 0.048 -10000 0 -0.2 15 15
FOXO1/FHL2/SIRT1 0.036 0.03 -10000 0 -0.19 8 8
HIST1H1E 0.014 0.022 0.21 2 -10000 0 2
SIRT1/p300 0.029 0.02 -10000 0 -0.25 2 2
muscle cell differentiation -0.022 0.037 0.22 9 -0.21 2 11
TP53 0.02 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.04 0.021 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.019 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.027 0.022 0.21 1 -0.25 2 3
ACSS2 -0.013 0.015 -10000 0 -0.25 2 2
SIRT1/PCAF/MYOD 0.022 0.037 0.21 2 -0.23 9 11
E-cadherin signaling in the nascent 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
CTTN -0.015 0.091 -10000 0 -0.27 57 57
KLHL20 -0.004 0.062 0.2 2 -0.2 29 31
CYFIP2 0.021 0.028 -10000 0 -0.35 3 3
Rac1/GDP 0.002 0.068 0.25 3 -0.27 7 10
ENAH -0.018 0.092 -10000 0 -0.28 58 58
AP1M1 0.022 0.005 -10000 0 -10000 0 0
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.028 -10000 0 -0.22 1 1
ABI1/Sra1/Nap1 -0.013 0.037 -10000 0 -0.14 32 32
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.028 -10000 0 -0.19 2 2
RAPGEF1 -0.011 0.079 0.22 2 -0.31 9 11
CTNND1 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.011 0.099 -10000 0 -0.28 63 63
CRK -0.008 0.081 -10000 0 -0.27 40 40
E-cadherin/gamma catenin/alpha catenin 0.039 0.027 -10000 0 -0.29 2 2
alphaE/beta7 Integrin 0.032 0.013 0.21 1 -10000 0 1
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.011 -10000 0 -10000 0 0
DLG1 -0.012 0.085 -10000 0 -0.28 49 49
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.016 -10000 0 -0.16 1 1
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.036 -10000 0 -0.18 12 12
PI3K -0.019 0.02 -10000 0 -0.21 1 1
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.028 0.027 -10000 0 -0.34 2 2
TIAM1 0.014 0.057 -10000 0 -0.35 13 13
E-cadherin(dimer)/Ca2+ 0.046 0.024 -10000 0 -0.17 2 2
AKT1 -0.011 0.021 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0.001 0.067 0.23 1 -0.27 5 6
actin cytoskeleton organization -0.002 0.047 0.16 4 -0.15 29 33
CDC42/GDP 0.003 0.068 0.25 3 -0.27 7 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.022 -10000 0 -0.32 2 2
ITGB7 0.023 0.011 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.026 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.035 0.019 -10000 0 -0.17 2 2
mol:GDP -0.01 0.073 0.25 3 -0.29 9 12
CDC42/GTP/IQGAP1 0.03 0.008 -10000 0 -10000 0 0
JUP 0.021 0.017 -10000 0 -0.35 1 1
p120 catenin/RhoA/GDP 0.009 0.069 0.24 1 -0.28 4 5
RAC1/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.03 0.011 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.004 0.037 0.15 7 -0.1 13 20
NME1 0.022 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.009 0.083 -10000 0 -0.27 47 47
regulation of cell-cell adhesion 0.008 0.023 -10000 0 -0.19 1 1
WASF2 -0.001 0.025 -10000 0 -10000 0 0
Rap1/GTP 0.018 0.038 -10000 0 -0.24 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.034 -10000 0 -0.25 2 2
CCND1 0.004 0.043 0.17 7 -0.12 16 23
VAV2 -0.028 0.16 -10000 0 -0.57 34 34
RAP1/GDP 0.018 0.06 0.25 4 -0.26 4 8
adherens junction assembly -0.01 0.083 -10000 0 -0.27 49 49
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.041 0.029 -10000 0 -0.24 2 2
E-cadherin/beta catenin 0.008 0.019 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.015 0.091 -10000 0 -0.28 56 56
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP -0.017 0.086 0.18 1 -0.31 31 32
E-cadherin/beta catenin/alpha catenin 0.039 0.022 -10000 0 -0.2 2 2
ITGAE 0.021 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.1 -10000 0 -0.29 63 63
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.022 0.043 0.35 4 -0.29 6 10
PI3K Class IB/PDE3B 0.022 0.043 0.29 6 -0.35 4 10
PDE3B 0.022 0.043 0.29 6 -0.35 4 10
Canonical NF-kappaB pathway

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
FBXW11 0.024 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 0.015 0.092 0.26 6 -0.3 19 25
ERC1 0.022 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.019 0.21 1 -0.25 1 2
NFKBIA -0.008 0.028 0.2 8 -10000 0 8
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.021 0.007 -10000 0 -10000 0 0
RIPK2 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.016 0.02 -10000 0 -10000 0 0
IKK complex/A20 0.033 0.11 0.26 3 -0.34 33 36
NEMO/A20/RIP2 0.021 0.007 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.01 0.11 0.26 1 -0.35 37 38
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.031 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.013 0.097 -10000 0 -0.32 35 35
BCL10/MALT1/TRAF6 0.043 0.013 -10000 0 -10000 0 0
NOD2 0.021 0.021 0.28 1 -0.35 1 2
NFKB1 0.023 0.017 -10000 0 -0.35 1 1
RELA 0.024 0.005 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.008 -10000 0 -10000 0 0
ATM 0.022 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.052 0.06 0.21 62 -0.25 2 64
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PRKCA 0 0.087 -10000 0 -0.35 31 31
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
TNF 0.053 0.088 0.28 66 -0.35 2 68
NF kappa B1 p50/RelA 0.047 0.018 -10000 0 -0.2 1 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.028 0.2 8 -10000 0 8
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.014 0.1 0.26 1 -0.34 35 36
CYLD 0.021 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.012 0.11 -10000 0 -0.35 33 33
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.02 -10000 0 -0.16 1 1
TRAF2/ASK1 0.028 0.013 -10000 0 -0.2 1 1
ATM 0.022 0.005 -10000 0 -10000 0 0
MAP2K3 -0.002 0.094 0.26 1 -0.33 28 29
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.006 0.088 0.26 4 -0.33 20 24
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.055 -10000 0 -0.35 12 12
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GADD45B 0.021 0.006 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
MAP3K6 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.022 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.014 -10000 0 -0.25 1 1
TAK1/TAB family 0.001 0.024 0.14 2 -0.15 4 6
RAC1/OSM/MEKK3 0.041 0.013 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.079 -10000 0 -0.31 17 17
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.063 0.097 0.28 86 -0.35 1 87
CCM2 0.023 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.052 0.057 0.19 77 -0.2 1 78
MAPK11 0.019 0.024 -10000 0 -0.35 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.063 0.057 0.19 79 -0.19 2 81
OSM/MEKK3 0.032 0.01 -10000 0 -10000 0 0
TAOK1 0.009 0.012 -10000 0 -0.26 1 1
TAOK2 0.01 0.003 -10000 0 -10000 0 0
TAOK3 0.01 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
MAP3K10 0.022 0.005 -10000 0 -10000 0 0
MAP3K3 0.022 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.013 0.03 -10000 0 -0.19 1 1
GADD45/MTK1/MTK1 0.043 0.037 -10000 0 -0.18 11 11
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.034 0.21 1 -0.19 7 8
HDAC3 0.023 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.031 0.007 -10000 0 -10000 0 0
GATA1/HDAC5 0.03 0.009 -10000 0 -10000 0 0
GATA2/HDAC5 0.006 0.08 -10000 0 -0.24 50 50
HDAC5/BCL6/BCoR 0.04 0.02 -10000 0 -0.21 1 1
HDAC9 0.016 0.048 -10000 0 -0.35 9 9
Glucocorticoid receptor/Hsp90/HDAC6 0.007 0.089 -10000 0 -0.21 77 77
HDAC4/ANKRA2 0.032 0.015 -10000 0 -0.25 1 1
HDAC5/YWHAB 0.031 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
GATA2 -0.012 0.11 -10000 0 -0.35 50 50
HDAC4/RFXANK 0.033 0.017 0.22 3 -10000 0 3
BCOR 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.021 0.007 -10000 0 -10000 0 0
HDAC5 0.022 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.037 0.21 1 -0.24 9 10
Histones 0.005 0.058 -10000 0 -0.29 6 6
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.015 -10000 0 -0.25 1 1
HDAC4/Ubc9 0.032 0.009 -10000 0 -10000 0 0
HDAC7 0.022 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.011 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.015 0.21 2 -10000 0 2
CAMK4 0.023 0.037 0.28 5 -0.35 3 8
Tubulin/HDAC6 0.045 0.02 0.2 3 -0.21 1 4
SUMO1 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
GATA1 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NR3C1 -0.031 0.13 -10000 0 -0.35 77 77
SUMO1/HDAC4 0.024 0.044 -10000 0 -0.19 12 12
SRF 0.023 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.032 0.009 -10000 0 -10000 0 0
Tubulin 0.033 0.023 0.21 3 -0.25 2 5
HDAC4/14-3-3 E 0.031 0.01 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.016 -10000 0 -0.25 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.044 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.024 0.2 4 -0.21 2 6
HDAC4/ER alpha 0.003 0.085 -10000 0 -0.24 56 56
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.005 0.058 -10000 0 -0.29 6 6
cell motility 0.044 0.02 0.2 3 -0.21 1 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.02 0.017 -10000 0 -0.35 1 1
HDAC4/CaMK II delta B 0.023 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.009 -10000 0 -10000 0 0
ESR1 -0.017 0.11 -10000 0 -0.35 56 56
HDAC6/HDAC11 0.032 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.042 -10000 0 -0.18 10 10
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C -0.01 0.1 -10000 0 -0.35 47 47
RAN 0.023 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.041 0.07 -10000 0 -0.18 45 45
GNG2 0.017 0.049 0.28 1 -0.35 9 10
NCOR2 0.023 0.004 -10000 0 -10000 0 0
TUBB2A 0.022 0.03 0.28 3 -0.35 2 5
HDAC11 0.023 0.014 0.33 1 -10000 0 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.017 -10000 0 -0.35 1 1
RFXANK 0.024 0.021 0.3 3 -10000 0 3
nuclear import -0.025 0.01 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.16 0.18 -10000 0 -0.35 257 257
CLTC 0.011 0.065 -10000 0 -0.47 8 8
calcium ion-dependent exocytosis 0.007 0.031 -10000 0 -0.22 7 7
Dynamin 2/GTP 0.019 0.007 -10000 0 -10000 0 0
EXOC4 0.022 0.005 -10000 0 -10000 0 0
CD59 0.005 0.046 -10000 0 -0.38 7 7
CPE -0.012 0.064 -10000 0 -0.2 53 53
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
membrane fusion 0.009 0.015 -10000 0 -10000 0 0
CTNND1 -0.009 0.029 0.18 12 -10000 0 12
DNM2 0.021 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.046 0.18 2 -0.34 5 7
TSHR 0.008 0.031 0.14 19 -0.2 3 22
INS -0.01 0.1 -10000 0 -0.48 24 24
BIN1 0.02 0.032 -10000 0 -0.35 4 4
mol:Choline 0.009 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.007 -10000 0 -10000 0 0
JUP 0.006 0.041 -10000 0 -0.39 5 5
ASAP2/amphiphysin II 0.04 0.021 -10000 0 -0.19 3 3
ARF6/GTP 0.017 0.003 -10000 0 -10000 0 0
CDH1 0.005 0.041 -10000 0 -0.39 5 5
clathrin-independent pinocytosis 0.017 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.005 -10000 0 -10000 0 0
positive regulation of endocytosis 0.017 0.003 -10000 0 -10000 0 0
EXOC2 0.022 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.038 -10000 0 -0.3 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.048 0.33 5 -0.25 1 6
positive regulation of phagocytosis 0.01 0.002 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.008 -10000 0 -10000 0 0
ACAP1 0.01 0.031 -10000 0 -0.18 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.006 0.04 -10000 0 -0.35 6 6
clathrin heavy chain/ACAP1 0.011 0.056 0.18 2 -0.38 7 9
JIP4/KLC1 0.04 0.013 -10000 0 -10000 0 0
EXOC1 0.023 0.003 -10000 0 -10000 0 0
exocyst 0.01 0.038 -10000 0 -0.3 3 3
RALA/GTP 0.017 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.017 0.003 -10000 0 -10000 0 0
CTNNA1 -0.009 0.026 0.18 10 -10000 0 10
NME1 0.009 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.069 0.26 1 -0.47 8 9
IL2RA 0.008 0.048 -10000 0 -0.36 7 7
VAMP3 0.01 0.002 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.057 0.095 -10000 0 -0.36 10 10
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.008 0.007 -10000 0 -10000 0 0
PLD2 0.009 0.005 -10000 0 -10000 0 0
EXOC5 0.023 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.038 -10000 0 -0.4 3 3
SDC1 0.019 0.044 -10000 0 -0.35 5 5
ARF6/GDP 0.019 0.005 -10000 0 -10000 0 0
EXOC7 0.022 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.029 0.05 0.26 1 -0.34 5 6
mol:Phosphatidic acid 0.009 0.015 -10000 0 -10000 0 0
endocytosis -0.039 0.02 0.19 3 -10000 0 3
SCAMP2 0.022 0.005 -10000 0 -10000 0 0
ADRB2 -0.019 0.087 0.3 1 -0.42 10 11
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ASAP2 0.022 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.022 0.009 -10000 0 -10000 0 0
KLC1 0.022 0.004 -10000 0 -10000 0 0
AVPR2 -0.038 0.1 0.23 6 -0.44 10 16
RALA 0.023 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.048 0.28 2 -0.35 4 6
Class I PI3K signaling events

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
ARF5/GTP -0.021 0.028 -10000 0 -10000 0 0
DAPP1 0.023 0.081 0.24 16 -0.36 7 23
Src family/SYK family/BLNK-LAT/BTK-ITK 0.016 0.1 0.31 4 -0.46 12 16
mol:DAG 0.013 0.06 0.22 21 -0.18 2 23
HRAS 0.023 0.007 -10000 0 -10000 0 0
RAP1A 0.024 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.072 -10000 0 -0.3 10 10
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARF5 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.017 0.026 0.14 12 -10000 0 12
ARF1/GTP -0.008 0.027 0.23 1 -10000 0 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.017 0.027 0.15 12 -10000 0 12
ADAP1 -0.019 0.025 0.15 2 -10000 0 2
ARAP3 -0.017 0.025 0.14 12 -10000 0 12
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PREX1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF6 0.015 0.055 -10000 0 -0.35 12 12
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.008 -10000 0 -10000 0 0
NRAS 0.024 0.005 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.016 0.051 -10000 0 -0.35 10 10
mol:Ca2+ 0.009 0.051 0.18 29 -10000 0 29
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.014 0.057 -10000 0 -0.35 13 13
ZAP70 0.029 0.05 0.28 16 -0.35 2 18
mol:IP3 0.009 0.061 0.21 29 -0.14 2 31
LYN 0.021 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.008 0.07 0.2 1 -0.28 10 11
RhoA/GDP 0.018 0.046 0.24 3 -0.22 1 4
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
actin cytoskeleton reorganization 0.002 0.066 0.25 12 -0.28 6 18
SRC 0.022 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.012 0.01 -10000 0 -0.21 1 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.01 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.03 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.027 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.02 0.06 0.21 4 -0.29 7 11
BLK 0.037 0.068 0.28 38 -10000 0 38
PDPK1 0.022 0.005 -10000 0 -10000 0 0
CYTH1 -0.018 0.027 0.15 2 -10000 0 2
HCK 0.025 0.03 0.28 7 -10000 0 7
CYTH3 -0.019 0.025 0.15 2 -10000 0 2
CYTH2 -0.019 0.026 0.14 3 -10000 0 3
KRAS 0.023 0.013 0.3 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.035 -10000 0 -0.36 2 2
SGK1 0.011 0.037 -10000 0 -0.38 2 2
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
mol:GDP -0.001 0.072 0.18 4 -0.25 21 25
SOS1 0.023 0.003 -10000 0 -10000 0 0
SYK 0.022 0.012 0.28 1 -10000 0 1
ARF6/GDP -0.012 0.042 0.22 4 -0.22 1 5
mol:PI-3-4-5-P3 -0.017 0.026 0.15 2 -10000 0 2
ARAP3/RAP1A/GTP -0.017 0.028 0.16 12 -10000 0 12
VAV1 0.023 0.03 0.28 5 -0.35 1 6
mol:PI-3-4-P2 -0.012 0.01 -10000 0 -0.25 1 1
RAS family/GTP/PI3K Class I 0.034 0.031 0.32 1 -0.16 1 2
PLEKHA1 -0.013 0.009 -10000 0 -0.21 1 1
Rac1/GDP 0.011 0.071 -10000 0 -0.3 10 10
LAT 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.079 -10000 0 -0.3 26 26
ITK -0.023 0.033 0.14 1 -0.18 11 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.013 0.068 0.27 13 -0.25 2 15
LCK 0.024 0.028 0.28 4 -0.35 1 5
BTK -0.02 0.028 0.15 2 -0.18 2 4
TRAIL signaling 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
TNFSF10 0.02 0.037 0.33 3 -0.35 3 6
positive regulation of NF-kappaB transcription factor activity 0.022 0.046 0.24 3 -0.24 12 15
MAP2K4 0.006 0.04 0.24 1 -0.24 6 7
IKBKB 0.021 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.02 0.008 -10000 0 -10000 0 0
SMPD1 0.008 0.015 0.15 3 -0.15 2 5
IKBKG 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.053 -10000 0 -0.35 11 11
TRAIL/TRAILR2 0.027 0.027 0.24 3 -0.25 2 5
TRAIL/TRAILR3 0.027 0.029 0.24 3 -0.25 3 6
TRAIL/TRAILR1 0.027 0.027 0.24 3 -0.25 2 5
TRAIL/TRAILR4 0.022 0.046 0.24 3 -0.25 12 15
TRAIL/TRAILR1/DAP3/GTP 0.028 0.028 0.22 2 -0.19 2 4
IKK complex 0.012 0.032 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.007 -10000 0 -10000 0 0
MAPK3 -0.01 0.029 0.3 3 -0.24 3 6
MAP3K1 0.012 0.038 0.26 1 -0.22 4 5
TRAILR4 (trimer) 0.012 0.053 -10000 0 -0.35 11 11
TRADD 0.02 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.027 0.17 1 -0.17 9 10
CFLAR 0.023 0.003 -10000 0 -10000 0 0
MAPK1 -0.01 0.026 0.3 2 -0.24 3 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.05 0.036 0.23 2 -0.18 2 4
mol:ceramide 0.008 0.015 0.15 3 -0.15 2 5
FADD 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.051 0.19 6 -0.24 6 12
TRAF2 0.022 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.018 -10000 0 -0.35 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.036 0.027 0.23 2 -0.21 2 4
DAP3 0.019 0.009 -10000 0 -10000 0 0
CASP10 0.009 0.059 0.17 49 -0.36 2 51
JNK cascade 0.022 0.046 0.24 3 -0.24 12 15
TRAIL (trimer) 0.02 0.037 0.33 3 -0.35 3 6
TNFRSF10C 0.019 0.018 -10000 0 -0.35 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.031 0.22 1 -0.18 2 3
TRAIL/TRAILR2/FADD 0.036 0.027 0.23 2 -0.21 2 4
cell death 0.008 0.015 0.15 3 -0.15 2 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.027 0.17 1 -0.17 9 10
TRAILR2 (trimer) 0.02 0.008 -10000 0 -10000 0 0
CASP8 0.013 0.038 -10000 0 -0.54 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.05 0.036 0.23 2 -0.18 2 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.057 0.071 0.23 2 -0.25 5 7
Ran/GTP/Exportin 1/HDAC1 -0.012 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.06 -10000 0 -0.28 8 8
SUMO1 0.023 0.003 -10000 0 -10000 0 0
ZFPM1 0.02 0.018 -10000 0 -0.35 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
FKBP3 0.023 0.004 -10000 0 -10000 0 0
Histones 0.055 0.038 -10000 0 -10000 0 0
YY1/LSF 0.007 0.069 -10000 0 -0.23 32 32
SMG5 0.019 0.009 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.029 0.17 7 -0.19 2 9
I kappa B alpha/HDAC1 0.032 0.034 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
RELA 0.025 0.035 0.19 7 -0.17 2 9
HDAC1/Smad7 0.042 0.02 -10000 0 -0.21 2 2
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.033 0.036 -10000 0 -0.16 7 7
NuRD/MBD3 Complex 0.027 0.042 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA 0.022 0.07 0.23 1 -0.29 13 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.012 0.11 -10000 0 -0.35 50 50
GATA1 0.02 0.005 -10000 0 -10000 0 0
Mad/Max 0.033 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.072 -10000 0 -0.35 7 7
RBBP7 0.023 0.003 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
MAX 0.023 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
NFKBIA 0.022 0.022 0.15 2 -10000 0 2
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.012 0.028 -10000 0 -10000 0 0
SIN3 complex 0.052 0.021 -10000 0 -10000 0 0
SMURF1 0.023 0.004 -10000 0 -10000 0 0
CHD3 0.021 0.006 -10000 0 -10000 0 0
SAP30 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.021 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.015 0.057 -10000 0 -0.28 8 8
YY1/HDAC2 0.009 0.065 -10000 0 -0.22 28 28
YY1/HDAC1 0.012 0.061 -10000 0 -0.22 25 25
NuRD/MBD2 Complex (MeCP1) 0.027 0.044 -10000 0 -0.3 2 2
PPARG 0.011 0.07 0.19 5 -0.26 25 30
HDAC8/hEST1B 0.036 0.02 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.032 0.035 -10000 0 -10000 0 0
MBD3L2 0.016 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.02 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.02 0.068 -10000 0 -0.29 13 13
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.022 0.15 6 -0.14 2 8
HDAC2 0.023 0.003 -10000 0 -10000 0 0
YY1 0.01 0.025 -10000 0 -0.22 6 6
HDAC8 0.023 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
NCOR2 0.023 0.004 -10000 0 -10000 0 0
MXD1 0.023 0.004 -10000 0 -10000 0 0
STAT3 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.065 -10000 0 -0.2 28 28
YY1/SAP30/HDAC1 0.024 0.061 -10000 0 -0.2 23 23
EP300 0.021 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.014 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.022 0.15 2 -10000 0 2
histone deacetylation 0.027 0.043 -10000 0 -0.3 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.033 -10000 0 -0.24 2 2
nuclear export -0.035 0.02 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GATAD2B 0.019 0.009 -10000 0 -10000 0 0
GATAD2A 0.022 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.013 0.069 -10000 0 -0.18 45 45
GATA1/HDAC1 0.03 0.008 -10000 0 -10000 0 0
GATA1/HDAC3 0.029 0.036 -10000 0 -0.16 2 2
CHD4 0.022 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.052 0.06 0.21 62 -0.25 2 64
SIN3/HDAC complex/Mad/Max 0.016 0.047 -10000 0 -0.32 5 5
NuRD Complex 0.023 0.063 -10000 0 -0.32 8 8
positive regulation of chromatin silencing 0.052 0.036 -10000 0 -10000 0 0
SIN3B 0.022 0.006 -10000 0 -10000 0 0
MTA2 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.025 0.042 -10000 0 -0.19 9 9
HDAC complex 0.054 0.024 -10000 0 -0.19 3 3
GATA1/Fog1 0.027 0.017 -10000 0 -0.25 1 1
FKBP25/HDAC1/HDAC2 0.044 0.012 -10000 0 -10000 0 0
TNF 0.053 0.088 0.28 66 -0.35 2 68
negative regulation of cell growth 0.016 0.047 -10000 0 -0.32 5 5
NuRD/MBD2/PRMT5 Complex 0.027 0.044 -10000 0 -0.3 2 2
Ran/GTP/Exportin 1 0.026 0.042 -10000 0 -0.18 10 10
NF kappa B/RelA/I kappa B alpha 0.02 0.055 0.18 6 -0.28 8 14
SIN3/HDAC complex/NCoR1 0.006 0.064 -10000 0 -0.4 8 8
TFCP2 0.019 0.039 -10000 0 -0.35 6 6
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.006 -10000 0 -10000 0 0
MBD2 0.022 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.016 0.24 2 -10000 0 2
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.016 0.24 2 -10000 0 2
MAPK12 -0.003 0.014 0.2 1 -0.18 1 2
CCND1 0.007 0.03 0.18 1 -0.33 3 4
p38 gamma/SNTA1 0.02 0.037 0.21 14 -0.17 1 15
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.014 0.2 1 -0.18 1 2
MAP2K6 0.001 0.015 0.24 1 -10000 0 1
MAPT -0.002 0.063 0.16 20 -0.24 25 45
MAPK13 -0.009 0.021 0.17 6 -10000 0 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.001 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.021 0.017 -10000 0 -0.35 1 1
PLK4 0.025 0.027 0.28 6 -10000 0 6
regulation of centriole replication -0.011 0.015 0.11 4 -0.25 1 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.012 -10000 0 -10000 0 0
DOCK1 0.017 0.042 -10000 0 -0.35 7 7
ITGA4 0.022 0.025 0.28 1 -0.35 2 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.034 0.017 0.21 2 -0.25 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.022 0.2 1 -0.21 2 3
alpha4/beta7 Integrin/Paxillin 0.034 0.018 0.19 2 -0.19 1 3
lamellipodium assembly -0.007 0.093 -10000 0 -0.39 23 23
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.027 0.029 -10000 0 -0.25 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.022 0.005 -10000 0 -10000 0 0
PXN -0.011 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
ARF6/GTP 0.041 0.023 -10000 0 -0.17 2 2
cell adhesion 0.041 0.023 0.19 1 -0.18 2 3
CRKL/CBL 0.032 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.032 0.019 0.19 1 -0.19 2 3
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.011 0.28 1 -10000 0 1
ARF6/GDP 0.021 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.03 0.06 0.2 1 -0.19 33 34
p130Cas/Crk/Dock1 0.036 0.033 -10000 0 -0.21 7 7
VCAM1 -0.004 0.097 -10000 0 -0.35 39 39
alpha4/beta1 Integrin/Paxillin/Talin 0.042 0.024 0.2 1 -0.18 2 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.023 0.2 1 -0.18 2 3
BCAR1 0.021 0.007 -10000 0 -10000 0 0
mol:GDP -0.041 0.023 0.18 2 -0.19 1 3
CBL 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.042 0.024 0.2 1 -0.18 2 3
Rac1/GTP -0.008 0.1 -10000 0 -0.44 23 23
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD2 0.002 0.042 0.22 6 -0.27 3 9
SMAD3 0.013 0.024 -10000 0 -0.25 1 1
SMAD3/SMAD4 0.019 0.094 -10000 0 -0.48 16 16
SMAD4/Ubc9/PIASy 0.041 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.053 0.24 3 -0.24 2 5
PPM1A 0.022 0.004 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.041 0.22 3 -0.24 4 7
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.029 0.034 -10000 0 -0.24 8 8
MAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.022 0.006 -10000 0 -10000 0 0
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
KPNB1 0.022 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.017 0.045 -10000 0 -0.35 8 8
UBE2I 0.022 0.005 -10000 0 -10000 0 0
NUP153 0.022 0.017 -10000 0 -0.35 1 1
KPNA2 0.035 0.059 0.3 25 -10000 0 25
PIAS4 0.021 0.007 -10000 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.015 0.022 -10000 0 -10000 0 0
regulation of axonogenesis -0.004 0.023 0.24 4 -10000 0 4
myoblast fusion -0.02 0.027 -10000 0 -10000 0 0
mol:GTP 0.017 0.023 -10000 0 -0.16 8 8
regulation of calcium-dependent cell-cell adhesion -0.037 0.042 0.19 12 -10000 0 12
ARF1/GTP 0.025 0.023 -10000 0 -10000 0 0
mol:GM1 0.007 0.016 -10000 0 -10000 0 0
mol:Choline 0.004 0.014 -10000 0 -0.19 1 1
lamellipodium assembly 0.007 0.05 -10000 0 -0.36 8 8
MAPK3 0.017 0.017 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.038 0.043 -10000 0 -0.19 12 12
ARF1 0.02 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.018 0.039 -10000 0 -0.21 8 8
ARF6 0.029 0.009 -10000 0 -10000 0 0
RAB11A 0.022 0.005 -10000 0 -10000 0 0
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.019 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.036 0.22 5 -10000 0 5
KALRN 0.008 0.022 -10000 0 -0.18 4 4
RAB11FIP3/RAB11A 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.036 -10000 0 -0.22 5 5
NME1 0.022 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.038 -10000 0 -0.22 8 8
substrate adhesion-dependent cell spreading 0.016 0.023 -10000 0 -0.16 8 8
cortical actin cytoskeleton organization 0.007 0.05 -10000 0 -0.36 8 8
RAC1 0.022 0.005 -10000 0 -10000 0 0
liver development 0.016 0.023 -10000 0 -0.16 8 8
ARF6/GTP 0.017 0.023 -10000 0 -0.16 8 8
RhoA/GTP 0.029 0.021 -10000 0 -10000 0 0
mol:GDP 0.009 0.028 -10000 0 -0.22 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.02 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.022 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.05 -10000 0 -0.36 8 8
ruffle organization 0.004 0.023 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.016 0.023 -10000 0 -0.16 8 8
PLD2 0.014 0.017 -10000 0 -0.21 1 1
PIP5K1A 0.004 0.023 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.004 0.014 -10000 0 -0.19 1 1
Rac1/GTP 0.007 0.05 -10000 0 -0.36 8 8
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.008 0.002 -10000 0 -10000 0 0
mol:DAG -0.011 0.013 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.01 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.02 0.032 -10000 0 -0.35 4 4
AKT1 0.002 0.054 0.48 1 -10000 0 1
PLCG1 -0.011 0.013 0.18 2 -10000 0 2
NOS3 0.013 0.049 0.43 2 -0.35 1 3
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:NO 0.02 0.065 0.38 7 -0.34 1 8
FLT1 0.011 0.003 -10000 0 -10000 0 0
PGF 0.023 0.012 0.28 1 -10000 0 1
VEGFR1 homodimer/NRP2/VEGFR121 0.026 0.047 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
eNOS/Hsp90 0.027 0.056 0.39 1 -0.32 1 2
endothelial cell proliferation -0.009 0.065 0.32 4 -0.28 4 8
mol:Ca2+ -0.011 0.013 0.18 2 -10000 0 2
MAPK3 -0.02 0.047 0.34 4 -10000 0 4
MAPK1 -0.02 0.047 0.34 4 -10000 0 4
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
PLGF homodimer 0.023 0.012 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
VEGFA homodimer 0.023 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.045 0.33 4 -10000 0 4
PI3K 0.041 0.03 -10000 0 -10000 0 0
PRKCA -0.021 0.037 0.17 1 -10000 0 1
PRKCB -0.021 0.037 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.024 0.011 -10000 0 -10000 0 0
VEGFA 0.023 0.003 -10000 0 -10000 0 0
VEGFB 0.022 0.004 -10000 0 -10000 0 0
mol:IP3 -0.011 0.013 0.18 2 -10000 0 2
RASA1 -0.012 0.024 0.18 4 -10000 0 4
NRP2 0.006 0.077 -10000 0 -0.35 24 24
VEGFR1 homodimer 0.011 0.003 -10000 0 -10000 0 0
VEGFB homodimer 0.022 0.004 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
eNOS/Caveolin-1 0.003 0.088 0.45 4 -0.3 3 7
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.029 -10000 0 -10000 0 0
mol:L-citrulline 0.02 0.065 0.38 7 -0.34 1 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.034 0.019 -10000 0 -10000 0 0
CD2AP 0.023 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.036 -10000 0 -10000 0 0
PDPK1 -0.002 0.053 0.33 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.012 -10000 0 -10000 0 0
mol:NADP 0.02 0.065 0.38 7 -0.34 1 8
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.014 0.047 -10000 0 -10000 0 0
Arf1 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
coatomer protein complex 0.008 0.032 0.15 24 -10000 0 24
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.056 0.14 78 -0.18 7 85
AP2 0.03 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.026 0.014 -10000 0 -10000 0 0
CLTB 0.023 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.008 -10000 0 -10000 0 0
CD4 0.023 0.012 0.28 1 -10000 0 1
CLTA 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP 0.021 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.005 0.004 -10000 0 -10000 0 0
mol:Choline 0.003 0.01 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.002 0.01 -10000 0 -0.15 1 1
ARF1/GDP 0.002 0.017 -10000 0 -0.11 3 3
AP2M1 0.021 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.004 0.011 -10000 0 -10000 0 0
Rac/GTP 0.019 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.025 0.016 -10000 0 -10000 0 0
ARFIP2 0.01 0.019 -10000 0 -10000 0 0
COPA 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.027 -10000 0 -0.24 1 1
ARF1/GTP/ARHGAP10 0.013 0.008 -10000 0 -10000 0 0
GGA3 0.022 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.007 0.048 -10000 0 -0.21 22 22
AP2A1 0.022 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.007 0.021 -10000 0 -0.18 6 6
ARF1/GDP/Membrin 0.008 0.057 -10000 0 -0.24 24 24
Arfaptin 2/Rac/GDP 0.021 0.018 -10000 0 -10000 0 0
CYTH2 0.027 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.025 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -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 0.011 0.019 -10000 0 -0.17 1 1
PLD2 0.003 0.01 -10000 0 -0.14 1 1
ARF-GAP1/v-SNARE -0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP/Membrin/GBF1/p115 0.011 0.022 -10000 0 -0.12 4 4
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.01 -10000 0 -0.14 1 1
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.006 0.025 -10000 0 -0.32 3 3
USO1 0.005 0.029 -10000 0 -0.32 4 4
GBF1 0.004 0.034 -10000 0 -0.34 5 5
ARF1/GTP/Arfaptin 2 0.025 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.041 0.018 0.2 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.011 0.28 1 -10000 0 1
ITGA4 0.022 0.025 0.28 1 -0.35 2 3
alpha4/beta7 Integrin 0.034 0.017 0.21 2 -0.25 1 3
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.25 2 3
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.014 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.024 0.045 -10000 0 -0.19 12 12
HDAC4 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.009 -10000 0 -10000 0 0
SUMO1 0.023 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.007 0.014 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0 0.021 -10000 0 -0.16 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.024 0.044 -10000 0 -0.19 12 12
SUMO1/HDAC1 0.025 0.042 -10000 0 -0.19 9 9
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.054 0.018 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.003 -10000 0 -10000 0 0
Ran/GTP 0.014 0.039 -10000 0 -0.17 12 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.013 0.041 0.18 5 -0.18 10 15
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0.032 0.012 0.21 1 -10000 0 1
FBXW11 0.023 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.035 0.19 5 -0.24 1 6
NFKBIA 0.012 0.022 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.013 -10000 0 -0.21 1 1
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.023 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.015 0.2 1 -0.21 1 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.019 0.013 -10000 0 -0.21 1 1
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
NF kappa B1 p50 dimer 0.014 0.016 0.24 1 -0.25 1 2
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
NFKB1 -0.011 0.011 -10000 0 -0.25 1 1
RELA 0.022 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.032 -10000 0 -0.25 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.035 -10000 0 -0.19 1 1
SRC 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.027 0.029 -10000 0 -0.25 5 5
NF kappa B1 p50/RelA 0.017 0.032 -10000 0 -0.25 2 2
IKBKB 0.021 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
SYK 0.022 0.012 0.28 1 -10000 0 1
I kappa B alpha/PIK3R1 0.022 0.044 0.2 6 -0.2 5 11
cell death 0.021 0.034 -10000 0 -0.19 1 1
NF kappa B1 p105/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
BCL3 0.023 0.012 0.28 1 -10000 0 1
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.038 0.027 -9999 0 -0.3 2 2
E-cadherin/beta catenin 0.029 0.021 -9999 0 -0.25 2 2
CTNNB1 0.022 0.004 -9999 0 -10000 0 0
JUP 0.021 0.017 -9999 0 -0.35 1 1
CDH1 0.019 0.024 -9999 0 -0.35 2 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.019 -10000 0 -10000 0 0
CLOCK 0.024 0.003 -10000 0 -10000 0 0
TIMELESS/CRY2 0.029 0.019 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.015 -10000 0 -0.25 1 1
ATR 0.022 0.004 -10000 0 -10000 0 0
NR1D1 0.013 0.01 -10000 0 -10000 0 0
ARNTL 0.023 0.017 -10000 0 -0.35 1 1
TIMELESS 0.014 0.016 -10000 0 -10000 0 0
NPAS2 0.021 0.036 -10000 0 -0.35 5 5
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.006 0.004 -10000 0 -0.073 1 1
CHEK1 0.022 0.005 -10000 0 -10000 0 0
mol:HEME 0.006 0.004 0.073 1 -10000 0 1
PER1 0.02 0.017 -10000 0 -0.35 1 1
BMAL/CLOCK/NPAS2 0.048 0.028 -10000 0 -0.2 5 5
BMAL1/CLOCK 0.013 0.05 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.019 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.02 -10000 0 -10000 0 0
mol:NADPH 0.006 0.004 0.073 1 -10000 0 1
PER1/TIMELESS 0.026 0.02 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.016 0.005 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.031 0.01 -9999 0 -10000 0 0
FBXW11 0.023 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -9999 0 -10000 0 0
CHUK 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.025 -9999 0 -10000 0 0
NFKB1 0.022 0.017 -9999 0 -0.35 1 1
MAP3K14 0.022 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.015 -9999 0 -0.25 1 1
RELB 0.022 0.005 -9999 0 -10000 0 0
NFKB2 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.029 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.028 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 537 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.SJ.A6ZJ TCGA.SJ.A6ZI
109_MAP3K5 -0.14 0.019 0.019 0.019
47_PPARGC1A -0.35 0.023 0.023 -0.35
105_BMP4 0.023 -0.35 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0 0.023 0.023
105_BMP2 0.023 -0.35 0.023 0.023
131_RELN/VLDLR -0.19 0 0.06 -0.19
30_TGFB1/TGF beta receptor Type II 0.023 0.023 0.02 0.023
84_STAT5B -0.031 0.028 -0.031 0.024
84_STAT5A -0.031 0.028 -0.031 0.024
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/UCEC-TP/22315277/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/UCEC-TP/22507127/Gistic2_Analysis_22507608/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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